Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016894.1 Corchorus olitorius cultivar O-4 contig16927, 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: 66531
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:798 original size:19 final size:18
Alignment explanation
Indices: 774--816 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
764 AAAAATAGTT
774 ATATATCTATATAAAAAAA
1 ATATATCTATAT-AAAAAA
* *
793 ATATATTTATATAAGAAA
1 ATATATCTATATAAAAAA
811 ATATAT
1 ATATAT
817 ACGGATTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (18 bp):
ATATATCTATATAAAAAA
Found at i:5595 original size:28 final size:28
Alignment explanation
Indices: 5553--5607 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
5543 CGTCGTGTTA
5553 GTTTATACTCAATCGCAGAGTTCTTATG
1 GTTTATACTCAATCGCAGAGTTCTTATG
* * **
5581 GTTTTTACTCCATCGTGGAGTTCTTAT
1 GTTTATACTCAATCGCAGAGTTCTTAT
5608 ACTCCATTCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.44
Consensus pattern (28 bp):
GTTTATACTCAATCGCAGAGTTCTTATG
Found at i:15324 original size:30 final size:29
Alignment explanation
Indices: 15279--15336 Score: 98
Period size: 30 Copynumber: 2.0 Consensus size: 29
15269 TTAACCTAGA
*
15279 TTTTAATTCCTTTTAATTTAGAATTACTT
1 TTTTAATTACTTTTAATTTAGAATTACTT
15308 TTTTAATTAACTTTTAATTTAGAATTACT
1 TTTTAATT-ACTTTTAATTTAGAATTACT
15337 AATTTTTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.31, C:0.09, G:0.03, T:0.57
Consensus pattern (29 bp):
TTTTAATTACTTTTAATTTAGAATTACTT
Found at i:17707 original size:29 final size:30
Alignment explanation
Indices: 17675--17744 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
17665 TTTCGTCCAT
*
17675 GTACTCAAAAAGC-GATCAATTTAATTCAC
1 GTACTCAAAAAGCAGATCAATTTAATGCAC
* * * *
17704 GTACTCACAAGATCAGGTCAATTTAATGCAT
1 GTACTCA-AAAAGCAGATCAATTTAATGCAC
17735 GTACTCAAAA
1 GTACTCAAAA
17745 GACTGGCTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
29 7 0.21
30 6 0.18
31 20 0.61
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (30 bp):
GTACTCAAAAAGCAGATCAATTTAATGCAC
Found at i:18996 original size:13 final size:13
Alignment explanation
Indices: 18978--19010 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
18968 CATTTTTTTC
18978 AATAAAAGT-AATA
1 AATAAAA-TAAATA
18991 AATAAAATAAATA
1 AATAAAATAAATA
19004 AATAAAA
1 AATAAAA
19011 AATACCCACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 1 0.05
13 18 0.95
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (13 bp):
AATAAAATAAATA
Found at i:19168 original size:6 final size:6
Alignment explanation
Indices: 19159--19189 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
19149 TCATGGTCAT
19159 GGGATG GGGATG GGGATG GGGAT- GGGATG GG
1 GGGATG GGGATG GGGATG GGGATG GGGATG GG
19190 ATGAGGTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.16, C:0.00, G:0.68, T:0.16
Consensus pattern (6 bp):
GGGATG
Found at i:29436 original size:6 final size:6
Alignment explanation
Indices: 29427--29451 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29417 CGACGGCGAT
29427 GATGAC GATGAC GATGAC GATGAC G
1 GATGAC GATGAC GATGAC GATGAC G
29452 GCAAAGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.36, T:0.16
Consensus pattern (6 bp):
GATGAC
Found at i:29463 original size:3 final size:3
Alignment explanation
Indices: 29455--29484 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
29445 GATGACGGCA
*
29455 AAG AAG AAG AAG AAG AAG AAG AAG GAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
29485 GAACGAGAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:32316 original size:17 final size:17
Alignment explanation
Indices: 32289--32321 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
32279 ATTGCACAGA
32289 TGAATTTAAACCAGAAAT
1 TGAATTTAAACC-GAAAT
32307 TGAA-TTAAACCGAAA
1 TGAATTTAAACCGAAA
32322 CCTTCGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (17 bp):
TGAATTTAAACCGAAAT
Found at i:34510 original size:15 final size:15
Alignment explanation
Indices: 34477--34510 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
34467 TGGAGTGATG
*
34477 GTCCTATGGACACGG
1 GTCCTATGGACACGA
*
34492 GTCCTATGGACTCGA
1 GTCCTATGGACACGA
34507 GTCC
1 GTCC
34511 GTGGGAGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.29, G:0.29, T:0.24
Consensus pattern (15 bp):
GTCCTATGGACACGA
Found at i:35804 original size:18 final size:18
Alignment explanation
Indices: 35781--35826 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
35771 TGAAATTAAT
35781 TAATTATTAATTAAATAA
1 TAATTATTAATTAAATAA
** *
35799 TAATTATTTTTTGAATAA
1 TAATTATTAATTAAATAA
*
35817 TTATTATTAA
1 TAATTATTAA
35827 ATTTCTAGTG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TAATTATTAATTAAATAA
Found at i:37276 original size:51 final size:50
Alignment explanation
Indices: 37175--37276 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 50
37165 GTTCTTCATA
* **
37175 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
*
37225 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGT
37276 T
1 T
37277 CTTCATTCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
50 7 0.16
51 37 0.82
52 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
Found at i:38832 original size:24 final size:24
Alignment explanation
Indices: 38800--38852 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
38790 GTTCATAGAT
38800 AGATATTTTATTTTATGAAGAAAA
1 AGATATTTTATTTTATGAAGAAAA
38824 AGATATTTTATTTTATGAAGAAAA
1 AGATATTTTATTTTATGAAGAAAA
38848 AGATA
1 AGATA
38853 ATCACAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (24 bp):
AGATATTTTATTTTATGAAGAAAA
Found at i:44721 original size:21 final size:21
Alignment explanation
Indices: 44676--44734 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
44666 CTATTTGACA
* *
44676 ACTGTACAGATGATATTA--C
1 ACTGTACAGATGAGATTATGT
*
44695 ACTGTACAGATTAGATTATGT
1 ACTGTACAGATGAGATTATGT
44716 ACTGTACAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
44735 TAGAGCAGCG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 16 0.47
21 18 0.53
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.34
Consensus pattern (21 bp):
ACTGTACAGATGAGATTATGT
Found at i:59414 original size:2 final size:2
Alignment explanation
Indices: 59407--59453 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
59397 GGATCTTTGT
59407 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
59449 TG TG T
1 TG TG T
59454 ATGATTTGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:62021 original size:2 final size:2
Alignment explanation
Indices: 62014--62041 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
62004 TTCAATTATT
62014 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
62042 CTACTTTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:63508 original size:84 final size:84
Alignment explanation
Indices: 63381--63542 Score: 272
Period size: 84 Copynumber: 1.9 Consensus size: 84
63371 AAATTATAAT
*
63381 ATATATCTAAGTTATGTAATTAAAATAGTAAAAAATGGTAAAAATAAAATAGTTATAAGGAGATT
1 ATATATCTAAGTTATGTAATTAAAATAGT-AAAAATGGTAAAAATAAAAAAGTTATAAGGAGATT
63446 AGATTTAATTAAAAAATCTA
65 AGATTTAATTAAAAAATCTA
* *
63466 ATATATCTAAGTTTTTTTAATTAAAATAGT-AAAATGGTAAAAATAAAAAAGTTATAAGGAGATT
1 ATATATCTAAG-TTATGTAATTAAAATAGTAAAAATGGTAAAAATAAAAAAGTTATAAGGAGATT
63530 AGATTTAATTAAA
65 AGATTTAATTAAA
63543 TAAAAATAGA
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
84 46 0.63
85 11 0.15
86 16 0.22
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.35
Consensus pattern (84 bp):
ATATATCTAAGTTATGTAATTAAAATAGTAAAAATGGTAAAAATAAAAAAGTTATAAGGAGATTA
GATTTAATTAAAAAATCTA
Done.