Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012551.1 Corchorus olitorius cultivar O-4 contig12584, 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: 15927
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:224 original size:2 final size:2
Alignment explanation
Indices: 219--321 Score: 93
Period size: 2 Copynumber: 56.0 Consensus size: 2
209 TCCAATGCGA
* *
219 AT AT AT AT AT ACT -T AT AT ACT AA AT AT AT AT AT AT AT AT GT -T
1 AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
261 AT AT -T AT AT AT -T AT AT AT -T AT AT AT AT -T AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
298 AT -T AT AT AT -T AT AT AT -T AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
322 TATTTGAAAG
Statistics
Matches: 85, Mismatches: 3, Indels: 26
0.75 0.03 0.23
Matches are distributed among these distances:
1 11 0.13
2 71 0.84
3 3 0.04
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (2 bp):
AT
Found at i:245 original size:21 final size:20
Alignment explanation
Indices: 219--324 Score: 133
Period size: 21 Copynumber: 5.1 Consensus size: 20
209 TCCAATGCGA
*
219 ATATATATATACTTATATACT
1 ATATATATATA-TTATATATT
* *
240 AAATATATATATATATATGTT
1 ATATATATATAT-TATATATT
261 ATAT-TATATATTATATATT
1 ATATATATATATTATATATT
280 ATATATATTATATTATATATT
1 ATATATA-TATATTATATATT
301 ATATATTATATATTATTATATT
1 ATATA-TATATATTA-TATATT
323 AT
1 AT
325 TTGAAAGACC
Statistics
Matches: 75, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
19 11 0.15
20 10 0.13
21 44 0.59
22 10 0.13
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (20 bp):
ATATATATATATTATATATT
Found at i:987 original size:13 final size:13
Alignment explanation
Indices: 963--997 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
953 GATACTTAAG
*
963 AAATAAATATAAA
1 AAATAAAGATAAA
*
976 AACTAAAGATAAA
1 AAATAAAGATAAA
989 AAATAAAGA
1 AAATAAAGA
998 GCTAGAGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.17
Consensus pattern (13 bp):
AAATAAAGATAAA
Found at i:1373 original size:2 final size:2
Alignment explanation
Indices: 1366--1394 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1356 ACCGGCTTAT
1366 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1395 GCAAGAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7757 original size:20 final size:20
Alignment explanation
Indices: 7732--7773 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
7722 CAATACACGC
*
7732 GCCGTTAACTATCCTACGTG
1 GCCGTTAACTATCCTACATG
* *
7752 GCCGTTAAGTCTCCTACATG
1 GCCGTTAACTATCCTACATG
7772 GC
1 GC
7774 TTTTTCAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.19, C:0.31, G:0.21, T:0.29
Consensus pattern (20 bp):
GCCGTTAACTATCCTACATG
Found at i:9111 original size:26 final size:24
Alignment explanation
Indices: 9052--9116 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 24
9042 TATTATTTAA
9052 ATAAAATAA-T-TATTTTTAAATT
1 ATAAAATAATTATATTTTTAAATT
*
9074 ATAAATTAATTAATATTTTTAAATCT
1 ATAAAATAATT-ATATTTTTAAAT-T
9100 -TAAAATATATTATATTT
1 ATAAAATA-ATTATATTT
9117 CATGTCCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
22 8 0.22
23 1 0.03
25 23 0.64
26 4 0.11
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
ATAAAATAATTATATTTTTAAATT
Found at i:10629 original size:17 final size:18
Alignment explanation
Indices: 10590--10627 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
10580 CACATAGATA
10590 TTTT-GTTTTCTTCTAGT
1 TTTTAGTTTTCTTCTAGT
10607 TTTTAGTTTTCTTCTAGT
1 TTTTAGTTTTCTTCTAGT
10625 TTT
1 TTT
10628 AGACAAGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.08, C:0.11, G:0.11, T:0.71
Consensus pattern (18 bp):
TTTTAGTTTTCTTCTAGT
Found at i:11407 original size:21 final size:21
Alignment explanation
Indices: 11370--11418 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
11360 TAGACTATGA
* *
11370 TTTAATTTACTTTGCTTTGTT
1 TTTAATTTACATTGCTTTCTT
11391 TTCTAATTTA-ATTGCTTTCTT
1 TT-TAATTTACATTGCTTTCTT
11412 TTTAATT
1 TTTAATT
11419 GTGATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.20
21 13 0.52
22 7 0.28
ACGTcount: A:0.18, C:0.10, G:0.06, T:0.65
Consensus pattern (21 bp):
TTTAATTTACATTGCTTTCTT
Found at i:12765 original size:22 final size:22
Alignment explanation
Indices: 12737--12778 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
12727 AAAATTTTGA
*
12737 TTTCAAAATAGCGGCGTTTCTG
1 TTTCAAAATAGCGGCATTTCTG
*
12759 TTTCAAAATAGTGGCATTTC
1 TTTCAAAATAGCGGCATTTC
12779 CGTAAAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (22 bp):
TTTCAAAATAGCGGCATTTCTG
Found at i:12811 original size:32 final size:32
Alignment explanation
Indices: 12767--12863 Score: 115
Period size: 32 Copynumber: 3.0 Consensus size: 32
12757 TGTTTCAAAA
* *
12767 TAGTGGCATTTCCGTA-AAAAAGCACCTCTATT
1 TAGTGGCGTTTCCGTACAAAAA-CACCGCTATT
* *
12799 TAGTGGCGTTTCCGTACAGAAACGCCGCTATT
1 TAGTGGCGTTTCCGTACAAAAACACCGCTATT
* * *
12831 TAGTGGCGTTTCCATACAGAAACGCCGCTATT
1 TAGTGGCGTTTCCGTACAAAAACACCGCTATT
12863 T
1 T
12864 TGGCTTCTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
32 55 0.93
33 4 0.07
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.30
Consensus pattern (32 bp):
TAGTGGCGTTTCCGTACAAAAACACCGCTATT
Found at i:12935 original size:2 final size:2
Alignment explanation
Indices: 12928--12957 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
12918 TTTAAATTGA
12928 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12958 AACATTGTAT
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.