Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012455.1 Corchorus olitorius cultivar O-4 contig12488, 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: 60489
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:12394 original size:1 final size:1
Alignment explanation
Indices: 12388--12415 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
12378 GACCCAAACT
12388 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
12416 CATCACCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:13611 original size:30 final size:30
Alignment explanation
Indices: 13575--13664 Score: 85
Period size: 29 Copynumber: 3.0 Consensus size: 30
13565 TCAGAAAAGA
13575 ACTTATTTGGCGTTTTATAAGAGTTCAGGG
1 ACTTATTTGGCGTTTTATAAGAGTTCAGGG
*** * *
13605 ACTTATTTGGC-TGCAATTAGAGTTCAGAG
1 ACTTATTTGGCGTTTTATAAGAGTTCAGGG
**
13634 ACTTATTTAACCGTTTTATATA-AGTTCAGGG
1 ACTTATTT-GGCGTTTTATA-AGAGTTCAGGG
13665 GCCTCTTTGA
Statistics
Matches: 45, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
29 21 0.47
30 12 0.27
31 11 0.24
32 1 0.02
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (30 bp):
ACTTATTTGGCGTTTTATAAGAGTTCAGGG
Found at i:13696 original size:2 final size:2
Alignment explanation
Indices: 13684--13721 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
13674 AGCAATAAAC
13684 AT AT A- AT AT AT AT AT AT AT AT AT AT 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
13722 GCTGGAATAC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:23954 original size:29 final size:31
Alignment explanation
Indices: 23884--23954 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 31
23874 AAGATAATTT
* *
23884 TCCCTTGAACTTGTAGTGATTGGACGTTTTG
1 TCCCATGAACTTGTAGTGATTGGACATTTTG
* * * *
23915 CCCCCTAAACTT-TAGT-TTTGGACATTTTG
1 TCCCATGAACTTGTAGTGATTGGACATTTTG
23944 TCCCATGAACT
1 TCCCATGAACT
23955 CTCAATTTTG
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
29 19 0.59
30 4 0.12
31 9 0.28
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (31 bp):
TCCCATGAACTTGTAGTGATTGGACATTTTG
Found at i:24746 original size:30 final size:31
Alignment explanation
Indices: 24712--24779 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 31
24702 GTCGTGGCCT
24712 TGCCACGTGGCA-TTTGGTCCAACATGACAC
1 TGCCACGTGGCATTTTGGTCCAACATGACAC
* * * *
24742 TGCCATGTGGCATTTTTTGTCCAACATGATAT
1 TGCCACGTGGCA-TTTTGGTCCAACATGACAC
24774 TGCCAC
1 TGCCAC
24780 ATCAGCAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 11 0.35
32 20 0.65
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.31
Consensus pattern (31 bp):
TGCCACGTGGCATTTTGGTCCAACATGACAC
Found at i:25392 original size:2 final size:2
Alignment explanation
Indices: 25385--25419 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
25375 GACTTCCATT
25385 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25420 GATGTAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:26177 original size:32 final size:29
Alignment explanation
Indices: 26124--26184 Score: 95
Period size: 32 Copynumber: 2.0 Consensus size: 29
26114 TTTTTGTTAG
26124 AAATATTTATTAATATGTAATAAATATTA
1 AAATATTTATTAATATGTAATAAATATTA
26153 AAATATTTATATAATATATGTAATAAATATTA
1 AAATATTTAT-T-A-ATATGTAATAAATATTA
26185 TTAGAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 10 0.34
30 1 0.03
31 1 0.03
32 17 0.59
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (29 bp):
AAATATTTATTAATATGTAATAAATATTA
Found at i:29781 original size:154 final size:154
Alignment explanation
Indices: 29497--29865 Score: 702
Period size: 154 Copynumber: 2.4 Consensus size: 154
29487 AAAAAGGTTG
29497 ATATACATATACTATTTTTGATCATTATTATTCATTAATCCACTTATGCAATTGCAAGCAATAAC
1 ATATACATATACTATTTTTGATCATTATTATTCATTAATCCACTTATGCAATTGCAAGCAATAAC
*
29562 CAGGTACGTGACGCGGGTCGGATCCGGATTAGTGGATACCGGATGAGATAAAAAAAAAAGGTTGA
66 CAGGTACGTGACGCGGGTCGGATCCGGATTAATGGATACCGGATGAGATAAAAAAAAAAGGTTGA
29627 TATATAAATATAGTTTAATTAAAT
131 TATATAAATATAGTTTAATTAAAT
*
29651 ATATACATATACTATTTTTGATCATTATTATTCATTAATCCATTTATGCAATTGCAAGCAATAAC
1 ATATACATATACTATTTTTGATCATTATTATTCATTAATCCACTTATGCAATTGCAAGCAATAAC
* *
29716 CAGGTGCGTGACGCGGGTCGGATCCGGATTAATGGATACCGGATGAGATAAAAAAAAAAGTTTGA
66 CAGGTACGTGACGCGGGTCGGATCCGGATTAATGGATACCGGATGAGATAAAAAAAAAAGGTTGA
29781 TATATAAATATAGTTTAATTAAAT
131 TATATAAATATAGTTTAATTAAAT
29805 ATATACATATACTATTTTTGATCATTATTATTCATTAATCCACTTATGCAATTGCAAGCAA
1 ATATACATATACTATTTTTGATCATTATTATTCATTAATCCACTTATGCAATTGCAAGCAA
29866 CTCTTCTGTT
Statistics
Matches: 210, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
154 210 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.34
Consensus pattern (154 bp):
ATATACATATACTATTTTTGATCATTATTATTCATTAATCCACTTATGCAATTGCAAGCAATAAC
CAGGTACGTGACGCGGGTCGGATCCGGATTAATGGATACCGGATGAGATAAAAAAAAAAGGTTGA
TATATAAATATAGTTTAATTAAAT
Found at i:29913 original size:43 final size:43
Alignment explanation
Indices: 29852--29937 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
29842 ATCCACTTAT
29852 GCAATTGCAAGCAACTCTTCTGTTCCACTGGCCAATGCCCCAA
1 GCAATTGCAAGCAACTCTTCTGTTCCACTGGCCAATGCCCCAA
*
29895 GCAATTGCAAGCAACTCTTCTGTTCCACTGGTCAATGCCCCAA
1 GCAATTGCAAGCAACTCTTCTGTTCCACTGGCCAATGCCCCAA
29938 ATTACATCCC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.26, C:0.34, G:0.16, T:0.24
Consensus pattern (43 bp):
GCAATTGCAAGCAACTCTTCTGTTCCACTGGCCAATGCCCCAA
Found at i:33094 original size:2 final size:2
Alignment explanation
Indices: 33089--33114 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
33079 ATAAAAAATA
33089 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
33115 TATTCCCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36236 original size:106 final size:102
Alignment explanation
Indices: 36098--36395 Score: 409
Period size: 93 Copynumber: 2.9 Consensus size: 102
36088 AACATCACGG
36098 TAATCAGTAATCATGGCACATAAGGGTATATATGATATTCCGCGCTACAATACCCAAATATCGTT
1 TAATCAGTAATCATGG-ACATAAGGGTATATATGATATTCCGCGCTACAATACCCAAA-AT-G-T
36163 ACTTCAGTTAAAACCCTCTCCTTATCCACAGGGGACGGTCCA
62 A-TTCAGTTAAAACCCTCTCCTTATCCACAGGGGACGGTCCA
*
36205 TAATCAGTAATCATGGACATAAGGGTATATATGATATTCCACGCTACAATACCC--AA---A--C
1 TAATCAGTAATCATGGACATAAGGGTATATATGATATTCCGCGCTACAATACCCAAAATGTATTC
36263 A--TAAAACCCTCTCCTTATCCACAGGGGACGGTCCA
66 AGTTAAAACCCTCTCCTTATCCACAGGGGACGGTCCA
*
36298 TAATCAGTAATCATGGACATAAGGGTATATATGATATTCCGTGCTACAATACCCAAACATGGATA
1 TAATCAGTAATCATGGACATAAGGGTATATATGATATTCCGCGCTACAATACCCAAA-AT-G-TA
*
36363 TTTCAGTTAAAACCCTC-CACTTATCCATAGGGG
63 -TTCAGTTAAAACCCTCTC-CTTATCCACAGGGG
36396 CGGACCGTCG
Statistics
Matches: 173, Mismatches: 4, Indels: 29
0.84 0.02 0.14
Matches are distributed among these distances:
93 86 0.50
95 3 0.02
96 1 0.01
98 1 0.01
101 1 0.01
103 1 0.01
104 3 0.02
105 1 0.01
106 60 0.35
107 16 0.09
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.27
Consensus pattern (102 bp):
TAATCAGTAATCATGGACATAAGGGTATATATGATATTCCGCGCTACAATACCCAAAATGTATTC
AGTTAAAACCCTCTCCTTATCCACAGGGGACGGTCCA
Found at i:39370 original size:27 final size:27
Alignment explanation
Indices: 39338--39393 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
39328 TGAAACTTGA
39338 TAAAGTAAAGTGAAAAA-GTGTTTGAGC
1 TAAAGTAAAGT-AAAAAGGTGTTTGAGC
39365 TAAAGTAAAGTAAAAAGGTGTTTGAGC
1 TAAAGTAAAGTAAAAAGGTGTTTGAGC
39392 TA
1 TA
39394 GCTAGTTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 5 0.18
27 23 0.82
ACGTcount: A:0.45, C:0.04, G:0.25, T:0.27
Consensus pattern (27 bp):
TAAAGTAAAGTAAAAAGGTGTTTGAGC
Done.