Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011288.1 Corchorus capsularis cultivar CVL-1 contig11309, 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: 38355
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:156 original size:22 final size:21
Alignment explanation
Indices: 126--187 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
116 AAAGTCGCAC
*
126 CCGGATCGCGACCCGCCACGG
1 CCGGGTCGCGACCCGCCACGG
**
147 TCCGGGTCGCGACCCAGCCGTGG
1 -CCGGGTCGCGACCC-GCCACGG
170 CCGGGTCGTGCGACCCGC
1 CCGGGTC--GCGACCCGC
188 TTTCTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 20 0.59
23 7 0.21
24 7 0.21
ACGTcount: A:0.10, C:0.44, G:0.37, T:0.10
Consensus pattern (21 bp):
CCGGGTCGCGACCCGCCACGG
Found at i:4809 original size:183 final size:183
Alignment explanation
Indices: 4501--4864 Score: 647
Period size: 183 Copynumber: 2.0 Consensus size: 183
4491 TGTTTTGAAG
4501 TTTGTAGTTGAGAGACCTTTGGTAAAGCAGTCTGCAAGTTGTAGTTGAGAAGTAATTGGCAGTAA
1 TTTGTAGTTGAGAGACCTTTGGTAAAGCAGTCTGCAAGTTGTAGTTGAGAAGTAATTGGCAGTAA
* *
4566 TTTGATAAATTCAGATTGTAGTTTACTTCTAACTTCTAACACATGACAATCTATGTCAATGTGCT
66 TTTGATAAATCCAGATTGTAGTTTACTTCTAACTTCTAACACATGACAATCAATGTCAATGTGCT
* * *
4631 TAGTCTTCTCGTGATATTAGGGGCGTAGCCACCTTATAAGGAGTGGGGTCACC
131 TAGTCCTCTCGTGAAATCAGGGGCGTAGCCACCTTATAAGGAGTGGGGTCACC
*
4684 TTTGTAGTTGAGAGACCTTTGGTAAAGCAGTCTGCGAGTTGTAGTTGAGAAGTAATTGGCAGTAA
1 TTTGTAGTTGAGAGACCTTTGGTAAAGCAGTCTGCAAGTTGTAGTTGAGAAGTAATTGGCAGTAA
* *
4749 TTTGATAAGTCCAGATTGTAGTTTACTTCTAACTTCTAACACGTGACAATCAATGTCAATGTGCT
66 TTTGATAAATCCAGATTGTAGTTTACTTCTAACTTCTAACACATGACAATCAATGTCAATGTGCT
*
4814 TAGTCCTCTCGTGAAATCAGGGGTGTAGCCACCTTATAAGGAGTGGGGTCA
131 TAGTCCTCTCGTGAAATCAGGGGCGTAGCCACCTTATAAGGAGTGGGGTCA
4865 ATTGACCCCA
Statistics
Matches: 172, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
183 172 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.33
Consensus pattern (183 bp):
TTTGTAGTTGAGAGACCTTTGGTAAAGCAGTCTGCAAGTTGTAGTTGAGAAGTAATTGGCAGTAA
TTTGATAAATCCAGATTGTAGTTTACTTCTAACTTCTAACACATGACAATCAATGTCAATGTGCT
TAGTCCTCTCGTGAAATCAGGGGCGTAGCCACCTTATAAGGAGTGGGGTCACC
Found at i:4956 original size:30 final size:30
Alignment explanation
Indices: 4922--4987 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
4912 ATTAGAGAAA
*
4922 TTATCA-ATTGACCCCACTAAATTTGAAGTT
1 TTATCATATTGA-CCCACTAAAATTGAAGTT
4952 TTATCATATTGACCCACTAAAATTGAAGTT
1 TTATCATATTGACCCACTAAAATTGAAGTT
4982 TTATCA
1 TTATCA
4988 CATCACCCTC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 29 0.85
31 5 0.15
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (30 bp):
TTATCATATTGACCCACTAAAATTGAAGTT
Found at i:5002 original size:30 final size:30
Alignment explanation
Indices: 4934--5004 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
4924 ATCAATTGAC
* * *
4934 CCCACTAAATTTGAAGTTTTATCATATTGA
1 CCCACTAAAATTGAAGTTTTATCACATTCA
4964 CCCACTAAAATTGAAGTTTTATCACA-TCA
1 CCCACTAAAATTGAAGTTTTATCACATTCA
*
4993 CCCTCCTAAAAT
1 CCC-ACTAAAAT
5005 AAAATATTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 5 0.14
30 31 0.86
ACGTcount: A:0.35, C:0.24, G:0.07, T:0.34
Consensus pattern (30 bp):
CCCACTAAAATTGAAGTTTTATCACATTCA
Found at i:10782 original size:18 final size:19
Alignment explanation
Indices: 10763--10798 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
10753 AATTAATTAT
10763 TTTA-ATATTA-ATTTTTA
1 TTTATATATTATATTTTTA
10780 TTTATATATTATATTTTTA
1 TTTATATATTATATTTTTA
10799 CTTAAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 6 0.35
19 7 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTATATATTATATTTTTA
Found at i:13628 original size:18 final size:18
Alignment explanation
Indices: 13601--13636 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
13591 TCAAAATTTT
* *
13601 ATTTATTTTTTTCTGAAA
1 ATTTAATTTTTTCGGAAA
13619 ATTTAATTTTTTCGGAAA
1 ATTTAATTTTTTCGGAAA
13637 TAAATTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.56
Consensus pattern (18 bp):
ATTTAATTTTTTCGGAAA
Found at i:14791 original size:29 final size:31
Alignment explanation
Indices: 14731--14801 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 31
14721 CTAAATATCT
* * *
14731 AAAAAAATCCCTTCTATTTTTCTTTTAGGAC
1 AAAATAATCCCTTATATTTTTCTTTGAGGAC
*
14762 AAAATAATCCCTTATA-TTTT-TTTGGGGAC
1 AAAATAATCCCTTATATTTTTCTTTGAGGAC
*
14791 AAATTAATCCC
1 AAAATAATCCC
14802 CTATGTTTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 17 0.49
30 4 0.11
31 14 0.40
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.39
Consensus pattern (31 bp):
AAAATAATCCCTTATATTTTTCTTTGAGGAC
Found at i:14905 original size:28 final size:28
Alignment explanation
Indices: 14872--14925 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
14862 ACGTGGATTT
*
14872 TCCACGTCAGGTTATCAGTCCACGTGAA
1 TCCACGTCAGCTTATCAGTCCACGTGAA
14900 TCCACGTCAGCTTATCAGTCCACGTG
1 TCCACGTCAGCTTATCAGTCCACGTG
14926 GCATGTGGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.26
Consensus pattern (28 bp):
TCCACGTCAGCTTATCAGTCCACGTGAA
Found at i:20151 original size:87 final size:86
Alignment explanation
Indices: 19986--20169 Score: 219
Period size: 87 Copynumber: 2.1 Consensus size: 86
19976 CAGGCACAAA
* * * *
19986 ATCCTCCACCAAATCAGTTTCCAAAGATTTTGCATCATTACTAACTAAAACTCCATTAGGAAGAT
1 ATCCTCCACCAAATCAGTTTCCAAAGATTTTGCACCATAACCAACCAAAACTCCATTAGGAAGAT
*
20051 CACTGAAATTTGAATTCAAACT
66 CAC-GAAAATTGAATTCAAACT
* * * *
20073 ATCCTCTACCATAAT-ATTTTCCAAAGATTTTGCACCATAACCACCCATAACTCCATTAGGAAGA
1 ATCCTCCACCA-AATCAGTTTCCAAAGATTTTGCACCATAACCAACCAAAACTCCATTAGGAAGA
*
20137 TCAC-AATCAATTGAATTCAAATT
65 TCACGAA--AATTGAATTCAAACT
*
20160 ATTCTCCACC
1 ATCCTCCACC
20170 CTAAAGGAGT
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
85 2 0.02
87 77 0.94
88 3 0.04
ACGTcount: A:0.37, C:0.26, G:0.08, T:0.30
Consensus pattern (86 bp):
ATCCTCCACCAAATCAGTTTCCAAAGATTTTGCACCATAACCAACCAAAACTCCATTAGGAAGAT
CACGAAAATTGAATTCAAACT
Found at i:22981 original size:1 final size:1
Alignment explanation
Indices: 22975--23000 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
22965 ATCTTAATAG
22975 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
23001 GCCAAACTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:25292 original size:38 final size:38
Alignment explanation
Indices: 25250--25440 Score: 310
Period size: 38 Copynumber: 5.0 Consensus size: 38
25240 GGCTGTGCAT
*
25250 AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATGGTAAG
*
25288 AGTGGACCCGTGCCTGAGGGGGTTAAACTGATGGTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATGGTAAG
25326 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATGGTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATGGTAAG
* * * *
25364 AATGGACCCGTGCCTTAGGGTGTTAAACTGTTGGTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATGGTAAG
* *
25402 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGCAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATGGTAAG
25440 A
1 A
25441 TTGTGATTGT
Statistics
Matches: 142, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 142 1.00
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.22
Consensus pattern (38 bp):
AGTGGACCCGTGCCTCAGGGGGTTAAACTGATGGTAAG
Found at i:25450 original size:6 final size:6
Alignment explanation
Indices: 25439--25475 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
25429 CTGTTGGCAA
* *
25439 GATTGT GATTGT AATTGT GATTGT GATTGC GATTGT G
1 GATTGT GATTGT GATTGT GATTGT GATTGT GATTGT G
25476 GTGCAGCCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.19, C:0.03, G:0.32, T:0.46
Consensus pattern (6 bp):
GATTGT
Found at i:30270 original size:30 final size:30
Alignment explanation
Indices: 30225--30282 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 30
30215 AGGCGGTTTT
30225 CAATACTTAAGAAATTGAAAT-AAGAAATTTA
1 CAATACTTAAGAAATT-AAATCAA-AAATTTA
30256 CAATACTT-AGAAATTAAATCAAAAATT
1 CAATACTTAAGAAATTAAATCAAAAATT
30283 ACTCTAAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 9 0.35
30 9 0.35
31 8 0.31
ACGTcount: A:0.55, C:0.09, G:0.07, T:0.29
Consensus pattern (30 bp):
CAATACTTAAGAAATTAAATCAAAAATTTA
Found at i:33497 original size:18 final size:19
Alignment explanation
Indices: 33452--33497 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
33442 ATGGATTCCC
33452 TTGGAGAAATATTCAAAGAA
1 TTGGA-AAATATTCAAAGAA
* *
33472 AT-GCAAATATTCAAA-AA
1 TTGGAAAATATTCAAAGAA
33489 TTGGAAAAT
1 TTGGAAAAT
33498 GGACAATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 4
0.72 0.14 0.14
Matches are distributed among these distances:
17 3 0.14
18 16 0.76
19 1 0.05
20 1 0.05
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.26
Consensus pattern (19 bp):
TTGGAAAATATTCAAAGAA
Done.