Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013394.1 Corchorus capsularis cultivar CVL-1 contig13415, 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: 64764
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:12055 original size:2 final size:2
Alignment explanation
Indices: 12048--12072 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12038 CATGGAAACC
12048 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
12073 AGCAACTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18312 original size:2 final size:2
Alignment explanation
Indices: 18305--18333 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
18295 AACGCATTTT
18305 TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18334 CTCAATCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:29586 original size:60 final size:60
Alignment explanation
Indices: 29522--29641 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
29512 TCTCATTTAA
29522 ATGTTTGGGCATAGAGATTTATTTGAATTGTAATGAGATTTCACTAGATTTGTTTGCTAG
1 ATGTTTGGGCATAGAGATTTATTTGAATTGTAATGAGATTTCACTAGATTTGTTTGCTAG
29582 ATGTTTGGGCATAGAGATTTATTTGAATTGTAATGAGATTTCACTAGATTTGTTTGCTAG
1 ATGTTTGGGCATAGAGATTTATTTGAATTGTAATGAGATTTCACTAGATTTGTTTGCTAG
29642 GGAAGGGGTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.27, C:0.07, G:0.23, T:0.43
Consensus pattern (60 bp):
ATGTTTGGGCATAGAGATTTATTTGAATTGTAATGAGATTTCACTAGATTTGTTTGCTAG
Found at i:29980 original size:166 final size:166
Alignment explanation
Indices: 29706--30037 Score: 601
Period size: 166 Copynumber: 2.0 Consensus size: 166
29696 TTTCTTCAAG
29706 AAATGAAAATGATTTTTATCTAAAAAAAATAGCAAAATGCAATTTTATTAGAAAGAACATCGGTG
1 AAATGAAAATGATTTTTATCTAAAAAAAATAGCAAAATGCAATTTTATTAGAAAGAACATCGGTG
*
29771 ATATGCCTATGCTCTAAAGTTACTTGGGTTCAGTTCATGTAAAATTCTGAACTTGTTAGATCAGT
66 ATATGCCTATGCTCTAAAGTTACTTGGGTTCAGTTCATGTAAAATTCCGAACTTGTTAGATCAGT
* * *
29836 CAAAATGAAATCGTTAAGTATGTTATTCAAATCCAA
131 CAAAATGAAATCATTAAGTATGTTACTCAAACCCAA
* *
29872 AAATGAAAATGATTTTTATCTAAAAAAAATAGTAAAATGCAATTTTATTAGAAAGAACATTGGTG
1 AAATGAAAATGATTTTTATCTAAAAAAAATAGCAAAATGCAATTTTATTAGAAAGAACATCGGTG
29937 ATATGCCTATGCTCTAAAGTTACTTGGGTTCAGTTCATGTAAAATTCCGAACTTGTTAGATCAGT
66 ATATGCCTATGCTCTAAAGTTACTTGGGTTCAGTTCATGTAAAATTCCGAACTTGTTAGATCAGT
*
30002 CAAATTGAAATCATTAAGTATGTTACTCAAACCCAA
131 CAAAATGAAATCATTAAGTATGTTACTCAAACCCAA
30038 CTCGCTTCTT
Statistics
Matches: 159, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
166 159 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (166 bp):
AAATGAAAATGATTTTTATCTAAAAAAAATAGCAAAATGCAATTTTATTAGAAAGAACATCGGTG
ATATGCCTATGCTCTAAAGTTACTTGGGTTCAGTTCATGTAAAATTCCGAACTTGTTAGATCAGT
CAAAATGAAATCATTAAGTATGTTACTCAAACCCAA
Found at i:30923 original size:30 final size:30
Alignment explanation
Indices: 30889--30956 Score: 118
Period size: 30 Copynumber: 2.2 Consensus size: 30
30879 AAAAATAGCG
*
30889 GGGTCAAAACTATAAACTTATCATTTTAAT
1 GGGTCAAAACTATAAACCTATCATTTTAAT
30919 GGGTCAAAACTATAAACCTATCATTTTAAT
1 GGGTCAAAACTATAAACCTATCATTTTAAT
30949 GAGGTCAA
1 G-GGTCAA
30957 TTGGCAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 30 0.83
31 6 0.17
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (30 bp):
GGGTCAAAACTATAAACCTATCATTTTAAT
Found at i:38852 original size:58 final size:57
Alignment explanation
Indices: 38771--38890 Score: 186
Period size: 58 Copynumber: 2.1 Consensus size: 57
38761 CAAGAACAGT
* *
38771 AAGTAAAACAACAAGTAAACCATGATAGTAGCCAAATGATAACAGAACAGATGAAAG
1 AAGTAAAACAACAAGTAAACCATGATAATAGCCAAATGATAACAGAACAGATGAAAA
* * *
38828 AAGTAAAACAACCAAGTAAGCCATGATAATAGCTAAATGATAACAGAAGAGATGAAAA
1 AAGTAAAACAA-CAAGTAAACCATGATAATAGCCAAATGATAACAGAACAGATGAAAA
38886 AAGTA
1 AAGTA
38891 GATAGCAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 11 0.19
58 46 0.81
ACGTcount: A:0.55, C:0.12, G:0.17, T:0.15
Consensus pattern (57 bp):
AAGTAAAACAACAAGTAAACCATGATAATAGCCAAATGATAACAGAACAGATGAAAA
Found at i:40458 original size:29 final size:29
Alignment explanation
Indices: 40387--40471 Score: 118
Period size: 29 Copynumber: 2.9 Consensus size: 29
40377 TGGGCTAAAT
40387 GCTCGATTTGGTCCTAAACCTTTCACGGTCC
1 GCTCGATTTGGTCCTAAACCTTTCAC-G-CC
*
40418 GCTCGATTTGGTCCTAAACCTTCTGAC-CC
1 GCTCGATTTGGTCCTAAACCTT-TCACGCC
*
40447 GCTCAATTTGGTCCTAAACCTTTCA
1 GCTCGATTTGGTCCTAAACCTTTCA
40472 ATTTCTTAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
28 2 0.04
29 23 0.46
31 22 0.44
32 3 0.06
ACGTcount: A:0.19, C:0.32, G:0.16, T:0.33
Consensus pattern (29 bp):
GCTCGATTTGGTCCTAAACCTTTCACGCC
Found at i:41839 original size:17 final size:17
Alignment explanation
Indices: 41813--41849 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
41803 AAAAAAATAT
*
41813 CATAACATACAGTCTTC
1 CATAAAATACAGTCTTC
41830 CATAAAATACAGTCTTC
1 CATAAAATACAGTCTTC
41847 CAT
1 CAT
41850 TAGTAGTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.30
Consensus pattern (17 bp):
CATAAAATACAGTCTTC
Found at i:46490 original size:31 final size:28
Alignment explanation
Indices: 46420--46504 Score: 116
Period size: 29 Copynumber: 2.9 Consensus size: 28
46410 GTTAAGAAAT
*
46420 TGAAAGGTTTAGGACCAAATTGAGCGGG
1 TGAAAGGTTTAGGACCAAATCGAGCGGG
*
46448 TCAGAAGGTTTAGGACCAAATCGAGCGGACCG
1 TGA-AAGGTTTAGGACCAAATCGAGCGG---G
46480 TGAAAGGTTTAGGACCAAATCGAGC
1 TGAAAGGTTTAGGACCAAATCGAGC
46505 ATTTAGCCTT
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
28 2 0.04
29 23 0.46
31 22 0.44
32 3 0.06
ACGTcount: A:0.33, C:0.16, G:0.32, T:0.19
Consensus pattern (28 bp):
TGAAAGGTTTAGGACCAAATCGAGCGGG
Found at i:46641 original size:35 final size:35
Alignment explanation
Indices: 46590--46661 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
46580 TGTTTTAATT
*
46590 TAATTTAATTTAATTTTATTATTAGTATGTAAGTA
1 TAATTTAATTTAATTTTATTATTAGTACGTAAGTA
* *
46625 TAATTTTATTTTATTTTATTATTAGTACGTAAGTA
1 TAATTTAATTTAATTTTATTATTAGTACGTAAGTA
46660 TA
1 TA
46662 TACTGTAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.35, C:0.01, G:0.08, T:0.56
Consensus pattern (35 bp):
TAATTTAATTTAATTTTATTATTAGTACGTAAGTA
Found at i:51121 original size:25 final size:25
Alignment explanation
Indices: 51093--51145 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
51083 GTTACTGCCC
51093 TTGTATAATTAGTTTACAATTTGTT
1 TTGTATAATTAGTTTACAATTTGTT
51118 TTGTATAATTAGTTTACAATTTGTT
1 TTGTATAATTAGTTTACAATTTGTT
51143 TTG
1 TTG
51146 GTTGATGATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.26, C:0.04, G:0.13, T:0.57
Consensus pattern (25 bp):
TTGTATAATTAGTTTACAATTTGTT
Found at i:59868 original size:3 final size:3
Alignment explanation
Indices: 59860--59903 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
59850 CTAAATGAAT
59860 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
59904 GTACATGAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:64650 original size:2 final size:2
Alignment explanation
Indices: 64643--64763 Score: 98
Period size: 2 Copynumber: 60.5 Consensus size: 2
64633 TGCTTCATTT
* * * * * *
64643 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TG TG TG TG TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * * * *
64685 TG TG TC TA TA TA TA TA TA TA TA TA TA TA TA TG TG TG TG TG TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
64727 TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
64764 C
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 113 1.00
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (2 bp):
TA
Done.