Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007411.1 Corchorus capsularis cultivar CVL-1 contig07432, 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: 36049
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:12129 original size:2 final size:2
Alignment explanation
Indices: 12122--12157 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
12112 GATTATTATC
12122 AT AT AT AT AT 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 AT AT AT AT AT
12158 TCTTCTGCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15563 original size:11 final size:11
Alignment explanation
Indices: 15547--15589 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
15537 TATACTATAT
15547 CTAATTAATAG
1 CTAATTAATAG
*
15558 CTAATTAATAT
1 CTAATTAATAG
15569 CTAATTAATAG
1 CTAATTAATAG
*
15580 TTAATTAATA
1 CTAATTAATA
15590 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:15569 original size:22 final size:22
Alignment explanation
Indices: 15543--15589 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
15533 CCATTATACT
15543 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
15565 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
15587 ATA
1 ATA
15590 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:16545 original size:19 final size:17
Alignment explanation
Indices: 16523--16567 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 17
16513 GTTACCGATG
16523 TATGTATATGTTATTTAAA
1 TATGTATATGTTA-TT-AA
*
16542 TATGTACATGTTATTAA
1 TATGTATATGTTATTAA
16559 TATGTATAT
1 TATGTATAT
16568 ATGATGTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 10 0.42
18 2 0.08
19 12 0.50
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (17 bp):
TATGTATATGTTATTAA
Found at i:17636 original size:16 final size:16
Alignment explanation
Indices: 17617--17675 Score: 75
Period size: 16 Copynumber: 3.8 Consensus size: 16
17607 ATTTTTGGGT
17617 ACCCGAACCCGAAATG
1 ACCCGAACCCGAAATG
* *
17633 ACCCGAATCC-AAACG
1 ACCCGAACCCGAAATG
* *
17648 ACCTGAACCCAAAATG
1 ACCCGAACCCGAAATG
17664 ACCCGAACCCGA
1 ACCCGAACCCGA
17676 TCAACCCGAC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
15 12 0.34
16 23 0.66
ACGTcount: A:0.39, C:0.39, G:0.15, T:0.07
Consensus pattern (16 bp):
ACCCGAACCCGAAATG
Found at i:19018 original size:31 final size:31
Alignment explanation
Indices: 18980--19040 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
18970 GTTATCAGTT
18980 TCCAGATCTTTAGATCTTGGATGTTTGAGTC
1 TCCAGATCTTTAGATCTTGGATGTTTGAGTC
19011 TCCAGATCTTTAGATCTTGGATGTTTGAGT
1 TCCAGATCTTTAGATCTTGGATGTTTGAGT
19041 TTGTTCAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.43
Consensus pattern (31 bp):
TCCAGATCTTTAGATCTTGGATGTTTGAGTC
Found at i:19063 original size:16 final size:16
Alignment explanation
Indices: 19039--19070 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
19029 GGATGTTTGA
*
19039 GTTTGTTCAGTTTGTT
1 GTTTATTCAGTTTGTT
19055 GTTTATTCAGTTTGTT
1 GTTTATTCAGTTTGTT
19071 TGATGTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.06, G:0.22, T:0.62
Consensus pattern (16 bp):
GTTTATTCAGTTTGTT
Found at i:19632 original size:16 final size:16
Alignment explanation
Indices: 19608--19638 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19598 AATTGTTACG
*
19608 ACCCGAACCCGAAAAA
1 ACCCAAACCCGAAAAA
19624 ACCCAAACCCGAAAA
1 ACCCAAACCCGAAAA
19639 CCCGAGGTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.39, G:0.10, T:0.00
Consensus pattern (16 bp):
ACCCAAACCCGAAAAA
Found at i:19726 original size:15 final size:15
Alignment explanation
Indices: 19672--19728 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
19662 TCCGAACCGT
*
19672 ATGACCCGAAACCGAAA
1 ATGACCCG-AACC-CAA
*
19689 ACGACCC-AACCCAGA
1 ATGACCCGAACCCA-A
19704 ATTGACCCGAACCCAA
1 A-TGACCCGAACCCAA
19720 ATGACCCGA
1 ATGACCCGA
19729 CATTTGAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
14 1 0.03
15 14 0.41
16 7 0.21
17 12 0.35
ACGTcount: A:0.40, C:0.37, G:0.16, T:0.07
Consensus pattern (15 bp):
ATGACCCGAACCCAA
Found at i:29647 original size:274 final size:274
Alignment explanation
Indices: 29158--29707 Score: 1055
Period size: 274 Copynumber: 2.0 Consensus size: 274
29148 CCTATATTAG
29158 TGAACAATGTCTATTGTTGGCTAAGATCTTTCTAGTTCTTAAAGCAACGGGTTACTTGAATCTAG
1 TGAACAATGTCTATTGTTGGCTAAGATCTTTCTAGTTCTTAAAGCAACGGGTTACTTGAATCTAG
*
29223 TAGACATTTGGAACTAAGTTATTACACCTGTTAGGATTTAGTTTAGGGTGTGAGCCAGTACTAAT
66 TAGACATTTGGAACTAAGTTAGTACACCTGTTAGGATTTAGTTTAGGGTGTGAGCCAGTACTAAT
*
29288 GAAGATTAAGGAAAAATAGGGATTAATGGTCAATGACGTTAATCTACATCATCTATTTACCAAGT
131 GAAGACTAAGGAAAAATAGGGATTAATGGTCAATGACGTTAATCTACATCATCTATTTACCAAGT
29353 TAGATATCAATTGATGCCAAGGATCAAATCCTTTTATCCCAAGAGTGTGATTGTCTTGAAATTGG
196 TAGATATCAATTGATGCCAAGGATCAAATCCTTTTATCCCAAGAGTGTGATTGTCTTGAAATTGG
29418 AATATTTATTTAAT
261 AATATTTATTTAAT
29432 TGAACAATGTCTATTGTTGGCTAAGATCTTTCTAGTTCTTAAAGCAACGGGTTACTTGAATCTAG
1 TGAACAATGTCTATTGTTGGCTAAGATCTTTCTAGTTCTTAAAGCAACGGGTTACTTGAATCTAG
*
29497 TAGACATTTGGAACTAAGTTAGTACACCTGTTAGGATTTAGTTTAGGGTGTGAGGCAGTACTAAT
66 TAGACATTTGGAACTAAGTTAGTACACCTGTTAGGATTTAGTTTAGGGTGTGAGCCAGTACTAAT
* *
29562 GAAGACTAAGGAAAGATAGGGATTAATGGTCAATGACGTTAATCTACGTCATCTATTTACCAAGT
131 GAAGACTAAGGAAAAATAGGGATTAATGGTCAATGACGTTAATCTACATCATCTATTTACCAAGT
29627 TAGATATCAATTGATGCCAAGGATCAAATCCTTTTATCCCAAGAGTGTGATTGTCTTGAAATTGG
196 TAGATATCAATTGATGCCAAGGATCAAATCCTTTTATCCCAAGAGTGTGATTGTCTTGAAATTGG
29692 AATATTTATTTAAT
261 AATATTTATTTAAT
29706 TG
1 TG
29708 TTTCTTTAAT
Statistics
Matches: 271, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
274 271 1.00
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (274 bp):
TGAACAATGTCTATTGTTGGCTAAGATCTTTCTAGTTCTTAAAGCAACGGGTTACTTGAATCTAG
TAGACATTTGGAACTAAGTTAGTACACCTGTTAGGATTTAGTTTAGGGTGTGAGCCAGTACTAAT
GAAGACTAAGGAAAAATAGGGATTAATGGTCAATGACGTTAATCTACATCATCTATTTACCAAGT
TAGATATCAATTGATGCCAAGGATCAAATCCTTTTATCCCAAGAGTGTGATTGTCTTGAAATTGG
AATATTTATTTAAT
Found at i:29976 original size:18 final size:17
Alignment explanation
Indices: 29933--29976 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
29923 GTTGCTTTCC
29933 TTTA-GTTTTGTTTTGT
1 TTTATGTTTTGTTTTGT
*
29949 TTTATATTTTGCTTTTGT
1 TTTATGTTTTG-TTTTGT
*
29967 TTTTTGTTTT
1 TTTATGTTTT
29977 TGTGTTTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 4 0.17
17 5 0.22
18 14 0.61
ACGTcount: A:0.07, C:0.02, G:0.14, T:0.77
Consensus pattern (17 bp):
TTTATGTTTTGTTTTGT
Found at i:32052 original size:12 final size:13
Alignment explanation
Indices: 32027--32059 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
32017 AGTGTCAAAA
32027 AAAAAAAGAAAGAG
1 AAAAAAAG-AAGAG
32041 AAAAAAAG-AGAG
1 AAAAAAAGAAGAG
32053 AAAAAAA
1 AAAAAAA
32060 TCAAGCTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
14 8 0.42
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAGAG
Found at i:33697 original size:69 final size:69
Alignment explanation
Indices: 33586--33723 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
33576 AGGGAATAAG
33586 AGAAAGACTCCAATACCCTAATACTTAATTTTATTAGTCTTAGACAATTATGTAATTCATTATTT
1 AGAAAGACTCCAATACCCTAATACTTAATTTTATTAGTCTTAGACAATTATGTAATTCATTATTT
33651 ATTA
66 ATTA
33655 AGAAAGACTCCAATACCCTAATACTTAATTTTATTAGTCTTAGACAATTATGTAATTCATTATTT
1 AGAAAGACTCCAATACCCTAATACTTAATTTTATTAGTCTTAGACAATTATGTAATTCATTATTT
33720 ATTA
66 ATTA
33724 TTTTAATTAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (69 bp):
AGAAAGACTCCAATACCCTAATACTTAATTTTATTAGTCTTAGACAATTATGTAATTCATTATTT
ATTA
Done.