Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009118.1 Kokia drynarioides strain JFW-HI SEQ_123820, 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: 20022
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Warning! 22 characters in sequence are not A, C, G, or T
Found at i:5322 original size:17 final size:17
Alignment explanation
Indices: 5286--5324 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
5276 TAGTAAATAA
*
5286 AAATATATAAAATAATT
1 AAATATATAAAATAAAT
5303 AAATAT-TAAAATAAAAT
1 AAATATATAAAAT-AAAT
5320 AAATA
1 AAATA
5325 ATTTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATATATAAAATAAAT
Found at i:5334 original size:21 final size:21
Alignment explanation
Indices: 5292--5333 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5282 ATAAAAATAT
*
5292 ATAAAATAATTAAATATTAAA
1 ATAAAATAAATAAATATTAAA
*
5313 ATAAAATAAAT-AATTTTAAA
1 ATAAAATAAATAAATATTAAA
5333 A
1 A
5334 AAATTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAAATAAATAAATATTAAA
Found at i:8731 original size:27 final size:26
Alignment explanation
Indices: 8640--8731 Score: 66
Period size: 27 Copynumber: 3.6 Consensus size: 26
8630 TACTCATTTT
* *
8640 ATTACTTAAAAAATATTTTTATTTAA
1 ATTAATTATAAAATATTTTTATTTAA
* ** **
8666 ATTTAATTATACAATGCTCGT-TTT--
1 A-TTAATTATAAAATATTTTTATTTAA
*
8690 ATTATTTA-AAAATATTTTTATTTAA
1 ATTAATTATAAAATATTTTTATTTAA
8715 ATCTAATTATAAAATAT
1 AT-TAATTATAAAATAT
8732 ATAAATGTTA
Statistics
Matches: 46, Mismatches: 14, Indels: 11
0.65 0.20 0.15
Matches are distributed among these distances:
22 6 0.13
23 9 0.20
24 1 0.02
25 2 0.04
26 9 0.20
27 19 0.41
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.50
Consensus pattern (26 bp):
ATTAATTATAAAATATTTTTATTTAA
Found at i:10164 original size:22 final size:21
Alignment explanation
Indices: 10134--10222 Score: 53
Period size: 21 Copynumber: 4.3 Consensus size: 21
10124 GTTTTGGTGT
*
10134 TGTTATTTTATTGTTTTGGTTA
1 TGTT-TTTTATTGTTTTAGTTA
** *
10156 CTGTTTTTTGCTGTATTAG-TA
1 -TGTTTTTTATTGTTTTAGTTA
*
10177 TTGTTTTTTATTGATTT-G--A
1 -TGTTTTTTATTGTTTTAGTTA
*
10196 T-TTTTTTACTGTTTTAGTTA
1 TGTTTTTTATTGTTTTAGTTA
10216 CTGTTTT
1 -TGTTTT
10223 GGTGATTTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 11
0.69 0.15 0.15
Matches are distributed among these distances:
17 12 0.24
18 2 0.04
19 1 0.02
20 2 0.04
21 15 0.30
22 14 0.28
23 4 0.08
ACGTcount: A:0.13, C:0.04, G:0.16, T:0.66
Consensus pattern (21 bp):
TGTTTTTTATTGTTTTAGTTA
Found at i:10265 original size:26 final size:24
Alignment explanation
Indices: 10207--10282 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
10197 TTTTTTACTG
* *
10207 TTTTAGTTACTG-TTTTGGTG--A
1 TTTTTGTTACTGTTTTTGTTGCTA
*
10228 TTTTT-TTACTGTTTTGATGTTGTTA
1 TTTTTGTTACTGTTTT--TGTTGCTA
*
10253 TTTTTGTTGCTGTTTTTGTTGCTA
1 TTTTTGTTACTGTTTTTGTTGCTA
10277 TTTTTG
1 TTTTTG
10283 CTGTTATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
20 6 0.13
21 7 0.16
23 4 0.09
24 13 0.29
25 6 0.13
26 9 0.20
ACGTcount: A:0.09, C:0.05, G:0.20, T:0.66
Consensus pattern (24 bp):
TTTTTGTTACTGTTTTTGTTGCTA
Found at i:10272 original size:24 final size:24
Alignment explanation
Indices: 10227--10299 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
10217 TGTTTTGGTG
*
10227 ATTTTT-TTACTGTTTTGATGTTGTT
1 ATTTTTGTTGCTGTTTT--TGTTGTT
*
10252 ATTTTTGTTGCTGTTTTTGTTGCT
1 ATTTTTGTTGCTGTTTTTGTTGTT
* * *
10276 ATTTTTGCTGTTATTTTTGTTGTT
1 ATTTTTGTTGCTGTTTTTGTTGTT
10300 TTGCTTTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
24 26 0.63
25 6 0.15
26 9 0.22
ACGTcount: A:0.08, C:0.05, G:0.18, T:0.68
Consensus pattern (24 bp):
ATTTTTGTTGCTGTTTTTGTTGTT
Found at i:10299 original size:12 final size:12
Alignment explanation
Indices: 10245--10299 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
10235 ACTGTTTTGA
10245 TGTTGTTATTTT
1 TGTTGTTATTTT
* *
10257 TGTTGCTGTTTT
1 TGTTGTTATTTT
*
10269 TGTTGCTATTTT
1 TGTTGTTATTTT
*
10281 TGCTGTTATTTT
1 TGTTGTTATTTT
10293 TGTTGTT
1 TGTTGTT
10300 TTGCTTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.05, C:0.05, G:0.20, T:0.69
Consensus pattern (12 bp):
TGTTGTTATTTT
Found at i:10502 original size:27 final size:25
Alignment explanation
Indices: 10472--10527 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 25
10462 TACAATTATC
10472 TTAATATAAAAT-TTTTTTAATGTATTT
1 TTAAT-TAAAATATTTTTTAA--TATTT
**
10499 TTAATTAATTTATTTTTTAATATTT
1 TTAATTAAAATATTTTTTAATATTT
10524 TTAA
1 TTAA
10528 GTTTATTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 9 0.35
26 4 0.15
27 13 0.50
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
TTAATTAAAATATTTTTTAATATTT
Found at i:11012 original size:18 final size:18
Alignment explanation
Indices: 10981--11015 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
10971 ATAAAGATTT
10981 TGTTTTTTTGAGTTTGAG
1 TGTTTTTTTGAGTTTGAG
10999 TGTTTGTTTT-AGTTTGA
1 TGTTT-TTTTGAGTTTGA
11016 AAGTGAGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.11, C:0.00, G:0.26, T:0.63
Consensus pattern (18 bp):
TGTTTTTTTGAGTTTGAG
Found at i:15434 original size:29 final size:28
Alignment explanation
Indices: 15393--15451 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
15383 CTATGAGAGA
*
15393 AATGATCGATTTAGTCCCT-TAACTATTG
1 AATGATCAATTTAGTCCCTGT-ACTATTG
*
15421 AATGAATCAATTTAGTTCCTGTACTATTG
1 AATG-ATCAATTTAGTCCCTGTACTATTG
15450 AA
1 AA
15452 AAAAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 4 0.15
29 22 0.81
30 1 0.04
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (28 bp):
AATGATCAATTTAGTCCCTGTACTATTG
Found at i:16680 original size:16 final size:16
Alignment explanation
Indices: 16646--16680 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
16636 ATTCGTACAT
*
16646 TTTGATTCGAATTTCA
1 TTTGATTCGAATTTAA
*
16662 TTTGATTCGATTTTAA
1 TTTGATTCGAATTTAA
16678 TTT
1 TTT
16681 TTACGGTACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.23, C:0.09, G:0.11, T:0.57
Consensus pattern (16 bp):
TTTGATTCGAATTTAA
Found at i:17025 original size:21 final size:20
Alignment explanation
Indices: 16994--17032 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
16984 AATTTACATT
16994 TTTTAAAGAATTTAAATCGA
1 TTTTAAAGAATTTAAATCGA
*
17014 TTTTAAATGAATTTGAATC
1 TTTTAAA-GAATTTAAATC
17033 CAACTGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (20 bp):
TTTTAAAGAATTTAAATCGA
Found at i:17669 original size:31 final size:31
Alignment explanation
Indices: 17626--17686 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
17616 ATCAATTTAG
* *
17626 TTTATATATTTTAATTTGATCAATTTTAGTT
1 TTTATATATTTTAAATTGATCAACTTTAGTT
*
17657 TTTATATTTTTTAAATTGATCAACTTTAGT
1 TTTATATATTTTAAATTGATCAACTTTAGT
17687 CCATTGTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.59
Consensus pattern (31 bp):
TTTATATATTTTAAATTGATCAACTTTAGTT
Found at i:17702 original size:32 final size:31
Alignment explanation
Indices: 17616--17703 Score: 92
Period size: 31 Copynumber: 2.9 Consensus size: 31
17606 TCCATCTAAT
* *
17616 ATCAA-TTTAGT--TTATATATTTTAATTTG
1 ATCAACTTTAGTCATTATATTTTTTAAATTG
* **
17644 ATCAATTTTAGTTTTTATATTTTTTAAATTG
1 ATCAACTTTAGTCATTATATTTTTTAAATTG
*
17675 ATCAACTTTAGTCCATTGTATTTTTTAAA
1 ATCAACTTTAGT-CATTATATTTTTTAAA
17704 CATAAAAGTT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.10
29 6 0.12
31 26 0.52
32 13 0.26
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.56
Consensus pattern (31 bp):
ATCAACTTTAGTCATTATATTTTTTAAATTG
Found at i:19064 original size:193 final size:193
Alignment explanation
Indices: 18843--19211 Score: 485
Period size: 194 Copynumber: 1.9 Consensus size: 193
18833 AAAATGATTT
* ** * *
18843 TTTTTTTCGTTTAAACTTTTTATAATTTATAAAATTTTAAATTAGTAATGGT-AAGTTACACTTT
1 TTTTTTTCATTTAAACCCTTTATAATTTATAAAATTTTAAATTAGTAATGGTAAAATTACACTCT
* * * * *
18907 AAT-CCTCTAAAAATAAT-AAAAATTTGATTTAATCTTTTAAAAAATATAAATATATAGACTATT
66 -ATCCCCCTAAAAATAATAAAAAATTAG-TTTAATCCTTTAAAAAATATAAAGATATAGACCATT
* * *
18970 AAAGTGGTGAACTTGCATTTTTACT-ATCATAAAAATATACAATTTAATTCTGCCCCTAAAATGA
129 AAAATGATGAAATTGCATTTTTA-TAATCAT-AAAATATACAATTTAATTCTGCCCCTAAAATGA
19034 AA
192 AA
* * *
19036 TTTTTTTCATTTAGACCCTTTATAATTTATAAAATTTTGAATTAGTAATGGTAAAATTGCACTCT
1 TTTTTTTCATTTAAACCCTTTATAATTTATAAAATTTTAAATTAGTAATGGTAAAATTACACTCT
* * * *
19101 GTCCCCCTCAAAATAATAAAAAATTAGTTTTATCCTTTAAAAATTATAAAGATATAGACCATTAA
66 ATCCCCCTAAAAATAATAAAAAATTAGTTTAATCCTTTAAAAAATATAAAGATATAGACCATTAA
*
19166 AATGATGAAATTGCATTTTTATAATCGTAAAATATACAATTTAATT
131 AATGATGAAATTGCATTTTTATAATCATAAAATATACAATTTAATT
19212 ATGTCCTCCC
Statistics
Matches: 151, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
193 67 0.44
194 76 0.50
195 8 0.05
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.41
Consensus pattern (193 bp):
TTTTTTTCATTTAAACCCTTTATAATTTATAAAATTTTAAATTAGTAATGGTAAAATTACACTCT
ATCCCCCTAAAAATAATAAAAAATTAGTTTAATCCTTTAAAAAATATAAAGATATAGACCATTAA
AATGATGAAATTGCATTTTTATAATCATAAAATATACAATTTAATTCTGCCCCTAAAATGAAA
Done.