Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013366.1 Corchorus olitorius cultivar O-4 contig13399, 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: 15386
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:260 original size:20 final size:20
Alignment explanation
Indices: 219--261 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
209 CTCTCACAAG
* *
219 TTTCTAGCCGTTGGAGCTCT
1 TTTCTAGCCGTTAGAGCACT
*
239 TTTCTAGCCGTTATAGCACT
1 TTTCTAGCCGTTAGAGCACT
259 TTT
1 TTT
262 TCCACTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (20 bp):
TTTCTAGCCGTTAGAGCACT
Found at i:2729 original size:28 final size:27
Alignment explanation
Indices: 2687--2741 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
2677 ACTGAGACTA
*
2687 GACTCGAAACTGACTCGAAAAAACAAACT
1 GACTCGAAACCGACTC--AAAAACAAACT
2716 GACTC-AAACCGACTCAAAAACAAACT
1 GACTCGAAACCGACTCAAAAACAAACT
2742 CAAATAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 11 0.44
28 9 0.36
29 5 0.20
ACGTcount: A:0.49, C:0.27, G:0.11, T:0.13
Consensus pattern (27 bp):
GACTCGAAACCGACTCAAAAACAAACT
Found at i:9922 original size:114 final size:112
Alignment explanation
Indices: 9720--9964 Score: 409
Period size: 114 Copynumber: 2.2 Consensus size: 112
9710 TGTAGCCATA
** *
9720 AGTGCCCTTCCTTGTTGATGATTTTGGCCAATGTAGCCCATTGAAAAAAAAATTATATTTTGACT
1 AGTGCCCTTCCTTGTTGATGATTACGGCCAATGTAGCCCATTAAAAAAAAAATTATATTTTGACT
9785 TGGAGTGAGTGCACCCTTAGGAGTGCTGCACTAGTTGCACCTCCAGG
66 TGGAGTGAGTGCACCCTTAGGAGTGCTGCACTAGTTGCACCTCCAGG
* *
9832 AGTGCCCTTCCTTGTTGATGATTACGGCCTATGTAGTCCATTAAAAAAAAGAATCTATATTTTGA
1 AGTGCCCTTCCTTGTTGATGATTACGGCCAATGTAGCCCATTAAAAAAAA-AAT-TATATTTTGA
* *
9897 CTTGGAGTGAGTGCACCCTTAGGAGTGTTGCACTGGTTGCACCTCCAGG
64 CTTGGAGTGAGTGCACCCTTAGGAGTGCTGCACTAGTTGCACCTCCAGG
9946 AGTGCCCTTCCTTGTTGAT
1 AGTGCCCTTCCTTGTTGAT
9965 ACTTCTAGCC
Statistics
Matches: 124, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
112 45 0.36
113 3 0.02
114 76 0.61
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (112 bp):
AGTGCCCTTCCTTGTTGATGATTACGGCCAATGTAGCCCATTAAAAAAAAAATTATATTTTGACT
TGGAGTGAGTGCACCCTTAGGAGTGCTGCACTAGTTGCACCTCCAGG
Found at i:9992 original size:114 final size:112
Alignment explanation
Indices: 9763--9993 Score: 315
Period size: 114 Copynumber: 2.0 Consensus size: 112
9753 TAGCCCATTG
9763 AAAAAAAAATTATATTTTGACTTGGAGTGAGTGCACCCTTAGGAGTGCTGCACTAGTTGCACCTC
1 AAAAAAAAATTATATTTTGACTTGGAGTGAGTGCACCCTTAGGAGTGCTGCACTAGTTGCACCTC
* * * * *
9828 CAGGAGTGCCCTTCCTTGTTGATGATTACGGCCTATGTAGTCCATTAA
66 CAGGAGTGCCCTTCCTTGTTGATGATTACAGCCGATGAACTCCA-AAA
* * *
9876 AAAAAAGAATCTATATTTTGACTTGGAGTGAGTGCACCCTTAGGAGTGTTGCACTGGTTGCACCT
1 AAAAAAAAAT-TATATTTTGACTTGGAGTGAGTGCACCCTTAGGAGTGCTGCACTAGTTGCACCT
*
9941 CCAGGAGTGCCCTTCCTTGTTGAT-ACTT-CTAGCCGATGCAACT-TAAAA
65 CCAGGAGTGCCCTTCCTTGTTGATGA-TTAC-AGCCGATG-AACTCCAAAA
9989 AAAAA
1 AAAAA
9994 GGCTTACAAT
Statistics
Matches: 105, Mismatches: 9, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
113 18 0.17
114 85 0.81
115 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (112 bp):
AAAAAAAAATTATATTTTGACTTGGAGTGAGTGCACCCTTAGGAGTGCTGCACTAGTTGCACCTC
CAGGAGTGCCCTTCCTTGTTGATGATTACAGCCGATGAACTCCAAAA
Found at i:10440 original size:159 final size:159
Alignment explanation
Indices: 10151--10471 Score: 633
Period size: 159 Copynumber: 2.0 Consensus size: 159
10141 AGACGGTGTC
10151 TTTTACTTATGAAATTAAATGATACTTACTTTCAACGTGATGGCGTATACTCTCTTCCATATGGT
1 TTTTACTTATGAAATTAAATGATACTTACTTTCAACGTGATGGCGTATACTCTCTTCCATATGGT
10216 GTTGGCCAATTATCATTTGCTTCCGAATATCATGAAGCACATCCTCATGGTGTTGGCGAATTACC
66 GTTGGCCAATTATCATTTGCTTCCGAATATCATGAAGCACATCCTCATGGTGTTGGCGAATTACC
10281 ACTTCTTCCAATGTGAAAAGTATATGGTG
131 ACTTCTTCCAATGTGAAAAGTATATGGTG
10310 TTTTACTTATGAAATTAAATGATACTTACTTTCAACGTGATGGCGTATACTCTCTTCCATATGGT
1 TTTTACTTATGAAATTAAATGATACTTACTTTCAACGTGATGGCGTATACTCTCTTCCATATGGT
*
10375 GTTGGCCAATTATCATTTGCTTCCGAATGTCATGAAGCACATCCTCATGGTGTTGGCGAATTACC
66 GTTGGCCAATTATCATTTGCTTCCGAATATCATGAAGCACATCCTCATGGTGTTGGCGAATTACC
10440 ACTTCTTCCAATGTGAAAAGTATATGGTG
131 ACTTCTTCCAATGTGAAAAGTATATGGTG
10469 TTT
1 TTT
10472 GCGGAACTAT
Statistics
Matches: 161, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
159 161 1.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (159 bp):
TTTTACTTATGAAATTAAATGATACTTACTTTCAACGTGATGGCGTATACTCTCTTCCATATGGT
GTTGGCCAATTATCATTTGCTTCCGAATATCATGAAGCACATCCTCATGGTGTTGGCGAATTACC
ACTTCTTCCAATGTGAAAAGTATATGGTG
Found at i:10613 original size:39 final size:39
Alignment explanation
Indices: 10565--10641 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
10555 TTCGCTTTAA
* *
10565 ACATCAAAGGCATGTGGTATTTGCAATGTGGTATTCGCG
1 ACATCAAAGGCATGTGGCATTCGCAATGTGGTATTCGCG
*
10604 ACATCAAAGGCATGTGGCATTCGCGATGTGGTATTCGC
1 ACATCAAAGGCATGTGGCATTCGCAATGTGGTATTCGC
10642 AATGTGGTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.29
Consensus pattern (39 bp):
ACATCAAAGGCATGTGGCATTCGCAATGTGGTATTCGCG
Found at i:10634 original size:14 final size:14
Alignment explanation
Indices: 10615--10658 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
10605 CATCAAAGGC
* *
10615 ATGTGGCATTCGCG
1 ATGTGGTATTCGCA
10629 ATGTGGTATTCGCA
1 ATGTGGTATTCGCA
*
10643 ATGTGGTATTCACA
1 ATGTGGTATTCGCA
10657 AT
1 AT
10659 ATATTATTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (14 bp):
ATGTGGTATTCGCA
Found at i:11111 original size:43 final size:42
Alignment explanation
Indices: 11051--11200 Score: 174
Period size: 43 Copynumber: 3.7 Consensus size: 42
11041 TCTTTCAATG
*
11051 TCAATTTCAAAGGCATATGGTGTTCGCGAGACTATGCCCTCTT
1 TCAATGTCAAAGGCATATGGTGTTCGCGA-ACTATGCCCTCTT
* *
11094 TCAATGTCAAAGACATATGGTGTT-------TGTG-CCTCTT
1 TCAATGTCAAAGGCATATGGTGTTCGCGAACTATGCCCTCTT
*
11128 TCAATGTCAAAGGCATATGGTGTTCGCGAAACTATCACCCTCTT
1 TCAATGTCAAAGGCATATGGTGTTCGCG-AACTAT-GCCCTCTT
11172 TCAATGTCAAA-GCATATGGTGTTCGCGAA
1 TCAATGTCAAAGGCATATGGTGTTCGCGAA
11201 GTACCACCTC
Statistics
Matches: 91, Mismatches: 6, Indels: 21
0.77 0.05 0.18
Matches are distributed among these distances:
34 29 0.32
35 3 0.03
42 4 0.04
43 38 0.42
44 17 0.19
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (42 bp):
TCAATGTCAAAGGCATATGGTGTTCGCGAACTATGCCCTCTT
Found at i:11144 original size:77 final size:77
Alignment explanation
Indices: 11051--11194 Score: 245
Period size: 77 Copynumber: 1.9 Consensus size: 77
11041 TCTTTCAATG
* * *
11051 TCAATTTCAAAGGCATATGGTGTTCGCGAGACTAT-GCCCTCTTTCAATGTCAAAGACATATGGT
1 TCAATGTCAAAGGCATATGGTGTTCGCGAAACTATCACCCTCTTTCAATGTCAAAG-CATATGGT
11115 GTTTGTGCCTCTT
65 GTTTGTGCCTCTT
11128 TCAATGTCAAAGGCATATGGTGTTCGCGAAACTATCACCCTCTTTCAATGTCAAAGCATATGGTG
1 TCAATGTCAAAGGCATATGGTGTTCGCGAAACTATCACCCTCTTTCAATGTCAAAGCATATGGTG
11193 TT
66 TT
11195 CGCGAAGTAC
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
77 44 0.70
78 19 0.30
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (77 bp):
TCAATGTCAAAGGCATATGGTGTTCGCGAAACTATCACCCTCTTTCAATGTCAAAGCATATGGTG
TTTGTGCCTCTT
Found at i:11223 original size:30 final size:30
Alignment explanation
Indices: 11187--11247 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
11177 GTCAAAGCAT
* *
11187 ATGGTGTTCGCGAAGTAC-CACCTCCTTCCA
1 ATGGTGTTAGCGAAGT-CTCACATCCTTCCA
11217 ATGGTGTTAGCGAAGTCTCACATCCTTCCA
1 ATGGTGTTAGCGAAGTCTCACATCCTTCCA
11247 A
1 A
11248 CGTCCTGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 1 0.04
30 27 0.96
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.28
Consensus pattern (30 bp):
ATGGTGTTAGCGAAGTCTCACATCCTTCCA
Found at i:11308 original size:51 final size:51
Alignment explanation
Indices: 11253--11373 Score: 188
Period size: 51 Copynumber: 2.4 Consensus size: 51
11243 TCCAACGTCC
* * *
11253 TGAAGCCTTTTGCATATGGTGTTCGCAAAATATCAACTCTTTCCAATATTA
1 TGAAGTCTTTTGCATATGGTGTTCACAAAATATCAACTCCTTCCAATATTA
*
11304 TGAAGTCTTTTGCATATGGTGTTCACAAAATATCACCTCCTTCCAATATTA
1 TGAAGTCTTTTGCATATGGTGTTCACAAAATATCAACTCCTTCCAATATTA
* *
11355 TGAAGTTTTTTGTATATGG
1 TGAAGTCTTTTGCATATGG
11374 CATTGGCGAA
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 64 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (51 bp):
TGAAGTCTTTTGCATATGGTGTTCACAAAATATCAACTCCTTCCAATATTA
Found at i:11389 original size:51 final size:51
Alignment explanation
Indices: 11253--11401 Score: 172
Period size: 51 Copynumber: 2.9 Consensus size: 51
11243 TCCAACGTCC
* ** * * *
11253 TGAAGCCTTTTGCATATGGTGTTCGCAAAATATCAACTCTTTCCAATATTA
1 TGAAGTCTTTTGCATATGGCATTCACAAAATATCACCTCCTTCCAATATTA
**
11304 TGAAGTCTTTTGCATATGGTGTTCACAAAATATCACCTCCTTCCAATATTA
1 TGAAGTCTTTTGCATATGGCATTCACAAAATATCACCTCCTTCCAATATTA
* * ** * *
11355 TGAAGTTTTTTGTATATGGCATTGGCGAACTATCACCTCCTTCCAAT
1 TGAAGTCTTTTGCATATGGCATTCACAAAATATCACCTCCTTCCAAT
11402 GTCGAAGGGT
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 86 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.38
Consensus pattern (51 bp):
TGAAGTCTTTTGCATATGGCATTCACAAAATATCACCTCCTTCCAATATTA
Found at i:11475 original size:31 final size:32
Alignment explanation
Indices: 11410--11497 Score: 124
Period size: 31 Copynumber: 2.8 Consensus size: 32
11400 ATGTCGAAGG
* *
11410 GTACATCCTCTTCCATATGGTGTTATCAAGAA
1 GTACACCCTCTTCCATATGGTGTTGTCAAGAA
*
11442 GTACACCCTCTTCCATATGATGTTGT-AAGAA
1 GTACACCCTCTTCCATATGGTGTTGTCAAGAA
* *
11473 GTACACCATCTTCCACATGGTGTTG
1 GTACACCCTCTTCCATATGGTGTTG
11498 GCAAACTATC
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
31 27 0.54
32 23 0.46
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (32 bp):
GTACACCCTCTTCCATATGGTGTTGTCAAGAA
Found at i:11884 original size:36 final size:36
Alignment explanation
Indices: 11650--11888 Score: 316
Period size: 36 Copynumber: 6.6 Consensus size: 36
11640 TGCTCTGTCT
* * * *
11650 TTGGCTATAATGCTGATGGCCTAAGTCGCCTAATAA
1 TTGGCTATAATGCCGCTGGCCTTAGTCGCCCAATAA
* *
11686 TTGGCTATAAAGCCGCTGGCCTTAGTCGCCCAATAC
1 TTGGCTATAATGCCGCTGGCCTTAGTCGCCCAATAA
* * *
11722 TTGGCTATAATGCCGATGGCCTAAGTCGCCCAGTAA
1 TTGGCTATAATGCCGCTGGCCTTAGTCGCCCAATAA
* *
11758 TTGGCTATAAAGCCGCTGGCCTTAGTCGCCCAATAC
1 TTGGCTATAATGCCGCTGGCCTTAGTCGCCCAATAA
* * *
11794 TTGGCTATAATGCCGATGGCCTAAGTCGCCCAGTAA
1 TTGGCTATAATGCCGCTGGCCTTAGTCGCCCAATAA
* *
11830 TTGGCTATAAAGCCGCTGGCCTTAGTCGCCCAATAT
1 TTGGCTATAATGCCGCTGGCCTTAGTCGCCCAATAA
**
11866 TTGGCTATAATGTTGCTGGCCTT
1 TTGGCTATAATGCCGCTGGCCTT
11889 TGATGCCATT
Statistics
Matches: 174, Mismatches: 29, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 174 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (36 bp):
TTGGCTATAATGCCGCTGGCCTTAGTCGCCCAATAA
Found at i:11887 original size:72 final size:72
Alignment explanation
Indices: 11650--11877 Score: 420
Period size: 72 Copynumber: 3.2 Consensus size: 72
11640 TGCTCTGTCT
* * *
11650 TTGGCTATAATGCTGATGGCCTAAGTCGCCTAATAATTGGCTATAAAGCCGCTGGCCTTAGTCGC
1 TTGGCTATAATGCCGATGGCCTAAGTCGCCCAGTAATTGGCTATAAAGCCGCTGGCCTTAGTCGC
11715 CCAATAC
66 CCAATAC
11722 TTGGCTATAATGCCGATGGCCTAAGTCGCCCAGTAATTGGCTATAAAGCCGCTGGCCTTAGTCGC
1 TTGGCTATAATGCCGATGGCCTAAGTCGCCCAGTAATTGGCTATAAAGCCGCTGGCCTTAGTCGC
11787 CCAATAC
66 CCAATAC
11794 TTGGCTATAATGCCGATGGCCTAAGTCGCCCAGTAATTGGCTATAAAGCCGCTGGCCTTAGTCGC
1 TTGGCTATAATGCCGATGGCCTAAGTCGCCCAGTAATTGGCTATAAAGCCGCTGGCCTTAGTCGC
*
11859 CCAATAT
66 CCAATAC
11866 TTGGCTATAATG
1 TTGGCTATAATG
11878 TTGCTGGCCT
Statistics
Matches: 152, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 152 1.00
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.27
Consensus pattern (72 bp):
TTGGCTATAATGCCGATGGCCTAAGTCGCCCAGTAATTGGCTATAAAGCCGCTGGCCTTAGTCGC
CCAATAC
Found at i:12122 original size:46 final size:46
Alignment explanation
Indices: 12051--12187 Score: 193
Period size: 46 Copynumber: 3.0 Consensus size: 46
12041 GAGATGCATT
* *
12051 TTATGTGAGCACCCTTCTTCTGAAAGAATACTCTATACAGTAGCTC
1 TTATGTGAGCACCCTTCTTCAGAAAGAATACTCTATACGGTAGCTC
** * *
12097 TTATGTGAGCACATTTCTTCAGAAAGAAAACTCTACACGGTAGCTC
1 TTATGTGAGCACCCTTCTTCAGAAAGAATACTCTATACGGTAGCTC
* * *
12143 TTATGTGAGCACCCATCTTTAGAAAGAATTCTCTATACGGTAGCT
1 TTATGTGAGCACCCTTCTTCAGAAAGAATACTCTATACGGTAGCT
12188 TCTTGCAAAG
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 78 1.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (46 bp):
TTATGTGAGCACCCTTCTTCAGAAAGAATACTCTATACGGTAGCTC
Found at i:12736 original size:45 final size:45
Alignment explanation
Indices: 12672--12773 Score: 125
Period size: 45 Copynumber: 2.3 Consensus size: 45
12662 CTCCAAGGTG
* * * *
12672 TTGAACATGGGAGATACACAAATGGT-TTCCACCATGATAAAGGCA
1 TTGAACCTGAGAGATACACAAATGGTCTT-CACCATGACAAAGACA
*
12717 TTGAACCTGAGAGATACACAAATTGTCTTCACCATGACAAAGACA
1 TTGAACCTGAGAGATACACAAATGGTCTTCACCATGACAAAGACA
* *
12762 CTAAACCTGAGA
1 TTGAACCTGAGA
12774 AATAAATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
45 47 0.96
46 2 0.04
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.22
Consensus pattern (45 bp):
TTGAACCTGAGAGATACACAAATGGTCTTCACCATGACAAAGACA
Found at i:13920 original size:27 final size:27
Alignment explanation
Indices: 13889--13952 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
13879 TAGGTATTGA
*
13889 TATTGCTAGAAGGTAATTGCCACATAG-
1 TATTGCAAGAAGGTAATTGCCACAT-GT
*
13916 TATTGCAAGAGGGTAATTGCCACATGT
1 TATTGCAAGAAGGTAATTGCCACATGT
13943 TATTGCAAGA
1 TATTGCAAGA
13953 TGGTGCAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 1 0.03
27 33 0.97
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (27 bp):
TATTGCAAGAAGGTAATTGCCACATGT
Done.