Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009866.1 Corchorus capsularis cultivar CVL-1 contig09887, 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: 13213
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Found at i:32 original size:6 final size:6
Alignment explanation
Indices: 21--51 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
11 TTATATATAA
21 AAATAT AAATAT AAATAT AAATAT AAA-AT AA
1 AAATAT AAATAT AAATAT AAATAT AAATAT AA
52 TAATATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAATAT
Found at i:34 original size:14 final size:14
Alignment explanation
Indices: 15--72 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
5 TTCCTTTTAT
15 ATATAAAAATATAA
1 ATATAAAAATATAA
29 ATAT--AAATATAA
1 ATATAAAAATATAA
41 ATAT-AAAATA-ATA
1 ATATAAAAATATA-A
* *
54 ATATAATAATAAAA
1 ATATAAAAATATAA
68 ATATA
1 ATATA
73 TTATATAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
12 13 0.33
13 10 0.26
14 15 0.38
15 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
ATATAAAAATATAA
Found at i:65 original size:25 final size:26
Alignment explanation
Indices: 21--81 Score: 56
Period size: 25 Copynumber: 2.3 Consensus size: 26
11 TTATATATAA
*
21 AAATATAAATATAAATATAAATATA-
1 AAATATAAATATAAATATAAAAATAT
46 AAATA-ATAATAT-AATAATAAAAATAT
1 AAATATA-AATATAAAT-ATAAAAATAT
*
72 ATTATATAAA
1 A-AATATAAA
82 ACATTATACA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
24 4 0.14
25 18 0.62
26 1 0.03
27 5 0.17
28 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (26 bp):
AAATATAAATATAAATATAAAAATAT
Found at i:1418 original size:19 final size:20
Alignment explanation
Indices: 1394--1432 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1384 ATGATCAAAA
1394 TTAGGT-CATGTGAGGAACC
1 TTAGGTACATGTGAGGAACC
* *
1413 TTAGGTATATGTGGGGAACC
1 TTAGGTACATGTGAGGAACC
1433 ATCTTCATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.26, C:0.13, G:0.33, T:0.28
Consensus pattern (20 bp):
TTAGGTACATGTGAGGAACC
Found at i:4819 original size:6 final size:6
Alignment explanation
Indices: 4808--4836 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
4798 CAGTTCAAAA
4808 ATTTTC ATTTTC ATTTTC ATTTTC ATTTT
1 ATTTTC ATTTTC ATTTTC ATTTTC ATTTT
4837 AGAATATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (6 bp):
ATTTTC
Found at i:6817 original size:3 final size:3
Alignment explanation
Indices: 6809--6864 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
6799 TTATAGCTAG
6809 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6857 TAA TAA TA
1 TAA TAA TA
6865 TAAGGAAGGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:8988 original size:33 final size:33
Alignment explanation
Indices: 8944--9050 Score: 187
Period size: 33 Copynumber: 3.2 Consensus size: 33
8934 TTCTTTTCAC
* *
8944 CCAAAACAGAATTATTTTCAATGTTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
*
8977 CCAAAATAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
9010 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
9043 CCAAAACA
1 CCAAAACA
9051 ATTTGTTTTC
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 70 1.00
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (33 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAA
Found at i:9097 original size:33 final size:32
Alignment explanation
Indices: 9042--9128 Score: 97
Period size: 33 Copynumber: 2.7 Consensus size: 32
9032 GCTATGATCA
** *
9042 ACCAAAACA-ATTT-GTTTTCATCACAATTAGC
1 ACCAAAACAGATTTAG-TTTCATCACAAACAAC
9073 ATCCAAAACAGATTTAGTTTCATCACAAACAAC
1 A-CCAAAACAGATTTAGTTTCATCACAAACAAC
*
9106 ACCTAAAACAGATTTAGTGTCAT
1 ACC-AAAACAGATTTAGTTTCAT
9129 TGCAAATATC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
31 1 0.02
32 10 0.21
33 36 0.75
34 1 0.02
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.29
Consensus pattern (32 bp):
ACCAAAACAGATTTAGTTTCATCACAAACAAC
Found at i:10940 original size:30 final size:30
Alignment explanation
Indices: 10900--10962 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
10890 TGTCTTCAAG
10900 TCCATAATAAGTCCTT-AGCGCATCATTCCC
1 TCCATAATAAG-CCTTGAGCGCATCATTCCC
* *
10930 TCCATGATAAGCCTTGGGCGCATCATTCCC
1 TCCATAATAAGCCTTGAGCGCATCATTCCC
10960 TCC
1 TCC
10963 CCCTTGAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 4 0.13
30 26 0.87
ACGTcount: A:0.22, C:0.35, G:0.14, T:0.29
Consensus pattern (30 bp):
TCCATAATAAGCCTTGAGCGCATCATTCCC
Found at i:11381 original size:33 final size:33
Alignment explanation
Indices: 11337--11445 Score: 191
Period size: 33 Copynumber: 3.3 Consensus size: 33
11327 TTCTTTTCAC
* *
11337 CCAAAACAGAATTATTTTCAATGTTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
*
11370 CCAAAATAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
11403 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
11436 CCAAAACAGA
1 CCAAAACAGA
11446 TTTGTTTTCA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 72 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (33 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAA
Found at i:11473 original size:66 final size:66
Alignment explanation
Indices: 11337--11478 Score: 169
Period size: 66 Copynumber: 2.2 Consensus size: 66
11327 TTCTTTTCAC
* * * * * *
11337 CCAAAACAGAATTATTTTCAATGTTATGATCAACCAAAATAGAATTATTTGCAATGCTATGATCA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTATTTGCAATACAATGAGCA
11402 A
66 A
* * * *
11403 CCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGATTTGTTTTC-ATCACAATTAGC
1 CCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTATTTGCAAT-ACAATGAGC
*
11467 AT
65 AA
11469 CCAAAACAGA
1 CCAAAACAGA
11479 TTTAGTTTCA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
65 2 0.03
66 62 0.97
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (66 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTATTTGCAATACAATGAGCA
A
Found at i:11508 original size:33 final size:33
Alignment explanation
Indices: 11438--11575 Score: 129
Period size: 33 Copynumber: 4.2 Consensus size: 33
11428 ATGATCAACC
** *
11438 AAAACAGATTT-GTTTTCATCACAATTAGCATCC-
1 AAAACAGATTTAG-TTTCATCACAAACAACA-CCT
11471 AAAACAGATTTAGTTTCATCACAAACAACACCT
1 AAAACAGATTTAGTTTCATCACAAACAACACCT
* **
11504 AAAACAGATTTAGTGTCATTGCAAACAACA-CT
1 AAAACAGATTTAGTTTCATCACAAACAACACCT
* * * * *
11536 CAAATCAGGTTTAGTATCATCGCAAACAACATCT
1 -AAAACAGATTTAGTTTCATCACAAACAACACCT
11570 AAAACA
1 AAAACA
11576 CTCTTTACAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
32 4 0.04
33 83 0.92
34 3 0.03
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (33 bp):
AAAACAGATTTAGTTTCATCACAAACAACACCT
Found at i:13077 original size:5 final size:5
Alignment explanation
Indices: 13067--13095 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
13057 TGGTCGAAAA
13067 TTTAT TTTAT TTTAT TTTAT TTT-T TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
13096 ATTTTTCGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTAT
Done.