Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014229.1 Kokia drynarioides strain JFW-HI SEQ_129262, 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: 552652
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 140 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:383789 original size:18 final size:18
Alignment explanation
Indices: 383766--383802 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
383756 TTTGGGGAGC
383766 CTAGCTCAATGAATAATT
1 CTAGCTCAATGAATAATT
*
383784 CTAGCTCAGTGAATAATT
1 CTAGCTCAATGAATAATT
383802 C
1 C
383803 CATTATCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (18 bp):
CTAGCTCAATGAATAATT
Found at i:385431 original size:16 final size:16
Alignment explanation
Indices: 385410--385440 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
385400 TGTAAGAATT
385410 GAACAACAAATTTAAC
1 GAACAACAAATTTAAC
385426 GAACAACAAATTTAA
1 GAACAACAAATTTAA
385441 TATGATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.16, G:0.06, T:0.19
Consensus pattern (16 bp):
GAACAACAAATTTAAC
Found at i:387043 original size:18 final size:18
Alignment explanation
Indices: 387020--387059 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
387010 ACATCAATTT
* *
387020 ATTATTCAAGTTATTGGA
1 ATTATTCAAATTATTCGA
387038 ATTATTCAAATTATTCGA
1 ATTATTCAAATTATTCGA
387056 ATTA
1 ATTA
387060 CAAATTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (18 bp):
ATTATTCAAATTATTCGA
Found at i:388532 original size:29 final size:29
Alignment explanation
Indices: 388495--388553 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
388485 CCGAAGTACT
388495 AAATAGAGAGCACATAAGTGGTGGCTAAC
1 AAATAGAGAGCACATAAGTGGTGGCTAAC
*
388524 AAATAGAGAGCACATAAGTGGTGGGTAAC
1 AAATAGAGAGCACATAAGTGGTGGCTAAC
388553 A
1 A
388554 GAAAGCACAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.12, G:0.29, T:0.17
Consensus pattern (29 bp):
AAATAGAGAGCACATAAGTGGTGGCTAAC
Found at i:388560 original size:25 final size:26
Alignment explanation
Indices: 388503--388562 Score: 68
Period size: 29 Copynumber: 2.2 Consensus size: 26
388493 CTAAATAGAG
*
388503 AGCACATAAGTGGTGGCTAACAAATAGAG
1 AGCACATAAGTGGTGGCTAAC--A-AGAA
*
388532 AGCACATAAGTGGTGGGTAAC-AGAA
1 AGCACATAAGTGGTGGCTAACAAGAA
388557 AGCACA
1 AGCACA
388563 CAAAGTGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 9 0.31
29 20 0.69
ACGTcount: A:0.42, C:0.15, G:0.28, T:0.15
Consensus pattern (26 bp):
AGCACATAAGTGGTGGCTAACAAGAA
Found at i:388578 original size:23 final size:23
Alignment explanation
Indices: 388550--388665 Score: 86
Period size: 23 Copynumber: 5.3 Consensus size: 23
388540 AGTGGTGGGT
* *
388550 AACAGAAAGCACACAAAGTGCTA
1 AACAGAGAGCACACGAAGTGCTA
* *
388573 AACAGAGAGTACAC-AA-AG-T-
1 AACAGAGAGCACACGAAGTGCTA
*
388592 -ACTGAG--CACACGAAGTGCTA
1 AACAGAGAGCACACGAAGTGCTA
*
388612 ATCAGAGAGCACACGAAGTGCTAA
1 AACAGAGAGCACACGAAGTGCT-A
*
388636 TAACAGAGAGCACGA-GACGTGCTA
1 -AACAGAGAGCAC-ACGAAGTGCTA
388660 AACAGA
1 AACAGA
388666 AAGCGCACTA
Statistics
Matches: 73, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
16 4 0.05
17 2 0.03
18 6 0.08
19 1 0.01
20 1 0.01
21 5 0.07
22 2 0.03
23 31 0.42
24 2 0.03
25 18 0.25
26 1 0.01
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACGAAGTGCTA
Found at i:388648 original size:25 final size:23
Alignment explanation
Indices: 388595--388665 Score: 90
Period size: 23 Copynumber: 3.0 Consensus size: 23
388585 ACAAAGTACT
388595 GAGCACACGAAGTGCTAATCAGA
1 GAGCACACGAAGTGCTAATCAGA
388618 GAGCACACGAAGTGCTAATAACAGA
1 GAGCACACGAAGTGCTAAT--CAGA
* *
388643 GAGCACGA-GACGTGCTAAACAGA
1 GAGCAC-ACGAAGTGCTAATCAGA
388666 AAGCGCACTA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
23 23 0.53
25 19 0.44
26 1 0.02
ACGTcount: A:0.41, C:0.21, G:0.27, T:0.11
Consensus pattern (23 bp):
GAGCACACGAAGTGCTAATCAGA
Found at i:389641 original size:33 final size:33
Alignment explanation
Indices: 389598--389686 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
389588 ACTTGTTCTT
389598 CTCTTATCCTTTGTCTTCAATTTGATCCTTATCC
1 CTCTT-TCCTTTGTCTTCAATTTGATCCTTATCC
389632 CTCTTTCCTTTGTCTTCAATTTGATCCTTATCC
1 CTCTTTCCTTTGTCTTCAATTTGATCCTTATCC
389665 CTCTTTCCTTCT-TCTTCAATTT
1 CTCTTTCCTT-TGTCTTCAATTT
389687 CATATAAACA
Statistics
Matches: 54, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
33 48 0.89
34 6 0.11
ACGTcount: A:0.12, C:0.30, G:0.04, T:0.53
Consensus pattern (33 bp):
CTCTTTCCTTTGTCTTCAATTTGATCCTTATCC
Found at i:391621 original size:29 final size:31
Alignment explanation
Indices: 391567--391636 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
391557 ATCTTAAAAT
391567 TATATATGAATTTTTATTTAATGTGTAATTA
1 TATATATGAATTTTTATTTAATGTGTAATTA
391598 TATATATGAATTTTTATTT-A-GTGTAATTA
1 TATATATGAATTTTTATTTAATGTGTAATTA
*
391627 TATATGTGAA
1 TATATATGAA
391637 ACTCTAAGTA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 18 0.47
30 1 0.03
31 19 0.50
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (31 bp):
TATATATGAATTTTTATTTAATGTGTAATTA
Found at i:400076 original size:21 final size:21
Alignment explanation
Indices: 400052--400101 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
400042 ACAAATTACA
* *
400052 AAAATTTCAAAATAATATT-TG
1 AAAATTT-AAAAAAAAATTATG
400073 AAAATTTAAAAAAAAATTATG
1 AAAATTTAAAAAAAAATTATG
400094 AAATATTT
1 AAA-ATTT
400102 TTCCAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.36
21 12 0.48
22 4 0.16
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (21 bp):
AAAATTTAAAAAAAAATTATG
Found at i:400076 original size:22 final size:22
Alignment explanation
Indices: 400051--400101 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 22
400041 AACAAATTAC
* *
400051 AAAAATTTCAAAATAATATT-TG
1 AAAAATTT-AAAAAAAAATTATG
400073 -AAAATTTAAAAAAAAATTATG
1 AAAAATTTAAAAAAAAATTATG
*
400094 AAATATTT
1 AAAAATTT
400102 TTCCAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 9 0.38
21 9 0.38
22 6 0.25
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (22 bp):
AAAAATTTAAAAAAAAATTATG
Found at i:400375 original size:20 final size:21
Alignment explanation
Indices: 400347--400385 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
400337 CTCAAATGAA
* *
400347 TTTATTCAACTCGA-TTCAAC
1 TTTACTCAAATCGAGTTCAAC
400367 TTTACTCAAATCGAGTTCA
1 TTTACTCAAATCGAGTTCA
400386 GATGATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (21 bp):
TTTACTCAAATCGAGTTCAAC
Found at i:403392 original size:6 final size:6
Alignment explanation
Indices: 403381--403422 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
403371 TACACCGACC
403381 TGGAGG TGGAGG TGGAGG TGGAGG TGGAGG TGGAGG TGGAGG
1 TGGAGG TGGAGG TGGAGG TGGAGG TGGAGG TGGAGG TGGAGG
403423 GAGTAGAAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.17, C:0.00, G:0.67, T:0.17
Consensus pattern (6 bp):
TGGAGG
Found at i:405074 original size:10 final size:10
Alignment explanation
Indices: 405050--405092 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
405040 TTATAATTTT
405050 TTAAAACATTA
1 TTAAAA-ATTA
405061 -TAAAAATTA
1 TTAAAAATTA
405070 TTAAAAATTA
1 TTAAAAATTA
*
405080 CTAAAAA-TA
1 TTAAAAATTA
405089 TTAA
1 TTAA
405093 TTTTAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 9 0.31
10 20 0.69
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:405085 original size:19 final size:20
Alignment explanation
Indices: 405050--405092 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
405040 TTATAATTTT
*
405050 TTAAAACATTATAAAAATTA
1 TTAAAACATTATAAAAAATA
405070 TTAAAA-ATTACT-AAAAATA
1 TTAAAACATTA-TAAAAAATA
405089 TTAA
1 TTAA
405093 TTTTAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
TTAAAACATTATAAAAAATA
Found at i:405307 original size:9 final size:9
Alignment explanation
Indices: 405287--405388 Score: 57
Period size: 10 Copynumber: 10.8 Consensus size: 9
405277 CCTCTTTGGC
405287 ATTTTTATTA
1 ATTTTTA-TA
405297 ATTTTTATA
1 ATTTTTATA
405306 ATTTTTTATA
1 A-TTTTTATA
* *
405316 GATTATTAATT
1 -ATT-TTTATA
*
405327 CTTTTTGA-A
1 ATTTTT-ATA
405336 ATTTTTATA
1 ATTTTTATA
*
405345 ATTGTTTA-C
1 ATT-TTTATA
* *
405354 ATATGTA-A
1 ATTTTTATA
405362 ATTTTTATAA
1 ATTTTTAT-A
405372 CATTTTTATA
1 -ATTTTTATA
405382 ATTTTTA
1 ATTTTTA
405389 AAAAATTATA
Statistics
Matches: 71, Mismatches: 12, Indels: 19
0.70 0.12 0.19
Matches are distributed among these distances:
8 9 0.13
9 23 0.32
10 26 0.37
11 13 0.18
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.61
Consensus pattern (9 bp):
ATTTTTATA
Found at i:406992 original size:27 final size:28
Alignment explanation
Indices: 406941--407002 Score: 99
Period size: 27 Copynumber: 2.2 Consensus size: 28
406931 AAAATGAAAC
406941 TTTTCGGATACTCGAGGGCAAAATGGTAA
1 TTTT-GGATACTCGAGGGCAAAATGGTAA
*
406970 TTTTGGATTCTCG-GGGCAAAATGGTAA
1 TTTTGGATACTCGAGGGCAAAATGGTAA
406997 TTTTGG
1 TTTTGG
407003 GAAAGTTAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 20 0.62
28 8 0.25
29 4 0.12
ACGTcount: A:0.26, C:0.11, G:0.29, T:0.34
Consensus pattern (28 bp):
TTTTGGATACTCGAGGGCAAAATGGTAA
Found at i:407097 original size:29 final size:28
Alignment explanation
Indices: 407016--407349 Score: 201
Period size: 29 Copynumber: 11.5 Consensus size: 28
407006 AGTTAGGGGT
* ** *
407016 TAAAAATGGAATTTTAGACATTCGGGGG
1 TAAAAATGGAATTTTGGAGGTTCGAGGG
* * * *
407044 T-GAAAGGGTAATTTTGAGAGTTTCGAGGT
1 TAAAAATGG-AATTTTG-GAGGTTCGAGGG
*
407073 TGAAAATGGAGATTTTGGAGGTTCGAGGG
1 TAAAAATGGA-ATTTTGGAGGTTCGAGGG
* *
407102 TAAAAATGGAATTTTTGGAAGTTTGAGGG
1 TAAAAATGGAA-TTTTGGAGGTTCGAGGG
* * *** *
407131 TAAAAATGGCATTTTTGGAAGTTTTTGGA
1 TAAAAATGG-AATTTTGGAGGTTCGAGGG
* * *
407160 TAAAAAAATGGAGTTTTTGGAAGTTTCG-GGA
1 T--AAAAATGGA-ATTTTGG-AGGTTCGAGGG
* *
407191 TCAAAAATGGAATTTTTGGAAGTTCGGGGG
1 T-AAAAATGGAA-TTTTGGAGGTTCGAGGG
* *
407221 TAAAAATGGAATTTTTGGAAGTTC-ATGG
1 TAAAAATGGAA-TTTTGGAGGTTCGAGGG
** *
407249 TCAAAAATGGAATTTTTGGAAATTTGAGGG
1 T-AAAAATGGAA-TTTTGGAGGTTCGAGGG
* * *
407279 TAAAAGTGGAATTTTTGGAAGTT-TAGGG
1 TAAAAATGGAA-TTTTGGAGGTTCGAGGG
* *
407307 TAAAAATGGAATTTTTGGAAGTT-TAGGG
1 TAAAAATGGAA-TTTTGGAGGTTCGAGGG
407335 TAAAAATGGAATTTT
1 TAAAAATGGAATTTT
407350 TGGAAGTTTT
Statistics
Matches: 256, Mismatches: 36, Indels: 29
0.80 0.11 0.09
Matches are distributed among these distances:
27 9 0.04
28 53 0.21
29 137 0.54
30 35 0.14
31 19 0.07
32 3 0.01
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.34
Consensus pattern (28 bp):
TAAAAATGGAATTTTGGAGGTTCGAGGG
Found at i:407115 original size:58 final size:59
Alignment explanation
Indices: 406987--407400 Score: 363
Period size: 58 Copynumber: 7.1 Consensus size: 59
406977 TTCTCGGGGC
* * * * *
406987 AAAATGGTAATTTTGGGAAAG-TTAGGGGTTAAAAATGGAA-TTTTAGACA-TTCGGGGGT-
1 AAAATGG-AATTTTTGG-AAGTTTCGAGGTTAAAAATGGAATTTTTGGA-AGTTCGAGGGTA
* * * *
407045 GAAAGGGTAA-TTTT-GAGAGTTTCGAGGTTGAAAATGGAGA-TTTTGGAGGTTCGAGGGTA
1 AAAATGG-AATTTTTGGA-AGTTTCGAGGTTAAAAATGGA-ATTTTTGGAAGTTCGAGGGTA
* * *** *
407104 AAAATGGAATTTTTGGAAGTTT-GAGGGTAAAAATGGCATTTTTGGAAGTTTTTGGATAAA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTTAAAAATGGAATTTTTGGAAGTTCGAGGGT--A
* * *
407164 AAAATGGAGTTTTTGGAAGTTTCG-GGATCAAAAATGGAATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGG-TTAAAAATGGAATTTTTGGAAGTTCGAGGGTA
* * *
407223 AAAATGGAATTTTTGGAAG-TTC-ATGGTCAAAAATGGAATTTTTGGAAATTTGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGA-GGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTA
* * *
407281 AAAGTGGAATTTTTGGAAGTTT--AGGGTAAAAATGGAATTTTTGGAAGTT-TAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTA
* * * **
407337 AAAATGGAATTTTTGGAAGTTTTG-GTGTCAAAAATGAAATTTTTGGAAGTTTAAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAG-GTTAAAAATGGAATTTTTGGAAGTTCGAGGGTA
407396 AAAAT
1 AAAAT
407401 TTATTTTTTG
Statistics
Matches: 296, Mismatches: 41, Indels: 37
0.79 0.11 0.10
Matches are distributed among these distances:
55 1 0.00
56 30 0.10
57 43 0.15
58 123 0.42
59 48 0.16
60 26 0.09
61 25 0.08
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTTCGAGGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTA
Found at i:407410 original size:29 final size:28
Alignment explanation
Indices: 407075--407400 Score: 384
Period size: 29 Copynumber: 11.2 Consensus size: 28
407065 TTCGAGGTTG
* *
407075 AAAATGGAGA-TTTTGGAGGTTCGAGGGTA
1 AAAATGGA-ATTTTTGGAAGTT-TAGGGTA
407104 AAAATGGAATTTTTGGAAGTTTGAGGGTA
1 AAAATGGAATTTTTGGAAGTTT-AGGGTA
* * *
407133 AAAATGGCATTTTTGGAAGTTTTTGGATAAA
1 AAAATGGAATTTTTGGAAG-TTTAGGGT--A
* *
407164 AAAATGGAGTTTTTGGAAGTTTCGGGATCA
1 AAAATGGAATTTTTGGAAGTTTAGGG-T-A
**
407194 AAAATGGAATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTT-TAGGGTA
* *
407223 AAAATGGAATTTTTGGAAGTTCATGGTCA
1 AAAATGGAATTTTTGGAAGTTTAGGGT-A
*
407252 AAAATGGAATTTTTGGAAATTTGAGGGTA
1 AAAATGGAATTTTTGGAAGTTT-AGGGTA
*
407281 AAAGTGGAATTTTTGGAAGTTTAGGGTA
1 AAAATGGAATTTTTGGAAGTTTAGGGTA
407309 AAAATGGAATTTTTGGAAGTTTAGGGTA
1 AAAATGGAATTTTTGGAAGTTTAGGGTA
*
407337 AAAATGGAATTTTTGGAAGTTTTGGTGTCA
1 AAAATGGAATTTTTGGAAGTTTAGG-GT-A
*
407367 AAAATGAAATTTTTGGAAGTTTAAGGGTA
1 AAAATGGAATTTTTGGAAGTTT-AGGGTA
407396 AAAAT
1 AAAAT
407401 TTATTTTTTG
Statistics
Matches: 260, Mismatches: 25, Indels: 24
0.84 0.08 0.08
Matches are distributed among these distances:
28 61 0.23
29 117 0.45
30 58 0.22
31 24 0.09
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.34
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTTAGGGTA
Found at i:408439 original size:20 final size:20
Alignment explanation
Indices: 408403--408440 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
408393 GTCATTAATG
*
408403 TTATTAATATTAGTAATATA
1 TTATTAATAATAGTAATATA
*
408423 TTATTAATAATATTAATA
1 TTATTAATAATAGTAATA
408441 CCATTTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TTATTAATAATAGTAATATA
Found at i:409140 original size:6 final size:6
Alignment explanation
Indices: 409129--409182 Score: 60
Period size: 6 Copynumber: 9.5 Consensus size: 6
409119 GTCTTAAGTC
* **
409129 AATTTA AATTT- AA-TTA AATTTA AATTTA AA-CTA AATTTA AAAATA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
409174 AATTTA AAT
1 AATTTA AAT
409183 CAATTTAATC
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
4 2 0.05
5 8 0.21
6 29 0.74
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (6 bp):
AATTTA
Found at i:409141 original size:16 final size:16
Alignment explanation
Indices: 409122--409169 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
409112 AAATTAAGTC
*
409122 TTAAGTCAATTTAAAT
1 TTAAGTAAATTTAAAT
*
409138 TTAATTAAATTTAAAT
1 TTAAGTAAATTTAAAT
*
409154 TTAAACTAAATTTAAA
1 TT-AAGTAAATTTAAA
409170 AATAAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 16 0.57
17 12 0.43
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (16 bp):
TTAAGTAAATTTAAAT
Found at i:409154 original size:11 final size:11
Alignment explanation
Indices: 409129--409182 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
409119 GTCTTAAGTC
*
409129 AATTTAAATTT
1 AATTTAAATTA
409140 AA-TTAAATTTA
1 AATTTAAA-TTA
*
409151 AATTTAAACTA
1 AATTTAAATTA
*
409162 AATTTAAAAATA
1 AATTT-AAATTA
409174 AATTTAAAT
1 AATTTAAAT
409183 CAATTTAATC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 5 0.14
11 16 0.44
12 15 0.42
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (11 bp):
AATTTAAATTA
Found at i:411373 original size:13 final size:13
Alignment explanation
Indices: 411352--411385 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
411342 ACAATATAAT
411352 AATAATAATCCTA
1 AATAATAATCCTA
*
411365 AATATTAATCCTA
1 AATAATAATCCTA
*
411378 AAAAATAA
1 AATAATAA
411386 AGGTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:412345 original size:18 final size:16
Alignment explanation
Indices: 412318--412360 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
412308 CACTTTTGTC
*
412318 TTCTTCTTTTTTTCTCAA
1 TTCTT-TTTTTTTTTC-A
412336 TTCTTTTTTTTTTTCA
1 TTCTTTTTTTTTTTCA
412352 TT-TTTTTTT
1 TTCTTTTTTT
412361 CTAAATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 3 0.12
17 9 0.38
18 5 0.21
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (16 bp):
TTCTTTTTTTTTTTCA
Found at i:413288 original size:11 final size:12
Alignment explanation
Indices: 413272--413318 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
413262 AATAGTGCAT
413272 AATT-AAAATAA
1 AATTAAAAATAA
413283 AATTAAAAATAA
1 AATTAAAAATAA
413295 AA-TAAAACA-AA
1 AATTAAAA-ATAA
*
413306 AATTGAAAATAA
1 AATTAAAAATAA
413318 A
1 A
413319 TATACTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
11 14 0.45
12 17 0.55
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (12 bp):
AATTAAAAATAA
Found at i:413307 original size:17 final size:17
Alignment explanation
Indices: 413275--413318 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
413265 AGTGCATAAT
**
413275 TAAAATAAAATTAAAAA
1 TAAAATAAAACAAAAAA
*
413292 TAAAATAAAACAAAAAT
1 TAAAATAAAACAAAAAA
413309 TGAAAATAAA
1 T-AAAATAAA
413319 TATACTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.20
Consensus pattern (17 bp):
TAAAATAAAACAAAAAA
Found at i:413360 original size:15 final size:16
Alignment explanation
Indices: 413330--413374 Score: 65
Period size: 15 Copynumber: 2.8 Consensus size: 16
413320 ATACTAAATT
413330 TTTTTTGAACTTTTCAAA
1 TTTTTT-AA-TTTTCAAA
413348 TTTTTT-ATTTTCAAA
1 TTTTTTAATTTTCAAA
413363 TTTTTTAATTTT
1 TTTTTTAATTTT
413375 TTTTTCAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 14 0.54
16 6 0.23
18 6 0.23
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (16 bp):
TTTTTTAATTTTCAAA
Found at i:413392 original size:22 final size:22
Alignment explanation
Indices: 413349--413389 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
413339 CTTTTCAAAT
413349 TTTTTATTTTCAAATTTTTTAA
1 TTTTTATTTTCAAATTTTTTAA
*
413371 TTTTT-TTTTCAATTTTTTT
1 TTTTTATTTTCAAATTTTTT
413390 TAAAAACATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTTATTTTCAAATTTTTTAA
Found at i:417442 original size:13 final size:13
Alignment explanation
Indices: 417421--417454 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
417411 ACAATATAAT
417421 AATAATAATCCTA
1 AATAATAATCCTA
*
417434 AATATTAATCCTA
1 AATAATAATCCTA
*
417447 AAAAATAA
1 AATAATAA
417455 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:418997 original size:40 final size:39
Alignment explanation
Indices: 418950--419025 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 39
418940 CTCATAAATT
418950 TAAATTTTATAAAATTTTATGATTTTTTAATTAATTTTTA
1 TAAATTTTATAAAATTTTATGA-TTTTTAATTAATTTTTA
*
418990 TAAATTTTATAAGATTTTATGATTTTTAATTAATTT
1 TAAATTTTATAAAATTTTATGATTTTTAATTAATTT
419026 CTAATGCTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 14 0.40
40 21 0.60
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (39 bp):
TAAATTTTATAAAATTTTATGATTTTTAATTAATTTTTA
Found at i:419008 original size:30 final size:31
Alignment explanation
Indices: 418949--419008 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
418939 GCTCATAAAT
* **
418949 TTAAATTTTATAAAATTTTATGATTTTTTAA
1 TTAAATTTTATAAAATTTTATAAGATTTTAA
*
418980 TTAATTTTTAT-AAATTTTATAAGATTTTA
1 TTAAATTTTATAAAATTTTATAAGATTTTA
419009 TGATTTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (31 bp):
TTAAATTTTATAAAATTTTATAAGATTTTAA
Found at i:419044 original size:20 final size:18
Alignment explanation
Indices: 418954--419060 Score: 72
Period size: 20 Copynumber: 5.6 Consensus size: 18
418944 TAAATTTAAA
418954 TTTTATAAAATTTTATGATT
1 TTTTAT-AAATTTTATGA-T
* * *
418974 TTTTAATTAATTTTTATAAA
1 TTTT-A-TAAATTTTATGAT
418994 TTTTATAAGATTTTATGAT
1 TTTTATAA-ATTTTATGAT
* *
419013 TTTTAATTAATTTCTAATGCT
1 TTTT-ATAAATTT-T-ATGAT
**
419034 TTTTATAAATTTTAAAAT
1 TTTTATAAATTTTATGAT
419052 TTTTA-AAAT
1 TTTTATAAAT
419061 GTCTTTTTAT
Statistics
Matches: 69, Mismatches: 12, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
17 4 0.06
18 10 0.14
19 17 0.25
20 19 0.28
21 18 0.26
22 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (18 bp):
TTTTATAAATTTTATGAT
Found at i:419046 original size:39 final size:38
Alignment explanation
Indices: 418950--419057 Score: 126
Period size: 39 Copynumber: 2.7 Consensus size: 38
418940 CTCATAAATT
*
418950 TAAATTTTATAAAATTTTATGATTTTTTAATTAATTTTTA
1 TAAATTTTAT-AAATTTTATGA-TTTTTAATTAATTTTAA
418990 TAAATTTTATAAGATTTTATGATTTTTAATTAATTTCTAA
1 TAAATTTTATAA-ATTTTATGATTTTTAATTAATTT-TAA
*** **
419030 TGCTTTTTATAAATTTTAAAATTTTTAA
1 TAAATTTTATAAATTTTATGATTTTTAA
419058 AATGTCTTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
39 30 0.50
40 30 0.50
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (38 bp):
TAAATTTTATAAATTTTATGATTTTTAATTAATTTTAA
Found at i:419634 original size:14 final size:13
Alignment explanation
Indices: 419600--419638 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
419590 TAAATAGTTG
*
419600 ACATATAAAAATT
1 ACATATAAAAAAT
419613 ACATATAAAGAAAT
1 ACATATAAA-AAAT
*
419627 ATATATAAAAAA
1 ACATATAAAAAA
419639 AATAGTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.26
Consensus pattern (13 bp):
ACATATAAAAAAT
Found at i:421055 original size:163 final size:163
Alignment explanation
Indices: 420872--421197 Score: 634
Period size: 163 Copynumber: 2.0 Consensus size: 163
420862 TGTAAAACCG
*
420872 AACCAAAGTCATATGTATCAATACTCTTGTAAATTATTGGTACCCAGATGTAGGGTATTGATACT
1 AACCAAAGTCATATGTATCAATACTCTTGTAAAGTATTGGTACCCAGATGTAGGGTATTGATACT
420937 TTAGTTTGGTATCGATACCAAATTGACATTTTGTTTAATTGAAAAACCATTTGAAAATACTAAGT
66 TTAGTTTGGTATCGATACCAAATTGACATTTTGTTTAATTGAAAAACCATTTGAAAATACTAAGT
421002 ATACATGCCTTTGCCAAGGTATCAATACTTAGT
131 ATACATGCCTTTGCCAAGGTATCAATACTTAGT
421035 AACCAAAGTCATATGTATCAATACTCTTGTAAAGTATTGGTACCCAGATGTAGGGTATTGATACT
1 AACCAAAGTCATATGTATCAATACTCTTGTAAAGTATTGGTACCCAGATGTAGGGTATTGATACT
*
421100 TTAGTTTGGTATCGATACCAAATTGACATTTTGTTTAATTGAAAAACCATTTGAAAATGCTAAGT
66 TTAGTTTGGTATCGATACCAAATTGACATTTTGTTTAATTGAAAAACCATTTGAAAATACTAAGT
421165 ATACATGCCTTTGCCAAGGTATCAATACTTAGT
131 ATACATGCCTTTGCCAAGGTATCAATACTTAGT
421198 GCCAAAATGT
Statistics
Matches: 161, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
163 161 1.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (163 bp):
AACCAAAGTCATATGTATCAATACTCTTGTAAAGTATTGGTACCCAGATGTAGGGTATTGATACT
TTAGTTTGGTATCGATACCAAATTGACATTTTGTTTAATTGAAAAACCATTTGAAAATACTAAGT
ATACATGCCTTTGCCAAGGTATCAATACTTAGT
Found at i:421569 original size:21 final size:21
Alignment explanation
Indices: 421514--421569 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
421504 ACAAAGGACA
*
421514 AAGTCTCGAAACTTTTGAGCT
1 AAGTCTCGAAACTTTTGAGCC
*
421535 AAGTATC-AATACTTTTGAGCC
1 AAGTCTCGAA-ACTTTTGAGCC
*
421556 AAGTCTCGAGACTT
1 AAGTCTCGAAACTT
421570 GCTCCATTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 2 0.07
21 26 0.90
22 1 0.03
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (21 bp):
AAGTCTCGAAACTTTTGAGCC
Found at i:441065 original size:25 final size:25
Alignment explanation
Indices: 441037--441090 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
441027 ATTTTCTAAG
*
441037 AAATAATTTTTTGAT-TTAATATTTT
1 AAATAATTTTTT-ATATTAAAATTTT
* *
441062 AAATGATTTTTTTTATTAAAATTTT
1 AAATAATTTTTTATATTAAAATTTT
441087 AAAT
1 AAAT
441091 TAAACAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.04
25 24 0.96
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (25 bp):
AAATAATTTTTTATATTAAAATTTT
Found at i:447551 original size:12 final size:11
Alignment explanation
Indices: 447536--447574 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
447526 AAATATTGTC
*
447536 TATATCATATGT
1 TATAT-ATATAT
447548 TATATATATAT
1 TATATATATAT
447559 ATATATATATAT
1 -TATATATATAT
447571 TATA
1 TATA
447575 AAGTTTAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (11 bp):
TATATATATAT
Found at i:454953 original size:23 final size:23
Alignment explanation
Indices: 454905--454962 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
454895 TGTCTCCATA
*
454905 TTTTTTCGTTTTGAGTAATTTAATT
1 TTTTTTC-TTTTGAGCAATTTAA-T
*
454930 TTTTTTCTTTTGAGCAGTTT-AT
1 TTTTTTCTTTTGAGCAATTTAAT
454952 TTTTTTCTTTT
1 TTTTTTCTTTT
454963 ATGTTCTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 12 0.39
23 1 0.03
24 11 0.35
25 7 0.23
ACGTcount: A:0.14, C:0.07, G:0.10, T:0.69
Consensus pattern (23 bp):
TTTTTTCTTTTGAGCAATTTAAT
Found at i:469333 original size:18 final size:18
Alignment explanation
Indices: 469310--469359 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
469300 GTGTAATTAT
*
469310 ATAATATATAGATTATAA
1 ATAATAAATAGATTATAA
* *
469328 ATAATAAATAGTTTATAC
1 ATAATAAATAGATTATAA
*
469346 ATTATAAATAGATT
1 ATAATAAATAGATT
469360 GTACATTTGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (18 bp):
ATAATAAATAGATTATAA
Found at i:469364 original size:18 final size:18
Alignment explanation
Indices: 469317--469366 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
469307 TATATAATAT
* *
469317 ATAGATTATAAATAATAA
1 ATAGATTATACATTATAA
*
469335 ATAGTTTATACATTATAA
1 ATAGATTATACATTATAA
*
469353 ATAGATTGTACATT
1 ATAGATTATACATT
469367 TGCTCTATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (18 bp):
ATAGATTATACATTATAA
Found at i:471519 original size:228 final size:228
Alignment explanation
Indices: 471122--471804 Score: 765
Period size: 228 Copynumber: 3.0 Consensus size: 228
471112 TCCAATCAAG
* * * * *
471122 ATGCAGATCTTCGTTAAGACCCTGACCGGCAAGACCATCACCCTCGAAGTCGAGAGTTCCGACAC
1 ATGCAGATCTTCGTCAAGACCCTGACCGGCAAGACCATAACCTTGGAAGTCGAGAGCTCCGACAC
* * * * * *
471187 GATCGACAACGTTAAGGCCAAAATCCAAGACAAGGAAGGGATCCCACCCGACCAACAACGTCTCA
66 GATCGACAACGTTAAGGCCAAGATCCAGGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTCA
* * *
471252 TCTTCGCCGGAAAACAGCTCGAAGATGGCCGGACCTTGGCCGATTACAACATCCAGAAGGAGTCC
131 TCTTTGCCGGGAAACAACTCGAAGATGGCCGGACCTTGGCCGATTACAACATCCAGAAGGAGTCC
* * *
471317 ACTCTCCATCTCGTCCTCCGTCTACGTGGTGGC
196 ACTCTCCATCTCGTCTTGCGTCTTCGTGGTGGC
* * * *
471350 ATGCAGATCTTCGTCAAAACCCTGACCGGCAAGACCATAACTTTGGAAGTCGAAAGCTCTGACAC
1 ATGCAGATCTTCGTCAAGACCCTGACCGGCAAGACCATAACCTTGGAAGTCGAGAGCTCCGACAC
* * *
471415 CATCGACAACGTCAAGGCCAAGATCCAGGACAAGGAAGGCATCCCACCAGACCAGCAAAGGCTCA
66 GATCGACAACGTTAAGGCCAAGATCCAGGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTCA
* * * * *
471480 TCTTTGCCGGGAAACAACTCGAGGACGGTCGCACCTTGGCCGATTACAACATCCAGAAGGAGTCG
131 TCTTTGCCGGGAAACAACTCGAAGATGGCCGGACCTTGGCCGATTACAACATCCAGAAGGAGTCC
* * * * * * *
471545 ACACTCCATTTGGTATTGAGGCTTCGTGGTGGG
196 ACTCTCCATCTCGTCTTGCGTCTTCGTGGTGGC
* ** * * * * * *
471578 ATGCAGATTTTCGTCAAGACGTTGACTGGGAAAACCATAACCTTGGAGGTGGAGAGCTCCGATAC
1 ATGCAGATCTTCGTCAAGACCCTGACCGGCAAGACCATAACCTTGGAAGTCGAGAGCTCCGACAC
* * * * * * * *
471643 GATCGACAATGTTAAGGCGAAGATTCAGGACAAAGAAGGGATTCCACCAGATCAGCAAAGGTTGA
66 GATCGACAACGTTAAGGCCAAGATCCAGGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTCA
* * * ** * * * * *
471708 T-TTTCGCTGGGAAACAATTGGAAGATGGGAGGACTTTGGCTGATTACAATATTCAGAAGGAATC
131 TCTTT-GCCGGGAAACAACTCGAAGATGGCCGGACCTTGGCCGATTACAACATCCAGAAGGAGTC
* *
471772 CACTCTCCACCTTGTCTTGCGTCTTCGTGGTGG
195 CACTCTCCATCTCGTCTTGCGTCTTCGTGGTGG
471805 TTTCTAAGTT
Statistics
Matches: 373, Mismatches: 81, Indels: 2
0.82 0.18 0.00
Matches are distributed among these distances:
227 3 0.01
228 370 0.99
ACGTcount: A:0.29, C:0.26, G:0.25, T:0.20
Consensus pattern (228 bp):
ATGCAGATCTTCGTCAAGACCCTGACCGGCAAGACCATAACCTTGGAAGTCGAGAGCTCCGACAC
GATCGACAACGTTAAGGCCAAGATCCAGGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTCA
TCTTTGCCGGGAAACAACTCGAAGATGGCCGGACCTTGGCCGATTACAACATCCAGAAGGAGTCC
ACTCTCCATCTCGTCTTGCGTCTTCGTGGTGGC
Found at i:481003 original size:24 final size:25
Alignment explanation
Indices: 480976--481031 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
480966 AAACAAAATT
* **
480976 AAAAAATCATTAAGGAT-CCAAAAA
1 AAAAAATCATAAAAAATCCCAAAAA
481000 AAAAAATCATAAAAAATCCCAAAAA
1 AAAAAATCATAAAAAATCCCAAAAA
481025 AAAAAAT
1 AAAAAAT
481032 GAAAACTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 14 0.50
25 14 0.50
ACGTcount: A:0.70, C:0.12, G:0.04, T:0.14
Consensus pattern (25 bp):
AAAAAATCATAAAAAATCCCAAAAA
Found at i:482827 original size:18 final size:18
Alignment explanation
Indices: 482783--482827 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
482773 TTGTTTATAT
482783 TATTTAT-TCAAATATTG
1 TATTTATATCAAATATTG
482800 TATTTAATAT-AAATATTTG
1 TATTT-ATATCAAATA-TTG
482819 TATTTATAT
1 TATTTATAT
482828 GTGTTTGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 5 0.20
18 11 0.44
19 9 0.36
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (18 bp):
TATTTATATCAAATATTG
Found at i:489583 original size:3 final size:3
Alignment explanation
Indices: 489575--489603 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
489565 TCTAAGAATC
489575 CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
489604 CTCTCTCCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:492976 original size:139 final size:139
Alignment explanation
Indices: 492746--493026 Score: 562
Period size: 139 Copynumber: 2.0 Consensus size: 139
492736 ATTTACACAT
492746 GAATACACTACGATAAAATTTTTAATATTGTATGAAAAATATGAAGCTTAATAAAAATGATAAAA
1 GAATACACTACGATAAAATTTTTAATATTGTATGAAAAATATGAAGCTTAATAAAAATGATAAAA
492811 ATAAAATTTAACTTTCAACTGTATGTAAAATTTACTTTCCTACAATTATTTACATAAATTATATT
66 ATAAAATTTAACTTTCAACTGTATGTAAAATTTACTTTCCTACAATTATTTACATAAATTATATT
492876 CTCATGACG
131 CTCATGACG
492885 GAATACACTACGATAAAATTTTTAATATTGTATGAAAAATATGAAGCTTAATAAAAATGATAAAA
1 GAATACACTACGATAAAATTTTTAATATTGTATGAAAAATATGAAGCTTAATAAAAATGATAAAA
492950 ATAAAATTTAACTTTCAACTGTATGTAAAATTTACTTTCCTACAATTATTTACATAAATTATATT
66 ATAAAATTTAACTTTCAACTGTATGTAAAATTTACTTTCCTACAATTATTTACATAAATTATATT
493015 CTCATGACG
131 CTCATGACG
493024 GAA
1 GAA
493027 GGAAAATAAT
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
139 142 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (139 bp):
GAATACACTACGATAAAATTTTTAATATTGTATGAAAAATATGAAGCTTAATAAAAATGATAAAA
ATAAAATTTAACTTTCAACTGTATGTAAAATTTACTTTCCTACAATTATTTACATAAATTATATT
CTCATGACG
Found at i:494623 original size:24 final size:23
Alignment explanation
Indices: 494596--494641 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
494586 TCAGCCCAAC
*
494596 TAGTTAATAGGGACTTTCAATTTA
1 TAGTTAATA-GCACTTTCAATTTA
* *
494620 TAGTTCATATCACTTTCAATTT
1 TAGTTAATAGCACTTTCAATTT
494642 CAATTTCACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (23 bp):
TAGTTAATAGCACTTTCAATTTA
Found at i:494800 original size:3 final size:3
Alignment explanation
Indices: 494792--494818 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
494782 TGCTAGCTAC
494792 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
494819 TTACACTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:495375 original size:16 final size:16
Alignment explanation
Indices: 495337--495380 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
495327 CTATTCTTCC
* *
495337 TTCTTTTGTTTCTTTT
1 TTCTTTTATTTCTTTA
* *
495353 TTTTTTTCTTTCTTTA
1 TTCTTTTATTTCTTTA
495369 TTCTTTTATTTC
1 TTCTTTTATTTC
495381 ATATATATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.80
Consensus pattern (16 bp):
TTCTTTTATTTCTTTA
Found at i:501877 original size:17 final size:17
Alignment explanation
Indices: 501855--501888 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
501845 AAAAATGAAA
*
501855 GGATTAAATTTAAAAAG
1 GGATTAAATTAAAAAAG
*
501872 GGATTAGATTAAAAAAG
1 GGATTAAATTAAAAAAG
501889 TATAAAAGGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26
Consensus pattern (17 bp):
GGATTAAATTAAAAAAG
Found at i:505869 original size:33 final size:33
Alignment explanation
Indices: 505827--505893 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
505817 TATGTGATGT
505827 GTGGGGCAGTACAGATGAGACAAAACATATCGA
1 GTGGGGCAGTACAGATGAGACAAAACATATCGA
505860 GTGGGGCAGTACAGATGAGACAAAACATATCGA
1 GTGGGGCAGTACAGATGAGACAAAACATATCGA
505893 G
1 G
505894 ACATCGCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.39, C:0.15, G:0.31, T:0.15
Consensus pattern (33 bp):
GTGGGGCAGTACAGATGAGACAAAACATATCGA
Found at i:507509 original size:23 final size:22
Alignment explanation
Indices: 507461--507504 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
507451 TCTCTCACTC
*
507461 TTCTGCTTCTCCCTCTATTTTA
1 TTCTGCTTCTCCATCTATTTTA
*
507483 TTCT-CTTCTCCATCTCTTTTA
1 TTCTGCTTCTCCATCTATTTTA
507504 T
1 T
507505 GTTCTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.09, C:0.32, G:0.02, T:0.57
Consensus pattern (22 bp):
TTCTGCTTCTCCATCTATTTTA
Found at i:507528 original size:17 final size:19
Alignment explanation
Indices: 507496--507530 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
507486 TCTTCTCCAT
507496 CTCTTTTATGTTCTTTTAA
1 CTCTTTTATGTTCTTTTAA
507515 CTCTTTT-T-TTCTTTTA
1 CTCTTTTATGTTCTTTTA
507531 CGTTACGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.11, C:0.17, G:0.03, T:0.69
Consensus pattern (19 bp):
CTCTTTTATGTTCTTTTAA
Found at i:507725 original size:35 final size:35
Alignment explanation
Indices: 507685--507760 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
507675 GGTATTTCGG
*
507685 CTTTTTACTTTTCAAAATAATATATTACTTTTCAA
1 CTTTTTACTTTTCAAAATAATATATTACTTGTCAA
* *
507720 CTTTTTATTTTTTAAAATAATATATTACTTGTCAA
1 CTTTTTACTTTTCAAAATAATATATTACTTGTCAA
507755 CTTTTT
1 CTTTTT
507761 TAAACTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.32, C:0.12, G:0.01, T:0.55
Consensus pattern (35 bp):
CTTTTTACTTTTCAAAATAATATATTACTTGTCAA
Found at i:508297 original size:35 final size:36
Alignment explanation
Indices: 508251--508329 Score: 142
Period size: 35 Copynumber: 2.2 Consensus size: 36
508241 AATGGATAAG
*
508251 ACATTTTTTAGTTTCAATTATT-ACGGAAAAAAAAA
1 ACATTTTTTAGTTTCAATTATTAACAGAAAAAAAAA
508286 ACATTTTTTAGTTTCAATTATTAACAGAAAAAAAAA
1 ACATTTTTTAGTTTCAATTATTAACAGAAAAAAAAA
508322 ACATTTTT
1 ACATTTTT
508330 AAAGCCTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 22 0.52
36 20 0.48
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.39
Consensus pattern (36 bp):
ACATTTTTTAGTTTCAATTATTAACAGAAAAAAAAA
Found at i:510342 original size:26 final size:26
Alignment explanation
Indices: 510313--510363 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
510303 TGGGGTCAAT
*
510313 TTTTTTAATTCCTTTAATTTCTAGGC
1 TTTTTTAATTCCTTTAATATCTAGGC
*
510339 TTTTTTAATTCTTTTAATATCTAGG
1 TTTTTTAATTCCTTTAATATCTAGG
510364 TAGGTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.22, C:0.12, G:0.08, T:0.59
Consensus pattern (26 bp):
TTTTTTAATTCCTTTAATATCTAGGC
Found at i:510394 original size:21 final size:23
Alignment explanation
Indices: 510370--510414 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
510360 TAGGTAGGTG
510370 ATTTTTCT-TTTCTTT-TTTTTA
1 ATTTTTCTATTTCTTTATTTTTA
510391 A-TTTTCTATTTCTTTATTTTTA
1 ATTTTTCTATTTCTTTATTTTTA
510413 AT
1 AT
510415 CAAATTTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 6 0.29
21 8 0.38
22 7 0.33
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.76
Consensus pattern (23 bp):
ATTTTTCTATTTCTTTATTTTTA
Found at i:510413 original size:22 final size:20
Alignment explanation
Indices: 510372--510414 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 20
510362 GGTAGGTGAT
510372 TTTTCTTTTCTTTTTTTTAA
1 TTTTCTTTTCTTTTTTTTAA
510392 TTTTCTATTTCTTTATTTTTAA
1 TTTTCT-TTTCTTT-TTTTTAA
510414 T
1 T
510415 CAAATTTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.29
21 7 0.33
22 8 0.38
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTCTTTTCTTTTTTTTAA
Found at i:510480 original size:16 final size:16
Alignment explanation
Indices: 510447--510479 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
510437 CCACCAATGG
*
510447 TTACAATTGATTTTTT
1 TTACAAGTGATTTTTT
510463 TTACAAGTG-TTTTTT
1 TTACAAGTGATTTTTT
510478 TT
1 TT
510480 TTCTAGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.21, C:0.06, G:0.09, T:0.64
Consensus pattern (16 bp):
TTACAAGTGATTTTTT
Found at i:512801 original size:19 final size:19
Alignment explanation
Indices: 512779--512822 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
512769 GAAGAAATTG
* *
512779 ATAATATTGATGAATCTCT
1 ATAAGATTGATAAATCTCT
* *
512798 ATAAGCTTGTTAAATCTCT
1 ATAAGATTGATAAATCTCT
512817 ATAAGA
1 ATAAGA
512823 ACTTAAACAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (19 bp):
ATAAGATTGATAAATCTCT
Found at i:524617 original size:18 final size:19
Alignment explanation
Indices: 524596--524633 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
524586 TATATATTAG
524596 TTCAAA-ATTATACATTTT
1 TTCAAATATTATACATTTT
* *
524614 TTCAAATGTTTTACATTTT
1 TTCAAATATTATACATTTT
524633 T
1 T
524634 CCTTCCCACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.55
Consensus pattern (19 bp):
TTCAAATATTATACATTTT
Found at i:527478 original size:55 final size:55
Alignment explanation
Indices: 527394--527548 Score: 177
Period size: 55 Copynumber: 2.8 Consensus size: 55
527384 GCTATGTAAC
* * * *
527394 AATCGATTTAAATATATAAATAATCGATTCAAAATAAG-TAATATTCTAATATGAA
1 AATCGATTTAAACATATAAACAATCGATTCAAAAGAAGCT-ATATTCTAACATGAA
* * * * *
527449 AATTGATTTAAACATGTAAACAATTGATTCAAAAGAAGCTGTATTCTAACATGAC
1 AATCGATTTAAACATATAAACAATCGATTCAAAAGAAGCTATATTCTAACATGAA
* * * *
527504 AATCGATTTAAACATAAAAACAATCTATCCAAAAGAAGCAATATT
1 AATCGATTTAAACATATAAACAATCGATTCAAAAGAAGCTATATT
527549 TTTTAAAAAT
Statistics
Matches: 82, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
55 81 0.99
56 1 0.01
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.30
Consensus pattern (55 bp):
AATCGATTTAAACATATAAACAATCGATTCAAAAGAAGCTATATTCTAACATGAA
Found at i:527939 original size:42 final size:42
Alignment explanation
Indices: 527892--527976 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
527882 TTTTTTACCT
527892 AACTAGTGGTACATAAGAGTATCATCATTAAAATATGCTAAC
1 AACTAGTGGTACATAAGAGTATCATCATTAAAATATGCTAAC
527934 AACTAGTGGTACATAAGAGTATCATCATTAAAATATGCTAAC
1 AACTAGTGGTACATAAGAGTATCATCATTAAAATATGCTAAC
527976 A
1 A
527977 TGGCATTGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (42 bp):
AACTAGTGGTACATAAGAGTATCATCATTAAAATATGCTAAC
Found at i:528302 original size:26 final size:26
Alignment explanation
Indices: 528248--528305 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
528238 ACATTTTTTT
* *
528248 TATATTTTTATATACTTTATATAAAA
1 TATATTTTTATATACTTTAGACAAAA
*
528274 TATATTTTTATATA-TTTGGAC-AAA
1 TATATTTTTATATACTTTAGACAAAA
528298 TATATTTT
1 TATATTTT
528306 ATAAATTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 11 0.38
25 4 0.14
26 14 0.48
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.55
Consensus pattern (26 bp):
TATATTTTTATATACTTTAGACAAAA
Found at i:532986 original size:61 final size:59
Alignment explanation
Indices: 532864--533303 Score: 417
Period size: 60 Copynumber: 7.3 Consensus size: 59
532854 GTCGGTCATG
* * * * * *
532864 TTATATGATAAAAAAAATTCAAATTTTTTTGGTATTGACC-GTGTAATGGCAGACACCCCTTT
1 TTATCTGATAAAAAAAA-TCAAA-TTTTTT-GTGTTGGCCATTG-CATGGCCGACACCCCTTT
532926 TTATCTGATAAAAAAAATCAAAGTTTTTTGTGTTGGCCATTGCATGGCCGACACCACCTTT
1 TTATCTGATAAAAAAAATCAAA-TTTTTTGTGTTGGCCATTGCATGGCCGACACC-CCTTT
* ** **
532987 TTAT-TTA-AAAAAAAATCAAATTTTTTGGTGTTGGCCATTGCATGGTTGACACCTTTTT
1 TTATCTGATAAAAAAAATCAAATTTTTT-GTGTTGGCCATTGCATGGCCGACACCCCTTT
* * *
533045 TTATCAGATAAAAAAATTCAAATTTTTTGGTGTTGGTCATTGCATGGCCGACACCCCTTT
1 TTATCTGATAAAAAAAATCAAATTTTTT-GTGTTGGCCATTGCATGGCCGACACCCCTTT
* * **
533105 TTATCTGATAAAAAAATTCAAATATTTTTTGTGTTGGTCA-TGCATTGATCGACACCCACTTT
1 TTATCTGATAAAAAAAATC-AA-ATTTTTTGTGTTGGCCATTGCA-TGGCCGACACCC-CTTT
* * * *
533167 TTATTTGAT-AAAAAAATCAAATATTTTGGTGTTGGTCATTGCATGACCGACACCACCTTTT
1 TTATCTGATAAAAAAAATCAAAT-TTTTTGTGTTGGCCATTGCATGGCCGACACC-CC-TTT
* * * *
533228 TTATCTGA-CAAAAAATTCAAAATTTTTGGTGTTGGCCA-TGCATTGGCCCACACCACCATTT
1 TTATCTGATAAAAAAAATC-AAATTTTTTGTGTTGGCCATTGCA-TGGCCGACACC-CC-TTT
*
533289 TTATCAGATAAAAAA
1 TTATCTGATAAAAAA
533304 TATTTTTTTT
Statistics
Matches: 326, Mismatches: 35, Indels: 34
0.83 0.09 0.09
Matches are distributed among these distances:
58 13 0.04
59 40 0.12
60 118 0.36
61 111 0.34
62 44 0.13
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (59 bp):
TTATCTGATAAAAAAAATCAAATTTTTTGTGTTGGCCATTGCATGGCCGACACCCCTTT
Found at i:533188 original size:121 final size:120
Alignment explanation
Indices: 532873--533325 Score: 501
Period size: 121 Copynumber: 3.8 Consensus size: 120
532863 GTTATATGAT
* * * * * * *
532873 AAAAAAAATTCAAATTTTTTTGGTATTGACCGTGTAATG-GCAGACACCCCTTTTTATCTGATAA
1 AAAAAAAATTCAAATATTTTTGGTGTTGGCCATGCATTGATC-GACACCCCTTTTTATCTGAT-A
* *
532937 AAAAAATCAAAGTTTTTT-GTGTTGGCCATTGCATGGCCGACACCACCTTTTTAT-TT
64 AAAAAATCAAA-TTTTTTGGTGTTGGTCATTGCATGGCCGACACCACCTTTTTATCTG
* * * ** *
532993 AAAAAAAAATCAAAT-TTTTTGGTGTTGGCCATTGCA-TGGTTGACACCTTTTTTTATCAGATAA
1 AAAAAAAATTCAAATATTTTTGGTGTTGGCCA-TGCATTGATCGACACCCCTTTTTATCTGATAA
533056 AAAAATTCAAATTTTTTGGTGTTGGTCATTGCATGGCCGACACC-CCTTTTTATCTG
65 AAAAA-TCAAATTTTTTGGTGTTGGTCATTGCATGGCCGACACCACCTTTTTATCTG
* * *
533112 ATAAAAAAATTCAAATATTTTTTGTGTTGGTCATGCATTGATCGACACCCACTTTTTATTTGATA
1 A-AAAAAAATTCAAATATTTTTGGTGTTGGCCATGCATTGATCGACACCC-CTTTTTATCTGATA
* *
533177 AAAAAATCAAATATTTTGGTGTTGGTCATTGCATGACCGACACCACCTTTTTTATCTG
64 AAAAAATCAAATTTTTTGGTGTTGGTCATTGCATGGCCGACACCACC-TTTTTATCTG
* ** * *
533235 ACAAAAAATTCAAA-ATTTTTGGTGTTGGCCATGCATTGGCCCACACCACCATTTTTATCAGAT-
1 AAAAAAAATTCAAATATTTTTGGTGTTGGCCATGCATTGATCGACACC-CC-TTTTTATCTGATA
** *
533298 AAAAAAT-ATTTTTTTTTGTGTTGGTCAT
64 AAAAAATCAAATTTTTTGGTGTTGGTCAT
533326 GTATTAGTCG
Statistics
Matches: 285, Mismatches: 35, Indels: 26
0.82 0.10 0.08
Matches are distributed among these distances:
118 22 0.08
119 64 0.22
120 51 0.18
121 95 0.33
122 42 0.15
123 11 0.04
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (120 bp):
AAAAAAAATTCAAATATTTTTGGTGTTGGCCATGCATTGATCGACACCCCTTTTTATCTGATAAA
AAAATCAAATTTTTTGGTGTTGGTCATTGCATGGCCGACACCACCTTTTTATCTG
Found at i:534850 original size:14 final size:15
Alignment explanation
Indices: 534826--534855 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
534816 GCATAATACC
534826 ACAAGAACCAAAACA
1 ACAAGAACCAAAACA
534841 ACAA-AACCAAAACA
1 ACAAGAACCAAAACA
534855 A
1 A
534856 AAGTTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.70, C:0.27, G:0.03, T:0.00
Consensus pattern (15 bp):
ACAAGAACCAAAACA
Found at i:541109 original size:17 final size:17
Alignment explanation
Indices: 541087--541167 Score: 81
Period size: 17 Copynumber: 4.7 Consensus size: 17
541077 ATTTTTTAAA
*
541087 TAAATTTGAATTTATTT
1 TAAATTTAAATTTATTT
* *
541104 TAAATTCAAATTCATTT
1 TAAATTTAAATTTATTT
* * * *
541121 TGAGTTTAGATTTACTT
1 TAAATTTAAATTTATTT
541138 TAAATTTAAATTTATTTT
1 TAAATTTAAATTTA-TTT
*
541156 TAAATTAAAATT
1 TAAATTTAAATT
541168 AAATTAAAGG
Statistics
Matches: 49, Mismatches: 14, Indels: 1
0.77 0.22 0.02
Matches are distributed among these distances:
17 36 0.73
18 13 0.27
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.53
Consensus pattern (17 bp):
TAAATTTAAATTTATTT
Found at i:542847 original size:28 final size:28
Alignment explanation
Indices: 542787--542922 Score: 116
Period size: 29 Copynumber: 4.7 Consensus size: 28
542777 ATACTGTTCA
* *
542787 AAAATTATATTTTGACCCCCAACTTAATC
1 AAAATTATATTTTGACCCCAAACTT-TTC
*
542816 AAAATTATATTTTGACCCCAAACTTTTG
1 AAAATTATATTTTGACCCCAAACTTTTC
*
542844 AAAATTACATTTT-ACCCCAAAC-TTTC
1 AAAATTATATTTTGACCCCAAACTTTTC
* *
542870 AAAAAAATTACCATTTT-ACCCCCAAACTTTCC
1 ---AAAATTA-TATTTTGA-CCCCAAACTTTTC
**
542902 AAAATTCCATTCTTGACCCCA
1 AAAATTATATT-TTGACCCCA
542923 TTTTTTCAAA
Statistics
Matches: 92, Mismatches: 7, Indels: 16
0.80 0.06 0.14
Matches are distributed among these distances:
26 3 0.03
27 9 0.10
28 17 0.18
29 44 0.48
30 8 0.09
31 8 0.09
32 3 0.03
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (28 bp):
AAAATTATATTTTGACCCCAAACTTTTC
Found at i:542905 original size:29 final size:28
Alignment explanation
Indices: 542815--543184 Score: 204
Period size: 29 Copynumber: 12.7 Consensus size: 28
542805 CCAACTTAAT
* *
542815 CAAAATTA-TATTTTGACCCCAAACTTTT
1 CAAAATTACCATTTT-ACCCCAAACTTTC
*
542843 GAAAATTA-CATTTTACCCCAAACTTTC
1 CAAAATTACCATTTTACCCCAAACTTTC
*
542870 AAAAAAATTACCATTTTACCCCCAAACTTTC
1 --CAAAATTACCATTTTA-CCCCAAACTTTC
***
542901 CAAAATT-CCATTCTTGACCCCATTTTTTC
1 CAAAATTACCATT-TT-ACCCCAAACTTTC
* * *
542930 AAAAATTACCATTTTACCTCGAACTTTC
1 CAAAATTACCATTTTACCCCAAACTTTC
* *** **
542958 CAGAATT-CCATTTTTTACCTTGATTTTTC
1 CAAAATTACCA--TTTTACCCCAAACTTTC
542987 CAAAAATTACCATTTTACCCTCAAAC-TTC
1 C-AAAATTACCATTTTACCC-CAAACTTTC
*
543016 CAAAAATT-CCATTTTTAACCCC-AATTTCTC
1 C-AAAATTACCA-TTTT-ACCCCAAACTT-TC
543046 CAAAAATTACCATTTTACCCCCAAAC-TTC
1 C-AAAATTACCATTTTA-CCCCAAACTTTC
*
543075 CAAAAATT-CCATTTTTGACCCC-AATTTCTC
1 C-AAAATTACCA-TTTT-ACCCCAAACTT-TC
* *
543105 CAAAAAATTA-CATTTTTACCCTCGAACTTCC
1 C--AAAATTACCA-TTTTACCC-CAAACTTTC
** ** * *
543136 CAAAATTACCAATTTGCCCCCCGAGTGTC
1 CAAAATTACC-ATTTTACCCCAAACTTTC
543165 CAAAATTACCATTTTACCCC
1 CAAAATTACCATTTTACCCC
543185 CGAGTATAAA
Statistics
Matches: 274, Mismatches: 39, Indels: 58
0.74 0.11 0.16
Matches are distributed among these distances:
27 15 0.05
28 48 0.18
29 112 0.41
30 57 0.21
31 38 0.14
32 4 0.01
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (28 bp):
CAAAATTACCATTTTACCCCAAACTTTC
Found at i:542907 original size:58 final size:58
Alignment explanation
Indices: 542831--543185 Score: 305
Period size: 59 Copynumber: 6.1 Consensus size: 58
542821 TATATTTTGA
** * *
542831 CCCCAAACTTTTGAAAATTACA-TTTT-ACCCCAAACTTTCAAAAAAATTACCATTTTAC
1 CCCCAAACTTTCCAAAATTCCATTTTTGACCCC-AATTTTC-AAAAAATTACCATTTTAC
* *
542889 CCCCAAACTTTCCAAAATTCCATTCTTGACCCCATTTTTTC-AAAAATTACCATTTTA-
1 CCCCAAACTTTCCAAAATTCCATTTTTGACCCCA-ATTTTCAAAAAATTACCATTTTAC
* * * * ** * *
542946 CCTCGAACTTTCCAGAATTCCATTTTTTACCTTGATTTTTCCAAAAATTACCATTTTAC
1 CCCCAAACTTTCCAAAATTCCATTTTTGACC-CCAATTTTCAAAAAATTACCATTTTAC
* * *
543005 CCTCAAAC-TTCCAAAAATTCCATTTTTAACCCCAATTTCTCCAAAAATTACCATTTTAC
1 CCCCAAACTTTCC-AAAATTCCATTTTTGACCCCAATTT-TCAAAAAATTACCATTTTAC
543064 CCCCAAAC-TTCCAAAAATTCCATTTTTGACCCCAATTTCTCCAAAAAATTA-CATTTTTAC
1 CCCCAAACTTTCC-AAAATTCCATTTTTGACCCCAATTT-T-CAAAAAATTACCA-TTTTAC
* * * * * * * * *
543124 CCTCGAACTTCCCAAAATTACCA-ATTTGCCCCCCGAGTGTC-CAAAATTACCATTTTAC
1 CCCCAAACTTTCCAAAATT-CCATTTTTG-ACCCCAATTTTCAAAAAATTACCATTTTAC
543182 CCCC
1 CCCC
543186 GAGTATAAAA
Statistics
Matches: 251, Mismatches: 32, Indels: 28
0.81 0.10 0.09
Matches are distributed among these distances:
57 32 0.13
58 76 0.30
59 90 0.36
60 41 0.16
61 12 0.05
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (58 bp):
CCCCAAACTTTCCAAAATTCCATTTTTGACCCCAATTTTCAAAAAATTACCATTTTAC
Found at i:543048 original size:59 final size:58
Alignment explanation
Indices: 542872--543142 Score: 332
Period size: 59 Copynumber: 4.6 Consensus size: 58
542862 AAACTTTCAA
* * * *
542872 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTCTTGACCCC-ATTTTTTC
1 AAAAATTACCATTTTACCCTCAAAC-TTCCAAAATTCCATTTTTGACCCCAATTTCTCC
* * * *** *
542930 AAAAATTACCATTTTA-CCTCGAACTTTCCAGAATTCCATTTTTTACCTTGATTTTTCC
1 AAAAATTACCATTTTACCCTCAAAC-TTCCAAAATTCCATTTTTGACCCCAATTTCTCC
*
542988 AAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCCCAATTTCTCC
1 AAAAATTACCATTTTACCCTCAAACTTCC-AAAATTCCATTTTTGACCCCAATTTCTCC
*
543047 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCAATTTCTCC
1 AAAAATTACCATTTTACCCTCAAACTTCC-AAAATTCCATTTTTGACCCCAATTTCTCC
*
543106 AAAAAATTA-CATTTTTACCCTCGAACTTCCCAAAATT
1 -AAAAATTACCA-TTTTACCCTCAAACTT-CCAAAATT
543143 ACCAATTTGC
Statistics
Matches: 188, Mismatches: 19, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
57 26 0.14
58 43 0.23
59 89 0.47
60 28 0.15
61 2 0.01
ACGTcount: A:0.33, C:0.29, G:0.02, T:0.36
Consensus pattern (58 bp):
AAAAATTACCATTTTACCCTCAAACTTCCAAAATTCCATTTTTGACCCCAATTTCTCC
Found at i:543187 original size:28 final size:29
Alignment explanation
Indices: 543135--543189 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
543125 CTCGAACTTC
*
543135 CCAAAATTACCAATTTGCCCCCCGAGTGT
1 CCAAAATTACCAATTTGACCCCCGAGTGT
*
543164 CCAAAATTACC-ATTTTACCCCCGAGT
1 CCAAAATTACCAATTTGACCCCCGAGT
543190 ATAAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.29, C:0.35, G:0.11, T:0.25
Consensus pattern (29 bp):
CCAAAATTACCAATTTGACCCCCGAGTGT
Found at i:543197 original size:28 final size:29
Alignment explanation
Indices: 543137--543197 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
543127 CGAACTTCCC
* * **
543137 AAAATTACCAATTTGCCCCCCGAGTGTCC
1 AAAATTACCAATTTGACCCCCGAGTATAA
*
543166 AAAATTACC-ATTTTACCCCCGAGTATAA
1 AAAATTACCAATTTGACCCCCGAGTATAA
543194 AAAA
1 AAAA
543198 ATCACATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.25
Consensus pattern (29 bp):
AAAATTACCAATTTGACCCCCGAGTATAA
Done.