Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006495.1 Corchorus capsularis cultivar CVL-1 contig06516, 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: 29222
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:166 original size:42 final size:42
Alignment explanation
Indices: 118--201 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
108 TCAAAAATTG
** *
118 CATTTTTCTGAAATCGTCATCAAAATACGGCACGTTATCGTT
1 CATTTTTCTGAAATCGTCATCAAAATACAACACGTTAACGTT
*
160 CATTTTTCTTAAATCGTCATCAAAATACAACACGTTAACGTT
1 CATTTTTCTGAAATCGTCATCAAAATACAACACGTTAACGTT
202 ATTCTACGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (42 bp):
CATTTTTCTGAAATCGTCATCAAAATACAACACGTTAACGTT
Found at i:720 original size:34 final size:34
Alignment explanation
Indices: 682--792 Score: 86
Period size: 34 Copynumber: 3.1 Consensus size: 34
672 TAATTTGAGA
682 TTAAACTTAGTGAAATTAATTTTATATTTTATTT
1 TTAAACTTAGTGAAATTAATTTTATATTTTATTT
* * *
716 TTAAAATCCTA-T--AATATAA-TTAAAATTTTAATTT
1 TT-AAA-CTTAGTGAAAT-TAATTTTATATTTT-ATTT
750 TGGGCTAAACTTAGTGAAATTAATTTTATATTTTATTT
1 T----TAAACTTAGTGAAATTAATTTTATATTTTATTT
*
788 CTAAA
1 TTAAA
793 ACCCTATAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 24
0.65 0.08 0.27
Matches are distributed among these distances:
33 11 0.19
34 14 0.24
35 4 0.07
36 6 0.10
37 4 0.07
38 8 0.14
39 11 0.19
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.50
Consensus pattern (34 bp):
TTAAACTTAGTGAAATTAATTTTATATTTTATTT
Found at i:733 original size:72 final size:72
Alignment explanation
Indices: 656--803 Score: 244
Period size: 72 Copynumber: 2.1 Consensus size: 72
646 TTACCCTTAA
* *
656 AATATAATTAAAATTTTAA-TTTGAGATTAAACTTAGTGAAATTAATTTTATATTTTATTTTTAA
1 AATATAATTAAAATTTTAATTTTG-GACTAAACTTAGTGAAATTAATTTTATATTTTATTTCTAA
*
720 AATCCTAT
65 AACCCTAT
*
728 AATATAATTAAAATTTTAATTTTGGGCTAAACTTAGTGAAATTAATTTTATATTTTATTTCTAAA
1 AATATAATTAAAATTTTAATTTTGGACTAAACTTAGTGAAATTAATTTTATATTTTATTTCTAAA
793 ACCCTAT
66 ACCCTAT
800 AATA
1 AATA
804 AAAAACCTTT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
72 67 0.94
73 4 0.06
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (72 bp):
AATATAATTAAAATTTTAATTTTGGACTAAACTTAGTGAAATTAATTTTATATTTTATTTCTAAA
ACCCTAT
Found at i:1936 original size:8 final size:8
Alignment explanation
Indices: 1925--1953 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1915 AGAAAAGAAA
1925 AAAAAAAC
1 AAAAAAAC
1933 AAAAAAAC
1 AAAAAAAC
1941 -AAAAAAC
1 AAAAAAAC
1948 AAAAAA
1 AAAAAA
1954 GAATTAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:1944 original size:15 final size:14
Alignment explanation
Indices: 1922--1953 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
1912 CTAAGAAAAG
1922 AAAAAAAAAACAAA
1 AAAAAAAAAACAAA
1936 AAAACAAAAAACAAA
1 AAAA-AAAAAACAAA
1951 AAA
1 AAA
1954 GAATTAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAACAAA
Found at i:2074 original size:16 final size:16
Alignment explanation
Indices: 2053--2110 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
2043 GTCAACGTCT
**
2053 CGAACCCGAAATTACC
1 CGAACCCGAAACAACC
* *
2069 CGAACCTGAGACAACC
1 CGAACCCGAAACAACC
*
2085 CGAACCCGAGACAACC
1 CGAACCCGAAACAACC
2101 CGAACCCGAA
1 CGAACCCGAA
2111 TCCGACCCGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.38, C:0.40, G:0.17, T:0.05
Consensus pattern (16 bp):
CGAACCCGAAACAACC
Found at i:3997 original size:16 final size:16
Alignment explanation
Indices: 3976--4095 Score: 140
Period size: 15 Copynumber: 7.7 Consensus size: 16
3966 TCGGCCCCGA
3976 ACCCGAACCCGAAAAT
1 ACCCGAACCCGAAAAT
3992 ACCCGAACCCG-AAAT
1 ACCCGAACCCGAAAAT
4007 ACCCGAACCCGACAAA-
1 ACCCGAACCCGA-AAAT
*
4023 ACCCGAACCTGAAAAT
1 ACCCGAACCCGAAAAT
*
4039 A-CCGAATCCGAAAAT
1 ACCCGAACCCGAAAAT
* *
4054 ACTCGAACCC-AAAGT
1 ACCCGAACCCGAAAAT
***
4069 ACCCGAACCCGAACCC
1 ACCCGAACCCGAAAAT
4085 ACCCGAACCCG
1 ACCCGAACCCG
4096 TCCAATTGCC
Statistics
Matches: 89, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
15 44 0.49
16 42 0.47
17 3 0.03
ACGTcount: A:0.40, C:0.40, G:0.13, T:0.07
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:4014 original size:31 final size:31
Alignment explanation
Indices: 3976--4095 Score: 138
Period size: 31 Copynumber: 3.9 Consensus size: 31
3966 TCGGCCCCGA
3976 ACCCGAACCCGAAAATACCCGAACCCGAAAT
1 ACCCGAACCCGAAAATACCCGAACCCGAAAT
*
4007 ACCCGAACCCGACAAA-ACCCGAACCTGAAAAT
1 ACCCGAACCCGA-AAATACCCGAACCCG-AAAT
* *
4039 A-CCGAATCCGAAAATACTCGAACCC-AAAGT
1 ACCCGAACCCGAAAATACCCGAACCCGAAA-T
***
4069 ACCCGAACCCGAACCCACCCGAACCCG
1 ACCCGAACCCGAAAATACCCGAACCCG
4096 TCCAATTGCC
Statistics
Matches: 74, Mismatches: 9, Indels: 11
0.79 0.10 0.12
Matches are distributed among these distances:
29 3 0.04
30 5 0.07
31 58 0.78
32 8 0.11
ACGTcount: A:0.40, C:0.40, G:0.13, T:0.07
Consensus pattern (31 bp):
ACCCGAACCCGAAAATACCCGAACCCGAAAT
Found at i:7096 original size:21 final size:21
Alignment explanation
Indices: 7043--7102 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
7033 TTTGGAGCAA
*
7043 GAATATTCCAATCGATTCTAT
1 GAATATTCCAATCGATTCTAG
** * *
7064 GTCTACTACAATCGATTCTAG
1 GAATATTCCAATCGATTCTAG
7085 GAATATTCCAATCGATTC
1 GAATATTCCAATCGATTC
7103 CAAGTTATAC
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.35
Consensus pattern (21 bp):
GAATATTCCAATCGATTCTAG
Found at i:9409 original size:27 final size:28
Alignment explanation
Indices: 9379--9453 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 28
9369 AGGGTCACAT
9379 AGGGGCATTTTGGTCATTTTTACATTC-
1 AGGGGCATTTTGGTCATTTTTACATTCA
* * *
9406 AGGGGTATTTAGGTCATTTTTGCATTCA
1 AGGGGCATTTTGGTCATTTTTACATTCA
*
9434 AGGGGCAATTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
9454 GAGTCCAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
27 24 0.59
28 17 0.41
ACGTcount: A:0.20, C:0.12, G:0.25, T:0.43
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTTACATTCA
Found at i:12700 original size:21 final size:21
Alignment explanation
Indices: 12659--12715 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
12649 ATTATGAGCT
* **
12659 AATTTT-AATTTAAAGGTTAA
1 AATTTTGAATTAAAAGACTAA
12679 AATTTTGAATTAAAAGACTAA
1 AATTTTGAATTAAAAGACTAA
* *
12700 ATTATTTGTATTAAAA
1 AAT-TTTGAATTAAAA
12716 ATCAACTCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 6 0.20
21 13 0.43
22 11 0.37
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (21 bp):
AATTTTGAATTAAAAGACTAA
Found at i:13980 original size:22 final size:21
Alignment explanation
Indices: 13945--13985 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
13935 AGTTTTGAAC
13945 CAGCATTTTTAAAAAATTTCA
1 CAGCATTTTTAAAAAATTTCA
13966 CAGCATTTTTAAAAAATTTC
1 CAGCATTTTTAAAAAATTTC
13986 TTCCCGGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.39
Consensus pattern (21 bp):
CAGCATTTTTAAAAAATTTCA
Found at i:18152 original size:17 final size:17
Alignment explanation
Indices: 18097--18180 Score: 65
Period size: 17 Copynumber: 5.2 Consensus size: 17
18087 AATTAGAGAA
*
18097 TATATCGTAATTAACAT
1 TATATCATAATTAACAT
* *
18114 TATAAT-GTAATGTTA-AT
1 TAT-ATCATAAT-TAACAT
18131 TATATCATAATTAACAT
1 TATATCATAATTAACAT
*
18148 TATAT-AT--TT--CAA
1 TATATCATAATTAACAT
18160 TATATCATAATTAACAT
1 TATATCATAATTAACAT
18177 TATA
1 TATA
18181 ATGTATTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 18
0.70 0.07 0.24
Matches are distributed among these distances:
12 7 0.13
13 2 0.04
14 2 0.04
15 2 0.04
16 6 0.11
17 30 0.57
18 4 0.08
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (17 bp):
TATATCATAATTAACAT
Found at i:18163 original size:29 final size:31
Alignment explanation
Indices: 18095--18180 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 31
18085 CTAATTAGAG
*
18095 AATATATCGTAATTAACATTATAATGTAATGTT
1 AATATATCATAATTAACATTAT-A-GTAATGTT
18128 AATTATATCATAATTAACATTATA-T-AT-TT
1 AA-TATATCATAATTAACATTATAGTAATGTT
18157 CAATATATCATAATTAACATTATA
1 -AATATATCATAATTAACATTATA
18181 ATGTATTTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 8
0.85 0.02 0.14
Matches are distributed among these distances:
29 23 0.46
30 4 0.08
31 1 0.02
33 3 0.06
34 19 0.38
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.43
Consensus pattern (31 bp):
AATATATCATAATTAACATTATAGTAATGTT
Found at i:19243 original size:310 final size:308
Alignment explanation
Indices: 18736--19308 Score: 925
Period size: 310 Copynumber: 1.9 Consensus size: 308
18726 TAAAACGAAT
*
18736 TGGTCAAGGTAAATATTATTTATTATTTATTTAAAGACGAAACAAAGACAAAACAATTAAATCAA
1 TGGTCAAGGGAAATATTATTTATTATTTATTTAAAGACGAAACAAAGACAAAACAATTAAATCAA
* *
18801 CATTCTTTCCCAAACCACGTGATCAGTAAGACCACACGACATTCCTAAATAGTCAAGAAACAAGA
66 CATTCTTTCCCAAACCACGTGATCAATAAGACCACACGACATCCCTAAATAGTCAAGAAACAAGA
*
18866 AGACTTCTCTAAAGAACATACCATATATGGATACCTAGTTGAAAAAGCAAATGAGTTCGCTCTTA
131 AGACTTCTCTAAAGAACACACCATATATGGATACCTAGTTGAAAAAGCAAATGAGTTCGCTCTTA
* * *
18931 ACTCCCGCTTTAGCCATCCCATCTGCAATCTTGGAGCATTAATCATATCTCTAGTATTTAGATTG
196 ACTCCCACTTTAGCCAGCCCATCTGCAATCTTGGAGCATTAATCATATCTCTAGCATTTAGATTG
18996 AGAGATCTAAAGCAAGTGATCTTGAAGCAAGTGATCTCTCAATCAAAG
261 AGAGATCTAAAGCAAGTGATCTTGAAGCAAGTGATCTCTCAATCAAAG
* * ** * *
19044 TGGTCAAGGGAATTATTATTTGTTATTTATTT-AAGACGGGATAAAGACAAAACAATTAAATCCA
1 TGGTCAAGGGAAATATTATTTATTATTTATTTAAAGACGAAACAAAGACAAAACAATTAAATCAA
* *
19108 CCTTCTTTCCCAAACCACGTGATCAATAGGACCACACGACATCCCTAAATAGTCAAGAATCAACC
66 CATTCTTTCCCAAACCACGTGATCAATAAGACCACACGACATCCCTAAATAGTCAAG-A--AA-C
* * *
19173 AA-AAGACTTTTCTAAAGAACACACCATATATGGATACCTAGTTTAAAAAGCAATTGAGTTCGCT
127 AAGAAGACTTCTCTAAAGAACACACCATATATGGATACCTAGTTGAAAAAGCAAATGAGTTCGCT
*
19237 CTTAACTCCCACTTTAGCCAGCCCATCTGCAATCTTGGAGCATTAATCATATGTCTAGCATTTAG
192 CTTAACTCCCACTTTAGCCAGCCCATCTGCAATCTTGGAGCATTAATCATATCTCTAGCATTTAG
19302 ATTGAGA
257 ATTGAGA
19309 TATCACATTA
Statistics
Matches: 242, Mismatches: 19, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
307 81 0.33
308 30 0.12
310 128 0.53
311 3 0.01
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (308 bp):
TGGTCAAGGGAAATATTATTTATTATTTATTTAAAGACGAAACAAAGACAAAACAATTAAATCAA
CATTCTTTCCCAAACCACGTGATCAATAAGACCACACGACATCCCTAAATAGTCAAGAAACAAGA
AGACTTCTCTAAAGAACACACCATATATGGATACCTAGTTGAAAAAGCAAATGAGTTCGCTCTTA
ACTCCCACTTTAGCCAGCCCATCTGCAATCTTGGAGCATTAATCATATCTCTAGCATTTAGATTG
AGAGATCTAAAGCAAGTGATCTTGAAGCAAGTGATCTCTCAATCAAAG
Found at i:20846 original size:27 final size:27
Alignment explanation
Indices: 20816--20867 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
20806 CATTTCAAGT
*
20816 TAGTCAAGACAG-TTCTCCATTCAAAAC
1 TAGTCAAAACAGTTTC-CCATTCAAAAC
20843 TAGTCAAAACAGTTTCCCATTCAAA
1 TAGTCAAAACAGTTTCCCATTCAAA
20868 GTCAGTTCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.27
Consensus pattern (27 bp):
TAGTCAAAACAGTTTCCCATTCAAAAC
Found at i:25365 original size:27 final size:27
Alignment explanation
Indices: 25309--25371 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
25299 GTCAGACTCT
* * *
25309 CATTCCAAGTTAGTCAAGACAGTTCTC
1 CATTCAAAGCTAGTCAAAACAGTTCTC
*
25336 CATTCAAAGCTAGTCAAAACAATT-TCC
1 CATTCAAAGCTAGTCAAAACAGTTCT-C
25363 CATTCAAAG
1 CATTCAAAG
25372 TCAGTTCCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 1 0.03
27 30 0.97
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.27
Consensus pattern (27 bp):
CATTCAAAGCTAGTCAAAACAGTTCTC
Done.