Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 173 of 213
Found at i:52061875 original size:29 final size:29
Alignment explanation
Indices: 52061833--52061922 Score: 171
Period size: 29 Copynumber: 3.1 Consensus size: 29
52061823 TTCTTCTCAG
52061833 ACTTAGCACAATAAACTTGACATTCAAAT
1 ACTTAGCACAATAAACTTGACATTCAAAT
52061862 ACTTAGCACAATAAACTTGACATTCAAAT
1 ACTTAGCACAATAAACTTGACATTCAAAT
*
52061891 ACTTAGCACAATAAACTTGACATTCAATT
1 ACTTAGCACAATAAACTTGACATTCAAAT
52061920 ACT
1 ACT
52061923 ACTGTATTAC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (29 bp):
ACTTAGCACAATAAACTTGACATTCAAAT
Found at i:52063404 original size:55 final size:55
Alignment explanation
Indices: 52063319--52063436 Score: 200
Period size: 55 Copynumber: 2.1 Consensus size: 55
52063309 TGGAAGTCGT
*
52063319 GATACCCCTAGTAGTGTTGAAACGAGAAGAATTGAAACCATCTACAGTGGTATTGC
1 GATA-CCCTAGTAGTGTTGAAACGAGAAGAATTGAAACCATCTACAGTGGTATCGC
* *
52063375 GATACCCTTGTAGTGTTGAAACGAGAAGAATTGAAGCCATCTACAGTGGTATCGC
1 GATACCCTAGTAGTGTTGAAACGAGAAGAATTGAAACCATCTACAGTGGTATCGC
52063430 GATACCC
1 GATACCC
52063437 AACCTCTAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
55 55 0.93
56 4 0.07
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (55 bp):
GATACCCTAGTAGTGTTGAAACGAGAAGAATTGAAACCATCTACAGTGGTATCGC
Found at i:52067044 original size:20 final size:20
Alignment explanation
Indices: 52067021--52067086 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
52067011 TTTTGGTGGC
*
52067021 TTGTCCACATTACTGGCTGT
1 TTGTCTACATTACTGGCTGT
*
52067041 TTGTCTACATTACTGG-TGGC
1 TTGTCTACATTACTGGCT-GT
* *
52067061 TTATCTACATTACTGGCAGT
1 TTGTCTACATTACTGGCTGT
52067081 TTGTCT
1 TTGTCT
52067087 GCAATATTAG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
19 1 0.03
20 37 0.97
ACGTcount: A:0.17, C:0.21, G:0.20, T:0.42
Consensus pattern (20 bp):
TTGTCTACATTACTGGCTGT
Found at i:52072952 original size:27 final size:26
Alignment explanation
Indices: 52072880--52072953 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 26
52072870 CATCCCTTTC
* *
52072880 CATAGACTGCCACAGAGGCTTTCATTT
1 CATAGA-TGCCACAAAGGCTTGCATTT
* * *
52072907 CAAATACGCCACAAAGGCTTGCATTT
1 CATAGATGCCACAAAGGCTTGCATTT
52072933 CATAGATGGCCACAAAGGCTT
1 CATAGAT-GCCACAAAGGCTT
52072954 CAATTTTCTG
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
26 21 0.55
27 17 0.45
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (26 bp):
CATAGATGCCACAAAGGCTTGCATTT
Found at i:52081951 original size:15 final size:16
Alignment explanation
Indices: 52081922--52081951 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52081912 AGAAGATGCT
52081922 TTAACACATTATCAAA
1 TTAACACATTATCAAA
52081938 TTAACACA-TATCAA
1 TTAACACATTATCAA
52081952 CAAGACACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:52083151 original size:25 final size:25
Alignment explanation
Indices: 52083081--52083151 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
52083071 TATGTACATA
52083081 TATGCTCACACGAGCTGTGAATAAG
1 TATGCTCACACGAGCTGTGAATAAG
* * *
52083106 TATGCTCAAATGAGCTATGAATAAG
1 TATGCTCACACGAGCTGTGAATAAG
*
52083131 TATGCTCACACGAGTTGTGAA
1 TATGCTCACACGAGCTGTGAA
52083152 AATGGGTCTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.27
Consensus pattern (25 bp):
TATGCTCACACGAGCTGTGAATAAG
Found at i:52088656 original size:13 final size:12
Alignment explanation
Indices: 52088638--52088707 Score: 50
Period size: 13 Copynumber: 5.3 Consensus size: 12
52088628 TGGGTAAACA
52088638 GAAATGGTGATAT
1 GAAATGGT-ATAT
*
52088651 GAAATGGATATGT
1 GAAATGG-TATAT
*
52088664 GAAATGATTATAT
1 GAAATG-GTATAT
*
52088677 GGAAATAGATATAT
1 -GAAAT-GGTATAT
*
52088691 GAAATGGCTATTT
1 GAAATGG-TATAT
52088704 GAAA
1 GAAA
52088708 AGGTTACTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
12 1 0.02
13 33 0.72
14 11 0.24
15 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.24, T:0.31
Consensus pattern (12 bp):
GAAATGGTATAT
Found at i:52088681 original size:27 final size:26
Alignment explanation
Indices: 52088638--52088696 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
52088628 TGGGTAAACA
* * *
52088638 GAAATGGTGATATGAAATGGATATGT
1 GAAATGATGATATGAAATAGATATAT
*
52088664 GAAATGATTATATGGAAATAGATATAT
1 GAAATGATGATAT-GAAATAGATATAT
52088691 GAAATG
1 GAAATG
52088697 GCTATTTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 11 0.39
27 17 0.61
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31
Consensus pattern (26 bp):
GAAATGATGATATGAAATAGATATAT
Found at i:52091580 original size:18 final size:18
Alignment explanation
Indices: 52091547--52091581 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52091537 CAAATTCATC
* *
52091547 AAAATTAAGTATAATTAT
1 AAAATTAAATAAAATTAT
52091565 AAAATTAAATAAAATTA
1 AAAATTAAATAAAATTA
52091582 AACATGTTCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
AAAATTAAATAAAATTAT
Found at i:52097311 original size:28 final size:28
Alignment explanation
Indices: 52097271--52097471 Score: 267
Period size: 28 Copynumber: 7.2 Consensus size: 28
52097261 TAAACACATG
* * *
52097271 AGAAAAAGGAAGCTTTTGTGGTGATCTA
1 AGAAAAGGGAAGCCTTTGTGGCGATCTA
*
52097299 AGAAAAGGGAAGCCTTTGTGGCGATTTA
1 AGAAAAGGGAAGCCTTTGTGGCGATCTA
* *
52097327 TGAAAAGAGAAGCCTTTGTGGCGATCTA
1 AGAAAAGGGAAGCCTTTGTGGCGATCTA
52097355 AGAAAAGGGAAGCCTTTGTGGCGATCTA
1 AGAAAAGGGAAGCCTTTGTGGCGATCTA
*
52097383 AGAAAAGGGAAGCCTTTGTGGCGATTTA
1 AGAAAAGGGAAGCCTTTGTGGCGATCTA
* * *
52097411 TGAAAAGAGAAGCCTTTGTGGCGATATA
1 AGAAAAGGGAAGCCTTTGTGGCGATCTA
** * *
52097439 TCAAAAGAGAAGCTTTTGTGGCGATCTA
1 AGAAAAGGGAAGCCTTTGTGGCGATCTA
*
52097467 TGAAA
1 AGAAA
52097472 TAGAAGCTTG
Statistics
Matches: 156, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 156 1.00
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.25
Consensus pattern (28 bp):
AGAAAAGGGAAGCCTTTGTGGCGATCTA
Found at i:52097412 original size:84 final size:84
Alignment explanation
Indices: 52097271--52097471 Score: 330
Period size: 84 Copynumber: 2.4 Consensus size: 84
52097261 TAAACACATG
* *
52097271 AGAAAAAGGAAGCTTTTGTGGTGATCTAAGAAAAGGGAAGCCTTTGTGGCGATTTATGAAAAGAG
1 AGAAAAGGGAAGCTTTTGTGGCGATCTAAGAAAAGGGAAGCCTTTGTGGCGATTTATGAAAAGAG
*
52097336 AAGCCTTTGTGGCGATCTA
66 AAGCCTTTGTGGCGATATA
*
52097355 AGAAAAGGGAAGCCTTTGTGGCGATCTAAGAAAAGGGAAGCCTTTGTGGCGATTTATGAAAAGAG
1 AGAAAAGGGAAGCTTTTGTGGCGATCTAAGAAAAGGGAAGCCTTTGTGGCGATTTATGAAAAGAG
52097420 AAGCCTTTGTGGCGATATA
66 AAGCCTTTGTGGCGATATA
** * *
52097439 TCAAAAGAGAAGCTTTTGTGGCGATCTATGAAA
1 AGAAAAGGGAAGCTTTTGTGGCGATCTAAGAAA
52097472 TAGAAGCTTG
Statistics
Matches: 108, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
84 108 1.00
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.25
Consensus pattern (84 bp):
AGAAAAGGGAAGCTTTTGTGGCGATCTAAGAAAAGGGAAGCCTTTGTGGCGATTTATGAAAAGAG
AAGCCTTTGTGGCGATATA
Found at i:52097505 original size:27 final size:27
Alignment explanation
Indices: 52097279--52097499 Score: 127
Period size: 28 Copynumber: 8.0 Consensus size: 27
52097269 TGAGAAAAAG
* * *
52097279 GAAGCTTTTGTGGTGATCTAAGAAA-A
1 GAAGCTTGTGTGGCGATCTATGAAATA
* *
52097305 GGGAAGCCTT-TGTGGCGATTTATGAAAAGA
1 --GAAG-CTTGTGTGGCGATCTATG-AAATA
*
52097335 GAAGCCTT-TGTGGCGATCTAAGAAA-A
1 GAAG-CTTGTGTGGCGATCTATGAAATA
*
52097361 GGGAAGCCTT-TGTGGCGATCTAAGAAA-A
1 --GAAG-CTTGTGTGGCGATCTATGAAATA
* *
52097389 GGGAAGCCTT-TGTGGCGATTTATGAAAAGA
1 --GAAG-CTTGTGTGGCGATCTATG-AAATA
* * *
52097419 GAAGCCTT-TGTGGCGATATATCAAAAGA
1 GAAG-CTTGTGTGGCGATCTAT-GAAATA
*
52097447 GAAGCTTTTGTGGCGATCTATGAAATA
1 GAAGCTTGTGTGGCGATCTATGAAATA
52097474 GAAGCTTGTGTGGCGGATC-ATGAAAT
1 GAAGCTTGTGTGGC-GATCTATGAAAT
52097500 GAAAGCCCTT
Statistics
Matches: 170, Mismatches: 13, Indels: 21
0.83 0.06 0.10
Matches are distributed among these distances:
26 1 0.01
27 30 0.18
28 128 0.75
29 9 0.05
30 2 0.01
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.27
Consensus pattern (27 bp):
GAAGCTTGTGTGGCGATCTATGAAATA
Found at i:52102757 original size:15 final size:16
Alignment explanation
Indices: 52102739--52102773 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
52102729 ATTAAAATAA
52102739 TCAAACTTAATTC-AT
1 TCAAACTTAATTCTAT
*
52102754 TCAAACTTCATTCTAT
1 TCAAACTTAATTCTAT
52102770 TCAA
1 TCAA
52102774 TTCAATCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (16 bp):
TCAAACTTAATTCTAT
Found at i:52106867 original size:10 final size:10
Alignment explanation
Indices: 52106852--52106889 Score: 58
Period size: 10 Copynumber: 3.6 Consensus size: 10
52106842 TAACATGATG
52106852 AATTTTAATT
1 AATTTTAATT
52106862 AATTTTATAGTT
1 AATTTTA-A-TT
52106874 AATTTTAATT
1 AATTTTAATT
52106884 AATTTT
1 AATTTT
52106890 GACTATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 15 0.58
11 2 0.08
12 9 0.35
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (10 bp):
AATTTTAATT
Found at i:52127905 original size:50 final size:50
Alignment explanation
Indices: 52127799--52128091 Score: 316
Period size: 50 Copynumber: 5.7 Consensus size: 50
52127789 GAGGATAAGA
* * * *
52127799 TCCCATGTAAGACCATGTCTGGGACATGGCATTTGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCA-C--CGAG---ATGAGAGG
*
52127855 TCCCATGTAAGACCATGTCTAGGACATGGCGTTGGAACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATGAGAGG
* ** *
52127905 TCCCATGTAAGACCATGTCTGGGACATGAAGTTGGCACTGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATGAGAGG
* *
52127955 TCCCATGTAAGACCATGTCCAGGACATGGCGTTGGCACCAAGATGAGAGG
1 TCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATGAGAGG
** * * * * * **
52128005 TCCCCCGTAAGACCTTGTCTAGGACATGGCATGGGCACCTATATGAGAAC
1 TCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATGAGAGG
* * * *
52128055 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 TCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCA
52128092 GTACAAGAAA
Statistics
Matches: 204, Mismatches: 33, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
50 167 0.82
53 3 0.01
55 1 0.00
56 33 0.16
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATGAGAGG
Found at i:52130883 original size:51 final size:51
Alignment explanation
Indices: 52130796--52131423 Score: 705
Period size: 51 Copynumber: 12.5 Consensus size: 51
52130786 ACAGCTAAAT
* * *
52130796 TTGCAGTGGAACAGATTAAAGCTAAAGGCAACGAATCTTATTTCCCTGGCT
1 TTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCG
* * * * * * *
52130847 TTACAATGGAATAGATTAAAACTGAAGGCAGTGAATCTT-TTTTCCTGGCA
1 TTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCG
** * * *
52130897 TTTTATTGGAACAGATTAAAGCTGAAAGCGGCGAATCTTATTTCCCTGGCG
1 TTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCG
* * *
52130948 TTGTAGTGGAACTGATTAAAGCTGAAGGCAGCGAATCTT-TTTCCCTAGCG
1 TTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCG
* * * * *
52130998 TTACAGT-----AGATTAAAGTTGAAGGCAGCAAATCTTATTTCCTTGGCA
1 TTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCG
** * *
52131044 TTGCAGTGGAACAGATTAAAGCTGAAGGCAGTAAATCTTATTTCCCTAGCA
1 TTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCG
* * * *
52131095 TTGCAGTAGAATAGATTAAAG-TAGAAGGCAACGAGTCTTATTTCCCTGGCG
1 TTGCAGTGGAACAGATTAAAGCT-GAAGGCAGCGAATCTTATTTCCCTGGCG
* * * * * * *
52131146 TTGTAGTGGAACAGATTAAAGCTAAAGACAGTGAATCTTATTTCCTTAGCA
1 TTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCG
** *
52131197 TTGCAGTGGAACAGATTAAAGCTGAAGGCAATGAATCTTATTTCCCTAGCG
1 TTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCG
** *
52131248 TTGCAGTGGAACAGATTAAAGCTGAAGGCAGTAAATATTATTTCCCTGGCG
1 TTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCG
* * * * *
52131299 TTGCAGTAGAGCAGATTAAAGCTGAGGGCAACGAATCTTATTTCCCTGGTG
1 TTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCG
* * *
52131350 TTGCAGTGGAATAGATTAAAGCTGAAGGCAGTGAATCTTATTTCCCTGGTG
1 TTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCG
* *
52131401 TTGCAGCGGAATAGATTAAAGCT
1 TTGCAGTGGAACAGATTAAAGCT
52131424 ACAAGTTATG
Statistics
Matches: 486, Mismatches: 82, Indels: 18
0.83 0.14 0.03
Matches are distributed among these distances:
45 24 0.05
46 14 0.03
50 56 0.12
51 391 0.80
52 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (51 bp):
TTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCG
Found at i:52132990 original size:3 final size:3
Alignment explanation
Indices: 52132982--52133014 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
52132972 TTTAATACTC
52132982 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
52133015 CTACTACTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:52148245 original size:25 final size:25
Alignment explanation
Indices: 52148217--52148309 Score: 107
Period size: 25 Copynumber: 3.7 Consensus size: 25
52148207 TGTAAACAGT
*
52148217 AAGCTCTTCTGAGCTGAATAATGGG
1 AAGCTCATCTGAGCTGAATAATGGG
*
52148242 AAGCTCATGTGAGCTGAATAATGGG
1 AAGCTCATCTGAGCTGAATAATGGG
* * *
52148267 AAGCTCATGC-GAGCGGAGTATTGGG
1 AAGCTCAT-CTGAGCTGAATAATGGG
**
52148292 AAGCTCATAAGAGCTGAA
1 AAGCTCATCTGAGCTGAA
52148310 ATCGATGACC
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
25 57 1.00
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (25 bp):
AAGCTCATCTGAGCTGAATAATGGG
Found at i:52150052 original size:18 final size:19
Alignment explanation
Indices: 52150022--52150061 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
52150012 AGAGTTGTAA
*
52150022 CAACCCAAAATTCTCGAGT
1 CAACCCAAAATTCTCAAGT
52150041 CAACCC-AAATTCTCAAGT
1 CAACCCAAAATTCTCAAGT
52150059 CAA
1 CAA
52150062 AATTTGAGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.40, C:0.33, G:0.07, T:0.20
Consensus pattern (19 bp):
CAACCCAAAATTCTCAAGT
Found at i:52170665 original size:29 final size:29
Alignment explanation
Indices: 52170602--52170669 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
52170592 TAATCAACCG
52170602 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
52170631 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
52170660 CGCACACTTA
1 CGCACACTTA
52170670 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:52170781 original size:174 final size:174
Alignment explanation
Indices: 52170491--52170992 Score: 959
Period size: 174 Copynumber: 2.9 Consensus size: 174
52170481 AACTCAAGGT
* *
52170491 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
* *
52170556 GAAAATATATATTGGGTTCCCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
52170621 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
52170665 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
52170730 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
52170795 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
52170839 GCTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
52170904 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
52170969 ACTTTAAACTCACACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
52170993 TGTACAATTT
Statistics
Matches: 323, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 323 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:52170986 original size:29 final size:30
Alignment explanation
Indices: 52170952--52171023 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
52170942 ATCAACCGCG
*
52170952 CACACTTAGTGCCATGTAC-TTTAAACTCA
1 CACACTTAGTGCCATGTACATTTAAACCCA
*
52170981 CACACTTAGTG-C-TGTACAATTTAAACCCG
1 CACACTTAGTGCCATGTAC-ATTTAAACCCA
52171010 CACACTTAGTGCCA
1 CACACTTAGTGCCA
52171024 ATCTCATGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
27 5 0.14
28 1 0.03
29 30 0.81
30 1 0.03
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.28
Consensus pattern (30 bp):
CACACTTAGTGCCATGTACATTTAAACCCA
Found at i:52191774 original size:7 final size:7
Alignment explanation
Indices: 52191763--52191808 Score: 83
Period size: 7 Copynumber: 6.6 Consensus size: 7
52191753 AATATATTTT
*
52191763 TTTTTAT
1 TTTTTAA
52191770 TTTTTAA
1 TTTTTAA
52191777 TTTTTAA
1 TTTTTAA
52191784 TTTTTAA
1 TTTTTAA
52191791 TTTTTAA
1 TTTTTAA
52191798 TTTTTAA
1 TTTTTAA
52191805 TTTT
1 TTTT
52191809 AAAATACTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTAA
Found at i:52192648 original size:33 final size:33
Alignment explanation
Indices: 52192562--52192659 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
52192552 AAAAAATATA
52192562 AAAACAAAATATTTTAAATATTTTAATATAATTT
1 AAAACAAAATATTTT-AATATTTTAATATAATTT
** ***
52192596 AGTACAAAACTA-AAAAATATTTTAATATAATTT
1 AAAACAAAA-TATTTTAATATTTTAATATAATTT
*
52192629 AAAATAAAATATTTTAATATATTTAATATAA
1 AAAACAAAATATTTTAATAT-TTTAATATAA
52192660 AAATAATTAT
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
32 2 0.04
33 29 0.58
34 17 0.34
35 2 0.04
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (33 bp):
AAAACAAAATATTTTAATATTTTAATATAATTT
Found at i:52192662 original size:25 final size:26
Alignment explanation
Indices: 52192608--52192664 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 26
52192598 TACAAAACTA
52192608 AAAAATATTTTAATATAATTTAAAAT
1 AAAAATATTTTAATATAATTTAAAAT
*
52192634 -AAAATATTTTAATAT-ATTTAATAT
1 AAAAATATTTTAATATAATTTAAAAT
52192658 AAAAATA
1 AAAAATA
52192665 ATTATATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 8 0.28
25 21 0.72
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
AAAAATATTTTAATATAATTTAAAAT
Found at i:52192797 original size:33 final size:33
Alignment explanation
Indices: 52192716--52192808 Score: 98
Period size: 33 Copynumber: 2.8 Consensus size: 33
52192706 TTAAATTATA
* *
52192716 AAAATATTTGAAACATTTTAATATAATTTAATAT
1 AAAATATTT-AAATATTTTAATATAATTTAAAAT
** *
52192750 AAAACTA-AAAAATATTTTAACATAATTTAAAAT
1 AAAA-TATTTAAATATTTTAATATAATTTAAAAT
*
52192783 AAAATATTTTAATATATTTAATATAA
1 AAAATATTTAAATAT-TTTAATATAA
52192809 AAATAATTAT
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
32 2 0.04
33 30 0.64
34 13 0.28
35 2 0.04
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (33 bp):
AAAATATTTAAATATTTTAATATAATTTAAAAT
Found at i:52192811 original size:25 final size:26
Alignment explanation
Indices: 52192757--52192813 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 26
52192747 TATAAAACTA
52192757 AAAAATATTTTAACATAATTTAAAAT
1 AAAAATATTTTAACATAATTTAAAAT
* *
52192783 -AAAATATTTTAATAT-ATTTAATAT
1 AAAAATATTTTAACATAATTTAAAAT
52192807 AAAAATA
1 AAAAATA
52192814 ATTATATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 8 0.29
25 20 0.71
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (26 bp):
AAAAATATTTTAACATAATTTAAAAT
Found at i:52192837 original size:149 final size:148
Alignment explanation
Indices: 52192567--52193037 Score: 827
Period size: 149 Copynumber: 3.2 Consensus size: 148
52192557 ATATAAAAAC
* * * *
52192567 AAAATATTTTAAATATTTTAATATAATTTAGTACAAAACTAAAAAATATTTTAATATAATTTAAA
1 AAAATATTTGAAATATTTTAATATAATTTAATATAAAACTAAAAAATATTTTAACATAATTTAAA
** * *
52192632 ATAAAATATTTTAATATATTTAATATAAAAATAATTATATTAAAATGTTATTAAATTATTTATTT
66 ATAAAATATTTTAATATATTTAATATAAAAATAATTATATTAATTTTTTATTAAATTATATATTT
52192697 TTATTTTTATTAAATTATA
131 TTA-TTTTATTAAATTATA
*
52192716 AAAATATTTGAAACATTTTAATATAATTTAATATAAAACTAAAAAATATTTTAACATAATTTAAA
1 AAAATATTTGAAATATTTTAATATAATTTAATATAAAACTAAAAAATATTTTAACATAATTTAAA
52192781 ATAAAATATTTTAATATATTTAATATAAAAATAATTATATTAATTTTTTATTAAATTATATATTT
66 ATAAAATATTTTAATATATTTAATATAAAAATAATTATATTAATTTTTTATTAAATTATATATTT
52192846 TTATTTTATTAAATTATA
131 TTATTTTATTAAATTATA
*
52192864 AAAATATTTGAAATATTTTAATATAATTTAATAT-AAACTAAAAAATATTTTGACATAATTTAAA
1 AAAATATTTGAAATATTTTAATATAATTTAATATAAAACTAAAAAATATTTTAACATAATTTAAA
52192928 ATAAAATATTTTAATATATTTAATATAAAAATAATTATATTAAATTTTTTATTAAATTATATATT
66 ATAAAATATTTTAATATATTTAATATAAAAATAATTATATT-AATTTTTTATTAAATTATATATT
52192993 TTTATTTTATTAAATTATA
130 TTTATTTTATTAAATTATA
52193012 AAAATATTTGAAATATTTTAATATAA
1 AAAATATTTGAAATATTTTAATATAA
52193038 AAATAATTAT
Statistics
Matches: 310, Mismatches: 11, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
147 70 0.23
148 116 0.37
149 124 0.40
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (148 bp):
AAAATATTTGAAATATTTTAATATAATTTAATATAAAACTAAAAAATATTTTAACATAATTTAAA
ATAAAATATTTTAATATATTTAATATAAAAATAATTATATTAATTTTTTATTAAATTATATATTT
TTATTTTATTAAATTATA
Found at i:52192842 original size:23 final size:23
Alignment explanation
Indices: 52192816--52192863 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
52192806 TAAAAATAAT
52192816 TATATTAATT-TTTTATTAAATTA
1 TATATT-ATTATTTTATTAAATTA
*
52192839 TATATTTTTATTTTATTAAATTA
1 TATATTATTATTTTATTAAATTA
52192862 TA
1 TA
52192864 AAAATATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TATATTATTATTTTATTAAATTA
Found at i:52192955 original size:24 final size:25
Alignment explanation
Indices: 52192905--52192957 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
52192895 TATAAACTAA
52192905 AAAATATTTTGACATAATTTAAAAT
1 AAAATATTTTGACATAATTTAAAAT
*
52192930 AAAATATTTT-A-ATATATTTAATAT
1 AAAATATTTTGACATA-ATTTAAAAT
52192954 AAAA
1 AAAA
52192958 ATAATTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 3 0.12
24 13 0.50
25 10 0.38
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (25 bp):
AAAATATTTTGACATAATTTAAAAT
Found at i:52192958 original size:25 final size:25
Alignment explanation
Indices: 52192904--52193042 Score: 77
Period size: 25 Copynumber: 5.3 Consensus size: 25
52192894 ATATAAACTA
*
52192904 AAAAATATTTTGACATA-ATTTAAAAT
1 AAAAATATTTT-A-ATATATTTAATAT
52192930 -AAAATATTTTAATATATTTAATAT
1 AAAAATATTTTAATATATTTAATAT
* * * **
52192954 AAAAATAATTATATTAAATTTTTTATT
1 AAAAAT-ATTTTAATATATTTAATA-T
* * *
52192981 AAATTATATATTTTTATTTTATTAAATTAT
1 AAA--A-ATA-TTTTAATATATTTAA-TAT
*
52193011 AAAAATATTTGAA-ATATTTTAATAT
1 AAAAATATTTTAATATA-TTTAATAT
52193036 AAAAATA
1 AAAAATA
52193043 ATTATATTAA
Statistics
Matches: 87, Mismatches: 16, Indels: 21
0.70 0.13 0.17
Matches are distributed among these distances:
23 3 0.03
24 9 0.10
25 27 0.31
26 21 0.24
27 7 0.08
28 1 0.01
29 2 0.02
30 15 0.17
31 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (25 bp):
AAAAATATTTTAATATATTTAATAT
Found at i:52193016 original size:82 final size:80
Alignment explanation
Indices: 52192930--52193080 Score: 223
Period size: 82 Copynumber: 1.9 Consensus size: 80
52192920 AATTTAAAAT
* ** * *
52192930 AAAATATTT-TAATATATTTAATATAAAAATAATTATATTAAATTTTTTATTAAATTATATATTT
1 AAAATATTTGAAATAT-TTTAATATAAAAATAATTATATTAAAAATGTCATTAAA-T-TATATTT
52192994 TTATTTTATTAAATTATA
63 TTATTTTATTAAATTATA
52193012 AAAATATTTGAAATATTTTAATATAAAAATAATTATATTAAAAATGTCATTAAATTATATTTTTA
1 AAAATATTTGAAATATTTTAATATAAAAATAATTATATTAAAAATGTCATTAAATTATATTTTTA
52193077 TTTT
66 TTTT
52193081 TTTATATTTA
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
80 14 0.22
81 1 0.02
82 43 0.68
83 5 0.08
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (80 bp):
AAAATATTTGAAATATTTTAATATAAAAATAATTATATTAAAAATGTCATTAAATTATATTTTTA
TTTTATTAAATTATA
Found at i:52193296 original size:16 final size:17
Alignment explanation
Indices: 52193277--52193308 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
52193267 GATTTATTCT
52193277 ATTACAGCTCT-TTTTC
1 ATTACAGCTCTATTTTC
52193293 ATTACAGCTCTATTTT
1 ATTACAGCTCTATTTT
52193309 TTTACAGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (17 bp):
ATTACAGCTCTATTTTC
Found at i:52196178 original size:3 final size:3
Alignment explanation
Indices: 52196170--52196240 Score: 124
Period size: 3 Copynumber: 23.7 Consensus size: 3
52196160 TGATTCTCCT
* *
52196170 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC ATC ATC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
52196218 TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TT
52196241 TAACCTAAGT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:52197822 original size:33 final size:33
Alignment explanation
Indices: 52197718--52197942 Score: 116
Period size: 33 Copynumber: 6.8 Consensus size: 33
52197708 GTTTCTTATT
* *
52197718 ATGCCATAGTCCAACTATGGTCTTA-CAT-ATGCA
1 ATGCCATAGCCCAGCTATGGTCTTATCATCA-G-A
* * * * * ** *
52197751 TTGCCATGGACCTGCCATGGTCTTATGTTCATA
1 ATGCCATAGCCCAGCTATGGTCTTATCATCAGA
* * *
52197784 GTGCCATAACCCAGTTATGGTCTTATCATCAGA
1 ATGCCATAGCCCAGCTATGGTCTTATCATCAGA
* * * *
52197817 ATGCCATAGCCCAACTATGGTCCTA-CATATAAA
1 ATGCCATAGCCCAGCTATGGTCTTATCAT-CAGA
* * * * * * *
52197850 CACTGTCATGGTCCAACCATGGTCTTA-CGTCCATA
1 -A-TGCCATAGCCCAGCTATGGTCTTATCAT-CAGA
* * * *
52197885 GTGCCATAACCCAGTTATGGTCTTATCATTAGA
1 ATGCCATAGCCCAGCTATGGTCTTATCATCAGA
52197918 ATGCCATAGCCCAGCTATGGTCTTA
1 ATGCCATAGCCCAGCTATGGTCTTA
52197943 CATATATACT
Statistics
Matches: 137, Mismatches: 49, Indels: 12
0.69 0.25 0.06
Matches are distributed among these distances:
32 3 0.02
33 106 0.77
34 4 0.03
35 24 0.18
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (33 bp):
ATGCCATAGCCCAGCTATGGTCTTATCATCAGA
Found at i:52197892 original size:101 final size:100
Alignment explanation
Indices: 52197718--52197978 Score: 362
Period size: 101 Copynumber: 2.6 Consensus size: 100
52197708 GTTTCTTATT
* * * ** * *
52197718 ATGCCATAGTCCAACTATGGTCTTACATAT-GCATTGCCATGGACCTGCCATGGTCTTATGTTCA
1 ATGCCATAGCCCAACTATGGTCTTACATATAACATTGCCATGGTCCAACCATGGTCTTACGTCCA
52197782 TAGTGCCATAACCCAGTTATGGTCTTATCATCAGA
66 TAGTGCCATAACCCAGTTATGGTCTTATCATCAGA
* * *
52197817 ATGCCATAGCCCAACTATGGTCCTACATATAAACACTGTCATGGTCCAACCATGGTCTTACGTCC
1 ATGCCATAGCCCAACTATGGTCTTACATAT-AACATTGCCATGGTCCAACCATGGTCTTACGTCC
*
52197882 ATAGTGCCATAACCCAGTTATGGTCTTATCATTAGA
65 ATAGTGCCATAACCCAGTTATGGTCTTATCATCAGA
* * * *
52197918 ATGCCATAGCCCAGCTATGGTCTTACATATATACTTTGCCATGGTCCAACTATGTTCTTAC
1 ATGCCATAGCCCAACTATGGTCTTACATATA-ACATTGCCATGGTCCAACCATGGTCTTAC
52197979 ATTTGAATAA
Statistics
Matches: 141, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
99 28 0.20
100 1 0.01
101 112 0.79
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.31
Consensus pattern (100 bp):
ATGCCATAGCCCAACTATGGTCTTACATATAACATTGCCATGGTCCAACCATGGTCTTACGTCCA
TAGTGCCATAACCCAGTTATGGTCTTATCATCAGA
Found at i:52201016 original size:26 final size:25
Alignment explanation
Indices: 52200962--52201016 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 25
52200952 TATATATATT
**
52200962 TTATGAAATTTTTATATTTGATATT
1 TTATGAAATTTTTATATTTGATAAA
*
52200987 TTATGAATATTTTTATAATTT-TTAAA
1 TTATGAA-ATTTTTAT-ATTTGATAAA
52201013 TTAT
1 TTAT
52201017 TTGTTGACGC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 7 0.28
26 14 0.56
27 4 0.16
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (25 bp):
TTATGAAATTTTTATATTTGATAAA
Found at i:52202222 original size:21 final size:22
Alignment explanation
Indices: 52202198--52202250 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 22
52202188 TTAATAATCA
*
52202198 AATTTAAGT-CAAAAATAAATT
1 AATTAAAGTACAAAAATAAATT
52202219 AATTAAAGTGACAAAAATAAATAAT
1 AATTAAAGT-ACAAAAATAAAT--T
52202244 AATTAAA
1 AATTAAA
52202251 TAGACAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 8 0.30
23 11 0.41
25 8 0.30
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (22 bp):
AATTAAAGTACAAAAATAAATT
Found at i:52202237 original size:23 final size:24
Alignment explanation
Indices: 52202207--52202259 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
52202197 AAATTTAAGT
52202207 CAAAAATAAAT-TAATTAAAGT-GA
1 CAAAAATAAATATAATTAAA-TAGA
52202230 CAAAAATAAATAATAATTAAATAGA
1 CAAAAATAAAT-ATAATTAAATAGA
52202255 CAAAA
1 CAAAA
52202260 TTTATCATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 11 0.41
24 1 0.04
25 15 0.56
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.23
Consensus pattern (24 bp):
CAAAAATAAATATAATTAAATAGA
Found at i:52202811 original size:24 final size:24
Alignment explanation
Indices: 52202782--52202829 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
52202772 AATTCATGGG
52202782 ACAGTCCCCTCCAATTTAATCCTA
1 ACAGTCCCCTCCAATTTAATCCTA
52202806 ACAGTCCCCTCCAATTTAATCCTA
1 ACAGTCCCCTCCAATTTAATCCTA
52202830 TCAGATTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.38, G:0.04, T:0.29
Consensus pattern (24 bp):
ACAGTCCCCTCCAATTTAATCCTA
Found at i:52206353 original size:14 final size:14
Alignment explanation
Indices: 52206336--52206367 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
52206326 TCCTATACTC
52206336 TCAATCCTCAATTT
1 TCAATCCTCAATTT
*
52206350 TCAATTCTCAATTT
1 TCAATCCTCAATTT
52206364 TCAA
1 TCAA
52206368 CTTTTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44
Consensus pattern (14 bp):
TCAATCCTCAATTT
Found at i:52206422 original size:25 final size:24
Alignment explanation
Indices: 52206384--52206431 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
52206374 TTAATTTTCT
*
52206384 CAAATTGTATACTTTATTTTACATTC
1 CAAATTGTACAC-TTA-TTTACATTC
52206410 CAAA-TGTACACTTATTTACATT
1 CAAATTGTACACTTATTTACATT
52206432 ATATGAAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 3 0.14
25 6 0.29
26 4 0.19
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (24 bp):
CAAATTGTACACTTATTTACATTC
Found at i:52217968 original size:16 final size:17
Alignment explanation
Indices: 52217936--52217975 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
52217926 AATCATTATC
52217936 AAATAATTACTAAAATAA
1 AAATAATTAC-AAAATAA
52217954 AAATAATTA-AAAATAA
1 AAATAATTACAAAATAA
*
52217970 TAATAA
1 AAATAA
52217976 ATGGTAGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.57
18 9 0.43
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (17 bp):
AAATAATTACAAAATAA
Found at i:52219059 original size:16 final size:16
Alignment explanation
Indices: 52219038--52219068 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52219028 GAAGAGATAA
*
52219038 AAATAAATAACGAAAC
1 AAATAAATAAAGAAAC
52219054 AAATAAATAAAGAAA
1 AAATAAATAAAGAAA
52219069 AATAAACAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.13
Consensus pattern (16 bp):
AAATAAATAAAGAAAC
Found at i:52225200 original size:27 final size:27
Alignment explanation
Indices: 52225161--52225406 Score: 257
Period size: 27 Copynumber: 9.2 Consensus size: 27
52225151 AATGGGCCTC
* *
52225161 TAAAATTACCGAAATACCCTTGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* * *
52225188 TAAAATGATCGAAATACCTTCGAAGAG
1 TAAAATGACCGAAATACCCTCGAAGGG
* *
52225215 TAAAATTATCGAAATACCCTCG-AGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
*
52225241 TAAAATGATCGAAATACCCTCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* * * *
52225268 TAAAATTATCAAAATACCCTCGAATGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* *
52225295 TAAAATGACCGAAATACCCTCAAAAGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* **
52225322 TAAAATGACCAAAATACCCT-GAAATG
1 TAAAATGACCGAAATACCCTCGAAGGG
* * *
52225348 TAAAATGACCAAAATACCC-CAAAAGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* *
52225374 TAAAATGACCAAAATACCC-CCATAGGG
1 TAAAATGACCGAAATACCCTCGA-AGGG
52225401 TAAAAT
1 TAAAAT
52225407 AACTGTTATA
Statistics
Matches: 192, Mismatches: 24, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
26 72 0.38
27 120 0.62
ACGTcount: A:0.46, C:0.20, G:0.15, T:0.20
Consensus pattern (27 bp):
TAAAATGACCGAAATACCCTCGAAGGG
Found at i:52225255 original size:53 final size:54
Alignment explanation
Indices: 52225161--52225366 Score: 247
Period size: 53 Copynumber: 3.9 Consensus size: 54
52225151 AATGGGCCTC
* * *
52225161 TAAAATTACCGAAATACCCTTGAAGGGTAAAATGATCGAAATACCTTCGAAGAG
1 TAAAATTATCGAAATACCCTCGAAGGGTAAAATGATCGAAATACCCTCGAAGAG
*
52225215 TAAAATTATCGAAATACCCTCG-AGGGTAAAATGATCGAAATACCCTCGAAGGG
1 TAAAATTATCGAAATACCCTCGAAGGGTAAAATGATCGAAATACCCTCGAAGAG
* * * *
52225268 TAAAATTATCAAAATACCCTCGAATGGTAAAATGACCGAAATACCCTC-AAAAGG
1 TAAAATTATCGAAATACCCTCGAAGGGTAAAATGATCGAAATACCCTCGAAGA-G
* * * ** * *
52225322 TAAAATGACCAAAATACCCT-GAAATGTAAAATGACCAAAATACCC
1 TAAAATTATCGAAATACCCTCGAAGGGTAAAATGATCGAAATACCC
52225367 CAAAAGGTAA
Statistics
Matches: 136, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
53 74 0.54
54 62 0.46
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.20
Consensus pattern (54 bp):
TAAAATTATCGAAATACCCTCGAAGGGTAAAATGATCGAAATACCCTCGAAGAG
Found at i:52225625 original size:26 final size:26
Alignment explanation
Indices: 52225562--52225625 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
52225552 TGTTACTATT
*
52225562 AGCTTTGCTGCGTTACTGATATTGGC
1 AGCTTTGCTGCGTTACTGATACTGGC
* *
52225588 AGCTCTACTGCGTTACT-ATTACTGGC
1 AGCTTTGCTGCGTTACTGA-TACTGGC
*
52225614 AGCTTTGTTGCG
1 AGCTTTGCTGCG
52225626 ATATTAGTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
25 1 0.03
26 30 0.97
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.38
Consensus pattern (26 bp):
AGCTTTGCTGCGTTACTGATACTGGC
Found at i:52225770 original size:30 final size:30
Alignment explanation
Indices: 52225733--52225848 Score: 133
Period size: 30 Copynumber: 3.9 Consensus size: 30
52225723 TACATTTGTA
52225733 CTGTTACTGTATTGGGCTAAGACCCACACT
1 CTGTTACTGTATTGGGCTAAGACCCACACT
* * *
52225763 TTGTTACTGTATTGGGCTAAGGCTCACACT
1 CTGTTACTGTATTGGGCTAAGACCCACACT
* * * *
52225793 CTGTTACTGTATTGGGCTATGGCCTACACA
1 CTGTTACTGTATTGGGCTAAGACCCACACT
** * *
52225823 CTACTACTGTATAGGGCTCAGACCCA
1 CTGTTACTGTATTGGGCTAAGACCCA
52225849 GACTGATTCT
Statistics
Matches: 71, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 71 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (30 bp):
CTGTTACTGTATTGGGCTAAGACCCACACT
Found at i:52226470 original size:25 final size:24
Alignment explanation
Indices: 52226434--52226531 Score: 99
Period size: 25 Copynumber: 4.0 Consensus size: 24
52226424 TACGAGCCAT
* * *
52226434 AATCAGTAAGCTCCTCCGAGCTGA
1 AATCGGTAAGCTCATACGAGCTGA
52226458 AATACGGTAAGCTCATACGAGCTGA
1 AAT-CGGTAAGCTCATACGAGCTGA
* * *
52226483 GAATCGTTAAGCTC-TCACGAGTTTCA
1 -AATCGGTAAGCTCAT-ACGAG-CTGA
52226509 AATCGGTAAGCTCATACGAGCTG
1 AATCGGTAAGCTCATACGAGCTG
52226532 TGGTGAGTTC
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
24 5 0.08
25 49 0.82
26 6 0.10
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.23
Consensus pattern (24 bp):
AATCGGTAAGCTCATACGAGCTGA
Found at i:52233108 original size:17 final size:17
Alignment explanation
Indices: 52233086--52233120 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
52233076 ATTACAAAAT
*
52233086 CAAATCTTATCAGATTA
1 CAAATCTTATAAGATTA
*
52233103 CAAATCTTCTAAGATTA
1 CAAATCTTATAAGATTA
52233120 C
1 C
52233121 TTTTCATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.34
Consensus pattern (17 bp):
CAAATCTTATAAGATTA
Found at i:52233857 original size:9 final size:8
Alignment explanation
Indices: 52233829--52233853 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
52233819 TATATTTCAT
52233829 ATATTAAA
1 ATATTAAA
52233837 ATATTAAA
1 ATATTAAA
52233845 ATATTAAA
1 ATATTAAA
52233853 A
1 A
52233854 ATATATGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
ATATTAAA
Found at i:52235710 original size:46 final size:45
Alignment explanation
Indices: 52235607--52235932 Score: 368
Period size: 46 Copynumber: 7.6 Consensus size: 45
52235597 TACGTATGAT
* *
52235607 CACTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTAT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAGGCTAC
52235650 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCT-AGGCTAC
* *
52235696 CACTTATCACTTTTTCACTTGATCAGATAAGTATAGCTGAGACTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCT-AGGCTAC
* *
52235742 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCT-AGGCTAC
**
52235788 CACTTATCACTTTGCCACTTGATCAGATAA--GTA--TA-G----
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAGGCTAC
*
52235824 CACTTATCACTTTTTCACTTGATCAAATAA--GTA--TA---T--
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAGGCTAC
*
52235860 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCT-AGGCTAC
* *
52235906 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTTTCACTTGATCAGA
52235933 AGTACTCAAA
Statistics
Matches: 252, Mismatches: 17, Indels: 25
0.86 0.06 0.09
Matches are distributed among these distances:
36 61 0.24
38 3 0.01
40 2 0.01
41 2 0.01
42 1 0.00
43 10 0.04
44 8 0.03
45 21 0.08
46 144 0.57
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (45 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAGGCTAC
Found at i:52235829 original size:36 final size:36
Alignment explanation
Indices: 52235788--52235896 Score: 173
Period size: 36 Copynumber: 3.0 Consensus size: 36
52235778 CTAAAGCTAC
**
52235788 CACTTATCACTTTGCCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
* *
52235824 CACTTATCACTTTTTCACTTGATCAAATAAGTATAT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
*
52235860 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
52235896 C
1 C
52235897 TAAAGCTACC
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (36 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
Found at i:52244065 original size:287 final size:287
Alignment explanation
Indices: 52243530--52244678 Score: 2266
Period size: 287 Copynumber: 4.0 Consensus size: 287
52243520 GATTATGAGC
52243530 ATTGACTCCCAATCTTGTC--TGATGAAAATTTTAATTCTGATCGAAATATTTATATCGACTTCT
1 ATTGACTCCCAATCTTGTCTGTGATGAAAATTTTAATTCTGATCGAAATATTTATATCGACTTCT
52243593 CTTCCACACCCTTTTTGGTAGGTGGAGATTGTCTGCCATATGGAGGCAGGGTTATAACGGTTAAG
66 CTTCCACACCCTTTTTGGTAGGTGGAGATTGTCTGCCATATGGAGGCAGGGTTATAACGGTTAAG
52243658 TATGGGGACTACACCCAAAGGATTGGTATCGACGGTACTACTGAAGCCATCAGAGAGGCAATTAA
131 TATGGGGACTACACCCAAAGGATTGGTATCGACGGTACTACTGAAGCCATCAGAGAGGCAATTAA
52243723 ATCTGCTTTTAGATTGAGAACTAAGCGTGCATTTTGGTTGGAGGATGAAGATCATATAATTCGTA
196 ATCTGCTTTTAGATTGAGAACTAAGCGTGCATTTTGGTTGGAGGATGAAGATCATATAATTCGTA
52243788 GTCTCGACAGGGAAATGCCTTTAGGGA
261 GTCTCGACAGGGAAATGCCTTTAGGGA
52243815 ATTGACTCCCAATCTTGTCTGTGATGAAAATTTTAATTCTGATCGAAATATTTATATCGACTTCT
1 ATTGACTCCCAATCTTGTCTGTGATGAAAATTTTAATTCTGATCGAAATATTTATATCGACTTCT
52243880 CTTCCACACCCTTTTTGGTAGGTGGAGATTGTCTGCCATATGGAGGCAGGGTTATAACGGTTAAG
66 CTTCCACACCCTTTTTGGTAGGTGGAGATTGTCTGCCATATGGAGGCAGGGTTATAACGGTTAAG
* *
52243945 TATGGGGACTACACCCAAAGGATTGGTATCTACGGTACTACTGAAGTCATCAGAGAGGCAATTAA
131 TATGGGGACTACACCCAAAGGATTGGTATCGACGGTACTACTGAAGCCATCAGAGAGGCAATTAA
52244010 ATCTGCTTTTAGATTGAGAACTAAGCGTGCATTTTGGTTGGAGGATGAAGATCATATAATTCGTA
196 ATCTGCTTTTAGATTGAGAACTAAGCGTGCATTTTGGTTGGAGGATGAAGATCATATAATTCGTA
52244075 GTCTCGACAGGGAAATGCCTTTAGGGA
261 GTCTCGACAGGGAAATGCCTTTAGGGA
52244102 ATTGACTCCCAATCTTGTCTGTGATGAAAATTTTAATTCTGATCGAAATATTTATATCGACTTCT
1 ATTGACTCCCAATCTTGTCTGTGATGAAAATTTTAATTCTGATCGAAATATTTATATCGACTTCT
52244167 CTTCCACACCCTTTTTGGTAGGTGGAGATTGTCTGCCATATGGAGGCAGGGTTATAACGGTTAAG
66 CTTCCACACCCTTTTTGGTAGGTGGAGATTGTCTGCCATATGGAGGCAGGGTTATAACGGTTAAG
52244232 TATGGGGACTACACCCAAAGGATTGGTATCGACGGTACTACTGAAGCCATCAGAGAGGCAATTAA
131 TATGGGGACTACACCCAAAGGATTGGTATCGACGGTACTACTGAAGCCATCAGAGAGGCAATTAA
52244297 ATCTGCTTTTAGATTGAGAACTAAGCGTGCATTTTGGTTGGAGGATGAAGATCATATAATTCGTA
196 ATCTGCTTTTAGATTGAGAACTAAGCGTGCATTTTGGTTGGAGGATGAAGATCATATAATTCGTA
52244362 GTCTCGACAGGGAAATGCCTTTAGGGA
261 GTCTCGACAGGGAAATGCCTTTAGGGA
52244389 ATTGACTCCCAATCTTGTCTGTGATGAAAATTTTAATTCTGATCGAAATATTTATATCGACTTCT
1 ATTGACTCCCAATCTTGTCTGTGATGAAAATTTTAATTCTGATCGAAATATTTATATCGACTTCT
52244454 CTTCCACACCCTTTTTGGTAGGTGGAGATTGTCTGCCATATGGAGGCAGGGTTATAACGGTTAAG
66 CTTCCACACCCTTTTTGGTAGGTGGAGATTGTCTGCCATATGGAGGCAGGGTTATAACGGTTAAG
52244519 TATGGGGACTACACCCAAAGGATTGGTATCGACGGTACTACTGAAGCCATCAGAGAGGCAATTAA
131 TATGGGGACTACACCCAAAGGATTGGTATCGACGGTACTACTGAAGCCATCAGAGAGGCAATTAA
52244584 ATCTGCTTTTAGATTGAGAACTAAGCGTGCATTTTGGTTGGAGGATGAAGATCATATAATTCGTA
196 ATCTGCTTTTAGATTGAGAACTAAGCGTGCATTTTGGTTGGAGGATGAAGATCATATAATTCGTA
52244649 GTCTCGACAGGGAAATGCCTTTAGGGA
261 GTCTCGACAGGGAAATGCCTTTAGGGA
52244676 ATT
1 ATT
52244679 ATAAACTCCA
Statistics
Matches: 858, Mismatches: 4, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
285 19 0.02
287 839 0.98
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (287 bp):
ATTGACTCCCAATCTTGTCTGTGATGAAAATTTTAATTCTGATCGAAATATTTATATCGACTTCT
CTTCCACACCCTTTTTGGTAGGTGGAGATTGTCTGCCATATGGAGGCAGGGTTATAACGGTTAAG
TATGGGGACTACACCCAAAGGATTGGTATCGACGGTACTACTGAAGCCATCAGAGAGGCAATTAA
ATCTGCTTTTAGATTGAGAACTAAGCGTGCATTTTGGTTGGAGGATGAAGATCATATAATTCGTA
GTCTCGACAGGGAAATGCCTTTAGGGA
Found at i:52248120 original size:17 final size:17
Alignment explanation
Indices: 52248090--52248124 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
52248080 TATTCTAGAC
*
52248090 ATTTTGTCATAAATTTT
1 ATTTTGTCAAAAATTTT
*
52248107 ATTTTTTCAAAAATTTT
1 ATTTTGTCAAAAATTTT
52248124 A
1 A
52248125 AATTTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (17 bp):
ATTTTGTCAAAAATTTT
Found at i:52248273 original size:49 final size:49
Alignment explanation
Indices: 52248213--52248325 Score: 124
Period size: 49 Copynumber: 2.3 Consensus size: 49
52248203 TTAAGTTTTC
* *
52248213 TTTTTGCAATTTTTGTAAATTTA-A-ATACCT-TTTTAAAAATTTTTATATT
1 TTTTTG-AATTTTT-TAAATTTATATATACATATTTTAAAAATTTATATA-T
* * *
52248262 TATTTTGAATTTTTAAAATTTATATTTACATATTTTAGAAATTTATATAT
1 T-TTTTGAATTTTTTAAATTTATATATACATATTTTAAAAATTTATATAT
52248312 TTTTTGAATTTTTT
1 TTTTTGAATTTTTT
52248326 TAAAAAAATT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
48 7 0.13
49 21 0.39
50 11 0.20
51 15 0.28
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (49 bp):
TTTTTGAATTTTTTAAATTTATATATACATATTTTAAAAATTTATATAT
Found at i:52249604 original size:20 final size:20
Alignment explanation
Indices: 52249588--52249626 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
52249578 GATAATTACG
52249588 CTTATTTTCTTTAAATTAAGA
1 CTTATTTT-TTTAAATTAAGA
*
52249609 GTTATTTTTTTAAATTAA
1 CTTATTTTTTTAAATTAA
52249627 TGTATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.56
Consensus pattern (20 bp):
CTTATTTTTTTAAATTAAGA
Found at i:52249641 original size:21 final size:20
Alignment explanation
Indices: 52249597--52249641 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
52249587 GCTTATTTTC
*
52249597 TTTAAATTAAGAGTTATTTT
1 TTTAAATTAAGAGTTATTTA
52249617 TTTAAATTAATGTA-TTATTTA
1 TTTAAATTAA-G-AGTTATTTA
52249638 TTTA
1 TTTA
52249642 TTTTATTACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 10 0.45
21 11 0.50
22 1 0.05
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (20 bp):
TTTAAATTAAGAGTTATTTA
Found at i:52250431 original size:18 final size:17
Alignment explanation
Indices: 52250399--52250443 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
52250389 CTTGTTTTCA
*
52250399 TTTTATTGTTTTTATATC
1 TTTTATT-TTATTATATC
*
52250417 TTTTTATTTTATTATCTC
1 -TTTTATTTTATTATATC
52250435 TTTTATTTT
1 TTTTATTTT
52250444 CGTTTTTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.38
18 8 0.33
19 7 0.29
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTTATTTTATTATATC
Found at i:52250432 original size:16 final size:16
Alignment explanation
Indices: 52250408--52250443 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
52250398 ATTTTATTGT
52250408 TTTTATATCT-TTTTA
1 TTTTATATCTCTTTTA
52250423 TTTTATTATCTCTTTTA
1 TTTTA-TATCTCTTTTA
52250440 TTTT
1 TTTT
52250444 CGTTTTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 5 0.26
17 9 0.47
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTATATCTCTTTTA
Found at i:52255109 original size:14 final size:13
Alignment explanation
Indices: 52255076--52255111 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
52255066 TGGAGGCAAT
52255076 AAAAAAACAAAAA
1 AAAAAAACAAAAA
52255089 AACAAAAACAAAAA
1 AA-AAAAACAAAAA
52255103 ATAAAAAAC
1 A-AAAAAAC
52255112 CTCTACTGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.10
14 18 0.86
15 1 0.05
ACGTcount: A:0.86, C:0.11, G:0.00, T:0.03
Consensus pattern (13 bp):
AAAAAAACAAAAA
Found at i:52255565 original size:13 final size:13
Alignment explanation
Indices: 52255547--52255589 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
52255537 TCATTTGAAA
52255547 AAAAAATGAAAAG
1 AAAAAATGAAAAG
52255560 AAAAAA-GAAAAG
1 AAAAAATGAAAAG
52255572 -AAAAATGAAAAAG
1 AAAAAATG-AAAAG
52255585 AAAAA
1 AAAAA
52255590 GGAGAGGCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 5 0.19
12 7 0.26
13 11 0.41
14 4 0.15
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (13 bp):
AAAAAATGAAAAG
Found at i:52255569 original size:12 final size:12
Alignment explanation
Indices: 52255542--52255589 Score: 71
Period size: 12 Copynumber: 4.0 Consensus size: 12
52255532 ATACTTCATT
52255542 TGAAAA-AAAAA
1 TGAAAAGAAAAA
52255553 TGAAAAGAAAAA
1 TGAAAAGAAAAA
*
52255565 AGAAAAGAAAAA
1 TGAAAAGAAAAA
52255577 TGAAAAAGAAAAA
1 TG-AAAAGAAAAA
52255590 GGAGAGGCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
11 6 0.18
12 17 0.52
13 10 0.30
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (12 bp):
TGAAAAGAAAAA
Found at i:52255570 original size:18 final size:17
Alignment explanation
Indices: 52255543--52255588 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
52255533 TACTTCATTT
52255543 GAAAAA-AAAATG-AAAA
1 GAAAAAGAAAA-GAAAAA
52255559 GAAAAAAGAAAAGAAAAA
1 G-AAAAAGAAAAGAAAAA
52255577 TGAAAAAGAAAA
1 -GAAAAAGAAAA
52255589 AGGAGAGGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 1 0.04
17 6 0.23
18 18 0.69
19 1 0.04
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.04
Consensus pattern (17 bp):
GAAAAAGAAAAGAAAAA
Found at i:52255580 original size:24 final size:24
Alignment explanation
Indices: 52255543--52255589 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
52255533 TACTTCATTT
52255543 GAAAAAAAAATG-AAAAGAAAAAA
1 GAAAAAAAAATGAAAAAGAAAAAA
52255566 GAAAAGAAAAATGAAAAAGAAAAA
1 GAAAA-AAAAATGAAAAAGAAAAA
52255590 GGAGAGGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 5 0.23
24 7 0.32
25 10 0.45
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (24 bp):
GAAAAAAAAATGAAAAAGAAAAAA
Found at i:52255989 original size:38 final size:38
Alignment explanation
Indices: 52255947--52256023 Score: 138
Period size: 38 Copynumber: 2.0 Consensus size: 38
52255937 GTTATCTTGA
52255947 TTGATTCATTCATTTCGAGCTTTGTTCTCAACAA-AACT
1 TTGATTCATTCATTTCGAGCTTTGTTCTCAA-AATAACT
52255985 TTGATTCATTCATTTCGAGCTTTGTTCTCAAAATAACT
1 TTGATTCATTCATTTCGAGCTTTGTTCTCAAAATAACT
52256023 T
1 T
52256024 CATCTTGTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 2 0.05
38 36 0.95
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.44
Consensus pattern (38 bp):
TTGATTCATTCATTTCGAGCTTTGTTCTCAAAATAACT
Found at i:52256953 original size:50 final size:50
Alignment explanation
Indices: 52256880--52257160 Score: 179
Period size: 50 Copynumber: 5.6 Consensus size: 50
52256870 GCAGTGGAGT
* * * * *
52256880 AGATTAAAGCTACAACGGCAAATCTTGCTTCCCCGACATTACAATTTAAA
1 AGATTGAAGCTGCAACGGTAAATCTTACTTCCCCGACATTGCAATTTAAA
* * ** * * ** **
52256930 AGATTGAAGCCGCAATGGTAAATCTTACTTCCATGGCGA-TGCAGTAGAGC
1 AGATTGAAGCTGCAACGGTAAATCTTACTTCCCCGAC-ATTGCAATTTAAA
* * * * * *
52256980 AGATTAAAGCTACAACAGCAAATCTTGCTTCCCTGACATTGCAATTTAAA
1 AGATTGAAGCTGCAACGGTAAATCTTACTTCCCCGACATTGCAATTTAAA
* * * * * * ** **
52257030 AGATTGAAGCCGCAACGGCAAATCTTACATCCACGGCGA-TGCAGTGGAGC
1 AGATTGAAGCTGCAACGGTAAATCTTACTTCCCCGAC-ATTGCAATTTAAA
* * * * * *
52257080 AGATTAAAGCTACAATGGTGAATCTTGCTTCTCCGACATTGCAATTTAAA
1 AGATTGAAGCTGCAACGGTAAATCTTACTTCCCCGACATTGCAATTTAAA
* *
52257130 AGATTGAGGCTGCAACGGTAGATCTTACTTC
1 AGATTGAAGCTGCAACGGTAAATCTTACTTC
52257161 TCTGGTGGTG
Statistics
Matches: 161, Mismatches: 66, Indels: 8
0.69 0.28 0.03
Matches are distributed among these distances:
49 2 0.01
50 157 0.98
51 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (50 bp):
AGATTGAAGCTGCAACGGTAAATCTTACTTCCCCGACATTGCAATTTAAA
Found at i:52257030 original size:100 final size:99
Alignment explanation
Indices: 52256869--52257212 Score: 447
Period size: 100 Copynumber: 3.4 Consensus size: 99
52256859 TCCCTGGTAG
* * *
52256869 TGCAGTGGAGTAGATTAAAGCTACAACGGCAAATCTTGCTTCCCCGACATTACAATTTAAAAGAT
1 TGCAGTGGAGCAGATTAAAGCTACAACAGCAAATCTTGCTT-CCCGACATTGCAATTTAAAAGAT
*
52256934 TGAAGCCGCAATGGTAAATCTTACTTCCATGGCGA
65 TGAAGCCGCAACGGTAAATCTTACTTCCATGGCGA
*
52256969 TGCAGTAGAGCAGATTAAAGCTACAACAGCAAATCTTGCTTCCCTGACATTGCAATTTAAAAGAT
1 TGCAGTGGAGCAGATTAAAGCTACAACAGCAAATCTTGCTTCCC-GACATTGCAATTTAAAAGAT
* * *
52257034 TGAAGCCGCAACGGCAAATCTTACATCCACGGCGA
65 TGAAGCCGCAACGGTAAATCTTACTTCCATGGCGA
** **
52257069 TGCAGTGGAGCAGATTAAAGCTACAATGGTGAATCTTGCTTCTCCGACATTGCAATTTAAAAGAT
1 TGCAGTGGAGCAGATTAAAGCTACAACAGCAAATCTTGCTTC-CCGACATTGCAATTTAAAAGAT
* * * * *
52257134 TGAGGCTGCAACGGTAGATCTTACTTCTC-TGGTGG
65 TGAAGCCGCAACGGTAAATCTTACTTC-CATGGCGA
* * * * *
52257169 TGTAATGGAACAGATTGAAGCTACAACAGCGAATCTTGCTTCCC
1 TGCAGTGGAGCAGATTAAAGCTACAACAGCAAATCTTGCTTCCC
52257213 CGGCATCGCA
Statistics
Matches: 213, Mismatches: 28, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
99 5 0.02
100 205 0.96
101 3 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (99 bp):
TGCAGTGGAGCAGATTAAAGCTACAACAGCAAATCTTGCTTCCCGACATTGCAATTTAAAAGATT
GAAGCCGCAACGGTAAATCTTACTTCCATGGCGA
Found at i:52257326 original size:45 final size:45
Alignment explanation
Indices: 52257254--52257901 Score: 801
Period size: 45 Copynumber: 14.4 Consensus size: 45
52257244 ACATTACAGA
*
52257254 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGA-TCAAAGATAGCAAG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACT-GAAGATAGCAAG
* * *
52257299 TCTTATCTTCCTGTATTAGCAGTGAAGTAGACTGAAGATAGCAAG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAGCAAG
* *
52257344 TCTTGTCTTCCTGTATTGGAAGCGAAGTAGACTGAAGATAAC-AG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAGCAAG
*
52257388 ATCTTGTCTTCCTGTATTGGCAGCGAAGTAGA-TCAAAGATAGCAAG
1 -TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACT-GAAGATAGCAAG
* * * * * *
52257434 TTTTGTCTTCCTATATTGGAAGCAAAGTAGACTGAAGATAACAAA
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAGCAAG
* * * *
52257479 TCTTGTCTTTCTGTATTGGCAACGAAGTAGA-TCGAAGATTGTAAG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACT-GAAGATAGCAAG
* * *
52257524 TCTTATCTTCCTGTATTAGCAGCGAAGTTGACTGAAGATAGCAAG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAGCAAG
* *
52257569 TCTTGTCTTCCTGTATTGGTAGCGAAGTAGACTGAAGATAAC-AG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAGCAAG
* * * * *
52257613 ATCTTGTGTTCATATATTGGCAGCGAAGTAGATTAAAGATAGCAAG
1 -TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAGCAAG
*
52257659 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAAC-AG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAGCAAG
* **
52257703 ATATTGTCTTCCTGTATTTACAGCGAAGTAGACTGAAGATAGCAAG
1 -TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAGCAAG
* *
52257749 TCTTGTCTTCCTGTATTAGCAGCGAAGTAGACTGAAGATAACATA-
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAGCA-AG
*
52257794 TCTTGTCTTCCTGTATTGGCAGCAAAGTAGA-TCGAAGATAGCAAG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACT-GAAGATAGCAAG
* * * *
52257839 TCTTGTCTTCCTATATTAGCAGTGAAGTAGACTGAAGATAAC-AG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAGCAAG
*
52257883 ATCTTGCCTTCCTGTATTG
1 -TCTTGTCTTCCTGTATTG
52257902 ATGGCGAAGT
Statistics
Matches: 514, Mismatches: 73, Indels: 32
0.83 0.12 0.05
Matches are distributed among these distances:
44 12 0.02
45 491 0.96
46 11 0.02
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (45 bp):
TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAGCAAG
Found at i:52258047 original size:50 final size:50
Alignment explanation
Indices: 52257993--52258088 Score: 147
Period size: 50 Copynumber: 1.9 Consensus size: 50
52257983 GTAGTGGAAC
* **
52257993 AGATTAAAGCTACAACGGCGAATCTTGTTTCCCCAACATTGCAATTTAAA
1 AGATTAAAGCTACAACGACGAATCTTACTTCCCCAACATTGCAATTTAAA
* *
52258043 AGATTGAAGCTACGACGACGAATCTTACTTCCCCAACATTGCAATT
1 AGATTAAAGCTACAACGACGAATCTTACTTCCCCAACATTGCAATT
52258089 AAACATATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (50 bp):
AGATTAAAGCTACAACGACGAATCTTACTTCCCCAACATTGCAATTTAAA
Found at i:52258157 original size:44 final size:43
Alignment explanation
Indices: 52258109--52258735 Score: 264
Period size: 44 Copynumber: 14.6 Consensus size: 43
52258099 AAGCCAAGCC
* * *
52258109 TATCTACTTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCT
1 TATCTCCTTGAAGTTGCAGTGGAGCAGA-CAAAACCACAGATCT
* * ** *
52258153 TATCTCTTTGAAGTTGCAGTAGAGCAGATC-GCATC-CAG-TCT
1 TATCTCCTTGAAGTTGCAGTGGAGCAGA-CAAAACCACAGATCT
** * ** *
52258194 TATCT-CTCT-AAGCAGTAGTGGAGCAGACAAAAGAAACCA-ATCC
1 TATCTCCT-TGAAGTTGCAGTGGAGCAGACAAAA-CCA-CAGATCT
* * * * *
52258237 TATCTCCCTAAAGTTGTAGTGGAGCGGATCAAAACTACAGATCT
1 TATCTCCTTGAAGTTGCAGTGGAGCAGA-CAAAACCACAGATCT
* * **
52258281 TATCT-CTCTAAAGTTGCAGTAGAGCA-A-ATTA-CATCTAG-TCT
1 TATCTCCT-TGAAGTTGCAGTGGAGCAGACAAAACCA-C-AGATCT
* * ** *
52258322 TATCTCCTTGAAGTTTCAGTGAAGCAGACAAAAGAAACCA-ATCC
1 TATCTCCTTGAAGTTGCAGTGGAGCAGACAAAA-CCA-CAGATCT
**
52258366 TATCTCCTTGAAGTTGCAGTGGAGTGGATCAAAACCACAGATCT
1 TATCTCCTTGAAGTTGCAGTGGAGCAGA-CAAAACCACAGATCT
** * * *
52258410 TATCT-CTCTGAAGTTGCAGTAAAGTAGATC-ACATC-CAG-TCT
1 TATCTCCT-TGAAGTTGCAGTGGAGCAGA-CAAAACCACAGATCT
* * * * ** *
52258451 TATCTCCCTAAATTTTCAGTGGAGCAGACAAAAGAAACCA-ATCC
1 TATCTCCTTGAAGTTGCAGTGGAGCAGACAAAA-CCA-CAGATCT
* * **
52258495 TATCTCCCTGAAGTTGTAGTGGAGTGGATCAAAACCACAGATCT
1 TATCTCCTTGAAGTTGCAGTGGAGCAGA-CAAAACCACAGATCT
* * * *
52258539 TATCT-CTCTGAAGTTGCAATAGAGCAGATC-ACATC-CAG-TCT
1 TATCTCCT-TGAAGTTGCAGTGGAGCAGA-CAAAACCACAGATCT
* * * ** *
52258580 TATCTCCCTAAAGTTTCAGTGGAGCAGACAAAAGAAACCA-ATCC
1 TATCTCCTTGAAGTTGCAGTGGAGCAGACAAAA-CCA-CAGATCT
* *
52258624 TATCTCCCTGAAGTTGCAGTGGAGCGGATCAAAACCACATG-TCT
1 TATCTCCTTGAAGTTGCAGTGGAGCAGA-CAAAACCACA-GATCT
* ** * *
52258668 TATCT-CTCTGAAGTTGCAGTAGAGCAGATC-GCATCA-AG-CCT
1 TATCTCCT-TGAAGTTGCAGTGGAGCAGA-CAAAACCACAGATCT
*
52258709 TATCTCCCTGAAGTTGCAGTGGAGCAG
1 TATCTCCTTGAAGTTGCAGTGGAGCAG
52258736 GTTGAAGATA
Statistics
Matches: 436, Mismatches: 105, Indels: 87
0.69 0.17 0.14
Matches are distributed among these distances:
39 1 0.00
40 19 0.04
41 110 0.25
42 18 0.04
43 37 0.08
44 229 0.53
45 22 0.05
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (43 bp):
TATCTCCTTGAAGTTGCAGTGGAGCAGACAAAACCACAGATCT
Found at i:52258455 original size:85 final size:85
Alignment explanation
Indices: 52258117--52258735 Score: 373
Period size: 85 Copynumber: 7.2 Consensus size: 85
52258107 CCTATCTACT
* * **
52258117 TGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTTTGAAGTTGCAGTAGAGCAGAT
1 TGAAGTTGCAGTGGAGCAGATCAAAACCACAG-TCTTATCTCCCTGAAGTTGCAGTAGAGCAGAT
** *
52258182 C-GCATCCAGTCTTATCTCTC
65 CAAAATCCAGTCTTATCTCCC
** * ** * * * * * *
52258202 T-AAGCAGTAGTGGAGCAGA-CAAAAGAAACCAATCCTATCTCCCTAAAGTTGTAGTGGAGCGGA
1 TGAAGTTGCAGTGGAGCAGATCAAAA-CCA-CAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGA
* *
52258265 TCAAAACTACAGATCTTATCTCTC
64 TCAAAA-TCCAG-TCTTATCTCCC
* * * * * * * * *
52258289 TAAAGTTGCAGTAGAGCAAAT-TACATC-TAGTCTTATCTCCTTGAAGTTTCAGT-GAAGCAGA-
1 TGAAGTTGCAGTGGAGCAGATCAAAACCACAGTCTTATCTCCCTGAAGTTGCAGTAG-AGCAGAT
* * * *
52258350 CAAAAGAAACCAATCCTATCTCCT
65 C--AA-AATCCAGTCTTATCTCCC
** * * *
52258374 TGAAGTTGCAGTGGAGTGGATCAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAAAGTAGAT
1 TGAAGTTGCAGTGGAGCAGATCAAAACCACAG-TCTTATCTCCCTGAAGTTGCAGTAGAGCAGAT
*
52258439 C-ACATCCAGTCTTATCTCCC
65 CAAAATCCAGTCTTATCTCCC
* * * ** * * * * **
52258459 TAAATTTTCAGTGGAGCAGA-CAAAAGAAACCAATCCTATCTCCCTGAAGTTGTAGTGGAGTGGA
1 TGAAGTTGCAGTGGAGCAGATCAAAA-CCA-CAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGA
* *
52258523 TCAAAACCACAGATCTTATCTCTC
64 TCAAAATC-CAG-TCTTATCTCCC
* * * * * * *
52258547 TGAAGTTGCAATAGAGCAGATC-ACATC-CAGTCTTATCTCCCTAAAGTTTCAGTGGAGCAGA-C
1 TGAAGTTGCAGTGGAGCAGATCAAAACCACAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGATC
* * *
52258609 AAAAGAAACCAATCCTATCTCCC
66 --AA-AATCCAGTCTTATCTCCC
* *
52258632 TGAAGTTGCAGTGGAGCGGATCAAAACCACATGTCTTATCTCTCTGAAGTTGCAGTAGAGCAGAT
1 TGAAGTTGCAGTGGAGCAGATCAAAACCACA-GTCTTATCTCCCTGAAGTTGCAGTAGAGCAGAT
** * *
52258697 C-GCATCAAGCCTTATCTCCC
65 CAAAATCCAGTCTTATCTCCC
52258717 TGAAGTTGCAGTGGAGCAG
1 TGAAGTTGCAGTGGAGCAG
52258736 GTTGAAGATA
Statistics
Matches: 392, Mismatches: 113, Indels: 58
0.70 0.20 0.10
Matches are distributed among these distances:
83 4 0.01
84 49 0.12
85 193 0.49
86 24 0.06
87 24 0.06
88 95 0.24
89 3 0.01
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (85 bp):
TGAAGTTGCAGTGGAGCAGATCAAAACCACAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGATC
AAAATCCAGTCTTATCTCCC
Found at i:52258751 original size:129 final size:129
Alignment explanation
Indices: 52258102--52258735 Score: 943
Period size: 129 Copynumber: 4.9 Consensus size: 129
52258092 CATATAAAAG
* * * * *
52258102 CCAAGCCTATCTACTTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTTTGAAGT
1 CCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATCAAAACCACAGATCTTATCTCTCTGAAGT
* *
52258167 TGCAGTAGAGCAGATCGCATCCAGTCTTATCTCTCTAAGCAG--T-AGTGGAGCAGACAAAAGAA
66 TGCAGTAGAGCAGATCACATCCAGTCTTATCTCCCTAA--AGTTTCAGTGGAGCAGACAAAAGAA
52258229 A
129 A
* * * *
52258230 CCAATCCTATCTCCCTAAAGTTGTAGTGGAGCGGATCAAAACTACAGATCTTATCTCTCTAAAGT
1 CCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATCAAAACCACAGATCTTATCTCTCTGAAGT
* * * * * *
52258295 TGCAGTAGAGCAAATTACATCTAGTCTTATCTCCTTGAAGTTTCAGTGAAGCAGACAAAAGAAA
66 TGCAGTAGAGCAGATCACATCCAGTCTTATCTCCCTAAAGTTTCAGTGGAGCAGACAAAAGAAA
* *
52258359 CCAATCCTATCTCCTTGAAGTTGCAGTGGAGTGGATCAAAACCACAGATCTTATCTCTCTGAAGT
1 CCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATCAAAACCACAGATCTTATCTCTCTGAAGT
* * *
52258424 TGCAGTAAAGTAGATCACATCCAGTCTTATCTCCCTAAATTTTCAGTGGAGCAGACAAAAGAAA
66 TGCAGTAGAGCAGATCACATCCAGTCTTATCTCCCTAAAGTTTCAGTGGAGCAGACAAAAGAAA
* *
52258488 CCAATCCTATCTCCCTGAAGTTGTAGTGGAGTGGATCAAAACCACAGATCTTATCTCTCTGAAGT
1 CCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATCAAAACCACAGATCTTATCTCTCTGAAGT
*
52258553 TGCAATAGAGCAGATCACATCCAGTCTTATCTCCCTAAAGTTTCAGTGGAGCAGACAAAAGAAA
66 TGCAGTAGAGCAGATCACATCCAGTCTTATCTCCCTAAAGTTTCAGTGGAGCAGACAAAAGAAA
52258617 CCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATCAAAACCACATG-TCTTATCTCTCTGAAG
1 CCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATCAAAACCACA-GATCTTATCTCTCTGAAG
* * * * *
52258681 TTGCAGTAGAGCAGATCGCATCAAGCCTTATCTCCCTGAAGTTGCAGTGGAGCAG
65 TTGCAGTAGAGCAGATCACATCCAGTCTTATCTCCCTAAAGTTTCAGTGGAGCAG
52258736 GTTGAAGATA
Statistics
Matches: 456, Mismatches: 46, Indels: 7
0.90 0.09 0.01
Matches are distributed among these distances:
126 2 0.00
128 88 0.19
129 365 0.80
130 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.26
Consensus pattern (129 bp):
CCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATCAAAACCACAGATCTTATCTCTCTGAAGT
TGCAGTAGAGCAGATCACATCCAGTCTTATCTCCCTAAAGTTTCAGTGGAGCAGACAAAAGAAA
Found at i:52259443 original size:10 final size:10
Alignment explanation
Indices: 52259428--52259459 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
52259418 CATTTTATTG
52259428 TTTTTATCTC
1 TTTTTATCTC
52259438 TTTTTAT-T-
1 TTTTTATCTC
52259446 TTTTTATCTC
1 TTTTTATCTC
52259456 TTTT
1 TTTT
52259460 ATTTTCGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.35
9 2 0.10
10 11 0.55
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTATCTC
Found at i:52259464 original size:16 final size:18
Alignment explanation
Indices: 52259420--52259464 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 18
52259410 CTTGTTTTCA
52259420 TTTTATTGTTTTTATCTCT
1 TTTTATT-TTTTTATCTCT
52259439 TTTTATTTTTTTATCTC-
1 TTTTATTTTTTTATCTCT
52259456 TTTTATTTT
1 TTTTATTTT
52259465 CGTTTTTGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 9 0.35
18 10 0.38
19 7 0.27
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTATTTTTTTATCTCT
Found at i:52261778 original size:17 final size:18
Alignment explanation
Indices: 52261756--52261792 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
52261746 ATGTCTATAA
*
52261756 AAGATATTAT-TTATTAT
1 AAGATATCATCTTATTAT
52261773 AAGATATCATCTTATTAT
1 AAGATATCATCTTATTAT
52261791 AA
1 AA
52261793 AATAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (18 bp):
AAGATATCATCTTATTAT
Found at i:52272843 original size:229 final size:229
Alignment explanation
Indices: 52272334--52272956 Score: 806
Period size: 229 Copynumber: 2.7 Consensus size: 229
52272324 TATTGAGAAA
* *
52272334 CGCCGCAAATAAGTTAAGCAAAACGACGTTGTTTTCTGTTGAGGTATAGGGACATTAGCGTCGCT
1 CGCCGCTAATAAGTTAAGCAAAACGACGTTGTTTTCTGTTGAGGTATAGGGACATTAGCGGCGCT
* * * * * * * * * *
52272399 TTCTATAAAACGCCACTAAATGTTAGGTAATAGCAGCGCACGTAAACAAACACTGCAAAAAATTT
66 TTTTGTAAAACGCCGCTAAAGGTTAGGTGATAGCGGCGCATGTAAACAAACGCCGC--AAAAGTT
* *
52272464 GATC-AAAATGGCAGCATTTTATTTCTTCGTTTTACTTAATTTAATGGCATTTTTTCTAAAAACG
129 GATCAAAAACGGCAGCATTTTATTTCTTCGCTTTACTTAATTTAATGGCA-TTTTTCTAAAAACG
* * * *
52272528 TCGCAACTTTCGGGCTTTACTAGCGCTTTTCTAAAAG
193 CCGCAACTTTCGAGCTTTACGAGCGCTTTTCCAAAAG
* * * * *
52272565 CGTCGCTAGTAAGTTAAGAAAAACGACATTGTTTTCTGTTGATGTATAGGGACATTAGCGGCGCT
1 CGCCGCTAATAAGTTAAGCAAAACGACGTTGTTTTCTGTTGAGGTATAGGGACATTAGCGGCGCT
* * *
52272630 TTTTGTAAAATGCCGCTAAAGGTTAGGTGATAGCGGCGCATGTAAACAGATGCCGCATAAAGTTG
66 TTTTGTAAAACGCCGCTAAAGGTTAGGTGATAGCGGCGCATGTAAACAAACGCCGCA-AAAGTTG
* *
52272695 ATCAAAAACGGCAGCATTTTATTTCTTCGCTTTACTTGATTTAGTGGCGA-TTTT-TAAAAACGC
130 ATCAAAAACGGCAGCATTTTATTTCTTCGCTTTACTTAATTTAATGGC-ATTTTTCTAAAAACGC
*
52272758 CGCAACTTTCGATCTTTACCGA-CGCTTTTCCAAAAG
194 CGCAACTTTCGAGCTTTA-CGAGCGCTTTTCCAAAAG
* * *
52272794 TGCCGTTAATAAGTTAAGCAAAACGACGTTGTTTTCTGTTGAGGTATAGGTACATTAGCGGCGCT
1 CGCCGCTAATAAGTTAAGCAAAACGACGTTGTTTTCTGTTGAGGTATAGGGACATTAGCGGCGCT
* *
52272859 TTTTGTAAAACGCCGCTAAAGGTTAGGTGTTAGCGGCGCATATAAACAAACGCCGCAAATATGTT
66 TTTTGTAAAACGCCGCTAAAGGTTAGGTGATAGCGGCGCATGTAAACAAACGCCGCAAA-A-GTT
* * *
52272924 GA-CAAAAACGGTAGCGTTTTATTTCTTTGCTTT
129 GATCAAAAACGGCAGCATTTTATTTCTTCGCTTT
52272957 GCTAATAAGT
Statistics
Matches: 341, Mismatches: 45, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
228 2 0.01
229 176 0.52
230 20 0.06
231 142 0.42
232 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (229 bp):
CGCCGCTAATAAGTTAAGCAAAACGACGTTGTTTTCTGTTGAGGTATAGGGACATTAGCGGCGCT
TTTTGTAAAACGCCGCTAAAGGTTAGGTGATAGCGGCGCATGTAAACAAACGCCGCAAAAGTTGA
TCAAAAACGGCAGCATTTTATTTCTTCGCTTTACTTAATTTAATGGCATTTTTCTAAAAACGCCG
CAACTTTCGAGCTTTACGAGCGCTTTTCCAAAAG
Found at i:52273360 original size:21 final size:22
Alignment explanation
Indices: 52273336--52273384 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
52273326 TAGTTTATGT
52273336 TTTATGAGTCAA-GGTTTAAGG
1 TTTATGAGTCAAGGGTTTAAGG
* *
52273357 TTTACGAGTTAAGGGTTTAAGG
1 TTTATGAGTCAAGGGTTTAAGG
*
52273379 ATTATG
1 TTTATG
52273385 GTTTGTGCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.39
Consensus pattern (22 bp):
TTTATGAGTCAAGGGTTTAAGG
Found at i:52273421 original size:21 final size:20
Alignment explanation
Indices: 52273395--52273433 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
52273385 GTTTGTGCAC
*
52273395 GGTTTATGGTTCAAGGGTTGG
1 GGTTTAAGGTT-AAGGGTTGG
52273416 GGTTTAAGGTTAAGGGTT
1 GGTTTAAGGTTAAGGGTT
52273434 TAGGATTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.18, C:0.03, G:0.41, T:0.38
Consensus pattern (20 bp):
GGTTTAAGGTTAAGGGTTGG
Found at i:52273572 original size:22 final size:22
Alignment explanation
Indices: 52273545--52273586 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
52273535 GGTTTAGAGG
52273545 TTAAGGATTAAGGG-ATAAGGTT
1 TTAAGGATT-AGGGTATAAGGTT
*
52273567 TTAAGGGTTAGGGTATAAGG
1 TTAAGGATTAGGGTATAAGG
52273587 GCTGGGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.31
Consensus pattern (22 bp):
TTAAGGATTAGGGTATAAGGTT
Found at i:52279441 original size:21 final size:21
Alignment explanation
Indices: 52279417--52279506 Score: 71
Period size: 21 Copynumber: 4.3 Consensus size: 21
52279407 CCTGCATAAT
52279417 AACTTACATAACTTATATATA
1 AACTTACATAACTTATATATA
* * *
52279438 AACTTAAATAAAATTTTTATATA
1 AACTTACAT--AACTTATATATA
* *
52279461 AAC-TA-ATTACATA-ATGCAT-
1 AACTTACATAACTTATAT--ATA
52279480 AACTTACATAACTTATATATA
1 AACTTACATAACTTATATATA
52279501 AACTTA
1 AACTTA
52279507 TATATAAACT
Statistics
Matches: 52, Mismatches: 9, Indels: 16
0.68 0.12 0.21
Matches are distributed among these distances:
18 2 0.04
19 5 0.10
20 6 0.12
21 22 0.42
22 4 0.08
23 13 0.25
ACGTcount: A:0.49, C:0.12, G:0.01, T:0.38
Consensus pattern (21 bp):
AACTTACATAACTTATATATA
Found at i:52279491 original size:9 final size:9
Alignment explanation
Indices: 52279477--52280009 Score: 205
Period size: 9 Copynumber: 62.0 Consensus size: 9
52279467 TTACATAATG
52279477 CATAACTTA
1 CATAACTTA
52279486 CATAACTTATA
1 CATAAC-T-TA
*
52279497 TATAAACTTATA
1 CAT-AAC-T-TA
* *
52279509 TATAAACTTG
1 CATA-ACTTA
52279519 CATAACTTA
1 CATAACTTA
52279528 CATAATAACTTA
1 C---ATAACTTA
52279540 CATAA--TA
1 CATAACTTA
* *
52279547 CATAGCCTA
1 CATAACTTA
* *
52279556 CATAGCCTA
1 CATAACTTA
52279565 CATAACTTA
1 CATAACTTA
*
52279574 CATGA--TA
1 CATAACTTA
*
52279581 CACAACTT-
1 CATAACTTA
* *
52279589 -ATTACATA
1 CATAACTTA
*
52279597 AATAACTTA
1 CATAACTTA
52279606 CATAA--TA
1 CATAACTTA
*
52279613 CATAACTTT
1 CATAACTTA
52279622 CATAACTTA
1 CATAACTTA
52279631 CAGT-A--TA
1 CA-TAACTTA
*
52279638 CACAACTTA
1 CATAACTTA
*
52279647 CATAAATTA
1 CATAACTTA
*
52279656 -AT-ATTATA
1 CATAACT-TA
*
52279664 CACAACTTA
1 CATAACTTA
52279673 CATAA--TA
1 CATAACTTA
*
52279680 CATTACTTA
1 CATAACTTA
52279689 CATAACTTA
1 CATAACTTA
*
52279698 CATTA--TA
1 CATAACTTA
*
52279705 CACAACTTA
1 CATAACTTA
*
52279714 CATAAATTA
1 CATAACTTA
*
52279723 -AT-ATTATA
1 CATAACT-TA
*
52279731 CACAACTTA
1 CATAACTTA
52279740 CATAA--TA
1 CATAACTTA
*
52279747 CATTACTTA
1 CATAACTTA
52279756 CATAACTTA
1 CATAACTTA
*
52279765 CATTA--TA
1 CATAACTTA
*
52279772 CACAACTTA
1 CATAACTTA
52279781 CATAACTTA
1 CATAACTTA
** *
52279790 TTTAATATTATA
1 CAT-A-ACT-TA
52279802 CATAACTTA
1 CATAACTTA
52279811 CATAA--TA
1 CATAACTTA
52279818 CATAACTTA
1 CATAACTTA
*
52279827 TATAACTTA
1 CATAACTTA
52279836 CATAA--TA
1 CATAACTTA
52279843 CATAACTTA
1 CATAACTTA
52279852 CATAAC-T-
1 CATAACTTA
* *
52279859 CACAAGTTA
1 CATAACTTA
52279868 CATAACTTA
1 CATAACTTA
* *
52279877 AATACATTATA
1 CATA-ACT-TA
**
52279888 CCCAACTTA
1 CATAACTTA
52279897 CAT-A--T-
1 CATAACTTA
52279902 -ATAACTTA
1 CATAACTTA
*
52279910 CATACCTTA
1 CATAACTTA
*
52279919 CAT-TC-TA
1 CATAACTTA
*
52279926 CACAACTTA
1 CATAACTTA
*
52279935 CATAACATA
1 CATAACTTA
52279944 CATAA--TA
1 CATAACTTA
*
52279951 CATAGCTTA
1 CATAACTTA
*
52279960 CACAA--TA
1 CATAACTTA
*
52279967 CACAACTTA
1 CATAACTTA
*
52279976 CATAGCTTA
1 CATAACTTA
52279985 CATAA--TA
1 CATAACTTA
*
52279992 CATGACTTA
1 CATAACTTA
*
52280001 CATAGCTTA
1 CATAACTTA
52280010 ATTATACTTA
Statistics
Matches: 390, Mismatches: 77, Indels: 114
0.67 0.13 0.20
Matches are distributed among these distances:
4 2 0.01
5 1 0.00
6 1 0.00
7 95 0.24
8 13 0.03
9 224 0.57
10 17 0.04
11 12 0.03
12 25 0.06
ACGTcount: A:0.45, C:0.20, G:0.02, T:0.33
Consensus pattern (9 bp):
CATAACTTA
Found at i:52279506 original size:12 final size:12
Alignment explanation
Indices: 52279489--52279517 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
52279479 TAACTTACAT
52279489 AACTTATATATA
1 AACTTATATATA
52279501 AACTTATATATA
1 AACTTATATATA
52279513 AACTT
1 AACTT
52279518 GCATAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (12 bp):
AACTTATATATA
Found at i:52279535 original size:12 final size:12
Alignment explanation
Indices: 52279520--52279546 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
52279510 ATAAACTTGC
52279520 ATAACTTACATA
1 ATAACTTACATA
52279532 ATAACTTACATA
1 ATAACTTACATA
52279544 ATA
1 ATA
52279547 CATAGCCTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:52279617 original size:16 final size:16
Alignment explanation
Indices: 52279532--52279979 Score: 138
Period size: 16 Copynumber: 27.8 Consensus size: 16
52279522 AACTTACATA
52279532 ATAACTTACATAATAC
1 ATAACTTACATAATAC
* * *
52279548 ATAGCCTACATAGCCTAC
1 ATAACTTACATA--ATAC
*
52279566 ATAACTTACATGATAC
1 ATAACTTACATAATAC
* * *
52279582 ACAACTTA-TTACATAA
1 ATAACTTACATA-ATAC
52279598 ATAACTTACATAATAC
1 ATAACTTACATAATAC
*
52279614 ATAACTTTCATAACTTAC
1 ATAACTTACATAA--TAC
*
52279632 AGTATAC--ACA-ACTTAC
1 A-TA-ACTTACATA-ATAC
*
52279648 ATAAATTA-ATATTATAC
1 ATAACTTACATA--ATAC
*
52279665 ACAACTTACATAATAC
1 ATAACTTACATAATAC
*
52279681 ATTACTTACATAACTTAC
1 ATAACTTACATAA--TAC
* *
52279699 ATTA--TACACAACTTAC
1 ATAACTTACATAA--TAC
*
52279715 ATAAATTA-ATATTATAC
1 ATAACTTACATA--ATAC
*
52279732 ACAACTTACATAATAC
1 ATAACTTACATAATAC
*
52279748 ATTACTTACATAACTTAC
1 ATAACTTACATAA--TAC
* *
52279766 ATTA--TACACAACTTAC
1 ATAACTTACATAA--TAC
*
52279782 ATAACTTATTTAATATTATAC
1 ATAACTTA---CATA--ATAC
52279803 ATAACTTACATAATAC
1 ATAACTTACATAATAC
52279819 ATAAC-T---T-AT--
1 ATAACTTACATAATAC
52279828 ATAACTTACATAATAC
1 ATAACTTACATAATAC
52279844 ATAACTTACATAACT-C
1 ATAACTTACATAA-TAC
* *
52279860 ACAAGTTACAT-A-AC
1 ATAACTTACATAATAC
* * *
52279874 TTAA-ATACATTATAC
1 ATAACTTACATAATAC
**
52279889 CCAACTTACAT-AT--
1 ATAACTTACATAATAC
*
52279902 ATAACTTACATACCTTAC
1 ATAACTTACATA--ATAC
* *
52279920 AT-TC-TACACAACTTAC
1 ATAACTTACATAA--TAC
*
52279936 ATAACATACATAATAC
1 ATAACTTACATAATAC
* *
52279952 ATAGCTTACACAATAC
1 ATAACTTACATAATAC
*
52279968 ACAACTTACATA
1 ATAACTTACATA
52279980 GCTTACATAA
Statistics
Matches: 323, Mismatches: 58, Indels: 102
0.67 0.12 0.21
Matches are distributed among these distances:
9 5 0.02
10 1 0.00
11 2 0.01
12 1 0.00
13 15 0.05
14 7 0.02
15 12 0.04
16 182 0.56
17 26 0.08
18 53 0.16
19 3 0.01
20 2 0.01
21 13 0.04
23 1 0.00
ACGTcount: A:0.45, C:0.21, G:0.01, T:0.32
Consensus pattern (16 bp):
ATAACTTACATAATAC
Found at i:52279626 original size:25 final size:25
Alignment explanation
Indices: 52279598--52279961 Score: 158
Period size: 25 Copynumber: 14.0 Consensus size: 25
52279588 TATTACATAA
*
52279598 ATAACTTACATAATACATAACTTTC
1 ATAACTTACATAATACATAACTTAC
*
52279623 ATAACTTACAGT-ATACACAACTTAC
1 ATAACTTACA-TAATACATAACTTAC
* *
52279648 ATAAATTA-ATATTATACACAACTTAC
1 ATAACTTACATA--ATACATAACTTAC
* * *
52279674 ATAATACATTACTTACATAACTTACATTATAC
1 AT-A-AC-TTACATA-AT-ACATA-ACT-TAC
* ** *
52279706 ACAACTTACATAAATTAAT-ATTATAC
1 ATAACTTACAT-AATACATAACT-TAC
* *
52279732 ACAACTTACATAATACATTACTTAC
1 ATAACTTACATAATACATAACTTAC
* *
52279757 ATAACTTACATTATACACAACTTAC
1 ATAACTTACATAATACATAACTTAC
*
52279782 ATAACTTATTTAATATTATACATAACTTAC
1 ATAACTTA---CATA--ATACATAACTTAC
*
52279812 ATAA--TACATAACTTATATAACTTAC
1 ATAACTTACATAA--TACATAACTTAC
52279837 ATAA--TACATAACTTACATAAC-T-C
1 ATAACTTACATAA--TACATAACTTAC
* * * *
52279860 ACAAGTTACATAACTTAAATACATTATAC
1 ATAACTTACATAA--TACATA-ACT-TAC
**
52279889 CCAACTTACAT-AT--ATAACTTAC
1 ATAACTTACATAATACATAACTTAC
* ** *
52279911 ATACCTTACATTCTACACAACTTAC
1 ATAACTTACATAATACATAACTTAC
* *
52279936 ATAACATACATAATACATAGCTTAC
1 ATAACTTACATAATACATAACTTAC
52279961 A
1 A
52279962 CAATACACAA
Statistics
Matches: 266, Mismatches: 44, Indels: 58
0.72 0.12 0.16
Matches are distributed among these distances:
22 11 0.04
23 9 0.03
24 5 0.02
25 141 0.53
26 38 0.14
27 1 0.00
28 8 0.03
29 22 0.08
30 24 0.09
31 3 0.01
32 4 0.02
ACGTcount: A:0.45, C:0.20, G:0.01, T:0.34
Consensus pattern (25 bp):
ATAACTTACATAATACATAACTTAC
Found at i:52279708 original size:67 final size:67
Alignment explanation
Indices: 52279600--52279856 Score: 406
Period size: 67 Copynumber: 3.8 Consensus size: 67
52279590 TTACATAAAT
* *
52279600 AACTTACATAATACATAACTTTCATAACTTACAGTATACACAACTTACATAAATTAATATTATAC
1 AACTTACATAATACATAACTTACATAACTTACATTATACACAACTTACATAAATTAATATTATAC
52279665 AC
66 AC
*
52279667 AACTTACATAATACATTACTTACATAACTTACATTATACACAACTTACATAAATTAATATTATAC
1 AACTTACATAATACATAACTTACATAACTTACATTATACACAACTTACATAAATTAATATTATAC
52279732 AC
66 AC
*
52279734 AACTTACATAATACATTACTTACATAACTTACATTATACACAACTTACATAACTTATTTAATATT
1 AACTTACATAATACATAACTTACATAACTTACATTATACACAACTTACATAA---A-TTAATATT
*
52279799 ATACAT
62 ATACAC
* * *
52279805 AACTTACATAATACATAACTTATATAACTTACATAATACATAACTTACATAA
1 AACTTACATAATACATAACTTACATAACTTACATTATACACAACTTACATAA
52279857 CTCACAAGTT
Statistics
Matches: 178, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
67 116 0.65
70 1 0.01
71 61 0.34
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (67 bp):
AACTTACATAATACATAACTTACATAACTTACATTATACACAACTTACATAAATTAATATTATAC
AC
Found at i:52279977 original size:25 final size:25
Alignment explanation
Indices: 52279949--52280009 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
52279939 ACATACATAA
52279949 TACATAGCTTACACAATACACAACT
1 TACATAGCTTACACAATACACAACT
* **
52279974 TACATAGCTTACATAATACATGACT
1 TACATAGCTTACACAATACACAACT
52279999 TACATAGCTTA
1 TACATAGCTTA
52280010 ATTATACTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.41, C:0.23, G:0.07, T:0.30
Consensus pattern (25 bp):
TACATAGCTTACACAATACACAACT
Found at i:52281421 original size:43 final size:43
Alignment explanation
Indices: 52281373--52281750 Score: 510
Period size: 43 Copynumber: 8.8 Consensus size: 43
52281363 CCAAAATTAC
* * *
52281373 CGGCGTTTGTGGAAAAAGCGCCACTAAAAGTCATGATCTATAG
1 CGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAG
* * * *
52281416 CGGCGTTTGTGAAAAAAACGCCGCTCAAGGTCATGGTCTGTAG
1 CGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAG
52281459 CGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAG
1 CGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAG
* * * *
52281502 CGGCGTTTTTGGGAAAAGCGCTGCTACAGGTCATGGTCTATAG
1 CGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAG
* * *
52281545 TGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCAAGGTCTATAG
1 CGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAG
** *
52281588 CGATGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTATAG
1 CGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAG
* *
52281631 CGGCGTTTGTGGGAAAAGCGCCGCTAAAGTTCATGGTCTATAG
1 CGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAG
* *
52281674 CTGCATTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAG
1 CGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAG
* *
52281717 CGGCATTTTTCTGG---AAGCGCCGCTAAAGGTCATG
1 CGGC--GTTTGTGGAAAAAGCGCCGCTAAAGGTCATG
52281751 AACTTTAGCG
Statistics
Matches: 299, Mismatches: 34, Indels: 5
0.88 0.10 0.01
Matches are distributed among these distances:
42 20 0.07
43 273 0.91
45 6 0.02
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (43 bp):
CGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAG
Found at i:52285516 original size:27 final size:27
Alignment explanation
Indices: 52285486--52285557 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 27
52285476 CAATCTAATT
* *
52285486 AGAGTACGCCACAAAGGCAATCCATGC
1 AGAGTACACCACAAAGGCAATCCATAC
* **
52285513 AGAGTACACCACAAAGGCTATTTATAC
1 AGAGTACACCACAAAGGCAATCCATAC
*
52285540 AAAGTACACCACAAAGGC
1 AGAGTACACCACAAAGGC
52285558 TGACAAGATG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.42, C:0.26, G:0.18, T:0.14
Consensus pattern (27 bp):
AGAGTACACCACAAAGGCAATCCATAC
Found at i:52291711 original size:19 final size:19
Alignment explanation
Indices: 52291687--52291726 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
52291677 AATGACTAAA
52291687 TTGCATAAAATAAATTGTC
1 TTGCATAAAATAAATTGTC
52291706 TTGCATAAAATAAATTGTC
1 TTGCATAAAATAAATTGTC
52291725 TT
1 TT
52291727 ACTATCTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (19 bp):
TTGCATAAAATAAATTGTC
Found at i:52292150 original size:21 final size:21
Alignment explanation
Indices: 52292124--52292205 Score: 60
Period size: 21 Copynumber: 3.9 Consensus size: 21
52292114 CAAGTGGATT
*
52292124 AGCTCTTTTGAGCTTCTGTTC
1 AGCTCTTTCGAGCTTCTGTTC
* *
52292145 AGCTCTTACGAGCTT-TAATTC
1 AGCTCTTTCGAGCTTCT-GTTC
* * *
52292166 AGCT-TTTACAAGCTTTTGTTA
1 AGCTCTTT-CGAGCTTCTGTTC
**
52292187 AGCTCTTTTTAGCTTCTGT
1 AGCTCTTTCGAGCTTCTGT
52292206 GGTGTGTTTG
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
20 3 0.06
21 40 0.85
22 4 0.09
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.46
Consensus pattern (21 bp):
AGCTCTTTCGAGCTTCTGTTC
Found at i:52293528 original size:31 final size:31
Alignment explanation
Indices: 52293493--52293569 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
52293483 AAATGTAAGT
52293493 ATGAATAATTGGTTGTGATTGAGGTGCCTAA
1 ATGAATAATTGGTTGTGATTGAGGTGCCTAA
52293524 ATGAATAATTGGTTGTGATTGAGGTGCCTAA
1 ATGAATAATTGGTTGTGATTGAGGTGCCTAA
52293555 ATGACAT-ATTGGTTG
1 ATGA-ATAATTGGTTG
52293570 AATGGACCTA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
31 43 0.96
32 2 0.04
ACGTcount: A:0.29, C:0.06, G:0.29, T:0.36
Consensus pattern (31 bp):
ATGAATAATTGGTTGTGATTGAGGTGCCTAA
Found at i:52297505 original size:7 final size:7
Alignment explanation
Indices: 52297495--52297527 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
52297485 CCTTTTTAGA
52297495 TTTTTA-
1 TTTTTAT
52297501 TTTTTATT
1 TTTTTA-T
52297509 TTTTTAT
1 TTTTTAT
52297516 TTTTTAT
1 TTTTTAT
52297523 TTTTT
1 TTTTT
52297528 TATTCTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.24
7 13 0.52
8 6 0.24
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:52297512 original size:8 final size:8
Alignment explanation
Indices: 52297501--52297542 Score: 59
Period size: 8 Copynumber: 5.1 Consensus size: 8
52297491 TAGATTTTTA
52297501 TTTTTATT
1 TTTTTATT
52297509 TTTTTA-T
1 TTTTTATT
52297516 TTTTTATT
1 TTTTTATT
52297524 TTTTTATT
1 TTTTTATT
52297532 CTTATTTATT
1 -TT-TTTATT
52297542 T
1 T
52297543 CTATTGTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 7 0.23
8 15 0.48
9 3 0.10
10 6 0.19
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTATT
Found at i:52297513 original size:15 final size:15
Alignment explanation
Indices: 52297495--52297538 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
52297485 CCTTTTTAGA
52297495 TTTTTATTTTTA-TT
1 TTTTTATTTTTATTT
52297509 TTTTTATTTTT-TATT
1 TTTTTATTTTTAT-TT
*
52297524 TTTTTATTCTTATTT
1 TTTTTATTTTTATTT
52297539 ATTTCTATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 11 0.42
15 14 0.54
16 1 0.04
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTATTTTTATTT
Found at i:52297525 original size:14 final size:14
Alignment explanation
Indices: 52297495--52297538 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
52297485 CCTTTTTAGA
52297495 TTTTTATTTTTATT
1 TTTTTATTTTTATT
52297509 TTTTTATTTTTTATT
1 TTTTTA-TTTTTATT
*
52297524 TTTTTATTCTTATT
1 TTTTTATTTTTATT
52297538 T
1 T
52297539 ATTTCTATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
14 14 0.50
15 14 0.50
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTATTTTTATT
Found at i:52297536 original size:21 final size:21
Alignment explanation
Indices: 52297495--52297538 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
52297485 CCTTTTTAGA
*
52297495 TTTTTATTTTTATTTTTTTAT
1 TTTTTATTTTTATTTTCTTAT
52297516 TTTTTATTTTT-TTATTCTTAT
1 TTTTTATTTTTATT-TTCTTAT
52297537 TT
1 TT
52297539 ATTTCTATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.84
Consensus pattern (21 bp):
TTTTTATTTTTATTTTCTTAT
Found at i:52297554 original size:29 final size:29
Alignment explanation
Indices: 52297495--52297559 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
52297485 CCTTTTTAGA
* * * *
52297495 TTTTTATTTTTATTTTTTTATTTTTTATT
1 TTTTTATTCTTATTTATTTATATTGTATT
* *
52297524 TTTTTATTCTTATTTATTTCTATTGTCTT
1 TTTTTATTCTTATTTATTTATATTGTATT
*
52297553 TTCTTAT
1 TTTTTAT
52297560 CATTCGTCTT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.78
Consensus pattern (29 bp):
TTTTTATTCTTATTTATTTATATTGTATT
Found at i:52297770 original size:11 final size:11
Alignment explanation
Indices: 52297741--52297777 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
52297731 TAAGTCTTGT
52297741 TTCTTTTAGTA
1 TTCTTTTAGTA
*
52297752 TTATTTTTAGTA
1 TT-CTTTTAGTA
52297764 TTCTTTTAGTA
1 TTCTTTTAGTA
52297775 TTC
1 TTC
52297778 ATATCATGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.19, C:0.08, G:0.08, T:0.65
Consensus pattern (11 bp):
TTCTTTTAGTA
Found at i:52299155 original size:6 final size:6
Alignment explanation
Indices: 52299139--52299178 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
52299129 TGTTTTGTTT
*
52299139 ATTTTA TTTTTA ATTTT- ATTTTA ATTTTA ATTTTA ATTTT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTT
52299179 TAGTTGTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (6 bp):
ATTTTA
Found at i:52299158 original size:17 final size:17
Alignment explanation
Indices: 52299136--52299178 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
52299126 ATTTGTTTTG
*
52299136 TTTATTTTATTTTTAAT
1 TTTATTTTAATTTTAAT
52299153 TTTATTTTAATTTTAAT
1 TTTATTTTAATTTTAAT
52299170 TTTAATTTT
1 TTT-ATTTT
52299179 TAGTTGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 19 0.79
18 5 0.21
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTATTTTAATTTTAAT
Found at i:52299194 original size:6 final size:6
Alignment explanation
Indices: 52299136--52299198 Score: 56
Period size: 6 Copynumber: 10.2 Consensus size: 6
52299126 ATTTGTTTTG
* * * *
52299136 TTTA-T TTTATT TTTAAT TTTATT TTAATT TTAATT TTAATT TTTAGTTGT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTA--T-T
52299186 TTTATT TTTATT T
1 TTTATT TTTATT T
52299199 CTTAGACTTC
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
5 4 0.08
6 39 0.78
7 1 0.02
8 1 0.02
9 5 0.10
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (6 bp):
TTTATT
Found at i:52301749 original size:18 final size:19
Alignment explanation
Indices: 52301726--52301763 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
52301716 TCTAGGTGGA
52301726 TTCTTTC-TTAGG-TATTAT
1 TTCTTTCATT-GGTTATTAT
52301744 TTCTTTCATTGGTTATTAT
1 TTCTTTCATTGGTTATTAT
52301763 T
1 T
52301764 CGATTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.16, C:0.11, G:0.11, T:0.63
Consensus pattern (19 bp):
TTCTTTCATTGGTTATTAT
Found at i:52326428 original size:18 final size:18
Alignment explanation
Indices: 52326405--52326444 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
52326395 TGTCTCCTTT
52326405 TTTTCTTCCTCTTTTCTG
1 TTTTCTTCCTCTTTTCTG
* *
52326423 TTTTCTTTCTTTTTTCTG
1 TTTTCTTCCTCTTTTCTG
52326441 TTTT
1 TTTT
52326445 TGTTGTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.05, T:0.75
Consensus pattern (18 bp):
TTTTCTTCCTCTTTTCTG
Found at i:52336183 original size:12 final size:13
Alignment explanation
Indices: 52336166--52336194 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
52336156 AGAGTTAGGG
52336166 TTTAAA-TATTTA
1 TTTAAAGTATTTA
52336178 TTTAAAGTATTTA
1 TTTAAAGTATTTA
52336191 TTTA
1 TTTA
52336195 GGTCATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
TTTAAAGTATTTA
Found at i:52337353 original size:15 final size:15
Alignment explanation
Indices: 52337333--52337370 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
52337323 CAATGAAAAG
52337333 GATGAAAAGGTTATC
1 GATGAAAAGGTTATC
52337348 GATGAAAAGGTTATC
1 GATGAAAAGGTTATC
52337363 GATTGAAA
1 GA-TGAAA
52337371 TATTTTATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.42, C:0.05, G:0.26, T:0.26
Consensus pattern (15 bp):
GATGAAAAGGTTATC
Found at i:52341409 original size:22 final size:22
Alignment explanation
Indices: 52341384--52341428 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
52341374 TCCACATAGT
* *
52341384 TATGAAAGCCTTTTACGGGTAG
1 TATGAAAGCCCTTTAAGGGTAG
*
52341406 TATGCAAGCCCTTTAAGGGTAG
1 TATGAAAGCCCTTTAAGGGTAG
52341428 T
1 T
52341429 GTGAGACTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (22 bp):
TATGAAAGCCCTTTAAGGGTAG
Found at i:52343247 original size:15 final size:15
Alignment explanation
Indices: 52343227--52343259 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
52343217 ATTTCCTCAC
*
52343227 ATTTTCATTTCTAAA
1 ATTTTCATATCTAAA
52343242 ATTTTCATATCTAAA
1 ATTTTCATATCTAAA
52343257 ATT
1 ATT
52343260 ACTTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTTTCATATCTAAA
Found at i:52346365 original size:45 final size:45
Alignment explanation
Indices: 52346275--52346447 Score: 260
Period size: 45 Copynumber: 3.9 Consensus size: 45
52346265 TTCATTTGAT
*
52346275 TCGTGATGCCATAGCATCTTTCAG-CTAT-GTCTTACTCGATAGAA
1 TCGTGATGCCATAACATCTTTCAGTC-ATGGTCTTACTCGATAGAA
* *
52346319 TCATAATGCCATAACATCTTTCAGTCATGGTCTTACTCGATAGAA
1 TCGTGATGCCATAACATCTTTCAGTCATGGTCTTACTCGATAGAA
* *
52346364 TCGTGATGTCATAACATCTTTCAGTCATGGTCTTACTTGATAGAA
1 TCGTGATGCCATAACATCTTTCAGTCATGGTCTTACTCGATAGAA
* *
52346409 TCGTGATGCCATAACGTCTTTCAGTCATGGTCTTGCTCG
1 TCGTGATGCCATAACATCTTTCAGTCATGGTCTTACTCG
52346448 TTTCTAGTAT
Statistics
Matches: 116, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
44 23 0.20
45 93 0.80
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (45 bp):
TCGTGATGCCATAACATCTTTCAGTCATGGTCTTACTCGATAGAA
Found at i:52348886 original size:20 final size:20
Alignment explanation
Indices: 52348863--52348902 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
52348853 TTGTCTAAAA
* *
52348863 AAAGGAAAAGAAAAGGTTGG
1 AAAGGAAAAAAAAAAGTTGG
*
52348883 AAAGTAAAAAAAAAAGTTGG
1 AAAGGAAAAAAAAAAGTTGG
52348903 GGAGGCCGCA
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:0.60, C:0.00, G:0.28, T:0.12
Consensus pattern (20 bp):
AAAGGAAAAAAAAAAGTTGG
Found at i:52352673 original size:20 final size:20
Alignment explanation
Indices: 52352648--52352690 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
52352638 CACATTCAGT
* *
52352648 ATTTTCGGTTTGATTTATTA
1 ATTTTCAGTTTAATTTATTA
52352668 ATTTTCAGTTTAATTTATTA
1 ATTTTCAGTTTAATTTATTA
52352688 ATT
1 ATT
52352691 ATCTTTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.09, T:0.60
Consensus pattern (20 bp):
ATTTTCAGTTTAATTTATTA
Found at i:52359269 original size:21 final size:20
Alignment explanation
Indices: 52359230--52359270 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
52359220 TAAAGAGAAC
* *
52359230 AAAATAAATAAATATATAAT
1 AAAATAAATAAAAACATAAT
52359250 AAAATAAAATAAAAACATAAT
1 AAAAT-AAATAAAAACATAAT
52359271 TATGTTTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAATAAATAAAAACATAAT
Found at i:52364615 original size:18 final size:18
Alignment explanation
Indices: 52364589--52364631 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
52364579 GACTGGGAAA
* *
52364589 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
52364607 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
52364625 AGGATAC
1 AGGATAC
52364632 GCACTTGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.28, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:52365228 original size:7 final size:7
Alignment explanation
Indices: 52365218--52365242 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
52365208 TTATATACAT
52365218 AATACTA
1 AATACTA
52365225 AATACTA
1 AATACTA
52365232 AATACTA
1 AATACTA
52365239 AATA
1 AATA
52365243 TGAAATGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:52367360 original size:11 final size:10
Alignment explanation
Indices: 52367341--52367389 Score: 59
Period size: 10 Copynumber: 5.1 Consensus size: 10
52367331 AATATTAATG
52367341 TATTTTTATA
1 TATTTTTATA
52367351 TATATTTTATA
1 TAT-TTTTATA
52367362 TATTTTTA-A
1 TATTTTTATA
52367371 -A-TTTTATA
1 TATTTTTATA
*
52367379 TATTATTATA
1 TATTTTTATA
52367389 T
1 T
52367390 GTTATGAACA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
7 5 0.15
8 2 0.06
9 2 0.06
10 15 0.44
11 10 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TATTTTTATA
Found at i:52367363 original size:9 final size:9
Alignment explanation
Indices: 52367349--52367389 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
52367339 TGTATTTTTA
52367349 TATATATTT
1 TATATATTT
52367358 TATATATTT
1 TATATATTT
*
52367367 T-TAAATTT
1 TATATATTT
52367375 TATATATTAT
1 TATATATT-T
52367385 TATAT
1 TATAT
52367390 GTTATGAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 7 0.25
9 15 0.54
10 6 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATATATTT
Found at i:52367394 original size:17 final size:17
Alignment explanation
Indices: 52367346--52367394 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
52367336 TAATGTATTT
52367346 TTATATATATTTTATATA
1 TTAT-TATATTTTATATA
* *
52367364 TTTTTAAATTTTATATA
1 TTATTATATTTTATATA
*
52367381 TTATTATATGTTAT
1 TTATTATATTTTAT
52367395 GAACAATTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 23 0.88
18 3 0.12
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TTATTATATTTTATATA
Found at i:52367871 original size:21 final size:21
Alignment explanation
Indices: 52367846--52367890 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
52367836 TAAGTAATTG
*
52367846 TAAATTTTAAGAAAGGTCTTT
1 TAAATTTTAAGAAAGGTCCTT
52367867 TAAATTTTAAGAAAGGTCCTT
1 TAAATTTTAAGAAAGGTCCTT
52367888 TAA
1 TAA
52367891 GTAGATTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (21 bp):
TAAATTTTAAGAAAGGTCCTT
Found at i:52379010 original size:6 final size:7
Alignment explanation
Indices: 52378976--52379007 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
52378966 TGGCAAGGAT
52378976 GGGGGAA
1 GGGGGAA
52378983 GGGGGAA
1 GGGGGAA
52378990 GGGGGAA
1 GGGGGAA
52378997 GGGGGAA
1 GGGGGAA
52379004 GGGG
1 GGGG
52379008 AAGAGGCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.25, C:0.00, G:0.75, T:0.00
Consensus pattern (7 bp):
GGGGGAA
Done.