Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014498.1 Corchorus olitorius cultivar O-4 contig14531, 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: 23623
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:4632 original size:5 final size:5
Alignment explanation
Indices: 4619--4674 Score: 51
Period size: 5 Copynumber: 10.6 Consensus size: 5
4609 ATAAATAAAT
* *
4619 AAAGT AAAGG AAAGG AAAGG TTGAAGG AAAAGG AAAGG AAA-G AAAGG
1 AAAGG AAAGG AAAGG AAAGG --AAAGG -AAAGG AAAGG AAAGG AAAGG
4666 AAAAGG AAA
1 -AAAGG AAA
4675 ATGGGAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
4 4 0.09
5 26 0.60
6 9 0.21
7 4 0.09
ACGTcount: A:0.61, C:0.00, G:0.34, T:0.05
Consensus pattern (5 bp):
AAAGG
Found at i:4682 original size:28 final size:28
Alignment explanation
Indices: 4619--4675 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
4609 ATAAATAAAT
* **
4619 AAAGTAAAGGAAAGGAAAGGTTGAAGGA
1 AAAGGAAAGGAAAGGAAAGGTAAAAGGA
4647 AAAGGAAAGGAAA-GAAAGG-AAAAGGA
1 AAAGGAAAGGAAAGGAAAGGTAAAAGGA
4673 AAA
1 AAA
4676 TGGGAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 8 0.31
27 6 0.23
28 12 0.46
ACGTcount: A:0.61, C:0.00, G:0.33, T:0.05
Consensus pattern (28 bp):
AAAGGAAAGGAAAGGAAAGGTAAAAGGA
Found at i:6635 original size:26 final size:26
Alignment explanation
Indices: 6586--6636 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
6576 TTTGTATGAA
*
6586 TTTCAACCAATAATTGAAAAAAAATG
1 TTTCAACCAATAATTAAAAAAAAATG
*
6612 TTTCGACCAA-AATTAAAAATAAAAT
1 TTTCAACCAATAATTAAAAA-AAAAT
6637 AGTTAAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.55, C:0.12, G:0.06, T:0.27
Consensus pattern (26 bp):
TTTCAACCAATAATTAAAAAAAAATG
Found at i:6888 original size:18 final size:18
Alignment explanation
Indices: 6865--6900 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
6855 AAATCCTTTT
6865 GATCATACCTCATCAATA
1 GATCATACCTCATCAATA
6883 GATCATACCTCATCAATA
1 GATCATACCTCATCAATA
6901 CAGAACCTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.28, G:0.06, T:0.28
Consensus pattern (18 bp):
GATCATACCTCATCAATA
Found at i:6957 original size:25 final size:25
Alignment explanation
Indices: 6929--6977 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
6919 CATTAGTTGA
6929 TTTTTTAGA-GAATATAATTAGCTCC
1 TTTTTTAGAGGAA-ATAATTAGCTCC
* *
6954 TTTTTTATAGGGAATAATTAGCTC
1 TTTTTTAGAGGAAATAATTAGCTC
6978 TTATTAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (25 bp):
TTTTTTAGAGGAAATAATTAGCTCC
Found at i:8665 original size:22 final size:22
Alignment explanation
Indices: 8356--8666 Score: 220
Period size: 22 Copynumber: 14.0 Consensus size: 22
8346 CATAGGAAGA
* ***
8356 TTATCAAAATTTCATAGTGTTA
1 TTATCAAAATTTCATAGAGAGG
* *
8378 TTACCAAAATTTTATATG-GAGG
1 TTATCAAAATTTCATA-GAGAGG
* *
8400 TTATCAAAACTTCATAGTGTA-G
1 TTATCAAAATTTCATAGAG-AGG
* *
8422 TTATCAAAATTTCATATAGAGA
1 TTATCAAAATTTCATAGAGAGG
* * *
8444 TTACCAAAATTTCATAAAAAGG
1 TTATCAAAATTTCATAGAGAGG
* *
8466 TTATCAAAATTTCTTAGGGAGG
1 TTATCAAAATTTCATAGAGAGG
*
8488 TTAACAAAATTTCATACGA-AGG
1 TTATCAAAATTTCATA-GAGAGG
* * * *
8510 TTATCAGAATTTTATAGTGTGG
1 TTATCAAAATTTCATAGAGAGG
*
8532 TTATCAAAATTTCATA-AGAAGA
1 TTATCAAAATTTCATAGAG-AGG
*
8554 TTAACAAAATTTCATAGGGAGGGAGG
1 TTATCAAAATTTCATA--GA--GAGG
* * *
8580 TTATCTAAATTTCCTAGGGAGG
1 TTATCAAAATTTCATAGAGAGG
* *
8602 TTAACAATATTTCATAG-GAAGG
1 TTATCAAAATTTCATAGAG-AGG
* *
8624 TTATGC-AAATTTTATGGAGAGG
1 TTAT-CAAAATTTCATAGAGAGG
*
8646 TTATCAAAATTACATAGAGAG
1 TTATCAAAATTTCATAGAGAG
8667 AATATCACAG
Statistics
Matches: 222, Mismatches: 51, Indels: 32
0.73 0.17 0.10
Matches are distributed among these distances:
21 6 0.03
22 193 0.87
23 5 0.02
24 1 0.00
25 1 0.00
26 15 0.07
27 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAGAGAGG
Found at i:8682 original size:114 final size:114
Alignment explanation
Indices: 8463--8670 Score: 303
Period size: 114 Copynumber: 1.8 Consensus size: 114
8453 TTTCATAAAA
* *
8463 AGGTTATCAAAATTTCTTAGGGAGGTTAACAAAATTTCATACGAAGGTTATCAGAATTTTATAGT
1 AGGTTATCAAAATTTCCTAGGGAGGTTAACAAAATTTCATACGAAGGTTATCAGAATTTTATAGA
* * *
8528 GTGGTTATCAAAATTTCATAAGAAGATTAACAAAATTTCATAGGGAGGG
66 GAGGTTATCAAAATTACATAAGAAGAATAACAAAATTTCATAGGGAGGG
* * * *
8577 AGGTTATCTAAATTTCCTAGGGAGGTTAACAATATTTCATAGGAAGGTTATGCA-AATTTTATGG
1 AGGTTATCAAAATTTCCTAGGGAGGTTAACAAAATTTCATACGAAGGTTAT-CAGAATTTTATAG
8641 AGAGGTTATCAAAATTACAT-AGAGAGAATA
65 AGAGGTTATCAAAATTACATAAGA-AGAATA
8671 TCACAGTTTC
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
113 3 0.04
114 78 0.94
115 2 0.02
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (114 bp):
AGGTTATCAAAATTTCCTAGGGAGGTTAACAAAATTTCATACGAAGGTTATCAGAATTTTATAGA
GAGGTTATCAAAATTACATAAGAAGAATAACAAAATTTCATAGGGAGGG
Found at i:9255 original size:11 final size:11
Alignment explanation
Indices: 9241--9278 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
9231 ATTCATAACA
9241 AATTTATAATT
1 AATTTATAATT
9252 AATTTATAATT
1 AATTTATAATT
9263 -ATTTGATAATT
1 AATTT-ATAATT
*
9274 TATTT
1 AATTT
9279 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:11157 original size:15 final size:16
Alignment explanation
Indices: 11121--11159 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
11111 AATTTTTCCG
11121 GGTCATTCGGGTTTCA
1 GGTCATTCGGGTTTCA
**
11137 ACTCATTCGGG-TTCA
1 GGTCATTCGGGTTTCA
11152 GGTCATTC
1 GGTCATTC
11160 AAGTCTCGGG
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.15, C:0.23, G:0.26, T:0.36
Consensus pattern (16 bp):
GGTCATTCGGGTTTCA
Found at i:15435 original size:2 final size:2
Alignment explanation
Indices: 15428--15457 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
15418 TATACTCTTT
15428 TC TC TC TC TC TC TC TC TC TC TC TC TAC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T-C TC T
15458 AAAATCTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:15979 original size:18 final size:18
Alignment explanation
Indices: 15953--15994 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
15943 CCGGTTACCG
* *
15953 GAAGAAAAAGAAAAAGAA
1 GAAGAAAAAAAAAAAAAA
*
15971 GAAGCAAAAAAAAAAAAA
1 GAAGAAAAAAAAAAAAAA
15989 G-AGAAA
1 GAAGAAA
15995 CAGTCCGCTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (18 bp):
GAAGAAAAAAAAAAAAAA
Found at i:16065 original size:29 final size:29
Alignment explanation
Indices: 16000--16056 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
15990 AGAAACAGTC
* *
16000 CGCTTGGGCCAGCCAGGCGCGAGGCCCAG
1 CGCTTGGGCCAGCCAAGAGCGAGGCCCAG
*
16029 CGCTTGGGCCAGCCAAGAGCGCGGCCCA
1 CGCTTGGGCCAGCCAAGAGCGAGGCCCA
16057 AGCTCTGGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.16, C:0.39, G:0.39, T:0.07
Consensus pattern (29 bp):
CGCTTGGGCCAGCCAAGAGCGAGGCCCAG
Found at i:17486 original size:13 final size:12
Alignment explanation
Indices: 17448--17489 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
17438 TTATTACAGT
17448 TTTTATATAAATG
1 TTTT-TATAAATG
17461 ATTTTTA-AAATG
1 -TTTTTATAAATG
17473 TTTTTGATAAATG
1 TTTTT-ATAAATG
17486 TTTT
1 TTTT
17490 GGGTGCATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 5 0.19
12 6 0.23
13 11 0.42
14 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (12 bp):
TTTTTATAAATG
Found at i:19490 original size:24 final size:23
Alignment explanation
Indices: 19438--19491 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
19428 ATAAATGATG
* * *
19438 CTGATAA-TCTTCTCTTTTATCT
1 CTGATAATTCTCCTCATTTATCA
19460 CTGATAATTCTCCTCATTTATCA
1 CTGATAATTCTCCTCATTTATCA
19483 CTTGATAAT
1 C-TGATAAT
19492 ATCTAGCCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 7 0.26
23 13 0.48
24 7 0.26
ACGTcount: A:0.24, C:0.22, G:0.06, T:0.48
Consensus pattern (23 bp):
CTGATAATTCTCCTCATTTATCA
Done.