Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021131.1 Corchorus olitorius cultivar O-4 contig21164, 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: 14012
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:1468 original size:179 final size:178
Alignment explanation
Indices: 1102--1480 Score: 528
Period size: 179 Copynumber: 2.1 Consensus size: 178
1092 CCATAAGCAC
* * * *
1102 AAATTATGTAATATTAAGTAGACTGTCTATTTCCGTTAACCGAAATAACTAATTCTTTGGAAGCA
1 AAATTATATAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAACAAATTCTTTGGAAGCA
* *
1167 TTTTTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAAC
66 TTTTTGATACCTTGAACATTAAATTTAATTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAAC
* * * *
1232 AACCTTTCAAGAGACACTTGAATCATCTCAATCAGACATCTGGAGTAA
131 AACCTTTCAAGAGACACTTAAATCACCTCAATCAGACAACCGGAGTAA
* * * * *
1280 AAGTTATATAACATTAAGTGGACCGTCTATTTCCCGTTAAGCGAAACAACAAATTTTTTGGAAGC
1 AAATTATATAATATTAAGTAGACCGTCTATTT-CCGTTAACCGAAACAACAAATTCTTTGGAAGC
1345 ATTTTTGATA-CTTGAAACATTAAATTTAATTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGA
65 ATTTTTGATACCTTG-AACATTAAATTTAATTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGA
* * * * *
1409 ACAATCTTTTAATAGACACTTAAATCACCTCAATCGGATAACCGGAG-AGA
129 ACAACCTTTCAAGAGACACTTAAATCACCTCAATCAGACAACCGGAGTA-A
*
1459 AAATTATATAATATTAAATAGA
1 AAATTATATAATATTAAGTAGA
1481 TCGTTTAGGC
Statistics
Matches: 174, Mismatches: 24, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
178 32 0.18
179 142 0.82
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (178 bp):
AAATTATATAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAACAAATTCTTTGGAAGCA
TTTTTGATACCTTGAACATTAAATTTAATTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAAC
AACCTTTCAAGAGACACTTAAATCACCTCAATCAGACAACCGGAGTAA
Found at i:2812 original size:184 final size:184
Alignment explanation
Indices: 2503--2872 Score: 740
Period size: 184 Copynumber: 2.0 Consensus size: 184
2493 AAATCGAAAC
2503 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATATGGCTAAGATTTGGTTAGATGAAT
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATATGGCTAAGATTTGGTTAGATGAAT
2568 ATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGCCGGACCCCGGAACGCGT
66 ATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGCCGGACCCCGGAACGCGT
2633 TTTTAGCCGAAAACTGTGATGGTTAGTACACGGTTTCAGCTAAAATTTTCCAAA
131 TTTTAGCCGAAAACTGTGATGGTTAGTACACGGTTTCAGCTAAAATTTTCCAAA
2687 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATATGGCTAAGATTTGGTTAGATGAAT
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATATGGCTAAGATTTGGTTAGATGAAT
2752 ATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGCCGGACCCCGGAACGCGT
66 ATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGCCGGACCCCGGAACGCGT
2817 TTTTAGCCGAAAACTGTGATGGTTAGTACACGGTTTCAGCTAAAATTTTCCAAA
131 TTTTAGCCGAAAACTGTGATGGTTAGTACACGGTTTCAGCTAAAATTTTCCAAA
2871 AA
1 AA
2873 TTGACTCGAA
Statistics
Matches: 186, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
184 186 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (184 bp):
AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATATGGCTAAGATTTGGTTAGATGAAT
ATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGCCGGACCCCGGAACGCGT
TTTTAGCCGAAAACTGTGATGGTTAGTACACGGTTTCAGCTAAAATTTTCCAAA
Found at i:3712 original size:330 final size:327
Alignment explanation
Indices: 2687--6720 Score: 3244
Period size: 332 Copynumber: 12.1 Consensus size: 327
2677 ATTTTCCAAA
* * * *
2687 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATATGGCTAAGATTTGGTTAGATGAAT
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
* * * *
2752 ATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGCC-GGACCCCGGAACGCG
66 ATAGATATTTCAAGAAGTCTTGGC-GCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCG
* * * *
2816 TTTTTAGCC--GAAAACTGTGATGGTTAGTACACGGTTTCAGCTAAAATTTTCCAAAAATTGACT
130 TTTTTAGCCAAAAAAACTGTGAT-G---GTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC-
* ** * * *
2879 C-GAAAAATTTTTCCTTGATTTCTAGCGAAAATACTCATAAAA-ATATATAATTCAATGCCAAAA
190 CAGAAATATTTTT-CTCAATTTTTAGCTAAAATACTCATAAAATATATATAATTCAACGCCAAAA
* * * ** * * **
2942 A-AATGAAAGCCTTTTTCACGCTTCAAATATCGTTTTCCTTATTTTCTTTCCAAATTAATTTCTA
254 AGATTGAAGGAC-TTTTCACGCTTTTAATATCGTTTT--TCATATT-TTTCTGAATTAATTTCTA
*
3006 ATTAAATCAAAAC
315 ATTAAATCGAAAC
* *** * * * *
3019 AAGATTTAGAAATTCGTAAAATCAAATCCTTAAATACAATGTTGCTGAGATTTGGTTAGATGAAT
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
* * * * *
3084 ATAGATATATTTTAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGACCCAGGACCCCGAAACG
66 ATAG--ATATTTCAAGAAGTCTTGGCG-CAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACG
* **
3149 CGTTTTTAGCAAAAAAAAAAAAAAACAATGATGGTACACGATTTCGGCTAAAATTTTGCAAAAAT
128 CGTTTTTAGC-------CAAAAAAACTGTGATGGTACACGATTTCGGCTAAAATTTTGCAAAAAT
* * * * *
3214 TAACCCGAAATATTTTTCTCAATTTTTAGCCACAATACTCATAAAAAATATATAATTCAACGCCA
186 TGACCAGAAATATTTTTCTCAATTTTTAGCTAAAATACTCATAAAATATATATAATTCAACGCCA
* * * * * *
3279 AAAAGATTGAAGGGCTCTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCAAATTAATTTCTA
251 AAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCT-GAATTAATTTCTA
3344 ATTAAATCGAAAC
315 ATTAAATCGAAAC
* * * * *
3357 ATGATTCAGATGCTCGCAAAAACAAATCCTTAAAT-CAAGTGTGGCTAAGGTTTGGTTAGATGAA
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA-TGTGGCTGAGATTTGATTAGATGAA
* * ** * * *
3421 TATAGATATTTCAAGAATTTTTACCACAAAAAATCATGCAAAACTGACCCGGGGCCCCGGAACGC
65 TATAGATATTTCAAGAAGTCTTGGCGC-AAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGC
* *
3486 GATTTTAGCCAAAAAAAACTGTGATGGTACACGATTTCGGATAAAATTTTGCAAAAATTGACCAG
129 GTTTTTAGCC-AAAAAAACTGTGATGGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCAG
* * * **
3551 AAATATTTTGTCTCAATTTTTAGCCACAACACTCATAAAATATATATAATTCAATACCAAAAAGA
193 AAATATTTT-TCTCAATTTTTAGCTAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGA
* *
3616 CTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAAT
257 TTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAAT
3681 CGAAAC
322 CGAAAC
* * * * *
3687 AAGATTCATAGGCTCGTAGAAACAAATCCTTAAATTCAATGTGGCTGAGATATGATTAGATGAAT
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
* * ** *
3752 ATAGATATTTCAAGAAGTCTCGGCGCAAAAAATCATGCAAAACTAAGCTTGGGCCTCGAAACGCG
66 ATAGATATTTCAAGAAGTCTTGGCGC-AAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCG
* * ** **
3817 TTTTTAGCC--AAAAACTATGATGGTAGTACATGATTTCAACTAATTTTTTGCAAAAATTGACCC
130 TTTTTAGCCAAAAAAACTGTGAT-G--GTACACGATTTCGGCTAAAATTTTGCAAAAATTGA-CC
* * * * * *
3880 A-AATTTTTTTTCCCAAAAATATTTGGCTAAAATACTCATAATATATATATATATATATAATTTA
191 AGAAATATTTTTCTC---AATTTTTAGCTAAAATACTC-----ATA-A-A-ATATATATAATTCA
* ** * * * *
3944 ATGGTAAAAAGATTGGAGAACTTTTCACGCTTTTAGTATCGTATTT-ATTATTTTTCTGAATTAA
245 ACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCA-TATTTTTCTGAATTAA
* *
4008 TTTTTAATTAAATCGAAAT
309 TTTCTAATTAAATCGAAAC
* * * * * *
4027 AAGATTCAGATGCTCATAAAAAAAAATTCTTAAATCCAATGTTGCTGATATTTTATTAGATGAAT
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
* * * * *
4092 ATGGATATCTCAAAAAGTCTTGGCACCAAAAATCATGCAAAACTGAGCCGGGGTCCCGAAACGCG
66 ATAGATATTTCAAGAAGTCTTGGC-GCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCG
** * * * * * * * *
4157 ACTTTAGCC--AAAAACCGTGATGATTATCAAACGATTTCTGTTAGAATTTTACAAAAATTTACT
130 TTTTTAGCCAAAAAAACTGTGATG-GTA-C--ACGATTTCGGCTAAAATTTTGCAAAAATTGACC
* * * * *
4220 TGAAAGT-TATTTTCTCAATTTTTAGCCACAACACTCATTAAAAT-TATATAATTCAACGCCAAT
191 AGAAA-TAT-TTTTCTCAATTTTTAGCTAAAATACTCA-TAAAATATATATAATTCAACGCCAAA
* * * *
4283 AAGATTGAAGGGCTTTTCATGCTTCTAATATCGTTTTTCATAATATTTT-TCGAATTAATTTCTG
253 AAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCAT-AT-TTTTCT-GAATTAATTTCTA
4347 ATTAAATCGAAAC
315 ATTAAATCGAAAC
* * *** * * *
4360 ATGATTCAGATGCTTGT-TTTAGAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAAATGAAT
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
** * * * *
4424 ATAGATATTTCAAGAAGTCTCAGCGTAAAAAATCATGCAACACTGTA-CCGGGACACCGAAACGC
66 ATAGATATTTCAAGAAGTCTTGGCG-CAAAAATCATGCAAAACTG-AGCCGGGGCCCCGAAACGC
* * * * *
4488 GTTTTTAGCAAAAAAAAAAAACCGTAATTTCGACTAACGTACACGATTTCGGCTAATATTTTGTA
129 GTTTTTAGC----CAAAAAAA-C----TGT-GA-T--GGTACACGATTTCGGCTAAAATTTTGCA
* *
4553 AAAATTGACCA-AAAGTATTATTCCTCAATTTTT-GTCTAAAATACTCATAAAATATATATATTT
181 AAAATTGACCAGAAA-TATT-TTTCTCAATTTTTAG-CTAAAATACTCATAAAATATATATAATT
* *
4616 CAACGCCAAAAAGATTGCAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTAAATTA
243 CAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTA
* *
4681 ATTTCAAATTAAATCAAAAC
308 ATTTCTAATTAAATCGAAAC
* * * * *
4701 AAGATTCAGATACTTGTAAAAACACATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATAAAT
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
* * * * * * *
4766 ATAGATTTTTCAAGGAGT-TCCGACGCCAAAAATCATGCAATACTAAGTCGGGG-CCCGAAACGC
66 ATAGATATTTCAAGAAGTCT-TGGCG-CAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGC
* * * * *
4829 GTTTTTTTTG-CAAAAAAACCGTGATGGTGTACACGATTTCGGCAAAAATTTTGCAAAAAATGAT
129 G--TTTTTAGCCAAAAAAACTGTGAT-G-GTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC
* * * * *
4893 CAAAAAAATTTCTCCTAAATTTTT-GACTAAAATACTCATGAAAATATATATAATTTAACGCCAA
190 CAGAAATATTT-TTCTCAATTTTTAG-CTAAAATACTCAT-AAAATATATATAATTCAACGCCAA
* * * * * * *
4957 GAAGATTGGAGGACTTTTCCCGCTTTTCATATCGTTTTTCATATTTTTTTTAATTAATTTGTAAT
252 AAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAAT
5022 TAAATCGAAAC
317 TAAATCGAAAC
* * * * * * * *
5033 AAAATACAGATACTCGTAAAAACAAATCATTAAATGCAATGTGGATGAAATTTGATTAGATTAAT
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
* * * * * *** * * *
5098 ATGGATATATCAAGGATTGTTAATGTCAAAAATCATGCAAAACTGA-CCTGGGGCCCTGGAACGT
66 ATAGATATTTCAAGAAGTCTTGGCG-CAAAAATCATGCAAAACTGAGCC-GGGGCCCCGAAACGC
* ** * *
5162 GTTTTTAGCC-AAAAATCGTGATGATTAATTACACGATTTCTGCTACAATTTTGCAAAAATTGAC
129 GTTTTTAGCCAAAAAAAC-TG-TGA-T-GGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC
* * * * * *
5226 CGAAAAAAAATATTTCCTCAATTTTT-GACTAAAATACTCATAAAAAATAGATAATTCATCGCCA
190 C--AGAAATAT-TTTTCTCAATTTTTAG-CTAAAATACTCATAAAATATATATAATTCAACGCCA
* ** * * * * *
5290 AAAATATTGAAGGGTTTTTTACGCTTGTAATATCTTTTTTCCTACTTTTTCCGAATTAATTTCTA
251 AAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCTGAATTAATTTCTA
5355 ATTAAATCGAAAC
315 ATTAAATCGAAAC
* * *
5368 AAGATTTAGATGCTCGTAAAAA-AAATCCTTAATTCCAATGTGGCTGAGATTTGTTTAGATGAAT
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
* * * * *
5432 ATAGATATTTGCATG-ATTTTTGGCGCCAAAAATCATACAAAACTGACCCGGGGCCCC-AGAACG
66 ATAGATATTT-CAAGAAGTCTTGGCG-CAAAAATCATGCAAAACTGAGCCGGGGCCCCGA-AACG
* * * *
5495 CAG-TTTTGGCCTAAAAAAAAAAACCGTGATGTTACACGATTTCGGCTAATATTTTGCAAAAATT
128 C-GTTTTTAGCC-----AAAAAAACTGTGATGGTACACGATTTCGGCTAAAATTTTGCAAAAATT
* * * *
5559 GTACCCA-AAATATTTTTCCTGAACTTTTTAGCCACAATACTCATAAAAAATATATAATTCAACG
187 G-A-CCAGAAATATTTTT-CTCAA-TTTTTAGCTAAAATACTCATAAAATATATATAATTCAACG
* ** * * * * *
5623 CCAAAAAGATTGAAGGGCTTTTCATTCTTCTGATA-CTGTTTTTTCTTTCTTTTTTTTTTCGAAT
248 CCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATC-G----TT-TTTCATATTTTTCT-GAAT
*
5687 TAATTTCTAATTAAAACGAAAC
306 TAATTTCTAATTAAATCGAAAC
* * * * * * *
5709 ATGATTCAGATTCTTGT------AAA-----AAA--CAA---GGCTGGGATTTGGTTAGATAAAA
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
* ** * * *
5758 ATAGATATTTCAAGGAGTCTT-G-GC--ACCTCATTCAAAACTGAACC-AGGCCCCGAAACGCGT
66 ATAGATATTTCAAGAAGTCTTGGCGCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGT
* * ** ** *
5818 TTGTAGCC-AAAAACCGTGATATGATTATTACACGATTTCAACTAAAATTTTGCAAAAATGGACC
131 TTTTAGCCAAAAAAAC-TG---TGA-TGGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACC
* * * * * *
5882 TGAAAGATATTTCCTCAATTTTTAGCCATAATACTCA-ATAAA-ATATATAATTCGACGCCAAAA
191 AGAAATAT-TTTTCTCAATTTTTAGCTAAAATACTCATA-AAATATATATAATTCAACGCCAAAA
* *
5945 AGATTGAAGGGCTTTTCGA-GCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAAC
254 AGATTGAAGGACTTTTC-ACGCTTTTAATATCGTTTTTCATA-TTTTTCTGAATTAATTTCTAAT
*
6009 TAAATCGAAAT
317 TAAATCGAAAC
* * *
6020 AAGATTCAGATGCTCGT-AAAACAAAT-CTTCAAATGCAATGTGGCTAAGATTTTATTAGATGAA
1 AAGATTCAGATGCTCGTAAAAACAAATCCTT-AAATCCAATGTGGCTGAGATTTGATTAGATGAA
*
6083 TATAGATATTTCAAGGAGTGTCTAT-GC-CAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAAC
65 TATAGATATTTCAA-GA-AGTCT-TGGCGCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAAC
* * * * * * * * *
6146 ACGTTTTTAG-CAAAAAACCATGATGGTTAGTACATGATTTTGGCTAAAATTCTGCAAAAAATAA
127 GCGTTTTTAGCCAAAAAAAC-TG-T-GATGGTACACGATTTCGGCTAAAATTTTGCAAAAATTGA
* * * *
6210 CCCGAAA-AGTTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTTAACGCCAA
189 CCAGAAATA-TTTTT-CTCAATTTTTAGCTAAAATACTCATAAAATATATATAATTCAACGCCAA
* * ** * *
6274 AACA-ATTGGAGGACTTTTCACGCTTATAATATTATTTTTCATA-TTTTCTCAATTAATTTCTCA
252 AA-AGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAA
6337 TTAAATCGAAAC
316 TTAAATCGAAAC
* * *
6349 AAGATTCAGATGCTTGTAAAAAAAAAAAT-CTTAAATCCAATGTGGCTGAAATTTGATTAGATGA
1 AAGATTCAGATGCTCGT--AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGA
* * * * * * ** *
6413 ATATGGATATCTCAAGGAGTCTTGGCGGCAAAAATCAGGCAAAACTGAGCC-AGGTCCTAAAACT
64 ATATAGATATTTCAAGAAGTCTTGGC-GCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACG
* * * **
6477 CATTTTTAACC--AAAAACTGTGATGGTTATTACACGATTTTGGCTAAAATTTTGTTAAAATTGA
128 CGTTTTTAGCCAAAAAAACTGTGATGG----TACACGATTTCGGCTAAAATTTTGCAAAAATTGA
* * * * *
6540 CCCGAAAGATGTTTTCTCAATTTTTGGTTAAAATACTCATAAAAAATATATAATTCAACGCCAAA
189 CCAGAAATAT-TTTTCTCAATTTTTAGCTAAAATACTCATAAAATATATATAATTCAACGCCAAA
* * * * **
6605 AAGATTGAATGG-CTTCTGACG-TTTCTAATATCGTTTTCCCTATTTTTTTCCCAATTAATTTCT
253 AAGATTGAA-GGACTTTTCACGCTTT-TAATATCGTTTT-TC-ATATTTTTCTGAATTAATTTCT
6668 AATTAAATCGAAAC
314 AATTAAATCGAAAC
* * *
6682 AAGATTTAGATGCTCGTAAAAACAAATTCATAAATCCAA
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
6721 GGCTAATTGC
Statistics
Matches: 3004, Mismatches: 520, Indels: 356
0.77 0.13 0.09
Matches are distributed among these distances:
311 42 0.01
312 8 0.00
314 6 0.00
315 1 0.00
316 49 0.02
317 25 0.01
318 13 0.00
319 35 0.01
320 17 0.01
321 20 0.01
323 4 0.00
324 1 0.00
325 4 0.00
326 66 0.02
327 13 0.00
328 8 0.00
329 71 0.02
330 416 0.14
331 369 0.12
332 417 0.14
333 132 0.04
334 185 0.06
335 122 0.04
336 155 0.05
337 13 0.00
338 105 0.03
339 46 0.02
340 308 0.10
341 129 0.04
342 100 0.03
343 109 0.04
344 11 0.00
345 2 0.00
346 2 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (327 bp):
AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
ATAGATATTTCAAGAAGTCTTGGCGCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGT
TTTTAGCCAAAAAAACTGTGATGGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCAGAAA
TATTTTTCTCAATTTTTAGCTAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGA
AGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAA
AC
Found at i:5004 original size:332 final size:328
Alignment explanation
Indices: 2687--6720 Score: 3328
Period size: 330 Copynumber: 12.1 Consensus size: 328
2677 ATTTTCCAAA
* * * *
2687 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATATGGCTAAGATTTGGTTAGATGAAT
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
* ** *
2752 ATAGATATTTCAAGGAG-TCTTGGCACCAAAAATCATGCAAAACTGAGCCGGACCCCGGAACGCG
66 ATAGATATTTCAAGGAGTTC-TGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCGAAACGCG
** * * * *
2816 TTTTTAGCCGAAAACTGTGATGGTTAGTACACGGTTTCAGCTAAAATTTTCCAAAAATTGACTCG
130 TTTTTAGCAAAAAACCGTGATGG-TAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC-C-
** * * *
2881 AAAAAT-TTTTCCTTGATTTCTAGCGAAAATACTCATAAAA-ATATATAATTCAATGCCAAAAA-
192 AAAAATATTTTCCTCAATTTTTAGCCAAAATACTCATAAAATATATATAATTCAACGCCAAAAAG
* * * ** * * **
2943 AATGAAAGCCTTTTTCACGCTTCAAATATCGTTTTCCTTATTTTCTTTCCAAATTAATTTCTAAT
257 ATTGAAGGAC-TTTTCACGCTTTTAATATCGTTTT--TCATATT-TTTCTGAATTAATTTCTAAT
*
3008 TAAATCAAAAC
318 TAAATCGAAAC
* *** * * * *
3019 AAGATTTAGAAATTCGTAAAATCAAATCCTTAAATACAATGTTGCTGAGATTTGGTTAGATGAAT
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
* * **
3084 ATAGATATATTTTAAGGAG-TCTTGGCGCCAAAAATCATGCAAAACTGACCCAGGACCCCGAAAC
66 ATAG--ATATTTCAAGGAGTTC-TGGCGCCAAAAATCATGCAAAACTGAGCC-GGGGCCCGAAAC
***** * *
3148 GCGTTTTTAGCAAAAAAAAAAAAAAACAATGATGGTACACGATTTCGGCTAAAATTTTGCAAAAA
127 GCGTTTTTAGC------AAAAAACCGTGATGGTAGTACACGATTTCGGCTAAAATTTTGCAAAAA
* ** * * *
3213 TTAACCCGAAATATTTTTCTCAATTTTTAGCCACAATACTCATAAAAAATATATAATTCAACGCC
186 TTGACCAAAAATATTTTCCTCAATTTTTAGCCAAAATACTCATAAAATATATATAATTCAACGCC
* * * * * *
3278 AAAAAGATTGAAGGGCTCTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCAAATTAATTTCT
251 AAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCT-GAATTAATTTCT
3343 AATTAAATCGAAAC
315 AATTAAATCGAAAC
* * * * *
3357 ATGATTCAGATGCTCGCAAAAACAAATCCTTAAAT-CAAGTGTGGCTAAGGTTTGGTTAGATGAA
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA-TGTGGCTGAGATTTGATTAGATGAA
* * * ** * * * *
3421 TATAGATATTTCAAGAATTTTTACCACAAAAAATCATGCAAAACTGACCCGGGGCCCCGGAACGC
65 TATAGATATTTCAAGGAGTTCTGGCGCCAAAAATCATGCAAAACTGAGCCGGGG-CCCGAAACGC
* * *
3486 GATTTTAGCCAAAAAAAACTGTGAT-G--GTACACGATTTCGGATAAAATTTTGCAAAAATTGAC
129 GTTTTTAG-C--AAAAAACCGTGATGGTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC
* * * * **
3548 CAGAAATATTTTGTCTCAATTTTTAGCCACAACACTCATAAAATATATATAATTCAATACCAAAA
191 CAAAAATATTTT-CCTCAATTTTTAGCCAAAATACTCATAAAATATATATAATTCAACGCCAAAA
* *
3613 AGACTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTA
255 AGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTA
3678 AATCGAAAC
320 AATCGAAAC
* * * * *
3687 AAGATTCATAGGCTCGTAGAAACAAATCCTTAAATTCAATGTGGCTGAGATATGATTAGATGAAT
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
* * * **
3752 ATAGATATTTCAAGAAG-TCTCGGCGCAAAAAATCATGCAAAACTAAGCTTGGGCCTCGAAACGC
66 ATAGATATTTCAAGGAGTTCT-GGCGCCAAAAATCATGCAAAACTGAGCCGGGGCC-CGAAACGC
* ** * ** **
3816 GTTTTTAGCCAAAAACTATGATGGTAGTACATGATTTCAACTAATTTTTTGCAAAAATTGACCCA
129 GTTTTTAGCAAAAAACCGTGATGGTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGA-CCA
** * * * * *
3881 AATTTTTTTTCC-CAAAAATATTTGGCTAAAATACTCATAATATATATATATATATATAATTTAA
193 AAAATATTTTCCTC---AATTTTTAGCCAAAATACTC-----ATA-A-A-ATATATATAATTCAA
* ** * * * *
3945 TGGTAAAAAGATTGGAGAACTTTTCACGCTTTTAGTATCGTATTT-ATTATTTTTCTGAATTAAT
247 CGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCA-TATTTTTCTGAATTAAT
* *
4009 TTTTAATTAAATCGAAAT
311 TTCTAATTAAATCGAAAC
* * * * * *
4027 AAGATTCAGATGCTCATAAAAAAAAATTCTTAAATCCAATGTTGCTGATATTTTATTAGATGAAT
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
* * ** *
4092 ATGGATATCTCAAAAAG-TCTTGGCACCAAAAATCATGCAAAACTGAGCCGGGGTCCCGAAACGC
66 ATAGATATTTCAAGGAGTTC-TGGCGCCAAAAATCATGCAAAACTGAGCCGGGG-CCCGAAACGC
** * * * * * * * *
4156 GACTTTAGCCAAAAACCGTGATGATTA-TCAAACGATTTCTGTTAGAATTTTACAAAAATTTACT
129 GTTTTTAGCAAAAAACCGTGATG-GTAGT-ACACGATTTCGGCTAAAATTTTGCAAAAATTGAC-
* ** * * *
4220 TGAAAGTTATTTT-CTCAATTTTTAGCCACAACACTCATTAAAAT-TATATAATTCAACGCCAAT
191 -CAAAAATATTTTCCTCAATTTTTAGCCAAAATACTCA-TAAAATATATATAATTCAACGCCAAA
* * * *
4283 AAGATTGAAGGGCTTTTCATGCTTCTAATATCGTTTTTCATAATATTTT-TCGAATTAATTTCTG
254 AAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCAT-AT-TTTTCT-GAATTAATTTCTA
4347 ATTAAATCGAAAC
316 ATTAAATCGAAAC
* * *** * * *
4360 ATGATTCAGATGCTTGT-TTTAGAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAAATGAAT
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
* * ** * *
4424 ATAGATATTTCAAGAAG-TCTCAGCGTAAAAAATCATGCAACACTGTA-CCGGGACACCGAAACG
66 ATAGATATTTCAAGGAGTTCT-GGCGCCAAAAATCATGCAAAACTG-AGCCGGGGC-CCGAAACG
* * * *
4487 CGTTTTTAGCAAAAAAAAAAAACCGTAATTTCGACTAACGTACACGATTTCGGCTAATATTTTGT
128 CGTTTTTAGC------AAAAAACCGTGA--T-G-GT-A-GTACACGATTTCGGCTAAAATTTTGC
* * *
4552 AAAAATTGACCAAAAGTATTATTCCTCAATTTTT-GTCTAAAATACTCATAAAATATATATATTT
181 AAAAATTGACCAAAAATATT-TTCCTCAATTTTTAG-CCAAAATACTCATAAAATATATATAATT
* *
4616 CAACGCCAAAAAGATTGCAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTAAATTA
244 CAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTA
* *
4681 ATTTCAAATTAAATCAAAAC
309 ATTTCTAATTAAATCGAAAC
* * * * *
4701 AAGATTCAGATACTTGTAAAAACACATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATAAAT
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
* * * * * *
4766 ATAGATTTTTCAAGGAGTTCCGACGCCAAAAATCATGCAATACTAAGTCGGGGCCCGAAACGCGT
66 ATAGATATTTCAAGGAGTTCTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCGAAACGCG-
* * * *
4831 TTTTTTTGCAAAAAAACCGTGATGGT-GTACACGATTTCGGCAAAAATTTTGCAAAAAATGATCA
130 -TTTTTAGC-AAAAAACCGTGATGGTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCA
* * * * *
4895 AAAAAATTTCTCCTAAATTTTT-GACTAAAATACTCATGAAAATATATATAATTTAACGCCAAGA
193 AAAATATTT-TCCTCAATTTTTAG-CCAAAATACTCAT-AAAATATATATAATTCAACGCCAAAA
* * * * * *
4959 AGATTGGAGGACTTTTCCCGCTTTTCATATCGTTTTTCATATTTTTTTTAATTAATTTGTAATTA
255 AGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTA
5024 AATCGAAAC
320 AATCGAAAC
* * * * * * * *
5033 AAAATACAGATACTCGTAAAAACAAATCATTAAATGCAATGTGGATGAAATTTGATTAGATTAAT
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
* * * *** * *
5098 ATGGATATATCAAGGA-TTGTTAATGTCAAAAATCATGCAAAACTGA-CCTGGGGCCCTGGAACG
66 ATAGATATTTCAAGGAGTT-CTGGCGCCAAAAATCATGCAAAACTGAGCC-GGGGCCC-GAAACG
* * * * * * *
5161 TGTTTTTAGCCAAAAATCGTGATGATTAATTACACGATTTCTGCTACAATTTTGCAAAAATTGAC
128 CGTTTTTAGCAAAAAACCGTGATG-GT-AGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC
* * * * *
5226 CGAAAAAAAATATTTCCTCAATTTTT-GACTAAAATACTCATAAAAAATAGATAATTCATCGCCA
191 C--AAAAATAT-TTTCCTCAATTTTTAG-CCAAAATACTCATAAAATATATATAATTCAACGCCA
* ** * * * * *
5290 AAAATATTGAAGGGTTTTTTACGCTTGTAATATCTTTTTTCCTACTTTTTCCGAATTAATTTCTA
252 AAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCTGAATTAATTTCTA
5355 ATTAAATCGAAAC
316 ATTAAATCGAAAC
* * *
5368 AAGATTTAGATGCTCGTAAAAA-AAATCCTTAATTCCAATGTGGCTGAGATTTGTTTAGATGAAT
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
* * * * * *
5432 ATAGATATTTGC-ATGATTTTTGGCGCCAAAAATCATACAAAACTGACCCGGGGCCCCAGAACGC
66 ATAGATATTT-CAAGGAGTTCTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCGA-AACGC
** *
5496 AGTTTTGGCCTAAAAAAAAAAACCGTGAT-GT--TACACGATTTCGGCTAATATTTTGCAAAAAT
129 -GTTTT----T--AGCAAAAAACCGTGATGGTAGTACACGATTTCGGCTAAAATTTTGCAAAAAT
* * * *
5558 TGTACCCAAAATATTTTTCCTGAACTTTTTAGCCACAATACTCATAAAAAATATATAATTCAACG
187 TG-ACCAAAAATA-TTTTCCTCAA-TTTTTAGCCAAAATACTCATAAAATATATATAATTCAACG
* ** * * * * *
5623 CCAAAAAGATTGAAGGGCTTTTCATTCTTCTGATA-CTGTTTTTTCTTTCTTTTTTTTTTCGAAT
249 CCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATC-G----TT-TTTCATATTTTTCT-GAAT
*
5687 TAATTTCTAATTAAAACGAAAC
307 TAATTTCTAATTAAATCGAAAC
* * * * * * *
5709 ATGATTCAGATTCTTGT------AAA-----AAA--CAA---GGCTGGGATTTGGTTAGATAAAA
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
* * * * *
5758 ATAGATATTTCAAGGAG-TCTTGGCACC-----TCATTCAAAACTGAACCAGGCCCCGAAACGCG
66 ATAGATATTTCAAGGAGTTC-TGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCGAAACGCG
* * * * ** *
5817 TTTGTAGCCAAAAACCGTGATATGATTATTACACGATTTCAACTAAAATTTTGCAAAAATGGACC
130 TTTTTAGCAAAAAACCGTG--ATG-GTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACC
* * *
5882 TGAAAGATA-TTTCCTCAATTTTTAGCCATAATACTCA-ATAAA-ATATATAATTCGACGCCAAA
192 --AAAAATATTTTCCTCAATTTTTAGCCAAAATACTCATA-AAATATATATAATTCAACGCCAAA
*
5944 AAGATTGAAGGGCTTTTCGA-GCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAA
254 AAGATTGAAGGACTTTTC-ACGCTTTTAATATCGTTTTTCATA-TTTTTCTGAATTAATTTCTAA
* *
6008 CTAAATCGAAAT
317 TTAAATCGAAAC
* * *
6020 AAGATTCAGATGCTCGT-AAAACAAAT-CTTCAAATGCAATGTGGCTAAGATTTTATTAGATGAA
1 AAGATTCAGATGCTCGTAAAAACAAATCCTT-AAATCCAATGTGGCTGAGATTTGATTAGATGAA
** *
6083 TATAGATATTTCAAGGAGTGTCT-ATGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACA
65 TATAGATATTTCAAGGAGT-TCTGGCGCCAAAAATCATGCAAAACTGAGCCGGGG-CCCGAAACG
* * * * * *
6147 CGTTTTTAGCAAAAAACCATGATGGTTAGTACATGATTTTGGCTAAAATTCTGCAAAAAATAACC
128 CGTTTTTAGCAAAAAACCGTGATGG-TAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGA-C
* * ** *
6212 CGAAAAGT-TTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTTAACGCCAAAA
191 C-AAAAATATTTTCCTCAATTTTTAGCCAAAATACTCATAAAATATATATAATTCAACGCCAAAA
* * ** * *
6276 CA-ATTGGAGGACTTTTCACGCTTATAATATTATTTTTCATA-TTTTCTCAATTAATTTCTCATT
255 -AGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATT
6339 AAATCGAAAC
319 AAATCGAAAC
* * *
6349 AAGATTCAGATGCTTGTAAAAAAAAAAAT-CTTAAATCCAATGTGGCTGAAATTTGATTAGATGA
1 AAGATTCAGATGCTCGT--AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGA
* * * * * * ** *
6413 ATATGGATATCTCAAGGAG-TCTTGGCGGCAAAAATCAGGCAAAACTGAGCCAGGTCCTAAAACT
64 ATATAGATATTTCAAGGAGTTC-TGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCGAAACG
* * * * * * **
6477 CATTTTTAACCAAAAACTGTGATGGTTATTACACGATTTTGGCTAAAATTTTGTTAAAATTGACC
128 CGTTTTTAGCAAAAAACCGTGATGG-TAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGA-C
* * * ** *
6542 CGAAAGATGTTTT-CTCAATTTTTGGTTAAAATACTCATAAAAAATATATAATTCAACGCCAAAA
191 C-AAAAATATTTTCCTCAATTTTTAGCCAAAATACTCATAAAATATATATAATTCAACGCCAAAA
* * * * **
6606 AGATTGAATGG-CTTCTGACG-TTTCTAATATCGTTTTCCCTATTTTTTTCCCAATTAATTTCTA
255 AGATTGAA-GGACTTTTCACGCTTT-TAATATCGTTTT-TC-ATATTTTTCTGAATTAATTTCTA
6669 ATTAAATCGAAAC
316 ATTAAATCGAAAC
* * *
6682 AAGATTTAGATGCTCGTAAAAACAAATTCATAAATCCAA
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
6721 GGCTAATTGC
Statistics
Matches: 3009, Mismatches: 528, Indels: 330
0.78 0.14 0.09
Matches are distributed among these distances:
311 42 0.01
312 8 0.00
313 11 0.00
315 3 0.00
316 49 0.02
317 24 0.01
318 11 0.00
319 33 0.01
320 10 0.00
321 24 0.01
323 3 0.00
325 2 0.00
326 74 0.02
327 12 0.00
328 3 0.00
329 58 0.02
330 420 0.14
331 383 0.13
332 409 0.14
333 135 0.04
334 176 0.06
335 132 0.04
336 150 0.05
337 15 0.00
338 111 0.04
339 48 0.02
340 295 0.10
341 160 0.05
342 99 0.03
343 108 0.04
344 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (328 bp):
AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
ATAGATATTTCAAGGAGTTCTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCGAAACGCGT
TTTTAGCAAAAAACCGTGATGGTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCAAAA
ATATTTTCCTCAATTTTTAGCCAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTG
AAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGA
AAC
Found at i:6763 original size:31 final size:31
Alignment explanation
Indices: 6728--6896 Score: 102
Period size: 31 Copynumber: 5.5 Consensus size: 31
6718 CAAGGCTAAT
*
6728 TGCTCAAATAAGGGCCCAATGTTTGTCAAAA
1 TGCTCAAATAAGGGCCTAATGTTTGTCAAAA
* * * **
6759 TGCTCAAATAAGGGTCTGATCTTTG--AATT
1 TGCTCAAATAAGGGCCTAATGTTTGTCAAAA
* *
6788 TGGCTCAAATAAGGGCCTAACG-TTATCGAAAA
1 T-GCTCAAATAAGGGCCTAATGTTTGTC-AAAA
* * * **
6820 TGCTCAAATAAGGG-TTCGATCTTT-T-AATTT
1 TGCTCAAATAAGGGCCT-AATGTTTGTCAA-AA
*
6850 TGC-CAAATAAGGGCCTAATG-TTATCGAAAA
1 TGCTCAAATAAGGGCCTAATGTTTGTC-AAAA
*
6880 TGCTCAAATAAGCGCCT
1 TGCTCAAATAAGGGCCT
6897 GGCGTCAGTT
Statistics
Matches: 101, Mismatches: 25, Indels: 24
0.67 0.17 0.16
Matches are distributed among these distances:
28 2 0.02
29 20 0.20
30 24 0.24
31 50 0.50
32 5 0.05
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAATGTTTGTCAAAA
Found at i:6796 original size:30 final size:29
Alignment explanation
Indices: 6759--6862 Score: 88
Period size: 30 Copynumber: 3.5 Consensus size: 29
6749 TTTGTCAAAA
6759 TGCTCAAATAAGGGTCTGATCTTTGAATT
1 TGCTCAAATAAGGGTCTGATCTTTGAATT
* * **
6788 TGGCTCAAATAAGGGCCT-AACGTTATCGAAAA
1 T-GCTCAAATAAGGGTCTGATC-TT-T-GAATT
*
6820 TGCTCAAATAAGGGT-TCGATCTTTTAATTT
1 TGCTCAAATAAGGGTCT-GATCTTTGAA-TT
6850 TGC-CAAATAAGGG
1 TGCTCAAATAAGGG
6863 CCTAATGTTA
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
29 15 0.25
30 22 0.37
31 16 0.27
32 6 0.10
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (29 bp):
TGCTCAAATAAGGGTCTGATCTTTGAATT
Found at i:6884 original size:60 final size:61
Alignment explanation
Indices: 6727--6891 Score: 246
Period size: 61 Copynumber: 2.7 Consensus size: 61
6717 CCAAGGCTAA
* *
6727 TTGCTCAAATAAGGGCCCAATGTTTGTC-AAAATGCTCAAATAAGGGTCTGATCTTTGAATT
1 TTGCTCAAATAAGGGCCTAATG-TTATCGAAAATGCTCAAATAAGGGTCTGATCTTTGAATT
* * *
6788 TGGCTCAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGT-TCGATCTTTTAATT
1 TTGCTCAAATAAGGGCCTAATGTTATCGAAAATGCTCAAATAAGGGTCT-GATCTTTGAATT
6849 TTGC-CAAATAAGGGCCTAATGTTATCGAAAATGCTCAAATAAG
1 TTGCTCAAATAAGGGCCTAATGTTATCGAAAATGCTCAAATAAG
6892 CGCCTGGCGT
Statistics
Matches: 95, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
60 43 0.45
61 52 0.55
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (61 bp):
TTGCTCAAATAAGGGCCTAATGTTATCGAAAATGCTCAAATAAGGGTCTGATCTTTGAATT
Found at i:6973 original size:31 final size:31
Alignment explanation
Indices: 6935--7102 Score: 127
Period size: 31 Copynumber: 5.5 Consensus size: 31
6925 TTTCGATGTC
* *
6935 AGGCCCTTATTTGAGTATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAAAGTT
** *
6966 AGGCCCTTATTTG-GCCAAATT---AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTGGCAAAAG-TT
*
6995 GGGCCCTTATTTGAGCATTTTGGCAAAAGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAAAGTT
** *
7026 AGGCCCTTATTTGA-CTAAATT-G--AAAGATC
1 AGGCCCTTATTTGAGC-ATTTTGGCAAAAG-TT
* * * *
7055 AGACCCTTATTTGAACATTTTGACAAACGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAAAGTT
7086 AGGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
7103 ATTAGCCTAA
Statistics
Matches: 104, Mismatches: 21, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
28 8 0.08
29 34 0.33
30 5 0.05
31 49 0.47
32 8 0.08
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCATTTTGGCAAAAGTT
Found at i:7029 original size:60 final size:60
Alignment explanation
Indices: 6933--7099 Score: 253
Period size: 60 Copynumber: 2.8 Consensus size: 60
6923 ATTTTCGATG
* *
6933 TCAGGCCCTTATTTGAGTATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGA
1 TCAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGACCAAATTAAAAGA
* * * *
6993 TCGGGCCCTTATTTGAGCATTTTGGCAAAAGTTAGGCCCTTATTTGACTAAATTGAAAGA
1 TCAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGACCAAATTAAAAGA
* * *
7053 TCAGACCCTTATTTGAACATTTTGACAAACGTTAGGCCCTTATTTGA
1 TCAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGA
7100 GCAATTAGCC
Statistics
Matches: 96, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 96 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (60 bp):
TCAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGACCAAATTAAAAGA
Found at i:7823 original size:29 final size:29
Alignment explanation
Indices: 7786--7845 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
7776 GTAAGATTAA
* **
7786 ATTAGAAAGTTATGTTTATATAAAAAGAC
1 ATTAGAAAGTCATGGGTATATAAAAAGAC
*
7815 ATTATAAAGTCATGGGTATATAAAAAGAC
1 ATTAGAAAGTCATGGGTATATAAAAAGAC
7844 AT
1 AT
7846 ATGTGATCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.48, C:0.05, G:0.15, T:0.32
Consensus pattern (29 bp):
ATTAGAAAGTCATGGGTATATAAAAAGAC
Found at i:9769 original size:38 final size:38
Alignment explanation
Indices: 9713--9789 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
9703 TTCAAAATCC
*
9713 TATATGATTTTTACAATACTTTCCAAGATTACACCAAA
1 TATACGATTTTTACAATACTTTCCAAGATTACACCAAA
9751 TATACGATTTTTACAATACTTTCCAAGATTACACCAAA
1 TATACGATTTTTACAATACTTTCCAAGATTACACCAAA
9789 T
1 T
9790 TTACTAAACA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.36
Consensus pattern (38 bp):
TATACGATTTTTACAATACTTTCCAAGATTACACCAAA
Found at i:11387 original size:22 final size:22
Alignment explanation
Indices: 11359--11402 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
11349 GCTTTAATTC
11359 CTACGACTCTATCTGATCCCAA
1 CTACGACTCTATCTGATCCCAA
11381 CTACGACTCTATCTGATCCCAA
1 CTACGACTCTATCTGATCCCAA
11403 TTGCAACCGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.36, G:0.09, T:0.27
Consensus pattern (22 bp):
CTACGACTCTATCTGATCCCAA
Found at i:11816 original size:29 final size:31
Alignment explanation
Indices: 11757--11824 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 31
11747 GAAAAAACAC
* *
11757 CAATTTGAGCTGATTTTGAAAGGTTCAGTAT
1 CAATTTGAGCAGACTTTGAAAGGTTCAGTAT
**
11788 CAATTTGAGCAG-CTTT-AAAGGTTTGGTAT
1 CAATTTGAGCAGACTTTGAAAGGTTCAGTAT
*
11817 CAAATTGA
1 CAATTTGA
11825 TCATTTCTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 18 0.56
30 3 0.09
31 11 0.34
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (31 bp):
CAATTTGAGCAGACTTTGAAAGGTTCAGTAT
Found at i:12265 original size:4 final size:4
Alignment explanation
Indices: 12256--12285 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
12246 CAAATGATTG
12256 AATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AA
12286 AATTACTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:13846 original size:15 final size:14
Alignment explanation
Indices: 13821--13865 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 14
13811 ATGTCATTTT
13821 TTTTATTAAAAAATG
1 TTTT-TTAAAAAATG
13836 ATTTTTTAAAAATATG
1 -TTTTTTAAAAA-ATG
13852 TTTTTTGAAAAAAT
1 TTTTTT-AAAAAAT
13866 TATTATTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (14 bp):
TTTTTTAAAAAATG
Done.