Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019354.1 Corchorus olitorius cultivar O-4 contig19387, 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: 62602
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:903 original size:15 final size:15
Alignment explanation
Indices: 883--912 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
873 ATCAGGCTGC
*
883 CACGATACACGATAT
1 CACGATACACAATAT
898 CACGATACACAATAT
1 CACGATACACAATAT
913 TTCAACCGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (15 bp):
CACGATACACAATAT
Found at i:7875 original size:17 final size:16
Alignment explanation
Indices: 7837--7896 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
7827 AGCTTACATG
* *
7837 GTGATCTAATCACTAT
1 GTGATCTAATCACCAA
*
7853 GTTGATCTAATCATCAA
1 G-TGATCTAATCACCAA
*
7870 GATGATATAATCACCAA
1 G-TGATCTAATCACCAA
*
7887 GGGATCTAAT
1 GTGATCTAAT
7897 TGATGGTGAT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
16 8 0.23
17 27 0.77
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.32
Consensus pattern (16 bp):
GTGATCTAATCACCAA
Found at i:11729 original size:107 final size:104
Alignment explanation
Indices: 11618--11899 Score: 413
Period size: 104 Copynumber: 2.7 Consensus size: 104
11608 TTATTACAGA
* *
11618 GTTTTAGAAATAAAATATAAAACTAATTTCATTAAGTTTAGCCCCAAATTAAAATTTTATTTTTA
1 GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTGTAG-CCCAAATTAAAATTTTATTTTTA
* *
11683 TTTTAAGAGTAAATTTCAAAATTAATAATTTATTGTTATAGG
65 TTTTAAGAGTAAATTCCAAAATTAATAA--TATTGTTATAAG
* * *
11725 GTTTTAGAAATAAAATAGAAAACTAATTTCACTAAGTGTAGCTCAAATTAAAAATTTATTTTTAT
1 GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTGTAGCCCAAATTAAAATTTTATTTTTAT
* *
11790 TTTAAGGGTAAATTCCATAATTAATAATATTGTTATAAG
66 TTTAAGAGTAAATTCCAAAATTAATAATATTGTTATAAG
* **
11829 GTTTTAGAAATAAAATATATAACTAA-TTCACTAAGTGTAGCCCAAATTAAAATTAAAATTTTTA
1 GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTGTAGCCCAAATTAAAATT-TTATTTTTA
11893 TTTTAAG
65 TTTTAAG
11900 GGTTAGAAAA
Statistics
Matches: 159, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
103 26 0.16
104 49 0.31
106 46 0.29
107 38 0.24
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.40
Consensus pattern (104 bp):
GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTGTAGCCCAAATTAAAATTTTATTTTTAT
TTTAAGAGTAAATTCCAAAATTAATAATATTGTTATAAG
Found at i:12674 original size:22 final size:22
Alignment explanation
Indices: 12648--12698 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
12638 TCACCAGATT
*
12648 CACCATAGCCCCCTTCCGGCAC
1 CACCACAGCCCCCTTCCGGCAC
12670 CACCACAGCCCCCTTCCGGCAC
1 CACCACAGCCCCCTTCCGGCAC
12692 CACCACA
1 CACCACA
12699 ACCACGCCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.22, C:0.57, G:0.12, T:0.10
Consensus pattern (22 bp):
CACCACAGCCCCCTTCCGGCAC
Found at i:15292 original size:2 final size:2
Alignment explanation
Indices: 15287--15316 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15277 CCATGGTCCT
15287 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15317 CTAGTTAAAG
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):
TA
Found at i:18214 original size:36 final size:36
Alignment explanation
Indices: 18167--18236 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
18157 TTCAATAACC
* *
18167 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
18203 TTACATCTTTTGTAATTTTGATTATTATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
18237 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:19174 original size:39 final size:40
Alignment explanation
Indices: 19120--19200 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
19110 ATACCTAAGA
19120 ATTTAAGTAATGTAAGTATTTCAGTTATTATA-ATATTAC
1 ATTTAAGTAATGTAAGTATTTCAGTTATTATATATATTAC
* *
19159 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAAGTAATGTAAGTATTTCAGTTATTATATATATTAC
19199 AT
1 AT
19201 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 30 0.77
40 9 0.23
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (40 bp):
ATTTAAGTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:24507 original size:32 final size:32
Alignment explanation
Indices: 24447--24539 Score: 111
Period size: 31 Copynumber: 3.0 Consensus size: 32
24437 GTGTCCAATG
*
24447 TGACACGCCACGTGTACCAAAAAA-TGACACA
1 TGACACGCCACGTGTATCAAAAAAGTGACACA
*
24478 T-ATCACGCCACGTGTATCAAAAAAGTGACACG
1 TGA-CACGCCACGTGTATCAAAAAAGTGACACA
* * *
24510 TGACATGCCATGTGTTTC-AAAAAGTGACAC
1 TGACACGCCACGTGTATCAAAAAAGTGACAC
24540 GTGGCATGCC
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
30 1 0.02
31 33 0.61
32 19 0.35
33 1 0.02
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (32 bp):
TGACACGCCACGTGTATCAAAAAAGTGACACA
Found at i:32617 original size:21 final size:20
Alignment explanation
Indices: 32578--32619 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
32568 CTATGTAATC
32578 TAAAATTACTAAAAAAATTA
1 TAAAATTACTAAAAAAATTA
* *
32598 TAAAAGTTATTAAAATAATTA
1 TAAAA-TTACTAAAAAAATTA
32619 T
1 T
32620 TCTACAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
TAAAATTACTAAAAAAATTA
Found at i:36875 original size:2 final size:2
Alignment explanation
Indices: 36868--36893 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
36858 AGAAGTTTTA
36868 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
36894 TCTTTTTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37279 original size:33 final size:33
Alignment explanation
Indices: 37232--37302 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
37222 TTACATTAAG
*
37232 AAAATTAATAAACATAAAGATTAGAAAGAAAAT
1 AAAAGTAATAAACATAAAGATTAGAAAGAAAAT
*
37265 AAAAGTAATAAACATGAAGATTAGAAAGAAAAT
1 AAAAGTAATAAACATAAAGATTAGAAAGAAAAT
37298 AAAAG
1 AAAAG
37303 AATGGTGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.66, C:0.03, G:0.13, T:0.18
Consensus pattern (33 bp):
AAAAGTAATAAACATAAAGATTAGAAAGAAAAT
Found at i:40899 original size:27 final size:27
Alignment explanation
Indices: 40869--40951 Score: 96
Period size: 27 Copynumber: 3.1 Consensus size: 27
40859 GAGGTTTGCG
*
40869 GGGGAACAGGAGAGAGACATGGAAGCT
1 GGGGAACAGGAGAGAGACGTGGAAGCT
* *
40896 GGGGAACAGGAGA-AGGACGTGGAAACA
1 GGGGAACAGGAGAGA-GACGTGGAAGCT
** *
40923 GAAGAACAGGAGAGGGACGTGGAAGCT
1 GGGGAACAGGAGAGAGACGTGGAAGCT
40950 GG
1 GG
40952 CCCTAGGTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
26 1 0.02
27 44 0.98
ACGTcount: A:0.37, C:0.11, G:0.46, T:0.06
Consensus pattern (27 bp):
GGGGAACAGGAGAGAGACGTGGAAGCT
Found at i:44746 original size:30 final size:30
Alignment explanation
Indices: 44712--44770 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
44702 TTTTTTTTAG
*
44712 ATTAATCTTTTTGTTGATAGTATTTTGTAC
1 ATTAATCTTTTTGTTGATAGCATTTTGTAC
*
44742 ATTAATTTTTTTGTTGATAGCATTTTGTA
1 ATTAATCTTTTTGTTGATAGCATTTTGTA
44771 AGTTTATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.24, C:0.05, G:0.14, T:0.58
Consensus pattern (30 bp):
ATTAATCTTTTTGTTGATAGCATTTTGTAC
Found at i:45849 original size:27 final size:27
Alignment explanation
Indices: 45808--45859 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
45798 CTAGGGCCCG
*
45808 CTTCCACGTCTCTCTCCTGTTCCCCAA
1 CTTCCACGTCCCTCTCCTGTTCCCCAA
45835 CTTCCACGTCCCTCTCCTGTTCCCC
1 CTTCCACGTCCCTCTCCTGTTCCCC
45860 CGCAAACCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.08, C:0.52, G:0.08, T:0.33
Consensus pattern (27 bp):
CTTCCACGTCCCTCTCCTGTTCCCCAA
Found at i:46920 original size:19 final size:20
Alignment explanation
Indices: 46896--46950 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
46886 TGATACACAT
46896 GAGTGAATCACGTAAG-TGA
1 GAGTGAATCACGTAAGTTGA
* ** *
46915 GAGTGAATCACTTGGGTTGG
1 GAGTGAATCACGTAAGTTGA
46935 GAGTGAATCACGTAAG
1 GAGTGAATCACGTAAG
46951 GTCTGAGGTC
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.31, C:0.11, G:0.35, T:0.24
Consensus pattern (20 bp):
GAGTGAATCACGTAAGTTGA
Found at i:55890 original size:102 final size:105
Alignment explanation
Indices: 55650--55926 Score: 341
Period size: 107 Copynumber: 2.6 Consensus size: 105
55640 TTTGTTTTTA
*
55650 TTATAGAGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTT
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAA-T-AAATTTT
* *
55715 ATTTTTATTTTAAGAGTAAATTTCAAAACTAATCATTTATTG
64 ATTTTTATTTTAAGAGTAAATTCCAAAACTAATCATATATTG
* ** *
55757 TTATAGGATTTTAGAAATAAAATGCAAAACTAATTTCATTAAGTTTAGCCCCAAAT-AATTTT-T
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATAAATTTTAT
* * *
55820 TTTTATTTTAAGGGTAAAATTCCATAATTAAT-A-ATATTG
66 TTTTATTTTAAGAGT-AAATTCCAAAACTAATCATATATTG
* * * *
55859 TTATAGGGTTTTAAAAATAAAATATATAACTAA-TTCACTAAATTTAG-CCCAAATTAAAATATT
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAA-T-AAATTTT
55922 ATTTT
64 ATTTT
55927 AAGGGTTAGG
Statistics
Matches: 147, Mismatches: 18, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
100 6 0.04
101 13 0.09
102 33 0.22
103 21 0.14
104 23 0.16
106 1 0.01
107 50 0.34
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (105 bp):
TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATAAATTTTAT
TTTTATTTTAAGAGTAAATTCCAAAACTAATCATATATTG
Found at i:57796 original size:149 final size:148
Alignment explanation
Indices: 57524--57818 Score: 428
Period size: 149 Copynumber: 2.0 Consensus size: 148
57514 CAAATTATAA
* * * ** * *
57524 GAAGTTAAATTACCAAAAAAATTGTCTAACCCAATCACGACATTTGTTTGGTTATTATTTAGCTT
1 GAAGTGAAAATACCAAAAAAATTGTCTAACCCAATCACCACATTCATTTGGTTACTATTTAACTT
* *
57589 GATTTTTTTATCAATTCAATCTTGATTTTTTAGCTCTTCTCACAAACTTCTAAGGGTATTTTTTA
66 GATTTTTTTATCAATTCAATCTTGATTTTTTAGCTCTTCTCACAAACTTCTAAAGGTATTTTTGA
*
57654 CTTTCTAGCATTTTAACT
131 CTTTCTAACATTTTAACT
57672 GAAGTGAAAATACCAAAAAAAATTGTCTAACCCAATCACCACATTCATTTGGTTACTATTTAACT
1 GAAGTGAAAATACC-AAAAAAATTGTCTAACCCAATCACCACATTCATTTGGTTACTATTTAACT
* * * * * * *
57737 TGGTTTTTTTGTCATTTCAATCTTGGTTTTTTAGTTCTTCTTACAAACTTTTAAAGGTATTTTTG
65 TGATTTTTTTATCAATTCAATCTTGATTTTTTAGCTCTTCTCACAAACTTCTAAAGGTATTTTTG
57802 ACTTTCTAACATTTTAA
130 ACTTTCTAACATTTTAA
57819 ATTATAATAT
Statistics
Matches: 129, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
148 12 0.09
149 117 0.91
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (148 bp):
GAAGTGAAAATACCAAAAAAATTGTCTAACCCAATCACCACATTCATTTGGTTACTATTTAACTT
GATTTTTTTATCAATTCAATCTTGATTTTTTAGCTCTTCTCACAAACTTCTAAAGGTATTTTTGA
CTTTCTAACATTTTAACT
Found at i:59180 original size:13 final size:13
Alignment explanation
Indices: 59162--59186 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59152 ATAAGTAAAT
59162 AATAAAAATAATA
1 AATAAAAATAATA
59175 AATAAAAATAAT
1 AATAAAAATAAT
59187 CACGTCGTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AATAAAAATAATA
Found at i:59751 original size:26 final size:26
Alignment explanation
Indices: 59715--59769 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
59705 ACAAATTACA
59715 AACAAACTCACATTCCGTGAGAGTTG
1 AACAAACTCACATTCCGTGAGAGTTG
59741 AACAAACTCACATTCCGTGAGAGTTG
1 AACAAACTCACATTCCGTGAGAGTTG
59767 AAC
1 AAC
59770 CCAAGACCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (26 bp):
AACAAACTCACATTCCGTGAGAGTTG
Found at i:62572 original size:24 final size:24
Alignment explanation
Indices: 62535--62580 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
62525 TTTGTCAGTC
** *
62535 TAAAACCAGGATAATATACCAATA
1 TAAAACCAAAATAATAAACCAATA
62559 TAAAACCAAAATAATAAACCAA
1 TAAAACCAAAATAATAAACCAA
62581 AATATCAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.61, C:0.17, G:0.04, T:0.17
Consensus pattern (24 bp):
TAAAACCAAAATAATAAACCAATA
Done.