Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 186 of 199
Found at i:54355137 original size:30 final size:30
Alignment explanation
Indices: 54354833--54355138 Score: 263
Period size: 30 Copynumber: 10.0 Consensus size: 30
54354823 CAGTTCGTGC
* * *
54354833 AAATGCAGCTCGTGTGACCTGC-CTTCATGT
1 AAATGCAGCTCATGCGA-CTGCAATTCATGT
* * * *
54354863 AAATGCAGCTCGTGCAATTGCACTTCATGT
1 AAATGCAGCTCATGCGACTGCAATTCATGT
* * *
54354893 AAATGCAGCTCATGCAACTGCAATCCGTGT
1 AAATGCAGCTCATGCGACTGCAATTCATGT
* * *
54354923 AAATGCAGCTCGTGCGACTGCAATCCGTGT
1 AAATGCAGCTCATGCGACTGCAATTCATGT
* * * *
54354953 AAATGCAGCTCGTGCAACTGCAATCCGTGT
1 AAATGCAGCTCATGCGACTGCAATTCATGT
* * *
54354983 AAATGCAGCTCATGTGACTGTAGTTCATGT
1 AAATGCAGCTCATGCGACTGCAATTCATGT
* * *
54355013 AAATGCAGCAGTTTATGTGACTGCAGTTCATGT
1 AAATGCAGC---TCATGCGACTGCAATTCATGT
* * *
54355046 AAATGCAGCACATGCAACTGCAGTTCATGT
1 AAATGCAGCTCATGCGACTGCAATTCATGT
* *
54355076 AAATGCAGCAGTTTATGCGACTGCAGTTCATGT
1 AAATGCAGC---TCATGCGACTGCAATTCATGT
* * *
54355109 AAATGCAGCTCGTGTGACTGCAAATCATGT
1 AAATGCAGCTCATGCGACTGCAATTCATGT
54355139 TTAAGCTGCT
Statistics
Matches: 237, Mismatches: 32, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
29 3 0.01
30 179 0.76
33 55 0.23
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (30 bp):
AAATGCAGCTCATGCGACTGCAATTCATGT
Found at i:54355137 original size:63 final size:60
Alignment explanation
Indices: 54354856--54355138 Score: 269
Period size: 63 Copynumber: 4.6 Consensus size: 60
54354846 GTGACCTGCC
* * *
54354856 TTCATGTAAATGCAGCTCGTGCAATTGCACTTCATGTAAATGCAGCTCATGCAACTGCAA
1 TTCATGTAAATGCAGCTCGTGCGACTGCAATTCATGTAAATGCAGCTCATGCAACTGCAA
* * * * *
54354916 TCCGTGTAAATGCAGCTCGTGCGACTGCAATCCGTGTAAATGCAGCTCGTGCAACTGCAA
1 TTCATGTAAATGCAGCTCGTGCGACTGCAATTCATGTAAATGCAGCTCATGCAACTGCAA
* * * * * * * ** *
54354976 TCCGTGTAAATGCAGCTCATGTGACTGTAGTTCATGTAAATGCAGCAGTTTATGTGACTGCAG
1 TTCATGTAAATGCAGCTCGTGCGACTGCAATTCATGTAAATGCAGC---TCATGCAACTGCAA
* * * * * * *
54355039 TTCATGTAAATGCAGCACATGCAACTGCAGTTCATGTAAATGCAGCAGTTTATGCGACTGCAG
1 TTCATGTAAATGCAGCTCGTGCGACTGCAATTCATGTAAATGCAGC---TCATGCAACTGCAA
* *
54355102 TTCATGTAAATGCAGCTCGTGTGACTGCAAATCATGT
1 TTCATGTAAATGCAGCTCGTGCGACTGCAATTCATGT
54355139 TTAAGCTGCT
Statistics
Matches: 188, Mismatches: 32, Indels: 3
0.84 0.14 0.01
Matches are distributed among these distances:
60 92 0.49
63 96 0.51
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Consensus pattern (60 bp):
TTCATGTAAATGCAGCTCGTGCGACTGCAATTCATGTAAATGCAGCTCATGCAACTGCAA
Found at i:54361039 original size:16 final size:16
Alignment explanation
Indices: 54361014--54361044 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54361004 TTCCATAAGT
54361014 TAAATACAAAATTAAA
1 TAAATACAAAATTAAA
*
54361030 TAAATTCAAAATTAA
1 TAAATACAAAATTAA
54361045 CGGAATCATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAATACAAAATTAAA
Found at i:54367437 original size:20 final size:20
Alignment explanation
Indices: 54367412--54367451 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
54367402 AATATTTTCC
*
54367412 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
54367432 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
54367452 TTATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:54367466 original size:34 final size:35
Alignment explanation
Indices: 54367400--54367466 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
54367390 CAAACACCAG
*
54367400 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
54367435 AAAACATTTTCCAG-AAATTATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
54367467 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:54373569 original size:22 final size:20
Alignment explanation
Indices: 54373491--54373570 Score: 67
Period size: 20 Copynumber: 3.9 Consensus size: 20
54373481 TCGAACCCTG
*
54373491 GGGTTCAAGGTTCAAATTTA
1 GGGTTCAAGGTTCAGATTTA
* *
54373511 -GGTTCGAGGCTACATG-TTT-
1 GGGTTCAAGG-TTCA-GATTTA
54373530 GGGTTCAAGGTTCAAGATTTAA
1 GGGTTCAAGGTTC-AGATTT-A
54373552 GGGTTCAAGGTTACAGATT
1 GGGTTCAAGGTT-CAGATT
54373571 ACGAGTTCGA
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
19 11 0.23
20 18 0.38
22 17 0.36
23 1 0.02
ACGTcount: A:0.26, C:0.11, G:0.29, T:0.34
Consensus pattern (20 bp):
GGGTTCAAGGTTCAGATTTA
Found at i:54376067 original size:26 final size:26
Alignment explanation
Indices: 54376017--54376069 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
54376007 TTTAAAATAC
*
54376017 TTTTAAAATATTTTTTTATTTTTTAT
1 TTTTAAAATATTTTTTTATTGTTTAT
54376043 TTTTAAAATATTTTTTT-TGTGTTTAT
1 TTTTAAAATATTTTTTTAT-TGTTTAT
54376069 T
1 T
54376070 AAAAATTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 1 0.04
26 24 0.96
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.72
Consensus pattern (26 bp):
TTTTAAAATATTTTTTTATTGTTTAT
Found at i:54376650 original size:27 final size:27
Alignment explanation
Indices: 54376612--54376667 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
54376602 AGTTCGAATC
54376612 TCTCAGGCGACGTCGAACTTTCTTTTT
1 TCTCAGGCGACGTCGAACTTTCTTTTT
54376639 TCTCAGGCGACGTCGAACTTTCTTTTT
1 TCTCAGGCGACGTCGAACTTTCTTTTT
54376666 TC
1 TC
54376668 CCTGTGTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.14, C:0.27, G:0.18, T:0.41
Consensus pattern (27 bp):
TCTCAGGCGACGTCGAACTTTCTTTTT
Found at i:54387752 original size:19 final size:17
Alignment explanation
Indices: 54387713--54387763 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
54387703 ACCGAAAGAA
54387713 AAAAAT-AAAAATAAAC
1 AAAAATAAAAAATAAAC
*
54387729 CAAAATAAAAAATATGAAC
1 AAAAATAAAAAATA--AAC
54387748 AAAAATAAATAAATAA
1 AAAAATAAA-AAATAA
54387764 TAGCATCAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 5 0.17
17 7 0.24
18 1 0.03
19 11 0.38
20 5 0.17
ACGTcount: A:0.76, C:0.06, G:0.02, T:0.16
Consensus pattern (17 bp):
AAAAATAAAAAATAAAC
Found at i:54389615 original size:44 final size:44
Alignment explanation
Indices: 54389330--54389995 Score: 233
Period size: 44 Copynumber: 14.9 Consensus size: 44
54389320 TCACTGTTTT
* * * ** *
54389330 AATCTACTCCATTGCGACTTCAGGGAGATAGGATTAACAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTC
* * * * * * *
54389374 AATCTGCTGCACTACAACTTCAAGGAGATAAGATTGGTATCTTA
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTC
* * * * * *
54389418 AACCTGCTCTACTGCAACTTTAGGGAGATAAGG-TTGGTCGTTTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGAT-AGGATTAGTAG-CTTC
* * *
54389463 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTGGACTT-
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGA----TTA--GTAG-CTTC
* * * * *
54389513 AATCCGAC-CTACTGCAACTTCTGAGGA-ATAGGATTCA-TCA-TTTT
1 AATCTG-CTCCACTGCAACTTCAG-GGAGATAGGATT-AGT-AGCTTC
* * *
54389557 AATCCGCTCCACTGCAACTTCAAGGAGATAGGATTAATAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTC
* * * **
54389601 AATCTGCTCAACTGCAACTTCAGGGAGATAAGATTGGTATTTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTC
* * * * *
54389645 AACCTGCTCCACTGTAACTTCAGGGAGATAAGG-TTGGTTGTATTC
1 AATCTGCTCCACTGCAACTTCAGGGAGAT-AGGATTAGTAG-CTTC
* * * * *
54389690 AGTCTGCTTCACTGTAACTTTAGGGAGATAAGACTTTTTATGGTAGACTT-
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGA----TTA--GTAG-CTTC
* * * * * * *
54389740 AAT-TCGAC-CTAATGCAACTTCCGAGG-TATAGGATTCA-TCGTTTT
1 AATCT-G-CTCCACTGCAACTTCAG-GGAGATAGGATT-AGTAGCTTC
* * * * *
54389784 AATCCGCTCCACAAG-AACTTTAGGGAGATAGGACTTGGTAACTTC
1 AATCTGCTCCAC-TGCAACTTCAGGGAGATAGGA-TTAGTAGCTTC
* * * ** *
54389829 AATCTGCTCCACTGCAACTTCAGGAAGATAAGATTAATTTATTTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATT-A-GTAGCTTC
* * * * *
54389875 AACCTGCTCCACTAC-ACTTCAGGGAGATAAGATTGGTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTC
* *
54389918 AA-CTTGCTCTACTGCAACTTCAGGGAGAT---A--AG--GCTTT
1 AATC-TGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTC
** * *
54389955 AATCTGCTCCACCACAACTTCAGGGAGATAAGATTTGTAGC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGC
54389996 ATGTCTTCAA
Statistics
Matches: 454, Mismatches: 117, Indels: 102
0.67 0.17 0.15
Matches are distributed among these distances:
37 27 0.06
38 1 0.00
39 1 0.00
40 1 0.00
41 1 0.00
42 2 0.00
43 29 0.06
44 199 0.44
45 109 0.24
46 21 0.05
47 2 0.00
49 5 0.01
50 39 0.09
51 17 0.04
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTC
Found at i:54389630 original size:227 final size:225
Alignment explanation
Indices: 54389235--54389949 Score: 864
Period size: 227 Copynumber: 3.1 Consensus size: 225
54389225 CCGCTATCTA
* * * * *
54389235 CAGTCTGCTCCACTACAACTTTAGGGAGATAATACTCGTTATGGTAGA-TTCAATCCAACCTACT
1 CAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTAGACTT-AATCCGACCTACT
** ** * *
54389299 AAAACTTCAGAGGTATAGGATTCA-CTGTTTTAATCTACTCCATTGCGACTTCAGGGAGATAGGA
65 GCAACTTCAGAGGTATAGGATTCATC-GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGA
* * * * *
54389363 TTAACAACTTCAATCTGCTGCACTACAACTTCAAGGAGATAAGATTGGTATCTTAAACCTGCTCT
129 TTAATAACTTCAATCTGCT-CACTGCAACTTCAGGGAGATAAGATTGGTATTTTAAACCTGCTCC
* *
54389428 ACTGCAACTTTAGGGAGATAAGGTTGGTCGTTTT
193 ACTGCAACTTCAGGGAGATAAGGTTGGT-GTATT
*
54389462 CAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTGGACTTAATCCGACCTACTG
1 CAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTAGACTTAATCCGACCTACTG
* * * *
54389527 CAACTTCTGAGGAATAGGATTCATCATTTTAATCCGCTCCACTGCAACTTCAAGGAGATAGGATT
66 CAACTTCAGAGGTATAGGATTCATCGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATT
* *
54389592 AATAGCTTCAATCTGCTCAACTGCAACTTCAGGGAGATAAGATTGGTATTTTCAACCTGCTCCAC
131 AATAACTTCAATCTGCTC-ACTGCAACTTCAGGGAGATAAGATTGGTATTTTAAACCTGCTCCAC
*
54389657 TGTAACTTCAGGGAGATAAGGTTGGTTGTATT
195 TGCAACTTCAGGGAGATAAGGTTGG-TGTATT
* * * * * *
54389689 CAGTCTGCTTCACTGTAACTTTAGGGAGATAAGACTTTTTATGGTAGACTTAATTCGACCTAATG
1 CAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTAGACTTAATCCGACCTACTG
* * *
54389754 CAACTTCCGAGGTATAGGATTCATCGTTTTAATCCGCTCCACAAG-AACTTTAGGGAGATAGGAC
66 CAACTTCAGAGGTATAGGATTCATCGTTTTAATCCGCTCCAC-TGCAACTTCAGGGAGATAGGA-
** * ** *
54389818 TTGGTAACTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTAATTTATTTTTAACCTGCT
129 TTAATAACTTCAATCTGCT-CACTGCAACTTCAGGGAGATAAGATT--GGTATTTTAAACCTGCT
* * * *
54389883 CCACTAC-ACTTCAGGGAGATAAGATTGGTATCTT
191 CCACTGCAACTTCAGGGAGATAAGGTTGGTGTATT
* *
54389917 CA-ACTTGCTCTACTGCAACTTCAGGGAGATAAG
1 CAGTC-TGCTCCACTGCAACTTCAGGGAGATAAG
54389950 GCTTTAATCT
Statistics
Matches: 422, Mismatches: 56, Indels: 19
0.85 0.11 0.04
Matches are distributed among these distances:
226 1 0.00
227 306 0.73
228 75 0.18
229 21 0.05
230 19 0.05
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (225 bp):
CAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTAGACTTAATCCGACCTACTG
CAACTTCAGAGGTATAGGATTCATCGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATT
AATAACTTCAATCTGCTCACTGCAACTTCAGGGAGATAAGATTGGTATTTTAAACCTGCTCCACT
GCAACTTCAGGGAGATAAGGTTGGTGTATT
Found at i:54390245 original size:123 final size:123
Alignment explanation
Indices: 54390026--54390248 Score: 320
Period size: 123 Copynumber: 1.8 Consensus size: 123
54390016 GATTCGTTGT
* * * * * *
54390026 CTTCAGCTTTAATTTGCTCCACTGCAATGCCAGAAAAACAAGATTCGCTACCTTTACCTTTAATT
1 CTTCAGCTTTAATCTACTCCACTACAATGCCAGAAAAACAAGATCCACTACCTTTACCTTTAATC
* ** *
54390091 TGTTCCACTGTAGCGCCAAGGAAATAGGATTCGCTACCTTCAGCTTTAATCCGCTTCA
66 TGTTCCACTGCAAAGCCAAGGAAATAAGATTCGCTACCTTCAGCTTTAATCCGCTTCA
* ** *
54390149 CTTCAGCTTTAATCTATTCCACTACAATGCCAGGGAAACAAGATCCACTACCTTTAGCTTTAATC
1 CTTCAGCTTTAATCTACTCCACTACAATGCCAGAAAAACAAGATCCACTACCTTTACCTTTAATC
54390214 TGTTCCACTGCAAAGCCAAGGAAATAAGATTCGCT
66 TGTTCCACTGCAAAGCCAAGGAAATAAGATTCGCT
54390249 GTATTTGATC
Statistics
Matches: 86, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
123 86 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.30
Consensus pattern (123 bp):
CTTCAGCTTTAATCTACTCCACTACAATGCCAGAAAAACAAGATCCACTACCTTTACCTTTAATC
TGTTCCACTGCAAAGCCAAGGAAATAAGATTCGCTACCTTCAGCTTTAATCCGCTTCA
Found at i:54390503 original size:88 final size:88
Alignment explanation
Indices: 54390411--54390598 Score: 261
Period size: 88 Copynumber: 2.1 Consensus size: 88
54390401 CTGTTTAGGG
* * * *
54390411 AGACAGGATCTATAATCTTCAACCTACTCTACTACTGCTCAAGGAGATAAGGCTGGTGTTTTCGA
1 AGACAAGATCTATAATCTTCAACCTACTCCACTACTGCTCAAGGAGAGAAGGCTGATGTTTTCGA
*
54390476 TCTAC-TTCACTGTCAGTACAAGA
66 TCT-CTTTCACTGCCAGTACAAGA
* ** *
54390499 AGACAAGATCTATAATCTTTAACCTACTCCACTGTTGCTCAGGGAGAGAAGGCTGATGTTTTCGA
1 AGACAAGATCTATAATCTTCAACCTACTCCACTACTGCTCAAGGAGAGAAGGCTGATGTTTTCGA
* *
54390564 TCTCTTTCACTGCCGGTACATGA
66 TCTCTTTCACTGCCAGTACAAGA
54390587 AGACAAGATCTA
1 AGACAAGATCTA
54390599 CAATATATAA
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
87 1 0.01
88 87 0.99
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (88 bp):
AGACAAGATCTATAATCTTCAACCTACTCCACTACTGCTCAAGGAGAGAAGGCTGATGTTTTCGA
TCTCTTTCACTGCCAGTACAAGA
Found at i:54390945 original size:24 final size:24
Alignment explanation
Indices: 54390911--54390969 Score: 91
Period size: 24 Copynumber: 2.4 Consensus size: 24
54390901 CGGATTGCCC
*
54390911 CCACTGTAATCTTCAGGGTTCAAT
1 CCACTGTAATCTTCAAGGTTCAAT
*
54390935 CTACTGTAATCTTCAAGGTTCAAT
1 CCACTGTAATCTTCAAGGTTCAAT
54390959 CCACTTGTAAT
1 CCAC-TGTAAT
54390970 TTTGGGACGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
24 25 0.81
25 6 0.19
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.36
Consensus pattern (24 bp):
CCACTGTAATCTTCAAGGTTCAAT
Found at i:54391630 original size:108 final size:109
Alignment explanation
Indices: 54391441--54391663 Score: 322
Period size: 108 Copynumber: 2.1 Consensus size: 109
54391431 GGAAAATGCT
* * *
54391441 TGAAAAAGATTATTACAATGGACGAGATGAAAATTTATTGAGAACAAAGCTCGAAATAAATAAAT
1 TGAAAAAGATTATCACAATGGACAAGATGAAAATTTATTGAGAACAAAGCTCGAAATAAACAAAT
* *
54391506 CAATCAAGATAGCAAATTTTGCTGAGATAC-AAGATGAATAAGA
66 CAATCAAGATAGCAAATTTTGCTAAGATACAAAAATGAATAAGA
* * * * * * *
54391549 TGAAAAAGATTATCACAATTGATAAGATGGAATTTTATTGAGAGCAAAGCTTGAAATGAACAAAT
1 TGAAAAAGATTATCACAATGGACAAGATGAAAATTTATTGAGAACAAAGCTCGAAATAAACAAAT
*
54391614 TAATCAAGATAGCAAATTTTGCTAAGATACAAAAATGAATAAGA
66 CAATCAAGATAGCAAATTTTGCTAAGATACAAAAATGAATAAGA
54391658 TGAAAA
1 TGAAAA
54391664 CAAGTGCCCC
Statistics
Matches: 101, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
108 83 0.82
109 18 0.18
ACGTcount: A:0.49, C:0.09, G:0.17, T:0.25
Consensus pattern (109 bp):
TGAAAAAGATTATCACAATGGACAAGATGAAAATTTATTGAGAACAAAGCTCGAAATAAACAAAT
CAATCAAGATAGCAAATTTTGCTAAGATACAAAAATGAATAAGA
Found at i:54391961 original size:15 final size:14
Alignment explanation
Indices: 54391929--54391968 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 14
54391919 TTGGCCTCTC
54391929 TTTCTTTTT-TTCT
1 TTTCTTTTTCTTCT
54391942 TTTCTTTTTCTTCTT
1 TTTCTTTTTCTTC-T
54391957 TTTCTTTTTCTT
1 TTTCTTTTTCTT
54391969 TTTGAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 9 0.36
14 3 0.12
15 13 0.52
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTCTTTTTCTTCT
Found at i:54393793 original size:9 final size:9
Alignment explanation
Indices: 54393781--54393839 Score: 75
Period size: 9 Copynumber: 6.4 Consensus size: 9
54393771 AAAATAAAAA
54393781 AATTCGGGT
1 AATTCGGGT
54393790 AATTCGGGT
1 AATTCGGGT
*
54393799 ATTTTTC-GGT
1 A--ATTCGGGT
*
54393809 AATTCGGTT
1 AATTCGGGT
54393818 AATTCGGGT
1 AATTCGGGT
54393827 AATTCGGGT
1 AATTCGGGT
54393836 AATT
1 AATT
54393840 TTTAACTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
8 3 0.07
9 33 0.77
10 4 0.09
11 3 0.07
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.41
Consensus pattern (9 bp):
AATTCGGGT
Found at i:54397891 original size:19 final size:17
Alignment explanation
Indices: 54397852--54397902 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
54397842 ACTGAAAGAA
54397852 AAAAAT-AAAAATAAAC
1 AAAAATAAAAAATAAAC
*
54397868 CAAAATAAAAAATATGAAC
1 AAAAATAAAAAATA--AAC
54397887 AAAAATAAATAAATAA
1 AAAAATAAA-AAATAA
54397903 TAGCATCAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 5 0.17
17 7 0.24
18 1 0.03
19 11 0.38
20 5 0.17
ACGTcount: A:0.76, C:0.06, G:0.02, T:0.16
Consensus pattern (17 bp):
AAAAATAAAAAATAAAC
Found at i:54399612 original size:19 final size:20
Alignment explanation
Indices: 54399572--54399613 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
54399562 TCATTACACC
* *
54399572 AATAAAATATATGTACAATT
1 AATAAAAAATATGTAAAATT
54399592 AATAAAAAATAT-TAAAATT
1 AATAAAAAATATGTAAAATT
54399611 AAT
1 AAT
54399614 TACCTTTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
AATAAAAAATATGTAAAATT
Found at i:54404320 original size:34 final size:31
Alignment explanation
Indices: 54404262--54404326 Score: 94
Period size: 34 Copynumber: 2.0 Consensus size: 31
54404252 GTTCAACAAC
54404262 AGATCCGATTTATACATCTATATATACATAT
1 AGATCCGATTTATACATCTATATATACATAT
*
54404293 AGATCCGATTTCATAAAGATCTATATATACATAT
1 AGATCCGATTT-AT--ACATCTATATATACATAT
54404327 GCATTCACCT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 11 0.37
32 2 0.07
34 17 0.57
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (31 bp):
AGATCCGATTTATACATCTATATATACATAT
Found at i:54408750 original size:28 final size:28
Alignment explanation
Indices: 54408710--54408766 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
54408700 TAATGGAAAA
54408710 TCATTTATCGATCCAATCCAAACTATGT
1 TCATTTATCGATCCAATCCAAACTATGT
54408738 TCATTTATCGATCCAATCCAAACTATGT
1 TCATTTATCGATCCAATCCAAACTATGT
54408766 T
1 T
54408767 TTCAAGATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.37
Consensus pattern (28 bp):
TCATTTATCGATCCAATCCAAACTATGT
Found at i:54413616 original size:4 final size:4
Alignment explanation
Indices: 54413602--54413654 Score: 79
Period size: 4 Copynumber: 13.2 Consensus size: 4
54413592 ACACTCGTAT
* * *
54413602 ACAC TCAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAT ACAT
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
54413650 ACAC A
1 ACAC A
54413655 TGCGTGTATA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.49, C:0.45, G:0.00, T:0.06
Consensus pattern (4 bp):
ACAC
Found at i:54413655 original size:6 final size:6
Alignment explanation
Indices: 54413602--54413654 Score: 79
Period size: 6 Copynumber: 8.8 Consensus size: 6
54413592 ACACTCGTAT
* * *
54413602 ACACTC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ATACAT
1 ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC
54413650 ACACA
1 ACACA
54413655 TGCGTGTATA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.49, C:0.45, G:0.00, T:0.06
Consensus pattern (6 bp):
ACACAC
Found at i:54413655 original size:10 final size:10
Alignment explanation
Indices: 54413602--54413654 Score: 79
Period size: 10 Copynumber: 5.3 Consensus size: 10
54413592 ACACTCGTAT
*
54413602 ACACTCACAC
1 ACACACACAC
54413612 ACACACACAC
1 ACACACACAC
54413622 ACACACACAC
1 ACACACACAC
54413632 ACACACACAC
1 ACACACACAC
* *
54413642 ACATACATAC
1 ACACACACAC
54413652 ACA
1 ACA
54413655 TGCGTGTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 40 1.00
ACGTcount: A:0.49, C:0.45, G:0.00, T:0.06
Consensus pattern (10 bp):
ACACACACAC
Found at i:54415199 original size:20 final size:20
Alignment explanation
Indices: 54415176--54415228 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
54415166 TTCTATCGGC
* *
54415176 AATTTACAATTTCTTTTTGA
1 AATTTACAATGTATTTTTGA
*
54415196 AATTTAAAATGTATTTTTGA
1 AATTTACAATGTATTTTTGA
*
54415216 TATTTATCAATGT
1 AATTTA-CAATGT
54415229 CTGAAATTGT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.34, C:0.06, G:0.08, T:0.53
Consensus pattern (20 bp):
AATTTACAATGTATTTTTGA
Found at i:54415517 original size:162 final size:162
Alignment explanation
Indices: 54415250--54415603 Score: 527
Period size: 162 Copynumber: 2.2 Consensus size: 162
54415240 TCAATAATAT
* * *
54415250 TTTTCATGCACTACTTCGTAACGAAATATGATACGTATGTTTAATTTAAAGAAGTCACGAACACA
1 TTTTCATGCACTATTTTGTAACGAAATATGATACGTATGTTTAATTGAAAGAAGTCACGAACACA
* *
54415315 CTAGGAGTATTTAACTTAAGAAGGCGCGGAAATAACGAATTTTTGAAATGTAACTTCAATACCTC
66 CTACGAGTATTTAACTTAAGAAGGCACGGAAATAACGAATTTTTGAAATGTAACTTCAATACCTC
*
54415380 TTTTCCCATATTCGACGTAATCTCTTTCGATG
131 TTTTCCCATATTCGACGTAATCTCTATCGATG
** *
54415412 TTTTCATGCACTATTTTGTAACGACGTATGATACGTGTGTTTAATTGAAAGAAGAT-AC-AA-AC
1 TTTTCATGCACTATTTTGTAACGAAATATGATACGTATGTTTAATTGAAAGAAG-TCACGAACAC
*
54415474 ACGTCACGAGTATTTAA-TATAAGAAGGTACGGAAATAACGAATTTTTGAAATGTAACTTCAATA
65 AC-T-ACGAGTATTTAACT-TAAGAAGGCACGGAAATAACGAATTTTTGAAATGTAACTTCAATA
* **
54415538 CCTCTTTTCCCATATTTGGGGTAATCTCTATCGATG
127 CCTCTTTTCCCATATTCGACGTAATCTCTATCGATG
54415574 TTTTCATGCACTATTTTGTAACGAAATATG
1 TTTTCATGCACTATTTTGTAACGAAATATG
54415604 GTAAACGTGT
Statistics
Matches: 173, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
160 4 0.02
161 4 0.02
162 164 0.95
163 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (162 bp):
TTTTCATGCACTATTTTGTAACGAAATATGATACGTATGTTTAATTGAAAGAAGTCACGAACACA
CTACGAGTATTTAACTTAAGAAGGCACGGAAATAACGAATTTTTGAAATGTAACTTCAATACCTC
TTTTCCCATATTCGACGTAATCTCTATCGATG
Found at i:54419413 original size:12 final size:12
Alignment explanation
Indices: 54419396--54419421 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54419386 CGACCCGCCC
54419396 ATATTAATTTTT
1 ATATTAATTTTT
54419408 ATATTAATTTTT
1 ATATTAATTTTT
54419420 AT
1 AT
54419422 GTAATTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:54419599 original size:30 final size:30
Alignment explanation
Indices: 54419555--54419617 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
54419545 ACTTAACAAG
*
54419555 CAAATGCCTCTAAAATAATAATAAAAATAA
1 CAAATGCCTCTAAAATAATAACAAAAATAA
* * *
54419585 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAAATAA
54419615 CAA
1 CAA
54419618 TAAAATAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.59, C:0.13, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAAATAA
Found at i:54423531 original size:225 final size:225
Alignment explanation
Indices: 54423140--54423586 Score: 876
Period size: 225 Copynumber: 2.0 Consensus size: 225
54423130 ATCAATAAAT
54423140 TTAAGATTATCTCTCAGGAATCATTTGGTAAAATTTAAGTCTAGATTTACAGATTTAAAAGACAA
1 TTAAGATTATCTCTCAGGAATCATTTGGTAAAATTTAAGTCTAGATTTACAGATTTAAAAGACAA
*
54423205 ACAAAGTGATGTAACCTTTTAGGGGTTACATATACAAACGAGTGGACCTTTTCTGTAATGGTTAT
66 ACAAAGTGATGTAACCTTTTAGGGGTTACATATACAAACGAGTGGACCCTTTCTGTAATGGTTAT
54423270 TGTGAAAAATATATATTAGGGTAAAGTTAGAAGAGAAATTTGAATGATTAATTCGAATTTTTATC
131 TGTGAAAAATATATATTAGGGTAAAGTTAGAAGAGAAATTTGAATGATTAATTCGAATTTTTATC
54423335 ATTTTTAGGGGGCCAAATTGCAATTTTTTA
196 ATTTTTAGGGGGCCAAATTGCAATTTTTTA
54423365 TTAAGATTATCTCTCAGGAATCATTTGGTAAAATTTAAGTCTAGATTTACAGATTTAAAAGACAA
1 TTAAGATTATCTCTCAGGAATCATTTGGTAAAATTTAAGTCTAGATTTACAGATTTAAAAGACAA
54423430 ACAAAGTGATGTAACCTTTTAGGGGTTACATATACAAACGAGTGGACCCTTTCTGTAATGGTTAT
66 ACAAAGTGATGTAACCTTTTAGGGGTTACATATACAAACGAGTGGACCCTTTCTGTAATGGTTAT
*
54423495 TGTGAAAAATATATATTAGGGTAAAGTTAGAAGAGAAATTTGAATGATTAATTTGAATTTTTATC
131 TGTGAAAAATATATATTAGGGTAAAGTTAGAAGAGAAATTTGAATGATTAATTCGAATTTTTATC
54423560 ATTTTTAGGGGGCCAAATTGCAATTTT
196 ATTTTTAGGGGGCCAAATTGCAATTTT
54423587 ACCTTTAAAA
Statistics
Matches: 220, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
225 220 1.00
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (225 bp):
TTAAGATTATCTCTCAGGAATCATTTGGTAAAATTTAAGTCTAGATTTACAGATTTAAAAGACAA
ACAAAGTGATGTAACCTTTTAGGGGTTACATATACAAACGAGTGGACCCTTTCTGTAATGGTTAT
TGTGAAAAATATATATTAGGGTAAAGTTAGAAGAGAAATTTGAATGATTAATTCGAATTTTTATC
ATTTTTAGGGGGCCAAATTGCAATTTTTTA
Found at i:54425871 original size:413 final size:417
Alignment explanation
Indices: 54424247--54426127 Score: 2448
Period size: 413 Copynumber: 4.5 Consensus size: 417
54424237 NNNNNNNNTG
*
54424247 ATTTTTTTCTAAAGAAAAAAAAACTATAATCCAAGTGAAACCGAAATCAATAAATTTGAGATTAT
1 ATTTTTTTCTAAAGAAAAAAAAACTATAATCCAAGTGAAACCGGAATCAATAAATTTGAGATTAT
* * * *
54424312 CTCTCAAGAATTATTTGGTAAAATTTAAGTCTAGATTT-ACAGATTTAAAAGGCAAACAAAGTGA
66 CTGTCAAGAATCATTTGGTAAAATTTAAGTCTAGATTTCA-ATATTTAAAAGACAAACAAAGTGA
* * * *
54424376 TGTAACCTTTTAGGGGTTACATATACAAATGAGTGGACCATTTCTATAATGGTTTTTGTG-AAAA
130 TGTAACCTTTTAGGGGTTACATATACAAACGAGTGAACCATCTCTATAATGGTTATTGTGAAAAA
* *
54424440 -ATA-TATAT-TA---GGGTAAAGTTAGAAGAGAAATTTGAAGGATT-AATTCAAATTTTTATCA
195 TATATTATATATATTGGGGTAAAGTTAGAAAAGAAATTTAAAGGATTAAATT-AAATTTTTATCA
* *
54424498 TTTTTAGGGGGGCCAAAGTGCAATTTTACCTTTACTAATGTAAAA-TTTAAAAAAATTAAAGGGC
259 TTTTTA-GGGGGCCAAAGTACAATTTTACCTTTACTAATTTAAAATTTTAAAAAAATTAAAGGGC
* * * ** *
54424562 CTAAATAAAAAATTTTCCATTTTAAGAGAGTCGGGGCCTTTGCCAGCCCCT-AGCTACTACAATA
323 CTAAATAGAAAATTTTCCATTTTAAGGGAGCCGGGGCCCCTGCCAGCCCCTGA-CTACTATAATA
* * *
54424626 AAAAATTCACTTATCTTTACATTAGAACCTG
387 AAAAATCCACTTATCTTTACATTCGAACCTA
** *
54424657 A-TTTTTTCTAAAGAAAAAAAAAACTATAATCCAAGTGAAACCAAAATCAATAAATTTGAGATCA
1 ATTTTTTTCTAAAG-AAAAAAAAACTATAATCCAAGTGAAACCGGAATCAATAAATTTGAGATTA
* * * ** *
54424721 TCTCTCATGAATCATTTGGTAAAATTGAAGTCTAGATTTCAATATTTAAAAGATGAACAAAGTAA
65 TCTGTCAAGAATCATTTGGTAAAATTTAAGTCTAGATTTCAATATTTAAAAGACAAACAAAGTGA
* *
54424786 TGTAACCTTTTAGGGTTTACATATACAAACGAGTGAACCCTCTCTATAATGGTTATTGTGAAAAT
130 TGTAACCTTTTAGGGGTTACATATACAAACGAGTGAACCATCTCTATAATGGTTATTGTGAAAA-
* * * * *
54424851 TATATATTATATATATTGGGATAGAGTTAGAAAAAAAAATTAAAGGATTAAATTGAATTTTTATC
194 -ATATATTATATATATTGGGGTAAAGTTAGAAAAGAAATTTAAAGGATTAAATTAAATTTTTATC
* ** * *
54424916 AATTTTAAGGGGG-CAAAGTGTAATTTTACTTTTATTAATTTAAAATTTTAAAAAAAATTAAAGG
258 -ATTTTTAGGGGGCCAAAGTACAATTTTACCTTTACTAATTTAAAATTTT-AAAAAAATTAAAGG
* ** * * * * * * * *
54424980 TCCTAAATAGAATTTTTTTCTATTTTGAGGGTGTCAGGCCCCCTGCCAACCCCTGGCTACTATAA
321 GCCTAAATAGAA-AATTTTCCATTTTAAGGGAGCCGGGGCCCCTGCCAGCCCCTGACTACTATAA
* * *
54425045 TAAAAAAAAATTCACTTATCTTAACATTCGAACCTG
385 T---AAAAAATCCACTTATCTTTACATTCGAACCTA
*
54425081 ATTTTTTTCT-AA-AAAAAAAAACTATAATTCAAGTGAAACCGGAATCAATAAATTTGAGATTAT
1 ATTTTTTTCTAAAGAAAAAAAAACTATAATCCAAGTGAAACCGGAATCAATAAATTTGAGATTAT
* * * *
54425144 CTGTGAGGAATCATTTGATAAAATTTAAGTCTAGATTTCAATATTTAAAAGACAAACAAA--G-C
66 CTGTCAAGAATCATTTGGTAAAATTTAAGTCTAGATTTCAATATTTAAAAGACAAACAAAGTGAT
* * *
54425206 GTAACCTTTTAGGGGTTACATATACAAACAAGTGGACCAACTCTATAATGGTTATTGTGAAAAAT
131 GTAACCTTTTAGGGGTTACATATACAAACGAGTGAACCATCTCTATAATGGTTATTGTGAAAAAT
* *
54425271 ATATTATATATATTGGGGTAAAGCTAGAAAAGAATTTTAAAGGATTAAATTAAATTTTTATCATT
196 ATATTATATATATTGGGGTAAAGTTAGAAAAGAAATTTAAAGGATTAAATTAAATTTTTATCATT
** * *
54425336 TTTAAGGGGGTTAAAGTATAATTTTACCTTTACTAATTTAAAATTTTACAAAAATTAAAGGGCCT
261 TTT-AGGGGGCCAAAGTACAATTTTACCTTTACTAATTTAAAATTTTAAAAAAATTAAAGGGCCT
*
54425401 AAATAGAAAATTTTCCATTTTAAGGGAGCCGGGGCCCCTACCAGCCCCTGACTACTATAATAAAA
325 AAATAGAAAATTTTCCATTTTAAGGGAGCCGGGGCCCCTGCCAGCCCCTGACTACTATAATAAAA
*
54425466 AATCCACTTATTTTTACATTCGAACCTA
390 AATCCACTTATCTTTACATTCGAACCTA
* * * * *
54425494 ATTTTATTCTAAA-AAGGAAAAAACTATAATTCAAGTGAAACTGGAATCAATAAATTTGATATTA
1 ATTTTTTTCTAAAGAA-AAAAAAACTATAATCCAAGTGAAACCGGAATCAATAAATTTGAGATTA
* *
54425558 TCTGTCAAGAATCATTTGGTAAAAATTATGTCTAGATTTCAATATTTAAAAGACAAACAAAGTGA
65 TCTGTCAAGAATCATTTGGTAAAATTTAAGTCTAGATTTCAATATTTAAAAGACAAACAAAGTGA
* *
54425623 TGTAACCTTTTAGGGGTTACATATACAAACGAGTGAACCATCTCTGTAATGATTATTGTG-AAAA
130 TGTAACCTTTTAGGGGTTACATATACAAACGAGTGAACCATCTCTATAATGGTTATTGTGAAAAA
* * *
54425687 -ATATTATATATATTGGGGTAAAGTTAGAAAAGAATTTTAAAAGATTAAATTGAATTTTTATCAT
195 TATATTATATATATTGGGGTAAAGTTAGAAAAGAAATTTAAAGGATTAAATTAAATTTTTATCAT
* * *
54425751 TTTTAGGTGG-CAAAGTACAAATTTACCTTTACTAATTTAAAATTTTAAAAAAA-TAAAGGACCT
260 TTTTAGGGGGCCAAAGTACAATTTTACCTTTACTAATTTAAAATTTTAAAAAAATTAAAGGGCCT
* * *
54425814 AAATAGAAAATTTTTCATTTTAGGGGAGCCGGGGCCCCTGCCAGCCCCTGACTACTATAATAAAG
325 AAATAGAAAATTTTCCATTTTAAGGGAGCCGGGGCCCCTGCCAGCCCCTGACTACTATAATAAAA
* * *
54425879 AA-CCTGCTTATCTTTATATTTGAACCTA
390 AATCC-ACTTATCTTTACATTCGAACCTA
54425907 ATTTTTTTCTAAAGAAAAAAAAACTATAATCCAAGTGAAACCGGAATCAATAAATTT-AGGATTA
1 ATTTTTTTCTAAAGAAAAAAAAACTATAATCCAAGTGAAACCGGAATCAATAAATTTGA-GATTA
* *
54425971 TCTGTCAGGAATCATTTGGTAAAATTTAAGTCTAGACTTT-AATATTTAAAAGACAAACAAAATG
65 TCTGTCAAGAATCATTTGGTAAAATTTAAGTCTAGA-TTTCAATATTTAAAAGACAAACAAAGTG
* * * * * * *
54426035 ATGTAACCTTTTAGGGTTTAAATATACAAACGAAT-AGACCCTCTCTACAGTGTTTATTGTGAAA
129 ATGTAACCTTTTAGGGGTTACATATACAAACGAGTGA-ACCATCTCTATAATGGTTATTGTG--A
*
54426099 AAAATATATTATATATATTTGGGTAAAGT
191 AAAATATATTATATATATTGGGGTAAAGT
54426128 CAAAATTTTT
Statistics
Matches: 1292, Mismatches: 142, Indels: 67
0.86 0.09 0.04
Matches are distributed among these distances:
409 12 0.01
410 158 0.12
411 4 0.00
412 4 0.00
413 290 0.22
414 51 0.04
415 111 0.09
416 118 0.09
417 115 0.09
418 114 0.09
419 101 0.08
420 34 0.03
421 39 0.03
422 100 0.08
424 33 0.03
425 8 0.01
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (417 bp):
ATTTTTTTCTAAAGAAAAAAAAACTATAATCCAAGTGAAACCGGAATCAATAAATTTGAGATTAT
CTGTCAAGAATCATTTGGTAAAATTTAAGTCTAGATTTCAATATTTAAAAGACAAACAAAGTGAT
GTAACCTTTTAGGGGTTACATATACAAACGAGTGAACCATCTCTATAATGGTTATTGTGAAAAAT
ATATTATATATATTGGGGTAAAGTTAGAAAAGAAATTTAAAGGATTAAATTAAATTTTTATCATT
TTTAGGGGGCCAAAGTACAATTTTACCTTTACTAATTTAAAATTTTAAAAAAATTAAAGGGCCTA
AATAGAAAATTTTCCATTTTAAGGGAGCCGGGGCCCCTGCCAGCCCCTGACTACTATAATAAAAA
ATCCACTTATCTTTACATTCGAACCTA
Found at i:54429038 original size:415 final size:409
Alignment explanation
Indices: 54428097--54429038 Score: 1171
Period size: 414 Copynumber: 2.3 Consensus size: 409
54428087 NNNNNNNNNN
* * * *
54428097 TATACAAACAAGTACACCCTCTCTACAAAGGTTATTGTGAAAAA-ATATTATATATATATTGGGG
1 TATACAAACGAGTAGACCCTCTCTATAATGGTTATTGTGAAAAATATATTATATATAT-TT-GGG
* * * * *
54428161 TAAAGTTAGAAAAGATTTTTAAAGGATTAAATCAAATTTTTACCATTTTAAGGGGCCAAAGTGTA
64 TAAAGTTAG-AAA-ATTTTTAAAGGATGAAATTAAA-TTTTA-TATTTTTAGGGGCCAAAGTGCA
* *
54428226 ATTTTACCTTTACTAATTTAAAATTTTTAAAACATTAAAGGGCCTAAACAAAAAATTTTTCATTT
125 ATTTTACCTTTACTAATTTAAAATTTTTAAAAAATTAAAGGGCCTAAACAAAAAATTTTCCATTT
* *
54428291 TAGGGGAGCCGGGGCCCCTGCCAGCCCCTTGTTACTATAATAAAAAAACTCACTTATCTTTACAT
190 TAGGGGAGCCGGGGCCCCTGCCAGCCCCTGGCTACTATAATAAAAAAACTCACTTATCTTTACAT
54428356 TCGAACCTAATTTTTTTCAAAAAAAAAACTATAATCCAAGTGAAACCATAATCAATAAAATTGAG
255 TCGAACCTAATTTTTTTCAAAAAAAAAACTATAATCCAAGTGAAACCATAATCAATAAAATTGAG
* *
54428421 ATTATCTGTCATGAATCATTTGGTAAAATTTAACTCTAGATTTCAATATTTAAAAGACAAATAAA
320 ATTATCTGTCAGGAATCATTTGGTAAAATTTAACTCTAGATTTCAATATTTAAAAGACAAACAAA
*
54428486 GTGACGTAACCTTTTAAGGGTTACA
385 GTAACGTAACCTTTTAAGGGTTACA
* * * *
54428511 TATACAAACGAGTAGACCGTCTCTGCT-ATGGTTATTGTGAAAAAATATATCATCTATA-TTGGG
1 TATACAAACGAGTAGACCCTCTCT-ATAATGGTTATTGTG-AAAAATATATTATATATATTTGGG
*** * *
54428574 CTAAAGTTAGAAAAAAATTAAAGGATGAAATCTAATTTTTATCATTTTTAGGGAGACTAAAGTGC
64 -TAAAGTTAGAAAATTTTTAAAGGATGAAAT-TAAATTTTAT-ATTTTTAGGG-G-CCAAAGTGC
* * *
54428639 AATTTTATCTTTACTAATTTAAAATTTTTAAAAAATTAAAGGGCCTAAATAGAAAATTTTCCATT
124 AATTTTACCTTTACTAATTTAAAATTTTTAAAAAATTAAAGGGCCTAAACAAAAAATTTTCCATT
* * * * *
54428704 TTAGGGGAGCCGGGG-CCGTGCTAGCCCCTGGCTATTATAATAAAAAAAATTCACTTATCTTTAT
189 TTAGGGGAGCCGGGGCCCCTGCCAGCCCCTGGCTACTATAAT-AAAAAAACTCACTTATCTTTAC
* * * * * *
54428768 ATTTGAACTTGATTTTTTTTAAAGAAAAAAATTATAATTCC-AGTGAAATCGA-AATCAAT-AAA
253 ATTCGAACCTAATTTTTTTCAAA-AAAAAAACTATAA-TCCAAGTGAAA-CCATAATCAATAAAA
* * * *
54428830 TTTAGAATTATCTGTTAGGAATCATTTGGTAAAATTTAAGTCTAGATTTTAATATTTAAAAGACA
315 TTGAG-ATTATCTGTCAGGAATCATTTGGTAAAATTTAACTCTAGATTTCAATATTTAAAAGACA
* * *
54428895 AACAAAGTAATGTAACTTTTTAGGGGTTACA
379 AACAAAGTAACGTAACCTTTTAAGGGTTACA
*
54428926 TATACAAACGAGTAGACCCTCTCTATAATGGTTATTATGAAAATATATATTATATATATTTGGGT
1 TATACAAACGAGTAGACCCTCTCTATAATGGTTATTGTGAAAA-ATATATTATATATATTTGGGT
* ** *
54428991 AAAGTCA-AAAATTTTTGTTGAGGATCGAAATTAAATTGTATATTTTTA
65 AAAGTTAGAAAA-TTTT-TAAAGGAT-GAAATTAAATTTTATATTTTTA
54429039 TGAAAGTAAA
Statistics
Matches: 450, Mismatches: 59, Indels: 37
0.82 0.11 0.07
Matches are distributed among these distances:
412 28 0.06
413 30 0.07
414 180 0.40
415 173 0.38
416 34 0.08
417 5 0.01
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (409 bp):
TATACAAACGAGTAGACCCTCTCTATAATGGTTATTGTGAAAAATATATTATATATATTTGGGTA
AAGTTAGAAAATTTTTAAAGGATGAAATTAAATTTTATATTTTTAGGGGCCAAAGTGCAATTTTA
CCTTTACTAATTTAAAATTTTTAAAAAATTAAAGGGCCTAAACAAAAAATTTTCCATTTTAGGGG
AGCCGGGGCCCCTGCCAGCCCCTGGCTACTATAATAAAAAAACTCACTTATCTTTACATTCGAAC
CTAATTTTTTTCAAAAAAAAAACTATAATCCAAGTGAAACCATAATCAATAAAATTGAGATTATC
TGTCAGGAATCATTTGGTAAAATTTAACTCTAGATTTCAATATTTAAAAGACAAACAAAGTAACG
TAACCTTTTAAGGGTTACA
Found at i:54429593 original size:30 final size:30
Alignment explanation
Indices: 54429557--54429619 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
54429547 ACTTAACAAG
54429557 CAAATGTCTCTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
*
54429587 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
54429617 CAA
1 CAA
54429620 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:54432002 original size:418 final size:419
Alignment explanation
Indices: 54430984--54432070 Score: 1553
Period size: 423 Copynumber: 2.6 Consensus size: 419
54430974 TTTTTAAAAC
* *
54430984 TTATAATAAAAAATTTCACTTATTTTTACATTCGAACCTGATTATTTTT-TAAAG-AAAAAAACT
1 TTATAATAAAAAA-TTCACTTATCTTTACATTCGAACCTGATT-TTTTTCTAAAGAAAAAAAAAT
* * * *
54431047 ATAATTCAAGTGAAACCAAAATCAATAAATTTGAGATTGTCTCTCAGGAATCATTTGGTAAAATT
64 ATAATCCAAGTGAAACCGAAATCAATAAATTTGAGATTATCTGTCAGGAATCATTTGGTAAAATT
*
54431112 TAAGTCTAGATTTCAATATTTAAAAGACAAACAAAGTGATGTAACATTTTAGGGGTTACATATAC
129 TAAGTCTAGATTTCAATATTTAAAAGACAAACAAAGTGATGTAACCTTTTAGGGGTTACATATAC
54431177 AAACGAGTGGACCCTCTCTATAATGGTTATTGTGAAAAATATATATGATATATATATTGGGGTAA
194 AAACGAGTGGACCCTCTCTATAATGGTTATTGTG-AAAATATATAT--TATATATATTGGGGTAA
* * * * *
54431242 AGTTAGAAAAGAATTTTAAAGGACTAAATCAAATTTTTATCATTTTTAGGGGGTCAAAGTGTACT
256 AGTTAGAAAAGAAATTTAAAGGACTAAATCAAATTTTTATAATTTTTAAGGGGCCAAAGTGTAAT
* **
54431307 TTTATCTTTACTAATTTAAAATTTCAAAAAAAATTAAAGGGCCTAAATAGAATTTTTTTTCATTT
321 TTTATCTTTACAAATTTAAAATTTCAAAAAAAATTAAAGGGCCTAAATAGAAAATTTTTTCATTT
**
54431372 TAAGGGAGTCAGGGCCTCTGTCAGCCCCTGACTA
386 TAAGGGAGTCAGGGCCTCTACCAGCCCCTGACTA
* * * * * * *
54431406 CTATAATAAAAAAAATTCACTTATCATTACATTCAAACCT-AATTTTTTCTAAATAAAAATAATT
1 TTATAAT--AAAAAATTCACTTATCTTTACATTCGAACCTGATTTTTTTCTAAAGAAAAAAAAAT
** * * * *
54431470 ATAATCCAAGTGAAATAGAAATCAATAAAATTGGGATTATCTGTCAGGAATAATTTAGTAAAATT
64 ATAATCCAAGTGAAACCGAAATCAATAAATTTGAGATTATCTGTCAGGAATCATTTGGTAAAATT
*
54431535 TAAGTCTAGATTTCAA-ATTTTAAAAGACAAACAAAGTGATGTAACCTTTTAGGGGTTATATATA
129 TAAGTCTAGATTTCAATA-TTTAAAAGACAAACAAAGTGATGTAACCTTTTAGGGGTTACATATA
*
54431599 CAAACGAGTGGACCCTCTCTGTAATGGTTATTGTGAAAAGTATATATTATATATATTGGGGTAAA
193 CAAACGAGTGGACCCTCTCTATAATGGTTATTGTGAAAA-TATATATTATATATATTGGGGTAAA
* * *
54431664 GTTAGAAAAGAAATTTAAAGGATTAACTCGAATTTTTATAATTTTTAAGGGGCCAAAGTGTAATT
257 GTTAGAAAAGAAATTTAAAGGACTAAATCAAATTTTTATAATTTTTAAGGGGCCAAAGTGTAATT
* *
54431729 TTA-CTTTTACAAATTTAAAATTT-TAAAAAAATTAAATGGCCTAAATAGAAAATTTTTT-ATTT
322 TTATC-TTTACAAATTTAAAATTTCAAAAAAAATTAAAGGGCCTAAATAGAAAATTTTTTCATTT
* *
54431791 TAGGGGAGTC-GAGGCCTCTACCAGCCCCTGGCTA
386 TAAGGGAGTCAG-GGCCTCTACCAGCCCCTGACTA
* *
54431825 TTATAATAAAAAATTCATTTATCTTTACATTCGAACCTGATTTTTTTCTAAAGAAAAAAAAATAA
1 TTATAATAAAAAATTCACTTATCTTTACATTCGAACCTGATTTTTTTCTAAAGAAAAAAAAATAT
* * *
54431890 AATCCAAGTGAAACCGGAATCAATAAATTTGAGATTATTTGTCTGGAATCATTTGGTAAAATTTA
66 AATCCAAGTGAAACCGAAATCAATAAATTTGAGATTATCTGTCAGGAATCATTTGGTAAAATTTA
*
54431955 AGTCTAGATTTCAATATTTAAAAGACAAACAAAGTGACGTAACCTTTTAGGGGTTACATATACAA
131 AGTCTAGATTTCAATATTTAAAAGACAAACAAAGTGATGTAACCTTTTAGGGGTTACATATACAA
* * * * * *
54432020 ACAAGTGCACCCTGTTTACAATGGTTATTGTGAAAA-AAATATTATATATAT
196 ACGAGTGGACCCTCTCTATAATGGTTATTGTGAAAATATATATTATATATAT
54432071 ATATATATAT
Statistics
Matches: 590, Mismatches: 65, Indels: 26
0.87 0.10 0.04
Matches are distributed among these distances:
416 14 0.02
417 28 0.05
418 169 0.29
419 39 0.07
420 32 0.05
421 100 0.17
422 17 0.03
423 185 0.31
424 6 0.01
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (419 bp):
TTATAATAAAAAATTCACTTATCTTTACATTCGAACCTGATTTTTTTCTAAAGAAAAAAAAATAT
AATCCAAGTGAAACCGAAATCAATAAATTTGAGATTATCTGTCAGGAATCATTTGGTAAAATTTA
AGTCTAGATTTCAATATTTAAAAGACAAACAAAGTGATGTAACCTTTTAGGGGTTACATATACAA
ACGAGTGGACCCTCTCTATAATGGTTATTGTGAAAATATATATTATATATATTGGGGTAAAGTTA
GAAAAGAAATTTAAAGGACTAAATCAAATTTTTATAATTTTTAAGGGGCCAAAGTGTAATTTTAT
CTTTACAAATTTAAAATTTCAAAAAAAATTAAAGGGCCTAAATAGAAAATTTTTTCATTTTAAGG
GAGTCAGGGCCTCTACCAGCCCCTGACTA
Found at i:54432067 original size:2 final size:2
Alignment explanation
Indices: 54432058--54432096 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
54432048 TGTGAAAAAA
54432058 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54432097 TGGGGTAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:54432485 original size:20 final size:20
Alignment explanation
Indices: 54432462--54432508 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
54432452 TAATTTTAAA
* *
54432462 ATAATTTATTATTATTTATT
1 ATAATTTATAATTAATTATT
*
54432482 ATAATTAATAATTAATTATT
1 ATAATTTATAATTAATTATT
*
54432502 TTAATTT
1 ATAATTT
54432509 TAAAATATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATAATTTATAATTAATTATT
Found at i:54432530 original size:10 final size:10
Alignment explanation
Indices: 54432505--54432544 Score: 57
Period size: 11 Copynumber: 4.1 Consensus size: 10
54432495 AATTATTTTA
54432505 ATTTTAAAAT
1 ATTTTAAAAT
54432515 ATTTTTAAAAT
1 A-TTTTAAAAT
54432526 ATTTT-AAAT
1 ATTTTAAAAT
54432535 -TTTTAAAAT
1 ATTTTAAAAT
54432544 A
1 A
54432545 AAATTTTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 4 0.15
9 8 0.30
10 5 0.19
11 10 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
ATTTTAAAAT
Found at i:54435310 original size:22 final size:22
Alignment explanation
Indices: 54435276--54435361 Score: 124
Period size: 22 Copynumber: 4.0 Consensus size: 22
54435266 GGCCCATTTT
54435276 TATTTTAAAA-T-TTTTAAAAA
1 TATTTTAAAAGTATTTTAAAAA
***
54435296 T-TAAAAAAAGTATTTTAAAAA
1 TATTTTAAAAGTATTTTAAAAA
54435317 TATTTTAAAAGTATTTTAAAAA
1 TATTTTAAAAGTATTTTAAAAA
54435339 TATTTTAAAAGTATTTTAAAAA
1 TATTTTAAAAGTATTTTAAAAA
54435361 T
1 T
54435362 NNNNNNNNNN
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
19 5 0.09
20 2 0.04
21 10 0.18
22 40 0.70
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (22 bp):
TATTTTAAAAGTATTTTAAAAA
Found at i:54435320 original size:11 final size:11
Alignment explanation
Indices: 54435276--54435361 Score: 99
Period size: 11 Copynumber: 8.1 Consensus size: 11
54435266 GGCCCATTTT
54435276 TATTTT-AAAA
1 TATTTTAAAAA
54435286 T-TTTT-AAAA
1 TATTTTAAAAA
**
54435295 -ATTAAAAAAA
1 TATTTTAAAAA
54435305 GTATTTTAAAAA
1 -TATTTTAAAAA
*
54435317 TATTTTAAAAG
1 TATTTTAAAAA
54435328 TATTTTAAAAA
1 TATTTTAAAAA
*
54435339 TATTTTAAAAG
1 TATTTTAAAAA
54435350 TATTTTAAAAA
1 TATTTTAAAAA
54435361 T
1 T
54435362 NNNNNNNNNN
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
9 10 0.16
10 5 0.08
11 41 0.64
12 8 0.12
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:54435731 original size:30 final size:28
Alignment explanation
Indices: 54435695--54435766 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
54435685 ACAATTGGAC
*
54435695 CTAAATTTTGAAAACTAAAAAGTATAGGCA
1 CTAAATTTT-AAAAAT-AAAAGTATAGGCA
* *
54435725 CTAAATTCTTAAAAATATAAGTATAGGGA
1 CTAAATT-TTAAAAATAAAAGTATAGGCA
*
54435754 TTAAATTTTAAAA
1 CTAAATTTTAAAA
54435767 TTTTGAAGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.16
29 17 0.46
30 12 0.32
31 2 0.05
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.32
Consensus pattern (28 bp):
CTAAATTTTAAAAATAAAAGTATAGGCA
Found at i:54448132 original size:46 final size:46
Alignment explanation
Indices: 54448031--54448384 Score: 324
Period size: 46 Copynumber: 7.6 Consensus size: 46
54448021 TACGTATGAT
54448031 CACTTATCACTTGTC-C-C-TGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTT-TCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
54448074 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
54448120 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* * *
54448166 CACTTATCACTTTCTCACCACTTATCACTTTCTCACTTGATCAGAT-AAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTCT---CAC-T-TGA-----TCA---GATAAG-TGTA-----GCTAAGGCTAC
* *
54448230 CACTTATCACTTTCTCACTTGATCAAATAAGTGTAGCTAAGGCTAA
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
54448276 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T-A-G----
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
54448312 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
54448358 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTCTCACTTGATCAGA
54448385 AGTACTCAAA
Statistics
Matches: 262, Mismatches: 15, Indels: 65
0.77 0.04 0.19
Matches are distributed among these distances:
36 29 0.11
38 3 0.01
40 2 0.01
41 2 0.01
42 3 0.01
43 13 0.05
44 4 0.02
45 19 0.07
46 130 0.50
49 3 0.01
50 2 0.01
51 7 0.03
54 3 0.01
56 3 0.01
59 8 0.03
60 2 0.01
61 3 0.01
64 26 0.10
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
Found at i:54448187 original size:18 final size:18
Alignment explanation
Indices: 54448164--54448201 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
54448154 AGCTAAGGCT
54448164 ACCACTTATCACTTTCTC
1 ACCACTTATCACTTTCTC
54448182 ACCACTTATCACTTTCTC
1 ACCACTTATCACTTTCTC
54448200 AC
1 AC
54448202 TTGATCAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.39, G:0.00, T:0.37
Consensus pattern (18 bp):
ACCACTTATCACTTTCTC
Found at i:54448197 original size:64 final size:64
Alignment explanation
Indices: 54448118--54448247 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
54448108 AGCTAAGGCT
54448118 ACCACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTCTC
1 ACCACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTCTC
54448182 ACCACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTCTC
1 ACCACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTCTC
54448246 AC
1 AC
54448248 TTGATCAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.27, C:0.28, G:0.11, T:0.34
Consensus pattern (64 bp):
ACCACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTCTC
Found at i:54448265 original size:110 final size:110
Alignment explanation
Indices: 54448072--54448293 Score: 408
Period size: 110 Copynumber: 2.0 Consensus size: 110
54448062 TAGCTAGGCT
*
54448072 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTCTCA
1 ACCACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTCTCA
* *
54448137 CTTGATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTCTC
66 CTTGATCAAATAAGTGTAGCTAAGGCTAACACTTATCACTTTCTC
54448182 ACCACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTCTCA
1 ACCACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTCTCA
*
54448247 CTTGATCAAATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTC
66 CTTGATCAAATAAGTGTAGCTAAGGCTAACACTTATCACTTTCTC
54448292 AC
1 AC
54448294 TTGATCAGAT
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
110 108 1.00
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (110 bp):
ACCACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTCTCA
CTTGATCAAATAAGTGTAGCTAAGGCTAACACTTATCACTTTCTC
Found at i:54448317 original size:36 final size:36
Alignment explanation
Indices: 54448276--54448348 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
54448266 CTAAGGCTAA
54448276 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
* *
54448312 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
54448348 C
1 C
54448349 TAAAGCTACC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.37
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
Found at i:54448367 original size:82 final size:82
Alignment explanation
Indices: 54448230--54448384 Score: 256
Period size: 82 Copynumber: 1.9 Consensus size: 82
54448220 CTAAGGCTAC
* *
54448230 CACTTATCACTTTCTCACTTGATCAAATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACT
1 CACTTATCACTTTCTCACTTGATCAAATAAGTGTAGCTAAAGCTAACACTTATCACTTTATCACT
54448295 TGATCAGATAAGTATAG
66 TGATCAGATAAGTATAG
* * * *
54448312 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
1 CACTTATCACTTTCTCACTTGATCAAATAAGTGTAGCTAAAGCTAACACTTATCACTTTATCACT
54448377 TGATCAGA
66 TGATCAGA
54448385 AGTACTCAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 67 1.00
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.35
Consensus pattern (82 bp):
CACTTATCACTTTCTCACTTGATCAAATAAGTGTAGCTAAAGCTAACACTTATCACTTTATCACT
TGATCAGATAAGTATAG
Found at i:54456925 original size:19 final size:19
Alignment explanation
Indices: 54456901--54456952 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
54456891 TAAACACGAG
54456901 AATTTTGAAACAC-AATAAT
1 AATTTTGAAACACGAA-AAT
54456920 AATTTTTGAAAACACGAAAAT
1 AA-TTTTG-AAACACGAAAAT
54456941 --TTTTGAAACACG
1 AATTTTGAAACACG
54456953 GAATTTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 7 0.23
18 5 0.17
19 2 0.07
20 5 0.17
21 9 0.30
22 2 0.07
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.31
Consensus pattern (19 bp):
AATTTTGAAACACGAAAAT
Found at i:54456943 original size:18 final size:18
Alignment explanation
Indices: 54456892--54457005 Score: 99
Period size: 18 Copynumber: 6.3 Consensus size: 18
54456882 TTTTGTTTTT
*
54456892 AAACACGAGAA-TTTTGA
1 AAACACGAAAATTTTTGA
**
54456909 AACACAATAATAATTTTTGA
1 AA-ACACGAA-AATTTTTGA
54456929 AAACACGAAAATTTTTG-
1 AAACACGAAAATTTTTGA
* *
54456946 AAACACGGAATTTTTTGA
1 AAACACGAAAATTTTTGA
* * *
54456964 AAACATGAAAATTTGT-C
1 AAACACGAAAATTTTTGA
*
54456981 AAACACGGAAATTTTTTGA
1 AAACAC-GAAAATTTTTGA
54457000 AAACAC
1 AAACAC
54457006 AATAACATCA
Statistics
Matches: 75, Mismatches: 16, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
17 22 0.29
18 32 0.43
19 13 0.17
20 8 0.11
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.29
Consensus pattern (18 bp):
AAACACGAAAATTTTTGA
Found at i:54456968 original size:35 final size:36
Alignment explanation
Indices: 54456922--54457005 Score: 134
Period size: 35 Copynumber: 2.4 Consensus size: 36
54456912 ACAATAATAA
* *
54456922 TTTTTGAAAACACGAAAATTTTTGAAACACGG-AAT
1 TTTTTGAAAACACGAAAATTTGTCAAACACGGAAAT
*
54456957 TTTTTGAAAACATGAAAATTTGTCAAACACGGAAAT
1 TTTTTGAAAACACGAAAATTTGTCAAACACGGAAAT
54456993 TTTTTGAAAACAC
1 TTTTTGAAAACAC
54457006 AATAACATCA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 29 0.66
36 15 0.34
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (36 bp):
TTTTTGAAAACACGAAAATTTGTCAAACACGGAAAT
Found at i:54457221 original size:17 final size:17
Alignment explanation
Indices: 54457198--54457247 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
54457188 TTATTATTAT
54457198 TATTTTGAAACACGAGAA
1 TATTTTGAAACACGA-AA
*
54457216 -ATTTTGAAGACATGAAA
1 TATTTTGAA-ACACGAAA
*
54457233 TTTTTTGAAACACGA
1 TATTTTGAAACACGA
54457248 TTTTTTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (17 bp):
TATTTTGAAACACGAAA
Found at i:54457638 original size:14 final size:13
Alignment explanation
Indices: 54457619--54457652 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
54457609 TACAATGTTT
54457619 AAATAAATGGACTA
1 AAATAAATGGA-TA
54457633 AAATAAATGGATA
1 AAATAAATGGATA
54457646 AAA-AAAT
1 AAATAAAT
54457653 TACCCAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.20
13 5 0.25
14 11 0.55
ACGTcount: A:0.65, C:0.03, G:0.12, T:0.21
Consensus pattern (13 bp):
AAATAAATGGATA
Found at i:54457821 original size:14 final size:13
Alignment explanation
Indices: 54457802--54457850 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
54457792 AGCTGCTAGA
54457802 CTGCTGAACTGGGC
1 CTGCTG-ACTGGGC
*
54457816 CTGCTG-CT-GGA
1 CTGCTGACTGGGC
54457827 CTGCTGCACTGGGC
1 CTGCTG-ACTGGGC
54457841 CTGCTG-CTGG
1 CTGCTGACTGG
54457851 ACTGCTTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
11 8 0.27
12 6 0.20
13 2 0.07
14 14 0.47
ACGTcount: A:0.08, C:0.31, G:0.37, T:0.24
Consensus pattern (13 bp):
CTGCTGACTGGGC
Found at i:54457821 original size:25 final size:25
Alignment explanation
Indices: 54457793--54457856 Score: 110
Period size: 25 Copynumber: 2.6 Consensus size: 25
54457783 TTGGGCTGAA
*
54457793 GCTGCTAGACTGCTGAACTGGGCCT
1 GCTGCTGGACTGCTGAACTGGGCCT
*
54457818 GCTGCTGGACTGCTGCACTGGGCCT
1 GCTGCTGGACTGCTGAACTGGGCCT
54457843 GCTGCTGGACTGCT
1 GCTGCTGGACTGCT
54457857 TCTTTCTTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.11, C:0.30, G:0.34, T:0.25
Consensus pattern (25 bp):
GCTGCTGGACTGCTGAACTGGGCCT
Found at i:54457876 original size:21 final size:22
Alignment explanation
Indices: 54457852--54457907 Score: 89
Period size: 21 Copynumber: 2.6 Consensus size: 22
54457842 TGCTGCTGGA
54457852 CTGCTTCTTTC-TTCTTTTTTT
1 CTGCTTCTTTCTTTCTTTTTTT
54457873 CTGCTTCTTTCTTTCTTTTTTT
1 CTGCTTCTTTCTTTCTTTTTTT
*
54457895 CTGCTGC-TTCTTT
1 CTGCTTCTTTCTTT
54457908 TTGGGCTGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
21 17 0.52
22 16 0.48
ACGTcount: A:0.00, C:0.25, G:0.07, T:0.68
Consensus pattern (22 bp):
CTGCTTCTTTCTTTCTTTTTTT
Found at i:54457894 original size:25 final size:25
Alignment explanation
Indices: 54457856--54457907 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
54457846 GCTGGACTGC
* *
54457856 TTCTTTCTTCTTTTTTTCTGCTTCT
1 TTCTTTCTTCTTTTCTGCTGCTTCT
*
54457881 TTCTTTCTTTTTTTCTGCTGCTTCT
1 TTCTTTCTTCTTTTCTGCTGCTTCT
54457906 TT
1 TT
54457908 TTGGGCTGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.00, C:0.23, G:0.06, T:0.71
Consensus pattern (25 bp):
TTCTTTCTTCTTTTCTGCTGCTTCT
Found at i:54458014 original size:7 final size:7
Alignment explanation
Indices: 54458004--54458077 Score: 51
Period size: 7 Copynumber: 10.3 Consensus size: 7
54457994 TTTCTTTCCC
54458004 CTTTTTT
1 CTTTTTT
*
54458011 CTTTCCTT
1 CTTT-TTT
54458019 -TTTTTT
1 CTTTTTT
*
54458025 CTTCTTT
1 CTTTTTT
* *
54458032 CTTCTCT
1 CTTTTTT
* *
54458039 GTTTCTT
1 CTTTTTT
54458046 CTTTCTTT
1 CTTT-TTT
54458054 CTTCTTTT
1 CTT-TTTT
54458062 CTTTTTT
1 CTTTTTT
*
54458069 CTTTCTT
1 CTTTTTT
54458076 CT
1 CT
54458078 CCGTTCAGCC
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
6 2 0.04
7 36 0.69
8 13 0.25
9 1 0.02
ACGTcount: A:0.00, C:0.24, G:0.01, T:0.74
Consensus pattern (7 bp):
CTTTTTT
Found at i:54458015 original size:4 final size:4
Alignment explanation
Indices: 54458004--54458075 Score: 52
Period size: 4 Copynumber: 19.8 Consensus size: 4
54457994 TTTCTTTCCC
* * *
54458004 CTTT -TTT CTTT CCTT -TTT -TTT C-TT CTTT C-TT CTCT GTTT C-TT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
54458046 CTTT CTTT C-TT CTTTT CTTT -TTT CTTT CTT
1 CTTT CTTT CTTT C-TTT CTTT CTTT CTTT CTT
54458076 CTCCGTTCAG
Statistics
Matches: 54, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
3 23 0.43
4 28 0.52
5 3 0.06
ACGTcount: A:0.00, C:0.24, G:0.01, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:54458045 original size:18 final size:18
Alignment explanation
Indices: 54458004--54458077 Score: 75
Period size: 19 Copynumber: 4.1 Consensus size: 18
54457994 TTTCTTTCCC
54458004 CTTTT-TTCTTTCCTT-TT
1 CTTTTCTTCTTT-CTTCTT
54458021 -TTTTCTTCTTTCTTC-T
1 CTTTTCTTCTTTCTTCTT
54458037 CTGTTTCTTCTTTCTTTCTT
1 CT-TTTCTTCTTTC-TTCTT
*
54458057 CTTTTCTTTTTTCTTTCTT
1 CTTTTCTTCTTTC-TTCTT
54458076 CT
1 CT
54458078 CCGTTCAGCC
Statistics
Matches: 50, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
16 8 0.16
17 7 0.14
18 11 0.22
19 21 0.42
20 3 0.06
ACGTcount: A:0.00, C:0.24, G:0.01, T:0.74
Consensus pattern (18 bp):
CTTTTCTTCTTTCTTCTT
Found at i:54458058 original size:14 final size:14
Alignment explanation
Indices: 54457992--54458077 Score: 68
Period size: 14 Copynumber: 6.0 Consensus size: 14
54457982 TTATTTTTTA
**
54457992 TTTTTCTTTCCCCT
1 TTTTTCTTTCTTCT
54458006 TTTTTCTTTCCTT-T
1 TTTTTCTTT-CTTCT
54458020 TTTTTC-TTCTTTCT
1 TTTTTCTTTC-TTCT
* * *
54458034 TCTCTGTTTCTTCT
1 TTTTTCTTTCTTCT
*
54458048 TTCTTTCTTCTTTTCT
1 TT-TTTCTT-TCTTCT
54458064 TTTTTCTTTCTTCT
1 TTTTTCTTTCTTCT
54458078 CCGTTCAGCC
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
12 1 0.02
13 4 0.07
14 30 0.54
15 14 0.25
16 7 0.12
ACGTcount: A:0.00, C:0.26, G:0.01, T:0.73
Consensus pattern (14 bp):
TTTTTCTTTCTTCT
Found at i:54458217 original size:25 final size:21
Alignment explanation
Indices: 54458162--54458228 Score: 84
Period size: 21 Copynumber: 3.1 Consensus size: 21
54458152 CTCTTCTCTC
54458162 TTTCTTCTTTGCTTGTTTTTT
1 TTTCTTCTTTGCTTGTTTTTT
54458183 TTTCTT-TTTGCTTGTTGTTTT
1 TTTCTTCTTTGCTTGTT-TTTT
54458204 TTTCTTTGACTTTGCTT-TTTTTT
1 TTTC-TT--CTTTGCTTGTTTTTT
54458227 TT
1 TT
54458229 ATTGGCTTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
20 10 0.24
21 14 0.34
22 2 0.05
23 6 0.15
24 2 0.05
25 7 0.17
ACGTcount: A:0.01, C:0.12, G:0.10, T:0.76
Consensus pattern (21 bp):
TTTCTTCTTTGCTTGTTTTTT
Found at i:54458347 original size:10 final size:11
Alignment explanation
Indices: 54458321--54458346 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
54458311 TTGCTGCTGT
54458321 TTTTTGCTTGA
1 TTTTTGCTTGA
54458332 TTTTTGCTTGA
1 TTTTTGCTTGA
54458343 TTTT
1 TTTT
54458347 GTTGTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.08, G:0.15, T:0.69
Consensus pattern (11 bp):
TTTTTGCTTGA
Found at i:54458692 original size:29 final size:30
Alignment explanation
Indices: 54458660--54458760 Score: 116
Period size: 30 Copynumber: 3.4 Consensus size: 30
54458650 TTAAAGGTTG
**
54458660 AAATGTAATTTTAGAAAAGT-TTGGGGTCA
1 AAATGTAATTTTAGAAAAGTACAGGGGTCA
* * *
54458689 AAATGTAAATTTCGAAAAGTACAAGGGTCA
1 AAATGTAATTTTAGAAAAGTACAGGGGTCA
*
54458719 AAATGTAAATTTCA-AAAAGTACAGGGGTCA
1 AAATGT-AATTTTAGAAAAGTACAGGGGTCA
*
54458749 AAATGCAATTTT
1 AAATGTAATTTT
54458761 TTTTAATTTT
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
29 23 0.39
30 32 0.54
31 4 0.07
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.29
Consensus pattern (30 bp):
AAATGTAATTTTAGAAAAGTACAGGGGTCA
Found at i:54459349 original size:152 final size:150
Alignment explanation
Indices: 54458909--54459612 Score: 984
Period size: 152 Copynumber: 4.6 Consensus size: 150
54458899 TTTTTACTTG
* * * * *
54458909 AAAA-ACAGAAATTGAAAATACCTCAGCGTGTGGCCCGAGGCTCAACTCACCTCTAGCAATATGA
1 AAAAGACATAAATTAAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCT-GTATTATGA
* * * * * * **
54458973 GTTGATTTTTGAAAAACAGAAATTTAAA--AGAAATACCTCGGCATGGTCCGAGGCTCAACTCAC
63 GTTGA-TTTTAAAAAAAAGACA--TAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCAC
*
54459036 CTCTGTATTATGAGTTGATTTTAAAA
125 CTCTGTATTATGAGTTGATTTAAAAA
* *
54459062 AAAAGACATAAATTAAAAATACCTTACCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
1 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
* * *
54459127 GATTTTTTAAAAAAAGACATAAATTAAAAATACCTCAGTGTGACCCGAGGCTCAACTCACCTTTG
66 GA-TTTTAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTG
**
54459192 TATTATGAGTTGATTTTTTTTAAA
130 TATTATGAGTTGA---TTTAAAAA
*
54459216 AAAAGACATAAATTAAAAATACATCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
1 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
* *
54459281 GA-TTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTTAACTCACCTCTGT
66 GATTTTAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGT
54459345 ATTATGAGTTGATTTAAAAA
131 ATTATGAGTTGATTTAAAAA
* * *
54459365 AAAAAACATAAATTAAAAATACATCAGCGTGACCCAAGGCTCAACTCACCTCTGTATTATGAGTT
1 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
*
54459430 GATTTTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGATGCTCAACTCACCTCT
66 GA-TTTT-AAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT
54459495 GTATTATGAGTTGATTTTAAAAA
129 GTATTATGAGTTGA-TTTAAAAA
54459518 AAAGAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGT
1 AAA-AGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGT
*
54459583 TGATTTTTTAAAAAAAGACATAAATTAAAA
65 TGA-TTTTAAAAAAAAGACATAAATTAAAA
54459613 NNNNNNNNNN
Statistics
Matches: 503, Mismatches: 37, Indels: 22
0.90 0.07 0.04
Matches are distributed among these distances:
149 75 0.15
151 74 0.15
152 162 0.32
153 36 0.07
154 156 0.31
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.28
Consensus pattern (150 bp):
AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
GATTTTAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGT
ATTATGAGTTGATTTAAAAA
Found at i:54459438 original size:77 final size:77
Alignment explanation
Indices: 54458909--54459612 Score: 1004
Period size: 77 Copynumber: 9.2 Consensus size: 77
54458899 TTTTTACTTG
* * * * *
54458909 AAAA-ACAGAAATTGAAAATACCTCAGCGTGTGGCCCGAGGCTCAACTCACCTCTAGCAATATGA
1 AAAAGACATAAATTAAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCT-GTATTATGA
54458973 GTTGATTTTTGAAAAA
63 GTTGATTTTT-AAAAA
* ** * * * **
54458989 CAGAA-ATTTAAA--AGAAATACCTCGGCATGGTCCGAGGCTCAACTCACCTCTGTATTATGAGT
1 -AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGT
54459051 TGA-TTTT-AAAA
65 TGATTTTTAAAAA
* *
54459062 AAAAGACATAAATTAAAAATACCTTACCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
1 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
*
54459127 GATTTTT-TAAA
66 GATTTTTAAAAA
* *
54459138 AAAAGACATAAATTAAAAATACCTCAGTGTGACCCGAGGCTCAACTCACCTTTGTATTATGAGTT
1 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
**
54459203 GATTTTTTTTAAA
66 GA-TTTTTAAAAA
*
54459216 AAAAGACATAAATTAAAAATACATCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
1 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
54459281 GA---TTAAAAA
66 GATTTTTAAAAA
*
54459290 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTTAACTCACCTCTGTATTATGAGTT
1 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
54459355 GA--TTTAAAAA
66 GATTTTTAAAAA
* * *
54459365 AAAAAACATAAATTAAAAATACATCAGCGTGACCCAAGGCTCAACTCACCTCTGTATTATGAGTT
1 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
54459430 GATTTTTAAAAA
66 GATTTTTAAAAA
*
54459442 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGATGCTCAACTCACCTCTGTATTATGAGTT
1 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
54459507 GA-TTTTAAAAA
66 GATTTTTAAAAA
54459518 AAAGAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGT
1 AAA-AGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGT
*
54459583 TGATTTTT-TAAA
65 TGATTTTTAAAAA
54459595 AAAAGACATAAATTAAAA
1 AAAAGACATAAATTAAAA
54459613 NNNNNNNNNN
Statistics
Matches: 569, Mismatches: 43, Indels: 27
0.89 0.07 0.04
Matches are distributed among these distances:
72 3 0.01
73 9 0.02
74 70 0.12
75 120 0.21
76 109 0.19
77 168 0.30
78 72 0.13
79 11 0.02
81 7 0.01
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.28
Consensus pattern (77 bp):
AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
GATTTTTAAAAA
Found at i:54459550 original size:303 final size:303
Alignment explanation
Indices: 54458909--54459612 Score: 1022
Period size: 303 Copynumber: 2.3 Consensus size: 303
54458899 TTTTTACTTG
* * * * *
54458909 AAAA-ACAGAAATTGAAAATACCTCAGCGTGTGGCCCGAGGCTCAACTCACCTCTAGCAATATGA
1 AAAAGACATAAATTAAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCT-GTATTATGA
* * * * * **
54458973 GTTGATTTTTGAAAAACAGAAATTTAAA--AGAAATACCTCGGCATGGTCCGAGGCTCAACTCAC
63 GTTGA-TTTTAAAAAAAAGACA--TAAATTAAAAATACCTCAGCATGACCCGAGGCTCAACTCAC
* * * * *
54459036 CTCTGTATTATGAGTTGATTTTAAAAAAAAGACATAAATTAAAAATACCTTACCGTGACCCGAGG
125 CTCTGTATTATGAGTTGATTTAAAAAAAAAAACATAAATTAAAAATACATCACCGTGACCCAAGG
* *
54459101 CTCAACTCACCTCTGTATTATGAGTTGATTTTTTAAAAAAAGACATAAATTAAAAATACCTCAGT
190 CTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAAGACATAAATTAAAAATACCTCAGC
* **
54459166 GTGACCCGAGGCTCAACTCACCTTTGTATTATGAGTTGATTTTTTTTAAA
255 GTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTAAAAA
*
54459216 AAAAGACATAAATTAAAAATACATCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
1 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
* * *
54459281 GA-TTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTTAACTCACCTCTGT
66 GATTTTAAAAAAAAGACATAAATTAAAAATACCTCAGCATGACCCGAGGCTCAACTCACCTCTGT
*
54459345 ATTATGAGTTGATTTAAAAAAAAAAACATAAATTAAAAATACATCAGCGTGACCCAAGGCTCAAC
131 ATTATGAGTTGATTTAAAAAAAAAAACATAAATTAAAAATACATCACCGTGACCCAAGGCTCAAC
54459410 TCACCTCTGTATTATGAGTTGATTTTTAAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGAC
196 TCACCTCTGTATTATGAGTTGATTTTT-AAAAAAAAGACATAAATTAAAAATACCTCAGCGTGAC
*
54459475 CCGATGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTAAAAA
260 CCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAA
54459518 AAAGAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGT
1 AAA-AGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGT
*
54459583 TGATTTTTTAAAAAAAGACATAAATTAAAA
65 TGA-TTTTAAAAAAAAGACATAAATTAAAA
54459613 NNNNNNNNNN
Statistics
Matches: 359, Mismatches: 31, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
301 4 0.01
302 10 0.03
303 195 0.54
304 67 0.19
305 35 0.10
306 24 0.07
307 4 0.01
308 20 0.06
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.28
Consensus pattern (303 bp):
AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
GATTTTAAAAAAAAGACATAAATTAAAAATACCTCAGCATGACCCGAGGCTCAACTCACCTCTGT
ATTATGAGTTGATTTAAAAAAAAAAACATAAATTAAAAATACATCACCGTGACCCAAGGCTCAAC
TCACCTCTGTATTATGAGTTGATTTTTAAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACC
CGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAA
Found at i:54460052 original size:77 final size:78
Alignment explanation
Indices: 54459922--54460277 Score: 505
Period size: 79 Copynumber: 4.6 Consensus size: 78
54459912 NNNNNNNNNN
* * *
54459922 ACCCGATGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAAAGAGAC-ATAAATTAAAA
1 ACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGAATTTAAAAAAAAAAGACAATAAATTAAAA
54459986 ATACCTCAGCGTG
66 ATACCTCAGCGTG
*
54459999 ACCCGAGGCTTAACTCACCTCTGTATTATGAGTTGAATTTAAAAAAAAAAGACAATAAAATTAAA
1 ACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGAATTTAAAAAAAAAAGACAAT-AAATTAAA
*
54460064 AATACCTCAGTGTG
65 AATACCTCAGCGTG
* * *
54460078 ACTCGAGGCTCAACTCACCTCTATATTATGAGTTG-ATTT----TAAAAAGACAATAAATT-AAA
1 ACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGAATTTAAAAAAAAAAGACAATAAATTAAAA
54460137 ATACCTCAGCGTG
66 ATACCTCAGCGTG
* * **
54460150 ACCCGAGGTTCAACTCACCTCTGTATTATGAGTTG-ATTTTAAAAAAAAAGAC-CGAAATTAAAA
1 ACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGAATTTAAAAAAAAAAGACAATAAATTAAAA
54460213 ATACCTCAGCGTG
66 ATACCTCAGCGTG
*
54460226 ACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATATTTGAAAAAAAAA
1 ACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGA-ATTTAAAAAAAAAA
54460278 TAGAAAGTGA
Statistics
Matches: 251, Mismatches: 18, Indels: 18
0.87 0.06 0.06
Matches are distributed among these distances:
72 51 0.20
73 5 0.02
74 11 0.04
75 5 0.02
76 45 0.18
77 62 0.25
78 6 0.02
79 66 0.26
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (78 bp):
ACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGAATTTAAAAAAAAAAGACAATAAATTAAAA
ATACCTCAGCGTG
Found at i:54460273 original size:151 final size:152
Alignment explanation
Indices: 54459922--54460273 Score: 525
Period size: 151 Copynumber: 2.3 Consensus size: 152
54459912 NNNNNNNNNN
* *
54459922 ACCCGATGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAAAGAGACATAAATTAAAAA
1 ACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTT---AAAAAGACACATAAATTAAAAA
54459987 TACCTCAGCGTGACCCGAGGCTTAACTCACCTCTGTATTATGAGTTGAATTTAAAAAAAAAAGAC
63 TACCTCAGCGTGACCCGAGGCTTAACTCACCTCTGTATTATGAGTTGAATTTAAAAAAAAAAGAC
* *
54460052 AATAAAATTAAAAATACCTCAGTGTG
128 -ACAAAATTAAAAATACCTCAGCGTG
* *
54460078 ACTCGAGGCTCAACTCACCTCTATATTATGAGTTGATTTTAAAAAGACA-ATAAATT-AAAATAC
1 ACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAGACACATAAATTAAAAATAC
*
54460141 CTCAGCGTGACCCGAGG-TTCAACTCACCTCTGTATTATGAGTTG-ATTTTAAAAAAAAAGAC-C
66 CTCAGCGTGACCCGAGGCTT-AACTCACCTCTGTATTATGAGTTGAATTTAAAAAAAAAAGACAC
*
54460203 GAAATTAAAAATACCTCAGCGTG
130 AAAATTAAAAATACCTCAGCGTG
54460226 ACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATATTTGAAAAA
1 ACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGAT-TTT-AAAAA
54460274 AAAATAGAAA
Statistics
Matches: 182, Mismatches: 10, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
148 42 0.23
149 14 0.08
150 21 0.12
151 53 0.29
152 7 0.04
153 8 0.04
156 37 0.20
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (152 bp):
ACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAGACACATAAATTAAAAATAC
CTCAGCGTGACCCGAGGCTTAACTCACCTCTGTATTATGAGTTGAATTTAAAAAAAAAAGACACA
AAATTAAAAATACCTCAGCGTG
Found at i:54461190 original size:31 final size:31
Alignment explanation
Indices: 54461144--54461216 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
54461134 TTCATCTTGA
*
54461144 TTTT-TTTCTTCTTCTT-TTCTTTTTCTAT-TT
1 TTTTGTTTCTTTTTCTTATT-TTTTTCT-TGTT
*
54461174 TTTTGTTTCTTTTTCTTATTTTTTTGTTGTT
1 TTTTGTTTCTTTTTCTTATTTTTTTCTTGTT
54461205 TTTTGTTT-TTTT
1 TTTTGTTTCTTTT
54461217 AGGCATAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
30 9 0.24
31 27 0.71
32 2 0.05
ACGTcount: A:0.03, C:0.10, G:0.05, T:0.82
Consensus pattern (31 bp):
TTTTGTTTCTTTTTCTTATTTTTTTCTTGTT
Found at i:54461216 original size:21 final size:21
Alignment explanation
Indices: 54461159--54461201 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
54461149 TTCTTCTTCT
54461159 TTTCTTTTTC-TATTTTTTTG
1 TTTCTTTTTCTTATTTTTTTG
54461179 TTTCTTTTTCTTATTTTTTTG
1 TTTCTTTTTCTTATTTTTTTG
54461200 TT
1 TT
54461202 GTTTTTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.05, C:0.09, G:0.05, T:0.81
Consensus pattern (21 bp):
TTTCTTTTTCTTATTTTTTTG
Found at i:54466821 original size:17 final size:17
Alignment explanation
Indices: 54466792--54466859 Score: 75
Period size: 18 Copynumber: 3.9 Consensus size: 17
54466782 ACACAATAAT
54466792 AATTTTTGAAAACACGA
1 AATTTTTGAAAACACGA
*
54466809 AGATTTTTG-AAACATGA
1 A-ATTTTTGAAAACACGA
*
54466826 ATTTTTTTGAAAACACGGA
1 A-ATTTTTGAAAACAC-GA
*
54466845 ATTTTTTGAAAACAC
1 AATTTTTGAAAACAC
54466860 AAAAATTTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
17 15 0.34
18 26 0.59
19 3 0.07
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.35
Consensus pattern (17 bp):
AATTTTTGAAAACACGA
Found at i:54466866 original size:19 final size:19
Alignment explanation
Indices: 54466775--54466867 Score: 61
Period size: 18 Copynumber: 5.1 Consensus size: 19
54466765 AACACGAGAA
*
54466775 TTTTG-AAACACAATAATAAT
1 TTTTGAAAACACAA-AA-ATT
* *
54466795 TTTTGAAAACACGAAGA-T
1 TTTTGAAAACACAAAAATT
** *
54466813 TTTTG-AAACA-TGAATTT
1 TTTTGAAAACACAAAAATT
**
54466830 TTTTGAAAACAC-GGAATT
1 TTTTGAAAACACAAAAATT
54466848 TTTTGAAAACACAAAAATT
1 TTTTGAAAACACAAAAATT
54466867 T
1 T
54466868 GTCAAACACG
Statistics
Matches: 58, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
16 1 0.02
17 11 0.19
18 27 0.47
19 6 0.10
20 6 0.10
21 7 0.12
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (19 bp):
TTTTGAAAACACAAAAATT
Found at i:54466967 original size:17 final size:17
Alignment explanation
Indices: 54466944--54466994 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
54466934 TGAAAACACG
54466944 AAAACACGAAATTTTTT
1 AAAACACGAAATTTTTT
* * *
54466961 CAAACACGGGAA-TTTTG
1 AAAACAC-GAAATTTTTT
54466978 AAAACACGAAATTTTTT
1 AAAACACGAAATTTTTT
54466995 TTTATTCACG
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
16 3 0.12
17 20 0.77
18 3 0.12
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (17 bp):
AAAACACGAAATTTTTT
Found at i:54467010 original size:36 final size:37
Alignment explanation
Indices: 54466943--54467029 Score: 101
Period size: 36 Copynumber: 2.4 Consensus size: 37
54466933 TTGAAAACAC
*
54466943 GAAAACACGAAA--TTTTTTCAAACACGGGAA-TTTT
1 GAAAACACGAAATTTTTTTTCAAACACGAGAATTTTT
* **
54466977 GAAAACACGAAATTTTTTTTTATTCACGAGAATTTTT
1 GAAAACACGAAATTTTTTTTCAAACACGAGAATTTTT
54467014 G-AAACACGGAAATTTT
1 GAAAACAC-GAAATTTT
54467030 AAAAAAAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
34 12 0.27
36 20 0.44
37 13 0.29
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (37 bp):
GAAAACACGAAATTTTTTTTCAAACACGAGAATTTTT
Found at i:54467127 original size:18 final size:17
Alignment explanation
Indices: 54467086--54467134 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
54467076 TATTATTATT
54467086 ATTTTGAAACACGAGAA
1 ATTTTGAAACACGAGAA
*
54467103 ATTTTGAAGACATGA-AA
1 ATTTTGAA-ACACGAGAA
54467120 ATTTTTGAAACACGA
1 A-TTTTGAAACACGA
54467135 TTTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (17 bp):
ATTTTGAAACACGAGAA
Found at i:54467527 original size:14 final size:13
Alignment explanation
Indices: 54467508--54467541 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
54467498 TACAATATTT
54467508 AAATAAATGGACTA
1 AAATAAATGGA-TA
54467522 AAATAAATGGATA
1 AAATAAATGGATA
54467535 AAA-AAAT
1 AAATAAAT
54467542 TACCCAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.20
13 5 0.25
14 11 0.55
ACGTcount: A:0.65, C:0.03, G:0.12, T:0.21
Consensus pattern (13 bp):
AAATAAATGGATA
Found at i:54467714 original size:14 final size:14
Alignment explanation
Indices: 54467695--54467740 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
54467685 AGCTGCTGGA
54467695 CTGCTGCACTGGGC
1 CTGCTGCACTGGGC
*
54467709 CTGCTG--CT-GGA
1 CTGCTGCACTGGGC
54467720 CTGCTGCACTGGGC
1 CTGCTGCACTGGGC
54467734 CTGCTGC
1 CTGCTGC
54467741 TGGACTGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
11 8 0.30
12 2 0.07
13 2 0.07
14 15 0.56
ACGTcount: A:0.07, C:0.35, G:0.35, T:0.24
Consensus pattern (14 bp):
CTGCTGCACTGGGC
Found at i:54467714 original size:25 final size:25
Alignment explanation
Indices: 54467686--54467749 Score: 128
Period size: 25 Copynumber: 2.6 Consensus size: 25
54467676 TTGGGCTAAA
54467686 GCTGCTGGACTGCTGCACTGGGCCT
1 GCTGCTGGACTGCTGCACTGGGCCT
54467711 GCTGCTGGACTGCTGCACTGGGCCT
1 GCTGCTGGACTGCTGCACTGGGCCT
54467736 GCTGCTGGACTGCT
1 GCTGCTGGACTGCT
54467750 TCTTTCTTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.08, C:0.31, G:0.36, T:0.25
Consensus pattern (25 bp):
GCTGCTGGACTGCTGCACTGGGCCT
Found at i:54467748 original size:11 final size:11
Alignment explanation
Indices: 54467686--54467749 Score: 56
Period size: 11 Copynumber: 5.3 Consensus size: 11
54467676 TTGGGCTAAA
54467686 GCTGCTGGACT
1 GCTGCTGGACT
*
54467697 GCTGCACTGGGCCT
1 GCTG--CT-GGACT
54467711 GCTGCTGGACT
1 GCTGCTGGACT
*
54467722 GCTGCACTGGGCCT
1 GCTG--CT-GGACT
54467736 GCTGCTGGACT
1 GCTGCTGGACT
54467747 GCT
1 GCT
54467750 TCTTTCTTCT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
11 19 0.44
12 4 0.09
13 4 0.09
14 16 0.37
ACGTcount: A:0.08, C:0.31, G:0.36, T:0.25
Consensus pattern (11 bp):
GCTGCTGGACT
Found at i:54467769 original size:21 final size:22
Alignment explanation
Indices: 54467745--54467800 Score: 89
Period size: 21 Copynumber: 2.6 Consensus size: 22
54467735 TGCTGCTGGA
54467745 CTGCTTCTTTC-TTCTTTTTTT
1 CTGCTTCTTTCTTTCTTTTTTT
54467766 CTGCTTCTTTCTTTCTTTTTTT
1 CTGCTTCTTTCTTTCTTTTTTT
*
54467788 CTGCTGC-TTCTTT
1 CTGCTTCTTTCTTT
54467801 TTGGGCTGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
21 17 0.52
22 16 0.48
ACGTcount: A:0.00, C:0.25, G:0.07, T:0.68
Consensus pattern (22 bp):
CTGCTTCTTTCTTTCTTTTTTT
Found at i:54467787 original size:25 final size:25
Alignment explanation
Indices: 54467749--54467800 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
54467739 GCTGGACTGC
* *
54467749 TTCTTTCTTCTTTTTTTCTGCTTCT
1 TTCTTTCTTCTTTTCTGCTGCTTCT
*
54467774 TTCTTTCTTTTTTTCTGCTGCTTCT
1 TTCTTTCTTCTTTTCTGCTGCTTCT
54467799 TT
1 TT
54467801 TTGGGCTGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.00, C:0.23, G:0.06, T:0.71
Consensus pattern (25 bp):
TTCTTTCTTCTTTTCTGCTGCTTCT
Found at i:54467915 original size:13 final size:14
Alignment explanation
Indices: 54467886--54467921 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
54467876 TATTTTTTTA
54467886 TTTTTCTTTCCCCT
1 TTTTTCTTTCCCCT
**
54467900 TTTTTCTTTCCTTT
1 TTTTTCTTTCCCCT
54467914 TTTTTCTT
1 TTTTTCTT
54467922 CTTTCTTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTTCTTTCCCCT
Found at i:54467956 original size:11 final size:11
Alignment explanation
Indices: 54467898--54467958 Score: 52
Period size: 11 Copynumber: 5.3 Consensus size: 11
54467888 TTTCTTTCCC
54467898 CTTTTTTCTTT
1 CTTTTTTCTTT
*
54467909 CCTTTTT-TTT
1 CTTTTTTCTTT
*
54467919 CTTCTTTCTTCT
1 CTTTTTTCTT-T
*
54467931 ATGTTTCTTCTTTT
1 CT-TTT-TTC-TTT
54467945 CTTTTTTCTTT
1 CTTTTTTCTTT
54467956 CTT
1 CTT
54467959 CTCCGTTCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
10 8 0.21
11 14 0.36
12 5 0.13
13 5 0.13
14 5 0.13
15 2 0.05
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75
Consensus pattern (11 bp):
CTTTTTTCTTT
Found at i:54467960 original size:14 final size:14
Alignment explanation
Indices: 54467886--54467960 Score: 60
Period size: 15 Copynumber: 5.0 Consensus size: 14
54467876 TATTTTTTTA
**
54467886 TTTTTCTTTCCCCT
1 TTTTTCTTTCTTCT
*
54467900 TTTTTCTTTCCTTTTT
1 TTTTTCTTT-C-TTCT
54467916 TTTCTTCTTTCTTCT
1 TTT-TTCTTTCTTCT
* *
54467931 ATGTTTCTTCTTTTCT
1 -TTTTTCTT-TCTTCT
54467947 TTTTTCTTTCTTCT
1 TTTTTCTTTCTTCT
54467961 CCGTTCAACC
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
14 14 0.29
15 16 0.33
16 12 0.25
17 6 0.12
ACGTcount: A:0.01, C:0.24, G:0.01, T:0.73
Consensus pattern (14 bp):
TTTTTCTTTCTTCT
Found at i:54468066 original size:19 final size:20
Alignment explanation
Indices: 54468044--54468105 Score: 76
Period size: 19 Copynumber: 3.1 Consensus size: 20
54468034 CTCTTCTCTC
54468044 TTTCTTCTTTGCTTG-TTTT
1 TTTCTTCTTTGCTTGCTTTT
*
54468063 TTTCTT-TTTGCTTGCTGTT
1 TTTCTTCTTTGCTTGCTTTT
54468082 TTT-TTCTTTGACTTTGCTTTT
1 TTTCTTCTTTG-C-TTGCTTTT
54468103 TTT
1 TTT
54468106 TTTATTGGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
18 10 0.27
19 16 0.43
20 1 0.03
21 10 0.27
ACGTcount: A:0.02, C:0.15, G:0.11, T:0.73
Consensus pattern (20 bp):
TTTCTTCTTTGCTTGCTTTT
Found at i:54468074 original size:18 final size:20
Alignment explanation
Indices: 54468044--54468090 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
54468034 CTCTTCTCTC
54468044 TTTCTTCTTTGC-T-TGTTTT
1 TTTCTT-TTTGCTTCTGTTTT
54468063 TTTCTTTTTGCTTGCTGTTTT
1 TTTCTTTTTGCTT-CTGTTTT
54468084 TTTCTTT
1 TTTCTTT
54468091 GACTTTGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.20
19 7 0.28
21 13 0.52
ACGTcount: A:0.00, C:0.15, G:0.11, T:0.74
Consensus pattern (20 bp):
TTTCTTTTTGCTTCTGTTTT
Found at i:54468098 original size:21 final size:21
Alignment explanation
Indices: 54468050--54468107 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 21
54468040 TCTCTTTCTT
54468050 CTTTGCTTGTTTTTTTCTTTTTG
1 CTTTGC-TGTTTTTTTC-TTTTG
54468073 C-TTGCTGTTTTTTTC-TTTG
1 CTTTGCTGTTTTTTTCTTTTG
*
54468092 ACTTTGCTTTTTTTTT
1 -CTTTGCTGTTTTTTT
54468108 TATTGGCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 4 0.12
20 1 0.03
21 22 0.69
22 4 0.12
23 1 0.03
ACGTcount: A:0.02, C:0.14, G:0.12, T:0.72
Consensus pattern (21 bp):
CTTTGCTGTTTTTTTCTTTTG
Found at i:54468117 original size:21 final size:20
Alignment explanation
Indices: 54468059--54468121 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
54468049 TCTTTGCTTG
54468059 TTTTTTTCTTTTT-GC-TTGC
1 TTTTTTT-TTTTTGGCTTTGC
* *
54468078 TGTTTTTTTCTTTGACTTTGC
1 T-TTTTTTTTTTTGGCTTTGC
54468099 TTTTTTTTTTATTGGCTTT-C
1 TTTTTTTTTT-TTGGCTTTGC
54468119 TTT
1 TTT
54468122 GTCTTTGGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
19 5 0.14
20 19 0.53
21 12 0.33
ACGTcount: A:0.03, C:0.13, G:0.11, T:0.73
Consensus pattern (20 bp):
TTTTTTTTTTTTGGCTTTGC
Found at i:54468227 original size:10 final size:11
Alignment explanation
Indices: 54468201--54468226 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
54468191 TTGCTGCTGC
54468201 TTTTTGCTTGA
1 TTTTTGCTTGA
54468212 TTTTTGCTTGA
1 TTTTTGCTTGA
54468223 TTTT
1 TTTT
54468227 GTTGTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.08, G:0.15, T:0.69
Consensus pattern (11 bp):
TTTTTGCTTGA
Found at i:54468533 original size:30 final size:31
Alignment explanation
Indices: 54468483--54468638 Score: 130
Period size: 30 Copynumber: 5.2 Consensus size: 31
54468473 AAATATGGGC
*
54468483 CAAAATGT-AATTTCT-TGAAAGTTTAGGGGT
1 CAAAATGTAAATTT-TGAGAAAGTTTAGGGGT
* * **
54468513 TAAAGTG-AAATTTTGAGAAAGTTTAAAGGT
1 CAAAATGTAAATTTTGAGAAAGTTTAGGGGT
**
54468543 TGAAATGT-AATTTT-AGAAAAGTTT-GGGGT
1 CAAAATGTAAATTTTGAG-AAAGTTTAGGGGT
* * *
54468572 CAAAATGTAAA-TTTCAAAAAGTATAGGGGT
1 CAAAATGTAAATTTTGAGAAAGTTTAGGGGT
**
54468602 CAAAATGTAAATTTTGA-AAAGTACAGGGGT
1 CAAAATGTAAATTTTGAGAAAGTTTAGGGGT
54468632 CAAAATG
1 CAAAATG
54468639 CAATTTTTTA
Statistics
Matches: 103, Mismatches: 15, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
29 21 0.20
30 78 0.76
31 4 0.04
ACGTcount: A:0.41, C:0.04, G:0.23, T:0.31
Consensus pattern (31 bp):
CAAAATGTAAATTTTGAGAAAGTTTAGGGGT
Found at i:54469658 original size:14 final size:14
Alignment explanation
Indices: 54469639--54469666 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
54469629 CAACTTTTAG
54469639 TTAGTATTTAGCAA
1 TTAGTATTTAGCAA
54469653 TTAGTATTTAGCAA
1 TTAGTATTTAGCAA
54469667 ATGTATGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (14 bp):
TTAGTATTTAGCAA
Found at i:54470819 original size:23 final size:23
Alignment explanation
Indices: 54470781--54470849 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
54470771 ATCTACCTTG
*
54470781 TTTGGACAGC-TCTTATACATCAA
1 TTTGGACAGCAT-TTATACACCAA
*
54470804 TTTGGACAGCATTTATATACCAA
1 TTTGGACAGCATTTATACACCAA
* **
54470827 ATTAAACAGCATTTATACACCAA
1 TTTGGACAGCATTTATACACCAA
54470850 AATTTAACAG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 38 0.97
24 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (23 bp):
TTTGGACAGCATTTATACACCAA
Found at i:54470852 original size:24 final size:23
Alignment explanation
Indices: 54470809--54471142 Score: 161
Period size: 23 Copynumber: 14.5 Consensus size: 23
54470799 ATCAATTTGG
* * *
54470809 ACAGCATTTATATACCAAATTAA
1 ACAGCATATATACACCAAATTTA
*
54470832 ACAGCATTTATACACCAAAATTTA
1 ACAGCATATATACACC-AAATTTA
**
54470856 ACAGCATATATACAGTAAA--TA
1 ACAGCATATATACACCAAATTTA
* * * *
54470877 GGCAGCATATACATATCC-ATTTTA
1 -ACAGCATATATACA-CCAAATTTA
*
54470901 ACAGCACT-TTTACACCAAAATTTA
1 ACAGCA-TATATACACC-AAATTTA
* *
54470925 ACAGCATATATATAGCAAA--TA
1 ACAGCATATATACACCAAATTTA
* *
54470946 GGCAGCATAT-TCATACCAAATTTA
1 -ACAGCATATAT-ACACCAAATTTA
*
54470970 ACAGCACT-TTTACACCAAAATTTA
1 ACAGCA-TATATACACC-AAATTTA
* **
54470994 ACAGCATATATACAACAAA-TGG
1 ACAGCATATATACACCAAATTTA
* * * *
54471016 GCAGCATATACATACCAAATTGA
1 ACAGCATATATACACCAAATTTA
* * *
54471039 ACAGCATTTTTACACAAAATTTA
1 ACAGCATATATACACCAAATTTA
*
54471062 ACAGCATATATACAACAAA--TA
1 ACAGCATATATACACCAAATTTA
* * * * *
54471083 GGCAGCATATACATACCAAACTGA
1 -ACAGCATATATACACCAAATTTA
* *
54471107 GCAGCA-ATTTTACACCAAATTTGA
1 ACAGCATA-TATACACCAAATTT-A
*
54471131 ACAGTATATATA
1 ACAGCATATATA
54471143 AAACAAATGG
Statistics
Matches: 231, Mismatches: 56, Indels: 47
0.69 0.17 0.14
Matches are distributed among these distances:
21 7 0.03
22 61 0.26
23 92 0.40
24 70 0.30
25 1 0.00
ACGTcount: A:0.45, C:0.20, G:0.09, T:0.27
Consensus pattern (23 bp):
ACAGCATATATACACCAAATTTA
Found at i:54470904 original size:69 final size:68
Alignment explanation
Indices: 54470810--54471166 Score: 477
Period size: 69 Copynumber: 5.2 Consensus size: 68
54470800 TCAATTTGGA
* * * **
54470810 CAGCATTTATATACCAAATTAAACAGCATTTATACACCAAAATTTAACAGCATATATACAGTAAA
1 CAGCATATACATACCAAATTGAACAGCATTT-TACACCAAAATTTAACAGCATATATACAACAAA
54470875 TAGG
65 TAGG
* * * *
54470879 CAGCATATACATATCC-ATTTTAACAGCACTTTTACACCAAAATTTAACAGCATATATATAGCAA
1 CAGCATATACATA-CCAAATTGAACAGCA-TTTTACACCAAAATTTAACAGCATATATACAACAA
54470943 ATAGG
64 ATAGG
* *
54470948 CAGCATATTCATACCAAATTTAACAGCACTTTTACACCAAAATTTAACAGCATATATACAACAAA
1 CAGCATATACATACCAAATTGAACAGCA-TTTTACACCAAAATTTAACAGCATATATACAACAAA
*
54471013 TGGG
65 TAGG
54471017 CAGCATATACATACCAAATTGAACAGCATTTTTACA-CAAAATTTAACAGCATATATACAACAAA
1 CAGCATATACATACCAAATTGAACAGCA-TTTTACACCAAAATTTAACAGCATATATACAACAAA
54471081 TAGG
65 TAGG
* * * *
54471085 CAGCATATACATACCAAACTGAGCAGCAATTTTACACC-AAATTTGAACAGTATATATAAAACAA
1 CAGCATATACATACCAAATTGAACAGC-ATTTTACACCAAAATTT-AACAGCATATATACAACAA
*
54471149 ATGGG
64 ATAGG
54471154 CAGCATATACATA
1 CAGCATATACATA
54471167 ATACATCATA
Statistics
Matches: 262, Mismatches: 20, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
68 71 0.27
69 186 0.71
70 5 0.02
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.26
Consensus pattern (68 bp):
CAGCATATACATACCAAATTGAACAGCATTTTACACCAAAATTTAACAGCATATATACAACAAAT
AGG
Found at i:54471120 original size:137 final size:138
Alignment explanation
Indices: 54470810--54471166 Score: 497
Period size: 137 Copynumber: 2.6 Consensus size: 138
54470800 TCAATTTGGA
* * **
54470810 CAGCATTTATATACCAAATTAAACAGC-ATTTATACACCAAAATTTAACAGCATATATACAGTAA
1 CAGCATATACATACCAAATTAAACAGCAATTT-TACACCAAAATTTAACAGCATATATACAACAA
* * * *
54470874 ATAGGCAGCATATACATATCCATTTTAACAGCACTTTTACACCAAAATTTAACAGCATATATATA
65 ATGGGCAGCATATACATATCCAATTGAACAGCACTTTTACACCAAAATTTAACAGCATATATACA
*
54470939 GCAAATAGG
130 ACAAATAGG
* * *
54470948 CAGCATATTCATACCAAATTTAACAGCACTTTTACACCAAAATTTAACAGCATATATACAACAAA
1 CAGCATATACATACCAAATTAAACAGCAATTTTACACCAAAATTTAACAGCATATATACAACAAA
*
54471013 TGGGCAGCATATACATA-CCAAATTGAACAGCATTTTTACA-CAAAATTTAACAGCATATATACA
66 TGGGCAGCATATACATATCC-AATTGAACAGCACTTTTACACCAAAATTTAACAGCATATATACA
54471076 ACAAATAGG
130 ACAAATAGG
* * * * *
54471085 CAGCATATACATACCAAACTGAGCAGCAATTTTACACC-AAATTTGAACAGTATATATAAAACAA
1 CAGCATATACATACCAAATTAAACAGCAATTTTACACCAAAATTT-AACAGCATATATACAACAA
54471149 ATGGGCAGCATATACATA
65 ATGGGCAGCATATACATA
54471167 ATACATCATA
Statistics
Matches: 196, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
136 6 0.03
137 100 0.51
138 87 0.44
139 3 0.02
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.26
Consensus pattern (138 bp):
CAGCATATACATACCAAATTAAACAGCAATTTTACACCAAAATTTAACAGCATATATACAACAAA
TGGGCAGCATATACATATCCAATTGAACAGCACTTTTACACCAAAATTTAACAGCATATATACAA
CAAATAGG
Found at i:54472112 original size:40 final size:41
Alignment explanation
Indices: 54471975--54472130 Score: 118
Period size: 41 Copynumber: 3.8 Consensus size: 41
54471965 TTCTATAAAA
* * * * * * * *
54471975 CACCGGCATAAAGCTTGCTAGGCACAAAGCCCGATACATTT
1 CACCAGCATAAAGCCTGCTAGACATAAAGTCTGATATAATT
**
54472016 CACTGGCATAAAGCCTGCTAGACATAAAGTCTGATATAATT
1 CACCAGCATAAAGCCTGCTAGACATAAAGTCTGATATAATT
** * * * * *
54472057 CACTGGCACAGAGCCTTCT-GATATCAAG-CTTGATATAATT
1 CACCAGCATAAAGCCTGCTAGACATAAAGTC-TGATATAATT
* *
54472097 CACCAGCATAAAGCCTGCTAGGCATAAAGCCTGA
1 CACCAGCATAAAGCCTGCTAGACATAAAGTCTGA
54472131 ACTTACAAAA
Statistics
Matches: 91, Mismatches: 21, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
39 1 0.01
40 31 0.34
41 58 0.64
42 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (41 bp):
CACCAGCATAAAGCCTGCTAGACATAAAGTCTGATATAATT
Found at i:54472740 original size:16 final size:16
Alignment explanation
Indices: 54472719--54472755 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
54472709 TTCACCTACT
54472719 AGCATCATAAAACTCA
1 AGCATCATAAAACTCA
54472735 AGCATCATAAAACTCA
1 AGCATCATAAAACTCA
54472751 AGCAT
1 AGCAT
54472756 TCATCAATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.24, G:0.08, T:0.19
Consensus pattern (16 bp):
AGCATCATAAAACTCA
Found at i:54478056 original size:19 final size:19
Alignment explanation
Indices: 54478034--54478076 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
54478024 AAATTCCTTT
54478034 AAAATAAAAAAAATCATAA
1 AAAATAAAAAAAATCATAA
** * *
54478053 AAAATGCAAAAATTCCTAA
1 AAAATAAAAAAAATCATAA
54478072 AAAAT
1 AAAAT
54478077 TCCAAAAAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.19
Consensus pattern (19 bp):
AAAATAAAAAAAATCATAA
Found at i:54482401 original size:31 final size:30
Alignment explanation
Indices: 54482362--54482444 Score: 96
Period size: 31 Copynumber: 2.7 Consensus size: 30
54482352 CATTTTAATG
54482362 ATAGAGTGACTAAAATTAACAACTTATCTA
1 ATAGAGTGACTAAAATTAACAACTTATCTA
* * *
54482392 ATAGAAGTGACTAAAATCAATAATTTATCTA
1 ATAG-AGTGACTAAAATTAACAACTTATCTA
* *
54482423 ACATGAGGGACTAAAA-TAACAA
1 ATA-GAGTGACTAAAATTAACAA
54482445 AATTTTGAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
30 8 0.18
31 35 0.80
32 1 0.02
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27
Consensus pattern (30 bp):
ATAGAGTGACTAAAATTAACAACTTATCTA
Found at i:54488465 original size:15 final size:15
Alignment explanation
Indices: 54488445--54488474 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54488435 TATAATTTTA
54488445 ATATTTTAATAATTT
1 ATATTTTAATAATTT
*
54488460 ATATTTTTATAATTT
1 ATATTTTAATAATTT
54488475 TTAAATGATT
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATATTTTAATAATTT
Found at i:54488554 original size:16 final size:18
Alignment explanation
Indices: 54488530--54488566 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
54488520 CATTTCACCA
*
54488530 TTATTAATT-TAAAA-TT
1 TTATAAATTATAAAAGTT
54488546 TTATAAATTATAAAAGTT
1 TTATAAATTATAAAAGTT
54488564 TTA
1 TTA
54488567 AATAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 5 0.28
18 5 0.28
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TTATAAATTATAAAAGTT
Found at i:54489765 original size:7 final size:7
Alignment explanation
Indices: 54489753--54489780 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
54489743 GGGCAATATT
54489753 CAAATGA
1 CAAATGA
54489760 CAAATGA
1 CAAATGA
54489767 CAAATGA
1 CAAATGA
54489774 CAAATGA
1 CAAATGA
54489781 TTAGATTTTT
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:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (7 bp):
CAAATGA
Found at i:54498013 original size:16 final size:16
Alignment explanation
Indices: 54497992--54498026 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
54497982 ATGTGATTGG
54497992 AGCTTGAAGGAAGTTA
1 AGCTTGAAGGAAGTTA
54498008 AGCTTGAAGGAAGTTA
1 AGCTTGAAGGAAGTTA
54498024 AGC
1 AGC
54498027 CCACTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.37, C:0.09, G:0.31, T:0.23
Consensus pattern (16 bp):
AGCTTGAAGGAAGTTA
Found at i:54503502 original size:24 final size:24
Alignment explanation
Indices: 54503475--54503526 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
54503465 TTAGTAAGTC
*
54503475 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
54503499 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
54503523 AAAT
1 AAAT
54503527 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:54515014 original size:11 final size:10
Alignment explanation
Indices: 54514987--54515011 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
54514977 CGACTCGCAA
54514987 ATTTTATTAG
1 ATTTTATTAG
54514997 ATTTTATTAG
1 ATTTTATTAG
54515007 ATTTT
1 ATTTT
54515012 TATATTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (10 bp):
ATTTTATTAG
Found at i:54516388 original size:24 final size:24
Alignment explanation
Indices: 54516350--54516413 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
54516340 CAGTCCCCAT
**
54516350 ATTTTTTTCGCTTTTAGTAATTTA
1 ATTTTTTTCTTTTTTAGTAATTTA
* **
54516374 ATTTTTTTCTTTTTTATTTTTTTA
1 ATTTTTTTCTTTTTTAGTAATTTA
54516398 ACTTTCTTTTCTTTTT
1 A-TTT-TTTTCTTTTT
54516414 CCCATTTTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
24 20 0.61
25 3 0.09
26 10 0.30
ACGTcount: A:0.14, C:0.09, G:0.03, T:0.73
Consensus pattern (24 bp):
ATTTTTTTCTTTTTTAGTAATTTA
Found at i:54520577 original size:18 final size:19
Alignment explanation
Indices: 54520543--54520578 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
54520533 TACAAAATAA
*
54520543 TCAAAATAATTTTTAAAAT
1 TCAAAATAATTTATAAAAT
54520562 TCAAAAT-ATTTATAAAA
1 TCAAAATAATTTATAAAA
54520579 AATTCAAATT
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:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (19 bp):
TCAAAATAATTTATAAAAT
Found at i:54520579 original size:19 final size:20
Alignment explanation
Indices: 54520543--54520586 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
54520533 TACAAAATAA
*
54520543 TCAAAATAATTTT-TAAAAT
1 TCAAAATAATTTTAAAAAAT
54520562 TCAAAAT-ATTTATAAAAAAT
1 TCAAAATAATTT-TAAAAAAT
54520582 TCAAA
1 TCAAA
54520587 TTTTATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 4 0.18
19 8 0.36
20 10 0.45
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (20 bp):
TCAAAATAATTTTAAAAAAT
Found at i:54520624 original size:12 final size:11
Alignment explanation
Indices: 54520600--54520633 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
54520590 TATATTTTTC
54520600 AAAAATTATAA
1 AAAAATTATAA
*
54520611 AAAAATTTTAA
1 AAAAATTATAA
*
54520622 AAAAATTCTAA
1 AAAAATTATAA
54520633 A
1 A
54520634 GAATATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:54537916 original size:13 final size:13
Alignment explanation
Indices: 54537898--54537925 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
54537888 TTCATCTCCT
54537898 TTAATTAACTTTG
1 TTAATTAACTTTG
54537911 TTAATTAACTTTG
1 TTAATTAACTTTG
54537924 TT
1 TT
54537926 GATATGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (13 bp):
TTAATTAACTTTG
Found at i:54544667 original size:22 final size:23
Alignment explanation
Indices: 54544614--54544668 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
54544604 ATTTGTCATT
*
54544614 ATAA-AAATAAAACAAATTTAGA
1 ATAATAAATATAACAAATTTAGA
* *
54544636 TTAATGAATATAACAAATTT-GA
1 ATAATAAATATAACAAATTTAGA
54544658 ATAATAAATAT
1 ATAATAAATAT
54544669 CTAAAATTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.31
Consensus pattern (23 bp):
ATAATAAATATAACAAATTTAGA
Found at i:54546882 original size:8 final size:9
Alignment explanation
Indices: 54546864--54546924 Score: 52
Period size: 9 Copynumber: 6.4 Consensus size: 9
54546854 AAAGTATTTT
54546864 AAAATTAAA
1 AAAATTAAA
54546873 AAAATTAAA
1 AAAATTAAA
54546882 AAAGTATTTTAAA
1 AAA--A--TTAAA
*
54546895 AAAATT-TA
1 AAAATTAAA
*
54546903 AAATTTAAA
1 AAAATTAAA
*
54546912 AAATTTAAA
1 AAAATTAAA
54546921 AAAA
1 AAAA
54546925 GTATTTTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
8 6 0.14
9 27 0.63
11 2 0.05
13 8 0.19
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAATTAAA
Found at i:54546883 original size:28 final size:31
Alignment explanation
Indices: 54546825--54546895 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 31
54546815 ACCAAAAATT
54546825 TATTTTAAAAATTAAAACAAAAATTAAAAAAAG
1 TATTTT-AAAATT-AAACAAAAATTAAAAAAAG
54546858 TATTTTAAAATT-AA-AAAAATT-AAAAAAG
1 TATTTTAAAATTAAACAAAAATTAAAAAAAG
54546886 TATTTTAAAA
1 TATTTTAAAA
54546896 AAATTTAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
28 17 0.45
29 7 0.18
30 2 0.05
32 6 0.16
33 6 0.16
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.32
Consensus pattern (31 bp):
TATTTTAAAATTAAACAAAAATTAAAAAAAG
Found at i:54546896 original size:40 final size:41
Alignment explanation
Indices: 54546852--54546955 Score: 153
Period size: 40 Copynumber: 2.6 Consensus size: 41
54546842 CAAAAATTAA
54546852 AAAAAGTATTTTAAAATTAAAAAAATT-AAAAAAGTATTTT
1 AAAAAGTATTTTAAAATTAAAAAAATTAAAAAAAGTATTTT
* *
54546892 AAAAA--AATTTAAAATTTAAAAAATTTAAAAAAAGTATTTT
1 AAAAAGTATTTTAAAA-TTAAAAAAATTAAAAAAAGTATTTT
54546932 -AAAAGTATTTTAAAATTAAAAAAA
1 AAAAAGTATTTTAAAATTAAAAAAA
54546956 ATAATAAATA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
38 8 0.14
39 14 0.25
40 26 0.46
41 8 0.14
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (41 bp):
AAAAAGTATTTTAAAATTAAAAAAATTAAAAAAAGTATTTT
Found at i:54549821 original size:112 final size:112
Alignment explanation
Indices: 54549612--54549832 Score: 354
Period size: 112 Copynumber: 2.0 Consensus size: 112
54549602 CAATTCGATT
54549612 AAAAAATATTAAAAATTTAGTTCACCCAATCTATATTGCTTCCCAAGTCAATTGTTTCAATGCCC
1 AAAAAATATTAAAAATTTAGTTCACCCAATCTATATTGCTTCCCAAGTCAATTGTTTCAATGCCC
* * * *
54549677 TTTTTTGGAATAGTACCTCGGCTAGAGTGGTCGGTCCAGTTCAATTA
66 TTTTCTGGAAGAGTACCTCGGATAGAGCGGTCGGTCCAGTTCAATTA
* *
54549724 AAAAAATATTAAAAATTTAGTTCACCCAATCTATATTGTTTCCCAAGTCAATTGTTTCAATGTCC
1 AAAAAATATTAAAAATTTAGTTCACCCAATCTATATTGCTTCCCAAGTCAATTGTTTCAATGCCC
* *
54549789 TTTTCTGGAACGA-TACCTTGGATCGAGCGGTCGGTCCAGTTCAA
66 TTTTCTGGAA-GAGTACCTCGGATAGAGCGGTCGGTCCAGTTCAA
54549833 ACAACCTTGA
Statistics
Matches: 100, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
112 99 0.99
113 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (112 bp):
AAAAAATATTAAAAATTTAGTTCACCCAATCTATATTGCTTCCCAAGTCAATTGTTTCAATGCCC
TTTTCTGGAAGAGTACCTCGGATAGAGCGGTCGGTCCAGTTCAATTA
Found at i:54550331 original size:36 final size:36
Alignment explanation
Indices: 54550284--54550357 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
54550274 AATTTCATGC
54550284 TTATTGAATGTTATCTCTTTTTATTGTTGATAAGGT
1 TTATTGAATGTTATCTCTTTTTATTGTTGATAAGGT
54550320 TTATTGAATGTTATCTCTTTTTATTGTTGATAAGGT
1 TTATTGAATGTTATCTCTTTTTATTGTTGATAAGGT
54550356 TT
1 TT
54550358 GAATTTTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.22, C:0.05, G:0.16, T:0.57
Consensus pattern (36 bp):
TTATTGAATGTTATCTCTTTTTATTGTTGATAAGGT
Found at i:54557052 original size:21 final size:21
Alignment explanation
Indices: 54557026--54557088 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
54557016 TTAATAAAAT
54557026 TATTTTATATTAATATTTAAA
1 TATTTTATATTAATATTTAAA
54557047 TATTTTATAATTAA-ATTTAAA
1 TATTTTAT-ATTAATATTTAAA
* *
54557068 AATATTT-T-TTATTATTTAAA
1 TAT-TTTATATTAATATTTAAA
54557088 T
1 T
54557089 CAAATTTAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
19 3 0.08
20 7 0.19
21 18 0.50
22 8 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTTATATTAATATTTAAA
Found at i:54557074 original size:23 final size:23
Alignment explanation
Indices: 54557020--54557081 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 23
54557010 AAATTATTAA
*
54557020 TAAAATTATTTTATATTAATATT
1 TAAAAATATTTTATATTAATATT
54557043 T--AAATATTTTATAATTAA-ATT
1 TAAAAATATTTTAT-ATTAATATT
*
54557064 TAAAAATATTTTTTATTA
1 TAAAAATATTTTATATTA
54557082 TTTAAATCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 14 0.41
22 9 0.26
23 11 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TAAAAATATTTTATATTAATATT
Found at i:54560993 original size:21 final size:20
Alignment explanation
Indices: 54560967--54561013 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
54560957 TGAATGCTGA
* *
54560967 TTTTTGGTTAAGATTTTTCAT
1 TTTTTGGATAAGAATTTT-AT
54560988 TTTTTGGATAAGAATTTTAT
1 TTTTTGGATAAGAATTTTAT
*
54561008 TGTTTG
1 TTTTTG
54561014 ATTTGTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.21, C:0.02, G:0.17, T:0.60
Consensus pattern (20 bp):
TTTTTGGATAAGAATTTTAT
Found at i:54565624 original size:13 final size:13
Alignment explanation
Indices: 54565572--54565624 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
54565562 TTTAAGCCAA
54565572 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* * *
54565585 ACCTCTCAAAATC
1 ACTTTTCAAAAGC
*
54565598 ACTTTTTC-ACAGC
1 AC-TTTTCAAAAGC
54565611 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
54565624 A
1 A
54565625 ACGAAAAATT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
12 5 0.17
13 22 0.73
14 3 0.10
ACGTcount: A:0.36, C:0.28, G:0.06, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:54565984 original size:20 final size:19
Alignment explanation
Indices: 54565954--54566004 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
54565944 AGTAAAGTAT
54565954 AAATA-ATTAAATGAAAAC
1 AAATACATTAAATGAAAAC
*
54565972 GAAATACATTAAACG-AAAC
1 -AAATACATTAAATGAAAAC
54565991 AAA-AC-TTAAATGAA
1 AAATACATTAAATGAA
54566005 TTAAATTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 6 0.21
17 3 0.11
18 3 0.11
19 9 0.32
20 7 0.25
ACGTcount: A:0.63, C:0.10, G:0.08, T:0.20
Consensus pattern (19 bp):
AAATACATTAAATGAAAAC
Found at i:54569668 original size:18 final size:17
Alignment explanation
Indices: 54569626--54569668 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
54569616 TTTTTAAGTT
*
54569626 TATAATATTTTATATTA
1 TATAATTTTTTATATTA
* *
54569643 TGTTATTTTTATATATTA
1 TATAATTTTT-TATATTA
54569661 TATAATTT
1 TATAATTT
54569669 AAAATACATT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Done.