Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013349.1 Corchorus olitorius cultivar O-4 contig13382, 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: 20217
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Found at i:4661 original size:18 final size:17
Alignment explanation
Indices: 4610--4659 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
4600 TGAGAAAGGG
4610 AAGGAAAAAGGAAAAGAA
1 AAGGAAAAA-GAAAAGAA
* *
4628 AAGAAAGAAAGAAAAGAG
1 AAGGAA-AAAGAAAAGAA
*
4646 TAGGAAAAAGAAAA
1 AAGGAAAAAGAAAA
4660 AGGAAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 8 0.30
18 16 0.59
19 3 0.11
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (17 bp):
AAGGAAAAAGAAAAGAA
Found at i:5557 original size:21 final size:21
Alignment explanation
Indices: 5532--5574 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
5522 GATTTTATTC
*
5532 TATTTT-ATTTGATTATTTTGG
1 TATTTTGATTTG-TTATCTTGG
5553 TATTTTGATTTGTTATCTTGG
1 TATTTTGATTTGTTATCTTGG
5574 T
1 T
5575 TTATTACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.16, C:0.02, G:0.16, T:0.65
Consensus pattern (21 bp):
TATTTTGATTTGTTATCTTGG
Found at i:9490 original size:21 final size:21
Alignment explanation
Indices: 9466--9535 Score: 52
Period size: 21 Copynumber: 3.3 Consensus size: 21
9456 AAGATTCATG
*
9466 ATAAGGTTACTAAAAATCTTA
1 ATAAGGTTACTAAAAAACTTA
*
9487 ATAA-GTTAAGGTAAAAAACTTA
1 ATAAGGTT-A-CTAAAAAACTTA
* * * * *
9509 ATGAGGTGACCAAAAAGCTTT
1 ATAAGGTTACTAAAAAACTTA
9530 ATAAGG
1 ATAAGG
9536 CCAAAAATAA
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
20 3 0.08
21 18 0.49
22 14 0.38
23 2 0.05
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.27
Consensus pattern (21 bp):
ATAAGGTTACTAAAAAACTTA
Found at i:11267 original size:280 final size:273
Alignment explanation
Indices: 10635--11447 Score: 1106
Period size: 280 Copynumber: 3.0 Consensus size: 273
10625 ATAAAGAAAC
* * *
10635 TTAATTAATTAAGTAAAAGGCATAATAATGTTACTTAAAACTTAAAAGTCTTTATGGTTATTACC
1 TTAATT-ATTAAGTAAAAGCCATAATAATGTTACTTAAAACTTAAAAGTGTTTATGGTTATTACG
* * * * * * *
10700 AAAAGGAAAATCACCATATCCACTATTAGTGTAG-TT--TAGTAGATTGTACAAACGGGATCAAA
65 AAAAGCAAAATTATCACATCCACTATCAGTGTAGTTTACTATTAGATTGTACAAACGGG-TTAAA
* * *
10762 GGATTGACACATGTGTCTTTTTAGTGTATATTTTTTTTAAGAAAAATTATCTTATTCACTGTTAG
129 GGATTG--ACATGTGTCTTTTTAGTGTATA--TTTTTTAAGGAAAATTATCTTATCCACCGTTAG
** * * *
10827 TGAAAATTAGCAGACTGCACATGCATTGTTAGGGTTAAAGGGTTGACATGTGTTCCCTTAGGGAA
190 TGAAGTTTAGCAGACTGCACATGCATGGTTAGAGTTAAAGGGTTGACATGTGTACCCTTAGGGAA
* *
10892 TA---AT-AGTTTTGAATA
255 TAGTTTTGAGTTTTGAACA
10907 TT-A-T-TTAAGTAAAAGCCATAATAATGTTACTTAAAACTTAAAAGTGTTTATGGTTATTACGA
1 TTAATTATTAAGTAAAAGCCATAATAATGTTACTTAAAACTTAAAAGTGTTTATGGTTATTACGA
* *
10969 AAAGCAAAATTATCACATCCACTATCAGTGTAGTTTACTATTAGATTGTGCAAACGAGGTTAAAA
66 AAAGCAAAATTATCACATCCACTATCAGTGTAGTTTACTATTAGATTGTACAAACG-GGTTAAAG
* *
11034 GATTGACATGTGTCTTTTCAGTGTATATTTTTTATGGAAAATTATCTTATCCACCGTTAGTGAAG
130 GATTGACATGTGTCTTTTTAGTGTATATTTTTTAAGGAAAATTATCTTATCCACCGTTAGTGAAG
* *
11099 TTTAGCAGACTGCACATGCAGGGTTAGAGTTAAAGGGTTGACATGTGTACCCTTAGGAAATAGTT
195 TTTAGCAGACTGCACATGCATGGTTAGAGTTAAAGGGTTGACATGTGTACCCTTAGGGAATAGTT
*
11164 TTGATTTTTGAACA
260 TTGAGTTTTGAACA
*
11178 TTAATTGATTAAGTAAAATGCCATAATGATGTTACTTAAATTAAACTTAAAAGTGTTTATGGTTA
1 TTAATT-ATTAAGTAAAA-GCCATAATAATGTTACTT--A--AAACTTAAAAGTGTTTATGGTTA
* * *
11243 TTACGAAAAGTAAAATTTTCACATCCACTATCAGTGTAGTTTACTATTAGATTGTACAAATGGGG
60 TTACGAAAAGCAAAATTATCACATCCACTATCAGTGTAGTTTACTATTAGATTGTACAAA-CGGG
* *
11308 TTAAAGGATTGACATGCGTCTTTTTAGTGTATATTTTTTAAGGAAAATTATCTTATCCACCATTA
124 TTAAAGGATTGACATGTGTCTTTTTAGTGTATATTTTTTAAGGAAAATTATCTTATCCACCGTTA
* * *
11373 GTGAAGTTTAACAGACTGCACATGCATGGTTAGAGTTAAAGGGTCGACATGTGTCCCCTTAGGGA
189 GTGAAGTTTAGCAGACTGCACATGCATGGTTAGAGTTAAAGGGTTGACATGTGTACCCTTAGGGA
11438 ATAGTTTTGA
254 ATAGTTTTGA
11448 ACATTAATAT
Statistics
Matches: 481, Mismatches: 42, Indels: 28
0.87 0.08 0.05
Matches are distributed among these distances:
267 89 0.19
268 83 0.17
269 23 0.05
270 2 0.00
271 37 0.08
272 5 0.01
273 1 0.00
275 10 0.02
276 17 0.04
278 1 0.00
280 212 0.44
281 1 0.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (273 bp):
TTAATTATTAAGTAAAAGCCATAATAATGTTACTTAAAACTTAAAAGTGTTTATGGTTATTACGA
AAAGCAAAATTATCACATCCACTATCAGTGTAGTTTACTATTAGATTGTACAAACGGGTTAAAGG
ATTGACATGTGTCTTTTTAGTGTATATTTTTTAAGGAAAATTATCTTATCCACCGTTAGTGAAGT
TTAGCAGACTGCACATGCATGGTTAGAGTTAAAGGGTTGACATGTGTACCCTTAGGGAATAGTTT
TGAGTTTTGAACA
Found at i:13769 original size:21 final size:22
Alignment explanation
Indices: 13745--13786 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
13735 CAAATCCAGT
*
13745 TTGCCATTTATAAAT-TAATAG
1 TTGCCATTTAAAAATATAATAG
*
13766 TTGCTATTTAAAAATATAATA
1 TTGCCATTTAAAAATATAATA
13787 AATTTTAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (22 bp):
TTGCCATTTAAAAATATAATAG
Found at i:17040 original size:41 final size:41
Alignment explanation
Indices: 16937--17267 Score: 359
Period size: 41 Copynumber: 7.9 Consensus size: 41
16927 CCATAAGAAG
* *
16937 AAATGCCTCTGTCTTATATATGTGTTTGAGGACTTTTG-TAAT
1 AAATGCCCCTGTGTTATATATGTGTTTGAGGAC-TTTGAT-AT
*
16979 AGAGATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGATAT
1 A-A-ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGATAT
*
17022 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTG-TAAT
1 AAATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGAT-AT
* *
17063 AGAGTTGCCCCTGTGTTATATATGTGTTTGGGGACTTTGATAT
1 A-A-ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGATAT
* *
17106 AGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTG-TAAT
1 AAATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGAT-AT
* * *
17147 AAAGGCGCCCCTGTG-T-TATATGTGTTTGGGGACTTAGATAT
1 AAA--TGCCCCTGTGTTATATATGTGTTTGAGGACTTTGATAT
** *
17188 AGGTGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGA-AT
1 AAATGCCCCTGTGTTATATATGTGTTTGAGGAC-TTT-GATAT
*
17230 AGAATTGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 A-AA-TGCCCCTGTGTTATATATGTGTTTGAGGACTTT
17268 TTGGTTATTG
Statistics
Matches: 245, Mismatches: 27, Indels: 33
0.80 0.09 0.11
Matches are distributed among these distances:
39 8 0.03
40 3 0.01
41 110 0.45
42 10 0.04
43 56 0.23
44 58 0.24
ACGTcount: A:0.21, C:0.11, G:0.26, T:0.42
Consensus pattern (41 bp):
AAATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGATAT
Found at i:17090 original size:84 final size:85
Alignment explanation
Indices: 16937--17267 Score: 535
Period size: 84 Copynumber: 3.9 Consensus size: 85
16927 CCATAAGAAG
* *
16937 AAATGCCTCTGTCTTATATATGTGTTTGAGGACTTTTGTAATAGAGATGCCCCTGTGTTATATAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGTTGCCCCTGTGTTATATAT
17002 GTGTTTGGGGACTTTGATAT
66 GTGTTTGGGGACTTTGATAT
17022 AAATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAGTTGCCCCTGTGTTATATAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGTTGCCCCTGTGTTATATAT
17086 GTGTTTGGGGACTTTGATAT
66 GTGTTTGGGGACTTTGATAT
* * **
17106 AGATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAAAGGCGCCCCTGTG-T-TATAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGTTGCCCCTGTGTTATATAT
*
17168 GTGTTTGGGGACTTAGATAT
66 GTGTTTGGGGACTTTGATAT
** * *
17188 AGGTGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAGAATTGCCCCTGTGTTATATAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGTTGCCCCTGTGTTATATAT
17253 GTGTTTGGGGACTTT
66 GTGTTTGGGGACTTT
17268 TTGGTTATTG
Statistics
Matches: 229, Mismatches: 14, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
82 56 0.24
83 19 0.08
84 103 0.45
85 51 0.22
ACGTcount: A:0.21, C:0.11, G:0.26, T:0.42
Consensus pattern (85 bp):
AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGTTGCCCCTGTGTTATATAT
GTGTTTGGGGACTTTGATAT
Found at i:17831 original size:16 final size:17
Alignment explanation
Indices: 17794--17833 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
17784 GATTTGCTAT
**
17794 CATTCTGCTGCAGGGGA
1 CATTCTGCTGCAGGCAA
17811 CATTCTGCTGC-GGCAA
1 CATTCTGCTGCAGGCAA
17827 CATTCTG
1 CATTCTG
17834 TTGTGGCAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.28
Consensus pattern (17 bp):
CATTCTGCTGCAGGCAA
Found at i:18732 original size:144 final size:144
Alignment explanation
Indices: 18473--18942 Score: 719
Period size: 144 Copynumber: 3.3 Consensus size: 144
18463 GATTAGTAGC
* * * ** *
18473 AAGGATTGTGCGAAGGACTGCC-AATGTGGGCACTGCCTCGGCTACAATTGAAATGA-GGAAGAT
1 AAGGATTGTGCGAAGGACTGCCAAACGTGGGAACTGCCTCGACTACAACCGCAAT-ACGGAAGAT
* *
18536 AATCACATAAGGATTGTGCGATGGACTGCCAAATGTGGGAACTACCTCGGCTACAACCGCAATAT
65 AATCACATAAGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAATAT
*
18601 GGAAGATTATCATGT
130 GGAAGATTATCACGT
* *
18616 AAGGATTGTGCGAAGGACTGCCAAACGTTGGAGCTGCCTCGACTACAACCGCAATACGGAAGATA
1 AAGGATTGTGCGAAGGACTGCCAAACGTGGGAACTGCCTCGACTACAACCGCAATACGGAAGATA
* * *
18681 ATCACATAAGGATTGTGCGAAGGACTGCCAAATGTGGCAACTGCCTTGGCTACAATCGCAATATG
66 ATCACATAAGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAATATG
*
18746 GAAAATTATCACGT
131 GAAGATTATCACGT
* * **
18760 AAGGATTGTGCGAAGGACTGCCAAACATTGGAACTGCCTCGTTTACAACCGCAATACGGAAGATA
1 AAGGATTGTGCGAAGGACTGCCAAACGTGGGAACTGCCTCGACTACAACCGCAATACGGAAGATA
*
18825 ATCACATAAGGATTGTGCGAAGGACTACCAAATGTGGGAACTGCCTCGGCTACAACCGCAATATG
66 ATCACATAAGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAATATG
18890 GAAGATTATCACGT
131 GAAGATTATCACGT
* *
18904 AAGGATTATGCGAAGGACTGCCAAATGTGGGAACTGCCT
1 AAGGATTGTGCGAAGGACTGCCAAACGTGGGAACTGCCT
18943 TGCCTTCAAT
Statistics
Matches: 297, Mismatches: 28, Indels: 3
0.91 0.09 0.01
Matches are distributed among these distances:
143 23 0.08
144 274 0.92
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.21
Consensus pattern (144 bp):
AAGGATTGTGCGAAGGACTGCCAAACGTGGGAACTGCCTCGACTACAACCGCAATACGGAAGATA
ATCACATAAGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAATATG
GAAGATTATCACGT
Found at i:18966 original size:72 final size:72
Alignment explanation
Indices: 18473--18942 Score: 647
Period size: 72 Copynumber: 6.5 Consensus size: 72
18463 GATTAGTAGC
* ** *
18473 AAGGATTGTGCGAAGGACTGCC-AATGTGGGCACTGCCTCGGCTACAATTGAAATGA-GGAAGAT
1 AAGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAAT-ATGGAAGAT
18536 AATCACAT
65 AATCACAT
* * *
18544 AAGGATTGTGCGATGGACTGCCAAATGTGGGAACTACCTCGGCTACAACCGCAATATGGAAGATT
1 AAGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAATATGGAAGATA
**
18609 ATCATGT
66 ATCACAT
* * * * *
18616 AAGGATTGTGCGAAGGACTGCCAAACGTTGGAGCTGCCTCGACTACAACCGCAATACGGAAGATA
1 AAGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAATATGGAAGATA
18681 ATCACAT
66 ATCACAT
* * * * *
18688 AAGGATTGTGCGAAGGACTGCCAAATGTGGCAACTGCCTTGGCTACAATCGCAATATGGAAAATT
1 AAGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAATATGGAAGATA
*
18753 ATCACGT
66 ATCACAT
** * ** *
18760 AAGGATTGTGCGAAGGACTGCCAAACATTGGAACTGCCTCGTTTACAACCGCAATACGGAAGATA
1 AAGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAATATGGAAGATA
18825 ATCACAT
66 ATCACAT
* *
18832 AAGGATTGTGCGAAGGACTACCAAATGTGGGAACTGCCTCGGCTACAACCGCAATATGGAAGATT
1 AAGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAATATGGAAGATA
*
18897 ATCACGT
66 ATCACAT
*
18904 AAGGATTATGCGAAGGACTGCCAAATGTGGGAACTGCCT
1 AAGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCT
18943 TGCCTTCAAT
Statistics
Matches: 344, Mismatches: 53, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
71 22 0.06
72 322 0.94
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.21
Consensus pattern (72 bp):
AAGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAATATGGAAGATA
ATCACAT
Done.