TQiSoft's Webgenetics(sm)

List Common Regions

This program is meant to aid you in manually doing multi-sequence alignment by listing common regions of certain length among sequences (either DNA or protein) so they can be used as anchor points. If you are unsatisfied with the multi-sequence alignment programs you have tried and like to try manual alignment, you may find this program helpful. Note that only top strands (the input sequences) are processed for DNA, so make sure that the input sequences are in correct orientation.

The regions are listed in order of their lengths in the following format:

length_of_the_common_region  sequence_of_the_region
sequence_name   number_of_occurrence: start_site(s)_of_the_common_region
sequence_name   number_of_occurrence: start_site(s)_of_the_common_region
sequence_name   number_of_occurrence: start_site(s)_of_the_common_region
...

Example output:

   10 GGAGGAGGAG
HSTFE3       3:    957   960  1256
HSTFAP       1:    813
S77532       1:    575
HUMIMENBPA   1:    900
HSTAL1AA     1:    515
RNCMYC       0:
CHKMAX       0:

    9 GAGGAGGAG
HSTFE3       4:    778   958   961  1257
HSTFAP       1:    814
S77532       1:    576
HUMIMENBPA   1:    901
HSTAL1AA     1:    516
RNCMYC       1:   6495
CHKMAX       0:

    9 GGAGGAGGA
HSTFE3       3:    957   960  1256
HSTFAP       1:    813
S77532       1:    575
HUMIMENBPA   1:    900
HSTAL1AA     1:    515
RNCMYC       0:
CHKMAX       2:   1481  1550

    8 CAGCTCCC
HSTFE3       1:    250
HSTFAP       0:
S77532       1:    116
HUMIMENBPA   1:   1271
HSTAL1AA     1:    653
RNCMYC       0:
CHKMAX       1:   1885

    8 CCAGCTGC
HSTFE3       0:
HSTFAP       0:
S77532       1:    440
HUMIMENBPA   1:    189
HSTAL1AA     1:    643
RNCMYC       1:   6119
CHKMAX       2:    175  4422

    8 AGGAGGAG
HSTFE3       5:    779   959   962  1255  1258
HSTFAP       1:    815
S77532       1:    577
HUMIMENBPA   1:    902
HSTAL1AA     2:    514   517
RNCMYC       1:   6496
CHKMAX       1:   2262

...