Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018668.1 Corchorus olitorius cultivar O-4 contig18701, 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: 75815
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:7767 original size:8 final size:8
Alignment explanation
Indices: 7754--7788 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
7744 GAGGAATGAT
7754 GAAGAAAA
1 GAAGAAAA
7762 GAAGAAAA
1 GAAGAAAA
*
7770 AAAGAAAA
1 GAAGAAAA
7778 GAAGAAAA
1 GAAGAAAA
7786 GAA
1 GAA
7789 ACAAATTGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (8 bp):
GAAGAAAA
Found at i:12942 original size:11 final size:11
Alignment explanation
Indices: 12928--12965 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
12918 ATTCATAACA
12928 AATTTATAATT
1 AATTTATAATT
12939 AATTTATAATT
1 AATTTATAATT
12950 -ATTTGATAATT
1 AATTT-ATAATT
*
12961 TATTT
1 AATTT
12966 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:20408 original size:26 final size:26
Alignment explanation
Indices: 20379--20428 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
20369 ATCTCTCTCT
20379 TAATTGTGTCTTCAG-GACCATTTACA
1 TAATTGTGTCTTCAGAG-CCATTTACA
*
20405 TAATTTTGTCTTCAGAGCCATTTA
1 TAATTGTGTCTTCAGAGCCATTTA
20429 AGGATTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (26 bp):
TAATTGTGTCTTCAGAGCCATTTACA
Found at i:21062 original size:33 final size:34
Alignment explanation
Indices: 21006--21075 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 34
20996 ATTTTTAATA
* *
21006 AAAAAAAAAGTAGAAGGAGGAGATTATGCATGAT
1 AAAAAAAAAGTAGAAGGAAGAGATCATGCATGAT
* *
21040 AAAAAAAAGGTAGAA-GAAGAGATCATGCATGTT
1 AAAAAAAAAGTAGAAGGAAGAGATCATGCATGAT
21073 AAA
1 AAA
21076 TAAACTTTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 18 0.56
34 14 0.44
ACGTcount: A:0.54, C:0.04, G:0.24, T:0.17
Consensus pattern (34 bp):
AAAAAAAAAGTAGAAGGAAGAGATCATGCATGAT
Found at i:24941 original size:26 final size:26
Alignment explanation
Indices: 24900--24952 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
24890 GCCCATATTT
24900 ATTTTTTAAAATAAAATAATAATTAA
1 ATTTTTTAAAATAAAATAATAATTAA
*
24926 ATTTTTTAATAA-AAAATAATATTTAA
1 ATTTTTTAA-AATAAAATAATAATTAA
24952 A
1 A
24953 CATTAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATTTTTTAAAATAAAATAATAATTAA
Found at i:32365 original size:2 final size:2
Alignment explanation
Indices: 32358--32385 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
32348 TGAGCGTTTA
32358 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
32386 GATTATTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34121 original size:16 final size:16
Alignment explanation
Indices: 34100--34145 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
34090 CATAGAAACT
34100 AAATTCCAGCTTTGGC
1 AAATTCCAGCTTTGGC
*
34116 AAATTCCAGCTTTCGC
1 AAATTCCAGCTTTGGC
34132 AAATTCCAGCTTTG
1 AAATTCCAGCTTTG
34146 AGAAGTTTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (16 bp):
AAATTCCAGCTTTGGC
Found at i:37456 original size:22 final size:22
Alignment explanation
Indices: 37428--37471 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
37418 GCAGGAGCTG
37428 GTTTGAGATGTGTGT-GATCTGT
1 GTTTGAGATGTGT-TCGATCTGT
37450 GTTTGAGATGTGTTCGATCTGT
1 GTTTGAGATGTGTTCGATCTGT
37472 CTGAAACTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.14, C:0.07, G:0.34, T:0.45
Consensus pattern (22 bp):
GTTTGAGATGTGTTCGATCTGT
Found at i:46733 original size:2 final size:2
Alignment explanation
Indices: 46726--47006 Score: 562
Period size: 2 Copynumber: 140.5 Consensus size: 2
46716 ACTACAAGCA
46726 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
46768 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
46810 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
46852 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
46894 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
46936 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
46978 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
47007 CAATTACTAT
Statistics
Matches: 279, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 279 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:47051 original size:2 final size:2
Alignment explanation
Indices: 47044--47075 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
47034 CTACAAGACA
47044 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
47076 CAAATTCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:47119 original size:2 final size:2
Alignment explanation
Indices: 47112--47137 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47102 ACTACAAGCA
47112 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
47138 CAAATTCTAT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:47147 original size:62 final size:62
Alignment explanation
Indices: 47050--47303 Score: 454
Period size: 62 Copynumber: 4.0 Consensus size: 62
47040 GACAGTGTGT
47050 GTGTGTGTGTGTGTGTGTGTGTGTGTCAAATTCTATGTGCTCTCTTCAACAAACTACAAGCA
1 GTGTGTGTGTGTGTGTGTGTGTGTGTCAAATTCTATGTGCTCTCTTCAACAAACTACAAGCA
47112 GTGTGTGTGTGTGTGTGTGTGTGTGTCAAATTCTATGTGCTCTCTTCAACAAACTACAAGCA
1 GTGTGTGTGTGTGTGTGTGTGTGTGTCAAATTCTATGTGCTCTCTTCAACAAACTACAAGCA
47174 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCAAATTCTATGTGCTCTCTTCAACAAACTACAA
1 ------GTGTGTGTGTGTGTGTGTGTGTGTGTCAAATTCTATGTGCTCTCTTCAACAAACTACAA
47239 GCA
60 GCA
47242 GTGTGTGTGTGTGTGTGTGTGTGTGTCAAATTCTATGTGCTCTCTTCAACAAACTACAAGCA
1 GTGTGTGTGTGTGTGTGTGTGTGTGTCAAATTCTATGTGCTCTCTTCAACAAACTACAAGCA
47304 ATCAAAACAG
Statistics
Matches: 186, Mismatches: 0, Indels: 12
0.94 0.00 0.06
Matches are distributed among these distances:
62 124 0.67
68 62 0.33
ACGTcount: A:0.20, C:0.16, G:0.26, T:0.37
Consensus pattern (62 bp):
GTGTGTGTGTGTGTGTGTGTGTGTGTCAAATTCTATGTGCTCTCTTCAACAAACTACAAGCA
Found at i:47181 original size:2 final size:2
Alignment explanation
Indices: 47174--47205 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
47164 ACTACAAGCA
47174 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
47206 CAAATTCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:47219 original size:130 final size:130
Alignment explanation
Indices: 46981--47303 Score: 605
Period size: 130 Copynumber: 2.5 Consensus size: 130
46971 GTGTGTGTGT
46981 GTGTGTGTGTGTGTGTGTGTGTGTGTC-AATTACTATGTGCTCTCTTCTAAC-AACTACAAGACA
1 GTGTGTGTGTGTGTGTGTGTGTGTGTCAAATT-CTATGTGCTCTCTTC-AACAAACTACAAG-CA
47044 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCAAATTCTATGTGCTCTCTTCAACAAACTACAA
63 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCAAATTCTATGTGCTCTCTTCAACAAACTACAA
47109 GCA
128 GCA
47112 GTGTGTGTGTGTGTGTGTGTGTGTGTCAAATTCTATGTGCTCTCTTCAACAAACTACAAGCAGTG
1 GTGTGTGTGTGTGTGTGTGTGTGTGTCAAATTCTATGTGCTCTCTTCAACAAACTACAAGCAGTG
47177 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTCAAATTCTATGTGCTCTCTTCAACAAACTACAAGCA
66 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTCAAATTCTATGTGCTCTCTTCAACAAACTACAAGCA
47242 GTGTGTGTGTGTGTGTGTGTGTGTGTCAAATTCTATGTGCTCTCTTCAACAAACTACAAGCA
1 GTGTGTGTGTGTGTGTGTGTGTGTGTCAAATTCTATGTGCTCTCTTCAACAAACTACAAGCA
47304 ATCAAAACAG
Statistics
Matches: 190, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
130 135 0.71
131 51 0.27
132 4 0.02
ACGTcount: A:0.20, C:0.15, G:0.27, T:0.38
Consensus pattern (130 bp):
GTGTGTGTGTGTGTGTGTGTGTGTGTCAAATTCTATGTGCTCTCTTCAACAAACTACAAGCAGTG
TGTGTGTGTGTGTGTGTGTGTGTGTGTGTCAAATTCTATGTGCTCTCTTCAACAAACTACAAGCA
Found at i:47249 original size:2 final size:2
Alignment explanation
Indices: 47242--47267 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47232 ACTACAAGCA
47242 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
47268 CAAATTCTAT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:56965 original size:57 final size:58
Alignment explanation
Indices: 56836--56988 Score: 191
Period size: 57 Copynumber: 2.6 Consensus size: 58
56826 ATCGATCTAA
* * * * *
56836 ATAAATGTCTCTAAGACCGTGTCTACTTTCCAGAGATAGATTTTGCTTATGTCTCTACGG
1 ATAAATGTCTCTAAGACCGTGTCTCCATT-CAGAGACAGA-TTTGCTTATGTCCCTACCG
56896 ATAAATGTCTCTAAGACCGTGTCTCCATTCAGAGACAGA-TTGCTTATGTCCCTACCG
1 ATAAATGTCTCTAAGACCGTGTCTCCATTCAGAGACAGATTTGCTTATGTCCCTACCG
* * * *
56953 ATAAACGTCTCTAAAACCATGTCTTCCATCCAGAGA
1 ATAAATGTCTCTAAGACCGTGTC-TCCATTCAGAGA
56989 TAGCTCACTT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
57 36 0.43
58 11 0.13
59 9 0.11
60 27 0.33
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.31
Consensus pattern (58 bp):
ATAAATGTCTCTAAGACCGTGTCTCCATTCAGAGACAGATTTGCTTATGTCCCTACCG
Found at i:57003 original size:58 final size:57
Alignment explanation
Indices: 56881--57003 Score: 147
Period size: 57 Copynumber: 2.1 Consensus size: 57
56871 ATAGATTTTG
* * * * * * **
56881 CTTATGTCTCTACGGATAAATGTCTCTAAGACCGTGTCTCCATTCAGAGACAGATTG
1 CTTATGTCCCTACCGATAAACGTCTCTAAAACCATGTCTCCATCCAGAGACAGATCA
* *
56938 CTTATGTCCCTACCGATAAACGTCTCTAAAACCATGTCTTCCATCCAGAGATAGCTCA
1 CTTATGTCCCTACCGATAAACGTCTCTAAAACCATGTC-TCCATCCAGAGACAGATCA
56996 CTTATGTC
1 CTTATGTC
57004 TCTAGCTCTT
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
57 33 0.60
58 22 0.40
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (57 bp):
CTTATGTCCCTACCGATAAACGTCTCTAAAACCATGTCTCCATCCAGAGACAGATCA
Found at i:65968 original size:2 final size:2
Alignment explanation
Indices: 65961--65990 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
65951 TAATTTGTTC
65961 AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
65991 AGTGATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:66809 original size:47 final size:47
Alignment explanation
Indices: 66740--66856 Score: 180
Period size: 47 Copynumber: 2.5 Consensus size: 47
66730 CAAATCTCAC
* *
66740 CATATTCGATGGGTGCAGGTTTTGTGCAGTTTTATATTGGCTTTGTG
1 CATATTCGATGTGTGCAGGTTTTGTGCAGCTTTATATTGGCTTTGTG
* *
66787 CATATTCGATGTGTGCAGGTTTTGTGTAGCTTTATGTTGGCTTTGTG
1 CATATTCGATGTGTGCAGGTTTTGTGCAGCTTTATATTGGCTTTGTG
* *
66834 CATATTTGATGTGTGTAGGTTTT
1 CATATTCGATGTGTGCAGGTTTT
66857 ATGTTGGTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 64 1.00
ACGTcount: A:0.15, C:0.09, G:0.29, T:0.47
Consensus pattern (47 bp):
CATATTCGATGTGTGCAGGTTTTGTGCAGCTTTATATTGGCTTTGTG
Found at i:67728 original size:10 final size:10
Alignment explanation
Indices: 67710--67740 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
67700 TTCTTGTCTC
67710 TTAATTTTTT
1 TTAATTTTTT
*
67720 TTTATTTTTT
1 TTAATTTTTT
67730 TTAATTTTTT
1 TTAATTTTTT
67740 T
1 T
67741 AAGATTGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTAATTTTTT
Found at i:69342 original size:23 final size:23
Alignment explanation
Indices: 69298--69344 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
69288 TTGTTCAATT
*
69298 AAGGTAATTCAAGTGTTAATTAA
1 AAGGTAATTCAACTGTTAATTAA
*
69321 AAGGTAATTTCAACT-TTCATTAA
1 AAGGTAA-TTCAACTGTTAATTAA
69344 A
1 A
69345 GACTTAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.36
Consensus pattern (23 bp):
AAGGTAATTCAACTGTTAATTAA
Found at i:71140 original size:20 final size:20
Alignment explanation
Indices: 71115--71177 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
71105 CGCATGAGTA
71115 AATATATAAAGATATTAATT
1 AATATATAAAGATATTAATT
71135 AATATAT--A-ATA-T-A-T
1 AATATATAAAGATATTAATT
71149 AATATATAAAGATATTAATT
1 AATATATAAAGATATTAATT
*
71169 ACTATATAA
1 AATATATAA
71178 TTAACACTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
14 8 0.22
15 1 0.03
16 2 0.06
17 6 0.17
18 2 0.06
19 1 0.03
20 16 0.44
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.40
Consensus pattern (20 bp):
AATATATAAAGATATTAATT
Found at i:74768 original size:25 final size:24
Alignment explanation
Indices: 74740--74796 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
74730 GTGGATTGTA
*
74740 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
74765 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
74789 AAA-AAATT
1 AAATAAATT
74797 CAAGGTTGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.32
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Done.