Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009845.1 Corchorus capsularis cultivar CVL-1 contig09866, 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: 116492
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1728 original size:11 final size:11
Alignment explanation
Indices: 1712--1736 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1702 TTTGCCTATC
1712 AAAAAAAAAAG
1 AAAAAAAAAAG
1723 AAAAAAAAAAG
1 AAAAAAAAAAG
1734 AAA
1 AAA
1737 GTAAAGGCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:3125 original size:72 final size:71
Alignment explanation
Indices: 3001--3232 Score: 243
Period size: 72 Copynumber: 3.2 Consensus size: 71
2991 TGTGGAGCAA
* * * * * *
3001 CTCCAGTCAAATTGTTGTGGGACAAGTCAAGAACTTC-AAGAGAAGTGGCATTGCATATGAGAGA
1 CTCCACTCAAACTGTTGTGGGACAAGTCAAG-ACTTCTAAGAAAACT-TCATTGCATATCAGAGA
3065 AGAGATTT
64 AGAGATTT
*
3073 CTCCACTCAAACTGTTGTGGGACAAGTCAAGACTTCTAAGAAAACTCTCATTGCATACCAGAGAA
1 CTCCACTCAAACTGTTGTGGGACAAGTCAAGACTTCTAAGAAAACT-TCATTGCATATCAGAGAA
*
3138 GAGATTC
65 GAGATTT
* * * * * *
3145 CTCCACTCAAATTGTTGTGGGACAAGTCAACAATT-TCAAGATAACTTCCATTAATGCAGATTAG
1 CTCCACTCAAACTGTTGTGGGACAAGTCAAGACTTCT-AAGAAAACTT-CA-T--TGCATATCAG
*
3209 AGGAGAGATTT
61 AGAAGAGATTT
3220 CTCCACTCAAACT
1 CTCCACTCAAACT
3233 ATTATTTGAG
Statistics
Matches: 135, Mismatches: 19, Indels: 9
0.83 0.12 0.06
Matches are distributed among these distances:
71 7 0.05
72 99 0.73
73 1 0.01
75 28 0.21
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (71 bp):
CTCCACTCAAACTGTTGTGGGACAAGTCAAGACTTCTAAGAAAACTTCATTGCATATCAGAGAAG
AGATTT
Found at i:22711 original size:2 final size:2
Alignment explanation
Indices: 22704--22733 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
22694 TGTGCTTTGA
22704 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
22734 GTTGAGTGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23183 original size:18 final size:18
Alignment explanation
Indices: 23160--23197 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
23150 AGTAAATTGT
23160 AATATTGTATAGACCAAA
1 AATATTGTATAGACCAAA
23178 AATATTGTATAGACCAAA
1 AATATTGTATAGACCAAA
23196 AA
1 AA
23198 CAAAGAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.26
Consensus pattern (18 bp):
AATATTGTATAGACCAAA
Found at i:23580 original size:27 final size:28
Alignment explanation
Indices: 23547--23600 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
23537 AGAAATTATG
23547 AGGGACAATTAAAAAGAAACA-AGGGAA
1 AGGGACAATTAAAAAGAAACAGAGGGAA
*
23574 AGGGACAATTAAAAAGGAACAGAGGGA
1 AGGGACAATTAAAAAGAAACAGAGGGA
23601 GTAATTAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.56, C:0.07, G:0.30, T:0.07
Consensus pattern (28 bp):
AGGGACAATTAAAAAGAAACAGAGGGAA
Found at i:27097 original size:15 final size:15
Alignment explanation
Indices: 27077--27112 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
27067 TACGAGGTAT
27077 ATTTTTATTCATT-TA
1 ATTTTTATT-ATTATA
27092 ATTTTTATTATTATA
1 ATTTTTATTATTATA
27107 ATTTTT
1 ATTTTT
27113 GGTTTATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTTTATTATTATA
Found at i:28820 original size:17 final size:19
Alignment explanation
Indices: 28784--28822 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
28774 TATAAATATT
28784 TATTTATATATATATAATA
1 TATTTATATATATATAATA
*
28803 TATTTA-ATATCT-TAATA
1 TATTTATATATATATAATA
28820 TAT
1 TAT
28823 GTGTTACATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 5 0.26
19 6 0.32
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTTATATATATATAATA
Found at i:62040 original size:83 final size:83
Alignment explanation
Indices: 61901--62065 Score: 303
Period size: 83 Copynumber: 2.0 Consensus size: 83
61891 AGCATAATGC
* *
61901 TATATCTCATGAAGAATCATAATTTGTGTAAAATCTACTGGGCAAGTAGCAAAATGGTCAATAAT
1 TATATCTCATGAAGAATCATAATATGTGTAAAATCTACTGGGCAACTAGCAAAATGGTCAATAAT
61966 TTAAAAAACTATGCAGCA
66 TTAAAAAACTATGCAGCA
*
61984 TATATCTCATGAAGAATCATAATATGTGTAATATCTACTGGGCAACTAGCAAAATGGTCAATAAT
1 TATATCTCATGAAGAATCATAATATGTGTAAAATCTACTGGGCAACTAGCAAAATGGTCAATAAT
62049 TTAAAAAACTATGCAGC
66 TTAAAAAACTATGCAGC
62066 GTCCCCCTGT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 79 1.00
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (83 bp):
TATATCTCATGAAGAATCATAATATGTGTAAAATCTACTGGGCAACTAGCAAAATGGTCAATAAT
TTAAAAAACTATGCAGCA
Found at i:89641 original size:19 final size:19
Alignment explanation
Indices: 89600--89643 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
89590 TTATCCCTCT
*
89600 TCTCTCTCCCCCCACTAAG
1 TCTCTCTCCCCCCACTAAC
* *
89619 TCTCTCTCCTCCCACTTAC
1 TCTCTCTCCCCCCACTAAC
89638 TCTCTC
1 TCTCTC
89644 ATAGTCAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.11, C:0.52, G:0.02, T:0.34
Consensus pattern (19 bp):
TCTCTCTCCCCCCACTAAC
Found at i:90526 original size:21 final size:21
Alignment explanation
Indices: 90495--90554 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
90485 ATGTGAGAGC
* *
90495 AAAATTGGTTACTATACGTAT
1 AAAATTTGTTACTATACATAT
* *
90516 TAAATTTGTTACTGTACATAT
1 AAAATTTGTTACTATACATAT
*
90537 AAAATTTGTTACTGTACA
1 AAAATTTGTTACTATACA
90555 GATGAGAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.42
Consensus pattern (21 bp):
AAAATTTGTTACTATACATAT
Found at i:92729 original size:10 final size:10
Alignment explanation
Indices: 92714--92747 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
92704 TATTCTTAAT
92714 TAATTAATAA
1 TAATTAATAA
* *
92724 TAATTATTAT
1 TAATTAATAA
92734 TAATTAATAA
1 TAATTAATAA
92744 TAAT
1 TAAT
92748 AATCTCCACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
TAATTAATAA
Found at i:98728 original size:29 final size:29
Alignment explanation
Indices: 98695--98751 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
98685 AATCTTTTAC
98695 TTTAGGGCTGTCCTTTTGTCTTTCATTTG
1 TTTAGGGCTGTCCTTTTGTCTTTCATTTG
98724 TTTAGGGCTGTCCTTTTGTCTTTCATTT
1 TTTAGGGCTGTCCTTTTGTCTTTCATTT
98752 CATGCAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.07, C:0.18, G:0.19, T:0.56
Consensus pattern (29 bp):
TTTAGGGCTGTCCTTTTGTCTTTCATTTG
Found at i:99382 original size:27 final size:27
Alignment explanation
Indices: 99347--99398 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
99337 TGATCATACA
99347 GGTGCGAAGAACATCACCACCTACAAG
1 GGTGCGAAGAACATCACCACCTACAAG
* *
99374 GGTGTGAAGAACATCGCCACCTACA
1 GGTGCGAAGAACATCACCACCTACA
99399 CCTCCAAGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.35, C:0.29, G:0.23, T:0.13
Consensus pattern (27 bp):
GGTGCGAAGAACATCACCACCTACAAG
Found at i:99407 original size:33 final size:34
Alignment explanation
Indices: 99364--99427 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
99354 AGAACATCAC
*
99364 CACCTACAAGGGTGTGAAG-AACATCGCCACCTA
1 CACCTACAAGGGTGCGAAGAAACATCGCCACCTA
*
99397 CACCTCCAAGGGTGCGAAGAAACATCGCCAC
1 CACCTACAAGGGTGCGAAGAAACATCGCCAC
99428 TTATAAGGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 17 0.61
34 11 0.39
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.12
Consensus pattern (34 bp):
CACCTACAAGGGTGCGAAGAAACATCGCCACCTA
Found at i:110171 original size:14 final size:13
Alignment explanation
Indices: 110139--110175 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
110129 TATACATATA
110139 AATAAT-ATAATT
1 AATAATAATAATT
110151 AAT-ATAATAATT
1 AATAATAATAATT
110163 AAGTAATAATAAT
1 AA-TAATAATAAT
110176 AGATTAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 2 0.09
12 11 0.50
13 1 0.05
14 8 0.36
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (13 bp):
AATAATAATAATT
Found at i:111046 original size:3 final size:3
Alignment explanation
Indices: 111034--111086 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
111024 TAATAACATA
111034 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
111081 ATT ATT
1 ATT ATT
111087 TTGGTGAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:114227 original size:25 final size:25
Alignment explanation
Indices: 114199--114251 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
114189 GTTAGTAGAT
114199 TGTTGCAAGTGGTGAGTGGTGATAA
1 TGTTGCAAGTGGTGAGTGGTGATAA
114224 TGTTGCAAGTGGTGAGTGGTGATAA
1 TGTTGCAAGTGGTGAGTGGTGATAA
114249 TGT
1 TGT
114252 AAACTGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.23, C:0.04, G:0.40, T:0.34
Consensus pattern (25 bp):
TGTTGCAAGTGGTGAGTGGTGATAA
Found at i:114826 original size:150 final size:150
Alignment explanation
Indices: 114629--114928 Score: 501
Period size: 150 Copynumber: 2.0 Consensus size: 150
114619 CTCTCTCTTA
*
114629 TCACGTTTCATTCCACCAATTAAAAAAAAAAACCTCCACTCTCTGAGCATCGTGATCTCCAATCT
1 TCACGTTTCATTCCACCAATTAAAAAAAAAAACCTCCACTCTCTGAGCATCGCGATCTCCAATCT
** * * *
114694 CGATCCAGAGTTTCCTCAAATTCCCTTGCATTTTTCTCGCTCCATCAGAAGGTAAGACACGTCGA
66 CGATCCAGAGTTTCCTCAAATTCCCCCGCATTTTTCCCGCTCCATCAGAAGGCAAGACACGTCAA
*
114759 AATATTAATCAATTTTGGTG
131 AATATTAATCAATTTCGGTG
* *
114779 TCACGTTTCATTCCATCAATTAAAAAAAAAAACCTCCACTCTCTGAGCATCGCGATCTCGAATCT
1 TCACGTTTCATTCCACCAATTAAAAAAAAAAACCTCCACTCTCTGAGCATCGCGATCTCCAATCT
* *
114844 CGATCTAGAGTTTCCTCAAATTCCCCCGCATTTTTCCCGCTCCATCAGAAGGCAAGGCACGTCAA
66 CGATCCAGAGTTTCCTCAAATTCCCCCGCATTTTTCCCGCTCCATCAGAAGGCAAGACACGTCAA
114909 AATATTAATCAATTTCGGTG
131 AATATTAATCAATTTCGGTG
114929 GAGAAGACCA
Statistics
Matches: 139, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
150 139 1.00
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (150 bp):
TCACGTTTCATTCCACCAATTAAAAAAAAAAACCTCCACTCTCTGAGCATCGCGATCTCCAATCT
CGATCCAGAGTTTCCTCAAATTCCCCCGCATTTTTCCCGCTCCATCAGAAGGCAAGACACGTCAA
AATATTAATCAATTTCGGTG
Found at i:115916 original size:333 final size:332
Alignment explanation
Indices: 115279--116492 Score: 1922
Period size: 333 Copynumber: 3.7 Consensus size: 332
115269 ATAGTAGCGC
* * * * * *
115279 TTCACATGCTCATAAAAAAAAATCCTTAAATCAATTGTGGCTGAGATTTGCCTGGATGGATACAG
1 TTCAGATGCTCGTAAAAACAAATCCTTAAATCAATTGTGGCTGAGATTTGGCTTGATGAATACAG
* * * * *
115344 ATATTTTAAGTAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCAAAACGCTTTTT
66 ATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAACCGGGGCCCCGAAACGCGTTTT
** **
115409 TAGTAAAAAACCGTGATGGTTATTACATAATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAA
131 TAGCCAAAAACCGTGATGGTTATTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAA
*
115474 AATTTTCCTCAATTTTTTGCCCCAATATTCAGAAAAAATATATAATTAAATTCCAAAAAAATTGA
196 ACTTTTCCTCAATTTTTTGCCCCAATATTCAGAAAAAATATATAATTAAATTCCAAAAAAATTGA
115539 AGAGTTTTTCACGCTTCTGATATCGTTTTTCAATATTTTTCCGAGTTTATTTCTAATTAAATCGA
261 AGAGTTTTTCACGCTTCTGATATCGTTTTTCAATATTTTTCCGAGTTTATTTCTAATTAAATCGA
115604 AACAAGA
326 AACAAGA
*
115611 TTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATTGTGGCTGAGATTTGACTTGATGAATACA
1 TTCAGATGCTCGTAAAAACAAATCCTTAAAT-CAATTGTGGCTGAGATTTGGCTTGATGAATACA
115676 GATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAACCGGGGCCCCGAAACGCGTTT
65 GATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAACCGGGGCCCCGAAACGCGTTT
*
115741 TTAGCCAAAAATCGTGATGGTTATTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAA
130 TTAGCCAAAAACCGTGATGGTTATTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAA
115806 AACTTTTCCTCAATTTTTTGCCCCAATATTCAGAAAAAATATATAATTAAATTCCAAAAAAATTG
195 AACTTTTCCTCAATTTTTTGCCCCAATATTCAGAAAAAATATATAATTAAATTCCAAAAAAATTG
*
115871 AAGAGTTTTTCACGCTTCTGATATCGTTTTTCAATATTTTTCCGAGTTTATTTCTAATTTAATCG
260 AAGAGTTTTTCACGCTTCTGATATCGTTTTTCAATATTTTTCCGAGTTTATTTCTAATTAAATCG
115936 AAACAAGA
325 AAACAAGA
*
115944 TTCAGATGCTCGTAAAAACAAATCCTTAAATCAATTGTGGCTGAGATTTGGCTAGATTG-ATACA
1 TTCAGATGCTCGTAAAAACAAATCCTTAAATCAATTGTGGCTGAGATTTGGCTTGA-TGAATACA
* * * * ** * *
116008 GATATTTTAATGAGCCTTTACACCAAAAATTGTGCAAAATTGAGA-CGGGGCCTCGAAACGCGTT
65 GATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGA-ACCGGGGCCCCGAAACGCGTT
* * * *
116072 TTTTGCTAAAAATCGTGATGGTTATTACACGATTTCAGCTAAAATTTTGCAAAAAATGACCCGAA
129 TTTAGCCAAAAACCGTGATGGTTATTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAA
* *
116137 AAACTTTTCCTCAATTTTTTGCCCCAA-ATTAAGAAAAAATATATAATTAAATTCCAAAAAAATA
194 AAACTTTTCCTCAATTTTTTGCCCCAATATTCAGAAAAAATATATAATTAAATTCCAAAAAAATT
* * * * *
116201 GAAGAGTTTTTCATGCTTCTGATATCATTTTTCAAT-TTTTT-TGAGTATATTTATAATTAAATC
259 GAAGAGTTTTTCACGCTTCTGATATCGTTTTTCAATATTTTTCCGAGTTTATTTCTAATTAAATC
116264 GAAACAAGA
324 GAAACAAGA
*
116273 TACAGATGCTCGTAAAAACAAATCCTTAAATCCAA-TGTGGCTGAGATTTGGCTTGATGAATACA
1 TTCAGATGCTCGTAAAAACAAATCCTTAAAT-CAATTGTGGCTGAGATTTGGCTTGATGAATACA
* * *
116337 GATATTTCAAGGAGACTTTACGCCAAAAATAATGCAAAAGCT-AGCCGGGGCCCCGAAACGCGTT
65 GATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAA-CTGAACCGGGGCCCCGAAACGCGTT
**
116401 TTTA-CCCCAAACCGTGATGGTTATTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAA
129 TTTAGCCAAAAACCGTGATGGTTATTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAA
116465 AAACTTTTCCTCAATTTTTTGCCCCAAT
194 AAACTTTTCCTCAATTTTTTGCCCCAAT
Statistics
Matches: 818, Mismatches: 56, Indels: 19
0.92 0.06 0.02
Matches are distributed among these distances:
328 84 0.10
329 137 0.17
330 9 0.01
331 69 0.08
332 199 0.24
333 320 0.39
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.32
Consensus pattern (332 bp):
TTCAGATGCTCGTAAAAACAAATCCTTAAATCAATTGTGGCTGAGATTTGGCTTGATGAATACAG
ATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAACCGGGGCCCCGAAACGCGTTTT
TAGCCAAAAACCGTGATGGTTATTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAA
ACTTTTCCTCAATTTTTTGCCCCAATATTCAGAAAAAATATATAATTAAATTCCAAAAAAATTGA
AGAGTTTTTCACGCTTCTGATATCGTTTTTCAATATTTTTCCGAGTTTATTTCTAATTAAATCGA
AACAAGA
Done.