Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021921.1 Corchorus olitorius cultivar O-4 contig21954, 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: 8220
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Found at i:162 original size:13 final size:13
Alignment explanation
Indices: 132--184 Score: 60
Period size: 12 Copynumber: 4.4 Consensus size: 13
122 CCCGTTGAGG
132 AAATG-TTT-TAT
1 AAATGCTTTATAT
*
143 AACTGCTTTATAT
1 AAATGCTTTATAT
156 AAATGCTTTATA-
1 AAATGCTTTATAT
*
168 AAATGTTTTA-AT
1 AAATGCTTTATAT
180 AAATG
1 AAATG
185 TTTTGGGTGC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 5 0.14
12 17 0.47
13 14 0.39
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (13 bp):
AAATGCTTTATAT
Found at i:1408 original size:36 final size:36
Alignment explanation
Indices: 1333--1408 Score: 82
Period size: 36 Copynumber: 2.1 Consensus size: 36
1323 TGAGAAAAGG
* * ** *
1333 CCAAGTACATAATTAAGTTGGCTTAATTCTATTGAC
1 CCAAATACATAATTAAGTTAGCCCAATTCTACTGAC
*
1369 CCAAATACATAATTAAGTTAGCCCAACTT-TACTGGC
1 CCAAATACATAATTAAGTTAGCCCAA-TTCTACTGAC
1405 CCAA
1 CCAA
1409 TACTACCAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
36 31 0.94
37 2 0.06
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (36 bp):
CCAAATACATAATTAAGTTAGCCCAATTCTACTGAC
Found at i:1568 original size:37 final size:37
Alignment explanation
Indices: 1527--1653 Score: 193
Period size: 37 Copynumber: 3.4 Consensus size: 37
1517 CCAAGAGTGA
* *
1527 AACAAGTCTTCATCAAAATTATTCATCAAAGTTCTTC
1 AACAAGTCTCCATCAAAGTTATTCATCAAAGTTCTTC
1564 AACAAGTCTCCA-CGAAAGTTATTCATCAAAGTTCTTC
1 AACAAGTCTCCATC-AAAGTTATTCATCAAAGTTCTTC
* *
1601 AACAAGTCCCCACCAAAGTTATTCATCAAAGTTCTTC
1 AACAAGTCTCCATCAAAGTTATTCATCAAAGTTCTTC
*
1638 AACAAGTCTTCATCAA
1 AACAAGTCTCCATCAA
1654 GTTGTTCTTC
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
36 1 0.01
37 80 0.98
38 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.08, T:0.30
Consensus pattern (37 bp):
AACAAGTCTCCATCAAAGTTATTCATCAAAGTTCTTC
Found at i:1653 original size:24 final size:24
Alignment explanation
Indices: 1548--1687 Score: 83
Period size: 24 Copynumber: 5.7 Consensus size: 24
1538 ATCAAAATTA
1548 TTCATCAAAGTTCTTCAACAAGTC
1 TTCATCAAAGTTCTTCAACAAGTC
* * *
1572 TCCA-CGAAAGTTATTCATCAAAGTTC
1 TTCATC-AAAGTTCTTCAAC-AAG-TC
* ** * *
1598 TTCAAC-AAG-TCCCCACCAAAGTTA
1 TTCATCAAAGTTCTTCAAC-AAG-TC
1622 TTCATCAAAGTTCTTCAACAAGTC
1 TTCATCAAAGTTCTTCAACAAGTC
* *
1646 TTCATCAAGTTGTTCTTCAACAAGTT
1 TTCATCAA--AGTTCTTCAACAAGTC
1672 TTCACTC--AGTTCTTCA
1 TTCA-TCAAAGTTCTTCA
1688 TCAAATTTTC
Statistics
Matches: 90, Mismatches: 17, Indels: 19
0.71 0.13 0.15
Matches are distributed among these distances:
23 9 0.10
24 38 0.42
25 12 0.13
26 28 0.31
27 3 0.03
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (24 bp):
TTCATCAAAGTTCTTCAACAAGTC
Found at i:1687 original size:23 final size:23
Alignment explanation
Indices: 1616--1697 Score: 76
Period size: 26 Copynumber: 3.3 Consensus size: 23
1606 GTCCCCACCA
1616 AAGTTATTCATCAAAGTTCTTCAAC
1 AAGTT-TTCATC-AAGTTCTTCAAC
*
1641 AAGTCTTCATCAAGTTGTTCTTCAAC
1 AAGTTTTCATCAA---GTTCTTCAAC
*
1667 AAGTTTTCACTC-AGTTCTTCATC
1 AAGTTTTCA-TCAAGTTCTTCAAC
*
1690 AAATTTTC
1 AAGTTTTC
1698 CACCAATCTA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
23 18 0.37
24 6 0.12
25 4 0.08
26 19 0.39
27 2 0.04
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (23 bp):
AAGTTTTCATCAAGTTCTTCAAC
Done.