Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 165 of 316
Found at i:52522797 original size:15 final size:15
Alignment explanation
Indices: 52522777--52522805 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
52522767 TGTAAAGAAA
52522777 AATGAATATTGTAAC
1 AATGAATATTGTAAC
52522792 AATGAATATTGTAA
1 AATGAATATTGTAA
52522806 AAATCTTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.14, T:0.34
Consensus pattern (15 bp):
AATGAATATTGTAAC
Found at i:52535909 original size:6 final size:7
Alignment explanation
Indices: 52535891--52535918 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
52535881 AAAATTTAAA
52535891 ATTTTTT
1 ATTTTTT
52535898 ATTTTTT
1 ATTTTTT
52535905 ATTTTTT
1 ATTTTTT
52535912 ATTTTTT
1 ATTTTTT
52535919 TTAAGACCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
ATTTTTT
Found at i:52535933 original size:17 final size:16
Alignment explanation
Indices: 52535912--52535946 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
52535902 TTTATTTTTT
52535912 ATTTTT-TTTAAGACCA
1 ATTTTTGTTT-AGACCA
52535928 ATTTTTGTTTAGACCA
1 ATTTTTGTTTAGACCA
52535944 ATT
1 ATT
52535947 ACAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (16 bp):
ATTTTTGTTTAGACCA
Found at i:52536503 original size:15 final size:15
Alignment explanation
Indices: 52536457--52536510 Score: 90
Period size: 15 Copynumber: 3.5 Consensus size: 15
52536447 TTTTTATGGT
52536457 TTTTTTTTGCTGGAAA
1 TTTTTTTTGCTGG-AA
*
52536473 GTTTTTTTGCTGGAA
1 TTTTTTTTGCTGGAA
52536488 TTTTTTTTGCTGGAA
1 TTTTTTTTGCTGGAA
52536503 TTTTTTTT
1 TTTTTTTT
52536511 TTGCTCTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
15 24 0.67
16 12 0.33
ACGTcount: A:0.13, C:0.06, G:0.19, T:0.63
Consensus pattern (15 bp):
TTTTTTTTGCTGGAA
Found at i:52536507 original size:16 final size:16
Alignment explanation
Indices: 52536456--52536511 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
52536446 CTTTTTATGG
52536456 TTTTTTTTTGCTGGAA
1 TTTTTTTTTGCTGGAA
**
52536472 AGTTTTTTTGCTGGAA
1 TTTTTTTTTGCTGGAA
52536488 -TTTTTTTTGCTGGAA
1 TTTTTTTTTGCTGGAA
52536503 TTTTTTTTT
1 TTTTTTTTT
52536512 TGCTCTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
15 14 0.39
16 22 0.61
ACGTcount: A:0.12, C:0.05, G:0.18, T:0.64
Consensus pattern (16 bp):
TTTTTTTTTGCTGGAA
Found at i:52536765 original size:29 final size:28
Alignment explanation
Indices: 52536719--52536819 Score: 76
Period size: 29 Copynumber: 3.4 Consensus size: 28
52536709 TTCTAGGGCT
*
52536719 AAATGTAATTTTTAGAAAATTTAGGGTTA
1 AAATGTAA-TTTAAGAAAATTTAGGGTTA
* * *
52536748 AAATGTAATTTAAGGAAAGTTTAAGGTTCT
1 AAATGTAATTTAA-GAAAATTTAGGGTT-A
* * *
52536778 AAGTGAAATTTAAAGAAAAGTTTAGGGGTCA
1 AAATGTAATTT-AAGAAAA-TTTA-GGGTTA
*
52536809 AAATGCAATTT
1 AAATGTAATTT
52536820 TTTATTTTTT
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
28 4 0.07
29 20 0.36
30 13 0.24
31 15 0.27
32 3 0.05
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.35
Consensus pattern (28 bp):
AAATGTAATTTAAGAAAATTTAGGGTTA
Found at i:52536819 original size:31 final size:29
Alignment explanation
Indices: 52536732--52536819 Score: 79
Period size: 31 Copynumber: 3.0 Consensus size: 29
52536722 TGTAATTTTT
* *
52536732 AGAAAA-TTTAGGGTTAAAATGTAATTTA
1 AGAAAAGTTTAGGGTCAAAATGAAATTTA
* * * *
52536760 AGGAAAGTTTAAGGTTCTAAGTGAAATTTAA
1 AGAAAAGTTT-AGGGTCAAAATGAAATTT-A
*
52536791 AGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAAGTTTA-GGGTCAAAATGAAATTT
52536820 TTTATTTTTT
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
28 5 0.11
29 3 0.07
30 14 0.31
31 23 0.51
ACGTcount: A:0.43, C:0.03, G:0.22, T:0.32
Consensus pattern (29 bp):
AGAAAAGTTTAGGGTCAAAATGAAATTTA
Found at i:52537410 original size:72 final size:72
Alignment explanation
Indices: 52537076--52537828 Score: 878
Period size: 72 Copynumber: 10.1 Consensus size: 72
52537066 AAAAGCCAAA
** * * ** * *
52537076 AAATTGAAAATACCTCAGTGTGTGACCTGAGGCTTAACTCACCTCTCGCAATACGAGTTGATTTT
1 AAATTGAAAATACCTCAACGTGT--CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--AT
*
52537141 TTTGACAACAG
62 TTTGAAAACAG
* * * ** *
52537152 AAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA----AT
* *
52537217 TTTGAAAGATAA
62 TTTGAAA-ACAG
* * * * *
52537229 AAATTGAAAATACCTCAGCATGTCTTAAGGCTCAACTCATTTCTCACAATATGAGTTGATTTTTC
1 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-----A
52537294 TTTTGAAAAACAG
61 TTTTG-AAAACAG
* * * *
52537307 AAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAGTATAAGTTGAATTTTG
1 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG
*
52537372 AAAATAG
66 AAAACAG
* * * *
52537379 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTAATTTCTTGCACTATGAGTTGAATTTTG
1 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG
52537444 AAAACAG
66 AAAACAG
52537451 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG
1 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG
52537516 AAAACAG
66 AAAACAG
*
52537523 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTG
1 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG
52537588 AAAAACATAAATTGAACAG
66 ---------AA---AACAG
** *
52537607 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTT
52537672 GAAAAGCAG
65 GAAAA-CAG
* *
52537681 AAATTGAAAATACCTCAATGTGTCTTGAGGCTCGACTCATTTCTCGCAATATGAGTTGAATTTTG
1 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG
52537746 AAAACAG
66 AAAACAG
* *
52537753 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTTGCAATATGAGTTGAATTTTT
1 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA-TTTT
52537818 G-AAACAG
65 GAAAACAG
52537825 AAAT
1 AAAT
52537829 AAAAGCATCA
Statistics
Matches: 610, Mismatches: 47, Indels: 44
0.87 0.07 0.06
Matches are distributed among these distances:
72 271 0.44
73 21 0.03
74 92 0.15
76 33 0.05
77 54 0.09
78 66 0.11
79 3 0.00
81 2 0.00
84 62 0.10
85 6 0.01
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Consensus pattern (72 bp):
AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG
AAAACAG
Found at i:52537721 original size:230 final size:229
Alignment explanation
Indices: 52537377--52537821 Score: 766
Period size: 230 Copynumber: 1.9 Consensus size: 229
52537367 TTTTGAAAAT
* ** * *
52537377 AGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTAATTTCTTGCACTATGAGTTGAATTT
1 AGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTAACCTCTCGCAATATGAGTTGAATTT
52537442 TGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGT
66 TGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGT
52537507 TGAATTTTGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAA
131 TGAATTTTGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAA
52537572 TATGAGTTG-ATTTTTGAAAAACATAAATTGAAC
196 TATGAGTTGAATTTTTGAAAAACATAAATTGAAC
* *
52537605 AGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 AGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTAACCTCTCGCAATATGAGTTGA-ATT
* *
52537670 TTGAAAAGCAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCGACTCATTTCTCGCAATATGA
65 TTGAAAA-CAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
* *
52537735 GTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTTGC
129 GTTGAATTTTGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGC
52537800 AATATGAGTTGAATTTTTGAAA
194 AATATGAGTTGAATTTTTGAAA
52537822 CAGAAATAAA
Statistics
Matches: 203, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
228 55 0.27
229 9 0.04
230 129 0.64
231 10 0.05
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (229 bp):
AGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTAACCTCTCGCAATATGAGTTGAATTT
TGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGT
TGAATTTTGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAA
TATGAGTTGAATTTTTGAAAAACATAAATTGAAC
Found at i:52548564 original size:14 final size:14
Alignment explanation
Indices: 52548545--52548597 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
52548535 TGAATGTTCC
**
52548545 TTTTTTTGGTTTTT
1 TTTTTTTGGAATTT
52548559 TTTTTTGCTGGAAATTT
1 TTTTTT--TGG-AATTT
*
52548576 TTTTGTTGGAATTT
1 TTTTTTTGGAATTT
52548590 TTTTTTTG
1 TTTTTTTG
52548598 CTTTTTTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
14 18 0.56
15 3 0.09
16 3 0.09
17 8 0.25
ACGTcount: A:0.09, C:0.02, G:0.17, T:0.72
Consensus pattern (14 bp):
TTTTTTTGGAATTT
Found at i:52548594 original size:15 final size:15
Alignment explanation
Indices: 52548557--52548594 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
52548547 TTTTTGGTTT
52548557 TTTTTTTTGCTGGAA
1 TTTTTTTTGCTGGAA
* *
52548572 ATTTTTTTGTTGGAA
1 TTTTTTTTGCTGGAA
52548587 TTTTTTTT
1 TTTTTTTT
52548595 TTGCTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.13, C:0.03, G:0.16, T:0.68
Consensus pattern (15 bp):
TTTTTTTTGCTGGAA
Found at i:52548856 original size:29 final size:29
Alignment explanation
Indices: 52548810--52548910 Score: 105
Period size: 31 Copynumber: 3.4 Consensus size: 29
52548800 TTCTGGGGCT
*
52548810 AAATGTAATTTTTAGAAAATTTA-GGGTTA
1 AAATGTAA-TTTAAGAAAATTTAGGGGTTA
* *
52548839 AAATGTAATTTAAGGAAAGTTTAGGGGTTT
1 AAATGTAATTTAA-GAAAATTTAGGGGTTA
* * *
52548869 AAGTGAAATTTAAAGAAAAGTTTAGGGGTCA
1 AAATGTAATTT-AAGAAAA-TTTAGGGGTTA
52548900 AAATGTAATTT
1 AAATGTAATTT
52548911 TTTTATTTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
28 4 0.07
29 16 0.28
30 18 0.31
31 20 0.34
ACGTcount: A:0.42, C:0.01, G:0.22, T:0.36
Consensus pattern (29 bp):
AAATGTAATTTAAGAAAATTTAGGGGTTA
Found at i:52555439 original size:47 final size:47
Alignment explanation
Indices: 52555348--52555567 Score: 175
Period size: 47 Copynumber: 4.7 Consensus size: 47
52555338 AGGGTAAGGT
** * *
52555348 GCCGATGCCATGTCTTAGACACGGTCTTACACTGGCTCAT-ATCTCAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACT-ATCATCTCAA
* * * * *
52555395 GTCGATGCCATATCTCAAACATGGTCTTACACTGACTATCATCTCGTA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATCTC-AA
*
52555443 GCCGATG-CATGTCCCAGACAT-GTCTTACACT-ACCCT-TCGTCTCAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGA--CTATCATCTCAA
* * * * ***
52555488 TGCCGATGCCATGTCCCAGACATTGTCTTACACTGGCTCTCATAATGTC
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTGACTATCAT-CTCAA
*
52555537 GCCGAT-ACATGTCCCAGACAT-GTCTTACACT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACT
52555568 AGCTCACACA
Statistics
Matches: 143, Mismatches: 20, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
45 2 0.01
46 35 0.24
47 79 0.55
48 26 0.18
49 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.29
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATCTCAA
Found at i:52555516 original size:94 final size:93
Alignment explanation
Indices: 52555389--52555568 Score: 245
Period size: 94 Copynumber: 1.9 Consensus size: 93
52555379 CTGGCTCATA
* * * *
52555389 TCTCAAGTCGATGCCATATCTCAAACATGGTCTTACACTGACTATCAT-CTCGTAGCCGATGCAT
1 TCTCAAGCCGATGCCATATCCCAAACATGGTCTTACACTGACTATCATAAT-GTAGCCGATACAT
52555453 GTCCCAGACATGTCTTACACTACCCTTCG
65 GTCCCAGACATGTCTTACACTACCCTTCG
* * * * * *
52555482 TCTCAATGCCGATGCCATGTCCCAGACATTGTCTTACACTGGCTCTCATAATGTCGCCGATACAT
1 TCTCAA-GCCGATGCCATATCCCAAACATGGTCTTACACTGACTATCATAATGTAGCCGATACAT
52555547 GTCCCAGACATGTCTTACACTA
65 GTCCCAGACATGTCTTACACTA
52555569 GCTCACACAC
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
93 6 0.08
94 68 0.91
95 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29
Consensus pattern (93 bp):
TCTCAAGCCGATGCCATATCCCAAACATGGTCTTACACTGACTATCATAATGTAGCCGATACATG
TCCCAGACATGTCTTACACTACCCTTCG
Found at i:52558890 original size:28 final size:30
Alignment explanation
Indices: 52558849--52558906 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 30
52558839 ACTTAACAAG
52558849 CAAATGCCTCTAAAATAA-AA-AAAATTAA
1 CAAATGCCTCTAAAATAATAATAAAATTAA
* *
52558877 CAAATGTCTTTAAAATAATAATAAAATTAA
1 CAAATGCCTCTAAAATAATAATAAAATTAA
52558907 TAATAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 16 0.62
29 2 0.08
30 8 0.31
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.28
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAATAAAATTAA
Found at i:52558909 original size:12 final size:12
Alignment explanation
Indices: 52558887--52558915 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
52558877 CAAATGTCTT
52558887 TAAAA-TAATAA
1 TAAAATTAATAA
52558898 TAAAATTAATAA
1 TAAAATTAATAA
52558910 TAAAAT
1 TAAAAT
52558916 AAGTTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAAATTAATAA
Found at i:52558964 original size:22 final size:22
Alignment explanation
Indices: 52558939--52558981 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
52558929 TATCCAAACA
52558939 ATAACAACAAAATAGTAGCAAT
1 ATAACAACAAAATAGTAGCAAT
* **
52558961 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
52558982 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAT
Found at i:52558985 original size:11 final size:11
Alignment explanation
Indices: 52558946--52558986 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
52558936 ACAATAACAA
52558946 CAAAATAGTAG
1 CAAAATAGTAG
* *
52558957 CAATATAATAG
1 CAAAATAGTAG
*
52558968 TAAAATAGTAG
1 CAAAATAGTAG
52558979 CAAAATAG
1 CAAAATAG
52558987 GGAGAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:52561193 original size:13 final size:13
Alignment explanation
Indices: 52561177--52561242 Score: 89
Period size: 13 Copynumber: 5.1 Consensus size: 13
52561167 TTTAAACCAA
52561177 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
52561190 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* *
52561203 AATTTTTC-ACAGC
1 -ACTTTTCAAAAGC
52561216 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
52561229 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
52561242 A
1 A
52561243 TTGCCAAACT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
12 6 0.13
13 34 0.76
14 5 0.11
ACGTcount: A:0.38, C:0.24, G:0.08, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:52561208 original size:39 final size:39
Alignment explanation
Indices: 52561164--52561242 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 39
52561154 TAAACACTCA
52561164 AATTTTAAACCA-AACTTTTCAAAAGCACTTCTCAAAAGC
1 AATTTTAAA-CAGAACTTTTCAAAAGCACTTCTCAAAAGC
** * *
52561203 AATTTTTCACAGCACTTTTCAAAAGCACTTTTCAAAAGC
1 AATTTTAAACAGAACTTTTCAAAAGCACTTCTCAAAAGC
52561242 A
1 A
52561243 TTGCCAAACT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 2 0.06
39 33 0.94
ACGTcount: A:0.41, C:0.23, G:0.06, T:0.30
Consensus pattern (39 bp):
AATTTTAAACAGAACTTTTCAAAAGCACTTCTCAAAAGC
Found at i:52563815 original size:48 final size:48
Alignment explanation
Indices: 52563750--52564526 Score: 1374
Period size: 48 Copynumber: 16.1 Consensus size: 48
52563740 GCTGAAATTG
*
52563750 ATGTATAAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
* *
52563798 ATGTATGAGATAAGTATATGTGGTAAAGTCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
* *
52563846 ATGTATGAGATAAGTATATGTGGTCAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
52563894 TTGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
* *
52563942 ATGTATGAGATAAGTGTATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
52563990 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
52564038 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
52564086 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
52564134 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
52564182 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
52564230 ATGTATGAGATAAGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
52564278 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
52564326 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG--A-A-AT
*
52564378 ATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
52564426 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTACTGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
* *
52564474 ATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
52564522 ATGTA
1 ATGTA
52564527 GGCGATGTGT
Statistics
Matches: 702, Mismatches: 23, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
48 654 0.93
49 1 0.00
50 2 0.00
51 1 0.00
52 44 0.06
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (48 bp):
ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
Found at i:52564781 original size:37 final size:37
Alignment explanation
Indices: 52564675--52564781 Score: 187
Period size: 37 Copynumber: 2.9 Consensus size: 37
52564665 AATTATATTT
*
52564675 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
1 CGGGTAAGACCCGATGACTACGTGTGGAGATTTTGTC
52564712 CGGGTAAGACCCGATGACTACGTGTGGAGATTTTGTC
1 CGGGTAAGACCCGATGACTACGTGTGGAGATTTTGTC
* *
52564749 CGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 CGGGTAAGACCCGATGACTACGTGTGGAGATTT
52564782 CATCTGAGCT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (37 bp):
CGGGTAAGACCCGATGACTACGTGTGGAGATTTTGTC
Found at i:52567208 original size:24 final size:24
Alignment explanation
Indices: 52567176--52567230 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
52567166 ACACCTTCAT
*
52567176 ATACATATACACATGAACACATAC
1 ATACATATACACATAAACACATAC
* **
52567200 ATACTTATACACATAAACACATTT
1 ATACATATACACATAAACACATAC
52567224 ATACATA
1 ATACATA
52567231 CCTTCCACAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.49, C:0.22, G:0.02, T:0.27
Consensus pattern (24 bp):
ATACATATACACATAAACACATAC
Found at i:52569150 original size:18 final size:18
Alignment explanation
Indices: 52569129--52569195 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
52569119 CCTTTAACTA
* *
52569129 AAAAAATAAAATTAATTC
1 AAAAAATAAAATAAATCC
*
52569147 AAAAATAAAAAATAAATCC
1 AAAAA-ATAAAATAAATCC
* **
52569166 AAAAGATAAAATAAATGA
1 AAAAAATAAAATAAATCC
52569184 AAAAAATGAAAA
1 AAAAAAT-AAAA
52569196 CTTTATAAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
18 21 0.54
19 18 0.46
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.18
Consensus pattern (18 bp):
AAAAAATAAAATAAATCC
Found at i:52569158 original size:19 final size:20
Alignment explanation
Indices: 52569136--52569176 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
52569126 CTAAAAAAAT
* *
52569136 AAAATTAATTCAAAA-ATAA
1 AAAATAAATCCAAAAGATAA
52569155 AAAATAAATCCAAAAGATAA
1 AAAATAAATCCAAAAGATAA
52569175 AA
1 AA
52569177 TAAATGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.71, C:0.07, G:0.02, T:0.20
Consensus pattern (20 bp):
AAAATAAATCCAAAAGATAA
Found at i:52574414 original size:19 final size:20
Alignment explanation
Indices: 52574385--52574423 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
52574375 CAAATTAGGC
*
52574385 TTTTCTGATGCATTTAAGGA
1 TTTTCTGATGCACTTAAGGA
52574405 TTTT-TGATGCACTTAAGGA
1 TTTTCTGATGCACTTAAGGA
52574424 GCTTTTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.44
Consensus pattern (20 bp):
TTTTCTGATGCACTTAAGGA
Found at i:52577683 original size:49 final size:47
Alignment explanation
Indices: 52577554--52578050 Score: 780
Period size: 47 Copynumber: 10.4 Consensus size: 47
52577544 CGGCCAAGAC
52577554 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
52577601 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
*
52577648 AAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTG
1 AAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
*
52577697 AAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTG
1 AAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
52577746 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
*
52577793 AAAGTGTATATATATGTGAGAAGG-CTAATGGCCGATGTGATGAATGTG
1 AAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
* *
52577841 AAAGTGTATATATGTGGTAAGGCCTAATAGCCGATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
*
52577888 AAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
*
52577935 AAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
* * ** * * * *
52577982 AAAGTGTATATATGTGACAGGGCAGAGTGGCCAAACGTGATGGATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCC-GATGTGATGAATGTG
*
52578030 AAAGTGTATAAATGTGATAAG
1 AAAGTGTATATATGTGATAAG
52578051 TCCCGAAGGG
Statistics
Matches: 423, Mismatches: 21, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
46 14 0.03
47 239 0.57
48 60 0.14
49 110 0.26
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
Found at i:52577960 original size:189 final size:188
Alignment explanation
Indices: 52577554--52578050 Score: 818
Period size: 189 Copynumber: 2.6 Consensus size: 188
52577544 CGGCCAAGAC
*
52577554 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAC
52577619 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGA
66 AAGG-CTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATAGCCGA
52577684 TGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTG
128 TGTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTG
52577746 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTG
* *
52577811 AGAAGGCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGGTAAGGCCTAATAGCCGAT
64 ACAAGGCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
52577876 GTGATGAATGTGAAAGTG-TATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTG
129 GTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTG
*
52577935 AAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAC
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAC
* * * * *
52578000 AGGGC-AGAGTGGCCAAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
66 AAGGCTA-A-TGGCC-GATGTGATGAATGTGAAAGTGTATATATGTGATAAG
52578051 TCCCGAAGGG
Statistics
Matches: 290, Mismatches: 10, Indels: 13
0.93 0.03 0.04
Matches are distributed among these distances:
186 1 0.00
187 16 0.06
188 5 0.02
189 124 0.43
191 46 0.16
192 53 0.18
193 30 0.10
194 15 0.05
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (188 bp):
AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAC
AAGGCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGT
GATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTG
Found at i:52580250 original size:38 final size:38
Alignment explanation
Indices: 52580186--52580260 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
52580176 AATCCGAGTT
*
52580186 TAAAGACCCGCTGACTATATGAAGAGATTATGTCCGGG
1 TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
* *
52580224 TAAAGACCCGATGGCTATGT-ACAGAGATTATGTCCGG
1 TAAAGACCCGATGACTATATGA-AGAGATTATGTCCGG
52580261 ATTAAAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (38 bp):
TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
Found at i:52580373 original size:40 final size:40
Alignment explanation
Indices: 52580318--52580713 Score: 605
Period size: 40 Copynumber: 9.9 Consensus size: 40
52580308 CTCGACAATG
*
52580318 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
52580358 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
52580398 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
52580438 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
52580478 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* ** *
52580518 ATCCGGGCTAAGTTCCGAAGAGCATTTGTGCTAGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
52580558 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* * * *
52580598 ATCCGGGCTAAGTTCTGAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* ** * * * * *
52580638 ATCCGTGCTAAACCCCGAAGAGCATTCGTACTGGT-TTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* * *
52580677 ATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
52580714 CGTGTATTCG
Statistics
Matches: 326, Mismatches: 29, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
39 31 0.10
40 295 0.90
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
Found at i:52584030 original size:47 final size:47
Alignment explanation
Indices: 52583976--52584423 Score: 707
Period size: 47 Copynumber: 9.4 Consensus size: 47
52583966 CGGCCAAGAC
52583976 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
* *
52584023 AAAGTGTATATATGTGATAAGGGCTAATGGCCAATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
*
52584070 AAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTG
1 AAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
52584119 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
*
52584166 AAAGTGTATATATATGTGAGAAGGCCTAATGGCCGATGTGATGAATGTG
1 AAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
* *
52584215 AAAGTGTATATATGTGGTAAGGCCTAATAGCCGATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
*
52584262 AAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
* *
52584309 AAAGTGTATATATGTGATGAGGCCTAATTGCCGATGTGATGAATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
* * * * * * *
52584356 AAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
*
52584403 AAAGTGTATAAATGTGATAAG
1 AAAGTGTATATATGTGATAAG
52584424 TCCCGAAGGG
Statistics
Matches: 372, Mismatches: 25, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
47 282 0.76
49 90 0.24
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
Found at i:52584090 original size:96 final size:94
Alignment explanation
Indices: 52583976--52584423 Score: 707
Period size: 96 Copynumber: 4.7 Consensus size: 94
52583966 CGGCCAAGAC
52583976 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
* *
52584041 AAGGGCTAATGGCCAATGTGATGAATGTG
66 AAGGCCTAATGGCCGATGTGATGAATGTG
*
52584070 AAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTG
1 AAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTG
52584135 ATAAGGCCTAATGGCCGATGTGATGAATGTG
64 ATAAGGCCTAATGGCCGATGTGATGAATGTG
*
52584166 AAAGTGTATATATATGTGAGAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTG
1 AAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTG
* *
52584231 GTAAGGCCTAATAGCCGATGTGATGAATGTG
64 ATAAGGCCTAATGGCCGATGTGATGAATGTG
*
52584262 AAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
* *
52584327 GAGGCCTAATTGCCGATGTGATGAATGTG
66 AAGGCCTAATGGCCGATGTGATGAATGTG
* * * * * * * *
52584356 AAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGAT
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
52584421 AAG
66 AAG
52584424 TCCCGAAGGG
Statistics
Matches: 330, Mismatches: 22, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
94 147 0.45
96 183 0.55
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (94 bp):
AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
AAGGCCTAATGGCCGATGTGATGAATGTG
Found at i:52584155 original size:143 final size:141
Alignment explanation
Indices: 52583976--52584423 Score: 716
Period size: 143 Copynumber: 3.1 Consensus size: 141
52583966 CGGCCAAGAC
52583976 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
* *
52584041 AAGGGCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGA
66 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATAGCCGA
52584106 TGTGATGAATGTG
129 TGTGATGAATGTG
52584119 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTG
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTG
* *
52584184 AGAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGGTAAGGCCTAATAGCCGA
64 ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGA
52584249 TGTGATGAATGTG
129 TGTGATGAATGTG
*
52584262 AAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
1 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
* * * * * * * * *
52584327 GAGGCCTAATTGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACG
66 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATG
*
52584392 TGATGGATGTG
131 TGATGAATGTG
*
52584403 AAAGTGTATAAATGTGATAAG
1 AAAGTGTATATATGTGATAAG
52584424 TCCCGAAGGG
Statistics
Matches: 285, Mismatches: 18, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
141 96 0.34
143 145 0.51
145 44 0.15
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (141 bp):
AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATG
TGATGAATGTG
Found at i:52588650 original size:48 final size:48
Alignment explanation
Indices: 52588590--52588871 Score: 210
Period size: 48 Copynumber: 5.9 Consensus size: 48
52588580 AACGGTGCAG
* * * * *
52588590 ATGCCATGTCCCAGACATGGTCTTATACGGGACCTCATATTGGTTCCA
1 ATGCCATATCCCAGATATGGTCTTATACGGGACCTCATACTGATGCCA
* * * *
52588638 ATTCCATATCCCAGATATGGTCTTATATGGGATCTCATACTGATGCCG
1 ATGCCATATCCCAGATATGGTCTTATACGGGACCTCATACTGATGCCA
* * * * * *
52588686 ATGCCATATCCTAGATATGGTCTTACACGAGATCTCAT-CTCGATGGCG
1 ATGCCATATCCCAGATATGGTCTTATACGGGACCTCATACT-GATGCCA
* * * * * * * *
52588734 ATGCCATATCGCAGATATAGTTTTACATGGGATCTCAT-TTCGATGCCG
1 ATGCCATATCCCAGATATGGTCTTATACGGGACCTCATACT-GATGCCA
* * * * * ***
52588782 ATGTCATATCCCATATATGGTCTTACACGGGATCTCAT-TTCGATGGTG
1 ATGCCATATCCCAGATATGGTCTTATACGGGACCTCATACT-GATGCCA
* *
52588830 ATGTCATATCCCAGATATGGTCTTATACGGGATCTCAATACT
1 ATGCCATATCCCAGATATGGTCTTATACGGGACCTC-ATACT
52588872 CACATGTCGT
Statistics
Matches: 197, Mismatches: 34, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
47 2 0.01
48 192 0.97
49 2 0.01
50 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (48 bp):
ATGCCATATCCCAGATATGGTCTTATACGGGACCTCATACTGATGCCA
Found at i:52588690 original size:96 final size:96
Alignment explanation
Indices: 52588589--52588872 Score: 313
Period size: 96 Copynumber: 2.9 Consensus size: 96
52588579 TAACGGTGCA
* * * * * ** *
52588589 GATGCCATGTCCCAGACATGGTCTTATACGGGACCTCATATTGGTTCCAATTCCATATCCCAGAT
1 GATGCCATATCCCAGATATGGTCTTACACGGGATCTCAT-TTGATGGCGATTCCATATCCCAGAT
52588654 ATGGTCTTATATGGGATCTCATACT-GATGCC
65 ATGGTCTTATATGGGATCTCATACTCGATGCC
* * * * *
52588685 GATGCCATATCCTAGATATGGTCTTACACGAGATCTCATCTCGATGGCGATGCCATATCGCAGAT
1 GATGCCATATCCCAGATATGGTCTTACACGGGATCTCAT-TTGATGGCGATTCCATATCCCAGAT
* * * *
52588750 ATAGTTTTACATGGGATCTCAT-TTCGATGCC
65 ATGGTCTTATATGGGATCTCATACTCGATGCC
* * *
52588781 GATGTCATATCCCATATATGGTCTTACACGGGATCTCATTTCGATGGTGATGT-CATATCCCAGA
1 GATGCCATATCCCAGATATGGTCTTACACGGGATCTCATTT-GATGGCGAT-TCCATATCCCAGA
*
52588845 TATGGTCTTATACGGGATCTCAATACTC
64 TATGGTCTTATATGGGATCTC-ATACTC
52588873 ACATGTCGTG
Statistics
Matches: 152, Mismatches: 31, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
95 2 0.01
96 146 0.96
97 2 0.01
98 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (96 bp):
GATGCCATATCCCAGATATGGTCTTACACGGGATCTCATTTGATGGCGATTCCATATCCCAGATA
TGGTCTTATATGGGATCTCATACTCGATGCC
Found at i:52588887 original size:96 final size:96
Alignment explanation
Indices: 52588641--52588872 Score: 315
Period size: 96 Copynumber: 2.4 Consensus size: 96
52588631 GGTTCCAATT
*
52588641 CCATATCCCAGATATGGTCTTATATGGGATCTCATACT-GATGCCGATGCCATATCCTAGATATG
1 CCATATCCCAGATATGGTCTTATATGGGATCTCATACTCGATGCCGATG-CATATCCCAGATATG
52588705 GTCTTACACGAGATCTCATCTCGATGGCGATG
65 GTCTTACACGAGATCTCATCTCGATGGCGATG
* * * * * *
52588737 CCATATCGCAGATATAGTTTTACATGGGATCTCAT-TTCGATGCCGATGTCATATCCCATATATG
1 CCATATCCCAGATATGGTCTTATATGGGATCTCATACTCGATGCCGATG-CATATCCCAGATATG
* * *
52588801 GTCTTACACGGGATCTCATTTCGATGGTGATG
65 GTCTTACACGAGATCTCATCTCGATGGCGATG
* *
52588833 TCATATCCCAGATATGGTCTTATACGGGATCTCAATACTC
1 CCATATCCCAGATATGGTCTTATATGGGATCTC-ATACTC
52588873 ACATGTCGTG
Statistics
Matches: 115, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
95 1 0.01
96 110 0.96
97 2 0.02
98 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (96 bp):
CCATATCCCAGATATGGTCTTATATGGGATCTCATACTCGATGCCGATGCATATCCCAGATATGG
TCTTACACGAGATCTCATCTCGATGGCGATG
Found at i:52594936 original size:47 final size:47
Alignment explanation
Indices: 52594767--52595215 Score: 710
Period size: 47 Copynumber: 9.6 Consensus size: 47
52594757 TATTTGAATA
* *
52594767 AATGTGAAAGTGTATATATGTGATAAGG-CGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
52594813 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
52594862 AATGTG-AAGTGTATATATGTGATAAGGCCGAATGG-C-ATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
52594906 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGG-CGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
52594954 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
52595001 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
52595048 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
52595095 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * *
52595142 AATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
52595189 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
52595216 TCCCGAAGGG
Statistics
Matches: 381, Mismatches: 14, Indels: 15
0.93 0.03 0.04
Matches are distributed among these distances:
44 14 0.04
45 6 0.02
46 58 0.15
47 240 0.63
48 41 0.11
49 22 0.06
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:52596673 original size:40 final size:40
Alignment explanation
Indices: 52596629--52596860 Score: 349
Period size: 40 Copynumber: 5.8 Consensus size: 40
52596619 GAGAATTGAG
52596629 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
52596669 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
52596709 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
*
52596749 AGTGATGTATCCGGACTAAGT-TCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCT-CGAAGAGCATTCGTGCT
* * ** *
52596789 AGTGATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
* * * * *
52596829 GGTGTTATATCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCA
52596861 ATCATGCTGG
Statistics
Matches: 177, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
39 1 0.01
40 176 0.99
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
Found at i:52600941 original size:47 final size:47
Alignment explanation
Indices: 52600887--52601195 Score: 501
Period size: 47 Copynumber: 6.6 Consensus size: 47
52600877 TATTTGAATA
52600887 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
52600934 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
52600981 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
52601028 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
52601075 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
52601122 AATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
52601169 GATGTGAAAGTGTATAAATTTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
52601196 TCCCGAAGGG
Statistics
Matches: 249, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 249 1.00
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:52606275 original size:42 final size:41
Alignment explanation
Indices: 52606167--52606286 Score: 118
Period size: 43 Copynumber: 2.9 Consensus size: 41
52606157 GTCTGAGACG
* *
52606167 TCGTGTAAGACCGTGTCTGGGACACAGGTCTCGATTGGGATT
1 TCGTGTAAGACCATGTCTGGGACACAGGTATCGATT-GGATT
* *
52606209 TACGTATAAGACCATGTCTAGGACATC-GGTATCGTATCT-GATT
1 T-CGTGTAAGACCATGTCTGGGACA-CAGGTATCG-AT-TGGATT
* * *
52606252 TCGTGTAAGACCCTGTCTGGGACAAAGGCATCGAT
1 TCGTGTAAGACCATGTCTGGGACACAGGTATCGAT
52606287 ATTGTACTAC
Statistics
Matches: 64, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
41 2 0.03
42 27 0.42
43 31 0.48
44 3 0.05
45 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (41 bp):
TCGTGTAAGACCATGTCTGGGACACAGGTATCGATTGGATT
Found at i:52615282 original size:14 final size:14
Alignment explanation
Indices: 52615263--52615292 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
52615253 GTTGTGTTCG
52615263 TAGTTAAATTAGAT
1 TAGTTAAATTAGAT
52615277 TAGTTAAATTAGAT
1 TAGTTAAATTAGAT
52615291 TA
1 TA
52615293 AAAACAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (14 bp):
TAGTTAAATTAGAT
Found at i:52618286 original size:49 final size:49
Alignment explanation
Indices: 52618185--52618309 Score: 160
Period size: 49 Copynumber: 2.5 Consensus size: 49
52618175 AGATGCCGAC
* * ** *
52618185 GCCATGTCCCAGACATGGTTTTACACTGGCTTTCATATAGTGAGGCCGAT
1 GCCATGTCCCAGACA-GGTCTTACACTGGCTCTCATATACCGAGGCCAAT
* * * *
52618235 GCCATGTCCTAGACAGGTCTTACACTGGCTCTCATCTACCGATGTCAAT
1 GCCATGTCCCAGACAGGTCTTACACTGGCTCTCATATACCGAGGCCAAT
52618284 GCCATGTCCCAGACAGGTCTTACACT
1 GCCATGTCCCAGACAGGTCTTACACT
52618310 AGCTTATCAA
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
49 51 0.78
50 14 0.22
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (49 bp):
GCCATGTCCCAGACAGGTCTTACACTGGCTCTCATATACCGAGGCCAAT
Found at i:52618353 original size:97 final size:99
Alignment explanation
Indices: 52618185--52618362 Score: 238
Period size: 97 Copynumber: 1.8 Consensus size: 99
52618175 AGATGCCGAC
* * * *
52618185 GCCATGTCCCAGACATGGTTTTACACTGGCTTTCATATAGTGAGGCCGATGCCATGTCCTAGACA
1 GCCATGTCCCAGACATGGTCTTACACTAGCTTTCATATAGTGAGGCCGATGACATGTCCCAGACA
*
52618250 GGTCTTACACTGGCTCTCATCTACCGATGTCAAT
66 GGTCTTACACTAGCTCTCATCTACCGATGTCAAT
* *
52618284 GCCATGTCCCAGACA-GGTCTTACACTAGCTTATCA-AT-GTCGAGGTCGAT-ATATGTCCCAGA
1 GCCATGTCCCAGACATGGTCTTACACTAGCTT-TCATATAGT-GAGGCCGATGACATGTCCCAGA
*
52618345 CATGTCTTACACTAGCTC
64 CAGGTCTTACACTAGCTC
52618363 GCGTCTCAAC
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
97 27 0.39
98 24 0.35
99 18 0.26
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.29
Consensus pattern (99 bp):
GCCATGTCCCAGACATGGTCTTACACTAGCTTTCATATAGTGAGGCCGATGACATGTCCCAGACA
GGTCTTACACTAGCTCTCATCTACCGATGTCAAT
Found at i:52618427 original size:143 final size:140
Alignment explanation
Indices: 52618231--52618499 Score: 294
Period size: 143 Copynumber: 1.9 Consensus size: 140
52618221 ATAGTGAGGC
* * * * * *
52618231 CGATGCCATGTCCTAGACAGGTCTTACACTGGCTCTCATCTACCGATGTCAATGCCATGTCCCAG
1 CGATGCCATGTCCTAGACAGATCTTACACTGGCTCTAATATACCGAGGCCAATG--ATGTACCAG
* * *
52618296 ACAGGTCTTACACTAGCTTATCA-ATGTCGAGGTCGATATATGTCCCAGACATGTCTTACACTAG
64 ACAGATCTTACACTAGC-TATCATAT-T-GAGGCCGATACATGTCCCAGACATGTCTTACACTAG
52618360 CTCGCGTCTCAACGT
126 CTCGCGTCTCAACGT
* *
52618375 CGATG-CATGTCCTAGACATATCTTACACTGGCT-TAA-ATATCTCGAGGCCAATGTTGTACCAG
1 CGATGCCATGTCCTAGACAGATCTTACACTGGCTCTAATATA-C-CGAGGCCAATGATGTACCAG
* * * * * *
52618437 ACATATCTTATACTGGCTCTCATATTGTGGCCGATGCATGTCCCAGACATGTCTTACACTAGC
64 ACAGATCTTACACTAGCTATCATATTGAGGCCGATACATGTCCCAGACATGTCTTACACTAGC
52618500 ACACACATCT
Statistics
Matches: 105, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
139 33 0.31
140 5 0.05
141 24 0.23
142 3 0.03
143 35 0.33
144 5 0.05
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.29
Consensus pattern (140 bp):
CGATGCCATGTCCTAGACAGATCTTACACTGGCTCTAATATACCGAGGCCAATGATGTACCAGAC
AGATCTTACACTAGCTATCATATTGAGGCCGATACATGTCCCAGACATGTCTTACACTAGCTCGC
GTCTCAACGT
Found at i:52621756 original size:79 final size:79
Alignment explanation
Indices: 52621645--52621867 Score: 260
Period size: 79 Copynumber: 2.8 Consensus size: 79
52621635 GCTCCTCGTT
* * * *
52621645 CAAATGCCTTCGGGACATCGCCCGG-TTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCG
*
52621709 GATTTAGTAACTCGCA
64 GAATTAGTAACTCGCA
52621725 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAAT-TCGCACAAATGCCTTCGGGACTTAGCCCGG
*
52621788 AATTAGTATCTCGCA
65 AATTAGTAACTCGCA
* * * *
52621803 CAAATGCCTTCGGATCTTAGTCCGGATATT-GTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCC
52621865 GGA
63 GGA
52621868 CATCATTCAA
Statistics
Matches: 126, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
78 46 0.37
79 56 0.44
80 23 0.18
81 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:52621762 original size:39 final size:40
Alignment explanation
Indices: 52621645--52621867 Score: 257
Period size: 39 Copynumber: 5.7 Consensus size: 40
52621635 GCTCCTCGTT
* * *
52621645 CAAATGCCTTCGGGACATCGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
52621685 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
52621725 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
52621764 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
52621803 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
52621844 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
52621868 CATCATTCAA
Statistics
Matches: 165, Mismatches: 10, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
38 2 0.01
39 89 0.54
40 63 0.38
41 11 0.07
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:52628052 original size:28 final size:28
Alignment explanation
Indices: 52628012--52628081 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
52628002 CTTGGCCTGA
*
52628012 CACACGCCCGTGTCCCCCACACAGCCAT
1 CACATGCCCGTGTCCCCCACACAGCCAT
*
52628040 CACATGCCCGTGTCCCTCACACAGCCAT
1 CACATGCCCGTGTCCCCCACACAGCCAT
*
52628068 TACATGCCCGTGTC
1 CACATGCCCGTGTC
52628082 TAAAAACCTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.20, C:0.47, G:0.16, T:0.17
Consensus pattern (28 bp):
CACATGCCCGTGTCCCCCACACAGCCAT
Found at i:52629149 original size:49 final size:49
Alignment explanation
Indices: 52629046--52629170 Score: 135
Period size: 49 Copynumber: 2.5 Consensus size: 49
52629036 AGATGCCGAC
* * * *
52629046 GCCATGTCCCAGACATGGTCTTACACTGGCTTTCATATAGTGAGGCCGAT
1 GCCATGTCCCAGACA-GGTCTTACACTGGCTCTCATATAGTCAGGCCAAA
* * * *
52629096 GCCATGTCCAAGACAGGTTTTACACTGGCTCTCATCTA-TCAGTGTCAAA
1 GCCATGTCCCAGACAGGTCTTACACTGGCTCTCATATAGTCAG-GCCAAA
* *
52629145 GCCATATCCCAGACATGTCTTACACT
1 GCCATGTCCCAGACAGGTCTTACACT
52629171 AGCTTTTTTA
Statistics
Matches: 62, Mismatches: 12, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
48 3 0.05
49 45 0.73
50 14 0.23
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (49 bp):
GCCATGTCCCAGACAGGTCTTACACTGGCTCTCATATAGTCAGGCCAAA
Found at i:52629195 original size:98 final size:98
Alignment explanation
Indices: 52629046--52629225 Score: 229
Period size: 97 Copynumber: 1.8 Consensus size: 98
52629036 AGATGCCGAC
* * *
52629046 GCCATGTCCCAGACATGGTCTTACACTGGCTTTCATATAGTGAGGCCGATGCCATGTCCAAGACA
1 GCCATATCCCAGACATGGTCTTACACTAGCTTTCATATACTGAGGCCGATG-CATGTCCAAGACA
* *
52629111 GGTTTTACACTGGCTCTCATCTATCAGTGTCAAA
65 GGTCTTACACTAGCTCTCATCTATCAGTGTCAAA
** ** *
52629145 GCCATATCCCAGACAT-GTCTTACACTAGCTTTTTTAT-CTCGAGGTTGATGCATGTCCCAGACA
1 GCCATATCCCAGACATGGTCTTACACTAGCTTTCATATACT-GAGGCCGATGCATGTCCAAGACA
*
52629208 TGTCTTACACTAGCTCTC
65 GGTCTTACACTAGCTCTC
52629226 GTCTCAACGC
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
97 28 0.41
98 26 0.38
99 15 0.22
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (98 bp):
GCCATATCCCAGACATGGTCTTACACTAGCTTTCATATACTGAGGCCGATGCATGTCCAAGACAG
GTCTTACACTAGCTCTCATCTATCAGTGTCAAA
Found at i:52634137 original size:42 final size:42
Alignment explanation
Indices: 52634068--52634201 Score: 146
Period size: 42 Copynumber: 3.1 Consensus size: 42
52634058 TCTTACATGT
*
52634068 AATCAAATATCGATGCCACTGTCCCAGACAGGGTCTTACACAA
1 AATCAAA-ATCGATGCCAATGTCCCAGACAGGGTCTTACACAA
* *
52634111 AATCAAACAT-GATGCCAATGTCCCAGACATGGTCTTACACGTA
1 AATCAAA-ATCGATGCCAATGTCCCAGACAGGGTCTTACAC-AA
* * * *
52634154 AATCTCAAATCGATGCCAACGTCCCAGA-TGTGGTCTTACACGA
1 AATC-AAAATCGATGCCAATGTCCCAGACAG-GGTCTTACACAA
52634197 AATCA
1 AATCA
52634202 CATATCGGAA
Statistics
Matches: 77, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
42 28 0.36
43 21 0.27
44 28 0.36
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.22
Consensus pattern (42 bp):
AATCAAAATCGATGCCAATGTCCCAGACAGGGTCTTACACAA
Found at i:52634181 original size:86 final size:85
Alignment explanation
Indices: 52634037--52634201 Score: 201
Period size: 86 Copynumber: 1.9 Consensus size: 85
52634027 AGCTCGTACA
* * * *
52634037 ATGCCAACGTCCTAGGCGTGGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGACAG-GG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAATCAAATATCGATGCCACTGTCCCAGA-AGTGG
52634101 TCTTACACAAAATCAAACATG
65 TCTTACACAAAATCAAACATG
* * *
52634122 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCTCAA-ATCGATGCCAAC-GTCCCAGATGT
1 ATGCCAACGTCCCAGACATGGTCTTACACGT-AATC-AAATATCGATGCC-ACTGTCCCAGAAGT
*
52634185 GGTCTTACACGAAATCA
63 GGTCTTACACAAAATCA
52634202 CATATCGGAA
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
85 27 0.40
86 37 0.54
87 4 0.06
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.24
Consensus pattern (85 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAATCAAATATCGATGCCACTGTCCCAGAAGTGGT
CTTACACAAAATCAAACATG
Found at i:52634583 original size:8 final size:8
Alignment explanation
Indices: 52634570--52634601 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
52634560 ATTAGCCCTC
*
52634570 ACATTTTT
1 ACATTTTA
52634578 ACATTTTA
1 ACATTTTA
52634586 ACATTTTA
1 ACATTTTA
52634594 ACATTTTA
1 ACATTTTA
52634602 GTCCCTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.53
Consensus pattern (8 bp):
ACATTTTA
Found at i:52643970 original size:81 final size:81
Alignment explanation
Indices: 52643846--52644461 Score: 629
Period size: 81 Copynumber: 7.6 Consensus size: 81
52643836 TTGCCCTATA
* * * * *
52643846 GGGGTATTTCGATAATTTTATAAA-TCGAGGATATTTCAATAATTTTACAAATTAAGGGTATTTC
1 GGGGTATTTCGGTAATTTTACAAACT-GAGGGTATTTCAGTAATTTTACAAATTGAGGGTATTTC
*
52643910 AGTAATTTTACAAATTG
65 AGTAATTTTACAAACTG
* * * ** *
52643927 GGGGTATTTCAGTAATTTTACAAACTAAGGGTACTTCAGTAATTTTACAAATCAAGGGTGTTTCA
1 GGGGTATTTCGGTAATTTTACAAACTGAGGGTATTTCAGTAATTTTACAAATTGAGGGTATTTCA
*
52643992 GTAATTTTATAAACTG
66 GTAATTTTACAAACTG
* * * * * * * * *
52644008 GGGTTATTTCAGCAATTTTACAAA-TCGGGGGTATTTTAGTAATGTTACAAATCGGGGGTCTTTC
1 GGGGTATTTCGGTAATTTTACAAACT-GAGGGTATTTCAGTAATTTTACAAATTGAGGGTATTTC
* * *
52644072 GGTAATTTTATAAA-TC
65 AGTAATTTTACAAACTG
*
52644088 GGGGTATTTCGGTAATTTTACAAATCGGA-GGTATTTC-GATAATTTTACAAATT-AGGGGTATT
1 GGGGTATTTCGGTAATTTTACAAA-CTGAGGGTATTTCAG-TAATTTTACAAATTGA-GGGTATT
*
52644150 TCAATAATTTTACAAA-TCG
63 TCAGTAATTTTACAAACT-G
* * * * * * * **
52644169 GGGGTATTTTGATAATTTTACAAACCGAGTGTATTTCAATTATTTTAAAAATTGAGGGTATTTTG
1 GGGGTATTTCGGTAATTTTACAAACTGAGGGTATTTCAGTAATTTTACAAATTGAGGGTATTTCA
52644234 GTAATTTTACAAACTG
66 GTAATTTTACAAACTG
* * * * * * *
52644250 GGGGTATTTTGGTAATTTGACAAACCGAAGGTATTTTAATAATTTTACAAACTGAGGGTATTTC-
1 GGGGTATTTCGGTAATTTTACAAACTGAGGGTATTTCAGTAATTTTACAAATTGAGGGTATTTCA
*
52644314 GATAATTTTACAAACTA
66 G-TAATTTTACAAACTG
* * *
52644331 GGGGTATTTCGATAATTTTACAAACTGAGGGTATTTC-GATAATTTTACAAACTGGGGGTATTTC
1 GGGGTATTTCGGTAATTTTACAAACTGAGGGTATTTCAG-TAATTTTACAAATTGAGGGTATTTC
* *
52644395 GGTAATTTTACAAACCG
65 AGTAATTTTACAAACTG
* * *
52644412 AGGGTATTTCGGTAATTTTACAAACTGGGGGTATTTCGGTAATTTTACAA
1 GGGGTATTTCGGTAATTTTACAAACTGAGGGTATTTCAGTAATTTTACAA
52644462 TCCGGGGTCT
Statistics
Matches: 450, Mismatches: 70, Indels: 30
0.82 0.13 0.05
Matches are distributed among these distances:
79 1 0.00
80 66 0.15
81 378 0.84
82 5 0.01
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (81 bp):
GGGGTATTTCGGTAATTTTACAAACTGAGGGTATTTCAGTAATTTTACAAATTGAGGGTATTTCA
GTAATTTTACAAACTG
Found at i:52644468 original size:27 final size:27
Alignment explanation
Indices: 52643846--52644461 Score: 553
Period size: 27 Copynumber: 22.9 Consensus size: 27
52643836 TTGCCCTATA
* *
52643846 GGGGTATTTCGATAATTTTATAAA-TCG
1 GGGGTATTTCGGTAATTTTACAAACT-G
* * ** * *
52643873 AGGATATTTCAATAATTTTACAAATTA
1 GGGGTATTTCGGTAATTTTACAAACTG
* * *
52643900 AGGGTATTTCAGTAATTTTACAAATTG
1 GGGGTATTTCGGTAATTTTACAAACTG
* *
52643927 GGGGTATTTCAGTAATTTTACAAACTA
1 GGGGTATTTCGGTAATTTTACAAACTG
* * * *
52643954 AGGGTACTTCAGTAATTTTACAAA-TCA
1 GGGGTATTTCGGTAATTTTACAAACT-G
* * * *
52643981 AGGGTGTTTCAGTAATTTTATAAACTG
1 GGGGTATTTCGGTAATTTTACAAACTG
* * *
52644008 GGGTTATTTCAGCAATTTTACAAA-TCG
1 GGGGTATTTCGGTAATTTTACAAACT-G
** *
52644035 GGGGTATTTTAGTAATGTTACAAA-TCG
1 GGGGTATTTCGGTAATTTTACAAACT-G
* * *
52644062 GGGGTCTTTCGGTAATTTTATAAA-TC
1 GGGGTATTTCGGTAATTTTACAAACTG
52644088 GGGGTATTTCGGTAATTTTACAAA-TCG
1 GGGGTATTTCGGTAATTTTACAAACT-G
* * * *
52644115 GAGGTATTTCGATAATTTTACAAATTA
1 GGGGTATTTCGGTAATTTTACAAACTG
**
52644142 GGGGTATTTCAATAATTTTACAAA-TCG
1 GGGGTATTTCGGTAATTTTACAAACT-G
* * *
52644169 GGGGTATTTTGATAATTTTACAAACCG
1 GGGGTATTTCGGTAATTTTACAAACTG
* * ** * * *
52644196 AGTGTATTTCAATTATTTTAAAAATTG
1 GGGGTATTTCGGTAATTTTACAAACTG
* *
52644223 AGGGTATTTTGGTAATTTTACAAACTG
1 GGGGTATTTCGGTAATTTTACAAACTG
* * *
52644250 GGGGTATTTTGGTAATTTGACAAACCG
1 GGGGTATTTCGGTAATTTTACAAACTG
** ***
52644277 AAGGTATTTTAATAATTTTACAAACTG
1 GGGGTATTTCGGTAATTTTACAAACTG
* * *
52644304 AGGGTATTTCGATAATTTTACAAACTA
1 GGGGTATTTCGGTAATTTTACAAACTG
*
52644331 GGGGTATTTCGATAATTTTACAAACTG
1 GGGGTATTTCGGTAATTTTACAAACTG
* *
52644358 AGGGTATTTCGATAATTTTACAAACTG
1 GGGGTATTTCGGTAATTTTACAAACTG
*
52644385 GGGGTATTTCGGTAATTTTACAAACCG
1 GGGGTATTTCGGTAATTTTACAAACTG
*
52644412 AGGGTATTTCGGTAATTTTACAAACTG
1 GGGGTATTTCGGTAATTTTACAAACTG
52644439 GGGGTATTTCGGTAATTTTACAA
1 GGGGTATTTCGGTAATTTTACAA
52644462 TCCGGGGTCT
Statistics
Matches: 500, Mismatches: 81, Indels: 16
0.84 0.14 0.03
Matches are distributed among these distances:
26 26 0.05
27 471 0.94
28 3 0.01
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (27 bp):
GGGGTATTTCGGTAATTTTACAAACTG
Found at i:52645007 original size:22 final size:22
Alignment explanation
Indices: 52644982--52645023 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
52644972 CATAGCATAC
52644982 GTCACACACCTGATCACGTACG
1 GTCACACACCTGATCACGTACG
52645004 GTCACACACCTGATCACGTA
1 GTCACACACCTGATCACGTA
52645024 GACTACTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.36, G:0.17, T:0.19
Consensus pattern (22 bp):
GTCACACACCTGATCACGTACG
Found at i:52658215 original size:8 final size:8
Alignment explanation
Indices: 52658192--52658244 Score: 70
Period size: 8 Copynumber: 6.6 Consensus size: 8
52658182 ATGTATCGGC
*
52658192 AAAAGCTG
1 AAAAGCCG
*
52658200 AAATGCCG
1 AAAAGCCG
52658208 AAAAGCCG
1 AAAAGCCG
52658216 AAAAGCCG
1 AAAAGCCG
*
52658224 AAAAGTCG
1 AAAAGCCG
*
52658232 AAATGCCG
1 AAAAGCCG
52658240 AAAAG
1 AAAAG
52658245 TAGAAAGTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 38 1.00
ACGTcount: A:0.49, C:0.19, G:0.25, T:0.08
Consensus pattern (8 bp):
AAAAGCCG
Found at i:52658245 original size:16 final size:16
Alignment explanation
Indices: 52658199--52658250 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
52658189 GGCAAAAGCT
*
52658199 GAAATGCCGAAAAGCC
1 GAAATGCCGAAAAGTC
*
52658215 GAAAAGCCGAAAAGTC
1 GAAATGCCGAAAAGTC
*
52658231 GAAATGCCGAAAAGTA
1 GAAATGCCGAAAAGTC
52658247 GAAA
1 GAAA
52658251 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.50, C:0.17, G:0.25, T:0.08
Consensus pattern (16 bp):
GAAATGCCGAAAAGTC
Found at i:52658509 original size:27 final size:29
Alignment explanation
Indices: 52658474--52658548 Score: 100
Period size: 29 Copynumber: 2.7 Consensus size: 29
52658464 TGAACGTGAC
* * *
52658474 TGGGCCTAACGGGCCATA-A-ATGTGATT
1 TGGGACTAATGGGCCATATACAGGTGATT
*
52658501 TGGGTCTAATGGGCCATATACAGGTGATT
1 TGGGACTAATGGGCCATATACAGGTGATT
52658530 TGGGACTAATGGGCCATAT
1 TGGGACTAATGGGCCATAT
52658549 GAATATGATA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 16 0.38
28 1 0.02
29 25 0.60
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.28
Consensus pattern (29 bp):
TGGGACTAATGGGCCATATACAGGTGATT
Found at i:52658557 original size:29 final size:28
Alignment explanation
Indices: 52658474--52658557 Score: 98
Period size: 29 Copynumber: 3.0 Consensus size: 28
52658464 TGAACGTGAC
* *
52658474 TGGGCCTAACGGGCCATA-AATGTGATT
1 TGGGACTAATGGGCCATATAATGTGATT
* *
52658501 TGGGTCTAATGGGCCATATACAGGTGATT
1 TGGGACTAATGGGCCATATA-ATGTGATT
*
52658530 TGGGACTAATGGGCCATATGAATATGAT
1 TGGGACTAATGGGCCATAT-AATGTGAT
52658558 AGGGCTTAGT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
27 16 0.33
28 1 0.02
29 30 0.62
30 1 0.02
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.29
Consensus pattern (28 bp):
TGGGACTAATGGGCCATATAATGTGATT
Found at i:52664711 original size:8 final size:8
Alignment explanation
Indices: 52664697--52664730 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
52664687 TAACACCCTA
52664697 AAAATCCC
1 AAAATCCC
* *
52664705 GAAATCCA
1 AAAATCCC
52664713 AAAATCCC
1 AAAATCCC
52664721 AAAATCCC
1 AAAATCCC
52664729 AA
1 AA
52664731 TTTTTTTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.53, C:0.32, G:0.03, T:0.12
Consensus pattern (8 bp):
AAAATCCC
Found at i:52666047 original size:29 final size:28
Alignment explanation
Indices: 52665991--52666089 Score: 92
Period size: 29 Copynumber: 3.5 Consensus size: 28
52665981 ATGAGCATGA
* * *
52665991 ATATGAATGTGA-CTGGGACTAACGGGCC
1 ATATAAATGTGATTTGGGACTAA-TGGCC
*
52666019 ATATAAATGTGATTTGGGCCTAATAGGCC
1 ATATAAATGTGATTTGGGACTAAT-GGCC
* *
52666048 ATATACAGGTGATTTGGGACTAATGAGCC
1 ATATAAATGTGATTTGGGACTAATG-GCC
* *
52666077 ATATGAATATGAT
1 ATATAAATGTGAT
52666090 AGGGCTTAGT
Statistics
Matches: 57, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
28 12 0.21
29 45 0.79
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.28
Consensus pattern (28 bp):
ATATAAATGTGATTTGGGACTAATGGCC
Found at i:52669960 original size:19 final size:19
Alignment explanation
Indices: 52669936--52669977 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
52669926 GCAAAAACCA
52669936 CATCCATGAAAGGCATCAT
1 CATCCATGAAAGGCATCAT
52669955 CATCCATGAAAGGCATCAT
1 CATCCATGAAAGGCATCAT
52669974 CATC
1 CATC
52669978 ATGCCAATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (19 bp):
CATCCATGAAAGGCATCAT
Found at i:52672502 original size:15 final size:15
Alignment explanation
Indices: 52672482--52672519 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
52672472 CCTTTAGAAA
*
52672482 TTAAATTAAACTAAG
1 TTAAATAAAACTAAG
52672497 TTAAATAAAACTAA-
1 TTAAATAAAACTAAG
52672511 TATAAATAA
1 T-TAAATAA
52672520 GTAAAATAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 1 0.05
15 20 0.95
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.32
Consensus pattern (15 bp):
TTAAATAAAACTAAG
Found at i:52673769 original size:25 final size:25
Alignment explanation
Indices: 52673741--52673810 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
52673731 CTCTTTTAAT
*
52673741 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
52673766 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
52673791 AACTGGGGCATAA-CCCTTTT
1 AACTGGGGCA-AAGCCCTTTT
52673811 AGCACTTCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
25 40 0.95
26 2 0.05
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:52674174 original size:27 final size:27
Alignment explanation
Indices: 52674042--52674177 Score: 200
Period size: 27 Copynumber: 5.0 Consensus size: 27
52674032 GTATCTCAAA
* *
52674042 AATTCTACCTTACAGGGGTATTTCAAT
1 AATTCTACCCTACAGGGGTATTTCGAT
*
52674069 AATTCTACCCTACAGGGGTATTTCAAT
1 AATTCTACCCTACAGGGGTATTTCGAT
* * *
52674096 AATTCTACCCTATAAGGGTATTTCGGT
1 AATTCTACCCTACAGGGGTATTTCGAT
*
52674123 AATTCTACCCTACAGGGGTATTTCGGT
1 AATTCTACCCTACAGGGGTATTTCGAT
*
52674150 AACTCTACCCTACAGGGGTATTTCGAT
1 AATTCTACCCTACAGGGGTATTTCGAT
52674177 A
1 A
52674178 TTTTACAAAT
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 100 1.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (27 bp):
AATTCTACCCTACAGGGGTATTTCGAT
Found at i:52674231 original size:27 final size:27
Alignment explanation
Indices: 52674162--52674288 Score: 134
Period size: 27 Copynumber: 4.8 Consensus size: 27
52674152 CTCTACCCTA
* *
52674162 CAGGGGTATTTCGAT-ATTTTACAAAT
1 CAGGGGTATTTTGGTAATTTTACAAAT
* * * *
52674188 C-GAGTTATTTTGATAATTTCACAAAT
1 CAGGGGTATTTTGGTAATTTTACAAAT
*
52674214 CAGGGGTATTTTGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAT
**
52674241 CAGGGGTATTTTGGTAATTTTACTGAT
1 CAGGGGTATTTTGGTAATTTTACAAAT
*
52674268 C-GAGGGCATTTTGGTAATTTT
1 CAG-GGGTATTTTGGTAATTTT
52674289 GAAAACCAAG
Statistics
Matches: 85, Mismatches: 13, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
25 10 0.12
26 13 0.15
27 62 0.73
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (27 bp):
CAGGGGTATTTTGGTAATTTTACAAAT
Found at i:52674259 original size:54 final size:54
Alignment explanation
Indices: 52674162--52674314 Score: 134
Period size: 54 Copynumber: 2.9 Consensus size: 54
52674152 CTCTACCCTA
* * * * * *
52674162 CAGGGGTATTTCGAT-ATTTTACAAATC-GAGTTATTTTGATAATTTCACAAAT
1 CAGGGGTATTTTGGTAATTTTACAAACCAGGGATATTTTGGTAATTTCACAAAT
* * **
52674214 CAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACTGAT
1 CAGGGGTATTTTGGTAATTTTACAAACCAGGGATATTTTGGTAATTTCACAAAT
* * **
52674268 C-GAGGGCATTTTGGTAATTTTGA-AAACCAAGGATATTTCAGTAATTT
1 CAG-GGGTATTTTGGTAATTTT-ACAAACCAGGGATATTTTGGTAATTT
52674315 TGTAAATCGA
Statistics
Matches: 83, Mismatches: 14, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
52 13 0.16
53 12 0.14
54 57 0.69
55 1 0.01
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.39
Consensus pattern (54 bp):
CAGGGGTATTTTGGTAATTTTACAAACCAGGGATATTTTGGTAATTTCACAAAT
Found at i:52674305 original size:27 final size:27
Alignment explanation
Indices: 52674193--52674315 Score: 113
Period size: 27 Copynumber: 4.6 Consensus size: 27
52674183 CAAATCGAGT
* * * *
52674193 TATTTTGATAATTTCACAAATCAGGGG
1 TATTTTGGTAATTTTACAAACCAAGGG
*
52674220 TATTTTGGTAATTTTACAAACCAGGGG
1 TATTTTGGTAATTTTACAAACCAAGGG
** * *
52674247 TATTTTGGTAATTTTACTGATCGAGGG
1 TATTTTGGTAATTTTACAAACCAAGGG
* *
52674274 CATTTTGGTAATTTTGA-AAACCAAGGA
1 TATTTTGGTAATTTT-ACAAACCAAGGG
**
52674301 TATTTCAGTAATTTT
1 TATTTTGGTAATTTT
52674316 GTAAATCGAG
Statistics
Matches: 78, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
27 77 0.99
28 1 0.01
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.41
Consensus pattern (27 bp):
TATTTTGGTAATTTTACAAACCAAGGG
Found at i:52679011 original size:24 final size:24
Alignment explanation
Indices: 52678974--52679042 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 24
52678964 TACTAATATA
*
52678974 TCAGCTCGTAAGAGCTTATTGTTT
1 TCAGCTCGAAAGAGCTTATTGTTT
** **
52678998 TCAGCTCGCCAGAGCTTACCG-TT
1 TCAGCTCGAAAGAGCTTATTGTTT
52679021 TCAGCTC-AATAGAGCTTATTGT
1 TCAGCTCGAA-AGAGCTTATTGT
52679043 CCATCAGCTC
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
23 18 0.51
24 17 0.49
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (24 bp):
TCAGCTCGAAAGAGCTTATTGTTT
Found at i:52679240 original size:19 final size:19
Alignment explanation
Indices: 52679218--52679294 Score: 57
Period size: 19 Copynumber: 4.0 Consensus size: 19
52679208 TGTTACACGG
52679218 ATAAATTACTGTTATATGA
1 ATAAATTACTGTTATATGA
* * * *
52679237 ATAAAGTACTATTTATAAGG
1 ATAAATTACT-GTTATATGA
* * *
52679257 ATGAGTTACTGTTAT-CGA
1 ATAAATTACTGTTATATGA
*
52679275 ATGAATTACTGTTTATATGA
1 ATAAATTACTG-TTATATGA
52679295 TTGAGAGTGA
Statistics
Matches: 43, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
18 11 0.26
19 17 0.40
20 15 0.35
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.40
Consensus pattern (19 bp):
ATAAATTACTGTTATATGA
Found at i:52682834 original size:14 final size:14
Alignment explanation
Indices: 52682815--52682848 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
52682805 AGGTATGGGC
52682815 ATTATGAATTTCTT
1 ATTATGAATTTCTT
*
52682829 ATTATGGATTTCTT
1 ATTATGAATTTCTT
*
52682843 GTTATG
1 ATTATG
52682849 CTTTCCAGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.06, G:0.15, T:0.56
Consensus pattern (14 bp):
ATTATGAATTTCTT
Found at i:52685093 original size:14 final size:14
Alignment explanation
Indices: 52685074--52685104 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
52685064 TTTTCTTAAC
*
52685074 CGGTTCGGTTCACT
1 CGGTTCGGTTCAAT
52685088 CGGTTCGGTTCAAT
1 CGGTTCGGTTCAAT
52685102 CGG
1 CGG
52685105 ACCATTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.26, G:0.32, T:0.32
Consensus pattern (14 bp):
CGGTTCGGTTCAAT
Found at i:52703145 original size:80 final size:78
Alignment explanation
Indices: 52702943--52703164 Score: 284
Period size: 80 Copynumber: 2.8 Consensus size: 78
52702933 TATTCGGATG
* * *
52702943 ATAACCGGGCTAAGTCCTGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGCCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTG-CTATA-T-CGGGCTAAGTCCCGAAGGC
52703007 ATTTGTGCGAGTTACT
63 ATTTGTGCGAGTTACT
* *
52703023 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCTGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TGCTATATC-GGGCTAAGTCCCGAAGGCA
52703088 TTTGTGCGAGTTACT
64 TTTGTGCGAGTTACT
** * * * *
52703103 ATAACCGGGCTAAGTCCCGAAGGCATTTGAACGAATCGCTATATCCGGCTAAATCTCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT-GCTATATCGGGCTAAGTCCCGAAGG
52703165 TACTTGGTTT
Statistics
Matches: 125, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
79 16 0.13
80 107 0.86
81 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.26
Consensus pattern (78 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGCTATATCGGGCTAAGTCCCGAAGGCATT
TGTGCGAGTTACT
Found at i:52703164 original size:39 final size:40
Alignment explanation
Indices: 52702947--52703131 Score: 300
Period size: 40 Copynumber: 4.6 Consensus size: 40
52702937 CGGATGATAA
* * *
52702947 CCGGGCTAAGTCCTGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
52702987 CCGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
52703027 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
52703067 CTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
52703107 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
52703132 AACGAATCGC
Statistics
Matches: 136, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
40 135 0.99
41 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:52706042 original size:31 final size:31
Alignment explanation
Indices: 52705983--52706042 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
52705973 ACCAAATGTT
* *
52705983 TAAAATATAAATTATATATTTAAAAATAACA
1 TAAAATATAAATTATAAAATTAAAAATAACA
*
52706014 TAAAATATATAATT-TAAAATTAATAATAA
1 TAAAATATA-AATTATAAAATTAAAAATAA
52706043 TAACACATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (31 bp):
TAAAATATAAATTATAAAATTAAAAATAACA
Found at i:52706081 original size:36 final size:33
Alignment explanation
Indices: 52705983--52706082 Score: 82
Period size: 38 Copynumber: 2.9 Consensus size: 33
52705973 ACCAAATGTT
* *
52705983 TAAAATATA-AA-TTATATATTTAAAAAT-AACA
1 TAAAATATATAATTTA-AAATTAAAAAATAAACA
52706014 TAAAATATATAATTTAAAATTAATAATAATAACACA
1 TAAAATATATAATTTAAAATTAA-AA-AATAA-ACA
*
52706050 TGAAATATATATGATATTAAAA-TAAAAAATAAA
1 T-AAA-ATATATAAT-TTAAAATTAAAAAATAAA
52706083 TTAAATTATA
Statistics
Matches: 57, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
31 9 0.16
32 7 0.12
33 5 0.09
34 3 0.05
35 2 0.04
36 9 0.16
37 5 0.09
38 11 0.19
39 6 0.11
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (33 bp):
TAAAATATATAATTTAAAATTAAAAAATAAACA
Found at i:52708867 original size:19 final size:19
Alignment explanation
Indices: 52708839--52708887 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
52708829 TCCTTTTTCT
* * *
52708839 TTTCTGGGTTCATTAAATA
1 TTTCTAGGTTCATCAAACA
*
52708858 TTTCTAGGTTCATCCAACA
1 TTTCTAGGTTCATCAAACA
52708877 TTTCTAGGTTC
1 TTTCTAGGTTC
52708888 CTTTGAAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.45
Consensus pattern (19 bp):
TTTCTAGGTTCATCAAACA
Found at i:52709652 original size:19 final size:19
Alignment explanation
Indices: 52709628--52709676 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
52709618 GAGAATTAAA
52709628 AGAAAAGAAAAAAGAAAAG
1 AGAAAAGAAAAAAGAAAAG
** *
52709647 AGAAAAGAAAATGGAAACG
1 AGAAAAGAAAAAAGAAAAG
52709666 AGAAAGAGAAA
1 AGAAA-AGAAA
52709677 GAGAAAGGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.71, C:0.02, G:0.24, T:0.02
Consensus pattern (19 bp):
AGAAAAGAAAAAAGAAAAG
Found at i:52709653 original size:7 final size:7
Alignment explanation
Indices: 52709628--52709682 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 7
52709618 GAGAATTAAA
52709628 AGAAAAG
1 AGAAAAG
52709635 A-AAAA-
1 AGAAAAG
52709640 AGAAAAG
1 AGAAAAG
52709647 AGAAAAG
1 AGAAAAG
*
52709654 A-AAATG
1 AGAAAAG
*
52709660 -GAAACG
1 AGAAAAG
52709666 AG-AAAG
1 AGAAAAG
52709672 AG-AAAG
1 AGAAAAG
52709678 AGAAA
1 AGAAA
52709683 GGGAAAGGGA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
5 1 0.03
6 27 0.68
7 12 0.30
ACGTcount: A:0.71, C:0.02, G:0.25, T:0.02
Consensus pattern (7 bp):
AGAAAAG
Found at i:52709663 original size:12 final size:12
Alignment explanation
Indices: 52709625--52709682 Score: 64
Period size: 12 Copynumber: 4.7 Consensus size: 12
52709615 GAGGAGAATT
*
52709625 AAAAGAAAAGAA
1 AAAAGAAAAGAG
52709637 AAAAGAAAAGAG
1 AAAAGAAAAGAG
52709649 AAAAGAAAATG-G
1 AAAAGAAAA-GAG
*
52709661 AAACGAGAAAGAG
1 AAAAGA-AAAGAG
52709674 AAAGAGAAA
1 AAA-AGAAA
52709683 GGGAAAGGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
12 27 0.69
13 10 0.26
14 2 0.05
ACGTcount: A:0.72, C:0.02, G:0.24, T:0.02
Consensus pattern (12 bp):
AAAAGAAAAGAG
Found at i:52709676 original size:6 final size:6
Alignment explanation
Indices: 52709638--52709706 Score: 54
Period size: 6 Copynumber: 11.5 Consensus size: 6
52709628 AGAAAAGAAA
*
52709638 AAAGA- AAAGAG AAA-AG AAA-ATGG AAACGAG AAAGAG AAAGAG AAAGGG
1 AAAGAG AAAGAG AAAGAG AAAGA--G AAA-GAG AAAGAG AAAGAG AAAGAG
* * *
52709686 AAAGGG AAAGGG AAAGTG AAA
1 AAAGAG AAAGAG AAAGAG AAA
52709707 AATGAAATAA
Statistics
Matches: 57, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
5 11 0.19
6 37 0.65
7 8 0.14
9 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.33, T:0.03
Consensus pattern (6 bp):
AAAGAG
Found at i:52711917 original size:60 final size:60
Alignment explanation
Indices: 52711852--52711977 Score: 157
Period size: 60 Copynumber: 2.1 Consensus size: 60
52711842 TTTTTTTTTA
* * *
52711852 TTTTTTAGTCACTCAACTATAAAAAAGTTACAAAATGGTCACCAAACTATTAGTAA-TTT-TC
1 TTTTTTAATCACCCAACTAT-AAAAAGATACAAAATGGTCACCAAACTATT--TAATTTTGTC
* * *
52711913 TTTTTTAATCACCCAACTATGAAAAGATACAAAATGGTTACCTAACTATTTAATTTTGTC
1 TTTTTTAATCACCCAACTATAAAAAGATACAAAATGGTCACCAAACTATTTAATTTTGTC
52711973 TTTTT
1 TTTTT
52711978 ATGGTCATTG
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
58 3 0.05
59 3 0.05
60 33 0.58
61 18 0.32
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.40
Consensus pattern (60 bp):
TTTTTTAATCACCCAACTATAAAAAGATACAAAATGGTCACCAAACTATTTAATTTTGTC
Found at i:52714540 original size:40 final size:40
Alignment explanation
Indices: 52714458--52714678 Score: 182
Period size: 40 Copynumber: 5.5 Consensus size: 40
52714448 CTCAAGAAAT
* *
52714458 CTTCGGGAT-TTAG-CCGGATATAA-CTACTTGCAC-AAGGC
1 CTTCGGG-TCTTAGCCCGGATATAATC-ACTAGCACAAATGC
* ** *
52714496 CTTCGGGTCTTAGCCCGGATGTGGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAATCACTAGCACAAATGC
* *
52714536 CTTCGGGACTTAGCCCGGATATAATCGCTAGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAATCACTAGCACAAATGC
* * ** *
52714576 GTTCGGGTCTTAGCCCGGATAT-AGCAACTCTCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCACAAATGC
* * * * * *
52714616 CTTCAGATCTTAGTCCGGTTATAGTCACCTAGCACAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAATCA-CTAGCACAAATGC
* *
52714657 CTTCGGGACTTAGCTCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
52714679 CATTCGAATA
Statistics
Matches: 140, Mismatches: 36, Indels: 11
0.75 0.19 0.06
Matches are distributed among these distances:
37 1 0.01
38 11 0.08
39 15 0.11
40 87 0.62
41 26 0.19
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAATCACTAGCACAAATGC
Found at i:52717005 original size:40 final size:40
Alignment explanation
Indices: 52716943--52717019 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
52716933 ACGGTACCAT
*
52716943 TTGGTGTGTAGGGTTGGATGGGTTGATTATATCCCCATAC
1 TTGGTGTGTAGGGCTGGATGGGTTGATTATATCCCCATAC
* *
52716983 TTGGTGTGTAGGGCTGGGTGGGTTGATTCTATCCCCA
1 TTGGTGTGTAGGGCTGGATGGGTTGATTATATCCCCA
52717020 CATGGTATGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.14, C:0.14, G:0.35, T:0.36
Consensus pattern (40 bp):
TTGGTGTGTAGGGCTGGATGGGTTGATTATATCCCCATAC
Found at i:52717323 original size:18 final size:18
Alignment explanation
Indices: 52717300--52717353 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
52717290 CCACCACCAA
52717300 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
*
52717318 CTCCACCA-CCA-A----
1 CTCCACTAGCCACACTTG
52717330 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
52717348 CTCCAC
1 CTCCAC
52717354 CACCTACTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 7 0.25
13 3 0.11
14 1 0.04
16 1 0.04
17 3 0.11
18 13 0.46
ACGTcount: A:0.24, C:0.50, G:0.07, T:0.19
Consensus pattern (18 bp):
CTCCACTAGCCACACTTG
Found at i:52717326 original size:30 final size:30
Alignment explanation
Indices: 52717290--52717386 Score: 167
Period size: 30 Copynumber: 3.2 Consensus size: 30
52717280 CTAGCCTTTC
52717290 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
52717320 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* **
52717350 CCACCACCTACTGTACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
52717380 CCACCAC
1 CCACCAC
52717387 TACTTGTACC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.26, C:0.49, G:0.07, T:0.18
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:52717565 original size:16 final size:16
Alignment explanation
Indices: 52717546--52717581 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
52717536 CAAGGAGAAG
*
52717546 AGTTATTGTAAAGGCT
1 AGTTATTGGAAAGGCT
*
52717562 AGTTTTTGGAAAGGCT
1 AGTTATTGGAAAGGCT
52717578 AGTT
1 AGTT
52717582 TTTTTTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.28, T:0.39
Consensus pattern (16 bp):
AGTTATTGGAAAGGCT
Found at i:52717905 original size:23 final size:23
Alignment explanation
Indices: 52717868--52717997 Score: 86
Period size: 25 Copynumber: 5.5 Consensus size: 23
52717858 TTTTTTTTGT
*
52717868 TATTAT-TATATTTCTTAATATTA
1 TATTATATATA-TTCTTAATACTA
* *
52717891 TATTATATATATTCTT-TTAATA
1 TATTATATATATTCTTAATACTA
** * *
52717913 TATTAGGTATATTCTAAATTCTA
1 TATTATATATATTCTTAATACTA
*
52717936 TATTACGTATATATATGTT-ATACTA
1 TATTA--TATATAT-TCTTAATACTA
* *
52717961 TTTTATGTATATATCTTTAATACTA
1 TATTATATATAT-TC-TTAATACTA
*
52717986 TATTATTTATAT
1 TATTATATATAT
52717998 ATATATATAT
Statistics
Matches: 82, Mismatches: 18, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
22 17 0.21
23 27 0.33
24 6 0.07
25 30 0.37
26 2 0.02
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (23 bp):
TATTATATATATTCTTAATACTA
Found at i:52718177 original size:25 final size:24
Alignment explanation
Indices: 52718149--52718204 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
52718139 GTTATATTTT
*
52718149 CACTATTTTAT-GTATATACTTCAAA
1 CACTATTATATAGTATAT--TTCAAA
*
52718174 CACTA-TATATAGTATATTTCTAA
1 CACTATTATATAGTATATTTCAAA
52718197 CACTATTA
1 CACTATTA
52718205 CTATTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.37
24 6 0.22
25 11 0.41
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (24 bp):
CACTATTATATAGTATATTTCAAA
Found at i:52719960 original size:125 final size:125
Alignment explanation
Indices: 52719713--52719953 Score: 351
Period size: 125 Copynumber: 1.9 Consensus size: 125
52719703 TTAAGAAAGA
* *
52719713 TTTCAAAATTTTAAAAATAAATTTACTTGTTTGGGTAAAAATATTGAAAAATTTTAGAACTTGTG
1 TTTCAAAATTCTAAAAATAAATTTACTTGTTTGGGTAAAAATATTGAAAAATTTCAGAACTTGTG
* * * *
52719778 AGTAATTTTAAAAGGGGATTTCAACAGCTCAATTTTCTTTTCCAAATTCTAACTAAAGGT
66 AGTAATTTCAAAAGGAGATTTCAAAAGATCAATTTTCTTTTCCAAATTCTAACTAAAGGT
* * *
52719838 TTTCAAAAATTCTAAAAATGAAATTT-CTTTTTTGGGTAAATATATTGGAAAATTTCA-AACTTG
1 TTTC-AAAATTCTAAAAAT-AAATTTACTTGTTTGGGTAAAAATATTGAAAAATTTCAGAACTTG
* *
52719901 TGAGTAATTTCAAAAGGAGATTTCAAAAGATGAATTTTCTTTTTCAAATTCTA
64 TGAGTAATTTCAAAAGGAGATTTCAAAAGATCAATTTTCTTTTCCAAATTCTA
52719954 CTTAAAGAGG
Statistics
Matches: 103, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
125 57 0.55
126 40 0.39
127 6 0.06
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (125 bp):
TTTCAAAATTCTAAAAATAAATTTACTTGTTTGGGTAAAAATATTGAAAAATTTCAGAACTTGTG
AGTAATTTCAAAAGGAGATTTCAAAAGATCAATTTTCTTTTCCAAATTCTAACTAAAGGT
Found at i:52720042 original size:13 final size:13
Alignment explanation
Indices: 52720024--52720049 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52720014 CAAAGTGAAC
52720024 CAAAAAAAAAATT
1 CAAAAAAAAAATT
52720037 CAAAAAAAAAATT
1 CAAAAAAAAAATT
52720050 ATTTAATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAAAAAAATT
Found at i:52729198 original size:34 final size:34
Alignment explanation
Indices: 52729155--52729222 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
52729145 GAGTCCTAGT
52729155 TGAGACTAGTTTCGACTTGCCCTTTCCCATAATA
1 TGAGACTAGTTTCGACTTGCCCTTTCCCATAATA
52729189 TGAGACTAGTTTCGACTTGCCCTTTCCCATAATA
1 TGAGACTAGTTTCGACTTGCCCTTTCCCATAATA
52729223 ATAATTTTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (34 bp):
TGAGACTAGTTTCGACTTGCCCTTTCCCATAATA
Found at i:52734505 original size:50 final size:49
Alignment explanation
Indices: 52734387--52734617 Score: 284
Period size: 50 Copynumber: 4.7 Consensus size: 49
52734377 CTAGTATGCA
* * *
52734387 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCTGGTACACG
** *
52734436 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCTGGTACACG
* * * ** *
52734486 TAGTAGCCTGCACTTAGTACTACACACATGATCGAAGTTATCGGGTATGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCTGGTACACG
* * *
52734537 TAGTAG-CTTCACTTAGTACTACACATGCGACCAATTATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCTGGTACACG
*
52734585 TAGTAGCCTGCACTTAGTACTACACACATGACC
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC
52734618 TCACAATAGA
Statistics
Matches: 150, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
48 16 0.11
49 56 0.37
50 64 0.43
51 14 0.09
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCTGGTACACG
Found at i:52734577 original size:99 final size:99
Alignment explanation
Indices: 52734387--52734617 Score: 304
Period size: 99 Copynumber: 2.3 Consensus size: 99
52734377 CTAGTATGCA
*** *
52734387 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACATGACCAATTATCCGGTACACATAGTAGCCTGCACTTA
*
52734452 GTACTACACACGTGACCTAACCATCTGATACACG
66 GTACTACACACGCGACCTAACCATCTGATACACG
* * ** *
52734486 TAGTAGCCTGCACTTAGTACTACACACATGATCGAAGTTATCGGGTATGCATAGTAG-CTTCACT
1 TAGTAGCCTGCACTTAGTACTACACACATGA-CCAA-TTATCCGGTACACATAGTAGCCTGCACT
* ** *
52734550 TAGTACTACACATGCGACC-AATTATCTGGTACACG
64 TAGTACTACACACGCGACCTAACCATCTGATACACG
52734585 TAGTAGCCTGCACTTAGTACTACACACATGACC
1 TAGTAGCCTGCACTTAGTACTACACACATGACC
52734618 TCACAATAGA
Statistics
Matches: 115, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
98 1 0.01
99 72 0.63
100 26 0.23
101 16 0.14
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACACATGACCAATTATCCGGTACACATAGTAGCCTGCACTTA
GTACTACACACGCGACCTAACCATCTGATACACG
Found at i:52734894 original size:27 final size:27
Alignment explanation
Indices: 52734864--52734917 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
52734854 TCATACAACC
* *
52734864 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
52734891 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
52734918 TCACAAGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:52739379 original size:47 final size:48
Alignment explanation
Indices: 52739310--52739571 Score: 176
Period size: 47 Copynumber: 5.5 Consensus size: 48
52739300 TTTGTGTGCT
* *
52739310 AGTGTAAGA-CATATCTGGGACAT-ACATCGGCCACATTATGAGAGGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGGC
* * *
52739356 AGTGTAAGACCATGTCTGGGACATGGCATTGG---CATTAAGACAAGAGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGA-GAG-GC
* ** * * *
52739403 TAGTGTAAGA-CATGTCTGGGATAT-ATATCGGCCTCGA-GATGTA-AGCC
1 -AGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC-ATTATG-AGAGGC
* * * *
52739450 AGTGTAAGACCATGTATGGGACATGGCATCGGCCTCGATT-TCGATAGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC-ATTAT-GAGAGGC
*
52739499 AGTGTAAGACCATGTATGGGACATGGCATC-G--AC-TTGATG-GATGGGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATT-ATGAGA--GGC
52739545 TAGTGTAAGACCATGTCTGGGACATGG
1 -AGTGTAAGACCATGTCTGGGACATGG
52739572 AATCAGTATT
Statistics
Matches: 174, Mismatches: 22, Indels: 39
0.74 0.09 0.17
Matches are distributed among these distances:
44 3 0.02
45 8 0.05
46 28 0.16
47 66 0.38
48 30 0.17
49 37 0.21
50 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGGC
Found at i:52739470 original size:94 final size:94
Alignment explanation
Indices: 52739307--52739478 Score: 249
Period size: 94 Copynumber: 1.8 Consensus size: 94
52739297 TCATTTGTGT
* * *
52739307 GCTAGTGTAAGACATATCTGGGACATACATCGGCCACATTATGAGAGGCAGTGTAAGACCATGTC
1 GCTAGTGTAAGACATATCTGGGACATACATCGGCCACATGATGAGAGCCAGTGTAAGACCATGTA
52739372 TGGGACATGGCATTGGCATTAAGACAAGA
66 TGGGACATGGCATTGGCATTAAGACAAGA
* * * *
52739401 GCTAGTGTAAGACATGTCTGGGATATATATCGGCCTCGA-GATGTA-AGCCAGTGTAAGACCATG
1 GCTAGTGTAAGACATATCTGGGACATACATCGGCCAC-ATGATG-AGAGCCAGTGTAAGACCATG
52739464 TATGGGACATGGCAT
64 TATGGGACATGGCAT
52739479 CGGCCTCGAT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
94 67 0.97
95 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.24
Consensus pattern (94 bp):
GCTAGTGTAAGACATATCTGGGACATACATCGGCCACATGATGAGAGCCAGTGTAAGACCATGTA
TGGGACATGGCATTGGCATTAAGACAAGA
Found at i:52739508 original size:49 final size:46
Alignment explanation
Indices: 52739449--52739571 Score: 156
Period size: 49 Copynumber: 2.6 Consensus size: 46
52739439 AGATGTAAGC
* *
52739449 CAGTGTAAGACCATGTATGGGACATGGCATCGGCCTCGATTTCGATAGT
1 CAGTGTAAGACCATGTATGGGACATGGCATC-GACTCGA--TCGATAGG
* * *
52739498 CAGTGTAAGACCATGTATGGGACATGGCATCGACTTGATGGATGGG
1 CAGTGTAAGACCATGTATGGGACATGGCATCGACTCGATCGATAGG
*
52739544 CTAGTGTAAGACCATGTCTGGGACATGG
1 C-AGTGTAAGACCATGTATGGGACATGG
52739572 AATCAGTATT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
46 6 0.09
47 25 0.37
48 5 0.07
49 31 0.46
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (46 bp):
CAGTGTAAGACCATGTATGGGACATGGCATCGACTCGATCGATAGG
Found at i:52740663 original size:40 final size:40
Alignment explanation
Indices: 52740598--52740691 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 40
52740588 CCAACTCCGT
* * *
52740598 CCAACCCAACACACC--ATGTGGGGATAAAATCGACCCAC
1 CCAACCCTACACACCAAATATGGGGATAAAATCAACCCAC
* * * *
52740636 CCATCCCTACACACCAAATATGGGGATAATATCAACCTAT
1 CCAACCCTACACACCAAATATGGGGATAAAATCAACCCAC
52740676 CCAACCCTACACACCA
1 CCAACCCTACACACCA
52740692 TAAGGTACCG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
38 13 0.28
40 33 0.72
ACGTcount: A:0.37, C:0.37, G:0.11, T:0.15
Consensus pattern (40 bp):
CCAACCCTACACACCAAATATGGGGATAAAATCAACCCAC
Found at i:52743800 original size:33 final size:33
Alignment explanation
Indices: 52743763--52743827 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
52743753 AATTGTAGGC
52743763 TAATAATAAAGGGTGTGTAAAAAAATTCTAAAT
1 TAATAATAAAGGGTGTGTAAAAAAATTCTAAAT
52743796 TAATAATAAAGGGTGTGTAAAAAAATTCTAAA
1 TAATAATAAAGGGTGTGTAAAAAAATTCTAAA
52743828 CCGAAAAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.52, C:0.03, G:0.15, T:0.29
Consensus pattern (33 bp):
TAATAATAAAGGGTGTGTAAAAAAATTCTAAAT
Found at i:52744403 original size:71 final size:70
Alignment explanation
Indices: 52744277--52744420 Score: 236
Period size: 71 Copynumber: 2.0 Consensus size: 70
52744267 AAATTTTTTG
*
52744277 ATTTTTAATATTAATATTTTTTATAATAAATTTGAAATAAATTAAAATTAAAAGTAATACAATAT
1 ATTTTTAATATTAATATTTTTTATAATAAATTTGAAATAAATTAAAATTAAAAGTAATAAAATAT
52744342 ACTAA
66 ACTAA
* *
52744347 ATTTTTAATTTTTAAT-TTTTTTATAATGAATTTGAAATAAAATTAAAATTAAAAGTAATAAAAT
1 ATTTTTAA-TATTAATATTTTTTATAATAAATTTGAAAT-AAATTAAAATTAAAAGTAATAAAAT
52744411 ATACTAA
64 ATACTAA
52744418 ATT
1 ATT
52744421 GAAGAAAGAA
Statistics
Matches: 69, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
70 29 0.42
71 40 0.58
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.44
Consensus pattern (70 bp):
ATTTTTAATATTAATATTTTTTATAATAAATTTGAAATAAATTAAAATTAAAAGTAATAAAATAT
ACTAA
Found at i:52754246 original size:13 final size:13
Alignment explanation
Indices: 52754228--52754253 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52754218 CCTAAAATCC
52754228 ACATGCTCGTGTG
1 ACATGCTCGTGTG
52754241 ACATGCTCGTGTG
1 ACATGCTCGTGTG
52754254 GGCCCACACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.31, T:0.31
Consensus pattern (13 bp):
ACATGCTCGTGTG
Found at i:52754934 original size:13 final size:13
Alignment explanation
Indices: 52754904--52754928 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52754894 TGTAAAAAGA
52754904 AATAAAAGAAAAT
1 AATAAAAGAAAAT
52754917 AATAAAAGAAAA
1 AATAAAAGAAAA
52754929 ATATAATCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (13 bp):
AATAAAAGAAAAT
Found at i:52761632 original size:6 final size:6
Alignment explanation
Indices: 52761621--52761663 Score: 50
Period size: 6 Copynumber: 6.7 Consensus size: 6
52761611 AAAGGTCAGA
*
52761621 TTTTAT TTTTATTT GTTTTAT TTTTAT TTTTCT TTTTAT TTTT
1 TTTTAT TTTTA--T -TTTTAT TTTTAT TTTTAT TTTTAT TTTT
52761664 GTGATATGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 25 0.78
7 1 0.03
8 1 0.03
9 5 0.16
ACGTcount: A:0.12, C:0.02, G:0.02, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:52761639 original size:15 final size:15
Alignment explanation
Indices: 52761621--52761649 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
52761611 AAAGGTCAGA
52761621 TTTTATTTTTATTTG
1 TTTTATTTTTATTTG
52761636 TTTTATTTTTATTT
1 TTTTATTTTTATTT
52761650 TTCTTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (15 bp):
TTTTATTTTTATTTG
Found at i:52766099 original size:55 final size:55
Alignment explanation
Indices: 52766015--52766124 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
52766005 TAATAACTCA
*
52766015 TTTGTAAAATTATTTCAGATCACTTCGGTGATCAATGTGACCTCTGAAATTCGGT
1 TTTGTAAAATTATTTCAGATCACTTCGGTGATCAATGTGACCTCCGAAATTCGGT
*
52766070 TTTGTAAAATTGTTTCAGATCACTTCGGTGATCAATGTGACCTCCGAAATTCGGT
1 TTTGTAAAATTATTTCAGATCACTTCGGTGATCAATGTGACCTCCGAAATTCGGT
52766125 CTAAACTCTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.37
Consensus pattern (55 bp):
TTTGTAAAATTATTTCAGATCACTTCGGTGATCAATGTGACCTCCGAAATTCGGT
Found at i:52767557 original size:19 final size:19
Alignment explanation
Indices: 52767533--52767571 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
52767523 TGACTCTTGA
52767533 TTTAATTTTAACCAATTAT
1 TTTAATTTTAACCAATTAT
*
52767552 TTTAATTTTAATCAATTAT
1 TTTAATTTTAACCAATTAT
52767571 T
1 T
52767572 AAAAGTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTAATTTTAACCAATTAT
Found at i:52770754 original size:26 final size:26
Alignment explanation
Indices: 52770725--52770805 Score: 153
Period size: 26 Copynumber: 3.1 Consensus size: 26
52770715 ATAAAAAATT
*
52770725 ATAATGGGTTAGGTAAATATTCCATG
1 ATAATGGGTTAGGTAAATGTTCCATG
52770751 ATAATGGGTTAGGTAAATGTTCCATG
1 ATAATGGGTTAGGTAAATGTTCCATG
52770777 ATAATGGGTTAGGTAAATGTTCCATG
1 ATAATGGGTTAGGTAAATGTTCCATG
52770803 ATA
1 ATA
52770806 GGCATTTCAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.35
Consensus pattern (26 bp):
ATAATGGGTTAGGTAAATGTTCCATG
Found at i:52772471 original size:54 final size:54
Alignment explanation
Indices: 52772389--52772533 Score: 220
Period size: 54 Copynumber: 2.7 Consensus size: 54
52772379 ATGGAGGAAG
*
52772389 TGTCCTGGAGGCTATGCCACAATTATCTAATCTGGTGGCTCTGCCACATATATC
1 TGTCCTGGTGGCTATGCCACAATTATCTAATCTGGTGGCTCTGCCACATATATC
*
52772443 TGTCCTGGTGGCTATGGCACAATTATCTAATCTGGTGGCTCTGCCACATATATC
1 TGTCCTGGTGGCTATGCCACAATTATCTAATCTGGTGGCTCTGCCACATATATC
* * * *
52772497 TATTCTGGTGGCTCTGCCACAA-TATCTGTATCTGGTG
1 TGTCCTGGTGGCTATGCCACAATTATCT-AATCTGGTG
52772534 ACTTCGTCAC
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
53 5 0.06
54 78 0.94
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (54 bp):
TGTCCTGGTGGCTATGCCACAATTATCTAATCTGGTGGCTCTGCCACATATATC
Found at i:52772529 original size:32 final size:27
Alignment explanation
Indices: 52772393--52772533 Score: 155
Period size: 27 Copynumber: 5.2 Consensus size: 27
52772383 AGGAAGTGTC
* *
52772393 CTGGAGGCTATGCCACA-ATTATCTAAT
1 CTGGTGGCTCTGCCACATA-TATCTAAT
*
52772420 CTGGTGGCTCTGCCACATATATCT-GT
1 CTGGTGGCTCTGCCACATATATCTAAT
* *
52772446 CCTGGTGGCTATGGCACA-ATTATCTAAT
1 -CTGGTGGCTCTGCCACATA-TATCTAAT
*
52772474 CTGGTGGCTCTGCCACATATATCTATT
1 CTGGTGGCTCTGCCACATATATCTAAT
*
52772501 CTGGTGGCTCTGCCACA-ATATCTGTAT
1 CTGGTGGCTCTGCCACATATATCT-AAT
52772528 CTGGTG
1 CTGGTG
52772534 ACTTCGTCAC
Statistics
Matches: 97, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
26 8 0.08
27 86 0.89
28 3 0.03
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATATATCTAAT
Found at i:52772545 original size:81 final size:80
Alignment explanation
Indices: 52772393--52772550 Score: 205
Period size: 81 Copynumber: 2.0 Consensus size: 80
52772383 AGGAAGTGTC
*
52772393 CTGGAGGCTATGCCACAATTATCTAATCTGGTGGCTCTGCCACATATATCTGTCCTGGTGGCTAT
1 CTGGAGGCTATGCCACAATTATCTAATCTGGTGGCTCTGCCACATATATCTGTCCTGGTGACTAT
52772458 GGCACAATTATCTAAT
66 GGCACAA-TATCTAAT
* * * *
52772474 CTGGTGGCTCTGCCAC-ATATATCTATTCTGGTGGCTCTGCCACA-ATATCTGTATCTGGTGACT
1 CTGGAGGCTATGCCACAAT-TATCTAATCTGGTGGCTCTGCCACATATATCTGT-CCTGGTGACT
*
52772537 -TCGTCACAATATCT
64 AT-GGCACAATATCT
52772551 GGCAACCTCG
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
80 16 0.24
81 52 0.76
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.34
Consensus pattern (80 bp):
CTGGAGGCTATGCCACAATTATCTAATCTGGTGGCTCTGCCACATATATCTGTCCTGGTGACTAT
GGCACAATATCTAAT
Found at i:52778747 original size:26 final size:26
Alignment explanation
Indices: 52778710--52778788 Score: 142
Period size: 26 Copynumber: 3.1 Consensus size: 26
52778700 GATAAAAATT
*
52778710 ATAAT-GGTTAGGTAAATATTCCATG
1 ATAATGGGTTAGGTAAATGTTCCATG
52778735 ATAATGGGTTAGGTAAATGTTCCATG
1 ATAATGGGTTAGGTAAATGTTCCATG
52778761 ATAATGGGTTAGGTAAATGTTCCATG
1 ATAATGGGTTAGGTAAATGTTCCATG
52778787 AT
1 AT
52778789 GGGCATTTCA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
25 5 0.10
26 47 0.90
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.35
Consensus pattern (26 bp):
ATAATGGGTTAGGTAAATGTTCCATG
Found at i:52780424 original size:27 final size:27
Alignment explanation
Indices: 52780384--52780470 Score: 115
Period size: 27 Copynumber: 3.2 Consensus size: 27
52780374 AGGAAGCGTC
*
52780384 CTGGTGGCTATGCCACAATTATTTGAT
1 CTGGTGGCTCTGCCACAATTATTTGAT
* *
52780411 CTGGTGGCTCTGCCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATTTGAT
52780438 CTGGTGGCTCTGCCACAA-TATTTGTAT
1 CTGGTGGCTCTGCCACAATTATTTG-AT
52780465 CTGGTG
1 CTGGTG
52780471 ACTTCGTCAC
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
26 7 0.13
27 44 0.85
28 1 0.02
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATTTGAT
Found at i:52785177 original size:27 final size:27
Alignment explanation
Indices: 52785146--52785323 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
52785136 TAAATTGTAC
52785146 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
52785173 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
52785199 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
52785227 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
52785255 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
52785282 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
52785309 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
52785324 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:52785260 original size:82 final size:81
Alignment explanation
Indices: 52785147--52785302 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
52785137 AAATTGTACA
* *
52785147 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
52785211 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
52785228 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
52785293 TGCGAGTTGA
65 TGCGAATTGA
52785303 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:52785314 original size:82 final size:81
Alignment explanation
Indices: 52785143--52785323 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
52785133 GATTAAATTG
* *
52785143 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
52785208 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
52785224 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
52785288 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
52785306 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
52785324 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:52794578 original size:21 final size:21
Alignment explanation
Indices: 52794536--52794579 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
52794526 CACAGTGTAG
*
52794536 CAAAGGTAGCCAAAAAGAAAAA
1 CAAAGGTA-CCAAAAAAAAAAA
*
52794558 CAAAGGTACAAAAAAATAAAAA
1 CAAAGGTACCAAAAAA-AAAAA
52794580 TAAAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.68, C:0.11, G:0.14, T:0.07
Consensus pattern (21 bp):
CAAAGGTACCAAAAAAAAAAA
Found at i:52794580 original size:6 final size:6
Alignment explanation
Indices: 52794569--52794597 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
52794559 AAAGGTACAA
52794569 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
52794598 GAGAAAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:52795209 original size:19 final size:19
Alignment explanation
Indices: 52795173--52795208 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
52795163 TTGAAACCTT
52795173 AAAAAATAAAAAGAAAAAG
1 AAAAAATAAAAAGAAAAAG
*
52795192 AAAAAAT-CAAAGAAAAA
1 AAAAAATAAAAAGAAAAA
52795209 ATAAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.83, C:0.03, G:0.08, T:0.06
Consensus pattern (19 bp):
AAAAAATAAAAAGAAAAAG
Found at i:52795214 original size:19 final size:19
Alignment explanation
Indices: 52795172--52795216 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
52795162 CTTGAAACCT
52795172 TAAAAAATAAAAAGAAAAA
1 TAAAAAATAAAAAGAAAAA
* *
52795191 GAAAAAAT-CAAAGAAAAAA
1 TAAAAAATAAAAAG-AAAAA
52795210 TAAAAAA
1 TAAAAAA
52795217 ATTTATTCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.82, C:0.02, G:0.07, T:0.09
Consensus pattern (19 bp):
TAAAAAATAAAAAGAAAAA
Done.