Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016287.1 Corchorus capsularis cultivar CVL-1 contig16308, 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: 39116
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:5147 original size:29 final size:27
Alignment explanation
Indices: 5114--5179 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 27
5104 TTGAAAAACT
*
5114 TTGAAAACTGGATGGGATCTTTCCCTAAA
1 TTGAAAACTGG--CGGATCTTTCCCTAAA
*
5143 TTGAATACTTGGCGGATCTTTCCCTAAA
1 TTGAAAAC-TGGCGGATCTTTCCCTAAA
5171 TTGAAAACT
1 TTGAAAACT
5180 TTTGGAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 1 0.03
28 22 0.67
29 7 0.21
30 3 0.09
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (27 bp):
TTGAAAACTGGCGGATCTTTCCCTAAA
Found at i:6904 original size:6 final size:6
Alignment explanation
Indices: 6893--6919 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6883 AAAGCAAAGC
6893 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
6920 GCAGATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:7869 original size:10 final size:10
Alignment explanation
Indices: 7854--7878 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
7844 AAGGACTCTA
7854 GAATTTTCTG
1 GAATTTTCTG
7864 GAATTTTCTG
1 GAATTTTCTG
7874 GAATT
1 GAATT
7879 GTGCGGCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:13659 original size:11 final size:11
Alignment explanation
Indices: 13643--13672 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
13633 GGTCTTCAAT
*
13643 TCTTCAAATTA
1 TCTTCAAATAA
13654 TCTTCAAATAA
1 TCTTCAAATAA
13665 TCTTCAAA
1 TCTTCAAA
13673 CACGAACTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (11 bp):
TCTTCAAATAA
Found at i:15255 original size:21 final size:21
Alignment explanation
Indices: 15230--15270 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
15220 CAATCAAGCA
15230 AATCA-AGCAATTCAAAGCATC
1 AATCATAGCAA-TCAAAGCATC
*
15251 AATCATAGTAATCAAAGCAT
1 AATCATAGCAATCAAAGCAT
15271 ATGAGTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.49, C:0.20, G:0.10, T:0.22
Consensus pattern (21 bp):
AATCATAGCAATCAAAGCATC
Found at i:15379 original size:16 final size:16
Alignment explanation
Indices: 15354--15385 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
15344 AGGAATAGAC
15354 AATCAATCAAAGCAAT
1 AATCAATCAAAGCAAT
*
15370 AATCACTCAAAGCAAT
1 AATCAATCAAAGCAAT
15386 GCAAGGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.22, G:0.06, T:0.19
Consensus pattern (16 bp):
AATCAATCAAAGCAAT
Found at i:16622 original size:15 final size:15
Alignment explanation
Indices: 16602--16632 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
16592 AGTTGCTCTT
16602 GTGGCTAATCTTCTG
1 GTGGCTAATCTTCTG
*
16617 GTGGCTTATCTTCTG
1 GTGGCTAATCTTCTG
16632 G
1 G
16633 CTTGGCAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.19, G:0.29, T:0.42
Consensus pattern (15 bp):
GTGGCTAATCTTCTG
Found at i:17069 original size:18 final size:18
Alignment explanation
Indices: 17046--17086 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
17036 CATCGCACGA
17046 GCCATCCGGCCACAACCG
1 GCCATCCGGCCACAACCG
17064 GCCATCCGGCCACAACCG
1 GCCATCCGGCCACAACCG
17082 GCCAT
1 GCCAT
17087 TCGACCCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.22, C:0.49, G:0.22, T:0.07
Consensus pattern (18 bp):
GCCATCCGGCCACAACCG
Found at i:19565 original size:33 final size:33
Alignment explanation
Indices: 19512--19584 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
19502 GTGTTTTAGA
* * * *
19512 TGTTGTTTGCGATGATACTAAACCTAATTTGAG
1 TGTTGTTAGCAATGACACTAAACCTAATTTAAG
* **
19545 TGTTGTTAGCAATGACACTAAATCTGTTTTAAG
1 TGTTGTTAGCAATGACACTAAACCTAATTTAAG
19578 TGTTGTT
1 TGTTGTT
19585 TGTGATGAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (33 bp):
TGTTGTTAGCAATGACACTAAACCTAATTTAAG
Found at i:19639 original size:33 final size:33
Alignment explanation
Indices: 19602--19771 Score: 258
Period size: 33 Copynumber: 5.2 Consensus size: 33
19592 AAAACAAATA
19602 TGTTTTGGTTGATCATAGCATTGCAAATAATTC
1 TGTTTTGGTTGATCATAGCATTGCAAATAATTC
*
19635 TGTTTTGGTTGATCATAGCATTGCAAACAATTC
1 TGTTTTGGTTGATCATAGCATTGCAAATAATTC
19668 TGTTTTGGTTGATCATAGCATTG-AACATAATTC
1 TGTTTTGGTTGATCATAGCATTGCAA-ATAATTC
*
19701 TGTTTTGGTTGATCATAACATTGCAAATAATTC
1 TGTTTTGGTTGATCATAGCATTGCAAATAATTC
* * *
19734 TGTTTTGGTTG---ATGGCATTGAAAATAAATC
1 TGTTTTGGTTGATCATAGCATTGCAAATAATTC
19764 TGTTTTGG
1 TGTTTTGG
19772 GTGACGAGAA
Statistics
Matches: 128, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
30 23 0.18
32 2 0.02
33 101 0.79
34 2 0.02
ACGTcount: A:0.27, C:0.11, G:0.19, T:0.42
Consensus pattern (33 bp):
TGTTTTGGTTGATCATAGCATTGCAAATAATTC
Found at i:21545 original size:21 final size:21
Alignment explanation
Indices: 21504--21548 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
21494 ATTGGAGATC
*
21504 ATGTCTTGGATGAACATGAAG
1 ATGTCTTGGATGAACAAGAAG
*
21525 ATGTCTTGGA-GATTCAAGAAG
1 ATGTCTTGGATGA-ACAAGAAG
21546 ATG
1 ATG
21549 CCACGGATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (21 bp):
ATGTCTTGGATGAACAAGAAG
Found at i:24047 original size:19 final size:18
Alignment explanation
Indices: 24010--24049 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
24000 TTTTTGACAT
*
24010 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
24028 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
24047 AAT
1 AAT
24050 AAATCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:25679 original size:21 final size:19
Alignment explanation
Indices: 25642--25680 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
25632 CAATCAAGCA
25642 AATCATGATTCAAAGCATC
1 AATCATGATTCAAAGCATC
*
25661 AATCATAGCATTCATAGCAT
1 AATCAT-G-ATTCAAAGCAT
25681 ATGAGTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 1 0.06
21 10 0.59
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (19 bp):
AATCATGATTCAAAGCATC
Found at i:27270 original size:35 final size:38
Alignment explanation
Indices: 27196--27274 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 38
27186 AAACAAGTAA
*
27196 AATTAACTAAGAAAGCAGTTAAGAAAATTAGAGAAAAC
1 AATTAACTAAGAAAGCAGTGAAGAAAATTAGAGAAAAC
* *
27234 AATTAACTAA-AAAGTAGTGAA-TAAATT-GAGAAAAC
1 AATTAACTAAGAAAGCAGTGAAGAAAATTAGAGAAAAC
27269 AATTAA
1 AATTAA
27275 AGAAAATCCT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 14 0.37
36 5 0.13
37 9 0.24
38 10 0.26
ACGTcount: A:0.58, C:0.06, G:0.14, T:0.22
Consensus pattern (38 bp):
AATTAACTAAGAAAGCAGTGAAGAAAATTAGAGAAAAC
Done.