Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019096.1 Corchorus olitorius cultivar O-4 contig19129, 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: 56209
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2178 original size:14 final size:15
Alignment explanation
Indices: 2155--2187 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2145 ATTCCCTCCC
*
2155 AATTATGGATTAATT
1 AATTATGGATTAAGT
2170 AATTA-GGATTAAGT
1 AATTATGGATTAAGT
2184 AATT
1 AATT
2188 TTAATGGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (15 bp):
AATTATGGATTAAGT
Found at i:9269 original size:104 final size:105
Alignment explanation
Indices: 9029--9288 Score: 400
Period size: 106 Copynumber: 2.5 Consensus size: 105
9019 AGTTTAGCCT
*
9029 TAATTTCACTAAATTTAGCCCCAAA-TAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAATTTAG-CCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
9093 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
65 AATAA-TTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
* *
9135 TAATTTCACTAAATTTAGCCCAAATTAAATTTTTATTTTTATTTTAAGGGTAAATTCCATAATTA
1 TAATTTCACTAAATTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
* *
9200 ATAA-TATTGTTATAGGGTTTTAGAAATAAAATATATAAC
66 ATAATTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
* ** *
9239 TAA-TTCACTAAGTTTAGCCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAATTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
9289 TAGAAAAATT
Statistics
Matches: 143, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
103 42 0.29
104 36 0.25
105 6 0.04
106 59 0.41
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (105 bp):
TAATTTCACTAAATTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
ATAATTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:10577 original size:10 final size:10
Alignment explanation
Indices: 10562--10588 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
10552 TAAACATTAG
10562 CAAATTGCAC
1 CAAATTGCAC
10572 CAAATTGCAC
1 CAAATTGCAC
10582 CAAATTG
1 CAAATTG
10589 GGCCTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.26, G:0.11, T:0.22
Consensus pattern (10 bp):
CAAATTGCAC
Found at i:11376 original size:31 final size:31
Alignment explanation
Indices: 11341--11417 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
11331 TTTTTCTGTT
* *
11341 TTTAGGCTCAAATTGAGCAATTTTTGAAA-TG
1 TTTAGGCTCAAATTGAGCAACTTTT-AAAGGG
*
11372 TTTAGACTCAAATTGAGCAACTTTTAAAGGG
1 TTTAGGCTCAAATTGAGCAACTTTTAAAGGG
*
11403 TTTAAGCTCAAATTG
1 TTTAGGCTCAAATTG
11418 GTAATTTGGC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 3 0.08
31 37 0.93
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (31 bp):
TTTAGGCTCAAATTGAGCAACTTTTAAAGGG
Found at i:14919 original size:106 final size:105
Alignment explanation
Indices: 14692--14978 Score: 418
Period size: 106 Copynumber: 2.7 Consensus size: 105
14682 TTTCTAACCT
* ** * *
14692 TTAAAATAAAATTTTAATTTTAATTT-GGGATAAACTTAGTG-AATTAGTTATATATTTTATTTC
1 TTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTC
*
14755 TAAAACCCTATAACAATATTATTAATTATGGAATTTACCC
66 TAAAACCCTATAACAATATTATTAATTATGAAATTTACCC
*
14795 TTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTTC
1 TTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTC
* *
14860 T-AAACCCTATAACAATAAATTATTAATTTTGAAATTTACCT
66 TAAAACCCTATAACAAT--ATTATTAATTATGAAATTTACCC
* * *
14901 TTACAATGAAAATAAAATTTTAATTTGGGGCTAAATTTAGTGAAATTAGTTTTATATTTTATTTC
1 TTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTC
*
14966 TAAAACTCTATAA
66 TAAAACCCTATAA
14979 TAAAAAAACC
Statistics
Matches: 165, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
103 23 0.14
104 29 0.18
105 21 0.13
106 82 0.50
107 10 0.06
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (105 bp):
TTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTC
TAAAACCCTATAACAATATTATTAATTATGAAATTTACCC
Found at i:15716 original size:26 final size:27
Alignment explanation
Indices: 15668--15719 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
15658 TAGATGAGTA
** *
15668 AAATCCAAAAATCATTTATAAAGATCC
1 AAATCCAAAAAGAATATATAAAGATCC
15695 AAATCCAAAAAGAATATA-AAAGATC
1 AAATCCAAAAAGAATATATAAAGATC
15720 AATAATGTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.58, C:0.15, G:0.06, T:0.21
Consensus pattern (27 bp):
AAATCCAAAAAGAATATATAAAGATCC
Found at i:18598 original size:44 final size:44
Alignment explanation
Indices: 18548--18688 Score: 174
Period size: 54 Copynumber: 3.0 Consensus size: 44
18538 TCTTCCTCTG
* *
18548 ATTAAACTAGTAATATCCCACATCTATTAAGTTTGACACGACTA
1 ATTAAACTAGTAATATCACACATCTGTTAAGTTTGACACGACTA
18592 ATTAAACTAGTAATATCACACATCTGTTAAGTTTGACACGACTGGGTACTCTTA
1 ATTAAACTAGTAATATCACACATCTGTTAAGTTTG--AC-AC---G-A--C-TA
18646 ATTAAACTAGTAATATCACACATCTGTTAAGTTTGACACGACT
1 ATTAAACTAGTAATATCACACATCTGTTAAGTTTGACACGACT
18689 GAGTCTCTTA
Statistics
Matches: 85, Mismatches: 2, Indels: 20
0.79 0.02 0.19
Matches are distributed among these distances:
44 34 0.40
45 1 0.01
46 2 0.02
47 3 0.04
48 1 0.01
50 1 0.01
51 3 0.04
52 2 0.02
53 1 0.01
54 37 0.44
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (44 bp):
ATTAAACTAGTAATATCACACATCTGTTAAGTTTGACACGACTA
Found at i:18672 original size:54 final size:53
Alignment explanation
Indices: 18590--18698 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 53
18580 TTGACACGAC
*
18590 TAATTAAACTAGTAATATCACACATCTGTTAAGTTTGACACGACTGGGTACTCT
1 TAATTAAACTAGTAATATCACACATCTGTTAAGTTTGACACGACTGAGT-CTCT
18644 TAATTAAACTAGTAATATCACACATCTGTTAAGTTTGACACGACTGAGTCTCT
1 TAATTAAACTAGTAATATCACACATCTGTTAAGTTTGACACGACTGAGTCTCT
18697 TA
1 TA
18699 TATCAAAACT
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 6 0.11
54 48 0.89
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (53 bp):
TAATTAAACTAGTAATATCACACATCTGTTAAGTTTGACACGACTGAGTCTCT
Found at i:24332 original size:12 final size:13
Alignment explanation
Indices: 24311--24343 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
24301 TAAATCATTG
24311 AAAGGAAAAA-AA
1 AAAGGAAAAAGAA
*
24323 AAAGGGAAAAGAA
1 AAAGGAAAAAGAA
24336 AAAGGAAA
1 AAAGGAAA
24344 GTTGGGAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAGGAAAAAGAA
Found at i:26183 original size:207 final size:207
Alignment explanation
Indices: 25815--26202 Score: 485
Period size: 207 Copynumber: 1.9 Consensus size: 207
25805 AAACCCTCTA
* * *
25815 CTTCAGATCGCATTGTGAACGTTTGTTTAGGCATCTGAGTTGGTAGAACTTCTGTCATCATGCCT
1 CTTCAGATCGCATTGTAAAAGTTTGTTTAGGCATCTGAGCTGGTAGAACTTCTGTCATCATGCCT
* * * **
25880 GTCAACTTACTTCGTCCATCATCAAAACGCAAATGGTCACTCTTTAAATATTGTTCTGATATCCC
66 GTCAACTTAATCCGTCCATCATCAAAACGCAAACGGTCACTCTTTAAATATTGTTCCAATATCCC
* * * *
25945 CATTTGCATGCTAGAACTAGCACCTTGAGACATTCTCTTAGGTGCTGCATTGCTCGATATCCTAG
131 CATTTGCATGCTAGAACTAGCACCCTGAGACATTCTATGAGCTGCTGCATTGCTCGATATCCTAG
26010 CATGGCCATTCT
196 CATGGCCATTCT
* * * **
26022 CTTCAGATTGGATTGTAAAAGTTTGTTTAGGCATCTGAGCTGGTATAACTTCTGTTGTCATGCCT
1 CTTCAGATCGCATTGTAAAAGTTTGTTTAGGCATCTGAGCTGGTAGAACTTCTGTCATCATGCCT
** * * * * *
26087 GTCAACTTAATCCGTCCATCATCAAAGTGTAACCGGTCA-TTTTGTACATGTTGTTCCAATA-CC
66 GTCAACTTAATCCGTCCATCATCAAAACGCAAACGGTCACTCTT-TAAATATTGTTCCAATATCC
** *
26150 CCTATTTGCATGCTAGATGT-GCCCCCCTGAGACATTCTATGAGCTGCTGCATT
130 CC-ATTTGCATGCTAGAACTAG-CACCCTGAGACATTCTATGAGCTGCTGCATT
26203 ACCTGGCATT
Statistics
Matches: 151, Mismatches: 27, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
206 8 0.05
207 143 0.95
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (207 bp):
CTTCAGATCGCATTGTAAAAGTTTGTTTAGGCATCTGAGCTGGTAGAACTTCTGTCATCATGCCT
GTCAACTTAATCCGTCCATCATCAAAACGCAAACGGTCACTCTTTAAATATTGTTCCAATATCCC
CATTTGCATGCTAGAACTAGCACCCTGAGACATTCTATGAGCTGCTGCATTGCTCGATATCCTAG
CATGGCCATTCT
Found at i:53056 original size:26 final size:26
Alignment explanation
Indices: 53016--53065 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
53006 CCTTATACAG
*
53016 AGAGATAAACACAATCCATGTCAAAA
1 AGAGAAAAACACAATCCATGTCAAAA
*
53042 AGAGAAAAACTCAATCCATGTCAA
1 AGAGAAAAACACAATCCATGTCAA
53066 TCCATGAGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.52, C:0.20, G:0.12, T:0.16
Consensus pattern (26 bp):
AGAGAAAAACACAATCCATGTCAAAA
Found at i:55851 original size:25 final size:23
Alignment explanation
Indices: 55819--55874 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 23
55809 GTGGATTGTA
*
55819 AAAAAATTGAATAATTAAGACATT
1 AAAAAATTGAAGAATTAA-ACATT
*
55843 AAATAAATTTAAGAATTAAACATT
1 AAA-AAATTGAAGAATTAAACATT
55867 AAAAAATT
1 AAAAAATT
55875 CAAGGCTGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 5 0.17
24 11 0.38
25 13 0.45
ACGTcount: A:0.61, C:0.04, G:0.05, T:0.30
Consensus pattern (23 bp):
AAAAAATTGAAGAATTAAACATT
Done.