Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015235.1 Kokia drynarioides strain JFW-HI SEQ_130280, 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: 263234
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 319 characters in sequence are not A, C, G, or T
Found at i:421 original size:12 final size:12
Alignment explanation
Indices: 406--430 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
396 AAATTAAAAT
406 ATTTTAAAATTA
1 ATTTTAAAATTA
418 ATTTTAAAATTA
1 ATTTTAAAATTA
430 A
1 A
431 CCATACTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTTAAAATTA
Found at i:632 original size:4 final size:4
Alignment explanation
Indices: 625--667 Score: 61
Period size: 4 Copynumber: 10.8 Consensus size: 4
615 TTCTTCCTTC
*
625 TTCT TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTC
668 CTTCAATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 29 0.83
5 3 0.09
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:1266 original size:21 final size:20
Alignment explanation
Indices: 1234--1276 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
1224 TGATATTACA
1234 ATATATTATTATGTGATATT
1 ATATATTATTATGTGATATT
* * *
1254 ATATCTTAGTTATTTGATTTT
1 ATATATTA-TTATGTGATATT
1275 AT
1 AT
1277 TATGAGATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.58
Consensus pattern (20 bp):
ATATATTATTATGTGATATT
Found at i:1277 original size:34 final size:34
Alignment explanation
Indices: 1239--1308 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 34
1229 TTACAATATA
* **
1239 TTATTATGTGATATTATATCTTAGTTATTTGATT
1 TTATTATGAGATATTATATCTTAGCAATTTGATT
* *
1273 TTATTATGAGATATTATTTTTTAGCAATTTGATT
1 TTATTATGAGATATTATATCTTAGCAATTTGATT
1307 TT
1 TT
1309 TACATAATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.27, C:0.03, G:0.11, T:0.59
Consensus pattern (34 bp):
TTATTATGAGATATTATATCTTAGCAATTTGATT
Found at i:6235 original size:129 final size:129
Alignment explanation
Indices: 6101--6360 Score: 520
Period size: 129 Copynumber: 2.0 Consensus size: 129
6091 ATTATATATA
6101 TATATATATATATTTTTATCATATGGTTATCAAGTGAGTTTTTTTTTTACTTTTAAAATGTTATA
1 TATATATATATATTTTTATCATATGGTTATCAAGTGAGTTTTTTTTTTACTTTTAAAATGTTATA
6166 CAAATAAATTTAACATAATAATTTTATCGAGGTTAACTGCTAACACTATAGTAAAATAGGTTTT
66 CAAATAAATTTAACATAATAATTTTATCGAGGTTAACTGCTAACACTATAGTAAAATAGGTTTT
6230 TATATATATATATTTTTATCATATGGTTATCAAGTGAGTTTTTTTTTTACTTTTAAAATGTTATA
1 TATATATATATATTTTTATCATATGGTTATCAAGTGAGTTTTTTTTTTACTTTTAAAATGTTATA
6295 CAAATAAATTTAACATAATAATTTTATCGAGGTTAACTGCTAACACTATAGTAAAATAGGTTTT
66 CAAATAAATTTAACATAATAATTTTATCGAGGTTAACTGCTAACACTATAGTAAAATAGGTTTT
6359 TA
1 TA
6361 ACGATATTTT
Statistics
Matches: 131, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
129 131 1.00
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.46
Consensus pattern (129 bp):
TATATATATATATTTTTATCATATGGTTATCAAGTGAGTTTTTTTTTTACTTTTAAAATGTTATA
CAAATAAATTTAACATAATAATTTTATCGAGGTTAACTGCTAACACTATAGTAAAATAGGTTTT
Found at i:6553 original size:14 final size:14
Alignment explanation
Indices: 6520--6556 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
6510 TGTCCCCCAG
*
6520 ATCCCAAATTTCTA
1 ATCCCTAATTTCTA
*
6534 ATCCCTAATTTTTA
1 ATCCCTAATTTCTA
6548 ATCCCTAAT
1 ATCCCTAAT
6557 CATTTCTCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.32, C:0.27, G:0.00, T:0.41
Consensus pattern (14 bp):
ATCCCTAATTTCTA
Found at i:7398 original size:34 final size:34
Alignment explanation
Indices: 7348--7421 Score: 121
Period size: 34 Copynumber: 2.2 Consensus size: 34
7338 AATTATTTAA
*
7348 TTAAATATTTAATTATTAAAAACAACCCAAATAT
1 TTAATTATTTAATTATTAAAAACAACCCAAATAT
* *
7382 TTAATTATTTAGTTATTAAAAACAACTCAAATAT
1 TTAATTATTTAATTATTAAAAACAACCCAAATAT
7416 TTAATT
1 TTAATT
7422 CAAAATATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.49, C:0.09, G:0.01, T:0.41
Consensus pattern (34 bp):
TTAATTATTTAATTATTAAAAACAACCCAAATAT
Found at i:7465 original size:40 final size:40
Alignment explanation
Indices: 7350--7457 Score: 120
Period size: 40 Copynumber: 2.9 Consensus size: 40
7340 TTATTTAATT
*
7350 AAATATTTAATTATTAAAAACAACCCAAATA-T---TT--
1 AAATATTTAATTATTAAAAACAACTCAAATATTCAATTCA
* * *
7384 AATTATTTAGTTATTAAAAACAACTCAAATATTTAATTCA
1 AAATATTTAATTATTAAAAACAACTCAAATATTCAATTCA
* *
7424 AAATATTTAATTATTAAAAACAATTTAAATATTC
1 AAATATTTAATTATTAAAAACAACTCAAATATTC
7458 GGTTCAAATT
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
34 28 0.47
35 1 0.02
38 2 0.03
40 29 0.48
ACGTcount: A:0.51, C:0.09, G:0.01, T:0.39
Consensus pattern (40 bp):
AAATATTTAATTATTAAAAACAACTCAAATATTCAATTCA
Found at i:7691 original size:6 final size:6
Alignment explanation
Indices: 7680--7706 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
7670 TAGGATGATA
7680 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
7707 CATATAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:11375 original size:43 final size:42
Alignment explanation
Indices: 11168--11376 Score: 125
Period size: 43 Copynumber: 4.9 Consensus size: 42
11158 TAATGTTAAT
* *
11168 GACGTTTGTGGGAAAAATG-CTGTTAAGGATTATGTTTTATAAC
1 GACGTTTGTGGGAAAAATGTC-GTTAAAGATAATG-TTTATAAC
* * * * * * *
11211 GTCGTTTGTGGGAAAAACGTCGCTAAAAACAATACTTTATAGAG
1 GACGTTTGTGGGAAAAATGTCGTTAAAGATAAT-GTTTATA-AC
* * ** *
11255 GA-GTTTGTGGGTAAAGTGTCGTTAAAGATCTTGCTTTATAGC
1 GACGTTTGTGGGAAAAATGTCGTTAAAGATAATG-TTTATAAC
* * * **** ** * *
11297 GGCGTTTCTGAGAAAAGCACCACTAAATATCATGTTCTATAAC
1 GACGTTTGTGGGAAAAATGTCGTTAAAGATAATGTT-TATAAC
11340 GACGTTTGTGGGAAAAATGTCGTTAAAGATAATGTTT
1 GACGTTTGTGGGAAAAATGTCGTTAAAGATAATGTTT
11377 TATAGCAGCG
Statistics
Matches: 116, Mismatches: 44, Indels: 13
0.67 0.25 0.08
Matches are distributed among these distances:
42 4 0.03
43 109 0.94
44 3 0.03
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (42 bp):
GACGTTTGTGGGAAAAATGTCGTTAAAGATAATGTTTATAAC
Found at i:11415 original size:86 final size:86
Alignment explanation
Indices: 11257--11423 Score: 190
Period size: 86 Copynumber: 1.9 Consensus size: 86
11247 TTATAGAGGA
* * ** * * *
11257 GTTTGTGGGTAAAGTGTCGTTAAAGATCTTGCTTTATAGCGGCGTTTCTGAGAAAAGCACCACTA
1 GTTTGTGGGAAAAATGTCGTTAAAGATAATGCTTTATAGCAGCGCTACTGAGAAAAGCACCACTA
* *
11322 AATATCATGTTCTATAACGAC
66 AAGATCATGATCTATAACGAC
* * * ** **
11343 GTTTGTGGGAAAAATGTCGTTAAAGATAATGTTTTATAGCAGCGCTAGTGGGAAAAGCGTCTTTA
1 GTTTGTGGGAAAAATGTCGTTAAAGATAATGCTTTATAGCAGCGCTACTGAGAAAAGCACCACTA
11408 AAGATCATGATCTATA
66 AAGATCATGATCTATA
11424 GGCGGCATTA
Statistics
Matches: 65, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
86 65 1.00
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.32
Consensus pattern (86 bp):
GTTTGTGGGAAAAATGTCGTTAAAGATAATGCTTTATAGCAGCGCTACTGAGAAAAGCACCACTA
AAGATCATGATCTATAACGAC
Found at i:14368 original size:23 final size:22
Alignment explanation
Indices: 14246--14370 Score: 88
Period size: 23 Copynumber: 5.5 Consensus size: 22
14236 AGTGCTGGGG
*
14246 AAACAGTAAGCACACACAGTGC
1 AAACAGTAAGCACACAAAGTGC
* * **
14268 AATCCAGTAGGCACACCTAGTGC
1 AA-ACAGTAAGCACACAAAGTGC
* ** * * *
14291 AATCAGTCGGCGCACATAGAGC
1 AAACAGTAAGCACACAAAGTGC
* * *
14313 AAATTAGTAGGCACACAAGGTGC
1 AAA-CAGTAAGCACACAAAGTGC
14336 GAAACAGTAAGCACACAAAGTGC
1 -AAACAGTAAGCACACAAAGTGC
14359 GAAACAGTAAGC
1 -AAACAGTAAGC
14371 GCTTGCGGTC
Statistics
Matches: 81, Mismatches: 19, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
22 19 0.23
23 59 0.73
24 3 0.04
ACGTcount: A:0.40, C:0.24, G:0.23, T:0.13
Consensus pattern (22 bp):
AAACAGTAAGCACACAAAGTGC
Found at i:14454 original size:23 final size:23
Alignment explanation
Indices: 14424--14467 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
14414 TAATTTATCT
14424 ACAAAGTGCGAAACAGTAAGCAC
1 ACAAAGTGCGAAACAGTAAGCAC
14447 ACAAAGTGCGAAACAGTAAGC
1 ACAAAGTGCGAAACAGTAAGC
14468 GCTTGCGGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.20, G:0.23, T:0.09
Consensus pattern (23 bp):
ACAAAGTGCGAAACAGTAAGCAC
Found at i:14498 original size:97 final size:97
Alignment explanation
Indices: 14327--14522 Score: 374
Period size: 97 Copynumber: 2.0 Consensus size: 97
14317 TAGTAGGCAC
*
14327 ACAAGGTGCGAAACAGTAAGCACACAAAGTGCGAAACAGTAAGCGCTTGCGGTCCTTAATGGCAT
1 ACAAAGTGCGAAACAGTAAGCACACAAAGTGCGAAACAGTAAGCGCTTGCGGTCCTTAATGGCAT
14392 GCCACTAATATCACAATGGTTCTAATTTATCT
66 GCCACTAATATCACAATGGTTCTAATTTATCT
14424 ACAAAGTGCGAAACAGTAAGCACACAAAGTGCGAAACAGTAAGCGCTTGCGGTCCTTAATGGCAT
1 ACAAAGTGCGAAACAGTAAGCACACAAAGTGCGAAACAGTAAGCGCTTGCGGTCCTTAATGGCAT
*
14489 GCCACTAATATCACAATGGTTCTAATTTGTCT
66 GCCACTAATATCACAATGGTTCTAATTTATCT
14521 AC
1 AC
14523 TTGGGCACAA
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 97 1.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.23
Consensus pattern (97 bp):
ACAAAGTGCGAAACAGTAAGCACACAAAGTGCGAAACAGTAAGCGCTTGCGGTCCTTAATGGCAT
GCCACTAATATCACAATGGTTCTAATTTATCT
Found at i:26640 original size:2 final size:2
Alignment explanation
Indices: 26635--26675 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
26625 TTCTCTCACT
26635 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
26676 TTGGATAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:42920 original size:59 final size:59
Alignment explanation
Indices: 42848--42967 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
42838 GCGCAAAGGA
42848 ATCACATGGCATTGGGTTGCTTATTTATAATTGCTAGAATGAATGGATTTAGCTCAACT
1 ATCACATGGCATTGGGTTGCTTATTTATAATTGCTAGAATGAATGGATTTAGCTCAACT
42907 ATCACATGGCATTGGGTTGCTTATTTATAATTGCTAGAATGAATGGATTTAGCTCAACT
1 ATCACATGGCATTGGGTTGCTTATTTATAATTGCTAGAATGAATGGATTTAGCTCAACT
42966 AT
1 AT
42968 GGAGGTATTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (59 bp):
ATCACATGGCATTGGGTTGCTTATTTATAATTGCTAGAATGAATGGATTTAGCTCAACT
Found at i:45655 original size:8 final size:9
Alignment explanation
Indices: 45636--45672 Score: 65
Period size: 9 Copynumber: 4.0 Consensus size: 9
45626 TAAACATTAT
45636 AAAAGAAGAA
1 AAAAGAA-AA
45646 AAAAGAAAA
1 AAAAGAAAA
45655 AAAAGAAAA
1 AAAAGAAAA
45664 AAAAGAAAA
1 AAAAGAAAA
45673 GAAATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 20 0.74
10 7 0.26
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:45701 original size:2 final size:2
Alignment explanation
Indices: 45696--45724 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
45686 ATATATATAT
45696 AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
45725 TAATGTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:50389 original size:2 final size:2
Alignment explanation
Indices: 50382--50408 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
50372 ACAATCAGTG
50382 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
50409 TAAACTTGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:62852 original size:2 final size:2
Alignment explanation
Indices: 62847--62876 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
62837 TAAAAAAAAA
*
62847 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62877 GTTGAAGGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:74615 original size:15 final size:16
Alignment explanation
Indices: 74595--74625 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
74585 TATTTAATAA
74595 ATTTA-TAAAATTTTT
1 ATTTATTAAAATTTTT
74610 ATTTATTAAAATTTTT
1 ATTTATTAAAATTTTT
74626 TATATAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTATTAAAATTTTT
Found at i:76978 original size:2 final size:2
Alignment explanation
Indices: 76971--77005 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
76961 ATTAAGTTTG
76971 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
77006 CCAAACCCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:77463 original size:19 final size:19
Alignment explanation
Indices: 77439--77486 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
77429 ATTTTTTAAA
77439 ATTTAAAAAATAAAAAAAT
1 ATTTAAAAAATAAAAAAAT
*
77458 ATTT-AAAAATAAAAAATT
1 ATTTAAAAAATAAAAAAAT
*
77476 A-ATAAAAAATA
1 ATTTAAAAAATA
77487 TATATATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 1 0.04
18 21 0.81
19 4 0.15
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
ATTTAAAAAATAAAAAAAT
Found at i:77472 original size:26 final size:27
Alignment explanation
Indices: 77433--77483 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
77423 TAATTTATTT
* *
77433 TTTAAAATTTAAAAAATAA-AAAAATA
1 TTTAAAAATAAAAAAATAATAAAAATA
*
77459 TTTAAAAATAAAAAATTAATAAAAA
1 TTTAAAAATAAAAAAATAATAAAAA
77484 ATATATATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (27 bp):
TTTAAAAATAAAAAAATAATAAAAATA
Found at i:77500 original size:28 final size:26
Alignment explanation
Indices: 77442--77512 Score: 63
Period size: 26 Copynumber: 2.7 Consensus size: 26
77432 TTTTAAAATT
* *
77442 TAAAAAATA-AAAAAATATTTAAAAA
1 TAAAAATTATAAAAAATATATAAAAA
* *
77467 TAAAAAATTAATAAAAAATATATATATA
1 T-AAAAATT-ATAAAAAATATATAAAAA
* *
77495 TTAAAATTTTAAAAAATA
1 TAAAAATTATAAAAAATA
77513 ATTAATTGCT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
25 1 0.03
26 15 0.41
27 7 0.19
28 14 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (26 bp):
TAAAAATTATAAAAAATATATAAAAA
Found at i:79111 original size:21 final size:21
Alignment explanation
Indices: 79067--79111 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
79057 TTTTGAACAA
*
79067 TTTAAATTTTTTTTATGTTTT
1 TTTAAATTTTTTTTATGTTCT
*
79088 TTTAACTTTTTTTTAT-TCTCT
1 TTTAAATTTTTTTTATGT-TCT
79109 TTT
1 TTT
79112 GCTTCTCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTAAATTTTTTTTATGTTCT
Found at i:81692 original size:19 final size:21
Alignment explanation
Indices: 81668--81706 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
81658 CAATTTATTT
81668 TTATAT-TGAATA-AATATAA
1 TTATATATGAATACAATATAA
*
81687 TTATATATGTATACAATATA
1 TTATATATGAATACAATATA
81707 TAAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (21 bp):
TTATATATGAATACAATATAA
Found at i:83368 original size:16 final size:16
Alignment explanation
Indices: 83334--83366 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
83324 TTAAAAAATT
*
83334 AATTATGTTTAATTTA
1 AATTATCTTTAATTTA
83350 AATTATCTTT-ATTTA
1 AATTATCTTTAATTTA
83365 AA
1 AA
83367 ATACACATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (16 bp):
AATTATCTTTAATTTA
Found at i:85010 original size:14 final size:14
Alignment explanation
Indices: 84991--85033 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
84981 TACATTACAG
*
84991 ATTAATATCACCCA
1 ATTAATATCACACA
85005 ATTAAT-TCAACACA
1 ATTAATATC-ACACA
*
85019 AATAATATCACACA
1 ATTAATATCACACA
85033 A
1 A
85034 AGAGATGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 2 0.08
14 21 0.84
15 2 0.08
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (14 bp):
ATTAATATCACACA
Found at i:85621 original size:22 final size:22
Alignment explanation
Indices: 85568--85613 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
85558 TCGAATTAGG
*
85568 TTTAGGGTTTGGGTGATTTGAT
1 TTTAAGGTTTGGGTGATTTGAT
*
85590 TTTAAGGTTTGGGT-ATTTGGT
1 TTTAAGGTTTGGGTGATTTGAT
85611 TTT
1 TTT
85614 TATGGTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.13, C:0.00, G:0.33, T:0.54
Consensus pattern (22 bp):
TTTAAGGTTTGGGTGATTTGAT
Found at i:89685 original size:3 final size:3
Alignment explanation
Indices: 89677--89707 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
89667 CCAACAAGTT
89677 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
89708 ATTTTTTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:92100 original size:21 final size:21
Alignment explanation
Indices: 92074--92113 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
92064 TACCCAAAAA
*
92074 GTCAATGATCAATGATCAACT
1 GTCAATGATCAACGATCAACT
*
92095 GTCAATGGTCAACGATCAA
1 GTCAATGATCAACGATCAA
92114 TGGTCGGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (21 bp):
GTCAATGATCAACGATCAACT
Found at i:92113 original size:14 final size:14
Alignment explanation
Indices: 92074--92118 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
92064 TACCCAAAAA
*
92074 GTCAATGATCAATG
1 GTCAACGATCAATG
*
92088 ATCAACTG-TCAATG
1 GTCAAC-GATCAATG
92102 GTCAACGATCAATG
1 GTCAACGATCAATG
92116 GTC
1 GTC
92119 GGGTTCGATC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 1 0.04
14 24 0.92
15 1 0.04
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (14 bp):
GTCAACGATCAATG
Found at i:92173 original size:21 final size:21
Alignment explanation
Indices: 92149--92200 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
92139 GGTCAAATCA
92149 AATTGGGTTTAAGGTTTGGAT
1 AATTGGGTTTAAGGTTTGGAT
* * *
92170 AATTTGGTTTTAGGGTTTGGGT
1 AA-TTGGGTTTAAGGTTTGGAT
92192 -ATTGGGTTT
1 AATTGGGTTT
92201 TTATGGTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 7 0.27
21 3 0.12
22 16 0.62
ACGTcount: A:0.17, C:0.00, G:0.35, T:0.48
Consensus pattern (21 bp):
AATTGGGTTTAAGGTTTGGAT
Found at i:92201 original size:21 final size:22
Alignment explanation
Indices: 92149--92201 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
92139 GGTCAAATCA
92149 AATTGGG-TTTAAGGTTTGGAT
1 AATTGGGTTTTAAGGTTTGGAT
* * *
92170 AATTTGGTTTTAGGGTTTGGGT
1 AATTGGGTTTTAAGGTTTGGAT
92192 -ATTGGGTTTT
1 AATTGGGTTTT
92202 TATGGTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.49
Consensus pattern (22 bp):
AATTGGGTTTTAAGGTTTGGAT
Found at i:93560 original size:23 final size:24
Alignment explanation
Indices: 93533--93580 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
93523 ATGTTATATT
*
93533 AAAAATTAATTT-AATTTAAAAAA
1 AAAAAATAATTTAAATTTAAAAAA
*
93556 AAAAAATATTTTAAAATTTAAAAAA
1 AAAAAATAATTT-AAATTTAAAAAA
93581 TTAATTAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 10 0.48
25 11 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
AAAAAATAATTTAAATTTAAAAAA
Found at i:98311 original size:237 final size:238
Alignment explanation
Indices: 97893--98367 Score: 848
Period size: 238 Copynumber: 2.0 Consensus size: 238
97883 TATGGACTTG
97893 ATCCTTTATTATTTCACTTCTGCCTTTCTTTTCAAAACGGAAAAAAATCCATTTTTTAGTTATTG
1 ATCCTTTATTATTTCACTTCTGCCTTTCTTTTCAAAACGGAAAAAAATCCATTTTTTAGTTATTG
* *
97958 GTAGGATTGTTTTTCTCAGCTAGAATTTCATACAAACCACAGTTGGTTTTTTCCAGTTTAATGGT
66 GTAGGATTGTTTTTCTCAGCTAGAATTCCATACAAACCACAGTTGGTTTTGTCCAGTTTAATGGT
98023 TCAACTCATTCTACTTCTAACAGAGGGGATAATATAATTATTATTTGTGTGACAATTATACATTT
131 TCAACTCATTCTACTTCTAACAGAGGGGATAATATAATTATTATTTGTGTGACAATTATACATTT
98088 GAACTTTTACTGTGATCTG-TTTTTGTGTGTTGACTCCTTTTT
196 GAACTTTTACTGTGATCTGTTTTTTGTGTGTTGACTCCTTTTT
* * *
98130 ATCCTTTATTATTTCACTTCTGTCTTTCTTTTCAAAATGGAAAAAAAATCCATTTTTTCA-TTTT
1 ATCCTTTATTATTTCACTTCTGCCTTTCTTTTCAAAACGG-AAAAAAATCCATTTTTT-AGTTAT
98194 TGGTAGGATTGTTTTTCTCAGCTAGAATTCCATACAAACCACAGTTGGTTTTGTCCAGTTTAATG
64 TGGTAGGATTGTTTTTCTCAGCTAGAATTCCATACAAACCACAGTTGGTTTTGTCCAGTTTAATG
* *
98259 GTTCAACTCATTCTGCTTCTAACAGA-GGGATAATATAATTATTATTTGTGTGACGATTATACAT
129 GTTCAACTCATTCTACTTCTAACAGAGGGGATAATATAATTATTATTTGTGTGACAATTATACAT
98323 TTGAACTTTTACTGTGATCTGTTTTTTGTGTGTTGACTCCTTTTT
194 TTGAACTTTTACTGTGATCTGTTTTTTGTGTGTTGACTCCTTTTT
98368 GTTCCTAAGT
Statistics
Matches: 228, Mismatches: 7, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
237 96 0.42
238 131 0.57
239 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (238 bp):
ATCCTTTATTATTTCACTTCTGCCTTTCTTTTCAAAACGGAAAAAAATCCATTTTTTAGTTATTG
GTAGGATTGTTTTTCTCAGCTAGAATTCCATACAAACCACAGTTGGTTTTGTCCAGTTTAATGGT
TCAACTCATTCTACTTCTAACAGAGGGGATAATATAATTATTATTTGTGTGACAATTATACATTT
GAACTTTTACTGTGATCTGTTTTTTGTGTGTTGACTCCTTTTT
Found at i:107091 original size:51 final size:51
Alignment explanation
Indices: 107032--107131 Score: 173
Period size: 51 Copynumber: 2.0 Consensus size: 51
107022 AGCCTTTAAC
* * *
107032 CTATAACTCACAGACATTATGACAGATGTCTGGTGTATGTGCCTCTGCCGT
1 CTATAACTCACAGACATTATGACAGATATATGATGTATGTGCCTCTGCCGT
107083 CTATAACTCACAGACATTATGACAGATATATGATGTATGTGCCTCTGCC
1 CTATAACTCACAGACATTATGACAGATATATGATGTATGTGCCTCTGCC
107132 TTCATCTTCA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (51 bp):
CTATAACTCACAGACATTATGACAGATATATGATGTATGTGCCTCTGCCGT
Found at i:114804 original size:2 final size:2
Alignment explanation
Indices: 114797--114825 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
114787 CTTAAGCTTT
114797 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
114826 TTGGGGGAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:119916 original size:23 final size:23
Alignment explanation
Indices: 119871--119916 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
119861 TATATTCTTT
* *
119871 AAAAATTTATAATAATTTTTAAA
1 AAAAATTTATAATAATATATAAA
119894 AAAAATTT-TAATTAATATATAAA
1 AAAAATTTATAA-TAATATATAAA
119917 GAAAGTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AAAAATTTATAATAATATATAAA
Found at i:121208 original size:6 final size:6
Alignment explanation
Indices: 121199--121227 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
121189 AAAAATGAAA
121199 AATGGG AATGGG AATGGG AATGGG AATGG
1 AATGGG AATGGG AATGGG AATGGG AATGG
121228 TACAGTGAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.48, T:0.17
Consensus pattern (6 bp):
AATGGG
Found at i:123204 original size:30 final size:28
Alignment explanation
Indices: 123166--123654 Score: 228
Period size: 30 Copynumber: 17.1 Consensus size: 28
123156 AAAATTATCA
123166 TTTTACCCCCGAACTTCCAAAAATCCCAT
1 TTTTA-CCCCGAACTTCCAAAAATCCCAT
* *
123195 TTTTGACCCCGAACTCTCTAAAAATTACCA-
1 TTTT-ACCCCGAACT-TCCAAAAA-TCCCAT
*
123225 TTTTA--CC---C--CCAAAAATCCTAT
1 TTTTACCCCGAACTTCCAAAAATCCCAT
* * *
123246 TTTTGACCCTGAACTCTCTAAAAATTACCA-
1 TTTT-ACCCCGAACT-TCCAAAAA-TCCCAT
* * *
123276 TTTTACCCCTAACTTCAAAAAATCCCCT
1 TTTTACCCCGAACTTCCAAAAATCCCAT
* *
123304 TTTTGACCCCGAACTCTCTAAAAATTACCA-
1 TTTT-ACCCCGAACT-TCCAAAAA-TCCCAT
123334 TTTTA--CC---C--CCAAAAATCCCAT
1 TTTTACCCCGAACTTCCAAAAATCCCAT
* * *
123355 TTTTGACGCCAAACTCTCCAAAAATTACCA-
1 TTTT-ACCCCGAACT-TCCAAAAA-TCCCAT
*
123385 TTTTACCCCCGAACTTCCAAAAATCCCCT
1 TTTTA-CCCCGAACTTCCAAAAATCCCAT
** * *
123414 TTTTGACCCTAAACTTTCCAAAACTTACCA-
1 TTTT-ACCCCGAAC-TTCCAAAA-ATCCCAT
* * *
123444 TTTTACCCTCAAATTTCCAAAAATCCAAT
1 TTTTACCC-CGAACTTCCAAAAATCCCAT
** * * *
123473 TTTTGACCCTAAACTTTCTAAAATTTACCA-
1 TTTT-ACCCCGAAC-TTCCAAAA-ATCCCAT
123503 TTTTACCCTCGAACTTCCAAAAATCCCAT
1 TTTTACCC-CGAACTTCCAAAAATCCCAT
** * *
123532 TTTTAACCTTGAACCTTCTAAAAATTACCAT
1 TTTT-ACCCCGAA-CTTCCAAAAA-TCCCAT
*
123563 TTTTACCCCCGAACTTCTAAAAATCCCAT
1 TTTTA-CCCCGAACTTCCAAAAATCCCAT
* ** *
123592 TTTTGACCTCGAACCTTTTAAAAATTACCA-
1 TTTT-ACCCCGAA-CTTCCAAAAA-TCCCAT
*
123622 TTTTACCCTCGAACTTCCAAAAATCACAT
1 TTTTACCC-CGAACTTCCAAAAATCCCAT
123651 TTTT
1 TTTT
123655 TATTCCAAAC
Statistics
Matches: 349, Mismatches: 61, Indels: 100
0.68 0.12 0.20
Matches are distributed among these distances:
20 7 0.02
21 20 0.06
22 2 0.01
24 5 0.01
27 9 0.03
28 24 0.07
29 118 0.34
30 126 0.36
31 38 0.11
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.33
Consensus pattern (28 bp):
TTTTACCCCGAACTTCCAAAAATCCCAT
Found at i:123248 original size:51 final size:51
Alignment explanation
Indices: 123182--123394 Score: 309
Period size: 51 Copynumber: 4.0 Consensus size: 51
123172 CCCCGAACTT
123182 CCAAAAATCCCATTTTTGACCCCGAACTCTCTAAAAATTACCATTTTACCC
1 CCAAAAATCCCATTTTTGACCCCGAACTCTCTAAAAATTACCATTTTACCC
* *
123233 CCAAAAATCCTATTTTTGACCCTGAACTCTCTAAAAATTACCATTTTACCCC
1 CCAAAAATCCCATTTTTGACCCCGAACTCTCTAAAAATTACCATTTTA-CCC
*
123285 TAACTTCAAAAAATCCCCTTTTTGACCCCGAACTCTCTAAAAATTACCATTTTACCC
1 ---C--C-AAAAATCCCATTTTTGACCCCGAACTCTCTAAAAATTACCATTTTACCC
* * *
123342 CCAAAAATCCCATTTTTGACGCCAAACTCTCCAAAAATTACCATTTTACCC
1 CCAAAAATCCCATTTTTGACCCCGAACTCTCTAAAAATTACCATTTTACCC
123393 CC
1 CC
123395 GAACTTCCAA
Statistics
Matches: 146, Mismatches: 9, Indels: 14
0.86 0.05 0.08
Matches are distributed among these distances:
51 93 0.64
52 4 0.03
54 1 0.01
55 1 0.01
57 4 0.03
58 43 0.29
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.30
Consensus pattern (51 bp):
CCAAAAATCCCATTTTTGACCCCGAACTCTCTAAAAATTACCATTTTACCC
Found at i:123347 original size:109 final size:110
Alignment explanation
Indices: 123145--123654 Score: 560
Period size: 109 Copynumber: 4.5 Consensus size: 110
123135 CGGAGGTCCT
* * *
123145 TAAACTTTCCAAAAATTATCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACT
1 TAAACTCTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACT
*
123210 CTCTAAAAATTACCATTTTACCCCCAAAAATCCTATTTTTGACCC
66 CTCTAAAAATTACCATTTTACCCCCAAAAATCCAATTTTTGACCC
* * * *
123255 TGAACTCTCTAAAAATTACCATTTTA-CCCCTAACTTCAAAAAATCCCCTTTTTGACCCCGAACT
1 TAAACTCTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACT
*
123319 CTCTAAAAATTACCATTTTACCCCCAAAAATCCCATTTTTGACGCC
66 CTCTAAAAATTACCATTTTACCCCCAAAAATCCAATTTTTGAC-CC
* * **
123365 -AAACTCTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCCTTTTTGACCCTAAACT
1 TAAACTCTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACT
* * *
123429 TTCCAAAACTTACCATTTTACCCTCAAATTTCCAAAAATCCAATTTTTGACCC
66 CTCTAAAAATTACCATTTTA-CC-C------CCAAAAATCCAATTTTTGACCC
* * * * **
123482 TAAACTTTCTAAAATTTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCTTGAAC-
1 TAAACTCTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACT
*
123546 CTTCTAAAAATTACCATTTTTACCCCCGAACTTCTAAAAATCCCATTTTTGACCTC
66 C-TCTAAAAATTACCA-TTTTA--CCC---C--C-AAAAATCCAATTTTTGACC-C
* * * * *
123602 GAACCT-TTTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCACATTTTT
1 TAAACTCTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTT
123655 TATTCCAAAC
Statistics
Matches: 344, Mismatches: 38, Indels: 27
0.84 0.09 0.07
Matches are distributed among these distances:
109 100 0.29
110 75 0.22
111 2 0.01
112 1 0.00
116 1 0.00
117 2 0.01
118 87 0.25
119 68 0.20
120 8 0.02
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.33
Consensus pattern (110 bp):
TAAACTCTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACT
CTCTAAAAATTACCATTTTACCCCCAAAAATCCAATTTTTGACCC
Found at i:123420 original size:59 final size:58
Alignment explanation
Indices: 123342--123689 Score: 385
Period size: 59 Copynumber: 5.9 Consensus size: 58
123332 CATTTTACCC
123342 CCAAAAATCCCATTTTTGACGCCAAA-CTCTCCAAAAATTACCATTTTACCCCCGAACTT
1 CCAAAAATCCCATTTTTGAC-CCAAACCT-TCCAAAAATTACCATTTTACCCCCGAACTT
* * * * * *
123401 CCAAAAATCCCCTTTTTGACCCTAAACTTTCCAAAACTTACCATTTTACCCTCAAATTT
1 CCAAAAATCCCATTTTTGACCC-AAACCTTCCAAAAATTACCATTTTACCCCCGAACTT
* * * * *
123460 CCAAAAATCCAATTTTTGACCCTAAACTTTCTAAAATTTACCATTTTACCCTCGAACTT
1 CCAAAAATCCCATTTTTGACCC-AAACCTTCCAAAAATTACCATTTTACCCCCGAACTT
* ** *
123519 CCAAAAATCCCATTTTTAACCTTGAACCTTCTAAAAATTACCATTTTTACCCCCGAACTT
1 CCAAAAATCCCATTTTTGACC-CAAACCTTCCAAAAATTACCA-TTTTACCCCCGAACTT
* * ** *
123579 CTAAAAATCCCATTTTTGACCTCGAACCTTTTAAAAATTACCATTTTACCCTCGAACTT
1 CCAAAAATCCCATTTTTGACC-CAAACCTTCCAAAAATTACCATTTTACCCCCGAACTT
* * * * *
123638 CCAAAAATCACATTTTTTATTCCAAACCTTCC-AAAACTACCATTTTGCCCCC
1 CCAAAAATCCCATTTTTGA-CCCAAACCTTCCAAAAATTACCATTTTACCCCC
123690 CGTGCATCCG
Statistics
Matches: 250, Mismatches: 34, Indels: 11
0.85 0.12 0.04
Matches are distributed among these distances:
58 19 0.08
59 175 0.70
60 56 0.22
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (58 bp):
CCAAAAATCCCATTTTTGACCCAAACCTTCCAAAAATTACCATTTTACCCCCGAACTT
Found at i:126299 original size:58 final size:58
Alignment explanation
Indices: 126189--126299 Score: 136
Period size: 59 Copynumber: 1.9 Consensus size: 58
126179 GTTTTGATAG
* * * *
126189 GTCTAATTAAAGTTTTCAAAATTTTTAGAGATTTTATGAAATTTTTCAAAAAAAAAAA
1 GTCTAATTAAAGTTTTCAAAATTTTTAAAGACTTAATGAAAATTTTCAAAAAAAAAAA
*
126247 GTCTAATTGAAAGTTTT-AAAATTTTTGAAAGGCTTAAT-AATAATTTTCAAAAA
1 GTCTAATT-AAAGTTTTCAAAATTTTT-AAAGACTTAATGAA-AATTTTCAAAAA
126300 TTTTGATAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
58 19 0.42
59 26 0.58
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (58 bp):
GTCTAATTAAAGTTTTCAAAATTTTTAAAGACTTAATGAAAATTTTCAAAAAAAAAAA
Found at i:126786 original size:69 final size:67
Alignment explanation
Indices: 126667--126821 Score: 213
Period size: 69 Copynumber: 2.3 Consensus size: 67
126657 ATAAACAATA
* ** *
126667 TAATGGTTTTGCCTTTTAACTTAATGAGTAAACATTTATCAAAACGACGTAATTTTGT-TTTTAA
1 TAATGGTTTTGACTTTTAACTTAAAAAGTAAACATTTATCAAAACAACGTAATTTTGTCTTTTAA
126731 CT
66 CT
126733 TAATGGTTTTGACTTTTAACTTTAGAAAATGTAAACATTTATCAAAACAACGTAATTTTGTCTTT
1 TAATGGTTTTGACTTTTAAC-TTA-AAAA-GTAAACATTTATCAAAACAACGTAATTTTGTCTTT
126798 TAACT
63 TAACT
* * *
126803 TAATGATTTTTATTTTTAA
1 TAATGGTTTTGACTTTTAA
126822 TTTGAGATAT
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
66 19 0.24
67 3 0.04
68 2 0.03
69 30 0.38
70 24 0.31
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (67 bp):
TAATGGTTTTGACTTTTAACTTAAAAAGTAAACATTTATCAAAACAACGTAATTTTGTCTTTTAA
CT
Found at i:127223 original size:58 final size:58
Alignment explanation
Indices: 127159--127273 Score: 221
Period size: 58 Copynumber: 2.0 Consensus size: 58
127149 ACTTAATTAA
127159 CCATTTAATTTAATAATATAATTAGCTTGGTGAATTTTTAAAATGAATATCAAGAATT
1 CCATTTAATTTAATAATATAATTAGCTTGGTGAATTTTTAAAATGAATATCAAGAATT
*
127217 CCATTTAATTTAATAATATAATTAGCTTGGTGAATTTTTAAAATGAATATCAGGAAT
1 CCATTTAATTTAATAATATAATTAGCTTGGTGAATTTTTAAAATGAATATCAAGAAT
127274 AATATTTTTG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (58 bp):
CCATTTAATTTAATAATATAATTAGCTTGGTGAATTTTTAAAATGAATATCAAGAATT
Found at i:129589 original size:4 final size:4
Alignment explanation
Indices: 129570--129624 Score: 69
Period size: 4 Copynumber: 14.2 Consensus size: 4
129560 CCAACGTGAG
* *
129570 AAGA AGGA AA-A AAGA AAGA AA-A AAAA AAGA AAGA AAGA AAGA AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
*
129616 AAGG AAGA A
1 AAGA AAGA A
129625 GGAAGGAGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
3 6 0.14
4 38 0.86
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:129807 original size:18 final size:18
Alignment explanation
Indices: 129784--129818 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
129774 TGAAGAAAGG
129784 TAAGTTTGATTAATTTTT
1 TAAGTTTGATTAATTTTT
*
129802 TAAGTTTGGTTAATTTT
1 TAAGTTTGATTAATTTT
129819 AAATTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (18 bp):
TAAGTTTGATTAATTTTT
Found at i:130813 original size:14 final size:15
Alignment explanation
Indices: 130794--130839 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
130784 AACCTAGCTA
130794 ATTAATTACCAAAAT
1 ATTAATTACCAAAAT
*
130809 A-TAATATA-AAAAAT
1 ATTAAT-TACCAAAAT
130823 AATTAATTACCAAAAT
1 -ATTAATTACCAAAAT
130839 A
1 A
130840 ATATCCCCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
14 9 0.36
15 7 0.28
16 9 0.36
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (15 bp):
ATTAATTACCAAAAT
Found at i:130837 original size:16 final size:16
Alignment explanation
Indices: 130792--130841 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
130782 TAAACCTAGC
130792 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
*
130808 T-A-TAATATA-AAAAA
1 TAATTAAT-TACCAAAA
130822 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
130838 TAAT
1 TAAT
130842 ATCCCCATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (16 bp):
TAATTAATTACCAAAA
Found at i:131860 original size:43 final size:43
Alignment explanation
Indices: 131778--131862 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
131768 ATTAACATGT
* *
131778 TAAATTATATTACTTGACTTGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTTGTATTAATATGCTTGCATGTTAC
*
131821 TAAATTATATTACTTTACTCT-TATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACT-TGTATTAATATGCTTG-CATGTTA
131863 TTAATTGTGC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 3 0.08
43 33 0.89
44 1 0.03
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.48
Consensus pattern (43 bp):
TAAATTATATTACTTGACTTGTATTAATATGCTTGCATGTTAC
Found at i:132732 original size:7 final size:7
Alignment explanation
Indices: 132717--132781 Score: 51
Period size: 7 Copynumber: 9.3 Consensus size: 7
132707 TAAATTTCAT
*
132717 AACCTTA
1 AACCCTA
132724 AACCCTA
1 AACCCTA
132731 AACCCTA
1 AACCCTA
***
132738 AATTTTAA
1 AACCCT-A
*
132746 AACACTA
1 AACCCTA
132753 AA-CCTA
1 AACCCTA
*
132759 AACCATA
1 AACCCTA
*
132766 AACCATA
1 AACCCTA
132773 AACCCTA
1 AACCCTA
132780 AA
1 AA
132782 TTTGATACCC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
6 5 0.11
7 37 0.80
8 4 0.09
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (7 bp):
AACCCTA
Found at i:132740 original size:29 final size:28
Alignment explanation
Indices: 132707--132767 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
132697 ATCATTTATT
* *
132707 TAAATTTCATAAC-CTTAAACCCTAAACCC
1 TAAATTTCAAAACAC-TAAA-CCTAAACCA
*
132736 TAAATTTTAAAACACTAAACCTAAACCA
1 TAAATTTCAAAACACTAAACCTAAACCA
132764 TAAA
1 TAAA
132768 CCATAAACCC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 12 0.43
29 15 0.54
30 1 0.04
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (28 bp):
TAAATTTCAAAACACTAAACCTAAACCA
Found at i:132745 original size:21 final size:21
Alignment explanation
Indices: 132721--132784 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
132711 TTTCATAACC
132721 TTAAACCCTAAACCCTAAATT
1 TTAAACCCTAAACCCTAAATT
* **
132742 TTAAAACACTAAA-CCTAAACC
1 TT-AAACCCTAAACCCTAAATT
* *
132763 ATAAACCATAAACCCTAAATT
1 TTAAACCCTAAACCCTAAATT
132784 T
1 T
132785 GATACCCAAA
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
20 8 0.25
21 15 0.47
22 9 0.28
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (21 bp):
TTAAACCCTAAACCCTAAATT
Found at i:135886 original size:20 final size:20
Alignment explanation
Indices: 135861--135919 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
135851 CATTACATTT
135861 CTCTCCTTCTTCTTTCTTTC
1 CTCTCCTTCTTCTTTCTTTC
*
135881 CTCTCCTTCTTCCTTC-TTC
1 CTCTCCTTCTTCTTTCTTTC
*
135900 CT-TCTTTCTTTCTTTCTTTC
1 CTCTCCTTC-TTCTTTCTTTC
135920 TTTTCTTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.15
19 11 0.32
20 18 0.53
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (20 bp):
CTCTCCTTCTTCTTTCTTTC
Found at i:135894 original size:7 final size:7
Alignment explanation
Indices: 135859--135905 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
135849 CACATTACAT
135859 TTCTCTCC
1 TTCT-TCC
*
135867 TTCTTCT
1 TTCTTCC
135874 TTCTTTCC
1 TTC-TTCC
135882 -TC-TCC
1 TTCTTCC
135887 TTCTTCC
1 TTCTTCC
135894 TTCTTCC
1 TTCTTCC
135901 TTCTT
1 TTCTT
135906 TCTTTCTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
5 3 0.09
6 2 0.06
7 22 0.65
8 7 0.21
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (7 bp):
TTCTTCC
Found at i:135898 original size:27 final size:26
Alignment explanation
Indices: 135858--135946 Score: 99
Period size: 27 Copynumber: 3.3 Consensus size: 26
135848 ACACATTACA
*
135858 TTTCTCTCCTTCTTCTTTCTTTCCTCTC
1 TTTCT-TCCTTCTTCTTTCTTT-CTTTC
* *
135886 CTTCTTCCTTCTTCCTTCTTTCTTTC
1 TTTCTTCCTTCTTCTTTCTTTCTTTC
*
135912 TTTCTTTCTT-TTCTTTTCTTTTCTTTC
1 TTTCTTCCTTCTTC-TTTC-TTTCTTTC
135939 TTTCTTCC
1 TTTCTTCC
135947 CCGTTTATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
25 3 0.06
26 15 0.29
27 30 0.58
28 4 0.08
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (26 bp):
TTTCTTCCTTCTTCTTTCTTTCTTTC
Found at i:135926 original size:5 final size:4
Alignment explanation
Indices: 135870--135944 Score: 64
Period size: 4 Copynumber: 18.2 Consensus size: 4
135860 TCTCTCCTTC
* * * *
135870 TTCT TTCT TTCCT CTCC TTC- TTCC TTC- TTCC TTCT TTCT TTCT TTCT
1 TTCT TTCT TT-CT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
135917 TTCTT TTCTT TTCTT TTCT TTCT TTCT T
1 TTC-T TTC-T TTC-T TTCT TTCT TTCT T
135945 CCCCGTTTAT
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
3 6 0.10
4 40 0.63
5 17 0.27
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
TTCT
Found at i:136487 original size:17 final size:17
Alignment explanation
Indices: 136456--136489 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
136446 TTAAAGTAAT
* *
136456 TTATATTTTATATTTTA
1 TTATATTTAAAATTTTA
136473 TTATATTTAAAATTTTA
1 TTATATTTAAAATTTTA
136490 AAATATTTCA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATATTTAAAATTTTA
Found at i:136497 original size:27 final size:28
Alignment explanation
Indices: 136465--136570 Score: 76
Period size: 27 Copynumber: 3.7 Consensus size: 28
136455 TTTATATTTT
136465 ATATTTTATTA-TATTTAAAATTTTAAA
1 ATATTTTATTATTATTTAAAATTTTAAA
* *
136492 ATATTTCA-TATATAATT-AAA-TTTACAA
1 ATATTTTATTAT-TATTTAAAATTTTA-AA
* *
136519 ATAATTTATTAATTATTAAAAAGTATATTAAA
1 ATATTTTATT-ATTATTTAAAA-T-T-TTAAA
* *
136551 TTATTTTAATATTATTTAAA
1 ATATTTTATTATTATTTAAA
136571 TTAATTTATT
Statistics
Matches: 59, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
26 6 0.10
27 18 0.31
28 8 0.14
29 5 0.08
31 9 0.15
32 10 0.17
33 3 0.05
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (28 bp):
ATATTTTATTATTATTTAAAATTTTAAA
Found at i:137174 original size:30 final size:30
Alignment explanation
Indices: 137140--137204 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
137130 TTTTATTTTA
* *
137140 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTATGTTACTATTTTAGAGGCAT
137170 TTGTTAATTATGTTACTATTTTAGAGGCAT
1 TTGTTAATTATGTTACTATTTTAGAGGCAT
137200 TTGTT
1 TTGTT
137205 TGTTAAGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.23, C:0.05, G:0.17, T:0.55
Consensus pattern (30 bp):
TTGTTAATTATGTTACTATTTTAGAGGCAT
Found at i:137215 original size:30 final size:30
Alignment explanation
Indices: 137140--137215 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
137130 TTTTATTTTA
** *
137140 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTAAGTTACTATTTTAGAGGCAT
*
137170 TTGTTAATTATGTTACTATTTTAGAGGCAT
1 TTGTTAATTAAGTTACTATTTTAGAGGCAT
**
137200 TTGTTTGTTAAGTTAC
1 TTGTTAATTAAGTTAC
137216 ATCTATTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.24, C:0.05, G:0.17, T:0.54
Consensus pattern (30 bp):
TTGTTAATTAAGTTACTATTTTAGAGGCAT
Found at i:138687 original size:23 final size:23
Alignment explanation
Indices: 138660--138774 Score: 106
Period size: 23 Copynumber: 5.0 Consensus size: 23
138650 TTTAATGTTC
*
138660 ACGAACATGTTCATTTAA-AATAA
1 ACGAACATGTTCA-TGAACAATAA
* *
138683 TCGAACATGTTCATGAACATTAA
1 ACGAACATGTTCATGAACAATAA
** * *
138706 ACGAACATGTTCACAAACATTAG
1 ACGAACATGTTCATGAACAATAA
* *
138729 ACAAATATGTTCATGAACATATAA
1 ACGAACATGTTCATGAACA-ATAA
**
138753 TTGAACATGTTCATGAACAATA
1 ACGAACATGTTCATGAACAATA
138775 TTAATGAATA
Statistics
Matches: 73, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
22 3 0.04
23 53 0.73
24 17 0.23
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (23 bp):
ACGAACATGTTCATGAACAATAA
Found at i:139800 original size:25 final size:27
Alignment explanation
Indices: 139741--139802 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 27
139731 AACAAAACAA
* * *
139741 AACAAAAAAAATGTGTTTTAAAACTCT
1 AACAAAAAAAATGAGATTTAAAACTCG
*
139768 AA-ATAAAAAAT-AGATTTAAAACT-G
1 AACAAAAAAAATGAGATTTAAAACTCG
139792 AACAAAAAAAA
1 AACAAAAAAAA
139803 ATCTTTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
24 2 0.07
25 17 0.59
26 8 0.28
27 2 0.07
ACGTcount: A:0.63, C:0.08, G:0.06, T:0.23
Consensus pattern (27 bp):
AACAAAAAAAATGAGATTTAAAACTCG
Found at i:140559 original size:28 final size:28
Alignment explanation
Indices: 140438--140704 Score: 248
Period size: 30 Copynumber: 9.2 Consensus size: 28
140428 ATTTTCTTTG
*
140438 AAATCACATTTTAACCCCTAAACTTTTCTA
1 AAATTACATTTTAA-CCC-AAACTTTTCTA
* *
140468 AAATTAAATTTTAATCCTTAAACTTTTCTA
1 AAATTACATTTTAA-CC-CAAACTTTTCTA
* *
140498 AAATCACATTTTAACCCTAAAATTTTCTA
1 AAATTACATTTTAACCC-AAACTTTTCTA
140527 AAATTACATTTTAACCCAAACTTTTCTA
1 AAATTACATTTTAACCCAAACTTTTCTA
* *
140555 AAATTACATTTTGACCCAAACTTTTCCA
1 AAATTACATTTTAACCCAAACTTTTCTA
* *
140583 AAATCACATTTTGACCCAAACTTTT-TA
1 AAATTACATTTTAACCCAAACTTTTCTA
* * *
140610 AAATTATATTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTT-AACCC-AAACTTTTCTA
* * * *
140640 AGATTGCATTTTAACTCTCAAACTTCTCCA
1 AAATTACATTTTAAC-C-CAAACTTTTCTA
** * * *
140670 AAATCCCATTTTGACCCCAAACTTCTCCA
1 AAATTACATTTT-AACCCAAACTTTTCTA
140699 AAATTA
1 AAATTA
140705 TGATTTTGCA
Statistics
Matches: 199, Mismatches: 30, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
27 11 0.06
28 63 0.32
29 54 0.27
30 68 0.34
31 3 0.02
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (28 bp):
AAATTACATTTTAACCCAAACTTTTCTA
Found at i:140651 original size:57 final size:58
Alignment explanation
Indices: 140438--140704 Score: 283
Period size: 57 Copynumber: 4.6 Consensus size: 58
140428 ATTTTCTTTG
* * * * * *
140438 AAATCACATTTTAACCCCTAAACTTTTCTAAAATTAAATTTTAATCCTTAAACTTTTCTA
1 AAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAA-CC-CAAACTTTTCTA
* * * *
140498 AAATCACATTTTAACCCTAAAA-TTTTCTAAAATTACATTTTAACCCAAACTTTTCTA
1 AAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCAAACTTTTCTA
* *
140555 AAATTACATTTTGA-CCC-AAACTTTTCCAAAATCACATTTTGACCCAAACTTTT-TA
1 AAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCAAACTTTTCTA
* * * * *
140610 AAATTATATTTTGACCCCAAAACTTTTCCAAGATTGCATTTTAACTCTCAAACTTCTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAAC-C-CAAACTTTTCTA
** *
140670 AAATCCCATTTTGACCCC-AAACTTCTCCAAAATTA
1 AAATTACATTTTGACCCCAAAACTTTTCCAAAATTA
140705 TGATTTTGCA
Statistics
Matches: 178, Mismatches: 23, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
55 18 0.10
56 34 0.19
57 45 0.25
58 3 0.02
59 42 0.24
60 36 0.20
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (58 bp):
AAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCAAACTTTTCTA
Found at i:140730 original size:29 final size:28
Alignment explanation
Indices: 140675--140801 Score: 101
Period size: 29 Copynumber: 4.3 Consensus size: 28
140665 CTCCAAAATC
* * *
140675 CCATTTTGACCCCAAACTTCTCCAAAATTA
1 CCATTTTG-CCCCGAACATC-CAAAAATTA
** *
140705 TGATTTTGCACCCGAATATCCAAAAATTA
1 CCATTTTGC-CCCGAACATCCAAAAATTA
* *
140734 CCATTTTACCCCCTCGAACATCCAACAATTA
1 CCATTTT--GCCC-CGAACATCCAAAAATTA
*
140765 CCATTTTGCCCCAGAACATCCAAAAATTT
1 CCATTTTGCCCC-GAACATCCAAAAATTA
*
140794 CAATTTTG
1 CCATTTTG
140802 ACCCTAAATT
Statistics
Matches: 77, Mismatches: 15, Indels: 11
0.75 0.15 0.11
Matches are distributed among these distances:
28 1 0.01
29 38 0.49
30 15 0.19
31 23 0.30
ACGTcount: A:0.34, C:0.30, G:0.06, T:0.30
Consensus pattern (28 bp):
CCATTTTGCCCCGAACATCCAAAAATTA
Found at i:140764 original size:31 final size:29
Alignment explanation
Indices: 140715--140792 Score: 102
Period size: 31 Copynumber: 2.6 Consensus size: 29
140705 TGATTTTGCA
*
140715 CCCGAATATCCAAAAATTACCATTTTACCC
1 CCCGAACATCCAAAAATTACCATTTT-CCC
* *
140745 CCTCGAACATCCAACAATTACCATTTTGCC
1 CC-CGAACATCCAAAAATTACCATTTTCCC
*
140775 CCAGAACATCCAAAAATT
1 CCCGAACATCCAAAAATT
140793 TCAATTTTGA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 14 0.33
30 6 0.14
31 22 0.52
ACGTcount: A:0.37, C:0.33, G:0.05, T:0.24
Consensus pattern (29 bp):
CCCGAACATCCAAAAATTACCATTTTCCC
Found at i:142248 original size:15 final size:15
Alignment explanation
Indices: 142201--142249 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
142191 TTTACATTAA
142201 TTCTCAACGAACAAG
1 TTCTCAACGAACAAG
* *
142216 TTCTTC-A-GCACGAG
1 TTC-TCAACGAACAAG
142230 TTCTCAACGAACAAG
1 TTCTCAACGAACAAG
142245 TTCTC
1 TTCTC
142250 CACCTCTTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
13 2 0.07
14 9 0.33
15 14 0.52
16 2 0.07
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.27
Consensus pattern (15 bp):
TTCTCAACGAACAAG
Found at i:147357 original size:410 final size:406
Alignment explanation
Indices: 146748--147562 Score: 1386
Period size: 410 Copynumber: 2.0 Consensus size: 406
146738 CCCAGGTTTG
* *
146748 AACTCTATATTCCATAATTTTTTTTTATGAATTAAAATAATAAAATAAAATCCGAATAAAAAGCA
1 AACTCTATATTCCATAATTTTTTTTTATGAATTAAAATAATAAAATAAAACCCGAATAAAAAACA
* * *
146813 CTACTAATATAATTCGAACTCAAATCACATGATAAATATTTTTAATCGTTTTATATTCCATAAGA
66 CTACTAATATAAATCGAACTCAAATCAAATGATAAACATTTTTAATCGTTTTATATTCCATAAGA
**
146878 TTTTTGTTTTTTTTTTTAAATTTAAAAAACTGACATTAACTGTACAGCCGACATACTGAACAATA
131 TTTTTGTTTTTTTTTAAAAATTTAAAAAACTGACATTAACTGTACAGCCGACATACTGAACAATA
146943 TTTGAAGGGAAAAAGTTAAACTGAAGTTG-AAAATCACCGTAGCAGACAGATGGTGACTGATCTA
196 TTTGAAGGGAAAAAGTTAAACTGAAGTTGAAAAATCACCGTAGCAGACAGATGGTGACTGATCTA
147007 CAAGTTGATAACTCCAAGAGATAAAA-CCCTATCTTTTTTTCTCCTGCACCACAGGATAAGGGAT
261 CAAGTTGATAACTCCAAGAGATAAAACCCCTATCTTTTTTTCTCCTGCACCACAGGATAAGGGAT
* *
147071 TTTTTTACAATAATAATAT-AAAAAAATTTAAATATTAAAATAATACACTTTTTTTATTATTTAT
326 TTTTTTACAATAATAATATAAAAAAAATTTAAATAATAAAATAATACACTTTTTTTATAATTTAT
147135 TAAAATGATACATTTA
391 TAAAATGATACATTTA
* *
147151 AACTCTATATTCCATAA-TTTTTTTTATGAATTAAAATAATAAAATAAAACCCTAATAAAAAATA
1 AACTCTATATTCCATAATTTTTTTTTATGAATTAAAATAATAAAATAAAACCCGAATAAAAAACA
* *
147215 TTACTAATATAAATCGAATTCAAATCATATTTAAAATGATAAACATTTTTAATCGTTTTATATTC
66 CTACTAATATAAATCGAACTCAAATC-------AAATGATAAACATTTTTAATCGTTTTATATTC
147280 CATAAGATTTTTGTTTTTCTTTTAAAAATTTAAAAAACTGACATTAACTGTACAGCCGACATACT
124 CATAAGATTTTTGTTTTT-TTTTAAAAATTTAAAAAACTGACATTAACTGTACAGCCGACATACT
*
147345 GAGCAATATTTGAAGGGAAAAAGTTAAACTGAAGTTGAAAAATCACCGTAGCAGACAGATGGTGA
188 GAACAATATTTGAAGGGAAAAAGTTAAACTGAAGTTGAAAAATCACCGTAGCAGACAGATGGTGA
* *
147410 CTGATGTACAAGTTGATAACTCCAAGAGATAAAACCCCTGTCTTTTTTTCTCCTGCACCACAGGA
253 CTGATCTACAAGTTGATAACTCCAAGAGATAAAACCCCTATCTTTTTTTCTCCTGCACCACAGGA
147475 TAAGGGATTTTTTTACAATAATAATATAAAAAAAATTTAAATAATAAAATAATACACTTTTTTTA
318 TAAGGGATTTTTTTACAATAATAATATAAAAAAAATTTAAATAATAAAATAATACACTTTTTTTA
147540 TAATTTATTAAAATGATACATTT
383 TAATTTATTAAAATGATACATTT
147563 GAGTAGTGGT
Statistics
Matches: 385, Mismatches: 16, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
402 66 0.17
403 17 0.04
409 48 0.12
410 80 0.21
411 60 0.16
412 56 0.15
413 58 0.15
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.36
Consensus pattern (406 bp):
AACTCTATATTCCATAATTTTTTTTTATGAATTAAAATAATAAAATAAAACCCGAATAAAAAACA
CTACTAATATAAATCGAACTCAAATCAAATGATAAACATTTTTAATCGTTTTATATTCCATAAGA
TTTTTGTTTTTTTTTAAAAATTTAAAAAACTGACATTAACTGTACAGCCGACATACTGAACAATA
TTTGAAGGGAAAAAGTTAAACTGAAGTTGAAAAATCACCGTAGCAGACAGATGGTGACTGATCTA
CAAGTTGATAACTCCAAGAGATAAAACCCCTATCTTTTTTTCTCCTGCACCACAGGATAAGGGAT
TTTTTTACAATAATAATATAAAAAAAATTTAAATAATAAAATAATACACTTTTTTTATAATTTAT
TAAAATGATACATTTA
Found at i:148809 original size:33 final size:33
Alignment explanation
Indices: 148771--148837 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
148761 AAAATTGAGA
**
148771 TTTTGAGTTAA-TCAAATTAAGTTGTTCGATTTT
1 TTTTGAGTTAATTCAAA-TAAGTAATTCGATTTT
148804 TTTTGAGTTAATTCAAATAAGTAATTCGATTTT
1 TTTTGAGTTAATTCAAATAAGTAATTCGATTTT
148837 T
1 T
148838 GTGTCGAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 26 0.84
34 5 0.16
ACGTcount: A:0.30, C:0.06, G:0.13, T:0.51
Consensus pattern (33 bp):
TTTTGAGTTAATTCAAATAAGTAATTCGATTTT
Found at i:148979 original size:9 final size:9
Alignment explanation
Indices: 148957--149015 Score: 52
Period size: 9 Copynumber: 6.7 Consensus size: 9
148947 AAAAAAAACC
148957 AAAATATTTAT
1 AAAA-ATTT-T
148968 AAAAATTTT
1 AAAAATTTT
148977 --AAATTTT
1 AAAAATTTT
* *
148984 ATATA-TTT
1 AAAAATTTT
*
148992 AAAAATTAT
1 AAAAATTTT
149001 AAAAATTTT
1 AAAAATTTT
149010 AAAAAT
1 AAAAAT
149016 CTAAAAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
7 7 0.17
8 6 0.15
9 19 0.47
10 4 0.10
11 4 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AAAAATTTT
Found at i:149020 original size:26 final size:26
Alignment explanation
Indices: 148977--149027 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
148967 TAAAAATTTT
* * * *
148977 AAATTTTATATATTTAAAAATTATAA
1 AAATTTTAAAAATCTAAAAAATATAA
149003 AAATTTTAAAAATCTAAAAAATATA
1 AAATTTTAAAAATCTAAAAAATATA
149028 TATAATAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (26 bp):
AAATTTTAAAAATCTAAAAAATATAA
Found at i:151889 original size:26 final size:28
Alignment explanation
Indices: 151855--151919 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
151845 TTGACCTGAC
*
151855 ATAT-ATTATAT-TA-TAAA-AATAATT
1 ATATAATTATATATATTAAATAATAAAT
151879 ATATTAATTATATATATTAAATAATAAAT
1 ATA-TAATTATATATATTAAATAATAAAT
*
151908 ATATATTTATAT
1 ATATAATTATAT
151920 CAAAACGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 3 0.09
25 1 0.03
26 7 0.21
27 2 0.06
28 12 0.35
29 9 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
ATATAATTATATATATTAAATAATAAAT
Found at i:152075 original size:39 final size:40
Alignment explanation
Indices: 152026--152106 Score: 130
Period size: 39 Copynumber: 2.0 Consensus size: 40
152016 ATATTTAAAC
*
152026 AATAAAACATTTATTATTTTTATTTTTA-T-TTTTTAATAT
1 AATAAAACATTTATTATTTTTA-TGTTAGTGTTTTTAATAT
152065 AATAAAACATTTATTATTTTTATGTTAGTGTTTTTAATAT
1 AATAAAACATTTATTATTTTTATGTTAGTGTTTTTAATAT
152105 AA
1 AA
152107 ATACTTTTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
38 4 0.10
39 23 0.59
40 12 0.31
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (40 bp):
AATAAAACATTTATTATTTTTATGTTAGTGTTTTTAATAT
Found at i:154156 original size:26 final size:27
Alignment explanation
Indices: 154086--154156 Score: 72
Period size: 31 Copynumber: 2.5 Consensus size: 27
154076 TTTTATTTTT
*
154086 TTTAT-TTAAAAATGAGTAAATTAATTA
1 TTTATGTTAAAAA-GAGTAAATTAAATA
*
154113 TTATATGTTAGATCAAAAAGTAAATTAAATA
1 TT-TATGTTA-A--AAAGAGTAAATTAAATA
154144 TTTATGTTAAAAA
1 TTTATGTTAAAAA
154157 TTTCATCCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
27 5 0.14
28 3 0.08
29 4 0.11
30 8 0.22
31 14 0.38
32 3 0.08
ACGTcount: A:0.49, C:0.01, G:0.08, T:0.41
Consensus pattern (27 bp):
TTTATGTTAAAAAGAGTAAATTAAATA
Found at i:157330 original size:106 final size:105
Alignment explanation
Indices: 157143--157353 Score: 395
Period size: 106 Copynumber: 2.0 Consensus size: 105
157133 ATATGGAGAA
*
157143 AGGTTATGAGACAAGGGATCAAGAACTAAGAAATGAACTGTAGCAGAAGAATGAAGATAATGGTT
1 AGGTTATGAGACAAGGGATCAAGAACTAAGAAATGAACTGTAGCAGAAGAATGAAGATAACGGTT
157208 CAAAGTCCATCCAGGATGAAGAAAGAAGTGAACATAGCTC
66 CAAAGTCCATCCAGGATGAAGAAAGAAGTGAACATAGCTC
157248 AGGTTATGAGACAAGGGGATCAAGAACTAAGAAATGAACTGTAGCAGAAGAATGAAGATAACGGT
1 AGGTTATGAGACAA-GGGATCAAGAACTAAGAAATGAACTGTAGCAGAAGAATGAAGATAACGGT
*
157313 TCAAAGTCCATCTAGGATGAAGAAAGAAGTGAACATAGCTC
65 TCAAAGTCCATCCAGGATGAAGAAAGAAGTGAACATAGCTC
157354 TAAGGTGATA
Statistics
Matches: 103, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
105 14 0.14
106 89 0.86
ACGTcount: A:0.44, C:0.12, G:0.26, T:0.18
Consensus pattern (105 bp):
AGGTTATGAGACAAGGGATCAAGAACTAAGAAATGAACTGTAGCAGAAGAATGAAGATAACGGTT
CAAAGTCCATCCAGGATGAAGAAAGAAGTGAACATAGCTC
Found at i:167961 original size:6 final size:6
Alignment explanation
Indices: 167948--167976 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
167938 AAAGAAATTG
167948 AAAT-A AAATAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA
167977 TGATAGATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:171321 original size:21 final size:21
Alignment explanation
Indices: 171281--171322 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
171271 GCAGGCTCTG
*
171281 TTTCTTCCTTCTCGTTCTCAT
1 TTTCTTCCTCCTCGTTCTCAT
171302 TTTCTTCCTCCTC-TTACTCAT
1 TTTCTTCCTCCTCGTT-CTCAT
171323 CTCCTTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.07, C:0.36, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTCTTCCTCCTCGTTCTCAT
Found at i:177272 original size:21 final size:21
Alignment explanation
Indices: 177246--177306 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
177236 TATTCCCGCA
177246 TAAAATTGAAAAGGTAAAAAG
1 TAAAATTGAAAAGGTAAAAAG
*
177267 TAAAATTGAAAATGTAAAAAG
1 TAAAATTGAAAAGGTAAAAAG
*
177288 TAAAAGTGAAAAGGTAAAA
1 TAAAATTGAAAAGGTAAAA
177307 GGAAATGTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.62, C:0.00, G:0.18, T:0.20
Consensus pattern (21 bp):
TAAAATTGAAAAGGTAAAAAG
Found at i:177318 original size:12 final size:14
Alignment explanation
Indices: 177246--177311 Score: 50
Period size: 14 Copynumber: 4.8 Consensus size: 14
177236 TATTCCCGCA
*
177246 TAAAATTGAAAAGG
1 TAAAAGTGAAAAGG
*
177260 TAAAAAGT-AAAA-T
1 T-AAAAGTGAAAAGG
*
177273 TGAAAA-TGTAAAAAG
1 T-AAAAGTG-AAAAGG
177288 TAAAAGTGAAAAGG
1 TAAAAGTGAAAAGG
177302 TAAAAG-GAAA
1 TAAAAGTGAAA
177312 TGTAAAATGC
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
12 1 0.02
13 9 0.21
14 24 0.57
15 8 0.19
ACGTcount: A:0.62, C:0.00, G:0.20, T:0.18
Consensus pattern (14 bp):
TAAAAGTGAAAAGG
Found at i:185769 original size:27 final size:27
Alignment explanation
Indices: 185719--185770 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
185709 TGGTAAATCA
* *
185719 TGTGGTAGCACTGGAGGAATATTATCC
1 TGTGGTAGCAATGGAGGAAGATTATCC
* *
185746 TGTGGTAGCAATGGTGGTAGATTAT
1 TGTGGTAGCAATGGAGGAAGATTAT
185771 TATTGTTGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.25, C:0.10, G:0.33, T:0.33
Consensus pattern (27 bp):
TGTGGTAGCAATGGAGGAAGATTATCC
Found at i:188052 original size:16 final size:17
Alignment explanation
Indices: 188025--188057 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
188015 TGTAATTAAA
188025 CTAAATGCAAATGATCC
1 CTAAATGCAAATGATCC
*
188042 CTAAA-GCAAATTATCC
1 CTAAATGCAAATGATCC
188058 TAAGTATGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.42, C:0.24, G:0.09, T:0.24
Consensus pattern (17 bp):
CTAAATGCAAATGATCC
Found at i:189417 original size:25 final size:25
Alignment explanation
Indices: 189383--189430 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
189373 GAAATATTTT
189383 ATATTAAATTATTAAATATAATCTC
1 ATATTAAATTATTAAATATAATCTC
* * *
189408 ATATTTAATTATTTAATTTAATC
1 ATATTAAATTATTAAATATAATC
189431 ATGCATGGCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (25 bp):
ATATTAAATTATTAAATATAATCTC
Found at i:192624 original size:21 final size:22
Alignment explanation
Indices: 192600--192640 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
192590 AAAATAAAAT
*
192600 TAAAACTAAAAC-TAAAAATAG
1 TAAAAATAAAACTTAAAAATAG
*
192621 TAAAAATATAACTTAAAAAT
1 TAAAAATAAAACTTAAAAAT
192641 TTAAAACCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.24
Consensus pattern (22 bp):
TAAAAATAAAACTTAAAAATAG
Found at i:192645 original size:21 final size:20
Alignment explanation
Indices: 192595--192646 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
192585 TAAACAAAAT
*
192595 AAAA-TTAAAACTAAAACTA
1 AAAATTTAAAAATAAAACTA
* *
192614 AAAATAGTAAAAATATAACTTA
1 AAAAT-TTAAAAATAAAAC-TA
192636 AAAATTTAAAA
1 AAAATTTAAAA
192647 CCTAATTAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 4 0.15
21 15 0.58
22 7 0.27
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (20 bp):
AAAATTTAAAAATAAAACTA
Found at i:195765 original size:12 final size:12
Alignment explanation
Indices: 195748--195797 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
195738 CAGGTTCTGT
195748 TTCTTCTTTCTC
1 TTCTTCTTTCTC
195760 TTCTTCCTTTC-C
1 TTCTT-CTTTCTC
*
195772 TTCTTCTTTTTC
1 TTCTTCTTTCTC
* *
195784 TTCATCCTTCTC
1 TTCTTCTTTCTC
195796 TT
1 TT
195798 TAGAACCTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 4 0.12
12 23 0.72
13 5 0.16
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (12 bp):
TTCTTCTTTCTC
Found at i:209862 original size:16 final size:16
Alignment explanation
Indices: 209843--209966 Score: 64
Period size: 16 Copynumber: 7.8 Consensus size: 16
209833 ACAACGAAAG
*
209843 AAAAAAAATAAATACT
1 AAAAAAAATAAATAAT
*
209859 AAAAAAAA-GAATAAT
1 AAAAAAAATAAATAAT
*
209874 AAAAAGAAATAAA-AAG
1 AAAAA-AAATAAATAAT
209890 AAAAGGCAAAATAAATGAAAT
1 AAAA---AAAATAAAT--AAT
* *
209911 TAAAAAAAT-GAT--T
1 AAAAAAAATAAATAAT
* *
209924 AAATAAAATAAAGAAT
1 AAAAAAAATAAATAAT
*
209940 -AAAATAA-AAATAAT
1 AAAAAAAATAAATAAT
209954 AAAATAAAATAAA
1 AAAA-AAAATAAA
209967 ATTAAGGGAA
Statistics
Matches: 79, Mismatches: 15, Indels: 27
0.65 0.12 0.22
Matches are distributed among these distances:
13 8 0.10
14 7 0.09
15 18 0.23
16 21 0.27
17 7 0.09
18 12 0.15
19 1 0.01
21 5 0.06
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (16 bp):
AAAAAAAATAAATAAT
Found at i:209940 original size:12 final size:11
Alignment explanation
Indices: 209924--209967 Score: 58
Period size: 12 Copynumber: 4.2 Consensus size: 11
209914 AAAAATGATT
209924 AAATAAAATAA
1 AAATAAAATAA
209935 AGAATAAAATAA
1 A-AATAAAATAA
209947 AAAT--AAT-A
1 AAATAAAATAA
209955 AAATAAAATAA
1 AAATAAAATAA
209966 AA
1 AA
209968 TTAAGGGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
8 5 0.17
9 3 0.10
10 3 0.10
11 7 0.24
12 11 0.38
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:209956 original size:14 final size:14
Alignment explanation
Indices: 209925--209962 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
209915 AAAATGATTA
209925 AATAAAAT--AAAG
1 AATAAAATAAAAAG
*
209937 AATAAAATAAAAAT
1 AATAAAATAAAAAG
209951 AATAAAATAAAA
1 AATAAAATAAAA
209963 TAAAATTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 8 0.35
14 15 0.65
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (14 bp):
AATAAAATAAAAAG
Found at i:209967 original size:5 final size:5
Alignment explanation
Indices: 209924--209968 Score: 56
Period size: 5 Copynumber: 8.8 Consensus size: 5
209914 AAAAATGATT
*
209924 AAATA AAATAA AGAATA AAATA AAA-A TAATA AAATA AAATA AAAT
1 AAATA AAAT-A A-AATA AAATA AAATA AAATA AAATA AAATA AAAT
209969 TAAGGGAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
4 3 0.09
5 25 0.71
6 4 0.11
7 3 0.09
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:210586 original size:75 final size:75
Alignment explanation
Indices: 210474--210659 Score: 205
Period size: 75 Copynumber: 2.5 Consensus size: 75
210464 AAAGCTCTAA
* * * * * * * *
210474 TGGTCACAGAGTCTAGCACATGCCCGTGTCTCTAGGTCGTGTGTCATTTTGAAATTTTATTCATA
1 TGGTCACACAATCTAGCACATGCCCGTGTGTCCAGGTCGTGTGTCATTTCGAAA-ATCATTCAAA
210539 AATACGCCCAAT
65 AATACGCCC-AT
* * ** *
210551 T-G-CACACAATCTAGCACACGCCAGTGTGTCCAGGTCGTGTGTTGTTTCGAAAATCATTTAAAA
1 TGGTCACACAATCTAGCACATGCCCGTGTGTCCAGGTCGTGTGTCATTTCGAAAATCATTCAAAA
210614 ATACGCCCAT
66 ATACGCCCAT
**
210624 TGGTCACACGGTCTAGCACATGCCCGTGTGTCCAGG
1 TGGTCACACAATCTAGCACATGCCCGTGTGTCCAGG
210660 CCGTTGGCCT
Statistics
Matches: 90, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
73 3 0.03
74 16 0.18
75 69 0.77
76 1 0.01
77 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.29
Consensus pattern (75 bp):
TGGTCACACAATCTAGCACATGCCCGTGTGTCCAGGTCGTGTGTCATTTCGAAAATCATTCAAAA
ATACGCCCAT
Found at i:216031 original size:18 final size:18
Alignment explanation
Indices: 216004--216052 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
215994 ATGGTTCGAC
* *
216004 GAGCAGGAAGAACAACAA
1 GAGCAAGAAGAACAAAAA
*
216022 GAGCAAGAAGAGCAAAAA
1 GAGCAAGAAGAACAAAAA
* *
216040 GAACAAGAGGAAC
1 GAGCAAGAAGAAC
216053 CCAATTATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.57, C:0.14, G:0.29, T:0.00
Consensus pattern (18 bp):
GAGCAAGAAGAACAAAAA
Found at i:216314 original size:26 final size:26
Alignment explanation
Indices: 216267--216316 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
216257 GAAAAATATT
** *
216267 AAAATATTAAAATTAAATTAAAAATG
1 AAAATATTAAAACAAAAATAAAAATG
216293 AAAATATTAAAACAAAAATAAAAA
1 AAAATATTAAAACAAAAATAAAAA
216317 ATGGCCAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (26 bp):
AAAATATTAAAACAAAAATAAAAATG
Found at i:220657 original size:63 final size:63
Alignment explanation
Indices: 220558--220686 Score: 249
Period size: 63 Copynumber: 2.0 Consensus size: 63
220548 AGGGTTTCTT
*
220558 AGCATTCATGTGAAGTAACTAGGACTGGGTCGATTTGAAACAATTTAATCTCATGAACCTAAA
1 AGCATTCATGTGAAGTAACAAGGACTGGGTCGATTTGAAACAATTTAATCTCATGAACCTAAA
220621 AGCATTCATGTGAAGTAACAAGGACTGGGTCGATTTGAAACAATTTAATCTCATGAACCTAAA
1 AGCATTCATGTGAAGTAACAAGGACTGGGTCGATTTGAAACAATTTAATCTCATGAACCTAAA
220684 AGC
1 AGC
220687 CATGCAAGGT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.27
Consensus pattern (63 bp):
AGCATTCATGTGAAGTAACAAGGACTGGGTCGATTTGAAACAATTTAATCTCATGAACCTAAA
Found at i:220757 original size:18 final size:18
Alignment explanation
Indices: 220709--220757 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
220699 TAGAGCTCAG
* *
220709 TCAATTTATTCTAAACTT
1 TCAATTCATTCTGAACTT
*
220727 TCAATTCAATCTGAACTT
1 TCAATTCATTCTGAACTT
220745 TCAATTCATTCTG
1 TCAATTCATTCTG
220758 GGTCGAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.45
Consensus pattern (18 bp):
TCAATTCATTCTGAACTT
Found at i:223667 original size:13 final size:14
Alignment explanation
Indices: 223649--223678 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
223639 ATTCGACTAA
223649 GGAAAAA-CAAATG
1 GGAAAAATCAAATG
223662 GGAAAAATCAAATG
1 GGAAAAATCAAATG
223676 GGA
1 GGA
223679 GCTAAAAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.57, C:0.07, G:0.27, T:0.10
Consensus pattern (14 bp):
GGAAAAATCAAATG
Found at i:233786 original size:21 final size:21
Alignment explanation
Indices: 233743--233792 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
233733 ATTTATTTAT
*
233743 TATTT-TAATTAAAATAATAA
1 TATTTATAAGTAAAATAATAA
* *
233763 TATTTATAAGTAATATAATTA
1 TATTTATAAGTAAAATAATAA
*
233784 TATATATAA
1 TATTTATAA
233793 AGAAAGAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TATTTATAAGTAAAATAATAA
Found at i:234604 original size:53 final size:55
Alignment explanation
Indices: 234538--234655 Score: 159
Period size: 55 Copynumber: 2.2 Consensus size: 55
234528 TAATGTTACG
* * * * *
234538 TTGGAATATTGCTTCTTTTGAATCGATT-TTT-TATGTTTAAATCGATTGTCATA
1 TTGGAATACTGCTTCTTTTAAATCGATTGTTTATATATTTAAATCAATTATCATA
*
234591 TTGGAATACTGCTTCTTTTAAATCGATTGTTTATATATTTAAATCAATTATCATG
1 TTGGAATACTGCTTCTTTTAAATCGATTGTTTATATATTTAAATCAATTATCATA
*
234646 TTGAAATACT
1 TTGGAATACT
234656 TTTATGTAGG
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
53 26 0.46
54 3 0.05
55 27 0.48
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48
Consensus pattern (55 bp):
TTGGAATACTGCTTCTTTTAAATCGATTGTTTATATATTTAAATCAATTATCATA
Found at i:235488 original size:34 final size:34
Alignment explanation
Indices: 235445--235512 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
235435 AAAACTTTTT
235445 TTAAAGTTTTTATAGATTGAACCCGTATTAAACA
1 TTAAAGTTTTTATAGATTGAACCCGTATTAAACA
*
235479 TTAAAGTTTTTATAGATTGAACCTGTATTAAACA
1 TTAAAGTTTTTATAGATTGAACCCGTATTAAACA
235513 GACTCAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (34 bp):
TTAAAGTTTTTATAGATTGAACCCGTATTAAACA
Found at i:237665 original size:22 final size:21
Alignment explanation
Indices: 237639--237687 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
237629 TTGTTGCTTT
237639 TTTCATCAGGTTTCCAT-TTAA
1 TTTCATCAGGTTT-CATGTTAA
**
237660 CTTTCATTTGGTTTCATGTTAA
1 -TTTCATCAGGTTTCATGTTAA
237682 TTTCAT
1 TTTCAT
237688 TTCGTAACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.20, C:0.16, G:0.10, T:0.53
Consensus pattern (21 bp):
TTTCATCAGGTTTCATGTTAA
Found at i:237687 original size:21 final size:22
Alignment explanation
Indices: 237647--237689 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
237637 TTTTTCATCA
237647 GGTTTCCATTTAACTTTCATTT
1 GGTTTCCATTTAACTTTCATTT
237669 GGTTT-CATGTTAA-TTTCATTT
1 GGTTTCCAT-TTAACTTTCATTT
237690 CGTAACACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.19, C:0.14, G:0.12, T:0.56
Consensus pattern (22 bp):
GGTTTCCATTTAACTTTCATTT
Found at i:241678 original size:55 final size:55
Alignment explanation
Indices: 241596--241729 Score: 196
Period size: 55 Copynumber: 2.4 Consensus size: 55
241586 GTTTAGATTG
* * * * *
241596 AATCGATTGTTATGCTGCAATATTGCTTCTTTTGAATCGATTGTTTTTATGTTTA
1 AATCGATTGTCATGTTGAAATACTGCTTCTTTTGAATCGATTGTTTTTATATTTA
* *
241651 AATCGATTGTCATGTTGGAATACTGCTTCTTTTGAATCGATTGTTTTTGTATTTA
1 AATCGATTGTCATGTTGAAATACTGCTTCTTTTGAATCGATTGTTTTTATATTTA
*
241706 AATCAATTGTCATGTTGAAATACT
1 AATCGATTGTCATGTTGAAATACT
241730 TTTATGCAGG
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 71 1.00
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.48
Consensus pattern (55 bp):
AATCGATTGTCATGTTGAAATACTGCTTCTTTTGAATCGATTGTTTTTATATTTA
Found at i:242505 original size:18 final size:18
Alignment explanation
Indices: 242482--242528 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
242472 ATGACAAAAT
242482 AATAAAATACATGAATAA
1 AATAAAATACATGAATAA
* * *
242500 AATAAATTAAATGAATAC
1 AATAAAATACATGAATAA
*
242518 AATTAAATACA
1 AATAAAATACA
242529 ATTAATAACA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (18 bp):
AATAAAATACATGAATAA
Found at i:243224 original size:13 final size:12
Alignment explanation
Indices: 243208--243250 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
243198 TTCTTTTTTC
243208 TTTTTATAAATTT
1 TTTTTAT-AATTT
*
243221 TTTTTCTAATTT
1 TTTTTATAATTT
*
243233 TTATTTATGATTT
1 TT-TTTATAATTT
243246 TTTTT
1 TTTTT
243251 GTTAACCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (12 bp):
TTTTTATAATTT
Found at i:243233 original size:27 final size:25
Alignment explanation
Indices: 243177--243250 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 25
243167 TCTACTGATT
*
243177 TTTTTATTTGA-AAATCTTTTTTTCTT
1 TTTTTATTT-ATAAAT-TTTTTTTCTA
*
243203 TTTTCTTTTTATAAATTTTTTTTCTAA
1 TTTT-TATTTATAAATTTTTTTTCT-A
*
243230 TTTTTATTTAT-GATTTTTTTT
1 TTTTTATTTATAAATTTTTTTT
243251 GTTAACCATT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
25 9 0.22
26 20 0.49
27 12 0.29
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (25 bp):
TTTTTATTTATAAATTTTTTTTCTA
Found at i:243595 original size:41 final size:42
Alignment explanation
Indices: 243549--243665 Score: 104
Period size: 41 Copynumber: 2.9 Consensus size: 42
243539 GATAGATAAA
243549 TAAATAAATAAACAAACAAGATAATAACAAT-AAATGCAAAT-
1 TAAATAAATAAACAAACAAGATAATAACAATAAAATG-AAATG
* * * *
243590 TAAATAAA-AAATAATAAAAGA-GATAACAATAAAATGACATG
1 TAAATAAATAAACAA-ACAAGATAATAACAATAAAATGAAATG
*
243631 AAAATAAAT-AAC-AACAAGATAAATAAACAA-AAAAT
1 TAAATAAATAAACAAACAAGAT-AAT-AACAATAAAAT
243666 AAGTAAAAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
39 5 0.08
40 17 0.28
41 34 0.56
42 5 0.08
ACGTcount: A:0.68, C:0.08, G:0.06, T:0.18
Consensus pattern (42 bp):
TAAATAAATAAACAAACAAGATAATAACAATAAAATGAAATG
Found at i:243667 original size:15 final size:15
Alignment explanation
Indices: 243631--243685 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
243621 AAATGACATG
243631 AAAATAAAT-AACAA
1 AAAATAAATAAACAA
*
243645 CAAGATAAATAAACAA
1 -AAAATAAATAAACAA
*
243661 AAAATAAGTAAA-AA
1 AAAATAAATAAACAA
*
243675 TAAA-AAATAAA
1 AAAATAAATAAA
243686 TTCTAAAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
13 6 0.18
14 5 0.15
15 18 0.53
16 5 0.15
ACGTcount: A:0.76, C:0.05, G:0.04, T:0.15
Consensus pattern (15 bp):
AAAATAAATAAACAA
Found at i:243710 original size:14 final size:13
Alignment explanation
Indices: 243689--243723 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
243679 AAATAAATTC
243689 TAAAATAAACAAA
1 TAAAATAAACAAA
243702 TAAATATAAACAAA
1 TAAA-ATAAACAAA
*
243716 AAAAATAA
1 TAAAATAA
243724 TTGGAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (13 bp):
TAAAATAAACAAA
Found at i:243721 original size:19 final size:18
Alignment explanation
Indices: 243659--243723 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 18
243649 ATAAATAAAC
* *
243659 AAAAAATAAGTA-AAAAT
1 AAAAAATAAATATAAAAA
*
243676 AAAAAATAAATTCTAAAATA
1 AAAAAATAAA-TATAAAA-A
*
243696 AACAAATAAATATAAACAA
1 AAAAAATAAATATAAA-AA
243715 AAAAAATAA
1 AAAAAATAA
243724 TTGGAATTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 9 0.24
18 1 0.03
19 18 0.47
20 10 0.26
ACGTcount: A:0.75, C:0.05, G:0.02, T:0.18
Consensus pattern (18 bp):
AAAAAATAAATATAAAAA
Found at i:243794 original size:25 final size:26
Alignment explanation
Indices: 243766--243814 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
243756 AATAAATAAA
243766 CAAAAAAAATCAA-TAAAT-TAAATGT
1 CAAAAAAAA-CAACTAAATATAAATGT
*
243791 CAAAATAAACAACTAAATATAAAT
1 CAAAAAAAACAACTAAATATAAAT
243815 AATAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 13 0.62
26 5 0.24
ACGTcount: A:0.65, C:0.10, G:0.02, T:0.22
Consensus pattern (26 bp):
CAAAAAAAACAACTAAATATAAATGT
Found at i:244035 original size:33 final size:33
Alignment explanation
Indices: 243993--244058 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
243983 ACAAATACAA
243993 ATTGATACCTCAATATTTACTTTGAATTTTCTT
1 ATTGATACCTCAATATTTACTTTGAATTTTCTT
*
244026 ATTGATACCTCAATATTTGCTTTGAATTTTCTT
1 ATTGATACCTCAATATTTACTTTGAATTTTCTT
244059 TGAATGTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.26, C:0.15, G:0.08, T:0.52
Consensus pattern (33 bp):
ATTGATACCTCAATATTTACTTTGAATTTTCTT
Found at i:244861 original size:45 final size:45
Alignment explanation
Indices: 244683--245403 Score: 725
Period size: 45 Copynumber: 15.8 Consensus size: 45
244673 GCTTTCTGTA
* * * *
244683 GCTTCAATCTGTCCCTCTAGATTTAGGGGTATAAGATTGGATGTGATA
1 GCTTCAATCTGCCCCTCT-GAATTAGGGGTAAAAGATTGGATG-G-TG
* * * * *
244731 GCTTAAATTTGCCCCTCTAGATTTAAGGGTATAAGATTGGAT-GTG
1 GCTTCAATCTGCCCCTCT-GAATTAGGGGTAAAAGATTGGATGGTG
* *
244776 GTAACTTCAATCTGCCCATCTAGATTTATGGGGTAAAAGATTGGATGGTG
1 G---CTTCAATCTGCCCCTCT-GAATTA-GGGGTAAAAGATTGGATGGTG
* * *
244826 GCTTCAATCTACCCCTCTGAATTAAGGGTAAAAGATTAGATGGTG
1 GCTTCAATCTGCCCCTCTGAATTAGGGGTAAAAGATTGGATGGTG
* * * * *
244871 GCTTAAATCCGCCCCTTTGGATTAGGGGTAAAAGATTGGATGGGG
1 GCTTCAATCTGCCCCTCTGAATTAGGGGTAAAAGATTGGATGGTG
* * * * * * *
244916 GCTTAAATTTGTCCCTTTGGATTAAGGGTAAAAGATTGGATGGCG
1 GCTTCAATCTGCCCCTCTGAATTAGGGGTAAAAGATTGGATGGTG
* * * **
244961 GCTTCAAT-TTCTCCCTTTGGATTAGGGGTAAAAGATTGGATGACG
1 GCTTCAATCTGC-CCCTCTGAATTAGGGGTAAAAGATTGGATGGTG
* *
245006 GCTTCAATCTACCCCTCT-AGATTAGGGGTAAAAGATTGGATGATG
1 GCTTCAATCTGCCCCTCTGA-ATTAGGGGTAAAAGATTGGATGGTG
* * *
245051 TCTTCAATCTACCCCTCT-AGATTAGGGGTAAAAGATTGGATGATG
1 GCTTCAATCTGCCCCTCTGA-ATTAGGGGTAAAAGATTGGATGGTG
* * *
245096 GTTTCAATCTGCCCCTCTGGATTAGGGGTGAAAGATTGGATGGTG
1 GCTTCAATCTGCCCCTCTGAATTAGGGGTAAAAGATTGGATGGTG
** * * *
245141 GCTTCAATCTATCCCTCTGGATTAGGGGTAAAAGATTGAATTTTGTG
1 GCTTCAATCTGCCCCTCTGAATTAGGGGTAAAAGATTGGA--TGGTG
* *
245188 ACTTCAATCTGCCCCT-TTAGATTAGGGGTAAAAGATTGGATGGTG
1 GCTTCAATCTGCCCCTCTGA-ATTAGGGGTAAAAGATTGGATGGTG
* * * * *
245233 GCTTTAATCTGCCCCTCTGGATAAGGGGTAAAAGACTAGATGGTG
1 GCTTCAATCTGCCCCTCTGAATTAGGGGTAAAAGATTGGATGGTG
* * * *
245278 GCTTCAATCTG-CCCTATGGATTAGGGGTAAAATATTGGATGGTA
1 GCTTCAATCTGCCCCTCTGAATTAGGGGTAAAAGATTGGATGGTG
* * *
245322 GCTTCAATCTGCCTCTCTAAATTAGGGGTAAAAGACTGGATGGTG
1 GCTTCAATCTGCCCCTCTGAATTAGGGGTAAAAGATTGGATGGTG
* *
245367 GCTTCAATATGCCCCTCTGGATTAGGGGTAAAAGATT
1 GCTTCAATCTGCCCCTCTGAATTAGGGGTAAAAGATT
245404 AGATTTGGTG
Statistics
Matches: 576, Mismatches: 83, Indels: 31
0.83 0.12 0.04
Matches are distributed among these distances:
44 39 0.07
45 398 0.69
46 10 0.02
47 51 0.09
48 59 0.10
49 15 0.03
50 4 0.01
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.31
Consensus pattern (45 bp):
GCTTCAATCTGCCCCTCTGAATTAGGGGTAAAAGATTGGATGGTG
Found at i:244956 original size:135 final size:135
Alignment explanation
Indices: 244683--245407 Score: 817
Period size: 135 Copynumber: 5.3 Consensus size: 135
244673 GCTTTCTGTA
* * * * * * * *
244683 GCTTCAATCTGTCCCTCTAGATTTAGGGGTATAAGATTGGATGTGATAGCTTAAATTTGCCCCTC
1 GCTTCAATCTGCCCCTCTGGA-TTAGGGGTAAAAGATTAGATG-G-TGGCTTCAATCTACCCCTC
* * * *
244748 TAGATTTAAGGGTATAAGATTGGAT-GTGGTAACTTCAATCTGCCCATCTAGATTTATGGGGTAA
63 TGGA-TTAGGGGTAAAAGATTGGATGGTGG---CTTCAATCTGCCCCTCTAGA-TTA-GGGGTAA
244812 AAGATTGGATGGTG
122 AAGATTGGATGGTG
* * * * ** *
244826 GCTTCAATCTACCCCTCTGAATTAAGGGTAAAAGATTAGATGGTGGCTTAAATCCGCCCCTTTGG
1 GCTTCAATCTGCCCCTCTGGATTAGGGGTAAAAGATTAGATGGTGGCTTCAATCTACCCCTCTGG
* * * * * * *
244891 ATTAGGGGTAAAAGATTGGATGGGGGCTTAAATTTGTCCCTTTGGATTAAGGGTAAAAGATTGGA
66 ATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTGCCCCTCTAGATTAGGGGTAAAAGATTGGA
*
244956 TGGCG
131 TGGTG
* * * ** *
244961 GCTTCAAT-TTCTCCCTTTGGATTAGGGGTAAAAGATTGGATGACGGCTTCAATCTACCCCTCTA
1 GCTTCAATCTGC-CCCTCTGGATTAGGGGTAAAAGATTAGATGGTGGCTTCAATCTACCCCTCTG
* * *
245025 GATTAGGGGTAAAAGATTGGATGATGTCTTCAATCTACCCCTCTAGATTAGGGGTAAAAGATTGG
65 GATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTGCCCCTCTAGATTAGGGGTAAAAGATTGG
*
245090 ATGATG
130 ATGGTG
* * * *
245096 GTTTCAATCTGCCCCTCTGGATTAGGGGTGAAAGATTGGATGGTGGCTTCAATCTATCCCTCTGG
1 GCTTCAATCTGCCCCTCTGGATTAGGGGTAAAAGATTAGATGGTGGCTTCAATCTACCCCTCTGG
* * * *
245161 ATTAGGGGTAAAAGATTGAATTTTGTGACTTCAATCTGCCCCTTTAGATTAGGGGTAAAAGATTG
66 ATTAGGGGTAAAAGATTGGA--TGGTGGCTTCAATCTGCCCCTCTAGATTAGGGGTAAAAGATTG
245226 GATGGTG
129 GATGGTG
* * * * *
245233 GCTTTAATCTGCCCCTCTGGATAAGGGGTAAAAGACTAGATGGTGGCTTCAATCT-GCCCTATGG
1 GCTTCAATCTGCCCCTCTGGATTAGGGGTAAAAGATTAGATGGTGGCTTCAATCTACCCCTCTGG
* * * * *
245297 ATTAGGGGTAAAATATTGGATGGTAGCTTCAATCTGCCTCTCTAAATTAGGGGTAAAAGACTGGA
66 ATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTGCCCCTCTAGATTAGGGGTAAAAGATTGGA
245362 TGGTG
131 TGGTG
*
245367 GCTTCAATATGCCCCTCTGGATTAGGGGTAAAAGATTAGAT
1 GCTTCAATCTGCCCCTCTGGATTAGGGGTAAAAGATTAGAT
245408 TTGGTGATGT
Statistics
Matches: 494, Mismatches: 83, Indels: 19
0.83 0.14 0.03
Matches are distributed among these distances:
134 82 0.17
135 200 0.40
136 30 0.06
137 107 0.22
139 18 0.04
140 21 0.04
141 1 0.00
142 18 0.04
143 17 0.03
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (135 bp):
GCTTCAATCTGCCCCTCTGGATTAGGGGTAAAAGATTAGATGGTGGCTTCAATCTACCCCTCTGG
ATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTGCCCCTCTAGATTAGGGGTAAAAGATTGGA
TGGTG
Found at i:245573 original size:101 final size:101
Alignment explanation
Indices: 245405--245644 Score: 263
Period size: 101 Copynumber: 2.4 Consensus size: 101
245395 TAAAAGATTA
* * * * * * *
245405 GATTTGGTGAT-GTAACTTTACTTCATTTCACTGTAACTTTAAGGAGATTGAGATCTGCTATTGT
1 GATTTGGTG-TGGTAACTTCACTCCATTCCACTATAACTTCAAGGAGATTGAGATCCGCTACTGT
* *
245469 AGTTTTAATCCGCTACACTGCAACTTCAGGAAGATGG
65 AGTTTTAAACCGCTACACTGCAACTTCAGGAAGATAG
* * *
245506 GATTTGGTGTGGTAACTTCGCTCCATTCCACTATAACTTCAAGGAGATTGAGGTCCGTTACTGTA
1 GATTTGGTGTGGTAACTTCACTCCATTCCACTATAACTTCAAGGAGATTGAGATCCGCTACTGTA
* * * *
245571 GTTTTAAACCGCTTCATTGCAACTTTAGGAATATAG
66 GTTTTAAACCGCTACACTGCAACTTCAGGAAGATAG
* * **
245607 AATTTGGTGTGG---CTTCACTCCGTTCCACTGCAACTTCA
1 GATTTGGTGTGGTAACTTCACTCCATTCCACTATAACTTCA
245645 GTGGGTGTTG
Statistics
Matches: 117, Mismatches: 21, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
98 22 0.19
100 1 0.01
101 94 0.80
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.35
Consensus pattern (101 bp):
GATTTGGTGTGGTAACTTCACTCCATTCCACTATAACTTCAAGGAGATTGAGATCCGCTACTGTA
GTTTTAAACCGCTACACTGCAACTTCAGGAAGATAG
Found at i:250224 original size:23 final size:23
Alignment explanation
Indices: 250194--250244 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
250184 ACCCCTAATA
250194 CTTTCCATATATTCAGTATAGTC
1 CTTTCCATATATTCAGTATAGTC
*
250217 CTTTCCATTTATTCAGTATAGTC
1 CTTTCCATATATTCAGTATAGTC
250240 CTTTC
1 CTTTC
250245 AACACAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.22, C:0.24, G:0.08, T:0.47
Consensus pattern (23 bp):
CTTTCCATATATTCAGTATAGTC
Found at i:252970 original size:17 final size:16
Alignment explanation
Indices: 252943--252995 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
252933 TATGTGAGGA
252943 TTTT-TATTTATTATT
1 TTTTATATTTATTATT
*
252958 TTTTATGATTTATGATT
1 TTTTAT-ATTTATTATT
*
252975 TTTTATTTTTATGTATT
1 TTTTATATTTAT-TATT
252992 TTTT
1 TTTT
252996 TCTGAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 4 0.12
16 6 0.19
17 22 0.69
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (16 bp):
TTTTATATTTATTATT
Found at i:257360 original size:12 final size:12
Alignment explanation
Indices: 257345--257371 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
257335 AATTAACCAT
257345 AAAGCATGATAC
1 AAAGCATGATAC
257357 AAAGCATGATAC
1 AAAGCATGATAC
257369 AAA
1 AAA
257372 CACAAGCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (12 bp):
AAAGCATGATAC
Done.