Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 167 of 313
Found at i:52376751 original size:32 final size:32
Alignment explanation
Indices: 52376715--52376778 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
52376705 TCCATACTTG
52376715 AATTC-ATTTCAATGTTCACATCTCAT-TTCATC
1 AATTCAATTTC-AT-TTCACATCTCATATTCATC
*
52376747 AATTCATATTTCATTTCCCATCTCATATTCAT
1 AATTCA-ATTTCATTTCACATCTCATATTCAT
52376779 TTTTCATCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
32 16 0.57
33 7 0.25
34 5 0.18
ACGTcount: A:0.28, C:0.25, G:0.02, T:0.45
Consensus pattern (32 bp):
AATTCAATTTCATTTCACATCTCATATTCATC
Found at i:52378047 original size:35 final size:34
Alignment explanation
Indices: 52377991--52378056 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 34
52377981 TTTTAATTTC
*
52377991 ATTCATTATTATTATATTATAATATATACATTAG
1 ATTCATTATTATTATATTATAACATATACATTAG
52378025 ATTCATT-TTATTTATTATTATAACATATACAT
1 ATTCATTATTA-TTA-TATTATAACATATACAT
52378057 ATCTATACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 3 0.10
34 10 0.34
35 16 0.55
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.52
Consensus pattern (34 bp):
ATTCATTATTATTATATTATAACATATACATTAG
Found at i:52395875 original size:5 final size:5
Alignment explanation
Indices: 52395865--52395891 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
52395855 TTTAAAGTTG
52395865 ATTGA ATTGA ATTGA ATTGA ATTGA AT
1 ATTGA ATTGA ATTGA ATTGA ATTGA AT
52395892 ATATGTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (5 bp):
ATTGA
Found at i:52406915 original size:77 final size:78
Alignment explanation
Indices: 52406822--52406978 Score: 298
Period size: 77 Copynumber: 2.0 Consensus size: 78
52406812 GTATTGGAAG
52406822 AAAGTATTAACAGAATTGTTATTTCTAAGATTTCCTATCA-TTGAAATGTCAGTACTTTGTTTTC
1 AAAGTATTAACAGAATTGTTATTTCTAAGATTTCCTATCATTTGAAATGTCAGTACTTTGTTTTC
52406886 AAAATTTGCTAAT
66 AAAATTTGCTAAT
*
52406899 AAAGTATTAACAGAATTGTTATTTCTAAGATTTCCTATCATTTGAGATGTCAGTACTTTGTTTTC
1 AAAGTATTAACAGAATTGTTATTTCTAAGATTTCCTATCATTTGAAATGTCAGTACTTTGTTTTC
52406964 AAAATTTGCTAAT
66 AAAATTTGCTAAT
52406977 AA
1 AA
52406979 CTAAGACTGA
Statistics
Matches: 78, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
77 40 0.51
78 38 0.49
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.43
Consensus pattern (78 bp):
AAAGTATTAACAGAATTGTTATTTCTAAGATTTCCTATCATTTGAAATGTCAGTACTTTGTTTTC
AAAATTTGCTAAT
Found at i:52409567 original size:20 final size:21
Alignment explanation
Indices: 52409542--52409586 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
52409532 GTGAGAACTT
52409542 TAAAAT-AAAATAATG-AAAAA
1 TAAAATGAAAATAA-GAAAAAA
*
52409562 TAAAATGAAAATTAGAAAAAA
1 TAAAATGAAAATAAGAAAAAA
52409583 TAAA
1 TAAA
52409587 TTGGTTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (21 bp):
TAAAATGAAAATAAGAAAAAA
Found at i:52416415 original size:19 final size:19
Alignment explanation
Indices: 52416381--52416427 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 19
52416371 ACACAGGTAA
52416381 TTTTAAAATTTTCAAAATAAT
1 TTTTAAAA-TTTCAAAAT-AT
52416402 TTTTAAAA-TTCAAAATAT
1 TTTTAAAATTTCAAAATAT
*
52416420 TTATAAAA
1 TTTTAAAA
52416428 ATCCAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 9 0.36
19 8 0.32
21 8 0.32
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTTAAAATTTCAAAATAT
Found at i:52416426 original size:18 final size:18
Alignment explanation
Indices: 52416391--52416441 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
52416381 TTTTAAAATT
*
52416391 TTCAAAATAATTTTTAAAA
1 TTCAAAAT-ATTTATAAAA
52416410 TTCAAAATATTTATAAAA
1 TTCAAAATATTTATAAAA
* *
52416428 ATCCAAA-ATTTATA
1 TTCAAAATATTTATA
52416442 TTTTTTAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 7 0.24
18 14 0.48
19 8 0.28
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (18 bp):
TTCAAAATATTTATAAAA
Found at i:52416428 original size:19 final size:19
Alignment explanation
Indices: 52416378--52416436 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
52416368 AATACACAGG
*
52416378 TAATTTTAAAATTTTCAAAA
1 TAATTTTAAAA-ATTCAAAA
*
52416398 TAATTTTTAAAATTCAAAA
1 TAATTTTAAAAATTCAAAA
*
52416417 T-ATTTATAAAAATCCAAAA
1 TAATTT-TAAAAATTCAAAA
52416436 T
1 T
52416437 TTATATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 4 0.12
19 20 0.59
20 10 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.41
Consensus pattern (19 bp):
TAATTTTAAAAATTCAAAA
Found at i:52416499 original size:20 final size:19
Alignment explanation
Indices: 52416463--52416518 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 19
52416453 ATATAGAAAT
52416463 TATAAAAAAATCCTAAAGAA
1 TATAAAAAAATCCTAAA-AA
**
52416483 TATAAAAAAATGTTAAAAA
1 TATAAAAAAATCCTAAAAA
*
52416502 -GTAAAAAAAT-CTAAAAA
1 TATAAAAAAATCCTAAAAA
52416519 AAACCTAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 6 0.19
18 9 0.28
19 2 0.06
20 15 0.47
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.21
Consensus pattern (19 bp):
TATAAAAAAATCCTAAAAA
Found at i:52425098 original size:26 final size:26
Alignment explanation
Indices: 52425065--52425122 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
52425055 ATATCAAAAT
52425065 TTATAGAGACCAATTTAAAATCTAGA
1 TTATAGAGACCAATTTAAAATCTAGA
*
52425091 TTATAGAGACCAATTTAATATCTAGA
1 TTATAGAGACCAATTTAAAATCTAGA
52425117 TTATAG
1 TTATAG
52425123 TTTGAGGATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.34
Consensus pattern (26 bp):
TTATAGAGACCAATTTAAAATCTAGA
Found at i:52427232 original size:27 final size:27
Alignment explanation
Indices: 52427194--52427292 Score: 96
Period size: 27 Copynumber: 3.6 Consensus size: 27
52427184 AAATCTTTCT
52427194 AACTATGGACAAGAAACCGATTCACAA
1 AACTATGGACAAGAAACCGATTCACAA
* * *
52427221 AACTATGGACAAGAAACCAATAACATAAA
1 AACTATGGACAAGAAACCGAT-TCA-CAA
*
52427250 GGAACTA---ACCCAGAAACCGATTCACAA
1 --AACTATGGA-CAAGAAACCGATTCACAA
52427277 AACTATGGACAAGAAA
1 AACTATGGACAAGAAA
52427293 ATATACCTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
25 5 0.09
27 28 0.50
28 6 0.11
29 12 0.21
31 5 0.09
ACGTcount: A:0.52, C:0.21, G:0.14, T:0.13
Consensus pattern (27 bp):
AACTATGGACAAGAAACCGATTCACAA
Found at i:52427725 original size:14 final size:14
Alignment explanation
Indices: 52427703--52427733 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
52427693 CACTGGAAAA
*
52427703 TCCGTAAAATATTT
1 TCCGGAAAATATTT
52427717 TCCGGAAAATATTT
1 TCCGGAAAATATTT
52427731 TCC
1 TCC
52427734 ACCAATCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (14 bp):
TCCGGAAAATATTT
Found at i:52428445 original size:23 final size:23
Alignment explanation
Indices: 52428415--52428459 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
52428405 TGTTATAACT
52428415 TTTTTTATTTACCAAAATATATA
1 TTTTTTATTTACCAAAATATATA
52428438 TTTTTTATTTACCAAAATATAT
1 TTTTTTATTTACCAAAATATAT
52428460 CAAAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTTTTATTTACCAAAATATATA
Found at i:52428585 original size:27 final size:27
Alignment explanation
Indices: 52428524--52428606 Score: 103
Period size: 27 Copynumber: 3.1 Consensus size: 27
52428514 AACTCCCTGG
*
52428524 GTGGAGGGAAGCAGGTTGGCAGCACCA
1 GTGGAGGGAAGCAGGTTGGCGGCACCA
**** *
52428551 AACAAGGGAAGCAGGTTGGCGGCACTA
1 GTGGAGGGAAGCAGGTTGGCGGCACCA
*
52428578 GTGGAGGGAACCAGGTTGGCGGCACCA
1 GTGGAGGGAAGCAGGTTGGCGGCACCA
52428605 GT
1 GT
52428607 CCTGCCAACC
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.27, C:0.19, G:0.42, T:0.12
Consensus pattern (27 bp):
GTGGAGGGAAGCAGGTTGGCGGCACCA
Found at i:52430016 original size:17 final size:17
Alignment explanation
Indices: 52429994--52430030 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
52429984 AATAAGATGT
52429994 CATGAATATTAGAATAG
1 CATGAATATTAGAATAG
52430011 CATGAATATTAGAATAG
1 CATGAATATTAGAATAG
52430028 CAT
1 CAT
52430031 CTTACCCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.08, G:0.16, T:0.30
Consensus pattern (17 bp):
CATGAATATTAGAATAG
Found at i:52431361 original size:19 final size:19
Alignment explanation
Indices: 52431339--52431375 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
52431329 GTGTTTTTCC
52431339 TATTTTCTTTA-TTTTTTTT
1 TATTTT-TTTACTTTTTTTT
52431358 TATTTTTTTACTTTTTTT
1 TATTTTTTTACTTTTTTT
52431376 GATATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.11, C:0.05, G:0.00, T:0.84
Consensus pattern (19 bp):
TATTTTTTTACTTTTTTTT
Found at i:52431407 original size:27 final size:29
Alignment explanation
Indices: 52431377--52431445 Score: 108
Period size: 28 Copynumber: 2.5 Consensus size: 29
52431367 ACTTTTTTTG
52431377 ATATATTTTGGTAAAT-AAAAAAA-TTAT
1 ATATATTTTGGTAAATAAAAAAAAGTTAT
*
52431404 ATATTTTTTGGTAAATAAAAAAAAGTTAT
1 ATATATTTTGGTAAATAAAAAAAAGTTAT
52431433 A-ATATTTTGGTAA
1 ATATATTTTGGTAA
52431446 TTTTTTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 15 0.39
28 18 0.47
29 5 0.13
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (29 bp):
ATATATTTTGGTAAATAAAAAAAAGTTAT
Found at i:52431506 original size:19 final size:18
Alignment explanation
Indices: 52431482--52431521 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
52431472 TATAAAACCC
52431482 ATAATAAAACATTACAAAA
1 ATAATAAAACATTA-AAAA
*
52431501 ATAATAAAATATTAAAAA
1 ATAATAAAACATTAAAAA
52431519 ATA
1 ATA
52431522 CCAAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (18 bp):
ATAATAAAACATTAAAAA
Found at i:52431520 original size:18 final size:19
Alignment explanation
Indices: 52431482--52431532 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
52431472 TATAAAACCC
*
52431482 ATAATAAAACATTACAAAA
1 ATAATAAAATATTACAAAA
52431501 ATAATAAAATATTA-AAAA
1 ATAATAAAATATTACAAAA
**
52431519 ATACCAAAATATTA
1 ATAATAAAATATTA
52431533 TATATATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 16 0.55
19 13 0.45
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (19 bp):
ATAATAAAATATTACAAAA
Found at i:52432285 original size:38 final size:38
Alignment explanation
Indices: 52432243--52432343 Score: 145
Period size: 38 Copynumber: 2.7 Consensus size: 38
52432233 TTCCCTCTTC
*
52432243 TTCTTT-CTT-TTTTT-TTTCTCTTCTCTTCTCCTTTCCTT
1 TTCTTTCCTTATTTTTCTTTCT-TTC-C-TCCCCTTTCCTT
52432281 TTCTTTCCTTATTTTTCTTTCTTTCCTCCCCTTTCCTT
1 TTCTTTCCTTATTTTTCTTTCTTTCCTCCCCTTTCCTT
52432319 TTCTTTCCTTATTTTTCTTTCTTTC
1 TTCTTTCCTTATTTTTCTTTCTTTC
52432344 GATTACAAAA
Statistics
Matches: 59, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
38 42 0.71
39 4 0.07
40 8 0.14
41 5 0.08
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (38 bp):
TTCTTTCCTTATTTTTCTTTCTTTCCTCCCCTTTCCTT
Found at i:52432288 original size:10 final size:10
Alignment explanation
Indices: 52432273--52432328 Score: 55
Period size: 10 Copynumber: 5.8 Consensus size: 10
52432263 TTCTCTTCTC
52432273 CTTTCCTTTT
1 CTTTCCTTTT
52432283 CTTTCCTTATT
1 CTTTCCTT-TT
52432294 -TTT-C-TTT
1 CTTTCCTTTT
***
52432301 CTTTCCTCCC
1 CTTTCCTTTT
52432311 CTTTCCTTTT
1 CTTTCCTTTT
52432321 CTTTCCTT
1 CTTTCCTT
52432329 ATTTTTCTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
7 2 0.06
8 4 0.11
9 2 0.06
10 26 0.72
11 2 0.06
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (10 bp):
CTTTCCTTTT
Found at i:52432373 original size:18 final size:19
Alignment explanation
Indices: 52432345--52432385 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
52432335 CTTTCTTTCG
*
52432345 ATTACAAAAATAATAAAAT
1 ATTACAAAAATAACAAAAT
*
52432364 ATTA-AAAAATACCAAAAT
1 ATTACAAAAATAACAAAAT
52432382 ATTA
1 ATTA
52432386 TATATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (19 bp):
ATTACAAAAATAACAAAAT
Found at i:52432571 original size:27 final size:27
Alignment explanation
Indices: 52432541--52432623 Score: 121
Period size: 27 Copynumber: 3.1 Consensus size: 27
52432531 GGTTGGCAGG
*
52432541 ACTGGTGCCGCCAACCTGGTTCCCTCC
1 ACTGGTGCCGCCAACCTGCTTCCCTCC
**
52432568 ACTGGTGCCGCCAACCTGCTTCCCTTG
1 ACTGGTGCCGCCAACCTGCTTCCCTCC
**
52432595 TTTGGTGCCGCCAACCTGCTTCCCTCC
1 ACTGGTGCCGCCAACCTGCTTCCCTCC
52432622 AC
1 AC
52432624 CCAGGGAGTT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.11, C:0.43, G:0.20, T:0.25
Consensus pattern (27 bp):
ACTGGTGCCGCCAACCTGCTTCCCTCC
Found at i:52432667 original size:13 final size:12
Alignment explanation
Indices: 52432649--52432682 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
52432639 ATCAGTTCAG
52432649 GTTTTTTTTTTCT
1 GTTTTTTTTTT-T
*
52432662 GTTTTTTTGTTT
1 GTTTTTTTTTTT
52432674 GTTTTTTTT
1 GTTTTTTTT
52432683 ATATATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.85
Consensus pattern (12 bp):
GTTTTTTTTTTT
Found at i:52433242 original size:10 final size:10
Alignment explanation
Indices: 52433229--52433416 Score: 53
Period size: 10 Copynumber: 19.1 Consensus size: 10
52433219 TCCTTCCCTC
52433229 TTCTTCTTCT
1 TTCTTCTTCT
* *
52433239 TTCTTTTTTT
1 TTCTTCTTCT
52433249 TCTCTTC-TCAT
1 T-TCTTCTTC-T
52433260 TTCATT-TTCT
1 TTC-TTCTTCT
*
52433270 TTC--CTTAT
1 TTCTTCTTCT
52433278 TT-TTCTTTCT
1 TTCTTC-TTCT
* **
52433288 TTCCTCCCCT
1 TTCTTCTTCT
52433298 TTCCTT-TTCT
1 TT-CTTCTTCT
*
52433308 TTC--CTTAT
1 TTCTTCTTCT
52433316 TT-TTCTTTCT
1 TTCTTC-TTCT
* **
52433326 TTCCTCCCCT
1 TTCTTCTTCT
52433336 TTCCTT-TTCT
1 TT-CTTCTTCT
52433346 TTC--CTTCT
1 TTCTTCTTCT
52433354 TT-TTCTTTCT
1 TTCTTC-TTCT
* *
52433364 TTCCTCTCCT
1 TTCTTCTTCT
*
52433374 TTCCTT-TTCC
1 TT-CTTCTTCT
*
52433384 TTCTTTTTCT
1 TTCTTCTTCT
52433394 TTCTTCCTTTCT
1 TTCTT-C-TTCT
52433406 TTCTTCTTCT
1 TTCTTCTTCT
52433416 T
1 T
52433417 CCCCTCTCCT
Statistics
Matches: 126, Mismatches: 27, Indels: 50
0.62 0.13 0.25
Matches are distributed among these distances:
8 16 0.13
9 8 0.06
10 70 0.56
11 23 0.18
12 9 0.07
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.66
Consensus pattern (10 bp):
TTCTTCTTCT
Found at i:52433255 original size:21 final size:21
Alignment explanation
Indices: 52433230--52433413 Score: 93
Period size: 18 Copynumber: 9.5 Consensus size: 21
52433220 CCTTCCCTCT
*
52433230 TCTTCTTCTTTCTTTTTTTTC
1 TCTTCTTCTTTCTTTTCTTTC
52433251 TCTTC-TCATTTCATTTTCTTTC
1 TCTTCTTC-TTTC-TTTTCTTTC
*
52433273 -CTTATT-TTTC-TTTCTTTC
1 TCTTCTTCTTTCTTTTCTTTC
**
52433291 -C-TCCCCTTTCCTTTTCTTTC
1 TCTTCTTCTTT-CTTTTCTTTC
*
52433311 -CTTATT-TTTC-TTTCTTTC
1 TCTTCTTCTTTCTTTTCTTTC
**
52433329 -C-TCCCCTTTCCTTTTCTTTC
1 TCTTCTTCTTT-CTTTTCTTTC
52433349 -CTTCTT-TTTC-TTTCTTTC
1 TCTTCTTCTTTCTTTTCTTTC
* *
52433367 -C-TCTCCTTTCCTTTTCCTTC
1 TCTTCTTCTTT-CTTTTCTTTC
*
52433387 T-TT-TTCTTTC-TTCCTTTC
1 TCTTCTTCTTTCTTTTCTTTC
52433405 T-TTCTTCTT
1 TCTTCTTCTT
52433414 CTTCCCCTCT
Statistics
Matches: 128, Mismatches: 18, Indels: 36
0.70 0.10 0.20
Matches are distributed among these distances:
17 5 0.04
18 45 0.35
19 11 0.09
20 42 0.33
21 16 0.12
22 9 0.07
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (21 bp):
TCTTCTTCTTTCTTTTCTTTC
Found at i:52433308 original size:38 final size:38
Alignment explanation
Indices: 52433259--52433404 Score: 222
Period size: 38 Copynumber: 3.8 Consensus size: 38
52433249 TCTCTTCTCA
*
52433259 TTTCATTTTCTTTCCTTATTTTTCTTTCTTTCCTCCCC
1 TTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCCCC
52433297 TTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCCCC
1 TTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCCCC
* *
52433335 TTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCC
1 TTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCCCC
* * *
52433373 TTTCCTTTTCCTT-CTTTTTCTTTCTTCCTTTC
1 TTTCCTTTTCTTTCCTTATT-TTTCTTTCTTTC
52433405 TTTCTTCTTC
Statistics
Matches: 101, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
37 5 0.05
38 96 0.95
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (38 bp):
TTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCCCC
Found at i:52433357 original size:14 final size:14
Alignment explanation
Indices: 52433340--52433413 Score: 55
Period size: 14 Copynumber: 5.1 Consensus size: 14
52433330 TCCCCTTTCC
52433340 TTTTCTTTCCTTCT
1 TTTTCTTTCCTTCT
*
52433354 TTTTCTTTCTTTCCT
1 TTTTCTTTCCTT-CT
52433369 CTCCTTTCCTTTTCCTTCT
1 -T--TTT-C-TTTCCTTCT
52433388 TTTTCTTT-CTTC-
1 TTTTCTTTCCTTCT
*
52433400 CTTTCTTT-CTTCT
1 TTTTCTTTCCTTCT
52433413 T
1 T
52433414 CTTCCCCTCT
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
12 11 0.22
13 4 0.08
14 14 0.29
15 3 0.06
16 4 0.08
18 4 0.08
19 3 0.06
20 6 0.12
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTCTTTCCTTCT
Found at i:52433365 original size:28 final size:28
Alignment explanation
Indices: 52433334--52433413 Score: 85
Period size: 34 Copynumber: 2.8 Consensus size: 28
52433324 CTTTCCTCCC
52433334 CTTTCCTTTTCTTTCCTTCTTTTTCTTT
1 CTTTCCTTTTCTTTCCTTCTTTTTCTTT
52433362 CTTTCCTCTCCTTTCCTTTTCCTTCTTTTTCTTT
1 CTTT-C-CT--TTT-C-TTTCCTTCTTTTTCTTT
52433396 C-TTCC-TTTCTTT-CTTCTT
1 CTTTCCTTTTCTTTCCTTCTT
52433414 CTTCCCCTCT
Statistics
Matches: 46, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
25 6 0.13
26 3 0.07
27 1 0.02
28 7 0.15
29 1 0.02
30 2 0.04
31 1 0.02
32 4 0.09
33 3 0.07
34 18 0.39
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (28 bp):
CTTTCCTTTTCTTTCCTTCTTTTTCTTT
Found at i:52433409 original size:22 final size:23
Alignment explanation
Indices: 52433374--52433416 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
52433364 TTCCTCTCCT
*
52433374 TTCCTTTTCCTTCTTTTTCTTTC
1 TTCCTTTTCCTTCTTCTTCTTTC
*
52433397 TTCC-TTTCTTTCTTCTTCTT
1 TTCCTTTTCCTTCTTCTTCTT
52433417 CCCCTCTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (23 bp):
TTCCTTTTCCTTCTTCTTCTTTC
Found at i:52433414 original size:28 final size:30
Alignment explanation
Indices: 52433336--52433417 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 30
52433326 TTCCTCCCCT
*
52433336 TTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCC
1 TTCC-TTTCTTT-CTTCTTCTTCTTTCTTTCC
*
52433368 TCTCCTTTCCTTT-TCCTTCTT-TTTCTTT-C
1 T-TCCTTT-CTTTCTTCTTCTTCTTTCTTTCC
52433397 TTCCTTTCTTTCTTCTTCTTC
1 TTCCTTTCTTTCTTCTTCTTC
52433418 CCCTCTCCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
27 4 0.09
28 13 0.30
29 2 0.05
30 7 0.16
31 6 0.14
32 4 0.09
33 7 0.16
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (30 bp):
TTCCTTTCTTTCTTCTTCTTCTTTCTTTCC
Found at i:52433415 original size:18 final size:17
Alignment explanation
Indices: 52433206--52433418 Score: 82
Period size: 18 Copynumber: 12.0 Consensus size: 17
52433196 TTACCTTATT
*
52433206 TTCTTTTT-TTCCTTCC
1 TTCTTTTTCTTTCTTCC
* * *
52433222 TTCCCTCTTC-TTCTTCT
1 TT-CTTTTTCTTTCTTCC
52433239 TTCTTTTT-TTTC-T-C
1 TTCTTTTTCTTTCTTCC
*
52433253 TTCTCATTTCATTTTCTTTCC
1 TTCT-TTTTC--TTTC-TTCC
*
52433274 TTATTTTTCTTTCTTTCC
1 TTCTTTTTCTTTC-TTCC
* * *
52433292 TCCCCTTTCCTTTTCTTTCC
1 T-TCTTTTTC-TTTC-TTCC
*
52433312 TTATTTTTCTTTCTTTCC
1 TTCTTTTTCTTTC-TTCC
* * *
52433330 TCCCCTTTCCTTTTCTTTCC
1 T-TCTTTTTC-TTTC-TTCC
52433350 TTCTTTTTCTTTCTTTCC
1 TTCTTTTTCTTTC-TTCC
* *
52433368 -TCTCCTTTCCTT-TTCC
1 TTCT-TTTTCTTTCTTCC
52433384 TTCTTTTTCTTTCTTCC
1 TTCTTTTTCTTTCTTCC
52433401 TTTCTTTCTTC-TTCTTCC
1 -TTCTTT-TTCTTTCTTCC
52433419 CCTCTCCTTC
Statistics
Matches: 149, Mismatches: 29, Indels: 36
0.70 0.14 0.17
Matches are distributed among these distances:
14 4 0.03
15 4 0.03
16 19 0.13
17 21 0.14
18 52 0.35
19 20 0.13
20 25 0.17
21 4 0.03
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (17 bp):
TTCTTTTTCTTTCTTCC
Found at i:52433427 original size:42 final size:40
Alignment explanation
Indices: 52433277--52433430 Score: 108
Period size: 38 Copynumber: 3.9 Consensus size: 40
52433267 TCTTTCCTTA
* * *
52433277 TTTTTCTTTCTTTCCTCCCCTT-TCCT-T--TTCTTTCCTTA
1 TTTTTCTTTCTTTCCTCTCCTTCCCCTCTCCTTCTTT--TTC
* *
52433315 TTTTTCTTTCTTTCCTCCCCTT-TCCT-T--TTCTTTCCTTC
1 TTTTTCTTTCTTTCCTCTCCTTCCCCTCTCCTTCTTT--TTC
* * *
52433353 TTTTTCTTTCTTTCCTCTCCTTTCCTTTTCCTTCTTTTTC
1 TTTTTCTTTCTTTCCTCTCCTTCCCCTCTCCTTCTTTTTC
* *
52433393 TTTCTTCCTTTCTTTCTTCTTCTTCCCCTCTCCTTCTT
1 TTT-TT-CTTTCTTTCCTCTCCTTCCCCTCTCCTTCTT
52433431 CCCCCCACCA
Statistics
Matches: 101, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
38 58 0.57
39 2 0.02
40 7 0.07
41 2 0.02
42 32 0.32
ACGTcount: A:0.01, C:0.36, G:0.00, T:0.64
Consensus pattern (40 bp):
TTTTTCTTTCTTTCCTCTCCTTCCCCTCTCCTTCTTTTTC
Found at i:52433503 original size:27 final size:27
Alignment explanation
Indices: 52433465--52433545 Score: 117
Period size: 27 Copynumber: 3.0 Consensus size: 27
52433455 AATTCAAGGG
*
52433465 TGGTGCCGCCAACCTGGTTCCCTCCAC
1 TGGTGCCGCCAACCTGCTTCCCTCCAC
****
52433492 TGGTGCCGCCAACCTGCTTCCCTTGTT
1 TGGTGCCGCCAACCTGCTTCCCTCCAC
52433519 TGGTGCCGCCAACCTGCTTCCCTCCAC
1 TGGTGCCGCCAACCTGCTTCCCTCCAC
52433546 CCAGGGAGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.10, C:0.43, G:0.21, T:0.26
Consensus pattern (27 bp):
TGGTGCCGCCAACCTGCTTCCCTCCAC
Found at i:52433589 original size:13 final size:12
Alignment explanation
Indices: 52433571--52433604 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
52433561 ATCAGTTCAG
52433571 GTTTTTTTTTTCT
1 GTTTTTTTTTT-T
*
52433584 GTTTTTTTGTTT
1 GTTTTTTTTTTT
52433596 GTTTTTTTT
1 GTTTTTTTT
52433605 ATATATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.85
Consensus pattern (12 bp):
GTTTTTTTTTTT
Found at i:52433627 original size:27 final size:27
Alignment explanation
Indices: 52433597--52433650 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
52433587 TTTTTGTTTG
52433597 TTTTTTTTATATATTTTGGTAAATAAA
1 TTTTTTTTATATATTTTGGTAAATAAA
52433624 TTTTTTTTATATATTTTGGTAAATAAA
1 TTTTTTTTATATATTTTGGTAAATAAA
52433651 AAAAGTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (27 bp):
TTTTTTTTATATATTTTGGTAAATAAA
Found at i:52434104 original size:10 final size:10
Alignment explanation
Indices: 52434089--52434227 Score: 82
Period size: 10 Copynumber: 14.5 Consensus size: 10
52434079 TTCTCTTCTC
52434089 CTTTCCTTTT
1 CTTTCCTTTT
52434099 CTTTCCTTATT
1 CTTTCCTT-TT
52434110 -TTT-C-TTT
1 CTTTCCTTTT
***
52434117 CTTTCCTCCC
1 CTTTCCTTTT
52434127 CTTTCCTTTT
1 CTTTCCTTTT
52434137 CTTTCCTTATT
1 CTTTCCTT-TT
52434148 -TTT-C-TTT
1 CTTTCCTTTT
* **
52434155 CTTT-CGTCC
1 CTTTCCTTTT
52434164 CATTTCCTTTT
1 C-TTTCCTTTT
52434175 CTTTCCTTCTT
1 CTTTCCTT-TT
52434186 -TTT-C-TTT
1 CTTTCCTTTT
* *
52434193 CTTTCCTCTC
1 CTTTCCTTTT
52434203 CTTTCCTTTT
1 CTTTCCTTTT
* *
52434213 CCTTCTTTTT
1 CTTTCCTTTT
52434223 CTTTC
1 CTTTC
52434228 TTCCTTTCTT
Statistics
Matches: 98, Mismatches: 18, Indels: 26
0.69 0.13 0.18
Matches are distributed among these distances:
7 6 0.06
8 13 0.13
9 7 0.07
10 63 0.64
11 9 0.09
ACGTcount: A:0.02, C:0.32, G:0.01, T:0.65
Consensus pattern (10 bp):
CTTTCCTTTT
Found at i:52434138 original size:38 final size:38
Alignment explanation
Indices: 52434088--52434235 Score: 217
Period size: 38 Copynumber: 3.9 Consensus size: 38
52434078 TTTCTCTTCT
52434088 CCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCC
1 CCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCC
*
52434126 CCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCGTCC
1 CCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCC
* * *
52434164 CATTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCT
1 CCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCC
* * *
52434202 CCTTTCCTTTTCCTT-CTTTTTCTTTCTTCCTTTC
1 CCTTTCCTTTTCTTTCCTTATT-TTTCTTTCTTTC
52434236 TTTCTTCTTC
Statistics
Matches: 100, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
37 5 0.05
38 95 0.95
ACGTcount: A:0.02, C:0.33, G:0.01, T:0.64
Consensus pattern (38 bp):
CCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCC
Found at i:52434188 original size:14 final size:14
Alignment explanation
Indices: 52434171--52434244 Score: 55
Period size: 14 Copynumber: 5.1 Consensus size: 14
52434161 TCCCATTTCC
52434171 TTTTCTTTCCTTCT
1 TTTTCTTTCCTTCT
*
52434185 TTTTCTTTCTTTCCT
1 TTTTCTTTCCTT-CT
52434200 CTCCTTTCCTTTTCCTTCT
1 -T--TTT-C-TTTCCTTCT
52434219 TTTTCTTT-CTTC-
1 TTTTCTTTCCTTCT
*
52434231 CTTTCTTT-CTTCT
1 TTTTCTTTCCTTCT
52434244 T
1 T
52434245 CTTCCCCTCT
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
12 11 0.22
13 4 0.08
14 14 0.29
15 3 0.06
16 4 0.08
18 4 0.08
19 3 0.06
20 6 0.12
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTCTTTCCTTCT
Found at i:52434197 original size:28 final size:28
Alignment explanation
Indices: 52434166--52434244 Score: 83
Period size: 34 Copynumber: 2.7 Consensus size: 28
52434156 TTTCGTCCCA
52434166 TTTCCTTTTCTTTCCTTCTTTTTCTTTC
1 TTTCCTTTTCTTTCCTTCTTTTTCTTTC
52434194 TTTCCTCTCCTTTCCTTTTCCTTCTTTTTCTTTC
1 TTT-C-CT--TTT-C-TTTCCTTCTTTTTCTTTC
52434228 -TTCC-TTTCTTT-CTTCTT
1 TTTCCTTTTCTTTCCTTCTT
52434245 CTTCCCCTCT
Statistics
Matches: 45, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
25 6 0.13
26 3 0.07
27 1 0.02
28 6 0.13
29 1 0.02
30 2 0.04
31 1 0.02
32 4 0.09
33 3 0.07
34 18 0.40
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (28 bp):
TTTCCTTTTCTTTCCTTCTTTTTCTTTC
Found at i:52434228 original size:10 final size:10
Alignment explanation
Indices: 52434176--52434247 Score: 54
Period size: 10 Copynumber: 6.6 Consensus size: 10
52434166 TTTCCTTTTC
*
52434176 TTTCCTTCTT
1 TTTCTTTCTT
52434186 TTTCTTTCTT
1 TTTCTTTCTT
*
52434196 TCCTCTCCTTTCCT
1 T--T-T-CTTTCTT
*
52434210 TTTCCTTCTT
1 TTTCTTTCTT
52434220 TTTCTTTCTT
1 TTTCTTTCTT
52434230 CCTTTCTTTCTT
1 --TTTCTTTCTT
*
52434242 CTTCTT
1 TTTCTT
52434248 CCCCTCTCCT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
10 29 0.58
11 1 0.02
12 12 0.24
13 1 0.02
14 7 0.14
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:52434240 original size:22 final size:23
Alignment explanation
Indices: 52434205--52434247 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
52434195 TTCCTCTCCT
*
52434205 TTCCTTTTCCTTCTTTTTCTTTC
1 TTCCTTTTCCTTCTTCTTCTTTC
*
52434228 TTCC-TTTCTTTCTTCTTCTT
1 TTCCTTTTCCTTCTTCTTCTT
52434248 CCCCTCTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (23 bp):
TTCCTTTTCCTTCTTCTTCTTTC
Found at i:52434245 original size:28 final size:30
Alignment explanation
Indices: 52434167--52434248 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 30
52434157 TTCGTCCCAT
*
52434167 TTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCC
1 TTCC-TTTCTTT-CTTCTTCTTCTTTCTTTCC
*
52434199 TCTCCTTTCCTTT-TCCTTCTT-TTTCTTT-C
1 T-TCCTTT-CTTTCTTCTTCTTCTTTCTTTCC
52434228 TTCCTTTCTTTCTTCTTCTTC
1 TTCCTTTCTTTCTTCTTCTTC
52434249 CCCTCTCCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
27 4 0.09
28 13 0.30
29 2 0.05
30 7 0.16
31 6 0.14
32 4 0.09
33 7 0.16
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (30 bp):
TTCCTTTCTTTCTTCTTCTTCTTTCTTTCC
Found at i:52434246 original size:18 final size:17
Alignment explanation
Indices: 52434172--52434249 Score: 72
Period size: 18 Copynumber: 4.5 Consensus size: 17
52434162 CCCATTTCCT
52434172 TTTCTTTCCTTCTTTTTC
1 TTTC-TTCCTTCTTTTTC
*
52434190 TTTCTTTCC-TCTCCTTTC
1 TTTC-TTCCTTCT-TTTTC
*
52434208 CTT-TTCCTTCTTTTTC
1 TTTCTTCCTTCTTTTTC
52434224 TTTCTTCCTTTCTTTCTTC
1 TTTCTTCC-TTCTTT-TTC
52434243 -TTCTTCC
1 TTTCTTCC
52434250 CCTCTCCTTC
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
16 10 0.20
17 10 0.20
18 28 0.55
19 3 0.06
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTCTTCCTTCTTTTTC
Found at i:52434258 original size:42 final size:40
Alignment explanation
Indices: 52434181--52434261 Score: 99
Period size: 42 Copynumber: 2.0 Consensus size: 40
52434171 TTTTCTTTCC
* * *
52434181 TTCTTTTTCTTTCTTTCCTCTCCTTTCCTTTTCCTTCTTT
1 TTCTTTTTCTTTCTTTCCTCTCCTTCCCCTCTCCTTCTTT
* *
52434221 TTCTTTCTTCCTTTCTTTCTTCTTCTTCCCCTCTCCTTCTT
1 TTCTTT-TT-CTTTCTTTCCTCTCCTTCCCCTCTCCTTCTT
52434262 CCCCCCACCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 6 0.18
41 2 0.06
42 26 0.76
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (40 bp):
TTCTTTTTCTTTCTTTCCTCTCCTTCCCCTCTCCTTCTTT
Found at i:52434334 original size:27 final size:27
Alignment explanation
Indices: 52434296--52434376 Score: 117
Period size: 27 Copynumber: 3.0 Consensus size: 27
52434286 AATTCAAGGG
*
52434296 TGGTGCCGCCAACCTGGTTCCCTCCAC
1 TGGTGCCGCCAACCTGCTTCCCTCCAC
****
52434323 TGGTGCCGCCAACCTGCTTCCCTTGTT
1 TGGTGCCGCCAACCTGCTTCCCTCCAC
52434350 TGGTGCCGCCAACCTGCTTCCCTCCAC
1 TGGTGCCGCCAACCTGCTTCCCTCCAC
52434377 CCAGGGAGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.10, C:0.43, G:0.21, T:0.26
Consensus pattern (27 bp):
TGGTGCCGCCAACCTGCTTCCCTCCAC
Found at i:52434420 original size:13 final size:12
Alignment explanation
Indices: 52434402--52434435 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
52434392 ATCAGTTCAG
52434402 GTTTTTTTTTTCT
1 GTTTTTTTTTT-T
*
52434415 GTTTTTTTGTTT
1 GTTTTTTTTTTT
52434427 GTTTTTTTT
1 GTTTTTTTT
52434436 ATATATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.85
Consensus pattern (12 bp):
GTTTTTTTTTTT
Found at i:52434440 original size:831 final size:838
Alignment explanation
Indices: 52433137--52434810 Score: 3218
Period size: 831 Copynumber: 2.0 Consensus size: 838
52433127 ACGTAAAATG
52433137 TACTTAACATTATTTTTTAACACACAAATATTACAAAAATCTTAAATTAATAATAAAAATTACCT
1 TACTTAACATTATTTTTTAACACACAAATATTACAAAAATCTTAAATTAATAATAAAAATTACCT
*
52433202 TATTTTCTTTTTTTCCTTCCTTCCCTCTTCTTCTTCTTTCTTTTTTTTCTCTTCTCATTTCATTT
66 TATTTTCTTTTTTTCCTTCCTT--CTCTGCTTCTTC-TTCTTTTTTTTCTCTTCTCATTTCATTT
52433267 TCTTTCCTTATTTTTCTTTCTTTCCTCCCCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTC
128 TCTTTCCTTATTTTTCTTTCTTTCCTCCCCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTC
*
52433332 CCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTTTCCTTTTCCTTCTTTTTCTTTC
193 CCATTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTTTCCTTTTCCTTCTTTTTCTTTC
52433397 TTCCTTTCTTTCTTCTTCTTCCCCTCTCCTTCTTCCCCCCACCAACCGACCACCCTTAAATTCAA
258 TTCCTTTCTTTCTTCTTCTTCCCCTCTCCTTCTTCCCCCCACCAACCGACCACCCTTAAATTCAA
52433462 GGGTGGTGCCGCCAACCTGGTTCCCTCCACTGGTGCCGCCAACCTGCTTCCCTTGTTTGGTGCCG
323 GGGTGGTGCCGCCAACCTGGTTCCCTCCACTGGTGCCGCCAACCTGCTTCCCTTGTTTGGTGCCG
52433527 CCAACCTGCTTCCCTCCACCCAGGGAGTTGTCAAATCAGTTCAGGTTTTTTTTTTCTGTTTTTTT
388 CCAACCTGCTTCCCTCCACCCAGGGAGTTGTCAAATCAGTTCAGGTTTTTTTTTTCTGTTTTTTT
52433592 GTTTGTTTTTTTTATATATTTTGGTAAATAAATTTTTTTTATATATTTTGGTAAATAAAAAAAGT
453 GTTTGTTTTTTTTATATATTTTGGTAAATAAATTTTTTTTATATATTTTGGTAAATAAAAAAAGT
52433657 TATAACATTTTGGTAATTTTTTATTTTTTTATATTATTTCTGTAAAAAACCCAAAATTATGCAAA
518 TATAACATTTTGGTAATTTTTTATTTTTTTATATTATTTCTGTAAAAAACCCAAAATTATGCAAA
52433722 CCCTTAATCGAAAGAGAGATTTTATCTAAGAATCATGGGGAACAAAATAACATAAAGTGAAATGA
583 CCCTTAATCGAAAGAGAGATTTTATCTAAGAATCATGGGGAACAAAATAACATAAAGTGAAATGA
52433787 TCTTAATTAATAAAAAATTGGGTTTTTAAGAAAAAAATTATTTTCCATGGGAATATTTCCCAATT
648 TCTTAATTAATAAAAAATTGGGTTTTTAAGAAAAAAATTATTTTCCATGGGAATATTTCCCAATT
52433852 ACAATTTTACACAAAATTTAAAACTTCATAGTTTATTGATTGGTCAAATGAGGTGAGTTTAGTAT
713 ACAATTTTACACAAAATTTAAAACTTCATAGTTTATTGATTGGTCAAATGAGGTGAGTTTAGTAT
52433917 AGATTTTGGGTGCAACTGCCAAGATTGGGTGAGCAAGAAGACCAATTGGAATGAACAATTT
778 AGATTTTGGGTGCAACTGCCAAGATTGGGTGAGCAAGAAGACCAATTGGAATGAACAATTT
52433978 TACTTAACATTATTTTTTAACACACAAATATTACAAAAATCTTAAATTAATAATAAAAATTACCT
1 TACTTAACATTATTTTTTAACACACAAATATTACAAAAATCTTAAATTAATAATAAAAATTACCT
* * *
52434043 TTTTTTCTTTTTTT-CTTCC-T-TC-GC-TCTTC-T-TTTTTTTTCTCTTCTCCTTTCCTTTTCT
66 TATTTTCTTTTTTTCCTTCCTTCTCTGCTTCTTCTTCTTTTTTTTCTCTTCTCATTTCATTTTCT
*
52434101 TTCCTTATTTTTCTTTCTTTCCTCCCCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCGTCCCA
131 TTCCTTATTTTTCTTTCTTTCCTCCCCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCCCA
52434166 TTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTTTCCTTTTCCTTCTTTTTCTTTCTTC
196 TTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTTTCCTTTTCCTTCTTTTTCTTTCTTC
52434231 CTTTCTTTCTTCTTCTTCCCCTCTCCTTCTTCCCCCCACCAACCGACCACCCTTAAATTCAAGGG
261 CTTTCTTTCTTCTTCTTCCCCTCTCCTTCTTCCCCCCACCAACCGACCACCCTTAAATTCAAGGG
52434296 TGGTGCCGCCAACCTGGTTCCCTCCACTGGTGCCGCCAACCTGCTTCCCTTGTTTGGTGCCGCCA
326 TGGTGCCGCCAACCTGGTTCCCTCCACTGGTGCCGCCAACCTGCTTCCCTTGTTTGGTGCCGCCA
52434361 ACCTGCTTCCCTCCACCCAGGGAGTTGTCAAATCAGTTCAGGTTTTTTTTTTCTGTTTTTTTGTT
391 ACCTGCTTCCCTCCACCCAGGGAGTTGTCAAATCAGTTCAGGTTTTTTTTTTCTGTTTTTTTGTT
52434426 TGTTTTTTTTATATATTTTGGTAAATAAATTTTTTTTATATATTTTGGTAAATAAAAAAAGTTAT
456 TGTTTTTTTTATATATTTTGGTAAATAAATTTTTTTTATATATTTTGGTAAATAAAAAAAGTTAT
52434491 AACATTTTGGTAATTTTTTATTTTTTTATATTATTTCTGTAAAAAACCCAAAATTATGCAAACCC
521 AACATTTTGGTAATTTTTTATTTTTTTATATTATTTCTGTAAAAAACCCAAAATTATGCAAACCC
52434556 TTAATCGAAAGAGAGATTTTATCTAAGAATCATGGGGAACAAAATAACATAAAGTGAAATGATCT
586 TTAATCGAAAGAGAGATTTTATCTAAGAATCATGGGGAACAAAATAACATAAAGTGAAATGATCT
52434621 TAATTAATAAAAAATTGGGTTTTTAAGAAAAAAATTATTTTCCATGGGAATATTTCCCAATTACA
651 TAATTAATAAAAAATTGGGTTTTTAAGAAAAAAATTATTTTCCATGGGAATATTTCCCAATTACA
52434686 ATTTTACACAAAATTTAAAACTTCATAGTTTATTGATTGGTCAAATGAGGTGAGTTTAGTATAGA
716 ATTTTACACAAAATTTAAAACTTCATAGTTTATTGATTGGTCAAATGAGGTGAGTTTAGTATAGA
52434751 TTTTGGGTGCAACTGCCAAGATTGGGTGAGCAAGAAGACCAATTGGAATGAACAATTT
781 TTTTGGGTGCAACTGCCAAGATTGGGTGAGCAAGAAGACCAATTGGAATGAACAATTT
52434809 TA
1 TA
52434811 AGATGGCATT
Statistics
Matches: 827, Mismatches: 6, Indels: 10
0.98 0.01 0.01
Matches are distributed among these distances:
831 734 0.89
832 1 0.00
834 5 0.01
835 1 0.00
836 2 0.00
839 1 0.00
840 5 0.01
841 78 0.09
ACGTcount: A:0.25, C:0.21, G:0.11, T:0.44
Consensus pattern (838 bp):
TACTTAACATTATTTTTTAACACACAAATATTACAAAAATCTTAAATTAATAATAAAAATTACCT
TATTTTCTTTTTTTCCTTCCTTCTCTGCTTCTTCTTCTTTTTTTTCTCTTCTCATTTCATTTTCT
TTCCTTATTTTTCTTTCTTTCCTCCCCTTTCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCCCA
TTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTTTCCTTTTCCTTCTTTTTCTTTCTTC
CTTTCTTTCTTCTTCTTCCCCTCTCCTTCTTCCCCCCACCAACCGACCACCCTTAAATTCAAGGG
TGGTGCCGCCAACCTGGTTCCCTCCACTGGTGCCGCCAACCTGCTTCCCTTGTTTGGTGCCGCCA
ACCTGCTTCCCTCCACCCAGGGAGTTGTCAAATCAGTTCAGGTTTTTTTTTTCTGTTTTTTTGTT
TGTTTTTTTTATATATTTTGGTAAATAAATTTTTTTTATATATTTTGGTAAATAAAAAAAGTTAT
AACATTTTGGTAATTTTTTATTTTTTTATATTATTTCTGTAAAAAACCCAAAATTATGCAAACCC
TTAATCGAAAGAGAGATTTTATCTAAGAATCATGGGGAACAAAATAACATAAAGTGAAATGATCT
TAATTAATAAAAAATTGGGTTTTTAAGAAAAAAATTATTTTCCATGGGAATATTTCCCAATTACA
ATTTTACACAAAATTTAAAACTTCATAGTTTATTGATTGGTCAAATGAGGTGAGTTTAGTATAGA
TTTTGGGTGCAACTGCCAAGATTGGGTGAGCAAGAAGACCAATTGGAATGAACAATTT
Found at i:52434458 original size:27 final size:27
Alignment explanation
Indices: 52434428--52434481 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
52434418 TTTTTGTTTG
52434428 TTTTTTTTATATATTTTGGTAAATAAA
1 TTTTTTTTATATATTTTGGTAAATAAA
52434455 TTTTTTTTATATATTTTGGTAAATAAA
1 TTTTTTTTATATATTTTGGTAAATAAA
52434482 AAAAGTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (27 bp):
TTTTTTTTATATATTTTGGTAAATAAA
Found at i:52443432 original size:56 final size:56
Alignment explanation
Indices: 52443366--52443564 Score: 250
Period size: 56 Copynumber: 3.7 Consensus size: 56
52443356 GGGAATGAGA
52443366 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
52443422 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
*** * * **
52443478 TCCCCCATAAGACCATGCCTGGGACATGGC-TTGGGCA-C---CA-A-TATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATT-GGCATCATTGAGATTATGAGAGG
* * *
52443528 TCCCATGTAAAACCATATCTGGGATATGGCATTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
52443565 GTACAGAAAA
Statistics
Matches: 127, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
50 34 0.27
51 3 0.02
52 1 0.01
55 3 0.02
56 86 0.68
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.25
Consensus pattern (56 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
Found at i:52443830 original size:12 final size:12
Alignment explanation
Indices: 52443813--52443851 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
52443803 ATGATTTATT
52443813 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
52443825 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
52443837 TAAGTGAGTAAG
1 TAAGTAAGCAAG
52443849 TAA
1 TAA
52443852 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:52445821 original size:13 final size:13
Alignment explanation
Indices: 52445803--52445829 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
52445793 GACATGTTTT
52445803 GATAAAATTATTC
1 GATAAAATTATTC
52445816 GATAAAATTATTC
1 GATAAAATTATTC
52445829 G
1 G
52445830 GTAATAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.37
Consensus pattern (13 bp):
GATAAAATTATTC
Found at i:52446980 original size:48 final size:48
Alignment explanation
Indices: 52446924--52447107 Score: 165
Period size: 48 Copynumber: 3.8 Consensus size: 48
52446914 CGCATGGAAT
*
52446924 GAGGCTTACGGAAAGTAATAAAGTGACCCTGCTCCCAGATGTAAGGGG
1 GAGGCTTACGGAAAGTAATAAAGTGACCCTGCTCCCAGACGTAAGGGG
* * * *
52446972 GAGGCTTAC-GAAAGCTAAGAAAGTGACCTTGCTCTCAGACGTATGGGG
1 GAGGCTTACGGAAAG-TAATAAAGTGACCCTGCTCCCAGACGTAAGGGG
* * * * * ** *
52447020 GAGGCTTATGGAAAGTAGTAAAGTGGCCTTACTCCC-GAACACATGGGGG
1 GAGGCTTACGGAAAGTAATAAAGTGACCCTGCTCCCAG-ACGTA-AGGGG
* * * * *
52447069 GAGGCTTATGAAAAGTAATAAACTAACCTTGCTCCCAGA
1 GAGGCTTACGGAAAGTAATAAAGTGACCCTGCTCCCAGA
52447108 TGCACGGAGG
Statistics
Matches: 111, Mismatches: 20, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
47 6 0.05
48 64 0.58
49 40 0.36
50 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.21
Consensus pattern (48 bp):
GAGGCTTACGGAAAGTAATAAAGTGACCCTGCTCCCAGACGTAAGGGG
Found at i:52447849 original size:20 final size:18
Alignment explanation
Indices: 52447799--52447850 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
52447789 AATGTAGATA
52447799 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
52447816 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
52447836 AATATTAAATTAATA
1 AATATTAAATTAATA
52447851 AAATGCCTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 3 0.10
20 15 0.50
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:52452456 original size:24 final size:25
Alignment explanation
Indices: 52452415--52452467 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
52452405 AAATATCCCT
*
52452415 GAAG-TAATAAGAGTTTAACTAGGAA
1 GAAGATAATAAGAATTTAACT-GGAA
52452440 -AAGATAAT-AGAATTTAACTGGAA
1 GAAGATAATAAGAATTTAACTGGAA
52452463 GAAGA
1 GAAGA
52452468 AACCCAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 4 0.16
24 17 0.68
25 4 0.16
ACGTcount: A:0.51, C:0.04, G:0.23, T:0.23
Consensus pattern (25 bp):
GAAGATAATAAGAATTTAACTGGAA
Found at i:52456175 original size:12 final size:12
Alignment explanation
Indices: 52456158--52456197 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
52456148 CCTTATATGA
*
52456158 TATATCTATATC
1 TATATCTATACC
52456170 TATATCTATACC
1 TATATCTATACC
52456182 TATATCTATACC
1 TATATCTATACC
52456194 TATA
1 TATA
52456198 CATGTGTGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.45
Consensus pattern (12 bp):
TATATCTATACC
Found at i:52456198 original size:6 final size:6
Alignment explanation
Indices: 52456158--52456197 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
52456148 CCTTATATGA
* *
52456158 TATATC TATATC TATATC TATACC TATATC TATACC TATA
1 TATATC TATATC TATATC TATATC TATATC TATATC TATA
52456198 CATGTGTGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.45
Consensus pattern (6 bp):
TATATC
Found at i:52456407 original size:6 final size:6
Alignment explanation
Indices: 52456396--52456434 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
52456386 TTTGGCCCTT
52456396 TATATG TATATG TATATG TATATG TATATG TATATG TAT
1 TATATG TATATG TATATG TATATG TATATG TATATG TAT
52456435 GGTGTTGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:52465514 original size:34 final size:34
Alignment explanation
Indices: 52465447--52465515 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 34
52465437 ATACACCATG
*
52465447 TAACCAACCAACACACCAATAGCTCGTAGGAGCA
1 TAACCAACCAACACACCAATAGCTCATAGGAGCA
*
52465481 TAACCATCCAACACACCAATAGCTCAATA-GAGCA
1 TAACCAACCAACACACCAATAGCTC-ATAGGAGCA
52465515 T
1 T
52465516 GGATCGAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 30 0.94
35 2 0.06
ACGTcount: A:0.42, C:0.32, G:0.12, T:0.14
Consensus pattern (34 bp):
TAACCAACCAACACACCAATAGCTCATAGGAGCA
Found at i:52470015 original size:16 final size:16
Alignment explanation
Indices: 52469994--52470024 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52469984 TTAATTTTAA
*
52469994 TTAATTAATTAATTTC
1 TTAATTAAATAATTTC
52470010 TTAATTAAATAATTT
1 TTAATTAAATAATTT
52470025 TCTCAACCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAATTAAATAATTTC
Found at i:52479282 original size:16 final size:16
Alignment explanation
Indices: 52479259--52479312 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
52479249 AAACTTTTAA
52479259 AGAAAATTAGAAAGAT
1 AGAAAATTAGAAAGAT
* *
52479275 AAAAAATT-GAAGGAT
1 AGAAAATTAGAAAGAT
* *
52479290 AGTAAATTAGAATGAT
1 AGAAAATTAGAAAGAT
52479306 AGAAAAT
1 AGAAAAT
52479313 ATATATATTC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
15 12 0.39
16 19 0.61
ACGTcount: A:0.59, C:0.00, G:0.19, T:0.22
Consensus pattern (16 bp):
AGAAAATTAGAAAGAT
Found at i:52488143 original size:44 final size:44
Alignment explanation
Indices: 52488095--52488185 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 44
52488085 GTAGGTCAAA
52488095 TAATATTAAAATAA-TCTACACTAATCAAAATTTAAGTGGAAAAC
1 TAATATTAAAATAACT-TACACTAATCAAAATTTAAGTGGAAAAC
* * *
52488139 TAATATTAAAATAACTTACACTAATTAAAGTTTAAGTGGTAAAC
1 TAATATTAAAATAACTTACACTAATCAAAATTTAAGTGGAAAAC
52488183 TAA
1 TAA
52488186 AAACATAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 42 0.98
45 1 0.02
ACGTcount: A:0.51, C:0.10, G:0.08, T:0.32
Consensus pattern (44 bp):
TAATATTAAAATAACTTACACTAATCAAAATTTAAGTGGAAAAC
Found at i:52491200 original size:604 final size:604
Alignment explanation
Indices: 52490052--52491260 Score: 2391
Period size: 604 Copynumber: 2.0 Consensus size: 604
52490042 TAATTGAGAA
52490052 AATTAGATCAATTGAGGGGTTAATTGAGAAAGGACCGAATTGTATAAACTGTGAAATTTGGGGGA
1 AATTAGATCAATTGAGGGGTTAATTGAGAAAGGACCGAATTGTATAAACTGTGAAATTTGGGGGA
52490117 AAATGGTAATTAACATCATGCACTAAAACAGTTTTGGACAGCAACATAACTCTAACTTTGAAAAA
66 AAATGGTAATTAACATCATGCACTAAAACAGTTTTGGACAGCAACATAACTCTAACTTTGAAAAA
52490182 TCACCAAAAATTGTAGATATTGAATTATAGGATGAATAAAATATGAAATTAAAGCTTATTGAGTC
131 TCACCAAAAATTGTAGATATTGAATTATAGGATGAATAAAATATGAAATTAAAGCTTATTGAGTC
52490247 TAGTTTCTTATAAAAGAAACGGTGTAAGCAATGGAATTATAAATCATGAGATATAATAGATTTTG
196 TAGTTTCTTATAAAAGAAACGGTGTAAGCAATGGAATTATAAATCATGAGATATAATAGATTTTG
52490312 TGAGACAATGTCAGAATGAATTCGGGTTCCCCTGTTCTGACTTTGAAAACTCATTCAAAATTGTA
261 TGAGACAATGTCAGAATGAATTCGGGTTCCCCTGTTCTGACTTTGAAAACTCATTCAAAATTGTA
52490377 AAAAAATTATTATGAGTTATAATTTATATGGTTAGAATCCTTAATGAGTCTATTTTCATAAGAAA
326 AAAAAATTATTATGAGTTATAATTTATATGGTTAGAATCCTTAATGAGTCTATTTTCATAAGAAA
52490442 CAAATAGAAACATCATCTGAATTTTGTACAATGAGATAATTAATTTTTAGTGAAGAGTGGTCGGA
391 CAAATAGAAACATCATCTGAATTTTGTACAATGAGATAATTAATTTTTAGTGAAGAGTGGTCGGA
52490507 ACTGTCAGACAACGAAATAGGAGAAATTTAAAGAATAAACTGTACTATTTGGATGAACCAAAAAT
456 ACTGTCAGACAACGAAATAGGAGAAATTTAAAGAATAAACTGTACTATTTGGATGAACCAAAAAT
52490572 TCTGAAAATTTTATGGTAAGAAGATATGTGAGTCTAGTTTCAGGGAAAATTTACATATCTTAATT
521 TCTGAAAATTTTATGGTAAGAAGATATGTGAGTCTAGTTTCAGGGAAAATTTACATATCTTAATT
52490637 TAGAACTCTGTAGCTCCAG
586 TAGAACTCTGTAGCTCCAG
* *
52490656 AATTAGATTAATTGATGGGTTAATTGAGAAAGGACCGAATTGTATAAACTGTGAAATTTGGGGGA
1 AATTAGATCAATTGAGGGGTTAATTGAGAAAGGACCGAATTGTATAAACTGTGAAATTTGGGGGA
52490721 AAATGGTAATTAACATCATGCACTAAAACAGTTTTGGACAGCAACATAACTCTAACTTTGAAAAA
66 AAATGGTAATTAACATCATGCACTAAAACAGTTTTGGACAGCAACATAACTCTAACTTTGAAAAA
52490786 TCACCAAAAATTGTAGATATTGAATTATAGGATGAATAAAATATGAAATTAAAGCTTATTGAGTC
131 TCACCAAAAATTGTAGATATTGAATTATAGGATGAATAAAATATGAAATTAAAGCTTATTGAGTC
52490851 TAGTTTCTTATAAAAGAAACGGTGTAAGCAATGGAATTATAAATCATGAGATATAATAGATTTTG
196 TAGTTTCTTATAAAAGAAACGGTGTAAGCAATGGAATTATAAATCATGAGATATAATAGATTTTG
52490916 TGAGACAATGTCAGAATGAATTCGGGTTCCCCTGTTCTGACTTTGAAAACTCATTCAAAATTGTA
261 TGAGACAATGTCAGAATGAATTCGGGTTCCCCTGTTCTGACTTTGAAAACTCATTCAAAATTGTA
52490981 AAAAAATTATTATGAGTTATAATTTATATGGTTAGAATCCTTAATGAGTCTATTTTCATAAGAAA
326 AAAAAATTATTATGAGTTATAATTTATATGGTTAGAATCCTTAATGAGTCTATTTTCATAAGAAA
52491046 CAAATAGAAACATCATCTGAATTTTGTACAATGAGATAATTAATTTTTAGTGAAGAGTGGTCGGA
391 CAAATAGAAACATCATCTGAATTTTGTACAATGAGATAATTAATTTTTAGTGAAGAGTGGTCGGA
52491111 ACTGTCAGACAACGAAATAGGAGAAATTTAAAGAATAAACTGTACTATTTGGATGAACCAAAAAT
456 ACTGTCAGACAACGAAATAGGAGAAATTTAAAGAATAAACTGTACTATTTGGATGAACCAAAAAT
*
52491176 TCTGAAAATTTTATGGTAAGAAGATATGTGAGTCTAGTTTCAGGGAACATTTACATATCTTAATT
521 TCTGAAAATTTTATGGTAAGAAGATATGTGAGTCTAGTTTCAGGGAAAATTTACATATCTTAATT
52491241 TAGAACTCTGTAGCTCCAG
586 TAGAACTCTGTAGCTCCAG
52491260 A
1 A
52491261 TAAAAATAAA
Statistics
Matches: 602, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
604 602 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.32
Consensus pattern (604 bp):
AATTAGATCAATTGAGGGGTTAATTGAGAAAGGACCGAATTGTATAAACTGTGAAATTTGGGGGA
AAATGGTAATTAACATCATGCACTAAAACAGTTTTGGACAGCAACATAACTCTAACTTTGAAAAA
TCACCAAAAATTGTAGATATTGAATTATAGGATGAATAAAATATGAAATTAAAGCTTATTGAGTC
TAGTTTCTTATAAAAGAAACGGTGTAAGCAATGGAATTATAAATCATGAGATATAATAGATTTTG
TGAGACAATGTCAGAATGAATTCGGGTTCCCCTGTTCTGACTTTGAAAACTCATTCAAAATTGTA
AAAAAATTATTATGAGTTATAATTTATATGGTTAGAATCCTTAATGAGTCTATTTTCATAAGAAA
CAAATAGAAACATCATCTGAATTTTGTACAATGAGATAATTAATTTTTAGTGAAGAGTGGTCGGA
ACTGTCAGACAACGAAATAGGAGAAATTTAAAGAATAAACTGTACTATTTGGATGAACCAAAAAT
TCTGAAAATTTTATGGTAAGAAGATATGTGAGTCTAGTTTCAGGGAAAATTTACATATCTTAATT
TAGAACTCTGTAGCTCCAG
Found at i:52492131 original size:46 final size:46
Alignment explanation
Indices: 52492064--52492186 Score: 219
Period size: 46 Copynumber: 2.7 Consensus size: 46
52492054 GATCAGTAAC
*
52492064 AAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAAGTGACA
1 AAGTGATAAGTGATAGCTTTAGCTACACTTATCTAATCAAGTGACA
*
52492110 AAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACA
1 AAGTGATAAGTGATAGCTTTAGCTACACTTATCTAATCAAGTGACA
*
52492156 AAGTGATAAGTGATAGCTTCAGCTACACTTA
1 AAGTGATAAGTGATAGCTTTAGCTACACTTA
52492187 GGGGTGTGCA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 74 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (46 bp):
AAGTGATAAGTGATAGCTTTAGCTACACTTATCTAATCAAGTGACA
Found at i:52492570 original size:9 final size:9
Alignment explanation
Indices: 52492558--52492625 Score: 66
Period size: 9 Copynumber: 7.4 Consensus size: 9
52492548 AAAATAAAAA
*
52492558 AATTTGGGT
1 AATTCGGGT
*
52492567 AATTCGGGC
1 AATTCGGGT
*
52492576 ATTTTTCGG-T
1 A-AT-TCGGGT
*
52492586 AATTCGGTT
1 AATTCGGGT
*
52492595 AATTCGGTT
1 AATTCGGGT
52492604 AATTCGGGT
1 AATTCGGGT
52492613 AATTCGGGT
1 AATTCGGGT
52492622 AATT
1 AATT
52492626 TTTAACCAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
8 4 0.08
9 40 0.80
10 2 0.04
11 4 0.08
ACGTcount: A:0.22, C:0.10, G:0.26, T:0.41
Consensus pattern (9 bp):
AATTCGGGT
Found at i:52492905 original size:45 final size:45
Alignment explanation
Indices: 52492811--52492969 Score: 205
Period size: 51 Copynumber: 3.4 Consensus size: 45
52492801 GAACACCCCT
52492811 AGCTACACTTATCTGATC-AG-GGACAAGTGATAAGTGATAGCTTC
1 AGCTACACTTATCTGATCAAGTGGA-AAGTGATAAGTGATAGCTTC
* *
52492855 AGCTACACTTATCTGATCAAGTGGAAAGTGATGAGTGATAGATTC
1 AGCTACACTTATCTGATCAAGTGGAAAGTGATAAGTGATAGCTTC
* *
52492900 GGCTACAATTATCTGATTAGTGACAAGTGGAAAGTGATAAGTGATAGCTTC
1 AGCTACACTTATCTG---A-T--CAAGTGGAAAGTGATAAGTGATAGCTTC
52492951 AGCTACACTTATCTGATCA
1 AGCTACACTTATCTGATCA
52492970 GTGTAGGTGG
Statistics
Matches: 99, Mismatches: 8, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
44 18 0.18
45 35 0.35
46 3 0.03
47 1 0.01
48 2 0.02
49 1 0.01
51 39 0.39
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.29
Consensus pattern (45 bp):
AGCTACACTTATCTGATCAAGTGGAAAGTGATAAGTGATAGCTTC
Found at i:52495340 original size:16 final size:17
Alignment explanation
Indices: 52495316--52495349 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
52495306 GTGAATTTCA
52495316 TCTTAGTTT-TTTTATT
1 TCTTAGTTTGTTTTATT
*
52495332 TCTTTGTTTGTTTTATT
1 TCTTAGTTTGTTTTATT
52495349 T
1 T
52495350 ATTTTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.09, C:0.06, G:0.09, T:0.76
Consensus pattern (17 bp):
TCTTAGTTTGTTTTATT
Found at i:52496089 original size:27 final size:26
Alignment explanation
Indices: 52496066--52496143 Score: 86
Period size: 27 Copynumber: 3.0 Consensus size: 26
52496056 ATAATATATT
* *
52496066 TATATATGCATTTTTTATATATATAG
1 TATATACGCATTTTTTATATATATAA
* *
52496092 CACATACGCATATTTTTATATATATAA
1 TATATACGCAT-TTTTTATATATATAA
*
52496119 TATATAGGCATTTTTT-TAATATATA
1 TATATACGCATTTTTTAT-ATATATA
52496144 CGTTTTTAAG
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
25 1 0.02
26 20 0.47
27 22 0.51
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (26 bp):
TATATACGCATTTTTTATATATATAA
Found at i:52496208 original size:14 final size:14
Alignment explanation
Indices: 52496189--52496222 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
52496179 CATTCATACG
52496189 ATTTTTATATATAT
1 ATTTTTATATATAT
52496203 ATTTTTATATATAT
1 ATTTTTATATATAT
52496217 ATTTTT
1 ATTTTT
52496223 TAAAACCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTTATATATAT
Found at i:52497765 original size:30 final size:28
Alignment explanation
Indices: 52497699--52497773 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
52497689 ATAAATACAC
*
52497699 ATATTTATATTA-TAAAAATAAAATATTC
1 ATATTT-TATTATTAAAAATAAAATATTA
* *
52497727 ATATTTTATTATTAAAAATATAATTTTTA
1 ATATTTTATTATTAAAAATA-AAATATTA
52497756 ATATATTTATTATTAAAA
1 ATAT-TTTATTATTAAAA
52497774 GAGTAATATA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
27 5 0.12
28 14 0.34
29 9 0.22
30 13 0.32
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (28 bp):
ATATTTTATTATTAAAAATAAAATATTA
Found at i:52498307 original size:29 final size:27
Alignment explanation
Indices: 52498263--52498317 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 27
52498253 TGCAATATAA
52498263 AATTATTTATTAAAATAATAAATTATGTT
1 AATTATTTATTAAAAT-ATAAA-TATGTT
52498292 AATTATGTTATT-AAATATAAATATGT
1 AATTAT-TTATTAAAATATAAATATGT
52498318 AAGTTTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 5 0.20
28 5 0.20
29 10 0.40
30 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (27 bp):
AATTATTTATTAAAATATAAATATGTT
Found at i:52499287 original size:17 final size:19
Alignment explanation
Indices: 52499267--52499305 Score: 55
Period size: 17 Copynumber: 2.1 Consensus size: 19
52499257 TTTGAACAAT
52499267 AATTATTT-TAT-AAAATA
1 AATTATTTATATAAAAATA
52499284 AATTATTTCATATAAAAATA
1 AATTATTT-ATATAAAAATA
52499304 AA
1 AA
52499306 CGAATCTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
19 3 0.16
20 8 0.42
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTATTTATATAAAAATA
Found at i:52501991 original size:37 final size:40
Alignment explanation
Indices: 52501907--52501991 Score: 95
Period size: 42 Copynumber: 2.1 Consensus size: 40
52501897 ATCAATCAAT
* *
52501907 ATAATCTTTTATACTATTTTAAAGTAAAGTGAACAAACAAGT
1 ATAATTTTTTATACTATTTTAAAGTAAAG-G-ACAAACAAGG
* *
52501949 TTAATTTTTTATTCTATTTTAAAGT-AA-G-CAAACAAGG
1 ATAATTTTTTATACTATTTTAAAGTAAAGGACAAACAAGG
52501986 ATAATT
1 ATAATT
52501992 GAATATGATG
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
37 13 0.34
39 1 0.03
41 2 0.05
42 22 0.58
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.40
Consensus pattern (40 bp):
ATAATTTTTTATACTATTTTAAAGTAAAGGACAAACAAGG
Found at i:52504832 original size:39 final size:39
Alignment explanation
Indices: 52504776--52504853 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
52504766 CTTCTCTTTG
*
52504776 CAAAATTTAATTACAGAAGAAATCAAATATATAAATTTT
1 CAAAATTTAATTACAGAAGAAATCAAAGATATAAATTTT
* *
52504815 CAAATTTTAATTGCAGAAGAAATCAAAGATATAAATTTT
1 CAAAATTTAATTACAGAAGAAATCAAAGATATAAATTTT
52504854 TGGTGCTACT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (39 bp):
CAAAATTTAATTACAGAAGAAATCAAAGATATAAATTTT
Found at i:52512727 original size:17 final size:18
Alignment explanation
Indices: 52512699--52512736 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
52512689 TAACTTAGAC
52512699 TATTGTTAATAT-TGTAAA
1 TATTGTTAATATATG-AAA
52512717 TATTG-TAATATATGAAA
1 TATTGTTAATATATGAAA
52512734 TAT
1 TAT
52512737 AAATTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (18 bp):
TATTGTTAATATATGAAA
Found at i:52513309 original size:20 final size:21
Alignment explanation
Indices: 52513253--52513309 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 21
52513243 GGAATTAAAA
52513253 ACAAATGTATCGATACC-TGTC
1 ACAAA-GTATCGATACCTTGTC
*
52513274 ACAAAGTATC--TACCTTTTC
1 ACAAAGTATCGATACCTTGTC
*
52513293 -CAAGGTATCGATACCTT
1 ACAAAGTATCGATACCTT
52513310 ACCTTCGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
18 12 0.39
19 3 0.10
20 11 0.35
21 5 0.16
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.32
Consensus pattern (21 bp):
ACAAAGTATCGATACCTTGTC
Found at i:52534558 original size:103 final size:103
Alignment explanation
Indices: 52534365--52534565 Score: 287
Period size: 103 Copynumber: 2.0 Consensus size: 103
52534355 GTGAATTGCT
* * *
52534365 GGTGGACATGACAAAATACTTTAAATGACTTTTGGAAAATGCTCCTTCCTATCTATTGGCACAAT
1 GGTGGACATGACAAAATACTTTAAATAACTTTTGGAAAATGCTCCTTCCAATCTATTGACACAAT
** *
52534430 ATCAATTGACCCTTATGGAGGGGTGTTTGATGTCTAAG
66 ATCAATTGACCCTTATAAAGAGGTGTTTGATGTCTAAG
** * *
52534468 GGTGGACATGGGAAAATACTTTGAATAACTTTTGGAAAATTCTCCTTCCAATCTATTGACACAAT
1 GGTGGACATGACAAAATACTTTAAATAACTTTTGGAAAATGCTCCTTCCAATCTATTGACACAAT
*
52534533 ATCTATTGATCCC-TATAAAGAGGTGTTTGATGT
66 ATCAATTGA-CCCTTATAAAGAGGTGTTTGATGT
52534566 AAGACCTATG
Statistics
Matches: 86, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
103 83 0.97
104 3 0.03
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (103 bp):
GGTGGACATGACAAAATACTTTAAATAACTTTTGGAAAATGCTCCTTCCAATCTATTGACACAAT
ATCAATTGACCCTTATAAAGAGGTGTTTGATGTCTAAG
Found at i:52541520 original size:12 final size:12
Alignment explanation
Indices: 52541503--52541528 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52541493 GATAAAGGTT
52541503 TCTGTTAATAAA
1 TCTGTTAATAAA
52541515 TCTGTTAATAAA
1 TCTGTTAATAAA
52541527 TC
1 TC
52541529 AAGTGGAGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (12 bp):
TCTGTTAATAAA
Found at i:52555030 original size:28 final size:28
Alignment explanation
Indices: 52554997--52555054 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
52554987 AGCCCCAACC
*
52554997 AACATGATATAAACAACAAAAGCTAATA
1 AACATGATATAAACAAAAAAAGCTAATA
52555025 AACATGATATAAACAAAAAAAGCTAATA
1 AACATGATATAAACAAAAAAAGCTAATA
52555053 AA
1 AA
52555055 ACAGCGGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.64, C:0.12, G:0.07, T:0.17
Consensus pattern (28 bp):
AACATGATATAAACAAAAAAAGCTAATA
Found at i:52556964 original size:18 final size:18
Alignment explanation
Indices: 52556941--52556977 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
52556931 GTCAAAAAAG
52556941 AAAAAAAACAATTAATGA
1 AAAAAAAACAATTAATGA
52556959 AAAAAAAACAATTAATGA
1 AAAAAAAACAATTAATGA
52556977 A
1 A
52556978 GAAATCAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.16
Consensus pattern (18 bp):
AAAAAAAACAATTAATGA
Found at i:52560883 original size:20 final size:21
Alignment explanation
Indices: 52560850--52560893 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
52560840 GTTATTGTAG
* *
52560850 TTTTTTAACTATTT-GGTTTT
1 TTTTTTAACAATTTCGCTTTT
*
52560870 TTTTTTTACAATTTCGCTTTT
1 TTTTTTAACAATTTCGCTTTT
52560891 TTT
1 TTT
52560894 AAATTTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.14, C:0.09, G:0.07, T:0.70
Consensus pattern (21 bp):
TTTTTTAACAATTTCGCTTTT
Found at i:52560952 original size:3 final size:3
Alignment explanation
Indices: 52560909--52560934 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
52560899 TATTTTCTCC
52560909 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
52560935 GGTATTGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:52561268 original size:6 final size:6
Alignment explanation
Indices: 52561257--52561287 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
52561247 TTTTATAATT
52561257 TACATA TACATA TACATA TACATA TACATA T
1 TACATA TACATA TACATA TACATA TACATA T
52561288 TTATTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.35
Consensus pattern (6 bp):
TACATA
Found at i:52561557 original size:13 final size:14
Alignment explanation
Indices: 52561523--52561559 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
52561513 TGCTTTCATA
52561523 TATATTCATTTCGTT
1 TATATT-ATTTCGTT
52561538 TAT-TTATTT-GTT
1 TATATTATTTCGTT
52561550 TATATTATTT
1 TATATTATTT
52561560 TTATGCTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 10 0.48
14 2 0.10
15 3 0.14
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (14 bp):
TATATTATTTCGTT
Found at i:52567221 original size:132 final size:132
Alignment explanation
Indices: 52567041--52567562 Score: 875
Period size: 132 Copynumber: 4.0 Consensus size: 132
52567031 CCTGTATTAA
* *
52567041 TAGTGGAGCAGATCGAATATGACGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCC
1 TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCC
* *
52567106 AGTAATTCTACTTCCCTAGGCAATAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGC
66 AGTAATTCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGC
52567171 AG
131 AG
*
52567173 TAGTGGATCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCC
1 TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCC
*
52567238 AATAATTCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGC
66 AGTAATTCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGC
52567303 AG
131 AG
*
52567305 CAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCC
1 TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCC
* *
52567370 AGTAATTCTACTTCCTTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGC
66 AGTAATTCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGC
52567435 AG
131 AG
* * * *
52567437 AAGTGGAGCAGATCGAAGATTGCGGATTTTCCCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
1 TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCC
* * * *
52567502 AGTAATTCTACTTCCCTGGGCAATAGTGAAATAGATTGAAGATTGTAAG-TTTTATCTCCCT
66 AGTAATTCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATT-TCAGATCTTATCTCCCT
52567563 GCAGTTGCAG
Statistics
Matches: 368, Mismatches: 21, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
132 365 0.99
133 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (132 bp):
TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCC
AGTAATTCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGC
AG
Found at i:52568701 original size:17 final size:18
Alignment explanation
Indices: 52568681--52568723 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
52568671 GTTATTGTAG
* *
52568681 TTTTTTAACTATTT-GTT
1 TTTTTTAACAATTTCGCT
*
52568698 TTTTTTTACAATTTCGCT
1 TTTTTTAACAATTTCGCT
52568716 TTTTTTAA
1 TTTTTTAA
52568724 ATTTATTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.19, C:0.09, G:0.05, T:0.67
Consensus pattern (18 bp):
TTTTTTAACAATTTCGCT
Found at i:52569359 original size:13 final size:14
Alignment explanation
Indices: 52569325--52569361 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
52569315 TGCTTTCATA
52569325 TATATTCATTTCGTT
1 TATATT-ATTTCGTT
52569340 TAT-TTATTT-GTT
1 TATATTATTTCGTT
52569352 TATATTATTT
1 TATATTATTT
52569362 TTATGCTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 10 0.48
14 2 0.10
15 3 0.14
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (14 bp):
TATATTATTTCGTT
Found at i:52575649 original size:49 final size:48
Alignment explanation
Indices: 52575547--52575649 Score: 120
Period size: 49 Copynumber: 2.1 Consensus size: 48
52575537 TTATTTAAGC
* *
52575547 CTATAAA-ATATTAAAATATTAAAAATATATATAAAATTATAGAAAAA
1 CTATAAATTTATTAAAATATTAAAAATATATAGAAAATTATAGAAAAA
* * *
52575594 CTATAAATTTATTACAAATGATTAAAAATAT-TAGAGAATTTTATAAAAA
1 CTATAAATTTATTA-AAAT-ATTAAAAATATATAGAAAATTATAGAAAAA
*
52575643 TTATAAA
1 CTATAAA
52575650 AAAATGTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
47 7 0.15
48 5 0.11
49 24 0.51
50 11 0.23
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.35
Consensus pattern (48 bp):
CTATAAATTTATTAAAATATTAAAAATATATAGAAAATTATAGAAAAA
Found at i:52578372 original size:16 final size:16
Alignment explanation
Indices: 52578347--52578380 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
52578337 ATGAATATAT
* *
52578347 ATGTGTAAATGTGATA
1 ATGTGCAAATATGATA
52578363 ATGTGCAAATATGATA
1 ATGTGCAAATATGATA
52578379 AT
1 AT
52578381 TGAATATTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (16 bp):
ATGTGCAAATATGATA
Found at i:52580270 original size:14 final size:15
Alignment explanation
Indices: 52580243--52580271 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
52580233 ATACATGAAA
52580243 TTTCACATTTATACC
1 TTTCACATTTATACC
52580258 TTTCACA-TTATACC
1 TTTCACATTTATACC
52580272 ATAAAAATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTCACATTTATACC
Found at i:52580596 original size:48 final size:48
Alignment explanation
Indices: 52580509--52580602 Score: 116
Period size: 48 Copynumber: 2.0 Consensus size: 48
52580499 TACAATAGTC
* * * *
52580509 TATACCATTCAATATATTACTATCAGGGATGGCCCAACTACGATGGTT
1 TATACCATTCAATATATTACCATCAGAGATAGCCAAACTACGATGGTT
* ** *
52580557 TATACCATTTAATATATTACCATCCTAGATAGCCAAACTATGATGG
1 TATACCATTCAATATATTACCATCAGAGATAGCCAAACTACGATGG
52580603 CTCACAATCT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (48 bp):
TATACCATTCAATATATTACCATCAGAGATAGCCAAACTACGATGGTT
Found at i:52582419 original size:43 final size:42
Alignment explanation
Indices: 52582356--52582481 Score: 114
Period size: 43 Copynumber: 2.9 Consensus size: 42
52582346 AGGATTCCGT
52582356 TATGTGTTATCGTGTAAGACCACGTCTGGGACGTTGGCATCAAC
1 TATGTGTTA-CGTGTAAGACCACGTCTGGGACGTTGGCATC-AC
* **
52582400 T-TGTGTTTACGTGTAAGACC-CTATCTGGGACAG-TGGCATCGT
1 TATGTG-TTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCAC
* * * *
52582442 TATGTGATTACATATAAGACAACGTCTAGGACGTTGGCAT
1 TATGTG-TTACGTGTAAGACCACGTCTGGGACGTTGGCAT
52582482 TGTACGATAT
Statistics
Matches: 67, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
42 3 0.04
43 58 0.87
44 6 0.09
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (42 bp):
TATGTGTTACGTGTAAGACCACGTCTGGGACGTTGGCATCAC
Found at i:52583482 original size:23 final size:23
Alignment explanation
Indices: 52583456--52583706 Score: 279
Period size: 23 Copynumber: 10.7 Consensus size: 23
52583446 ATTGGGTATA
* *
52583456 TATATATGTTGTCCAATTTGGTG
1 TATAAATGCTGTCCAATTTGGTG
* *
52583479 TATATATGCTGTTCAATTTGGTG
1 TATAAATGCTGTCCAATTTGGTG
52583502 TATAAAATGCTGTCCAATTTGGTG
1 TAT-AAATGCTGTCCAATTTGGTG
**
52583526 TATAAATATTGTCCAATTTGGTG
1 TATAAATGCTGTCCAATTTGGTG
*
52583549 TATAAATGTTGTCCAATTTGGTG
1 TATAAATGCTGTCCAATTTGGTG
* * *
52583572 TATATATTTGCTATCCAATTGGGTG
1 TATA-A-ATGCTGTCCAATTTGGTG
*
52583597 TATAAATTCTGTCCAATTTGGTG
1 TATAAATGCTGTCCAATTTGGTG
* * *
52583620 TATAAATGCTATCCACTTTGGTA
1 TATAAATGCTGTCCAATTTGGTG
*
52583643 TATATATATGCTGTCCAATTGGGTG
1 TATA-A-ATGCTGTCCAATTTGGTG
* **
52583668 TATAAATGCTGTCCGATTTAATG
1 TATAAATGCTGTCCAATTTGGTG
52583691 TATAAGA-GCTGTCCAA
1 TATAA-ATGCTGTCCAA
52583707 ATAGGGTAGA
Statistics
Matches: 194, Mismatches: 28, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
23 132 0.68
24 26 0.13
25 36 0.19
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (23 bp):
TATAAATGCTGTCCAATTTGGTG
Found at i:52583620 original size:71 final size:71
Alignment explanation
Indices: 52583465--52583706 Score: 319
Period size: 71 Copynumber: 3.4 Consensus size: 71
52583455 ATATATATGT
* * * *
52583465 TGTCCAATTTGGTGTATATATGCTGTTCAATTTGGTGTATA-AAATGCTGTCCAATTTGGTGTAT
1 TGTCCAATTTGGTGTATAAATGCTGTCCAATTTGGTGTATATATATGCTGTCCAATTGGGTGTAT
52583529 AAATAT-
66 AAAT-TC
* * *
52583535 TGTCCAATTTGGTGTATAAATGTTGTCCAATTTGGTGTATATATTTGCTATCCAATTGGGTGTAT
1 TGTCCAATTTGGTGTATAAATGCTGTCCAATTTGGTGTATATATATGCTGTCCAATTGGGTGTAT
52583600 AAATTC
66 AAATTC
* * *
52583606 TGTCCAATTTGGTGTATAAATGCTATCCACTTTGGTATATATATATGCTGTCCAATTGGGTGTAT
1 TGTCCAATTTGGTGTATAAATGCTGTCCAATTTGGTGTATATATATGCTGTCCAATTGGGTGTAT
*
52583671 AAATGC
66 AAATTC
* **
52583677 TGTCCGATTTAATGTATAAGA-GCTGTCCAA
1 TGTCCAATTTGGTGTATAA-ATGCTGTCCAA
52583707 ATAGGGTAGA
Statistics
Matches: 150, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
70 39 0.26
71 110 0.73
72 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (71 bp):
TGTCCAATTTGGTGTATAAATGCTGTCCAATTTGGTGTATATATATGCTGTCCAATTGGGTGTAT
AAATTC
Found at i:52583672 original size:48 final size:46
Alignment explanation
Indices: 52583456--52583706 Score: 270
Period size: 48 Copynumber: 5.3 Consensus size: 46
52583446 ATTGGGTATA
* * * * *
52583456 TATATATGTTGTCCAATTTGGTGTATATATGCTGTTCAATTTGGTG
1 TATAAATGCTGTCCAATTTGGTGTATAAATGCTATCCAATTTGGTG
** *
52583502 TATAAAATGCTGTCCAATTTGGTGTATAAATATTGTCCAATTTGGTG
1 TAT-AAATGCTGTCCAATTTGGTGTATAAATGCTATCCAATTTGGTG
* * *
52583549 TATAAATGTTGTCCAATTTGGTGTATATATTTGCTATCCAATTGGGTG
1 TATAAATGCTGTCCAATTTGGTGTATA-A-ATGCTATCCAATTTGGTG
* * *
52583597 TATAAATTCTGTCCAATTTGGTGTATAAATGCTATCCACTTTGGTA
1 TATAAATGCTGTCCAATTTGGTGTATAAATGCTATCCAATTTGGTG
* * * **
52583643 TATATATATGCTGTCCAATTGGGTGTATAAATGCTGTCCGATTTAATG
1 TATA-A-ATGCTGTCCAATTTGGTGTATAAATGCTATCCAATTTGGTG
52583691 TATAAGA-GCTGTCCAA
1 TATAA-ATGCTGTCCAA
52583707 ATAGGGTAGA
Statistics
Matches: 173, Mismatches: 27, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
46 53 0.31
47 45 0.26
48 75 0.43
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (46 bp):
TATAAATGCTGTCCAATTTGGTGTATAAATGCTATCCAATTTGGTG
Found at i:52587136 original size:41 final size:41
Alignment explanation
Indices: 52586992--52587138 Score: 233
Period size: 41 Copynumber: 3.6 Consensus size: 41
52586982 TTTAACATAT
*
52586992 TCACCGGCACTTAACCTGCTA-AGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGA-CTTATAGCCTGATTCAGA
** *
52587033 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGACTTATAGCCTGATTCAGA
*
52587074 TCACCGGCACTTAGCCTGCTAGACTTATAGCCTGTTTCAGA
1 TCACCGGCACTTAGCCTGCTAGACTTATAGCCTGATTCAGA
52587115 TCACCGGCACTTAGCCTGCTAGAC
1 TCACCGGCACTTAGCCTGCTAGAC
52587139 GTAAAGTCTG
Statistics
Matches: 97, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
41 97 1.00
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGACTTATAGCCTGATTCAGA
Found at i:52587192 original size:40 final size:40
Alignment explanation
Indices: 52587074--52587176 Score: 111
Period size: 41 Copynumber: 2.5 Consensus size: 40
52587064 CTGATTCAGA
* * ** *
52587074 TCACCGGCACTTAGCCTGCTAGACTTATAGCCTGTTTCAGA-
1 TCACCGGCACTTAGCCTGCTAGACGTAAAGCCTG--AAAAAT
*
52587115 TCACCGGCACTTAGCCTGCTAGACGTAAAGTCTGAAAAAT
1 TCACCGGCACTTAGCCTGCTAGACGTAAAGCCTGAAAAAT
52587155 TCACCGGCA-TTAAGCCTGCTAG
1 TCACCGGCACTT-AGCCTGCTAG
52587177 GCGCTTAGCC
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
39 4 0.07
40 19 0.35
41 31 0.57
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
TCACCGGCACTTAGCCTGCTAGACGTAAAGCCTGAAAAAT
Found at i:52587789 original size:114 final size:115
Alignment explanation
Indices: 52587623--52587848 Score: 391
Period size: 114 Copynumber: 1.9 Consensus size: 115
52587613 TCATATATAC
* *
52587623 ATATTCGAACTTCATTTATGCATATATATATATAACATTCATACTTAACTAATTTTAATTTATAT
1 ATATTCGAACTTCATTTATGC--A-ATATATATAACATTCATACTTAACTAATTTCAATTCATAT
52587688 ACTTTTAATTATAGCTCATCAAATATACAATAGATATACATATATATTTACAT
63 ACTTTTAATTATAGCTCATCAAATATACAATAGATATACATATATATTTACAT
*
52587741 ATATTCGAACTTCATTTATGC-ATATATATAACATTCATACTTAACTAATTTCAATTCATATATT
1 ATATTCGAACTTCATTTATGCAATATATATAACATTCATACTTAACTAATTTCAATTCATATACT
52587805 TTTAATTATAGCTCATCAAATATACAATAGATATACATATATAT
66 TTTAATTATAGCTCATCAAATATACAATAGATATACATATATAT
52587849 ATATATATGC
Statistics
Matches: 105, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
114 84 0.80
118 21 0.20
ACGTcount: A:0.41, C:0.13, G:0.04, T:0.42
Consensus pattern (115 bp):
ATATTCGAACTTCATTTATGCAATATATATAACATTCATACTTAACTAATTTCAATTCATATACT
TTTAATTATAGCTCATCAAATATACAATAGATATACATATATATTTACAT
Found at i:52590375 original size:24 final size:24
Alignment explanation
Indices: 52590343--52590409 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
52590333 CAAACAATGT
52590343 TGAAAAGTACCCAAACAATACTTG
1 TGAAAAGTACCCAAACAATACTTG
*
52590367 TGAATAGTACCCAAACAATACTTG
1 TGAAAAGTACCCAAACAATACTTG
* * * *
52590391 TCAACAGTATCTAAACAAT
1 TGAAAAGTACCCAAACAAT
52590410 GATAAGAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.45, C:0.21, G:0.10, T:0.24
Consensus pattern (24 bp):
TGAAAAGTACCCAAACAATACTTG
Found at i:52590965 original size:30 final size:31
Alignment explanation
Indices: 52590931--52590988 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
52590921 AATATGTAAC
*
52590931 AAATATTATCAACATAT-TATAGAAAATATG
1 AAATATTATAAACATATATATAGAAAATATG
*
52590961 AAATATTATAAATATATATATAGAAAAT
1 AAATATTATAAACATATATATAGAAAAT
52590989 TATATAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.34
Consensus pattern (31 bp):
AAATATTATAAACATATATATAGAAAATATG
Found at i:52591049 original size:9 final size:9
Alignment explanation
Indices: 52591023--52591071 Score: 53
Period size: 9 Copynumber: 5.1 Consensus size: 9
52591013 AAAAAAGAAC
52591023 ATTATTAAAGA
1 ATTATT-AA-A
52591034 ATTATTAAA
1 ATTATTAAA
*
52591043 CTTATTAAA
1 ATTATTAAA
*
52591052 ATTTTTGAAA
1 ATTATT-AAA
52591062 ATTATTAAA
1 ATTATTAAA
52591071 A
1 A
52591072 AATTATAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 17 0.52
10 10 0.30
11 6 0.18
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (9 bp):
ATTATTAAA
Found at i:52591049 original size:20 final size:20
Alignment explanation
Indices: 52591023--52591077 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
52591013 AAAAAAGAAC
52591023 ATTATTAAAGAATTATT-AAA
1 ATTATTAAA-AATTATTGAAA
* *
52591043 CTTATT-AAAATTTTTGAAA
1 ATTATTAAAAATTATTGAAA
52591062 ATTATTAAAAAATTAT
1 ATTATT-AAAAATTAT
52591078 AAAAAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 5 0.18
21 7 0.25
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (20 bp):
ATTATTAAAAATTATTGAAA
Found at i:52591082 original size:20 final size:20
Alignment explanation
Indices: 52591023--52591082 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
52591013 AAAAAAGAAC
* *
52591023 ATTATTAAAGAATTATTAAA
1 ATTATTAAAAAATTATAAAA
* * * *
52591043 CTTATT-AAAATTTTTGAAA
1 ATTATTAAAAAATTATAAAA
52591062 ATTATTAAAAAATTATAAAA
1 ATTATTAAAAAATTATAAAA
52591082 A
1 A
52591083 AAAATAAAAA
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (20 bp):
ATTATTAAAAAATTATAAAA
Found at i:52591416 original size:21 final size:21
Alignment explanation
Indices: 52591390--52591437 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
52591380 AAATCATTAT
52591390 AAAAATTT-TAGAAAATTATAA
1 AAAAATTTATA-AAAATTATAA
* *
52591411 AAAAATTTATATAAATTATTA
1 AAAAATTTATAAAAATTATAA
52591432 AAAAAT
1 AAAAAT
52591438 ATAAGATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
AAAAATTTATAAAAATTATAA
Found at i:52592824 original size:16 final size:16
Alignment explanation
Indices: 52592797--52592831 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
52592787 ATTTAAAAGA
52592797 AAAAGAACAAAAACAAG
1 AAAAGAACAAAAAC-AG
52592814 AAAAG-ACAAAAACAG
1 AAAAGAACAAAAACAG
52592829 AAA
1 AAA
52592832 GTCAAATTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 8 0.44
17 5 0.28
ACGTcount: A:0.77, C:0.11, G:0.11, T:0.00
Consensus pattern (16 bp):
AAAAGAACAAAAACAG
Found at i:52594416 original size:49 final size:49
Alignment explanation
Indices: 52594329--52594425 Score: 119
Period size: 49 Copynumber: 2.0 Consensus size: 49
52594319 TATGGTTTAA
*
52594329 CCAAACAAATAATATAAATATTTTTTTACTTTGCTAA-T-TTTATCTAT
1 CCAAACAAATAATATAAATATTTTTTTACTTTGATAATTATTTATCTAT
* *
52594376 CCAAACAAAATAAATATAATTAATTTTTTT-CTTTTATAATTATTTATCTA
1 CCAAAC-AAAT-AATATAAAT-ATTTTTTTACTTTGATAATTATTTATCTA
52594426 AACTTATAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
47 6 0.14
48 4 0.10
49 15 0.36
50 9 0.21
51 8 0.19
ACGTcount: A:0.40, C:0.11, G:0.01, T:0.47
Consensus pattern (49 bp):
CCAAACAAATAATATAAATATTTTTTTACTTTGATAATTATTTATCTAT
Found at i:52596605 original size:16 final size:16
Alignment explanation
Indices: 52596584--52596617 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
52596574 GCTCAGCCTC
*
52596584 TCATTTCCTTCTCATT
1 TCATTTCCTCCTCATT
52596600 TCATTTCCTCCTCATT
1 TCATTTCCTCCTCATT
52596616 TC
1 TC
52596618 CTCTTCGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.00, T:0.53
Consensus pattern (16 bp):
TCATTTCCTCCTCATT
Found at i:52605688 original size:19 final size:20
Alignment explanation
Indices: 52605651--52605688 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
52605641 TGATTATAAT
* *
52605651 TAAAATTTAATTATGTTTAA
1 TAAAATTTAATGATATTTAA
52605671 TAAAA-TTAATGATATTTA
1 TAAAATTTAATGATATTTA
52605689 TTTTCAAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
TAAAATTTAATGATATTTAA
Found at i:52613683 original size:28 final size:28
Alignment explanation
Indices: 52613643--52613696 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
52613633 TATAACTTTT
52613643 TTTATTTACCAAAATATATAAAAAAAAA
1 TTTATTTACCAAAATATATAAAAAAAAA
52613671 TTTATTTACCAAAATATATAAAAAAA
1 TTTATTTACCAAAATATATAAAAAAA
52613697 CAAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.33
Consensus pattern (28 bp):
TTTATTTACCAAAATATATAAAAAAAAA
Found at i:52613800 original size:27 final size:28
Alignment explanation
Indices: 52613752--52613809 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
52613742 ACTAGCCACG
**
52613752 CCAATGGTTGCCAATGGGATTGGCGGCA
1 CCAATGGTTGCCAATACGATTGGCGGCA
*
52613780 CCAATGG-TGCCAATACTATTGGCGGCA
1 CCAATGGTTGCCAATACGATTGGCGGCA
52613807 CCA
1 CCA
52613810 GTTAATAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.24, C:0.26, G:0.29, T:0.21
Consensus pattern (28 bp):
CCAATGGTTGCCAATACGATTGGCGGCA
Found at i:52613861 original size:4 final size:4
Alignment explanation
Indices: 52613852--52614028 Score: 102
Period size: 4 Copynumber: 43.8 Consensus size: 4
52613842 GAAGGAGAGG
* * * *
52613852 GAAA GAAA GAAA GAAA GAGA GAAA GAAA GGAA GAAA GGAGAG GGAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA
* * *
52613902 GAAAA CGAAG GAAA GAAA GGGAAA G-GA GAAGA GAAA AAAA GAAA GAAA
1 G-AAA -GAAA GAAA GAAA --GAAA GAAA GAA-A GAAA GAAA GAAA GAAA
* *
52613950 G-AA G-AA GAAGA GAAG GAAAA GAGAA GAAA -AAA GAAA GAAA GAAG GAAA
1 GAAA GAAA GAA-A GAAA G-AAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA
*
52613998 G-AA -AAA GAAA G-GA GAAGA GAAA -AAA -AAA GAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAA
52614029 GAAGAGGGAA
Statistics
Matches: 135, Mismatches: 20, Indels: 36
0.71 0.10 0.19
Matches are distributed among these distances:
3 23 0.17
4 79 0.59
5 27 0.20
6 6 0.04
ACGTcount: A:0.68, C:0.01, G:0.32, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:52613922 original size:27 final size:25
Alignment explanation
Indices: 52613858--52613924 Score: 73
Period size: 27 Copynumber: 2.6 Consensus size: 25
52613848 GAGGGAAAGA
* *
52613858 AAGAAAGAAAGAG-AGAAAGAAAGG
1 AAGAAAGAAAGGGAAGAAAGAAACG
*
52613882 AAGAAAGGAGAGGGAAGAAAGAAAACG
1 AAGAAA-GAAAGGGAAGAAAG-AAACG
52613909 AAGGAAAGAAAGGGAA
1 AA-GAAAGAAAGGGAA
52613925 AGGAGAAGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 6 0.17
25 5 0.14
26 6 0.17
27 14 0.40
28 4 0.11
ACGTcount: A:0.63, C:0.01, G:0.36, T:0.00
Consensus pattern (25 bp):
AAGAAAGAAAGGGAAGAAAGAAACG
Found at i:52613943 original size:40 final size:39
Alignment explanation
Indices: 52613855--52614032 Score: 136
Period size: 39 Copynumber: 4.5 Consensus size: 39
52613845 GGAGAGGGAA
*
52613855 AGAAAGAAAG-AAAG-AGAGAAAGAAAGGAAGAAAGGAG-AG
1 AGAAAAAAAGAAAAGAAG-GAAAGAAAGG--GAAAGGAGAAG
* *
52613894 -GGAAGAAAGAAAACGAAGGAAAGAAAGGGAAAGGAGAAG
1 AGAAAAAAAGAAAA-GAAGGAAAGAAAGGGAAAGGAGAAG
* *
52613933 AGAAAAAAAG-AAAGAAAGAAGAAGAAGAGAAGGAAAAGAGAAG
1 AGAAAAAAAGAAAAG-AAGGA-AAGAA-AG--GGAAAGGAGAAG
* **
52613976 AAAAAAGAAAG-AAAGAAGGAAAGAAAAAGAAAGGAGAAG
1 AGAAAA-AAAGAAAAGAAGGAAAGAAAGGGAAAGGAGAAG
52614015 AGAAAAAAA-AAGAAGAAG
1 AGAAAAAAAGAA-AAGAAG
52614033 AGGGAAGGAG
Statistics
Matches: 115, Mismatches: 11, Indels: 26
0.76 0.07 0.17
Matches are distributed among these distances:
38 21 0.18
39 33 0.29
40 23 0.20
41 5 0.04
42 5 0.04
43 20 0.17
44 8 0.07
ACGTcount: A:0.67, C:0.01, G:0.32, T:0.00
Consensus pattern (39 bp):
AGAAAAAAAGAAAAGAAGGAAAGAAAGGGAAAGGAGAAG
Found at i:52613945 original size:44 final size:42
Alignment explanation
Indices: 52613843--52614023 Score: 175
Period size: 40 Copynumber: 4.4 Consensus size: 42
52613833 GGGGGGGCAG
* *
52613843 AAGGAG-AGGGAAAGAAAGAAAGAAAG-AGAGAAAGAAAGGAAGA
1 AAGGAGAAGAGAAAAAAAGAAAGAAAGAAG-GAAAGAAA-G-AGA
* * * *
52613886 AAGGAG-AG-GGAAGAAAG-AA-AACGAAGGAAAGAAAGGGA
1 AAGGAGAAGAGAAAAAAAGAAAGAAAGAAGGAAAGAAAGAGA
52613924 AAGGAGAAGAGAAAAAAAGAAAGAAAGAA-G-AAG-AAGAG-
1 AAGGAGAAGAGAAAAAAAGAAAGAAAGAAGGAAAGAAAGAGA
* *
52613962 AAGGAAAAGAGAAGAAAAAAGAAAGAAAGAAGGAAAGAAAAAGA
1 AAGGAGAAGAG-A-AAAAAAGAAAGAAAGAAGGAAAGAAAGAGA
52614006 AAGGAGAAGAGAAAAAAA
1 AAGGAGAAGAGAAAAAAA
52614024 AAGAAGAAGA
Statistics
Matches: 117, Mismatches: 10, Indels: 23
0.78 0.07 0.15
Matches are distributed among these distances:
38 18 0.15
39 8 0.07
40 38 0.32
41 8 0.07
42 22 0.19
43 13 0.11
44 10 0.09
ACGTcount: A:0.66, C:0.01, G:0.33, T:0.00
Consensus pattern (42 bp):
AAGGAGAAGAGAAAAAAAGAAAGAAAGAAGGAAAGAAAGAGA
Found at i:52613977 original size:29 final size:28
Alignment explanation
Indices: 52613928--52614015 Score: 99
Period size: 29 Copynumber: 3.1 Consensus size: 28
52613918 AAGGGAAAGG
*
52613928 AGAAGAGAA-AAAAAGAAAGAAAGAAGA
1 AGAAGAGAAGGAAAAGAAAGAAAGAAGA
*
52613955 AGAAGAGAAGGAAAAGAGAAGAAAAAAGAA
1 AGAAGAGAAGGAAAAGA-AAGAAAGAAG-A
* *
52613985 AGAA-AGAAGGAAAGAAAAAGAAAGGAGA
1 AGAAGAGAAGGAAA-AGAAAGAAAGAAGA
52614013 AGA
1 AGA
52614016 GAAAAAAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
27 9 0.17
28 10 0.19
29 26 0.50
30 7 0.13
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (28 bp):
AGAAGAGAAGGAAAAGAAAGAAAGAAGA
Found at i:52613986 original size:70 final size:69
Alignment explanation
Indices: 52613849--52614001 Score: 161
Period size: 70 Copynumber: 2.2 Consensus size: 69
52613839 GCAGAAGGAG
* * * *
52613849 AGGGAAAGAAAGAAAGAAAGAGAGAAAGAAAGGAAGAAAGGAGAGGGAAGAAAGAAAACGAAGGA
1 AGGGAAAGAAAGAAAGAAAAAAAGAAAGAAAGGAAGAAAAGAGAGGAAAGAAAGAAAAC-AAGGA
52613914 AAGAA
65 AAGAA
*
52613919 AGGGAAAG-GAGAAGAGAAAAAAAGAAAGAAA-GAAGAAGAAGAGAAGGAAAAGAGAAGAAAA-A
1 AGGGAAAGAAAGAA-AGAAAAAAAGAAAGAAAGGAAGAA-AAGAG-AGG-AAAGA-AAGAAAACA
52613981 A-GAAAGAA
61 AGGAAAGAA
52613989 AGAAGGAAAGAAA
1 AG--GGAAAGAAA
52614002 AAGAAAGGAG
Statistics
Matches: 69, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
69 10 0.14
70 36 0.52
71 5 0.07
72 10 0.14
73 8 0.12
ACGTcount: A:0.66, C:0.01, G:0.33, T:0.00
Consensus pattern (69 bp):
AGGGAAAGAAAGAAAGAAAAAAAGAAAGAAAGGAAGAAAAGAGAGGAAAGAAAGAAAACAAGGAA
AGAA
Found at i:52613994 original size:82 final size:83
Alignment explanation
Indices: 52613853--52614059 Score: 239
Period size: 82 Copynumber: 2.5 Consensus size: 83
52613843 AAGGAGAGGG
* ***
52613853 AAAGAAAGAAAGAAAGAGAGAA-AGAAAGGAAGAAAGGAGAGGGAAGAAAGAAAACGAAGGAAAG
1 AAAGAAAGAAAG-AAGAGAGAAGAG-AAGGAA-AAAGAAGAAAAAAGAAAGAAAACGAAGGAAAG
**
52613917 AAAGGGAAAGGAGAAGAGAAAA
63 AAAAAGAAAGGAGAAGAG-AAA
52613939 AAAGAAAGAAAGAAGA-AGAAGAGAAGGAAAAGAGAAGAAAAAAGAAAG-AAA-GAAGGAAAGAA
1 AAAGAAAGAAAGAAGAGAGAAGAGAAGGAAAA-AGAAGAAAAAAGAAAGAAAACGAAGGAAAGAA
52614001 AAAGAAAGGAGAAGAGAAA
65 AAAGAAAGGAGAAGAGAAA
* * *
52614020 AAA-AAAG-AAGAAGAGGGAAG-GAGGGAAAAAAAAGAAAAAA
1 AAAGAAAGAAAGAAGAGAGAAGAGAAGGAAAAAGAAGAAAAAA
52614060 ATGTAATTTT
Statistics
Matches: 109, Mismatches: 9, Indels: 14
0.83 0.07 0.11
Matches are distributed among these distances:
78 10 0.09
79 15 0.14
80 8 0.07
81 6 0.06
82 25 0.23
83 5 0.05
84 22 0.20
85 6 0.06
86 12 0.11
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (83 bp):
AAAGAAAGAAAGAAGAGAGAAGAGAAGGAAAAAGAAGAAAAAAGAAAGAAAACGAAGGAAAGAAA
AAGAAAGGAGAAGAGAAA
Found at i:52614024 original size:44 final size:44
Alignment explanation
Indices: 52613852--52614028 Score: 161
Period size: 44 Copynumber: 4.1 Consensus size: 44
52613842 GAAGGAGAGG
* * * ***
52613852 GAAAGAAAGAAAGAAAGAGAGAAAGAAAGGAAGAA-AGGAGAGGGAA
1 GAAAGAAAGAAGGAAAGA-A-AAAGAAAGG-AGAAGAGAAAAAAAAA
**
52613898 GAAAGAAAACGAAGGAAAGAAAGGGAAAGGAGAAGAG--AAAAAAA
1 GAAAG-AAA-GAAGGAAAGAAAAAGAAAGGAGAAGAGAAAAAAAAA
* * *
52613942 GAAAGAAAGAA-G-AAG-AAGAG-AAGGAAAAGAGAAGAAAAAA
1 GAAAGAAAGAAGGAAAGAAAAAGAAAGGAGAAGAGAAAAAAAAA
52613982 GAAAGAAAGAAGGAAAGAAAAAGAAAGGAGAAGAGAAAAAAAAA
1 GAAAGAAAGAAGGAAAGAAAAAGAAAGGAGAAGAGAAAAAAAAA
52614026 GAA
1 GAA
52614029 GAAGAGGGAA
Statistics
Matches: 109, Mismatches: 13, Indels: 20
0.77 0.09 0.14
Matches are distributed among these distances:
38 10 0.09
39 4 0.04
40 20 0.18
41 2 0.02
42 6 0.06
43 7 0.06
44 29 0.27
45 4 0.04
46 14 0.13
47 4 0.04
48 9 0.08
ACGTcount: A:0.68, C:0.01, G:0.32, T:0.00
Consensus pattern (44 bp):
GAAAGAAAGAAGGAAAGAAAAAGAAAGGAGAAGAGAAAAAAAAA
Found at i:52614026 original size:18 final size:18
Alignment explanation
Indices: 52613941--52614034 Score: 77
Period size: 18 Copynumber: 5.1 Consensus size: 18
52613931 AGAGAAAAAA
*
52613941 AGAAAGAAAGAAGAAGAAG
1 AGAAA-AAAAAAGAAGAAG
* *
52613960 AGAAGGAAAAGAGAAGAA-
1 AGAA-AAAAAAAGAAGAAG
52613978 A-AAAGAAAGAAAGAAGGAA-
1 AGAAA-AAA-AAAGAA-GAAG
* *
52613997 AGAAAAAGAAAGGAGAAG
1 AGAAAAAAAAAGAAGAAG
52614015 AGAAAAAAAAAGAAGAAG
1 AGAAAAAAAAAGAAGAAG
52614033 AG
1 AG
52614035 GGAAGGAGGG
Statistics
Matches: 60, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
17 8 0.13
18 29 0.48
19 20 0.33
20 3 0.05
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (18 bp):
AGAAAAAAAAAGAAGAAG
Found at i:52619724 original size:15 final size:12
Alignment explanation
Indices: 52619687--52619717 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
52619677 GAAAAAATTT
*
52619687 ATACTCAAAATA
1 ATACACAAAATA
52619699 ATACACAAAATA
1 ATACACAAAATA
52619711 ATACACA
1 ATACACA
52619718 CTAAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.61, C:0.19, G:0.00, T:0.19
Consensus pattern (12 bp):
ATACACAAAATA
Done.