Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 110 of 198
Found at i:35349449 original size:16 final size:16
Alignment explanation
Indices: 35349430--35349460 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35349420 TAAATAATTT
*
35349430 TTTTATTTAATTAAAG
1 TTTTATCTAATTAAAG
35349446 TTTTATCTAATTAAA
1 TTTTATCTAATTAAA
35349461 TTCCAAATGT
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:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (16 bp):
TTTTATCTAATTAAAG
Found at i:35351898 original size:7 final size:7
Alignment explanation
Indices: 35351886--35351911 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
35351876 AACAAATATT
35351886 GGGTTTA
1 GGGTTTA
35351893 GGGTTTA
1 GGGTTTA
35351900 GGGTTTA
1 GGGTTTA
35351907 GGGTT
1 GGGTT
35351912 GGGTTGGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.46, T:0.42
Consensus pattern (7 bp):
GGGTTTA
Found at i:35352228 original size:11 final size:11
Alignment explanation
Indices: 35352212--35352237 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
35352202 AACCATCTGT
35352212 ATATAACCAAA
1 ATATAACCAAA
35352223 ATATAACCAAA
1 ATATAACCAAA
35352234 ATAT
1 ATAT
35352238 CATCCAGCAA
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:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (11 bp):
ATATAACCAAA
Found at i:35352554 original size:18 final size:19
Alignment explanation
Indices: 35352517--35352560 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
35352507 GTTGCAATCC
*
35352517 AAGGGGAAGGGAAAATGG-
1 AAGGGGAAGGGAAAAGGGA
*
35352535 AAGGGGAAGGGAAAGGGGA
1 AAGGGGAAGGGAAAAGGGA
35352554 AAGGGGA
1 AAGGGGA
35352561 GAAGAAGGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.43, C:0.00, G:0.55, T:0.02
Consensus pattern (19 bp):
AAGGGGAAGGGAAAAGGGA
Found at i:35353608 original size:21 final size:21
Alignment explanation
Indices: 35353566--35353606 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
35353556 CCATTAAAAG
35353566 AACAAATCAATTTAGCACTTT
1 AACAAATCAATTTAGCACTTT
35353587 AACAAAT-AA-TTAGCATCTTT
1 AACAAATCAATTTAGCA-CTTT
35353607 TACTTTTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 6 0.32
21 7 0.37
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (21 bp):
AACAAATCAATTTAGCACTTT
Found at i:35354926 original size:18 final size:18
Alignment explanation
Indices: 35354903--35354938 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
35354893 CGATCTCAAG
*
35354903 CTTCGTATAAAATTTCAC
1 CTTCGTATAAAATCTCAC
*
35354921 CTTCGTGTAAAATCTCAC
1 CTTCGTATAAAATCTCAC
35354939 GACGAAACTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (18 bp):
CTTCGTATAAAATCTCAC
Found at i:35358361 original size:39 final size:39
Alignment explanation
Indices: 35358278--35358369 Score: 105
Period size: 39 Copynumber: 2.4 Consensus size: 39
35358268 AAAATTGGGA
* * * * *
35358278 ATTAGCGGTGCTTCTGAGAAAGCCCCGCTAAAAATGAGC
1 ATTAGCGGCGTTTCTAAGAAAACCCCACTAAAAATGAGC
* *
35358317 TTTAGCGGCGTTTCTAAGAAAACGCCACTAAAAAT-ATGC
1 ATTAGCGGCGTTTCTAAGAAAACCCCACTAAAAATGA-GC
35358356 ATTAGCGGCGTTTC
1 ATTAGCGGCGTTTC
35358370 CGCCAAAAAC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
38 1 0.02
39 43 0.98
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (39 bp):
ATTAGCGGCGTTTCTAAGAAAACCCCACTAAAAATGAGC
Found at i:35359085 original size:2 final size:2
Alignment explanation
Indices: 35359033--35359067 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
35359023 AGGTTTAAGG
35359033 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35359068 GATTATTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35359648 original size:34 final size:34
Alignment explanation
Indices: 35359609--35359724 Score: 92
Period size: 34 Copynumber: 3.3 Consensus size: 34
35359599 TGGAAGGTAT
* *
35359609 TTTAAGGAGTAGGGGGTATGGATTAGGGTTTGGGA
1 TTTAAGG-GTAGGGGGTAGGGATTAGGGTTAGGGA
* * * *
35359644 -TTAAGGTTTAGAGGTTAGGGGTTAGGGTTAGGGA
1 TTTAAGG-GTAGGGGGTAGGGATTAGGGTTAGGGA
*
35359678 TTTAAGGGTTAGGGGGATTTAGGGGTTAGAGGTTAGGGA
1 TTTAAGGG-TAGGGGG---TAGGGATTAG-GGTTAGGGA
35359717 TTT-AGGGT
1 TTTAAGGGT
35359725 TTAGGGTGTC
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
34 27 0.42
35 11 0.17
37 1 0.02
38 14 0.22
39 12 0.18
ACGTcount: A:0.22, C:0.00, G:0.45, T:0.33
Consensus pattern (34 bp):
TTTAAGGGTAGGGGGTAGGGATTAGGGTTAGGGA
Found at i:35359672 original size:21 final size:21
Alignment explanation
Indices: 35359618--35359730 Score: 72
Period size: 21 Copynumber: 5.2 Consensus size: 21
35359608 TTTTAAGGAG
* *
35359618 TAGGGGGTATGGA-TTAGGGT
1 TAGGGGTTAGGGATTTAGGGT
* * *
35359638 TTGGGATTAAGG-TTTAGAGGT
1 TAGGGGTTAGGGATTTAG-GGT
35359659 TAGGGGTTAGGG--TTAGGGATT
1 TAGGGGTTAGGGATTTAGGG--T
*
35359680 TAAGGGTTAGGGGGATTTAGGGGT
1 TAGGGGTTA--GGGATTTA-GGGT
*
35359704 TAGAGGTTAGGGATTTAGGGTT
1 TAGGGGTTAGGGATTTAGGG-T
35359726 TAGGG
1 TAGGG
35359731 TGTCAAGGGT
Statistics
Matches: 72, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
19 2 0.03
20 16 0.22
21 24 0.33
22 13 0.18
23 3 0.04
24 8 0.11
25 3 0.04
26 3 0.04
ACGTcount: A:0.21, C:0.00, G:0.46, T:0.33
Consensus pattern (21 bp):
TAGGGGTTAGGGATTTAGGGT
Found at i:35359685 original size:15 final size:15
Alignment explanation
Indices: 35359667--35359706 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
35359657 GTTAGGGGTT
35359667 AGGGTTAGGGATTTA
1 AGGGTTAGGGATTTA
35359682 AGGGTTAGGGGGATTTA
1 AGGGTTA--GGGATTTA
*
35359699 GGGGTTAG
1 AGGGTTAG
35359707 AGGTTAGGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 8 0.36
17 14 0.64
ACGTcount: A:0.23, C:0.00, G:0.47, T:0.30
Consensus pattern (15 bp):
AGGGTTAGGGATTTA
Found at i:35359696 original size:17 final size:17
Alignment explanation
Indices: 35359674--35359706 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35359664 GTTAGGGTTA
35359674 GGGATTTAAGGGTTAGG
1 GGGATTTAAGGGTTAGG
*
35359691 GGGATTTAGGGGTTAG
1 GGGATTTAAGGGTTAG
35359707 AGGTTAGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.48, T:0.30
Consensus pattern (17 bp):
GGGATTTAAGGGTTAGG
Found at i:35359728 original size:15 final size:13
Alignment explanation
Indices: 35359631--35359731 Score: 71
Period size: 13 Copynumber: 7.1 Consensus size: 13
35359621 GGGGTATGGA
35359631 TTAGGGTTT-GGG
1 TTAGGGTTTAGGG
*
35359643 ATTAAGGTTTAGAGG
1 -TTAGGGTTTAG-GG
*
35359658 TTAGGGGTTAGGG
1 TTAGGGTTTAGGG
35359671 TTAGGGATTTAAGGG
1 TTAGGG-TTT-AGGG
35359686 TTAGGGGGATTTAGGGG
1 TTA--GGG-TTTA-GGG
35359703 TTAGAGG-TTAGGG
1 TTAG-GGTTTAGGG
35359716 ATTTAGGGTTTAGGG
1 --TTAGGGTTTAGGG
35359731 T
1 T
35359732 GTCAAGGGTA
Statistics
Matches: 73, Mismatches: 4, Indels: 22
0.74 0.04 0.22
Matches are distributed among these distances:
13 20 0.27
14 17 0.23
15 20 0.27
16 3 0.04
17 13 0.18
ACGTcount: A:0.21, C:0.00, G:0.45, T:0.35
Consensus pattern (13 bp):
TTAGGGTTTAGGG
Found at i:35359731 original size:7 final size:7
Alignment explanation
Indices: 35359631--35359731 Score: 59
Period size: 7 Copynumber: 14.0 Consensus size: 7
35359621 GGGGTATGGA
35359631 TTAGGGT
1 TTAGGGT
*
35359638 TT-GGGA
1 TTAGGGT
*
35359644 TTAAGGT
1 TTAGGGT
35359651 TTAGAGG-
1 TTAG-GGT
*
35359658 TTAGGGG
1 TTAGGGT
35359665 TTAGGG-
1 TTAGGGT
35359671 TTAGGGAT
1 TTAGGG-T
35359679 TTAAGGG-
1 TT-AGGGT
35359686 TTAGGGGGAT
1 TTA--GGG-T
*
35359696 TTAGGGG
1 TTAGGGT
35359703 TTAGAGG-
1 TTAG-GGT
35359710 TTAGGGAT
1 TTAGGG-T
35359718 TTAGGGT
1 TTAGGGT
35359725 TTAGGGT
1 TTAGGGT
35359732 GTCAAGGGTA
Statistics
Matches: 76, Mismatches: 5, Indels: 26
0.71 0.05 0.24
Matches are distributed among these distances:
6 16 0.21
7 35 0.46
8 18 0.24
9 4 0.05
10 3 0.04
ACGTcount: A:0.21, C:0.00, G:0.45, T:0.35
Consensus pattern (7 bp):
TTAGGGT
Found at i:35361190 original size:24 final size:24
Alignment explanation
Indices: 35361156--35361201 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
35361146 CGAAAAAGCT
35361156 ATTTTCTCCCCAAAAATTCCCCCCA
1 ATTTTCTCCCCAAAAA-TCCCCCCA
35361181 ATTTT-TCCCCAAAAATCCCCC
1 ATTTTCTCCCCAAAAATCCCCC
35361202 AAATCTAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 6 0.29
24 10 0.48
25 5 0.24
ACGTcount: A:0.28, C:0.43, G:0.00, T:0.28
Consensus pattern (24 bp):
ATTTTCTCCCCAAAAATCCCCCCA
Found at i:35361621 original size:12 final size:12
Alignment explanation
Indices: 35361604--35361628 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35361594 AGTTTGAAAC
35361604 TGTTCATAATTT
1 TGTTCATAATTT
35361616 TGTTCATAATTT
1 TGTTCATAATTT
35361628 T
1 T
35361629 CACTATCTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (12 bp):
TGTTCATAATTT
Found at i:35361683 original size:17 final size:17
Alignment explanation
Indices: 35361656--35361695 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
35361646 TATAGAAAAC
35361656 AATAA-AATGTTATTA-G
1 AATAATAATGTTA-TACG
35361672 AATAATAATGTTATACG
1 AATAATAATGTTATACG
35361689 AATAATA
1 AATAATA
35361696 TTATGAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.53, C:0.03, G:0.10, T:0.35
Consensus pattern (17 bp):
AATAATAATGTTATACG
Found at i:35362032 original size:26 final size:26
Alignment explanation
Indices: 35362003--35362060 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
35361993 CTCGTTGCAT
*
35362003 AATAATTCTTACTCTATAGCTTATGA
1 AATAATTCTTACTCTATAGCTTATAA
35362029 AATAATTCTTACTCTATAGCTTATAA
1 AATAATTCTTACTCTATAGCTTATAA
35362055 AATAAT
1 AATAAT
35362061 ATAAATCTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.41
Consensus pattern (26 bp):
AATAATTCTTACTCTATAGCTTATAA
Found at i:35364652 original size:44 final size:45
Alignment explanation
Indices: 35364584--35364668 Score: 129
Period size: 44 Copynumber: 1.9 Consensus size: 45
35364574 GAAGTAAAAT
* *
35364584 TTGCTATTCTCGGTCTGCCCCACTGCAA-CTGTAGGGAGATATGAC
1 TTGCTATTCTCAGTCTACCCCACTGCAACCT-TAGGGAGATATGAC
35364629 TTGCT-TTCTCAGTCTACCCCACTGCAACCTTAGGGAGATA
1 TTGCTATTCTCAGTCTACCCCACTGCAACCTTAGGGAGATA
35364669 AGACCTGATG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
44 30 0.81
45 7 0.19
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.29
Consensus pattern (45 bp):
TTGCTATTCTCAGTCTACCCCACTGCAACCTTAGGGAGATATGAC
Found at i:35364772 original size:44 final size:44
Alignment explanation
Indices: 35364690--35365540 Score: 418
Period size: 44 Copynumber: 19.6 Consensus size: 44
35364680 GATCTACCCT
* * *
35364690 ACTGCAACTTC-GGAGAGATAAGATCTAT-TATTTTAATCTGCTCC
1 ACTGCAACTTCAGG-GAGATAAGAT-TATCAACTTCAATCTGCTCC
* ** *
35364734 TCTGCAACTTCAGGGAGATGGGATTATCAACTTCAATCTGCACC
1 ACTGCAACTTCAGGGAGATAAGATTATCAACTTCAATCTGCTCC
* * * * *
35364778 ACTGCAACCTCAGGGAGATAAGATTGA-CATCTTCGATTTGCCCC
1 ACTGCAACTTCAGGGAGATAAGATT-ATCAACTTCAATCTGCTCC
** * * * **
35364822 ACTGCAACTTCAGGTG-GATAAGA-GCT-GA-TGCGATCCACTCC
1 ACTGCAACTTCAGG-GAGATAAGATTATCAACTTCAATCTGCTCC
* * * * * *
35364863 ACTACAACTTC-GGAGAGATCAGATCTAT-TATTTTAATCCGCTCC
1 ACTGCAACTTCAGG-GAGATAAGAT-TATCAACTTCAATCTGCTCC
*
35364907 ACTGCAACTTCAGGGAGATAGGATTATCAACTTCAATCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATTATCAACTTCAATCTGCTCC
* * *
35364951 ACTGCAACCTCAGGGAGATAAGATT-TGCCATA-TTCGATCTGCCCC
1 ACTGCAACTTCAGGGAGATAAGATTAT--CA-ACTTCAATCTGCTCC
* * * * ** *
35364996 ACTGCAACTTCAGTGG-GATAAGACT-T-GA-TGCTATCCACTCT
1 ACTGCAACTTCAG-GGAGATAAGATTATCAACTTCAATCTGCTCC
* * * * * *
35365037 ACTGCAACTTAAGAGACATAAGATCTAT-TACTTTAATCCGCTCC
1 ACTGCAACTTCAGGGAGATAAGAT-TATCAACTTCAATCTGCTCC
** *
35365081 ACTGCAACTTCAGGGAGATGGGATTATCAACATCAATCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATTATCAACTTCAATCTGCTCC
* * *
35365125 ACTGCAACCTCAGGGAGATAAGATT-TGCCATCTTCGATCTGC-CC
1 ACTGCAACTTCAGGGAGATAAGATTAT--CAACTTCAATCTGCTCC
* ** * * * ** *
35365169 ACTGCAACTTCAGGGGGATAAGA-CCT-GA-TGCGATCCACTCT
1 ACTGCAACTTCAGGGAGATAAGATTATCAACTTCAATCTGCTCC
* * * *
35365210 ACTGCAAC-TCCGGAGAAATAAGATCTAT-TACTTTAAT-TCGCTCC
1 ACTGCAACTTCAGG-GAGATAAGAT-TATCAACTTCAATCT-GCTCC
* ** *
35365254 ACTGTAACTTCAGGGAGATGGGATTATCAACTTCAATCTACTCC
1 ACTGCAACTTCAGGGAGATAAGATTATCAACTTCAATCTGCTCC
* * * * *
35365298 ACTACAACCTCAGGGAGATAAGATT-TGCCATCTTCGATCTGCCCC
1 ACTGCAACTTCAGGGAGATAAGATTAT--CAACTTCAATCTGCTCC
* * * * * *
35365343 ACTGCAACTTCAGGGGGATAAGACCT-GCTTAC-TCAGTCTGCTCT
1 ACTGCAACTTCAGGGAGATAAGA-TTATC-AACTTCAATCTGCTCC
* ** * *** ** *
35365387 GCTGCAACTTCAGGGAGATAAGA-CCT-GA-TGGGATCCACTCT
1 ACTGCAACTTCAGGGAGATAAGATTATCAACTTCAATCTGCTCC
* * *
35365428 ACTGCAACTTCAGAGAGATAAGATCTAT-TACTTTAATCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGAT-TATCAACTTCAATCTGCTCC
* * *
35365472 ACTGTAACTTCAGGGAGATAGGATTATCGA-TCTCAATCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATTATCAACT-TCAATCTGCTCC
* *
35365516 -CTTGCAACCTCAGGGAGGTAAGATT
1 AC-TGCAACTTCAGGGAGATAAGATT
35365541 TGCCATCTTC
Statistics
Matches: 603, Mismatches: 160, Indels: 88
0.71 0.19 0.10
Matches are distributed among these distances:
40 15 0.02
41 94 0.16
42 1 0.00
43 28 0.05
44 371 0.62
45 90 0.15
46 4 0.01
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.27
Consensus pattern (44 bp):
ACTGCAACTTCAGGGAGATAAGATTATCAACTTCAATCTGCTCC
Found at i:35364892 original size:173 final size:174
Alignment explanation
Indices: 35364645--35365369 Score: 1134
Period size: 173 Copynumber: 4.2 Consensus size: 174
35364635 TCTCAGTCTA
* *
35364645 CCCCACTGCAACCTT-AGGGAGATAAGACCTGATGCGATCTAC-CCTACTGCAACTTCGGAGAGA
1 CCCCACTGCAA-CTTCAGGGGGATAAGACCTGATGCGATCCACTCC-ACTGCAACTTCGGAGAGA
* * *
35364708 TAAGATCTATTATTTTAATCTGCTCCTCTGCAACTTCAGGGAGATGGGATTATCAACTTCAATCT
64 TAAGATCTATTACTTTAATCCGCTCCACTGCAACTTCAGGGAGATGGGATTATCAACTTCAATCT
* * *
35364773 GCACCACTGCAACCTCAGGGAGATAAGA-TTGACATCTTCGATTTG
129 GCTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGATCTG
* * * *
35364818 CCCCACTGCAACTTCAGGTGGATAAGAGCTGATGCGATCCACTCCACTACAACTTCGGAGAGATC
1 CCCCACTGCAACTTCAGGGGGATAAGACCTGATGCGATCCACTCCACTGCAACTTCGGAGAGATA
* *
35364883 AGATCTATTATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCAACTTCAATCTGC
66 AGATCTATTACTTTAATCCGCTCCACTGCAACTTCAGGGAGATGGGATTATCAACTTCAATCTGC
*
35364948 TCCACTGCAACCTCAGGGAGATAAGATTTGCCATATTCGATCTG
131 TCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGATCTG
* * * * ** *
35364992 CCCCACTGCAACTTCAGTGGGATAAGACTTGATGCTATCCACTCTACTGCAACTTAAGAGACATA
1 CCCCACTGCAACTTCAGGGGGATAAGACCTGATGCGATCCACTCCACTGCAACTTCGGAGAGATA
*
35365057 AGATCTATTACTTTAATCCGCTCCACTGCAACTTCAGGGAGATGGGATTATCAACATCAATCTGC
66 AGATCTATTACTTTAATCCGCTCCACTGCAACTTCAGGGAGATGGGATTATCAACTTCAATCTGC
35365122 TCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGATCTG
131 TCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGATCTG
* * *
35365166 -CCCACTGCAACTTCAGGGGGATAAGACCTGATGCGATCCACTCTACTGCAACTCCGGAGAAATA
1 CCCCACTGCAACTTCAGGGGGATAAGACCTGATGCGATCCACTCCACTGCAACTTCGGAGAGATA
* * *
35365230 AGATCTATTACTTTAATTCGCTCCACTGTAACTTCAGGGAGATGGGATTATCAACTTCAATCTAC
66 AGATCTATTACTTTAATCCGCTCCACTGCAACTTCAGGGAGATGGGATTATCAACTTCAATCTGC
*
35365295 TCCACTACAACCTCAGGGAGATAAGATTTGCCATCTTCGATCTG
131 TCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGATCTG
35365339 CCCCACTGCAACTTCAGGGGGATAAGACCTG
1 CCCCACTGCAACTTCAGGGGGATAAGACCTG
35365370 CTTACTCAGT
Statistics
Matches: 508, Mismatches: 40, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
172 3 0.01
173 300 0.59
174 205 0.40
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (174 bp):
CCCCACTGCAACTTCAGGGGGATAAGACCTGATGCGATCCACTCCACTGCAACTTCGGAGAGATA
AGATCTATTACTTTAATCCGCTCCACTGCAACTTCAGGGAGATGGGATTATCAACTTCAATCTGC
TCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGATCTG
Found at i:35365280 original size:347 final size:346
Alignment explanation
Indices: 35364645--35365369 Score: 1139
Period size: 347 Copynumber: 2.1 Consensus size: 346
35364635 TCTCAGTCTA
* ** *
35364645 CCCCACTGCAACCTT-AGGGAGATAAGACCTGATGCGATCTACCCTACTGCAACTTCGGAGAGAT
1 CCCCACTGCAA-CTTCAGGG-GATAAGACCTGATGCGATCCACCCTACTGCAACTTAAGAGACAT
* * * *
35364709 AAGATCTATTATTTTAATCTGCTCCTCTGCAACTTCAGGGAGATGGGATTATCAACTTCAATCTG
64 AAGATCTATTACTTTAATCCGCTCCACTGCAACTTCAGGGAGATGGGATTATCAACATCAATCTG
* *
35364774 CACCACTGCAACCTCAGGGAGATAAGATTGACATCTTCGATTTGCCCCACTGCAACTTCAGGTGG
129 CACCACTGCAACCTCAGGGAGATAAGATTGACATCTTCGATCTGCCCCACTGCAACTTCAGGGGG
* * * * *
35364839 ATAAGAGCTGATGCGATCCACTCCACTACAACTTCGGAGAGATCAGATCTATTATTTTAATCCGC
194 ATAAGACCTGATGCGATCCACTCCACTACAACTCCGGAGAAATAAGATCTATTACTTTAATCCGC
* *
35364904 TCCACTGCAACTTCAGGGAGATAGGATTATCAACTTCAATCTGCTCCACTGCAACCTCAGGGAGA
259 TCCACTGCAACTTCAGGGAGATAGGATTATCAACTTCAATCTACTCCACTACAACCTCAGGGAGA
35364969 TAAGATTTGCCATATTCGATCTG
324 TAAGATTTGCCATATTCGATCTG
* * *
35364992 CCCCACTGCAACTTCAGTGGGATAAGACTTGATGCTATCCACTCTACTGCAACTTAAGAGACATA
1 CCCCACTGCAACTTCAG-GGGATAAGACCTGATGCGATCCACCCTACTGCAACTTAAGAGACATA
35365057 AGATCTATTACTTTAATCCGCTCCACTGCAACTTCAGGGAGATGGGATTATCAACATCAATCTGC
65 AGATCTATTACTTTAATCCGCTCCACTGCAACTTCAGGGAGATGGGATTATCAACATCAATCTGC
* *
35365122 TCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGATCTG-CCCACTGCAACTTCAGGGGG
130 ACCACTGCAACCTCAGGGAGATAAGA-TTGACATCTTCGATCTGCCCCACTGCAACTTCAGGGGG
* * *
35365186 ATAAGACCTGATGCGATCCACTCTACTGCAACTCCGGAGAAATAAGATCTATTACTTTAATTCGC
194 ATAAGACCTGATGCGATCCACTCCACTACAACTCCGGAGAAATAAGATCTATTACTTTAATCCGC
* *
35365251 TCCACTGTAACTTCAGGGAGATGGGATTATCAACTTCAATCTACTCCACTACAACCTCAGGGAGA
259 TCCACTGCAACTTCAGGGAGATAGGATTATCAACTTCAATCTACTCCACTACAACCTCAGGGAGA
*
35365316 TAAGATTTGCCATCTTCGATCTG
324 TAAGATTTGCCATATTCGATCTG
35365339 CCCCACTGCAACTTCAGGGGGATAAGACCTG
1 CCCCACTGCAACTTCA-GGGGATAAGACCTG
35365370 CTTACTCAGT
Statistics
Matches: 345, Mismatches: 29, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
346 3 0.01
347 324 0.94
348 18 0.05
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (346 bp):
CCCCACTGCAACTTCAGGGGATAAGACCTGATGCGATCCACCCTACTGCAACTTAAGAGACATAA
GATCTATTACTTTAATCCGCTCCACTGCAACTTCAGGGAGATGGGATTATCAACATCAATCTGCA
CCACTGCAACCTCAGGGAGATAAGATTGACATCTTCGATCTGCCCCACTGCAACTTCAGGGGGAT
AAGACCTGATGCGATCCACTCCACTACAACTCCGGAGAAATAAGATCTATTACTTTAATCCGCTC
CACTGCAACTTCAGGGAGATAGGATTATCAACTTCAATCTACTCCACTACAACCTCAGGGAGATA
AGATTTGCCATATTCGATCTG
Found at i:35365434 original size:347 final size:348
Alignment explanation
Indices: 35364645--35365496 Score: 1088
Period size: 347 Copynumber: 2.5 Consensus size: 348
35364635 TCTCAGTCTA
* * * * * ** *
35364645 CCCCACTGCAACCTT-AGGGAGATAAGACCTGATGCGATCTACCCTACTGCAACTTCGGAGAGAT
1 CCCCACTGCAA-CTTCAGGGGGATAAGACCTGATACTATCCACTCTACTGCAACTTAAGAGACAT
* * ** ** *
35364709 AAGATCTATTATTTTAATCTGCTCCTCTGCAACTTCAGGGAGATGGGATTATCAACTTCAATCTG
65 AAGATCTATGACTGGAATCCACTCCACTGCAACTTCAGGGAGATGGGATTATCAACTTCAATCTG
* * *
35364774 CACCACTGCAACCTCAGGGAGATAAGA-TTGACATCTTCGATTTGCCCCACTGCAACTTCAGGTG
130 CTCCACTGCAACCTCAGGGAGATAAGATTTGACATCTTCGATCTGCCCCACTGCAACTTCAGGGG
* * * * *
35364838 GATAAGAGCTGATGCGATCCACTCCACTACAACTTCGGAGAGATCAGATCTATTATTTTAATCCG
195 GATAAGACCTGATGCGATCCACTCCACTACAACTCCGGAGAAATAAGATCTATTACTTTAATCCG
* *
35364903 CTCCACTGCAACTTCAGGGAGATAGGATTATCAACTTCAATCTGCTCCACTGCAACCTCAGGGAG
260 CTCCACTGCAACTTCAGGGAGATAGGATTATCAACTTCAATCTACTCCACTACAACCTCAGGGAG
35364968 ATAAGATTTGCCATATTCGATCTG
325 ATAAGATTTGCCATATTCGATCTG
* * *
35364992 CCCCACTGCAACTTCAGTGGGATAAGACTTGATGCTATCCACTCTACTGCAACTTAAGAGACATA
1 CCCCACTGCAACTTCAGGGGGATAAGACCTGATACTATCCACTCTACTGCAACTTAAGAGACATA
* ** * *
35365057 AGATCTATTACTTTAATCCGCTCCACTGCAACTTCAGGGAGATGGGATTATCAACATCAATCTGC
66 AGATCTATGACTGGAATCCACTCCACTGCAACTTCAGGGAGATGGGATTATCAACTTCAATCTGC
*
35365122 TCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGATCTG-CCCACTGCAACTTCAGGGGG
131 TCCACTGCAACCTCAGGGAGATAAGATTTGACATCTTCGATCTGCCCCACTGCAACTTCAGGGGG
* * *
35365186 ATAAGACCTGATGCGATCCACTCTACTGCAACTCCGGAGAAATAAGATCTATTACTTTAATTCGC
196 ATAAGACCTGATGCGATCCACTCCACTACAACTCCGGAGAAATAAGATCTATTACTTTAATCCGC
* *
35365251 TCCACTGTAACTTCAGGGAGATGGGATTATCAACTTCAATCTACTCCACTACAACCTCAGGGAGA
261 TCCACTGCAACTTCAGGGAGATAGGATTATCAACTTCAATCTACTCCACTACAACCTCAGGGAGA
*
35365316 TAAGATTTGCCATCTTCGATCTG
326 TAAGATTTGCCATATTCGATCTG
* ** * * * *
35365339 CCCCACTGCAACTTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCTGCTGCAACTTCAGGGAG
1 CCCCACTGCAACTTCAGGGGGATAAGACCTG-ATACT-A-TCCACTCTACTGCAACTTAAGAGAC
* * * * ** * *
35365404 ATAAGA-C-CTGA-TGGGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTAT-TACTTTAAT
63 ATAAGATCTATGACTGGAATCCACTCCACTGCAACTTCAGGGAGATGGGAT-TATCAACTTCAAT
* * *
35365465 CTGCTCCACTGTAACTTCAGGGAGATAGGATT
127 CTGCTCCACTGCAACCTCAGGGAGATAAGATT
35365497 ATCGATCTCA
Statistics
Matches: 443, Mismatches: 56, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
346 3 0.01
347 390 0.88
348 23 0.05
349 2 0.00
350 25 0.06
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (348 bp):
CCCCACTGCAACTTCAGGGGGATAAGACCTGATACTATCCACTCTACTGCAACTTAAGAGACATA
AGATCTATGACTGGAATCCACTCCACTGCAACTTCAGGGAGATGGGATTATCAACTTCAATCTGC
TCCACTGCAACCTCAGGGAGATAAGATTTGACATCTTCGATCTGCCCCACTGCAACTTCAGGGGG
ATAAGACCTGATGCGATCCACTCCACTACAACTCCGGAGAAATAAGATCTATTACTTTAATCCGC
TCCACTGCAACTTCAGGGAGATAGGATTATCAACTTCAATCTACTCCACTACAACCTCAGGGAGA
TAAGATTTGCCATATTCGATCTG
Found at i:35365682 original size:217 final size:218
Alignment explanation
Indices: 35365162--35365714 Score: 830
Period size: 218 Copynumber: 2.5 Consensus size: 218
35365152 CCATCTTCGA
* * * *
35365162 TCTGC-CCACTGCAACTTCAGGGGGATAAGACCTGATGCGATCCACTCTACTGCAACTCCGGAGA
1 TCTGCTCCGCTGCAACTTCAGGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGA-A
*
35365226 A-ATAAGATCTATTACTTTAAT-TCGCTCCACTGTAACTTCAGGGAGATGGGATTATCAACTTCA
65 AGATAAGATCTATTACTTTAATCT-GCTCCACTGTAACTTCAGGGAGATAGGATTATCAACTTCA
* *
35365289 ATCTACTCCACTACAACCTCAGGGAGATAAGATTTGCCATCTTCGATCTGCCCCACTGCAACTTC
129 ATCTACTCCACTACAACCTCAGGGAGATAAGATTTGCCATCTTCGATATGCCCCACTACAACTTC
*
35365354 AGGGGGATAAGACCTGCTTACTCAG
194 AGCGGGATAAGACCTGCTTACTCAG
* * *
35365379 TCTGCTCTGCTGCAACTTCAGGGAGATAAGACCTGATGGGATCCACTCTACTGCAACTTCAGAGA
1 TCTGCTCCGCTGCAACTTCAGGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAAA
*
35365444 GATAAGATCTATTACTTTAATCTGCTCCACTGTAACTTCAGGGAGATAGGATTATCGA-TCTCAA
66 GATAAGATCTATTACTTTAATCTGCTCCACTGTAACTTCAGGGAGATAGGATTATCAACT-TCAA
* * *
35365508 TCTGCTCC-CTTGCAACCTCAGGGAGGTAAGATTTGCCATCTTCGATATGCCCCA-TACAACTTC
130 TCTACTCCAC-TACAACCTCAGGGAGATAAGATTTGCCATCTTCGATATGCCCCACTACAACTTC
*
35365571 AGCGGGATAAGACCTGCTTTCTCAG
194 AGCGGGATAAGACCTGCTTACTCAG
* *
35365596 TCTGCTCCGCTGCAACTTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTTAGAAA
1 TCTGCTCCGCTGCAACTTCAGGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAAA
* * * *
35365661 GATAAGATCTATTATTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTA
66 GATAAGATCTATTACTTTAATCTGCTCCACTGTAACTTCAGGGAGATAGGATTA
35365715 GTGGTTTCAC
Statistics
Matches: 306, Mismatches: 25, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
217 149 0.49
218 156 0.51
219 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (218 bp):
TCTGCTCCGCTGCAACTTCAGGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAAA
GATAAGATCTATTACTTTAATCTGCTCCACTGTAACTTCAGGGAGATAGGATTATCAACTTCAAT
CTACTCCACTACAACCTCAGGGAGATAAGATTTGCCATCTTCGATATGCCCCACTACAACTTCAG
CGGGATAAGACCTGCTTACTCAG
Found at i:35365691 original size:391 final size:389
Alignment explanation
Indices: 35364820--35365714 Score: 1015
Period size: 391 Copynumber: 2.3 Consensus size: 389
35364810 TCGATTTGCC
* * * * * *
35364820 CCACTGCAACTTCAGGTG-GATAAGAGCTGATGCGATCCACTCCACTACAACTTCGGAGAGATCA
1 CCACTGCAACTTCAGGAGAGATAAGACCTGATGCGATCTACTCCACTGCAACTTCAGAGAGATAA
*
35364884 GATCTATTATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCAACTTCAATCTGCT
66 GATCTATTATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCAACTTCAATCTGCC
** *
35364949 CCACTGCAACCTCAGGGAGATAAGATTTGCCATATTCGATCTGCCCCACTGCAACTTCAGTGGGA
131 CCACTGCAACCTCAGGGAGATAAGACCTGCCATACTCGATCTGCCCCACTGCAACTTCAGTGGGA
* *
35365014 TAAGACTTGATGCTATCCACTCTACTGCAACTTAAGAGACATAAGATCTATTACTTTAATCCGCT
196 TAAGACCTGATGCGATCCACTCTACTGCAACTTAAGAGACATAAGATCTATTACTTTAATCCGCT
*
35365079 CCACTGCAACTTCAGGGAGATGGGATTATCAACATCAATCTGCTCCACTGCAACCTCAGGGAGAT
261 CCACTGCAACTTCAGGGAGATAGGATTATCAACATCAATCTGCTCCACTGCAACCTCAGGGAGAT
* * * *
35365144 AAGATTTGCCATCTTCGATCTGCCCACTGCAACTTCAGGGGGATAAGACCTGATGCGATCCACT
326 AAGATTTGCCATCTTCGATATGCCCACTACAACTTCAGCGGGATAAGACCTGATGCCATCCACT
* * * * * * * * *
35365208 CTACTGCAAC-TCCGGAGAAATAAGATCT-ATTACTTTAAT-TCGCTCCACTGTAACTTCAGGGA
1 CCACTGCAACTTCAGGAGAGATAAGACCTGA-TGC---GATCT-ACTCCACTGCAACTTCAGAGA
** * * * ** * * * *
35365270 GATGGGAT-TATCAACTTCAATCTACTCCACTACAACCTCAGGGAGATAAGATT-TGCCATCTTC
61 GATAAGATCTAT-TATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAT--CAACTTC
* * * * * **
35365333 GATCTGCCCCACTGCAACTTCAGGGGGATAAGACCTG-CTTACTC-AGTCTGCTCTGCTGCAACT
123 AATCTGCCCCACTGCAACCTCAGGGAGATAAGACCTGCCATACTCGA-TCTGCCCCACTGCAACT
* * *
35365396 TCAG-GGAGATAAGACCTGATGGGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACT
187 TCAGTGG-GATAAGACCTGATGCGATCCACTCTACTGCAACTTAAGAGACATAAGATCTATTACT
* * *
35365460 TTAATCTGCTCCACTGTAACTTCAGGGAGATAGGATTATCGATC-TCAATCTGCTCC-CTTGCAA
251 TTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATC-AACATCAATCTGCTCCAC-TGCAA
*
35365523 CCTCAGGGAGGTAAGATTTGCCATCTTCGATATGCCC-CATACAACTTCAGCGGGATAAGACCTG
314 CCTCAGGGAGATAAGATTTGCCATCTTCGATATGCCCAC-TACAACTTCAGCGGGATAAGACCTG
* * **
35365587 CTTTCTCAGTCTGCT
378 -ATGC-CA-TCCACT
* * * *
35365602 CCGCTGCAACTTCAGG-GAGATAAGACCTGATGCGATCTACTCTACTGCAACTTTAGAAAGATAA
1 CCACTGCAACTTCAGGAGAGATAAGACCTGATGCGATCTACTCCACTGCAACTTCAGAGAGATAA
*
35365666 GATCTATTATTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTA
66 GATCTATTATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTA
35365715 GTGGTTTCAC
Statistics
Matches: 408, Mismatches: 77, Indels: 40
0.78 0.15 0.08
Matches are distributed among these distances:
387 6 0.01
388 19 0.05
390 9 0.02
391 299 0.73
392 45 0.11
393 1 0.00
394 24 0.06
395 5 0.01
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (389 bp):
CCACTGCAACTTCAGGAGAGATAAGACCTGATGCGATCTACTCCACTGCAACTTCAGAGAGATAA
GATCTATTATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCAACTTCAATCTGCC
CCACTGCAACCTCAGGGAGATAAGACCTGCCATACTCGATCTGCCCCACTGCAACTTCAGTGGGA
TAAGACCTGATGCGATCCACTCTACTGCAACTTAAGAGACATAAGATCTATTACTTTAATCCGCT
CCACTGCAACTTCAGGGAGATAGGATTATCAACATCAATCTGCTCCACTGCAACCTCAGGGAGAT
AAGATTTGCCATCTTCGATATGCCCACTACAACTTCAGCGGGATAAGACCTGATGCCATCCACT
Found at i:35366982 original size:7 final size:7
Alignment explanation
Indices: 35366967--35367017 Score: 59
Period size: 7 Copynumber: 7.4 Consensus size: 7
35366957 GGCCTCTTCA
*
35366967 TTTCTTT
1 TTTCATT
35366974 TTTCATT
1 TTTCATT
*
35366981 TTTCGTT
1 TTTCATT
35366988 TTTCA-T
1 TTTCATT
35366994 TTTCATT
1 TTTCATT
*
35367001 TTTTATT
1 TTTCATT
*
35367008 TTTTATT
1 TTTCATT
35367015 TTT
1 TTT
35367018 TTCTGACTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
6 6 0.15
7 33 0.85
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.78
Consensus pattern (7 bp):
TTTCATT
Found at i:35367009 original size:20 final size:20
Alignment explanation
Indices: 35366973--35367016 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
35366963 TTCATTTCTT
*
35366973 TTTTCATTTTTCGTTTTTCA
1 TTTTCATTTTTCATTTTTCA
* *
35366993 TTTTCATTTTTTATTTTTTA
1 TTTTCATTTTTCATTTTTCA
35367013 TTTT
1 TTTT
35367017 TTTCTGACTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTTCATTTTTCATTTTTCA
Found at i:35367924 original size:26 final size:25
Alignment explanation
Indices: 35367895--35367943 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
35367885 TTTCTCATAT
35367895 TTTTCATTTTCACTTTTTGACTTTGA
1 TTTTCATTTTCACTTTTT-ACTTTGA
* **
35367921 TTTTGATTTTTTCTTTTTACTTT
1 TTTTCATTTTCACTTTTTACTTT
35367944 TGCTTTTGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 5 0.25
26 15 0.75
ACGTcount: A:0.12, C:0.12, G:0.06, T:0.69
Consensus pattern (25 bp):
TTTTCATTTTCACTTTTTACTTTGA
Found at i:35367927 original size:6 final size:6
Alignment explanation
Indices: 35367909--35367974 Score: 51
Period size: 6 Copynumber: 10.7 Consensus size: 6
35367899 CATTTTCACT
* ** * * * *
35367909 TTTTGA CTTTGA TTTTGA TTTTTTC TTTTTA CTTTTGC TTTTGC TTTTGC
1 TTTTGA TTTTGA TTTTGA -TTTTGA TTTTGA -TTTTGA TTTTGA TTTTGA
35367959 TTTTGA TTTTGA TTTT
1 TTTTGA TTTTGA TTTT
35367975 TTTCTTCCCC
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
6 42 0.84
7 8 0.16
ACGTcount: A:0.09, C:0.09, G:0.12, T:0.70
Consensus pattern (6 bp):
TTTTGA
Found at i:35372808 original size:21 final size:21
Alignment explanation
Indices: 35372779--35372829 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
35372769 NNNNNNNNNN
*
35372779 GAAGCAGAGGCTACAGCGAGG
1 GAAGCAGAGGCTACAACGAGG
* * *
35372800 GAAGTAGAGGCTGCAATGAGG
1 GAAGCAGAGGCTACAACGAGG
35372821 GAAGCAGAG
1 GAAGCAGAG
35372830 CAGCGTAGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.14, G:0.43, T:0.08
Consensus pattern (21 bp):
GAAGCAGAGGCTACAACGAGG
Found at i:35373248 original size:43 final size:43
Alignment explanation
Indices: 35373177--35373268 Score: 114
Period size: 43 Copynumber: 2.1 Consensus size: 43
35373167 AAAAACACCA
* * * **
35373177 CTAAAGGTCATGGTCTTTTGCGGTGTTTG-TGGGAAAAGCGCCG
1 CTAAAGATCAGGGTCTTTAGCGACGTTTGTTGGG-AAAGCGCCG
*
35373220 CTAAAGATCAGGGTCTTTAGCGACGTTTGTTTGGAAAGCGCCG
1 CTAAAGATCAGGGTCTTTAGCGACGTTTGTTGGGAAAGCGCCG
35373263 CTAAAG
1 CTAAAG
35373269 GTTGTCGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 39 0.93
44 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (43 bp):
CTAAAGATCAGGGTCTTTAGCGACGTTTGTTGGGAAAGCGCCG
Found at i:35379961 original size:3 final size:3
Alignment explanation
Indices: 35379953--35379977 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35379943 TAAAATGGAC
35379953 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
35379978 TATATATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:35380076 original size:43 final size:43
Alignment explanation
Indices: 35380029--35380354 Score: 388
Period size: 43 Copynumber: 7.6 Consensus size: 43
35380019 GGGTTATTAC
* * *
35380029 AAAGGTTATTGTCTTTAGCGGCGTTTCTCGGATAAGCGCCGCT
1 AAAGGTCATGGTCTTTAGCGGCGTTTGTCGGATAAGCGCCGCT
* * *
35380072 AAAGGTCATGGTCTTTAGCGGCGTTTGTTGGAAAAGCGCTGCT
1 AAAGGTCATGGTCTTTAGCGGCGTTTGTCGGATAAGCGCCGCT
* *
35380115 AAAGGTCATTGTCTTTAGCGGCGTTTGTCGGATAAGTGCCGCT
1 AAAGGTCATGGTCTTTAGCGGCGTTTGTCGGATAAGCGCCGCT
*
35380158 AAAGGTCATGGTC-TTATCCGGCGTTTGTCGGATAAGCGCCGCT
1 AAAGGTCATGGTCTTTA-GCGGCGTTTGTCGGATAAGCGCCGCT
* * * *
35380201 AAAGGTCTTGGTCTTTAGCGGTGTTTGTCGGAAAAGTGCCGCT
1 AAAGGTCATGGTCTTTAGCGGCGTTTGTCGGATAAGCGCCGCT
* * * *
35380244 AAAGGTCATAGCCTTTAGCGGCGTTTGTGGGA-AAGCGCCACT
1 AAAGGTCATGGTCTTTAGCGGCGTTTGTCGGATAAGCGCCGCT
** ** * * *
35380286 AAAGACCATGACCTTTAGCGGCGTTTGTGGTGA-AAGAGCTGCT
1 AAAGGTCATGGTCTTTAGCGGCGTTTGTCG-GATAAGCGCCGCT
*
35380329 AAAGGTCTTGGTCTTTAGCGGCGTTT
1 AAAGGTCATGGTCTTTAGCGGCGTTT
35380355 ATTTCTAAAA
Statistics
Matches: 242, Mismatches: 38, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
42 37 0.15
43 202 0.83
44 3 0.01
ACGTcount: A:0.20, C:0.19, G:0.31, T:0.30
Consensus pattern (43 bp):
AAAGGTCATGGTCTTTAGCGGCGTTTGTCGGATAAGCGCCGCT
Found at i:35390721 original size:19 final size:18
Alignment explanation
Indices: 35390699--35390741 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
35390689 CATTAATTTT
*
35390699 TTATTAAAAATCTAATTAG
1 TTATTAAAAATAT-ATTAG
* *
35390718 TTATAAAAAATATTTTAG
1 TTATTAAAAATATATTAG
35390736 TTATTA
1 TTATTA
35390742 TTTAATTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (18 bp):
TTATTAAAAATATATTAG
Found at i:35392405 original size:15 final size:16
Alignment explanation
Indices: 35392385--35392417 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
35392375 TATATATTAA
*
35392385 TTGTATGTTAA-ATAT
1 TTGTATATTAATATAT
35392400 TTGTATATTAATATAT
1 TTGTATATTAATATAT
35392416 TT
1 TT
35392418 AATTTAACGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (16 bp):
TTGTATATTAATATAT
Found at i:35392648 original size:166 final size:175
Alignment explanation
Indices: 35392468--35392791 Score: 495
Period size: 179 Copynumber: 1.9 Consensus size: 175
35392458 AGTTCATCAC
* * *
35392468 CCAAAATGTGGCTTGGATTCGAGTCGTGTTACATTTAGGATTTACTCTCCTCTTAT-ATT-TC-A
1 CCAAAATGTGGCTTGGATTCAAGTCGTGTTACATTAAGGATTTACTCTCCTCTTATAATTCACAA
* * *
35392530 T-TA-A-AT-TA-A-ATATATATTTAATTTAATGAAAGTTGCAATTTTAAATTATTAATATTAAT
66 TATATATATATATATATATATATTTAATTTAACGAAAGTTGCAATTTTAAATTATTAATAGTAAG
35392589 TGTATGTTATTTAACAAAAGTTGTACTGGCTTGATGATCAGGGAG
131 TGTATGTTATTTAACAAAAGTTGTACTGGCTTGATGATCAGGGAG
35392634 CCAAAATGTGGCTTGGATTCAAGTCGTGTTACATTAAGGATTTACTCTCCTCTTATAATTCACCA
1 CCAAAATGTGGCTTGGATTCAAGTCGTGTTACATTAAGGATTTACTCTCCTCTTATAATT---CA
35392699 CAAATATATATATATATATATATATATTTAATTTAACGAAAGTTGCAATTTTAAATTATTAATAG
63 C-AATATATATATATATATATATATATTTAATTTAACGAAAGTTGCAATTTTAAATTATTAATAG
35392764 TAAGTGTATGTTATTTAACAAAAGTTGT
127 TAAGTGTATGTTATTTAACAAAAGTTGT
35392792 GTAAGGCGAT
Statistics
Matches: 139, Mismatches: 6, Indels: 13
0.88 0.04 0.08
Matches are distributed among these distances:
166 54 0.39
167 3 0.02
171 1 0.01
173 2 0.01
174 2 0.01
175 1 0.01
176 2 0.01
177 2 0.01
178 1 0.01
179 71 0.51
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.41
Consensus pattern (175 bp):
CCAAAATGTGGCTTGGATTCAAGTCGTGTTACATTAAGGATTTACTCTCCTCTTATAATTCACAA
TATATATATATATATATATATATTTAATTTAACGAAAGTTGCAATTTTAAATTATTAATAGTAAG
TGTATGTTATTTAACAAAAGTTGTACTGGCTTGATGATCAGGGAG
Found at i:35394458 original size:19 final size:18
Alignment explanation
Indices: 35394436--35394479 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
35394426 TTGAATTAGA
35394436 AATTAGTTGTT-GAATGTT
1 AATTAGTTGTTCG-ATGTT
*
35394454 GAATTAATTGTTCGATGTT
1 -AATTAGTTGTTCGATGTT
35394473 AATTAGT
1 AATTAGT
35394480 ATGAATTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 6 0.27
19 15 0.68
20 1 0.05
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.48
Consensus pattern (18 bp):
AATTAGTTGTTCGATGTT
Found at i:35396905 original size:25 final size:25
Alignment explanation
Indices: 35396874--35396943 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
35396864 CGTTCTGACC
35396874 CACAGCTCGTGTGAGCATACCGATT
1 CACAGCTCGTGTGAGCATACCGATT
* * *
35396899 TACAGCTTGTGTGAGCATATCGATT
1 CACAGCTCGTGTGAGCATACCGATT
35396924 CACAGCTCGTGTGAGCATAC
1 CACAGCTCGTGTGAGCATAC
35396944 ATGTACAAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (25 bp):
CACAGCTCGTGTGAGCATACCGATT
Found at i:35404465 original size:25 final size:25
Alignment explanation
Indices: 35404401--35404542 Score: 158
Period size: 25 Copynumber: 5.6 Consensus size: 25
35404391 CAACCCATAG
* * * *
35404401 CTCGTTTGAGCAGACCCATTTTCACAG
1 CTCGTGTGAGCATACCGA-TTT-ACAA
*
35404428 CTCGTGTGAGCATACCAATTTACAA
1 CTCGTGTGAGCATACCGATTTACAA
*
35404453 CTCGTGTGGGCATACCGATTTACAA
1 CTCGTGTGAGCATACCGATTTACAA
* * *
35404478 CTCATGTGAGGATACCGATTTACAG
1 CTCGTGTGAGCATACCGATTTACAA
* * *
35404503 CTCATGTGAGCATACCGATTTATAG
1 CTCGTGTGAGCATACCGATTTACAA
35404528 CTCGTGTGAGCATAC
1 CTCGTGTGAGCATAC
35404543 ATGTCCAGGA
Statistics
Matches: 102, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
25 84 0.82
26 3 0.03
27 15 0.15
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (25 bp):
CTCGTGTGAGCATACCGATTTACAA
Found at i:35409382 original size:16 final size:16
Alignment explanation
Indices: 35409358--35409406 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
35409348 TTCGCTGTAT
35409358 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
* *
35409374 TGGATTAGAGGTGTAA
1 TGGAATAGAGGCGTAA
35409390 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
35409406 T
1 T
35409407 AGCAAATCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.35, C:0.04, G:0.37, T:0.24
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:35409436 original size:45 final size:44
Alignment explanation
Indices: 35409385--35409475 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 44
35409375 GGATTAGAGG
35409385 TGTAATGGAATAGAGGCGTAATAGCAAATCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATC-ATGTGTTTGGTTGAA
* *
35409430 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAA
35409474 TG
1 TG
35409476 GAATAGAGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 18 0.42
45 24 0.56
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAA
Found at i:35409657 original size:16 final size:16
Alignment explanation
Indices: 35409620--35409661 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
35409610 TTAATCATAT
*
35409620 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
35409636 TT-AAATATATTATAA
1 TTAAAATATATTATAA
35409651 TTAAAATATAT
1 TTAAAATATAT
35409662 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:35409668 original size:14 final size:15
Alignment explanation
Indices: 35409629--35409670 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
35409619 TTTAAACATA
*
35409629 ATTATTATTAAATAT
1 ATTATAATTAAATAT
35409644 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
35409658 A-TATAATTTAATA
1 ATTATAATTAAATA
35409671 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:35409767 original size:15 final size:16
Alignment explanation
Indices: 35409735--35409781 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 16
35409725 TACTATAAAA
*
35409735 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
35409751 TATTATTAAAA-ATAT
1 TATAATTAAAATATAT
35409766 TATAATTAAAATATAT
1 TATAATTAAAATATAT
35409782 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 1 0.04
15 17 0.65
16 8 0.31
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:35409853 original size:61 final size:61
Alignment explanation
Indices: 35409668--35409854 Score: 158
Period size: 61 Copynumber: 3.1 Consensus size: 61
35409658 ATATAATTTA
* * * *
35409668 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAAGCATAAGATATGATACT
1 ATAAAATTCTTAATAATTAATATTCTAATATGAATTTACTCAAATCATAATATATGATACT
* * * * *
35409729 ATAAAATATAATTTAACATAATTATTA-T-TAA-A--AATATTA-T--AATTAAAATATATAAT-
1 ATAAAAT-T--CTT-A-ATAATTAATATTCTAATATGAAT-TTACTCAAATCATAATATATGATA
*
35409785 TT
60 CT
35409787 AATAAAATTCTTAATAATTAATATTCTAATATGAATTTACTCAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATTAATATTCTAATATGAATTTACTCAAATCATAATATATGATACT
35409849 ATAAAA
1 ATAAAA
35409855 GATAATTTAA
Statistics
Matches: 94, Mismatches: 16, Indels: 32
0.66 0.11 0.23
Matches are distributed among these distances:
54 9 0.10
55 2 0.02
56 5 0.05
57 1 0.01
58 5 0.05
59 22 0.23
61 30 0.32
62 5 0.05
63 1 0.01
64 4 0.04
65 2 0.02
66 8 0.09
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (61 bp):
ATAAAATTCTTAATAATTAATATTCTAATATGAATTTACTCAAATCATAATATATGATACT
Found at i:35409901 original size:18 final size:17
Alignment explanation
Indices: 35409880--35409914 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35409870 TTATTATTAA
*
35409880 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
35409898 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
35409915 TTAAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:35409925 original size:54 final size:53
Alignment explanation
Indices: 35409858--35410016 Score: 152
Period size: 54 Copynumber: 3.1 Consensus size: 53
35409848 TATAAAAGAT
* *
35409858 AATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAA
1 AATTTAAAATAATTATTATTAAATATAATTTAATTAAAATATATAATTT-ATAA
* * * * * * *
35409912 AATTTAAAATAATTATAACT-AATAAAATTT-CTT---ATAT-GAATTTGTAT
1 AATTTAAAATAATTATTATTAAATATAATTTAATTAAAATATATAATTTATAA
*
35409959 AATTTAAAATAATTATTATTACATATAATTTAA-TAATAATATATAATTTCATAA
1 AATTTAAAATAATTATTATTAAATATAATTTAATTAA-AATATATAATTT-ATAA
35410013 AATT
1 AATT
35410017 ATTGATAATA
Statistics
Matches: 80, Mismatches: 17, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
47 20 0.25
48 14 0.17
49 4 0.05
52 6 0.08
53 13 0.16
54 23 0.29
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.45
Consensus pattern (53 bp):
AATTTAAAATAATTATTATTAAATATAATTTAATTAAAATATATAATTTATAA
Found at i:35409926 original size:120 final size:120
Alignment explanation
Indices: 35409618--35409915 Score: 524
Period size: 120 Copynumber: 2.5 Consensus size: 120
35409608 ATTTAATCAT
35409618 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* * *
35409683 ATCAATATTCTTATATGAATTTACTCAAAGCATAAGATATGATACTATAAAATATA
65 ATTAATATTCTAATATGAATTTACTCAAAGCATAAGATATGATACTATAAAAGATA
*
35409739 ATTTAACATAATTATTATTAAAAATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
* *
35409804 TTAATATTCTAATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 TTAATATTCTAATATGAATTTACTCAAAGCATAAGATATGATACTATAAAAGATA
*
35409859 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
35409916 TAAAATAATT
Statistics
Matches: 169, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
120 165 0.98
121 4 0.02
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.42
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
TTAATATTCTAATATGAATTTACTCAAAGCATAAGATATGATACTATAAAAGATA
Found at i:35409963 original size:47 final size:46
Alignment explanation
Indices: 35409897--35410064 Score: 159
Period size: 47 Copynumber: 3.7 Consensus size: 46
35409887 TTAATTAAAA
*
35409897 TATAT-AATTTAATAAAATTTAAAATAATTATAACTAATAAAATTTCT
1 TATATGAATTT-ATATAATTTAAAATAATTATAA-TAATAAAATTTCT
* * * **
35409944 TATATGAATTTGTATAATTTAAAATAATTATTATTACATATAATTTAA
1 TATATGAATTTATATAATTTAAAATAATTA-TAATA-ATAAAATTTCT
* * *
35409992 TA-AT-AA--TATATAATTTCATAA-AATTATTGATAATAAATTTTCT
1 TATATGAATTTATATAATTT-AAAATAATTA-TAATAATAAAATTTCT
35410035 TATATGAATTTATATAATTTAAAATAATTA
1 TATATGAATTTATATAATTTAAAATAATTA
35410065 ATATTAAATA
Statistics
Matches: 97, Mismatches: 15, Indels: 18
0.75 0.12 0.14
Matches are distributed among these distances:
43 9 0.09
44 20 0.21
45 5 0.05
46 5 0.05
47 41 0.42
48 17 0.18
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATAATAATAAAATTTCT
Found at i:35409987 original size:26 final size:28
Alignment explanation
Indices: 35409956--35410016 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
35409946 TATGAATTTG
*
35409956 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
35409982 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
35410010 TAAAATT
1 TATAATT
35410017 ATTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:35409995 original size:91 final size:91
Alignment explanation
Indices: 35409912--35410085 Score: 253
Period size: 91 Copynumber: 1.9 Consensus size: 91
35409902 AATTTAATAA
* *
35409912 AATTT-AAAATAATTA-TAACTAATAAAATTTCTTATATGAATTTGTATAATTTAAAATAATTAT
1 AATTTCAAAA-AATTATTAA-TAATAAAATTTCTTATATGAATTTATATAATTTAAAATAATTAA
*
35409975 TATTACATATAATTTAATAATAATATAT
64 TATTAAATATAATTTAATAATAATATAT
* * *
35410003 AATTTCATAAAATTATTGATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATA
1 AATTTCAAAAAATTATTAATAATAAAATTTCTTATATGAATTTATATAATTTAAAATAATTAATA
*
35410068 TTAAATATAATTTCATAA
66 TTAAATATAATTTAATAA
35410086 AATTGATTCT
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
91 69 0.93
92 5 0.07
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.45
Consensus pattern (91 bp):
AATTTCAAAAAATTATTAATAATAAAATTTCTTATATGAATTTATATAATTTAAAATAATTAATA
TTAAATATAATTTAATAATAATATAT
Found at i:35414294 original size:25 final size:24
Alignment explanation
Indices: 35414238--35414391 Score: 157
Period size: 25 Copynumber: 6.2 Consensus size: 24
35414228 AGACACACCA
*
35414238 CAGCTCGTATGAGCTTACCGATTT
1 CAGCTCATATGAGCTTACCGATTT
*
35414262 CAGCTCATGA-GAGGTTACCGATTCT
1 CAGCTCAT-ATGAGCTTACCGATT-T
35414287 CAGCTCATATGAGCTTACCGATTAT
1 CAGCTCATATGAGCTTACCGATT-T
* *
35414312 TAGCTCATATGAGCTTACCGTTTGT
1 CAGCTCATATGAGCTTACCGATT-T
* *
35414337 TAGCTCGTATGAGCTTACCGATTGT
1 CAGCTCATATGAGCTTACCGATT-T
* ** *
35414362 AAGCTTGTATGAGCTTACCAATTT
1 CAGCTCATATGAGCTTACCGATTT
35414386 CCAGCT
1 -CAGCT
35414392 TGTGAGAGCA
Statistics
Matches: 113, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
24 21 0.19
25 92 0.81
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (24 bp):
CAGCTCATATGAGCTTACCGATTT
Found at i:35414373 original size:75 final size:74
Alignment explanation
Indices: 35414239--35414380 Score: 178
Period size: 75 Copynumber: 1.9 Consensus size: 74
35414229 GACACACCAC
* * *
35414239 AGCTCGTATGAGCTTACCGATTTCAGCTCATGAGAGGTTACCGATTCTCAGCTCATATGAGCTTA
1 AGCTCATATGAGCTTACCGATTTCAGCTCATGAGAGCTTACCGATTCTAAGCTCATATGAGCTTA
35414304 CCGATTATT
66 CCGATTATT
* * * * **
35414313 AGCTCATATGAGCTTACCGTTTGTTAGCTCGT-ATGAGCTTACCGATTGTAAGCTTGTATGAGCT
1 AGCTCATATGAGCTTACCGATT-TCAGCTCATGA-GAGCTTACCGATTCTAAGCTCATATGAGCT
35414377 TACC
64 TACC
35414381 AATTTCCAGC
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
74 21 0.37
75 36 0.63
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (74 bp):
AGCTCATATGAGCTTACCGATTTCAGCTCATGAGAGCTTACCGATTCTAAGCTCATATGAGCTTA
CCGATTATT
Found at i:35418590 original size:19 final size:20
Alignment explanation
Indices: 35418566--35418607 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
35418556 AGGGCATTGA
**
35418566 CTTCTTAGGTTTG-TTCCTT
1 CTTCTTAGGCCTGCTTCCTT
35418585 CTTCTTAGGCCTGCTTCCTT
1 CTTCTTAGGCCTGCTTCCTT
35418605 CTT
1 CTT
35418608 TGTATGGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.05, C:0.29, G:0.14, T:0.52
Consensus pattern (20 bp):
CTTCTTAGGCCTGCTTCCTT
Found at i:35421764 original size:42 final size:42
Alignment explanation
Indices: 35421680--35421856 Score: 250
Period size: 42 Copynumber: 4.2 Consensus size: 42
35421670 ACCGACACTT
* *
35421680 AGCCTGCTAGACATATAA-TCTGA-AATGTTTCACTGGCATTA
1 AGCCTGCTAGACGTA-AAGTCTGATATTGTTTCACTGGCATTA
*
35421721 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACTGGAATTA
1 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACTGGCATTA
* * *
35421763 AGCCTGCTAGACGTAAAGTCTGAAATTATTTCACCGGCATTA
1 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACTGGCATTA
* *
35421805 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACTGTCAATA
1 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACTGGCATTA
*
35421847 AGCTTGCTAG
1 AGCCTGCTAG
35421857 GCGTTAAGCC
Statistics
Matches: 121, Mismatches: 13, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
40 2 0.02
41 19 0.16
42 100 0.83
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (42 bp):
AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACTGGCATTA
Found at i:35424995 original size:26 final size:26
Alignment explanation
Indices: 35424959--35425024 Score: 105
Period size: 26 Copynumber: 2.5 Consensus size: 26
35424949 TAAATTTTTC
35424959 AAGTATGTTTTAATCATTTCTTCCAT
1 AAGTATGTTTTAATCATTTCTTCCAT
* *
35424985 AAGTATGTTTTTATCATTTCTTTCAT
1 AAGTATGTTTTAATCATTTCTTCCAT
*
35425011 AAGTTTGTTTTAAT
1 AAGTATGTTTTAAT
35425025 AAATGAATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.55
Consensus pattern (26 bp):
AAGTATGTTTTAATCATTTCTTCCAT
Found at i:35437421 original size:3 final size:3
Alignment explanation
Indices: 35437413--35437443 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
35437403 CATAAAGAAT
35437413 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
35437444 ATGAAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:35438983 original size:42 final size:42
Alignment explanation
Indices: 35438877--35438983 Score: 110
Period size: 42 Copynumber: 2.5 Consensus size: 42
35438867 GGTAAGGCAT
* ** * *
35438877 ATGGGTGTGTGTCTAGACCGTGTGAGTCACCTAGACAAGGAC
1 ATGGGTGTGTGTCCAGGTCGTGTGAGCCACCGAGACAAGGAC
* **
35438919 ATAGGCATGTGTCCA-GTCCGTGTGAGCCACACGAG-CAAGGAC
1 ATGGGTGTGTGTCCAGGT-CGTGTGAGCCAC-CGAGACAAGGAC
35438961 ATGGGTGTGTGTCCAGGTCGTGT
1 ATGGGTGTGTGTCCAGGTCGTGT
35438984 CACATATAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
42 46 0.90
43 5 0.10
ACGTcount: A:0.21, C:0.21, G:0.35, T:0.23
Consensus pattern (42 bp):
ATGGGTGTGTGTCCAGGTCGTGTGAGCCACCGAGACAAGGAC
Found at i:35445672 original size:42 final size:42
Alignment explanation
Indices: 35445598--35445709 Score: 118
Period size: 42 Copynumber: 2.7 Consensus size: 42
35445588 ATACGACTAG
* * ** * *
35445598 GGACATGGGCGTGTGCCCAAGCTGTGTCAGTCATAC-GAAAAA
1 GGACATGGGCGTGTGTCCAGGCCATGTGAGTCACACTG-AAAA
**
35445640 GGACATGGGCGTGTGTCCAGGCCATGTGAGTCACACTGGCAA
1 GGACATGGGCGTGTGTCCAGGCCATGTGAGTCACACTGAAAA
* *
35445682 GGACATAGGCGTGTGTCCAGGTCATGTG
1 GGACATGGGCGTGTGTCCAGGCCATGTG
35445710 GCATATAAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 58 0.98
43 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.35, T:0.21
Consensus pattern (42 bp):
GGACATGGGCGTGTGTCCAGGCCATGTGAGTCACACTGAAAA
Found at i:35459464 original size:31 final size:30
Alignment explanation
Indices: 35459423--35459481 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
35459413 AGAATGAAAA
*
35459423 AAAAACAAAGTTTAAAACCT-AAGAGAAAGG
1 AAAAACAAAGTCTAAAA-CTAAAGAGAAAGG
35459453 AAAAACTAAAGTCTAAAACTAAAGAGAAA
1 AAAAAC-AAAGTCTAAAACTAAAGAGAAA
35459482 ATTATACAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.63, C:0.10, G:0.14, T:0.14
Consensus pattern (30 bp):
AAAAACAAAGTCTAAAACTAAAGAGAAAGG
Found at i:35459965 original size:20 final size:21
Alignment explanation
Indices: 35459940--35459982 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
35459930 CAACTTACAC
*
35459940 ATTTATTAAAAT-TAACTAAA
1 ATTTATCAAAATATAACTAAA
*
35459960 ATTTATCAAAATATAATTAAA
1 ATTTATCAAAATATAACTAAA
35459981 AT
1 AT
35459983 GCAACAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTTATCAAAATATAACTAAA
Found at i:35460627 original size:22 final size:22
Alignment explanation
Indices: 35460596--35460640 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
35460586 CTCTCCACAT
35460596 AGGAGACACAACATAATATAAC
1 AGGAGACACAACATAATATAAC
*
35460618 AGGAGTCACAACATAATATAAC
1 AGGAGACACAACATAATATAAC
35460640 A
1 A
35460641 ATCATGGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.53, C:0.18, G:0.13, T:0.16
Consensus pattern (22 bp):
AGGAGACACAACATAATATAAC
Found at i:35478704 original size:15 final size:16
Alignment explanation
Indices: 35478684--35478727 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
35478674 GAAGAAAATA
35478684 TTGAGACAA-AAGCTG
1 TTGAGACAAGAAGCTG
*
35478699 TTGAGA-AAGAATCTG
1 TTGAGACAAGAAGCTG
35478714 TTGAGGACAAGAAG
1 TTGA-GACAAGAAG
35478728 TAGCTGATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 2 0.08
15 15 0.62
16 2 0.08
17 5 0.21
ACGTcount: A:0.41, C:0.09, G:0.30, T:0.20
Consensus pattern (16 bp):
TTGAGACAAGAAGCTG
Found at i:35486845 original size:17 final size:17
Alignment explanation
Indices: 35486823--35486856 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
35486813 TTAAGATAAT
35486823 TAAATATAAAATT-TTAA
1 TAAATA-AAAATTATTAA
35486840 TAAATAAAAATTATTAA
1 TAAATAAAAATTATTAA
35486857 ATATTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATAAAAATTATTAA
Found at i:35486857 original size:14 final size:16
Alignment explanation
Indices: 35486821--35486866 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
35486811 TGTTAAGATA
35486821 ATTAAATATAAAATTTT
1 ATTAAATATAAAA-TTT
*
35486838 AATAAATA-AAAA-TT
1 ATTAAATATAAAATTT
*
35486852 ATTAAATATTAAATT
1 ATTAAATATAAAATT
35486867 AAAATAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
14 9 0.38
15 3 0.12
16 5 0.21
17 7 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTAAATATAAAATTT
Found at i:35486864 original size:21 final size:22
Alignment explanation
Indices: 35486840--35486882 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
35486830 AAAATTTTAA
*
35486840 TAAATAAAAATTAT-TAAATAT
1 TAAATAAAAATAATATAAATAT
*
35486861 TAAATTAAAATAATATAAATAT
1 TAAATAAAAATAATATAAATAT
35486883 ATTTTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAATAAAAATAATATAAATAT
Found at i:35487987 original size:31 final size:32
Alignment explanation
Indices: 35487952--35488022 Score: 99
Period size: 31 Copynumber: 2.2 Consensus size: 32
35487942 TAAAAGGGTT
*
35487952 TATTAATTTCATGTAAATATCTTTTATA-TTA
1 TATTAATTTAATGTAAATATCTTTTATACTTA
* *
35487983 TATTAATTTAATGTAAATATTTTTTGTACTTA
1 TATTAATTTAATGTAAATATCTTTTATACTTA
35488015 TCATTAAT
1 T-ATTAAT
35488023 CACTATTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 25 0.71
32 4 0.11
33 6 0.17
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (32 bp):
TATTAATTTAATGTAAATATCTTTTATACTTA
Found at i:35490153 original size:23 final size:23
Alignment explanation
Indices: 35490118--35490161 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
35490108 TTATGCATAT
35490118 TCATTTGAGTATTTTAAATATTA
1 TCATTTGAGTATTTTAAATATTA
35490141 TCATATTGA-TATTTTAAATAT
1 TCAT-TTGAGTATTTTAAATAT
35490162 AATATTAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (23 bp):
TCATTTGAGTATTTTAAATATTA
Found at i:35492749 original size:38 final size:39
Alignment explanation
Indices: 35492697--35492830 Score: 96
Period size: 38 Copynumber: 3.4 Consensus size: 39
35492687 AATATAAATA
*
35492697 TTTTCATTATATTATAACTAATGGCAATATTTATTTCAC
1 TTTTCATTAAATTATAACTAATGGCAATATTTATTTCAC
** * * ** *
35492736 TTTT-ATTAAATTATGTCATAAT--CTAGTTTTTTAATATAAATA
1 TTTTCATTAAATTATAAC-TAATGGC-A-ATATTT-AT-TTCA-C
*
35492778 TTTTCATTATATTATAACTAATGGCAATATTTATTTCAC
1 TTTTCATTAAATTATAACTAATGGCAATATTTATTTCAC
*
35492817 TTTT-AATAAATTAT
1 TTTTCATTAAATTAT
35492831 TTTTTATTAT
Statistics
Matches: 68, Mismatches: 18, Indels: 19
0.65 0.17 0.18
Matches are distributed among these distances:
37 1 0.01
38 19 0.28
39 16 0.24
40 4 0.06
41 4 0.06
42 12 0.18
43 11 0.16
44 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (39 bp):
TTTTCATTAAATTATAACTAATGGCAATATTTATTTCAC
Found at i:35492758 original size:81 final size:81
Alignment explanation
Indices: 35492668--35492830 Score: 317
Period size: 81 Copynumber: 2.0 Consensus size: 81
35492658 GATGAGTATG
35492668 TGTCATAATCTAGTTTTTTAATATAAATATTTTCATTATATTATAACTAATGGCAATATTTATTT
1 TGTCATAATCTAGTTTTTTAATATAAATATTTTCATTATATTATAACTAATGGCAATATTTATTT
*
35492733 CACTTTTATTAAATTA
66 CACTTTTAATAAATTA
35492749 TGTCATAATCTAGTTTTTTAATATAAATATTTTCATTATATTATAACTAATGGCAATATTTATTT
1 TGTCATAATCTAGTTTTTTAATATAAATATTTTCATTATATTATAACTAATGGCAATATTTATTT
35492814 CACTTTTAATAAATTA
66 CACTTTTAATAAATTA
35492830 T
1 T
35492831 TTTTTATTAT
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (81 bp):
TGTCATAATCTAGTTTTTTAATATAAATATTTTCATTATATTATAACTAATGGCAATATTTATTT
CACTTTTAATAAATTA
Found at i:35503574 original size:56 final size:50
Alignment explanation
Indices: 35503478--35503774 Score: 231
Period size: 50 Copynumber: 5.8 Consensus size: 50
35503468 ATTTGGGTAA
* * * * *
35503478 AGAGATCCCATGTAAGACCATGTCTGGGACATGACATTGGCATCATTGTGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C----CGA-GATG
*
35503534 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * *
35503584 AGAGGTCTCATATAAGACCATGTCTGGGACATGGAGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * * * * *
35503634 AGAGGTCTCC-CGTAAGACCATGTATGGGACATGACATGGGCACCGATATG
1 AGAGGTC-CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * * * * * *
35503684 AGAACTCCCATGCAAGACCATATTTGGGATATGGCATTGGCA--GTACAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCG-AGATG
* ** * * *
35503733 AAACATCCCGTGTAAGACCATGTCTGAGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
35503775 TGTTATTATC
Statistics
Matches: 198, Mismatches: 40, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
48 1 0.01
49 37 0.19
50 118 0.60
51 3 0.02
55 1 0.01
56 38 0.19
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:35503586 original size:50 final size:50
Alignment explanation
Indices: 35503478--35503725 Score: 239
Period size: 50 Copynumber: 4.8 Consensus size: 50
35503468 ATTTGGGTAA
* * * * *
35503478 AGAGATCCCATGTAAGACCATGTCTGGGACATGACATTGGCATCATTGTGATTATG
1 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCA-C----CGA-GATG
*
35503534 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGATG
* * *
35503584 AGAGGTCTCATATAAGACCATGTCTGGGACATGG-AGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCA-TTGGCACCGAGATG
* * * * *
35503634 AGAGGTCTCC-CGTAAGACCATGTATGGGACATGACATGGGCACCGATATG
1 AGAGGTC-CCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGATG
** * * *
35503684 AGAACTCCCATGCAAGACCATATTTGGGATATGGCATTGGCA
1 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCA
35503726 GTACAAGAAA
Statistics
Matches: 162, Mismatches: 26, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
49 2 0.01
50 117 0.72
51 4 0.02
55 1 0.01
56 38 0.23
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGATG
Found at i:35505565 original size:25 final size:22
Alignment explanation
Indices: 35505524--35505587 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 22
35505514 AGCTTGGGGC
*
35505524 AGAAA-AAATAAAAAGGAAAGAGA
1 AGAAAGAAAGAAAAAGG-AAGA-A
35505547 AGAAAGAAAGAAAGAAGGAAGAA
1 AGAAAGAAAGAAA-AAGGAAGAA
35505570 AGAAAATGAAAGAAAAAG
1 AG-AAA-GAAAGAAAAAG
35505588 AATGAAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
23 8 0.22
24 16 0.44
25 12 0.33
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03
Consensus pattern (22 bp):
AGAAAGAAAGAAAAAGGAAGAA
Found at i:35505568 original size:15 final size:15
Alignment explanation
Indices: 35505544--35505584 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
35505534 AAAAGGAAAG
35505544 AGAAGAAAGAAAGAA
1 AGAAGAAAGAAAGAA
*
35505559 AGAAGGAAGAAAGAA
1 AGAAGAAAGAAAGAA
*
35505574 A-ATGAAAGAAA
1 AGAAGAAAGAAA
35505585 AAGAATGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (15 bp):
AGAAGAAAGAAAGAA
Found at i:35505596 original size:10 final size:10
Alignment explanation
Indices: 35505533--35505596 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
35505523 CAGAAAAAAT
35505533 AAAAAGGAAAG
1 AAAAA-GAAAG
*
35505544 -AGAAGAAAG
1 AAAAAGAAAG
35505553 --AAAGAAAG
1 AAAAAGAAAG
*
35505561 AAGGAAGAAAG
1 AA-AAAGAAAG
*
35505572 AAAATGAAAG
1 AAAAAGAAAG
*
35505582 AAAAAGAATG
1 AAAAAGAAAG
35505592 AAAAA
1 AAAAA
35505597 TTTCCATAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
8 7 0.16
9 5 0.12
10 22 0.51
11 9 0.21
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:35507652 original size:40 final size:40
Alignment explanation
Indices: 35507586--35507687 Score: 161
Period size: 40 Copynumber: 2.5 Consensus size: 40
35507576 ACCAGTGTTC
*
35507586 CATTTCATATATCTATT-TTCATATAACCGATTCATATAAA
1 CATTTCATATATC-ATTCTTCACATAACCGATTCATATAAA
*
35507626 CATTTCATATATCATTCTTCACATAACCGATTCATATAAC
1 CATTTCATATATCATTCTTCACATAACCGATTCATATAAA
*
35507666 CATTTCATAAATCATTCTTCAC
1 CATTTCATATATCATTCTTCAC
35507688 CCGATGAACC
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
39 3 0.05
40 55 0.95
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (40 bp):
CATTTCATATATCATTCTTCACATAACCGATTCATATAAA
Found at i:35507672 original size:13 final size:13
Alignment explanation
Indices: 35507585--35507674 Score: 69
Period size: 13 Copynumber: 6.8 Consensus size: 13
35507575 AACCAGTGTT
*
35507585 CCATTTCATATAT
1 CCATTTCATATAA
*
35507598 CTATTTTCATATAA
1 CCA-TTTCATATAA
35507612 CCGA-TTCATATAA
1 CC-ATTTCATATAA
*
35507625 ACATTTCATAT-A
1 CCATTTCATATAA
* *
35507637 TCATTCTTCACATAA
1 CCA-T-TTCATATAA
35507652 CCGA-TTCATATAA
1 CC-ATTTCATATAA
35507665 CCATTTCATA
1 CCATTTCATA
35507675 AATCATTCTT
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
12 5 0.08
13 36 0.59
14 16 0.26
15 3 0.05
16 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.02, T:0.40
Consensus pattern (13 bp):
CCATTTCATATAA
Found at i:35509805 original size:17 final size:17
Alignment explanation
Indices: 35509783--35509816 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
35509773 GTAGTCAATC
35509783 GGAAGCTTGTTCGAGTT
1 GGAAGCTTGTTCGAGTT
*
35509800 GGAAGCTTGTTGGAGTT
1 GGAAGCTTGTTCGAGTT
35509817 ATATCACACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.09, G:0.38, T:0.35
Consensus pattern (17 bp):
GGAAGCTTGTTCGAGTT
Found at i:35510012 original size:71 final size:71
Alignment explanation
Indices: 35509932--35510073 Score: 266
Period size: 71 Copynumber: 2.0 Consensus size: 71
35509922 CCAATGTGTT
* *
35509932 TTGACTTGAGAATTTGGTATTTTGAATGTTTGAAATGGTTGAATACATTTTTATGTGTATGTGGC
1 TTGACTTGAGAATTTGGTATTTTGAATGTTTGAAATGGTTGAATACATTGTTATGTGTATATGGC
35509997 CTTATA
66 CTTATA
35510003 TTGACTTGAGAATTTGGTATTTTGAATGTTTGAAATGGTTGAATACATTGTTATGTGTATATGGC
1 TTGACTTGAGAATTTGGTATTTTGAATGTTTGAAATGGTTGAATACATTGTTATGTGTATATGGC
35510068 CTTATA
66 CTTATA
35510074 ATGGTTGAAT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.46
Consensus pattern (71 bp):
TTGACTTGAGAATTTGGTATTTTGAATGTTTGAAATGGTTGAATACATTGTTATGTGTATATGGC
CTTATA
Found at i:35512246 original size:13 final size:13
Alignment explanation
Indices: 35512228--35512259 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
35512218 TTGACTCGTA
35512228 AATATTAAATAAT
1 AATATTAAATAAT
35512241 AATATTAAATAAT
1 AATATTAAATAAT
35512254 AATATT
1 AATATT
35512260 TACGGGCTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AATATTAAATAAT
Found at i:35521136 original size:40 final size:39
Alignment explanation
Indices: 35521075--35521208 Score: 141
Period size: 40 Copynumber: 3.5 Consensus size: 39
35521065 TTTATCAGTC
* * * *
35521075 TATCTGACTAGTGCAGAGCACACCATTATATCTGTCAGTT
1 TATCTGACTAGCGCTGGGCACA-CATTATATCTGTCAATT
* *
35521115 TATCCGACTAGCGCTGGGCACA-ACT-T-TC-GTCAATT
1 TATCTGACTAGCGCTGGGCACACATTATATCTGTCAATT
* * *
35521150 TATCTGACTAGTGCTGGGCACAACATTATATTTTTCAATT
1 TATCTGACTAGCGCTGGGCAC-ACATTATATCTGTCAATT
35521190 TATCTGACTAGCGCTGGGC
1 TATCTGACTAGCGCTGGGC
35521209 GCAAATCTTC
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
35 25 0.32
36 3 0.04
37 3 0.04
38 3 0.04
39 1 0.01
40 42 0.55
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (39 bp):
TATCTGACTAGCGCTGGGCACACATTATATCTGTCAATT
Found at i:35521159 original size:35 final size:36
Alignment explanation
Indices: 35521108--35521242 Score: 119
Period size: 40 Copynumber: 3.7 Consensus size: 36
35521098 CATTATATCT
* *
35521108 GTCAGTTTATCCGACTAGCGCTGGGCACAACT-TTC
1 GTCAATTTATCTGACTAGCGCTGGGCACAACTATTC
* *
35521143 GTCAATTTATCTGACTAGTGCTGGGCACAACATTATATTT
1 GTCAATTTATCTGACTAGCGCTGGGCACAAC----TATTC
* * * *
35521183 TTCAATTTATCTGACTAGCGCTGGGCGCAAATCTTC
1 GTCAATTTATCTGACTAGCGCTGGGCACAACTATTC
* * * *
35521219 ATCAGTTTATTTGACTAGTGCTGG
1 GTCAATTTATCTGACTAGCGCTGG
35521243 TCGCAAATCT
Statistics
Matches: 81, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
35 28 0.35
36 23 0.28
39 1 0.01
40 29 0.36
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (36 bp):
GTCAATTTATCTGACTAGCGCTGGGCACAACTATTC
Found at i:35521192 original size:75 final size:76
Alignment explanation
Indices: 35521075--35521242 Score: 221
Period size: 75 Copynumber: 2.2 Consensus size: 76
35521065 TTTATCAGTC
* * * * *
35521075 TATCTGACTAGTGCAGAGCACACCATTATATCTGTCAGTTTATCCGACTAGCGCTGGGCACAACT
1 TATCTGACTAGTGCTGGGCACAACATTATATCTGTCAATTTATCCGACTAGCGCTGGGCACAAAT
*
35521140 -TTCGTCAATT
66 CTTCATCAATT
* * * *
35521150 TATCTGACTAGTGCTGGGCACAACATTATATTTTTCAATTTATCTGACTAGCGCTGGGCGCAAAT
1 TATCTGACTAGTGCTGGGCACAACATTATATCTGTCAATTTATCCGACTAGCGCTGGGCACAAAT
*
35521215 CTTCATCAGTT
66 CTTCATCAATT
*
35521226 TATTTGACTAGTGCTGG
1 TATCTGACTAGTGCTGG
35521243 TCGCAAATCT
Statistics
Matches: 80, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
75 56 0.70
76 24 0.30
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (76 bp):
TATCTGACTAGTGCTGGGCACAACATTATATCTGTCAATTTATCCGACTAGCGCTGGGCACAAAT
CTTCATCAATT
Found at i:35521262 original size:36 final size:36
Alignment explanation
Indices: 35521109--35521275 Score: 131
Period size: 36 Copynumber: 4.6 Consensus size: 36
35521099 ATTATATCTG
* * * * *
35521109 TCAGTTTATCCGACTAGCGCTGGGCACAACT-TTCG
1 TCAGTTTATCTGACTAGTGCTGGGCGCAAATCTTCA
* * * **
35521144 TCAATTTATCTGACTAGTGCTGGGCACAACATTATATTTT
1 TCAGTTTATCTGACTAGTGCTGGGCGC-A-A--ATCTTCA
* *
35521184 TCAATTTATCTGACTAGCGCTGGGCGCAAATCTTCA
1 TCAGTTTATCTGACTAGTGCTGGGCGCAAATCTTCA
* * **
35521220 TCAGTTTATTTGACTAGTGCTGGTCGCAAATCTTTG
1 TCAGTTTATCTGACTAGTGCTGGGCGCAAATCTTCA
*
35521256 TTAGTTTA-CTGACTAGTGCT
1 TCAGTTTATCTGACTAGTGCT
35521276 AGGCACACTC
Statistics
Matches: 108, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
35 35 0.32
36 42 0.39
37 1 0.01
38 1 0.01
39 2 0.02
40 27 0.25
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.37
Consensus pattern (36 bp):
TCAGTTTATCTGACTAGTGCTGGGCGCAAATCTTCA
Found at i:35525126 original size:14 final size:15
Alignment explanation
Indices: 35525107--35525146 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
35525097 ACTGATAAGA
*
35525107 TCTTGCGA-AGATGT
1 TCTTGCGATAGAAGT
35525121 TCTTGC-ATAGAAGT
1 TCTTGCGATAGAAGT
35525135 TCTTGCG-TAGAA
1 TCTTGCGATAGAA
35525147 ACTTCACAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 1 0.04
14 22 0.96
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (15 bp):
TCTTGCGATAGAAGT
Found at i:35536862 original size:27 final size:27
Alignment explanation
Indices: 35536824--35536877 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
35536814 ATACTAATAA
35536824 AATATAATATCTTAATATTTTGATACT
1 AATATAATATCTTAATATTTTGATACT
35536851 AATATAATATCTTAATATTTTGATACT
1 AATATAATATCTTAATATTTTGATACT
35536878 TATCTTCTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (27 bp):
AATATAATATCTTAATATTTTGATACT
Found at i:35539782 original size:28 final size:28
Alignment explanation
Indices: 35539750--35539835 Score: 84
Period size: 28 Copynumber: 3.1 Consensus size: 28
35539740 CTTTAATCCC
* *
35539750 TAACGGATATTCCACCCAAGATAGTCTT
1 TAACGGACATTCCACTCAAGATAGTCTT
* *
35539778 TAAC-GAGCATTCCACTTAAGATAGTCCT
1 TAACGGA-CATTCCACTCAAGATAGTCTT
* * * *
35539806 TGATGGACATTCCATTGAAGATAGTCTT
1 TAACGGACATTCCACTCAAGATAGTCTT
35539834 TA
1 TA
35539836 GCGAACTTGT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
27 2 0.04
28 42 0.91
29 2 0.04
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31
Consensus pattern (28 bp):
TAACGGACATTCCACTCAAGATAGTCTT
Found at i:35540989 original size:53 final size:53
Alignment explanation
Indices: 35540923--35541026 Score: 136
Period size: 53 Copynumber: 2.0 Consensus size: 53
35540913 AGCGCTAAAT
* * *
35540923 ACCATATCGTGTAAGACCATAACTGGTGGGTTATGGCATCACATGAAAAAAAG
1 ACCATATCATGTAAGACCATAACCGGTGGGTTATGACATCACATGAAAAAAAG
*** * *
35540976 ACCATATCATGTAAGATTGTAACCGGTGGGTTATGACATCATATGGAAAAA
1 ACCATATCATGTAAGACCATAACCGGTGGGTTATGACATCACATGAAAAAA
35541027 TCTAAATTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (53 bp):
ACCATATCATGTAAGACCATAACCGGTGGGTTATGACATCACATGAAAAAAAG
Found at i:35541236 original size:28 final size:28
Alignment explanation
Indices: 35541204--35541267 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
35541194 TACTTAATGG
35541204 AAAGGACA-CATTTGTAGCAACCTCTATT
1 AAAGGA-AGCATTTGTAGCAACCTCTATT
* * * *
35541232 AAAGGAAGCATTTGTGGCAATCTTTGTT
1 AAAGGAAGCATTTGTAGCAACCTCTATT
35541260 AAAGGAAG
1 AAAGGAAG
35541268 GCTTTGTGGC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 1 0.03
28 30 0.97
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (28 bp):
AAAGGAAGCATTTGTAGCAACCTCTATT
Found at i:35542079 original size:18 final size:19
Alignment explanation
Indices: 35542058--35542095 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
35542048 TTAGAGGTAG
35542058 AATAAGT-GGAGTA-ATGTA
1 AATAAGTAGGA-TATATGTA
35542076 AATAAGTAGGATATATGTA
1 AATAAGTAGGATATATGTA
35542095 A
1 A
35542096 TTGTAAATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
AATAAGTAGGATATATGTA
Found at i:35542772 original size:33 final size:34
Alignment explanation
Indices: 35542721--35542830 Score: 87
Period size: 35 Copynumber: 3.2 Consensus size: 34
35542711 CCAACTTCAG
* * *
35542721 AGAGTCAGGAAACCATTTTCATGGTGTCGCTCC-
1 AGAGCCAGCAAACAATTTTCATGGTGTCGCTCCA
* * * ** *
35542754 AGAGCCTGCAAATAATTTTTATATTATCGCTCCA
1 AGAGCCAGCAAACAATTTTCATGGTGTCGCTCCA
* * *
35542788 TAGAGCCAGTAAACCATTTTCATGGTGTCGCTCCGT
1 -AGAGCCAGCAAACAATTTTCATGGTGTCGCTCC-A
35542824 AGAGCCA
1 AGAGCCA
35542831 ATAGATTATT
Statistics
Matches: 56, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
33 24 0.43
35 32 0.57
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (34 bp):
AGAGCCAGCAAACAATTTTCATGGTGTCGCTCCA
Found at i:35544887 original size:13 final size:14
Alignment explanation
Indices: 35544857--35544898 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
35544847 CAATTGTGTC
*
35544857 AATATCTAATTATA
1 AATATTTAATTATA
35544871 AATATTTAATT-TA
1 AATATTTAATTATA
*
35544884 AATATTTAAATATA
1 AATATTTAATTATA
35544898 A
1 A
35544899 TTTATATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
AATATTTAATTATA
Found at i:35544901 original size:19 final size:20
Alignment explanation
Indices: 35544877--35544922 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
35544867 TATAAATATT
35544877 TAATTTAAATATT-TAAATA
1 TAATTTAAATATTCTAAATA
* *
35544896 TAATTTATATATTCTAATTA
1 TAATTTAAATATTCTAAATA
35544916 -AATTTAA
1 TAATTTAA
35544923 TAAATAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATTTAAATATTCTAAATA
Found at i:35545796 original size:3 final size:3
Alignment explanation
Indices: 35545788--35545813 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
35545778 TTCTAGATGA
35545788 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
35545814 TAGTTTAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:35557344 original size:7 final size:7
Alignment explanation
Indices: 35557332--35557372 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
35557322 TTACACCCTT
35557332 TTTTTTC
1 TTTTTTC
35557339 TTTTTTC
1 TTTTTTC
35557346 TTTTTTC
1 TTTTTTC
35557353 TTTTTTC
1 TTTTTTC
35557360 TTTTTTC
1 TTTTTTC
35557367 TTTTTT
1 TTTTTT
35557373 AATTCTCTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:35561200 original size:68 final size:68
Alignment explanation
Indices: 35561091--35561230 Score: 253
Period size: 68 Copynumber: 2.1 Consensus size: 68
35561081 GTATAGGACC
*
35561091 TCTTTATAATGGTAGTTCTTGTATGTGTTAAGGATCAAATTGGCATGAATATGCTTTTGGAGTTT
1 TCTTTATAATGGTAGTTCTTGTATGCGTTAAGGATCAAATTGGCATGAATATGCTTTTGGAGTTT
35561156 ATG
66 ATG
* *
35561159 TCTTTATAATGGTAGTTCTTGTATGCGTTAATGATCAAATTGGTATGAATATGCTTTTGGAGTTT
1 TCTTTATAATGGTAGTTCTTGTATGCGTTAAGGATCAAATTGGCATGAATATGCTTTTGGAGTTT
35561224 ATG
66 ATG
35561227 TCTT
1 TCTT
35561231 GTTTGATGGA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.46
Consensus pattern (68 bp):
TCTTTATAATGGTAGTTCTTGTATGCGTTAAGGATCAAATTGGCATGAATATGCTTTTGGAGTTT
ATG
Found at i:35562644 original size:51 final size:51
Alignment explanation
Indices: 35562575--35562682 Score: 173
Period size: 51 Copynumber: 2.1 Consensus size: 51
35562565 AATATTATTC
*
35562575 CAATATTTGATAGTACAAAATTAGTCGAAAGCT-TCAGAAGAGTTAATATAT
1 CAATATTTGATAGTACAAAATTAGTCGAAAGCTCT-AGAAGAGCTAATATAT
* *
35562626 CAATATTTGGTAGTACAAAATTAGTTGAAAGCTCTAGAAGAGCTAATATAT
1 CAATATTTGATAGTACAAAATTAGTCGAAAGCTCTAGAAGAGCTAATATAT
35562677 CAATAT
1 CAATAT
35562683 CTAAAAATAA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
51 52 0.98
52 1 0.02
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (51 bp):
CAATATTTGATAGTACAAAATTAGTCGAAAGCTCTAGAAGAGCTAATATAT
Found at i:35565724 original size:27 final size:27
Alignment explanation
Indices: 35565692--35565780 Score: 110
Period size: 27 Copynumber: 3.3 Consensus size: 27
35565682 ATTCGTGGGC
*
35565692 AAATGACTGAAATACCCTCGATGGGTA
1 AAATGACTGAAATACCCTCGAAGGGTA
35565719 AAATGA-TAGAAATACCCT-GAAGGGTA
1 AAATGACT-GAAATACCCTCGAAGGGTA
* * * *
35565745 AAATGACCGAAATACCCCCAAAAGGTA
1 AAATGACTGAAATACCCTCGAAGGGTA
35565772 AAATGACTG
1 AAATGACTG
35565781 TTATACCCCT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
26 23 0.43
27 30 0.57
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (27 bp):
AAATGACTGAAATACCCTCGAAGGGTA
Found at i:35566042 original size:32 final size:26
Alignment explanation
Indices: 35565955--35566057 Score: 161
Period size: 26 Copynumber: 4.0 Consensus size: 26
35565945 TTGCCACATA
* *
35565955 TACTGTTACTGGTAGCTTTGCTGCGT
1 TACTATTACTGGCAGCTTTGCTGCGT
35565981 TACTATTACTGGCAGCTTTGCTGCGT
1 TACTATTACTGGCAGCTTTGCTGCGT
35566007 TACTATTACTGGCAGCTTTGCTGCGT
1 TACTATTACTGGCAGCTTTGCTGCGT
* * *
35566033 CATTATTACTAGCAGCTTTGCTGCG
1 TACTATTACTGGCAGCTTTGCTGCG
35566058 ATATTGGTGT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 72 1.00
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.39
Consensus pattern (26 bp):
TACTATTACTGGCAGCTTTGCTGCGT
Found at i:35566203 original size:28 final size:28
Alignment explanation
Indices: 35566163--35566224 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
35566153 ACTGCATTGT
35566163 ACTGTTACGGTATTAGGCTAAGGCCCAC
1 ACTGTTACGGTATTAGGCTAAGGCCCAC
* *
35566191 ACTGTTACTGTATTGGGCTAAGGCCCAC
1 ACTGTTACGGTATTAGGCTAAGGCCCAC
35566219 ACTGTT
1 ACTGTT
35566225 GCCGCATAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (28 bp):
ACTGTTACGGTATTAGGCTAAGGCCCAC
Found at i:35566236 original size:28 final size:28
Alignment explanation
Indices: 35566178--35566259 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 28
35566168 TACGGTATTA
* * *
35566178 GGCTAAGGCCCACACTGTTACTGTATTG
1 GGCTAAGGCCCACACTGTTACCGCATAG
*
35566206 GGCTAAGGCCCACACTGTTGCCGCATAG
1 GGCTAAGGCCCACACTGTTACCGCATAG
* * * *
35566234 GGCTCAGGCCCAGACTGCTACTGCAT
1 GGCTAAGGCCCACACTGTTACCGCAT
35566260 GTTGTATACT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.21, C:0.30, G:0.27, T:0.22
Consensus pattern (28 bp):
GGCTAAGGCCCACACTGTTACCGCATAG
Found at i:35570756 original size:34 final size:33
Alignment explanation
Indices: 35570683--35570794 Score: 138
Period size: 34 Copynumber: 3.4 Consensus size: 33
35570673 GATTTAGTGT
*
35570683 TATTTTTTAAAAATTAATTAAA-TTAGGGTTTAG
1 TATTTTTAAAAAATTAATTAAATTTA-GGTTTAG
**
35570716 -GGTTTTAAATAAATTAATTAAATTTAGGTTTAG
1 TATTTTTAAA-AAATTAATTAAATTTAGGTTTAG
*
35570749 TATTTTTAAGAAAATTAATTAAATTTTGGTTTAG
1 TATTTTTAA-AAAATTAATTAAATTTAGGTTTAG
*
35570783 TTTTTTTAAAAA
1 TATTTTTAAAAA
35570795 TAATATTGTG
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
32 6 0.09
33 22 0.32
34 39 0.57
35 1 0.01
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (33 bp):
TATTTTTAAAAAATTAATTAAATTTAGGTTTAG
Found at i:35571210 original size:125 final size:125
Alignment explanation
Indices: 35570854--35571492 Score: 879
Period size: 125 Copynumber: 5.1 Consensus size: 125
35570844 GGATTTTGAT
*
35570854 TTTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAA
1 TTTTTT-TACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTTTGAACAAATAGTGTCAAA
* ** *
35570919 AACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCACACATAGACGCTC
65 AACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTG-AAAAAGCTCCCATGTGGACGCTC
* * *
35570981 ATTTTCTT-CAGTAGTTCCTGAAAAAATAATTTTGAGATGACGGTTCTGAACAAATAGTGTCAAA
1 -TTTTTTTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTTTGAACAAATAGTGTCAAA
35571045 AACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAGAGCTCCCATGTGGACGCT-
65 AACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAA-AGCTCCCATGTGGACGCTC
*
35571106 TTTTTTTACTGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTTTGAACAAATAGTGTCAAAA
1 TTTTTTTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTTTGAACAAATAGTGTCAAAA
* * *
35571171 ACACTTCAAGTAGGATGCACTATCAGCAAAATTGA-TGAAAAAAGCTCCCATGTGGACGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATT-ACTG-AAAAAGCTCCCATGTGGACGCTC
* *
35571232 TTTTTATACAGTAGTTCCTG-AAAAATAATTTTGAGAAGA-TGTTTCTGAACAAATAGTGTCAAA
1 TTTTTTTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTT-TGAACAAATAGTGTCAAA
* * * * *
35571295 AATGCTTCAAGAAGTATGCACTGTCAGCAAAATTACTG-AAAA--T---AGGTGGACACTC
65 AACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAGCTCCCATGTGGACGCTC
* * * *
35571350 TTTTTCTACAGTAGTTCCTGAAAAGATAATTTTGAGAAGAC-ATTTCTGAAAAAATAGTGTCAAA
1 TTTTTTTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTT-TGAACAAATAGTGTCAAA
*
35571414 AACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAGAAAAGCTCCCATGTGGGCGCTC
65 AACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGA-AAAAGCTCCCATGTGGACGCTC
* *
35571476 TTTTTCTACAATAGTTC
1 TTTTTTTACAGTAGTTC
35571493 GTGTTTGGCC
Statistics
Matches: 461, Mismatches: 34, Indels: 34
0.87 0.06 0.06
Matches are distributed among these distances:
118 29 0.06
119 74 0.16
121 5 0.01
123 5 0.01
124 11 0.02
125 176 0.38
126 155 0.34
127 1 0.00
128 5 0.01
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (125 bp):
TTTTTTTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTTTGAACAAATAGTGTCAAAA
ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAGCTCCCATGTGGACGCTC
Found at i:35574446 original size:26 final size:25
Alignment explanation
Indices: 35574398--35574446 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
35574388 ACTTCTATTT
*
35574398 TATTAAAAATATAAAAATAATTTAC
1 TATTAAAAATATAAAAAGAATTTAC
35574423 TATT-AAAATATTAAAAACGAATTT
1 TATTAAAAATA-TAAAAA-GAATTT
35574447 TATTTTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 10 0.48
26 5 0.24
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (25 bp):
TATTAAAAATATAAAAAGAATTTAC
Found at i:35574450 original size:24 final size:23
Alignment explanation
Indices: 35574394--35574450 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 23
35574384 AAGAACTTCT
*
35574394 ATTTTATTAAAAATATAAAAATA
1 ATTTTATTAAAAATATAAAAAGA
35574417 ATTTACTATT-AAAATATTAAAAACGA
1 ATTT--TATTAAAAATA-TAAAAA-GA
35574443 ATTTTATT
1 ATTTTATT
35574451 TTATTAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 4 0.14
24 10 0.34
25 10 0.34
26 5 0.17
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (23 bp):
ATTTTATTAAAAATATAAAAAGA
Found at i:35576700 original size:30 final size:30
Alignment explanation
Indices: 35576646--35576710 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
35576636 ATTAATTAAA
*
35576646 GAGAGCTTTGAGAAATTTAAGGAGAAGTTT
1 GAGAGCTTTGAGAAATTTAAGGAGAAATTT
**
35576676 GAGAGCTTTGAGAAATTTTGGGAGAAATTT
1 GAGAGCTTTGAGAAATTTAAGGAGAAATTT
*
35576706 TAGAG
1 GAGAG
35576711 TTTTTTGCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.35, C:0.03, G:0.31, T:0.31
Consensus pattern (30 bp):
GAGAGCTTTGAGAAATTTAAGGAGAAATTT
Found at i:35577191 original size:6 final size:6
Alignment explanation
Indices: 35577180--35577208 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
35577170 ATTTTATTAC
35577180 TTTTAA TTTTAA TTTTAA TTTTAA TTTTA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTA
35577209 TTTCAAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:35577547 original size:22 final size:22
Alignment explanation
Indices: 35577519--35577570 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
35577509 TGGGCATCGA
*
35577519 AAATTGACCA-AATAAACCAATT
1 AAATTGAACATAA-AAACCAATT
* *
35577541 AAATTGAACATGAAAATCAATT
1 AAATTGAACATAAAAACCAATT
35577563 AAATTGAA
1 AAATTGAA
35577571 AAATCGAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.56, C:0.12, G:0.08, T:0.25
Consensus pattern (22 bp):
AAATTGAACATAAAAACCAATT
Found at i:35577573 original size:17 final size:17
Alignment explanation
Indices: 35577553--35577590 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
35577543 ATTGAACATG
*
35577553 AAAATC-AATTAAATTGA
1 AAAATCGAA-TAAACTGA
35577570 AAAATCGAATAAACTGA
1 AAAATCGAATAAACTGA
35577587 AAAA
1 AAAA
35577591 ATTCAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.21
Consensus pattern (17 bp):
AAAATCGAATAAACTGA
Found at i:35580502 original size:19 final size:19
Alignment explanation
Indices: 35580422--35580502 Score: 65
Period size: 19 Copynumber: 4.3 Consensus size: 19
35580412 GGGTAATTAA
* *
35580422 CACACAACGTGCATACTTG
1 CACACAAAGTGCATACTAG
* *
35580441 CATACAAAAG-GCATCCTAG
1 CACAC-AAAGTGCATACTAG
** * *
35580460 TGCACAAAGCGCATACTGG
1 CACACAAAGTGCATACTAG
*
35580479 CACACAAAGTGCATCCTAG
1 CACACAAAGTGCATACTAG
35580498 CACAC
1 CACAC
35580503 GAAGCGTATA
Statistics
Matches: 46, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
18 4 0.09
19 39 0.85
20 3 0.07
ACGTcount: A:0.36, C:0.31, G:0.17, T:0.16
Consensus pattern (19 bp):
CACACAAAGTGCATACTAG
Found at i:35580508 original size:38 final size:38
Alignment explanation
Indices: 35580422--35580534 Score: 102
Period size: 38 Copynumber: 2.9 Consensus size: 38
35580412 GGGTAATTAA
* * * *
35580422 CACACAACGTGCATACTTGCATACAAAAG-GCATCCTAG
1 CACACAAAGCGCATACTGGCACAC-AAAGTGCATCCTAG
**
35580460 TGCACAAAGCGCATACTGGCACACAAAGTGCATCCTAG
1 CACACAAAGCGCATACTGGCACACAAAGTGCATCCTAG
* * * * *
35580498 CACACGAAGCGTATATTTGGCACACGAGGTGCATCCT
1 CACACAAAGCGCATA-CTGGCACACAAAGTGCATCCT
35580535 GACAAATTAA
Statistics
Matches: 60, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
37 4 0.07
38 38 0.63
39 18 0.30
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.19
Consensus pattern (38 bp):
CACACAAAGCGCATACTGGCACACAAAGTGCATCCTAG
Found at i:35581687 original size:25 final size:25
Alignment explanation
Indices: 35581652--35581788 Score: 134
Period size: 25 Copynumber: 5.4 Consensus size: 25
35581642 CCACAAAAGG
* *
35581652 TTTTCCAGATAATACACCATATAGGC
1 TTTT-CAGATAATACGCCACATAGGC
* *
35581678 TTTTCAGATAATATGCAACATAGGC
1 TTTTCAGATAATACGCCACATAGGC
* * *
35581703 -TTTCTAGATAATACACCACATATGT
1 TTTTC-AGATAATACGCCACATAGGC
* * *
35581728 TTTTTAGATAACT-TGCCACAAAGGC
1 TTTTCAGATAA-TACGCCACATAGGC
*
35581753 TTTTCAGATAATACGCCACATAGTC
1 TTTTCAGATAATACGCCACATAGGC
35581778 TTTTCAGATAA
1 TTTTCAGATAA
35581789 CTTACCACAA
Statistics
Matches: 88, Mismatches: 19, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
24 5 0.06
25 75 0.85
26 8 0.09
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (25 bp):
TTTTCAGATAATACGCCACATAGGC
Found at i:35581737 original size:50 final size:49
Alignment explanation
Indices: 35581631--35581802 Score: 168
Period size: 50 Copynumber: 3.4 Consensus size: 49
35581621 ACAGGCTTTC
* * * * * *
35581631 CAGATGACTTGCCACAAAAGGTTTTCCAGATAATACACCATATAGGCTTTT
1 CAGATAACTTGCAAC-AAAGGCTTTCTAGATAATACACCACATA-GTTTTT
*
35581682 CAGATAA-TATGCAACATAGGCTTTCTAGATAATACACCACATATGTTTTT
1 CAGATAACT-TGCAACAAAGGCTTTCTAGATAATACACCACATA-GTTTTT
* * *
35581732 TAGATAACTTGCCACAAAGGCTTT-TCAGATAATACGCCACATAGTCTTTT
1 CAGATAACTTGCAACAAAGGCTTTCT-AGATAATACACCACATAGT-TTTT
* *
35581782 CAGATAACTTACCACAAAGGC
1 CAGATAACTTGCAACAAAGGC
35581803 ACTGCATAAA
Statistics
Matches: 103, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
49 3 0.03
50 88 0.85
51 12 0.12
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.30
Consensus pattern (49 bp):
CAGATAACTTGCAACAAAGGCTTTCTAGATAATACACCACATAGTTTTT
Found at i:35581796 original size:25 final size:25
Alignment explanation
Indices: 35581717--35581797 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
35581707 TAGATAATAC
*
35581717 ACCACATATGT-TTTTTAGATAACTT
1 ACCACATA-GTCTTTTCAGATAACTT
* * *
35581742 GCCACAAAGGCTTTTCAGATAA--T
1 ACCACATAGTCTTTTCAGATAACTT
35581765 ACGCCACATAGTCTTTTCAGATAACTT
1 A--CCACATAGTCTTTTCAGATAACTT
35581792 ACCACA
1 ACCACA
35581798 AAGGCACTGC
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
23 1 0.02
24 1 0.02
25 40 0.91
27 2 0.05
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.32
Consensus pattern (25 bp):
ACCACATAGTCTTTTCAGATAACTT
Found at i:35589709 original size:29 final size:29
Alignment explanation
Indices: 35589623--35589725 Score: 88
Period size: 27 Copynumber: 3.7 Consensus size: 29
35589613 TTGCATCACG
* * *
35589623 AAGGCATTTCTTTTTCAGATATAGCTACA
1 AAGGCATTTCTTTTACAGAGATAGCCACA
* * **
35589652 AAGGC--TTCTTTTACGGAGATTGTGACA
1 AAGGCATTTCTTTTACAGAGATAGCCACA
*
35589679 AAGGC-TTTCTTTTGACAGAGATCGCCACA
1 AAGGCATTTCTTTT-ACAGAGATAGCCACA
*
35589708 AAGGCATTTCATTT-CAGA
1 AAGGCATTTCTTTTACAGA
35589726 TATTTTCCAC
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
27 21 0.35
28 11 0.18
29 21 0.35
30 7 0.12
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (29 bp):
AAGGCATTTCTTTTACAGAGATAGCCACA
Found at i:35589854 original size:29 final size:29
Alignment explanation
Indices: 35589816--35589917 Score: 87
Period size: 29 Copynumber: 3.4 Consensus size: 29
35589806 ACATCCAGTA
35589816 TTTGCCACAAAGGCTTTCCTGTCTAAAGT
1 TTTGCCACAAAGGCTTTCCTGTCTAAAGT
* * * **
35589845 TTTGCCACAAATGCTATCCTTTACATCCAGT
1 TTTGCCACAAAGGCTTTCCTGT-C-TAAAGT
* * * *
35589876 ACTCGCCACAAAGGCTTTCCTGTCCAAAGA
1 -TTTGCCACAAAGGCTTTCCTGTCTAAAGT
*
35589906 TTTACCACAAAG
1 TTTGCCACAAAG
35589918 ACTATGCTTT
Statistics
Matches: 53, Mismatches: 17, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
29 28 0.53
30 3 0.06
31 5 0.09
32 17 0.32
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.29
Consensus pattern (29 bp):
TTTGCCACAAAGGCTTTCCTGTCTAAAGT
Found at i:35589884 original size:61 final size:59
Alignment explanation
Indices: 35589780--35589978 Score: 227
Period size: 61 Copynumber: 3.3 Consensus size: 59
35589770 TTACCTTTCC
* * * * *
35589780 AAAGTTTCGCCACAAAGGTTGTCTTTACATCCAGTATTTGCCACAAAGGCTTTCCTGTCT
1 AAAGTTTTGCCACAAA-GCTATCTTTACATCCAGTACTCGCCACAAAGGCTTTCCTGTCT
*
35589840 AAAGTTTTGCCACAAATGCTATCCTTTACATCCAGTACTCGCCACAAAGGCTTTCCTGTCC
1 AAAGTTTTGCCACAAA-GCTAT-CTTTACATCCAGTACTCGCCACAAAGGCTTTCCTGTCT
* * * * * *
35589901 AAAGATTTACCACAAAGACTATGCTTTATATCCATTACTCGCCAAAAAGGCTTTCCTATCT
1 AAAGTTTTGCCACAAAG-CTAT-CTTTACATCCAGTACTCGCCACAAAGGCTTTCCTGTCT
* *
35589962 AGAGTTTTGCCAAAAAG
1 AAAGTTTTGCCACAAAG
35589979 GCGTTCCTTA
Statistics
Matches: 118, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
60 19 0.16
61 99 0.84
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.31
Consensus pattern (59 bp):
AAAGTTTTGCCACAAAGCTATCTTTACATCCAGTACTCGCCACAAAGGCTTTCCTGTCT
Found at i:35590206 original size:53 final size:53
Alignment explanation
Indices: 35590109--35590252 Score: 148
Period size: 53 Copynumber: 2.7 Consensus size: 53
35590099 TCCCCACAAA
* * * *
35590109 ATGCCATAACTCACTAGTTACAGTCTTACACT-ATATCGTCTTCTTCCCACATG
1 ATGCCATAACTCACCAGTTACGGTCTTACA-TGATATGGTATTCTTCCCACATG
* * *
35590162 ATGCCATAAAC-CACCAGTTACGGTCTTACATGATATGGTATTCTTTCTATATG
1 ATGCCAT-AACTCACCAGTTACGGTCTTACATGATATGGTATTCTTCCCACATG
** * * *
35590215 ATGTTATAACTCACCAATTACGGCCTTACACGATATGG
1 ATGCCATAACTCACCAGTTACGGTCTTACATGATATGG
35590253 CCATGGACAT
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
52 4 0.05
53 69 0.91
54 3 0.04
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (53 bp):
ATGCCATAACTCACCAGTTACGGTCTTACATGATATGGTATTCTTCCCACATG
Found at i:35619290 original size:43 final size:43
Alignment explanation
Indices: 35619163--35619291 Score: 129
Period size: 44 Copynumber: 3.0 Consensus size: 43
35619153 TTAGGATTCT
*
35619163 GTTATGTG-TTATCGTGTAAGACCACGTCTGGGATGTTGGCATC
1 GTTATGTGATTA-CGTGTAAGACCACGTCTGGGACGTTGGCATC
* * **
35619206 GACT-TGTGACTTACGTGTAAGACC-CTATCTGGGACAATGGCATC
1 G-TTATGTGA-TTACGTGTAAGACCAC-GTCTGGGACGTTGGCATC
* **
35619250 GTTATGTGATTACATGTAAGACCACGTCTAAGACGTTGGCAT
1 GTTATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
35619292 TTTATGAAAT
Statistics
Matches: 68, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
43 32 0.47
44 33 0.49
45 3 0.04
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (43 bp):
GTTATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATC
Found at i:35623385 original size:13 final size:14
Alignment explanation
Indices: 35623367--35623395 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
35623357 AAAATTGCTT
35623367 AAAAATCAAG-CAA
1 AAAAATCAAGTCAA
35623380 AAAAATCAAGTCAA
1 AAAAATCAAGTCAA
35623394 AA
1 AA
35623396 GCCACTAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.69, C:0.14, G:0.07, T:0.10
Consensus pattern (14 bp):
AAAAATCAAGTCAA
Done.