Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012008.1 Corchorus olitorius cultivar O-4 contig12041, 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: 37999
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1813 original size:22 final size:22
Alignment explanation
Indices: 1788--1835 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1778 GACTTCAAGT
*
1788 GAAGGAATTAATCAACT-AAGAG
1 GAAGAAATT-ATCAACTCAAGAG
*
1810 GAAGAAATTTTCAACTCAAGAG
1 GAAGAAATTATCAACTCAAGAG
1832 GAAG
1 GAAG
1836 CAAACCGTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.48, C:0.10, G:0.23, T:0.19
Consensus pattern (22 bp):
GAAGAAATTATCAACTCAAGAG
Found at i:2760 original size:21 final size:21
Alignment explanation
Indices: 2734--2777 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2724 CCAATTTAGG
*
2734 TTTAGATTTCA-ATTTATTGTT
1 TTTAGATTTAAGATTTATT-TT
2755 TTTAGATTTAAGATTTATTTT
1 TTTAGATTTAAGATTTATTTT
2776 TT
1 TT
2778 ATACATCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.25, C:0.02, G:0.09, T:0.64
Consensus pattern (21 bp):
TTTAGATTTAAGATTTATTTT
Found at i:13178 original size:433 final size:430
Alignment explanation
Indices: 12305--13143 Score: 952
Period size: 433 Copynumber: 1.9 Consensus size: 430
12295 TCAAGTGTCT
* ** * * **
12305 ATTAAAAGGTAATTTCATGATCTACAATTTTCATTTAGAACTCAAAAGTCAATTTTTGTTTTGAT
1 ATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGAACTCAAAAGTCAATTTTTATGTCAAT
* * * ** * * *
12370 TCTAAAAATTGCTTCTGAAATTTTGTGGTTTTGATTGCCAGTTAATTTAATATCATATAATTTTT
66 TCAAAAAAATGCTTCTGAAATTTGGTCATTTCGATTGCCAGTTAATTTAATACCATATAAATTTT
* * * * * * *
12435 TGTCCACATCTCCGATTGAAGTTATTGAAGTGTCGGTTTAAAGGTTATTGCATGATTTACGACTT
131 GGTCCACATCTCCAATTAAAGTTATTCAAGTGTCGGTTAAAAGGTTATTGCATAATCTACGACTT
* * * * *
12500 TCATGAAGGACCCGAAAGCTAAATTTGATCTACGAGTTTCGTTAAGGGTTCAAAAGGGAATTTTT
196 TCATGAAGAACCCGAAAGCTAAATTTAATCTACGAGTTTCATGAAGGATTCAAAAGGGAATTTTT
* * **
12565 ACGTTTCAAGATCTCCATTAACAAACATTTTCTTATTTGAATTATTTATCAAATGGCCCTCATAC
261 ACGTTTCAAGATCTCAATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATAC
* * *
12630 TTTTCTACTTTATACTACTTAATTCTTTACAAATTCTATCTAATCTAACGTTTAAGCTTTATTTT
326 TTTTCTACTTTATACTACTTAATCCTTTACAAATTCTATCTAATCT-ACGTTTAAACTTCATTTT
**** * ** * * *
12695 TTTTCTTTTTTCTATTTGTCCAATGAAGTTGATTCATGTGTC
390 TTTGAAATGTAATATTTGTCCAATCAAGTT-ATTCATGAGAC
*
12737 TATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGGACTCAAAAG-CAAATTTTTATGTCA
1 -ATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGAACTCAAAAGTC-AATTTTTATGTCA
***
12801 ATTCAAAAAAATGCTTCCT-AAATTTGGTCATTTCGATTGTTGGTCT-ATTTAATACCATATAAA
64 ATTCAAAAAAATGCTT-CTGAAATTTGGTCATTTCGATTGCCAGT-TAATTTAATACCATATAAA
* *
12864 TTTTGGTCCACATGTCCAATTAAAGTTATTCAAGTGTCGGTTAAAAGGTTATTGTATAATCTACG
127 TTTTGGTCCACATCTCCAATTAAAGTTATTCAAGTGTCGGTTAAAAGGTTATTGCATAATCTACG
** ** *
12929 ACTTTCATGAAGAATTCGAAAG-TTGATTTAATCTACGAGTTTCATGAATGATTCAAAAGGGAAT
192 ACTTTCATGAAGAACCCGAAAGCTAAATTTAATCTACGAGTTTCATGAAGGATTCAAAAGGGAA-
* *
12993 TTTTTATGTTTCAAGATCTTCATTAATTAACAAATATTTTCTTATTTGAATTAGTTATCAAATCA
256 TTTTTACGTTTCAAGATC-TC---AATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCA
* * * * * *
13058 CCCTTATACTTTTTTATTTTATGCTACTTAGTCCTTTACAAATTCTATCTTA-CT-CGATTTAAC
317 CCCTCATACTTTTCTACTTTATACTACTTAATCCTTTACAAATTCTATCTAATCTACG-TTTAA-
13121 ACTTCATTTTTTTGAAATGTAAT
380 ACTTCATTTTTTTGAAATGTAAT
13144 TTTATGATCT
Statistics
Matches: 336, Mismatches: 60, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
432 35 0.10
433 192 0.57
434 7 0.02
435 5 0.01
436 16 0.05
437 81 0.24
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (430 bp):
ATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGAACTCAAAAGTCAATTTTTATGTCAAT
TCAAAAAAATGCTTCTGAAATTTGGTCATTTCGATTGCCAGTTAATTTAATACCATATAAATTTT
GGTCCACATCTCCAATTAAAGTTATTCAAGTGTCGGTTAAAAGGTTATTGCATAATCTACGACTT
TCATGAAGAACCCGAAAGCTAAATTTAATCTACGAGTTTCATGAAGGATTCAAAAGGGAATTTTT
ACGTTTCAAGATCTCAATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATAC
TTTTCTACTTTATACTACTTAATCCTTTACAAATTCTATCTAATCTACGTTTAAACTTCATTTTT
TTGAAATGTAATATTTGTCCAATCAAGTTATTCATGAGAC
Found at i:19734 original size:39 final size:40
Alignment explanation
Indices: 19670--19750 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
19660 TTTAATTCCT
*
19670 ATGTAATATATATAATCACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
19710 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
19749 AT
1 AT
19751 TCTTAGGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:19777 original size:25 final size:24
Alignment explanation
Indices: 19741--19787 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
19731 AATACTTACA
*
19741 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCTTAGCTATTTTT
19765 TTAATTCAAATTCTTAGCTATTT
1 TTAATT-AAATTCTTAGCTATTT
19788 GTGCAAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (24 bp):
TTAATTAAATTCTTAGCTATTTTT
Found at i:20103 original size:205 final size:199
Alignment explanation
Indices: 19859--20267 Score: 737
Period size: 205 Copynumber: 2.0 Consensus size: 199
19849 TTCCTTAATA
19859 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
1 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
*
19924 ATTTAATAAATCAACCACTAATGTTCAACTAAATTTTTTTTGGTATAGTTCTATAGATATAATAG
66 ATTTAATAAATCAACCACTAATGTTCAACT-AATTTTTTTT-GTATAGTT-T-TAGATATAATAA
19989 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
127 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTT-AAAAATTAATAACAT
*
20054 TCACCATTG
191 TCACCAGTG
20063 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
*
20128 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGTATAGTTTTATATATAATAATAA
65 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGTATAGTTTTAGATATAATAATAA
20193 TGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAATTAATAACATTCAC
130 TGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAATTAATAACATTCAC
20258 CAGTG
195 CAGTG
20263 ATAAA
1 ATAAA
20268 GTTATTAAGC
Statistics
Matches: 201, Mismatches: 3, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
200 28 0.14
201 59 0.29
202 1 0.00
203 8 0.04
204 26 0.13
205 79 0.39
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.44
Consensus pattern (199 bp):
ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGTATAGTTTTAGATATAATAATAAT
GTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAATTAATAACATTCACC
AGTG
Found at i:25761 original size:21 final size:22
Alignment explanation
Indices: 25735--25776 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
25725 TTAGCCCTGT
25735 TTCGACCCAGA-GAAGGTCGAG
1 TTCGACCCAGATGAAGGTCGAG
*
25756 TTCGACCCTGATGAAGGTCGA
1 TTCGACCCAGATGAAGGTCGA
25777 AACAGGGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.26, C:0.24, G:0.31, T:0.19
Consensus pattern (22 bp):
TTCGACCCAGATGAAGGTCGAG
Found at i:29052 original size:12 final size:12
Alignment explanation
Indices: 29035--29060 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29025 AGGCAAAGGC
29035 ATGAAAAATCCA
1 ATGAAAAATCCA
29047 ATGAAAAATCCA
1 ATGAAAAATCCA
29059 AT
1 AT
29061 TCAAACTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.15, G:0.08, T:0.19
Consensus pattern (12 bp):
ATGAAAAATCCA
Found at i:31357 original size:21 final size:22
Alignment explanation
Indices: 31331--31372 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
31321 TTAGCCCTGT
31331 TTCGACCCAGA-GAAGGTCGAG
1 TTCGACCCAGATGAAGGTCGAG
*
31352 TTCGACCCTGATGAAGGTCGA
1 TTCGACCCAGATGAAGGTCGA
31373 AACATGGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.26, C:0.24, G:0.31, T:0.19
Consensus pattern (22 bp):
TTCGACCCAGATGAAGGTCGAG
Found at i:35095 original size:36 final size:36
Alignment explanation
Indices: 35048--35126 Score: 140
Period size: 36 Copynumber: 2.2 Consensus size: 36
35038 AAAAAAAAAG
35048 AGCAAAACCCAAAATCAAAATTTCTTAGCAAATCAC
1 AGCAAAACCCAAAATCAAAATTTCTTAGCAAATCAC
* *
35084 AGCAAAACCCAAAATCACAATTTCTTAGCAAATCGC
1 AGCAAAACCCAAAATCAAAATTTCTTAGCAAATCAC
35120 AGCAAAA
1 AGCAAAA
35127 GAGCCAAATC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.49, C:0.25, G:0.08, T:0.18
Consensus pattern (36 bp):
AGCAAAACCCAAAATCAAAATTTCTTAGCAAATCAC
Found at i:37945 original size:24 final size:25
Alignment explanation
Indices: 37907--37957 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
37897 ATTGGAGTAT
*
37907 TTATTTATCTTGTTTCTTAATTTTA
1 TTATTTATCTTGTTTATTAATTTTA
*
37932 TTATTT-TCTTGTTTATTTATTTTA
1 TTATTTATCTTGTTTATTAATTTTA
37956 TT
1 TT
37958 GTTACTCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.73
Consensus pattern (25 bp):
TTATTTATCTTGTTTATTAATTTTA
Done.