Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012840.1 Corchorus capsularis cultivar CVL-1 contig12861, 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: 97568
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2440 original size:331 final size:327
Alignment explanation
Indices: 2035--7586 Score: 4051
Period size: 331 Copynumber: 16.8 Consensus size: 327
2025 TGTTTTGTTT
* * * **
2035 TTTAATTAGAAATGAATTCTGAAAAAAGATAGGAAAAACGATATTAAAAGCGAGAAAAGCCCTTC
1 TTTAATTAGAAATTAATTC-G-AAAAA-ATAGG-AAAATGATATTAAAAGCGTGAAAATACCTTC
* *
2100 AATATTTTTGGCGTTGAATTATATATTTTTTACGAGTATTGTGGCTAAAAATTGAGGGAAAGTAT
62 AATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGA-GGAAA-TAT
* * * * * * *** *
2165 -TTT-GGG-AAATTTTTGCAAAATATTAGCCAAAATTGT-TAACATCATGATTTTTTTTTTTTTG
125 CTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAAAATCATCA----CGGTTTTTGG
* * * * * * *
2226 CAAAAAAATGCGTTCTTTGGACCCGAGAT-AGTTTTGCATGATTTTTAGTGTCAAGACTCCCTGA
186 C-AAAAAACGCGTTC-TGGGACCCG-GGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGA
*
2290 AATATCTATATTCATC-ATCAAATCTCAACCACATTGCATTTAAGGATTTGTTTTTACGAGCATC
248 AATATCTATATTCATCAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATC
* *
2354 TAAATCTAGTTTCGA
313 TGAATCTTGTTTCGA
2369 TTTAATTAGAAATTAATTCGAAAAAAGTAGGAAAATGATATTAAAAGCGT-AAAATACCCTTCAA
1 TTTAATTAGAAATTAATTCGAAAAAA-TAGGAAAATGATATTAAAAGCGTGAAAATA-CCTTCAA
* * * *
2433 TATTTTTGGTGTTGAATTATATATTTTTTTATGAGTATTTTAGCCAAAAAATTCAGGAAATATCT
64 TATTTTTGGCGTTGAATTATATA-TTTTTTATGAGTATTTT-GGCTAAAAATTGAGGAAATATCT
* *
2498 TTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACGGTTTTTGGCTAAA
127 TTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAA-AATCATCACGGTTTTTGGCAAAA
* * * * * * * *
2563 CACACGTTCCAGGGCCCCGGGTCAGTTTTGCCTTATTTTAGGC-CCTAAGACT-CTTGAGATAT-
191 AACGCGTT-CTGGGACCCGGGTCAGTTTTGCATGATTTTTGGCGCC-AAGACTCCTTGAAATATC
* * * *
2625 TCATATTCATCTAATCAAATCTTAGGCACATTGCATTTAATGATTT-TTTTTACGAGCATCTGGA
254 T-ATATTCATC-AATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAA
2689 TCTTGTTTCGA
317 TCTTGTTTCGA
* * * * *
2700 TTTAATTTGAAATTAATTCATAAAAAATATGAAAAATGATATGAAAAGCTTGAAAAGT-CCTTCA
1 TTTAATTAGAAATTAATTC-GAAAAAATA-GGAAAATGATATTAAAAGCGTGAAAA-TACCTTCA
* * *
2764 ATCTTTTTGGC-TCTGAATTATATATTTTTTATGACTATTTTAGCTAAAAATT-ATGGAAATATC
63 ATATTTTTGGCGT-TGAATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGA-GGAAATATC
* * *** *
2827 TTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAA-CTATTAAAATTTTTAGCTA
126 TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAA-AATC-ATCACGGTTTTTGGC-A
* * * * *
2891 AAAAA-GCGTTCTCGGACCC-CGACTATGTTTTCCATGATTTTT-G-G-C--G------T-AGAT
188 AAAAACGCGTTCTGGGACCCGGGTC-A-GTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAAT
* * * * * **
2942 ATCCATATTCATCTAATCAAATCTCAGTCAAATTGGATTTAAGAATTTGTTTTTAAAAGCATCTG
251 ATCTATATTCATC-AATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTG
*
3007 AATTTTGTTTCGA
315 AATCTTGTTTCGA
* * * * * * * *
3020 TTTAATTGGAAATCAATGCAAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGT-TCTCCAA
1 TTTAATTAGAAATTAATTCGAAAAAATA-GGAAAATGATATTAAAAGCGTGAAAA-TACCTTCAA
* * * * ** *
3084 TTTTTTTTGCGTTAAATTATATATTTGTTATGAGTATTTTGTTTAAAAATTGATGAAATAT-TCT
64 TATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGAGGAAATATCT-T
* * * * * *
3148 TCGGGTCATTTTTTGTAAAATTTTAG-AGAACATCATGTACTAA-CTATCACGGTTTTTTGGCTA
128 TCGGGTCAATTTTTGCAAAATTTTAGCCGAA-ATCGTGTA-AAATC-ATCACGG-TTTTTGGCAA
* * * * *
3211 AAAACGCATT-TCGAGG-CCAGGACTCATTTTTCCATGATTTTTGGCGCCGAA-ACTCCTTGAAA
189 AAAACGCGTTCT-G-GGACCCGG-GTCAGTTTTGCATGATTTTTGGCGCC-AAGACTCCTTGAAA
* * ** *
3273 TATCTATATTTATCCAATAAAATCTTTGCTACA-TGACATTTAAGGATTTGTTTTTACGAGCATC
250 TATCTATATTCAT-CAATCAAATCTCAGCCACATTG-CATTTAAGGATTTGTTTTTACGAGCATC
*
3337 TGATTCTTGTTTCGA
313 TGAATCTTGTTTCGA
* *
3352 TTTTATTAGAAATTAATTC-AGAAAAATATGAAAAAATGATATTAAAAGCGTGAAAA-ATCCTTC
1 TTTAATTAGAAATTAATTCGA-AAAAATA-G-GAAAATGATATTAAAAGCGTGAAAATA-CCTTC
** * * * * * *
3415 AACCTTTATGGCGTTTAATTATATATTTTTCATCAGTATTATGGCTAAAAATTGAGGAAATATAT
62 AATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGAGGAAATATCT
* *
3480 TTCGGGTCAATTTTTGCAAAACTTTAGCCGAAATCGTGTAATAATCATCACACGGTTTTTGGCTA
127 TTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAA-AATCAT--CACGGTTTTTGGCAA
* * * * * * * * * *
3545 AACACGCGTTCCGGG-CACGGTTCAATTTTGAATAATTTTTGACACCCAGACTCCTTGAAATATC
189 AAAACGCGTTCTGGGACCCGGGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATC
* * *
3609 TATATTCATCTAACCAAATCTCAG---C----C--------A-TTGTTTTTACAAGCATATGAAT
254 TATATTCATC-AATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAAT
* *
3658 CATGTTTCGT
318 CTTGTTTCGA
* * *
3668 TTTAATTAGAAATCAATTTGGAAAAAAATAGGAAAAATGATATTAAAAGCGTGAAAAGACCTTCA
1 TTTAATTAGAAATTAA-TTCG-AAAAAATAGG-AAAATGATATTAAAAGCGTGAAAATACCTTCA
*
3733 ATATTTTTGGCGTAGAATATTTTTGGCGTAGAATTATATATTTTTTTATGAGTATTGTGGCTAAA
63 ATATTTTTGGC---G--------T----T-GAATTATATA-TTTTTTATGAGTATTTTGGCTAAA
* *** * * *
3798 ACTTGAGGAAA-AGTAAATCGGGTCAATTTTTGCAAAATATTAGCTGAAATTGTGTAACATCACG
111 AATTGAGGAAATA-TCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAA-A--A--
* * *** *** * * * *
3862 GTTTTAATTTTTATTTTTTATTTTTTTTAATAAAAGGCGTTCCGGGGCCCTGGGTCAGTTTTCCA
170 ----TCA---TCA----CGGTTTTTGGCAA-AAAACGCGTTCTGGGACCC-GGGTCAGTTTTGCA
* * * * *
3927 TGATTTTTAGTG-CAAGACTTCTTGAAATGTCTATATTCATCTAATCAAATCTCAGCCACATTGG
222 TGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATC-AATCAAATCTCAGCCACATTGC
* * *
3991 ATTTAAGGATTTGTTTTT-TGAGCATCTAAATCTTGTTTCAA
286 ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGA
* *
4032 TTTAATTAGAAATTAATTCGGAAAAAGTAGGAAAAACGATATTAAAAGCGT-AAAATATCCTTCA
1 TTTAATTAGAAATTAATTC-GAAAAAATAGG-AAAATGATATTAAAAGCGTGAAAATA-CCTTCA
* * * * *
4096 ATATTTTTGGCGTTAAATTGTATATTTTTTATGAGTATTTTAGCCAATAATTGAGGAAATATCTT
63 ATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGAGGAAATATCTT
* * * * * *
4161 TCCGGTTAGTTTTTTCAAAATTTTAGCCGAAATCGTGTAATAATCATCATGGTTTTTGGCTAAAA
128 TCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAA-AATCATCACGGTTTTTGGCAAAAA
* * * * * ** * *
4226 A-GCGTTTCAGGGTCCCAGGTCAATTTTGCATTATTTTTGGCGATAAGACTCCTTGAGATATCCA
192 ACGCG-TTCTGGGACCCGGGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTA
* * * * *
4290 GATTCATCTAATCAAATCTCAGGCACATTGCATTTAATGATTT-TTTTTGCGAGCATCTGTATCT
256 TATTCATC-AATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCT
*
4354 TGTTGCGA
320 TGTTTCGA
* ** * * *
4362 TTTAATTAGAAATTAATTC-ATAAAAATATGAAAAACAATATGAAAAGCTTGAAAAGT-TCTTCA
1 TTTAATTAGAAATTAATTCGA-AAAAATA-GGAAAATGATATTAAAAGCGTGAAAA-TACCTTCA
* * * * * *
4425 ATCTTTTTGGCTTTGAATTATATATATTTTATGACTATTTTAGCTAAAAATTGAGAAAATATCTT
63 ATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGAGGAAATATCTT
* * * *** * *
4490 TCGGGTCAATTTTTACAAAATTTTAGCTGAAATCGGGTAATAACTC-TCATAATTTTTAGCTAAA
128 TCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAA-AA-TCATCACGGTTTTTGGCAAAA
* * ** * * * * *
4554 AATGGGTTCTGGGACCCCGACTCTGTTTTCCATTATTTTTGGCGCCAAGACTCCTTGAGATATCC
191 AACGCGTTCTGGGA-CCCGGGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCT
* * * ** *
4619 ATATTCATCTAATCAAATCTCAGGCACATTGGATTTAAGAATTTGTTTTTAAAAGCATTTGAATC
255 ATATTCATC-AATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATC
4684 TTGTTTCGA
319 TTGTTTCGA
* * * * * *
4693 TTTAATTGGAAATTAATT-TAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGT-TCTCCA
1 TTTAATTAGAAATTAATTCGA-AAAAATA-GGAAAATGATATTAAAAGCGTGAAAA-TACCTTCA
* * * * *
4756 ATATTTTTGGCGTTAAATTATAT-TTTTGTTATGAGTATTTTGTCCAAAAATTGAGGAAAAATTT
63 ATATTTTTGGCGTTGAATTATATATTTT-TTATGAGTATTTTGGCTAAAAATTGAGGAAATATCT
* * * * * * *
4820 TTCGGGTCATTTTTTGC-AAATTTCTAGCCAAAATCATGTACTAACCATCACGGTTTTTGACTAA
127 TTCGGGTCAATTTTTGCAAAATTT-TAGCCGAAATCGTGTA-AAATCATCACGGTTTTTGGCAAA
** * * * * *
4884 AAACGTATT-TCGAGG-CCAGGGCTCAGTTTTCCATGATTTTCGGCGCCGACACTCCTTGAAATA
190 AAACGCGTTCT-G-GGACCCGGG-TCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATA
* ** *
4947 TCTATATTCATCTAATAAAATCTTTGCTACA-TGACATTTAAGGATTTGTTTTTACGAGCATCTG
252 TCTATATTCATC-AATCAAATCTCAGCCACATTG-CATTTAAGGATTTGTTTTTACGAGCATCTG
* *
5011 ATTCTTGTTTCAA
315 AATCTTGTTTCGA
* * *
5024 TTT-TTTAAAAAATTAATTCAGAAAAAATATGAAAAATGATATTAAAAGCGTGAAAA-ACCCTTC
1 TTTAATT-AGAAATTAATTC-GAAAAAATA-GGAAAATGATATTAAAAGCGTGAAAATA-CCTTC
* * * * *
5087 AATATTTTTGGTGTTTAATTATATA-TTTTCATCAGTATTATGGCTAAAAATTGAGGAAATATCT
62 AATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGAGGAAATATCT
* *
5151 TTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACACCGTTTTTGGCTA
127 TTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAA-AATCAT--CACGGTTTTTGGCAA
* * * * * * *
5216 AAAACGCGTTCTGGG-CCCGGTTCAATTTTGAATAATTTTTTGCACCAAGAATCCTTGAAATATC
189 AAAACGCGTTCTGGGACCCGGGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATC
* * *
5280 TATATTCATCTAACCAAA--T---CC-CA--GC-------CA-TTGTTTTTACAAGCATCTGAAT
254 TATATTCATC-AATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAAT
* * *
5329 CATGTTTTGTTT
318 CTTGTTTCG--A
* *
5341 TTTAATTAGAAATGAATTCTGAAACAAGATAGGAAAAACGATATTAAAAGCGTGAAAA-ACCCTT
1 TTTAATTAGAAATTAATTC-GAAA-AA-ATAGG-AAAATGATATTAAAAGCGTGAAAATA-CCTT
*
5405 CAATATTTTTGGCGTTGAATTATATATTTTTTTATGAGTATTGTGGCTAAAAATTGAGGGAAAGT
61 CAATATTTTTGGCGTTGAATTATATA-TTTTTTATGAGTATTTTGGCTAAAAATTGA-GGAAA-T
* * * *****
5470 AT-TTT-GGGTCAATTTTTGCAAAATATTAGCCGAAATTGT-TAACATCATGGTTTTTTTTTGTT
123 ATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAAAATCAT-CACGGTTTTTG--
* * *
5532 GCAAAAAACGCGTTCTGGGGACCCGTGAT-AGTTTTGCATGATTTTTAGTGCCAAGACT-CTCTG
185 GCAAAAAACGCGTTCT-GGGACCCG-GGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCT-TG
*
5595 AAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCA
247 AAATATCTATATTCATC-AATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCA
* *
5660 TCTAAATCTAGTTTCGA
311 TCTGAATCTTGTTTCGA
* * *
5677 TTTAATTAGAAATTCATTCAGAAAAAGTAGGAAAAACGATATTAAAAGCGT-AAAATACCCTTCA
1 TTTAATTAGAAATTAATTC-GAAAAAATAGG-AAAATGATATTAAAAGCGTGAAAATA-CCTTCA
* * * * *
5741 ATATTTTT-TCTGTTGAATTATATATTTTTTATGAGTATTTTAGCCT-TAAATTAAAGAAATATC
63 ATATTTTTGGC-GTTGAATTATATATTTTTTATGAGTATTTT-GGCTAAAAATTGAGGAAATATC
* *
5804 TTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACGGTTTTTGGCTAA
126 TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAA-AATCATCACGGTTTTTGGCAAA
* * * * *
5869 AAACGCGTTTCAGGGCCCCGGGTCAGTTTTGCAT-TTTTTTTGC-CCTAAGACTCCTTGAGATAT
190 AAACGCG-TTCTGGGACCCGGGTCAGTTTTGCATGATTTTTGGCGCC-AAGACTCCTTGAAATAT
* * * * * * * *
5932 -TCATATTTATCTAATCAAATCTTAGGCAAATTGCATTTAATG-TTTTTTTTTACTAGCATCTGG
253 CT-ATATTCATC-AATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGA
5995 ATCTTGTTTCGA
316 ATCTTGTTTCGA
* * * * *
6007 TTTAATTTGAAATTAATTCATAAAAAAATATGAAAATGATATGAAAAGCTTGAAAAGT-CCTTCA
1 TTTAATTAGAAATTAATTC--GAAAAAATAGGAAAATGATATTAAAAGCGTGAAAA-TACCTTCA
* * * * *
6071 ATCTTTTTGGCTTTGAATTATTTATTTTTTATGACTATTTTAGCTAAAAATT-ATGGAAATATCT
63 ATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGA-GGAAATATCT
* * ** *
6135 TTCGGCTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAA-CTATCACAATTTTTAGCTAA
127 TTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAA-AATC-ATCACGGTTTTTGGC-AA
** * * * *
6199 AAAA-GCGTTCTGGGATCCCGACTCTGTTTTTCCATGATTTTT---G----G--T--AT-AGATA
189 AAAACGCGTTCTGGGA-CCCGGGTCAG-TTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATA
* *
6251 TCCATATTCATCTAATCAAATCTCAG---C----C--------ATTT-TTTTTACAAGCATCTGA
252 TCTATATTCATC-AATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGA
* *
6300 ATCATGTTTCGT
316 ATCTTGTTTCGA
* * * * * * *
6312 TTTAATTAGAAGTCAATTTGGAAAATAATAGGAAAAACGATATTAATAGCGTGAAAAGACCTTTA
1 TTTAATTAGAAATTAA-TTCGAAAA-AATAGG-AAAATGATATTAAAAGCGTGAAAATACCTTCA
* *
6377 ATATTTTTGGTGTTGAATTATATATAATTTTTATGAGTATTGTGGCTAAAAATTGAGGGAAATTA
63 ATATTTTTGGCGTTGAATTATATAT--TTTTTATGAGTATTTTGGCTAAAAATTGA-GGAAA-T-
* * * * ** * *****
6442 AGTATTTCAGATCAATTTTTGCAAAATATTAGCCGAAATTATGTAACATCACTGTTTTTTTTTCT
123 A-TCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAAAATCA-------TCACGGT
* * * * * *
6507 TTTTTGCAAAAAACGCGTTCCGGTGCCCCGGGTCAGTTTTGCATGATTTTTAGTGTCAAGACTCC
180 TTTTGGCAAAAAACGCGTTCTGG-GACCCGGGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC
* **
6572 TTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTTTGA
244 TTGAAATATCTATATTCATC-AATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGA
**
6637 GCATCCAAATCTTGTTTCGA
308 GCATCTGAATCTTGTTTCGA
* *
6657 TTTAATTAGAAATTAATTCGGAAAAAGTAGGAAAAACT-ATATTAAAAGCAT-AAAATATCCTTC
1 TTTAATTAGAAATTAATTC-GAAAAAATAGG-AAAA-TGATATTAAAAGCGTGAAAATA-CCTTC
* * * * *
6720 AATATTTTTGGTGTTGAATTATATACTTTTAATGAGTA-TTTAGCCAAAAATTGAGGAAATATCT
62 AATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGAGGAAATATCT
* * * *
6784 TTCCGGTCAATTTTTGCAAAATTTTAGCCGAAATCGAGTAATAATCATCACGGTTTTTTGCTAAA
127 TTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAA-AATCATCACGGTTTTTGGCAAAA
* * * * * *
6849 AACGCATTTCAGGG-CCCAGGGTCTGTTTTGCATTATTTTTGGCGCTAAGACTCCTTGAGATATC
191 AACGC-GTTCTGGGACCC-GGGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATC
** * * * * *
6913 CGTATTCATCTAATCAAATCTCAGGCACATTGCATTTAATGATTTTTTTTTTACGAGCATTTGGA
254 TATATTCATC-AATCAAATCTCAGCCACATTGCATTTAAGGA-TTTGTTTTTACGAGCATCTGAA
*
6978 TCATGTTTCGA
317 TCTTGTTTCGA
* * *
6989 TTTAATTAGAAATTAATTC---ATAA-A--AAAAT-ATATGAAAAGCTTGAAAAGT-CCTTCAAT
1 TTTAATTAGAAATTAATTCGAAAAAATAGGAAAATGATATTAAAAGCGTGAAAA-TACCTTCAAT
* * * * *
7046 CTTTTTGG-GTTTGAATCATATATTTTTTATGACTATTTTAGCTAAAAATTGAGGAAATATCTTC
65 ATTTTTGGCG-TTGAATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGAGGAAATATCTTT
* * * *
7110 CGGGTCAATTTTTACAAAATTTTAGCCAAAATCGTGTAATAA-CTATCA-GAATTTTTAGCTAAA
129 CGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAA-AATC-ATCACG-GTTTTTGGC-AAA
* ** * * * * *
7173 AAA-GCGTTCTAGGACCCCGCCTCAATTTTCCATGATTTATGGCGTCAAGACTCCTTGAGATATC
190 AAACGCGTTCTGGGA-CCCGGGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATC
* * * **
7237 TATATTCATCTAATCAAATCTTAGCCACATTGGATTTAAGAATTTGTTTTTAAAAGCATCTGAAT
254 TATATTCATC-AATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAAT
7302 CTTGTTTCGA
318 CTTGTTTCGA
* * * * *
7312 TTTAATTGGAAATTAATTC-AGAAAAATATGAAAAATGATATTAAAAGTGTGAAAAGT-TC-TCC
1 TTTAATTAGAAATTAATTCGA-AAAAATA-GGAAAATGATATTAAAAGCGTGAAAA-TACCTTCA
* * * * ** * * *
7374 ATTTTTTTGGTGTTAAATTATATATTTGTTATGAGTATTTTCTCCAAAAATTGAGGAAAAATTTT
63 ATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGAGGAAATATCTT
* * * ** * *
7439 TCGGGTCAATTTTTGTAAAATTTTTGCCAAAATCAAGTAATAACCATCACGGTTTTTGGCTAAAA
128 TCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAA-AATCATCACGGTTTTTGGCAAAAA
* * * * * *
7504 ACGCATT-TCGAGG-TCAGGGCTCAGTTTTACATGATTTTTGGCGCCGACACTCCTTG-AATATC
192 ACGCGTTCT-G-GGACCCGGG-TCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATC
*
7566 TATATTCATCTAATAAAATCT
254 TATATTCATC-AATCAAATCT
7587 TTGCTACATG
Statistics
Matches: 4184, Mismatches: 739, Indels: 595
0.76 0.13 0.11
Matches are distributed among these distances:
304 4 0.00
305 43 0.01
306 51 0.01
308 24 0.01
309 6 0.00
310 1 0.00
311 3 0.00
312 38 0.01
313 1 0.00
315 26 0.01
316 42 0.01
317 79 0.02
318 46 0.01
319 238 0.06
320 119 0.03
321 68 0.02
322 63 0.02
323 108 0.03
324 160 0.04
325 14 0.00
326 5 0.00
327 4 0.00
328 10 0.00
329 256 0.06
330 651 0.16
331 763 0.18
332 425 0.10
333 230 0.05
334 205 0.05
335 17 0.00
336 28 0.01
337 38 0.01
338 33 0.01
339 1 0.00
340 5 0.00
341 13 0.00
342 13 0.00
343 6 0.00
344 57 0.01
345 42 0.01
346 65 0.02
347 15 0.00
348 14 0.00
349 41 0.01
350 17 0.00
352 2 0.00
360 1 0.00
362 5 0.00
363 47 0.01
364 33 0.01
365 8 0.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (327 bp):
TTTAATTAGAAATTAATTCGAAAAAATAGGAAAATGATATTAAAAGCGTGAAAATACCTTCAATA
TTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGAGGAAATATCTTTCG
GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAAAATCATCACGGTTTTTGGCAAAAAACGC
GTTCTGGGACCCGGGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTC
ATCAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTC
GA
Found at i:3753 original size:16 final size:16
Alignment explanation
Indices: 3732--3766 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
3722 AAAGACCTTC
3732 AATATTTTTGGCGTAG
1 AATATTTTTGGCGTAG
3748 AATATTTTTGGCGTAG
1 AATATTTTTGGCGTAG
3764 AAT
1 AAT
3767 TATATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.43
Consensus pattern (16 bp):
AATATTTTTGGCGTAG
Found at i:7843 original size:13 final size:12
Alignment explanation
Indices: 7824--7853 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
7814 TAGTATTTAG
7824 CCAAAGCCCAAA
1 CCAAAGCCCAAA
7836 CACAAAGCCCAAA
1 C-CAAAGCCCAAA
7849 CCAAA
1 CCAAA
7854 TCTAATCCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.53, C:0.40, G:0.07, T:0.00
Consensus pattern (12 bp):
CCAAAGCCCAAA
Found at i:7927 original size:13 final size:13
Alignment explanation
Indices: 7909--7933 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7899 TAATTTGATA
7909 AAAAAAAAAACTG
1 AAAAAAAAAACTG
7922 AAAAAAAAAACT
1 AAAAAAAAAACT
7934 AAGTCTAACG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.08, G:0.04, T:0.08
Consensus pattern (13 bp):
AAAAAAAAAACTG
Found at i:10497 original size:988 final size:979
Alignment explanation
Indices: 8572--10499 Score: 2254
Period size: 988 Copynumber: 2.0 Consensus size: 979
8562 GTTTTTTATT
* * *
8572 CATTGCATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTTATTAGAAATTAAT
1 CATTGCATTTAAGGATTTGTTTTTACAAGCATATAAATCTTGTTTCGATTTAATTAGAAATTAAT
* *
8637 TCAGAAAAAATATGAAAAACGATATTAAAAGCATGAAAAGCCCTTCAATCTTTTTGGCGTTGAAT
66 TAAGAAAAAATATGAAAAACGATATGAAAAGCATGAAAAGCCCTTCAATCTTTTTGGCGTTGAAT
* ** * *
8702 TATATATTTTTCATCAGTATTATGGCTAAAAATTGAGGAAACATCTTTTGAGTCAATTTTTGCAA
131 TATATATTTTTCATCACTATTATACCTAAAAATTGAGGAAACATCTTTCGAGTCAATTTTTACAA
* * * ** * **
8767 AATTTTAGCCGAAATCGTGTAATAATCATCACATGATTTTTGGCTAAAAATGTGTTTCGGGCACG
196 AATTTTAACCGAAATCGTGTAATAATCATCACA-GATTTTTAGCTAAAAAAGCATTTAGACCACG
** * * *
8832 GTTCAATTTTGAATAATTTTTGGCACCGAGACTCCTTGAAATATCTATCTATATTCATCTAACCA
260 ACTCAATTTTCAATAATTTTTGGCACCAAGACTCCTTGAAATATCTATCTATACTCATCTAACCA
* * * * * * ** *
8897 AATCCCAGCCATTGTTTTTATAAGCATCTGAATGATGTTTCGTTTTAATTAGAAATCAGTTCGGA
325 AATACAAGCAATTGTTTTTAAAAGCATCCGAATCATGTTTCAATTTAATTAGAAATCAATTC-G-
* ** * *
8962 AAAAAAATAGGAAAAACGATATTAAAAGCGTGGAAAGCCGTTTAATATTTTTAGCATTGAATTAT
388 AAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGCCGTCCAATATTGTTAGCATTAAATTAT
* * *
9027 ATATTTTTATGAGTATTGTGGCTAAAAATTGAGAAAAAGTATTTCGGGTCAATTTTTGCAAAATA
453 ATATTTTTATGAGTATTGTGGCCAAAAATTGAGAAAAAATATTTAGGGTCAATTTTTGCAAAATA
* * ** * * *
9092 TTAGCCGAAATTGTGTAACATCACGGTTTTTTTTTTTTTGCAAAAAACGCGTTCCAGGGCGCCGG
518 GTAGCCAAAATCATGTAACATCACGG------TTTTTTGGCAAAAAACGCGTTCCAGGGCCCCGA
* * * * * * *
9157 GTCAGTTTTGCATGATTTTTAGTGTCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCT
577 CTCAGTTTTACATGATTTTTAGCGCCAACACTCCTCGAAATATCTATATTCATCTAATAAAATCT
* * * **
9222 CTGCCACATTGGATTTAGGGATTTGTTTTTTTGAGCATTTAAATCTTGTTTCGATTTAATTAGAA
642 ATGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATTTAAATCTTGTTTCGATTTAATTAGAA
* * * *
9287 GTTAATTCGGAAAAAGTAGGAAAAACGATATTAAAAGCGTAAAATACTCTTCAATATTTTTGGCG
707 ATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTAAAATACCCTTCAATATTTTTGGCG
* * *
9352 TTGAATTATATAATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCCGGTCATTT
772 TTGAATTATATAATTTTTCATCAGTATTATAGCCAAAAATTGAGGAAATATCTTTCCGGTCATTT
* **
9417 TTGCAAAATTTTAGCCGAAATCATGTAATAATCATCACGATTTTTGTCTAAAAACGTGTTCCAGG
837 TTGCAAAATTTTAGCCGAAATCATGTAATAATCATCACGATTTTTGGCTAAAAACAAGTTCCAGG
* *
9482 GCTCCGGGTCAGTTCTACATTATTTTTTGCGCTAAGAATCTTTTAGATATCCATATTCATCTAAT
902 GATCCGGGTCAGTTCTACATGATTTTTTGCGCTAAGAATCTTTTAGATATCCATATTCATCTAAT
9547 CAAAAATCAGGCA
967 CAAAAATCAGGCA
* *
9560 CATTGCATTTAATGA-TT-TTTTTACGAGCATATAAATCTTGTTTCGATTTAATTAGAAATTAAT
1 CATTGCATTTAAGGATTTGTTTTTACAAGCATATAAATCTTGTTTCGATTTAATTAGAAATTAAT
* * *
9623 TAATAAAAAATATGAAAAACGATATGAAAAGCTTGAAAAGTCCTTCAATCTTTTTGGCGTTGAAT
66 TAAGAAAAAATATGAAAAACGATATGAAAAGCATGAAAAGCCCTTCAATCTTTTTGGCGTTGAAT
* * * * *
9688 TATATATTTTT-TTGACTATTTTACCTAAAAATTGAGGAAATATCTTTCGAGTCACTTTTTACAA
131 TATATATTTTTCATCACTATTATACCTAAAAATTGAGGAAACATCTTTCGAGTCAATTTTTACAA
* *
9752 AATTTTAACCGAAATCGTGTAATATAT-TTCACA-ATTTTTAGCTAAAAAAGCATTATAGAACCC
196 AATTTTAACCGAAATCGTGTAATA-ATCATCACAGATTTTTAGCTAAAAAAGCATT-TAG-ACCA
* * * * * *
9815 CGACTCAGTTTTCCATGATTTTTGGCGCCAAGAACT-CTTGAGATATCCATATTCATCTACTCAA
258 CGACTCAATTTTCAATAATTTTTGGCACCAAG-ACTCCTTGAAATAT-C-TA-TC-TATACTC--
* * * *
9879 ATTTCAGCCAGATTTGATATAAG-AATTTGTTTTTAAAAGCATCCGAATCTTGTTTCAATTTAAT
316 ATCT-AACCA-A----ATACAAGCAA-TTGTTTTTAAAAGCATCCGAATCATGTTTCAATTTAAT
* * * * *
9943 TAGAAATTAATTC-AGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTTC-TCCAATCTTG
374 TAGAAATCAATTCGAAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAG-CCGTCCAATATTG
* * *
10006 TTGGCATTAAATTATATATTTTTTATGAGTATTTTGTCCAAAAATTGAGGAAAAAAT-TTTAGGG
438 TTAGCATTAAATTATATA-TTTTTATGAGTATTGTGGCCAAAAATTGA-GAAAAAATATTTAGGG
* * * *
10070 TCATTTTTTGCAAACT-GTAGCCAAAATCATGTACCCATCACGG-TTTTTGGCTAAAAACGCGTT
501 TCAATTTTTGCAAAATAGTAGCCAAAATCATGTA-ACATCACGGTTTTTTGGCAAAAAACGCGTT
* * * *
10133 TCGGGGCCCCGACTCAGTTTTACATGATTTTTGGCGCCGACACTCCTCGAAATATCTATATTCAT
565 CCAGGGCCCCGACTCAGTTTTACATGATTTTTAGCGCCAACACTCCTCGAAATATCTATATTCAT
* * * *
10198 CTAATAAAATCTATGCTACA-TGACATTTAAGGATTTGTTTTTACGAGTATTTCAATTTTGTTTC
630 CTAATAAAATCTATGCCACATTG-CATTTAAGGATTTGTTTTTACGAGCATTTAAATCTTGTTTC
** * *
10262 GATTTTGTTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAA-GCCCTT
694 GATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGT-AAAATACCCTT
* * *
10326 CAATCTTTTTGGCGTTGAATTATAT-ATTTTTCATCAGTATTATGGCTAAAAATTGAGGAAATAT
758 CAATATTTTTGGCGTTGAATTATATAATTTTTCATCAGTATTATAGCCAAAAATTGAGGAAATAT
** * *
10390 CTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACACGGTTTTTGGC
823 CTTTCCGGTC-ATTTTTGCAAAATTTTAGCCGAAATCATGTAATAATCAT--CACGATTTTTGGC
* * * *
10455 TAAAAACAAG-TCC-TGGATTCGGTTCAGTTTTGA-ATGATTTTTTGC
885 TAAAAACAAGTTCCAGGGATCCGGGTCAGTTCT-ACATGATTTTTTGC
10500 ACCGAGACTC
Statistics
Matches: 785, Mismatches: 128, Indels: 54
0.81 0.13 0.06
Matches are distributed among these distances:
983 17 0.02
984 2 0.00
985 105 0.13
986 119 0.15
987 48 0.06
988 275 0.35
989 13 0.02
990 19 0.02
991 3 0.00
992 4 0.01
993 1 0.00
994 69 0.09
995 55 0.07
996 8 0.01
997 47 0.06
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.37
Consensus pattern (979 bp):
CATTGCATTTAAGGATTTGTTTTTACAAGCATATAAATCTTGTTTCGATTTAATTAGAAATTAAT
TAAGAAAAAATATGAAAAACGATATGAAAAGCATGAAAAGCCCTTCAATCTTTTTGGCGTTGAAT
TATATATTTTTCATCACTATTATACCTAAAAATTGAGGAAACATCTTTCGAGTCAATTTTTACAA
AATTTTAACCGAAATCGTGTAATAATCATCACAGATTTTTAGCTAAAAAAGCATTTAGACCACGA
CTCAATTTTCAATAATTTTTGGCACCAAGACTCCTTGAAATATCTATCTATACTCATCTAACCAA
ATACAAGCAATTGTTTTTAAAAGCATCCGAATCATGTTTCAATTTAATTAGAAATCAATTCGAAA
AAAATAGGAAAAACGATATTAAAAGCGTGAAAAGCCGTCCAATATTGTTAGCATTAAATTATATA
TTTTTATGAGTATTGTGGCCAAAAATTGAGAAAAAATATTTAGGGTCAATTTTTGCAAAATAGTA
GCCAAAATCATGTAACATCACGGTTTTTTGGCAAAAAACGCGTTCCAGGGCCCCGACTCAGTTTT
ACATGATTTTTAGCGCCAACACTCCTCGAAATATCTATATTCATCTAATAAAATCTATGCCACAT
TGCATTTAAGGATTTGTTTTTACGAGCATTTAAATCTTGTTTCGATTTAATTAGAAATTAATTCA
GAAAAAATAGGAAAAACGATATTAAAAGCGTAAAATACCCTTCAATATTTTTGGCGTTGAATTAT
ATAATTTTTCATCAGTATTATAGCCAAAAATTGAGGAAATATCTTTCCGGTCATTTTTGCAAAAT
TTTAGCCGAAATCATGTAATAATCATCACGATTTTTGGCTAAAAACAAGTTCCAGGGATCCGGGT
CAGTTCTACATGATTTTTTGCGCTAAGAATCTTTTAGATATCCATATTCATCTAATCAAAAATCA
GGCA
Found at i:11620 original size:217 final size:216
Alignment explanation
Indices: 11226--11622 Score: 507
Period size: 217 Copynumber: 1.8 Consensus size: 216
11216 TGCATTTAAT
* *
11226 GATTTTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAGAAATTAATTCATAAAAATATGA
1 GATTTTTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATTAATTCAGAAAAATATGA
* * * *
11291 AAAACGATATGAAAAGCTCGAAAAGTCCTCCAGTATTTTTGGCGTTAAATTTTATATATTTCAAG
66 AAAACGATATGAAAAGCTCGAAAAGTCCTCCAATATTTTTGCCATTAAATTATATATATTTCAAG
* * *
11356 AGTATTTCAGCCAAAATTTCAGGAAAAAAATTTCTAGTCATTTTTTGCAAAACTTTATGCTTTTC
131 AGTATTTCAGCCAAAAATTCAGGAAAAAAATTTCGAGTCAATTTTTGCAAAACTTTATGCTTTTC
11421 GGGGGCCCGACTTAGTTTTGC
196 GGGGGCCCGACTTAGTTTTGC
* *
11442 GATTTGTTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATTTATTTAGAAAAATATG
1 GATTT-TTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATTAATTCAGAAAAATATG
* ** *
11507 AAAAACGATATTAAAAGCAT-GAAAAG-CTCTTTAATCTTTTTGCCATTGAAA-TATATA-ATTT
65 AAAAACGATATGAAAAGC-TCGAAAAGTC-CTCCAATATTTTTGCCATT-AAATTATATATA-TT
* * * * * * *
11568 TTATGAGTATTGT-GGCTAAAAATTGAGGAAATAATTTTCGAGTCAATTTTTGCAA
126 TCAAGAGTATT-TCAGCCAAAAATTCAGGAAAAAAATTTCGAGTCAATTTTTGCAA
11623 GATTCTAGCC
Statistics
Matches: 153, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
216 7 0.05
217 141 0.92
218 5 0.03
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (216 bp):
GATTTTTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATTAATTCAGAAAAATATGA
AAAACGATATGAAAAGCTCGAAAAGTCCTCCAATATTTTTGCCATTAAATTATATATATTTCAAG
AGTATTTCAGCCAAAAATTCAGGAAAAAAATTTCGAGTCAATTTTTGCAAAACTTTATGCTTTTC
GGGGGCCCGACTTAGTTTTGC
Found at i:12142 original size:335 final size:331
Alignment explanation
Indices: 11443--12627 Score: 1242
Period size: 335 Copynumber: 3.6 Consensus size: 331
11433 TAGTTTTGCG
* * * *
11443 ATTTGTTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATTTATTTAGAAAAATATGA
1 ATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAATATGA
* * ** * *
11508 AAAACGATATTAAAAGCATGAAAAGCTCTTTAATCTTTTTGCCATTGAAA-TATATA-ATTTTTA
66 AAAACGATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTT-AAATTATATATA-TTTTA
* * * *
11571 TGAGTATTGTGGCTAAAAATTGAGGAAATAAT-TTTCGAGTCAATTTTTGCAAGA-TTCTAGCCG
129 TGAGTATTGTAGCTAAAAATTGA-GAAAAAATATTTCGAGTCAATTTTTGCAAAATTTC-AGCTG
* * * * * * *
11634 AAGTCGTGT--TATAATCATCACGGTTTTTTTTGGCTAAAAACTCGTTCCGAGGCCCCGACTAAG
192 AAATCGTGTCATGTTACCATCACGG---TTTTTGGCT-AAAACGCGTTCCGGGGCCCCGAATAAG
* ** * * * *
11697 TTTTGCATGATTTTTGGCGTCAAGACTATTTGAGATATCCATATTCTTCTATTCAAATCTTAGCT
253 TTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTTAGCT
*
11762 ACATTGGATTTAAGA
318 ACATT-GAATTAAGA
* *
11777 ATTTGTTTTTATGGGCATCTAAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAATATGA
1 ATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAATATGA
** *
11842 AAAACGATATTAAAAGCGTGAAAAGTTCTCCAATCTTTTTGGTGTTAAATTATATATATTTTATG
66 AAAACGATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTAAATTATATATATTTTATG
* * * * * *
11907 ATTATTTTATC-CAAAATTAACGAAAAAAT-TTTCGGGT-AATTTTTTGCAAAATTTCAGCTGAA
131 AGTATTGTAGCTAAAAATTGA-GAAAAAATATTTCGAGTCAA-TTTTTGCAAAATTTCAGCTGAA
* * * *
11969 ATCGTGTACATGTTTAGCCATCACGGTTTTTGGCTAAACCCGCATTTCGGGGCCCCGAATTAGTT
194 ATCGTGT-CATG-TTA-CCATCACGGTTTTTGGCTAAA-ACGCGTTCCGGGGCCCCGAATAAGTT
* * * * * **
12034 TTACATGATTTTTGGCGCCCAGACTCCTTGAAATATCTATATTCATCCAATCAGATCTCAGCCGC
255 TTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTTAGCTAC
12099 ATTGAATTAGAGA
320 ATTGAATTA-AGA
* *
12112 ATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAAAAACTAATTCAAAAAAATATGA
1 ATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAATATGA
* * *
12177 AAAACGATATTGAAAGCGTGAAAAGTCCTCCATTAATCTTTTTGGCGTTGAATTATATATA--TT
66 AAAACGATATTAAAAGCGTGAAAAGCCCTCC---AATCTTTTTGGCGTTAAATTATATATATTTT
*
12240 ATGAGTATTGTGGCTAAAAATTGAG-AAAAATATTTCGAGTCAATTTTTGCAAAATTTCAG-TCG
128 ATGAGTATTGTAGCTAAAAATTGAGAAAAAATATTTCGAGTCAATTTTTGCAAAATTTCAGCT-G
* * * *
12303 AAA-----TCATG-TACCAATCACGATTTTTTGGCTAGAAACGCGTTCCGGGACCTCGAGTAAGT
192 AAATCGTGTCATGTTACC-ATCACG-GTTTTTGGCTA-AAACGCGTTCCGGGGCCCCGAATAAGT
* * * * * *
12362 TTTGCATGATTATTGGTGGCAAAACTCCTTGAAATATCTATATTCATCTAATCAAATTTTAACTA
254 TTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTTAGCTA
12427 CATTGAATTTAAGA
319 CATTGAA-TTAAGA
* * * *
12441 ATTTGTTTTTACGAGTATCTAAATCTTGTCTCGATTTAATTAGAAATTAATTCAGAAAAAAATAG
1 ATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAATAT-G
* * * ** * *
12506 AAAAAACAATATTAAAAGCGTTAAAAGCCCTTCAATCTTTTTGATGTCAAATTATATATTTTTTA
65 -AAAAACGATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTAAATTATATATATTTTA
* * *
12571 TGAGTATTCTAG-TCAAAAATTGAGAAAATATATTTC-AGGTTAATTTTTGCAAAATTT
129 TGAGTATTGTAGCT-AAAAATTGAGAAAAAATATTTCGA-GTCAATTTTTGCAAAATTT
12628 TAGCCGAATT
Statistics
Matches: 716, Mismatches: 106, Indels: 61
0.81 0.12 0.07
Matches are distributed among these distances:
327 2 0.00
328 30 0.04
329 148 0.21
330 34 0.05
331 56 0.08
332 2 0.00
333 46 0.06
334 129 0.18
335 183 0.26
336 42 0.06
337 11 0.02
338 33 0.05
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.38
Consensus pattern (331 bp):
ATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAATATGA
AAAACGATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTAAATTATATATATTTTATG
AGTATTGTAGCTAAAAATTGAGAAAAAATATTTCGAGTCAATTTTTGCAAAATTTCAGCTGAAAT
CGTGTCATGTTACCATCACGGTTTTTGGCTAAAACGCGTTCCGGGGCCCCGAATAAGTTTTGCAT
GATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTTAGCTACATTGAA
TTAAGA
Found at i:19873 original size:6 final size:6
Alignment explanation
Indices: 19862--19908 Score: 85
Period size: 6 Copynumber: 7.8 Consensus size: 6
19852 ATTTGGGAAC
*
19862 CCCATA CCCATA CCCATA CCCATA CTCATA CCCATA CCCATA CCCAT
1 CCCATA CCCATA CCCATA CCCATA CCCATA CCCATA CCCATA CCCAT
19909 TTGCATTCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.32, C:0.49, G:0.00, T:0.19
Consensus pattern (6 bp):
CCCATA
Found at i:27296 original size:13 final size:13
Alignment explanation
Indices: 27278--27302 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27268 GATTAATTTT
27278 TGAATTTTTCTTC
1 TGAATTTTTCTTC
27291 TGAATTTTTCTT
1 TGAATTTTTCTT
27303 TTCCTGGACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.12, G:0.08, T:0.64
Consensus pattern (13 bp):
TGAATTTTTCTTC
Found at i:36346 original size:1 final size:1
Alignment explanation
Indices: 36342--36366 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
36332 ATTAAAAATT
36342 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
36367 CTCGTCAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:37549 original size:23 final size:22
Alignment explanation
Indices: 37505--37550 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
37495 TTTGACTGAC
*
37505 AAAAAAAAAACAACTGTAAATT
1 AAAAAAAAAACAACTATAAATT
37527 AAAAAAAGAAACAA-TATATAATT
1 AAAAAAA-AAACAACTATA-AATT
37550 A
1 A
37551 TATATATCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.70, C:0.07, G:0.04, T:0.20
Consensus pattern (22 bp):
AAAAAAAAAACAACTATAAATT
Found at i:45165 original size:3 final size:3
Alignment explanation
Indices: 45157--45192 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
45147 TGATTTAACA
45157 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
45193 TTGAGTTAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:52049 original size:2 final size:2
Alignment explanation
Indices: 52042--52150 Score: 55
Period size: 2 Copynumber: 61.0 Consensus size: 2
52032 AAGTTTTATG
*
52042 AT AT AT AT AT AT AT AT AT AT CT -T AT AT -T AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
52081 AA AT -T AT AA AA AC AA AT AT AT AT A- AT A- AT AT A- AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
52118 AT AT AA AA AT -T A- AT A- AT -T AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52151 TTATTGGTCG
Statistics
Matches: 85, Mismatches: 9, Indels: 26
0.71 0.08 0.22
Matches are distributed among these distances:
1 13 0.15
2 72 0.85
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:52113 original size:34 final size:37
Alignment explanation
Indices: 52063--52149 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 37
52053 TATATATATC
*
52063 TTATATTATATATATAATAA-ATTATAAAAACAAAT-A
1 TTATATAATATATATAATAATA-TATAAAAACAAATAA
* **
52099 -TATATAATA-ATATAATTATATATAAAAATTAATAA
1 TTATATAATATATATAATAATATATAAAAACAAATAA
52134 TTATATAATATATATA
1 TTATATAATATATATA
52150 TTTATTGGTC
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
34 19 0.44
35 10 0.23
36 9 0.21
37 5 0.12
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (37 bp):
TTATATAATATATATAATAATATATAAAAACAAATAA
Found at i:52120 original size:18 final size:18
Alignment explanation
Indices: 52097--52154 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
52087 TAAAAACAAA
52097 TATATATAATAATATAAT
1 TATATATAATAATATAAT
*
52115 TATATATAAAAAT-TAAT
1 TATATATAATAATATAAT
* *
52132 AATTATATAATATATATATT
1 TA-TATATAATA-ATATAAT
52152 TAT
1 TAT
52155 TGGTCGGTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
17 5 0.16
18 20 0.62
19 3 0.09
20 4 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATATATAATAATATAAT
Found at i:52121 original size:20 final size:20
Alignment explanation
Indices: 52096--52154 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
52086 ATAAAAACAA
52096 ATATATATAATAATATAATT
1 ATATATATAATAATATAATT
*
52116 ATATATA-AA-AAT-TAATA
1 ATATATATAATAATATAATT
*
52133 AT-TATATAATATATATATTT
1 ATATATATAATA-ATATAATT
52153 AT
1 AT
52155 TGGTCGGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 4 0.12
17 8 0.25
18 4 0.12
19 4 0.12
20 12 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATATATAATAATATAATT
Found at i:52890 original size:11 final size:11
Alignment explanation
Indices: 52876--52913 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
52866 ATTCATAACA
52876 AATTTATAATT
1 AATTTATAATT
52887 AATTTATAATT
1 AATTTATAATT
52898 -ATTTGATAATT
1 AATTT-ATAATT
*
52909 TATTT
1 AATTT
52914 TATATATAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:63509 original size:259 final size:259
Alignment explanation
Indices: 63050--63825 Score: 1480
Period size: 259 Copynumber: 3.0 Consensus size: 259
63040 CCCCCCTTCC
* * *
63050 TTTTCCTGCTACCCTTTTTTGTAATTGCCCATTTCTCTTCCTTAATTGCTTTTAGTTAATGTTTC
1 TTTTCCTGCTACCCTTTTTTGTAATTACACATCTCTCTTCCTTAATTGCTTTTAGTTAATGTTTC
*
63115 TACCTCCTTTCCTTTTTTCCTCCCACCAACTCAGCTGCTGCTTCCTTTCAACTCCTCAGTGCTGA
66 TACCTCCTTTCCTTTTTTCCTCCCACCAACTCAGCTGCTGCTTCCTTTCAACTCCTCAGTGCCGA
63180 TCAATCTTCAGGTTTGCCAAAAATCAAACATTTCATTACTCCCCTCGATTATCACCTTCACATCT
131 TCAATCTTCAGGTTTGCCAAAAATCAAACATTTCATTACTCCCCTCGATTATCACCTTCACATCT
63245 CTTTCTTTTACTTCTCCTTCCCCACCCCTTCACCATGGACCGTTCAATGTTTTTCTCATTCTGT
196 CTTTCTTTTACTTCTCCTTCCCCACCCCTTCACCATGGACCGTTCAATGTTTTTCTCATTCTGT
63309 TTTTCCTGCTACCCTTTTTTGTAATTACACATCTCTCTTCCTTAATTGCTTTTAGTTAATGTTTC
1 TTTTCCTGCTACCCTTTTTTGTAATTACACATCTCTCTTCCTTAATTGCTTTTAGTTAATGTTTC
63374 TACCTCCTTTCCTTTTTTCCTCCCACCAACTCAGCTGCTGCTTCCTTTCAACTCCTCAGTGCCGA
66 TACCTCCTTTCCTTTTTTCCTCCCACCAACTCAGCTGCTGCTTCCTTTCAACTCCTCAGTGCCGA
* *
63439 TCAATCTTCAGGTTTGCTAAAAATCAAACATTTCATTACTCCCCTCGATTATCACATTCACATCT
131 TCAATCTTCAGGTTTGCCAAAAATCAAACATTTCATTACTCCCCTCGATTATCACCTTCACATCT
*
63504 CTTTCTTTTACTTCTCCTTCCCCACCCCTTCACCATGGACCGTTCAATGTTTTTCTTATTCTGT
196 CTTTCTTTTACTTCTCCTTCCCCACCCCTTCACCATGGACCGTTCAATGTTTTTCTCATTCTGT
63568 TTTTCCTGCTACCCTTTTTTGTAATTACACATCTCTCTTCCTTAATTGCTTTTAGTTAATGTTTC
1 TTTTCCTGCTACCCTTTTTTGTAATTACACATCTCTCTTCCTTAATTGCTTTTAGTTAATGTTTC
63633 TACCTCCTTTCCTTTTTTCCTCCCACCAACTCAGCTGCTGCTTCCTTTCAACTCCTCAGTGCCGA
66 TACCTCCTTTCCTTTTTTCCTCCCACCAACTCAGCTGCTGCTTCCTTTCAACTCCTCAGTGCCGA
*
63698 TCAATCTTCAAGTTTGCCAAAAATCAAACATTTCATTACTCCCCTCGATTATCACCTTCACATCT
131 TCAATCTTCAGGTTTGCCAAAAATCAAACATTTCATTACTCCCCTCGATTATCACCTTCACATCT
63763 CTTTCTTTTACTTCTCCTTCCCCACCCCTTCACCATGGACCGTTCAATGTTTTTCTCATTCTG
196 CTTTCTTTTACTTCTCCTTCCCCACCCCTTCACCATGGACCGTTCAATGTTTTTCTCATTCTG
63826 AATTAAATTA
Statistics
Matches: 506, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
259 506 1.00
ACGTcount: A:0.18, C:0.32, G:0.08, T:0.42
Consensus pattern (259 bp):
TTTTCCTGCTACCCTTTTTTGTAATTACACATCTCTCTTCCTTAATTGCTTTTAGTTAATGTTTC
TACCTCCTTTCCTTTTTTCCTCCCACCAACTCAGCTGCTGCTTCCTTTCAACTCCTCAGTGCCGA
TCAATCTTCAGGTTTGCCAAAAATCAAACATTTCATTACTCCCCTCGATTATCACCTTCACATCT
CTTTCTTTTACTTCTCCTTCCCCACCCCTTCACCATGGACCGTTCAATGTTTTTCTCATTCTGT
Found at i:64797 original size:30 final size:31
Alignment explanation
Indices: 64761--64830 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 31
64751 TGGCAATTTA
** *
64761 GAAATATATTTTTTAAAAA-GGGTATAATCG
1 GAAATATATTTTAGAAAAATGGGTACAATCG
64791 GAAATATATTTTAGAAAAATGGGTACAATCG
1 GAAATATATTTTAGAAAAATGGGTACAATCG
64822 GAAAATATA
1 G-AAATATA
64831 AAGTTTCCCC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
30 17 0.49
31 11 0.31
32 7 0.20
ACGTcount: A:0.47, C:0.04, G:0.17, T:0.31
Consensus pattern (31 bp):
GAAATATATTTTAGAAAAATGGGTACAATCG
Found at i:70257 original size:11 final size:11
Alignment explanation
Indices: 70230--70267 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
70220 ATGACAAGCC
70230 AAAAGAAGAAAA
1 AAAAGAA-AAAA
*
70242 GAAAGAAAAAA
1 AAAAGAAAAAA
70253 AAAAGAAAAAA
1 AAAAGAAAAAA
70264 AAAA
1 AAAA
70268 CCCTTTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 18 0.75
12 6 0.25
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:70258 original size:15 final size:14
Alignment explanation
Indices: 70238--70267 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
70228 CCAAAAGAAG
70238 AAAAGAAAGAAAAAA
1 AAAAGAAA-AAAAAA
70253 AAAAGAAAAAAAAA
1 AAAAGAAAAAAAAA
70267 A
1 A
70268 CCCTTTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAAAA
Found at i:82727 original size:13 final size:13
Alignment explanation
Indices: 82709--82734 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
82699 AAAAGGANAA
82709 GGGGGGGGGGGTG
1 GGGGGGGGGGGTG
82722 GGGGGGGGGGGTG
1 GGGGGGGGGGGTG
82735 CTGAACCTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.92, T:0.08
Consensus pattern (13 bp):
GGGGGGGGGGGTG
Found at i:87201 original size:43 final size:43
Alignment explanation
Indices: 87126--87211 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
87116 TAGTTTAAGC
87126 AAATATTTTTCCTGTTTATTTTTAACTTTTAATTCCTCTCAAGA
1 AAATATTTTTCCTGTTTA-TTTTAACTTTTAATTCCTCTCAAGA
*
87170 AAATTTTTGTTCCTGTTTA-TTTAACTTTTAATTCCTCTCAAG
1 AAATATTT-TTCCTGTTTATTTTAACTTTTAATTCCTCTCAAG
87212 TCTCAACTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
43 23 0.57
44 7 0.17
45 10 0.25
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.52
Consensus pattern (43 bp):
AAATATTTTTCCTGTTTATTTTAACTTTTAATTCCTCTCAAGA
Done.