Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009691.1 Corchorus capsularis cultivar CVL-1 contig09712, 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: 44051
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:47 original size:19 final size:20
Alignment explanation
Indices: 23--60 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
13 TGATTACTAA
23 AAAACAATTAT-AGGTTATC
1 AAAACAATTATAAGGTTATC
42 AAAACAATTATAAGGTTAT
1 AAAACAATTATAAGGTTAT
61 TTATAAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.32
Consensus pattern (20 bp):
AAAACAATTATAAGGTTATC
Found at i:2982 original size:21 final size:19
Alignment explanation
Indices: 2957--3012 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 19
2947 GCTGCTCTAA
2957 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
2978 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
2997 TAATCTCATCTGTACA
1 TAATCTCATCTGTACA
3013 ATTGCTAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 15 0.47
21 17 0.53
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:11968 original size:88 final size:87
Alignment explanation
Indices: 11811--12042 Score: 333
Period size: 88 Copynumber: 2.6 Consensus size: 87
11801 TAGTTTCTTC
* * * *
11811 GCCGTAGGTATATCCCCCATCAAACC-TGTTGGTT-GTTTATGGCTATACCAACGCCTCCCGCTG
1 GCCGTAGGTATATCTCCAATCATACCAT-TT--TTGGTTTATGGCTATACCAACGCCACCCGCTG
* *
11874 TTGGTATATATCTATAGCAACGTAA
63 TCGGTATACATCTATAGCAACGTAA
* * *
11899 GCTGTAGGTATATCTCCAATCATACCATTTTTTGGTTTGTGGCTATACCAATGCCACCCGCTGTC
1 GCCGTAGGTATATCTCCAATCATACCA-TTTTTGGTTTATGGCTATACCAACGCCACCCGCTGTC
11964 GGTATACATCTATAGCAACGTAA
65 GGTATACATCTATAGCAACGTAA
11987 GCCGTAGGTATATCTCCAATCATACCATTTTTGGTTTATGGCTATACCAACGCCAC
1 GCCGTAGGTATATCTCCAATCATACCATTTTTGGTTTATGGCTATACCAACGCCAC
12043 AGTCCATTTG
Statistics
Matches: 129, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
87 29 0.22
88 97 0.75
89 2 0.02
90 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (87 bp):
GCCGTAGGTATATCTCCAATCATACCATTTTTGGTTTATGGCTATACCAACGCCACCCGCTGTCG
GTATACATCTATAGCAACGTAA
Found at i:12490 original size:17 final size:17
Alignment explanation
Indices: 12454--12491 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
12444 AAAGTAGTGG
*
12454 GAATATTGAACTTAGGA
1 GAATATTGAACTTAGAA
12471 GAATATTGAA-TTATGAA
1 GAATATTGAACTTA-GAA
12488 GAAT
1 GAAT
12492 GTCTGAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (17 bp):
GAATATTGAACTTAGAA
Found at i:17269 original size:2 final size:2
Alignment explanation
Indices: 17262--17287 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17252 TTCAATTTAA
17262 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
17288 TTCAGTAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21337 original size:489 final size:489
Alignment explanation
Indices: 20289--21338 Score: 1337
Period size: 488 Copynumber: 2.2 Consensus size: 489
20279 AGGTAATATT
* * * * * * * *
20289 TGTAGAAATTAAGCTTTACTGATTTATCGAGAAGA-AAAAAGTTGTATATTTAATTTACCATGAT
1 TGTAGAAAATAAGCCTCAATGAATTATCAAGAAGAGGAAAAGTTGTATATTTCATTTACCATGAT
* * *
20353 CAGTGTATATATATACAAAGAGTTTTAATGTAGATAAACTACAACAACAGTATTTATCTAAAATA
66 CAGTGTATAAATATAAAAAGAGTTTTAATGTAGATAAACTACAACAACAATATTTATCTAAAATA
* * * *
20418 ACAGTAGGTTTTCTTTTATCTGATATGGCAGTAGCCTTTAACTAAGAAAAGACAATAGCATTATC
131 ACAGTAGGTCTTCTTTTATCTAATATGACAGTAGCCTTTAACTAAGAAAAGACAATAGAATTATC
* * * *
20483 TTAAGCTATAGCATCATCCTTAACACGCCCCCTCAAAATTGAGACACCCTTGAAAACTCCAATCT
196 TTAAGATATAACATCATCATTAACACGACCCCTCAAAATTGAGACACCCTTGAAAACTCCAATCT
* * * *
20548 TGGACAACAACAGATTGAACGATGACGAGTTAAAGGCTTGGTTAAAAGGTTAGCTAGTTGGTCTT
261 TGGACAACAACAGAATGAACGATGACAAGTTAAAGGCTTGGCTAAAAGGTCAGCTAGTTGGTCTT
* * *
20613 GTGTAGGCACATGCTTTACTTGAAGAAACCCATTGTTCAATTTATCACGAACGAAGCGAAAATCA
326 GTGTAGGAACATGCTTTACTTGAAGAAACCCATTGTTCAATTTATCACAAACGAAGCAAAAATCA
* *
20678 ATGGCTATATGTTTCATTTTGGAGTGGTAAGCTGGATTGCCTGACATAGGATTATGATCAATGAT
391 ATGGCTATATGTTTCATTTTGGAGTGGTAAGCTGGATTGCCTGACACAGGATTATGATCAATAAT
* * **
20743 TTATCTAGATTTATTAGGATTGGCTCTGATATTA
456 TTATCAAGATTTATCAGGATTGGCTCTGATACCA
* * * *
20777 TGTAGAAATTAAGCCTCAGTGATTTATCAAGAAGAGGAAAA-TTGTATATTTCATTTACTATGAT
1 TGTAGAAAATAAGCCTCAATGAATTATCAAGAAGAGGAAAAGTTGTATATTTCATTTACCATGAT
* * *
20841 CAGTGTATAAATATAAAAAGAGTTTTAATGTAGATCAACTACAACAACAATATTTATTTGAAATA
66 CAGTGTATAAATATAAAAAGAGTTTTAATGTAGATAAACTACAACAACAATATTTATCTAAAATA
* * * * * * * * * *
20906 GCTGTA-GTCTTGTATTTATCTAATATGACAGTAGCTTTTGACTAGGATAAGGCAGTAGAATTTT
131 ACAGTAGGTCTTCT-TTTATCTAATATGACAGTAGCCTTTAACTAAGAAAAGACAATAGAATTAT
* * *
20970 C-TATAGATGTAACATCATCATTAACACGACCCCTCAAGATTGAGACACCCTTGGAAACTCCAAT
195 CTTA-AGATATAACATCATCATTAACACGACCCCTCAAAATTGAGACACCCTTGAAAACTCCAAT
**
21034 CTTAGG-CATTAACAGAATGAATCGATGACAAGTTAAAGGCTTGGCTAAAAGGTCAGCTAGTTGG
259 CTT-GGACAACAACAGAATGAA-CGATGACAAGTTAAAGGCTTGGCTAAAAGGTCAGCTAGTTGG
* * *
21098 TCTTGTGTAGGAACATGCTTTACTTGAAGAAATCCCTTTGTTCACTTTATCACAAACGAAGTAAA
322 TCTTGTGTAGGAACATGCTTTACTTGAAGAAA-CCCATTGTTCAATTTATCACAAACGAAGCAAA
* * * * * *
21163 AATCAATGGCTATATGTTTTATTTTGGAGTGTTAAGTTGGATTGGCTGGCACATGATTATGAT-A
386 AATCAATGGCTATATGTTTCATTTTGGAGTGGTAAGCTGGATTGCCTGACACAGGATTATGATCA
21227 AGTAATTTATCAAGATTTATCAGGATT-GCTCTGATACCA
451 A-TAATTTATCAAGATTTATCAGGATTGGCTCTGATACCA
* * * * *
21266 TGTAGAAAATAAGTCTTAATGAATTATTGTAA-AA-A-GAAAAGTTGTATATTTCATTCACCATT
1 TGTAGAAAATAAGCCTCAATGAATTA-T-CAAGAAGAGGAAAAGTTGTATATTTCATTTACCATG
*
21328 ATTAGTGTATA
64 ATCAGTGTATA
21339 TATTTACGAG
Statistics
Matches: 484, Mismatches: 68, Indels: 19
0.85 0.12 0.03
Matches are distributed among these distances:
487 7 0.01
488 229 0.47
489 138 0.29
490 108 0.22
491 2 0.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (489 bp):
TGTAGAAAATAAGCCTCAATGAATTATCAAGAAGAGGAAAAGTTGTATATTTCATTTACCATGAT
CAGTGTATAAATATAAAAAGAGTTTTAATGTAGATAAACTACAACAACAATATTTATCTAAAATA
ACAGTAGGTCTTCTTTTATCTAATATGACAGTAGCCTTTAACTAAGAAAAGACAATAGAATTATC
TTAAGATATAACATCATCATTAACACGACCCCTCAAAATTGAGACACCCTTGAAAACTCCAATCT
TGGACAACAACAGAATGAACGATGACAAGTTAAAGGCTTGGCTAAAAGGTCAGCTAGTTGGTCTT
GTGTAGGAACATGCTTTACTTGAAGAAACCCATTGTTCAATTTATCACAAACGAAGCAAAAATCA
ATGGCTATATGTTTCATTTTGGAGTGGTAAGCTGGATTGCCTGACACAGGATTATGATCAATAAT
TTATCAAGATTTATCAGGATTGGCTCTGATACCA
Found at i:26332 original size:20 final size:20
Alignment explanation
Indices: 26307--26348 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
26297 GAAAGGGATT
26307 TTATCGGATTTTTCTTTTTC
1 TTATCGGATTTTTCTTTTTC
26327 TTATCGGATTTTTCTTTTTC
1 TTATCGGATTTTTCTTTTTC
26347 TT
1 TT
26349 TTTATGGGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.10, C:0.14, G:0.10, T:0.67
Consensus pattern (20 bp):
TTATCGGATTTTTCTTTTTC
Found at i:29162 original size:48 final size:48
Alignment explanation
Indices: 29091--29340 Score: 235
Period size: 48 Copynumber: 5.2 Consensus size: 48
29081 CCTCTCGAGT
* *
29091 CTCATCCGTATCAGAATCATTTAGTCCATCATCT-TCTTGCTCTTCAGC
1 CTCATCCATATCAGAATCATTTAGTCCATCA-CTGTCTTGCTCTTCAGA
* * * * *
29139 CTCATCCATATCAAAATCATTTAGGCCGTCATTGTCTTGGTCTTC-GAA
1 CTCATCCATATCAGAATCATTTAGTCCATCACTGTCTTGCTCTTCAG-A
* * * * *
29187 CTCATCCATATCAAAATCATTTAGGCCATCACTGCCTTGCTCTTTAAA
1 CTCATCCATATCAGAATCATTTAGTCCATCACTGTCTTGCTCTTCAGA
*
29235 CTCATCCATATCAGAATAATATGT-GT-CATCACTGTCTTGCTCTTC-GAA
1 CTCATCCATATCAGAATCAT-T-TAGTCCATCACTGTCTTGCTCTTCAG-A
* * * *
29283 CTCATCCATATCAGAATAATTT-GTGTCATCACTGCCTTGCTCTTGAG-
1 CTCATCCATATCAGAATCATTTAGT-CCATCACTGTCTTGCTCTTCAGA
29330 CTTCATCCATA
1 C-TCATCCATA
29341 ACACCATTTA
Statistics
Matches: 171, Mismatches: 21, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
46 3 0.02
47 4 0.02
48 160 0.94
49 3 0.02
50 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.36
Consensus pattern (48 bp):
CTCATCCATATCAGAATCATTTAGTCCATCACTGTCTTGCTCTTCAGA
Found at i:29216 original size:96 final size:96
Alignment explanation
Indices: 29091--29340 Score: 290
Period size: 96 Copynumber: 2.6 Consensus size: 96
29081 CCTCTCGAGT
* * *
29091 CTCATCCGTATCAGAATCATTTAGTCCATCATCT-TCTTGCTCTTCAGCCTCATCCATATCAAAA
1 CTCATCCATATCAGAATCATTTAGGCCATCA-CTGCCTTGCTCTTCAGCCTCATCCATATCAAAA
* * * * *
29155 TCATTTAG-GCCGTCATTGTCTTGGTCTTCGAA
65 TAATAT-GTGCCATCACTGTCTTGCTCTTCGAA
* * ** *
29187 CTCATCCATATCAAAATCATTTAGGCCATCACTGCCTTGCTCTTTAAACTCATCCATATCAGAAT
1 CTCATCCATATCAGAATCATTTAGGCCATCACTGCCTTGCTCTTCAGCCTCATCCATATCAAAAT
*
29252 AATATGTGTCATCACTGTCTTGCTCTTCGAA
66 AATATGTGCCATCACTGTCTTGCTCTTCGAA
* * * *
29283 CTCATCCATATCAGAATAATTT-GTGTCATCACTGCCTTGCTCTTGAGCTTCATCCATA
1 CTCATCCATATCAGAATCATTTAG-GCCATCACTGCCTTGCTCTTCAGCCTCATCCATA
29341 ACACCATTTA
Statistics
Matches: 130, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
95 4 0.03
96 126 0.97
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.36
Consensus pattern (96 bp):
CTCATCCATATCAGAATCATTTAGGCCATCACTGCCTTGCTCTTCAGCCTCATCCATATCAAAAT
AATATGTGCCATCACTGTCTTGCTCTTCGAA
Found at i:32585 original size:520 final size:520
Alignment explanation
Indices: 31546--32586 Score: 1933
Period size: 520 Copynumber: 2.0 Consensus size: 520
31536 TGAAAACTAC
31546 TAGATCTTAACAGGTCCATAAGAAAATCAATAACTAAATATGATGTGGGGTTGAGAGTTGAGACA
1 TAGATCTTAACAGGTCCATAAGAAAATCAATAACTAAATATGATGTGGGGTTGAGAGTTGAGACA
*
31611 TTCAATTGTTTTTTCTTCATTTTTTTTAAGAGCTAGCAAACCAAACCTTTCTTGTTAGGTGAAAA
66 TTCAATTGTTTTTTCTTCATTTTTTTTAAGAGCTAGCAAACCAAACCTTTCTTGTCAGGTGAAAA
31676 AATGCTTCAATTATGCTACAGACATCGAATCAGGTTTCAAGGATTCGCCCATACAGACACATTAT
131 AATGCTTCAATTATGCTACAGACATCGAATCAGGTTTCAAGGATTCGCCCATACAGACACATTAT
*
31741 ATCGAAACCAAACACAAAGAGCAGTAGATGACCTATAAAATCACCTATTCGACCACTTAGAAATC
196 ATCGAAACCAAACACAAAGAGCAGCAGATGACCTATAAAATCACCTATTCGACCACTTAGAAATC
*
31806 GAATCTAGTTCAAGTTGCTTCACATACTATATTTACAGAACAATTAACTCATAACCCAACCATTC
261 GAATCTAGTTCAAGTTGCTTCACATACTATATTTACAGAACAATCAACTCATAACCCAACCATTC
* * *
31871 CAAGACCGAACGACAAAAAAAAAAAAGAAGACATAATCAAAGACCCGATTCCAAGAAGCAAATTC
326 CAAGACCAAACGACAAAAAAAAAAAAGAAGAAATAATCAAAAACCCGATTCCAAGAAGCAAATTC
*
31936 CCAAACAAAAAGGTTAAAATTAATAAAATCAAAATTAAAATAGGGCAGATTGGTCATCATACCAG
391 CCAAACAAAAAGGTTAAAATTAATAAAATCAAAATTAAAATAGGGCAGATTGATCATCATACCAG
32001 AAGAGTTTGCATGTTTAGGTGGGCCTTCATTCAAGTCAATAAGCGGCTGGGTTGGTGATGGACGA
456 AAGAGTTTGCATGTTTAGGTGGGCCTTCATTCAAGTCAATAAGCGGCTGGGTTGGTGATGGACGA
32066 TAGATCTTAACAGGTCCATAAGAAAATCAATAACTAAATATGATGTGGGGTTGAGAGTTGAGACA
1 TAGATCTTAACAGGTCCATAAGAAAATCAATAACTAAATATGATGTGGGGTTGAGAGTTGAGACA
32131 TTCAATTGTTTTTTCTTCATTTTTTTT-AGAGCTAGCAAACCAAACCTTTCTTGTCAGGTGAAAA
66 TTCAATTGTTTTTTCTTCATTTTTTTTAAGAGCTAGCAAACCAAACCTTTCTTGTCAGGTGAAAA
* *
32195 AATGCTTCAATTATGCTACAGACATCGAATCAGGTTTCAAGGATTCGGCCATACTGACACATTAT
131 AATGCTTCAATTATGCTACAGACATCGAATCAGGTTTCAAGGATTCGCCCATACAGACACATTAT
32260 ATCGAAACC-AACACAAAGAGCAGCAGATGACCTATAAAATCACCTATTCGACCACTTAGAAATC
196 ATCGAAACCAAACACAAAGAGCAGCAGATGACCTATAAAATCACCTATTCGACCACTTAGAAATC
*
32324 GAATCTAGTTCAAGTTGCTTCACATACTATATTTACAGAATAATCAACTCATAACCCAACCATTC
261 GAATCTAGTTCAAGTTGCTTCACATACTATATTTACAGAACAATCAACTCATAACCCAACCATTC
* *
32389 CAAGACCAAACGACAAAAAAAGAAGAAGAAGAAATAATCAAAAACCCGATTCCAGGAAGCAAATT
326 CAAGACCAAACGACAAAAAAA-AAAAAGAAGAAATAATCAAAAACCCGATTCCAAGAAGCAAATT
*
32454 CCCAAACAAAAAGGTTAAAATTAATAAAATCAAAACTTAAAATAGGGCAGATTGATCATTATACC
390 CCCAAACAAAAAGGTTAAAATTAATAAAATCAAAA-TTAAAATAGGGCAGATTGATCATCATACC
32519 AGAAGAGTTTGCATGTTTAGGTGGGCCTTCATTCAAGTCAATAAGCGGCTGGGTTGGTGATGGAC
454 AGAAGAGTTTGCATGTTTAGGTGGGCCTTCATTCAAGTCAATAAGCGGCTGGGTTGGTGATGGAC
32584 GA
519 GA
32586 T
1 T
32587 CAGCCAAAGG
Statistics
Matches: 506, Mismatches: 13, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
518 137 0.27
519 182 0.36
520 187 0.37
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (520 bp):
TAGATCTTAACAGGTCCATAAGAAAATCAATAACTAAATATGATGTGGGGTTGAGAGTTGAGACA
TTCAATTGTTTTTTCTTCATTTTTTTTAAGAGCTAGCAAACCAAACCTTTCTTGTCAGGTGAAAA
AATGCTTCAATTATGCTACAGACATCGAATCAGGTTTCAAGGATTCGCCCATACAGACACATTAT
ATCGAAACCAAACACAAAGAGCAGCAGATGACCTATAAAATCACCTATTCGACCACTTAGAAATC
GAATCTAGTTCAAGTTGCTTCACATACTATATTTACAGAACAATCAACTCATAACCCAACCATTC
CAAGACCAAACGACAAAAAAAAAAAAGAAGAAATAATCAAAAACCCGATTCCAAGAAGCAAATTC
CCAAACAAAAAGGTTAAAATTAATAAAATCAAAATTAAAATAGGGCAGATTGATCATCATACCAG
AAGAGTTTGCATGTTTAGGTGGGCCTTCATTCAAGTCAATAAGCGGCTGGGTTGGTGATGGACGA
Found at i:33261 original size:27 final size:27
Alignment explanation
Indices: 33231--33282 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
33221 CAACAACAGT
33231 ATTTATCTGAAATAGCAGTAGCCTTGC
1 ATTTATCTGAAATAGCAGTAGCCTTGC
* *
33258 ATTTATCTGATATGGCAGTAGCCTT
1 ATTTATCTGAAATAGCAGTAGCCTT
33283 TGACTAGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (27 bp):
ATTTATCTGAAATAGCAGTAGCCTTGC
Found at i:33759 original size:27 final size:27
Alignment explanation
Indices: 33729--33780 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
33719 CAACAATAGT
*
33729 ATTTATCTAAAATAGTAGTAGCCTTGC
1 ATTTATCTAAAATAGCAGTAGCCTTGC
* *
33756 ATTTATCTAATATGGCAGTAGCCTT
1 ATTTATCTAAAATAGCAGTAGCCTT
33781 TGACTAAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (27 bp):
ATTTATCTAAAATAGCAGTAGCCTTGC
Found at i:34179 original size:498 final size:493
Alignment explanation
Indices: 33117--34320 Score: 1534
Period size: 494 Copynumber: 2.4 Consensus size: 493
33107 GAGGGAGTAG
* *
33117 AAATTAAGCCTCAGTGATTTATTGAGAAGAGAAAAGTTATATTTTTCATTTACTATAATCAGTGT
1 AAATTAAGCCTCAGTGATTTATT-AGAAGAGAAAAGTTGTATATTTCATTTACTATAATCAGTGT
* *
33182 ATATATATATACATA-A-AGAGTTTTAATGTAGATCAACTACAACAACAGTATTTATCTGAAATA
65 ATATATATATATATACACAAAGTTTTAATGTAGATCAACTACAACAACAGTATTTATCTGAAATA
* *
33245 GCAGTAGCCTTGCATTTATCTGATATGGCAGTAGCCTTTGACTAGGATAAGACAGTAGCATTATC
130 GTAGTAGCCTTGCATTTATCTGATATGGCAGTAGCCTTTGACTAGGATAAGACAATAGCATTATC
* * * *
33310 TAAAGTTGTAGCATCATCCTTAACACGCCCATTCAAGATTGAGATACCCTTAGAGACTCCATTCT
195 TATAGTTGTAGCATCATCCTTAACACGCCCACTCAAGATTGAGACACCCTTAGAGACTCCAATCT
* **
33375 AGAACACAAACGATTGAATCGATATCGAGCAAAAGGCTTGGTTAAATGGTCAGCTAGAATTGATA
260 AGAACACAAACGATTGAATCGATATCGAACAAAAGGCTTGGTTAAAAAGTCAGCTAG-ATTGATA
* *
33440 TTCTGTAGACACATGCATTACTTAAATAAATCTATTATTCAATTTATCATGAACGAAGTGAAAAT
324 TTCTGTAGACACATGCATTACTTAAAGAAATCTATTATTCAATTTATCACGAACGAAGTGAAAAT
** *
33505 CAATGGCTATATGTTTCATTTTGGAGTGGTAAGCTGGATTGGCTGACTCAGAATTACGATCAGTG
389 CAATGGCTATATGTTTCATTTTGGAGTGGTAAGCTAAATTGGCTGACACAGAATTACGATCAGTG
* * * *
33570 ATGTACCGAGATTTATCAGGATTGCTCTGATACCATGTAG
454 ATGTACCGAGATTTATCAAGATTGCTCTCATACCATATAA
* * *
33610 AAATTAGGCCTCAGTGATTTATTAGAAAAGAGAAAAGTTGTATATTTCATTTACTATGATCAGTC
1 AAATTAAGCCTCAGTGATTTATTAG--AAGAGAAAAGTTGTATATTTCATTTACTATAATCAGTG
* * *
33675 TATATATATATATATACACAAATTGTTTTAATGTACATCAACTACAACAATAGTATTTATCTAAA
64 TATATATATATATATACACAAA--GTTTTAATGTAGATCAACTACAACAACAGTATTTATCTGAA
* * * *
33740 ATAGTAGTAGCCTTGCATTTATCTAATATGGCAGTAGCCTTTGACTAAGATAAGACATTAGAATT
127 ATAGTAGTAGCCTTGCATTTATCTGATATGGCAGTAGCCTTTGACTAGGATAAGACAATAGCATT
* * * * * *
33805 ATTTATTGTTGTAGCATCATCCTTAACTCGCCC-CTCAAGATTGAGACACCTTTGGAGACTTCAA
192 ATCTATAGTTGTAGCATCATCCTTAACACGCCCACTCAAGATTGAGACACCCTTAGAGACTCCAA
* * * * * * *
33869 TCTTGGACACCAACAGATTGAATCGATGTTGAACTAAAGGTTTGGTTAAAAAGTCAGCTAG-TTG
257 TCTAGAACACAAAC-GATTGAATCGATATCGAACAAAAGGCTTGGTTAAAAAGTCAGCTAGATTG
* * * * * * * *
33933 GTCTTGTGTATGTC-CATGCTTTACTTGAAGAAA-CTCATTGTTTAA-TT-TCACGAACGAAGTG
321 ATATTCTGTA-GACACATGCATTACTTAAAGAAATCT-ATTATTCAATTTATCACGAACGAAGTG
* * *
33994 AAAATCAATGGCTATATGTTTTATTTTGGAGTGGTAAGCTAAATTGGCTGACACAGGATTATGAT
384 AAAATCAATGGCTATATGTTTCATTTTGGAGTGGTAAGCTAAATTGGCTGACACAGAATTACGAT
* * *
34059 CAGTGAAT-TATCGAGATTTATCAAGATTTGCTCTCATGCCTTATAA
449 CAGTG-ATGTACCGAGATTTATCAAGA-TTGCTCTCATACCATATAA
* *
34105 AAATTAAGCCTCAGTGATTTATTCAGAAGAGAAAAGTTGTATATTTCATGTACTACAATCAGTG-
1 AAATTAAGCCTCAGTGATTTATT-AGAAGAGAAAAGTTGTATATTTCATTTACTATAATCAGTGT
* * *
34169 -TATATATATATACACA-AAGAGTTTTAATGTAGATCAATTACAACAACAGTATTTATCTGAAGT
65 ATATATATATATATACACAA-AGTTTTAATGTAGATCAACTACAACAACAGTATTTATCTGAAAT
* *** ** * *
34232 AGCT-GCAGCCTTGCATTTATCTGATATTATAGTAGTGTTTAACTAGGATAAGGCAATAGCATTA
129 AG-TAGTAGCCTTGCATTTATCTGATATGGCAGTAGCCTTTGACTAGGATAAGACAATAGCATTA
*
34296 TCTATAGCTGTAGCATCATCCTTAA
193 TCTATAGTTGTAGCATCATCCTTAA
34321 TAATATTAAC
Statistics
Matches: 613, Mismatches: 84, Indels: 31
0.84 0.12 0.04
Matches are distributed among these distances:
490 110 0.18
491 3 0.00
492 18 0.03
493 22 0.04
494 176 0.29
495 43 0.07
496 37 0.06
497 38 0.06
498 166 0.27
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (493 bp):
AAATTAAGCCTCAGTGATTTATTAGAAGAGAAAAGTTGTATATTTCATTTACTATAATCAGTGTA
TATATATATATATACACAAAGTTTTAATGTAGATCAACTACAACAACAGTATTTATCTGAAATAG
TAGTAGCCTTGCATTTATCTGATATGGCAGTAGCCTTTGACTAGGATAAGACAATAGCATTATCT
ATAGTTGTAGCATCATCCTTAACACGCCCACTCAAGATTGAGACACCCTTAGAGACTCCAATCTA
GAACACAAACGATTGAATCGATATCGAACAAAAGGCTTGGTTAAAAAGTCAGCTAGATTGATATT
CTGTAGACACATGCATTACTTAAAGAAATCTATTATTCAATTTATCACGAACGAAGTGAAAATCA
ATGGCTATATGTTTCATTTTGGAGTGGTAAGCTAAATTGGCTGACACAGAATTACGATCAGTGAT
GTACCGAGATTTATCAAGATTGCTCTCATACCATATAA
Found at i:44030 original size:2 final size:2
Alignment explanation
Indices: 44025--44051 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
44015 AACGAATTGG
44025 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.