Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013739.1 Kokia drynarioides strain JFW-HI SEQ_128767, 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: 11812
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:150 original size:14 final size:14
Alignment explanation
Indices: 131--164 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
121 AACCCAAAAC
131 CAAAATAATAATAA
1 CAAAATAATAATAA
145 CAAAATAATAATAA
1 CAAAATAATAATAA
*
159 TAAAAT
1 CAAAAT
165 GATGTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (14 bp):
CAAAATAATAATAA
Found at i:1267 original size:7 final size:7
Alignment explanation
Indices: 1257--1286 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1247 AGTCAANNNN
1257 TCAACGG
1 TCAACGG
*
1264 TCAACGA
1 TCAACGG
1271 TCAACGG
1 TCAACGG
1278 TCAACGG
1 TCAACGG
1285 TC
1 TC
1287 GGTCAACGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.17
Consensus pattern (7 bp):
TCAACGG
Found at i:3040 original size:26 final size:26
Alignment explanation
Indices: 2997--3048 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
2987 ATTCTGGGTG
*
2997 CAATTCTGGACACGTTCATGCAGCGA
1 CAATTCTGGACACATTCATGCAGCGA
* *
3023 CAATTCTGTACATATTCATGCAGCGA
1 CAATTCTGGACACATTCATGCAGCGA
3049 TATTCCTGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (26 bp):
CAATTCTGGACACATTCATGCAGCGA
Found at i:4058 original size:23 final size:23
Alignment explanation
Indices: 4026--4069 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
4016 ACTACCATTT
4026 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
4049 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
4070 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:4062 original size:13 final size:11
Alignment explanation
Indices: 4030--4072 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
4020 CCATTTTCTA
*
4030 AATAAAATAAT
1 AATAAAATATT
4041 AAT-AAATATCT
1 AATAAAATAT-T
4052 AAGTAAAATATT
1 AA-TAAAATATT
4064 AATAAAATA
1 AATAAAATA
4073 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:4453 original size:3 final size:3
Alignment explanation
Indices: 4445--4489 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
4435 CTACTTCTTA
4445 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4490 TATTTTACAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5684 original size:21 final size:21
Alignment explanation
Indices: 5658--5700 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
5648 CTTAATAAAT
*
5658 GAACATAAATGAACGTTATAC
1 GAACATAAACGAACGTTATAC
5679 GAACATAAACGAACGTTATAC
1 GAACATAAACGAACGTTATAC
5700 G
1 G
5701 TTCTGTTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (21 bp):
GAACATAAACGAACGTTATAC
Found at i:5790 original size:24 final size:24
Alignment explanation
Indices: 5762--5823 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 24
5752 AGAAATAATC
5762 TTTCAGTTAAACTCTATTTATTTG
1 TTTCAGTTAAACTCTATTTATTTG
* *
5786 TTTCAATTAAACT-TGTTTATTTG
1 TTTCAGTTAAACTCTATTTATTTG
* *
5809 TTTTAGTCAAACTCT
1 TTTCAGTTAAACTCT
5824 TATTAGTCTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 19 0.59
24 13 0.41
ACGTcount: A:0.26, C:0.13, G:0.08, T:0.53
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTATTTG
Done.