Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017259.1 Corchorus olitorius cultivar O-4 contig17292, 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: 50982
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:171 original size:29 final size:29
Alignment explanation
Indices: 138--225 Score: 149
Period size: 29 Copynumber: 3.0 Consensus size: 29
128 GAACTAGTAG
* * *
138 ATGACCATAATGCCCCTGAATGTGTAAAA
1 ATGACCAAAATGCCCCTGGATGTGCAAAA
167 ATGACCAAAATGCCCCTGGATGTGCAAAA
1 ATGACCAAAATGCCCCTGGATGTGCAAAA
196 ATGACCAAAATGCCCCTGGATGTGCAAAA
1 ATGACCAAAATGCCCCTGGATGTGCAAAA
225 A
1 A
226 GGTCAATTGA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (29 bp):
ATGACCAAAATGCCCCTGGATGTGCAAAA
Found at i:3857 original size:22 final size:22
Alignment explanation
Indices: 3828--3892 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
3818 TGAATATTTT
*
3828 TATGAAATTTTGATAACTACCC
1 TATGAAATTTTGATAACTACCA
*
3850 TATTAAATTTTGATAACTACCA
1 TATGAAATTTTGATAACTACCA
3872 TATGAAATTTTGATAACTACC
1 TATGAAATTTTGATAACTACC
3893 TAACAATGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACTACCA
Found at i:5687 original size:2 final size:2
Alignment explanation
Indices: 5680--5712 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5670 GTAGTTAGAA
5680 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5713 ATAGTTTGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6489 original size:27 final size:25
Alignment explanation
Indices: 6451--6511 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 25
6441 CTAAATTTTC
6451 ATTATTTTAATAATGGAATAATTAAAA
1 ATTA-TTTAATAATGGAA-AATTAAAA
*
6478 TATTATTTAATAATGGAAATTTAAAA
1 -ATTATTTAATAATGGAAAATTAAAA
6504 ATATATTT
1 AT-TATTT
6512 GAAAAAAGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 2 0.06
26 12 0.39
27 13 0.42
28 4 0.13
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (25 bp):
ATTATTTAATAATGGAAAATTAAAA
Found at i:9154 original size:28 final size:27
Alignment explanation
Indices: 9116--9172 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 27
9106 TTGTATTTTA
9116 TTTATTCTTACATCTCAT-TTAGTCTCAT
1 TTTATTCTTACAT-T-ATATTAGTCTCAT
9144 TTTATTCTTACATTATACTTAGTCTCAT
1 TTTATTCTTACATTATA-TTAGTCTCAT
9172 T
1 T
9173 AGTAATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 2 0.07
27 1 0.04
28 24 0.89
ACGTcount: A:0.23, C:0.19, G:0.04, T:0.54
Consensus pattern (27 bp):
TTTATTCTTACATTATATTAGTCTCAT
Found at i:11309 original size:15 final size:15
Alignment explanation
Indices: 11277--11328 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 15
11267 TAAAGAAATG
11277 GTAA-TTAG-TTTTA
1 GTAATTTAGATTTTA
*
11290 ATAATTTAGATTTTA
1 GTAATTTAGATTTTA
*
11305 GTAATTT-CATTTTA
1 GTAATTTAGATTTTA
*
11319 GAAATTTAGA
1 GTAATTTAGA
11329 GTTAATTTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
13 3 0.10
14 16 0.52
15 12 0.39
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.50
Consensus pattern (15 bp):
GTAATTTAGATTTTA
Found at i:13498 original size:26 final size:25
Alignment explanation
Indices: 13459--13524 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
13449 AAAAGTATTG
*
13459 TTTTGATCAATTTTTGCA-CTAGGGGAA
1 TTTTGGTC-ATTTTTGCATC-A-GGGAA
* * *
13486 TTTTGGTCATTTTCGTATCAGGGCA
1 TTTTGGTCATTTTTGCATCAGGGAA
13511 TTTTGGTCATTTTT
1 TTTTGGTCATTTTT
13525 CAGCCCATGG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
25 17 0.52
26 8 0.24
27 8 0.24
ACGTcount: A:0.18, C:0.12, G:0.21, T:0.48
Consensus pattern (25 bp):
TTTTGGTCATTTTTGCATCAGGGAA
Found at i:15457 original size:13 final size:13
Alignment explanation
Indices: 15439--15472 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
15429 CTCAAAAACA
15439 GGGTAAAAGATGT
1 GGGTAAAAGATGT
15452 GGGTAAAAGATGT
1 GGGTAAAAGATGT
15465 GGGTAAAA
1 GGGTAAAA
15473 TTACAGTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.38, T:0.21
Consensus pattern (13 bp):
GGGTAAAAGATGT
Found at i:17514 original size:19 final size:18
Alignment explanation
Indices: 17481--17516 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
17471 TTGAAATAAT
17481 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
17499 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
17517 TGCGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:17826 original size:15 final size:16
Alignment explanation
Indices: 17808--17837 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17798 AATGTGTAAG
17808 TCAAAA-ATCAATTTT
1 TCAAAAGATCAATTTT
17823 TCAAAAGATCAATTT
1 TCAAAAGATCAATTT
17838 GAATTCATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (16 bp):
TCAAAAGATCAATTTT
Found at i:19039 original size:23 final size:23
Alignment explanation
Indices: 19013--19058 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
19003 AATTAAACTT
19013 GGAAAA-TAAAGACATAAAATAAA
1 GGAAAATTAAA-ACATAAAATAAA
*
19036 GGAAAATTAAAACATAAACTAAA
1 GGAAAATTAAAACATAAAATAAA
19059 TAACTAATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.67, C:0.07, G:0.11, T:0.15
Consensus pattern (23 bp):
GGAAAATTAAAACATAAAATAAA
Found at i:26199 original size:158 final size:158
Alignment explanation
Indices: 25794--26187 Score: 673
Period size: 158 Copynumber: 2.5 Consensus size: 158
25784 TTATTAATTG
*
25794 CCCGGAGGTTTCTGAATTTGTGCCCGGAGGTCTTACCAATGTAAACTCTAAATAGAGACCTTGAC
1 CCCGGAGGTTTCTGAATTTGTGCCCGGAGGTCTTACCAATGTAAACTTTAAATAGAGACCTTGAC
*
25859 CAAGGATTTTAAACTTTTTAATGAAAATCATGATGAAATGAAATGTCAGCCGGAGGTTTTATTAA
66 CAAGGATTTTAAACTTTTTAATGAAAATCATGATGAAATGAAATGTCACCCGGAGGTTTTATTAA
25924 TTGCCTGGAGGACTTATCAGAATTAATA
131 TTGCCTGGAGGACTTATCAGAATTAATA
* * * *
25952 CCCGGAGGTTTTTGAATTTGTGCCCGGAGGTCTTACCAATGTGAACTTTTAATAGAGAACTTGAC
1 CCCGGAGGTTTCTGAATTTGTGCCCGGAGGTCTTACCAATGTAAACTTTAAATAGAGACCTTGAC
26017 CAAGGATTTTAAACTTTTTAATGAAAATCATGATGAAATGAAATGAT-ACCCGGAGGTTTTATTA
66 CAAGGATTTTAAACTTTTTAATGAAAATCATGATGAAATGAAATG-TCACCCGGAGGTTTTATTA
26081 ATTGCCTGGAGGACTTATCAGAATTAATA
130 ATTGCCTGGAGGACTTATCAGAATTAATA
* * * * *
26110 CCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAATGCAAACTTTGAATTGAGACCTTGAA
1 CCCGGAGGTTTCTGAATTTGTGCCCGGAGGTCTTACCAATGTAAACTTTAAATAGAGACCTTGAC
26175 CAAGGATTTTAAA
66 CAAGGATTTTAAA
26188 TTTAAACATG
Statistics
Matches: 221, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
158 220 1.00
159 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (158 bp):
CCCGGAGGTTTCTGAATTTGTGCCCGGAGGTCTTACCAATGTAAACTTTAAATAGAGACCTTGAC
CAAGGATTTTAAACTTTTTAATGAAAATCATGATGAAATGAAATGTCACCCGGAGGTTTTATTAA
TTGCCTGGAGGACTTATCAGAATTAATA
Found at i:26499 original size:69 final size:69
Alignment explanation
Indices: 26426--26811 Score: 535
Period size: 69 Copynumber: 5.6 Consensus size: 69
26416 CCAGTGTTTA
* * * * ** *
26426 AACTGACTCGCATGGAAACGAGTTTGACCTATGGAAAAATCTATATGGCTTGGATGGAACCAAGG
1 AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGG
*
26491 TTTG
66 CTTG
*
26495 AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTTTGTGGCTTGGATGGAACCAAGG
1 AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGG
26560 CTTG
66 CTTG
* *
26564 AACTGACTCATATGGAAATGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGG
1 AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGG
*
26629 CTTA
66 CTTG
** * *
26633 AACTGACTCACATGGAAACGAGTTTCGCTTGTGGCAAAGCCTATGTGGCTTGGATGGAACCAAGG
1 AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGG
26698 CTTG
66 CTTG
* * * *
26702 AAGTGACTCGTATGGAAACGAGTTTGGCTTGTTGAAAAGCCCACGTGGCTTGG--GCGAACCCAA
1 AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATG-GAA-CCAA
*
26765 GGCGT-
64 GGCTTG
26770 AAGCTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
1 AA-CTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
26812 AAAGTATTCG
Statistics
Matches: 285, Mismatches: 29, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
67 1 0.00
68 5 0.02
69 279 0.98
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.25
Consensus pattern (69 bp):
AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGG
CTTG
Found at i:26549 original size:138 final size:137
Alignment explanation
Indices: 26380--26811 Score: 541
Period size: 138 Copynumber: 3.1 Consensus size: 137
26370 CTCATTAAAC
* * * * *
26380 TTGGCTTATGGAAAAGCCTTTGCT-G-TATGGATCGAACC-AGTGTTTAAACTGACTCGCATGGA
1 TTGGCTTGTGGAAAAGCCTTTG-TGGCT-TGGATGGAACCAAG-GCTTGAACTGACTCGTATGGA
* * * ** * *
26442 AACGAGTTTGACCTATGGAAAAATCTATATGGCTTGGATGGAACCAAGGTTTGAACTGACTCGTA
63 AACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTT-AACTGACTCGTA
26507 TGGAAACGAGT
127 TGGAAACGAGT
* *
26518 TTGGCTTGTGGAAAAGCCTTTGTGGCTTGGATGGAACCAAGGCTTGAACTGACTCATATGGAAAT
1 TTGGCTTGTGGAAAAGCCTTTGTGGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
**
26583 GAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCACATGG
66 GAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTT-AACTGACTCGTATGG
26648 AAACGAGT
130 AAACGAGT
* * * *
26656 TTCGCTTGTGGCAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTGAAGTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTTTGTGGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
* * * *
26721 GAGTTTGGCTTGTTGAAAAGCCCACGTGGCTTGG--GCGAACCCAAGGCGTAAGCTGACTCGTAT
66 GAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATG-GAA-CCAAGGCTTAA-CTGACTCGTAT
26784 GGAAACGAGT
128 GGAAACGAGT
26794 TTGGCTTGTGGAAAAGCC
1 TTGGCTTGTGGAAAAGCC
26812 AAAGTATTCG
Statistics
Matches: 257, Mismatches: 31, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
136 1 0.00
137 6 0.02
138 247 0.96
139 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.26
Consensus pattern (137 bp):
TTGGCTTGTGGAAAAGCCTTTGTGGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
GAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAACTGACTCGTATGGA
AACGAGT
Found at i:26741 original size:207 final size:207
Alignment explanation
Indices: 26380--26811 Score: 572
Period size: 207 Copynumber: 2.1 Consensus size: 207
26370 CTCATTAAAC
* * * *
26380 TTGGCTTATGGAAAAGCCTTTGCTGTATGGATCGAACCAGTGTTTAAACTGACTCGCATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGCTGTATGGATCGAACCAGTGCTTAAACTGACTCACATGGAAAC
* *
26445 GAGTTTGACCTATGGAAAAATCTATATGGCTTGGATGGAACCAAGGTTTGAACTGACTCGTATGG
66 GAGTTTGACCTATGGAAAAACCTATATGGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGG
*** *
26510 AAACGAGTTTGGCTTGTGGAAAAGCCTTTGTGGCTTGGATG-GAA-CCAAGGCTTGAA-CTGACT
131 AAACGAGTTTGGCTTGTGGAAAAGCCCACGTGGCTTGG--GCGAACCCAAGGCGT-AAGCTGACT
*
26572 CATATGGAAATGAGT
193 CATATGGAAACGAGT
*
26587 TTGGCTTGTGGAAAAGCCTATG-TGGCT-TGGATGGAACCAAG-GCTTAAACTGACTCACATGGA
1 TTGGCTTGTGGAAAAGCCTATGCT-G-TATGGATCGAACC-AGTGCTTAAACTGACTCACATGGA
* * * * * *
26649 AACGAGTTTCG-CTTGTGGCAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTGAAGTGACTCGT
63 AACGAGTTT-GACCTATGGAAAAACCTATATGGCTTGGATGGAACCAAGGCTTGAACTGACTCGT
*
26713 ATGGAAACGAGTTTGGCTTGTTGAAAAGCCCACGTGGCTTGGGCGAACCCAAGGCGTAAGCTGAC
127 ATGGAAACGAGTTTGGCTTGTGGAAAAGCCCACGTGGCTTGGGCGAACCCAAGGCGTAAGCTGAC
*
26778 TCGTATGGAAACGAGT
192 TCATATGGAAACGAGT
26794 TTGGCTTGTGGAAAAGCC
1 TTGGCTTGTGGAAAAGCC
26812 AAAGTATTCG
Statistics
Matches: 198, Mismatches: 20, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
205 1 0.01
206 6 0.03
207 187 0.94
208 4 0.02
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.26
Consensus pattern (207 bp):
TTGGCTTGTGGAAAAGCCTATGCTGTATGGATCGAACCAGTGCTTAAACTGACTCACATGGAAAC
GAGTTTGACCTATGGAAAAACCTATATGGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGG
AAACGAGTTTGGCTTGTGGAAAAGCCCACGTGGCTTGGGCGAACCCAAGGCGTAAGCTGACTCAT
ATGGAAACGAGT
Found at i:26830 original size:69 final size:69
Alignment explanation
Indices: 26380--26811 Score: 479
Period size: 69 Copynumber: 6.3 Consensus size: 69
26370 CTCATTAAAC
* * * * * *
26380 TTGGCTTATGGAAAAGCCTTTGCTG-TATGGATCGAACC-AGTG-TTTAAACTGACTCGCATGGA
1 TTGGCTTGTGGAAAAGCCTATG-TGCT-TGGATGGAACCAAG-GCTTGAAGCTGACTCGTATGGA
26442 AACGAGT
63 AACGAGT
* * * ** * *
26449 TTGACCTATGGAAAAATCTATATGGCTTGGATGGAACCAAGGTTTGAA-CTGACTCGTATGGAAA
1 TTGGCTTGTGGAAAAGCCTATGT-GCTTGGATGGAACCAAGGCTTGAAGCTGACTCGTATGGAAA
26513 CGAGT
65 CGAGT
* *
26518 TTGGCTTGTGGAAAAGCCTTTGTGGCTTGGATGGAACCAAGGCTTGAA-CTGACTCATATGGAAA
1 TTGGCTTGTGGAAAAGCCTATGT-GCTTGGATGGAACCAAGGCTTGAAGCTGACTCGTATGGAAA
*
26582 TGAGT
65 CGAGT
* **
26587 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTT-AAACTGACTCACATGGAAA
1 TTGGCTTGTGGAAAAGCCTATGT-GCTTGGATGGAACCAAGGCTTGAAGCTGACTCGTATGGAAA
26651 CGAGT
65 CGAGT
* *
26656 TTCGCTTGTGGCAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTGAAG-TGACTCGTATGGAAA
1 TTGGCTTGTGGAAAAGCCTATGT-GCTTGGATGGAACCAAGGCTTGAAGCTGACTCGTATGGAAA
26720 CGAGT
65 CGAGT
* * * *
26725 TTGGCTTGTTGAAAAGCCCACGTGGCTTGG--GCGAACCCAAGGCGT-AAGCTGACTCGTATGGA
1 TTGGCTTGTGGAAAAGCCTATGT-GCTTGGATG-GAA-CCAAGGCTTGAAGCTGACTCGTATGGA
26787 AACGAGT
63 AACGAGT
26794 TTGGCTTGTGGAAAAGCC
1 TTGGCTTGTGGAAAAGCC
26812 AAAGTATTCG
Statistics
Matches: 320, Mismatches: 34, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
67 1 0.00
68 9 0.03
69 301 0.94
70 9 0.03
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.26
Consensus pattern (69 bp):
TTGGCTTGTGGAAAAGCCTATGTGCTTGGATGGAACCAAGGCTTGAAGCTGACTCGTATGGAAAC
GAGT
Found at i:28074 original size:7 final size:7
Alignment explanation
Indices: 28056--28098 Score: 50
Period size: 8 Copynumber: 5.7 Consensus size: 7
28046 ATTCTTTCCC
28056 TTTTTCT
1 TTTTTCT
28063 CTTTTTCT
1 -TTTTTCT
28071 TTTTTCTT
1 TTTTTC-T
*
28079 TTTTTCA
1 TTTTTCT
28086 TTTTTCAT
1 TTTTTC-T
28094 TTTTT
1 TTTTT
28099 TGTGCACTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 12 0.39
8 19 0.61
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTCT
Found at i:28076 original size:15 final size:15
Alignment explanation
Indices: 28056--28091 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
28046 ATTCTTTCCC
*
28056 TTTTTCTCTTTTTCT
1 TTTTTCTCTTTTTCA
*
28071 TTTTTCTTTTTTTCA
1 TTTTTCTCTTTTTCA
28086 TTTTTC
1 TTTTTC
28092 ATTTTTTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTCTCTTTTTCA
Found at i:28096 original size:15 final size:15
Alignment explanation
Indices: 28064--28098 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28054 CCTTTTTCTC
* *
28064 TTTTTCTTTTTTCTT
1 TTTTTCATTTTTCAT
28079 TTTTTCATTTTTCAT
1 TTTTTCATTTTTCAT
28094 TTTTT
1 TTTTT
28099 TGTGCACTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTCATTTTTCAT
Found at i:28416 original size:22 final size:23
Alignment explanation
Indices: 28385--28429 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
28375 TCCATCAATC
28385 AATTCTTTTTCGA-TTTTGATTTT
1 AATTCTTTTT-GATTTTTGATTTT
28408 AATT-TTTTTGATTTTTGATTTT
1 AATTCTTTTTGATTTTTGATTTT
28430 TTTATGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 2 0.10
22 15 0.71
23 4 0.19
ACGTcount: A:0.18, C:0.04, G:0.09, T:0.69
Consensus pattern (23 bp):
AATTCTTTTTGATTTTTGATTTT
Found at i:28418 original size:15 final size:16
Alignment explanation
Indices: 28398--28432 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28388 TCTTTTTCGA
28398 TTTTGA-TTTTAATTT
1 TTTTGATTTTTAATTT
*
28413 TTTTGATTTTTGATTT
1 TTTTGATTTTTAATTT
28429 TTTT
1 TTTT
28433 ATGCTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.14, C:0.00, G:0.09, T:0.77
Consensus pattern (16 bp):
TTTTGATTTTTAATTT
Found at i:28479 original size:38 final size:37
Alignment explanation
Indices: 28386--28481 Score: 99
Period size: 38 Copynumber: 2.5 Consensus size: 37
28376 CCATCAATCA
**
28386 ATTCTTTTTCGATTTTGATTTTAATTTTTTTGATTTTT
1 ATTCTTTTT-GATTTTTTTTTTAATTTTTTTGATTTTT
28424 GATT-TTTTT-ATGCTTTTTTTTTAATTTTTGATTGATTTTT
1 -ATTCTTTTTGAT--TTTTTTTTTAATTTTT--TTGATTTTT
28464 -TTCTTTTTGATTTTTTTT
1 ATTCTTTTTGATTTTTTTT
28482 GTTTTGGAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
36 2 0.04
38 28 0.57
39 8 0.16
40 11 0.22
ACGTcount: A:0.14, C:0.04, G:0.08, T:0.74
Consensus pattern (37 bp):
ATTCTTTTTGATTTTTTTTTTAATTTTTTTGATTTTT
Found at i:28481 original size:19 final size:19
Alignment explanation
Indices: 28437--28481 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
28427 TTTTTTATGC
28437 TTTTTTTTTAATTTTTGAT
1 TTTTTTTTTAATTTTTGAT
* *
28456 TGATTTTTTT-CTTTTTGAT
1 T-TTTTTTTTAATTTTTGAT
28475 TTTTTTT
1 TTTTTTT
28482 GTTTTGGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 5 0.23
19 10 0.45
20 7 0.32
ACGTcount: A:0.11, C:0.02, G:0.07, T:0.80
Consensus pattern (19 bp):
TTTTTTTTTAATTTTTGAT
Found at i:28916 original size:7 final size:7
Alignment explanation
Indices: 28848--28908 Score: 113
Period size: 7 Copynumber: 8.6 Consensus size: 7
28838 AGTGCCTTTA
28848 TTTTCAT
1 TTTTCAT
28855 TTTTCAT
1 TTTTCAT
28862 TTTTCAT
1 TTTTCAT
28869 TTTTCAT
1 TTTTCAT
28876 TTTTCAT
1 TTTTCAT
28883 TTTTCAT
1 TTTTCAT
28890 TTTTCATT
1 TTTTCA-T
28898 TTTTCAT
1 TTTTCAT
28905 TTTT
1 TTTT
28909 TTATTTTTAT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
7 46 0.87
8 7 0.13
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTCAT
Found at i:30913 original size:15 final size:15
Alignment explanation
Indices: 30895--30954 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
30885 CGCCAATGAT
*
30895 GTTTCCACCTATGGC
1 GTTTCCACCTATGCC
* *
30910 GTTTCAACCTTTGCC
1 GTTTCCACCTATGCC
* * *
30925 GTATCCGCGTATGCC
1 GTTTCCACCTATGCC
*
30940 GTTGCCACCTATGCC
1 GTTTCCACCTATGCC
30955 ATACCAACCC
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.13, C:0.35, G:0.20, T:0.32
Consensus pattern (15 bp):
GTTTCCACCTATGCC
Found at i:35819 original size:9 final size:8
Alignment explanation
Indices: 35771--35817 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
35761 TGATTTTCTG
*
35771 ATTTTTCC
1 ATTTTTTC
35779 ATTTTTTTC
1 A-TTTTTTC
35788 ATTTTTTC
1 ATTTTTTC
* *
35796 CTTTCTTC
1 ATTTTTTC
35804 -TTTTTTC
1 ATTTTTTC
35811 ATTTTTT
1 ATTTTTT
35818 TCTTCAACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 6 0.18
8 20 0.61
9 7 0.21
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (8 bp):
ATTTTTTC
Found at i:35828 original size:22 final size:23
Alignment explanation
Indices: 35781--35828 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
35771 ATTTTTCCAT
**
35781 TTTTTTCATTTTTTCCTTTCTTC
1 TTTTTTCATTTTTTCCTTTCAAC
*
35804 TTTTTTCATTTTTTTC-TTCAAC
1 TTTTTTCATTTTTTCCTTTCAAC
35826 TTT
1 TTT
35829 GACCTAAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTTTCATTTTTTCCTTTCAAC
Found at i:42583 original size:12 final size:12
Alignment explanation
Indices: 42566--42602 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
42556 TAAAATTAAC
42566 TAAGAAAACAAT
1 TAAGAAAACAAT
42578 TAAGAAAAC--T
1 TAAGAAAACAAT
*
42588 AAAGAAAACAAT
1 TAAGAAAACAAT
42600 TAA
1 TAA
42603 TCAGAAAGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
10 9 0.43
12 12 0.57
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (12 bp):
TAAGAAAACAAT
Found at i:44945 original size:15 final size:15
Alignment explanation
Indices: 44927--44985 Score: 63
Period size: 15 Copynumber: 4.1 Consensus size: 15
44917 TCGAAATTTT
44927 ATTTTTCAAAAATCA
1 ATTTTTCAAAAATCA
44942 ATTTTTCCAAAAA--A
1 ATTTTT-CAAAAATCA
*
44956 A-TTATCAAAAATC-
1 ATTTTTCAAAAATCA
44969 ATATTTTCAAAAATCA
1 AT-TTTTCAAAAATCA
44985 A
1 A
44986 GGGAATAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
12 6 0.17
13 4 0.11
14 2 0.06
15 17 0.47
16 7 0.19
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.36
Consensus pattern (15 bp):
ATTTTTCAAAAATCA
Found at i:47525 original size:52 final size:52
Alignment explanation
Indices: 47439--47668 Score: 299
Period size: 52 Copynumber: 4.4 Consensus size: 52
47429 ATTTCCCAAT
* * *
47439 TTAAAAACTTTGAAAATTGAATGGGAACTTTCCCAATTTGAAAATCG-GCTAAA
1 TTAAATACTTTGAAAACTG-ATGGGAACTTTCCCAACTTGAAAA-CGAGCTAAA
47492 TTAAATACTTTGAAAACTGATGGGAACTTTCCCAA-TATGAAAACCG-GCTAAA
1 TTAAATACTTTGAAAACTGATGGGAACTTTCCCAACT-TGAAAA-CGAGCTAAA
*
47544 TTAAATACTTTGAAAACTGATGAGAACTTTCCCAACTTGAAAA-GAGCTAAA
1 TTAAATACTTTGAAAACTGATGGGAACTTTCCCAACTTGAAAACGAGCTAAA
* * * *
47595 TTGAATACTTTGGAAAA-TTATGGGAACTTTCCCAACTTGAAAAAGAGCGAAA
1 TTAAATACTTT-GAAAACTGATGGGAACTTTCCCAACTTGAAAACGAGCTAAA
*
47647 TTGAATACTTTGAAAACTGATG
1 TTAAATACTTTGAAAACTGATG
47669 AAATTCTTTT
Statistics
Matches: 162, Mismatches: 9, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
50 1 0.01
51 46 0.28
52 97 0.60
53 18 0.11
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (52 bp):
TTAAATACTTTGAAAACTGATGGGAACTTTCCCAACTTGAAAACGAGCTAAA
Found at i:47620 original size:103 final size:103
Alignment explanation
Indices: 47439--47669 Score: 299
Period size: 103 Copynumber: 2.2 Consensus size: 103
47429 ATTTCCCAAT
* * * *
47439 TTAAAAACTTTGAAAATTGAATGGGAACTTTCCCAATTTGAAAATCGGCTAAATTAAATACTTTG
1 TTAAATACTTTGAAAACTG-ATGAGAACTTTCCCAACTTGAAAA-CGGCTAAATTAAATACTTTG
* *
47504 AAAACTGATGGGAACTTTCCCAA-TATGAAAACCG-GCTAAA
64 AAAACTGATGGGAACTTTCCCAACT-TGAAAA-AGAGCGAAA
*
47544 TTAAATACTTTGAAAACTGATGAGAACTTTCCCAACTTGAAAA-GAGCTAAATTGAATACTTTGG
1 TTAAATACTTTGAAAACTGATGAGAACTTTCCCAACTTGAAAACG-GCTAAATTAAATACTTT-G
*
47608 AAAA-TTATGGGAACTTTCCCAACTTGAAAAAGAGCGAAA
64 AAAACTGATGGGAACTTTCCCAACTTGAAAAAGAGCGAAA
*
47647 TTGAATACTTTGAAAACTGATGA
1 TTAAATACTTTGAAAACTGATGA
47670 AATTCTTTTT
Statistics
Matches: 113, Mismatches: 9, Indels: 10
0.86 0.07 0.08
Matches are distributed among these distances:
102 2 0.02
103 66 0.58
104 28 0.25
105 17 0.15
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (103 bp):
TTAAATACTTTGAAAACTGATGAGAACTTTCCCAACTTGAAAACGGCTAAATTAAATACTTTGAA
AACTGATGGGAACTTTCCCAACTTGAAAAAGAGCGAAA
Done.