Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011851.1 Corchorus olitorius cultivar O-4 contig11884, 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: 32463
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:151 original size:78 final size:78
Alignment explanation
Indices: 22--190 Score: 277
Period size: 78 Copynumber: 2.2 Consensus size: 78
12 TTGTTTAAAC
* * *
22 TTTTA-TAGTTTTACTCAACTAAAAGCTCTATATTTATTTAATTAAATCTAATATCTTTATAACT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATATTTATTTAATTAAATCTAATATCCTTAAAACT
*
86 ATTTTATTTTACCA
65 ATTTTAGTTTACCA
*
100 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTAAAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATATTTATTTAATTAAATCTAATATCCTTAAAACTA
165 TTTTAGTTTACCA
66 TTTTAGTTTACCA
178 TTTTACTATTTTA
1 TTTTACTATTTTA
191 ATTAAAAAAA
Statistics
Matches: 85, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
78 83 0.98
79 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.02, T:0.50
Consensus pattern (78 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATATTTATTTAATTAAATCTAATATCCTTAAAACTA
TTTTAGTTTACCA
Found at i:729 original size:16 final size:16
Alignment explanation
Indices: 704--749 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
694 CTTTCTCTGA
704 TCATTCGGGTTTTGGC
1 TCATTCGGGTTTTGGC
* *
720 TCATTAGGG-TTTGGG
1 TCATTCGGGTTTTGGC
*
735 TCATTCGGGTCTTGG
1 TCATTCGGGTTTTGG
750 GTCTGCTAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.09, C:0.15, G:0.35, T:0.41
Consensus pattern (16 bp):
TCATTCGGGTTTTGGC
Found at i:750 original size:16 final size:15
Alignment explanation
Indices: 704--752 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
694 CTTTCTCTGA
*
704 TCATTCGGGTTTTGGC
1 TCATTCGGG-TTTGGG
*
720 TCATTAGGGTTTGGG
1 TCATTCGGGTTTGGG
735 TCATTCGGGTCTTGGG
1 TCATTCGGGT-TTGGG
751 TC
1 TC
753 TGCTAGGTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 14 0.48
16 15 0.52
ACGTcount: A:0.08, C:0.16, G:0.35, T:0.41
Consensus pattern (15 bp):
TCATTCGGGTTTGGG
Found at i:2022 original size:16 final size:17
Alignment explanation
Indices: 2001--2034 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1991 GTATGTATAA
*
2001 ATTATAT-TTAATAAAT
1 ATTATATATCAATAAAT
2017 ATTATATATCAATAAAT
1 ATTATATATCAATAAAT
2034 A
1 A
2035 AAAATAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTATATATCAATAAAT
Found at i:2591 original size:30 final size:31
Alignment explanation
Indices: 2557--2629 Score: 112
Period size: 30 Copynumber: 2.4 Consensus size: 31
2547 TTATCCTGAC
**
2557 AAAAGAAATTTGCTTATGATTCTTTTTG-AA
1 AAAAGAAATTTGCTTATGAAGCTTTTTGAAA
2587 AAAAGAAATTTGCTTATGAAGCTTTTTGAAA
1 AAAAGAAATTTGCTTATGAAGCTTTTTGAAA
*
2618 AAAAAAAATTTG
1 AAAAGAAATTTG
2630 ATATCGACTA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 26 0.67
31 13 0.33
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (31 bp):
AAAAGAAATTTGCTTATGAAGCTTTTTGAAA
Found at i:2735 original size:32 final size:32
Alignment explanation
Indices: 2694--2796 Score: 163
Period size: 32 Copynumber: 3.2 Consensus size: 32
2684 TTGAGTCAGG
2694 TCGGGTTAAATTTGGATCAGGTTGATTCGGGT
1 TCGGGTTAAATTTGGATCAGGTTGATTCGGGT
*
2726 TCGGGTTAAATTTGGGTCAGGTTGATTCGGGT
1 TCGGGTTAAATTTGGATCAGGTTGATTCGGGT
* *
2758 TCGGGTCAAATTT-GAGTCAGGTTAATTCGGGT
1 TCGGGTTAAATTTGGA-TCAGGTTGATTCGGGT
2790 TCGGGTT
1 TCGGGTT
2797 GGGTTTTGGC
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
31 1 0.02
32 64 0.98
ACGTcount: A:0.17, C:0.11, G:0.35, T:0.37
Consensus pattern (32 bp):
TCGGGTTAAATTTGGATCAGGTTGATTCGGGT
Found at i:2963 original size:20 final size:20
Alignment explanation
Indices: 2930--2968 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2920 CATAAATGAA
*
2930 ATTTTCAGAAATTATTATTT
1 ATTTTCAGAAATTAGTATTT
2950 ATTTTCA-AATATTAGTATT
1 ATTTTCAGAA-ATTAGTATT
2969 GAATTCGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTCAGAAATTAGTATTT
Found at i:5579 original size:2 final size:2
Alignment explanation
Indices: 5572--5600 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5562 ATATGCCATT
5572 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
5601 TTATTAATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:7846 original size:14 final size:14
Alignment explanation
Indices: 7827--7854 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
7817 TTTTTTCTTA
7827 AATAATAATAAATT
1 AATAATAATAAATT
7841 AATAATAATAAATT
1 AATAATAATAAATT
7855 TAATCACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATAATAATAAATT
Found at i:9271 original size:45 final size:45
Alignment explanation
Indices: 9207--9299 Score: 159
Period size: 45 Copynumber: 2.1 Consensus size: 45
9197 ATTTTTCAAA
*
9207 GGAGTTGAATTTTTAAACGTAAAATCATACTATAAGAACTAAACC
1 GGAGTTGAATTTTAAAACGTAAAATCATACTATAAGAACTAAACC
* *
9252 GGAGTTGAATTTTAAAACGTATAATCATACTATAAGAGCTAAACC
1 GGAGTTGAATTTTAAAACGTAAAATCATACTATAAGAACTAAACC
9297 GGA
1 GGA
9300 TTAGATTGCC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (45 bp):
GGAGTTGAATTTTAAAACGTAAAATCATACTATAAGAACTAAACC
Found at i:9978 original size:29 final size:30
Alignment explanation
Indices: 9945--10017 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 30
9935 AGAGCTTAAT
* ** *
9945 AGCCAAATAAGCCCCTGAACT-TTTATTAC
1 AGCCAAATAAGCCCCTGAACTCTTGAAAAA
9974 AGCCAAATAAGCCCCTGAACTCTTGAAAAA
1 AGCCAAATAAGCCCCTGAACTCTTGAAAAA
10004 AGCCAAATAAGCCC
1 AGCCAAATAAGCCC
10018 TTTTTTCTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 21 0.54
30 18 0.46
ACGTcount: A:0.40, C:0.29, G:0.12, T:0.19
Consensus pattern (30 bp):
AGCCAAATAAGCCCCTGAACTCTTGAAAAA
Found at i:10113 original size:14 final size:14
Alignment explanation
Indices: 10096--10146 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
10086 GCCACATGGA
10096 AAAAATAAATTTTG
1 AAAAATAAATTTTG
***
10110 AAAAA-AAATTGACAA
1 AAAAATAAATT--TTG
10125 AAAAATAAATTTTG
1 AAAAATAAATTTTG
10139 AAAAATAA
1 AAAAATAA
10147 GATAAAAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
13 5 0.18
14 13 0.46
15 5 0.18
16 5 0.18
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (14 bp):
AAAAATAAATTTTG
Found at i:10114 original size:16 final size:16
Alignment explanation
Indices: 10095--10143 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
10085 TGCCACATGG
10095 AAAAAATAAATTTTG-
1 AAAAAATAAATTTTGA
***
10110 -AAAAA-AAATTGACA
1 AAAAAATAAATTTTGA
10124 AAAAAATAAATTTTGA
1 AAAAAATAAATTTTGA
10140 AAAA
1 AAAA
10144 TAAGATAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 5
0.69 0.17 0.14
Matches are distributed among these distances:
13 5 0.20
14 5 0.20
15 5 0.20
16 10 0.40
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.24
Consensus pattern (16 bp):
AAAAAATAAATTTTGA
Found at i:13858 original size:22 final size:22
Alignment explanation
Indices: 13824--13907 Score: 75
Period size: 21 Copynumber: 3.9 Consensus size: 22
13814 ACTATAGTAT
* * *
13824 CAAAAAATTATAGGGAGATTAA
1 CAAAATATCATAGGGAGGTTAA
*
13846 CAAAATCTCATAGGGAGGTTATA
1 CAAAATATCATAGGGAGGTTA-A
*
13869 -AAAA-ATCATAGGAAGGTT-A
1 CAAAATATCATAGGGAGGTTAA
* *
13888 CAAAATTTCATAGGAAGGTT
1 CAAAATATCATAGGGAGGTT
13908 TATTAAAACT
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.02
20 4 0.08
21 25 0.48
22 21 0.40
23 1 0.02
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.25
Consensus pattern (22 bp):
CAAAATATCATAGGGAGGTTAA
Found at i:13930 original size:44 final size:42
Alignment explanation
Indices: 13825--13944 Score: 123
Period size: 43 Copynumber: 2.8 Consensus size: 42
13815 CTATAGTATC
* * * * *
13825 AAAAAATTATAGGGAGATTAACAAAATCTCATAGGGAGGTTAT
1 AAAAAATCATAGGAAGGTT-ACAAAATTTCATAGGAAGGTTAT
13868 AAAAAATCATAGGAAGGTTACAAAATTTCATAGGAAGGTTTATT
1 AAAAAATCATAGGAAGGTTACAAAATTTCATAGGAAGG-TTA-T
** **
13912 AAAACTTCATAGTTAGGTTATCAAAATTTCATA
1 AAAAAATCATAGGAAGGTTA-CAAAATTTCATA
13945 TGGAGTTTAT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
42 17 0.26
43 19 0.29
44 17 0.26
45 12 0.18
ACGTcount: A:0.45, C:0.08, G:0.17, T:0.30
Consensus pattern (42 bp):
AAAAAATCATAGGAAGGTTACAAAATTTCATAGGAAGGTTAT
Found at i:13937 original size:22 final size:22
Alignment explanation
Indices: 13846--14005 Score: 116
Period size: 21 Copynumber: 7.4 Consensus size: 22
13836 GGGAGATTAA
* *
13846 CAAAATCTCATAGGGAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
**
13868 -AAAAAATCATAGGAAGGTTA-
1 CAAAATTTCATAGGAAGGTTAT
13888 CAAAATTTCATAGGAAGGTTTAT
1 CAAAATTTCATAGGAAGG-TTAT
* * **
13911 TAAAACTTCATAGTTAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
*
13933 CAAAATTTCATATGG-AGTTTAT
1 CAAAATTTCATA-GGAAGGTTAT
* * *
13955 CACATTTTTATAGGTAA--TTAT
1 CAAAATTTCATAGG-AAGGTTAT
* *
13976 CAAAATTTAATAGGGTA-GTTAT
1 CAAAATTTCATA-GGAAGGTTAT
13998 CAAAATTT
1 CAAAATTT
14006 TATAAAAATA
Statistics
Matches: 110, Mismatches: 20, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
21 48 0.44
22 46 0.42
23 16 0.15
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:13953 original size:44 final size:42
Alignment explanation
Indices: 13825--13954 Score: 118
Period size: 44 Copynumber: 3.0 Consensus size: 42
13815 CTATAGTATC
* * * * *
13825 AAAAAATTATAGGGAGATTAACAAAATCTCATAGGGAGGTTA-T
1 AAAAAATCATAGGAAGGTT-ACAAAATTTCATA-GGAGTTTATT
13868 AAAAAATCATAGGAAGGTTACAAAATTTCATAGGAAGGTTTATT
1 AAAAAATCATAGGAAGGTTACAAAATTTCATAGG-A-GTTTATT
** **
13912 AAAACTTCATAGTTAGGTTATCAAAATTTCATATGGAGTTTAT
1 AAAAAATCATAGGAAGGTTA-CAAAATTTCATA-GGAGTTTAT
13955 CACATTTTTA
Statistics
Matches: 73, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
41 2 0.03
42 13 0.18
43 20 0.27
44 23 0.32
45 13 0.18
46 2 0.03
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.32
Consensus pattern (42 bp):
AAAAAATCATAGGAAGGTTACAAAATTTCATAGGAGTTTATT
Found at i:13975 original size:21 final size:22
Alignment explanation
Indices: 13929--14009 Score: 78
Period size: 22 Copynumber: 3.7 Consensus size: 22
13919 CATAGTTAGG
*
13929 TTATCAAAATTTCATATGGAGT--
1 TTATCAAAATTTTATA-GG-GTAA
* *
13951 TTATCACATTTTTATA-GGTAA
1 TTATCAAAATTTTATAGGGTAA
* *
13972 TTATCAAAATTTAATAGGGTAG
1 TTATCAAAATTTTATAGGGTAA
13994 TTATCAAAATTTTATA
1 TTATCAAAATTTTATA
14010 AAAATATTCA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.04
20 1 0.02
21 13 0.27
22 32 0.67
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.43
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGGTAA
Found at i:14636 original size:16 final size:16
Alignment explanation
Indices: 14615--14646 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
14605 AGAAATTGTA
14615 ATTGTAACAAAGAGAT
1 ATTGTAACAAAGAGAT
14631 ATTGTAACAAAGAGAT
1 ATTGTAACAAAGAGAT
14647 TTTATTAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (16 bp):
ATTGTAACAAAGAGAT
Found at i:20158 original size:93 final size:93
Alignment explanation
Indices: 20037--20362 Score: 589
Period size: 93 Copynumber: 3.5 Consensus size: 93
20027 AGCTCTAATG
20037 ACTTATCCGCTTTTCAAGGCTCGTAAAGTGGCATGAGGTTCATCATGGTCGTCTAATTGAGCTCT
1 ACTTATCCGCTTTTCAAGGCTCGTAAAGTGGCATGAGGTTCATCATGGTCGTCTAATTGAGCTCT
20102 AATGCCACTTGTTAGGAGAGCACTCGGA
66 AATGCCACTTGTTAGGAGAGCACTCGGA
* * *
20130 ACTTATCCGCTTTTCAAGGCTCGTAAAGTGGCATGAGGTCCATCATGATTGTCTAATTGAGCTCT
1 ACTTATCCGCTTTTCAAGGCTCGTAAAGTGGCATGAGGTTCATCATGGTCGTCTAATTGAGCTCT
20195 AATGCCACTTGTTAGGAGAGCACTCGGA
66 AATGCCACTTGTTAGGAGAGCACTCGGA
20223 ACTTATCCGCTTTTCAAGGCTCGTAAAGTGGCATGAGGTTCATCATGGTCGTCTAATTGAGCTCT
1 ACTTATCCGCTTTTCAAGGCTCGTAAAGTGGCATGAGGTTCATCATGGTCGTCTAATTGAGCTCT
20288 AATGCCACTTGTTAGGAGAGCACTCGGA
66 AATGCCACTTGTTAGGAGAGCACTCGGA
* ***
20316 ACTTATCTGCTTTTCAAGGCTCACCAAGTGGCATGAGGTTCATCATG
1 ACTTATCCGCTTTTCAAGGCTCGTAAAGTGGCATGAGGTTCATCATG
20363 ATCTTAGTTA
Statistics
Matches: 223, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 223 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (93 bp):
ACTTATCCGCTTTTCAAGGCTCGTAAAGTGGCATGAGGTTCATCATGGTCGTCTAATTGAGCTCT
AATGCCACTTGTTAGGAGAGCACTCGGA
Found at i:29875 original size:45 final size:45
Alignment explanation
Indices: 29800--29896 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 45
29790 AGTGTATTAC
* **
29800 CTAA-ATTCTAGTACTCCATCTATAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTACTCCATCTATACATAATTCATCAAAATAAAG
* * *
29844 CTAATATTCTACTCCTCCATCTCTACATAATTCATTAAAATAAAG
1 CTAATATTCTACTACTCCATCTATACATAATTCATCAAAATAAAG
29889 CTAATATT
1 CTAATATT
29897 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 4 0.09
45 42 0.91
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.35
Consensus pattern (45 bp):
CTAATATTCTACTACTCCATCTATACATAATTCATCAAAATAAAG
Found at i:31278 original size:26 final size:26
Alignment explanation
Indices: 31249--31299 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
31239 TACAATTAAT
31249 TTGGATTTAATTAAATTTACCAGACA
1 TTGGATTTAATTAAATTTACCAGACA
* *
31275 TTGGATTTGATTAAATTTACTAGAC
1 TTGGATTTAATTAAATTTACCAGAC
31300 TCCTTTACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (26 bp):
TTGGATTTAATTAAATTTACCAGACA
Found at i:31407 original size:2 final size:2
Alignment explanation
Indices: 31367--31393 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31357 ACTCAAATAA
31367 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
31394 GCTTCGCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Done.