Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012052.1 Kokia drynarioides strain JFW-HI SEQ_127050, 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: 25885
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:1423 original size:22 final size:22
Alignment explanation
Indices: 1389--1442 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1379 GAAAATGATA
* *
1389 ATAATC-CATAAATGAAATAAG
1 ATAATCACAAAAATAAAATAAG
1410 ATAATCACAAAAATAAAATAAG
1 ATAATCACAAAAATAAAATAAG
*
1432 ATAATTACAAA
1 ATAATCACAAA
1443 TCAAAGTAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.63, C:0.09, G:0.06, T:0.22
Consensus pattern (22 bp):
ATAATCACAAAAATAAAATAAG
Found at i:2232 original size:62 final size:62
Alignment explanation
Indices: 2132--2247 Score: 155
Period size: 62 Copynumber: 1.9 Consensus size: 62
2122 ACACTTTATA
* *
2132 TTTGTATTCATTTTGATTTAGATATAAAAGAGATAAAAAAACATAGTAAAATAGAGAAATAG
1 TTTGTATTCATTCTAATTTAGATATAAAAGAGATAAAAAAACATAGTAAAATAGAGAAATAG
* * * *
2194 TTTGTATTTATTCTAATTTATATATAAGAA-A-ATAAAAAAATATAGTAAGATAGA
1 TTTGTATTCATTCTAATTTAGATATAA-AAGAGATAAAAAAACATAGTAAAATAGA
2248 TAGATAAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
61 21 0.45
62 24 0.51
63 2 0.04
ACGTcount: A:0.50, C:0.03, G:0.12, T:0.35
Consensus pattern (62 bp):
TTTGTATTCATTCTAATTTAGATATAAAAGAGATAAAAAAACATAGTAAAATAGAGAAATAG
Found at i:2676 original size:22 final size:20
Alignment explanation
Indices: 2639--2682 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
2629 TTAATTTTTG
*
2639 TTGACATAAAAAAAATTAAT
1 TTGACATAAAAAAAATAAAT
2659 TTGACAGTAAAAATAAATAAAT
1 TTGACA-TAAAAA-AAATAAAT
2681 TT
1 TT
2683 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.29
21 6 0.29
22 9 0.43
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
TTGACATAAAAAAAATAAAT
Found at i:4138 original size:3 final size:3
Alignment explanation
Indices: 4132--4156 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4122 ACACCAACAA
4132 CAG CAG CAG CAG CAG CAG CAG CAG C
1 CAG CAG CAG CAG CAG CAG CAG CAG C
4157 TTAGACAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.32, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:6392 original size:112 final size:112
Alignment explanation
Indices: 6246--6470 Score: 450
Period size: 112 Copynumber: 2.0 Consensus size: 112
6236 CTTTTGTATA
6246 TTTGAAGTCCTCGTACTTTTATTTTTAAAAATTTTAATTTTTTTAACTTTTGAATTTAAAAATTT
1 TTTGAAGTCCTCGTACTTTTATTTTTAAAAATTTTAATTTTTTTAACTTTTGAATTTAAAAATTT
6311 GGGTTCGGATATTAATATACTTAGAATTCTTTTCTTAAATTAATTGG
66 GGGTTCGGATATTAATATACTTAGAATTCTTTTCTTAAATTAATTGG
6358 TTTGAAGTCCTCGTACTTTTATTTTTAAAAATTTTAATTTTTTTAACTTTTGAATTTAAAAATTT
1 TTTGAAGTCCTCGTACTTTTATTTTTAAAAATTTTAATTTTTTTAACTTTTGAATTTAAAAATTT
6423 GGGTTCGGATATTAATATACTTAGAATTCTTTTCTTAAATTAATTGG
66 GGGTTCGGATATTAATATACTTAGAATTCTTTTCTTAAATTAATTGG
6470 T
1 T
6471 ATGATACTCT
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 113 1.00
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.51
Consensus pattern (112 bp):
TTTGAAGTCCTCGTACTTTTATTTTTAAAAATTTTAATTTTTTTAACTTTTGAATTTAAAAATTT
GGGTTCGGATATTAATATACTTAGAATTCTTTTCTTAAATTAATTGG
Found at i:6500 original size:112 final size:112
Alignment explanation
Indices: 6272--6500 Score: 336
Period size: 112 Copynumber: 2.0 Consensus size: 112
6262 TTTTATTTTT
6272 AAAAATTTTAATTTTTTTAACTTTTGAATTTAAAAATTTGGGTTCGGATATTAATATACTTAGAA
1 AAAAATTTTAATTTTTTTAACTTTTGAATTTAAAAATTTGGGTTCGGATATTAATATACTTAGAA
* * * * ** *** *
6337 TTCTTTTCTTAAATTAATTGGTTTGAAGTCCTCGTACTTTTATTTTT
66 TTCTTTTCTTAAATTAATTGGTATGAACTCCTCGAAATTAAAAAATA
6384 AAAAATTTTAATTTTTTTAACTTTTGAATTTAAAAATTTGGGTTCGGATATTAATATACTTAGAA
1 AAAAATTTTAATTTTTTTAACTTTTGAATTTAAAAATTTGGGTTCGGATATTAATATACTTAGAA
6449 TTCTTTTCTTAAATTAATTGGTATGATACT-CT-GAAAATTAAAAAATA
66 TTCTTTTCTTAAATTAATTGGTATGA-ACTCCTCG-AAATTAAAAAATA
6496 AAAAA
1 AAAAA
6501 ACCTCGCTTA
Statistics
Matches: 105, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
111 1 0.01
112 102 0.97
113 2 0.02
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.47
Consensus pattern (112 bp):
AAAAATTTTAATTTTTTTAACTTTTGAATTTAAAAATTTGGGTTCGGATATTAATATACTTAGAA
TTCTTTTCTTAAATTAATTGGTATGAACTCCTCGAAATTAAAAAATA
Found at i:11846 original size:4 final size:4
Alignment explanation
Indices: 11837--11862 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
11827 GAGATCCTAA
11837 ATCT ATCT ATCT ATCT ATCT ATCT AT
1 ATCT ATCT ATCT ATCT ATCT ATCT AT
11863 GTATATATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (4 bp):
ATCT
Found at i:15574 original size:3 final size:3
Alignment explanation
Indices: 15566--15593 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
15556 GGGCACAAAC
15566 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
15594 GTTCTGTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:16045 original size:173 final size:169
Alignment explanation
Indices: 15756--16101 Score: 500
Period size: 173 Copynumber: 2.0 Consensus size: 169
15746 GGCCTATATC
* * * *
15756 AACTGATGATGGTGAAACCAAATTGGGTTGGTTCGGTTGGCTCGTGTTCACTAGCGTCTTGGTAA
1 AACTGATGATGGTGAAACCAAATTAGGTTGATTCAGTTGGCTCGTGTTCACTAGCGTCTTGGCAA
* * * *
15821 GCGACGCGGTTCGAATCTTGCTAGTATGTTTATTTGGTGGGTGATCTATATGATCATAAATCAAT
66 GCAACGCGGTTCGAATCTTGCTAGCATGCTTATTTGGTGGGTGACCTATATGATCAT--A--AAT
*
15886 CACACTTTGATTTAAAAAGGGTT-ATATCATTATTTAGGGCTTG
127 CACACTTTGATTTAAAAAGGATTGA-ATCATTATTTAGGGCTTG
* *
15929 AACTGATG-TGGGTGAAACCAACTTAGGTTGATTCAGTTGGCTCGTGTTCATTAGCGTCTTGGCA
1 AACTGATGAT-GGTGAAACCAAATTAGGTTGATTCAGTTGGCTCGTGTTCACTAGCGTCTTGGCA
*
15993 AGCAACGCGGTTCGAATCTTGCTAGCACT-CTTATTTGGTGGGTGACCTATATGATCATAAGTCA
65 AGCAACGCGGTTCGAATCTTGCTAGCA-TGCTTATTTGGTGGGTGACCTATATGATCATAAATCA
16057 CACTTTGATTTAAAAAGGATTGAATCATTATTTAGGGCTTG
129 CACTTTGATTTAAAAAGGATTGAATCATTATTTAGGGCTTG
16098 AACT
1 AACT
16102 TGGTAATAAC
Statistics
Matches: 158, Mismatches: 12, Indels: 10
0.88 0.07 0.06
Matches are distributed among these distances:
169 46 0.29
170 1 0.01
171 1 0.01
172 1 0.01
173 108 0.68
174 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (169 bp):
AACTGATGATGGTGAAACCAAATTAGGTTGATTCAGTTGGCTCGTGTTCACTAGCGTCTTGGCAA
GCAACGCGGTTCGAATCTTGCTAGCATGCTTATTTGGTGGGTGACCTATATGATCATAAATCACA
CTTTGATTTAAAAAGGATTGAATCATTATTTAGGGCTTG
Found at i:19242 original size:16 final size:16
Alignment explanation
Indices: 19197--19248 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
19187 GTGCATATAT
*
19197 ATTTCGATTATCAATTG
1 ATTTTGATTAT-AATTG
*
19214 TATTTT-ATAATAATTG
1 -ATTTTGATTATAATTG
19230 ATTTTGATTATAATT-
1 ATTTTGATTATAATTG
19245 ATTT
1 ATTT
19249 GTAATTGCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 9 0.30
16 13 0.43
17 4 0.13
18 4 0.13
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.56
Consensus pattern (16 bp):
ATTTTGATTATAATTG
Found at i:19891 original size:5 final size:5
Alignment explanation
Indices: 19876--19904 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
19866 TTTAAAAATA
19876 GTTTT -TTTT GTTTT GTTTT GTTTT GTTTT
1 GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT
19905 TCTTATCCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (5 bp):
GTTTT
Found at i:23025 original size:29 final size:30
Alignment explanation
Indices: 22986--23049 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
22976 TTAATTTATT
* * *
22986 AAATTAAATT-ATGACACATATATTTATAA
1 AAATAAAATTAATAACAAATATATTTATAA
*
23015 AAATAAAATTACATAATAAATATATTTATAA
1 AAATAAAATTA-ATAACAAATATATTTATAA
23046 AAAT
1 AAAT
23050 TTAAATGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 9 0.31
31 20 0.69
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.36
Consensus pattern (30 bp):
AAATAAAATTAATAACAAATATATTTATAA
Found at i:23157 original size:18 final size:21
Alignment explanation
Indices: 23122--23165 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
23112 TAAATACTCT
23122 TAAAATAATATATTTATTTT-A
1 TAAAATAATATA-TTATTTTAA
23143 TAAAATAATA-A-TATTTTAA
1 TAAAATAATATATTATTTTAA
23162 TAAA
1 TAAA
23166 TATCTAACTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.27
19 5 0.23
20 1 0.05
21 10 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAAATAATATATTATTTTAA
Found at i:24633 original size:25 final size:22
Alignment explanation
Indices: 24566--24636 Score: 74
Period size: 24 Copynumber: 3.1 Consensus size: 22
24556 TAACCCTTAA
24566 AAAATAATAAAAATATAAACTATT
1 AAAATAATAAAAATATAAA-T-TT
24590 AAAATAAT-AAAAT-TAAATTT
1 AAAATAATAAAAATATAAATTT
*
24610 ATATTATAATAAAAATATATAATTT
1 A-A-AATAATAAAAATATA-AATTT
24635 AA
1 AA
24637 TACTGACCCC
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
20 3 0.07
21 2 0.05
22 9 0.22
23 10 0.24
24 11 0.27
25 6 0.15
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAATAATAAAAATATAAATTT
Done.