Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023825.1 Corchorus olitorius cultivar O-4 contig23858, 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: 34586
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Found at i:466 original size:22 final size:22
Alignment explanation
Indices: 441--487 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
431 GCTAAATTTC
* * *
441 TAAGTTTAAATAGTCATCTCTA
1 TAAGTTTAAACAATCAACTCTA
463 TAAGTTTAAACAATCAACTCTA
1 TAAGTTTAAACAATCAACTCTA
485 TAA
1 TAA
488 AGCTAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.36
Consensus pattern (22 bp):
TAAGTTTAAACAATCAACTCTA
Found at i:6942 original size:42 final size:42
Alignment explanation
Indices: 6883--6971 Score: 169
Period size: 42 Copynumber: 2.1 Consensus size: 42
6873 GGAAAAAGAA
6883 AGCATGAGATCTTTTGTCAGGTTTATATCTTTTGCTACTGGG
1 AGCATGAGATCTTTTGTCAGGTTTATATCTTTTGCTACTGGG
6925 AGCATGAGATCTTTTGTCAGGTTTATATCTTTTGCTACTGGG
1 AGCATGAGATCTTTTGTCAGGTTTATATCTTTTGCTACTGGG
*
6967 TGCAT
1 AGCAT
6972 TTTTATTCTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.43
Consensus pattern (42 bp):
AGCATGAGATCTTTTGTCAGGTTTATATCTTTTGCTACTGGG
Found at i:12854 original size:19 final size:19
Alignment explanation
Indices: 12830--12870 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
12820 TACTAATTAA
12830 TTATTTTAATATTATATTT
1 TTATTTTAATATTATATTT
*
12849 TTATTTTTATATTATATTT
1 TTATTTTAATATTATATTT
12868 TTA
1 TTA
12871 CTTAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTATTTTAATATTATATTT
Found at i:17427 original size:16 final size:16
Alignment explanation
Indices: 17409--17484 Score: 82
Period size: 16 Copynumber: 4.8 Consensus size: 16
17399 AATTTTGGGT
*
17409 ACCCGAACCCGAAATT
1 ACCCGAACCCGAAATG
* *
17425 ACCCGAATCC-AAACG
1 ACCCGAACCCGAAATG
17440 ACCCGAACCCGAAAATG
1 ACCCGAACCCG-AAATG
* *
17457 ACCCAAACCCAAAATG
1 ACCCGAACCCGAAATG
*
17473 ACCCAAACCCGA
1 ACCCGAACCCGA
17485 TCAACCCAAC
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
15 12 0.24
16 25 0.50
17 13 0.26
ACGTcount: A:0.42, C:0.39, G:0.12, T:0.07
Consensus pattern (16 bp):
ACCCGAACCCGAAATG
Found at i:18522 original size:67 final size:67
Alignment explanation
Indices: 18439--18588 Score: 291
Period size: 67 Copynumber: 2.2 Consensus size: 67
18429 CATGAACAAA
18439 AGAGACATGGCCTAAAATAAAAAAACCAGATTTGAAAGTCTATTATATAATATATATAGTATAAA
1 AGAGACATGGCCTAAAATAAAAAAACCAGATTTGAAAGTCTATTATATAATATATATAGTATAAA
18504 TC
66 TC
*
18506 AGAGACATGACCTAAAATAAAAAAACCAGATTTGAAAGTCTATTATATAATATATATAGTATAAA
1 AGAGACATGGCCTAAAATAAAAAAACCAGATTTGAAAGTCTATTATATAATATATATAGTATAAA
18571 TC
66 TC
18573 AGAGACATGGCCTAAA
1 AGAGACATGGCCTAAA
18589 TATATATACT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 81 1.00
ACGTcount: A:0.49, C:0.11, G:0.13, T:0.27
Consensus pattern (67 bp):
AGAGACATGGCCTAAAATAAAAAAACCAGATTTGAAAGTCTATTATATAATATATATAGTATAAA
TC
Found at i:19203 original size:16 final size:16
Alignment explanation
Indices: 19157--19210 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 16
19147 GAATCGTACA
* *
19157 ACCCGAAACCGAAAACG
1 ACCCG-AACCCAAAATG
19174 ACCC-AACCCAAAATTG
1 ACCCGAACCCAAAA-TG
19190 ACCCGAACCC-AAATG
1 ACCCGAACCCAAAATG
19205 ACCCGA
1 ACCCGA
19211 CATTTGAGCG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 16 0.48
16 8 0.24
17 9 0.27
ACGTcount: A:0.43, C:0.39, G:0.13, T:0.06
Consensus pattern (16 bp):
ACCCGAACCCAAAATG
Found at i:20946 original size:11 final size:11
Alignment explanation
Indices: 20930--20959 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
20920 TGATATGAAA
20930 GCCATTGATGC
1 GCCATTGATGC
20941 GCCATTGATGC
1 GCCATTGATGC
20952 GCCATTGA
1 GCCATTGA
20960 GGAGCTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (11 bp):
GCCATTGATGC
Found at i:25820 original size:29 final size:27
Alignment explanation
Indices: 25744--25829 Score: 120
Period size: 27 Copynumber: 3.1 Consensus size: 27
25734 TATTTCTTAA
*
25744 TTGGTCATTTGCAC-TCTCAGAGGCATT
1 TTGGTCATTTGCACAT-TCAGGGGCATT
25771 TTGGTCATTTGCACATTCAGGGGCATT
1 TTGGTCATTTGCACATTCAGGGGCATT
*
25798 TTGGTCATTTTTGCATATTCAGGGGCATT
1 TTGGTCA--TTTGCACATTCAGGGGCATT
25827 TTG
1 TTG
25830 CATACTCGGG
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
27 31 0.57
28 1 0.02
29 22 0.41
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.41
Consensus pattern (27 bp):
TTGGTCATTTGCACATTCAGGGGCATT
Found at i:28285 original size:178 final size:178
Alignment explanation
Indices: 27967--28290 Score: 447
Period size: 178 Copynumber: 1.8 Consensus size: 178
27957 AAGGTGATTT
* * *
27967 AAGTGTCTATTGAAAGATTGTTTAATGATCTACAACTTTCATGAAGGATTCGAAAACTAAATTTA
1 AAGTGTCTATTGAAAGACTGTTCAATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTA
* * * * **
28032 ATGTTTTAAGAATCAAAAATGCTTCCGAAAGATTTGTTGTTTCGGTTAACGGGAATAGACGATTG
66 ATGTTTCAAGAATAAAAAATGATTCCGAAAGATTAGTTGTTTCGGTTAACGAAAATAGACGATTG
* *
28097 ACTTAATATTATATAACTTTTACTCCAGATGTCTGATTGAGATAATTC
131 ACTCAATATTACATAACTTTTACTCCAGATGTCTGATTGAGATAATTC
* * *
28145 AAGTGTCTCTTGAAAGGCTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTA
1 AAGTGTCTATTGAAAGACTGTTCAATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTA
* * *
28210 ATG-TTCAAGGTATAAAAAATGATTCC-AAAGAATTAGTTGTTTCGGTTAATGAAAATAGACGGT
66 ATGTTTCAA-GAATAAAAAATGATTCCGAAAG-ATTAGTTGTTTCGGTTAACGAAAATAGACGAT
28273 CT-ACTCAATATTACATAA
129 -TGACTCAATATTACATAA
28291 TTTGTGCTTA
Statistics
Matches: 126, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
177 8 0.06
178 117 0.93
179 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (178 bp):
AAGTGTCTATTGAAAGACTGTTCAATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTA
ATGTTTCAAGAATAAAAAATGATTCCGAAAGATTAGTTGTTTCGGTTAACGAAAATAGACGATTG
ACTCAATATTACATAACTTTTACTCCAGATGTCTGATTGAGATAATTC
Found at i:28789 original size:1 final size:1
Alignment explanation
Indices: 28783--28810 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
28773 GGTAGGGTAG
28783 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
28811 GCTTTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:30931 original size:17 final size:18
Alignment explanation
Indices: 30896--30932 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
30886 AAAAGGTAAT
30896 AAAAGGTTTTTTTCTCAA
1 AAAAGGTTTTTTTCTCAA
*
30914 AAAAGTTTTTTTTC-CAA
1 AAAAGGTTTTTTTCTCAA
30931 AA
1 AA
30933 TCATGTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (18 bp):
AAAAGGTTTTTTTCTCAA
Found at i:32404 original size:15 final size:16
Alignment explanation
Indices: 32384--32423 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
32374 TCGTCTTTTC
32384 TCCTTTTCTTG-TTCT
1 TCCTTTTCTTGCTTCT
32399 TCC-TTT-TTGCTTCT
1 TCCTTTTCTTGCTTCT
*
32413 TTCTTTTCTTG
1 TCCTTTTCTTG
32424 ATCAAAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
13 3 0.14
14 9 0.43
15 6 0.29
16 3 0.14
ACGTcount: A:0.00, C:0.25, G:0.07, T:0.68
Consensus pattern (16 bp):
TCCTTTTCTTGCTTCT
Done.