Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020366.1 Corchorus olitorius cultivar O-4 contig20399, 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: 169351
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4854 original size:60 final size:60
Alignment explanation
Indices: 4695--4856 Score: 227
Period size: 60 Copynumber: 2.7 Consensus size: 60
4685 GCTAATTGCT
* * * *
4695 CAAATAAGGGCCAAAC-TTTTGCCAAAATGCTCAAATAAGAGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTAT-CGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
* * * *
4755 CAAATAAGGGACTAATGTTATGGAAAATGCTCAAATAAGGGCCCGATCTTTTTATTTGGC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
*
4815 CAAATAAGGGCCTAACGTTATCGAAAATGCTGAAATAAGGGC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGC
4857 TTGACGTCAG
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
60 86 0.97
61 3 0.03
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:4935 original size:31 final size:28
Alignment explanation
Indices: 4897--5062 Score: 84
Period size: 31 Copynumber: 5.5 Consensus size: 28
4887 TTTCGACAAC
4897 AGGCCCTTATTTGAGCATTTTCCATAATGTT
1 AGGCCCTTATTTGAGCATTTT--A-AATGTT
** * *
4928 AGGCCCTTATTTG-GCCAAATTAAAAGATC
1 AGGCCCTTATTTGAG-CATTTTAAATG-TT
* * *
4957 GGGTCCTTATTTGAGCATTTTCAATAACGTT
1 AGGCCCTTATTTGAGCATTTT--A-AATGTT
* * * *
4988 AGGCCCTTATTTG-GCTAAATTAAAATATC
1 AGGCCCTTATTTGAGC--ATTTTAAATGTT
* *
5017 AGACCCTTATTTGAGCATTTTGGCAAAGGTT
1 AGGCCCTTATTTGAGCATTTT---AAATGTT
5048 AGGCCCTTATTTGAG
1 AGGCCCTTATTTGAG
5063 TAATTAGCCT
Statistics
Matches: 99, Mismatches: 24, Indels: 24
0.67 0.16 0.16
Matches are distributed among these distances:
28 6 0.06
29 32 0.32
30 7 0.07
31 48 0.48
32 6 0.06
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (28 bp):
AGGCCCTTATTTGAGCATTTTAAATGTT
Found at i:4994 original size:60 final size:59
Alignment explanation
Indices: 4900--5060 Score: 216
Period size: 60 Copynumber: 2.7 Consensus size: 59
4890 CGACAACAGG
* * *
4900 CCCTTATTTGAGCATTTTCCATAATGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGG
1 CCCTTATTTGAGCATTTT-CATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
* * *
4960 TCCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTTGGCTAAATTAAAATATCAGA
1 CCCTTATTTGAGCATTTTC-ATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
*
5020 CCCTTATTTGAGCATTTTGGCA-AAGGTTAGGCCCTTATTTG
1 CCCTTATTTGAGCATTTT--CATAACGTTAGGCCCTTATTTG
5061 AGTAATTAGC
Statistics
Matches: 90, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
59 1 0.01
60 87 0.97
61 1 0.01
62 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (59 bp):
CCCTTATTTGAGCATTTTCATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
Found at i:6715 original size:2 final size:2
Alignment explanation
Indices: 6708--6737 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6698 CCGGGTGAGA
6708 AT AT 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 AT AT
6738 TGTCTCAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8039 original size:16 final size:16
Alignment explanation
Indices: 8018--8051 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
8008 TTTACTTAAT
8018 ATTATACAAAACAATA
1 ATTATACAAAACAATA
8034 ATTATACAAAACAATA
1 ATTATACAAAACAATA
8050 AT
1 AT
8052 AGGAAGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.26
Consensus pattern (16 bp):
ATTATACAAAACAATA
Found at i:9857 original size:21 final size:22
Alignment explanation
Indices: 9817--9857 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
9807 GACAAACTCG
*
9817 TAACCCGAATAACCCGAGAAGA
1 TAACCCGAATAACCCAAGAAGA
*
9839 TAACCCG-ATGACCCAAGAA
1 TAACCCGAATAACCCAAGAA
9858 TATTATAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.44, C:0.29, G:0.17, T:0.10
Consensus pattern (22 bp):
TAACCCGAATAACCCAAGAAGA
Found at i:10111 original size:31 final size:32
Alignment explanation
Indices: 10050--10116 Score: 86
Period size: 31 Copynumber: 2.1 Consensus size: 32
10040 CCGAGCCTGC
*
10050 ATGACCCTAAATCTAGCAGACCTGAGACCCGA
1 ATGACCCTAAATCTAGCAGACCTGAAACCCGA
10082 ATGA-CCTAAATCTAG-ATGAGCC-GAAACCCGA
1 ATGACCCTAAATCTAGCA-GA-CCTGAAACCCGA
10113 ATGA
1 ATGA
10117 TCTGAGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
30 1 0.03
31 25 0.78
32 6 0.19
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.16
Consensus pattern (32 bp):
ATGACCCTAAATCTAGCAGACCTGAAACCCGA
Found at i:16706 original size:22 final size:22
Alignment explanation
Indices: 16678--16728 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
16668 AAGAGCAAAT
16678 CACGGAGATTCCTGAGA-AA-AAG
1 CACGGAGATT--TGAGAGAATAAG
*
16700 CACGGAGCTTTGAGAGAATAAG
1 CACGGAGATTTGAGAGAATAAG
16722 CACGGAG
1 CACGGAG
16729 CTTGATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 5 0.19
21 2 0.08
22 19 0.73
ACGTcount: A:0.37, C:0.18, G:0.31, T:0.14
Consensus pattern (22 bp):
CACGGAGATTTGAGAGAATAAG
Found at i:20290 original size:16 final size:16
Alignment explanation
Indices: 20269--20299 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20259 ACAAGAACAG
*
20269 AAAAGAAGAGAATAGA
1 AAAAGAAAAGAATAGA
20285 AAAAGAAAAGAATAG
1 AAAAGAAAAGAATAG
20300 GGCTCAAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (16 bp):
AAAAGAAAAGAATAGA
Found at i:22959 original size:10 final size:10
Alignment explanation
Indices: 22944--22988 Score: 56
Period size: 10 Copynumber: 4.4 Consensus size: 10
22934 CATCTACCTA
22944 ATTAAGCTCT
1 ATTAAGCTCT
22954 ATTAAGCTCT
1 ATTAAGCTCT
22964 ATTATA-CTCT
1 ATTA-AGCTCT
*
22974 AGCTAAGCTCT
1 A-TTAAGCTCT
22985 ATTA
1 ATTA
22989 TGTGAGATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (10 bp):
ATTAAGCTCT
Found at i:23919 original size:45 final size:45
Alignment explanation
Indices: 23863--23963 Score: 184
Period size: 45 Copynumber: 2.2 Consensus size: 45
23853 GTCAAACCAG
*
23863 AAACTTTGACCACCCAGTTCGACTCAAATCAGACCGGTTCACAGA
1 AAACTTAGACCACCCAGTTCGACTCAAATCAGACCGGTTCACAGA
23908 AAACTTAGACCACCCAGTTCGACTCAAATCAGACCGGTTCACAGA
1 AAACTTAGACCACCCAGTTCGACTCAAATCAGACCGGTTCACAGA
*
23953 AAATTTAGACC
1 AAACTTAGACC
23964 GGTTCCTAAG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.36, C:0.30, G:0.15, T:0.20
Consensus pattern (45 bp):
AAACTTAGACCACCCAGTTCGACTCAAATCAGACCGGTTCACAGA
Found at i:26937 original size:22 final size:22
Alignment explanation
Indices: 26898--26939 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
26888 GACAAATCTG
**
26898 TAACCCGAATGATTCAAGAAGC
1 TAACCCGAATGACCCAAGAAGC
*
26920 TAACCCGGATGACCCAAGAA
1 TAACCCGAATGACCCAAGAA
26940 TATTATAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.26, G:0.19, T:0.14
Consensus pattern (22 bp):
TAACCCGAATGACCCAAGAAGC
Found at i:28559 original size:127 final size:127
Alignment explanation
Indices: 28329--28557 Score: 345
Period size: 127 Copynumber: 1.8 Consensus size: 127
28319 AAATATTTTT
* *
28329 AAAAATTATAATAGATCTAAGTTTTTTAATTAAATTAGTAAAATGGTAAAAATAAAAATAGGTAT
1 AAAAATTATAATAGATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAAATAGGTAT
28394 AAGGATATTAGATTTAATTAAATAAAAAATAAAGTTTTTAGTCGAATAAAACTATAAAAGTA
66 AAGGATATTAGATTTAATTAAATAAAAAATAAAGTTTTTAGTCGAATAAAACTATAAAAGTA
* * * * * *
28456 AAAAATTTTAATATATATAAGTTTTTTAATTAAAATAGTAAATTGGTAAAAAT-TAAATAGTTGT
1 AAAAATTATAATAGATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAAATAGGTAT
** *
28520 GGGGATATTAGATTTAATTAAAT-AAAAATAGAGTTTTT
66 AAGGATATTAGATTTAATTAAATAAAAAATAAAGTTTTT
28558 TTTGCATCAA
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
125 14 0.15
126 29 0.32
127 48 0.53
ACGTcount: A:0.50, C:0.01, G:0.12, T:0.37
Consensus pattern (127 bp):
AAAAATTATAATAGATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAAATAGGTAT
AAGGATATTAGATTTAATTAAATAAAAAATAAAGTTTTTAGTCGAATAAAACTATAAAAGTA
Found at i:32504 original size:21 final size:21
Alignment explanation
Indices: 32478--32521 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
32468 TAACATCAGG
32478 TTGGTTTTCGCCATGGAGGAA
1 TTGGTTTTCGCCATGGAGGAA
32499 TTGGTTTTCGCCATGGAGGAA
1 TTGGTTTTCGCCATGGAGGAA
32520 TT
1 TT
32522 AGACTCCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.14, G:0.32, T:0.36
Consensus pattern (21 bp):
TTGGTTTTCGCCATGGAGGAA
Found at i:35109 original size:18 final size:18
Alignment explanation
Indices: 35086--35120 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35076 TCCATGATCT
35086 TTAAAAAAATTCATGACA
1 TTAAAAAAATTCATGACA
*
35104 TTAAAAAAATTTATGAC
1 TTAAAAAAATTCATGAC
35121 TTTTATCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.09, G:0.06, T:0.31
Consensus pattern (18 bp):
TTAAAAAAATTCATGACA
Found at i:45929 original size:92 final size:93
Alignment explanation
Indices: 45833--46001 Score: 279
Period size: 92 Copynumber: 1.8 Consensus size: 93
45823 TAGTAATATC
*
45833 GTAAAAATAAAACA-TATATAAGGATATTAGATTTAATTAAATAAA-ATAGAGTTTTTAGTTGAG
1 GTAAAAATAAAACAGT-TATAAGGATATTAGATTTAATTAAATAAATATAGAGTTTTTAGTTGAC
45896 TAAAACTATAAAAGTAAAATAGTGAAATG
65 TAAAACTATAAAAGTAAAATAGTGAAATG
* * *
45925 GTAAAAATAATATAGTTATAAGGATATTAGATTTAATTAAATAAATATAGTGTTTTTAGTTGACT
1 GTAAAAATAAAACAGTTATAAGGATATTAGATTTAATTAAATAAATATAGAGTTTTTAGTTGACT
45990 AAAACTATAAAA
66 AAAACTATAAAA
46002 ATTTAAACAA
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
92 41 0.58
93 30 0.42
ACGTcount: A:0.50, C:0.02, G:0.13, T:0.34
Consensus pattern (93 bp):
GTAAAAATAAAACAGTTATAAGGATATTAGATTTAATTAAATAAATATAGAGTTTTTAGTTGACT
AAAACTATAAAAGTAAAATAGTGAAATG
Found at i:53454 original size:2 final size:2
Alignment explanation
Indices: 53447--53472 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
53437 TTTAATTTAC
53447 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
53473 TGTATATCAC
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:56580 original size:54 final size:55
Alignment explanation
Indices: 56508--56611 Score: 142
Period size: 54 Copynumber: 1.9 Consensus size: 55
56498 CATAATTACT
* * *
56508 TTGTTAATTTGTCTTTACAT-C-ATTAAT-TCGGTTGTAATTTTGTTTTTATATGAG
1 TTGTAAATTTGTCATTACATGCAATTAATGTC--TTGTAAATTTGTTTTTATATGAG
56562 TTGTAAATTTGTCATTACATGCAATTAATGTCTTGTAAATTTGTTTTTAT
1 TTGTAAATTTGTCATTACATGCAATTAATGTCTTGTAAATTTGTTTTTAT
56612 CTCATTTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
54 18 0.41
55 18 0.41
56 6 0.14
57 2 0.05
ACGTcount: A:0.25, C:0.08, G:0.13, T:0.54
Consensus pattern (55 bp):
TTGTAAATTTGTCATTACATGCAATTAATGTCTTGTAAATTTGTTTTTATATGAG
Found at i:65504 original size:24 final size:25
Alignment explanation
Indices: 65477--65532 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
65467 TGACAAGATC
**
65477 GAAACCCCACCAAGGGAGG-AGAAA
1 GAAACCCCACCAAAAGAGGAAGAAA
*
65501 GAAACCCCATCAAAAGAGGAAGAAA
1 GAAACCCCACCAAAAGAGGAAGAAA
65526 -AAACCCC
1 GAAACCCC
65533 CCACTTAGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 23 0.82
25 5 0.18
ACGTcount: A:0.50, C:0.27, G:0.21, T:0.02
Consensus pattern (25 bp):
GAAACCCCACCAAAAGAGGAAGAAA
Found at i:66373 original size:10 final size:10
Alignment explanation
Indices: 66344--66374 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
66334 ATTGCTATTA
*
66344 TTTTCTTTTC
1 TTTTCTTTTT
66354 TTTTCTTTTT
1 TTTTCTTTTT
66364 TTTTCTTTTT
1 TTTTCTTTTT
66374 T
1 T
66375 GAGTTGGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:68883 original size:11 final size:10
Alignment explanation
Indices: 68867--68919 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 10
68857 GAAGTTCGTG
68867 ATTGAAGACTT
1 ATTGAAGA-TT
*
68878 ATTGAAGATA
1 ATTGAAGATT
68888 ATTTGAAGA-T
1 A-TTGAAGATT
68898 -TTGAAGATT
1 ATTGAAGATT
68907 ATTGAAGAATT
1 ATTGAAG-ATT
68918 AT
1 AT
68920 CTCAAGACGC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
8 7 0.19
9 1 0.03
10 8 0.22
11 20 0.56
ACGTcount: A:0.42, C:0.02, G:0.19, T:0.38
Consensus pattern (10 bp):
ATTGAAGATT
Found at i:68903 original size:19 final size:18
Alignment explanation
Indices: 68879--68914 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
68869 TGAAGACTTA
68879 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
68898 TTGAAGATTATTGAAGA
1 TTGAAGATAATTGAAGA
68915 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:73614 original size:17 final size:18
Alignment explanation
Indices: 73592--73627 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
73582 GAAGGGTAGT
*
73592 TAAAAA-AATTGTTTTCA
1 TAAAAAGAAGTGTTTTCA
73609 TAAAAAGAAGTGTTTTCA
1 TAAAAAGAAGTGTTTTCA
73627 T
1 T
73628 GCAAGAGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (18 bp):
TAAAAAGAAGTGTTTTCA
Found at i:74743 original size:19 final size:18
Alignment explanation
Indices: 74719--74754 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
74709 TGAAAACTTA
74719 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
74738 TTGAAGATTATTGAAGA
1 TTGAAGATAATTGAAGA
74755 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:90464 original size:29 final size:28
Alignment explanation
Indices: 90420--90475 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
90410 TTCTTCAAAC
*
90420 TTTCTAATTTCAAGAACGCTCAAGAACA
1 TTTCTAATTTCAAGAACGCTAAAGAACA
90448 TTTCTAATCTTCAAGAACGCTAAAGAAC
1 TTTCTAAT-TTCAAGAACGCTAAAGAAC
90476 GTGGAATAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (28 bp):
TTTCTAATTTCAAGAACGCTAAAGAACA
Found at i:91888 original size:31 final size:29
Alignment explanation
Indices: 91845--92011 Score: 106
Period size: 31 Copynumber: 5.6 Consensus size: 29
91835 AAAGGCTAAT
* *
91845 TGCTTAAATAAGGTCCTAACGTTTGGTAAAA
1 TGCTCAAATAAGGGCCTAACGTTT--TAAAA
* * * **
91876 TGTTCAAATAAGGGCATGATC-TTTTAATT
1 TGCTCAAATAAGGGCCT-AACGTTTTAAAA
* *
91905 TGGTCAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTT--TAAAA
* * * **
91936 TGCTCAAATAAGGATCCGATC-TTTTAATT
1 TGCTCAAATAAGG-GCCTAACGTTTTAAAA
91965 TGGC-CAAATAAGGGCCTAACGTTTGTCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTT-T-AAAA
91996 TGCTCAAATAAGGGCC
1 TGCTCAAATAAGGGCC
92012 CGACATCGAA
Statistics
Matches: 101, Mismatches: 25, Indels: 20
0.69 0.17 0.14
Matches are distributed among these distances:
28 6 0.06
29 36 0.36
30 5 0.05
31 48 0.48
32 6 0.06
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Consensus pattern (29 bp):
TGCTCAAATAAGGGCCTAACGTTTTAAAA
Found at i:91923 original size:60 final size:61
Alignment explanation
Indices: 91850--92010 Score: 231
Period size: 60 Copynumber: 2.7 Consensus size: 61
91840 CTAATTGCTT
* * *
91850 AAATAAGGTCCTAACGTTTGGTAAAATGTTCAAATAAGGGCAT-GATCTTTTAATTTGGTC
1 AAATAAGGGCCTAACGTTTGGTAAAATGCTCAAATAAGGGCATCGATCTTTTAATTTGGCC
**
91910 AAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAA-GG-ATCCGATCTTTTAATTTGGCC
1 AAATAAGGGCCTAACGTTTGGTAAAATGCTCAAATAAGGGCAT-CGATCTTTTAATTTGGCC
91970 AAATAAGGGCCTAACGTTT-GTCAAAATGCTCAAATAAGGGC
1 AAATAAGGGCCTAACGTTTGGT-AAAATGCTCAAATAAGGGC
92011 CCGACATCGA
Statistics
Matches: 89, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
58 2 0.02
59 2 0.02
60 83 0.93
61 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (61 bp):
AAATAAGGGCCTAACGTTTGGTAAAATGCTCAAATAAGGGCATCGATCTTTTAATTTGGCC
Found at i:92151 original size:60 final size:60
Alignment explanation
Indices: 92054--92193 Score: 228
Period size: 60 Copynumber: 2.3 Consensus size: 60
92044 TGATATGTCA
* * *
92054 GGCCCTTATTTGAACATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAAATCG
*
92114 GGCCCTTATTTGAGCATATTT-GATAACGTTAGACCCTTATTTGGTCAAATTAAAAAATCG
1 GGCCCTTATTTGAGCAT-TTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAAATCG
92174 GGCCCTTATTTGAGCATTTT
1 GGCCCTTATTTGAGCATTTT
92194 AACAAACATT
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
59 3 0.04
60 69 0.92
61 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.36
Consensus pattern (60 bp):
GGCCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAAATCG
Found at i:92195 original size:29 final size:29
Alignment explanation
Indices: 92084--92221 Score: 91
Period size: 29 Copynumber: 4.6 Consensus size: 29
92074 CGATAACGTT
*
92084 AGGCCCTTATTTG-GCCAAATTAAAAGATC
1 AGGCCCTTATTTGAG-CAAATTAAAAAATC
* * * ** *
92113 GGGCCCTTATTTGAGCATATTTGATAACGTT
1 AGGCCCTTATTTGAGCA-AATT-AAAAAATC
*
92144 AGACCCTTATTTG-GTCAAATTAAAAAATC
1 AGGCCCTTATTTGAG-CAAATTAAAAAATC
* ** *
92173 GGGCCCTTATTTGAGCATTTTAACAAACATT
1 AGGCCCTTATTTGAGCAAATTAA-AAA-ATC
*
92204 AGGCCCTTATTTAAGCAA
1 AGGCCCTTATTTGAGCAA
92222 TTAGCCAATA
Statistics
Matches: 81, Mismatches: 21, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
29 35 0.43
30 12 0.15
31 34 0.42
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Consensus pattern (29 bp):
AGGCCCTTATTTGAGCAAATTAAAAAATC
Found at i:92211 original size:60 final size:59
Alignment explanation
Indices: 92054--92215 Score: 211
Period size: 60 Copynumber: 2.7 Consensus size: 59
92044 TGATATGTCA
* *
92054 GGCCCTTATTTGAACATTTT-CGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTAC-A-AACGTTAGGCCCTTATTTGGCCAAATTAAAAAATCG
* * *
92114 GGCCCTTATTTGAGCATATTTGA-TAACGTTAGACCCTTATTTGGTCAAATTAAAAAATCG
1 GGCCCTTATTTGAGCAT-TTT-ACAAACGTTAGGCCCTTATTTGGCCAAATTAAAAAATCG
*
92174 GGCCCTTATTTGAGCATTTTAACAAACATTAGGCCCTTATTT
1 GGCCCTTATTTGAGCATTTT-ACAAACGTTAGGCCCTTATTT
92216 AAGCAATTAG
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
59 4 0.04
60 82 0.92
61 3 0.03
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (59 bp):
GGCCCTTATTTGAGCATTTTACAAACGTTAGGCCCTTATTTGGCCAAATTAAAAAATCG
Found at i:92212 original size:31 final size:30
Alignment explanation
Indices: 92053--92220 Score: 101
Period size: 31 Copynumber: 5.6 Consensus size: 30
92043 CTGATATGTC
* * * *
92053 AGGCCCTTATTTGAACATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTT-AAAAACATT
** * *
92084 AGGCCCTTATTTG-GCCAAATT-AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTAAAAACATT
* * * *
92113 GGGCCCTTATTTGAGCATATTTGATAACGTT
1 AGGCCCTTATTTGAGCAT-TTTAAAAACATT
* ** *
92144 AGACCCTTATTTG-GTCAAATTAAAAA-ATC
1 AGGCCCTTATTTGAG-CATTTTAAAAACATT
*
92173 GGGCCCTTATTTGAGCATTTTAACAAACATT
1 AGGCCCTTATTTGAGCATTTTAA-AAACATT
*
92204 AGGCCCTTATTTAAGCA
1 AGGCCCTTATTTGAGCA
92221 ATTAGCCAAT
Statistics
Matches: 100, Mismatches: 29, Indels: 16
0.69 0.20 0.11
Matches are distributed among these distances:
29 36 0.36
30 13 0.13
31 51 0.51
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (30 bp):
AGGCCCTTATTTGAGCATTTTAAAAACATT
Found at i:98543 original size:25 final size:25
Alignment explanation
Indices: 98505--98556 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
98495 ATGCAATCTC
98505 TCATAAAAAGACACATTTTCATGTT
1 TCATAAAAAGACACATTTTCATGTT
* * *
98530 TCATAGAAATACACCTTTTCATGTT
1 TCATAAAAAGACACATTTTCATGTT
98555 TC
1 TC
98557 TGCAGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (25 bp):
TCATAAAAAGACACATTTTCATGTT
Found at i:100500 original size:28 final size:27
Alignment explanation
Indices: 100460--100532 Score: 94
Period size: 26 Copynumber: 2.7 Consensus size: 27
100450 GGGTCATCTC
* *
100460 GGGGCATTTTGGTTATTTTGCGCATTCA
1 GGGGCATTTTGGTCATTTTGCAC-TTCA
*
100488 GGGGCATTTTGGTCA-TTTGTACTTCA
1 GGGGCATTTTGGTCATTTTGCACTTCA
*
100514 GGGACATTTTGGTCATTTT
1 GGGGCATTTTGGTCATTTT
100533 TTATATTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
26 18 0.45
27 8 0.20
28 14 0.35
ACGTcount: A:0.15, C:0.14, G:0.27, T:0.44
Consensus pattern (27 bp):
GGGGCATTTTGGTCATTTTGCACTTCA
Found at i:108725 original size:8 final size:8
Alignment explanation
Indices: 108712--108736 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
108702 GAACTTGCAC
108712 AGTAAGGA
1 AGTAAGGA
108720 AGTAAGGA
1 AGTAAGGA
108728 AGTAAGGA
1 AGTAAGGA
108736 A
1 A
108737 AAATAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.36, T:0.12
Consensus pattern (8 bp):
AGTAAGGA
Found at i:119040 original size:20 final size:21
Alignment explanation
Indices: 118997--119041 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
118987 AAAAAATCTA
*
118997 AAAATTTTAATTTTTTTTCTG
1 AAAATTTTAATTTTTTTTCGG
119018 AAAA-TTTAA-TTTTTTTCGG
1 AAAATTTTAATTTTTTTTCGG
*
119037 GAAAT
1 AAAAT
119042 ATATTTTGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 12 0.57
20 5 0.24
21 4 0.19
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.53
Consensus pattern (21 bp):
AAAATTTTAATTTTTTTTCGG
Found at i:120747 original size:20 final size:21
Alignment explanation
Indices: 120705--120745 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
120695 AGTGTTTGAA
120705 AGAATGTTTCTTTTTTTTTTT
1 AGAATGTTTCTTTTTTTTTTT
120726 AGAATGTTTCTTTTTTTTTT
1 AGAATGTTTCTTTTTTTTTT
120746 AGTGAGTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.15, C:0.05, G:0.10, T:0.71
Consensus pattern (21 bp):
AGAATGTTTCTTTTTTTTTTT
Found at i:121909 original size:34 final size:38
Alignment explanation
Indices: 121839--121915 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
121829 GACATCCACA
**
121839 ACATACATGTATATTTATAACAAATTTATAATTAATTT
1 ACATACATGTATATGCATAACAAATTTATAATTAATTT
121877 ACATACATGTATATGCATAACAAATTTATAATTAATTT
1 ACATACATGTATATGCATAACAAATTTATAATTAATTT
121915 A
1 A
121916 TAATTATTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (38 bp):
ACATACATGTATATGCATAACAAATTTATAATTAATTT
Found at i:121913 original size:11 final size:11
Alignment explanation
Indices: 121899--121936 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
121889 ATGCATAACA
121899 AATTTATAATT
1 AATTTATAATT
121910 AATTTATAATT
1 AATTTATAATT
121921 -ATTTGATAATT
1 AATTT-ATAATT
*
121932 TATTT
1 AATTT
121937 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:124519 original size:16 final size:16
Alignment explanation
Indices: 124488--124521 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
124478 GGGTTTCCAC
**
124488 TTTCCTTTTTTTTTTT
1 TTTCCTTTTTCATTTT
124504 TTTCCTTTTTCATTTT
1 TTTCCTTTTTCATTTT
124520 TT
1 TT
124522 CCCTCCTGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTCCTTTTTCATTTT
Found at i:126253 original size:21 final size:21
Alignment explanation
Indices: 126197--126253 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
126187 AGTTTGGTGA
* * *
126197 TTCTCCCCGGTTTAACTTTGG
1 TTCTCCCAGGTTTACCATTGG
*
126218 TTCCCCCAGGTTTACCATTGG
1 TTCTCCCAGGTTTACCATTGG
126239 TTCTCCCAGGTTTAC
1 TTCTCCCAGGTTTAC
126254 TAATTCTCCC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.12, C:0.32, G:0.18, T:0.39
Consensus pattern (21 bp):
TTCTCCCAGGTTTACCATTGG
Found at i:144184 original size:25 final size:25
Alignment explanation
Indices: 144150--144200 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
144140 AGTTGGTTTG
144150 TGATCTGAAAACTGATGAAAATTCT
1 TGATCTGAAAACTGATGAAAATTCT
144175 TGATCTGAAAACTGATGAAAATTCT
1 TGATCTGAAAACTGATGAAAATTCT
144200 T
1 T
144201 ACCATTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (25 bp):
TGATCTGAAAACTGATGAAAATTCT
Found at i:144331 original size:13 final size:13
Alignment explanation
Indices: 144313--144338 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
144303 GCTCTGAATT
144313 TTCTTTGATGTTA
1 TTCTTTGATGTTA
144326 TTCTTTGATGTTA
1 TTCTTTGATGTTA
144339 GTTGTTACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (13 bp):
TTCTTTGATGTTA
Found at i:145450 original size:25 final size:26
Alignment explanation
Indices: 145416--145464 Score: 91
Period size: 25 Copynumber: 1.9 Consensus size: 26
145406 CCACGTCAGT
145416 TTATGGTATATTTTCC-GAAAAAACA
1 TTATGGTATATTTTCCGGAAAAAACA
145441 TTATGGTATATTTTCCGGAAAAAA
1 TTATGGTATATTTTCCGGAAAAAA
145465 TTTAAAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (26 bp):
TTATGGTATATTTTCCGGAAAAAACA
Found at i:154520 original size:11 final size:11
Alignment explanation
Indices: 154496--154530 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
154486 CAGACAATGC
154496 AACAAAAACAA
1 AACAAAAACAA
* *
154507 AACGAAAACGA
1 AACAAAAACAA
154518 AACAAAAACAA
1 AACAAAAACAA
154529 AA
1 AA
154531 AAACAGAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:167445 original size:14 final size:15
Alignment explanation
Indices: 167410--167448 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 15
167400 CGAACCCGAT
167410 TATGAAAATATACTA
1 TATGAAAATATACTA
167425 TAT---AATATA-TA
1 TATGAAAATATACTA
167436 TATGAAAATATAC
1 TATGAAAATATAC
167449 AGTAGTGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 8
0.71 0.00 0.29
Matches are distributed among these distances:
11 5 0.25
12 6 0.30
14 6 0.30
15 3 0.15
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (15 bp):
TATGAAAATATACTA
Found at i:167704 original size:3 final size:3
Alignment explanation
Indices: 167696--167720 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
167686 ACATTCTCAT
167696 TCC TCC TCC TCC TCC TCC TCC TCC T
1 TCC TCC TCC TCC TCC TCC TCC TCC T
167721 TCTTCTTCTC
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:0.64, G:0.00, T:0.36
Consensus pattern (3 bp):
TCC
Done.