Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000415.1 Kokia drynarioides strain JFW-HI SEQ_111242, 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: 15572
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:5980 original size:56 final size:56
Alignment explanation
Indices: 5917--6024 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
5907 GGTACAGGAA
* * * *
5917 ACACACGGGCTGGGCACACAGGTGTGTGCCAGACCGTGTGTGTATACTGTTTAGTG
1 ACACACGGGCTGGGCACACAGGCGTGTGCCAAACCGTGTGTGCATACCGTTTAGTG
* * *
5973 ACACACGGGTTGGGCACACGGGCGTGTGTCAAACCGTGTGTGCATACCGTTT
1 ACACACGGGCTGGGCACACAGGCGTGTGCCAAACCGTGTGTGCATACCGTTT
6025 TGGGAATTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
56 45 1.00
ACGTcount: A:0.19, C:0.23, G:0.33, T:0.24
Consensus pattern (56 bp):
ACACACGGGCTGGGCACACAGGCGTGTGCCAAACCGTGTGTGCATACCGTTTAGTG
Found at i:6589 original size:40 final size:40
Alignment explanation
Indices: 6529--6637 Score: 148
Period size: 40 Copynumber: 2.7 Consensus size: 40
6519 ATATTTATTG
*
6529 AACTAGCAGTGACACTGTAAACACTG-AAAAATTACAACTA
1 AACTGGCAGTGACACTGTAAACACTGCAAAAA-TACAACTA
* *
6569 AACTGGCAGTGACACTGTAAACACTGCAAGAATACCACTA
1 AACTGGCAGTGACACTGTAAACACTGCAAAAATACAACTA
* * *
6609 AACTGGCAATGAAACTATAAACACTGCAA
1 AACTGGCAGTGACACTGTAAACACTGCAA
6638 TGTGTTAGAT
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
40 58 0.94
41 4 0.06
ACGTcount: A:0.45, C:0.22, G:0.15, T:0.18
Consensus pattern (40 bp):
AACTGGCAGTGACACTGTAAACACTGCAAAAATACAACTA
Found at i:10325 original size:24 final size:24
Alignment explanation
Indices: 10245--10313 Score: 120
Period size: 24 Copynumber: 2.9 Consensus size: 24
10235 TAATCTTTAG
* *
10245 TTAAACTCTGTTTAATTGTTTCAA
1 TTAAACTCTATTTATTTGTTTCAA
10269 TTAAACTCTATTTATTTGTTTCAA
1 TTAAACTCTATTTATTTGTTTCAA
10293 TTAAACTCTATTTATTTGTTT
1 TTAAACTCTATTTATTTGTTT
10314 GAGTCAAACT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.28, C:0.12, G:0.06, T:0.55
Consensus pattern (24 bp):
TTAAACTCTATTTATTTGTTTCAA
Found at i:10332 original size:24 final size:24
Alignment explanation
Indices: 10247--10325 Score: 104
Period size: 24 Copynumber: 3.3 Consensus size: 24
10237 ATCTTTAGTT
* * *
10247 AAACTCTGTTTAATTGTTTCAATT
1 AAACTCTATTTATTTGTTTCAATC
*
10271 AAACTCTATTTATTTGTTTCAATT
1 AAACTCTATTTATTTGTTTCAATC
* *
10295 AAACTCTATTTATTTGTTTGAGTC
1 AAACTCTATTTATTTGTTTCAATC
10319 AAACTCT
1 AAACTCT
10326 TATTATTCTA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (24 bp):
AAACTCTATTTATTTGTTTCAATC
Found at i:12293 original size:24 final size:24
Alignment explanation
Indices: 12207--12281 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
12197 AGAAATAATC
* * *
12207 TTTCAGTTAAACTCTGTTTAATTA
1 TTTCAATTAAACTCTGTTTATTTG
* *
12231 TTTCAATTAAACTCTATTTGTTTG
1 TTTCAATTAAACTCTGTTTATTTG
12255 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
12279 TTT
1 TTT
12282 GAGTCAAACT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:13392 original size:17 final size:17
Alignment explanation
Indices: 13372--13507 Score: 71
Period size: 17 Copynumber: 8.3 Consensus size: 17
13362 TATTTTCCAT
13372 TAAAAATTATTAAAAAA
1 TAAAAATTATTAAAAAA
13389 TAAAAA--A-TAAAAAA
1 TAAAAATTATTAAAAAA
*
13403 TATAAAAATA-TAAAAATTA
1 TA-AAAATTATTAAAAA--A
* *
13422 TAAAAATTATTAAATAT
1 TAAAAATTATTAAAAAA
* *
13439 TAAAAAATATT-ACAAA
1 TAAAAATTATTAAAAAA
*
13455 TATGAAA-T-TT--AAAA
1 TA-AAAATTATTAAAAAA
13469 T-AAAATT-TTAAAAAA
1 TAAAAATTATTAAAAAA
13484 TATAAATATTA-TAAAAATA
1 TA-AAA-ATTATTAAAAA-A
13503 TAAAA
1 TAAAA
13508 GAATCTAATA
Statistics
Matches: 94, Mismatches: 10, Indels: 29
0.71 0.08 0.22
Matches are distributed among these distances:
12 3 0.03
13 3 0.03
14 13 0.14
15 12 0.13
16 5 0.05
17 29 0.31
18 18 0.19
19 11 0.12
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.31
Consensus pattern (17 bp):
TAAAAATTATTAAAAAA
Found at i:13400 original size:6 final size:7
Alignment explanation
Indices: 13382--13419 Score: 58
Period size: 7 Copynumber: 5.1 Consensus size: 7
13372 TAAAAATTAT
13382 TAAAAAA
1 TAAAAAA
13389 TAAAAAA
1 TAAAAAA
13396 TAAAAAA
1 TAAAAAA
13403 TATAAAAA
1 TA-AAAAA
13411 TATAAAAA
1 TA-AAAAA
13419 T
1 T
13420 TATAAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 16 0.53
8 14 0.47
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAAAAA
Found at i:13424 original size:26 final size:26
Alignment explanation
Indices: 13383--13537 Score: 84
Period size: 26 Copynumber: 5.7 Consensus size: 26
13373 AAAAATTATT
*
13383 AAAAAATAAAAA-ATAAAAAATAT-A
1 AAAATATAAAAATATAAAAAATATAA
* *
13407 AAAATATAAAAATTATAAAAATTATTA
1 AAAATATAAAAA-TATAAAAAATATAA
* * *
13434 AATAT-TAAAAAATATTACAAATATGAA
1 AAAATAT-AAAAATATAAAAAATAT-AA
* *
13461 ATTTAAA-ATAAAATTTTAAAAAATATAA
1 A---AAATATAAAAATATAAAAAATATAA
* * *
13489 ATATTATAAAAATATAAAAGAATCTAA
1 AAAATATAAAAATATAAAA-AATATAA
*
13516 TAAATTATAAAAGATTATAAAA
1 -AAAATATAAAA-A-TATAAAA
13538 TTAATAAAAC
Statistics
Matches: 99, Mismatches: 18, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
24 11 0.11
25 1 0.01
26 32 0.32
27 18 0.18
28 13 0.13
29 14 0.14
30 10 0.10
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (26 bp):
AAAATATAAAAATATAAAAAATATAA
Found at i:13534 original size:10 final size:9
Alignment explanation
Indices: 13372--13546 Score: 100
Period size: 9 Copynumber: 19.6 Consensus size: 9
13362 TATTTTCCAT
13372 TAAAAATTA
1 TAAAAATTA
13381 TTAAAAA--A
1 -TAAAAATTA
13389 TAAAAA--A
1 TAAAAATTA
*
13396 TAAAAAATA
1 TAAAAATTA
13405 TAAAAA-TA
1 TAAAAATTA
13413 TAAAAATTA
1 TAAAAATTA
13422 TAAAAATTA
1 TAAAAATTA
*
13431 TTAAATATTA
1 -TAAAAATTA
13441 -AAAAA-TA
1 TAAAAATTA
*
13448 TTACAAA-TA
1 -TAAAAATTA
* *
13457 TGAAATTTAA
1 TAAAAATT-A
* *
13467 AATAAAATTT
1 TA-AAAATTA
*
13477 TAAAAAATA
1 TAAAAATTA
*
13486 TAAATATTA
1 TAAAAATTA
13495 TAAAAA-TA
1 TAAAAATTA
* *
13503 TAAAAGAATC
1 TAAAA-ATTA
13513 TAATAAATTA
1 TAA-AAATTA
13523 TAAAAGATTA
1 TAAAA-ATTA
13533 T-AAAATTAA
1 TAAAAATT-A
13542 TAAAA
1 TAAAA
13547 CATATTTAAA
Statistics
Matches: 131, Mismatches: 19, Indels: 30
0.73 0.11 0.17
Matches are distributed among these distances:
7 15 0.11
8 26 0.20
9 50 0.38
10 33 0.25
11 7 0.05
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (9 bp):
TAAAAATTA
Found at i:13587 original size:20 final size:20
Alignment explanation
Indices: 13533--13587 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
13523 TAAAAGATTA
* *
13533 TAAAATTAATAAAACATATT
1 TAAAATTTATAAAACACATT
*
13553 TAAAATTTACCAAAACACA-T
1 TAAAATTTA-TAAAACACATT
13573 TAAAATTCTATAAAA
1 TAAAATT-TATAAAA
13588 ATCATAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 20 0.69
21 9 0.31
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAAATTTATAAAACACATT
Found at i:13803 original size:9 final size:9
Alignment explanation
Indices: 13789--13821 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
13779 AATAGAATTG
13789 ATTTTTTTA
1 ATTTTTTTA
*
13798 ATTTTTTTG
1 ATTTTTTTA
13807 A-TTTTTTA
1 ATTTTTTTA
13815 ATTTTTT
1 ATTTTTT
13822 ATTTAATTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (9 bp):
ATTTTTTTA
Found at i:13813 original size:17 final size:18
Alignment explanation
Indices: 13786--13821 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
13776 AACAATAGAA
13786 TTGATTTTTTTAATTTTT
1 TTGATTTTTTTAATTTTT
13804 TTGA-TTTTTTAATTTTT
1 TTGATTTTTTTAATTTTT
13821 T
1 T
13822 ATTTAATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.78
Consensus pattern (18 bp):
TTGATTTTTTTAATTTTT
Found at i:14107 original size:18 final size:20
Alignment explanation
Indices: 14076--14118 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
14066 GTTTAGTTCA
* *
14076 AATTTTTCTGATTTTTTAT-
1 AATTTTTCTAATTTTATATC
14095 AATTTTT-TAATTTTATATC
1 AATTTTTCTAATTTTATATC
14114 AATTT
1 AATTT
14119 AATATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (20 bp):
AATTTTTCTAATTTTATATC
Found at i:14238 original size:19 final size:19
Alignment explanation
Indices: 14216--14264 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
14206 ATTTATTAGA
14216 ATTTTTATA-TTTTTATAAT
1 ATTTTTA-AGTTTTTATAAT
*
14235 ATTTATAAGTTTTTATAAT
1 ATTTTTAAGTTTTTATAAT
14254 -TTTTATAAGTT
1 ATTTT-TAAGTT
14265 AGTGTGAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (19 bp):
ATTTTTAAGTTTTTATAAT
Found at i:14241 original size:17 final size:18
Alignment explanation
Indices: 14219--14260 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
14209 TATTAGAATT
14219 TTTATA-TTTTTATAATA
1 TTTATAGTTTTTATAATA
*
14236 TTTATAAGTTTTTATAATT
1 TTTAT-AGTTTTTATAATA
14255 TTTATA
1 TTTATA
14261 AGTTAGTGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 5 0.23
18 2 0.09
19 15 0.68
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTATAGTTTTTATAATA
Found at i:14295 original size:17 final size:18
Alignment explanation
Indices: 14273--14311 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
14263 TTAGTGTGAA
14273 TTTTAAAATTT-TAATTT
1 TTTTAAAATTTATAATTT
*
14290 TTTTAACATTTAATAATTT
1 TTTTAAAATTT-ATAATTT
14309 TTT
1 TTT
14312 ATGATTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
19 9 0.47
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTAAAATTTATAATTT
Found at i:14707 original size:16 final size:17
Alignment explanation
Indices: 14667--14708 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
14657 AGTGTAAAAC
*
14667 TATTAAAAATTATAAAT
1 TATTAAAAATAATAAAT
* *
14684 GATAAAAAATAAT-AAT
1 TATTAAAAATAATAAAT
14700 TATTAAAAA
1 TATTAAAAA
14709 AAATTTAAAC
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
TATTAAAAATAATAAAT
Found at i:15089 original size:17 final size:17
Alignment explanation
Indices: 15067--15101 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
15057 AAATTATCTC
15067 TTATAAATTTTGAAATA
1 TTATAAATTTTGAAATA
15084 TTATAAATTTTGAAATA
1 TTATAAATTTTGAAATA
15101 T
1 T
15102 GCAAATTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (17 bp):
TTATAAATTTTGAAATA
Found at i:15150 original size:3 final size:3
Alignment explanation
Indices: 15142--15166 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
15132 CCTTTTTTGT
15142 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
15167 GGTTAGGTGT
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:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.