Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019773.1 Corchorus olitorius cultivar O-4 contig19806, 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: 67863
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Found at i:9878 original size:24 final size:24
Alignment explanation
Indices: 9846--9903 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
9836 CTTATGCACC
*
9846 TAAAACATTTAT-TAAAACATTTTA
1 TAAAACATTTATATAAAACA-GTTA
* *
9870 TAAAGCATTTATATAAAGCAGTTA
1 TAAAACATTTATATAAAACAGTTA
9894 TAAAACATTT
1 TAAAACATTT
9904 CCTCAACGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 23 0.79
25 6 0.21
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (24 bp):
TAAAACATTTATATAAAACAGTTA
Found at i:9884 original size:13 final size:13
Alignment explanation
Indices: 9846--9903 Score: 61
Period size: 12 Copynumber: 4.8 Consensus size: 13
9836 CTTATGCACC
9846 TAAAACATTTAT-
1 TAAAACATTTATA
9858 TAAAACATTT-TA
1 TAAAACATTTATA
*
9870 TAAAGCATTTATA
1 TAAAACATTTATA
* *
9883 TAAAGCA-GT-TA
1 TAAAACATTTATA
9894 TAAAACATTT
1 TAAAACATTT
9904 CCTCAACGGG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
11 9 0.23
12 21 0.54
13 9 0.23
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (13 bp):
TAAAACATTTATA
Found at i:10347 original size:28 final size:28
Alignment explanation
Indices: 10315--10368 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
10305 AATTTAGTCA
* * *
10315 ACCAAGGGTAAAATGGTAATTTTAACCG
1 ACCAAGGGCAAAATCGTAATTATAACCG
*
10343 ACCAAGGGCAAATTCGTAATTATAAC
1 ACCAAGGGCAAAATCGTAATTATAAC
10369 ATCCTAAGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.24
Consensus pattern (28 bp):
ACCAAGGGCAAAATCGTAATTATAACCG
Found at i:18841 original size:1 final size:1
Alignment explanation
Indices: 18835--18863 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
18825 TTGCAATATC
18835 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
18864 ATAAATTCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:25025 original size:15 final size:15
Alignment explanation
Indices: 25007--25041 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
24997 CCTTTGAAAT
25007 CTAAAATGCTGAATA
1 CTAAAATGCTGAATA
25022 CTAAAATGCTGAATA
1 CTAAAATGCTGAATA
25037 CTAAA
1 CTAAA
25042 TAAATGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (15 bp):
CTAAAATGCTGAATA
Found at i:32928 original size:6 final size:6
Alignment explanation
Indices: 32917--32950 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
32907 TTACCAATTG
32917 AAATAA AAATAA AAATAA AAATAA AAATAGA AAA
1 AAATAA AAATAA AAATAA AAATAA AAATA-A AAA
32951 GTGTAATAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 23 0.85
7 4 0.15
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:32966 original size:3 final size:3
Alignment explanation
Indices: 32958--32995 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
32948 AAAGTGTAAT
32958 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
32996 TAATAATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:33009 original size:15 final size:15
Alignment explanation
Indices: 32991--33019 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
32981 CAACAACAAC
32991 AACAATAATAATAAT
1 AACAATAATAATAAT
33006 AACAATAATAATAA
1 AACAATAATAATAA
33020 CATTAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (15 bp):
AACAATAATAATAAT
Found at i:33012 original size:12 final size:12
Alignment explanation
Indices: 32997--33027 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
32987 CAACAACAAT
32997 AATAATAATAAC
1 AATAATAATAAC
33009 AATAATAATAAC
1 AATAATAATAAC
*
33021 ATTAATA
1 AATAATA
33028 TTCAAAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (12 bp):
AATAATAATAAC
Found at i:37178 original size:53 final size:53
Alignment explanation
Indices: 37116--37278 Score: 308
Period size: 53 Copynumber: 3.1 Consensus size: 53
37106 TTTTTAAATC
*
37116 CAATAGTTCATTGCATTTTGTATTATTTGATATGTGTGCTTATTTAATAGGTT
1 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
*
37169 CAATAGTTCATTGCATTTTGTAATATTTGGTATGTGTGCTTATTTAATAGGTT
1 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
37222 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
1 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
37275 CAAT
1 CAAT
37279 TGAATAAACA
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 107 1.00
ACGTcount: A:0.25, C:0.08, G:0.18, T:0.50
Consensus pattern (53 bp):
CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
Found at i:39629 original size:14 final size:14
Alignment explanation
Indices: 39610--39638 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
39600 TTTTTCACGG
39610 TCTTGTTTAATTTA
1 TCTTGTTTAATTTA
39624 TCTTGTTTAATTTA
1 TCTTGTTTAATTTA
39638 T
1 T
39639 TTTAATTACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (14 bp):
TCTTGTTTAATTTA
Found at i:41860 original size:736 final size:730
Alignment explanation
Indices: 40443--42481 Score: 2946
Period size: 736 Copynumber: 2.8 Consensus size: 730
40433 AGTTTTAGTG
40443 ACTTGAATTTTCTTTTTTGAATTTTATTATCAGGAACAACTATGGTTCTTGTACAACCATTAGGG
1 ACTTGAATTTTCTTTTTTGAATTTTATTATCAGGAACAACTATGGTTCTTGTACAACCATTAGGG
40508 ATACATGTAATACCCTCACTAATTGGGATATTTGTCTCAA-TTTACCTTAATCAACTGTGGCGAT
66 ATACATGTAATACCCTCACTAATT-GGATATTTGTCTCAATTTTA-CTTAATCAACTGTGGCGAT
*
40572 CGAAATTGGATCATATTGATATGGCGAAAGTTAAGAAGGATGTGTCAACTCTGACATATCATATA
129 CGAAATTGGATCATATTGATATGGCGAAAGTTAAGAAGGATGCGTCAACTCTGACATATCATATA
* *
40637 TTTCAATCGAAAATTAGACTCGATAAGCATCTGATACAGGACATTATGGATCTTTTACCCATAAC
194 TTTCAATCGAAAATTAGGCTCGATAAGCATCTGATACAGGACATTATGGATCTTTTACCCGTAAC
* *
40702 TTATTTGGCAAACGAATTATTTTATTTTATCCAATTAATTCGACCCACAGATCAGAGAAAGAGAT
259 TTATTTGGCCAACG-ATTATTTTATCTTATCCAATTAATTCGACCCACAGATCAGAGAAAGAGAT
* *
40767 CGTTGGTGCAAAAATTGAATATTTGTTTTAATGCACTAGCCTATATATGTATCTTGTTTTATGTG
323 CGTTGGTGCAAAAA-TGAATATTTGTTTTAATGCACTAGCCTATATATGTATCTTGTTTTGTGTT
* *
40832 TTAGTAATTTCATGGCAGACACTTCTTGATATCGTTATCTCCATACTTTCAACGTTTGGAATAGC
387 TTA-T-GTTTCATGG-AGATACTTCTTGATATCGTTATCTCCATACTTTCAACGTTTGGAATAGC
* *
40897 ATGAGCGTCTATTTACCCATTGTTTCTTCGTTTTGTCAATCCCAAGTTGCCATTTATGTCAAAGA
449 AGGAGCGTCTATTTACCCATCGTTTCTTCGTTTTGTCAATCCCAAGTTGCCATTTATGTCAAAGA
* * *** *
40962 TATCTTGCAATTGAATGATTAAATTCAATTGGGAGGAAACACATACATAGTGCGTGATGTGACAA
514 TATCTTGCAATTAAATGATTAAATTCAATTGGGAGGAGACACATACATAAAACATGATGTGACAA
* * *
41027 TATTGAATACAGATCTCGTCAGATCTGATGGAGATATATGTATGTACCAATTGCAAAATATGATA
579 TATTGAATACAGATCTCGTCAGATCTGATGGAGATATATGCATGTACCAACTACAAAATATGATA
* * * * *
41092 GTTTTTATTTAAGTGACTTGAATTTGCTTTGTTGAAG-TGTATGTATAATATAAGCATTGCAAAA
644 GATTCTATTTAAGTGACTTGAATTTACTTTGTTGAAGCT-TATATATAATATAAGCATTGAAAAA
*
41156 TACGATTGTTTCTACTTTTTCTA
708 TACGATTGTTTCTACTTTTACTA
* * *
41179 ACTTGAATTTGT-TTTTTTGAATTTTATTATCAGCAACAACTATGGTTCATGTACAACCATTATG
1 ACTTGAATTT-TCTTTTTTGAATTTTATTATCAGGAACAACTATGGTTCTTGTACAACCATTAGG
* * * * * * *
41243 GATACGTGTAATACCCTCAATAATTAGGATATTTGTCTCAATTTTTCTTAATCATCTCTAGTGAT
65 GATACATGTAATACCCTCACTAATT-GGATATTTGTCTCAATTTTACTTAATCAACTGTGGCGAT
* * ** *
41308 CGAAATTGGATTATATTGATATGGCGAACGTTGGGAAGGATG-GGCAGACTCTGACATATCATAT
129 CGAAATTGGATCATATTGATATGGCGAAAGTTAAGAAGGATGCGTCA-ACTCTGACATATCATAT
* * * *
41372 GTTTCAATCGAAAATT-GTGCTCGATCAA-CATCTGATACAGTAAATTATAGATCTTTTACCCGT
193 ATTTCAATCGAAAATTAG-GCTCGAT-AAGCATCTGATACAGGACATTATGGATCTTTTACCCGT
* *
41435 AACTTATTTGGCCAACAGATTATTTTATCTTATCCAATTAATTCGACCCAAAGATCAGAGAAAGG
256 AACTTATTTGGCCAAC-GATTATTTTATCTTATCCAATTAATTCGACCCACAGATCAGAGAAAGA
* *
41500 GATCGTCGGTGCTGAAAAA-GAAT-TTT-TTTTAAAAGCACTAGCCTATATATGTATCTTGTTTT
320 GATCGTTGGTGC--AAAAATGAATATTTGTTTT-AATGCACTAGCCTATATATGTATCTTGTTTT
* * * * *
41562 GTGTATTTATGTGTTCATGGTGGATACTTCTTGCTATCATTATCTCCATTCTTTCAATGTTTGGA
382 GTGT-TTTATGT-TTCATGG-AGATACTTCTTGATATCGTTATCTCCATACTTTCAACGTTTGGA
* * * * *
41627 ATAGCAGGAGCGTTTATTTACCCATCGTTTCTTCGTTTTGTCGATCTCAAGTTGTCATTTATCTC
444 ATAGCAGGAGCGTCTATTTACCCATCGTTTCTTCGTTTTGTCAATCCCAAGTTGCCATTTATGTC
* * * *
41692 AAAGATATCTTGCAATTAAATAATTAAATTTAATTAGGAGGAGACACATACATAAAACATGATTT
509 AAAGATATCTTGCAATTAAATGATTAAATTCAATTGGGAGGAGACACATACATAAAACATGATGT
* * * * *
41757 GACAATATTGGATAGAGATCTCGTTAGATCTGATGGAGATATATGCATGTATCAACTACCAAATA
574 GACAATATTGAATACAGATCTCGTCAGATCTGATGGAGATATATGCATGTACCAACTACAAAATA
* * * * *
41822 TGATTGATTCTAGTTTTAGTGACTTGAATTTACTTTGTTGAAGCTTATATGTAATTTAGGCATTG
639 TGATAGATTCTA-TTTAAGTGACTTGAATTTACTTTGTTGAAGCTTATATATAATATAAGCATTG
* * *
41887 AAAAATATGATTGTTTCTAGTTTTACTG
703 AAAAATACGATTGTTTCTACTTTTACTA
*
41915 ACTTGAATTTTCTTTTTTGAATTTTATTATCAGGAACATCTATGGTTCTTGTACAACCATTAGGG
1 ACTTGAATTTTCTTTTTTGAATTTTATTATCAGGAACAACTATGGTTCTTGTACAACCATTAGGG
*
41980 ATACATGTAATACCCTCACTAATTGCTATATTTGTCTCAA-TTTACTTTAATCAACTGTGGCGAT
66 ATACATGTAATACCCTCACTAATTG-GATATTTGTCTCAATTTTAC-TTAATCAACTGTGGCGAT
* *
42044 CGAAATTGGATCATATTGATAAGGCGAAAGTTAAGAAGGATGCGTCAACTCTGACATATCATATC
129 CGAAATTGGATCATATTGATATGGCGAAAGTTAAGAAGGATGCGTCAACTCTGACATATCATATA
42109 TTTCAATCGAAAATTAGGCTCGATAAGCATCTGATACAGGACATTATGGATCTTTTACCCGTAAC
194 TTTCAATCGAAAATTAGGCTCGATAAGCATCTGATACAGGACATTATGGATCTTTTACCCGTAAC
* *
42174 TTATTTGGCCAACGGATTATTTTATCTTATCCAATTAATTCGACCCACAGATCAAAGAAAGAAAT
259 TTATTTGGCCAAC-GATTATTTTATCTTATCCAATTAATTCGACCCACAGATCAGAGAAAGAGAT
* * *
42239 CGTTGGCGCAAAAATTGAATATTTGTTTTAATGCATTAGCCTATATATGTAGCTTGTTTTGTGTG
323 CGTTGGTGCAAAAA-TGAATATTTGTTTTAATGCACTAGCCTATATATGTATCTTGTTTTGTGT-
* * ***
42304 TTAATAATTTCCCAGAGATACTTCTTGATATCGTTATCTCCATACTTTCAACGTTTGGAATAGCA
386 TTTAT-GTTTCATGGAGATACTTCTTGATATCGTTATCTCCATACTTTCAACGTTTGGAATAGCA
42369 GGAGCGTCTATTTACCCATCGTTTCTTCGTTTTGTCAATCCCAAGTTGCCATTTATGTCAAAGAT
450 GGAGCGTCTATTTACCCATCGTTTCTTCGTTTTGTCAATCCCAAGTTGCCATTTATGTCAAAGAT
*
42434 ATCTTGCAATCAAATGATTAAATTCAATTGGGAGGAGACACATACATA
515 ATCTTGCAATTAAATGATTAAATTCAATTGGGAGGAGACACATACATA
42482 GTGCATTGTA
Statistics
Matches: 1150, Mismatches: 129, Indels: 48
0.87 0.10 0.04
Matches are distributed among these distances:
734 10 0.01
735 273 0.24
736 802 0.70
737 55 0.05
738 10 0.01
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (730 bp):
ACTTGAATTTTCTTTTTTGAATTTTATTATCAGGAACAACTATGGTTCTTGTACAACCATTAGGG
ATACATGTAATACCCTCACTAATTGGATATTTGTCTCAATTTTACTTAATCAACTGTGGCGATCG
AAATTGGATCATATTGATATGGCGAAAGTTAAGAAGGATGCGTCAACTCTGACATATCATATATT
TCAATCGAAAATTAGGCTCGATAAGCATCTGATACAGGACATTATGGATCTTTTACCCGTAACTT
ATTTGGCCAACGATTATTTTATCTTATCCAATTAATTCGACCCACAGATCAGAGAAAGAGATCGT
TGGTGCAAAAATGAATATTTGTTTTAATGCACTAGCCTATATATGTATCTTGTTTTGTGTTTTAT
GTTTCATGGAGATACTTCTTGATATCGTTATCTCCATACTTTCAACGTTTGGAATAGCAGGAGCG
TCTATTTACCCATCGTTTCTTCGTTTTGTCAATCCCAAGTTGCCATTTATGTCAAAGATATCTTG
CAATTAAATGATTAAATTCAATTGGGAGGAGACACATACATAAAACATGATGTGACAATATTGAA
TACAGATCTCGTCAGATCTGATGGAGATATATGCATGTACCAACTACAAAATATGATAGATTCTA
TTTAAGTGACTTGAATTTACTTTGTTGAAGCTTATATATAATATAAGCATTGAAAAATACGATTG
TTTCTACTTTTACTA
Found at i:46227 original size:15 final size:16
Alignment explanation
Indices: 46203--46242 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
46193 AGAGGTTGAA
*
46203 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
46218 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
46234 AGAAAACAA
1 AGAAAACAA
46243 AGCAAAGTAA
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:65212 original size:36 final size:36
Alignment explanation
Indices: 65096--65212 Score: 101
Period size: 36 Copynumber: 3.2 Consensus size: 36
65086 AATGATCATC
* * *
65096 TGCCACATATTGCTTCTCTGT-CGCAGATTGATGCTC
1 TGCCACATGTTGCTTCTCT-TCCGCAAATTGATGCTA
* * * * * *
65132 TGTCATATGTTGCTTTTCTGCCGCAAACTGATGATA
1 TGCCACATGTTGCTTCTCTTCCGCAAATTGATGCTA
* * * *
65168 TGCGACATGTTACTTCTCTTCCACAAATTGATGCTT
1 TGCCACATGTTGCTTCTCTTCCGCAAATTGATGCTA
65204 TGCCACATG
1 TGCCACATG
65213 ATTTTTCTCT
Statistics
Matches: 60, Mismatches: 20, Indels: 2
0.73 0.24 0.02
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.37
Consensus pattern (36 bp):
TGCCACATGTTGCTTCTCTTCCGCAAATTGATGCTA
Done.