Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018897.1 Corchorus olitorius cultivar O-4 contig18930, 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: 21582
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:820 original size:57 final size:57
Alignment explanation
Indices: 732--848 Score: 225
Period size: 57 Copynumber: 2.1 Consensus size: 57
722 TCCCTCTAGG
732 CCTATTCAGCTATTCTCCCAGTGTTATCTCAGCCTGATTTAACCTAGTTCTTTTAGT
1 CCTATTCAGCTATTCTCCCAGTGTTATCTCAGCCTGATTTAACCTAGTTCTTTTAGT
*
789 CCTATTCAGCTATTCTCCCAGTGTTATCTCAGTCTGATTTAACCTAGTTCTTTTAGT
1 CCTATTCAGCTATTCTCCCAGTGTTATCTCAGCCTGATTTAACCTAGTTCTTTTAGT
846 CCT
1 CCT
849 CGTTAGTGTT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.19, C:0.26, G:0.12, T:0.43
Consensus pattern (57 bp):
CCTATTCAGCTATTCTCCCAGTGTTATCTCAGCCTGATTTAACCTAGTTCTTTTAGT
Found at i:1183 original size:7 final size:7
Alignment explanation
Indices: 1171--1211 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
1161 ATGGGCTCCT
1171 TTTTTAA
1 TTTTTAA
1178 TTTTTAA
1 TTTTTAA
1185 TTTTTAA
1 TTTTTAA
1192 TTTTTAA
1 TTTTTAA
1199 TTTTTAA
1 TTTTTAA
1206 TTTTTA
1 TTTTTA
1212 TTGAGATCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTAA
Found at i:2069 original size:51 final size:53
Alignment explanation
Indices: 1918--2178 Score: 354
Period size: 54 Copynumber: 5.0 Consensus size: 53
1908 AGGAGTCTTG
* * * **
1918 ATAATTACCATAATTATTTCTAATAATATAAAAAGATAATATGGTTAATAAAT-
1 ATAATCACCATAATTATCTCTAAT-ATATATACGGATAATATGGTTAATAAATA
*
1971 ATAATCACCATAATTATCTCTAATATATAT--GGATAATGTGGTTAAT-AAT-
1 ATAATCACCATAATTATCTCTAATATATATACGGATAATATGGTTAATAAATA
* *
2020 ATAATCACCATAATTATCTC-ATATATATATATGGATGATATGGTTAATAATATA
1 ATAATCACCATAATTATCTCTA-ATATATATACGGATAATATGGTTAATAA-ATA
*
2074 ATAATCACCATAATTATCTCTAATATATTTACGGATAATATGGTTAATAATATA
1 ATAATCACCATAATTATCTCTAATATATATACGGATAATATGGTTAATAA-ATA
*
2128 ATAATCACCATAATTATCTCTAATATATTTACGGATAATATGGTTAATAAA
1 ATAATCACCATAATTATCTCTAATATATATACGGATAATATGGTTAATAAA
2179 GGTAACTGGT
Statistics
Matches: 191, Mismatches: 10, Indels: 14
0.89 0.05 0.07
Matches are distributed among these distances:
48 1 0.01
49 31 0.16
50 14 0.07
51 14 0.07
52 6 0.03
53 25 0.13
54 99 0.52
55 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (53 bp):
ATAATCACCATAATTATCTCTAATATATATACGGATAATATGGTTAATAAATA
Found at i:2097 original size:27 final size:27
Alignment explanation
Indices: 2067--2154 Score: 76
Period size: 27 Copynumber: 3.3 Consensus size: 27
2057 ATATGGTTAA
2067 TAATATAATAATCACCATAATTATCTC
1 TAATATAATAATCACCATAATTATCTC
* * * *
2094 TAATAT-AT--TTACGGATAA-TATGGTTAA
1 TAATATAATAATCAC-CATAATTAT--CT-C
2121 TAATATAATAATCACCATAATTATCTC
1 TAATATAATAATCACCATAATTATCTC
2148 TAATATA
1 TAATATA
2155 TTTACGGATA
Statistics
Matches: 45, Mismatches: 8, Indels: 16
0.65 0.12 0.23
Matches are distributed among these distances:
24 6 0.13
25 4 0.09
26 3 0.07
27 19 0.42
28 3 0.07
29 4 0.09
30 6 0.13
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (27 bp):
TAATATAATAATCACCATAATTATCTC
Found at i:4160 original size:45 final size:45
Alignment explanation
Indices: 4109--4235 Score: 218
Period size: 45 Copynumber: 2.8 Consensus size: 45
4099 AATTCTACTT
4109 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTC
1 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTC
** *
4154 CATCTCTAGGTTGTTCATCAAAATAAAGCTAATATTCTACTCCTC
1 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTC
*
4199 CATCTCTAGGTAATTCATCAAAATAAACCTAATATTA
1 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTA
4236 ATTATTGCTT
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 75 1.00
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34
Consensus pattern (45 bp):
CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTC
Found at i:11338 original size:31 final size:31
Alignment explanation
Indices: 11303--11364 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
11293 AAAGTCATTA
11303 ATGAATATTGTGATTATTCATGAATCAAGAG
1 ATGAATATTGTGATTATTCATGAATCAAGAG
11334 ATGAATATTGTGATTATTCATGAATCAAGAG
1 ATGAATATTGTGATTATTCATGAATCAAGAG
11365 TTCTCTTGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.35
Consensus pattern (31 bp):
ATGAATATTGTGATTATTCATGAATCAAGAG
Found at i:15216 original size:22 final size:22
Alignment explanation
Indices: 15182--15232 Score: 77
Period size: 24 Copynumber: 2.3 Consensus size: 22
15172 CAGCAAGTCA
15182 TAAACAGAACTC-AAAAACAGT
1 TAAACAGAACTCAAAAAACAGT
15203 TAAACAGGAACTCAAAAAAACAGT
1 TAAACA-GAACTC-AAAAAACAGT
15227 TAAACA
1 TAAACA
15233 AAGGGGAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.22
22 6 0.22
24 15 0.56
ACGTcount: A:0.59, C:0.18, G:0.10, T:0.14
Consensus pattern (22 bp):
TAAACAGAACTCAAAAAACAGT
Found at i:15406 original size:64 final size:63
Alignment explanation
Indices: 15204--15531 Score: 323
Period size: 63 Copynumber: 5.2 Consensus size: 63
15194 AAAAACAGTT
*
15204 AAACAGGAACTCAAAAAAACAGTTAAACAAAG-GGGAA-TCCAAAAACAGGAAGTAATGAACTAA
1 AAACAGGAACT-AAAAAAACAGTTAAAC-CAGCGGGAACT-CAAAAACAGGAAGTAATGAACTAA
15267 A
63 A
* ** *
15268 AGACAGGAACTAAAAAAACAGTTAAACCAGCATGAACTCAAAAATAGGAAGTAATGAACTAAA
1 AAACAGGAACTAAAAAAACAGTTAAACCAGCGGGAACTCAAAAACAGGAAGTAATGAACTAAA
*
15331 AAACAGGAACTAAAAAAACAGTTAAACCAGCGGGAACTCAAAAACAGGAGGTAATGAACTAAAA
1 AAACAGGAACTAAAAAAACAGTTAAACCAGCGGGAACTCAAAAACAGGAAGTAATGAACT-AAA
* * * * *
15395 AAACAGGAACT-AAAAAACAGTTAAATAAACACTAAACAGG--CTCAAAAACAAGAGGTAAGGAA
1 AAACAGGAACTAAAAAAACAG-T---TAAAC-C--AGCGGGAACTCAAAAACAGGAAGTAATGAA
*
15457 CTAGA
59 CTAAA
** * * ** *
15462 AAACAGGAACT--AAAAACAGTTAAATAAACAGG--CTCAAAAACAACAAGTAAGGAACTAAA
1 AAACAGGAACTAAAAAAACAGTTAAACCAGCGGGAACTCAAAAACAGGAAGTAATGAACTAAA
15521 AAACAGGAACT
1 AAACAGGAACT
15532 CACAAATAGG
Statistics
Matches: 234, Mismatches: 20, Indels: 25
0.84 0.07 0.09
Matches are distributed among these distances:
59 41 0.18
62 6 0.03
63 107 0.46
64 26 0.11
65 1 0.00
66 8 0.03
67 18 0.08
68 23 0.10
70 4 0.02
ACGTcount: A:0.57, C:0.15, G:0.16, T:0.12
Consensus pattern (63 bp):
AAACAGGAACTAAAAAAACAGTTAAACCAGCGGGAACTCAAAAACAGGAAGTAATGAACTAAA
Found at i:15479 original size:13 final size:14
Alignment explanation
Indices: 15452--15480 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
15442 ACAAGAGGTA
15452 AGGAACTAGAAAAC
1 AGGAACTAGAAAAC
15466 AGGAACTA-AAAAC
1 AGGAACTAGAAAAC
15479 AG
1 AG
15481 TTAAATAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.14, G:0.21, T:0.07
Consensus pattern (14 bp):
AGGAACTAGAAAAC
Found at i:15530 original size:14 final size:14
Alignment explanation
Indices: 15511--15554 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
15501 ACAACAAGTA
*
15511 AGGAACTAAAAAAC
1 AGGAACTCAAAAAC
* *
15525 AGGAACTCACAAAT
1 AGGAACTCAAAAAC
*
15539 AGGAAATCAAAAAC
1 AGGAACTCAAAAAC
15553 AG
1 AG
15555 CAAATCAATG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.59, C:0.16, G:0.16, T:0.09
Consensus pattern (14 bp):
AGGAACTCAAAAAC
Found at i:15559 original size:14 final size:14
Alignment explanation
Indices: 15519--15562 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
15509 TAAGGAACTA
*
15519 AAAAACAGGAACTC
1 AAAAACAGGAAATC
* *
15533 ACAAATAGGAAATC
1 AAAAACAGGAAATC
*
15547 AAAAACAGCAAATC
1 AAAAACAGGAAATC
15561 AA
1 AA
15563 TGACTAAAGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.61, C:0.18, G:0.11, T:0.09
Consensus pattern (14 bp):
AAAAACAGGAAATC
Found at i:18056 original size:21 final size:22
Alignment explanation
Indices: 18031--18076 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
18021 GCAAACACAT
18031 AAACTGATCAAAAC-AGATCAG
1 AAACTGATCAAAACAAGATCAG
*
18052 AAACTGATCAAAACAAGTTCAG
1 AAACTGATCAAAACAAGATCAG
18074 AAA
1 AAA
18077 TTGAAACTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.54, C:0.17, G:0.13, T:0.15
Consensus pattern (22 bp):
AAACTGATCAAAACAAGATCAG
Found at i:18060 original size:11 final size:10
Alignment explanation
Indices: 18031--18065 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
18021 GCAAACACAT
18031 AAACTGATCA
1 AAACTGATCA
*
18041 AAACAGATCA
1 AAACTGATCA
18051 GAAACTGATCA
1 -AAACTGATCA
18062 AAAC
1 AAAC
18066 AAGTTCAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.54, C:0.20, G:0.11, T:0.14
Consensus pattern (10 bp):
AAACTGATCA
Found at i:18130 original size:29 final size:27
Alignment explanation
Indices: 18051--18131 Score: 78
Period size: 29 Copynumber: 2.9 Consensus size: 27
18041 AAACAGATCA
18051 GAAACTGATCAAAACA-AGTTCAGAAATT
1 GAAACTGATCAAAACATA--TCAGAAATT
*
18079 GAAACTGATCAAAAC-TGACCAGAAATGT
1 GAAACTGATCAAAACAT-ATCAGAAAT-T
18107 AGACAA-TGATCAAAACATATCAGAA
1 -GA-AACTGATCAAAACATATCAGAA
18132 TTCAGAATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
27 7 0.16
28 16 0.36
29 19 0.42
30 3 0.07
ACGTcount: A:0.51, C:0.16, G:0.15, T:0.19
Consensus pattern (27 bp):
GAAACTGATCAAAACATATCAGAAATT
Found at i:18234 original size:29 final size:29
Alignment explanation
Indices: 18202--18257 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
18192 CGTCAAAATT
18202 AACACAAAAATACAGTATGG-AAATACATA
1 AACA-AAAAATACAGTATGGAAAATACATA
**
18231 AACAGGAAATACAGTATGGAAAATACA
1 AACAAAAAATACAGTATGGAAAATACA
18258 ATATACATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.57, C:0.12, G:0.14, T:0.16
Consensus pattern (29 bp):
AACAAAAAATACAGTATGGAAAATACATA
Found at i:18372 original size:28 final size:27
Alignment explanation
Indices: 18339--18420 Score: 73
Period size: 28 Copynumber: 3.0 Consensus size: 27
18329 TACAGTATAC
18339 AATATACATATACATATATATTAACAT
1 AATATACATATACATATATATTAACAT
*
18366 ATATATACA-ATATCAGTATACA-T-ACAGT
1 A-ATATACATATA-CA-TATATATTAACA-T
*
18394 AA-ATACAGTATACACATATATTAACAT
1 AATATACA-TATACATATATATTAACAT
18421 TACAGTTACA
Statistics
Matches: 44, Mismatches: 3, Indels: 16
0.70 0.05 0.25
Matches are distributed among these distances:
26 9 0.20
27 12 0.27
28 18 0.41
29 5 0.11
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (27 bp):
AATATACATATACATATATATTAACAT
Found at i:19517 original size:23 final size:23
Alignment explanation
Indices: 19466--19518 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
19456 TTTTATTCAT
19466 TTATATATAATAAAATTATAAAA
1 TTATATATAATAAAATTATAAAA
** * *
19489 ACATATATAATATATTTATAAAA
1 TTATATATAATAAAATTATAAAA
19512 TTATATA
1 TTATATA
19519 GTCGGGTTCG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
TTATATATAATAAAATTATAAAA
Found at i:21416 original size:73 final size:75
Alignment explanation
Indices: 21328--21467 Score: 198
Period size: 75 Copynumber: 1.9 Consensus size: 75
21318 TTTCTATCAA
*
21328 TAAATTCCAGAGTGAG-AAA-ACCGAAA-CAAGGCGAAAA-GATTCTCCCACGTTAAAAGTTGAT
1 TAAATTCCAGAGTGAGAAAAGACC-AAATCAAGGCGAAAATG-TTCTCACACGTTAAAAGTTGAT
21389 GGGAGCTGTTGG
64 GGGAGCTGTTGG
* * *
21401 TAAATTCCAGTGTGAGAAAAGACCAAATTAGGGCGAAAATGTTCTCACACGTTAAAAGTTGATGG
1 TAAATTCCAGAGTGAGAAAAGACCAAATCAAGGCGAAAATGTTCTCACACGTTAAAAGTTGATGG
21466 GA
66 GA
21468 ACTATCAGTA
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
73 15 0.25
74 6 0.10
75 37 0.63
76 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (75 bp):
TAAATTCCAGAGTGAGAAAAGACCAAATCAAGGCGAAAATGTTCTCACACGTTAAAAGTTGATGG
GAGCTGTTGG
Done.