Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013268.1 Corchorus olitorius cultivar O-4 contig13301, 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: 58055
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1017 original size:58 final size:58
Alignment explanation
Indices: 923--1037 Score: 187
Period size: 58 Copynumber: 2.0 Consensus size: 58
913 ATTAATCAAA
*
923 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCGAGGCT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCGAGGCT
* *
981 TATCAAGTGACATGTTTTTCTATTAGATGCCT-AAAAAAGACGTTTTAGGACCGAGGC
1 TATCAAGTGACATGTTCTT-TATTAGATGCATAAAAAAAGACGTTTTAGGACCGAGGC
1038 ATGATGCTAT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
58 42 0.79
59 11 0.21
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCGAGGCT
Found at i:1653 original size:30 final size:30
Alignment explanation
Indices: 1619--1706 Score: 77
Period size: 26 Copynumber: 3.2 Consensus size: 30
1609 AGTCATCTTA
1619 CATCCTTATTGAAGACCGAGTCAGGGTTAG
1 CATCCTTATTGAAGACCGAGTCAGGGTTAG
* *
1649 CATCC----TG-AGGCCGTAGTTA---TT-G
1 CATCCTTATTGAAGACCG-AGTCAGGGTTAG
*
1671 CATCCTTATTGAAGATCGAGTCAGGGTTAG
1 CATCCTTATTGAAGACCGAGTCAGGGTTAG
1701 CATCCT
1 CATCCT
1707 GAGGCCGTAG
Statistics
Matches: 43, Mismatches: 5, Indels: 20
0.63 0.07 0.29
Matches are distributed among these distances:
22 6 0.14
23 2 0.05
25 5 0.12
26 12 0.28
27 4 0.09
29 2 0.05
30 12 0.28
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.30
Consensus pattern (30 bp):
CATCCTTATTGAAGACCGAGTCAGGGTTAG
Found at i:1697 original size:52 final size:52
Alignment explanation
Indices: 1619--1723 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
1609 AGTCATCTTA
1619 CATCCTTATTGAAGACCGAGTCAGGGTTAGCATCCTGAGGCCGTAGTTATTG
1 CATCCTTATTGAAGACCGAGTCAGGGTTAGCATCCTGAGGCCGTAGTTATTG
*
1671 CATCCTTATTGAAGATCGAGTCAGGGTTAGCATCCTGAGGCCGTAGTTATTG
1 CATCCTTATTGAAGACCGAGTCAGGGTTAGCATCCTGAGGCCGTAGTTATTG
1723 C
1 C
1724 CATCTCTTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.30
Consensus pattern (52 bp):
CATCCTTATTGAAGACCGAGTCAGGGTTAGCATCCTGAGGCCGTAGTTATTG
Found at i:2404 original size:36 final size:36
Alignment explanation
Indices: 2357--2426 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
2347 TTCAATAACC
*
2357 TTACATCTTTTGTGATTTCTG-TTATCATATTTCTTA
1 TTACATCTTTTGTAATTT-TGATTATCATATTTCTTA
*
2393 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
2427 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 2 0.06
36 29 0.94
ACGTcount: A:0.21, C:0.11, G:0.07, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:3500 original size:206 final size:203
Alignment explanation
Indices: 3117--3530 Score: 695
Period size: 206 Copynumber: 2.0 Consensus size: 203
3107 GCTTAATAAC
3117 TTTATCAATGGTGAATGTTATTAATTTTTCAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTCAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* * *
3182 GATTCAACACATTATTATTATATATAAAACTATACCAAAAAAAAATTAGTTGAACATTAGTGGTT
66 GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAAATTAGTTGAAAATTAGTGGTT
* *
3247 GATTTATTAAATTAAATTAGATAAATGTCAAACAAAATTTCAAAATTATACAAGATATTAAAGAT
131 GATTTATTAAATTAAATTAGATAAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAAAT
3312 CCGATTTA
196 CCGATTTA
* * *
3320 TTTATCAATGGTGAATGTTTTTTTATTTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAAT
1 TTTATCAATGGTGAATG--TTATTAATTTTTCAAGTCTAAGATTACTAACAAAGTTGTAGTGAAT
*
3385 AAGATACAACACATTACTATTATATATATAGAACTATACC-AAAAAATATTAGTTGAAAATTAGT
64 AAGATACAACACATTACTATTATATATA-A-AACTATACCAAAAAAAAATTAGTTGAAAATTAGT
*
3449 GGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAA
127 GGTTGATTTATTAAATTAAATTAGATAAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAA
3514 AAATCCGATTTA
192 AAATCCGATTTA
3526 TTTAT
1 TTTAT
3531 TATTAAGGAA
Statistics
Matches: 197, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
203 17 0.09
205 69 0.35
206 102 0.52
207 9 0.05
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.37
Consensus pattern (203 bp):
TTTATCAATGGTGAATGTTATTAATTTTTCAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAAATTAGTTGAAAATTAGTGGTT
GATTTATTAAATTAAATTAGATAAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAAAT
CCGATTTA
Found at i:3638 original size:25 final size:24
Alignment explanation
Indices: 3604--3650 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
3594 ACGTTTGCAC
3604 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
3629 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
3651 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:3697 original size:22 final size:21
Alignment explanation
Indices: 3641--3699 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 21
3631 ATACCTAAGA
*
3641 ATTTAATTAATGTAAGTATTTC
1 ATTT-ATTAATGTAAGTATTAC
*
3663 AGTTATT-A--T-AGTATTAC
1 ATTTATTAATGTAAGTATTAC
3680 ATTTCATTAATGTAAGTATT
1 ATTT-ATTAATGTAAGTATT
3700 TTAGTTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 10
0.69 0.07 0.24
Matches are distributed among these distances:
17 10 0.34
18 4 0.14
19 1 0.03
20 1 0.03
21 4 0.14
22 9 0.31
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (21 bp):
ATTTATTAATGTAAGTATTAC
Found at i:3700 original size:39 final size:40
Alignment explanation
Indices: 3641--3721 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
3631 ATACCTAAGA
*
3641 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
* *
3680 ATTTCATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
3720 AT
1 AT
3722 AGGAATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:6003 original size:69 final size:69
Alignment explanation
Indices: 5892--6030 Score: 210
Period size: 69 Copynumber: 2.0 Consensus size: 69
5882 TTGCTTGAAA
*
5892 TGCATTGTTTTTATATGTAATTTTAGCATTTGGATGAAATTAATGGTGTTC-CTACCATTTTTTC
1 TGCATTGTCTTTATATGTAATTTTAGCATTTGGATGAAATTAATGGTGTTCTC-ACCATTTTTTC
*
5956 CTTAG
65 CATAG
* *
5961 TGCATTGTCTTTATATGTAATTTTAGCA-TTGAGATGTAATTAATGGTGTTCTCACTATTTTTTC
1 TGCATTGTCTTTATATGTAATTTTAGCATTTG-GATGAAATTAATGGTGTTCTCACCATTTTTTC
6025 CATAG
65 CATAG
6030 T
1 T
6031 TGTTAGTTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
68 3 0.05
69 60 0.94
70 1 0.02
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.49
Consensus pattern (69 bp):
TGCATTGTCTTTATATGTAATTTTAGCATTTGGATGAAATTAATGGTGTTCTCACCATTTTTTCC
ATAG
Found at i:6520 original size:2 final size:2
Alignment explanation
Indices: 6513--6537 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6503 GGCTTTAGAA
6513 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6538 ATTATCTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6747 original size:31 final size:30
Alignment explanation
Indices: 6712--6788 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 30
6702 TTACCGTACA
6712 GGTCCCTCTACTTACAAAAAAGGATCAATTT
1 GGTCCCTCTACTTACAAAAAAGG-TCAATTT
* * **
6743 GGTCCCTGTAC-TATAAAAACTGTCAATTT
1 GGTCCCTCTACTTACAAAAAAGGTCAATTT
*
6772 GGTACCTCTACTTACAA
1 GGTCCCTCTACTTACAA
6789 TTTGGTATTA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 16 0.42
30 12 0.32
31 10 0.26
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.31
Consensus pattern (30 bp):
GGTCCCTCTACTTACAAAAAAGGTCAATTT
Found at i:7153 original size:31 final size:30
Alignment explanation
Indices: 7084--7156 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
7074 CACCAAATTG
* * *
7084 TAAGTAGAGGGACCAAATTGACAGTTTTTG
1 TAAGTAGAGGGACCAAATTGACACTTTCTA
*
7114 T-AGTAGAGGGACCAAATTGATCCCTTTCTA
1 TAAGTAGAGGGACCAAATTGA-CACTTTCTA
7144 TAAGTAGAGGGAC
1 TAAGTAGAGGGAC
7157 TTGTACGGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 19 0.51
30 7 0.19
31 11 0.30
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (30 bp):
TAAGTAGAGGGACCAAATTGACACTTTCTA
Found at i:12225 original size:16 final size:16
Alignment explanation
Indices: 12200--12261 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
12190 ATGGAGTTCC
*
12200 TTTCCCTTCCTCCCTA
1 TTTCCTTTCCTCCCTA
**
12216 TTTCCTTTCCCTTGCTA
1 TTTCCTTT-CCTCCCTA
* *
12233 TTTTCTTTCCTTCCTA
1 TTTCCTTTCCTCCCTA
12249 TTT-CTTTCCTCCC
1 TTTCCTTTCCTCCC
12262 AACCAAACAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
15 9 0.23
16 17 0.44
17 13 0.33
ACGTcount: A:0.05, C:0.40, G:0.02, T:0.53
Consensus pattern (16 bp):
TTTCCTTTCCTCCCTA
Found at i:21000 original size:105 final size:105
Alignment explanation
Indices: 20820--21029 Score: 402
Period size: 105 Copynumber: 2.0 Consensus size: 105
20810 CATATTTATA
20820 AAAAAGCATTTGTCACTCACACCAGCTAGTTCAATAAGGCTTGGACCGGCCTGTTTTTTTTTTTT
1 AAAAAGCATTTGTCACTCACACCAGCTAGTTCAATAAGGCTTGGACCGGCCTGTTTTTTTTTTTT
20885 TTTCAGGCACCAGCTTGGACCGGCCTTTACTCATTATCAT
66 TTTCAGGCACCAGCTTGGACCGGCCTTTACTCATTATCAT
20925 AAAAAGCATTTGTCACTCACACCAGCTAGTTCAATAAGGCTTGGACCGGCCTGTTTTTTTTTTTT
1 AAAAAGCATTTGTCACTCACACCAGCTAGTTCAATAAGGCTTGGACCGGCCTGTTTTTTTTTTTT
**
20990 TTTTTGGCACCAGCTTGGACCGGCCTTTACTCATTATCAT
66 TTTCAGGCACCAGCTTGGACCGGCCTTTACTCATTATCAT
21030 TGCCAAGTTT
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 103 1.00
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.36
Consensus pattern (105 bp):
AAAAAGCATTTGTCACTCACACCAGCTAGTTCAATAAGGCTTGGACCGGCCTGTTTTTTTTTTTT
TTTCAGGCACCAGCTTGGACCGGCCTTTACTCATTATCAT
Found at i:31399 original size:31 final size:31
Alignment explanation
Indices: 31364--31484 Score: 145
Period size: 31 Copynumber: 3.9 Consensus size: 31
31354 TGTGCACGTC
* **
31364 GCATGCTACGTGTCACTTTTTGAAACACATG
1 GCATGATACGTGTCACTTTTTGGTACACATG
** *
31395 GCATGCCATGTGTCACTTTTTGGTACACATG
1 GCATGATACGTGTCACTTTTTGGTACACATG
*
31426 GCGTGATACGTGTCACTTTTTGGTACA-ATTG
1 GCATGATACGTGTCACTTTTTGGTACACA-TG
* *
31457 GCGTGATACGTGTCGCTTTTTGGTACAC
1 GCATGATACGTGTCACTTTTTGGTACAC
31485 GTTGCGTGCC
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
30 1 0.01
31 78 0.99
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.36
Consensus pattern (31 bp):
GCATGATACGTGTCACTTTTTGGTACACATG
Found at i:39012 original size:23 final size:23
Alignment explanation
Indices: 38986--39032 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
38976 CTAAATTTCT
* * *
38986 AAGTTTAAATAGTCATCTCTATA
1 AAGTTTAAACAATCAACTCTATA
39009 AAGTTTAAACAATCAACTCTATA
1 AAGTTTAAACAATCAACTCTATA
39032 A
1 A
39033 TGCTAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.34
Consensus pattern (23 bp):
AAGTTTAAACAATCAACTCTATA
Found at i:46102 original size:16 final size:16
Alignment explanation
Indices: 46084--46157 Score: 78
Period size: 16 Copynumber: 4.6 Consensus size: 16
46074 AATTTTGGGT
* *
46084 ACCCGAACCCGAAATT
1 ACCCGAACCCAAAATG
* *
46100 ACCCGAATCC-AAACG
1 ACCCGAACCCAAAATG
46115 ACCCGAACCCTAAAATG
1 ACCCGAACCC-AAAATG
*
46132 ACCCAAACCCAAAATG
1 ACCCGAACCCAAAATG
*
46148 ATCCGAACCC
1 ACCCGAACCC
46158 GATCAACCCG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
15 12 0.25
16 23 0.48
17 13 0.27
ACGTcount: A:0.41, C:0.39, G:0.11, T:0.09
Consensus pattern (16 bp):
ACCCGAACCCAAAATG
Found at i:46140 original size:17 final size:16
Alignment explanation
Indices: 46114--46148 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
46104 GAATCCAAAC
*
46114 GACCCGAACCCTAAAAT
1 GACCCAAACCC-AAAAT
46131 GACCCAAACCCAAAAT
1 GACCCAAACCCAAAAT
46147 GA
1 GA
46149 TCCGAACCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.46, C:0.34, G:0.11, T:0.09
Consensus pattern (16 bp):
GACCCAAACCCAAAAT
Found at i:47781 original size:15 final size:15
Alignment explanation
Indices: 47727--47783 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
47717 TCCGAACCGT
*
47727 ATGACCCGAAACCGAAA
1 ATGACCCG-AACC-CAA
*
47744 ACGACCC-AACCCAGA
1 ATGACCCGAACCCA-A
47759 ATTGACCCGAACCCAA
1 A-TGACCCGAACCCAA
47775 ATGACCCGA
1 ATGACCCGA
47784 CATTTGAACG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
14 1 0.03
15 14 0.41
16 7 0.21
17 12 0.35
ACGTcount: A:0.40, C:0.37, G:0.16, T:0.07
Consensus pattern (15 bp):
ATGACCCGAACCCAA
Found at i:53005 original size:38 final size:38
Alignment explanation
Indices: 52954--53026 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
52944 CCCAACTATG
* *
52954 TTTTCACCATTTTTTAACTTTTAAACTGGTTCAATATT
1 TTTTCACCATTTTTAAACATTTAAACTGGTTCAATATT
*
52992 TTTTCACCTTTTTTAAACATTTAAACTGGTTCAAT
1 TTTTCACCATTTTTAAACATTTAAACTGGTTCAAT
53027 CCCGGCCCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.27, C:0.16, G:0.05, T:0.51
Consensus pattern (38 bp):
TTTTCACCATTTTTAAACATTTAAACTGGTTCAATATT
Found at i:53153 original size:71 final size:69
Alignment explanation
Indices: 53032--53169 Score: 213
Period size: 71 Copynumber: 2.0 Consensus size: 69
53022 TCAATCCCGG
* * *
53032 CCCAATTCAGTTTCTAACATTTTATCCGGAGCGTATAGGTTACCGTTTCTCAGTTGAATCGGTCC
1 CCCAATTCAGTTTCTAACATTTTATCCGAAGCGTATAGGTCACCGATTCTCAGTTGAATCGGTCC
53097 GAGA
66 GAGA
* *
53101 CCCAATTCAGTTTCTAACCTTGTTTATTCGAAGCGTATAGGTCACCGATTCTCAGTTGAATCGGT
1 CCCAATTCAGTTTCTAA-CAT-TTTATCCGAAGCGTATAGGTCACCGATTCTCAGTTGAATCGGT
53166 CCGA
64 CCGA
53170 CCAACCGATC
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
69 17 0.27
70 2 0.03
71 43 0.69
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (69 bp):
CCCAATTCAGTTTCTAACATTTTATCCGAAGCGTATAGGTCACCGATTCTCAGTTGAATCGGTCC
GAGA
Done.