Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013070.1 Corchorus olitorius cultivar O-4 contig13103, 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: 48264
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1155 original size:21 final size:21
Alignment explanation
Indices: 1130--1174 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1120 TCAGAATATT
* *
1130 CATCACTATCAGTAGCAGCAA
1 CATCACTATCAGCAGCAACAA
1151 CATCACTATCAGCAGCAACAA
1 CATCACTATCAGCAGCAACAA
1172 CAT
1 CAT
1175 TAACACCAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.31, G:0.11, T:0.18
Consensus pattern (21 bp):
CATCACTATCAGCAGCAACAA
Found at i:4573 original size:20 final size:19
Alignment explanation
Indices: 4548--4588 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
4538 AACAATTGAA
4548 TTGCTAAATACCGCCCCCTT
1 TTGCTAAATACCG-CCCCTT
**
4568 TTGCTATTTACCGCCCCTT
1 TTGCTAAATACCGCCCCTT
4587 TT
1 TT
4589 TTACACTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.15, C:0.37, G:0.10, T:0.39
Consensus pattern (19 bp):
TTGCTAAATACCGCCCCTT
Found at i:4818 original size:10 final size:10
Alignment explanation
Indices: 4805--4888 Score: 56
Period size: 10 Copynumber: 9.0 Consensus size: 10
4795 TTTTTATTTT
4805 TTAATTATTA
1 TTAATTATTA
4815 TTAATTA-T-
1 TTAATTATTA
4823 TT-A--ATTA
1 TTAATTATTA
4830 TTAATTATTA
1 TTAATTATTA
*
4840 TTAATT-TAAA
1 TTAATTAT-TA
*
4850 TT-GTTATTA
1 TTAATTATTA
*
4859 TTAATTATAA
1 TTAATTATTA
* *
4869 TTAATAATAA
1 TTAATTATTA
*
4879 TTAATAATTA
1 TTAATTATTA
4889 AAAAAAAACA
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
5 1 0.02
6 1 0.02
7 3 0.05
8 3 0.05
9 7 0.12
10 44 0.75
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (10 bp):
TTAATTATTA
Found at i:4821 original size:7 final size:7
Alignment explanation
Indices: 4811--4889 Score: 65
Period size: 7 Copynumber: 11.1 Consensus size: 7
4801 TTTTTTAATT
4811 ATTATTA
1 ATTATTA
4818 ATTATTTA
1 ATTA-TTA
4826 ATTATTA
1 ATTATTA
4833 ATTATT-
1 ATTATTA
4839 ATTAATTTAA
1 ATT-A-TT-A
*
4849 ATTGTT-
1 ATTATTA
4855 ATTATTA
1 ATTATTA
4862 ATTA-TA
1 ATTATTA
*
4868 ATTAATA
1 ATTATTA
*
4875 ATAATTA
1 ATTATTA
*
4882 ATAATTA
1 ATTATTA
4889 A
1 A
4890 AAAAAAACAA
Statistics
Matches: 61, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
6 14 0.23
7 33 0.54
8 11 0.18
10 3 0.05
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (7 bp):
ATTATTA
Found at i:4833 original size:25 final size:27
Alignment explanation
Indices: 4805--4873 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 27
4795 TTTTTATTTT
4805 TTAATTATTATTAATT-ATT-TAATTA
1 TTAATTATTATTAATTAATTGTAATTA
*
4830 TTAATTATTATTAATTTAAATTGTTATTA
1 TTAATTATTATTAA-TT-AATTGTAATTA
*
4859 TTAATTATAATTAAT
1 TTAATTATTATTAAT
4874 AATAATTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
25 14 0.37
26 2 0.05
28 4 0.11
29 18 0.47
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (27 bp):
TTAATTATTATTAATTAATTGTAATTA
Found at i:4994 original size:33 final size:33
Alignment explanation
Indices: 4909--5005 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 33
4899 ATGCCGTCCT
* ** *
4909 ATGGTCATACCGCCCAAGGAGAATGGCATGATC
1 ATGGTCATGCCGCCCAAGGAGGGTGGCATGACC
*
4942 ATGGTCATGCAGCCCAAGGAGGGTGGCATGACC
1 ATGGTCATGCCGCCCAAGGAGGGTGGCATGACC
** *
4975 ATGGTCATGCCGCTTAAGGAGGGCGGCATGA
1 ATGGTCATGCCGCCCAAGGAGGGTGGCATGA
5006 GTGGCACGTC
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.26, C:0.23, G:0.34, T:0.18
Consensus pattern (33 bp):
ATGGTCATGCCGCCCAAGGAGGGTGGCATGACC
Found at i:6890 original size:1 final size:1
Alignment explanation
Indices: 6884--6910 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
6874 GAGTTTTCTT
6884 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
6911 CTTCAAGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:10209 original size:20 final size:20
Alignment explanation
Indices: 10184--10272 Score: 178
Period size: 20 Copynumber: 4.5 Consensus size: 20
10174 TTTGGTTGGG
10184 GGTGATCTTTGATCACCTGT
1 GGTGATCTTTGATCACCTGT
10204 GGTGATCTTTGATCACCTGT
1 GGTGATCTTTGATCACCTGT
10224 GGTGATCTTTGATCACCTGT
1 GGTGATCTTTGATCACCTGT
10244 GGTGATCTTTGATCACCTGT
1 GGTGATCTTTGATCACCTGT
10264 GGTGATCTT
1 GGTGATCTT
10273 GGCAGGTGAT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.15, C:0.19, G:0.26, T:0.40
Consensus pattern (20 bp):
GGTGATCTTTGATCACCTGT
Found at i:10434 original size:17 final size:16
Alignment explanation
Indices: 10394--10436 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
10384 CATGTAATCT
*
10394 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
10410 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
10427 TTAGATCACT
1 TT-GATCACT
10437 AATGATTTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 20 0.83
18 1 0.04
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:10703 original size:53 final size:53
Alignment explanation
Indices: 10610--10710 Score: 134
Period size: 53 Copynumber: 1.9 Consensus size: 53
10600 TATGGGCATG
*
10610 TGGGTTTGATTTAAAGTCACCTTAGGATTTGTTTAAATTATTAAACCTACTAT
1 TGGGTTTGATTTAAAGTCACCTTAGGATTTGTTTAAATTATCAAACCTACTAT
* * *
10663 TGGGTATTGATTTAATGTCACGGTT-GGA-TTGTTTATATTATCAAACCT
1 TGGGT-TTGATTTAAAGTCAC-CTTAGGATTTGTTTAAATTATCAAACCT
10711 GCTGGATCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
53 23 0.55
54 17 0.40
55 2 0.05
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.44
Consensus pattern (53 bp):
TGGGTTTGATTTAAAGTCACCTTAGGATTTGTTTAAATTATCAAACCTACTAT
Found at i:12356 original size:44 final size:44
Alignment explanation
Indices: 12307--12395 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
12297 TATCATATAT
*
12307 TACTTTATAATATATGATATATATAATTTAAATAAAAATAAAAA
1 TACTTTATAATATATAATATATATAATTTAAATAAAAATAAAAA
*
12351 TACTTTATAATATATAATATATATAATTTAAATAAAAATCAAAA
1 TACTTTATAATATATAATATATATAATTTAAATAAAAATAAAAA
12395 T
1 T
12396 CAAAATCAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.39
Consensus pattern (44 bp):
TACTTTATAATATATAATATATATAATTTAAATAAAAATAAAAA
Found at i:16530 original size:51 final size:51
Alignment explanation
Indices: 16433--16531 Score: 119
Period size: 51 Copynumber: 1.9 Consensus size: 51
16423 TTCAATATTT
** * **
16433 CCTTGTTTCAATCTTGTCTCCGAACACCCAAACACTCTTTTAGTGTTTTTC
1 CCTTGTTTCAATCTTGTCTCCGAACACAAAAACACTCGTACAGTGTTTTTC
* *
16484 CCTTGTTTCAATCTTGTCTCCGGACATAAAAACACT-GTACACGTGTTT
1 CCTTGTTTCAATCTTGTCTCCGAACACAAAAACACTCGTACA-GTGTTT
16532 CCCTCTCAGT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
50 2 0.05
51 38 0.95
ACGTcount: A:0.22, C:0.27, G:0.12, T:0.38
Consensus pattern (51 bp):
CCTTGTTTCAATCTTGTCTCCGAACACAAAAACACTCGTACAGTGTTTTTC
Found at i:20688 original size:31 final size:31
Alignment explanation
Indices: 20650--20708 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
20640 TTTGTAAAAC
*
20650 TTTTGAAACGTCTATTGTACCCTTATTTAAT
1 TTTTGAAACGTCTATTATACCCTTATTTAAT
*
20681 TTTTGAAACGTCTATTATATCCTTATTT
1 TTTTGAAACGTCTATTATACCCTTATTT
20709 GTCTAACATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.25, C:0.15, G:0.08, T:0.51
Consensus pattern (31 bp):
TTTTGAAACGTCTATTATACCCTTATTTAAT
Found at i:21571 original size:22 final size:22
Alignment explanation
Indices: 21530--21571 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
21520 GTTTATAATA
* *
21530 TTCTTGGGTCATTCATGTTAAC
1 TTCTTAGGTCATTCAGGTTAAC
*
21552 TTCTTAGGTCATTTAGGTTA
1 TTCTTAGGTCATTCAGGTTA
21572 CAAGTTTGTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.48
Consensus pattern (22 bp):
TTCTTAGGTCATTCAGGTTAAC
Found at i:23184 original size:24 final size:25
Alignment explanation
Indices: 23151--23207 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
23141 GTCAGCCTTG
*
23151 AATTT-TTTAATGT-TTAATTCTTA
1 AATTTATTTAATGTCTTAATTATTA
*
23174 AATTTATTTAATGTCTTAATTATTC
1 AATTTATTTAATGTCTTAATTATTA
23199 AATTTATTT
1 AATTTATTT
23208 TACAATCCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60
Consensus pattern (25 bp):
AATTTATTTAATGTCTTAATTATTA
Found at i:23490 original size:31 final size:31
Alignment explanation
Indices: 23452--23513 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
23442 GAGTTTTGTA
*
23452 AAACTTTTGAATCGCCTATTATACCCTTATT
1 AAACTTTTGAATCGCCTATCATACCCTTATT
*
23483 AAACTTTTGAATCGCCTATCATATCCTTATT
1 AAACTTTTGAATCGCCTATCATACCCTTATT
23514 TTAATCAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (31 bp):
AAACTTTTGAATCGCCTATCATACCCTTATT
Found at i:23666 original size:93 final size:93
Alignment explanation
Indices: 23512--23688 Score: 282
Period size: 93 Copynumber: 1.9 Consensus size: 93
23502 CATATCCTTA
*
23512 TTTTAATCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAATTTTTTATTT
1 TTTTAATCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAATATTTTATTT
* * *
23577 TTACCATTTTACTATTTTACTTTTATAG
66 TAACCATATTACTAATTTACTTTTATAG
* **
23605 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATATCTATTTTATTT
1 TTTTAATCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAATATTTTATTT
*
23670 TAACGATATTACTAATTTA
66 TAACCATATTACTAATTTA
23689 ATTAAAAAGT
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.34, C:0.12, G:0.01, T:0.52
Consensus pattern (93 bp):
TTTTAATCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAATATTTTATTT
TAACCATATTACTAATTTACTTTTATAG
Found at i:26970 original size:7 final size:7
Alignment explanation
Indices: 26938--26963 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
26928 AACTTAGATT
26938 TAAAAAA
1 TAAAAAA
26945 TAAAAAA
1 TAAAAAA
26952 TAAAAAA
1 TAAAAAA
26959 TAAAA
1 TAAAA
26964 TAAAAAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:38150 original size:2 final size:2
Alignment explanation
Indices: 38143--38204 Score: 108
Period size: 2 Copynumber: 31.5 Consensus size: 2
38133 ACGGTAGATT
38143 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
38185 TC TC -C CC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC T
38205 GTGTTGAATT
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:41924 original size:11 final size:10
Alignment explanation
Indices: 41899--41940 Score: 54
Period size: 9 Copynumber: 4.4 Consensus size: 10
41889 TAAAATTAAA
41899 AAAAAATTAT
1 AAAAAATTAT
41909 -AAAAATTAT
1 AAAAAATTAT
41918 AACAAAATT-T
1 AA-AAAATTAT
41928 AAAAAA-TAT
1 AAAAAATTAT
41937 AAAA
1 AAAA
41941 TTGGATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 1 0.03
9 18 0.62
10 4 0.14
11 6 0.21
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:41933 original size:20 final size:21
Alignment explanation
Indices: 41890--41940 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
41880 TGTAGTCGTT
41890 AAAATTA-AAAAAAAATTATA
1 AAAATTATAAAAAAAATTATA
*
41910 AAAATTAT-AACAAAATT-TA
1 AAAATTATAAAAAAAATTATA
*
41929 AAAAATATAAAA
1 AAAATTATAAAA
41941 TTGGATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (21 bp):
AAAATTATAAAAAAAATTATA
Found at i:43090 original size:72 final size:72
Alignment explanation
Indices: 43002--43145 Score: 198
Period size: 72 Copynumber: 2.0 Consensus size: 72
42992 GTCAACTTTT
* *** ** *
43002 TAGGATAGTTTGTTGCTTCATGGACTTCATGTTGTGTATGTAAGATATTCAGATTGTTCTTTAAT
1 TAGGATAGTTTATTGCTTCATGGACCAAATGTTGCATATGTAAGATACTCAGATTGTTCTTTAAT
*
43067 TTTACTA
66 TTAACTA
* *
43074 TAGGATAGTTTATTGCTTCATGGACCAAATGTTGCATATGTAAGATACTCAGTTTGTTCTTTTAT
1 TAGGATAGTTTATTGCTTCATGGACCAAATGTTGCATATGTAAGATACTCAGATTGTTCTTTAAT
43139 TTAACTA
66 TTAACTA
43146 ACTCAGTTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.45
Consensus pattern (72 bp):
TAGGATAGTTTATTGCTTCATGGACCAAATGTTGCATATGTAAGATACTCAGATTGTTCTTTAAT
TTAACTA
Found at i:47141 original size:15 final size:15
Alignment explanation
Indices: 47118--47160 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
47108 ATAAAAATTA
47118 AATAT-TTTTATTTT
1 AATATATTTTATTTT
47132 AATATATTTTATTTT
1 AATATATTTTATTTT
*
47147 ATTGATA-TTTATTT
1 AAT-ATATTTTATTT
47161 ATAAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 5 0.19
15 18 0.69
16 3 0.12
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
AATATATTTTATTTT
Found at i:48102 original size:15 final size:15
Alignment explanation
Indices: 48070--48099 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
48060 TAAATTTCAA
48070 TAAAATAAAATATAT
1 TAAAATAAAATATAT
48085 TAAAATAAAA-ATAT
1 TAAAATAAAATATAT
48099 T
1 T
48100 TAATTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAAATAAAATATAT
Done.