Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023772.1 Corchorus olitorius cultivar O-4 contig23805, 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: 80238
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2181 original size:22 final size:22
Alignment explanation
Indices: 2134--2292 Score: 126
Period size: 22 Copynumber: 7.2 Consensus size: 22
2124 TCTCTTTGTA
** *
2134 GTTATCAAAATTTCATAACGAG
1 GTTATCAAAATTTCATAGTGTG
* * *
2156 GTTATCGAAATTTCATATTGTT
1 GTTATCAAAATTTCATAGTGTG
*
2178 GTTATCAAAATTTCTTAGTGTG
1 GTTATCAAAATTTCATAGTGTG
*
2200 GTTATCAAAA-TTCATAGCGAT-
1 GTTATCAAAATTTCATAGTG-TG
*
2221 GTTATCAAAAATTTCATAGTATG
1 GTTATC-AAAATTTCATAGTGTG
* * * **
2244 ATTA-GAAAATTTTCATAGGGCA
1 GTTATCAAAA-TTTCATAGTGTG
* *
2266 ATTATCAAAATTTCATAGTGTA
1 GTTATCAAAATTTCATAGTGTG
2288 GTTAT
1 GTTAT
2293 GTGACACCAT
Statistics
Matches: 108, Mismatches: 23, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
21 17 0.16
22 77 0.71
23 14 0.13
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGTGTG
Found at i:4102 original size:22 final size:22
Alignment explanation
Indices: 4077--4119 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
4067 TAAGATGATA
4077 TAATAATT-TTTAGATGATGGAT
1 TAATAATTATTTA-ATGATGGAT
* *
4099 TAATTATTATTTAATTATGGA
1 TAATAATTATTTAATGATGGA
4120 AAGTGTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (22 bp):
TAATAATTATTTAATGATGGAT
Found at i:4719 original size:2 final size:2
Alignment explanation
Indices: 4714--4739 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4704 TGTTAGAGAG
4714 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
4740 TGTCTTGATT
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:6024 original size:22 final size:21
Alignment explanation
Indices: 5909--6449 Score: 195
Period size: 22 Copynumber: 24.8 Consensus size: 21
5899 TATTAGGAGC
*
5909 AAGGTTATTAAAATTTCAGT-G
1 AAGGTTATCAAAATTTCA-TAG
* *
5930 -TGGTTATCAAAATTTCTTAG
1 AAGGTTATCAAAATTTCATAG
* **
5950 AGACGTTATCCGAATTTCAT-G
1 A-AGGTTATCAAAATTTCATAG
** * *
5971 GTGTGATTATCAAAATTTTATAAAA
1 AAG-G-TTATCAAAATTTCAT--AG
*
5996 AAGGTTATCAAAGTTTCATAAG
1 AAGGTTATCAAAATTTCAT-AG
6018 AAGGTTATCAAAATTTCATAG
1 AAGGTTATCAAAATTTCATAG
** *
6039 TGTGGTTATCAAAATTTCATCTG
1 -AAGGTTATCAAAATTTCAT-AG
* * *
6062 AAGATTACCAAAATTTTATAG
1 AAGGTTATCAAAATTTCATAG
* *
6083 GAGGTTATCAAAATTTCATTGG
1 AAGGTTATCAAAATTTCA-TAG
* ** *
6105 TAGGTTGCCAAAATATTTATA-
1 AAGGTTATCAAAAT-TTCATAG
** * *
6126 TTGTGATATTAAAATTTCATATGG
1 AAG-GTTATCAAAATTTCATA--G
* *
6150 ATGG-TA-CTAAAATTTTATAG
1 AAGGTTATC-AAAATTTCATAG
*
6170 -TGTGATTATCAAAATTT-ATTAG
1 AAG-G-TTATCAAAATTTCA-TAG
*
6192 ATAGG-CAGTC-AAATTTCATAAG
1 A-AGGTTA-TCAAAATTTCAT-AG
* ** * *
6214 GAGGCAATCGAAATTTCGTAG
1 AAGGTTATCAAAATTTCATAG
*
6235 AGAGTTTATCAAAATTTCATAG
1 A-AGGTTATCAAAATTTCATAG
* *
6257 AGAGATTATCAAGATTTCATAG
1 A-AGGTTATCAAAATTTCATAG
* * *
6279 AGTGGTT-TCCAAAGTTTCATAA
1 A-AGGTTAT-CAAAATTTCATAG
6301 AGAGGTTATCAAAATTTCATAG
1 A-AGGTTATCAAAATTTCATAG
** * *
6323 TGTGGTTACCAAAATTTCATACA
1 -AAGGTTATCAAAATTTCATA-G
* *
6346 AACGTTATCAAATTTTCATAG
1 AAGGTTATCAAAATTTCATAG
** * *
6367 TACTGTTATTAAAATTTTATAGG
1 -AAGGTTATCAAAATTTCATA-G
* ** *
6390 GATATTATCAAAATTTCATGGG
1 AAGGTTATCAAAATTTCAT-AG
*
6412 GAGGTTATCAAAATTTCATATG
1 AAGGTTATCAAAATTTCATA-G
*
6434 CAGGTTATCAAAATTT
1 AAGGTTATCAAAATTT
6450 TATAATGTGA
Statistics
Matches: 387, Mismatches: 95, Indels: 75
0.69 0.17 0.13
Matches are distributed among these distances:
19 3 0.01
20 17 0.04
21 43 0.11
22 297 0.77
23 22 0.06
24 4 0.01
25 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (21 bp):
AAGGTTATCAAAATTTCATAG
Found at i:6560 original size:120 final size:118
Alignment explanation
Indices: 6349--6574 Score: 276
Period size: 120 Copynumber: 1.9 Consensus size: 118
6339 TCATACAAAC
* * * * *
6349 GTTATCAAATTTTCATAGTACTGTTATTAAAATTTTATAGGGATATTATCAAAATTTCATGGGGA
1 GTTATCAAATTTTCATAGGACGGTTATTAAAATTTTATAAGGAGATTATCAAAATTTCATAGGGA
* *
6414 GGTTATCAAAATTTCATATGCAGGTTATCAAAATTTTATAATGTGATACAATG
66 GGTTAACAAAATTTCATATGCAGGTTATCAAAATTTCATAATGTGATACAATG
* *
6467 GTTATCGAATTTTCATAAGGA-GGTTATTATATAATTTTATAATGAGATTATCAAAATTTCATAG
1 GTTATCAAATTTTCAT-AGGACGGTTATTA-A-AATTTTATAAGGAGATTATCAAAATTTCATAG
* * ** *
6531 GGAGGTTAAGAAAATTTCGT-TGTGTGGTTATCAATATTTCATAA
63 GGAGGTTAACAAAATTTCATATG-CAGGTTATCAAAATTTCATAA
6575 GAATGTTATC
Statistics
Matches: 90, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
118 22 0.24
119 6 0.07
120 62 0.69
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (118 bp):
GTTATCAAATTTTCATAGGACGGTTATTAAAATTTTATAAGGAGATTATCAAAATTTCATAGGGA
GGTTAACAAAATTTCATATGCAGGTTATCAAAATTTCATAATGTGATACAATG
Found at i:8013 original size:18 final size:18
Alignment explanation
Indices: 7979--8013 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
7969 ACTTTTATTT
*
7979 TATATTTATATAATTATA
1 TATATTTAGATAATTATA
*
7997 TATATTTAGATATTTAT
1 TATATTTAGATAATTAT
8014 GATTGATATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TATATTTAGATAATTATA
Found at i:10229 original size:18 final size:18
Alignment explanation
Indices: 10208--10244 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
10198 ATTAATTAAG
10208 AGGGATAAGATTTATTAT
1 AGGGATAAGATTTATTAT
*
10226 AGGGATAGGATTTATTAT
1 AGGGATAAGATTTATTAT
10244 A
1 A
10245 ACATTTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (18 bp):
AGGGATAAGATTTATTAT
Found at i:13163 original size:27 final size:28
Alignment explanation
Indices: 13133--13186 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
13123 CTAAAATGAA
*
13133 ATTCTCCCTATTAG-TTTTGAGTTTTTC
1 ATTCTCCCTATAAGTTTTTGAGTTTTTC
13160 ATTCTCCCTATAAGTTTTTGAGTTTTT
1 ATTCTCCCTATAAGTTTTTGAGTTTTT
13187 ATTTTATGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.56
Consensus pattern (28 bp):
ATTCTCCCTATAAGTTTTTGAGTTTTTC
Found at i:17299 original size:32 final size:35
Alignment explanation
Indices: 17218--17297 Score: 103
Period size: 35 Copynumber: 2.4 Consensus size: 35
17208 ATTATTTTTC
** *
17218 TTTTC-CTTTCCTTTTATTTTTATTTTTTTATTTA
1 TTTTCTCTTTCCCCTTATTATTATTTTTTTATTTA
17252 TTTTCTCTTTCCCCTTATTATTATTTTTTTA-TT-
1 TTTTCTCTTTCCCCTTATTATTATTTTTTTATTTA
*
17285 TTTTCTTTTTCCC
1 TTTTCTCTTTCCC
17298 TTTTCAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
33 12 0.29
34 7 0.17
35 22 0.54
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.72
Consensus pattern (35 bp):
TTTTCTCTTTCCCCTTATTATTATTTTTTTATTTA
Found at i:21543 original size:21 final size:20
Alignment explanation
Indices: 21504--21548 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
21494 AAATAACAAT
* *
21504 TAAAAAGAAAGCAATTAAAC
1 TAAAAACAAAGCAAGTAAAC
*
21524 TAAAAACAAAGCAAAGTAAAT
1 TAAAAACAAAGC-AAGTAAAC
21545 TAAA
1 TAAA
21549 TCTAAACTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.16
Consensus pattern (20 bp):
TAAAAACAAAGCAAGTAAAC
Found at i:24372 original size:13 final size:13
Alignment explanation
Indices: 24344--24386 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
24334 AAGTATATAT
24344 ATTAACTAATAAATA
1 ATTAA-TAA-AAATA
24359 ATTAATAAAAATA
1 ATTAATAAAAATA
* *
24372 ATAAATAAATATA
1 ATTAATAAAAATA
24385 AT
1 AT
24387 ATATATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 18 0.69
14 3 0.12
15 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (13 bp):
ATTAATAAAAATA
Found at i:24955 original size:185 final size:186
Alignment explanation
Indices: 24635--24999 Score: 608
Period size: 185 Copynumber: 2.0 Consensus size: 186
24625 TATTTGAAAG
*
24635 ACCCAGGGAATTTACCAAAGGCCCCTTTTGAGGATCGATGAGTAGGCTCCATTTGAACTTTTTTT
1 ACCCAGGGAATTTACCAAAGGCCCCTTTTGAGGATCGATGAGGAGGCTCCATTTGAACTTTTTTT
* * **
24700 TGTCATTTTCGGTCTTTTCTCACTTGCCAAATTACTAAGAAGACCCTAGGTTAGTTTCTAGTTAG
66 TATCATTTTCGATCTTTTCTCACTTGCCAAATTACTAAGAAGACCCTAGGTTAGTTTCTAGCCAG
24765 TTCTTGCAC-TTGAGCCCTATTTTGTAATTATCCTTTCCTTTCACATAAATATTACA
131 TTCTTGC-CTTTGAGCCCTATTTTGTAATTATCCTTTCCTTTCACATAAATATTACA
24821 ACCCAGGGAATTTACCAAAGGCCCCTTTTGAGGATCGATGAGGAGGCTCCATTTGAAC-TTTTTT
1 ACCCAGGGAATTTACCAAAGGCCCCTTTTGAGGATCGATGAGGAGGCTCCATTTGAACTTTTTTT
* *
24885 TATCCTTTTCTATCTTTTCTCACTTGCCAAATTACTAAGAAGACCCTAGGTTAGTTTCTAGCCAG
66 TATCATTTTCGATCTTTTCTCACTTGCCAAATTACTAAGAAGACCCTAGGTTAGTTTCTAGCCAG
* * * *
24950 TTCTTGCCTTTGAGTCTTTTTTTGTAATTATCCTTTCTTTTCACATAAAT
131 TTCTTGCCTTTGAGCCCTATTTTGTAATTATCCTTTCCTTTCACATAAAT
25000 GTTATAATAA
Statistics
Matches: 167, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
184 1 0.01
185 109 0.65
186 57 0.34
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (186 bp):
ACCCAGGGAATTTACCAAAGGCCCCTTTTGAGGATCGATGAGGAGGCTCCATTTGAACTTTTTTT
TATCATTTTCGATCTTTTCTCACTTGCCAAATTACTAAGAAGACCCTAGGTTAGTTTCTAGCCAG
TTCTTGCCTTTGAGCCCTATTTTGTAATTATCCTTTCCTTTCACATAAATATTACA
Found at i:26502 original size:45 final size:42
Alignment explanation
Indices: 26451--26546 Score: 149
Period size: 45 Copynumber: 2.2 Consensus size: 42
26441 AGCAACAATT
26451 AATATTAGATTTATTTTGATGAATTATCTAGAGATGGAGGAGTAG
1 AATATTAGATTTATTTTGATGAATTATCTAGAGAT-GA--AGTAG
*
26496 AATATTAGCTTTATTTTGATGAATTATCTAGAGATGAAGTAG
1 AATATTAGATTTATTTTGATGAATTATCTAGAGATGAAGTAG
26538 AAT-TTAGAT
1 AATATTAGAT
26547 AATGCACTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
41 5 0.10
42 8 0.16
44 2 0.04
45 34 0.69
ACGTcount: A:0.36, C:0.03, G:0.21, T:0.40
Consensus pattern (42 bp):
AATATTAGATTTATTTTGATGAATTATCTAGAGATGAAGTAG
Found at i:28353 original size:29 final size:29
Alignment explanation
Indices: 28311--28377 Score: 134
Period size: 29 Copynumber: 2.3 Consensus size: 29
28301 TAGAAAGTAG
28311 ATTCAAGACTTTCGGCCAAAAAAAAATCA
1 ATTCAAGACTTTCGGCCAAAAAAAAATCA
28340 ATTCAAGACTTTCGGCCAAAAAAAAATCA
1 ATTCAAGACTTTCGGCCAAAAAAAAATCA
28369 ATTCAAGAC
1 ATTCAAGAC
28378 ACTTTCCCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.48, C:0.21, G:0.10, T:0.21
Consensus pattern (29 bp):
ATTCAAGACTTTCGGCCAAAAAAAAATCA
Found at i:37041 original size:23 final size:21
Alignment explanation
Indices: 36996--37041 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
36986 GTTGTTTGAC
**
36996 AAAATTGAAAATTAAGTGTTG
1 AAAATTGAAAATTAAGTACTG
37017 AAAACTTGAAATATTAAGTACTG
1 AAAA-TTGAAA-ATTAAGTACTG
37040 AA
1 AA
37042 TTTTTAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 6 0.29
23 11 0.52
ACGTcount: A:0.50, C:0.04, G:0.15, T:0.30
Consensus pattern (21 bp):
AAAATTGAAAATTAAGTACTG
Found at i:40065 original size:15 final size:16
Alignment explanation
Indices: 40045--40083 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
40035 TTTCCTTATT
40045 TTCCTTTTTT-TTTCC
1 TTCCTTTTTTCTTTCC
*
40060 TTCCTTTTTTCTTTTC
1 TTCCTTTTTTCTTTCC
*
40076 TTTCTTTT
1 TTCCTTTT
40084 CCTTTCTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TTCCTTTTTTCTTTCC
Found at i:40069 original size:13 final size:13
Alignment explanation
Indices: 40043--40122 Score: 69
Period size: 13 Copynumber: 6.3 Consensus size: 13
40033 AATTTCCTTA
40043 TTTTCC-TT-TTT
1 TTTTCCTTTCTTT
*
40054 TTTTCC-TTCCTT
1 TTTTCCTTTCTTT
*
40066 TTTTCTTTTCTTT
1 TTTTCCTTTCTTT
*
40079 CTTTTCCTTTCTAT
1 -TTTTCCTTTCTTT
* *
40093 TTTTCTTTTCTAT
1 TTTTCCTTTCTTT
40106 TTTT-CTCTTCTTT
1 TTTTCCT-TTCTTT
40119 TTTT
1 TTTT
40123 TTCTCCCATT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
11 8 0.14
12 8 0.14
13 30 0.53
14 11 0.19
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTCCTTTCTTT
Found at i:40073 original size:22 final size:23
Alignment explanation
Indices: 40036--40101 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 23
40026 AATCTTTAAT
40036 TTCCTTATTTTCCTTTTT-TTTTCC
1 TTCCTT-TTTT-CTTTTTCTTTTCC
40060 TTCCTTTTTTCTTTTCTTTCTTTTCC
1 TTCCTTTTTTC--TT-TTTCTTTTCC
*
40086 TTTCTATTTTTCTTTT
1 TTCCT-TTTTTCTTTT
40102 CTATTTTTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
22 1 0.03
23 4 0.11
24 10 0.28
25 5 0.14
26 10 0.28
27 6 0.17
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (23 bp):
TTCCTTTTTTCTTTTTCTTTTCC
Found at i:40123 original size:27 final size:27
Alignment explanation
Indices: 40054--40122 Score: 81
Period size: 26 Copynumber: 2.6 Consensus size: 27
40044 TTTCCTTTTT
* *
40054 TTTTCC-TTCCTTTTTTCTTTTCTTTC
1 TTTTCCTTTCTTTTTTTCTTTTCTATC
*
40080 TTTTCCTTTCTATTTTTCTTTTCTAT-
1 TTTTCCTTTCTTTTTTTCTTTTCTATC
40106 TTTT-CTCTTCTTTTTTT
1 TTTTCCT-TTCTTTTTTT
40123 TTCTCCCATT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 2 0.05
26 19 0.51
27 16 0.43
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (27 bp):
TTTTCCTTTCTTTTTTTCTTTTCTATC
Found at i:46062 original size:106 final size:106
Alignment explanation
Indices: 45941--46153 Score: 338
Period size: 106 Copynumber: 2.0 Consensus size: 106
45931 TAAATACTAA
* *
45941 AGATTTGCACTAAAGAATAGCACTCATACTTTTTTACCTTAAATTTGTATGCCTACAAACAACTA
1 AGATTTGCACTAAAGAATAACACTCACACTTTTTTACCTTAAATTTGTATGCCTACAAACAACTA
*
46006 AAAAATATATCCTTGTATTC-AAACACCTAAATATCCATTAT
66 AAAAATATATCATTGTA-TCGAAACACCTAAATATCCATTAT
* * *
46047 AGATTTGCACTAAAGAATAACACTCACACTTTTTTACCTTAAATTTGTATGTCTCCAAACAACTG
1 AGATTTGCACTAAAGAATAACACTCACACTTTTTTACCTTAAATTTGTATGCCTACAAACAACTA
* *
46112 AAAAATATATCATTGTATCGAAACACCTCAATATCTATTAT
66 AAAAATATATCATTGTATCGAAACACCTAAATATCCATTAT
46153 A
1 A
46154 TTTATGTAGA
Statistics
Matches: 98, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
105 2 0.02
106 96 0.98
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (106 bp):
AGATTTGCACTAAAGAATAACACTCACACTTTTTTACCTTAAATTTGTATGCCTACAAACAACTA
AAAAATATATCATTGTATCGAAACACCTAAATATCCATTAT
Found at i:47496 original size:26 final size:26
Alignment explanation
Indices: 47459--47513 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
47449 CTGATGTGAG
47459 ATTATATATATTTAATAATAAGAACC
1 ATTATATATATTTAATAATAAGAACC
*
47485 ATTATATCTATTTAATAATAAGAACC
1 ATTATATATATTTAATAATAAGAACC
47511 ATT
1 ATT
47514 GAAAATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (26 bp):
ATTATATATATTTAATAATAAGAACC
Found at i:47522 original size:26 final size:26
Alignment explanation
Indices: 47459--47523 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
47449 CTGATGTGAG
*
47459 ATTATATATATTTAATAATAAGAACC
1 ATTATAAATATTTAATAATAAGAACC
**
47485 ATTATATCTATTTAATAATAAGAACC
1 ATTATAAATATTTAATAATAAGAACC
47511 ATTGA-AAATATTT
1 ATT-ATAAATATTT
47524 TTGACCAGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
26 34 0.97
27 1 0.03
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.40
Consensus pattern (26 bp):
ATTATAAATATTTAATAATAAGAACC
Found at i:47657 original size:29 final size:29
Alignment explanation
Indices: 47621--47681 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
47611 TCTTAATATG
47621 ATGTTTTAATAGTTTATAATCCATTAATT
1 ATGTTTTAATAGTTTATAATCCATTAATT
47650 ATGTTTTAATAGTTTATAATCCATTAATT
1 ATGTTTTAATAGTTTATAATCCATTAATT
47679 ATG
1 ATG
47682 ATAACATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.51
Consensus pattern (29 bp):
ATGTTTTAATAGTTTATAATCCATTAATT
Found at i:49193 original size:22 final size:22
Alignment explanation
Indices: 49168--49283 Score: 114
Period size: 22 Copynumber: 5.3 Consensus size: 22
49158 TATTTTTATA
*
49168 AAATTTTGATAACTACCCTATT
1 AAATTTTGATAACTACCCTATG
*
49190 AAATTTTGATAA-TCACGCTATG
1 AAATTTTGATAACT-ACCCTATG
*
49212 AAATTTTGATAATTA-CCTATG
1 AAATTTTGATAACTACCCTATG
* *
49233 AAATTGTGATAAACT-CCATATG
1 AAATTTTGAT-AACTACCCTATG
* *
49255 AATTTTTGATAACCTA-ACTATG
1 AAATTTTGATAA-CTACCCTATG
49277 AAATTTT
1 AAATTTT
49284 ACCTTCCTAT
Statistics
Matches: 77, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
21 17 0.22
22 59 0.77
23 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAACTACCCTATG
Found at i:49233 original size:21 final size:21
Alignment explanation
Indices: 49168--49349 Score: 108
Period size: 22 Copynumber: 8.6 Consensus size: 21
49158 TATTTTTATA
* *
49168 AAATTTTGATAACTACCCTATT
1 AAATTTTGATAATTA-CCTATG
*
49190 AAATTTTGATAATCACGCTATG
1 AAATTTTGATAATTAC-CTATG
49212 AAATTTTGATAATTACCTATG
1 AAATTTTGATAATTACCTATG
* *
49233 AAATTGTGATAAACT-CCATATG
1 AAATTTTGAT-AATTACC-TATG
* * *
49255 AATTTTTGATAACCTAACTATG
1 AAATTTTGATAA-TTACCTATG
**
49277 AAATTTT-A-CCTT-CCTATG
1 AAATTTTGATAATTACCTATG
49295 AAATTTT-ATAACCTT-CCTATG
1 AAATTTTGATAA--TTACCTATG
* * *
49316 -ATTTTTTATAATCTCCCTATG
1 AAATTTTGATAAT-TACCTATG
* *
49337 AGATTTTGTTAAT
1 AAATTTTGATAAT
49350 CTCCCTATAA
Statistics
Matches: 127, Mismatches: 21, Indels: 24
0.74 0.12 0.14
Matches are distributed among these distances:
18 13 0.10
19 2 0.02
20 6 0.05
21 38 0.30
22 67 0.53
23 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (21 bp):
AAATTTTGATAATTACCTATG
Found at i:49243 original size:43 final size:43
Alignment explanation
Indices: 49168--49281 Score: 131
Period size: 43 Copynumber: 2.6 Consensus size: 43
49158 TATTTTTATA
* * *
49168 AAATTTTGATAACTACCCTATTAAATTTTGATAATCACGC-TATG
1 AAATTTTGATAACTA-CCTATGAAATTGTGATAAACAC-CATATG
* *
49212 AAATTTTGATAATTACCTATGAAATTGTGATAAACTCCATATG
1 AAATTTTGATAACTACCTATGAAATTGTGATAAACACCATATG
* *
49255 AATTTTTGATAACCTAACTATGAAATT
1 AAATTTTGATAA-CTACCTATGAAATT
49282 TTACCTTCCT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 1 0.02
43 33 0.55
44 26 0.43
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.39
Consensus pattern (43 bp):
AAATTTTGATAACTACCTATGAAATTGTGATAAACACCATATG
Found at i:49293 original size:18 final size:21
Alignment explanation
Indices: 49207--49343 Score: 97
Period size: 21 Copynumber: 6.6 Consensus size: 21
49197 GATAATCACG
49207 CTATGAAATTTTGATAA--TTAC
1 CTATGAAATTTT-ATAACCTT-C
* *
49228 CTATGAAATTGTGATAAAC-TC
1 CTATGAAATT-TTATAACCTTC
* **
49249 CATATGAATTTTTGATAACCTAA
1 C-TATGAAATTTT-ATAACCTTC
49272 CTATGAAA-TTT-T-ACCTTC
1 CTATGAAATTTTATAACCTTC
49290 CTATGAAATTTTATAACCTTC
1 CTATGAAATTTTATAACCTTC
** * *
49311 CTATGATTTTTTATAATCTCC
1 CTATGAAATTTTATAACCTTC
*
49332 CTATGAGATTTT
1 CTATGAAATTTT
49344 GTTAATCTCC
Statistics
Matches: 92, Mismatches: 15, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
18 12 0.13
19 4 0.04
20 1 0.01
21 53 0.58
22 21 0.23
23 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (21 bp):
CTATGAAATTTTATAACCTTC
Found at i:49365 original size:22 final size:22
Alignment explanation
Indices: 49310--49369 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
49300 TTATAACCTT
49310 CCTATGATTTTTT-ATAATCTC
1 CCTATGATTTTTTGATAATCTC
** *
49331 CCTATGAGATTTTGTTAATCTC
1 CCTATGATTTTTTGATAATCTC
*
49353 CCTATAATTTTTTGATA
1 CCTATGATTTTTTGATA
49370 CTATAGTATG
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 11 0.35
22 20 0.65
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (22 bp):
CCTATGATTTTTTGATAATCTC
Found at i:50238 original size:45 final size:45
Alignment explanation
Indices: 50205--50340 Score: 218
Period size: 45 Copynumber: 3.0 Consensus size: 45
50195 GGCAATCTAA
50205 TCCGATTTAGCTCTTATAGTATGATTATACTTTTAAAAATTCAAC
1 TCCGATTTAGCTCTTATAGTATGATTATACTTTTAAAAATTCAAC
* *
50250 TCCGATTTAGTTCTTATAGTATGATTATACATTTAAAAATTCAAC
1 TCCGATTTAGCTCTTATAGTATGATTATACTTTTAAAAATTCAAC
* ** *
50295 TCCGGTTTAATTCTTATAGTATGATTATACATTTAAAAATTCAAC
1 TCCGATTTAGCTCTTATAGTATGATTATACTTTTAAAAATTCAAC
50340 T
1 T
50341 ACTTCGAAAA
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 87 1.00
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.43
Consensus pattern (45 bp):
TCCGATTTAGCTCTTATAGTATGATTATACTTTTAAAAATTCAAC
Found at i:58663 original size:30 final size:31
Alignment explanation
Indices: 58612--58670 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
58602 AAAACTCTCA
*
58612 AACATTTATACTTTATGCAATTTAATCCTCG
1 AACATTTATACTTTATACAATTTAATCCTCG
* *
58643 AACATTT-TATTTTATACAATTTAGTCCT
1 AACATTTATACTTTATACAATTTAATCCT
58671 TAATTGTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.32, C:0.17, G:0.05, T:0.46
Consensus pattern (31 bp):
AACATTTATACTTTATACAATTTAATCCTCG
Found at i:64227 original size:22 final size:22
Alignment explanation
Indices: 64127--64591 Score: 131
Period size: 22 Copynumber: 21.1 Consensus size: 22
64117 ACCAACATTA
* *
64127 CATAGAAAGATTATCAAAATTT
1 CATAGAGAGGTTATCAAAATTT
* * * *
64149 CGTAGTGTGGTTACCAAAATTT
1 CATAGAGAGGTTATCAAAATTT
* * * *
64171 CATATAAAGATTATCAAAACTT
1 CATAGAGAGGTTATCAAAATTT
*
64193 CATAGTGTA-GTTATCAAAATTT
1 CATAGAG-AGGTTATCAAAATTT
* *
64215 CATACAGAGGTTACCAAAACTTT
1 CATAGAGAGGTTATCAAAA-TTT
*
64238 -ATAGGGAGGGAGGTTACCAAAA-TT
1 CATA--GA--GAGGTTATCAAAATTT
* *
64262 --T---GTGCTTATCAAAATTT
1 CATAGAGAGGTTATCAAAATTT
* * *
64279 CCTAGAGGGGTTAACAAAATTT
1 CATAGAGAGGTTATCAAAATTT
* *
64301 -ATAGGGAGGTTATAAAAATTT
1 CATAGAGAGGTTATCAAAATTT
* * * *
64322 TATGGAGAGCTTATCGAAAA-TA
1 CATAGAGAGGTTATC-AAAATTT
* *
64344 CATAGAGAGGATATCACAGTTTCATTCT
1 CATAGAGAGGTTATCA-A----AATT-T
* *
64372 CATAGGGAGGTTATCGAAATTT
1 CATAGAGAGGTTATCAAAATTT
* * *
64394 CATGGTGTGGTTATCAAAATTTT
1 CATAGAGAGGTTATCAAAA-TTT
* * *
64417 CATAGTGCGGTTA-C-CAATTT
1 CATAGAGAGGTTATCAAAATTT
* * * * *
64437 TATTTAGTGTGATTATTAAAATTT
1 CA--TAGAGAGGTTATCAAAATTT
* *
64461 TATAG-GTAGATTATCAAAATTT
1 CATAGAG-AGGTTATCAAAATTT
* * * *
64483 CACACTA-AGGTTATCGAAATAT
1 CATA-GAGAGGTTATCAAAATTT
*
64505 CATAGTATGA--TTACCAAAATTT
1 CATAG-A-GAGGTTATCAAAATTT
* * *
64527 C--AGTGTGGTTATCAAATTTT
1 CATAGAGAGGTTATCAAAATTT
* *
64547 CATAGGGAGGTTATCGAAATTT
1 CATAGAGAGGTTATCAAAATTT
* *
64569 CATA-TGAGGTTATCAAATTTT
1 CATAGAGAGGTTATCAAAATTT
64590 CA
1 CA
64592 AAATGTGGTT
Statistics
Matches: 321, Mismatches: 85, Indels: 75
0.67 0.18 0.16
Matches are distributed among these distances:
16 10 0.03
17 2 0.01
18 1 0.00
19 1 0.00
20 17 0.05
21 37 0.12
22 187 0.58
23 26 0.08
24 11 0.03
26 14 0.04
27 2 0.01
28 13 0.04
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (22 bp):
CATAGAGAGGTTATCAAAATTT
Found at i:64590 original size:21 final size:21
Alignment explanation
Indices: 64533--64611 Score: 88
Period size: 22 Copynumber: 3.6 Consensus size: 21
64523 ATTTCAGTGT
*
64533 GGTTATCAAATTTTCATAGGGA
1 GGTTATCAAATTTTCATA-TGA
64555 GGTTATCGAAA-TTTCATATGA
1 GGTTATC-AAATTTTCATATGA
* *
64576 GGTTATCAAATTTTCAAAATGT
1 GGTTATCAAATTTTC-ATATGA
64598 GGTTATCAATATTT
1 GGTTATCAA-ATTT
64612 CTACATTGGA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
20 3 0.06
21 13 0.26
22 27 0.54
23 7 0.14
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.41
Consensus pattern (21 bp):
GGTTATCAAATTTTCATATGA
Found at i:66385 original size:22 final size:22
Alignment explanation
Indices: 66360--66887 Score: 128
Period size: 22 Copynumber: 23.6 Consensus size: 22
66350 ACATAGGAAT
*
66360 GTTATTAAAATTTCATAGTGTG
1 GTTATCAAAATTTCATAGTGTG
* *
66382 GTTACCAAAATTTCATA-TGGAG
1 GTTATCAAAATTTCATAGT-GTG
* * *
66404 GTTATCAAAACTTCGTAGTGTA
1 GTTATCAAAATTTCATAGTGTG
** *
66426 GTTATCAAAATTTCATACAGAG
1 GTTATCAAAATTTCATAGTGTG
* *****
66448 GTTACCAAAATTTCATAAAAAA
1 GTTATCAAAATTTCATAGTGTG
* *
66470 ATTATCAAAATTTCTTA-TG-G
1 GTTATCAAAATTTCATAGTGTG
**
66490 AGATTATCAAAATTTCATACG-AAG
1 -G-TTATCAAAATTTCATA-GTGTG
** * * *
66514 GTTATTGAACTTTTATAGTTTG
1 GTTATCAAAATTTCATAGTGTG
* * **
66536 ATTATCAAAA-TTAATTAGAAT-
1 GTTATCAAAATTTCA-TAGTGTG
* *
66557 GTTGA-CAAAATTTCATAGGGAG
1 GTT-ATCAAAATTTCATAGTGTG
* * * *
66579 GTTATGAAAATATT-ATGGAGAG
1 GTTATCAAAAT-TTCATAGTGTG
* **
66601 GTTATCAAAATTACATA-TAAAG
1 GTTATCAAAATTTCATAGT-GTG
** * * **
66623 AATATCACAGTTTCATTCTCATAGGGAA
1 GTTATCA-A----AATT-TCATAGTGTG
* *
66651 GTTATCGAAATTTCATGGTGTG
1 GTTATCAAAATTTCATAGTGTG
*
66673 GTTATCAAAATTTTCATAGTGCG
1 GTTATCAAAA-TTTCATAGTGTG
* * * * *
66696 ATTA-C-CAATTTTATAATATG
1 GTTATCAAAATTTCATAGTGTG
* *
66716 ATTATCAAAATTTCATAGACACTGAG
1 GTTATCAAAATTTCATAG----TGTG
* *
66742 GTTATCAAAACTTCATTGTGTG
1 GTTATCAAAATTTCATAGTGTG
* * *
66764 GTTAGCAGAATTTCACAGTGTG
1 GTTATCAAAATTTCATAGTGTG
*
66786 GTTATCAAAACTTTACAT--TATG
1 GTTATCAAAA-TTT-CATAGTGTG
* * *
66808 GTTATCAAATTTTCATAGGGAG
1 GTTATCAAAATTTCATAGTGTG
* * * * **
66830 GTTATCGAGATTTCACAATAAG
1 GTTATCAAAATTTCATAGTGTG
* **
66852 GTTATCAAATTTTCGCAGTGTG
1 GTTATCAAAATTTCATAGTGTG
*
66874 GTTATCAATATTTC
1 GTTATCAAAATTTC
66888 TACGTTGGAG
Statistics
Matches: 357, Mismatches: 115, Indels: 68
0.66 0.21 0.13
Matches are distributed among these distances:
20 15 0.04
21 23 0.06
22 262 0.73
23 24 0.07
24 3 0.01
26 17 0.05
27 4 0.01
28 9 0.03
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGTGTG
Found at i:66408 original size:44 final size:43
Alignment explanation
Indices: 66341--66508 Score: 147
Period size: 44 Copynumber: 3.8 Consensus size: 43
66331 TGACATTCAA
* * * *
66341 ACCAAAATTACATAGGAATGTTATTAAAATTTCATAGTGTGGTT
1 ACCAAAATTTCATAGG-AGGTTATCAAAATTTCATAGTGTAGTT
* *
66385 ACCAAAATTTCATATGGAGGTTATCAAAACTTCGTAGTGTAGTT
1 ACCAAAATTTCATA-GGAGGTTATCAAAATTTCATAGTGTAGTT
* * * **** *
66429 ATCAAAATTTCATACAGAGGTTACCAAAATTTCATAAAAAAATT
1 ACCAAAATTTCATA-GGAGGTTATCAAAATTTCATAGTGTAGTT
* * *
66473 ATCAAAATTTCTTATGGAGATTATCAAAATTTCATA
1 ACCAAAATTTCATA-GGAGGTTATCAAAATTTCATA
66509 CGAAGGTTAT
Statistics
Matches: 101, Mismatches: 22, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
44 99 0.98
45 2 0.02
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (43 bp):
ACCAAAATTTCATAGGAGGTTATCAAAATTTCATAGTGTAGTT
Found at i:66451 original size:66 final size:64
Alignment explanation
Indices: 66360--66517 Score: 172
Period size: 66 Copynumber: 2.4 Consensus size: 64
66350 ACATAGGAAT
* * * *** ** *
66360 GTTATTAAAATTTCATAGTGTGGTTACCAAAATTTCATATGGAGGTTATCAAAACTTCGTAGTGT
1 GTTATCAAAATTTCATA-CGAGGTTACCAAAATTTCATAAAAAAATTATCAAAACTTCGTA-TGG
66425 A
64 A
* *
66426 GTTATCAAAATTTCATACAGAGGTTACCAAAATTTCATAAAAAAATTATCAAAATTTCTTATGGA
1 GTTATCAAAATTTCATAC-GAGGTTACCAAAATTTCATAAAAAAATTATCAAAACTTCGTATGGA
66491 GATTATCAAAATTTCATACGAAGGTTA
1 G-TTATCAAAATTTCATACG-AGGTTA
66518 TTGAACTTTT
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
65 5 0.06
66 73 0.94
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.35
Consensus pattern (64 bp):
GTTATCAAAATTTCATACGAGGTTACCAAAATTTCATAAAAAAATTATCAAAACTTCGTATGGA
Found at i:74630 original size:24 final size:24
Alignment explanation
Indices: 74598--74679 Score: 90
Period size: 24 Copynumber: 3.8 Consensus size: 24
74588 GAGGAAGGAG
74598 AGTTAAACACATTATCAGCAACCA
1 AGTTAAACACATTATCAGCAACCA
*
74622 AGTTAAACACATAATCAG--A-C-
1 AGTTAAACACATTATCAGCAACCA
*
74642 --TTAAATA-A-TATCAGCAACCA
1 AGTTAAACACATTATCAGCAACCA
74662 AGTTAAACACATTATCAG
1 AGTTAAACACATTATCAG
74680 AATGCATCTT
Statistics
Matches: 46, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
16 5 0.11
17 1 0.02
18 7 0.15
19 1 0.02
21 1 0.02
22 7 0.15
23 1 0.02
24 23 0.50
ACGTcount: A:0.48, C:0.21, G:0.09, T:0.23
Consensus pattern (24 bp):
AGTTAAACACATTATCAGCAACCA
Found at i:79937 original size:27 final size:27
Alignment explanation
Indices: 79899--79954 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
79889 CATGTTTGGG
79899 TTAATGAGGGGCTAGATTATTAAATAT
1 TTAATGAGGGGCTAGATTATTAAATAT
79926 TTAATGAGGGGCTAGATTATTAAATAT
1 TTAATGAGGGGCTAGATTATTAAATAT
79953 TT
1 TT
79955 TAGTTTTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.39
Consensus pattern (27 bp):
TTAATGAGGGGCTAGATTATTAAATAT
Done.