Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007984.1 Hibiscus syriacus cultivar Beakdansim tig00110429_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: 12923621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 28 of 65
Found at i:5551394 original size:23 final size:24
Alignment explanation
Indices: 5551368--5551413 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5551358 GAAAAAGAAA
5551368 AAAAAAGAA-AAAA-AAGAAAAAGG
1 AAAAAAGAAGAAAATAA-AAAAAGG
5551391 AAAAAAGAAGAAAATAAAAAAAG
1 AAAAAAGAAGAAAATAAAAAAAG
5551414 AGGGTCCAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.43
24 10 0.48
25 2 0.10
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (24 bp):
AAAAAAGAAGAAAATAAAAAAAGG
Found at i:5551397 original size:14 final size:13
Alignment explanation
Indices: 5551348--5551399 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 13
5551338 ATTATGCTTG
5551348 AAGAAAAAATGAAA
1 AAGAAAAAA-GAAA
5551362 AAGAAAAAA-AAA
1 AAGAAAAAAGAAA
5551374 GAA-AAAAAAGAAA
1 -AAGAAAAAAGAAA
5551387 AAGGAAAAAAGAA
1 AA-GAAAAAAGAA
5551400 GAAAATAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
12 11 0.32
13 5 0.15
14 18 0.53
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (13 bp):
AAGAAAAAAGAAA
Found at i:5551413 original size:16 final size:15
Alignment explanation
Indices: 5551347--5551414 Score: 64
Period size: 16 Copynumber: 4.1 Consensus size: 15
5551337 TATTATGCTT
5551347 GAAGAAAAAATGAAAAA
1 GAAGAAAAAA--AAAAA
*
5551364 GAAAAAAAAAGAAAAA
1 GAAGAAAAAA-AAAAA
*
5551380 AAAGAAAAAGGAAAAAA
1 GAAGAAAAA--AAAAAA
5551397 GAAGAAAATAAAAAAA
1 GAAGAAAA-AAAAAAA
5551413 GA
1 GA
5551415 GGGTCCAGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
16 21 0.48
17 21 0.48
18 2 0.05
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (15 bp):
GAAGAAAAAAAAAAA
Found at i:5553151 original size:113 final size:113
Alignment explanation
Indices: 5552953--5553404 Score: 649
Period size: 113 Copynumber: 4.0 Consensus size: 113
5552943 TAGCAAAGAT
* *
5552953 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTTATAATGAGAAGAACTTATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * *
5553018 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACATTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAAAAGAACTTGTTCAACCTTTTGC
*
5553066 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
5553131 AGAAGGAAGAAGAAGTTCATAATGAAAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAAAAGAACTTGTTCAACCTTTTGC
* *
5553179 TCAAATCCATCACTTGATGGATCA-ATATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCCG
1 TCAAATCCATCACTTGATGGATCAGCT-TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
* * ** *
5553243 AAGAAGGAAGAAGAAGTTCATAATAAAAAGAATTTACTCAACCTTTTGT
65 AAGAAGGAAGAAGAAGTTCATAATGAAAAGAACTTGTTCAACCTTTTGC
** * * * * * *
5553292 TTGAATTCATTATTTGATGGATCAGCATTGCCAGA-AGGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGA-AAGTTCATAATGAGAAGAACTCATCTG
*
5553356 AAAAAGGAAG-AGAAAGTTCATAATGAAAAGAACTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAG-AAGTTCATAATGAAAAGAACTTGTTCAACCTTTTGC
5553405 ATAACTCTAT
Statistics
Matches: 305, Mismatches: 30, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
112 4 0.01
113 301 0.99
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.27
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAAAAGAACTTGTTCAACCTTTTGC
Found at i:5553544 original size:120 final size:124
Alignment explanation
Indices: 5553312--5553548 Score: 315
Period size: 120 Copynumber: 1.9 Consensus size: 124
5553302 TATTTGATGG
*
5553312 ATCAGCATTGCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAGAAAGTTCAT
1 ATCAACATTGCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAGAAAGTTCAT
* *
5553377 AATGAAAAGAACTTGTTCAACCTTTTGCATAACTCTATCACAAAAGGAGATATATCATC
66 AAGGAAAAGAACTTATTCAACCTTTTGCATAACTCTATCACAAAAGGAGATATATCATC
* * *
5553436 ATCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAA-G-A-AG-AATTTCAT
1 ATCAACATTGCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAGAAAGTTCAT
** * * *
5553497 AAGGAGGAGAATTTATTCAACTTTTTGC-TAGATTAC-ATCACAAAAGGAGATA
66 AAGGAAAAGAACTTATTCAACCTTTTGCATA-ACT-CTATCACAAAAGGAGATA
5553549 AATTGTCATC
Statistics
Matches: 100, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
119 2 0.02
120 47 0.47
121 3 0.03
122 1 0.01
123 1 0.01
124 46 0.46
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (124 bp):
ATCAACATTGCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAGAAAGTTCAT
AAGGAAAAGAACTTATTCAACCTTTTGCATAACTCTATCACAAAAGGAGATATATCATC
Found at i:5553759 original size:3 final size:3
Alignment explanation
Indices: 5553751--5553806 Score: 62
Period size: 3 Copynumber: 18.7 Consensus size: 3
5553741 TTGTTTTTAA
* *
5553751 TAT TAT TAT TAA TA- TAT TAT TAT AAT T-T TATT TAT TAT TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT -TAT
5553796 TAT TAT TAT TA
1 TAT TAT TAT TA
5553807 AATAATTACA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
2 4 0.09
3 36 0.78
4 6 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:5553782 original size:25 final size:27
Alignment explanation
Indices: 5553748--5553801 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
5553738 CATTTGTTTT
5553748 TAATATTA-TTATTA-ATATATTATTA
1 TAATATTATTTATTATATATATTATTA
*
5553773 TAATTTTATTTATTATTATATATTATTA
1 TAATATTATTTATTA-TATATATTATTA
5553801 T
1 T
5553802 TATTAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 7 0.28
26 6 0.24
28 12 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
TAATATTATTTATTATATATATTATTA
Found at i:5555898 original size:23 final size:23
Alignment explanation
Indices: 5555868--5555921 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
5555858 ACAACAACAA
*
5555868 CAAGCATCAATGTACCAATTCAG
1 CAAGCATCAATGCACCAATTCAG
** * *
5555891 CAAGCATCGTTGCATCGATTCAG
1 CAAGCATCAATGCACCAATTCAG
5555914 CAAGCATC
1 CAAGCATC
5555922 CTGCATTAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (23 bp):
CAAGCATCAATGCACCAATTCAG
Found at i:5558021 original size:61 final size:61
Alignment explanation
Indices: 5557949--5558080 Score: 180
Period size: 61 Copynumber: 2.2 Consensus size: 61
5557939 ATATTTATTT
*
5557949 AATTTAGTCCAAATTTAATGATT-TAATATATTAATTTAAGCCTT-ATATTTCAAAATTT-TTC
1 AATTTAATCCAAATTTAATG-TTATAATATATTAATTTAAG-CTTCATATTT-AAAATTTGTTC
* *
5558010 CATTTAATCCAAATTTAATGTTATAATTTATTAATTTAAGCTTCATATTTAAAATTTGTTC
1 AATTTAATCCAAATTTAATGTTATAATATATTAATTTAAGCTTCATATTTAAAATTTGTTC
*
5558071 AATTTGATCC
1 AATTTAATCC
5558081 TTACATATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
60 12 0.19
61 51 0.81
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.48
Consensus pattern (61 bp):
AATTTAATCCAAATTTAATGTTATAATATATTAATTTAAGCTTCATATTTAAAATTTGTTC
Found at i:5558187 original size:51 final size:51
Alignment explanation
Indices: 5558132--5558410 Score: 317
Period size: 51 Copynumber: 5.3 Consensus size: 51
5558122 ATTAATAAAT
*
5558132 TAATATATAGTTTATATATATTTTATAGTTTATATATACTAATGAACTATA
1 TAATATATAGTTTATATATATTATATAGTTTATATATACTAATGAACTATA
*
5558183 TAATATATAGTTTGTATATACCATATACTATATAGGTTATATATACTAATGAACTATA
1 TAATATATAG-TT-TATAT---ATAT--TATATAGTTTATATATACTAATGAACTATA
* **
5558241 TAATATATAATTTATATATACAATATAGTTTATATATACTAATGAACTATA
1 TAATATATAGTTTATATATATTATATAGTTTATATATACTAATGAACTATA
* * **
5558292 TAATATATAGTTTATATATACTATATAGTTTATATATAATGTATAGTTTA-TATA
1 TAATATATAGTTTATATATATTATATAGTTTATATAT-A-CTA-A-TGAACTATA
** * * *
5558346 TACCATATAGTCTATATATATTATATAGTTTATATATACTAATAAATTATA
1 TAATATATAGTTTATATATATTATATAGTTTATATATACTAATGAACTATA
*
5558397 TAATGTATAGTTTA
1 TAATATATAGTTTA
5558411 GGGTTTAGGG
Statistics
Matches: 194, Mismatches: 22, Indels: 24
0.81 0.09 0.10
Matches are distributed among these distances:
50 2 0.01
51 88 0.45
52 5 0.03
53 11 0.06
54 38 0.20
55 2 0.01
56 9 0.05
57 2 0.01
58 37 0.19
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.46
Consensus pattern (51 bp):
TAATATATAGTTTATATATATTATATAGTTTATATATACTAATGAACTATA
Found at i:5558192 original size:33 final size:33
Alignment explanation
Indices: 5558146--5558261 Score: 122
Period size: 33 Copynumber: 3.8 Consensus size: 33
5558136 ATATAGTTTA
* *
5558146 TATATATTTTATAGTTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
*
5558179 TATATAATATATAGTTTGTATATAC-------C
1 TATATAATATATAGTTTATATATACTAATGAAC
* *
5558205 -ATATACTATATAGGTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
*
5558237 TATATAATATATAATTTATATATAC
1 TATATAATATATAGTTTATATATAC
5558262 AATATAGTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 16
0.73 0.10 0.18
Matches are distributed among these distances:
25 21 0.32
26 1 0.02
32 1 0.02
33 43 0.65
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (33 bp):
TATATAATATATAGTTTATATATACTAATGAAC
Found at i:5558202 original size:18 final size:18
Alignment explanation
Indices: 5558132--5558383 Score: 173
Period size: 18 Copynumber: 14.1 Consensus size: 18
5558122 ATTAATAAAT
5558132 TAATATATAGTTTATATA
1 TAATATATAGTTTATATA
* *
5558150 TATTTTATAGTTTATATA
1 TAATATATAGTTTATATA
* *
5558168 TACTA-AT-G--AACTATA
1 TAATATATAGTTTA-TATA
*
5558183 TAATATATAGTTTGTATA
1 TAATATATAGTTTATATA
** * *
5558201 TACCATATACTATATAGGT-
1 TAATATATAGTTTATA--TA
* **
5558220 TATATATACTAATGAACTATA
1 TA-ATATA-TAGTTTA-TATA
*
5558241 TAATATATAATTTATATA
1 TAATATATAGTTTATATA
5558259 TACA-ATATAGTTTATATA
1 TA-ATATATAGTTTATATA
* *
5558277 TACTA-AT-G--AACTATA
1 TAATATATAGTTTA-TATA
5558292 TAATATATAGTTTATATA
1 TAATATATAGTTTATATA
*
5558310 TACTATATAGTTTATATA
1 TAATATATAGTTTATATA
*
5558328 TAATGTATAGTTTATATA
1 TAATATATAGTTTATATA
** *
5558346 TACCATATAGTCTATATA
1 TAATATATAGTTTATATA
*
5558364 TATTATATAGTTTATATA
1 TAATATATAGTTTATATA
5558382 TA
1 TA
5558384 CTAATAAATT
Statistics
Matches: 181, Mismatches: 35, Indels: 36
0.72 0.14 0.14
Matches are distributed among these distances:
14 2 0.01
15 16 0.09
16 6 0.03
17 6 0.03
18 124 0.69
19 9 0.05
20 10 0.06
21 6 0.03
22 2 0.01
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (18 bp):
TAATATATAGTTTATATA
Found at i:5558214 original size:25 final size:25
Alignment explanation
Indices: 5558180--5558228 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
5558170 CTAATGAACT
* *
5558180 ATATAATATATAGTTTGTATATACC
1 ATATAATATATAGGTTATATATACC
*
5558205 ATATACTATATAGGTTATATATAC
1 ATATAATATATAGGTTATATATAC
5558229 TAATGAACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (25 bp):
ATATAATATATAGGTTATATATACC
Found at i:5558247 original size:109 final size:105
Alignment explanation
Indices: 5558132--5558410 Score: 344
Period size: 109 Copynumber: 2.6 Consensus size: 105
5558122 ATTAATAAAT
* *
5558132 TAATATATAGTTTATATATATTTTATAGTTTATATATACTAATGAACTATATAATATATAGTTTG
1 TAATATATAGTTTATATATATTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTA
5558197 TATATACCATATACTATATAGGT-TATATATACTAATGAACTATA
66 TATATACCATATACTATATA--TATA-ATATA-TAATGAA-TATA
* **
5558241 TAATATATAATTTATATATACAATATAGTTTATATATACTAATGAACTATATAATATATAGTTTA
1 TAATATATAGTTTATATATATTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTA
* * * * * **
5558306 TATATACTATATAGTTTATATATAATGTATAGTTTATATA
66 TATATACCATATACTATATATATAATATATAATGAATATA
** * * * *
5558346 TACCATATAGTCTATATATATTATATAGTTTATATATACTAATAAATTATATAATGTATAGTTTA
1 TAATATATAGTTTATATATATTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTA
5558411 GGGTTTAGGG
Statistics
Matches: 148, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
105 60 0.41
106 4 0.03
107 5 0.03
108 2 0.01
109 77 0.52
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.46
Consensus pattern (105 bp):
TAATATATAGTTTATATATATTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTA
TATATACCATATACTATATATATAATATATAATGAATATA
Found at i:5558307 original size:9 final size:9
Alignment explanation
Indices: 5558295--5558381 Score: 56
Period size: 9 Copynumber: 9.7 Consensus size: 9
5558285 AACTATATAA
5558295 TATATAGTT
1 TATATAGTT
*
5558304 TATATA-TAC
1 TATATAGT-T
5558313 TATATAGTT
1 TATATAGTT
*
5558322 TATATA-TAA
1 TATATAGT-T
*
5558331 TGTATAGTT
1 TATATAGTT
*
5558340 TATATA-TAC
1 TATATAGT-T
* *
5558349 CATATAGTC
1 TATATAGTT
5558358 TATATA-TAT
1 TATATAGT-T
5558367 TATATAGTT
1 TATATAGTT
5558376 TATATA
1 TATATA
5558382 TACTAATAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 16
0.70 0.12 0.19
Matches are distributed among these distances:
8 4 0.07
9 52 0.87
10 4 0.07
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (9 bp):
TATATAGTT
Found at i:5558499 original size:18 final size:18
Alignment explanation
Indices: 5558468--5558510 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
5558458 TCATATGTAA
* *
5558468 ATATTAACTATAGTTTAT
1 ATATAAACTATAGTTCAT
* *
5558486 ATGTAAACTGTAGTTCAT
1 ATATAAACTATAGTTCAT
5558504 ATATAAA
1 ATATAAA
5558511 TATCAACCTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (18 bp):
ATATAAACTATAGTTCAT
Found at i:5558547 original size:67 final size:67
Alignment explanation
Indices: 5558476--5558642 Score: 300
Period size: 67 Copynumber: 2.5 Consensus size: 67
5558466 AAATATTAAC
*
5558476 TATAGTTTATATGTAAACTGTAGTTCATATATAAATATCAACCTTAGTATATATATATATT-TAT
1 TATAGTTTATATGTAAACTATAGTTCATATATAAATATCAACCTTAGTATATATATAT-TTATAT
5558540 ATA
65 ATA
*
5558543 TATAGTTTACATGTAAACTATAGTTCATATATAAATATCAACCTTAGTATATATATATTTATATA
1 TATAGTTTATATGTAAACTATAGTTCATATATAAATATCAACCTTAGTATATATATATTTATATA
5558608 TA
66 TA
5558610 TATAGTTTATATGTAAACTATAGTTCATATATA
1 TATAGTTTATATGTAAACTATAGTTCATATATA
5558643 TAGTATATAA
Statistics
Matches: 96, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
66 2 0.02
67 94 0.98
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (67 bp):
TATAGTTTATATGTAAACTATAGTTCATATATAAATATCAACCTTAGTATATATATATTTATATA
TA
Found at i:5558649 original size:18 final size:17
Alignment explanation
Indices: 5558590--5558649 Score: 54
Period size: 18 Copynumber: 3.6 Consensus size: 17
5558580 TCAACCTTAG
5558590 TATATATATA-TT--TA
1 TATATATATAGTTCATA
*
5558604 TATATATATAGTTTATA
1 TATATATATAGTTCATA
* *
5558621 TGTAAACTATAGTTCATA
1 TATATA-TATAGTTCATA
5558639 TATATAGTATA
1 TATATA-TATA
5558650 TAAATATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 10 0.28
15 2 0.06
17 6 0.17
18 18 0.50
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (17 bp):
TATATATATAGTTCATA
Found at i:5558660 original size:33 final size:33
Alignment explanation
Indices: 5558605--5558689 Score: 113
Period size: 33 Copynumber: 2.7 Consensus size: 33
5558595 ATATATTTAT
* *
5558605 ATATATATAGT-T-TATATGTAAACTATAGTTC
1 ATATATATAGTATATAAATATAAACTATAGTTC
*
5558636 ATATATATAGTATATAAATATAAACTATAGTTT
1 ATATATATAGTATATAAATATAAACTATAGTTC
*
5558669 ATATAAATAGTATA-AAATATA
1 ATATATATAGTATATAAATATA
5558690 GTATATAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
31 11 0.23
32 8 0.17
33 29 0.60
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (33 bp):
ATATATATAGTATATAAATATAAACTATAGTTC
Found at i:5558664 original size:20 final size:20
Alignment explanation
Indices: 5558640--5558713 Score: 85
Period size: 20 Copynumber: 3.5 Consensus size: 20
5558630 TAGTTCATAT
5558640 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
5558660 CTATAGTTTATATAAATAGTATAAA
1 ATATAG--TATAT-AA-A-TATAAA
5558685 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
5558705 TTATAGTAT
1 ATATAGTAT
5558714 GTAGTTTATA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
20 19 0.41
21 1 0.02
22 7 0.15
23 7 0.15
24 1 0.02
25 11 0.24
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (20 bp):
ATATAGTATATAAATATAAA
Found at i:5558689 original size:25 final size:23
Alignment explanation
Indices: 5558640--5558700 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
5558630 TAGTTCATAT
5558640 ATATAGTATAT-AA-A-TATAAA
1 ATATAGTATATAAATAGTATAAA
*
5558660 CTATAGTTTATATAAATAGTATAAA
1 ATATAG--TATATAAATAGTATAAA
5558685 ATATAGTATATAAATA
1 ATATAGTATATAAATA
5558701 TAAATTATAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 5 0.15
22 5 0.15
23 12 0.35
24 1 0.03
25 11 0.32
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.38
Consensus pattern (23 bp):
ATATAGTATATAAATAGTATAAA
Found at i:5558692 original size:12 final size:13
Alignment explanation
Indices: 5558653--5558702 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
5558643 TAGTATATAA
5558653 ATATAAACTATAGT
1 ATATAAA-TATAGT
*
5558667 TTATATAA-ATAGT
1 ATATA-AATATAGT
5558680 ATA-AAATATAGT
1 ATATAAATATAGT
5558692 ATATAAATATA
1 ATATAAATATA
5558703 AATTATAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 2 0.06
12 9 0.29
13 14 0.45
14 4 0.13
15 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (13 bp):
ATATAAATATAGT
Found at i:5558701 original size:29 final size:29
Alignment explanation
Indices: 5558669--5558737 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
5558659 ACTATAGTTT
5558669 ATATAAATAGTATAAAATATAG-TATATAA
1 ATATAAATA-TATAAAATATAGTTATATAA
** *
5558698 ATATAAAT-TATAGTATGTAGTTTATATAA
1 ATATAAATATATAAAATATAG-TTATATAA
5558727 ATATAAATATA
1 ATATAAATATA
5558738 AACCCTAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 9 0.26
29 23 0.68
30 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (29 bp):
ATATAAATATATAAAATATAGTTATATAA
Found at i:5558879 original size:13 final size:11
Alignment explanation
Indices: 5558769--5558881 Score: 62
Period size: 11 Copynumber: 10.6 Consensus size: 11
5558759 ATATATAAAC
5558769 TATATAATTTA
1 TATATAATTTA
**
5558780 TAT-TAATAAA
1 TATATAATTTA
5558790 CTATATAATTTA
1 -TATATAATTTA
*
5558802 TACAATATATATTA
1 TA-TATA-AT-TTA
*
5558816 TTTATAA-TTA
1 TATATAATTTA
*
5558826 TACATAA--TA
1 TATATAATTTA
*
5558835 TATA-AA-TTG
1 TATATAATTTA
*
5558844 T-T-TAGTTTA
1 TATATAATTTA
*
5558853 TATATAATTCA
1 TATATAATTTA
5558864 TATATAATTTA
1 TATATAATTTA
5558875 TATATAA
1 TATATAA
5558882 ACTATGTAGT
Statistics
Matches: 76, Mismatches: 16, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
8 4 0.05
9 10 0.13
10 14 0.18
11 30 0.39
12 9 0.12
13 5 0.07
14 4 0.05
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (11 bp):
TATATAATTTA
Found at i:5558985 original size:2 final size:2
Alignment explanation
Indices: 5558973--5559009 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
5558963 TTTATACATA
5558973 AT AT AT A- AT AT AT AT AT -T AT AT AT AT -T 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
5559010 TAGTTGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.09
2 29 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5558985 original size:9 final size:9
Alignment explanation
Indices: 5558973--5559007 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
5558963 TTTATACATA
*
5558973 ATATATAAT
1 ATATATATT
5558982 ATATATATT
1 ATATATATT
5558991 ATATATATT
1 ATATATATT
5559000 ATATATAT
1 ATATATAT
5559008 ATTAGTTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
ATATATATT
Found at i:5559010 original size:11 final size:11
Alignment explanation
Indices: 5558973--5559011 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
5558963 TTTATACATA
*
5558973 ATATATAATAT
1 ATATATTATAT
5558984 ATATA-T-TAT
1 ATATATTATAT
5558993 ATATATTATAT
1 ATATATTATAT
5559004 ATATATTA
1 ATATATTA
5559012 GTTGTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 8 0.32
10 1 0.04
11 16 0.64
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
ATATATTATAT
Found at i:5559416 original size:208 final size:213
Alignment explanation
Indices: 5559049--5559835 Score: 1166
Period size: 208 Copynumber: 3.7 Consensus size: 213
5559039 TATTTATATT
* *
5559049 AATTGGCCCATAACTTTTTAAATGAGTATAATTTAGTACATTTTTGTATTAATTTCAACCTCAAA
1 AATTGGCCCATAACTTTTTAAATGAGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACA
* * *
5559114 ATTTAAAATTATTTTGATTTGATCCCT-T-T-TGTGCTGTTTATTATATTTAAATTTTTATTTGT
66 ATTTAAAATTATTTCGATTTGATCCCTATATGTGTGTTGTTTAATATATTTAAATTTTTATTTGT
* * *
5559176 AATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTACACCTGAAATTGACCCACACTTAT
131 AATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTGACCCATACTTAT
5559241 TACTTATTTATATTTTTA
196 TACTTATTTATATTTTTA
* *
5559259 AATTGGTCCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCA-A
1 AATTGGCCCATAACTTTTTAAATGAGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACA
* *
5559323 ATTT-AAATTATTTTGATTTGATCCCT-T-T-TGTGTTATTTAATATATTTAAATTTTTATTTGT
66 ATTTAAAATTATTTCGATTTGATCCCTATATGTGTGTTGTTTAATATATTTAAATTTTTATTTGT
5559384 AATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTGACCCATACTTAT
131 AATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTGACCCATACTTAT
*
5559449 TACTTATTTCTATTTTTA
196 TACTTATTTATATTTTTA
* * *
5559467 AATTGACCCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACA
1 AATTGGCCCATAACTTTTTAAATGAGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACA
* *
5559532 ATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAATTTTTAAT
66 ATTTAAAATTATTTCGATTTGATCCCT-AT--ATGTGTGTTGTTTAATATATTTAAATTTTTATT
* * * *
5559597 TGTAATTTCATATTTGTTCAATTCAGTTCTCCAAATTTTATTTGCATATGAAATTGATCCATACT
128 TGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTGACCCATACT
*
5559662 TATTACTTAATTCTAT-TTTTTT
193 TATTACTT-ATT-TATATTTTTA
* * *
5559684 AATTGGCCCAGAACTTTTTAAATGAGTATAATTTAGTACTTTTTTGTATTAATTTCAAACTCATA
1 AATTGGCCCATAACTTTTTAAATGAGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACA
*
5559749 ATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAATTTTTATT
66 ATTTAAAATTATTTCGATTTGATCCCT-AT--ATGTGTGTTGTTTAATATATTTAAATTTTTATT
*
5559814 TGTAA---AATATTTGTTCAATTTA
128 TGTAATTTCATATTTGTTCAATTTA
5559836 ATTCTTAAAT
Statistics
Matches: 535, Mismatches: 32, Indels: 16
0.92 0.05 0.03
Matches are distributed among these distances:
208 193 0.36
209 10 0.02
210 81 0.15
212 1 0.00
214 15 0.03
215 1 0.00
216 96 0.18
217 136 0.25
218 2 0.00
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (213 bp):
AATTGGCCCATAACTTTTTAAATGAGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACA
ATTTAAAATTATTTCGATTTGATCCCTATATGTGTGTTGTTTAATATATTTAAATTTTTATTTGT
AATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTGACCCATACTTAT
TACTTATTTATATTTTTA
Found at i:5560452 original size:26 final size:26
Alignment explanation
Indices: 5560423--5560480 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
5560413 ACACAAAAAT
*
5560423 AATATAATTA-ATAAATAAAAATTAAG
1 AATATAATTACATAAATAAAAA-TAAA
** *
5560449 AATATTTTTACATTAATAAAAATAAA
1 AATATAATTACATAAATAAAAATAAA
5560475 AATATA
1 AATATA
5560481 CAAAATATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (26 bp):
AATATAATTACATAAATAAAAATAAA
Found at i:5560575 original size:25 final size:24
Alignment explanation
Indices: 5560508--5560575 Score: 61
Period size: 25 Copynumber: 2.8 Consensus size: 24
5560498 ATTTAATATT
*
5560508 ATATATATTTATTAATATAATAGGA
1 ATATATATTTATTAATATATTA-GA
* *
5560533 ATATATA-ATA-TAAAATATTA-A
1 ATATATATTTATTAATATATTAGA
5560554 AGTCATATATTTATTAATATAT
1 A-T-ATATATTTATTAATATAT
5560576 GCGAATAGGA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
21 2 0.06
22 1 0.03
23 13 0.38
24 4 0.12
25 14 0.41
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.44
Consensus pattern (24 bp):
ATATATATTTATTAATATATTAGA
Found at i:5561453 original size:384 final size:387
Alignment explanation
Indices: 5560692--5561470 Score: 1061
Period size: 389 Copynumber: 2.0 Consensus size: 387
5560682 AAAGTAAAAT
* *
5560692 AAATTTGGTCCTCCAATCAAATGATAAAACTTGTCATTATTTTAATTTATTAAAATGAGGACCAA
1 AAATTTAGTCATCCAATCAAATGATAAAACTTGTCATTATTTTAATTTATTAAAATGAGGACCAA
* *
5560757 ATTGAAAGAATATATAAGTAACATGGAAAAATTATGTAATTATACCAAAATGTTTTTAACTGCCA
66 ATTGAAAGAATATATAAGTAACATGGAAAAATTATGTAATTATACCAAAATATTTTCAACTGCCA
* * * *
5560822 TGTCACCTATTCATTTAACTGTTAATGGATGATGACTTGATTGAAGCATTTAGATAGTTGGATGG
131 TGTCACCTATTCAGTTAACTATTAACGGATGATGACTTGATTGAAGCATTTAGATAGTTGAATGG
* * * *
5560887 TCTTTTTGATTAAATTGAAACATCAATGGTCAAAATGATTTTTAACCATAGTTGGGTGGTCACCT
196 TCTTTTTGATCAAATTGAAACATCAATGGTCAAAATAATTTTTAACAATAGTT-GGTGATCA-C-
* * *
5560952 GTTTACTTTTTTTTATAATTATGTTTTTCTTTCCTTGGATTGGGGAAAATTCTAGACTGCATGTC
258 GTTTACTTTTTTATATAATTATGTTTTTCTTTCCTTGGATTAGGGAAAATTCTAGAATGCATGTC
* * *
5561017 CATTCATTGCAATTTACCGCTAATTTTATAATGTAAAATTTACAAATGGTCATTAAATTATGTCA
323 CATTAATTGCAATTTACCACTAATTTTATAACGTAAAATTTACAAATGGTCATTAAATTATGTCA
* *
5561082 AAATTTAGTCATCCAATCAAATGATGACACGTT-TCATTATTTTAATTTATTAAAATGAGGACCA
1 AAATTTAGTCATCCAATCAAATGATAAAAC-TTGTCATTATTTTAATTTATTAAAATGAGGACCA
* * * ** *
5561146 AATTGAAATATTATATAAGTAATATGG-ACGATTATGTAATTATACCAAAATATTTTCAACTTCC
65 AATTGAAAGAATATATAAGTAACATGGAAAAATTATGTAATTATACCAAAATATTTTCAACTGCC
* * *
5561210 ATGTCA-CTTTTTACGTTAACTATTAACGG-TGGATGGCTTGATTGAAGCATTTAGATAGTTGAA
130 ATGTCACCTATTCA-GTTAACTATTAACGGAT-GATGACTTGATTGAAGCATTTAGATAGTTGAA
* ** * *
5561273 TGGTCTTTTTGATCCAATTGAAACATCGGTGGTTAAAATAATTTTTGACAATAGTT-G-GAT-A-
193 TGGTCTTTTTGATCAAATTGAAACATCAATGGTCAAAATAATTTTTAACAATAGTTGGTGATCAC
* * *
5561334 GTTTACCCTTTTTTATATACTTATGTTTTTCTTTCCTTGGATTAGGGAAAATTCTGGAATGTATG
258 GTTTA--CTTTTTTATATAATTATGTTTTTCTTTCCTTGGATTAGGGAAAATTCTAGAATGCATG
* * *
5561399 TCCATTAATTGGAATTTACTACTAATTTTATAGCGTAAAATTTACAAATGGTCATTAAATTATGT
321 TCCATTAATTGCAATTTACCACTAATTTTATAACGTAAAATTTACAAATGGTCATTAAATTATGT
*
5561464 TA
386 CA
5561466 AAATT
1 AAATT
5561471 ATTCTTTTGA
Statistics
Matches: 343, Mismatches: 41, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
382 5 0.01
384 117 0.34
385 1 0.00
386 2 0.01
387 1 0.00
388 6 0.02
389 128 0.37
390 81 0.24
391 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.40
Consensus pattern (387 bp):
AAATTTAGTCATCCAATCAAATGATAAAACTTGTCATTATTTTAATTTATTAAAATGAGGACCAA
ATTGAAAGAATATATAAGTAACATGGAAAAATTATGTAATTATACCAAAATATTTTCAACTGCCA
TGTCACCTATTCAGTTAACTATTAACGGATGATGACTTGATTGAAGCATTTAGATAGTTGAATGG
TCTTTTTGATCAAATTGAAACATCAATGGTCAAAATAATTTTTAACAATAGTTGGTGATCACGTT
TACTTTTTTATATAATTATGTTTTTCTTTCCTTGGATTAGGGAAAATTCTAGAATGCATGTCCAT
TAATTGCAATTTACCACTAATTTTATAACGTAAAATTTACAAATGGTCATTAAATTATGTCA
Found at i:5567864 original size:44 final size:44
Alignment explanation
Indices: 5567732--5567867 Score: 143
Period size: 44 Copynumber: 3.2 Consensus size: 44
5567722 AGGTCTTATG
* * *
5567732 GATGGCCCGAACGA--CTT-ATCATCTTGCTCGAAAGACTTACA
1 GATGGCCCGAAGGATTCTTAATCATCATGCTCGAAAGACTTACT
* * ** * *
5567773 AATGACAAGAAGGATTTTTAATCATCATGCTCGAAATACTTACT
1 GATGGCCCGAAGGATTCTTAATCATCATGCTCGAAAGACTTACT
* * *
5567817 GATGGCCCGAAGGATTCTTAATCATCATGTTTGAAAGACTTATT
1 GATGGCCCGAAGGATTCTTAATCATCATGCTCGAAAGACTTACT
5567861 GATGGCC
1 GATGGCC
5567868 TGCACGACTT
Statistics
Matches: 74, Mismatches: 18, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
41 9 0.12
43 2 0.03
44 63 0.85
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (44 bp):
GATGGCCCGAAGGATTCTTAATCATCATGCTCGAAAGACTTACT
Found at i:5567985 original size:194 final size:194
Alignment explanation
Indices: 5567608--5568062 Score: 671
Period size: 194 Copynumber: 2.4 Consensus size: 194
5567598 CTTATCATTT
** ** * *
5567608 TGCTCGAAAGACTTACAAATGAACCGAAAGA-T-TTCATCATCATGCTCGAAAGACTTATTGATG
1 TGCTCGAAAGACTTACTGATGGCCCGAAAAATTCTTAATCATCATGCTCGAAAGACTTATTGATG
*
5567671 ACCCACAAGACTTACTAAATTCTTTTTTTTTTGTGAAAACATCCTACCCGAAGGTCTTATGGATG
66 GCCCACAAGACTTACTAAATTCTTTTTTTTTTGTGAAAACATCCTACCCGAAGGTCTTATGGATG
* * *
5567736 GCCCGAACGACTTATCATCTTGCTCGAAAGACTTACAAATGACAAGAAGGATTTTTAATCATCA
131 GCCCGAACGACTTATCATCTTGCTCAAAAGACTTACAAATAACAAGAAGGATTTTTAATCATAA
* ** * *
5567800 TGCTCGAAATACTTACTGATGGCCCGAAGGATTCTTAATCATCATGTTTGAAAGACTTATTGATG
1 TGCTCGAAAGACTTACTGATGGCCCGAAAAATTCTTAATCATCATGCTCGAAAGACTTATTGATG
** *
5567865 GCCTGCACGACTTACTAAATTCTTTTTTTTTTGTGAAAACATCCTACCCGAAGGTCTTATGGATG
66 GCCCACAAGACTTACTAAATTCTTTTTTTTTTGTGAAAACATCCTACCCGAAGGTCTTATGGATG
* * ** *
5567930 GCCTGATCGACTTATCATCTTGCTCAAAAGACTTACAAATAACCCGAATGATTTTTAATCATAA
131 GCCCGAACGACTTATCATCTTGCTCAAAAGACTTACAAATAACAAGAAGGATTTTTAATCATAA
* *
5567994 TGCTCGAAAGGCTTACTGATGGCCCGAAAAATTCTTAATCATCATGCTCAAAAGACTTATTGATG
1 TGCTCGAAAGACTTACTGATGGCCCGAAAAATTCTTAATCATCATGCTCGAAAGACTTATTGATG
5568059 GCCC
66 GCCC
5568063 GAAGGACTTA
Statistics
Matches: 232, Mismatches: 29, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
192 25 0.11
193 1 0.00
194 206 0.89
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (194 bp):
TGCTCGAAAGACTTACTGATGGCCCGAAAAATTCTTAATCATCATGCTCGAAAGACTTATTGATG
GCCCACAAGACTTACTAAATTCTTTTTTTTTTGTGAAAACATCCTACCCGAAGGTCTTATGGATG
GCCCGAACGACTTATCATCTTGCTCAAAAGACTTACAAATAACAAGAAGGATTTTTAATCATAA
Found at i:5568020 original size:44 final size:44
Alignment explanation
Indices: 5567950--5568065 Score: 133
Period size: 44 Copynumber: 2.6 Consensus size: 44
5567940 CTTATCATCT
** ** ** *
5567950 TGCTCAAAAGACTTACAAATAACCCGAATGATTTTTAATCATAA
1 TGCTCAAAAGACTTACTGATGGCCCGAAAAATTCTTAATCATAA
* * *
5567994 TGCTCGAAAGGCTTACTGATGGCCCGAAAAATTCTTAATCATCA
1 TGCTCAAAAGACTTACTGATGGCCCGAAAAATTCTTAATCATAA
*
5568038 TGCTCAAAAGACTTATTGATGGCCCGAA
1 TGCTCAAAAGACTTACTGATGGCCCGAA
5568066 GGACTTATAA
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 59 1.00
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.28
Consensus pattern (44 bp):
TGCTCAAAAGACTTACTGATGGCCCGAAAAATTCTTAATCATAA
Found at i:5568280 original size:42 final size:41
Alignment explanation
Indices: 5568180--5568285 Score: 113
Period size: 42 Copynumber: 2.6 Consensus size: 41
5568170 CCCGAAGGTT
* * * * *
5568180 TTATGGATGGCCCGAAGGACTTATCATCTTACTCTAAAGGC
1 TTATAGATGGCCCGAAGGACTTAGCATCATACTCGAAAGAC
* * * *
5568221 TTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGAC
1 TTATAGATGGCCCGAAGGACTT-AGCATCATACTCGAAAGAC
*
5568263 TTATTGATGGCCCGAAGGACTTA
1 TTATAGATGGCCCGAAGGACTTA
5568286 CTAAATGTGA
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
41 19 0.37
42 32 0.63
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (41 bp):
TTATAGATGGCCCGAAGGACTTAGCATCATACTCGAAAGAC
Found at i:5568387 original size:215 final size:215
Alignment explanation
Indices: 5568000--5568954 Score: 1186
Period size: 215 Copynumber: 4.3 Consensus size: 215
5567990 ATAATGCTCG
* * ** * * *
5568000 AAAGGCTTACTGATGGCCCGAAAAATTCTTAATCATCATGCTCAAAAGACTTATTGATGGCCCGA
1 AAAGGCTTACAGATGACCCGAAGGA-T-TTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGA
* * * * *
5568065 AGGACTTATAAA-GTGCGAAA-TATGGAAATCGCCTTCTTACTTTTCAAATATCTCATTTTTTTA
64 AGGACTTATAAATGTG-AAAATTTTGGAAATCGCCTTCTTACTTTTCAAAGATTTCATTTTCTTA
* * *
5568128 AAACATCACTT-TCATTTTTCAAATTCATGTCAAAACATCCTACCCGAAGGTTTTATGGATGGCC
128 AAACATCATTTCTCATTTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCC
*
5568192 CGAAGGACTTATCATCTTACTCT
193 CGAAGGACTTATCATCTTACTCA
*
5568215 AAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCCGAAG
1 AAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAG
* * *
5568280 GACTTACTAAATGTG-AAATTTTGGAAATCGCCTTCTTAGTTTTCAAAAATTTCATCTTCTTAAA
66 GACTTA-TAAATGTGAAAATTTTGGAAATCGCCTTCTTACTTTTCAAAGATTTCATTTTCTTAAA
*
5568344 ACATCATTTTCTCA-TTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCC
130 ACATCA-TTTCTCATTTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCC
*
5568408 GAAGGACTTATCATCTTGCTCA
194 GAAGGACTTATCATCTTACTCA
* *
5568430 AAAGGCTTACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTAATGATGGCCCGAAG
1 AAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAG
* ** * *
5568495 GACTTATATA-GTGCGAATTATTGGAAATCTCCTTCTTACTTCTCAAAGATTTCATTTTCTTAAA
66 GACTTATAAATGTGAAAATT-TTGGAAATCGCCTTCTTACTTTTCAAAGATTTCATTTTCTTAAA
* * *
5568559 ACAATAATTTCTCATTTTTCAATTTCAAGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCC
130 AC-ATCATTTCTCATTTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCC
* *
5568624 GAATGACTTATCATCTTGCTTAAAAGGCTTTA
194 GAAGGACTTATCA---T-CTT---A--C-TCA
*
5568656 AAAGGCTTACAGATGACCCGAAGGATTTAAGCATCAAGCTCGAAAGACTTACTGATGGCCCGAAG
1 AAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAG
* * * *
5568721 GACTTATAAATTTCGAAAATAGTTTACTAGGTAAGAAAC-CTTTCTTACTTTTCAAAGATTCCAT
66 GACTTATAAATGT-G-AAA-A-TTT--T-GG--A-AATCGCCTTCTTACTTTTCAAAGATTTCAT
* *
5568785 TTTCTTAAAACATTACTTTCTCCTTTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTAT
121 TTTCTTAAAACATCA-TTTCTCATTTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTAT
* *
5568850 GGATGGCCCAAAGGACTTATCATCTTGCTCA
185 GGATGGCCCGAAGGACTTATCATCTTACTCA
* * * *
5568881 AAAGGCTTACACATGACTCGAAGGATTTAAGCATCAAGCTCGAAAGACTTACCGATGGCCCGAAG
1 AAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAG
5568946 GACTTATAA
66 GACTTATAA
5568955 TATTTGGAAA
Statistics
Matches: 655, Mismatches: 54, Indels: 52
0.86 0.07 0.07
Matches are distributed among these distances:
213 49 0.07
214 57 0.09
215 212 0.32
216 65 0.10
219 1 0.00
220 3 0.00
225 74 0.11
226 74 0.11
227 1 0.00
228 1 0.00
229 1 0.00
230 2 0.00
231 5 0.01
232 2 0.00
233 2 0.00
234 3 0.00
235 100 0.15
236 3 0.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Consensus pattern (215 bp):
AAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAG
GACTTATAAATGTGAAAATTTTGGAAATCGCCTTCTTACTTTTCAAAGATTTCATTTTCTTAAAA
CATCATTTCTCATTTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGA
AGGACTTATCATCTTACTCA
Found at i:5568470 original size:42 final size:41
Alignment explanation
Indices: 5568400--5568501 Score: 134
Period size: 42 Copynumber: 2.5 Consensus size: 41
5568390 AGGTTTTATG
* *
5568400 GATGGCCCGAAGGACTTATCATCTTGCTCAAAAGGCTTACA-
1 GATGGCCCGAAGGACTTATCATCATGCTCAAAAGACTTA-AT
* * *
5568441 GATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTAAT
1 GATGGCCCGAAGGACTT-ATCATCATGCTCAAAAGACTTAAT
5568483 GATGGCCCGAAGGACTTAT
1 GATGGCCCGAAGGACTTAT
5568502 ATAGTGCGAA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
41 18 0.35
42 34 0.65
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTATCATCATGCTCAAAAGACTTAAT
Found at i:5572200 original size:18 final size:17
Alignment explanation
Indices: 5572156--5572207 Score: 86
Period size: 17 Copynumber: 2.9 Consensus size: 17
5572146 CAAACAAGAT
5572156 GTTTCAAATGACAAAAA
1 GTTTCAAATGACAAAAA
5572173 GTTTCAAATGACAAAAA
1 GTTTCAAATGACAAAAA
5572190 GTTTCATAATGAACAAAA
1 GTTTCA-AATG-ACAAAA
5572208 TGATTTCTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 23 0.70
18 4 0.12
19 6 0.18
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.25
Consensus pattern (17 bp):
GTTTCAAATGACAAAAA
Found at i:5578605 original size:14 final size:14
Alignment explanation
Indices: 5578586--5578618 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
5578576 ACATCGGTTC
5578586 CCTCTCTAGCCCTA
1 CCTCTCTAGCCCTA
5578600 CCTCTCTAGCCCTA
1 CCTCTCTAGCCCTA
5578614 -CTCTC
1 CCTCTC
5578619 CTCTCCGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.12, C:0.52, G:0.06, T:0.30
Consensus pattern (14 bp):
CCTCTCTAGCCCTA
Found at i:5580302 original size:15 final size:15
Alignment explanation
Indices: 5580265--5580311 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
5580255 GAAGAATATC
**
5580265 AAGAAAAA-AAGATG
1 AAGAAAAAGAAGAAA
*
5580279 AAG-AAAAGAAGGAA
1 AAGAAAAAGAAGAAA
5580293 AAGAAAAAGAAGAAA
1 AAGAAAAAGAAGAAA
5580308 AAGA
1 AAGA
5580312 TCGGTGTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 4 0.15
14 9 0.33
15 14 0.52
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (15 bp):
AAGAAAAAGAAGAAA
Found at i:5584527 original size:31 final size:31
Alignment explanation
Indices: 5584489--5584561 Score: 119
Period size: 31 Copynumber: 2.4 Consensus size: 31
5584479 TGGGGCTCTA
*
5584489 AATCAAGCAAAGAAAAAATGTCATCTTCATT
1 AATCAAGCAAAGAAAAAATGTCATCTTCATC
*
5584520 AATCAAGCAAAGAAAAGATGTCATCTTCATC
1 AATCAAGCAAAGAAAAAATGTCATCTTCATC
*
5584551 AATAAAGCAAA
1 AATCAAGCAAA
5584562 ATACATCAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.51, C:0.16, G:0.11, T:0.22
Consensus pattern (31 bp):
AATCAAGCAAAGAAAAAATGTCATCTTCATC
Found at i:5585704 original size:14 final size:15
Alignment explanation
Indices: 5585654--5585707 Score: 74
Period size: 15 Copynumber: 3.7 Consensus size: 15
5585644 GGTTTAGTCA
* *
5585654 CCGAGTTAAATCAGT
1 CCGAGTCAACTCAGT
5585669 CCGAGTCAACTCAGT
1 CCGAGTCAACTCAGT
*
5585684 CCAAGTCAACTC-GT
1 CCGAGTCAACTCAGT
5585698 CCGAGTCAAC
1 CCGAGTCAAC
5585708 CCATTGACTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
14 11 0.31
15 24 0.69
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.20
Consensus pattern (15 bp):
CCGAGTCAACTCAGT
Found at i:5586627 original size:28 final size:27
Alignment explanation
Indices: 5586566--5586628 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
5586556 ATAGAATTAC
* *
5586566 CCCCTGAAGTAAAAAATGACCAAAATG
1 CCCCTAAAGTAAAAAATGACCAAAATA
* *
5586593 CCCCTAAAGTGAAAAATGACCTAAAGTA
1 CCCCTAAAGTAAAAAATGACC-AAAATA
*
5586621 CCTCTAAA
1 CCCCTAAA
5586629 CCCTAGAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 19 0.63
28 11 0.37
ACGTcount: A:0.46, C:0.24, G:0.13, T:0.17
Consensus pattern (27 bp):
CCCCTAAAGTAAAAAATGACCAAAATA
Found at i:5600844 original size:20 final size:20
Alignment explanation
Indices: 5600777--5600855 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 20
5600767 TATGTACACT
5600777 TAGTATCGATATTGTTCATC
1 TAGTATCGATATTGTTCATC
* * * * * * *
5600797 CAATACCAATACTGTTCTTTGT
1 TAGTATCGATATTGTTC-AT-C
5600819 TAGTATCGATATTGTTCATC
1 TAGTATCGATATTGTTCATC
5600839 TAGTATCGATATTGTTC
1 TAGTATCGATATTGTTC
5600856 TTGCAGCCTT
Statistics
Matches: 43, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
20 29 0.67
21 2 0.05
22 12 0.28
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.44
Consensus pattern (20 bp):
TAGTATCGATATTGTTCATC
Found at i:5603480 original size:21 final size:21
Alignment explanation
Indices: 5603463--5603531 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
5603453 ATGTAGTATC
5603463 GATACTACTTAGTG-TAGTACT
1 GATACT-CTTAGTGATAGTACT
*
5603484 GATACTCTTAGTGATGGTACT
1 GATACTCTTAGTGATAGTACT
* *
5603505 GATACTCTTAGTGATGGTACC
1 GATACTCTTAGTGATAGTACT
5603526 GATACT
1 GATACT
5603532 ACCTTTTTGG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.16
21 38 0.84
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (21 bp):
GATACTCTTAGTGATAGTACT
Found at i:5605789 original size:15 final size:15
Alignment explanation
Indices: 5605771--5605808 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
5605761 AACCAGAGAA
5605771 AAAGAAAGAAGAGCC
1 AAAGAAAGAAGAGCC
*
5605786 AAAGAAAGAGGAGCC
1 AAAGAAAGAAGAGCC
*
5605801 CAAGAAAG
1 AAAGAAAG
5605809 TAGAAGAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.58, C:0.13, G:0.29, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAGAGCC
Found at i:5608815 original size:19 final size:20
Alignment explanation
Indices: 5608782--5608821 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
5608772 TCAAGAGAAG
*
5608782 AAAAAACTCAAAAAGGAAATA
1 AAAAAACTC-AAAAGCAAATA
5608803 AAAAAACTC-AAAGCAAATA
1 AAAAAACTCAAAAGCAAATA
5608822 TCCTATGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.70, C:0.12, G:0.07, T:0.10
Consensus pattern (20 bp):
AAAAAACTCAAAAGCAAATA
Found at i:5621488 original size:21 final size:22
Alignment explanation
Indices: 5621464--5621530 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 22
5621454 AACAATGATG
5621464 TAGTATC-GATACTACTTAGTG-
1 TAGTATCTGATACT-CTTAGTGA
5621485 TAGTAGTACTGATACTCTTAGTGA
1 TAGTA-T-CTGATACTCTTAGTGA
*
5621509 TGGTA-CTGATACTCTTAGTGA
1 TAGTATCTGATACTCTTAGTGA
5621530 T
1 T
5621531 GGTACCGATA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
21 22 0.54
22 1 0.02
23 8 0.20
24 10 0.24
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (22 bp):
TAGTATCTGATACTCTTAGTGA
Found at i:5621531 original size:21 final size:21
Alignment explanation
Indices: 5621471--5621542 Score: 99
Period size: 21 Copynumber: 3.3 Consensus size: 21
5621461 ATGTAGTATC
*
5621471 GATACTACTTAGTGTAGTAGTACT
1 GATACT-CTTAGTG-A-TGGTACT
5621495 GATACTCTTAGTGATGGTACT
1 GATACTCTTAGTGATGGTACT
*
5621516 GATACTCTTAGTGATGGTACC
1 GATACTCTTAGTGATGGTACT
5621537 GATACT
1 GATACT
5621543 ACCTTTTTGG
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
21 32 0.70
22 1 0.02
23 7 0.15
24 6 0.13
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.36
Consensus pattern (21 bp):
GATACTCTTAGTGATGGTACT
Found at i:5623801 original size:15 final size:15
Alignment explanation
Indices: 5623783--5623820 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
5623773 AACCAGAGAA
5623783 AAAGAAAGAAGAGCC
1 AAAGAAAGAAGAGCC
*
5623798 AAAGAAAGAGGAGCC
1 AAAGAAAGAAGAGCC
*
5623813 CAAGAAAG
1 AAAGAAAG
5623821 TAGAAGAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.58, C:0.13, G:0.29, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAGAGCC
Found at i:5626829 original size:19 final size:20
Alignment explanation
Indices: 5626796--5626835 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
5626786 TCAAGAGAAG
*
5626796 AAAAAACTCAAAAAGGAAATA
1 AAAAAACTC-AAAAGCAAATA
5626817 AAAAAACTC-AAAGCAAATA
1 AAAAAACTCAAAAGCAAATA
5626836 TCCTATGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.70, C:0.12, G:0.07, T:0.10
Consensus pattern (20 bp):
AAAAAACTCAAAAGCAAATA
Found at i:5633962 original size:28 final size:27
Alignment explanation
Indices: 5633906--5633962 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
5633896 TTGCCCACTG
*
5633906 AAGTGAAAAATGACCAAAATGCCCCTA
1 AAGTGAAAAATGACCAAAATACCCCTA
* *
5633933 AAGTGAAAAATGACCTAAAGTACCTCTA
1 AAGTGAAAAATGACC-AAAATACCCCTA
5633961 AA
1 AA
5633963 CCCTAGAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 15 0.58
28 11 0.42
ACGTcount: A:0.49, C:0.19, G:0.14, T:0.18
Consensus pattern (27 bp):
AAGTGAAAAATGACCAAAATACCCCTA
Found at i:5638721 original size:25 final size:24
Alignment explanation
Indices: 5638664--5638721 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
5638654 AAGTAAAGGG
* **
5638664 AAGTATTTTTTCAAGTAAACTTGG
1 AAGTTTTTTTTCAAGTAAACTTAA
*
5638688 GAGTATTTTTTTCAAGTAAATCTTAA
1 AAGT-TTTTTTTCAAGTAAA-CTTAA
5638714 AAGTTTTT
1 AAGTTTTT
5638722 AAATTTTTGT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
24 3 0.11
25 18 0.67
26 6 0.22
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.47
Consensus pattern (24 bp):
AAGTTTTTTTTCAAGTAAACTTAA
Found at i:5639195 original size:21 final size:21
Alignment explanation
Indices: 5639146--5639223 Score: 95
Period size: 21 Copynumber: 3.6 Consensus size: 21
5639136 TACCATATAC
*
5639146 GGTATTGATACTACTTAGTGTAGT
1 GGTACTGATACT-CTTAGTG-A-T
*
5639170 AGTACTGATACTCTTAGTGAT
1 GGTACTGATACTCTTAGTGAT
5639191 GGTACTGATACTCTTAGTGAT
1 GGTACTGATACTCTTAGTGAT
5639212 GGTA-TCGATACT
1 GGTACT-GATACT
5639224 ACCTTTTTGG
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.02
21 31 0.62
22 1 0.02
23 7 0.14
24 10 0.20
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (21 bp):
GGTACTGATACTCTTAGTGAT
Found at i:5641481 original size:15 final size:15
Alignment explanation
Indices: 5641463--5641500 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
5641453 AACCAGAGAA
5641463 AAAGAAAGAAGAGCC
1 AAAGAAAGAAGAGCC
*
5641478 AAAGAAAGAGGAGCC
1 AAAGAAAGAAGAGCC
*
5641493 CAAGAAAG
1 AAAGAAAG
5641501 TAGAAGAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.58, C:0.13, G:0.29, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAGAGCC
Found at i:5644508 original size:19 final size:20
Alignment explanation
Indices: 5644475--5644514 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
5644465 TCAAGAGAAG
*
5644475 AAAAAACTCAAAAAGGAAATA
1 AAAAAACTC-AAAAGCAAATA
5644496 AAAAAACTC-AAAGCAAATA
1 AAAAAACTCAAAAGCAAATA
5644515 TCCTATGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.70, C:0.12, G:0.07, T:0.10
Consensus pattern (20 bp):
AAAAAACTCAAAAGCAAATA
Found at i:5649925 original size:3 final size:3
Alignment explanation
Indices: 5649917--5649943 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5649907 ACTAGGTCCA
5649917 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
5649944 AAAAAACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5651305 original size:22 final size:23
Alignment explanation
Indices: 5651233--5651305 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
5651223 TGACCCTAAG
* * *
5651233 GACCGCATAGAATATTTCTCGAAA
1 GACCACATAGAA-ATGTCCCGAAA
* * *
5651257 GACCACGTAGAAATGTCCTGAAG
1 GACCACATAGAAATGTCCCGAAA
* *
5651280 GACCACATAG-ATTGTCCCGAAC
1 GACCACATAGAAATGTCCCGAAA
5651302 GACC
1 GACC
5651306 TTGTAGAACC
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
22 13 0.33
23 16 0.41
24 10 0.26
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19
Consensus pattern (23 bp):
GACCACATAGAAATGTCCCGAAA
Found at i:5651542 original size:15 final size:16
Alignment explanation
Indices: 5651522--5651551 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5651512 ATATATATAT
5651522 ATATAACA-TTTTCAA
1 ATATAACACTTTTCAA
5651537 ATATAACACTTTTCA
1 ATATAACACTTTTCA
5651552 CGTAGAACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAACACTTTTCAA
Found at i:5651631 original size:17 final size:17
Alignment explanation
Indices: 5651609--5651642 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5651599 ATAGAACTTG
5651609 TTCTCATAACATTTATT
1 TTCTCATAACATTTATT
*
5651626 TTCTCATAGCATTTATT
1 TTCTCATAACATTTATT
5651643 CAATATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.18, G:0.03, T:0.53
Consensus pattern (17 bp):
TTCTCATAACATTTATT
Found at i:5657616 original size:15 final size:15
Alignment explanation
Indices: 5657592--5657642 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
5657582 ATATATATAT
*
5657592 ATATATAACATTTTC
1 ATATAGAACATTTTC
5657607 ATATAGAACACTTTTC
1 ATATAGAACA-TTTTC
* *
5657623 ACT-TAGCACATTATC
1 A-TATAGAACATTTTC
5657638 ATATA
1 ATATA
5657643 TATATAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
16 12 0.40
17 1 0.03
ACGTcount: A:0.39, C:0.18, G:0.04, T:0.39
Consensus pattern (15 bp):
ATATAGAACATTTTC
Found at i:5657677 original size:64 final size:62
Alignment explanation
Indices: 5657542--5657679 Score: 215
Period size: 62 Copynumber: 2.2 Consensus size: 62
5657532 CACTTATCAC
* *
5657542 ATTCACGTAGAACCTTTTCACTTAGCACATTATCATATATATATATATATATATATAACATT
1 ATTCACATAGAACCTTTTCACTTAGCACATTATCATATATATATAAATATATATATAACATT
* *
5657604 -TTCATATAGAACACTTTTCACTTAGCACATTATCATATATATATAAATATATATATATCATTT
1 ATTCACATAGAAC-CTTTTCACTTAGCACATTATCATATATATATAAATATATATATAACA-TT
5657667 ATTCACATAGAAC
1 ATTCACATAGAAC
5657680 TTGTTCTCAT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
61 10 0.15
62 45 0.66
63 2 0.03
64 11 0.16
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (62 bp):
ATTCACATAGAACCTTTTCACTTAGCACATTATCATATATATATAAATATATATATAACATT
Found at i:5658163 original size:22 final size:22
Alignment explanation
Indices: 5658133--5658203 Score: 55
Period size: 22 Copynumber: 3.5 Consensus size: 22
5658123 CCCTTCTATA
*
5658133 GTACCGATACTTATCTCTTATG
1 GTACTGATACTTATCTCTTATG
* * *
5658155 GTACTGATAC---CCCCTCA--
1 GTACTGATACTTATCTCTTATG
5658172 GTA-TCGATACTTATCTCTTATG
1 GTACT-GATACTTATCTCTTATG
5658194 GTACTGATAC
1 GTACTGATAC
5658204 CCCCTCAGTA
Statistics
Matches: 35, Mismatches: 7, Indels: 14
0.62 0.12 0.25
Matches are distributed among these distances:
16 1 0.03
17 8 0.23
19 4 0.11
20 4 0.11
22 17 0.49
23 1 0.03
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.37
Consensus pattern (22 bp):
GTACTGATACTTATCTCTTATG
Found at i:5658181 original size:39 final size:39
Alignment explanation
Indices: 5658132--5658220 Score: 169
Period size: 39 Copynumber: 2.3 Consensus size: 39
5658122 CCCCTTCTAT
*
5658132 AGTACCGATACTTATCTCTTATGGTACTGATACCCCCTC
1 AGTATCGATACTTATCTCTTATGGTACTGATACCCCCTC
5658171 AGTATCGATACTTATCTCTTATGGTACTGATACCCCCTC
1 AGTATCGATACTTATCTCTTATGGTACTGATACCCCCTC
5658210 AGTATCGATAC
1 AGTATCGATAC
5658221 CATTTTGGCA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.34
Consensus pattern (39 bp):
AGTATCGATACTTATCTCTTATGGTACTGATACCCCCTC
Found at i:5661600 original size:27 final size:30
Alignment explanation
Indices: 5661569--5661636 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
5661559 AAACCTTTTA
5661569 TCTTC-CT-TCATTTTCTTCTCTT-T-ATTT
1 TCTTCTCTCTCATTTTCTTCT-TTCTCATTT
*
5661596 TCTTCTTTCTCATTTTCTTCTTTCTCATTT
1 TCTTCTCTCTCATTTTCTTCTTTCTCATTT
5661626 TCTTCTCTCTC
1 TCTTCTCTCTC
5661637 GTTTCCCTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 5 0.14
28 3 0.09
29 13 0.37
30 14 0.40
ACGTcount: A:0.06, C:0.29, G:0.00, T:0.65
Consensus pattern (30 bp):
TCTTCTCTCTCATTTTCTTCTTTCTCATTT
Found at i:5661612 original size:15 final size:15
Alignment explanation
Indices: 5661576--5661636 Score: 90
Period size: 15 Copynumber: 4.1 Consensus size: 15
5661566 TTATCTTCCT
5661576 TCATTTTCTTCTCTT-
1 TCATTTTCTTCT-TTC
5661591 T-ATTTTCTTCTTTC
1 TCATTTTCTTCTTTC
5661605 TCATTTTCTTCTTTC
1 TCATTTTCTTCTTTC
*
5661620 TCATTTTCTTCTCTC
1 TCATTTTCTTCTTTC
5661635 TC
1 TC
5661637 GTTTCCCTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
13 2 0.05
14 11 0.26
15 30 0.70
ACGTcount: A:0.07, C:0.28, G:0.00, T:0.66
Consensus pattern (15 bp):
TCATTTTCTTCTTTC
Found at i:5671906 original size:18 final size:18
Alignment explanation
Indices: 5671883--5671920 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
5671873 AACTCGACTC
5671883 GAACTCGAAAACCGATTT
1 GAACTCGAAAACCGATTT
5671901 GAACTCGAAAACCGATTT
1 GAACTCGAAAACCGATTT
5671919 GA
1 GA
5671921 TAATTCGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (18 bp):
GAACTCGAAAACCGATTT
Found at i:5677857 original size:285 final size:283
Alignment explanation
Indices: 5677350--5677919 Score: 1043
Period size: 285 Copynumber: 2.0 Consensus size: 283
5677340 CCTCTGAAGA
5677350 ATAGAATCAAAGAAAATTAAACCCCTCTTAATGGCTAACAGCTCCATCAAAATAGAACCTGGACC
1 ATAGAATCAAAGAAAATTAAACCCCTCTTAATGGCTAACAGCTCCATCAAAATAGAACCTGGACC
*
5677415 CGCAGCCTCTTGGAAAGAACCCTTCATCTTACCAACCTCATTCCTTAGTAAACCACCTATACCAC
66 CGCAGCCTCTTGGAAAGAACCCTTCATCTTACCAACCTCATTCCTTAATAAACCACCTATACCAC
*
5677480 TCTTTCGCCAATCTCCACAAACAGCTGCATCCACATTCAATTTTAAAAAACCCTTTAGAGGAGGA
131 TCTTTCGCCAATCTCCACAAACAGCTGCATCCACATTCAATTTTAAAAAACCCTTTAGAGGAGAA
5677545 ACCCAAGACACGATTTTATGAATCGAATTTCTGGAAGAATAGCATAAATCTCCAATAGAGGGATC
196 ACCCAAGACACGATTTTATGAATCGAATTTCTGGAAGAATAGCATAAATCTCCAATAGAGGGATC
5677610 GCTAAT-GAGAGTCCTTAGAAAT
261 GCTAATAGAGAGTCCTTAGAAAT
5677632 ATAGAATCAAAGAAAATTAAACCCCTCTTAATGGCTAACAGCTCCATCAAAATAGGAGAACCTGG
1 ATAGAATCAAAGAAAATTAAACCCCTCTTAATGGCTAACAGCTCCATCAAAAT---AGAACCTGG
* * *
5677697 ACCCGTAGCCTCTTGGAAAGAACCCTTCATCTTGCCAACCTCATTCCTTAATAAACCACTTATAC
63 ACCCGCAGCCTCTTGGAAAGAACCCTTCATCTTACCAACCTCATTCCTTAATAAACCACCTATAC
*
5677762 CACTCTTTCGCCAATCTCCACAAACAGCTGCATCCACATTCAATTTTAAAAAACCCTTTGGAGGA
128 CACTCTTTCGCCAATCTCCACAAACAGCTGCATCCACATTCAATTTTAAAAAACCCTTTAGAGGA
5677827 GAAACCCAAGACACGATTTTATGAATCGAATTTCTGGAAGAATAGCATAAATCTCCAATAGAGGG
193 GAAACCCAAGACACGATTTTATGAATCGAATTTCTGGAAGAATAGCATAAATCTCCAATAGAGGG
5677892 ATCGCTAATGAGAGAGTCCTTAGAAAT
258 ATCGCTAAT-AGAGAGTCCTTAGAAAT
5677919 A
1 A
5677920 GCAACTTCCT
Statistics
Matches: 277, Mismatches: 6, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
282 53 0.19
285 207 0.75
287 17 0.06
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.24
Consensus pattern (283 bp):
ATAGAATCAAAGAAAATTAAACCCCTCTTAATGGCTAACAGCTCCATCAAAATAGAACCTGGACC
CGCAGCCTCTTGGAAAGAACCCTTCATCTTACCAACCTCATTCCTTAATAAACCACCTATACCAC
TCTTTCGCCAATCTCCACAAACAGCTGCATCCACATTCAATTTTAAAAAACCCTTTAGAGGAGAA
ACCCAAGACACGATTTTATGAATCGAATTTCTGGAAGAATAGCATAAATCTCCAATAGAGGGATC
GCTAATAGAGAGTCCTTAGAAAT
Found at i:5680051 original size:3 final size:3
Alignment explanation
Indices: 5680033--5680073 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
5680023 TGGTCAAACC
* * *
5680033 TCA TCA TAA TCT TCA TCA TCA TCG TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
5680074 TTCAATATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.29, C:0.32, G:0.02, T:0.37
Consensus pattern (3 bp):
TCA
Found at i:5680053 original size:15 final size:15
Alignment explanation
Indices: 5680033--5680094 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
5680023 TGGTCAAACC
5680033 TCATCATAATCTTCA
1 TCATCATAATCTTCA
** *
5680048 TCATCATCGTCATCA
1 TCATCATAATCTTCA
*
5680063 TCATCATCATCTTCAA
1 TCATCATAATCTTC-A
5680079 T-ATCA-ATATCTTCA
1 TCATCATA-ATCTTCA
5680093 TC
1 TC
5680095 GTCAATTTCC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
14 2 0.05
15 34 0.89
16 2 0.05
ACGTcount: A:0.31, C:0.29, G:0.02, T:0.39
Consensus pattern (15 bp):
TCATCATAATCTTCA
Found at i:5683141 original size:30 final size:30
Alignment explanation
Indices: 5683100--5683166 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
5683090 ATTCTTTCTA
*
5683100 TGGCAATCTTGAGATATAGTCATCTATTAT
1 TGGCCATCTTGAGATATAGTCATCTATTAT
5683130 TGGCCATCTTGAGATATAGTCATCTATTAT
1 TGGCCATCTTGAGATATAGTCATCTATTAT
5683160 TGGCCAT
1 TGGCCAT
5683167 ACTTTTGTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (30 bp):
TGGCCATCTTGAGATATAGTCATCTATTAT
Found at i:5684683 original size:111 final size:110
Alignment explanation
Indices: 5684484--5684810 Score: 432
Period size: 111 Copynumber: 3.0 Consensus size: 110
5684474 GTCAGAATTC
* * **
5684484 AAGTAAAGCAGCTACAGGAATTTGATAAAACTGCCAAAGGCATCACTGAGGACAAGGAAACTGAA
1 AAGTAAAGCAGCTACAGGAACTTGATAAAATTGCCAAAGGTGTCACTGAGGACAAGGAAACTGAA
* * *
5684549 GAGATTTCGAGTTTAGAGCATGAGGAAGTAGAAGCAAGTTCAAATA
66 AAGAATTCGAGTTTAGAGAATGAGGAAGT-GAAGCAAGTTCAAATA
* *
5684595 AAGTAAAGCAGCTACAGGAACTTGATAAAATTGCCAAAGGTGTCACTGAGGACAATGAAACTAAA
1 AAGTAAAGCAGCTACAGGAACTTGATAAAATTGCCAAAGGTGTCACTGAGGACAAGGAAACTGAA
* *
5684660 AAGAATTCAAATTTAGAGAAT---G-AG-GAAGCAAGTTCAAATA
66 AAGAATTCGAGTTTAGAGAATGAGGAAGTGAAGCAAGTTCAAATA
* * *
5684700 AATTAAAGCAACTACAGGAAGTTGATAAAATTGCCAAAGGTGTCACTGAGGACAAGGAAACTGAA
1 AAGTAAAGCAGCTACAGGAACTTGATAAAATTGCCAAAGGTGTCACTGAGGACAAGGAAACTGAA
* * *
5684765 ACGAATTTGAGTTTA-AAACATGAGGAAGCTGAAGCAAGTTCAAATA
66 AAGAATTCGAGTTTAGAGA-ATGAGGAAG-TGAAGCAAGTTCAAATA
5684811 CATTCACCAC
Statistics
Matches: 188, Mismatches: 21, Indels: 14
0.84 0.09 0.06
Matches are distributed among these distances:
104 2 0.01
105 89 0.47
107 2 0.01
108 2 0.01
109 2 0.01
111 91 0.48
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.20
Consensus pattern (110 bp):
AAGTAAAGCAGCTACAGGAACTTGATAAAATTGCCAAAGGTGTCACTGAGGACAAGGAAACTGAA
AAGAATTCGAGTTTAGAGAATGAGGAAGTGAAGCAAGTTCAAATA
Found at i:5692247 original size:16 final size:17
Alignment explanation
Indices: 5692221--5692280 Score: 61
Period size: 16 Copynumber: 3.5 Consensus size: 17
5692211 AATGATAAAA
5692221 ATATATATATATTAAATT
1 ATAT-TATATATTAAATT
5692239 AT-TTATATA-TAAATT
1 ATATTATATATTAAATT
* *
5692254 TTATTATATATATATATAT
1 ATATTATATAT-TAAAT-T
5692273 ATATTATA
1 ATATTATA
5692281 AATAATAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
15 7 0.20
16 13 0.37
17 1 0.03
18 6 0.17
19 8 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATTATATATTAAATT
Found at i:5692247 original size:20 final size:20
Alignment explanation
Indices: 5692221--5692272 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
5692211 AATGATAAAA
5692221 ATATATATATATTAAATTAT
1 ATATATATATATTAAATTAT
* * **
5692241 TTATATATAAATTTTATTAT
1 ATATATATATATTAAATTAT
5692261 ATATATATATAT
1 ATATATATATAT
5692273 ATATTATAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATATATATATATTAAATTAT
Found at i:5692279 original size:22 final size:20
Alignment explanation
Indices: 5692221--5692279 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
5692211 AATGATAAAA
5692221 ATATATATATATTAAATTATTT
1 ATATATATATATT--ATTATTT
* * *
5692243 ATATATAAATTTTATTATAT
1 ATATATATATATTATTATTT
5692263 ATATATATATA-TATTAT
1 ATATATATATATTATTAT
5692280 AAATAATAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
19 6 0.19
20 15 0.47
22 11 0.34
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATATATATATATTATTATTT
Found at i:5693197 original size:42 final size:42
Alignment explanation
Indices: 5693137--5693216 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
5693127 CTTTGGGTGG
5693137 ATCCTCTTCCTTTGCTTCATCAATGTCACCTAAGGGAATAAC
1 ATCCTCTTCCTTTGCTTCATCAATGTCACCTAAGGGAATAAC
**
5693179 ATCCTCTTCCTCTT-CTTCATCAATGTCATTTAAGGGAA
1 ATCCTCTTCCT-TTGCTTCATCAATGTCACCTAAGGGAA
5693217 CAAGATGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.25, C:0.28, G:0.11, T:0.36
Consensus pattern (42 bp):
ATCCTCTTCCTTTGCTTCATCAATGTCACCTAAGGGAATAAC
Found at i:5702009 original size:25 final size:25
Alignment explanation
Indices: 5701972--5702037 Score: 96
Period size: 25 Copynumber: 2.6 Consensus size: 25
5701962 AAGTGATCAA
5701972 ATTATATTATTTTTCTCATTTATGT
1 ATTATATTATTTTTCTCATTTATGT
*
5701997 ATTATATTGTTTTTCTCATTTATGT
1 ATTATATTATTTTTCTCATTTATGT
* *
5702022 GTTTACATTATTTTTC
1 -ATTATATTATTTTTC
5702038 GATCAATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
25 24 0.67
26 12 0.33
ACGTcount: A:0.21, C:0.09, G:0.06, T:0.64
Consensus pattern (25 bp):
ATTATATTATTTTTCTCATTTATGT
Found at i:5702987 original size:112 final size:110
Alignment explanation
Indices: 5702761--5702964 Score: 266
Period size: 112 Copynumber: 1.8 Consensus size: 110
5702751 AAAGGGCCTC
* * *
5702761 AAAAAAGTATATATAGTGGCGTTTTTTCAATAAACGCCACTATAGATGGACCTATTGCGACATTT
1 AAAAAAGTATATATAGTGGCGTTTTTCCAATAAACACCACTATAGATGGACCTATTGCGACAGTT
* * *** **
5702826 TTTTCAAAAAACGTCACTATTATTGTGCAGGCCCAAACAAGCCCA
66 TTTTCAAAAAAAGCCACTATTATTACCCAGAACCAAACAAGCCCA
* *
5702871 AAAAAAGTATATATATAGTGGCGTTTTTCCAATAAACACCACTATAGATTGACCTATTGCGTC-G
1 AAAAAAG--TATATATAGTGGCGTTTTTCCAATAAACACCACTATAGATGGACCTATTGCGACAG
*
5702935 TTTTTTCAAAAAAAGCCACTATTGTTACCC
64 TTTTTTCAAAAAAAGCCACTATTATTACCC
5702965 CGAAATCGAA
Statistics
Matches: 81, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
110 7 0.09
111 24 0.30
112 50 0.62
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (110 bp):
AAAAAAGTATATATAGTGGCGTTTTTCCAATAAACACCACTATAGATGGACCTATTGCGACAGTT
TTTTCAAAAAAAGCCACTATTATTACCCAGAACCAAACAAGCCCA
Found at i:5703166 original size:22 final size:22
Alignment explanation
Indices: 5703152--5703193 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
5703142 ATCTATCTTG
5703152 TAATAATTATCTATCTTATTAA
1 TAATAATTATCTATCTTATTAA
*
5703174 TAATAATTATCTACCTTATT
1 TAATAATTATCTATCTTATT
5703194 GTATTAACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATAATTATCTATCTTATTAA
Found at i:5703185 original size:18 final size:18
Alignment explanation
Indices: 5703133--5703168 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5703123 AATATGCCTC
5703133 GTAATAATTATCTATCTT
1 GTAATAATTATCTATCTT
5703151 GTAATAATTATCTATCTT
1 GTAATAATTATCTATCTT
5703169 ATTAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (18 bp):
GTAATAATTATCTATCTT
Found at i:5703322 original size:21 final size:21
Alignment explanation
Indices: 5703296--5703358 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
5703286 TTTGCTATTT
5703296 GACTCGTTACTCGTTAAGCTC
1 GACTCGTTACTCGTTAAGCTC
*
5703317 GACTCGTTGCTCGTTAAGCTC
1 GACTCGTTACTCGTTAAGCTC
*
5703338 GACTCGTTGA-TTGTTAAGCTC
1 GACTCGTT-ACTCGTTAAGCTC
5703359 ACTAAAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.17, C:0.25, G:0.22, T:0.35
Consensus pattern (21 bp):
GACTCGTTACTCGTTAAGCTC
Found at i:5703499 original size:40 final size:42
Alignment explanation
Indices: 5703452--5703539 Score: 110
Period size: 44 Copynumber: 2.1 Consensus size: 42
5703442 AAATAATGTT
5703452 ATTAGTTAA-TA-ATATTTTATTATTTATTAAAAAAT-AATA
1 ATTAGTTAACTATATATTTTATTATTTATTAAAAAATCAATA
* *
5703491 GATTAGTTAACTTATTATTTTTTATTATTTATTAATAAATCAATA
1 -ATTAGTTAAC-TA-TATATTTTATTATTTATTAAAAAATCAATA
5703536 ATTA
1 ATTA
5703540 TTATTTAGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
40 9 0.22
42 2 0.05
44 26 0.63
45 4 0.10
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.51
Consensus pattern (42 bp):
ATTAGTTAACTATATATTTTATTATTTATTAAAAAATCAATA
Found at i:5706744 original size:3 final size:3
Alignment explanation
Indices: 5706738--5706790 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
5706728 ATTATTTATT
* *
5706738 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA TAT TAA -AA CAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5706782 TAA TAA TAA
1 TAA TAA TAA
5706791 ATAAAACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 8 0.18
3 36 0.82
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:5706763 original size:22 final size:21
Alignment explanation
Indices: 5706716--5706794 Score: 74
Period size: 22 Copynumber: 3.8 Consensus size: 21
5706706 TGTAAAAATG
* * *
5706716 TAATAATAATAAATTATTTATT
1 TAATAATAATAAATAATATA-A
5706738 TAATAATAATAATATAATATAA
1 TAATAATAATAA-ATAATATAA
*
5706760 TAATAATATTAAA-ACA-A-AA
1 TAATAATAATAAATA-ATATAA
5706779 TAATAATAATAAATAA
1 TAATAATAATAAATAA
5706795 AACTAATGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
19 15 0.31
20 3 0.06
21 2 0.04
22 23 0.47
23 6 0.12
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (21 bp):
TAATAATAATAAATAATATAA
Found at i:5706801 original size:19 final size:18
Alignment explanation
Indices: 5706739--5706801 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 18
5706729 TTATTTATTT
*
5706739 AATAATAATAATATAATAT
1 AATAATAATAATA-AATAA
* *
5706758 AATAATAATATTAAAACAA
1 AATAATAATAAT-AAATAA
5706777 AATAATAATAATAAATAA
1 AATAATAATAATAAATAA
5706795 AACTAAT
1 AA-TAAT
5706802 GAAATAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 7 0.19
19 29 0.78
20 1 0.03
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
AATAATAATAATAAATAA
Found at i:5707254 original size:113 final size:114
Alignment explanation
Indices: 5707118--5707648 Score: 725
Period size: 113 Copynumber: 4.7 Consensus size: 114
5707108 TGTGATAGAG
* *
5707118 TCAAAC-AAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCT
1 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* *
5707181 TCTCATTATGAACTCTTCTCTGGAAAAGTTGATCCATCGAGTGATGAAT
66 TCTCATTATGAACTCTTCTCTGGAAAAGTTAATCCATCAAGTGATGAAT
* * * * * *
5707230 TCAAACAAAAAGTTGAACAAATTCTTATCATTATGAATTTCTTCCTCTTTCTTCAGATGAGTTAT
1 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
*
5707295 TCTCATTATGAACTC-TCTTTGGAAAAGTTAATCCATCAAGTGATGAAT
66 TCTCATTATGAACTCTTCTCTGGAAAAGTTAATCCATCAAGTGATGAAT
* * * *
5707343 TCGAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * * *
5707408 TCTCATTATGAACACTT-T-TGGAAATGTTGATCCATCAAGTGATGGAT
66 TCTCATTATGAACTCTTCTCTGGAAAAGTTAATCCATCAAGTGATGAAT
** * * * * *
5707455 TTGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTTAGACGAGTTCT
1 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * * **
5707520 TCTCATTATGAACT-TTTTCTGGCAATGTTAATCCATCGGGTGATGAAT
66 TCTCATTATGAACTCTTCTCTGGAAAAGTTAATCCATCAAGTGATGAAT
5707568 T-AAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
1 TCAAA-CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
5707632 TTCTCATTATGAACTCT
65 TTCTCATTATGAACTCT
5707649 ACCTGGCATG
Statistics
Matches: 370, Mismatches: 42, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
111 2 0.01
112 107 0.29
113 230 0.62
114 31 0.08
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (114 bp):
TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
TCTCATTATGAACTCTTCTCTGGAAAAGTTAATCCATCAAGTGATGAAT
Found at i:5707488 original size:225 final size:225
Alignment explanation
Indices: 5707124--5707684 Score: 768
Period size: 225 Copynumber: 2.5 Consensus size: 225
5707114 AGAGTCAAAC
* *
5707124 AAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
5707188 ATGAACTCTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAAAAAGTTGAACAAATT
66 ATGAACTCTT-T-TGGAAATGTTGATCCATCAAGTGATGGATTCAAACAAAAAGTTGAACAAATT
* * * *
5707253 CTTATCATTATGAATTTCTTCCTCTTTCTTCAGATGAGTTATTCTCATTATGAACTCTCTT-TGG
129 CTTATCATTATGAACTTCCTCCTCCTTCTTCAGACGAGTTATTCTCATTATGAACT-TCTTCTGG
**
5707317 AAAAGTTAATCCATCAAGTGATGAATTCGAGCA
193 AAAAGTTAATCCATCAAGTGATGAATTAAAGCA
* *
5707350 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* ** * * *
5707415 ATGAACACTTTTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGTTCT
66 ATGAACTCTTTTGGAAATGTTGATCCATCAAGTGATGGATTCAAACAAAAAGTTGAACAAATTCT
* * * * * *
5707480 TCTCATTATGAACTTCCTCTTCCTTCTTTAGACGAGTTCTTCTCATTATGAACTTTTTCTGGCAA
131 TATCATTATGAACTTCCTCCTCCTTCTTCAGACGAGTTATTCTCATTATGAACTTCTTCTGGAAA
* **
5707545 TGTTAATCCATCGGGTGATGAATTAAAGCA
196 AGTTAATCCATCAAGTGATGAATTAAAGCA
5707575 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
** * * *
5707640 ATGAACTCTACCTGG-CATGTTGATCCATTAAGTAATGGATTCAAA
66 ATGAACTCT-TTTGGAAATGTTGATCCATCAAGTGATGGATTCAAA
5707685 TCTTTGCTAA
Statistics
Matches: 293, Mismatches: 39, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
224 3 0.01
225 217 0.74
226 42 0.14
227 31 0.11
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (225 bp):
AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCTTTTGGAAATGTTGATCCATCAAGTGATGGATTCAAACAAAAAGTTGAACAAATTCT
TATCATTATGAACTTCCTCCTCCTTCTTCAGACGAGTTATTCTCATTATGAACTTCTTCTGGAAA
AGTTAATCCATCAAGTGATGAATTAAAGCA
Found at i:5708554 original size:53 final size:54
Alignment explanation
Indices: 5708448--5708554 Score: 128
Period size: 53 Copynumber: 2.0 Consensus size: 54
5708438 AGAATAACTG
* * *
5708448 GTTTGTAAAACATTTGACAACACATTCATCATCTCATGTGGTATCTGCTCAGAT
1 GTTTGTAAAACATTTGACAACACATTCATCATCTCATGTGCTATCTACACAGAT
** * *
5708502 GTTTGTAAAGTATTTGACAA-ACATTCATCATTTCTTGTGACT-TCTACACAGAT
1 GTTTGTAAAACATTTGACAACACATTCATCATCTCATGTG-CTATCTACACAGAT
5708555 TTCTGGTCAG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
53 26 0.58
54 19 0.42
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (54 bp):
GTTTGTAAAACATTTGACAACACATTCATCATCTCATGTGCTATCTACACAGAT
Found at i:5717106 original size:20 final size:21
Alignment explanation
Indices: 5717069--5717117 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
5717059 AATACTTGAT
*
5717069 AAATAAAATAAAACATTAAT-A
1 AAATAATATAAAACATT-ATGA
*
5717090 AAATAATAT-AAATATTATGA
1 AAATAATATAAAACATTATGA
5717110 AAATAATA
1 AAATAATA
5717118 AATATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 15 0.60
21 8 0.32
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (21 bp):
AAATAATATAAAACATTATGA
Found at i:5717120 original size:18 final size:19
Alignment explanation
Indices: 5717097--5717132 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5717087 ATAAAATAAT
*
5717097 ATAAATAT-TATGAAAATA
1 ATAAATATATATAAAAATA
5717115 ATAAATATATATAAAAAT
1 ATAAATATATATAAAAAT
5717133 TTTGAAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
ATAAATATATATAAAAATA
Found at i:5717126 original size:28 final size:28
Alignment explanation
Indices: 5717085--5717140 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
5717075 AATAAAACAT
*
5717085 TAATAAAATAATATAAATATTATGAAAA
1 TAATAAAATAATATAAAAATTATGAAAA
*
5717113 TAAT-AAATATATATAAAAATTTTGAAAA
1 TAATAAAATA-ATATAAAAATTATGAAAA
5717141 GAAAGAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (28 bp):
TAATAAAATAATATAAAAATTATGAAAA
Found at i:5719379 original size:3 final size:3
Alignment explanation
Indices: 5719373--5719425 Score: 69
Period size: 3 Copynumber: 19.0 Consensus size: 3
5719363 ATTATTTATT
*
5719373 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA TAA TAA -AA CAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5719417 TAA TAA TAA
1 TAA TAA TAA
5719426 ATAAAACTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 8 0.17
3 38 0.83
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:5719379 original size:22 final size:21
Alignment explanation
Indices: 5719351--5719429 Score: 83
Period size: 22 Copynumber: 3.8 Consensus size: 21
5719341 TGTAAAAATG
* * *
5719351 TAATAATAATAAATTATTTATT
1 TAATAATAATAAATAATATA-A
5719373 TAATAATAATAATATAATATAA
1 TAATAATAATAA-ATAATATAA
5719395 TAATAATAATAAA-ACA-A-AA
1 TAATAATAATAAATA-ATATAA
5719414 TAATAATAATAAATAA
1 TAATAATAATAAATAA
5719430 AACTAATGAA
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
19 16 0.31
20 3 0.06
21 2 0.04
22 24 0.47
23 6 0.12
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (21 bp):
TAATAATAATAAATAATATAA
Found at i:5719436 original size:19 final size:19
Alignment explanation
Indices: 5719376--5719452 Score: 79
Period size: 19 Copynumber: 4.1 Consensus size: 19
5719366 ATTTATTTAA
*
5719376 TAATAATAATATAATATAA-
1 TAATAATAATA-AATAAAAC
*
5719395 TAATAATAATAAA-ACAAAA
1 TAATAATAATAAATA-AAAC
5719414 TAATAATAATAAATAAAAC
1 TAATAATAATAAATAAAAC
* *
5719433 TAATGA-AATAAAAAAAAC
1 TAATAATAATAAATAAAAC
5719451 TA
1 TA
5719453 GTGTCTTCAA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
17 1 0.02
18 17 0.33
19 32 0.63
20 1 0.02
ACGTcount: A:0.69, C:0.04, G:0.01, T:0.26
Consensus pattern (19 bp):
TAATAATAATAAATAAAAC
Found at i:5720103 original size:7 final size:7
Alignment explanation
Indices: 5720091--5720120 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
5720081 TATTTGAGCG
5720091 CAAGTGA
1 CAAGTGA
5720098 CAAGTGA
1 CAAGTGA
5720105 CAAGTGA
1 CAAGTGA
5720112 CAAGTGA
1 CAAGTGA
5720119 CA
1 CA
5720121 TTGTTGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.27, T:0.13
Consensus pattern (7 bp):
CAAGTGA
Found at i:5751533 original size:12 final size:11
Alignment explanation
Indices: 5751514--5751549 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
5751504 TCTTCGATAT
5751514 TAAAAAATAAA
1 TAAAAAATAAA
5751525 TAAACAAATAAA
1 TAAA-AAATAAA
*
5751537 TAAAAAATTAA
1 TAAAAAATAAA
5751548 TA
1 TA
5751550 TATAATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (11 bp):
TAAAAAATAAA
Found at i:5751629 original size:123 final size:120
Alignment explanation
Indices: 5751421--5751650 Score: 291
Period size: 123 Copynumber: 1.9 Consensus size: 120
5751411 AAAAATTATT
* * * *
5751421 AATTTATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAATGACTTCTAGGT
1 AATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGACATCCAGGT
* *
5751486 GCCTTAAGACAGCTATTTTCTTCGATATTAAAAAATAAATAAACAAATAAATAAAA
66 GCCTTAAGACAGCTACTTTCTT-AATATTAAAAAATAAATAAACAAATAAATAAAA
**
5751542 AATTAATATATAATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCA
1 AATTAATATAT-ATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAAT-GACATCCA
* ** * * *
5751607 GTTGTTTTAAGACTG-TCCTTTCTTAATATTGAAAAATAAATAAA
63 GGTGCCTTAAGACAGCTACTTTCTTAATATTAAAAAATAAATAAA
5751651 TATTAAAACA
Statistics
Matches: 92, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
121 10 0.11
122 24 0.26
123 41 0.45
124 17 0.18
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (120 bp):
AATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGACATCCAGGT
GCCTTAAGACAGCTACTTTCTTAATATTAAAAAATAAATAAACAAATAAATAAAA
Found at i:5751847 original size:21 final size:20
Alignment explanation
Indices: 5751821--5751862 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
5751811 CTATATATTT
*
5751821 AAAATAAATAAAATTTGTAAA
1 AAAATAAATAAAAATTG-AAA
5751842 AAAATAAATAAAAATTGAAA
1 AAAATAAATAAAAATTGAAA
5751862 A
1 A
5751863 TAGTGACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (20 bp):
AAAATAAATAAAAATTGAAA
Found at i:5753154 original size:3 final size:3
Alignment explanation
Indices: 5753148--5753224 Score: 95
Period size: 3 Copynumber: 25.7 Consensus size: 3
5753138 TATTTTTTTT
5753148 TAA TAA TAA TAA TAA T-A TATA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
* * *
5753193 TTA TTA TTA TAA TAA TAA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
5753225 TTCAAATGAA
Statistics
Matches: 68, Mismatches: 2, Indels: 8
0.87 0.03 0.10
Matches are distributed among these distances:
2 4 0.06
3 59 0.87
4 5 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:5753671 original size:113 final size:113
Alignment explanation
Indices: 5753488--5754273 Score: 1116
Period size: 113 Copynumber: 6.9 Consensus size: 113
5753478 AGAATCATGC
*
5753488 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAG-TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
5753553 TATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCA
65 TATGAACTCTCTCTGGAAAAGCTGATCCATCGAGTGATGAATTCAAGCA
* *
5753602 AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTTATT
1 AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * *
5753667 ATGAACTCGCCCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCA
66 ATGAACTCTCTCTGGAAAAGCTGATCCATCGAGTGATGAATTCAAGCA
5753715 AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * *
5753780 ATGAACTCGAC-CTGGCAATGCTGATCCATCGAATGATGAATTCAAGCG
66 ATGAACTC-TCTCTGGAAAAGCTGATCCATCGAGTGATGAATTCAAGCA
* *
5753828 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATC
1 AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* ** * * * *
5753893 ATGAACTCTTTCACTGGGGATGCTGATCCATCAAATGATGAATTCAAAC-
66 ATGAACTC--TCTCTGGAAAAGCTGATCCATCGAGTGATGAATTCAAGCA
*
5753942 AAAAGTTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAG-TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
5754007 TATGAACTATCTCTGGAAAAGCTGATCCATCAAGTGATGAATT----CA
65 TATGAACTCTCTCTGGAAAAGCTGATCCATCGAGTGATGAATTCAAGCA
*
5754052 AAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * **
5754117 ATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCA
66 ATGAACTCTCTCTGGAAAAGCTGATCCATCGAGTGATGAATTCAAGCA
* * *
5754165 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
5754230 ATGAACTCTTTCACTGGAAAAGCTGATCTATCGAGTGATGAATT
66 ATGAACTC--TCTCTGGAAAAGCTGATCCATCGAGTGATGAATT
5754274 TGAGCCTTTG
Statistics
Matches: 615, Mismatches: 46, Indels: 21
0.90 0.07 0.03
Matches are distributed among these distances:
109 98 0.16
110 5 0.01
113 375 0.61
114 12 0.02
115 125 0.20
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (113 bp):
AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCTCTCTGGAAAAGCTGATCCATCGAGTGATGAATTCAAGCA
Found at i:5754190 original size:337 final size:338
Alignment explanation
Indices: 5753486--5754273 Score: 1187
Period size: 337 Copynumber: 2.3 Consensus size: 338
5753476 ATAGAATCAT
*
5753486 GCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
5753551 ATTATGAACTC--TCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCAAAAAGTTGAACA
66 ATTATGAACTCTTTCACTGGAAAAGCTGATCCATCGAGTGATGAATTCAAACAAAAAGTTGAACA
* *
5753614 AATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTTATTATGAACTCGCCC
131 AATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTAGCCC
* *
5753679 TGGCAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAATTCTTCTCATTATGA
196 TGGAAAAGCTGATCCATCGAATGATGAATT--A-CAAAAAGTTGAACAAATTCTTCTCATTATGA
* *
5753744 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCAT
258 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGAAAAGCTGATCCAT
5753809 CGAATGATGAATTCAA
323 CGAATGATGAATTCAA
5753825 GCGAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 GC-AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* ** * * *
5753889 CATCATGAACTCTTTCACTGGGGATGCTGATCCATCAAATGATGAATTCAAAC-AAAAGTTTGAA
65 CATTATGAACTCTTTCACTGGAAAAGCTGATCCATCGAGTGATGAATTCAAACAAAAAG-TTGAA
*
5753953 CAAATTCTTCTCATTATGAACTTCTTCTT-TCTTCTTCAGATGAGTTCTTCTCATTATGAACTAT
129 CAAATTCTTCTCATTATGAACTTCTTCTTCT-TTCTTCAGATGAGTTCTTCTCATTATGAACTAG
*
5754017 CTCTGGAAAAGCTGATCCATC-AAGTGATGAATT-CAAAAAGTTGAACAAATTCTTCTCATTATG
193 CCCTGGAAAAGCTGATCCATCGAA-TGATGAATTACAAAAAGTTGAACAAATTCTTCTCATTATG
* ****
5754080 AATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCA
257 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGAAAAGCTGATCCA
* **
5754145 TC-AAGTGATGGATTTGA
322 TCGAA-TGATGAATTCAA
*
5754162 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
5754227 ATTATGAACTCTTTCACTGGAAAAGCTGATCTATCGAGTGATGAATT
66 ATTATGAACTCTTTCACTGGAAAAGCTGATCCATCGAGTGATGAATT
5754274 TGAGCCTTTG
Statistics
Matches: 406, Mismatches: 35, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
336 6 0.01
337 198 0.49
339 69 0.17
340 12 0.03
341 121 0.30
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (338 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCTTTCACTGGAAAAGCTGATCCATCGAGTGATGAATTCAAACAAAAAGTTGAACA
AATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTAGCCC
TGGAAAAGCTGATCCATCGAATGATGAATTACAAAAAGTTGAACAAATTCTTCTCATTATGAACT
TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGAAAAGCTGATCCATCGA
ATGATGAATTCAA
Found at i:5754701 original size:22 final size:22
Alignment explanation
Indices: 5754676--5754730 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
5754666 GATAAAGCTT
*
5754676 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
5754698 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
5754720 TCATCTTTGAA
1 TCATCTTTGAA
5754731 GAGTGTAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:5759848 original size:15 final size:15
Alignment explanation
Indices: 5759830--5759903 Score: 62
Period size: 15 Copynumber: 4.7 Consensus size: 15
5759820 ATTTCTCCCC
*
5759830 TTTTTCTTTTTCCCTT
1 TTTTTCTTTTT-CCAT
5759846 TTTTTCATTTTT-CAT
1 TTTTTC-TTTTTCCAT
5759861 TTTTTCATTTTT-CAT
1 TTTTTC-TTTTTCCAT
* *
5759876 TTTTCCTTTTTCATCTT
1 TTTTTCTTTTTC--CAT
5759893 TTTTTCTTTTT
1 TTTTTCTTTTT
5759904 TTTCTTTCTT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
14 5 0.10
15 22 0.44
16 6 0.12
17 17 0.34
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTCTTTTTCCAT
Found at i:5759856 original size:7 final size:7
Alignment explanation
Indices: 5759846--5759894 Score: 71
Period size: 7 Copynumber: 6.7 Consensus size: 7
5759836 TTTTTCCCTT
5759846 TTTTTCA
1 TTTTTCA
5759853 TTTTTCA
1 TTTTTCA
5759860 TTTTTTCA
1 -TTTTTCA
5759868 TTTTTCA
1 TTTTTCA
*
5759875 TTTTTCC
1 TTTTTCA
5759882 TTTTTCA
1 TTTTTCA
5759889 TCTTTT
1 T-TTTT
5759895 TTTCTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
7 27 0.71
8 11 0.29
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTCA
Found at i:5759902 original size:7 final size:7
Alignment explanation
Indices: 5759830--5759962 Score: 63
Period size: 7 Copynumber: 17.3 Consensus size: 7
5759820 ATTTCTCCCC
5759830 TTTTTCT
1 TTTTTCT
*
5759837 TTTTCCCTT
1 TTTT-TC-T
*
5759846 TTTTTCA
1 TTTTTCT
5759853 TTTTTCAT
1 TTTTTC-T
*
5759861 TTTTTCA
1 TTTTTCT
*
5759868 TTTTTCA
1 TTTTTCT
*
5759875 TTTTTCC
1 TTTTTCT
5759882 TTTTTCAT
1 TTTTTC-T
*
5759890 CTTTT-T
1 TTTTTCT
*
5759896 TTCTT-T
1 TTTTTCT
5759902 TTTTTCT
1 TTTTTCT
5759909 TTCTTTGCT
1 TT-TTT-CT
5759918 GGATTTTTCT
1 ---TTTTTCT
5759928 TTTTTCT
1 TTTTTCT
5759935 TTATTTGCT
1 TT-TTT-CT
5759944 GGATTTTTCT
1 ---TTTTTCT
5759954 TTTTTCT
1 TTTTTCT
5759961 TT
1 TT
5759963 CTTTGCTGGA
Statistics
Matches: 100, Mismatches: 11, Indels: 30
0.71 0.08 0.21
Matches are distributed among these distances:
6 9 0.09
7 50 0.50
8 18 0.18
9 9 0.09
10 4 0.04
11 6 0.06
12 4 0.04
ACGTcount: A:0.06, C:0.16, G:0.05, T:0.74
Consensus pattern (7 bp):
TTTTTCT
Found at i:5759930 original size:26 final size:26
Alignment explanation
Indices: 5759901--5759973 Score: 137
Period size: 26 Copynumber: 2.8 Consensus size: 26
5759891 TTTTTTTCTT
5759901 TTTTTTCTTTCTTTGCTGGATTTTTC
1 TTTTTTCTTTCTTTGCTGGATTTTTC
*
5759927 TTTTTTCTTTATTTGCTGGATTTTTC
1 TTTTTTCTTTCTTTGCTGGATTTTTC
5759953 TTTTTTCTTTCTTTGCTGGAT
1 TTTTTTCTTTCTTTGCTGGAT
5759974 GAGTATAAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.05, C:0.14, G:0.12, T:0.68
Consensus pattern (26 bp):
TTTTTTCTTTCTTTGCTGGATTTTTC
Found at i:5763618 original size:14 final size:14
Alignment explanation
Indices: 5763599--5763634 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
5763589 AAGATGCCAG
5763599 ATGTAAATATGCAA
1 ATGTAAATATGCAA
* *
5763613 ATGTAAAAATGTAA
1 ATGTAAATATGCAA
5763627 ATGTAAAT
1 ATGTAAAT
5763635 TATTTAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.14, T:0.31
Consensus pattern (14 bp):
ATGTAAATATGCAA
Found at i:5765926 original size:4 final size:4
Alignment explanation
Indices: 5765913--5765946 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
5765903 TCTTCGATAT
5765913 TAAA -AAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
5765947 TATATAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:5765964 original size:123 final size:122
Alignment explanation
Indices: 5765824--5766051 Score: 307
Period size: 123 Copynumber: 1.9 Consensus size: 122
5765814 ATTATTAATT
* * *
5765824 TATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAT-GACTTCTAGGTGCC
1 TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGGTGCC
* *
5765888 TTAAGACAGCTCTTTTCTTCGATATTAAAAAATAAATAAATAAATAAATAAATAAATAA
66 TTAAGACAG-TCCTTTCTT-AATATTAAAAAATAAATAAATAAATAAATAAATAAATAA
** * *
5765947 TATATA-ATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGTTGT
1 TATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGGTGC
* * *
5766011 TTTAAGACTGTCCTTTCTTAATATTGAAAAATAAATAAATA
65 CTTAAGACAGTCCTTTCTTAATATTAAAAAATAAATAAATA
5766052 TTAAAACATG
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
122 26 0.29
123 48 0.53
124 17 0.19
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (122 bp):
TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGGTGCC
TTAAGACAGTCCTTTCTTAATATTAAAAAATAAATAAATAAATAAATAAATAAATAA
Found at i:5766249 original size:23 final size:22
Alignment explanation
Indices: 5766223--5766266 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
5766213 CTATATATTT
*
5766223 AAAATAAATAAAATTTGTAAAAA
1 AAAATAAATAAAAATTG-AAAAA
5766246 AAAATAAATAAAAATTGAAAA
1 AAAATAAATAAAAATTGAAAA
5766267 TAGTGACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (22 bp):
AAAATAAATAAAAATTGAAAAA
Found at i:5767565 original size:3 final size:3
Alignment explanation
Indices: 5767559--5767651 Score: 84
Period size: 3 Copynumber: 30.7 Consensus size: 3
5767549 TTATTTTTTT
5767559 TAA TAA TAA TAA TAA T-A TATA TAA TAA T-A TATA TAA TAA T-A TATA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TA-A
* * * * *
5767604 TATA TAA TAA TAA TAA TTA TTA TTA TTA TTA TAA TAA TAA TAA TAA
1 TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5767650 TA
1 TA
5767652 TTCAAATGAA
Statistics
Matches: 82, Mismatches: 2, Indels: 12
0.85 0.02 0.12
Matches are distributed among these distances:
2 6 0.07
3 63 0.77
4 13 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:5767710 original size:23 final size:23
Alignment explanation
Indices: 5767684--5767731 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
5767674 TCTTCAGTCA
5767684 TTATATGATCTTAAGTTACTAGT
1 TTATATGATCTTAAGTTACTAGT
*
5767707 TTATGTGATCTTAAGTTACTAGT
1 TTATATGATCTTAAGTTACTAGT
5767730 TT
1 TT
5767732 TGTTTCAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.50
Consensus pattern (23 bp):
TTATATGATCTTAAGTTACTAGT
Found at i:5767758 original size:2 final size:2
Alignment explanation
Indices: 5767740--5767778 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
5767730 TTTGTTTCAA
* *
5767740 AT AT GT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5767779 AAGTTTAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5768636 original size:25 final size:24
Alignment explanation
Indices: 5768607--5768655 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
5768597 TTTTAAAAAA
* *
5768607 TATTTTTATATATAATAAACTTTTT
1 TATTTTTATA-AAAATAAAATTTTT
*
5768632 TATTTTTTTAAAAATAAAATTTTT
1 TATTTTTATAAAAATAAAATTTTT
5768656 AAAATTATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
TATTTTTATAAAAATAAAATTTTT
Found at i:5769577 original size:37 final size:37
Alignment explanation
Indices: 5769526--5769630 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
5769516 CCTATTCATC
** *
5769526 CTACTAAGATTCAAACTTATAAAAATAGGATATAATT
1 CTACTAAGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
5769563 TTACTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAAGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
5769600 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAAGATTCAAACTCCTAAAAATAGGAT
5769631 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.31
Consensus pattern (37 bp):
CTACTAAGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:5770237 original size:24 final size:24
Alignment explanation
Indices: 5770210--5770309 Score: 88
Period size: 24 Copynumber: 4.3 Consensus size: 24
5770200 CTTTGCATTT
5770210 TTATTATTACTATTATATTTATTA
1 TTATTATTACTATTATATTTATTA
*
5770234 TTATTTTTACTATTATATTT-TCT-
1 TTATTATTACTATTATATTTAT-TA
*
5770257 TT-TTATT-CTACT-TATTTA-TA
1 TTATTATTACTATTATATTTATTA
*
5770277 TTATATATGTA-TATTTTATTTTATTA
1 TTAT-TAT-TACTATTATA-TTTATTA
5770303 TTATTAT
1 TTATTAT
5770310 ATATTTTTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 19
0.73 0.05 0.22
Matches are distributed among these distances:
19 1 0.02
20 7 0.11
21 5 0.08
22 7 0.11
23 7 0.11
24 22 0.35
25 7 0.11
26 6 0.10
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.66
Consensus pattern (24 bp):
TTATTATTACTATTATATTTATTA
Found at i:5770312 original size:23 final size:24
Alignment explanation
Indices: 5770268--5770320 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
5770258 TTTATTCTAC
*
5770268 TTATTTATATTATATATGTATATT
1 TTATTTATATTATATATATATATT
5770292 TTATTT-TATTAT-TATTATATATT
1 TTATTTATATTATATA-TATATATT
5770315 TT-TTTA
1 TTATTTA
5770321 CTTTCTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 5 0.19
23 15 0.58
24 6 0.23
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (24 bp):
TTATTTATATTATATATATATATT
Found at i:5770659 original size:28 final size:29
Alignment explanation
Indices: 5770583--5770683 Score: 75
Period size: 30 Copynumber: 3.4 Consensus size: 29
5770573 TACTTTGTTA
*
5770583 TTATTATTTTGTTTATTTGTTT-TATTTATT
1 TTATTA-TTTGTTTATTT-TTTATATATATT
* * * *
5770613 TTCTTTTTCTTTTTCTTTTTTATATATATT
1 TTATTATT-TGTTTATTTTTTATATATATT
5770643 TTATTATTTGTTT-TTTTTTACT-TACTATT
1 TTATTATTTGTTTATTTTTTA-TATA-TATT
*
5770672 TTA-TCTTTGTTT
1 TTATTATTTGTTT
5770684 TCTTCATTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
28 17 0.29
29 17 0.29
30 24 0.41
ACGTcount: A:0.15, C:0.06, G:0.04, T:0.75
Consensus pattern (29 bp):
TTATTATTTGTTTATTTTTTATATATATT
Found at i:5770684 original size:28 final size:27
Alignment explanation
Indices: 5770616--5770684 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 27
5770606 ATTTATTTTC
*
5770616 TTTT-TCTTT-TTCTTTTTTATATATA
1 TTTTATCTTTGTTTTTTTTTATATATA
*
5770641 TTTTATTATTTGTTTTTTTTTACT-TACTA
1 TTTTA-TCTTTGTTTTTTTTTA-TATA-TA
5770670 TTTTATCTTTGTTTT
1 TTTTATCTTTGTTTT
5770685 CTTCATTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
25 4 0.11
27 4 0.11
28 20 0.56
29 8 0.22
ACGTcount: A:0.14, C:0.07, G:0.03, T:0.75
Consensus pattern (27 bp):
TTTTATCTTTGTTTTTTTTTATATATA
Found at i:5771780 original size:19 final size:20
Alignment explanation
Indices: 5771744--5771781 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5771734 ACCTTACTAA
*
5771744 CTCTTTTCATTTTTTTTCCT
1 CTCTTTTCATTTTATTTCCT
5771764 CTCTTTT-ATTTTATTTCC
1 CTCTTTTCATTTTATTTCC
5771782 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (20 bp):
CTCTTTTCATTTTATTTCCT
Done.