Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012421.1 Corchorus olitorius cultivar O-4 contig12454, 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: 16079
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Found at i:876 original size:16 final size:15
Alignment explanation
Indices: 838--879 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
828 ACAGAGGTTG
*
838 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
853 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
868 ACTAGAAAACAA
1 AC-AGAAAACAA
880 AGCAAAGTAA
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:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:3560 original size:19 final size:18
Alignment explanation
Indices: 3522--3566 Score: 81
Period size: 18 Copynumber: 2.4 Consensus size: 18
3512 TACGAAAAAA
3522 TTATGGCATATTTAGATTT
1 TTAT-GCATATTTAGATTT
3541 TTATGCATATTTAGATTT
1 TTATGCATATTTAGATTT
3559 TTATGCAT
1 TTATGCAT
3567 GCAGACTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (18 bp):
TTATGCATATTTAGATTT
Found at i:7212 original size:16 final size:15
Alignment explanation
Indices: 7174--7215 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
7164 ACAGAGGTTG
*
7174 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
7189 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
7204 ACTAGAAAACAA
1 AC-AGAAAACAA
7216 AGCAAAGTAA
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:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:9235 original size:13 final size:13
Alignment explanation
Indices: 9217--9241 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9207 ATAAAAAACT
9217 CAAAAGTGTTTTC
1 CAAAAGTGTTTTC
9230 CAAAAGTGTTTT
1 CAAAAGTGTTTT
9242 TATGTATGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (13 bp):
CAAAAGTGTTTTC
Found at i:13499 original size:8 final size:8
Alignment explanation
Indices: 13486--13584 Score: 175
Period size: 8 Copynumber: 12.5 Consensus size: 8
13476 AATGAATGGA
13486 AAAAAATG
1 AAAAAATG
13494 AAAAAAATG
1 -AAAAAATG
13503 AAAAAATG
1 AAAAAATG
13511 AAAAAATG
1 AAAAAATG
13519 AAAAAATG
1 AAAAAATG
13527 AAAAAATG
1 AAAAAATG
13535 AAAAAATG
1 AAAAAATG
13543 AAAAAATG
1 AAAAAATG
13551 AAAAAATG
1 AAAAAATG
13559 AAAAAATG
1 AAAAAATG
13567 -AAAAATG
1 AAAAAATG
13574 -AAAAATG
1 AAAAAATG
13581 AAAA
1 AAAA
13585 TAAATGCACT
Statistics
Matches: 89, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
7 14 0.16
8 67 0.75
9 8 0.09
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:14359 original size:11 final size:11
Alignment explanation
Indices: 14343--14389 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
14333 CACAAAAATG
14343 AAAAAATGAAA
1 AAAAAATGAAA
14354 AAAAAATGAAA
1 AAAAAATGAAA
*
14365 AAAAGA-GAAGA
1 AAAAAATGAA-A
*
14376 AAAAAAGGAAA
1 AAAAAATGAAA
14387 AAA
1 AAA
14390 TAGAGCTCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 3 0.09
11 26 0.81
12 3 0.09
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (11 bp):
AAAAAATGAAA
Found at i:14378 original size:21 final size:21
Alignment explanation
Indices: 14336--14394 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
14326 TCAAGTGCAC
*
14336 AAAAATG-AAAAAA-TGAAAA
1 AAAAATGAAAAAAAGAGAAAA
14355 AAAAATGAAAAAAAGAGAAGAA
1 AAAAATGAAAAAAAGAGAA-AA
*
14377 AAAAAGGAAAAAATAGAG
1 AAAAATGAAAAAA-AGAG
14395 CTCTAGGGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.21
20 6 0.18
21 3 0.09
22 14 0.41
23 4 0.12
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (21 bp):
AAAAATGAAAAAAAGAGAAAA
Found at i:15070 original size:19 final size:18
Alignment explanation
Indices: 15046--15081 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
15036 TGAAGATTTA
15046 TTGAAGATAATTTGAAGAC
1 TTGAAGATAA-TTGAAGAC
*
15065 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
15082 ATTATTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAC
Done.