Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 172 of 425
Found at i:52119461 original size:46 final size:45
Alignment explanation
Indices: 52119286--52119461 Score: 176
Period size: 46 Copynumber: 3.8 Consensus size: 45
52119276 TGTAACCCGC
* * * *
52119286 CCATAAGCGAACTCAGACTCAACTCAACGAGCTTGGGCATTCGCAT
1 CCATAA-CGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
* * * *
52119332 CCATGAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCAT-AACGAACTCGGACTCAACTCAACGAGCTCGGA---C-ATTTGCAT
* *
52119382 -C-TCACGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAACGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
*
52119425 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
1 CCATAA-CGAACTCGGACTCAACTCAACGAGCTCGGA
52119462 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 15, Indels: 16
0.78 0.11 0.12
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 57 0.53
47 32 0.30
48 1 0.01
49 2 0.02
50 5 0.05
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (45 bp):
CCATAACGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
Found at i:52119480 original size:46 final size:45
Alignment explanation
Indices: 52119294--52119480 Score: 125
Period size: 46 Copynumber: 4.0 Consensus size: 45
52119284 GCCCATAAGC
* * * * * * *
52119294 GAACTCAGACTCAACTCAACGAGCTTGGGCATTCGCATCCAT-GAAT
1 GAACTCGGACTCAACTCAACGAG-TTCGG-ATGCTCAACCATCTAGT
*
52119340 GAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATCTCA-C
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCT-AGT
* * *
52119387 GAACTCGGACTCAACTCAACGAGTTCGGACAT-TTGCATCCAT-AAGT
1 GAACTCGGACTCAACTCAACGAGTTCGG--ATGCT-CAACCATCTAGT
*
52119433 GAACTCGGACTCAACTCAACGAGCTCGGATGCTCAACCATCCTAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT-CTAGT
52119479 GA
1 GA
52119481 CATGTCACTT
Statistics
Matches: 112, Mismatches: 14, Indels: 30
0.72 0.09 0.19
Matches are distributed among these distances:
43 1 0.01
44 12 0.11
45 6 0.05
46 57 0.51
47 31 0.28
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (45 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCTAGT
Found at i:52121392 original size:29 final size:29
Alignment explanation
Indices: 52121290--52121391 Score: 125
Period size: 29 Copynumber: 3.5 Consensus size: 29
52121280 GTGACGAGAT
52121290 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
52121319 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
52121348 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
52121377 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
52121392 GGGTTTAAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
29 61 0.98
30 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:52121448 original size:28 final size:28
Alignment explanation
Indices: 52121379--52121479 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
52121369 GAAGGGTATG
* * * *
52121379 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
52121409 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
52121437 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
52121466 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
52121480 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:52129314 original size:29 final size:29
Alignment explanation
Indices: 52129212--52129313 Score: 125
Period size: 29 Copynumber: 3.5 Consensus size: 29
52129202 GTGACGAGAT
52129212 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
52129241 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
52129270 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
52129299 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
52129314 GGGTTTAAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
29 61 0.98
30 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:52129370 original size:28 final size:28
Alignment explanation
Indices: 52129301--52129400 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
52129291 GAAGGGTATG
* * * *
52129301 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
52129331 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
52129359 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
52129388 GCACTAAGTGTGC
1 GCACTAAGTGTGC
52129401 AGATTCACTA
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 18 0.29
30 18 0.29
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:52141722 original size:23 final size:23
Alignment explanation
Indices: 52141696--52141740 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
52141686 TTAAAATGTA
*
52141696 TGTTCTTAATTGT-AATATAATTG
1 TGTTATTAATTGTGAA-ATAATTG
*
52141719 TGTTATTCATTGTGAAATAATT
1 TGTTATTAATTGTGAAATAATT
52141741 TATGAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.31, C:0.04, G:0.13, T:0.51
Consensus pattern (23 bp):
TGTTATTAATTGTGAAATAATTG
Found at i:52148085 original size:27 final size:27
Alignment explanation
Indices: 52147556--52148084 Score: 672
Period size: 27 Copynumber: 19.6 Consensus size: 27
52147546 AAAGTACTCC
52147556 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
52147583 C-AGTTTATAGAATTACTGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
** *
52147610 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
52147637 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* **
52147664 -TAGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
52147691 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
52147718 C-AGTTTACAGAATTATTGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* *
52147745 TGATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
52147772 CGATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** * *
52147799 CGATTTGTAAAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
52147826 CGATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
52147853 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* *
52147880 CAATTTATAGAATTACCGTTTTACCC-
1 CGATTTACAGAATTACCGTTTTACCCT
* * * *
52147906 CTAATTTACATAATTACCATTTTACCCC
1 C-GATTTACAGAATTACCGTTTTACCCT
* *
52147934 CGATTTACATAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
52147961 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
52147988 CGATTTACAGAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
52148015 CGATTTATAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
52148042 TGATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
52148069 CGATTTACAAAATTAC
1 CGATTTACAGAATTAC
52148085 TAAAATACCC
Statistics
Matches: 442, Mismatches: 50, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
26 5 0.01
27 432 0.98
28 5 0.01
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (27 bp):
CGATTTACAGAATTACCGTTTTACCCT
Found at i:52149421 original size:9 final size:9
Alignment explanation
Indices: 52149409--52149465 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
52149399 TTTGATAAAC
52149409 ATGATATGT
1 ATGATATGT
*
52149418 ATGATATGCAC
1 ATGATATG--T
52149429 ATGATATGT
1 ATGATATGT
*
52149438 ATGATATGCAC
1 ATGATATG--T
*
52149449 ATGACATGT
1 ATGATATGT
52149458 ATGATATG
1 ATGATATG
52149466 CACACGATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:52149432 original size:20 final size:20
Alignment explanation
Indices: 52149407--52149489 Score: 139
Period size: 20 Copynumber: 4.2 Consensus size: 20
52149397 ATTTTGATAA
52149407 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
52149427 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
52149447 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
* *
52149467 ACACGATATGTATGCTATGC
1 ACATGATATGTATGATATGC
52149487 ACA
1 ACA
52149490 CGAGATGTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.31
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:52149434 original size:11 final size:11
Alignment explanation
Indices: 52149418--52149476 Score: 54
Period size: 11 Copynumber: 5.7 Consensus size: 11
52149408 CATGATATGT
52149418 ATGATATGCAC
1 ATGATATGCAC
*
52149429 ATGATATG--T
1 ATGATATGCAC
52149438 ATGATATGCAC
1 ATGATATGCAC
* *
52149449 ATGACATG--T
1 ATGATATGCAC
52149458 ATGATATGCAC
1 ATGATATGCAC
*
52149469 ACGATATG
1 ATGATATG
52149477 TATGCTATGC
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
9 15 0.41
11 22 0.59
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:52149599 original size:24 final size:24
Alignment explanation
Indices: 52149543--52149731 Score: 269
Period size: 24 Copynumber: 8.0 Consensus size: 24
52149533 GAGGAAGTGA
52149543 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
52149566 TAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
52149590 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
52149614 AAAAGGGCTTATG-CCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
*
52149637 AAAAGGGCTTACGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
* *
52149660 TAAAGGGCTTATGCCCCAGTTATA
1 AAAAGGGCTTATGCCCCAGTTATC
* *
52149684 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
52149708 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
52149732 ATGATAAAGC
Statistics
Matches: 151, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
23 65 0.43
24 75 0.50
25 11 0.07
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:52149612 original size:47 final size:47
Alignment explanation
Indices: 52149543--52149710 Score: 284
Period size: 47 Copynumber: 3.6 Consensus size: 47
52149533 GAGGAAGTGA
52149543 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATC
*
52149590 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATG-CCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-TAAAGGGCTTATGCCCCAGTTATC
* *
52149637 AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATA
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATC
*
52149684 AAAAGGGCTTTTGCCCCAGTTATTAAA
1 AAAAGGGCTTATGCCCCAGTTATTAAA
52149711 AGAGGCTAGG
Statistics
Matches: 113, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
46 12 0.11
47 89 0.79
48 12 0.11
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATC
Found at i:52149958 original size:31 final size:31
Alignment explanation
Indices: 52149923--52149986 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
52149913 CGTTTACCGT
*
52149923 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
52149954 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
52149985 AA
1 AA
52149987 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:52153313 original size:27 final size:27
Alignment explanation
Indices: 52152787--52153312 Score: 679
Period size: 27 Copynumber: 19.6 Consensus size: 27
52152777 CAAAGTACTC
52152787 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* * *
52152814 C-AGTTATAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
52152840 C-ATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
52152866 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
52152893 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
52152920 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
52152947 C-AGTTTACAGAATTATTGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* *
52152974 TGATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
52153001 CGATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
52153028 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
52153055 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
52153082 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
52153109 CGATTTATAGAATTACCGTTTTACCC-
1 CGATTTACAGAATTACCGTTTTACCCT
* * *
52153135 CTAATTTACATAATTACCATTTTACCC-
1 C-GATTTACAGAATTACCGTTTTACCCT
* *
52153162 CGATTTACATAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
52153189 CGATTTACAGAATTACAATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
52153216 CGATTTACAGAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
52153243 CGATTTATAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
52153270 TGATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
52153297 CGATTTACAAAATTAC
1 CGATTTACAGAATTAC
52153313 TAAAATACCC
Statistics
Matches: 440, Mismatches: 50, Indels: 18
0.87 0.10 0.04
Matches are distributed among these distances:
26 71 0.16
27 366 0.83
28 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.40
Consensus pattern (27 bp):
CGATTTACAGAATTACCGTTTTACCCT
Found at i:52154650 original size:9 final size:9
Alignment explanation
Indices: 52154638--52154691 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
52154628 TTTGATAAAC
52154638 ATGATATGT
1 ATGATATGT
*
52154647 ATGATATGCAC
1 ATGATATG--T
52154658 ATGATATGT
1 ATGATATGT
*
52154667 ATGATATGC
1 ATGATATGT
*
52154676 AT-ACATGT
1 ATGATATGT
52154684 ATGATATG
1 ATGATATG
52154692 CACACGATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
8 6 0.17
9 22 0.61
11 8 0.22
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.37
Consensus pattern (9 bp):
ATGATATGT
Found at i:52154661 original size:20 final size:20
Alignment explanation
Indices: 52154636--52154715 Score: 112
Period size: 20 Copynumber: 4.2 Consensus size: 20
52154626 ATTTTGATAA
52154636 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
52154656 ACATGATATGTATGATATG-
1 ACATGATATGTATGATATGC
*
52154675 -CAT-ACATGTATGATATGC
1 ACATGATATGTATGATATGC
* *
52154693 ACACGATATGTATGATGTGC
1 ACATGATATGTATGATATGC
52154713 ACA
1 ACA
52154716 CGAGATGTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
17 13 0.25
18 3 0.06
19 2 0.04
20 35 0.66
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:52154684 original size:37 final size:37
Alignment explanation
Indices: 52154643--52154713 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
52154633 TAAACATGAT
*
52154643 ATGTATGATATGCACATGATATGTATGATATGCATAC
1 ATGTATGATATGCACACGATATGTATGATATGCATAC
*
52154680 ATGTATGATATGCACACGATATGTATGATGTGCA
1 ATGTATGATATGCACACGATATGTATGATATGCA
52154714 CACGAGATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (37 bp):
ATGTATGATATGCACACGATATGTATGATATGCATAC
Found at i:52154812 original size:23 final size:23
Alignment explanation
Indices: 52154769--52154955 Score: 222
Period size: 23 Copynumber: 8.0 Consensus size: 23
52154759 GGAGGAAGTG
*
52154769 AAAAAGGCTTATG-CCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
52154791 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
52154814 CAAAA-GGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
52154837 CAAAAGGGCTTATG-CCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
52154860 CAAAAGGGCTTACGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
52154884 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
52154907 AAAAAGGGCTTTTG-CCCAGTTATT
1 -AAAAGGGCTTATGCCCCAGTTA-T
*
52154931 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
52154955 A
1 A
52154956 TGATAAAGCA
Statistics
Matches: 146, Mismatches: 10, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
22 11 0.08
23 90 0.62
24 38 0.26
25 7 0.05
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:52154855 original size:46 final size:46
Alignment explanation
Indices: 52154769--52154954 Score: 234
Period size: 47 Copynumber: 4.0 Consensus size: 46
52154759 GGAGGAAGTG
* *
52154769 AAAAAGGCTTATGCCCAGTTATTAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
52154815 AAAA-GGCTTATGCCCCAGTTATCAAAAGGGCTTATG-CCCAGTTATC
1 AAAAGGGCTTATG-CCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
* * *
52154861 AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATA
1 AAAAGGGCTTATG-CCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* *
52154908 AAAAGGGCTTTTGCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
52154955 ATGATAAAGC
Statistics
Matches: 125, Mismatches: 8, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
45 8 0.06
46 47 0.38
47 59 0.47
48 11 0.09
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (46 bp):
AAAAGGGCTTATGCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:52154881 original size:70 final size:69
Alignment explanation
Indices: 52154769--52154954 Score: 259
Period size: 70 Copynumber: 2.7 Consensus size: 69
52154759 GGAGGAAGTG
* *
52154769 AAAAA-GGCTTATGCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGCTTATGCCCCAG
1 AAAAAGGGCTTATGCCCAGTTATAAAAGGGCTTACGCCCCAGTTATCAAAAGGCTTATGCCCCAG
52154833 TTAT
66 TTAT
* * *
52154837 CAAAAGGGCTTATGCCCAGTTATCAAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCA
1 AAAAAGGGCTTATGCCCAGTTAT-AAAAGGGCTTACGCCCCAGTTATCAAAAGGCTTATGCCCCA
52154902 GTTAT
65 GTTAT
* *
52154907 AAAAAGGGCTTTTGCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAAGGGCTTATGCCCAGTTA-TAAAAG-GGCTTACGCC-CCAGTTAT
52154955 ATGATAAAGC
Statistics
Matches: 105, Mismatches: 8, Indels: 7
0.88 0.07 0.06
Matches are distributed among these distances:
68 4 0.04
69 17 0.16
70 72 0.69
71 12 0.11
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (69 bp):
AAAAAGGGCTTATGCCCAGTTATAAAAGGGCTTACGCCCCAGTTATCAAAAGGCTTATGCCCCAG
TTAT
Found at i:52155193 original size:30 final size:31
Alignment explanation
Indices: 52155148--52155210 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 31
52155138 CGTTTACCGT
*
52155148 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
52155179 AAAGGCTT-GGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
52155209 AA
1 AA
52155211 TATGAAAAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 21 0.72
31 8 0.28
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:52163539 original size:68 final size:71
Alignment explanation
Indices: 52163467--52163625 Score: 175
Period size: 68 Copynumber: 2.3 Consensus size: 71
52163457 CATCATGTGT
** ** * * * *
52163467 ACAAGAGAGCTACGAGATACTATGTA-GTAGCTAGGTCACATGTGTGA-T-ACGGGATGTATC-C
1 ACAAGAGAGCTACGAGATAAGATAAATGTAGCTAGGTCAAATGTGTGATTCAAGGGAAGGA-CAC
52163528 CATGTAG
65 CATGTAG
* *
52163535 ACAAGAGAGCTACGGGA-AAGATAAATGTAGCTAGGTCAAATGTGTGATTCCAAGTGAAGGACAC
1 ACAAGAGAGCTACGAGATAAGATAAATGTAGCTAGGTCAAATGTGTGATT-CAAGGGAAGGACAC
52163599 CATGTAG
65 CATGTAG
52163606 ACAAGAGAGCTACGAGATAA
1 ACAAGAGAGCTACGAGATAA
52163626 ATTGGCTAGG
Statistics
Matches: 74, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
67 4 0.05
68 36 0.49
69 1 0.01
70 1 0.01
71 30 0.41
72 2 0.03
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.21
Consensus pattern (71 bp):
ACAAGAGAGCTACGAGATAAGATAAATGTAGCTAGGTCAAATGTGTGATTCAAGGGAAGGACACC
ATGTAG
Found at i:52170972 original size:27 final size:26
Alignment explanation
Indices: 52170931--52171040 Score: 130
Period size: 27 Copynumber: 4.1 Consensus size: 26
52170921 AAGCATGGCT
* * *
52170931 ACCAGAACAGGTAATGTGACAGAGTC
1 ACCAGAACAGATAATGTGGCAGAGCC
52170957 ACCAGATACAGATAATCGTGGCAGAGCC
1 ACCAGA-ACAGATAAT-GTGGCAGAGCC
*
52170985 ACCAGAACAGATATATGTGGCAGAACC
1 ACCAGAACAGATA-ATGTGGCAGAGCC
* *
52171012 ACCAGATCAGATAATTGTGGCATAGCC
1 ACCAGAACAGATAA-TGTGGCAGAGCC
52171039 AC
1 AC
52171041 TAGGACGCTT
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
26 7 0.10
27 49 0.67
28 17 0.23
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.16
Consensus pattern (26 bp):
ACCAGAACAGATAATGTGGCAGAGCC
Found at i:52171023 original size:54 final size:54
Alignment explanation
Indices: 52170931--52171040 Score: 150
Period size: 54 Copynumber: 2.0 Consensus size: 54
52170921 AAGCATGGCT
* **
52170931 ACCAGAACAGGTAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCC
1 ACCAGAACAGATAATGTGACAGAACCACCAGATACAGATAATCGTGGCAGAGCC
* * *
52170985 ACCAGAACAGATATATGTGGCAGAACCACCAGAT-CAGATAATTGTGGCATAGCC
1 ACCAGAACAGATA-ATGTGACAGAACCACCAGATACAGATAATCGTGGCAGAGCC
52171039 AC
1 AC
52171041 TAGGACGCTT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
54 32 0.65
55 17 0.35
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.16
Consensus pattern (54 bp):
ACCAGAACAGATAATGTGACAGAACCACCAGATACAGATAATCGTGGCAGAGCC
Found at i:52172966 original size:30 final size:30
Alignment explanation
Indices: 52172932--52172992 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
52172922 TTAATACACC
52172932 TCATTGCATGTAAAACTCATCTCATCGGTT
1 TCATTGCATGTAAAACTCATCTCATCGGTT
52172962 TCATTGCATGTAAAACTCATCTCATCGGTT
1 TCATTGCATGTAAAACTCATCTCATCGGTT
52172992 T
1 T
52172993 TCATACATGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (30 bp):
TCATTGCATGTAAAACTCATCTCATCGGTT
Found at i:52181858 original size:133 final size:133
Alignment explanation
Indices: 52181658--52181927 Score: 414
Period size: 133 Copynumber: 2.0 Consensus size: 133
52181648 ATTTAATTCT
* * * * * ** *
52181658 ATGAAGTGTTATGCGATCATGATAGATGAAATGGAAAATGTTGGCATAATTTTTTTGGTTGGAAT
1 ATGAAATGTTATGAGATCATGATAGATGAAAAGGAAAATATTGGCATAAATGATTTGATTGGAAT
* *
52181723 GAGTAATGCAAATTGGAATTGGATGAATGAAATGTATATTGAGATGTTACTAGTACATGTTTTAT
66 GAGTAATGCAAATTGGAATTGGATGAATAAAATGTATATTGAGATATTACTAGTACATGTTTTAT
52181788 ATA
131 ATA
52181791 ATGAAATGTTATGAGATCATGATAGATGAAAAGGAAAATATTGGCATAAATGATTTGATTGGAAT
1 ATGAAATGTTATGAGATCATGATAGATGAAAAGGAAAATATTGGCATAAATGATTTGATTGGAAT
* * *
52181856 GAGTAATGCAAATTGGAATTTGATTAATAAAATGTATATTGAGATATTATTAGTACATGTTTTAT
66 GAGTAATGCAAATTGGAATTGGATGAATAAAATGTATATTGAGATATTACTAGTACATGTTTTAT
*
52181921 TTA
131 ATA
52181924 ATGA
1 ATGA
52181928 TAAGATTATA
Statistics
Matches: 123, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
133 123 1.00
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.37
Consensus pattern (133 bp):
ATGAAATGTTATGAGATCATGATAGATGAAAAGGAAAATATTGGCATAAATGATTTGATTGGAAT
GAGTAATGCAAATTGGAATTGGATGAATAAAATGTATATTGAGATATTACTAGTACATGTTTTAT
ATA
Found at i:52189995 original size:37 final size:37
Alignment explanation
Indices: 52189945--52190018 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
52189935 ATAAATATTC
**
52189945 TTTTGATAAGTACATTCGTTGTTCTAAGAGAAAAAAA
1 TTTTGATAAGTACATTCACTGTTCTAAGAGAAAAAAA
52189982 TTTTGATAAGTACATTCACTGTTCTAAGAGAAAAAAA
1 TTTTGATAAGTACATTCACTGTTCTAAGAGAAAAAAA
52190019 AAATATGGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (37 bp):
TTTTGATAAGTACATTCACTGTTCTAAGAGAAAAAAA
Found at i:52193327 original size:49 final size:48
Alignment explanation
Indices: 52193263--52193560 Score: 467
Period size: 49 Copynumber: 6.2 Consensus size: 48
52193253 ATGATAGTAT
52193263 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
52193311 CATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 -ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
52193360 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 -ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
*
52193409 TATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT-
1 -ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* *
52193457 ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT-
1 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* * * * * *
52193504 ATGTGATAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A
1 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
52193551 ATGTGATAAG
1 ATGTGATAAG
52193561 TCCCGAAGGG
Statistics
Matches: 238, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
47 95 0.40
49 143 0.60
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (48 bp):
ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
Found at i:52196333 original size:23 final size:23
Alignment explanation
Indices: 52196284--52196334 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
52196274 CAGTTAGAGT
* *
52196284 ACACGGTTGTATGGTTCAAGACT
1 ACACGATTGTATGGTTCAAGACC
52196307 ACACGATTGTATGGTTC-AGCACC
1 ACACGATTGTATGGTTCAAG-ACC
52196330 ACACG
1 ACACG
52196335 GCATCAGCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 2 0.08
23 23 0.92
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (23 bp):
ACACGATTGTATGGTTCAAGACC
Found at i:52206214 original size:26 final size:25
Alignment explanation
Indices: 52206165--52206217 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 25
52206155 AATGGTAGTT
52206165 AAATGTTAAATTTATATGCTGTTATG
1 AAATGTTAAATTTATATGC-GTTATG
52206191 AAATGTTAGAATTTATATTG-GTTATG
1 AAATGTTA-AATTTATA-TGCGTTATG
52206217 A
1 A
52206218 CTAAATATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 15 0.60
27 8 0.32
28 2 0.08
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.45
Consensus pattern (25 bp):
AAATGTTAAATTTATATGCGTTATG
Found at i:52207417 original size:37 final size:37
Alignment explanation
Indices: 52207362--52207542 Score: 308
Period size: 37 Copynumber: 4.9 Consensus size: 37
52207352 AGCTCAGACG
* * *
52207362 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGAAA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
52207399 AAATCTCCACACGTAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
52207436 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
52207473 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
52207510 TAATCTCCACACGTAGTCATCGGGTCTTACCCG
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCG
52207543 AAATATATTT
Statistics
Matches: 140, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 140 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:52207815 original size:48 final size:48
Alignment explanation
Indices: 52207690--52208018 Score: 570
Period size: 48 Copynumber: 6.8 Consensus size: 48
52207680 GCACATCGCC
*
52207690 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--A
* * *
52207740 TATATATTTCACATT-GACCATTTGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCA
52207788 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
52207836 TACATATTTCACATTAGCCATTTGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
52207884 TACATATTTCACATTAGCCATTCGACTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
52207932 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
52207980 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
52208019 TGCATGTTCA
Statistics
Matches: 266, Mismatches: 11, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
48 223 0.84
49 2 0.01
50 41 0.15
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.36
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:52208062 original size:47 final size:47
Alignment explanation
Indices: 52207989--52208134 Score: 193
Period size: 47 Copynumber: 3.1 Consensus size: 47
52207979 ATACATATTT
* * * *
52207989 CACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCAC
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAC
*
52208036 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAT
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAC
* * * ** *
52208083 CACATCGGCCATTCGGCCTTATCTCATATATACACATTCACATTCAT
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAC
52208130 CACAT
1 CACAT
52208135 AAAATCCTAA
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 89 1.00
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.33
Consensus pattern (47 bp):
CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAC
Found at i:52208116 original size:144 final size:142
Alignment explanation
Indices: 52207690--52208070 Score: 511
Period size: 144 Copynumber: 2.6 Consensus size: 142
52207680 GCACATCGCC
*
52207690 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--ATATATA--TCACATT
* * *
52207755 GACCATTTGGCTTTAC-CACATATGCATATCTCATACATATTTCACATTAGCCATTCGGCTTTAC
62 GGCCATTCGGCTTTACACATATATGCATATCTCA-ACATATTTCACATTAGCCATTCGGCTTTAC
52207819 CACATATACATATCTCA
126 CACATATACATATCTCA
* * *
52207836 TACATATTTCACATTAGCCATTTGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCAT--ATATATCACATTGG
*
52207901 CCATTCGACTTTACCACATATA--CATATCTCATACATATTTCACATTAGCCATTCGGCTTTACC
64 CCATTCGGCTTTA-CACATATATGCATATCTCA-ACATATTTCACATTAGCCATTCGGCTTTACC
52207964 ACATATACATATCTCA
127 ACATATACATATCTCA
* *
52207980 TACATATTTCACATTAGCCATTCGGCTTTACCACATATATGCATGT-TCATAT-TCACCACATTG
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA--CATATCTCATATAT-ATCACATTG
*
52208043 GCCATTCGGCCTTATCACATATATGCAT
63 GCCATTCGGCTTTA-CACATATATGCAT
52208071 GTTCACATTC
Statistics
Matches: 210, Mismatches: 16, Indels: 19
0.86 0.07 0.08
Matches are distributed among these distances:
142 1 0.00
143 28 0.13
144 115 0.55
145 8 0.04
146 58 0.28
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.36
Consensus pattern (142 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATCACATTGGCC
ATTCGGCTTTACACATATATGCATATCTCAACATATTTCACATTAGCCATTCGGCTTTACCACAT
ATACATATCTCA
Found at i:52212080 original size:40 final size:40
Alignment explanation
Indices: 52212036--52212387 Score: 533
Period size: 40 Copynumber: 8.8 Consensus size: 40
52212026 CCAGCATGAT
* * * * *
52212036 TGCTCTTCGGGACCTAGCCCAGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
52212076 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
52212116 TGCTCTTCGGGACTTAGTCCGGATACATCACTAGCACAAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
52212156 TGCTCTTCGGGACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
52212196 TGCTCTTCGGGACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
52212236 TGCTCTTTGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
52212276 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * *
52212316 TGCTCTTTGGGACTTAGCCCGGATACATGACTAGTACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
52212356 TGCTCTTCGGGACATAGCCCGGATATATCACT
1 TGCTCTTCGGGACTTAGCCCGGATACATCACT
52212388 CTCAATTCTC
Statistics
Matches: 290, Mismatches: 22, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 290 1.00
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:52213711 original size:37 final size:37
Alignment explanation
Indices: 52213656--52213836 Score: 308
Period size: 37 Copynumber: 4.9 Consensus size: 37
52213646 AGCTCAGACG
* *
52213656 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
52213693 AAATCTCCACACGTAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
52213730 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
52213767 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
52213804 TAATCTTCACACGTAGTCATCGGGTCTTACCCG
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCG
52213837 AAATATATTT
Statistics
Matches: 140, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 140 1.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:52214109 original size:48 final size:48
Alignment explanation
Indices: 52213984--52214360 Score: 675
Period size: 48 Copynumber: 7.8 Consensus size: 48
52213974 GCACATCGCC
*
52213984 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--A
* * *
52214034 TATATATTTCACATT-GACCATTTGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCA
52214082 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
52214130 TACATATTTCACATTAGCCATTTGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
52214178 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
52214226 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
52214274 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
52214322 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
52214361 TGCATGTTCA
Statistics
Matches: 316, Mismatches: 9, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
48 273 0.86
49 2 0.01
50 41 0.13
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:52214404 original size:47 final size:47
Alignment explanation
Indices: 52214331--52214476 Score: 193
Period size: 47 Copynumber: 3.1 Consensus size: 47
52214321 ATACATATTT
* * * *
52214331 CACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCAC
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAC
*
52214378 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAT
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAC
* * * ** *
52214425 CACATCGGCCATTCGGCCTTATCTCATATATACACATTCACATTCAT
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAC
52214472 CACAT
1 CACAT
52214477 AAAATCCTAA
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 89 1.00
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.33
Consensus pattern (47 bp):
CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAC
Found at i:52214458 original size:144 final size:142
Alignment explanation
Indices: 52213985--52214454 Score: 533
Period size: 144 Copynumber: 3.3 Consensus size: 142
52213975 CACATCGCCT
* * *
52213985 ACATATTTCACA-CTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
1 ACATATATCACATC-AGCCATTCGGCCTTACCACATATACATATCTC--ATACATATTTCACATT
* * ** *
52214049 -GACCATTTGGCTTTACCACATATGCATATCTCATACATATTTCACATTAGCCATTCGGCTTTAC
63 AG-CCATTCGGCTTTACCACATATACATATCTCATA-ATATACCACATTAGCCATTCGGCCTTAC
52214113 CACATATACATATCTCA
126 CACATATACATATCTCA
* * * *
52214130 TACATATTTCACATTAGCCATTTGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
1 -ACATATATCACATCAGCCATTCGGCCTTACCACATATACATATCTCATACATATTTCACATTAG
** *
52214195 CCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
65 CCATTCGGCTTTACCACATATACATATCTCATA-ATATACCACATTAGCCATTCGGCCTTACCAC
52214260 ATATACATATCTCA
129 ATATACATATCTCA
* * *
52214274 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
1 -ACATATATCACATCAGCCATTCGGCCTTACCACATATACATATCTCATACATATTTCACATTAG
* * *
52214339 CCATTCGGCTTTACCACATATATGCATGT-TCAT-AT-TCACCACATTGGCCATTCGGCCTTATC
65 CCATTCGGCTTTACCACATATA--CATATCTCATAATAT-ACCACATTAGCCATTCGGCCTTACC
*
52214401 ACATATATGCATGT-TC-
127 ACATATA--CATATCTCA
* * *
52214417 ACAT-TCATCACATCGGCCATTCGGCCTTATCTCATATA
1 ACATAT-ATCACATCAGCCATTCGGCCTTACCACATATA
52214455 TACACATTCA
Statistics
Matches: 297, Mismatches: 19, Indels: 20
0.88 0.06 0.06
Matches are distributed among these distances:
141 1 0.00
142 31 0.10
143 29 0.10
144 180 0.61
145 9 0.03
146 47 0.16
ACGTcount: A:0.30, C:0.27, G:0.08, T:0.36
Consensus pattern (142 bp):
ACATATATCACATCAGCCATTCGGCCTTACCACATATACATATCTCATACATATTTCACATTAGC
CATTCGGCTTTACCACATATACATATCTCATAATATACCACATTAGCCATTCGGCCTTACCACAT
ATACATATCTCA
Found at i:52221691 original size:20 final size:20
Alignment explanation
Indices: 52221668--52221706 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
52221658 TATTCATTTA
52221668 TTTATATAAATTTTATAAAT
1 TTTATATAAATTTTATAAAT
* **
52221688 TTTATGTATTTTTTATAAA
1 TTTATATAAATTTTATAAA
52221707 ATCTTATGTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTATATAAATTTTATAAAT
Found at i:52221703 original size:31 final size:32
Alignment explanation
Indices: 52221663--52221723 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
52221653 ATATATATTC
*
52221663 ATTTATTTATATAAATTTTAT-AAATTTTATGT
1 ATTTATTTATA-AAATCTTATGAAATTTTATGT
*
52221695 ATTT-TTTATAAAATCTTATGTAATTTTAT
1 ATTTATTTATAAAATCTTATGAAATTTTAT
52221724 TGAAAAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 14 0.54
32 4 0.15
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (32 bp):
ATTTATTTATAAAATCTTATGAAATTTTATGT
Found at i:52221713 original size:21 final size:20
Alignment explanation
Indices: 52221678--52221721 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
52221668 TTTATATAAA
* *
52221678 TTTTATAAATTTTATGTATT
1 TTTTATAAATCTTATGTAAT
52221698 TTTTATAAAATCTTATGTAAT
1 TTTTAT-AAATCTTATGTAAT
52221719 TTT
1 TTT
52221722 ATTGAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTTATAAATCTTATGTAAT
Found at i:52221721 original size:20 final size:19
Alignment explanation
Indices: 52221676--52221723 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
52221666 TATTTATATA
*
52221676 AATTTTATAAATTTTATGT
1 AATTTTATAAATCTTATGT
*
52221695 ATTTTTTATAAAATCTTATGT
1 A-ATTTTAT-AAATCTTATGT
52221716 AATTTTAT
1 AATTTTAT
52221724 TGAAAAATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 12 0.50
21 11 0.46
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.58
Consensus pattern (19 bp):
AATTTTATAAATCTTATGT
Found at i:52226865 original size:28 final size:28
Alignment explanation
Indices: 52226831--52226886 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
52226821 GTACGAGTAA
52226831 GACCATGGCATCGATATGTGATTCCAAT
1 GACCATGGCATCGATATGTGATTCCAAT
52226859 GACCATGGCATCGATATGTGATTCCAAT
1 GACCATGGCATCGATATGTGATTCCAAT
52226887 ATGTGTTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (28 bp):
GACCATGGCATCGATATGTGATTCCAAT
Found at i:52229946 original size:44 final size:43
Alignment explanation
Indices: 52229894--52230077 Score: 226
Period size: 44 Copynumber: 4.2 Consensus size: 43
52229884 AGCCTTGACC
*
52229894 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGATCAAGGCTT
1 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCAAGGC-T
** * *
52229938 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGGTTAAGGCT
1 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAA-GGTCAAGGCT
*** * *
52229982 TTTAGCGGCGCTTT-TCCCACAAACGCCGCTAAAGGTCAAGGCT
1 TTTAGCGGCG-TTTGTGGGAGAAGCGCCGCTAAAGGTCAAGGCT
* *
52230025 TTTAGCGGCGTTTTTGGGAGAAGTGCCGCTAAAGGTCAAGGCT
1 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCAAGGCT
52230068 TTTAGCGGCG
1 TTTAGCGGCG
52230078 CTTTTTTTAC
Statistics
Matches: 120, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
42 3 0.03
43 52 0.43
44 55 0.46
45 10 0.08
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.26
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCAAGGCT
Found at i:52230053 original size:43 final size:43
Alignment explanation
Indices: 52229831--52230083 Score: 227
Period size: 43 Copynumber: 5.8 Consensus size: 43
52229821 TGGAAAAAAA
* * *** * *
52229831 CGCCGCTAAAGGTTAAGGCTTTTAGCGGCGCTTTTCCCACAAA
1 CGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTTTGGGAGAAG
* * * ** * * *
52229874 CGCTGCTAAAAGCCTTGACCTTTAGCGGCGTTTGTGGGAGAAG
1 CGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTTTGGGAGAAG
* * ** *
52229917 CGCCGCTAAAGATCAAGGCTTTTTAGCGGCGTTTGTGATAAAAG
1 CGCCGCTAAAGGTCAAGGC-TTTTAGCGGCGTTTTTGGGAGAAG
* * *** * *
52229961 CGCCGCTAAAGGGTTAAGGCTTTTAGCGGCGCTTTTCCCACAAA
1 CGCCGCTAAA-GGTCAAGGCTTTTAGCGGCGTTTTTGGGAGAAG
52230005 CGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTTTGGGAGAAG
1 CGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTTTGGGAGAAG
*
52230048 TGCCGCTAAAGGTCAAGGCTTTTAGCGGCGCTTTTT
1 CGCCGCTAAAGGTCAAGGCTTTTAGCGGCG-TTTTT
52230084 TTACAAACGC
Statistics
Matches: 164, Mismatches: 43, Indels: 5
0.77 0.20 0.02
Matches are distributed among these distances:
43 95 0.58
44 62 0.38
45 7 0.04
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.27
Consensus pattern (43 bp):
CGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTTTGGGAGAAG
Found at i:52230090 original size:86 final size:88
Alignment explanation
Indices: 52229917--52230100 Score: 255
Period size: 86 Copynumber: 2.1 Consensus size: 88
52229907 GTGGGAGAAG
* *
52229917 CGCCGCTAAAGATCAAGGCTTTTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGGTTAAGGCT
1 CGCCGCTAAAGATCAAGGCTTTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGGTCAAGGCT
52229982 TTTAGCGGCGCTTTTCCCACAAA
66 TTTAGCGGCGCTTTTCCCACAAA
* * * * *
52230005 CGCCGCTAAAGGTCAAGGC-TTTTAGCGGCGTTTTTGGGAGAAGTGCCGCTAAA-GGTCAAGGCT
1 CGCCGCTAAAGATCAAGGCTTTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGGTCAAGGCT
***
52230068 TTTAGCGGCGCTTTTTTTACAAA
66 TTTAGCGGCGCTTTTCCCACAAA
*
52230091 CGCCGTTAAA
1 CGCCGCTAAA
52230101 TTTGGCAGAT
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
86 38 0.45
87 29 0.34
88 18 0.21
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (88 bp):
CGCCGCTAAAGATCAAGGCTTTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGGTCAAGGCT
TTTAGCGGCGCTTTTCCCACAAA
Found at i:52230186 original size:31 final size:31
Alignment explanation
Indices: 52230151--52230231 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 31
52230141 CTTCCTGCAT
* *
52230151 TAAAATCCAACCAAATACAACAAATATAATA
1 TAAAATCCAACCAAAAACAACAAATATAACA
* * * *
52230182 TAAAATGCAGCCAAAAACAGCAAATTTAACA
1 TAAAATCCAACCAAAAACAACAAATATAACA
*
52230213 TAAAAAATACAACCAAAAA
1 T--AAAATCCAACCAAAAA
52230232 TATTAATTCT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 26 0.65
33 14 0.35
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.16
Consensus pattern (31 bp):
TAAAATCCAACCAAAAACAACAAATATAACA
Found at i:52231949 original size:13 final size:13
Alignment explanation
Indices: 52231931--52231955 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52231921 AACCAAGAAG
52231931 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
52231944 AAAAAAAAAAAA
1 AAAAAAAAAAAA
52231956 TTTGTTCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.96, C:0.04, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:52233254 original size:40 final size:40
Alignment explanation
Indices: 52233195--52233386 Score: 194
Period size: 40 Copynumber: 4.8 Consensus size: 40
52233185 AAATTGAATG
* *
52233195 ATATCCGGGCTAA-ATCCCGAAGACAATT-ATGCTG-GAAATT
1 ATATCCGGGCTAAGA-CCCGAAGGC-ATTCGTGC-GAGAAATT
* * ****
52233235 ATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGAAATT
* *
52233275 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGATATT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGAAATT
* *
52233315 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGACATT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGAAATT
* *
52233355 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGC
52233387 ACATGATTAT
Statistics
Matches: 130, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
39 3 0.02
40 126 0.97
41 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGAAATT
Found at i:52233400 original size:40 final size:41
Alignment explanation
Indices: 52233232--52233402 Score: 208
Period size: 40 Copynumber: 4.3 Consensus size: 41
52233222 TATGCTGGAA
* *
52233232 ATTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAG-TG
1 ATTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGATG
** *
52233272 GCTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGAT-
1 ATTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGATG
* *
52233312 ATTCTATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-C
1 ATTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGATG
* * *
52233352 ATTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGATG
52233392 ATTATATCCGG
1 ATTATATCCGG
52233403 TTATATTCCG
Statistics
Matches: 114, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
39 5 0.04
40 108 0.95
41 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (41 bp):
ATTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGATG
Found at i:52239449 original size:9 final size:9
Alignment explanation
Indices: 52239435--52239683 Score: 152
Period size: 9 Copynumber: 27.6 Consensus size: 9
52239425 TATTTAAGTA
52239435 TTATGTAAG
1 TTATGTAAG
*
52239444 TTATGTAAT
1 TTATGTAAG
*
52239453 TTATGATATG
1 TTATG-TAAG
* * *
52239463 ATATAT-AT
1 TTATGTAAG
*
52239471 TTATGTAAA
1 TTATGTAAG
* *
52239480 TTATAT-AT
1 TTATGTAAG
*
52239488 TTATCTAAG
1 TTATGTAAG
*
52239497 TTATATAAG
1 TTATGTAAG
52239506 TTATGTAAG
1 TTATGTAAG
*
52239515 TTATGTAAA
1 TTATGTAAG
*
52239524 TTATGATATAAAA
1 TTATG---T-AAG
*
52239537 TATATTTAAG
1 T-TATGTAAG
52239547 TATTATGTAAG
1 --TTATGTAAG
52239558 TTATGTAAG
1 TTATGTAAG
* *
52239567 TTATAT-AT
1 TTATGTAAG
*
52239575 TTATCTAAG
1 TTATGTAAG
*
52239584 TTATATAAG
1 TTATGTAAG
*
52239593 -TATATAAG
1 TTATGTAAG
52239601 TTATGT-AG
1 TTATGTAAG
52239609 TTA--TAAG
1 TTATGTAAG
52239616 TTATGTAAG
1 TTATGTAAG
* *
52239625 TTATATATG
1 TTATGTAAG
*
52239634 TTATATAAG
1 TTATGTAAG
52239643 TTATGTAAG
1 TTATGTAAG
* *
52239652 TTATATATG
1 TTATGTAAG
*
52239661 TTATATAAG
1 TTATGTAAG
*
52239670 TTATGTAAA
1 TTATGTAAG
52239679 TTATG
1 TTATG
52239684 ATATCAAATA
Statistics
Matches: 190, Mismatches: 35, Indels: 30
0.75 0.14 0.12
Matches are distributed among these distances:
6 1 0.01
7 5 0.03
8 29 0.15
9 131 0.69
10 7 0.04
11 8 0.04
12 2 0.01
13 4 0.02
14 3 0.02
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:52239514 original size:18 final size:18
Alignment explanation
Indices: 52239435--52239682 Score: 168
Period size: 18 Copynumber: 13.7 Consensus size: 18
52239425 TATTTAAGTA
* *
52239435 TTATGTAAGTTATGTAAT
1 TTATGTAAGTTATATAAG
* * *
52239453 TTATGATATGATATAT-AT
1 TTATG-TAAGTTATATAAG
* *
52239471 TTATGTAAATTATAT-AT
1 TTATGTAAGTTATATAAG
*
52239488 TTATCTAAGTTATATAAG
1 TTATGTAAGTTATATAAG
* *
52239506 TTATGTAAGTTATGTAAA
1 TTATGTAAGTTATATAAG
* *
52239524 TTATGATATAAAATATATTTAAG
1 TTATG---T-AAGT-TATATAAG
*
52239547 TATTATGTAAGTTATGTAAG
1 --TTATGTAAGTTATATAAG
* * *
52239567 TTATAT-ATTTATCTAAG
1 TTATGTAAGTTATATAAG
*
52239584 TTATATAAG-TATATAAG
1 TTATGTAAGTTATATAAG
52239601 TTATGT-AG-T-TATAAG
1 TTATGTAAGTTATATAAG
*
52239616 TTATGTAAGTTATATATG
1 TTATGTAAGTTATATAAG
* *
52239634 TTATATAAGTTATGTAAG
1 TTATGTAAGTTATATAAG
* *
52239652 TTATATATGTTATATAAG
1 TTATGTAAGTTATATAAG
*
52239670 TTATGTAAATTAT
1 TTATGTAAGTTAT
52239683 GATATCAAAT
Statistics
Matches: 185, Mismatches: 32, Indels: 26
0.76 0.13 0.11
Matches are distributed among these distances:
15 12 0.06
16 5 0.03
17 50 0.27
18 85 0.46
19 7 0.04
20 7 0.04
21 4 0.02
22 4 0.02
23 6 0.03
25 5 0.03
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.48
Consensus pattern (18 bp):
TTATGTAAGTTATATAAG
Found at i:52239527 original size:27 final size:27
Alignment explanation
Indices: 52239488--52239683 Score: 168
Period size: 27 Copynumber: 7.2 Consensus size: 27
52239478 AATTATATAT
*
52239488 TTATCTAAGTTATATAAGTTATGTAAG
1 TTATGTAAGTTATATAAGTTATGTAAG
* * *
52239515 TTATGTAAATTATGATATAAAATATATTTAAG
1 TTATGT-AAGT-T-ATAT-AAGT-TATGTAAG
* * *
52239547 TATTATGTAAGTTATGTAAGTTATAT-AT
1 --TTATGTAAGTTATATAAGTTATGTAAG
* *
52239575 TTATCTAAGTTATATAAG-TATATAAG
1 TTATGTAAGTTATATAAGTTATGTAAG
52239601 TTATGT-AG-T-TATAAGTTATGTAAG
1 TTATGTAAGTTATATAAGTTATGTAAG
* *
52239625 TTATATATGTTATATAAGTTATGTAAG
1 TTATGTAAGTTATATAAGTTATGTAAG
* * *
52239652 TTATATATGTTATATAAGTTATGTAAA
1 TTATGTAAGTTATATAAGTTATGTAAG
52239679 TTATG
1 TTATG
52239684 ATATCAAATA
Statistics
Matches: 139, Mismatches: 18, Indels: 24
0.77 0.10 0.13
Matches are distributed among these distances:
23 6 0.04
24 13 0.09
25 8 0.06
26 23 0.17
27 50 0.36
28 4 0.03
29 5 0.04
30 7 0.05
31 6 0.04
32 8 0.06
33 3 0.02
34 6 0.04
ACGTcount: A:0.39, C:0.01, G:0.14, T:0.46
Consensus pattern (27 bp):
TTATGTAAGTTATATAAGTTATGTAAG
Found at i:52239583 original size:26 final size:25
Alignment explanation
Indices: 52239549--52239598 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
52239539 TATTTAAGTA
* *
52239549 TTATGTAAGTTATGTAAGTTATATAT
1 TTATCTAAGTTATATAAG-TATATAT
52239575 TTATCTAAGTTATATAAGTATATA
1 TTATCTAAGTTATATAAGTATATA
52239599 AGTTATGTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (25 bp):
TTATCTAAGTTATATAAGTATATAT
Found at i:52239634 original size:114 final size:114
Alignment explanation
Indices: 52239411--52239628 Score: 286
Period size: 114 Copynumber: 1.9 Consensus size: 114
52239401 ACTAGTTATG
* * * * *
52239411 TATGATATGATATATATTTAAGTATTATGTAAGTTATGTAATTTATGATATGATATATATTTATG
1 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATGATATATAGTTATA
*
52239476 TAAATTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAAT
66 TAAATTATATAGTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAAT
* *
52239525 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTAT-ATAT-TTATCTAAGTTAT
1 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATGATATAT-AGTTAT
* *
52239588 AT-AAGTATATAAGTTATGT-AG-T-TATAAGTTATGTAAGTTAT
65 ATAAATTATAT-AGTTATCTAAGTTATATAAGTTATGTAAGTTAT
52239629 ATATGTTATA
Statistics
Matches: 92, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
110 19 0.21
111 1 0.01
112 13 0.14
113 16 0.17
114 43 0.47
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.47
Consensus pattern (114 bp):
TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATGATATATAGTTATA
TAAATTATATAGTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAAT
Found at i:52239807 original size:15 final size:15
Alignment explanation
Indices: 52239787--52239841 Score: 71
Period size: 14 Copynumber: 3.8 Consensus size: 15
52239777 AAGTAGCGGG
52239787 ATTAAATAATATTTA
1 ATTAAATAATATTTA
52239802 ATTAAATAATATTTTA
1 ATTAAATAATA-TTTA
*
52239818 A--AAATTAT-TTTA
1 ATTAAATAATATTTA
52239830 ATTAAATAATAT
1 ATTAAATAATAT
52239842 ACATATTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
12 5 0.15
14 12 0.35
15 12 0.35
16 5 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTAAATAATATTTA
Found at i:52241461 original size:21 final size:21
Alignment explanation
Indices: 52241435--52241474 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
52241425 ACACTAATTC
*
52241435 ATACTTAAGTTGAATCAAATA
1 ATACTTAAGTTGAACCAAATA
52241456 ATACTTAAGTTGAACCAAA
1 ATACTTAAGTTGAACCAAA
52241475 ATATAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.30
Consensus pattern (21 bp):
ATACTTAAGTTGAACCAAATA
Found at i:52243703 original size:134 final size:129
Alignment explanation
Indices: 52243528--52243774 Score: 422
Period size: 134 Copynumber: 1.9 Consensus size: 129
52243518 GAATTCAACA
*
52243528 ATATAAAACGTGAGCAACAAGAATATAACTCTTAAATCAATCTAAGTCCACACTAAACACATAAG
1 ATATAAAACGTGAGCAACAAGAAAATAACTCTTAAATCAATCTAAGTCCACACTAAACACATAAG
52243593 TTGGATAGAAACATGAAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTTATT
66 TTGGATAGAAACATG-AAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTTATT
52243658 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
1 ATATAAAACGTGAGCAACAAGA-A--AAT-AACTCTTAAATCAATCTAAGTCCACACTAAACACA
* *
52243723 TAAGTTGGATAGAAACATGAAAACAGACCAAAATAACGTCTAAATAACCAAA
62 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAA
52243775 TGGAATCACC
Statistics
Matches: 110, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
130 22 0.20
131 1 0.01
133 33 0.30
134 54 0.49
ACGTcount: A:0.51, C:0.18, G:0.10, T:0.20
Consensus pattern (129 bp):
ATATAAAACGTGAGCAACAAGAAAATAACTCTTAAATCAATCTAAGTCCACACTAAACACATAAG
TTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTTATT
Found at i:52249842 original size:80 final size:80
Alignment explanation
Indices: 52249758--52249906 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
52249748 TATGGTAACC
* * * *
52249758 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
52249822 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
52249838 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
52249903 CCGG
66 CCGG
52249907 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:52249848 original size:40 final size:38
Alignment explanation
Indices: 52249799--52249906 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
52249789 ATCACGATTT
*
52249799 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
52249839 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
52249879 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
52249907 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:52256905 original size:49 final size:49
Alignment explanation
Indices: 52256800--52257106 Score: 223
Period size: 49 Copynumber: 6.5 Consensus size: 49
52256790 AGATGCCGAC
* * *
52256800 GCCATGTCCCAGGCATGGTCTTACACTGGCTAGTACAT-TA--AA-GTCGAT
1 GCCATGTCCCAGACA-GGTCTTACACTAGCT-CT-CATATATCAAGGTCGAT
* * *
52256848 GCCGTGTCCCAGACAGGTCTTACACTAGCTTTCATATATCGAGGTCGAT
1 GCCATGTCCCAGACAGGTCTTACACTAGCTCTCATATATCAAGGTCGAT
* * *
52256897 GCCATGTCCCAGACAAGTCTTACACTAGCTCTCATTTATCAATGTCGAT
1 GCCATGTCCCAGACAGGTCTTACACTAGCTCTCATATATCAAGGTCGAT
* * * * *
52256946 GCCATGTCCCAGATAGGTCTTACACT-G-ACACATA-A-CAAGCT-GAC
1 GCCATGTCCCAGACAGGTCTTACACTAGCTCTCATATATCAAGGTCGAT
* ** * *
52256990 GCCATGTCCCAGATAGGTCTTACACTA--TCTTGTATATCCCGAGG-CTAAT
1 GCCATGTCCCAGACAGGTCTTACACTAGCTCTCATATAT--CAAGGTC-GAT
* * * * *
52257039 G-CATGTCCCAAACATGTCTTACACTAGCTCTC--ATCTCAATGCCGAT
1 GCCATGTCCCAGACAGGTCTTACACTAGCTCTCATATATCAAGGTCGAT
*
52257085 G-CATGTCCCAGACATGTCTTAC
1 GCCATGTCCCAGACAGGTCTTAC
52257107 GTTGGCTCAC
Statistics
Matches: 209, Mismatches: 36, Indels: 30
0.76 0.13 0.11
Matches are distributed among these distances:
44 31 0.15
45 8 0.04
46 30 0.14
47 19 0.09
48 43 0.21
49 75 0.36
50 3 0.01
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (49 bp):
GCCATGTCCCAGACAGGTCTTACACTAGCTCTCATATATCAAGGTCGAT
Found at i:52263543 original size:28 final size:28
Alignment explanation
Indices: 52263488--52263543 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
52263478 TACAGGGGTT
* *
52263488 TTCACATGGCCTGATACACGCTCGTGTCC
1 TTCACATGGCCTGA-ACACGCCCATGTCC
52263517 TTCACATGGCCATG-ACACGCCCATGTC
1 TTCACATGGCC-TGAACACGCCCATGTC
52263544 TTAGCCCGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.46
29 11 0.46
30 2 0.08
ACGTcount: A:0.20, C:0.36, G:0.20, T:0.25
Consensus pattern (28 bp):
TTCACATGGCCTGAACACGCCCATGTCC
Found at i:52275413 original size:11 final size:11
Alignment explanation
Indices: 52275397--52275423 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
52275387 CAAATCCGAG
52275397 ATTTTAAATTT
1 ATTTTAAATTT
52275408 ATTTTAAATTT
1 ATTTTAAATTT
52275419 ATTTT
1 ATTTT
52275424 TAGTGTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTTTAAATTT
Found at i:52275906 original size:26 final size:26
Alignment explanation
Indices: 52275870--52275922 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
52275860 ACTAAATGAT
52275870 TCAATTTGCCATTTTAGTATCCTAGG
1 TCAATTTGCCATTTTAGTATCCTAGG
52275896 TCAATTTGCCATTTTAGTATCCTAGG
1 TCAATTTGCCATTTTAGTATCCTAGG
52275922 T
1 T
52275923 AAGTTCGTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (26 bp):
TCAATTTGCCATTTTAGTATCCTAGG
Found at i:52281730 original size:20 final size:20
Alignment explanation
Indices: 52281705--52281743 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
52281695 AGAGACTAAA
* *
52281705 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
52281725 ATGAAAAATTCTAAAATTT
1 ATGAAAAATTCTAAAATTT
52281744 TGTATAACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:52284268 original size:30 final size:30
Alignment explanation
Indices: 52284234--52284294 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
52284224 TCCTTAACTC
52284234 AAACTTTAGAAAAATTACAATTTTGCCCCT
1 AAACTTTAGAAAAATTACAATTTTGCCCCT
* * * * *
52284264 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTAGAAAAATTACAATTTTGCCCCT
52284294 A
1 A
52284295 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.38
Consensus pattern (30 bp):
AAACTTTAGAAAAATTACAATTTTGCCCCT
Found at i:52289979 original size:13 final size:13
Alignment explanation
Indices: 52289961--52290014 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
52289951 TGAATGTGAT
52289961 AATGATATATGAA
1 AATGATATATGAA
52289974 AATGAT-TATG--
1 AATGATATATGAA
* * *
52289984 CATGA-ATGTGAT
1 AATGATATATGAA
52289996 AATGATATATGAA
1 AATGATATATGAA
52290009 AATGAT
1 AATGAT
52290015 TAAATGTTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
10 7 0.22
12 8 0.25
13 17 0.53
ACGTcount: A:0.46, C:0.02, G:0.19, T:0.33
Consensus pattern (13 bp):
AATGATATATGAA
Found at i:52289984 original size:35 final size:35
Alignment explanation
Indices: 52289945--52290016 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
52289935 AGTGTTAAAG
52289945 TATGCATGAATGTGATAATGATATATGAAAATGAT
1 TATGCATGAATGTGATAATGATATATGAAAATGAT
52289980 TATGCATGAATGTGATAATGATATATGAAAATGAT
1 TATGCATGAATGTGATAATGATATATGAAAATGAT
52290015 TA
1 TA
52290017 AATGTTGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.35
Consensus pattern (35 bp):
TATGCATGAATGTGATAATGATATATGAAAATGAT
Found at i:52294642 original size:43 final size:42
Alignment explanation
Indices: 52294521--52294656 Score: 131
Period size: 41 Copynumber: 3.3 Consensus size: 42
52294511 CGTTTGCAAT
* * *
52294521 AAAACGCCG-TAAAAAACTGAGCAATAGCGGCTTTTTTAGTCCA
1 AAAACGCCGCT-AAAAACTGAGCAATAGCTGCGTTTTT-GGCCA
* *
52294564 AATA--CCGCTAAAAACTGAGCAATA-ATGACGTTTTTGGACCA
1 AAAACGCCGCTAAAAACTGAGCAATAGCTG-CGTTTTTGG-CCA
* *
52294605 AAAACGCCGCTAAAAACTGAACAATAGCTGCGCTTTTGG--A
1 AAAACGCCGCTAAAAACTGAGCAATAGCTGCGTTTTTGGCCA
52294645 AAAACGCCGCTA
1 AAAACGCCGCTA
52294657 TAGATCAAGG
Statistics
Matches: 78, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
40 15 0.19
41 30 0.38
42 1 0.01
43 30 0.38
44 2 0.03
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.21
Consensus pattern (42 bp):
AAAACGCCGCTAAAAACTGAGCAATAGCTGCGTTTTTGGCCA
Found at i:52294711 original size:50 final size:50
Alignment explanation
Indices: 52294636--52294736 Score: 168
Period size: 50 Copynumber: 2.0 Consensus size: 50
52294626 CAATAGCTGC
52294636 GCTTTTGGAAAAACGCCGCTATAGATCAAGGTTTTAGC-AGCGCTTCTAGA
1 GCTTTTGGAAAAACGCCGCTATAGATCAAGGTTTTAGCGA-CGCTTCTAGA
* *
52294686 GCTTTTGGAAAAACGCCGCTATAGATCGAGGTTTTAGCGACGCTTTTAGA
1 GCTTTTGGAAAAACGCCGCTATAGATCAAGGTTTTAGCGACGCTTCTAGA
52294736 G
1 G
52294737 AAACGCCGCT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
50 47 0.98
51 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.29
Consensus pattern (50 bp):
GCTTTTGGAAAAACGCCGCTATAGATCAAGGTTTTAGCGACGCTTCTAGA
Found at i:52294743 original size:41 final size:41
Alignment explanation
Indices: 52294686--52294805 Score: 195
Period size: 41 Copynumber: 2.9 Consensus size: 41
52294676 CGCTTCTAGA
*
52294686 GCTTTTGGAAAAACGCCGCTATAGATCGAGGTTTTAGCGAC
1 GCTTTTGGAGAAACGCCGCTATAGATCGAGGTTTTAGCGAC
* * *
52294727 GCTTTTAGAGAAACGCCGCTATAGATTGAGGTTTTAGCGGC
1 GCTTTTGGAGAAACGCCGCTATAGATCGAGGTTTTAGCGAC
*
52294768 GCTTTTGGAGAAATGCCGCTATAGATCGAGGTTTTAGC
1 GCTTTTGGAGAAACGCCGCTATAGATCGAGGTTTTAGC
52294806 TGTGCTTTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.29
Consensus pattern (41 bp):
GCTTTTGGAGAAACGCCGCTATAGATCGAGGTTTTAGCGAC
Found at i:52295389 original size:7 final size:7
Alignment explanation
Indices: 52295371--52295409 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
52295361 GGGTTAAGGA
52295371 TTTATGG
1 TTTATGG
* *
52295378 CTTATGT
1 TTTATGG
*
52295385 TTTATGT
1 TTTATGG
52295392 TTTATGG
1 TTTATGG
52295399 TTTATGG
1 TTTATGG
52295406 TTTA
1 TTTA
52295410 AAGTTTAGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.15, C:0.03, G:0.21, T:0.62
Consensus pattern (7 bp):
TTTATGG
Found at i:52295542 original size:14 final size:14
Alignment explanation
Indices: 52295532--52295582 Score: 84
Period size: 14 Copynumber: 3.6 Consensus size: 14
52295522 AATGTTTATT
52295532 GTTTTTGGTTTAGA
1 GTTTTTGGTTTAGA
*
52295546 GTTTTTGGTTTAGG
1 GTTTTTGGTTTAGA
*
52295560 GTTTATGGTTTAGA
1 GTTTTTGGTTTAGA
52295574 GTTTTTGGT
1 GTTTTTGGT
52295583 CTTTTGTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.12, C:0.00, G:0.31, T:0.57
Consensus pattern (14 bp):
GTTTTTGGTTTAGA
Found at i:52295556 original size:28 final size:28
Alignment explanation
Indices: 52295525--52295592 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
52295515 ATCATATAAT
52295525 GTTTATTGTTTTTGGTTTAGAGTTTTTG
1 GTTTATTGTTTTTGGTTTAGAGTTTTTG
** *
52295553 GTTTAGGGTTTATGGTTTAGAGTTTTTG
1 GTTTATTGTTTTTGGTTTAGAGTTTTTG
52295581 GTCTT-TTGTTTT
1 GT-TTATTGTTTT
52295593 ACAGTTAGGA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 31 0.94
29 2 0.06
ACGTcount: A:0.10, C:0.01, G:0.26, T:0.62
Consensus pattern (28 bp):
GTTTATTGTTTTTGGTTTAGAGTTTTTG
Found at i:52295782 original size:20 final size:20
Alignment explanation
Indices: 52295759--52295798 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
52295749 ATATATATAT
*
52295759 ATATATATTTAGGGTTTAGG
1 ATATAGATTTAGGGTTTAGG
* *
52295779 ATATAGGTTTATGGTTTAGG
1 ATATAGATTTAGGGTTTAGG
52295799 GTTTACTGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (20 bp):
ATATAGATTTAGGGTTTAGG
Found at i:52296029 original size:17 final size:18
Alignment explanation
Indices: 52296007--52296043 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
52295997 AATATTTATT
52296007 TTAATATA-TTAAAATTA
1 TTAATATAGTTAAAATTA
*
52296024 TTAATATAGTTTAAATTA
1 TTAATATAGTTAAAATTA
52296042 TT
1 TT
52296044 TAAGAGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TTAATATAGTTAAAATTA
Found at i:52296046 original size:19 final size:18
Alignment explanation
Indices: 52296006--52296046 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
52295996 TAATATTTAT
52296006 TTTAATATATTAAAATTA
1 TTTAATATATTAAAATTA
*
52296024 -TTAATATAGTTTAAATTA
1 TTTAATATA-TTAAAATTA
52296042 TTTAA
1 TTTAA
52296047 GAGATAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 8 0.40
18 8 0.40
19 4 0.20
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TTTAATATATTAAAATTA
Found at i:52300858 original size:40 final size:40
Alignment explanation
Indices: 52300802--52301019 Score: 305
Period size: 40 Copynumber: 5.5 Consensus size: 40
52300792 CGGATGATAA
*
52300802 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
*
52300842 TCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
* * *
52300882 CCGGGCTAAGTCCCAAAGGCATTTGTGCTAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
* * * * *
52300922 CCAGGCTAAGTCCCGAAGGCATTTGGGCTAGTTACTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
* *
52300962 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGCTTTAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
52301002 CC-GGCTAA-ATCCCGAAGG
1 CCGGGCTAAGA-CCCGAAGG
52301020 TACTTGGGTT
Statistics
Matches: 160, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
38 1 0.01
39 14 0.09
40 145 0.91
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
Found at i:52303454 original size:40 final size:40
Alignment explanation
Indices: 52303352--52303519 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
52303342 AAATTGAATG
* * * * *
52303352 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAATT
* ***
52303392 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAATT
* *
52303432 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAATT
* * * *
52303472 CTATCCGGGCTAAGACCCAAAGGCATTTGTGC-ACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTA-GTAATT
52303512 ATATCCGG
1 ATATCCGG
52303520 TTATATTCCG
Statistics
Matches: 106, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
39 4 0.04
40 100 0.94
41 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAATT
Found at i:52306448 original size:15 final size:15
Alignment explanation
Indices: 52306428--52306457 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
52306418 AAATTCAATT
52306428 TATAATTTGTTGCTA
1 TATAATTTGTTGCTA
52306443 TATAATTTGTTGCTA
1 TATAATTTGTTGCTA
52306458 ATATTCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (15 bp):
TATAATTTGTTGCTA
Found at i:52307304 original size:12 final size:11
Alignment explanation
Indices: 52307271--52307304 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
52307261 TTTAATTTGA
52307271 TAAT-GAATTT
1 TAATAGAATTT
52307281 TAATAGAATTT
1 TAATAGAATTT
52307292 TAATAGAAATTT
1 TAATAG-AATTT
52307304 T
1 T
52307305 TTATATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 4 0.18
11 12 0.55
12 6 0.27
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (11 bp):
TAATAGAATTT
Found at i:52308987 original size:12 final size:12
Alignment explanation
Indices: 52308970--52308994 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52308960 CTTTTAAGAA
52308970 TAATCATATTAT
1 TAATCATATTAT
52308982 TAATCATATTAT
1 TAATCATATTAT
52308994 T
1 T
52308995 TTTAGGACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TAATCATATTAT
Found at i:52319933 original size:28 final size:26
Alignment explanation
Indices: 52319893--52319948 Score: 85
Period size: 28 Copynumber: 2.1 Consensus size: 26
52319883 CCTAGGATTC
*
52319893 GCTAGTTAAGTTGCGAACTGGAGGGTTT
1 GCTAGTTAAGTTGCAAACT-G-GGGTTT
52319921 GCTAGTTAAGTTGCAAACTGGGGTTT
1 GCTAGTTAAGTTGCAAACTGGGGTTT
52319947 GC
1 GC
52319949 CAATCACAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 8 0.30
27 1 0.04
28 18 0.67
ACGTcount: A:0.21, C:0.12, G:0.34, T:0.32
Consensus pattern (26 bp):
GCTAGTTAAGTTGCAAACTGGGGTTT
Found at i:52329560 original size:30 final size:30
Alignment explanation
Indices: 52329526--52329585 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
52329516 ATTTACTACG
52329526 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
52329556 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
52329586 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:52333038 original size:2 final size:2
Alignment explanation
Indices: 52333031--52333066 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
52333021 AATTTTTGTA
52333031 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52333067 TAAAAATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52333284 original size:20 final size:20
Alignment explanation
Indices: 52333240--52333276 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
52333230 AGGTAAATTT
52333240 ATTATTATATTACTTTTTAA
1 ATTATTATATTACTTTTTAA
52333260 ATTATTATATTA-TTTTT
1 ATTATTATATTACTTTTT
52333277 TCTGTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTATTATATTACTTTTTAA
Found at i:52334547 original size:21 final size:22
Alignment explanation
Indices: 52334521--52334562 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
52334511 AATGTAATCT
52334521 AGTTATTTAAATC-GA-GTTTTA
1 AGTTA-TTAAATCTGAGGTTTTA
52334542 AGTTATTAAATCTGAGGTTTT
1 AGTTATTAAATCTGAGGTTTT
52334563 GTGTAAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 7 0.37
22 5 0.26
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.48
Consensus pattern (22 bp):
AGTTATTAAATCTGAGGTTTTA
Found at i:52336881 original size:24 final size:24
Alignment explanation
Indices: 52336854--52336924 Score: 79
Period size: 24 Copynumber: 2.9 Consensus size: 24
52336844 CAGCTCGAAA
* *
52336854 GAGCATCCCGTTATTAGCTCTTAT
1 GAGCTTCCCGTTATTAGCTCTTAC
* * *
52336878 GAGCTTCCCGTTATATGGTTCTTGC
1 GAGCTTCCCGTTAT-TAGCTCTTAC
*
52336903 GAGCTTCCCGTTAATAGCTCTT
1 GAGCTTCCCGTTATTAGCTCTT
52336925 TGGAGTATCT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
24 19 0.50
25 19 0.50
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.38
Consensus pattern (24 bp):
GAGCTTCCCGTTATTAGCTCTTAC
Found at i:52338804 original size:39 final size:39
Alignment explanation
Indices: 52338761--52338901 Score: 212
Period size: 39 Copynumber: 3.6 Consensus size: 39
52338751 CATATTCACT
* * *
52338761 TTTAAGCA-AGTATCACATTACACATATAATCACATAACA
1 TTTAAGCATA-TATCACAATACTCATATAATAACATAACA
52338800 TTTAAGCATATATCACAATACTCATATAATAACATAACA
1 TTTAAGCATATATCACAATACTCATATAATAACATAACA
* *
52338839 TTTAAGCATATATCACAATGCTCATATAATAACATAACG
1 TTTAAGCATATATCACAATACTCATATAATAACATAACA
*
52338878 TTCAAGCATATATCACAATACTCA
1 TTTAAGCATATATCACAATACTCA
52338902 AAAACATGTT
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
39 93 0.99
40 1 0.01
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACTCATATAATAACATAACA
Found at i:52340130 original size:24 final size:24
Alignment explanation
Indices: 52340098--52340144 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
52340088 CTGTCAGGAG
**
52340098 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGCAGATAAGGGAT
52340122 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGCAGATAAGGGA
52340145 GGAAATCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.38, T:0.23
Consensus pattern (24 bp):
AGGATTTAGGAGCAGATAAGGGAT
Found at i:52341602 original size:27 final size:26
Alignment explanation
Indices: 52341562--52341673 Score: 134
Period size: 27 Copynumber: 4.2 Consensus size: 26
52341552 AGGAAGCGTC
*
52341562 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
52341589 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
52341616 CTGGTGGTTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
52341644 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
52341670 CTGG
1 CTGG
52341674 CAGCCATGCT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
26 7 0.09
27 51 0.69
28 16 0.22
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:52341666 original size:54 final size:54
Alignment explanation
Indices: 52341562--52341673 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
52341552 AGGAAGCGTC
*
52341562 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * * *
52341616 CTGGTGGTTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
52341670 CTGG
1 CTGG
52341674 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:52345746 original size:51 final size:51
Alignment explanation
Indices: 52345691--52345790 Score: 137
Period size: 51 Copynumber: 2.0 Consensus size: 51
52345681 CTACCTTATA
* ** *
52345691 ACATGTAACACATCCATAATGAACTCGGACCTTTCAATGAGCTCAGATGTT
1 ACATGTAACACATCCATAATGAACTCAGACCACTCAACGAGCTCAGATGTT
* * *
52345742 ACATGTATCACATCCATTATGAACTCAGACCACTCAACGAGCTCGGATG
1 ACATGTAACACATCCATAATGAACTCAGACCACTCAACGAGCTCAGATG
52345791 CCACATATAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (51 bp):
ACATGTAACACATCCATAATGAACTCAGACCACTCAACGAGCTCAGATGTT
Found at i:52345802 original size:51 final size:51
Alignment explanation
Indices: 52345699--52345802 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 51
52345689 TAACATGTAA
* ** * ** *
52345699 CACATCCATAATGAACTCGGACCTTTCAATGAGCTCAGATGTTACATGTAT
1 CACATCCATAATGAACTCAGACCACTCAACGAGCTCAGATGCCACATATAT
* *
52345750 CACATCCATTATGAACTCAGACCACTCAACGAGCTCGGATGCCACATATAT
1 CACATCCATAATGAACTCAGACCACTCAACGAGCTCAGATGCCACATATAT
52345801 CA
1 CA
52345803 TGAACTTGGA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.25
Consensus pattern (51 bp):
CACATCCATAATGAACTCAGACCACTCAACGAGCTCAGATGCCACATATAT
Found at i:52354348 original size:12 final size:12
Alignment explanation
Indices: 52354331--52354355 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52354321 TTTGGACAGC
52354331 AGCAGTAGTCTA
1 AGCAGTAGTCTA
52354343 AGCAGTAGTCTA
1 AGCAGTAGTCTA
52354355 A
1 A
52354356 CTTTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (12 bp):
AGCAGTAGTCTA
Found at i:52358789 original size:29 final size:29
Alignment explanation
Indices: 52358755--52358832 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
52358745 GTGACGAGAT
* *
52358755 CGGCACTAAGTGTGCGTGCTGGAAATATA
1 CGGCACTAAGTGTGCGAGCTGGAAAAATA
* *
52358784 TGGCACTAAGTGTGCAAGCTGGAAAAATA
1 CGGCACTAAGTGTGCGAGCTGGAAAAATA
**
52358813 CGGCACTGGGTGTGCGAGCT
1 CGGCACTAAGTGTGCGAGCT
52358833 CGGAGGGTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.27, C:0.18, G:0.33, T:0.22
Consensus pattern (29 bp):
CGGCACTAAGTGTGCGAGCTGGAAAAATA
Found at i:52366680 original size:28 final size:29
Alignment explanation
Indices: 52366604--52366680 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
52366594 GTGACGAGAT
*
52366604 CGGCACTAAGTGTGCGTGCTGGAAATATA
1 CGGCACTAAGTGTGCGAGCTGGAAATATA
* *
52366633 TGGCACTAAGTGTGCAAGCTGGAAA-ATA
1 CGGCACTAAGTGTGCGAGCTGGAAATATA
**
52366661 CGGCACTGGGTGTGCGAGCT
1 CGGCACTAAGTGTGCGAGCT
52366681 CGGAGGGTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 19 0.46
29 22 0.54
ACGTcount: A:0.26, C:0.18, G:0.34, T:0.22
Consensus pattern (29 bp):
CGGCACTAAGTGTGCGAGCTGGAAATATA
Found at i:52370442 original size:40 final size:40
Alignment explanation
Indices: 52370267--52370486 Score: 277
Period size: 40 Copynumber: 5.5 Consensus size: 40
52370257 CGGATGTAAC
52370267 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
*
52370307 AACCCA-CACGAATACCTTCGGGACTTAACCCGGTTATAAT
1 AA-CCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
* *
52370347 AACCCGCACGAATACCTTC-GGACTTAACCCGGTTATAAT
1 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
* *
52370386 AACCCGTACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
* ** * *
52370426 AACTAGCAC-AATTGCCTTC-GGATCTTAGTCCGGATATAGT
1 AACCAGCACGAA-TGCCTTCGGGA-CTTAACCCGGTTATAAT
* *
52370466 AACTAGCACAAATGCCTTCGG
1 AACCAGCACGAATGCCTTCGG
52370487 ATCTTAGTCC
Statistics
Matches: 162, Mismatches: 11, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
39 44 0.27
40 112 0.69
41 6 0.04
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (40 bp):
AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
Found at i:52370444 original size:79 final size:79
Alignment explanation
Indices: 52370267--52370452 Score: 284
Period size: 79 Copynumber: 2.3 Consensus size: 79
52370257 CGGATGTAAC
52370267 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAATAACCCACACGAATACCTTCGGGACT
1 AACCAGCACGAATGCCTTC-GGACTTAACCCGGTTATAATAACCCACACGAATACCTTCGGGACT
52370332 TAACCCGGTTATAAT
65 TAACCCGGTTATAAT
* * ** *
52370347 AACCCGCACGAATACCTTCGGACTTAACCCGGTTATAATAACCCGTACGAATGCCTTCGGGACTT
1 AACCAGCACGAATGCCTTCGGACTTAACCCGGTTATAATAACCCACACGAATACCTTCGGGACTT
52370412 AACCCGGTTATAAT
66 AACCCGGTTATAAT
*
52370426 AACTAGCAC-AATTGCCTTCGGATCTTA
1 AACCAGCACGAA-TGCCTTCGGA-CTTA
52370453 GTCCGGATAT
Statistics
Matches: 96, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
78 2 0.02
79 73 0.76
80 21 0.22
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (79 bp):
AACCAGCACGAATGCCTTCGGACTTAACCCGGTTATAATAACCCACACGAATACCTTCGGGACTT
AACCCGGTTATAAT
Found at i:52370485 original size:119 final size:120
Alignment explanation
Indices: 52370274--52370492 Score: 293
Period size: 119 Copynumber: 1.8 Consensus size: 120
52370264 AACAACCAGC
52370274 ACGAATGCCTTCGGGACTTAACCCGGTTATAATAACCCACACGAATACCTTCGGGACTTAACCCG
1 ACGAATGCCTTCGGGACTTAACCCGGTTATAATAACCCACACGAATACCTTCGGGACTTAACCCG
* * *
52370339 GTTATAATAACCCGCACGAATACCTTCGGA-CTTAACCCGGTTATAATAACCCGT
66 GATATAATAACCAGCACAAATACCTTCGGATCTTAACCCGGTTATAATAACCCGT
* * **
52370393 ACGAATGCCTTCGGGACTTAACCCGGTTATAATAA-CTAGCAC-AATTGCCTTC-GGATCTTAGT
1 ACGAATGCCTTCGGGACTTAACCCGGTTATAATAACCCA-CACGAA-TACCTTCGGGA-CTTAAC
* * *
52370455 CCGGATATAGTAACTAGCACAAATGCCTTCGGATCTTA
63 CCGGATATAATAACCAGCACAAATACCTTCGGATCTTA
52370493 GTCCGGATAT
Statistics
Matches: 86, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
118 7 0.08
119 75 0.87
120 4 0.05
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (120 bp):
ACGAATGCCTTCGGGACTTAACCCGGTTATAATAACCCACACGAATACCTTCGGGACTTAACCCG
GATATAATAACCAGCACAAATACCTTCGGATCTTAACCCGGTTATAATAACCCGT
Found at i:52370487 original size:40 final size:40
Alignment explanation
Indices: 52370257--52370502 Score: 160
Period size: 40 Copynumber: 6.2 Consensus size: 40
52370247 GAATTTGGCT
* * * * **
52370257 CGGATGTAACAACCAGCACGAATGCCTTCGGGA-CTTAACC
1 CGGATATAATAACTAGCACAAATGCCTTC-GGATCTTAGTC
* * * * **
52370297 CGGTTATAATAACCCA-CACGAATACCTTCGGGA-CTTAACC
1 CGGATATAATAA-CTAGCACAAATGCCTTC-GGATCTTAGTC
* ** * * **
52370337 CGGTTATAATAACCCGCACGAATACCTTCGGA-CTTAACC
1 CGGATATAATAACTAGCACAAATGCCTTCGGATCTTAGTC
* ** * * **
52370376 CGGTTATAATAACCCGTACGAATGCCTTCGGGA-CTTAACC
1 CGGATATAATAACTAGCACAAATGCCTTC-GGATCTTAGTC
* *
52370416 CGGTTATAATAACTAGCACAATTGCCTTCGGATCTTAGTC
1 CGGATATAATAACTAGCACAAATGCCTTCGGATCTTAGTC
*
52370456 CGGATATAGTAACTAGCACAAATGCCTTCGGATCTTAGTC
1 CGGATATAATAACTAGCACAAATGCCTTCGGATCTTAGTC
52370496 CGGATAT
1 CGGATAT
52370503 CATCCGAATA
Statistics
Matches: 185, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
39 42 0.23
40 140 0.76
41 3 0.02
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.25
Consensus pattern (40 bp):
CGGATATAATAACTAGCACAAATGCCTTCGGATCTTAGTC
Found at i:52377916 original size:40 final size:40
Alignment explanation
Indices: 52377740--52377960 Score: 277
Period size: 40 Copynumber: 5.5 Consensus size: 40
52377730 CGGATGTAAC
52377740 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
*
52377780 AACCCA-CACGAATACCTTCGGGACTTAACCCGGTTATAAT
1 AA-CCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
* * *
52377820 AACCCGCACGAATACCTTCAGGACTTAACCCGGTTATAAT
1 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
* *
52377860 AACCCGTACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
* ** * *
52377900 AACTAGCAC-AATTGCCTTC-GGATCTTAGTCCGGATATAGT
1 AACCAGCACGAA-TGCCTTCGGGA-CTTAACCCGGTTATAAT
* *
52377940 AACTAGCACAAATGCCTTCGG
1 AACCAGCACGAATGCCTTCGG
52377961 ATCTTAGTCC
Statistics
Matches: 162, Mismatches: 13, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
39 7 0.04
40 149 0.92
41 6 0.04
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (40 bp):
AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
Found at i:52377961 original size:40 final size:40
Alignment explanation
Indices: 52377730--52377976 Score: 153
Period size: 40 Copynumber: 6.2 Consensus size: 40
52377720 GAATTTGGCT
* * * * **
52377730 CGGATGTAACAACCAGCACGAATGCCTTCGGGA-CTTAACC
1 CGGATATAATAACTAGCACAAATGCCTTC-GGATCTTAGTC
* * * * **
52377770 CGGTTATAATAACCCA-CACGAATACCTTCGGGA-CTTAACC
1 CGGATATAATAA-CTAGCACAAATGCCTTC-GGATCTTAGTC
* ** * * **
52377810 CGGTTATAATAACCCGCACGAATACCTTCAGGA-CTTAACC
1 CGGATATAATAACTAGCACAAATGCCTTC-GGATCTTAGTC
* ** * * **
52377850 CGGTTATAATAACCCGTACGAATGCCTTCGGGA-CTTAACC
1 CGGATATAATAACTAGCACAAATGCCTTC-GGATCTTAGTC
* *
52377890 CGGTTATAATAACTAGCACAATTGCCTTCGGATCTTAGTC
1 CGGATATAATAACTAGCACAAATGCCTTCGGATCTTAGTC
*
52377930 CGGATATAGTAACTAGCACAAATGCCTTCGGATCTTAGTC
1 CGGATATAATAACTAGCACAAATGCCTTCGGATCTTAGTC
52377970 CGGATAT
1 CGGATAT
52377977 CATCTGAATA
Statistics
Matches: 185, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
39 5 0.03
40 177 0.96
41 3 0.02
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.25
Consensus pattern (40 bp):
CGGATATAATAACTAGCACAAATGCCTTCGGATCTTAGTC
Found at i:52381231 original size:40 final size:40
Alignment explanation
Indices: 52381176--52381313 Score: 129
Period size: 37 Copynumber: 3.5 Consensus size: 40
52381166 ACCAGTTTGG
*
52381176 CACCCAGTGTCTCATCGAATAATTCAAAGTAGTAAATTGA
1 CACCCAATGTCTCATCGAATAATTCAAAGTAGTAAATTGA
** * * *
52381216 CACCCAATGTCTCATCGGTTAA-ACCAA--AGTAAATTGG
1 CACCCAATGTCTCATCGAATAATTCAAAGTAGTAAATTGA
* ** * *
52381253 CACCCAATGCCTCATCGAATAAATTCGGAGTAATAAACTGA
1 CACCCAATGTCTCATCGAAT-AATTCAAAGTAGTAAATTGA
* *
52381294 AACCCAGTGTCTCATCGAAT
1 CACCCAATGTCTCATCGAAT
52381314 CGAAGTCGAA
Statistics
Matches: 76, Mismatches: 18, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
37 26 0.34
38 2 0.03
39 5 0.07
40 19 0.25
41 24 0.32
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (40 bp):
CACCCAATGTCTCATCGAATAATTCAAAGTAGTAAATTGA
Found at i:52381742 original size:16 final size:14
Alignment explanation
Indices: 52381686--52381752 Score: 57
Period size: 16 Copynumber: 4.6 Consensus size: 14
52381676 GTCTTTCTCC
52381686 TTTC-TTTCTTTC-
1 TTTCTTTTCTTTCT
*
52381698 TTTCTTTCCTTTCT
1 TTTCTTTTCTTTCT
*
52381712 GTTTCGTTTTTTTTCT
1 -TTTC-TTTTCTTTCT
52381728 ATTTCTATTTCTTTCT
1 -TTTCT-TTTCTTTCT
52381744 TCTTCTTTT
1 T-TTCTTTT
52381753 TTTTTAAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
12 4 0.09
13 7 0.16
15 9 0.20
16 24 0.55
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.73
Consensus pattern (14 bp):
TTTCTTTTCTTTCT
Found at i:52381742 original size:32 final size:31
Alignment explanation
Indices: 52381698--52381757 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
52381688 TCTTTCTTTC
52381698 TTTCTTTCCTTTCTGT-TTCGTTTTTTTTCTA
1 TTTCTTTCCTTTCT-TCTTCGTTTTTTTTCTA
* *
52381729 TTTCTATTTCTTTCTTCTTCTTTTTTTTT
1 TTTCT-TTCCTTTCTTCTTCGTTTTTTTT
52381758 AAATTTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 6 0.24
32 19 0.76
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.75
Consensus pattern (31 bp):
TTTCTTTCCTTTCTTCTTCGTTTTTTTTCTA
Found at i:52381749 original size:22 final size:23
Alignment explanation
Indices: 52381690--52381749 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 23
52381680 TTCTCCTTTC
* *
52381690 TTTCTTTCTTTCTT-TCCTTTCTG
1 TTTCTTTC-TTCTTCTCATTTCTA
*
52381713 TTTCGTTT-TTTTTCT-ATTTCTA
1 TTTC-TTTCTTCTTCTCATTTCTA
52381735 TTTCTTTCTTCTTCT
1 TTTCTTTCTTCTTCT
52381750 TTTTTTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
21 3 0.10
22 19 0.63
23 5 0.17
24 3 0.10
ACGTcount: A:0.03, C:0.22, G:0.03, T:0.72
Consensus pattern (23 bp):
TTTCTTTCTTCTTCTCATTTCTA
Found at i:52382904 original size:19 final size:19
Alignment explanation
Indices: 52382880--52382918 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
52382870 AAATGTTAAC
*
52382880 ATCAATTTTCAATAGTTGT
1 ATCAATTTTCAATAATTGT
52382899 ATCAATTTTCAATAATTGT
1 ATCAATTTTCAATAATTGT
52382918 A
1 A
52382919 CCATCCTACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (19 bp):
ATCAATTTTCAATAATTGT
Found at i:52383922 original size:28 final size:28
Alignment explanation
Indices: 52383882--52383940 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
52383872 ACTAGTTTGG
52383882 CAACCTTTGAGGACAAGGTTCAACCTTA
1 CAACCTTTGAGGACAAGGTTCAACCTTA
52383910 CAACCTTTGAGGACAAGGTTCAACCTTA
1 CAACCTTTGAGGACAAGGTTCAACCTTA
52383938 CAA
1 CAA
52383941 TCTCTCTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (28 bp):
CAACCTTTGAGGACAAGGTTCAACCTTA
Found at i:52384751 original size:33 final size:33
Alignment explanation
Indices: 52384714--52384779 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
52384704 GAATAGATTA
*
52384714 CTCCCCCT-TAATAAAAGTCATTTTCAATTTAAG
1 CTCCCCCTAT-ATAAAAATCATTTTCAATTTAAG
52384747 CTCCCCCTATATAAAAATCATTTTCAATTTAAG
1 CTCCCCCTATATAAAAATCATTTTCAATTTAAG
52384780 GCATAAAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.36
Consensus pattern (33 bp):
CTCCCCCTATATAAAAATCATTTTCAATTTAAG
Found at i:52392128 original size:39 final size:40
Alignment explanation
Indices: 52392028--52392219 Score: 205
Period size: 40 Copynumber: 4.8 Consensus size: 40
52392018 TCGAATGATG
* * *
52392028 TCCGGTCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
*
52392067 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
** * *
52392108 TCCAAGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
52392147 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
52392186 AACCGGGCTATGTCCCGAAGGCATTTGAGCGAGT
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
52392220 AGCTATATCC
Statistics
Matches: 129, Mismatches: 17, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
39 34 0.26
40 85 0.66
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:52392234 original size:79 final size:79
Alignment explanation
Indices: 52392029--52392235 Score: 219
Period size: 79 Copynumber: 2.6 Consensus size: 79
52392019 CGAATGATGT
* * *
52392029 CCGGTCTAAGTCCCGAAGGC-TTTGTGCTAAGT-GACTATATCCGGACTAAGATCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTAG-CTATATCCGG-TTAAGATCCGAAGGCATT
*
52392092 TGTGCGAGTTACTAATT
63 TGTGCGAGTTACTAATA
** * *
52392109 CCAAGCTAAG-CCCGAAGGCATTGGTGCGAGTTA-CTAAATCCGGGTTAAG-TCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TAGCTATATCC-GGTTAAGAT-CCGAAGGCATT
52392171 TGTGCGAGTTACT-ATAA
63 TGTGCGAGTTACTAAT-A
* *
52392188 CCGGGCTATGTCCCGAAGGCATTTGAGCGAGTAGCTATATCCGGTTAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTTAA
52392236 AGTCTGAAGG
Statistics
Matches: 105, Mismatches: 14, Indels: 17
0.77 0.10 0.12
Matches are distributed among these distances:
78 3 0.03
79 61 0.58
80 41 0.39
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTTAAGATCCGAAGGCATTTGT
GCGAGTTACTAATA
Found at i:52397453 original size:38 final size:38
Alignment explanation
Indices: 52397401--52397476 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
52397391 GTAATAGAAA
*
52397401 ATGTTAATGAGTGACTAATTTG-CAACTTTTTGATAACG
1 ATGTTAATGAGTGACTAATTTGTC-ACTTTTCGATAACG
*
52397439 ATGTTAATGGGTGACTAATTTGTCACTTTTCGATAACG
1 ATGTTAATGAGTGACTAATTTGTCACTTTTCGATAACG
52397477 TTAGTGACTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 34 0.97
39 1 0.03
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (38 bp):
ATGTTAATGAGTGACTAATTTGTCACTTTTCGATAACG
Found at i:52397839 original size:5 final size:5
Alignment explanation
Indices: 52397829--52397876 Score: 62
Period size: 5 Copynumber: 9.4 Consensus size: 5
52397819 TAAATTTTAA
*
52397829 TTATT TTATT TTATT TTATT TTATT TCTATCT TTATT TT-TT CTATT TT
1 TTATT TTATT TTATT TTATT TTATT T-TAT-T TTATT TTATT TTATT TT
52397877 TGCTTTCATC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
4 3 0.08
5 27 0.71
6 6 0.16
7 2 0.05
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:52400738 original size:21 final size:22
Alignment explanation
Indices: 52400712--52400752 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
52400702 ATTTTGCTTG
*
52400712 CTGTGTTGCGACATC-CAAGCT
1 CTGTGTTGCAACATCACAAGCT
52400733 CTGTGTTGCAACATCACAAG
1 CTGTGTTGCAACATCACAAG
52400753 TAGTCCACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (22 bp):
CTGTGTTGCAACATCACAAGCT
Found at i:52406184 original size:21 final size:21
Alignment explanation
Indices: 52406160--52406232 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
52406150 ACAGGGGAAA
*
52406160 TCTTTAGAAATTTTGGTAAAT
1 TCTTTAGAAATTTTAGTAAAT
*
52406181 TCTTTAGAAATTTTAGTAAAA
1 TCTTTAGAAATTTTAGTAAAT
52406202 T-TTTAGAAATTTTAGTAAAT
1 TCTTTAGAAATTTTAGTAAAT
* *
52406222 CCTTTAAAAAT
1 TCTTTAGAAAT
52406233 ATAGATATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 18 0.39
21 28 0.61
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (21 bp):
TCTTTAGAAATTTTAGTAAAT
Found at i:52406202 original size:11 final size:11
Alignment explanation
Indices: 52406167--52406220 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 11
52406157 AAATCTTTAG
*
52406167 AAATTTTGGTA
1 AAATTTTAGTA
*
52406178 AATTCTTTAG--
1 AAAT-TTTAGTA
52406188 AAATTTTAGTA
1 AAATTTTAGTA
52406199 AAATTTTAG--
1 AAATTTTAGTA
52406208 AAATTTTAGTA
1 AAATTTTAGTA
52406219 AA
1 AA
52406221 TCCTTTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
9 14 0.40
10 3 0.09
11 14 0.40
12 4 0.11
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.44
Consensus pattern (11 bp):
AAATTTTAGTA
Found at i:52406208 original size:20 final size:21
Alignment explanation
Indices: 52406157--52406292 Score: 104
Period size: 20 Copynumber: 6.6 Consensus size: 21
52406147 GACACAGGGG
*
52406157 AAATCTTTAGAAATTTTGGTA
1 AAATCTTTAGAAATTTTAGTA
*
52406178 AATTCTTTAGAAATTTTAGTA
1 AAATCTTTAGAAATTTTAGTA
52406199 AAAT-TTTAGAAATTTTAGT-
1 AAATCTTTAGAAATTTTAGTA
* *
52406218 AAATCCTTTA-AAAATATAGATA
1 AAAT-CTTTAGAAATTTTAG-TA
* * *
52406240 TAA-CCTTAGAGAA-TTTGGT-
1 AAATCTTTAGA-AATTTTAGTA
* *
52406259 AAATGTTTAGATATTTTAGTA
1 AAATCTTTAGAAATTTTAGTA
*
52406280 TAAATCCTTAGAA
1 -AAATCTTTAGAA
52406293 TTATTGATAA
Statistics
Matches: 88, Mismatches: 17, Indels: 19
0.71 0.14 0.15
Matches are distributed among these distances:
19 7 0.08
20 37 0.42
21 31 0.35
22 13 0.15
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (21 bp):
AAATCTTTAGAAATTTTAGTA
Done.