Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006696.1 Corchorus capsularis cultivar CVL-1 contig06717, 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: 29196
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:904 original size:19 final size:20
Alignment explanation
Indices: 880--943 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 20
870 CTACATGGCA
880 TTTTTAAATACTTTTTT-AT
1 TTTTTAAATACTTTTTTAAT
*
899 TTTTTAAATATTTTTTTAAT
1 TTTTTAAATACTTTTTTAAT
*
919 TTTTT--TTAC-TTTTTAAT
1 TTTTTAAATACTTTTTTAAT
*
936 ATTTTAAA
1 TTTTTAAA
944 CCAGCTCAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
17 12 0.32
18 2 0.05
19 16 0.43
20 7 0.19
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTTAAATACTTTTTTAAT
Found at i:912 original size:29 final size:27
Alignment explanation
Indices: 879--940 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 27
869 TCTACATGGC
*
879 ATTTTTAAATACTTTTTTATTTTTTAAAT
1 ATTTTTAAAT-CTTTTTTACTTTTT-AAT
* *
908 ATTTTTTTAATTTTTTTTACTTTTTAAT
1 A-TTTTTAAATCTTTTTTACTTTTTAAT
936 ATTTT
1 ATTTT
941 AAACCAGCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 4 0.14
28 4 0.14
29 13 0.45
30 8 0.28
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (27 bp):
ATTTTTAAATCTTTTTTACTTTTTAAT
Found at i:973 original size:30 final size:31
Alignment explanation
Indices: 937--1005 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
927 CTTTTTAATA
937 TTTT-AAACCAGCTCAAATAGGTACCAAACG
1 TTTTAAAACCAGCTCAAATAGGTACCAAACG
*** *
967 TTTTAAAATTGGCTCAAATAGGTACTAAACG
1 TTTTAAAACCAGCTCAAATAGGTACCAAACG
*
998 TTTCAAAA
1 TTTTAAAA
1006 TTGGATCAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29
Consensus pattern (31 bp):
TTTTAAAACCAGCTCAAATAGGTACCAAACG
Found at i:984 original size:31 final size:31
Alignment explanation
Indices: 947--1014 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
937 TTTTAAACCA
*
947 GCTCAAATAGGTACCAAACGTTTTAAAATTG
1 GCTCAAATAGGTACCAAACGTTTCAAAATTG
*
978 GCTCAAATAGGTACTAAACGTTTCAAAATTG
1 GCTCAAATAGGTACCAAACGTTTCAAAATTG
*
1009 GATCAA
1 GCTCAA
1015 TTTAGATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (31 bp):
GCTCAAATAGGTACCAAACGTTTCAAAATTG
Found at i:4921 original size:27 final size:28
Alignment explanation
Indices: 4890--4945 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
4880 TGCCAAATAG
*
4890 AATTCCTT-GAAATAAAATGTCCAAAAC
1 AATTCCTTAGAAACAAAATGTCCAAAAC
* *
4917 AATTCTTTAGGAACAAAATGTCCAAAAC
1 AATTCCTTAGAAACAAAATGTCCAAAAC
4945 A
1 A
4946 CCATCGTTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.48, C:0.18, G:0.09, T:0.25
Consensus pattern (28 bp):
AATTCCTTAGAAACAAAATGTCCAAAAC
Found at i:8321 original size:15 final size:15
Alignment explanation
Indices: 8301--8329 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
8291 AAACCGAGAA
8301 AGTCGGGCTCGGTGC
1 AGTCGGGCTCGGTGC
8316 AGTCGGGCTCGGTG
1 AGTCGGGCTCGGTG
8330 TAATCGAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.24, G:0.48, T:0.21
Consensus pattern (15 bp):
AGTCGGGCTCGGTGC
Found at i:9339 original size:13 final size:14
Alignment explanation
Indices: 9286--9346 Score: 51
Period size: 13 Copynumber: 4.6 Consensus size: 14
9276 AGGTTAGGTG
9286 AATAT-TTA-ATAT
1 AATATATTATATAT
9298 ACATATATATATATAT
1 A-ATATAT-TATATAT
* *
9314 AACAGA-T-TATAT
1 AATATATTATATAT
9326 AAT-TATTATATAT
1 AATATATTATATAT
9339 AATATATT
1 AATATATT
9347 TAATTTCTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
11 1 0.03
12 9 0.24
13 13 0.34
14 5 0.13
15 5 0.13
16 5 0.13
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (14 bp):
AATATATTATATAT
Found at i:10829 original size:28 final size:29
Alignment explanation
Indices: 10785--10839 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
10775 CAACTCATAA
*
10785 AAACATAAGAGAAAAAGACAAAAATAGAT
1 AAACATAAGAGAAAAAGAAAAAAATAGAT
*
10814 AAACATAGGAG-AAAAGAAAAAAATAG
1 AAACATAAGAGAAAAAGAAAAAAATAG
10840 GTTAGTTATC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.69, C:0.05, G:0.16, T:0.09
Consensus pattern (29 bp):
AAACATAAGAGAAAAAGAAAAAAATAGAT
Found at i:11640 original size:102 final size:102
Alignment explanation
Indices: 11462--11666 Score: 365
Period size: 102 Copynumber: 2.0 Consensus size: 102
11452 TCGAATTAAG
* *
11462 ATCGAGGCACAGGAAAGCGCTGCTATATATTATTTTCCTTTTAAAAATGCGCCAATTTTTAGGGC
1 ATCGAGGCACAGGAAAGCGCTGCTATATATTATTTTCCTTTTAAAAATGCGCCAATTTCTAAGGC
*
11527 GCTTCAGGTTAACGTCGGGATTCCTTTAAATGCCACT
66 GCTTCAAGTTAACGTCGGGATTCCTTTAAATGCCACT
* *
11564 ATCGAGGCACATGAAAGTGCTGCTATATATTATTTTCCTTTTAAAAATGCGCCAATTTCTAAGGC
1 ATCGAGGCACAGGAAAGCGCTGCTATATATTATTTTCCTTTTAAAAATGCGCCAATTTCTAAGGC
11629 GCTTCAAGTTAACGTCGGGATTCCTTTAAATGCCACT
66 GCTTCAAGTTAACGTCGGGATTCCTTTAAATGCCACT
11666 A
1 A
11667 AATTAGGAGA
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 98 1.00
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (102 bp):
ATCGAGGCACAGGAAAGCGCTGCTATATATTATTTTCCTTTTAAAAATGCGCCAATTTCTAAGGC
GCTTCAAGTTAACGTCGGGATTCCTTTAAATGCCACT
Found at i:13326 original size:473 final size:471
Alignment explanation
Indices: 12381--13329 Score: 1758
Period size: 473 Copynumber: 2.0 Consensus size: 471
12371 TATTTCATCT
*
12381 ATTTATACTATATATAAAAGTACGAGTTTTGTGAAACTTTTGAATCGACCATTATACCCACATTT
1 ATTTTTACTATATATAAAAGTACGAGTTTTGTGAAACTTTTGAATCGACCATTATACCCACATTT
*
12446 TTTTGAATATATTTCTTAAATACCTTTGCTTAAACTATTGTAGTTTTATTTTACTAAAACTCTAT
66 TTTTGAATATATTTCTTAAATACCTTTGCTTAAACTATTGTAGTTTTATTCTACTAAAACTCTAT
* *
12511 TTTTATTCAATTATTAAATCTAATATCTTTATAATTTCTTTATTTTTACCATTTTACTATTTTGA
131 TTTTACTCAATAATTAAATCTAATATCTTTATAATTTCTTTATTTTTACCATTTTACTATTTTGA
12576 ATTAAAATTGGATATATTAAAATTTTTAATATACAGTTTTATTCTACTAAAAACTCTACTTTCAT
196 ATTAAAATTGGATATATTAAAATTTTTAATATACAGTTTTATTCTACTAAAAACTCTACTTTCAT
12641 TTAATTAAATTCAATATTTTATAATTATTTTATCTTTACCATTTTAATTTAAAAGGTTATTTTGA
261 TTAATTAAATTCAATATTTTATAATTATTTTATCTTTACCATTTTAATTTAAAAGGTTATTTTGA
12706 CTGACATGTTCTATTTGATAGTTTAATGTATTATGATTAAAATTTATTATTTCTATAATTATTTT
326 CTGACATGTTCTATTTGATAGTTTAATGTATTATGATTAAAATTTATTATTTCTATAATTATTTT
*
12771 ATTTGATTTATAATTAATTTTTTTGCTAGATAAATGTAACCCTTAATGTGGGTTTAAATTTACTA
391 ATTTGATTTATAATTAATTTTTTTGCTAGATAAATGTAACCCTTAATGAGGGTTTAAATTTACTA
*
12836 TTTTACTTTGTTAATA
456 TTTTACTTTGCTAATA
*
12852 ATTTTTACTATATATAAAAGTACGAGTTTTGTGAAACTTTTGAATCGACCATTATACCCTCATTT
1 ATTTTTACTATATATAAAAGTACGAGTTTTGTGAAACTTTTGAATCGACCATTATACCCACATTT
12917 TTTTGAATATATTTCTTAAATACCTTTGCTTAAACTATTGTAGTTTTATTCTACTCAAAACTCTA
66 TTTTGAATATATTTCTTAAATACCTTTGCTTAAACTATTGTAGTTTTATTCTACT-AAAACTCTA
12982 TTTTTACTCAATAATTAAATCTAATATCTTTATAATTTCTTTATTTTTACCATTTTACTATTTTT
130 TTTTTACTCAATAATTAAATCTAATATCTTTATAATTTCTTTATTTTTACCATTTTACTA-TTTT
13047 GAATTAAAATTGGATATATTAAAATTTTTAATATACAGTTTTATTCTACTAAAAACTCTACTTTC
194 GAATTAAAATTGGATATATTAAAATTTTTAATATACAGTTTTATTCTACTAAAAACTCTACTTTC
13112 ATTTAATTAAAATTCAATATTTTATAATTATTTTAGT-TTTACCATTTTAATTTAAAAGGTTATT
259 ATTTAATT-AAATTCAATATTTTATAATTATTTTA-TCTTTACCATTTTAATTTAAAAGGTTATT
* * *
13176 TTGATTGACATGTTCTATTTGATAGTTTAATGTATTATGATTAAAATTTATTATTTTTGTAATTA
322 TTGACTGACATGTTCTATTTGATAGTTTAATGTATTATGATTAAAATTTATTATTTCTATAATTA
13241 TTTTATTTGATTTATAATTAA-TTTTTTGCTAGATAAATGTAACCCTTAATGAGGGTTTAAATTT
387 TTTTATTTGATTTATAATTAATTTTTTTGCTAGATAAATGTAACCCTTAATGAGGGTTTAAATTT
13305 ACTATTTTACTTTGCTAATA
452 ACTATTTTACTTTGCTAATA
13325 ATTTT
1 ATTTT
13330 CTTTAAAGCT
Statistics
Matches: 464, Mismatches: 10, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
471 117 0.25
472 67 0.14
473 143 0.31
474 136 0.29
475 1 0.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (471 bp):
ATTTTTACTATATATAAAAGTACGAGTTTTGTGAAACTTTTGAATCGACCATTATACCCACATTT
TTTTGAATATATTTCTTAAATACCTTTGCTTAAACTATTGTAGTTTTATTCTACTAAAACTCTAT
TTTTACTCAATAATTAAATCTAATATCTTTATAATTTCTTTATTTTTACCATTTTACTATTTTGA
ATTAAAATTGGATATATTAAAATTTTTAATATACAGTTTTATTCTACTAAAAACTCTACTTTCAT
TTAATTAAATTCAATATTTTATAATTATTTTATCTTTACCATTTTAATTTAAAAGGTTATTTTGA
CTGACATGTTCTATTTGATAGTTTAATGTATTATGATTAAAATTTATTATTTCTATAATTATTTT
ATTTGATTTATAATTAATTTTTTTGCTAGATAAATGTAACCCTTAATGAGGGTTTAAATTTACTA
TTTTACTTTGCTAATA
Found at i:14102 original size:2 final size:2
Alignment explanation
Indices: 14095--14120 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14085 AACAACACAA
14095 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
14121 GCACAATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18177 original size:23 final size:25
Alignment explanation
Indices: 18150--18196 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
18140 CTTTCTCTTT
18150 CTCATGTAA-TG-TTTTTCTTTTCA
1 CTCATGTAAGTGTTTTTTCTTTTCA
18173 CTCATGTAAGTTGTTTTTTCTTTT
1 CTCATGTAAG-TGTTTTTTCTTTT
18197 AAATTTTGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.43
25 2 0.10
26 10 0.48
ACGTcount: A:0.15, C:0.15, G:0.11, T:0.60
Consensus pattern (25 bp):
CTCATGTAAGTGTTTTTTCTTTTCA
Found at i:24673 original size:2 final size:2
Alignment explanation
Indices: 24666--24697 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
24656 GGCTGCTCCC
24666 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
24698 TTCGTTATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25190 original size:50 final size:50
Alignment explanation
Indices: 25093--25192 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 50
25083 TTATACTATT
*
25093 AAATTAAATGTGATAGAATAATAATAATAAACTTTAACTACGTTTACATG
1 AAATTAAATGTGATAGAATAATAATAATAAACCTTAACTACGTTTACATG
* * *
25143 AAATTAAATGTGATTGGAATAATAATATTAAACCTTAACTATG-TTACATG
1 AAATTAAATGTGA-TAGAATAATAATAATAAACCTTAACTACGTTTACATG
25193 GTCATACAAC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 20 0.44
51 25 0.56
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.35
Consensus pattern (50 bp):
AAATTAAATGTGATAGAATAATAATAATAAACCTTAACTACGTTTACATG
Done.