Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004010.1 Kokia drynarioides strain JFW-HI SEQ_117129, 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: 9694
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Found at i:4047 original size:17 final size:17
Alignment explanation
Indices: 4027--4064 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
4017 CCGTAATTAA
4027 TATTTTTACA-TAATATT
1 TATTTTTACATTAAT-TT
*
4044 TATTTTTATATTAATTT
1 TATTTTTACATTAATTT
4061 TATT
1 TATT
4065 CCTTACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTTTTACATTAATTT
Found at i:4280 original size:33 final size:33
Alignment explanation
Indices: 4218--4281 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 33
4208 AAAAAGTTTC
* *
4218 AACATTTAATATTTTAATTATGTTTTATTAAAA
1 AACATTTAATATTTTAATTATATTATATTAAAA
4251 AACATTTAATTATGTTTAA-TA-ATTATATTAA
1 AACATTTAA-TAT-TTTAATTATATTATATTAA
4282 TTTTTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 17 0.63
34 5 0.19
35 5 0.19
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (33 bp):
AACATTTAATATTTTAATTATATTATATTAAAA
Found at i:4630 original size:15 final size:15
Alignment explanation
Indices: 4605--4665 Score: 63
Period size: 15 Copynumber: 4.1 Consensus size: 15
4595 ATAACTTAAA
*
4605 TTCAACCCTTAATTT
1 TTCAACACTTAATTT
* *
4620 TTCAATACTTATTTT
1 TTCAACACTTAATTT
*
4635 TTCAACACAT-ATTT
1 TTCAACACTTAATTT
4649 TTCAACA-TCTAATTT
1 TTCAACACT-TAATTT
4664 TT
1 TT
4666 TTAATTTATC
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
14 11 0.30
15 26 0.70
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.51
Consensus pattern (15 bp):
TTCAACACTTAATTT
Found at i:5513 original size:17 final size:18
Alignment explanation
Indices: 5475--5513 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
5465 AGGGTTAAAT
5475 TAATAATTTTAATAATGA
1 TAATAATTTTAATAATGA
*
5493 -AATAATTTTATTAAT-A
1 TAATAATTTTAATAATGA
5509 TAATA
1 TAATA
5514 TTGATAGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 1 0.05
17 18 0.95
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
TAATAATTTTAATAATGA
Found at i:6953 original size:114 final size:113
Alignment explanation
Indices: 6753--7216 Score: 479
Period size: 114 Copynumber: 4.2 Consensus size: 113
6743 ATCTGAAGTT
* * * * *
6753 ATCTCGGCTGCACAAATTTCTCCAGGAGCAG-CTGGGGGAGGGTCTCCTCAGGTTCAGCATTCTG
1 ATCTCGGCTGCCCAAATGTCACCAGGAG-GGTCT-GGGGAGGGTCTCCTCAGGCTCAGCATTCTG
* * *
6817 GACTGTTGGGCACTGCTTCTGGATTCATCAAGCAGATCTCTTCCGATGCC
64 GACTGTTGGGCACTGCCTCTGGATTCATCAAGCAGGTCTCATCCGATGCC
* * * * *
6867 ATCTCGGCTGCCCAATTGTCTCCTGGAGTGT-TCGAGGGAGGGTCTCCTCAGGCTCAGCCTTCTG
1 ATCTCGGCTGCCCAAATGTCACCAGGAGGGTCT-G-GGGAGGGTCTCCTCAGGCTCAGCATTCTG
* * *
6931 GACTGTTGGGTACTGCCTCTGGATTCATCAATCAGGTCTCATCCGATCCC
64 GACTGTTGGGCACTGCCTCTGGATTCATCAAGCAGGTCTCATCCGATGCC
* *
6981 ATCTCGGTTGCCCAAATGTCACCAGGAGGGTCTGGGGAAGGGTCTCCTCAGGCTCAGAATTCTGG
1 ATCTCGGCTGCCCAAATGTCACCAGGAGGGTCTGGGG-AGGGTCTCCTCAGGCTCAGCATTCTGG
* *
7046 ACTGTTGGGCACTGCCTCTGGGTTCATCAAGCAGGTCTCATCTGATGCC
65 ACTGTTGGGCACTGCCTCTGGATTCATCAAGCAGGTCTCATCCGATGCC
* ** * *
7095 ATCTCGACTGCCCAAA-GCTCTTCAGGA----CT------GG-CTACTCAGGCCCAGCATTCTGG
1 ATCTCGGCTGCCCAAATG-TCACCAGGAGGGTCTGGGGAGGGTCTCCTCAGGCTCAGCATTCTGG
* ** * *
7148 ACTGTTCGGTGCTGCCTCTGGATTGATCAAGCAGGTCTCATCTGATGCC
65 ACTGTTGGGCACTGCCTCTGGATTCATCAAGCAGGTCTCATCCGATGCC
* *
7197 GTCTCAGCTGCCCATAATGT
1 ATCTCGGCTGCCCA-AATGT
7217 AGCTACTGAT
Statistics
Matches: 302, Mismatches: 41, Indels: 25
0.82 0.11 0.07
Matches are distributed among these distances:
102 74 0.25
103 5 0.02
104 1 0.00
110 2 0.01
113 7 0.02
114 212 0.70
115 1 0.00
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.27
Consensus pattern (113 bp):
ATCTCGGCTGCCCAAATGTCACCAGGAGGGTCTGGGGAGGGTCTCCTCAGGCTCAGCATTCTGGA
CTGTTGGGCACTGCCTCTGGATTCATCAAGCAGGTCTCATCCGATGCC
Found at i:7208 original size:102 final size:102
Alignment explanation
Indices: 7027--7210 Score: 280
Period size: 102 Copynumber: 1.8 Consensus size: 102
7017 GAAGGGTCTC
* * *
7027 CTCAGGCTCAGAATTCTGGACTGTTGGGCACTGCCTCTGGGTTCATCAAGCAGGTCTCATCTGAT
1 CTCAGGCCCAGAATTCTGGACTGTTCGGCACTGCCTCTGGATTCATCAAGCAGGTCTCATCTGAT
7092 GCCATCTCGACTGCCCAAAGCTCTTCAGGACTGGCTA
66 GCCATCTCGACTGCCCAAAGCTCTTCAGGACTGGCTA
* ** *
7129 CTCAGGCCCAGCATTCTGGACTGTTCGGTGCTGCCTCTGGATTGATCAAGCAGGTCTCATCTGAT
1 CTCAGGCCCAGAATTCTGGACTGTTCGGCACTGCCTCTGGATTCATCAAGCAGGTCTCATCTGAT
*
7194 GCCGTCTC-AGCTGCCCA
66 GCCATCTCGA-CTGCCCA
7211 TAATGTAGCT
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 1 0.01
102 72 0.99
ACGTcount: A:0.18, C:0.30, G:0.25, T:0.27
Consensus pattern (102 bp):
CTCAGGCCCAGAATTCTGGACTGTTCGGCACTGCCTCTGGATTCATCAAGCAGGTCTCATCTGAT
GCCATCTCGACTGCCCAAAGCTCTTCAGGACTGGCTA
Done.