Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020873.1 Corchorus olitorius cultivar O-4 contig20906, 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: 117163
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7129 original size:68 final size:68
Alignment explanation
Indices: 7047--7185 Score: 278
Period size: 68 Copynumber: 2.0 Consensus size: 68
7037 TCAAGTCTTG
7047 GAAAGCCGGTTATTGGCTTAAGACTTGACGGGTTGGGCCGTACGGGGGAGAGATGAGGACTCACA
1 GAAAGCCGGTTATTGGCTTAAGACTTGACGGGTTGGGCCGTACGGGGGAGAGATGAGGACTCACA
7112 AGT
66 AGT
7115 GAAAGCCGGTTATTGGCTTAAGACTTGACGGGTTGGGCCGTACGGGGGAGAGATGAGGACTCACA
1 GAAAGCCGGTTATTGGCTTAAGACTTGACGGGTTGGGCCGTACGGGGGAGAGATGAGGACTCACA
7180 AGT
66 AGT
7183 GAA
1 GAA
7186 TCGGGAGAGA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 71 1.00
ACGTcount: A:0.26, C:0.16, G:0.38, T:0.20
Consensus pattern (68 bp):
GAAAGCCGGTTATTGGCTTAAGACTTGACGGGTTGGGCCGTACGGGGGAGAGATGAGGACTCACA
AGT
Found at i:16144 original size:40 final size:40
Alignment explanation
Indices: 16084--16163 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
16074 AGTTAATGAC
* *
16084 TTTCTTTTCTTAACTAAATTTTCTTAAAAACACTTATAAA
1 TTTCATTTCTTAACTAAATTTTCTTAAAAAAACTTATAAA
16124 TTTCATTTCTTAACTAAATTTTCTTAAAAAAACTTATAAA
1 TTTCATTTCTTAACTAAATTTTCTTAAAAAAACTTATAAA
16164 ATAAAACAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (40 bp):
TTTCATTTCTTAACTAAATTTTCTTAAAAAAACTTATAAA
Found at i:16592 original size:21 final size:21
Alignment explanation
Indices: 16568--16608 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16558 GTTGCTCTCG
*
16568 AAAATT-AGGTTAAATAAAATT
1 AAAATTAAAGTTAAA-AAAATT
16589 AAAATTAAAGTTAAAAAAAT
1 AAAATTAAAGTTAAAAAAAT
16609 GGGTTAGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.29
Consensus pattern (21 bp):
AAAATTAAAGTTAAAAAAATT
Found at i:24423 original size:22 final size:22
Alignment explanation
Indices: 24398--24444 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
24388 TCCACAGCAT
24398 GTTGAATCAAAGGAATCATATG
1 GTTGAATCAAAGGAATCATATG
24420 GTTGAATCAAAGGAATCATATG
1 GTTGAATCAAAGGAATCATATG
24442 GTT
1 GTT
24445 ATCTATAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (22 bp):
GTTGAATCAAAGGAATCATATG
Found at i:25724 original size:42 final size:42
Alignment explanation
Indices: 25642--25726 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
25632 GGCAAAGTCC
* * * * *
25642 TGATTAATCCGGATTCGACCCGTGTTATACACTTGGTTATGG
1 TGATTAATCCGGATCCGACCCGTGTCACACACCTGATTATGG
* * *
25684 TGATTAATCCGGATCCGACTCGTGTCGCGCACCTGATTATGG
1 TGATTAATCCGGATCCGACCCGTGTCACACACCTGATTATGG
25726 T
1 T
25727 AGGTAAGTCT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (42 bp):
TGATTAATCCGGATCCGACCCGTGTCACACACCTGATTATGG
Found at i:49150 original size:15 final size:15
Alignment explanation
Indices: 49111--49166 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
49101 TGGTTGGGGT
*
49111 GGTGGTGCTGGTGGC
1 GGTGGTGGTGGTGGC
49126 GGCT--TAGGTGGTGGC
1 GG-TGGT-GGTGGTGGC
*
49141 GGTGGTGGTGGTGGA
1 GGTGGTGGTGGTGGC
*
49156 GGTGGGGGTGG
1 GGTGGTGGTGG
49167 AGGTGGCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
14 2 0.06
15 30 0.88
16 2 0.06
ACGTcount: A:0.04, C:0.07, G:0.64, T:0.25
Consensus pattern (15 bp):
GGTGGTGGTGGTGGC
Found at i:49159 original size:12 final size:12
Alignment explanation
Indices: 49131--49172 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
49121 GTGGCGGCTT
*
49131 AGGTGGTGGCGG
1 AGGTGGTGGTGG
*
49143 TGGTGGTGGTGG
1 AGGTGGTGGTGG
*
49155 AGGTGGGGGTGG
1 AGGTGGTGGTGG
49167 AGGTGG
1 AGGTGG
49173 CAATGGGGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.07, C:0.02, G:0.69, T:0.21
Consensus pattern (12 bp):
AGGTGGTGGTGG
Found at i:52670 original size:12 final size:12
Alignment explanation
Indices: 52644--52685 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
52634 TAAGTGGCAA
52644 TGGAGG-GGAAGG
1 TGGAGGAGG-AGG
*
52656 TGGTGGAGGAGG
1 TGGAGGAGGAGG
52668 TGGAGGAGGAGG
1 TGGAGGAGGAGG
*
52680 AGGAGG
1 TGGAGG
52686 TGGTGGTGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 24 0.92
13 2 0.08
ACGTcount: A:0.24, C:0.00, G:0.67, T:0.10
Consensus pattern (12 bp):
TGGAGGAGGAGG
Found at i:52671 original size:9 final size:9
Alignment explanation
Indices: 52657--52688 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
52647 AGGGGAAGGT
52657 GGTGGAGGA
1 GGTGGAGGA
52666 GGTGGAGGA
1 GGTGGAGGA
*
52675 GGAGGAGGA
1 GGTGGAGGA
52684 GGTGG
1 GGTGG
52689 TGGTGGGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.22, C:0.00, G:0.69, T:0.09
Consensus pattern (9 bp):
GGTGGAGGA
Found at i:52739 original size:123 final size:122
Alignment explanation
Indices: 52534--52805 Score: 366
Period size: 123 Copynumber: 2.2 Consensus size: 122
52524 GAGTAGGAAT
* * * * *
52534 GGGAGGAGGAGGGGGAGGTGGAGGTGGTGGTGGGGGTGGGGAGGTTTAGGTTCAGGTGGAGGAAA
1 GGGAGGAGGAGGTGGAGGAGGAGGAGGAGGTGGGGGTGGGGAGGTATAGGTTCAGGTGGAGGAAA
* * * *
52599 TGGCCATGGTAGTGGTTATGGAGCGGGTGGTGGTGTAAGTGGCAATGGAGG-GGAAGG
66 TGGCCATGGAAGTGGTTACGGAGCAGGTGGGGGTGTAAGTGGCAATGGAGGAGG-AGG
* * * * *
52656 TGGTGGAGGAGGTGGAGGAGGAGGAGGAGGTGGTGGTGGGAGTGGTATAGGTTCAGGTGGAGGAT
1 GGGAGGAGGAGGTGGAGGAGGAGGAGGAGGTGGGGGTGGG-GAGGTATAGGTTCAGGTGGAGGAA
*
52721 ATGGCCATGGAAGTGGTTACGGAGCAGGTGGGGGTGTAGGTGGCAATGGAGGAGGAGG
65 ATGGCCATGGAAGTGGTTACGGAGCAGGTGGGGGTGTAAGTGGCAATGGAGGAGGAGG
* *
52779 GGGAGGGGGAGGTGGTGGAGGAGGAGG
1 GGGAGGAGGAGGTGGAGGAGGAGGAGG
52806 TGGCAGTACT
Statistics
Matches: 129, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
122 33 0.26
123 94 0.73
124 2 0.02
ACGTcount: A:0.20, C:0.04, G:0.58, T:0.18
Consensus pattern (122 bp):
GGGAGGAGGAGGTGGAGGAGGAGGAGGAGGTGGGGGTGGGGAGGTATAGGTTCAGGTGGAGGAAA
TGGCCATGGAAGTGGTTACGGAGCAGGTGGGGGTGTAAGTGGCAATGGAGGAGGAGG
Found at i:52798 original size:15 final size:15
Alignment explanation
Indices: 52768--52808 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
52758 AGGTGGCAAT
* *
52768 GGAGGAGGAGGGGGA
1 GGAGGAGGTGGTGGA
*
52783 GGGGGAGGTGGTGGA
1 GGAGGAGGTGGTGGA
52798 GGAGGAGGTGG
1 GGAGGAGGTGG
52809 CAGTACTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.20, C:0.00, G:0.73, T:0.07
Consensus pattern (15 bp):
GGAGGAGGTGGTGGA
Found at i:69566 original size:2 final size:2
Alignment explanation
Indices: 69559--69588 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
69549 CTTTGAAGTC
69559 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
69589 TGGAAATTAT
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:79804 original size:27 final size:28
Alignment explanation
Indices: 79752--79818 Score: 134
Period size: 28 Copynumber: 2.4 Consensus size: 28
79742 GTCTTTTAAT
79752 AACCTTTTTTTCTTTGGTCCCAAAAAAA
1 AACCTTTTTTTCTTTGGTCCCAAAAAAA
79780 AACCTTTTTTTCTTTGGTCCCAAAAAAA
1 AACCTTTTTTTCTTTGGTCCCAAAAAAA
79808 AACCTTTTTTT
1 AACCTTTTTTT
79819 TTCTTCTGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.43
Consensus pattern (28 bp):
AACCTTTTTTTCTTTGGTCCCAAAAAAA
Found at i:87822 original size:22 final size:23
Alignment explanation
Indices: 87797--87845 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
87787 AATTGAACAC
* *
87797 ATTGAA-CCGAGTAATCTGAAGT
1 ATTGAACCCGACTAATCCGAAGT
87819 ATTGAACCCCGACTAATCCGAAGT
1 ATTGAA-CCCGACTAATCCGAAGT
87843 ATT
1 ATT
87846 CGGATATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 6 0.26
24 17 0.74
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (23 bp):
ATTGAACCCGACTAATCCGAAGT
Found at i:90141 original size:33 final size:33
Alignment explanation
Indices: 90103--90170 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
90093 CTATATATTT
90103 AAAGTATTTATCATCATCATTATTCTAGTTTTA
1 AAAGTATTTATCATCATCATTATTCTAGTTTTA
90136 AAAGTATTTATCATCATCATTATTCTAGTTTTA
1 AAAGTATTTATCATCATCATTATTCTAGTTTTA
90169 AA
1 AA
90171 GGTCAACCTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (33 bp):
AAAGTATTTATCATCATCATTATTCTAGTTTTA
Done.