Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016240.1 Corchorus olitorius cultivar O-4 contig16273, 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: 145277
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3612 original size:62 final size:64
Alignment explanation
Indices: 3496--3771 Score: 422
Period size: 67 Copynumber: 4.3 Consensus size: 64
3486 TTTAAATTTA
*
3496 ATTGACACCAGAAGTTGTCATAT-TAA--ATTATCTTGACACCAGAAGTTGTCA-TGA-AAATT
1 ATTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCACTGAGAAATT
*
3555 ATTGACACCAGAAGTTGTCATACCAAATTATTATCTTGACACCAGAAGTTGTCA-TGA-AAATT
1 ATTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCACTGAGAAATT
*
3617 ATTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACATCAGAAGTTGTCATGCTGAGGAAA
1 ATTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCA--CTGA-GAAA
3682 TT
63 TT
3684 ATTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGCTGAGGAAA
1 ATTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCA--CTGA-GAAA
3749 TT
63 TT
3751 ATTGACACCAGAAGTTGTCAT
1 ATTGACACCAGAAGTTGTCAT
3772 CCCGAGATTG
Statistics
Matches: 204, Mismatches: 5, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
59 22 0.11
60 2 0.01
62 85 0.42
65 3 0.01
67 92 0.45
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (64 bp):
ATTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCACTGAGAAATT
Found at i:3711 original size:129 final size:123
Alignment explanation
Indices: 3496--3771 Score: 412
Period size: 129 Copynumber: 2.2 Consensus size: 123
3486 TTTAAATTTA
*
3496 ATTGACACCAGAAGTTGTCATATTAAATTATCTTGACACCAGAAGTTGTCATGAAAATTATTGAC
1 ATTGACACCAGAAGTTGTCATATAAAATTATCTTGACACCAGAAGTTGTCATGAAAATTATTGAC
3561 ACCAGAAGTTGTCATACCAAATTATTATCTTGACACCAGAAGTTGTCA-TGA-AAATT
66 ACCAGAAGTTGTCATACCAAATTATTATCTTGACACCAGAAGTTGTCACTGAGAAATT
*
3617 ATTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACATCAGAAGTTGTCATGCTGAGGAAA
1 ATTGACACCAGAAGTTGTCATAT-AAA--ATTATCTTGACACCAGAAGTTGTCA---TGA--AAA
*
3682 TTATTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGCTGAGGA
58 TTATTGACACCAGAAGTTGTCATACCAAATTATTATCTTGACACCAGAAGTTGTCA--CTGA-GA
3747 AATT
120 AATT
3751 ATTGACACCAGAAGTTGTCAT
1 ATTGACACCAGAAGTTGTCAT
3772 CCCGAGATTG
Statistics
Matches: 139, Mismatches: 3, Indels: 13
0.90 0.02 0.08
Matches are distributed among these distances:
121 23 0.17
122 2 0.01
124 24 0.17
127 3 0.02
129 58 0.42
132 3 0.02
134 26 0.19
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (123 bp):
ATTGACACCAGAAGTTGTCATATAAAATTATCTTGACACCAGAAGTTGTCATGAAAATTATTGAC
ACCAGAAGTTGTCATACCAAATTATTATCTTGACACCAGAAGTTGTCACTGAGAAATT
Found at i:14391 original size:29 final size:29
Alignment explanation
Indices: 14333--14394 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
14323 GGTATTTTTT
* * ***
14333 AAAGAGGGTTTAGGGTTTTTTTCCTGAAA
1 AAAGAGGGTTTAGGGTTTATTGCAAAAAA
14362 AAAGAGGGTTTAGGGTTTATTGCAAAAAA
1 AAAGAGGGTTTAGGGTTTATTGCAAAAAA
14391 AAAG
1 AAAG
14395 GTTTAGGATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.37, C:0.05, G:0.27, T:0.31
Consensus pattern (29 bp):
AAAGAGGGTTTAGGGTTTATTGCAAAAAA
Found at i:40835 original size:32 final size:30
Alignment explanation
Indices: 40799--40876 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 30
40789 ATACCGTACA
40799 GGTCCCTCTATTTACAAAAAAATGATCAATTT
1 GGTCCCTCTA-TTACAAAAAAATG-TCAATTT
* * *
40831 GGTCCCTCTAGTA-TAAAAACTGTCAATTT
1 GGTCCCTCTATTACAAAAAAATGTCAATTT
*
40860 GCTCCCTCTACTTACAA
1 GGTCCCTCTA-TTACAA
40877 TTTGGTGTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
29 16 0.42
30 9 0.24
31 3 0.08
32 10 0.26
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.33
Consensus pattern (30 bp):
GGTCCCTCTATTACAAAAAAATGTCAATTT
Found at i:42234 original size:12 final size:12
Alignment explanation
Indices: 42217--42243 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
42207 AAATTGGAAT
42217 TGGGCGTCGGCG
1 TGGGCGTCGGCG
42229 TGGGCGTCGGCG
1 TGGGCGTCGGCG
42241 TGG
1 TGG
42244 CTGCTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.22, G:0.59, T:0.19
Consensus pattern (12 bp):
TGGGCGTCGGCG
Found at i:47294 original size:14 final size:14
Alignment explanation
Indices: 47267--47304 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
47257 TCATTTACCC
*
47267 CTTGA-ATACGTAA
1 CTTGATATACATAA
47280 CTTGATATACATAA
1 CTTGATATACATAA
47294 CTTGATATACA
1 CTTGATATACA
47305 ATATTCGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 5 0.22
14 18 0.78
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (14 bp):
CTTGATATACATAA
Found at i:49053 original size:20 final size:20
Alignment explanation
Indices: 49028--49076 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
49018 GTCTCTATAT
49028 ATGGTATATGGTGCTTCGAC
1 ATGGTATATGGTGCTTCGAC
49048 ATGGTATATGGTGCTTCGAC
1 ATGGTATATGGTGCTTCGAC
49068 ATGGTATAT
1 ATGGTATAT
49077 ATGCTTATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.12, G:0.29, T:0.37
Consensus pattern (20 bp):
ATGGTATATGGTGCTTCGAC
Found at i:49559 original size:20 final size:20
Alignment explanation
Indices: 49534--49574 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
49524 AAGTTGGTGA
49534 CTCTAAAAGTTGTTTAAAGC
1 CTCTAAAAGTTGTTTAAAGC
49554 CTCTAAAAGTTGTTTAAAGC
1 CTCTAAAAGTTGTTTAAAGC
49574 C
1 C
49575 ATTATAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (20 bp):
CTCTAAAAGTTGTTTAAAGC
Found at i:50023 original size:21 final size:21
Alignment explanation
Indices: 49997--50036 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
49987 GGTCGCGACC
* *
49997 GAATCGCGACTTGACCATGCT
1 GAATCGCAACCTGACCATGCT
50018 GAATCGCAACCTGACCATG
1 GAATCGCAACCTGACCATG
50037 GCCCGAACGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.20
Consensus pattern (21 bp):
GAATCGCAACCTGACCATGCT
Found at i:58519 original size:6 final size:6
Alignment explanation
Indices: 58508--58549 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
58498 ACCTAATGAT
58508 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
58550 GAGATAAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:64358 original size:14 final size:14
Alignment explanation
Indices: 64339--64369 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
64329 ATGGAGAAGG
64339 AGAAGAAAGAGGAA
1 AGAAGAAAGAGGAA
*
64353 AGAAGAAAGATGAA
1 AGAAGAAAGAGGAA
64367 AGA
1 AGA
64370 GATATGAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (14 bp):
AGAAGAAAGAGGAA
Found at i:64980 original size:2 final size:2
Alignment explanation
Indices: 64967--65003 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
64957 ACTAAAAATA
64967 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
65004 GTTGTAGACA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:67366 original size:11 final size:12
Alignment explanation
Indices: 67329--67370 Score: 50
Period size: 11 Copynumber: 3.4 Consensus size: 12
67319 CCTACTACAG
67329 TATATATATATATA
1 TATATA-ATATA-A
*
67343 TATATAATCTAA
1 TATATAATATAA
67355 TA-ATAATATAA
1 TATATAATATAA
67366 TATAT
1 TATAT
67371 CATTATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 10 0.40
12 5 0.20
13 4 0.16
14 6 0.24
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (12 bp):
TATATAATATAA
Found at i:71416 original size:23 final size:22
Alignment explanation
Indices: 71390--71433 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
71380 TTAAATCTAA
* *
71390 TATCCTTATATCTATTTTATTTT
1 TATCATTATA-CTATGTTATTTT
*
71413 TATCATTTTACTATGTTATTT
1 TATCATTATACTATGTTATTT
71434 AAAAAACTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.23, C:0.11, G:0.02, T:0.64
Consensus pattern (22 bp):
TATCATTATACTATGTTATTTT
Found at i:71456 original size:130 final size:123
Alignment explanation
Indices: 71215--71468 Score: 375
Period size: 122 Copynumber: 2.0 Consensus size: 123
71205 CATTGTTTAA
*
71215 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATGAT
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATGAT
*
71280 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAA-TTTTTAAATAT
66 TTTTACCATTTTACTATGTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
*
71337 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATATC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATAT-C---T-T-
* * *
71402 TATTTTATTTTTATCATTTTACTATGTTATTTAAAAAACTTATATATATTAGAATTTTTTAAATA
60 TA--TGATTTTTACCATTTTACTATGTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA
71467 T
123 T
71468 A
1 A
71469 TTTCTTAAAT
Statistics
Matches: 117, Mismatches: 6, Indels: 9
0.89 0.05 0.07
Matches are distributed among these distances:
122 54 0.46
123 1 0.01
126 1 0.01
127 1 0.01
128 2 0.02
130 46 0.39
131 12 0.10
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.50
Consensus pattern (123 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATGAT
TTTTACCATTTTACTATGTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:71490 original size:14 final size:13
Alignment explanation
Indices: 71454--71492 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
71444 TATATATTAG
71454 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
71467 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
71481 AATTTTTTAAAT
1 AATTTTTTAAAT
71493 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:73714 original size:32 final size:32
Alignment explanation
Indices: 73668--73728 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
73658 AAATATGTTT
*
73668 GAAAAATAAAGGTATAATGATCGATTCAATTA
1 GAAAAATAAAGGTATAATAATCGATTCAATTA
*
73700 GAAAAATAAGGGTATAATAATCGATTCAA
1 GAAAAATAAAGGTATAATAATCGATTCAA
73729 AAGTTTTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.26
Consensus pattern (32 bp):
GAAAAATAAAGGTATAATAATCGATTCAATTA
Found at i:74514 original size:24 final size:24
Alignment explanation
Indices: 74482--74551 Score: 115
Period size: 24 Copynumber: 2.9 Consensus size: 24
74472 GAAAAATAAC
*
74482 AAGTTTCAATTCATATATGAATTG
1 AAGTTTCAATTCTTATATGAATTG
74506 AAGTTTCAATTCTTATA-GAAATTG
1 AAGTTTCAATTCTTATATG-AATTG
74530 AAGTTTCAATTCTTATATGAAT
1 AAGTTTCAATTCTTATATGAAT
74552 GGAATAATAG
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
23 1 0.02
24 41 0.95
25 1 0.02
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (24 bp):
AAGTTTCAATTCTTATATGAATTG
Found at i:83661 original size:18 final size:17
Alignment explanation
Indices: 83629--83663 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
83619 CAGATGGGAT
83629 GGGAAGGGAAAGGAAAG
1 GGGAAGGGAAAGGAAAG
*
83646 GGGAAGGAGGAAGGAAAG
1 GGGAAGG-GAAAGGAAAG
83664 AGTCTTTAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (17 bp):
GGGAAGGGAAAGGAAAG
Found at i:84093 original size:26 final size:27
Alignment explanation
Indices: 84057--84116 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 27
84047 TTATTTTGTT
*
84057 AGGAGATACAATAATTAAT-GGAATCA
1 AGGAGATACAATAATTAATAGAAATCA
84083 AGGAGATACAATAATTAATAGAAATCA
1 AGGAGATACAATAATTAATAGAAATCA
84110 AGGAGAT
1 AGGAGAT
84117 TAATGATACA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 19 0.59
27 13 0.41
ACGTcount: A:0.52, C:0.07, G:0.20, T:0.22
Consensus pattern (27 bp):
AGGAGATACAATAATTAATAGAAATCA
Found at i:101090 original size:7 final size:7
Alignment explanation
Indices: 101078--101103 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
101068 CAAAATTAGA
101078 GGAGACT
1 GGAGACT
101085 GGAGACT
1 GGAGACT
101092 GGAGACT
1 GGAGACT
101099 GGAGA
1 GGAGA
101104 GGGCTAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.46, T:0.12
Consensus pattern (7 bp):
GGAGACT
Found at i:103331 original size:16 final size:17
Alignment explanation
Indices: 103305--103337 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
103295 TACAAAAATA
103305 TAATGAGAACAAAATGG
1 TAATGAGAACAAAATGG
*
103322 TAATGA-AACATAATGG
1 TAATGAGAACAAAATGG
103338 CCATTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.52, C:0.06, G:0.21, T:0.21
Consensus pattern (17 bp):
TAATGAGAACAAAATGG
Found at i:111475 original size:114 final size:114
Alignment explanation
Indices: 111273--111500 Score: 375
Period size: 114 Copynumber: 2.0 Consensus size: 114
111263 TGACCGGTAA
* * * *
111273 TTGGCTTGAAACTCGGCGGGTTGGGTCGCACGGGGAGAGATGAGGACTCACAAGTGAATCGGGGG
1 TTGGCTTGAAACTCGACGGGTTGGGCCGCACAGGGAGAGATGAGGACTCACAAGTGAATCGAGGG
*
111338 AGATTGTTAAGGGATTCACATGTGAGGGAACATCCCACATCATGAAGAG
66 AGATTGTTAAGGGATTCACATGTGAAGGAACATCCCACATCATGAAGAG
* * *
111387 TTGGCTTGAGACTTGACGGGTTGGGCCGCACAGGGAGAGATGAGGACTCATAAGTGAATCGAGGG
1 TTGGCTTGAAACTCGACGGGTTGGGCCGCACAGGGAGAGATGAGGACTCACAAGTGAATCGAGGG
*
111452 AGATTGTTAAGGGATTCATATGTGAAGGAACATCCCACATCATGAAGAG
66 AGATTGTTAAGGGATTCACATGTGAAGGAACATCCCACATCATGAAGAG
111501 ATGAGTTGTT
Statistics
Matches: 105, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 105 1.00
ACGTcount: A:0.29, C:0.16, G:0.35, T:0.21
Consensus pattern (114 bp):
TTGGCTTGAAACTCGACGGGTTGGGCCGCACAGGGAGAGATGAGGACTCACAAGTGAATCGAGGG
AGATTGTTAAGGGATTCACATGTGAAGGAACATCCCACATCATGAAGAG
Found at i:118006 original size:16 final size:16
Alignment explanation
Indices: 117970--118006 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
117960 ATTGTTAATC
*
117970 AAATTCAATTCCTTCT
1 AAATTCAATTCCCTCT
*
117986 CAATTCAATTCCCTCT
1 AAATTCAATTCCCTCT
118002 AAATT
1 AAATT
118007 ACTTTTCAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.27, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATTCAATTCCCTCT
Found at i:120161 original size:26 final size:26
Alignment explanation
Indices: 120125--120178 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
120115 TGCATCCTCG
120125 TTATTAATTGTTAAAACTTCAGACTT
1 TTATTAATTGTTAAAACTTCAGACTT
120151 TTATTAATTGTTAAAACTTCAGACTT
1 TTATTAATTGTTAAAACTTCAGACTT
120177 TT
1 TT
120179 TGTGGGAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.48
Consensus pattern (26 bp):
TTATTAATTGTTAAAACTTCAGACTT
Found at i:124046 original size:6 final size:6
Alignment explanation
Indices: 124037--124061 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
124027 GGAGACGGAG
124037 AGGTTC AGGTTC AGGTTC AGGTTC A
1 AGGTTC AGGTTC AGGTTC AGGTTC A
124062 ATCAACTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.32
Consensus pattern (6 bp):
AGGTTC
Found at i:129073 original size:31 final size:31
Alignment explanation
Indices: 129038--129101 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
129028 TTTTTAGTAG
129038 TATAAAACTATAATAGTTAAATAATGACATT
1 TATAAAACTATAATAGTTAAATAATGACATT
129069 TATAAAACTATAATAGTTAAATAATGACATT
1 TATAAAACTATAATAGTTAAATAATGACATT
129100 TA
1 TA
129102 AGAAATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (31 bp):
TATAAAACTATAATAGTTAAATAATGACATT
Found at i:129585 original size:8 final size:8
Alignment explanation
Indices: 129572--129599 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
129562 ACCATAAATT
129572 TTTTTTTG
1 TTTTTTTG
129580 TTTTTTTG
1 TTTTTTTG
129588 TTTTTTTG
1 TTTTTTTG
129596 TTTT
1 TTTT
129600 GGTGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (8 bp):
TTTTTTTG
Found at i:131602 original size:9 final size:9
Alignment explanation
Indices: 131588--131619 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
131578 AATTACAATC
131588 AACAATCAT
1 AACAATCAT
131597 AACAATC--
1 AACAATCAT
131604 AACAATCAT
1 AACAATCAT
131613 AACAATC
1 AACAATC
131620 TCTCTAGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
7 7 0.33
9 14 0.67
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.19
Consensus pattern (9 bp):
AACAATCAT
Found at i:131603 original size:16 final size:16
Alignment explanation
Indices: 131582--131619 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
131572 TCAATCAATT
131582 ACAATCAACAATCATA
1 ACAATCAACAATCATA
131598 ACAATCAACAATCATA
1 ACAATCAACAATCATA
131614 ACAATC
1 ACAATC
131620 TCTCTAGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.18
Consensus pattern (16 bp):
ACAATCAACAATCATA
Found at i:133300 original size:31 final size:31
Alignment explanation
Indices: 133262--133323 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
133252 GAGTTCTGTA
* *
133262 AAACTTTTGAATTGCCTACTATATCCTTATT
1 AAACTTTTGAATCGCCTACTATACCCTTATT
*
133293 AAACTTTTGAATCGCCTATTATACCCTTATT
1 AAACTTTTGAATCGCCTACTATACCCTTATT
133324 TTTTTAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (31 bp):
AAACTTTTGAATCGCCTACTATACCCTTATT
Found at i:133461 original size:93 final size:93
Alignment explanation
Indices: 133359--133543 Score: 307
Period size: 93 Copynumber: 2.0 Consensus size: 93
133349 TTGTTTAAAT
* * *
133359 TTTTATAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATGTGCTTATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
* *
133424 TTTTATTTTTACCATTTTACTATTTTAC
66 TTTTATTTTTACCATATTACTAATTTAC
*
133452 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
*
133517 TTTTATTTTTACGATATTACTAATTTA
66 TTTTATTTTTACCATATTACTAATTTA
133544 ATTAAAAAGC
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 85 1.00
ACGTcount: A:0.32, C:0.12, G:0.03, T:0.52
Consensus pattern (93 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTTTATTTTTACCATATTACTAATTTAC
Found at i:139044 original size:35 final size:37
Alignment explanation
Indices: 138996--139111 Score: 132
Period size: 36 Copynumber: 3.2 Consensus size: 37
138986 AGATATGAAA
138996 TAAATATAAAATATATATTATATATAAAGATCAATTC
1 TAAATATAAAATATATATTATATATAAAGATCAATTC
* * * * *
139033 TAAA-AT-TAATATATATATATATATCAGATATGAA--A
1 TAAATATAAAATATATAT-TATATAT-AAAGATCAATTC
139068 TAAATATAAAATATATATTATATATAAAGATCAGATTC
1 TAAATATAAAATATATATTATATATAAAGATCA-ATTC
139106 TAAATA
1 TAAATA
139112 ATCAAATTCT
Statistics
Matches: 62, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
35 18 0.29
36 19 0.31
37 19 0.31
38 6 0.10
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (37 bp):
TAAATATAAAATATATATTATATATAAAGATCAATTC
Found at i:139060 original size:72 final size:74
Alignment explanation
Indices: 138968--139109 Score: 261
Period size: 72 Copynumber: 1.9 Consensus size: 74
138958 AGTTTTAGGT
138968 TATATATATATATCAATCAGATATGAAATAAATATAAAATATATATTATATATAAAGATCA-ATT
1 TATATATATATAT-AATCAGATATGAAATAAATATAAAATATATATTATATATAAAGATCAGATT
139032 CTAAAATTAA
65 CTAAAATTAA
139042 TATATATATATAT-ATCAGATATGAAATAAATATAAAATATATATTATATATAAAGATCAGATTC
1 TATATATATATATAATCAGATATGAAATAAATATAAAATATATATTATATATAAAGATCAGATTC
139106 TAAA
66 TAAA
139110 TAATCAAATT
Statistics
Matches: 67, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
72 46 0.69
73 8 0.12
74 13 0.19
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (74 bp):
TATATATATATATAATCAGATATGAAATAAATATAAAATATATATTATATATAAAGATCAGATTC
TAAAATTAA
Found at i:139140 original size:22 final size:23
Alignment explanation
Indices: 139106--139168 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 23
139096 GATCAGATTC
* *
139106 TAAATA-ATCAAAT-TCTAAATT
1 TAAATATATCAAATATATAAAAT
139127 TAAAATATAT-AAATATATAAAAT
1 T-AAATATATCAAATATATAAAAT
*
139150 TAAATATATTATAATATAT
1 TAAATATATCA-AATATAT
139169 GGATTGGTCG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
21 1 0.03
22 17 0.49
23 10 0.29
24 7 0.20
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAATATATCAAATATATAAAAT
Found at i:139141 original size:72 final size:73
Alignment explanation
Indices: 138988--139167 Score: 192
Period size: 72 Copynumber: 2.5 Consensus size: 73
138978 TATCAATCAG
* *
138988 ATATGAAATAAATATAAAATATATATTATATATAAAGATCAATTCTAAAATTAATATATATATAT
1 ATAT-AAATAAATATAAAATATATATTATATATAAAGATCAATTCTAAAATTAATAAATATATAA
* *
139053 ATATCAGAT
65 ATATAAAAT
* *
139062 AT-GAAATAAATATAAAATATATATTATATATAAAGATCAGATTCT-AAA-TAATCAAAT-TCTA
1 ATATAAATAAATATAAAATATATATTATATATAAAGATCA-ATTCTAAAATTAAT-AAATATATA
*
139123 AATTTAAAAT
64 AATATAAAAT
139133 ATATAAAT--ATATAAAATTAAATATATTATAATATA
1 ATATAAATAAATATAAAA-T--ATATATTAT-ATATA
139168 TGGATTGGTC
Statistics
Matches: 91, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
70 8 0.09
71 16 0.18
72 46 0.51
73 14 0.15
74 7 0.08
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (73 bp):
ATATAAATAAATATAAAATATATATTATATATAAAGATCAATTCTAAAATTAATAAATATATAAA
TATAAAAT
Found at i:139158 original size:24 final size:23
Alignment explanation
Indices: 139121--139168 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
139111 AATCAAATTC
*
139121 TAAATTTAAAATA-TATAAATATA
1 TAAAATTAAAATATTAT-AATATA
139144 TAAAATTAAATATATTATAATATA
1 TAAAATTAAA-ATATTATAATATA
139168 T
1 T
139169 GGATTGGTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 9 0.41
24 10 0.45
25 3 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TAAAATTAAAATATTATAATATA
Found at i:139711 original size:28 final size:30
Alignment explanation
Indices: 139657--139730 Score: 98
Period size: 28 Copynumber: 2.5 Consensus size: 30
139647 GCTAAATACC
*
139657 CAAAAAAATCCCTTATGTTTTGCTTTTGGAA
1 CAAAATAATCCCTTATGTTTT-CTTTTGGAA
*
139688 CAAAATAATCCCTTATG-TTT-TTTTGGGA
1 CAAAATAATCCCTTATGTTTTCTTTTGGAA
*
139716 CAAATTAATCCCTTA
1 CAAAATAATCCCTTA
139731 CATTTCAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 21 0.52
30 3 0.08
31 16 0.40
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTTCTTTTGGAA
Found at i:139897 original size:30 final size:32
Alignment explanation
Indices: 139863--139928 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 32
139853 AAGAGACTAA
* *
139863 TTTGTCCCATAA-AATAACATAAGGG-ATTAT
1 TTTGTCCCAAAAGAAAAACATAAGGGAATTAT
*
139893 TTTGTCCCAAAAGAAAAACATAAGGGAATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGAATTAT
139925 TTTG
1 TTTG
139929 AAATTTAGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 11 0.35
31 12 0.39
32 8 0.26
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.33
Consensus pattern (32 bp):
TTTGTCCCAAAAGAAAAACATAAGGGAATTAT
Found at i:142928 original size:2 final size:2
Alignment explanation
Indices: 142921--142985 Score: 53
Period size: 2 Copynumber: 32.5 Consensus size: 2
142911 TGTTGCAAAA
* * * *
142921 AT AT AT AT AT AT AT AT AT AT AT AT A- AT TT TT GAG AT CA- AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT -AT AT AT
*
142963 AG AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
142986 ATTTGATAAC
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
1 2 0.04
2 49 0.94
3 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:143359 original size:16 final size:16
Alignment explanation
Indices: 143340--143377 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
143330 TAAATTTATT
143340 TAGTTTGCTTTATTTC
1 TAGTTTGCTTTATTTC
143356 TAGTTTGCTTTATTTC
1 TAGTTTGCTTTATTTC
143372 TAGTTT
1 TAGTTT
143378 AATTACTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.13, C:0.11, G:0.13, T:0.63
Consensus pattern (16 bp):
TAGTTTGCTTTATTTC
Done.