Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014783.1 Corchorus capsularis cultivar CVL-1 contig14804, 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: 18926
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Found at i:543 original size:21 final size:21
Alignment explanation
Indices: 517--559 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
507 TGAAGACAAT
*
517 AGCAATCAAAGTAATTTATTG
1 AGCAATCAAAGTAATTGATTG
538 AGCAATCAAAGTAATTGATTG
1 AGCAATCAAAGTAATTGATTG
559 A
1 A
560 CTTGCCTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.30
Consensus pattern (21 bp):
AGCAATCAAAGTAATTGATTG
Found at i:665 original size:17 final size:17
Alignment explanation
Indices: 643--677 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
633 AACATAGCTA
*
643 TGTGAATGTAATCCCAT
1 TGTGAACGTAATCCCAT
660 TGTGAACGTAATCCCAT
1 TGTGAACGTAATCCCAT
677 T
1 T
678 AAGTTATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (17 bp):
TGTGAACGTAATCCCAT
Found at i:8625 original size:57 final size:57
Alignment explanation
Indices: 8496--8652 Score: 248
Period size: 57 Copynumber: 2.8 Consensus size: 57
8486 ATCTTGTCCA
* * * *
8496 CATCACAATCCAATAGCTCCTGCTGATCCAAACTGCCTAT--C-TCGTCCACATCAC
1 CATCACAATCCAACAGCTCCTGATGATCCAAATTGCCTATCGCATCCTCCACATCAC
*
8550 CATCACAATCCAACAGCTCCTGATGATCCAAATTGCCTATCGCATCCTCCGCATCAC
1 CATCACAATCCAACAGCTCCTGATGATCCAAATTGCCTATCGCATCCTCCACATCAC
8607 CATCACAATCCAACAGCTCCTGATGATCCAAATTGCCTATCGCATC
1 CATCACAATCCAACAGCTCCTGATGATCCAAATTGCCTATCGCATC
8653 GCCATCATAA
Statistics
Matches: 95, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
54 37 0.39
56 1 0.01
57 57 0.60
ACGTcount: A:0.29, C:0.38, G:0.10, T:0.24
Consensus pattern (57 bp):
CATCACAATCCAACAGCTCCTGATGATCCAAATTGCCTATCGCATCCTCCACATCAC
Found at i:8848 original size:21 final size:21
Alignment explanation
Indices: 8803--8855 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
8793 TCTCGTCAGA
* * *
8803 ATCATAATCCATCTTGTCTGC
1 ATCACAATCCATCATGTCCGC
*
8824 ATCACAATCCATCATGTCCGT
1 ATCACAATCCATCATGTCCGC
*
8845 ATCACTATCCA
1 ATCACAATCCA
8856 CAATTGGGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.32, G:0.08, T:0.32
Consensus pattern (21 bp):
ATCACAATCCATCATGTCCGC
Found at i:10192 original size:23 final size:23
Alignment explanation
Indices: 10147--10193 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
10137 AGAAGTTAGG
10147 GTTTTAATTTTTTTTTGCCACATT
1 GTTTTAATTTTTTTTTG-CACATT
10171 GTTTTAATTTGTTTTTTG-ACATT
1 GTTTTAATTT-TTTTTTGCACATT
10194 TTTGAGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.23
24 10 0.45
25 7 0.32
ACGTcount: A:0.17, C:0.09, G:0.11, T:0.64
Consensus pattern (23 bp):
GTTTTAATTTTTTTTTGCACATT
Found at i:10936 original size:2 final size:2
Alignment explanation
Indices: 10925--10961 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
10915 ATATTAAAGA
10925 AT AT -T 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 AT AT
10962 CTTAGCAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:12094 original size:25 final size:25
Alignment explanation
Indices: 12066--12144 Score: 97
Period size: 25 Copynumber: 3.2 Consensus size: 25
12056 TGCGCTGGGT
* * *
12066 AAACGCTCATGTTCTTGCGTTTGGC
1 AAACGATCATGTGCTTGCGTTTAGC
*
12091 AAACGAGCATGTGCTTGCGTTTAGC
1 AAACGATCATGTGCTTGCGTTTAGC
*
12116 AAACGAGTC-TGTGCTTGCGTTTAGA
1 AAACGA-TCATGTGCTTGCGTTTAGC
12141 AAAC
1 AAAC
12145 ACATAGACTA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
25 46 0.98
26 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.30
Consensus pattern (25 bp):
AAACGATCATGTGCTTGCGTTTAGC
Found at i:16592 original size:15 final size:15
Alignment explanation
Indices: 16574--16603 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16564 CAGCTTCCTT
16574 CAAAACTTCTTCTTC
1 CAAAACTTCTTCTTC
*
16589 CAAAGCTTCTTCTTC
1 CAAAACTTCTTCTTC
16604 GATTTCATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.33, G:0.03, T:0.40
Consensus pattern (15 bp):
CAAAACTTCTTCTTC
Done.