Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010538.1 Kokia drynarioides strain JFW-HI SEQ_125456, 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: 16092
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Warning! 38 characters in sequence are not A, C, G, or T
Found at i:2998 original size:28 final size:27
Alignment explanation
Indices: 2953--3006 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 27
2943 TTTTGAGAAA
*
2953 TCAAACATAGCCAGAGTGTATTCAAAGC
1 TCAAACATAGACAGAGTG-ATTCAAAGC
* * *
2981 TCAAACATAGAGATAGTGATTGAAAG
1 TCAAACATAGACAGAGTGATTCAAAG
3007 ATAAAACAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 7 0.32
28 15 0.68
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.22
Consensus pattern (27 bp):
TCAAACATAGACAGAGTGATTCAAAGC
Found at i:3268 original size:24 final size:21
Alignment explanation
Indices: 3216--3269 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
3206 GTTTTAGTAA
3216 ATAATTAATAAATAATAAAAT
1 ATAATTAATAAATAATAAAAT
* *
3237 AT-AGTAATAAATACCTAATAAT
1 ATAATTAATAAATA-ATAA-AAT
3259 ACTAATTAATA
1 A-TAATTAATA
3270 TTAAATAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 10 0.38
21 5 0.19
22 4 0.15
23 1 0.04
24 6 0.23
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (21 bp):
ATAATTAATAAATAATAAAAT
Found at i:4207 original size:30 final size:30
Alignment explanation
Indices: 4163--4482 Score: 236
Period size: 30 Copynumber: 10.9 Consensus size: 30
4153 CCTAGTAATG
* ** *
4163 CCCT-AAACTTTCCAAAAATCATGTTTTGA
1 CCCTAAAACTTTCCTAAAATCACATTTTAA
* *
4192 CCCTAAAAGTTTCC-AAAATTACATTTTAA
1 CCCTAAAACTTTCCTAAAATCACATTTTAA
* ** *
4221 CTCCCAAAACTTTTTTAAAATCACATTTTCA
1 C-CCTAAAACTTTCCTAAAATCACATTTTAA
* *
4252 CCCTAAAA-TTTTC-AAAATCATATTTTAA
1 CCCTAAAACTTTCCTAAAATCACATTTTAA
*
4280 CCCCTTAAACTTTCCTAAAATCACATTTTAA
1 -CCCTAAAACTTTCCTAAAATCACATTTTAA
*
4311 CCCTAAAACTTTCCTAAAATCACATTTTGA
1 CCCTAAAACTTTCCTAAAATCACATTTTAA
* * *
4341 CCCAAAAACTTTTCTAAAATTACATTTTAA
1 CCCTAAAACTTTCCTAAAATCACATTTTAA
* *
4371 CCCCT-AAAC-TTCTCTAAAATCAAAATTTAA
1 -CCCTAAAACTTTC-CTAAAATCACATTTTAA
* * * * *
4401 CCCCT-AAACCTTCCCAATATCATA-TTTGA
1 -CCCTAAAACTTTCCTAAAATCACATTTTAA
* * *
4430 CCCCAAAA-TTCTCC-AAAATCTCA-TTT-C
1 CCCTAAAACTT-TCCTAAAATCACATTTTAA
*
4457 CCCT-AAA-TTTCCAAAAATCACATTTT
1 CCCTAAAACTTTCCTAAAATCACATTTT
4483 CGATCTTAAA
Statistics
Matches: 237, Mismatches: 41, Indels: 28
0.77 0.13 0.09
Matches are distributed among these distances:
25 3 0.01
26 13 0.05
27 6 0.03
28 26 0.11
29 39 0.16
30 116 0.49
31 34 0.14
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (30 bp):
CCCTAAAACTTTCCTAAAATCACATTTTAA
Found at i:4308 original size:90 final size:90
Alignment explanation
Indices: 4163--4482 Score: 277
Period size: 89 Copynumber: 3.6 Consensus size: 90
4153 CCTAGTAATG
* * * * * * *
4163 CCCTAAACTTTCCAAAAATCATGTTTTGA-CCCTAAAAGTTTCC-AAAATTACATTTTAACTCCC
1 CCCTAAAATTTTCAAAAATCATATTTTAACCCCTTAAACTTTCCTAAAATCACATTTTAAC-CCC
**
4226 AAAACTTTTTTAAAATCACATTTTCA
65 AAAACTTTCCTAAAATCACATTTTCA
*
4252 CCCTAAAATTTTC-AAAATCATATTTTAACCCCTTAAACTTTCCTAAAATCACATTTTAACCCTA
1 CCCTAAAATTTTCAAAAATCATATTTTAACCCCTTAAACTTTCCTAAAATCACATTTTAACCCCA
*
4316 AAACTTTCCTAAAATCACATTTTGA
66 AAACTTTCCTAAAATCACATTTTCA
* * * * * *
4341 CCCAAAAACTTTTCTAAAATTACATTTTAACCCC-TAAAC-TTCTCTAAAATCAAAATTTAACCC
1 CCCTAAAA-TTTTCAAAAATCATATTTTAACCCCTTAAACTTTC-CTAAAATCACATTTTAACCC
* * * * * *
4404 CTAAACCTTCCCAATATCATA-TTTGA
64 CAAAACTTTCCTAAAATCACATTTTCA
* * * *
4430 CCCCAAAATTCTCCAAAATC-TCA-TTT--CCCC-TAAA-TTTCCAAAAATCACATTTT
1 CCCTAAAATTTTCAAAAATCAT-ATTTTAACCCCTTAAACTTTCCTAAAATCACATTTT
4483 CGATCTTAAA
Statistics
Matches: 194, Mismatches: 30, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
84 12 0.06
85 11 0.06
87 3 0.02
88 23 0.12
89 70 0.36
90 58 0.30
91 17 0.09
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (90 bp):
CCCTAAAATTTTCAAAAATCATATTTTAACCCCTTAAACTTTCCTAAAATCACATTTTAACCCCA
AAACTTTCCTAAAATCACATTTTCA
Found at i:4464 original size:26 final size:26
Alignment explanation
Indices: 4430--4481 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
4420 TCATATTTGA
*
4430 CCCCAAAATTCTCC-AAAATCTCATTT
1 CCCCAAAATT-TCCAAAAATCACATTT
*
4456 CCCCTAAATTTCCAAAAATCACATTT
1 CCCCAAAATTTCCAAAAATCACATTT
4482 TCGATCTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 3 0.13
26 20 0.87
ACGTcount: A:0.37, C:0.33, G:0.00, T:0.31
Consensus pattern (26 bp):
CCCCAAAATTTCCAAAAATCACATTT
Found at i:8725 original size:24 final size:24
Alignment explanation
Indices: 8698--8751 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
8688 GATGCAGTAT
*
8698 CAAATGCAGGAGCAATTACAGGAA
1 CAAATGCAAGAGCAATTACAGGAA
* *
8722 CAAATGCAAGAGCAGTTGCAGGAA
1 CAAATGCAAGAGCAATTACAGGAA
8746 CAAATG
1 CAAATG
8752 ACGATGATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.44, C:0.17, G:0.26, T:0.13
Consensus pattern (24 bp):
CAAATGCAAGAGCAATTACAGGAA
Found at i:15981 original size:39 final size:39
Alignment explanation
Indices: 15912--16086 Score: 151
Period size: 39 Copynumber: 4.5 Consensus size: 39
15902 ACTATCACTC
* * *
15912 AATCTCTTACCCCGAGCTTGAGGCAAATTGCAGCCATCT
1 AATCTCTTACCCCGAGCCTAAGGCAGATTGCAGCCATCT
* * * * *
15951 AATCTTTTACCCCGAGCCTAGGGTAGATTGCAGTCATCC
1 AATCTCTTACCCCGAGCCTAAGGCAGATTGCAGCCATCT
* ** *
15990 GATCTCTTACCCTAAGCCTAAGGTAGA-T-CA-CCATCAGT
1 AATCTCTTACCCCGAGCCTAAGGCAGATTGCAGCCATC--T
*
16028 CAATCTCTTACCCCGAGCCTAAGGCAGATTACAGCCAT-T
1 -AATCTCTTACCCCGAGCCTAAGGCAGATTGCAGCCATCT
* *
16067 CGATCTCTTACCCTGAGCCT
1 -AATCTCTTACCCCGAGCCT
16087 TCGGCA
Statistics
Matches: 109, Mismatches: 21, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
36 4 0.04
37 2 0.02
38 1 0.01
39 95 0.87
40 1 0.01
41 2 0.02
42 4 0.04
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.26
Consensus pattern (39 bp):
AATCTCTTACCCCGAGCCTAAGGCAGATTGCAGCCATCT
Done.