Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019186.1 Corchorus olitorius cultivar O-4 contig19219, 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: 71645
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1966 original size:12 final size:12
Alignment explanation
Indices: 1937--1970 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1927 TTTTTATCAA
1937 TAAATAAAT-AC
1 TAAATAAATAAC
*
1948 AAAATAAATAAC
1 TAAATAAATAAC
1960 TAAATAAATAA
1 TAAATAAATAA
1971 AATGATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (12 bp):
TAAATAAATAAC
Found at i:2203 original size:7 final size:7
Alignment explanation
Indices: 2193--2217 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2183 TAGTTCTTCA
2193 ATCTTGG
1 ATCTTGG
2200 ATCTTGG
1 ATCTTGG
2207 ATCTTGG
1 ATCTTGG
2214 ATCT
1 ATCT
2218 GAGTTCTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.44
Consensus pattern (7 bp):
ATCTTGG
Found at i:14428 original size:433 final size:436
Alignment explanation
Indices: 13415--14430 Score: 1302
Period size: 438 Copynumber: 2.3 Consensus size: 436
13405 TATTTTTGTA
*
13415 TTTT-TTT-TTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATC
1 TTTTCTTTGTTCTATTTGTCCGATTAAGCTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATC
* * * ** * *
13478 TACAATTTTCAT-TAAGAACTCAAAAG-TCAATTTTAATATTTTGATTCTAAAAAATACTTCCGA
66 TACAACTTTCATGAAAG-ACTCAAAAGCT-AATTTTTATATTTCAATTCTAAAAAATGCTTCTGA
** * * * * *
13541 AATTTTGTGGTTTTAATTGCCGGTTGATTTAATATCGTATAATTTTTTGTCCACATGTCCGATTG
129 AATTTTGT-GTTTCGATTGCCGGTTGATTTAATACCATATAATTTTTCGTCCACATGTCCAATTA
* * * *
13606 AAGTTATTGAAGTGTCGGTTAAAAGGTTATTGCATGATTTACGACTTTCATGAAGGACCCGAAAG
193 AAGTTATTCAAGTGTCGGTTAAAAGGTTACTGCATAATTTACGACTTTCATGAAGAACCCGAAAG
* * *
13671 CTAAATTTGACCTATGAGTTTCGTGAAGGGTTCAAAAGGGAATTTCTATGTTTCAAGATCACCAT
258 CTAAATTTGACCTACGAGTTTCATGAAGGATTCAAAAGGGAATTTCTATGTTTCAAGATCACCAT
* * *
13736 TAACAAACATTTTCTTATTTGGATTATTTATCAAATGACCCTCATACTTTTCTACTTTATACTAC
323 TAACAAACATTTTCTTATTTAGATTAGTTATCAAATCACCCTCATACTTTTCTACTTTATACTAC
* ** *
13801 TTAGTCCTTTACAAATTCTATCTTAATCTAACGTTTAAGTTTTATATTTT
388 TTAATCCTTTACAAATTCTATCTTAATCTAAC-TTTAAACTTCATATTTT
* * * *
13851 TATTCTTTGTTCTATTTATCCGATTAAGTTGATTCATGTGTCTATTAAAAGGTAATTTCATGATC
1 TTTTCTTTGTTCTATTTGTCCGATTAAGCTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATC
* * * *
13916 TACAACTTTCATGAAGGACTCAAAAGCAAATTTTTATGTTTCAATTCAAAAAAATGCTTCCT-AA
66 TACAACTTTCATGAAAGACTCAAAAGCTAATTTTTATATTTCAATTCTAAAAAATGCTT-CTGAA
* **
13980 ATTTGTTTGTTTCGATTGTTGGTCT-ATTTAATACCATATAA-TTTTCGATCCACATGTCCAATT
130 ATTT-TGTGTTTCGATTGCCGGT-TGATTTAATACCATATAATTTTTCG-TCCACATGTCCAATT
*
14043 AAAGTTATTCAAGTGTCGGTTAAAAGGTTACTGTATAATTTACGACTTTCATGAAGAACCCGAAA
192 AAAGTTATTCAAGTGTCGGTTAAAAGGTTACTGCATAATTTACGACTTTCATGAAGAACCCGAAA
* * * * * *
14108 G-TTAATTTGATCTGCGAGTTTCATGAAGGATTCAAAAGGGAATTTTTATGTTTTAAGATCTCCA
257 GCTAAATTTGACCTACGAGTTTCATGAAGGATTCAAAAGGGAATTTCTATGTTTCAAGATCACCA
* * **
14172 TTAACAAATATTTTCTTATTTCAG-TTAGTTAT-AAATCACCCTCATACTTTTCTATTTTATGTT
322 TTAACAAACATTTTCTTATTT-AGATTAGTTATCAAATCACCCTCATACTTTTCTACTTTATACT
* *
14235 ACTTAATCCTTTCCAAATTCTATCTTACTC-AA-TTTAACACTTCAT-TTTT
386 ACTTAATCCTTTACAAATTCTATCTTAATCTAACTTTAA-ACTTCATATTTT
* * * *
14284 TTTTCTTTGTTCTATTTGTCCAATTAAGCTAATTCAAGTGTCTATTAAAAGATAATTTTATGATC
1 TTTTCTTTGTTCTATTTGTCCGATTAAGCTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATC
* * *
14349 TACAACTTTCATGAAAGACACAAAAGCTAATTTTTATATCTCAATTCTAAAAAATGCTTTTGAAA
66 TACAACTTTCATGAAAGACTCAAAAGCTAATTTTTATATTTCAATTCTAAAAAATGCTTCTGAAA
14414 TTTTGTGATTTCGATTG
131 TTTTGTG-TTTCGATTG
14431 AAAATCTATT
Statistics
Matches: 500, Mismatches: 68, Indels: 27
0.84 0.11 0.05
Matches are distributed among these distances:
432 4 0.01
433 134 0.27
434 4 0.01
435 2 0.00
436 57 0.11
437 89 0.18
438 204 0.41
439 6 0.01
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.42
Consensus pattern (436 bp):
TTTTCTTTGTTCTATTTGTCCGATTAAGCTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATC
TACAACTTTCATGAAAGACTCAAAAGCTAATTTTTATATTTCAATTCTAAAAAATGCTTCTGAAA
TTTTGTGTTTCGATTGCCGGTTGATTTAATACCATATAATTTTTCGTCCACATGTCCAATTAAAG
TTATTCAAGTGTCGGTTAAAAGGTTACTGCATAATTTACGACTTTCATGAAGAACCCGAAAGCTA
AATTTGACCTACGAGTTTCATGAAGGATTCAAAAGGGAATTTCTATGTTTCAAGATCACCATTAA
CAAACATTTTCTTATTTAGATTAGTTATCAAATCACCCTCATACTTTTCTACTTTATACTACTTA
ATCCTTTACAAATTCTATCTTAATCTAACTTTAAACTTCATATTTT
Found at i:17050 original size:40 final size:40
Alignment explanation
Indices: 17004--17122 Score: 112
Period size: 40 Copynumber: 3.1 Consensus size: 40
16994 TACGTTATTT
17004 TATTGTTGTTAAAAGAATTATATTTTACGCAACAACTCAA
1 TATTGTTGTTAAAAGAATTATATTTTACGCAACAACTCAA
* *
17044 TATTGTTGCGT--AA-AA--ATATTTT----AACAACGTCATTT
1 TATTGTTG-TTAAAAGAATTATATTTTACGCAACAAC-TCA--A
*
17079 TATTATTGTTAAAAGAATTATATTTTACGCAACAACTCAA
1 TATTGTTGTTAAAAGAATTATATTTTACGCAACAACTCAA
17119 TATT
1 TATT
17123 ATTGCGAAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 26
0.66 0.05 0.28
Matches are distributed among these distances:
32 6 0.10
33 3 0.05
34 1 0.02
35 7 0.11
36 9 0.15
37 2 0.03
38 2 0.03
39 9 0.15
40 12 0.20
41 1 0.02
42 3 0.05
43 6 0.10
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (40 bp):
TATTGTTGTTAAAAGAATTATATTTTACGCAACAACTCAA
Found at i:17094 original size:75 final size:74
Alignment explanation
Indices: 16995--17145 Score: 266
Period size: 75 Copynumber: 2.0 Consensus size: 74
16985 TCTTTTCGTT
* * *
16995 ACGTTATTTTATTGTTGTTAAAAGAATTATATTTTACGCAACAACTCAATATTGTTGCGTAAAAA
1 ACGTCATTTTATTATTGTTAAAAGAATTATATTTTACGCAACAACTCAATATTATTGCG-AAAAA
17060 TATTTTAACA
65 TATTTTAACA
17070 ACGTCATTTTATTATTGTTAAAAGAATTATATTTTACGCAACAACTCAATATTATTGCGAAAAAT
1 ACGTCATTTTATTATTGTTAAAAGAATTATATTTTACGCAACAACTCAATATTATTGCGAAAAAT
17135 ATTTTAACA
66 ATTTTAACA
17144 AC
1 AC
17146 AACATATATT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
74 17 0.23
75 56 0.77
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (74 bp):
ACGTCATTTTATTATTGTTAAAAGAATTATATTTTACGCAACAACTCAATATTATTGCGAAAAAT
ATTTTAACA
Found at i:17140 original size:35 final size:34
Alignment explanation
Indices: 17023--17148 Score: 87
Period size: 35 Copynumber: 3.5 Consensus size: 34
17013 TAAAAGAATT
*
17023 ATATTTTACGCAACAACTCAATATTGTTGCGTAAAA
1 ATATTTTA-GCAACAACTCAATATTATTGCG-AAAA
* **
17059 ATATTTT---AACAACGTCATTTTATTATTGTTAAAAGAA
1 ATATTTTAGCAACAAC-TCA--ATATTATTG--CGAA-AA
17096 TTATATTTTACGCAACAACTCAATATTATTGCGAAAA
1 --ATATTTTA-GCAACAACTCAATATTATTGCGAAAA
*
17133 ATATTTTAACAACAAC
1 ATATTTTAGCAACAAC
17149 ATATATTCGT
Statistics
Matches: 70, Mismatches: 8, Indels: 26
0.67 0.08 0.25
Matches are distributed among these distances:
32 6 0.09
33 3 0.04
34 7 0.10
35 15 0.21
36 9 0.13
37 4 0.06
38 2 0.03
39 7 0.10
40 8 0.11
42 3 0.04
43 6 0.09
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (34 bp):
ATATTTTAGCAACAACTCAATATTATTGCGAAAA
Found at i:17817 original size:134 final size:133
Alignment explanation
Indices: 17479--17785 Score: 370
Period size: 134 Copynumber: 2.3 Consensus size: 133
17469 AACGACATAA
* ** * ** ***
17479 CAAAATTATTTTGGTTGTAAATACTTTTCGGTAACGATATTTATTGGTTATTTAAAGTTTTTTAT
1 CAAAATTATTTTGGTTGTAAATACTTTACGACAACAATATTTATTAATTGCCTAAAGTTTTTTAT
** * ** * * * *
17544 AACGATAT-TAAGTTGGTTGCGGATAATTTTTTAAAACGACAAAATGTTGTTGTCAAAATGTTTA
66 AATAATATCT-AGTTGGTTACAAATGACTTTTTAAAACAACAAAATGTTGTTGTCAAAATATTTA
17608 CACAG
130 -ACAG
*
17613 CAAAATTATTTTGGTTGTAAATACTTTATGACAACAATATTTATTAATTGCCTAAAGTTTTTTAT
1 CAAAATTATTTTGGTTGTAAATACTTTACGACAACAATATTTATTAATTGCCTAAAGTTTTTTAT
17678 AATAATATCTAGTTGGTTACAAATGACTTTTTAAAACAACAAAATGTTGTTGTCAAAATATTT-A
66 AATAATATCTAGTTGGTTACAAATGACTTTTTAAAACAACAAAATGTTGTTGTCAAAATATTTAA
17742 CA-
131 CAG
* *
17744 CAACATTATTTTGGTTGTAAATACTCTTACG-TAACAATATTT
1 CAAAATTATTTTGGTTGTAAATACT-TTACGACAACAATATTT
17786 TAATTATTGT
Statistics
Matches: 149, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
131 34 0.23
132 7 0.05
134 107 0.72
135 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.42
Consensus pattern (133 bp):
CAAAATTATTTTGGTTGTAAATACTTTACGACAACAATATTTATTAATTGCCTAAAGTTTTTTAT
AATAATATCTAGTTGGTTACAAATGACTTTTTAAAACAACAAAATGTTGTTGTCAAAATATTTAA
CAG
Found at i:18571 original size:32 final size:33
Alignment explanation
Indices: 18506--18572 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
18496 TTGGTAGTTA
* **
18506 TATAGATGAAATTAGAGATTTGGCAATGGTAAT
1 TATAGATGAAATTAGACATTTGGCAATCCTAAT
18539 TATAGATGAAATTAGACA-TTGGCAATCCTAAT
1 TATAGATGAAATTAGACATTTGGCAATCCTAAT
18571 TA
1 TA
18573 ATTTATGTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 14 0.45
33 17 0.55
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.33
Consensus pattern (33 bp):
TATAGATGAAATTAGACATTTGGCAATCCTAAT
Found at i:20323 original size:75 final size:74
Alignment explanation
Indices: 20157--20420 Score: 317
Period size: 75 Copynumber: 3.6 Consensus size: 74
20147 GAAGGCGAAG
* ** ** * *
20157 TCATTTGCTGATGATTTTGAACCAAGGCCCAATGTTTCTGCTTATGGTGATGAT--TC-TCAA--
1 TCATTTGCTGAAGATTTTGAACCAAGGCCCAACATTTCTGCTTACAGTGATGGTGATCTTAAAGG
*
20217 GAGAA-ATCA
66 GAGAAGA-AA
* * *
20226 TCATTTGCTAAAGAATTTGAACCAAGGCCCAATATTTCTGCTTACAGTGATGGTGATCTTAAAGG
1 TCATTTGCTGAAGATTTTGAACCAAGGCCCAACATTTCTGCTTACAGTGATGGTGATCTTAAAGG
20291 TGAGAAGAAA
66 -GAGAAGAAA
* *
20301 TCATTTGTTGAAGATTTTGAACCAAGGCCCAACATTTCTGCTTACAGTGATGGTGATCTTAAGGG
1 TCATTTGCTGAAGATTTTGAACCAAGGCCCAACATTTCTGCTTACAGTGATGGTGATCTTAA-AG
20366 GGAGAAGAAA
65 GGAGAAGAAA
*
20376 TCATTTGCT-AATGATTTTGAACCAAGGCCCAACATTTCTACTTAC
1 TCATTTGCTGAA-GATTTTGAACCAAGGCCCAACATTTCTGCTTAC
20421 CATGATTAAA
Statistics
Matches: 170, Mismatches: 16, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
69 47 0.28
71 2 0.01
72 3 0.02
74 2 0.01
75 113 0.66
76 3 0.02
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (74 bp):
TCATTTGCTGAAGATTTTGAACCAAGGCCCAACATTTCTGCTTACAGTGATGGTGATCTTAAAGG
GAGAAGAAA
Found at i:55668 original size:3 final size:3
Alignment explanation
Indices: 55662--55688 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
55652 TCAATAGGAG
55662 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
55689 AGATACCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:66442 original size:25 final size:25
Alignment explanation
Indices: 66414--66463 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
66404 AAGGTAGAGA
66414 CTTTTAGCTTAAATCATGTTAAATC
1 CTTTTAGCTTAAATCATGTTAAATC
66439 CTTTTAGCTTAAATCATGTTAAATC
1 CTTTTAGCTTAAATCATGTTAAATC
66464 TTCTCTAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (25 bp):
CTTTTAGCTTAAATCATGTTAAATC
Done.