Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024264.1 Corchorus olitorius cultivar O-4 contig24297, 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: 24548
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:2888 original size:2 final size:2
Alignment explanation
Indices: 2881--2929 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
2871 CTTTAACTAG
* * *
2881 TA TA TA TA TA TA TA TA CA TA TG TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2923 TA TA TA T
1 TA TA TA T
2930 TTTGTAATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2908 original size:18 final size:18
Alignment explanation
Indices: 2881--2929 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
2871 CTTTAACTAG
2881 TATATATATATATATACA
1 TATATATATATATATACA
*
2899 TATGTATATATATATACA
1 TATATATATATATATACA
2917 TATATATATATAT
1 TATATATATATAT
2930 TTTGTAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (18 bp):
TATATATATATATATACA
Found at i:19434 original size:52 final size:51
Alignment explanation
Indices: 19371--19554 Score: 266
Period size: 52 Copynumber: 3.6 Consensus size: 51
19361 GATCAATTTA
* * * *
19371 TTTGAATTGTCTTCCACTCTAATATATTAAAAGGACCGTCTTCCGCTTATCC
1 TTTGAACTGTCTACCAAT-TAATATCTTAAAAGGACCGTCTTCCGCTTATCC
*
19423 TTTGAACTGTCTACCAATTTA-ATCTTAAAAGGACCGTCTTCCGCTTATCC
1 TTTGAACTGTCTACCAATTAATATCTTAAAAGGACCGTCTTCCGCTTATCC
19473 TTTGAACTGTCTACCAATTCAAT-TCTATAAAAGGACCGTCTTCCGCTTATCC
1 TTTGAACTGTCTACCAATT-AATATCT-TAAAAGGACCGTCTTCCGCTTATCC
*
19525 TTTGAACTGTCTACCAATTCA-ATCTTAAAA
1 TTTGAACTGTCTACCAATTAATATCTTAAAA
19555 AAAGTAATGC
Statistics
Matches: 121, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
50 52 0.43
51 10 0.08
52 59 0.49
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (51 bp):
TTTGAACTGTCTACCAATTAATATCTTAAAAGGACCGTCTTCCGCTTATCC
Found at i:19457 original size:50 final size:50
Alignment explanation
Indices: 19397--19554 Score: 289
Period size: 50 Copynumber: 3.1 Consensus size: 50
19387 CTCTAATATA
*
19397 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTTAATC
1 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
19447 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTC
1 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAA-TC
19498 TATAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
1 T-TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
19549 TTAAAA
1 TTAAAA
19555 AAAGTAATGC
Statistics
Matches: 105, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
50 52 0.50
51 6 0.06
52 47 0.45
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (50 bp):
TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
Found at i:19674 original size:50 final size:50
Alignment explanation
Indices: 19610--19747 Score: 267
Period size: 50 Copynumber: 2.8 Consensus size: 50
19600 AGGTTTGAAA
*
19610 TGACTCGTATGGAAACGAGTTCGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
19660 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
19710 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
19748 AAAGCATTCG
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 87 1.00
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.30
Consensus pattern (50 bp):
TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
Found at i:20388 original size:50 final size:50
Alignment explanation
Indices: 20334--20533 Score: 319
Period size: 50 Copynumber: 4.0 Consensus size: 50
20324 CTTAAATGCC
* * * **
20334 CTTTGAAGAGCGAATTTTGATCTTGGACTCACAAATGGAATGGAATCCTA
1 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATTTTA
*
20384 CTTTGAAAAGCGAATTTTGATCTTGGACTTACAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATTTTA
*
20434 CTTTGAAAAGCGAATTTTGATCTTGGACTTACAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATTTTA
* *
20484 CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATTTTA
20534 TTGTAAAACT
Statistics
Matches: 141, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 141 1.00
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.33
Consensus pattern (50 bp):
CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATTTTA
Found at i:20819 original size:1 final size:1
Alignment explanation
Indices: 20813--20837 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
20803 GAGCTCTTCC
20813 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
20838 GCAAACGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:21152 original size:18 final size:17
Alignment explanation
Indices: 21129--21165 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
21119 ATCAATTCTC
21129 TTTTGATTTTAATTTTGA
1 TTTTGATTTT-ATTTTGA
*
21147 TTTTGATTTTTTTTTGA
1 TTTTGATTTTATTTTGA
21164 TT
1 TT
21166 GATTGACTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.16, C:0.00, G:0.11, T:0.73
Consensus pattern (17 bp):
TTTTGATTTTATTTTGA
Found at i:21579 original size:8 final size:8
Alignment explanation
Indices: 21562--21615 Score: 60
Period size: 8 Copynumber: 7.0 Consensus size: 8
21552 AGTGCCTTTA
*
21562 TTTTCCTT
1 TTTTCATT
21570 TTTTCA--
1 TTTTCATT
21576 TTTTCATT
1 TTTTCATT
21584 TTTTCATTT
1 TTTTCA-TT
21593 TTTTCATT
1 TTTTCATT
*
21601 TTTTC-CT
1 TTTTCATT
21608 TTTTCATT
1 TTTTCATT
21616 ATTGGGAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
6 6 0.15
7 6 0.15
8 19 0.49
9 8 0.21
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTCATT
Found at i:21596 original size:9 final size:9
Alignment explanation
Indices: 21576--21604 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
21566 CCTTTTTTCA
21576 TTTTCA-TT
1 TTTTCATTT
21584 TTTTCATTT
1 TTTTCATTT
21593 TTTTCATTT
1 TTTTCATTT
21602 TTT
1 TTT
21605 CCTTTTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTCATTT
Found at i:21598 original size:17 final size:17
Alignment explanation
Indices: 21576--21611 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
21566 CCTTTTTTCA
21576 TTTTCATTTTTTCATTT
1 TTTTCATTTTTTCATTT
*
21593 TTTTCATTTTTTCCTTT
1 TTTTCATTTTTTCATTT
21610 TT
1 TT
21612 CATTATTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTCATTTTTTCATTT
Found at i:21610 original size:14 final size:14
Alignment explanation
Indices: 21561--21593 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
21551 AAGTGCCTTT
*
21561 ATTTTCCTTTTTTC
1 ATTTTCATTTTTTC
21575 ATTTTCATTTTTTC
1 ATTTTCATTTTTTC
21589 ATTTT
1 ATTTT
21594 TTTCATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (14 bp):
ATTTTCATTTTTTC
Found at i:22036 original size:50 final size:50
Alignment explanation
Indices: 21977--22105 Score: 177
Period size: 50 Copynumber: 2.6 Consensus size: 50
21967 ATTTTTGTCC
* * *
21977 CTATCAACATAGCCTTTTCCACAAGCCAAGGTCGTTTCCATACGAGCCAA
1 CTATCAACATAGACTTTTCCACAAGCCAAGCTCATTTCCATACGAGCCAA
* * * *
22027 CTATCAACATAGGCTTTTCCACAAGCAAAGCTCATTTCCATACGGGTCAA
1 CTATCAACATAGACTTTTCCACAAGCCAAGCTCATTTCCATACGAGCCAA
* *
22077 TTATCAACATAGAGTTTTCCACAAGCCAA
1 CTATCAACATAGACTTTTCCACAAGCCAA
22106 ATTCGAGGAT
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 69 1.00
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.26
Consensus pattern (50 bp):
CTATCAACATAGACTTTTCCACAAGCCAAGCTCATTTCCATACGAGCCAA
Found at i:22430 original size:28 final size:27
Alignment explanation
Indices: 22389--22488 Score: 94
Period size: 28 Copynumber: 3.6 Consensus size: 27
22379 TCATCTATGT
*
22389 GGCATTTTGGGTCATTTTCATAATCCAGG
1 GGCATTTT-AGTCATTTTCA-AATCCAGG
* * *
22418 GGCGTTTTAGTCATTTGCACATCCAGG
1 GGCATTTTAGTCATTTTCAAATCCAGG
* * *
22445 GGCATTTTGGTCATTTTTACA-CCTAGGG
1 GGCATTTTAGTCATTTTCAAATCC-A-GG
22473 GGCATTTTAGTCATTT
1 GGCATTTTAGTCATTT
22489 GTGCTTCAGG
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
26 2 0.03
27 25 0.42
28 26 0.43
29 7 0.12
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (27 bp):
GGCATTTTAGTCATTTTCAAATCCAGG
Found at i:22499 original size:27 final size:27
Alignment explanation
Indices: 22412--22523 Score: 102
Period size: 27 Copynumber: 4.1 Consensus size: 27
22402 ATTTTCATAA
* *
22412 TCCA-GGGGCGTTTTAGTCATTTGCAC
1 TCCAGGGGGCATTTTAGTCATTTGTAC
* *
22438 ATCCA-GGGGCATTTTGGTCATTTTTAC
1 -TCCAGGGGGCATTTTAGTCATTTGTAC
* *
22465 ACCTAGGGGGCATTTTAGTCATTTGTGC
1 TCC-AGGGGGCATTTTAGTCATTTGTAC
* * * *
22493 TTCAGGGGGCATTGTGGTCATTTCTAC
1 TCCAGGGGGCATTTTAGTCATTTGTAC
22520 TCCA
1 TCCA
22524 TTGCTCAAGT
Statistics
Matches: 68, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
26 2 0.03
27 46 0.68
28 20 0.29
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.37
Consensus pattern (27 bp):
TCCAGGGGGCATTTTAGTCATTTGTAC
Done.