Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 169 of 250
Found at i:54296412 original size:23 final size:25
Alignment explanation
Indices: 54296367--54296413 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
54296357 AATAAATATA
*
54296367 CATAAAATATATGGAAATGATGAAG
1 CATAAAATATATGGAAATAATGAAG
*
54296392 CATAAAATAT-T-GATATAATGAA
1 CATAAAATATATGGAAATAATGAA
54296414 ATGAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (25 bp):
CATAAAATATATGGAAATAATGAAG
Found at i:54306210 original size:21 final size:21
Alignment explanation
Indices: 54306184--54306224 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54306174 ATCTGCTCAA
* *
54306184 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
54306205 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
54306225 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:54312159 original size:29 final size:29
Alignment explanation
Indices: 54312116--54312173 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
54312106 CATTTAATAC
* *
54312116 AACTTTGGCAAAATTACATTTTTGCCCTA
1 AACTTTGGCAAAATTACACTTTTCCCCTA
* *
54312145 AACTTTTGCATAATTACACTTTTCCCCTA
1 AACTTTGGCAAAATTACACTTTTCCCCTA
54312174 GGCTCGGGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (29 bp):
AACTTTGGCAAAATTACACTTTTCCCCTA
Found at i:54329851 original size:18 final size:18
Alignment explanation
Indices: 54329810--54329876 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 18
54329800 AAGTTTATAA
*
54329810 ATTTTAAATTTTTTTAAT
1 ATTTTTAATTTTTTTAAT
*
54329828 AATTTTAATGTTTTTT-AT
1 ATTTTTAAT-TTTTTTAAT
*
54329846 ATTTTT-ATTTTTACTAATT
1 ATTTTTAATTTTT-TTAA-T
54329865 ATCTTTTAATTT
1 AT-TTTTAATTT
54329877 CATAAAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
16 4 0.10
17 3 0.08
18 15 0.38
19 9 0.23
20 4 0.10
21 4 0.10
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.67
Consensus pattern (18 bp):
ATTTTTAATTTTTTTAAT
Found at i:54344911 original size:38 final size:38
Alignment explanation
Indices: 54344868--54345063 Score: 266
Period size: 38 Copynumber: 5.2 Consensus size: 38
54344858 AACACACTAG
*
54344868 ACAGAAGCTCATAAGAGTTGATCCAACCGAAACACCAA
1 ACAGAAGCTCATAAGAGCTGATCCAACCGAAACACCAA
* ****
54344906 ACAGAAGCTCATAAGAGCTAATCCAACCGATTTTCCAA
1 ACAGAAGCTCATAAGAGCTGATCCAACCGAAACACCAA
* * *
54344944 ATAGAAGCTCATAAGAGCTAATCCAACCAAAACACCAA
1 ACAGAAGCTCATAAGAGCTGATCCAACCGAAACACCAA
* * *
54344982 ACAGAAGCTCATAAGAGTTGATCCAACCGAATCGCCAA
1 ACAGAAGCTCATAAGAGCTGATCCAACCGAAACACCAA
* *
54345020 ACAAAAGCTCATAAGAGCTGATCCAACCGAAACGCCAA
1 ACAGAAGCTCATAAGAGCTGATCCAACCGAAACACCAA
54345058 ACAGAA
1 ACAGAA
54345064 AGTATAACAC
Statistics
Matches: 136, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 136 1.00
ACGTcount: A:0.44, C:0.27, G:0.15, T:0.14
Consensus pattern (38 bp):
ACAGAAGCTCATAAGAGCTGATCCAACCGAAACACCAA
Found at i:54344996 original size:76 final size:76
Alignment explanation
Indices: 54344868--54345063 Score: 293
Period size: 76 Copynumber: 2.6 Consensus size: 76
54344858 AACACACTAG
*
54344868 ACAGAAGCTCATAAGAGTTGATCCAACCGAAACACCAAACAGAAGCTCATAAGAGCTAATCCAAC
1 ACAGAAGCTCATAAGAGCTGATCCAACCGAAACACCAAACAGAAGCTCATAAGAGCTAATCCAAC
* **
54344933 CGATTTTCCAA
66 CGAATCGCCAA
* * * * *
54344944 ATAGAAGCTCATAAGAGCTAATCCAACCAAAACACCAAACAGAAGCTCATAAGAGTTGATCCAAC
1 ACAGAAGCTCATAAGAGCTGATCCAACCGAAACACCAAACAGAAGCTCATAAGAGCTAATCCAAC
54345009 CGAATCGCCAA
66 CGAATCGCCAA
* *
54345020 ACAAAAGCTCATAAGAGCTGATCCAACCGAAACGCCAAACAGAA
1 ACAGAAGCTCATAAGAGCTGATCCAACCGAAACACCAAACAGAA
54345064 AGTATAACAC
Statistics
Matches: 106, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
76 106 1.00
ACGTcount: A:0.44, C:0.27, G:0.15, T:0.14
Consensus pattern (76 bp):
ACAGAAGCTCATAAGAGCTGATCCAACCGAAACACCAAACAGAAGCTCATAAGAGCTAATCCAAC
CGAATCGCCAA
Found at i:54346042 original size:24 final size:23
Alignment explanation
Indices: 54345998--54346042 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
54345988 TTATTTTATT
* **
54345998 TTACTAATTATCTCTTTATTAAA
1 TTACTAATTACCTCTCAATTAAA
54346021 TTACTAATTTACCTCTCAATTA
1 TTACTAA-TTACCTCTCAATTA
54346043 TACATGCATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49
Consensus pattern (23 bp):
TTACTAATTACCTCTCAATTAAA
Found at i:54351670 original size:9 final size:9
Alignment explanation
Indices: 54351628--54351687 Score: 52
Period size: 10 Copynumber: 6.6 Consensus size: 9
54351618 AAAAAAACTT
54351628 ATTTTTATGA
1 ATTTTTAT-A
*
54351638 GTTTTTAGTA
1 ATTTTTA-TA
*
54351648 ATTTTAATA
1 ATTTTTATA
54351657 ATTTTTAT-
1 ATTTTTATA
*
54351665 ATTTTTCTAA
1 ATTTTTAT-A
54351675 ATTTTTA-A
1 ATTTTTATA
54351683 ATTTT
1 ATTTT
54351688 AAAAATTAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
8 13 0.32
9 9 0.22
10 18 0.44
11 1 0.02
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (9 bp):
ATTTTTATA
Found at i:54351693 original size:17 final size:18
Alignment explanation
Indices: 54351639--54351694 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
54351629 TTTTTATGAG
*
54351639 TTTTTAGTAATTTTAATAA
1 TTTTTA-TAATTTTAAAAA
* **
54351658 TTTTTATATTTTTCTAAA
1 TTTTTATAATTTTAAAAA
54351676 TTTTTA-AATTTTAAAAA
1 TTTTTATAATTTTAAAAA
54351693 TT
1 TT
54351695 AATTAACTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 10 0.33
18 14 0.47
19 6 0.20
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTTTATAATTTTAAAAA
Found at i:54354889 original size:26 final size:26
Alignment explanation
Indices: 54354853--54354936 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
54354843 TGATACAAAT
*
54354853 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
54354879 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
54354905 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
54354931 TGATAA
1 TGATAA
54354937 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:54357364 original size:19 final size:19
Alignment explanation
Indices: 54357321--54357360 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
54357311 TACAAAAATG
*
54357321 AAATTCAAAATAATTTCTA
1 AAATTCAAAATAATTTATA
54357340 AAATTCAAAAT-ATTTATA
1 AAATTCAAAATAATTTATA
54357358 AAA
1 AAA
54357361 ATTCCAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATTCAAAATAATTTATA
Found at i:54361268 original size:21 final size:22
Alignment explanation
Indices: 54361238--54361294 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
54361228 TTGATACAAG
*
54361238 ATTTTAATATTTTAAATTAATT
1 ATTTTTATATTTTAAATTAATT
**
54361260 -TTTTTATATTTTTATCTTAATT
1 ATTTTTATA-TTTTAAATTAATT
54361282 ATTTTTAT-TTTTA
1 ATTTTTATATTTTA
54361295 TTTATAATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 12 0.40
22 11 0.37
23 7 0.23
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (22 bp):
ATTTTTATATTTTAAATTAATT
Found at i:54361302 original size:22 final size:22
Alignment explanation
Indices: 54361254--54361295 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
54361244 ATATTTTAAA
*
54361254 TTAATTTTTTTATATTTTTATC
1 TTAATTATTTTATATTTTTATC
54361276 TTAATTATTTT-TATTTTTAT
1 TTAATTATTTTATATTTTTAT
54361296 TTATAATCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (22 bp):
TTAATTATTTTATATTTTTATC
Found at i:54361753 original size:30 final size:30
Alignment explanation
Indices: 54361696--54361753 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
54361686 AATAGAAAAG
* * *
54361696 AACAAAAGAAAATTATTGCTTATAAATGTC
1 AACAAAAGAAAATAATGGCTTAAAAATGTC
54361726 AACAAAAGAAAATCAATGGC-TAAAAATG
1 AACAAAAGAAAAT-AATGGCTTAAAAATG
54361754 GAGTTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.22
Consensus pattern (30 bp):
AACAAAAGAAAATAATGGCTTAAAAATGTC
Found at i:54372943 original size:18 final size:20
Alignment explanation
Indices: 54372922--54372990 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
54372912 TGTATTTACC
54372922 ATTATT-TATAT-TATTATT
1 ATTATTATATATGTATTATT
*
54372940 ATTATTAGTATATGTTTTATT
1 ATTATTA-TATATGTATTATT
* * *
54372961 ATTATGCATATATTTATGTAGT
1 ATTAT-TATATATGTAT-TATT
54372983 ATTATTAT
1 ATTATTAT
54372991 TAGTCGTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
18 6 0.15
20 5 0.12
21 20 0.50
22 9 0.22
ACGTcount: A:0.32, C:0.01, G:0.07, T:0.59
Consensus pattern (20 bp):
ATTATTATATATGTATTATT
Found at i:54373131 original size:22 final size:22
Alignment explanation
Indices: 54373086--54373183 Score: 71
Period size: 22 Copynumber: 4.4 Consensus size: 22
54373076 ATGTTATTTT
54373086 TTTTAATATTAATTTA-TTAT-TA
1 TTTTAATATT-A-TTAGTTATATA
54373108 TTATT-ATATTATTACG-TATATA
1 TT-TTAATATTATTA-GTTATATA
54373130 TTTTAATATTATTAGTTATATA
1 TTTTAATATTATTAGTTATATA
* * *
54373152 TCTTTTATACTATT-GTATGTATA
1 T-TTTAATATTATTAGT-TATATA
54373175 TTTCTAATA
1 TTT-TAATA
54373184 CTGTATTGTA
Statistics
Matches: 63, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
20 3 0.05
21 7 0.11
22 31 0.49
23 22 0.35
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (22 bp):
TTTTAATATTATTAGTTATATA
Found at i:54373305 original size:22 final size:22
Alignment explanation
Indices: 54373280--54373345 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
54373270 ATCATTTCTA
54373280 ATATATATATTGTATATGTTTT
1 ATATATATATTGTATATGTTTT
*
54373302 ATATATAT-TATGTATATATTTT
1 ATATATATAT-TGTATATGTTTT
54373324 -TA-ATATTATTAGTTATATGTTT
1 ATATATA-TATT-G-TATATGTTT
54373346 CTTATACTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
20 3 0.08
21 5 0.14
22 21 0.57
23 8 0.22
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (22 bp):
ATATATATATTGTATATGTTTT
Found at i:54373356 original size:23 final size:23
Alignment explanation
Indices: 54373292--54373393 Score: 68
Period size: 23 Copynumber: 4.2 Consensus size: 23
54373282 ATATATATTG
54373292 TATATGTTTTATATATATTATGTA
1 TATATGTTTT-TATATATTATGTA
*
54373316 TATAT-TTTTAATATTATTA-GT-
1 TATATGTTTTTATA-TATTATGTA
*
54373337 TATATGTTTCTTATACTATTCCAGGTA
1 TATATGTTT-TTATA-TATT--ATGTA
*
54373364 CATAT-TTTTTATATCATCTTATGTA
1 TATATGTTTTTATAT-A--TTATGTA
54373389 TATAT
1 TATAT
54373394 TCTTAAATAC
Statistics
Matches: 62, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
21 5 0.08
22 8 0.13
23 17 0.27
24 6 0.10
25 15 0.24
26 5 0.08
27 6 0.10
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (23 bp):
TATATGTTTTTATATATTATGTA
Found at i:54374277 original size:130 final size:133
Alignment explanation
Indices: 54373925--54374419 Score: 350
Period size: 134 Copynumber: 3.7 Consensus size: 133
54373915 TAAAATACGC
* * * *
54373925 GTGAAATTCCGAAA-GAGATATTCGATTATTTTGAACAAACGGGAGATTGCAACCCAGCACGATA
1 GTGAAATACC-AAAGGA-ATATTCGATTATTTTGAACAAACGAGAAATCGCAACCCAGCACGATA
* **** *
54373989 GGGCACT-ATTCCACGAATTGCCAAACATCGAACATTTTTTTTCTGTTTTAAAGAGTTTTTAGAA
64 GGGCA-TGATTCC-CGAATTGCCAAACATCGAACAGTCGCCTTCTGTTTTAAAGAGATTTTAGAA
*
54374053 AACGTGA
127 AACATGA
* * * * * * * * *
54374060 GTGAAATTCCGAAGGGATCTTCAATCATTTTGAACAAATGAAAAAGCGCAACCCAGCACGATAGG
1 GTGAAATACCAAAGGAATATTCGATTATTTTGAACAAACGAGAAATCGCAACCCAGCACGATAGG
** *
54374125 GC-TCGATTTTCAAATTGCCAAACATCGAAC-GTCGCCTTC-GTTTTGAAA-A-ATTTTA-ATAA
66 GCAT-GATTCCCGAATTGCCAAACATCGAACAGTCGCCTTCTGTTTT-AAAGAGATTTTAGA-AA
54374184 ACATGA
128 ACATGA
* *
54374190 GTGAAA-ACCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCACAACCCAGCACGATAG
1 GTGAAATACC-AAAGGAATATTCGATTATTTTGAACAAACGAGAAATCGCAACCCAGCACGATAG
** * **
54374254 GGCATGATTCCCGAATTATCAAACACCGATTA-TCGCCTT-TGTTTTAAA-AGATTTTTTTTAGA
65 GGCATGATTCCCGAATTGCCAAACATCGAACAGTCGCCTTCTGTTTTAAAGAGA----TTTTAGA
* *
54374316 AGATATGA
126 AAACATGA
* **** * * * * * *
54374324 ATGAAATTTTGAAGGGATACTCGATTATTTTGAGCAAACGCA-AAATTGCAACCCAACACGTTAG
1 GTGAAATACCAAAGGAATATTCGATTATTTTGAACAAACG-AGAAATCGCAACCCAGCACGATAG
* * * *
54374388 GGAACGATTCCGCGAATTGCTAAATATCGAAC
65 GGCATGATTCC-CGAATTGCCAAACATCGAAC
54374420 TTCGTCTTCG
Statistics
Matches: 278, Mismatches: 64, Indels: 36
0.74 0.17 0.10
Matches are distributed among these distances:
129 7 0.03
130 96 0.35
131 7 0.03
132 8 0.03
133 19 0.07
134 115 0.41
135 26 0.09
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (133 bp):
GTGAAATACCAAAGGAATATTCGATTATTTTGAACAAACGAGAAATCGCAACCCAGCACGATAGG
GCATGATTCCCGAATTGCCAAACATCGAACAGTCGCCTTCTGTTTTAAAGAGATTTTAGAAAACA
TGA
Found at i:54377038 original size:44 final size:44
Alignment explanation
Indices: 54376990--54377806 Score: 931
Period size: 44 Copynumber: 18.2 Consensus size: 44
54376980 CTCAGGAACA
54376990 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
*
54377034 CCAAATCTGCTATCTTCGATCTGCTCTCTGCCAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* *
54377078 CCCAATCTGCTATCTTTGATCTGCTCTCCGCCAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* *
54377122 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCACTACAGAGATG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* *
54377166 CCAAATCTGTTATCTTCGATCTGCTCTCCGCCACTACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* *
54377210 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCACTACAGAGATG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
*
54377254 CCAAATCTGCTATATTCGATCTGCTCTCCGCCAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* *
54377298 CCAAATCTGCTATCTTCGATCTGCTCTCCGTCAACACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
*
54377342 CCAAATCTGCTATCTTCGATCTGCTCTCTGCCAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* *
54377386 CCAAATCTGCTA-CTTTCGATCTACTCTCTGCCAATACAGAGACG
1 CCAAATCTGCTATC-TTCGATCTGCTCTCCGCCAATACAGAGACG
* * * * *
54377430 CCAAATCTGCTATATTTGATCTACTCTCCGTCAATACAGAGATG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* * * * * *** *
54377474 CCAAATCTATAAAGACGCCAAATCTACTATCTTCGATCTGCTCTCCGCCACTACAGA-G
1 CCAAATC--T------G-C-TATCTTCGATC-T-GCTCT-C-CGCCAATAC-AGAGACG
**** ** * * *
54377532 ATGCCAAAT-CTGTTGTCTTCGATCTGCTCTCCGCCACTACAGAGATG
1 -CCAAATCTGC---TATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* * * *
54377579 CCAAATCTGTTATCTTCGATCTTCTCTCCGCCACTACAGAGATG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* * *
54377623 CCAAATCTGTTATCTTCGATCTGCTCTCCGCCACTACAGAGATG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* * * **
54377667 CCAAATCTGTTATCTTCGATCTACTCTCCGCCACTACAGAGATA
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
*
54377711 CCAAATCTGCTATATTCGATCTGCTCTCCGCCAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* * * *
54377755 CCAAATCTGCTATCTTCGATTTGCTCTCCACTACTACA-AGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
54377798 CCAAATCTG
1 CCAAATCTG
54377807 TCTGTTCTTG
Statistics
Matches: 672, Mismatches: 79, Indels: 45
0.84 0.10 0.06
Matches are distributed among these distances:
43 15 0.02
44 605 0.90
46 7 0.01
47 7 0.01
48 1 0.00
49 5 0.01
50 1 0.00
51 7 0.01
52 1 0.00
53 1 0.00
54 6 0.01
55 1 0.00
56 3 0.00
57 2 0.00
58 5 0.01
59 5 0.01
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (44 bp):
CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
Found at i:54377191 original size:132 final size:132
Alignment explanation
Indices: 54376990--54377806 Score: 1089
Period size: 132 Copynumber: 6.1 Consensus size: 132
54376980 CTCAGGAACA
54376990 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATC
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATC
* * * *
54377055 TGCTCTCTGCCAATACAGAGACGCCCAATCTGCTATCTTTGATCTGCTCTCCGCCAATACAGAGA
66 TGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCACTACAGAGA
54377120 CG
131 CG
* * *
54377122 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCACTACAGAGATGCCAAATCTGTTATCTTCGATC
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATC
*
54377187 TGCTCTCCGCCACTACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCACTACAGAGA
66 TGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCACTACAGAGA
*
54377252 TG
131 CG
*
54377254 CCAAATCTGCTATATTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATC
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATC
* * * *
54377319 TGCTCTCCGTCAACACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGCCAATACAGAGA
66 TGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCACTACAGAGA
54377384 CG
131 CG
* * * *
54377386 CCAAATCTGCTA-CTTTCGATCTACTCTCTGCCAATACAGAGACGCCAAATCTGCTATATTTGAT
1 CCAAATCTGCTATC-TTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGAT
* * *
54377450 CTACTCTCCGTCAATACAGAGATGCCAAATCTATAAAGACGCCAAATCTACTATCTTCGATCTGC
65 CTGCTCTCCGCCAATACAGAGACGCCAAATC--T------G---------CTATCTTCGATCTGC
*
54377515 TCTCCGCCACTACAGAGATG
113 TCTCCGCCACTACAGAGACG
* * * * *
54377535 CCAAATCTGTTGTCTTCGATCTGCTCTCCGCCACTACAGAGATGCCAAATCTGTTATCTTCGATC
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATC
* * * *
54377600 TTCTCTCCGCCACTACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCACTACAGAGA
66 TGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCACTACAGAGA
*
54377665 TG
131 CG
* * * ** *
54377667 CCAAATCTGTTATCTTCGATCTACTCTCCGCCACTACAGAGATACCAAATCTGCTATATTCGATC
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATC
* * *
54377732 TGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATTTGCTCTCCACTACTACA-AGA
66 TGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCACTACAGAGA
54377796 CG
131 CG
54377798 CCAAATCTG
1 CCAAATCTG
54377807 TCTGTTCTTG
Statistics
Matches: 610, Mismatches: 56, Indels: 39
0.87 0.08 0.06
Matches are distributed among these distances:
131 13 0.02
132 479 0.79
134 1 0.00
140 1 0.00
141 1 0.00
147 1 0.00
149 113 0.19
150 1 0.00
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (132 bp):
CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATC
TGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCACTACAGAGA
CG
Found at i:54377512 original size:61 final size:61
Alignment explanation
Indices: 54377425--54377542 Score: 182
Period size: 61 Copynumber: 1.9 Consensus size: 61
54377415 GCCAATACAG
* * *
54377425 AGACGCCAAATCTGCTATATTTGATCTACTCTCCGTCAATACAGAGATGCCAAATCTATAA
1 AGACGCCAAATCTACTATATTCGATCTACTCTCCGCCAATACAGAGATGCCAAATCTATAA
* * *
54377486 AGACGCCAAATCTACTATCTTCGATCTGCTCTCCGCCACTACAGAGATGCCAAATCT
1 AGACGCCAAATCTACTATATTCGATCTACTCTCCGCCAATACAGAGATGCCAAATCT
54377543 GTTGTCTTCG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (61 bp):
AGACGCCAAATCTACTATATTCGATCTACTCTCCGCCAATACAGAGATGCCAAATCTATAA
Found at i:54377563 original size:105 final size:105
Alignment explanation
Indices: 54377381--54377586 Score: 288
Period size: 105 Copynumber: 2.0 Consensus size: 105
54377371 GCCAATACAG
* *
54377381 AGACGCCAAATCTGCTACTTTCGATCTACTCTCTGCCAATACAGAGACGCCAAATCTGCTATATT
1 AGACGCCAAATCTACTACTTTCGATCTACTCTCCGCCAATACAGAGACGCCAAATCTGCTATATT
* *
54377446 TGATCTACTCTCCGTCAATACAGAGATGCCAAATCTATAA
66 CGATCTACTCTCCGCCAATACAGAGATGCCAAATCTATAA
* * * * * *
54377486 AGACGCCAAATCTACTA-TCTTCGATCTGCTCTCCGCCACTACAGAGATGCCAAATCTGTTGTCT
1 AGACGCCAAATCTACTACT-TTCGATCTACTCTCCGCCAATACAGAGACGCCAAATCTGCTATAT
* *
54377550 TCGATCTGCTCTCCGCCACTACAGAGATGCCAAATCT
65 TCGATCTACTCTCCGCCAATACAGAGATGCCAAATCT
54377587 GTTATCTTCG
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
104 1 0.01
105 87 0.99
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.27
Consensus pattern (105 bp):
AGACGCCAAATCTACTACTTTCGATCTACTCTCCGCCAATACAGAGACGCCAAATCTGCTATATT
CGATCTACTCTCCGCCAATACAGAGATGCCAAATCTATAA
Found at i:54377607 original size:149 final size:149
Alignment explanation
Indices: 54377337--54377630 Score: 428
Period size: 149 Copynumber: 2.0 Consensus size: 149
54377327 GTCAACACAG
* *
54377337 AGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGCCAATACAGAGACGCCAAATCTGCTACTTT
1 AGACGCCAAATCTACTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTACTTT
* * *
54377402 CGATCTACTCTCTGCCAATACAGAGACGCCAAATCTGCTATATTTGATCTACTCTCCGTCAATAC
66 CGATCTACTCTCCGCCAATACAGAGACGCCAAATCTGCTATATTCGATCTACTCTCCGCCAATAC
54377467 AGAGATGCCAAATCTATAA
131 AGAGATGCCAAATCTATAA
* * **
54377486 AGACGCCAAATCTACTATCTTCGATCTGCTCTCCGCCACTACAGAGATGCCAAATCTG-TTGTCT
1 AGACGCCAAATCTACTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTACT-T
* * * * * * *
54377550 TCGATCTGCTCTCCGCCACTACAGAGATGCCAAATCTGTTATCTTCGATCTTCTCTCCGCCACTA
65 TCGATCTACTCTCCGCCAATACAGAGACGCCAAATCTGCTATATTCGATCTACTCTCCGCCAATA
54377615 CAGAGATGCCAAATCT
130 CAGAGATGCCAAATCT
54377631 GTTATCTTCG
Statistics
Matches: 128, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
148 2 0.02
149 126 0.98
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.28
Consensus pattern (149 bp):
AGACGCCAAATCTACTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTACTTT
CGATCTACTCTCCGCCAATACAGAGACGCCAAATCTGCTATATTCGATCTACTCTCCGCCAATAC
AGAGATGCCAAATCTATAA
Found at i:54377672 original size:237 final size:237
Alignment explanation
Indices: 54377253--54377806 Score: 691
Period size: 237 Copynumber: 2.4 Consensus size: 237
54377243 CTACAGAGAT
*
54377253 GCCAAATCTGCTATATTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGAT
1 GCCAAATCTACTATATTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGAT
*
54377318 CTGCTCTCCGTCAACACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGCCAATACAGAG
66 CTGCTCTCCGTCAACACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAG
* *
54377383 ACGCCAAATCTGCTACTTTCGATCTACTCTCTGCCAATACAGAGACGCCAAATCTGCTATATTTG
131 ACGCCAAATCTGCTACTTTCGATCTACTCTCCGCCAATACAGAGACGCCAAATCTGCTATATTCG
* *
54377448 ATCTACTCTCCGTCAATACAGAGATGCCAAATCTATAAAGAC
196 ATCTACTCTCCGCCAATACAGAGATACCAAATCTATAAAGAC
* * * * *
54377490 GCCAAATCTACTATCTTCGATCTGCTCTCCGCCACTACAGAGATGCCAAATCTGTTGTCTTCGAT
1 GCCAAATCTACTATATTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGAT
* * * * *
54377555 CTGCTCTCCG-CCACTACAGAGATGCCAAATCTGTTATCTTCGATCTTCTCTCCGCCACTACAGA
66 CTGCTCTCCGTCAAC-ACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGA
* * * * * * *
54377619 GATGCCAAATCTGTTA-TCTTCGATCTGCTCTCCGCCACTACAGAGATGCCAAATCTGTTATCTT
130 GACGCCAAATCTGCTACT-TTCGATCTACTCTCCGCCAATACAGAGACGCCAAATCTGCTATATT
*
54377683 CGATCTACTCTCCGCCACTACAGAGATACCAAATC--T------
194 CGATCTACTCTCCGCCAATACAGAGATACCAAATCTATAAAGAC
54377719 G---------CTATATTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGAT
1 GCCAAATCTACTATATTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGAT
* * *
54377775 TTGCTCTCC-ACTACTACA-AGACGCCAAATCTG
66 CTGCTCTCCGTCAAC-ACAGAGACGCCAAATCTG
54377807 TCTGTTCTTG
Statistics
Matches: 282, Mismatches: 32, Indels: 24
0.83 0.09 0.07
Matches are distributed among these distances:
219 13 0.05
220 65 0.23
229 1 0.00
235 1 0.00
236 4 0.01
237 198 0.70
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (237 bp):
GCCAAATCTACTATATTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGAT
CTGCTCTCCGTCAACACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAG
ACGCCAAATCTGCTACTTTCGATCTACTCTCCGCCAATACAGAGACGCCAAATCTGCTATATTCG
ATCTACTCTCCGCCAATACAGAGATACCAAATCTATAAAGAC
Found at i:54378290 original size:129 final size:131
Alignment explanation
Indices: 54377986--54378354 Score: 435
Period size: 131 Copynumber: 2.8 Consensus size: 131
54377976 TCGAGAAGAT
* * * *
54377986 AAGACCTACAATCATCAGCCCACTTCATTACAACTTTAGGGAGCTAGGACTTGCTTAAATCTGCT
1 AAGATCTACAATCATCAGCCTACTCCACTACAACTTTAGGGAGCTAGGACTTGCTTAAATCTGCT
* * * ** * * *
54378051 TCGCTGCATCTTCAGGAAGCCAAGATTTATTGTCTTTGAT-TTGCCTCACTGCAACTTCAGGGAG
66 TCACTGCAACTTCAGGAAGCCTAGA-TTACCGTCTTCGATCTGGCCTCACTGCAACTTCAGGGAA
54378115 AC
130 AC
* * *
54378117 GAGATCTACAATCCTCAGCCTACTCCACTACAACTTTAGAGAGCTAGGACTTGCTTAAATCTGCT
1 AAGATCTACAATCATCAGCCTACTCCACTACAACTTTAGGGAGCTAGGACTTGCTTAAATCTGCT
* *
54378182 TTACTGCAACATCAGGAAGCCTAGATT-CCGTCTTCGATCTGGCC-CACTGCAATCTT-AGGGAA
66 TCACTGCAACTTCAGGAAGCCTAGATTACCGTCTTCGATCTGGCCTCACTGCAA-CTTCAGGGAA
54378244 AC
130 AC
* * *
54378246 AAGATCTATAATCTTCAGCCTACTCCACTACAACTTTAGGGAGCTA-GAATGGTGGCTTAAATCT
1 AAGATCTACAATCATCAGCCTACTCCACTACAACTTTAGGGAGCTAGGACT--T-GCTTAAATCT
* *
54378310 ACTTCACTGCAACTTCAGGAAG-CTCAGATTCACCATCTTCGATCT
63 GCTTCACTGCAACTTCAGGAAGCCT-AGATT-ACCGTCTTCGATCT
54378355 ATTTCACTGT
Statistics
Matches: 204, Mismatches: 26, Indels: 14
0.84 0.11 0.06
Matches are distributed among these distances:
128 3 0.01
129 65 0.32
130 12 0.06
131 112 0.55
133 12 0.06
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.28
Consensus pattern (131 bp):
AAGATCTACAATCATCAGCCTACTCCACTACAACTTTAGGGAGCTAGGACTTGCTTAAATCTGCT
TCACTGCAACTTCAGGAAGCCTAGATTACCGTCTTCGATCTGGCCTCACTGCAACTTCAGGGAAA
C
Found at i:54378415 original size:45 final size:45
Alignment explanation
Indices: 54378306--54378720 Score: 175
Period size: 45 Copynumber: 9.5 Consensus size: 45
54378296 GGTGGCTTAA
* *
54378306 ATCTACTTCACTGCAACTTCAGGAAGCTCAGATTCACCATCTTCG
1 ATCTATTTCACTGCAACTTTAGGAAGCTCAGATTCACCATCTTCG
* * *
54378351 ATCTATTTCACTGTAACTTTAGGAAGCTCAGATTCGCCGTCTTCG
1 ATCTATTTCACTGCAACTTTAGGAAGCTCAGATTCACCATCTTCG
* * * * * * *
54378396 ATCTGTTTCACTGCAACTTTAGGGAAAC-AAGATCTGA-AATTTTAG
1 ATCTATTTCACTGCAACTTTA-GGAAGCTCAGAT-TCACCATCTTCG
* * * * * * ***** **
54378441 -CCTACTCCACTACAACTTTAGGGAGCT-AGGTT-GGTGGCTTAA
1 ATCTATTTCACTGCAACTTTAGGAAGCTCAGATTCACCATCTTCG
** * *
54378483 ATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCACCGTCTTCG
1 ATCTATTTCACTGCAACTTTAGGAAGCTCAGATTCACCATCTTCG
* * **
54378528 ----A--T--CTGCAA-TCTTAGGGAAAC-AAGA-TCTATAATCTTC-
1 ATCTATTTCACTGCAACT-TTA-GGAAGCTCAGATTC-ACCATCTTCG
* * * * * * ***** **
54378564 AGCCTACTCCACTACAACTTTAGGGAGCT-AGAAT-GGTGGCTTAA
1 A-TCTATTTCACTGCAACTTTAGGAAGCTCAGATTCACCATCTTCG
* *
54378608 ATCTACTTCACTGCAACTTCAGGAAGCTCAGATTCACCATCTTCG
1 ATCTATTTCACTGCAACTTTAGGAAGCTCAGATTCACCATCTTCG
* * *
54378653 ATCTATTTCACTGTAACTTTAGGAAGCTCAGATTCGCCGTCTTCG
1 ATCTATTTCACTGCAACTTTAGGAAGCTCAGATTCACCATCTTCG
*
54378698 ATCTGTTTCACTGCAACTTTAGG
1 ATCTATTTCACTGCAACTTTAGG
54378721 GAAACAAGAT
Statistics
Matches: 266, Mismatches: 79, Indels: 50
0.67 0.20 0.13
Matches are distributed among these distances:
36 3 0.01
37 17 0.06
38 5 0.02
39 1 0.00
41 1 0.00
42 4 0.02
43 53 0.20
44 31 0.12
45 144 0.54
46 7 0.03
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.31
Consensus pattern (45 bp):
ATCTATTTCACTGCAACTTTAGGAAGCTCAGATTCACCATCTTCG
Found at i:54378506 original size:177 final size:178
Alignment explanation
Indices: 54378209--54378531 Score: 535
Period size: 177 Copynumber: 1.8 Consensus size: 178
54378199 AGCCTAGATT
54378209 CCGTCTTCGATCTGGCCCACTGCAATCTTAGGGAAACAAGATCTATAATCTTCAGCCTACTCCAC
1 CCGTCTTCGATCTGGCCCACTGCAATCTTAGGGAAACAAGATCTATAATCTTCAGCCTACTCCAC
54378274 TACAACTTTAGGGAGCTAGAATGGTGGCTTAAATCTACTTCACTGCAACTTCAGGAAGCTCAGAT
66 TACAACTTTAGGGAGCTAGAATGGTGGCTTAAATCTACTTCACTGCAACTTCAGGAAGCTCAGAT
54378339 TCACCATCTTCGATCTATTTCACTGTAACTTTAGGAAGCTCAGATTCG
131 TCACCATCTTCGATCTATTTCACTGTAACTTTAGGAAGCTCAGATTCG
*** *
54378387 CCGTCTTCGATCTGTTTCACTGCAA-CTTTAGGGAAACAAGATCTGA-AAT-TTTAGCCTACTCC
1 CCGTCTTCGATCTGGCCCACTGCAATC-TTAGGGAAACAAGATCT-ATAATCTTCAGCCTACTCC
** *
54378449 ACTACAACTTTAGGGAGCTAGGTTGGTGGCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAG
64 ACTACAACTTTAGGGAGCTAGAATGGTGGCTTAAATCTACTTCACTGCAACTTCAGGAAGCTCAG
*
54378514 ATTCACCGTCTTCGATCT
129 ATTCACCATCTTCGATCT
54378532 GCAATCTTAG
Statistics
Matches: 135, Mismatches: 8, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
177 92 0.68
178 42 0.31
179 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.30
Consensus pattern (178 bp):
CCGTCTTCGATCTGGCCCACTGCAATCTTAGGGAAACAAGATCTATAATCTTCAGCCTACTCCAC
TACAACTTTAGGGAGCTAGAATGGTGGCTTAAATCTACTTCACTGCAACTTCAGGAAGCTCAGAT
TCACCATCTTCGATCTATTTCACTGTAACTTTAGGAAGCTCAGATTCG
Found at i:54378606 original size:125 final size:127
Alignment explanation
Indices: 54378351--54378656 Score: 431
Period size: 125 Copynumber: 2.4 Consensus size: 127
54378341 ACCATCTTCG
* * * *
54378351 ATCTATTTCACTGTAACTTTAGGAAGCTCAGATTCGCCGTCTTCGATCTGTTTCACTGCAACTTT
1 ATCTACTTCACTGCAACTTCAGGAAGCTCAGATTCACCGTCTTCGATCTG--TCA---CAACTTT
* **
54378416 AGGGAAACAAGATCTGAAATTTTAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGCTT
61 AGGGAAACAAGATCTGAAATTTCAGCCTACTCCACTACAACTTTAGGGAGCTAGAATGGTGGCTT
54378481 AA
126 AA
* *
54378483 ATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCACCGTCTTCGATCTG-CA-ATC-TTAGGGA
1 ATCTACTTCACTGCAACTTCAGGAAGCTCAGATTCACCGTCTTCGATCTGTCACAACTTTAGGGA
54378545 AACAAGATCT-ATAATCTTCAGCCTACTCCACTACAACTTTAGGGAGCTAGAATGGTGGCTTAA
66 AACAAGATCTGA-AAT-TTCAGCCTACTCCACTACAACTTTAGGGAGCTAGAATGGTGGCTTAA
*
54378608 ATCTACTTCACTGCAACTTCAGGAAGCTCAGATTCACCATCTTCGATCT
1 ATCTACTTCACTGCAACTTCAGGAAGCTCAGATTCACCGTCTTCGATCT
54378657 ATTTCACTGT
Statistics
Matches: 161, Mismatches: 11, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
123 1 0.01
124 20 0.12
125 93 0.58
129 2 0.01
132 45 0.28
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (127 bp):
ATCTACTTCACTGCAACTTCAGGAAGCTCAGATTCACCGTCTTCGATCTGTCACAACTTTAGGGA
AACAAGATCTGAAATTTCAGCCTACTCCACTACAACTTTAGGGAGCTAGAATGGTGGCTTAA
Found at i:54378774 original size:302 final size:302
Alignment explanation
Indices: 54378096--54378980 Score: 1338
Period size: 302 Copynumber: 2.9 Consensus size: 302
54378086 TTGATTTGCC
* * * * * *
54378096 TCACTGCAACTTCAGGGAGACGAGATCT-ACAATCCTCAGCCTACTCCACTACAACTTTAGAGAG
1 TCACTGCAACTTTAGGGAAACAAGATCTGA-AAT-TTTAGCCTACTCCACTACAACTTTAGGGAG
* * *
54378160 CTAGGACT--T-GCTTAAATCTGCTTTACTGCAACATCAGGAAGC-CTAGATT--CCGTCTTCGA
64 CTAGG-TTGGTGGCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTC-AGATTCACCGTCTTCGA
54378219 TCTGGCCCACTGCAATCTTAGGGAAACAAGATCTATAATCTTCAGCCTACTCCACTACAACTTTA
127 --T------CTGCAATCTTAGGGAAACAAGATCTATAATCTTCAGCCTACTCCACTACAACTTTA
54378284 GGGAGCTAGAATGGTGGCTTAAATCTACTTCACTGCAACTTCAGGAAGCTCAGATTCACCATCTT
184 GGGAGCTAGAATGGTGGCTTAAATCTACTTCACTGCAACTTCAGGAAGCTCAGATTCACCATCTT
54378349 CGATCTATTTCACTGTAACTTTAGGAAGCTCAGATTCGCCGTCTTCGATCTGTT
249 CGATCTATTTCACTGTAACTTTAGGAAGCTCAGATTCGCCGTCTTCGATCTGTT
54378403 TCACTGCAACTTTAGGGAAACAAGATCTGAAATTTTAGCCTACTCCACTACAACTTTAGGGAGCT
1 TCACTGCAACTTTAGGGAAACAAGATCTGAAATTTTAGCCTACTCCACTACAACTTTAGGGAGCT
54378468 AGGTTGGTGGCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCACCGTCTTCGATCTG
66 AGGTTGGTGGCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCACCGTCTTCGATCTG
54378533 CAATCTTAGGGAAACAAGATCTATAATCTTCAGCCTACTCCACTACAACTTTAGGGAGCTAGAAT
131 CAATCTTAGGGAAACAAGATCTATAATCTTCAGCCTACTCCACTACAACTTTAGGGAGCTAGAAT
54378598 GGTGGCTTAAATCTACTTCACTGCAACTTCAGGAAGCTCAGATTCACCATCTTCGATCTATTTCA
196 GGTGGCTTAAATCTACTTCACTGCAACTTCAGGAAGCTCAGATTCACCATCTTCGATCTATTTCA
54378663 CTGTAACTTTAGGAAGCTCAGATTCGCCGTCTTCGATCTGTT
261 CTGTAACTTTAGGAAGCTCAGATTCGCCGTCTTCGATCTGTT
54378705 TCACTGCAACTTTAGGGAAACAAGATCTGAAATTTTAGCCTACTCCACTACAACTTTAGGGAGCT
1 TCACTGCAACTTTAGGGAAACAAGATCTGAAATTTTAGCCTACTCCACTACAACTTTAGGGAGCT
54378770 AGGTTGGTGGCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCACCGTCTTCGATCTG
66 AGGTTGGTGGCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCACCGTCTTCGATCTG
* * * *
54378835 CTTCACTGTAACTTCAGGGAAACAAGATTTGA-AAT-TTTAGCCTACTCTACTACAACTTTAGGG
131 ---CA----ATCTT-AGGGAAACAAGATCT-ATAATCTTCAGCCTACTCCACTACAACTTTAGGG
** * * *
54378898 AGCTAGGTTGGTGGCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGTCTTCGA
187 AGCTAGAATGGTGGCTTAAATCTACTTCACTGCAACTTCAGGAAGCTCAGATTCACCATCTTCGA
* *
54378963 TCTACTTCACTGCAACTT
252 TCTATTTCACTGTAACTT
54378981 CAGGGAAATA
Statistics
Matches: 542, Mismatches: 20, Indels: 30
0.92 0.03 0.05
Matches are distributed among these distances:
302 305 0.56
305 3 0.01
306 32 0.06
307 29 0.05
308 38 0.07
309 107 0.20
310 27 0.05
311 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (302 bp):
TCACTGCAACTTTAGGGAAACAAGATCTGAAATTTTAGCCTACTCCACTACAACTTTAGGGAGCT
AGGTTGGTGGCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCACCGTCTTCGATCTG
CAATCTTAGGGAAACAAGATCTATAATCTTCAGCCTACTCCACTACAACTTTAGGGAGCTAGAAT
GGTGGCTTAAATCTACTTCACTGCAACTTCAGGAAGCTCAGATTCACCATCTTCGATCTATTTCA
CTGTAACTTTAGGAAGCTCAGATTCGCCGTCTTCGATCTGTT
Found at i:54378780 original size:177 final size:170
Alignment explanation
Indices: 54378483--54378852 Score: 537
Period size: 177 Copynumber: 2.1 Consensus size: 170
54378473 GGTGGCTTAA
* * *
54378483 ATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCACCGTCTTCGATCTGCAATCTTAGGGAAAC
1 ATCTACTTCACTGTAACTTCAGGAAGCTCAGATTCACCGTCTTCGATCTGCAAACTTAGGGAAAC
54378548 AAGATCTATAATCTTCAGCCTACTCCACTACAACTTTAGGGAGCTAGAATGGTGGCTTAAATCTA
66 AAGATCTATAATCTTCAGCCTACTCCACTACAACTTTAGGGAGCTAGAATGGTGGCTTAAATCTA
54378613 CTTCACTGCAACTTCAGGAAGCTCAGATTCACCATCTTCG
131 CTTCACTGCAACTTCAGGAAGCTCAGATTCACCATCTTCG
* * *
54378653 ATCTATTTCACTGTAACTTTAGGAAGCTCAGATTCGCCGTCTTCGATCTGTTTCACTGCAACTTT
1 ATCTACTTCACTGTAACTTCAGGAAGCTCAGATTCACCGTCTTCGATCTG---CA----AAC-TT
* **
54378718 AGGGAAACAAGATCTGA-AAT-TTTAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGC
58 AGGGAAACAAGATCT-ATAATCTTCAGCCTACTCCACTACAACTTTAGGGAGCTAGAATGGTGGC
* *
54378781 TTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCACCGTCTTCG
122 TTAAATCTACTTCACTGCAACTTCAGGAAGCTCAGATTCACCATCTTCG
*
54378830 ATCTGCTTCACTGTAACTTCAGG
1 ATCTACTTCACTGTAACTTCAGG
54378853 GAAACAAGAT
Statistics
Matches: 177, Mismatches: 14, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
170 45 0.25
173 2 0.01
177 109 0.62
178 20 0.11
179 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.30
Consensus pattern (170 bp):
ATCTACTTCACTGTAACTTCAGGAAGCTCAGATTCACCGTCTTCGATCTGCAAACTTAGGGAAAC
AAGATCTATAATCTTCAGCCTACTCCACTACAACTTTAGGGAGCTAGAATGGTGGCTTAAATCTA
CTTCACTGCAACTTCAGGAAGCTCAGATTCACCATCTTCG
Found at i:54378819 original size:132 final size:132
Alignment explanation
Indices: 54378659--54379009 Score: 612
Period size: 132 Copynumber: 2.7 Consensus size: 132
54378649 TTCGATCTAT
* * * *
54378659 TTCACTGTAACTTTAGGAAGCTCAGATTCGCCGTCTTCGATCTGTTTCACTGCAACTTTAGGGAA
1 TTCACTGCAACTTCAGGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGCAACTTCAGGGAA
54378724 ACAAGATCTGAAATTTTAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGCTTAAATCT
66 ACAAGATCTGAAATTTTAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGCTTAAATCT
54378789 GC
131 GC
* *
54378791 TTCACTGCAACTTCAGGAAGCTCAGATTCACCGTCTTCGATCTGCTTCACTGTAACTTCAGGGAA
1 TTCACTGCAACTTCAGGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGCAACTTCAGGGAA
* *
54378856 ACAAGATTTGAAATTTTAGCCTACTCTACTACAACTTTAGGGAGCTAGGTTGGTGGCTTAAATCT
66 ACAAGATCTGAAATTTTAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGCTTAAATCT
54378921 GC
131 GC
*
54378923 TTCACTGCAACTTCAGGAAGCTCAGATTCGCCGTCTTCGATCTACTTCACTGCAACTTCAGGGAA
1 TTCACTGCAACTTCAGGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGCAACTTCAGGGAA
*
54378988 ATAAGATCTGAAATTTTAGCCT
66 ACAAGATCTGAAATTTTAGCCT
54379010 CATAGGCCCA
Statistics
Matches: 206, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 206 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (132 bp):
TTCACTGCAACTTCAGGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGCAACTTCAGGGAA
ACAAGATCTGAAATTTTAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGCTTAAATCT
GC
Found at i:54378835 original size:45 final size:45
Alignment explanation
Indices: 54378603--54378984 Score: 174
Period size: 45 Copynumber: 8.6 Consensus size: 45
54378593 AGAATGGTGG
* * *
54378603 CTTAAATCTACTTCACTGCAACTTCAGGAAGCTCAGATTCACCAT
1 CTTAGATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCACCGT
* ** * * *
54378648 CTTCGATCTATTTCACTGTAACTTTAGGAAGCTCAGATTCGCCGT
1 CTTAGATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCACCGT
* * * * * * **
54378693 CTTCGATCTGTTTCACTGCAACTTTAGGGAAAC-AAGATCTGA-AAT
1 CTTAGATCTGCTTCACTGCAACTTCA-GGAAGCTCAGAT-TCACCGT
* * * * * * * * *** *
54378738 TTTAG-CCTACTCCACTACAACTTTAGGGAGCT-AGGTT-GGTGG
1 CTTAGATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCACCGT
*
54378780 CTTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCACCGT
1 CTTAGATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCACCGT
* * * * * **
54378825 CTTCGATCTGCTTCACTGTAACTTCAGGGAAAC-AAGATTTGA-AAT
1 CTTAGATCTGCTTCACTGCAACTTCA-GGAAGCTCAGA-TTCACCGT
* * * * * * * *** *
54378870 TTTAG-CCTAC-TCTACTACAACTTTAGGGAGCT-AGGTT-GGTGG
1 CTTAGATCTGCTTC-ACTGCAACTTCAGGAAGCTCAGATTCACCGT
* *
54378912 CTTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGT
1 CTTAGATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCACCGT
* *
54378957 CTTCGATCTACTTCACTGCAACTTCAGG
1 CTTAGATCTGCTTCACTGCAACTTCAGG
54378985 GAAATAAGAT
Statistics
Matches: 243, Mismatches: 78, Indels: 32
0.69 0.22 0.09
Matches are distributed among these distances:
42 9 0.04
43 55 0.23
44 37 0.15
45 128 0.53
46 14 0.06
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (45 bp):
CTTAGATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCACCGT
Found at i:54382665 original size:5 final size:5
Alignment explanation
Indices: 54382655--54382720 Score: 68
Period size: 5 Copynumber: 13.6 Consensus size: 5
54382645 AATGCAAATG
* *
54382655 ATGCA ATGCA ATGCA ATGTAA AT--T ATGCA ATGCA ATGCA ATGCA ATGCAA
1 ATGCA ATGCA ATGCA ATG-CA ATGCA ATGCA ATGCA ATGCA ATGCA ATGC-A
54382705 ATG-- ATGCA ATGCA ATG
1 ATGCA ATGCA ATGCA ATG
54382721 TAAATGCATG
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
3 5 0.10
5 40 0.77
6 7 0.13
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (5 bp):
ATGCA
Found at i:54382677 original size:24 final size:24
Alignment explanation
Indices: 54382645--54382726 Score: 89
Period size: 24 Copynumber: 3.4 Consensus size: 24
54382635 TGGGAAATTT
*
54382645 AATGCAAATGATGCAATGCAATGC
1 AATGTAAATGATGCAATGCAATGC
*
54382669 AATGTAAATTATGCAATGCAATGC
1 AATGTAAATGATGCAATGCAATGC
*
54382693 AATG-CAATGCAAATG--ATGCAATGC
1 AATGTAAATG---ATGCAATGCAATGC
54382717 AATGTAAATG
1 AATGTAAATG
54382727 CATGGGATGA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
23 3 0.06
24 39 0.80
25 4 0.08
26 3 0.06
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.24
Consensus pattern (24 bp):
AATGTAAATGATGCAATGCAATGC
Found at i:54382697 original size:29 final size:29
Alignment explanation
Indices: 54382655--54382720 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
54382645 AATGCAAATG
* *
54382655 ATGCAATGCAATGCAATGTAAATTATGCA
1 ATGCAATGCAATGCAATGCAAATGATGCA
54382684 ATGCAATGCAATGCAATGCAAATGATGCA
1 ATGCAATGCAATGCAATGCAAATGATGCA
54382713 ATGCAATG
1 ATGCAATG
54382721 TAAATGCATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (29 bp):
ATGCAATGCAATGCAATGCAAATGATGCA
Found at i:54384626 original size:130 final size:132
Alignment explanation
Indices: 54384264--54384626 Score: 321
Period size: 130 Copynumber: 2.7 Consensus size: 132
54384254 CTTACTTCAT
* * * * *
54384264 AAAATACGCGTGAAATTCCGAAA-GAGATATTCGATTATTTTGAACAAACGAGAGATTGCAACCC
1 AAAACACGAGTGAAATACC-AAAGGA-ATATTCGATTATTTTGAACAAACGAGAAATCGCAACCC
* * ****
54384328 AGCACGATAGGGCACT-ATTCCCCGAATTGCCAAACATCAAACATTTTTTTTCTGTTTTAAAGAG
64 AGCACGATAGGGCA-TGATT-CCCGAATT-TCAAACATCAAACAGTCACATTCTGTTTTAAAGAG
*
54384392 TTTTTAG
126 ATTTTAG
* * * * * * * *
54384399 AAAACGCGAGTGAAATTCCAAAGGGATCTTCGATTGTTTTGAACAAATGAAAAAACGCAACCCAG
1 AAAACACGAGTGAAATACCAAAGGAATATTCGATTATTTTGAACAAACGAGAAATCGCAACCCAG
** * *
54384464 CACGATAGGGC-TCGATTTTCAAATTTCCAAACATCGAAC-GTCACATTC-GTTTTGAAA-A-AT
66 CACGATAGGGCAT-GATTCCCGAATTT-CAAACATCAAACAGTCACATTCTGTTTT-AAAGAGAT
54384524 TTTA-
128 TTTAG
* * *
54384528 ATAAACATGAGTGAAA-ACCTAAAGGAATATTCGATTATTTTGAACAAGCGAGAAATCACAACCC
1 A-AAACACGAGTGAAATACC-AAAGGAATATTCGATTATTTTGAACAAACGAGAAATCGCAACCC
54384592 AGCACGATAGGGCATGATTCCCGAATTATCAAACA
64 AGCACGATAGGGCATGATTCCCGAATT-TCAAACA
54384627 CCGATTATCG
Statistics
Matches: 183, Mismatches: 36, Indels: 23
0.76 0.15 0.10
Matches are distributed among these distances:
129 3 0.02
130 81 0.44
131 8 0.04
132 8 0.04
133 16 0.09
134 50 0.27
135 17 0.09
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (132 bp):
AAAACACGAGTGAAATACCAAAGGAATATTCGATTATTTTGAACAAACGAGAAATCGCAACCCAG
CACGATAGGGCATGATTCCCGAATTTCAAACATCAAACAGTCACATTCTGTTTTAAAGAGATTTT
AG
Found at i:54391141 original size:22 final size:22
Alignment explanation
Indices: 54391116--54391160 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
54391106 ATTCATGACT
54391116 AACATTCATTCGTCATTTATTC
1 AACATTCATTCGTCATTTATTC
**
54391138 AACATTCATTTTTCATTTATTC
1 AACATTCATTCGTCATTTATTC
54391160 A
1 A
54391161 TTCATCCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.02, T:0.49
Consensus pattern (22 bp):
AACATTCATTCGTCATTTATTC
Found at i:54398653 original size:44 final size:44
Alignment explanation
Indices: 54398589--54398748 Score: 241
Period size: 44 Copynumber: 3.6 Consensus size: 44
54398579 TTATGCCTAA
*
54398589 AAAAAGAGATCAATGTGAAAACCCGAAAAGGGCGTCTTGATGAAC
1 AAAAA-AGATCAAGGTGAAAACCCGAAAAGGGCGTCTTGATGAAC
54398634 AAAAAAGATCAAGGTGAAAACCCGAAAAGGGCGTCTTGATGAAC
1 AAAAAAGATCAAGGTGAAAACCCGAAAAGGGCGTCTTGATGAAC
* * *
54398678 AAAAAGGATCAAGGTGAAAACCCAAAAAGGGCGTCTTGATTAAC
1 AAAAAAGATCAAGGTGAAAACCCGAAAAGGGCGTCTTGATGAAC
* *
54398722 ACAAAAGAT-TAGGATGAAAACCCGAAA
1 AAAAAAGATCAAGG-TGAAAACCCGAAA
54398749 TGGCGTTCTA
Statistics
Matches: 106, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
43 3 0.03
44 98 0.92
45 5 0.05
ACGTcount: A:0.47, C:0.16, G:0.23, T:0.14
Consensus pattern (44 bp):
AAAAAAGATCAAGGTGAAAACCCGAAAAGGGCGTCTTGATGAAC
Found at i:54399757 original size:77 final size:74
Alignment explanation
Indices: 54399540--54399757 Score: 258
Period size: 75 Copynumber: 2.9 Consensus size: 74
54399530 TTCTGTTTTC
* * * * *
54399540 AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGTCTCAAGACAAGTTGAGGTATTTTAAATTTC
1 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTC-AGACACGTTGAGGTATTTTTAATTTC
* *
54399605 CGTCTTTCAA
65 TGTCATTCAA
* *
54399615 AAAAATCAATTCATATTGTGAGAGGTGAGTTGAGCCTCAGAACACGTTGAGGTAATTTTAATTTC
1 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAG-ACACGTTGAGGTATTTTTAATTTC
54399680 TGTTCATT-AA
65 TG-TCATTCAA
* * * *
54399690 AAAAATCAACTCATATTGTGAGATGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTTAGTT
1 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTC-AG--ACACGTTGAGGTATTTTTAATT
54399755 TCT
63 TCT
54399758 ATCAACTCAT
Statistics
Matches: 123, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
74 2 0.02
75 94 0.76
76 5 0.04
77 22 0.18
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (74 bp):
AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGACACGTTGAGGTATTTTTAATTTCT
GTCATTCAA
Found at i:54399795 original size:64 final size:64
Alignment explanation
Indices: 54399694--54399823 Score: 206
Period size: 64 Copynumber: 2.0 Consensus size: 64
54399684 CATTAAAAAA
* * * * *
54399694 ATCAACTCATATTGTGAGATGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTTAGTTTCT
1 ATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGGGTCACACGCTGAGGTATTTTCAATTTCT
*
54399758 ATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGGGTCACATGCTGAGGTATTTTCAATTTCT
1 ATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGGGTCACACGCTGAGGTATTTTCAATTTCT
54399822 AT
1 AT
54399824 TTTTTTTAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (64 bp):
ATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGGGTCACACGCTGAGGTATTTTCAATTTCT
Found at i:54399936 original size:17 final size:17
Alignment explanation
Indices: 54399914--54399949 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
54399904 TCAAATTCTG
*
54399914 TTTTTAATTTCTGTTTT
1 TTTTTAATTTCTATTTT
54399931 TTTTTAATTTCTATTTT
1 TTTTTAATTTCTATTTT
54399948 TT
1 TT
54399950 AAAAAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTTTAATTTCTATTTT
Found at i:54400234 original size:55 final size:56
Alignment explanation
Indices: 54400101--54400248 Score: 237
Period size: 56 Copynumber: 2.7 Consensus size: 56
54400091 TCTATTCGCC
*
54400101 AAAAATCGACTCATATTGTGAGAAGTGAGTTGAGCCTTTTAGTCTCTGATTTTTCA
1 AAAAATCGACTCATATTGCGAGAAGTGAGTTGAGCCTTTTAGTCTCTGATTTTTCA
*
54400157 AAAAATTGACTCATATTGCGAGAAGT-AGGTTGAGCCTTTTAGTCTCTG-TTTTTCA
1 AAAAATCGACTCATATTGCGAGAAGTGA-GTTGAGCCTTTTAGTCTCTGATTTTTCA
* *
54400212 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 AAAAATCGACTCATATTGCGAGAAGTGAGTTGAGCCT
54400249 CAGGTCACAC
Statistics
Matches: 85, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
55 40 0.47
56 45 0.53
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (56 bp):
AAAAATCGACTCATATTGCGAGAAGTGAGTTGAGCCTTTTAGTCTCTGATTTTTCA
Found at i:54401936 original size:3 final size:3
Alignment explanation
Indices: 54401930--54402029 Score: 62
Period size: 3 Copynumber: 31.7 Consensus size: 3
54401920 ATTTTTTTAA
* *
54401930 TAT TATT TAT TAT T-T TATT TAC CAT TAT T-T ATAT TAT TAT TAT TAT
1 TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT -TAT TAT TAT TAT TAT
* * *
54401976 TAT TAG TA- TAT GTTT TAT TAT TAT GTAT ATACT TAT GTAG TAT TAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT -TAT -TA-T TAT -TAT TAT TAT
54402022 TAT TAT TA
1 TAT TAT TA
54402030 GTCGTTTTTA
Statistics
Matches: 77, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
2 5 0.06
3 53 0.69
4 18 0.23
5 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:54402037 original size:46 final size:50
Alignment explanation
Indices: 54401967--54402063 Score: 114
Period size: 49 Copynumber: 2.0 Consensus size: 50
54401957 TTTATATTAT
* *
54401967 TATTATTATTATTAGTATATG-TTTTA-T-TATTATGTATATACTTATGTAG
1 TATTATTATTATTAG-ATACGTTTTTATTCTAATATGTATATA-TTATGTAG
54402016 TATTATTATTATTAG-T-CGTTTTTATTTCTAATATGTATATATTATGTA
1 TATTATTATTATTAGATACGTTTTTA-TTCTAATATGTATATATTATGTA
54402064 AATATTTTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
46 1 0.02
47 6 0.14
49 23 0.55
50 12 0.29
ACGTcount: A:0.30, C:0.03, G:0.09, T:0.58
Consensus pattern (50 bp):
TATTATTATTATTAGATACGTTTTTATTCTAATATGTATATATTATGTAG
Found at i:54402172 original size:22 final size:24
Alignment explanation
Indices: 54402135--54402183 Score: 68
Period size: 22 Copynumber: 2.1 Consensus size: 24
54402125 AATATTAATT
54402135 TATTATTATATATTATTACG-TATA
1 TATTATTATATATTATTA-GTTATA
54402159 TATT-TTA-ATATTATTAGTTATA
1 TATTATTATATATTATTAGTTATA
54402181 TAT
1 TAT
54402184 CTTTTATACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 1 0.04
22 16 0.67
23 3 0.12
24 4 0.17
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (24 bp):
TATTATTATATATTATTAGTTATA
Found at i:54402333 original size:22 final size:22
Alignment explanation
Indices: 54402308--54402374 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
54402298 TCATTTCTAA
54402308 TATATATATATTGTATATGTTT
1 TATATATATATTGTATATGTTT
*
54402330 TATATATAT-TATGTATATATTT
1 TATATATATAT-TGTATATGTTT
54402352 T-TA-ATATTATTAGTTATATGTTT
1 TATATATA-TATT-G-TATATGTTT
54402375 CTTATACTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
20 3 0.08
21 5 0.13
22 22 0.58
23 8 0.21
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (22 bp):
TATATATATATTGTATATGTTT
Found at i:54402445 original size:26 final size:26
Alignment explanation
Indices: 54402411--54402472 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
54402401 TTATATCATC
* *
54402411 TTATGTATATATTCTTAAATA-CTATG
1 TTATATATATATTCTTAAATACCT-TA
* *
54402437 TTATATATATATTTTTTAATACCTTA
1 TTATATATATATTCTTAAATACCTTA
54402463 TTATATATAT
1 TTATATATAT
54402473 TATTATTACA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 29 0.94
27 2 0.06
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (26 bp):
TTATATATATATTCTTAAATACCTTA
Found at i:54409883 original size:22 final size:22
Alignment explanation
Indices: 54409857--54409926 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
54409847 TCCAATACTA
54409857 AAATCACCACATTACCAAGATC
1 AAATCACCACATTACCAAGATC
* *
54409879 AAATCGA--A-AGTA-C-AGTCATA
1 AAATC-ACCACATTACCAAG--ATC
54409899 AAATCACCACATTACCAAGATC
1 AAATCACCACATTACCAAGATC
54409921 AAATCA
1 AAATCA
54409927 GAAGTACAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 10 0.28
21 2 0.06
22 16 0.44
23 2 0.06
24 2 0.06
ACGTcount: A:0.49, C:0.26, G:0.07, T:0.19
Consensus pattern (22 bp):
AAATCACCACATTACCAAGATC
Found at i:54409914 original size:42 final size:42
Alignment explanation
Indices: 54409855--54409939 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
54409845 ATTCCAATAC
54409855 TAAAATCACCACATTACCAAGATCAAATC-GAAAGTACAGTCA
1 TAAAATCACCACATTACCAAGATCAAATCAG-AAGTACAGTCA
54409897 TAAAATCACCACATTACCAAGATCAAATCAGAAGTACAGTCA
1 TAAAATCACCACATTACCAAGATCAAATCAGAAGTACAGTCA
54409939 T
1 T
54409940 GCTTATAATG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
42 41 0.98
43 1 0.02
ACGTcount: A:0.47, C:0.24, G:0.09, T:0.20
Consensus pattern (42 bp):
TAAAATCACCACATTACCAAGATCAAATCAGAAGTACAGTCA
Found at i:54413307 original size:20 final size:20
Alignment explanation
Indices: 54413284--54413321 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
54413274 TACTTTGCTT
54413284 AAAGTATCGATACCTTTAAC
1 AAAGTATCGATACCTTTAAC
* *
54413304 AAAGTTTCGATATCTTTA
1 AAAGTATCGATACCTTTA
54413322 TTCTGGTATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (20 bp):
AAAGTATCGATACCTTTAAC
Found at i:54427978 original size:539 final size:540
Alignment explanation
Indices: 54426943--54428023 Score: 2083
Period size: 539 Copynumber: 2.0 Consensus size: 540
54426933 AAATTATTCT
54426943 AATACCGACAAAAAGAAGAATTACAACGTGAATTGAAGCAAAAAAACCATTAGAATGCAGAAATC
1 AATACCGACAAAAAGAAGAATTACAACGTGAATTGAAGCAAAAAAACCATTAGAATGCAGAAATC
54427008 GTTGAAGAAAATTAACAAAATCAATAAAATCTCTAACAACATTTACATAAATTTCAAAACAAAAA
66 GTTGAAGAAAATTAACAAAATCAATAAAATCTCTAACAACATTTACATAAATTTCAAAACAAAAA
*
54427073 AGGAGGCAAAAATAACTTTAAAGAAGACAACCTAGAATATATACACCTATCTCCCATAACATATC
131 AGGAGGCAAAAATAACTTTAAAGAAGACAACCTAGAATATATACACCTATCTCCCAAAACATATC
54427138 GTTTTGAAGAACAAGCAACATCCAATAGCAACTTACCACCTGTTACAAAAGGCTATTGTTTATCA
196 GTTTTGAAGAACAAGCAACATCCAATAGCAACTTACCACCTGTTACAAAAGGCTATTGTTTATCA
54427203 TTATCGTGGCTCCTTAGAAGTGCAATTCTCAAGGTACATTTATGATAAAATCTCAACAAATGAGA
261 TTATCGTGGCTCCTTAGAAGTGCAATTCTCAAGGTACATTTATGATAAAATCTCAACAAATGAGA
54427268 TATAATGTTCCATCGTGGAATAAAGCCACCATTGAGAACAACCTAGAAAGAAGAAGTTATCAGAG
326 TATAATGTTCCATCGTGGAATAAAGCCACCATTGAGAACAACCTAGAAAGAAGAAGTTATCAGAG
54427333 CAGGGTGTTTTGAGGAAGGCCATATAACCCATCTCTCGACTCAAAAAGAGGGGGATATTGTTATG
391 CAGGGTGTTTTGAGGAAGGCCATATAACCCATCTCTCGACTCAAAAAGAGGGGGATATTGTTATG
54427398 CCCCCATTCGTGACAAGCCATGTGGCAAGCTTGGGAGACGTCTTAATAGTAAGCCTACCATTAAC
456 CCCCCATTCGTGACAAGCCATGTGGCAAGCTTGGGAGACGTCTTAATAGTAAGCCTACCATTAAC
54427463 AAGTCGGGAGGTCACTTGTG
521 AAGTCGGGAGGTCACTTGTG
*
54427483 AATACCGACAAAAAGAA-AATTACAACGTGAATTGAAGCAAACAAACCATTAGAATGCAGAAATC
1 AATACCGACAAAAAGAAGAATTACAACGTGAATTGAAGCAAAAAAACCATTAGAATGCAGAAATC
*
54427547 GTTGAAGAAAATTAACAAAATCAATAAAATCTCTAACAACATTTGCATAAATTTCAAAACAAAAA
66 GTTGAAGAAAATTAACAAAATCAATAAAATCTCTAACAACATTTACATAAATTTCAAAACAAAAA
* *
54427612 AGGAGGCAAAAATAACTTTGAAGAAGACAACCTAGAATATATACACCTATCTCCCAAAACGTATC
131 AGGAGGCAAAAATAACTTTAAAGAAGACAACCTAGAATATATACACCTATCTCCCAAAACATATC
54427677 GTTTTGAAGAACAAGCAACATCCAATAGCAACTTACCACCTGTTACAAAAGGCTATTGTTTATCA
196 GTTTTGAAGAACAAGCAACATCCAATAGCAACTTACCACCTGTTACAAAAGGCTATTGTTTATCA
*
54427742 TTATCGTGGCTCCTTAGAAGTGCAATTCTCAAGGTACATTTATGATAAAATCTTAACAAATGAGA
261 TTATCGTGGCTCCTTAGAAGTGCAATTCTCAAGGTACATTTATGATAAAATCTCAACAAATGAGA
*
54427807 TATAATGTTCCATCGTGGAATAAAGCCATCATTGAGAACAACCTAGAAAGAAGAAGTTATCAGAG
326 TATAATGTTCCATCGTGGAATAAAGCCACCATTGAGAACAACCTAGAAAGAAGAAGTTATCAGAG
54427872 CAGGGTGTTTTGAGGAAGGCCATATAACCCATCTCTCGACTCAAAAAGAGGGGGATATTGTTATG
391 CAGGGTGTTTTGAGGAAGGCCATATAACCCATCTCTCGACTCAAAAAGAGGGGGATATTGTTATG
*
54427937 CCCCCATTCGTGACAAGCCATGTGGCAAGCTTGGGAGACGTCTTAATAGTAAGCTTACCATTAAC
456 CCCCCATTCGTGACAAGCCATGTGGCAAGCTTGGGAGACGTCTTAATAGTAAGCCTACCATTAAC
54428002 AAGTCGGGAGGTCACTTGTG
521 AAGTCGGGAGGTCACTTGTG
54428022 AA
1 AA
54428024 CTTACCCTTT
Statistics
Matches: 533, Mismatches: 8, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
539 516 0.97
540 17 0.03
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (540 bp):
AATACCGACAAAAAGAAGAATTACAACGTGAATTGAAGCAAAAAAACCATTAGAATGCAGAAATC
GTTGAAGAAAATTAACAAAATCAATAAAATCTCTAACAACATTTACATAAATTTCAAAACAAAAA
AGGAGGCAAAAATAACTTTAAAGAAGACAACCTAGAATATATACACCTATCTCCCAAAACATATC
GTTTTGAAGAACAAGCAACATCCAATAGCAACTTACCACCTGTTACAAAAGGCTATTGTTTATCA
TTATCGTGGCTCCTTAGAAGTGCAATTCTCAAGGTACATTTATGATAAAATCTCAACAAATGAGA
TATAATGTTCCATCGTGGAATAAAGCCACCATTGAGAACAACCTAGAAAGAAGAAGTTATCAGAG
CAGGGTGTTTTGAGGAAGGCCATATAACCCATCTCTCGACTCAAAAAGAGGGGGATATTGTTATG
CCCCCATTCGTGACAAGCCATGTGGCAAGCTTGGGAGACGTCTTAATAGTAAGCCTACCATTAAC
AAGTCGGGAGGTCACTTGTG
Found at i:54429935 original size:75 final size:75
Alignment explanation
Indices: 54429812--54429961 Score: 282
Period size: 75 Copynumber: 2.0 Consensus size: 75
54429802 GTTTGCCATT
54429812 GAAGTTGAAAAGTGATCCGAAAGAAAACTTTTTAAGAACGCTATTAAAAGTTGCTTATGAAAAGA
1 GAAGTTGAAAAGTGATCCGAAAGAAAACTTTTTAAGAACGCTATTAAAAGTTGCTTATGAAAAGA
54429877 TAAAATGAAG
66 TAAAATGAAG
* *
54429887 GAAGTTGAAAAGTGATCCGAAAGAAAATTTTTTAAGAACTCTATTAAAAGTTGCTTATGAAAAGA
1 GAAGTTGAAAAGTGATCCGAAAGAAAACTTTTTAAGAACGCTATTAAAAGTTGCTTATGAAAAGA
54429952 TAAAATGAAG
66 TAAAATGAAG
54429962 AATTAATAGA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.27
Consensus pattern (75 bp):
GAAGTTGAAAAGTGATCCGAAAGAAAACTTTTTAAGAACGCTATTAAAAGTTGCTTATGAAAAGA
TAAAATGAAG
Found at i:54437749 original size:18 final size:19
Alignment explanation
Indices: 54437713--54437750 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
54437703 TTGAAGCTTT
*
54437713 ATTTTAATATTTTTTATAC
1 ATTTTAATATTTATTATAC
54437732 ATTTTAAT-TTTATTATAC
1 ATTTTAATATTTATTATAC
54437750 A
1 A
54437751 CATTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTAATATTTATTATAC
Found at i:54437755 original size:20 final size:19
Alignment explanation
Indices: 54437713--54437757 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
54437703 TTGAAGCTTT
*
54437713 ATTTTAATATTTTTTATAC
1 ATTTTAATATTTTTTACAC
54437732 ATTTTAAT-TTTATTATACAC
1 ATTTTAATATTT-TT-TACAC
54437752 ATTTTA
1 ATTTTA
54437758 TTACTTCGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 3 0.13
19 10 0.43
20 10 0.43
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTTAATATTTTTTACAC
Found at i:54440520 original size:20 final size:19
Alignment explanation
Indices: 54440476--54440520 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
54440466 GCTAGGTTTG
*
54440476 ATATCTTTTCTTTTTTATTA
1 ATAT-TTTTCTTTTTTATGA
*
54440496 TTATTTTTCTTTTTTAATGA
1 ATATTTTTCTTTTTT-ATGA
54440516 ATATT
1 ATATT
54440521 ACTATCTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.69
Consensus pattern (19 bp):
ATATTTTTCTTTTTTATGA
Found at i:54446299 original size:15 final size:16
Alignment explanation
Indices: 54446281--54446331 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
54446271 TAAAATTTCA
54446281 ATAAA-TAAAAAATAT
1 ATAAATTAAAAAATAT
**
54446296 ATAAAATTATTAAATAT
1 AT-AAATTAAAAAATAT
*
54446313 -TAAATTAAAAATTAT
1 ATAAATTAAAAAATAT
54446328 ATAA
1 ATAA
54446332 TATTTTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
15 13 0.46
16 7 0.25
17 8 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAAATTAAAAAATAT
Found at i:54446349 original size:34 final size:32
Alignment explanation
Indices: 54446282--54446354 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
54446272 AAAATTTCAA
*
54446282 TAAA-TAAAAAATATATAAAATTATTAAATAT
1 TAAATTAAAAAATATATAAAATTATTAAAAAT
* * *
54446313 TAAATTAAAAATTATATAATATTTTTAAAAAAAT
1 TAAATTAAAAAATATATAAAATTATT--AAAAAT
54446347 TAAATTAA
1 TAAATTAA
54446355 TATGAGTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 4 0.11
32 18 0.51
34 13 0.37
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (32 bp):
TAAATTAAAAAATATATAAAATTATTAAAAAT
Found at i:54448908 original size:9 final size:9
Alignment explanation
Indices: 54448894--54448925 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
54448884 AAGTTTCTTT
54448894 TTTTTTTAC
1 TTTTTTTAC
54448903 TTTTTTTAC
1 TTTTTTTAC
54448912 -TTTTTTAC
1 TTTTTTTAC
54448920 TTTTTT
1 TTTTTT
54448926 GAGTTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTAC
Found at i:54448915 original size:7 final size:8
Alignment explanation
Indices: 54448895--54448925 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
54448885 AGTTTCTTTT
54448895 TTTTTTAC
1 TTTTTTAC
54448903 TTTTTTTAC
1 -TTTTTTAC
54448912 TTTTTTAC
1 TTTTTTAC
54448920 TTTTTT
1 TTTTTT
54448926 GAGTTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTAC
Found at i:54448932 original size:17 final size:17
Alignment explanation
Indices: 54448895--54448932 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
54448885 AGTTTCTTTT
*
54448895 TTTTTTACTTTTTTTAC
1 TTTTTTACTTTTTTGAC
*
54448912 TTTTTTACTTTTTTGAG
1 TTTTTTACTTTTTTGAC
54448929 TTTT
1 TTTT
54448933 ATTTTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.08, G:0.05, T:0.76
Consensus pattern (17 bp):
TTTTTTACTTTTTTGAC
Found at i:54448948 original size:23 final size:24
Alignment explanation
Indices: 54448912--54448967 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
54448902 CTTTTTTTAC
* *
54448912 TTTTTTACTTTTTTGAGTTTTAT-T
1 TTTTTTA-TGTTTTGACTTTTATCT
*
54448936 TTTTTTATGTTTTGTCTTTTATCT
1 TTTTTTATGTTTTGACTTTTATCT
*
54448960 TTATTTAT
1 TTTTTTAT
54448968 TTATTTATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 12 0.44
24 15 0.56
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.75
Consensus pattern (24 bp):
TTTTTTATGTTTTGACTTTTATCT
Found at i:54449056 original size:28 final size:28
Alignment explanation
Indices: 54449001--54449056 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
54448991 AAAATTTGAA
* *
54449001 ATATATATTTGAAATATTTTATTAATAT
1 ATATATATTTGAAATATTTAAATAATAT
*
54449029 ATATATATTTTAAAT-TTTAAAT-ATAT
1 ATATATATTTGAAATATTTAAATAATAT
54449055 AT
1 AT
54449057 TTTTAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 6 0.24
27 5 0.20
28 14 0.56
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
ATATATATTTGAAATATTTAAATAATAT
Found at i:54449071 original size:22 final size:22
Alignment explanation
Indices: 54449027--54449075 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
54449017 TTTTATTAAT
* *
54449027 ATATATATATTTTAAATTTTAA
1 ATATATATATTTTAAAATATAA
54449049 ATATATAT-TTTTAATAATATAA
1 ATATATATATTTTAA-AATATAA
54449071 A-ATAT
1 ATATAT
54449076 TTAAATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATATATATATTTTAAAATATAA
Found at i:54449178 original size:11 final size:11
Alignment explanation
Indices: 54449162--54449187 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
54449152 TTAAATTATG
54449162 ATTTTTAAATT
1 ATTTTTAAATT
54449173 ATTTTTAAATT
1 ATTTTTAAATT
54449184 ATTT
1 ATTT
54449188 AAAGATATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTTTAAATT
Found at i:54449354 original size:26 final size:28
Alignment explanation
Indices: 54449302--54449357 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 28
54449292 AAATGAATTT
*
54449302 ATTTAAATATATATATTAAAAAATAAAA
1 ATTTAAATATATAAATTAAAAAATAAAA
*
54449330 ATTTAAAT-T-TAAATTAAAAATTAAAA
1 ATTTAAATATATAAATTAAAAAATAAAA
54449356 AT
1 AT
54449358 ATATATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 17 0.65
27 1 0.04
28 8 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
ATTTAAATATATAAATTAAAAAATAAAA
Found at i:54449744 original size:20 final size:21
Alignment explanation
Indices: 54449700--54449759 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 21
54449690 ATATCTTTAA
54449700 AAATAAT-TTAAAAATCATAATT
1 AAATAATATTAAAAAT-A-AATT
*
54449722 TAA-AATATTATAAAATAAATT
1 AAATAATATTA-AAAATAAATT
54449743 AAATAATATTAAAAATA
1 AAATAATATTAAAAATA
54449760 TTAAAAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
21 15 0.45
22 13 0.39
23 5 0.15
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATAATATTAAAAATAAATT
Found at i:54449762 original size:19 final size:21
Alignment explanation
Indices: 54449716--54449764 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
54449706 TTTAAAAATC
*
54449716 ATAATTTAA-AATATTATAAA
1 ATAATTAAATAATATTATAAA
54449736 ATAAATTAAATAATATTA-AAA
1 AT-AATTAAATAATATTATAAA
54449757 AT-ATTAAA
1 ATAATTAAA
54449765 AAACTAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 6 0.23
20 2 0.08
21 11 0.42
22 7 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
ATAATTAAATAATATTATAAA
Found at i:54449765 original size:9 final size:9
Alignment explanation
Indices: 54449723--54449766 Score: 52
Period size: 9 Copynumber: 4.4 Consensus size: 9
54449713 ATCATAATTT
54449723 AAAATATTA
1 AAAATATTA
54449732 TAAAATAAATTA
1 -AAAAT--ATTA
54449744 AATAATATTA
1 AA-AATATTA
54449754 AAAATATTA
1 AAAATATTA
54449763 AAAA
1 AAAA
54449767 ACTAATAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 11 0.35
10 11 0.35
11 2 0.06
12 7 0.23
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAATATTA
Found at i:54449846 original size:21 final size:23
Alignment explanation
Indices: 54449816--54449873 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 23
54449806 TAAATATTTT
54449816 ATATTATTAAAAATAT-ATATT-A
1 ATATT-TTAAAAATATAATATTCA
54449838 ATATTTTAAAAA-ATAATATTCA
1 ATATTTTAAAAATATAATATTCA
*
54449860 AAATTTTAAAAATA
1 ATATTTTAAAAATA
54449874 ATTTAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 2 0.06
21 12 0.38
22 17 0.53
23 1 0.03
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
ATATTTTAAAAATATAATATTCA
Found at i:54449874 original size:21 final size:20
Alignment explanation
Indices: 54449822--54449881 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 20
54449812 TTTTATATTA
*
54449822 TTAAAAATATATATTAATATT
1 TTAAAAATA-ATATTAAAATT
54449843 TTAAAAAATAATATTCAAAATT
1 TT-AAAAATAATATT-AAAATT
54449865 TTAAAAATAAT-TTAAAA
1 TTAAAAATAATATTAAAA
54449882 ATAATTTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 4 0.11
20 2 0.06
21 16 0.44
22 14 0.39
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TTAAAAATAATATTAAAATT
Found at i:54449880 original size:33 final size:33
Alignment explanation
Indices: 54449837--54449927 Score: 98
Period size: 33 Copynumber: 2.7 Consensus size: 33
54449827 AATATATATT
*
54449837 AATATTTTAAAAAATAATATTCAAAA-TTTTAAA
1 AATAATTTAAAAAATAAT-TTCAAAATTTTTAAA
*
54449870 AATAATTT-AAAAATAATTTTTAAAATTTTTAAA
1 AATAATTTAAAAAATAA-TTTCAAAATTTTTAAA
*
54449903 AATATATATTATAAAAT-ATTTCAAA
1 AATA-AT-TTAAAAAATAATTTCAAA
54449928 TATAGATTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
32 14 0.29
33 19 0.39
34 8 0.16
35 3 0.06
36 5 0.10
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (33 bp):
AATAATTTAAAAAATAATTTCAAAATTTTTAAA
Found at i:54449887 original size:23 final size:23
Alignment explanation
Indices: 54449862--54449940 Score: 79
Period size: 23 Copynumber: 3.3 Consensus size: 23
54449852 AATATTCAAA
54449862 ATTTTAAAAATAATTTAAAAATA-
1 ATTTTAAAAAT-ATTTAAAAATAG
* * *
54449885 ATTTTTAAAATTTTTAAAAATAT
1 ATTTTAAAAATATTTAAAAATAG
* *
54449908 ATATTATAAAATATTTCAAATATAG
1 ATTTTA-AAAATATTT-AAAAATAG
54449933 ATTTTAAA
1 ATTTTAAA
54449941 TTTTTTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
22 10 0.22
23 14 0.31
24 10 0.22
25 11 0.24
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (23 bp):
ATTTTAAAAATATTTAAAAATAG
Found at i:54449951 original size:23 final size:22
Alignment explanation
Indices: 54449875--54449955 Score: 67
Period size: 23 Copynumber: 3.6 Consensus size: 22
54449865 TTAAAAATAA
54449875 TTTAAAA-ATAATTTTTAAAATTT
1 TTTAAAATATAA-TTTT-AAATTT
* * * *
54449898 TTAAAAATATATATTATAAAATA
1 TTTAAAATATA-ATTTTAAATTT
*
54449921 TTTCAAATATAGATTTTAAATTT
1 TTTAAAATATA-ATTTTAAATTT
54449944 TTTAAAAT-TAAT
1 TTTAAAATATAAT
54449956 AACAAAAAAT
Statistics
Matches: 45, Mismatches: 11, Indels: 6
0.73 0.18 0.10
Matches are distributed among these distances:
21 2 0.04
22 2 0.04
23 34 0.76
24 6 0.13
25 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (22 bp):
TTTAAAATATAATTTTAAATTT
Found at i:54449966 original size:10 final size:9
Alignment explanation
Indices: 54449953--54450056 Score: 52
Period size: 9 Copynumber: 11.2 Consensus size: 9
54449943 TTTTAAAATT
54449953 AATAACAAAA
1 AATAA-AAAA
*
54449963 AATAAATAA
1 AATAAAAAA
54449972 AATAAATACAA
1 AATAAA-A-AA
*
54449983 AAT-AAAAT
1 AATAAAAAA
54449991 AAT--AAAA
1 AATAAAAAA
*
54449998 AATATAAAA
1 AATAAAAAA
**
54450007 CTTAAAAAA
1 AATAAAAAA
*
54450016 ATTAAAGAAA
1 AATAAA-AAA
* *
54450026 AAGACAAAA
1 AATAAAAAA
*
54450035 GATAATAAAA
1 AATAA-AAAA
54450045 AAGTAAAAAA
1 AA-TAAAAAA
54450055 AA
1 AA
54450057 AAGTGAAAGA
Statistics
Matches: 72, Mismatches: 15, Indels: 14
0.71 0.15 0.14
Matches are distributed among these distances:
7 6 0.08
8 4 0.06
9 30 0.42
10 24 0.33
11 8 0.11
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (9 bp):
AATAAAAAA
Found at i:54449999 original size:15 final size:16
Alignment explanation
Indices: 54449966--54450001 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
54449956 AACAAAAAAT
*
54449966 AAATAAAATAAATACA
1 AAATAAAATAAATAAA
54449982 AAATAAAAT-AATAAA
1 AAATAAAATAAATAAA
54449997 AAATA
1 AAATA
54450002 TAAAACTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (16 bp):
AAATAAAATAAATAAA
Found at i:54453722 original size:20 final size:20
Alignment explanation
Indices: 54453697--54453740 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
54453687 TAAGATACGG
54453697 TGAAGG-AAAAGAAATAACTT
1 TGAAGGTAAAAGAAATAA-TT
**
54453717 TGAAGGTAAAATTAATAATT
1 TGAAGGTAAAAGAAATAATT
54453737 TGAA
1 TGAA
54453741 TTCATTTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.52, C:0.02, G:0.18, T:0.27
Consensus pattern (20 bp):
TGAAGGTAAAAGAAATAATT
Found at i:54459155 original size:18 final size:19
Alignment explanation
Indices: 54459128--54459177 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
54459118 TTTATTACAT
*
54459128 TTTA-TTTTTGTTTT-TAG
1 TTTATTTTTTGTTTTCTAA
54459145 TTTATTTTTTGTTTTCTAA
1 TTTATTTTTTGTTTTCTAA
54459164 TTT-TTCTTTTGTTT
1 TTTATT-TTTTGTTT
54459178 GCTCTTGGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 4 0.14
18 12 0.41
19 13 0.45
ACGTcount: A:0.10, C:0.04, G:0.08, T:0.78
Consensus pattern (19 bp):
TTTATTTTTTGTTTTCTAA
Found at i:54463028 original size:19 final size:18
Alignment explanation
Indices: 54463004--54463042 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
54462994 CTTTTTTTTG
*
54463004 TTATTTTTTATTTATTTAT
1 TTATTTTTTAATTA-TTAT
54463023 TTATTTTTTAATTATTAT
1 TTATTTTTTAATTATTAT
54463041 TT
1 TT
54463043 TCTTTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (18 bp):
TTATTTTTTAATTATTAT
Found at i:54464243 original size:22 final size:21
Alignment explanation
Indices: 54464218--54464260 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
54464208 AATTATTAAC
*
54464218 ATAATGAATTTTAATTAATTTT
1 ATAATAAATTTTAATT-ATTTT
*
54464240 ATAATAAATTTTGATTATTTT
1 ATAATAAATTTTAATTATTTT
54464261 CGACAGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (21 bp):
ATAATAAATTTTAATTATTTT
Found at i:54466647 original size:25 final size:25
Alignment explanation
Indices: 54466601--54466648 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
54466591 TTTCTTTTTA
* *
54466601 TTTTTATTTTTTTAGACTTATTTCT
1 TTTTTATCTTTTGAGACTTATTTCT
54466626 TTTTTATCTTTTGA-ACTATATTT
1 TTTTTATCTTTTGAGACT-TATTT
54466649 AATTTTATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 3 0.15
25 17 0.85
ACGTcount: A:0.19, C:0.08, G:0.04, T:0.69
Consensus pattern (25 bp):
TTTTTATCTTTTGAGACTTATTTCT
Found at i:54466654 original size:25 final size:25
Alignment explanation
Indices: 54466600--54466654 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
54466590 CTTTCTTTTT
* * *
54466600 ATTTTTATTTTTTTAGACTTATTTC
1 ATTTTTATCTTTTGAGACTTATTTA
*
54466625 TTTTTTATCTTTTGA-ACTATATTTA
1 ATTTTTATCTTTTGAGACT-TATTTA
54466650 ATTTT
1 ATTTT
54466655 ATGTTTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.22, C:0.07, G:0.04, T:0.67
Consensus pattern (25 bp):
ATTTTTATCTTTTGAGACTTATTTA
Found at i:54470225 original size:25 final size:25
Alignment explanation
Indices: 54470212--54470352 Score: 158
Period size: 25 Copynumber: 5.6 Consensus size: 25
54470202 CTTCCGAGTC
54470212 ATATAACGGGAAGCTCATGTGAGCT
1 ATATAACGGGAAGCTCATGTGAGCT
*
54470237 GTATAACGGGAAGCTCATGTGAGCT
1 ATATAACGGGAAGCTCATGTGAGCT
54470262 ATATAACGGGAAGCTCATGTGAGCT
1 ATATAACGGGAAGCTCATGTGAGCT
* * * * *
54470287 GTATAACAGGAAGCTCTTGCGAGCC
1 ATATAACGGGAAGCTCATGTGAGCT
* * * * * *
54470312 AAATATCGAGAAGCTCAAGAGAGCC
1 ATATAACGGGAAGCTCATGTGAGCT
54470337 AT-TAATCGGGAAGCTC
1 ATATAA-CGGGAAGCTC
54470353 GTGAAAGCTA
Statistics
Matches: 97, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
24 2 0.02
25 95 0.98
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (25 bp):
ATATAACGGGAAGCTCATGTGAGCT
Found at i:54470325 original size:50 final size:50
Alignment explanation
Indices: 54470197--54470328 Score: 183
Period size: 50 Copynumber: 2.6 Consensus size: 50
54470187 TGTAAACGGA
* * *
54470197 AAGCTCTTCCGAGTCATATAACGGGAAGCTCATGTGAGCTGTATAACGGG
1 AAGCTCTTGCGAGCCATATAACGGGAAGCTCATGTGAGCTGTATAACAGG
* * *
54470247 AAGCTCATGTGAGCTATATAACGGGAAGCTCATGTGAGCTGTATAACAGG
1 AAGCTCTTGCGAGCCATATAACGGGAAGCTCATGTGAGCTGTATAACAGG
* * *
54470297 AAGCTCTTGCGAGCCAAATATCGAGAAGCTCA
1 AAGCTCTTGCGAGCCATATAACGGGAAGCTCA
54470329 AGAGAGCCAT
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 70 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.23
Consensus pattern (50 bp):
AAGCTCTTGCGAGCCATATAACGGGAAGCTCATGTGAGCTGTATAACAGG
Found at i:54470325 original size:75 final size:75
Alignment explanation
Indices: 54470246--54470412 Score: 174
Period size: 75 Copynumber: 2.2 Consensus size: 75
54470236 TGTATAACGG
* * * ** ** * **
54470246 GAAGCTCATGTGAGCTATATAA-CGGGAAGCTCATGTGAGCTGTATAACAGGAAGCTCTTGCGAG
1 GAAGCTCAAGAGAGCCAT-TAATCGGGAAGCTCATGAAAGCTAAATAACAGGAAACTCTTAAGAG
54470310 CCAAATATCGA
65 CCAAATATCGA
* **
54470321 GAAGCTCAAGAGAGCCATTAATCGGGAAGCTCGTGAAAGCTAAATAATGGGAAACTCTTAAGAGC
1 GAAGCTCAAGAGAGCCATTAATCGGGAAGCTCATGAAAGCTAAATAACAGGAAACTCTTAAGAGC
*
54470386 CAAGTATCGA
66 CAAATATCGA
**
54470396 GAAGCTCTTGAGAGCCA
1 GAAGCTCAAGAGAGCCA
54470413 AATATCAGGA
Statistics
Matches: 75, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
74 3 0.04
75 72 0.96
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.20
Consensus pattern (75 bp):
GAAGCTCAAGAGAGCCATTAATCGGGAAGCTCATGAAAGCTAAATAACAGGAAACTCTTAAGAGC
CAAATATCGA
Found at i:54470409 original size:25 final size:25
Alignment explanation
Indices: 54470296--54470418 Score: 106
Period size: 25 Copynumber: 4.9 Consensus size: 25
54470286 TGTATAACAG
*
54470296 GAAGCTCTTGCGAGCCAAATATCGA
1 GAAGCTCTTGAGAGCCAAATATCGA
** * *
54470321 GAAGCTCAAGAGAGCC-ATTAATCGG
1 GAAGCTCTTGAGAGCCAAAT-ATCGA
* * * *
54470346 GAAGCTCGTGAAAGCTAAATAAT-GG
1 GAAGCTCTTGAGAGCCAAAT-ATCGA
* * *
54470371 GAAACTCTTAAGAGCCAAGTATCGA
1 GAAGCTCTTGAGAGCCAAATATCGA
54470396 GAAGCTCTTGAGAGCCAAATATC
1 GAAGCTCTTGAGAGCCAAATATC
54470419 AGGACGCTTA
Statistics
Matches: 75, Mismatches: 20, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
24 4 0.05
25 66 0.88
26 5 0.07
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (25 bp):
GAAGCTCTTGAGAGCCAAATATCGA
Found at i:54476891 original size:31 final size:30
Alignment explanation
Indices: 54476856--54476932 Score: 73
Period size: 31 Copynumber: 2.5 Consensus size: 30
54476846 GTTAAAGATA
54476856 AAATTGATACTCGAATTTATTTATTTCTCCT
1 AAATTGATACTCGAATTT-TTTATTTCTCCT
* * * * * *
54476887 AAATTGGTACTTGTGATTTTTTTTTTGTTCT
1 AAATTGATACTCG-AATTTTTTATTTCTCCT
*
54476918 AGATTGATACTCGAA
1 AAATTGATACTCGAA
54476933 CTTGTATTAG
Statistics
Matches: 35, Mismatches: 10, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
30 1 0.03
31 30 0.86
32 4 0.11
ACGTcount: A:0.26, C:0.12, G:0.13, T:0.49
Consensus pattern (30 bp):
AAATTGATACTCGAATTTTTTATTTCTCCT
Found at i:54477422 original size:191 final size:195
Alignment explanation
Indices: 54477061--54477438 Score: 462
Period size: 191 Copynumber: 2.0 Consensus size: 195
54477051 GAAAAATAAT
* * * *
54477061 GAGGTATAAGAGGACGTCACGTGGCAGTGTTCGATTAGCTAGCACTGCCACGTCAGCAAAAAAAT
1 GAGGTATAAGAGGACGTCACGCGGCAGTGTTCGATTAGCTAACAATACCACGTCAGC-AAAAAAT
* ** ** *
54477126 TAACATTCTTAGTCTCAGGTATCAATATAGTGGACAAAAAAAAGTTTGGGTATCAATATGGGAAA
65 TAACATTCTTAGTCTCAAGTATCAATATAGCAGACAAAAAAAAGTTTGAATATCAATATGCGAAA
* * * *
54477191 AAAAAAATCATAAGTATCAATTTGGGAGAAATGGACAAATTCGAGTACCAATTTTATTAAGAAAA
130 AAAAAAACCATAAGTATAAATTTGGGAGAAATGAACAAATTCGAATACCAATTTTATTAAGAAAA
54477256 G
195 G
* *
54477257 GAGGTATAAGAGGACGTCACGCGGCGGCATG-T-GATTGGCTAACAATACCACGTCAGC-AAAAA
1 GAGGTATAAGAGGACGTCACGCGGCAG--TGTTCGATTAGCTAACAATACCACGTCAGCAAAAAA
* * * * * * *
54477319 TTAACGTTGTTAGTCTTAAGTATCGATATAGCAGACAGAAAAAATTTTGAATAT-AA-AT-CTAA
64 TTAACATTCTTAGTCTCAAGTATCAATATAGCAGACAAAAAAAAGTTTGAATATCAATATGCGAA
* *
54477381 AAAAAAAACCATAAGTATAAATTTGGGAGAAGTGAACAAATTCGAATACTAATTTTAT
129 AAAAAAAACCATAAGTATAAATTTGGGAGAAATGAACAAATTCGAATACCAATTTTAT
54477439 ATTTAACCCT
Statistics
Matches: 155, Mismatches: 25, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
191 54 0.35
192 2 0.01
193 2 0.01
194 48 0.31
196 46 0.30
197 1 0.01
198 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.25
Consensus pattern (195 bp):
GAGGTATAAGAGGACGTCACGCGGCAGTGTTCGATTAGCTAACAATACCACGTCAGCAAAAAATT
AACATTCTTAGTCTCAAGTATCAATATAGCAGACAAAAAAAAGTTTGAATATCAATATGCGAAAA
AAAAAACCATAAGTATAAATTTGGGAGAAATGAACAAATTCGAATACCAATTTTATTAAGAAAAG
Found at i:54481706 original size:20 final size:20
Alignment explanation
Indices: 54481681--54481723 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
54481671 AAAATTATAC
54481681 TTTTAAAACTA-ATTTAATTT
1 TTTTAAAA-TATATTTAATTT
*
54481701 TTTTAAAATATTTTTAATTT
1 TTTTAAAATATATTTAATTT
54481721 TTT
1 TTT
54481724 AATTTATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTAAAATATATTTAATTT
Found at i:54484311 original size:23 final size:23
Alignment explanation
Indices: 54484284--54484328 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
54484274 CCCGTTACAT
*
54484284 GGCTCTTTGTGAGCTTCCTGATA
1 GGCTCTTCGTGAGCTTCCTGATA
54484307 GGCTCTTCGTGAGCTTCCTGAT
1 GGCTCTTCGTGAGCTTCCTGAT
54484329 TAAAAGTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.11, C:0.24, G:0.27, T:0.38
Consensus pattern (23 bp):
GGCTCTTCGTGAGCTTCCTGATA
Found at i:54484422 original size:23 final size:26
Alignment explanation
Indices: 54484393--54484450 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
54484383 AGCCCGGATA
54484393 AGCTTCCTGA-TAA-G-CTCTTTGTG
1 AGCTTCCTGATTAATGACTCTTTGTG
**
54484416 AGCTTCCCAATTAATGACTCTTTGTG
1 AGCTTCCTGATTAATGACTCTTTGTG
54484442 AGCTTCCTG
1 AGCTTCCTG
54484451 TTATATGGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 8 0.29
24 3 0.11
25 1 0.04
26 16 0.57
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (26 bp):
AGCTTCCTGATTAATGACTCTTTGTG
Found at i:54491133 original size:21 final size:21
Alignment explanation
Indices: 54491074--54491134 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
54491064 GATTATATGA
* * *
54491074 ATTGGATTGAATATTGATTAT
1 ATTGAATTGATTATTGAATAT
54491095 ATTGAATTGATT-TATGAATAT
1 ATTGAATTGATTAT-TGAATAT
54491116 ATGTGAATTG-TTATTGAAT
1 AT-TGAATTGATTATTGAAT
54491135 TGAAATTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.03
21 25 0.74
22 8 0.24
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (21 bp):
ATTGAATTGATTATTGAATAT
Found at i:54491992 original size:45 final size:45
Alignment explanation
Indices: 54491928--54492199 Score: 380
Period size: 45 Copynumber: 6.2 Consensus size: 45
54491918 CTGTTACTGC
*
54491928 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATTTTGT
1 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
* *
54491973 TACTGCTACTATTACCGATTCGACACTTTGTGTGTCGAATATTGT
1 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
*
54492018 TACTGCTACTGTTACCGATTCGGCACTGTGTGTGTCGAATATTGT
1 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
*
54492063 TACTGCTACTGTTACCGATTCGGCACTGTGTGTGTCGAATATTGT
1 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
*
54492108 TACTGTTACTGTTA-C----C-G--CTTTGTGTGTCGAATATTGT
1 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
* * * * *
54492145 TACTGTTACCGTTACCGATTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
*
54492190 TACTGTTACT
1 TACTGCTACT
54492200 ATTATTGTTA
Statistics
Matches: 207, Mismatches: 12, Indels: 16
0.88 0.05 0.07
Matches are distributed among these distances:
37 32 0.15
38 1 0.00
39 1 0.00
40 1 0.00
42 1 0.00
43 1 0.00
44 1 0.00
45 169 0.82
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.41
Consensus pattern (45 bp):
TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
Found at i:54492141 original size:37 final size:37
Alignment explanation
Indices: 54492091--54492161 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
54492081 TTCGGCACTG
*
54492091 TGTGTGTCGAATATTGTTACTGTTACTGTTACCGCTT
1 TGTGTGTCGAATATTGTTACTGTTACCGTTACCGCTT
54492128 TGTGTGTCGAATATTGTTACTGTTACCGTTACCG
1 TGTGTGTCGAATATTGTTACTGTTACCGTTACCG
54492162 ATTCAGCACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.44
Consensus pattern (37 bp):
TGTGTGTCGAATATTGTTACTGTTACCGTTACCGCTT
Found at i:54492195 original size:6 final size:6
Alignment explanation
Indices: 54492184--54492220 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
54492174 GTGTGTTGAA
* *
54492184 TACTGT TACTGT TACTAT TATTGT TACTGT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT T
54492221 CCGGATTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.54
Consensus pattern (6 bp):
TACTGT
Found at i:54492411 original size:18 final size:18
Alignment explanation
Indices: 54492384--54492666 Score: 162
Period size: 18 Copynumber: 15.3 Consensus size: 18
54492374 AAAGGTATAA
* *
54492384 AATAACTGATTATTACTG
1 AATAATTGATTGTTACTG
54492402 AATAATTGATTGTTACTG
1 AATAATTGATTGTTACTG
* *
54492420 GATAATTGACTGTTACT-
1 AATAATTGATTGTTACTG
*
54492437 AGAT-ATTAGACTGTTACTG
1 A-ATAATT-GATTGTTACTG
* * * *
54492456 AATAACTAAATATTACTG
1 AATAATTGATTGTTACTG
**
54492474 AATAATTGATCATTACTG
1 AATAATTGATTGTTACTG
* *
54492492 AATAACTGATTGTCACTG
1 AATAATTGATTGTTACTG
* *
54492510 AATGAA-TGACTGCTACTG
1 AAT-AATTGATTGTTACTG
* *
54492528 AATAACTTAATAGTTACTG
1 AATAA-TTGATTGTTACTG
54492547 AAT-ATCTGATT-TTACTG
1 AATAAT-TGATTGTTACTG
*
54492564 AATAATTGACTGTTACTGG
1 AATAATTGATTGTTACT-G
* *
54492583 ATAACCGATCAATTGATCGATACTG
1 ---A---AT-AATTGATTGTTACTG
** * * *
54492608 AATAACCGGTTATTATTG
1 AATAATTGATTGTTACTG
*
54492626 AATAATTGATTGTTACCG
1 AATAATTGATTGTTACTG
* *
54492644 AATAACTGACTGTTACTG
1 AATAATTGATTGTTACTG
54492662 AATAA
1 AATAA
54492667 ATAATTATTC
Statistics
Matches: 201, Mismatches: 46, Indels: 36
0.71 0.16 0.13
Matches are distributed among these distances:
17 19 0.09
18 147 0.73
19 19 0.09
22 2 0.01
25 3 0.01
26 11 0.05
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (18 bp):
AATAATTGATTGTTACTG
Found at i:54492664 original size:36 final size:36
Alignment explanation
Indices: 54492384--54492666 Score: 189
Period size: 36 Copynumber: 7.6 Consensus size: 36
54492374 AAAGGTATAA
* *
54492384 AATAACTGATTATTACTGAATAATTGATTGTTACTG
1 AATAACTGACTGTTACTGAATAATTGATTGTTACTG
* * *
54492420 GATAATTGACTGTTACT-AGAT-ATTAGACTGTTACTG
1 AATAACTGACTGTTACTGA-ATAATT-GATTGTTACTG
* * * **
54492456 AATAACTAAATATTACTGAATAATTGATCATTACTG
1 AATAACTGACTGTTACTGAATAATTGATTGTTACTG
* * * *
54492492 AATAACTGATTGTCACTGAATGAA-TGACTGCTACTG
1 AATAACTGACTGTTACTGAAT-AATTGATTGTTACTG
* *
54492528 AATAACTTAATAGTTACTGAAT-ATCTGATT-TTACTG
1 AATAACTGACT-GTTACTGAATAAT-TGATTGTTACTG
* * *
54492564 AATAATTGACTGTTACTGGATAACCGATCAATTGATCGATACTG
1 AATAACTGACTGTTACT-G---A---AT-AATTGATTGTTACTG
* ** * * *
54492608 AATAACCGGTTATTATTGAATAATTGATTGTTACCG
1 AATAACTGACTGTTACTGAATAATTGATTGTTACTG
54492644 AATAACTGACTGTTACTGAATAA
1 AATAACTGACTGTTACTGAATAA
54492667 ATAATTATTC
Statistics
Matches: 184, Mismatches: 45, Indels: 36
0.69 0.17 0.14
Matches are distributed among these distances:
35 11 0.06
36 125 0.68
37 21 0.11
39 1 0.01
40 1 0.01
42 2 0.01
43 5 0.03
44 18 0.10
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (36 bp):
AATAACTGACTGTTACTGAATAATTGATTGTTACTG
Found at i:54495282 original size:23 final size:23
Alignment explanation
Indices: 54495256--54495301 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
54495246 ATAATAATTA
54495256 AAATTAATCAAATTAAAGTGTTG
1 AAATTAATCAAATTAAAGTGTTG
54495279 AAATTAATCAAATTAAAGTGTTG
1 AAATTAATCAAATTAAAGTGTTG
54495302 GACTAAATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35
Consensus pattern (23 bp):
AAATTAATCAAATTAAAGTGTTG
Found at i:54495310 original size:23 final size:23
Alignment explanation
Indices: 54495256--54495310 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
54495246 ATAATAATTA
*
54495256 AAATTAATCAAATTAAAGTGTTG
1 AAATAAATCAAATTAAAGTGTTG
*
54495279 AAATTAATCAAATTAAAGTGTTG
1 AAATAAATCAAATTAAAGTGTTG
* *
54495302 GACTAAATC
1 AAATAAATC
54495311 CGTAACTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (23 bp):
AAATAAATCAAATTAAAGTGTTG
Found at i:54495775 original size:12 final size:13
Alignment explanation
Indices: 54495755--54495780 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54495745 GTCCTTTTCC
54495755 TTTGTTTTTTTTT
1 TTTGTTTTTTTTT
54495768 TTTGTTTTTTTTT
1 TTTGTTTTTTTTT
54495781 CTAATTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (13 bp):
TTTGTTTTTTTTT
Found at i:54496975 original size:317 final size:320
Alignment explanation
Indices: 54496381--54497063 Score: 855
Period size: 317 Copynumber: 2.1 Consensus size: 320
54496371 CAACGGTTTT
*
54496381 CTAATAGGG-AGGCTTTATGCTTATTCGATAATTGTGGCATTGCCAACGTTGTCCATGTAGGTTG
1 CTAATAGGGCA-GCTTTATGCTTATTCGATAATTGTGGCATTGCCAACGTTGTCCATGTAGGTTC
* *
54496445 TTACATTTTATTAAAGAGAGAACATATATTCAGTAATGGAGTCCTTCTGTGGTGGGGGAAGGGCA
65 TTACATTTTATTAAAGAAAGAACATATATTCAGTAATGGAGTCCTTCTATGGTGGGGGAAGGGCA
* * * *
54496510 AGGGCAGTCTACTCGTTGTCAGGTTGCAATAAGAAATGAAAACTAGTCATTGGAGGGAACACAAG
130 AGGGCAGTCTACTCCTTGTCAGGTTGAAACAAGAAACGAAAACTAGTCATTGGAGGGAACACAAG
** * * *
54496575 GCTAGAGGAGAGTGGCTTTGCATACGAGCCTTACTCTATAGGGTCATTAGAGTGCTACAGCTAGC
195 GCTAGAGGAGAGTGGCTTCACATAAGAGCCTTACTCTATAGGGACATTAGAGTGCTACAACTAGC
* * *
54496640 ACTTTGAAGCCCGCTGAAAAACAGATG--TGCTCTACTAGCGCGCAATGG-TTTGAAGCTTTG
260 ACCTTGAAGCCAGCTGAAAAACAGATGCTTG--CTACTAGCGCGCAATGGATTTCAAGCTTTG
* * * *** * ** *
54496700 CTGATAGGGCAGCTTTATGCTTATTCAATAATTGTGGTATTGCCTTGGATTTTCTGTTTAGGTTC
1 CTAATAGGGCAGCTTTATGCTTATTCGATAATTGTGGCATTGCCAACG-TTGTCCATGTAGGTTC
*
54496765 TTACATTTTATTAAATAAAGAACATATATTCAGTAATGGAGTCCTTAC-ATGGTGGGGGAAGGGC
65 TTACATTTTATTAAAGAAAGAACATATATTCAGTAATGGAGTCCTT-CTATGGTGGGGGAAGGGC
** * * *
54496829 AAGGGCAG-C-A-TCCTTGTTGGGTTGAAACAAGAAACGGAAACTAGTCGTTGGAGGGAACACGA
129 AAGGGCAGTCTACTCCTTGTCAGGTTGAAACAAGAAACGAAAACTAGTCATTGGAGGGAACACAA
* * * * *
54496891 GGCTTGTGGA-ATGTGG-TTCCACATAAGAGCCTTACTCTATAGTGACGTTAGTGTGCTACAACT
194 GGCTAGAGGAGA-GTGGCTT-CACATAAGAGCCTTACTCTATAGGGACATTAGAGTGCTACAACT
* * * *
54496954 AGCACCTTGAAGCCAGCTGAAAAACTGATGCTTGCTATTGGTGCGCAATGGATTTCAAGCTTTG
257 AGCACCTTGAAGCCAGCTGAAAAACAGATGCTTGCTACTAGCGCGCAATGGATTTCAAGCTTTG
*
54497018 CTAATAGGGCAGCTTTATTGCTTATTCGATAATTGTGCCATTGCCA
1 CTAATAGGGCAGCTTTA-TGCTTATTCGATAATTGTGGCATTGCCA
54497064 GCATTTTCCA
Statistics
Matches: 310, Mismatches: 45, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
316 3 0.01
317 132 0.43
318 28 0.09
319 67 0.22
320 79 0.25
321 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (320 bp):
CTAATAGGGCAGCTTTATGCTTATTCGATAATTGTGGCATTGCCAACGTTGTCCATGTAGGTTCT
TACATTTTATTAAAGAAAGAACATATATTCAGTAATGGAGTCCTTCTATGGTGGGGGAAGGGCAA
GGGCAGTCTACTCCTTGTCAGGTTGAAACAAGAAACGAAAACTAGTCATTGGAGGGAACACAAGG
CTAGAGGAGAGTGGCTTCACATAAGAGCCTTACTCTATAGGGACATTAGAGTGCTACAACTAGCA
CCTTGAAGCCAGCTGAAAAACAGATGCTTGCTACTAGCGCGCAATGGATTTCAAGCTTTG
Found at i:54499287 original size:14 final size:15
Alignment explanation
Indices: 54499268--54499296 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
54499258 GATTTGCAAC
54499268 AGTTAAATT-TATTA
1 AGTTAAATTATATTA
54499282 AGTTAAATTATATTA
1 AGTTAAATTATATTA
54499297 TTTTCAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (15 bp):
AGTTAAATTATATTA
Found at i:54500216 original size:18 final size:16
Alignment explanation
Indices: 54500195--54500233 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
54500185 TAATATTAAC
54500195 AAATTCTATAAAAACGTT
1 AAATT-TATAAAAA-GTT
54500213 AAA-TTATAAAAAGTT
1 AAATTTATAAAAAGTT
54500228 AAATTT
1 AAATTT
54500234 CTTTTTCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 6 0.30
16 10 0.50
17 1 0.05
18 3 0.15
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (16 bp):
AAATTTATAAAAAGTT
Found at i:54500228 original size:15 final size:16
Alignment explanation
Indices: 54500201--54500232 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
54500191 TAACAAATTC
54500201 TATAAAAACGTTAAAT
1 TATAAAAACGTTAAAT
54500217 TATAAAAA-GTTAAAT
1 TATAAAAACGTTAAAT
54500232 T
1 T
54500233 TCTTTTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.34
Consensus pattern (16 bp):
TATAAAAACGTTAAAT
Found at i:54508800 original size:24 final size:24
Alignment explanation
Indices: 54508752--54508813 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
54508742 ACCTCTTTGT
* *
54508752 TTGAACCGTTATATCAATCATTTC
1 TTGAACCATTATATCAATCAGTTC
* *
54508776 TTGAACCATTATATCGATTAGTTC
1 TTGAACCATTATATCAATCAGTTC
* *
54508800 TTGGACTATTATAT
1 TTGAACCATTATAT
54508814 TGATCAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (24 bp):
TTGAACCATTATATCAATCAGTTC
Found at i:54510054 original size:30 final size:30
Alignment explanation
Indices: 54510014--54510074 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
54510004 TAGAGTAAAA
54510014 TTTTACTATTAATTATGATTTTTA-ATAATT
1 TTTTACTATTAATTATGA-TTTTACATAATT
* * *
54510044 TTTTCCTATTAATTTTTATTTTACATAATT
1 TTTTACTATTAATTATGATTTTACATAATT
54510074 T
1 T
54510075 AATTTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 5 0.19
30 22 0.81
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.62
Consensus pattern (30 bp):
TTTTACTATTAATTATGATTTTACATAATT
Found at i:54512266 original size:31 final size:31
Alignment explanation
Indices: 54512231--54512293 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
54512221 TTCATGGAGC
*
54512231 TAAGGTCCAAAATATGGAAGAAACAGGTGTT
1 TAAGGTCCAAAATATAGAAGAAACAGGTGTT
54512262 TAAGGTCCAAAATATAGAAGAAACAGGTGTT
1 TAAGGTCCAAAATATAGAAGAAACAGGTGTT
54512293 T
1 T
54512294 CCACAACTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.43, C:0.10, G:0.24, T:0.24
Consensus pattern (31 bp):
TAAGGTCCAAAATATAGAAGAAACAGGTGTT
Found at i:54524518 original size:32 final size:32
Alignment explanation
Indices: 54524482--54524600 Score: 154
Period size: 32 Copynumber: 3.8 Consensus size: 32
54524472 AAATGAGTGG
54524482 TTTTGTGAAATGATAACAAATATCAACTTTCA
1 TTTTGTGAAATGATAACAAATATCAACTTTCA
*
54524514 TTTTGTGAAATGCTAACAAAT-TACAAC-TTCAA
1 TTTTGTGAAATGATAACAAATAT-CAACTTTC-A
* *
54524546 TTTTGTAAAATGATAACAAATATCAACTTTAA
1 TTTTGTGAAATGATAACAAATATCAACTTTCA
* *
54524578 TTTTGTTAAATGATGAC-AATATC
1 TTTTGTGAAATGATAACAAATATC
54524601 CCTCTGAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
31 10 0.13
32 64 0.83
33 3 0.04
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (32 bp):
TTTTGTGAAATGATAACAAATATCAACTTTCA
Found at i:54527583 original size:42 final size:42
Alignment explanation
Indices: 54527519--54527600 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
54527509 TTTTTGAGGC
*
54527519 TTTTCATAACTCAACATCAAAGACGAAGTGTTTTCTCAAAAT
1 TTTTCATAACTCAACATCAAAGACCAAGTGTTTTCTCAAAAT
* *
54527561 TTTTCATAATTCAACATGAAAGACCAAGTGTTTTCTCAAA
1 TTTTCATAACTCAACATCAAAGACCAAGTGTTTTCTCAAA
54527601 TGATTTATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (42 bp):
TTTTCATAACTCAACATCAAAGACCAAGTGTTTTCTCAAAAT
Found at i:54528874 original size:30 final size:30
Alignment explanation
Indices: 54528840--54528902 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
54528830 ACTTATTTTA
54528840 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
54528870 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
54528900 TTG
1 TTG
54528903 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.24, C:0.03, G:0.16, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:54528915 original size:30 final size:30
Alignment explanation
Indices: 54528840--54528919 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
54528830 ACTTATTTTA
**
54528840 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTAAGTTATTATTTTAAAGGCAT
** *
54528870 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTAAGTTATTATTTTAAAGGCAT
*
54528900 TTGCTT-GTTAAGTTA-TATTT
1 TTG-TTAATTAAGTTATTATTT
54528920 ATCTTAGTGT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
29 5 0.11
30 38 0.84
31 2 0.04
ACGTcount: A:0.24, C:0.04, G:0.15, T:0.57
Consensus pattern (30 bp):
TTGTTAATTAAGTTATTATTTTAAAGGCAT
Found at i:54535321 original size:14 final size:14
Alignment explanation
Indices: 54535285--54535327 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
54535275 ACTAAAAAAC
*
54535285 AAATTCAAGAATAAAA
1 AAATTCAA-AAT-TAA
54535301 AAATTCAAAATTAA
1 AAATTCAAAATTAA
*
54535315 AATTTCAAAATTA
1 AAATTCAAAATTA
54535328 GATAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 14 0.56
15 3 0.12
16 8 0.32
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (14 bp):
AAATTCAAAATTAA
Found at i:54535396 original size:31 final size:31
Alignment explanation
Indices: 54535357--54535425 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
54535347 AATTAAAAGG
* * *
54535357 TGAA-AGATCGATTGAATAAACAAATGGATA
1 TGAATAGATCAATCGAATAAACAAATAGATA
54535387 TGAATAGATCAATCGAATAAACAAATAGATA
1 TGAATAGATCAATCGAATAAACAAATAGATA
54535418 TGAATAGA
1 TGAATAGA
54535426 AGATAGTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 4 0.11
31 31 0.89
ACGTcount: A:0.52, C:0.07, G:0.17, T:0.23
Consensus pattern (31 bp):
TGAATAGATCAATCGAATAAACAAATAGATA
Found at i:54539955 original size:18 final size:18
Alignment explanation
Indices: 54539934--54539999 Score: 114
Period size: 18 Copynumber: 3.7 Consensus size: 18
54539924 TCCATCAGTT
54539934 TGAACATCATTTGAAATG
1 TGAACATCATTTGAAATG
54539952 TGAACATCATTTGAAATG
1 TGAACATCATTTGAAATG
*
54539970 TGAACATCATTTAAAATG
1 TGAACATCATTTGAAATG
*
54539988 CGAACATCATTT
1 TGAACATCATTT
54540000 CTCACATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (18 bp):
TGAACATCATTTGAAATG
Found at i:54542462 original size:12 final size:12
Alignment explanation
Indices: 54542445--54542469 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54542435 GAAGATGAGA
54542445 AGAACAAATCAG
1 AGAACAAATCAG
54542457 AGAACAAATCAG
1 AGAACAAATCAG
54542469 A
1 A
54542470 CAAGAAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.16, T:0.08
Consensus pattern (12 bp):
AGAACAAATCAG
Found at i:54546842 original size:20 final size:20
Alignment explanation
Indices: 54546814--54546861 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
54546804 GTCCAATTTT
*
54546814 TTATTTTTAAAAATAATTAA
1 TTATATTTAAAAATAATTAA
* * *
54546834 TTTTATTTAATATTAATTAA
1 TTATATTTAAAAATAATTAA
54546854 TTATATTT
1 TTATATTT
54546862 GACTACAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATATTTAAAAATAATTAA
Found at i:54547026 original size:23 final size:27
Alignment explanation
Indices: 54546977--54547029 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
54546967 TATATGATAT
54546977 AAATAATATAATATATAAACCAAATGAA
1 AAATAATATAATATATAAACC-AATGAA
54547005 AAATAATAT-AT-TATAAA-C-ATGAA
1 AAATAATATAATATATAAACCAATGAA
54547028 AA
1 AA
54547030 CAAGTCAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 7 0.28
25 1 0.04
26 6 0.24
27 2 0.08
28 9 0.36
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (27 bp):
AAATAATATAATATATAAACCAATGAA
Found at i:54549495 original size:20 final size:21
Alignment explanation
Indices: 54549427--54549518 Score: 73
Period size: 20 Copynumber: 4.3 Consensus size: 21
54549417 TTTCTTTAAC
* *
54549427 TTTTTTAAAAATTGTTAT-AA
1 TTTTTTAAAAATTATTTTGAA
*
54549447 TTTTTTTAAAAAATATAACTTTTGGA
1 -TTTTTT-AAAAAT-T-A-TTTTGAA
*
54549473 TTTTTTATAAA-TATTTTGAA
1 TTTTTTAAAAATTATTTTGAA
*
54549493 -TTTTGAAAAATTATTTTGAA
1 TTTTTTAAAAATTATTTTGAA
54549513 TTTTTT
1 TTTTTT
54549519 TTATAATTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
19 8 0.14
20 15 0.27
21 11 0.20
22 7 0.12
23 1 0.02
24 4 0.07
25 9 0.16
26 1 0.02
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTTTTAAAAATTATTTTGAA
Found at i:54550324 original size:27 final size:27
Alignment explanation
Indices: 54550286--54550340 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
54550276 TGACAATTGG
*
54550286 CATTGTCACAACTTAAGCACGATGTAT
1 CATTGTCACAACTCAAGCACGATGTAT
54550313 CATTGTCACAACTCAAGCACGATGTAT
1 CATTGTCACAACTCAAGCACGATGTAT
54550340 C
1 C
54550341 TAGAGTGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (27 bp):
CATTGTCACAACTCAAGCACGATGTAT
Found at i:54554812 original size:48 final size:48
Alignment explanation
Indices: 54554760--54554856 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
54554750 TAAACTGTTA
54554760 GTTCTAGTGCTTATGAAGATTCCGGATTTGTGGAATCACTCATTTTCT
1 GTTCTAGTGCTTATGAAGATTCCGGATTTGTGGAATCACTCATTTTCT
*
54554808 GTTCTAGTGCTTATGACGATTCCGGATTTGTGGAATCACTCATTTTCT
1 GTTCTAGTGCTTATGAAGATTCCGGATTTGTGGAATCACTCATTTTCT
54554856 G
1 G
54554857 CCTCATTCTG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.41
Consensus pattern (48 bp):
GTTCTAGTGCTTATGAAGATTCCGGATTTGTGGAATCACTCATTTTCT
Done.