Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012614.1 Corchorus capsularis cultivar CVL-1 contig12635, 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: 29698
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:8480 original size:21 final size:21
Alignment explanation
Indices: 8454--8493 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
8444 ACAATAATTT
*
8454 AGATTGATACACAGCCAAAAA
1 AGATTGATACACAACCAAAAA
8475 AGATTGATACACAACCAAA
1 AGATTGATACACAACCAAA
8494 GCAGAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.20, G:0.12, T:0.15
Consensus pattern (21 bp):
AGATTGATACACAACCAAAAA
Found at i:9756 original size:11 final size:11
Alignment explanation
Indices: 9740--9781 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
9730 ATAATATATC
9740 TAATTAATAGA
1 TAATTAATAGA
**
9751 TAATTAATATC
1 TAATTAATAGA
*
9762 TAATTAATAGT
1 TAATTAATAGA
9773 TAATTAATA
1 TAATTAATA
9782 ATGAATAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (11 bp):
TAATTAATAGA
Found at i:9762 original size:22 final size:22
Alignment explanation
Indices: 9735--9781 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
9725 CCATTATAAT
9735 ATATCTAATTAATAGATAATTA
1 ATATCTAATTAATAGATAATTA
*
9757 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGATAATTA
9779 ATA
1 ATA
9782 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGATAATTA
Found at i:10504 original size:130 final size:130
Alignment explanation
Indices: 10353--10613 Score: 513
Period size: 130 Copynumber: 2.0 Consensus size: 130
10343 AAGTTTTTCA
10353 ACCATTGACTGATAGTTTTTTCATTCTAGCATTGTATTGTTAATTTTATATAGTTGCAGTATTTC
1 ACCATTGACTGATAGTTTTTTCATTCTAGCATTGTATTGTTAATTTTATATAGTTGCAGTATTTC
10418 ATTTGTACCCTAAATTCCAAGGAAATTTCTTGAGAGATCTACTTTTTCCAATATATCGTATTTGT
66 ATTTGTACCCTAAATTCCAAGGAAATTTCTTGAGAGATCTACTTTTTCCAATATATCGTATTTGT
10483 ACCATTGACTGATAGTTTTTTCATTCTAGCATTGTATTGTTAATTTTATATAGTTGCAGTATTTC
1 ACCATTGACTGATAGTTTTTTCATTCTAGCATTGTATTGTTAATTTTATATAGTTGCAGTATTTC
*
10548 ATTTGTACCCTAAATTCCAAGGAAATTTCTTGAGAGATCTACTTTTTTCAATATATCGTATTTGT
66 ATTTGTACCCTAAATTCCAAGGAAATTTCTTGAGAGATCTACTTTTTCCAATATATCGTATTTGT
10613 A
1 A
10614 ACTCATATTA
Statistics
Matches: 130, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
130 130 1.00
ACGTcount: A:0.27, C:0.14, G:0.13, T:0.46
Consensus pattern (130 bp):
ACCATTGACTGATAGTTTTTTCATTCTAGCATTGTATTGTTAATTTTATATAGTTGCAGTATTTC
ATTTGTACCCTAAATTCCAAGGAAATTTCTTGAGAGATCTACTTTTTCCAATATATCGTATTTGT
Found at i:11301 original size:56 final size:59
Alignment explanation
Indices: 11212--11323 Score: 203
Period size: 56 Copynumber: 1.9 Consensus size: 59
11202 TCGATTATTT
11212 ATTTATTTATTTATTTTGAGTGAGCACATGTGAAATCTCATTACAATCAGAATAAAGAC
1 ATTTATTTATTTATTTTGAGTGAGCACATGTGAAATCTCATTACAATCAGAATAAAGAC
11271 ATTTATTT-TTT-TTTT-AGTGAGCACATGTGAAATCTCATTACAATCAGAATAAA
1 ATTTATTTATTTATTTTGAGTGAGCACATGTGAAATCTCATTACAATCAGAATAAA
11324 TCTTTATATG
Statistics
Matches: 53, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
56 38 0.72
57 4 0.08
58 3 0.06
59 8 0.15
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (59 bp):
ATTTATTTATTTATTTTGAGTGAGCACATGTGAAATCTCATTACAATCAGAATAAAGAC
Found at i:11824 original size:3 final size:3
Alignment explanation
Indices: 11816--11845 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
11806 TATTATATAG
11816 TAA TAA TAA TAA TAA TTAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TA
11846 TATCAATTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:11837 original size:13 final size:13
Alignment explanation
Indices: 11819--11844 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11809 TATATAGTAA
11819 TAATAATAATAAT
1 TAATAATAATAAT
11832 TAATAATAATAAT
1 TAATAATAATAAT
11845 ATATCAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAATAATAATAAT
Found at i:11952 original size:21 final size:21
Alignment explanation
Indices: 11928--11969 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
11918 CTAGAGCTAT
11928 GGTATGAAATTAATCAATGGA
1 GGTATGAAATTAATCAATGGA
11949 GGTATGAAATTAATCAATGGA
1 GGTATGAAATTAATCAATGGA
11970 TTTTGATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.05, G:0.24, T:0.29
Consensus pattern (21 bp):
GGTATGAAATTAATCAATGGA
Found at i:22588 original size:24 final size:24
Alignment explanation
Indices: 22561--22607 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
22551 TATGTGTTGC
22561 TAGTTTATCATGCATATCGTATTA
1 TAGTTTATCATGCATATCGTATTA
*
22585 TAGTTTATCATGCATATTGTATT
1 TAGTTTATCATGCATATCGTATT
22608 CTAACTCTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.49
Consensus pattern (24 bp):
TAGTTTATCATGCATATCGTATTA
Found at i:27934 original size:24 final size:24
Alignment explanation
Indices: 27898--27944 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
27888 TATGAGTTGT
*
27898 TAGTTTGTAATGCATATCGTATTA
1 TAGTTTATAATGCATATCGTATTA
* *
27922 TAGTTTATCATGCATATTGTATT
1 TAGTTTATAATGCATATCGTATT
27945 CTAACTAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.49
Consensus pattern (24 bp):
TAGTTTATAATGCATATCGTATTA
Done.