Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014919.1 Kokia drynarioides strain JFW-HI SEQ_129962, 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: 7000
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Warning! 47 characters in sequence are not A, C, G, or T
Found at i:141 original size:30 final size:30
Alignment explanation
Indices: 103--252 Score: 141
Period size: 30 Copynumber: 5.0 Consensus size: 30
93 CAAACATTCG
103 GGGGTAAAAGGGTAATTTTTGGAAGGTTCA
1 GGGGTAAAAGGGTAATTTTTGGAAGGTTCA
*
133 GGGTTAAAAATGGG--ATTTTTGGAA-GTTCA
1 GGGGT-AAAA-GGGTAATTTTTGGAAGGTTCA
* *
162 GGGGGTAAAATGGTAATTTTAGGAAGGTTC-
1 -GGGGTAAAAGGGTAATTTTTGGAAGGTTCA
* *
192 GGGGTAAAAAAATGGG-ACTTTTTGGAA-GTTCG
1 GGGGT---AAAA-GGGTAATTTTTGGAAGGTTCA
*
224 GGGGTAAAATGGTAATTTTTGGAAGGTTC
1 GGGGTAAAAGGGTAATTTTTGGAAGGTTC
253 GAAGTCAAAA
Statistics
Matches: 98, Mismatches: 9, Indels: 26
0.74 0.07 0.20
Matches are distributed among these distances:
28 4 0.04
29 28 0.29
30 31 0.32
31 12 0.12
32 21 0.21
33 2 0.02
ACGTcount: A:0.30, C:0.04, G:0.35, T:0.31
Consensus pattern (30 bp):
GGGGTAAAAGGGTAATTTTTGGAAGGTTCA
Found at i:151 original size:29 final size:30
Alignment explanation
Indices: 117--278 Score: 136
Period size: 30 Copynumber: 5.4 Consensus size: 30
107 TAAAAGGGTA
117 ATTTTTGGAAGGTTCAGGGTTAAAAATGGG
1 ATTTTTGGAAGGTTCAGGGTTAAAAATGGG
* *
147 ATTTTTGGAA-GTTCAGGGGGT-AAAATGGTA
1 ATTTTTGGAAGGTTCA-GGGTTAAAAATGG-G
* * *
177 ATTTTAGGAAGGTTCGGGGTAAAAAAATGGG
1 ATTTTTGGAAGGTTCAGGGT-TAAAAATGGG
* * *
208 ACTTTTTGGAA-GTTCGGGGGT-AAAATGGTA
1 A-TTTTTGGAAGGTTCAGGGTTAAAAATGG-G
* *
238 ATTTTTGGAAGGTTC-GAAGTCAAAAATGGG
1 ATTTTTGGAAGGTTCAG-GGTTAAAAATGGG
*
268 ATTTCTGGAAG
1 ATTTTTGGAAG
279 TTTGGGGGTA
Statistics
Matches: 106, Mismatches: 16, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
29 29 0.27
30 42 0.40
31 20 0.19
32 15 0.14
ACGTcount: A:0.31, C:0.05, G:0.33, T:0.31
Consensus pattern (30 bp):
ATTTTTGGAAGGTTCAGGGTTAAAAATGGG
Found at i:166 original size:60 final size:58
Alignment explanation
Indices: 99--305 Score: 297
Period size: 60 Copynumber: 3.5 Consensus size: 58
89 ATTTCAAACA
* *
99 TTCGGGGGTAAAAGGGTAATTTTTGGAAGGTTCAGGGTTAAAAATGGGATTTTTGGAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTC-GGGTAAAAAATGGGATTTTTGGAAG
*
158 TTCAGGGGGTAAAATGGTAATTTTAGGAAGGTTCGGGGTAAAAAAATGGGACTTTTTGGAAG
1 TTC-GGGGGTAAAATGGTAATTTTTGGAAGGTTC-GGGT-AAAAAATGGGA-TTTTTGGAAG
* * *
220 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGAAGTCAAAAATGGGATTTCTGGAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCG-GGTAAAAAATGGGATTTTTGGAAG
*
279 TTTGGGGGTAAAATGGTAATTTTTGGA
1 TTCGGGGGTAAAATGGTAATTTTTGGA
306 TAGTTTAGGG
Statistics
Matches: 135, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
59 38 0.28
60 43 0.32
61 41 0.30
62 13 0.10
ACGTcount: A:0.30, C:0.04, G:0.34, T:0.32
Consensus pattern (58 bp):
TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGTAAAAAATGGGATTTTTGGAAG
Found at i:710 original size:12 final size:12
Alignment explanation
Indices: 695--724 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
685 CTAAGTCGGA
695 TCGGGTCGGATT
1 TCGGGTCGGATT
707 TCGGGTCGGATT
1 TCGGGTCGGATT
719 TCGGGT
1 TCGGGT
725 AATAGCTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.07, C:0.17, G:0.43, T:0.33
Consensus pattern (12 bp):
TCGGGTCGGATT
Found at i:3409 original size:61 final size:60
Alignment explanation
Indices: 3368--3566 Score: 262
Period size: 60 Copynumber: 3.3 Consensus size: 60
3358 ATTTCAAACA
*
3368 TTCGGGGGTAAAAGGGTAATTTTTGGAAGGTTCAGGGTT--AAAAATGGGATTTTTGGAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTC-GGGTTAAAAAAATGGGATTTTTGGAAG
* * *
3427 TTCAGGGGATAAAATGGTAATTTTAGGAAGGTTCGGGGTAAAAAAATGGGACTTTTTGGAAG
1 TTC-GGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGTTAAAAAAATGGGA-TTTTTGGAAG
* *
3489 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGAAG-T-CAAAAATGGGATTTTTGGAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCG-GGTTAAAAAAATGGGATTTTTGGAAG
*
3548 TTTGGGGGGTAAAATGGTA
1 -TTCGGGGGTAAAATGGTA
3567 CATATGTTAT
Statistics
Matches: 125, Mismatches: 9, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
59 17 0.14
60 54 0.43
61 40 0.32
62 14 0.11
ACGTcount: A:0.31, C:0.04, G:0.34, T:0.31
Consensus pattern (60 bp):
TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGTTAAAAAAATGGGATTTTTGGAAG
Found at i:3420 original size:29 final size:30
Alignment explanation
Indices: 3386--3547 Score: 145
Period size: 30 Copynumber: 5.4 Consensus size: 30
3376 TAAAAGGGTA
3386 ATTTTTGGAAGGTTCAGGGTTAAAAATGGG
1 ATTTTTGGAAGGTTCAGGGTTAAAAATGGG
* *
3416 ATTTTTGGAA-GTTCAGGG-GATAAAATGGTA
1 ATTTTTGGAAGGTTCAGGGTTA-AAAATGG-G
* * *
3446 ATTTTAGGAAGGTTCGGGGTAAAAAAATGGG
1 ATTTTTGGAAGGTTCAGGGT-TAAAAATGGG
* * *
3477 ACTTTTTGGAA-GTTCGGGGGT-AAAATGGTA
1 A-TTTTTGGAAGGTTCAGGGTTAAAAATGG-G
* *
3507 ATTTTTGGAAGGTTC-GAAGTCAAAAATGGG
1 ATTTTTGGAAGGTTCAG-GGTTAAAAATGGG
3537 ATTTTTGGAAG
1 ATTTTTGGAAG
3548 TTTGGGGGGT
Statistics
Matches: 108, Mismatches: 14, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
28 1 0.01
29 32 0.30
30 36 0.33
31 23 0.21
32 15 0.14
33 1 0.01
ACGTcount: A:0.31, C:0.04, G:0.32, T:0.32
Consensus pattern (30 bp):
ATTTTTGGAAGGTTCAGGGTTAAAAATGGG
Found at i:6503 original size:17 final size:17
Alignment explanation
Indices: 6478--6558 Score: 90
Period size: 17 Copynumber: 4.6 Consensus size: 17
6468 TAAATAGATT
*
6478 TAAACTTTAAATTTATAA
1 TAAA-TTTAAATTTAAAA
* *
6496 TAAATTTAAATTTTTAAG
1 TAAATTTAAA-TTTAAAA
*
6514 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
6531 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
*
6548 TGAATTTAAAT
1 TAAATTTAAAT
6559 CCTGTTGGGC
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
17 34 0.65
18 18 0.35
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:6533 original size:35 final size:34
Alignment explanation
Indices: 6478--6557 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 34
6468 TAAATAGATT
* * * *
6478 TAAACTTTAAATTTATAATAAATTTAAATTTTTAAG
1 TAAA-TTTAAACTTAAAATAAATTT-AATTTTAAAA
6514 TAAATTTAAACTTAAAATAAATTTAATTTTAAAA
1 TAAATTTAAACTTAAAATAAATTTAATTTTAAAA
*
6548 TGAATTTAAA
1 TAAATTTAAA
6558 TCCTGTTGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 17 0.44
35 18 0.46
36 4 0.10
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (34 bp):
TAAATTTAAACTTAAAATAAATTTAATTTTAAAA
Done.