Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012173.1 Corchorus olitorius cultivar O-4 contig12206, 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: 33658
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7528 original size:20 final size:21
Alignment explanation
Indices: 7505--7581 Score: 79
Period size: 20 Copynumber: 3.7 Consensus size: 21
7495 GATGTAATTT
*
7505 TTAATAATTATATA-TAATTA
1 TTAATAATTATATATTAATAA
*
7525 TTAAAAATTAT-TATTAATAA
1 TTAATAATTATATATTAATAA
*
7545 TT-ATAAATTTTATCATTAATAA
1 TTAAT-AATTATAT-ATTAATAA
*
7567 GTAATAATTATATAT
1 TTAATAATTATATAT
7582 AACCAATCGA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
19 3 0.07
20 22 0.48
21 3 0.07
22 16 0.35
23 2 0.04
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (21 bp):
TTAATAATTATATATTAATAA
Found at i:7557 original size:22 final size:23
Alignment explanation
Indices: 7518--7566 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
7508 ATAATTATAT
*
7518 ATAATTATTAAAAATTATTATTA
1 ATAATTATTAAAAATTATCATTA
**
7541 ATAATTA-TAAATTTTATCATTA
1 ATAATTATTAAAAATTATCATTA
7563 ATAA
1 ATAA
7567 GTAATAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
ATAATTATTAAAAATTATCATTA
Found at i:13513 original size:8 final size:8
Alignment explanation
Indices: 13502--13535 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
13492 TACTTTATTT
13502 TTTTTTTG
1 TTTTTTTG
13510 TTTTTTTG
1 TTTTTTTG
*
13518 TTTTTGTG
1 TTTTTTTG
13526 TTCTTTTTG
1 TT-TTTTTG
13535 T
1 T
13536 AACTTTGCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 17 0.74
9 6 0.26
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (8 bp):
TTTTTTTG
Found at i:19599 original size:21 final size:21
Alignment explanation
Indices: 19565--19614 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
19555 CTCCAGCTAG
** *
19565 GCACCCAGGTCGTAAGACTGA
1 GCACCCAGCCCGTAAGACGGA
* *
19586 GCACCCAGCCCGTAGGCCGGA
1 GCACCCAGCCCGTAAGACGGA
19607 GCACCCAG
1 GCACCCAG
19615 GCTCAAGCTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.38, G:0.30, T:0.08
Consensus pattern (21 bp):
GCACCCAGCCCGTAAGACGGA
Found at i:25281 original size:6 final size:6
Alignment explanation
Indices: 25270--25299 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
25260 CAATATTTGC
*
25270 TTTAGT TTTAGT CTTAGT TTTAGT TTTAGT
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT
25300 GTTTCATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.03, G:0.17, T:0.63
Consensus pattern (6 bp):
TTTAGT
Found at i:27689 original size:39 final size:39
Alignment explanation
Indices: 27632--28067 Score: 497
Period size: 39 Copynumber: 10.9 Consensus size: 39
27622 CGACACCAGT
* *
27632 TTTTCAGAGTTTTGAATTTAGGGAAAGATCCCATCCAA-
1 TTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCCAAG
* * *
27670 CTTTCAAAAGTTTTCAATTTAGTGAAAGATCCCATCAAGAAG
1 TTTTC-AAAGTTTTCAATTTAGGGAAAGATCCCATC--CAAG
**
27712 TTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATTAAGAAG
1 -TTTTCAAAGTTTTCAATTTAGGGAAAGATCCCA-T-CCAAG
*
27754 TTTTGCAAAGTTTTCAATTTAGGAAAAGATCCCATCC-AG
1 TTTT-CAAAGTTTTCAATTTAGGGAAAGATCCCATCCAAG
**
27793 TTTTCAAAAGTTTTCAATTTAGGGAAAGATCCCATTAAGAAG
1 TTTTC-AAAGTTTTCAATTTAGGGAAAGATCCCA-T-CCAAG
27835 TTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCC-AG
1 -TTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCCAAG
* * *
27874 TTTTTAAAAGTTTTTAATTTAGGGAAAGATTCCATCATCAAG
1 -TTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATC--CAAG
* *
27916 TTTTTCAAAGTTTTTAATTTAGGGAAAGATCTCAT-CAAG
1 -TTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCCAAG
27955 TTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCAT-CAAG
1 -TTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCCAAG
* * * *
27994 TTTTTTAAGGTTTTCAATTTAGAGAAAGATCCCATTC-AG
1 -TTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCCAAG
*
28033 TTTTCAAAGTTTTCAATTAAGGGAAAGATCCCATC
1 TTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATC
28068 AAAAAGCATT
Statistics
Matches: 349, Mismatches: 32, Indels: 34
0.84 0.08 0.08
Matches are distributed among these distances:
38 35 0.10
39 170 0.49
40 2 0.01
41 9 0.03
42 123 0.35
43 10 0.03
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (39 bp):
TTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCCAAG
Found at i:27795 original size:81 final size:81
Alignment explanation
Indices: 27627--28084 Score: 542
Period size: 81 Copynumber: 5.7 Consensus size: 81
27617 TGTTGCGACA
* * * *
27627 CCAGTTTTTCAGAGTTTTGAATTTAGGGAAAGATCCCA-T-CCAA--CTTTCAAAAGTTTTCAAT
1 CCAGTTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATTAACAAGTTTTTC-AAAGTTTTCAAT
27688 TTAGTG-AAAGATCCCAT
65 TTAG-GAAAAGATCCCAT
* * *
27705 CAAGAAGTTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATTAAGAAGTTTTGCAAAGTTTTCA
1 C---CAGTTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATTAACAAGTTTTTCAAAGTTTTCA
27770 ATTTAGGAAAAGATCCCAT
63 ATTTAGGAAAAGATCCCAT
*
27789 CCAG-TTTTCAAAAGTTTTCAATTTAGGGAAAGATCCCATTAAGAAGTTTTTCAAAGTTTTCAAT
1 CCAGTTTTTC-AAAGTTTTCAATTTAGGGAAAGATCCCATTAACAAGTTTTTCAAAGTTTTCAAT
*
27853 TTAGGGAAAGATCCCAT
65 TTAGGAAAAGATCCCAT
* * * * * *
27870 CCAGTTTTTAAAAGTTTTTAATTTAGGGAAAGATTCCATCATCAAGTTTTTCAAAGTTTTTAATT
1 CCAGTTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATTAACAAGTTTTTCAAAGTTTTCAATT
* *
27935 TAGGGAAAGATCTCAT
66 TAGGAAAAGATCCCAT
* * *
27951 CAAGTTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCA-T--CAAGTTTTTTAAGGTTTTCAATT
1 CCAGTTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATTAACAAGTTTTTCAAAGTTTTCAATT
28013 TA-GAGAAAGATCCCAT
66 TAGGA-AAAGATCCCAT
* * * *
28029 TCAG-TTTTCAAAGTTTTCAATTAAGGGAAAGATCCCATCAAAAAGCATTTTTCAAA
1 CCAGTTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATTAACAAG--TTTTTCAAA
28085 AAGAGTCGTT
Statistics
Matches: 329, Mismatches: 35, Indels: 28
0.84 0.09 0.07
Matches are distributed among these distances:
77 33 0.10
78 35 0.11
80 8 0.02
81 207 0.63
82 12 0.04
83 3 0.01
84 28 0.09
85 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (81 bp):
CCAGTTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATTAACAAGTTTTTCAAAGTTTTCAATT
TAGGAAAAGATCCCAT
Found at i:27848 original size:123 final size:119
Alignment explanation
Indices: 27629--28084 Score: 587
Period size: 123 Copynumber: 3.8 Consensus size: 119
27619 TTGCGACACC
* * * ** *
27629 AGTTTTTCAGAGTTTTGAATTTAGGGAAAGATCCCATCCAACTTTCAAAAGTTTTCAATTTAGTG
1 AGTTTTTCAAAGTTTTCAATTTAGGAAAAGATCCCATCCAGTTTTC-AAAGTTTTCAATTTAGGG
*
27694 AAAGATCCCATCAAGAAGTTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATTAAGA
65 AAAGATCCCATCAAGAAGTTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCA-T--CA
*
27752 AGTTTTGCAAAGTTTTCAATTTAGGAAAAGATCCCATCCAGTTTTCAAAAGTTTTCAATTTAGGG
1 AGTTTTTCAAAGTTTTCAATTTAGGAAAAGATCCCATCCAGTTTTC-AAAGTTTTCAATTTAGGG
* *
27817 AAAGATCCCATTAAGAAGTTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCC
65 AAAGATCCCATCAAGAAGTTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCA
* * * * *
27872 AGTTTTTAAAAGTTTTTAATTTAGGGAAAGATTCCATCATCAAGTTTTTCAAAGTTTTTAATTTA
1 AGTTTTTCAAAGTTTTCAATTTAGGAAAAGA-TCC--CATCCAG-TTTTCAAAGTTTTCAATTTA
*
27937 GGGAAAGATCTCATC---AAGTTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCA
62 GGGAAAGATCCCATCAAGAAGTTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCA
* * * *
27992 AGTTTTTTAAGGTTTTCAATTTA-GAGAAAGATCCCATTCAGTTTTCAAAGTTTTCAATTAAGGG
1 AGTTTTTCAAAGTTTTCAATTTAGGA-AAAGATCCCATCCAGTTTTCAAAGTTTTCAATTTAGGG
*
28056 AAAGATCCCATCAAAAAGCATTTTTCAAA
65 AAAGATCCCATCAAGAAG--TTTTTCAAA
28085 AAGAGTCGTT
Statistics
Matches: 295, Mismatches: 28, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
116 32 0.11
117 5 0.02
119 7 0.02
120 91 0.31
121 12 0.04
122 1 0.00
123 142 0.48
124 5 0.02
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (119 bp):
AGTTTTTCAAAGTTTTCAATTTAGGAAAAGATCCCATCCAGTTTTCAAAGTTTTCAATTTAGGGA
AAGATCCCATCAAGAAGTTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCA
Found at i:30070 original size:7 final size:8
Alignment explanation
Indices: 30051--30079 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
30041 TGTCACTGTA
30051 AAAAATAC
1 AAAAATAC
30059 AAAAATAC
1 AAAAATAC
30067 AAAAATAC
1 AAAAATAC
30075 AAAAA
1 AAAAA
30080 CATAGAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAATAC
Found at i:30088 original size:16 final size:16
Alignment explanation
Indices: 30051--30104 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
30041 TGTCACTGTA
*
30051 AAAAATACAAAAATAC
1 AAAAATACAAAAACAC
*
30067 AAAAATACAAAAACAT
1 AAAAATACAAAAACAC
*
30083 AGAAATTA-AAAAATCAC
1 A-AAAATACAAAAA-CAC
30100 AAAAA
1 AAAAA
30105 AAGGGGGTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 23 0.74
17 8 0.26
ACGTcount: A:0.74, C:0.11, G:0.02, T:0.13
Consensus pattern (16 bp):
AAAAATACAAAAACAC
Found at i:33613 original size:2 final size:2
Alignment explanation
Indices: 33606--33643 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
33596 TTTAAATTGA
* *
33606 AT AT AT AT GT GT AT AT AT AT AT AT -T AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33644 AGCATTGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Done.