Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018804.1 Corchorus olitorius cultivar O-4 contig18837, 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: 17519
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:4345 original size:60 final size:59
Alignment explanation
Indices: 4281--4394 Score: 140
Period size: 59 Copynumber: 1.9 Consensus size: 59
4271 TTTCATACAG
* * *
4281 AGGTTAT-GAATATTTCATAAAAAAAATTATCAAAATTTCTTAAGGAGGTTAACAATTCTA
1 AGGTTATCGAA-ATTTCAT-AAAAAAACTATCAAAATTTCATAAGAAGGTTAACAATTCTA
* * * *
4341 AGGTTATCGAAATTTTATAATATAGCTATCAAAATTTCATAAGAAGGTTAACAA
1 AGGTTATCGAAATTTCATAAAAAAACTATCAAAATTTCATAAGAAGGTTAACAA
4395 AATTTCATAG
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
59 30 0.65
60 13 0.28
61 3 0.07
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (59 bp):
AGGTTATCGAAATTTCATAAAAAAACTATCAAAATTTCATAAGAAGGTTAACAATTCTA
Found at i:4494 original size:22 final size:21
Alignment explanation
Indices: 4430--4510 Score: 65
Period size: 22 Copynumber: 3.7 Consensus size: 21
4420 AAATGTCTAC
*
4430 TTATCAAAATTTCATAGGAAAG
1 TTATCAAAATTTCATA-GAGAG
* *
4452 TTATGAAAATTTTAT-GAAGAG
1 TTATCAAAATTTCATAG-AGAG
*
4473 TTTATCAAAATTACATAGAGAGG
1 -TTATCAAAATTTCATAGAGA-G
* *
4496 ATATCAAAGTTTCAT
1 TTATCAAAATTTCAT
4511 TCTCGTAGGG
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
20 1 0.02
21 3 0.07
22 40 0.87
23 2 0.04
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.35
Consensus pattern (21 bp):
TTATCAAAATTTCATAGAGAG
Found at i:4655 original size:22 final size:22
Alignment explanation
Indices: 4520--4775 Score: 184
Period size: 22 Copynumber: 11.8 Consensus size: 22
4510 TTCTCGTAGG
* * **
4520 GAGGTTATCGAAATTGCATGGT
1 GAGGTTATCAAAATTTCATAAT
* *
4542 GTGGCTATCAAAATTT--T-AT
1 GAGGTTATCAAAATTTCATAAT
*
4561 GAGGTTATCAAAATTTTCATAGT
1 GAGGTTATCAAAA-TTTCATAAT
* * *
4584 GCGGTTA-C-CAATTTTAT-AT
1 GAGGTTATCAAAATTTCATAAT
* * **
4603 CGTGATTATCAAAATTTCATAGG
1 -GAGGTTATCAAAATTTCATAAT
**
4626 GAAATTATCAAAATTTCATAAT
1 GAGGTTATCAAAATTTCATAAT
* * *
4648 AAGGTTATCAAAATTTCTTAGT
1 GAGGTTATCAAAATTTCATAAT
* * *
4670 GTGGTTATCAAATTTTCATAAG
1 GAGGTTATCAAAATTTCATAAT
* *
4692 GAGGTTATCGAAATTTAATAAT
1 GAGGTTATCAAAATTTCATAAT
* *
4714 GAGGTTATCAAATTTTCACAGAT
1 GAGGTTATCAAAATTTCATA-AT
*
4737 -AGGTTATCGAAATTTCATAAT
1 GAGGTTATCAAAATTTCATAAT
*
4758 GAGGTTATCAAATTTTCA
1 GAGGTTATCAAAATTTCA
4776 GTGTGATTAT
Statistics
Matches: 177, Mismatches: 47, Indels: 20
0.73 0.19 0.08
Matches are distributed among these distances:
19 13 0.07
20 14 0.08
21 5 0.03
22 136 0.77
23 9 0.05
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAAT
Found at i:4658 original size:44 final size:43
Alignment explanation
Indices: 4562--4775 Score: 209
Period size: 44 Copynumber: 4.9 Consensus size: 43
4552 AAATTTTATG
* *
4562 AGGTTATCAAAATTTTCATAGTGCGGTTA-CCAATTTT-AT-AT
1 AGGTTATCAAAA-TTTCATAGTGAGGTTATCAAATTTTCATAAT
* * ** *
4603 CGTGATTATCAAAATTTCATAGGGAAATTATCAAAATTTCATAAT
1 AG-G-TTATCAAAATTTCATAGTGAGGTTATCAAATTTTCATAAT
* * *
4648 AAGGTTATCAAAATTTCTTAGTGTGGTTATCAAATTTTCATAAGG
1 -AGGTTATCAAAATTTCATAGTGAGGTTATCAAATTTTCATAA-T
* * * *
4693 AGGTTATCGAAATTTAATAATGAGGTTATCAAATTTTCACAGAT
1 AGGTTATCAAAATTTCATAGTGAGGTTATCAAATTTTCATA-AT
* *
4737 AGGTTATCGAAATTTCATAATGAGGTTATCAAATTTTCA
1 AGGTTATCAAAATTTCATAGTGAGGTTATCAAATTTTCA
4776 GTGTGATTAT
Statistics
Matches: 142, Mismatches: 23, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
41 1 0.01
42 13 0.09
43 15 0.11
44 108 0.76
45 4 0.03
46 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (43 bp):
AGGTTATCAAAATTTCATAGTGAGGTTATCAAATTTTCATAAT
Found at i:8604 original size:23 final size:22
Alignment explanation
Indices: 8569--8730 Score: 103
Period size: 22 Copynumber: 7.3 Consensus size: 22
8559 TCTAACGTAT
* * *
8569 AAATATTGGTAACCACACTGTCA
1 AAATTTTGATAACCACACTAT-A
*
8592 AAATTTTGATAACCTC-CTTATGA
1 AAATTTTGATAACCACAC-TAT-A
* * *
8615 AAA-TTTGATAACCACATTGTG
1 AAATTTTGATAACCACACTATA
*** * * *
8636 AAATTTTGATAACTTGAGTCTG
1 AAATTTTGATAACCACACTATA
* * *
8658 AAATTTTGATAATCTCCCTATA
1 AAATTTTGATAACCACACTATA
* *
8680 AAATTTTGAAAACCACACTATGT
1 AAATTTTGATAACCACACTAT-A
*
8703 AAATTTTGATAACCACACTATG
1 AAATTTTGATAACCACACTATA
8725 AAATTT
1 AAATTT
8731 CAATAACCTC
Statistics
Matches: 107, Mismatches: 28, Indels: 9
0.74 0.19 0.06
Matches are distributed among these distances:
21 3 0.03
22 65 0.61
23 39 0.36
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.35
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATA
Found at i:8728 original size:22 final size:22
Alignment explanation
Indices: 8592--9088 Score: 232
Period size: 22 Copynumber: 22.4 Consensus size: 22
8582 CACACTGTCA
8592 AAATTTTGATAACCTC-CTTATG
1 AAATTTTGATAACCTCAC-TATG
* * * *
8614 AAAATTTGATAACCACATTGTG
1 AAATTTTGATAACCTCACTATG
* * * *
8636 AAATTTTGATAACTTGAGTCTG
1 AAATTTTGATAACCTCACTATG
* * *
8658 AAATTTTGATAATCTCCCTATA
1 AAATTTTGATAACCTCACTATG
* *
8680 AAATTTTGAAAACCACACTATG
1 AAATTTTGATAACCTCACTATG
*
8702 TAAATTTTGATAACCACACTATG
1 -AAATTTTGATAACCTCACTATG
** *
8725 AAATTTCAATAACCTCCCTATG
1 AAATTTTGATAACCTCACTATG
* * * *
8747 AGAATGAAACTGTGATATCTTCTCTATG
1 A-AAT-----TTTGATAACCTCACTATG
* * *
8775 TAATTTTGATAACCTCTCCAT-
1 AAATTTTGATAACCTCACTATG
* * * *
8796 AAATTTTTCATAACCTCCCGATA
1 AAA-TTTTGATAACCTCACTATG
* * *
8819 AAATTTTGTTAACCTCCCTAGG
1 AAATTTTGATAACCTCACTATG
* *
8841 ATATTTTGATAA--GCAC----
1 AAATTTTGATAACCTCACTATG
*
8857 AAATTTTGATAACTTCCCTCCCTATG
1 AAATTTTGATAA----CCTCACTATG
** *
8883 AAATTTTTTTAACCTTC-TTATG
1 AAATTTTGATAACC-TCACTATG
*
8905 AAATTTTGATAA-CTACACTATA
1 AAATTTTGATAACCT-CACTATG
** *
8927 AAATTTCAATAACCTTC-GTATG
1 AAATTTTGATAACC-TCACTATG
* *
8949 AAATTTT-ATTAACCTCGCTAAG
1 AAATTTTGA-TAACCTCACTATG
***
8971 AAATTTTGATAACCTTTTTATG
1 AAATTTTGATAACCTCACTATG
*
8993 GAATTTTGATAA-CTACACTATG
1 AAATTTTGATAACCT-CACTATG
* *
9015 AAGTTTTGATAATCTCTA-TATG
1 AAATTTTGATAACCTC-ACTATG
* * *
9037 AAATTTTGGTAACCACACTAAG
1 AAATTTTGATAACCTCACTATG
9059 AAATTTTGATAACCTTC-CTATG
1 AAATTTTGATAACC-TCACTATG
*
9081 TAATTTTG
1 AAATTTTG
9089 GTTTGATTAT
Statistics
Matches: 355, Mismatches: 87, Indels: 66
0.70 0.17 0.13
Matches are distributed among these distances:
16 11 0.03
20 3 0.01
21 10 0.03
22 269 0.76
23 36 0.10
24 1 0.00
26 10 0.03
27 3 0.01
28 12 0.03
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAACCTCACTATG
Found at i:8742 original size:67 final size:65
Alignment explanation
Indices: 8568--8747 Score: 182
Period size: 67 Copynumber: 2.7 Consensus size: 65
8558 TTCTAACGTA
* * * * * *
8568 TAAATATTGGTAACCACACTGTCAAAATTTTGATAACCTCCTTATGAAAATTTGATAACCACATT
1 TAAATTTTGATAACCACACTAT-GAAATTTTGATAACCTCCCTATGAAAATTTGAAAACCACATT
8633 G
65 G
*** * * *
8634 TGAAATTTTGATAACTTGAGTCTGAAATTTTGATAATCTCCCTAT-AAAATTTTGAAAACCACAC
1 T-AAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCTATGAAAA-TTTGAAAACCACA-
8698 TATG
63 T-TG
**
8702 TAAATTTTGATAACCACACTATGAAATTTCAATAACCTCCCTATGA
1 TAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCTATGA
8748 GAATGAAACT
Statistics
Matches: 90, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
65 4 0.04
66 32 0.36
67 50 0.56
68 4 0.04
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (65 bp):
TAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCTATGAAAATTTGAAAACCACATTG
Found at i:8746 original size:45 final size:44
Alignment explanation
Indices: 8569--8747 Score: 128
Period size: 45 Copynumber: 4.0 Consensus size: 44
8559 TCTAACGTAT
* * * *
8569 AAATATTGGTAACCACACTGTCAAAATTTTGATAACCTC-CTTATG
1 AAATTTTGATAACCACACTAT-AAAATTTTAATAACCTCAC-TATG
* * * * * * * * *
8614 AAAATTTGATAACCACATTGTGAAATTTTGATAACTTGAGTCTG
1 AAATTTTGATAACCACACTATAAAATTTTAATAACCTCACTATG
* * * *
8658 AAATTTTGATAATCTCCCTATAAAATTTTGAA-AACCACACTATG
1 AAATTTTGATAACCACACTATAAAATTTT-AATAACCTCACTATG
* * *
8702 TAAATTTTGATAACCACACTATGAAATTTCAATAACCTCCCTATG
1 -AAATTTTGATAACCACACTATAAAATTTTAATAACCTCACTATG
8747 A
1 A
8748 GAATGAAACT
Statistics
Matches: 101, Mismatches: 29, Indels: 9
0.73 0.21 0.06
Matches are distributed among these distances:
44 49 0.49
45 52 0.51
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (44 bp):
AAATTTTGATAACCACACTATAAAATTTTAATAACCTCACTATG
Found at i:10599 original size:439 final size:440
Alignment explanation
Indices: 9767--10738 Score: 1526
Period size: 439 Copynumber: 2.2 Consensus size: 440
9757 CCCGCTATCA
* * *
9767 ATAAATAAATACTTTTTTGTTGG-TCTATTTATCAAATGAT--TCATATATTTTTATACTTTATG
1 ATAAACAAATATTTTTTTGTTGGAT-TATTTATCAAATGATCCTCA-A-ATTTTTATGCTTTATG
*
9829 CTATTTAGTCCTTCACAATTTCTGGGTTGGACGACTGAACGTTTCGGCTTTAATTCTTTTATTTT
63 CTATTTAGTCCCTCACAATTTCTGGGTTGGACGACTGAACGTTTCGGCTTTAATTCTTTTATTTT
* *
9894 TTGTTTTGCTTATCCGATCAAGGTGATTCAAGTGTCTATTAAAACGTAATTTCGTGATCTACAAC
128 TTCTTTTGCTTATCCGATCAAGGTGATTCAAGTGTCTATTAAAACGTAATTTCATGATCTACAAC
* *
9959 TTTCATAAAGGACTCAAAAGCCAATTTTAATGTTTTGATTTTAAAAAAATACTTTTGAAATTTTG
193 TTCCATAAAGGACTCAAAAGCCAAATTTAATGTTTTGATTTTAAAAAAATACTTTTGAAATTTTG
10024 TGGTCTTGATTGCCGGTCTATTTGATATCCTATAATTTTTGTTCCACTTGTCCGATTGAGGTTAT
258 TGGTCTTGATTGCCGGTCTATTTGATATCCTATAATTTTTGTTCCACTTGTCCGATTGAGGTTAT
* * * * *
10089 TCAAGTGCCGGTTTAAAGGTTATTGTGTGATCTATGCCTTTCGTTAAGAGCTTCAAAGCTGGATT
323 TCAAGTGCCGGTTAAAAGGTTATTGTGTGATCTACGCCTTTCGTTAAGAGCCTCAAAACTGAATT
*
10154 TGATTAATAATTTTCGTGGAGGGTTCAAGAGGGAAATTTTATGTTTGGTCTCC
388 TGATTAATAAGTTTCGTGGAGGGTTCAAGAGGGAAATTTTATGTTTGGTCTCC
*
10207 ATAAACAAATATTTTTTTTGTTGGATTATTTATCAAATGATCCTCAAACTTTTATGCTTTATGCT
1 ATAAACAAATA-TTTTTTTGTTGGATTATTTATCAAATGATCCTCAAATTTTTATGCTTTATGCT
*
10272 ATTTAGTCCCTCACAATTTCTGGGTTGGACGACTGAACGTTTTGGCTTTAATTCTTTTA-TTTTT
65 ATTTAGTCCCTCACAATTTCTGGGTTGGACGACTGAACGTTTCGGCTTTAATTCTTTTATTTTTT
* *
10336 CTTTTGCTTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTT
130 CTTTTGCTTATCCGATCAAGGTGATTCAAGTGTCTATTAAAACGTAATTTCATGATCTACAACTT
* * *
10401 CCATGAAGGATTCAAAAGCCAAATTTAATGTTTTGATTTT-AAAAAATGCTTTTGAAATTTTGTG
195 CCATAAAGGACTCAAAAGCCAAATTTAATGTTTTGATTTTAAAAAAATACTTTTGAAATTTTGTG
* *
10465 GTCTTGATTGTCGGTCTATTTGATATCGTATAATTTTT-TGTCCACTTGTCCGATTGAGGTTATT
260 GTCTTGATTGCCGGTCTATTTGATATCCTATAATTTTTGT-TCCACTTGTCCGATTGAGGTTATT
* * *
10529 CAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGGCTTTCGTTAAGGGCCTCAAAACTGAATTT
324 CAAGTGCCGGTTAAAAGGTTATTGTGTGATCTACGCCTTTCGTTAAGAGCCTCAAAACTGAATTT
* * *
10594 GATTAATGAGTTTCTTGGAGGGTTCAAGAGGGAATTTTTATGTTTGGTCTCC
389 GATTAATAAGTTTCGTGGAGGGTTCAAGAGGGAAATTTTATGTTTGGTCTCC
* * *
10646 ATAAACAAATATTTTTTTGCTAGATTATTTATCAAATGATCCTCAGATTTTTATGCTTTATGCTA
1 ATAAACAAATATTTTTTTGTTGGATTATTTATCAAATGATCCTCAAATTTTTATGCTTTATGCTA
* * * *
10711 TTTAATCTCTCATAA-TTATGGGTTGGAC
66 TTTAGTCCCTCACAATTTCTGGGTTGGAC
10739 CATTTAATGC
Statistics
Matches: 490, Mismatches: 37, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
437 12 0.02
438 63 0.13
439 199 0.41
440 112 0.23
441 99 0.20
442 2 0.00
443 3 0.01
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (440 bp):
ATAAACAAATATTTTTTTGTTGGATTATTTATCAAATGATCCTCAAATTTTTATGCTTTATGCTA
TTTAGTCCCTCACAATTTCTGGGTTGGACGACTGAACGTTTCGGCTTTAATTCTTTTATTTTTTC
TTTTGCTTATCCGATCAAGGTGATTCAAGTGTCTATTAAAACGTAATTTCATGATCTACAACTTC
CATAAAGGACTCAAAAGCCAAATTTAATGTTTTGATTTTAAAAAAATACTTTTGAAATTTTGTGG
TCTTGATTGCCGGTCTATTTGATATCCTATAATTTTTGTTCCACTTGTCCGATTGAGGTTATTCA
AGTGCCGGTTAAAAGGTTATTGTGTGATCTACGCCTTTCGTTAAGAGCCTCAAAACTGAATTTGA
TTAATAAGTTTCGTGGAGGGTTCAAGAGGGAAATTTTATGTTTGGTCTCC
Found at i:16021 original size:107 final size:108
Alignment explanation
Indices: 15887--16090 Score: 311
Period size: 107 Copynumber: 1.9 Consensus size: 108
15877 CTCACGCTGG
* * * *
15887 CGCGTTGAGTATTCTTGATTTGTGGCTAACAAATTATTTTAGTTTTAGAG-TTTTTTTCTCTCGA
1 CGCGTCGAGTATTCTTGATATGTGGCTAACAAATCATTTTAGTTATAGAGTTTTTTTTCTCTCGA
15951 TTCTTATCATATATGTGAGTAGGTGGTTATCGACTCGCACTAC
66 TTCTTATCATATATGTGAGTAGGTGGTTATCGACTCGCACTAC
*
15994 CGCGTCGAGTATTCTTGATATGTGGCTAGCAAATCATTTTAGTTATAGAGTTTTTTTTTTTCTCT
1 CGCGTCGAGTATTCTTGATATGTGGCTAACAAATCATTTTAGTTATAGAG---TTTTTTTTCTCT
* *
16059 CGGTTCTTATCATATGTGTGAGTAGGTGGTTA
63 CGATTCTTATCATATATGTGAGTAGGTGGTTA
16091 GCAAATTCGG
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
107 45 0.52
111 41 0.48
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.45
Consensus pattern (108 bp):
CGCGTCGAGTATTCTTGATATGTGGCTAACAAATCATTTTAGTTATAGAGTTTTTTTTCTCTCGA
TTCTTATCATATATGTGAGTAGGTGGTTATCGACTCGCACTAC
Found at i:16298 original size:23 final size:23
Alignment explanation
Indices: 16271--16316 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
16261 GGAGGATATC
16271 ATCTTTATAAGACTATAATCATT
1 ATCTTTATAAGACTATAATCATT
16294 ATCTTTATAAGACTATAATCATT
1 ATCTTTATAAGACTATAATCATT
16317 CTATTTGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.04, T:0.43
Consensus pattern (23 bp):
ATCTTTATAAGACTATAATCATT
Done.