Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024046.1 Corchorus olitorius cultivar O-4 contig24079, 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: 100298
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:146 original size:19 final size:18
Alignment explanation
Indices: 122--157 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
112 TGAAGACTTA
122 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
141 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
158 ATTATTTCCA
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:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:2671 original size:12 final size:12
Alignment explanation
Indices: 2654--2683 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2644 GCAACAAACA
2654 TTTTGCCACAAC
1 TTTTGCCACAAC
*
2666 TTTTGCCACATC
1 TTTTGCCACAAC
2678 TTTTGC
1 TTTTGC
2684 AAATACCCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.30, G:0.10, T:0.43
Consensus pattern (12 bp):
TTTTGCCACAAC
Found at i:2957 original size:21 final size:21
Alignment explanation
Indices: 2931--2995 Score: 76
Period size: 26 Copynumber: 2.9 Consensus size: 21
2921 TTGGTTTCAC
2931 TTGTTTGATGGAATATTACAA
1 TTGTTTGATGGAATATTACAA
*
2952 TTGTTTGATGAAATTGTGTATTACAA
1 TTGTTTGATGGAA-----TATTACAA
2978 TTGTTTGATGGAATATTA
1 TTGTTTGATGGAATATTA
2996 TATCATCTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
21 17 0.46
26 20 0.54
ACGTcount: A:0.31, C:0.03, G:0.20, T:0.46
Consensus pattern (21 bp):
TTGTTTGATGGAATATTACAA
Found at i:4138 original size:516 final size:517
Alignment explanation
Indices: 3165--4599 Score: 2543
Period size: 529 Copynumber: 2.8 Consensus size: 517
3155 CTAGTTACAA
*
3165 TTAAAAACCGTGGGAAAAGTCGTGGCTATTTGGCACGGCCTTTGCCACGACTTTTCAATTTACCA
1 TTAAAAACCGTGGGAAAAGTCGTGGCTATTTGGCACGGCCTTTGCCACGACTTTTCAATTTTCCA
*
3230 CGGGTTTTGCAGCAGGTTTACAGATTCCCGTGGCAAAAGCTGTGGCAAATTGAGAGATGATTGAC
66 CGGGTTTTGCAGCGGGTTTACAGATTCCCGTGGCAAAAGCTGTGGCAAATTGAGAGATGATTGAC
3295 CTCAAACCCTACACTTATATGAGTTAGTAATTGGCTAATGATCACATAATTGCATTTATATCATC
131 CTCAAACCCTACACTTATATGAGTTAGTAATTGGCTAATGATCACATAATTGCATTTATATCATC
*
3360 TCAAAATTCTATATTGTCTCCAAAAAAATGTGTAATTTCTAATTACTTAAAAAAATTTAATTGAA
196 TCAAAATTCTATATTGTCTCC-AAAAATTGTGTAATTTCTAATTACTT-AAAAAATTTAATTGAA
3425 TCTTTACACAATGTCATAATATACAAATGTGTTAGTAGTGTGTTCATAGATAGTATTACAAATAC
259 TCTTTACACAATGTCATAATATACAAATGTGTTAGTAGTGTGTTCATAGATAGTATTACAAATAC
3490 ATTTAGCCAATTAAGTCTAGTTACAATTTTGA-TTTTTTTTACTCCCAAACTATTTTACATTAAA
324 ATTTAGCCAATTAAGTCTAGTTACAATTTTGATTTTTTTTTACTCCCAAACTATTTTACATTAAA
3554 TTCTACATCAAATACTCGAGCTAAACACAATAGGGTACCATAAAAACCTTTAATTTTATGGGAAC
389 TTCTACATCAAATACTCGAGCTAAACACAATAGGGTACCATAAAAACCTTTAATTTTATGGGAAC
3619 TTCAAATTATCTTTGTTTAGAGTAAAATTCTTAGAGATGAAGTCTATATTTGCC-ACGCTTTTC
454 TTCAAATTATCTTTGTTTAGAGTAAAATTCTTAGAGATGAAGTCTATATTTGCCTACGCTTTTC
*
3682 TTAAAAACCGTGGGAAAAGTCGTGGCTATTTGGCACGGCCTTTGCCACGACTTTTTAATTTTCCA
1 TTAAAAACCGTGGGAAAAGTCGTGGCTATTTGGCACGGCCTTTGCCACGACTTTTCAATTTTCCA
* * *
3747 CGGGTATTGCAGCGGGTTTATAGATTCCCGTTGCAAAAGCTGTGGC-AATTGAGAGATGATTGAC
66 CGGGTTTTGCAGCGGGTTTACAGATTCCCGTGGCAAAAGCTGTGGCAAATTGAGAGATGATTGAC
3811 CTCAAACCCTACACTTATATGAGTTAGTAATTGGCTAATGATCACATAATTGCATTTATATCATC
131 CTCAAACCCTACACTTATATGAGTTAGTAATTGGCTAATGATCACATAATTGCATTTATATCATC
*
3876 TCAAAATTCTATATTGTCTTCAAAAATTGTGTAATTTCTAATTACTTAAAAAATTTAATTGAATC
196 TCAAAATTCTATATTGTCTCCAAAAATTGTGTAATTTCTAATTACTTAAAAAATTTAATTGAATC
*
3941 TTTACACAATGTCATAATATACAAATGTGTTAGTAGTGTGTTCATAGATAGTATTACACATACAT
261 TTTACACAATGTCATAATATACAAATGTGTTAGTAGTGTGTTCATAGATAGTATTACAAATACAT
4006 TTAGCCAATTAAGTCTAGTTACAATTTTGATTTTTTTTTTACTCCCAAACTATTTTACATTAAAT
326 TTAGCCAATTAAGTCTAGTTACAATTTTGA-TTTTTTTTTACTCCCAAACTATTTTACATTAAAT
4071 TCTACATCAAATACTCGAGCTAAACACAATAGGGTACCATAAAAACCTTTAATTTTATGGGAACT
390 TCTACATCAAATACTCGAGCTAAACACAATAGGGTACCATAAAAACCTTTAATTTTATGGGAACT
4136 TCAAATTATCTTTGTTTAGAGTAAAATTCTTAGAGATGAAGTCTATATTTGCCATGGTTTTTGAA
455 TCAAATTATCTTTGTTTAGAGTAAAATTCTTAGAGATGAAGTCTATATTTGCC--------T---
*
4201 ACGGTTTTC
509 ACGCTTTTC
4210 TTAAAAACCGTGGGAAAAGTCGTGGCTATTTGGCACGGCCTTTGCCACGACTTTTCAATTTTCCA
1 TTAAAAACCGTGGGAAAAGTCGTGGCTATTTGGCACGGCCTTTGCCACGACTTTTCAATTTTCCA
*
4275 CGGGTTTTGCAGGGGGTTTACAGATTCCCGTGGCAAAAGCTGTGGCAAATTGAGAGATGATTGAC
66 CGGGTTTTGCAGCGGGTTTACAGATTCCCGTGGCAAAAGCTGTGGCAAATTGAGAGATGATTGAC
* *
4340 CTCAAACCGTACACTTATATGAGTTAGTAATTGGCTAATGATCACAAAATTGCATTTATATCATC
131 CTCAAACCCTACACTTATATGAGTTAGTAATTGGCTAATGATCACATAATTGCATTTATATCATC
* *
4405 TCAAAATTCTATATTGTCTCCAAAAATTGTGTAATTTCTATTTACTTAAAAATTTTAATTGAATC
196 TCAAAATTCTATATTGTCTCCAAAAATTGTGTAATTTCTAATTACTTAAAAAATTTAATTGAATC
* *
4470 TTTACACAATGTCATAATATAGAAATGTGTTAGTAGTGTATTCATAGATAGTATTACAAATACAT
261 TTTACACAATGTCATAATATACAAATGTGTTAGTAGTGTGTTCATAGATAGTATTACAAATACAT
**
4535 TTAGCCAATTAAGTCTAGTTACAATTTTGATTTTTTTCCACTCCCCAAACTATTTTACATTAAAT
326 TTAGCCAATTAAGTCTAGTTACAATTTTGATTTTTTTTTACT-CCCAAACTATTTTACATTAAAT
4600 ACTCGAGCTA
Statistics
Matches: 877, Mismatches: 25, Indels: 20
0.95 0.03 0.02
Matches are distributed among these distances:
514 112 0.13
515 25 0.03
516 254 0.29
517 105 0.12
528 124 0.14
529 257 0.29
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (517 bp):
TTAAAAACCGTGGGAAAAGTCGTGGCTATTTGGCACGGCCTTTGCCACGACTTTTCAATTTTCCA
CGGGTTTTGCAGCGGGTTTACAGATTCCCGTGGCAAAAGCTGTGGCAAATTGAGAGATGATTGAC
CTCAAACCCTACACTTATATGAGTTAGTAATTGGCTAATGATCACATAATTGCATTTATATCATC
TCAAAATTCTATATTGTCTCCAAAAATTGTGTAATTTCTAATTACTTAAAAAATTTAATTGAATC
TTTACACAATGTCATAATATACAAATGTGTTAGTAGTGTGTTCATAGATAGTATTACAAATACAT
TTAGCCAATTAAGTCTAGTTACAATTTTGATTTTTTTTTACTCCCAAACTATTTTACATTAAATT
CTACATCAAATACTCGAGCTAAACACAATAGGGTACCATAAAAACCTTTAATTTTATGGGAACTT
CAAATTATCTTTGTTTAGAGTAAAATTCTTAGAGATGAAGTCTATATTTGCCTACGCTTTTC
Found at i:9596 original size:14 final size:14
Alignment explanation
Indices: 9577--9618 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
9567 TTTCTTCAAC
9577 TAGAGTTATAAAGT
1 TAGAGTTATAAAGT
*
9591 TAGAGTTATAGAGT
1 TAGAGTTATAAAGT
*
9605 TAGGAATTATAAAG
1 TA-GAGTTATAAAG
9619 AGGGAGTGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 15 0.62
15 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.24, T:0.33
Consensus pattern (14 bp):
TAGAGTTATAAAGT
Found at i:10157 original size:26 final size:26
Alignment explanation
Indices: 10093--10186 Score: 95
Period size: 26 Copynumber: 3.7 Consensus size: 26
10083 GTTGGGCTTC
* *
10093 TATTTCATTTATGCTTT-GGTTTTTT
1 TATTTCATTTATGCTTTGGGCTTTAT
* * *
10118 TATTCCCTTGATGCTTTGGGCTTTAT
1 TATTTCATTTATGCTTTGGGCTTTAT
*
10144 TATTTCATTTATGCTTTGGGCATCTAT
1 TATTTCATTTATGCTTTGGGC-TTTAT
*
10171 T-TTT-ATTTGTGCTTTG
1 TATTTCATTTATGCTTTG
10187 AGTTTCTGCT
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
25 25 0.44
26 27 0.47
27 5 0.09
ACGTcount: A:0.13, C:0.13, G:0.16, T:0.59
Consensus pattern (26 bp):
TATTTCATTTATGCTTTGGGCTTTAT
Found at i:10242 original size:19 final size:19
Alignment explanation
Indices: 10198--10243 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
10188 GTTTCTGCTC
10198 ATGATTT-GGACTTTATTT
1 ATGATTTGGGACTTTATTT
* *
10216 ATATATTTGGGTCTTTATTT
1 AT-GATTTGGGACTTTATTT
10236 ATGATTTG
1 ATGATTTG
10244 AGTTTTTGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 2 0.09
19 9 0.39
20 12 0.52
ACGTcount: A:0.22, C:0.04, G:0.17, T:0.57
Consensus pattern (19 bp):
ATGATTTGGGACTTTATTT
Found at i:11045 original size:19 final size:20
Alignment explanation
Indices: 11012--11050 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
11002 TAAAAAGGTT
*
11012 TTCAAAAATCCAAAA-AAAA
1 TTCAAAAATCAAAAATAAAA
*
11031 TTCAAAATTCAAAAATAAAA
1 TTCAAAAATCAAAAATAAAA
11051 AAGAATTTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.21
Consensus pattern (20 bp):
TTCAAAAATCAAAAATAAAA
Found at i:11239 original size:52 final size:52
Alignment explanation
Indices: 11065--11231 Score: 264
Period size: 51 Copynumber: 3.2 Consensus size: 52
11055 ATTTCCTTCA
* * * *
11065 AAGTGTTCAAAGTATTCAATTTAGCTCTTTTTTAAAGTGGTAAAGTTCCCATC
1 AAGTTTTCAAAGTATTCAATTTAGGTC-TTTTCAAAGTGGGAAAGTTCCCATC
*
11118 AAGTTTTCAAAGTATTCAATTTAGGTC-TTTCAATGTGGGAAAGTTCCCATC
1 AAGTTTTCAAAGTATTCAATTTAGGTCTTTTCAAAGTGGGAAAGTTCCCATC
*
11169 AAGTTTTCAAAGTGTTCAATTTAGGTCTTTTCAAAGTGGGAAAGTTCCCATC
1 AAGTTTTCAAAGTATTCAATTTAGGTCTTTTCAAAGTGGGAAAGTTCCCATC
11221 AAGTTTTCAAA
1 AAGTTTTCAAA
11232 ACATTCAAAC
Statistics
Matches: 106, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
51 47 0.44
52 34 0.32
53 25 0.24
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.38
Consensus pattern (52 bp):
AAGTTTTCAAAGTATTCAATTTAGGTCTTTTCAAAGTGGGAAAGTTCCCATC
Found at i:11252 original size:103 final size:104
Alignment explanation
Indices: 11065--11253 Score: 254
Period size: 103 Copynumber: 1.8 Consensus size: 104
11055 ATTTCCTTCA
* * *
11065 AAGTGTTCAAAGTATTCAATTTAGCTCTTTTTTAAAGTGGTAAAGTTCCCATCAAGTTTTCAAAG
1 AAGTGTTCAAAGTATTCAATTTAGCTCTTTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAA
* *** **
11130 TATTCAATTTAGGTCTTTCAATGTGGGAAAGTTCCCATC
66 CATTCAAACAACATCTTTCAATGTGGGAAAGTTCCCATC
* * *
11169 AAGTTTTCAAAGTGTTCAATTTAGGTC-TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAA
1 AAGTGTTCAAAGTATTCAATTTAGCTCTTTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAA
*
11233 CATTCAAACAACATTTTTCAA
66 CATTCAAACAACATCTTTCAA
11254 ATAGAGTTGT
Statistics
Matches: 72, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
103 48 0.67
104 24 0.33
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (104 bp):
AAGTGTTCAAAGTATTCAATTTAGCTCTTTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAA
CATTCAAACAACATCTTTCAATGTGGGAAAGTTCCCATC
Found at i:18437 original size:30 final size:30
Alignment explanation
Indices: 18403--18459 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
18393 ATTCTTTCTC
* *
18403 CTTGAAATATTTCTTCAA-TGATCTTCATGA
1 CTTGAAAT-TGTCTTCAATTAATCTTCATGA
18433 CTTGAAATTGTCTTCAATTAATCTTCA
1 CTTGAAATTGTCTTCAATTAATCTTCA
18460 ATCATGAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.44
Consensus pattern (30 bp):
CTTGAAATTGTCTTCAATTAATCTTCATGA
Found at i:19915 original size:38 final size:38
Alignment explanation
Indices: 19864--19940 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
19854 TTATATCTCT
19864 ATTTCAATTTCATCAAGTGCTAACAAAACTGACACATG
1 ATTTCAATTTCATCAAGTGCTAACAAAACTGACACATG
19902 ATTTCAATTTCATCAAGTGCTAACAAAACTGACACATG
1 ATTTCAATTTCATCAAGTGCTAACAAAACTGACACATG
19940 A
1 A
19941 GACTTCATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (38 bp):
ATTTCAATTTCATCAAGTGCTAACAAAACTGACACATG
Found at i:31367 original size:46 final size:45
Alignment explanation
Indices: 31300--31392 Score: 134
Period size: 46 Copynumber: 2.0 Consensus size: 45
31290 CCCTGTCAAG
*
31300 ACGGCGTCCTATAATGATGGG-TAAAACCAAGTAAAAGGAAATATTA
1 ACGGCGTCCTATAATGATGGGTTAAAACAAAG-AAAA-GAAATATTA
* *
31346 ACGGCGTCCTATACTGATGGGTTAAAACAAAGAGAAGAAATATTA
1 ACGGCGTCCTATAATGATGGGTTAAAACAAAGAAAAGAAATATTA
31391 AC
1 AC
31393 CTTTTGAACA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
45 11 0.26
46 23 0.53
47 9 0.21
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.22
Consensus pattern (45 bp):
ACGGCGTCCTATAATGATGGGTTAAAACAAAGAAAAGAAATATTA
Found at i:32166 original size:25 final size:25
Alignment explanation
Indices: 32135--32183 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
32125 CCGAACATTG
32135 ATGGCAAAATGAATTGGACGTGGCT
1 ATGGCAAAATGAATTGGACGTGGCT
32160 ATGGCAAAATGAATTGGACGTGGC
1 ATGGCAAAATGAATTGGACGTGGC
32184 CCGAACATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.33, T:0.22
Consensus pattern (25 bp):
ATGGCAAAATGAATTGGACGTGGCT
Found at i:34054 original size:37 final size:37
Alignment explanation
Indices: 34013--34121 Score: 200
Period size: 37 Copynumber: 2.9 Consensus size: 37
34003 TTGAAGCTGA
34013 ATTTTGTAGTGGATTGTTAAATTCTAGTGGGCCTTGG
1 ATTTTGTAGTGGATTGTTAAATTCTAGTGGGCCTTGG
* *
34050 ATTTTGGAGTGGATTGTTAAATTGTAGTGGGCCTTGG
1 ATTTTGTAGTGGATTGTTAAATTCTAGTGGGCCTTGG
34087 ATTTTGTAGTGGATTGTTAAATTCTAGTGGGCCTT
1 ATTTTGTAGTGGATTGTTAAATTCTAGTGGGCCTT
34122 TTAGATGATT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.19, C:0.07, G:0.30, T:0.43
Consensus pattern (37 bp):
ATTTTGTAGTGGATTGTTAAATTCTAGTGGGCCTTGG
Found at i:38910 original size:20 final size:20
Alignment explanation
Indices: 38885--38972 Score: 158
Period size: 20 Copynumber: 4.4 Consensus size: 20
38875 GGAAAGCCAG
*
38885 TTGGGCTCGCTCAGCGGGGC
1 TTGGGCTCGCTCAGCGAGGC
*
38905 TTGGGCTCGCTCAGCGCGGC
1 TTGGGCTCGCTCAGCGAGGC
38925 TTGGGCTCGCTCAGCGAGGC
1 TTGGGCTCGCTCAGCGAGGC
38945 TTGGGCTCGCTCAGCGAGGC
1 TTGGGCTCGCTCAGCGAGGC
38965 TTGGGCTC
1 TTGGGCTC
38973 ATAAAGGCCC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.07, C:0.31, G:0.41, T:0.22
Consensus pattern (20 bp):
TTGGGCTCGCTCAGCGAGGC
Found at i:39937 original size:21 final size:20
Alignment explanation
Indices: 39893--39953 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 20
39883 TTTTGATAAT
*
39893 CTCATTAAATTTCGATAACCAC
1 CTCA-TAAATTT-GATAACAAC
39915 CTCATAAATTTGATAACTAAC
1 CTCATAAATTTGATAAC-AAC
39936 CT-ATGAAATGTTGATAAC
1 CTCAT-AAAT-TTGATAAC
39954 CTCCCCATGA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
20 8 0.23
21 15 0.43
22 12 0.34
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (20 bp):
CTCATAAATTTGATAACAAC
Found at i:44970 original size:24 final size:23
Alignment explanation
Indices: 44935--44986 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 23
44925 AAAACGCAGA
*
44935 CAAAAAT-TTTTTTTTTTATGACG
1 CAAAAATATTTTTTTTTT-CGACG
44958 CAAAAACTATTTTTTTTTTCGACG
1 CAAAAA-TATTTTTTTTTTCGACG
44982 CAAAA
1 CAAAA
44987 CACAAAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 6 0.23
24 10 0.38
25 10 0.38
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (23 bp):
CAAAAATATTTTTTTTTTCGACG
Found at i:45368 original size:16 final size:15
Alignment explanation
Indices: 45330--45371 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
45320 ACAGAGATTG
*
45330 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
45345 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
45360 ACTAGAAAACAA
1 AC-AGAAAACAA
45372 ACCAGAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:52397 original size:38 final size:38
Alignment explanation
Indices: 52346--52513 Score: 246
Period size: 38 Copynumber: 4.4 Consensus size: 38
52336 TCAGTTTGTT
* *
52346 AAGTTTAATGTGTTGATTAAGCAGGATGGTTAAGCTTA
1 AAGTTTAATGTGTTGATTAAGCAGGATGTTTAACCTTA
*
52384 AAGTTTAATGTGTTGATTAAGCAGGATGTTTAAGCTTA
1 AAGTTTAATGTGTTGATTAAGCAGGATGTTTAACCTTA
* * *
52422 AAGTTTATTGTGTTGATTAAGCATGATGTTTTACCTTA
1 AAGTTTAATGTGTTGATTAAGCAGGATGTTTAACCTTA
* * *
52460 AAGTTTATTGTGTTCATTAAGCAGGATGTTTTACCTTA
1 AAGTTTAATGTGTTGATTAAGCAGGATGTTTAACCTTA
*
52498 AAGTTTAATGTTTTGA
1 AAGTTTAATGTGTTGA
52514 ATATTAGTTT
Statistics
Matches: 120, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 120 1.00
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (38 bp):
AAGTTTAATGTGTTGATTAAGCAGGATGTTTAACCTTA
Found at i:58270 original size:2 final size:2
Alignment explanation
Indices: 58263--58314 Score: 63
Period size: 2 Copynumber: 27.0 Consensus size: 2
58253 TATAGTGTAC
* *
58263 AT AT AT AT AT AT AT AT -T AT AT AC AT AT AT A- AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
58303 AT AT AT GT AT AT
1 AT AT AT AT AT AT
58315 CAATGTAACA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58283 original size:17 final size:17
Alignment explanation
Indices: 58263--58308 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
58253 TATAGTGTAC
58263 ATATATATATATATAT-T
1 ATATATATATATA-ATGT
*
58280 ATATACATATATAATGT
1 ATATATATATATAATGT
58297 ATATATATATAT
1 ATATATATATAT
58309 GTATATCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 2 0.08
17 24 0.92
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (17 bp):
ATATATATATATAATGT
Found at i:62176 original size:24 final size:25
Alignment explanation
Indices: 62144--62193 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
62134 GCCCAACATC
*
62144 TTAAGGTGTAAATTATTAAC-GATA
1 TTAAGGTGTAAATTACTAACTGATA
62168 TTAAGGTGTAAATTACTAACTGATA
1 TTAAGGTGTAAATTACTAACTGATA
62193 T
1 T
62194 GTTATCGCGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.38
Consensus pattern (25 bp):
TTAAGGTGTAAATTACTAACTGATA
Found at i:65571 original size:23 final size:23
Alignment explanation
Indices: 65545--65589 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
65535 ATGTAATTAC
65545 TCAACAGAAAATGCTTGAATATA
1 TCAACAGAAAATGCTTGAATATA
65568 TCAACAGAAAATGCTTGAATAT
1 TCAACAGAAAATGCTTGAATAT
65590 CTTTTTTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (23 bp):
TCAACAGAAAATGCTTGAATATA
Found at i:68214 original size:38 final size:39
Alignment explanation
Indices: 68121--68223 Score: 138
Period size: 39 Copynumber: 2.7 Consensus size: 39
68111 ATTTTATTAA
* * *
68121 TTTCCAAAATCTTCTTTTGGGA-TATCTTAAACTTTTATT
1 TTTCCAAAATCTTCTTTTGGAATTA-CCTAAACCTTTATT
68160 TTTCCAAAATCTTCTTTTGGAATTACCTAAACCTTTA-T
1 TTTCCAAAATCTTCTTTTGGAATTACCTAAACCTTTATT
* *
68198 TTTCCATAATCGTCTTTTGGAATTAC
1 TTTCCAAAATCTTCTTTTGGAATTAC
68224 TCAATTAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
38 25 0.43
39 31 0.53
40 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.48
Consensus pattern (39 bp):
TTTCCAAAATCTTCTTTTGGAATTACCTAAACCTTTATT
Found at i:71015 original size:27 final size:27
Alignment explanation
Indices: 70985--71054 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
70975 AGTGAACTTA
* *
70985 AAATGACCAAAATGTCCCTGAATGTGT
1 AAATGACCAAAATGCCCCTGAATGTGC
* *
71012 AAATTACCAAAATGCCCCTGGATGTGC
1 AAATGACCAAAATGCCCCTGAATGTGC
*
71039 GAATGACCAAAATGCC
1 AAATGACCAAAATGCC
71055 TCTGGATGAC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAATGTGC
Found at i:71059 original size:27 final size:26
Alignment explanation
Indices: 70985--71062 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 26
70975 AGTGAACTTA
* *
70985 AAATGACCAAAATGTCCCTGAATGTGT
1 AAATGACCAAAATG-CCCTGGATGTGC
*
71012 AAATTACCAAAATGCCCCTGGATGTGC
1 AAATGACCAAAATG-CCCTGGATGTGC
*
71039 GAATGACCAAAATGCCTCTGGATG
1 AAATGACCAAAATGCC-CTGGATG
71063 ACCCTAATGC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
26 2 0.05
27 42 0.95
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.23
Consensus pattern (26 bp):
AAATGACCAAAATGCCCTGGATGTGC
Found at i:71075 original size:27 final size:27
Alignment explanation
Indices: 71017--71076 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
71007 TGTGTAAATT
**
71017 ACCAAAATGCCCCTGGATGTGCGAATG
1 ACCAAAATGCCCCTGGATGCCCGAATG
* *
71044 ACCAAAATGCCTCTGGATGACCCTAATG
1 ACCAAAATGCCCCTGGATG-CCCGAATG
71072 -CCAAA
1 ACCAAA
71077 TAAGAAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 23 0.82
28 5 0.18
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.18
Consensus pattern (27 bp):
ACCAAAATGCCCCTGGATGCCCGAATG
Found at i:88480 original size:34 final size:34
Alignment explanation
Indices: 88431--88501 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
88421 ATGCAATTAT
* *
88431 ATATATTATAGTAGTATGCAGTAAGAAAATACAA
1 ATATATAATACTAGTATGCAGTAAGAAAATACAA
*
88465 ATATATAATACTAGTATGCAGTAAGAAAATACGA
1 ATATATAATACTAGTATGCAGTAAGAAAATACAA
88499 ATA
1 ATA
88502 AAGTTTTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.51, C:0.07, G:0.14, T:0.28
Consensus pattern (34 bp):
ATATATAATACTAGTATGCAGTAAGAAAATACAA
Found at i:93535 original size:478 final size:478
Alignment explanation
Indices: 92633--93592 Score: 1866
Period size: 478 Copynumber: 2.0 Consensus size: 478
92623 ATTTTTTAAT
92633 TTATATAATAACTATTTTCTCCAGGAAGTTTCTACAACAATCTTAAAGAGTATGTCCAAGGAAAA
1 TTATATAATAACTATTTTCTCCAGGAAGTTTCTACAACAATCTTAAAGAGTATGTCCAAGGAAAA
*
92698 CGAAACCATTCTTCTAACCACCGCTGAGTCTGCTGCTGCCACCAAAAATGGCCAAACATCCAACA
66 CGAAACCATTCTTCTAACCACCGCCGAGTCTGCTGCTGCCACCAAAAATGGCCAAACATCCAACA
92763 ATGACACTGCCCCTCTGCCCATTCCGGCGCATGTTACCTTCGCCAAACCATTTCCAGACATCTCC
131 ATGACACTGCCCCTCTGCCCATTCCGGCGCATGTTACCTTCGCCAAACCATTTCCAGACATCTCC
92828 AAAATTGAAGTGTTCGATGGCAACAACTTCAGACGCTGGATGGAAAGTGTCTATTCTGCTCTTGA
196 AAAATTGAAGTGTTCGATGGCAACAACTTCAGACGCTGGATGGAAAGTGTCTATTCTGCTCTTGA
* *
92893 CATGCATGGAATGGTGTTTTCTCTAACAGATGCTAAGCCCACTGACGACAGCCTTCTTAACCAAT
261 CATGCATGGAATGGTGTTTGCTCTAACAAATGCTAAGCCCACTGACGACAGCCTTCTTAACCAAT
*
92958 AGACCCATGCTAATAAGGTATGCTGACGCACCATCATTAGCACTTTATCTAATGAGCTCTTTGAT
326 AGACCCATGCTAATAAGGTATGCTGACACACCATCATTAGCACTTTATCTAATGAGCTCTTTGAT
93023 GTCTACAGTCCATACAAAGAAGCAAAACAGATTTGGAACTCCATGATTACAAAATACACTGCTGA
391 GTCTACAGTCCATACAAAGAAGCAAAACAGATTTGGAACTCCATGATTACAAAATACACTGCTGA
93088 GGAAGTGGGCAAACAGAAGTTTG
456 GGAAGTGGGCAAACAGAAGTTTG
93111 TTATATAATAACTATTTTCTCCAGGAAGTTTCTACAACAATCTTAAAGAGTATGTCCAAGGAAAA
1 TTATATAATAACTATTTTCTCCAGGAAGTTTCTACAACAATCTTAAAGAGTATGTCCAAGGAAAA
93176 CGAAACCATTCTTCTAACCACCGCCGAGTCTGCTGCTGCCACCAAAAATGGCCAAACATCCAACA
66 CGAAACCATTCTTCTAACCACCGCCGAGTCTGCTGCTGCCACCAAAAATGGCCAAACATCCAACA
*
93241 ATGACACTGCCCCTCTGCCCATTCCGGCGCCTGTTACCTTCGCCAAACCATTTCCAGACATCTCC
131 ATGACACTGCCCCTCTGCCCATTCCGGCGCATGTTACCTTCGCCAAACCATTTCCAGACATCTCC
93306 AAAATTGAAGTGTTCGATGGCAACAACTTCAGACGCTGGATGGAAAGTGTCTATTCTGCTCTTGA
196 AAAATTGAAGTGTTCGATGGCAACAACTTCAGACGCTGGATGGAAAGTGTCTATTCTGCTCTTGA
93371 CATGCATGGAATGGTGTTTGCTCTAACAAATGCTAAGCCCACTGACGACAGCCTTCTTAACCAAT
261 CATGCATGGAATGGTGTTTGCTCTAACAAATGCTAAGCCCACTGACGACAGCCTTCTTAACCAAT
93436 AGACCCATGCTAATAAGGTATGCTGACACACCATCATTAGCACTTTATCTAATGAGCTCTTTGAT
326 AGACCCATGCTAATAAGGTATGCTGACACACCATCATTAGCACTTTATCTAATGAGCTCTTTGAT
*
93501 GTCTACAGTCCATACAAAGAAGCAAAATAGATTTGGAACTCCATGATTACAAAATACACTGCTGA
391 GTCTACAGTCCATACAAAGAAGCAAAACAGATTTGGAACTCCATGATTACAAAATACACTGCTGA
93566 GGAAGTGGGCAAACAGAAGTTTG
456 GGAAGTGGGCAAACAGAAGTTTG
93589 TTAT
1 TTAT
93593 TGGCAACTGC
Statistics
Matches: 476, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
478 476 1.00
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (478 bp):
TTATATAATAACTATTTTCTCCAGGAAGTTTCTACAACAATCTTAAAGAGTATGTCCAAGGAAAA
CGAAACCATTCTTCTAACCACCGCCGAGTCTGCTGCTGCCACCAAAAATGGCCAAACATCCAACA
ATGACACTGCCCCTCTGCCCATTCCGGCGCATGTTACCTTCGCCAAACCATTTCCAGACATCTCC
AAAATTGAAGTGTTCGATGGCAACAACTTCAGACGCTGGATGGAAAGTGTCTATTCTGCTCTTGA
CATGCATGGAATGGTGTTTGCTCTAACAAATGCTAAGCCCACTGACGACAGCCTTCTTAACCAAT
AGACCCATGCTAATAAGGTATGCTGACACACCATCATTAGCACTTTATCTAATGAGCTCTTTGAT
GTCTACAGTCCATACAAAGAAGCAAAACAGATTTGGAACTCCATGATTACAAAATACACTGCTGA
GGAAGTGGGCAAACAGAAGTTTG
Found at i:96611 original size:25 final size:27
Alignment explanation
Indices: 96574--96629 Score: 71
Period size: 25 Copynumber: 2.1 Consensus size: 27
96564 AGGCGCCCCG
* * *
96574 AATTTTTTTTTATTTATTT-ATTTT-A
1 AATTTATTATTATTAATTTAATTTTGA
96599 AATTTATTATTATTAATTTAATTTTGA
1 AATTTATTATTATTAATTTAATTTTGA
96626 AATT
1 AATT
96630 GTTAAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 16 0.62
26 5 0.19
27 5 0.19
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (27 bp):
AATTTATTATTATTAATTTAATTTTGA
Found at i:96694 original size:22 final size:18
Alignment explanation
Indices: 96647--96681 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
96637 TTTATTAAGG
96647 TTAATTAGTGTTAATTAA
1 TTAATTAGTGTTAATTAA
*
96665 CTAATTAGTGTTAATTA
1 TTAATTAGTGTTAATTA
96682 GTGTATTAAT
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:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAATTAGTGTTAATTAA
Found at i:98016 original size:19 final size:18
Alignment explanation
Indices: 97992--98058 Score: 82
Period size: 19 Copynumber: 3.6 Consensus size: 18
97982 ACCATCATAC
97992 AAAAACAAAAAAAAAACAG
1 AAAAACAAAAAAAAAA-AG
*
98011 AAAAACAAAAACAAAAAAC
1 AAAAACAAAAA-AAAAAAG
98030 AAAAACAGAAAGAAAAAAAG
1 AAAAACA-AAA-AAAAAAAG
98050 AAAAA-AAAA
1 AAAAACAAAA
98059 GAAAGGGAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
18 3 0.07
19 20 0.47
20 19 0.44
21 1 0.02
ACGTcount: A:0.85, C:0.09, G:0.06, T:0.00
Consensus pattern (18 bp):
AAAAACAAAAAAAAAAAG
Found at i:98020 original size:13 final size:12
Alignment explanation
Indices: 97992--98058 Score: 75
Period size: 13 Copynumber: 5.4 Consensus size: 12
97982 ACCATCATAC
97992 AAAAACA-AAAA
1 AAAAACAGAAAA
98003 AAAAACAGAAAAA
1 AAAAACAG-AAAA
*
98016 CAAAAACAAAAAA
1 -AAAAACAGAAAA
98029 CAAAAACAGAAAGA
1 -AAAAACAGAAA-A
98043 AAAAA-AGAAAA
1 AAAAACAGAAAA
98054 AAAAA
1 AAAAA
98059 GAAAGGGAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
11 13 0.26
12 5 0.10
13 24 0.48
14 8 0.16
ACGTcount: A:0.85, C:0.09, G:0.06, T:0.00
Consensus pattern (12 bp):
AAAAACAGAAAA
Found at i:98024 original size:25 final size:26
Alignment explanation
Indices: 97990--98058 Score: 97
Period size: 27 Copynumber: 2.7 Consensus size: 26
97980 AGACCATCAT
97990 ACAAAAACAAAAAAAAAACAGAAA-A
1 ACAAAAACAAAAAAAAAACAGAAAGA
98015 ACAAAAACAAAAAACAAAAACAGAAAGA
1 ACAAAAAC-AAAAA-AAAAACAGAAAGA
*
98043 A-AAAAAGAAAAAAAAA
1 ACAAAAACAAAAAAAAA
98059 GAAAGGGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
25 12 0.30
26 10 0.25
27 16 0.40
28 2 0.05
ACGTcount: A:0.84, C:0.10, G:0.06, T:0.00
Consensus pattern (26 bp):
ACAAAAACAAAAAAAAAACAGAAAGA
Found at i:98054 original size:6 final size:6
Alignment explanation
Indices: 97990--98046 Score: 62
Period size: 6 Copynumber: 9.2 Consensus size: 6
97980 AGACCATCAT
*
97990 ACAAAA ACAAAA A-AAAA ACAGAAAA ACAAAA ACAAAAA ACAAAA ACAGAA
1 ACAAAA ACAAAA ACAAAA AC--AAAA ACAAAA AC-AAAA ACAAAA ACAAAA
*
98040 AGAAAA A
1 ACAAAA A
98047 AAGAAAAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
5 5 0.11
6 27 0.61
7 6 0.14
8 6 0.14
ACGTcount: A:0.82, C:0.12, G:0.05, T:0.00
Consensus pattern (6 bp):
ACAAAA
Found at i:98942 original size:28 final size:28
Alignment explanation
Indices: 98874--98943 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
98864 TATGGGCATA
*
98874 AAATTACCGTTTTACCCTAAGAATGAAT
1 AAATTACAGTTTTACCCTAAGAATGAAT
* **
98902 AAATTACCA-TTTTACCCTTAGAA-GGTT
1 AAATTA-CAGTTTTACCCTAAGAATGAAT
98929 AAATTTACAGTTTTA
1 AAA-TTACAGTTTTA
98944 ACTTTGTACT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
27 7 0.20
28 27 0.77
29 1 0.03
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (28 bp):
AAATTACAGTTTTACCCTAAGAATGAAT
Found at i:99443 original size:13 final size:12
Alignment explanation
Indices: 99425--99468 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 12
99415 TTTTATTACC
99425 GTTTTATTAAATT
1 GTTTTA-TAAATT
*
99438 GTTTTATAAATG
1 GTTTTATAAATT
99450 GTTTTAAATAAATT
1 GTTTT--ATAAATT
99464 GTTTT
1 GTTTT
99469 GGGTGCATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 10 0.37
13 6 0.22
14 11 0.41
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (12 bp):
GTTTTATAAATT
Done.