Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012999.1 Corchorus olitorius cultivar O-4 contig13032, 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: 74186
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:350 original size:14 final size:16
Alignment explanation
Indices: 326--367 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
316 GTTGAAAGAT
* *
326 TAAGCACTGAAT-TTT
1 TAAGTACTGAATATTG
341 TAA-TACTGAATATTG
1 TAAGTACTGAATATTG
356 TAAGTACTGAAT
1 TAAGTACTGAAT
368 CCAAACTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.30
15 8 0.35
16 8 0.35
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (16 bp):
TAAGTACTGAATATTG
Found at i:4312 original size:31 final size:29
Alignment explanation
Indices: 4234--4312 Score: 72
Period size: 31 Copynumber: 2.7 Consensus size: 29
4224 CTTCGCGTCA
* *
4234 AGGATGTTTTG-TACCTAAATTTCAAATC
1 AGGATATTTTGCTCCCTAAATTTCAAATC
* * *
4262 AAGACATTTTGC-CTACTAAATTTCCAAATTC
1 AGGATATTTTGCTC-CCTAAATTT-CAAA-TC
4293 AGGATATTTTGCTCCCTAAA
1 AGGATATTTTGCTCCCTAAA
4313 CTTAAAAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
28 8 0.21
29 8 0.21
30 4 0.11
31 17 0.45
32 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (29 bp):
AGGATATTTTGCTCCCTAAATTTCAAATC
Found at i:12446 original size:13 final size:13
Alignment explanation
Indices: 12428--12464 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
12418 AAGAACTGTT
12428 TTGAAATTTTCGC
1 TTGAAATTTTCGC
*
12441 TTGAAATTATCGC
1 TTGAAATTTTCGC
12454 TTGAAATTTTC
1 TTGAAATTTTC
12465 TCTCATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.46
Consensus pattern (13 bp):
TTGAAATTTTCGC
Found at i:15928 original size:15 final size:15
Alignment explanation
Indices: 15910--15939 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15900 ACTGCAAAGC
15910 ACATAATTTGAATCA
1 ACATAATTTGAATCA
*
15925 ACATGATTTGAATCA
1 ACATAATTTGAATCA
15940 CAATTTAAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (15 bp):
ACATAATTTGAATCA
Found at i:16393 original size:6 final size:6
Alignment explanation
Indices: 16384--16418 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
16374 TAGATATAGA
16384 TATATC TATATC TATATC TATATC TATATAC TATA
1 TATATC TATATC TATATC TATATC TATAT-C TATA
16419 CTAGTCTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (6 bp):
TATATC
Found at i:16512 original size:28 final size:28
Alignment explanation
Indices: 16468--16521 Score: 83
Period size: 27 Copynumber: 1.9 Consensus size: 28
16458 CGTTTAAATA
*
16468 AAAAAATTAAAATAATTAAAATTATTAAT
1 AAAAAATTAAAAGAATT-AAATTATTAAT
16497 AAAAAATT-AAAGAATTAAATTATTA
1 AAAAAATTAAAAGAATTAAATTATTA
16522 TATTGTATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 9 0.38
28 7 0.29
29 8 0.33
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (28 bp):
AAAAAATTAAAAGAATTAAATTATTAAT
Found at i:17335 original size:25 final size:26
Alignment explanation
Indices: 17292--17341 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
17282 GGTACTGTAC
17292 AAATTGAATTTTTCTAAATAAAATAA
1 AAATTGAATTTTTCTAAATAAAATAA
17318 AAATTGAA-TTTTCTAAATAAAATA
1 AAATTGAATTTTTCTAAATAAAATA
17342 TTTTAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (26 bp):
AAATTGAATTTTTCTAAATAAAATAA
Found at i:20773 original size:36 final size:36
Alignment explanation
Indices: 20726--20795 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
20716 GAGATTTTGG
*
20726 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATTACAAAAAATGTAATA
20762 AGAAATATGATAACCAAAATTACAAAAAATGTAA
1 AGAAATATGATAACCAAAATTACAAAAAATGTAA
20796 GGTTATTGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.61, C:0.07, G:0.09, T:0.23
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATTACAAAAAATGTAATA
Found at i:21550 original size:179 final size:178
Alignment explanation
Indices: 21251--21594 Score: 582
Period size: 179 Copynumber: 1.9 Consensus size: 178
21241 TTACTAATGT
21251 TATTAAGAATGTAAGGATTGGTAAATACAATTTTACAAACTTTTATAGCTTTTTAGTAGATTACT
1 TATTAAGAATGTAAGGATTGGTAAATACAATTTTACAAACTTTTATAGCTTTTTAGTAGATTACT
* * *
21316 CAAGTAATTAAATTGGTAACTTTCATTATTAATCATAAAAAGTTACTAAAATTAATAAGGATGTA
66 CAAGTAATTAAATTGGCAACTTTCATTATTAATCACAAAAAGTTACTAAAATTAATAAAGATGTA
21381 AGATTACTTGAATCTAGATAGTACTATAATGTTTTTCGGGAAAAAAAA
131 AGATTACTTGAATCTAGATAGTACTATAATGTTTTTCGGGAAAAAAAA
* *
21429 TATTAAGAATGTAAGGATTGGTAAATGCAATTTTA-ATAACTTTTTTAGCTTTTATAGTAGATTA
1 TATTAAGAATGTAAGGATTGGTAAATACAATTTTACA-AACTTTTATAGCTTTT-TAGTAGATTA
* * *
21493 CTTAAGTAATTAAATTGGCAACTTTCATTATTGATCACACAAAGTTACTAAAATTAATAAAGATG
64 CTCAAGTAATTAAATTGGCAACTTTCATTATTAATCACAAAAAGTTACTAAAATTAATAAAGATG
*
21558 TAAGATTATTTGAATCTAGATAGTACTATAATGTTTT
129 TAAGATTACTTGAATCTAGATAGTACTATAATGTTTT
21595 CATAACTTTT
Statistics
Matches: 155, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
177 1 0.01
178 49 0.32
179 105 0.68
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (178 bp):
TATTAAGAATGTAAGGATTGGTAAATACAATTTTACAAACTTTTATAGCTTTTTAGTAGATTACT
CAAGTAATTAAATTGGCAACTTTCATTATTAATCACAAAAAGTTACTAAAATTAATAAAGATGTA
AGATTACTTGAATCTAGATAGTACTATAATGTTTTTCGGGAAAAAAAA
Found at i:23316 original size:3 final size:3
Alignment explanation
Indices: 23310--23356 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
23300 AGTAAATTCT
23310 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
23357 GCATCAGAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:23862 original size:51 final size:51
Alignment explanation
Indices: 23786--23888 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
23776 ATTGATTGTT
23786 GGTCCACCTTGAATCCCACCTACTGCTTGTTTATCTCCTTTTACATCACCA
1 GGTCCACCTTGAATCCCACCTACTGCTTGTTTATCTCCTTTTACATCACCA
23837 GGTCCACCTTGAATCCCACCTACTGCTTGTTTATCTCCTTTTACATCACCA
1 GGTCCACCTTGAATCCCACCTACTGCTTGTTTATCTCCTTTTACATCACCA
23888 G
1 G
23889 AAAAGCAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.19, C:0.35, G:0.11, T:0.35
Consensus pattern (51 bp):
GGTCCACCTTGAATCCCACCTACTGCTTGTTTATCTCCTTTTACATCACCA
Found at i:29885 original size:25 final size:25
Alignment explanation
Indices: 29857--29921 Score: 87
Period size: 24 Copynumber: 2.6 Consensus size: 25
29847 TAAAATCAGT
*
29857 AAATATAAGAATTTTTAAGAAATAA
1 AAATATAAGAATTTTTAAAAAATAA
* *
29882 AAATGTAAG-TTTTTTAAAAAATAA
1 AAATATAAGAATTTTTAAAAAATAA
*
29906 AAATACAAGAATTTTT
1 AAATATAAGAATTTTT
29922 GCTTGAGTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 20 0.61
25 13 0.39
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (25 bp):
AAATATAAGAATTTTTAAAAAATAA
Found at i:52417 original size:12 final size:13
Alignment explanation
Indices: 52386--52418 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
52376 AGAGAAGGTG
52386 GGAAATGGTAAAT
1 GGAAATGGTAAAT
52399 GGAAATGGT-AAT
1 GGAAATGGTAAAT
*
52411 GGTAATGG
1 GGAAATGG
52419 GGTATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.39, C:0.00, G:0.36, T:0.24
Consensus pattern (13 bp):
GGAAATGGTAAAT
Found at i:59040 original size:21 final size:20
Alignment explanation
Indices: 59002--59053 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
58992 TCCTTCTCAA
*
59002 ATTGTAATG-T-TGTTTCTG
1 ATTGTAATGTTCTATTTCTG
59020 ATTGTAATGCTTCTATTTCTG
1 ATTGTAATG-TTCTATTTCTG
59041 ATTGTAATGTTCT
1 ATTGTAATGTTCT
59054 TGCTTGTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 9 0.30
20 5 0.17
21 16 0.53
ACGTcount: A:0.19, C:0.10, G:0.17, T:0.54
Consensus pattern (20 bp):
ATTGTAATGTTCTATTTCTG
Found at i:62009 original size:11 final size:11
Alignment explanation
Indices: 61993--62018 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
61983 GATTAAATTT
61993 GTTATGAGTTA
1 GTTATGAGTTA
62004 GTTATGAGTTA
1 GTTATGAGTTA
62015 GTTA
1 GTTA
62019 ATTTTACAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (11 bp):
GTTATGAGTTA
Done.