Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014013.1 Corchorus capsularis cultivar CVL-1 contig14034, 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: 20714
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:13 original size:2 final size:2
Alignment explanation
Indices: 7--50 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1 TTCTAC
7 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49 TA
1 TA
51 CCCTTAAATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1895 original size:21 final size:19
Alignment explanation
Indices: 1871--1926 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 19
1861 GCTGCTCTAA
* *
1871 TAATTTCATCTGTACAGTACT
1 TAATCTCATCTGTACAGT--G
*
1892 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTG
1911 TAATCTCATCTGTACA
1 TAATCTCATCTGTACA
1927 ATTGCTAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTG
Found at i:1916 original size:19 final size:20
Alignment explanation
Indices: 1878--1926 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
1868 TAATAATTTC
*
1878 ATCTGTACAGTACTTAATCTA
1 ATCTGTACAGTA-GTAATCTA
*
1899 ATCTGTACAGT-GTAATCTC
1 ATCTGTACAGTAGTAATCTA
1918 ATCTGTACA
1 ATCTGTACA
1927 ATTGCTAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 15 0.58
21 11 0.42
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (20 bp):
ATCTGTACAGTAGTAATCTA
Found at i:2296 original size:2 final size:2
Alignment explanation
Indices: 2289--2317 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2279 CAAGCATTAT
2289 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2318 CACGAATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8155 original size:15 final size:16
Alignment explanation
Indices: 8130--8159 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
8120 GAGTTTGGAT
8130 TAAAGTAATAAATAAA
1 TAAAGTAATAAATAAA
8146 TAAA-TAATAAATAA
1 TAAAGTAATAAATAA
8160 TAAGGAGTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (16 bp):
TAAAGTAATAAATAAA
Found at i:15893 original size:70 final size:71
Alignment explanation
Indices: 15761--15994 Score: 176
Period size: 72 Copynumber: 3.3 Consensus size: 71
15751 AGTTTTACCA
* * * * *** *
15761 ATTAAATAATTGAAATGAAACATAAGGAT-AAAGTTGGAAAGTAATAATTTTGGTG-ATCTGGTT
1 ATTAAATAATTG-AA-GAGAGATAAGGATAAAAG-TGGAAAATAATAATATCATTGAATATGGTT
* * *
15824 TTCATTGTC
63 TCCACTATC
*
15833 ATTAAATAATTGAAGAGAGATAAGGATAAAAGTGGAAATTAATAATATCATTGAAT-TGGTTTCC
1 ATTAAATAATTGAAGAGAGATAAGGATAAAAGTGGAAAATAATAATATCATTGAATATGGTTTCC
*
15897 ACTATT
66 ACTATC
* * * * *
15903 TTTAAAT-ATCGGAGTAGAGAGATAAGGGTAAAATTGGAAAAT-ACAA-A-CATTGATGATATGG
1 ATTAAATAAT-TGA--AGAGAGATAAGGATAAAAGTGGAAAATAATAATATCATTGA--ATATGG
*
15964 TTTCCACTCTC
61 TTTCCACTATC
15975 ATTAAATAATTGAAGAGAGA
1 ATTAAATAATTGAAGAGAGA
15995 GATAAGGGTA
Statistics
Matches: 132, Mismatches: 21, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
69 8 0.06
70 53 0.40
71 13 0.10
72 56 0.42
73 2 0.02
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (71 bp):
ATTAAATAATTGAAGAGAGATAAGGATAAAAGTGGAAAATAATAATATCATTGAATATGGTTTCC
ACTATC
Found at i:15965 original size:72 final size:72
Alignment explanation
Indices: 15831--16008 Score: 188
Period size: 72 Copynumber: 2.5 Consensus size: 72
15821 GTTTTCATTG
* * * * *
15831 TCATTAAATAATTG-A-AGAGAGATAAGGATAAAAGTGGAAATTAATAATATCATTGAATTGGTT
1 TCATTAAATAATCGAAGAGAGAGATAAGGGTAAAATTGGAAAATAACAATATCATTGAATTGGTT
15894 TCCACTA
66 TCCACTA
** *
15901 TTTTTAAAT-ATCGGAGTAGAGAGATAAGGGTAAAATTGGAAAAT-ACAA-A-CATTGATGATAT
1 TCATTAAATAATCGAAG-AGAGAGATAAGGGTAAAATTGGAAAATAACAATATCATTGA--AT-T
*
15962 GGTTTCCACTC
62 GGTTTCCACTA
*
15973 TCATTAAATAATTGAAGAGAGAGATAAGGGTAAAAT
1 TCATTAAATAATCGAAGAGAGAGATAAGGGTAAAAT
16009 AAAAAAGGAA
Statistics
Matches: 89, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
69 9 0.10
70 9 0.10
71 5 0.06
72 61 0.69
73 5 0.06
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (72 bp):
TCATTAAATAATCGAAGAGAGAGATAAGGGTAAAATTGGAAAATAACAATATCATTGAATTGGTT
TCCACTA
Found at i:17271 original size:17 final size:18
Alignment explanation
Indices: 17249--17283 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
17239 TTATTTATAT
17249 CATTTAA-AAAAACTACC
1 CATTTAATAAAAACTACC
17266 CATTTAATAAAAACTACC
1 CATTTAATAAAAACTACC
17284 ACAAACTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (18 bp):
CATTTAATAAAAACTACC
Found at i:17747 original size:31 final size:29
Alignment explanation
Indices: 17689--17747 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
17679 GTTTTTTTTG
*
17689 GGTGAAATAAAAATTTTTTTATGACAAAT
1 GGTGAAATAAAAATTTTTTTATAACAAAT
*
17718 GGTGAAATAAAATGTTTTTTTAATAACAAA
1 GGTGAAATAAAA-ATTTTTTT-ATAACAAA
17748 AAAATATAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 12 0.46
30 7 0.27
31 7 0.27
ACGTcount: A:0.46, C:0.03, G:0.14, T:0.37
Consensus pattern (29 bp):
GGTGAAATAAAAATTTTTTTATAACAAAT
Found at i:20112 original size:13 final size:13
Alignment explanation
Indices: 20096--20121 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20086 TGTATTTGAT
20096 CCTCCAATTTGTC
1 CCTCCAATTTGTC
20109 CCTCCAATTTGTC
1 CCTCCAATTTGTC
20122 TCTCATAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.38, G:0.08, T:0.38
Consensus pattern (13 bp):
CCTCCAATTTGTC
Done.