Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011825.1 Corchorus capsularis cultivar CVL-1 contig11846, 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: 53413
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:25 original size:2 final size:2
Alignment explanation
Indices: 18--51 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
8 CGATATAACA
18 AT 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 AT
52 TTGGCTTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13999 original size:10 final size:10
Alignment explanation
Indices: 13984--14020 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 10
13974 AAAAGGATGG
13984 GAGAGAAAGA
1 GAGAGAAAGA
13994 GAGAGAAGGAGA
1 GAGAGAA--AGA
14006 GAGAGAAAGA
1 GAGAGAAAGA
14016 GAGAG
1 GAGAG
14021 GGAGTTGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 15 0.60
12 10 0.40
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (10 bp):
GAGAGAAAGA
Found at i:14006 original size:12 final size:12
Alignment explanation
Indices: 13991--14020 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
13981 TGGGAGAGAA
*
13991 AGAGAGAGAAGG
1 AGAGAGAGAAAG
14003 AGAGAGAGAAAG
1 AGAGAGAGAAAG
14015 AGAGAG
1 AGAGAG
14021 GGAGTTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (12 bp):
AGAGAGAGAAAG
Found at i:18253 original size:58 final size:59
Alignment explanation
Indices: 18189--18309 Score: 208
Period size: 59 Copynumber: 2.1 Consensus size: 59
18179 TTTTAATTTG
* * *
18189 GGAAAA-TTTGTATCTCTAACTAATTGATTAAATTTGGTCAATTTGGGGCACATGGAAA
1 GGAAAATTTTGCATCTCTAACTAATTGATTAAAATTGGCCAATTTGGGGCACATGGAAA
18247 GGAAAATTTTGCATCTCTAACTAATTGATTAAAATTGGCCAATTTGGGGCACATGGAAA
1 GGAAAATTTTGCATCTCTAACTAATTGATTAAAATTGGCCAATTTGGGGCACATGGAAA
18306 GGAA
1 GGAA
18310 GGGTGGGTCA
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
58 6 0.10
59 53 0.90
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (59 bp):
GGAAAATTTTGCATCTCTAACTAATTGATTAAAATTGGCCAATTTGGGGCACATGGAAA
Found at i:36454 original size:17 final size:17
Alignment explanation
Indices: 36434--36467 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
36424 CGAGAGGTTA
*
36434 ATTCAATCGGTTAGTTC
1 ATTCAAGCGGTTAGTTC
36451 ATTCAAGCGGTTAGTTC
1 ATTCAAGCGGTTAGTTC
36468 GTTCTTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.38
Consensus pattern (17 bp):
ATTCAAGCGGTTAGTTC
Found at i:37340 original size:30 final size:32
Alignment explanation
Indices: 37292--37373 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 32
37282 CATGGACAGG
* * *
37292 CCGCCCCACTGGTGCGGCTTTGC-CACGGCAAA
1 CCGCCCCA-TGGGGCGGCTTCGCGCAAGGCAAA
**
37324 CCG-CCCATGGGGCGGCTTCGCGCAAGGCAGG
1 CCGCCCCATGGGGCGGCTTCGCGCAAGGCAAA
37355 CCGCCCTCATGGGGCGGCT
1 CCGCCC-CATGGGGCGGCT
37374 AGAGCTAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
30 12 0.29
31 13 0.31
32 5 0.12
33 12 0.29
ACGTcount: A:0.12, C:0.39, G:0.35, T:0.13
Consensus pattern (32 bp):
CCGCCCCATGGGGCGGCTTCGCGCAAGGCAAA
Found at i:37368 original size:33 final size:31
Alignment explanation
Indices: 37262--37373 Score: 100
Period size: 33 Copynumber: 3.5 Consensus size: 31
37252 GGCGGAGCCT
* * *
37262 CCCCACTGGGGTGGCTTCACCATGGACAGGCCG
1 CCCCA-TGGGGCGGCTTCGCCAAGG-CAGGCCG
* * * **
37295 CCCCACTGGTGCGGCTTTGCCACGGCAAACCG
1 CCCCA-TGGGGCGGCTTCGCCAAGGCAGGCCG
37327 -CCCATGGGGCGGCTTCGCGCAAGGCAGGCCG
1 CCCCATGGGGCGGCTTCGC-CAAGGCAGGCCG
37358 CCCTCATGGGGCGGCT
1 CCC-CATGGGGCGGCT
37374 AGAGCTAAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
30 12 0.19
31 13 0.20
32 7 0.11
33 32 0.50
ACGTcount: A:0.13, C:0.38, G:0.35, T:0.14
Consensus pattern (31 bp):
CCCCATGGGGCGGCTTCGCCAAGGCAGGCCG
Found at i:37540 original size:34 final size:33
Alignment explanation
Indices: 37452--37575 Score: 135
Period size: 34 Copynumber: 3.8 Consensus size: 33
37442 CCCACCGGCA
* * *
37452 CGGCCTG-CCGTGGCGAAGCCGCCCCAGTGGGG
1 CGGCCTGCCCATGGTGAAGCCGCCCTAGTGGGG
** *** *
37484 CCACCTATTCATAGTGAAGCCGCCCTAGTGGGG
1 CGGCCTGCCCATGGTGAAGCCGCCCTAGTGGGG
*
37517 TGGCCTGCCCAATGGTGAAGCCGCCCTAGTGGGG
1 CGGCCTGCCC-ATGGTGAAGCCGCCCTAGTGGGG
37551 CGGCCTGCCCATGGT-AAGCCGCCCT
1 CGGCCTGCCCATGGTGAAGCCGCCCT
37576 CTTGGGGCAG
Statistics
Matches: 74, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
32 14 0.19
33 29 0.39
34 31 0.42
ACGTcount: A:0.15, C:0.35, G:0.35, T:0.16
Consensus pattern (33 bp):
CGGCCTGCCCATGGTGAAGCCGCCCTAGTGGGG
Found at i:41358 original size:21 final size:21
Alignment explanation
Indices: 41325--41364 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
41315 AGGAAATAAA
41325 TTAAACTCTGGTTTAGCCCCC
1 TTAAACTCTGGTTTAGCCCCC
41346 TTAAA-TCTAGGTTTAGCCC
1 TTAAACTCT-GGTTTAGCCC
41365 TTAGTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.35
Consensus pattern (21 bp):
TTAAACTCTGGTTTAGCCCCC
Found at i:42108 original size:13 final size:13
Alignment explanation
Indices: 42090--42114 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42080 TTATAGTAGT
42090 ATTAATTAAATAA
1 ATTAATTAAATAA
42103 ATTAATTAAATA
1 ATTAATTAAATA
42115 CTGGCATATA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTAATTAAATAA
Found at i:47236 original size:12 final size:12
Alignment explanation
Indices: 47219--47243 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
47209 TTGTAAGTTT
47219 TTTTTTTTTAAA
1 TTTTTTTTTAAA
47231 TTTTTTTTTAAA
1 TTTTTTTTTAAA
47243 T
1 T
47244 AAATACTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTTTTTAAA
Done.