Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024242.1 Corchorus olitorius cultivar O-4 contig24275, 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: 10549
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1412 original size:16 final size:15
Alignment explanation
Indices: 1370--1417 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
1360 TTCCATTTAC
*
1370 TTTTTCTTTGCATTG-
1 TTTTGCTTTG-ATTGA
*
1385 TTTTGCTCTGATTGA
1 TTTTGCTTTGATTGA
1400 TTATTGCTTTGATTGA
1 TT-TTGCTTTGATTGA
1416 TT
1 TT
1418 GCCTATTCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 4 0.14
15 10 0.36
16 14 0.50
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.60
Consensus pattern (15 bp):
TTTTGCTTTGATTGA
Found at i:1737 original size:25 final size:25
Alignment explanation
Indices: 1700--1748 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
1690 TAGAGAGTCT
1700 GCATGCATCATAATCTTAAAATATG
1 GCATGCATCATAATCTTAAAATATG
*
1725 GCATGCATTATAATCTTAAAATAT
1 GCATGCATCATAATCTTAAAATAT
1749 ACCATAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (25 bp):
GCATGCATCATAATCTTAAAATATG
Found at i:4426 original size:15 final size:16
Alignment explanation
Indices: 4399--4428 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4389 CTTTGCTTTG
4399 TTTTCTAGTTTAATTA
1 TTTTCTAGTTTAATTA
4415 TTTTCT-GTTTAATT
1 TTTTCTAGTTTAATT
4429 GCTTTCTGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (16 bp):
TTTTCTAGTTTAATTA
Found at i:4684 original size:61 final size:61
Alignment explanation
Indices: 4609--4731 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
4599 TGAGATCAAA
4609 TGAAAGCTTTAGAGAATATGCAGTGAGATGGAGGGATATGACGTTGCAAGTTAAACCTTCT
1 TGAAAGCTTTAGAGAATATGCAGTGAGATGGAGGGATATGACGTTGCAAGTTAAACCTTCT
4670 TGAAAGCTTTAGAGAATATGCAGTGAGATGGAGGGATATGACGTTGCAAGTTAAACCTTCT
1 TGAAAGCTTTAGAGAATATGCAGTGAGATGGAGGGATATGACGTTGCAAGTTAAACCTTCT
4731 T
1 T
4732 TACCTGAAAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (61 bp):
TGAAAGCTTTAGAGAATATGCAGTGAGATGGAGGGATATGACGTTGCAAGTTAAACCTTCT
Found at i:6479 original size:6 final size:6
Alignment explanation
Indices: 6437--6495 Score: 50
Period size: 6 Copynumber: 9.7 Consensus size: 6
6427 GTAAATATGC
* * *
6437 AAAA-A AAAA-A AAAACA ACAACA AACAGCA ACAACA AAAACAA AAAACAA
1 AAAACA AAAACA AAAACA AAAACA AA-AACA AAAACA AAAAC-A AAAAC-A
6486 AAAACA AAAA
1 AAAACA AAAA
6496 AAAGTGAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
5 9 0.20
6 19 0.42
7 17 0.38
ACGTcount: A:0.81, C:0.17, G:0.02, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:6494 original size:7 final size:7
Alignment explanation
Indices: 6437--6496 Score: 54
Period size: 7 Copynumber: 8.7 Consensus size: 7
6427 GTAAATATGC
6437 AAAAA-A
1 AAAAACA
6443 AAAAA-A
1 AAAAACA
*
6449 AACAACA
1 AAAAACA
*
6456 ACAAACA
1 AAAAACA
*
6463 GCAACAAC-
1 --AAAAACA
6471 AAAAACA
1 AAAAACA
6478 AAAAACA
1 AAAAACA
6485 AAAAACA
1 AAAAACA
6492 AAAAA
1 AAAAA
6497 AAGTGAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
6 15 0.34
7 25 0.57
9 4 0.09
ACGTcount: A:0.82, C:0.17, G:0.02, T:0.00
Consensus pattern (7 bp):
AAAAACA
Found at i:6520 original size:19 final size:19
Alignment explanation
Indices: 6496--6532 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
6486 AAAACAAAAA
6496 AAAGTGAAAATTGAAAATG
1 AAAGTGAAAATTGAAAATG
*
6515 AAAGTGGAAATTGAAAAT
1 AAAGTGAAAATTGAAAAT
6533 TTAAAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.22, T:0.22
Consensus pattern (19 bp):
AAAGTGAAAATTGAAAATG
Found at i:6806 original size:8 final size:8
Alignment explanation
Indices: 6793--6826 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
6783 AAACATTATA
6793 AAAAAATG
1 AAAAAATG
6801 AAAAAATG
1 AAAAAATG
6809 AAGAAAAATG
1 -A-AAAAATG
6819 AAAAAATG
1 AAAAAATG
6827 TTTCAGGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 15 0.62
9 2 0.08
10 7 0.29
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:6901 original size:14 final size:14
Alignment explanation
Indices: 6882--6909 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6872 AACGGGGGTG
6882 AATGAAAAAATGAA
1 AATGAAAAAATGAA
6896 AATGAAAAAATGAA
1 AATGAAAAAATGAA
6910 GAGAAGAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AATGAAAAAATGAA
Found at i:8121 original size:148 final size:147
Alignment explanation
Indices: 7853--8237 Score: 646
Period size: 148 Copynumber: 2.6 Consensus size: 147
7843 CAAAGTTGCA
* * *
7853 TTTAAATTTCAAAAGCACCTTGCTCAAGGTTGAGTTCGCATTTGTAAGTCCTCCGGGCACAATTT
1 TTTAAGTTTCAAAAG-ACCTTGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCGGGCACAATTT
*
7918 CAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATTTCATTTCATCAAATTTTTA
65 CAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCAGGTATCATTTCATTTCATCAAATTTTTA
7983 ATCAAAGCTGCGTTTAAG
130 ATCAAAGCTGCGTTTAAG
*
8001 TTTAAGTTTCAAAAGTACCTTGCTCAAGGTTGAGTTTGCATTTGTAAGACCTTCGGGCACAATTT
1 TTTAAGTTTCAAAAG-ACCTTGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCGGGCACAATTT
* * *
8066 CAGAAACCTCCGGATATAAATTCTGATAAATCCTCCAGGTATCATTTCATTTCATCCAATTTTTA
65 CAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCAGGTATCATTTCATTTCATCAAATTTTTA
8131 ATCAAAGCTGCGTTTAAG
130 ATCAAAGCTGCGTTTAAG
* * *
8149 TTTAAGTTTCAAAA-ACCTTTCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCGGGCACCATTTT
1 TTTAAGTTTCAAAAGACCTTGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCGGGCACAATTTC
8213 AGAAACCTCCGGGTATTAATTCTGA
66 AGAAACCTCCGGGTATTAATTCTGA
8238 CAAGTCCTTC
Statistics
Matches: 222, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
146 69 0.31
148 153 0.69
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (147 bp):
TTTAAGTTTCAAAAGACCTTGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCGGGCACAATTTC
AGAAACCTCCGGGTATTAATTCTGATAAATCCTCCAGGTATCATTTCATTTCATCAAATTTTTAA
TCAAAGCTGCGTTTAAG
Found at i:8422 original size:40 final size:40
Alignment explanation
Indices: 8371--9304 Score: 1267
Period size: 40 Copynumber: 23.3 Consensus size: 40
8361 TTATTAGTCG
* *
8371 ATTTCAGAATCCTGCTCAGAATCATTGCTTTATCAAATTA
1 ATTTCAAAATCCTGCTCAGGATCATTGCTTTATCAAATTA
* * *
8411 ATTTCAGAATCCTGCTCAAGATCATCT-TTTTATCAAATTA
1 ATTTCAAAATCCTGCTCAGGATCAT-TGCTTTATCAAATTA
*
8451 ATTTCAAAACCCTGCTCAGGATCATTGCTTTATCAAATTA
1 ATTTCAAAATCCTGCTCAGGATCATTGCTTTATCAAATTA
*
8491 ATTTCAAAACCCTGCTCAGGATCATTGCTTTATCAAATTA
1 ATTTCAAAATCCTGCTCAGGATCATTGCTTTATCAAATTA
* *
8531 ATTTCAGAATCCTGCTCAGGATCATCT-TTTTATCAAATTA
1 ATTTCAAAATCCTGCTCAGGATCAT-TGCTTTATCAAATTA
* * * *
8571 ATTTCAGAATCCTACTCAGAATCATCT-TTTTATCAAATTA
1 ATTTCAAAATCCTGCTCAGGATCAT-TGCTTTATCAAATTA
* *
8611 ATTTCAAAACCCTGCTCAGGATCATTGTTTTATCAAATTA
1 ATTTCAAAATCCTGCTCAGGATCATTGCTTTATCAAATTA
* *
8651 ATTTCAGAATCCTGCTCAGGATCATCT-TTTTATCAAATTA
1 ATTTCAAAATCCTGCTCAGGATCAT-TGCTTTATCAAATTA
*
8691 ATTTCAAAACCCTGCTCAGGATCATTGCTTTATCAAATTA
1 ATTTCAAAATCCTGCTCAGGATCATTGCTTTATCAAATTA
* * *
8731 ATTTCAGAATCTTGCTCAGGATCATCT-TTTTATCAAATTA
1 ATTTCAAAATCCTGCTCAGGATCAT-TGCTTTATCAAATTA
*
8771 ATTTCAAAACCCTGCTCAGGATCATTGCTTTATCAAATTA
1 ATTTCAAAATCCTGCTCAGGATCATTGCTTTATCAAATTA
* * *
8811 ATTTCAAAACCCTGCTCAGGATTATTGATTTATCAAATTA
1 ATTTCAAAATCCTGCTCAGGATCATTGCTTTATCAAATTA
* * *
8851 ATTTCAGAATCCTACTCAGGATCATCT-TTTTATCAAATTA
1 ATTTCAAAATCCTGCTCAGGATCAT-TGCTTTATCAAATTA
* * *
8891 ATTTCAAAACCCTGCTCAAGATCATTGTTTTATCAAATTA
1 ATTTCAAAATCCTGCTCAGGATCATTGCTTTATCAAATTA
* * *
8931 ATTTCAGAATCCTACTCAGGATCATCT-TTTTATCAAATTA
1 ATTTCAAAATCCTGCTCAGGATCAT-TGCTTTATCAAATTA
* * *
8971 ATTTCAAAACCCTACTCAGGATCATTGTTTTATCAAATTA
1 ATTTCAAAATCCTGCTCAGGATCATTGCTTTATCAAATTA
*
9011 ATTTCAAAATCCTGCTCAGGATCATCT-TTTTATCAAATTA
1 ATTTCAAAATCCTGCTCAGGATCAT-TGCTTTATCAAATTA
9051 ATTTC-AAATCCCTGCTCAGGATCATTGCTTTATCAAATTA
1 ATTTCAAAAT-CCTGCTCAGGATCATTGCTTTATCAAATTA
*
9091 ATTTCAAAATCCTACTCAGGATCATTGCTTTATCAAATTA
1 ATTTCAAAATCCTGCTCAGGATCATTGCTTTATCAAATTA
*
9131 ATTTCAAAATCCTACTCAGGATCATTGCTTTATCAAATTA
1 ATTTCAAAATCCTGCTCAGGATCATTGCTTTATCAAATTA
9171 ATTTCAAAATCCTGCTCAGGATCATTGCTTTATCAAATTA
1 ATTTCAAAATCCTGCTCAGGATCATTGCTTTATCAAATTA
* * * *
9211 ATTTCAAAATCCTACTCGGGATCATTGCTTTATCAAGTGA
1 ATTTCAAAATCCTGCTCAGGATCATTGCTTTATCAAATTA
* * * *
9251 ATTTCAGAATCCTGTTCAGGATCATTTGCTTTATC-AGTCA
1 ATTTCAAAATCCTGCTCAGGATCA-TTGCTTTATCAAATTA
9291 ATTTCAAAAATCCT
1 ATTTC-AAAATCCT
9305 ATTCAGGACC
Statistics
Matches: 815, Mismatches: 61, Indels: 35
0.89 0.07 0.04
Matches are distributed among these distances:
39 11 0.01
40 776 0.95
41 28 0.03
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.38
Consensus pattern (40 bp):
ATTTCAAAATCCTGCTCAGGATCATTGCTTTATCAAATTA
Found at i:9336 original size:40 final size:41
Alignment explanation
Indices: 9090--9328 Score: 138
Period size: 40 Copynumber: 6.0 Consensus size: 41
9080 TTATCAAATT
* * * * *
9090 AATTTC-AAAATCCTACTCAGGATCA-TTGCTTTATCAAATT
1 AATTTCAAAAATCCTATTCAGGACCAGTGGCTTTATC-AGTC
* * * * *
9130 AATTTC-AAAATCCTACTCAGGATCA-TTGCTTTATCAAATT
1 AATTTCAAAAATCCTATTCAGGACCAGTGGCTTTATC-AGTC
** * * * *
9170 AATTTC-AAAATCCTGCTCAGGATCA-TTGCTTTATCAAATT
1 AATTTCAAAAATCCTATTCAGGACCAGTGGCTTTATC-AGTC
* * * * *
9210 AATTTC-AAAATCCTACTCGGGATCA-TTGCTTTATCAAGTG
1 AATTTCAAAAATCCTATTCAGGACCAGTGGCTTTATC-AGTC
* * * * *
9250 AATTTC-AGAATCCTGTTCAGGATCATTTGCTTTATCAGTC
1 AATTTCAAAAATCCTATTCAGGACCAGTGGCTTTATCAGTC
9290 AATTTCAAAAATCCTATTCAGGACCAGTGGC-TTATCAGT
1 AATTTCAAAAATCCTATTCAGGACCAGTGGCTTTATCAGT
9329 TGATTTCAGC
Statistics
Matches: 182, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
40 153 0.84
41 29 0.16
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (41 bp):
AATTTCAAAAATCCTATTCAGGACCAGTGGCTTTATCAGTC
Done.