Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015061.1 Corchorus capsularis cultivar CVL-1 contig15082, 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: 16735
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:83 original size:3 final size:3
Alignment explanation
Indices: 75--116 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
65 AATAAGCAAC
75 TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA -ATA TATA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TA-A TAA TAA
117 ATGAATAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 3 0.08
3 28 0.78
4 5 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:97 original size:17 final size:17
Alignment explanation
Indices: 77--131 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
67 TAAGCAACTA
77 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
94 ATAATAAT-A-AATATAT
1 ATAATAATAATAATA-AT
*
110 ATAATAAATGAATAAAAAT
1 ATAAT-AAT-AATAATAAT
129 ATA
1 ATA
132 GAGATCAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
15 4 0.12
16 8 0.25
17 11 0.34
19 6 0.19
20 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Found at i:113 original size:21 final size:21
Alignment explanation
Indices: 75--131 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
65 AATAAGCAAC
75 TAATAAT-AATA-ATAATAATA
1 TAATAATAAATATAT-ATAATA
95 TAATAATAAATATATATAATA
1 TAATAATAAATATATATAATA
*
116 -AATGAATAAAAATATA
1 TAAT-AATAAATATATA
132 GAGATCAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
20 10 0.30
21 21 0.64
22 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
TAATAATAAATATATATAATA
Found at i:1500 original size:19 final size:19
Alignment explanation
Indices: 1476--1513 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1466 CAAAAGCTGA
1476 CCCGAACCCACCCAACCCG
1 CCCGAACCCACCCAACCCG
**
1495 CCCGAACCTGCCCAACCCG
1 CCCGAACCCACCCAACCCG
1514 ATTTGATCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.61, G:0.13, T:0.03
Consensus pattern (19 bp):
CCCGAACCCACCCAACCCG
Found at i:1577 original size:16 final size:16
Alignment explanation
Indices: 1553--1683 Score: 117
Period size: 16 Copynumber: 8.2 Consensus size: 16
1543 CCCGTCCGAT
*
1553 CCGAGACCCGAATGAC
1 CCGAAACCCGAATGAC
1569 CC-ATAACCC-AGATGAC
1 CCGA-AACCCGA-ATGAC
*
1585 CCGAGACCCGAATGAC
1 CCGAAACCCGAATGAC
*
1601 CCGTAACCC-AGATGAC
1 CCGAAACCCGA-ATGAC
1617 CCGAAACCCGAATGAC
1 CCGAAACCCGAATGAC
* * *
1633 CCGTAA-TCGAGTGAC
1 CCGAAACCCGAATGAC
* *
1648 CCGAGACCCGTATGAC
1 CCGAAACCCGAATGAC
* *
1664 CCGAAACCCAAATAAC
1 CCGAAACCCGAATGAC
1680 CCGA
1 CCGA
1684 GAAGTTAACC
Statistics
Matches: 91, Mismatches: 17, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
15 14 0.15
16 74 0.81
17 3 0.03
ACGTcount: A:0.34, C:0.37, G:0.20, T:0.10
Consensus pattern (16 bp):
CCGAAACCCGAATGAC
Found at i:1586 original size:9 final size:8
Alignment explanation
Indices: 1553--1667 Score: 66
Period size: 9 Copynumber: 14.5 Consensus size: 8
1543 CCCGTCCGAT
1553 CCGA-GAC
1 CCGATGAC
1560 CCGAATGAC
1 CCG-ATGAC
*
1569 CC-ATAAC
1 CCGATGAC
1576 CCAGATGAC
1 CC-GATGAC
1585 CCGA-GAC
1 CCGATGAC
1592 CCGAATGAC
1 CCG-ATGAC
*
1601 CCG-TAAC
1 CCGATGAC
1608 CCAGATGAC
1 CC-GATGAC
*
1617 CCGA-AAC
1 CCGATGAC
1624 CCGAATGAC
1 CCG-ATGAC
*
1633 CCG-T-AA
1 CCGATGAC
*
1639 TCGAGTGAC
1 CCGA-TGAC
1648 CCGA-GAC
1 CCGATGAC
1655 CCGTATGAC
1 CCG-ATGAC
1664 CCGA
1 CCGA
1668 AACCCAAATA
Statistics
Matches: 83, Mismatches: 10, Indels: 29
0.68 0.08 0.24
Matches are distributed among these distances:
6 3 0.04
7 32 0.39
8 11 0.13
9 37 0.45
ACGTcount: A:0.31, C:0.37, G:0.22, T:0.10
Consensus pattern (8 bp):
CCGATGAC
Found at i:1589 original size:32 final size:32
Alignment explanation
Indices: 1553--1685 Score: 171
Period size: 32 Copynumber: 4.2 Consensus size: 32
1543 CCCGTCCGAT
1553 CCGAGACCCGAATGACCCATAACCCAGATGAC
1 CCGAGACCCGAATGACCCATAACCCAGATGAC
*
1585 CCGAGACCCGAATGACCCGTAACCCAGATGAC
1 CCGAGACCCGAATGACCCATAACCCAGATGAC
* * * *
1617 CCGAAACCCGAATGACCCGTAATCGAG-TGAC
1 CCGAGACCCGAATGACCCATAACCCAGATGAC
* * *
1648 CCGAGACCCGTATGACCCGA-AACCCAAATAAC
1 CCGAGACCCGAATGACCC-ATAACCCAGATGAC
1680 CCGAGA
1 CCGAGA
1686 AGTTAACCCG
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
31 24 0.27
32 64 0.73
ACGTcount: A:0.34, C:0.36, G:0.20, T:0.10
Consensus pattern (32 bp):
CCGAGACCCGAATGACCCATAACCCAGATGAC
Found at i:1666 original size:47 final size:46
Alignment explanation
Indices: 1553--1685 Score: 130
Period size: 47 Copynumber: 2.8 Consensus size: 46
1543 CCCGTCCGAT
1553 CCGAGACCCGAATGACCC-ATAACCCAGATGACCCGAGACCCGAATGAC
1 CCGAGACCCG-ATGACCCGA-AACCCA-ATGACCCGAGACCCGAATGAC
* *
1601 CCGTA-ACCCAGATGACCCGAAACCCGAATGACCCGTA-A-TCGAGTGAC
1 CCG-AGACCC-GATGACCCGAAACCC-AATGACCCG-AGACCCGAATGAC
*
1648 CCGAGACCCGTATGACCCGAAACCCAAATAACCCGAGA
1 CCGAGACCCG-ATGACCCGAAACCC-AATGACCCGAGA
1686 AGTTAACCCG
Statistics
Matches: 73, Mismatches: 4, Indels: 17
0.78 0.04 0.18
Matches are distributed among these distances:
46 3 0.04
47 37 0.51
48 28 0.38
49 5 0.07
ACGTcount: A:0.34, C:0.36, G:0.20, T:0.10
Consensus pattern (46 bp):
CCGAGACCCGATGACCCGAAACCCAATGACCCGAGACCCGAATGAC
Found at i:2277 original size:42 final size:42
Alignment explanation
Indices: 2209--2290 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
2199 ATTTGACACA
* * *
2209 TACCCCACTTGATAATTAATTATGTATTTAATATTTAAAACC
1 TACCCCACCTGATAATCAATTATGTATTTAATATTCAAAACC
* *
2251 TACCTCACCTGATAATCGATTATGTATTTAATATTCAAAA
1 TACCCCACCTGATAATCAATTATGTATTTAATATTCAAAA
2291 TTAATATCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.39
Consensus pattern (42 bp):
TACCCCACCTGATAATCAATTATGTATTTAATATTCAAAACC
Found at i:2558 original size:32 final size:32
Alignment explanation
Indices: 2522--2584 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
2512 CCAACTCGAG
* * * *
2522 ACCCGCATGACCTGGAACCCGTATGACCCGAT
1 ACCCGAATGACCCGAAACCCGAATGACCCGAT
2554 ACCCGAATGACCCGAAACCCGAATGACCCGA
1 ACCCGAATGACCCGAAACCCGAATGACCCGA
2585 GAAAACTGCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.30, C:0.38, G:0.21, T:0.11
Consensus pattern (32 bp):
ACCCGAATGACCCGAAACCCGAATGACCCGAT
Found at i:2582 original size:16 final size:16
Alignment explanation
Indices: 2522--2584 Score: 81
Period size: 16 Copynumber: 3.9 Consensus size: 16
2512 CCAACTCGAG
* * *
2522 ACCCGCATGACCTGGA
1 ACCCGAATGACCCGAA
* *
2538 ACCCGTATGACCCGAT
1 ACCCGAATGACCCGAA
2554 ACCCGAATGACCCGAA
1 ACCCGAATGACCCGAA
2570 ACCCGAATGACCCGA
1 ACCCGAATGACCCGA
2585 GAAAACTGCC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.30, C:0.38, G:0.21, T:0.11
Consensus pattern (16 bp):
ACCCGAATGACCCGAA
Found at i:3307 original size:30 final size:30
Alignment explanation
Indices: 3273--3331 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
3263 TCTCATGGAA
3273 TGTGAGTTTTCTTTGTAATTTATTTGTTTG
1 TGTGAGTTTTCTTTGTAATTTATTTGTTTG
3303 TGTGAGTTTTCTTTGTAATTTATTTGTTT
1 TGTGAGTTTTCTTTGTAATTTATTTGTTT
3332 TTATATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.14, C:0.03, G:0.19, T:0.64
Consensus pattern (30 bp):
TGTGAGTTTTCTTTGTAATTTATTTGTTTG
Found at i:4422 original size:30 final size:30
Alignment explanation
Indices: 4386--4443 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
4376 ATCTTCAAGC
4386 CCATGATAAGTCCTT-GGCGCATCATTCCTT
1 CCATGATAAG-CCTTGGGCGCATCATTCCTT
4416 CCATGATAAGCCTTGGGCGCATCATTCC
1 CCATGATAAGCCTTGGGCGCATCATTCC
4444 CTCCCCCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.21, C:0.31, G:0.19, T:0.29
Consensus pattern (30 bp):
CCATGATAAGCCTTGGGCGCATCATTCCTT
Found at i:4917 original size:33 final size:33
Alignment explanation
Indices: 4880--4965 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 33
4870 ATGATCAACC
** * *
4880 AAAACAGA-TTTGTTTTCATCACAATTAGCATCT
1 AAAACAGATTTTG-TTTCATCACAAACAACACCT
4913 AAAACAGATTTTGTTTCATCACAAACAACACCT
1 AAAACAGATTTTGTTTCATCACAAACAACACCT
* *
4946 AAAACAGATTTAGTGTCATC
1 AAAACAGATTTTGTTTCATC
4966 GCAGACTACA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 42 0.91
34 4 0.09
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (33 bp):
AAAACAGATTTTGTTTCATCACAAACAACACCT
Found at i:6435 original size:11 final size:10
Alignment explanation
Indices: 6402--6437 Score: 63
Period size: 10 Copynumber: 3.5 Consensus size: 10
6392 TCTAGTCGAT
6402 TTTTTTTTAA
1 TTTTTTTTAA
6412 TTTTTTTTAA
1 TTTTTTTTAA
6422 TTTTTTTTATA
1 TTTTTTTTA-A
6433 TTTTT
1 TTTTT
6438 CGATATAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 19 0.76
11 6 0.24
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTTTAA
Done.