Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024542.1 Corchorus olitorius cultivar O-4 contig24575, 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: 16695
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2370 original size:25 final size:24
Alignment explanation
Indices: 2342--2399 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
2332 AATAATAAAA
*
2342 AAATAGGTATAGAGATAAAATAGAT
1 AAATAGGTACAGAGA-AAAATAGAT
* *
2367 AAATAGATACAGAGAATAATAGAT
1 AAATAGGTACAGAGAAAAATAGAT
2391 AAATAGGTA
1 AAATAGGTA
2400 GCTAAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 16 0.55
25 13 0.45
ACGTcount: A:0.57, C:0.02, G:0.19, T:0.22
Consensus pattern (24 bp):
AAATAGGTACAGAGAAAAATAGAT
Found at i:2423 original size:4 final size:4
Alignment explanation
Indices: 2402--2599 Score: 71
Period size: 4 Copynumber: 50.8 Consensus size: 4
2392 AATAGGTAGC
* * ** *
2402 TAAA AAAA T-AA T-AA TAAA TAAA TATA T-AA TAGC TAAA TTAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* * * ** *
2447 TAAA -AAGA TAAA T-AG TAAG TAAA TAGA T-AA TAGC TAAA TTAA TAAA
1 TAAA TAA-A TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* * *
2493 TAAA -AAGA TAAA T-AG TAAA TAAA TAGA TAATA GTTAA -AAA TAAA TAAA
1 TAAA TAA-A TAAA TAAA TAAA TAAA TAAA TAA-A -TAAA TAAA TAAA TAAA
* * *
2541 -AAGA TAAA T-AG TAAA TAAA TAGA TAATA GTTAA -AAA TAAA TAAA -AAGA
1 TAA-A TAAA TAAA TAAA TAAA TAAA TAA-A -TAAA TAAA TAAA TAAA TAA-A
*
2589 TAAA TAGA TAA
1 TAAA TAAA TAA
2600 TAGTTAAAAA
Statistics
Matches: 140, Mismatches: 34, Indels: 40
0.65 0.16 0.19
Matches are distributed among these distances:
3 28 0.20
4 96 0.69
5 12 0.09
6 4 0.03
ACGTcount: A:0.65, C:0.01, G:0.08, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:2457 original size:27 final size:27
Alignment explanation
Indices: 2413--2522 Score: 87
Period size: 27 Copynumber: 4.4 Consensus size: 27
2403 AAAAAAATAA
* *
2413 TAATAAATAAATATAT-AATAGCTAAAT
1 TAATAAATAAAAAGATAAATAG-TAAAT
2440 TAATAAATAAAAAGATAAATAGT--A-
1 TAATAAATAAAAAGATAAATAGTAAAT
*
2464 -AGTAAAT----AGAT-AATAGCTAAAT
1 TAATAAATAAAAAGATAAATAG-TAAAT
2486 TAATAAATAAAAAGATAAATAGTAAAT
1 TAATAAATAAAAAGATAAATAGTAAAT
* *
2513 AAATAGATAA
1 TAATAAATAA
2523 TAGTTAAAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 22
0.70 0.06 0.23
Matches are distributed among these distances:
18 5 0.08
19 5 0.08
21 1 0.02
23 12 0.18
25 1 0.02
27 32 0.48
28 10 0.15
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27
Consensus pattern (27 bp):
TAATAAATAAAAAGATAAATAGTAAAT
Found at i:2474 original size:19 final size:19
Alignment explanation
Indices: 2429--2594 Score: 98
Period size: 19 Copynumber: 9.0 Consensus size: 19
2419 ATAAATATAT
* *
2429 AATAGCTAAATTAATAAATA
1 AATAGATAAA-TAGTAAATA
* *
2449 AAAAGATAAATAGTAAGTA
1 AATAGATAAATAGTAAATA
*
2468 AATAGAT-AATAGCTAAATT
1 AATAGATAAATAG-TAAATA
* *
2487 AATAAATAAA-A--AGATA
1 AATAGATAAATAGTAAATA
* *
2503 AATAG-TAAATAAATAGAT-
1 AATAGATAAAT-AGTAAATA
* *
2521 AATAGTTAAA-AATAAATA
1 AATAGATAAATAGTAAATA
*
2539 AAAAGATAAATAGTAAATA
1 AATAGATAAATAGTAAATA
*
2558 AATAGAT-AATAGTTAA-A
1 AATAGATAAATAGTAAATA
* *
2575 AATAAATAAAAAGATAAATA
1 AATAGATAAATAG-TAAATA
2595 GATAATAGTT
Statistics
Matches: 114, Mismatches: 20, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
15 4 0.04
16 7 0.06
17 14 0.12
18 30 0.26
19 48 0.42
20 11 0.10
ACGTcount: A:0.64, C:0.01, G:0.09, T:0.25
Consensus pattern (19 bp):
AATAGATAAATAGTAAATA
Found at i:2550 original size:44 final size:44
Alignment explanation
Indices: 2512--2595 Score: 168
Period size: 44 Copynumber: 1.9 Consensus size: 44
2502 AAATAGTAAA
2512 TAAATAGATAATAGTTAAAAATAAATAAAAAGATAAATAGTAAA
1 TAAATAGATAATAGTTAAAAATAAATAAAAAGATAAATAGTAAA
2556 TAAATAGATAATAGTTAAAAATAAATAAAAAGATAAATAG
1 TAAATAGATAATAGTTAAAAATAAATAAAAAGATAAATAG
2596 ATAATAGTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (44 bp):
TAAATAGATAATAGTTAAAAATAAATAAAAAGATAAATAGTAAA
Found at i:10183 original size:15 final size:16
Alignment explanation
Indices: 10150--10183 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
10140 TTACTTTGCT
10150 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
10166 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
10181 TTG
1 TTG
10184 CTTCCTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.18, C:0.06, G:0.15, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:10546 original size:22 final size:22
Alignment explanation
Indices: 10516--10567 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
10506 TTCTAAAAAA
*
10516 AATTATTTTTCTTTGCGTCTTT
1 AATTTTTTTTCTTTGCGTCTTT
* *
10538 AATTTTTTTTTTTTGCGTTTTT
1 AATTTTTTTTCTTTGCGTCTTT
10560 AATTTTTT
1 AATTTTTT
10568 GTGTTGCGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.13, C:0.08, G:0.08, T:0.71
Consensus pattern (22 bp):
AATTTTTTTTCTTTGCGTCTTT
Found at i:10565 original size:21 final size:21
Alignment explanation
Indices: 10516--10580 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 21
10506 TTCTAAAAAA
* *
10516 AATTATTTTTCTTTGCGTCTTT
1 AATT-TTTTTTTTTGCGTTTTT
10538 AATTTTTTTTTTTTGCGTTTTT
1 AA-TTTTTTTTTTTGCGTTTTT
* *
10560 AATTTTTTGTGTTGCGTTTTT
1 AATTTTTTTTTTTGCGTTTTT
10581 GAAAAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 17 0.45
22 19 0.50
23 2 0.05
ACGTcount: A:0.11, C:0.08, G:0.12, T:0.69
Consensus pattern (21 bp):
AATTTTTTTTTTTGCGTTTTT
Found at i:10580 original size:22 final size:22
Alignment explanation
Indices: 10528--10580 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
10518 TTATTTTTCT
* * *
10528 TTGCGTCTTTAATTTTTTTTTT
1 TTGCGTTTTTAATTTTTTTGTG
10550 TTGCGTTTTTAA-TTTTTTGTG
1 TTGCGTTTTTAATTTTTTTGTG
10571 TTGCGTTTTT
1 TTGCGTTTTT
10581 GAAAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.08, C:0.08, G:0.15, T:0.70
Consensus pattern (22 bp):
TTGCGTTTTTAATTTTTTTGTG
Found at i:13821 original size:21 final size:21
Alignment explanation
Indices: 13797--13851 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
13787 CCGCCAAAAG
* *
13797 CCGTGCCACCACTGGTTGA-GC
1 CCGTGCCACCACCGG-CGATGC
13818 CCGTGCCACCACCGGCGATGC
1 CCGTGCCACCACCGGCGATGC
*
13839 CCGTGCCATCACC
1 CCGTGCCACCACC
13852 ATTCCATGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.15, C:0.45, G:0.25, T:0.15
Consensus pattern (21 bp):
CCGTGCCACCACCGGCGATGC
Done.