Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020285.1 Corchorus olitorius cultivar O-4 contig20318, 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: 46227
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:945 original size:30 final size:28
Alignment explanation
Indices: 909--1006 Score: 83
Period size: 29 Copynumber: 3.3 Consensus size: 28
899 CCGAAAAGAA
909 CTTATTTGGCCTTTTTCAAGAGTTCAGGGG
1 CTTATTTGGCCTTTTT-AA-AGTTCAGGGG
**
939 CTTATTTGG-CTGCAATTAAAGTTCAGGGG
1 CTTATTTGGCCT--TTTTAAAGTTCAGGGG
*
968 CTTATTTGGCCGTTTTGTGTAAGTTCAGGGG
1 CTTATTTGGCC-TTTT-T-AAAGTTCAGGGG
999 TCTT-TTTG
1 -CTTATTTG
1007 AGCAATAAGC
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
29 22 0.39
30 13 0.23
31 18 0.32
32 3 0.05
ACGTcount: A:0.16, C:0.14, G:0.28, T:0.42
Consensus pattern (28 bp):
CTTATTTGGCCTTTTTAAAGTTCAGGGG
Found at i:1191 original size:44 final size:44
Alignment explanation
Indices: 1141--1230 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
1131 CGCTACATGA
*
1141 TTAGCTACATTACCGAAACGCTAATCTATGAGCCAACAAACCCC
1 TTAGCTACATTACCGAAACGCTAATCTATGAACCAACAAACCCC
*
1185 TTAGCTACATTACTGAAACGCTAATCTATGAACCAACAAACCCC
1 TTAGCTACATTACCGAAACGCTAATCTATGAACCAACAAACCCC
1229 TT
1 TT
1231 CCCCAACAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.37, C:0.30, G:0.10, T:0.23
Consensus pattern (44 bp):
TTAGCTACATTACCGAAACGCTAATCTATGAACCAACAAACCCC
Found at i:1709 original size:2 final size:2
Alignment explanation
Indices: 1704--1738 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1694 AGTAGCAAAT
1704 TA TA 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 TA TA T
1739 TTGAGGTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6577 original size:20 final size:20
Alignment explanation
Indices: 6552--6605 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
6542 TTTCTTTTCT
6552 ATTATGAATGTTCAGCTTGG
1 ATTATGAATGTTCAGCTTGG
6572 ATTATGAATGTTCAGCTTGG
1 ATTATGAATGTTCAGCTTGG
6592 ATTATGAATGTTCA
1 ATTATGAATGTTCA
6606 TTGTCCAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTATGAATGTTCAGCTTGG
Found at i:10983 original size:12 final size:12
Alignment explanation
Indices: 10966--11009 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
10956 GGAAGAGGGA
*
10966 GAAGAAAGTGGG
1 GAAGAAAGTGAG
10978 GAAGAAAGTGAG
1 GAAGAAAGTGAG
10990 GAAGAATTAGATGAG
1 GAAGAA--AG-TGAG
11005 GAAGA
1 GAAGA
11010 GGAAGAGGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 17 0.61
14 2 0.07
15 9 0.32
ACGTcount: A:0.48, C:0.00, G:0.41, T:0.11
Consensus pattern (12 bp):
GAAGAAAGTGAG
Found at i:11722 original size:27 final size:27
Alignment explanation
Indices: 11679--11731 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
11669 AAACTTTCTG
*
11679 TTTTTTGTTTCAAACTTGTTGTTTTTC
1 TTTTTTGTCTCAAACTTGTTGTTTTTC
*
11706 TTTTTTGTCTCATACTTGTTGTTTTT
1 TTTTTTGTCTCAAACTTGTTGTTTTT
11732 TCTGAAACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.09, C:0.11, G:0.11, T:0.68
Consensus pattern (27 bp):
TTTTTTGTCTCAAACTTGTTGTTTTTC
Found at i:11861 original size:26 final size:27
Alignment explanation
Indices: 11820--11873 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
11810 AAACTTACTG
*
11820 TTTTTTGTTCAAACTTGCTG-TTTCTC
1 TTTTTTGCTCAAACTTGCTGTTTTCTC
* *
11846 TTTTTTGCTCATACTTGTTGTTTTCTC
1 TTTTTTGCTCAAACTTGCTGTTTTCTC
11873 T
1 T
11874 GAAACTTGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.09, C:0.19, G:0.11, T:0.61
Consensus pattern (27 bp):
TTTTTTGCTCAAACTTGCTGTTTTCTC
Found at i:11910 original size:139 final size:139
Alignment explanation
Indices: 11593--11993 Score: 730
Period size: 139 Copynumber: 2.9 Consensus size: 139
11583 AAGGTTAGTT
*
11593 TGAAACTTGCTGAAATTTACTTAATTATTTCTGTTTCGGGAGGCTAATTCTGAAACTTAATTGCT
1 TGAAACTTGCTGAAATTTACTTAATTATTTCTGTTTTGGGAGGCTAATTCTGAAACTTAATTGCT
*
11658 CAAAGTTGCTGAAACTTTCTGTTTTTTGTTTCAAACTTGTTGTTTTTCTTTTTTGTCTCATACTT
66 CAAAGTTGCTGAAACTTACTGTTTTTTG-TTCAAACTTGTTGTTTTTCTTTTTTG-CTCATACTT
*
11723 GTTGTTTTTTC
129 GTTGTTTTCTC
11734 TGAAACTTGCTGAAATTTACTTAATTATTTCTGTTTTGGGAGGCTAATTCTGAAACTTAATTGCT
1 TGAAACTTGCTGAAATTTACTTAATTATTTCTGTTTTGGGAGGCTAATTCTGAAACTTAATTGCT
* *
11799 CAAAGTTGCTGAAACTTACTGTTTTTTGTTCAAACTTGCTGTTTCTCTTTTTTGCTCATACTTGT
66 CAAAGTTGCTGAAACTTACTGTTTTTTGTTCAAACTTGTTGTTTTTCTTTTTTGCTCATACTTGT
11864 TGTTTTCTC
131 TGTTTTCTC
11873 TGAAACTTGCTGAAATTTACTTAATTATTTCTGTTTTGGGAGGCTAATTCTGAAACTTAATTGCT
1 TGAAACTTGCTGAAATTTACTTAATTATTTCTGTTTTGGGAGGCTAATTCTGAAACTTAATTGCT
*
11938 CAAAGTTGCTGAAACTTACTATTTTTTGTTCAAACTTGTTGTTTTTCTTTTTTGCT
66 CAAAGTTGCTGAAACTTACTGTTTTTTGTTCAAACTTGTTGTTTTTCTTTTTTGCT
11994 ATATTTCTGT
Statistics
Matches: 252, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
139 137 0.54
140 24 0.10
141 91 0.36
ACGTcount: A:0.22, C:0.14, G:0.15, T:0.49
Consensus pattern (139 bp):
TGAAACTTGCTGAAATTTACTTAATTATTTCTGTTTTGGGAGGCTAATTCTGAAACTTAATTGCT
CAAAGTTGCTGAAACTTACTGTTTTTTGTTCAAACTTGTTGTTTTTCTTTTTTGCTCATACTTGT
TGTTTTCTC
Found at i:14485 original size:21 final size:21
Alignment explanation
Indices: 14448--14496 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
14438 TATTCTTATA
14448 TGCTACGAGCTTATTTACAGT
1 TGCTACGAGCTTATTTACAGT
*
14469 TGCTACGAGCTTATTTACATT
1 TGCTACGAGCTTATTTACAGT
14490 TGCTACG
1 TGCTACG
14497 GACATTATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.39
Consensus pattern (21 bp):
TGCTACGAGCTTATTTACAGT
Found at i:17648 original size:2 final size:2
Alignment explanation
Indices: 17641--17684 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
17631 CACCAAGTAG
17641 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
17683 AT
1 AT
17685 GGATGGATGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29220 original size:15 final size:15
Alignment explanation
Indices: 29200--29230 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29190 TTAGAAGAAT
*
29200 AATAATTTTCCAGCC
1 AATAATTATCCAGCC
29215 AATAATTATCCAGCC
1 AATAATTATCCAGCC
29230 A
1 A
29231 GCAAAAAGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.26, G:0.06, T:0.29
Consensus pattern (15 bp):
AATAATTATCCAGCC
Found at i:32579 original size:63 final size:63
Alignment explanation
Indices: 32480--32611 Score: 255
Period size: 63 Copynumber: 2.1 Consensus size: 63
32470 TCTATTTCTC
*
32480 CCTCCTCCACATCATTTCCTTGATTTGGAACACTAGGTGGCTCGCCTTCTTCTTCCTCTTCAT
1 CCTCCTCCACATCATTTCCTTGATTTGGAACACTAGGTGGCTCGCCTTCTTCTTCCTCCTCAT
32543 CCTCCTCCACATCATTTCCTTGATTTGGAACACTAGGTGGCTCGCCTTCTTCTTCCTCCTCAT
1 CCTCCTCCACATCATTTCCTTGATTTGGAACACTAGGTGGCTCGCCTTCTTCTTCCTCCTCAT
32606 CCTCCT
1 CCTCCT
32612 TCATGTACAA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 68 1.00
ACGTcount: A:0.14, C:0.37, G:0.12, T:0.37
Consensus pattern (63 bp):
CCTCCTCCACATCATTTCCTTGATTTGGAACACTAGGTGGCTCGCCTTCTTCTTCCTCCTCAT
Found at i:35321 original size:2 final size:2
Alignment explanation
Indices: 35314--35347 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
35304 CACTTGGCAA
* *
35314 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35348 TAATTACTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39455 original size:11 final size:11
Alignment explanation
Indices: 39412--39449 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
39402 TTCCTATATA
*
39412 AAATAAATTAT
1 AAATTAATTAT
39423 CAAA-TAATTAT
1 -AAATTAATTAT
39434 AAATTAATTAT
1 AAATTAATTAT
39445 AAATT
1 AAATT
39450 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:39828 original size:28 final size:31
Alignment explanation
Indices: 39771--39831 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
39761 CAATATTTAT
* *
39771 TTTTTTGTGTATTATTAGTATGTAACATTAA
1 TTTTTTGTGTATTATTAATATATAACATTAA
39802 TTTTTTGTGTATTA-TAATA-ATAA-ATTAA
1 TTTTTTGTGTATTATTAATATATAACATTAA
39830 TT
1 TT
39832 ATAGTTTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.25
29 3 0.11
30 4 0.14
31 14 0.50
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.56
Consensus pattern (31 bp):
TTTTTTGTGTATTATTAATATATAACATTAA
Found at i:40660 original size:5 final size:5
Alignment explanation
Indices: 40650--40685 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
40640 CTAATCTTAC
40650 TATCT TATCT TATCT TATCT TATCT TA--T TATCT TAT
1 TATCT TATCT TATCT TATCT TATCT TATCT TATCT TAT
40686 TATTATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.10
5 26 0.90
ACGTcount: A:0.22, C:0.17, G:0.00, T:0.61
Consensus pattern (5 bp):
TATCT
Found at i:40670 original size:15 final size:13
Alignment explanation
Indices: 40643--40685 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
40633 ACAAGTTCTA
*
40643 ATCTTACTATCTT
1 ATCTTATTATCTT
40656 ATCTTATCTTATCTT
1 ATCTTA--TTATCTT
40671 ATCTTATTATCTT
1 ATCTTATTATCTT
40684 AT
1 AT
40686 TATTATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 15 0.56
15 12 0.44
ACGTcount: A:0.23, C:0.19, G:0.00, T:0.58
Consensus pattern (13 bp):
ATCTTATTATCTT
Found at i:40699 original size:14 final size:14
Alignment explanation
Indices: 40674--40716 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
40664 TTATCTTATC
*
40674 TTATTATCTTATTA
1 TTATTATATTATTA
* *
40688 TTATTTTTTTATTA
1 TTATTATATTATTA
40702 TTATTATATTATTA
1 TTATTATATTATTA
40716 T
1 T
40717 ACTATATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (14 bp):
TTATTATATTATTA
Done.