Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007851.1 Corchorus capsularis cultivar CVL-1 contig07872, 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: 53049
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:6604 original size:3 final size:3
Alignment explanation
Indices: 6596--6622 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
6586 GAAAAGCAAT
6596 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
6623 CTGGTGTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:16150 original size:11 final size:11
Alignment explanation
Indices: 16134--16158 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16124 AAAAAAAACA
16134 ATGTTTATTTG
1 ATGTTTATTTG
16145 ATGTTTATTTG
1 ATGTTTATTTG
16156 ATG
1 ATG
16159 AGAAGTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (11 bp):
ATGTTTATTTG
Found at i:18028 original size:24 final size:26
Alignment explanation
Indices: 17995--18046 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 26
17985 AGTGCTCAAA
* * *
17995 GATTGGTTAGGTTTGGTTTAGA-ATT
1 GATTGGTTAGATTGGGTTGAGAGATT
18020 GATT-GTTAGATTGGGTTGAGAGATT
1 GATTGGTTAGATTGGGTTGAGAGATT
18045 GA
1 GA
18047 GTGAGAGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.23, C:0.00, G:0.35, T:0.42
Consensus pattern (26 bp):
GATTGGTTAGATTGGGTTGAGAGATT
Found at i:24196 original size:20 final size:20
Alignment explanation
Indices: 24159--24200 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
24149 ATAAACTATG
24159 AACTAGAATTGAAATAATTA
1 AACTAGAATTGAAATAATTA
*
24179 AACTA-AATTGCAAGTAATTA
1 AACTAGAATTG-AAATAATTA
24199 AA
1 AA
24201 AAAGAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.29
Consensus pattern (20 bp):
AACTAGAATTGAAATAATTA
Found at i:26360 original size:21 final size:22
Alignment explanation
Indices: 26334--26375 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
26324 AAAAAGTGAA
*
26334 TTACTAAATACCGC-CCCCTTT
1 TTACTAAACACCGCTCCCCTTT
*
26355 TTACTAGACACCGCTCCCCTT
1 TTACTAAACACCGCTCCCCTT
26376 GAACTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.21, C:0.40, G:0.07, T:0.31
Consensus pattern (22 bp):
TTACTAAACACCGCTCCCCTTT
Found at i:29167 original size:18 final size:19
Alignment explanation
Indices: 29129--29168 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
29119 TTGAAGATTT
*
29129 ATTGAAGACATATTCAAGA
1 ATTGAAGACACATTCAAGA
*
29148 ATTGAAGAC-CATTGAAGA
1 ATTGAAGACACATTCAAGA
29166 ATT
1 ATT
29169 ACTTCAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.28
Consensus pattern (19 bp):
ATTGAAGACACATTCAAGA
Found at i:42441 original size:17 final size:17
Alignment explanation
Indices: 42419--42451 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42409 GTTTAAGAGA
42419 TTTTAAATATTTTGGAC
1 TTTTAAATATTTTGGAC
*
42436 TTTTAATTATTTTGGA
1 TTTTAAATATTTTGGA
42452 ATGATAGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.03, G:0.12, T:0.58
Consensus pattern (17 bp):
TTTTAAATATTTTGGAC
Found at i:44565 original size:122 final size:122
Alignment explanation
Indices: 44348--44594 Score: 494
Period size: 122 Copynumber: 2.0 Consensus size: 122
44338 CTTTCTTCAG
44348 AAGGTATTGAATTAATCTTTTCTATAATGGTTGATTAATGATGTAATTTTTTATTTTTAATTTGT
1 AAGGTATTGAATTAATCTTTTCTATAATGGTTGATTAATGATGTAATTTTTTATTTTTAATTTGT
44413 TTTGTAACTCATTTCTCAACTTTTTATTGCCAATTTTTAAAAATCTTGGTGTAAAAC
66 TTTGTAACTCATTTCTCAACTTTTTATTGCCAATTTTTAAAAATCTTGGTGTAAAAC
44470 AAGGTATTGAATTAATCTTTTCTATAATGGTTGATTAATGATGTAATTTTTTATTTTTAATTTGT
1 AAGGTATTGAATTAATCTTTTCTATAATGGTTGATTAATGATGTAATTTTTTATTTTTAATTTGT
44535 TTTGTAACTCATTTCTCAACTTTTTATTGCCAATTTTTAAAAATCTTGGTGTAAAAC
66 TTTGTAACTCATTTCTCAACTTTTTATTGCCAATTTTTAAAAATCTTGGTGTAAAAC
44592 AAG
1 AAG
44595 ATATAGATGC
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
122 125 1.00
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (122 bp):
AAGGTATTGAATTAATCTTTTCTATAATGGTTGATTAATGATGTAATTTTTTATTTTTAATTTGT
TTTGTAACTCATTTCTCAACTTTTTATTGCCAATTTTTAAAAATCTTGGTGTAAAAC
Found at i:45944 original size:2 final size:2
Alignment explanation
Indices: 45937--45968 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
45927 GACTTAATAC
45937 AT AT AT AT AT AT AT AT 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
45969 GCGTTTACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48254 original size:18 final size:18
Alignment explanation
Indices: 48233--48312 Score: 92
Period size: 18 Copynumber: 4.4 Consensus size: 18
48223 GAGCTAACTC
*
48233 TGAATGGGGAACTGACTT
1 TGAATGAGGAACTGACTT
48251 TGAATGAGGAACT-AGCTTT
1 TGAATGAGGAACTGA-C-TT
*
48270 TGAATG-GAGAAGTGACTT
1 TGAATGAG-GAACTGACTT
*
48288 TGAATGAGAAACTGACTT
1 TGAATGAGGAACTGACTT
48306 TGAATGA
1 TGAATGA
48313 TCCTTAACAT
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
17 1 0.02
18 37 0.70
19 14 0.26
20 1 0.02
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.29
Consensus pattern (18 bp):
TGAATGAGGAACTGACTT
Found at i:49599 original size:18 final size:19
Alignment explanation
Indices: 49576--49613 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
49566 GAAATAGGAT
49576 TTCAAATCCAACAGA-AGA
1 TTCAAATCCAACAGATAGA
*
49594 TTCAAATTCAACAGATAGA
1 TTCAAATCCAACAGATAGA
49613 T
1 T
49614 AGGATAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (19 bp):
TTCAAATCCAACAGATAGA
Found at i:52029 original size:10 final size:10
Alignment explanation
Indices: 52014--52038 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
52004 GTTCCTGCAC
52014 AATTCCAGAA
1 AATTCCAGAA
52024 AATTCCAGAA
1 AATTCCAGAA
52034 AATTC
1 AATTC
52039 TAGAGTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Done.