Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013471.1 Corchorus capsularis cultivar CVL-1 contig13492, 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: 54354
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1075 original size:2 final size:2
Alignment explanation
Indices: 1068--1101 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1058 TATTTTCGAT
1068 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1102 ATGAAAAATA
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):
TA
Found at i:8892 original size:15 final size:15
Alignment explanation
Indices: 8872--8901 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
8862 TTGTCATCAG
8872 GGAGATACCATCCAA
1 GGAGATACCATCCAA
8887 GGAGATACCATCCAA
1 GGAGATACCATCCAA
8902 ATAAAGTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.27, G:0.20, T:0.13
Consensus pattern (15 bp):
GGAGATACCATCCAA
Found at i:10735 original size:2 final size:2
Alignment explanation
Indices: 10728--10757 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10718 TTGATGTGAA
10728 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
10758 GTGGGGGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14631 original size:22 final size:22
Alignment explanation
Indices: 14606--14647 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
14596 ATTGAGGTAA
*
14606 ATAATAAGGTGTGGCAGTATAT
1 ATAATAAGGCGTGGCAGTATAT
14628 ATAATAAGGCGTGGCAGTAT
1 ATAATAAGGCGTGGCAGTAT
14648 TGCATTCTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.07, G:0.29, T:0.29
Consensus pattern (22 bp):
ATAATAAGGCGTGGCAGTATAT
Found at i:15503 original size:36 final size:36
Alignment explanation
Indices: 15456--15525 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
15446 TCTCTTCAGG
15456 GATTTCATTAGAGCTTACAAAGACATATCCCTGAAC
1 GATTTCATTAGAGCTTACAAAGACATATCCCTGAAC
15492 GATTTCATTAGAGCTTACAAAGACATATCCCTGA
1 GATTTCATTAGAGCTTACAAAGACATATCCCTGA
15526 CGAAGACTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (36 bp):
GATTTCATTAGAGCTTACAAAGACATATCCCTGAAC
Found at i:29408 original size:29 final size:28
Alignment explanation
Indices: 29371--29426 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
29361 ACCAATTAAA
*
29371 ACAAGGTACTATGAGTTTTTTTTTTGGC
1 ACAAGGTACTAAGAGTTTTTTTTTTGGC
29399 ACAATGGTACTAAGAGTTTTTTTTTTGG
1 ACAA-GGTACTAAGAGTTTTTTTTTTGG
29427 TTGAAACATG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.23, C:0.09, G:0.21, T:0.46
Consensus pattern (28 bp):
ACAAGGTACTAAGAGTTTTTTTTTTGGC
Found at i:42881 original size:76 final size:78
Alignment explanation
Indices: 42755--42910 Score: 280
Period size: 76 Copynumber: 2.0 Consensus size: 78
42745 AACATCTTCC
42755 AACAATTTTTACCAAACACTACCAGCATTAATTCAAGAACAGAACTCCATC-TT-TCCATCAATG
1 AACAATTTTTACCAAACACTACCAGCATTAATTCAAGAACAGAACTCCATCTTTCTCCATCAATG
42818 AACCACAAACTAT
66 AACCACAAACTAT
42831 AACAATTTTTACCAAACACTACCAGCATTAATTCAAGAACAGAACTCCATCTTTCCATCCATCAA
1 AACAATTTTTACCAAACACTACCAGCATTAATTCAAGAACAGAACTCCATCTTT-C-TCCATCAA
42896 TGAACCACAAACTAT
64 TGAACCACAAACTAT
42911 GTAAATTACA
Statistics
Matches: 76, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
76 51 0.67
77 2 0.03
80 23 0.30
ACGTcount: A:0.42, C:0.28, G:0.05, T:0.25
Consensus pattern (78 bp):
AACAATTTTTACCAAACACTACCAGCATTAATTCAAGAACAGAACTCCATCTTTCTCCATCAATG
AACCACAAACTAT
Found at i:49549 original size:13 final size:14
Alignment explanation
Indices: 49524--49553 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
49514 AAAAGTTGAA
49524 AAATAACTTAATTT
1 AAATAACTTAATTT
49538 AAATAA-TTAATTT
1 AAATAACTTAATTT
49551 AAA
1 AAA
49554 GTTTAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (14 bp):
AAATAACTTAATTT
Found at i:53419 original size:20 final size:19
Alignment explanation
Indices: 53394--53431 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
53384 GAATTTATTA
53394 ATAACCTTATAATTGTTTTG
1 ATAACC-TATAATTGTTTTG
*
53414 ATAACCTCTAATTGTTTT
1 ATAACCTATAATTGTTTT
53432 TTTAGTAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (19 bp):
ATAACCTATAATTGTTTTG
Done.