Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023630.1 Corchorus olitorius cultivar O-4 contig23663, 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: 40218
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:514 original size:41 final size:41
Alignment explanation
Indices: 464--558 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 41
454 ACAAAAATAA
* * *
464 GGACCAAATTGAATAAAATAGTGACTAGAATCCTAAATCAG
1 GGACCAAATTGAAGAAAATAGTAAATAGAATCCTAAATCAG
* * * * *
505 GGACTAAATTGTAGCAAATATTAAATAGAATCTTAAATCAG
1 GGACCAAATTGAAGAAAATAGTAAATAGAATCCTAAATCAG
*
546 GGACCATATTGAA
1 GGACCAAATTGAA
559 CACGGAAATA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.25
Consensus pattern (41 bp):
GGACCAAATTGAAGAAAATAGTAAATAGAATCCTAAATCAG
Found at i:7934 original size:15 final size:15
Alignment explanation
Indices: 7910--7940 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
7900 AATTTGCATC
*
7910 ATATATAATATTAAT
1 ATATAGAATATTAAT
7925 ATATAGAATATTAAT
1 ATATAGAATATTAAT
7940 A
1 A
7941 ATCTAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
ATATAGAATATTAAT
Found at i:10748 original size:27 final size:26
Alignment explanation
Indices: 10707--10766 Score: 84
Period size: 27 Copynumber: 2.3 Consensus size: 26
10697 AGTCAACTGC
* *
10707 CTGGGCCATGTGGCTGGCCCAAGCCAG
1 CTGGGCCACGCGGCTGGCCCAAGCC-G
10734 CTGGGCCACGCGGCTGGCCCAAGCCG
1 CTGGGCCACGCGGCTGGCCCAAGCCG
*
10760 TTGGGCC
1 CTGGGCC
10767 TGCTGCAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 7 0.23
27 23 0.77
ACGTcount: A:0.12, C:0.37, G:0.38, T:0.13
Consensus pattern (26 bp):
CTGGGCCACGCGGCTGGCCCAAGCCG
Found at i:17644 original size:6 final size:6
Alignment explanation
Indices: 17633--17665 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
17623 AATCCTATCT
*
17633 CATCGC CATCGC CATCGC CATC-C CATCTC CATC
1 CATCGC CATCGC CATCGC CATCGC CATCGC CATC
17666 ACCACTGCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.18, C:0.52, G:0.09, T:0.21
Consensus pattern (6 bp):
CATCGC
Found at i:19456 original size:36 final size:36
Alignment explanation
Indices: 19416--19490 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
19406 AAATTTGTAT
19416 TTACTTGTTTCTCCACTCCATTGTCATCAACTATCA
1 TTACTTGTTTCTCCACTCCATTGTCATCAACTATCA
19452 TTACTTGTTTCTCCACTCCATTGTCATCAACTATCA
1 TTACTTGTTTCTCCACTCCATTGTCATCAACTATCA
19488 TTA
1 TTA
19491 TAAAAAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.23, C:0.29, G:0.05, T:0.43
Consensus pattern (36 bp):
TTACTTGTTTCTCCACTCCATTGTCATCAACTATCA
Found at i:23242 original size:25 final size:24
Alignment explanation
Indices: 23206--23252 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
23196 TCCTTCTATT
23206 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
23229 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
23253 AATTTTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:24207 original size:15 final size:15
Alignment explanation
Indices: 24187--24218 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
24177 CCTTGGGGGT
24187 TCAAAATCAACAAGC
1 TCAAAATCAACAAGC
24202 TCAAAATCAACAAGC
1 TCAAAATCAACAAGC
24217 TC
1 TC
24219 CACTTAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.28, G:0.06, T:0.16
Consensus pattern (15 bp):
TCAAAATCAACAAGC
Found at i:24850 original size:33 final size:33
Alignment explanation
Indices: 24805--24885 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 33
24795 GTGTTTTAGA
* *
24805 TGTTGTTAGTGATGATACTAAAACTAATTTGA-G
1 TGTTGTTTGTGATGACACTAAAACT-ATTTGAGG
* * *
24838 TGTTGTTTGTGATGACACTAAATCTGTTTTAGG
1 TGTTGTTTGTGATGACACTAAAACTATTTGAGG
24871 TGTTGTTTGTGATGA
1 TGTTGTTTGTGATGA
24886 AACAAATTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
32 4 0.10
33 38 0.90
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.44
Consensus pattern (33 bp):
TGTTGTTTGTGATGACACTAAAACTATTTGAGG
Found at i:24899 original size:33 final size:33
Alignment explanation
Indices: 24796--24900 Score: 99
Period size: 33 Copynumber: 3.2 Consensus size: 33
24786 TTGCAAAGAG
* * *
24796 TGTTTTAGATGTTGTTAGTGATGATACTAAA-A
1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATA
** * *
24828 CTAATTT-GAGTGTTGTTTGTGATGACACTAAATC
1 -TGTTTTAG-GTGTTGTTTGTGATGAAACTAAATA
24862 TGTTTTAGGTGTTGTTTGTGATGAAAC-AAATTA
1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAA-TA
24895 TGTTTT
1 TGTTTT
24901 GGATGCTAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
32 4 0.07
33 53 0.91
34 1 0.02
ACGTcount: A:0.27, C:0.06, G:0.22, T:0.46
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGTGATGAAACTAAATA
Found at i:28021 original size:16 final size:15
Alignment explanation
Indices: 27992--28027 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
27982 GTTACTAACC
27992 TTTTTATTATTTTTA
1 TTTTTATTATTTTTA
*
28007 TTTTTATTTTATTTTA
1 TTTTTATTAT-TTTTA
28023 TTTTT
1 TTTTT
28028 CAAAGAGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTATTATTTTTA
Found at i:29288 original size:21 final size:21
Alignment explanation
Indices: 29264--29310 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
29254 GCTCGCGCCT
* *
29264 GGTGCTCCGGCCTACGAGCTG
1 GGTGCTCAGGCCTACGACCTG
* *
29285 GGTGCTCAGTCTTACGACCTG
1 GGTGCTCAGGCCTACGACCTG
29306 GGTGC
1 GGTGC
29311 CCAGCTGGAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.11, C:0.30, G:0.36, T:0.23
Consensus pattern (21 bp):
GGTGCTCAGGCCTACGACCTG
Found at i:32375 original size:6 final size:6
Alignment explanation
Indices: 32364--32396 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
32354 CACTTAAACG
*
32364 AAAAAT AAAAAT AAAAGT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAA
32397 GTAACGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:32387 original size:18 final size:17
Alignment explanation
Indices: 32364--32400 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
32354 CACTTAAACG
32364 AAAAATAAAAATAAAAGT
1 AAAAATAAAAAT-AAAGT
32382 AAAAATAAAAATAAAGT
1 AAAAATAAAAATAAAGT
32399 AA
1 AA
32401 CGAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.16
Consensus pattern (17 bp):
AAAAATAAAAATAAAGT
Found at i:35924 original size:21 final size:21
Alignment explanation
Indices: 35900--35970 Score: 133
Period size: 21 Copynumber: 3.4 Consensus size: 21
35890 TGCTAGGAGT
35900 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
35921 TCATTGGAGAAAGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
35942 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
35963 TCATTGGA
1 TCATTGGA
35971 ATTGCCTAAG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:36957 original size:32 final size:32
Alignment explanation
Indices: 36894--36958 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
36884 AAATTATATA
* * *
36894 TAGCGGCGTTTTGTTTAATAAATGCCACTATT
1 TAGCGGCGTTTTCTTCAATAAACGCCACTATT
* *
36926 TAGCGGCGTTTTCTTCAATAGACGCCGCTATT
1 TAGCGGCGTTTTCTTCAATAAACGCCACTATT
36958 T
1 T
36959 TTCAGCTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (32 bp):
TAGCGGCGTTTTCTTCAATAAACGCCACTATT
Found at i:39494 original size:15 final size:15
Alignment explanation
Indices: 39464--39505 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
39454 TTACTTTGCT
39464 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
39480 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
39495 TTGCTTTCTGT
1 TTGTTTTCTGT
39506 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Done.