Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012822.1 Corchorus olitorius cultivar O-4 contig12855, 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: 24594
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:2760 original size:19 final size:20
Alignment explanation
Indices: 2736--2773 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2726 GCAATTAATT
*
2736 TTACCTAA-ATATACCTAAA
1 TTACCTAACATATAACTAAA
2755 TTACCTAACATATAACTAA
1 TTACCTAACATATAACTAA
2774 TGCATGTACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (20 bp):
TTACCTAACATATAACTAAA
Found at i:5555 original size:25 final size:25
Alignment explanation
Indices: 5521--5582 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
5511 CAGAGAGGAC
*
5521 TATAAAGTTTCTCACCATATTCTCT
1 TATAAAGTTTCTCACCACATTCTCT
5546 TATAAAGTTTCTCACCACATTCTCT
1 TATAAAGTTTCTCACCACATTCTCT
5571 TATAAAGTTTCT
1 TATAAAGTTTCT
5583 TTGGCAGTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.29, C:0.23, G:0.05, T:0.44
Consensus pattern (25 bp):
TATAAAGTTTCTCACCACATTCTCT
Found at i:8622 original size:42 final size:42
Alignment explanation
Indices: 8449--8640 Score: 241
Period size: 40 Copynumber: 4.6 Consensus size: 42
8439 CAAAGCTGAC
* **
8449 GGGATCTTTCCCTAAAGTGAAAACTTTTTGAAAAACTTCTTGAT
1 GGGATCTTTCCCTAAATTGAAAAC--TTTGAAAAACTTGATGAT
*
8493 GGGTTCTTTCCCTAAATTGAAAACTTTTGAAAAA-TT--TGAT
1 GGGATCTTTCCCTAAATTGAAAAC-TTTGAAAAACTTGATGAT
* * * **
8533 GGGATCTTTCCCTAATTTGGAAAC--TGGACGACTTGATGAT
1 GGGATCTTTCCCTAAATTGAAAACTTTGAAAAACTTGATGAT
8573 GGGATCTTTCCCTAAATTGAAAACTTTGAAAAACTTGATGAT
1 GGGATCTTTCCCTAAATTGAAAACTTTGAAAAACTTGATGAT
8615 GGGATCTTTCCCTAAATTGAAAACTT
1 GGGATCTTTCCCTAAATTGAAAACTT
8641 GAATTGATTT
Statistics
Matches: 130, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
37 4 0.03
38 2 0.02
40 51 0.39
42 41 0.32
43 10 0.08
44 22 0.17
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (42 bp):
GGGATCTTTCCCTAAATTGAAAACTTTGAAAAACTTGATGAT
Found at i:12115 original size:31 final size:31
Alignment explanation
Indices: 12080--12141 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
12070 CTAAGCCCAA
12080 TGTCCAAATGCAAGCCCAAAAGTCCAAGATC
1 TGTCCAAATGCAAGCCCAAAAGTCCAAGATC
*
12111 TGTCCAAATGCAAGCCCAAAAGTCTAAGATC
1 TGTCCAAATGCAAGCCCAAAAGTCCAAGATC
12142 CCAAAATGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.27, G:0.16, T:0.18
Consensus pattern (31 bp):
TGTCCAAATGCAAGCCCAAAAGTCCAAGATC
Found at i:12854 original size:61 final size:60
Alignment explanation
Indices: 12754--13123 Score: 400
Period size: 61 Copynumber: 6.2 Consensus size: 60
12744 TTGACTTTCA
* * * *
12754 TGAACTGTCTTTAGATTCA-TTTCTAAATATCATTGAGGAACTGTCTTCAGATCCATCTTCG
1 TGAACTGTCTTTAGATTCACTCT-TAAATACCTTTTAGGAACTGTCTTCAGATCCATCTT-G
* *
12815 TGAACTGTCTTAAGATTCACTCTTAAATACCTTTTAGGAACTGTCTTCAGAACCTATCTTCG
1 TGAACTGTCTTTAGATTCACTCTTAAATACCTTTTAGGAACTGTCTTCAGATCC-ATCTT-G
* *
12877 TGAACTGTCTTCAGTTTCACTCTTAAATACCTTTTAGGAACTGTCTT-AGAATCCATCTTTG
1 TGAACTGTCTTTAGATTCACTCTTAAATACCTTTTAGGAACTGTCTTCAG-ATCCATC-TTG
* * *
12938 TAAACTGTCTTCAGATTCACTCTTAAATACCTTTTAGGAGCTGTCTTCAGATCCATC-TG
1 TGAACTGTCTTTAGATTCACTCTTAAATACCTTTTAGGAACTGTCTTCAGATCCATCTTG
* * * * *
12997 TGAGCTGTCTTTAG-TCTCAATCTTAAA-ATCTTTAAGCAACTGTCTTCAGATCCATC-TG
1 TGAACTGTCTTTAGAT-TCACTCTTAAATACCTTTTAGGAACTGTCTTCAGATCCATCTTG
* * * *
13055 TGAGCTGTCTTTAG-TCTAAATCTTAAA-ATCC-TTAAGGAACTGTCTTCAGATCCAT-TTG
1 TGAACTGTCTTTAGAT-TCACTCTTAAATA-CCTTTTAGGAACTGTCTTCAGATCCATCTTG
*
13113 TGAGCTGTCTT
1 TGAACTGTCTT
13124 CAGTCTCAAT
Statistics
Matches: 278, Mismatches: 23, Indels: 19
0.87 0.07 0.06
Matches are distributed among these distances:
58 91 0.33
59 24 0.09
61 102 0.37
62 61 0.22
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (60 bp):
TGAACTGTCTTTAGATTCACTCTTAAATACCTTTTAGGAACTGTCTTCAGATCCATCTTG
Found at i:12973 original size:123 final size:120
Alignment explanation
Indices: 12754--13127 Score: 415
Period size: 123 Copynumber: 3.1 Consensus size: 120
12744 TTGACTTTCA
* * * * * *
12754 TGAACTGTCTTTAGATTCATTTCTAAATATCATTGAGGAACTGTCTTCAGATCCATCTTCGTGAA
1 TGAACTGTCTTCAGTTTCATCT-TAAATATCTTTAAGGAACTGTCTTCAGATCCATCTTTGTGAA
*
12819 CTGTCTTAAGATTCACTCTTAAATACCTTTTAGGAACTGTCTTCAGAACCTATCTTCG
65 CTGTCTTAAGATTCACTCTTAAATACCTTTTAGGAACTGTCTTCAGATCC-ATCTT-G
* * *
12877 TGAACTGTCTTCAGTTTCACTCTTAAATACCTTTTAGGAACTGTCTT-AGAATCCATCTTTGTAA
1 TGAACTGTCTTCAGTTTCA-TCTTAAATATCTTTAAGGAACTGTCTTCAG-ATCCATCTTTGTGA
* *
12941 ACTGTCTTCAGATTCACTCTTAAATACCTTTTAGGAGCTGTCTTCAGATCCATC-TG
64 ACTGTCTTAAGATTCACTCTTAAATACCTTTTAGGAACTGTCTTCAGATCCATCTTG
* * * * *
12997 TGAGCTGTCTTTAGTCTCAATCTTAAA-ATCTTTAAGCAACTGTCTTCAGATCCATC--TGTGAG
1 TGAACTGTCTTCAGTTTC-ATCTTAAATATCTTTAAGGAACTGTCTTCAGATCCATCTTTGTGAA
* * * *
13059 CTGTCTTTAG-TCTAAATCTTAAA-ATCC-TTAAGGAACTGTCTTCAGATCCAT-TTG
65 CTGTCTTAAGAT-TCACTCTTAAATA-CCTTTTAGGAACTGTCTTCAGATCCATCTTG
*
13113 TGAGCTGTCTTCAGT
1 TGAACTGTCTTCAGT
13128 CTCAATAATA
Statistics
Matches: 219, Mismatches: 25, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
116 40 0.18
117 24 0.11
119 23 0.11
120 25 0.11
121 2 0.01
122 5 0.02
123 98 0.45
124 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (120 bp):
TGAACTGTCTTCAGTTTCATCTTAAATATCTTTAAGGAACTGTCTTCAGATCCATCTTTGTGAAC
TGTCTTAAGATTCACTCTTAAATACCTTTTAGGAACTGTCTTCAGATCCATCTTG
Found at i:13049 original size:58 final size:60
Alignment explanation
Indices: 12789--13133 Score: 393
Period size: 58 Copynumber: 5.8 Consensus size: 60
12779 AATATCATTG
* *
12789 AGGAACTGTCTTCAGATCCATCTTCGTGAACTGTCTTAAGAT-TCACTCTTAAATACCTTTT
1 AGGAACTGTCTTCAGATCCATCTT-GTGAACTGTCTTCAG-TCTCAATCTTAAATACCTTTT
* * *
12850 AGGAACTGTCTTCAGAACCTATCTTCGTGAACTGTCTTCAGTTTCACTCTTAAATACCTTTT
1 AGGAACTGTCTTCAGATCC-ATCTT-GTGAACTGTCTTCAGTCTCAATCTTAAATACCTTTT
* *
12912 AGGAACTGTCTT-AGAATCCATCTTTGTAAACTGTCTTCAGAT-TCACTCTTAAATACCTTTT
1 AGGAACTGTCTTCAG-ATCCATC-TTGTGAACTGTCTTCAG-TCTCAATCTTAAATACCTTTT
* * * * *
12973 AGGAGCTGTCTTCAGATCCATC-TGTGAGCTGTCTTTAGTCTCAATCTTAAA-ATCTTTA
1 AGGAACTGTCTTCAGATCCATCTTGTGAACTGTCTTCAGTCTCAATCTTAAATACCTTTT
* * * * *
13031 AGCAACTGTCTTCAGATCCATC-TGTGAGCTGTCTTTAGTCTAAATCTTAAA-ATCC-TTA
1 AGGAACTGTCTTCAGATCCATCTTGTGAACTGTCTTCAGTCTCAATCTTAAATA-CCTTTT
*
13089 AGGAACTGTCTTCAGATCCAT-TTGTGAGCTGTCTTCAGTCTCAAT
1 AGGAACTGTCTTCAGATCCATCTTGTGAACTGTCTTCAGTCTCAAT
13134 AATAAAAGGA
Statistics
Matches: 257, Mismatches: 18, Indels: 21
0.87 0.06 0.07
Matches are distributed among these distances:
58 99 0.39
59 24 0.09
61 75 0.29
62 59 0.23
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (60 bp):
AGGAACTGTCTTCAGATCCATCTTGTGAACTGTCTTCAGTCTCAATCTTAAATACCTTTT
Found at i:13775 original size:64 final size:62
Alignment explanation
Indices: 13571--13808 Score: 233
Period size: 65 Copynumber: 3.7 Consensus size: 62
13561 TTCTTAAGAT
* * * * *
13571 ATCGTCTTCTGATCAACTTCTGAAAACTCTTTGAGAAACAATCTTCCGGTGCATCTTTTAACAAA
1 ATCGTCTTCCGATCAACTTCTGAAAA-TTTTTGAGAAACTATCTTTC-GTGCA-CTTTTAACAAG
* ** * * * *
13636 ATCGTCTTCCTATCAACTTCTGAATCCTTTTCGAGAAGCTATCTTCTGGTGTACTTTTTAACAAG
1 ATCGTCTTCCGATCAACTTCTGAA-AATTTTTGAGAAACTATCTT-TCGTGCAC-TTTTAACAAG
* * * * *
13701 ATTGTCTTCCGATCAACTTCTGAATATTTTTGAGAAACTATATTATCGTGGACTTCTTGACAAG
1 ATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGAAACTATCTT-TCGTGCACTT-TTAACAAG
* *
13765 ATCGTCTTCCGATCATCTTCTGAAAATTTTTGAGAAACCATCTT
1 ATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGAAACTATCTT
13809 CTGGTGTACT
Statistics
Matches: 141, Mismatches: 28, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
63 2 0.01
64 68 0.48
65 71 0.50
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.38
Consensus pattern (62 bp):
ATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGAAACTATCTTTCGTGCACTTTTAACAAG
Found at i:13786 original size:129 final size:129
Alignment explanation
Indices: 13574--13819 Score: 300
Period size: 129 Copynumber: 1.9 Consensus size: 129
13564 TTAAGATATC
* *
13574 GTCTTCTGATCAACTTCTGAAAACTCTTTGAGAAACAATCTTCCGGTGCATCTTTTAACAAAATC
1 GTCTTCCGATCAACTTCTGAAAACTCTTTGAGAAACAATATTCCGGTGCATCTTTTAACAAAATC
* ** * *
13639 GTCTTCCTATCAACTTCTGAATCCTTTTCGAGAAGCTATCTTCTGGTGTACTTTTTAACAAGATT
66 GTCTTCCGATCAACTTCTGAA-AATTTTCGAGAAACCATCTTCTGGTGTACTTTTTAACAAGATT
* * * * * * *
13704 GTCTTCCGATCAACTTCTGAATA-TTTTTGAGAAACTATATTATC-GTGGA-CTTCTTGACAAGA
1 GTCTTCCGATCAACTTCTGAAAACTCTTTGAGAAACAATATT-CCGGTGCATCTT-TTAACAAAA
* *
13766 TCGTCTTCCGATCATCTTCTGAAAATTTTTGAGAAACCATCTTCTGGTGTACTT
64 TCGTCTTCCGATCAACTTCTGAAAATTTTCGAGAAACCATCTTCTGGTGTACTT
13820 CTAAAAATTC
Statistics
Matches: 98, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
128 29 0.30
129 47 0.48
130 22 0.22
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.38
Consensus pattern (129 bp):
GTCTTCCGATCAACTTCTGAAAACTCTTTGAGAAACAATATTCCGGTGCATCTTTTAACAAAATC
GTCTTCCGATCAACTTCTGAAAATTTTCGAGAAACCATCTTCTGGTGTACTTTTTAACAAGATT
Found at i:13820 original size:64 final size:64
Alignment explanation
Indices: 13571--13821 Score: 279
Period size: 64 Copynumber: 3.9 Consensus size: 64
13561 TTCTTAAGAT
* * * * *
13571 ATCGTCTTCTGATCAACTTCTGAAAACTCTTTGAGAAACAATCTTCCGGTGCATCTT-TTAACAA
1 ATCGTCTTCCGATCAACTTCTGAAAA-TTTTTGAGAAACTATCTTCTGGTGTA-CTTCTTAACAA
*
13635 A
64 G
* ** * * *
13636 ATCGTCTTCCTATCAACTTCTGAATCCTTTTCGAGAAGCTATCTTCTGGTGTACTTTTTAACAAG
1 ATCGTCTTCCGATCAACTTCTGAA-AATTTTTGAGAAACTATCTTCTGGTGTACTTCTTAACAAG
* * * * * * *
13701 ATTGTCTTCCGATCAACTTCTGAATATTTTTGAGAAACTATATTATCGTGGACTTCTTGACAAG
1 ATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGAAACTATCTTCTGGTGTACTTCTTAACAAG
* *
13765 ATCGTCTTCCGATCATCTTCTGAAAATTTTTGAGAAACCATCTTCTGGTGTACTTCT
1 ATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGAAACTATCTTCTGGTGTACTTCT
13822 AAAAATTCTC
Statistics
Matches: 153, Mismatches: 31, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
64 82 0.54
65 71 0.46
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (64 bp):
ATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGAAACTATCTTCTGGTGTACTTCTTAACAAG
Found at i:15135 original size:15 final size:16
Alignment explanation
Indices: 15115--15144 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
15105 GGTTTATCTT
15115 TTCTTTTTT-CTTTTG
1 TTCTTTTTTCCTTTTG
15130 TTCTTTTTTCCTTTT
1 TTCTTTTTTCCTTTT
15145 TGATTTCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (16 bp):
TTCTTTTTTCCTTTTG
Found at i:15260 original size:22 final size:23
Alignment explanation
Indices: 15232--15285 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
15222 TTTCTCTAAA
*
15232 TCCTTTTGAGAAAAAC-ATTTTT
1 TCCTTTTGAGAAAAACAATTTCT
*
15254 TCCTTTTGA-AAAATCAATTTCT
1 TCCTTTTGAGAAAAACAATTTCT
*
15276 TCTTTTTGAG
1 TCCTTTTGAG
15286 CAATCCTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.48
Consensus pattern (23 bp):
TCCTTTTGAGAAAAACAATTTCT
Found at i:15861 original size:14 final size:14
Alignment explanation
Indices: 15842--15892 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
15832 CTCAAAAACC
15842 TTTTGAAAACTCAT
1 TTTTGAAAACTCAT
*
15856 TTTTGAAAAC-CTT
1 TTTTGAAAACTCAT
15869 TTCTTGAAAACAT-AT
1 TT-TTGAAAAC-TCAT
*
15884 TTTTCAAAA
1 TTTTGAAAA
15893 ATCTCTTGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 4 0.13
14 24 0.77
15 3 0.10
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (14 bp):
TTTTGAAAACTCAT
Found at i:15976 original size:22 final size:22
Alignment explanation
Indices: 15948--15996 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
15938 TGCAATCCAA
* *
15948 TTTCTTTT-TTCCTTTTTTTTGT
1 TTTCTTTTCTT-CTTTTTATTCT
15970 TTTCTTTTCTTCTTTTTATTCT
1 TTTCTTTTCTTCTTTTTATTCT
15992 TTTCT
1 TTTCT
15997 GATGGGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (22 bp):
TTTCTTTTCTTCTTTTTATTCT
Found at i:19094 original size:28 final size:28
Alignment explanation
Indices: 19053--19128 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 28
19043 TTAAGATGTC
** *
19053 AAAATTACTGTTTTGCCCTTGGTCGGCT
1 AAAATTACAATTTTACCCTTGGTCGGCT
* * * *
19081 AAAATTACCATTTTACCCCTGGTTGTCT
1 AAAATTACAATTTTACCCTTGGTCGGCT
19109 -AAATTACAATTTTACCCTTG
1 AAAATTACAATTTTACCCTTG
19129 AATGCCGGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
27 18 0.45
28 22 0.55
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.39
Consensus pattern (28 bp):
AAAATTACAATTTTACCCTTGGTCGGCT
Done.