Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009532.1 Corchorus olitorius cultivar O-4 contig09564, 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: 20162
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Found at i:970 original size:17 final size:17
Alignment explanation
Indices: 944--978 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
934 AAAGGGTAGT
944 TAAAAAAAGT-TTTTCA
1 TAAAAAAAGTGTTTTCA
960 TAAAAAGAAGTGTTTTCA
1 TAAAAA-AAGTGTTTTCA
978 T
1 T
979 GAAACCTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 4 0.24
18 7 0.41
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (17 bp):
TAAAAAAAGTGTTTTCA
Found at i:1806 original size:11 final size:10
Alignment explanation
Indices: 1775--1822 Score: 55
Period size: 11 Copynumber: 4.8 Consensus size: 10
1765 AAAGTTCGTG
1775 ATTGAAGATTA
1 ATTGAAGA-TA
1786 ATTGAAGATA
1 ATTGAAGATA
1796 ATTTGAAGAT-
1 A-TTGAAGATA
*
1806 A-TGAAGATC
1 ATTGAAGATA
1815 ATTGAAGA
1 ATTGAAGA
1823 ATTATTTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.21
9 1 0.03
10 10 0.29
11 16 0.47
ACGTcount: A:0.46, C:0.02, G:0.21, T:0.31
Consensus pattern (10 bp):
ATTGAAGATA
Found at i:3729 original size:50 final size:51
Alignment explanation
Indices: 3661--3778 Score: 148
Period size: 50 Copynumber: 2.3 Consensus size: 51
3651 AATTTAGCAT
* * ** **
3661 AAAAAGGATTAAAATTTGGTATGTTAGAGTTAAAAATATGATCTTT-AGTTC
1 AAAAA-GATTAAATTTTGGCATGTTAGAAATAAAAATACCATCTTTAAGTTC
*
3712 AAAAAGATTAAATTTTGGCATGTTTGAAATAAAAATACCATCTTTAAGTTC
1 AAAAAGATTAAATTTTGGCATGTTAGAAATAAAAATACCATCTTTAAGTTC
*
3763 AAAAAGATTAAGTTTT
1 AAAAAGATTAAATTTT
3779 AGTAGGTTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
50 33 0.57
51 25 0.43
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.36
Consensus pattern (51 bp):
AAAAAGATTAAATTTTGGCATGTTAGAAATAAAAATACCATCTTTAAGTTC
Found at i:3793 original size:51 final size:50
Alignment explanation
Indices: 3691--3793 Score: 134
Period size: 51 Copynumber: 2.0 Consensus size: 50
3681 ATGTTAGAGT
** * * *
3691 TAAAAATATGATCTTTAGTTCAAAAAGATTAAATTTTGGCATGTTTGAAA
1 TAAAAATACCATCTTTAGTTCAAAAAGATTAAATTTTAGCAGGTTTAAAA
* *
3741 TAAAAATACCATCTTTAAGTTCAAAAAGATTAAGTTTTAGTAGGTTTAAAA
1 TAAAAATACCATCTTT-AGTTCAAAAAGATTAAATTTTAGCAGGTTTAAAA
3792 TA
1 TA
3794 GAAGTTGGGT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
50 14 0.31
51 31 0.69
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.37
Consensus pattern (50 bp):
TAAAAATACCATCTTTAGTTCAAAAAGATTAAATTTTAGCAGGTTTAAAA
Found at i:4411 original size:35 final size:35
Alignment explanation
Indices: 4330--4462 Score: 130
Period size: 35 Copynumber: 3.9 Consensus size: 35
4320 GTGAATCAGT
* * * *
4330 AATAAGCAACTTAATTTACGGTAATTAAGTCAGTC
1 AATAAGCAACTTAATTCAAGGTAATTAAGTAATTC
* * * *
4365 AGT-A--AA-TTAATTCAGGGTAATCAAGTAATTT
1 AATAAGCAACTTAATTCAAGGTAATTAAGTAATTC
* *
4396 ACTAAGCAACTTAATTCATGGTAATTAAGTAATTC
1 AATAAGCAACTTAATTCAAGGTAATTAAGTAATTC
* *
4431 AATAAGTAACTTAATTCAAGATAATTAAGTAA
1 AATAAGCAACTTAATTCAAGGTAATTAAGTAA
4463 ATAAAATGAC
Statistics
Matches: 79, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
31 21 0.27
32 3 0.04
34 3 0.04
35 52 0.66
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.33
Consensus pattern (35 bp):
AATAAGCAACTTAATTCAAGGTAATTAAGTAATTC
Found at i:17816 original size:95 final size:95
Alignment explanation
Indices: 17543--17823 Score: 360
Period size: 89 Copynumber: 3.0 Consensus size: 95
17533 GTCATTTAAC
* * * *
17543 ATAGATTTTGAAAACCAACAAAGACTCAGCAGAAACATAGATCTATTACCAAGAAAATAACTAAA
1 ATAGA-TTTGAGAACCAACAAAGACTCGGCAGAAACATAGATCTATTACCAGGAAAATAACCAAA
* *
17608 CAAAACCAGAACTTCCAGAGCCAAATAGC--
65 CAAAACCAAAACTTACAGAGCCAAATAGCAA
17637 A-AG---TGAGAACCAACAAAGACTCGGCAGAAACATAGATCTATTACCAGGAAAAATAACCAAA
1 ATAGATTTGAGAACCAACAAAGACTCGGCAGAAACATAGATCTATTACCAGG-AAAATAACCAAA
* *
17698 CAAAAACAAAACTTACAAAGCCAAATAGCAA
65 CAAAACCAAAACTTACAGAGCCAAATAGCAA
* * * *
17729 ATAGATATTGAGAACCAACAAAGACT-GGCAAAAACATCGATTTATTACCAGGAAATTAACCAAA
1 ATAGAT-TTGAGAACCAACAAAGACTCGGCAGAAACATAGATCTATTACCAGGAAAATAACCAAA
* *
17793 CAAAACCAAAACCTACGGAGCCAAATAGCAA
65 CAAAACCAAAACTTACAGAGCCAAATAGCAA
17824 GTAATGCACC
Statistics
Matches: 163, Mismatches: 16, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
89 42 0.26
90 36 0.22
92 1 0.01
93 4 0.02
94 1 0.01
95 38 0.23
96 23 0.14
97 18 0.11
ACGTcount: A:0.51, C:0.21, G:0.13, T:0.15
Consensus pattern (95 bp):
ATAGATTTGAGAACCAACAAAGACTCGGCAGAAACATAGATCTATTACCAGGAAAATAACCAAAC
AAAACCAAAACTTACAGAGCCAAATAGCAA
Found at i:19773 original size:19 final size:20
Alignment explanation
Indices: 19745--19784 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
19735 TATGTATTAC
19745 ATATATATATATTCTTAATT
1 ATATATATATATTCTTAATT
19765 ATATA-ATATATTCTTAATT
1 ATATATATATATTCTTAATT
19784 A
1 A
19785 AAATATTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATATATATATTCTTAATT
Found at i:19817 original size:2 final size:2
Alignment explanation
Indices: 19801--19838 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
19791 TTACATACTT
* *
19801 TA TA -A TA TT TA TA TA TA TA TG TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19839 GTTTGAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Done.