Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010400.1 Corchorus capsularis cultivar CVL-1 contig10421, 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: 16473
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:7516 original size:3 final size:3
Alignment explanation
Indices: 7508--7532 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
7498 AATCAATGTC
7508 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
7533 AGTTTCTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:9427 original size:27 final size:27
Alignment explanation
Indices: 9394--9448 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
9384 TCTGGAAAAT
9394 AAGGGAAATG-GACAATTAAAAAGAAAC
1 AAGGGAAA-GAGACAATTAAAAAGAAAC
*
9421 AAGGGAAAGAGACAATTAAAAAGGAAC
1 AAGGGAAAGAGACAATTAAAAAGAAAC
9448 A
1 A
9449 GAGGAGTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.60, C:0.07, G:0.24, T:0.09
Consensus pattern (27 bp):
AAGGGAAAGAGACAATTAAAAAGAAAC
Found at i:10210 original size:7 final size:7
Alignment explanation
Indices: 10200--10232 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
10190 CTTTTTTCCC
10200 TTCTTCT
1 TTCTTCT
10207 TTCTTCT
1 TTCTTCT
10214 TTCTT-T
1 TTCTTCT
*
10220 TTCTTTT
1 TTCTTCT
10227 TTCTTC
1 TTCTTC
10233 CTCCCTCATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TTCTTCT
Found at i:12204 original size:333 final size:329
Alignment explanation
Indices: 11546--13977 Score: 3169
Period size: 333 Copynumber: 7.3 Consensus size: 329
11536 GTTTTTAGTA
* * * *
11546 AAAAATCGTGATGAT-TAATACACGATTTCGGCTAAAATATTGCAAAAATTT-ACCCGTAAGATT
1 AAAAACCGTGAT-ATATAATACACGATTTCGGCT-AAATTTTGC-AAAATTTGACCCGAAATATT
** *
11609 TTTCCTCAATTTTCAGCCACAATACTCATAAAAAAAATATAATTC-AATGCAAAAAAGATTGAAG
63 TTTCCTCAATTTTTTGCCACAATACTCAT-AAAAATATATAATTCAAAT-C-AAAAAGATTGAA-
* * * * * *
11673 GGCTTTTCATGCTTCTAATACCATTTT-CCTTT-GTTTTGCCGAATTAAATTCTCATTAAATCGG
124 GGTTTTTCATGCTTTTTATACCATTTTCCCTTTACTTTT-TCGAATTAATTTCTCATTAAATC-G
* * * *
11736 AAA-AGGATTCAAATGCTCGTAAAAGCAAATAT-AGAAATT-CAACATGGCTGAGATTTTGTT-A
187 AAACGGGATTCAAATACTCGTAAAACCAAAT-TCAG-AATTCCAACGTGGCTGAGATTTT-TTAA
* * * * * *
11797 GATGAATA-ATGATATTTCAAGGAGTCTTGGCGCCAAAAGTCATGCAAATATGAG-CAGGTGCCT
249 GATGAATATA-GATATTTCAAGGAGTCTTAGCGCAAAAAATCATGCAAATCTGAGCCGGGT-CCC
* *
11860 CAAAACACGTTTTTAACA
312 CGAAACACGTTTTTAACC
* * * *
11878 AAAAACCGTAATATATAATACACGATTTCGGCTAGAATTTTGTAAATTTTCACCCGAAA-ATTTT
1 AAAAACCGTGATATATAATACACGATTTCGGCTA-AATTTTGCAAAATTTGACCCGAAATA-TTT
* * * *
11942 TTCCTCAATTATTTGCCGCAATACTCATCAAAAGTATATAATTCAACCTCAAAAAGATTGAAGGA
64 TTCCTCAATTTTTTGCCACAATACTCAT-AAAAATATATAATTCAA-ATCAAAAAGATTGAAGG-
*
12007 TTTTTCATGCTTTTTATACCATTTTCCCTTAACTTTTTCGAATTAATTTCTCATTAAATCGAAAC
126 TTTTTCATGCTTTTTATACCATTTTCCCTTTACTTTTTCGAATTAATTTCTCATTAAATCGAAAC
*
12072 GGGATTCAGATACTCGTAAAACCAAATTCAGAATTCCAACGTGGCTGAGATTTTTTAAGATGAAT
191 GGGATTCAAATACTCGTAAAACCAAATTCAGAATTCCAACGTGGCTGAGATTTTTTAAGATGAAT
* *
12137 ATAGATATTTCAAGGAGTCTTAGTGCAAAAAATCATGCAAATGTGAGCCGGGTCCCCGAAACACG
256 ATAGATATTTCAAGGAGTCTTAGCGCAAAAAATCATGCAAATCTGAGCCGGGTCCCCGAAACACG
12202 TTTTTAACC
321 TTTTTAACC
* *
12211 AAAAACCGTGATAATATAATACACGATTTCGGCTAAAATTTTACAAAAATTGACCCGAAATATTT
1 AAAAACCGTGAT-ATATAATACACGATTTCGGCT-AAATTTTGCAAAATTTGACCCGAAATATTT
* * *
12276 TTCCTCAATTTTTTGTCACAATACTCATAAAAATATATAATTTAAATGCCAAAAATATTGAAGTG
64 TTCCTCAATTTTTTGCCACAATACTCATAAAAATATATAATTCAAAT--CAAAAAGATTGAAG-G
* *
12341 TTTTCCATGCTTTTTATACCATTTTCCCTTTAC-TTTTCGAATTAATTTCTCATTAAATCGTAAC
126 TTTTTCATGCTTTTTATACCATTTTCCCTTTACTTTTTCGAATTAATTTCTCATTAAATCGAAAC
*
12405 GGGATTCAAATACTCGTAAAACCAAATTCAGAATTCCAACGTGGCTGGGATTTTTTAAGATGAAT
191 GGGATTCAAATACTCGTAAAACCAAATTCAGAATTCCAACGTGGCTGAGATTTTTTAAGATGAAT
*
12470 ATAGATATTTCAAGGAGTCTTAGCGAAAAAAATCATGCAAATCTGAGCCGGGTCCCCGAAACACG
256 ATAGATATTTCAAGGAGTCTTAGCGCAAAAAATCATGCAAATCTGAGCCGGGTCCCCGAAACACG
12535 TTTTTAACC
321 TTTTTAACC
*
12544 AAAAACCGTGATATATAATACACGATTTCGGTTAATATTTTGCAAAATTTGACCCGAAATATTTT
1 AAAAACCGTGATATATAATACACGATTTCGGCTAA-ATTTTGCAAAATTTGACCCGAAATATTTT
* **
12609 TCCTCAATTTTTTTGCCACAATAATCATTAAACGTATATAATTC-AATGCCAAAAAGATTGAAGG
65 TCCTCAA-TTTTTTGCCACAATACTCA-TAAAAATATATAATTCAAAT--CAAAAAGATTGAAGG
* *
12673 ATTTTTCATGCTGTTTATACTATTTTCCCTTTA-TTTTTCGAATTAATTTCTCATTAAATCGAAA
126 -TTTTTCATGCTTTTTATACCATTTTCCCTTTACTTTTTCGAATTAATTTCTCATTAAATCGAAA
* * * * * * *
12737 CAGGATTGAAATGCTCGTAAAAACAAATTTAGAATTCCAACGTGACTGAGATTTTTTTAGATGAA
190 CGGGATTCAAATACTCGTAAAACCAAATTCAGAATTCCAACGTGGCTGAGATTTTTTAAGATGAA
* * * * * **
12802 TATATATATTTTATGGAGTCTTAGCGCAAAAAATCAAGCAAATCTGAGCCGGGACCCCGAAATGC
255 TATAGATATTTCAAGGAGTCTTAGCGCAAAAAATCATGCAAATCTGAGCCGGGTCCCCGAAACAC
* *
12867 ATTCTTAACC
320 GTTTTTAACC
* *
12877 AAAAACCGTGATATATAATACACGATTTCGGCTAGAATTTTGCAAATTTTGACCGGAAATATTTT
1 AAAAACCGTGATATATAATACACGATTTCGGCTA-AATTTTGCAAAATTTGACCCGAAATATTTT
** * * * *
12942 TCCTCAATTTTTTTGCCTGAATACTCATTAAAAGTATATAATTCAACCTAAAAAATATTGAAGTG
65 TCCTCAA-TTTTTTGCCACAATACTCA-TAAAAATATATAATTCAA-ATCAAAAAGATTGAAG-G
* *
13007 TTTTTCATGCTTTTTATACCATTTCCCCTTTAC-TTTTCGAATCAATTTCTCATTAAATCGAAAC
126 TTTTTCATGCTTTTTATACCATTTTCCCTTTACTTTTTCGAATTAATTTCTCATTAAATCGAAAC
*
13071 GGGATTCAAATACTCGTAAAACCAAATTCAGAATTCCAACGTGGCTGGGATTTTTTAAGATGAAT
191 GGGATTCAAATACTCGTAAAACCAAATTCAGAATTCCAACGTGGCTGAGATTTTTTAAGATGAAT
*
13136 ATAGATATTTCAAGGAGTCTTAGCGCAAAAAATCATGCAAATCTGAGTCGGGTCCCCGAAACACG
256 ATAGATATTTCAAGGAGTCTTAGCGCAAAAAATCATGCAAATCTGAGCCGGGTCCCCGAAACACG
13201 TTTTTTAACC
321 -TTTTTAACC
* *
13211 -AAAACCGTGATATATAATACACAATTTCGGGT-AATATTTGCAAAATTTGACCCGAAATATTTT
1 AAAAACCGTGATATATAATACACGATTTCGGCTAAAT-TTTGCAAAATTTGACCCGAAATATTTT
* * * ** * *
13274 TCCTAAATTTTTTTCCACAATATTCATTAAAAGCATATAATTCAACATAAAAAAAATTGAA-GTA
65 TCCTCAATTTTTTGCCACAATACTCA-TAAAAATATATAATTCAA-ATCAAAAAGATTGAAGGT-
* * * *
13338 CTTTTCATGTTTTTTATAGCATTTTCCCTTTA-TATTTCGAATTAATTTCTCATTAAATTCGGAA
127 -TTTTCATGCTTTTTATACCATTTTCCCTTTACTTTTTCGAATTAATTTCTCATTAAA-TCGAAA
** * * * * *
13402 CAAGATTCAAATTCTCGTAAAACAAAATTCAGAATTCCAAAGTGGCCGAGATTTTTTTTAGATGA
190 CGGGATTCAAATACTCGTAAAACCAAATTCAGAATTCCAACGTGGCTGAGA-TTTTTTAAGATG-
* * * * ** *
13467 ATATATATATATTTCATGGAGTCTTAGCGCAAAAAATCAAGCAAATCTGAGCCCGGAGCGCGAAA
253 A-ATATAGATATTTCAAGGAGTCTTAGCGCAAAAAATCATGCAAATCTGAGCCGGGTCCCCGAAA
*
13532 CGCGTTTTTAACC
317 CACGTTTTTAACC
* *
13545 AAAAACCGTGATATATAATACACGATTTCGGCTAAAATTTTACAAAAATTGACCCGAAATATTTT
1 AAAAACCGTGATATATAATACACGATTTCGGCT-AAATTTTGCAAAATTTGACCCGAAATATTTT
** * *
13610 TCCTCAATTTTTTTTCACAATACTCATAAAAATATATAATTTAAATGCCAAAAATATTGAAGTGT
65 TCCTCAATTTTTTGCCACAATACTCATAAAAATATATAATTCAAAT--CAAAAAGATTGAAG-GT
*
13675 TTTTCATGCTTTTTATACCATTTTCCCTTTAC-TTTTCGAATTAATTTCTCATTAATTCGAAACG
127 TTTTCATGCTTTTTATACCATTTTCCCTTTACTTTTTCGAATTAATTTCTCATTAAATCGAAACG
** *
13739 GGATTCAAATACTCGTAAAACCAAATTCAGAATTCCAATATGGCTGAGATTTTTTAGGATGAATA
192 GGATTCAAATACTCGTAAAACCAAATTCAGAATTCCAACGTGGCTGAGATTTTTTAAGATGAATA
* *
13804 TAGATATTTCAAGGAGTTTTAGCGCAAAAAATCATGCAAATCTGAGCCGGGTCCCTGAAACACGT
257 TAGATATTTCAAGGAGTCTTAGCGCAAAAAATCATGCAAATCTGAGCCGGGTCCCCGAAACACGT
13869 TTTTAACC
322 TTTTAACC
*
13877 AAAAACCGTGATATATAATACACGATTTCGGCTAATATTTTGCAAAATTTGACCCGATATATTTT
1 AAAAACCGTGATATATAATACACGATTTCGGCTAA-ATTTTGCAAAATTTGACCCGAAATATTTT
*
13942 TCCTCAATTTTTTGTCACAATACTCATAAAAATATA
65 TCCTCAATTTTTTGCCACAATACTCATAAAAATATA
13978 CTCCCTCTGT
Statistics
Matches: 1857, Mismatches: 194, Indels: 98
0.86 0.09 0.05
Matches are distributed among these distances:
329 2 0.00
331 116 0.06
332 422 0.23
333 878 0.47
334 168 0.09
335 156 0.08
336 110 0.06
337 3 0.00
338 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (329 bp):
AAAAACCGTGATATATAATACACGATTTCGGCTAAATTTTGCAAAATTTGACCCGAAATATTTTT
CCTCAATTTTTTGCCACAATACTCATAAAAATATATAATTCAAATCAAAAAGATTGAAGGTTTTT
CATGCTTTTTATACCATTTTCCCTTTACTTTTTCGAATTAATTTCTCATTAAATCGAAACGGGAT
TCAAATACTCGTAAAACCAAATTCAGAATTCCAACGTGGCTGAGATTTTTTAAGATGAATATAGA
TATTTCAAGGAGTCTTAGCGCAAAAAATCATGCAAATCTGAGCCGGGTCCCCGAAACACGTTTTT
AACC
Found at i:14068 original size:24 final size:25
Alignment explanation
Indices: 14036--14082 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
14026 ACCCTTCTTG
14036 AAACATGCATTTAATTA-AAAGATC
1 AAACATGCATTTAATTAGAAAGATC
*
14060 AAACATGCATTTAGTTAGAAAGA
1 AAACATGCATTTAATTAGAAAGA
14083 AGCAATGGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.49, C:0.11, G:0.13, T:0.28
Consensus pattern (25 bp):
AAACATGCATTTAATTAGAAAGATC
Found at i:14841 original size:333 final size:330
Alignment explanation
Indices: 14219--15879 Score: 2450
Period size: 331 Copynumber: 5.0 Consensus size: 330
14209 GGGAGTATAA
* * *
14219 TTTCATGCTTTTTATACCATTTACCCTTTACTTTTCGAATTAATTTCTCATTAAATCGAAACGGG
1 TTTCATGCTGTTTATACCATTTTCCCTTTA-TTTTCGAATTAATTTCTCATTAAATCGAAACAGG
* * * *
14284 ATTCAAATACTTGTAAAACCAAATTCAGAATTCCAACATGGCTGAGATTTTTTAGGATGAATATA
65 ATTCAAATGCTCGTAAAACCAAATTCAGAATTCCAACGTGACTGAGATTTTTTA-GATGAATATA
* * *
14349 GATATTTCAAGGAGTTTTAGCGCAAAAAATCATGCAATTCTGAGACGGGTCCCCGAAACACGTTT
129 GATATTTCAAGGAGTCTTAGCGCAAAAAATCATGCAAATCTGAGCCGGGTCCCCGAAACACGTTT
14414 TTAACCAAAAACTGTGATATATAATACACGATTTCGGCTAATATTTTGCAAAATTTGACCCGAAA
194 TTAACCAAAAACTGTGATATATAATACACGATTTCGGCTAATATTTTGCAAAATTTGACCCGAAA
* * * *
14479 TATTTTTACTCAATTTTTTTTCAACAATACTCATTAAACGTATATAATTGAATGCCAAAAAGATT
259 TATTTTTCCTCAATTTTTTTGCCACAATACTCATTAAACGTATATAATTCAATGCCAAAAAGATT
14544 GAATGATT
324 GAA-GATT
14552 TTTCATGCTGTTTATACCATTTTCCCTTTATATTTCGAATTAATTTCTCATTAAATCGAAACAGG
1 TTTCATGCTGTTTATACCATTTTCCCTTTAT-TTTCGAATTAATTTCTCATTAAATCGAAACAGG
* * *
14617 ATTGAAATGCTCGTAAAACCAAATTCAGAATTCCAACGTGACTGAGATTTGTATAGATAAATATA
65 ATTCAAATGCTCGTAAAACCAAATTCAGAATTCCAACGTGACTGAGATTT-TTTAGATGAATATA
14682 GATATTTCAAGGAGTCTTAGCGCAAAAAAATCATGCAAATCTGAGCCGGGTCCCCGAAACACGTT
129 GATATTTCAAGGAGTCTTAGCGC-AAAAAATCATGCAAATCTGAGCCGGGTCCCCGAAACACGTT
14747 TTTAACCAAAAACTGTGATATATAATACACGATTTCGGCTAATATTTTGCAAAATTTGACCCGAA
193 TTTAACCAAAAACTGTGATATATAATACACGATTTCGGCTAATATTTTGCAAAATTTGACCCGAA
14812 ATATTTTTCCTCAA-TTTTTTGCCACAATACTCATTAAACGTATATAATTCAATGCCAAAAAGAT
258 ATATTTTTCCTCAATTTTTTTGCCACAATACTCATTAAACGTATATAATTCAATGCCAAAAAGAT
14876 TGAAGGA-T
323 TGAA-GATT
*
14884 TTTCATGCTGTTTATACCATTTTCCCTTTATTTTCGAATTAATTTCTCATTAAATCGAAACAAGA
1 TTTCATGCTGTTTATACCATTTTCCCTTTATTTTCGAATTAATTTCTCATTAAATCGAAACAGGA
*
14949 TTCAAATGCTCGTAAAACCAAATTCAGAATTCCAAAGTGACTGAGATTTTTTTTAGATGAATATA
66 TTCAAATGCTCGTAAAACCAAATTCAGAATTCCAACGTGACTGAGA--TTTTTTAGATGAATATA
* * *
15014 TATATTTCATGGAGTCTTAGCGCAAAAAATCATGCAAATCTGAGCCGGGTCCCCGAAACTCGTTT
129 GATATTTCAAGGAGTCTTAGCGCAAAAAATCATGCAAATCTGAGCCGGGTCCCCGAAACACGTTT
* * *
15079 TTAACCAAAAACCGTGATATAAAATACACGATTTCGGGTAATATTTTGCAAAATTTGACCCGAAA
194 TTAACCAAAAACTGTGATATATAATACACGATTTCGGCTAATATTTTGCAAAATTTGACCCGAAA
* ** * * ***
15144 TATTTTTCCT-AAATTTTTCACCACAATATTCATTAAAAGTATATAATTCAACATCAAAAAGATT
259 TATTTTTCCTCAATTTTTTTGCCACAATACTCATTAAACGTATATAATTCAATGCCAAAAAGATT
* *
15208 CAAGTACT
324 GAAG-ATT
* * * *
15216 TTTCATGTTTTTTATACCATTTTCCCTTTATATTTCGAATTAATTTCTCATTAAATCAAAACAAG
1 TTTCATGCTGTTTATACCATTTTCCCTTTAT-TTTCGAATTAATTTCTCATTAAATCGAAACAGG
* * * ** *
15281 ATTCAAATTCTCGTAAAACCAAATTCAGAATTCCAAAGTGGCTGAGATTTTTTTTA-G-AT-GA-
65 ATTCAAATGCTCGTAAAACCAAATTCAGAATTCCAACGTGACTGAGATTTTTTAGATGAATATAG
* * * * *
15342 ATATTTCATGGAGTCTTAGCGCAAAAAATCATGCAAATCTGAGCCCGGACCGCGAAACGCGTTTT
130 ATATTTCAAGGAGTCTTAGCGCAAAAAATCATGCAAATCTGAGCCGGGTCCCCGAAACACGTTTT
* ** * *
15407 TAACCAAAAACCGTGATATATAATACACGATTTCGTATAGA-ATTTTGCAAAAATTGA-ACG--A
195 TAACCAAAAACTGTGATATATAATACACGATTTCGGCTA-ATATTTTGCAAAATTTGACCCGAAA
*
15468 TATTTTTCCAT-AATTTTTTTCCCACAATACTCATTAAACGTATATAATTCAATGCCAAAAAGAT
259 TATTTTTCC-TCAATTTTTTTGCCACAATACTCATTAAACGTATATAATTCAATGCCAAAAAGAT
15532 TGAAGAATT
323 TGAAG-ATT
*
15541 TTTCATGCTGTTTATCCCATTTTCCCTTTATTTTTCGAATTAATTTCTCATTAAATCGAAACAGG
1 TTTCATGCTGTTTATACCATTTTCCCTTTA-TTTTCGAATTAATTTCTCATTAAATCGAAACAGG
*
15606 ATTGAAATGCTCGTAAAACCAAATTCAGAATTTCCAACGTGACTGAGATTTTTTTTAGATGAATA
65 ATTCAAATGCTCGTAAAACCAAATTCAGAA-TTCCAACGTGACTGAGA--TTTTTTAGATGAATA
* * * * *
15671 TAGATATTTTAAGGAG-CTTAGCGCAAAAAAACCATGCAAATCTGAGCCGGGACCCCGAAACGCA
127 TAGATATTTCAAGGAGTCTTAGCGC-AAAAAATCATGCAAATCTGAGCCGGGTCCCCGAAACACG
15735 TTTTT-ACCAAAAACTGTGATATATAATACACGATTTTCGGCTAATATTTTGCAAAATTTGACCC
191 TTTTTAACCAAAAACTGTGATATATAATACACGA-TTTCGGCTAATATTTTGCAAAATTTGACCC
*
15799 GAAATATTTTTCCTCAATTTTTTTTGCCACAATACTCATTAAACGTATATAATTGAATGCCAAAA
255 GAAATATTTTTCCTCAA-TTTTTTTGCCACAATACTCATTAAACGTATATAATTCAATGCCAAAA
15864 AGATTGAATGATT
319 AGATTGAA-GATT
15877 TTT
1 TTT
15880 TCCTTAATTT
Statistics
Matches: 1210, Mismatches: 90, Indels: 53
0.89 0.07 0.04
Matches are distributed among these distances:
324 10 0.01
325 138 0.11
326 18 0.01
327 112 0.09
328 9 0.01
329 3 0.00
330 6 0.00
331 281 0.23
332 169 0.14
333 271 0.22
334 121 0.10
335 12 0.01
336 59 0.05
337 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.34
Consensus pattern (330 bp):
TTTCATGCTGTTTATACCATTTTCCCTTTATTTTCGAATTAATTTCTCATTAAATCGAAACAGGA
TTCAAATGCTCGTAAAACCAAATTCAGAATTCCAACGTGACTGAGATTTTTTAGATGAATATAGA
TATTTCAAGGAGTCTTAGCGCAAAAAATCATGCAAATCTGAGCCGGGTCCCCGAAACACGTTTTT
AACCAAAAACTGTGATATATAATACACGATTTCGGCTAATATTTTGCAAAATTTGACCCGAAATA
TTTTTCCTCAATTTTTTTGCCACAATACTCATTAAACGTATATAATTCAATGCCAAAAAGATTGA
AGATT
Found at i:15063 original size:331 final size:333
Alignment explanation
Indices: 14219--15879 Score: 2480
Period size: 333 Copynumber: 5.0 Consensus size: 333
14209 GGGAGTATAA
* * *
14219 TTTCATGCTTTTTATACCATTTACCCTTTACTTTTCGAATTAATTTCTCATTAAATCGAAACGGG
1 TTTCATGCTGTTTATACCATTTTCCCTTTA-TTTTCGAATTAATTTCTCATTAAATCGAAACAGG
* * *
14284 ATTCAAATACTTGTAAAACCAAATTCAGAATTCCAACA-TGGCTGAGA--TTTTTTAGGATGAAT
65 ATTCAAATGCTCGTAAAACCAAATTCAGAATTCCAA-AGTGACTGAGATTTTTTTTA-GATGAAT
* * *
14346 ATAGATATTTCAAGGAGTTTTAGCGCAAAAAATCATGCAATTCTGAGACGGGTCCCCGAAACACG
128 ATAGATATTTCAAGGAGTCTTAGCGCAAAAAATCATGCAAATCTGAGCCGGGTCCCCGAAACACG
14411 TTTTTAACCAAAAACTGTGATATATAATACACGATTTCGGCTAATATTTTGCAAAATTTGACCCG
193 TTTTTAACCAAAAACTGTGATATATAATACACGATTTCGGCTAATATTTTGCAAAATTTGACCCG
* * * *
14476 AAATATTTTTACTCAATTTTTTTTCAACAATACTCATTAAACGTATATAATTGAATGCCAAAAAG
258 AAATATTTTTCCTCAATTTTTTTGCCACAATACTCATTAAACGTATATAATTCAATGCCAAAAAG
*
14541 ATTGAATGATT
323 ATTGAAGGATT
14552 TTTCATGCTGTTTATACCATTTTCCCTTTATATTTCGAATTAATTTCTCATTAAATCGAAACAGG
1 TTTCATGCTGTTTATACCATTTTCCCTTTAT-TTTCGAATTAATTTCTCATTAAATCGAAACAGG
* * * * *
14617 ATTGAAATGCTCGTAAAACCAAATTCAGAATTCCAACGTGACTGAGA-TTTGTATAGATAAATAT
65 ATTCAAATGCTCGTAAAACCAAATTCAGAATTCCAAAGTGACTGAGATTTTTTTTAGATGAATAT
14681 AGATATTTCAAGGAGTCTTAGCGCAAAAAAATCATGCAAATCTGAGCCGGGTCCCCGAAACACGT
130 AGATATTTCAAGGAGTCTTAGCGC-AAAAAATCATGCAAATCTGAGCCGGGTCCCCGAAACACGT
14746 TTTTAACCAAAAACTGTGATATATAATACACGATTTCGGCTAATATTTTGCAAAATTTGACCCGA
194 TTTTAACCAAAAACTGTGATATATAATACACGATTTCGGCTAATATTTTGCAAAATTTGACCCGA
14811 AATATTTTTCCTCAA-TTTTTTGCCACAATACTCATTAAACGTATATAATTCAATGCCAAAAAGA
259 AATATTTTTCCTCAATTTTTTTGCCACAATACTCATTAAACGTATATAATTCAATGCCAAAAAGA
14875 TTGAAGGA-T
324 TTGAAGGATT
*
14884 TTTCATGCTGTTTATACCATTTTCCCTTTATTTTCGAATTAATTTCTCATTAAATCGAAACAAGA
1 TTTCATGCTGTTTATACCATTTTCCCTTTATTTTCGAATTAATTTCTCATTAAATCGAAACAGGA
14949 TTCAAATGCTCGTAAAACCAAATTCAGAATTCCAAAGTGACTGAGATTTTTTTTAGATGAATATA
66 TTCAAATGCTCGTAAAACCAAATTCAGAATTCCAAAGTGACTGAGATTTTTTTTAGATGAATATA
* * *
15014 TATATTTCATGGAGTCTTAGCGCAAAAAATCATGCAAATCTGAGCCGGGTCCCCGAAACTCGTTT
131 GATATTTCAAGGAGTCTTAGCGCAAAAAATCATGCAAATCTGAGCCGGGTCCCCGAAACACGTTT
* * *
15079 TTAACCAAAAACCGTGATATAAAATACACGATTTCGGGTAATATTTTGCAAAATTTGACCCGAAA
196 TTAACCAAAAACTGTGATATATAATACACGATTTCGGCTAATATTTTGCAAAATTTGACCCGAAA
* ** * * ***
15144 TATTTTTCCT-AAATTTTTCACCACAATATTCATTAAAAGTATATAATTCAACATCAAAAAGATT
261 TATTTTTCCTCAATTTTTTTGCCACAATACTCATTAAACGTATATAATTCAATGCCAAAAAGATT
* * *
15208 CAAGTACT
326 GAAGGATT
* * * *
15216 TTTCATGTTTTTTATACCATTTTCCCTTTATATTTCGAATTAATTTCTCATTAAATCAAAACAAG
1 TTTCATGCTGTTTATACCATTTTCCCTTTAT-TTTCGAATTAATTTCTCATTAAATCGAAACAGG
* *
15281 ATTCAAATTCTCGTAAAACCAAATTCAGAATTCCAAAGTGGCTGAGATTTTTTTTAGATG-----
65 ATTCAAATGCTCGTAAAACCAAATTCAGAATTCCAAAGTGACTGAGATTTTTTTTAGATGAATAT
* * * * *
15341 A-ATATTTCATGGAGTCTTAGCGCAAAAAATCATGCAAATCTGAGCCCGGACCGCGAAACGCGTT
130 AGATATTTCAAGGAGTCTTAGCGCAAAAAATCATGCAAATCTGAGCCGGGTCCCCGAAACACGTT
* ** * *
15405 TTTAACCAAAAACCGTGATATATAATACACGATTTCGTATAGA-ATTTTGCAAAAATTGA-ACG-
195 TTTAACCAAAAACTGTGATATATAATACACGATTTCGGCTA-ATATTTTGCAAAATTTGACCCGA
*
15467 -ATATTTTTCCAT-AATTTTTTTCCCACAATACTCATTAAACGTATATAATTCAATGCCAAAAAG
259 AATATTTTTCC-TCAATTTTTTTGCCACAATACTCATTAAACGTATATAATTCAATGCCAAAAAG
*
15530 ATTGAAGAATT
323 ATTGAAGGATT
*
15541 TTTCATGCTGTTTATCCCATTTTCCCTTTATTTTTCGAATTAATTTCTCATTAAATCGAAACAGG
1 TTTCATGCTGTTTATACCATTTTCCCTTTA-TTTTCGAATTAATTTCTCATTAAATCGAAACAGG
* *
15606 ATTGAAATGCTCGTAAAACCAAATTCAGAATTTCCAACGTGACTGAGATTTTTTTTAGATGAATA
65 ATTCAAATGCTCGTAAAACCAAATTCAGAA-TTCCAAAGTGACTGAGATTTTTTTTAGATGAATA
* * * * *
15671 TAGATATTTTAAGGAG-CTTAGCGCAAAAAAACCATGCAAATCTGAGCCGGGACCCCGAAACGCA
129 TAGATATTTCAAGGAGTCTTAGCGC-AAAAAATCATGCAAATCTGAGCCGGGTCCCCGAAACACG
15735 TTTTT-ACCAAAAACTGTGATATATAATACACGATTTTCGGCTAATATTTTGCAAAATTTGACCC
193 TTTTTAACCAAAAACTGTGATATATAATACACGA-TTTCGGCTAATATTTTGCAAAATTTGACCC
*
15799 GAAATATTTTTCCTCAATTTTTTTTGCCACAATACTCATTAAACGTATATAATTGAATGCCAAAA
257 GAAATATTTTTCCTCAA-TTTTTTTGCCACAATACTCATTAAACGTATATAATTCAATGCCAAAA
*
15864 AGATTGAATGATT
321 AGATTGAAGGATT
15877 TTT
1 TTT
15880 TCCTTAATTT
Statistics
Matches: 1213, Mismatches: 89, Indels: 49
0.90 0.07 0.04
Matches are distributed among these distances:
324 10 0.01
325 138 0.11
326 31 0.03
327 112 0.09
328 2 0.00
330 2 0.00
331 275 0.23
332 172 0.14
333 277 0.23
334 123 0.10
335 12 0.01
336 59 0.05
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.34
Consensus pattern (333 bp):
TTTCATGCTGTTTATACCATTTTCCCTTTATTTTCGAATTAATTTCTCATTAAATCGAAACAGGA
TTCAAATGCTCGTAAAACCAAATTCAGAATTCCAAAGTGACTGAGATTTTTTTTAGATGAATATA
GATATTTCAAGGAGTCTTAGCGCAAAAAATCATGCAAATCTGAGCCGGGTCCCCGAAACACGTTT
TTAACCAAAAACTGTGATATATAATACACGATTTCGGCTAATATTTTGCAAAATTTGACCCGAAA
TATTTTTCCTCAATTTTTTTGCCACAATACTCATTAAACGTATATAATTCAATGCCAAAAAGATT
GAAGGATT
Found at i:15891 original size:70 final size:70
Alignment explanation
Indices: 15804--15950 Score: 242
Period size: 70 Copynumber: 2.1 Consensus size: 70
15794 GACCCGAAAT
* *
15804 ATTTTTCCTCAATTTTTTTTGCCACAATACTCATTAAACGTATATAATTGAATGCCAAAAAGATT
1 ATTTTTCCTCAATTTTTTTTCCCACAATACTCATTAAACGTATATAATTCAATGCCAAAAAGATT
15869 GAATGA
66 GAA-GA
* *
15875 TTTTTTCCTTAA-TTTTTTTCCCACAATACTCATTAAACGTATATAATTCAATGCCAAAAAGATT
1 ATTTTTCCTCAATTTTTTTTCCCACAATACTCATTAAACGTATATAATTCAATGCCAAAAAGATT
15939 GAAGA
66 GAAGA
15944 ATTTTTC
1 ATTTTTC
15951 ATGCTGTTTA
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
69 8 0.11
70 53 0.75
71 10 0.14
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.40
Consensus pattern (70 bp):
ATTTTTCCTCAATTTTTTTTCCCACAATACTCATTAAACGTATATAATTCAATGCCAAAAAGATT
GAAGA
Found at i:16228 original size:406 final size:406
Alignment explanation
Indices: 15455--16269 Score: 1417
Period size: 406 Copynumber: 2.0 Consensus size: 406
15445 AGAATTTTGC
15455 AAAA-ATTGAACGATATTTTTCCATAATTTTTTTCCCACAATACTCATTAAACGTATATAATTCA
1 AAAAGATTGAACGATATTTTTCCATAATTTTTTTCCCACAATACTCATTAAACGTATATAATTCA
* *
15519 ATGCCAAAAAGATTGAAGAATTTTTCATGCTGTTTATCCCATTTTCCCTTTATTTTTCGAATTAA
66 ATGCCAAAAAGATTGAAGAATTTTTCATGCTGTTTATACCATTTTCCATTTATTTTTCGAATTAA
*
15584 TTTCTCATTAAATCGAAACAGGATTGAAATGCTCGTAAAACCAAATTCAGAATTTCCAACGTGAC
131 TTTCTCATTAAATAGAAACAGGATTGAAATGCTCGTAAAACCAAATTCAGAATTTCCAACGTGAC
*
15649 TGAGATTTTTTTTAGATGAATATAGATATTTTAAGGAGCTTAGCGCAAAAAAACCATGCAAATCT
196 TGAGATTTTTTTTAGATGAATATAGATATTTCAAGGAGCTTAGCGCAAAAAAACCATGCAAATCT
* * *
15714 GAGCCGGGACCCCGAAACGCATTTTTACCAAAAACTGTGATATATAATACACGATTTTCGGCTAA
261 GAACCGGGACCCCGAAACACATTTTTACCAAAAACCGTGATATATAATACACGATTTTCGGCTAA
15779 TATTTTGCAAAATTTGACCCGAAATATTTTTCCTCAATTTTTTTTGCCACAATACTCATTAAACG
326 TATTTTGCAAAATTTGACCCGAAATATTTTTCCTCAATTTTTTTT-CCACAATACTCATTAAACG
*
15844 TATATAATTGAATGCCA
390 TATATAATTCAATGCCA
* *
15861 AAAAGATTGAATGAT-TTTTTCCTTAATTTTTTTCCCACAATACTCATTAAACGTATATAATTCA
1 AAAAGATTGAACGATATTTTTCCATAATTTTTTTCCCACAATACTCATTAAACGTATATAATTCA
15925 ATGCCAAAAAGATTGAAGAATTTTTCATGCTGTTTATACCATTTTCCATTTATTTTTCGAATTAA
66 ATGCCAAAAAGATTGAAGAATTTTTCATGCTGTTTATACCATTTTCCATTTATTTTTCGAATTAA
15990 TTTCTCATTAAATAGAAACAGGATTGAAATGCTCGTAAAACCAAATTCAGAA-TTCCAACGTGAC
131 TTTCTCATTAAATAGAAACAGGATTGAAATGCTCGTAAAACCAAATTCAGAATTTCCAACGTGAC
*
16054 TGAGA-TTTTTTTAGATTGAATATAGATATTTCAAGGAGTCTTAGCGC-AAAAAATCATGCAAAT
196 TGAGATTTTTTTTAGA-TGAATATAGATATTTCAAGGAG-CTTAGCGCAAAAAAACCATGCAAAT
* * *
16117 CTGAATCGGGTCCCCGAAACACGTTTTTAACCAAAAACCGTGATATATAATACACGA-TTTCGGC
259 CTGAACCGGGACCCCGAAACACATTTTT-ACCAAAAACCGTGATATATAATACACGATTTTCGGC
*
16181 TAATATTTTGCAAAATTTGACCCGAAATATTTTTCCTTAATTTTTTTTCCACAATACTCATTAAA
323 TAATATTTTGCAAAATTTGACCCGAAATATTTTTCCTCAATTTTTTTTCCACAATACTCATTAAA
16246 CGTATATAATTCAATGCCA
388 CGTATATAATTCAATGCCA
16265 AAAAG
1 AAAAG
16270 TTCCAACGTG
Statistics
Matches: 390, Mismatches: 15, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
404 50 0.13
405 130 0.33
406 201 0.52
407 9 0.02
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (406 bp):
AAAAGATTGAACGATATTTTTCCATAATTTTTTTCCCACAATACTCATTAAACGTATATAATTCA
ATGCCAAAAAGATTGAAGAATTTTTCATGCTGTTTATACCATTTTCCATTTATTTTTCGAATTAA
TTTCTCATTAAATAGAAACAGGATTGAAATGCTCGTAAAACCAAATTCAGAATTTCCAACGTGAC
TGAGATTTTTTTTAGATGAATATAGATATTTCAAGGAGCTTAGCGCAAAAAAACCATGCAAATCT
GAACCGGGACCCCGAAACACATTTTTACCAAAAACCGTGATATATAATACACGATTTTCGGCTAA
TATTTTGCAAAATTTGACCCGAAATATTTTTCCTCAATTTTTTTTCCACAATACTCATTAAACGT
ATATAATTCAATGCCA
Found at i:16438 original size:227 final size:229
Alignment explanation
Indices: 16042--16473 Score: 708
Period size: 227 Copynumber: 1.9 Consensus size: 229
16032 AAATTCAGAA
16042 TTCCAACGTGACTGAGATTTTTTTAGATTGAATATAGATATTTCAAGGAGTCTTAGCGCAAAAAA
1 TTCCAACGTGACTGAGATTTTTTTAGATTGAATATAGATATTTCAAGGAGTCTTAGCGCAAAAAA
* * *
16107 TCATGCAAATCTGAATCGGGTCCCCGAAACACGTTTTTAACCAAAAACCGTGATATATAATACAC
66 TCATGCAAATCTGAACCGGGACCCCGAAACACATTTTTAACCAAAAACCGTGATATATAATACAC
* *
16172 GATTTCGGCTAATATTTTGCAAAATTTGACCCGAAATATTTTTCCTTAATTT-TTTTTCCACAAT
131 GATTTCGGCTAATATTTTGCAAAATTTGACCCGAAATATTTTTCCTCAATTTCTTTTGCCACAAT
16236 ACTCATTAAACGTATATAATTCAATGCCAAAAAG
196 ACTCATTAAACGTATATAATTCAATGCCAAAAAG
* *
16270 TTCCAACGTGACTGAGATTTTTTTAGA-TGAATATAGATATTTTATGGAGTCTTAGCGCAAAAAA
1 TTCCAACGTGACTGAGATTTTTTTAGATTGAATATAGATATTTCAAGGAGTCTTAGCGCAAAAAA
* **
16334 TCATGCAAATCTGAGCCGGGACCCCGAAATGCATTTTTAACCAAAAACCGTGATATATAATACAC
66 TCATGCAAATCTGAACCGGGACCCCGAAACACATTTTTAACCAAAAACCGTGATATATAATACAC
* * *
16399 GATTTCGGCTAGA-ATTTTGCAAATTTTGACCGGAAATATTTTTCCTCAATTTCTTTTGCCAGAA
131 GATTTCGGCTA-ATATTTTGCAAAATTTGACCCGAAATATTTTTCCTCAATTTCTTTTGCCACAA
*
16463 TATTCATTAAA
195 TACTCATTAAA
Statistics
Matches: 188, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
227 141 0.75
228 47 0.25
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (229 bp):
TTCCAACGTGACTGAGATTTTTTTAGATTGAATATAGATATTTCAAGGAGTCTTAGCGCAAAAAA
TCATGCAAATCTGAACCGGGACCCCGAAACACATTTTTAACCAAAAACCGTGATATATAATACAC
GATTTCGGCTAATATTTTGCAAAATTTGACCCGAAATATTTTTCCTCAATTTCTTTTGCCACAAT
ACTCATTAAACGTATATAATTCAATGCCAAAAAG
Done.