Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014767.1 Corchorus olitorius cultivar O-4 contig14800, 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: 25534
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:28 original size:2 final size:2
Alignment explanation
Indices: 21--47 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11 TGAAATTAGT
21 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
48 TATATATATA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1849 original size:36 final size:36
Alignment explanation
Indices: 1802--1871 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
1792 TTCAATAACC
* *
1802 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
1838 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
1872 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:2959 original size:39 final size:40
Alignment explanation
Indices: 2905--2985 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
2895 CTACCTAAGA
*
2905 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
2944 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
2984 AT
1 AT
2986 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:3305 original size:22 final size:22
Alignment explanation
Indices: 3276--3379 Score: 113
Period size: 22 Copynumber: 4.8 Consensus size: 22
3266 TGAATATTTT
3276 TATGAAATTTTGATAACTACCC
1 TATGAAATTTTGATAACTACCC
* *
3298 TATTAAATTTTGATAACTATCC
1 TATGAAATTTTGATAACTACCC
* * *
3320 TAAGAAATTTTGATAATTA-CG
1 TATGAAATTTTGATAACTACCC
* *
3341 TATGAAATTGTGATAAACT-CCA
1 TATGAAATTTTGAT-AACTACCC
*
3363 TATGAAACTTTGATAAC
1 TATGAAATTTTGATAAC
3380 CTAATTATAA
Statistics
Matches: 68, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
21 16 0.24
22 52 0.76
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACTACCC
Found at i:8798 original size:31 final size:31
Alignment explanation
Indices: 8763--8848 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 31
8753 TCATGTGTAC
* *
8763 CAAAAAGTGACACATGGCATGCTATATATTT
1 CAAAAAGTGACACGTGGCATGCCATATATTT
* * * *
8794 CAAAAAGTGACATGTGGTATGCCATGTGTTT
1 CAAAAAGTGACACGTGGCATGCCATATATTT
* *
8825 CCAAAAGTGACACGTGACATGCCA
1 CAAAAAGTGACACGTGGCATGCCA
8849 CGTGCACAAA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.26
Consensus pattern (31 bp):
CAAAAAGTGACACGTGGCATGCCATATATTT
Found at i:11192 original size:20 final size:20
Alignment explanation
Indices: 11137--11193 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 20
11127 AAGTCCGCCC
11137 ATTTTATTAATTGAATATATATT
1 ATTTTATTAATT-AAT-TAT-TT
11160 A-TTT-TTAA-T--TTATTT
1 ATTTTATTAATTAATTATTT
11175 ATTTTATTAATTAATTATT
1 ATTTTATTAATTAATTATT
11194 ACTTTATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 13
0.69 0.00 0.31
Matches are distributed among these distances:
15 3 0.10
16 6 0.21
17 5 0.17
18 1 0.03
20 6 0.21
21 4 0.14
22 3 0.10
23 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
ATTTTATTAATTAATTATTT
Found at i:11856 original size:84 final size:85
Alignment explanation
Indices: 11715--11880 Score: 298
Period size: 84 Copynumber: 2.0 Consensus size: 85
11705 ATAAAATTAC
*
11715 TTATTAATGACACTATTTATTACCGAAATAGTCAATTACCAAAATAGGGCAGAGGG-AAGAAAGT
1 TTATTAATGACACTATTTATTACCAAAATAGTCAATTACCAAAATAGGGCAGAGGGAAAGAAAGT
11779 GTAAGAAACTAATTGAGAGA
66 GTAAGAAACTAATTGAGAGA
* *
11799 TTATTAATGACACTATTTATTACCAAAATAGTCAATTACCAAATTAGGGCAGGGGGAAAGAAAGT
1 TTATTAATGACACTATTTATTACCAAAATAGTCAATTACCAAAATAGGGCAGAGGGAAAGAAAGT
11864 GTAAGAAACTAATTGAG
66 GTAAGAAACTAATTGAG
11881 GGGCTTCTCA
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
84 53 0.68
85 25 0.32
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (85 bp):
TTATTAATGACACTATTTATTACCAAAATAGTCAATTACCAAAATAGGGCAGAGGGAAAGAAAGT
GTAAGAAACTAATTGAGAGA
Found at i:12335 original size:21 final size:19
Alignment explanation
Indices: 12309--12366 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
12299 GCTGCATTAA
*
12309 TAATCTCATATGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
12330 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
12349 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
12367 TGCTAAACAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:20405 original size:19 final size:19
Alignment explanation
Indices: 20381--20417 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
20371 ATACAGTATC
20381 TAATCTAATTTGTACAGTG
1 TAATCTAATTTGTACAGTG
*
20400 TAATCTCATTTGTACAGT
1 TAATCTAATTTGTACAGT
20418 TACTAAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (19 bp):
TAATCTAATTTGTACAGTG
Found at i:24593 original size:24 final size:23
Alignment explanation
Indices: 24566--24697 Score: 76
Period size: 24 Copynumber: 5.7 Consensus size: 23
24556 TTTATTATAA
24566 ATATATTAAATATATTTAAGATAT
1 ATATATTAAATATATTTAA-ATAT
*
24590 ATATATTATATATA-TT--ATAT
1 ATATATTAAATATATTTAAATAT
* * *
24610 AT-TAGT-AATCAGTTTTTATTATAT
1 ATATATTAAAT-A-TATTTA-AATAT
* * *
24634 ATATATAAATATATATTTTATTAT
1 ATATATTAA-ATATATTTAAATAT
* *
24658 AAATGTTAAATATATTTAAGATAT
1 ATATATTAAATATATTTAA-ATAT
**
24682 ATATATTGTATATATT
1 ATATATTAAATATATT
24698 ATATATTAGT
Statistics
Matches: 79, Mismatches: 19, Indels: 20
0.67 0.16 0.17
Matches are distributed among these distances:
18 2 0.03
19 4 0.05
20 7 0.09
21 2 0.03
23 11 0.14
24 43 0.54
25 6 0.08
26 2 0.03
27 2 0.03
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.51
Consensus pattern (23 bp):
ATATATTAAATATATTTAAATAT
Found at i:24599 original size:20 final size:20
Alignment explanation
Indices: 24548--24688 Score: 58
Period size: 20 Copynumber: 7.5 Consensus size: 20
24538 GAAAACCCAA
*
24548 ATATATATTTTATTATAAAT
1 ATATATATTATATTATAAAT
*
24568 ATAT-TAAATATATT-TAAGAT
1 ATATAT-ATTATATTATAA-AT
24588 ATATATATTATA-TAT--AT
1 ATATATATTATATTATAAAT
* *
24605 -TATATATTAGTA--ATCAGT
1 ATATATATTA-TATTATAAAT
*
24623 -T-TTTATTATATATATATAA-
1 ATATATATTATAT-TATA-AAT
*
24642 ATATATATTTTATTATAAAT
1 ATATATATTATATTATAAAT
* *
24662 GT-TA-AATATATT-TAAGAT
1 ATATATATTATATTATAA-AT
24680 ATATATATT
1 ATATATATT
24689 GTATATATTA
Statistics
Matches: 90, Mismatches: 14, Indels: 34
0.65 0.10 0.25
Matches are distributed among these distances:
16 13 0.14
17 13 0.14
18 11 0.12
19 13 0.14
20 31 0.34
21 9 0.10
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.51
Consensus pattern (20 bp):
ATATATATTATATTATAAAT
Found at i:24633 original size:42 final size:41
Alignment explanation
Indices: 24587--24733 Score: 106
Period size: 46 Copynumber: 3.3 Consensus size: 41
24577 ATATTTAAGA
24587 TATATATATTATATATATTATATATTAGTAATCAGTTTTTAT
1 TATATATATTATATATATTATATATTAGTAAT-AGTTTTTAT
*
24629 TATATATATATAAATATATATT-T-TATTA-TAA-ATGTTAAATATATT
1 TATATATAT-T--ATATATATTATATATTAGTAATA-GTT---TTTA-T
*
24674 TAAGATATATATATTGTATATATTATATATTAGTAATAAGTTTTTAT
1 T-ATATATAT-TA---TATATATTATATATTAGTAAT-AGTTTTTAT
24721 TATATATA-TATAT
1 TATATATATTATAT
24734 TAAAGATAAT
Statistics
Matches: 84, Mismatches: 4, Indels: 35
0.68 0.03 0.28
Matches are distributed among these distances:
40 1 0.01
41 6 0.07
42 12 0.14
43 6 0.07
44 7 0.08
45 11 0.13
46 15 0.18
47 10 0.12
48 4 0.05
49 5 0.06
50 3 0.04
51 3 0.04
52 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (41 bp):
TATATATATTATATATATTATATATTAGTAATAGTTTTTAT
Found at i:24733 original size:94 final size:94
Alignment explanation
Indices: 24546--24732 Score: 333
Period size: 92 Copynumber: 2.0 Consensus size: 94
24536 TCGAAAACCC
24546 AAATATATATTTTATTATAAATATATTAAATATATTTAAGATATATATATTATATATATTATATA
1 AAATATATATTTTATTATAAATATATTAAATATATTTAAGATATATATATTATATATATTATATA
*
24611 TTAGTAATCAGTTTTTATTATATATATAT
66 TTAGTAATAAGTTTTTATTATATATATAT
* *
24640 AAATATATATTTTATTAT-AA-ATGTTAAATATATTTAAGATATATATATTGTATATATTATATA
1 AAATATATATTTTATTATAAATATATTAAATATATTTAAGATATATATATTATATATATTATATA
24703 TTAGTAATAAGTTTTTATTATATATATAT
66 TTAGTAATAAGTTTTTATTATATATATAT
24732 A
1 A
24733 TTAAAGATAA
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
92 70 0.78
93 2 0.02
94 18 0.20
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (94 bp):
AAATATATATTTTATTATAAATATATTAAATATATTTAAGATATATATATTATATATATTATATA
TTAGTAATAAGTTTTTATTATATATATAT
Done.