Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006494.1 Corchorus capsularis cultivar CVL-1 contig06515, 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: 28216
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Found at i:2797 original size:11 final size:11
Alignment explanation
Indices: 2783--2809 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2773 AGTTATATCG
2783 AAAATATAAAA
1 AAAATATAAAA
2794 AAAATATAAAA
1 AAAATATAAAA
2805 AAAAT
1 AAAAT
2810 TTCGACCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAATATAAAA
Found at i:6554 original size:33 final size:32
Alignment explanation
Indices: 6495--6571 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 32
6485 AAGCCGCGCA
* *
6495 ACACCGGCCACGCGACTTGGAGATGCCCGGCC
1 ACACCGGCCACGCGACATGGACATGCCCGGCC
*
6527 ATCACCGGCCACGCGACAT-GACCATGCCTGGCC
1 A-CACCGGCCACGCGACATGGA-CATGCCCGGCC
6560 ACAACCGGCCAC
1 AC-ACCGGCCAC
6572 ATGACTCGGC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
32 4 0.10
33 35 0.90
ACGTcount: A:0.22, C:0.43, G:0.26, T:0.09
Consensus pattern (32 bp):
ACACCGGCCACGCGACATGGACATGCCCGGCC
Found at i:8013 original size:11 final size:11
Alignment explanation
Indices: 7997--8032 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
7987 ATCGACTTGA
7997 TTTGAATTGTG
1 TTTGAATTGTG
8008 TTTGAATTGTG
1 TTTGAATTGTG
*
8019 TTTGAATTGAG
1 TTTGAATTGTG
8030 TTT
1 TTT
8033 AGTGCAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.25, T:0.56
Consensus pattern (11 bp):
TTTGAATTGTG
Found at i:13026 original size:33 final size:33
Alignment explanation
Indices: 12984--13087 Score: 122
Period size: 33 Copynumber: 3.2 Consensus size: 33
12974 CGCAACACCT
*
12984 GCCACGCGACTTGGAGATGCCCGGCCATC-ACCG
1 GCCACGCGACTTGGACATGCCCGGCCA-CAACCG
*
13017 GCCACGCGACAT-GACCATGCCCGGCCACAACCG
1 GCCACGCGACTTGGA-CATGCCCGGCCACAACCG
** * *
13050 GCCACATGACTCGGCCATGCCCGGCCACAACCG
1 GCCACGCGACTTGGACATGCCCGGCCACAACCG
13083 GCCAC
1 GCCAC
13088 ACGATCCTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 57 0.93
34 1 0.02
ACGTcount: A:0.21, C:0.44, G:0.26, T:0.09
Consensus pattern (33 bp):
GCCACGCGACTTGGACATGCCCGGCCACAACCG
Found at i:13052 original size:10 final size:10
Alignment explanation
Indices: 13037--13088 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
13027 ATGACCATGC
13037 CCGGCCACAA
1 CCGGCCACAA
13047 CCGGCCACATGA
1 CCGGCCACA--A
***
13059 CTCGGCCATGC
1 C-CGGCCACAA
13070 CCGGCCACAA
1 CCGGCCACAA
13080 CCGGCCACA
1 CCGGCCACA
13089 CGATCCTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
10 24 0.73
11 1 0.03
12 2 0.06
13 6 0.18
ACGTcount: A:0.23, C:0.48, G:0.23, T:0.06
Consensus pattern (10 bp):
CCGGCCACAA
Found at i:13088 original size:33 final size:33
Alignment explanation
Indices: 13000--13091 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 33
12990 CGACTTGGAG
*
13000 ATGCCCGGCCATC-ACCGGCCACGCGACATGACC
1 ATGCCCGGCCA-CAACCGGCCACACGACATGACC
* *
13033 ATGCCCGGCCACAACCGGCCACATGAC-TCGGCC
1 ATGCCCGGCCACAACCGGCCACACGACAT-GACC
13066 ATGCCCGGCCACAACCGGCCACACGA
1 ATGCCCGGCCACAACCGGCCACACGA
13092 TCCTTTAACT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
32 2 0.04
33 51 0.96
ACGTcount: A:0.23, C:0.46, G:0.24, T:0.08
Consensus pattern (33 bp):
ATGCCCGGCCACAACCGGCCACACGACATGACC
Found at i:19467 original size:30 final size:29
Alignment explanation
Indices: 19399--19476 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
19389 TGTTGGTTTA
* *
19399 TCAAGTGCGGGTTGTGCACTTGTGTTGAT
1 TCAAGTGTGGGTTGTGCACTTGGGTTGAT
*
19428 TCAAGTGTGGGTTGTGCACTTGGGATTGTT
1 TCAAGTGTGGGTTGTGCACTTGGG-TTGAT
**
19458 TTGAGTGTGGGTT-TGCACT
1 TCAAGTGTGGGTTGTGCACT
19477 CGGTGTCAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 28 0.65
30 15 0.35
ACGTcount: A:0.13, C:0.12, G:0.36, T:0.40
Consensus pattern (29 bp):
TCAAGTGTGGGTTGTGCACTTGGGTTGAT
Found at i:20026 original size:19 final size:19
Alignment explanation
Indices: 20002--20042 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
19992 CTCTCTTTGA
20002 TGGCACCAACTACCAGTTC
1 TGGCACCAACTACCAGTTC
20021 TGGCACCAACTACCAGTTC
1 TGGCACCAACTACCAGTTC
20040 TGG
1 TGG
20043 AAGTCTCGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.34, G:0.20, T:0.22
Consensus pattern (19 bp):
TGGCACCAACTACCAGTTC
Found at i:26958 original size:27 final size:29
Alignment explanation
Indices: 26911--26968 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
26901 TTTCCTTACT
* *
26911 CTTTTTTTTTATTGATTACCA-CGTTTTA
1 CTTTTTTCTTATTGATTACCACCATTTTA
26939 CTTTTTTCTTA-T-ATTGACCACCATTTTA
1 CTTTTTTCTTATTGATT-ACCACCATTTTA
26967 CT
1 CT
26969 CTCTGAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 3 0.12
27 5 0.19
28 18 0.69
ACGTcount: A:0.19, C:0.19, G:0.05, T:0.57
Consensus pattern (29 bp):
CTTTTTTCTTATTGATTACCACCATTTTA
Found at i:27017 original size:22 final size:22
Alignment explanation
Indices: 26992--27072 Score: 78
Period size: 22 Copynumber: 3.7 Consensus size: 22
26982 ATCACCTTTC
26992 ACTCTTTACAGATTACTATTTT
1 ACTCTTTACAGATTACTATTTT
* *
27014 ACTC-TTACTA-ATAACCATTTT
1 ACTCTTTAC-AGATTACTATTTT
* *
27035 GCTCTTTACTGATTACTATTTT
1 ACTCTTTACAGATTACTATTTT
*
27057 AC-CTTTTACTGATTAC
1 ACTC-TTTACAGATTAC
27073 CTTTTTTTAC
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
21 17 0.35
22 31 0.65
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.48
Consensus pattern (22 bp):
ACTCTTTACAGATTACTATTTT
Found at i:27033 original size:21 final size:22
Alignment explanation
Indices: 26992--27062 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 22
26982 ATCACCTTTC
* *
26992 ACTCTTTAC-AGATTACTATTTT
1 ACTCTTTACTA-ATAACCATTTT
27014 ACTC-TTACTAATAACCATTTT
1 ACTCTTTACTAATAACCATTTT
* * * *
27035 GCTCTTTACTGATTACTATTTT
1 ACTCTTTACTAATAACCATTTT
27057 AC-CTTT
1 ACTCTTT
27063 TACTGATTAC
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
21 20 0.50
22 20 0.50
ACGTcount: A:0.25, C:0.21, G:0.04, T:0.49
Consensus pattern (22 bp):
ACTCTTTACTAATAACCATTTT
Found at i:27165 original size:22 final size:22
Alignment explanation
Indices: 27079--27447 Score: 232
Period size: 22 Copynumber: 18.1 Consensus size: 22
27069 TTACCTTTTT
* *
27079 TTACTATTTTA-TTCTTTATTGA
1 TTACCATTTTACTT-TTTACTGA
*
27101 TTACC-TTCTTACTTTTTACTGT
1 TTACCATT-TTACTTTTTACTGA
* ** *
27123 TTACTATTTCGC-TCTTACTGA
1 TTACCATTTTACTTTTTACTGA
27144 TTACCATTTTACTTTTTACTGA
1 TTACCATTTTACTTTTTACTGA
* *
27166 TTATCA--TCACTTTTTACT-A
1 TTACCATTTTACTTTTTACTGA
* *
27185 TT--C----TACTCTATACTGA
1 TTACCATTTTACTTTTTACTGA
27201 TTA-CATTCTTACTTTTTACTGA
1 TTACCATT-TTACTTTTTACTGA
* *
27223 TTACTATTTTACTCTTTACTGA
1 TTACCATTTTACTTTTTACTGA
*
27245 TTACTATTTTAC-TTTTACTGA
1 TTACCATTTTACTTTTTACTGA
*
27266 TTATCA--TTACTTTTTAC---
1 TTACCATTTTACTTTTTACTGA
*
27283 -T---ATTTTACTCTTTACTGA
1 TTACCATTTTACTTTTTACTGA
27301 TTACC-TTCTTACTTTTTACTGA
1 TTACCATT-TTACTTTTTACTGA
* *
27323 TTACTATTTTACTCTTTACTGA
1 TTACCATTTTACTTTTTACTGA
**
27345 TTATTATTTTAC-TTTTACTGA
1 TTACCATTTTACTTTTTACTGA
*
27366 TTATCA--TTACTTTTTAC---
1 TTACCATTTTACTTTTTACTGA
*
27383 -T---ATTTTACTCTTTACTGA
1 TTACCATTTTACTTTTTACTGA
27401 TTACC-TTCTTACTTTTTACTGA
1 TTACCATT-TTACTTTTTACTGA
* *
27423 TTACTATTTTACTCTTTACTGA
1 TTACCATTTTACTTTTTACTGA
27445 TTA
1 TTA
27448 TCATCACTTT
Statistics
Matches: 276, Mismatches: 35, Indels: 72
0.72 0.09 0.19
Matches are distributed among these distances:
13 2 0.01
15 28 0.10
16 5 0.02
17 2 0.01
19 13 0.05
20 23 0.08
21 47 0.17
22 145 0.53
23 11 0.04
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.56
Consensus pattern (22 bp):
TTACCATTTTACTTTTTACTGA
Found at i:27290 original size:8 final size:7
Alignment explanation
Indices: 27209--27442 Score: 89
Period size: 7 Copynumber: 32.7 Consensus size: 7
27199 GATTACATTC
27209 TTACTTT
1 TTACTTT
**
27216 TTACTGA
1 TTACTTT
27223 TTACTATT
1 TTACT-TT
*
27231 TTACTCT
1 TTACTTT
**
27238 TTACTGA
1 TTACTTT
27245 TTACTATT
1 TTACT-TT
27253 TTAC-TT
1 TTACTTT
**
27259 TTACTGA
1 TTACTTT
**
27266 TTA-TCA
1 TTACTTT
27272 TTACTTT
1 TTACTTT
27279 TTACTATT
1 TTACT-TT
*
27287 TTACTCT
1 TTACTTT
**
27294 TTACTGA
1 TTACTTT
*
27301 TTACCTTC
1 TTA-CTTT
27309 TTACTTT
1 TTACTTT
**
27316 TTACTGA
1 TTACTTT
27323 TTACTATT
1 TTACT-TT
*
27331 TTACTCT
1 TTACTTT
**
27338 TTACTGA
1 TTACTTT
*
27345 TTATTATT
1 TTACT-TT
27353 TTAC-TT
1 TTACTTT
**
27359 TTACTGA
1 TTACTTT
**
27366 TTA-TCA
1 TTACTTT
27372 TTACTTT
1 TTACTTT
27379 TTACTATT
1 TTACT-TT
*
27387 TTACTCT
1 TTACTTT
**
27394 TTACTGA
1 TTACTTT
*
27401 TTACCTTC
1 TTA-CTTT
27409 TTACTTT
1 TTACTTT
**
27416 TTACTGA
1 TTACTTT
27423 TTACTATT
1 TTACT-TT
*
27431 TTACTCT
1 TTACTTT
27438 TTACT
1 TTACT
27443 GATTATCATC
Statistics
Matches: 167, Mismatches: 47, Indels: 26
0.70 0.20 0.11
Matches are distributed among these distances:
6 22 0.13
7 99 0.59
8 46 0.28
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.57
Consensus pattern (7 bp):
TTACTTT
Found at i:27313 original size:78 final size:78
Alignment explanation
Indices: 27115--27442 Score: 261
Period size: 78 Copynumber: 4.2 Consensus size: 78
27105 CTTCTTACTT
** * * *
27115 TTTACTGTTTACTATTTCGCTC-TTACTGATTACCATTTTACTTTTTACTGATTA-TCA--TCAC
1 TTTACT-TTTACTATTTTACTCTTTACTGATTACTATTTTACTCTTTACTGATTACT-ATTTTAC
27176 TTTTTACT-ATTCTACTC-
64 -TTTTACTGA-T-TA-TCA
* * *
27193 TATACTGATTAC-ATTCTTACTTTTTACTGATTACTATTTTACTCTTTACTGATTACTATTTTAC
1 TTTACT-TTTACTATT-TTACTCTTTACTGATTACTATTTTACTCTTTACTGATTACTATTTTAC
27257 TTTTACTGATTATCA
64 TTTTACTGATTATCA
* *
27272 -TTACTTTTTACTATTTTACTCTTTACTGATTACCT-TCTTACTTTTTACTGATTACTATTTTAC
1 TTTAC-TTTTACTATTTTACTCTTTACTGATTA-CTATTTTACTCTTTACTGATTACTATTTTAC
*
27335 TCTTTACTGATTATTA
64 T-TTTACTGATTATCA
* ** *
27351 TTTTACTTTTACTGA--TTA-TCATTACTTTTTACTATTTTACTCTTTACTGATTACCT-TCTTA
1 -TTTACTTTTACT-ATTTTACTCTTTACTGATTACTATTTTACTCTTTACTGATTA-CTATTTTA
27412 CTTTTTACTGATTA-CTA
63 C-TTTTACTGATTATC-A
27429 TTTTACTCTTTACT
1 -TTTACT-TTTACT
27443 GATTATCATC
Statistics
Matches: 210, Mismatches: 21, Indels: 37
0.78 0.08 0.14
Matches are distributed among these distances:
77 5 0.02
78 116 0.55
79 64 0.30
80 16 0.08
81 9 0.04
ACGTcount: A:0.22, C:0.19, G:0.04, T:0.55
Consensus pattern (78 bp):
TTTACTTTTACTATTTTACTCTTTACTGATTACTATTTTACTCTTTACTGATTACTATTTTACTT
TTACTGATTATCA
Found at i:27448 original size:100 final size:100
Alignment explanation
Indices: 27030--27447 Score: 673
Period size: 100 Copynumber: 4.2 Consensus size: 100
27020 ACTAATAACC
* * *
27030 ATTTTGCTCTTTACTGATTACTATTTTACCTTTTACTGATTA-CCTT--TTTTTACTATTTTATT
1 ATTTTACTCTTTACTGATTACTATTTTA-CTTTTACTGATTATCATTACTTTTTACTATTTTACT
* *
27092 CTTTATTGATTACCTTCTTACTTTTTACTGTTTACT
65 CTTTACTGATTACCTTCTTACTTTTTACTGATTACT
** * * *
27128 ATTTCGCTC-TTACTGATTACCATTTTACTTTTTACTGATTATCATCACTTTTTACTATTCTACT
1 ATTTTACTCTTTACTGATTACTATTTTAC-TTTTACTGATTATCATTACTTTTTACTATTTTACT
* *
27192 CTATACTGATTACATTCTTACTTTTTACTGATTACT
65 CTTTACTGATTACCTTCTTACTTTTTACTGATTACT
27228 ATTTTACTCTTTACTGATTACTATTTTACTTTTACTGATTATCATTACTTTTTACTATTTTACTC
1 ATTTTACTCTTTACTGATTACTATTTTACTTTTACTGATTATCATTACTTTTTACTATTTTACTC
27293 TTTACTGATTACCTTCTTACTTTTTACTGATTACT
66 TTTACTGATTACCTTCTTACTTTTTACTGATTACT
*
27328 ATTTTACTCTTTACTGATTATTATTTTACTTTTACTGATTATCATTACTTTTTACTATTTTACTC
1 ATTTTACTCTTTACTGATTACTATTTTACTTTTACTGATTATCATTACTTTTTACTATTTTACTC
27393 TTTACTGATTACCTTCTTACTTTTTACTGATTACT
66 TTTACTGATTACCTTCTTACTTTTTACTGATTACT
27428 ATTTTACTCTTTACTGATTA
1 ATTTTACTCTTTACTGATTA
27448 TCATCACTTT
Statistics
Matches: 297, Mismatches: 18, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
96 1 0.00
97 29 0.10
98 10 0.03
100 239 0.80
101 18 0.06
ACGTcount: A:0.22, C:0.18, G:0.05, T:0.56
Consensus pattern (100 bp):
ATTTTACTCTTTACTGATTACTATTTTACTTTTACTGATTATCATTACTTTTTACTATTTTACTC
TTTACTGATTACCTTCTTACTTTTTACTGATTACT
Done.