Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016275.1 Corchorus olitorius cultivar O-4 contig16308, 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: 31210
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--27 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
28 TAAACACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:118 original size:2 final size:2
Alignment explanation
Indices: 102--135 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
92 TACTTACCAA
102 AT AT -T AT AT -T 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 AT AT AT
136 TTTGGTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:5548 original size:1 final size:1
Alignment explanation
Indices: 5542--5576 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
5532 TGTCATCTGG
5542 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5577 GTTTCAGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:15469 original size:16 final size:16
Alignment explanation
Indices: 15448--15486 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
15438 TCTCTATAAG
15448 CCAACAAACTCTTTCC
1 CCAACAAACTCTTTCC
15464 CCAACAAACTCTTTCC
1 CCAACAAACTCTTTCC
15480 CCAACAA
1 CCAACAA
15487 TTACAATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.36, C:0.44, G:0.00, T:0.21
Consensus pattern (16 bp):
CCAACAAACTCTTTCC
Found at i:19028 original size:138 final size:140
Alignment explanation
Indices: 18687--19076 Score: 522
Period size: 138 Copynumber: 2.8 Consensus size: 140
18677 CCGGCGCAAA
* *
18687 CTACGATTAGCCCCCCACAATATATCGGCGCAGATGCAT-ATGGGGCCAAAAGCAATCTCGTTCA
1 CTACGATTAGCCCCCCACAATATATCGGCGCGGATGCATGATGGGGCCAAAAGCAATCTCGTCCA
* *
18751 TTGAAAAAGGCT-GCGCCATATGAGAGCCATCTGTTTTGAGTACTCACAGTTTTTTTTGTCACCG
66 TTGAAAAAGG-TGGCGCCATATGAGAGCCATCTGTTTTGAGTACTTAC-GTATTTTTTGTCACCG
* *
18815 AAAAGGCGCGGG
129 AAAAGGCACGAG
* * * *
18827 CTACGATTAACCCCTCACAATATGTCTGCGCGGATGCATG-TGGGGCCAAAAGCAATCTCGTCCA
1 CTACGATTAGCCCCCCACAATATATCGGCGCGGATGCATGATGGGGCCAAAAGCAATCTCGTCCA
* *
18891 TTGAAAAAGGTGGTGCCATATGAGAGCCATCTGTTTTGAGTACTTACG-ATTTTTTGTCACTGAA
66 TTGAAAAAGGTGGCGCCATATGAGAGCCATCTGTTTTGAGTACTTACGTATTTTTTGTCACCGAA
*
18955 AGGGCACGAG
131 AAGGCACGAG
* *** *
18965 CTACGATTAGCCCCCCACAGTATATCGGTATGGATGCATGAT-GGGCCAAAAGCAATCTTGTCCA
1 CTACGATTAGCCCCCCACAATATATCGGCGCGGATGCATGATGGGGCCAAAAGCAATCTCGTCCA
* * *
19029 TT-AAAATAGGCGGCACCATATGAGAGCCATCCGTTTTGAGTACTTACG
66 TTGAAAA-AGGTGGCGCCATATGAGAGCCATCTGTTTTGAGTACTTACG
19077 GGCTTTTTTC
Statistics
Matches: 220, Mismatches: 26, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
137 4 0.02
138 113 0.51
139 3 0.01
140 100 0.45
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (140 bp):
CTACGATTAGCCCCCCACAATATATCGGCGCGGATGCATGATGGGGCCAAAAGCAATCTCGTCCA
TTGAAAAAGGTGGCGCCATATGAGAGCCATCTGTTTTGAGTACTTACGTATTTTTTGTCACCGAA
AAGGCACGAG
Found at i:21399 original size:21 final size:21
Alignment explanation
Indices: 21373--21414 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
21363 TTAGTGCTTT
21373 AAACTATATATAAATCTTGAG
1 AAACTATATATAAATCTTGAG
21394 AAACTATATATAAATCTTGAG
1 AAACTATATATAAATCTTGAG
21415 TCTTGACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (21 bp):
AAACTATATATAAATCTTGAG
Found at i:26384 original size:63 final size:62
Alignment explanation
Indices: 26317--26616 Score: 197
Period size: 63 Copynumber: 4.9 Consensus size: 62
26307 GTACTGGTGG
* *
26317 TGGTGGAGGTAGTGCTGGTGGAGCTTCAGGTTATGGAAGTGGAGGTGGCGAAGGAGGTGGAGC
1 TGGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGTGGCGAAGGAGGTGG-GC
* * * * **** * * *
26380 TGGTGGTGCCGGA-T-ATGGAGGAGCAGGGGGCTATGGAGGTGGAGGTGGTGGAGGCAAAGGT-G
1 TGGTGGAG--GTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGTGGCGAAGG---AGGTGG
26442 GC
61 GC
* *
26444 -GGTGGAGGTAGTGCCGGTGGAGCTTCAGGATATGGAGGTGGAGGCGGCGAAGGAGGTGGGGC
1 TGGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGTGGCGAAGGAGGT-GGGC
* * * * * **** * * *
26506 TGGTGGTGCTGGTTAC-GGAGGAGCAGGGGGGTATGGAGGTGGTGGAGGC-AA-G-GGT-GGC
1 TGGTGGAGGTAG-TGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGTGGCGAAGGAGGTGGGC
* *
26564 -GGTGGAGGTAGTGCTGGTGGAGCTTCTGGATATGGAGGTGGAGGAGGCGAAGG
1 TGGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGTGGCGAAGG
26617 CGGCGGAGTT
Statistics
Matches: 175, Mismatches: 48, Indels: 32
0.69 0.19 0.13
Matches are distributed among these distances:
56 2 0.01
57 34 0.19
58 5 0.03
59 1 0.01
60 7 0.04
61 3 0.02
62 6 0.03
63 105 0.60
64 5 0.03
65 3 0.02
66 4 0.02
ACGTcount: A:0.18, C:0.09, G:0.54, T:0.19
Consensus pattern (62 bp):
TGGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGTGGCGAAGGAGGTGGGC
Found at i:26481 original size:57 final size:57
Alignment explanation
Indices: 26419--26622 Score: 183
Period size: 57 Copynumber: 3.5 Consensus size: 57
26409 GCTATGGAGG
*
26419 TGGAGGTGGTGGAGGCAAAGGTGGCGGTGGAGGTAGTGCCGGTGGAGCTTCAGGATA
1 TGGAGGTGGAGGAGGCAAAGGTGGCGGTGGAGGTAGTGCCGGTGGAGCTTCAGGATA
* * * * ** * **** *
26476 TGGAGGTGGAGGCGGCGAAGGAGGTGGGGCTGGTGGTGCTGGTTACGGAGGAGCAGGGGGGTA
1 TGGAGGTGGAGGAGGC-AA--AGGT--GGC-GGTGGAGGTAGTGCCGGTGGAGCTTCAGGATA
* * * *
26539 TGGAGGTGGTGGAGGCAAGGGTGGCGGTGGAGGTAGTGCTGGTGGAGCTTCTGGATA
1 TGGAGGTGGAGGAGGCAAAGGTGGCGGTGGAGGTAGTGCCGGTGGAGCTTCAGGATA
* *
26596 TGGAGGTGGAGGAGGCGAAGGCGGCGG
1 TGGAGGTGGAGGAGGCAAAGGTGGCGG
26623 AGTTGGCGGT
Statistics
Matches: 109, Mismatches: 32, Indels: 12
0.71 0.21 0.08
Matches are distributed among these distances:
57 57 0.52
58 5 0.05
60 7 0.06
62 5 0.05
63 35 0.32
ACGTcount: A:0.17, C:0.10, G:0.55, T:0.18
Consensus pattern (57 bp):
TGGAGGTGGAGGAGGCAAAGGTGGCGGTGGAGGTAGTGCCGGTGGAGCTTCAGGATA
Found at i:26583 original size:120 final size:120
Alignment explanation
Indices: 26312--26719 Score: 487
Period size: 120 Copynumber: 3.4 Consensus size: 120
26302 TGGTGGTACT
* * * *
26312 GGTGGTGGTGGAGGTAGTGCTGGTGGAGCTTCAGGTTATGGAAGTGGAGGTGGCGAAGGAGGTGG
1 GGTGGCGGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGAGGCGAAGGAGGTGG
* * * *
26377 AGCTGGTGGTGCCGGATATGGAGGAGCAGGGGGCTATGGAGGTGGAGGTGGTGGAGGCAAA
66 AGCTGGTGGTGCTGGATACGGAGGAGCAGGGGG----GTA--TGGAGGTGGTGGAGGCAAG
* *
26438 GGTGGCGGTGGAGGTAGTGCCGGTGGAGCTTCAGGATATGGAGGTGGAGGCGGCGAAGGAGGTGG
1 GGTGGCGGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGAGGCGAAGGAGGTGG
* *
26503 GGCTGGTGGTGCTGGTTACGGAGGAGCAGGGGGGTATGGAGGTGGTGGAGGCAAG
66 AGCTGGTGGTGCTGGATACGGAGGAGCAGGGGGGTATGGAGGTGGTGGAGGCAAG
* * *
26558 GGTGGCGGTGGAGGTAGTGCTGGTGGAGCTTCTGGATATGGAGGTGGAGGAGGCGAAGGCGGCGG
1 GGTGGCGGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGAGGCGAAGGAGGTGG
* * * * * * * *
26623 AGTTGGCGGTGCTGGGTACGGAGGAGC-CGGTGGTCACGGAGGCGGTGGTGGC-AG
66 AGCTGGTGGTGCTGGATACGGAGGAGCAGGGGGGT-ATGGAGGTGGTGGAGGCAAG
* * * *
26677 TGGAGGTGGAGGAGGTAGTGCTGGTGGAGCTTCTGGATATGGA
1 -GGTGGCGGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGA
26720 AGCGGGGGTG
Statistics
Matches: 252, Mismatches: 28, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
119 7 0.03
120 154 0.61
122 2 0.01
126 89 0.35
ACGTcount: A:0.17, C:0.10, G:0.54, T:0.19
Consensus pattern (120 bp):
GGTGGCGGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGAGGCGAAGGAGGTGG
AGCTGGTGGTGCTGGATACGGAGGAGCAGGGGGGTATGGAGGTGGTGGAGGCAAG
Found at i:26796 original size:12 final size:13
Alignment explanation
Indices: 26777--26814 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
26767 TGCTGGTTCA
26777 GGAGGTGGTGGAG
1 GGAGGTGGTGGAG
26790 GGA-GTGGTGG-G
1 GGAGGTGGTGGAG
*
26801 GGAGGTGGAGGAG
1 GGAGGTGGTGGAG
26814 G
1 G
26815 ATATGGGGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
11 4 0.18
12 13 0.59
13 5 0.23
ACGTcount: A:0.16, C:0.00, G:0.71, T:0.13
Consensus pattern (13 bp):
GGAGGTGGTGGAG
Found at i:27818 original size:16 final size:17
Alignment explanation
Indices: 27798--27835 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
27788 AGTCAATTTG
27798 CTTTTATCGAGTCAGTT
1 CTTTTATCGAGTCAGTT
* *
27815 -TTTTTTCTAGTCAGTT
1 CTTTTATCGAGTCAGTT
27831 CTTTT
1 CTTTT
27836 TGAATTTGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.13, C:0.16, G:0.13, T:0.58
Consensus pattern (17 bp):
CTTTTATCGAGTCAGTT
Found at i:29892 original size:16 final size:16
Alignment explanation
Indices: 29871--29906 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
29861 TGGCGCTGCG
29871 AATGCTTTTGGCATGC
1 AATGCTTTTGGCATGC
29887 AATGCTTTTGGCATGC
1 AATGCTTTTGGCATGC
29903 AATG
1 AATG
29907 TGGTGGTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (16 bp):
AATGCTTTTGGCATGC
Found at i:30547 original size:26 final size:26
Alignment explanation
Indices: 30493--30591 Score: 166
Period size: 26 Copynumber: 3.8 Consensus size: 26
30483 GTGTTTTTTC
30493 TTCTCTTAGAGTTG-TT-AGTTGATTT
1 TTCTCTTAGAGTTGATTGA-TTGATTT
30518 TTCTCTTAGAGTTGATTGATTGATTT
1 TTCTCTTAGAGTTGATTGATTGATTT
*
30544 TTCTCTTAGAGTTCATTGATTGATTT
1 TTCTCTTAGAGTTGATTGATTGATTT
30570 TTCTCTTAGAGTTGATTGATTG
1 TTCTCTTAGAGTTGATTGATTG
30592 CCATTTTCGA
Statistics
Matches: 70, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
25 14 0.20
26 55 0.79
27 1 0.01
ACGTcount: A:0.18, C:0.09, G:0.19, T:0.54
Consensus pattern (26 bp):
TTCTCTTAGAGTTGATTGATTGATTT
Done.