Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021956.1 Corchorus olitorius cultivar O-4 contig21989, 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: 31133
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.29
Found at i:3733 original size:29 final size:29
Alignment explanation
Indices: 3688--3755 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
3678 CACAAATAAT
3688 ATTTTCAATTTGATCCTTACATTTTTCAA
1 ATTTTCAATTTGATCCTTACATTTTTCAA
* *
3717 TTTTTCAATTTGGTCCTTACATTTTTCAA
1 ATTTTCAATTTGATCCTTACATTTTTCAA
3746 ATTTTCAATT
1 ATTTTCAATT
3756 CCATCCCCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.25, C:0.16, G:0.04, T:0.54
Consensus pattern (29 bp):
ATTTTCAATTTGATCCTTACATTTTTCAA
Found at i:4301 original size:12 final size:14
Alignment explanation
Indices: 4284--4318 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
4274 TGAAAAGCCC
4284 GTGGCAAAA-A-TT
1 GTGGCAAAATAGTT
4296 GTGGCAAAATAGTT
1 GTGGCAAAATAGTT
4310 GTGGCAAAA
1 GTGGCAAAA
4319 CCCGCGGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.43
13 1 0.05
14 11 0.52
ACGTcount: A:0.40, C:0.09, G:0.29, T:0.23
Consensus pattern (14 bp):
GTGGCAAAATAGTT
Found at i:8930 original size:107 final size:108
Alignment explanation
Indices: 8731--8937 Score: 353
Period size: 107 Copynumber: 1.9 Consensus size: 108
8721 ATCAAAGCAC
* * ** *
8731 AATTTGGCTATGCCACGTGGCATGTTTGATGATATTTTCATGCCATACCATCATGTCAGGTTATA
1 AATTTGGCTATGCCACGTGGCATATTTGATGACATTTTCATGCCA-ACCATCATGTCAAATGATA
8796 TCTTAGATGATATGGCCTATCATATCATCATGCCATAACTTGAT
65 TCTTAGATGATATGGCCTATCATATCATCATGCCATAACTTGAT
8840 AATTTGGCTATGCCACGTGGCATATTTGATGACATTTTCATGCC-ACCATCATGTCAAATGATAT
1 AATTTGGCTATGCCACGTGGCATATTTGATGACATTTTCATGCCAACCATCATGTCAAATGATAT
8904 CTTAGATGATATGGCCTATCATATCATCATGCCA
66 CTTAGATGATATGGCCTATCATATCATCATGCCA
8938 CGTGGCATGA
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
107 51 0.55
109 42 0.45
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (108 bp):
AATTTGGCTATGCCACGTGGCATATTTGATGACATTTTCATGCCAACCATCATGTCAAATGATAT
CTTAGATGATATGGCCTATCATATCATCATGCCATAACTTGAT
Found at i:11353 original size:22 final size:22
Alignment explanation
Indices: 11328--11492 Score: 129
Period size: 22 Copynumber: 7.5 Consensus size: 22
11318 GGGAGATGAA
11328 CAAAATTTCATAGGGAGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
* * *
11350 CAAAA-ATCATAAGAAGGTTA-
1 CAAAATTTCATAGGGAGGTTAT
*
11370 CAAAATTTCATAAGGAAGGTTTAT
1 CAAAATTTCAT-AGGGAGG-TTAT
* ***
11394 TAAAATTTCATATTTAGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
* * *
11416 CAAAGTTTCATATGGAGTTTAT
1 CAAAATTTCATAGGGAGGTTAT
** * *
11438 CACGATTTCATAGGTA-ATTAT
1 CAAAATTTCATAGGGAGGTTAT
* * *
11459 TAAAATTTCATAGCGTGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
11481 CAAAATTTCATA
1 CAAAATTTCATA
11493 AAAATATTCA
Statistics
Matches: 110, Mismatches: 28, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
20 5 0.05
21 30 0.27
22 58 0.53
23 7 0.06
24 10 0.09
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
CAAAATTTCATAGGGAGGTTAT
Found at i:11367 original size:21 final size:22
Alignment explanation
Indices: 11327--11390 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
11317 AGGGAGATGA
* *
11327 ACAAAATTTCAT-AGGGAGGTT
1 ACAAAATATCATAAGGAAGGTT
11348 ATCAAAA-ATCATAA-GAAGGTT
1 A-CAAAATATCATAAGGAAGGTT
*
11369 ACAAAATTTCATAAGGAAGGTT
1 ACAAAATATCATAAGGAAGGTT
11391 TATTAAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
20 5 0.14
21 18 0.50
22 13 0.36
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.27
Consensus pattern (22 bp):
ACAAAATATCATAAGGAAGGTT
Found at i:14614 original size:30 final size:30
Alignment explanation
Indices: 14574--14630 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
14564 TCTAACTTTT
*
14574 ACTACCTACTAATTACACAAAA-TGAAATAA
1 ACTACATACTAATTACA-AAAATTGAAATAA
*
14604 ACTACATACTAATTTCAAAAATTGAAA
1 ACTACATACTAATTACAAAAATTGAAA
14631 ACAATGAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.53, C:0.18, G:0.04, T:0.26
Consensus pattern (30 bp):
ACTACATACTAATTACAAAAATTGAAATAA
Found at i:16027 original size:2 final size:2
Alignment explanation
Indices: 16020--16051 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16010 AGGAGCCAAG
16020 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16052 ATAAAATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17497 original size:41 final size:41
Alignment explanation
Indices: 17410--17655 Score: 291
Period size: 41 Copynumber: 5.8 Consensus size: 41
17400 CAATAACCAA
*
17410 AAAGTCCCCAAACACATATATAACACAG-GAGCACCT-TCATTAC
1 AAAGTCCCCAAACACATATATAACACAGAG-GCATCTAT-A-T-C
*
17453 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATC
*
17494 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTACTA-C
1 AAAGTCCCCAAACACATATATAACACAGAGGC-A-TCTA-TATC
* * *
17537 AAAGTACTCAAACACATATATAACACAGAGGCATTTATATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATC
* * *
17578 AAAGTCCCCAAACACATATATAACACAGGGGTATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATA-T-C
*
17621 AAAAGTCCTCAAACACATATATAACACAGAGGCAT
1 -AAAGTCCCCAAACACATATATAACACAGAGGCAT
17656 TTCTCCTTAT
Statistics
Matches: 177, Mismatches: 17, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
40 2 0.01
41 68 0.38
42 4 0.02
43 68 0.38
44 35 0.20
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.20
Consensus pattern (41 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATC
Found at i:17505 original size:84 final size:84
Alignment explanation
Indices: 17410--17655 Score: 404
Period size: 84 Copynumber: 2.9 Consensus size: 84
17400 CAATAACCAA
* *
17410 AAAGTCCCCAAACACATATATAACACAGGAGCACCT-TCATTACAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCT-ATTACAAAGTCCTCAAACACATATAT
17474 AACACAGAGGCATCTATATC
65 AACACAGAGGCATCTATATC
* *
17494 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTACTACAAAGTACTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
*
17559 ACACAGAGGCATTTATATC
66 ACACAGAGGCATCTATATC
* *
17578 AAAGTCCCCAAACACATATATAACACAGGGGTATCTCTATTACAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC-AAAGTCCTCAAACACATATAT
17643 AACACAGAGGCAT
65 AACACAGAGGCAT
17656 TTCTCCTTAT
Statistics
Matches: 151, Mismatches: 9, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
84 117 0.77
85 34 0.23
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.20
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC
Found at i:17794 original size:2 final size:2
Alignment explanation
Indices: 17789--17826 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
17779 TATATATATA
17789 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
17827 ACAAAGGCCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Done.