Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006906.1 Corchorus capsularis cultivar CVL-1 contig06927, 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: 8183
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:121 original size:11 final size:11
Alignment explanation
Indices: 105--147 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
95 TATAATATAT
105 CTAATTAATAG
1 CTAATTAATAG
*
116 CTAATTAATAT
1 CTAATTAATAG
127 CTAATTAATAG
1 CTAATTAATAG
*
138 TTAATTAATA
1 CTAATTAATA
148 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:128 original size:22 final size:22
Alignment explanation
Indices: 101--147 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
91 CCATTATAAT
101 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
123 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
145 ATA
1 ATA
148 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:4184 original size:29 final size:29
Alignment explanation
Indices: 4147--4235 Score: 119
Period size: 29 Copynumber: 3.1 Consensus size: 29
4137 GGATCGCCCA
4147 GGGGCATTTTGGTCATTTTCTGCATTTAG
1 GGGGCATTTTGGTCATTTTCTGCATTTAG
* *
4176 GGGGCATTTTGGTCATTTTC-ACATCTA-
1 GGGGCATTTTGGTCATTTTCTGCATTTAG
* *
4203 GGGGCATTTAGGTCATTTTTTTGCATTTAG
1 GGGGCATTTTGGTCA-TTTTCTGCATTTAG
4233 GGG
1 GGG
4236 TGTCTTGGGT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
27 14 0.27
28 9 0.18
29 25 0.49
30 3 0.06
ACGTcount: A:0.16, C:0.13, G:0.28, T:0.43
Consensus pattern (29 bp):
GGGGCATTTTGGTCATTTTCTGCATTTAG
Found at i:4373 original size:23 final size:22
Alignment explanation
Indices: 4347--4425 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 22
4337 TAGAGTTTTT
4347 GCATATTTTCATTTAGTGATTTG
1 GCATATTTTCATTTAGT-ATTTG
* *
4370 GCATTATGGTGTTTTCAATTAGTATTGTT
1 GCA-TA-----TTTTCATTTAGTATT-TG
4399 GCATATTTTCATTTAGTAATTTG
1 GCATATTTTCATTTAGT-ATTTG
4422 GCAT
1 GCAT
4426 TGTTACACTC
Statistics
Matches: 44, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
23 19 0.43
24 5 0.11
28 5 0.11
29 15 0.34
ACGTcount: A:0.23, C:0.09, G:0.18, T:0.51
Consensus pattern (22 bp):
GCATATTTTCATTTAGTATTTG
Found at i:4995 original size:2 final size:2
Alignment explanation
Indices: 4988--5019 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4978 AGTTGATTGA
4988 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5020 GCGCTTGGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6468 original size:16 final size:16
Alignment explanation
Indices: 6435--6467 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
6425 AAACGGGGGC
6435 AACTAGGGTTCTTGAA
1 AACTAGGGTTCTTGAA
6451 AACTAGGGTT-TTGAA
1 AACTAGGGTTCTTGAA
6466 AA
1 AA
6468 AAAAAGAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.30
Consensus pattern (16 bp):
AACTAGGGTTCTTGAA
Found at i:7310 original size:49 final size:49
Alignment explanation
Indices: 7254--7399 Score: 168
Period size: 49 Copynumber: 3.0 Consensus size: 49
7244 GAAGCTTTTT
* *
7254 GTAAAAATGCCATCTTTGGGTAAAAGATTGAATTTTTAGTAATTAGTAA
1 GTAAAAATGTCATCTTTGAGTAAAAGATTGAATTTTTAGTAATTAGTAA
* ** * *
7303 GTAAAAATGTCATCTTTGAGTGAAAGATTGAAACTTTAGTGATTAGCAA
1 GTAAAAATGTCATCTTTGAGTAAAAGATTGAATTTTTAGTAATTAGTAA
* * * *
7352 GTAAAGATGTCACCTTAGAGCAAAAGATTG-ATTTTTAGAGTAATTAGT
1 GTAAAAATGTCATCTTTGAGTAAAAGATTGAATTTTT--AGTAATTAGT
7400 GAATAGAGAT
Statistics
Matches: 79, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
48 4 0.05
49 67 0.85
50 8 0.10
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.34
Consensus pattern (49 bp):
GTAAAAATGTCATCTTTGAGTAAAAGATTGAATTTTTAGTAATTAGTAA
Done.