Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002599.1 Kokia drynarioides strain JFW-HI SEQ_114810, 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: 24404
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Found at i:302 original size:17 final size:18
Alignment explanation
Indices: 280--317 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
270 TTTATATATG
280 ATATTA-ATTATTACAAA
1 ATATTATATTATTACAAA
* *
297 ATATTATTTTATTATAAA
1 ATATTATATTATTACAAA
315 ATA
1 ATA
318 AATCTCGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATTATATTATTACAAA
Found at i:5536 original size:45 final size:45
Alignment explanation
Indices: 5485--5624 Score: 190
Period size: 45 Copynumber: 3.1 Consensus size: 45
5475 AGCGAAACGT
* *
5485 ATATCATGCATATCGTATAGCATAATCAATCAAATAATATTTACC
1 ATATCATGCATATCATATAGCATAATAAATCAAATAATATTTACC
* * *
5530 ATATCATGCATATTATATAGCATAATTAATCAAATAATGTTTACC
1 ATATCATGCATATCATATAGCATAATAAATCAAATAATATTTACC
* * * * *
5575 ATATCGTGCATATCTTATAGCACAATAAATTAAATAATATTTATC
1 ATATCATGCATATCATATAGCATAATAAATCAAATAATATTTACC
5620 ATATC
1 ATATC
5625 TCTTATTCAA
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 83 1.00
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.36
Consensus pattern (45 bp):
ATATCATGCATATCATATAGCATAATAAATCAAATAATATTTACC
Found at i:5707 original size:33 final size:33
Alignment explanation
Indices: 5669--5744 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
5659 TATATCGCAC
* *
5669 ATCATAGCATCAA-TCACAAGTTTATGTCATAAA
1 ATCATAGCATCAATTCACAAATTCATGTCAT-AA
* *
5702 ATCATAG-AACAATTCACAAATTCATGTCATCA
1 ATCATAGCATCAATTCACAAATTCATGTCATAA
5734 ATCATAAGCAT
1 ATCAT-AGCAT
5745 ATAGTTCATA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
32 10 0.29
33 24 0.69
34 1 0.03
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (33 bp):
ATCATAGCATCAATTCACAAATTCATGTCATAA
Found at i:6454 original size:30 final size:30
Alignment explanation
Indices: 6380--6477 Score: 99
Period size: 30 Copynumber: 3.3 Consensus size: 30
6370 TTTATTGCAA
* * *
6380 TTTAATAAAATTGAGGGTATTTATCATAAT
1 TTTACTAAAATTGAGGGCATTTACCATAAT
* *
6410 TTTACTAGAGTTGAGGGCATTTACCATAAT
1 TTTACTAAAATTGAGGGCATTTACCATAAT
* * * * *
6440 TTTATTAAATTTGAGAGC-GTTACTATAAT
1 TTTACTAAAATTGAGGGCATTTACCATAAT
6469 TTTACTAAA
1 TTTACTAAA
6478 GTTGGGCGTG
Statistics
Matches: 56, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
29 17 0.30
30 39 0.70
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (30 bp):
TTTACTAAAATTGAGGGCATTTACCATAAT
Found at i:12173 original size:28 final size:29
Alignment explanation
Indices: 12125--12358 Score: 113
Period size: 30 Copynumber: 7.9 Consensus size: 29
12115 ACGGGGTCGA
* * *
12125 AAAATGAAATTTCGAAGAATTT-GTGGTC
1 AAAATGTAATTTTGAAGAATTTAGGGGTC
*
12153 AAAATGTAATTTTGTAA-AATTTAGGGGTT
1 AAAATGTAATTTTG-AAGAATTTAGGGGTC
* * * *
12182 AAAATGTAATTTTTCGAA-AAGTTCA-AGTTT
1 AAAATGTAA-TTTT-GAAGAA-TTTAGGGGTC
* *
12212 AAAATGTAATTTTGAAAAATTTTAGGGATC
1 AAAATGTAATTTTGAAGAA-TTTAGGGGTC
* * * *
12242 AAAATGAAATTTGGAAGAGTTTGAGGGCT-
1 AAAATGTAATTTTGAAGAATTT-AGGGGTC
* *
12271 AAAATGTAATTTTAGAAGAGTTTAAGGG-C
1 AAAATGTAATTTT-GAAGAATTTAGGGGTC
** * * *
12300 TAAAATAAAATTTTTAAAAAGTTT-GAGGGTT
1 -AAAATGTAATTTTGAAGAA-TTTAG-GGGTC
*
12331 AAAATGTAATTTTGGAAGAGTTTGAGGG
1 AAAATGTAATTTT-GAAGAATTT-AGGG
12359 CTCTTTTATG
Statistics
Matches: 156, Mismatches: 33, Indels: 31
0.71 0.15 0.14
Matches are distributed among these distances:
28 20 0.13
29 44 0.28
30 82 0.53
31 9 0.06
32 1 0.01
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTGAAGAATTTAGGGGTC
Found at i:12180 original size:59 final size:58
Alignment explanation
Indices: 12125--12344 Score: 167
Period size: 59 Copynumber: 3.7 Consensus size: 58
12115 ACGGGGTCGA
* * *
12125 AAAATGAAATTTCGAAGAATTTGTGGTCAAAATGTAATTTTGTAAAA-TTTAGGGGTT
1 AAAATGAAATTTCGAAGAATTTGAGGTCAAAATGTAATTTTGAAAAATTTTAGGGGTC
* ** * * *
12182 AAAATGTAATTTTTCGAA-AAGTTCAAGTTTAAAATGTAATTTTGAAAAATTTTAGGGATC
1 AAAATG-AA-ATTTCGAAGAA-TTTGAGGTCAAAATGTAATTTTGAAAAATTTTAGGGGTC
* * * * * * *
12242 AAAATGAAATTTGGAAGAGTTTGAGGGCTAAAATGTAATTTTAGAAGAGTTTAAGGGCT-
1 AAAATGAAATTTCGAAGAATTTGAGGTC-AAAATGTAATTTT-GAAAAATTTTAGGGGTC
* ** * *
12301 AAAATAAAATTTTTAAAAAGTTTGAGGGTTAAAATGTAATTTTG
1 AAAATGAAATTTCGAAGAA-TTTGA-GGTCAAAATGTAATTTTG
12345 GAAGAGTTTG
Statistics
Matches: 126, Mismatches: 28, Indels: 16
0.74 0.16 0.09
Matches are distributed among these distances:
57 6 0.05
58 14 0.11
59 60 0.48
60 44 0.35
61 2 0.02
ACGTcount: A:0.41, C:0.03, G:0.20, T:0.36
Consensus pattern (58 bp):
AAAATGAAATTTCGAAGAATTTGAGGTCAAAATGTAATTTTGAAAAATTTTAGGGGTC
Found at i:12246 original size:30 final size:30
Alignment explanation
Indices: 12153--12360 Score: 140
Period size: 30 Copynumber: 7.0 Consensus size: 30
12143 ATTTGTGGTC
* *
12153 AAAATGTAATTTTGTAAAATTT-AGGGGTT
1 AAAATGTAATTTTGAAAAATTTGAGGGCTT
* * * *
12182 AAAATGTAATTTTTCG-AAAAGTTCA-AGTTT
1 AAAATGTAA-TTTT-GAAAAATTTGAGGGCTT
* * *
12212 AAAATGTAATTTTGAAAAATTTTAGGGATC
1 AAAATGTAATTTTGAAAAATTTGAGGGCTT
* * * *
12242 AAAATGAAATTTGGAAGAGTTTGAGGGC-T
1 AAAATGTAATTTTGAAAAATTTGAGGGCTT
* * *
12271 AAAATGTAATTTTAGAAGAGTTTAAGGGC-T
1 AAAATGTAATTTT-GAAAAATTTGAGGGCTT
** *
12301 AAAATAAAATTTTTAAAAAGTTTGAGGG-TT
1 AAAATGTAATTTTGAAAAA-TTTGAGGGCTT
* *
12331 AAAATGTAATTTTGGAAGAGTTTGAGGGCT
1 AAAATGTAATTTT-GAAAAATTTGAGGGCT
12361 CTTTTATGCA
Statistics
Matches: 140, Mismatches: 29, Indels: 18
0.75 0.16 0.10
Matches are distributed among these distances:
28 1 0.01
29 34 0.24
30 99 0.71
31 6 0.04
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.36
Consensus pattern (30 bp):
AAAATGTAATTTTGAAAAATTTGAGGGCTT
Found at i:12274 original size:89 final size:90
Alignment explanation
Indices: 12149--12360 Score: 227
Period size: 89 Copynumber: 2.4 Consensus size: 90
12139 AAGAATTTGT
* * * * * **
12149 GGTCAAAATGTAATTTTGTAA-AATTT-AGGGGTTAAAATGTAATTTTTCGAAAAGTTCAA-GTT
1 GGTCAAAATGTAAATTTGGAAGAGTTTGA-GGGCTAAAATGTAA-TTTTAGAAAAGTTCAAGGGC
** *
12211 TAAAATGTAATTTTGAAAAA-TTTTAG
64 TAAAATAAAATTTTGAAAAAGTTTGAG
* *
12237 GGATCAAAATG-AAATTTGGAAGAGTTTGAGGGCTAAAATGTAATTTTAGAAGAGTTTAAGGGCT
1 GG-TCAAAATGTAAATTTGGAAGAGTTTGAGGGCTAAAATGTAATTTTAGAAAAGTTCAAGGGCT
*
12301 AAAATAAAATTTTTAAAAAGTTTGAG
65 AAAATAAAATTTTGAAAAAGTTTGAG
* *
12327 GGTTAAAATGTAATTTTGGAAGAGTTTGAGGGCT
1 GGTCAAAATGTAAATTTGGAAGAGTTTGAGGGCT
12361 CTTTTATGCA
Statistics
Matches: 103, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
88 23 0.22
89 50 0.49
90 30 0.29
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.35
Consensus pattern (90 bp):
GGTCAAAATGTAAATTTGGAAGAGTTTGAGGGCTAAAATGTAATTTTAGAAAAGTTCAAGGGCTA
AAATAAAATTTTGAAAAAGTTTGAG
Found at i:12342 original size:60 final size:59
Alignment explanation
Indices: 12210--12361 Score: 180
Period size: 60 Copynumber: 2.5 Consensus size: 59
12200 AAGTTCAAGT
* * * * * * *
12210 TTAAAATGTAATTTTGAAAAATTTTAGGGATCAAAATGAAATTTGGAAGAGTTTGAGGG
1 TTAAAATGTAATTTTGAAGAGTTTAAGGGCTCAAAATAAAATTTGAAAAAGTTTGAGGG
* *
12269 CTAAAATGTAATTTTAGAAGAGTTTAAGGGCT-AAAATAAAATTTTTAAAAAGTTTGAGGG
1 TTAAAATGTAATTTT-GAAGAGTTTAAGGGCTCAAAATAAAA-TTTGAAAAAGTTTGAGGG
*
12329 TTAAAATGTAATTTTGGAAGAGTTTGAGGGCTC
1 TTAAAATGTAATTTT-GAAGAGTTTAAGGGCTC
12362 TTTTATGCAA
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
59 22 0.28
60 56 0.72
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.34
Consensus pattern (59 bp):
TTAAAATGTAATTTTGAAGAGTTTAAGGGCTCAAAATAAAATTTGAAAAAGTTTGAGGG
Found at i:16484 original size:14 final size:14
Alignment explanation
Indices: 16461--16502 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
16451 AAGAACCTAT
*
16461 AAAATAAAATAAAA
1 AAAATTAAATAAAA
*
16475 AAAATTAAATTAAA
1 AAAATTAAATAAAA
*
16489 AAAA-TATATAAAA
1 AAAATTAAATAAAA
16502 A
1 A
16503 TAAAAATGGC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAATTAAATAAAA
Found at i:17593 original size:25 final size:23
Alignment explanation
Indices: 17565--17610 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
17555 GTTGGATCCA
17565 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
17590 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
17611 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:18450 original size:21 final size:23
Alignment explanation
Indices: 18414--18456 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
18404 CAGCAAATGA
*
18414 TTTTAAAATTATTAAATTTATTT
1 TTTTAAAATTATTAAAATTATTT
18437 TTTTAAAA-TA-TAAAATTATT
1 TTTTAAAATTATTAAAATTATT
18457 AAATTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 2 0.11
23 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTTAAAATTATTAAAATTATTT
Found at i:22457 original size:16 final size:17
Alignment explanation
Indices: 22424--22456 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
22414 ACTTTGGTTA
*
22424 ATTTTTTAATGCATTTT
1 ATTTTTTAATACATTTT
22441 ATTTTTTAATACATTT
1 ATTTTTTAATACATTT
22457 AGATGGATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (17 bp):
ATTTTTTAATACATTTT
Done.