Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000158.1 Kokia drynarioides strain JFW-HI SEQ_110822, 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: 22942
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:867 original size:3 final size:3
Alignment explanation
Indices: 859--907 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
849 TTAGTTTTAA
859 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
907 A
1 A
908 AGAAACCATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1276 original size:16 final size:17
Alignment explanation
Indices: 1257--1290 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1247 TTTTACATAT
1257 TTATAA-ATTTAAAAAA
1 TTATAATATTTAAAAAA
*
1273 TTATAATTTTTAAAAAA
1 TTATAATATTTAAAAAA
1290 T
1 T
1291 AAGTCTAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTATAATATTTAAAAAA
Found at i:2926 original size:18 final size:17
Alignment explanation
Indices: 2905--2947 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
2895 ATTTTAGTTC
*
2905 TTTTATATATTTATATAT
1 TTTTATAAATTTATA-AT
2923 TTTTATAAATTTATAAT
1 TTTTATAAATTTATAAT
2940 TTTT-TAAA
1 TTTTATAAA
2948 AAATATTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 4 0.17
17 6 0.25
18 14 0.58
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTATAAATTTATAAT
Found at i:3267 original size:23 final size:21
Alignment explanation
Indices: 3203--3282 Score: 63
Period size: 23 Copynumber: 3.6 Consensus size: 21
3193 AAAACTTAAT
*
3203 TAAAAATAAAATT-TGAAAATGCT
1 TAAAAA-AAAATTAT-AAAAT-CA
*
3226 TAAATAAAAAATTATAAAATTA
1 TAAA-AAAAAATTATAAAATCA
3248 TAAAAAAAAATTGATAAAAATCA
1 TAAAAAAAAATT-AT-AAAATCA
**
3271 TAAGCAAAAATT
1 TAAAAAAAAATT
3283 TGGAAAATAA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
21 8 0.17
22 6 0.12
23 31 0.65
24 3 0.06
ACGTcount: A:0.64, C:0.04, G:0.05, T:0.28
Consensus pattern (21 bp):
TAAAAAAAAATTATAAAATCA
Found at i:3422 original size:6 final size:6
Alignment explanation
Indices: 3411--3451 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
3401 TAAAAATTAA
*
3411 AAAAAT AGAAAT AGAAAAT AAAAAT AAAAAT AAAAAAT AAA
1 AAAAAT AAAAAT A-AAAAT AAAAAT AAAAAT -AAAAAT AAA
3452 GAAAATTTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 20 0.65
7 11 0.35
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:3430 original size:13 final size:12
Alignment explanation
Indices: 3411--3451 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
3401 TAAAAATTAA
*
3411 AAAAATAGAAAT
1 AAAAATAAAAAT
3423 AGAAAATAAAAAT
1 A-AAAATAAAAAT
3436 AAAAATAAAAAAT
1 AAAAAT-AAAAAT
3449 AAA
1 AAA
3452 GAAAATTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 6 0.23
13 20 0.77
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (12 bp):
AAAAATAAAAAT
Found at i:3435 original size:19 final size:19
Alignment explanation
Indices: 3411--3451 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
3401 TAAAAATTAA
* *
3411 AAAAATAGAAATAGAAAAT
1 AAAAATAAAAATAAAAAAT
3430 AAAAATAAAAATAAAAAAT
1 AAAAATAAAAATAAAAAAT
3449 AAA
1 AAA
3452 GAAAATTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (19 bp):
AAAAATAAAAATAAAAAAT
Found at i:8048 original size:31 final size:31
Alignment explanation
Indices: 8013--8078 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
8003 AAAAAAGTCC
* *
8013 TGAACTATTCGAAAGTTTTTATTCAAGTCAT
1 TGAACTATTCAAAAGTTGTTATTCAAGTCAT
*
8044 TGAACTATTCAAAAGTTGTTATTTAAGTCAT
1 TGAACTATTCAAAAGTTGTTATTCAAGTCAT
8075 TGAA
1 TGAA
8079 TTGTTAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.41
Consensus pattern (31 bp):
TGAACTATTCAAAAGTTGTTATTCAAGTCAT
Found at i:8797 original size:21 final size:21
Alignment explanation
Indices: 8771--8812 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
8761 TTAAAATTTA
*
8771 ATTAAAAAGTAAAAATTAAAT
1 ATTAAAAACTAAAAATTAAAT
* *
8792 ATTAAAGACTAAAGATTAAAT
1 ATTAAAAACTAAAAATTAAAT
8813 TTATAATTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (21 bp):
ATTAAAAACTAAAAATTAAAT
Found at i:9908 original size:11 final size:11
Alignment explanation
Indices: 9892--9916 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9882 GGCTGGTTGT
9892 TGAAGTAGTAA
1 TGAAGTAGTAA
9903 TGAAGTAGTAA
1 TGAAGTAGTAA
9914 TGA
1 TGA
9917 CCTTTTCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (11 bp):
TGAAGTAGTAA
Found at i:20581 original size:22 final size:23
Alignment explanation
Indices: 20549--20597 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
20539 TGATCTAAGG
*
20549 AAAAATAAAAAAAAAACAGAATT
1 AAAAATAAAAAAAAAACAGAATC
* *
20572 AAAAAT-AAAAGAAAATAGAATC
1 AAAAATAAAAAAAAAACAGAATC
20594 AAAA
1 AAAA
20598 GAAATGGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.78, C:0.04, G:0.06, T:0.12
Consensus pattern (23 bp):
AAAAATAAAAAAAAAACAGAATC
Found at i:21435 original size:19 final size:19
Alignment explanation
Indices: 21411--21453 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
21401 AAACATAAAT
21411 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATATTAAATAA
* *
21430 TAAATAATATATTAAATAT
1 TAAATAAAATATTAAATAA
21449 TAAAT
1 TAAAT
21454 CCTATAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATATTAAATAA
Found at i:22113 original size:21 final size:22
Alignment explanation
Indices: 22075--22222 Score: 97
Period size: 23 Copynumber: 6.5 Consensus size: 22
22065 TATACGGAAA
* *
22075 AACAGAGAGTACCA-AAGTACT-
1 AACAGAGAGCA-CATAAGTGCTG
22096 AACAGAGAGCACATAAGTGCTGGG
1 AACAGAGAGCACATAAGTGCT--G
* *
22120 CAACAGAGAACACATACAGTGCTA
1 -AACAGAGAGCACATA-AGTGCTG
*
22144 AACAGAGAGCACACAAAGTGCT-
1 AACAGAGAGCACA-TAAGTGCTG
*
22166 AATCAGAGAGCACACAAAGTGCTG
1 AA-CAGAGAGCACA-TAAGTGCTG
* * *
22190 ATCAGAGGGCACGA-AACGTGCTA
1 AACAGAGAGCAC-ATAA-GTGCTG
22213 AACAGAGAGC
1 AACAGAGAGC
22223 CCGCTAGTGT
Statistics
Matches: 105, Mismatches: 11, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
20 2 0.02
21 16 0.15
22 4 0.04
23 60 0.57
24 3 0.03
25 14 0.13
26 6 0.06
ACGTcount: A:0.43, C:0.21, G:0.25, T:0.11
Consensus pattern (22 bp):
AACAGAGAGCACATAAGTGCTG
Found at i:22147 original size:23 final size:23
Alignment explanation
Indices: 22121--22222 Score: 116
Period size: 23 Copynumber: 4.4 Consensus size: 23
22111 AGTGCTGGGC
* * *
22121 AACAGAGAACACATACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
22144 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
22167 ATCAGAGAGCACACAAAGTGCTG
1 AACAGAGAGCACACAAAGTGCTA
* * *
22190 ATCAGAGGGCACGA-AACGTGCTA
1 AACAGAGAGCAC-ACAAAGTGCTA
22213 AACAGAGAGC
1 AACAGAGAGC
22223 CCGCTAGTGT
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 67 0.99
24 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:22196 original size:69 final size:68
Alignment explanation
Indices: 22074--22222 Score: 169
Period size: 69 Copynumber: 2.2 Consensus size: 68
22064 ATATACGGAA
* * *
22074 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAACAGAGAACAC-ATACA
1 AAACAGAGAGCACCAAAGTACTAACAGAGAGCACAAAAGTGCT-GGCAACAGAGAACACGAAAC-
22138 GTGCT
64 GTGCT
* * **
22143 AAACAGAGAGCACACAAAGTGCTAATCAGAGAGCACACAAAGTGCT-G-ATCAGAGGGCACGAAA
1 AAACAGAGAGCAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGGCAACAGAGAACACGAAA
22206 CGTGCT
63 CGTGCT
22212 AAACAGAGAGC
1 AAACAGAGAGC
22223 CCGCTAGTGT
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
69 37 0.54
70 14 0.20
71 11 0.16
72 7 0.10
ACGTcount: A:0.43, C:0.21, G:0.25, T:0.11
Consensus pattern (68 bp):
AAACAGAGAGCACCAAAGTACTAACAGAGAGCACAAAAGTGCTGGCAACAGAGAACACGAAACGT
GCT
Found at i:22221 original size:46 final size:46
Alignment explanation
Indices: 22074--22222 Score: 126
Period size: 46 Copynumber: 3.2 Consensus size: 46
22064 ATATACGGAA
* * *
22074 AAACAGAGAGTAC-CAAAGTACT-AACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTGCT
* * * *
22117 GGGCAACAGAGAACACATACAGTGCTAAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTGCT
* * * * *
22166 AATCAGAGAGCACACAAAGTGCTGATCAGAGGGCACGA-AACGTGCT
1 AAACAGAGAGCACACAAAGTGCTAAACAGAGAGCAC-ACAAAGTGCT
22212 AAACAGAGAGC
1 AAACAGAGAGC
22223 CCGCTAGTGT
Statistics
Matches: 82, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
46 55 0.67
47 7 0.09
48 13 0.16
49 7 0.09
ACGTcount: A:0.43, C:0.21, G:0.25, T:0.11
Consensus pattern (46 bp):
AAACAGAGAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTGCT
Done.