Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018672.1 Corchorus olitorius cultivar O-4 contig18705, 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: 30666
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:1880 original size:26 final size:26
Alignment explanation
Indices: 1851--1901 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
1841 GAAAGCCCAA
1851 AGAAATGGACTTGAACAAAAGATAAG
1 AGAAATGGACTTGAACAAAAGATAAG
*
1877 AGAAATGGACTTGACCAAAAGATAA
1 AGAAATGGACTTGAACAAAAGATAA
1902 AAGAGAGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.53, C:0.10, G:0.22, T:0.16
Consensus pattern (26 bp):
AGAAATGGACTTGAACAAAAGATAAG
Found at i:3656 original size:13 final size:13
Alignment explanation
Indices: 3638--3662 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3628 TTGTTACCAC
3638 CTTAAAATTATTG
1 CTTAAAATTATTG
3651 CTTAAAATTATT
1 CTTAAAATTATT
3663 TTTTGGCAAA
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:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (13 bp):
CTTAAAATTATTG
Found at i:5621 original size:18 final size:18
Alignment explanation
Indices: 5598--5643 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
5588 TGAAATTAAT
5598 TAATTATTAATTAAATAA
1 TAATTATTAATTAAATAA
** *
5616 TAATTATTTTTTGAATAA
1 TAATTATTAATTAAATAA
*
5634 TTATTATTAA
1 TAATTATTAA
5644 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:7094 original size:51 final size:50
Alignment explanation
Indices: 6993--7094 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 50
6983 GTTCTTCATA
* **
6993 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
* *
7043 TTTTCTCTTGTTTCA-ATCTTGTCTCTGGACATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGT
7094 T
1 T
7095 CTTCATTCAG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 7 0.16
51 36 0.82
52 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.42
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
Found at i:8368 original size:17 final size:18
Alignment explanation
Indices: 8346--8379 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
8336 TTACTATATC
8346 AAAAAATTAA-TAAAATA
1 AAAAAATTAATTAAAATA
8363 AAAAAATTAATTAAAAT
1 AAAAAATTAATTAAAAT
8380 TTGCAGCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAAATTAATTAAAATA
Found at i:9626 original size:78 final size:77
Alignment explanation
Indices: 9510--9663 Score: 236
Period size: 78 Copynumber: 2.0 Consensus size: 77
9500 TTTTAAATTA
* * *
9510 AAATAGTAAAATGGTAAACTTAATAGTTATAAAAATATTATATTTAATTAAATAAAAATAGAGTA
1 AAATAGTAAAATGGTAAAATAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAATAGAGTA
9575 TTTAGTTGAGTT
66 TTTAGTTGAGTT
* * *
9587 AAATTGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAATATAGAGT
1 AAATAGTAAAATGGTAAAAT-AAATAGTTATAAAAATATTAGATTTAATTAAATAAAAATAGAGT
*
9652 TTTTAGTTGAGT
65 ATTTAGTTGAGT
9664 AAAACTATAA
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
77 18 0.26
78 51 0.74
ACGTcount: A:0.49, C:0.01, G:0.13, T:0.38
Consensus pattern (77 bp):
AAATAGTAAAATGGTAAAATAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAATAGAGTA
TTTAGTTGAGTT
Found at i:11253 original size:31 final size:30
Alignment explanation
Indices: 11210--11267 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
11200 CGGTTAAGCC
* *
11210 AAATTATTATTAAAAAATGATTTTTTTGGTG
1 AAATCATTATTAAAAAAT-ATTTATTTGGTG
11241 AAATCATTATTAAAAAATATTTATTTG
1 AAATCATTATTAAAAAATATTTATTTG
11268 ACTTTTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.47
Consensus pattern (30 bp):
AAATCATTATTAAAAAATATTTATTTGGTG
Found at i:12439 original size:19 final size:18
Alignment explanation
Indices: 12417--12468 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
12407 GGGCTGAAAT
12417 TAATTAATTATTAAATAAA
1 TAATT-ATTATTAAATAAA
* * *
12436 TAATTATTATTTTATTGAA
1 TAATTATTA-TTAAATAAA
12455 TAATTATTATTAAA
1 TAATTATTATTAAA
12469 AATACCACAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 7 0.26
19 20 0.74
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TAATTATTATTAAATAAA
Found at i:12450 original size:23 final size:22
Alignment explanation
Indices: 12424--12466 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
12414 AATTAATTAA
12424 TTATTAAATAAATAATTATTATT
1 TTATTAAAT-AATAATTATTATT
* *
12447 TTATTGAATAATTATTATTA
1 TTATTAAATAATAATTATTA
12467 AAAATACCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TTATTAAATAATAATTATTATT
Found at i:22852 original size:2 final size:2
Alignment explanation
Indices: 22845--22884 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
22835 CTCTTATAGA
*
22845 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22885 GTTATAAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:27394 original size:33 final size:32
Alignment explanation
Indices: 27319--27473 Score: 136
Period size: 32 Copynumber: 4.9 Consensus size: 32
27309 TTGAAAGGTG
* ** *
27319 AAATCATGACAACTTCTGGCGTCAATTGAATA
1 AAATCATGACATCTTCAAGTGTCAATTGAATA
* *
27351 AAATTATGACATCTTCAAGTGTCTATTGAA-A
1 AAATCATGACATCTTCAAGTGTCAATTGAATA
* * *
27382 ATTTATCATGACAACTTCTAGTGTCAATTGAATA
1 A--AATCATGACATCTTCAAGTGTCAATTGAATA
* *
27416 AAATGATGACATCTTCAAGTGTCAATTG--CA
1 AAATCATGACATCTTCAAGTGTCAATTGAATA
* * **
27446 AGATCATGACAGCTTCTGGTGTCAATTG
1 AAATCATGACATCTTCAAGTGTCAATTG
27474 CAACATCATG
Statistics
Matches: 99, Mismatches: 21, Indels: 8
0.77 0.16 0.06
Matches are distributed among these distances:
30 24 0.24
31 2 0.02
32 47 0.47
33 24 0.24
34 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (32 bp):
AAATCATGACATCTTCAAGTGTCAATTGAATA
Found at i:27397 original size:65 final size:62
Alignment explanation
Indices: 27321--27593 Score: 248
Period size: 60 Copynumber: 4.4 Consensus size: 62
27311 GAAAGGTGAA
* * * *
27321 ATCATGACAACTTCTGGCGTCAATTGAATAAAATTATGACATCTTCAAGTGTCTATTGAAAATTT
1 ATCATGACAACTTCTGGTGTCAATTGAATAAAATGATGACATCTTCAAGTGTCAATTG-AAA--G
* *
27386 ATCATGACAACTTCTAGTGTCAATTGAATAAAATGATGACATCTTCAAGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGAATAAAATGATGACATCTTCAAGTGTCAATTGAAAG
* * * * * * ** *
27448 ATCATGACAGCTTCTGGTGTCAATTG--CAACATCATGATAGCTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGAATAAAATGATGACATCTTCAAGTGTCAATTGAAAG
* * * **** * ** * *
27508 ACCATGACAACTTCTGGTGTCATTTG--CAAGGCCATGACAACTTCTGGTGTCATTTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGAATAAAATGATGACATCTTCAAGTGTCAATTGAAAG
27568 ATCATGACAACTTCTGGTGTCAATTG
1 ATCATGACAACTTCTGGTGTCAATTG
27594 CAAGATCATG
Statistics
Matches: 182, Mismatches: 26, Indels: 5
0.85 0.12 0.02
Matches are distributed among these distances:
60 102 0.56
62 24 0.13
64 2 0.01
65 54 0.30
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (62 bp):
ATCATGACAACTTCTGGTGTCAATTGAATAAAATGATGACATCTTCAAGTGTCAATTGAAAG
Found at i:27468 original size:30 final size:30
Alignment explanation
Indices: 27386--27619 Score: 306
Period size: 30 Copynumber: 7.7 Consensus size: 30
27376 TTGAAAATTT
* * *
27386 ATCATGACAACTTCTAGTGTCAATTGAATAAA
1 ATCATGACAACTTCTGGTGTCAATTG--CAAG
* * **
27418 ATGATGACATCTTCAAGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* *
27448 ATCATGACAGCTTCTGGTGTCAATTGCAAC
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* *
27478 ATCATGATAGCTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* *
27508 ACCATGACAACTTCTGGTGTCATTTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
** *
27538 GCCATGACAACTTCTGGTGTCATTTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
27568 ATCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
27598 ATCATGACAACTTCTGGTGTCA
1 ATCATGACAACTTCTGGTGTCA
27620 TTTAGAGAGT
Statistics
Matches: 182, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
30 159 0.87
32 23 0.13
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (30 bp):
ATCATGACAACTTCTGGTGTCAATTGCAAG
Done.