Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 101 of 186
Found at i:33136374 original size:30 final size:30
Alignment explanation
Indices: 33136339--33136396 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
33136329 TTTGTAAATT
* *
33136339 TCCCTATAATTCATATTTGTCCAATTGTAA
1 TCCCTACAATTCACATTTGTCCAATTGTAA
*
33136369 TCCCTACAATTCACATTTGTTCAATTGT
1 TCCCTACAATTCACATTTGTCCAATTGT
33136397 GGTGAATTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.28, C:0.22, G:0.07, T:0.43
Consensus pattern (30 bp):
TCCCTACAATTCACATTTGTCCAATTGTAA
Found at i:33139303 original size:46 final size:46
Alignment explanation
Indices: 33139245--33139357 Score: 201
Period size: 46 Copynumber: 2.5 Consensus size: 46
33139235 AGTGTGCTCT
33139245 CTGATA-GAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
33139291 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
33139337 CTGATATGAAACGTGTAAGAC
1 CTGATATGAAATGTGTAAGAC
33139358 TTGACATGAA
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
46 64 0.98
47 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:33139378 original size:67 final size:67
Alignment explanation
Indices: 33139296--33139424 Score: 231
Period size: 67 Copynumber: 1.9 Consensus size: 67
33139286 GCAACCTGAT
*
33139296 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAACGTGTAAGACTTG
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAACGTGTAAGACTTG
33139361 AC
66 AC
* *
33139363 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAATGTGTAAGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAACGTGTAAGAC
33139425 CATGGTTGAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (67 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAACGTGTAAGACTTG
AC
Found at i:33139409 original size:46 final size:46
Alignment explanation
Indices: 33139359--33139539 Score: 247
Period size: 46 Copynumber: 3.9 Consensus size: 46
33139349 GTGTAAGACT
*
33139359 TGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACG
*
33139405 TGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACG
* ** * * *
33139451 TAACGGGAAATGAATAAGACCATGGTTGAATGATACCATGGCAACA
1 TGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACG
* * *
33139497 TGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 TGACATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
33139540 TCATGTCGAA
Statistics
Matches: 120, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
45 1 0.01
46 119 0.99
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (46 bp):
TGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACG
Found at i:33139469 original size:113 final size:113
Alignment explanation
Indices: 33139253--33139470 Score: 346
Period size: 113 Copynumber: 1.9 Consensus size: 113
33139243 CTCTGATAGA
*
33139253 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGT
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATGTGTAAGACCATGGT
* * * **
33139318 TGAAAGATACCATGGCAACCTGATATGAAACGTGTAAGACTTGACATG
66 TGAAAGATACCATGGCAACCTAACAGGAAACGAATAAGACTTGACATG
*
33139366 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAATGTGTAAGACCATGGT
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATGTGTAAGACCATGGT
* * *
33139431 TGAAAGATACCATGGCAACGTAACGGGAAATGAATAAGAC
66 TGAAAGATACCATGGCAACCTAACAGGAAACGAATAAGAC
33139471 CATGGTTGAA
Statistics
Matches: 95, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
113 95 1.00
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.22
Consensus pattern (113 bp):
AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATGTGTAAGACCATGGT
TGAAAGATACCATGGCAACCTAACAGGAAACGAATAAGACTTGACATG
Found at i:33141008 original size:3 final size:3
Alignment explanation
Indices: 33141002--33141031 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
33140992 CCTTCTTCTT
*
33141002 CTC CTC CTC CTC CTC CTC CTC CTC CGC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
33141032 TTTCTCTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.67, G:0.03, T:0.30
Consensus pattern (3 bp):
CTC
Found at i:33144382 original size:15 final size:15
Alignment explanation
Indices: 33144362--33144391 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
33144352 TTCACTATCA
*
33144362 TGTCTTTTGTATTTT
1 TGTCTTTTATATTTT
33144377 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
33144392 GCATGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.07, G:0.10, T:0.73
Consensus pattern (15 bp):
TGTCTTTTATATTTT
Found at i:33151115 original size:20 final size:18
Alignment explanation
Indices: 33151091--33151142 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
33151081 AATAGCATTT
33151091 TATTAATTTAATATTAAA
1 TATTAATTTAATATTAAA
33151109 GTGATT-ATCTTAATATTAAA
1 -T-ATTAAT-TTAATATTAAA
33151129 TA-TAATTTAATATT
1 TATTAATTTAATATT
33151143 TATCTACAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 9 0.30
18 3 0.10
19 4 0.13
20 14 0.47
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (18 bp):
TATTAATTTAATATTAAA
Found at i:33161799 original size:24 final size:24
Alignment explanation
Indices: 33161766--33161817 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
33161756 TTTGTAGTTC
**
33161766 AAATAAATTATGTTAATAAATACT
1 AAATAAATTATACTAATAAATACT
*
33161790 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
33161814 AAAT
1 AAAT
33161818 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:33170539 original size:31 final size:31
Alignment explanation
Indices: 33170503--33170570 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
33170493 TAAATTTGGT
* *
33170503 CGTGTGGTCCCACACGA-GTAAACCACATGGG
1 CGTGTGGGCCCACA-GAGGTAAACCACACGGG
*
33170534 CGTGTGGGCCCACATAGGTAAACCACACGGG
1 CGTGTGGGCCCACAGAGGTAAACCACACGGG
33170565 CGTGTG
1 CGTGTG
33170571 AGATTCTAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 1 0.03
31 32 0.97
ACGTcount: A:0.24, C:0.28, G:0.32, T:0.16
Consensus pattern (31 bp):
CGTGTGGGCCCACAGAGGTAAACCACACGGG
Found at i:33170682 original size:18 final size:17
Alignment explanation
Indices: 33170642--33170682 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
33170632 CAATTTGTGC
33170642 CGTGTGGGCCACACGGG
1 CGTGTGGGCCACACGGG
* *
33170659 CCTGTGGGCCTACATGGG
1 CGTGTGGGCC-ACACGGG
33170677 CGTGTG
1 CGTGTG
33170683 CGCCCATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.10, C:0.27, G:0.44, T:0.20
Consensus pattern (17 bp):
CGTGTGGGCCACACGGG
Found at i:33171185 original size:27 final size:28
Alignment explanation
Indices: 33171147--33171201 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
33171137 TATAATTTTG
33171147 AAATTGTATCTGTAA-GGGCTCAGGCCC
1 AAATTGTATCTGTAAGGGGCTCAGGCCC
33171174 AAATTG-ATTCTGTAAGGGGCTCAGGCCC
1 AAATTGTA-TCTGTAAGGGGCTCAGGCCC
33171202 GGACTGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 1 0.04
27 13 0.50
28 12 0.46
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (28 bp):
AAATTGTATCTGTAAGGGGCTCAGGCCC
Found at i:33174889 original size:3 final size:3
Alignment explanation
Indices: 33174871--33174914 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
33174861 TTTACTTTTA
33174871 ATT ATT A-T ATT A-T ATT ATT ATT A-T ATT -TT AGTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
33174913 AT
1 AT
33174915 ATTTTACTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
2 8 0.22
3 25 0.69
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:33174908 original size:20 final size:20
Alignment explanation
Indices: 33174883--33174920 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
33174873 TATTATATTA
33174883 TATTATTATTATATTTTAGT
1 TATTATTATTATATTTTAGT
33174903 TATTATTATTATATTTTA
1 TATTATTATTATATTTTA
33174921 CTTAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (20 bp):
TATTATTATTATATTTTAGT
Found at i:33176935 original size:20 final size:19
Alignment explanation
Indices: 33176912--33176956 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
33176902 ATACCGATAC
*
33176912 AAAAATATCGACACTTTATA
1 AAAAATATCGACAC-TTACA
*
33176932 AAAAGTATCGACACTTACA
1 AAAAATATCGACACTTACA
33176951 AAAAAT
1 AAAAAT
33176957 TATTGATACC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.53, C:0.16, G:0.07, T:0.24
Consensus pattern (19 bp):
AAAAATATCGACACTTACA
Found at i:33176953 original size:19 final size:19
Alignment explanation
Indices: 33176909--33176954 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
33176899 TTGATACCGA
33176909 TACAAAAATATCGACACTT
1 TACAAAAATATCGACACTT
*
33176928 TATAAAAAGTATCGACAC-T
1 TACAAAAA-TATCGACACTT
33176947 TACAAAAA
1 TACAAAAA
33176955 ATTATTGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.52, C:0.17, G:0.07, T:0.24
Consensus pattern (19 bp):
TACAAAAATATCGACACTT
Found at i:33179932 original size:20 final size:21
Alignment explanation
Indices: 33179906--33179994 Score: 103
Period size: 20 Copynumber: 4.4 Consensus size: 21
33179896 TATCGATCCT
33179906 ATATCAATTCTTTTTGTCAAG
1 ATATCAATTCTTTTTGTCAAG
*** *
33179927 -TATCAATAGATTTTGTTAAG
1 ATATCAATTCTTTTTGTCAAG
*
33179947 ATATCAATTCTTTTTTTC-AG
1 ATATCAATTCTTTTTGTCAAG
*
33179967 ATATCAATTCTTTTTTTCAAG
1 ATATCAATTCTTTTTGTCAAG
33179988 -TATCAAT
1 ATATCAAT
33179995 AGATTTTGTT
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
20 43 0.75
21 14 0.25
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.49
Consensus pattern (21 bp):
ATATCAATTCTTTTTGTCAAG
Found at i:33180001 original size:20 final size:20
Alignment explanation
Indices: 33179916--33180019 Score: 79
Period size: 20 Copynumber: 5.1 Consensus size: 20
33179906 ATATCAATTC
33179916 TTTTTGTCAAGTATCAATAGA
1 TTTTT-TCAAGTATCAATAGA
***
33179937 TTTTGTT-AAGATATCAATTCT
1 TTTT-TTCAAG-TATCAATAGA
***
33179958 TTTTTTC-AGATATCAATTCT
1 TTTTTTCAAG-TATCAATAGA
33179978 TTTTTTCAAGTATCAATAGA
1 TTTTTTCAAGTATCAATAGA
*
33179998 TTTTGTT-AAGTATCGATAGA
1 TTTT-TTCAAGTATCAATAGA
33180018 TT
1 TT
33180020 CAAATTTATC
Statistics
Matches: 71, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
20 50 0.70
21 20 0.28
22 1 0.01
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.49
Consensus pattern (20 bp):
TTTTTTCAAGTATCAATAGA
Found at i:33182153 original size:14 final size:14
Alignment explanation
Indices: 33182134--33182172 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
33182124 TTGTTTCACT
33182134 GAAAATGACTTCTA
1 GAAAATGACTTCTA
*
33182148 GAAAATGA-TATCTG
1 GAAAATGACT-TCTA
33182162 GAAAATGACTT
1 GAAAATGACTT
33182173 ACTTTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.28
Consensus pattern (14 bp):
GAAAATGACTTCTA
Found at i:33182689 original size:16 final size:16
Alignment explanation
Indices: 33182670--33182700 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33182660 AATTTATTAA
33182670 AATAATTAATTATATT
1 AATAATTAATTATATT
*
33182686 AATAATTTATTATAT
1 AATAATTAATTATAT
33182701 GACTAGATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATAATTAATTATATT
Found at i:33182689 original size:29 final size:30
Alignment explanation
Indices: 33182632--33182697 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 30
33182622 AAAACATTTC
33182632 TTATTAAAATAAAATTAAAATATTAAATAAT
1 TTATTAAAAT-AAATTAAAATATTAAATAAT
*
33182663 TTATTAAAAT-AATTAATTATATT-AATAAT
1 TTATTAAAATAAATTAA-AATATTAAATAAT
33182692 TTATTA
1 TTATTA
33182698 TATGACTAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 18 0.55
30 5 0.15
31 10 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
TTATTAAAATAAATTAAAATATTAAATAAT
Found at i:33184086 original size:37 final size:40
Alignment explanation
Indices: 33184026--33184103 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 40
33184016 TGCCAATAAA
33184026 TAAATAAATATATTTTTTCAAAATTATT-TTATAATT-AAATT
1 TAAATAAATATA-TTTTTCAAAA-TATTATT-TAATTGAAATT
33184067 TAAATAAA-ATA-TTTT-AAAATATTATTTAATTGAAATT
1 TAAATAAATATATTTTTCAAAATATTATTTAATTGAAATT
33184104 AGAATTGAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
36 9 0.26
37 11 0.31
38 4 0.11
40 3 0.09
41 8 0.23
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (40 bp):
TAAATAAATATATTTTTCAAAATATTATTTAATTGAAATT
Found at i:33192413 original size:43 final size:42
Alignment explanation
Indices: 33192330--33192443 Score: 133
Period size: 43 Copynumber: 2.7 Consensus size: 42
33192320 TGTGATTACA
33192330 TGTAAGACCATGTCTGGGACATTGGCATTATATTAAGATTTCG
1 TGTAAGACCATGTCTGGGACATTGGCA-TATATTAAGATTTCG
* * *
33192373 TGTAAAACCATGTCTGGGACATTGGCAT-TGTTAATCGATTTTG
1 TGTAAGACCATGTCTGGGACATTGGCATATATTAA--GATTTCG
* *
33192416 TGTAAGACCCTGT-TGGGGACAGTGGCAT
1 TGTAAGACCATGTCT-GGGACATTGGCAT
33192444 CAATTTATGA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
41 5 0.08
42 2 0.03
43 55 0.89
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.33
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACATTGGCATATATTAAGATTTCG
Found at i:33196934 original size:20 final size:20
Alignment explanation
Indices: 33196911--33196948 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
33196901 TTACCAACCT
*
33196911 TTTTTATTTTTTAATTTTGA
1 TTTTGATTTTTTAATTTTGA
33196931 TTTTGATTTTTTAATTTT
1 TTTTGATTTTTTAATTTT
33196949 TATAACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.76
Consensus pattern (20 bp):
TTTTGATTTTTTAATTTTGA
Found at i:33197846 original size:32 final size:32
Alignment explanation
Indices: 33197803--33197879 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
33197793 CAAAATAAAT
** *
33197803 TATGAAAAGTTACGAATGTGAAGAGGCTTGAA
1 TATGAAAAGTTACGAATGCAAAGAGACTTGAA
* **
33197835 TATGAAGAGTTAATAATGCAAAGAGACTTGAA
1 TATGAAAAGTTACGAATGCAAAGAGACTTGAA
*
33197867 GATGAAAAGTTAC
1 TATGAAAAGTTAC
33197880 ACACATGCAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.44, C:0.06, G:0.25, T:0.25
Consensus pattern (32 bp):
TATGAAAAGTTACGAATGCAAAGAGACTTGAA
Found at i:33199788 original size:13 final size:13
Alignment explanation
Indices: 33199770--33199794 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33199760 AGGCCGTGTG
33199770 AAGGACACGGGCC
1 AAGGACACGGGCC
33199783 AAGGACACGGGC
1 AAGGACACGGGC
33199795 GTGTGCTTGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.28, G:0.40, T:0.00
Consensus pattern (13 bp):
AAGGACACGGGCC
Found at i:33208144 original size:30 final size:30
Alignment explanation
Indices: 33208014--33208156 Score: 101
Period size: 30 Copynumber: 4.8 Consensus size: 30
33208004 TCCTATAGGG
* * * *
33208014 AACTCTCCCATGGTGATCTCAGTTATGTCA
1 AACTCCCCCATGGCGAACTCACTTATGTCA
* * * *
33208044 AACTCCACTATGGCGAACTCACTTTTGGCA
1 AACTCCCCCATGGCGAACTCACTTATGTCA
* * * * * * *
33208074 AA-TGCACCTACGGCAAACTCTCCTATAG-CG
1 AACT-CCCCCATGGCGAACTCACTTAT-GTCA
* *
33208104 AGCTCTCCCATGGCGAACTCACTTATGTCA
1 AACTCCCCCATGGCGAACTCACTTATGTCA
33208134 AACTCCCCCATGGCGAACTCACT
1 AACTCCCCCATGGCGAACTCACT
33208157 ATTGGCGAAT
Statistics
Matches: 83, Mismatches: 26, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
29 2 0.02
30 79 0.95
31 2 0.02
ACGTcount: A:0.26, C:0.33, G:0.16, T:0.25
Consensus pattern (30 bp):
AACTCCCCCATGGCGAACTCACTTATGTCA
Found at i:33208181 original size:45 final size:45
Alignment explanation
Indices: 33208037--33208181 Score: 141
Period size: 45 Copynumber: 3.2 Consensus size: 45
33208027 TGATCTCAGT
* * *
33208037 TATGTCAAACTCCACTATGGCGAACTCACTTTTGGCAAATGCACC
1 TATGTCAAACTCCCCTATGGCGAACTCACTATTGGCGAATGCACC
* * * * * * * *
33208082 TACGGCAAACTCTCCTATAGCGAGCTCTCCCA-TGGCGAACT-CACT
1 TATGTCAAACTCCCCTATGGCGAACTC-ACTATTGGCGAA-TGCACC
*
33208127 TATGTCAAACTCCCCCATGGCGAACTCACTATTGGCGAATGCACC
1 TATGTCAAACTCCCCTATGGCGAACTCACTATTGGCGAATGCACC
*
33208172 TATGACAAAC
1 TATGTCAAAC
33208182 AAACATAATA
Statistics
Matches: 75, Mismatches: 21, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
44 3 0.04
45 70 0.93
46 2 0.03
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (45 bp):
TATGTCAAACTCCCCTATGGCGAACTCACTATTGGCGAATGCACC
Found at i:33208181 original size:90 final size:90
Alignment explanation
Indices: 33207990--33208181 Score: 285
Period size: 90 Copynumber: 2.1 Consensus size: 90
33207980 TAGGCATAGC
* * * * *
33207990 CCTATGGCAAACTCTCCTATAGGGAACTCTCCCATGGTGATCTCAGTTATGTCAAACTCCACTAT
1 CCTATGGCAAACTCTCCTATAGCGAACTCTCCCATGGCGAACTCACTTATGTCAAACTCCACCAT
*
33208055 GGCGAACTCACTTTTGGCAAATGCA
66 GGCGAACTCACTATTGGCAAATGCA
* * *
33208080 CCTACGGCAAACTCTCCTATAGCGAGCTCTCCCATGGCGAACTCACTTATGTCAAACTCCCCCAT
1 CCTATGGCAAACTCTCCTATAGCGAACTCTCCCATGGCGAACTCACTTATGTCAAACTCCACCAT
*
33208145 GGCGAACTCACTATTGGCGAATGCA
66 GGCGAACTCACTATTGGCAAATGCA
*
33208170 CCTATGACAAAC
1 CCTATGGCAAAC
33208182 AAACATAATA
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
90 90 1.00
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.24
Consensus pattern (90 bp):
CCTATGGCAAACTCTCCTATAGCGAACTCTCCCATGGCGAACTCACTTATGTCAAACTCCACCAT
GGCGAACTCACTATTGGCAAATGCA
Found at i:33209981 original size:41 final size:44
Alignment explanation
Indices: 33209942--33210027 Score: 104
Period size: 47 Copynumber: 1.9 Consensus size: 44
33209932 CTTCAGGTGC
33209942 GAATAA-TACCTTGATTTGGCTAC-GAGCCATGGTATAGGTGCTCCG
1 GAATAAGTACCTTGATTTGGCTACAG-GCCATGGTATAGGTG--CCG
* *
33209987 GGATAAGTTACCTTGATTTGGCTACAGGCCGTGGTATAGGT
1 GAATAAG-TACCTTGATTTGGCTACAGGCCATGGTATAGGT
33210028 ATGTAACGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
45 5 0.14
47 30 0.83
48 1 0.03
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.30
Consensus pattern (44 bp):
GAATAAGTACCTTGATTTGGCTACAGGCCATGGTATAGGTGCCG
Found at i:33210976 original size:30 final size:30
Alignment explanation
Indices: 33210936--33211003 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
33210926 TGTGGCTTGA
* *
33210936 CCGTATGTGACACATGGCTTTGGTATACAG
1 CCGTGTGTGACACATGGCCTTGGTATACAG
*
33210966 CCGTGTGTGACACATGGCCTTGGTATACGG
1 CCGTGTGTGACACATGGCCTTGGTATACAG
33210996 CCGTGTGT
1 CCGTGTGT
33211004 CCTGTAAGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.18, C:0.22, G:0.31, T:0.29
Consensus pattern (30 bp):
CCGTGTGTGACACATGGCCTTGGTATACAG
Found at i:33213040 original size:46 final size:45
Alignment explanation
Indices: 33212972--33213138 Score: 144
Period size: 46 Copynumber: 3.6 Consensus size: 45
33212962 TGTAACCCGC
* *
33212972 CCATAAGCGAACTCAGAATCAACTCAACGAGCTCAGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAG-TCAGGCGTTCGCAT
* * *
33213018 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAG-TC--A-GGC--GTTCGCAT
* * **
33213068 --TTCA-CGAACTCGGACTCAACTCAACGAGTTTGGACGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTCAGG-CGTTCGCAT
*
33213111 CCATAAGTGAACTCGGACTCAACTCAAC
1 CCATAAGCGAACTCGGACTCAACTCAAC
33213139 AAGTTCGGAT
Statistics
Matches: 95, Mismatches: 16, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
44 1 0.01
45 2 0.02
46 51 0.54
47 23 0.24
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.22
Consensus pattern (45 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTCAGGCGTTCGCAT
Found at i:33213095 original size:93 final size:93
Alignment explanation
Indices: 33212979--33213149 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
33212969 CGCCCATAAG
33212979 CGAACTCAGAATCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCAGAATCAACTCAACGAG-TCAGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTC
*
33213043 AACGAGTTCGGATGCCTAGTTACATTTCA
65 AACAAGTTCGGATGCCTAGTTACATTTCA
* * **
33213072 CGAACTCGGACTCAACTCAACGAGTTTGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGAATCAACTCAACGAGTCAGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
33213137 ACAAGTTCGGATG
66 ACAAGTTCGGATG
33213150 ACCAAATATC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 3 0.04
93 69 0.96
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.22
Consensus pattern (93 bp):
CGAACTCAGAATCAACTCAACGAGTCAGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACAAGTTCGGATGCCTAGTTACATTTCA
Found at i:33215927 original size:15 final size:15
Alignment explanation
Indices: 33215909--33215947 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
33215899 TCCAAGATTG
33215909 AGAAACCCAGAATAA
1 AGAAACCCAGAATAA
* *
33215924 AGAAATCTAGAATAA
1 AGAAACCCAGAATAA
33215939 AGAAACCCA
1 AGAAACCCA
33215948 AGATACGATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.59, C:0.18, G:0.13, T:0.10
Consensus pattern (15 bp):
AGAAACCCAGAATAA
Found at i:33219024 original size:93 final size:93
Alignment explanation
Indices: 33218896--33219068 Score: 249
Period size: 93 Copynumber: 1.9 Consensus size: 93
33218886 CGCCCATAAG
** * *
33218896 CGAACTCGGACTCAACTCAATGAGCTCAGGCGTTCGCATCCATAAGTGAACTCGGATTCAACTCA
1 CGAACTCGGACTCAACTCAACAAGCTCAGGCGTTCGCATCCATAAGTGAACTCGGACTCAAATCA
*
33218961 ACGAGTTCGGATGCCTAATTACATTTCA
66 ACAAGTTCGGATGCCTAATTACATTTCA
** *
33218989 CGAACTCGGACTCAACTCAACAAG-TTTGGATGTTCGCATCCATAAGTGAACTCGGACTCAAATC
1 CGAACTCGGACTCAACTCAACAAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAAATC
*
33219053 AACAAGTTTGGATGCC
65 AACAAGTTCGGATGCC
33219069 CAAATATCTG
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
92 3 0.04
93 67 0.96
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACAAGCTCAGGCGTTCGCATCCATAAGTGAACTCGGACTCAAATCA
ACAAGTTCGGATGCCTAATTACATTTCA
Found at i:33224632 original size:40 final size:40
Alignment explanation
Indices: 33224577--33224704 Score: 197
Period size: 40 Copynumber: 3.2 Consensus size: 40
33224567 ATATATTATA
* *
33224577 TATATCCAGGTCAAATCCCACAGGCTTCGTGCTGGTAATG
1 TATATCCGGGTCAAATCCCGCAGGCTTCGTGCTGGTAATG
33224617 TATATCCGGGTCAAATCCCGCAGGCTTCGTGCTGGTAATG
1 TATATCCGGGTCAAATCCCGCAGGCTTCGTGCTGGTAATG
* * *
33224657 TATATCCGGGTTAAATCTCGCAGGCTTAGTGCTGGT-AT-
1 TATATCCGGGTCAAATCCCGCAGGCTTCGTGCTGGTAATG
33224695 TATATCCGGG
1 TATATCCGGG
33224705 CTTAAAGTTT
Statistics
Matches: 83, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
38 10 0.12
39 2 0.02
40 71 0.86
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.30
Consensus pattern (40 bp):
TATATCCGGGTCAAATCCCGCAGGCTTCGTGCTGGTAATG
Found at i:33224718 original size:40 final size:40
Alignment explanation
Indices: 33224577--33224719 Score: 182
Period size: 40 Copynumber: 3.6 Consensus size: 40
33224567 ATATATTATA
* * * *
33224577 TATATCCAGGTCAAATCCCACAGGCTTCGTGCTGGTAATG
1 TATATCCGGGTTAAATCTCGCAGGCTTCGTGCTGGTAATG
* *
33224617 TATATCCGGGTCAAATCCCGCAGGCTTCGTGCTGGTAATG
1 TATATCCGGGTTAAATCTCGCAGGCTTCGTGCTGGTAATG
*
33224657 TATATCCGGGTTAAATCTCGCAGGCTTAGTGCTGGT-AT-
1 TATATCCGGGTTAAATCTCGCAGGCTTCGTGCTGGTAATG
*
33224695 TATATCCGGGCTTAAAGTTTCGCAG
1 TATATCCGGG-TTAAA-TCTCGCAG
33224720 ACTTTGAGCT
Statistics
Matches: 95, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
38 10 0.11
39 7 0.07
40 78 0.82
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.30
Consensus pattern (40 bp):
TATATCCGGGTTAAATCTCGCAGGCTTCGTGCTGGTAATG
Found at i:33229103 original size:47 final size:47
Alignment explanation
Indices: 33229006--33229130 Score: 153
Period size: 47 Copynumber: 2.7 Consensus size: 47
33228996 GAATAATACC
* * * * * * *
33229006 TTGATTTGGCTAC-AGCCATGGTATATGTATTCTGAGAGGAGTTGCC
1 TTGATTTGGCTACGGGCAATGGTATAGGTACTCTGAGAGAAGTTACA
* *
33229052 TTGATTTGGCTACGGGCAATGGTATAGGTACTCTGGGATAAGTTACA
1 TTGATTTGGCTACGGGCAATGGTATAGGTACTCTGAGAGAAGTTACA
*
33229099 TTGATTTGGCTACGGGCTATGGTATAGGTACT
1 TTGATTTGGCTACGGGCAATGGTATAGGTACT
33229131 TATCGATTGT
Statistics
Matches: 68, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
46 13 0.19
47 55 0.81
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.34
Consensus pattern (47 bp):
TTGATTTGGCTACGGGCAATGGTATAGGTACTCTGAGAGAAGTTACA
Found at i:33230276 original size:66 final size:66
Alignment explanation
Indices: 33230188--33230318 Score: 185
Period size: 66 Copynumber: 2.0 Consensus size: 66
33230178 GTAGCTGGCC
* **
33230188 GTGTGACCCAAGTTAGTAACCCCTCCAGTTTTCTCGCA-G-CCATGGTATACGGGCGTGTTCTCG
1 GTGTGACCCAAGTCAGTAACCCCTCCAGTTTTC-C-CACGACCATGACATACGGGCGTGTTCTCG
33230251 GCG
64 GCG
* *
33230254 GTGTGACCTAAGTCAGTAACCCCTCTAGTTTTCCCACGACCATGACATACGGGCGTGTTCTCGGC
1 GTGTGACCCAAGTCAGTAACCCCTCCAGTTTTCCCACGACCATGACATACGGGCGTGTTCTCGGC
33230319 CCTGTTTTCA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
64 2 0.03
65 2 0.03
66 54 0.93
ACGTcount: A:0.18, C:0.30, G:0.25, T:0.27
Consensus pattern (66 bp):
GTGTGACCCAAGTCAGTAACCCCTCCAGTTTTCCCACGACCATGACATACGGGCGTGTTCTCGGC
G
Found at i:33234390 original size:42 final size:41
Alignment explanation
Indices: 33234331--33234499 Score: 198
Period size: 42 Copynumber: 4.0 Consensus size: 41
33234321 GACATTAGGG
*
33234331 TTAT-TGAGATTAT-GTGTAAGACCACATCTGGGATATGGCA
1 TTATATGAGATT-TCGTGTAAGACCATATCTGGGATATGGCA
*
33234371 TTATTATGAGATTTCGTGTAAGACCATATCTGGGGTATGGCA
1 TTA-TATGAGATTTCGTGTAAGACCATATCTGGGATATGGCA
* * *
33234413 TTGATATGAGATTTCGTGTAAGTCCATAGCTGGGCTATTGGCA
1 TT-ATATGAGATTTCGTGTAAGACCATATCTGGGATA-TGGCA
* ** *
33234456 TCGATATGAGATCCCATGTAAGACCATATCTGGGATATGGCA
1 T-TATATGAGATTTCGTGTAAGACCATATCTGGGATATGGCA
33234498 TT
1 TT
33234500 GGAGTGGTAC
Statistics
Matches: 110, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
40 3 0.03
41 2 0.02
42 70 0.64
43 35 0.32
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.33
Consensus pattern (41 bp):
TTATATGAGATTTCGTGTAAGACCATATCTGGGATATGGCA
Found at i:33238369 original size:106 final size:106
Alignment explanation
Indices: 33238184--33238395 Score: 406
Period size: 106 Copynumber: 2.0 Consensus size: 106
33238174 TATCAACTGA
*
33238184 GCGAATACTTATTTGTAAGGCCTCAACTAAATTCAAGCACATACGAAACATACCTCAATGTTGGG
1 GCGAATACTTATTTGTAAGGCCTCAACTAAATTCAAGCACATACGAAACATAACTCAATGTTGGG
33238249 ATGTTTCGAGAGTATTAACTGGAATTTTACAGCAAGTTCAT
66 ATGTTTCGAGAGTATTAACTGGAATTTTACAGCAAGTTCAT
33238290 GCGAATACTTATTTGTAAGGCCTCAACTAAATTCAAGCACATACGAAACATAACTCAATGTTGGG
1 GCGAATACTTATTTGTAAGGCCTCAACTAAATTCAAGCACATACGAAACATAACTCAATGTTGGG
*
33238355 ATGTTTTGAGAGTATTAACTGGAATTTTACAGCAAGTTCAT
66 ATGTTTCGAGAGTATTAACTGGAATTTTACAGCAAGTTCAT
33238396 TCATTCCCAA
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 104 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (106 bp):
GCGAATACTTATTTGTAAGGCCTCAACTAAATTCAAGCACATACGAAACATAACTCAATGTTGGG
ATGTTTCGAGAGTATTAACTGGAATTTTACAGCAAGTTCAT
Found at i:33238491 original size:40 final size:40
Alignment explanation
Indices: 33238447--33238539 Score: 134
Period size: 40 Copynumber: 2.3 Consensus size: 40
33238437 GCTCCTCGTT
* * *
33238447 CAAATGCCTTCGGGACATAGCCTGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATT-TAGTAACTCGCA
*
33238487 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
33238527 CAAATGCCTTCGG
1 CAAATGCCTTCGG
33238540 ATCTTAGTCT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 46 0.96
41 2 0.04
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:33246400 original size:40 final size:40
Alignment explanation
Indices: 33246356--33246619 Score: 360
Period size: 40 Copynumber: 6.7 Consensus size: 40
33246346 GCTCCTCGTT
* *
33246356 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
33246396 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
33246436 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
33246476 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
33246516 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
33246555 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGTAAC-TCGCA
33246596 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
33246620 CATCATTCAA
Statistics
Matches: 206, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
38 2 0.01
39 49 0.24
40 146 0.71
41 9 0.04
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:33253614 original size:42 final size:42
Alignment explanation
Indices: 33253487--33253595 Score: 191
Period size: 42 Copynumber: 2.6 Consensus size: 42
33253477 AGACCATGCA
* *
33253487 TAAGACCATATCTGGGATATGACATCAATATGAGACTTCGTG
1 TAAGACCATATCTGGGATATGGCATCGATATGAGACTTCGTG
*
33253529 TAAGACCATATCTGGGATATGGCATCGATATGAGATTTCGTG
1 TAAGACCATATCTGGGATATGGCATCGATATGAGACTTCGTG
33253571 TAAGACCATATCTGGGATATGGCAT
1 TAAGACCATATCTGGGATATGGCAT
33253596 TGGTATGATA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (42 bp):
TAAGACCATATCTGGGATATGGCATCGATATGAGACTTCGTG
Found at i:33253756 original size:16 final size:15
Alignment explanation
Indices: 33253731--33253760 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
33253721 GCACGAAAAA
33253731 CTCATATGTGATGAG
1 CTCATATGTGATGAG
33253746 CTCATTATGTGATGA
1 CTCA-TATGTGATGA
33253761 ACCCTCGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (15 bp):
CTCATATGTGATGAG
Found at i:33262150 original size:7 final size:7
Alignment explanation
Indices: 33262138--33262170 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
33262128 AAATCAAATG
33262138 AGAAAAA
1 AGAAAAA
33262145 AGAAAAA
1 AGAAAAA
33262152 AGAAAAA
1 AGAAAAA
33262159 A-ATAAAA
1 AGA-AAAA
33262166 AGAAA
1 AGAAA
33262171 GAAAAGGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 1 0.04
7 22 0.92
8 1 0.04
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (7 bp):
AGAAAAA
Found at i:33262157 original size:14 final size:14
Alignment explanation
Indices: 33262138--33262175 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
33262128 AAATCAAATG
33262138 AGAAAAAAGA-AAAA
1 AGAAAAAA-ATAAAA
33262152 AGAAAAAAATAAAA
1 AGAAAAAAATAAAA
33262166 AGAAAGAAAA
1 AGAAA-AAAA
33262176 GGGAAGTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 17 0.77
15 4 0.18
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (14 bp):
AGAAAAAAATAAAA
Found at i:33264717 original size:25 final size:24
Alignment explanation
Indices: 33264689--33264736 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
33264679 GCAAGGGAAT
33264689 AAGGGAAGGAA-ATGAAGAAAAATGG
1 AAGGGAAGGAAGA--AAGAAAAATGG
*
33264714 AAGGGAATGAAGAAAGAAAAATG
1 AAGGGAAGGAAGAAAGAAAAATG
33264737 AGAGAAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 10 0.48
25 10 0.48
26 1 0.05
ACGTcount: A:0.58, C:0.00, G:0.33, T:0.08
Consensus pattern (24 bp):
AAGGGAAGGAAGAAAGAAAAATGG
Found at i:33269133 original size:48 final size:47
Alignment explanation
Indices: 33269098--33269384 Score: 238
Period size: 48 Copynumber: 6.0 Consensus size: 47
33269088 GTCAACCACA
33269098 TTATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCAATG
1 TTATGAGAGCCAGTGTAAGACCATGTTTGGAACATGG-ATCGGCAATG
*
33269146 TTATGAGAGCCAGTGTAAGACCATGTTTGGAACATAGCATCGGCAATG
1 TTATGAGAGCCAGTGTAAGACCATGTTTGGAACAT-GGATCGGCAATG
* * * *
33269194 TTGTGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTG
1 TTATGAGAGCCAGTGTAAGACCATGTTTGGAACATGG-ATCGGCAATG
* * * * * * *
33269242 ATT-TGTGTGCTAGTGTAAGACCATGTCTAGG-ACATGGCATCGACATTA
1 -TTATGAGAGCCAGTGTAAGACCATGT-TTGGAACATGG-ATCGGCAATG
** * * * * * * *
33269290 AGACGAGAGCTAGTGTCAGACCATGTCTGGGACATGGCATCGGC-CTCA
1 TTATGAGAGCCAGTGTAAGACCATGTTTGGAACATGG-ATCGGCAAT-G
** * * *
33269338 ACATGTGAGCCAGTGTAAGACCATATTTGGAACATGGCATCGACAAT
1 TTATGAGAGCCAGTGTAAGACCATGTTTGGAACATGG-ATCGGCAAT
33269385 TCACCCTCTT
Statistics
Matches: 198, Mismatches: 33, Indels: 15
0.80 0.13 0.06
Matches are distributed among these distances:
47 4 0.02
48 188 0.95
49 6 0.03
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (47 bp):
TTATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGATCGGCAATG
Found at i:33269229 original size:96 final size:97
Alignment explanation
Indices: 33269100--33269385 Score: 332
Period size: 96 Copynumber: 3.0 Consensus size: 97
33269090 CAACCACATT
* * *
33269100 ATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCAATGTTATGAGAGCCAGTGTAAG
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAATGTTATGTGAGCCAGTGTAAG
* * *
33269165 ACCATGTTTGGAACATAGCATCGGCAATGT-TG
66 ACCATGTTTGGAACATGGCATCGACAAT-TAAG
* * *
33269197 -TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATT-TGTGTGCTAGTGTAA
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAATG-TTATGTGAGCCAGTGTAA
*
33269260 GACCATGTCTAGG-ACATGGCATCGAC-ATTAAG
65 GACCATGT-TTGGAACATGGCATCGACAATTAAG
* * * * ***
33269292 ACGAGAGCTAGTGTCAGACCATGTCTGGGACATGGCATCGGC-CTCAACATGTGAGCCAGTGTAA
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAAT-GTTATGTGAGCCAGTGTAA
*
33269356 GACCATATTTGGAACATGGCATCGACAATT
65 GACCATGTTTGGAACATGGCATCGACAATT
33269386 CACCCTCTTG
Statistics
Matches: 160, Mismatches: 21, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
94 1 0.01
95 7 0.04
96 144 0.90
97 8 0.05
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (97 bp):
ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAATGTTATGTGAGCCAGTGTAAG
ACCATGTTTGGAACATGGCATCGACAATTAAG
Found at i:33271805 original size:35 final size:35
Alignment explanation
Indices: 33271761--33271855 Score: 104
Period size: 35 Copynumber: 2.7 Consensus size: 35
33271751 TCCTCATTGA
33271761 AATACCATACCTACATTTTACAACTCAGTATGGGA-
1 AATACCATACCTACATTTTACAACTCAGTAT-GGAT
** * * *
33271796 AATGTCATACCTACGTTTCT-TAGCTCAGTATGGAT
1 AATACCATACCTACATTT-TACAACTCAGTATGGAT
*
33271831 AATACCATACCTACATTTCACAACT
1 AATACCATACCTACATTTTACAACT
33271856 TTGCCATGAA
Statistics
Matches: 46, Mismatches: 11, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
34 3 0.07
35 42 0.91
36 1 0.02
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32
Consensus pattern (35 bp):
AATACCATACCTACATTTTACAACTCAGTATGGAT
Found at i:33275694 original size:92 final size:92
Alignment explanation
Indices: 33275537--33275720 Score: 332
Period size: 92 Copynumber: 2.0 Consensus size: 92
33275527 TCTTTGAATA
*
33275537 GACCAATATGTCATCAATAAATACCACCACAAATCTATCCAAATAAGGCTGAAAAATCCAATTCA
1 GACCAATATGTCATCAATAAATACCACCACAAATCTATCCAAATAAGGATGAAAAATCCAATTCA
33275602 TTAAATCCATAAATACAGCAGGGGCAT
66 TTAAATCCATAAATACAGCAGGGGCAT
*
33275629 GACCAATATGTCATTAATAAATACCACCACAAATCTATCCAAATAAGGATGAAAAATCCAATTCA
1 GACCAATATGTCATCAATAAATACCACCACAAATCTATCCAAATAAGGATGAAAAATCCAATTCA
* *
33275694 TTAAATCCATAAATGCCGCAGGGGCAT
66 TTAAATCCATAAATACAGCAGGGGCAT
33275721 TTGTTAAACC
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 88 1.00
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.22
Consensus pattern (92 bp):
GACCAATATGTCATCAATAAATACCACCACAAATCTATCCAAATAAGGATGAAAAATCCAATTCA
TTAAATCCATAAATACAGCAGGGGCAT
Found at i:33277138 original size:13 final size:13
Alignment explanation
Indices: 33277120--33277150 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
33277110 ACTAGAATCA
33277120 TCTTTTGTATACC
1 TCTTTTGTATACC
33277133 TCTTTTGTATACC
1 TCTTTTGTATACC
33277146 TCTTT
1 TCTTT
33277151 ACCTCTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.06, T:0.58
Consensus pattern (13 bp):
TCTTTTGTATACC
Found at i:33279321 original size:35 final size:34
Alignment explanation
Indices: 33279241--33279405 Score: 152
Period size: 35 Copynumber: 4.7 Consensus size: 34
33279231 TTCTCATTGA
**
33279241 AATACCATACCTATATTTTACAACTCAATATGGGA-
1 AATACCATACCTA-CGTTTACAACTCAATAT-GGAT
*** *
33279276 AATGTTATACCTACGTTTATTAACTCAATATGGAT
1 AATACCATACCTACGTTTA-CAACTCAATATGGAT
* * *
33279311 AATACCATACCTACGTTGCACAACTCAGTATGGTT
1 AATACCATACCTACGTT-TACAACTCAATATGGAT
* *
33279346 AATAGCATACCTATGTTTCACAACTCAATATGGAT
1 AATACCATACCTACGTTT-ACAACTCAATATGGAT
* *
33279381 GATACCATACCTATGTTTCACAACT
1 AATACCATACCTACGTTT-ACAACT
33279406 TTACCATGGA
Statistics
Matches: 106, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
34 7 0.07
35 98 0.92
36 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (34 bp):
AATACCATACCTACGTTTACAACTCAATATGGAT
Found at i:33279423 original size:35 final size:35
Alignment explanation
Indices: 33279297--33279423 Score: 121
Period size: 35 Copynumber: 3.6 Consensus size: 35
33279287 TACGTTTATT
* * * *
33279297 AACTCAATATGGATAATACCATACCTACGTTGCAC
1 AACTCAACATGGATCATACCATACCTATGTTTCAC
** * * *
33279332 AACTCAGTATGGTTAATAGCATACCTATGTTTCAC
1 AACTCAACATGGATCATACCATACCTATGTTTCAC
* *
33279367 AACTCAATATGGATGATACCATACCTATGTTTCAC
1 AACTCAACATGGATCATACCATACCTATGTTTCAC
* *
33279402 AACTTTACCATGGATCA-ACCAT
1 AAC-TCAACATGGATCATACCAT
33279424 GGTCTTATCC
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
35 69 0.88
36 9 0.12
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.30
Consensus pattern (35 bp):
AACTCAACATGGATCATACCATACCTATGTTTCAC
Found at i:33284197 original size:30 final size:30
Alignment explanation
Indices: 33284141--33284199 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
33284131 GCCTTTTAAA
* *
33284141 AATATTTATAAAAAGAGGCATCTAATTTTT
1 AATATTTACAAAAAGAGGCAACTAATTTTT
33284171 AATATTTACAAAAAGA-GCAACATAATTTT
1 AATATTTACAAAAAGAGGCAAC-TAATTTT
33284200 GGAAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.36
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGCAACTAATTTTT
Found at i:33284786 original size:19 final size:18
Alignment explanation
Indices: 33284762--33284798 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
33284752 TGGACACAGG
33284762 GACACGCCCGTGTGCTCCA
1 GACACGCCCGTGT-CTCCA
*
33284781 GACACGCCTGTGTCTCCA
1 GACACGCCCGTGTCTCCA
33284799 AGCCGTGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.16, C:0.41, G:0.24, T:0.19
Consensus pattern (18 bp):
GACACGCCCGTGTCTCCA
Found at i:33287864 original size:31 final size:31
Alignment explanation
Indices: 33287826--33287896 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
33287816 TTACTCGGCT
*
33287826 GAAGCCTTTTCATAAATCATATCACTGGGCC
1 GAAGCCTTTTAATAAATCATATCACTGGGCC
* *
33287857 GCAGCCTTTTAATAAATCATATCATTGGGCC
1 GAAGCCTTTTAATAAATCATATCACTGGGCC
33287888 GAAGCCTTT
1 GAAGCCTTT
33287897 ACTGTAAACG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (31 bp):
GAAGCCTTTTAATAAATCATATCACTGGGCC
Found at i:33288143 original size:25 final size:26
Alignment explanation
Indices: 33288102--33288211 Score: 129
Period size: 25 Copynumber: 4.3 Consensus size: 26
33288092 CTGGAGGCCT
33288102 AGCCTCTTTT-AAT-AACTGGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATA
**
33288126 AGCCCTTTTCGGTAAACTGGGGCA-A
1 AGCCCTTTTCAATAAACTGGGGCATA
* *
33288151 AACCCTTTTCAATAAACTTGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
**
33288177 AGCTATTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
33288203 AGCCCTTTT
1 AGCCCTTTT
33288212 GCACTTCCTC
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.07
24 5 0.07
25 31 0.44
26 30 0.42
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:33288186 original size:51 final size:49
Alignment explanation
Indices: 33288107--33288211 Score: 122
Period size: 51 Copynumber: 2.1 Consensus size: 49
33288097 GGCCTAGCCT
* **
33288107 CTTTTAATAACTGGGGCAAAGCCCTTTTCGGTAAACTGGGGCA-AAACC
1 CTTTTAATAACTGGGGCAAAGCCATTTTCAATAAACTGGGGCATAAACC
* * *
33288155 CTTTTCAATAAACTTGGGCATAAGCTATTTTCAATAAACTGGGGCATAAGCC
1 CTTTT-AAT-AACTGGGGCA-AAGCCATTTTCAATAAACTGGGGCATAAACC
33288207 CTTTT
1 CTTTT
33288212 GCACTTCCTC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
48 5 0.11
49 3 0.06
50 9 0.19
51 21 0.45
52 9 0.19
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (49 bp):
CTTTTAATAACTGGGGCAAAGCCATTTTCAATAAACTGGGGCATAAACC
Found at i:33289100 original size:27 final size:27
Alignment explanation
Indices: 33289016--33289103 Score: 115
Period size: 27 Copynumber: 3.3 Consensus size: 27
33289006 CATTCGTTAT
* *
33289016 TTTACCATACAGGGG-TATTACGGTCAC
1 TTTACCTTACAGGGGCT-TTACGGTCTC
*
33289043 TTTACCCTACAGGGGCTTTACGGTCTC
1 TTTACCTTACAGGGGCTTTACGGTCTC
* *
33289070 TTTACCTTACAGGGGCTTTACGATCTT
1 TTTACCTTACAGGGGCTTTACGGTCTC
33289097 TTTACCT
1 TTTACCT
33289104 AATAGGGGTA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
27 54 0.98
28 1 0.02
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.36
Consensus pattern (27 bp):
TTTACCTTACAGGGGCTTTACGGTCTC
Found at i:33289260 original size:27 final size:27
Alignment explanation
Indices: 33289244--33289452 Score: 210
Period size: 27 Copynumber: 7.8 Consensus size: 27
33289234 CTTTGTAAAT
33289244 TAGGGGTATTTTGGTAATTTTACAAA-
1 TAGGGGTATTTTGGTAATTTTACAAAC
* * * *
33289270 TTGAGGGTATTTCGATAATTTCACAAAC
1 TAG-GGGTATTTTGGTAATTTTACAAAC
* *
33289298 CAGTGGTATTTTGGTAATTTTACAAAC
1 TAGGGGTATTTTGGTAATTTTACAAAC
33289325 TAGGGGTATTTTGGTAATTTTACAAA-
1 TAGGGGTATTTTGGTAATTTTACAAAC
* * *
33289351 TTGAGGGTGTTTCGGTAATTTTACAAAC
1 TAG-GGGTATTTTGGTAATTTTACAAAC
* * * * *
33289379 CAAGGGTATTTTAGCAATTTTACAGAC
1 TAGGGGTATTTTGGTAATTTTACAAAC
**
33289406 TA-GGGTATTTTGGTAATTTTACTGA-
1 TAGGGGTATTTTGGTAATTTTACAAAC
*
33289431 TCGAGGGTATTTTGGTAATTTT
1 TAG-GGGTATTTTGGTAATTTT
33289453 GTAAACCGAT
Statistics
Matches: 149, Mismatches: 28, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
25 1 0.01
26 24 0.16
27 123 0.83
28 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (27 bp):
TAGGGGTATTTTGGTAATTTTACAAAC
Found at i:33289306 original size:54 final size:53
Alignment explanation
Indices: 33289247--33289493 Score: 228
Period size: 54 Copynumber: 4.6 Consensus size: 53
33289237 TGTAAATTAG
* * *
33289247 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGATAATTTCACAAACCA
1 GGGTATTTTGGTAATTTTACAAATCGAGGGTATTTTGATAATTTTACAAACCA
* * **
33289300 GTGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAATTGA
1 G-GGTATTTTGGTAATTTTACAAATCGA-GGGTATTTTGATAATTTTACAAA-CCA
* * * * * * *
33289355 GGGTGTTTCGGTAATTTTACAAACCAAGGGTATTTT-AGCAATTTTACAGACTA
1 GGGTATTTTGGTAATTTTACAAATCGAGGGTATTTTGA-TAATTTTACAAACCA
** * **
33289408 GGGTATTTTGGTAATTTTACTGATCGAGGGTATTTTGGTAATTTTGTAAACCGA
1 GGGTATTTTGGTAATTTTACAAATCGAGGGTATTTTGATAATTTTACAAACC-A
* * **
33289462 TGGTATTTTAGTAATTTTGTAAATCGAGGGTA
1 GGGTATTTTGGTAATTTTACAAATCGAGGGTA
33289494 AAACAGTAAT
Statistics
Matches: 154, Mismatches: 33, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
53 42 0.27
54 108 0.70
55 4 0.03
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (53 bp):
GGGTATTTTGGTAATTTTACAAATCGAGGGTATTTTGATAATTTTACAAACCA
Found at i:33289334 original size:81 final size:81
Alignment explanation
Indices: 33289244--33289479 Score: 325
Period size: 81 Copynumber: 2.9 Consensus size: 81
33289234 CTTTGTAAAT
* *
33289244 TAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGATAATTTCACAAACCAGTGGTATTT
1 TAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAACCAGTGGTATTT
*
33289309 TGGTAATTTTACAAAC
66 TAGTAATTTTACAAAC
*
33289325 TAGGGGTATTTTGGTAATTTTACAAATTGAGGGTGTTTCGGTAATTTTACAAACCAAG-GGTATT
1 TAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAACC-AGTGGTATT
* *
33289389 TTAGCAATTTTACAGAC
65 TTAGTAATTTTACAAAC
** * * **
33289406 TA-GGGTATTTTGGTAATTTTACTGATCGAGGGTATTTTGGTAATTTTGTAAACC-GATGGTATT
1 TAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAACCAG-TGGTATT
33289469 TTAGTAATTTT
65 TTAGTAATTTT
33289480 GTAAATCGAG
Statistics
Matches: 138, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
78 1 0.01
80 61 0.44
81 74 0.54
82 2 0.01
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (81 bp):
TAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAACCAGTGGTATTT
TAGTAATTTTACAAAC
Found at i:33289466 original size:27 final size:27
Alignment explanation
Indices: 33289219--33289493 Score: 157
Period size: 27 Copynumber: 10.2 Consensus size: 27
33289209 TAGAAAGTCA
* *
33289219 AGGGTATTTCT-GTAACTTTGTAAAT-T
1 AGGGTATTT-TGGTAATTTTGTAAATCG
** *
33289245 AGGGGTATTTTGGTAATTTTACAAATTG
1 A-GGGTATTTTGGTAATTTTGTAAATCG
* * *** *
33289273 AGGGTATTTCGATAATTTCACAAA-CC
1 AGGGTATTTTGGTAATTTTGTAAATCG
** *
33289299 AGTGGTATTTTGGTAATTTTACAAA-CT
1 AG-GGTATTTTGGTAATTTTGTAAATCG
** *
33289326 AGGGGTATTTTGGTAATTTTACAAATTG
1 A-GGGTATTTTGGTAATTTTGTAAATCG
* * ** * *
33289354 AGGGTGTTTCGGTAATTTTACAAACCA
1 AGGGTATTTTGGTAATTTTGTAAATCG
* * ** * *
33289381 AGGGTATTTTAGCAATTTTACAGA-CT
1 AGGGTATTTTGGTAATTTTGTAAATCG
* *
33289407 AGGGTATTTTGGTAATTTTACT-GATCG
1 AGGGTATTTTGGTAATTTT-GTAAATCG
*
33289434 AGGGTATTTTGGTAATTTTGTAAACCG
1 AGGGTATTTTGGTAATTTTGTAAATCG
* *
33289461 ATGGTATTTTAGTAATTTTGTAAATCG
1 AGGGTATTTTGGTAATTTTGTAAATCG
33289488 AGGGTA
1 AGGGTA
33289494 AAACAGTAAT
Statistics
Matches: 202, Mismatches: 38, Indels: 17
0.79 0.15 0.07
Matches are distributed among these distances:
26 25 0.12
27 174 0.86
28 3 0.01
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (27 bp):
AGGGTATTTTGGTAATTTTGTAAATCG
Found at i:33289501 original size:27 final size:27
Alignment explanation
Indices: 33289471--33289601 Score: 190
Period size: 27 Copynumber: 4.9 Consensus size: 27
33289461 ATGGTATTTT
*
33289471 AGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
33289498 AGTAATTCTGTAAATCAATGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
33289525 AGTAATTCTATAAATTGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
33289552 GGTAATTCTGTAAATCAAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
33289579 AGTAATTCTATAAATCGAGGGTA
1 AGTAATTCTGTAAATCGAGGGTA
33289602 CTTTGGTAAT
Statistics
Matches: 90, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 90 1.00
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.29
Consensus pattern (27 bp):
AGTAATTCTGTAAATCGAGGGTAAAAC
Found at i:33289612 original size:54 final size:54
Alignment explanation
Indices: 33289471--33289601 Score: 217
Period size: 54 Copynumber: 2.4 Consensus size: 54
33289461 ATGGTATTTT
* * * *
33289471 AGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCAATGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAAC
*
33289525 AGTAATTCTATAAATTGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAAC
33289579 AGTAATTCTATAAATCGAGGGTA
1 AGTAATTCTATAAATCGAGGGTA
33289602 CTTTGGTAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 71 1.00
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.29
Consensus pattern (54 bp):
AGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAAC
Found at i:33289638 original size:81 final size:81
Alignment explanation
Indices: 33289430--33289639 Score: 204
Period size: 81 Copynumber: 2.6 Consensus size: 81
33289420 AATTTTACTG
* * ** * * * *
33289430 ATCGAGGGTATTTTGGTAATTTTGTAAACCGATGGTATTTTAGTAATTTTGTAAATCGAGGGTAA
1 ATCGAGGGTAATTTGGTAATTTTATAAATTGAAGGTATTTCAGTAATTCTGTAAATCAAGGGTAA
*
33289495 AACAGTAATTCTGTAA
66 AACAGTAATTCTATAA
* * **** * * *** *
33289511 ATCAATGGTAAAACAGTAATTCTATAAATTGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAA
1 ATCGAGGGTAATTTGGTAATTTTATAAATTGAAGGTATTTCAGTAATTCTGTAAATCAAGGGTAA
33289576 AACAGTAATTCTATAA
66 AACAGTAATTCTATAA
* * *
33289592 ATCGAGGGTACTTTGGTAATTTTACAATTTGAAGGTATTTCAGTAATT
1 ATCGAGGGTAATTTGGTAATTTTATAAATTGAAGGTATTTCAGTAATT
33289640 TGGTAAACTA
Statistics
Matches: 94, Mismatches: 35, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
81 94 1.00
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.35
Consensus pattern (81 bp):
ATCGAGGGTAATTTGGTAATTTTATAAATTGAAGGTATTTCAGTAATTCTGTAAATCAAGGGTAA
AACAGTAATTCTATAA
Found at i:33297742 original size:25 final size:24
Alignment explanation
Indices: 33297714--33297760 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
33297704 AAGGGAATAG
33297714 GGGAA-GGAAATGAAGAAAAATGAAA
1 GGGAATGGAAA-G-AGAAAAATGAAA
*
33297739 GGGAATGGAGAGAGAAAAATGA
1 GGGAATGGAAAGAGAAAAATGA
33297761 GAGAGATGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 10 0.50
25 6 0.30
26 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.36, T:0.09
Consensus pattern (24 bp):
GGGAATGGAAAGAGAAAAATGAAA
Found at i:33300981 original size:27 final size:26
Alignment explanation
Indices: 33300942--33301045 Score: 127
Period size: 27 Copynumber: 3.8 Consensus size: 26
33300932 GGAAGCGTCT
*
33300942 TGGTGGCTATGCCACAATTATCTAATC
1 TGGTGGCTCTGCCAC-ATTATCTAATC
**
33300969 TGGTGGCTCTGCCACATATATCTGTTC
1 TGGTGGCTCTGCCACAT-TATCTAATC
33300996 TGGTGGCTCTGCCACGATTATCTATATC
1 TGGTGGCTCTGCCAC-ATTATCTA-ATC
* *
33301024 TGGTGACTCTGTCACATTATCT
1 TGGTGGCTCTGCCACATTATCT
33301046 GTTCTGGCAG
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
26 2 0.03
27 48 0.72
28 17 0.25
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.37
Consensus pattern (26 bp):
TGGTGGCTCTGCCACATTATCTAATC
Found at i:33301045 original size:54 final size:54
Alignment explanation
Indices: 33300942--33301052 Score: 170
Period size: 54 Copynumber: 2.1 Consensus size: 54
33300932 GGAAGCGTCT
*
33300942 TGGTGGCTATGCCACAATTATCTAATCTGGTGGCTCTGCCACATATATCTGTTC
1 TGGTGGCTATGCCACAATTATCTAATCTGGTGACTCTGCCACATATATCTGTTC
* * *
33300996 TGGTGGCTCTGCCACGATTATCTATATCTGGTGACTCTGTCACAT-TATCTGTTC
1 TGGTGGCTATGCCACAATTATCTA-ATCTGGTGACTCTGCCACATATATCTGTTC
33301050 TGG
1 TGG
33301053 CAGTCATGCT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.37
Consensus pattern (54 bp):
TGGTGGCTATGCCACAATTATCTAATCTGGTGACTCTGCCACATATATCTGTTC
Found at i:33301668 original size:16 final size:17
Alignment explanation
Indices: 33301637--33301675 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
33301627 CTTCCGCAAT
33301637 GATTTTCGGAAAACAAA
1 GATTTTCGGAAAACAAA
33301654 GATTTTCGG-AAACAAA
1 GATTTTCGGAAAACAAA
*
33301670 AATTTT
1 GATTTT
33301676 ATAAAGATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (17 bp):
GATTTTCGGAAAACAAA
Found at i:33303618 original size:17 final size:17
Alignment explanation
Indices: 33303596--33303629 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
33303586 ACTTGGCATT
33303596 TGTAAGTCAATCGGAAG
1 TGTAAGTCAATCGGAAG
*
33303613 TGTAAGTGAATCGGAAG
1 TGTAAGTCAATCGGAAG
33303630 AGGAAGGTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.09, G:0.32, T:0.24
Consensus pattern (17 bp):
TGTAAGTCAATCGGAAG
Found at i:33307597 original size:49 final size:49
Alignment explanation
Indices: 33307538--33307634 Score: 176
Period size: 49 Copynumber: 2.0 Consensus size: 49
33307528 CATCAGAATT
*
33307538 GAGTAGGAGTTAACTGGAATCATTAACTGAAGGAACCAGTGGTAAGATC
1 GAGTAAGAGTTAACTGGAATCATTAACTGAAGGAACCAGTGGTAAGATC
*
33307587 GAGTAAGAGTTAACTGGAATCATTGACTGAAGGAACCAGTGGTAAGAT
1 GAGTAAGAGTTAACTGGAATCATTAACTGAAGGAACCAGTGGTAAGAT
33307635 TTTGAACATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.23
Consensus pattern (49 bp):
GAGTAAGAGTTAACTGGAATCATTAACTGAAGGAACCAGTGGTAAGATC
Found at i:33308502 original size:27 final size:26
Alignment explanation
Indices: 33308459--33308546 Score: 95
Period size: 27 Copynumber: 3.2 Consensus size: 26
33308449 AGGAAGCGTC
*
33308459 CTGGTGGCTATGACACAATTATCTAAT
1 CTGGTGGCTATGCCAC-ATTATCTAAT
* *
33308486 CTGGTGGCTTTGCCACATATATCTATT
1 CTGGTGGCTATGCCACAT-TATCTAAT
* *
33308513 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTATGCCAC-ATTATCT-AAT
33308541 CTGGTG
1 CTGGTG
33308547 ACTCTATCAC
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
26 2 0.04
27 41 0.79
28 9 0.17
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (26 bp):
CTGGTGGCTATGCCACATTATCTAAT
Found at i:33308560 original size:27 final size:26
Alignment explanation
Indices: 33308498--33308570 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 26
33308488 GGTGGCTTTG
* * *
33308498 CCACATATATCTATTCTGGTGGCTCTG
1 CCACAT-TATCTGTTCTGGTGACTCTA
33308525 CCACGATTATCTGTATCTGGTGACTCTA
1 CCAC-ATTATCTGT-TCTGGTGACTCTA
*
33308553 TCACATTATCTGTTCTGG
1 CCACATTATCTGTTCTGG
33308571 AAGCCATGCT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
26 5 0.12
27 19 0.47
28 16 0.40
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (26 bp):
CCACATTATCTGTTCTGGTGACTCTA
Found at i:33308563 original size:54 final size:54
Alignment explanation
Indices: 33308459--33308570 Score: 127
Period size: 54 Copynumber: 2.1 Consensus size: 54
33308449 AGGAAGCGTC
* * *
33308459 CTGGTGGCTATGACACAATTATCTAATCTGGTGGCTTTGCCACATATATCTATT
1 CTGGTGGCTATGACACAATTATCTAATCTGGTGACTCTACCACATATATCTATT
* * * * * *
33308513 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTATCACAT-TATCTGTT
1 CTGGTGGCTATGACACAATTATCT-AATCTGGTGACTCTACCACATATATCTATT
33308567 CTGG
1 CTGG
33308571 AAGCCATGCT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
54 32 0.67
55 16 0.33
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGACACAATTATCTAATCTGGTGACTCTACCACATATATCTATT
Found at i:33308982 original size:131 final size:131
Alignment explanation
Indices: 33308748--33309146 Score: 798
Period size: 131 Copynumber: 3.0 Consensus size: 131
33308738 AATTCTGTTC
33308748 TGGGCTAAGGCCAACTTATTCTGTTCTCTGTGGTTTGAACCGATATAGGCTATGGTTGGGTTAAT
1 TGGGCTAAGGCCAACTTATTCTGTTCTCTGTGGTTTGAACCGATATAGGCTATGGTTGGGTTAAT
33308813 TTACACACTGAGTTTCCCCAAACTCACCACTTTATTTTCATCCACACAGGTAATCCCCAACCATA
66 TTACACACTGAGTTTCCCCAAACTCACCACTTTATTTTCATCCACACAGGTAATCCCCAACCATA
33308878 G
131 G
33308879 TGGGCTAAGGCCAACTTATTCTGTTCTCTGTGGTTTGAACCGATATAGGCTATGGTTGGGTTAAT
1 TGGGCTAAGGCCAACTTATTCTGTTCTCTGTGGTTTGAACCGATATAGGCTATGGTTGGGTTAAT
33308944 TTACACACTGAGTTTCCCCAAACTCACCACTTTATTTTCATCCACACAGGTAATCCCCAACCATA
66 TTACACACTGAGTTTCCCCAAACTCACCACTTTATTTTCATCCACACAGGTAATCCCCAACCATA
33309009 G
131 G
33309010 TGGGCTAAGGCCAACTTATTCTGTTCTCTGTGGTTTGAACCGATATAGGCTATGGTTGGGTTAAT
1 TGGGCTAAGGCCAACTTATTCTGTTCTCTGTGGTTTGAACCGATATAGGCTATGGTTGGGTTAAT
33309075 TTACACACTGAGTTTCCCCAAACTCACCACTTTATTTTCATCCACACAGGTAATCCCCAACCATA
66 TTACACACTGAGTTTCCCCAAACTCACCACTTTATTTTCATCCACACAGGTAATCCCCAACCATA
33309140 G
131 G
33309141 TGGGCT
1 TGGGCT
33309147 TAGAGCTGTG
Statistics
Matches: 268, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
131 268 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (131 bp):
TGGGCTAAGGCCAACTTATTCTGTTCTCTGTGGTTTGAACCGATATAGGCTATGGTTGGGTTAAT
TTACACACTGAGTTTCCCCAAACTCACCACTTTATTTTCATCCACACAGGTAATCCCCAACCATA
G
Found at i:33313020 original size:38 final size:38
Alignment explanation
Indices: 33312975--33313059 Score: 134
Period size: 38 Copynumber: 2.2 Consensus size: 38
33312965 GGCTTAAAGA
* *
33312975 CCCGCAGGCTTCGTGCTGGTAAAATATCCGGGTTAAAT
1 CCCGCAGGCTTCGTACTGGTAAAATATCCGGGATAAAT
**
33313013 CCCGCAGGCTTCGTACTGGTATTATATCCGGGATAAAT
1 CCCGCAGGCTTCGTACTGGTAAAATATCCGGGATAAAT
33313051 CCCGCAGGC
1 CCCGCAGGC
33313060 CTAATGCTGG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.22, C:0.27, G:0.26, T:0.25
Consensus pattern (38 bp):
CCCGCAGGCTTCGTACTGGTAAAATATCCGGGATAAAT
Found at i:33313070 original size:38 final size:38
Alignment explanation
Indices: 33312988--33313077 Score: 117
Period size: 38 Copynumber: 2.4 Consensus size: 38
33312978 GCAGGCTTCG
** * * **
33312988 TGCTGGTAAAATATCCGGGTTAAATCCCGCAGGCTTCG
1 TGCTGGTATTATATCCGGGATAAATCCCGCAGGCCTAA
*
33313026 TACTGGTATTATATCCGGGATAAATCCCGCAGGCCTAA
1 TGCTGGTATTATATCCGGGATAAATCCCGCAGGCCTAA
33313064 TGCTGGTATTATAT
1 TGCTGGTATTATAT
33313078 TCGAGCCTTC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (38 bp):
TGCTGGTATTATATCCGGGATAAATCCCGCAGGCCTAA
Found at i:33313152 original size:43 final size:42
Alignment explanation
Indices: 33313054--33313156 Score: 127
Period size: 43 Copynumber: 2.5 Consensus size: 42
33313044 GATAAATCCC
*
33313054 GCAGGCCTAATGCTGGT-ATTATATTCGAGCCTTCGTGCCTA
1 GCAGGCCTAATGCCGGTGATTATATTCGAGCCTTCGTGCCTA
* ** * *
33313095 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCCTAATGCCGGTGAT-TATATTCGAGCCTTCGTGCCTA
*
33313138 GCAGGCGTAATGCCGGTGA
1 GCAGGCCTAATGCCGGTGA
33313157 AATGATATGT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 13 0.25
42 2 0.04
43 36 0.71
ACGTcount: A:0.16, C:0.24, G:0.32, T:0.28
Consensus pattern (42 bp):
GCAGGCCTAATGCCGGTGATTATATTCGAGCCTTCGTGCCTA
Found at i:33313508 original size:227 final size:227
Alignment explanation
Indices: 33313113--33313560 Score: 896
Period size: 227 Copynumber: 2.0 Consensus size: 227
33313103 CGTGCCGGTG
33313113 ATGTGTATTCGGGCCTTCGTGCCTAGCAGGCGTAATGCCGGTGAAATGATATGTTATGTGAATTC
1 ATGTGTATTCGGGCCTTCGTGCCTAGCAGGCGTAATGCCGGTGAAATGATATGTTATGTGAATTC
33313178 GGTGTTCCTTGTAAGATAAGGGTTTAGCCGAATGTTAAAGATGAAATGATAGTGTATTGTATCAT
66 GGTGTTCCTTGTAAGATAAGGGTTTAGCCGAATGTTAAAGATGAAATGATAGTGTATTGTATCAT
33313243 GCTTATATGGCCTAATGGCAAGTATAACATGTTGGTAAATATGCAATGTGCTTTTATAATCGAAT
131 GCTTATATGGCCTAATGGCAAGTATAACATGTTGGTAAATATGCAATGTGCTTTTATAATCGAAT
33313308 GATATGTTTGAAATGAATGTGAGTGACCAGTT
196 GATATGTTTGAAATGAATGTGAGTGACCAGTT
33313340 ATGTGTATTCGGGCCTTCGTGCCTAGCAGGCGTAATGCCGGTGAAATGATATGTTATGTGAATTC
1 ATGTGTATTCGGGCCTTCGTGCCTAGCAGGCGTAATGCCGGTGAAATGATATGTTATGTGAATTC
33313405 GGTGTTCCTTGTAAGATAAGGGTTTAGCCGAATGTTAAAGATGAAATGATAGTGTATTGTATCAT
66 GGTGTTCCTTGTAAGATAAGGGTTTAGCCGAATGTTAAAGATGAAATGATAGTGTATTGTATCAT
33313470 GCTTATATGGCCTAATGGCAAGTATAACATGTTGGTAAATATGCAATGTGCTTTTATAATCGAAT
131 GCTTATATGGCCTAATGGCAAGTATAACATGTTGGTAAATATGCAATGTGCTTTTATAATCGAAT
33313535 GATATGTTTGAAATGAATGTGAGTGA
196 GATATGTTTGAAATGAATGTGAGTGA
33313561 AATGTTATGC
Statistics
Matches: 221, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
227 221 1.00
ACGTcount: A:0.29, C:0.11, G:0.26, T:0.34
Consensus pattern (227 bp):
ATGTGTATTCGGGCCTTCGTGCCTAGCAGGCGTAATGCCGGTGAAATGATATGTTATGTGAATTC
GGTGTTCCTTGTAAGATAAGGGTTTAGCCGAATGTTAAAGATGAAATGATAGTGTATTGTATCAT
GCTTATATGGCCTAATGGCAAGTATAACATGTTGGTAAATATGCAATGTGCTTTTATAATCGAAT
GATATGTTTGAAATGAATGTGAGTGACCAGTT
Found at i:33316802 original size:15 final size:16
Alignment explanation
Indices: 33316777--33316824 Score: 64
Period size: 15 Copynumber: 3.0 Consensus size: 16
33316767 TCAAAGGAGT
33316777 AAAAAGAAGAAAGAAA
1 AAAAAGAAGAAAGAAA
33316793 AAAAAG-AGAAAGAAA
1 AAAAAGAAGAAAGAAA
33316808 AAGGAAAGAAG-AAGAAA
1 AA--AAAGAAGAAAGAAA
33316825 GAGTATAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 11 0.38
16 6 0.21
17 10 0.34
18 2 0.07
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AAAAAGAAGAAAGAAA
Found at i:33316808 original size:11 final size:10
Alignment explanation
Indices: 33316779--33316826 Score: 51
Period size: 11 Copynumber: 4.5 Consensus size: 10
33316769 AAAGGAGTAA
33316779 AAAGAAGAAAG
1 AAAGAA-AAAG
*
33316790 AAAAAAAAGAG
1 AAAGAAAA-AG
33316801 AAAGAAAAAGG
1 AAAGAAAAA-G
*
33316812 AAAGAAGAAG
1 AAAGAAAAAG
33316822 AAAGA
1 AAAGA
33316827 GTATAGAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
10 9 0.28
11 23 0.72
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:33319397 original size:105 final size:105
Alignment explanation
Indices: 33319215--33319531 Score: 607
Period size: 105 Copynumber: 3.0 Consensus size: 105
33319205 TATCTGCAAG
* *
33319215 ACTTTTGCTATGAACCCACAGTCAAAAGTAGATTCCAACCGCAAGGACTTGCTATGTGTCCACAG
1 ACTTTTACTATGAACCCACAGTCAAAGGTAGATTCCAACCGCAAGGACTTGCTATGTGTCCACAG
33319280 CCAATATGGCAGTTGTTATTTGCAAACTAATAGTAGTTTA
66 CCAATATGGCAGTTGTTATTTGCAAACTAATAGTAGTTTA
33319320 ACTTTTACTATGAACCCACAGTCAAAGGTAGATTCCAACCGCAAGGACTTGCTATGTGTCCACAG
1 ACTTTTACTATGAACCCACAGTCAAAGGTAGATTCCAACCGCAAGGACTTGCTATGTGTCCACAG
33319385 CCAATATGGCAGTTGTTATTTGCAAACTAATAGTAGTTTA
66 CCAATATGGCAGTTGTTATTTGCAAACTAATAGTAGTTTA
33319425 ACTTTTACTATGAACCCACAGTCAAAGGTAGATTCCAACCGCAAGGACTTGCTATGTGTCCACAG
1 ACTTTTACTATGAACCCACAGTCAAAGGTAGATTCCAACCGCAAGGACTTGCTATGTGTCCACAG
*
33319490 CCAATATGGCAGTTGTTATTTGCAGACTAATAGTAGTTTA
66 CCAATATGGCAGTTGTTATTTGCAAACTAATAGTAGTTTA
33319530 AC
1 AC
33319532 AACGTGGCGT
Statistics
Matches: 209, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 209 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.29
Consensus pattern (105 bp):
ACTTTTACTATGAACCCACAGTCAAAGGTAGATTCCAACCGCAAGGACTTGCTATGTGTCCACAG
CCAATATGGCAGTTGTTATTTGCAAACTAATAGTAGTTTA
Found at i:33334257 original size:15 final size:15
Alignment explanation
Indices: 33334237--33334268 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
33334227 AAATTTAGCC
33334237 TTCAATGGTTATATA
1 TTCAATGGTTATATA
33334252 TTCAATGGTTATATA
1 TTCAATGGTTATATA
33334267 TT
1 TT
33334269 TTGTCATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50
Consensus pattern (15 bp):
TTCAATGGTTATATA
Found at i:33338056 original size:41 final size:41
Alignment explanation
Indices: 33337964--33338107 Score: 227
Period size: 41 Copynumber: 3.5 Consensus size: 41
33337954 GACAAATCAG
* * *
33337964 CTATATGTGGCACTTAGTGTGCGA-TTCGACATAGCTTCGA
1 CTATATATGGCACTTAGTGTGCGAGATCGAGATAGCTTCGA
* *
33338004 CTATATATGGCACTTAGTGTGCGAGATCAAGATAGATTCGA
1 CTATATATGGCACTTAGTGTGCGAGATCGAGATAGCTTCGA
33338045 CTATATATGGCACTTAGTGTGCGAGATCGAGATAGCTTCGA
1 CTATATATGGCACTTAGTGTGCGAGATCGAGATAGCTTCGA
*
33338086 TTATATATGGCACTTAGTGTGC
1 CTATATATGGCACTTAGTGTGC
33338108 AATTTAAGAT
Statistics
Matches: 95, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 23 0.24
41 72 0.76
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (41 bp):
CTATATATGGCACTTAGTGTGCGAGATCGAGATAGCTTCGA
Found at i:33338140 original size:81 final size:82
Alignment explanation
Indices: 33337974--33338152 Score: 229
Period size: 81 Copynumber: 2.2 Consensus size: 82
33337964 CTATATGTGG
*
33337974 CACTTAGTGTGCGA-TTCGACATAGCTTCGACTATATATGGCACTTAGTGTGCGAGATCAAGATA
1 CACTTAGTGTGCGAGATCGACATAGCTTCGACTATATATGGCACTTAGTGTGCGAGATCAAGATA
***
33338038 GATTCGACTATATATGG
66 GATTCGACTATATACAA
* * *
33338055 CACTTAGTGTGCGAGATCGAGATAGCTTCGATTATATATGGCACTTAGTGTGC-A-ATTTAAGAT
1 CACTTAGTGTGCGAGATCGACATAGCTTCGACTATATATGGCACTTAGTGTGCGAGA-TCAAGAT
* * *
33338118 AGCTTCGGCTATGTACAA
65 AGATTCGACTATATACAA
*
33338136 CACTTAGTGTGTGAGAT
1 CACTTAGTGTGCGAGAT
33338153 ATTGAGTATT
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
80 1 0.01
81 49 0.58
82 35 0.41
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (82 bp):
CACTTAGTGTGCGAGATCGACATAGCTTCGACTATATATGGCACTTAGTGTGCGAGATCAAGATA
GATTCGACTATATACAA
Found at i:33342183 original size:5 final size:5
Alignment explanation
Indices: 33342175--33342331 Score: 314
Period size: 5 Copynumber: 31.4 Consensus size: 5
33342165 TTAGTTTAGT
33342175 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
33342225 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
33342275 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
33342325 TATAA TA
1 TATAA TA
33342332 ATATTCTTAT
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 152 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:33344753 original size:180 final size:180
Alignment explanation
Indices: 33344482--33344807 Score: 481
Period size: 180 Copynumber: 1.8 Consensus size: 180
33344472 ATTTTTTATA
* * * * * *
33344482 AAACTATACTCATATATCTTATTACCATAAAATTTTCATAGTTTTTGGTTTAGCCAATTAGTACA
1 AAACTAGACTCACATATATTATTACCATAAAATTTTCAGAATTTTTAGTTTAGCCAATTAGTACA
* * ** *
33344547 GTCTATTCATTAAAGATATCCCTATTTCATTGTCTGACAGTTCCGACTTCTCTTCACTAAAAATT
66 GTCTATTCATTAAAGATACCCCTATTTCACTGTCCAACAGTTCCGACCTCTCTTCACTAAAAATT
*
33344612 ATTTATTTCATGGTACGGGACTCCAAATTGAGAACAACTAATTTTACCAT
131 ATTTATCTCATGGTACGGGACTCCAAATTGAGAACAACTAATTTTACCAT
* * *
33344662 AAACTAGACTCACATATATTCTTACCATAAATTTTTTAGAATTTTTAGTTTAGCCAATTAGTACA
1 AAACTAGACTCACATATATTATTACCATAAAATTTTCAGAATTTTTAGTTTAGCCAATTAGTACA
* * * *
33344727 GTTTATTCATTAAATATACCCCTATTTCACTGTCCAATAGTTTCGACCTCTCTTCACTAAAAATT
66 GTCTATTCATTAAAGATACCCCTATTTCACTGTCCAACAGTTCCGACCTCTCTTCACTAAAAATT
33344792 ATTTATCTCATGGTAC
131 ATTTATCTCATGGTAC
33344808 AACTCTCAGA
Statistics
Matches: 127, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
180 127 1.00
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (180 bp):
AAACTAGACTCACATATATTATTACCATAAAATTTTCAGAATTTTTAGTTTAGCCAATTAGTACA
GTCTATTCATTAAAGATACCCCTATTTCACTGTCCAACAGTTCCGACCTCTCTTCACTAAAAATT
ATTTATCTCATGGTACGGGACTCCAAATTGAGAACAACTAATTTTACCAT
Found at i:33345464 original size:50 final size:50
Alignment explanation
Indices: 33345387--33345626 Score: 266
Period size: 50 Copynumber: 4.8 Consensus size: 50
33345377 ACCGAAGCTC
* * *
33345387 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAACAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAAACAA
* * * * * *
33345437 TTTGGTACATGTAGTAGCCTACACTTAGTACTACACACGTGACCTAACCA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAAACAA
* * ** * *
33345487 TC-GGATACACGTAGTAGCTTGCACTTAGTACTACACACGTGATTGAAGCTA
1 TCTGG-TACACGTAGTAGCCTGCACTTAGTACTACACACGCGA-CCAAACAA
* * * *
33345538 TCGGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAAACAA
* *
33345588 TCTGGTACAAGTAGTAGCCTACACTTAGTACTACACACG
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACG
33345627 TGATCTAAAA
Statistics
Matches: 155, Mismatches: 32, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
49 2 0.01
50 113 0.73
51 38 0.25
52 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (50 bp):
TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAAACAA
Found at i:33345572 original size:101 final size:101
Alignment explanation
Indices: 33345448--33345630 Score: 287
Period size: 101 Copynumber: 1.8 Consensus size: 101
33345438 TTGGTACATG
* * * * *
33345448 TAGTAGCCTACACTTAGTACTACACACGTGACCTAACCATC-GGATACACGTAGTAGCTTGCACT
1 TAGTAGCCTACACTTAGTACTACACACGCGACCTAACAATCTGG-TACAAGTAGTAGCCTACACT
33345512 TAGTACTACACACGTGATTGAAGCTATCGGGTACACA
65 TAGTACTACACACGTGATTGAAGCTATCGGGTACACA
* *
33345549 TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGTACAAGTAGTAGCCTACACTT
1 TAGTAGCCTACACTTAGTACTACACACGCGACCTAACAATCTGGTACAAGTAGTAGCCTACACTT
33345614 AGTACTACACACGTGAT
66 AGTACTACACACGTGAT
33345631 CTAAAACCGT
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
101 72 0.97
102 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (101 bp):
TAGTAGCCTACACTTAGTACTACACACGCGACCTAACAATCTGGTACAAGTAGTAGCCTACACTT
AGTACTACACACGTGATTGAAGCTATCGGGTACACA
Found at i:33348240 original size:32 final size:34
Alignment explanation
Indices: 33348204--33348268 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 34
33348194 TAACAGTGGT
*
33348204 ACTGGACCAGAG-CCCTT-TTCAGATTACAATAA
1 ACTGGACCAGAGCCCCTTATTCAGATAACAATAA
* **
33348236 ACTGGGCCTTAGCCCCTTATTCAGATAACAATA
1 ACTGGACCAGAGCCCCTTATTCAGATAACAATA
33348269 TGGCCCATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 9 0.33
33 5 0.19
34 13 0.48
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (34 bp):
ACTGGACCAGAGCCCCTTATTCAGATAACAATAA
Found at i:33350150 original size:26 final size:26
Alignment explanation
Indices: 33350114--33350223 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
33350104 CATGAAATTC
33350114 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
33350140 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
33350166 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
33350192 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
33350218 TTATCA
1 TTATCA
33350224 ATTTGTATCA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:33352714 original size:20 final size:19
Alignment explanation
Indices: 33352668--33352714 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
33352658 ACATTTCAGG
*
33352668 TATA-ATTAATTTTATAAA
1 TATATATTAATTTTAAAAA
*
33352686 TAAATTATTAATTATTAAAAA
1 TATA-TATTAATT-TTAAAAA
33352707 TATATATT
1 TATATATT
33352715 TTATGTACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 3 0.13
20 11 0.48
21 9 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TATATATTAATTTTAAAAA
Found at i:33353499 original size:19 final size:19
Alignment explanation
Indices: 33353474--33353557 Score: 80
Period size: 22 Copynumber: 4.1 Consensus size: 19
33353464 TGTTTTTTTA
33353474 AATTATAAAAAATATTAGAT
1 AATTATAAAAAATATTA-AT
33353494 -ATTATAAAATAAATATGTAAT
1 AATTAT-AAA-AAATAT-TAAT
*
33353515 AATTTTAAAAAATATTAAT
1 AATTATAAAAAATATTAAT
*
33353534 AATTTATAATAAAAAAATTAAT
1 AA-TTAT-A-AAAAATATTAAT
33353556 AA
1 AA
33353558 AAATTGTAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
19 11 0.20
20 12 0.22
21 12 0.22
22 19 0.35
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
AATTATAAAAAATATTAAT
Found at i:33353556 original size:41 final size:41
Alignment explanation
Indices: 33353474--33353557 Score: 102
Period size: 41 Copynumber: 2.0 Consensus size: 41
33353464 TGTTTTTTTA
*
33353474 AATTATAAAAAATATTAGATATTATAAAATAAATATGTAAT
1 AATTATAAAAAATATTAGATATTATAAAATAAAAATGTAAT
*
33353515 AATTTTAAAAAATATTA-ATAATTTATAATAA-AAAAAT-TAAT
1 AATTATAAAAAATATTAGAT-A-TTATAA-AATAAAAATGTAAT
33353556 AA
1 AA
33353558 AAATTGTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
40 2 0.05
41 23 0.61
42 11 0.29
43 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (41 bp):
AATTATAAAAAATATTAGATATTATAAAATAAAAATGTAAT
Found at i:33354594 original size:19 final size:20
Alignment explanation
Indices: 33354572--33354611 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
33354562 TTTTTGAATA
*
33354572 TTTACGATTTTTATA-TATT
1 TTTAAGATTTTTATATTATT
*
33354591 TTTAATATTTTTATATTATT
1 TTTAAGATTTTTATATTATT
33354611 T
1 T
33354612 ATTGGTATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (20 bp):
TTTAAGATTTTTATATTATT
Found at i:33354610 original size:11 final size:10
Alignment explanation
Indices: 33354578--33354611 Score: 52
Period size: 9 Copynumber: 3.4 Consensus size: 10
33354568 AATATTTACG
33354578 ATTTTTATAT
1 ATTTTTATAT
33354588 ATTTTTA-AT
1 ATTTTTATAT
33354597 ATTTTTATATT
1 ATTTTTATA-T
33354608 ATTT
1 ATTT
33354612 ATTGGTATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.41
10 8 0.36
11 5 0.23
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
ATTTTTATAT
Found at i:33355129 original size:15 final size:16
Alignment explanation
Indices: 33355102--33355139 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
33355092 GCAAAATGTG
33355102 ATTT-TTTTT-AAATA
1 ATTTATTTTTAAAATA
33355116 A-TTATTTTTAAAATA
1 ATTTATTTTTAAAATA
33355131 ATTTATTTT
1 ATTTATTTT
33355140 AGGATTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.10
14 6 0.29
15 6 0.29
16 7 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTTATTTTTAAAATA
Found at i:33357238 original size:15 final size:15
Alignment explanation
Indices: 33357201--33357243 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
33357191 TATTTATATG
*
33357201 CATATATTATTTTGA
1 CATATATTATTTTTA
33357216 -ATATATTATTTTTA
1 CATATATTATTTTTA
*
33357230 CATACATTATTTTT
1 CATATATTATTTTT
33357244 TCCATGCACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (15 bp):
CATATATTATTTTTA
Found at i:33357944 original size:120 final size:120
Alignment explanation
Indices: 33357731--33357955 Score: 297
Period size: 120 Copynumber: 1.9 Consensus size: 120
33357721 AAAGTTTTTC
* * * * * ** *
33357731 AAAATAAGACAATATTTCGTGTTTGGAAGTTTGAGAAATCGTGCCTTACCGTGCTGGGTTTCGAT
1 AAAATAAGACAATATTTCGTATTTAGAAATTCGAGAAATCATGCCCAACCGTGCTGGATTTCGAT
* * * *
33357796 TTTCCGTTCAACCGAATAACTGAATATCCTTTTGAAATTTCATCCATGTTTTCTT
66 TTACCATTCAACCAAATAACTAAATATCCTTTTGAAATTTCATCCATGTTTTCTT
* * *
33357851 AAAATGAGACAATATTTCGTATTTAGAAATTCGAGAAATCATGCCCAATCGTGTTGGATTTCGAT
1 AAAATAAGACAATATTTCGTATTTAGAAATTCGAGAAATCATGCCCAACCGTGCTGGATTTCGAT
* *
33357916 TTACCATTTAACCAAATAGCTAAATATCCTTTTGAAATTT
66 TTACCATTCAACCAAATAACTAAATATCCTTTTGAAATTT
33357956 GAAATGCATA
Statistics
Matches: 88, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
120 88 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (120 bp):
AAAATAAGACAATATTTCGTATTTAGAAATTCGAGAAATCATGCCCAACCGTGCTGGATTTCGAT
TTACCATTCAACCAAATAACTAAATATCCTTTTGAAATTTCATCCATGTTTTCTT
Found at i:33360820 original size:11 final size:11
Alignment explanation
Indices: 33360804--33360828 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
33360794 ATAGAAATTC
33360804 TGAGGGTAAAT
1 TGAGGGTAAAT
33360815 TGAGGGTAAAT
1 TGAGGGTAAAT
33360826 TGA
1 TGA
33360829 AGGAATTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.28
Consensus pattern (11 bp):
TGAGGGTAAAT
Found at i:33361769 original size:24 final size:23
Alignment explanation
Indices: 33361720--33361769 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
33361710 ACTATACACA
* *
33361720 TTTTTTTATTTTGGTACCTAATT
1 TTTTTTTATGTTGGTACCTAAAT
**
33361743 TTTTTCTTATGTTGGTATTTAAAT
1 TTTTT-TTATGTTGGTACCTAAAT
33361767 TTT
1 TTT
33361770 GCATTATTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.18, C:0.06, G:0.10, T:0.66
Consensus pattern (23 bp):
TTTTTTTATGTTGGTACCTAAAT
Found at i:33362301 original size:10 final size:9
Alignment explanation
Indices: 33362269--33362315 Score: 58
Period size: 9 Copynumber: 5.0 Consensus size: 9
33362259 ATATGTACAC
33362269 TTAAAAATT
1 TTAAAAATT
*
33362278 TTAAAAGTT
1 TTAAAAATT
*
33362287 ATAAAAATT
1 TTAAAAATT
33362296 CTTAAAAATT
1 -TTAAAAATT
33362306 TGTAAAAATT
1 T-TAAAAATT
33362316 GTTTAGAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
9 16 0.50
10 16 0.50
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (9 bp):
TTAAAAATT
Found at i:33365832 original size:30 final size:30
Alignment explanation
Indices: 33365796--33365855 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
33365786 TAATTAGTTA
33365796 AGTTAGTTTTTACTGTAGCTTAGGTTTATT
1 AGTTAGTTTTTACTGTAGCTTAGGTTTATT
33365826 AGTTAGTTTTTACTGTAGCTTAGGTTTATT
1 AGTTAGTTTTTACTGTAGCTTAGGTTTATT
33365856 TACATGTCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.53
Consensus pattern (30 bp):
AGTTAGTTTTTACTGTAGCTTAGGTTTATT
Found at i:33369836 original size:271 final size:271
Alignment explanation
Indices: 33369344--33370156 Score: 1536
Period size: 271 Copynumber: 3.0 Consensus size: 271
33369334 GAACATTGCC
*
33369344 GCCTCCAAAACCCTTTCTATCATCGTCAAACGAAGCCCCGATCTTGTGTCCAAACCAAATAGTAA
1 GCCTCCAAAACCCTTTCTATCATCGTCAAACGAAGCCCCGATCTTGTGTCCAAACCAAAAAGTAA
* *
33369409 CCACCAACCACCACATTGTCACTACCCCGAGCACCATTGTTGCTCGACCGAAATCAATAATCCGA
66 CCACCAACCACCACATTGTCACTACCCCGAGCACTATTGTTGATCGACCGAAATCAATAATCCGA
** *
33369474 CGATAGTTGAATACCTTCGGCCATCCCTTTTATGCTCATTGATGAGCAAAACTACCTCCGACACT
131 CGATAGTTGAATACCTTCGGCCATCCCTTTTACACTCATTGATGAGCAAAACTACCTCTGACACT
33369539 CTGAAAACGCACACCAAAGTCGCTCATATGAGCCTTGCTGATAATGCTCTAGAATAACATATTTT
196 CTGAAAACGCACACCAAAGTCGCTCATATGAGCCTTGCTGATAATGCTCTAGAATAACATATTTT
33369604 TATGTATTAAT
261 TATGTATTAAT
33369615 GCCTCCAAAACCCTTTCTATCATCGTCAAACGAAGCCCCGATCTTGTGTCCAAACCAAAAAGTAA
1 GCCTCCAAAACCCTTTCTATCATCGTCAAACGAAGCCCCGATCTTGTGTCCAAACCAAAAAGTAA
33369680 CCACCAACCACCACATTGTCACTACCCCGAGCACTATTGTTGATCGACCGAAATCAATAATCCGA
66 CCACCAACCACCACATTGTCACTACCCCGAGCACTATTGTTGATCGACCGAAATCAATAATCCGA
*
33369745 CGATAGTTGAATACCTTCGGCCATCCCTTTTACACTCATTGCTGAGCAAAACTACCTCTGACACT
131 CGATAGTTGAATACCTTCGGCCATCCCTTTTACACTCATTGATGAGCAAAACTACCTCTGACACT
* *
33369810 CTGAAAACGCACCCCAAAGACGCTCATATGAGCCTTGCTGATAATGCTCTAGAATAACATATTTT
196 CTGAAAACGCACACCAAAGTCGCTCATATGAGCCTTGCTGATAATGCTCTAGAATAACATATTTT
33369875 TATGTATTAAT
261 TATGTATTAAT
33369886 GCCTCCAAAACCCTTTCTATCATCGTCAAACGAAGCCCCGATCTTGTGTCCAAACCAAAAAGTAA
1 GCCTCCAAAACCCTTTCTATCATCGTCAAACGAAGCCCCGATCTTGTGTCCAAACCAAAAAGTAA
33369951 CCACCAACCACCACATTGTCACTACCCCGAGCACTATTGTTGATCGACCGAAATCAATAATCCGA
66 CCACCAACCACCACATTGTCACTACCCCGAGCACTATTGTTGATCGACCGAAATCAATAATCCGA
33370016 CGATAGTTGAATACCTTCGGCCATCCCTTTTACACTCATTGATGAGCAAAACTACCTCTGACACT
131 CGATAGTTGAATACCTTCGGCCATCCCTTTTACACTCATTGATGAGCAAAACTACCTCTGACACT
*
33370081 CTGAAAACGCACACCAAAGTCGCTCATATGAGCCTTGCTGATAATACTCTAGAATAACATATTTT
196 CTGAAAACGCACACCAAAGTCGCTCATATGAGCCTTGCTGATAATGCTCTAGAATAACATATTTT
33370146 TATGTATTAAT
261 TATGTATTAAT
33370157 CATGTGTTTA
Statistics
Matches: 529, Mismatches: 13, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
271 529 1.00
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (271 bp):
GCCTCCAAAACCCTTTCTATCATCGTCAAACGAAGCCCCGATCTTGTGTCCAAACCAAAAAGTAA
CCACCAACCACCACATTGTCACTACCCCGAGCACTATTGTTGATCGACCGAAATCAATAATCCGA
CGATAGTTGAATACCTTCGGCCATCCCTTTTACACTCATTGATGAGCAAAACTACCTCTGACACT
CTGAAAACGCACACCAAAGTCGCTCATATGAGCCTTGCTGATAATGCTCTAGAATAACATATTTT
TATGTATTAAT
Found at i:33370411 original size:15 final size:15
Alignment explanation
Indices: 33370391--33370420 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
33370381 CATTTTATTT
33370391 ATATTAAGATAATTA
1 ATATTAAGATAATTA
33370406 ATATTAAGATAATTA
1 ATATTAAGATAATTA
33370421 TTAGGATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:33376893 original size:26 final size:25
Alignment explanation
Indices: 33376864--33376932 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 25
33376854 AATTTTAAAT
*
33376864 TTTATTTCTATTTTTTATTATTT-TTA
1 TTTATTT-TATTTATT-TTATTTCTTA
33376890 TTTA-TTTATTTATTTTATTTCTTA
1 TTTATTTTATTTATTTTATTTCTTA
33376914 TTGTATTTTATTTCATTTT
1 TT-TATTTTATTT-ATTTT
33376933 GTTTTATTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
23 6 0.16
24 12 0.32
25 4 0.11
26 11 0.29
27 5 0.13
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.75
Consensus pattern (25 bp):
TTTATTTTATTTATTTTATTTCTTA
Found at i:33376915 original size:30 final size:29
Alignment explanation
Indices: 33376872--33376963 Score: 71
Period size: 32 Copynumber: 3.0 Consensus size: 29
33376862 ATTTTATTTC
*
33376872 TATTTT-TTATTATTTTTATTTATTTATT
1 TATTTTATTTTTATTTTTATTTATTTATT
*
33376900 TATTTTATTTCTTA-TTGTATTTTATTTCATTT
1 TATTTTATTT-TTATTTTTA-TTTATTT-A-TT
*
33376932 TGTTTTATTTTTAAATATTTTATTATATTTAT
1 TATTTTATTTTT--AT-TTTTATT-TATTTAT
33376964 AAATTTCTCT
Statistics
Matches: 50, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
28 6 0.12
29 6 0.12
30 10 0.20
31 3 0.06
32 11 0.22
33 2 0.04
34 3 0.06
35 9 0.18
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (29 bp):
TATTTTATTTTTATTTTTATTTATTTATT
Found at i:33376927 original size:17 final size:16
Alignment explanation
Indices: 33376864--33376955 Score: 73
Period size: 17 Copynumber: 5.7 Consensus size: 16
33376854 AATTTTAAAT
*
33376864 TTTATTTCTATTTTTTA
1 TTTATTT-TATTTCTTA
*
33376881 -TTATTTTTATTTATTTA
1 TTTA-TTTTATTT-CTTA
33376898 TTTATTTTATTTCTTA
1 TTTATTTTATTTCTTA
*
33376914 TTGTATTTTATTTCAT-
1 TT-TATTTTATTTCTTA
*
33376930 TTTGTTTTATTT-TTA
1 TTTATTTTATTTCTTA
**
33376945 AATATTTTATT
1 TTTATTTTATT
33376956 ATATTTATAA
Statistics
Matches: 63, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
14 1 0.02
15 17 0.27
16 15 0.24
17 27 0.43
18 3 0.05
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (16 bp):
TTTATTTTATTTCTTA
Found at i:33376955 original size:5 final size:5
Alignment explanation
Indices: 33376862--33376942 Score: 62
Period size: 5 Copynumber: 16.0 Consensus size: 5
33376852 TTAATTTTAA
33376862 ATTTT ATTTCT ATTTT -TTATT ATTTT -TATTT A-TTT A-TTT ATTTT
1 ATTTT ATTT-T ATTTT ATT-TT ATTTT AT-TTT ATTTT ATTTT ATTTT
* * *
33376906 ATTTCTT ATTGT ATTTT ATTTC ATTTT GTTTT ATTTT
1 A-TT-TT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
33376943 TAAATATTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
4 11 0.18
5 37 0.60
6 11 0.18
7 3 0.05
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (5 bp):
ATTTT
Found at i:33378686 original size:36 final size:36
Alignment explanation
Indices: 33378639--33378709 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
33378629 ACAACTGTTA
**
33378639 TTTTCCCTACATGGCTTTAATGCTCCTATTTCAGAC
1 TTTTCCCTACATGGCACTAATGCTCCTATTTCAGAC
33378675 TTTTCCCTACATGGCACTAATGCTCCTATTTCAGA
1 TTTTCCCTACATGGCACTAATGCTCCTATTTCAGA
33378710 ATTACATGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.21, C:0.28, G:0.11, T:0.39
Consensus pattern (36 bp):
TTTTCCCTACATGGCACTAATGCTCCTATTTCAGAC
Found at i:33379729 original size:99 final size:99
Alignment explanation
Indices: 33379552--33379730 Score: 281
Period size: 99 Copynumber: 1.8 Consensus size: 99
33379542 TAATTTCTAA
*
33379552 GAATGTGTTGGGCCGAGTAACCGGGATGAGGTGCTTGGGTTGTCATCTCTCTTCGCGTCAAAAGG
1 GAATGTGCTGGGCCGAGTAACCGGGATGAGGTGCTTGGGTTGTCATCTCTCTTCGCGTCAAAAGG
* *
33379617 TTCGATATGTTCCTAGGAATAATAAAAAAATTAG
66 TGCGATATATTCCTAGGAATAATAAAAAAATTAG
* *
33379651 GAATGTGCTGGGCTGAGTAACCAGGG-TGGGGTGCTTGGGTTGTCATCTCTCTTCGCGTCAAAAG
1 GAATGTGCTGGGCCGAGTAACC-GGGATGAGGTGCTTGGGTTGTCATCTCTCTTCGCGTCAAAAG
33379715 GTGC-AGTATATTCCTA
65 GTGCGA-TATATTCCTA
33379731 AGTAAAAATA
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
98 1 0.01
99 69 0.95
100 3 0.04
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (99 bp):
GAATGTGCTGGGCCGAGTAACCGGGATGAGGTGCTTGGGTTGTCATCTCTCTTCGCGTCAAAAGG
TGCGATATATTCCTAGGAATAATAAAAAAATTAG
Found at i:33379787 original size:10 final size:11
Alignment explanation
Indices: 33379767--33379791 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
33379757 ATTCTATAAC
33379767 AAAAAGAAAAA
1 AAAAAGAAAAA
33379778 AAAAAGAAAAA
1 AAAAAGAAAAA
33379789 AAA
1 AAA
33379792 GTCATATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:33380380 original size:15 final size:15
Alignment explanation
Indices: 33380360--33380389 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
33380350 CATTTTATTT
*
33380360 ATATTAGGATAATTA
1 ATATTAAGATAATTA
33380375 ATATTAAGATAATTA
1 ATATTAAGATAATTA
33380390 TTAGGATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:33382720 original size:37 final size:37
Alignment explanation
Indices: 33382679--33382761 Score: 112
Period size: 37 Copynumber: 2.2 Consensus size: 37
33382669 TTCTACTTGT
* *
33382679 TTGAGTTTCACTCTGTATAACAATAGGATTTGCTAGA
1 TTGAGCTTCACTCAGTATAACAATAGGATTTGCTAGA
* * *
33382716 TTGAGCTTCATTCAGTATAACAGTAGGATTTGCTCGA
1 TTGAGCTTCACTCAGTATAACAATAGGATTTGCTAGA
*
33382753 TTAAGCTTC
1 TTGAGCTTC
33382762 TTTTCGTAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (37 bp):
TTGAGCTTCACTCAGTATAACAATAGGATTTGCTAGA
Found at i:33385206 original size:12 final size:12
Alignment explanation
Indices: 33385189--33385221 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
33385179 CGCCCAGCCC
33385189 ATATTAATTTTT
1 ATATTAATTTTT
33385201 ATATT-ATTTTT
1 ATATTAATTTTT
33385212 ATA-TAATTTT
1 ATATTAATTTT
33385222 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:33388182 original size:104 final size:104
Alignment explanation
Indices: 33388002--33388201 Score: 310
Period size: 104 Copynumber: 1.9 Consensus size: 104
33387992 TTTAAGGTCC
* * *
33388002 AAGCAATTTGAAATGGTAAACTTGTGTTTTAAGGTTCATTTTAAGGCCACATGGCCTAAGACACT
1 AAGCAATTTGAAATGGTAAACTTGAGTTTTAAAGTTCATTTTAAGGCCACATGGCCTAAGACACG
33388067 GGCGTGTGTCTCAGCAGTGTCTAGCACACGGTCGTGTTG
66 GGCGTGTGTCTCAGCAGTGTCTAGCACACGGTCGTGTTG
* * *
33388106 AAGCAATTTGAAATGGTAAACTTGAGTTTTAAAGTTTATTTTGAGGCCACATGGCCTGAGACACG
1 AAGCAATTTGAAATGGTAAACTTGAGTTTTAAAGTTCATTTTAAGGCCACATGGCCTAAGACACG
* * * *
33388171 GGTGTTTGTCTCAGCCGTGTGTAGCACACGG
66 GGCGTGTGTCTCAGCAGTGTCTAGCACACGG
33388202 CCTGGCACGC
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
104 86 1.00
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (104 bp):
AAGCAATTTGAAATGGTAAACTTGAGTTTTAAAGTTCATTTTAAGGCCACATGGCCTAAGACACG
GGCGTGTGTCTCAGCAGTGTCTAGCACACGGTCGTGTTG
Found at i:33393384 original size:19 final size:19
Alignment explanation
Indices: 33393331--33393384 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 19
33393321 ATCGCGTTCA
33393331 ATTTATTTCTAGTATTT-ATT
1 ATTTATTT-TA-TATTTAATT
*
33393351 -TTTATTTGA-ATTTTAATT
1 ATTTATTTTATA-TTTAATT
33393369 ATTTATTTTATATTTA
1 ATTTATTTTATATTTA
33393385 GATTTAATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
16 1 0.04
17 3 0.11
18 4 0.14
19 19 0.68
20 1 0.04
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (19 bp):
ATTTATTTTATATTTAATT
Done.