Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013008.1 Corchorus capsularis cultivar CVL-1 contig13029, 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: 20084
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:152 original size:23 final size:23
Alignment explanation
Indices: 125--230 Score: 122
Period size: 23 Copynumber: 4.4 Consensus size: 23
115 AACTTTACTT
125 TATTACATAGAAAAGAATTTACA
1 TATTACATAGAAAAGAATTTACA
148 TATTACATAGAAAAGAATTTACA
1 TATTACATAGAAAAGAATTTACA
* *** *
171 TATTACATATAGGGGTCCAACTTTACTT
1 TATTACATAGAAAAG---AA-TTTAC-A
199 TATTACATAGAAAAGAATTTACA
1 TATTACATAGAAAAGAATTTACA
222 TATTACATA
1 TATTACATA
231 TATCTAAAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
23 43 0.63
24 5 0.07
25 2 0.03
26 2 0.03
27 5 0.07
28 11 0.16
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.34
Consensus pattern (23 bp):
TATTACATAGAAAAGAATTTACA
Found at i:3235 original size:75 final size:74
Alignment explanation
Indices: 3066--3240 Score: 174
Period size: 75 Copynumber: 2.3 Consensus size: 74
3056 ACTCTCATTC
* * *
3066 TCAGGTTGCTAATTCAAATTCAAATAATAAGTTTTCTGATGGTGTTAGGCAAAATCTTAAAGATG
1 TCAGGTTCCT-ATTCGAATTCAAATAATAAGTTTTCTGATGATGTTAGGCAAAATCTTAAAGATG
3131 ATTCACCTGA
65 ATTCACCTGA
** * * * * *
3141 TCAAATTCCTATTTTGAATTCAAATACA-AAGTTTTCTGATGATGATT-TGCAACATCTTGAAGT
1 TCAGGTTCCTA-TTCGAATTCAAATA-ATAAGTTTTCTGATGATG-TTAGGCAAAATCTTAAAGA
* *
3204 TGATTCACTTTA
63 TGATTCACCTGA
*
3216 TCAGGTTTCTGATTCGAATTCAAAT
1 TCAGGTTCCT-ATTCGAATTCAAAT
3241 TTTAAGCATC
Statistics
Matches: 80, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
74 1 0.01
75 75 0.94
76 4 0.05
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (74 bp):
TCAGGTTCCTATTCGAATTCAAATAATAAGTTTTCTGATGATGTTAGGCAAAATCTTAAAGATGA
TTCACCTGA
Found at i:3339 original size:75 final size:75
Alignment explanation
Indices: 3189--3341 Score: 164
Period size: 75 Copynumber: 2.0 Consensus size: 75
3179 ATGATGATTT
* * * **
3189 GCAACATCTTGAAGTTGATTCACTTTATCAGGTTTCTGATTCGAATTCAAATTTTAAGCATCATA
1 GCAACATCTTGAAGTTGATTCACTTAATCAGGATGCTGATTCGAATTCAAATACTAAGCATCATA
**
3254 ACGATGATAG
66 ACGACAATAG
* * * * * *
3264 GCAACATCTTGAAGTTGATTCTCTTAATCAGGATGCTG-TCTCGAATTCTAGTACTGAGCTTCCT
1 GCAACATCTTGAAGTTGATTCACTTAATCAGGATGCTGAT-TCGAATTCAAATACTAAGCATCAT
*
3328 AATGACAATAG
65 AACGACAATAG
3339 GCA
1 GCA
3342 TTTTGAAAAT
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
74 1 0.02
75 62 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (75 bp):
GCAACATCTTGAAGTTGATTCACTTAATCAGGATGCTGATTCGAATTCAAATACTAAGCATCATA
ACGACAATAG
Found at i:5452 original size:12 final size:12
Alignment explanation
Indices: 5420--5460 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
5410 AGTGTTCCAT
*
5420 TTTTTTTTTCAC
1 TTTTTTTTTCTC
*
5432 TTTTGTTTTCTC
1 TTTTTTTTTCTC
5444 TTTTTTTTT-T-
1 TTTTTTTTTCTC
5454 TTTTTTT
1 TTTTTTT
5461 CATTTGGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
10 7 0.27
11 1 0.04
12 18 0.69
ACGTcount: A:0.02, C:0.10, G:0.02, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTCTC
Found at i:8044 original size:3 final size:3
Alignment explanation
Indices: 8036--8064 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
8026 CTGCCTTTCA
8036 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
8065 GGCTCAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:8608 original size:26 final size:27
Alignment explanation
Indices: 8579--8640 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 27
8569 GCCTTAATGC
*
8579 AAATGCAATGCATGCAAACA-AAA-AGA
1 AAATGCAATACATGCAAACATAAACA-A
* * *
8605 AAATGAAAAATATGCAAACATAAACAA
1 AAATGCAATACATGCAAACATAAACAA
8632 AAATGCAAT
1 AAATGCAAT
8641 TTTTTTACCC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
26 16 0.57
27 11 0.39
28 1 0.04
ACGTcount: A:0.61, C:0.13, G:0.11, T:0.15
Consensus pattern (27 bp):
AAATGCAATACATGCAAACATAAACAA
Found at i:14211 original size:36 final size:36
Alignment explanation
Indices: 14134--14212 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 36
14124 GGCTGCGCAG
* * * * *
14134 ATGGTGCATGAGATGATGACCCGACATTTGGGGCTG
1 ATGGAGCATGAGATGATGACCCGACATGTGGCGATA
*
14170 GTGGAGCATGAGATGATGACCCGACATGTGGCGATA
1 ATGGAGCATGAGATGATGACCCGACATGTGGCGATA
14206 ATGGAGC
1 ATGGAGC
14213 TGGGGAAGGA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.16, G:0.37, T:0.22
Consensus pattern (36 bp):
ATGGAGCATGAGATGATGACCCGACATGTGGCGATA
Found at i:14292 original size:9 final size:9
Alignment explanation
Indices: 14278--14331 Score: 81
Period size: 9 Copynumber: 6.0 Consensus size: 9
14268 GATGAAGTGT
14278 GTGCAGCTG
1 GTGCAGCTG
14287 GTGCAGCTG
1 GTGCAGCTG
*
14296 GTGCAGCTA
1 GTGCAGCTG
14305 GTGCAGCTG
1 GTGCAGCTG
*
14314 GTGCAGCTA
1 GTGCAGCTG
*
14323 GTGTAGCTG
1 GTGCAGCTG
14332 ACTTACGATG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 40 1.00
ACGTcount: A:0.15, C:0.20, G:0.41, T:0.24
Consensus pattern (9 bp):
GTGCAGCTG
Found at i:14301 original size:18 final size:18
Alignment explanation
Indices: 14278--14331 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
14268 GATGAAGTGT
*
14278 GTGCAGCTGGTGCAGCTG
1 GTGCAGCTAGTGCAGCTG
14296 GTGCAGCTAGTGCAGCTG
1 GTGCAGCTAGTGCAGCTG
*
14314 GTGCAGCTAGTGTAGCTG
1 GTGCAGCTAGTGCAGCTG
14332 ACTTACGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.15, C:0.20, G:0.41, T:0.24
Consensus pattern (18 bp):
GTGCAGCTAGTGCAGCTG
Found at i:18015 original size:13 final size:13
Alignment explanation
Indices: 17999--18023 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17989 GTCTCATTTT
17999 CTTTTCTCCTTTC
1 CTTTTCTCCTTTC
18012 CTTTTCTCCTTT
1 CTTTTCTCCTTT
18024 TTGTAATACG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (13 bp):
CTTTTCTCCTTTC
Done.