Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022936.1 Corchorus olitorius cultivar O-4 contig22969, 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: 44403
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:10306 original size:20 final size:20
Alignment explanation
Indices: 10259--10300 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
10249 AATTTTTAAG
*
10259 TAAAAATATAATATTATAAA
1 TAAAAATTTAATATTATAAA
10279 TAAAAATTTAATATTA-AAA
1 TAAAAATTTAATATTATAAA
10298 TAA
1 TAA
10301 TTAATTAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAAAATTTAATATTATAAA
Found at i:11731 original size:153 final size:151
Alignment explanation
Indices: 11468--11770 Score: 468
Period size: 153 Copynumber: 2.0 Consensus size: 151
11458 TATAATCACC
* * *
11468 TTATTTTTACTATTTTACTATTTTTCATTTAAAACTATGATATATTAAAGCTTTTTAATATACAG
1 TTATTTTTACCATTTTACTATTTTTCATTAAAAACTATGATATATTAAAGATTTTTAATATACAG
*
11533 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAATTAATATTTTTATAATAATTATTTCA
66 TTTTATTATACTAAAAACTCTATTTTCATTTAATTAAAATTAATA-TTTT-T-ATAATTATTTCA
11598 TTTTTACCATTTTAATTTAAAAGT
128 TTTTTACCATTTTAATTTAAAAGT
* *
11622 TTATTTTTACCATTTTGCTATTTTTCATTAAAAACT-TGGATATATTAAA-ATTTTTAATATGCA
1 TTATTTTTACCATTTTACTATTTTTCATTAAAAACTAT-GATATATTAAAGATTTTTAATATACA
* *
11685 GTTTTATTATACTAAAAACTCTATTTTCATTT-ATTCAAATTCAATATTTTTATAATTATTTTAT
65 GTTTTATTATACTAAAAACTCTATTTTCATTTAATTAAAATT-AATATTTTTATAATTATTTCAT
11749 TTTTACCATTTTAATTTAAAAG
129 TTTTACCATTTTAATTTAAAAG
11771 GTTTTTGTGC
Statistics
Matches: 139, Mismatches: 8, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
150 34 0.24
151 1 0.01
152 12 0.09
153 48 0.35
154 44 0.32
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.52
Consensus pattern (151 bp):
TTATTTTTACCATTTTACTATTTTTCATTAAAAACTATGATATATTAAAGATTTTTAATATACAG
TTTTATTATACTAAAAACTCTATTTTCATTTAATTAAAATTAATATTTTTATAATTATTTCATTT
TTACCATTTTAATTTAAAAGT
Found at i:21437 original size:3 final size:3
Alignment explanation
Indices: 21429--21557 Score: 258
Period size: 3 Copynumber: 43.0 Consensus size: 3
21419 TATTAGTGCT
21429 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
21477 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
21525 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
21558 TATACAAGTG
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 126 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:22740 original size:21 final size:21
Alignment explanation
Indices: 22716--22782 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
22706 AATTCTCTGT
22716 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * **
22737 AAATCATAGAAAATTCTTTA-T-
1 AAATTA-AG-AAATACTCAACTC
22758 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
22779 AAAT
1 AAAT
22783 CCTGATCCTT
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
19 7 0.21
20 3 0.09
21 14 0.41
22 3 0.09
23 7 0.21
ACGTcount: A:0.52, C:0.15, G:0.04, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:22762 original size:42 final size:42
Alignment explanation
Indices: 22703--22783 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
22693 GCTAAGTCTT
*
22703 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTATAAATTAAGAAATACTCAACTCAAATCATA
*
22745 GAAAATTCTTTATAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTCTCTATAAATTAAGAAATACTCAACTCAAATC
22784 CTGATCCTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.48, C:0.16, G:0.06, T:0.30
Consensus pattern (42 bp):
GAAAATTCTCTATAAATTAAGAAATACTCAACTCAAATCATA
Found at i:22921 original size:56 final size:56
Alignment explanation
Indices: 22851--23011 Score: 286
Period size: 56 Copynumber: 2.8 Consensus size: 56
22841 TATTTTGTAG
22851 AATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAAAA
1 AATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAAAA
* *
22907 AATAATTAAGTAGAGATAGGGGGATATGATTTATTATAACATTTATTGTGTGAAAG
1 AATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAAAA
22963 AATAATTAAGTAGAGATAAGGGGGGATAGGATTTATTATAACATTTATT
1 AATAATTAAGTAGAGAT-A-GGGGGATAGGATTTATTATAACATTTATT
23012 TATTTTGTGA
Statistics
Matches: 100, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
56 71 0.71
57 1 0.01
58 28 0.28
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.35
Consensus pattern (56 bp):
AATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAAAA
Found at i:26235 original size:15 final size:16
Alignment explanation
Indices: 26202--26241 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
26192 TTAATTTGCT
26202 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
26218 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
26233 TTGCTTTCT
1 TTGTTTTCT
26242 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:28467 original size:41 final size:41
Alignment explanation
Indices: 28422--28511 Score: 128
Period size: 41 Copynumber: 2.2 Consensus size: 41
28412 AATAAGGACC
*
28422 AAATTGAATCAATTAATAAAT-GAAATACTAAATTAGAGACT
1 AAATTGAATCAAATAATAAATAG-AATACTAAATTAGAGACT
* * *
28463 AAATTGTATCAAATAATAAATAGAATCCTAAATTAGTGACT
1 AAATTGAATCAAATAATAAATAGAATACTAAATTAGAGACT
28504 AAATTGAA
1 AAATTGAA
28512 CACGAAAAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 42 0.98
42 1 0.02
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (41 bp):
AAATTGAATCAAATAATAAATAGAATACTAAATTAGAGACT
Found at i:31370 original size:29 final size:29
Alignment explanation
Indices: 31336--31497 Score: 159
Period size: 29 Copynumber: 5.7 Consensus size: 29
31326 TGTGAACTTG
*
31336 AAATGACCAAAATGCCCCTGAATGTGCAA
1 AAATGACCAAAATGCCCCTGAATATGCAA
* * *
31365 AAATGACCATAATGCCCCTGGATATGCAG
1 AAATGACCAAAATGCCCCTGAATATGCAA
* * ***
31394 AAATGACAAAAATACCCCTGAATATGTGG
1 AAATGACCAAAATGCCCCTGAATATGCAA
* *
31423 AAATGACTAAAATGCCCCTGAAAATGCAA
1 AAATGACCAAAATGCCCCTGAATATGCAA
* * * * *
31452 AAAAGACCATAATGCCACTG-A-GTG-TA
1 AAATGACCAAAATGCCCCTGAATATGCAA
31478 AAATGACCAAAATGCCCCTG
1 AAATGACCAAAATGCCCCTG
31498 GGAGACCCTA
Statistics
Matches: 108, Mismatches: 25, Indels: 3
0.79 0.18 0.02
Matches are distributed among these distances:
26 18 0.17
27 2 0.02
28 1 0.01
29 87 0.81
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (29 bp):
AAATGACCAAAATGCCCCTGAATATGCAA
Found at i:37702 original size:15 final size:16
Alignment explanation
Indices: 37678--37717 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
37668 AGAGGTTGAA
*
37678 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
37693 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
37709 AGAAAACAA
1 AGAAAACAA
37718 AGCAAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:38750 original size:343 final size:343
Alignment explanation
Indices: 38060--39019 Score: 1739
Period size: 343 Copynumber: 2.8 Consensus size: 343
38050 ATAAAATCCG
38060 ATCAATGTCTTTAGCAAAATTATAAGCAGATTGGATAAAGAAATGGCTATTGGCATATCTTTTCC
1 ATCAATGTCTTTAGCAAAATTATAAGCAGATTGGATAAAGAAATGGCTATTGGCATATCTTTTCC
* *
38125 AAAAAAGAGAATTAGCCTTGGTTTCAAGGTCTTCAAAAAGGCACAACTAAAATATTGCCAAAGAT
66 AAAAGAGAGAATTAGCCTTGGTTTCAAGGTCTT-GAAAAGGCACAACTAAAATATTGCCAAAGAT
38190 ATGATCAGGAATGGGGAAGGAAATGAGAGAGGAGTTGGAAAAAACTGATTTACAGTAACAAAATC
130 ATGATCAGGAATGGGGAAGGAAATGAGAGAGGAGTTGGAAAAAACTGATTTACAGTAACAAAATC
38255 CTCACCAAGCATTAAAGGACCATGCATGAGGGATCTAAAAAGGTCCT-A--AGTCCAATCTTTAG
195 CTCACCAAGCATTAAAGGACCATGCATGAGGGATCTAAAAAGGTCCTAATCAGTCCAATCTTTAG
*
38317 ACAGAAAAATGCAACTGTAAAGGACCATGCATCAGGTAGAAAGTTAGACTTCCAAAGCCAATCCC
260 ACAGAAAAATGCAACTATAAAGGACCATGCATCAGGTAGAAAGTTAGACTTCCAAAGCCAATCCC
38382 AACACATCAAGGGTTTGTT
325 AACACATCAAGGGTTTGTT
38401 ATCAATGTCTTTAGCAAAATTATAAGCAGATTGGATAAAGAAATGGCTATTGGCATATCTTTTCC
1 ATCAATGTCTTTAGCAAAATTATAAGCAGATTGGATAAAGAAATGGCTATTGGCATATCTTTTCC
* *
38466 AAAAGAGAGAATTAGCCTTGGTTTCAAGGTCTTGAAAAGGCACATCTAAAATAGTGCCAAAGATA
66 AAAAGAGAGAATTAGCCTTGGTTTCAAGGTCTTGAAAAGGCACAACTAAAATATTGCCAAAGATA
*
38531 TGATCAGGAAT-GGGAAGGAAATGAGAGAGGAGTTGGAAAAAACTGATTTACAATAACAAAATCC
131 TGATCAGGAATGGGGAAGGAAATGAGAGAGGAGTTGGAAAAAACTGATTTACAGTAACAAAATCC
* *
38595 TCACCAAGCATGAAAGGACCATGCATGAGGGATCTAAAAAGGTACTAATCTAGTCCAATCTTTAG
196 TCACCAAGCATTAAAGGACCATGCATGAGGGATCTAAAAAGGTCCTAATC-AGTCCAATCTTTAG
* *
38660 ACAAAAAAATGCAACTATAAAGGACCATGCATGAGGTAGAAAGTTAGACTTCCAAAGCCAATCCC
260 ACAGAAAAATGCAACTATAAAGGACCATGCATCAGGTAGAAAGTTAGACTTCCAAAGCCAATCCC
38725 AACACATCAAGGGTTTGTT
325 AACACATCAAGGGTTTGTT
* *
38744 ATCAATGTCTTTAGCAAAATTATAAGCATATTGGATAAAGAAATGGCTATTGGCAGATCTTTTCC
1 ATCAATGTCTTTAGCAAAATTATAAGCAGATTGGATAAAGAAATGGCTATTGGCATATCTTTTCC
*
38809 AAAAGAGAGAATTAGCCTTGGTTTCAAGGTCTTGAAAAGGCACAGCTAAAATATTGCCAAAGATA
66 AAAAGAGAGAATTAGCCTTGGTTTCAAGGTCTTGAAAAGGCACAACTAAAATATTGCCAAAGATA
38874 TGATCAGGAATGGGGAAGGAAATGAGAGAGGAGTTGGAAAAAACTGATTTACAGTAACAAAATCC
131 TGATCAGGAATGGGGAAGGAAATGAGAGAGGAGTTGGAAAAAACTGATTTACAGTAACAAAATCC
*
38939 TCACCAAGCATTAAAGGACCATGCATGAGGGATCTTAAAAGGTCCTAATCCAGTCCAATCTTTAG
196 TCACCAAGCATTAAAGGACCATGCATGAGGGATCTAAAAAGGTCCTAAT-CAGTCCAATCTTTAG
39004 ACAGAAAAATGCAACT
260 ACAGAAAAATGCAACT
39020 TTCCCATTAG
Statistics
Matches: 594, Mismatches: 19, Indels: 9
0.95 0.03 0.01
Matches are distributed among these distances:
339 96 0.16
340 41 0.07
341 97 0.16
343 232 0.39
344 127 0.21
345 1 0.00
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.24
Consensus pattern (343 bp):
ATCAATGTCTTTAGCAAAATTATAAGCAGATTGGATAAAGAAATGGCTATTGGCATATCTTTTCC
AAAAGAGAGAATTAGCCTTGGTTTCAAGGTCTTGAAAAGGCACAACTAAAATATTGCCAAAGATA
TGATCAGGAATGGGGAAGGAAATGAGAGAGGAGTTGGAAAAAACTGATTTACAGTAACAAAATCC
TCACCAAGCATTAAAGGACCATGCATGAGGGATCTAAAAAGGTCCTAATCAGTCCAATCTTTAGA
CAGAAAAATGCAACTATAAAGGACCATGCATCAGGTAGAAAGTTAGACTTCCAAAGCCAATCCCA
ACACATCAAGGGTTTGTT
Found at i:42007 original size:21 final size:21
Alignment explanation
Indices: 41983--42033 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
41973 GTGACACTGC
41983 CCACCTGGGTACTCAA-GCAAA
1 CCACCTGGGTACTCAAGGC-AA
* *
42004 CCACATGGGTGCTCAAGGCAA
1 CCACCTGGGTACTCAAGGCAA
*
42025 CCATCTGGG
1 CCACCTGGG
42034 CGCCCAGGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.27, C:0.31, G:0.25, T:0.16
Consensus pattern (21 bp):
CCACCTGGGTACTCAAGGCAA
Done.