Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020176.1 Corchorus olitorius cultivar O-4 contig20209, 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: 62091
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:3790 original size:21 final size:21
Alignment explanation
Indices: 3751--3799 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
3741 TCAATGCTTT
**
3751 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
3773 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
3794 A-GAAGC
1 AGGAAGC
3800 TACAGTTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Found at i:8664 original size:4 final size:4
Alignment explanation
Indices: 8655--8681 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
8645 TCTTTAAAAA
8655 AATT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AAT
8682 AAAAAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:28972 original size:25 final size:26
Alignment explanation
Indices: 28929--28977 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
28919 TATTTAATAT
* *
28929 ATTTAAAAATATAAGTAATTTATAAC
1 ATTTAAAAATACAAGTAATATATAAC
*
28955 ATTTAAAATTACAA-TAATATATA
1 ATTTAAAAATACAAGTAATATATA
28978 TTATTTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 8 0.40
26 12 0.60
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (26 bp):
ATTTAAAAATACAAGTAATATATAAC
Found at i:28983 original size:25 final size:26
Alignment explanation
Indices: 28927--28983 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
28917 TTTATTTAAT
* *
28927 ATATTTAAAAATATAAGTAATTTATA
1 ATATTTAAAAATACAAGTAATATATA
* *
28953 ACATTTAAAATTACAA-TAATATATA
1 ATATTTAAAAATACAAGTAATATATA
*
28978 TTATTT
1 ATATTT
28984 TTAATGTTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (26 bp):
ATATTTAAAAATACAAGTAATATATA
Found at i:30138 original size:13 final size:13
Alignment explanation
Indices: 30120--30145 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30110 ACAGATATCC
30120 ACGGATATATCGA
1 ACGGATATATCGA
30133 ACGGATATATCGA
1 ACGGATATATCGA
30146 GGTATCGATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
ACGGATATATCGA
Found at i:32254 original size:19 final size:18
Alignment explanation
Indices: 32226--32261 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
32216 AATTAATTGT
32226 TTTAATATTAAATTTTTC
1 TTTAATATTAAATTTTTC
*
32244 TTTATATATTATATTTTT
1 TTTA-ATATTAAATTTTT
32262 ACTTAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTAATATTAAATTTTTC
Found at i:35033 original size:134 final size:131
Alignment explanation
Indices: 34890--35156 Score: 417
Period size: 134 Copynumber: 2.0 Consensus size: 131
34880 GTCATTTAAG
* * * *
34890 AAATATATTTTAAAAATTCTAATATATCTAAGTTTTTTAATTAAATTAGTAAATTGATAAAAATA
1 AAATATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATA
34955 AAATAGGTATAAGGATATTAGATTTAATTAAATAATAAAAATAGAGTTTTTAGTTGAGTAAAACT
66 AAATAGGTATAAGGATATTAGATTTAATT--A-AATAAAAATAGAGTTTTTAGTTGAGTAAAACT
35020 AAAA
128 AAAA
* * *
35024 AAATATATTTAAAAAATTCTAATATATATAATTTTTTTAATTAAAATAGTAAAATGGTAAAAATT
1 AAATATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATA
* * *
35089 AAATAGTTATAAGGATATTATATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATA
66 AAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTAAA
35154 A
131 A
35155 AA
1 AA
35157 GTCTAAACAA
Statistics
Matches: 123, Mismatches: 10, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
131 37 0.30
132 1 0.01
134 85 0.69
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.39
Consensus pattern (131 bp):
AAATATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATA
AAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTAAA
A
Found at i:35502 original size:23 final size:25
Alignment explanation
Indices: 35444--35502 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 25
35434 ATTTTACTAT
*
35444 TTTAATTAAAATACTTTATAGTTTTA
1 TTTAATTAAAATACTCTATA-TTTTA
* * *
35470 CTCAACTAAAA-ACTCTAT-TTTTA
1 TTTAATTAAAATACTCTATATTTTA
35493 TTTAATTAAA
1 TTTAATTAAA
35503 TCTAATATCT
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
23 12 0.46
25 6 0.23
26 8 0.31
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (25 bp):
TTTAATTAAAATACTCTATATTTTA
Found at i:42370 original size:2 final size:2
Alignment explanation
Indices: 42363--42392 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
42353 GGTGTATCAA
42363 AT AT 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 AT AT
42393 GTATTATTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42546 original size:13 final size:13
Alignment explanation
Indices: 42528--42553 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42518 AAAGTAATAA
42528 TACTATTATTAAT
1 TACTATTATTAAT
42541 TACTATTATTAAT
1 TACTATTATTAAT
42554 ATTATTTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
TACTATTATTAAT
Found at i:49598 original size:212 final size:212
Alignment explanation
Indices: 49231--49658 Score: 856
Period size: 212 Copynumber: 2.0 Consensus size: 212
49221 TCATAGTGAC
49231 AGGTGACCGAATCTGAATGACTCAACCCATATGACCTGAACATCAAACCCAAAAACCTGTACTCG
1 AGGTGACCGAATCTGAATGACTCAACCCATATGACCTGAACATCAAACCCAAAAACCTGTACTCG
49296 CATGACCTGAGATAGGAATGAGCCAAATCCAACCCAACCTGAAACTGAAATGACCCGAATTTCTC
66 CATGACCTGAGATAGGAATGAGCCAAATCCAACCCAACCTGAAACTGAAATGACCCGAATTTCTC
49361 TAAACCTGGAACTGACTCAATCTGTCGTCCATCTGCCACATCTAGTTTCGACCCTTTTTGCACCC
131 TAAACCTGGAACTGACTCAATCTGTCGTCCATCTGCCACATCTAGTTTCGACCCTTTTTGCACCC
49426 TAGCAAACATGCATTTA
196 TAGCAAACATGCATTTA
49443 AGGTGACCGAATCTGAATGACTCAACCCATATGACCTGAACATCAAACCCAAAAACCTGTACTCG
1 AGGTGACCGAATCTGAATGACTCAACCCATATGACCTGAACATCAAACCCAAAAACCTGTACTCG
49508 CATGACCTGAGATAGGAATGAGCCAAATCCAACCCAACCTGAAACTGAAATGACCCGAATTTCTC
66 CATGACCTGAGATAGGAATGAGCCAAATCCAACCCAACCTGAAACTGAAATGACCCGAATTTCTC
49573 TAAACCTGGAACTGACTCAATCTGTCGTCCATCTGCCACATCTAGTTTCGACCCTTTTTGCACCC
131 TAAACCTGGAACTGACTCAATCTGTCGTCCATCTGCCACATCTAGTTTCGACCCTTTTTGCACCC
49638 TAGCAAACATGCATTTA
196 TAGCAAACATGCATTTA
49655 AGGT
1 AGGT
49659 TCAGAGCTAA
Statistics
Matches: 216, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
212 216 1.00
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.23
Consensus pattern (212 bp):
AGGTGACCGAATCTGAATGACTCAACCCATATGACCTGAACATCAAACCCAAAAACCTGTACTCG
CATGACCTGAGATAGGAATGAGCCAAATCCAACCCAACCTGAAACTGAAATGACCCGAATTTCTC
TAAACCTGGAACTGACTCAATCTGTCGTCCATCTGCCACATCTAGTTTCGACCCTTTTTGCACCC
TAGCAAACATGCATTTA
Found at i:53046 original size:18 final size:18
Alignment explanation
Indices: 53023--53057 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
53013 TTTTATTTTT
53023 TTGGCAGTTAAACATGAA
1 TTGGCAGTTAAACATGAA
53041 TTGGCAGTTAAACATGA
1 TTGGCAGTTAAACATGA
53058 TAGTAAGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (18 bp):
TTGGCAGTTAAACATGAA
Found at i:55982 original size:3 final size:3
Alignment explanation
Indices: 55974--55999 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
55964 GGTGGGGTTT
55974 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
56000 TTTTTTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:56014 original size:15 final size:15
Alignment explanation
Indices: 55981--56026 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
55971 TTTTTCTTCT
* * *
55981 TCTTCTTCTTCTTCT
1 TCTTTTTCTTTTTCC
*
55996 TCTTTTTTTTTTTCC
1 TCTTTTTCTTTTTCC
56011 TCTTTTTCTTTTTCC
1 TCTTTTTCTTTTTCC
56026 T
1 T
56027 TTCTGTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
TCTTTTTCTTTTTCC
Found at i:60984 original size:39 final size:40
Alignment explanation
Indices: 60928--61008 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
60918 TTTAATTCCT
60928 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
60968 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
61007 AT
1 AT
61009 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:61036 original size:24 final size:25
Alignment explanation
Indices: 60999--61045 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
60989 AATACTTACA
60999 TTAATTAAATTC-TTAGGTATTTTT
1 TTAATTAAATTCTTTAGGTATTTTT
61023 TTAATTCAAA-TCTTTAGGTATTT
1 TTAATT-AAATTCTTTAGGTATTT
61046 GTGCAAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (25 bp):
TTAATTAAATTCTTTAGGTATTTTT
Found at i:61500 original size:203 final size:203
Alignment explanation
Indices: 61123--61516 Score: 684
Period size: 203 Copynumber: 1.9 Consensus size: 203
61113 TTAATAATAA
*
61123 ATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTT
1 ATAAATCAGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTT
* **
61188 AATAAATCAACCACTAATGTTTAACTAATTTTTTTTGGTATAGTTCTATATATATAATAGTAATG
66 AATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAACAATG
61253 TGTTGTATCTTACTCACTACAACTTTGTTAGTAATATTAGACTTAAAAAATTAATAACATTGACC
131 TGTTGTATCTTACTCACTACAACTTTGTTAGTAATATTAGACTTAAAAAATTAATAACATTGACC
61318 ATTGATAT
196 ATTGATAT
61326 ATAAATCAGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTAGACATTGATCTAATTTAAT
1 ATAAATCAGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTT-GACATTGATCTAATTTAAT
*
61391 TTAATAAATCAACCACTAATGTTCAACTACTTTTTTTTGGTATAGTT-T-TATATATAATAACAA
64 TTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAACAA
* * *
61454 TGTGTTGTATCTTATTCACTGCAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATT
129 TGTGTTGTATCTTACTCACTACAACTTTGTTAGTAATATTAGACTTAAAAAATTAATAACATT
61517 CATCATCGAT
Statistics
Matches: 181, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
203 84 0.46
204 33 0.18
205 64 0.35
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.45
Consensus pattern (203 bp):
ATAAATCAGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTT
AATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAACAATG
TGTTGTATCTTACTCACTACAACTTTGTTAGTAATATTAGACTTAAAAAATTAATAACATTGACC
ATTGATAT
Done.