Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 114 of 204
Found at i:35400928 original size:39 final size:39
Alignment explanation
Indices: 35400812--35400933 Score: 158
Period size: 40 Copynumber: 3.1 Consensus size: 39
35400802 GTTTGTACAA
* **
35400812 AAAACGTCGCTAAAAATCGAGCATTAGCGGCGCATTAGTT-
1 AAAACGCCGCTAAAAATCGAGCATTAGCGGCG--TTTTTTG
* *
35400852 AAAACGCCACTAAAGATCGAGCATTAGCGGCGCTTTTTTG
1 AAAACGCCGCTAAAAATCGAGCATTAGCGGCG-TTTTTTG
35400892 AAAACGCCGCTAAAAAT-GAGCATTAGCGGCGTTTTTTG
1 AAAACGCCGCTAAAAATCGAGCATTAGCGGCGTTTTTTG
35400930 AAAA
1 AAAA
35400934 AACGCCACAA
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
38 11 0.15
39 18 0.25
40 44 0.60
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (39 bp):
AAAACGCCGCTAAAAATCGAGCATTAGCGGCGTTTTTTG
Found at i:35400936 original size:40 final size:41
Alignment explanation
Indices: 35400794--35400939 Score: 156
Period size: 40 Copynumber: 3.6 Consensus size: 41
35400784 AGCGGCACTT
* * *
35400794 TTAGCGGCGTTTGTACAAAAAACGTCGCTAAAAATCGAGCA
1 TTAGCGGCGTTTTTAGAAAAAACGCCGCTAAAAATCGAGCA
** ** * *
35400835 TTAGCGGCG-CATTAGTTAAAACGCCACTAAAGATCGAGCA
1 TTAGCGGCGTTTTTAGAAAAAACGCCGCTAAAAATCGAGCA
*
35400875 TTAGCGGCGCTTTTTTG--AAAACGCCGCTAAAAAT-GAGCA
1 TTAGCGGCG-TTTTTAGAAAAAACGCCGCTAAAAATCGAGCA
*
35400914 TTAGCGGCGTTTTTTGAAAAAACGCC
1 TTAGCGGCGTTTTTAGAAAAAACGCC
35400940 ACAAAAAACC
Statistics
Matches: 87, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
38 7 0.08
39 14 0.16
40 54 0.62
41 9 0.10
42 3 0.03
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.24
Consensus pattern (41 bp):
TTAGCGGCGTTTTTAGAAAAAACGCCGCTAAAAATCGAGCA
Found at i:35401063 original size:41 final size:41
Alignment explanation
Indices: 35400984--35401143 Score: 178
Period size: 41 Copynumber: 3.9 Consensus size: 41
35400974 CCTTTCGGGG
* * *
35400984 CTTTAGCGACGTTTTTAAAAAAAGCGCCGCTAAAGCTCAGAT
1 CTTTAGCGGCGTTTTT-AGAAAAGCGCCGCTAATGCTCAGAT
* *
35401026 CTTTAGCGGCGTTTTTTGAAAAGCGCCACTAATGCTCAGAT
1 CTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGCTCAGAT
* * * * **
35401067 CTTTAGCGGCGATTCTAGAAATGCGCCGCTAATGCTCGGGG
1 CTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGCTCAGAT
* *
35401108 CTTTAGCGGCGTTTTCCA-ATAAGCGCCGCTAATGCT
1 CTTTAGCGGCGTTTT-TAGAAAAGCGCCGCTAATGCT
35401144 TAAGGCTTTA
Statistics
Matches: 99, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
41 83 0.84
42 16 0.16
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGCTCAGAT
Found at i:35401652 original size:14 final size:14
Alignment explanation
Indices: 35401622--35401687 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 14
35401612 GGGTTGTGAT
* *
35401622 TTAAGGTTTATGGG
1 TTAAGGGTTAGGGG
*
35401636 TTAGGGGTTAGGGG
1 TTAAGGGTTAGGGG
* *
35401650 TTAATGGTTAGAGG
1 TTAAGGGTTAGGGG
* * *
35401664 TTAAGAGTTAAGGA
1 TTAAGGGTTAGGGG
*
35401678 TTTAGGGTTA
1 TTAAGGGTTA
35401688 TGCATTCGGT
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
14 39 1.00
ACGTcount: A:0.26, C:0.00, G:0.38, T:0.36
Consensus pattern (14 bp):
TTAAGGGTTAGGGG
Found at i:35401673 original size:21 final size:21
Alignment explanation
Indices: 35401634--35401674 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
35401624 AAGGTTTATG
* * *
35401634 GGTTAGGGGTTAGGGGTTAAT
1 GGTTAGAGGTTAAGAGTTAAT
35401655 GGTTAGAGGTTAAGAGTTAA
1 GGTTAGAGGTTAAGAGTTAA
35401675 GGATTTAGGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.41, T:0.32
Consensus pattern (21 bp):
GGTTAGAGGTTAAGAGTTAAT
Found at i:35401814 original size:7 final size:7
Alignment explanation
Indices: 35401798--35401829 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
35401788 AGAGTTAGGG
*
35401798 TTAGGGT
1 TTAGGAT
35401805 TTAGGAT
1 TTAGGAT
35401812 TTAGGAT
1 TTAGGAT
35401819 TTAGGAT
1 TTAGGAT
35401826 TTAG
1 TTAG
35401830 ACTAATTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (7 bp):
TTAGGAT
Found at i:35403000 original size:147 final size:149
Alignment explanation
Indices: 35402793--35403106 Score: 456
Period size: 147 Copynumber: 2.1 Consensus size: 149
35402783 ATAATTTTTT
* * *
35402793 GCGGCGTTTTTATGAAAAACGCCACAAAAAATAATTTTACTTTAAAAAAATAGCGCCATTTTAGC
1 GCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAAATAACGCCATTTTAAC
* * * * **
35402858 ATAGCAAAACAGTGTCGTTTTATTCCAAATAAAATAATTTTTTTGCGGC-ATTTTTATGAAAACG
66 ATAACAAAACAGTATCGTTTTACTCCAAATAAAATAATTTTTTTACGGCGATTTTTACAAAAACG
* *
35402922 CTGCAAAATG-TAAGCAATA
131 CCGCAAAA-GATAAGCAAAA
* * *
35402941 GCGGCGTTTTTATAAAAAACGCCA-TAAAATTAATTTTACTTTAAAAAAATAACGTCATTTTAAC
1 GCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAAATAACGCCATTTTAAC
*
35403005 ATAACAAAACAGTATCGTTTTACTCCAAATAAAATAATTTTTTTACGGCGTTTTTTACAAAAACG
66 ATAACAAAACAGTATCGTTTTACTCCAAATAAAATAATTTTTTTACGGCGATTTTTACAAAAACG
35403070 CCGCAAAAGATAAGCAAAA
131 CCGCAAAAGATAAGCAAAA
35403089 G-GGCGTTTTTATAAAAAA
1 GCGGCGTTTTTATAAAAAA
35403107 AAACGCCACA
Statistics
Matches: 149, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
147 98 0.66
148 51 0.34
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.32
Consensus pattern (149 bp):
GCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAAATAACGCCATTTTAAC
ATAACAAAACAGTATCGTTTTACTCCAAATAAAATAATTTTTTTACGGCGATTTTTACAAAAACG
CCGCAAAAGATAAGCAAAA
Found at i:35407675 original size:43 final size:43
Alignment explanation
Indices: 35407623--35407936 Score: 430
Period size: 43 Copynumber: 7.3 Consensus size: 43
35407613 AGATTATGTT
* *
35407623 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATAGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* * * * *
35407666 TATGGCGGCGTTTGAGGGAAAAGTGCCACTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
** * * *
35407709 AATAGCGGCGTTTGTTGGAAAAGCGCCACTAATGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* * *
35407752 TATAGCGGCGTTTTTGGGAAAAGCGCCGCTAATGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* * * *
35407795 TTTAGCGGCGTTTTTTGAAAAAGCGCCGCTAAAGGTTATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* *
35407838 TTTAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
*
35407881 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
35407924 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
35407937 ATTTTTAAAA
Statistics
Matches: 242, Mismatches: 29, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 242 1.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:35409985 original size:202 final size:202
Alignment explanation
Indices: 35409633--35410041 Score: 687
Period size: 202 Copynumber: 2.0 Consensus size: 202
35409623 AAATTTTATC
** * * *
35409633 AAAATAATTTATGATTCGTGAATAGCATTATATGGAAAGTTGAAAGACTAATTAATAGTTACTTA
1 AAAATAAAGTATGATTCATGAATAGCATTATAGGGAAAGTTGAAAGACTAATTAATAGTTAATTA
*
35409698 AATTAGATAATTATGAAAAGCTTAATGATTAAGGACTCAATTGTGAAAAATCTATTTGGTTGGAA
66 AATTAGATAATTATGAAAAGCTTAATGATTAAGGACTAAATTGTGAAAAATCTATTTGGTTGGAA
*
35409763 TATTTATTTATTATTTATTTTAATTAATAAATTAAGTATATATTTTTATAGAATATTACAGAAAG
131 TATTTAATTATTATTTATTTTAATTAATAAATTAAGTATATATTTTTATAGAATATTACAGAAAG
35409828 ATGATGA
196 ATGATGA
* *
35409835 AAAATAAAGTATGATTCATGAATGGCATTATAGGGAAAGTTGAAGGACTAATTAATAGTTAATTA
1 AAAATAAAGTATGATTCATGAATAGCATTATAGGGAAAGTTGAAAGACTAATTAATAGTTAATTA
*
35409900 AATTAGATAATTATGAAAAGCTTAATGATTAAGGGCTAAATTGTGAAAAATCTAATTT-GTTGGA
66 AATTAGATAATTATGAAAAGCTTAATGATTAAGGACTAAATTGTGAAAAATCT-ATTTGGTTGGA
*
35409964 ATATTTAATTATT-TGTTATTTTAATTAATAAATTAAGTATATATTTTTATAGAATATTATAGAA
130 ATATTTAATTATTAT-TTATTTTAATTAATAAATTAAGTATATATTTTTATAGAATATTACAGAA
35410028 AGATGATGA
194 AGATGATGA
35410037 AAAAT
1 AAAAT
35410042 CATCCATGTC
Statistics
Matches: 194, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
201 1 0.01
202 189 0.97
203 4 0.02
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.39
Consensus pattern (202 bp):
AAAATAAAGTATGATTCATGAATAGCATTATAGGGAAAGTTGAAAGACTAATTAATAGTTAATTA
AATTAGATAATTATGAAAAGCTTAATGATTAAGGACTAAATTGTGAAAAATCTATTTGGTTGGAA
TATTTAATTATTATTTATTTTAATTAATAAATTAAGTATATATTTTTATAGAATATTACAGAAAG
ATGATGA
Found at i:35418914 original size:2 final size:2
Alignment explanation
Indices: 35418907--35418937 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
35418897 GTCTGCTATT
*
35418907 TC TC TC TC TC CC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
35418938 TGAAGCTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:35419474 original size:22 final size:22
Alignment explanation
Indices: 35419449--35419493 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
35419439 AATAATCTTG
35419449 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
35419471 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
35419493 T
1 T
35419494 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:35423247 original size:22 final size:22
Alignment explanation
Indices: 35423219--35423263 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
35423209 AGGGGGAGTG
35423219 TAGGAATATCCTGTAAATATTT
1 TAGGAATATCCTGTAAATATTT
** *
35423241 TAGGAATATTTTGTAGATATTT
1 TAGGAATATCCTGTAAATATTT
35423263 T
1 T
35423264 TTTATTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (22 bp):
TAGGAATATCCTGTAAATATTT
Found at i:35425431 original size:9 final size:9
Alignment explanation
Indices: 35425411--35425486 Score: 102
Period size: 9 Copynumber: 8.4 Consensus size: 9
35425401 GTAGTGATTC
35425411 AATTCGGTT
1 AATTCGGTT
35425420 AATTCAGG-T
1 AATTC-GGTT
35425429 AATTCGGTT
1 AATTCGGTT
35425438 AATTCGGTT
1 AATTCGGTT
*
35425447 AATTTAGG-T
1 AA-TTCGGTT
35425456 AATTCGGTT
1 AATTCGGTT
35425465 AATTCGGTT
1 AATTCGGTT
*
35425474 AATTCGGGT
1 AATTCGGTT
35425483 AATT
1 AATT
35425487 TTTAACCAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
8 6 0.10
9 48 0.80
10 6 0.10
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:35425443 original size:27 final size:27
Alignment explanation
Indices: 35425411--35425486 Score: 134
Period size: 27 Copynumber: 2.8 Consensus size: 27
35425401 GTAGTGATTC
35425411 AATTCGGTTAATTCAGGTAATTCGGTT
1 AATTCGGTTAATTCAGGTAATTCGGTT
*
35425438 AATTCGGTTAATTTAGGTAATTCGGTT
1 AATTCGGTTAATTCAGGTAATTCGGTT
*
35425465 AATTCGGTTAATTCGGGTAATT
1 AATTCGGTTAATTCAGGTAATT
35425487 TTTAACCAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.42
Consensus pattern (27 bp):
AATTCGGTTAATTCAGGTAATTCGGTT
Found at i:35447607 original size:17 final size:17
Alignment explanation
Indices: 35447576--35447624 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 17
35447566 TAGAATTGTG
*
35447576 TTGAGAAAATTATTTAAT
1 TTGA-AAAATAATTTAAT
35447594 TTGAAAAATAATTT-AT
1 TTGAAAAATAATTTAAT
*
35447610 TT--AAATTAATTTAAT
1 TTGAAAAATAATTTAAT
35447625 AAATAATACT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 9 0.32
15 2 0.07
16 4 0.14
17 9 0.32
18 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
TTGAAAAATAATTTAAT
Found at i:35450184 original size:17 final size:17
Alignment explanation
Indices: 35450139--35450180 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
35450129 GTAATATATA
35450139 TAATTGATATTTATGAT
1 TAATTGATATTTATGAT
35450156 TGAATTGTATATTTATG-T
1 T-AATTG-ATATTTATGAT
35450174 TAATTGA
1 TAATTGA
35450181 ATATATTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 1 0.04
17 6 0.26
18 7 0.30
19 9 0.39
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.52
Consensus pattern (17 bp):
TAATTGATATTTATGAT
Found at i:35450188 original size:19 final size:19
Alignment explanation
Indices: 35450140--35450184 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
35450130 TAATATATAT
35450140 AATTG-ATATTTATGATTG
1 AATTGTATATTTATGATTG
35450158 AATTGTATATTTATG-TT-
1 AATTGTATATTTATGATTG
*
35450175 AATTGAATAT
1 AATTGTATAT
35450185 ATTTTGAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 9 0.36
18 7 0.28
19 9 0.36
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (19 bp):
AATTGTATATTTATGATTG
Found at i:35452252 original size:25 final size:23
Alignment explanation
Indices: 35452208--35452253 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
35452198 ATGTTAATTG
35452208 ATTTAATTTTAAATAAAATAATA
1 ATTTAATTTTAAATAAAATAATA
* *
35452231 ATTTACATATTTAGATAGAATAA
1 ATTTA-AT-TTTAAATAAAATAA
35452254 ATATGTTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 2 0.11
25 12 0.63
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (23 bp):
ATTTAATTTTAAATAAAATAATA
Found at i:35461669 original size:24 final size:24
Alignment explanation
Indices: 35461635--35461681 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
35461625 TCATATTGTA
*
35461635 CTATTGCTTTTGGA-TTGCTTTTTT
1 CTATTGATTTTGGACTT-CTTTTTT
35461659 CTATTGATTTTGGACTTCTTTTT
1 CTATTGATTTTGGACTTCTTTTT
35461682 CTTTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.11, C:0.13, G:0.15, T:0.62
Consensus pattern (24 bp):
CTATTGATTTTGGACTTCTTTTTT
Found at i:35463654 original size:45 final size:45
Alignment explanation
Indices: 35463578--35463684 Score: 144
Period size: 45 Copynumber: 2.4 Consensus size: 45
35463568 GTAATGGTAG
*
35463578 CAGTAACAGTAACAGTAACAGAATTCAACACACAAAGTG-CTGAAT
1 CAGTAATAGTAACAGTAACAGAATTCAACACACAAAGTGTC-GAAT
* * * * *
35463623 CTGTCATAGTAACGGTAACAGTATTCGACACACAAAGTGTCGAAT
1 CAGTAATAGTAACAGTAACAGAATTCAACACACAAAGTGTCGAAT
35463668 CAGTAATAGTAACAGTA
1 CAGTAATAGTAACAGTA
35463685 GTAAGCATCT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
45 51 0.98
46 1 0.02
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (45 bp):
CAGTAATAGTAACAGTAACAGAATTCAACACACAAAGTGTCGAAT
Found at i:35463944 original size:40 final size:40
Alignment explanation
Indices: 35463884--35463970 Score: 111
Period size: 40 Copynumber: 2.2 Consensus size: 40
35463874 AATTCATTAC
* * *
35463884 TTCAGTAATTTCACAGTTCAATGCAATACACATAACAATA
1 TTCAGTAACTTCACAATTCAATGCAATACACAAAACAATA
* * * *
35463924 TTCAGTAACTTCACAATTCAATTCAGTACTCAAAAGAATA
1 TTCAGTAACTTCACAATTCAATGCAATACACAAAACAATA
35463964 TTCAGTA
1 TTCAGTA
35463971 TTCCATAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (40 bp):
TTCAGTAACTTCACAATTCAATGCAATACACAAAACAATA
Found at i:35464762 original size:5 final size:5
Alignment explanation
Indices: 35464752--35464778 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
35464742 TTACCTATTT
35464752 ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA AT
35464779 CTTATTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:35466502 original size:34 final size:34
Alignment explanation
Indices: 35466459--35466529 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
35466449 GATTTCGAAA
35466459 TCTCAAACAATCATGATCATCAACACTAAAATTT
1 TCTCAAACAATCATGATCATCAACACTAAAATTT
35466493 TCTCAAACAATCATGATCATCAACACTAAAATTT
1 TCTCAAACAATCATGATCATCAACACTAAAATTT
35466527 TCT
1 TCT
35466530 ACTGGGCCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.42, C:0.24, G:0.03, T:0.31
Consensus pattern (34 bp):
TCTCAAACAATCATGATCATCAACACTAAAATTT
Found at i:35470912 original size:45 final size:45
Alignment explanation
Indices: 35470817--35470916 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 45
35470807 TAACGGTAGT
* * **
35470817 AGTAACAGTAACAGTATTCAACGCAAAAAGTGTTGAATCTGTAAC
1 AGTAACAGTAACAGTATTCAACACAAAAAGTGTCGAATCAATAAC
* * *
35470862 AGTAACGGTAACAGTATTCGACACACAAAGTGTCGAATCAATAAC
1 AGTAACAGTAACAGTATTCAACACAAAAAGTGTCGAATCAATAAC
*
35470907 TGTAACAGTA
1 AGTAACAGTA
35470917 GTCGGCATAA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (45 bp):
AGTAACAGTAACAGTATTCAACACAAAAAGTGTCGAATCAATAAC
Found at i:35472000 original size:5 final size:5
Alignment explanation
Indices: 35471990--35472153 Score: 314
Period size: 5 Copynumber: 33.2 Consensus size: 5
35471980 TTTCTTTACC
35471990 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
35472040 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TAT-A TAT-A
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
35472088 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
35472138 TATAA TATAA TATAA T
1 TATAA TATAA TATAA T
35472154 CTTATTTATT
Statistics
Matches: 158, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
4 8 0.05
5 150 0.95
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:35474951 original size:20 final size:20
Alignment explanation
Indices: 35474928--35474982 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
35474918 GTGACAAGGC
*
35474928 ACACGCCCGTGTGACTGAGG
1 ACACGCCCATGTGACTGAGG
**
35474948 ACACTTCCATGTGACTGAAGG
1 ACACGCCCATGTGACTG-AGG
* *
35474969 TCACACCCATGTGA
1 ACACGCCCATGTGA
35474983 GTAGGCCGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.25, C:0.29, G:0.25, T:0.20
Consensus pattern (20 bp):
ACACGCCCATGTGACTGAGG
Found at i:35474980 original size:21 final size:20
Alignment explanation
Indices: 35474937--35474982 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
35474927 CACACGCCCG
**
35474937 TGTGACTGAGGACACTTCCA
1 TGTGACTGAGGACACACCCA
*
35474957 TGTGACTGAAGGTCACACCCA
1 TGTGACTG-AGGACACACCCA
35474978 TGTGA
1 TGTGA
35474983 GTAGGCCGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (20 bp):
TGTGACTGAGGACACACCCA
Found at i:35475875 original size:15 final size:16
Alignment explanation
Indices: 35475855--35475884 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
35475845 GAAATTTCCT
35475855 ACTAACTCG-ACAATC
1 ACTAACTCGCACAATC
35475870 ACTAACTCGCACAAT
1 ACTAACTCGCACAAT
35475885 TTGCTACCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.33, G:0.07, T:0.20
Consensus pattern (16 bp):
ACTAACTCGCACAATC
Found at i:35488661 original size:41 final size:41
Alignment explanation
Indices: 35488602--35488816 Score: 288
Period size: 41 Copynumber: 5.2 Consensus size: 41
35488592 AGAATATCCT
*
35488602 TGAATTGCACATACGTGCCCCTGTTTGTACTTTGATACCCC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
* * *
35488643 TGAATTGCACATATGTGCCTCTGTTTGTACTTCGGTACCCC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
* * *
35488684 TGAATTGCACATACGTGCCCTTTTTTTTTACTTTGGTACCCC
1 TGAATTGCACATACGTGCCC-CTGTTTGTACTTTGGTACCCC
* ** *
35488726 CGAATTGCACATATATGCCCCTATTTGTACTTTGGTACCCC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
* * *
35488767 TGAATTGCACATACGTGCCCCTTTTTGTACTATAGTACCCC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
35488808 TGAA-TGCAC
1 TGAATTGCAC
35488817 TTTTGTACCC
Statistics
Matches: 151, Mismatches: 22, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
40 5 0.03
41 112 0.74
42 34 0.23
ACGTcount: A:0.20, C:0.28, G:0.16, T:0.36
Consensus pattern (41 bp):
TGAATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
Found at i:35488753 original size:83 final size:82
Alignment explanation
Indices: 35488602--35488797 Score: 293
Period size: 83 Copynumber: 2.4 Consensus size: 82
35488592 AGAATATCCT
* * * * * *
35488602 TGAATTGCACATACGTGCCCCTGTTTGTACTTTGATACCCCTGAATTGCACATATGTGCCTCTGT
1 TGAATTGCACATACGTGCCCTTTTTTGTACTTTGATACCCCCGAATTGCACATATATGCCCCTAT
35488667 TTGTACTTCGGTACCCC
66 TTGTACTTCGGTACCCC
* *
35488684 TGAATTGCACATACGTGCCCTTTTTTTTTACTTTGGTACCCCCGAATTGCACATATATGCCCCTA
1 TGAATTGCACATACGTGCCC-TTTTTTGTACTTTGATACCCCCGAATTGCACATATATGCCCCTA
*
35488749 TTTGTACTTTGGTACCCC
65 TTTGTACTTCGGTACCCC
*
35488767 TGAATTGCACATACGTGCCCCTTTTTGTACT
1 TGAATTGCACATACGTGCCCTTTTTTGTACT
35488798 ATAGTACCCC
Statistics
Matches: 102, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
82 29 0.28
83 73 0.72
ACGTcount: A:0.19, C:0.28, G:0.16, T:0.37
Consensus pattern (82 bp):
TGAATTGCACATACGTGCCCTTTTTTGTACTTTGATACCCCCGAATTGCACATATATGCCCCTAT
TTGTACTTCGGTACCCC
Found at i:35489556 original size:15 final size:15
Alignment explanation
Indices: 35489538--35489572 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
35489528 AGTCGTGTGT
35489538 GACATACAGCCTGGC
1 GACATACAGCCTGGC
35489553 GACATACAGCCTGGC
1 GACATACAGCCTGGC
35489568 GACAT
1 GACAT
35489573 GGCCGTGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (15 bp):
GACATACAGCCTGGC
Found at i:35492313 original size:165 final size:165
Alignment explanation
Indices: 35492041--35492366 Score: 598
Period size: 165 Copynumber: 2.0 Consensus size: 165
35492031 AGTATAGACA
*
35492041 AAAACTTAAGTTACTTATACAATTTACAATTAATTATAACTTTACTACACATTCCCACTCAAACT
1 AAAACTTAAGCTACTTATACAATTTACAATTAATTATAACTTTACTACACATTCCCACTCAAACT
*
35492106 AATTTACACATGCATAGACAATAGGTAAATACAATTGCAGTACATGGTAATTTAATTAGAAGAAA
66 AATTTACACATGCATACACAATAGGTAAATACAATTGCAGTACATGGTAATTTAATTAGAAGAAA
* **
35492171 TCTGAATTGAAATTCTCCTCTATTATAGTTGTCCT
131 TATGAATTGAAACCCTCCTCTATTATAGTTGTCCT
*
35492206 AAAACTTAAGCTACTTATACAATTTACAATTAATTATAACTTTACTACACATTCCTACTCAAACT
1 AAAACTTAAGCTACTTATACAATTTACAATTAATTATAACTTTACTACACATTCCCACTCAAACT
35492271 AATTTACACATGCATACACAATAGGTAAATACAATTGCAGTACATGGTAATTTAATTAGAAGAAA
66 AATTTACACATGCATACACAATAGGTAAATACAATTGCAGTACATGGTAATTTAATTAGAAGAAA
35492336 TATGAATTGAAACCCTCCTCTATTATAGTTG
131 TATGAATTGAAACCCTCCTCTATTATAGTTG
35492367 CCCCAAAATT
Statistics
Matches: 155, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
165 155 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (165 bp):
AAAACTTAAGCTACTTATACAATTTACAATTAATTATAACTTTACTACACATTCCCACTCAAACT
AATTTACACATGCATACACAATAGGTAAATACAATTGCAGTACATGGTAATTTAATTAGAAGAAA
TATGAATTGAAACCCTCCTCTATTATAGTTGTCCT
Found at i:35493123 original size:28 final size:25
Alignment explanation
Indices: 35493092--35493153 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 25
35493082 ATAGAGGTGT
35493092 TTCTTTCAGTTTATCGCTACAAAGGCTA
1 TTCTTTCAGTTTA-C-C-ACAAAGGCTA
*
35493120 TTCTTTTAGAGTTTACCACAAAGGCTA
1 TTC-TTT-CAGTTTACCACAAAGGCTA
35493147 TTCTTTC
1 TTCTTTC
35493154 TTAAATCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
26 3 0.10
27 13 0.43
28 4 0.13
29 4 0.13
30 6 0.20
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (25 bp):
TTCTTTCAGTTTACCACAAAGGCTA
Found at i:35495167 original size:31 final size:31
Alignment explanation
Indices: 35495118--35495631 Score: 664
Period size: 31 Copynumber: 16.7 Consensus size: 31
35495108 GTATATGTTT
* * *
35495118 TATACATTGTC-AAATTGATTTGTATAAAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* * *
35495148 TATACATTGTCGAATTTGATTTGTTTATAGG
1 TATACATTGCCGAATTTGATTTGTATATAGA
** * * *
35495179 TATACATTGTTGAAATTGAATTGTTTATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
35495210 TATACATTGTC-AAATTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
35495240 TATACATTGCCGAATTTGATTTGTATATGGT
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
35495271 TATACATTGCCGAATTTAATTTGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* * *
35495302 TATATATTGCCTAA-TTGATTTTTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
35495332 TATACATTGCCGAATTTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* * *
35495363 TATACATTGTCGAATTTGATTTGTATATGGT
1 TATACATTGCCGAATTTGATTTGTATATAGA
35495394 TATACATTGCCGAATTTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
*
35495425 TATACATTCCCGAA-TTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
*
35495455 TATACATTGCC-AAATTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
35495485 TATACATTGCCGAATTTGATTTGTATATGGT
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
35495516 TATACATTGCCAAATTTGATTTGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
35495547 TATTCATTGCC-AAATTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
*
35495577 TATACATTGCCGAATTTGATTTGTATATGAATA
1 TATACATTGCCGAATTTGATTTGTATAT--AGA
*
35495610 TATATATTGCCGAA-TTGATTTG
1 TATACATTGCCGAATTTGATTTG
35495632 AGCATTGAAT
Statistics
Matches: 431, Mismatches: 45, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
29 2 0.00
30 143 0.33
31 263 0.61
32 8 0.02
33 15 0.03
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.44
Consensus pattern (31 bp):
TATACATTGCCGAATTTGATTTGTATATAGA
Found at i:35495238 original size:61 final size:62
Alignment explanation
Indices: 35495118--35495631 Score: 664
Period size: 61 Copynumber: 8.4 Consensus size: 62
35495108 GTATATGTTT
* * * * *
35495118 TATACATTGTC-AAATTGATTTGTATAAAGATATACATTGTCGAATTTGATTTGTTTATAGG
1 TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
** * * * *
35495179 TATACATTGTTGAAATTGAATTGTTTATAGATATACATTGTC-AAATTGATTTGTATATAGA
1 TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* * * * *
35495240 TATACATTGCCGAATTTGATTTGTATATGGTTATACATTGCCGAATTTAATTTGTATATGGA
1 TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* * *
35495302 TATATATTGCC-TAATTGATTTTTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
1 TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* * * *
35495363 TATACATTGTCGAATTTGATTTGTATATGGTTATACATTGCCGAATTTGATTTGTATATAGA
1 TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* *
35495425 TATACATTCCCG-AATTGATTTGTATATAGATATACATTGCC-AAATTGATTTGTATATAGA
1 TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* * * * *
35495485 TATACATTGCCGAATTTGATTTGTATATGGTTATACATTGCCAAATTTGATTTGTATATGGA
1 TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* *
35495547 TATTCATTGCC-AAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGAATA
1 TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATAT--AGA
*
35495610 TATATATTGCCG-AATTGATTTG
1 TATACATTGCCGAAATTGATTTG
35495632 AGCATTGAAT
Statistics
Matches: 391, Mismatches: 54, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
60 29 0.07
61 207 0.53
62 135 0.35
63 20 0.05
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.44
Consensus pattern (62 bp):
TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
Found at i:35495254 original size:92 final size:92
Alignment explanation
Indices: 35495118--35495631 Score: 637
Period size: 92 Copynumber: 5.6 Consensus size: 92
35495108 GTATATGTTT
* * * *
35495118 TATACATTGTC-AAATTGATTTGTATAAAGATATACATTGTCGAATTTGATTTGTTTATAGGTAT
1 TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGGTAT
* * *
35495182 ACATTGTTGAAATTGAATTGTTTATAGA
66 ACATTG-CGAAATTGATTTGTATATAGA
*
35495210 TATACATTGTC-AAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATAT-GGTTA
1 TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGG-TA
* * *
35495273 TACATTGCCGAATTTAATTTGTATATGGA
65 TACATTG-CGAAATTGATTTGTATATAGA
* * * *
35495302 TATATATTGCC-TAATTGATTTTTATATAGATATACATTGCCGAATTTGATTTGTATATAGATAT
1 TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGGTAT
* * *
35495366 ACATTGTCGAATTTGATTTGTATATGGT
66 ACATTG-CGAAATTGATTTGTATATAGA
* * *
35495394 TATACATTGCCGAATTTGATTTGTATATAGATATACATTCCCGAA-TTGATTTGTATATAGATAT
1 TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGGTAT
*
35495458 ACATTGCCAAATTGATTTGTATATAGA
66 ACATTGCGAAATTGATTTGTATATAGA
* * * *
35495485 TATACATTGCCGAATTTGATTTGTATATGGTTATACATTGCCAAATTTGATTTGTATAT-GGATA
1 TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGG-TA
* *
35495549 TTCATTGCCAAATTGATTTGTATATAGA
65 TACATTGCGAAATTGATTTGTATATAGA
* * *
35495577 TATACATTGCCGAATTTGATTTGTATATGAATATATATATTGCCGAA-TTGATTTG
1 TATACATTGCCGAAATTGATTTGTATAT--AGATATACATTGCCGAATTTGATTTG
35495632 AGCATTGAAT
Statistics
Matches: 377, Mismatches: 38, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
91 61 0.16
92 266 0.71
93 38 0.10
94 12 0.03
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.44
Consensus pattern (92 bp):
TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGGTAT
ACATTGCGAAATTGATTTGTATATAGA
Found at i:35497383 original size:30 final size:31
Alignment explanation
Indices: 35497347--35497432 Score: 104
Period size: 30 Copynumber: 2.8 Consensus size: 31
35497337 ATAGTACGAG
**
35497347 GTATGAATATGTTAATATGAATG-TTACAAT
1 GTATGAATATGAAAATATGAATGATTACAAT
*
35497377 GTATGAATATGAAAATATGAATGATTAC-AG
1 GTATGAATATGAAAATATGAATGATTACAAT
* * *
35497407 GTAAGAAAATAAAAATATGAATGATT
1 GTATGAATATGAAAATATGAATGATT
35497433 GATGCCCATA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
30 45 0.92
31 4 0.08
ACGTcount: A:0.48, C:0.02, G:0.17, T:0.33
Consensus pattern (31 bp):
GTATGAATATGAAAATATGAATGATTACAAT
Found at i:35504695 original size:16 final size:15
Alignment explanation
Indices: 35504674--35504703 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
35504664 GAACAGATCA
35504674 AAAAATAAATAAAAAT
1 AAAAATAAA-AAAAAT
35504690 AAAAATAAAAAAAA
1 AAAAATAAAAAAAA
35504704 CTTTGAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAAATAAAAAAAAT
Found at i:35506438 original size:169 final size:169
Alignment explanation
Indices: 35505773--35506412 Score: 998
Period size: 169 Copynumber: 3.8 Consensus size: 169
35505763 CATCGTTGCG
* * *
35505773 GCTTTAATCTATTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTCGATCCGCTC
1 GCTTTAATCTGTTCCACTATAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTCAATCCGCTC
35505838 CACCTCAGCTATTCTAAGTCTCAACGCCAGGGAGATAAGATCCGCTGCCCTCAGCTTTAATCTGC
66 CACCTCAGCTATTCTAAGTCTCAACGCCAGGGAGATAAGATCCGCTGCCCTCAGCTTTAATCTGC
*
35505903 TCCGCTGCAACACTAGGGAAACAAGATTCGCTACATTTA
131 TCCGCTGCAACACTAGGGAAACAAGATTCGCTACCTTTA
*
35505942 GCTTTAATCTGTTCCACTATAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTCGATCCGCTC
1 GCTTTAATCTGTTCCACTATAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTCAATCCGCTC
35506007 CACCTCAGCTATTCTAAGTCTCAACGCCAGGGAGATAAGATCCGCTGCCCTCAGCTTTAATCTGC
66 CACCTCAGCTATTCTAAGTCTCAACGCCAGGGAGATAAGATCCGCTGCCCTCAGCTTTAATCTGC
35506072 TCCGCTGCAACACTAGGGAAACAAGATTCGCTACCTTTA
131 TCCGCTGCAACACTAGGGAAACAAGATTCGCTACCTTTA
* * *
35506111 GCTTTAATCCGTTCCACTATAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTTAATCTGCTC
1 GCTTTAATCTGTTCCACTATAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTCAATCCGCTC
* * * * * *
35506176 CACTTCAGCTATT-TCAACTCTTAACACCAGGGAGATAAGATTCGCTGCCCTCAACTTTAATCTG
66 CACCTCAGCTATTCT-AAGTCTCAACGCCAGGGAGATAAGATCCGCTGCCCTCAGCTTTAATCTG
*
35506240 CTCCGCTGCAACGCTAGGGAAACAAGATTCGCTACCTTTA
130 CTCCGCTGCAACACTAGGGAAACAAGATTCGCTACCTTTA
* * *
35506280 ACTTTAATCTGTTCCACTATAATTCCAAAGAGATAGGA-TCTGCTGCCCACAGCTTTAATCCGCT
1 GCTTTAATCTGTTCCACTATAATGCCAAAGAGATAGGATTC-GCTGCCCACAGCTTCAATCCGCT
* * * * * * *
35506344 CTACTTCATCTATT-TCAAGTCTTAACGCCAGGGAGATAAGATTCGTTACCCTCAGCTTTAATCT
65 CCACCTCAGCTATTCT-AAGTCTCAACGCCAGGGAGATAAGATCCGCTGCCCTCAGCTTTAATCT
*
35506408 TCTCC
129 GCTCC
35506413 ACTATAATGT
Statistics
Matches: 443, Mismatches: 26, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
168 3 0.01
169 440 0.99
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.28
Consensus pattern (169 bp):
GCTTTAATCTGTTCCACTATAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTCAATCCGCTC
CACCTCAGCTATTCTAAGTCTCAACGCCAGGGAGATAAGATCCGCTGCCCTCAGCTTTAATCTGC
TCCGCTGCAACACTAGGGAAACAAGATTCGCTACCTTTA
Found at i:35506483 original size:44 final size:44
Alignment explanation
Indices: 35506434--35506520 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
35506424 AGGAAAGTAA
35506434 GATTCACAATCTTCAACCTATTCCACTGCTAACCAGGGAGATAG
1 GATTCACAATCTTCAACCTATTCCACTGCTAACCAGGGAGATAG
* * * *
35506478 GATTCACAATCTTTAACTTATTCCGCTGCTGACCAGGGAGATA
1 GATTCACAATCTTCAACCTATTCCACTGCTAACCAGGGAGATA
35506521 AGGCTAGGGG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (44 bp):
GATTCACAATCTTCAACCTATTCCACTGCTAACCAGGGAGATAG
Found at i:35509461 original size:9 final size:9
Alignment explanation
Indices: 35509447--35509531 Score: 116
Period size: 9 Copynumber: 9.4 Consensus size: 9
35509437 TTTGGTTAAA
35509447 AATTAACCG
1 AATTAACCG
*
35509456 AATTAACCA
1 AATTAACCG
35509465 AATTAACCG
1 AATTAACCG
*
35509474 AATTACCCG
1 AATTAACCG
35509483 AATTAACCG
1 AATTAACCG
*
35509492 AATTAATCG
1 AATTAACCG
*
35509501 AATTACCCG
1 AATTAACCG
*
35509510 AATTAACCA
1 AATTAACCG
*
35509519 AATTAACCA
1 AATTAACCG
35509528 AATT
1 AATT
35509532 GAATCACTAT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 67 1.00
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:35509483 original size:27 final size:27
Alignment explanation
Indices: 35509447--35509531 Score: 134
Period size: 27 Copynumber: 3.1 Consensus size: 27
35509437 TTTGGTTAAA
*
35509447 AATTAACCGAATTAACCAAATTAACCG
1 AATTACCCGAATTAACCAAATTAACCG
* *
35509474 AATTACCCGAATTAACCGAATTAATCG
1 AATTACCCGAATTAACCAAATTAACCG
*
35509501 AATTACCCGAATTAACCAAATTAACCA
1 AATTACCCGAATTAACCAAATTAACCG
35509528 AATT
1 AATT
35509532 GAATCACTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.25
Consensus pattern (27 bp):
AATTACCCGAATTAACCAAATTAACCG
Found at i:35509678 original size:18 final size:18
Alignment explanation
Indices: 35509638--35509681 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
35509628 TAATTTTATG
**
35509638 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
35509656 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
35509674 CTTGGGTT
1 ATTGGGTT
35509682 TAGATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:35523145 original size:21 final size:22
Alignment explanation
Indices: 35523102--35523148 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
35523092 AAATTTAGTA
*
35523102 TATTTTAAATTTATTACCATAT
1 TATTTTAAATTTATTAACATAT
35523124 TATTTT-AATATTA-TAACATAT
1 TATTTTAAAT-TTATTAACATAT
35523145 TATT
1 TATT
35523149 GTTCTAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTTTAAATTTATTAACATAT
Found at i:35524927 original size:52 final size:52
Alignment explanation
Indices: 35524855--35524959 Score: 120
Period size: 52 Copynumber: 2.0 Consensus size: 52
35524845 AAATATTTAG
* * * * **
35524855 AATTAGAACTAAATTGACAAAATTTGTAAATGTTGAGGGCTAAATTTATTAA
1 AATTAGAACTAAAATAACAAAATTTATAAATATTGAAAGCTAAATTTATTAA
* * * *
35524907 AATTTGAACTAAAATAACAAATTTTATCAATATTGAAAGCTAAATTTGTTAA
1 AATTAGAACTAAAATAACAAAATTTATAAATATTGAAAGCTAAATTTATTAA
35524959 A
1 A
35524960 TTTTTATATT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.35
Consensus pattern (52 bp):
AATTAGAACTAAAATAACAAAATTTATAAATATTGAAAGCTAAATTTATTAA
Found at i:35525546 original size:15 final size:16
Alignment explanation
Indices: 35525519--35525549 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
35525509 ACTTTATTCT
35525519 AATAATAAATTTTAAA
1 AATAATAAATTTTAAA
35525535 AATAAT-AATTTTAAA
1 AATAATAAATTTTAAA
35525550 TTATATTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAATAAATTTTAAA
Found at i:35525610 original size:15 final size:15
Alignment explanation
Indices: 35525586--35525618 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
35525576 ATTTGATATT
*
35525586 AATATTTTAATAATA
1 AATATATTAATAATA
35525601 AATATATTAATAATA
1 AATATATTAATAATA
35525616 AAT
1 AAT
35525619 GTTCTGTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATATTAATAATA
Found at i:35547802 original size:13 final size:13
Alignment explanation
Indices: 35547784--35547835 Score: 59
Period size: 13 Copynumber: 3.7 Consensus size: 13
35547774 AGGGTCACAC
35547784 GGCCATGTGGTCA
1 GGCCATGTGGTCA
*
35547797 GGCCATGTGACTCACA
1 GGCCATGTG-GT--CA
35547813 CGGCCATGTGGTCA
1 -GGCCATGTGGTCA
35547827 GGCCATGTG
1 GGCCATGTG
35547836 ACTCACACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
13 18 0.55
14 3 0.09
16 3 0.09
17 9 0.27
ACGTcount: A:0.17, C:0.27, G:0.35, T:0.21
Consensus pattern (13 bp):
GGCCATGTGGTCA
Found at i:35547814 original size:30 final size:30
Alignment explanation
Indices: 35547778--35547845 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
35547768 CATTGCAGGG
35547778 TCACACGGCCATGTGGTCAGGCCATGTGAC
1 TCACACGGCCATGTGGTCAGGCCATGTGAC
35547808 TCACACGGCCATGTGGTCAGGCCATGTGAC
1 TCACACGGCCATGTGGTCAGGCCATGTGAC
35547838 TCACACGG
1 TCACACGG
35547846 TTTGGAGACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.21, C:0.31, G:0.29, T:0.19
Consensus pattern (30 bp):
TCACACGGCCATGTGGTCAGGCCATGTGAC
Found at i:35549104 original size:21 final size:21
Alignment explanation
Indices: 35549080--35549127 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
35549070 AAGGCTGCAG
*
35549080 AGAAGCACATAAGTGCTAAAC
1 AGAAGCACATAAGGGCTAAAC
* * *
35549101 AGAAACCCATAAGGGCTGAAC
1 AGAAGCACATAAGGGCTAAAC
*
35549122 GGAAGC
1 AGAAGC
35549128 TCGTAAGAGC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.10
Consensus pattern (21 bp):
AGAAGCACATAAGGGCTAAAC
Found at i:35549118 original size:42 final size:42
Alignment explanation
Indices: 35549081--35549237 Score: 118
Period size: 42 Copynumber: 3.8 Consensus size: 42
35549071 AGGCTGCAGA
*
35549081 GAAGCACATAAGTGCTAAACAGAAACCCATAAGGGCTGAACG
1 GAAGCACATAAGAGCTAAACAGAAACCCATAAGGGCTGAACG
* * * * * * **
35549123 GAAGCTCGTAAGAGCTGAACGGAAACCCATAAGGGTTAAATT
1 GAAGCACATAAGAGCTAAACAGAAACCCATAAGGGCTGAACG
** * * ** * *
35549165 GAAGCTTAAAAG-GCTAAACGGAAACCCATAAGGATTAAACT
1 GAAGCACATAAGAGCTAAACAGAAACCCATAAGGGCTGAACG
* * * *
35549206 GAAGCTCAAAAGAGCTGAACAAAAACCCATAA
1 GAAGCACATAAGAGCTAAACAGAAACCCATAA
35549238 AGGTTAAACT
Statistics
Matches: 95, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
41 37 0.39
42 58 0.61
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.15
Consensus pattern (42 bp):
GAAGCACATAAGAGCTAAACAGAAACCCATAAGGGCTGAACG
Found at i:35549155 original size:21 final size:21
Alignment explanation
Indices: 35549087--35549155 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
35549077 CAGAGAAGCA
* * *
35549087 CATAAGTGCTAAACAGAAACC
1 CATAAGAGCTGAACGGAAACC
* * *
35549108 CATAAGGGCTGAACGGAAGCT
1 CATAAGAGCTGAACGGAAACC
*
35549129 CGTAAGAGCTGAACGGAAACC
1 CATAAGAGCTGAACGGAAACC
35549150 CATAAG
1 CATAAG
35549156 GGTTAAATTG
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.41, C:0.22, G:0.25, T:0.13
Consensus pattern (21 bp):
CATAAGAGCTGAACGGAAACC
Found at i:35549210 original size:83 final size:83
Alignment explanation
Indices: 35549094--35549250 Score: 215
Period size: 83 Copynumber: 1.9 Consensus size: 83
35549084 GCACATAAGT
* * ** ** *
35549094 GCTAAACAGAAACCCATAAGGGCTGAACGGAAGCTCGTAAGAGCTGAACGGAAACCCATAAGGGT
1 GCTAAACAGAAACCCATAAGGACTAAACGGAAGCTCAAAAGAGCTGAACAAAAACCCATAAAGGT
*
35549159 TAAATTGAAGCTTAAAAG
66 TAAACTGAAGCTTAAAAG
* * *
35549177 GCTAAACGGAAACCCATAAGGATTAAACTGAAGCTCAAAAGAGCTGAACAAAAACCCATAAAGGT
1 GCTAAACAGAAACCCATAAGGACTAAACGGAAGCTCAAAAGAGCTGAACAAAAACCCATAAAGGT
35549242 TAAACTGAA
66 TAAACTGAA
35549251 ACTCATATGA
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
83 63 1.00
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (83 bp):
GCTAAACAGAAACCCATAAGGACTAAACGGAAGCTCAAAAGAGCTGAACAAAAACCCATAAAGGT
TAAACTGAAGCTTAAAAG
Found at i:35549245 original size:42 final size:42
Alignment explanation
Indices: 35549098--35549255 Score: 167
Period size: 42 Copynumber: 3.8 Consensus size: 42
35549088 ATAAGTGCTA
* * * * **
35549098 AACAGAAACCCATAAGGGCTGAACGGAAGCTCGTAAGAGCTG
1 AACAGAAACCCATAAAGGTTAAACTGAAGCTCAAAAGAGCTG
* * * * *
35549140 AACGGAAACCCATAAGGGTTAAATTGAAGCTTAAAAG-GCTA
1 AACAGAAACCCATAAAGGTTAAACTGAAGCTCAAAAGAGCTG
*
35549181 AACGGAAACCCAT-AAGGATTAAACTGAAGCTCAAAAGAGCTG
1 AACAGAAACCCATAAAGG-TTAAACTGAAGCTCAAAAGAGCTG
* *
35549223 AACAAAAACCCATAAAGGTTAAACTGAAACTCA
1 AACAGAAACCCATAAAGGTTAAACTGAAGCTCA
35549256 TATGAGTTAA
Statistics
Matches: 97, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
40 3 0.03
41 33 0.34
42 57 0.59
43 4 0.04
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (42 bp):
AACAGAAACCCATAAAGGTTAAACTGAAGCTCAAAAGAGCTG
Found at i:35549252 original size:21 final size:21
Alignment explanation
Indices: 35549144--35549257 Score: 63
Period size: 21 Copynumber: 5.5 Consensus size: 21
35549134 GAGCTGAACG
* *
35549144 GAAACCCATAAGGGTTAAATT
1 GAAACCCATAAAGGTTAAACT
* ** * *
35549165 GAAGCTTA-AAAGGCTAAACG
1 GAAACCCATAAAGGTTAAACT
35549185 GAAACCCAT-AAGGATTAAACT
1 GAAACCCATAAAGG-TTAAACT
* * * * *
35549206 GAAGCTCA-AAAGAGCTGAACA
1 GAAACCCATAAAG-GTTAAACT
*
35549227 AAAACCCATAAAGGTTAAACT
1 GAAACCCATAAAGGTTAAACT
*
35549248 GAAACTCATA
1 GAAACCCATA
35549258 TGAGTTAATA
Statistics
Matches: 63, Mismatches: 25, Indels: 10
0.64 0.26 0.10
Matches are distributed among these distances:
20 17 0.27
21 41 0.65
22 5 0.08
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (21 bp):
GAAACCCATAAAGGTTAAACT
Found at i:35549533 original size:45 final size:46
Alignment explanation
Indices: 35549448--35549535 Score: 115
Period size: 45 Copynumber: 1.9 Consensus size: 46
35549438 TTTTCAATTC
* * * * *
35549448 ATAATTTAACAATATTTCATTTTTTTAACAATATGCTAAATACATA
1 ATAATTTAACAACATTCCATTTTTTCAAAAATATACTAAATACATA
*
35549494 ATAATTTAACAACATTCCA-TTTTTCAAAAATATATTAAATAC
1 ATAATTTAACAACATTCCATTTTTTCAAAAATATACTAAATAC
35549536 GTAACATCAT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 19 0.53
46 17 0.47
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.41
Consensus pattern (46 bp):
ATAATTTAACAACATTCCATTTTTTCAAAAATATACTAAATACATA
Found at i:35551250 original size:13 final size:13
Alignment explanation
Indices: 35551225--35551251 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35551215 TTTATTGTTC
35551225 TATTTTATTTATT
1 TATTTTATTTATT
35551238 TATTTTATTTATT
1 TATTTTATTTATT
35551251 T
1 T
35551252 TAATTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TATTTTATTTATT
Found at i:35551673 original size:17 final size:18
Alignment explanation
Indices: 35551636--35551674 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
35551626 TAAATCTAAA
35551636 TAAAACTATTAAGTATAC
1 TAAAACTATTAAGTATAC
* *
35551654 TAAAACT-TTAATTATCC
1 TAAAACTATTAAGTATAC
35551671 TAAA
1 TAAA
35551675 CAAAAAGTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.36
Consensus pattern (18 bp):
TAAAACTATTAAGTATAC
Found at i:35574716 original size:30 final size:30
Alignment explanation
Indices: 35574649--35574717 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
35574639 ATGTCTCTTA
*
35574649 GCCGTGTAAGTCACACGGCCTGGCCACATT
1 GCCGTGTGAGTCACACGGCCTGGCCACATT
*
35574679 TCCGTGTGAGTCACACGGCCTGGCCACATT
1 GCCGTGTGAGTCACACGGCCTGGCCACATT
35574709 GCCGTGTGA
1 GCCGTGTGA
35574718 CCCCTACAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.17, C:0.32, G:0.29, T:0.22
Consensus pattern (30 bp):
GCCGTGTGAGTCACACGGCCTGGCCACATT
Found at i:35577462 original size:41 final size:40
Alignment explanation
Indices: 35577416--35577508 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 40
35577406 ACCGGCACAT
* **
35577416 AGCCTGCTAGGCTTAAAGCCTGCTTCAGTACACCGACATTA
1 AGCCTGCTAGGCGTAAAGCCTGAAT-AGTACACCGACATTA
* * * * *
35577457 AGCCTGCTAGACGTAAAGTCTGAATATTTCACCGGCATTA
1 AGCCTGCTAGGCGTAAAGCCTGAATAGTACACCGACATTA
35577497 AGCCTGCTAGGC
1 AGCCTGCTAGGC
35577509 ACAAGCCTGA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
40 23 0.53
41 20 0.47
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
AGCCTGCTAGGCGTAAAGCCTGAATAGTACACCGACATTA
Found at i:35583939 original size:50 final size:50
Alignment explanation
Indices: 35583861--35584049 Score: 279
Period size: 50 Copynumber: 3.8 Consensus size: 50
35583851 GGGTAAAGAG
35583861 GTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAA
1 GTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAA
* ** *
35583911 GTACCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATGAGAG
1 GTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAA
* * * *
35583961 GTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACTGACATGAGAA
1 GTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAA
* *
35584011 CATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 -GTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
35584050 TGTTATTATT
Statistics
Matches: 122, Mismatches: 16, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
50 88 0.72
51 34 0.28
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (50 bp):
GTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAA
Found at i:35598159 original size:39 final size:39
Alignment explanation
Indices: 35598119--35598295 Score: 246
Period size: 39 Copynumber: 4.5 Consensus size: 39
35598109 ATTCACTTTT
* * *
35598119 AAGCATATATCACATTACACATATAATCACATAACATTT
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* *
35598158 AAGCATATATCACAATACTCATATAATTACATAACGTTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* * * *
35598197 AAGCATATGTCGCAATACTCATATGATTACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* *
35598236 AAGCATATATCGCAATACTTATATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
*
35598275 AAGCATATGTCACAATACTCA
1 AAGCATATATCACAATACTCA
35598296 AAAACATGTT
Statistics
Matches: 122, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 122 1.00
ACGTcount: A:0.43, C:0.21, G:0.06, T:0.30
Consensus pattern (39 bp):
AAGCATATATCACAATACTCATATAATCACATAACATTC
Found at i:35620459 original size:10 final size:10
Alignment explanation
Indices: 35620443--35620490 Score: 60
Period size: 10 Copynumber: 4.8 Consensus size: 10
35620433 ATAGATATCT
35620443 TAAAAAATTA
1 TAAAAAATTA
*
35620453 TAGAAAATTA
1 TAAAAAATTA
* *
35620463 TTAAAAATCA
1 TAAAAAATTA
*
35620473 TAAAAAAGTA
1 TAAAAAATTA
35620483 TAAAAAAT
1 TAAAAAAT
35620491 AGTAAAATTG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:35620496 original size:20 final size:19
Alignment explanation
Indices: 35620443--35620497 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
35620433 ATAGATATCT
* *
35620443 TAAAAAATTATAGAAAATTA
1 TAAAAAA-TATAAAAAAGTA
*
35620463 TTAAAAATCATAAAAAAGTA
1 TAAAAAAT-ATAAAAAAGTA
35620483 TAAAAAATAGTAAAA
1 TAAAAAATA-TAAAA
35620498 TTGTTCTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 27 0.93
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.25
Consensus pattern (19 bp):
TAAAAAATATAAAAAAGTA
Found at i:35627664 original size:20 final size:19
Alignment explanation
Indices: 35627639--35627693 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 19
35627629 AGATTATTTG
35627639 CACTTCTGTGTCTCTTCTTA
1 CACTTC-GTGTCTCTTCTTA
*
35627659 CACTTCGATGCCTCTTCTTA
1 CACTTCG-TGTCTCTTCTTA
35627679 CACTTCGGTGTCTCT
1 CACTTC-GTGTCTCT
35627694 GTTAAAACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.11, C:0.33, G:0.13, T:0.44
Consensus pattern (19 bp):
CACTTCGTGTCTCTTCTTA
Found at i:35627730 original size:20 final size:20
Alignment explanation
Indices: 35627656--35627836 Score: 98
Period size: 20 Copynumber: 9.1 Consensus size: 20
35627646 GTGTCTCTTC
* *
35627656 TTACACTTCGATGCCTCTT-C
1 TTACACTTCGGTGCCT-TTAT
* * *
35627676 TTACACTTCGGTGTCTCTGT
1 TTACACTTCGGTGCCTTTAT
* * * *
35627696 TAAAACTTTGATGCCTTTAT
1 TTACACTTCGGTGCCTTTAT
* * **
35627716 TTGCACTTCAGTGCCTTTGC
1 TTACACTTCGGTGCCTTTAT
* *
35627736 TTACACTTTGGTGTCTTTGAT
1 TTACACTTCGGTGCCTTT-AT
*
35627757 TT-CACTTTGGTGCCTTTAT
1 TTACACTTCGGTGCCTTTAT
* * **
35627776 TTACACTTCGGTGCATCTGC
1 TTACACTTCGGTGCCTTTAT
* * *
35627796 TTACACTTTGGTGTCTCTGAT
1 TTACACTTCGGTGCCT-TTAT
*
35627817 TT-CACTTCGGTGCCTCTAT
1 TTACACTTCGGTGCCTTTAT
35627836 T
1 T
35627837 AGTACTAAGG
Statistics
Matches: 115, Mismatches: 42, Indels: 9
0.69 0.25 0.05
Matches are distributed among these distances:
19 8 0.07
20 103 0.90
21 4 0.03
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.45
Consensus pattern (20 bp):
TTACACTTCGGTGCCTTTAT
Found at i:35627744 original size:40 final size:40
Alignment explanation
Indices: 35627632--35627783 Score: 114
Period size: 40 Copynumber: 3.8 Consensus size: 40
35627622 TTACGATAGA
* * *
35627632 TTATTTGCACTTCTGTGTCTCTT-CTTACACTTCGATGCCT
1 TTATTTGCACTTCGGTGCCT-TTGCTTACACTTTGATGCCT
* * * * *
35627672 CTT-CTTACACTTCGGTGTCTCTG-TTAAAACTTTGATGCCT
1 -TTATTTGCACTTCGGTGCCTTTGCTT-ACACTTTGATGCCT
* * *
35627712 TTATTTGCACTTCAGTGCCTTTGCTTACACTTTGGTGTCT
1 TTATTTGCACTTCGGTGCCTTTGCTTACACTTTGATGCCT
* **
35627752 TTGATTT-CACTTTGGTGCCTTTATTTACACTT
1 TT-ATTTGCACTTCGGTGCCTTTGCTTACACTT
35627784 CGGTGCATCT
Statistics
Matches: 88, Mismatches: 18, Indels: 11
0.75 0.15 0.09
Matches are distributed among these distances:
39 5 0.06
40 75 0.85
41 8 0.09
ACGTcount: A:0.14, C:0.24, G:0.14, T:0.47
Consensus pattern (40 bp):
TTATTTGCACTTCGGTGCCTTTGCTTACACTTTGATGCCT
Found at i:35627818 original size:60 final size:60
Alignment explanation
Indices: 35627656--35627836 Score: 229
Period size: 60 Copynumber: 3.0 Consensus size: 60
35627646 GTGTCTCTTC
* * * ** *
35627656 TTACACTTCGATGCCTCTTCTTACACTTCGGTGTCTCTG-TTAAAACTTTGATGCCTTTAT
1 TTACACTTCGGTGCCTCTGCTTACACTTTGGTGTCTCTGATT-TCACTTTGGTGCCTTTAT
* * * *
35627716 TTGCACTTCAGTGCCTTTGCTTACACTTTGGTGTCTTTGATTTCACTTTGGTGCCTTTAT
1 TTACACTTCGGTGCCTCTGCTTACACTTTGGTGTCTCTGATTTCACTTTGGTGCCTTTAT
* * *
35627776 TTACACTTCGGTGCATCTGCTTACACTTTGGTGTCTCTGATTTCACTTCGGTGCCTCTAT
1 TTACACTTCGGTGCCTCTGCTTACACTTTGGTGTCTCTGATTTCACTTTGGTGCCTTTAT
35627836 T
1 T
35627837 AGTACTAAGG
Statistics
Matches: 103, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
60 101 0.98
61 2 0.02
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.45
Consensus pattern (60 bp):
TTACACTTCGGTGCCTCTGCTTACACTTTGGTGTCTCTGATTTCACTTTGGTGCCTTTAT
Found at i:35627849 original size:60 final size:60
Alignment explanation
Indices: 35627733--35627849 Score: 164
Period size: 60 Copynumber: 1.9 Consensus size: 60
35627723 TCAGTGCCTT
* * * **
35627733 TGCTTACACTTTGGTGTCTTTGATTTCACTTTGGTGCCTTTATTTACACTTCGGTGCATC
1 TGCTTACACTTTGGTGTCTCTGATTTCACTTCGGTGCCTCTATTTACACTAAGGTGCATC
*
35627793 TGCTTACACTTTGGTGTCTCTGATTTCACTTCGGTGCCTCTA-TTAGTACTAAGGTGC
1 TGCTTACACTTTGGTGTCTCTGATTTCACTTCGGTGCCTCTATTTA-CACTAAGGTGC
35627850 CTCCGTATAG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
59 3 0.06
60 47 0.94
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.44
Consensus pattern (60 bp):
TGCTTACACTTTGGTGTCTCTGATTTCACTTCGGTGCCTCTATTTACACTAAGGTGCATC
Found at i:35631000 original size:11 final size:11
Alignment explanation
Indices: 35630986--35631027 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
35630976 TAAATATTAC
35630986 TTTATTAATAT
1 TTTATTAATAT
*
35630997 TTTAATGAGATAT
1 TTT-ATTA-ATAT
35631010 TTTATTAATAT
1 TTTATTAATAT
35631021 TTTATTA
1 TTTATTA
35631028 TAAATAGCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 14 0.52
12 6 0.22
13 7 0.26
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (11 bp):
TTTATTAATAT
Found at i:35631076 original size:15 final size:15
Alignment explanation
Indices: 35631052--35631081 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35631042 AAAAGGAGAG
*
35631052 AAAGATGAAGAAAGA
1 AAAGAAGAAGAAAGA
35631067 AAAGAAGAAGAAAGA
1 AAAGAAGAAGAAAGA
35631082 TGATCCTCCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (15 bp):
AAAGAAGAAGAAAGA
Found at i:35634557 original size:22 final size:22
Alignment explanation
Indices: 35634527--35634568 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
35634517 ACAGCAGAAC
*
35634527 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
35634549 AGGCCTTTAGCGGCGCTTTT
1 AGGCCTTTAGCGGCGCTTTT
35634569 AAGCGCCGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.10, C:0.21, G:0.29, T:0.40
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:35634761 original size:42 final size:43
Alignment explanation
Indices: 35634715--35634812 Score: 126
Period size: 43 Copynumber: 2.3 Consensus size: 43
35634705 AGACAAAGAC
* *
35634715 CTTTAGCGCCGCTTTAGT-GGAAGCGCCGCTAAAGATCAGGGT
1 CTTTAGCGGCGCTTTAGTGGGAAACGCCGCTAAAGATCAGGGT
** * **
35634757 CTTTAGCGGCATTTTTGTGGGAAACGCCGCTAAAGATTGGGGT
1 CTTTAGCGGCGCTTTAGTGGGAAACGCCGCTAAAGATCAGGGT
35634800 CTTTAGCGGCGCT
1 CTTTAGCGGCGCT
35634813 CTTACTACAA
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 14 0.30
43 32 0.70
ACGTcount: A:0.19, C:0.21, G:0.32, T:0.28
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTAGTGGGAAACGCCGCTAAAGATCAGGGT
Found at i:35634850 original size:43 final size:42
Alignment explanation
Indices: 35634803--35634939 Score: 186
Period size: 43 Copynumber: 3.2 Consensus size: 42
35634793 TTGGGGTCTT
*
35634803 TAGCGGCGCTCTTACTACAAACGCCGCAATAGACCCTGATCTA
1 TAGCGGCGCT-TTACTAAAAACGCCGCAATAGACCCTGATCTA
* *
35634846 TAGCGGCGCATTTTCTAAAAACGCCGTAATAGACACC-GATCTA
1 TAGCGGCGC-TTTACTAAAAACGCCGCAATAGAC-CCTGATCTA
* *
35634889 TAGCGGCGCTTTTACAAAAAACGCCGCAGTAGACCCTGATCTA
1 TAGCGGCGC-TTTACTAAAAACGCCGCAATAGACCCTGATCTA
35634932 TAGCGGCG
1 TAGCGGCG
35634940 ATTCGGATAA
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
42 2 0.02
43 78 0.94
44 3 0.04
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.21
Consensus pattern (42 bp):
TAGCGGCGCTTTACTAAAAACGCCGCAATAGACCCTGATCTA
Found at i:35634952 original size:43 final size:42
Alignment explanation
Indices: 35634803--35634956 Score: 166
Period size: 43 Copynumber: 3.6 Consensus size: 42
35634793 TTGGGGTCTT
* * *
35634803 TAGCGGCGCTCTTACTACAAACGCCGCAATAGACCCTGATCTA
1 TAGCGGCGATTTTA-TAAAAACGCCGCAATAGACCCTGATCTA
* *
35634846 TAGCGGCGCATTTTCTAAAAACGCCGTAATAGACACC-GATCTA
1 TAGCGGCG-ATTTTATAAAAACGCCGCAATAGAC-CCTGATCTA
* * *
35634889 TAGCGGCGCTTTTACAAAAAACGCCGCAGTAGACCCTGATCTA
1 TAGCGGCGATTTTA-TAAAAACGCCGCAATAGACCCTGATCTA
**
35634932 TAGCGGCGATTCGGATAAAAACGCC
1 TAGCGGCGATT-TTATAAAAACGCC
35634957 ACTAAAGATC
Statistics
Matches: 92, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
42 6 0.07
43 80 0.87
44 6 0.07
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.21
Consensus pattern (42 bp):
TAGCGGCGATTTTATAAAAACGCCGCAATAGACCCTGATCTA
Found at i:35634985 original size:86 final size:85
Alignment explanation
Indices: 35634778--35634987 Score: 235
Period size: 86 Copynumber: 2.4 Consensus size: 85
35634768 TTTTTGTGGG
*** * * *
35634778 AAACGCCGCTAAAGATTGGGGTCTTTAGCGGCGCTCTTACTACAAACGCCGCAATAGACCCTGAT
1 AAACGCC-CTAAAGATCACGGTCTTTAGCGGCGCTTTTACAAAAAACGCCGCAATAGACCCTGAT
***
35634843 CTATAGCGGCGCATTTTCTAA
65 CTATAGCGGCGCATTGGATAA
* * * *
35634864 AAACGCCGTAATAGA-CACCGATCTATAGCGGCGCTTTTACAAAAAACGCCGCAGTAGACCCTGA
1 AAACGCCCTAA-AGATCA-CGGTCTTTAGCGGCGCTTTTACAAAAAACGCCGCAATAGACCCTGA
35634928 TCTATAGCGGCG-ATTCGGATAA
64 TCTATAGCGGCGCATT-GGATAA
*
35634950 AAACGCCACTAAAGATCATGGTCTTTAGCGGCGCTTTT
1 AAACGCC-CTAAAGATCACGGTCTTTAGCGGCGCTTTT
35634988 CCCGAAAACA
Statistics
Matches: 102, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
85 6 0.06
86 91 0.89
87 5 0.05
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (85 bp):
AAACGCCCTAAAGATCACGGTCTTTAGCGGCGCTTTTACAAAAAACGCCGCAATAGACCCTGATC
TATAGCGGCGCATTGGATAA
Found at i:35634996 original size:43 final size:42
Alignment explanation
Indices: 35634949--35635048 Score: 128
Period size: 43 Copynumber: 2.3 Consensus size: 42
35634939 GATTCGGATA
* *
35634949 AAAACGCCACTAAAGATCATGGTCTTTAGCGGCGCTTTTCCC
1 AAAACGCCACTAAAGACCATGATCTTTAGCGGCGCTTTTCCC
* * * *
35634991 GAAAACACCGCTAAAGACCATGATCTTTAGTGGCGCTTTTTCC
1 -AAAACGCCACTAAAGACCATGATCTTTAGCGGCGCTTTTCCC
35635034 ACAAACGCCACTAAA
1 A-AAACGCCACTAAA
35635049 TTTGGCAGAT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 1 0.02
43 47 0.98
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (42 bp):
AAAACGCCACTAAAGACCATGATCTTTAGCGGCGCTTTTCCC
Found at i:35634996 original size:86 final size:84
Alignment explanation
Indices: 35634778--35635026 Score: 216
Period size: 86 Copynumber: 2.9 Consensus size: 84
35634768 TTTTTGTGGG
*** * * *
35634778 AAACGCCGCTAAAGATTGGGGTCTTTAGCGGCGCTCTTACTACAAACGCCGCAATAGACCCTGAT
1 AAACGCC-CTAAAGATCACGGTCTTTAGCGGCGCT-TTTCCAAAAACGCCGCAATAGACCCTGAT
***
35634843 CTATAGCGGCGCATTTTCTAA
64 CTATAGCGGCGCATTGGATAA
* * * * *
35634864 AAACGCCGTAATAGA-CACCGATCTATAGCGGCGCTTTTACAAAAAACGCCGCAGTAGACCCTGA
1 AAACGCCCTAA-AGATCA-CGGTCTTTAGCGGCGCTTTT-CCAAAAACGCCGCAATAGACCCTGA
35634928 TCTATAGCGGCG-ATTCGGATAA
63 TCTATAGCGGCGCATT-GGATAA
* * * *
35634950 AAACGCCACTAAAGATCATGGTCTTTAGCGGCGCTTTTCCCGAAAACACCGCTAA-AGACCATGA
1 AAACGCC-CTAAAGATCACGGTCTTTAGCGGCGCTTTT-CCAAAAACGCCGC-AATAGACCCTGA
* *
35635014 TCTTTAGTGGCGC
63 TCTATAGCGGCGC
35635027 TTTTTCCACA
Statistics
Matches: 130, Mismatches: 25, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
85 8 0.06
86 116 0.89
87 6 0.05
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (84 bp):
AAACGCCCTAAAGATCACGGTCTTTAGCGGCGCTTTTCCAAAAACGCCGCAATAGACCCTGATCT
ATAGCGGCGCATTGGATAA
Found at i:35635416 original size:42 final size:42
Alignment explanation
Indices: 35635356--35635448 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
35635346 TTTGACGCTG
* * *
35635356 CTCTGCTTACCTCGCTGCAGCCTATACTTGC-CTCGCTACAGC
1 CTCTGCTTCCCTCACTGCAACCTATACTT-CTCTCGCTACAGC
* * *
35635398 CTCTGCTTCCCTCACTGCAACCTGTACTTCTCTCGCTGCCGC
1 CTCTGCTTCCCTCACTGCAACCTATACTTCTCTCGCTACAGC
35635440 CTCTGCTTC
1 CTCTGCTTC
35635449 TCTTGCTGCC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
41 1 0.02
42 43 0.98
ACGTcount: A:0.11, C:0.43, G:0.15, T:0.31
Consensus pattern (42 bp):
CTCTGCTTCCCTCACTGCAACCTATACTTCTCTCGCTACAGC
Found at i:35635448 original size:21 final size:20
Alignment explanation
Indices: 35635356--35635467 Score: 80
Period size: 21 Copynumber: 5.3 Consensus size: 20
35635346 TTTGACGCTG
35635356 CTCTGCTTACCTCGCTGCAGC
1 CTCTGCTT-CCTCGCTGCAGC
* * *
35635377 CTATACTTGCCTCGCTACAGC
1 CTCTGCTT-CCTCGCTGCAGC
* *
35635398 CTCTGCTTCCCTCACTGCAAC
1 CTCTGCTT-CCTCGCTGCAGC
* * *
35635419 CTGTACTTCTCTCGCTGCCGC
1 CTCTGCTTC-CTCGCTGCAGC
* *
35635440 CTCTGCTTCTCTTGCTGCCGC
1 CTCTGCTTC-CTCGCTGCAGC
*
35635461 ATCTGCT
1 CTCTGCT
35635468 CTAAGCTGGT
Statistics
Matches: 71, Mismatches: 19, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
20 1 0.01
21 70 0.99
ACGTcount: A:0.10, C:0.42, G:0.16, T:0.32
Consensus pattern (20 bp):
CTCTGCTTCCTCGCTGCAGC
Found at i:35635532 original size:66 final size:66
Alignment explanation
Indices: 35635439--35635585 Score: 224
Period size: 66 Copynumber: 2.2 Consensus size: 66
35635429 CTCGCTGCCG
* * *
35635439 CCTCTGCTTCTCTTGCTGCCGCATCTGCTCTAAGCTGGTGCTGGAGTTCTTCATA-CTTTCGTTG
1 CCTCAGCTTCTCTCGCTGCCGCATCTGCTCTAAGCTGCTGCTGGAGTTCTTCATATCTTT-GTTG
35635503 AA
65 AA
* * *
35635505 CCTCAGCTTCTCTCGTTGCTGCATCTGCTCTAAGCTGCTGCTGGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTCGCTGCCGCATCTGCTCTAAGCTGCTGCTGGAGTTCTTCATATCTTTGTTGA
35635570 A
66 A
35635571 CCTCAGCTTCTCTCG
1 CCTCAGCTTCTCTCG
35635586 ATGTTGCCTC
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
66 70 0.95
67 4 0.05
ACGTcount: A:0.12, C:0.30, G:0.19, T:0.39
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCCGCATCTGCTCTAAGCTGCTGCTGGAGTTCTTCATATCTTTGTTGA
A
Found at i:35641040 original size:18 final size:18
Alignment explanation
Indices: 35641017--35641052 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
35641007 ATAGTTAAGC
35641017 TATGTAAGTTATGTATTA
1 TATGTAAGTTATGTATTA
*
35641035 TATGTAAGTTATTTATTA
1 TATGTAAGTTATGTATTA
35641053 CCCAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (18 bp):
TATGTAAGTTATGTATTA
Found at i:35641102 original size:9 final size:9
Alignment explanation
Indices: 35641090--35641250 Score: 72
Period size: 9 Copynumber: 18.7 Consensus size: 9
35641080 AAAATTATGC
35641090 TATGTAAGT
1 TATGTAAGT
35641099 TATGTAAGT
1 TATGTAAGT
* ** *
35641108 CACATAAGC
1 TATGTAAGT
35641117 TATGTAAG-
1 TATGTAAGT
*
35641125 AAGTTGTAAGT
1 TA--TGTAAGT
35641136 TATGTAAGT
1 TATGTAAGT
*
35641145 TAT-TTA-T
1 TATGTAAGT
* *
35641152 TATGAAAAT
1 TATGTAAGT
*
35641161 TAAGTAAGT
1 TATGTAAGT
**
35641170 TATGTACTT
1 TATGTAAGT
*
35641179 TACG-AA-T
1 TATGTAAGT
* **
35641186 AAT-TAAAA
1 TATGTAAGT
*
35641194 AAATGTAAGT
1 TA-TGTAAGT
*
35641204 TATGT-AGA
1 TATGTAAGT
35641212 T-TGTAAGT
1 TATGTAAGT
35641220 TATGTAAG-
1 TATGTAAGT
35641228 T-TGTAAGT
1 TATGTAAGT
35641236 TATGTAAGT
1 TATGTAAGT
35641245 TATGTA
1 TATGTA
35641251 TAATATTAAT
Statistics
Matches: 111, Mismatches: 28, Indels: 26
0.67 0.17 0.16
Matches are distributed among these distances:
7 17 0.15
8 15 0.14
9 68 0.61
10 10 0.09
11 1 0.01
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.40
Consensus pattern (9 bp):
TATGTAAGT
Found at i:35641218 original size:16 final size:16
Alignment explanation
Indices: 35641197--35641245 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
35641187 ATTAAAAAAA
35641197 TGTAAGTTATGT-AGAT
1 TGTAAGTTATGTAAG-T
35641213 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
35641229 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
35641245 T
1 T
35641246 ATGTATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
16 30 0.94
17 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.45
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:35641224 original size:25 final size:25
Alignment explanation
Indices: 35641196--35641250 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
35641186 AATTAAAAAA
35641196 ATGTAAGTTATGT-AGAT-TGTAAGTT
1 ATGTAAG-T-TGTAAGATATGTAAGTT
*
35641221 ATGTAAGTTGTAAGTTATGTAAGTT
1 ATGTAAGTTGTAAGATATGTAAGTT
35641246 ATGTA
1 ATGTA
35641251 TAATATTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 3 0.11
24 4 0.15
25 20 0.74
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.44
Consensus pattern (25 bp):
ATGTAAGTTGTAAGATATGTAAGTT
Found at i:35641286 original size:34 final size:34
Alignment explanation
Indices: 35641231--35641439 Score: 252
Period size: 34 Copynumber: 6.3 Consensus size: 34
35641221 ATGTAAGTTG
*
35641231 TAAGTTATGTAAGTTATGTATAATATTAATTAAC
1 TAAGTTATGTAATTTATGTATAATATTAATTAAC
* * *
35641265 TAACTTATGTAATTTAAGTATAATATTAA-T--G
1 TAAGTTATGTAATTTATGTATAATATTAATTAAC
* *
35641296 TAAGTTATGTAATTAATGTATAATATTAATTAAT
1 TAAGTTATGTAATTTATGTATAATATTAATTAAC
* *
35641330 TAAGTCATGTAATTTATGTATAATATTAA-T-GC
1 TAAGTTATGTAATTTATGTATAATATTAATTAAC
* *
35641362 -AAGTTATGTAATATATGTATAATATTAATTAAT
1 TAAGTTATGTAATTTATGTATAATATTAATTAAC
* *
35641395 TAAGTTATGTAATTTATGTATAATACTAAATAA-
1 TAAGTTATGTAATTTATGTATAATATTAATTAAC
35641428 TCAAGTTATGTA
1 T-AAGTTATGTA
35641440 TAATATTAAT
Statistics
Matches: 149, Mismatches: 19, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
31 52 0.35
32 2 0.01
33 3 0.02
34 92 0.62
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (34 bp):
TAAGTTATGTAATTTATGTATAATATTAATTAAC
Found at i:35641307 original size:65 final size:64
Alignment explanation
Indices: 35641229--35641419 Score: 310
Period size: 65 Copynumber: 2.9 Consensus size: 64
35641219 TTATGTAAGT
* * *
35641229 TGTAAGTTATGTAAGTTATGTATAATATTAATTAACTAACTTATGTAATTTAAGTATAATATTAA
1 TGTAAGTTATGTAA-TTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
*
35641294 TGTAAGTTATGTAATTAATGTATAATATTAATTAATTAAGTCATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATT-ATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
*
35641359 TGCAAGTTATGTAATATATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATA
1 TGTAAGTTATGTAAT-TATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATA
35641420 CTAAATAATC
Statistics
Matches: 118, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
64 2 0.02
65 115 0.97
66 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (64 bp):
TGTAAGTTATGTAATTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
Found at i:35641349 original size:99 final size:98
Alignment explanation
Indices: 35641231--35641439 Score: 269
Period size: 99 Copynumber: 2.1 Consensus size: 98
35641221 ATGTAAGTTG
*
35641231 TAAGTTATGTAAGTTATGTATAATATTAATTAACTAACTTATGTAATTTAAGTATAATATTAA-T
1 TAAGTTATGTAAGTTATGTATAATATTAA-T-AC-AACTTATGTAATATAAGTATAATATTAATT
* *
35641295 -GTAAGTTATGTAATTAATGTATAATATTAATTAAT
63 AGTAAGTTATGTAATTAATGTATAATACTAAATAAT
* * * * * *
35641330 TAAGTCATGTAATTTATGTATAATATTAATGCAAGTTATGTAATATATGTATAATATTAATTAAT
1 TAAGTTATGTAAGTTATGTATAATATTAATACAACTTATGTAATATAAGTATAATATTAATT-AG
*
35641395 TAAGTTATGTAATTTATGTATAATACTAAATAAT
65 TAAGTTATGTAATTAATGTATAATACTAAATAAT
*
35641429 CAAGTTATGTA
1 TAAGTTATGTA
35641440 TAATATTAAT
Statistics
Matches: 95, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
96 25 0.26
97 2 0.02
98 1 0.01
99 67 0.71
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (98 bp):
TAAGTTATGTAAGTTATGTATAATATTAATACAACTTATGTAATATAAGTATAATATTAATTAGT
AAGTTATGTAATTAATGTATAATACTAAATAAT
Found at i:35642356 original size:18 final size:19
Alignment explanation
Indices: 35642318--35642362 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
35642308 GGAAATTGGG
*
35642318 AACCCCTAGCTAAATCCTA
1 AACCCCTAGCTAAACCCTA
35642337 AACCCCTAGCT-AACCCTA
1 AACCCCTAGCTAAACCCTA
*
35642355 AATCCCTA
1 AACCCCTA
35642363 ACCCCTAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.36, C:0.40, G:0.04, T:0.20
Consensus pattern (19 bp):
AACCCCTAGCTAAACCCTA
Found at i:35643111 original size:113 final size:114
Alignment explanation
Indices: 35642912--35643622 Score: 924
Period size: 114 Copynumber: 6.3 Consensus size: 114
35642902 AGATAAAATG
* * * * * *
35642912 TTTTTGCGGCGC-TTTATAAAAAACGCCGCTAAAGGCATCAGCATTAGCGGCGCTTATTCA-GAA
1 TTTTTGCGGCGCTTTTA-AAAAAACGCCGCTAAAGACCTGAACATTAGCGGCGCTT-TACATAAA
* *
35642975 ACGCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGTCGTTAGGCTTAGGC
64 ACGCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* *
35643026 -TTTTGCGGCGCATTTAAAAAAACGCCGTTAAAGACCTGAACATTAGCGGCGCTTTACATAAAAC
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAACATTAGCGGCGCTTTACATAAAAC
* *
35643090 GCCACTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGTTTAGGC
66 GCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* * * * **
35643139 TTTTTGCGGCGCTTTTGAAAAAACGCCGCTAAAGACCTCAGCATTAGCGACGCTTT--ATAGATG
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAACATTAGCGGCGCTTTACATA-AAA
* *
35643202 CACCGCTAAAGACCCCTAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGT
65 CGCCGCTAAAGACCCC-AAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
**
35643253 TTTTTGCGGCGCAATTAAAAAAACGCCGCTAAAGACCTGAACATTAGCGGCGCTTTACAT-AAAC
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAACATTAGCGGCGCTTTACATAAAAC
* * * *
35643317 ACCGCGAAAGACCCCAAAAACTCAAAAAACGGTGCCGTTGAGCTTAGGC
66 GCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* * *
35643366 TTTTTGC-GCGC-TTTAAAAAAACGCCGCTAAAGACATGAGCATTAGCGGCACTTTACATAAAAC
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAACATTAGCGGCGCTTTACATAAAAC
* * * *
35643429 GCCACTAAAGACCCC-AAAACTTAGAAAACGGTGCCGTTGGGTTTAGAC
66 GCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* *
35643477 TTTTTGCGGCGCTTTTAAAACAACGCCGCTAAAGACCT-AAGCATTAGCGGCGCTTTTACA-GAA
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAA-CATTAGCGGCGC-TTTACATAAA
* * *
35643540 ACGCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGACGTTTGTCTTTA-GC
64 ACGCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGC-TTAGGC
*
35643591 TTTTTGCGGCGCTTTTATAAAAACGCCGCTAA
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAA
35643623 TGCTTATTTT
Statistics
Matches: 522, Mismatches: 61, Indels: 28
0.85 0.10 0.05
Matches are distributed among these distances:
111 78 0.15
112 31 0.06
113 198 0.38
114 210 0.40
115 3 0.01
116 2 0.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (114 bp):
TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAACATTAGCGGCGCTTTACATAAAAC
GCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
Found at i:35651811 original size:25 final size:25
Alignment explanation
Indices: 35651782--35651831 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
35651772 TTTAAAAAAA
* *
35651782 TAAATATAT-TAATTTATTTTTATAT
1 TAAATAAATATAA-TTATTTATATAT
35651807 TAAATAAATATAATTATTTATATAT
1 TAAATAAATATAATTATTTATATAT
35651832 CTAATATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TAAATAAATATAATTATTTATATAT
Found at i:35655830 original size:21 final size:20
Alignment explanation
Indices: 35655806--35655856 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
35655796 ATTCATAACA
*
35655806 TATTCAATTCTCATCACTTGC
1 TATTCAAATCTCAT-ACTTGC
*
35655827 TATTTCAAATCTCATATTTGC
1 TA-TTCAAATCTCATACTTGC
35655848 TATTCAAAT
1 TATTCAAAT
35655857 AGTTTTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 7 0.26
21 9 0.33
22 11 0.41
ACGTcount: A:0.29, C:0.22, G:0.04, T:0.45
Consensus pattern (20 bp):
TATTCAAATCTCATACTTGC
Found at i:35657047 original size:17 final size:18
Alignment explanation
Indices: 35657015--35657050 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
35657005 GAAACCCTGG
35657015 CTTTTTCTCCTTTCTTTCT
1 CTTTTTCT-CTTTCTTTCT
35657034 CTTTTTCT-TTTCTTTCT
1 CTTTTTCTCTTTCTTTCT
35657051 TTCCTTCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
19 8 0.47
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (18 bp):
CTTTTTCTCTTTCTTTCT
Found at i:35657156 original size:21 final size:22
Alignment explanation
Indices: 35657104--35657156 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
35657094 TTCTATTTCT
*
35657104 TTATTTGTTTTGTTTTAATTAC
1 TTATTTATTTTGTTTTAATTAC
35657126 TTATTTATTTTGTTTT-ATTA-
1 TTATTTATTTTGTTTTAATTAC
35657146 TTATTTCATTT
1 TTATTT-ATTT
35657157 ACTTTGTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 6 0.21
21 8 0.28
22 15 0.52
ACGTcount: A:0.19, C:0.04, G:0.06, T:0.72
Consensus pattern (22 bp):
TTATTTATTTTGTTTTAATTAC
Found at i:35659997 original size:98 final size:98
Alignment explanation
Indices: 35659822--35660018 Score: 322
Period size: 98 Copynumber: 2.0 Consensus size: 98
35659812 TAAGTAAAGA
* * *
35659822 ATTTGAGATGAAAGGTTTGGGACCAGCAAAGAAGATACTTAGTATGAAGATTCTCAGAGATAGAA
1 ATTTGAGATAAAAGATTTGGGACCAGCAAAGAAGATACTTAGTATAAAGATTCTCAGAGATAGAA
* *
35659887 AAGAAAGTAAATTGTACCTAAGTCAAAAGGGGT
66 AAGAAAGCAAATTGCACCTAAGTCAAAAGGGGT
*
35659920 ATTTGAGATAAAAGATTTGGGACCAGCAAAGAAGATACTTGGTATAAAGATTCTCAGAGATAGAA
1 ATTTGAGATAAAAGATTTGGGACCAGCAAAGAAGATACTTAGTATAAAGATTCTCAGAGATAGAA
* *
35659985 AAGTAAGCAAATTGCACCTAAGTCAGAAGGGGT
66 AAGAAAGCAAATTGCACCTAAGTCAAAAGGGGT
35660018 A
1 A
35660019 CATTGAGAAA
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.42, C:0.10, G:0.25, T:0.23
Consensus pattern (98 bp):
ATTTGAGATAAAAGATTTGGGACCAGCAAAGAAGATACTTAGTATAAAGATTCTCAGAGATAGAA
AAGAAAGCAAATTGCACCTAAGTCAAAAGGGGT
Found at i:35667496 original size:24 final size:24
Alignment explanation
Indices: 35667464--35667511 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
35667454 GAGTATAACC
35667464 CAATCTACCAAGGATAAAGCTAGG
1 CAATCTACCAAGGATAAAGCTAGG
35667488 CAATCTACCAAGGATAAAGCTAGG
1 CAATCTACCAAGGATAAAGCTAGG
35667512 ATTAGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.21, G:0.21, T:0.17
Consensus pattern (24 bp):
CAATCTACCAAGGATAAAGCTAGG
Found at i:35669533 original size:29 final size:29
Alignment explanation
Indices: 35669438--35669534 Score: 106
Period size: 29 Copynumber: 3.3 Consensus size: 29
35669428 AAACTACACC
*
35669438 ACACTAGGTTGCTCGTCCAAGCTAAAATT
1 ACACTAGGTTGCTAGTCCAAGCTAAAATT
* * * *
35669467 TCA-TAAGGTTGCTAGTCTAGGCTAAAAGT
1 ACACT-AGGTTGCTAGTCCAAGCTAAAATT
* * *
35669496 ATACAAGGTTGCTTGTCCAAGCTAAAATT
1 ACACTAGGTTGCTAGTCCAAGCTAAAATT
35669525 ACACTAGGTT
1 ACACTAGGTT
35669535 AGGTTACTAA
Statistics
Matches: 52, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
28 1 0.02
29 51 0.98
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (29 bp):
ACACTAGGTTGCTAGTCCAAGCTAAAATT
Found at i:35678508 original size:3 final size:3
Alignment explanation
Indices: 35678500--35678527 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
35678490 ATGAAAGACC
35678500 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
35678528 GAAAATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:35684961 original size:16 final size:15
Alignment explanation
Indices: 35684940--35684969 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
35684930 AAGATATTAG
35684940 AAGTTGAAAGTGAAAA
1 AAGTTGAAAG-GAAAA
35684956 AAGTTGAAAGGAAA
1 AAGTTGAAAGGAAA
35684970 GTGAAAGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.17
Consensus pattern (15 bp):
AAGTTGAAAGGAAAA
Found at i:35687242 original size:27 final size:26
Alignment explanation
Indices: 35687211--35687268 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
35687201 AATTCATACA
* *
35687211 TTTTTCATGCACATTAATTTATTTAG
1 TTTTTCATGAACATTAAATTATTTAG
* * *
35687237 TGTTTTGATGAACTTTAAATTCTTTAG
1 T-TTTTCATGAACATTAAATTATTTAG
35687264 TTTTT
1 TTTTT
35687269 AAGTGTTAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.24, C:0.09, G:0.10, T:0.57
Consensus pattern (26 bp):
TTTTTCATGAACATTAAATTATTTAG
Found at i:35691038 original size:6 final size:6
Alignment explanation
Indices: 35691027--35691057 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
35691017 CAGTGAGAAG
35691027 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT G
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT G
35691058 GCGAAAGGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.35, T:0.16
Consensus pattern (6 bp):
GAAGAT
Found at i:35692060 original size:16 final size:16
Alignment explanation
Indices: 35692039--35692073 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
35692029 AGTTAAAAAT
*
35692039 TATTTAAATTATATAA
1 TATTTAAATAATATAA
*
35692055 TATTTAAATAATTTAA
1 TATTTAAATAATATAA
35692071 TAT
1 TAT
35692074 AATGATACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TATTTAAATAATATAA
Found at i:35695031 original size:26 final size:27
Alignment explanation
Indices: 35695002--35695091 Score: 96
Period size: 26 Copynumber: 3.3 Consensus size: 27
35694992 TATATACATG
*
35695002 TACATATATA-AATAATAATAATTATA
1 TACATATATATAATAATAATAATAATA
* *
35695028 TACATATATATAGATTATAA-AAAAATAA
1 TACATATATATA-ATAATAATAATAAT-A
*
35695056 TTACATATATATAAAAATAATAATAAT-
1 -TACATATATATAATAATAATAATAATA
35695083 TACATATAT
1 TACATATAT
35695092 TGAAATTAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
26 19 0.36
27 5 0.09
28 12 0.23
29 17 0.32
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (27 bp):
TACATATATATAATAATAATAATAATA
Found at i:35696060 original size:19 final size:19
Alignment explanation
Indices: 35696036--35696072 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
35696026 CTTGTTACAA
*
35696036 AATAAAATAATAAAAAAAG
1 AATAAAAAAATAAAAAAAG
35696055 AATAAAAAAATAAAAAAA
1 AATAAAAAAATAAAAAAA
35696073 TAGACGCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.14
Consensus pattern (19 bp):
AATAAAAAAATAAAAAAAG
Found at i:35697085 original size:44 final size:43
Alignment explanation
Indices: 35697026--35697142 Score: 137
Period size: 43 Copynumber: 2.7 Consensus size: 43
35697016 GATGTGATCT
* * * * *
35697026 ACTCTACTACAACTTCAGAGAGGTAAGA-TATTTGGTTTTAATCC
1 ACTCCACTGCAACTTCAGGGAGATAAGATTA-TTGGCTTT-ATCC
* * *
35697070 GCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTATCT
1 ACTCCACTGCAACTTCAGGGAGATAAGATTATTGGCTTTATCC
35697113 ACTCCACTGCAACTTCAGGGAGATAAGATT
1 ACTCCACTGCAACTTCAGGGAGATAAGATT
35697143 TGCCATCTTC
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
43 31 0.50
44 29 0.47
45 2 0.03
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (43 bp):
ACTCCACTGCAACTTCAGGGAGATAAGATTATTGGCTTTATCC
Found at i:35697122 original size:43 final size:45
Alignment explanation
Indices: 35697022--35697142 Score: 149
Period size: 44 Copynumber: 2.8 Consensus size: 45
35697012 ACCCGATGTG
* * * * *
35697022 ATCTACTCTACTACAACTTCAGAGAGGTAAGA-TATTTGGTTTTA
1 ATCTACTCCACTGCAACTTCAGGGAGATAAGATTATTTGGCTTTA
** *
35697066 ATCCGCTCCACTGCAACTTCAGGGAGATAGGATTA-TTGGCTTT-
1 ATCTACTCCACTGCAACTTCAGGGAGATAAGATTATTTGGCTTTA
35697109 ATCTACTCCACTGCAACTTCAGGGAGATAAGATT
1 ATCTACTCCACTGCAACTTCAGGGAGATAAGATT
35697143 TGCCATCTTC
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
43 31 0.48
44 32 0.49
45 2 0.03
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (45 bp):
ATCTACTCCACTGCAACTTCAGGGAGATAAGATTATTTGGCTTTA
Found at i:35697229 original size:50 final size:50
Alignment explanation
Indices: 35697175--35697364 Score: 152
Period size: 50 Copynumber: 3.8 Consensus size: 50
35697165 TGCAATGTTG
35697175 GGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACATCGCCA
1 GGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACATCGCCA
** * * ** * ** * * **
35697225 GGGAAGTAAGATTCGTCGTTGCGGCTTCAATCTTTTTAATTGCAAT-G-TG
1 GGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTAC-ATCGCCA
* * *
35697274 GGGAAACGAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACCGCCA
1 GGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACATCGCCA
** * * *
35697324 -GGAGAGTAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACT
1 GGGA-AACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACT
35697365 GTAATGCAAA
Statistics
Matches: 100, Mismatches: 36, Indels: 8
0.69 0.25 0.06
Matches are distributed among these distances:
48 1 0.01
49 34 0.34
50 63 0.63
51 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (50 bp):
GGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACATCGCCA
Found at i:35697295 original size:99 final size:100
Alignment explanation
Indices: 35697149--35697356 Score: 321
Period size: 99 Copynumber: 2.1 Consensus size: 100
35697139 GATTTGCCAT
* *
35697149 CTTCAGTCTTTTAAATTGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTAAATTGCAATGTTGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCA
* *
35697214 CTACATCGCCAGG-GAAGTAAGATTCGTCGTTGCGG
66 CTACACCGCCAGGAG-AGTAAGATTCGCCGTTGCGG
* *
35697249 CTTCAATCTTTTTAATTGCAATG-TGGGGAAACGAGATTCACCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTAAATTGCAATGTTGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCA
*
35697313 CTACACCGCCAGGAGAGTAAGATTCGCCGTTGTGG
66 CTACACCGCCAGGAGAGTAAGATTCGCCGTTGCGG
*
35697348 CTTTAATCT
1 CTTCAATCT
35697357 GTTCCACTGT
Statistics
Matches: 99, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
99 77 0.78
100 22 0.22
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (100 bp):
CTTCAATCTTTTAAATTGCAATGTTGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCA
CTACACCGCCAGGAGAGTAAGATTCGCCGTTGCGG
Found at i:35697652 original size:44 final size:44
Alignment explanation
Indices: 35697559--35697716 Score: 207
Period size: 44 Copynumber: 3.7 Consensus size: 44
35697549 TGCTACTTTT
* * *
35697559 AACCTACTCCACTGCT-ACTCACGGAGATATGATT---AATCTTC
1 AACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCACAATCTTC
35697600 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTC
1 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTC
35697644 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTC
1 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTC
* * * * *
35697688 AGCCTATTCCATTGTTGTCTAGGGAGATA
1 AACCTATTCCACTGCTGACCAGGGAGATA
35697717 TGGCTGGGGT
Statistics
Matches: 105, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
41 28 0.27
42 2 0.02
44 75 0.71
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (44 bp):
AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTC
Found at i:35700103 original size:25 final size:25
Alignment explanation
Indices: 35700053--35700112 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
35700043 AAGAAAATCC
* *
35700053 AAAAGAATGAAAGAATAATTATTAA
1 AAAAGAATGAAAAAATAATTACTAA
*
35700078 AAAAGAATGAAAAAAT-ATTGGCTAA
1 AAAAGAATGAAAAAATAATT-ACTAA
35700103 AAAATGAATG
1 AAAA-GAATG
35700113 CAAAGATGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 3 0.10
25 22 0.73
26 5 0.17
ACGTcount: A:0.62, C:0.02, G:0.15, T:0.22
Consensus pattern (25 bp):
AAAAGAATGAAAAAATAATTACTAA
Found at i:35704292 original size:31 final size:33
Alignment explanation
Indices: 35704237--35704326 Score: 103
Period size: 31 Copynumber: 2.7 Consensus size: 33
35704227 AAAAATATTC
*
35704237 ATTAGAAAAATATATAAATATATACATGTACAT-
1 ATTATAAAAATA-ATAAATATATACATGTACATA
* *
35704270 A-TATAAAAATAATAATTATATACATGTATATA
1 ATTATAAAAATAATAAATATATACATGTACATA
*
35704302 GATTATAAAAATAATTACATATATA
1 -ATTATAAAAATAA-TAAATATATA
35704327 AAAACAAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
31 18 0.38
32 9 0.19
33 2 0.04
34 11 0.23
35 8 0.17
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (33 bp):
ATTATAAAAATAATAAATATATACATGTACATA
Found at i:35704524 original size:17 final size:17
Alignment explanation
Indices: 35704504--35704538 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
35704494 GAAATAAAAA
*
35704504 AAAATGTATATGTATAT
1 AAAATGTAAATGTATAT
35704521 AAAATGTAAATGTATAT
1 AAAATGTAAATGTATAT
35704538 A
1 A
35704539 TATGTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.37
Consensus pattern (17 bp):
AAAATGTAAATGTATAT
Found at i:35704662 original size:3 final size:3
Alignment explanation
Indices: 35704656--35704712 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
35704646 TATGCGTATG
35704656 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35704704 TAA TAA TAA
1 TAA TAA TAA
35704713 AATTGGTACT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:35709081 original size:16 final size:16
Alignment explanation
Indices: 35709060--35709116 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 16
35709050 TTGAATTACT
*
35709060 GATTACAATTTTATTC
1 GATTACAACTTTATTC
35709076 GATTACAACTTTATTC
1 GATTACAACTTTATTC
* *
35709092 AATTACAACTCTATTC
1 GATTACAACTTTATTC
*
35709108 CATTACAAC
1 GATTACAAC
35709117 CCTATCTCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (16 bp):
GATTACAACTTTATTC
Found at i:35709081 original size:46 final size:44
Alignment explanation
Indices: 35708993--35709081 Score: 108
Period size: 46 Copynumber: 2.0 Consensus size: 44
35708983 ATCTATTTCA
* *
35708993 TTCAACCAAACACAATAATACTATTACAGTTCTATTCTATTACG
1 TTCAACCAAACACAATAATACTATTACAATTCTATTCGATTACG
* *
35709037 TTCAACCAAACA-ATTGAATTACTGATTACAATTTTATTCGATTAC
1 TTCAACCAAACACAAT-AA-TACT-ATTACAATTCTATTCGATTAC
35709082 AACTTTATTC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
43 2 0.05
44 14 0.37
45 4 0.11
46 18 0.47
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (44 bp):
TTCAACCAAACACAATAATACTATTACAATTCTATTCGATTACG
Found at i:35713722 original size:25 final size:27
Alignment explanation
Indices: 35713691--35713748 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 27
35713681 TTAAGTTAAT
35713691 ATTATAA-T-TATATATAATTGTCTTA
1 ATTATAATTATATATATAATTGTCTTA
35713716 ATTATAATTAAATATATATAATTGTCTTA
1 ATTATAATT--ATATATATAATTGTCTTA
35713745 ATTA
1 ATTA
35713749 AGTTAATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 7 0.24
26 1 0.03
29 21 0.72
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (27 bp):
ATTATAATTATATATATAATTGTCTTA
Found at i:35714136 original size:20 final size:20
Alignment explanation
Indices: 35714094--35714129 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
35714084 AGGTAAAATA
35714094 AATCAAAGATTAAGTTAATT
1 AATCAAAGATTAAGTTAATT
35714114 AATCAAAG-TTAA-TTAA
1 AATCAAAGATTAAGTTAA
35714130 GATTAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.25
19 4 0.25
20 8 0.50
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.33
Consensus pattern (20 bp):
AATCAAAGATTAAGTTAATT
Found at i:35716869 original size:26 final size:26
Alignment explanation
Indices: 35716840--35716898 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
35716830 TACCCCTAGC
*
35716840 AAAATTTTGATGATTTTACCTC-TGGT
1 AAAATTTTGATCATTTT-CCTCTTGGT
*
35716866 AAAATTTTGATCATTTTGCTCTTGGT
1 AAAATTTTGATCATTTTCCTCTTGGT
35716892 AAAATTT
1 AAAATTT
35716899 CAAAAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 3 0.10
26 27 0.90
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (26 bp):
AAAATTTTGATCATTTTCCTCTTGGT
Found at i:35717062 original size:12 final size:12
Alignment explanation
Indices: 35717045--35717092 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
35717035 TGCAAATGGA
*
35717045 TCATTTCCCTTT
1 TCATTTCCATTT
*
35717057 TCATTTTCATTT
1 TCATTTCCATTT
*
35717069 CCATTTCCATTT
1 TCATTTCCATTT
35717081 TCATTTCCATTT
1 TCATTTCCATTT
35717093 CTAGAAACCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.15, C:0.27, G:0.00, T:0.58
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:35717065 original size:6 final size:6
Alignment explanation
Indices: 35717046--35717093 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
35717036 GCAAATGGAT
* * * *
35717046 CATTTC CCTTTT CATTTT CATTTC CATTTC CATTTT CATTTC CATTTC
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC
35717094 TAGAAACCTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.15, C:0.29, G:0.00, T:0.56
Consensus pattern (6 bp):
CATTTC
Done.