Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023448.1 Corchorus olitorius cultivar O-4 contig23481, 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: 65617
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:5352 original size:21 final size:21
Alignment explanation
Indices: 5314--5357 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5304 AGAACAATTG
*
5314 AAAATAAAAGCAATTAAACTA
1 AAAATAAAAGCAAGTAAACTA
*
5335 AAAAT-AAAGCAAAGTAAATTA
1 AAAATAAAAGC-AAGTAAACTA
5356 AA
1 AA
5358 TCTAAACTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.68, C:0.07, G:0.07, T:0.18
Consensus pattern (21 bp):
AAAATAAAAGCAAGTAAACTA
Found at i:8830 original size:27 final size:26
Alignment explanation
Indices: 8800--8895 Score: 106
Period size: 27 Copynumber: 3.7 Consensus size: 26
8790 TCACGCTCAT
8800 GGGCATTTTGGTCATTTGAACACTTAG
1 GGGCATTTTGGTCATTTG-ACACTTAG
* **
8827 GGGCATTTTGGTAATTTGTACACCCAG
1 GGGCATTTTGGTCATTTG-ACACTTAG
**
8854 GGGCATTTTGGTCATTTTG-CA-TTTT
1 GGGCATTTTGGTCA-TTTGACACTTAG
8879 GGGCATTTTGGTCATTT
1 GGGCATTTTGGTCATTT
8896 TGGTCATTGT
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
24 3 0.05
25 14 0.24
26 2 0.03
27 36 0.61
28 4 0.07
ACGTcount: A:0.18, C:0.15, G:0.26, T:0.42
Consensus pattern (26 bp):
GGGCATTTTGGTCATTTGACACTTAG
Found at i:8871 original size:9 final size:9
Alignment explanation
Indices: 8857--8903 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
8847 CACCCAGGGG
8857 CATTTTGGT
1 CATTTTGGT
8866 CATTTT-G-
1 CATTTTGGT
*
8873 CATTTTGGG
1 CATTTTGGT
8882 CATTTTGGT
1 CATTTTGGT
8891 CATTTTGGT
1 CATTTTGGT
8900 CATT
1 CATT
8904 GTACACTTAG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
7 6 0.17
8 2 0.06
9 27 0.77
ACGTcount: A:0.13, C:0.13, G:0.21, T:0.53
Consensus pattern (9 bp):
CATTTTGGT
Found at i:8877 original size:16 final size:17
Alignment explanation
Indices: 8855--8903 Score: 73
Period size: 16 Copynumber: 2.9 Consensus size: 17
8845 TACACCCAGG
8855 GGCATTTTGGTCATTTT
1 GGCATTTTGGTCATTTT
*
8872 -GCATTTTGGGCATTTT
1 GGCATTTTGGTCATTTT
8888 GGTCATTTTGGTCATT
1 GG-CATTTTGGTCATT
8904 GTACACTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 15 0.54
17 1 0.04
18 12 0.43
ACGTcount: A:0.12, C:0.12, G:0.24, T:0.51
Consensus pattern (17 bp):
GGCATTTTGGTCATTTT
Found at i:16714 original size:28 final size:28
Alignment explanation
Indices: 16683--16785 Score: 136
Period size: 28 Copynumber: 3.7 Consensus size: 28
16673 AGTGAACTTA
*
16683 AAATAACCAAAATGCCCCCTGAATGTGC
1 AAATGACCAAAATGCCCCCTGAATGTGC
16711 AAATGACCAAAATG-CCCCTGAATGTGC
1 AAATGACCAAAATGCCCCCTGAATGTGC
* * * *
16738 AAATGACCAAAATGCCCCTTGGACGTGT
1 AAATGACCAAAATGCCCCCTGAATGTGC
* *
16766 AAATGACTAACATGCCCCCT
1 AAATGACCAAAATGCCCCCT
16786 ATGCGACCCT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
27 27 0.41
28 39 0.59
ACGTcount: A:0.36, C:0.28, G:0.17, T:0.19
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCCTGAATGTGC
Found at i:30752 original size:47 final size:48
Alignment explanation
Indices: 30658--31505 Score: 927
Period size: 47 Copynumber: 17.5 Consensus size: 48
30648 TATTTCTGCT
* * *
30658 TTTTACTTTTTAGTTTAATTACTCAGAATT-AACTAATTACCGCTTACTCTTTC
1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAA-TA-CTC-T--TC-TTC
* * * *
30711 TTTTACTCTTTAGTTTAATTACCCAAAATTAAACTAATTACTTTTTATTTCTTG
1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAA-TAC----T-CTTCTTC
* *
30765 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATTATTGTTTACTTCTTC
1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAA-TA----CT-CTTCTTC
* * *
30819 TTTTACTCTTTAGTTTAATTACCCAGAATTAAATTAATTATTGTTTACTTCTTC
1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAA-TA----CT-CTTCTTC
* *
30873 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAA-CCTCTTCTTC
1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATACTCTTCTTC
* *
30920 TTTTACTATTTAGTTTAATTACCCAGAATCAAACTAACA-TCTTCTTC
1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATACTCTTCTTC
* * *
30967 TTTTACTATTTAGTTTAATTACCCAGAAATAAAATAA-CCTCTTCTTC
1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATACTCTTCTTC
* *
31014 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAA-CCTCTCCTTC
1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATACTCTTCTTC
* * *
31061 TTTTACTATTTAGTTTAATTACCCAGATTTAAACTAACA-TCTCCTTC
1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATACTCTTCTTC
*
31108 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAA-CCTCTT-TATC
1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATACTCTTCT-TC
* * * *
31155 TTTTGCTATTTAGTTAAATTACCCAGAATTAAACTAA-CCTCTCCTTC
1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATACTCTTCTTC
* *
31202 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACA-TCTCCTTC
1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATACTCTTCTTC
* * *** *
31249 TTTTGCTCTTTAGTTTAATT-CTGGGTAATTAAACTAACA-TCTTCTTC
1 TTTTACTATTTAGTTTAATTACCCAG-AATTAAACTAATACTCTTCTTC
* *
31296 TTTTGCTATTTAGTTTAATTACCCAGAATTAAACTAA-CCTCTTCTTC
1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATACTCTTCTTC
* * *
31343 TTTTACTATTTAGTTTAATTACACAGAATTAAACTAA-CCTCTCCTTC
1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATACTCTTCTTC
* *
31390 TTTTCCTATTTAGTTTAATTACCCAGAATTAAACTAA-CCTCTTCTTC
1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATACTCTTCTTC
* *
31437 TTTTACTATTTAGTTTAATTACACAGAATTAAACTAA-ACTCTCCTTC
1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATACTCTTCTTC
*
31484 TTTTACTATTTAGTTCAATTAC
1 TTTTACTATTTAGTTTAATTAC
31506 TCTTCTAATT
Statistics
Matches: 718, Mismatches: 57, Indels: 46
0.87 0.07 0.06
Matches are distributed among these distances:
46 3 0.00
47 534 0.74
48 4 0.01
53 28 0.04
54 146 0.20
55 2 0.00
57 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.46
Consensus pattern (48 bp):
TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATACTCTTCTTC
Found at i:31036 original size:141 final size:141
Alignment explanation
Indices: 30658--31505 Score: 1043
Period size: 141 Copynumber: 5.8 Consensus size: 141
30648 TATTTCTGCT
* * * * *
30658 TTTTACTTTTTAGTTTAATTACTCAGAATTAACTAATTACCGCTTACTCTTTCTTTTACTCTTTA
1 TTTTACTATTTAGTTTAATTACCCAGAATTAA--AATAACCTC-T--TC-TTCTTTTACTATTTA
* * * * * *
30723 GTTTAATTACCCAAAATTAAACTAATTACTTTTTATTTCTTGTTTTACTCTTTAGTTTAATTACC
60 GTTTAATTACCCAGAATTAAACT-A--AC---CT-CTCCTTCTTTTACTATTTAGTTTAATTACC
* *
30788 CAGAATTAAACTAATTATTGTTTACTTCTTC
118 CAGAATTAAACTAA-CA-----T-CTCCTTC
* *** *
30819 TTTTACTCTTTAGTTTAATTACCCAGAATTAAATTAATTATTGTTTACTTCTTCTTTTACTCTTT
1 TTTTACTATTTAGTTTAATTACCCAGAATT-AA--AA-TA--ACCT-CTTCTTCTTTTACTATTT
*
30884 AGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTATTTAGTTTAATTACCCAGAAT
59 AGTTTAATTACCCAGAATTAAACTAACCTCTCCTTCTTTTACTATTTAGTTTAATTACCCAGAAT
* *
30949 CAAACTAACATCTTCTTC
124 TAAACTAACATCTCCTTC
*
30967 TTTTACTATTTAGTTTAATTACCCAGAAATAAAATAACCTCTTCTTCTTTTACTATTTAGTTTAA
1 TTTTACTATTTAGTTTAATTACCCAGAATTAAAATAACCTCTTCTTCTTTTACTATTTAGTTTAA
*
31032 TTACCCAGAATTAAACTAACCTCTCCTTCTTTTACTATTTAGTTTAATTACCCAGATTTAAACTA
66 TTACCCAGAATTAAACTAACCTCTCCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTA
31097 ACATCTCCTTC
131 ACATCTCCTTC
* * *
31108 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTT-TATCTTTTGCTATTTAGTTAA
1 TTTTACTATTTAGTTTAATTACCCAGAATTAAAATAACCTCTTCT-TCTTTTACTATTTAGTTTA
31172 ATTACCCAGAATTAAACTAACCTCTCCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACT
65 ATTACCCAGAATTAAACTAACCTCTCCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACT
31237 AACATCTCCTTC
130 AACATCTCCTTC
* * *** * * *
31249 TTTTGCTCTTTAGTTTAATT-CTGGGTAATTAAACTAACATCTTCTTCTTTTGCTATTTAGTTTA
1 TTTTACTATTTAGTTTAATTACCCAG-AATTAAAATAACCTCTTCTTCTTTTACTATTTAGTTTA
* *
31313 ATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTATTTAGTTTAATTACACAGAATTAAACT
65 ATTACCCAGAATTAAACTAACCTCTCCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACT
*
31378 AACCTCTCCTTC
130 AACATCTCCTTC
* *
31390 TTTTCCTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTATTTAGTTTAA
1 TTTTACTATTTAGTTTAATTACCCAGAATTAAAATAACCTCTTCTTCTTTTACTATTTAGTTTAA
* * *
31455 TTACACAGAATTAAACTAAACTCTCCTTCTTTTACTATTTAGTTCAATTAC
66 TTACCCAGAATTAAACTAACCTCTCCTTCTTTTACTATTTAGTTTAATTAC
31506 TCTTCTAATT
Statistics
Matches: 627, Mismatches: 51, Indels: 38
0.88 0.07 0.05
Matches are distributed among these distances:
140 3 0.00
141 458 0.73
142 4 0.01
144 2 0.00
145 2 0.00
147 2 0.00
148 35 0.06
149 1 0.00
154 1 0.00
155 40 0.06
156 1 0.00
159 2 0.00
161 29 0.05
162 42 0.07
163 3 0.00
165 1 0.00
166 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.46
Consensus pattern (141 bp):
TTTTACTATTTAGTTTAATTACCCAGAATTAAAATAACCTCTTCTTCTTTTACTATTTAGTTTAA
TTACCCAGAATTAAACTAACCTCTCCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTA
ACATCTCCTTC
Found at i:31570 original size:22 final size:22
Alignment explanation
Indices: 31507--31566 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
31497 TTCAATTACT
* **
31507 CTTCTAATTACTCTTTATTTTA
1 CTTCTAATTACTCTTTCTCCTA
31529 CTTCTAATTACTCTTTCTCCTA
1 CTTCTAATTACTCTTTCTCCTA
*
31551 CTTCTGATTACT-TTTC
1 CTTCTAATTACTCTTTC
31567 CTCCATTTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 4 0.12
22 30 0.88
ACGTcount: A:0.18, C:0.25, G:0.02, T:0.55
Consensus pattern (22 bp):
CTTCTAATTACTCTTTCTCCTA
Found at i:32285 original size:8 final size:8
Alignment explanation
Indices: 32272--32296 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
32262 TTCTCCTCTT
32272 CCTCCAAA
1 CCTCCAAA
32280 CCTCCAAA
1 CCTCCAAA
32288 CCTCCAAA
1 CCTCCAAA
32296 C
1 C
32297 TCTAGCCGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.52, G:0.00, T:0.12
Consensus pattern (8 bp):
CCTCCAAA
Found at i:33952 original size:8 final size:7
Alignment explanation
Indices: 33931--33979 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
33921 GAGCTCTATC
33931 TTTTCTT
1 TTTTCTT
33938 TTTTCTT
1 TTTTCTT
33945 TATTTC-T
1 T-TTTCTT
33952 TTTTC--
1 TTTTCTT
33957 TTTTCTT
1 TTTTCTT
33964 TATTTCTT
1 T-TTTCTT
33972 TTTT-TT
1 TTTTCTT
33978 TT
1 TT
33980 AACTAGTTGC
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
5 5 0.13
6 8 0.21
7 14 0.37
8 11 0.29
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTCTT
Found at i:33979 original size:19 final size:19
Alignment explanation
Indices: 33929--33979 Score: 84
Period size: 19 Copynumber: 2.6 Consensus size: 19
33919 TAGAGCTCTA
33929 TCTTTTCTTTTTTCTTTATT
1 TCTTTT-TTTTTTCTTTATT
*
33949 TCTTTTTCTTTTCTTTATT
1 TCTTTTTTTTTTCTTTATT
33968 TCTTTTTTTTTT
1 TCTTTTTTTTTT
33980 AACTAGTTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 23 0.79
20 6 0.21
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (19 bp):
TCTTTTTTTTTTCTTTATT
Found at i:42019 original size:15 final size:15
Alignment explanation
Indices: 41989--42030 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
41979 TTACTTTGCT
41989 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
42005 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
42020 TTGCTTTCTGT
1 TTGTTTTCTGT
42031 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:46022 original size:28 final size:28
Alignment explanation
Indices: 45990--46123 Score: 191
Period size: 28 Copynumber: 4.7 Consensus size: 28
45980 GGTTACTTAG
45990 GGGGCATTTTGGTCATTTTGCACA-TCTA
1 GGGGCATTTTGGTCATTTTGCACATTC-A
*
46018 GGGGCATTTTGGTCATTTTGCATATTCA
1 GGGGCATTTTGGTCATTTTGCACATTCA
46046 GGGGCATTTTGGTCATTTTTGCACA-TCTA
1 GGGGCATTTTGGTCA-TTTTGCACATTC-A
*
46075 GGGGCATTTTAGTCATTTTTGCACATTCA
1 GGGGCATTTTGGTCA-TTTTGCACATTCA
46104 TGGGGCATTTTGGTCATTTT
1 -GGGGCATTTTGGTCATTTT
46124 AAGTTCACGT
Statistics
Matches: 97, Mismatches: 4, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
28 41 0.42
29 40 0.41
30 16 0.16
ACGTcount: A:0.17, C:0.16, G:0.25, T:0.43
Consensus pattern (28 bp):
GGGGCATTTTGGTCATTTTGCACATTCA
Found at i:46076 original size:57 final size:59
Alignment explanation
Indices: 45990--46123 Score: 229
Period size: 57 Copynumber: 2.3 Consensus size: 59
45980 GGTTACTTAG
* *
45990 GGGGCATTTTGGTCA-TTTTGCACATCTAGGGGCATTTTGGTCA-TTTTGCATATTCA-
1 GGGGCATTTTGGTCATTTTTGCACATCTAGGGGCATTTTAGTCATTTTTGCACATTCAT
46046 GGGGCATTTTGGTCATTTTTGCACATCTAGGGGCATTTTAGTCATTTTTGCACATTCAT
1 GGGGCATTTTGGTCATTTTTGCACATCTAGGGGCATTTTAGTCATTTTTGCACATTCAT
46105 GGGGCATTTTGGTCATTTT
1 GGGGCATTTTGGTCATTTT
46124 AAGTTCACGT
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
56 15 0.21
57 27 0.37
58 12 0.16
59 19 0.26
ACGTcount: A:0.17, C:0.16, G:0.25, T:0.43
Consensus pattern (59 bp):
GGGGCATTTTGGTCATTTTTGCACATCTAGGGGCATTTTAGTCATTTTTGCACATTCAT
Found at i:64309 original size:20 final size:21
Alignment explanation
Indices: 64284--64325 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
64274 CATGCCACGT
64284 GTCAC-TTTTTGAAACACATG
1 GTCACTTTTTTGAAACACATG
*
64304 GTCACTTTTTTGATACACATG
1 GTCACTTTTTTGAAACACATG
64325 G
1 G
64326 CGTGATATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (21 bp):
GTCACTTTTTTGAAACACATG
Found at i:64352 original size:31 final size:31
Alignment explanation
Indices: 64297--64388 Score: 103
Period size: 31 Copynumber: 2.9 Consensus size: 31
64287 ACTTTTTGAA
*
64297 ACACATGGTCACTTTTTTGATACACATGGCGTG
1 ACACAT-GTCAC-TTTTTGGTACACATGGCGTG
* **
64330 ATATGTGTCACTTTTTGGTACACATGGCGTG
1 ACACATGTCACTTTTTGGTACACATGGCGTG
* * *
64361 CCACATGTCGCTTTTTGGTACACGTGGC
1 ACACATGTCACTTTTTGGTACACATGGC
64389 ATGCCATCGT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
31 41 0.84
32 5 0.10
33 3 0.06
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.35
Consensus pattern (31 bp):
ACACATGTCACTTTTTGGTACACATGGCGTG
Found at i:64888 original size:23 final size:23
Alignment explanation
Indices: 64854--64897 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
64844 AAAAATTAAA
*
64854 TATTTTTTAATAAAATAAAAATT
1 TATTTTTAAATAAAATAAAAATT
64877 TATTTTTAAATAAAATAAAAA
1 TATTTTTAAATAAAATAAAAA
64898 GAAGAAATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATTTTTAAATAAAATAAAAATT
Done.