Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008716.1 Hibiscus syriacus cultivar Beakdansim tig00111769_pilon, whole genome shotgun sequence
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: 5677467
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 24
Found at i:3240198 original size:41 final size:41
Alignment explanation
Indices: 3240152--3240231 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
3240142 CAGATTGCCT
*
3240152 AGGGGGTACAGATTCCCCCCCAGGGGGTA-CAGATTCCCCCC
1 AGGGGGAACAGATTCCCCCCCAGGGGGTATC-GATTCCCCCC
* *
3240193 AGGGGGAATAGATTTCCCCCCAGGGGGTATCGATTCCCC
1 AGGGGGAACAGATTCCCCCCCAGGGGGTATCGATTCCCC
3240232 GGGAACAGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 34 0.97
42 1 0.03
ACGTcount: A:0.20, C:0.33, G:0.30, T:0.17
Consensus pattern (41 bp):
AGGGGGAACAGATTCCCCCCCAGGGGGTATCGATTCCCCCC
Found at i:3240705 original size:34 final size:34
Alignment explanation
Indices: 3240661--3240735 Score: 132
Period size: 34 Copynumber: 2.2 Consensus size: 34
3240651 CCTATTGTAA
*
3240661 AGGGGAAGGTTCTAGCTTATCCCGTGTAAAAGAT
1 AGGGAAAGGTTCTAGCTTATCCCGTGTAAAAGAT
*
3240695 AGGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCT
1 AGGGAAAGGTTCTAGCTTATCCCGTGTAAAAGAT
3240729 AGGGAAA
1 AGGGAAA
3240736 TGTTATAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.24
Consensus pattern (34 bp):
AGGGAAAGGTTCTAGCTTATCCCGTGTAAAAGAT
Found at i:3241770 original size:19 final size:20
Alignment explanation
Indices: 3241748--3241787 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3241738 CTTCTTCTAG
* *
3241748 AAATGAAAATGGAAT-TTGA
1 AAATCAAAATGAAATCTTGA
3241767 AAATCAAAATGAAATCTTGA
1 AAATCAAAATGAAATCTTGA
3241787 A
1 A
3241788 GAAGGATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.55, C:0.05, G:0.15, T:0.25
Consensus pattern (20 bp):
AAATCAAAATGAAATCTTGA
Found at i:3243411 original size:21 final size:22
Alignment explanation
Indices: 3243378--3243420 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
3243368 ATTTGAATAT
*
3243378 TATGAAGGGGGTATCGATTCCC
1 TATGAAGGGGGTACCGATTCCC
3243400 TATGAA-GGGGTACCGATTCCC
1 TATGAAGGGGGTACCGATTCCC
3243421 CCCATTCTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (22 bp):
TATGAAGGGGGTACCGATTCCC
Found at i:3243742 original size:34 final size:32
Alignment explanation
Indices: 3243703--3243772 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
3243693 TATTGTAAAG
* *
3243703 GGGAAAGGTTATAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTATAGCTTAGCCCG-G-AAAAACTA
* *
3243737 GGGAAATGTTATAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
3243769 GGGA
1 GGGA
3243773 GATGTAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.34, C:0.13, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
Found at i:3245067 original size:24 final size:20
Alignment explanation
Indices: 3245011--3245068 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
3245001 TTCCTCTTGA
*
3245011 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
*
3245031 AGTGCATCAATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
3245054 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
3245069 CTACCCATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 15 0.48
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:3245179 original size:64 final size:63
Alignment explanation
Indices: 3245056--3245192 Score: 154
Period size: 64 Copynumber: 2.2 Consensus size: 63
3245046 TCTTTAACAT
* *
3245056 GTGCATCGATGCACTACCCATGCATCGATACACCAATCATCTTCGATGTTTTCATTTTAAGGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACCAATCATCTTCGATGTTTTCATTTTAA-AGA
* * * * *
3245120 GTGCATCGATGCACT-CCTTATGCATCGATGCACTAATTA-CATTCGATG-TTTCTTCTTTAAAG
1 GTGCATCGATGCACTACC-CATGCATCGATACACCAATCATC-TTCGATGTTTTCAT-TTTAAAG
3245182 A
63 A
3245183 GTGCATCGAT
1 GTGCATCGAT
3245193 ACACATTGAA
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
63 19 0.30
64 44 0.70
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACCAATCATCTTCGATGTTTTCATTTTAAAGA
Found at i:3252345 original size:56 final size:56
Alignment explanation
Indices: 3252256--3252368 Score: 199
Period size: 56 Copynumber: 2.0 Consensus size: 56
3252246 TTAACATCTC
* *
3252256 TCAAAAAGTTGCAATTTGTTGATATGATTTTTAACATGTCCACGCGACTCACCAAA
1 TCAAAAAGTCGCAATTTGTTGATATGATCTTTAACATGTCCACGCGACTCACCAAA
*
3252312 TCAAAAAGTCGCAATTTGTTGATATGATCTTTAACATGTCCACGCGACTTACCAAA
1 TCAAAAAGTCGCAATTTGTTGATATGATCTTTAACATGTCCACGCGACTCACCAAA
3252368 T
1 T
3252369 TAAATTTATC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (56 bp):
TCAAAAAGTCGCAATTTGTTGATATGATCTTTAACATGTCCACGCGACTCACCAAA
Found at i:3261270 original size:2 final size:2
Alignment explanation
Indices: 3261263--3261304 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3261253 AAATATGTAC
3261263 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3261305 GCATAAACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3282058 original size:27 final size:27
Alignment explanation
Indices: 3282020--3282078 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
3282010 GAATAGAGAT
3282020 TTGGGTTTTACATCTTTACTACAAATA
1 TTGGGTTTTACATCTTTACTACAAATA
*
3282047 TTGGGTTTTACATCTTTACTGCAAATA
1 TTGGGTTTTACATCTTTACTACAAATA
3282074 TTGGG
1 TTGGG
3282079 AACTTTAGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (27 bp):
TTGGGTTTTACATCTTTACTACAAATA
Found at i:3282125 original size:19 final size:20
Alignment explanation
Indices: 3282101--3282143 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
3282091 TTAAACTATG
*
3282101 TTAT-GGATTGTAATTTTAA
1 TTATGGGATTGTAACTTTAA
3282120 TTATGGGATTGTAACTTTAA
1 TTATGGGATTGTAACTTTAA
3282140 TTAT
1 TTAT
3282144 CCAGTATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.30, C:0.02, G:0.16, T:0.51
Consensus pattern (20 bp):
TTATGGGATTGTAACTTTAA
Found at i:3282406 original size:19 final size:20
Alignment explanation
Indices: 3282366--3282408 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3282356 TCAAGATGTA
* *
3282366 TTACTAGAGATCTAACATTT
1 TTACCAGAGACCTAACATTT
3282386 TTACCAGAGACCTAA-ATTT
1 TTACCAGAGACCTAACATTT
3282405 TTAC
1 TTAC
3282409 ACAATTTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (20 bp):
TTACCAGAGACCTAACATTT
Found at i:3285515 original size:53 final size:49
Alignment explanation
Indices: 3285434--3285548 Score: 133
Period size: 50 Copynumber: 2.3 Consensus size: 49
3285424 GACATGGCTT
* *
3285434 ACACGT-TGGTATAGCGCCCCCCTTATCCACGCTATACGCCATGTTTATCTG
1 ACACGTGTGGTATAGCGCCCCCCTGATCCACGCTATA--CC-TATTTATCTG
** *
3285485 ACACGTGTGGTATAGCGTGGCCCCTGATCCACGCTATATCTATTTATCTG
1 ACACGTGTGGTATAGCG-CCCCCCTGATCCACGCTATACCTATTTATCTG
*
3285535 ACACGTGGGGTATA
1 ACACGTGTGGTATA
3285549 ACACGGTACA
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
50 22 0.39
51 7 0.12
52 10 0.18
53 17 0.30
ACGTcount: A:0.21, C:0.28, G:0.22, T:0.30
Consensus pattern (49 bp):
ACACGTGTGGTATAGCGCCCCCCTGATCCACGCTATACCTATTTATCTG
Found at i:3285740 original size:17 final size:18
Alignment explanation
Indices: 3285704--3285744 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3285694 ATATTATGTA
*
3285704 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
3285722 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
3285739 TTTACT
1 TTTACT
3285745 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:3286509 original size:51 final size:51
Alignment explanation
Indices: 3286406--3286520 Score: 144
Period size: 51 Copynumber: 2.3 Consensus size: 51
3286396 TCCCTACGTG
* **
3286406 GCGTATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGTAAGCCATGTCA
1 GCGTATAGCGCGGATCAAGGGGCGCGCTATACCCACGTGTAAGCCAAATCA
**
3286457 GCGTATAGCGCGG-TACAAGGGGCGCGCTATACCCCACGTG-GCGCCAAATCA
1 GCGTATAGCGCGGAT-CAAGGGGCGCGCTATA-CCCACGTGTAAGCCAAATCA
*
3286508 GCATATAGCGCGG
1 GCGTATAGCGCGG
3286521 GGCAGGGAAC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
50 1 0.02
51 47 0.84
52 8 0.14
ACGTcount: A:0.23, C:0.29, G:0.33, T:0.16
Consensus pattern (51 bp):
GCGTATAGCGCGGATCAAGGGGCGCGCTATACCCACGTGTAAGCCAAATCA
Found at i:3290030 original size:29 final size:28
Alignment explanation
Indices: 3289976--3290030 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
3289966 CTTAATAACG
*
3289976 AAATATTACCTTTTAAGCATCATTTTTC
1 AAATATTACCATTTAAGCATCATTTTTC
*
3290004 AAATATTACCGATTTAA-TATCATTTTT
1 AAATATTACC-ATTTAAGCATCATTTTT
3290031 AACAAAGCGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.35, C:0.15, G:0.04, T:0.47
Consensus pattern (28 bp):
AAATATTACCATTTAAGCATCATTTTTC
Found at i:3290640 original size:29 final size:27
Alignment explanation
Indices: 3290584--3290640 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 27
3290574 TTTTAGTAGC
*
3290584 TAATATTTTTATTATATTATAATCATT
1 TAATATTTTTATTATATTATAATAATT
* *
3290611 TAATAGTTTGTTATTTTATTATACTAATT
1 TAATA-TTT-TTATTATATTATAATAATT
3290640 T
1 T
3290641 TTATTATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 5 0.20
28 3 0.12
29 17 0.68
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (27 bp):
TAATATTTTTATTATATTATAATAATT
Found at i:3290680 original size:175 final size:175
Alignment explanation
Indices: 3290356--3290714 Score: 603
Period size: 175 Copynumber: 2.0 Consensus size: 175
3290346 TCTATCTATC
3290356 ATTCTATCAAGTTTTAAGAAGATATAGTTATCATTTTTAGTAGCTAATTTTTTATTATATTATAA
1 ATTCTATCAAGTTTTAAGAAGATATAGTTATCATTTTTAGTAGCTAATTTTTTATTATATTATAA
3290421 TCATTTAATAGTTTGTTATTTTATTTTATTTTATTATACTAATTTTTATTATATTTTGCAGTTAT
66 TCATTTAATAGTTTG---------TTTATTTTATTATACTAATTTTTATTATATTTTGCAGTTAT
3290486 AAAATGACAGATAGGTTGTTGTGTTTATATGATAATTATATATCGAGTCATTTT
122 AAAATGACAGATAGGTTGTTGTGTTTATATGATAATTATATATCGAGTCATTTT
3290540 ATTCTATCAAGTTTTAAGAAGATATAGTTATCATTTTTAGTAGCTAATATTTTTATTATATTATA
1 ATTCTATCAAGTTTTAAGAAGATATAGTTATCATTTTTAGTAGCTAAT-TTTTTATTATATTATA
*
3290605 ATCATTTAATAGTTTG-TTATTTTATTATACTAATTTTTATTATATTTTGCAGTTATAAAATGGC
65 ATCATTTAATAGTTTGTTTATTTTATTATACTAATTTTTATTATATTTTGCAGTTATAAAATGAC
*
3290669 AGATGGGTTGTTGTGTTTATATGATAATTATATATCGAGTCATTTT
130 AGATAGGTTGTTGTGTTTATATGATAATTATATATCGAGTCATTTT
3290715 GCTGACACGA
Statistics
Matches: 172, Mismatches: 2, Indels: 11
0.93 0.01 0.06
Matches are distributed among these distances:
175 92 0.53
184 48 0.28
185 32 0.19
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.51
Consensus pattern (175 bp):
ATTCTATCAAGTTTTAAGAAGATATAGTTATCATTTTTAGTAGCTAATTTTTTATTATATTATAA
TCATTTAATAGTTTGTTTATTTTATTATACTAATTTTTATTATATTTTGCAGTTATAAAATGACA
GATAGGTTGTTGTGTTTATATGATAATTATATATCGAGTCATTTT
Found at i:3292320 original size:21 final size:21
Alignment explanation
Indices: 3292286--3292346 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
3292276 TTATATTCTG
* *
3292286 CAGTCGTTTCAGATGCCACCA
1 CAGTCATTTTAGATGCCACCA
3292307 CAGTCATTTTAGATGCCACCA
1 CAGTCATTTTAGATGCCACCA
*
3292328 CAATCATTTTAGATGCCAC
1 CAGTCATTTTAGATGCCAC
3292347 AATCGTAGGG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.28
Consensus pattern (21 bp):
CAGTCATTTTAGATGCCACCA
Found at i:3292770 original size:25 final size:25
Alignment explanation
Indices: 3292736--3292817 Score: 72
Period size: 25 Copynumber: 3.6 Consensus size: 25
3292726 CAATAGACTT
3292736 GTTTTTATTTATTTTGTTTCTTAAC
1 GTTTTTATTTATTTTGTTTCTTAAC
*
3292761 GTTTTTATTTAATTATG------AAC
1 GTTTTTATTT-ATTTTGTTTCTTAAC
*
3292781 -TTTTTATTTATTTTGTTTCTTAAT
1 GTTTTTATTTATTTTGTTTCTTAAC
*
3292805 ATTTTTA-TTATTT
1 GTTTTTATTTATTT
3292818 AATTGTTTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 17
0.70 0.05 0.26
Matches are distributed among these distances:
18 5 0.11
19 9 0.20
20 3 0.07
24 8 0.17
25 16 0.35
26 5 0.11
ACGTcount: A:0.21, C:0.05, G:0.06, T:0.68
Consensus pattern (25 bp):
GTTTTTATTTATTTTGTTTCTTAAC
Found at i:3303024 original size:51 final size:51
Alignment explanation
Indices: 3302946--3303075 Score: 217
Period size: 50 Copynumber: 2.6 Consensus size: 51
3302936 TTACTTAGAT
*
3302946 GACTTCTTTTTCCCGGGTTTGGACTTTTTCATACTTACAGATTCTTTCTCG
1 GACTTCTTTTTCCCGGGTTTGGACTTTTTCATACTTACAGATTCTTTCTCA
* *
3302997 GACTTC-TTTTCCCGGGTTTGGACCTTTTCGTACTTACAGATTCTTTCTCA
1 GACTTCTTTTTCCCGGGTTTGGACTTTTTCATACTTACAGATTCTTTCTCA
*
3303047 GACTTCTTTTTCCCGGATTTGGACTTTTT
1 GACTTCTTTTTCCCGGGTTTGGACTTTTT
3303076 AGTTTTCATC
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
50 47 0.64
51 26 0.36
ACGTcount: A:0.13, C:0.24, G:0.16, T:0.47
Consensus pattern (51 bp):
GACTTCTTTTTCCCGGGTTTGGACTTTTTCATACTTACAGATTCTTTCTCA
Found at i:3310574 original size:31 final size:31
Alignment explanation
Indices: 3310536--3310599 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
3310526 ATCCAGTTGC
*
3310536 CTGATGTTATAAACGTTACTATCTTAGGTGT
1 CTGATGTTATAAACATTACTATCTTAGGTGT
* *
3310567 CTGATGTTATAAACATTATTATTTTAGGTGT
1 CTGATGTTATAAACATTACTATCTTAGGTGT
3310598 CT
1 CT
3310600 CGTGGCTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.45
Consensus pattern (31 bp):
CTGATGTTATAAACATTACTATCTTAGGTGT
Found at i:3310872 original size:23 final size:23
Alignment explanation
Indices: 3310846--3310897 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
3310836 TCAAAATCTA
*
3310846 AAAATTTTAAAT-CTCTAATCCCT
1 AAAATTTCAAATACTC-AATCCCT
*
3310869 AAAATTTCAAATACTCAATCTCT
1 AAAATTTCAAATACTCAATCCCT
*
3310892 TAAATT
1 AAAATT
3310898 AATTTAATCG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 22 0.88
24 3 0.12
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.38
Consensus pattern (23 bp):
AAAATTTCAAATACTCAATCCCT
Found at i:3316936 original size:102 final size:102
Alignment explanation
Indices: 3316841--3317126 Score: 286
Period size: 102 Copynumber: 2.8 Consensus size: 102
3316831 TTTAATTAGA
* *
3316841 AACTGTTAAGATTATTTGTTTCAAACCATTTTTATTA-GGAAACAATACA-ACAAAACATGTTGA
1 AACTGTTAAGATTATATGTTTCAAACC-TTTTTATTATGGAAACAATACAGACAAAACA-GTTTA
*
3316904 TAAGTCTAACATTATA-GTTAACACCTTTTTTTAATTGTC
64 TAAGTCTAACATTATAGGAT-ACACCTTTTTTTAATTGTC
* * * *
3316943 AACTGTTTAAG-TTATATGTTTGAAA-CTTTTCATATTATGCAAA-AGTA-AGACTAAACAAGTT
1 AACTG-TTAAGATTATATGTTTCAAACCTTTT--TATTATGGAAACAATACAGACAAAAC-AGTT
* * * *
3317004 TATAAGTATAACATTATAGGATGCACGTTTTTTAAATTGTC
62 TATAAGTCTAACATTATAGGATACACCTTTTTTTAATTGTC
* *
3317045 AA-TCGTTAAAATCATATGTTTCAAACCGTTTTTTATTATGG-AACAAT-CAGACAAAACGAGTT
1 AACT-GTTAAGATTATATGTTTCAAACC--TTTTTATTATGGAAACAATACAGACAAAAC-AGTT
3317107 TATAAGTCTAACATTATAGG
62 TATAAGTCTAACATTATAGG
3317127 TTGCGTCGTC
Statistics
Matches: 151, Mismatches: 19, Indels: 27
0.77 0.10 0.14
Matches are distributed among these distances:
100 4 0.03
101 7 0.05
102 83 0.55
103 53 0.35
105 4 0.03
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (102 bp):
AACTGTTAAGATTATATGTTTCAAACCTTTTTATTATGGAAACAATACAGACAAAACAGTTTATA
AGTCTAACATTATAGGATACACCTTTTTTTAATTGTC
Found at i:3317067 original size:204 final size:205
Alignment explanation
Indices: 3316742--3317125 Score: 468
Period size: 204 Copynumber: 1.9 Consensus size: 205
3316732 CTTATTCATC
*
3316742 GTTTATGTTATACGTTTGAAACCTTTTATATTTGAACAAAAGTAAGATAGAACATATTTATAAGT
1 GTTTAAGTTATACGTTTGAAACCTTTTATATTTG-ACAAAAGTAAGATAGAACATATTTATAAGT
* * * * * *
3316807 TTACCATTGTAGATTGCACATTCTTTTAATTAGAAACTGTTAAGATTATTTGTTTCAAACC-ATT
65 ATAACATTATAGATTGCACATTCTTTTAATTAGAAACTGTTAAAATCATATGTTTCAAACCGATT
3316871 TTTATTA-GGAAACAATACA-ACAAAAC-ATGTTGATAAGTCTAACATTATAGTTAACACCTTTT
130 TTTATTATGG-AACAAT-CAGACAAAACGA-GTTGATAAGTCTAACATTATAGTTAACACCTTTT
3316933 TTTAATTGTCAACT
192 TTTAATTGTCAACT
*
3316947 GTTTAAGTTATATGTTTGAAA-CTTTTCATATTATG-CAAAAGTAAGACTA-AACA-AGTTTATA
1 GTTTAAGTTATACGTTTGAAACCTTTT-ATATT-TGACAAAAGTAAGA-TAGAACATA-TTTATA
* *
3317008 AGTATAACATTATAGGA-TGCACGTT-TTTTAAATT-GTCAA-TCGTTAAAATCATATGTTTCAA
62 AGTATAACATTATA-GATTGCACATTCTTTT-AATTAG-AAACT-GTTAAAATCATATGTTTCAA
* *
3317069 ACCGTTTTTTATTATGGAACAATCAGACAAAACGAGTTTATAAGTCTAACATTATAG
123 ACCGATTTTTATTATGGAACAATCAGACAAAACGAGTTGATAAGTCTAACATTATAG
3317126 GTTGCGTCGT
Statistics
Matches: 155, Mismatches: 12, Indels: 24
0.81 0.06 0.13
Matches are distributed among these distances:
203 7 0.05
204 72 0.46
205 71 0.46
206 5 0.03
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (205 bp):
GTTTAAGTTATACGTTTGAAACCTTTTATATTTGACAAAAGTAAGATAGAACATATTTATAAGTA
TAACATTATAGATTGCACATTCTTTTAATTAGAAACTGTTAAAATCATATGTTTCAAACCGATTT
TTATTATGGAACAATCAGACAAAACGAGTTGATAAGTCTAACATTATAGTTAACACCTTTTTTTA
ATTGTCAACT
Found at i:3317294 original size:41 final size:41
Alignment explanation
Indices: 3317237--3317315 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
3317227 CCCAATATTT
*
3317237 ATTTGAAATCAAAACTTAGGTTGTAACATTTTACAAAAATA
1 ATTTGAAATCAAAACTTAAGTTGTAACATTTTACAAAAATA
3317278 ATTTGAAATCAAAACTTAAGTTGTAACATTTTACAAAA
1 ATTTGAAATCAAAACTTAAGTTGTAACATTTTACAAAA
3317316 CAAACTTGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.47, C:0.10, G:0.09, T:0.34
Consensus pattern (41 bp):
ATTTGAAATCAAAACTTAAGTTGTAACATTTTACAAAAATA
Found at i:3328704 original size:18 final size:18
Alignment explanation
Indices: 3328681--3328720 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3328671 AAACTGAATA
* *
3328681 AATTAATATTTCTTATAT
1 AATTAAGATATCTTATAT
*
3328699 AATTAAGATATCTTATCT
1 AATTAAGATATCTTATAT
3328717 AATT
1 AATT
3328721 TGAACTTACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (18 bp):
AATTAAGATATCTTATAT
Found at i:3329012 original size:37 final size:35
Alignment explanation
Indices: 3328940--3329012 Score: 83
Period size: 35 Copynumber: 2.0 Consensus size: 35
3328930 AATTGATTTA
* *
3328940 AAAAAAAATTTAGATAAGATAAATTTATGTAAAAT
1 AAAAAAAATTTAAATAAGATAAATTTAAGTAAAAT
* * *
3328975 AAAAACAATTTAAATAGAGATTCAATTTAAGTTAAAT
1 AAAAAAAATTTAAATA-AGA-TAAATTTAAGTAAAAT
3329012 A
1 A
3329013 GATTTGATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 14 0.45
36 3 0.10
37 14 0.45
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.32
Consensus pattern (35 bp):
AAAAAAAATTTAAATAAGATAAATTTAAGTAAAAT
Found at i:3330189 original size:29 final size:29
Alignment explanation
Indices: 3330155--3330213 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
3330145 ACCAAATATG
*
3330155 TGTAATTACAAATTAATTAAAAATATAAA
1 TGTAATTACAAATTAACTAAAAATATAAA
3330184 TGTAATTACAAATTAACTAAAAATATAAA
1 TGTAATTACAAATTAACTAAAAATATAAA
3330213 T
1 T
3330214 ATAAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (29 bp):
TGTAATTACAAATTAACTAAAAATATAAA
Found at i:3330601 original size:9 final size:9
Alignment explanation
Indices: 3330587--3330617 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
3330577 TCATATTAAA
3330587 TATTTTTTT
1 TATTTTTTT
3330596 TATTTTTTTT
1 TA-TTTTTTT
3330606 TATTTTTTT
1 TATTTTTTT
3330615 TAT
1 TAT
3330618 AATTACAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (9 bp):
TATTTTTTT
Found at i:3330604 original size:10 final size:10
Alignment explanation
Indices: 3330589--3330615 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
3330579 ATATTAAATA
3330589 TTTTTTTTAT
1 TTTTTTTTAT
3330599 TTTTTTTTAT
1 TTTTTTTTAT
3330609 TTTTTTT
1 TTTTTTT
3330616 ATAATTACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:3335091 original size:21 final size:21
Alignment explanation
Indices: 3335066--3335105 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3335056 TTTGATATTA
*
3335066 TGTTTGATATTTATAAATTTG
1 TGTTTGATATATATAAATTTG
*
3335087 TGTTTGATATATATTAATT
1 TGTTTGATATATATAAATT
3335106 AATTCAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (21 bp):
TGTTTGATATATATAAATTTG
Found at i:3335552 original size:18 final size:18
Alignment explanation
Indices: 3335508--3335544 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3335498 GTATTGAATC
*
3335508 TAGATTATATATTAAATT
1 TAGATTTTATATTAAATT
*
3335526 TAGATTTTATATTAGATT
1 TAGATTTTATATTAAATT
3335544 T
1 T
3335545 GAGTTTTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (18 bp):
TAGATTTTATATTAAATT
Found at i:3339316 original size:21 final size:21
Alignment explanation
Indices: 3339256--3339318 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
3339246 AATCAAGATC
3339256 AATTAAGGTAGGTACAAAT-A
1 AATTAAGGTAGGTACAAATGA
* * *
3339276 AATTAGGGTGGGCACAAATGA
1 AATTAAGGTAGGTACAAATGA
*
3339297 AATTAAGGTAGGTACGAATGA
1 AATTAAGGTAGGTACAAATGA
3339318 A
1 A
3339319 TCAGACGACA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
20 16 0.46
21 19 0.54
ACGTcount: A:0.44, C:0.06, G:0.27, T:0.22
Consensus pattern (21 bp):
AATTAAGGTAGGTACAAATGA
Found at i:3339586 original size:53 final size:52
Alignment explanation
Indices: 3339506--3339610 Score: 183
Period size: 53 Copynumber: 2.0 Consensus size: 52
3339496 CGCTTTAACA
*
3339506 CCGTTAAATATTTAATAGCTGAATGATAAAAAAACACTAATTATAATAAATTC
1 CCGTTAAATATTTAACAGCTGAATGAT-AAAAAACACTAATTATAATAAATTC
*
3339559 CCGTTAAATATTTAACAGCTGAATGATAAAAAACACTAATTATATTAAATTC
1 CCGTTAAATATTTAACAGCTGAATGATAAAAAACACTAATTATAATAAATTC
3339611 GGTGAAAACT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 24 0.48
53 26 0.52
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (52 bp):
CCGTTAAATATTTAACAGCTGAATGATAAAAAACACTAATTATAATAAATTC
Found at i:3340159 original size:201 final size:197
Alignment explanation
Indices: 3339814--3340211 Score: 697
Period size: 201 Copynumber: 2.0 Consensus size: 197
3339804 AATCTTTTCA
* *
3339814 ATCTATGGTTCAATCTTTACACATGGAAAATGAGTTATAGTCGATAAATGTTATGGATACGATTA
1 ATCTATGATTCAATCTTTACACATGGAAAATGAGTTATAATCGATAAATGTTATGGATACGATTA
* *
3339879 ACATTTTAGGTTTCGTCAAGAACGTCATGGTTCATTAAAAAATAAATTATGATCTTTAATATTAA
66 ACATTTTAGGTTTCATCAAGAACGTCATGATTCATTAAAAAATAAATTATGATCTTTAATATTAA
3339944 TATTTTTATTAATTATTCAAAAGTATTTATAGATTCTAATCCTTTGATTGATTCAAATATATTAT
131 TATTTTTATTAATTATTCAAAAGTATTTATAGATTCTAATCC--T--TTGATTCAAATATATTAT
3340009 TTTAAT
192 TTTAAT
*
3340015 ATCTATGATTCAATCTTTGCACATGGAAAATGAGTTATAATCGATAAATGTTATGGATACGATTA
1 ATCTATGATTCAATCTTTACACATGGAAAATGAGTTATAATCGATAAATGTTATGGATACGATTA
* *
3340080 ACGTTTTAGGTTTCATCAAGAATGTCATGATTCATTAAAAAATAAATTATGATCTTTAATATTAA
66 ACATTTTAGGTTTCATCAAGAACGTCATGATTCATTAAAAAATAAATTATGATCTTTAATATTAA
3340145 TATTTTTATTAATTATTCAAAAGTATTTATAGATTCTAATCCTTTGATTCAAATATATTATTTTA
131 TATTTTTATTAATTATTCAAAAGTATTTATAGATTCTAATCCTTTGATTCAAATATATTATTTTA
3340210 AT
196 AT
3340212 TTTTAAAATG
Statistics
Matches: 190, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
197 24 0.13
199 1 0.01
201 165 0.87
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.42
Consensus pattern (197 bp):
ATCTATGATTCAATCTTTACACATGGAAAATGAGTTATAATCGATAAATGTTATGGATACGATTA
ACATTTTAGGTTTCATCAAGAACGTCATGATTCATTAAAAAATAAATTATGATCTTTAATATTAA
TATTTTTATTAATTATTCAAAAGTATTTATAGATTCTAATCCTTTGATTCAAATATATTATTTTA
AT
Found at i:3340266 original size:13 final size:12
Alignment explanation
Indices: 3340251--3340291 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
3340241 TAAATTATAG
3340251 ATTTGATTTAGT
1 ATTTGATTTAGT
3340263 GATTTGA-TTA-T
1 -ATTTGATTTAGT
3340274 ATGTTGATTTAGT
1 AT-TTGATTTAGT
3340287 ATTTG
1 ATTTG
3340292 TAAATTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
10 2 0.08
11 5 0.20
12 9 0.36
13 9 0.36
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (12 bp):
ATTTGATTTAGT
Found at i:3341089 original size:21 final size:21
Alignment explanation
Indices: 3341051--3341090 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3341041 GTAAAAATAA
*
3341051 CTAAAACATTATTATTTTTAC
1 CTAAAACATTAATATTTTTAC
*
3341072 CTAAAACATTAATGTTTTT
1 CTAAAACATTAATATTTTT
3341091 TAACATTTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (21 bp):
CTAAAACATTAATATTTTTAC
Found at i:3351202 original size:14 final size:14
Alignment explanation
Indices: 3351183--3351221 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3351173 TAATGGGGAG
3351183 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
3351197 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
3351211 GAATCTCTGCA
1 TAATCCCTGCA
3351222 TATAGACAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:3360451 original size:29 final size:28
Alignment explanation
Indices: 3360403--3360536 Score: 126
Period size: 29 Copynumber: 4.5 Consensus size: 28
3360393 ATGGCAAGAA
*
3360403 AAAATATATTTTAACTTTTTATTCAACTTAT
1 AAAATATATTTT-A-TTTTTATTTAACTT-T
*
3360434 TAAATATATTTTATTTTTATTATAACTTT
1 AAAATATATTTTATTTTTATT-TAACTTT
* * *
3360463 AAAATGTATTTAATTTTTATCTTGACTTT
1 AAAATATATTTTATTTTTAT-TTAACTTT
*
3360492 AAAAATATATTTTATTCTTT-TATTAACTTA
1 -AAAATATATTTTATT-TTTAT-TTAACTTT
*
3360522 AAAATATTTTTTATT
1 AAAATATATTTTATT
3360537 AACTTATCTT
Statistics
Matches: 87, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
29 46 0.53
30 27 0.31
31 14 0.16
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.56
Consensus pattern (28 bp):
AAAATATATTTTATTTTTATTTAACTTT
Found at i:3360669 original size:29 final size:29
Alignment explanation
Indices: 3360586--3360780 Score: 143
Period size: 29 Copynumber: 6.8 Consensus size: 29
3360576 ACTTAAAGTA
* *
3360586 ATAATAA-AAAATACAATTTTAAGTTAAT
1 ATAATAATAAAATATATTTTTAAGTTAAT
* * *
3360614 A-AAAAATAATATATATATATTTGAAGTTAAG
1 ATAATAATAA-A-ATATAT-TTTTAAGTTAAT
*
3360645 ATAATAACAAAATATATTTTTAAGTTAAT
1 ATAATAATAAAATATATTTTTAAGTTAAT
* * *
3360674 AAAAGAATAAAATATA-TTTAAAGTTAAT
1 ATAATAATAAAATATATTTTTAAGTTAAT
*
3360702 AT-ATAA-GAAATATATATTTTAAGTTAAT
1 ATAATAATAAAATATAT-TTTTAAGTTAAT
* * * * *
3360730 A-AAAAATGAAATATATATTTAAAGATAAG
1 ATAATAATAAAATATAT-TTTTAAGTTAAT
* *
3360759 ATAAGAATAAAACAT-TTTTTAA
1 ATAATAATAAAATATATTTTTAA
3360781 ATAAAAAATA
Statistics
Matches: 132, Mismatches: 25, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
26 7 0.05
27 7 0.05
28 35 0.27
29 45 0.34
30 20 0.15
31 12 0.09
32 6 0.05
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (29 bp):
ATAATAATAAAATATATTTTTAAGTTAAT
Found at i:3360716 original size:28 final size:28
Alignment explanation
Indices: 3360626--3360753 Score: 118
Period size: 28 Copynumber: 4.5 Consensus size: 28
3360616 AAAATAATAT
* * *
3360626 ATATATATTTGAAGTTAAGATAATAACAA
1 ATATATATTTAAAGTTAATAT-ATAAGAA
*
3360655 A-ATATATTTTTAAGTTAATA-A-AAGAATA
1 ATATATA-TTTAAAGTTAATATATAAG-A-A
*
3360683 AAATATATTTAAAGTTAATATATAAGAA
1 ATATATATTTAAAGTTAATATATAAGAA
* * *
3360711 ATATATATTTTAAGTTAATAAAAAATGAA
1 ATATATATTTAAAGTTAATATATAA-GAA
3360740 ATATATATTTAAAG
1 ATATATATTTAAAG
3360754 ATAAGATAAG
Statistics
Matches: 83, Mismatches: 9, Indels: 14
0.78 0.08 0.13
Matches are distributed among these distances:
26 2 0.02
27 2 0.02
28 41 0.49
29 35 0.42
30 3 0.04
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.38
Consensus pattern (28 bp):
ATATATATTTAAAGTTAATATATAAGAA
Found at i:3360717 original size:57 final size:55
Alignment explanation
Indices: 3360578--3360798 Score: 208
Period size: 57 Copynumber: 4.0 Consensus size: 55
3360568 TTTTTTTAAC
*
3360578 TTAAAG-TAATA-ATAAAAAATACAATTTTAAGTTAATAAAAAATAATATATATATAT
1 TTAAAGTTAATATATAAAAAATA-TATTTTAAGTTAATAAAAAATAA-A-ATATATAT
* *
3360634 TTGAAGTTAAGATAATAACAAAATATATTTTTAAGTTAATAAAAGAAT-AAA-ATATAT
1 TTAAAGTTAATAT-ATAA-AAAATATA-TTTTAAGTTAATAAAA-AATAAAATATATAT
*
3360691 TTAAAGTTAATATATAAGAAATATATATTTTAAGTTAATAAAAAATGAAATATATAT
1 TTAAAGTTAATATATAA-AAA-ATATATTTTAAGTTAATAAAAAATAAAATATATAT
* * *
3360748 TTAAAGATAAGATA-AGAATAAA-ACATTTT---TTAAATAAAAAATAAAATATAT
1 TTAAAGTTAATATATA-AA-AAATATATTTTAAGTT-AATAAAAAATAAAATATAT
3360799 TTAATAAGTT
Statistics
Matches: 143, Mismatches: 10, Indels: 27
0.79 0.06 0.15
Matches are distributed among these distances:
52 2 0.01
53 18 0.13
55 9 0.06
56 34 0.24
57 47 0.33
58 1 0.01
59 6 0.04
60 23 0.16
61 3 0.02
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.35
Consensus pattern (55 bp):
TTAAAGTTAATATATAAAAAATATATTTTAAGTTAATAAAAAATAAAATATATAT
Found at i:3374993 original size:21 final size:21
Alignment explanation
Indices: 3374951--3374993 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3374941 TTTCTGGGCT
* * *
3374951 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
3374972 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
3374993 A
1 A
3374994 ACGAACCAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:3376617 original size:23 final size:23
Alignment explanation
Indices: 3376591--3376658 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
3376581 ATTATTATAT
*
3376591 GGCACTACGGTGCAATTCTATGC
1 GGCACTACGGTGCAATTCTACGC
* *
3376614 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
3376637 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
3376659 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:3378843 original size:21 final size:21
Alignment explanation
Indices: 3378817--3378860 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
3378807 CTTTAATAGT
3378817 GAAGAAGGCTTATATTTGTGG
1 GAAGAAGGCTTATATTTGTGG
3378838 GAAGAAGGCTTATATTTGTGG
1 GAAGAAGGCTTATATTTGTGG
3378859 GA
1 GA
3378861 TACTAAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.32
Consensus pattern (21 bp):
GAAGAAGGCTTATATTTGTGG
Found at i:3379640 original size:2 final size:2
Alignment explanation
Indices: 3379635--3379660 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3379625 AAAAAGGAAA
3379635 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3379661 CAAAGTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3380150 original size:2 final size:2
Alignment explanation
Indices: 3380143--3380197 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
3380133 AAAATAATTA
3380143 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3380185 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
3380198 CATGAATAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3381526 original size:105 final size:105
Alignment explanation
Indices: 3381225--3382202 Score: 1491
Period size: 105 Copynumber: 9.3 Consensus size: 105
3381215 CATTGTTCCA
* * ** *
3381225 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACAA
* * * *
3381289 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** * *
3381331 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
3381391 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** * * *
3381431 AGTCCAATATATTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGATAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
*
3381496 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
3381536 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
3381601 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
3381641 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
* *
3381706 AGCGGTCCCTTCGTCATGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
3381746 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
3381811 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
3381851 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
3381916 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
3381956 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGG-AAGTTG-TTGTTGACAA
*
3382021 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGG
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
3382063 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAC
* * * *
3382128 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
3382169 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
3382203 CGCGGATGGC
Statistics
Matches: 811, Mismatches: 50, Indels: 19
0.92 0.06 0.02
Matches are distributed among these distances:
100 82 0.10
101 1 0.00
102 7 0.01
104 5 0.01
105 499 0.62
106 97 0.12
107 98 0.12
109 22 0.03
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:3383116 original size:67 final size:67
Alignment explanation
Indices: 3383036--3383194 Score: 230
Period size: 67 Copynumber: 2.4 Consensus size: 67
3383026 GAAACGAAAT
* * *
3383036 TTTGTTTTAAGGGAGATAAAT-TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCATGGGAGACA
1 TTTGTTTCAAGGGAAAT-AATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACA
3383100 AAA
65 AAA
* * **
3383103 TTTGTTTCGAGGGAAATAATCTCAAAGGTTTTGTGTTTCAAGAGAAGTTGTCTCAAGGGAGACAA
1 TTTGTTTCAAGGGAAATAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAA
3383168 AA
66 AA
*
3383170 TTTGTTTCAAGGGAAATTATCTCAA
1 TTTGTTTCAAGGGAAATAATCTCAA
3383195 GAGAGACGAA
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
66 3 0.04
67 79 0.96
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (67 bp):
TTTGTTTCAAGGGAAATAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAA
AA
Found at i:3383309 original size:102 final size:102
Alignment explanation
Indices: 3383069--3383528 Score: 652
Period size: 102 Copynumber: 4.5 Consensus size: 102
3383059 AAAGATTTTG
* * * * ** * ** * *
3383069 TGTTTCAAGAGAAACTGTCTCATGGGAGACAAAATTTGTTTCGAGGGAAATAATCTCAAAGGTTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTC-AATG-TT
* ** *
3383134 TGTGTTTCAAGAGAAGTTGTCTCAAGGGAGACAAAA-TT
64 TATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
* * *
3383172 TGTTTCAAGGGAAATTATCTCAAGAGAGACGAAATTCATTTCTAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
3383237 TGTTTCAGGAGAAACTGTCTCAAGGGAGATAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
*
3383274 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
3383339 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
*
3383376 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
3383441 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAG-AAAAAATTT
* * **
3383479 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTTTGTTTCAAGGGAAA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
3383529 CTGTCTCAAG
Statistics
Matches: 324, Mismatches: 31, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
101 33 0.10
102 192 0.59
103 99 0.31
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (102 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
Found at i:3383425 original size:204 final size:206
Alignment explanation
Indices: 3383069--3383528 Score: 692
Period size: 205 Copynumber: 2.2 Consensus size: 206
3383059 AAAGATTTTG
* * * *
3383069 TGTTTCAAGAGAAACTGTCTCATGGGAGACAAAATTTGTTTCGAGGGAAATAATCTCAAAGGTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATAATCTCAAAGGTTT
* ** * *
3383134 TGTGTTTCAAGAGAAGTTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATTATCTCAAGAGA
66 TATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTGTTTCAAGGGAAACTATCTCAAGAGA
* * * *
3383199 GACGAAATTCATTTCTAGGGAAATGTTTTCAATGTTTATGTTTCAGGAGAAACTGTCTCAAGGGA
131 GACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGA
*
3383264 G-ATAAAATTT
196 GAAAAAAATTT
* ** * * * *
3383274 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAAT-GTTTCCAATG-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATAATCTCAAAGGTTT
3383337 TATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAG
66 TATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAA-TTTGTTTCAAGGGAAACTATCTCAAGAG
3383402 AGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGG
130 AGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGG
3383467 AGAAAAAAATTT
195 AGAAAAAAATTT
*
3383479 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTTTGTTTCAAGGGAAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
3383529 CTGTCTCAAG
Statistics
Matches: 228, Mismatches: 25, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
203 34 0.15
204 96 0.42
205 98 0.43
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (206 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATAATCTCAAAGGTTT
TATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTGTTTCAAGGGAAACTATCTCAAGAGA
GACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGA
GAAAAAAATTT
Found at i:3383493 original size:38 final size:37
Alignment explanation
Indices: 3383441--3383543 Score: 145
Period size: 36 Copynumber: 2.8 Consensus size: 37
3383431 TCAATGTTTA
* *
3383441 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAA-GGAGAAAAAAAGTT
* *
3383479 TGTTTCAAGGGAAACTGTCTCAA-GAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGGAGAAAAAAAGTT
3383515 TGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGGGAAACTGTCTCAAG-GAGA
3383544 CAATGGTGAG
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
36 33 0.56
38 26 0.44
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGGAGAAAAAAAGTT
Found at i:3385068 original size:20 final size:21
Alignment explanation
Indices: 3385044--3385105 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
3385034 TTTTTTGTTC
*
3385044 CCTTTTTTATTTTTGTTCTTT
1 CCTTTTTTATTCTTGTTCTTT
* *
3385065 -CTTTTTTGTTCTTGTTTTTT
1 CCTTTTTTATTCTTGTTCTTT
*
3385085 CCTTTTTTGCTTCTT-TTCTTT
1 CCTTTTTT-ATTCTTGTTCTTT
3385106 TTTCTTTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 12 0.35
22 5 0.15
ACGTcount: A:0.02, C:0.16, G:0.06, T:0.76
Consensus pattern (21 bp):
CCTTTTTTATTCTTGTTCTTT
Found at i:3385116 original size:22 final size:22
Alignment explanation
Indices: 3385062--3385114 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
3385052 ATTTTTGTTC
3385062 TTTCTTTTTTG-TTCTTGTTTT
1 TTTCTTTTTTGCTTCTTGTTTT
* *
3385083 TTCCTTTTTTGCTTCTTTTCTTT
1 TTTCTTTTTTGCTTCTTGT-TTT
3385106 TTTCTTTTT
1 TTTCTTTTT
3385115 GCCCTTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 10 0.37
22 6 0.22
23 11 0.41
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (22 bp):
TTTCTTTTTTGCTTCTTGTTTT
Found at i:3386284 original size:8 final size:8
Alignment explanation
Indices: 3386271--3386306 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
3386261 GTAGATGAAG
3386271 ATGCAAAA
1 ATGCAAAA
3386279 ATGCAAAA
1 ATGCAAAA
3386287 ATGC-AAA
1 ATGCAAAA
*
3386294 ATGCAAGA
1 ATGCAAAA
3386302 ATGCA
1 ATGCA
3386307 TGAAATGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.56, C:0.14, G:0.17, T:0.14
Consensus pattern (8 bp):
ATGCAAAA
Found at i:3386296 original size:15 final size:15
Alignment explanation
Indices: 3386271--3386306 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
3386261 GTAGATGAAG
3386271 ATGCAAAAATGCAAAA
1 ATGC-AAAATGCAAAA
*
3386287 ATGCAAAATGCAAGA
1 ATGCAAAATGCAAAA
3386302 ATGCA
1 ATGCA
3386307 TGAAATGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.56, C:0.14, G:0.17, T:0.14
Consensus pattern (15 bp):
ATGCAAAATGCAAAA
Found at i:3388288 original size:2 final size:2
Alignment explanation
Indices: 3388186--3388269 Score: 161
Period size: 2 Copynumber: 42.5 Consensus size: 2
3388176 AAAAAGGAAA
3388186 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3388228 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3388269 A
1 A
3388270 AAATAATATA
Statistics
Matches: 81, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 80 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3388700 original size:2 final size:2
Alignment explanation
Indices: 3388688--3388735 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
3388678 TAAAATAATA
3388688 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3388729 AT AT AT A
1 AT AT AT A
3388736 ATAATAACAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3388766 original size:17 final size:18
Alignment explanation
Indices: 3388733--3388768 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3388723 ATATATATAT
*
3388733 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
3388751 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
3388768 A
1 A
3388769 AATATCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:3389284 original size:20 final size:20
Alignment explanation
Indices: 3389237--3389570 Score: 235
Period size: 20 Copynumber: 16.2 Consensus size: 20
3389227 AATGACCAAC
* *
3389237 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
*
3389256 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* * **
3389276 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTTAG
* * **
3389296 AAGATCGCAACACGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
* * *
3389317 AAGAATCGCAATGCGATTCAT
1 AA-AATCGCAACGCGATTTAG
**
3389338 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
3389359 AAGAATCGCAACGCGATTCAG
1 AA-AATCGCAACGCGATTTAG
**
3389380 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
3389401 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTTAG
*
3389422 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-TAG
* * *
3389442 AGAATCGCAATGCGATTCAG
1 AAAATCGCAACGCGATTTAG
*
3389462 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-TAG
* **
3389482 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
3389503 AAGAATCGCAACGCGATTCAG
1 AA-AATCGCAACGCGATTTAG
**
3389524 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
3389545 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTTAG
3389566 AAAAT
1 AAAAT
3389571 GAGTAAATTC
Statistics
Matches: 246, Mismatches: 52, Indels: 33
0.74 0.16 0.10
Matches are distributed among these distances:
19 20 0.08
20 126 0.51
21 33 0.13
22 67 0.27
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:3389345 original size:42 final size:42
Alignment explanation
Indices: 3389294--3389561 Score: 329
Period size: 42 Copynumber: 6.4 Consensus size: 42
3389284 AACGTTGAAA
* * *
3389294 AGAAGATCGCAACACGATCTTCCAAGAATCGCAATGCGATTC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
*
3389336 ATAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
*
3389378 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTA
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
*
3389420 AGAAAATCGCAACGCGA--TTCCAAGAATCGCAATGCGATTC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
3389460 AGAAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATCTTCC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGA--TT-C
* *
3389503 A-AGAATCGCAACGCGA--TT-CAGAAAATCGCAACGCGATCTTCC
1 AGAAAATCGCAACGCGATCTTCCA-AGAATCGCAACGCGA--TT-C
*
3389545 A-AGAATCGCAACGCGAT
1 AGAAAATCGCAACGCGAT
3389562 TAAGAAAATG
Statistics
Matches: 210, Mismatches: 11, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
40 57 0.27
41 2 0.01
42 149 0.71
43 2 0.01
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (42 bp):
AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
Found at i:3389347 original size:62 final size:59
Alignment explanation
Indices: 3389240--3389539 Score: 275
Period size: 62 Copynumber: 4.9 Consensus size: 59
3389230 GACCAACAAA
* * * * *
3389240 ATCGCAACGCGATAT-CAA-AACCGCAACGCGATTTAGAAAAGCGCAACGTTGAAAAGAAG
1 ATCGCAACGCGAT-TCCAAGAATCGCAACGCGATTCAGAAAATCGCAACG-CGATAAGAAG
* * * ***
3389299 ATCGCAACACGATCTTCCAAGAATCGCAATGCGATTCATAAAATCGCAACGCGATCTTCCAAG
1 ATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGA--TAAGAAG
* * *
3389362 AATCGCAACGCGATT-CAGAAAATCGCAACGCGATCTTCCA-AGAATCGCAACGCGATTAAGAAA
1 -ATCGCAACGCGATTCCA-AGAATCGCAACGCGA--TT-CAGAAAATCGCAACGCGA-TAAGAAG
* ***
3389425 ATCGCAACGCGATTCCAAGAATCGCAATGCGATTCAGAAAATCGCAACGCGATTCCAAG
1 ATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATAAGAAG
3389484 AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGAT
1 -ATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGAT
3389540 CTTCCAAGAA
Statistics
Matches: 197, Mismatches: 28, Indels: 29
0.78 0.11 0.11
Matches are distributed among these distances:
59 16 0.08
60 29 0.15
61 8 0.04
62 107 0.54
63 8 0.04
64 27 0.14
65 2 0.01
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (59 bp):
ATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATAAGAAG
Found at i:3389677 original size:6 final size:6
Alignment explanation
Indices: 3389666--3389730 Score: 102
Period size: 6 Copynumber: 11.5 Consensus size: 6
3389656 GACACGTATT
3389666 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
3389713 ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACC
3389731 CGAGACGGCG
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 20 0.34
6 39 0.66
ACGTcount: A:0.29, C:0.54, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:3390239 original size:6 final size:6
Alignment explanation
Indices: 3390219--3390389 Score: 307
Period size: 6 Copynumber: 29.3 Consensus size: 6
3390209 CCGTCGTCTC
3390219 GTCG-G GTCG-G GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
3390265 GTC--- GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
3390310 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
3390358 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
3390390 AATACGTGTC
Statistics
Matches: 162, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
3 3 0.02
5 9 0.06
6 150 0.93
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
GTCGTG
Found at i:3390541 original size:20 final size:20
Alignment explanation
Indices: 3390485--3390964 Score: 426
Period size: 20 Copynumber: 23.2 Consensus size: 20
3390475 GAATTTACTC
3390485 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
3390505 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
*
3390527 ATTTACTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
3390547 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
3390567 ATTTTCTTGGAAGATCGCGTTGCG
1 ATTTTC-T-G-A-ATCGCGTTGCG
*
3390591 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
3390611 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
*
3390633 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
3390653 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
*
3390675 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
3390695 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
3390715 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
3390735 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
3390755 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
3390775 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
3390797 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
3390817 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
3390837 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
* *
3390859 ATTTTATGAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
*
3390879 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
* ** *
3390901 ATCTTCT-TTTCAACGTTGCG
1 ATTTTCTGAATC-GCGTTGCG
* *
3390921 CTTTTCTAAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
3390941 -GTTT-TGATATCGCGTTGCG
1 ATTTTCTGA-ATCGCGTTGCG
3390960 ATTTT
1 ATTTT
3390965 GTTGGTCATT
Statistics
Matches: 388, Mismatches: 38, Indels: 68
0.79 0.08 0.14
Matches are distributed among these distances:
18 2 0.01
19 20 0.05
20 219 0.56
21 38 0.10
22 90 0.23
23 2 0.01
24 17 0.04
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
ATTTTCTGAATCGCGTTGCG
Found at i:3390549 original size:42 final size:41
Alignment explanation
Indices: 3390492--3390964 Score: 430
Period size: 42 Copynumber: 11.4 Consensus size: 41
3390482 CTCATTTTCT
* *
3390492 GAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTAC-T-
1 GAATCGCGTTGCGATT-TTCGTA-ATCGCGTTGCGATTT-CTTG
*
3390534 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTTTCTTG
1 GAATCGCGTTGCGATTTTCGTAATCGCGTTGCGA-TTTCTTG
*
3390576 GAAGATCGCGTTGCGATTTTCTTAATCGCGTTGCGA-TTCTTG
1 G-A-ATCGCGTTGCGATTTTCGTAATCGCGTTGCGATTTCTTG
*
3390618 GAAGATCGCGTTGCGATTTTCTTAATCGCGTTGCGA-TTCTTG
1 G-A-ATCGCGTTGCGATTTTCGTAATCGCGTTGCGATTTCTTG
*
3390660 GAAGATCGCGTTGCGATTCTT-GGAATCGCGTTGCGA-TTCTTG
1 G-A-ATCGCGTTGCGATT-TTCGTAATCGCGTTGCGATTTCTTG
3390702 GAATCGCGTTGCGATTTTC-TGAATCGCGTTGCGA-TTCTTG
1 GAATCGCGTTGCGATTTTCGT-AATCGCGTTGCGATTTCTTG
*
3390742 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGA-TTCTTG
1 GAATCGCGTTGCGATTTTCGTAATCGCGTTGCGATTTCTTG
3390782 GAAGATCGCGTTGCGATTTTC-TGAATCGCGTTGCGATTT-TCT-
1 G-A-ATCGCGTTGCGATTTTCGT-AATCGCGTTGCGATTTCT-TG
* *
3390824 GAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTT-TAT-
1 GAATCGCGTTGCGATT-TTCGTA-ATCGCGTTGCGATTTCT-TG
* * *
3390866 GAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATCTTCTT-
1 GAATCGCGTTGCGATT-TTCGTA-ATCGCGTTGCGAT-TTCTTG
* * * *
3390909 --TTCAACGTTGCGCTTTTC-TAAATCGCGTTGCG-GTT-TT-
1 GAATC-GCGTTGCGATTTTCGT-AATCGCGTTGCGATTTCTTG
3390946 GATATCGCGTTGCGATTTT
1 GA-ATCGCGTTGCGATTTT
3390965 GTTGGTCATT
Statistics
Matches: 387, Mismatches: 20, Indels: 51
0.84 0.04 0.11
Matches are distributed among these distances:
37 2 0.01
38 2 0.01
39 13 0.03
40 112 0.29
41 20 0.05
42 196 0.51
43 9 0.02
44 33 0.09
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.38
Consensus pattern (41 bp):
GAATCGCGTTGCGATTTTCGTAATCGCGTTGCGATTTCTTG
Found at i:3390561 original size:62 final size:58
Alignment explanation
Indices: 3390485--3390963 Score: 398
Period size: 62 Copynumber: 7.7 Consensus size: 58
3390475 GAATTTACTC
3390485 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTACTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATT-TTGG-A-ATCGCGTTGCGATTT-CTGAATCGCGTTGCG
* *
3390547 ATTTTCTTAATCGCGTTGCGATTTTCTTGGAAGATCGCGTTGCGATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGA--TT-TTGG-A-ATCGCGTTGCGA-TTTCTGAATCGCGTTGCG
* **
3390611 ATTCTT-GGAAGATCGCGTTGCGATTTTCTTAATCGCGTTGCGA-TTCTTGGAAGATCGCGTTGC
1 ATT-TTCTG-A-ATCGCGTTGCGATTTT-GGAATCGCGTTGCGATTTC-T-G-A-ATCGCGTTGC
3390674 G
58 G
*
3390675 ATTCTT-GGAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCGATT-TTGGAATCGCGTTGCGA-TTTCTGAATCGCGTTGCG
* **
3390735 ATTCTT-GGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGA-TTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCGATTTT-GGAATCGCGTTGCGATTTC-T-G-A-ATCGCGTTGCG
*
3390797 ATTTTCTGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGA-TTCTTGGAAGATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTTT-GGAATCGCGTTGCGATTTC-T-G-A-ATCGCGTTGCG
* * ** *
3390859 ATTTTATGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATCTTCT-TTTCAACGTTGCG
1 ATTTTCTGAATCGCGTTGCGATT-TTGG-A-ATCGCGTTGCGAT-TTCTGAATC-GCGTTGCG
* * *
3390921 CTTTTCTAAATCGCGTTGCGGTTTT-GATATCGCGTTGCGATTT
1 ATTTTCTGAATCGCGTTGCGATTTTGGA-ATCGCGTTGCGATTT
3390964 TGTTGGTCAT
Statistics
Matches: 366, Mismatches: 25, Indels: 56
0.82 0.06 0.13
Matches are distributed among these distances:
58 5 0.01
59 17 0.05
60 52 0.14
61 9 0.02
62 175 0.48
63 11 0.03
64 75 0.20
65 7 0.02
66 15 0.04
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.38
Consensus pattern (58 bp):
ATTTTCTGAATCGCGTTGCGATTTTGGAATCGCGTTGCGATTTCTGAATCGCGTTGCG
Found at i:3406536 original size:30 final size:28
Alignment explanation
Indices: 3406458--3406545 Score: 95
Period size: 28 Copynumber: 3.1 Consensus size: 28
3406448 AAAAAGTTTG
* * **
3406458 AATAGTTTAGGTACCTATTTTGACTCAA
1 AATACTTTAGGTACTTATTTTGACAAAA
*
3406486 AATACTTTAGGTATTTATTTTGACAAAA
1 AATACTTTAGGTACTTATTTTGACAAAA
* *
3406514 AGATACTTTTAAGTACTTATTTTGATAAAA
1 A-ATAC-TTTAGGTACTTATTTTGACAAAA
3406544 AA
1 AA
3406546 AATGCTTTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
28 24 0.48
29 5 0.10
30 21 0.42
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (28 bp):
AATACTTTAGGTACTTATTTTGACAAAA
Found at i:3406555 original size:30 final size:29
Alignment explanation
Indices: 3406484--3406560 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 29
3406474 ATTTTGACTC
* * *
3406484 AAAATACTTTAGGTATTTATTTTGACAAA
1 AAAATACTTTAAGTACTTATTTTGAAAAA
*
3406513 AAGATACTTTTAAGTACTTATTTTGATAAAA
1 AAAATAC-TTTAAGTACTTATTTTGA-AAAA
*
3406544 AAAATGCTTTAAGTACT
1 AAAATACTTTAAGTACT
3406561 GAAATAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 6 0.15
30 26 0.65
31 8 0.20
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (29 bp):
AAAATACTTTAAGTACTTATTTTGAAAAA
Found at i:3415786 original size:28 final size:28
Alignment explanation
Indices: 3415746--3415845 Score: 91
Period size: 28 Copynumber: 3.6 Consensus size: 28
3415736 CGTAGGTAGT
* * *
3415746 CATGCTTCCGGGCGACTTTATAAGTTGC
1 CATGCATCCGGGCGACCTTATAAGTCGC
* *
3415774 CATGCATCCGGGCGACCTTGTAGGTCGC
1 CATGCATCCGGGCGACCTTATAAGTCGC
* *
3415802 CATGCA-CTCGGG-GACC-TGTAGGTCGC
1 CATGCATC-CGGGCGACCTTATAAGTCGC
3415828 CATGCA-CTCGGGCGACCT
1 CATGCATC-CGGGCGACCT
3415846 ACCCTTGCTC
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
26 22 0.34
27 9 0.14
28 33 0.52
ACGTcount: A:0.16, C:0.31, G:0.30, T:0.23
Consensus pattern (28 bp):
CATGCATCCGGGCGACCTTATAAGTCGC
Found at i:3415828 original size:26 final size:27
Alignment explanation
Indices: 3415772--3415845 Score: 116
Period size: 26 Copynumber: 2.7 Consensus size: 27
3415762 TTTATAAGTT
3415772 GCCATGCA-TCCGGGCGACCTTGTAGGTC
1 GCCATGCACT-CGGGCGACC-TGTAGGTC
3415800 GCCATGCACTCGGG-GACCTGTAGGTC
1 GCCATGCACTCGGGCGACCTGTAGGTC
3415826 GCCATGCACTCGGGCGACCT
1 GCCATGCACTCGGGCGACCT
3415846 ACCCTTGCTC
Statistics
Matches: 44, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
26 22 0.50
27 9 0.20
28 12 0.27
29 1 0.02
ACGTcount: A:0.15, C:0.34, G:0.32, T:0.19
Consensus pattern (27 bp):
GCCATGCACTCGGGCGACCTGTAGGTC
Found at i:3415938 original size:29 final size:29
Alignment explanation
Indices: 3415899--3415966 Score: 109
Period size: 29 Copynumber: 2.3 Consensus size: 29
3415889 GTCATGCTAT
* *
3415899 CGGGCGACCTTGTAGGTCGTCATACCCTC
1 CGGGCGACCTTGTAGGTCGCCATACACTC
*
3415928 CGGGCGACCTTGTAGGTCGCCATGCACTC
1 CGGGCGACCTTGTAGGTCGCCATACACTC
3415957 CGGGCGACCT
1 CGGGCGACCT
3415967 ACCCTCGTCG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.13, C:0.35, G:0.31, T:0.21
Consensus pattern (29 bp):
CGGGCGACCTTGTAGGTCGCCATACACTC
Found at i:3426814 original size:31 final size:31
Alignment explanation
Indices: 3426776--3426837 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
3426766 TCTAGGAAGT
3426776 AAGATTCTACCTTGCCATCGCCAAACTGAGC
1 AAGATTCTACCTTGCCATCGCCAAACTGAGC
3426807 AAGATTCTACCTTGCCATCGCCAAACTGAGC
1 AAGATTCTACCTTGCCATCGCCAAACTGAGC
3426838 TCGATAAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.23
Consensus pattern (31 bp):
AAGATTCTACCTTGCCATCGCCAAACTGAGC
Found at i:3430405 original size:28 final size:28
Alignment explanation
Indices: 3430373--3430447 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
3430363 GAAAAAAATT
* *
3430373 AAATATTTTATGTACTTATTTTGACCAA
1 AAATATTTTAGGTACTTATTTTGACAAA
* *
3430401 AAATATTTTAGGTATTTCTTTTGACAAAA
1 AAATATTTTAGGTACTTATTTTGAC-AAA
* *
3430430 AAATACTATAGGTACTTA
1 AAATATTTTAGGTACTTA
3430448 GATAAAAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
28 22 0.58
29 16 0.42
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (28 bp):
AAATATTTTAGGTACTTATTTTGACAAA
Found at i:3432382 original size:2 final size:2
Alignment explanation
Indices: 3432375--3432401 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3432365 ACTGTAATTG
3432375 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 T
3432402 GTTCTGGCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3434944 original size:2 final size:2
Alignment explanation
Indices: 3434937--3434962 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3434927 CGAATAGATG
3434937 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3434963 TTTCGGGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3441897 original size:42 final size:42
Alignment explanation
Indices: 3441829--3441908 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
3441819 GGGTTTCAGT
* *
3441829 TGGTGAATTGACTGATGTAGTATTGGATGGAGGTGGTGATGC
1 TGGTGAATTGACTGATATAGTATTGGATGGAGATGGTGATGC
* * *
3441871 TGGTGCATTGATTGATATAGTCTTGGATGGAGATGGTG
1 TGGTGAATTGACTGATATAGTATTGGATGGAGATGGTG
3441909 CATTGTTGCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.21, C:0.05, G:0.39, T:0.35
Consensus pattern (42 bp):
TGGTGAATTGACTGATATAGTATTGGATGGAGATGGTGATGC
Found at i:3449433 original size:80 final size:80
Alignment explanation
Indices: 3449333--3449487 Score: 215
Period size: 80 Copynumber: 1.9 Consensus size: 80
3449323 AAGGGTAGCC
* *
3449333 AACCTAAGAATATACCTTGGGTA-TACCCAAGGACATCATTAGATCCGTAGGGTTACCTTATGCA
1 AACCTAAGAATATACCTTGGGGACTAACCAA-GACATCATTAGATCCGTAGGGTTACCTTATGCA
3449397 CACAACAAAGGAAACT
65 CACAACAAAGGAAACT
* * * * *
3449413 AACCTAATG-ATATGCCTTGGGGACTAACCAAGATATCCTTAGGTTCGTAGGGTTACCTTATGCA
1 AACCTAA-GAATATACCTTGGGGACTAACCAAGACATCATTAGATCCGTAGGGTTACCTTATGCA
3449477 CACAACAAAGG
65 CACAACAAAGG
3449488 GAACCAATGT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
80 59 0.89
81 7 0.11
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (80 bp):
AACCTAAGAATATACCTTGGGGACTAACCAAGACATCATTAGATCCGTAGGGTTACCTTATGCAC
ACAACAAAGGAAACT
Found at i:3464398 original size:18 final size:18
Alignment explanation
Indices: 3464375--3464424 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
3464365 GAGATAACTT
*
3464375 TTATTTTTTTATTTTGAA
1 TTATTTATTTATTTTGAA
3464393 TTATTTATTTATTTTGAA
1 TTATTTATTTATTTTGAA
*
3464411 TCATTTATTTATTT
1 TTATTTATTTATTT
3464425 ATTTTGAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (18 bp):
TTATTTATTTATTTTGAA
Found at i:3464424 original size:44 final size:44
Alignment explanation
Indices: 3464374--3464469 Score: 128
Period size: 44 Copynumber: 2.3 Consensus size: 44
3464364 GGAGATAACT
* * * *
3464374 TTTATTTTTTTATTTTGAAT-TATT--T-ATTTATTTTGAATCA
1 TTTATTTATTTATTTTGAATAAATTAGTGATTTATTTCGAATAA
3464414 TTTATTTATTTATTTTGAATAAATTAGTGATTTATTTCGAATAA
1 TTTATTTATTTATTTTGAATAAATTAGTGATTTATTTCGAATAA
3464458 TTTATTTATTTA
1 TTTATTTATTTA
3464470 ATTAAAGGGG
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
40 19 0.40
41 3 0.06
43 1 0.02
44 25 0.52
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.62
Consensus pattern (44 bp):
TTTATTTATTTATTTTGAATAAATTAGTGATTTATTTCGAATAA
Found at i:3464446 original size:26 final size:22
Alignment explanation
Indices: 3464374--3464469 Score: 110
Period size: 22 Copynumber: 4.5 Consensus size: 22
3464364 GGAGATAACT
*
3464374 TTTATTTTTTTATTTTG---AA
1 TTTATTTATTTATTTTGAATAA
*
3464393 -TTATTTATTTATTTTGAATCA
1 TTTATTTATTTATTTTGAATAA
3464414 TTTATTTATTTATTTTGAATAA
1 TTTATTTATTTATTTTGAATAA
* * * *
3464436 ATTAGTGATTTATTTCGAATAA
1 TTTATTTATTTATTTTGAATAA
3464458 TTTATTTATTTA
1 TTTATTTATTTA
3464470 ATTAAAGGGG
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
18 15 0.24
21 1 0.02
22 47 0.75
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.62
Consensus pattern (22 bp):
TTTATTTATTTATTTTGAATAA
Found at i:3464921 original size:14 final size:13
Alignment explanation
Indices: 3464904--3464951 Score: 62
Period size: 14 Copynumber: 3.6 Consensus size: 13
3464894 ATTTTTATTT
3464904 ATTTATTTCGAATA
1 ATTTATTTC-AATA
*
3464918 ATTTATTT-TATA
1 ATTTATTTCAATA
3464930 ATTTATTTCAAATA
1 ATTTATTTC-AATA
3464944 ATTTATTT
1 ATTTATTT
3464952 ATTTATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 11 0.37
14 19 0.63
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.58
Consensus pattern (13 bp):
ATTTATTTCAATA
Found at i:3464963 original size:26 final size:26
Alignment explanation
Indices: 3464897--3465008 Score: 122
Period size: 26 Copynumber: 4.4 Consensus size: 26
3464887 GGAGGTAATT
*
3464897 TTTATTTATTTATTTCGAATAATTTA
1 TTTATTTATTAATTTCGAATAATTTA
* * *
3464923 TTT-TATAATTTATTTCAAATAATTTA
1 TTTAT-TTATTAATTTCGAATAATTTA
* *
3464949 TTTATTTATTAATTTTGAATAA--TG
1 TTTATTTATTAATTTCGAATAATTTA
* *
3464973 TTTATTTATTAATTTTGAATAAATTA
1 TTTATTTATTAATTTCGAATAATTTA
3464999 TTTATTTATT
1 TTTATTTATT
3465009 TTTATTAATT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
24 23 0.31
25 1 0.01
26 49 0.66
27 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.61
Consensus pattern (26 bp):
TTTATTTATTAATTTCGAATAATTTA
Found at i:3465013 original size:32 final size:32
Alignment explanation
Indices: 3464977--3465040 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
3464967 ATAATGTTTA
3464977 TTTATTAATTTTGAATAAATTATTT-ATTTATT
1 TTTATTAATTTTGAAT-AATTATTTAATTTATT
*
3465009 TTTATTAATTTTGAATAATTTTTTAATTTATT
1 TTTATTAATTTTGAATAATTATTTAATTTATT
3465041 CGTTTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 7 0.23
32 23 0.77
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (32 bp):
TTTATTAATTTTGAATAATTATTTAATTTATT
Found at i:3465037 original size:50 final size:51
Alignment explanation
Indices: 3464897--3465033 Score: 127
Period size: 54 Copynumber: 2.6 Consensus size: 51
3464887 GGAGGTAATT
* * *
3464897 TTTATTTATTTATTTCGAATAATTTATTT-TATAA-TTT-ATTTCAAATAATTTA
1 TTTATTTATTAATTTTGAATAA-TTATTTAT-TAATTTTGA-AT-AAATAATTTA
*
3464949 TTTATTTATTAATTTTGAATAATGTTTATTTATTAATTTTGAATAAATTATTTA
1 TTTATTTATTAATTTTGAATAA---TTATTTATTAATTTTGAATAAATAATTTA
*
3465003 TTTATTTTTATTAATTTTGAATAATTTTTTA
1 TTTA--TTTATTAATTTTGAATAATTATTTA
3465034 ATTTATTCGT
Statistics
Matches: 73, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
52 20 0.27
53 6 0.08
54 23 0.32
55 5 0.07
56 19 0.26
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (51 bp):
TTTATTTATTAATTTTGAATAATTATTTATTAATTTTGAATAAATAATTTA
Found at i:3470165 original size:23 final size:22
Alignment explanation
Indices: 3470135--3470178 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
3470125 TTTTGTGCTG
3470135 AAAACAAGATAAAAAATAAGATT
1 AAAACAAGATAAAAAA-AAGATT
*
3470158 AAAACAAGATAAAGAAAAGAT
1 AAAACAAGATAAAAAAAAGAT
3470179 AAAGGAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.70, C:0.05, G:0.11, T:0.14
Consensus pattern (22 bp):
AAAACAAGATAAAAAAAAGATT
Found at i:3470687 original size:25 final size:22
Alignment explanation
Indices: 3470658--3470703 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3470648 TTTTTAACCC
3470658 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
3470683 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
3470704 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:3473287 original size:2 final size:2
Alignment explanation
Indices: 3473282--3473315 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3473272 ATATACTTGA
3473282 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3473316 TGAAAATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3473643 original size:3 final size:3
Alignment explanation
Indices: 3473637--3473666 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3473627 GTTCCAAATC
3473637 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
3473667 ATTTTCATGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:3473751 original size:2 final size:2
Alignment explanation
Indices: 3473746--3473792 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
3473736 TCTCTCTCTC
3473746 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3473788 TA TA T
1 TA TA T
3473793 GCTAGTATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3475433 original size:21 final size:21
Alignment explanation
Indices: 3475407--3475448 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3475397 TATAGTGATG
3475407 GATCTAGAAA-TTTAATATTAA
1 GATCTA-AAATTTTAATATTAA
*
3475428 GATCTAAAATTTTAATTTTAA
1 GATCTAAAATTTTAATATTAA
3475449 TTTTTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (21 bp):
GATCTAAAATTTTAATATTAA
Found at i:3477437 original size:3 final size:3
Alignment explanation
Indices: 3477422--3477455 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
3477412 AGTTTCTCTT
*
3477422 TTA TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3477456 CAATGTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:3494586 original size:36 final size:36
Alignment explanation
Indices: 3494539--3494630 Score: 175
Period size: 36 Copynumber: 2.6 Consensus size: 36
3494529 TTAAAAATGC
3494539 ACGATTTAAGACCAAAGACAATTGATTTGAGATTAT
1 ACGATTTAAGACCAAAGACAATTGATTTGAGATTAT
3494575 ACGATTTAAGACCAAAGACAATTGATTTGAGATTAT
1 ACGATTTAAGACCAAAGACAATTGATTTGAGATTAT
*
3494611 ACGATTTAAGACGAAAGACA
1 ACGATTTAAGACCAAAGACA
3494631 CAATTAGTGA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.27
Consensus pattern (36 bp):
ACGATTTAAGACCAAAGACAATTGATTTGAGATTAT
Found at i:3504717 original size:42 final size:42
Alignment explanation
Indices: 3504660--3504789 Score: 219
Period size: 42 Copynumber: 3.1 Consensus size: 42
3504650 ACTATCACAA
*
3504660 TGCGA-TT-TTCCAAATTCATTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
* *
3504700 TGCGATTTATTCCAAATTCGTTGTGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
3504742 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
3504784 TGCGAT
1 TGCGAT
3504790 AGTCGAAGTT
Statistics
Matches: 83, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
40 5 0.06
41 2 0.02
42 76 0.92
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (42 bp):
TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
Found at i:3504785 original size:63 final size:62
Alignment explanation
Indices: 3504687--3504961 Score: 256
Period size: 63 Copynumber: 4.3 Consensus size: 62
3504677 ATTGCGATAG
* * * *
3504687 TCCAAGTTCGCGTTGCGATTTATTCCAAATT-CGTTGTGATAGTCGAAGTTCGCGTTGCGATTTA
1 TCCAAGTT--CGTTGCGA--TAGTCCAAGTTGCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTA
3504751 T
62 T
* *
3504752 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCCAAGTT-GCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTAT
* * * * * *
3504815 TCCAAGTTTGTTGCGATAGTCGAAGTTTGCGTTGCGATTTATTCCAAATT--CGTTGGGA--TAG
1 TCCAAGTTCGTTGCGATAGTCCAAG-TTGCGTTGCGA--TAGTCCAAGTTCGCGTTGCGATTTAT
* * *
3504876 TCGAAGTTCGCGTTGCGATTTATTCCAAATT-CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTA
1 TCCAAGTT--CGTTGCGA--TAGTCCAAGTTGCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTA
3504940 T
62 T
*
3504941 TCCAAGTTCGTTGCGAAAGTC
1 TCCAAGTTCGTTGCGATAGTC
3504962 AAATATGTAA
Statistics
Matches: 173, Mismatches: 24, Indels: 30
0.76 0.11 0.13
Matches are distributed among these distances:
61 30 0.17
63 109 0.63
64 4 0.02
65 30 0.17
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (62 bp):
TCCAAGTTCGTTGCGATAGTCCAAGTTGCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTAT
Found at i:3504806 original size:42 final size:43
Alignment explanation
Indices: 3504678--3504950 Score: 230
Period size: 42 Copynumber: 6.5 Consensus size: 43
3504668 TCCAAATTCA
* * *
3504678 TTGCGA-TAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT--CG
1 TTGCGATTATTCCAAGTTCGCGTTGCGA--TAGTCCAAGTTCGCG
* * * * *
3504720 TTGTGA-TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT--CG
1 TTGCGATTATTCCAAGTTCGCGTTGCGA--TAGTCCAAGTTCGCG
* *
3504762 TTGCGA-TAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCG
1 TTGCGATTATTCCAAGTTCGCGTTGCGATAGTCCAAGTTCGCG
* * *
3504804 TTGCGATTTATTCCAAGTT--TGTTGCGATAGTCGAAGTTTGCG
1 TTGCGA-TTATTCCAAGTTCGCGTTGCGATAGTCCAAGTTCGCG
* * *
3504846 TTGCGATTTATTCCAAATT--CGTTGGGATAGTCGAAGTTCGCG
1 TTGCGA-TTATTCCAAGTTCGCGTTGCGATAGTCCAAGTTCGCG
*
3504888 TTGCGATTTATTCCAAATT--CGTTGCGATAGTCCAAGTTCGCG
1 TTGCGA-TTATTCCAAGTTCGCGTTGCGATAGTCCAAGTTCGCG
3504930 TTGCGATTTATTCCAAGTTCG
1 TTGCGA-TTATTCCAAGTTCG
3504951 TTGCGAAAGT
Statistics
Matches: 208, Mismatches: 17, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
40 8 0.04
42 190 0.91
44 10 0.05
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.36
Consensus pattern (43 bp):
TTGCGATTATTCCAAGTTCGCGTTGCGATAGTCCAAGTTCGCG
Found at i:3504812 original size:105 final size:105
Alignment explanation
Indices: 3504678--3504894 Score: 371
Period size: 105 Copynumber: 2.1 Consensus size: 105
3504668 TCCAAATTCA
*
3504678 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGTGATAGTCGAAGTTCGCGTT
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
3504743 GCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
66 GCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
* * * *
3504783 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTTGTTGCGATAGTCGAAGTTTGCGTT
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
* *
3504848 GCGATTTATTCCAAATTCGTTGGGATAGTCGAAGTTCGCG
66 GCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
3504888 TTGCGAT
1 TTGCGAT
3504895 TTATTCCAAA
Statistics
Matches: 105, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
105 105 1.00
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (105 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
GCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
Found at i:3504951 original size:42 final size:42
Alignment explanation
Indices: 3504771--3504961 Score: 301
Period size: 42 Copynumber: 4.5 Consensus size: 42
3504761 GTTGCGATAG
3504771 TCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* *
3504815 TCCAAGTTTGTTGCGATAGTCGAAGTTTGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* *
3504857 TCCAAATTCGTTGGGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* *
3504899 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
*
3504941 TCCAAGTTCGTTGCGAAAGTC
1 TCCAAGTTCGTTGCGATAGTC
3504962 AAATATGTAA
Statistics
Matches: 137, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
42 129 0.94
44 8 0.06
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (42 bp):
TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
Found at i:3506667 original size:21 final size:20
Alignment explanation
Indices: 3506621--3506670 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
3506611 TTTCAACTTT
* *
3506621 TTGTAACTCTTGTAATTACT
1 TTGTAACTCATGTAATTACC
3506641 TGTGTAACTCATGTAATTACAC
1 T-TGTAACTCATGTAATTAC-C
3506663 TTGTAACT
1 TTGTAACT
3506671 GGCATAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (20 bp):
TTGTAACTCATGTAATTACC
Found at i:3507259 original size:21 final size:21
Alignment explanation
Indices: 3507235--3507283 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
3507225 TTCAACTCTT
* **
3507235 TGTAACTCTTGTAATTACTTG
1 TGTAACTCTTGAAATTACACG
3507256 TGTAACTCTTGAAATTACACG
1 TGTAACTCTTGAAATTACACG
3507277 TGTAACT
1 TGTAACT
3507284 AACATAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (21 bp):
TGTAACTCTTGAAATTACACG
Found at i:3507770 original size:613 final size:613
Alignment explanation
Indices: 3506515--3508090 Score: 2694
Period size: 613 Copynumber: 2.6 Consensus size: 613
3506505 TAGAACTCTT
* * * * * * * * *
3506515 TAAATTTGATTAATTTATGAATTTAATATCATGTTTGAAACTGCTTACATAAAAAAAATGAACTT
1 TAAATATGACTAATTTTTTAATTTAATCTCATGTTTGAAACTGCTAAAAT-AAAAAATTGAACCT
* * * *
3506580 GGCCTCTAACCTATTCA-ATTTGTTG-CTTAATTTTCAACTTTTTGTAACTCTTGTAATTACTTG
65 GG-CTCTAACCCATCCAGATTTG-CGACTTAATTTTCAACTCTTTGTAACTCTTGTAATTACTTG
* * * ** * * *
3506643 TGTAACTCATGTAATTACACTTGTAACTGGCATAATAAACAACTCATTATTCACTCTAAACAGAG
128 TGTAACTCTTGAAATTACACGTGTAACTAACATAATAAACAACTCATTATTCACTTTGAACAAAG
*
3506708 TTGAAAAACCATGTCGGTACACTCAAACGTTCACAAATTAAAATTCAGAAACTGATTGTTTAAAT
193 CTGAAAAACCATGTCGGTACACTCAAACGTTCACAAATTAAAATTCAGAAACTGATTGTTTAAAT
3506773 TTTAATTTTTAGAAATCAGAATAGAATTAGCATATAAATATCATAATAAAATTCTTTCACAATAT
258 TTTAATTTTTAGAAATCAGAATAGAATTAGCATATAAATATCATAATAAAATTCTTTCACAATAT
*
3506838 TTTATGCTTGAGAAAAATCCTTACGAATTTTCTCTAAAAAAATAGTATTCGCACGGACATGCAAG
323 TTTATGCTTGAGAAAAATCCTTAAGAATTTTCTCTAAAAAAATAGTATTCGCACGGACATGCAAG
3506903 CGAATTGTCTCCAGAGGTTAACACGGTCACTCCAAATTCTGTACACCCGAAATCGGAATGGACTG
388 CGAATTGTCTCCAGAGGTTAACACGGTCACTCCAAATTCTGTACACCCGAAATCGGAATGGACTG
*
3506968 CCGGTGATACCTATTCTTCTGATAGCAACCGAGAAAAGAGACTTAGAACTCTTTAAATTTAATAG
453 CCGGTGATACCTATTCTTCTGATAGCAACCGAGAAAAGAGACTTAGAACTCTTTAAATTTAAGAG
3507033 AATTGCGAGTATTGAATGAAATTAGTGAGTTGAGAAGCTAATGAAGCTCTCTATTTATAGGCTCA
518 AATTGCGAGTATTGAATGAAATTAGTGAGTTGAGAAGCTAATGAAGCTCTCTATTTATAGGCTCA
*
3507098 GGGGTAAAATCATCCATAGCAAAATCAAATA
583 AGGGTAAAATCATCCATAGCAAAATCAAATA
3507129 TAAATATGACTAATTTTTTAATTTAATCTCATGTTTGAAACTGCTAAAATAAAAAATTGAACCTG
1 TAAATATGACTAATTTTTTAATTTAATCTCATGTTTGAAACTGCTAAAATAAAAAATTGAACCTG
3507194 GCTCTAACCCATCCAGATTTGCGACTTAATTTTCAACTCTTTGTAACTCTTGTAATTACTTGTGT
66 GCTCTAACCCATCCAGATTTGCGACTTAATTTTCAACTCTTTGTAACTCTTGTAATTACTTGTGT
3507259 AACTCTTGAAATTACACGTGTAACTAACATAATAAACAACTCATTATTCACTTTGAACAAAGCTG
131 AACTCTTGAAATTACACGTGTAACTAACATAATAAACAACTCATTATTCACTTTGAACAAAGCTG
3507324 AAAAACCATGTCGGTACACTCAAACGTTCACAAATTAAAATTCAGAAACTGATTGTTTAAATTTT
196 AAAAACCATGTCGGTACACTCAAACGTTCACAAATTAAAATTCAGAAACTGATTGTTTAAATTTT
*
3507389 AATTTTCAGAAATCAGAATAGAATTAGCATATAAATATCATAATAAAATTCTTTCACAATATTTT
261 AATTTTTAGAAATCAGAATAGAATTAGCATATAAATATCATAATAAAATTCTTTCACAATATTTT
*
3507454 ATGCTTGAGAAAAATCCTTAAGAATTTTCTCTAAAAAAATAGTATTCGCACGGACGTGCAAGCGA
326 ATGCTTGAGAAAAATCCTTAAGAATTTTCTCTAAAAAAATAGTATTCGCACGGACATGCAAGCGA
3507519 ATTGTCTCCAGAGGTTAACACGGTCACTCCAAATTCTGTACACCCGAAATCGGAATGGACTGCCG
391 ATTGTCTCCAGAGGTTAACACGGTCACTCCAAATTCTGTACACCCGAAATCGGAATGGACTGCCG
3507584 GTGATACCTATTCTTCTGATAGCAACCGAGAAAAGAGACTTAGAACTCTTTAAATTTAAGAGAAT
456 GTGATACCTATTCTTCTGATAGCAACCGAGAAAAGAGACTTAGAACTCTTTAAATTTAAGAGAAT
3507649 TGCGAGTATTGAATGAAATTAGTGAGTTGAGAAGCTAATGAAGCTCTCTATTTATAGGCTCAAGG
521 TGCGAGTATTGAATGAAATTAGTGAGTTGAGAAGCTAATGAAGCTCTCTATTTATAGGCTCAAGG
3507714 GTAAAATCATCCATAGCAAAATCAAATA
586 GTAAAATCATCCATAGCAAAATCAAATA
3507742 TAAATATGACTAATTTTTTAATTTAATCTCATGTTTGAAACTGCTAAAATAAAAAATTGAACCTG
1 TAAATATGACTAATTTTTTAATTTAATCTCATGTTTGAAACTGCTAAAATAAAAAATTGAACCTG
3507807 GCTCTAACCCATCCAGATTTGCGACTTAATTTTCAACTCTTTGTAACTCTTGTAATTACTCT-TG
66 GCTCTAACCCATCCAGATTTGCGACTTAATTTTCAACTCTTTGTAACTCTTGTAATTACT-TGTG
3507871 TAACTCTTGAAATTACACGTGTAACTAACATAATAAACAACTCATTATTCACTTTGAACAAAGCT
130 TAACTCTTGAAATTACACGTGTAACTAACATAATAAACAACTCATTATTCACTTTGAACAAAGCT
* * *
3507936 G-AAAACCAT-CCAGATACACTCAAACGTTCACAAATTAAAATTCAGAAACTGACTGTTTAAATT
195 GAAAAACCATGTC-GGTACACTCAAACGTTCACAAATTAAAATTCAGAAACTGATTGTTTAAATT
* * * * *
3507999 TTAATTTTTAGAAATCAGAACAGAAGCTAATTAACATATAAATATTAGAATGAAATTCTTTCACA
259 TTAATTTTTAGAAATCAG-A-A-TAG--AATTAGCATATAAATATCATAATAAAATTCTTTCACA
* *
3508064 ATTTTTTATGCTTGAGAAATATCCTTA
319 ATATTTTATGCTTGAGAAAAATCCTTA
3508091 CGATTTTTTT
Statistics
Matches: 915, Mismatches: 38, Indels: 15
0.95 0.04 0.02
Matches are distributed among these distances:
611 1 0.00
612 87 0.10
613 722 0.79
614 45 0.05
615 2 0.00
617 58 0.06
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.33
Consensus pattern (613 bp):
TAAATATGACTAATTTTTTAATTTAATCTCATGTTTGAAACTGCTAAAATAAAAAATTGAACCTG
GCTCTAACCCATCCAGATTTGCGACTTAATTTTCAACTCTTTGTAACTCTTGTAATTACTTGTGT
AACTCTTGAAATTACACGTGTAACTAACATAATAAACAACTCATTATTCACTTTGAACAAAGCTG
AAAAACCATGTCGGTACACTCAAACGTTCACAAATTAAAATTCAGAAACTGATTGTTTAAATTTT
AATTTTTAGAAATCAGAATAGAATTAGCATATAAATATCATAATAAAATTCTTTCACAATATTTT
ATGCTTGAGAAAAATCCTTAAGAATTTTCTCTAAAAAAATAGTATTCGCACGGACATGCAAGCGA
ATTGTCTCCAGAGGTTAACACGGTCACTCCAAATTCTGTACACCCGAAATCGGAATGGACTGCCG
GTGATACCTATTCTTCTGATAGCAACCGAGAAAAGAGACTTAGAACTCTTTAAATTTAAGAGAAT
TGCGAGTATTGAATGAAATTAGTGAGTTGAGAAGCTAATGAAGCTCTCTATTTATAGGCTCAAGG
GTAAAATCATCCATAGCAAAATCAAATA
Found at i:3507873 original size:21 final size:21
Alignment explanation
Indices: 3507842--3507896 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
3507832 TTAATTTTCA
*
3507842 ACTCTTTGTAACTCTTGTAATT
1 ACTC-TTGTAACTCTTGAAATT
3507864 ACTCTTGTAACTCTTGAAATT
1 ACTCTTGTAACTCTTGAAATT
* *
3507885 ACACGTGTAACT
1 ACTCTTGTAACT
3507897 AACATAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 26 0.87
22 4 0.13
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.42
Consensus pattern (21 bp):
ACTCTTGTAACTCTTGAAATT
Found at i:3513407 original size:23 final size:22
Alignment explanation
Indices: 3513376--3513420 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
3513366 AGAAATTTAA
*
3513376 CTTTCTTTG-AATGCTTTAGTTT
1 CTTTCTTTGTAATACTTT-GTTT
3513398 CTTTCCTTTGTAATACTTTGTTT
1 CTTT-CTTTGTAATACTTTGTTT
3513421 TTGCACAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 9 0.45
24 7 0.35
ACGTcount: A:0.13, C:0.16, G:0.11, T:0.60
Consensus pattern (22 bp):
CTTTCTTTGTAATACTTTGTTT
Found at i:3513863 original size:5 final size:5
Alignment explanation
Indices: 3513853--3513877 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3513843 CACATCGTTG
3513853 CAGAC CAGAC CAGAC CAGAC CAGAC
1 CAGAC CAGAC CAGAC CAGAC CAGAC
3513878 TGGAAATAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.40, G:0.20, T:0.00
Consensus pattern (5 bp):
CAGAC
Found at i:3516008 original size:11 final size:11
Alignment explanation
Indices: 3515990--3516025 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
3515980 TGCTTTTGTG
3515990 TTTCTTTTCTT
1 TTTCTTTTCTT
*
3516001 TTTTTTTTCTT
1 TTTCTTTTCTT
*
3516012 TTTCTCTTCTT
1 TTTCTTTTCTT
3516023 TTT
1 TTT
3516026 GAGGCCTGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:3516008 original size:22 final size:22
Alignment explanation
Indices: 3515983--3516025 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3515973 GGTGCTCTGC
* *
3515983 TTTTGTGTTTCTTTTCTTTTTT
1 TTTTCTGTTTCTCTTCTTTTTT
*
3516005 TTTTCTTTTTCTCTTCTTTTT
1 TTTTCTGTTTCTCTTCTTTTT
3516026 GAGGCCTGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (22 bp):
TTTTCTGTTTCTCTTCTTTTTT
Found at i:3520868 original size:47 final size:47
Alignment explanation
Indices: 3520805--3520940 Score: 202
Period size: 47 Copynumber: 2.9 Consensus size: 47
3520795 AAATTATCGA
* * *
3520805 ATCAATTGAGTTAAATTTAGTATTTATACG-TAGAATTAAATAAATTT
1 ATCAATTGAGTTAAATTTAATATTTATACGAT-GAATCAAATAAACTT
* *
3520852 ATCAATTGAGTTAAATTTAATAATTATATGATGAATCAAATAAACTT
1 ATCAATTGAGTTAAATTTAATATTTATACGATGAATCAAATAAACTT
*
3520899 ATCAATTGAGTTAAATTTAATATTTATATGATGAATCAAATA
1 ATCAATTGAGTTAAATTTAATATTTATACGATGAATCAAATA
3520941 GGTTTGATAA
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
47 81 0.99
48 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (47 bp):
ATCAATTGAGTTAAATTTAATATTTATACGATGAATCAAATAAACTT
Found at i:3520873 original size:27 final size:26
Alignment explanation
Indices: 3520838--3520920 Score: 70
Period size: 27 Copynumber: 3.3 Consensus size: 26
3520828 TTATACGTAG
3520838 AATTAAATAAATTTATCAATTGAGTTA
1 AATTAAATAAA-TTATCAATTGAGTTA
* *
3520865 AATTTAAT-AATTAT--A-TGA--TG
1 AATTAAATAAATTATCAATTGAGTTA
*
3520885 AATCAAATAAACTTATCAATTGAGTTA
1 AATTAAATAAA-TTATCAATTGAGTTA
*
3520912 AATTTAATA
1 AATTAAATA
3520921 TTTATATGAT
Statistics
Matches: 42, Mismatches: 7, Indels: 14
0.67 0.11 0.22
Matches are distributed among these distances:
20 7 0.17
21 2 0.05
22 7 0.17
23 1 0.02
24 1 0.02
25 7 0.17
26 2 0.05
27 15 0.36
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (26 bp):
AATTAAATAAATTATCAATTGAGTTA
Found at i:3520892 original size:25 final size:25
Alignment explanation
Indices: 3520864--3520939 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
3520854 CAATTGAGTT
3520864 AAATTTAATAATTATATGATGAATC
1 AAATTTAATAATTATATGATGAATC
* * *
3520889 AAA--TAA-ACTTATCA--ATTGAGTT
1 AAATTTAATAATTAT-ATGA-TGAATC
*
3520911 AAATTTAATATTTATATGATGAATC
1 AAATTTAATAATTATATGATGAATC
3520936 AAAT
1 AAAT
3520940 AGGTTTGATA
Statistics
Matches: 38, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
21 1 0.03
22 12 0.32
23 4 0.11
24 4 0.11
25 16 0.42
26 1 0.03
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.39
Consensus pattern (25 bp):
AAATTTAATAATTATATGATGAATC
Found at i:3520914 original size:22 final size:22
Alignment explanation
Indices: 3520840--3520914 Score: 55
Period size: 22 Copynumber: 3.3 Consensus size: 22
3520830 ATACGTAGAA
*
3520840 TTAAATAAATTTATCAATTGAG
1 TTAAATAAAATTATCAATTGAG
*
3520862 TTAAATTTAATAATTAT--ATGATGAA
1 TTAAA--TAA-AATTATCAAT--TGAG
* *
3520887 TCAAATAAACTTATCAATTGAG
1 TTAAATAAAATTATCAATTGAG
3520909 TTAAAT
1 TTAAAT
3520915 TTAATATTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 18 0.45
23 5 0.12
24 5 0.12
25 12 0.30
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (22 bp):
TTAAATAAAATTATCAATTGAG
Found at i:3521274 original size:19 final size:19
Alignment explanation
Indices: 3521252--3521303 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
3521242 TTATTTTTGA
3521252 AAAATATAATTATAAAAAT-
1 AAAA-ATAATTATAAAAATG
*
3521271 AAAAAT-ATGATAAAAATG
1 AAAAATAATTATAAAAATG
3521289 AAAAAATAATT-TAAA
1 -AAAAATAATTATAAA
3521304 TATGGAAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 10 0.36
18 2 0.07
19 14 0.50
20 2 0.07
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (19 bp):
AAAAATAATTATAAAAATG
Found at i:3525689 original size:92 final size:92
Alignment explanation
Indices: 3525532--3525705 Score: 303
Period size: 92 Copynumber: 1.9 Consensus size: 92
3525522 AAACTCTTAC
* * *
3525532 TCAGATTCTTCTTTTTTTCCTCCAACAGCTGTGTCCTTAGCAAAACATCTCCCAATTTCTGTTGC
1 TCAGATTCTTCTTGTTTTCCTCCAACAGCTGTGCCCTTAGCAAAACATCTCCCAAGTTCTGTTGC
3525597 ACAATTGTAGCTATAAGGCTGGTTCAT
66 ACAATTGTAGCTATAAGGCTGGTTCAT
*
3525624 TCAGATTCTTCTTGTTTTCCTCTAACAGCTGTGCCCTTAGCAAAACATCTCCCAAGTTCTGTTGC
1 TCAGATTCTTCTTGTTTTCCTCCAACAGCTGTGCCCTTAGCAAAACATCTCCCAAGTTCTGTTGC
*
3525689 ACAATTGTAGTTATAAG
66 ACAATTGTAGCTATAAG
3525706 AGTGGCTCAT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
92 77 1.00
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.37
Consensus pattern (92 bp):
TCAGATTCTTCTTGTTTTCCTCCAACAGCTGTGCCCTTAGCAAAACATCTCCCAAGTTCTGTTGC
ACAATTGTAGCTATAAGGCTGGTTCAT
Found at i:3531482 original size:21 final size:22
Alignment explanation
Indices: 3531435--3531492 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
3531425 TATTTCAAAT
* * *
3531435 AATATATAAATTTTAACATTATT
1 AATAT-TAATTTTTAAAATTATA
3531458 AATATTAATTTTTAAAATTA-A
1 AATATTAATTTTTAAAATTATA
*
3531479 AATATTATTTTTTA
1 AATATTAATTTTTA
3531493 GAGTTACTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
AATATTAATTTTTAAAATTATA
Found at i:3534222 original size:20 final size:20
Alignment explanation
Indices: 3534193--3534240 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
3534183 CTTCTCTACC
3534193 CAAGAACCCTAAATTGAATT
1 CAAGAACCCTAAATTGAATT
* *
3534213 CAAGAGCCCTAAATTTAATT
1 CAAGAACCCTAAATTGAATT
3534233 CAAGAACC
1 CAAGAACC
3534241 TACTGTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.44, C:0.23, G:0.10, T:0.23
Consensus pattern (20 bp):
CAAGAACCCTAAATTGAATT
Found at i:3541732 original size:28 final size:28
Alignment explanation
Indices: 3541701--3541756 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
3541691 TGGTTGAAGC
*
3541701 AGGGTAAATGTTGAAGAAGAATCTTGGT
1 AGGGTAAATGTTGAAGAAGAAACTTGGT
*
3541729 AGGGTATATGTTGAAGAAGAAACTTGGT
1 AGGGTAAATGTTGAAGAAGAAACTTGGT
3541757 GAGGTGTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.36, C:0.04, G:0.32, T:0.29
Consensus pattern (28 bp):
AGGGTAAATGTTGAAGAAGAAACTTGGT
Found at i:3541785 original size:52 final size:52
Alignment explanation
Indices: 3541729--3541837 Score: 146
Period size: 52 Copynumber: 2.1 Consensus size: 52
3541719 GAATCTTGGT
* * * * *
3541729 AGGGTATATGTTGAAGAAGAAACTTGGTGAGGTGTTGAAAGCTGGTTGGAGC
1 AGGGTAAATGTTGAAGAACAAACTTAGTGAGGTGTTGAAAGCTAGTTGAAGC
** *
3541781 AGGGTAAATGTTGAAGGTCAAGCTTAGTGAGGTGTTGAAAGCTAGTTGAAGC
1 AGGGTAAATGTTGAAGAACAAACTTAGTGAGGTGTTGAAAGCTAGTTGAAGC
3541833 AGGGT
1 AGGGT
3541838 GCTGTTGAAG
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.29, C:0.06, G:0.38, T:0.27
Consensus pattern (52 bp):
AGGGTAAATGTTGAAGAACAAACTTAGTGAGGTGTTGAAAGCTAGTTGAAGC
Found at i:3541868 original size:51 final size:52
Alignment explanation
Indices: 3541729--3541881 Score: 132
Period size: 52 Copynumber: 3.0 Consensus size: 52
3541719 GAATCTTGGT
* ** * * * *
3541729 AGGGTATATGTTGAAGAAGAAACTT-GGTGAGGTGTTGAAAGCTGGTTGGAGC
1 AGGGTAAATGTTGAAGATCAAGCTTAGG-GAGCTGTTGAAAGCTAGTTGAAGC
* * *
3541781 AGGGTAAATGTTGAAGGTCAAGCTTAGTGAGGTGTTGAAAGCTAGTTGAAGC
1 AGGGTAAATGTTGAAGATCAAGCTTAGGGAGCTGTTGAAAGCTAGTTGAAGC
** * * * *
3541833 AGGGT-GCTGTTGAAGATCTAGCTTGGGGTGCTGTTG-AAGTTAGTTGAAG
1 AGGGTAAATGTTGAAGATCAAGCTTAGGGAGCTGTTGAAAGCTAGTTGAAG
3541882 TTAGTTGAAG
Statistics
Matches: 83, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
50 12 0.14
51 23 0.28
52 47 0.57
53 1 0.01
ACGTcount: A:0.27, C:0.07, G:0.37, T:0.29
Consensus pattern (52 bp):
AGGGTAAATGTTGAAGATCAAGCTTAGGGAGCTGTTGAAAGCTAGTTGAAGC
Found at i:3541880 original size:10 final size:10
Alignment explanation
Indices: 3541865--3541898 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
3541855 TTGGGGTGCT
3541865 GTTGAAGTTA
1 GTTGAAGTTA
3541875 GTTGAAGTTA
1 GTTGAAGTTA
*
3541885 GTTGAAGTTT
1 GTTGAAGTTA
3541895 GTTG
1 GTTG
3541899 GGTTTGTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (10 bp):
GTTGAAGTTA
Found at i:3549329 original size:22 final size:21
Alignment explanation
Indices: 3549301--3549343 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3549291 TTTTTAGAAC
3549301 GCTACAGGGGTACCGATACCCT
1 GCTACA-GGGTACCGATACCCT
* *
3549323 GCTACAGTGTAGCGATACCCT
1 GCTACAGGGTACCGATACCCT
3549344 CATTGTTCGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.23, C:0.30, G:0.26, T:0.21
Consensus pattern (21 bp):
GCTACAGGGTACCGATACCCT
Done.