Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020758.1 Corchorus olitorius cultivar O-4 contig20791, 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: 26475
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:2517 original size:26 final size:26
Alignment explanation
Indices: 2474--2524 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
2464 GGTAAATGTA
2474 CTTGATCAGAAATAATTGTAAAATTTT
1 CTTGATCAGAAATAATTG-AAAATTTT
*
2501 CTTGATGAGAAAT-ATTGAAAATTT
1 CTTGATCAGAAATAATTGAAAATTT
2525 CTTACTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.30
26 4 0.17
27 12 0.52
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (26 bp):
CTTGATCAGAAATAATTGAAAATTTT
Found at i:2962 original size:126 final size:122
Alignment explanation
Indices: 2722--2978 Score: 322
Period size: 126 Copynumber: 2.0 Consensus size: 122
2712 ATTAGTATTC
*
2722 ATAATAGCACTAAAGATTATTACAAAGCTGAAAGTATTGATCCATCATCCATCTAAAGTTGAAAG
1 ATAATAGCACTAAAGATTATTACAAAGCTGAAAGTATTAAT-C-TCATCCATCTAAAGTTGAAAG
*
2787 TGATGGAAGGCTATAATAATTATAGATAGATCATATAATTGCAGACATGATCTTATCATAT
64 TGATGGAAGGCTATAATAATTATAGATAGATCA-ATAATAGCAGACATGATCTTAT-ATAT
* *
2848 ATAATAGCACTAAAGATTATTACAAA-ATCGAAAGTATTAAT-TGATCCATCTAAAGTTGAAAGT
1 ATAATAGCACTAAAGATTATTACAAAGCT-GAAAGTATTAATCTCATCCATCTAAAGTTGAAAGT
* * * *
2911 GGTGGGAGGTTAATCTTTATAATTATAGATAGATC-ATAATAGCAGATCATGATCTTATATAT
65 GATGGAAGGCT-A---TAATAATTATAGATAGATCAATAATAGCAGA-CATGATCTTATATAT
*
2973 ACAATA
1 ATAATA
2979 TTGTCCCAAA
Statistics
Matches: 116, Mismatches: 9, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
123 29 0.25
124 1 0.01
125 20 0.17
126 48 0.41
127 18 0.16
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (122 bp):
ATAATAGCACTAAAGATTATTACAAAGCTGAAAGTATTAATCTCATCCATCTAAAGTTGAAAGTG
ATGGAAGGCTATAATAATTATAGATAGATCAATAATAGCAGACATGATCTTATATAT
Found at i:14885 original size:17 final size:17
Alignment explanation
Indices: 14863--14901 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
14853 TTAGGGAGAA
14863 GGAAAAGAGAAGAAAAG
1 GGAAAAGAGAAGAAAAG
14880 GGAAAAGAGAAGAAAAG
1 GGAAAAGAGAAGAAAAG
14897 GGAAA
1 GGAAA
14902 GGGTAGACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (17 bp):
GGAAAAGAGAAGAAAAG
Found at i:15318 original size:21 final size:21
Alignment explanation
Indices: 15292--15335 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
15282 CCAAACTGAA
*
15292 TTGCTAAATACTGCCCCCCTT
1 TTGCTAAATACCGCCCCCCTT
**
15313 TTGCTACTTACCGCCCCCCTT
1 TTGCTAAATACCGCCCCCCTT
15334 TT
1 TT
15336 TACACTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.41, G:0.09, T:0.36
Consensus pattern (21 bp):
TTGCTAAATACCGCCCCCCTT
Found at i:15574 original size:7 final size:7
Alignment explanation
Indices: 15562--15636 Score: 66
Period size: 7 Copynumber: 10.6 Consensus size: 7
15552 TTTTTTTAAT
15562 ATTATTA
1 ATTATTA
15569 ATTATTTA
1 ATTA-TTA
15577 ATTATTA
1 ATTATTA
15584 ATTATT-
1 ATTATTA
15590 ATTAATTTAA
1 ATT-A-TT-A
*
15600 ATTGTT-
1 ATTATTA
15606 ATTATTA
1 ATTATTA
15613 ATTA-TA
1 ATTATTA
*
15619 ATTAATA
1 ATTATTA
*
15626 ATTAATA
1 ATTATTA
15633 ATTA
1 ATTA
15637 AAAACAAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
6 14 0.24
7 31 0.53
8 11 0.19
10 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (7 bp):
ATTATTA
Found at i:15590 original size:10 final size:10
Alignment explanation
Indices: 15562--15636 Score: 55
Period size: 10 Copynumber: 7.4 Consensus size: 10
15552 TTTTTTTAAT
15562 ATTATTAATTA
1 ATTATT-ATTA
*
15573 TTTAATTATTA
1 ATT-ATTATTA
15584 ATTATTATTA
1 ATTATTATTA
*
15594 ATT-TAAATT-
1 ATTAT-TATTA
*
15603 GTTATTATTA
1 ATTATTATTA
*
15613 ATTATAATTA
1 ATTATTATTA
* *
15623 ATAATTAATA
1 ATTATTATTA
15633 ATTA
1 ATTA
15637 AAAACAAAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
9 6 0.12
10 32 0.65
11 8 0.16
12 3 0.06
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (10 bp):
ATTATTATTA
Found at i:15745 original size:33 final size:33
Alignment explanation
Indices: 15668--15745 Score: 129
Period size: 33 Copynumber: 2.4 Consensus size: 33
15658 CCACCCTCCT
* *
15668 AGGGCGTCACCACCATGGTCATGCCGCCCTAGG
1 AGGGCGGCACCGCCATGGTCATGCCGCCCTAGG
*
15701 AGGGCGGCACCGCCATGGTCATTCCGCCCTAGG
1 AGGGCGGCACCGCCATGGTCATGCCGCCCTAGG
15734 AGGGCGGCACCG
1 AGGGCGGCACCG
15746 GTTATTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.17, C:0.36, G:0.35, T:0.13
Consensus pattern (33 bp):
AGGGCGGCACCGCCATGGTCATGCCGCCCTAGG
Found at i:15852 original size:21 final size:21
Alignment explanation
Indices: 15810--15854 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
15800 GCAAAATTAT
* ***
15810 CAAAAGGGGGGCGGTGTTTAG
1 CAAAAAGGGGGCGGTAAATAG
15831 CAAAAAGGGGGCGGTAAATAG
1 CAAAAAGGGGGCGGTAAATAG
15852 CAA
1 CAA
15855 CTCCCTTGGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.11, G:0.40, T:0.13
Consensus pattern (21 bp):
CAAAAAGGGGGCGGTAAATAG
Found at i:17613 original size:19 final size:18
Alignment explanation
Indices: 17568--17639 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 18
17558 ACAACAAGTG
*
17568 GTATTA-TTATTTATTAGT
1 GTATTATTTA-TTATTAAT
*
17586 CGTAATATTTATTATTAAT
1 -GTATTATTTATTATTAAT
17605 GTTATTA-TTATTTATTAAT
1 G-TATTATTTA-TTATTAAT
17624 GTATTCATTTATTATT
1 GTATT-ATTTATTATT
17640 TCCGCAGGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
18 8 0.18
19 31 0.69
20 6 0.13
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.60
Consensus pattern (18 bp):
GTATTATTTATTATTAAT
Found at i:20782 original size:26 final size:27
Alignment explanation
Indices: 20718--20785 Score: 88
Period size: 26 Copynumber: 2.6 Consensus size: 27
20708 CCTTCCACCC
* *
20718 TAAATAAATAATAATAATTAATTCTAG
1 TAAATAAATAATTATAATTAATTCTAA
20745 TAAATAAA-AATTATAATTAATTAC-AA
1 TAAATAAATAATTATAATTAATT-CTAA
20771 T-AATAAATAATTATA
1 TAAATAAATAATTATA
20786 GTAAATAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
25 6 0.16
26 22 0.59
27 9 0.24
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (27 bp):
TAAATAAATAATTATAATTAATTCTAA
Found at i:20798 original size:17 final size:17
Alignment explanation
Indices: 20757--20812 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
20747 AATAAAAATT
* *
20757 ATAATTAATTACAAT-A
1 ATAATTAATTATAGTAA
*
20773 ATAAATAATTATAGTAA
1 ATAATTAATTATAGTAA
20790 ATAATTAATTATAGTCAA
1 ATAATTAATTATAGT-AA
20808 ATAAT
1 ATAAT
20813 AAAATAACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
16 12 0.35
17 15 0.44
18 7 0.21
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (17 bp):
ATAATTAATTATAGTAA
Found at i:20848 original size:37 final size:37
Alignment explanation
Indices: 20745--20851 Score: 103
Period size: 38 Copynumber: 2.8 Consensus size: 37
20735 TTAATTCTAG
*
20745 TAAATAAAAATT-ATAATTAATTACAATAAT-AAATAAT
1 TAAATAAAAATTAATAATTAATT--AATAATAAAATAAC
* * * *
20782 TATAGTAAATAATTAATTA-TAGTCAAATAATAAAATAAC
1 TA-AATAAA-AATTAATAATTAAT-TAATAATAAAATAAC
20821 TAAATAAAAATTAATAATTAATTAATAATAA
1 TAAATAAAAATTAATAATTAATTAATAATAA
20852 TTAATTTTAA
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
37 18 0.33
38 19 0.35
39 15 0.27
40 3 0.05
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.35
Consensus pattern (37 bp):
TAAATAAAAATTAATAATTAATTAATAATAAAATAAC
Found at i:20993 original size:21 final size:21
Alignment explanation
Indices: 20969--21015 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
20959 ATTTATAAAA
*
20969 AAATTATATT-TTACATTTTTT
1 AAATAATATTATTA-ATTTTTT
*
20990 AAATAATATTATTATTTTTTT
1 AAATAATATTATTAATTTTTT
21011 AAATA
1 AAATA
21016 TGTGGCGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
AAATAATATTATTAATTTTTT
Found at i:21237 original size:19 final size:19
Alignment explanation
Indices: 21213--21251 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
21203 CATGATGTTC
21213 TTGAAGAAGTTTAGAGAGT
1 TTGAAGAAGTTTAGAGAGT
*
21232 TTGAAGAAGTTTTGAGAGT
1 TTGAAGAAGTTTAGAGAGT
21251 T
1 T
21252 AGAAAATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.36
Consensus pattern (19 bp):
TTGAAGAAGTTTAGAGAGT
Found at i:21829 original size:29 final size:29
Alignment explanation
Indices: 21786--21890 Score: 79
Period size: 29 Copynumber: 3.6 Consensus size: 29
21776 CCAAAATATT
**
21786 CAAATAAGGTTCTAATCTTTTAATTTGGC
1 CAAATAAGGGCCTAATCTTTTAATTTGGC
* ** **
21815 CAAATAAGGGCCTAA-CGTTATCGAAAATGAT
1 CAAATAAGGGCCTAATC-TT-T-TAATTTGGC
* *
21846 CAAATAAGGGTCC-GATCTTTTAATTTAGC
1 CAAATAAGGG-CCTAATCTTTTAATTTGGC
21875 CAAATAAGGGCCTAAT
1 CAAATAAGGGCCTAAT
21891 GTTATCGAAA
Statistics
Matches: 55, Mismatches: 15, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
28 3 0.05
29 30 0.55
30 2 0.04
31 17 0.31
32 3 0.05
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.30
Consensus pattern (29 bp):
CAAATAAGGGCCTAATCTTTTAATTTGGC
Found at i:21849 original size:60 final size:60
Alignment explanation
Indices: 21756--21915 Score: 216
Period size: 60 Copynumber: 2.7 Consensus size: 60
21746 CTAATTGCTT
* * * *
21756 AAATAAGGGCCTAATGTT-TGCCAAAAT-ATTCAAATAAGGTTCTAATCTTTTAATTTGGCC
1 AAATAAGGGCCTAATGTTAT-CGAAAATGA-TCAAATAAGGGTCCAATCTTTTAATTTAGCC
* *
21816 AAATAAGGGCCTAACGTTATCGAAAATGATCAAATAAGGGTCCGATCTTTTAATTTAGCC
1 AAATAAGGGCCTAATGTTATCGAAAATGATCAAATAAGGGTCCAATCTTTTAATTTAGCC
* *
21876 AAATAAGGGCCTAATGTTATCGAAAATGTTAAAATAAGGG
1 AAATAAGGGCCTAATGTTATCGAAAATGATCAAATAAGGG
21916 ACTGACGTAA
Statistics
Matches: 89, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
60 87 0.98
61 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (60 bp):
AAATAAGGGCCTAATGTTATCGAAAATGATCAAATAAGGGTCCAATCTTTTAATTTAGCC
Found at i:22057 original size:60 final size:59
Alignment explanation
Indices: 21960--22121 Score: 193
Period size: 60 Copynumber: 2.7 Consensus size: 59
21950 TGAAGCTAGG
* *
21960 CCCTTATTTGA-ACATTTTCGATAACGTTAGACTCTTATTTGACAAAATTAAAAGATCAGA
1 CCCTTATTTGAGA-ATTTTCGATAACGTTAGGCCCTTATTTGAC-AAATTAAAAGATCAGA
* * *
22020 CCCTTATTTGAGAATTTTCGATAATGTTAGGCCCTTATTTGGTCAAATTAAAAGATCATA
1 CCCTTATTTGAGAATTTTCGATAACGTTAGGCCCTTATTT-GACAAATTAAAAGATCAGA
* * * *
22080 ACCTTATTTGAGCATTTTGGCA-AACGTTAGGGCCTTATTTGA
1 CCCTTATTTGAGAATTTTCG-ATAACGTTAGGCCCTTATTTGA
22122 ACAATTAGCC
Statistics
Matches: 88, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
59 1 0.01
60 83 0.94
61 4 0.05
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (59 bp):
CCCTTATTTGAGAATTTTCGATAACGTTAGGCCCTTATTTGACAAATTAAAAGATCAGA
Found at i:22058 original size:31 final size:30
Alignment explanation
Indices: 21960--22060 Score: 82
Period size: 31 Copynumber: 3.3 Consensus size: 30
21950 TGAAGCTAGG
*
21960 CCCTTATTTGAACATTTTCGATAACGTTAGA
1 CCCTTATTTGAA-ATTTTCGATAAAGTTAGA
* ** *
21991 CTCTTATTTGACAAAATT--A-AAAGATCAGA
1 CCCTTATTTGA-AATTTTCGATAAAG-TTAGA
* *
22020 CCCTTATTTGAGAATTTTCGATAATGTTAGG
1 CCCTTATTTGA-AATTTTCGATAAAGTTAGA
22051 CCCTTATTTG
1 CCCTTATTTG
22061 GTCAAATTAA
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
28 3 0.06
29 19 0.36
31 27 0.51
32 4 0.08
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.39
Consensus pattern (30 bp):
CCCTTATTTGAAATTTTCGATAAAGTTAGA
Done.