Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014368.1 Corchorus olitorius cultivar O-4 contig14401, 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: 25522
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:584 original size:16 final size:17
Alignment explanation
Indices: 549--592 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
539 GTTATATATT
*
549 AAATCAATATATTTAAGC
1 AAATCAAT-TATTCAAGC
567 AAATCAATT-TTCAAGC
1 AAATCAATTATTCAAGC
*
583 AAACCAATTA
1 AAATCAATTA
593 AACAAATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 14 0.61
17 1 0.04
18 8 0.35
ACGTcount: A:0.50, C:0.16, G:0.05, T:0.30
Consensus pattern (17 bp):
AAATCAATTATTCAAGC
Found at i:11646 original size:178 final size:178
Alignment explanation
Indices: 11382--11889 Score: 840
Period size: 178 Copynumber: 2.9 Consensus size: 178
11372 CCAATTAAGG
11382 TGATTTAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
1 TGATTTAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
* *
11447 AATTTAATGTTTCAAGTATCAAAAATGCTTCCGAAAAATTTGTTGTTTCGGTTAACGGGCATATA
66 AATTTAATGTTTCAAGTATCAAAAATGCTTCCGAAAAATTTGTTGTTTCGGTTAACGGGAATAGA
* *
11512 TGGTCCACTTAATATTATATAACTTTTGCTCCAGATGTCTGATTGAGA
131 CGGTCTACTTAATATTATATAACTTTTGCTCCAGATGTCTGATTGAGA
*
11560 TGATTTAAGTGTTTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
1 TGATTTAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
*
11625 AATTTAATGTTTCAAGTATCAAAAATGCTTCCGAAAAATTTGTTGTTTCGATTAACGGGAATAGA
66 AATTTAATGTTTCAAGTATCAAAAATGCTTCCGAAAAATTTGTTGTTTCGGTTAACGGGAATAGA
*
11690 CGGTCTACTTAATATTATGTAACTTTTGCTCCAGATGTCTGATTGAGA
131 CGGTCTACTTAATATTATATAACTTTTGCTCCAGATGTCTGATTGAGA
* * * * *
11738 TGATTCAAGTATCTATTGAAAGGTTGTTCCATGATCTATAACTTTCATGAAGGACTCGAAAACTA
1 TGATTTAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
* * *
11803 AATTTAATG-TTCAAGGTATAAAAAATGCTTCC-AAAGAATTAGTTGTTTCGGTTAACGGAAATA
66 AATTTAATGTTTCAA-GTATCAAAAATGCTTCCGAAA-AATTTGTTGTTTCGGTTAACGGGAATA
*
11866 GACGGTCTACTTAATATTACATAA
129 GACGGTCTACTTAATATTATATAA
11890 TTTGAGCTTA
Statistics
Matches: 309, Mismatches: 19, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
177 8 0.03
178 301 0.97
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36
Consensus pattern (178 bp):
TGATTTAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
AATTTAATGTTTCAAGTATCAAAAATGCTTCCGAAAAATTTGTTGTTTCGGTTAACGGGAATAGA
CGGTCTACTTAATATTATATAACTTTTGCTCCAGATGTCTGATTGAGA
Found at i:15541 original size:26 final size:26
Alignment explanation
Indices: 15503--15560 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
15493 CTTCACTAAC
15503 TGGGCCAACGGGCTAAAATCCTTAGA
1 TGGGCCAACGGGCTAAAATCCTTAGA
*
15529 TGGGCCAATGGGCTAAAATCCTTAGA
1 TGGGCCAACGGGCTAAAATCCTTAGA
15555 TGGGCC
1 TGGGCC
15561 TATTTTAGGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.21
Consensus pattern (26 bp):
TGGGCCAACGGGCTAAAATCCTTAGA
Found at i:16253 original size:199 final size:199
Alignment explanation
Indices: 15901--16362 Score: 698
Period size: 199 Copynumber: 2.3 Consensus size: 199
15891 CTGCATGGGA
*
15901 TATGTGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATA
1 TATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATA
* * * **
15966 ATATCATATAAAAAAAATTATACAATACACCGTCAGTGGAATTTAGCAGATTGCATGTGCAAGCT
66 ATATCATATAAAAAAAAGTATACAATACACCGTCAGTGGAATTCAGCAGACTGCACATGCAAGCT
*
16031 TAAGGGTTGACATGTGTCCCTTAGGGAATATGTATTAATAATTT-ATATTTAATTAATTATAAAA
131 TAAGGATTGACATGTGTCCCTTAGGGAATATGTATTAAT-ATTTAATATTTAATTAATTATAAAA
16095 TAGGG
195 TAGGG
* * * * *
16100 TATTTGTCAACTTCTTAACTCGCTTATGGAGTTCAAAATTTACACTGTCAGTGTATTGTATAA-C
1 TATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATA
* *
16164 A-ATCCTATAAAAAAAAGTATACAATACACCGTCAGT-GAAGTTCAGCAGACTGCACATGCATGG
66 ATATCATATAAAAAAAAGTATACAATACACCGTCAGTGGAA-TTCAGCAGACTGCACATGCA-AG
* *
16227 TTTAAGGATTGACATGTGTCCCCTTAGGGAATATTTATTAATATTTAATATTTAATTAATTATAA
129 CTTAAGGATTGACATGTGT-CCCTTAGGGAATATGTATTAATATTTAATATTTAATTAATTATAA
16292 AATAGGG
193 AATAGGG
* *
16299 TATGTGTCAATTTCTTAACCCGCTTATGGAGTCCAAAATTTACATTGACAGTGTATTGTATAAT
1 TATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAAT
16363 GATCTTTATT
Statistics
Matches: 236, Mismatches: 22, Indels: 9
0.88 0.08 0.03
Matches are distributed among these distances:
196 3 0.01
197 49 0.21
198 23 0.10
199 161 0.68
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (199 bp):
TATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATA
ATATCATATAAAAAAAAGTATACAATACACCGTCAGTGGAATTCAGCAGACTGCACATGCAAGCT
TAAGGATTGACATGTGTCCCTTAGGGAATATGTATTAATATTTAATATTTAATTAATTATAAAAT
AGGG
Found at i:16737 original size:16 final size:16
Alignment explanation
Indices: 16712--16742 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16702 TCTACACATT
16712 ATAAAGATTTAGTAAA
1 ATAAAGATTTAGTAAA
*
16728 ATAAATATTTAGTAA
1 ATAAAGATTTAGTAA
16743 TATTTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (16 bp):
ATAAAGATTTAGTAAA
Found at i:17354 original size:20 final size:19
Alignment explanation
Indices: 17328--17383 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 19
17318 AATGTCACCG
17328 GATATCCGTCGATATATCC
1 GATATCCGTCGATATATCC
17347 GTATATCCGTCGATATTAT-C
1 G-ATATCCGTCGATA-TATCC
17367 GATA-CC-TCGATATATCC
1 GATATCCGTCGATATATCC
17384 CTAAATATCC
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.09
17 7 0.21
18 2 0.06
19 4 0.12
20 15 0.44
21 3 0.09
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (19 bp):
GATATCCGTCGATATATCC
Found at i:18317 original size:12 final size:13
Alignment explanation
Indices: 18300--18335 Score: 65
Period size: 12 Copynumber: 2.8 Consensus size: 13
18290 CATCGATACC
18300 TCGATATATCCG-
1 TCGATATATCCGT
18312 TCGATATATCCGT
1 TCGATATATCCGT
18325 TCGATATATCC
1 TCGATATATCC
18336 TTGGATATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (13 bp):
TCGATATATCCGT
Found at i:18342 original size:12 final size:12
Alignment explanation
Indices: 18300--18343 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
18290 CATCGATACC
*
18300 TCGATATATCCG
1 TCGATATATCCT
18312 TCGATATATCCGT
1 TCGATATATCC-T
18325 TCGATATATCCT
1 TCGATATATCCT
*
18337 TGGATAT
1 TCGATAT
18344 CTATATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (12 bp):
TCGATATATCCT
Found at i:19453 original size:12 final size:13
Alignment explanation
Indices: 19436--19471 Score: 65
Period size: 12 Copynumber: 2.8 Consensus size: 13
19426 CATCGATACC
19436 TCGATATATCCG-
1 TCGATATATCCGT
19448 TCGATATATCCGT
1 TCGATATATCCGT
19461 TCGATATATCC
1 TCGATATATCC
19472 TTGGATATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (13 bp):
TCGATATATCCGT
Found at i:19478 original size:12 final size:12
Alignment explanation
Indices: 19436--19479 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
19426 CATCGATACC
*
19436 TCGATATATCCG
1 TCGATATATCCT
19448 TCGATATATCCGT
1 TCGATATATCC-T
19461 TCGATATATCCT
1 TCGATATATCCT
*
19473 TGGATAT
1 TCGATAT
19480 CTGTATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (12 bp):
TCGATATATCCT
Found at i:20197 original size:221 final size:219
Alignment explanation
Indices: 19802--20202 Score: 465
Period size: 221 Copynumber: 1.8 Consensus size: 219
19792 TAGATCATAC
**
19802 TTAAAGGGTATTAATAAGTAAAATAAAAAATCTTTTAAAAAATAAGGGAAATAAAGTTAAAGGAT
1 TTAAAGGGTATTAATAAGTAAAATAAAAAATCTTTTAAAAAATAAAAGAAATAAAGTTAAAGGAT
* * * * ** *
19867 TGAATTATTTATAGTAAAATACTAGTTGCACTAAATTGCATAGAATAAAAATAGTTGAGTGCTTT
66 TGAACTATATAAAATAAAATACTAGTT-CACTAAATCACATAGAAGAAAAATAGTTGAGTGCTTT
* *
19932 CTATGAAAGGAATAAAGTTGAAGGGTTAAATAGTATAAAAAGAAATAATAGAGAGACTAAATAAA
130 CTATGAAAAGAATAAAGTTGAAGGGCTAAATAGTATAAAAAGAAATAATAGAGAGACTAAATAAA
19997 ATAAAATAAATATTTAAAATTATAT
195 ATAAAATAAATATTTAAAATTATAT
* * * *
20022 TTAAAGGGTATTAATAAGTAAAATTTAAACATCTTTTTAGAAATAAAAGAAATACAA-TTAAAGG
1 TTAAAGGGTATTAATAAGTAAAA-TAAAAAATCTTTTAAAAAATAAAAGAAATA-AAGTTAAAGG
* * *
20086 ATTGAACTGTATAAAATAAAATATTTAAGTT-ACTAGATCACAGT-GAAGAAAAAT-GTCTGAG-
64 ATTGAACTATATAAAATAAAATA-CT-AGTTCACTAAATCACA-TAGAAGAAAAATAGT-TGAGT
* * * *
20147 GTCATTTCTGTGAAAAGAATTAA-TTGAAGGGCTATAT-GATATATAAAGAAATAATA
125 G-C-TTTCTATGAAAAGAATAAAGTTGAAGGGCTAAATAG-TATAAAAAGAAATAATA
20203 TAAAGGCTAA
Statistics
Matches: 150, Mismatches: 22, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
220 27 0.18
221 99 0.66
222 20 0.13
223 4 0.03
ACGTcount: A:0.50, C:0.05, G:0.15, T:0.30
Consensus pattern (219 bp):
TTAAAGGGTATTAATAAGTAAAATAAAAAATCTTTTAAAAAATAAAAGAAATAAAGTTAAAGGAT
TGAACTATATAAAATAAAATACTAGTTCACTAAATCACATAGAAGAAAAATAGTTGAGTGCTTTC
TATGAAAAGAATAAAGTTGAAGGGCTAAATAGTATAAAAAGAAATAATAGAGAGACTAAATAAAA
TAAAATAAATATTTAAAATTATAT
Found at i:20361 original size:13 final size:14
Alignment explanation
Indices: 20330--20361 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
20320 CTATTACATA
20330 AGTTTATGATTATG
1 AGTTTATGATTATG
20344 A-TTTATGATT-TG
1 AGTTTATGATTATG
20356 AGTTTA
1 AGTTTA
20362 CAAAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 13 0.76
14 1 0.06
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (14 bp):
AGTTTATGATTATG
Found at i:21950 original size:86 final size:86
Alignment explanation
Indices: 21853--22031 Score: 313
Period size: 86 Copynumber: 2.1 Consensus size: 86
21843 AATCTTGTAA
21853 ATTTTCTTGGTAAGCTTATAAAGTTTTCATTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAAT
1 ATTTT-TTGGTAAGCTTATAAAGTTTTCATTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAAT
*
21918 TTATTTAATCACCTCGTTTAAG
65 TTATTCAATCACCTCGTTTAAG
* * *
21940 ATTTTTTGGTAAGCTTATAAATTTTTCATTAAACTTAAAAGGTTTTTAAATAGTTTTCTTGAATT
1 ATTTTTTGGTAAGCTTATAAAGTTTTCATTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAATT
22005 TATTCAATCACCTCGTTTAAG
66 TATTCAATCACCTCGTTTAAG
22026 ATTTTT
1 ATTTTT
22032 AGTGATCTTA
Statistics
Matches: 88, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
86 83 0.94
87 5 0.06
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.49
Consensus pattern (86 bp):
ATTTTTTGGTAAGCTTATAAAGTTTTCATTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAATT
TATTCAATCACCTCGTTTAAG
Found at i:22045 original size:22 final size:22
Alignment explanation
Indices: 22020--22075 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 22
22010 AATCACCTCG
* *
22020 TTTAAGATTTTTAGTGATCTTA
1 TTTAAGATTTTTAGAGACCTTA
*
22042 TTT-ACATGTTTTAGAGACCTTA
1 TTTAAGAT-TTTTAGAGACCTTA
*
22064 CTTAAG-TTTTTA
1 TTTAAGATTTTTA
22076 TTTAGTGACC
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
21 8 0.30
22 18 0.67
23 1 0.04
ACGTcount: A:0.27, C:0.09, G:0.12, T:0.52
Consensus pattern (22 bp):
TTTAAGATTTTTAGAGACCTTA
Found at i:22156 original size:22 final size:23
Alignment explanation
Indices: 22112--22162 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
22102 TAACTTATGA
*
22112 GTTTTATAGTGACCTTATGGAGT
1 GTTTTATAGTAACCTTATGGAGT
* * *
22135 TTTTTTTAGTAACCTTGT-GAGT
1 GTTTTATAGTAACCTTATGGAGT
22157 GTTTTA
1 GTTTTA
22163 GAAATCTTAT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.20, C:0.08, G:0.22, T:0.51
Consensus pattern (23 bp):
GTTTTATAGTAACCTTATGGAGT
Found at i:22462 original size:21 final size:22
Alignment explanation
Indices: 22416--22489 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 22
22406 ATTTATAAGC
* * *
22416 TTTTAAGTAA-CCTTACTAAAC
1 TTTTTAGTAACCCTTATTAAAA
* *
22437 GTTTTAGTAACCCTTATTACAA
1 TTTTTAGTAACCCTTATTAAAA
** *
22459 TTTTTAGTAGTCTTTATTAAAA
1 TTTTTAGTAACCCTTATTAAAA
22481 -TTTTAGTAA
1 TTTTTAGTAA
22490 TCTTGTGTAA
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
21 16 0.39
22 25 0.61
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46
Consensus pattern (22 bp):
TTTTTAGTAACCCTTATTAAAA
Found at i:22493 original size:21 final size:22
Alignment explanation
Indices: 22438--22493 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
22428 TTACTAAACG
* * *
22438 TTTTAGTAACCCTTATTACAAT
1 TTTTAGTAATCTTTATTACAAA
*
22460 TTTTAGTAGTCTTTATTA-AAA
1 TTTTAGTAATCTTTATTACAAA
22481 TTTTAGTAATCTT
1 TTTTAGTAATCTT
22494 GTGTAAGCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 14 0.48
22 15 0.52
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (22 bp):
TTTTAGTAATCTTTATTACAAA
Done.