Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013552.1 Kokia drynarioides strain JFW-HI SEQ_128578, 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: 60159
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 33 characters in sequence are not A, C, G, or T
Found at i:254 original size:15 final size:15
Alignment explanation
Indices: 236--291 Score: 85
Period size: 15 Copynumber: 3.7 Consensus size: 15
226 CATTGGGTCG
*
236 TTTGTATTTGGGCCA
1 TTTGTAATTGGGCCA
*
251 TTTGTATTTGGGCCA
1 TTTGTAATTGGGCCA
*
266 TTTGTAATTGGGTCA
1 TTTGTAATTGGGCCA
281 TTTGTAATTGG
1 TTTGTAATTGG
292 ACTTTGTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.16, C:0.09, G:0.27, T:0.48
Consensus pattern (15 bp):
TTTGTAATTGGGCCA
Found at i:262 original size:30 final size:30
Alignment explanation
Indices: 227--291 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
217 ACTTTGGGCC
* * *
227 ATTGGGTCGTTTGTATTTGGGCCATTTGTA
1 ATTGGGCCATTTGTAATTGGGCCATTTGTA
* *
257 TTTGGGCCATTTGTAATTGGGTCATTTGTA
1 ATTGGGCCATTTGTAATTGGGCCATTTGTA
287 ATTGG
1 ATTGG
292 ACTTTGTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.15, C:0.09, G:0.29, T:0.46
Consensus pattern (30 bp):
ATTGGGCCATTTGTAATTGGGCCATTTGTA
Found at i:316 original size:13 final size:14
Alignment explanation
Indices: 281--321 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
271 AATTGGGTCA
281 TTTG-TAATTGGAC
1 TTTGTTAATTGGAC
294 TTTGTT--TTGGAC
1 TTTGTTAATTGGAC
306 TTT-TTAATTGGAC
1 TTTGTTAATTGGAC
319 TTT
1 TTT
322 CTAAATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.08
12 9 0.36
13 13 0.52
14 1 0.04
ACGTcount: A:0.17, C:0.07, G:0.20, T:0.56
Consensus pattern (14 bp):
TTTGTTAATTGGAC
Found at i:361 original size:34 final size:33
Alignment explanation
Indices: 323--395 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 33
313 TTGGACTTTC
** * *
323 TAAATTTAATTTTATAATAAATTTAAATTTCAAA
1 TAAATTTAAAATTAAAATAAACTTAAATTT-AAA
*
357 TAAATTTAAAATTAAAATTAACTTAAATTTAAA
1 TAAATTTAAAATTAAAATAAACTTAAATTTAAA
390 TAAATT
1 TAAATT
396 CGATTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 9 0.26
34 25 0.74
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (33 bp):
TAAATTTAAAATTAAAATAAACTTAAATTTAAA
Found at i:366 original size:17 final size:16
Alignment explanation
Indices: 323--395 Score: 83
Period size: 17 Copynumber: 4.4 Consensus size: 16
313 TTGGACTTTC
*
323 TAAATTTAATTTTATAA
1 TAAATTTAAATTTA-AA
340 TAAATTTAAATTTCAAA
1 TAAATTTAAATTT-AAA
*
357 TAAATTTAAAATTAAAA
1 TAAATTT-AAATTTAAA
* *
374 TTAACTTAAATTTAAA
1 TAAATTTAAATTTAAA
390 TAAATT
1 TAAATT
396 CGATTTCCAA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
16 12 0.26
17 29 0.62
18 6 0.13
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:366 original size:23 final size:23
Alignment explanation
Indices: 340--390 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
330 AATTTTATAA
*
340 TAAATTTAAATTTCAA-ATAAATT
1 TAAATTTAAAATT-AACATAAATT
* *
363 TAAAATTAAAATTAACTTAAATT
1 TAAATTTAAAATTAACATAAATT
386 TAAAT
1 TAAAT
391 AAATTCGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (23 bp):
TAAATTTAAAATTAACATAAATT
Found at i:3048 original size:26 final size:26
Alignment explanation
Indices: 3020--3070 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
3010 TATTATAACA
*
3020 TTTTTAATGTATTTTAAATTTATTTAT
1 TTTTTAATGT-TTTTAAATGTATTTAT
3047 TTTTTAATGTTTTTAAATGTATTT
1 TTTTTAATGTTTTTAAATGTATTT
3071 GATATATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (26 bp):
TTTTTAATGTTTTTAAATGTATTTAT
Found at i:9366 original size:22 final size:19
Alignment explanation
Indices: 9328--9373 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
9318 AAGGCTACAA
9328 CTTTTTTTCTATTTCTTTT
1 CTTTTTTTCTATTTCTTTT
9347 CCTTTTTTTCTATTTATCTTTT
1 -CTTTTTTTCTA-TT-TCTTTT
9369 CTTTT
1 CTTTT
9374 ATCTTGCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.46
21 7 0.29
22 6 0.25
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (19 bp):
CTTTTTTTCTATTTCTTTT
Found at i:10867 original size:74 final size:74
Alignment explanation
Indices: 10746--10893 Score: 260
Period size: 74 Copynumber: 2.0 Consensus size: 74
10736 ACTAAAAAAA
10746 TAGTCACTTTTATTTGCCTCAAACTATATTCTAATCAATTATGTTTGAAATGTTTCGTTTTAGTC
1 TAGTCACTTTTATTTGCCTCAAACTATATTCTAATCAATTATGTTTGAAATGTTTCGTTTTAGTC
10811 ATTTATGTT
66 ATTTATGTT
* * * *
10820 TAGTCACTTTTATTTGCCTCAAACTATATTTTAGTCACTTATGTTTGAAATGTTTTGTTTTAGTC
1 TAGTCACTTTTATTTGCCTCAAACTATATTCTAATCAATTATGTTTGAAATGTTTCGTTTTAGTC
10885 ATTTATGTT
66 ATTTATGTT
10894 GTCGTTTTAT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.24, C:0.13, G:0.11, T:0.51
Consensus pattern (74 bp):
TAGTCACTTTTATTTGCCTCAAACTATATTCTAATCAATTATGTTTGAAATGTTTCGTTTTAGTC
ATTTATGTT
Found at i:12511 original size:30 final size:30
Alignment explanation
Indices: 12436--12511 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
12426 ATTTTCGAGG
* *
12436 AATTTGAGGTCAAAATTGAAATTTTGGGAA
1 AATTTGAGGTTAAAATCGAAATTTTGGGAA
*
12466 AATTTG-GGATTAAAATCGAACTTTT-GGAA
1 AATTTGAGG-TTAAAATCGAAATTTTGGGAA
12495 AATTTGAGGTTGAAAAT
1 AATTTGAGGTT-AAAAT
12512 GTGACTTTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 14 0.35
30 26 0.65
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.34
Consensus pattern (30 bp):
AATTTGAGGTTAAAATCGAAATTTTGGGAA
Found at i:12519 original size:30 final size:29
Alignment explanation
Indices: 12436--12523 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 29
12426 ATTTTCGAGG
* *
12436 AATTTGAGGTCAAAAT-TGAAATTTTGGGAA
1 AATTTGAGGTTAAAATGTG-ACTTTT-GGAA
*
12466 AATTTG-GGATTAAAATCG-AACTTTTGGAA
1 AATTTGAGG-TTAAAAT-GTGACTTTTGGAA
12495 AATTTGAGGTTGAAAATGTGACTTTTGGA
1 AATTTGAGGTT-AAAATGTGACTTTTGGA
12524 GATTTAGGGG
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
29 15 0.31
30 33 0.69
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (29 bp):
AATTTGAGGTTAAAATGTGACTTTTGGAA
Found at i:12627 original size:58 final size:58
Alignment explanation
Indices: 12554--12694 Score: 160
Period size: 58 Copynumber: 2.4 Consensus size: 58
12544 ACTTTGGATG
* * * * *
12554 AGGGTTAAAATGTAATTTTGGAGAAGTTTGGGATCAAAATGGGAGTTTAGAGAAGTTC
1 AGGGGTAAAATGTAATTTTGGAAAAATTTGGGATCAAAATGAGAGTTTAGAAAAGTTC
* * *
12612 AGGGGTAAAATGTAATTTTGGAAAAATTTGGGGTTAAAATGAGATTTTAGAAAAGTT-
1 AGGGGTAAAATGTAATTTTGGAAAAATTTGGGATCAAAATGAGAGTTTAGAAAAGTTC
* *
12669 TGAGGTGAAAATG-AGATTTTGGAAAA
1 AGGGGT-AAAATGTA-ATTTTGGAAAA
12695 GTTCGGGTGT
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
57 5 0.07
58 66 0.93
ACGTcount: A:0.38, C:0.01, G:0.29, T:0.31
Consensus pattern (58 bp):
AGGGGTAAAATGTAATTTTGGAAAAATTTGGGATCAAAATGAGAGTTTAGAAAAGTTC
Found at i:12649 original size:29 final size:29
Alignment explanation
Indices: 12555--12750 Score: 136
Period size: 29 Copynumber: 6.8 Consensus size: 29
12545 CTTTGGATGA
*
12555 GGGTTAAAATGTAATTTTGGAGAAGTTTG
1 GGGTTAAAATGTAATTTTGGAAAAGTTTG
* * ** * * * *
12584 GGATCAAAATGGGAGTTTAGAGAAGTTCAG
1 GGGTTAAAATGTAATTTTGGAAAAGTT-TG
*
12614 GGG-TAAAATGTAATTTTGGAAAAATTTG
1 GGGTTAAAATGTAATTTTGGAAAAGTTTG
*
12642 GGGTTAAAATG-AGATTTTAGAAAAGTTTG
1 GGGTTAAAATGTA-ATTTTGGAAAAGTTTG
* * *
12671 AGGTGAAAATG-AGATTTTGGAAAAG-TTC
1 GGGTTAAAATGTA-ATTTTGGAAAAGTTTG
12699 GGGTGT--AATGTAATTTTTGG-AAAGTTTAG
1 GGGT-TAAAATGTAA-TTTTGGAAAAGTTT-G
* *
12728 GGGTAAAAATATAATTTTTGGAA
1 GGGTTAAAATGTAA-TTTTGGAA
12751 GTTCAGAGGC
Statistics
Matches: 129, Mismatches: 27, Indels: 20
0.73 0.15 0.11
Matches are distributed among these distances:
27 9 0.07
28 19 0.15
29 84 0.65
30 16 0.12
31 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.34
Consensus pattern (29 bp):
GGGTTAAAATGTAATTTTGGAAAAGTTTG
Found at i:12659 original size:87 final size:86
Alignment explanation
Indices: 12555--12745 Score: 203
Period size: 87 Copynumber: 2.2 Consensus size: 86
12545 CTTTGGATGA
* * * *
12555 GGGTTAAAATGTAATTTTGGAGAAGTTTG-GGATCAAAATGGGAGTTTAGAGAAGTTCAGGG-GT
1 GGGTTAAAATGTAATTTTAGAAAAGTTTGAGG-TCAAAATGAGAGTTTAGAAAAGTTC-GGGTGT
12618 AAAATGTAA-TTTTGGAAAAATTTG
64 --AATGTAATTTTTGGAAAAATTTG
* * *
12642 GGGTTAAAATG-AGATTTTAGAAAAGTTTGAGGTGAAAATGAGATTTTGGAAAAGTTCGGGTGTA
1 GGGTTAAAATGTA-ATTTTAGAAAAGTTTGAGGTCAAAATGAGAGTTTAGAAAAGTTCGGGTGTA
*
12706 ATGTAATTTTTGG-AAAGTTTAG
65 ATGTAATTTTTGGAAAAATTT-G
* *
12728 GGGTAAAAATATAATTTT
1 GGGTTAAAATGTAATTTT
12746 TGGAAGTTCA
Statistics
Matches: 88, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
85 13 0.15
86 25 0.28
87 48 0.55
88 2 0.02
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34
Consensus pattern (86 bp):
GGGTTAAAATGTAATTTTAGAAAAGTTTGAGGTCAAAATGAGAGTTTAGAAAAGTTCGGGTGTAA
TGTAATTTTTGGAAAAATTTG
Found at i:12745 original size:30 final size:31
Alignment explanation
Indices: 12709--12835 Score: 115
Period size: 30 Copynumber: 4.3 Consensus size: 31
12699 GGGTGTAATG
12709 TAATTTTTGGA-AAGTTTAGGGGTAAAAATA
1 TAATTTTTGGAGAAGTTTAGGGGTAAAAATA
* * *
12739 TAATTTTT-G-GAAGTTCAGAGGCAAAAATGA
1 TAATTTTTGGAGAAGTTTAGGGGTAAAAAT-A
* *
12769 -AATTTTT-GAGAAGTTTAAGGGTAAAAATG
1 TAATTTTTGGAGAAGTTTAGGGGTAAAAATA
** *
12798 TAA-TTTTAAAGAAGTTT-GATGGTAAAAATA
1 TAATTTTTGGAGAAGTTTAG-GGGTAAAAATA
12828 TAATTTTT
1 TAATTTTT
12836 TAAACAAAAC
Statistics
Matches: 78, Mismatches: 12, Indels: 13
0.76 0.12 0.13
Matches are distributed among these distances:
29 28 0.36
30 46 0.59
31 4 0.05
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (31 bp):
TAATTTTTGGAGAAGTTTAGGGGTAAAAATA
Found at i:14431 original size:6 final size:6
Alignment explanation
Indices: 14422--14456 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
14412 TAAACATAAA
*
14422 TAAATT TAAATT TAAA-A TAAATT TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
14457 CTATTTGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
TAAATT
Found at i:14462 original size:17 final size:17
Alignment explanation
Indices: 14419--14454 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
14409 TAGTAAACAT
14419 AAATAAATTTAAATTTA
1 AAATAAATTTAAATTTA
14436 AAATAAATTTAAATTTA
1 AAATAAATTTAAATTTA
14453 AA
1 AA
14455 TTCTATTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATAAATTTAAATTTA
Found at i:14976 original size:13 final size:13
Alignment explanation
Indices: 14958--14984 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
14948 GGAGTGTGGT
14958 CTAGAGGTGACAC
1 CTAGAGGTGACAC
14971 CTAGAGGTGACAC
1 CTAGAGGTGACAC
14984 C
1 C
14985 ACTATTCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.26, G:0.30, T:0.15
Consensus pattern (13 bp):
CTAGAGGTGACAC
Found at i:18185 original size:19 final size:18
Alignment explanation
Indices: 18158--18193 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
18148 ATCTGAATTA
*
18158 TTCATTATTTAATATTTAT
1 TTCAATATTT-ATATTTAT
18177 TTCAATATTTATATTTA
1 TTCAATATTTATATTTA
18194 AAGTGAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (18 bp):
TTCAATATTTATATTTAT
Found at i:18303 original size:6 final size:6
Alignment explanation
Indices: 18292--18330 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
18282 TGATCAAAAT
* * *
18292 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
18331 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:22997 original size:28 final size:27
Alignment explanation
Indices: 22889--23223 Score: 198
Period size: 29 Copynumber: 11.7 Consensus size: 27
22879 GGCTACACTT
* * *
22889 TTCC-AAAATCACATTTGACCCCCGAAC
1 TTCCAAAAATTACATTTTA-CCCCAAAC
* * *
22916 TTTACAAAAATTATATTTTGACCCTCGAAC
1 -TTCCAAAAATTACATTTT-ACCC-CAAAC
22946 TTTCCAAAAATTACATTTTGACCCCAAAC
1 -TTCCAAAAATTACATTTT-ACCCCAAAC
*
22975 TTCCCAAAAGTTACATTTTACCCCTAAAC
1 TT-CCAAAAATTACATTTTACCCC-AAAC
* *
23004 TTCAAAAAATCACATTTTTAACCCCAAAC
1 TTCCAAAAATTACA-TTTT-ACCCCAAAC
* *
23033 TTCTAAAAATTATCATTTTATCCCCGAA-
1 TTCCAAAAATTA-CATTTTA-CCCCAAAC
*
23061 TATCC-AAAATTACCATTTTACCCCCGAA-
1 T-TCCAAAAATTA-CATTTTA-CCCCAAAC
23089 TATCC-AAAATTACATTTTTGACCCCAAAC
1 T-TCCAAAAATTACA-TTTT-ACCCCAAAC
* *
23118 TTTCC-AAAGTTACCATTTTACCCTCGAAC
1 -TTCCAAAAATTA-CATTTTACCC-CAAAC
* * *
23147 ATCCAAAAATTACCATTTTACTCTCGAA-
1 TTCCAAAAATTA-CATTTTAC-CCCAAAC
*
23175 TGTCCAAAAATTACATTTTTGACCCCGAAC
1 T-TCCAAAAATTACA-TTTT-ACCCCAAAC
* *
23205 TTTTCAAAAATTACCTTTT
1 -TTCCAAAAATTACATTTT
23224 TACCTCGTGC
Statistics
Matches: 257, Mismatches: 27, Indels: 45
0.78 0.08 0.14
Matches are distributed among these distances:
27 2 0.01
28 73 0.28
29 129 0.50
30 52 0.20
31 1 0.00
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (27 bp):
TTCCAAAAATTACATTTTACCCCAAAC
Found at i:23181 original size:57 final size:55
Alignment explanation
Indices: 22920--23227 Score: 173
Period size: 57 Copynumber: 5.3 Consensus size: 55
22910 CCGAACTTTA
* * * *
22920 CAAAAATTA-TATTTTGACCCTCGAACTTTCCAAAAATTA-CATTTTGACCCCAAACTTCC
1 CAAAAATTACCATTTT-ACCC-CGAA-TATCC-AAAATTACCATTTT-ACCCCGAACAT-C
* * * * * *
22979 CAAAAGTTA-CATTTTACCCCTAA-ACTTCAAAA-AATCACATTTTTAACCCCAAACTTC
1 CAAAAATTACCATTTTACCCCGAATA-TCCAAAATTA-C-CA-TTTT-ACCCCGAACATC
* * *
23036 TAAAAATTATCATTTTATCCCCGAATATCCAAAATTACCATTTTACCCCCGAATATC
1 CAAAAATTACCATTTTA-CCCCGAATATCCAAAATTACCATTTTA-CCCCGAACATC
* * *
23093 C-AAAATTA-CATTTTTGACCCCAAACTTTCCAAAGTTACCATTTTACCCTCGAACATC
1 CAAAAATTACCA-TTTT-ACCCCGAA-TATCCAAAATTACCATTTTACCC-CGAACATC
* * * *
23150 CAAAAATTACCATTTTACTCTCGAATGTCCAAAAATTA-CATTTTTGACCCCGAACTTTT
1 CAAAAATTACCATTTTAC-CCCGAATATCC-AAAATTACCA-TTTT-ACCCCGAAC-ATC
*
23209 CAAAAATTACCTTTTTACC
1 CAAAAATTACCATTTTACC
23228 TCGTGCGTCC
Statistics
Matches: 201, Mismatches: 27, Indels: 43
0.74 0.10 0.16
Matches are distributed among these distances:
54 1 0.00
55 6 0.03
56 23 0.11
57 60 0.30
58 59 0.29
59 50 0.25
60 2 0.01
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (55 bp):
CAAAAATTACCATTTTACCCCGAATATCCAAAATTACCATTTTACCCCGAACATC
Found at i:23308 original size:135 final size:136
Alignment explanation
Indices: 23130--23390 Score: 289
Period size: 135 Copynumber: 1.9 Consensus size: 136
23120 TCCAAAGTTA
* *
23130 CCATTTTACCCTCGAACATCCAAAAATTACCATTTTACTCTCGAA-TGTCCAAAAATTACATTTT
1 CCATTTTACCCTCGAACATCCAAAAAGTACCATTTTACTCTCGAACTGTCCAAAAATTACAATTT
* * * ** * *
23194 TGAC-CCCGAACTTTTCAAAAATTACCTTTTTA-CCTCGTGCGTCCAAAAATTATCGTTTTACTC
66 TG-CTCCCGAAC-ATACAAAAATTACCGTTTTACCCTCGAACATCCAAAAATTATCATTTTACTC
23257 TTGGACAT
129 TTGGACAT
* * ** * * *
23265 CCATTTTACCCTTGGATGTCCAAAAAGTA-CATTTTTGAC-CTCGAACTTTTCAAAAATTATAAT
1 CCATTTTACCCTCGAACATCCAAAAAGTACCA-TTTT-ACTCTCGAACTGTCCAAAAATTACAAT
* *
23328 TTTGCTCCCGAGCATACAAAAATTACCGTTTTACCCTCGAACATCCAAAAATTTTCATTTTAC
64 TTTGCTCCCGAACATACAAAAATTACCGTTTTACCCTCGAACATCCAAAAATTATCATTTTAC
23391 CCCGGATGTC
Statistics
Matches: 103, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
134 2 0.02
135 52 0.50
136 49 0.48
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.35
Consensus pattern (136 bp):
CCATTTTACCCTCGAACATCCAAAAAGTACCATTTTACTCTCGAACTGTCCAAAAATTACAATTT
TGCTCCCGAACATACAAAAATTACCGTTTTACCCTCGAACATCCAAAAATTATCATTTTACTCTT
GGACAT
Found at i:23376 original size:29 final size:29
Alignment explanation
Indices: 23344--23579 Score: 158
Period size: 29 Copynumber: 8.3 Consensus size: 29
23334 CCCGAGCATA
*
23344 CAAAAATTACCGTTTTACCCTCGAACATC
1 CAAAAATTACCATTTTACCCTCGAACATC
** * **
23373 CAAAAATTTTCATTTTACCC-CGGATGTC
1 CAAAAATTACCATTTTACCCTCGAACATC
* * * * * *
23401 C-AAAATTATCGTTTTATCCTCAAACGTT
1 CAAAAATTACCATTTTACCCTCGAACATC
* * *** *
23429 TAAAAATTACCATTTTGCCCTCGAGTGTA
1 CAAAAATTACCATTTTACCCTCGAACATC
* * *
23458 C-AAAATTACCGTTTTACCCCCGATCATC
1 CAAAAATTACCATTTTACCCTCGAACATC
* *
23486 CCAAAATTACCATTTTACCCTCGAGCATC
1 CAAAAATTACCATTTTACCCTCGAACATC
* * * * *
23515 TAAAAATTA-CATTTTTGCCC-CAAACTTT
1 CAAAAATTACCA-TTTTACCCTCGAACATC
* *
23543 CAAAAATTACCATTTTGCCCTCGAGCATC
1 CAAAAATTACCATTTTACCCTCGAACATC
23572 CAAAAATT
1 CAAAAATT
23580 GCATTTTTAA
Statistics
Matches: 156, Mismatches: 45, Indels: 12
0.73 0.21 0.06
Matches are distributed among these distances:
27 15 0.10
28 53 0.34
29 88 0.56
ACGTcount: A:0.33, C:0.27, G:0.08, T:0.32
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCTCGAACATC
Found at i:23472 original size:57 final size:58
Alignment explanation
Indices: 23346--23567 Score: 202
Period size: 57 Copynumber: 3.9 Consensus size: 58
23336 CGAGCATACA
* * ** *
23346 AAAATTACCGTTTTACCCTCGAACATCCAAAAATTTTCATTTTACCC-CG-GATGTCC
1 AAAATTACCGTTTTACCCCCAAACATCCAAAAATTACCATTTTACCCTCGAGATGTAC
* * * * ** *
23402 AAAATTATCGTTTTATCCTCAAACGTTTAAAAATTACCATTTTGCCCTCGAG-TGTAC
1 AAAATTACCGTTTTACCCCCAAACATCCAAAAATTACCATTTTACCCTCGAGATGTAC
* * * *
23459 AAAATTACCGTTTTACCCCCGATCATCCCAAAATTACCATTTTACCCTCGAGCATCTA-
1 AAAATTACCGTTTTACCCCCAAACATCCAAAAATTACCATTTTACCCTCGAG-ATGTAC
* ** * * *
23517 AAAATTA-CATTTTTGCCCCAAACTTTCAAAAATTACCATTTTGCCCTCGAG
1 AAAATTACCGTTTTACCCCCAAACATCCAAAAATTACCATTTTACCCTCGAG
23568 CATCCAAAAA
Statistics
Matches: 132, Mismatches: 30, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
56 38 0.29
57 83 0.63
58 8 0.06
59 3 0.02
ACGTcount: A:0.32, C:0.27, G:0.09, T:0.33
Consensus pattern (58 bp):
AAAATTACCGTTTTACCCCCAAACATCCAAAAATTACCATTTTACCCTCGAGATGTAC
Found at i:23568 original size:57 final size:57
Alignment explanation
Indices: 23421--23587 Score: 178
Period size: 57 Copynumber: 2.9 Consensus size: 57
23411 GTTTTATCCT
* * *
23421 CAAACGTTT-AAAAATTACCATTTTGCCCTCGAG--TGTACAAAATTACCGTTTTACCCC
1 CAAAC-TTTCAAAAATTACCATTTTGCCCTCGAGCATCTA-AAAATTA-CATTTTTCCCC
* * * * * * *
23478 CGATCATCCCAAAATTACCATTTTACCCTCGAGCATCTAAAAATTACATTTTTGCCC
1 CAAACTTTCAAAAATTACCATTTTGCCCTCGAGCATCTAAAAATTACATTTTTCCCC
* *
23535 CAAACTTTCAAAAATTACCATTTTGCCCTCGAGCATCCAAAAATTGCATTTTT
1 CAAACTTTCAAAAATTACCATTTTGCCCTCGAGCATCTAAAAATTACATTTTT
23588 AACTCCGTTT
Statistics
Matches: 89, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
56 1 0.01
57 78 0.88
58 7 0.08
59 3 0.03
ACGTcount: A:0.32, C:0.27, G:0.08, T:0.32
Consensus pattern (57 bp):
CAAACTTTCAAAAATTACCATTTTGCCCTCGAGCATCTAAAAATTACATTTTTCCCC
Found at i:23576 original size:114 final size:113
Alignment explanation
Indices: 23265--23576 Score: 319
Period size: 114 Copynumber: 2.7 Consensus size: 113
23255 TCTTGGACAT
* * * * * **
23265 CCATTTTACCCTTGGATGTCCAAAAAGTACATTTTTGACCTCGAACTTTTCAAAAATTATAATTT
1 CCATTTTACCC-CGGATCT-CAAAAATTACATTTTTG-CCTCAAACGTTTCAAAAATTACCATTT
* * *
23330 TGCTCC-CGAGCATACAAAAATTACCGTTTTACCCTCGAACATCCAAAAATTT
63 TGC-CCTCGAGCAT-CCAAAATTACCGTTTTACCCCCGAACATCCAAAAATTA
* * * *
23382 TCATTTTACCCCGGATGTCCAAAATTATCGTTTTAT-CCTCAAACGTTT-AAAAATTACCATTTT
1 CCATTTTACCCCGGATCTCAAAAATTA-CATTTT-TGCCTCAAACGTTTCAAAAATTACCATTTT
** * * *
23445 GCCCTCGAGTGTACAAAATTACCGTTTTACCCCCGATCATCCCAAAATTA
64 GCCCTCGAGCATCCAAAATTACCGTTTTACCCCCGAACATCCAAAAATTA
*
23495 CCATTTTACCCTCGAGCATCT-AAAAATTACATTTTTGCCCCAAAC-TTTCAAAAATTACCATTT
1 CCATTTTACCC-CG-G-ATCTCAAAAATTACATTTTTGCCTCAAACGTTTCAAAAATTACCATTT
23558 TGCCCTCGAGCATCCAAAA
63 TGCCCTCGAGCATCCAAAA
23577 ATTGCATTTT
Statistics
Matches: 162, Mismatches: 25, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
113 48 0.30
114 64 0.40
115 25 0.15
116 14 0.09
117 11 0.07
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.33
Consensus pattern (113 bp):
CCATTTTACCCCGGATCTCAAAAATTACATTTTTGCCTCAAACGTTTCAAAAATTACCATTTTGC
CCTCGAGCATCCAAAATTACCGTTTTACCCCCGAACATCCAAAAATTA
Found at i:23586 original size:28 final size:29
Alignment explanation
Indices: 23315--23579 Score: 150
Period size: 29 Copynumber: 9.3 Consensus size: 29
23305 TCGAACTTTT
** *
23315 CAAAAATTATAATTTTGCTCC-CGAGCATA
1 CAAAAATTACCATTTTGC-CCTCGAGCATC
* * *
23344 CAAAAATTACCGTTTTACCCTCGAACATC
1 CAAAAATTACCATTTTGCCCTCGAGCATC
** *
23373 CAAAAATTTTCATTTTACCC-CG-G-ATGTC
1 CAAAAATTACCATTTTGCCCTCGAGCA--TC
* * ** * * * *
23401 C-AAAATTATCGTTTTATCCTCAAACGTT
1 CAAAAATTACCATTTTGCCCTCGAGCATC
* ** *
23429 TAAAAATTACCATTTTGCCCTCGAGTGTA
1 CAAAAATTACCATTTTGCCCTCGAGCATC
* * * *
23458 C-AAAATTACCGTTTTACCCCCGATCATC
1 CAAAAATTACCATTTTGCCCTCGAGCATC
* *
23486 CCAAAATTACCATTTTACCCTCGAGCATC
1 CAAAAATTACCATTTTGCCCTCGAGCATC
* * * * *
23515 TAAAAATTA-CATTTTTGCCC-CAAACTTT
1 CAAAAATTACCA-TTTTGCCCTCGAGCATC
23543 CAAAAATTACCATTTTGCCCTCGAGCATC
1 CAAAAATTACCATTTTGCCCTCGAGCATC
23572 CAAAAATT
1 CAAAAATT
23580 GCATTTTTAA
Statistics
Matches: 176, Mismatches: 49, Indels: 22
0.71 0.20 0.09
Matches are distributed among these distances:
26 1 0.01
27 15 0.09
28 52 0.30
29 108 0.61
ACGTcount: A:0.33, C:0.26, G:0.08, T:0.32
Consensus pattern (29 bp):
CAAAAATTACCATTTTGCCCTCGAGCATC
Found at i:27204 original size:25 final size:23
Alignment explanation
Indices: 27190--27244 Score: 83
Period size: 25 Copynumber: 2.3 Consensus size: 23
27180 TTTATTTTAA
27190 GTTATATATATATAAATAATTTT
1 GTTATATATATATAAATAATTTT
27213 GTTATATATGTATATAAATAATTTTT
1 GTTATATA--TATATAAATAA-TTTT
27239 GTTATA
1 GTTATA
27245 CACTAATCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
23 8 0.28
25 11 0.38
26 10 0.34
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (23 bp):
GTTATATATATATAAATAATTTT
Found at i:28892 original size:41 final size:41
Alignment explanation
Indices: 28833--28928 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 41
28823 GAATTTTATT
* * *
28833 TTAACAAGAATTCCAGTCATCTAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
* *
28874 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTTCATC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
* *
28915 TTGACAAAAATTCT
1 TTAACAAGAATTCT
28929 CCATGAACAA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.38, C:0.26, G:0.05, T:0.31
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
Found at i:32006 original size:17 final size:18
Alignment explanation
Indices: 31968--32008 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
31958 CTTTACTTTT
* *
31968 ATTTTATTTTACCACTGA
1 ATTTTATTTTAACACAGA
31986 ATTTTATTTTAACA-AGA
1 ATTTTATTTTAACACAGA
32003 ATTTTA
1 ATTTTA
32009 GTCATCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (18 bp):
ATTTTATTTTAACACAGA
Found at i:32097 original size:7 final size:7
Alignment explanation
Indices: 32085--32114 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
32075 TAGCAATAAC
32085 TATGAAG
1 TATGAAG
32092 TATGAAG
1 TATGAAG
32099 TATGAAG
1 TATGAAG
*
32106 TACGAAG
1 TATGAAG
32113 TA
1 TA
32115 CACTTTGTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.43, C:0.03, G:0.27, T:0.27
Consensus pattern (7 bp):
TATGAAG
Found at i:34434 original size:21 final size:20
Alignment explanation
Indices: 34402--34452 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
34392 AAATTTTAAC
34402 TTTATTTATATATTCTTTACAA
1 TTTATTT-TATATT-TTTACAA
*
34424 TTTATTTTATATTTTTATAA
1 TTTATTTTATATTTTTACAA
*
34444 TTTCTTTTA
1 TTTATTTTA
34453 AATATAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 14 0.52
21 6 0.22
22 7 0.26
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTATTTTATATTTTTACAA
Found at i:48212 original size:13 final size:13
Alignment explanation
Indices: 48194--48218 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48184 AAACGAACTT
48194 AATTAAACTTACA
1 AATTAAACTTACA
48207 AATTAAACTTAC
1 AATTAAACTTAC
48219 CAAAAACATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (13 bp):
AATTAAACTTACA
Found at i:49884 original size:14 final size:14
Alignment explanation
Indices: 49865--49894 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
49855 ATCCAAACAA
49865 TAGCAATAAAATAG
1 TAGCAATAAAATAG
*
49879 TAGCAATATAATAG
1 TAGCAATAAAATAG
49893 TA
1 TA
49895 AAATGGCAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (14 bp):
TAGCAATAAAATAG
Found at i:50027 original size:12 final size:11
Alignment explanation
Indices: 50008--50033 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
49998 GAAAATGGGC
50008 CCCATTTTTTG
1 CCCATTTTTTG
50019 CCCATTTTTTG
1 CCCATTTTTTG
50030 CCCA
1 CCCA
50034 ATCCCAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.12, C:0.35, G:0.08, T:0.46
Consensus pattern (11 bp):
CCCATTTTTTG
Found at i:51230 original size:43 final size:43
Alignment explanation
Indices: 51169--51255 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
51159 CATTACAAAC
51169 TTTTCTTCAGTTTCTGGCAATTTCTCTCTTTATCTAAAGTTGA
1 TTTTCTTCAGTTTCTGGCAATTTCTCTCTTTATCTAAAGTTGA
*
51212 TTTTCTTCAGTTTCTGGCACTTTCTCTCTTTATCTAAAGTTGA
1 TTTTCTTCAGTTTCTGGCAATTTCTCTCTTTATCTAAAGTTGA
51255 T
1 T
51256 GCCTTTCTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.17, C:0.20, G:0.11, T:0.52
Consensus pattern (43 bp):
TTTTCTTCAGTTTCTGGCAATTTCTCTCTTTATCTAAAGTTGA
Found at i:54879 original size:56 final size:56
Alignment explanation
Indices: 54801--54934 Score: 187
Period size: 56 Copynumber: 2.4 Consensus size: 56
54791 AAACAAAGCA
* *
54801 ATGAACAGGAGATATTCCCTGCAAGAAAAAACAAAATGAATAGCGACATTCTCTGGC
1 ATGAACAGTA-ATATTCCCTGCAAGAAAAAACAAAATGAATAGCGACATTCTCTGAC
* * * * * *
54858 ATGAATAGTAATATTCTCTGCAAGAAAAAACAAAATGAATTGTGAGATTCTCTGAT
1 ATGAACAGTAATATTCCCTGCAAGAAAAAACAAAATGAATAGCGACATTCTCTGAC
54914 ATGAACAGTAATATTCCCTGC
1 ATGAACAGTAATATTCCCTGC
54935 CATGAATAGT
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
56 59 0.88
57 8 0.12
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.25
Consensus pattern (56 bp):
ATGAACAGTAATATTCCCTGCAAGAAAAAACAAAATGAATAGCGACATTCTCTGAC
Found at i:55493 original size:22 final size:22
Alignment explanation
Indices: 55465--55531 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
55455 AAAAACCAAA
*
55465 ATGAACAGTGAGATTCTTTAGC
1 ATGAACAGTGAGATTCTCTAGC
* * * *
55487 ATGAACAGTAATATTATCTGGC
1 ATGAACAGTGAGATTCTCTAGC
* *
55509 ATGAATAATGAGATTCTCTAGC
1 ATGAACAGTGAGATTCTCTAGC
55531 A
1 A
55532 ATATTCTTGA
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.31
Consensus pattern (22 bp):
ATGAACAGTGAGATTCTCTAGC
Found at i:55595 original size:22 final size:22
Alignment explanation
Indices: 55568--55620 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 22
55558 ATGAATTGTG
55568 AGATTCTCTGACATGAAAAGTA
1 AGATTCTCTGACATGAAAAGTA
* *
55590 ATATTC-C---CATGAATAGTA
1 AGATTCTCTGACATGAAAAGTA
55608 AGATTCTCTGACA
1 AGATTCTCTGACA
55621 ATATTCTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 8
0.69 0.09 0.23
Matches are distributed among these distances:
18 15 0.62
19 1 0.04
21 1 0.04
22 7 0.29
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (22 bp):
AGATTCTCTGACATGAAAAGTA
Found at i:56320 original size:31 final size:29
Alignment explanation
Indices: 56285--56348 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 29
56275 TAAAATATGT
* *
56285 TTTAGT-TCTTGTACTTTGATAAATTCTAAAA
1 TTTAGTCTC-TGTACTTT-AAAAATT-AAAAA
56316 TTTAGTCTCTGTACTTTAAAAATTAAAAA
1 TTTAGTCTCTGTACTTTAAAAATTAAAAA
56345 TTTA
1 TTTA
56349 ATCCTTTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 8 0.27
30 6 0.20
31 14 0.47
32 2 0.07
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (29 bp):
TTTAGTCTCTGTACTTTAAAAATTAAAAA
Done.