Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007972.1 Corchorus capsularis cultivar CVL-1 contig07993, 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: 25622
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:760 original size:13 final size:13
Alignment explanation
Indices: 742--769 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
732 ACCATCAAGG
742 TACTTTTTTTCTC
1 TACTTTTTTTCTC
755 TACTTTTTTTCTC
1 TACTTTTTTTCTC
768 TA
1 TA
770 GTCGAATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.11, C:0.21, G:0.00, T:0.68
Consensus pattern (13 bp):
TACTTTTTTTCTC
Found at i:1776 original size:31 final size:31
Alignment explanation
Indices: 1731--1838 Score: 87
Period size: 31 Copynumber: 3.5 Consensus size: 31
1721 GCTAAATAAC
* * **
1731 CAATTCAGGGTATAACGTTTGCTG-CCACGAT
1 CAATTTAGGATATAACGTTT-CTGAAAACGAT
* *
1762 CAATTTGGGATATAACGTTTCTGAAAATGAT
1 CAATTTAGGATATAACGTTTCTGAAAACGAT
* * *
1793 CATTTTAGGATATAACGTTTC-AAAAAGTGAT
1 CAATTTAGGATATAACGTTTCTGAAAA-CGAT
1824 C-ATTTCAGGATATAA
1 CAATTT-AGGATATAA
1839 AGAATGATCA
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
30 10 0.16
31 54 0.84
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (31 bp):
CAATTTAGGATATAACGTTTCTGAAAACGAT
Found at i:2026 original size:30 final size:29
Alignment explanation
Indices: 1992--2049 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1982 TTGATTTGAT
* *
1992 CGTTTCAAGTAACGTTATATCCTAAATTGG
1 CGTTTC-AGAAACGTTATATCCCAAATTGG
*
2022 CGTTTCTGAAACGTTATATCCCAAATTG
1 CGTTTCAGAAACGTTATATCCCAAATTG
2050 ATCCGCGCGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (29 bp):
CGTTTCAGAAACGTTATATCCCAAATTGG
Found at i:3994 original size:30 final size:29
Alignment explanation
Indices: 3930--3997 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
3920 ACACAAGACG
* ** *
3930 GCCAAATAAGCCCCTAAACTTTTATTACA
1 GCCAAATAAGCCCCTAAACTCTTAAAAAA
*
3959 GCCAAATAAGCCCCTGAACTCTTAGAAAAA
1 GCCAAATAAGCCCCTAAACTCTTA-AAAAA
3989 GCCAAATAA
1 GCCAAATAA
3998 ACCCTTTTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
29 22 0.67
30 11 0.33
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.21
Consensus pattern (29 bp):
GCCAAATAAGCCCCTAAACTCTTAAAAAA
Found at i:5917 original size:17 final size:15
Alignment explanation
Indices: 5893--5944 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 15
5883 ATTGTTCTTA
5893 TTTTTCAAAATTTATT
1 TTTTTCAAAA-TTATT
5909 TTTTGTCAAAA--ATT
1 TTTT-TCAAAATTATT
*
5923 TTTTTCCAAAATTAAT
1 TTTTT-CAAAATTATT
5939 TTTTTC
1 TTTTTC
5945 CACGTGGCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
13 1 0.03
14 12 0.39
15 1 0.03
16 11 0.35
17 6 0.19
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.58
Consensus pattern (15 bp):
TTTTTCAAAATTATT
Found at i:6423 original size:69 final size:70
Alignment explanation
Indices: 6297--6446 Score: 239
Period size: 69 Copynumber: 2.2 Consensus size: 70
6287 GAGGTTGCTA
* *
6297 ATTTAAATAAGTAAAATATACTTCAATTTTCAACAAAGAATATACCCGAAATGCTTTGGTAAAAA
1 ATTTAAATAGGTAAAATATACTTCAATTTTCAACAAAGAATATACCAGAAATGCTTTGGTAAAAA
6362 AACAT
66 AACAT
* * * *
6367 ATTT-AATAGGTAAGATATACTTCAATTTTCAATAAAGAATATACGAGAAATTCTTTGGTAAAAA
1 ATTTAAATAGGTAAAATATACTTCAATTTTCAACAAAGAATATACCAGAAATGCTTTGGTAAAAA
6431 AACAT
66 AACAT
6436 ATTTAAATAGG
1 ATTTAAATAGG
6447 GAAAGGCTTT
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
69 63 0.86
70 10 0.14
ACGTcount: A:0.47, C:0.10, G:0.11, T:0.32
Consensus pattern (70 bp):
ATTTAAATAGGTAAAATATACTTCAATTTTCAACAAAGAATATACCAGAAATGCTTTGGTAAAAA
AACAT
Found at i:6693 original size:30 final size:30
Alignment explanation
Indices: 6659--6716 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
6649 AGTACTACTA
6659 AATCTTCCACTACTATTTTAAATTGGAACT
1 AATCTTCCACTACTATTTTAAATTGGAACT
6689 AATCTTCCACTACTATTTTAAATTGGAA
1 AATCTTCCACTACTATTTTAAATTGGAA
6717 TTACTACACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (30 bp):
AATCTTCCACTACTATTTTAAATTGGAACT
Found at i:8186 original size:13 final size:13
Alignment explanation
Indices: 8168--8203 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
8158 GAGCCAATAG
8168 TGAACTAAGGTCT
1 TGAACTAAGGTCT
8181 TGAACTAAGGTCT
1 TGAACTAAGGTCT
8194 TGAACTAAGG
1 TGAACTAAGG
8204 CTGCTTTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (13 bp):
TGAACTAAGGTCT
Found at i:21869 original size:51 final size:49
Alignment explanation
Indices: 21799--21900 Score: 159
Period size: 51 Copynumber: 2.0 Consensus size: 49
21789 AAGATCCAAG
*
21799 GAAGATTATAAAAATTTACAGAAGTTCGCTTTCAAGAAATTTTTATTTT
1 GAAGATTATAAAAATTTACAGAAGCTCGCTTTCAAGAAATTTTTATTTT
* *
21848 GAAGAATTATCAAAGATTTACAGGAGCTCGCTTTCAAGAAATTTTTATTTT
1 GAAG-ATTAT-AAAAATTTACAGAAGCTCGCTTTCAAGAAATTTTTATTTT
21899 GA
1 GA
21901 TCTTCATCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
49 4 0.08
50 5 0.10
51 39 0.81
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (49 bp):
GAAGATTATAAAAATTTACAGAAGCTCGCTTTCAAGAAATTTTTATTTT
Found at i:22075 original size:55 final size:57
Alignment explanation
Indices: 22009--22122 Score: 151
Period size: 62 Copynumber: 1.9 Consensus size: 57
21999 AAGACCCTCG
*
22009 AATCAAATCAAACTC-CCTCATCAA-TTCAAGATCAAGTCATTTGACCCTTGAATTA
1 AATCAAATCAAACTCACATCATCAAGTTCAAGATCAAGTCATTTGACCCTTGAATTA
*
22064 AATCAAATCAAACTCTGAAATTATCATCAAGTTCAAGATCAAGTCATTTGACCCTTGAA
1 AATCAAATCAAACTC----A-CATCATCAAGTTCAAGATCAAGTCATTTGACCCTTGAA
22123 GCAAATCTTG
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
55 15 0.30
61 7 0.14
62 28 0.56
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.29
Consensus pattern (57 bp):
AATCAAATCAAACTCACATCATCAAGTTCAAGATCAAGTCATTTGACCCTTGAATTA
Found at i:24836 original size:2 final size:2
Alignment explanation
Indices: 24829--24892 Score: 89
Period size: 2 Copynumber: 32.5 Consensus size: 2
24819 ATTCAACATT
24829 TA TA TA TA TA -A TA TA TA -A TA TA TA TA TA TA TA TCA TA TCA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T-A TA
24871 TA -A TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
24893 TAAAACTGAG
Statistics
Matches: 57, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.05
2 50 0.88
3 4 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:24871 original size:29 final size:30
Alignment explanation
Indices: 24829--24892 Score: 96
Period size: 31 Copynumber: 2.2 Consensus size: 30
24819 ATTCAACATT
24829 TATATATATAATAT-ATA-ATATATATATA
1 TATATATATAATATAATATATATATATATA
*
24857 TATATCATATCATATAATATATATATATATA
1 TATAT-ATATAATATAATATATATATATATA
24888 TATAT
1 TATAT
24893 TAAAACTGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 5 0.16
29 8 0.25
30 3 0.09
31 16 0.50
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (30 bp):
TATATATATAATATAATATATATATATATA
Done.