Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008924.1 Corchorus capsularis cultivar CVL-1 contig08945, 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: 40177
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:4698 original size:6 final size:6
Alignment explanation
Indices: 4687--4713 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4677 TTAATTTTGC
4687 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
4714 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:5375 original size:32 final size:31
Alignment explanation
Indices: 5310--5375 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
5300 AGTAAATTGA
*
5310 TAATTAAGAGTCAAGGTAAGAGATTAATCAG
1 TAATTAAGAGTCAAGGTAAGAAATTAATCAG
5341 TAATTAAGAGTCAAGGTAA-AAATAGTAATCAG
1 TAATTAAGAGTCAAGGTAAGAAAT--TAATCAG
5373 TAA
1 TAA
5376 ATCAGTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 3 0.09
31 19 0.59
32 10 0.31
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (31 bp):
TAATTAAGAGTCAAGGTAAGAAATTAATCAG
Found at i:5495 original size:14 final size:14
Alignment explanation
Indices: 5458--5497 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
5448 AATGGTAAAG
*
5458 AGTAAAGAATAATC
1 AGTAAAGAGTAATC
* *
5472 AGTAAGGAGTAATT
1 AGTAAAGAGTAATC
5486 AGTAAAGAGTAA
1 AGTAAAGAGTAA
5498 AATGATAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.53, C:0.03, G:0.23, T:0.23
Consensus pattern (14 bp):
AGTAAAGAGTAATC
Found at i:5552 original size:35 final size:35
Alignment explanation
Indices: 5472--5599 Score: 159
Period size: 35 Copynumber: 3.6 Consensus size: 35
5462 AAGAATAATC
* * *
5472 AGTAAGGAGTAATTAGTAAAGAGTAA-AATGATAAAA
1 AGTAAAGAGTAATCAGTAAA-AG-AAGAATGGTAAAA
*
5508 AGTATAGAGTAATCAGTAAAAGAAGAATGGTAAAA
1 AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
* *
5543 AGTAAAGAGTAATCAGTAAAGGAAGAATGGTAAAG
1 AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
*
5578 AGTAAAAGGGTAATCAGTAAAA
1 AGT-AAAGAGTAATCAGTAAAA
5600 AGTAAAAAGA
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
34 2 0.02
35 46 0.57
36 33 0.41
ACGTcount: A:0.54, C:0.02, G:0.24, T:0.20
Consensus pattern (35 bp):
AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
Found at i:5597 original size:22 final size:22
Alignment explanation
Indices: 5572--5784 Score: 132
Period size: 22 Copynumber: 9.5 Consensus size: 22
5562 AGGAAGAATG
*
5572 GTAAAGAGTAAAAGGGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
* * *
5594 GTAAAAAGTAAAAAGATAATCA
1 GTAAAGAGTAAAATGGTAATCA
*
5616 GTAAAGAATGAAATAGTAGAAGGTAATCA
1 GTAAAGAGT-AAA-A-T----GGTAATCA
* * * *
5645 ATAAAAAGT--AATGATAATTA
1 GTAAAGAGTAAAATGGTAATCA
**
5665 GTAAA-AGGTAAAATATTAATCA
1 GTAAAGA-GTAAAATGGTAATCA
*
5687 GT-AAGAGCAAAATGGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
* * *
5708 AT-GAGAGCAAAATGGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
* *
5729 GTAAAGAGTAAAATAGTAATCG
1 GTAAAGAGTAAAATGGTAATCA
* *
5751 GTAAAAAGTAAGAA-GGTAATCG
1 GTAAAGAGTAA-AATGGTAATCA
5773 GTAAAGAGTAAA
1 GTAAAGAGTAAA
5785 GTAGTGATCA
Statistics
Matches: 149, Mismatches: 29, Indels: 27
0.73 0.14 0.13
Matches are distributed among these distances:
19 1 0.01
20 12 0.08
21 35 0.23
22 79 0.53
23 5 0.03
24 2 0.01
25 1 0.01
26 1 0.01
29 13 0.09
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (22 bp):
GTAAAGAGTAAAATGGTAATCA
Found at i:5604 original size:85 final size:85
Alignment explanation
Indices: 5419--5604 Score: 214
Period size: 85 Copynumber: 2.2 Consensus size: 85
5409 CTAAAGGGAG
* * *
5419 AAAGTAAAATTAGTGATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAATAATCAGTAAGGAGTAA
1 AAAGTAAAA--AGTAATCAGTAAAAGAAAAATGGTAAAAAGTAAAGAATAATCAGTAAGGAGTAA
*
5484 TTAGTAAAGAGTAAAATGATAA
64 TTAGTAAAGAGTAAAAGGATAA
* * * *
5506 AAAGTATAGAGTAATCAGTAAAAGAAGAATGGTAAAAAGTAAAGAGTAATCAGTAAAGGAAG-AA
1 AAAGTAAAAAGTAATCAGTAAAAGAAAAATGGTAAAAAGTAAAGAATAATCAGT-AAGG-AGTAA
* *
5570 -TGGTAAAGAGTAAAAGGGTAA
64 TTAGTAAAGAGTAAAAGGATAA
**
5591 TCAGTAAAAAGTAA
1 AAAGTAAAAAGTAA
5605 AAAGATAATC
Statistics
Matches: 83, Mismatches: 14, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
85 68 0.82
86 6 0.07
87 9 0.11
ACGTcount: A:0.54, C:0.03, G:0.23, T:0.20
Consensus pattern (85 bp):
AAAGTAAAAAGTAATCAGTAAAAGAAAAATGGTAAAAAGTAAAGAATAATCAGTAAGGAGTAATT
AGTAAAGAGTAAAAGGATAA
Found at i:5705 original size:21 final size:21
Alignment explanation
Indices: 5681--5754 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
5671 GGTAAAATAT
5681 TAATCAGTAAGAGCAAAATGG
1 TAATCAGTAAGAGCAAAATGG
* *
5702 TAATCAATGAGAGCAAAATGG
1 TAATCAGTAAGAGCAAAATGG
* *
5723 TAATCAGTAAAGAGTAAAATAG
1 TAATCAGT-AAGAGCAAAATGG
*
5745 TAATCGGTAA
1 TAATCAGTAA
5755 AAAGTAAGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 28 0.62
22 17 0.38
ACGTcount: A:0.49, C:0.08, G:0.22, T:0.22
Consensus pattern (21 bp):
TAATCAGTAAGAGCAAAATGG
Found at i:5803 original size:36 final size:35
Alignment explanation
Indices: 5763--5943 Score: 166
Period size: 36 Copynumber: 4.9 Consensus size: 35
5753 AAAAAGTAAG
* * *
5763 AAGGTAATCGGTAAAGAGTAAAGTAGTGATCAGCAA
1 AAGGTAATCAGT-AAGAGTAAAATAGTAATCAGCAA
*
5799 AAGGTAATCAGTAAGAGTAAAATAGTAATCAGTC-G
1 AAGGTAATCAGTAAGAGTAAAATAGTAATCAG-CAA
* *
5834 AAGGTAATCAGTAAAGAGTAAAATACTAATCAGTAA
1 AAGGTAATCAGT-AAGAGTAAAATAGTAATCAGCAA
* * *
5870 AAGATAATCAGTAAGAGTAAAACAGTAACCAGTAAGAACAA
1 AAGGTAATCAGTAAGAGTAAAATAGT-A--A-TCAG--CAA
* *
5911 AGTGGTAATTAGTAAGAGTAAAATAGTAATCAG
1 A-AGGTAATCAGTAAGAGTAAAATAGTAATCAG
5944 TAAAGAGTAA
Statistics
Matches: 118, Mismatches: 17, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
35 42 0.36
36 43 0.36
38 4 0.03
39 4 0.03
41 4 0.03
42 21 0.18
ACGTcount: A:0.49, C:0.08, G:0.22, T:0.21
Consensus pattern (35 bp):
AAGGTAATCAGTAAGAGTAAAATAGTAATCAGCAA
Found at i:5819 original size:35 final size:36
Alignment explanation
Indices: 5763--5897 Score: 168
Period size: 35 Copynumber: 3.8 Consensus size: 36
5753 AAAAAGTAAG
* * *
5763 AAGGTAATCGGTAAAGAGTAAAGTAGTGATCAGCAA
1 AAGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAA
*
5799 AAGGTAATCAGT-AAGAGTAAAATAGTAATCAGTC-G
1 AAGGTAATCAGTAAAGAGTAAAATAGTAATCAG-CAA
* *
5834 AAGGTAATCAGTAAAGAGTAAAATACTAATCAGTAA
1 AAGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAA
* *
5870 AAGATAATCAGT-AAGAGTAAAACAGTAA
1 AAGGTAATCAGTAAAGAGTAAAATAGTAA
5898 CCAGTAAGAA
Statistics
Matches: 86, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
35 44 0.51
36 42 0.49
ACGTcount: A:0.50, C:0.08, G:0.21, T:0.21
Consensus pattern (36 bp):
AAGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAA
Found at i:5879 original size:14 final size:15
Alignment explanation
Indices: 5850--5883 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5840 ATCAGTAAAG
*
5850 AGTAAAATACTAATC
1 AGTAAAAGACTAATC
5865 AGTAAAAGA-TAATC
1 AGTAAAAGACTAATC
5879 AGTAA
1 AGTAA
5884 GAGTAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.24
Consensus pattern (15 bp):
AGTAAAAGACTAATC
Found at i:5890 original size:71 final size:71
Alignment explanation
Indices: 5762--5902 Score: 210
Period size: 71 Copynumber: 2.0 Consensus size: 71
5752 TAAAAAGTAA
* * * * * *
5762 GAAGGTAATCGGTAAAGAGTAAAGTAGTGATCAGCAAAAGGTAATCAGTAAGAGTAAAATAGTAA
1 GAAGGTAATCAGTAAAGAGTAAAATACTAATCAGCAAAAGATAATCAGTAAGAGTAAAACAGTAA
*
5827 TCAGTC
66 CCAGTC
*
5833 GAAGGTAATCAGTAAAGAGTAAAATACTAATCAGTAAAAGATAATCAGTAAGAGTAAAACAGTAA
1 GAAGGTAATCAGTAAAGAGTAAAATACTAATCAGCAAAAGATAATCAGTAAGAGTAAAACAGTAA
5898 CCAGT
66 CCAGT
5903 AAGAACAAAG
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
71 62 1.00
ACGTcount: A:0.48, C:0.09, G:0.22, T:0.21
Consensus pattern (71 bp):
GAAGGTAATCAGTAAAGAGTAAAATACTAATCAGCAAAAGATAATCAGTAAGAGTAAAACAGTAA
CCAGTC
Found at i:5904 original size:21 final size:21
Alignment explanation
Indices: 5865--5955 Score: 94
Period size: 21 Copynumber: 4.3 Consensus size: 21
5855 AATACTAATC
*
5865 AGTAAAAGA-TAATCAGTAAG
1 AGTAAAATAGTAATCAGTAAG
* *
5885 AGTAAAACAGTAACCAGTAAG
1 AGTAAAATAGTAATCAGTAAG
** * * *
5906 AACAAAGTGGTAATTAGTAAG
1 AGTAAAATAGTAATCAGTAAG
5927 AGTAAAATAGTAATCAGTAAAG
1 AGTAAAATAGTAATCAGT-AAG
5949 AGTAAAA
1 AGTAAAA
5956 GGTGATCAGT
Statistics
Matches: 55, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 8 0.15
21 37 0.67
22 10 0.18
ACGTcount: A:0.54, C:0.07, G:0.20, T:0.20
Consensus pattern (21 bp):
AGTAAAATAGTAATCAGTAAG
Found at i:5967 original size:42 final size:41
Alignment explanation
Indices: 5865--5967 Score: 116
Period size: 42 Copynumber: 2.5 Consensus size: 41
5855 AATACTAATC
*
5865 AGTAAAAGATAATCAGTAAGAGTAAAACAGTAACCAGTAAG
1 AGTAAAAGGTAATCAGTAAGAGTAAAACAGTAACCAGTAAG
** * * * *
5906 AACAAAGTGGTAATTAGTAAGAGTAAAATAGTAATCAGTAAAG
1 AGTAAA-AGGTAATCAGTAAGAGTAAAACAGTAACCAGT-AAG
*
5949 AGTAAAAGGTGATCAGTAA
1 AGTAAAAGGTAATCAGTAA
5968 TTCAAAAGAG
Statistics
Matches: 48, Mismatches: 12, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
41 4 0.08
42 37 0.77
43 7 0.15
ACGTcount: A:0.51, C:0.07, G:0.21, T:0.20
Consensus pattern (41 bp):
AGTAAAAGGTAATCAGTAAGAGTAAAACAGTAACCAGTAAG
Found at i:6088 original size:29 final size:29
Alignment explanation
Indices: 6027--6090 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 29
6017 GTGGTGATAA
* **
6027 ATAAAAGAGGGTAAGAAAAGAGTAATTAG
1 ATAAAAGAGAGTAAGAAAAGAGTAAAAAG
6056 -TAAAA-AGAGTAAGAAAAGAGTAAAAATG
1 ATAAAAGAGAGTAAGAAAAGAGTAAAAA-G
6084 ATAAAAG
1 ATAAAAG
6091 TAGCAAAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 18 0.62
28 6 0.21
29 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.23, T:0.16
Consensus pattern (29 bp):
ATAAAAGAGAGTAAGAAAAGAGTAAAAAG
Found at i:18764 original size:19 final size:21
Alignment explanation
Indices: 18728--18769 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
18718 TTTCTTCTAT
18728 TTTAATTACTTGCAA-TTTAG
1 TTTAATTACTTGCAATTTTAG
*
18748 TTTAATTA-TTTCAATTTTAG
1 TTTAATTACTTGCAATTTTAG
18768 TT
1 TT
18770 CATAGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTAATTACTTGCAATTTTAG
Found at i:18785 original size:53 final size:53
Alignment explanation
Indices: 18727--18888 Score: 126
Period size: 53 Copynumber: 3.2 Consensus size: 53
18717 CTTTCTTCTA
18727 TTTTAATTACTTGCAATTTAGTTTAATTATTTCAATTTTAGTTCATAGTTTAT
1 TTTTAATTACTTGCAATTTAGTTTAATTATTTCAATTTTAGTTCATAGTTTAT
* * **** * * * ** *
18780 TTTTAATTA-AT-CAA---AATCCCCCTGATTT--ACTTT-GTTGCTTAG-AAAGA
1 TTTTAATTACTTGCAATTTAGT-TTAATTATTTCAATTTTAGTT-CATAGTTTA-T
18827 TTTTAATTACTTGCAATTTAGTTTAATTATTTCAATTTTAGTTCATAGTTTAT
1 TTTTAATTACTTGCAATTTAGTTTAATTATTTCAATTTTAGTTCATAGTTTAT
18880 TTTTAATTA
1 TTTTAATTA
18889 ATAAAAATCC
Statistics
Matches: 73, Mismatches: 24, Indels: 24
0.60 0.20 0.20
Matches are distributed among these distances:
46 4 0.05
47 17 0.23
48 3 0.04
49 8 0.11
51 8 0.11
52 3 0.04
53 26 0.36
54 4 0.05
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (53 bp):
TTTTAATTACTTGCAATTTAGTTTAATTATTTCAATTTTAGTTCATAGTTTAT
Found at i:18851 original size:100 final size:100
Alignment explanation
Indices: 18726--18925 Score: 391
Period size: 100 Copynumber: 2.0 Consensus size: 100
18716 TCTTTCTTCT
18726 ATTTTAATTACTTGCAATTTAGTTTAATTATTTCAATTTTAGTTCATAGTTTATTTTTAATTAAT
1 ATTTTAATTACTTGCAATTTAGTTTAATTATTTCAATTTTAGTTCATAGTTTATTTTTAATTAAT
*
18791 CAAAATCCCCCTGATTTACTTTGTTGCTTAGAAAG
66 AAAAATCCCCCTGATTTACTTTGTTGCTTAGAAAG
18826 ATTTTAATTACTTGCAATTTAGTTTAATTATTTCAATTTTAGTTCATAGTTTATTTTTAATTAAT
1 ATTTTAATTACTTGCAATTTAGTTTAATTATTTCAATTTTAGTTCATAGTTTATTTTTAATTAAT
18891 AAAAATCCCCCTGATTTACTTTGTTGCTTAGAAAG
66 AAAAATCCCCCTGATTTACTTTGTTGCTTAGAAAG
18926 TAGTTAGTGA
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 99 1.00
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.49
Consensus pattern (100 bp):
ATTTTAATTACTTGCAATTTAGTTTAATTATTTCAATTTTAGTTCATAGTTTATTTTTAATTAAT
AAAAATCCCCCTGATTTACTTTGTTGCTTAGAAAG
Found at i:18864 original size:19 final size:21
Alignment explanation
Indices: 18828--18869 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
18818 TTAGAAAGAT
18828 TTTAATTACTTGCAA-TTTAG
1 TTTAATTACTTGCAATTTTAG
*
18848 TTTAATTA-TTTCAATTTTAG
1 TTTAATTACTTGCAATTTTAG
18868 TT
1 TT
18870 CATAGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTAATTACTTGCAATTTTAG
Found at i:24538 original size:22 final size:22
Alignment explanation
Indices: 24510--24553 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
24500 CAAAACTAAA
24510 TTGCATTGCATCTTCTATACTT
1 TTGCATTGCATCTTCTATACTT
** *
24532 TTGCATTGTGTCTTCTCTACTT
1 TTGCATTGCATCTTCTATACTT
24554 ATGGTCTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.23, G:0.11, T:0.52
Consensus pattern (22 bp):
TTGCATTGCATCTTCTATACTT
Found at i:26823 original size:220 final size:220
Alignment explanation
Indices: 26441--26881 Score: 882
Period size: 220 Copynumber: 2.0 Consensus size: 220
26431 AGGCGGTAGA
26441 AAGAAAAGAAGCTAGGGTTTTAGGAAAGAAGCTGCTATCATAAGGAACAATTTTTAAAAAATTGA
1 AAGAAAAGAAGCTAGGGTTTTAGGAAAGAAGCTGCTATCATAAGGAACAATTTTTAAAAAATTGA
26506 GGAGTTTGAAGGGTTCTAGAAAAAAGGGAAGTTGTAGAGAAGAGTTGTCAAGGGAAGTTTAGGGT
66 GGAGTTTGAAGGGTTCTAGAAAAAAGGGAAGTTGTAGAGAAGAGTTGTCAAGGGAAGTTTAGGGT
26571 TTTAGCAAGAGAAAAGACAGAGGGTTTAGAGGAAAAGCTCGGGTTTAAGTTTTTCTAAGGTTTTC
131 TTTAGCAAGAGAAAAGACAGAGGGTTTAGAGGAAAAGCTCGGGTTTAAGTTTTTCTAAGGTTTTC
26636 ATTTTTAGGTCTTCTTGGTTGAAAT
196 ATTTTTAGGTCTTCTTGGTTGAAAT
26661 AAGAAAAGAAGCTAGGGTTTTAGGAAAGAAGCTGCTATCATAAGGAACAATTTTTAAAAAATTGA
1 AAGAAAAGAAGCTAGGGTTTTAGGAAAGAAGCTGCTATCATAAGGAACAATTTTTAAAAAATTGA
26726 GGAGTTTGAAGGGTTCTAGAAAAAAGGGAAGTTGTAGAGAAGAGTTGTCAAGGGAAGTTTAGGGT
66 GGAGTTTGAAGGGTTCTAGAAAAAAGGGAAGTTGTAGAGAAGAGTTGTCAAGGGAAGTTTAGGGT
26791 TTTAGCAAGAGAAAAGACAGAGGGTTTAGAGGAAAAGCTCGGGTTTAAGTTTTTCTAAGGTTTTC
131 TTTAGCAAGAGAAAAGACAGAGGGTTTAGAGGAAAAGCTCGGGTTTAAGTTTTTCTAAGGTTTTC
26856 ATTTTTAGGTCTTCTTGGTTGAAAT
196 ATTTTTAGGTCTTCTTGGTTGAAAT
26881 A
1 A
26882 CGAGAGGGTG
Statistics
Matches: 221, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
220 221 1.00
ACGTcount: A:0.36, C:0.07, G:0.28, T:0.29
Consensus pattern (220 bp):
AAGAAAAGAAGCTAGGGTTTTAGGAAAGAAGCTGCTATCATAAGGAACAATTTTTAAAAAATTGA
GGAGTTTGAAGGGTTCTAGAAAAAAGGGAAGTTGTAGAGAAGAGTTGTCAAGGGAAGTTTAGGGT
TTTAGCAAGAGAAAAGACAGAGGGTTTAGAGGAAAAGCTCGGGTTTAAGTTTTTCTAAGGTTTTC
ATTTTTAGGTCTTCTTGGTTGAAAT
Found at i:28196 original size:48 final size:48
Alignment explanation
Indices: 28125--28685 Score: 847
Period size: 48 Copynumber: 11.7 Consensus size: 48
28115 AAAAATTGAA
28125 ATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTTT
1 ATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTTT
* * * *
28173 ATTTCCAGTTTTGGCCTTCCCGGTCGGAAGGTGCAATCTTCGGTGTTT
1 ATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTTT
** *
28221 ATTTCCAACTTTGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTCT
1 ATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTTT
*
28269 ATTTCCAATTTTGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTTT
1 ATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTTT
* * * *
28317 ATTTCCA-TATTTGCCCTTCCCAGTCGGAAGGTGCAGTCTTCGGTATTT
1 ATTTCCAGT-TTTGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTTT
* * *
28365 ATTTCCCGTTTTGCCATTCCCGGTCGGAAGGTGCAGTTTTCAATGTTT
1 ATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTTT
* *
28413 ATTTCCAGTTTTGCTCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTCT
1 ATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTTT
28461 ATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTTT
1 ATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTTT
* * *
28509 ATTTCCAGATTTG-CCTTCCCGGTCGGAAGGTGCAGTCTTCGGTGTTT
1 ATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTTT
* * * *
28556 ATTTCCAGTTTTGCCCTTCCCGGTCAGAAGGTGAAGTTTTCATTGTCT
1 ATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTTT
* * * *
28604 ATTTCCAGTTATGCCCTTCCCGGTCGGAATGTGCAGTGTTCGGTGTTT
1 ATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTTT
28652 ATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGC
1 ATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGC
28686 TAGATTTGTC
Statistics
Matches: 459, Mismatches: 51, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
47 45 0.10
48 413 0.90
49 1 0.00
ACGTcount: A:0.14, C:0.24, G:0.24, T:0.38
Consensus pattern (48 bp):
ATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAGTGTTT
Found at i:29862 original size:12 final size:11
Alignment explanation
Indices: 29845--29887 Score: 54
Period size: 12 Copynumber: 3.9 Consensus size: 11
29835 AATTTCTCCT
29845 TTTTCATTTTC
1 TTTTCATTTTC
29856 ATTTTCATTTTC
1 -TTTTCATTTTC
29868 --TTCATTTTC
1 TTTTCATTTTC
29877 TCTTTCATTTT
1 T-TTTCATTTT
29888 ATCCATTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 9 0.32
12 19 0.68
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTCATTTTC
Found at i:29871 original size:21 final size:21
Alignment explanation
Indices: 29847--29887 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
29837 TTTCTCCTTT
29847 TTCATTTTCAT-TTTCATTTTC
1 TTCATTTTC-TCTTTCATTTTC
29868 TTCATTTTCTCTTTCATTTT
1 TTCATTTTCTCTTTCATTTT
29888 ATCCATTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (21 bp):
TTCATTTTCTCTTTCATTTTC
Found at i:29894 original size:21 final size:21
Alignment explanation
Indices: 29849--29894 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
29839 TCTCCTTTTT
* *
29849 CATTTTCATTTTCATTTTCTT
1 CATTTTCATTTTCATTTTATC
29870 CATTTTC-TCTTTCATTTTATC
1 CATTTTCAT-TTTCATTTTATC
29891 CATT
1 CATT
29895 CTTTTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (21 bp):
CATTTTCATTTTCATTTTATC
Found at i:30030 original size:12 final size:11
Alignment explanation
Indices: 30013--30055 Score: 54
Period size: 12 Copynumber: 3.9 Consensus size: 11
30003 AATTTCTCCT
30013 TTTTCATTTTC
1 TTTTCATTTTC
30024 ATTTTCATTTTC
1 -TTTTCATTTTC
30036 --TTCATTTTC
1 TTTTCATTTTC
30045 TCTTTCATTTT
1 T-TTTCATTTT
30056 ATCCGTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 9 0.32
12 19 0.68
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTCATTTTC
Found at i:30039 original size:21 final size:21
Alignment explanation
Indices: 30015--30055 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
30005 TTTCTCCTTT
30015 TTCATTTTCAT-TTTCATTTTC
1 TTCATTTTC-TCTTTCATTTTC
30036 TTCATTTTCTCTTTCATTTT
1 TTCATTTTCTCTTTCATTTT
30056 ATCCGTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (21 bp):
TTCATTTTCTCTTTCATTTTC
Found at i:30067 original size:168 final size:168
Alignment explanation
Indices: 29786--30121 Score: 663
Period size: 168 Copynumber: 2.0 Consensus size: 168
29776 GTGAAAAATC
29786 TTGTCACACTTGTTGTTTCCTCCATCCTTTTCGATTTCTTTCCTTTTCAAATTTCTCCTTTTTCA
1 TTGTCACACTTGTTGTTTCCTCCATCCTTTTCGATTTCTTTCCTTTTCAAATTTCTCCTTTTTCA
29851 TTTTCATTTTCATTTTCTTCATTTTCTCTTTCATTTTATCCATTCTTTTTTATTCTCCCCTCCTT
66 TTTTCATTTTCATTTTCTTCATTTTCTCTTTCATTTTATCCATTCTTTTTTATTCTCCCCTCCTT
29916 TGTTGATTTTTGACTTGAATTTCTTGATGAAGTGATCT
131 TGTTGATTTTTGACTTGAATTTCTTGATGAAGTGATCT
29954 TTGTCACACTTGTTGTTTCCTCCATCCTTTTCGATTTCTTTCCTTTTCAAATTTCTCCTTTTTCA
1 TTGTCACACTTGTTGTTTCCTCCATCCTTTTCGATTTCTTTCCTTTTCAAATTTCTCCTTTTTCA
*
30019 TTTTCATTTTCATTTTCTTCATTTTCTCTTTCATTTTATCCGTTCTTTTTTATTCTCCCCTCCTT
66 TTTTCATTTTCATTTTCTTCATTTTCTCTTTCATTTTATCCATTCTTTTTTATTCTCCCCTCCTT
30084 TGTTGATTTTTGACTTGAATTTCTTGATGAAGTGATCT
131 TGTTGATTTTTGACTTGAATTTCTTGATGAAGTGATCT
30122 CAATGCCTCT
Statistics
Matches: 167, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
168 167 1.00
ACGTcount: A:0.13, C:0.23, G:0.07, T:0.57
Consensus pattern (168 bp):
TTGTCACACTTGTTGTTTCCTCCATCCTTTTCGATTTCTTTCCTTTTCAAATTTCTCCTTTTTCA
TTTTCATTTTCATTTTCTTCATTTTCTCTTTCATTTTATCCATTCTTTTTTATTCTCCCCTCCTT
TGTTGATTTTTGACTTGAATTTCTTGATGAAGTGATCT
Found at i:30535 original size:8 final size:8
Alignment explanation
Indices: 30514--30557 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
30504 TCCAAGTGCC
30514 TTTTTTCT
1 TTTTTTCT
30522 TCTTTTTC-
1 T-TTTTTCT
*
30530 TTTTTTCA
1 TTTTTTCT
30538 TTTTTTCAT
1 TTTTTTC-T
30547 TTTTTTCT
1 TTTTTTCT
30555 TTT
1 TTT
30558 GATGGGAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
7 6 0.19
8 13 0.41
9 13 0.41
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTCT
Done.