Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020181.1 Corchorus olitorius cultivar O-4 contig20214, 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: 20153
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:173 original size:36 final size:35
Alignment explanation
Indices: 109--206 Score: 90
Period size: 35 Copynumber: 2.7 Consensus size: 35
99 TGTAGAAATT
*
109 ATTAAATAAAATAATAATAAAGAGAAGTTAAA-AATAAA
1 ATTAAATAAAA-AATAAT--TGA-AAGTTAAATAATAAA
*
147 TATTTAAATAAAAAATAATTGAAAGTTAAATTATAAA
1 -A-TTAAATAAAAAATAATTGAAAGTTAAATAATAAA
* * *
184 AATCAATAAAAAATAATTAAAAG
1 ATTAAATAAAAAATAATTGAAAG
207 ATAATTTTAG
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
35 19 0.37
36 9 0.17
37 7 0.13
39 7 0.13
40 10 0.19
ACGTcount: A:0.65, C:0.01, G:0.06, T:0.28
Consensus pattern (35 bp):
ATTAAATAAAAAATAATTGAAAGTTAAATAATAAA
Found at i:1699 original size:11 final size:11
Alignment explanation
Indices: 1650--1707 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
1640 AATATTTAAA
1650 TAAAAAATAAT
1 TAAAAAATAAT
* *
1661 TGAAAATTAAAT
1 TAAAAAAT-AAT
1673 TATAAAAATCAA-
1 TA-AAAAAT-AAT
1685 TAAAAAATAAT
1 TAAAAAATAAT
*
1696 TAAAAGATAAT
1 TAAAAAATAAT
1707 T
1 T
1708 TTAGATTTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
10 2 0.05
11 23 0.61
12 6 0.16
13 7 0.18
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (11 bp):
TAAAAAATAAT
Found at i:5831 original size:19 final size:20
Alignment explanation
Indices: 5800--5837 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
5790 TATTGACATT
5800 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
5819 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
5838 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:11192 original size:107 final size:107
Alignment explanation
Indices: 11004--11213 Score: 393
Period size: 107 Copynumber: 2.0 Consensus size: 107
10994 AATAAATAAA
*
11004 AAAACAATAATAAGAGAAAGTGAAAATACACAAAAACCAATCAAAAGATTGAACCTTATCAAATT
1 AAAACAATAATAAGAGAAAGTGAAAATACACAAAAAACAATCAAAAGATTGAACCTTATCAAATT
*
11069 GAGTATTGTTGGATTGGACTTGATGGTCATTTCAAGTCATAG
66 GAGTATTGTTGAATTGGACTTGATGGTCATTTCAAGTCATAG
*
11111 AAAACAATAATAAGAGAAAGTGAAAATACACAAAAAACAATCAAAAGATTGAACCTTATCGAATT
1 AAAACAATAATAAGAGAAAGTGAAAATACACAAAAAACAATCAAAAGATTGAACCTTATCAAATT
11176 GAGTATTGTTGAATTGGACTTGATGGTCATTTCAAGTC
66 GAGTATTGTTGAATTGGACTTGATGGTCATTTCAAGTC
11214 TATTCAATAA
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 100 1.00
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (107 bp):
AAAACAATAATAAGAGAAAGTGAAAATACACAAAAAACAATCAAAAGATTGAACCTTATCAAATT
GAGTATTGTTGAATTGGACTTGATGGTCATTTCAAGTCATAG
Found at i:14069 original size:36 final size:35
Alignment explanation
Indices: 14020--14087 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 35
14010 TTTTAATTTT
* *
14020 AAATATATTATATATGTTATAA-ATTAAAAATCTGA
1 AAATATATAATATAT-ATATAACATTAAAAATCTGA
*
14055 AAATATATAAATATATATATAACATTAATAATC
1 AAATATAT-AATATATATATAACATTAAAAATC
14088 AAAAAATCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
35 13 0.46
36 15 0.54
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.38
Consensus pattern (35 bp):
AAATATATAATATATATATAACATTAAAAATCTGA
Found at i:14601 original size:18 final size:18
Alignment explanation
Indices: 14578--14618 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
14568 TGTTTATGTT
*
14578 CTTCTTGTTCTCATTGTG
1 CTTCTTATTCTCATTGTG
14596 CTTCTTATTCTCATTGTG
1 CTTCTTATTCTCATTGTG
14614 CTTCT
1 CTTCT
14619 GTTTAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.07, C:0.24, G:0.12, T:0.56
Consensus pattern (18 bp):
CTTCTTATTCTCATTGTG
Found at i:15076 original size:11 final size:11
Alignment explanation
Indices: 15052--15086 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
15042 TTGACAGCAC
15052 AACAAAAACAA
1 AACAAAAACAA
* *
15063 AACGAAAACGA
1 AACAAAAACAA
15074 AACAAAAACAA
1 AACAAAAACAA
15085 AA
1 AA
15087 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:18664 original size:22 final size:22
Alignment explanation
Indices: 18638--18684 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
18628 TTTTCTTTTA
*
18638 GTAACCTTGAATAAGAAGAATG
1 GTAACATTGAATAAGAAGAATG
*
18660 GTAACATTGAATAAGAAGATTG
1 GTAACATTGAATAAGAAGAATG
18682 GTA
1 GTA
18685 TAAGCTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.45, C:0.06, G:0.23, T:0.26
Consensus pattern (22 bp):
GTAACATTGAATAAGAAGAATG
Done.