Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008235.1 Hibiscus syriacus cultivar Beakdansim tig00110879_pilon, 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: 820011
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:471595 original size:13 final size:13
Alignment explanation
Indices: 471558--471597 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
471548 TTGATATTGA
471558 AAAATAAATA-TT
1 AAAATAAATATTT
*
471570 AAAATAATTTATTT
1 AAAATAA-ATATTT
471584 AAAATAAATATTT
1 AAAATAAATATTT
471597 A
1 A
471598 TATATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:472997 original size:3 final size:3
Alignment explanation
Indices: 472979--473081 Score: 136
Period size: 3 Copynumber: 33.7 Consensus size: 3
472969 ATATGTATTT
* *
472979 TAA TATA TAT TAA TAA TAA TAA TAA T-A TGA TAA TAA TAA TATA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
* *
473025 TAA TATA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
473071 TAA TAA TAA TA
1 TAA TAA TAA TA
473082 TTTATAATAT
Statistics
Matches: 89, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
2 2 0.02
3 79 0.89
4 8 0.09
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:474544 original size:39 final size:39
Alignment explanation
Indices: 474490--474571 Score: 164
Period size: 39 Copynumber: 2.1 Consensus size: 39
474480 GCTGATATCC
474490 AAACATAGTCTTTCAAACTATGATCCTCCTATCTTTTAG
1 AAACATAGTCTTTCAAACTATGATCCTCCTATCTTTTAG
474529 AAACATAGTCTTTCAAACTATGATCCTCCTATCTTTTAG
1 AAACATAGTCTTTCAAACTATGATCCTCCTATCTTTTAG
474568 AAAC
1 AAAC
474572 TTTGTGCGGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (39 bp):
AAACATAGTCTTTCAAACTATGATCCTCCTATCTTTTAG
Found at i:481186 original size:22 final size:23
Alignment explanation
Indices: 481155--481230 Score: 88
Period size: 22 Copynumber: 3.4 Consensus size: 23
481145 AATTAATGTT
481155 AAATAATAATTAGTAAAAGCTAA
1 AAATAATAATTAGTAAAAGCTAA
***
481178 AAAT-ATAA-TA-TAATATTTTAA
1 AAATAATAATTAGTAA-AAGCTAA
481199 AAATAATAATTAGTAAAAGCTAA
1 AAATAATAATTAGTAAAAGCTAA
481222 AAA-AATAAT
1 AAATAATAAT
481231 ATAATATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
20 3 0.07
21 10 0.23
22 14 0.33
23 13 0.30
24 3 0.07
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (23 bp):
AAATAATAATTAGTAAAAGCTAA
Found at i:481214 original size:44 final size:44
Alignment explanation
Indices: 481155--481242 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
481145 AATTAATGTT
*
481155 AAATAATAATTAGTAAAAGCTAAAAATATAATATAATATTTTAA
1 AAATAATAATTAGTAAAAGCTAAAAAAATAATATAATATTTTAA
481199 AAATAATAATTAGTAAAAGCTAAAAAAATAATATAATATTTTAA
1 AAATAATAATTAGTAAAAGCTAAAAAAATAATATAATATTTTAA
481243 TTTAATATTC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (44 bp):
AAATAATAATTAGTAAAAGCTAAAAAAATAATATAATATTTTAA
Found at i:487203 original size:18 final size:16
Alignment explanation
Indices: 487158--487198 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
487148 CATAAGGTAG
487158 GTTGCATATTAGTATA
1 GTTGCATATTAGTATA
487174 GTTGCATATTAGTATA
1 GTTGCATATTAGTATA
487190 GTTGCATAT
1 GTTGCATAT
487199 ATTAGATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.29, C:0.07, G:0.20, T:0.44
Consensus pattern (16 bp):
GTTGCATATTAGTATA
Found at i:487351 original size:12 final size:12
Alignment explanation
Indices: 487331--487368 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
487321 TCATGTTGAA
487331 TTGCATTTCATG
1 TTGCATTTCATG
*
487343 TTTCATTTCATG
1 TTGCATTTCATG
*
487355 TTGCATTGCATG
1 TTGCATTTCATG
487367 TT
1 TT
487369 AAATAGTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.53
Consensus pattern (12 bp):
TTGCATTTCATG
Found at i:488315 original size:21 final size:21
Alignment explanation
Indices: 488273--488315 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
488263 TTTCTGGGCT
* *
488273 AGGGGAATCGATACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
488294 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
488315 A
1 A
488316 ACGAACCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.30, G:0.23, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:488388 original size:23 final size:22
Alignment explanation
Indices: 488344--488388 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
488334 AATGTCATGG
*
488344 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
488366 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
488389 AAGTTATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:489962 original size:23 final size:22
Alignment explanation
Indices: 489936--489998 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
489926 ATTATTATAT
489936 GGCACTATGGTGCAATTCTACGC
1 GGCACT-TGGTGCAATTCTACGC
* * *
489959 GGCACTCCGGTGTAATTCTACGT
1 GGCACT-TGGTGCAATTCTACGC
489982 GGCACTTCGGTGCAATT
1 GGCACTT-GGTGCAATT
489999 ATACAAGCTG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.29
Consensus pattern (22 bp):
GGCACTTGGTGCAATTCTACGC
Found at i:494429 original size:161 final size:162
Alignment explanation
Indices: 494164--494489 Score: 618
Period size: 161 Copynumber: 2.0 Consensus size: 162
494154 TTGATTGCTT
494164 GGATAGTTGTTCTCTTACTTCTTCAAGTGTCATTAGCTTGTATTTATAGCTTGGAATGTGTTTGA
1 GGATAGTTGTTCTCTTACTTCTTCAAGTGTCATTAGCTTGTATTTATAGCTTGGAATGTGTTTGA
*
494229 AGTCGTATATAGCTGTTGGGGATGTTTTGGAGCCGTTTGGATATGAAAATCAATTAATAAAACAG
66 AGTCGTATATAGCTGTTGGGGATGTTTTGGAGACGTTTGGATATGAAAATCAATTAATAAAACAG
494294 CTTGGA-GTGGGGGAATAGGTACCCCCTCATG
131 CTTGGACGTGGGGGAATAGGTACCCCCTCATG
*
494325 GGATAGTTGTTCTCTTACTTCTTCAAGTGTCCTTAGCTTGTATTTATAGCTTGGAATGTGTTTGA
1 GGATAGTTGTTCTCTTACTTCTTCAAGTGTCATTAGCTTGTATTTATAGCTTGGAATGTGTTTGA
494390 AGTCGTATATAGCTGTTGGGGATGTTTTGGAGACGTTTGGATATGAAAATCAATTAATAAAACAG
66 AGTCGTATATAGCTGTTGGGGATGTTTTGGAGACGTTTGGATATGAAAATCAATTAATAAAACAG
494455 CTTGGAGCGTGGGGGAATAGGTACCCCCTCATG
131 CTTGGA-CGTGGGGGAATAGGTACCCCCTCATG
494488 GG
1 GG
494490 GAATCGGTTC
Statistics
Matches: 161, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
161 134 0.83
163 27 0.17
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.36
Consensus pattern (162 bp):
GGATAGTTGTTCTCTTACTTCTTCAAGTGTCATTAGCTTGTATTTATAGCTTGGAATGTGTTTGA
AGTCGTATATAGCTGTTGGGGATGTTTTGGAGACGTTTGGATATGAAAATCAATTAATAAAACAG
CTTGGACGTGGGGGAATAGGTACCCCCTCATG
Found at i:494556 original size:21 final size:21
Alignment explanation
Indices: 494532--494573 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
494522 CCGTTAGACA
494532 GGGGAATCGGTACCCCCTGGG
1 GGGGAATCGGTACCCCCTGGG
* *
494553 GGGGAATCTGTTCCCCCTGGG
1 GGGGAATCGGTACCCCCTGGG
494574 CAATCTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.29, G:0.40, T:0.19
Consensus pattern (21 bp):
GGGGAATCGGTACCCCCTGGG
Found at i:494847 original size:13 final size:13
Alignment explanation
Indices: 494829--494858 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
494819 CTTAGTTGCG
494829 AAAATTAAAATTT
1 AAAATTAAAATTT
*
494842 AAAATTGAAATTT
1 AAAATTAAAATTT
494855 AAAA
1 AAAA
494859 ATTCGGTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:495026 original size:5 final size:5
Alignment explanation
Indices: 495012--495053 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
495002 TATACCAAAG
* *
495012 AAATA AAATA CAATA AAATTA AAATT AAATA AAA-A AAATA AA
1 AAATA AAATA AAATA AAA-TA AAATA AAATA AAATA AAATA AA
495054 GAAGTATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
4 4 0.13
5 22 0.71
6 5 0.16
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:495135 original size:22 final size:21
Alignment explanation
Indices: 495110--495170 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
495100 CCATATGAGG
*
495110 TAAAAAAAATACTAATAATAAT
1 TAAAAAAAATA-TAATAATAAA
*
495132 TAAAAAACATGATAATAATAAA
1 TAAAAAAAAT-ATAATAATAAA
* *
495154 TAAATAAAATAAAATAA
1 TAAAAAAAATATAATAA
495171 GAATTTAGGG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
21 6 0.18
22 26 0.79
23 1 0.03
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.25
Consensus pattern (21 bp):
TAAAAAAAATATAATAATAAA
Found at i:496271 original size:3 final size:3
Alignment explanation
Indices: 496263--496313 Score: 70
Period size: 3 Copynumber: 17.3 Consensus size: 3
496253 TAAATATGAC
*
496263 ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA GTA ATA A-A ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
496307 ATA ATA A
1 ATA ATA A
496314 ATCTATATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 4 0.09
3 36 0.84
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:496314 original size:12 final size:12
Alignment explanation
Indices: 496237--496314 Score: 63
Period size: 14 Copynumber: 6.2 Consensus size: 12
496227 GAGAAAAGAA
496237 AAAATAAATAA-
1 AAAATAAATAAT
496248 ATAAATAAAT-AT
1 A-AAATAAATAAT
* *
496260 GACAT-AATAAT
1 AAAATAAATAAT
496271 AATAATATAATAAT
1 AA-AATA-AATAAT
496285 AATAATAATAGTAAT
1 AA-AATAA-A-TAAT
496300 AAAATAAATAAT
1 AAAATAAATAAT
496312 AAA
1 AAA
496315 TCTATATAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 15
0.74 0.05 0.20
Matches are distributed among these distances:
10 3 0.05
11 8 0.15
12 17 0.31
13 2 0.04
14 19 0.35
15 6 0.11
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (12 bp):
AAAATAAATAAT
Found at i:496517 original size:37 final size:36
Alignment explanation
Indices: 496469--496619 Score: 209
Period size: 37 Copynumber: 4.2 Consensus size: 36
496459 CAAAATGTCT
* * *
496469 TATATAATATAAATATTTTCAAAAATGTTTTCAAAAC
1 TATATATTATATATATTTTC-AAAATGTTTTAAAAAC
*
496506 TATATA-T-TATA-ATTTTCAAAATGTTTTCAAAAC
1 TATATATTATATATATTTTCAAAATGTTTTAAAAAC
496539 TATATATTATATATAATTTTCAAAATGTTTTAAAAAC
1 TATATATTATATAT-ATTTTCAAAATGTTTTAAAAAC
496576 TATATATTATATATATTTTCAAAATGACTTTTAAAAAC
1 TATATATTATATATATTTTCAAAATG--TTTTAAAAAC
496614 TATATA
1 TATATA
496620 ATTTGAAAAA
Statistics
Matches: 106, Mismatches: 2, Indels: 11
0.89 0.02 0.09
Matches are distributed among these distances:
33 22 0.21
34 7 0.07
35 7 0.07
36 13 0.12
37 41 0.39
38 16 0.15
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (36 bp):
TATATATTATATATATTTTCAAAATGTTTTAAAAAC
Found at i:496532 original size:33 final size:33
Alignment explanation
Indices: 496435--496619 Score: 186
Period size: 37 Copynumber: 5.5 Consensus size: 33
496425 TCAAAAATAT
496435 TTTTAAAAACTATATA-TAT-ATTTTCAAAATG
1 TTTTAAAAACTATATATTATAATTTTCAAAATG
* *
496466 TCTTATATAA-TATA-A--AT-ATTTTCAAAAATG
1 TTTTA-AAAACTATATATTATAATTTTC-AAAATG
*
496496 TTTTCAAAACTATATATTATAATTTTCAAAATG
1 TTTTAAAAACTATATATTATAATTTTCAAAATG
*
496529 TTTTCAAAACTATATATTATATATAATTTTCAAAATG
1 TTTTAAAAAC--TATA-TAT-TATAATTTTCAAAATG
496566 TTTTAAAAACTATATATTATATATATTTTCAAAATG
1 TTTTAAAAACTATATA-T-TATA-ATTTTCAAAATG
496602 ACTTTTAAAAACTATATA
1 --TTTTAAAAACTATATA
496620 ATTTGAAAAA
Statistics
Matches: 133, Mismatches: 6, Indels: 23
0.82 0.04 0.14
Matches are distributed among these distances:
29 11 0.08
30 14 0.11
31 9 0.07
32 3 0.02
33 18 0.14
34 8 0.06
35 14 0.11
36 15 0.11
37 25 0.19
38 16 0.12
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.45
Consensus pattern (33 bp):
TTTTAAAAACTATATATTATAATTTTCAAAATG
Found at i:496576 original size:70 final size:74
Alignment explanation
Indices: 496469--496621 Score: 217
Period size: 70 Copynumber: 2.1 Consensus size: 74
496459 CAAAATGTCT
*
496469 TATATAATATAAATATTTTCAAAAATGTTTTCAAAACTATATA-T-TATA-ATTTTCAAAATG-T
1 TATATAATATAAATATTTTCAAAAATGTTTTAAAAACTATATATTATATATATTTTCAAAATGAT
*
496530 TTTCAAAAC
66 TTTAAAAAC
* *
496539 TATATATTATATATAATTTTC-AAAATGTTTTAAAAACTATATATTATATATATTTTCAAAATGA
1 TATATAATATAAAT-ATTTTCAAAAATGTTTTAAAAACTATATATTATATATATTTTCAAAATGA
496603 CTTTTAAAAAC
65 -TTTTAAAAAC
496614 TATATAAT
1 TATATAAT
496622 TTGAAAAACC
Statistics
Matches: 72, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
70 33 0.46
71 7 0.10
72 4 0.06
73 12 0.17
75 16 0.22
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (74 bp):
TATATAATATAAATATTTTCAAAAATGTTTTAAAAACTATATATTATATATATTTTCAAAATGAT
TTTAAAAAC
Found at i:496673 original size:37 final size:35
Alignment explanation
Indices: 496490--496673 Score: 145
Period size: 37 Copynumber: 5.3 Consensus size: 35
496480 AATATTTTCA
496490 AAAATGTTTTC-AAAACTATATATTATAATTT-TC
1 AAAATGTTTTCTAAAACTATATATTATAATTTGTC
*
496523 AAAATGTTTTC-AAAACTATATATTATATATAATTTTC
1 AAAATGTTTTCTAAAACTATATATTATA-AT--TTGTC
* *
496560 AAAATGTTTT-AAAAACTATATATTATATATATTTTC
1 AAAATGTTTTCTAAAACTATATATTATA-AT-TTGTC
* * *
496596 AAAATGACTTT-TAAAA--A-CTA-TATAATTTG-A
1 AAAATG-TTTTCTAAAACTATATATTATAATTTGTC
* *
496626 AAAACCGTTTTCTGAAAACTATATATTATACTTTGTC
1 AAAA-TGTTTTCT-AAAACTATATATTATAATTTGTC
496663 AAAAATGTTTT
1 -AAAATGTTTT
496674 GAGAAAAAAG
Statistics
Matches: 125, Mismatches: 11, Indels: 26
0.77 0.07 0.16
Matches are distributed among these distances:
30 7 0.06
31 4 0.03
32 6 0.05
33 31 0.25
34 5 0.04
35 3 0.02
36 22 0.18
37 43 0.34
38 4 0.03
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (35 bp):
AAAATGTTTTCTAAAACTATATATTATAATTTGTC
Found at i:496691 original size:2 final size:2
Alignment explanation
Indices: 496686--496717 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
496676 GAAAAAAGAC
496686 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
496718 ATAAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:497545 original size:84 final size:84
Alignment explanation
Indices: 497324--498214 Score: 810
Period size: 84 Copynumber: 10.7 Consensus size: 84
497314 GAATATAATT
* * * * * * **
497324 GAACTCGGAGGTCTTCGGTTGACAGATAACCCTTCTAGCCTTGAGTTATATTGTGAATGATGTGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTG-
* * * * *
497389 CCTCCAAGCTGAGAGTAATT
65 CCTTCGAGCTGAGTGTAGTC
* * * *
497409 GAACTCGAGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGC
* *
497470 CTTAGAGCTGAGCGTAGTC
66 CTTCGAGCTGAGTGTAGTC
* * * *
497489 GAACTCGAAGGTCTTTGGTTGGCAGACAACCCTTCTAGA-TTCAAGTTGTACTGCAAATAATATG
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTT-AAGTTATACTGCAAATGATGTG
* *
497553 CCTTGGAGCTGAGCGTAGTC
65 CCTTCGAGCTGAGTGTAGTC
* ** * * *
497573 GAACTCGAAGATCTTTTGG-TCACAGATAACCCTTCTAGCCTTGAGTTATGA-TGTAAATGATGT
1 GAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTAT-ACTGCAAATGATGT
* *
497636 GCCCTCGAAGCTGAGTGTAATC
64 GCCTTCG-AGCTGAGTGTAGTC
* * * * *** *
497658 AAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGCGCTGCAAATGATATGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGC
* *
497723 CCTCGAAGCTGAGTGTAATC
66 CTTCG-AGCTGAGTGTAGTC
* * * * *
497743 GAACTCGAAGGTC--T--TTGGCAGATAGCCTTTCTATACTTAAGCTATGCTGCAAATGATGTGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGC
* *
497804 CTTGGAGCTGAGCGTAGTC
66 CTTCGAGCTGAGTGTAGTC
** * * *
497823 GAACTCGAAGGTCTTTTGG-TCACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTG
1 GAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTG
* *
497887 CCCTCGAAGCTGAGTGTAATC
65 CCTTCG-AGCTGAGTGTAGTC
** * * * * *
497908 GAACTCGGGGGTCTTTTGTTGGCAGAAAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGC
*
497973 CTTGGAGCTGAGTGTAGTC
66 CTTCGAGCTGAGTGTAGTC
* *
497992 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGT
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTG-
* *
498057 CGTT-GAGCTGAGCGTAGTC
65 CCTTCGAGCTGAGTGTAGTC
* ** * * *
498076 GAACTCAAAGGTCTTTTGG-TCACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTG
1 GAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTG
* *
498140 CCCTCGAAGCTGAGTGTAATC
65 CCTTCG-AGCTGAGTGTAGTC
** * * * *
498161 GAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAAT
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAAT
498215 AGTTTGTTTA
Statistics
Matches: 652, Mismatches: 131, Indels: 50
0.78 0.16 0.06
Matches are distributed among these distances:
80 51 0.08
81 109 0.17
82 2 0.00
83 6 0.01
84 284 0.44
85 200 0.31
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (84 bp):
GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGC
CTTCGAGCTGAGTGTAGTC
Found at i:497681 original size:169 final size:170
Alignment explanation
Indices: 497324--498178 Score: 844
Period size: 169 Copynumber: 5.1 Consensus size: 170
497314 GAATATAATT
* * * * * * * ** *
497324 GAACTCGGAGGTCTTCGGTTGACAGATAACCCTTCTAGCCTTGAGTTATATTGTGAATGATGTGC
1 GAACTCGAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTATACTGCAAATGATATGC
* * * * * *
497389 CCTCCAAGCTGAGAGTAATTGAACTCGAGGGTC-TTTGG---CAGATAGCCCTTCTCGACTTAAG
66 CCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAAG
* * * *
497450 CTAT-ACTGCAAATGATGTGCCTTAG-AGCTGAGCGTAGTC
131 TTATGA-TGCAAATGATGTGCCCTCGAAGCTGAGTGTAGTC
* *
497489 GAACTCGAAGGTCTTTGGTTGGCAGACAACCCTTCTAGA-TTCAAGTTGTACTGCAAATAATATG
1 GAACTCGAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTT-AAGTTATACTGCAAATGATATG
* * * * * *
497553 -CCTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTTGGTCACAGATAACCCTTCTAGCCTTGA
65 CCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAA
* *
497617 GTTATGATGTAAATGATGTGCCCTCGAAGCTGAGTGTAATC
130 GTTATGATGCAAATGATGTGCCCTCGAAGCTGAGTGTAGTC
* * * ***
497658 AAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGCGCTGCAAATGATATGC
1 GAACTCGAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTATACTGCAAATGATATGC
* * * *
497723 CCTCGAAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGG---CAGATAGCCTTTCTATACTTAAG
66 CCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAAG
* * * * *
497784 CTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTC
131 TTATGATGCAAATGATGTGCCCTCGAAGCTGAGTGTAGTC
** * * * * *
497823 GAACTCGAAGGTCTTTTGG-TCACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTG
1 GAACTCGAAGGTC-TTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTATACTGCAAATGATATG
* ** * ** *
497887 CCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTTGTTGGCAGAAAACCCTTCTAGACTTAA
65 CCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAA
* * * * *
497952 GTTGTGCTGCAAATGATATG-CCTTGGAGCTGAGTGTAGTC
130 GTTATGATGCAAATGATGTGCCCTCGAAGCTGAGTGTAGTC
* * * * *
497992 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGT
1 GAACTCGAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTATACTGCAAATGATATGC
* * * * * *
498057 CGTTG-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
66 CCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAAG
* *
498121 TTAT-ACTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATC
131 TTATGA-TGCAAATGATGTGCCCTCGAAGCTGAGTGTAGTC
**
498161 GAACTCGGGGGTCTTTGG
1 GAACTCGAAGGTCTTTGG
498179 CAGATAGCCC
Statistics
Matches: 566, Mismatches: 107, Indels: 30
0.81 0.15 0.04
Matches are distributed among these distances:
164 27 0.05
165 148 0.26
166 42 0.07
168 105 0.19
169 214 0.38
170 30 0.05
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (170 bp):
GAACTCGAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTATACTGCAAATGATATGC
CCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAAG
TTATGATGCAAATGATGTGCCCTCGAAGCTGAGTGTAGTC
Found at i:497749 original size:334 final size:333
Alignment explanation
Indices: 497332--498178 Score: 935
Period size: 334 Copynumber: 2.5 Consensus size: 333
497322 TTGAACTCGG
* * * * * *** ** *
497332 AGGTCTTCGGTTGACAGATAACCCTTCTAGCCTTGAGTTATATTGTGAATGATGTGCCCTCCAAG
1 AGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTACGCTGCAAATGATGTGCCCTCGAAG
* * *
497397 CTGAGAGTAATTGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAA
66 CTGAGAGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTAGACTTAAGCTATACTGCAAA
**
497462 TGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGACAACCCTTCTAG
131 TGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TCACAGACAACCCTTCTAG
* * * *
497527 -ATTCAAGTTGTACTGCAAATAATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTT
195 CATT-AAGTTATACTGCAAATAATATGCCCTCGAAGCTGAGCGTAATCGAACTCGAAGATCTTTT
* * * * *
497590 GGTCACAGATAACCCTTCTAGCCTTGAGTTATGATGTAAATGATGTGCCCTCGAAGCTGAGTGTA
259 GGTCACAGAAAACCCTTCTAGACTTAAGTTATGATGCAAATGATATG-CCTCGAAGCTGAGTGTA
497655 ATCAAACTCAA
323 ATCAAACTCAA
* * *
497666 AGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGCGCTGCAAATGATATGCCCTCGAAG
1 AGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTACGCTGCAAATGATGTGCCCTCGAAG
* * * *
497731 CTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCTTTCTATACTTAAGCTATGCTGCAAA
66 CTGAGAGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTAGACTTAAGCTATACTGCAAA
* *
497796 TGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAG
131 TGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTCACAGACAACCCTTCTAG
* * * * * * ** *
497861 CCTTGAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTTG
195 CATTAAGTTATACTGCAAATAATATGCCCTCGAAGCTGAGCGTAATCGAACTCGAAGATCTTTTG
* ** * * * * *
497926 TTGGCAGAAAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGTGTAGT
260 GTCACAGAAAACCCTTCTAGACTTAAGTTATGATGCAAATGATATGCCTCGAAGCTGAGTGTAAT
* *
497991 CGAACTCGA
325 CAAACTCAA
* * * * * *
498000 AGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGTCGTTG-AG
1 AGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTACGCTGCAAATGATGTGCCCTCGAAG
* * * * * * *
498064 CTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATACTG
66 CTGAGAGTAATCGAACTCGAAGGTC-TTTGG---CAGATAGCCCTTCTAGACTTAAGCTATACTG
* * * * * **
498129 TAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
127 CAAATGATGTGCCTTAG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
498179 CAGATAGCCC
Statistics
Matches: 426, Mismatches: 79, Indels: 13
0.82 0.15 0.03
Matches are distributed among these distances:
333 24 0.06
334 262 0.62
335 74 0.17
337 43 0.10
338 23 0.05
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (333 bp):
AGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTACGCTGCAAATGATGTGCCCTCGAAG
CTGAGAGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTAGACTTAAGCTATACTGCAAA
TGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCACAGACAACCCTTCTAGC
ATTAAGTTATACTGCAAATAATATGCCCTCGAAGCTGAGCGTAATCGAACTCGAAGATCTTTTGG
TCACAGAAAACCCTTCTAGACTTAAGTTATGATGCAAATGATATGCCTCGAAGCTGAGTGTAATC
AAACTCAA
Found at i:503262 original size:13 final size:13
Alignment explanation
Indices: 503244--503273 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
503234 CTTAGTTGCG
503244 AAAATTAAAATTT
1 AAAATTAAAATTT
*
503257 AAAATTGAAATTT
1 AAAATTAAAATTT
503270 AAAA
1 AAAA
503274 ATTCGGTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:503441 original size:5 final size:5
Alignment explanation
Indices: 503427--503468 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
503417 TATACCAAAG
* *
503427 AAATA AAATA CAATA AAATTA AAATT AAATA AAA-A AAATA AA
1 AAATA AAATA AAATA AAA-TA AAATA AAATA AAATA AAATA AA
503469 GAAGTATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
4 4 0.13
5 22 0.71
6 5 0.16
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:503551 original size:19 final size:19
Alignment explanation
Indices: 503530--503565 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
503520 TGATGTAAAA
503530 AAAATAC-TGATAATAATT
1 AAAATACATGATAATAATT
503548 AAAATACATGATAATAAT
1 AAAATACATGATAATAAT
503566 AAATAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (19 bp):
AAAATACATGATAATAATT
Found at i:504542 original size:3 final size:3
Alignment explanation
Indices: 504534--504572 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
504524 ATAAATAAGA
504534 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
504573 CTATATAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:504720 original size:36 final size:34
Alignment explanation
Indices: 504654--504880 Score: 205
Period size: 33 Copynumber: 6.5 Consensus size: 34
504644 TCAGAAACGT
* * ** *
504654 TTTTAAAAACATATACAATATATAACTTCAAAAATAT
1 TTTTAAAAAC-TATATATTATATATTTTC-AAAAT-G
504691 TTTTAAAAACTATATATTATATATTTTC-AAATG
1 TTTTAAAAACTATATATTATATATTTTCAAAATG
* * *
504724 TCTTATATAA-TATATA--ATGT-TTTTCAAAAAATG
1 TTTTA-AAAACTATATATTATATATTTTC--AAAATG
*
504757 TTTTCAAAACTATATATTATA-ATTTTCAAAATG
1 TTTTAAAAACTATATATTATATATTTTCAAAATG
*
504790 TTTTCAAAACTATATATTATATATAATTTTCAAAATG
1 TTTTAAAAACTATATA-T-TATAT-ATTTTCAAAATG
504827 TTTTAAAAACTATATATTATATATATTTTCAAAATG
1 TTTTAAAAACTATATA-T-TATATATTTTCAAAATG
504863 ACTTTTAAAAACTATATA
1 --TTTTAAAAACTATATA
504881 ATTTGAAAAA
Statistics
Matches: 163, Mismatches: 13, Indels: 27
0.80 0.06 0.13
Matches are distributed among these distances:
30 5 0.03
31 3 0.02
32 3 0.02
33 46 0.28
34 8 0.05
35 11 0.07
36 26 0.16
37 45 0.28
38 16 0.10
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (34 bp):
TTTTAAAAACTATATATTATATATTTTCAAAATG
Found at i:504824 original size:37 final size:37
Alignment explanation
Indices: 504751--504880 Score: 189
Period size: 37 Copynumber: 3.6 Consensus size: 37
504741 TGTTTTTCAA
*
504751 AAAATGTTTTCAAAAC--TATA-TAT-TATAATTTTC
1 AAAATGTTTTAAAAACTATATATTATATATAATTTTC
*
504784 AAAATGTTTTCAAAACTATATATTATATATAATTTTC
1 AAAATGTTTTAAAAACTATATATTATATATAATTTTC
504821 AAAATGTTTTAAAAACTATATATTATATAT-ATTTTC
1 AAAATGTTTTAAAAACTATATATTATATATAATTTTC
504857 AAAATGACTTTTAAAAACTATATA
1 AAAATG--TTTTAAAAACTATATA
504881 ATTTGAAAAA
Statistics
Matches: 90, Mismatches: 1, Indels: 7
0.92 0.01 0.07
Matches are distributed among these distances:
33 16 0.18
35 4 0.04
36 15 0.17
37 39 0.43
38 16 0.18
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (37 bp):
AAAATGTTTTAAAAACTATATATTATATATAATTTTC
Found at i:504934 original size:37 final size:35
Alignment explanation
Indices: 504751--504934 Score: 145
Period size: 37 Copynumber: 5.3 Consensus size: 35
504741 TGTTTTTCAA
504751 AAAATGTTTTC-AAAACTATATATTATAATTT-TC
1 AAAATGTTTTCTAAAACTATATATTATAATTTGTC
*
504784 AAAATGTTTTC-AAAACTATATATTATATATAATTTTC
1 AAAATGTTTTCTAAAACTATATATTATA-AT--TTGTC
* *
504821 AAAATGTTTT-AAAAACTATATATTATATATATTTTC
1 AAAATGTTTTCTAAAACTATATATTATA-AT-TTGTC
* * *
504857 AAAATGACTTT-TAAAA--A-CTA-TATAATTTG-A
1 AAAATG-TTTTCTAAAACTATATATTATAATTTGTC
* *
504887 AAAACCGTTTTCTGAAAACTATATATTATACTTTGTC
1 AAAA-TGTTTTCT-AAAACTATATATTATAATTTGTC
504924 AAAAATGTTTT
1 -AAAATGTTTT
504935 GAGAAAAAGA
Statistics
Matches: 125, Mismatches: 11, Indels: 26
0.77 0.07 0.16
Matches are distributed among these distances:
30 7 0.06
31 4 0.03
32 6 0.05
33 31 0.25
34 5 0.04
35 3 0.02
36 22 0.18
37 43 0.34
38 4 0.03
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (35 bp):
AAAATGTTTTCTAAAACTATATATTATAATTTGTC
Found at i:504953 original size:2 final size:2
Alignment explanation
Indices: 504946--504987 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
504936 AGAAAAAGAC
504946 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
504988 ATAATAATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:505046 original size:2 final size:2
Alignment explanation
Indices: 505039--505083 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
505029 GAATGTCTAC
505039 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
505080 AT AT
1 AT AT
505084 TGTTTCAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:505450 original size:27 final size:27
Alignment explanation
Indices: 505415--505467 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
505405 TATTTAAATT
505415 TTTACTTC-TAAATATATATTTGTTCAA
1 TTTACTTCTTAAATATATATTT-TTCAA
* *
505442 TTTAGTTCTTAAATTTATATTTTTCA
1 TTTACTTCTTAAATATATATTTTTCA
505468 TAAAATTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.30, C:0.09, G:0.04, T:0.57
Consensus pattern (27 bp):
TTTACTTCTTAAATATATATTTTTCAA
Found at i:505962 original size:23 final size:23
Alignment explanation
Indices: 505909--505964 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
505899 GACCTAACAG
* *
505909 TATCCGACTGAAACTTGAACGAT
1 TATCCGATTTAAACTTGAACGAT
505932 TATCCGATTTAAACTTGAACGAT
1 TATCCGATTTAAACTTGAACGAT
505955 TATCCGATTT
1 TATCCGATTT
505965 TGCATCCCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (23 bp):
TATCCGATTTAAACTTGAACGAT
Found at i:511326 original size:27 final size:28
Alignment explanation
Indices: 511287--511353 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 28
511277 CACACATATT
* *
511287 AATATTATAAAAAATTT-ATATGAA-ATA
1 AATATAATTAAAAATTTAATATGAACA-A
*
511314 AATATAATTAAAATTTTCAATATGAACAA
1 AATATAATTAAAAATTT-AATATGAACAA
*
511343 AATAAAATTAA
1 AATATAATTAA
511354 TTAATTAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 14 0.42
29 18 0.55
30 1 0.03
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (28 bp):
AATATAATTAAAAATTTAATATGAACAA
Found at i:517004 original size:163 final size:163
Alignment explanation
Indices: 516734--517059 Score: 643
Period size: 163 Copynumber: 2.0 Consensus size: 163
516724 GTAATCGCAA
516734 ATCTAAATCCAATCAGATTTTCCAAAACAGAAAAGATAAGCAATATAATAAATAAGTATCATCTT
1 ATCTAAATCCAATCAGATTTTCCAAAACAGAAAAGATAAGCAATATAATAAATAAGTATCATCTT
*
516799 GATCAATCGAAGCGTTGTCAAATTCAATCATGATAAAAAGATAAAATGTAAATAACAATCAAATA
66 GATCAATCGAAGCGTTGTCAAATTCAATCATGAGAAAAAGATAAAATGTAAATAACAATCAAATA
516864 ACTAGGGATGGGCATGAGACCCGAATCCGATAG
131 ACTAGGGATGGGCATGAGACCCGAATCCGATAG
516897 ATCTAAATCCAATCAGATTTTCCAAAACAGAAAAGATAAGCAATATAATAAATAAGTATCATCTT
1 ATCTAAATCCAATCAGATTTTCCAAAACAGAAAAGATAAGCAATATAATAAATAAGTATCATCTT
516962 GATCAATCGAAGCGTTGTCAAATTCAATCATGAGAAAAAGATAAAATGTAAATAACAATCAAATA
66 GATCAATCGAAGCGTTGTCAAATTCAATCATGAGAAAAAGATAAAATGTAAATAACAATCAAATA
517027 ACTAGGGATGGGCATGAGACCCGAATCCGATAG
131 ACTAGGGATGGGCATGAGACCCGAATCCGATAG
517060 GTTCTGATTG
Statistics
Matches: 162, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
163 162 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (163 bp):
ATCTAAATCCAATCAGATTTTCCAAAACAGAAAAGATAAGCAATATAATAAATAAGTATCATCTT
GATCAATCGAAGCGTTGTCAAATTCAATCATGAGAAAAAGATAAAATGTAAATAACAATCAAATA
ACTAGGGATGGGCATGAGACCCGAATCCGATAG
Found at i:517421 original size:23 final size:24
Alignment explanation
Indices: 517395--517443 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
517385 AACATCCCAC
517395 AAGACAAAGAAAAATGTATCA-AA
1 AAGACAAAGAAAAATGTATCATAA
* * *
517418 AAGACAGATAAAAATGTGTCATAA
1 AAGACAAAGAAAAATGTATCATAA
517442 AA
1 AA
517444 ATAAAGTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.61, C:0.08, G:0.14, T:0.16
Consensus pattern (24 bp):
AAGACAAAGAAAAATGTATCATAA
Found at i:519491 original size:19 final size:19
Alignment explanation
Indices: 519467--519505 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
519457 TATGTGGGTG
*
519467 TTTTTTT-TTTGTTTTTGAA
1 TTTTTTTATTT-TTTTAGAA
519486 TTTTTTTATTTTTTTAGAA
1 TTTTTTTATTTTTTTAGAA
519505 T
1 T
519506 GGTAGAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (19 bp):
TTTTTTTATTTTTTTAGAA
Found at i:520593 original size:12 final size:12
Alignment explanation
Indices: 520573--520602 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
520563 ATTGTTCCCG
*
520573 TTAAGAATCAAT
1 TTAACAATCAAT
520585 TTAACAATCAAT
1 TTAACAATCAAT
520597 TTAACA
1 TTAACA
520603 GTACTTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.33
Consensus pattern (12 bp):
TTAACAATCAAT
Found at i:526705 original size:25 final size:24
Alignment explanation
Indices: 526676--526722 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
526666 TAACTTTAAC
526676 TATTTGATAGAAATTTTGTTAACAA
1 TATTTGATA-AAATTTTGTTAACAA
* * *
526701 TATTTTATAAGATTTTTTTAAC
1 TATTTGATAAAATTTTGTTAAC
526723 TGAGAGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (24 bp):
TATTTGATAAAATTTTGTTAACAA
Found at i:535927 original size:43 final size:43
Alignment explanation
Indices: 535860--536033 Score: 171
Period size: 43 Copynumber: 4.1 Consensus size: 43
535850 TGAGAACTAA
* *
535860 AAACGCCGC-AATAGGTCAAGATCTACT-GCGGTGCTTTT-GGAAC
1 AAACGCCGCTAA-AGGTCGATATCTA-TAGCGGTG-TTTTAGGAAC
535903 AAACGCCGCTAAAGGTCGATATCTATAGCGGTGTTTTAGGAAC
1 AAACGCCGCTAAAGGTCGATATCTATAGCGGTGTTTTAGGAAC
* * * * *
535946 AAACGCCGCTAAAAGTTGATATATATAGCGGCGTTTTCA-TAAC
1 AAACGCCGCTAAAGGTCGATATCTATAGCGGTGTTTT-AGGAAC
* * *
535989 AAACGCCGCAAAATGTC-ATATCTATAGCGGCGTTTTTA-GAAC
1 AAACGCCGCTAAAGGTCGATATCTATAGCGGTG-TTTTAGGAAC
536031 AAA
1 AAA
536034 AGGTCGTTCT
Statistics
Matches: 114, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
42 26 0.23
43 85 0.75
44 3 0.03
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGGTCGATATCTATAGCGGTGTTTTAGGAAC
Found at i:536256 original size:42 final size:42
Alignment explanation
Indices: 536085--536433 Score: 361
Period size: 43 Copynumber: 8.2 Consensus size: 42
536075 AGAACAACAT
* * * *
536085 CAAAAGCCGCTAAAGGTCGATATCTATAGCGGC-ATTTTAGGAA
1 CAAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTA-GAA
* * * **
536128 CAAACGCCGCTAAAA-GTCGATATATATAGCGGGGTTTTCGGAA
1 CAAACGCCGC-AAAAGGTC-AGATCTATAGCGGCGTTTTTAGAA
* * *
536171 CAAACGCCACAAAAGGT-AGTGATATATAGCGGCGTTTTCAGAA
1 CAAACGCCGCAAAAGGTCA--GATCTATAGCGGCGTTTTTAGAA
*
536214 CAAACGCCGCAAAATGTCAGATCTATAGCGGCGTTTTTAGAA
1 CAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTAGAA
* * *
536256 CAAAATGCCGCAAAAGGTCA-TTCTATAGCGGC-ATTTT-GATA
1 C-AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTAGA-A
* * *
536297 CAAACGCCGCAAAAGGTCAGATCTATAGCGACATTTTTTGAA
1 CAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTAGAA
* * *
536339 CAAACGCCACAAAAGGTCAGAATCTATAGCGGCATTTTTTGAA
1 CAAACGCCGCAAAAGGTCAG-ATCTATAGCGGCGTTTTTAGAA
536382 CAAACGCCGCAAAAGGTCA-ATTCTATAGCGGCGTTTTTAGAA
1 CAAACGCCGCAAAAGGTCAGA-TCTATAGCGGCGTTTTTAGAA
536424 CAAACGCCGC
1 CAAACGCCGC
536434 TAATTGAAAC
Statistics
Matches: 265, Mismatches: 28, Indels: 27
0.83 0.09 0.08
Matches are distributed among these distances:
40 19 0.07
41 18 0.07
42 90 0.34
43 131 0.49
44 7 0.03
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (42 bp):
CAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTAGAA
Found at i:536387 original size:168 final size:170
Alignment explanation
Indices: 536085--536433 Score: 460
Period size: 168 Copynumber: 2.1 Consensus size: 170
536075 AGAACAACAT
* *
536085 CAAAAGCCGCTAAAGGTCGATATCTATAGCGGCATTTTAGGAACAAACGCCGCTAAAAGTCGATA
1 CAAAAGCCGCAAAAGGTCGATATCTATAGCGGCATTTTA-GAACAAACGCCGCTAAAAGTCGAGA
*** * *
536150 TATATAGCGGGGTTTTCGGAACAAACGCCACAAAAGGTAGTGATATATAGCGGCGTTTTCAGAAC
65 TATATAGCGACATTTTCGGAACAAACGCCACAAAAGGTAGTAATATATAGCGGCATTTTCAGAAC
*
536215 AAACGCCGCAAAATGTCAGA-TCTATAGCGGCGTTTTTAGAA
130 AAACGCCGCAAAAGGTCA-ATTCTATAGCGGCGTTTTTAGAA
536256 CAAAATGCCGCAAAAGGTC-AT-TCTATAGCGGCATTTT-GATACAAACGCCGC-AAAAGGTC-A
1 CAAAA-GCCGCAAAAGGTCGATATCTATAGCGGCATTTTAGA-ACAAACGCCGCTAAAA-GTCGA
* ** * **
536316 GATCTATAGCGACATTTTTTGAACAAACGCCACAAAAGGTCAG-AATCTATAGCGGCATTTTTTG
63 GATATATAGCGACATTTTCGGAACAAACGCCACAAAAGGT-AGTAATATATAGCGGCATTTTCAG
536380 AACAAACGCCGCAAAAGGTCAATTCTATAGCGGCGTTTTTAGAA
127 AACAAACGCCGCAAAAGGTCAATTCTATAGCGGCGTTTTTAGAA
*
536424 CAAACGCCGC
1 CAAAAGCCGC
536434 TAATTGAAAC
Statistics
Matches: 158, Mismatches: 15, Indels: 14
0.84 0.08 0.07
Matches are distributed among these distances:
167 6 0.04
168 101 0.64
169 16 0.10
170 16 0.10
171 7 0.04
172 12 0.08
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (170 bp):
CAAAAGCCGCAAAAGGTCGATATCTATAGCGGCATTTTAGAACAAACGCCGCTAAAAGTCGAGAT
ATATAGCGACATTTTCGGAACAAACGCCACAAAAGGTAGTAATATATAGCGGCATTTTCAGAACA
AACGCCGCAAAAGGTCAATTCTATAGCGGCGTTTTTAGAA
Found at i:536958 original size:20 final size:20
Alignment explanation
Indices: 536933--536987 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
536923 ATACTAAGCT
536933 AAAATGAGAAAATTCATTTA
1 AAAATGAGAAAATTCATTTA
536953 AAAATGATG-AAATTCATTTA
1 AAAATGA-GAAAATTCATTTA
*
536973 AAAATGATAAAATTC
1 AAAATGAGAAAATTC
536988 CAAACAAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.31
Consensus pattern (20 bp):
AAAATGAGAAAATTCATTTA
Found at i:540011 original size:41 final size:41
Alignment explanation
Indices: 539958--540180 Score: 268
Period size: 41 Copynumber: 5.4 Consensus size: 41
539948 TTATAAATAC
* ** *
539958 AAACGCCACTAAAGTACTAGTGTATAGCAATGTTTGTATAC
1 AAACGCCACTAAAGTACAAGTGTATAGCGGTGTTTGTATAA
* *
539999 AAACGCCACTAAAGTACAAGTGTATAGCAGTGTTTATATAA
1 AAACGCCACTAAAGTACAAGTGTATAGCGGTGTTTGTATAA
* * * * * * *
540040 AAACGCCACTAATGTACAAGTCTTTCGCGGCGTTTATAAACAA
1 AAACGCCACTAAAGTACAAGTGTATAGCGGTGTTTGT--ATAA
*
540083 AAACGCCACTAAAGTACAATTGTATAG-GGTGTTTGTATAA
1 AAACGCCACTAAAGTACAAGTGTATAGCGGTGTTTGTATAA
* * *
540123 AAATGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACAAGTGTATAGCGGTGTTTGTATAA
540164 AAACGCCACTAAAGTAC
1 AAACGCCACTAAAGTAC
540181 TACTCAGTTG
Statistics
Matches: 155, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
40 27 0.17
41 96 0.62
42 7 0.05
43 25 0.16
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.26
Consensus pattern (41 bp):
AAACGCCACTAAAGTACAAGTGTATAGCGGTGTTTGTATAA
Found at i:540140 original size:83 final size:82
Alignment explanation
Indices: 539958--540180 Score: 268
Period size: 83 Copynumber: 2.7 Consensus size: 82
539948 TTATAAATAC
* * *** * * *
539958 AAACGCCACTAAAGTACTAGTGTATAGCAATGTTTGTATACAAACGCCACTAAAGTACAAGTGTA
1 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTATACAAAAACGCCACTAAAGTACAAGTGTA
540023 TAGCAGTGTTTATATAA
66 TAGCAGTGTTTATATAA
* * * *
540040 AAACGCCACTAATGTACAAGTCTTTCGCGGCGTTTATAAACAAAAACGCCACTAAAGTACAATTG
1 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTAT--ACAAAAACGCCACTAAAGTACAAGTG
* *
540105 TATAG-GGTGTTTGTATAA
64 TATAGCAGTGTTTATATAA
* * *
540123 AAATGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTAC
1 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTATACAAAAACGCCACTAAAGTAC
540181 TACTCAGTTG
Statistics
Matches: 119, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
81 20 0.17
82 28 0.24
83 43 0.36
84 28 0.24
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.26
Consensus pattern (82 bp):
AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTATACAAAAACGCCACTAAAGTACAAGTGTA
TAGCAGTGTTTATATAA
Found at i:540163 original size:124 final size:125
Alignment explanation
Indices: 539941--540180 Score: 356
Period size: 124 Copynumber: 1.9 Consensus size: 125
539931 TTATAAATTT
* * * *
539941 GCGGCGTTTATAAATACAAACGCCACTAAAGTACTAGTGTATAGCAATGTTTGTATACAAACGCC
1 GCGGCGTTTATAAACAAAAACGCCACTAAAGTACAAGTGTATAGCAATGTTTGTATAAAAACGCC
* * *
540006 ACTAAAGTACAAGTGTATAGCAGTGTTTATATAAAAACGCCACTAATGTACAAGTCTTTC
66 ACTAAAGTACAAGTCTATAGCAGCGTTTATATAAAAACGCCACTAAAGTACAAGTCTTTC
* ** *
540066 GCGGCGTTTATAAACAAAAACGCCACTAAAGTACAATTGTATAG-GGTGTTTGTATAAAAATGCC
1 GCGGCGTTTATAAACAAAAACGCCACTAAAGTACAAGTGTATAGCAATGTTTGTATAAAAACGCC
* *
540130 ACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTAC
66 ACTAAAGTACAAGTCTATAGCAGCGTTTATATAAAAACGCCACTAAAGTAC
540181 TACTCAGTTG
Statistics
Matches: 102, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
124 62 0.61
125 40 0.39
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.27
Consensus pattern (125 bp):
GCGGCGTTTATAAACAAAAACGCCACTAAAGTACAAGTGTATAGCAATGTTTGTATAAAAACGCC
ACTAAAGTACAAGTCTATAGCAGCGTTTATATAAAAACGCCACTAAAGTACAAGTCTTTC
Found at i:540198 original size:41 final size:41
Alignment explanation
Indices: 540113--540257 Score: 168
Period size: 41 Copynumber: 3.5 Consensus size: 41
540103 TGTATAGGGT
* * *
540113 GTTTGTATAAAAATGCCACTAAAGTACAAGTCTA-TAGCGGC
1 GTTTGTATAAAAATGCCACTAAAGTACTACTC-AGTTGCGGC
* *
540154 GTTTGTATAAAAACGCCACTAAAGTACTACTCAGTTGCGAC
1 GTTTGTATAAAAATGCCACTAAAGTACTACTCAGTTGCGGC
* * * *
540195 GTTTTTCTAGAAATGCCACTAAAGTACTACTCTGTTGCGGC
1 GTTTGTATAAAAATGCCACTAAAGTACTACTCAGTTGCGGC
540236 GTTTGT-TGAAAAAATGCCACTA
1 GTTTGTAT--AAAAATGCCACTA
540258 TTGATGAACC
Statistics
Matches: 88, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
40 2 0.02
41 74 0.84
42 12 0.14
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (41 bp):
GTTTGTATAAAAATGCCACTAAAGTACTACTCAGTTGCGGC
Found at i:549391 original size:18 final size:18
Alignment explanation
Indices: 549368--549403 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
549358 TATATATATT
*
549368 ATTATTATCGTTATTTTA
1 ATTATTATCATTATTTTA
*
549386 ATTATTATTATTATTTTA
1 ATTATTATCATTATTTTA
549404 TTTACATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (18 bp):
ATTATTATCATTATTTTA
Found at i:552959 original size:31 final size:32
Alignment explanation
Indices: 552923--552984 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
552913 ATTTTACATG
552923 TACTAACTTATTT-TTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
552954 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
552985 CATTTTGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.61
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
Found at i:557568 original size:27 final size:28
Alignment explanation
Indices: 557517--557576 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
557507 GACAATTTTG
*
557517 TGAAAAAAATCTTTGAGATTGTTTC-TT
1 TGAAAAAAATCTTTGAGATTATTTCTTT
557544 TGAAAAAAATCTTTGAG-TCTATTTCTTT
1 TGAAAAAAATCTTTGAGAT-TATTTCTTT
557572 TGAAA
1 TGAAA
557577 CAAAGTTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 1 0.03
27 22 0.73
28 7 0.23
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.43
Consensus pattern (28 bp):
TGAAAAAAATCTTTGAGATTATTTCTTT
Found at i:557701 original size:30 final size:31
Alignment explanation
Indices: 557665--557795 Score: 108
Period size: 30 Copynumber: 4.1 Consensus size: 31
557655 TTTGTAAAAA
*
557665 AAAAATCTTTGAGAT-TGTTTCTTTTGAAAC
1 AAAAATCTTTGAGATCTGTTTCTTTGGAAAC
557695 AAAAATCTTTGAG-TCTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATCTGTTTCTTTGGAAAC
* * ** *
557725 AAAATTTTGTCTCTCTTAAGAT-AATTTCTTTTGAAAC
1 AAAA------ATCT-TTGAGATCTGTTTCTTTGGAAAC
*
557762 AAAAATCTTTG-GGTCTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATCTGTTTCTTTGGAAAC
557792 AAAA
1 AAAA
557796 TTTTGTCTCT
Statistics
Matches: 79, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
29 3 0.04
30 49 0.62
31 3 0.04
36 3 0.04
37 20 0.25
38 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (31 bp):
AAAAATCTTTGAGATCTGTTTCTTTGGAAAC
Found at i:557738 original size:147 final size:142
Alignment explanation
Indices: 557484--557752 Score: 448
Period size: 147 Copynumber: 1.9 Consensus size: 142
557474 GAATCTTTTA
*
557484 AAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAAATCTTTGAGATTGTTTCTTTGAAA
1 AAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTAAAAAAAATCTTTGAGATTGTTTCTTTGAAA
* *
557549 AAAATCTTTGAGTCTATTTCTTTTGAAACAAAGTTTTGTCTCTCTTAAGACAATTTCGTGAAAAA
66 AAAATCTTTGAGTCTATTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGACAATTTCGTGAAAAA
557614 TCTTTGAGTCTG
131 TCTTTGAGTCTG
557626 AAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTAAAAAAAAAATCTTTGAGATTGTTTCTTTTG
1 AAACAAAGTTTTGTCTCTCTTGAGACAATTTTGT--AAAAAAAATCTTTGAGATTGTTTC-TTTG
* *
557691 AAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTC
63 -AA-AAAAATCTTTGAGTCTATTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGACAATTTC
557753 TTTTGAAACA
Statistics
Matches: 117, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
142 34 0.29
144 23 0.20
145 4 0.03
146 2 0.02
147 54 0.46
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.41
Consensus pattern (142 bp):
AAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTAAAAAAAATCTTTGAGATTGTTTCTTTGAAA
AAAATCTTTGAGTCTATTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGACAATTTCGTGAAAAA
TCTTTGAGTCTG
Found at i:557757 original size:67 final size:67
Alignment explanation
Indices: 557682--557850 Score: 302
Period size: 67 Copynumber: 2.5 Consensus size: 67
557672 TTTGAGATTG
557682 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
557747 AA
66 AA
*
557749 TTTCTTTTGAAACAAAAATCTTTGGGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
*
557814 AT
66 AA
* *
557816 TTTCTTTTGAAAAAAAAATCTTTGAATCTGTTTCT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCT
557851 CTTAAAATGA
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 97 1.00
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (67 bp):
TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
AA
Found at i:557762 original size:37 final size:36
Alignment explanation
Indices: 557712--557832 Score: 105
Period size: 37 Copynumber: 3.5 Consensus size: 36
557702 TTTGAGTCTG
557712 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
1 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT-A
* **
557749 TTTCTTTTGAAACAAAAATCTTTG--GGTC-T--G---
1 TTTCTTTGGAAAC-AAAAT-TTTGTCTCTCTTAAGATA
557779 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
* *
557815 TTTTCTTTTGAAAAAAAA
1 -TTTCTTTGGAAACAAAA
557833 ATCTTTGAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 22
0.68 0.08 0.23
Matches are distributed among these distances:
28 4 0.06
29 5 0.08
30 14 0.22
31 1 0.02
33 1 0.02
34 1 0.02
36 1 0.02
37 29 0.45
38 5 0.08
39 4 0.06
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (36 bp):
TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
Found at i:557886 original size:66 final size:66
Alignment explanation
Indices: 557676--557892 Score: 285
Period size: 67 Copynumber: 3.3 Consensus size: 66
557666 AAAATCTTTG
*
557676 AGATTGTTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTT-GAAACAAAATTTTGTCTCTCT
557741 TA
65 TA
* *
557743 AGATAATTTCTTTTGAAACAAAAATCTTTGGGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTT-GAAACAAAATTTTGTCTCTCT
557808 TA
65 TA
* * * * *
557810 AGATATTTTCTTTTGAAAAAAAAATCTTTGAATCTGTTTCTCTT-AAA-ATGAATTTTGTATCTC
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCT-TTGAAACA-AAATTTTGTCTCTC
*
557873 TTG
64 TTA
* *
557876 AGACAGTTTCTCTTGAA
1 AGATAGTTTCTTTTGAA
557893 GTAAATCTTT
Statistics
Matches: 135, Mismatches: 13, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
65 1 0.01
66 31 0.23
67 101 0.75
68 2 0.01
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (66 bp):
AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGAAACAAAATTTTGTCTCTCTT
A
Found at i:557942 original size:25 final size:27
Alignment explanation
Indices: 557881--557942 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 27
557871 TCTTGAGACA
557881 GTTTCTCTTGAAGTAAATCTTTGAATAT
1 GTTTCTCTTGAAG-AAATCTTTGAATAT
* *
557909 G-TTCATCTTG-A-AAATCTTTGAGTTT
1 GTTTC-TCTTGAAGAAATCTTTGAATAT
557934 GTTTCTCTT
1 GTTTCTCTT
557943 AACAAAATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
25 17 0.57
26 3 0.10
27 4 0.13
28 6 0.20
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.50
Consensus pattern (27 bp):
GTTTCTCTTGAAGAAATCTTTGAATAT
Found at i:558510 original size:101 final size:102
Alignment explanation
Indices: 558380--558630 Score: 427
Period size: 101 Copynumber: 2.5 Consensus size: 102
558370 TAAAACAGTT
* *
558380 TCTTTTGAAGAAAAAT--CTGAGTCTATTTCTTTGGAAACAAAATTTTGTCTCACTAAGATACAA
1 TCTTTTAAAAAAAAATCACTGAGTCTATTTCTTTGGAAACAAAATTTTGTCTCACTAAGATACAA
558443 TTTTCTGAAAAACAAAGTTTTGTCTCTTATGAAAATG
66 TTTTCTGAAAAACAAAGTTTTGTCTCTTATGAAAATG
*
558480 TCTTTT-AAAAAAAATCACTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCACTAAGATACAA
1 TCTTTTAAAAAAAAATCACTGAGTCTATTTCTTTGGAAACAAAATTTTGTCTCACTAAGATACAA
558544 TTTTCTGAAAAACAAAGTTTTGTCTCTTATGAAAATG
66 TTTTCTGAAAAACAAAGTTTTGTCTCTTATGAAAATG
* * *
558581 TCTTTTAAAAAAAAATCATTGAATCTCTTTCTTTGGAAACAAAATTTTGT
1 TCTTTTAAAAAAAAATCACTGAGTCTATTTCTTTGGAAACAAAATTTTGT
558631 TTCTCTCGAG
Statistics
Matches: 143, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
99 8 0.06
100 6 0.04
101 89 0.62
102 40 0.28
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.39
Consensus pattern (102 bp):
TCTTTTAAAAAAAAATCACTGAGTCTATTTCTTTGGAAACAAAATTTTGTCTCACTAAGATACAA
TTTTCTGAAAAACAAAGTTTTGTCTCTTATGAAAATG
Found at i:558804 original size:66 final size:65
Alignment explanation
Indices: 558734--558910 Score: 162
Period size: 66 Copynumber: 2.7 Consensus size: 65
558724 AACAAACATC
*
558734 TTTGAGATCGTTTCCCTTGAAATGAATTTTGTCTCATTTGAGACAGCTTCCCATGAAAC-ACAGA
1 TTTGAGATCGTTTCCCTTGAAATGAATTTTGTCTC-TTTGAGACAGATTCCCATGAAACGACAGA
558798 T
65 T
* * ** * * * *
558799 ATTTGAGAACGTTTCCCTTAAAAACAAATTTTGTCTCGCTTGAGACA-ATTCCCTTTAAACGTCA
1 -TTTGAGATCGTTTCCCTT-GAAATGAATTTTGTCTC-TTTGAGACAGATTCCCATGAAACGACA
**
558863 TCT
63 GAT
* **
558866 TTTGAG-TTGTTTCATTTGAAATGAATTTTGTCTCTTTCGAGACAG
1 TTTGAGATCGTTTCCCTTGAAATGAATTTTGTCTCTTT-GAGACAG
558911 TTGCTTTTGA
Statistics
Matches: 87, Mismatches: 20, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
63 2 0.02
64 20 0.23
65 7 0.08
66 33 0.38
67 25 0.29
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (65 bp):
TTTGAGATCGTTTCCCTTGAAATGAATTTTGTCTCTTTGAGACAGATTCCCATGAAACGACAGAT
Found at i:558963 original size:28 final size:28
Alignment explanation
Indices: 558914--558990 Score: 86
Period size: 28 Copynumber: 2.6 Consensus size: 28
558904 GAGACAGTTG
*
558914 CTTTTGAAACACATTATATTTGAG-CTTGTTT
1 CTTTTGAAACA-A--ATCTTTGAGTC-TGTTT
558945 -TTCTTGAAACAAATCTTTGAGTCTGTTT
1 CTT-TTGAAACAAATCTTTGAGTCTGTTT
558973 CTTTTGAAACAAATCTTT
1 CTTTTGAAACAAATCTTT
558991 AATTTGGTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
28 28 0.67
29 3 0.07
30 3 0.07
31 8 0.19
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.47
Consensus pattern (28 bp):
CTTTTGAAACAAATCTTTGAGTCTGTTT
Found at i:559000 original size:28 final size:28
Alignment explanation
Indices: 558940--559010 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
558930 TATTTGAGCT
* *
558940 TGTTTTTCTTGAAACAAATCTTTGAGTC
1 TGTTTCTCTTGAAACAAATCTTTGAATC
* *
558968 TGTTTCTTTTGAAACAAATCTTT-AATT
1 TGTTTCTCTTGAAACAAATCTTTGAATC
558995 TGGTTTCTCTTGAAAC
1 T-GTTTCTCTTGAAAC
559011 CATAACTCCT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 3 0.08
28 34 0.92
ACGTcount: A:0.25, C:0.14, G:0.13, T:0.48
Consensus pattern (28 bp):
TGTTTCTCTTGAAACAAATCTTTGAATC
Found at i:559091 original size:40 final size:40
Alignment explanation
Indices: 559036--559353 Score: 212
Period size: 40 Copynumber: 7.5 Consensus size: 40
559026 TGGCCAGCCG
* *
559036 TCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCATCCCTAGACCAGATC
* * * *
559076 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAACCGTGTCATCCCTAG---ACCAGATC
* *
559118 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAACCGTGTCATC-CC--TAGA---CCAGATC
* * *
559165 TCTTCATCACGTATGAGCCGTGTCATTCCC-AGACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCA-TCCCTAGACCAGATC
* * * *
559205 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAACCGTGTCATCCCTAG---ACCAGATC
* *
559247 ATCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAACCGTGTCATC-CC--TAGA---CCAGATC
* * * * *
559294 TCTTCATCACGTATGAGCCGTGTCATTCCC-CGACCAGATT
1 TCCTCATCACGTAGGAACCGTGTCA-TCCCTAGACCAGATC
559334 TCCTCATCACGTAGGAACCG
1 TCCTCATCACGTAGGAACCG
559354 CGTTAACCTT
Statistics
Matches: 217, Mismatches: 36, Indels: 50
0.72 0.12 0.17
Matches are distributed among these distances:
39 2 0.01
40 80 0.37
42 2 0.01
43 65 0.30
44 2 0.01
46 60 0.28
47 6 0.03
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (40 bp):
TCCTCATCACGTAGGAACCGTGTCATCCCTAGACCAGATC
Found at i:559175 original size:46 final size:45
Alignment explanation
Indices: 559023--559319 Score: 216
Period size: 46 Copynumber: 6.9 Consensus size: 45
559013 TAACTCCTAA
* * * *
559023 AGATGGCCAG-CCGTCCTCATCATGTAGGAACCGTGTCATC-CC-C
1 AGATGGCCAGAAC-TCCTCATCACGTAGGAGCCGTGTCATCACCTT
* *
559066 AGA---CCAGATCTCCTCATCACGTAGGAGCCGTGTCA--ACCAT
1 AGATGGCCAGAACTCCTCATCACGTAGGAGCCGTGTCATCACCTT
** * * *
559106 AGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
1 AGATGGCCAGAAC-TCCTCATCACGTAGGAGCCGTGTCATCACC-TT
* *
559152 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTC-CC--
1 AGATGGCCAGAACTCCTCATCACGTAGGAGCCGTGTCA-TCACCTT
* *
559195 AGA---CCAGATCTCCTCATCACGTAGGAGCCGTGTCA--ACCAT
1 AGATGGCCAGAACTCCTCATCACGTAGGAGCCGTGTCATCACCTT
** * * *
559235 AGATAACCAG-CCATCCTCATCACGTAGGAACCGTGTTATCACCTTT
1 AGATGGCCAGAAC-TCCTCATCACGTAGGAGCCGTGTCATCACC-TT
* *
559281 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCAT
1 AGATGGCCAGAACTCCTCATCACGTAGGAGCCGTGTCAT
559320 TCCCCGACCA
Statistics
Matches: 202, Mismatches: 29, Indels: 43
0.74 0.11 0.16
Matches are distributed among these distances:
38 2 0.01
39 2 0.01
40 62 0.31
41 1 0.00
42 2 0.01
43 60 0.30
45 6 0.03
46 63 0.31
47 4 0.02
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.24
Consensus pattern (45 bp):
AGATGGCCAGAACTCCTCATCACGTAGGAGCCGTGTCATCACCTT
Found at i:559253 original size:129 final size:129
Alignment explanation
Indices: 559039--559349 Score: 559
Period size: 129 Copynumber: 2.4 Consensus size: 129
559029 CCAGCCGTCC
* * * *
559039 TCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
1 TCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
*
559104 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
66 ATAGATAACCAGCCATCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
559168 TCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
1 TCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
559233 ATAGATAACCAGCCATCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
66 ATAGATAACCAGCCATCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
* *
559297 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATTTCCTCATCACGTAGGA
1 TCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTCATCACGTAGGA
559350 ACCGCGTTAA
Statistics
Matches: 175, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
129 175 1.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (129 bp):
TCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
ATAGATAACCAGCCATCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
Found at i:559560 original size:3 final size:3
Alignment explanation
Indices: 559554--559610 Score: 55
Period size: 3 Copynumber: 19.3 Consensus size: 3
559544 TTTTTATATA
** * *
559554 TAT TAT TAT CGT TAT T-T TAAT TAT TAT TAT TAT TAG CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT
559599 TAT TAT T-T TAT T
1 TAT TAT TAT TAT T
559611 TACATATTAC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
2 4 0.09
3 37 0.86
4 2 0.05
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:559586 original size:18 final size:18
Alignment explanation
Indices: 559555--559608 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
559545 TTTTATATAT
**
559555 ATTATTATCGTTATTTTA
1 ATTATTATTATTATTTTA
***
559573 ATTATTATTATTATTAGC
1 ATTATTATTATTATTTTA
559591 ATTATTATTATTATTTTA
1 ATTATTATTATTATTTTA
559609 TTTACATATT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (18 bp):
ATTATTATTATTATTTTA
Found at i:566279 original size:20 final size:20
Alignment explanation
Indices: 566241--566280 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
566231 TAATCCTATT
**
566241 CACTGGTAATCTTTTATTCC
1 CACTGGTAATCTTACATTCC
566261 CACTGGTAATCTTACATTCC
1 CACTGGTAATCTTACATTCC
566281 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.28, G:0.10, T:0.40
Consensus pattern (20 bp):
CACTGGTAATCTTACATTCC
Found at i:570542 original size:36 final size:37
Alignment explanation
Indices: 570482--570567 Score: 111
Period size: 36 Copynumber: 2.3 Consensus size: 37
570472 GGACGTATCT
* *
570482 TAAAATGTTATTTTTTTTCCTAACATTTTTAGTTGAACC
1 TAAAATGTTA-TTTTTTT-CTAACATTTTCACTTGAACC
*
570521 TAAAATGTTATTTTTTT-TAACATTTTCACTTGAACT
1 TAAAATGTTATTTTTTTCTAACATTTTCACTTGAACC
*
570557 TAAAATTTTAT
1 TAAAATGTTAT
570568 CTTATTCATG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 26 0.60
38 7 0.16
39 10 0.23
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.52
Consensus pattern (37 bp):
TAAAATGTTATTTTTTTCTAACATTTTCACTTGAACC
Found at i:577524 original size:13 final size:12
Alignment explanation
Indices: 577500--577530 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
577490 ATAATTTAAA
577500 TTTTTTAAATAT
1 TTTTTTAAATAT
577512 TTTTTTAATATAT
1 TTTTTTAA-ATAT
577525 TTTTTT
1 TTTTTT
577531 TGAGTTGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTTAAATAT
Found at i:583699 original size:21 final size:22
Alignment explanation
Indices: 583663--583703 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
583653 TTAGAAATTA
583663 TAAAGGAAGTACCGATACTCAT
1 TAAAGGAAGTACCGATACTCAT
*
583685 TAAAGG-AGTATCGATACTC
1 TAAAGGAAGTACCGATACTC
583704 CTTGTCTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (22 bp):
TAAAGGAAGTACCGATACTCAT
Found at i:583920 original size:34 final size:34
Alignment explanation
Indices: 583872--583940 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
583862 AGAGAAGAGC
*
583872 TTTGCAATCTTATTTTCCTTTCTCTTGTAAATAT
1 TTTGAAATCTTATTTTCCTTTCTCTTGTAAATAT
583906 TTTGAAATCTTATTTTCCTTTCTCTTGTAAATAT
1 TTTGAAATCTTATTTTCCTTTCTCTTGTAAATAT
583940 T
1 T
583941 AGTGTGTTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.22, C:0.16, G:0.06, T:0.57
Consensus pattern (34 bp):
TTTGAAATCTTATTTTCCTTTCTCTTGTAAATAT
Found at i:585227 original size:15 final size:15
Alignment explanation
Indices: 585199--585237 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
585189 TGGCCCCAAA
*
585199 AGCCGAGAAGAAGCC
1 AGCCGAGAAAAAGCC
*
585214 AGCTGAGAAAAAGCC
1 AGCCGAGAAAAAGCC
585229 AGCCGAGAA
1 AGCCGAGAA
585238 GGCCCCAGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.44, C:0.23, G:0.31, T:0.03
Consensus pattern (15 bp):
AGCCGAGAAAAAGCC
Found at i:585235 original size:30 final size:31
Alignment explanation
Indices: 585198--585275 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 31
585188 ATGGCCCCAA
585198 AAGCCGAGAAGAAGCCAGCTGAGAAAAAGCC
1 AAGCCGAGAAGAAGCCAGCTGAGAAAAAGCC
*** *
585229 -AGCCGAGAAGGCCCCAGCTGAGAAGAAGCC
1 AAGCCGAGAAGAAGCCAGCTGAGAAAAAGCC
585259 AAGAGCCGAGAAGAAGC
1 -A-AGCCGAGAAGAAGC
585276 TGCCCAAAGA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
30 26 0.70
33 11 0.30
ACGTcount: A:0.41, C:0.24, G:0.32, T:0.03
Consensus pattern (31 bp):
AAGCCGAGAAGAAGCCAGCTGAGAAAAAGCC
Found at i:590408 original size:18 final size:18
Alignment explanation
Indices: 590385--590421 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
590375 AGCAACCATG
590385 ACATTCCGTGCTCGGGAC
1 ACATTCCGTGCTCGGGAC
590403 ACATTCCGTGCTCGGGAC
1 ACATTCCGTGCTCGGGAC
590421 A
1 A
590422 TTGTGATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.19, C:0.32, G:0.27, T:0.22
Consensus pattern (18 bp):
ACATTCCGTGCTCGGGAC
Found at i:590929 original size:18 final size:18
Alignment explanation
Indices: 590906--590942 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
590896 AGCAACCATG
590906 ACATTCCGTGCTCGGGAC
1 ACATTCCGTGCTCGGGAC
590924 ACATTCCGTGCTCGGGAC
1 ACATTCCGTGCTCGGGAC
590942 A
1 A
590943 TTGTGATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.19, C:0.32, G:0.27, T:0.22
Consensus pattern (18 bp):
ACATTCCGTGCTCGGGAC
Found at i:591337 original size:521 final size:521
Alignment explanation
Indices: 590356--591403 Score: 2096
Period size: 521 Copynumber: 2.0 Consensus size: 521
590346 CCTGCAGAGG
590356 CAAAAGCTAGTAACCCAGAAGCAACCATGACATTCCGTGCTCGGGACACATTCCGTGCTCGGGAC
1 CAAAAGCTAGTAACCCAGAAGCAACCATGACATTCCGTGCTCGGGACACATTCCGTGCTCGGGAC
590421 ATTGTGATTCTAAACCAACTTCAACAAGAGGGAGACCTACAACATGTTAAACAACTTATTGACAT
66 ATTGTGATTCTAAACCAACTTCAACAAGAGGGAGACCTACAACATGTTAAACAACTTATTGACAT
590486 TTCCAATACCAATACGAAATTCTACATGTTAATTCATACATTCTATATAGTAAATAAACGAAAAC
131 TTCCAATACCAATACGAAATTCTACATGTTAATTCATACATTCTATATAGTAAATAAACGAAAAC
590551 AATATTCTTGAATTATAGATTATAGCTCGAACCACCAGAAAATGAGGGTCGAAAAGAGATCTAGA
196 AATATTCTTGAATTATAGATTATAGCTCGAACCACCAGAAAATGAGGGTCGAAAAGAGATCTAGA
590616 ATTGCCAAGTTCGATCTCAAGAGCAATTTCCACACTTACCTACCACCAACAGGAAAGTAAAGCAC
261 ATTGCCAAGTTCGATCTCAAGAGCAATTTCCACACTTACCTACCACCAACAGGAAAGTAAAGCAC
590681 AAAACTTTCCAGTCAGCAATGGATTCTTACAAATGATCAAAACCAACATGCCCCGGAACTCTCGA
326 AAAACTTTCCAGTCAGCAATGGATTCTTACAAATGATCAAAACCAACATGCCCCGGAACTCTCGA
590746 TTCTCAGTTCAAGGAGGCTCGTGTATGATAAAGAGTTCAAGACAAGTGGCCTCAGCAACTATGTA
391 TTCTCAGTTCAAGGAGGCTCGTGTATGATAAAGAGTTCAAGACAAGTGGCCTCAGCAACTATGTA
590811 CACCATAATTCCCAGAATTCAATACCACCCTTTCATAATTGCAAATTGGGATAACCTAAATAGAC
456 CACCATAATTCCCAGAATTCAATACCACCCTTTCATAATTGCAAATTGGGATAACCTAAATAGAC
590876 C
521 C
590877 CAAAAGCTAGTAACCCAGAAGCAACCATGACATTCCGTGCTCGGGACACATTCCGTGCTCGGGAC
1 CAAAAGCTAGTAACCCAGAAGCAACCATGACATTCCGTGCTCGGGACACATTCCGTGCTCGGGAC
590942 ATTGTGATTCTAAACCAACTTCAACAAGAGGGAGACCTACAACATGTTAAACAACTTATTGACAT
66 ATTGTGATTCTAAACCAACTTCAACAAGAGGGAGACCTACAACATGTTAAACAACTTATTGACAT
591007 TTCCAATACCAATACGAAATTCTACATGTTAATTCATACATTCTATATAGTAAATAAACGAAAAC
131 TTCCAATACCAATACGAAATTCTACATGTTAATTCATACATTCTATATAGTAAATAAACGAAAAC
591072 AATATTCTTGAATTATAGATTATAGCTCGAACCACCAGAAAATGAGGGTCGAAAAGAGATCTAGA
196 AATATTCTTGAATTATAGATTATAGCTCGAACCACCAGAAAATGAGGGTCGAAAAGAGATCTAGA
591137 ATTGCCAAGTTCGATCTCAAGAGCAATTTCCACACTTACCTACCACCAACAGGAAAGTAAAGCAC
261 ATTGCCAAGTTCGATCTCAAGAGCAATTTCCACACTTACCTACCACCAACAGGAAAGTAAAGCAC
591202 AAAACTTTCCAGTCAGCAATGGATTCTTACAAATGATCAAAACCAACATGCCCCGGAACTCTCGA
326 AAAACTTTCCAGTCAGCAATGGATTCTTACAAATGATCAAAACCAACATGCCCCGGAACTCTCGA
591267 TTCTCAGTTCAAGGAGGCTCGTGTATGATAAAGAGTTCAAGACAAGTGGCCTCAGCAACTATGTA
391 TTCTCAGTTCAAGGAGGCTCGTGTATGATAAAGAGTTCAAGACAAGTGGCCTCAGCAACTATGTA
591332 CACCATAATTCCCAGAATTCAATACCACCCTTTCATAATTGCAAATTGGGATAACCTAAATAGAC
456 CACCATAATTCCCAGAATTCAATACCACCCTTTCATAATTGCAAATTGGGATAACCTAAATAGAC
591397 C
521 C
591398 CAAAAG
1 CAAAAG
591404 TCGGAGATTT
Statistics
Matches: 527, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
521 527 1.00
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (521 bp):
CAAAAGCTAGTAACCCAGAAGCAACCATGACATTCCGTGCTCGGGACACATTCCGTGCTCGGGAC
ATTGTGATTCTAAACCAACTTCAACAAGAGGGAGACCTACAACATGTTAAACAACTTATTGACAT
TTCCAATACCAATACGAAATTCTACATGTTAATTCATACATTCTATATAGTAAATAAACGAAAAC
AATATTCTTGAATTATAGATTATAGCTCGAACCACCAGAAAATGAGGGTCGAAAAGAGATCTAGA
ATTGCCAAGTTCGATCTCAAGAGCAATTTCCACACTTACCTACCACCAACAGGAAAGTAAAGCAC
AAAACTTTCCAGTCAGCAATGGATTCTTACAAATGATCAAAACCAACATGCCCCGGAACTCTCGA
TTCTCAGTTCAAGGAGGCTCGTGTATGATAAAGAGTTCAAGACAAGTGGCCTCAGCAACTATGTA
CACCATAATTCCCAGAATTCAATACCACCCTTTCATAATTGCAAATTGGGATAACCTAAATAGAC
C
Found at i:594059 original size:6 final size:6
Alignment explanation
Indices: 594048--594086 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
594038 GAGACGAAGC
594048 GTGTGG GTGTGG GTGT-G G-GTGG GTGTGG GTGTGG GTGTG
1 GTGTGG GTGTGG GTGTGG GTGTGG GTGTGG GTGTGG GTGTG
594087 CGTGGCGAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 2 0.06
5 4 0.13
6 25 0.81
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (6 bp):
GTGTGG
Found at i:594071 original size:16 final size:16
Alignment explanation
Indices: 594050--594084 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
594040 GACGAAGCGT
594050 GTGGGTGTGGGTGTGG
1 GTGGGTGTGGGTGTGG
594066 GTGGGTGTGGGTGTGG
1 GTGGGTGTGGGTGTGG
594082 GTG
1 GTG
594085 TGCGTGGCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.69, T:0.31
Consensus pattern (16 bp):
GTGGGTGTGGGTGTGG
Found at i:594076 original size:22 final size:22
Alignment explanation
Indices: 594048--594091 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
594038 GAGACGAAGC
*
594048 GTGTGGGTGTGGGTGTGGGTGG
1 GTGTGGGTGTGGGTGTGCGTGG
594070 GTGTGGGTGTGGGTGTGCGTGG
1 GTGTGGGTGTGGGTGTGCGTGG
594092 CGAGGGAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.00, C:0.02, G:0.66, T:0.32
Consensus pattern (22 bp):
GTGTGGGTGTGGGTGTGCGTGG
Found at i:594091 original size:16 final size:16
Alignment explanation
Indices: 594050--594091 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
594040 GACGAAGCGT
*
594050 GTGGGTGTGGGTGTGG
1 GTGGGCGTGGGTGTGG
*
594066 GTGGGTGTGGGTGTGG
1 GTGGGCGTGGGTGTGG
*
594082 GTGTGCGTGG
1 GTGGGCGTGG
594092 CGAGGGAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.00, C:0.02, G:0.67, T:0.31
Consensus pattern (16 bp):
GTGGGCGTGGGTGTGG
Found at i:596434 original size:24 final size:24
Alignment explanation
Indices: 596381--596434 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
596371 CACCACTGTT
* *
596381 CATATAATTTGCACCGAAGTGCCA
1 CATAGAATATGCACCGAAGTGCCA
* *
596405 CGTAGAATATGCACCGAAGTGCCG
1 CATAGAATATGCACCGAAGTGCCA
596429 CATAGA
1 CATAGA
596435 TTTATCCCGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.20
Consensus pattern (24 bp):
CATAGAATATGCACCGAAGTGCCA
Found at i:596467 original size:25 final size:24
Alignment explanation
Indices: 596434--596496 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 24
596424 TGCCGCATAG
* * *
596434 ATTTATCCCGAAGGATCGGGTAAAA
1 ATTTGTCCCGAAGGACCAGGT-AAA
* *
596459 ATTTGTCCCGAAGGACCATGTAGA
1 ATTTGTCCCGAAGGACCAGGTAAA
596483 ATTTGTCCCGAAGG
1 ATTTGTCCCGAAGG
596497 GCCGCTTAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
24 16 0.48
25 17 0.52
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (24 bp):
ATTTGTCCCGAAGGACCAGGTAAA
Found at i:598999 original size:22 final size:21
Alignment explanation
Indices: 598961--599019 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
598951 TATTAAATTA
*
598961 TTTAA-AATATATTTATTAATAT
1 TTTAATAATATA-ATATT-ATAT
598983 TTTAATAATATAATATTATAT
1 TTTAATAATATAATATTATAT
*
599004 TTCTAATATTATAATA
1 TT-TAATAATATAATA
599020 AAATAATCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 6 0.18
22 21 0.64
23 6 0.18
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTAATAATATAATATTATAT
Found at i:599038 original size:23 final size:23
Alignment explanation
Indices: 599009--599062 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
598999 TATATTTCTA
599009 ATATTATAATAAAATAATCA-ATT
1 ATATTATAATAAAATAA-CATATT
*
599032 ATATTATAATAAAATAAGATATT
1 ATATTATAATAAAATAACATATT
599055 ATATTATA
1 ATATTATA
599063 TTTTTATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 1 0.03
23 28 0.97
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
ATATTATAATAAAATAACATATT
Found at i:599208 original size:23 final size:23
Alignment explanation
Indices: 599188--599232 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
599178 AATAATATTT
599188 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
599211 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
599233 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:599349 original size:14 final size:14
Alignment explanation
Indices: 599301--599350 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
599291 AAAATATACC
*
599301 AATATTAATATTTT
1 AATAATAATATTTT
* * *
599315 ATTAATAAAATTAT
1 AATAATAATATTTT
*
599329 AAAAATAATATTTT
1 AATAATAATATTTT
599343 AATAATAA
1 AATAATAA
599351 ATAAATTATT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATAATAATATTTT
Found at i:599521 original size:14 final size:14
Alignment explanation
Indices: 599499--599533 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
599489 CAAACATAGT
*
599499 AAAACGTTTTTCAG
1 AAAATGTTTTTCAG
599513 AAAATGTTTTTCAG
1 AAAATGTTTTTCAG
*
599527 AAGATGT
1 AAAATGT
599534 AATTCATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (14 bp):
AAAATGTTTTTCAG
Found at i:602399 original size:28 final size:28
Alignment explanation
Indices: 602342--602410 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 28
602332 ATATTATTGA
* *
602342 AAAAAACTT-AAACTTAATTTATTTATT
1 AAAAAACTTAAAACTTAATTAAATTATT
*
602369 AAAAAACTTAAAATTTTAATTAAATTA-T
1 AAAAAACTTAAAA-CTTAATTAAATTATT
602397 AAAAAACTCTAAAA
1 AAAAAACT-TAAAA
602411 AAACTAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 9 0.25
28 12 0.33
29 15 0.42
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (28 bp):
AAAAAACTTAAAACTTAATTAAATTATT
Found at i:608134 original size:210 final size:210
Alignment explanation
Indices: 607772--608195 Score: 830
Period size: 210 Copynumber: 2.0 Consensus size: 210
607762 ATGTTAATGA
607772 TCAAATTTTGGATGGGGACCGGCAAGAAAATATTGCGAATGTATCGTCCCTTGAAACTTTACAGA
1 TCAAATTTTGGATGGGGACCGGCAAGAAAATATTGCGAATGTATCGTCCCTTGAAACTTTACAGA
*
607837 ATGAAGCGAGAGAACATAGTGGTGAAGCATCTTATGTACATTTTCCCCAAGATGGTGAGAGAAGT
66 ATGAAGCGAGAGAACATAGTGGTGAAGCATCGTATGTACATTTTCCCCAAGATGGTGAGAGAAGT
607902 GGGACCTACTGGTTACCTGATGACAGAGAAAATTTAGAACAGAATCTAGTTCAATATATTGACGG
131 GGGACCTACTGGTTACCTGATGACAGAGAAAATTTAGAACAGAATCTAGTTCAATATATTGACGG
607967 GCAGGAATCTGCTTC
196 GCAGGAATCTGCTTC
607982 TCAAATTTTGGATGGGGACCGGCAAGAAAATATTGCGAATGTATCGTCCCTTGAAACTTTACAGA
1 TCAAATTTTGGATGGGGACCGGCAAGAAAATATTGCGAATGTATCGTCCCTTGAAACTTTACAGA
608047 ATGAAGCGAGAGAACATAGTGGTGAAGCATCGTATGTACATTTTCCCCAAGATGGTGAGAGAAGT
66 ATGAAGCGAGAGAACATAGTGGTGAAGCATCGTATGTACATTTTCCCCAAGATGGTGAGAGAAGT
*
608112 GGGACCTACTGGTTACCTGATGACAGAGAAAATTTAGAACAGAATCTAGTTCAATATATTGATGG
131 GGGACCTACTGGTTACCTGATGACAGAGAAAATTTAGAACAGAATCTAGTTCAATATATTGACGG
608177 GCAGGAATCTGCTTC
196 GCAGGAATCTGCTTC
608192 TCAA
1 TCAA
608196 GTTGAAGGAC
Statistics
Matches: 212, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
210 212 1.00
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (210 bp):
TCAAATTTTGGATGGGGACCGGCAAGAAAATATTGCGAATGTATCGTCCCTTGAAACTTTACAGA
ATGAAGCGAGAGAACATAGTGGTGAAGCATCGTATGTACATTTTCCCCAAGATGGTGAGAGAAGT
GGGACCTACTGGTTACCTGATGACAGAGAAAATTTAGAACAGAATCTAGTTCAATATATTGACGG
GCAGGAATCTGCTTC
Found at i:610456 original size:29 final size:29
Alignment explanation
Indices: 610414--610471 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
610404 TAGTTGTTGA
610414 ACTGTTGTCGGTTGACAAATGTTAATGTC
1 ACTGTTGTCGGTTGACAAATGTTAATGTC
*
610443 ACTGTTGTCGGTTGGCAAATGTTAATGTC
1 ACTGTTGTCGGTTGACAAATGTTAATGTC
610472 TTGTGTCGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.22, C:0.14, G:0.26, T:0.38
Consensus pattern (29 bp):
ACTGTTGTCGGTTGACAAATGTTAATGTC
Found at i:611184 original size:15 final size:16
Alignment explanation
Indices: 611157--611192 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
611147 AACCATCGAA
*
611157 TTCCCCTCTCTTCTTC
1 TTCCCCTCTCTTCCTC
611173 TTCCCC-CTCTTCCTC
1 TTCCCCTCTCTTCCTC
611188 TTCCC
1 TTCCC
611193 ATTCTCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (16 bp):
TTCCCCTCTCTTCCTC
Found at i:614019 original size:30 final size:31
Alignment explanation
Indices: 613978--614045 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
613968 TTAAAACTTA
* * *
613978 CAATATAATCCC-CAATATTTAGTCTATTTG
1 CAATATGATCCCTCAACATTTAGTCCATTTG
614008 CAATATGATCCCTCAACATTTAGTCCATTTG
1 CAATATGATCCCTCAACATTTAGTCCATTTG
614039 CAATATG
1 CAATATG
614046 GTCCTTGATG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 11 0.32
31 23 0.68
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (31 bp):
CAATATGATCCCTCAACATTTAGTCCATTTG
Found at i:623454 original size:15 final size:15
Alignment explanation
Indices: 623369--623446 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
623359 TTATCATTTG
623369 TTCACAT-TGAACATA
1 TTCACATAT-AACATA
*
623384 TTCACTTAGT-ACATA
1 TTCACATA-TAACATA
* *
623399 TTCACATAAAACATT
1 TTCACATATAACATA
* *
623414 TTCACAAAGAACATA
1 TTCACATATAACATA
623429 TTCACATATAACATA
1 TTCACATATAACATA
623444 TTC
1 TTC
623447 TTATATAAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
15 50 0.98
17 1 0.02
ACGTcount: A:0.42, C:0.21, G:0.04, T:0.33
Consensus pattern (15 bp):
TTCACATATAACATA
Found at i:630115 original size:15 final size:16
Alignment explanation
Indices: 630077--630117 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
630067 ACAGAGCCTC
* *
630077 TGAATCATTTAGCATT
1 TGAATCATTCAGCACT
630093 TGAATCATTCAGCACT
1 TGAATCATTCAGCACT
630109 T-AATCATTC
1 TGAATCATTC
630118 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.39
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:636035 original size:40 final size:40
Alignment explanation
Indices: 635977--636054 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 40
635967 GGCTAAGACA
*
635977 CGGTGCATAGGGCGCGCCTTATGCCACGTAGGGTATAGCG
1 CGGTGCATAGGGCACGCCTTATGCCACGTAGGGTATAGCG
*
636017 CGGTGCAT-GGGTCACGCCTTATGTCACGTAGGGTATAG
1 CGGTGCATAGGG-CACGCCTTATGCCACGTAGGGTATAG
636055 TACGGAGCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 3 0.09
40 32 0.91
ACGTcount: A:0.18, C:0.23, G:0.36, T:0.23
Consensus pattern (40 bp):
CGGTGCATAGGGCACGCCTTATGCCACGTAGGGTATAGCG
Found at i:636065 original size:40 final size:40
Alignment explanation
Indices: 635991--636076 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
635981 GCATAGGGCG
* * *
635991 CGCCTTATGCCACGTAGGGTATAGCGCGGTGCATGGGTCA
1 CGCCTTATGCCACGTAGGGTATAGCACGGAGCATGGGCCA
* * *
636031 CGCCTTATGTCACGTAGGGTATAGTACGGAGCATGGGCCG
1 CGCCTTATGCCACGTAGGGTATAGCACGGAGCATGGGCCA
636071 CGCCTT
1 CGCCTT
636077 CCTGCAATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.17, C:0.26, G:0.34, T:0.23
Consensus pattern (40 bp):
CGCCTTATGCCACGTAGGGTATAGCACGGAGCATGGGCCA
Found at i:642071 original size:17 final size:18
Alignment explanation
Indices: 642043--642076 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
642033 TAGTTAAATA
642043 AAATACTAATAAAATATT
1 AAATACTAATAAAATATT
642061 AAATA-TAATAAAATAT
1 AAATACTAATAAAATAT
642077 ACATTAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATACTAATAAAATATT
Found at i:643173 original size:2 final size:2
Alignment explanation
Indices: 643166--643237 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
643156 TTCTATAACC
643166 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
643208 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
643238 CTTTTTCATA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:645174 original size:230 final size:229
Alignment explanation
Indices: 644715--645432 Score: 1311
Period size: 230 Copynumber: 3.1 Consensus size: 229
644705 ATTATATTGT
* * *
644715 AAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGT-GAAAATATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
644779 ATCTTTGGTTAATATTGTTAAATTTAAATTCT--A-AATATTTTATAAAATATCAAAACAATCAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAA-AATCAA
*
644841 ATAATTTTGTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTA
130 ATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTA
644906 AAAAAAATTGAAACATAAATTACATAACTTTAAAA
195 AAAAAAATTGAAACATAAATTACATAACTTTAAAA
*
644941 AAAGTATATATCATTTTTATAAAAGTGTACATACTTATTTCACTGTGGAAAACATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
645006 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAA
645071 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
131 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-A
645136 AAAAAAATTGAAACATAAATTACATAACTTTAAAA
195 AAAAAAATTGAAACATAAATTACATAACTTTAAAA
*
645171 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACCGTGGAAAACATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
*
645236 ATCTTTGGTTAATATTGTTAAATTGAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAA
*
645301 TAATTTTTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-A
131 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
645365 AAAAAATTGAAACATAAATTACATAACTTTAAAA
196 AAAAAATTGAAACATAAATTACATAACTTTAAAA
645399 AAAGTATATATCATTTTTATAAAAGTGTCCATAC
1 AAAGTATATATCATTTTTATAAAAGTGTCCATAC
645433 GTATAAAAGT
Statistics
Matches: 478, Mismatches: 9, Indels: 8
0.97 0.02 0.02
Matches are distributed among these distances:
226 43 0.09
227 49 0.10
228 69 0.14
229 70 0.15
230 247 0.52
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (229 bp):
AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAA
TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
AAAAAATTGAAACATAAATTACATAACTTTAAAA
Found at i:645521 original size:21 final size:20
Alignment explanation
Indices: 645482--645528 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
645472 GGTATACCAA
645482 GTAAAAATATGATAAAACCG
1 GTAAAAATATGATAAAACCG
645502 GTAACAAA-ATGATAAAAACCG
1 GTAA-AAATATGAT-AAAACCG
645523 GTAAAA
1 GTAAAA
645529 CGTTACCGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.57, C:0.11, G:0.15, T:0.17
Consensus pattern (20 bp):
GTAAAAATATGATAAAACCG
Found at i:646311 original size:23 final size:23
Alignment explanation
Indices: 646285--646343 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
646275 TGTAAAAATG
646285 ATGTAATAGGTAGCGCTTATATA
1 ATGTAATAGGTAGCGCTTATATA
* *
646308 ATGTAATAGGTATCGTTTATATA
1 ATGTAATAGGTAGCGCTTATATA
*
646331 ATATAATAGGTAG
1 ATGTAATAGGTAG
646344 TTGTAAAGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.37
Consensus pattern (23 bp):
ATGTAATAGGTAGCGCTTATATA
Found at i:646540 original size:476 final size:482
Alignment explanation
Indices: 645886--647224 Score: 2448
Period size: 476 Copynumber: 2.8 Consensus size: 482
645876 CAAAATATAA
*
645886 TTTAGTAAAAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTG
1 TTTA-TAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTG
645951 AGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATAT
65 AGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATAT
646016 ATTATTATTAAATTAAAAACAATAAACATATATATTACATA--T-TTATTATCTTTGGTTAATAT
130 ATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATAT
*
646078 TGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTGTGTGTA
195 TGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTA
*
646143 AATGAAATTATTAAATTAATATTGTAGGTAGAAAACATGAAACACTATT-AAAAAAATTGAAACA
260 AATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACA
*
646207 TAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATA
325 TAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTCAATATA
*
646272 ATATGT-AAAA-ATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATAT
390 ATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATAT
646335 AATAGGTAGTTGTAAAGTATCTATCCTT
455 AATAGGTAGTTGTAAAGTATCTATCCTT
* *
646363 TTTATAAGAGTGTCCATACTTTTTTCACTGTGAAAAACATTAATTTAAGGTTATCTTTTGAGTGA
1 TTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGA
646428 GTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA-TTTTTACGTTACGATATATA
66 GTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATA
*
646492 TTA-TATT-AATTAAAAACAATAAACATATATATTACATATTTATTATTATATTTGGTTAATATT
131 TTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATT
646555 GTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAA
196 GTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAA
646620 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
261 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
646685 AAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTCAATATAA
326 AAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTCAATATAA
* *
646750 TAGGTAAAAATATGATGTAATAGGTAGCGTTTATATAATGTAATAGGTATCGTTTATATAATGTA
391 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATATA
646815 ATAGGTAGTTGTAAAGTATCTATCCTT
456 ATAGGTAGTTGTAAAGTATCTATCCTT
646842 TTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGA
1 TTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGA
*
646907 GTTTTAAGATATTAATTTAGTAATTATATGCGTCTAATGATTTATTTTTTACGTTACGATATATA
66 GTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATA
*
646972 TTATTATTAAATTAAAAATAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATT
131 TTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATT
*
647037 GTTAAATTTAAATTCTAAATA-TATTTTATAAAATATCAAAACAATC-AATAATTTTTTGTGCAA
196 GTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAA
647100 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
261 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
* * *
647165 AAATTACATAACTTTTAAAAAATTATCGATCATTTTTATAAAAAGTATGGATACTTTCAA
326 AAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTCAA
647225 CATATTATAA
Statistics
Matches: 834, Mismatches: 19, Indels: 15
0.96 0.02 0.02
Matches are distributed among these distances:
473 31 0.04
474 4 0.00
475 24 0.03
476 233 0.28
477 88 0.11
478 4 0.00
479 185 0.22
480 161 0.19
481 29 0.03
482 75 0.09
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (482 bp):
TTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGA
GTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATA
TTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATT
GTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAA
ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
AAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTCAATATAA
TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATATA
ATAGGTAGTTGTAAAGTATCTATCCTT
Found at i:646790 original size:23 final size:23
Alignment explanation
Indices: 646759--646822 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
646749 ATAGGTAAAA
*
646759 ATATGATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGTTT
*
646782 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGTTT
646805 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
646823 TTGTAAAGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.39
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGTTT
Found at i:649539 original size:14 final size:14
Alignment explanation
Indices: 649520--649547 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
649510 TTTGATAAAC
649520 CGTTGTTGTTATAA
1 CGTTGTTGTTATAA
649534 CGTTGTTGTTATAA
1 CGTTGTTGTTATAA
649548 TCTTATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.50
Consensus pattern (14 bp):
CGTTGTTGTTATAA
Found at i:653934 original size:339 final size:339
Alignment explanation
Indices: 653314--653993 Score: 1351
Period size: 339 Copynumber: 2.0 Consensus size: 339
653304 CTGGCAGTCA
653314 TCATAAATGAATTAGGAGATATAGAAGAGGTACAGTTTGTCATTTTCAATTGGAGTTCTTTCTGC
1 TCATAAATGAATTAGGAGATATAGAAGAGGTACAGTTTGTCATTTTCAATTGGAGTTCTTTCTGC
653379 TTTCAGCTATTGCTTAATATTTGTGTTTCTGGTAATTTTATGGATTAGTACCAAAGATAGAAGTG
66 TTTCAGCTATTGCTTAATATTTGTGTTTCTGGTAATTTTATGGATTAGTACCAAAGATAGAAGTG
653444 TATTTATCCTCCGCAGGCTGTAGAATTTGTGACCATGCAGCATGATGATGATCTTTGGGAAGAAC
131 TATTTATCCTCCGCAGGCTGTAGAATTTGTGACCATGCAGCATGATGATGATCTTTGGGAAGAAC
*
653509 TTATTCACCAATGCCTCCACTAACCTGAAATGGTAATGCCATAAAATGCAGACTGGAAATATGCT
196 TTATTCACCAATGCCTCCACAAACCTGAAATGGTAATGCCATAAAATGCAGACTGGAAATATGCT
653574 TGTCTTGTCTGATGATTAGCCATATTCCTCTTGTTTTGAACTTGTTCTTACTAGTCTCTCACTGA
261 TGTCTTGTCTGATGATTAGCCATATTCCTCTTGTTTTGAACTTGTTCTTACTAGTCTCTCACTGA
653639 TTGGCAGGTGGGCG
326 TTGGCAGGTGGGCG
653653 TCATAAATGAATTAGGAGATATAGAAGAGGTACAGTTTGTCATTTTCAATTGGAGTTCTTTCTGC
1 TCATAAATGAATTAGGAGATATAGAAGAGGTACAGTTTGTCATTTTCAATTGGAGTTCTTTCTGC
653718 TTTCAGCTATTGCTTAATATTTGTGTTTCTGGTAATTTTATGGATTAGTACCAAAGATAGAAGTG
66 TTTCAGCTATTGCTTAATATTTGTGTTTCTGGTAATTTTATGGATTAGTACCAAAGATAGAAGTG
653783 TATTTATCCTCCGCAGGCTGTAGAATTTGTGACCATGCAGCATGATGATGATCTTTGGGAAGAAC
131 TATTTATCCTCCGCAGGCTGTAGAATTTGTGACCATGCAGCATGATGATGATCTTTGGGAAGAAC
653848 TTATTCACCAATGCCTCCACAAACCTGAAATGGTAATGCCATAAAATGCAGACTGGAAATATGCT
196 TTATTCACCAATGCCTCCACAAACCTGAAATGGTAATGCCATAAAATGCAGACTGGAAATATGCT
653913 TGTCTTGTCTGATGATTAGCCATATTCCTCTTGTTTTGAACTTGTTCTTACTAGTCTCTCACTGA
261 TGTCTTGTCTGATGATTAGCCATATTCCTCTTGTTTTGAACTTGTTCTTACTAGTCTCTCACTGA
653978 TTGGCAGGTGGGCG
326 TTGGCAGGTGGGCG
653992 TC
1 TC
653994 TTATTGGAAC
Statistics
Matches: 340, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
339 340 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.36
Consensus pattern (339 bp):
TCATAAATGAATTAGGAGATATAGAAGAGGTACAGTTTGTCATTTTCAATTGGAGTTCTTTCTGC
TTTCAGCTATTGCTTAATATTTGTGTTTCTGGTAATTTTATGGATTAGTACCAAAGATAGAAGTG
TATTTATCCTCCGCAGGCTGTAGAATTTGTGACCATGCAGCATGATGATGATCTTTGGGAAGAAC
TTATTCACCAATGCCTCCACAAACCTGAAATGGTAATGCCATAAAATGCAGACTGGAAATATGCT
TGTCTTGTCTGATGATTAGCCATATTCCTCTTGTTTTGAACTTGTTCTTACTAGTCTCTCACTGA
TTGGCAGGTGGGCG
Found at i:657875 original size:27 final size:27
Alignment explanation
Indices: 657837--657897 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
657827 ATTCTTATTC
657837 ATAGATCATCTTCGGACTCATCACTGA
1 ATAGATCATCTTCGGACTCATCACTGA
*
657864 ATAGATCATCTTCGGATTCATCACTGA
1 ATAGATCATCTTCGGACTCATCACTGA
657891 ATAGATC
1 ATAGATC
657898 TTAAGGAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (27 bp):
ATAGATCATCTTCGGACTCATCACTGA
Found at i:662105 original size:2 final size:2
Alignment explanation
Indices: 662098--662129 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
662088 GCTTCATGAA
662098 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
662130 TTAAATTACG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:663723 original size:2 final size:2
Alignment explanation
Indices: 663718--663751 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
663708 ATAAAAAATC
663718 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
663752 AGATCGTTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:663927 original size:2 final size:2
Alignment explanation
Indices: 663920--663945 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
663910 ATAGTATCGC
663920 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
663946 CGTAAGTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:674899 original size:23 final size:23
Alignment explanation
Indices: 674832--674899 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
674822 ATGCCATATA
* * *
674832 TTTGTCCCGAAAGACTACATAGT
1 TTTGTCCCGAAGGACCACATAGG
*
674855 TTTGTCCCGAAGGATCACATAGG
1 TTTGTCCCGAAGGACCACATAGG
674878 TTTGTCCCGAAGGACCACATAG
1 TTTGTCCCGAAGGACCACATAG
674900 AACCCTTGAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (23 bp):
TTTGTCCCGAAGGACCACATAGG
Found at i:675693 original size:17 final size:15
Alignment explanation
Indices: 675671--675714 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
675661 GTTTTTTCGG
675671 TTCGGTTCGGTTTTT
1 TTCGGTTCGGTTTTT
*
675686 TTAACGGTTCGG-GTTT
1 TT--CGGTTCGGTTTTT
675702 TTCGGTTCGGTTT
1 TTCGGTTCGGTTT
675715 ATCGGTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
14 8 0.33
15 3 0.12
16 5 0.21
17 8 0.33
ACGTcount: A:0.05, C:0.14, G:0.30, T:0.52
Consensus pattern (15 bp):
TTCGGTTCGGTTTTT
Found at i:679225 original size:14 final size:14
Alignment explanation
Indices: 679206--679235 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
679196 TGAATTATTG
*
679206 GAAGTTGATTTCAA
1 GAAGTTAATTTCAA
679220 GAAGTTAATTTCAA
1 GAAGTTAATTTCAA
679234 GA
1 GA
679236 TCGAGGACGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (14 bp):
GAAGTTAATTTCAA
Found at i:683228 original size:58 final size:58
Alignment explanation
Indices: 683153--683293 Score: 246
Period size: 58 Copynumber: 2.4 Consensus size: 58
683143 TCCAGTTTCG
*
683153 CAACACAGTTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACACAACTATTCA
1 CAACTCAGTTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACACAACTATTCA
*
683211 CAACTCAGTTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACACAACTATTCG
1 CAACTCAGTTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACACAACTATTCA
* *
683269 TAACTCAGTTTTCAAATTCGAAACG
1 CAACTCAGTTTTCAAATTCGCAACG
683294 TGAATTTCGT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 79 1.00
ACGTcount: A:0.38, C:0.23, G:0.11, T:0.28
Consensus pattern (58 bp):
CAACTCAGTTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACACAACTATTCA
Found at i:683308 original size:20 final size:20
Alignment explanation
Indices: 683285--683323 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
683275 AGTTTTCAAA
683285 TTCGAAACGT-GAATTTCGTT
1 TTCGAAAC-TCGAATTTCGTT
*
683305 TTCGCAACTCGAATTTCGT
1 TTCGAAACTCGAATTTCGT
683324 AACGCTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (20 bp):
TTCGAAACTCGAATTTCGTT
Found at i:689674 original size:30 final size:31
Alignment explanation
Indices: 689638--689698 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 31
689628 AAAAAGAAAT
689638 ATCTGATTGAG-AGCTATTTATAGGTCTAAA
1 ATCTGATTGAGAAGCTATTTATAGGTCTAAA
* *
689668 ATCTGATTGAGACAGTTATTTGTAGGTCTAA
1 ATCTGATTGAGA-AGCTATTTATAGGTCTAA
689699 TAACATTACC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 11 0.41
32 16 0.59
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (31 bp):
ATCTGATTGAGAAGCTATTTATAGGTCTAAA
Found at i:693801 original size:3 final size:3
Alignment explanation
Indices: 693793--693898 Score: 140
Period size: 3 Copynumber: 34.7 Consensus size: 3
693783 TCATTTAAAT
** * *
693793 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA TTA TTA TTA GTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
693841 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA ATA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
693887 TATA TTA TTA TT
1 T-TA TTA TTA TT
693899 TAATAAATAA
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
3 83 0.93
4 6 0.07
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:703155 original size:114 final size:114
Alignment explanation
Indices: 702954--703175 Score: 390
Period size: 114 Copynumber: 1.9 Consensus size: 114
702944 CACGTTCTCG
* *
702954 TAGTAGGAATAAGGAGATCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 TAGTAGAAATAAGGAGATCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
*
703019 GGTATAAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
66 GGTATAAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTGCTCA
703068 TAGTAGAAATAAGGAGATCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGGAGATCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
* * *
703133 GGTATGAACCCTAAAACTAATCATTGGAATTGAAAGATGAATT
66 GGTATAAACCCCAAAACCAATCATTGGAATTGAAAGATGAATT
703176 GCATGATCGT
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 102 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGATCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
GGTATAAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTGCTCA
Found at i:705334 original size:54 final size:54
Alignment explanation
Indices: 705179--705397 Score: 325
Period size: 54 Copynumber: 4.1 Consensus size: 54
705169 CAATGATTGA
* * *
705179 GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGTGTTATC-AATGATTGA-
1 GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGTGTTGTCAAATGTTTTAC
*
705231 GAACATCTGAGCAGAAGCCACAAAAAAATGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAGCCAC-AAAAAAGGATGAATGTGTTGTCAAATGTTTTAC
705286 GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGTGTTGTCAAATGTTTTAC
** * ***
705340 GAACATCTGAGCAGAAGCCACAGGAAAGGATAAATGCACTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGTGTTGTCAAATGTTTTAC
705394 GAAC
1 GAAC
705398 CTGCGATTCT
Statistics
Matches: 153, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
52 21 0.14
53 20 0.13
54 91 0.59
55 21 0.14
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (54 bp):
GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGTGTTGTCAAATGTTTTAC
Done.