Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009438.1 Corchorus capsularis cultivar CVL-1 contig09459, 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: 59662
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:3597 original size:80 final size:80
Alignment explanation
Indices: 3464--3619 Score: 296
Period size: 80 Copynumber: 1.9 Consensus size: 80
3454 CCCAACAAGG
3464 TGAGAACACAAAAGGCTTTAATCTTTCACACTCCTATTTCGAAAGAGATTAATCACCGTCCAAGG
1 TGAGAACACAAAAGGCTTTAATCTTTCACACTCCTATTTCGAAAGAGATTAATCACCGTCCAAGG
3529 GGACATTTGGTAAGC
66 GGACATTTGGTAAGC
3544 TGAGAACACAAAAGGCTTTAATCTTTCACAC-CTCTATTTCGAAAGAGATTAATCACCGTCCAAG
1 TGAGAACACAAAAGGCTTTAATCTTTCACACTC-CTATTTCGAAAGAGATTAATCACCGTCCAAG
3608 GGGACATTTGGT
65 GGGACATTTGGT
3620 TAGGGGTCAT
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
79 1 0.01
80 74 0.99
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (80 bp):
TGAGAACACAAAAGGCTTTAATCTTTCACACTCCTATTTCGAAAGAGATTAATCACCGTCCAAGG
GGACATTTGGTAAGC
Found at i:3927 original size:2 final size:2
Alignment explanation
Indices: 3920--3947 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3910 AGAGTGAATT
3920 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3948 ATGGAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35688 original size:18 final size:18
Alignment explanation
Indices: 35661--35704 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
35651 TGGTGGGTCC
* * *
35661 GTTAAAGGCGGCTCCATG
1 GTTAACGGCGGATCAATG
35679 GTTAACGGCGGATCAATG
1 GTTAACGGCGGATCAATG
*
35697 GTGAACGG
1 GTTAACGG
35705 ATCGGATATC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.18, G:0.36, T:0.20
Consensus pattern (18 bp):
GTTAACGGCGGATCAATG
Found at i:39652 original size:42 final size:42
Alignment explanation
Indices: 39588--39671 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
39578 AACGTAGAAT
* **
39588 AACGTTAACGTGTTGTATTTTGATGACGATTTAAGAAAAATG
1 AACGATAACGTGCCGTATTTTGATGACGATTTAAGAAAAATG
*
39630 AACGATAACGTGCCGTATTTTGATGACGATTTCAGAAAAATG
1 AACGATAACGTGCCGTATTTTGATGACGATTTAAGAAAAATG
39672 CAATTTTTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (42 bp):
AACGATAACGTGCCGTATTTTGATGACGATTTAAGAAAAATG
Found at i:39758 original size:32 final size:32
Alignment explanation
Indices: 39722--39822 Score: 98
Period size: 33 Copynumber: 3.1 Consensus size: 32
39712 CCAAGAGGGA
*
39722 GGCTTACCATGGGCAGGCCGCCCCACTGGGGC
1 GGCTTACCATGGGTAGGCCGCCCCACTGGGGC
* ** *
39754 GGCTTCACTATGAATAGGCCGCCCCACTAGGGC
1 GGCTT-ACCATGGGTAGGCCGCCCCACTGGGGC
**
39787 GGCTT-CGC-TAGGGTAGGCCGCCCCGGTGGGGC
1 GGCTTAC-CAT-GGGTAGGCCGCCCCACTGGGGC
39819 GGCT
1 GGCT
39823 CGGCTATTTT
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
31 2 0.04
32 26 0.47
33 27 0.49
ACGTcount: A:0.13, C:0.34, G:0.38, T:0.16
Consensus pattern (32 bp):
GGCTTACCATGGGTAGGCCGCCCCACTGGGGC
Found at i:39778 original size:33 final size:32
Alignment explanation
Indices: 39736--39822 Score: 111
Period size: 33 Copynumber: 2.7 Consensus size: 32
39726 TACCATGGGC
39736 AGGCCGCCCCACTGGGGCGGCTTCACTATGAAT
1 AGGCCGCCCCACTGGGGCGGCTTCACTA-GAAT
* * **
39769 AGGCCGCCCCACTAGGGCGGCTTCGCTAGGGT
1 AGGCCGCCCCACTGGGGCGGCTTCACTAGAAT
**
39801 AGGCCGCCCCGGTGGGGCGGCT
1 AGGCCGCCCCACTGGGGCGGCT
39823 CGGCTATTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 21 0.45
33 26 0.55
ACGTcount: A:0.13, C:0.34, G:0.38, T:0.15
Consensus pattern (32 bp):
AGGCCGCCCCACTGGGGCGGCTTCACTAGAAT
Found at i:39955 original size:33 final size:33
Alignment explanation
Indices: 39904--39991 Score: 124
Period size: 33 Copynumber: 2.7 Consensus size: 33
39894 CCCATGGTGA
* * *
39904 AGCCGCCCCAGTGGGGAGGCTCCGCCGTGATTG
1 AGCCTCCCTAGTGGGGAGGCTCCGCCGTGACTG
*
39937 AGCCTCCCTAGTGGGGAGGCTCCGCCGTGGCTG
1 AGCCTCCCTAGTGGGGAGGCTCCGCCGTGACTG
39970 AGCCGT-CCTAGTGGGGAGGCTC
1 AGCC-TCCCTAGTGGGGAGGCTC
39992 AGTGTAAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
33 49 0.98
34 1 0.02
ACGTcount: A:0.11, C:0.32, G:0.40, T:0.17
Consensus pattern (33 bp):
AGCCTCCCTAGTGGGGAGGCTCCGCCGTGACTG
Found at i:41025 original size:32 final size:32
Alignment explanation
Indices: 40946--41062 Score: 171
Period size: 32 Copynumber: 3.6 Consensus size: 32
40936 AGCCACGCGG
* *
40946 AGCCTCCCCACTAAGACGGCTCTGCCACGGCGG
1 AGCCTCCCCACTAGGACGGCTCTGCCACGGC-T
40979 AGCCTCCCCACTAGGACGGCTCTGCCACGGCT
1 AGCCTCCCCACTAGGACGGCTCTGCCACGGCT
* *
41011 AGCCACCCCACTAGGACGGCTCTACCACGGCT
1 AGCCTCCCCACTAGGACGGCTCTGCCACGGCT
* *
41043 AGCCGCCCCACTAGGGCGGC
1 AGCCTCCCCACTAGGACGGC
41063 AAAGTCTTTT
Statistics
Matches: 78, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
32 48 0.62
33 30 0.38
ACGTcount: A:0.18, C:0.44, G:0.26, T:0.12
Consensus pattern (32 bp):
AGCCTCCCCACTAGGACGGCTCTGCCACGGCT
Found at i:41167 original size:33 final size:32
Alignment explanation
Indices: 41125--41294 Score: 121
Period size: 32 Copynumber: 5.2 Consensus size: 32
41115 TAGTACCGGT
* *
41125 GCCGCCCCAGGGGGGCGGTCTATCCATGGCAGA
1 GCCGCCCCAGGGGGGCGGCCT-GCCATGGCAGA
* * *
41158 GCCGCCCCAGGGAGGCGGCCTGCCATGGTAGT
1 GCCGCCCCAGGGGGGCGGCCTGCCATGGCAGA
* * *
41190 GTCGCCCCAGGAGGGCGGCTTGGCCATGGCA-A
1 GCCGCCCCAGGGGGGCGGCCT-GCCATGGCAGA
* ** * * *
41222 GTCGTCCCC-CTGGTGCGGCCTGCCATGGTAGT
1 GCCG-CCCCAGGGGGGCGGCCTGCCATGGCAGA
* * *
41254 GTCGCCCCAGGAGGGCGGCTTGGCCATGGCA-A
1 GCCGCCCCAGGGGGGCGGCCT-GCCATGGCAGA
41286 GCCGTCCCC
1 GCCG-CCCC
41295 CTGGTGCGGC
Statistics
Matches: 105, Mismatches: 26, Indels: 12
0.73 0.18 0.08
Matches are distributed among these distances:
31 12 0.11
32 50 0.48
33 43 0.41
ACGTcount: A:0.12, C:0.35, G:0.38, T:0.15
Consensus pattern (32 bp):
GCCGCCCCAGGGGGGCGGCCTGCCATGGCAGA
Found at i:41196 original size:32 final size:32
Alignment explanation
Indices: 41160--41282 Score: 128
Period size: 32 Copynumber: 3.8 Consensus size: 32
41150 ATGGCAGAGC
41160 CGCCCCAGGGAGGCGGCCT-GCCATGGTAGTGT
1 CGCCCCA-GGAGGCGGCCTGGCCATGGTAGTGT
* *
41192 CGCCCCAGGAGGGCGGCTTGGCCATGGCAAGTCGT
1 CGCCCCAGGA-GGCGGCCTGGCCATGG-TAGT-GT
* *
41227 C-CCCCTGG-TGCGGCCT-GCCATGGTAGTGT
1 CGCCCCAGGAGGCGGCCTGGCCATGGTAGTGT
*
41256 CGCCCCAGGAGGGCGGCTTGGCCATGG
1 CGCCCCAGGA-GGCGGCCTGGCCATGG
41283 CAAGCCGTCC
Statistics
Matches: 74, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
29 3 0.04
30 9 0.12
31 10 0.14
32 26 0.35
33 14 0.19
34 9 0.12
35 3 0.04
ACGTcount: A:0.11, C:0.33, G:0.40, T:0.16
Consensus pattern (32 bp):
CGCCCCAGGAGGCGGCCTGGCCATGGTAGTGT
Found at i:41258 original size:64 final size:64
Alignment explanation
Indices: 41172--41314 Score: 259
Period size: 64 Copynumber: 2.2 Consensus size: 64
41162 CCCCAGGGAG
*
41172 GCGGCCTGCCATGGTAGTGTCGCCCCAGGAGGGCGGCTTGGCCATGGCAAGTCGTCCCCCTGGT
1 GCGGCCTGCCATGGTAGTGTCGCCCCAGGAGGGCGGCTTGGCCATGGCAAGCCGTCCCCCTGGT
41236 GCGGCCTGCCATGGTAGTGTCGCCCCAGGAGGGCGGCTTGGCCATGGCAAGCCGTCCCCCTGGT
1 GCGGCCTGCCATGGTAGTGTCGCCCCAGGAGGGCGGCTTGGCCATGGCAAGCCGTCCCCCTGGT
*
41300 GCGGCCCTACCATGG
1 GCGG-CCTGCCATGG
41315 CTCAGCCGCC
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
64 67 0.88
65 9 0.12
ACGTcount: A:0.11, C:0.34, G:0.37, T:0.17
Consensus pattern (64 bp):
GCGGCCTGCCATGGTAGTGTCGCCCCAGGAGGGCGGCTTGGCCATGGCAAGCCGTCCCCCTGGT
Found at i:42599 original size:16 final size:15
Alignment explanation
Indices: 42578--42613 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
42568 AGTTTTTTTG
42578 ATATAATTAATAATTA
1 ATATAA-TAATAATTA
42594 ATATAATAATAATTA
1 ATATAATAATAATTA
42609 A-ATAA
1 ATATAA
42614 AGGTGACCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 4 0.20
15 10 0.50
16 6 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
ATATAATAATAATTA
Found at i:44538 original size:3 final size:3
Alignment explanation
Indices: 44488--44521 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
44478 TGGTCTTACT
*
44488 TGG TGG TGG TGG TGG TGG TGG TGG GGG TGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG T
44522 TGCAGCGGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.68, T:0.32
Consensus pattern (3 bp):
TGG
Found at i:55476 original size:20 final size:20
Alignment explanation
Indices: 55434--55485 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
55424 AAGGTAAAAA
* *
55434 TAAACGACATTGAAAATATTT
1 TAAACGTCA-TGAAAATAATT
*
55455 TAAACGTCATGAGAATAATT
1 TAAACGTCATGAAAATAATT
*
55475 TAAACATCATG
1 TAAACGTCATG
55486 TTTTGTGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.31
Consensus pattern (20 bp):
TAAACGTCATGAAAATAATT
Found at i:56329 original size:22 final size:24
Alignment explanation
Indices: 56299--56344 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
56289 TACATCATAC
* *
56299 ATAATTTTAGAGC-TAAA-AATGG
1 ATAAATTTAAAGCATAAAGAATGG
56321 ATAAATTTAAAGCATAAAGAATGG
1 ATAAATTTAAAGCATAAAGAATGG
56345 GTAATGGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 11 0.55
23 4 0.20
24 5 0.25
ACGTcount: A:0.50, C:0.04, G:0.17, T:0.28
Consensus pattern (24 bp):
ATAAATTTAAAGCATAAAGAATGG
Found at i:56419 original size:57 final size:57
Alignment explanation
Indices: 56326--56443 Score: 191
Period size: 57 Copynumber: 2.1 Consensus size: 57
56316 AATGGATAAA
* *
56326 TTTAAAGCATAAAGAATGGGTAATGGGGTATAAGATATGTGATTGGGTATATTAGAT
1 TTTAAAGCATAAAGAATGGGTAATGGGGAATAAGATATGTAATTGGGTATATTAGAT
* * *
56383 TTTAAAGCATAAAGAATGGGTCATGGGGAATGAGATATGTAATTGGGTGTATTAGAT
1 TTTAAAGCATAAAGAATGGGTAATGGGGAATAAGATATGTAATTGGGTATATTAGAT
56440 TTTA
1 TTTA
56444 GGGTTTTAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.34
Consensus pattern (57 bp):
TTTAAAGCATAAAGAATGGGTAATGGGGAATAAGATATGTAATTGGGTATATTAGAT
Found at i:56635 original size:48 final size:48
Alignment explanation
Indices: 56581--56688 Score: 189
Period size: 48 Copynumber: 2.2 Consensus size: 48
56571 ATCCTAACCA
*
56581 TGTCCGACACGATCCGGACACGAGACACGATAAGCCAAACACGAAACG
1 TGTCCGACACGATCCAGACACGAGACACGATAAGCCAAACACGAAACG
* *
56629 TGTCCGACACGATTCAGACACGAGACACGATAAGCCAAACACGAACCG
1 TGTCCGACACGATCCAGACACGAGACACGATAAGCCAAACACGAAACG
56677 TGTCCGACACGA
1 TGTCCGACACGA
56689 AACACGATAA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 57 1.00
ACGTcount: A:0.36, C:0.31, G:0.22, T:0.10
Consensus pattern (48 bp):
TGTCCGACACGATCCAGACACGAGACACGATAAGCCAAACACGAAACG
Found at i:56842 original size:20 final size:20
Alignment explanation
Indices: 56817--56857 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
56807 AATTGGCCTA
56817 CGGTGATTTCTTCTACAAGT
1 CGGTGATTTCTTCTACAAGT
*
56837 CGGTGATTTCTTCTATAAGT
1 CGGTGATTTCTTCTACAAGT
56857 C
1 C
56858 ACCAATGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (20 bp):
CGGTGATTTCTTCTACAAGT
Found at i:57351 original size:18 final size:16
Alignment explanation
Indices: 57309--57344 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
57299 ATGTGTGTTA
57309 ACATACA-TATAAAAG
1 ACATACACTATAAAAG
57324 ACATACACTATAAAAG
1 ACATACACTATAAAAG
57340 ACATA
1 ACATA
57345 AACACTAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.58, C:0.17, G:0.06, T:0.19
Consensus pattern (16 bp):
ACATACACTATAAAAG
Found at i:57366 original size:22 final size:22
Alignment explanation
Indices: 57340--57384 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
57330 ACTATAAAAG
**
57340 ACATAAACACTAGTAGCACTAT
1 ACATAAACACTACCAGCACTAT
57362 ACATAAACACTACCAGCACTAT
1 ACATAAACACTACCAGCACTAT
57384 A
1 A
57385 TAAGAAACAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.27, G:0.07, T:0.20
Consensus pattern (22 bp):
ACATAAACACTACCAGCACTAT
Found at i:57458 original size:22 final size:22
Alignment explanation
Indices: 57433--57477 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
57423 CATATAAAAG
57433 ACATAAACACTACTAGCACTAT
1 ACATAAACACTACTAGCACTAT
57455 ACATAAACACTACTAGCACTAT
1 ACATAAACACTACTAGCACTAT
57477 A
1 A
57478 TAAGAAACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.27, G:0.04, T:0.22
Consensus pattern (22 bp):
ACATAAACACTACTAGCACTAT
Found at i:57493 original size:23 final size:22
Alignment explanation
Indices: 57437--57487 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
57427 TAAAAGACAT
* *
57437 AAACACTACTAGCACTATACAT
1 AAACACTACTAGCACTATAAAG
57459 AAACACTACTAGCACTATATAAG
1 AAACACTACTAGCACTATA-AAG
57482 AAACAC
1 AAACAC
57488 ATCTAGTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.49, C:0.25, G:0.06, T:0.20
Consensus pattern (22 bp):
AAACACTACTAGCACTATAAAG
Found at i:57535 original size:21 final size:22
Alignment explanation
Indices: 57511--57556 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
57501 AGATATAAAA
*
57511 ACATAAACCCTA-TAGCACCAT
1 ACATAAACACTACTAGCACCAT
*
57532 ACATAAACACTACTAGCACTAT
1 ACATAAACACTACTAGCACCAT
57554 ACA
1 ACA
57557 AGAAACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.46, C:0.30, G:0.04, T:0.20
Consensus pattern (22 bp):
ACATAAACACTACTAGCACCAT
Found at i:57543 original size:77 final size:79
Alignment explanation
Indices: 57410--57563 Score: 249
Period size: 77 Copynumber: 2.0 Consensus size: 79
57400 ACACTGGATT
* *
57410 TCTAGTTAACATTCATATAAAAGACATAAACACTACTAGCACTATACATAAACACTACTAGCACT
1 TCTAGTTAACATACATATAAAAGACATAAACACTACTAGCACCATACATAAACACTACTAGCACT
*
57475 ATATAAGAAACACA
66 ATACAAGAAACACA
* *
57489 TCTAGTTAACATAGATATAAAA-ACATAAACCCTA-TAGCACCATACATAAACACTACTAGCACT
1 TCTAGTTAACATACATATAAAAGACATAAACACTACTAGCACCATACATAAACACTACTAGCACT
57552 ATACAAGAAACA
66 ATACAAGAAACA
57564 AAAAAACACT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
77 39 0.56
78 11 0.16
79 20 0.29
ACGTcount: A:0.49, C:0.22, G:0.06, T:0.23
Consensus pattern (79 bp):
TCTAGTTAACATACATATAAAAGACATAAACACTACTAGCACCATACATAAACACTACTAGCACT
ATACAAGAAACACA
Found at i:58666 original size:329 final size:327
Alignment explanation
Indices: 58013--59662 Score: 1851
Period size: 329 Copynumber: 5.0 Consensus size: 327
58003 CTTTTTCTAC
* * **
58013 ATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAATAAATCCTTAAATCCAACG
1 ATTAATTTCTAATTAAATCGAAACATGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATA
* * * *
58078 TGGTTGATATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTGGGTGCCAAAAATCAAGCAAA
66 TGGTCGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGCCAAAAATCAAGCAAA
* * * * * * * * * **
58143 ACAGAACTGGGGCCCTGGAATGTGTTTTTAGCCAAAATCGTGATGCAAAAAATGTACACAAGCTC
131 ACTGAGCCGGGGCCCTGGAACGCGTTTTTAGCAAAAAAC-CG-T-----AAA-GTACACGATTTC
* * * * **
58208 GGCTAAAATTTTACAAAAAAAGACCCAAAAATTTTTTCCTAAATTTTTGGTCACAATACTCATAA
188 GGCTAAAATTTTGCAAAAAATGA-CCAAAAAATTTTTCCTCAATTTTTGACCACAATACTCATAA
*
58273 AAAATATATAATTCAACGCCAAAAAGATTAACGGGCTTTTCAAGCATCTAATATCGATTTTCCTA
252 AAAATATATAATTCAACGCCAAAAAGATTAACGGGCTTTTCAAGCATCTAATATCGCTTTTCCTA
58338 TTTTTTCCTGA
317 TTTTTTCCTGA
* * * *
58349 ATTAATTTCTAATTAAATCGAAATATGATTCAGATGCTTGTAAAAACAAATCCTTAAATCCATTA
1 ATTAATTTCTAATTAAATCGAAACATGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATA
* * *
58414 TGGTCGAGATTTGGTTAGATGAATATAGATATTTCAAGCAGACCGGGCGCCAAAAATCAAGCAAA
66 TGGTCGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGCCAAAAATCAAGCAAA
* * *
58479 ACTGAGCCGGGACCCTGAAACGCGTTTTTAGCAAAAAAACCGTAACGTACACGATTTCGGCTAAA
131 ACTGAGCCGGGGCCCTGGAACGCGTTTTTAGC-AAAAAACCGTAAAGTACACGATTTCGGCTAAA
* *
58544 ATTTTGCAAAAAATGACCTAAAAAATTTTTCCTCAATTTTTGAACAGAATACTCATAAAAAATAT
195 ATTTTGCAAAAAATGACC-AAAAAATTTTTCCTCAATTTTTGACCACAATACTCATAAAAAATAT
* *
58609 ATAATTCAACACTAAAAAGATTAACGGGCTTTTCAAGCATCTAATATCGCTTTTCCTATTTTTTT
259 ATAATTCAACGCCAAAAAGATTAACGGGCTTTTCAAGCATCTAATATCGCTTTTCCTA-TTTTTT
58674 CCTGA
323 CCTGA
* * *
58679 ATTAGTTTCTAATTAAATCAAAACATGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATG
1 ATTAATTTCTAATTAAATCGAAACATGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATA
* * * * * *
58744 TGCTCGAAATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGTGTCAAAAATAAAACAAA
66 TGGTCGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGCCAAAAATCAAGCAAA
* ** * * * *
58809 ACAGAGCCGGGGCCCTGGAACATGATTTTAGTAAAAAACCGTGATGGTTAGTACACGATTACGGC
131 ACTGAGCCGGGGCCCTGGAACGCGTTTTTAGCAAAAAACCGT-A----AAGTACACGATTTCGGC
*
58874 TAAAATTTTGC-AAAAATGACC-AAAAATTTTTCCTTAATTTTT-ACCACAATACTCAT-AAAAA
191 TAAAATTTTGCAAAAAATGACCAAAAAATTTTTCCTCAATTTTTGACCACAATACTCATAAAAAA
*
58935 TATATAAATCAACGCCAAAAAGATTAACGGGCTTTTCAAGCATCTAATATCGCTTTTCCTA-TTT
256 TATATAATTCAACGCCAAAAAGATTAACGGGCTTTTCAAGCATCTAATATCGCTTTTCCTATTTT
58999 TTCCTGA
321 TTCCTGA
* * *
59006 ATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTC
1 ATTAATTTCTAATTAAATCGAAACATGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATA
* *
59071 TGGTAGAGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTGGGCGCCAAAAATCAAGCAAA
66 TGGTCGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGCCAAAAATCAAGCAAA
* * * * * *
59136 ACTGACCCGGTGTCCTGGAACGCGTTTTTAGCCAAAAACCGTGATGATTAGTACATGATTTCTGC
131 ACTGAGCCGGGGCCCTGGAACGCGTTTTTAGCAAAAAACCGT-A--A--AGTACACGATTTCGGC
* * * ** * * * *
59201 TAAAACTTTGTAAAAGATGACCAGAAATTTTTTTTTCTCAAATTTTGACCACAATACTTATTAAA
191 TAAAATTTTGCAAAAAATGACCA-AAA-AATTTTTCCTCAATTTTTGACCACAATACTCATAAAA
* * **
59266 AATATATAATTCAATG-GAAGAAAGATTGAA-GGGCTTTTCGCGCATCTAATAT--C--TT--T-
254 AATATATAATTCAACGCCAA-AAAGATT-AACGGGCTTTTCAAGCATCTAATATCGCTTTTCCTA
59322 TTTTTT-CTGA
317 TTTTTTCCTGA
* * ** *
59332 ATTAATTTCTAATTAAATAGAAACAAGATTTAGAAACTCGTAAAAACAAATCCTTAAATCCAACA
1 ATTAATTTCTAATTAAATCGAAACATGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATA
* * * * * * * * *
59397 TGATTGAGATTTGGTTAGATGCATATATATGTTTGAAGAAGTCTGCGCGCCAAAAATAAAGCAAA
66 TGGTCGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGCCAAAAATCAAGCAAA
* * * * ** *
59462 ACTGAGCCGGGGCCCCGTAATGCGTTTTTAGCCAAAAATTA-TGATGGTTAGTATACGATTTCGG
131 ACTGAGCCGGGGCCCTGGAACGCGTTTTTAG-CAAAAA--ACCG-T--AAAGTACACGATTTCGG
* * * * *
59526 TTAAAATTTTGCAAAAAATAACCCGAAGAATTTTTCCTCAATTTTTGACCACTATACTCATAAAA
190 CTAAAATTTTGCAAAAAATGA-CCAAAAAATTTTTCCTCAATTTTTGACCACAATACTCATAAAA
* * * * * *
59591 ATTATATAATTCAATGCCAAAAAGGTTAACAGGCTTTTTAAGCATCTAATA-CTCTTTTCCTA-T
254 AATATATAATTCAACGCCAAAAAGATTAACGGGCTTTTCAAGCATCTAATATCGCTTTTCCTATT
59654 TTTTCCTGA
319 TTTTCCTGA
Statistics
Matches: 1114, Mismatches: 165, Indels: 75
0.82 0.12 0.06
Matches are distributed among these distances:
324 2 0.00
325 68 0.06
326 174 0.16
327 197 0.18
328 14 0.01
329 203 0.18
330 175 0.16
331 38 0.03
332 15 0.01
333 54 0.05
334 27 0.02
335 1 0.00
336 141 0.13
337 5 0.00
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (327 bp):
ATTAATTTCTAATTAAATCGAAACATGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATA
TGGTCGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGCCAAAAATCAAGCAAA
ACTGAGCCGGGGCCCTGGAACGCGTTTTTAGCAAAAAACCGTAAAGTACACGATTTCGGCTAAAA
TTTTGCAAAAAATGACCAAAAAATTTTTCCTCAATTTTTGACCACAATACTCATAAAAAATATAT
AATTCAACGCCAAAAAGATTAACGGGCTTTTCAAGCATCTAATATCGCTTTTCCTATTTTTTCCT
GA
Found at i:59085 original size:327 final size:328
Alignment explanation
Indices: 58013--59662 Score: 1934
Period size: 327 Copynumber: 5.0 Consensus size: 328
58003 CTTTTTCTAC
* * *
58013 ATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAATAAATCCTTAAATCCAACG
1 ATTAATTTCTAATTAAATCGAAACATGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCATC-
* * * *
58078 TGGTTGATATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTGGGTGCCAAAAATCAAGCAAA
65 TGGTCGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGCCAAAAATCAAGCAAA
* * * * * * ** * **
58143 ACAGAACTGGGGCCCTGGAATGTGTTTTTAGCC-AAAATCGTGATGCAAAAAATGTACACAAGCT
130 ACTGAGCCGGGGCCCTGGAACGCGTTTTTAGCCAAAAACCGTGATG---ATTA-GTACACGATTT
* * **
58207 CGGCTAAAATTTTACAAAAAAAGACCCAAAAATTTTTTCCTAAATTTTTGGTCACAATACTCATA
191 CGGCTAAAATTTTGCAAAAAATGA-CCAAAAA-TTTTTCCTAAATTTTTGACCACAATACTCAT-
*
58272 AAAAATATATAATTCAACGCCAAAAAGATTAACGGGCTTTTCAAGCATCTAATATCGATTTTCCT
253 AAAAATATATAATTCAACGCCAAAAAGATTAACGGGCTTTTCAAGCATCTAATATCGCTTTTCCT
58337 ATTTTTTCCTGA
318 A-TTTTTCCTGA
* * * *
58349 ATTAATTTCTAATTAAATCGAAATATGATTCAGATGCTTGTAAAAACAAATCCTTAAATCCATTA
1 ATTAATTTCTAATTAAATCGAAACATGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCA-TC
* * *
58414 TGGTCGAGATTTGGTTAGATGAATATAGATATTTCAAGCAGACCGGGCGCCAAAAATCAAGCAAA
65 TGGTCGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGCCAAAAATCAAGCAAA
* * * *
58479 ACTGAGCCGGGACCCTGAAACGCGTTTTTAGCAAAAAAACCGT-A--A--CGTACACGATTTCGG
130 ACTGAGCCGGGGCCCTGGAACGCGTTTTTAGC-CAAAAACCGTGATGATTAGTACACGATTTCGG
* * *
58539 CTAAAATTTTGCAAAAAATGACCTAAAAAATTTTTCCTCAATTTTTGAACAGAATACTCATAAAA
194 CTAAAATTTTGCAAAAAATGACC--AAAAATTTTTCCTAAATTTTTGACCACAATACTCAT-AAA
* *
58604 AATATATAATTCAACACTAAAAAGATTAACGGGCTTTTCAAGCATCTAATATCGCTTTTCCTATT
256 AATATATAATTCAACGCCAAAAAGATTAACGGGCTTTTCAAGCATCTAATATCGCTTTTCCTA--
58669 TTTTTCCTGA
319 TTTTTCCTGA
* * *
58679 ATTAGTTTCTAATTAAATCAAAACATGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATG
1 ATTAATTTCTAATTAAATCGAAACATGATTTAGATGCTCGTAAAAACAAATCCTTAAATCC-ATC
* * * * * *
58744 TGCTCGAAATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGTGTCAAAAATAAAACAAA
65 TGGTCGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGCCAAAAATCAAGCAAA
* ** * ** * *
58809 ACAGAGCCGGGGCCCTGGAACATGATTTTAGTAAAAAACCGTGATGGTTAGTACACGATTACGGC
130 ACTGAGCCGGGGCCCTGGAACGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGC
*
58874 TAAAATTTTGC-AAAAATGACCAAAAATTTTTCCTTAATTTTT-ACCACAATACTCATAAAAATA
195 TAAAATTTTGCAAAAAATGACCAAAAATTTTTCCTAAATTTTTGACCACAATACTCATAAAAATA
*
58937 TATAAATCAACGCCAAAAAGATTAACGGGCTTTTCAAGCATCTAATATCGCTTTTCCTATTTTTC
260 TATAATTCAACGCCAAAAAGATTAACGGGCTTTTCAAGCATCTAATATCGCTTTTCCTATTTTTC
59002 CTGA
325 CTGA
*
59006 ATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTC
1 ATTAATTTCTAATTAAATCGAAACATGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCA-TC
* *
59071 TGGTAGAGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTGGGCGCCAAAAATCAAGCAAA
65 TGGTCGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGCCAAAAATCAAGCAAA
* * * * *
59136 ACTGACCCGGTGTCCTGGAACGCGTTTTTAGCCAAAAACCGTGATGATTAGTACATGATTTCTGC
130 ACTGAGCCGGGGCCCTGGAACGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGC
* * * * * *
59201 TAAAACTTTGTAAAAGATGACCAGAAATTTTTTTTTCTCAAA-TTTTGACCACAATACTTATTAA
195 TAAAATTTTGCAAAAAATGACCA-AAA--ATTTTTCCT-AAATTTTTGACCACAATACTCA-TAA
* * **
59265 AAATATATAATTCAATG-GAAGAAAGATTGAA-GGGCTTTTCGCGCATCTAATAT--C-TTT--T
255 AAATATATAATTCAACGCCAA-AAAGATT-AACGGGCTTTTCAAGCATCTAATATCGCTTTTCCT
59323 -TTTTT-CTGA
318 ATTTTTCCTGA
* * ** *
59332 ATTAATTTCTAATTAAATAGAAACAAGATTTAGAAACTCGTAAAAACAAATCCTTAAATCCAACA
1 ATTAATTTCTAATTAAATCGAAACATGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCATC-
* * * * * * * * *
59397 TGATTGAGATTTGGTTAGATGCATATATATGTTTGAAGAAGTCTGCGCGCCAAAAATAAAGCAAA
65 TGGTCGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGCCAAAAATCAAGCAAA
* * * *** * * *
59462 ACTGAGCCGGGGCCCCGTAATGCGTTTTTAGCCAAAAATTATGATGGTTAGTATACGATTTCGGT
130 ACTGAGCCGGGGCCCTGGAACGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGC
* * * *
59527 TAAAATTTTGCAAAAAATAACCCGAAGAATTTTTCCTCAATTTTTGACCACTATACTCATAAAAA
195 TAAAATTTTGCAAAAAATGA-CC-AAAAATTTTTCCTAAATTTTTGACCACAATACTCATAAAAA
* * * * *
59592 TTATATAATTCAATGCCAAAAAGGTTAACAGGCTTTTTAAGCATCTAATA-CTCTTTTCCTATTT
258 -TATATAATTCAACGCCAAAAAGATTAACGGGCTTTTCAAGCATCTAATATCGCTTTTCCTATTT
59656 TTCCTGA
322 TTCCTGA
Statistics
Matches: 1128, Mismatches: 150, Indels: 77
0.83 0.11 0.06
Matches are distributed among these distances:
324 10 0.01
325 61 0.05
326 187 0.17
327 199 0.18
328 14 0.01
329 198 0.18
330 175 0.16
331 37 0.03
332 17 0.02
333 55 0.05
334 27 0.02
336 140 0.12
337 1 0.00
338 7 0.01
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (328 bp):
ATTAATTTCTAATTAAATCGAAACATGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCATCT
GGTCGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGCCAAAAATCAAGCAAAA
CTGAGCCGGGGCCCTGGAACGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCT
AAAATTTTGCAAAAAATGACCAAAAATTTTTCCTAAATTTTTGACCACAATACTCATAAAAATAT
ATAATTCAACGCCAAAAAGATTAACGGGCTTTTCAAGCATCTAATATCGCTTTTCCTATTTTTCC
TGA
Done.