Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006373.1 Kokia drynarioides strain JFW-HI SEQ_120949, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6863
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Found at i:736 original size:216 final size:215
Alignment explanation
Indices: 34--6859 Score: 6224
Period size: 216 Copynumber: 31.8 Consensus size: 215
24 CCAAACTTTG
* * * *
34 CAAACTTTTTCGAGTTCTTTTATAACTTTGGTTCTTTAAAGTATTCAAGATGATCCATTTCTTCG
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
* * * * *
99 AACAATTTTTCGAACATTCCATTCTCGGGAAATTGCATCATTTGGTCCAAATAATTTGTTATTTT
66 AGCAATTTTTCGAACATTCCA-TCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTT
* * *
164 GTAAACAACTTTTGGT-TCTTGGATTGAAAA-TATATTTATCTGAGAATTGTTTCTCTCTTGGTT
130 GTAAACAACTTTTGGTCT-TTGAATTAAAAACT-TATTTATGTGAGAATTGTTTCTCTCTTGGTT
227 CTTGGCCGAAC-TTCTGAACTTGT
193 CTTGGCCGAACTTTC-GAACTTGT
* * * *
250 GAAACTTTTTCGAGTACTTTTATAACTTCGGTTCCTTAAAGTATTCAAGAAGATCGATTCCTTCG
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
* * * *
315 AGCAA-TTTTCTAAACATTCAATTCTC-AGGAAATCGCATCATTTGGTCCAAATAATTAGTCCA-
66 AGCAATTTTTC-GAACATTCCA-TCTCGA-GAAATCGCATCATTTGGTCCAAATAGTTTGT-CAT
* * * * * * * **
377 TTTGTAAAAAACTTTCGGTTTTTTAATTAAAAACTTATTTTATGTGAGAATTATTGCACTCTCAG
127 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTA-TTTATGTGAGAATTGTTTCTCTCTTGG
* * * *
442 TTCTAGGCCGAACTTCCAAAGTT-T
191 TTCTTGGCCGAACTTTCGAACTTGT
** * * * * *
466 GCAAACTTTTTCTTGTTCTTATATAACTTTGGATCCTTTAAGTATTCAAGACGATCCATTTCTTC
1 -CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTC
* * * * * *
531 GAACAATTTTTTGAACATTCTGATCTCGAGAAATTGCATCATTTGGTCCAAATAATCTGTCATTT
65 GAGCAATTTTTCGAACATTC-CATCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTT
* * * * *
596 TGTAAACAACTTTTGGTCTTTGGATTAAAAATTTATTTATGTGATAATTGTTTATCACTTGGTTC
129 TGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTC
* *
661 TTGACCGAACTTTCGAACTTAT
194 TTGGCCGAACTTTCGAACTTGT
* * * *
683 CAAACTTTTTCGAGTACTTTTATAACTTCGGTTCCTTAAAGTATTGAAGACGATCGATTCCTTTG
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
* * *** ** * *
748 ACCAA-TTTTCAGAACTTTCCATTCTTTCGAAATCATATCATTTGGTCCAAATAATTAGTCATTT
66 AGCAATTTTTC-GAACATTCCA-TCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTT
* * * * *
812 TGTAAAAAACTTTCGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATTTCACTCTTGGTTC
129 TGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTC
* * * *
877 TAGGCTGAATTTTCAAACTT-T
194 TTGGCCGAACTTTCGAACTTGT
* * * * * *
898 GAAAATTTTTTCGAGTTCATTTATATCTTTGGTTCCTTAAAGTATTCAAGACGATCCATTACTTC
1 -CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTC
* * * * * *
963 --G--A--TTT----CATT-C-T-T-GGGAAATTGCATCATTTGGTACAAATAATCTGTTATTTT
65 GAGCAATTTTTCGAACATTCCATCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTT
** * * *
1014 GTAAACAACTTTCAGTTTTTGGATTAAAAAATTATTTATGTGAGAATTGTTTCTCTCTTGGTTCT
130 GTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCT
*
1079 TGGCCGAACTTTTGAACTTGT
195 TGGCCGAACTTTCGAACTTGT
* * * **
1100 CAAACTTTTTCAAGTACTTTTATAACTTCGGTTCCTTAAAGTATTCAAGATGATAGATTCC-TCA
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTC-
* * * ** * *
1164 TAGCAATTTTCCTAACATTTTAGCCTCGAGAAATCGCA-CGATTTGGTCCAAATAGTTTGTCCTT
65 GAGCAATTTTTCGAACATTCCA-TCTCGAGAAATCGCATC-ATTTGGTCCAAATAGTTTGTCATT
* * * * * *
1228 TTGTAAAAAACTTTCGATCTTTTAATTAGAAACTTATTTATTTGAGAATTGTTTCTCTCTTGGTT
128 TTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTT
* * * *
1293 CTTGGCC-AATCTTCCAAAGTTTT
193 CTTGGCCGAA-CTTTCGAACTTGT
* * * * * * *
1316 TAAACTTTATCGAGTTCTTTTATAACTGCGGTTCCTTAAATTTTTCAAGACGATCCTTTCATTCG
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
* * * * * * * * *
1381 AGTAATTTTTCGAACATTCGATTCTCGGGAAATTGAATCATTTGATCCAAATAATATGTTATTTT
66 AGCAATTTTTCGAACATTCCA-TCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTT
* * * * *
1446 GTAAACAACTTTTGGTCTTTGGATTAAAAATTTATTTATGGGAGAATTATTTCTCTCTTGATTCT
130 GTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCT
** *
1511 T---ATAGCTTTCGAACTTGT
195 TGGCCGAACTTTCGAACTTGT
* * * * *
1529 CAAACTTTTACGAGTTCTTTT-TAAATTAGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCT
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
* * * * * *
1593 AGCAATTTCTCGAGCATTCCATGCTCAATAAATCGCATCCTTTGGTCCAAATAGTTTGTCATTTC
66 AGCAATTTTTCGAACATTCCAT-CTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTT
* * *
1658 GT-AACAACTTTTGGTCTTTGAATTAAAGACTTATTTATGTGAGAATTGTTTCTTTCTTGTTTCT
130 GTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCT
* *
1722 TGGCCGAAC-ATCTGAACATGT
195 TGGCCGAACTTTC-GAACTTGT
* *** * * * **
1743 AAAACTTTTAAAAGTTCTTTTATAACTTTGGTTCCTTAAAGTAATCATGACGATCCGCTCCTTCG
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
** * * * * * *
1808 AGCAATTTTTTTAGCATT-CATTCTCGAGAAAGCGTATCATTT-CTACCAAGTAGTTTATCATTT
66 AGCAATTTTTCGAACATTCCA-TCTCGAGAAATCGCATCATTTGGT-CCAAATAGTTTGTCATTT
* * * ** * *
1871 TGTAAACAACTTTTGCTCTTTGAATTAAAAACATATTAACATTAGAATTGTTTCTCTCTTGGCTC
129 TGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTC
* * * * *
1936 TTGGTCAAACTTCCAAACTTTT
194 TTGGCCGAACTTTCGAACTTGT
* * * * * * * *
1958 CAAACTTTTTCGAGTCCTATTATAGCATCGATTCTTTACAGTATTCAAGACGATCCATTCCTTCA
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
* * * * * *
2023 AGCAATTTTTTGAACATTCCAAGCTCAAGAAATCGGACCATTTGGTCCAAATAGTTTGTCACTTT
66 AGCAATTTTTCGAACATTCC-ATCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTT
** ** * * *
2088 GTAAACAACTTTTGGTCTTAAAATTAAAAACTTATTTACCTAAGAATGGTTTCTCCCTTGGTTCT
130 GTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCT
* *
2153 TGACTGAACTTTCGAA-TTAGT
195 TGGCCGAACTTTCGAACTT-GT
* * * * * *
2174 CAAACTTTTACGTGTTATTTTATAACTTTGGTTCCTTAAAGTATTCAAGATGATCTATTCCTTCG
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
* * * * * * *
2239 TGCAATTTTCCAAACATTCCATGCTC-AGGAAATCGCATCATTTGGTCTAAATATTTTATCGTTT
66 AGCAATTTTTCGAACATTCCAT-CTCGA-GAAATCGCATCATTTGGTCCAAATAGTTTGTCATTT
* *
2303 TGTAAACAACTTTCGGTCTTTGAATTAAAAACTTATTTATTTGAGAATTGTTTCTCTCTTGGTTC
129 TGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTC
* * *
2368 TTGGTCGAACTTCCGAACTTAT
194 TTGGCCGAACTTTCGAACTTGT
* * * *
2390 CAAACTTTTTTGAGTTCTTCTATAACTTCGATTCCTTAAAGTATTCAAGATGATCAATCAATTCC
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATC---C-ATTCC
* * * * * *
2455 TTCGAGCAATTTTTCGAATATTCCATTCTCGGGAAATCGAATCACTTGGTCCAAATAGTTAGTCC
62 TTCGAGCAATTTTTCGAACATTCCA-TCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCA
* * * * * * * * * ** *
2520 TTTTGTAAAAAACTTAT--T-TAT--A-TGAGAA-TTATTTCTCT----CTTGGTTCTAGGC--C
126 TTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCT-CTCTTG
** *
2572 GAACTT--CCGAACTTTGCAAACTT-T
190 GTTCTTGGCCGAACTTT-CGAACTTGT
** * * *
2596 --------TTCGAGTTCTTTTATAACTTTTGTTCCTTAAAGTATTTAAGACGATTCATTTCTTCG
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
** ** * *
2653 AATAATTTTTCGAACATTACGTTCTCTG-GAAATCGCATCATTTGGTCCAAATAATCTGTCATTT
66 AGCAATTTTTCGAACATT-CCATCTC-GAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTT
* * *
2717 TGTAAACAACTTTTGGTCTTTGGACTAAAAATTTATTTATGTGAGAATTGTTTCTCTCATT-GTT
129 TGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTC-TTGGTT
* *
2781 CTTGGCCGAACTTTTGAACATGT
193 CTTGGCCGAACTTTCGAACTTGT
* * * * *
2804 CAAAC-TTTTCTATGTTCTTTTATAACTTCGATTTCTTAAAGTATTTAAGACGATCAATTCCTTC
1 CAAACTTTTTCGA-GTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTC
* * * * * * *
2868 GAGCAATTTTCCGAACATTCTATTCTC-AGGAAATTGCATCCTTTGGTCCAAATGGTTAGTCCTT
65 GAGCAATTTTTCGAACATTCCA-TCTCGA-GAAATCGCATCATTTGGTCCAAATAGTTTGTCATT
* * *
2932 TAGTAAAAAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTATTTCTCTCTTGGTT
128 TTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTT
* ** * *
2997 CTAGGAAGAACTTCCGAACTTTT
193 CTTGGCCGAACTTTCGAACTTGT
* * * * * * *
3020 CAATCTTTTTTTGAGTTCTTTTATAACTTTGATTCCTTAAAGTATTCAAGACAATCCATTTCTTT
1 CAAAC-TTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTC
* * * * *
3085 GAACAATTTTTCGAACATT-CAGT-TCTTAGGAAATCACATCATTTGGTCCAAATAATCTGTCAT
65 GAGCAATTTTTCGAACATTCCA-TCTC-GA-GAAATCGCATCATTTGGTCCAAATAGTTTGTCAT
* * *
3148 TTTGTAAACAAATTTTGGTCTTTGGATTAAAAATTTATTTATGTGAGAATTGTTTCTCT-TTGGG
127 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTT-GG
*** *
3212 TTCTTGATTGAACTTCCGAACTTGT
191 TTCTTGGCCGAACTTTCGAACTTGT
* * * * * *
3237 CAAACTTTTTCGAGTTGTTTTATAACTTCGATTCCTGAAAGTATTCATGACTATCGATTCCTTCG
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
* * * * * *
3302 AGCAA-TTATCTGAACGTTTCGTGCTTG-GTAAATCGCATCATTTGGTGCAAATAGTTTGTCATT
66 AGCAATTTTTC-GAACATTCCAT-CTCGAG-AAATCGCATCATTTGGTCCAAATAGTTTGTCATT
** * *** ** *
3365 TTGTAAACAACTTTTTTTCTTAGAATTAAAAACTTATTTACACGAGAA-TGACCTCTCCCTTGGT
128 TTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTG-TTTCTCTCTTGGT
* * * *
3429 TCATGACTGAACTTTCAAACTTGT
192 TCTTGGCCGAACTTTCGAACTTGT
* * * * *
3453 CAAACTTTTACGATTTATTTTACAACTTCGGTTCCTTAAAGTATTCAAGACAATCCATTCCTTCG
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
* ** * * * ** * * *
3518 AGTAATTTCCCAAACATTTCATGCTCGGGAAATCGCATCATTTGGT-TGAATATTTTATCCTTTT
66 AGCAATTTTTCGAACATTCCAT-CTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTT
* *
3582 ATAAACAACTTTCT-GTCTTTGAATTAAAAACTTATTTATGTAAGAATTGTTTCTCTCTTGGTTC
130 GTAAACAACTTT-TGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTC
* * *
3646 TTGGTCGAATTTTCGAACTTAT
194 TTGGCCGAACTTTCGAACTTGT
* * ** *
3668 TAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACAATAGATTCTTTCG
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
* * * * * * * * *
3733 AGCAATTTTCCTAACATTTCAGCCTCGAGAAATTGTACCATTTGGTCCAAATAGTTCGTCCTTTT
66 AGCAATTTTTCGAACATTCCA-TCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTT
* * * * * *
3798 GTAAAAAACCTTCGGTATTTGAATTAAAAACTTATTTATTTGAGAATTGTTTCTCTCAT-GTTCT
130 GTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCT
* *
3862 TGGCCGAACATTCGAACTTTT
195 TGGCCGAACTTTCGAACTTGT
* *
3883 CAAACTTTTTCGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACAATCCATTCCTTCG
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
* * * * *** * * * *
3948 AGCCATTTTTCTAACATTCGATTCTCGGGAAATTAAATCATTT-TTCCAAATAATCTGTTATTTT
66 AGCAATTTTTCGAACATTCCA-TCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTT
* * * * * * *
4012 GTAAAAAACTTTTGGTCTTTGGATTAAAAACTTATTTACGTGAGAATTATTTTTCTCTGGGTTAT
130 GTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCT
** * *
4077 TAACCGAACTTCCGAACTAGT
195 TGGCCGAACTTTCGAACTTGT
* * * * * *
4098 CAAACTTCTACGAGTTATTTT-TAACTTCAGTTCCTT-AAGTTTTCAAGACGATCCATTCCTTCT
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
* * * * * *
4161 AGCAATTTTTCGAACATTCCATGCTCAAGAAATCACATCCTTTGGTCCAAATAGTTTCTTATTTC
66 AGCAATTTTTCGAACATTCCAT-CTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTT
* *
4226 GTAAACAACTTTTGGTCTTTGAATTAAAGACTTATTTATGTGAGAATTATTTCTCTCTTGGTTCT
130 GTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCT
* *
4291 TGGACGAACTTCCGAACTTGT
195 TGGCCGAACTTTCGAACTTGT
* * * * *
4312 CAAACTTTTTCGAGTTCTTTTATAATTTTGGTTCCTTATAGTATTCAAGACGGTCCATTCCTTCA
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
** * * * * * * *
4377 AGCAA-TTTTCTGAGTATTCCATGCTCAAGAAATCGTATCGTTTCGACCAAGTAGTTTGTTATTT
66 AGCAATTTTTC-GAACATTCCAT-CTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTT
* * ** * * **
4441 TGTAAGCAAGTTTTACTCATTGAATT-AAAACTTATTTACGTGAGAAAGGTTTCTCTCTTGGTTC
129 TGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTC
* * *
4505 TTGGTCGAACTTCCAAACCTT-T
194 TTGGCCGAACTTTCGAA-CTTGT
* * * * *
4527 CAAACTTTTTTGAGTTCTATTATAGCTTCGATTCCTTACAA-TATTCAAGACGATCCATTCCTTT
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTA-AAGTATTCAAGACGATCCATTCCTTC
* * * * * * *
4591 GTGCAATTTCTCAAACATTTCAAACTCGAGAAATAGCATCATTTGGTCTAAATAGTTTGTCATTT
65 GAGCAATTTTTCGAACA-TTCCATCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTT
* * * * *
4656 TGTAAATAACTTTTGGTCTTAGAATTAAAAACTTATTTACGTGAGAATGGTTTCTCCCTTGGTTC
129 TGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTC
* * * *
4721 TT-GACTAAGC-TTCGAAATTTT
194 TTGGCCGAA-CTTTCGAACTTGT
* * * * *
4742 CAAACTTTTACGAGTTGTTTTATAACTTCGGTTTCTTAAAGTATTCAAGACAATTCATTCCTTCG
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
** * * * * * * *
4807 AGCAATTTACCAAACATTCCATGCT-TAGGAAATTGCATCATTAGGTCCAAATATTTTATCCTTT
66 AGCAATTTTTCGAACATTCCAT-CTCGA-GAAATCGCATCATTTGGTCCAAATAGTTTGTCATTT
* *
4871 TGTAAACAACTTTCGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTACTCTCTTGGTTC
129 TGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTC
*
4936 TTGGCCGAACTTCCGAACTTGT
194 TTGGCCGAACTTTCGAACTTGT
* * * * *
4958 TAAACTTTTTCGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATGCAAGATGATCGATTCACTT-
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTC-CTTC
* * * * *
5022 GAACAATTTTTCGAACATTCCATTCTCGAGAAATCTCATCATTTGGTCCAAATAGTTAGCCCTTT
65 GAGCAATTTTTCGAACATTCCA-TCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTT
* * * * *
5087 TGTAAAAAACTTTCGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATTTTTCTCTTGGTTC
129 TGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTC
* * **
5152 TAGGTCGAACTTTAAAACGTTG-
194 TTGGCCGAACTTTCGAAC-TTGT
* * * * * * *
5174 CAAACTTTTTCGAGTTTTTTTATAACTTTGGTTCCTTAAGGTGTTCAAGATGATCCATTTCTTTG
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
* * *** * * * * *
5239 AACAAATTTTCGAACATTTGTTCT-AAGGAAATCACAT-ATTTTGGTCCAAATAATCTATCATTT
66 AGCAATTTTTCGAACATTCCATCTCGA-GAAATCGCATCA-TTTGGTCCAAATAGTTTGTCATTT
* * * * * * * * *
5302 TGAAAATAACTTTTGGT-TCATGGATTAAAAATTTATTTTTTTGAGAAGTGTTTCTCTTTTGGTT
129 TGTAAACAACTTTTGGTCT-TTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTT
*
5366 CTTGGCCGAAC-TTCTGAACATGT
193 CTTGGCCGAACTTTC-GAACTTGT
* * * ** * * * *
5389 CGAACTTTTTCTAGTACTTTTATAACTTCTTTTCCTTAAACTATTCATGACTA-CAGATTCCTTC
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATC-CATTCCTTC
* * * * * * * ** *
5453 GGGCAATTATCCAAACATTCCATGCTCGATAAATTGCATCAGTTGGTTAAAATAGTTCGTCATTT
65 GAGCAATTTTTCGAACATTCCAT-CTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTT
* * * * *
5518 TGTAAACAACTTTTGGTCTTAGAATTAAAAACTTATTTACGTGACAATGGTTTCTCCCTTGGTTC
129 TGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTC
* *** *
5583 ATGATTGAACTTTCAAACTTGT
194 TTGGCCGAACTTTCGAACTTGT
* * * * ** *
5605 CAAACTTTTACGATTTATGTTATAACTTCGGTTCCTTAAAGTATTCAAGTTGATCCATTCCTTCA
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
** * * * * * *
5670 AAAAATTTTCCAAACATTCCATACTCGAGAAATCGCATCATTTGGCCCAAATATTTTATCCTTTT
66 AGCAATTTTTCGAACATTCCAT-CTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTT
* *
5735 GTAAACAACTTTCGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTTTCTCTTGGTTCT
130 GTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCT
*
5800 TGGTCGAACTTTCGAACTTGT
195 TGGCCGAACTTTCGAACTTGT
* * * * * * * * *
5821 CAAACTTTTACGAGTTCATTTATAACTTTGGTTCTTTAAAGTACTCAAAATGATCAATTCCTTTG
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
* * * *
5886 AGCAATTTTCCAAACATTCCATACTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCCTTTT
66 AGCAATTTTTCGAACATTCCAT-CTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTT
* * * * **
5951 GTAAAAAAATTTTGGTCTTTGAATTAAATACTTATTTACGTGAGAATTGTTTCTCTCTTATTTCT
130 GTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCT
* *
6016 TAGCCGAACTTTCGAATTTGT
195 TGGCCGAACTTTCGAACTTGT
* * * * *
6037 CAAACTTTTTACGACTTCTTTTATAACTTCAGTTTCTTAATGTATTCAAGAC-AACTCATTCCTT
1 CAAACTTTTT-CGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATC-CATTCCTT
** * * * * * * * *
6101 TTAGAAAATTTCCAAACATTCCATGCTTGGGAAATCGTATCATTTGGTCCAAATAG-TTGTCAGT
64 CGAGCAATTTTTCGAACATTCCAT-CTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATT
* * * *
6165 TTGTAAAGAAATTTTGGTCTTTAAATTAAAAACTTATTTACGTG-GAATTGTTTCTCTCTTGGTT
128 TTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTT
* * *
6229 CTTGGCTGAAC-ATCTAAACTTGT
193 CTTGGCCGAACTTTC-GAACTTGT
* * ** * * *
6252 CAAACTTTTACAAGTTCTTTTATAACTTCTATTCCTTAAGGTATTCAATACGATCCATTCATTCG
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
* * * * *
6317 AGTAATTTTTTGAACATTCCTTGCTCGAGAAATCGCATCATTTCGTCCAAATAATTTGTCATTTT
66 AGCAATTTTTCGAACATTCCAT-CTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTT
* ** * *
6382 GT-AA-TACTTTTGGTCTTAAAATTAAAAACTTATTT-TCGTGGGAATGGTTTCTC-CATTGGTT
130 GTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAT-GTGAGAATTGTTTCTCTC-TTGGTT
* *
6443 CTTGACTGAACTTTCGAACTTGT
193 CTTGGCCGAACTTTCGAACTTGT
* * * * * * *
6466 CAATCTTTTACGAGTTCTTTTGTAACTTCAGTTTCTTAAAGTATTCAAGACGATTCATTCCTTTG
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
* *
6531 AGCAATTTTTC-AATCATTCCATGCTCGAGAAATCGCATCATTTGGTCCAAATATTTTGTCCTTT
66 AGCAATTTTTCGAA-CATTCCAT-CTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTT
* * * *
6595 TGTATACAACTTTCGATCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTTTCTTGGTTC
129 TGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTC
* *
6660 TTCGCCGAAC-TTCTAAACTTGT
194 TTGGCCGAACTTTC-GAACTTGT
* * * * * *
6682 CAAACTTTTTGGAGCTCTTTTTTAACTTCGGTTCCTTAAAGTATTCATGATGATCGATTCCTTCG
1 CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
* ** *
6747 AGCAA-TTTTCAGAACATTCCATTCTTGAGAAATCATATCATTTGGTCCAAATAGTTTGTCCTTT
66 AGCAATTTTTC-GAACATTCCA-TCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTT
* * * *
6811 TGTAAA-AGACTTTCGGTCTATGAATTAAAAACTTATATACGTGAGAATT
129 TGTAAACA-ACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATT
6860 ATTT
Statistics
Matches: 5329, Mismatches: 1114, Indels: 334
0.79 0.16 0.05
Matches are distributed among these distances:
194 69 0.01
195 3 0.00
196 1 0.00
197 2 0.00
198 39 0.01
199 1 0.00
200 6 0.00
201 159 0.03
202 2 0.00
203 2 0.00
204 1 0.00
205 9 0.00
206 15 0.00
207 12 0.00
208 14 0.00
209 7 0.00
210 1 0.00
211 64 0.01
212 86 0.02
213 129 0.02
214 504 0.09
215 1102 0.21
216 2555 0.48
217 461 0.09
218 15 0.00
220 69 0.01
221 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (215 bp):
CAAACTTTTTCGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
AGCAATTTTTCGAACATTCCATCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTG
TAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTT
GGCCGAACTTTCGAACTTGT
Found at i:2210 original size:431 final size:432
Alignment explanation
Indices: 16--6859 Score: 6473
Period size: 431 Copynumber: 16.0 Consensus size: 432
6 AGGCTCTAGG
* * * *
16 CTGAACTTCCAAACTT-TGCAAACTTTTTCGAGTTCTTTTATAACTTTGGTTCTTTAAAGTATTC
1 CTGAACTTTCGAACTTGT-CAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTC
* * * * *
80 AAGATGATCCATTTCTTCGAACAATTTTTCGAACATTCCATTCTCGGGAAATTGCATCATTTGGT
65 AAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATTCTCGAGAAATCGCATCATTTGGT
* * * *
145 CCAAATAATTTGTTATTTTGTAAACAACTTTTGGT-TCTTGGATTGAAAA-TATATTTATCTGAG
130 CCAAATAATTTGTCATTTTGTAAACAACTTTTGGTCT-TTGAATTAAAAACT-TATTTATGTGAG
* * *
208 AATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCTGAACTTGTGAAACTTTTTCGAGTACTTTTAT
193 AATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTTTCGAGTTCTTTTAT
* * ** * *
273 AACTTCGGTTCCTTAAAGTATTCAAGAAGATCGATTCCTTCGAGCAATTTTCTAAACATTCAATT
258 AACTTCGATTCCTTAAAGTATTCAAGACGATCGATTCCTTCGAGCAATTTTCCGAACATTCCATG
* * * * *
338 CTC-AGGAAATCGCATCATTTGGTCCAAATAATTAGTC-CATTTGTAAAAAACTTTCGGTTTTTT
323 CTCGA-GAAATCGCATCATTTGGTCCAAATAGTTTGTCAC-TTTGTAAAAAACTTTTGGTCTTTG
* * * * ** * *
401 AATTAAAAACTTATTTTATGTGAGAATTATTGCACTCTCAGTTCTAGG
386 AATTAAAAACTTA-TTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGA
* * * * * ** * * *
449 CCGAACTTCCAAAGTT-TGCAAACTTTTTCTTGTTCTTATATAACTTTGGATCCTTTAAGTATTC
1 CTGAACTTTCGAACTTGT-CAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTC
* * * * *
513 AAGACGATCCATTTCTTCGAACAATTTTTTGAACATTCTGA-TCTCGAGAAATTGCATCATTTGG
65 AAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTC-CATTCTCGAGAAATCGCATCATTTGG
* * * *
577 TCCAAATAATCTGTCATTTTGTAAACAACTTTTGGTCTTTGGATTAAAAATTTATTTATGTGATA
129 TCCAAATAATTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGA
* * * * * *
642 ATTGTTTATCACTTGGTTCTTGACCGAACTTTCGAACTTATCAAACTTTTTCGAGTACTTTTATA
194 ATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTTTCGAGTTCTTTTATA
* * * * * * *
707 ACTTCGGTTCCTTAAAGTATTGAAGACGATCGATTCCTTTGACCAATTTTCAGAACTTTCCATTC
259 ACTTCGATTCCTTAAAGTATTCAAGACGATCGATTCCTTCGAGCAATTTTCCGAACATTCCATGC
*** ** * * * *
772 TTTCGAAATCATATCATTTGGTCCAAATAATTAGTCATTTTGTAAAAAACTTTCGGTCTTTGAAT
324 TCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCACTTTGTAAAAAACTTTTGGTCTTTGAAT
* * * *
837 TAAAAACTTATTTACGTGAGAATTATTTCACTCTTGGTTCTAGG
389 TAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGA
* * * * * * *
881 CTGAATTTTCAAACTT-TGAAAATTTTTTCGAGTTCATTTATATCTTTGGTTCCTTAAAGTATTC
1 CTGAACTTTCGAACTTGT-CAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTC
* * *
945 AAGACGATCCATTACTTC--G--A--TTT----CATT-C--T-T-GGGAAATTGCATCATTTGGT
65 AAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATTCTCGAGAAATCGCATCATTTGGT
* * * ** * * *
995 ACAAATAATCTGTTATTTTGTAAACAACTTTCAGTTTTTGGATTAAAAAATTATTTATGTGAGAA
130 CCAAATAATTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAA
** * *
1060 TTGTTTCTCTCTTGGTTCTTGGCCGAACTTTTGAACTTGTCAAACTTTTTCAAGTACTTTTATAA
195 TTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTTTCGAGTTCTTTTATAA
* * * * * **
1125 CTTCGGTTCCTTAAAGTATTCAAGATGATAGATTCC-TCATAGCAATTTTCCTAACATTTTA-GC
260 CTTCGATTCCTTAAAGTATTCAAGACGATCGATTCCTTC-GAGCAATTTTCCGAACATTCCATG-
* * *
1188 CTCGAGAAATCGCA-CGATTTGGTCCAAATAGTTTGTC-CTTTTGTAAAAAACTTTCGATCTTTT
323 CTCGAGAAATCGCATC-ATTTGGTCCAAATAGTTTGTCAC-TTTGTAAAAAACTTTTGGTCTTTG
* ** *
1251 AATTAGAAACTTATTTATTTGAGAATTGTTTCTCTCTTGGTTCTTGG
386 AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGA
* * * * * * ** * *
1298 C-CAATCTTCCAAAGTTTTTAAAC-TTTATCGAGTTCTTTTATAACTGCGGTTCCTTAAATTTTT
1 CTGAA-CTTTCGAACTTGTCAAACTTTTA-CGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATT
* * * * * * * *
1361 CAAGACGATCCTTTCATTCGAGTAATTTTTCGAACATTCGATTCTCGGGAAATTGAATCATTTGA
64 CAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATTCTCGAGAAATCGCATCATTTGG
* * * * *
1426 TCCAAATAATATGTTATTTTGTAAACAACTTTTGGTCTTTGGATTAAAAATTTATTTATGGGAGA
129 TCCAAATAATTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGA
* * ** * * *
1491 ATTATTTCTCTCTTGATTCTT---ATAGCTTTCGAACTTGTCAAACTTTTACGAGTTCTTTT-TA
194 ATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTTTCGAGTTCTTTTATA
* * * * *
1552 AATTAGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCTAGCAA-TTTCTCGAGCATTCCATG
259 ACTTCGATTCCTTAAAGTATTCAAGACGATCGATTCCTTCGAGCAATTTTC-CGAACATTCCATG
* * * *
1616 CTCAATAAATCGCATCCTTTGGTCCAAATAGTTTGTCA-TTTCGT-AACAACTTTTGGTCTTTGA
323 CTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCACTTT-GTAAAAAACTTTTGGTCTTTGA
* * * * *
1679 ATTAAAGACTTATTTATGTGAGAATTGTTTCTTTCTTGTTTCTTGG
387 ATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGA
* * * * ** *
1725 CCGAAC-ATCTGAACATGTAAAACTTTTAAAAGTTCTTTTATAACTTTGGTTCCTTAAAGTAATC
1 CTGAACTTTC-GAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTC
* ** ** * * * *
1789 ATGACGATCCGCTCCTTCGAGCAATTTTTTTAGCATT-CATTCTCGAGAAAGCGTATCATTT-CT
65 AAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATTCTCGAGAAATCGCATCATTTGGT
* * * * * * ** *
1852 ACCAAGTAGTTTATCATTTTGTAAACAACTTTTGCTCTTTGAATTAAAAACATATTAACATTAGA
130 -CCAAATAATTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGA
* * * * * * *
1917 ATTGTTTCTCTCTTGGCTCTTGGTCAAACTTCCAAACTTTTCAAACTTTTTCGAGTCCTATTATA
194 ATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTTTCGAGTTCTTTTATA
* * * * * * ** *
1982 GCATCGATTCTTTACAGTATTCAAGACGATCCATTCCTTCAAGCAATTTTTTGAACATTCCAAGC
259 ACTTCGATTCCTTAAAGTATTCAAGACGATCGATTCCTTCGAGCAATTTTCCGAACATTCCATGC
* * * * **
2047 TCAAGAAATCGGACCATTTGGTCCAAATAGTTTGTCACTTTGTAAACAACTTTTGGTCTTAAAAT
324 TCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCACTTTGTAAAAAACTTTTGGTCTTTGAAT
* * * *
2112 TAAAAACTTATTTACCTAAGAATGGTTTCTCCCTTGGTTCTTGA
389 TAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGA
* *
2156 CTGAACTTTCGAA-TTAGTCAAACTTTTACGTGTTATTTTATAACTTTGGTTCCTTAAAGTATTC
1 CTGAACTTTCGAACTT-GTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTC
* * * * * *
2220 AAGATGATCTATTCCTTCGTGCAATTTTCCAAACATTCCATGCTC-AGGAAATCGCATCATTTGG
65 AAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATTCTCGA-GAAATCGCATCATTTGG
* * * * * *
2284 TCTAAATATTTTATCGTTTTGTAAACAACTTTCGGTCTTTGAATTAAAAACTTATTTATTTGAGA
129 TCCAAATAATTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGA
* * * *
2349 ATTGTTTCTCTCTTGGTTCTTGGTCGAACTTCCGAACTTATCAAACTTTTTTGAGTTCTTCTATA
194 ATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTTTCGAGTTCTTTTATA
* * * *
2414 ACTTCGATTCCTTAAAGTATTCAAGATGATCAATCAATTCCTTCGAGCAATTTTTCGAATATTCC
259 ACTTCGATTCCTTAAAGTATTC-A-A-GA-CGATCGATTCCTTCGAGCAATTTTCCGAACATTCC
* * * * *
2479 ATTCTCGGGAAATCGAATCACTTGGTCCAAATAGTTAGTC-CTTTTGTAAAAAA--------C-T
320 ATGCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCAC-TTTGTAAAAAACTTTTGGTCTT
* * *
2534 T--A-T------TTA--TA--TGAGAATTATTTCTCTCTTGGTTCTAGG
384 TGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGA
* * * * *
2570 CCGAACTTCCGAACTT-TGCAAACTTTTTCGAGTTCTTTTATAACTTTTGTTCCTTAAAGTATTT
1 CTGAACTTTCGAACTTGT-CAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTC
* * ** * *
2634 AAGACGATTCATTTCTTCGAATAATTTTTCGAACATTACGTTCTCTG-GAAATCGCATCATTTGG
65 AAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATTCTC-GAGAAATCGCATCATTTGG
* * * *
2698 TCCAAATAATCTGTCATTTTGTAAACAACTTTTGGTCTTTGGACTAAAAATTTATTTATGTGAGA
129 TCCAAATAATTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGA
** * *
2763 ATTGTTTCTCTCATT-GTTCTTGGCCGAACTTTTGAACATGTCAAAC-TTTTCTATGTTCTTTTA
194 ATTGTTTCTCTC-TTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTTTCGA-GTTCTTTTA
* * * *
2826 TAACTTCGATTTCTTAAAGTATTTAAGACGATCAATTCCTTCGAGCAATTTTCCGAACATTCTAT
257 TAACTTCGATTCCTTAAAGTATTCAAGACGATCGATTCCTTCGAGCAATTTTCCGAACATTCCAT
* * * * *
2891 TCTC-AGGAAATTGCATCCTTTGGTCCAAATGGTTAGTC-CTTTAGTAAAAAACTTTTGGTCTTT
322 GCTCGA-GAAATCGCATCATTTGGTCCAAATAGTTTGTCACTTT-GTAAAAAACTTTTGGTCTTT
* * *
2954 GAATTAAAAACTTATTTATGTGAGAATTATTTCTCTCTTGGTTCTAGGA
385 GAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCT-TGA
* * * * ** *
3003 -AGAACTTCCGAACTTTTCAATCTTTTTTTGAGTTCTTTTATAACTTTGATTCCTTAAAGTATTC
1 CTGAACTTTCGAACTTGTCAAAC-TTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTC
* * * * * *
3067 AAGACAATCCATTTCTTTGAACAATTTTTCGAACATT-CAGTTCT-TAGGAAATCACATCATTTG
65 AAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCA-TTCTCGA-GAAATCGCATCATTTG
* * * *
3130 GTCCAAATAATCTGTCATTTTGTAAACAAATTTTGGTCTTTGGATTAAAAATTTATTTATGTGAG
128 GTCCAAATAATTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAG
*** *
3195 AATTGTTTCTCT-TTGGGTTCTTGATTGAACTTCCGAACTTGTCAAACTTTTTCGAGTTGTTTTA
193 AATTGTTTCTCTCTT-GGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTTTCGAGTTCTTTTA
* * * * * * * *
3259 TAACTTCGATTCCTGAAAGTATTCATGACTATCGATTCCTTCGAGCAATTATCTGAACGTTTCGT
257 TAACTTCGATTCCTTAAAGTATTCAAGACGATCGATTCCTTCGAGCAATTTTCCGAACATTCCAT
* * * * ** *
3324 GCTTG-GTAAATCGCATCATTTGGTGCAAATAGTTTGTCATTTTGTAAACAACTTTTTTTCTTAG
322 GCTCGAG-AAATCGCATCATTTGGTCCAAATAGTTTGTCACTTTGTAAAAAACTTTTGGTCTTTG
** ** * *
3388 AATTAAAAACTTATTTACACGAGAA-TGACCTCTCCCTTGGTTCATGA
386 AATTAAAAACTTATTTACGTGAGAATTG-TTTCTCTCTTGGTTCTTGA
* * * * *
3435 CTGAACTTTCAAACTTGTCAAACTTTTACGATTTATTTTACAACTTCGGTTCCTTAAAGTATTCA
1 CTGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCA
* * ** * * * *
3500 AGACAATCCATTCCTTCGAGTAATTTCCCAAACATTTCATGCTCGGGAAATCGCATCATTTGGT-
66 AGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATTCTCGAGAAATCGCATCATTTGGTC
** * * * * *
3564 TGAATATTTTATCCTTTTATAAACAACTTTCT-GTCTTTGAATTAAAAACTTATTTATGTAAGAA
131 CAAATAATTTGTCATTTTGTAAACAACTTT-TGGTCTTTGAATTAAAAACTTATTTATGTGAGAA
* * * * *
3628 TTGTTTCTCTCTTGGTTCTTGGTCGAATTTTCGAACTTATTAAACTTTTTCGAGTTCTTTTATAA
195 TTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTTTCGAGTTCTTTTATAA
* * * * * *
3693 CTTCGGTTCCTTAAAGTATTCAAGACAATAGATTCTTTCGAGCAATTTTCCTAACATTTCA-GCC
260 CTTCGATTCCTTAAAGTATTCAAGACGATCGATTCCTTCGAGCAATTTTCCGAACATTCCATG-C
* * * * * * *
3757 TCGAGAAATTGTACCATTTGGTCCAAATAGTTCGTC-CTTTTGTAAAAAACCTTCGGTATTTGAA
324 TCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCAC-TTTGTAAAAAACTTTTGGTCTTTGAA
** * *
3821 TTAAAAACTTATTTATTTGAGAATTGTTTCTCTCAT-GTTCTTGG
388 TTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGA
* * * *
3865 CCGAACATTCGAACTTTTCAAACTTTTTCGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCA
1 CTGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCA
* * * * * *** *
3930 AGACAATCCATTCCTTCGAGCCATTTTTCTAACATTCGATTCTCGGGAAATTAAATCATTT-TTC
66 AGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATTCTCGAGAAATCGCATCATTTGGTC
* * * * *
3994 CAAATAATCTGTTATTTTGTAAAAAACTTTTGGTCTTTGGATTAAAAACTTATTTACGTGAGAAT
131 CAAATAATTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAAT
* * * * ** * * * *
4059 TATTTTTCTCTGGGTTATTAACCGAACTTCCGAACTAGTCAAACTTCTACGAGTTATTTT-TAAC
196 TGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTTTCGAGTTCTTTTATAAC
* * * *
4123 TTC-AGTTCCTT-AAGTTTTCAAGACGATCCATTCCTTCTAGCAATTTTTCGAACATTCCATGCT
261 TTCGA-TTCCTTAAAGTATTCAAGACGATCGATTCCTTCGAGCAATTTTCCGAACATTCCATGCT
* * * * * *
4186 CAAGAAATCACATCCTTTGGTCCAAATAGTTTCTTA-TTTCGTAAACAACTTTTGGTCTTTGAAT
325 CGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCACTTT-GTAAAAAACTTTTGGTCTTTGAAT
* * *
4250 TAAAGACTTATTTATGTGAGAATTATTTCTCTCTTGGTTCTTGGA
389 TAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTT-GA
* * * *
4295 C-GAACTTCCGAACTTGTCAAACTTTTTCGAGTTCTTTTATAATTTTGGTTCCTTATAGTATTCA
1 CTGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCA
* * ** * * * * * *
4359 AGACGGTCCATTCCTTCAAGCAA-TTTTCTGAGTATTCCATGCTCAAGAAATCGTATCGTTTCGA
66 AGACGATCCATTCCTTCGAGCAATTTTTC-GAACATTCCATTCTCGAGAAATCGCATCATTTGGT
* * * * * ** * *
4423 CCAAGTAGTTTGTTATTTTGTAAGCAAGTTTTACTCATTGAATT-AAAACTTATTTACGTGAGAA
130 CCAAATAATTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAA
** * * * *
4487 AGGTTTCTCTCTTGGTTCTTGGTCGAACTTCCAAACCTT-TCAAACTTTTTTGAGTTCTATTATA
195 TTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAA-CTTGTCAAACTTTTTCGAGTTCTTTTATA
* * * * * * *
4551 GCTTCGATTCCTTACAA-TATTCAAGACGATCCATTCCTTTGTGCAA-TTTCTCAAACATTTCAA
259 ACTTCGATTCCTTA-AAGTATTCAAGACGATCGATTCCTTCGAGCAATTTTC-CGAACATTCCAT
* * * * * *
4614 ACTCGAGAAATAGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAATAACTTTTGGTCTTAGA
322 GCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCACTTTGTAAAAAACTTTTGGTCTTTGA
* *
4679 ATTAAAAACTTATTTACGTGAGAATGGTTTCTCCCTTGGTTCTTGA
387 ATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGA
* * * * *
4725 CT-AAGC-TTCGAAATTTTCAAACTTTTACGAGTTGTTTTATAACTTCGGTTTCTTAAAGTATTC
1 CTGAA-CTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTC
* * ** * * * * *
4788 AAGACAATTCATTCCTTCGAGCAATTTACCAAACATTCCATGCT-TAGGAAATTGCATCATTAGG
65 AAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATTCTCGA-GAAATCGCATCATTTGG
* * * *
4852 TCCAAATATTTTATCCTTTTGTAAACAACTTTCGGTCTTTGAATTAAAAACTTATTTATGTGAGA
129 TCCAAATAATTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGA
* *
4917 ATTGTTACTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTTAAACTTTTTCGAGTTCTTTTATA
194 ATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTTTCGAGTTCTTTTATA
* * * * * * *
4982 ACTTTGGTTCCTTAAAGTATGCAAGATGATCGATTCACTT-GAACAATTTTTCGAACATTCCATT
259 ACTTCGATTCCTTAAAGTATTCAAGACGATCGATTC-CTTCGAGCAATTTTCCGAACATTCCATG
* * * *
5046 CTCGAGAAATCTCATCATTTGGTCCAAATAGTTAG-CCCTTTTGTAAAAAACTTTCGGTCTTTGA
323 CTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCAC-TTTGTAAAAAACTTTTGGTCTTTGA
* * *
5110 ATTAAAAACTTATTTACGTGAGAATTATTTTTCTCTTGGTTCTAG-
387 ATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGA
* ** * * * *
5155 GTCGAACTTTAAAACGTTG-CAAACTTTTTCGAGTTTTTTTATAACTTTGGTTCCTTAAGGTGTT
1 CT-GAACTTTCGAAC-TTGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATT
* * * * * ** * *
5219 CAAGATGATCCATTTCTTTGAACAAATTTTCGAACATT-TGTTCT-AAGGAAATCACAT-ATTTT
64 CAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATTCTCGA-GAAATCGCATCA-TTT
* * * * * * * * *
5281 GGTCCAAATAATCTATCATTTTGAAAATAACTTTTGGT-TCATGGATTAAAAATTTATTTTTTTG
127 GGTCCAAATAATTTGTCATTTTGTAAACAACTTTTGGTCT-TTGAATTAAAAACTTATTTATGTG
* * * * * * *
5345 AGAAGTGTTTCTCTTTTGGTTCTTGGCCGAACTTCTGAACATGTCGAACTTTTTCTAGTACTTTT
191 AGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTTTCGAGTTCTTTT
** * * * * * *
5410 ATAACTTCTTTTCCTTAAACTATTCATGACTA-CAGATTCCTTCGGGCAATTATCCAAACATTCC
256 ATAACTTCGATTCCTTAAAGTATTCAAGACGATC-GATTCCTTCGAGCAATTTTCCGAACATTCC
* * * ** * * * *
5474 ATGCTCGATAAATTGCATCAGTTGGTTAAAATAGTTCGTCATTTTGTAAACAACTTTTGGTCTTA
320 ATGCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCACTTTGTAAAAAACTTTTGGTCTTT
* * * *
5539 GAATTAAAAACTTATTTACGTGACAATGGTTTCTCCCTTGGTTCATGA
385 GAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGA
* * * * * *
5587 TTGAACTTTCAAACTTGTCAAACTTTTACGATTTATGTTATAACTTCGGTTCCTTAAAGTATTCA
1 CTGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCA
** * ** * * * *
5652 AGTTGATCCATTCCTTCAAAAAATTTTCCAAACATTCCATACTCGAGAAATCGCATCATTTGGCC
66 AGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATTCTCGAGAAATCGCATCATTTGGTC
* * * *
5717 CAAATATTTTATCCTTTTGTAAACAACTTTCGGTCTTTGAATTAAAAACTTATTTATGTGAGAAT
131 CAAATAATTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAAT
* * * * *
5782 TGTTTTTCTCTTGGTTCTTGGTCGAACTTTCGAACTTGTCAAACTTTTACGAGTTCATTTATAAC
196 TGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTTTCGAGTTCTTTTATAAC
* * * * * * * * * *
5847 TTTGGTTCTTTAAAGTACTCAAAATGATCAATTCCTTTGAGCAATTTTCCAAACATTCCATACTC
261 TTCGATTCCTTAAAGTATTCAAGACGATCGATTCCTTCGAGCAATTTTCCGAACATTCCATGCTC
* *
5912 GGGAAATCGCATCATTTGGTCCAAATAGTTTGTC-CTTTTGTAAAAAAATTTTGGTCTTTGAATT
326 GAGAAATCGCATCATTTGGTCCAAATAGTTTGTCAC-TTTGTAAAAAACTTTTGGTCTTTGAATT
* **
5976 AAATACTTATTTACGTGAGAATTGTTTCTCTCTTATTTCTT-A
390 AAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGA
* * * ** * *
6018 GCCGAACTTTCGAATTTGTCAAACTTTTTACGACTTCTTTTATAACTTCAGTTTCTTAATGTATT
1 -CTGAACTTTCGAACTTGTCAAAC-TTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATT
* ** * * * * * * * *
6083 CAAGAC-AACTCATTCCTTTTAGAAAATTTCCAAACATTCCATGCTTGGGAAATCGTATCATTTG
64 CAAGACGATC-CATTCCTTCGAGCAATTTTTCGAACATTCCATTCTCGAGAAATCGCATCATTTG
* * * * * *
6147 GTCCAAAT-AGTTGTCAGTTTGTAAAGAAATTTTGGTCTTTAAATTAAAAACTTATTTACGTG-G
128 GTCCAAATAATTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAG
* * ** * *
6210 AATTGTTTCTCTCTTGGTTCTTGGCTGAACATCTAAACTTGTCAAACTTTTACAAGTTCTTTTAT
193 AATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTTTCGAGTTCTTTTAT
* * * * * * ** *
6275 AACTTCTATTCCTTAAGGTATTCAATACGATCCATTCATTCGAGTAATTTTTTGAACATTCCTTG
258 AACTTCGATTCCTTAAAGTATTCAAGACGATCGATTCCTTCGAGCAATTTTCCGAACATTCCATG
* * * * **
6340 CTCGAGAAATCGCATCATTTCGTCCAAATAATTTGTCATTTTGT--AATACTTTTGGTCTTAAAA
323 CTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCACTTTGTAAAAAACTTTTGGTCTTTGAA
* * *
6403 TTAAAAACTTATTTTCGTGGGAATGGTTTCTC-CATTGGTTCTTGA
388 TTAAAAACTTATTTACGTGAGAATTGTTTCTCTC-TTGGTTCTTGA
* * ** *
6448 CTGAACTTTCGAACTTGTCAATCTTTTACGAGTTCTTTTGTAACTTCAGTTTCTTAAAGTATTCA
1 CTGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCA
* * *
6513 AGACGATTCATTCCTTTGAGCAATTTTTC-AATCATTCCATGCTCGAGAAATCGCATCATTTGGT
66 AGACGATCCATTCCTTCGAGCAATTTTTCGAA-CATTCCATTCTCGAGAAATCGCATCATTTGGT
* * * * *
6577 CCAAATATTTTGTCCTTTTGTATACAACTTTCGATCTTTGAATTAAAAACTTATTTATGTGAGAA
130 CCAAATAATTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAA
* * ** * * *
6642 TTGTTTCTTTCTTGGTTCTTCGCCGAACTTCTAAACTTGTCAAACTTTTTGGAGCTCTTTTTTAA
195 TTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTTTCGAGTTCTTTTATAA
* * * * *
6707 CTTCGGTTCCTTAAAGTATTCATGATGATCGATTCCTTCGAGCAATTTTCAGAACATTCCATTCT
260 CTTCGATTCCTTAAAGTATTCAAGACGATCGATTCCTTCGAGCAATTTTCCGAACATTCCATGCT
* ** * * *
6772 TGAGAAATCATATCATTTGGTCCAAATAGTTTGTC-CTTTTGTAAAAGACTTTCGGTCTATGAAT
325 CGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCAC-TTTGTAAAAAACTTTTGGTCTTTGAAT
*
6836 TAAAAACTTATATACGTGAGAATT
389 TAAAAACTTATTTACGTGAGAATT
6860 ATTT
Statistics
Matches: 5245, Mismatches: 1003, Indels: 327
0.80 0.15 0.05
Matches are distributed among these distances:
409 3 0.00
410 73 0.01
411 2 0.00
412 1 0.00
413 7 0.00
414 247 0.05
415 4 0.00
416 9 0.00
417 332 0.06
418 6 0.00
419 4 0.00
421 2 0.00
422 5 0.00
423 3 0.00
424 1 0.00
425 2 0.00
426 91 0.02
427 141 0.03
428 310 0.06
429 361 0.07
430 645 0.12
431 1186 0.23
432 922 0.18
433 800 0.15
434 13 0.00
435 3 0.00
436 72 0.01
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (432 bp):
CTGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCA
AGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATTCTCGAGAAATCGCATCATTTGGTC
CAAATAATTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAAT
TGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTTTCGAGTTCTTTTATAAC
TTCGATTCCTTAAAGTATTCAAGACGATCGATTCCTTCGAGCAATTTTCCGAACATTCCATGCTC
GAGAAATCGCATCATTTGGTCCAAATAGTTTGTCACTTTGTAAAAAACTTTTGGTCTTTGAATTA
AAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGA
Found at i:2577 original size:198 final size:194
Alignment explanation
Indices: 2329--2728 Score: 527
Period size: 198 Copynumber: 2.0 Consensus size: 194
2319 TCTTTGAATT
* * * *
2329 AAAAACTTATTTATTTGAGAATTGTTTCTCTCTTGGTTCTTGGTCGAACTTCCGAACTTAT-CAA
1 AAAAACTTATTTATATGAGAATTATTTCTCTCTTGGTTCTAGGCCGAACTTCCGAACTT-TGCAA
* *
2393 ACTTTTTTGAGTTCTTCTATAAC-TTCGATTCCTTAAAGTATTCAAGATGATCAATCAATTCCTT
65 ACTTTTTCGAGTTCTTCTATAACTTTCG-TTCCTTAAAGTATTCAAGACGAT---TC-ATTCCTT
* * * * *
2457 CGAGCAATTTTTCGAATATTCCATTCTCGGGAAATCGAATCACTTGGTCCAAATAGT-TAGTCCT
125 CGAACAATTTTTCGAACATTACATTCTCGGGAAATCGAATCACTTGGTCCAAATAATCT-GTCAT
2521 TTTGTA
189 TTTGTA
2527 AAAAACTTATTTATATGAGAATTATTTCTCTCTTGGTTCTAGGCCGAACTTCCGAACTTTGCAAA
1 AAAAACTTATTTATATGAGAATTATTTCTCTCTTGGTTCTAGGCCGAACTTCCGAACTTTGCAAA
* * * * *
2592 CTTTTTCGAGTTCTTTTATAACTTTTGTTCCTTAAAGTATTTAAGACGATTCATTTCTTCGAATA
66 CTTTTTCGAGTTCTTCTATAACTTTCGTTCCTTAAAGTATTCAAGACGATTCATTCCTTCGAACA
* * * *
2657 ATTTTTCGAACATTACGTTCTCTGGAAATCGCATCATTTGGTCCAAATAATCTGTCATTTTGTA
131 ATTTTTCGAACATTACATTCTCGGGAAATCGAATCACTTGGTCCAAATAATCTGTCATTTTGTA
*
2721 AACAACTT
1 AAAAACTT
2729 TTGGTCTTTG
Statistics
Matches: 178, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
194 71 0.40
195 3 0.02
197 1 0.01
198 100 0.56
199 3 0.02
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (194 bp):
AAAAACTTATTTATATGAGAATTATTTCTCTCTTGGTTCTAGGCCGAACTTCCGAACTTTGCAAA
CTTTTTCGAGTTCTTCTATAACTTTCGTTCCTTAAAGTATTCAAGACGATTCATTCCTTCGAACA
ATTTTTCGAACATTACATTCTCGGGAAATCGAATCACTTGGTCCAAATAATCTGTCATTTTGTA
Done.