Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021414.1 Corchorus olitorius cultivar O-4 contig21447, 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: 27996
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2091 original size:25 final size:24
Alignment explanation
Indices: 2063--2110 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2053 AATTGGTTAT
*
2063 TGTTGTCCATAAATATTTTGGTGGG
1 TGTT-TCCAAAAATATTTTGGTGGG
*
2088 TGTTTTCAAAAATATTTTGGTGG
1 TGTTTCCAAAAATATTTTGGTGG
2111 TAGCGATGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.23, C:0.06, G:0.25, T:0.46
Consensus pattern (24 bp):
TGTTTCCAAAAATATTTTGGTGGG
Found at i:2794 original size:35 final size:35
Alignment explanation
Indices: 2748--2817 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
2738 TTAAGATTCG
*
2748 AACCCTTCTTATACCAAACTTAAGTTCGAGTCCTT
1 AACCCTTCTTATACCAAACTTAAGTTCAAGTCCTT
*
2783 AACCCTTCTTATACCAAATTTAAGTTCAAGTCCTT
1 AACCCTTCTTATACCAAACTTAAGTTCAAGTCCTT
2818 TATCTATAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (35 bp):
AACCCTTCTTATACCAAACTTAAGTTCAAGTCCTT
Found at i:3376 original size:20 final size:20
Alignment explanation
Indices: 3351--3390 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3341 CATATAAAAT
*
3351 AATAATAACTAATTTTTAAA
1 AATAATAACTAATTATTAAA
3371 AATAATAACTAATTATTAAA
1 AATAATAACTAATTATTAAA
3391 TTTAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAATAACTAATTATTAAA
Found at i:12789 original size:76 final size:77
Alignment explanation
Indices: 12698--12862 Score: 323
Period size: 76 Copynumber: 2.2 Consensus size: 77
12688 AGTTTGGACG
12698 GAGGGGTGACGTGGTATGTTAAGTCCTATTTTTTCACCTAAAATATTTCTTTTAATTTGATTTAA
1 GAGGGGTGACGTGGTATGTTAAGTCCTATTTTTTCACCTAAAATATTTCTTTTAATTTGATTTAA
12763 -TTTTTTATTAC
66 TTTTTTTATTAC
12774 GAGGGGTGACGTGGTATGTTAAGTCCTATTTTTTCACCTAAAATATTTCTTTTAATTTGATTTAA
1 GAGGGGTGACGTGGTATGTTAAGTCCTATTTTTTCACCTAAAATATTTCTTTTAATTTGATTTAA
12839 TTTTTTTATTAC
66 TTTTTTTATTAC
12851 GAGGGGTGACGT
1 GAGGGGTGACGT
12863 CTTTGTATGG
Statistics
Matches: 88, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 65 0.74
77 23 0.26
ACGTcount: A:0.24, C:0.10, G:0.19, T:0.47
Consensus pattern (77 bp):
GAGGGGTGACGTGGTATGTTAAGTCCTATTTTTTCACCTAAAATATTTCTTTTAATTTGATTTAA
TTTTTTTATTAC
Found at i:12904 original size:22 final size:22
Alignment explanation
Indices: 12876--13411 Score: 166
Period size: 22 Copynumber: 24.7 Consensus size: 22
12866 TGTATGGTTG
12876 TCAAAATTTCATAGTGTGATTA
1 TCAAAATTTCATAGTGTGATTA
* *
12898 TCAAAATTTCATAATGTGGTTA
1 TCAAAATTTCATAGTGTGATTA
*
12920 TCAAAATTTCATAGTGTAATTA
1 TCAAAATTTCATAGTGTGATTA
* * *
12942 TCAAAATTTCATACTGAGGTTA
1 TCAAAATTTCATAGTGTGATTA
* * *
12964 TCACAATTTTATGGTGT-AGTTA
1 TCAAAATTTCATAGTGTGA-TTA
*
12986 TCGAAATTTCATAGTATGGTG-TTA
1 TCAAAATTTCATAG--T-GTGATTA
* * *
13010 CCACAATTTCAT-GATG-CAGTTA
1 TCAAAATTTCATAG-TGTGA-TTA
* * *
13032 CCAAAATTTCATA-AGAGATTA
1 TCAAAATTTCATAGTGTGATTA
* **
13053 TCAAAA--T--T--TGTAAAAA
1 TCAAAATTTCATAGTGTGATTA
* * *
13069 CCAAAATTTTAT-G-GGGAAGTTA
1 TCAAAATTTCATAGTGTG-A-TTA
* *
13091 TCAAAATTTCGTAG-G-AACGTTA
1 TCAAAATTTCATAGTGTGA--TTA
* *
13113 TCAAAATTTTATTGTGT-AGTTA
1 TCAAAATTTCATAGTGTGA-TTA
* * * * * *
13135 TCAAATTTTCTTACTGAGGTTT
1 TCAAAATTTCATAGTGTGATTA
* * *
13157 TCAAAATTTCACAAG-GAGATTG
1 TCAAAATTTCA-TAGTGTGATTA
*
13179 TCAAAATTTCATAG-G-GAAGTA
1 TCAAAATTTCATAGTGTG-ATTA
* *
13200 CCAAAATTTCATAGTGTGGTTA
1 TCAAAATTTCATAGTGTGATTA
** * * * **
13222 TTGAATTTTCATAGAGAGGCTA
1 TCAAAATTTCATAGTGTGATTA
* * *
13244 TCAGAATTTCATAG-GAAGGTTA
1 TCAAAATTTCATAGTG-TGATTA
* *
13266 TCAAAATTTCATAGTGTGGTTG
1 TCAAAATTTCATAGTGTGATTA
* *
13288 TCAAAATTTCAT--TGGGATGTG
1 TCAAAATTTCATAGTGTGAT-TA
* *
13309 CCAAAATTTCATAGTTTGATTA
1 TCAAAATTTCATAGTGTGATTA
* * *
13331 TCAAAATTTCATAGGGAGGTTA
1 TCAAAATTTCATAGTGTGATTA
* * * *
13353 TCACAAGTTGATAGTGTGGTTA
1 TCAAAATTTCATAGTGTGATTA
* ** *
13375 CCAACGTTTTATA-TG-GAGGTTA
1 TCAAAATTTCATAGTGTGA--TTA
13397 TCAAAATTTCATAGT
1 TCAAAATTTCATAGT
13412 ATAGTTATCA
Statistics
Matches: 375, Mismatches: 106, Indels: 65
0.69 0.19 0.12
Matches are distributed among these distances:
16 8 0.02
17 1 0.00
18 1 0.00
19 1 0.00
20 8 0.02
21 46 0.12
22 282 0.75
23 13 0.03
24 13 0.03
25 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (22 bp):
TCAAAATTTCATAGTGTGATTA
Found at i:12924 original size:44 final size:44
Alignment explanation
Indices: 12871--13528 Score: 231
Period size: 44 Copynumber: 15.2 Consensus size: 44
12861 GTCTTTGTAT
* *
12871 GGTTGTCAAAATTTCATAGTGTGATTATCAAAATTTCATAATGT
1 GGTTATCAAAATTTCATAGTGTGATTATCAAAATTTCATAATGA
* *
12915 GGTTATCAAAATTTCATAGTGTAATTATCAAAATTTCATACTGA
1 GGTTATCAAAATTTCATAGTGTGATTATCAAAATTTCATAATGA
* * * *
12959 GGTTATCACAATTTTATGGTGT-AGTTATCGAAATTTCATAGTATG-
1 GGTTATCAAAATTTCATAGTGTGA-TTATCAAAATTTCATA--ATGA
* * * *
13004 GTGTTACCACAATTTCAT-GATG-CAGTTACCAAAATTTCATAA-GA
1 G-GTTATCAAAATTTCATAG-TGTGA-TTATCAAAATTTCATAATGA
* * ** * * ***
13048 GATTATCAAAA--T--T--TGTAAAAACCAAAATTTTATGGGGA
1 GGTTATCAAAATTTCATAGTGTGATTATCAAAATTTCATAATGA
* * * * **
13086 AGTTATCAAAATTTCGTAG-G-AACGTTATCAAAATTTTATTGTGTA
1 GGTTATCAAAATTTCATAGTGTGA--TTATCAAAATTTCATAATG-A
* * * * * * * *
13131 -GTTATCAAATTTTCTTACTGAGGTTTTCAAAATTTCACAAGGA
1 GGTTATCAAAATTTCATAGTGTGATTATCAAAATTTCATAATGA
* * * * * *
13174 GATTGTCAAAATTTCATAG-G-GAAGTACCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGTG-ATTATCAAAATTTCATAATGA
** * * * ** * *
13217 GGTTATTGAATTTTCATAGAGAGGCTATCAGAATTTCAT-AGGAA
1 GGTTATCAAAATTTCATAGTGTGATTATCAAAATTTCATAATG-A
* *
13261 GGTTATCAAAATTTCATAGTGTGGTTGTCAAAATTTCAT--TG-
1 GGTTATCAAAATTTCATAGTGTGATTATCAAAATTTCATAATGA
** * **
13302 GGATGTGCCAAAATTTCATAGTTTGATTATCAAAATTTCATAGGGA
1 GG-T-TATCAAAATTTCATAGTGTGATTATCAAAATTTCATAATGA
* * * * * ** *
13348 GGTTATCACAAGTTGATAGTGTGGTTACCAACGTTTTAT-ATGGA
1 GGTTATCAAAATTTCATAGTGTGATTATCAAAATTTCATAAT-GA
* *
13392 GGTTATCAAAATTTCATAGTAT-AGTTATCAAGATTT--T-A--A
1 GGTTATCAAAATTTCATAGTGTGA-TTATCAAAATTTCATAATGA
* * * * *
13431 GGTTATCAAATTTTCATA-TGAAGGTTGTCAAATTTTCCATAATGA
1 GGTTATCAAAATTTCATAGTG-TGATTATCAAAATTT-CATAATGA
* ** * * * *
13476 GATTATTGAAATTTCGTAATGTGGA-TATCAAAATTTCTTAAGGA
1 GGTTATCAAAATTTCATAGTGT-GATTATCAAAATTTCATAATGA
*
13520 GATTATCAA
1 GGTTATCAA
13529 CATTATTATA
Statistics
Matches: 451, Mismatches: 121, Indels: 84
0.69 0.18 0.13
Matches are distributed among these distances:
37 14 0.03
38 13 0.03
39 28 0.06
40 1 0.00
41 3 0.01
42 8 0.02
43 73 0.16
44 242 0.54
45 30 0.07
46 39 0.09
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAGTGTGATTATCAAAATTTCATAATGA
Found at i:12953 original size:66 final size:66
Alignment explanation
Indices: 12876--13512 Score: 225
Period size: 66 Copynumber: 9.8 Consensus size: 66
12866 TGTATGGTTG
* *
12876 TCAAAATTTCATAGTGTGATTATCAAAATTTCATAATGTGGTTATCAAAATTTCATAGTGTAATT
1 TCAAAATTTCATAGTGAGATTATCAAAATTTCATAATGAGGTTATCAAAATTTCATAGTGTAATT
12941 A
66 A
* * * * ** *
12942 TCAAAATTTCATACTGAGGTTATCACAATTTTATGGTGTA-GTTATCGAAATTTCATAGTATGGT
1 TCAAAATTTCATAGTGAGATTATCAAAATTTCATAATG-AGGTTATCAAAATTTCATAG--T-GT
*
13006 -GTTA
62 AATTA
* * * *
13010 CCACAATTTCAT-GATGCAG-TTACCAAAATTTCATAA-GAGATTATCAAAA--T--T--TGTAA
1 TCAAAATTTCATAG-TG-AGATTATCAAAATTTCATAATGAGGTTATCAAAATTTCATAGTGTAA
**
13066 AAA
64 TTA
* * * * * * * * * *
13069 CCAAAATTTTATGGGGA-AGTTATCAAAATTTCGT-AGGAACGTTATCAAAATTTTATTGTGTAG
1 TCAAAATTTCATAGTGAGA-TTATCAAAATTTCATAATG-AGGTTATCAAAATTTCATAGTGTAA
13132 TTA
64 TTA
* * * * * * * * * * *
13135 TCAAATTTTCTTACTGAGGTTTTCAAAATTTCACAAGGAGATTGTCAAAATTTCATAG-GGAAGT
1 TCAAAATTTCATAGTGAGATTATCAAAATTTCATAATGAGGTTATCAAAATTTCATAGTGTAATT
13199 A
66 A
* * * ** * * *
13200 CCAAAATTTCATAGTGTGGTTATTGAATTTTCATAGA-GAGGCTATCAGAATTTCATAG-G-AAG
1 TCAAAATTTCATAGTGAGATTATCAAAATTTCATA-ATGAGGTTATCAAAATTTCATAGTGTAA-
13262 GTTA
64 -TTA
* * * ** * *
13266 TCAAAATTTCATAGTGTGGTTGTCAAAATTTCAT--TG-GGATGTGCCAAAATTTCATAGTTTGA
1 TCAAAATTTCATAGTGAGATTATCAAAATTTCATAATGAGG-T-TATCAAAATTTCATAGTGTAA
13328 TTA
64 TTA
* * * * * * * * ** * * *
13331 TCAAAATTTCATAGGGAGGTTATCACAAGTTGATAGTGTGGTTACCAACGTTTTATA-TGGAGGT
1 TCAAAATTTCATAGTGAGATTATCAAAATTTCATAATGAGGTTATCAAAATTTCATAGTGTA-AT
13395 TA
65 TA
* * *
13397 TCAAAATTTCATAGT-ATAGTTATCAAGATTT--T-A--AGGTTATCAAATTTTCATA-TG-AAG
1 TCAAAATTTCATAGTGAGA-TTATCAAAATTTCATAATGAGGTTATCAAAATTTCATAGTGTAA-
*
13454 GTTG
64 -TTA
* * ** * * *
13458 TCAAATTTTCCATAATGAGATTATTGAAATTTCGTAATGTGGATATCAAAATTTC
1 TCAAAATTT-CATAGTGAGATTATCAAAATTTCATAATGAGGTTATCAAAATTTC
13513 TTAAGGAGAT
Statistics
Matches: 413, Mismatches: 115, Indels: 85
0.67 0.19 0.14
Matches are distributed among these distances:
58 4 0.01
59 27 0.07
60 12 0.03
61 26 0.06
62 15 0.04
63 5 0.01
64 6 0.01
65 95 0.23
66 160 0.39
67 29 0.07
68 30 0.07
69 4 0.01
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.38
Consensus pattern (66 bp):
TCAAAATTTCATAGTGAGATTATCAAAATTTCATAATGAGGTTATCAAAATTTCATAGTGTAATT
A
Found at i:13246 original size:109 final size:109
Alignment explanation
Indices: 13151--13355 Score: 268
Period size: 109 Copynumber: 1.9 Consensus size: 109
13141 TTTCTTACTG
*
13151 AGGTTTTCAAAATTTCACAAG-GAGATTGTCAAAATTTCATAGGGAAGTACCAAAATTTCATAGT
1 AGGTTATCAAAATTTCA-AAGTGAGATTGTCAAAATTTCATAGGGAAGTACCAAAATTTCATAGT
* ** *
13215 GTGGTTATTGAATTTTCATAGAGAGGCTATCAGAATTTCATAGGA
65 GTGATTATCAAAATTTCATAGAGAGGCTATCAGAATTTCATAGGA
* * * * * * *
13260 AGGTTATCAAAATTTCATAGTGTGGTTGTCAAAATTTCATTGGGATGTGCCAAAATTTCATAGTT
1 AGGTTATCAAAATTTCAAAGTGAGATTGTCAAAATTTCATAGGGAAGTACCAAAATTTCATAGTG
* *
13325 TGATTATCAAAATTTCATAGGGAGGTTATCA
66 TGATTATCAAAATTTCATAGAGAGGCTATCA
13356 CAAGTTGATA
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
108 2 0.02
109 79 0.98
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (109 bp):
AGGTTATCAAAATTTCAAAGTGAGATTGTCAAAATTTCATAGGGAAGTACCAAAATTTCATAGTG
TGATTATCAAAATTTCATAGAGAGGCTATCAGAATTTCATAGGA
Found at i:13401 original size:109 final size:109
Alignment explanation
Indices: 13179--13410 Score: 252
Period size: 109 Copynumber: 2.1 Consensus size: 109
13169 AAGGAGATTG
* ** *
13179 TCAAAATTTCATAGGGAAGTACCAAAATTTCATAGTGTGGTTATTGAATTTTCATAGAGAGGCTA
1 TCAAAATTTCATAGGGAAGTACCAAAATTTCATAGTGTGATTATCAAAATTTCATAGAGAGGCTA
* * * * *
13244 TCAGAATTTCATAGGAAGGTTATCAAAATTTCATAGTGTGGTTG
66 TCACAAGTTCATAGGAAGGTTACCAAAATTTCATAGTGAGGTTA
* * * * * *
13288 TCAAAATTTCATTGGGATGTGCCAAAATTTCATAGTTTGATTATCAAAATTTCATAGGGAGGTTA
1 TCAAAATTTCATAGGGAAGTACCAAAATTTCATAGTGTGATTATCAAAATTTCATAGAGAGGCTA
* * ** *
13353 TCACAAGTTGATAGTG-TGGTTACCAACGTTTTATA-TGGAGGTTA
66 TCACAAGTTCATAG-GAAGGTTACCAAAATTTCATAGT-GAGGTTA
13397 TCAAAATTTCATAG
1 TCAAAATTTCATAG
13411 TATAGTTATC
Statistics
Matches: 100, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
108 1 0.01
109 98 0.98
110 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (109 bp):
TCAAAATTTCATAGGGAAGTACCAAAATTTCATAGTGTGATTATCAAAATTTCATAGAGAGGCTA
TCACAAGTTCATAGGAAGGTTACCAAAATTTCATAGTGAGGTTA
Found at i:16326 original size:18 final size:20
Alignment explanation
Indices: 16302--16339 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
16292 CATGTCCCAC
16302 AAAAA-ATTCCATGTCAGCT
1 AAAAATATTCCATGTCAGCT
16321 AAAAATATTCCATGTCAGC
1 AAAAATATTCCATGTCAGC
16340 AATTAACTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (20 bp):
AAAAATATTCCATGTCAGCT
Found at i:16740 original size:32 final size:32
Alignment explanation
Indices: 16683--16745 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
16673 TCATTCTTGA
* * *
16683 AATGCCTTACTTATGCTGTTCGATAATTTTGT
1 AATGCATTACTTACGCTGTTCGATAACTTTGT
16715 AATGCATTACTTACGCTG-TCTGATAACTTTG
1 AATGCATTACTTACGCTGTTC-GATAACTTTG
16746 CTGCATCCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 2 0.07
32 25 0.93
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.43
Consensus pattern (32 bp):
AATGCATTACTTACGCTGTTCGATAACTTTGT
Found at i:20743 original size:15 final size:16
Alignment explanation
Indices: 20714--20743 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20704 TCTTTCCTAC
20714 TCAAAATCTAATATAA
1 TCAAAATCTAATATAA
20730 TCAAAATC-AATATA
1 TCAAAATCTAATATA
20744 GTTTTGTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (16 bp):
TCAAAATCTAATATAA
Found at i:21076 original size:2 final size:2
Alignment explanation
Indices: 21069--21116 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
21059 ATGAATATAC
*
21069 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT CT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
21111 GT GT GT
1 GT GT GT
21117 TTCTACATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.02, G:0.48, T:0.50
Consensus pattern (2 bp):
GT
Found at i:21143 original size:45 final size:43
Alignment explanation
Indices: 21093--21180 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
21083 GTGTGTGTGT
21093 GTGTGTGTGTGTCTGTGTGTGTGTTTCTACATTTCCTTTTTCTCA
1 GTGTGTGTGTGTC--TGTGTGTGTTTCTACATTTCCTTTTTCTCA
21138 GTGTGTGTGTGTCTGTGTGTGTTTCTACATTTCCTTTTTCTCA
1 GTGTGTGTGTGTCTGTGTGTGTTTCTACATTTCCTTTTTCTCA
21181 AACTAACTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
43 30 0.70
45 13 0.30
ACGTcount: A:0.07, C:0.16, G:0.24, T:0.53
Consensus pattern (43 bp):
GTGTGTGTGTGTCTGTGTGTGTTTCTACATTTCCTTTTTCTCA
Done.