Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014901.1 Corchorus capsularis cultivar CVL-1 contig14922, 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: 34087
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:1108 original size:37 final size:37
Alignment explanation
Indices: 1058--1129 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
1048 TGGTCCTGAT
1058 TAATCCGGATCCGACCCGCGTCGCGAACCTGGTTAAC
1 TAATCCGGATCCGACCCGCGTCGCGAACCTGGTTAAC
* *
1095 TAATCCGGATCCGACCTGCGTCGCGCACCTGGTTA
1 TAATCCGGATCCGACCCGCGTCGCGAACCTGGTTA
1130 TGGTGGGTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.19, C:0.35, G:0.25, T:0.21
Consensus pattern (37 bp):
TAATCCGGATCCGACCCGCGTCGCGAACCTGGTTAAC
Found at i:2965 original size:33 final size:34
Alignment explanation
Indices: 2928--2996 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 34
2918 GTTGAATAAC
2928 CTCTGAATTTCAAAAATAATACAAGACA-CTTTG
1 CTCTGAATTTCAAAAATAATACAAGACACCTTTG
2961 CTCTGAATTTCAAAAATAATACAAGACACCTTTG
1 CTCTGAATTTCAAAAATAATACAAGACACCTTTG
2995 CT
1 CT
2997 AATAGCCCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 28 0.80
34 7 0.20
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (34 bp):
CTCTGAATTTCAAAAATAATACAAGACACCTTTG
Found at i:3072 original size:25 final size:25
Alignment explanation
Indices: 3025--3072 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3015 AACACACTTA
* *
3025 AAAACCTAATTCTTGTAGGAAAAGT
1 AAAACCTAATCCTTGTAGAAAAAGT
*
3050 AAAACCTAATCCTTTTAGAAAAA
1 AAAACCTAATCCTTGTAGAAAAA
3073 AACCCCTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.27
Consensus pattern (25 bp):
AAAACCTAATCCTTGTAGAAAAAGT
Found at i:15268 original size:2 final size:2
Alignment explanation
Indices: 15261--15288 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
15251 CTTTTCAATT
15261 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15289 CCTAACAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17172 original size:30 final size:29
Alignment explanation
Indices: 17136--17214 Score: 79
Period size: 30 Copynumber: 2.7 Consensus size: 29
17126 CCCTTTTGGT
17136 AACGTTATATCCTGAATTGTCACATCCT-CA
1 AACGTTATATCCTGAATTG-CA-ATCCTACA
* * * * *
17166 AACGTTATATTCTCAATTGGATTTCTGACA
1 AACGTTATATCCTGAATTGCAATCCT-ACA
17196 AACGTTATATCCTGAATTG
1 AACGTTATATCCTGAATTG
17215 GTCATTTAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 3 0.08
29 1 0.03
30 36 0.90
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (29 bp):
AACGTTATATCCTGAATTGCAATCCTACA
Found at i:21294 original size:24 final size:24
Alignment explanation
Indices: 21258--21303 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
21248 ATTGAAAAAG
*
21258 AAAAAAAGGAAAAAGAAA-ATGGA
1 AAAAAAAAGAAAAAGAAATATGGA
21281 AAAAAAAAGAAAAAGAAATATGG
1 AAAAAAAAGAAAAAGAAATATGG
21304 CTAAATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.07
Consensus pattern (24 bp):
AAAAAAAAGAAAAAGAAATATGGA
Found at i:22249 original size:11 final size:11
Alignment explanation
Indices: 22220--22249 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
22210 AGGTATATAG
22220 ATAGAGATAAA
1 ATAGAGATAAA
22231 AT-GAGATAAA
1 ATAGAGATAAA
22241 ATAGAGATA
1 ATAGAGATA
22250 GAGATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (11 bp):
ATAGAGATAAA
Found at i:23044 original size:22 final size:22
Alignment explanation
Indices: 23019--23083 Score: 67
Period size: 27 Copynumber: 2.7 Consensus size: 22
23009 GTAATACAAG
23019 GAATCTGAAATAGAAATGTATT
1 GAATCTGAAATAGAAATGTATT
* *
23041 GAATCGATTTAAGAACAGAAATGTATT
1 GAATC----TGA-AATAGAAATGTATT
23068 GAATCTGAAATAGAAA
1 GAATCTGAAATAGAAA
23084 GACGCCCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
22 12 0.35
23 2 0.06
26 2 0.06
27 18 0.53
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.28
Consensus pattern (22 bp):
GAATCTGAAATAGAAATGTATT
Found at i:25835 original size:2 final size:2
Alignment explanation
Indices: 25828--25853 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25818 AGAAAAATGC
25828 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
25854 CAATACATTT
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:29972 original size:15 final size:14
Alignment explanation
Indices: 29932--29980 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
29922 ATTTGGACAA
29932 ATAATACTATATAT
1 ATAATACTATATAT
* *
29946 AGTATTATTATATACT
1 A-TAATACTATATA-T
29962 ATAATACTATAGTAT
1 ATAATACTATA-TAT
29977 ATAA
1 ATAA
29981 GAAAATATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
14 1 0.04
15 23 0.82
16 4 0.14
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (14 bp):
ATAATACTATATAT
Found at i:32676 original size:2 final size:2
Alignment explanation
Indices: 32669--32699 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
32659 ACTATGTATG
32669 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 T
32700 TTTTGGTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32986 original size:20 final size:21
Alignment explanation
Indices: 32961--33002 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
32951 TCTTGGGTTC
*
32961 TACTCTCACGGAA-TGTGAGT
1 TACTCTCACGCAATTGTGAGT
32981 TACTCTCACGCAATTGTGAGT
1 TACTCTCACGCAATTGTGAGT
33002 T
1 T
33003 TTCTTTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.33
Consensus pattern (21 bp):
TACTCTCACGCAATTGTGAGT
Found at i:33041 original size:2 final size:2
Alignment explanation
Indices: 33034--33058 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33024 GTGTATTTAG
33034 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 T
33059 GTTGGTAGTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33524 original size:28 final size:28
Alignment explanation
Indices: 33493--33561 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 28
33483 ACTTGTAGAA
*
33493 TTTGGACGTTTGTCCCCTGAATTTCAAT
1 TTTGGACGTTTGTCCCCTGAACTTCAAT
* *
33521 TTTGGACATTTTGTCTCCTGAACTTCAAT
1 TTTGGAC-GTTTGTCCCCTGAACTTCAAT
33550 TTTGAGACGTTT
1 TTTG-GACGTTT
33562 TATCCCCTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.20
29 25 0.71
30 3 0.09
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.45
Consensus pattern (28 bp):
TTTGGACGTTTGTCCCCTGAACTTCAAT
Found at i:33540 original size:29 final size:28
Alignment explanation
Indices: 33493--33569 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 28
33483 ACTTGTAGAA
* *
33493 TTTGGACGTTTGTCCCCTGAATTTCAAT
1 TTTGGACTTTTGTCCCCTGAACTTCAAT
*
33521 TTTGGACATTTTGTCTCCTGAACTTCAAT
1 TTTGGAC-TTTTGTCCCCTGAACTTCAAT
*
33550 TTTGAGACGTTTTATCCCCT
1 TTTG-GAC-TTTTGTCCCCT
33570 CAACCTAATG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 7 0.17
29 22 0.54
30 12 0.29
ACGTcount: A:0.18, C:0.22, G:0.16, T:0.44
Consensus pattern (28 bp):
TTTGGACTTTTGTCCCCTGAACTTCAAT
Done.