Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006114.1 Corchorus capsularis cultivar CVL-1 contig06132, 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: 34557
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:7 original size:1 final size:1
Alignment explanation
Indices: 2--26 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1 T
2 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
27 GAAAGAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:765 original size:12 final size:12
Alignment explanation
Indices: 750--783 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
740 GTGAACAACA
750 AACGAACAATCT
1 AACGAACAATCT
762 AACGAACAATCT
1 AACGAACAATCT
774 AACGAACAAT
1 AACGAACAAT
784 ACACTACAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.53, C:0.24, G:0.09, T:0.15
Consensus pattern (12 bp):
AACGAACAATCT
Found at i:6405 original size:15 final size:16
Alignment explanation
Indices: 6372--6418 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
6362 AACTTTAATT
6372 TAAATA-TATTATTAA
1 TAAATATTATTATTAA
6387 -AAATATTATT-TTAA
1 TAAATATTATTATTAA
* *
6401 TAAATTTTATTAATAA
1 TAAATATTATTATTAA
6417 TA
1 TA
6419 CACAAGACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 9 0.33
15 13 0.48
16 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAAATATTATTATTAA
Found at i:14792 original size:6 final size:6
Alignment explanation
Indices: 14781--14820 Score: 62
Period size: 6 Copynumber: 6.3 Consensus size: 6
14771 CCGGCTCTTC
14781 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCTAT TTTTCT TT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTC--T TTTTCT TT
14821 CATGTTTTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 26 0.81
8 6 0.19
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:16678 original size:30 final size:30
Alignment explanation
Indices: 16644--16701 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
16634 TAGTTTGACC
* *
16644 TGAAAATGCTGGTTTAACATTCAGCTTACT
1 TGAAAATGCTGCTGTAACATTCAGCTTACT
*
16674 TGAAAATGCTGCTGTATCATTCAGCTTA
1 TGAAAATGCTGCTGTAACATTCAGCTTA
16702 ATAACCTTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36
Consensus pattern (30 bp):
TGAAAATGCTGCTGTAACATTCAGCTTACT
Found at i:17947 original size:27 final size:29
Alignment explanation
Indices: 17917--17974 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 29
17907 AATTTACTTT
17917 GCAC-AAACACAATA-ACTCTTAAATATA
1 GCACTAAACACAATATACTCTTAAATATA
** * *
17944 GCACTTTACACTATATTCTCTTAAATATA
1 GCACTAAACACAATATACTCTTAAATATA
17973 GC
1 GC
17975 TCAACACTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 4 0.16
28 7 0.28
29 14 0.56
ACGTcount: A:0.41, C:0.22, G:0.05, T:0.31
Consensus pattern (29 bp):
GCACTAAACACAATATACTCTTAAATATA
Found at i:22851 original size:75 final size:75
Alignment explanation
Indices: 22728--22878 Score: 302
Period size: 75 Copynumber: 2.0 Consensus size: 75
22718 CTGATCTAAG
22728 TCGATTTTGTAACGTTGGAAATTTAATTAACCAAATTATAAAAGTTATGCCCTTATTTAAACATT
1 TCGATTTTGTAACGTTGGAAATTTAATTAACCAAATTATAAAAGTTATGCCCTTATTTAAACATT
22793 TTCGTAAACA
66 TTCGTAAACA
22803 TCGATTTTGTAACGTTGGAAATTTAATTAACCAAATTATAAAAGTTATGCCCTTATTTAAACATT
1 TCGATTTTGTAACGTTGGAAATTTAATTAACCAAATTATAAAAGTTATGCCCTTATTTAAACATT
22868 TTCGTAAACA
66 TTCGTAAACA
22878 T
1 T
22879 TACAAATCGA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (75 bp):
TCGATTTTGTAACGTTGGAAATTTAATTAACCAAATTATAAAAGTTATGCCCTTATTTAAACATT
TTCGTAAACA
Found at i:26180 original size:15 final size:15
Alignment explanation
Indices: 26154--26228 Score: 123
Period size: 15 Copynumber: 5.0 Consensus size: 15
26144 TCCATGCTTC
26154 CTCCTCCATCAAGAA
1 CTCCTCCATCAAGAA
* *
26169 CTCCTTCTTCAAGAA
1 CTCCTCCATCAAGAA
26184 CTCCTCCATCAAGAA
1 CTCCTCCATCAAGAA
*
26199 CTCCTTCATCAAGAA
1 CTCCTCCATCAAGAA
26214 CTCCTCCATCAAGAA
1 CTCCTCCATCAAGAA
26229 GAAGATTAGA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 54 1.00
ACGTcount: A:0.32, C:0.37, G:0.07, T:0.24
Consensus pattern (15 bp):
CTCCTCCATCAAGAA
Found at i:26190 original size:30 final size:30
Alignment explanation
Indices: 26154--26228 Score: 141
Period size: 30 Copynumber: 2.5 Consensus size: 30
26144 TCCATGCTTC
*
26154 CTCCTCCATCAAGAACTCCTTCTTCAAGAA
1 CTCCTCCATCAAGAACTCCTTCATCAAGAA
26184 CTCCTCCATCAAGAACTCCTTCATCAAGAA
1 CTCCTCCATCAAGAACTCCTTCATCAAGAA
26214 CTCCTCCATCAAGAA
1 CTCCTCCATCAAGAA
26229 GAAGATTAGA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.32, C:0.37, G:0.07, T:0.24
Consensus pattern (30 bp):
CTCCTCCATCAAGAACTCCTTCATCAAGAA
Found at i:26248 original size:45 final size:45
Alignment explanation
Indices: 26215--26304 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
26205 CATCAAGAAC
* * *
26215 TCCTCCATCAAGAAGAAGATTAGAATCTTCTCCTTCACAAACAAA
1 TCCTCCATCAAGAACAAAATCAGAATCTTCTCCTTCACAAACAAA
* * *
26260 TCCTTCATCAAGAACAAAATCAGATTGTTCTCCTTCACAAACAAA
1 TCCTCCATCAAGAACAAAATCAGAATCTTCTCCTTCACAAACAAA
26305 GAGATCAGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.26
Consensus pattern (45 bp):
TCCTCCATCAAGAACAAAATCAGAATCTTCTCCTTCACAAACAAA
Found at i:33783 original size:17 final size:17
Alignment explanation
Indices: 33758--33796 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
33748 GCAGATGCAG
*
33758 CCTATCACCTCATACTA
1 CCTAGCACCTCATACTA
33775 CCTAGCACCTCATACTA
1 CCTAGCACCTCATACTA
33792 CCTAG
1 CCTAG
33797 GTACCATGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.28, C:0.41, G:0.05, T:0.26
Consensus pattern (17 bp):
CCTAGCACCTCATACTA
Found at i:33972 original size:20 final size:20
Alignment explanation
Indices: 33947--34003 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
33937 AAGAGTTCGC
33947 CTTCCTCAGCAAGTAAATGA
1 CTTCCTCAGCAAGTAAATGA
*
33967 CTTCCTCAGCAAGTAAATGC
1 CTTCCTCAGCAAGTAAATGA
33987 CTTCCTCAGCAAGTAAA
1 CTTCCTCAGCAAGTAAA
34004 GCCCGCCAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.25
Consensus pattern (20 bp):
CTTCCTCAGCAAGTAAATGA
Done.