Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 171 of 318
Found at i:54046418 original size:17 final size:17
Alignment explanation
Indices: 54046396--54046515 Score: 59
Period size: 17 Copynumber: 6.8 Consensus size: 17
54046386 TTAACTATTT
54046396 TTTTTTATAATTTTAAA
1 TTTTTTATAATTTTAAA
* *
54046413 TTTTTTAGAATTTAATTAA
1 TTTTTTATAATTT--TAAA
* *
54046432 TCTTTTAT-ATTTTTAA
1 TTTTTTATAATTTTAAA
* **
54046448 TTTTTCTATACTTTTTGGA
1 TTTTT-TATA-ATTTTAAA
*
54046467 TTTTTT-TACGTTTCT-AA
1 TTTTTTATA-ATTT-TAAA
*
54046484 TATTTTAT-ATTTTAAA
1 TTTTTTATAATTTTAAA
54046500 TTTTTCTATACATTTT
1 TTTTT-TATA-ATTTT
54046516 CTTAACTTTT
Statistics
Matches: 79, Mismatches: 13, Indels: 20
0.71 0.12 0.18
Matches are distributed among these distances:
15 1 0.01
16 17 0.22
17 30 0.38
18 7 0.09
19 24 0.30
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (17 bp):
TTTTTTATAATTTTAAA
Found at i:54046569 original size:19 final size:19
Alignment explanation
Indices: 54046547--54046589 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
54046537 AATATTATTT
*
54046547 ATTTTTATAAAAATTTTGA
1 ATTTTTATAAAAATTTAGA
* *
54046566 ATTTTTATATATATTTAGA
1 ATTTTTATAAAAATTTAGA
54046585 ATTTT
1 ATTTT
54046590 AGGATTTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
ATTTTTATAAAAATTTAGA
Found at i:54047630 original size:16 final size:16
Alignment explanation
Indices: 54047595--54047660 Score: 55
Period size: 16 Copynumber: 4.1 Consensus size: 16
54047585 AATTATAATT
** *
54047595 TAAAAATACAAATTAT
1 TAAAAATACAAAAAAA
54047611 TAAAAATACAAAAAAA
1 TAAAAATACAAAAAAA
*
54047627 T-AAAATAAAAAAAATTA
1 TAAAAATACAAAAAA--A
54047644 TAAAAAATA-AAAAAAA
1 T-AAAAATACAAAAAAA
54047660 T
1 T
54047661 TACTATGAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
15 12 0.29
16 16 0.38
17 2 0.05
18 6 0.14
19 6 0.14
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (16 bp):
TAAAAATACAAAAAAA
Found at i:54047639 original size:24 final size:23
Alignment explanation
Indices: 54047612--54047659 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
54047602 ACAAATTATT
54047612 AAAAA-TACAAAAAAATAAAATAAA
1 AAAAATTA-AAAAAAATAAAA-AAA
*
54047636 AAAAATTATAAAAAATAAAAAAA
1 AAAAATTAAAAAAAATAAAAAAA
54047659 A
1 A
54047660 TTACTATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 4 0.18
24 16 0.73
25 2 0.09
ACGTcount: A:0.83, C:0.02, G:0.00, T:0.15
Consensus pattern (23 bp):
AAAAATTAAAAAAAATAAAAAAA
Found at i:54050022 original size:17 final size:17
Alignment explanation
Indices: 54050000--54050034 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
54049990 AACTGGAAAA
54050000 ACATGTTATATATTTTT
1 ACATGTTATATATTTTT
54050017 ACATGTTATATATTTTT
1 ACATGTTATATATTTTT
54050034 A
1 A
54050035 GTTTCATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (17 bp):
ACATGTTATATATTTTT
Found at i:54050564 original size:20 final size:19
Alignment explanation
Indices: 54050541--54050610 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
54050531 ATTACAAAAC
54050541 AAAATTTAAAATAATTTTCA
1 AAAATTTAAAATAATTTT-A
54050561 AAAATTTAAAATAAATTTT-
1 AAAATTTAAAAT-AATTTTA
*
54050580 AAAATTCAAAAT-ATTTATAA
1 AAAATTTAAAATAATTT-T-A
54050600 AAAATTTAAAA
1 AAAATTTAAAA
54050611 ATTTATATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.09
18 1 0.02
19 11 0.25
20 22 0.50
21 6 0.14
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATTTAAAATAATTTTA
Found at i:54050604 original size:28 final size:27
Alignment explanation
Indices: 54050557--54050613 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
54050547 TAAAATAATT
*
54050557 TTCAAAAATTTAAAATAAATTTTAAAA
1 TTCAAAAATTTAAAATAAATTTAAAAA
54050584 TTCAAAATATTTATAAA-AAATTTAAAAA
1 TTCAAAA-ATTTA-AAATAAATTTAAAAA
54050612 TT
1 TT
54050614 TATATTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 7 0.26
28 17 0.63
29 3 0.11
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.39
Consensus pattern (27 bp):
TTCAAAAATTTAAAATAAATTTAAAAA
Found at i:54050614 original size:19 final size:20
Alignment explanation
Indices: 54050580--54050617 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54050570 AATAAATTTT
54050580 AAAATTCAAAATATTTATAA
1 AAAATTCAAAATATTTATAA
*
54050600 AAAATTTAAAA-ATTTATA
1 AAAATTCAAAATATTTATA
54050618 TTTTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATTCAAAATATTTATAA
Found at i:54050618 original size:25 final size:27
Alignment explanation
Indices: 54050590--54050644 Score: 87
Period size: 25 Copynumber: 2.1 Consensus size: 27
54050580 AAAATTCAAA
54050590 ATATTTATAAAAAATT-TAAAAATT-T
1 ATATTTATAAAAAATTCTAAAAATTAT
*
54050615 ATATTTTTAAAAAATTCTAAAAATTAT
1 ATATTTATAAAAAATTCTAAAAATTAT
54050642 ATA
1 ATA
54050645 AAAAGTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 15 0.56
26 8 0.30
27 4 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (27 bp):
ATATTTATAAAAAATTCTAAAAATTAT
Found at i:54050666 original size:45 final size:45
Alignment explanation
Indices: 54050580--54050667 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 45
54050570 AATAAATTTT
* *
54050580 AAAATTCAAAATATTTATAAAAAATTTAAAAATTTATATTTTTAA
1 AAAATTCAAAATATTTATAAAAAAGTTAAAAATTTAAATTTTTAA
54050625 AAAATTCTAAAA-A-TTATATAAAAAGTT-AAAATTTAAAATTTTT
1 AAAATTC-AAAATATTTATA-AAAAAGTTAAAAATTT-AAATTTTT
54050668 TCTAAAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
44 12 0.32
45 22 0.58
46 4 0.11
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (45 bp):
AAAATTCAAAATATTTATAAAAAAGTTAAAAATTTAAATTTTTAA
Found at i:54057909 original size:12 final size:12
Alignment explanation
Indices: 54057892--54057916 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54057882 TAAGCCTCTC
54057892 ATTTGTGTTTTA
1 ATTTGTGTTTTA
54057904 ATTTGTGTTTTA
1 ATTTGTGTTTTA
54057916 A
1 A
54057917 CTCCCTTGAA
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:0.20, C:0.00, G:0.16, T:0.64
Consensus pattern (12 bp):
ATTTGTGTTTTA
Found at i:54067590 original size:41 final size:41
Alignment explanation
Indices: 54067545--54067628 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
54067535 TTCAAGAAAG
54067545 ACTTAAAGATTCCAATCCTATTAGGGCTACCGTTTTTAGCT
1 ACTTAAAGATTCCAATCCTATTAGGGCTACCGTTTTTAGCT
54067586 ACTTAAAGATTCCAATCCTATTAGGGCTACCGTTTTTAGCT
1 ACTTAAAGATTCCAATCCTATTAGGGCTACCGTTTTTAGCT
54067627 AC
1 AC
54067629 CTCTCGAGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (41 bp):
ACTTAAAGATTCCAATCCTATTAGGGCTACCGTTTTTAGCT
Found at i:54068945 original size:43 final size:43
Alignment explanation
Indices: 54068898--54069018 Score: 138
Period size: 43 Copynumber: 2.8 Consensus size: 43
54068888 CCTCGATTGA
* * *
54068898 GATTTACGTATAAGACCATGTCCGGGACATCGGCATCG-TATCT
1 GATTTACATGTAAGACCATGTCTGGGACATCGGCATCGATAT-T
* **
54068941 GATTT-CATGTAAGACCCTGTCTGGGACAGAGGCATCGATATT
1 GATTTACATGTAAGACCATGTCTGGGACATCGGCATCGATATT
* * *
54068983 GAATTACATGTAAGACCACGTCTGGGACGTCGGCAT
1 GATTTACATGTAAGACCATGTCTGGGACATCGGCAT
54069019 TGTACTTATT
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
42 31 0.48
43 33 0.52
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (43 bp):
GATTTACATGTAAGACCATGTCTGGGACATCGGCATCGATATT
Found at i:54072697 original size:184 final size:185
Alignment explanation
Indices: 54072398--54072743 Score: 613
Period size: 184 Copynumber: 1.9 Consensus size: 185
54072388 ATAATATGTG
*
54072398 ATATGTGATATGTGAGCATGTTTACATGGAAATGTGTAAAATTGAGAAATATGCATTAAGTGAGA
1 ATATGTGATATGTGAGCATGTTTACATGAAAATGTGTAAAATTGAGAAATATGCATTAAGTGAGA
*
54072463 CTATGAGCATGATTACATGTGAAAAATGATTAAATGTGTTAAATTTGAAAATGGCCATATCACAT
66 CTATGAGCATGACTACATGTGAAAAATGATTAAATGTGTTAAATTTGAAAATGGCCATATCACAT
*
54072528 G-ATGGAGTGGGTCTGGTGAAAGGTGGAAGTTCTAAAGTGAATAAAAAGTGAATA
131 GCATGGAGTGGGTCTGGTGAAAGGTAGAAGTTCTAAAGTGAATAAAAAGTGAATA
* **
54072582 ATATGTGATATGTGAGTATGTTTACATGAAAATGTGTAAAATTGAGAAATATGTGTTAAGTGAGA
1 ATATGTGATATGTGAGCATGTTTACATGAAAATGTGTAAAATTGAGAAATATGCATTAAGTGAGA
*
54072647 CTATGAGCATGACTACATGTGAAAAATGATTAAATGTGTTAAATTTGAAAATGGTCATATCACAT
66 CTATGAGCATGACTACATGTGAAAAATGATTAAATGTGTTAAATTTGAAAATGGCCATATCACAT
*
54072712 GCATGGAGTGGGTCTTGTGAAAGGTAGAAGTT
131 GCATGGAGTGGGTCTGGTGAAAGGTAGAAGTT
54072744 ATCTGGCAGT
Statistics
Matches: 153, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
184 125 0.82
185 28 0.18
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.31
Consensus pattern (185 bp):
ATATGTGATATGTGAGCATGTTTACATGAAAATGTGTAAAATTGAGAAATATGCATTAAGTGAGA
CTATGAGCATGACTACATGTGAAAAATGATTAAATGTGTTAAATTTGAAAATGGCCATATCACAT
GCATGGAGTGGGTCTGGTGAAAGGTAGAAGTTCTAAAGTGAATAAAAAGTGAATA
Found at i:54072772 original size:22 final size:21
Alignment explanation
Indices: 54072742--54072792 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
54072732 AAGGTAGAAG
* * *
54072742 TTATCTGGCAGTTTATCTGCGA
1 TTATGTGGCAG-TTATCGGCAA
*
54072764 TTATGTGGCCGTTATCGGCAA
1 TTATGTGGCAGTTATCGGCAA
54072785 TTATGTGG
1 TTATGTGG
54072793 TGGCTTGTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (21 bp):
TTATGTGGCAGTTATCGGCAA
Found at i:54080571 original size:26 final size:26
Alignment explanation
Indices: 54080516--54080571 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
54080506 TTATGATTTT
* *
54080516 TTAATAATAATTTTATTAAATTATAT
1 TTAATAATAATTTTATTAAAATATAG
*
54080542 TTAATAATAATTATT-TTAAAATATGG
1 TTAATAATAATT-TTATTAAAATATAG
54080568 TTAA
1 TTAA
54080572 ATTATTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (26 bp):
TTAATAATAATTTTATTAAAATATAG
Found at i:54088471 original size:38 final size:38
Alignment explanation
Indices: 54088363--54088482 Score: 152
Period size: 38 Copynumber: 3.1 Consensus size: 38
54088353 ATTTGATGTG
* * * *
54088363 TATCCGGGCTTAAAGACCCGCAGG-CTATATGCTAGAATTA
1 TATCCGGG-TTAAA-TCCCGCAGGCCTA-GTGCTGGTATTA
* *
54088403 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCCTAGTGCTGGTATTA
54088441 TATCCGGGTTAAATCCCGCAGGCCTAGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCCTAGTGCTGGTATTA
54088479 TATC
1 TATC
54088483 TAAGTTTAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
38 57 0.80
39 6 0.08
40 8 0.11
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.29
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCCTAGTGCTGGTATTA
Found at i:54088511 original size:40 final size:38
Alignment explanation
Indices: 54088399--54088519 Score: 143
Period size: 38 Copynumber: 3.1 Consensus size: 38
54088389 ATATGCTAGA
**
54088399 ATTATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGT
1 ATTATATCAAGGTTAAATCCCGCAGGCTTCGTGCTGGT
** * *
54088437 ATTATATCCGGGTTAAATCCCGCAGGCCTAGTGCTGGT
1 ATTATATCAAGGTTAAATCCCGCAGGCTTCGTGCTGGT
* *
54088475 ATTATATCTAAGTTTAAAGTCCCGTAGGCTTCGTGCTGGT
1 ATTATATC-AAGGTTAAA-TCCCGCAGGCTTCGTGCTGGT
*
54088515 GTTAT
1 ATTAT
54088520 GTTCGGGTTT
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
38 44 0.61
39 6 0.08
40 22 0.31
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.34
Consensus pattern (38 bp):
ATTATATCAAGGTTAAATCCCGCAGGCTTCGTGCTGGT
Found at i:54098542 original size:18 final size:18
Alignment explanation
Indices: 54098521--54098559 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
54098511 ATTATATATT
*
54098521 ATTTA-TTACATTTGGTTA
1 ATTTAGTTA-ATTCGGTTA
54098539 ATTTAGTTAATTCGGTTA
1 ATTTAGTTAATTCGGTTA
54098557 ATT
1 ATT
54098560 GGTCAATTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.28, C:0.05, G:0.13, T:0.54
Consensus pattern (18 bp):
ATTTAGTTAATTCGGTTA
Found at i:54100014 original size:18 final size:17
Alignment explanation
Indices: 54099988--54100021 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
54099978 CAAAACTTTT
54099988 GGAGAAAGAAAAATGAG
1 GGAGAAAGAAAAATGAG
*
54100005 GGAGACAAGAAGAATGA
1 GGAGA-AAGAAAAATGA
54100022 TAGAAGATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.56, C:0.03, G:0.35, T:0.06
Consensus pattern (17 bp):
GGAGAAAGAAAAATGAG
Found at i:54100980 original size:90 final size:90
Alignment explanation
Indices: 54100838--54101074 Score: 304
Period size: 90 Copynumber: 2.6 Consensus size: 90
54100828 TCAGTGAATG
* * * *
54100838 CATCAAGTTTGCCTCACTAGGACCACCCAAAGC-CTGGGATATGAA-TTCATTAAGAACATTTAG
1 CATCAAGTTTGTCTCAATAGGACCACCCAAA-CTCTGGGCTATGAACTT-ATTAAGAACATCTAG
*
54100901 TGGCTT-ATCCTATAAATTTGGT-AAGTT
64 TAG-TTCATCCTATAAATTTGGTGAAG-T
*
54100928 CATCAAGTTTGTCTCAATAGGACCACCCAAACTCTGGGCTATGAACTTATTAAAAACATCTAGTA
1 CATCAAGTTTGTCTCAATAGGACCACCCAAACTCTGGGCTATGAACTTATTAAGAACATCTAGTA
54100993 GTTCATCCTATAAATTTGGTGAAGT
66 GTTCATCCTATAAATTTGGTGAAGT
* * * * *
54101018 CATCAAGTCTGTCTTAGTAGGACCATCCAAA-TCTGGGCTATGAACTCATTAAGAACA
1 CATCAAGTTTGTCTCAATAGGACCACCCAAACTCTGGGCTATGAACTTATTAAGAACA
54101075 CGGAGCTCAT
Statistics
Matches: 131, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
89 27 0.21
90 99 0.76
91 5 0.04
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (90 bp):
CATCAAGTTTGTCTCAATAGGACCACCCAAACTCTGGGCTATGAACTTATTAAGAACATCTAGTA
GTTCATCCTATAAATTTGGTGAAGT
Found at i:54104258 original size:26 final size:26
Alignment explanation
Indices: 54104229--54104279 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
54104219 AAATCAAATA
54104229 GTTTAAAATAAATAATATATAAAAGG
1 GTTTAAAATAAATAATATATAAAAGG
* *
54104255 GTTTAAGATAAATAATATGTAAAAG
1 GTTTAAAATAAATAATATATAAAAG
54104280 AGATATTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (26 bp):
GTTTAAAATAAATAATATATAAAAGG
Found at i:54104295 original size:29 final size:25
Alignment explanation
Indices: 54104234--54104304 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 25
54104224 AAATAGTTTA
*
54104234 AAATAAATAATATATAAAAGGGTTT
1 AAATAAATAATATATAAAAGGATTT
*
54104259 AAGATAAATAATATGTAAAAGAGATATTT
1 AA-ATAAATAATATATAAAAG-G--ATTT
*
54104288 GAAATAAATAATGTATA
1 -AAATAAATAATATATA
54104305 CATATGTAGG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
25 2 0.05
26 17 0.46
27 1 0.03
29 15 0.41
30 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (25 bp):
AAATAAATAATATATAAAAGGATTT
Found at i:54105905 original size:23 final size:23
Alignment explanation
Indices: 54105862--54105905 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
54105852 TTTTACTGCC
*
54105862 TTTGCTACTATTTTGTCTTGCTT
1 TTTGCTACTATTTCGTCTTGCTT
*
54105885 TTTG-TACTATTTGCGTGTTGC
1 TTTGCTACTATTT-CGTCTTGC
54105906 CTTGTCACTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.09, C:0.16, G:0.18, T:0.57
Consensus pattern (23 bp):
TTTGCTACTATTTCGTCTTGCTT
Found at i:54109738 original size:9 final size:9
Alignment explanation
Indices: 54109724--54109767 Score: 52
Period size: 9 Copynumber: 4.4 Consensus size: 9
54109714 TTATACTTAA
54109724 ATAATTTTT
1 ATAATTTTT
54109733 ATAATTTTT
1 ATAATTTTT
54109742 ATTATATATTTT
1 A-TA-AT-TTTT
54109754 ATAATTTATT
1 ATAATTT-TT
54109764 ATAA
1 ATAA
54109768 GTAGAGATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 12 0.39
10 10 0.32
11 4 0.13
12 5 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
ATAATTTTT
Found at i:54117172 original size:27 final size:27
Alignment explanation
Indices: 54117141--54117194 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
54117131 GTTGAAAGGA
*
54117141 TGCACAGTAACTCTGCTATGAAACAAT
1 TGCACAGTAACCCTGCTATGAAACAAT
*
54117168 TGCACAGTAACCCTGTTATGAAACAAT
1 TGCACAGTAACCCTGCTATGAAACAAT
54117195 GGCATACCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (27 bp):
TGCACAGTAACCCTGCTATGAAACAAT
Found at i:54118650 original size:13 final size:13
Alignment explanation
Indices: 54118632--54118656 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54118622 TCACTACTAT
54118632 TACTATTATTATA
1 TACTATTATTATA
54118645 TACTATTATTAT
1 TACTATTATTAT
54118657 CATTTTTTAC
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:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (13 bp):
TACTATTATTATA
Found at i:54119092 original size:20 final size:20
Alignment explanation
Indices: 54119058--54119095 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
54119048 TTTTTTAAAT
**
54119058 TATTTTAAAGGAAAGTTTAA
1 TATTTTAAAACAAAGTTTAA
54119078 TATTTTAAAACAAAGTTT
1 TATTTTAAAACAAAGTTT
54119096 TGATTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.42
Consensus pattern (20 bp):
TATTTTAAAACAAAGTTTAA
Found at i:54119155 original size:52 final size:49
Alignment explanation
Indices: 54119037--54119160 Score: 124
Period size: 52 Copynumber: 2.4 Consensus size: 49
54119027 TGAAAAAAAT
* * *
54119037 AAAAATATGTTTTTTTTAAATTATTTTAAAGGAAAGTTTAATATTTTAA
1 AAAAATATGTTTTTTTTAAACTATTTCAAAGAAAAGTTTAATATTTTAA
* * *
54119086 AACAAAGTTTTGATTTTTTTCAACTATTTCAAAGTAAAAGCTTTAATA-TTTAA
1 AA-AAA--TATGTTTTTTTTAAACTATTTCAAAG-AAAAG-TTTAATATTTTAA
54119139 GAAAAATAGTGTTTTTTTTAAA
1 -AAAAATA-TGTTTTTTTTAAA
54119161 AGAGAAAGTT
Statistics
Matches: 59, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
49 2 0.03
50 3 0.05
51 1 0.02
52 32 0.54
53 12 0.20
54 9 0.15
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (49 bp):
AAAAATATGTTTTTTTTAAACTATTTCAAAGAAAAGTTTAATATTTTAA
Found at i:54119230 original size:147 final size:150
Alignment explanation
Indices: 54118984--54119424 Score: 602
Period size: 147 Copynumber: 2.9 Consensus size: 150
54118974 TTGATTTTGG
* *
54118984 GAAAAATAGTGTTTTTTTTAAAAAAGGGAGAAAGTTTAGATTTTGAAAAAAATAAAAATATGTTT
1 GAAAAATAGTGTTTTTTTT-AAAAA-GGAGAAAGTTTAGATTTTG--AAAAATAAAAATCTGATT
* *
54119049 TTTTTAAATTATTTTAAAGGAAAGTTTAATATTTTAAAACAAAGTTTTGATTTTTTTCAACTATT
62 TTTTTAAGTTATTTTAAAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTT-AACTATT
* *
54119114 TCAAAGTAAAAGCTTTAATATTTAA
126 TCAAAATAAAAACTTTAATATTTAA
54119139 GAAAAATAGTGTTTTTTTT-AAAA-GAGAAAGTTTAGATTTTGAAAAATAAAAATCT-ATTTTTT
1 GAAAAATAGTGTTTTTTTTAAAAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATCTGATTTTTT
* *
54119201 T-AGTTATTTTAATGGAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTTAACTACTTCAA
66 TAAGTTATTTTAAAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGA-TTTTTTTAACTATTTCAA
*
54119265 AATAAAAACTTTAATCTTTAA
130 AATAAAAACTTTAATATTTAA
* *
54119286 GAAAAATAATTTTTTTTTTAAAAAAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATCTGCATTT
1 GAAAAATAGTGTTTTTTTT--AAAAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATCTG-A-TT
* * * **
54119351 TTTTTAAAGTCATTTTAAAGGAAAGTTTAAATTTTTAAAAAAAAGTTTTGATTCGTTTAACTATT
62 TTTTT-AAGTTATTTTAAAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTAACTATT
*
54119416 TCGAAATAA
126 TCAAAATAA
54119425 GGTTTTGATT
Statistics
Matches: 257, Mismatches: 19, Indels: 20
0.87 0.06 0.07
Matches are distributed among these distances:
147 86 0.33
148 14 0.05
149 13 0.05
150 4 0.02
151 50 0.19
153 5 0.02
154 7 0.03
155 38 0.15
156 40 0.16
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.42
Consensus pattern (150 bp):
GAAAAATAGTGTTTTTTTTAAAAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATCTGATTTTTT
TAAGTTATTTTAAAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTAACTATTTCAAA
ATAAAAACTTTAATATTTAA
Found at i:54119483 original size:22 final size:21
Alignment explanation
Indices: 54119449--54119491 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
54119439 CGAAAAGTAA
* *
54119449 TGATTTTTTAAAATAAAATTT
1 TGATTTTTAAAAAAAAAATTT
54119470 TGATTTTGTAAAAAAAAAATTT
1 TGATTTT-TAAAAAAAAAATTT
54119492 AGCCACCGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (21 bp):
TGATTTTTAAAAAAAAAATTT
Found at i:54121647 original size:42 final size:41
Alignment explanation
Indices: 54121598--54121711 Score: 165
Period size: 42 Copynumber: 2.7 Consensus size: 41
54121588 TTCATTTTCT
** * *
54121598 TGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A
*
54121640 TGATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
54121681 TCGATGCCATAGCCCAGCTATGGTCTTACAC
1 T-GATGCCATAGCCCAGCTATGGTCTTACAC
54121712 GAATCACATA
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
41 2 0.03
42 64 0.97
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (41 bp):
TGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
Found at i:54121783 original size:47 final size:46
Alignment explanation
Indices: 54121682--54121805 Score: 158
Period size: 47 Copynumber: 2.7 Consensus size: 46
54121672 ATTCATATAT
* * * * *
54121682 CGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
* * * *
54121728 TGATGCCATATCCTAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACAC
54121775 CGATGCCATATCCCAGATATGGTCTTATACG
1 CGATGCCATATCCCAGATATGGTCTTATACG
54121806 GAAATCACTT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
46 26 0.39
47 40 0.61
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
Found at i:54121865 original size:31 final size:31
Alignment explanation
Indices: 54121830--54121978 Score: 217
Period size: 31 Copynumber: 4.8 Consensus size: 31
54121820 CTTGTCACTT
*
54121830 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
54121861 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
54121892 GTAGCCGAAGCTACCACTTTTCACTGATCAC
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * *
54121923 GTAGCAGAAACTACCACTTTTCACTAATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
54121954 GTAGCTGAAGCTACCACTTCTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
54121979 TGTCATTTGT
Statistics
Matches: 105, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 105 1.00
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:54122064 original size:50 final size:51
Alignment explanation
Indices: 54121954--54122082 Score: 181
Period size: 50 Copynumber: 2.5 Consensus size: 51
54121944 CACTAATCAG
* * *
54121954 GTAGCTGAAGCTACCACTTCTCACTTGTCATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTACCACTTATCACTTGTCATTTGTCATTGATCAAATAAGT
* * *
54122005 GTAGTCGAAGCTATCACTTATCACTT-TCACTTT-TCCTTGATCAAATAAGT
1 GTAGCCGAAGCTACCACTTATCACTTGTCA-TTTGTCATTGATCAAATAAGT
54122055 GTAGCCGAAGCTACCACTTATCACTTGT
1 GTAGCCGAAGCTACCACTTATCACTTGT
54122083 TGCCATGGTC
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
50 42 0.62
51 26 0.38
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (51 bp):
GTAGCCGAAGCTACCACTTATCACTTGTCATTTGTCATTGATCAAATAAGT
Found at i:54124283 original size:42 final size:41
Alignment explanation
Indices: 54124224--54124589 Score: 358
Period size: 42 Copynumber: 8.7 Consensus size: 41
54124214 TCGATTTGAT
* *
54124224 ATTTACGTGTAAGACCATGTCTGAGACATCTACATCGTATCTG
1 ATTT-CGTGTAAGACCATGTCTGGGACAT-TGCATCGTATCTG
*
54124267 ATTTCGTGTAAGACCATGTCTGGGACATTGGCATCATATCTG
1 ATTTCGTGTAAGACCATGTCTGGGACATT-GCATCGTATCTG
* * *
54124309 ATTACGTGTAAGACCATGTCTGGGATAGTGGCATCGTATCTG
1 ATTTCGTGTAAGACCATGTCTGGGACA-TTGCATCGTATCTG
* *
54124351 ATTTCGTGTAAGACCATGTATAGGACATTGGCATCGTATCTG
1 ATTTCGTGTAAGACCATGTCTGGGACATT-GCATCGTATCTG
* * * * * *
54124393 ACTACATGTAAGACCATTTCTGGGACATCAGCATCGTATCCG
1 ATTTCGTGTAAGACCATGTCTGGGACAT-TGCATCGTATCTG
* * *
54124435 ATTTCGTGTAAGACCATGTCTGAGACATCGGCATCGTATCTA
1 ATTTCGTGTAAGACCATGTCTGGGACAT-TGCATCGTATCTG
* * *
54124477 ATTTCGTGTAAAACCATGTTTGGGACATTAGCATCGTATTTG
1 ATTTCGTGTAAGACCATGTCTGGGACATT-GCATCGTATCTG
* * ** *
54124519 ATTTTGTGTAAGATCC-TGTTTGGGACAGAGACATTG-ATACTG
1 ATTTCGTGTAAGA-CCATGTCTGGGACATTG-CATCGTAT-CTG
* * *
54124561 AATTACATGTAAGACCACGTCTGGGACAT
1 -ATTTCGTGTAAGACCATGTCTGGGACAT
54124590 CGTCATTATA
Statistics
Matches: 267, Mismatches: 46, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
41 5 0.02
42 236 0.88
43 26 0.10
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.32
Consensus pattern (41 bp):
ATTTCGTGTAAGACCATGTCTGGGACATTGCATCGTATCTG
Found at i:54124328 original size:84 final size:85
Alignment explanation
Indices: 54124226--54124590 Score: 418
Period size: 84 Copynumber: 4.3 Consensus size: 85
54124216 GATTTGATAT
*
54124226 TTACGTGTAAGACCATGTCTGAGACATCTA-CATCGTATCTGATTTCGTGTAAGACCATGTCTGG
1 TTACGTGTAAGACCATGTCTGGGACATCTAGCATCGTATCTGATTTCGTGTAAGACCATGTCTGG
54124290 GACATTGGCATCATATCTGA
66 GACATTGGCATCATATCTGA
* * * * *
54124310 TTACGTGTAAGACCATGTCTGGGATA-GTGGCATCGTATCTGATTTCGTGTAAGACCATGTATAG
1 TTACGTGTAAGACCATGTCTGGGACATCTAGCATCGTATCTGATTTCGTGTAAGACCATGTCTGG
*
54124374 GACATTGGCATCGTATCTGA
66 GACATTGGCATCATATCTGA
* * * * *
54124394 CTACATGTAAGACCATTTCTGGGACATC-AGCATCGTATCCGATTTCGTGTAAGACCATGTCTGA
1 TTACGTGTAAGACCATGTCTGGGACATCTAGCATCGTATCTGATTTCGTGTAAGACCATGTCTGG
* * *
54124458 GACATCGGCATCGTATCTAA
66 GACATTGGCATCATATCTGA
* * * * * *
54124478 TTTCGTGTAAAACCATGTTTGGGACAT-TAGCATCGTATTTGATTTTGTGTAAGATCC-TGTTTG
1 TTACGTGTAAGACCATGTCTGGGACATCTAGCATCGTATCTGATTTCGTGTAAGA-CCATGTCTG
** * *
54124541 GGACAGAGACATTGATA-CTGAA
65 GGACATTGGCA-TCATATCTG-A
* *
54124563 TTACATGTAAGACCACGTCTGGGACATC
1 TTACGTGTAAGACCATGTCTGGGACATC
54124591 GTCATTATAC
Statistics
Matches: 233, Mismatches: 41, Indels: 12
0.81 0.14 0.04
Matches are distributed among these distances:
83 1 0.00
84 204 0.88
85 28 0.12
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.32
Consensus pattern (85 bp):
TTACGTGTAAGACCATGTCTGGGACATCTAGCATCGTATCTGATTTCGTGTAAGACCATGTCTGG
GACATTGGCATCATATCTGA
Found at i:54138607 original size:40 final size:41
Alignment explanation
Indices: 54138524--54138669 Score: 167
Period size: 40 Copynumber: 3.6 Consensus size: 41
54138514 TTGAATGATG
* * * *
54138524 TCCGGGCTAAGTCCCAAAGGC-TTTGTGCTAAGTGACCAT-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
*
54138564 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-AA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
54138604 TCCGGGTTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
54138645 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
54138670 AACGAGGAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
39 1 0.01
40 80 0.88
41 10 0.11
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.27
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:54138687 original size:80 final size:80
Alignment explanation
Indices: 54138524--54138702 Score: 186
Period size: 80 Copynumber: 2.2 Consensus size: 80
54138514 TTGAATGATG
* * *
54138524 TCCGGGCTAAGTCCCAAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
** *
54138589 GTGCGAGTTACTAAA
66 GAACGAGTGACTAAA
* * * *
54138604 TCCGGGTTAAGTCCCGAAGGCATTTGTGCT-AGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCAT
*
54138667 TTGAACGAG-GAGCTATA
64 TTGAACGAGTGA-CTAAA
* *
54138684 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
54138703 TACGTGATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 7
0.81 0.13 0.07
Matches are distributed among these distances:
79 16 0.19
80 59 0.71
81 8 0.10
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
GAACGAGTGACTAAA
Found at i:54146429 original size:40 final size:40
Alignment explanation
Indices: 54146346--54146531 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
54146336 TTGAATGATG
* * * * *
54146346 TCCGGGCTAAGTCCCAAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
54146386 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
54146426 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
54146466 TCCGGGTTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
54146507 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
54146532 AACGAGGAGC
Statistics
Matches: 129, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 118 0.91
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:54146549 original size:80 final size:79
Alignment explanation
Indices: 54146346--54146564 Score: 203
Period size: 80 Copynumber: 2.7 Consensus size: 79
54146336 TTGAATGATG
* ** * * * *
54146346 TCCGGGCTAAGTCCCAAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGAAC-GAGTGACTAAATCCGG-TTAA-ATCCCGAAGGCAT
54146409 TTGTGCGAGATACTAAA
63 TTGTGCGAGATACTAAA
* ** * *
54146426 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAATCC-GGTTAAATCCCGAAGGCATTT
* *
54146491 GTGCTAGTTACTATAA
65 GTGCGAGATACTA-AA
* * *
54146507 -CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCCGGTTAAATTCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGTTAAATCCCGAAGG
54146565 TACGTGATTT
Statistics
Matches: 116, Mismatches: 18, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
79 16 0.14
80 89 0.77
81 11 0.09
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAATCCGGTTAAATCCCGAAGGCATTTG
TGCGAGATACTAAA
Found at i:54148255 original size:15 final size:16
Alignment explanation
Indices: 54148223--54148255 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
54148213 TCAAGATGGA
*
54148223 ATTTTGAATTCATCTG
1 ATTTTGAATTCATATG
54148239 ATTTTGAA-TCATATG
1 ATTTTGAATTCATATG
54148254 AT
1 AT
54148256 ACTTTTGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.48
Consensus pattern (16 bp):
ATTTTGAATTCATATG
Found at i:54151377 original size:26 final size:26
Alignment explanation
Indices: 54151339--54151424 Score: 91
Period size: 27 Copynumber: 3.2 Consensus size: 26
54151329 TGATGTTCAC
54151339 ATACCCCCAGATTGTAAAATTATCGAA
1 ATACCCCC-GATTGTAAAATTATCGAA
*
54151366 ATACCCCCGATTTGTAAAATTATTGAA
1 ATACCCCCGA-TTGTAAAATTATCGAA
* ** * *
54151393 ATAACCTTGTAGTGTAAAATTACCGAA
1 ATACCCCCG-ATTGTAAAATTATCGAA
54151420 ATACC
1 ATACC
54151425 TCTGTAGGGT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
26 2 0.04
27 46 0.94
28 1 0.02
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.29
Consensus pattern (26 bp):
ATACCCCCGATTGTAAAATTATCGAA
Found at i:54151408 original size:27 final size:27
Alignment explanation
Indices: 54151378--54151438 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
54151368 ACCCCCGATT
**
54151378 TGTAAAATTATTGAAATAACCT-TGTAG
1 TGTAAAATTACCGAAAT-ACCTCTGTAG
54151405 TGTAAAATTACCGAAATACCTCTGTAG
1 TGTAAAATTACCGAAATACCTCTGTAG
*
54151432 GGTAAAA
1 TGTAAAA
54151439 GATAGTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 4 0.13
27 26 0.87
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.31
Consensus pattern (27 bp):
TGTAAAATTACCGAAATACCTCTGTAG
Found at i:54152017 original size:26 final size:25
Alignment explanation
Indices: 54151960--54152017 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
54151950 TGTAAGCAGT
*
54151960 ATATATATATCTGGTAGCTTTGCTGC
1 ATAT-TATATCTGGTAGCTATGCTGC
*
54151986 ATTATTATTTCTGGTAGCTATGCTGC
1 A-TATTATATCTGGTAGCTATGCTGC
54152012 GATATT
1 -ATATT
54152018 GGTGTGCTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 24 0.86
27 4 0.14
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (25 bp):
ATATTATATCTGGTAGCTATGCTGC
Found at i:54153214 original size:94 final size:93
Alignment explanation
Indices: 54153093--54153266 Score: 294
Period size: 94 Copynumber: 1.9 Consensus size: 93
54153083 GATAAAAAGG
* * *
54153093 GGATTTGATATATTCCTTATCAAATAAGGAAATAAAATTTAATTATTATTTAAAAGAGTTTTATA
1 GGATATGATATATTCCTTAACAAATAAGGAAATAAAATTTAATTATT-TTTAAAAGAGTTTTAAA
54153158 TAAATAATAATTAAAATTCAAAATCAAAA
65 TAAATAATAATTAAAATTCAAAATCAAAA
* *
54153187 GGATATGATATATTCCTTAACAGATAAGGAAATAGAATTTAATTATTTTTAAAAGAGTTTTAAAT
1 GGATATGATATATTCCTTAACAAATAAGGAAATAAAATTTAATTATTTTTAAAAGAGTTTTAAAT
54153252 AAATAATAATTAAAA
66 AAATAATAATTAAAA
54153267 AATTTAATTA
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
93 32 0.43
94 43 0.57
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (93 bp):
GGATATGATATATTCCTTAACAAATAAGGAAATAAAATTTAATTATTTTTAAAAGAGTTTTAAAT
AAATAATAATTAAAATTCAAAATCAAAA
Found at i:54153321 original size:49 final size:47
Alignment explanation
Indices: 54153222--54153347 Score: 150
Period size: 49 Copynumber: 2.7 Consensus size: 47
54153212 AAGGAAATAG
54153222 AATTT-AATTATT-TTTAAAAGAGTTTTAAATAAATAATAATTAAAA
1 AATTTAAATTATTATTTAAAAGAGTTTTAAATAAATAATAATTAAAA
*
54153267 AATTTAATTATTATTATTTAAAAGAGTTTTAAATAAA-AGATAATTAAAT
1 AATTTAA--ATTATTATTTAAAAGAGTTTTAAATAAATA-ATAATTAAAA
* * * *
54153316 TATTTAAAATATTATTGAAAAAAGTATTTAAA
1 AATTTAAATTATTATTTAAAAGAGT-TTTAAA
54153348 AGTCAAGATA
Statistics
Matches: 70, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
45 5 0.07
46 1 0.01
47 15 0.21
48 13 0.19
49 36 0.51
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (47 bp):
AATTTAAATTATTATTTAAAAGAGTTTTAAATAAATAATAATTAAAA
Found at i:54154809 original size:19 final size:19
Alignment explanation
Indices: 54154787--54154823 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
54154777 CAATGATCCC
* *
54154787 TCATCCCTTCATTCCTTAA
1 TCATCCCTACATCCCTTAA
54154806 TCATCCCTACATCCCTTA
1 TCATCCCTACATCCCTTA
54154824 TTCAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.41, G:0.00, T:0.38
Consensus pattern (19 bp):
TCATCCCTACATCCCTTAA
Found at i:54158522 original size:45 final size:45
Alignment explanation
Indices: 54158473--54158580 Score: 135
Period size: 45 Copynumber: 2.4 Consensus size: 45
54158463 GATGCCGATG
* * * *
54158473 TCCCAGACATGGACTTACACGTAACCAGATATATCAATGCCAACA
1 TCCCAGACGTGGTCTTACACGTAACCAAATATATCAACGCCAACA
* * * *
54158518 TCCCAGACGTGGTTTTACACGTATCCAAATATATCGACGCCAACG
1 TCCCAGACGTGGTCTTACACGTAACCAAATATATCAACGCCAACA
*
54158563 TACCAGACGTGGTCTTAC
1 TCCCAGACGTGGTCTTAC
54158581 TCGAAAACAC
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (45 bp):
TCCCAGACGTGGTCTTACACGTAACCAAATATATCAACGCCAACA
Found at i:54158886 original size:15 final size:15
Alignment explanation
Indices: 54158862--54158891 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54158852 GTTCTTGATC
54158862 TAAACATATTCAAAT
1 TAAACATATTCAAAT
*
54158877 TAAACTTATTCAAAT
1 TAAACATATTCAAAT
54158892 ATATTTTCAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAACATATTCAAAT
Found at i:54162172 original size:10 final size:10
Alignment explanation
Indices: 54162159--54162197 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
54162149 ATATATGAAT
54162159 ATATCATGGC
1 ATATCATGGC
54162169 ATATCATGTGC
1 ATATCATG-GC
*
54162180 ATATCATTGC
1 ATATCATGGC
54162190 ATATCATG
1 ATATCATG
54162198 TATAAAACAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (10 bp):
ATATCATGGC
Found at i:54162185 original size:21 final size:21
Alignment explanation
Indices: 54162159--54162198 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
54162149 ATATATGAAT
54162159 ATATCATGGCATATCATGTGC
1 ATATCATGGCATATCATGTGC
*
54162180 ATATCATTGCATATCATGT
1 ATATCATGGCATATCATGT
54162199 ATAAAACAGT
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:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
ATATCATGGCATATCATGTGC
Found at i:54165913 original size:27 final size:26
Alignment explanation
Indices: 54165878--54165989 Score: 134
Period size: 27 Copynumber: 4.2 Consensus size: 26
54165868 AGCATGGCTG
* *
54165878 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
54165904 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
54165932 CCAGAACAGAAATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
** *
54165959 CCAGATTAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
54165986 CCAG
1 CCAG
54165990 GATGCTTCCT
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
26 6 0.08
27 52 0.69
28 17 0.23
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:54165941 original size:54 final size:54
Alignment explanation
Indices: 54165878--54165989 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
54165868 AGCATGGCTG
* *
54165878 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGAAATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
54165932 CCAGAACAGAAATATGTGGCAGAGCCACCAGATTAGATAATTGTGGCATAGCCA
1 CCAGAACAGAAATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
54165986 CCAG
1 CCAG
54165990 GATGCTTCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 33 0.65
55 18 0.35
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (54 bp):
CCAGAACAGAAATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:54167941 original size:40 final size:40
Alignment explanation
Indices: 54167851--54168070 Score: 259
Period size: 40 Copynumber: 5.5 Consensus size: 40
54167841 ACCCAAGTAT
* ** * * *
54167851 CTTCGGGATTTAG-CCGGATATAACCACTCGCAC-AAGGT
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
54167889 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
54167929 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
54167969 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * *
54168009 CTTC-GGATCTTAGTCCGGATATAGTCACTAGCATAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCACTAGCACAAATGC
54168049 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
54168071 CATTCGAATA
Statistics
Matches: 154, Mismatches: 22, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
38 11 0.07
39 18 0.12
40 121 0.79
41 4 0.03
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:54170749 original size:24 final size:24
Alignment explanation
Indices: 54170722--54170792 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
54170712 CTAGATTTCC
** *
54170722 TCCCTTATCTGCTCCTAAATCGTA
1 TCCCTTATCAACTCCTAAATCCTA
54170746 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
*
54170770 TCCTTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
54170793 CTCCTGACAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.25, C:0.35, G:0.03, T:0.37
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:54179905 original size:14 final size:14
Alignment explanation
Indices: 54179886--54179916 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
54179876 ACACACAGCC
54179886 GTGTCTCAGCTTAT
1 GTGTCTCAGCTTAT
54179900 GTGTCTCAGCTTAT
1 GTGTCTCAGCTTAT
54179914 GTG
1 GTG
54179917 GCTAACACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.13, C:0.19, G:0.26, T:0.42
Consensus pattern (14 bp):
GTGTCTCAGCTTAT
Found at i:54181757 original size:49 final size:48
Alignment explanation
Indices: 54181665--54181783 Score: 134
Period size: 48 Copynumber: 2.5 Consensus size: 48
54181655 TCAATTTGAT
* *
54181665 GCCATGTCCCAGACATGGTCTTACACTGACTATTAAAACCGAGGCCGAC
1 GCCATGTCCCAGACAT-GTCTTAAACTGACTATCAAAACCGAGGCCGAC
* * * *
54181714 GCCATGTCCCAGACATGTCTTAAACTGGCT-TGCATATCTCGAGGCCGAT
1 GCCATGTCCCAGACATGTCTTAAACTGACTAT-CAAAAC-CGAGGCCGAC
*
54181763 G-CATGTGCCAGACATGTCTTA
1 GCCATGTCCCAGACATGTCTTA
54181784 CACTAGCTCT
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
47 1 0.02
48 34 0.56
49 26 0.43
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (48 bp):
GCCATGTCCCAGACATGTCTTAAACTGACTATCAAAACCGAGGCCGAC
Found at i:54185551 original size:30 final size:29
Alignment explanation
Indices: 54185508--54185583 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 29
54185498 CAACCATATG
* *
54185508 ATTCATATATATATATGTCACATAT-TTC-C
1 ATTCATTTGTATATAT-T-ACATATATTCTC
*
54185537 AATTCATTTGTATATATTGCATATATTCTC
1 -ATTCATTTGTATATATTACATATATTCTC
54185567 ATTCATTTGTCATATAT
1 ATTCATTTGT-ATATAT
54185584 CATCACTTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.12
29 14 0.35
30 21 0.52
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.49
Consensus pattern (29 bp):
ATTCATTTGTATATATTACATATATTCTC
Found at i:54185866 original size:42 final size:43
Alignment explanation
Indices: 54185758--54185867 Score: 150
Period size: 43 Copynumber: 2.6 Consensus size: 43
54185748 TCGTACAATG
* * *
54185758 CCAACGTCCCAGACATGGTCTTACATGTAATCAAATATCGATG
1 CCAATGTCCCAGACATGGTCTTACATGAAATCAAATATCGATA
* * *
54185801 CCACTATCCCAGACAAGGTCTTACATGAAATCAAATA-CGATA
1 CCAATGTCCCAGACATGGTCTTACATGAAATCAAATATCGATA
*
54185843 CCAATGTCCCAGACGTGGTCTTACA
1 CCAATGTCCCAGACATGGTCTTACA
54185868 CGATAACTCA
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
42 25 0.44
43 32 0.56
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (43 bp):
CCAATGTCCCAGACATGGTCTTACATGAAATCAAATATCGATA
Found at i:54188756 original size:48 final size:48
Alignment explanation
Indices: 54188687--54189166 Score: 771
Period size: 48 Copynumber: 10.0 Consensus size: 48
54188677 AGATAAATAT
* *
54188687 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* *
54188735 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* * *
54188783 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
*
54188831 ATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
54188879 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* * *
54188927 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* * *
54188975 ATATGTATGAGATATGTATATGTGGTAAAACCGAATGACTAATGTGAA
1 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
*
54189023 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGATAATGTGAA
1 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* * *
54189071 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* * *
54189119 ATATGTATGAGATAAGAATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
54189167 TGTTGTAACA
Statistics
Matches: 403, Mismatches: 29, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 403 1.00
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (48 bp):
ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
Found at i:54188957 original size:144 final size:144
Alignment explanation
Indices: 54188697--54189166 Score: 877
Period size: 144 Copynumber: 3.3 Consensus size: 144
54188687 ATATATGTGT
* *
54188697 GATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATATGTATATGTGGTA
1 GATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGTGGTA
54188762 AAGCCGAATGGCTAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATG
66 AAGCCGAATGGCTAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATG
54188827 TGAAATATGTATGA
131 TGAAATATGTATGA
54188841 GATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGTGGTA
1 GATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGTGGTA
54188906 AAGCCGAATGGCTAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATG
66 AAGCCGAATGGCTAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATG
54188971 TGAAATATGTATGA
131 TGAAATATGTATGA
* *
54188985 GATATGTATATGTGGTAAAACCGAATGACTAATGTGAAATATATATGAGATATGTATATGTGGTA
1 GATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGTGGTA
*
54189050 AAGCCGAATGGATAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATG
66 AAGCCGAATGGCTAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATG
54189115 TGAAATATGTATGA
131 TGAAATATGTATGA
* *
54189129 GATAAGAATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 GATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
54189167 TGTTGTAACA
Statistics
Matches: 317, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
144 317 1.00
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (144 bp):
GATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGTGGTA
AAGCCGAATGGCTAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATG
TGAAATATGTATGA
Found at i:54189269 original size:37 final size:37
Alignment explanation
Indices: 54189219--54189318 Score: 173
Period size: 37 Copynumber: 2.7 Consensus size: 37
54189209 ATTCCGAGTG
54189219 AGACCCGATGACTACGTGTGGAGATTATGTCCGGGTA
1 AGACCCGATGACTACGTGTGGAGATTATGTCCGGGTA
*
54189256 AGACCCGATGACTACGTGTGGAGAGTATGTCCGGGTA
1 AGACCCGATGACTACGTGTGGAGATTATGTCCGGGTA
* *
54189293 AGACCCGATAACTTCGTGTGGAGATT
1 AGACCCGATGACTACGTGTGGAGATT
54189319 TCGTCTGAGC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (37 bp):
AGACCCGATGACTACGTGTGGAGATTATGTCCGGGTA
Found at i:54213901 original size:46 final size:45
Alignment explanation
Indices: 54213834--54213999 Score: 156
Period size: 46 Copynumber: 3.6 Consensus size: 45
54213824 CGCCCCTAAG
* *
54213834 TGAACTTGGACTCAACTCAACGAGCTCGGGCGTTCGTATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGGC-TTCGTATCCATAAA
* * * **
54213880 TGAACTCAGACTCAACTCAACGAGTTCAGATGGC-TAGT-TACATCTCA
1 TGAACTCGGACTCAACTCAACGAGTTC-G--GGCTTCGTATCCAT-AAA
** * * *
54213927 TGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCGTAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGGC-TTCGTATCCATAAA
54213973 TGAACTCGGACTCAACTCAACGAGTTC
1 TGAACTCGGACTCAACTCAACGAGTTC
54214000 AGATGCTCAA
Statistics
Matches: 96, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
44 1 0.01
46 58 0.60
47 34 0.35
49 3 0.03
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.23
Consensus pattern (45 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGGCTTCGTATCCATAAA
Found at i:54213945 original size:93 final size:93
Alignment explanation
Indices: 54213834--54214004 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
54213824 CGCCCCTAAG
* ** * *
54213834 TGAACTTGGACTCAACTCAACGAGCTCGGGCGTTCGTATCCATAAATGAACTCAGACTCAACTCA
1 TGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAATGAACTCAGACTCAACTCA
54213899 ACGAGTTCAGATGGCTAGTTACATCTCA
66 ACGAGTTCAGATGGCTAGTTACATCTCA
* * * *
54213927 TGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCGTAAGTGAACTCGGACTCAACTCA
1 TGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAATGAACTCAGACTCAACTCA
54213992 ACGAGTTCAGATG
66 ACGAGTTCAGATG
54214005 CTCAACCATC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.23
Consensus pattern (93 bp):
TGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAATGAACTCAGACTCAACTCA
ACGAGTTCAGATGGCTAGTTACATCTCA
Found at i:54214021 original size:46 final size:46
Alignment explanation
Indices: 54213828--54214021 Score: 134
Period size: 46 Copynumber: 4.2 Consensus size: 46
54213818 GTAACCCGCC
* * * ** * **
54213828 CCTAAGTGAACTTGGACTCAACTCAACGAGCTCGGGCGTTC-GTAT
1 CCTAAGTGAACTCGGACTCAACTCAACGAGTTCAGATGCTCAACAT
* *
54213873 CCATAAATGAACTCAGACTCAACTCAACGAGTTCAGATGGCT-AGTTACAT
1 CC-TAAGTGAACTCGGACTCAACTCAACGAGTTCAGAT-GCTCA---ACAT
* * *
54213923 -CTCA-TGAACTCGGACTCAACTCAACGAGTTC-GA-ACATTC-GCAT
1 CCTAAGTGAACTCGGACTCAACTCAACGAGTTCAGATGC--TCAACAT
54213966 CCGTAAGTGAACTCGGACTCAACTCAACGAGTTCAGATGCTCAACCAT
1 CC-TAAGTGAACTCGGACTCAACTCAACGAGTTCAGATGCTCAA-CAT
54214014 CCT-AGTGA
1 CCTAAGTGA
54214022 CATGTCACTT
Statistics
Matches: 116, Mismatches: 17, Indels: 31
0.71 0.10 0.19
Matches are distributed among these distances:
43 3 0.03
44 2 0.02
45 4 0.03
46 65 0.56
47 31 0.27
48 8 0.07
49 1 0.01
50 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.23
Consensus pattern (46 bp):
CCTAAGTGAACTCGGACTCAACTCAACGAGTTCAGATGCTCAACAT
Found at i:54218237 original size:17 final size:17
Alignment explanation
Indices: 54218215--54218247 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
54218205 ACTTCCCTTC
54218215 TCATCTTTTCTTTTCTT
1 TCATCTTTTCTTTTCTT
54218232 TCATCTTTTCTTTTCT
1 TCATCTTTTCTTTTCT
54218248 CCATAGCCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.70
Consensus pattern (17 bp):
TCATCTTTTCTTTTCTT
Found at i:54219191 original size:27 final size:27
Alignment explanation
Indices: 54219161--54219218 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
54219151 TACTAAAATA
* *
54219161 CCCTAAGTATG-AAAATTACCATTATGC
1 CCCTAAG-ATGCAAAATGACCATTATAC
*
54219188 CCCT-AGGTGCAAAATGACCATTATAC
1 CCCTAAGATGCAAAATGACCATTATAC
54219214 CCCTA
1 CCCTA
54219219 GAGTTGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 2 0.08
26 20 0.77
27 4 0.15
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (27 bp):
CCCTAAGATGCAAAATGACCATTATAC
Found at i:54219363 original size:28 final size:28
Alignment explanation
Indices: 54219323--54219431 Score: 139
Period size: 28 Copynumber: 3.9 Consensus size: 28
54219313 GGAGGAAGCG
*
54219323 TTCTGGTGGCTCTGGCACAAATATCTGT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
*
54219351 TTCTGGTGGCTCTGCCACAAATATTTGT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
* * *
54219379 TTCTAGTGGCCCTGCCACAATTATCTGT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
* * *
54219407 ATCTGGTGACTCTGTCAC-AATATCT
1 TTCTGGTGGCTCTGCCACAAATATCT
54219432 ATTCTGGCAG
Statistics
Matches: 69, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
27 6 0.09
28 63 0.91
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.37
Consensus pattern (28 bp):
TTCTGGTGGCTCTGCCACAAATATCTGT
Found at i:54220927 original size:49 final size:50
Alignment explanation
Indices: 54220730--54220927 Score: 202
Period size: 50 Copynumber: 4.0 Consensus size: 50
54220720 ATCTATTGTG
* *
54220730 AGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTT
1 AGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAA-TT
* * * * * * **
54220781 CGATC-AAGTGTGTAGTACTAAGTGCAGGCTAATACGTGTATCAGATGGTT
1 AGGTCGCA-TGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
* * * * **
54220831 AGGTCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACTGGATAATT
1 AGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
* *
54220881 -GGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAA
1 AGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAA
54220928 CCTTGTCTAC
Statistics
Matches: 116, Mismatches: 29, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
49 39 0.34
50 41 0.35
51 36 0.31
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.29
Consensus pattern (50 bp):
AGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
Found at i:54222351 original size:21 final size:21
Alignment explanation
Indices: 54222325--54222364 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
54222315 TTGAGCTCGT
*
54222325 TTTAGCTCGTTTGAGCTCAAA
1 TTTAGCTCGTTTCAGCTCAAA
54222346 TTTAGCTCGTTTCAGCTCA
1 TTTAGCTCGTTTCAGCTCA
54222365 TTCCTTTTTC
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:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (21 bp):
TTTAGCTCGTTTCAGCTCAAA
Found at i:54222606 original size:13 final size:13
Alignment explanation
Indices: 54222588--54222616 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
54222578 AATAGTTGTG
54222588 TGTTATTTAATTA
1 TGTTATTTAATTA
54222601 TGTTATTTAATTA
1 TGTTATTTAATTA
54222614 TGT
1 TGT
54222617 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:54224328 original size:15 final size:15
Alignment explanation
Indices: 54224295--54224324 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
54224285 TATTTTCTAT
54224295 ATTTATTATGTGTGA
1 ATTTATTATGTGTGA
54224310 ATTTA-TATGTGTGA
1 ATTTATTATGTGTGA
54224324 A
1 A
54224325 ATTTTCGTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (15 bp):
ATTTATTATGTGTGA
Found at i:54225064 original size:45 final size:43
Alignment explanation
Indices: 54224980--54225144 Score: 120
Period size: 45 Copynumber: 3.8 Consensus size: 43
54224970 TAAGATTTCC
* ** * *
54224980 TATATGTGTTCTCGTGTAAGACCACATTTGGGACGTTGGCATCAA
1 TATATGTGAT-TCGTGTAAGACCATGTCTGGGACATTGGCATC-A
* *
54225025 TATATGTGGTTACGTGTAAGACCATGTCTGAGACATTGGCAT--
1 TATATGTGATT-CGTGTAAGACCATGTCTGGGACATTGGCATCA
* * * *
54225067 TGTATTTGATTCGTGTAAGACCCTGTCTGGGACAGTGGCATC-
1 TATATGTGATTCGTGTAAGACCATGTCTGGGACATTGGCATCA
* * * * * *
54225109 GATATGAGATAGCATGTAAAACCATGTTTGGGACAT
1 TATATGTGAT-TCGTGTAAGACCATGTCTGGGACAT
54225145 GATACGTACT
Statistics
Matches: 95, Mismatches: 22, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
41 27 0.28
42 14 0.15
43 19 0.20
44 1 0.01
45 34 0.36
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (43 bp):
TATATGTGATTCGTGTAAGACCATGTCTGGGACATTGGCATCA
Found at i:54227955 original size:6 final size:6
Alignment explanation
Indices: 54227944--54228000 Score: 87
Period size: 6 Copynumber: 9.5 Consensus size: 6
54227934 GCTTCGTACC
* * *
54227944 CACTCT CACTCT CACTCT CATTCT CGCTCT CGCTCT CACTCT CACTCT
1 CACTCT CACTCT CACTCT CACTCT CACTCT CACTCT CACTCT CACTCT
54227992 CACTCT CAC
1 CACTCT CAC
54228001 ATGTGAAACT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.14, C:0.49, G:0.04, T:0.33
Consensus pattern (6 bp):
CACTCT
Found at i:54230827 original size:6 final size:6
Alignment explanation
Indices: 54230816--54230878 Score: 99
Period size: 6 Copynumber: 10.5 Consensus size: 6
54230806 AGTTTCACAT
* * *
54230816 GTGAGA GTGAGA GTGAGA GTGAGA GTGAGA GCGAGA GCGAGA ATGAGA
1 GTGAGA GTGAGA GTGAGA GTGAGA GTGAGA GTGAGA GTGAGA GTGAGA
54230864 GTGAGA GTGAGA GTG
1 GTGAGA GTGAGA GTG
54230879 GGTACGAAGC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.33, C:0.03, G:0.49, T:0.14
Consensus pattern (6 bp):
GTGAGA
Found at i:54232444 original size:14 final size:14
Alignment explanation
Indices: 54232425--54232469 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
54232415 AACTCATCTT
*
54232425 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
54232439 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
54232452 AATTTAATTTAATG
1 AGTTTAATTTAATG
54232466 AGTT
1 AGTT
54232470 ACTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:54233479 original size:29 final size:29
Alignment explanation
Indices: 54233446--54233505 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
54233436 ATAACCAAAC
*
54233446 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
54233475 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
54233504 CT
1 CT
54233506 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:54233498 original size:15 final size:15
Alignment explanation
Indices: 54233452--54233499 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
54233442 AAACCTACAA
*
54233452 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
54233467 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
54233481 AAACTTCATATCCAT
1 AAACTTCATATCCAT
54233496 AAAC
1 AAAC
54233500 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:54240595 original size:15 final size:14
Alignment explanation
Indices: 54240576--54240618 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
54240566 ACTCTTTCTA
54240576 CTCTTTTTCTTTT-
1 CTCTTTTTCTTTTG
*
54240589 CATTCTTTTTATTTTG
1 C--TCTTTTTCTTTTG
54240605 CTCTTTTTCTTTTG
1 CTCTTTTTCTTTTG
54240619 ATCTCTCCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
13 1 0.04
14 12 0.48
15 11 0.44
16 1 0.04
ACGTcount: A:0.05, C:0.19, G:0.05, T:0.72
Consensus pattern (14 bp):
CTCTTTTTCTTTTG
Found at i:54242705 original size:11 final size:10
Alignment explanation
Indices: 54242688--54242716 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
54242678 TTTCTAAAAT
54242688 ATTTTTTTGA
1 ATTTTTTTGA
54242698 ATTTTTTTGA
1 ATTTTTTTGA
54242708 ATTTTTTTG
1 ATTTTTTTG
54242717 CTAATATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.72
Consensus pattern (10 bp):
ATTTTTTTGA
Found at i:54249763 original size:20 final size:20
Alignment explanation
Indices: 54249737--54249802 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
54249727 ATGTTCAAAT
54249737 TTTTTTTCAATTTTTTTTGAA
1 TTTTTTTCAA-TTTTTTTGAA
*
54249758 TTTTTTTGAATTTTTTTGAA
1 TTTTTTTCAATTTTTTTGAA
* *
54249778 TTTTTTTC-GTTTTTTT-CA
1 TTTTTTTCAATTTTTTTGAA
54249796 TTTTTTT
1 TTTTTTT
54249803 TTGTTTTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
18 8 0.20
19 7 0.17
20 17 0.41
21 9 0.22
ACGTcount: A:0.14, C:0.05, G:0.06, T:0.76
Consensus pattern (20 bp):
TTTTTTTCAATTTTTTTGAA
Found at i:54249803 original size:10 final size:10
Alignment explanation
Indices: 54249737--54249802 Score: 73
Period size: 10 Copynumber: 6.7 Consensus size: 10
54249727 ATGTTCAAAT
54249737 TTTTTTTCAA
1 TTTTTTTCAA
*
54249747 TTTTTTTTGAA
1 -TTTTTTTCAA
*
54249758 TTTTTTTGAA
1 TTTTTTTCAA
*
54249768 TTTTTTTGAA
1 TTTTTTTCAA
*
54249778 TTTTTTTC-G
1 TTTTTTTCAA
54249787 TTTTTTTC-A
1 TTTTTTTCAA
54249796 TTTTTTT
1 TTTTTTT
54249803 TTGTTTTTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
9 15 0.29
10 27 0.53
11 9 0.18
ACGTcount: A:0.14, C:0.05, G:0.06, T:0.76
Consensus pattern (10 bp):
TTTTTTTCAA
Found at i:54253732 original size:19 final size:20
Alignment explanation
Indices: 54253688--54253734 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
54253678 AGTAAGCGCG
54253688 ATTGAGCTCAAACGAGCTGA
1 ATTGAGCTCAAACGAGCTGA
* *
54253708 AATGAGCTCAAATGAG-TGA
1 ATTGAGCTCAAACGAGCTGA
54253727 ATTGAGCT
1 ATTGAGCT
54253735 GGACGGAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (20 bp):
ATTGAGCTCAAACGAGCTGA
Found at i:54257008 original size:46 final size:46
Alignment explanation
Indices: 54256852--54257265 Score: 311
Period size: 47 Copynumber: 8.8 Consensus size: 46
54256842 TTGGATTTCT
* * **
54256852 TGAGTGCCAGTGTAAGACATGTCTGGGACATACATCGGCCACA-TTA
1 TGAGTGCCAGTGTAAGACATGTCTGGGACATGCATCGG-CATAGAGA
* *
54256898 TGAGTGCCAGTATAAGACCATGTCTGGGACATGGCATTGGCATAGAGA
1 TGAGTGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATAGAGA
* **
54256946 TGAGTGCCAGTGTAAGACATGTTTGGGACATGCATCGGCCATA-TTA
1 TGAGTGCCAGTGTAAGACATGTCTGGGACATGCATCGG-CATAGAGA
* * **
54256992 TGAGTACCAGTATAAGACCATGTCTGGGACATGGCATCGGTGTAGAGA
1 TGAGTGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATAGAGA
* * * *
54257040 TGAGTGCCAATGTAAGACATGTCTGGGACATGCATCAGCCTCGATGA
1 TGAGTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATAGA-GA
* * *
54257087 TGA-TAGCTAGTGTAAGACGTGTCTGGGACACGCATCGGC-TA-AGA
1 TGAGT-GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATAGAGA
* * * * * * *
54257131 -GTTGTGCTAGTGTAAGACGTGTCTAGGACATGCATCAGCATGTATATA
1 TG-AGTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCA--TAGAGA
* * * * * *
54257179 TGAGAGCTAGTATAAGACCATGTCTGGGACATGGCATTGGCTTCGATGA
1 TGAGTGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATAGA-GA
* *
54257228 TG-CTAGCCAGTGTAGGACCATGTCTGGGACATGGCATC
1 TGAGT-GCCAGTGTAAGA-CATGTCTGGGACAT-GCATC
54257266 AAAAACTTAT
Statistics
Matches: 295, Mismatches: 53, Indels: 37
0.77 0.14 0.10
Matches are distributed among these distances:
43 1 0.00
44 33 0.11
45 2 0.01
46 49 0.17
47 99 0.34
48 60 0.20
49 45 0.15
50 6 0.02
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.25
Consensus pattern (46 bp):
TGAGTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATAGAGA
Found at i:54257013 original size:94 final size:94
Alignment explanation
Indices: 54256852--54257266 Score: 438
Period size: 94 Copynumber: 4.4 Consensus size: 94
54256842 TTGGATTTCT
* * *
54256852 TGAGTGCCAGTGTAAGACATGTCTGGGACATACATCGGCCACATTATGAGT-GCCAGTATAAGAC
1 TGAGTGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCATATTATGAGTAGCCAGTATAAGAC
*
54256916 CATGTCTGGGACATGGCATTGGCATAGAGA
66 CATGTCTGGGACATGGCATCGGC-TAGAGA
* *
54256946 TGAGTGCCAGTGTAAGACATGTTTGGGACATGCATCGGCCATATTATGAGTA-CCAGTATAAGAC
1 TGAGTGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCATATTATGAGTAGCCAGTATAAGAC
*
54257010 CATGTCTGGGACATGGCATCGGTGTAGAGA
66 CATGTCTGGGACATGGCATCGG-CTAGAGA
* * * *
54257040 TGAGTGCCAATGTAAGACATGTCTGGGACATGCATCAGCC-TCGATGATGA-TAGCTAGTGTAAG
1 TGAGTGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCAT--ATTATGAGTAGCCAGTATAAG
* *
54257103 A-CGTGTCTGGGACA-CGCATCGGCTA-AGA
64 ACCATGTCTGGGACATGGCATCGGCTAGAGA
* * * * *
54257131 -GTTGTGCTAGTGTAAGACGTGTCTAGGACATGCATCAG-CATGTATATATGAG-AGCTAGTATA
1 TG-AGTGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCA--TAT-TATGAGTAGCCAGTATA
* *
54257193 AGACCATGTCTGGGACATGGCATTGGCTTCGATGA
62 AGACCATGTCTGGGACATGGCATCGGC-TAGA-GA
* *
54257228 TG-CTAGCCAGTGTAGGACCATGTCTGGGACATGGCATCA
1 TGAGT-GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCA
54257267 AAAACTTATC
Statistics
Matches: 271, Mismatches: 30, Indels: 35
0.81 0.09 0.10
Matches are distributed among these distances:
90 2 0.01
91 36 0.13
92 18 0.07
93 21 0.08
94 145 0.54
95 16 0.06
96 2 0.01
97 12 0.04
98 13 0.05
99 6 0.02
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.25
Consensus pattern (94 bp):
TGAGTGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCATATTATGAGTAGCCAGTATAAGAC
CATGTCTGGGACATGGCATCGGCTAGAGA
Found at i:54257225 original size:141 final size:143
Alignment explanation
Indices: 54256896--54257258 Score: 384
Period size: 141 Copynumber: 2.6 Consensus size: 143
54256886 TCGGCCACAT
*
54256896 TATGAGTGCCAGTATAAGACCATGTCTGGGACATGGCATTGGCATAGA-GATGAGT-GCCAGTGT
1 TATGAGTGCCAGTATAAGACCATGTCTGGGACATGGCATTGGCATCGATGATGA-TAGCCAGTGT
* * ** *
54256959 AAGACATGTTTGGGACATGCATCGGCCATATTATGAGTACCAGTATAAGACCATGTCTGGGACAT
65 AAGACATGTCTGGGACACGCATCGGCCATAAGATGAGTACCAGTATAAGACCATGTCTAGGACAT
*
54257024 GGCATCGGTGTAGA
130 GGCATCGATGTAGA
* * * ** * *
54257038 GATGAGTGCCAATGTAAGA-CATGTCTGGGACAT-GCATCAGCCTCGATGATGATAGCTAGTGTA
1 TATGAGTGCCAGTATAAGACCATGTCTGGGACATGGCATTGGCATCGATGATGATAGCCAGTGTA
* * * * * *
54257101 AGACGTGTCTGGGACACGCATCGG-C-TAAGA-GTTGTGCTAGTGTAAGA-CGTGTCTAGGACAT
66 AGACATGTCTGGGACACGCATCGGCCATAAGATG-AGTACCAGTATAAGACCATGTCTAGGACAT
*
54257162 -GCATCAGCATGTATA
130 GGCATC-G-ATGTAGA
* * * *
54257177 TATGAGAGCTAGTATAAGACCATGTCTGGGACATGGCATTGGCTTCGATGATGCTAGCCAGTGTA
1 TATGAGTGCCAGTATAAGACCATGTCTGGGACATGGCATTGGCATCGATGATGATAGCCAGTGTA
*
54257242 GGACCATGTCTGGGACA
66 AGA-CATGTCTGGGACA
54257259 TGGCATCAAA
Statistics
Matches: 180, Mismatches: 33, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
137 5 0.03
138 14 0.08
139 33 0.18
140 25 0.14
141 75 0.42
142 28 0.16
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (143 bp):
TATGAGTGCCAGTATAAGACCATGTCTGGGACATGGCATTGGCATCGATGATGATAGCCAGTGTA
AGACATGTCTGGGACACGCATCGGCCATAAGATGAGTACCAGTATAAGACCATGTCTAGGACATG
GCATCGATGTAGA
Found at i:54258156 original size:55 final size:55
Alignment explanation
Indices: 54258030--54258158 Score: 186
Period size: 55 Copynumber: 2.3 Consensus size: 55
54258020 TAAAATTTTT
* *
54258030 AGTCAGTGTTGTACACGGGTAGGCCACACGGGCGTGTGCCATGGCCGTGTCTTAA
1 AGTCAGTGTTGTACACGGGAAGGCCACACAGGCGTGTGCCATGGCCGTGTCTTAA
* * * * *
54258085 AGTCAGTATCGTACACGGGAAGGTCACACAGGCGTGTGCCATGGCCGTGTGTTGA
1 AGTCAGTGTTGTACACGGGAAGGCCACACAGGCGTGTGCCATGGCCGTGTCTTAA
*
54258140 AGTCAGTGTTGCACACGGG
1 AGTCAGTGTTGTACACGGG
54258159 CTAAGGGCAT
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 64 1.00
ACGTcount: A:0.20, C:0.22, G:0.35, T:0.22
Consensus pattern (55 bp):
AGTCAGTGTTGTACACGGGAAGGCCACACAGGCGTGTGCCATGGCCGTGTCTTAA
Found at i:54259265 original size:18 final size:19
Alignment explanation
Indices: 54259229--54259300 Score: 80
Period size: 18 Copynumber: 3.9 Consensus size: 19
54259219 TTTCTCGCAC
54259229 TCTTTCTTTTCTTTCTTCAA
1 TCTTTCTTTTCTTT-TTCAA
*
54259249 TCTTT-TTTGCTTTTTCAA
1 TCTTTCTTTTCTTTTTCAA
54259267 T-TTTCTTTTCTTTTTC-A
1 TCTTTCTTTTCTTTTTCAA
*
54259284 -CATTCTTTTTCTTTTTC
1 TCTTTC-TTTTCTTTTTC
54259301 TTTCTCTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
17 7 0.15
18 27 0.59
19 7 0.15
20 5 0.11
ACGTcount: A:0.08, C:0.21, G:0.01, T:0.69
Consensus pattern (19 bp):
TCTTTCTTTTCTTTTTCAA
Found at i:54259301 original size:12 final size:11
Alignment explanation
Indices: 54259267--54259314 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 11
54259257 GCTTTTTCAA
54259267 TTTTCTTTTCT
1 TTTTCTTTTCT
**
54259278 TTTTCACATTCT
1 TTTTC-TTTTCT
54259290 TTTTCTTTTTCT
1 TTTTC-TTTTCT
*
54259302 TTCTCTTTTCT
1 TTTTCTTTTCT
54259313 TT
1 TT
54259315 CAAGCTCTCT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
11 13 0.43
12 17 0.57
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:54259983 original size:36 final size:36
Alignment explanation
Indices: 54259936--54260023 Score: 158
Period size: 36 Copynumber: 2.4 Consensus size: 36
54259926 AAAGAAAATT
*
54259936 CACTCACTTGGCTTTTGTTCACTTGAATAGACTCAC
1 CACTCTCTTGGCTTTTGTTCACTTGAATAGACTCAC
54259972 CACTCTCTTGGCTTTTGTTCACTTGAATAGACTCAC
1 CACTCTCTTGGCTTTTGTTCACTTGAATAGACTCAC
*
54260008 CACTCTCTTGCCTTTT
1 CACTCTCTTGGCTTTT
54260024 CCGCTCAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.18, C:0.30, G:0.12, T:0.40
Consensus pattern (36 bp):
CACTCTCTTGGCTTTTGTTCACTTGAATAGACTCAC
Found at i:54261480 original size:16 final size:17
Alignment explanation
Indices: 54261455--54261502 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 17
54261445 ATAAGCACAA
54261455 TTAAACAAG-TAAATGT
1 TTAAACAAGTTAAATGT
*
54261471 TTAAATAAGTTAAATGGT
1 TTAAACAAGTTAAAT-GT
*
54261489 TGTAAACAATTTAA
1 T-TAAACAAGTTAA
54261503 TTAAGCTGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 8 0.31
17 5 0.19
18 3 0.12
19 10 0.38
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.35
Consensus pattern (17 bp):
TTAAACAAGTTAAATGT
Found at i:54261633 original size:50 final size:50
Alignment explanation
Indices: 54261529--54261678 Score: 241
Period size: 49 Copynumber: 3.0 Consensus size: 50
54261519 TAATTGCCAA
* *
54261529 AATTAGTTAAGCAACTAAAGAAAATTAAAAA-AACTTAATTAATTAAACT
1 AATTATTTAAGCAACTAAAGACAATTAAAAACAACTTAATTAATTAAACT
54261578 AATTATTTAAGCAACTAAAGACAATTAAAAACAACTTAATTAATTAAACT
1 AATTATTTAAGCAACTAAAGACAATTAAAAACAACTTAATTAATTAAACT
* * *
54261628 AATTATTTAAGAAACTAAAGACAAAT-AAAACAACTTAATTAATTAAGCT
1 AATTATTTAAGCAACTAAAGACAATTAAAAACAACTTAATTAATTAAACT
54261677 AA
1 AA
54261679 AATAACTAAA
Statistics
Matches: 95, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
49 53 0.56
50 42 0.44
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.29
Consensus pattern (50 bp):
AATTATTTAAGCAACTAAAGACAATTAAAAACAACTTAATTAATTAAACT
Found at i:54263321 original size:20 final size:20
Alignment explanation
Indices: 54263296--54263350 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
54263286 TGTGGTTCAA
*
54263296 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
54263316 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
54263336 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
54263351 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:54266660 original size:43 final size:43
Alignment explanation
Indices: 54266612--54266782 Score: 161
Period size: 43 Copynumber: 4.0 Consensus size: 43
54266602 GGTTACCGAG
*
54266612 ATGTGATTACATGTAAGACCATGCCTAGGACATTGGCATTGTA
1 ATGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTA
* *
54266655 ATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCAT-TA
1 ATGTGATTACATGTAAGACCATGTCTAGGACATTGGCAT--TGTA
* * * * * * *
54266699 AT-CGATTACGTGTAAGACCCTGTCTGGGACAGTGACATCG-A
1 ATGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTA
** * *
54266740 TATGTGACAACATGTAAGACCATATCTAGGATA-TGGCATTGTA
1 -ATGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTA
54266783 CGAGCTATAT
Statistics
Matches: 104, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
41 1 0.01
42 8 0.08
43 90 0.87
44 4 0.04
45 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (43 bp):
ATGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTA
Found at i:54267585 original size:15 final size:15
Alignment explanation
Indices: 54267565--54267612 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
54267555 TCAAAGATGG
54267565 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
54267580 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
54267594 GTTTATGGATATAAA
1 GTTTATGGATATGAA
54267609 GTTT
1 GTTT
54267613 TTGTAGGGTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:54267599 original size:14 final size:14
Alignment explanation
Indices: 54267559--54267602 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
54267549 AAGGATTCAA
54267559 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
54267573 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
54267588 AGATGGGTTTATGG
1 AGATGGGTTTATGG
54267602 A
1 A
54267603 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:54267628 original size:29 final size:29
Alignment explanation
Indices: 54267559--54267618 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
54267549 AAGGATTCAA
*
54267559 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
54267588 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
54267617 AG
1 AG
54267619 GGTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:54270906 original size:30 final size:28
Alignment explanation
Indices: 54270853--54270908 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
54270843 TTCTTCCACG
* *
54270853 CTTTCTTTTTGCTCACTCTCTTTTTCAA
1 CTTTCTTTTTGCACACACTCTTTTTCAA
54270881 CTTTACTTTCTTGCACACACTCTTTTTC
1 CTTT-CTTT-TTGCACACACTCTTTTTC
54270909 TTTTTCGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.12, C:0.30, G:0.04, T:0.54
Consensus pattern (28 bp):
CTTTCTTTTTGCACACACTCTTTTTCAA
Found at i:54272233 original size:15 final size:15
Alignment explanation
Indices: 54272213--54272260 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
54272203 TCAAAGATGG
54272213 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
54272228 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
54272243 -TTTATGGATATAAA
1 GTTTATGGATATGAA
54272257 GTTT
1 GTTT
54272261 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:54272240 original size:29 final size:29
Alignment explanation
Indices: 54272207--54272266 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
54272197 AAGGATTCAA
* *
54272207 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTTATGGATATAAAGTTTATGT
*
54272236 AGATGGATTTATGGATATAAAGTTTTTGT
1 AGATGGATTTATGGATATAAAGTTTATGT
54272265 AG
1 AG
54272267 GTTTGGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATGGATATAAAGTTTATGT
Found at i:54286040 original size:51 final size:50
Alignment explanation
Indices: 54285906--54286040 Score: 162
Period size: 50 Copynumber: 2.7 Consensus size: 50
54285896 GAAGCTATCT
* * *
54285906 GGTATGCATAGTAGCCTGCACTTAGTACTACACACGTGACCTCACCATCT
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACCACACCATCG
** * * * ***
54285956 AATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCG
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACCACA-CCATCG
54286007 GGTACGCATAGTAGCCTGCACTTAGTACTACACA
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACA
54286041 TGCGACCTCA
Statistics
Matches: 69, Mismatches: 15, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
50 37 0.54
51 32 0.46
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (50 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACCACACCATCG
Found at i:54292077 original size:14 final size:14
Alignment explanation
Indices: 54292040--54292083 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
54292030 ATTCTCTTCC
54292040 TTGCTATTTTTGTT
1 TTGCTATTTTTGTT
54292054 TT-C-ATCTTTTGTT
1 TTGCTAT-TTTTGTT
*
54292067 TTGCTATTTTTCTT
1 TTGCTATTTTTGTT
54292081 TTG
1 TTG
54292084 GTAGCCGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 2 0.08
13 10 0.38
14 12 0.46
15 2 0.08
ACGTcount: A:0.07, C:0.11, G:0.11, T:0.70
Consensus pattern (14 bp):
TTGCTATTTTTGTT
Found at i:54293557 original size:11 final size:11
Alignment explanation
Indices: 54293541--54293566 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
54293531 CGAAGCCCAC
54293541 ATCACAATAAT
1 ATCACAATAAT
54293552 ATCACAATAAT
1 ATCACAATAAT
54293563 ATCA
1 ATCA
54293567 TACATGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (11 bp):
ATCACAATAAT
Found at i:54302127 original size:40 final size:40
Alignment explanation
Indices: 54302072--54302254 Score: 294
Period size: 40 Copynumber: 4.6 Consensus size: 40
54302062 ATTTGAATAC
54302072 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
54302112 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* *
54302152 ATCCGGGCTAAGACCCGAAGACAATTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* * * *
54302192 ATCCGGGCTAAGACCCTAAGGCATTCGTGCGAGTTGCTAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* *
54302232 ACCCGGGTTAAGACCCGAAGGCA
1 ATCCGGGCTAAGACCCGAAGGCA
54302255 ATTGAGCTTG
Statistics
Matches: 132, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 132 1.00
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.22
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
Found at i:54307959 original size:13 final size:13
Alignment explanation
Indices: 54307941--54307965 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54307931 TAACCTACAA
54307941 AATTAAATAACAT
1 AATTAAATAACAT
54307954 AATTAAATAACA
1 AATTAAATAACA
54307966 CACAACTATT
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AATTAAATAACAT
Found at i:54308223 original size:10 final size:10
Alignment explanation
Indices: 54308190--54308238 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
54308180 AAAAAGGAAT
*
54308190 GAGCTGAAAC
1 GAGCTCAAAC
54308200 GAGCT-AAATTC
1 GAGCTCAAA--C
54308211 GAGCTCAAAC
1 GAGCTCAAAC
*
54308221 GAGCTAAAAC
1 GAGCTCAAAC
54308231 GAGCTCAA
1 GAGCTCAA
54308239 GTGAGCTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 3 0.09
10 22 0.65
11 6 0.18
12 3 0.09
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:54308245 original size:20 final size:21
Alignment explanation
Indices: 54308190--54308238 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
54308180 AAAAAGGAAT
* *
54308190 GAGCTGAAACGAGCTAAATTC
1 GAGCTCAAACGAGCTAAATAC
54308211 GAGCTCAAACGAGCTAAA-AC
1 GAGCTCAAACGAGCTAAATAC
54308231 GAGCTCAA
1 GAGCTCAA
54308239 GTGAGCTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (21 bp):
GAGCTCAAACGAGCTAAATAC
Found at i:54314994 original size:6 final size:6
Alignment explanation
Indices: 54314985--54315063 Score: 81
Period size: 6 Copynumber: 12.8 Consensus size: 6
54314975 AATTAAAATG
*
54314985 AGAATC AGAATC AGAATC AGAATC AG-GTGAC AGAATC AGAATC AGAATC
1 AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC
* *
54315034 AGTATC AGGTAA-C AGAATC AAAATC AGAAT
1 AGAATC A-G-AATC AGAATC AGAATC AGAAT
54315064 GTGAATGCAA
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
5 3 0.05
6 50 0.82
7 6 0.10
8 2 0.03
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.18
Consensus pattern (6 bp):
AGAATC
Found at i:54314994 original size:18 final size:18
Alignment explanation
Indices: 54314973--54315063 Score: 69
Period size: 19 Copynumber: 4.9 Consensus size: 18
54314963 TATAAGAACT
* *
54314973 AGAATTAAAATGAGAATC
1 AGAATCAAAATCAGAATC
*
54314991 AGAATCAGAATCAGAATC
1 AGAATCAAAATCAGAATC
* *
54315009 AG-GTGACAGAATCAGAATC
1 AGAAT--CAAAATCAGAATC
**
54315028 AGAATCAGTATCAGGTAA-C
1 AGAATCAAAATCA-G-AATC
54315047 AGAATCAAAATCAGAAT
1 AGAATCAAAATCAGAAT
54315064 GTGAATGCAA
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
17 3 0.05
18 25 0.42
19 28 0.47
20 3 0.05
ACGTcount: A:0.49, C:0.13, G:0.19, T:0.19
Consensus pattern (18 bp):
AGAATCAAAATCAGAATC
Found at i:54315020 original size:31 final size:31
Alignment explanation
Indices: 54314985--54315063 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
54314975 AATTAAAATG
*
54314985 AGAATCAGAATCAGAATCAGAATCAGGTGAC
1 AGAATCAGAATCAGAATCAGAATCAGGTAAC
*
54315016 AGAATCAGAATCAGAATCAGTATCAGGTAAC
1 AGAATCAGAATCAGAATCAGAATCAGGTAAC
*
54315047 AGAATCAAAATCAGAAT
1 AGAATCAGAATCAGAAT
54315064 GTGAATGCAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.18
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGAATCAGGTAAC
Found at i:54315053 original size:25 final size:24
Alignment explanation
Indices: 54314990--54315036 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
54314980 AAATGAGAAT
54314990 CAGAATCAGAATCAGAATCAGGTGA
1 CAGAATCAGAATCAGAATCA-GTGA
54315015 CAGAATCAGAATCAGAATCAGT
1 CAGAATCAGAATCAGAATCAGT
54315037 ATCAGGTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.17
Consensus pattern (24 bp):
CAGAATCAGAATCAGAATCAGTGA
Found at i:54315286 original size:71 final size:67
Alignment explanation
Indices: 54315209--54315350 Score: 185
Period size: 67 Copynumber: 2.1 Consensus size: 67
54315199 TCACCAGATA
* * * * *
54315209 CAGATATTGTGGCTAGGCCACCAGAACAGATATATATATGTGGCGAAGCCATCAGATTGCAGCGA
1 CAGATATTGTGACGAAGCCACCAGAACAG----ATATATGTGGCGAAGCCACCAGATTGCAGCAA
54315274 GGCTGC
62 GGCTGC
* *
54315280 CAGATATTGTGACGAAGTCACCAGAACAGATATATGTGGCGAGGCCACCAGATTGCAGCAAGGCT
1 CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCAAGGCT
54315345 GC
66 GC
54315347 CAGA
1 CAGA
54315351 ACGCTTCCTC
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
67 39 0.61
71 25 0.39
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.19
Consensus pattern (67 bp):
CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCAAGGCT
GC
Found at i:54315328 original size:27 final size:26
Alignment explanation
Indices: 54315280--54315331 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
54315270 GCGAGGCTGC
*
54315280 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
54315306 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
54315332 TTGCAGCAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:54315598 original size:27 final size:27
Alignment explanation
Indices: 54315568--54315758 Score: 240
Period size: 27 Copynumber: 7.1 Consensus size: 27
54315558 AACACCCTAG
*
54315568 GGGTAAAACGGTAATTCTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
54315595 GGGTAAAATAGTAATTTTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
54315622 GGGTAAAATAGTAATTTTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
*
54315649 GGGTAAAACAGTAATTCTGTCAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
54315676 GGGTAAAAC-GATAATTCTATAAATTGA
1 GGGTAAAACAG-TAATTCTGTAAATCGA
* * *
54315703 GGGTAAAACAATAATTCTATAAATTGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* * *
54315730 GGGTAAAACGGTAATTTTGTAAATTGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
54315757 GG
1 GG
54315759 ATATTTGGGT
Statistics
Matches: 148, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
26 1 0.01
27 147 0.99
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (27 bp):
GGGTAAAACAGTAATTCTGTAAATCGA
Found at i:54315772 original size:81 final size:80
Alignment explanation
Indices: 54315568--54315788 Score: 235
Period size: 81 Copynumber: 2.7 Consensus size: 80
54315558 AACACCCTAG
* * * *
54315568 GGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAATAG
1 GGGTAAAACGGTAATTCTGTAAATCGAGGGT-AAATGGTAATTTTATAAATCGAGGGTAAAACAA
* *
54315633 TAATTTTGTAAATCGA
65 TAATTCTATAAATCGA
* * * * * *
54315649 GGGTAAAACAGTAATTCTGTCAATCGAGGGTAAAACGATAATTCTATAAATTGAGGGTAAAACAA
1 GGGTAAAACGGTAATTCTGTAAATCGAGGGT-AAATGGTAATTTTATAAATCGAGGGTAAAACAA
*
54315714 TAATTCTATAAATTGA
65 TAATTCTATAAATCGA
* * * ** * *
54315730 GGGTAAAACGGTAATTTTGTAAATTGAGGATATTTGGGTAATTTTATAAACCGGGGGTA
1 GGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAT-GGTAATTTTATAAATCGAGGGTA
54315789 CTTTGGTAAT
Statistics
Matches: 113, Mismatches: 26, Indels: 2
0.80 0.18 0.01
Matches are distributed among these distances:
80 1 0.01
81 112 0.99
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (80 bp):
GGGTAAAACGGTAATTCTGTAAATCGAGGGTAAATGGTAATTTTATAAATCGAGGGTAAAACAAT
AATTCTATAAATCGA
Found at i:54317799 original size:6 final size:6
Alignment explanation
Indices: 54317790--54317840 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
54317780 AATTAAAATG
* * *
54317790 AGAATC AGAATC AGAATC AG-GTGAC AGAATT AGAATC AGAATC AGTATC
1 AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC AGAATC
54317839 AG
1 AG
54317841 GTAACAGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
5 1 0.03
6 32 0.86
7 3 0.08
8 1 0.03
ACGTcount: A:0.45, C:0.14, G:0.22, T:0.20
Consensus pattern (6 bp):
AGAATC
Found at i:54317827 original size:31 final size:31
Alignment explanation
Indices: 54317790--54317848 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
54317780 AATTAAAATG
*
54317790 AGAATCAGAATCAGAATCAGGTGACAGAATT
1 AGAATCAGAATCAGAATCAGGTAACAGAATT
*
54317821 AGAATCAGAATCAGTATCAGGTAACAGA
1 AGAATCAGAATCAGAATCAGGTAACAGA
54317849 TTCAAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.22, T:0.19
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGGTAACAGAATT
Found at i:54317862 original size:31 final size:31
Alignment explanation
Indices: 54317792--54317862 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
54317782 TTAAAATGAG
* *
54317792 AATCAGAATCAGAATCAGGTGACAGAATTAG
1 AATCAGAATCAGAATCAGGTAACAGAATTAA
*
54317823 AATCAGAATCAGTATCAGGTAACAG-ATTCAA
1 AATCAGAATCAGAATCAGGTAACAGAATT-AA
*
54317854 AATTAGAAT
1 AATCAGAAT
54317863 GTGAATGCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 3 0.09
31 32 0.91
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.23
Consensus pattern (31 bp):
AATCAGAATCAGAATCAGGTAACAGAATTAA
Found at i:54318397 original size:27 final size:27
Alignment explanation
Indices: 54318367--54318557 Score: 231
Period size: 27 Copynumber: 7.1 Consensus size: 27
54318357 AATACCCTAG
** *
54318367 GGGTAAAATGGTAATTCTGTAAATCAA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
54318394 GGGTAAAACAGTAATTTTGTAAATTGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* * *
54318421 GGGTAAAATAATAATTTTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
*
54318448 GGGTAAAACAGTAATTCTGTCAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
54318475 GGGTAAAAC-GATAATTCTGTAAATCGA
1 GGGTAAAACAG-TAATTCTGTAAATCGA
* * * *
54318502 GGGTAAAATAATAATTCTATAAATTGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
* *
54318529 GGGTAAAACGGTAATTTTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
54318556 GG
1 GG
54318558 ATATTTGGAT
Statistics
Matches: 139, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
26 1 0.01
27 138 0.99
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (27 bp):
GGGTAAAACAGTAATTCTGTAAATCGA
Done.