Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 138 of 335
Found at i:40600390 original size:13 final size:13
Alignment explanation
Indices: 40600374--40600398 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40600364 AATATTAAAT
40600374 AATAATATTTACG
1 AATAATATTTACG
40600387 AATAATATTTAC
1 AATAATATTTAC
40600399 ATACTTACTC
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:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (13 bp):
AATAATATTTACG
Found at i:40600600 original size:20 final size:20
Alignment explanation
Indices: 40600577--40600627 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
40600567 TTTGAAAAAT
40600577 AATATTTATTTTAATTAT-AA
1 AATATTTATTTT-ATTATAAA
* *
40600597 AATATATAATTTATTATAAA
1 AATATTTATTTTATTATAAA
40600617 AATATTTATTT
1 AATATTTATTT
40600628 ATTTTTAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATATTTATTTTATTATAAA
Found at i:40608899 original size:22 final size:23
Alignment explanation
Indices: 40608846--40608900 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
40608836 ACACTTCAAT
40608846 AATATAAATAATATAAAATGTGA
1 AATATAAATAATATAAAATGTGA
*
40608869 AAT-TTAATAATAT-AAATAGT-A
1 AATATAAATAATATAAAAT-GTGA
*
40608890 TATATAAATAA
1 AATATAAATAA
40608901 AATTATTACT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.26
22 17 0.63
23 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (23 bp):
AATATAAATAATATAAAATGTGA
Found at i:40609024 original size:17 final size:17
Alignment explanation
Indices: 40608974--40609031 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
40608964 GGGTGAGAAG
*
40608974 TAAAAGTTTAGGAGGAAAA
1 TAAAAGTTT--GAGGGAAA
*
40608993 TAAAAAGTTT-TGGGAAA
1 T-AAAAGTTTGAGGGAAA
40609010 TAAAAGTTTGAGGGAAA
1 TAAAAGTTTGAGGGAAA
40609027 GTAAA
1 -TAAA
40609032 TGGGGGGTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 8 0.24
17 12 0.36
18 4 0.12
19 1 0.03
20 8 0.24
ACGTcount: A:0.50, C:0.00, G:0.26, T:0.24
Consensus pattern (17 bp):
TAAAAGTTTGAGGGAAA
Found at i:40612533 original size:63 final size:63
Alignment explanation
Indices: 40612427--40612552 Score: 198
Period size: 63 Copynumber: 2.0 Consensus size: 63
40612417 TCCCTTTGGT
*** *
40612427 TATGCACTAGTTGATGGTCTGAGAGTCAATCGATTGTAGAAGTTGGGTAGAATCCGTCTAAAA
1 TATGCACTAGTTGATGGTCTGAGAGTCAATCGACCATAGAAGTTGGGTAGAATCCGACTAAAA
* *
40612490 TATGCACTAGTTGATGGTCTGAGAGTCAATCGACCATATAAGTTGGGTAGAATCTGACTAAAA
1 TATGCACTAGTTGATGGTCTGAGAGTCAATCGACCATAGAAGTTGGGTAGAATCCGACTAAAA
40612553 CAGAAAGGAC
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.29
Consensus pattern (63 bp):
TATGCACTAGTTGATGGTCTGAGAGTCAATCGACCATAGAAGTTGGGTAGAATCCGACTAAAA
Found at i:40613828 original size:20 final size:20
Alignment explanation
Indices: 40613780--40613840 Score: 88
Period size: 19 Copynumber: 3.1 Consensus size: 20
40613770 AGTTGAATAA
40613780 GCTAGCTATAGCCGTAAAAG
1 GCTAGCTATAGCCGTAAAAG
40613800 GCT-GCTATAGCCGTAAAAG
1 GCTAGCTATAGCCGTAAAAG
* * *
40613819 GTTAGCTATAACTGTAAAAG
1 GCTAGCTATAGCCGTAAAAG
40613839 GC
1 GC
40613841 AAGTTTAGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
19 18 0.50
20 18 0.50
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (20 bp):
GCTAGCTATAGCCGTAAAAG
Found at i:40621655 original size:19 final size:19
Alignment explanation
Indices: 40621633--40621669 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
40621623 TCACTATCAC
40621633 CCACTGTAATCAAATTTGT
1 CCACTGTAATCAAATTTGT
40621652 CCACTGTAATCAAATTTG
1 CCACTGTAATCAAATTTG
40621670 AATAATTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (19 bp):
CCACTGTAATCAAATTTGT
Found at i:40624379 original size:124 final size:124
Alignment explanation
Indices: 40624150--40624495 Score: 487
Period size: 124 Copynumber: 2.8 Consensus size: 124
40624140 AACCTTGGTC
* * * * * *
40624150 TCTGCTCATAATTTGGCAATATGCCTCTCATTCGACTCAATGTAAGAGGTGAGTTGATCAATCAT
1 TCTGCTCGTAATTTGGCAACATGCCTTTCATTCGACTCATTATAGGAGGTGAGTTGATCAATCAT
* * *
40624215 TCGTTCTTGAATGCTTGTGGGAATAGACTTGGGGCTTGAGCTAGTGAGCACTCATTGAG
66 TCGTTCTTGAATGCTTGTGGGAATAGCCTTGGGACCTGAGCTAGTGAGCACTCATTGAG
40624274 TCTGCTCGTAATTTGGCAACATGCCTTTCATTCGACTCATTATAGGAGGTGAGTTGATCAATCAT
1 TCTGCTCGTAATTTGGCAACATGCCTTTCATTCGACTCATTATAGGAGGTGAGTTGATCAATCAT
* * * * *
40624339 TCGTTCTTGAATACTTGTGGGAGTAGCCTTTGGACCTGAGCTAGTGAGCATTCCTTGAG
66 TCGTTCTTGAATGCTTGTGGGAATAGCCTTGGGACCTGAGCTAGTGAGCACTCATTGAG
* * * * * *
40624398 TCTGCTCGTAATCTGGAAACATGCCTCTT-ATTCTACTCATTATAGAAGGTGAGTAGATTAATCA
1 TCTGCTCGTAATTTGGCAACATGCCT-TTCATTCGACTCATTATAGGAGGTGAGTTGATCAATCA
*
40624462 TTCATTCTTGAATGCTTGTGGGAATAGCCTTGGG
65 TTCGTTCTTGAATGCTTGTGGGAATAGCCTTGGG
40624496 GCCACTCCTT
Statistics
Matches: 197, Mismatches: 24, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
124 195 0.99
125 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (124 bp):
TCTGCTCGTAATTTGGCAACATGCCTTTCATTCGACTCATTATAGGAGGTGAGTTGATCAATCAT
TCGTTCTTGAATGCTTGTGGGAATAGCCTTGGGACCTGAGCTAGTGAGCACTCATTGAG
Found at i:40624596 original size:110 final size:110
Alignment explanation
Indices: 40624403--40624608 Score: 301
Period size: 110 Copynumber: 1.9 Consensus size: 110
40624393 TTGAGTCTGC
* * **
40624403 TCGTAATCTGGAAACATGCCTCTTATTCTACTCATTATAGAAGGTGAGTAGATTAATCATTCATT
1 TCGTAATCTGGAAACATGCCTCTCATTCTAATCATTATAGAAGGTGAGTAGACCAATCATTCATT
* *
40624468 CTTGAATGCTTGTGGGAATAGCCTTGGGGCCACTCCTTAAGGCTA
66 CTTGAATGCCTGTGGGAATAACCTTGGGGCCACTCCTTAAGGCTA
*
40624513 TCGTAATCTGGAAACATGCCTCTCATT-TGAATCACTT-TA-AGAGGTGAGTTGACCAATCATTC
1 TCGTAATCTGGAAACATGCCTCTCATTCT-AATCA-TTATAGA-AGGTGAGTAGACCAATCATTC
40624575 ATTCTTGAATGCCTGTGGGAATAACCTTGGGGCC
63 ATTCTTGAATGCCTGTGGGAATAACCTTGGGGCC
40624609 TGAAGTAATC
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
109 2 0.02
110 82 0.95
111 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (110 bp):
TCGTAATCTGGAAACATGCCTCTCATTCTAATCATTATAGAAGGTGAGTAGACCAATCATTCATT
CTTGAATGCCTGTGGGAATAACCTTGGGGCCACTCCTTAAGGCTA
Found at i:40629068 original size:29 final size:29
Alignment explanation
Indices: 40628996--40629071 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
40628986 ACCAGTACAT
* * * *
40628996 AGTACCTGATAATTATAACACTGGTACAA
1 AGTACCTGATAACTGTAACACTAGCACAA
*
40629025 AGTGCCTGATAACTGTAACACTAGCACAA
1 AGTACCTGATAACTGTAACACTAGCACAA
*
40629054 AGTACCTAATAACTGTAA
1 AGTACCTGATAACTGTAA
40629072 TCACCGGCAC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (29 bp):
AGTACCTGATAACTGTAACACTAGCACAA
Found at i:40633810 original size:94 final size:94
Alignment explanation
Indices: 40633710--40633989 Score: 234
Period size: 94 Copynumber: 3.1 Consensus size: 94
40633700 TCTGGATATT
40633710 TGAATGAAATATATGACTAACAAGAGTGATGAAGATATGTGTTAGGGCTTGTGATCAAATTGGTT
1 TGAATGAAATATATGACTAACAAGAGTGATGAAGATATGTGTTAGGGCTTGTGATCAAATTGGTT
40633775 GATTGTGTCTTGCATGTTTATCTTGAACA
66 GATTGTGTCTTGCATGTTTATCTTGAACA
* * * * ** * *
40633804 TGAATG-AATGGTAAG-TTAATTACCA-TG-T-AAG-TATATG-TA----TATG-GA--AATTTG
1 TGAATGAAAT-ATATGACTAA-CAAGAGTGATGAAGATATGTGTTAGGGCT-TGTGATCAAATTG
* * * * * **
40633855 GTT-ATTGTTGAGCCCATACAT-ATT-TCTAGAATT
63 GTTGATTG-T--G-TCTTGCATGTTTATCTTGAACA
*
40633888 TGAATGAAATATATGACTAACAAGAGTGATGAGGATATGTGTTAGGGCTTGTGATCAAATTGGTT
1 TGAATGAAATATATGACTAACAAGAGTGATGAAGATATGTGTTAGGGCTTGTGATCAAATTGGTT
40633953 GATTGTGTCTTGCATGTTTATCTTGAACA
66 GATTGTGTCTTGCATGTTTATCTTGAACA
40633982 TGAATGAA
1 TGAATGAA
40633990 TGGTAAGTTA
Statistics
Matches: 131, Mismatches: 31, Indels: 48
0.62 0.15 0.23
Matches are distributed among these distances:
82 4 0.03
83 9 0.07
84 17 0.13
85 14 0.11
86 8 0.06
87 2 0.02
88 5 0.04
89 4 0.03
90 5 0.04
91 3 0.02
92 8 0.06
93 14 0.11
94 25 0.19
95 9 0.07
96 4 0.03
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.37
Consensus pattern (94 bp):
TGAATGAAATATATGACTAACAAGAGTGATGAAGATATGTGTTAGGGCTTGTGATCAAATTGGTT
GATTGTGTCTTGCATGTTTATCTTGAACA
Found at i:40633953 original size:178 final size:179
Alignment explanation
Indices: 40633653--40634009 Score: 689
Period size: 178 Copynumber: 2.0 Consensus size: 179
40633643 ATGATGTGGA
*
40633653 AAGTATATGTATATGGAAATTTGGTTATTGTTGAGCCCATACATATTTCTGGATATTTGAATGAA
1 AAGTATATGTATATGGAAATTTGGTTATTGTTGAGCCCATACATATTTCTAGATATTTGAATGAA
40633718 ATATATGACTAACAAGAGTGATGAAGATATGTGTTAGGGCTTGTGATCAAATTGGTTGATTGTGT
66 ATATATGACTAACAAGAGTGATGAAGATATGTGTTAGGGCTTGTGATCAAATTGGTTGATTGTGT
40633783 CTTGCATGTTTATCTTGAACATGAATGAATGGTAAGTTAATTACCATGT
131 CTTGCATGTTTATCTTGAACATGAATGAATGGTAAGTTAATTACCATGT
40633832 AAGTATATGTATATGGAAATTTGGTTATTGTTGAGCCCATACATATTTCTAGA-ATTTGAATGAA
1 AAGTATATGTATATGGAAATTTGGTTATTGTTGAGCCCATACATATTTCTAGATATTTGAATGAA
*
40633896 ATATATGACTAACAAGAGTGATGAGGATATGTGTTAGGGCTTGTGATCAAATTGGTTGATTGTGT
66 ATATATGACTAACAAGAGTGATGAAGATATGTGTTAGGGCTTGTGATCAAATTGGTTGATTGTGT
40633961 CTTGCATGTTTATCTTGAACATGAATGAATGGTAAGTTAATTACCATGT
131 CTTGCATGTTTATCTTGAACATGAATGAATGGTAAGTTAATTACCATGT
40634010 TATACGAACT
Statistics
Matches: 176, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
178 124 0.70
179 52 0.30
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.38
Consensus pattern (179 bp):
AAGTATATGTATATGGAAATTTGGTTATTGTTGAGCCCATACATATTTCTAGATATTTGAATGAA
ATATATGACTAACAAGAGTGATGAAGATATGTGTTAGGGCTTGTGATCAAATTGGTTGATTGTGT
CTTGCATGTTTATCTTGAACATGAATGAATGGTAAGTTAATTACCATGT
Found at i:40634047 original size:28 final size:28
Alignment explanation
Indices: 40634005--40634067 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
40633995 AGTTAATTAC
*
40634005 CATG-TTATACGAACTTACTAAACATTT
1 CATGCTTATACAAACTTACTAAACATTT
*
40634032 CATGCTTATACAAACTTACTAAGCATTT
1 CATGCTTATACAAACTTACTAAACATTT
40634060 CATGCTTA
1 CATGCTTA
40634068 CTCTATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
27 4 0.12
28 29 0.88
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.37
Consensus pattern (28 bp):
CATGCTTATACAAACTTACTAAACATTT
Found at i:40637790 original size:2 final size:2
Alignment explanation
Indices: 40637783--40637815 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
40637773 AAAGATATGA
40637783 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40637816 ACTTTTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40639194 original size:2 final size:2
Alignment explanation
Indices: 40639187--40639222 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
40639177 ACAGTTGTAT
40639187 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40639223 AAAGAGAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40647630 original size:2 final size:2
Alignment explanation
Indices: 40647623--40647654 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
40647613 TTTATACCAA
40647623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40647655 CAATTACCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40652576 original size:2 final size:2
Alignment explanation
Indices: 40652571--40652599 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
40652561 CATATATAGG
40652571 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40652600 GCCTTATGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40653226 original size:30 final size:30
Alignment explanation
Indices: 40653192--40653251 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
40653182 TTATAGGCTG
40653192 AATAAAATATGTAATCAAAGCTTAATTAGT
1 AATAAAATATGTAATCAAAGCTTAATTAGT
40653222 AATAAAATATGTAATCAAAGCTTAATTAGT
1 AATAAAATATGTAATCAAAGCTTAATTAGT
40653252 CTAGTTTCTT
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:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (30 bp):
AATAAAATATGTAATCAAAGCTTAATTAGT
Found at i:40653861 original size:48 final size:48
Alignment explanation
Indices: 40653790--40654173 Score: 619
Period size: 48 Copynumber: 8.0 Consensus size: 48
40653780 GAAGATAAAT
* * *
40653790 ATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* * *
40653838 ATATGTATGTGTGGTAAAGCCGAATAGCTAATATGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
40653886 ATATATATATGTGGTAAAGCCGAATGACTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
40653934 --ATGTATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
40653980 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
40654028 ATATGTATATGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
40654076 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
40654124 ATATGTATATTTGGTAAAGCCGAATGGCTAATGTGAAATATGTAGGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
40654172 AT
1 AT
40654174 GTGTGTATAT
Statistics
Matches: 315, Mismatches: 19, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
46 43 0.14
48 272 0.86
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:40654122 original size:190 final size:191
Alignment explanation
Indices: 40653790--40654173 Score: 635
Period size: 190 Copynumber: 2.0 Consensus size: 191
40653780 GAAGATAAAT
* *
40653790 ATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATGTGTGGTAA
1 ATATATATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAA
*
40653855 AGCCGAATAGCTAATATGAAATATGTATGAGATATATATATGTGGTAAAGCCGAATGACTAATGT
66 AGCCAAATAGCTAATATGAAATATGTATGAGATATATATATGTGGTAAAGCCGAATGACTAATGT
*
40653920 GAAATATGTATGAG-ATGTATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTATGAG
131 GAAATATGTATGAGAATGTATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTAGGAG
*
40653980 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAA
1 ATATATATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAA
* * * * * *
40654045 AGCCAAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGT
66 AGCCAAATAGCTAATATGAAATATGTATGAGATATATATATGTGGTAAAGCCGAATGACTAATGT
* *
40654110 GAAATATGTATGAGATATGTATATTTGGTAAAGCCGAATGGCTAATGTGAAATATGTAGGAG
131 GAAATATGTATGAGA-ATGTATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTAGGAG
40654172 AT
1 AT
40654174 GTGTGTATAT
Statistics
Matches: 179, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
190 134 0.75
192 45 0.25
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (191 bp):
ATATATATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAA
AGCCAAATAGCTAATATGAAATATGTATGAGATATATATATGTGGTAAAGCCGAATGACTAATGT
GAAATATGTATGAGAATGTATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTAGGAG
Found at i:40654364 original size:37 final size:37
Alignment explanation
Indices: 40654314--40654416 Score: 179
Period size: 37 Copynumber: 2.8 Consensus size: 37
40654304 GGAAATATAT
*
40654314 TCCGGGTAAGACCCAATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
40654351 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
40654388 TCCGGGTAAGACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
40654417 GGACTATTCG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:40658921 original size:43 final size:44
Alignment explanation
Indices: 40658858--40658941 Score: 134
Period size: 43 Copynumber: 1.9 Consensus size: 44
40658848 ATCGAAATAT
*
40658858 GATATTCGGGCTTCGGGCCTAGCAGGCTATAATGCCAGTGAGAC
1 GATATTCGGGCTTCGAGCCTAGCAGGCTATAATGCCAGTGAGAC
* *
40658902 GATA-TCGGGCTTTGAGCCTAGCAGGCTATAATGCCGGTGA
1 GATATTCGGGCTTCGAGCCTAGCAGGCTATAATGCCAGTGA
40658942 AATAAAATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
43 33 0.89
44 4 0.11
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (44 bp):
GATATTCGGGCTTCGAGCCTAGCAGGCTATAATGCCAGTGAGAC
Found at i:40659283 original size:38 final size:40
Alignment explanation
Indices: 40659222--40659302 Score: 112
Period size: 38 Copynumber: 2.1 Consensus size: 40
40659212 ATTTGATGTG
* * *
40659222 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTATTA
1 TATCCGGGCTTAAAGACCCGCAGGCCTAGTACTGGTATTA
*
40659262 TATCCGGG-TTAAA-TCCCGCAGGCCTAGTACTGGTATTA
1 TATCCGGGCTTAAAGACCCGCAGGCCTAGTACTGGTATTA
40659300 TAT
1 TAT
40659303 TCAGGCCTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
38 24 0.65
39 5 0.14
40 8 0.22
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (40 bp):
TATCCGGGCTTAAAGACCCGCAGGCCTAGTACTGGTATTA
Found at i:40659355 original size:45 final size:45
Alignment explanation
Indices: 40659299--40659413 Score: 146
Period size: 45 Copynumber: 2.6 Consensus size: 45
40659289 TACTGGTATT
* * *
40659299 ATATTCAGGCCTTTGAGCCTAGCAGGCTATTATGCCAGTGAGAT-
1 ATATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCAGTGACATG
* *
40659343 ACTATTCGGGCCTTTGAGCCTAGTAGGCTATAATGCCGGTGACATG
1 A-TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCAGTGACATG
*
40659389 ATA-TCGAGCC-TTGAGCCTAGCAGGC
1 ATATTCGGGCCTTTGAGCCTAGCAGGC
40659414 GAAATGCTGG
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
43 14 0.23
44 7 0.11
45 40 0.65
46 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (45 bp):
ATATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCAGTGACATG
Found at i:40664803 original size:30 final size:30
Alignment explanation
Indices: 40664769--40664837 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
40664759 CACGGGTAGA
40664769 GACACGGCCGCGTGTCTCAGCAGTGTAGGG
1 GACACGGCCGCGTGTCTCAGCAGTGTAGGG
* * *
40664799 GACACGGCCGTGTGTCTCAGCTGTGTGGGG
1 GACACGGCCGCGTGTCTCAGCAGTGTAGGG
40664829 GACACGGCC
1 GACACGGCC
40664838 TTAGCACATG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.14, C:0.28, G:0.41, T:0.17
Consensus pattern (30 bp):
GACACGGCCGCGTGTCTCAGCAGTGTAGGG
Found at i:40667433 original size:26 final size:26
Alignment explanation
Indices: 40667404--40667457 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
40667394 CCCTAGCCAC
40667404 CAATATAACTCACGAAGGTCTTGGTA
1 CAATATAACTCACGAAGGTCTTGGTA
*
40667430 CAATATAACTCATGAAGGTCTTGGTA
1 CAATATAACTCACGAAGGTCTTGGTA
40667456 CA
1 CA
40667458 TCTTATTTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (26 bp):
CAATATAACTCACGAAGGTCTTGGTA
Found at i:40670946 original size:25 final size:23
Alignment explanation
Indices: 40670916--40670972 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 23
40670906 TTAACTATAG
40670916 TTTTCAGTATGTACTAACTAGAGTA
1 TTTTCAGTA--TACTAACTAGAGTA
*
40670941 TTTTCACAGTATACTAACTATAGTA
1 TTTT--CAGTATACTAACTAGAGTA
*
40670966 GTTTCAG
1 TTTTCAG
40670973 GATAGCATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 3 0.11
25 20 0.71
27 5 0.18
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (23 bp):
TTTTCAGTATACTAACTAGAGTA
Found at i:40673989 original size:23 final size:23
Alignment explanation
Indices: 40673963--40674007 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
40673953 TAGGTATGTG
*
40673963 ATGACGTTATCTT-ATAAATATGC
1 ATGAAGTTATCTTGA-AAATATGC
*
40673986 ATGAATTTATCTTGAAAATATG
1 ATGAAGTTATCTTGAAAATATG
40674008 TTGAATTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (23 bp):
ATGAAGTTATCTTGAAAATATGC
Found at i:40674808 original size:34 final size:34
Alignment explanation
Indices: 40674750--40674829 Score: 115
Period size: 34 Copynumber: 2.4 Consensus size: 34
40674740 CCATCTCAAT
* * *
40674750 ACAGTATCAATATGCAGTAAGGCCTTAGCCCATC
1 ACAGTATCAGTATACAGTAAGGCCTTAGCCCATA
* *
40674784 ACAGTATCAGTATACATTAGGGCCTTAGCCCATA
1 ACAGTATCAGTATACAGTAAGGCCTTAGCCCATA
40674818 ACAGTATCAGTA
1 ACAGTATCAGTA
40674830 GCAATCATGC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (34 bp):
ACAGTATCAGTATACAGTAAGGCCTTAGCCCATA
Found at i:40675418 original size:12 final size:12
Alignment explanation
Indices: 40675399--40675432 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
40675389 AGGCCGTGTG
40675399 CAACCACACGGC
1 CAACCACACGGC
* *
40675411 CTACCACACGGG
1 CAACCACACGGC
40675423 CAACCACACG
1 CAACCACACG
40675433 CTTGTGTGGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.32, C:0.47, G:0.18, T:0.03
Consensus pattern (12 bp):
CAACCACACGGC
Found at i:40679701 original size:22 final size:21
Alignment explanation
Indices: 40679671--40679736 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 21
40679661 TACAAATTAA
40679671 ATCTCCAAGATTACAAGATCAT
1 ATCTCCAAGATTAC-AGATCAT
* * *
40679693 ATCTTCAAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
* *
40679714 ATCT--AAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
40679733 ATCT
1 ATCT
40679737 AAGATTGTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
19 19 0.46
21 10 0.24
22 12 0.29
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (21 bp):
ATCTCCAAGATTACAGATCAT
Found at i:40679723 original size:19 final size:19
Alignment explanation
Indices: 40679688--40679785 Score: 164
Period size: 19 Copynumber: 5.2 Consensus size: 19
40679678 AGATTACAAG
40679688 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
40679709 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
40679728 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
40679745 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
40679764 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
40679783 ATC
1 ATC
40679786 CTTAAAGATT
Statistics
Matches: 75, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.23
19 49 0.65
20 1 0.01
21 8 0.11
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:40679752 original size:36 final size:37
Alignment explanation
Indices: 40679688--40679785 Score: 153
Period size: 36 Copynumber: 2.6 Consensus size: 37
40679678 AGATTACAAG
40679688 ATCATATCTTCAAGATTGCATATCATATCTAAGATTGCAT
1 ATCATATC-T-AAGATTG-ATATCATATCTAAGATTGCAT
40679728 ATCATATCTAAGATTG-TATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGATATCATATCTAAGATTGCAT
40679764 ATCATATCTAAGATTGCATATC
1 ATCATATCTAAGATTG-ATATC
40679786 CTTAAAGATT
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
36 36 0.64
38 11 0.20
39 1 0.02
40 8 0.14
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (37 bp):
ATCATATCTAAGATTGATATCATATCTAAGATTGCAT
Found at i:40679939 original size:21 final size:20
Alignment explanation
Indices: 40679902--40679940 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
40679892 GAACTTGGAC
**
40679902 TTTTTTTTTGGGTTTATTGT
1 TTTTTTTTTGGACTTATTGT
40679922 TTTTGTTTTTGGACTTATT
1 TTTT-TTTTTGGACTTATT
40679941 TCTGGGCCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.08, C:0.03, G:0.18, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTGGACTTATTGT
Found at i:40680018 original size:28 final size:28
Alignment explanation
Indices: 40679974--40680058 Score: 116
Period size: 28 Copynumber: 3.0 Consensus size: 28
40679964 GTCTACAAAA
* *
40679974 GTGATTAGGCCTAATGGGCCATATGAAT
1 GTGATTGGGCCTGATGGGCCATATGAAT
40680002 GTGATTGGGCCTGATGGGCCATATGAAT
1 GTGATTGGGCCTGATGGGCCATATGAAT
* * *
40680030 GAGATTGGGCCTGAAGGGGCCAAATGAAT
1 GTGATTGGGCCTG-ATGGGCCATATGAAT
40680059 AAGTATGGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 38 0.75
29 13 0.25
ACGTcount: A:0.27, C:0.14, G:0.34, T:0.25
Consensus pattern (28 bp):
GTGATTGGGCCTGATGGGCCATATGAAT
Found at i:40689331 original size:11 final size:11
Alignment explanation
Indices: 40689315--40689339 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40689305 ATTAAATAAT
40689315 AATAAAAATTA
1 AATAAAAATTA
40689326 AATAAAAATTA
1 AATAAAAATTA
40689337 AAT
1 AAT
40689340 TGCAAGGAAA
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAAAAATTA
Found at i:40697121 original size:16 final size:16
Alignment explanation
Indices: 40697111--40697153 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
40697101 TGAAATGCCT
40697111 AAAAGCCGAAATACCG
1 AAAAGCCGAAATACCG
*
40697127 AAAAGCTGAAATACCG
1 AAAAGCCGAAATACCG
*
40697143 AAAAACCGAAA
1 AAAAGCCGAAA
40697154 GTTTGGCTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.56, C:0.21, G:0.16, T:0.07
Consensus pattern (16 bp):
AAAAGCCGAAATACCG
Found at i:40697380 original size:28 final size:28
Alignment explanation
Indices: 40697347--40697449 Score: 143
Period size: 28 Copynumber: 3.7 Consensus size: 28
40697337 ATTGCATGAC
* *
40697347 TATGAATGTGATTGGGCTTGACGGGCCA
1 TATGAATGTGATTGGGCCTGATGGGCCA
* *
40697375 TATGAAAGTGATTGGGCCTAATGGGCCA
1 TATGAATGTGATTGGGCCTGATGGGCCA
* *
40697403 TATGAATTTGATTGGGCCCGATGGGCCA
1 TATGAATGTGATTGGGCCTGATGGGCCA
*
40697431 TATGAATGAGATTGGGCCT
1 TATGAATGTGATTGGGCCT
40697450 AAAAGGGCCA
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 64 1.00
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.28
Consensus pattern (28 bp):
TATGAATGTGATTGGGCCTGATGGGCCA
Found at i:40697415 original size:56 final size:57
Alignment explanation
Indices: 40697347--40697466 Score: 161
Period size: 56 Copynumber: 2.1 Consensus size: 57
40697337 ATTGCATGAC
** * *
40697347 TATGAATGTGATTGGGCTTGACGGGCCATATGAAAGTGATTGGGCCT-AATGGGCCA
1 TATGAATGTGATTGGGCCCGACGGGCCATATGAAAGAGATTGGGCCTAAAAGGGCCA
* * *
40697403 TATGAATTTGATTGGGCCCGATGGGCCATATGAATGAGATTGGGCCTAAAAGGGCCA
1 TATGAATGTGATTGGGCCCGACGGGCCATATGAAAGAGATTGGGCCTAAAAGGGCCA
*
40697460 AATGAAT
1 TATGAAT
40697467 AAGTATGGAT
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
56 41 0.75
57 14 0.25
ACGTcount: A:0.28, C:0.14, G:0.32, T:0.26
Consensus pattern (57 bp):
TATGAATGTGATTGGGCCCGACGGGCCATATGAAAGAGATTGGGCCTAAAAGGGCCA
Found at i:40698719 original size:18 final size:17
Alignment explanation
Indices: 40698698--40698731 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40698688 TTTGAAGAAG
40698698 GGTTTTCAAATAAAACAA
1 GGTTTTC-AATAAAACAA
*
40698716 GGTTTTCGATAAAACA
1 GGTTTTCAATAAAACA
40698732 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (17 bp):
GGTTTTCAATAAAACAA
Found at i:40700193 original size:16 final size:16
Alignment explanation
Indices: 40700172--40700206 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
40700162 GTTTGTATAA
40700172 AACCAAATTACACTCT
1 AACCAAATTACACTCT
40700188 AACCAAATTACACTCT
1 AACCAAATTACACTCT
40700204 AAC
1 AAC
40700207 AAGTTCCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (16 bp):
AACCAAATTACACTCT
Found at i:40701912 original size:224 final size:224
Alignment explanation
Indices: 40701522--40701941 Score: 718
Period size: 224 Copynumber: 1.9 Consensus size: 224
40701512 ATGGAGTAAG
*
40701522 CATATAAAAACCTTAGTAAGTTCATAGGTATTAAAAAAAACTTACCTTATCTTTCATTTAAATAC
1 CATATAAAAACCTTAGTAAGTTCATAGGTATTAAAAAAAACTTACATTATCTTTCATTTAAATAC
*
40701587 AATAAGCTACCATATTGTTGGCATAGTTTGGCTAGACATGGCAATTCAGAACATTAACTAGGTGA
66 AATAAGCTACCATATTGTTGGCATAGTTTGGCTAGACATGGCAATTCACAACATTAACTAGGTGA
* *
40701652 GTATTAACTTGTAAATAAAACATATGACACCACAAACACATATCATTCTAATTGATCATGCCTCG
131 GTATTAACTTGTAAATAAAACATATGACACCACAAACACATATCATGCCAATTGATCATGCCTCG
40701717 ATGTGCGTGCATCGGGGCTCGTAAATCTA
196 ATGTGCGTGCATCGGGGCTCGTAAATCTA
**
40701746 CATATAAAATGCTTAGTAAGTTCATAGGTATTAAACAAAAACTTACATTATCTTTCATTTAAATA
1 CATATAAAAACCTTAGTAAGTTCATAGGTATTAAA-AAAAACTTACATTATCTTTCATTTAAATA
*
40701811 -AATTAAGCTATCATATTGTTGGCATAGTTTGGCTAGACATGGCAATTCACAACATTAACTAGGT
65 CAA-TAAGCTACCATATTGTTGGCATAGTTTGGCTAGACATGGCAATTCACAACATTAACTAGGT
* * *
40701875 -TGTATTAACTTGTAAATAAAATATATGACACCACAAACACATATCATGCCAATTGATCGTGCCT
129 GAGTATTAACTTGTAAATAAAACATATGACACCACAAACACATATCATGCCAATTGATCATGCCT
40701939 CGA
194 CGA
40701942 CGTGTATGCG
Statistics
Matches: 184, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
224 97 0.53
225 87 0.47
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (224 bp):
CATATAAAAACCTTAGTAAGTTCATAGGTATTAAAAAAAACTTACATTATCTTTCATTTAAATAC
AATAAGCTACCATATTGTTGGCATAGTTTGGCTAGACATGGCAATTCACAACATTAACTAGGTGA
GTATTAACTTGTAAATAAAACATATGACACCACAAACACATATCATGCCAATTGATCATGCCTCG
ATGTGCGTGCATCGGGGCTCGTAAATCTA
Found at i:40703560 original size:26 final size:26
Alignment explanation
Indices: 40703531--40703584 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
40703521 TTGGTATAGG
40703531 TATGTTTTGACCATGTTTAAAACACT
1 TATGTTTTGACCATGTTTAAAACACT
*
40703557 TATGTTTTGACCATGTTTAAAATACT
1 TATGTTTTGACCATGTTTAAAACACT
40703583 TA
1 TA
40703585 GATAGGTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.44
Consensus pattern (26 bp):
TATGTTTTGACCATGTTTAAAACACT
Found at i:40713535 original size:2 final size:2
Alignment explanation
Indices: 40713489--40713518 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
40713479 AGCAGATGTT
40713489 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40713519 AATCTATGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40722132 original size:75 final size:75
Alignment explanation
Indices: 40722009--40722159 Score: 266
Period size: 75 Copynumber: 2.0 Consensus size: 75
40721999 TCAGATGACA
*
40722009 AGACAAAGTACACTTTTGAACTATTTCAAAGGTTTTTTGAAGAGTCAAGGGTTGAACACCAATTC
1 AGACAAAGTACACTTTTGAACTATTTCAAAGGTTTTGTGAAGAGTCAAGGGTTGAACACCAATTC
40722074 ACCAACACCT
66 ACCAACACCT
* * *
40722084 AGACAAAGTACACTTTTGAATTGTTTCAAAGGTTTTGTGAAGAGTCAAGGGTTGAACACCAGTTC
1 AGACAAAGTACACTTTTGAACTATTTCAAAGGTTTTGTGAAGAGTCAAGGGTTGAACACCAATTC
40722149 ACCAACACCT
66 ACCAACACCT
40722159 A
1 A
40722160 CACACCTCAA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (75 bp):
AGACAAAGTACACTTTTGAACTATTTCAAAGGTTTTGTGAAGAGTCAAGGGTTGAACACCAATTC
ACCAACACCT
Found at i:40726896 original size:24 final size:25
Alignment explanation
Indices: 40726869--40726922 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
40726859 TAGACAAGTC
40726869 ACATTTTCG-TATAATATTTTAACA
1 ACATTTTCGTTATAATATTTTAACA
* * * *
40726893 ACA-TCTCGTTATCATATTTTTACT
1 ACATTTTCGTTATAATATTTTAACA
40726917 ACATTT
1 ACATTT
40726923 CCCTTTTTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
23 4 0.17
24 18 0.78
25 1 0.04
ACGTcount: A:0.31, C:0.17, G:0.04, T:0.48
Consensus pattern (25 bp):
ACATTTTCGTTATAATATTTTAACA
Found at i:40727081 original size:34 final size:34
Alignment explanation
Indices: 40727003--40727097 Score: 118
Period size: 34 Copynumber: 2.8 Consensus size: 34
40726993 TGGTGACTTG
* * * * *
40727003 TAACAACATATTCAACCAACACACTAGTGGCTTA
1 TAACAACATATCCAACCAACACACCAATAGCTCA
40727037 TAACAACATATCCAACCAACACACCAATAGCTCA
1 TAACAACATATCCAACCAACACACCAATAGCTCA
* * *
40727071 TAAGAGCATATCCATCCAACACACCAA
1 TAACAACATATCCAACCAACACACCAA
40727098 GGCACATAAG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.44, C:0.32, G:0.06, T:0.18
Consensus pattern (34 bp):
TAACAACATATCCAACCAACACACCAATAGCTCA
Found at i:40727136 original size:54 final size:54
Alignment explanation
Indices: 40727077--40727179 Score: 143
Period size: 54 Copynumber: 1.9 Consensus size: 54
40727067 CTCATAAGAG
*
40727077 CATATCCATCCAACACACCAAGGCACATAAGTGCAAGACCCAAAGGCATCATAT
1 CATATCCATCCAACACACCAAGGAACATAAGTGCAAGACCCAAAGGCATCATAT
* ** * * *
40727131 CATATCCTTTTAACATACCAAGGAACGTAAGTGCAAGACCCGAAGGCAT
1 CATATCCATCCAACACACCAAGGAACATAAGTGCAAGACCCAAAGGCAT
40727180 ATAACTCTGT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 42 1.00
ACGTcount: A:0.39, C:0.28, G:0.16, T:0.17
Consensus pattern (54 bp):
CATATCCATCCAACACACCAAGGAACATAAGTGCAAGACCCAAAGGCATCATAT
Found at i:40730253 original size:11 final size:11
Alignment explanation
Indices: 40730237--40730272 Score: 54
Period size: 11 Copynumber: 3.1 Consensus size: 11
40730227 GATTGGTTAG
40730237 AATATTTTATT
1 AATATTTTATT
40730248 AATATTTTATCAT
1 AATATTTTAT--T
40730261 AATATTTTATT
1 AATATTTTATT
40730272 A
1 A
40730273 TAAGAAGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 12 0.52
13 11 0.48
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (11 bp):
AATATTTTATT
Found at i:40730265 original size:13 final size:12
Alignment explanation
Indices: 40730237--40730275 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
40730227 GATTGGTTAG
40730237 AATATTTTAT-T
1 AATATTTTATAT
40730248 AATATTTTATCAT
1 AATATTTTAT-AT
40730261 AATATTTTATTAT
1 AATATTTTA-TAT
40730274 AA
1 AA
40730276 GAAGTTGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.40
13 14 0.56
14 1 0.04
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (12 bp):
AATATTTTATAT
Found at i:40733560 original size:48 final size:48
Alignment explanation
Indices: 40733404--40733611 Score: 260
Period size: 48 Copynumber: 4.3 Consensus size: 48
40733394 TATGTGTGCT
* * * * *
40733404 AGTGTAAGACATGTCTAGGACATGCATTGGCCAC-A-TTATGA-GAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATAT-ACAAGCC
* *
40733450 AGTATAAGACATGTTTGGGACATGCATCGGCCTCGAGATATATACAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAG--ATATACAAGCC
*
40733500 AGTGTAAGACATGTCTGGGACATGCATCGGCCTTGAGATATACAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACAAGCC
* * *
40733548 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAAATATACAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACAAGCC
*
40733596 AGTGTAAGACCTGTCT
1 AGTGTAAGACATGTCT
40733612 AGAACATGGC
Statistics
Matches: 142, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
46 29 0.20
47 1 0.01
48 70 0.49
49 1 0.01
50 41 0.29
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACAAGCC
Found at i:40733697 original size:49 final size:49
Alignment explanation
Indices: 40733441--40733811 Score: 187
Period size: 48 Copynumber: 7.7 Consensus size: 49
40733431 TGGCCACATT
* * * * * * *
40733441 ATGAGAGCCAGTATAAGACATGTTTGGGACAT-GCATCGGCCTCGAGATAT
1 ATGAAAGCCAGTGTAAGACCTATCTGGGACATGGCATCGACCTC--GATAG
* * * * * *
40733491 AT-ACAAGCCAGTGTAAGACATGTCTGGGACAT-GCATCGGCCTTGAGAT
1 ATGA-AAGCCAGTGTAAGACCTATCTGGGACATGGCATCGACCTCGATAG
* * * *
40733539 AT-ACAAGCCAGTGTAAGACATGTCTGGGACAT-GCATC-AGCCTCGAAAT
1 ATGA-AAGCCAGTGTAAGACCTATCTGGGACATGGCATCGA-CCTCGATAG
* * * * * * *
40733587 AT-ACAAGCTAGTGTAAGACCTGTCTAGAACATGGCATC-AGCTTG-TTG
1 ATGA-AAGCCAGTGTAAGACCTATCTGGGACATGGCATCGACCTCGATAG
* *
40733634 -TG--TGTCAGTGTAAGACCTATCTGGGACATGGCATCGACAC-CGATAG
1 ATGAAAGCCAGTGTAAGACCTATCTGGGACATGGCATCGAC-CTCGATAG
* * * * * * *
40733680 ATGAGAGCCAGTGTAAGACCTGTCTGGGACATGACATTGGCCTTGATAT
1 ATGAAAGCCAGTGTAAGACCTATCTGGGACATGGCATCGACCTCGATAG
** * * *
40733729 ATGAAATTCAGTGTAAGACCTATCTGGGACATGGCAGCGACTTTGAT-G
1 ATGAAAGCCAGTGTAAGACCTATCTGGGACATGGCATCGACCTCGATAG
** * *
40733777 -TGCTAGCCAGTGTAAGACCATGTTTGGGACATGGC
1 ATGAAAGCCAGTGTAAGACC-TATCTGGGACATGGC
40733812 GTCGGCATCT
Statistics
Matches: 259, Mismatches: 50, Indels: 26
0.77 0.15 0.08
Matches are distributed among these distances:
44 27 0.10
45 2 0.01
46 4 0.02
47 17 0.07
48 93 0.36
49 79 0.31
50 37 0.14
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.25
Consensus pattern (49 bp):
ATGAAAGCCAGTGTAAGACCTATCTGGGACATGGCATCGACCTCGATAG
Found at i:40737393 original size:39 final size:40
Alignment explanation
Indices: 40737350--40737442 Score: 118
Period size: 39 Copynumber: 2.4 Consensus size: 40
40737340 CGTTTAAATG
*
40737350 AAAAACGCCGCTAAAGAAT-GAGTATTAGCAGCAC-TTTTT
1 AAAAACGCCGCTAAA-AATCAAGTATTAGCAGCACTTTTTT
* * * *
40737389 AAAAACGTCGTTAAAAATCAAGTATTAGCGGCGCTTTTTT
1 AAAAACGCCGCTAAAAATCAAGTATTAGCAGCACTTTTTT
40737429 AAAAACGCCGCTAA
1 AAAAACGCCGCTAA
40737443 TGCTTGATCC
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
38 3 0.07
39 25 0.56
40 17 0.38
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATCAAGTATTAGCAGCACTTTTTT
Found at i:40737572 original size:40 final size:40
Alignment explanation
Indices: 40737486--40737589 Score: 120
Period size: 40 Copynumber: 2.6 Consensus size: 40
40737476 CCTTTAGTGG
* *
40737486 CTTTAGCGGCGTTTTTTAAAAAACGCCGCTATATGTACAC
1 CTTTAGCAGCGTTTTTCAAAAAACGCCGCTATATGTACAC
* * ** *
40737526 CATTAGCAGCGCTTTTCAAAAAACGCCGCTA-ATGCTTGAT
1 CTTTAGCAGCGTTTTTCAAAAAACGCCGCTATATG-TACAC
40737566 CTTTAGCAGCGTTTTTGCAAAAAA
1 CTTTAGCAGCGTTTTT-CAAAAAA
40737590 ATTTTGCAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
39 3 0.06
40 43 0.81
41 7 0.13
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (40 bp):
CTTTAGCAGCGTTTTTCAAAAAACGCCGCTATATGTACAC
Found at i:40738087 original size:7 final size:7
Alignment explanation
Indices: 40738077--40738113 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
40738067 GGTTTAAGGT
*
40738077 TTAGGTG
1 TTAGGGG
40738084 TTAGGGG
1 TTAGGGG
40738091 TTAGGGG
1 TTAGGGG
40738098 TTAGGGG
1 TTAGGGG
*
40738105 TTAAGGG
1 TTAGGGG
40738112 TT
1 TT
40738114 CATAGTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.16, C:0.00, G:0.49, T:0.35
Consensus pattern (7 bp):
TTAGGGG
Found at i:40738155 original size:7 final size:7
Alignment explanation
Indices: 40738053--40738158 Score: 54
Period size: 7 Copynumber: 15.0 Consensus size: 7
40738043 GTTTAAGGGT
40738053 GGTTTAAG
1 GGTTT-AG
*
40738061 GG-TTGG
1 GGTTTAG
*
40738067 GGTTTAA
1 GGTTTAG
40738074 GGTTTA-
1 GGTTTAG
40738080 GGTGTTAG
1 GGT-TTAG
*
40738088 GGGTTAG
1 GGTTTAG
*
40738095 GGGTTAGG
1 GGTTTA-G
*
40738103 GGTTAAG
1 GGTTTAG
* *
40738110 GGTTCAT
1 GGTTTAG
* *
40738117 AGTTCAG
1 GGTTTAG
*
40738124 GGTTTAT
1 GGTTTAG
*
40738131 GTTTTAG
1 GGTTTAG
* *
40738138 GATTTAT
1 GGTTTAG
40738145 GGTTTAG
1 GGTTTAG
40738152 GGTTTAG
1 GGTTTAG
40738159 TGATTAAGAG
Statistics
Matches: 75, Mismatches: 19, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
6 6 0.08
7 60 0.80
8 9 0.12
ACGTcount: A:0.18, C:0.02, G:0.40, T:0.41
Consensus pattern (7 bp):
GGTTTAG
Found at i:40738363 original size:15 final size:15
Alignment explanation
Indices: 40738343--40738390 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
40738333 ACTATTTTAA
40738343 GGTTTATGAATTATG
1 GGTTTATGAATTATG
* *
40738358 GGTTTAAGGATTAT-
1 GGTTTATGAATTATG
* *
40738372 GGTTTATGATTTAAG
1 GGTTTATGAATTATG
40738387 GGTT
1 GGTT
40738391 GGCGTTTAAG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (15 bp):
GGTTTATGAATTATG
Found at i:40738378 original size:22 final size:21
Alignment explanation
Indices: 40738338--40738387 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
40738328 GAGTTACTAT
* *
40738338 TTTAAGGTTTATGAATTATGGG
1 TTTAAGGATTATGAATTAT-GA
**
40738360 TTTAAGGATTATGGTTTATGA
1 TTTAAGGATTATGAATTATGA
40738381 TTTAAGG
1 TTTAAGG
40738388 GTTGGCGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (21 bp):
TTTAAGGATTATGAATTATGA
Found at i:40739171 original size:8 final size:8
Alignment explanation
Indices: 40739160--40739261 Score: 99
Period size: 8 Copynumber: 12.9 Consensus size: 8
40739150 TTTATATGAT
40739160 AATTTAAA
1 AATTTAAA
40739168 AATTATAAA
1 AATT-TAAA
40739177 AATCTTCAAAAA
1 AAT-TT---AAA
40739189 AATTTAAA
1 AATTTAAA
40739197 AATTT-AA
1 AATTTAAA
40739204 AATTT-AA
1 AATTTAAA
40739211 AATTT-AA
1 AATTTAAA
40739218 AATTT-AA
1 AATTTAAA
40739225 AATTTAAA
1 AATTTAAA
40739233 AATTTAAA
1 AATTTAAA
40739241 AA--TAAA
1 AATTTAAA
*
40739247 AACTTAAA
1 AATTTAAA
*
40739255 TATTTAA
1 AATTTAA
40739262 TATTTAATAT
Statistics
Matches: 84, Mismatches: 2, Indels: 16
0.82 0.02 0.16
Matches are distributed among these distances:
6 6 0.07
7 28 0.33
8 33 0.39
9 8 0.10
10 1 0.01
11 2 0.02
12 6 0.07
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (8 bp):
AATTTAAA
Found at i:40739205 original size:7 final size:7
Alignment explanation
Indices: 40739187--40739273 Score: 102
Period size: 7 Copynumber: 12.0 Consensus size: 7
40739177 AATCTTCAAA
40739187 AAAATTT
1 AAAATTT
40739194 AAAAATTT
1 -AAAATTT
40739202 AAAATTT
1 AAAATTT
40739209 AAAATTT
1 AAAATTT
40739216 AAAATTT
1 AAAATTT
40739223 AAAATTT
1 AAAATTT
40739230 AAAAATTT
1 -AAAATTT
* *
40739238 AAAAATA
1 AAAATTT
*
40739245 AAAACTT
1 AAAATTT
40739252 AAATATTT
1 AAA-ATTT
*
40739260 AATATTT
1 AAAATTT
*
40739267 AATATTT
1 AAAATTT
40739274 TAGTCTATAT
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
7 52 0.73
8 19 0.27
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (7 bp):
AAAATTT
Found at i:40739215 original size:22 final size:22
Alignment explanation
Indices: 40739187--40739261 Score: 100
Period size: 22 Copynumber: 3.4 Consensus size: 22
40739177 AATCTTCAAA
40739187 AAAATTTAAAAATTTAAAATTT
1 AAAATTTAAAAATTTAAAATTT
40739209 AAAATTT-AAAATTTAAAATTT
1 AAAATTTAAAAATTTAAAATTT
* *
40739230 AAAAATTTAAAAA-TAAAAACTT
1 -AAAATTTAAAAATTTAAAATTT
40739252 AAATATTTAA
1 AAA-ATTTAA
40739262 TATTTAATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
21 17 0.35
22 27 0.56
23 4 0.08
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAATTTAAAAATTTAAAATTT
Found at i:40739521 original size:1 final size:1
Alignment explanation
Indices: 40739483--40739513 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
40739473 CGCTAATAAC
40739483 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
40739514 CTGAAAAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:40739580 original size:10 final size:10
Alignment explanation
Indices: 40739565--40739593 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
40739555 AAGAAAACCC
40739565 TTCACTGTTA
1 TTCACTGTTA
40739575 TTCACTGTTA
1 TTCACTGTTA
40739585 TTCACTGTT
1 TTCACTGTT
40739594 TTCGCCAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.17, C:0.21, G:0.10, T:0.52
Consensus pattern (10 bp):
TTCACTGTTA
Found at i:40740742 original size:40 final size:40
Alignment explanation
Indices: 40740681--40740757 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
40740671 TCCATGGCAT
* *
40740681 CTCTATACTTATGCTTGGCTAAA-AATGTATGTATGTACAC
1 CTCTATACTTATGCTTAGCTAAAGAA-ATATGTATGTACAC
*
40740721 CTCTGTACTTATGCTTAGCTAAAGAAATATGTATGTA
1 CTCTATACTTATGCTTAGCTAAAGAAATATGTATGTA
40740758 TGTATGCAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 31 0.94
41 2 0.06
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (40 bp):
CTCTATACTTATGCTTAGCTAAAGAAATATGTATGTACAC
Found at i:40740842 original size:28 final size:27
Alignment explanation
Indices: 40740802--40740854 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
40740792 ATAATTTATA
*
40740802 AAATTTTAAATTAATAATGATAAAATT
1 AAATTTTAAATTAAAAATGATAAAATT
*
40740829 AAATTTTCACATTAAAAATGATAAAA
1 AAATTTT-AAATTAAAAATGATAAAA
40740855 ATATATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (27 bp):
AAATTTTAAATTAAAAATGATAAAATT
Found at i:40745138 original size:43 final size:43
Alignment explanation
Indices: 40745077--40745223 Score: 156
Period size: 43 Copynumber: 3.4 Consensus size: 43
40745067 TTGTGAGAAA
*
40745077 AGCGGCGTTTTGGGGAAAAGTGTCGCTAAATGTCATGGTTTTT
1 AGCGGCGTTTTGGGGAAAAGTGTCGCTAAATGTCATGGTCTTT
* *
40745120 AGCGGCGTTTTGGGGAAAAGTGTCGTTAAATGTTATGGTCTTT
1 AGCGGCGTTTTGGGGAAAAGTGTCGCTAAATGTCATGGTCTTT
* * * * * *
40745163 AGTGGCG-TTTGAAGAAAAAGCG-CTGTTAAAGGTCATGGTCTTT
1 AGCGGCGTTTTG-GGGAAAAGTGTC-GCTAAATGTCATGGTCTTT
* *
40745206 ATCGGCG-TTTGAGGAAAA
1 AGCGGCGTTTTGGGGAAAA
40745224 AGCGCCACAA
Statistics
Matches: 90, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
42 11 0.12
43 79 0.88
ACGTcount: A:0.24, C:0.11, G:0.32, T:0.33
Consensus pattern (43 bp):
AGCGGCGTTTTGGGGAAAAGTGTCGCTAAATGTCATGGTCTTT
Found at i:40746949 original size:12 final size:12
Alignment explanation
Indices: 40746932--40746964 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
40746922 TTCTCTGTAA
40746932 AATAGTAAAAAT
1 AATAGTAAAAAT
40746944 AATAGTAAAAAT
1 AATAGTAAAAAT
40746956 AATAGTAAA
1 AATAGTAAA
40746965 GGGGAAGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (12 bp):
AATAGTAAAAAT
Found at i:40747894 original size:10 final size:10
Alignment explanation
Indices: 40747875--40747934 Score: 70
Period size: 10 Copynumber: 6.0 Consensus size: 10
40747865 TGAAATTCTA
40747875 AAAGATAAAT
1 AAAGATAAAT
40747885 ACAA-ATAAAT
1 A-AAGATAAAT
* *
40747895 AAATATAATT
1 AAAGATAAAT
40747905 AAAGATAAAT
1 AAAGATAAAT
40747915 AAAGATAAAT
1 AAAGATAAAT
40747925 GAAA-ATAAAT
1 -AAAGATAAAT
40747935 CCTAAAATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
9 2 0.05
10 37 0.84
11 5 0.11
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.23
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:40747909 original size:30 final size:30
Alignment explanation
Indices: 40747875--40747932 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
40747865 TGAAATTCTA
40747875 AAAGATAAATACAA-ATAAAT-AAATATAATT
1 AAAGATAAATA-AAGATAAATGAAA-ATAATT
40747905 AAAGATAAATAAAGATAAATGAAAATAA
1 AAAGATAAATAAAGATAAATGAAAATAA
40747933 ATCCTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 2 0.08
30 21 0.81
31 3 0.12
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.22
Consensus pattern (30 bp):
AAAGATAAATAAAGATAAATGAAAATAATT
Found at i:40750017 original size:53 final size:53
Alignment explanation
Indices: 40749930--40750039 Score: 193
Period size: 53 Copynumber: 2.1 Consensus size: 53
40749920 CTTGGTCTAG
*
40749930 TATAATAGAGTTCATCATTTATGACCATACAATGCTTCATACAGTGCCATGTT
1 TATAATAGAGTTCATCATTTATGACCATACAATGCATCATACAGTGCCATGTT
* *
40749983 TATAGTAGAGTTCATCATTTATGACCATATAATGCATCATACAGTGCCATGTT
1 TATAATAGAGTTCATCATTTATGACCATACAATGCATCATACAGTGCCATGTT
40750036 TATA
1 TATA
40750040 CTCGATTGAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (53 bp):
TATAATAGAGTTCATCATTTATGACCATACAATGCATCATACAGTGCCATGTT
Found at i:40758492 original size:20 final size:19
Alignment explanation
Indices: 40758467--40758514 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 19
40758457 TCATGTTGAA
40758467 TAAATTGA-AGAATTAGAGGT
1 TAAATTGATAGAATTA-A-GT
40758487 TAAATTGATAGAATTAAGT
1 TAAATTGATAGAATTAAGT
40758506 TAGAATTGA
1 TA-AATTGA
40758515 GAAAAGGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.15
20 15 0.58
21 7 0.27
ACGTcount: A:0.46, C:0.00, G:0.21, T:0.33
Consensus pattern (19 bp):
TAAATTGATAGAATTAAGT
Found at i:40758952 original size:5 final size:5
Alignment explanation
Indices: 40758944--40758991 Score: 69
Period size: 5 Copynumber: 9.6 Consensus size: 5
40758934 GTATTATGGT
* * *
40758944 ATTGA ATTGA ATTAA ATTAA ATTGA ATTGA GTTGA ATTGA ATTGA ATT
1 ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATT
40758992 ATGAATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.42
Consensus pattern (5 bp):
ATTGA
Found at i:40759398 original size:22 final size:23
Alignment explanation
Indices: 40759347--40759398 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
40759337 GGTAATTAAA
40759347 TGAAATGACATTATGATTGATAT
1 TGAAATGACATTATGATTGATAT
* *
40759370 TG-GATGATATTAT-ATGTGAT-T
1 TGAAATGACATTATGAT-TGATAT
40759391 TGAAATGA
1 TGAAATGA
40759399 GAAAGTGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
21 5 0.21
22 17 0.71
23 2 0.08
ACGTcount: A:0.37, C:0.02, G:0.21, T:0.40
Consensus pattern (23 bp):
TGAAATGACATTATGATTGATAT
Found at i:40764681 original size:29 final size:29
Alignment explanation
Indices: 40764649--40764721 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
40764639 CTTTGAGCTC
* *
40764649 GCACACCCAGTGCCGTATTTTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
40764678 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
40764707 GCACACTTAGTGCCA
1 GCACACCCAGTGCCA
40764722 ATCTCGTCAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (29 bp):
GCACACCCAGTGCCATATATTTCCAGCAT
Found at i:40768647 original size:6 final size:6
Alignment explanation
Indices: 40768638--40768676 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
40768628 AATAAAATTG
*
40768638 AAATGA AAATAA AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAA
40768677 AGATAGGAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:40775018 original size:16 final size:15
Alignment explanation
Indices: 40774991--40775031 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
40774981 ATCTTAAAAC
40774991 TTTATTTTTATTTGA
1 TTTATTTTTATTTGA
*
40775006 TTTATTATTTATTTTA
1 TTTATT-TTTATTTGA
40775022 TTTTATTTTT
1 -TTTATTTTT
40775032 TTAAAAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 6 0.26
16 11 0.48
17 6 0.26
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (15 bp):
TTTATTTTTATTTGA
Found at i:40775685 original size:17 final size:17
Alignment explanation
Indices: 40775663--40775701 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
40775653 TGGTAAAAGC
40775663 CACACAGCCGTGTGTGA
1 CACACAGCCGTGTGTGA
40775680 CACACAGCCGTGTGTGA
1 CACACAGCCGTGTGTGA
40775697 CACAC
1 CACAC
40775702 GGTCTAGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.26, C:0.33, G:0.26, T:0.15
Consensus pattern (17 bp):
CACACAGCCGTGTGTGA
Found at i:40775783 original size:32 final size:32
Alignment explanation
Indices: 40775746--40775817 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
40775736 GATGTGTGTA
* *
40775746 GGCCGTGTGAGCCACACGAGCATAGAAATTTT
1 GGCCGTGTGAGCCACACGAGAATAGAAATTTG
* *
40775778 GGCCGTATGAGCCACACGAGAATGGAAATTTG
1 GGCCGTGTGAGCCACACGAGAATAGAAATTTG
40775810 GGCCGTGT
1 GGCCGTGT
40775818 AGGCATACGG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.26, C:0.21, G:0.32, T:0.21
Consensus pattern (32 bp):
GGCCGTGTGAGCCACACGAGAATAGAAATTTG
Found at i:40776633 original size:13 final size:13
Alignment explanation
Indices: 40776611--40776641 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
40776601 TTTGGGATTG
*
40776611 TTTTTGTTTTGGA
1 TTTTTATTTTGGA
40776624 TTTTTATTTTGGA
1 TTTTTATTTTGGA
40776637 TTTTT
1 TTTTT
40776642 GACATTACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.10, C:0.00, G:0.16, T:0.74
Consensus pattern (13 bp):
TTTTTATTTTGGA
Found at i:40778761 original size:13 final size:13
Alignment explanation
Indices: 40778751--40778779 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
40778741 GATGGAGATA
40778751 TTGTTTGGAGAAT
1 TTGTTTGGAGAAT
40778764 TTGTTTGGAGAAT
1 TTGTTTGGAGAAT
40778777 TTG
1 TTG
40778780 GTCTGATTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (13 bp):
TTGTTTGGAGAAT
Found at i:40782357 original size:19 final size:19
Alignment explanation
Indices: 40782329--40782426 Score: 146
Period size: 19 Copynumber: 5.2 Consensus size: 19
40782319 AATCTTTAAG
*
40782329 GATATTCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
40782348 GATATGCAATCTTAGATGT
1 GATATGCAATCTTAGATAT
40782367 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40782384 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40782403 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
40782424 GAT
1 GAT
40782427 CTTGTAATCT
Statistics
Matches: 72, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
17 16 0.22
19 47 0.65
21 9 0.12
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:40782359 original size:36 final size:37
Alignment explanation
Indices: 40782335--40782426 Score: 125
Period size: 36 Copynumber: 2.4 Consensus size: 37
40782325 TAAGGATATT
40782335 CAATCTTAGATATGATATGCAATC-TTAGATGTGATA
1 CAATCTTAGATATGATATGCAATCTTTAGATGTGATA
*
40782371 CAATCTTAGATATGATATGCAATC-TTAGATATGATA
1 CAATCTTAGATATGATATGCAATCTTTAGATGTGATA
40782407 TGCAATCTTGAAGATATGAT
1 --CAATCTT--AGATATGAT
40782427 CTTGTAATCT
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
36 35 0.69
38 7 0.14
40 9 0.18
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (37 bp):
CAATCTTAGATATGATATGCAATCTTTAGATGTGATA
Found at i:40786976 original size:13 final size:13
Alignment explanation
Indices: 40786954--40786984 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
40786944 TTTGTGATTG
*
40786954 TTTTTGTTTTGGA
1 TTTTTATTTTGGA
40786967 TTTTTATTTTGGA
1 TTTTTATTTTGGA
40786980 TTTTT
1 TTTTT
40786985 GACATGATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.10, C:0.00, G:0.16, T:0.74
Consensus pattern (13 bp):
TTTTTATTTTGGA
Found at i:40787154 original size:24 final size:25
Alignment explanation
Indices: 40787127--40787189 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 25
40787117 ACGATTTTAA
*
40787127 TTAAATAAG-TATGACAAACACATT
1 TTAAATAAGCGATGACAAACACATT
*
40787151 TTAAATAAAGCGATGACAAACACGTT
1 TTAAAT-AAGCGATGACAAACACATT
40787177 TTAAATAAAGCGA
1 TTAAAT-AAGCGA
40787190 GCTTTTTAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 6 0.17
25 3 0.09
26 26 0.74
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (25 bp):
TTAAATAAGCGATGACAAACACATT
Found at i:40787166 original size:26 final size:26
Alignment explanation
Indices: 40787137--40787189 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
40787127 TTAAATAAGT
40787137 ATGACAAACACATTTTAAATAAAGCG
1 ATGACAAACACATTTTAAATAAAGCG
*
40787163 ATGACAAACACGTTTTAAATAAAGCG
1 ATGACAAACACATTTTAAATAAAGCG
40787189 A
1 A
40787190 GCTTTTTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.49, C:0.15, G:0.13, T:0.23
Consensus pattern (26 bp):
ATGACAAACACATTTTAAATAAAGCG
Found at i:40789698 original size:14 final size:15
Alignment explanation
Indices: 40789663--40789700 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
40789653 TTTACATGTT
40789663 ATAAATTT-TTTATA
1 ATAAATTTATTTATA
*
40789677 ATATATTTATTTATA
1 ATAAATTTATTTATA
40789692 A-AAATTTAT
1 ATAAATTTAT
40789701 GGTCAAGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAAATTTATTTATA
Found at i:40792883 original size:24 final size:24
Alignment explanation
Indices: 40792818--40793003 Score: 100
Period size: 24 Copynumber: 7.9 Consensus size: 24
40792808 AGAAATAAGT
* * *
40792818 TTAAAATAGATATTATAAAATAAAT
1 TTAAAATAAATAATATAAAA-AAAC
* * **
40792843 TTAAAGTGAATGGTATAAAAAAAC
1 TTAAAATAAATAATATAAAAAAAC
* *
40792867 TTAAAATAATTAATATACAAAACAAT
1 TTAAAATAAATAATATA-AAAA-AAC
**
40792893 TTAAAAT--A-AA-ATAAAGCAAC
1 TTAAAATAAATAATATAAAAAAAC
* * *
40792913 TTAAAATAAATAATATATAACAAT
1 TTAAAATAAATAATATAAAAAAAC
* * **
40792937 TTAAAAT-AA-CATATAGAAAGTC
1 TTAAAATAAATAATATAAAAAAAC
*
40792959 -TAAAATAAATAATATGTAAAAAA-
1 TTAAAATAAATAATAT-AAAAAAAC
*
40792982 TTAAAATAAATAATATTAAAAA
1 TTAAAATAAATAATATAAAAAA
40793004 TATAAAATAG
Statistics
Matches: 121, Mismatches: 30, Indels: 22
0.70 0.17 0.13
Matches are distributed among these distances:
20 9 0.07
21 8 0.07
22 13 0.11
23 16 0.13
24 47 0.39
25 19 0.16
26 9 0.07
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.29
Consensus pattern (24 bp):
TTAAAATAAATAATATAAAAAAAC
Found at i:40792914 original size:46 final size:44
Alignment explanation
Indices: 40792857--40792991 Score: 148
Period size: 46 Copynumber: 3.0 Consensus size: 44
40792847 AGTGAATGGT
* *
40792857 ATAAAAAAACTTAAAATAATTAATATACAAAACAATTTAAAATAAA
1 ATAAAGAAACTTAAAATAAATAATAT--AAAACAATTTAAAATAAA
* * *
40792903 ATAAAGCAACTTAAAATAAATAATATATAACAATTTAAAATAAC
1 ATAAAGAAACTTAAAATAAATAATATAAAACAATTTAAAATAAA
* *
40792947 ATATAGAAAGTCTAAAATAAATAATATGTAAAA-AA-TTAAAATAAA
1 ATAAAGAAACT-TAAAATAAATAATA--TAAAACAATTTAAAATAAA
40792992 TAATATTAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
44 24 0.32
45 23 0.30
46 25 0.33
47 4 0.05
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (44 bp):
ATAAAGAAACTTAAAATAAATAATATAAAACAATTTAAAATAAA
Found at i:40792969 original size:25 final size:24
Alignment explanation
Indices: 40792940--40793152 Score: 84
Period size: 25 Copynumber: 8.7 Consensus size: 24
40792930 TAACAATTTA
* *
40792940 AAATAACATATAGAAAGTCTAAAAT
1 AAATAACATATAAAAAAT-TAAAAT
* *
40792965 AAATAATATGTAAAAAATTAAAAT
1 AAATAACATATAAAAAATTAAAAT
*
40792989 AAAT-A-ATATTAAAAATATAAAAT
1 AAATAACATATAAAAAAT-TAAAAT
* * * *
40793012 AGTTTAATAATAAACAAAAAATTTAAAAC
1 A----AATAACATATAAAAAA-TTAAAAT
* *
40793041 AATTAACATATAAAACAATATAAACT
1 AAATAACATATAAAA-AAT-TAAAAT
*
40793067 AAATAAC--ATAAAAATTTAAAAT
1 AAATAACATATAAAAAATTAAAAT
* **
40793089 AGATAA-A-AT---AGTTTAAAAT
1 AAATAACATATAAAAAATTAAAAT
* *
40793108 AAATAAAATATGTAAAATATTTAAAAT
1 AAATAACATA--TAAAA-AATTAAAAT
*
40793135 AAATAATATATAATAAAA
1 AAATAACATATAA-AAAA
40793153 CAGTTTAAAG
Statistics
Matches: 143, Mismatches: 25, Indels: 40
0.69 0.12 0.19
Matches are distributed among these distances:
19 14 0.10
20 1 0.01
21 1 0.01
22 21 0.15
23 11 0.08
24 16 0.11
25 29 0.20
26 15 0.10
27 20 0.14
28 1 0.01
29 13 0.09
30 1 0.01
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (24 bp):
AAATAACATATAAAAAATTAAAAT
Found at i:40792973 original size:45 final size:44
Alignment explanation
Indices: 40792857--40792991 Score: 153
Period size: 45 Copynumber: 3.0 Consensus size: 44
40792847 AGTGAATGGT
* * *
40792857 ATAAAAAAACTTAAAATAATTAATATACAAAACAATTTAAAATAAA
1 ATAAAGAAACTTAAAATAAATAATAT--ATAACAATTTAAAATAAA
* *
40792903 ATAAAGCAACTTAAAATAAATAATATATAACAATTTAAAATAAC
1 ATAAAGAAACTTAAAATAAATAATATATAACAATTTAAAATAAA
* * * * *
40792947 ATATAGAAAGTCTAAAATAAATAATATGTAAAAAATTAAAATAAA
1 ATAAAGAAACT-TAAAATAAATAATATATAACAATTTAAAATAAA
40792992 TAATATTAAA
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
44 24 0.32
45 29 0.38
46 23 0.30
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (44 bp):
ATAAAGAAACTTAAAATAAATAATATATAACAATTTAAAATAAA
Found at i:40793105 original size:19 final size:18
Alignment explanation
Indices: 40792982--40793126 Score: 78
Period size: 18 Copynumber: 8.4 Consensus size: 18
40792972 ATGTAAAAAA
40792982 TTAAAATAAAT--AATA-
1 TTAAAATAAATAAAATAT
*
40792997 TTAAAA-ATATAAAATAGT
1 TTAAAATAAATAAAATA-T
* *
40793015 TTAATAATAAACAAAAAAT
1 TTAA-AATAAATAAAATAT
* * *
40793034 TTAAAACAATTAACATA-
1 TTAAAATAAATAAAATAT
* *
40793051 -TAAAA-CAATATAA-A-
1 TTAAAATAAATAAAATAT
*
40793065 CT-AAATAACATAAAA-AT
1 TTAAAATAA-ATAAAATAT
*
40793082 TTAAAATAGATAAAATAGT
1 TTAAAATAAATAAAATA-T
40793101 TTAAAATAAATAAAATAT
1 TTAAAATAAATAAAATAT
*
40793119 GTAAAATA
1 TTAAAATA
40793127 TTTAAAATAA
Statistics
Matches: 98, Mismatches: 19, Indels: 23
0.70 0.14 0.16
Matches are distributed among these distances:
14 7 0.07
15 12 0.12
16 15 0.15
17 7 0.07
18 26 0.27
19 24 0.24
20 7 0.07
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (18 bp):
TTAAAATAAATAAAATAT
Found at i:40793138 original size:27 final size:29
Alignment explanation
Indices: 40793083--40793161 Score: 110
Period size: 28 Copynumber: 2.8 Consensus size: 29
40793073 CATAAAAATT
40793083 TAAAATA-GATAAAATAGTTTAAAATAAA
1 TAAAATATGATAAAATAGTTTAAAATAAA
40793111 TAAAATATG-TAAAATA-TTTAAAATAAA
1 TAAAATATGATAAAATAGTTTAAAATAAA
* * *
40793138 TAATATATAATAAAACAGTTTAAA
1 TAAAATATGATAAAATAGTTTAAA
40793162 GTATAGGGTC
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
27 18 0.40
28 20 0.44
29 7 0.16
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (29 bp):
TAAAATATGATAAAATAGTTTAAAATAAA
Found at i:40794775 original size:46 final size:46
Alignment explanation
Indices: 40794723--40794842 Score: 131
Period size: 46 Copynumber: 2.7 Consensus size: 46
40794713 GTAATTTCAA
* * *
40794723 CCTGCTCCACTACAACTTCAGAGAGATAAGGT-TTGTGTATCTT-TAT
1 CCTGCTCCACTACAACTTCAGAGAGATAAGGTATTATG--GCTTCGAT
* * *
40794769 CCTGCTCTACTGCAACTTCAAAGAGATAA-GTATTATGGCTTCGAT
1 CCTGCTCCACTACAACTTCAGAGAGATAAGGTATTATGGCTTCGAT
*
40794814 -CTGCTCCACTACAACTTCAGGGAGATAAG
1 CCTGCTCCACTACAACTTCAGAGAGATAAG
40794843 ACTTCTGCTC
Statistics
Matches: 61, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
44 27 0.44
45 4 0.07
46 30 0.49
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.30
Consensus pattern (46 bp):
CCTGCTCCACTACAACTTCAGAGAGATAAGGTATTATGGCTTCGAT
Found at i:40794839 original size:44 final size:43
Alignment explanation
Indices: 40794718--40795244 Score: 236
Period size: 44 Copynumber: 11.9 Consensus size: 43
40794708 AATTGGTAAT
* * *
40794718 TTCAACCTGCTCCACTACAACTTCAGAGAGATAAGGTT-TGTG-
1 TTCAATCTGCTCCACTACAACTTCAGGGAGATAAGATTATG-GC
* * * **
40794760 TATCTTTATCCTGCTCTACTGCAACTTCAAAGAGATAAGTATTATGGC
1 T-TC--AAT-CTGCTCCACTACAACTTCAGGGAGATAAG-ATTATGGC
*
40794808 TTCGATCTGCTCCACTACAACTTCAGGGAGATAAG---A---C
1 TTCAATCTGCTCCACTACAACTTCAGGGAGATAAGATTATGGC
* * * *
40794845 -T---TCTGCTCCACTGCAACTTCAAGGAGATAAGACT-TGCTAC
1 TTCAATCTGCTCCACTACAACTTCAGGGAGATAAGATTATG--GC
* * * * *
40794885 TTCAACCTGCTCCACTATAACTTTAGGGAGATAAGGTT-TGTGTTT
1 TTCAATCTGCTCCACTACAACTTCAGGGAGATAAGATTATG-G--C
** * * * *
40794930 TTTTATCCTGCTCTACTGCAACTTCAGAGAGATAAAGATTATGGT
1 TTCAAT-CTGCTCCACTACAACTTCAGGGAGAT-AAGATTATGGC
* * * *
40794975 TTCGATCTACTCCACTGCAACTTCAGGGAGATAAGACTTGTGGC
1 TTCAATCTGCTCCACTACAACTTCAGGGAGATAAGA-TTATGGC
* *
40795019 TTCAATCTACTCCACTACAACTTCAGGAAGATAAGATTCACCATGATTTGTAGC
1 TTCAATCTGCTCCACTACAACTTCAGGGAGATAAGA-T-----T-A--TG--GC
* * * * * **
40795073 TTTAATCTGTTCCACTGCAACTTTAGGGAAATAAGATTCACTATC
1 TTCAATCTGCTCCACTACAACTTCAGGGAGATAAGATT-A-TGGC
* * * * *
40795118 TTTAGTCTGCTCCACTGCAACTTCAGGGAAATAAGATTCACTGTC
1 TTCAATCTGCTCCACTACAACTTCAGGGAGATAAGATT-A-TGGC
* * * * *
40795163 TTTAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGACTTGTGGC
1 TTCAATCTGCTCCACTACAACTTCAGGGAGATAAGA-TTATGGC
* * *
40795207 TTCAATCTACTCCACTGCAACTTCACGGAGATAAGATT
1 TTCAATCTGCTCCACTACAACTTCAGGGAGATAAGATT
40795245 CGTCATGATT
Statistics
Matches: 382, Mismatches: 67, Indels: 71
0.73 0.13 0.14
Matches are distributed among these distances:
33 28 0.07
36 1 0.00
37 1 0.00
40 2 0.01
41 1 0.00
42 1 0.00
43 9 0.02
44 149 0.39
45 87 0.23
46 49 0.13
47 12 0.03
48 7 0.02
49 1 0.00
52 2 0.01
53 1 0.00
54 31 0.08
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (43 bp):
TTCAATCTGCTCCACTACAACTTCAGGGAGATAAGATTATGGC
Found at i:40794855 original size:33 final size:33
Alignment explanation
Indices: 40794813--40794879 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
40794803 ATGGCTTCGA
*
40794813 TCTGCTCCACTACAACTTCAGGGAGATAAGACT
1 TCTGCTCCACTACAACTTCAAGGAGATAAGACT
*
40794846 TCTGCTCCACTGCAACTTCAAGGAGATAAGACT
1 TCTGCTCCACTACAACTTCAAGGAGATAAGACT
40794879 T
1 T
40794880 GCTACTTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (33 bp):
TCTGCTCCACTACAACTTCAAGGAGATAAGACT
Found at i:40794897 original size:77 final size:77
Alignment explanation
Indices: 40794770--40794919 Score: 196
Period size: 77 Copynumber: 1.9 Consensus size: 77
40794760 TATCTTTATC
* * * *
40794770 CTGCTCTACTGCAACTTCAAAGAGATAAGTATTATGGCTTCGATCTGCTCCACTACAACTTCAGG
1 CTGCTCCACTGCAACTTCAAAGAGATAAGTATTATGACTTCAACCTGCTCCACTACAACTTCAGG
40794835 GAGATAAGACTT
66 GAGATAAGACTT
* * * *
40794847 CTGCTCCACTGCAACTTCAAGGAGATAAG-ACT-TGCTACTTCAACCTGCTCCACTATAACTTTA
1 CTGCTCCACTGCAACTTCAAAGAGATAAGTATTATG--ACTTCAACCTGCTCCACTACAACTTCA
40794910 GGGAGATAAG
64 GGGAGATAAG
40794920 GTTTGTGTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
75 2 0.03
76 2 0.03
77 59 0.94
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (77 bp):
CTGCTCCACTGCAACTTCAAAGAGATAAGTATTATGACTTCAACCTGCTCCACTACAACTTCAGG
GAGATAAGACTT
Found at i:40794998 original size:167 final size:168
Alignment explanation
Indices: 40794691--40795013 Score: 506
Period size: 167 Copynumber: 1.9 Consensus size: 168
40794681 ATTCCGCTGG
* * *
40794691 AACTTCAAGGAGGTAAGAATTGGTAATTTCAACCTGCTCCACTACAACTTCAGAGAGATAAGGTT
1 AACTTCAAGGAGATAAGAATTGCTAACTTCAACCTGCTCCACTACAACTTCAGAGAGATAAGGTT
*
40794756 TGTGTATCTTTATCCTGCTCTACTGCAACTTCAAAGAGATAAGTATTATGGCTTCGATCTGCTCC
66 TGTGTATCTTTATCCTGCTCTACTGCAACTTCAAAGAGATAAGTATTATGGCTTCGATCTACTCC
40794821 ACTACAACTTCAGGGAGATAAGACTTCTGCTCCACTGC
131 ACTACAACTTCAGGGAGATAAGACTTCTGCTCCACTGC
* * * *
40794859 AACTTCAAGGAGATAAGACTTGCT-ACTTCAACCTGCTCCACTATAACTTTAGGGAGATAAGGTT
1 AACTTCAAGGAGATAAGAATTGCTAACTTCAACCTGCTCCACTACAACTTCAGAGAGATAAGGTT
* * * *
40794923 TGTGTTTTTTTATCCTGCTCTACTGCAACTTCAGAGAGATAAAG-ATTATGGTTTCGATCTACTC
66 TGTGTATCTTTATCCTGCTCTACTGCAACTTCAAAGAGAT-AAGTATTATGGCTTCGATCTACTC
*
40794987 CACTGCAACTTCAGGGAGATAAGACTT
130 CACTACAACTTCAGGGAGATAAGACTT
40795014 GTGGCTTCAA
Statistics
Matches: 141, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
167 117 0.83
168 24 0.17
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (168 bp):
AACTTCAAGGAGATAAGAATTGCTAACTTCAACCTGCTCCACTACAACTTCAGAGAGATAAGGTT
TGTGTATCTTTATCCTGCTCTACTGCAACTTCAAAGAGATAAGTATTATGGCTTCGATCTACTCC
ACTACAACTTCAGGGAGATAAGACTTCTGCTCCACTGC
Found at i:40795107 original size:54 final size:46
Alignment explanation
Indices: 40795072--40795245 Score: 178
Period size: 45 Copynumber: 3.9 Consensus size: 46
40795062 TGATTTGTAG
* *
40795072 CTTTAATCTGTTCCACTGCAACTTTAGGGAAATAAGATTCA-CTAT
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCACCTAT
* *
40795117 CTTTAGTCTGCTCCACTGCAACTTCAGGGAAATAAGATTCA-CTGT
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCACCTAT
* * * * **
40795162 CTTTAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGACTT---GTGG
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGA-TTCACCTAT
* * * *
40795206 CTTCAATCTACTCCACTGCAACTTCACGGAGATAAGATTC
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTC
40795246 GTCATGATTA
Statistics
Matches: 114, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
43 2 0.02
44 34 0.30
45 76 0.67
46 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (46 bp):
CTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCACCTAT
Found at i:40795136 original size:45 final size:45
Alignment explanation
Indices: 40795072--40795198 Score: 200
Period size: 45 Copynumber: 2.8 Consensus size: 45
40795062 TGATTTGTAG
* * *
40795072 CTTTAATCTGTTCCACTGCAACTTTAGGGAAATAAGATTCACTAT
1 CTTTAGTCTGCTCCACTGCAACTTCAGGGAAATAAGATTCACTAT
*
40795117 CTTTAGTCTGCTCCACTGCAACTTCAGGGAAATAAGATTCACTGT
1 CTTTAGTCTGCTCCACTGCAACTTCAGGGAAATAAGATTCACTAT
* *
40795162 CTTTAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGA
1 CTTTAGTCTGCTCCACTGCAACTTCAGGGAAATAAGA
40795199 CTTGTGGCTT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 76 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (45 bp):
CTTTAGTCTGCTCCACTGCAACTTCAGGGAAATAAGATTCACTAT
Found at i:40795781 original size:46 final size:46
Alignment explanation
Indices: 40795640--40795787 Score: 156
Period size: 46 Copynumber: 3.2 Consensus size: 46
40795630 AATTTGTGGT
* * * ** *
40795640 TTCTTCTATCCACCCCATTGCAACTCAATGGTATAGGATGTGTATC
1 TTCTTCAATCCATCCCACTGCAACTCAGGGGTATAGGATTTGTATC
* * * *
40795686 ATCTTCAATCCATCTCACTGCAACTTATGGGTATAGGATTTGTATC
1 TTCTTCAATCCATCCCACTGCAACTCAGGGGTATAGGATTTGTATC
* *
40795732 TTCTTCAATTCATCCCACTGCAGCTCAGGGGTATAGGACTTATG-A-C
1 TTCTTCAATCCATCCCACTGCAACTCAGGGGTATAGGA-TT-TGTATC
40795778 TTCTTCAATC
1 TTCTTCAATC
40795788 AATTGATCTG
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
46 79 0.94
47 3 0.04
48 2 0.02
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (46 bp):
TTCTTCAATCCATCCCACTGCAACTCAGGGGTATAGGATTTGTATC
Found at i:40796264 original size:53 final size:53
Alignment explanation
Indices: 40796184--40796340 Score: 260
Period size: 53 Copynumber: 3.0 Consensus size: 53
40796174 AGGAGCATAG
* *
40796184 CTTGAAATGAATAAATTAATCAAAGATAGCAAATGCAATAAGAAGGAAATTAA
1 CTTGAAATGAATAAGTTAATCAAAGATAGCAAATGTAATAAGAAGGAAATTAA
*
40796237 CTTGAAATGAATAAGTTAATCAAAGATAGCAAATGTAATAAGAAGGCAATTAA
1 CTTGAAATGAATAAGTTAATCAAAGATAGCAAATGTAATAAGAAGGAAATTAA
* * *
40796290 CTCGAAATGAGTAAGTTAATCAAAGATAGCAAATGTAATAAAAAGGAAATT
1 CTTGAAATGAATAAGTTAATCAAAGATAGCAAATGTAATAAGAAGGAAATT
40796341 GGTTGGGAGC
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 97 1.00
ACGTcount: A:0.52, C:0.08, G:0.17, T:0.24
Consensus pattern (53 bp):
CTTGAAATGAATAAGTTAATCAAAGATAGCAAATGTAATAAGAAGGAAATTAA
Found at i:40796278 original size:27 final size:26
Alignment explanation
Indices: 40796188--40796330 Score: 75
Period size: 26 Copynumber: 5.4 Consensus size: 26
40796178 GCATAGCTTG
*
40796188 AAATGAATAAATTAATCAAAGATAGC
1 AAATGAATAAGTTAATCAAAGATAGC
** * *
40796214 AAATGCAATAAG--AAGGAAA-TTAAC
1 AAATG-AATAAGTTAATCAAAGATAGC
40796238 TTGAAATGAATAAGTTAATCAAAGATAGC
1 ---AAATGAATAAGTTAATCAAAGATAGC
* *
40796267 AAATGTAATAAG--AAGGCAATTA-ACTCG-
1 AAATG-AATAAGTTAA-TCAA--AGA-TAGC
*
40796294 AAATGAGTAAGTTAATCAAAGATAGC
1 AAATGAATAAGTTAATCAAAGATAGC
40796320 AAATGTAATAA
1 AAATG-AATAA
40796331 AAAGGAAATT
Statistics
Matches: 85, Mismatches: 15, Indels: 33
0.64 0.11 0.25
Matches are distributed among these distances:
24 3 0.04
25 10 0.12
26 30 0.35
27 29 0.34
28 10 0.12
29 3 0.04
ACGTcount: A:0.53, C:0.08, G:0.16, T:0.23
Consensus pattern (26 bp):
AAATGAATAAGTTAATCAAAGATAGC
Found at i:40799835 original size:13 final size:13
Alignment explanation
Indices: 40799817--40799862 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
40799807 AAACCCAACT
*
40799817 ACCCAACTACCCA
1 ACCCAATTACCCA
40799830 ACCCAATTACCCA
1 ACCCAATTACCCA
* *
40799843 ACCTAATTTCCCA
1 ACCCAATTACCCA
40799856 ACCCAAT
1 ACCCAAT
40799863 AAATTTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.37, C:0.46, G:0.00, T:0.17
Consensus pattern (13 bp):
ACCCAATTACCCA
Found at i:40803398 original size:17 final size:17
Alignment explanation
Indices: 40803378--40803512 Score: 67
Period size: 17 Copynumber: 7.4 Consensus size: 17
40803368 ATTTCAAGAC
40803378 TTATGTAATGTTTTTAA
1 TTATGTAATGTTTTTAA
* ***
40803395 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
*
40803414 CTTATGTAATGTTTTTTA
1 -TTATGTAATGTTTTTAA
*
40803432 TTATGT-A-GTTATTCAAAGA
1 TTATGTAATGTT-TT--TA-A
40803451 CTTATGTAATGTTTTTAA
1 -TTATGTAATGTTTTTAA
* ***
40803469 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
40803488 CTTATGTAATGTTTTTAA
1 -TTATGTAATGTTTTTAA
40803506 TTATGTA
1 TTATGTA
40803513 GTGATTTAAT
Statistics
Matches: 85, Mismatches: 20, Indels: 26
0.65 0.15 0.20
Matches are distributed among these distances:
15 3 0.04
16 3 0.04
17 31 0.36
18 9 0.11
19 9 0.11
20 24 0.28
21 3 0.04
22 3 0.04
ACGTcount: A:0.31, C:0.04, G:0.15, T:0.50
Consensus pattern (17 bp):
TTATGTAATGTTTTTAA
Found at i:40803414 original size:37 final size:37
Alignment explanation
Indices: 40803373--40803518 Score: 274
Period size: 37 Copynumber: 3.9 Consensus size: 37
40803363 TGTTAATTTC
40803373 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
* *
40803410 AAGACTTATGTAATGTTTTTTATTATGTAGTTATTCA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
40803447 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
40803484 AAGACTTATGTAATGTTTTTAATTATGTAGTGATT
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATT
40803519 TAATTCGGTT
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 105 1.00
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.48
Consensus pattern (37 bp):
AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
Found at i:40803420 original size:20 final size:20
Alignment explanation
Indices: 40803395--40803495 Score: 70
Period size: 20 Copynumber: 5.3 Consensus size: 20
40803385 ATGTTTTTAA
40803395 TTATGTAGTGATTCAAAGAC
1 TTATGTAGTGATTCAAAGAC
* ****
40803415 TTATGTAATG-TT-TTTTA-
1 TTATGTAGTGATTCAAAGAC
*
40803432 TTATGTAGTTATTCAAAGAC
1 TTATGTAGTGATTCAAAGAC
* ***
40803452 TTATGTAATG-TTTTTA-A-
1 TTATGTAGTGATTCAAAGAC
40803469 TTATGTAGTGATTCAAAGAC
1 TTATGTAGTGATTCAAAGAC
40803489 TTATGTA
1 TTATGTA
40803496 ATGTTTTTAA
Statistics
Matches: 55, Mismatches: 20, Indels: 12
0.63 0.23 0.14
Matches are distributed among these distances:
17 17 0.31
18 7 0.13
19 7 0.13
20 24 0.44
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.47
Consensus pattern (20 bp):
TTATGTAGTGATTCAAAGAC
Found at i:40803456 original size:74 final size:75
Alignment explanation
Indices: 40803356--40803514 Score: 279
Period size: 74 Copynumber: 2.1 Consensus size: 75
40803346 ATTACATTTC
40803356 AATTATGT-GTTAATTTCAAGACTTATGTAATGTTTTTAATTATGTAGTGATTCAAAGACTTATG
1 AATTATGTAGTTAATTTCAAGACTTATGTAATGTTTTTAATTATGTAGTGATTCAAAGACTTATG
40803420 TAATGTTTTT
66 TAATGTTTTT
*
40803430 TATTATGTAGTT-A-TTCAAAGACTTATGTAATGTTTTTAATTATGTAGTGATTCAAAGACTTAT
1 AATTATGTAGTTAATTTC-AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCAAAGACTTAT
40803493 GTAATGTTTTT
65 GTAATGTTTTT
40803504 AATTATGTAGT
1 AATTATGTAGT
40803515 GATTTAATTC
Statistics
Matches: 81, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
73 3 0.04
74 75 0.93
75 3 0.04
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.48
Consensus pattern (75 bp):
AATTATGTAGTTAATTTCAAGACTTATGTAATGTTTTTAATTATGTAGTGATTCAAAGACTTATG
TAATGTTTTT
Found at i:40803532 original size:9 final size:9
Alignment explanation
Indices: 40803518--40803559 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
40803508 ATGTAGTGAT
40803518 TTAATTCGG
1 TTAATTCGG
*
40803527 TTAATTTGG
1 TTAATTCGG
**
40803536 TTAATTCAA
1 TTAATTCGG
40803545 TTAATTCGG
1 TTAATTCGG
40803554 TTAATT
1 TTAATT
40803560 TTTAACCAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (9 bp):
TTAATTCGG
Found at i:40806780 original size:26 final size:26
Alignment explanation
Indices: 40806744--40806799 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
40806734 TGAAATTCCA
40806744 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
40806770 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
40806796 ATCA
1 ATCA
40806800 ATTTGTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.27, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:40807409 original size:19 final size:20
Alignment explanation
Indices: 40807385--40807429 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
40807375 TTGTGACATT
*
40807385 CAATGCATATG-ATGAAATG
1 CAATGCAGATGCATGAAATG
40807404 CAATGCAGATGCATGAAATG
1 CAATGCAGATGCATGAAATG
40807424 -AATGCA
1 CAATGCA
40807430 AAAAGAGACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.22
Consensus pattern (20 bp):
CAATGCAGATGCATGAAATG
Found at i:40809616 original size:27 final size:26
Alignment explanation
Indices: 40809579--40809693 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
40809569 AGCATGGCTG
* *
40809579 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
40809605 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
40809633 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
40809660 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
40809687 CCAGAAC
1 CCAGAAC
40809694 GCTTCCTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:40809638 original size:54 final size:54
Alignment explanation
Indices: 40809579--40809693 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
40809569 AGCATGGCTG
*
40809579 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
40809633 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
40809687 CCAGAAC
1 CCAGAAC
40809694 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:40811391 original size:25 final size:26
Alignment explanation
Indices: 40811297--40811405 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
40811287 CATGAAATTC
40811297 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
40811323 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
40811349 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
40811375 TTATCATG-AACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
40811400 TTATCA
1 TTATCA
40811406 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
25 23 0.28
26 58 0.72
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:40815352 original size:27 final size:26
Alignment explanation
Indices: 40815315--40815429 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
40815305 AGCATGGCTG
* *
40815315 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
40815341 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
40815369 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
40815396 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
40815423 CCAGAAC
1 CCAGAAC
40815430 GCTTCCTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:40815374 original size:54 final size:54
Alignment explanation
Indices: 40815315--40815429 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
40815305 AGCATGGCTG
*
40815315 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
40815369 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
40815423 CCAGAAC
1 CCAGAAC
40815430 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:40817100 original size:26 final size:25
Alignment explanation
Indices: 40817031--40817138 Score: 189
Period size: 25 Copynumber: 4.2 Consensus size: 25
40817021 CATGAAATTC
40817031 TTATCATGAAACATTTACCTAACCCA
1 TTATCATG-AACATTTACCTAACCCA
40817057 TTATCATGAACATTTACCTAACCCA
1 TTATCATGAACATTTACCTAACCCA
*
40817082 TTATCATGGAACATTTACCTAACCTA
1 TTATCAT-GAACATTTACCTAACCCA
40817108 TTATCATGAACATTTACCTAACCCA
1 TTATCATGAACATTTACCTAACCCA
40817133 TTATCA
1 TTATCA
40817139 ATTTGTATCA
Statistics
Matches: 79, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
25 47 0.59
26 32 0.41
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (25 bp):
TTATCATGAACATTTACCTAACCCA
Found at i:40817111 original size:51 final size:51
Alignment explanation
Indices: 40817031--40817138 Score: 198
Period size: 51 Copynumber: 2.1 Consensus size: 51
40817021 CATGAAATTC
40817031 TTATCATGAAACATTTACCTAACCCATTATCATGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCATTATCATGAACATTTACCTAACCCA
* *
40817082 TTATCATGGAACATTTACCTAACCTATTATCATGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCATTATCATGAACATTTACCTAACCCA
40817133 TTATCA
1 TTATCA
40817139 ATTTGTATCA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (51 bp):
TTATCATGAAACATTTACCTAACCCATTATCATGAACATTTACCTAACCCA
Found at i:40818232 original size:46 final size:44
Alignment explanation
Indices: 40818176--40818264 Score: 124
Period size: 46 Copynumber: 2.0 Consensus size: 44
40818166 TGTGAATGGT
*
40818176 ATAAAACAACTTAAAATAATTAATACACAAAACAATTTAAAATAAA
1 ATAAAACAACTTAAAATAAATAAT--ACAAAACAATTTAAAATAAA
* * *
40818222 ATAAAGCAACTTAAAATAAATAATATATAACAATTTAAAATAA
1 ATAAAACAACTTAAAATAAATAATACAAAACAATTTAAAATAA
40818265 CATATAGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 17 0.44
46 22 0.56
ACGTcount: A:0.64, C:0.09, G:0.01, T:0.26
Consensus pattern (44 bp):
ATAAAACAACTTAAAATAAATAATACAAAACAATTTAAAATAAA
Found at i:40818242 original size:24 final size:24
Alignment explanation
Indices: 40818215--40818264 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
40818205 AAACAATTTA
40818215 AAATAAAATA-AAGCAACTTAAAAT
1 AAATAAAATATAA-CAACTTAAAAT
* *
40818239 AAATAATATATAACAATTTAAAAT
1 AAATAAAATATAACAACTTAAAAT
40818263 AA
1 AA
40818265 CATATAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (24 bp):
AAATAAAATATAACAACTTAAAAT
Found at i:40818374 original size:28 final size:28
Alignment explanation
Indices: 40818321--40818375 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
40818311 AATAATATTT
* *
40818321 AAAAATATAAAACAGTTTAATAATAAAC
1 AAAAATATAAAACAATTAAATAATAAAC
*
40818349 AAAAATTTAAAACAATTAACAT-ATAAA
1 AAAAATATAAAACAATTAA-ATAATAAA
40818376 ACAGTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.25
Consensus pattern (28 bp):
AAAAATATAAAACAATTAAATAATAAAC
Done.