Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 115 of 297
Found at i:41248763 original size:21 final size:22
Alignment explanation
Indices: 41248739--41248779 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
41248729 ATTTTGAGCC
41248739 TCTTAATAT-TTATTTTAAATT
1 TCTTAATATATTATTTTAAATT
*
41248760 TCTTTATATATTATTTTAAA
1 TCTTAATATATTATTTTAAA
41248780 CTTGCCTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (22 bp):
TCTTAATATATTATTTTAAATT
Found at i:41248775 original size:26 final size:26
Alignment explanation
Indices: 41248640--41248775 Score: 81
Period size: 25 Copynumber: 5.4 Consensus size: 26
41248630 AATTTTCATG
* * *
41248640 TATAATATTTAATTTAAACTGT-TTTA
1 TATATTATTTATTTTAAA-TTTCTTTA
* * *
41248666 TATGTTATTCACTTTAAATTT-TTTA
1 TATATTATTTATTTTAAATTTCTTTA
41248691 TATATTATTTATTTTAAATTTCTCTTTTA
1 TATATTATTTATTTTAAA-TT-TC-TTTA
* * ** *
41248720 CATATTA-TTATTTT-GA-GCCTCT-
1 TATATTATTTATTTTAAATTTCTTTA
41248742 TA-A-TATTTATTTTAAATTTCTTTA
1 TATATTATTTATTTTAAATTTCTTTA
41248766 TATATTATTT
1 TATATTATTT
41248776 TAAACTTGCC
Statistics
Matches: 82, Mismatches: 18, Indels: 20
0.68 0.15 0.17
Matches are distributed among these distances:
20 2 0.02
21 8 0.10
22 2 0.02
23 5 0.06
24 3 0.04
25 22 0.27
26 21 0.26
27 2 0.02
28 7 0.09
29 10 0.12
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (26 bp):
TATATTATTTATTTTAAATTTCTTTA
Found at i:41250543 original size:25 final size:23
Alignment explanation
Indices: 41250515--41250561 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
41250505 AAAAAAAAAA
41250515 TTAAAAAAATTATATTTATAAAATT
1 TTAAAAAAA-TA-ATTTATAAAATT
* *
41250540 TTAAATAAATAATTTTTAAAAT
1 TTAAAAAAATAATTTATAAAAT
41250562 AAAATTTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 2 0.10
25 8 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TTAAAAAAATAATTTATAAAATT
Found at i:41253108 original size:14 final size:13
Alignment explanation
Indices: 41253079--41253131 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
41253069 TCAGTAAAAA
*
41253079 AAATTAAAAATTTT
1 AAATTAAAAA-ATT
41253093 AAATCTAAAAAATT
1 AAAT-TAAAAAATT
*
41253107 AAAATTAATAAAAAT
1 -AAATTAA-AAAATT
41253122 AAATTAAAAA
1 AAATTAAAAA
41253132 CTATAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
13 3 0.09
14 16 0.47
15 15 0.44
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATTAAAAAATT
Found at i:41253111 original size:15 final size:14
Alignment explanation
Indices: 41253078--41253131 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 14
41253068 GTCAGTAAAA
*
41253078 AAAATTAAAAATTT
1 AAAATTAAAAAATT
*
41253092 TAAATCTAAAAAATT
1 AAAAT-TAAAAAATT
*
41253107 AAAATTAATAAAAAT
1 AAAATTAA-AAAATT
41253122 -AAATTAAAAA
1 AAAATTAAAAA
41253132 CTATAAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
13 3 0.09
14 14 0.41
15 17 0.50
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAATTAAAAAATT
Found at i:41253124 original size:23 final size:23
Alignment explanation
Indices: 41253076--41253142 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 23
41253066 CTGTCAGTAA
* **
41253076 AAAAAATTAAAAATTTTAAATCT
1 AAAAAATTAAAAATTATAAAAAT
41253099 AAAAAATT-AAAATTAATAAAAAT
1 AAAAAATTAAAAATT-ATAAAAAT
*
41253122 ---AAATTAAAAACTATAAAAAT
1 AAAAAATTAAAAATTATAAAAAT
41253142 A
1 A
41253143 TTATAAAAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 13 0.35
21 5 0.14
22 6 0.16
23 13 0.35
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (23 bp):
AAAAAATTAAAAATTATAAAAAT
Found at i:41253219 original size:16 final size:17
Alignment explanation
Indices: 41253189--41253222 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
41253179 GTGTAAAATT
41253189 ATTAAAAAAATTTAATA
1 ATTAAAAAAATTTAATA
*
41253206 ATTATAAAAA-TTAATA
1 ATTAAAAAAATTTAATA
41253222 A
1 A
41253223 ACATCATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTAAAAAAATTTAATA
Found at i:41253240 original size:22 final size:23
Alignment explanation
Indices: 41253206--41253265 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 23
41253196 AAATTTAATA
41253206 ATTATAAAA-ATTAATAAACA-TC
1 ATTA-AAAATATTAATAAACATTC
*
41253228 ATTAAAAATATT-ATAAAGATTC
1 ATTAAAAATATTAATAAACATTC
*
41253250 A-TAAATATATTAATAA
1 ATTAAAAATATTAATAA
41253266 TTTATAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 19 0.58
22 14 0.42
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (23 bp):
ATTAAAAATATTAATAAACATTC
Found at i:41253244 original size:31 final size:30
Alignment explanation
Indices: 41253206--41253274 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 30
41253196 AAATTTAATA
41253206 ATTATAAAAATTAATAAACATCATTAAAAAT
1 ATTATAAAAATTAATAAACAT-ATTAAAAAT
* * * *
41253237 ATTATAAAGATTCATAAATATATTAATAAT
1 ATTATAAAAATTAATAAACATATTAAAAAT
41253267 -TTATAAAA
1 ATTATAAAA
41253275 TAAAAAATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 7 0.21
30 8 0.24
31 18 0.55
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (30 bp):
ATTATAAAAATTAATAAACATATTAAAAAT
Found at i:41254071 original size:18 final size:18
Alignment explanation
Indices: 41254048--41254083 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
41254038 AATGTATTCA
41254048 TATCATATGATA-TATATT
1 TATCATAT-ATATTATATT
41254066 TATCATATATATTATATT
1 TATCATATATATTATATT
41254084 ATAAGGTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.53
Consensus pattern (18 bp):
TATCATATATATTATATT
Found at i:41263815 original size:170 final size:170
Alignment explanation
Indices: 41263533--41263873 Score: 655
Period size: 170 Copynumber: 2.0 Consensus size: 170
41263523 GTATTTTTTT
41263533 TAAAACTCTTCAAATTTTCAATTTTCGACACTAAGACAATGATTAATCAACTAGGTACCAATTTT
1 TAAAACTCTTCAAATTTTCAATTTTCGACACTAAGACAATGATTAATCAACTAGGTACCAATTTT
* * *
41263598 GTGCGTATCGAGGGTGCTAATCCTTCCTCGTGCGTAACCGACTCCCGAACCCTTTTTTTTTTAAT
66 GGGCGTATCGAGGGTGCTAATCCTTCCTCGTGCGTAACCGACTCCCGAACCCTTTTTTTCTGAAT
41263663 TTCGTAGACCAAAATCGTTATTTCAATAAAAATTAAATCG
131 TTCGTAGACCAAAATCGTTATTTCAATAAAAATTAAATCG
41263703 TAAAACTCTTCAAATTTTCAATTTTCGACACTAAGACAATGATTAATCAACTAGGTACCAATTTT
1 TAAAACTCTTCAAATTTTCAATTTTCGACACTAAGACAATGATTAATCAACTAGGTACCAATTTT
41263768 GGGCGTATCGAGGGTGCTAATCCTTCCTCGTGCGTAACCGACTCCCGAACCCTTTTTTTCTGAAT
66 GGGCGTATCGAGGGTGCTAATCCTTCCTCGTGCGTAACCGACTCCCGAACCCTTTTTTTCTGAAT
41263833 TTCGTAGACCAAAATCGTTATTTCAATAAAAATTAAATCG
131 TTCGTAGACCAAAATCGTTATTTCAATAAAAATTAAATCG
41263873 T
1 T
41263874 TTATTAAAAA
Statistics
Matches: 168, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
170 168 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.34
Consensus pattern (170 bp):
TAAAACTCTTCAAATTTTCAATTTTCGACACTAAGACAATGATTAATCAACTAGGTACCAATTTT
GGGCGTATCGAGGGTGCTAATCCTTCCTCGTGCGTAACCGACTCCCGAACCCTTTTTTTCTGAAT
TTCGTAGACCAAAATCGTTATTTCAATAAAAATTAAATCG
Found at i:41289552 original size:132 final size:131
Alignment explanation
Indices: 41289315--41289576 Score: 303
Period size: 132 Copynumber: 2.0 Consensus size: 131
41289305 AAGGAACAGA
* * *
41289315 TCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGATCTTGTCTTCCCATATTGCTGG
1 TCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGAAGCAAATCTTGTCTTCACATATTGC-GG
* * * * * *
41289380 CGAAGTAGATCGCAGAAAACAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAGC
65 CGAAGTAGATCGAAGAAAACAGATCCTATCTTCATATATTGGTAG-GAAGTAGATCGAAGAAAGC
41289444 AGG
129 AGG
* **
41289447 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGAAAGCAAATCTTGTCTTCATGTATTG-GC
1 TCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAG-AAGCAAATCTTGTCTTCACATATTGCG-
* ** * * * *
41289511 GTGAAGTAGATCGAAGGTAGCAGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGAAAGC
64 GCGAAGTAGATCGAAGAAAACAGATCCTATCTTCATATATTGGTAGGAAGTAGATCGAAGAAAGC
41289576 A
129 A
41289577 AATCTTGTCT
Statistics
Matches: 108, Mismatches: 19, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
131 1 0.01
132 86 0.80
133 21 0.19
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (131 bp):
TCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGAAGCAAATCTTGTCTTCACATATTGCGGC
GAAGTAGATCGAAGAAAACAGATCCTATCTTCATATATTGGTAGGAAGTAGATCGAAGAAAGCAG
G
Found at i:41289588 original size:132 final size:132
Alignment explanation
Indices: 41289513--41290641 Score: 2028
Period size: 132 Copynumber: 8.6 Consensus size: 132
41289503 GTATTGGCGT
* * * * * * * * *
41289513 GAAGTAGATCGAAGGTAGCAGGTCCTATCTTCCTATATTGGTAG-GAAGTGGATCGAAGAAAGCA
1 GAAGTGGATCGAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGTA
41289577 AATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGGTCCTATCTTCCTATATTGG
65 AATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGGTCCTATCTTCCTATATTGG
41289642 TAG
130 TAG
41289645 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGTAA
1 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGTAA
41289710 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGGTCCTATCTTCCTATATTGGT
66 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGGTCCTATCTTCCTATATTGGT
41289775 AG
131 AG
41289777 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGTAA
1 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGTAA
41289842 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGGTCCTATCTTCCTATATTGGT
66 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGGTCCTATCTTCCTATATTGGT
41289907 AG
131 AG
41289909 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGTAA
1 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGTAA
41289974 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGGTCCTATCTTCCTATATTGGT
66 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGGTCCTATCTTCCTATATTGGT
41290039 AG
131 AG
41290041 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGTAA
1 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGTAA
41290106 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGGTCCTATCTTCCTATATTGGT
66 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGGTCCTATCTTCCTATATTGGT
41290171 AG
131 AG
41290173 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGTAA
1 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGTAA
41290238 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGGTCCTATCTTCCTATATTGGT
66 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGGTCCTATCTTCCTATATTGGT
41290303 AG
131 AG
41290305 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGTAA
1 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGTAA
* *
41290370 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCTTATATTGGT
66 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGGTCCTATCTTCCTATATTGGT
41290435 AG
131 AG
* *
41290437 GAAGCGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC-ACAGAAAGCA
1 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA-AGAAAGTA
* * *
41290501 GATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGA
65 AATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGGTCCTATCTTCCTATATTGG
41290566 TAG
130 TAG
* * * * * *
41290569 GAAGTGGATCCAAGATACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAG
1 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGTAA
41290634 ATCTTGTC
66 ATCTTGTC
41290642 CCTGTATTTG
Statistics
Matches: 971, Mismatches: 23, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
131 23 0.02
132 947 0.98
133 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.30
Consensus pattern (132 bp):
GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGTAA
ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGGTCCTATCTTCCTATATTGGT
AG
Found at i:41290815 original size:40 final size:42
Alignment explanation
Indices: 41290770--41290877 Score: 123
Period size: 40 Copynumber: 2.6 Consensus size: 42
41290760 CCGATAACTC
* * *
41290770 ATCTCCCTAAGCAGTAGTGGAGCAGATCG-CATCA-AG-TCTT
1 ATCTCCCTAAGCAGTAGTGGAGCAGA-AGAAACCACAGATCTT
* *
41290810 ATCTCCTTAAGCAGTAGCGGAGCAGAAGAAACCACAGATCTT
1 ATCTCCCTAAGCAGTAGTGGAGCAGAAGAAACCACAGATCTT
**
41290852 ATCTCCCTAAATAGTAGTGGAGCAGA
1 ATCTCCCTAAGCAGTAGTGGAGCAGA
41290878 CTAAAAACAC
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
39 1 0.02
40 27 0.48
41 2 0.04
42 26 0.46
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.22
Consensus pattern (42 bp):
ATCTCCCTAAGCAGTAGTGGAGCAGAAGAAACCACAGATCTT
Found at i:41305587 original size:495 final size:495
Alignment explanation
Indices: 41304657--41310405 Score: 11426
Period size: 495 Copynumber: 11.6 Consensus size: 495
41304647 AACAAGAAGN
41304657 TAATATAAATAAGCAATTGCAACTCAAATCTCGATCTCAGTTGTCACAAATCACTCACCCAAGTT
1 TAATATAAATAAGCAATTGCAACTCAAATCTCGATCTCAGTTGTCACAAATCACTCACCCAAGTT
41304722 TAAAAAAATGAAATTATCCCATTAATGATCTTGAGTATTTATCAACTAAAAATCATCATAAATTA
66 TAAAAAAATGAAATTATCCCATTAATGATCTTGAGTATTTATCAACTAAAAATCATCATAAATTA
41304787 GTCTTTTAACGATACCAAAACTCTCTCAAAAGATAAACATTATCATTACTTTAAACTTCTTAATA
131 GTCTTTTAACGATACCAAAACTCTCTCAAAAGATAAACATTATCATTACTTTAAACTTCTTAATA
41304852 TGACTAGTTAAAGAGATGAAAAGTCCTACAAAACTCCATTGAATAAACATGATATTTATCACTAA
196 TGACTAGTTAAAGAGATGAAAAGTCCTACAAAACTCCATTGAATAAACATGATATTTATCACTAA
41304917 AACAATATTTTTATCATCTAGAGCTAATAAAACTTTCATGTTTACTTTTAAAATCTTTTTAGTTT
261 AACAATATTTTTATCATCTAGAGCTAATAAAACTTTCATGTTTACTTTTAAAATCTTTTTAGTTT
41304982 CAAAGCTGAAAAATAATTAGCCTAAAAATACGATAAATCAACAATTAGAACAAAAGCATATAATG
326 CAAAGCTGAAAAATAATTAGCCTAAAAATACGATAAATCAACAATTAGAACAAAAGCATATAATG
41305047 TAAAAAATAAGAGCAGAAAAGAACCAACACAAACGTTATTTGTTAATGCAATTCAAACACAAGGA
391 TAAAAAATAAGAGCAGAAAAGAACCAACACAAACGTTATTTGTTAATGCAATTCAAACACAAGGA
41305112 TTTTATATCTGCAGAGTCTTGACTTAAGCTCAATTCACCC
456 TTTTATATCTGCAGAGTCTTGACTTAAGCTCAATTCACCC
41305152 TAATATAAATAAGCAATTGCAACTCAAATCTCGATCTCAGTTGTCACAAATCACTCACCCAAGTT
1 TAATATAAATAAGCAATTGCAACTCAAATCTCGATCTCAGTTGTCACAAATCACTCACCCAAGTT
41305217 TAAAAAAATGAAATTATCCCATTAATGATCTTGAGTATTTATCAACTAAAAATCATCATAAATTA
66 TAAAAAAATGAAATTATCCCATTAATGATCTTGAGTATTTATCAACTAAAAATCATCATAAATTA
41305282 GTCTTTTAACGATACCAAAACTCTCTCAAAAGATAAACATTATCATTACTTTAAACTTCTTAATA
131 GTCTTTTAACGATACCAAAACTCTCTCAAAAGATAAACATTATCATTACTTTAAACTTCTTAATA
41305347 TGACTAGTTAAAGAGATGAAAAGTCCTACAAAACTCCATTGAATAAACATGATATTTATCACTAA
196 TGACTAGTTAAAGAGATGAAAAGTCCTACAAAACTCCATTGAATAAACATGATATTTATCACTAA
41305412 AACAATATTTTTATCATCTAGAGCTAATAAAACTTTCATGTTTACTTTTAAAATCTTTTTAGTTT
261 AACAATATTTTTATCATCTAGAGCTAATAAAACTTTCATGTTTACTTTTAAAATCTTTTTAGTTT
41305477 CAAAGCTGAAAAATAATTAGCCTAAAAATACGATAAATCAACAATTAGAACAAAAGCATATAATG
326 CAAAGCTGAAAAATAATTAGCCTAAAAATACGATAAATCAACAATTAGAACAAAAGCATATAATG
41305542 TAAAAAATAAGAGCAGAAAAGAACCAACACAAACGTTATTTGTTAATGCAATTCAAACACAAGGA
391 TAAAAAATAAGAGCAGAAAAGAACCAACACAAACGTTATTTGTTAATGCAATTCAAACACAAGGA
41305607 TTTTATATCTGCAGAGTCTTGACTTAAGCTCAATTCACCC
456 TTTTATATCTGCAGAGTCTTGACTTAAGCTCAATTCACCC
41305647 TAATATAAATAAGCAATTGCAACTCAAATCTCGATCTCAGTTGTCACAAATCACTCACCCAAGTT
1 TAATATAAATAAGCAATTGCAACTCAAATCTCGATCTCAGTTGTCACAAATCACTCACCCAAGTT
41305712 TAAAAAAATGAAATTATCCCATTAATGATCTTGAGTATTTATCAACTAAAAATCATCATAAATTA
66 TAAAAAAATGAAATTATCCCATTAATGATCTTGAGTATTTATCAACTAAAAATCATCATAAATTA
41305777 GTCTTTTAACGATACCAAAACTCTCTCAAAAGATAAACATTATCATTACTTTAAACTTCTTAATA
131 GTCTTTTAACGATACCAAAACTCTCTCAAAAGATAAACATTATCATTACTTTAAACTTCTTAATA
41305842 TGACTAGTTAAAGAGATGAAAAGTCCTACAAAACTCCATTGAATAAACATGATATTTATCACTAA
196 TGACTAGTTAAAGAGATGAAAAGTCCTACAAAACTCCATTGAATAAACATGATATTTATCACTAA
41305907 AACAATATTTTTATCATCTAGAGCTAATAAAACTTTCATGTTTACTTTTAAAATCTTTTTAGTTT
261 AACAATATTTTTATCATCTAGAGCTAATAAAACTTTCATGTTTACTTTTAAAATCTTTTTAGTTT
41305972 CAAAGCTGAAAAATAATTAGCCTAAAAATACGATAAATCAACAATTAGAACAAAAGCATATAATG
326 CAAAGCTGAAAAATAATTAGCCTAAAAATACGATAAATCAACAATTAGAACAAAAGCATATAATG
41306037 TAAAAAATAAGAGCAGAAAAGAACCAACACAAACGTTATTTGTTAATGCAATTCAAACACAAGGA
391 TAAAAAATAAGAGCAGAAAAGAACCAACACAAACGTTATTTGTTAATGCAATTCAAACACAAGGA
41306102 TTTTATATCTGCAGAGTCTTGACTTAAGCTCAATTCACCC
456 TTTTATATCTGCAGAGTCTTGACTTAAGCTCAATTCACCC
41306142 TAATATAAATAAGCAATTGCAACTCAAATCTCGATCTCAGTTGTCACAAATCACTCACCCAAGTT
1 TAATATAAATAAGCAATTGCAACTCAAATCTCGATCTCAGTTGTCACAAATCACTCACCCAAGTT
41306207 TAAAAAAATGAAATTATCCCATTAATGATCTTGAGTATTTATCAACTAAAAATCATCATAAATTA
66 TAAAAAAATGAAATTATCCCATTAATGATCTTGAGTATTTATCAACTAAAAATCATCATAAATTA
41306272 GTCTTTTAACGATACCAAAACTCTCTCAAAAGATAAACATTATCATTACTTTAAACTTCTTAATA
131 GTCTTTTAACGATACCAAAACTCTCTCAAAAGATAAACATTATCATTACTTTAAACTTCTTAATA
41306337 TGACTAGTTAAAGAGATGAAAAGTCCTACAAAACTCCATTGAATAAACATGATATTTATCACTAA
196 TGACTAGTTAAAGAGATGAAAAGTCCTACAAAACTCCATTGAATAAACATGATATTTATCACTAA
41306402 AACAATATTTTTATCATCTAGAGCTAATAAAACTTTCATGTTTACTTTTAAAATCTTTTTAGTTT
261 AACAATATTTTTATCATCTAGAGCTAATAAAACTTTCATGTTTACTTTTAAAATCTTTTTAGTTT
41306467 CAAAGCTGAAAAATAATTAGCCTAAAAATACGATAAATCAACAATTAGAACAAAAGCATATAATG
326 CAAAGCTGAAAAATAATTAGCCTAAAAATACGATAAATCAACAATTAGAACAAAAGCATATAATG
41306532 TAAAAAATAAGAGCAGAAAAGAACCAACACAAACGTTATTTGTTAATGCAATTCAAACACAAGGA
391 TAAAAAATAAGAGCAGAAAAGAACCAACACAAACGTTATTTGTTAATGCAATTCAAACACAAGGA
41306597 TTTTATATCTGCAGAGTCTTGACTTAAGCTCAATTCACCC
456 TTTTATATCTGCAGAGTCTTGACTTAAGCTCAATTCACCC
41306637 TAATATAAATAAGCAATTGCAACTCAAATCTCGATCTCAGTTGTCACAAATCACTCACCCAAGTT
1 TAATATAAATAAGCAATTGCAACTCAAATCTCGATCTCAGTTGTCACAAATCACTCACCCAAGTT
41306702 TAAAAAAATGAAATTATCCCATTAATGATCTTGAGTATTTATCAACTAAAAATCATCATAAATTA
66 TAAAAAAATGAAATTATCCCATTAATGATCTTGAGTATTTATCAACTAAAAATCATCATAAATTA
41306767 GTCTTTTAACGATACCAAAACTCTCTCAAAAGATAAACATTATCATTACTTTAAACTTCTTAATA
131 GTCTTTTAACGATACCAAAACTCTCTCAAAAGATAAACATTATCATTACTTTAAACTTCTTAATA
41306832 TGACTAGTTAAAGAGATGAAAAGTCCTACAAAACTCCATTGAATAAACATGATATTTATCACTAA
196 TGACTAGTTAAAGAGATGAAAAGTCCTACAAAACTCCATTGAATAAACATGATATTTATCACTAA
41306897 AACAATATTTTTATCATCTAGAGCTAATAAAACTTTCATGTTTACTTTTAAAATCTTTTTAGTTT
261 AACAATATTTTTATCATCTAGAGCTAATAAAACTTTCATGTTTACTTTTAAAATCTTTTTAGTTT
41306962 CAAAGCTGAAAAATAATTAGCCTAAAAATACGATAAATCAACAATTAGAACAAAAGCATATAATG
326 CAAAGCTGAAAAATAATTAGCCTAAAAATACGATAAATCAACAATTAGAACAAAAGCATATAATG
41307027 TAAAAAATAAGAGCAGAAAAGAACCAACACAAACGTTATTTGTTAATGCAATTCAAACACAAGGA
391 TAAAAAATAAGAGCAGAAAAGAACCAACACAAACGTTATTTGTTAATGCAATTCAAACACAAGGA
41307092 TTTTATATCTGCAGAGTCTTGACTTAAGCTCAATTCACCC
456 TTTTATATCTGCAGAGTCTTGACTTAAGCTCAATTCACCC
41307132 TAATATAAATAAGCAATTGCAACTCAAATCTCGATCTCAGTTGTCACAAATCACTCACCCAAGTT
1 TAATATAAATAAGCAATTGCAACTCAAATCTCGATCTCAGTTGTCACAAATCACTCACCCAAGTT
41307197 TAAAAAAATGAAATTATCCCATTAATGATCTTGAGTATTTATCAACTAAAAATCATCATAAATTA
66 TAAAAAAATGAAATTATCCCATTAATGATCTTGAGTATTTATCAACTAAAAATCATCATAAATTA
41307262 GTCTTTTAACGATACCAAAACTCTCTCAAAAGATAAACATTATCATTACTTTAAACTTCTTAATA
131 GTCTTTTAACGATACCAAAACTCTCTCAAAAGATAAACATTATCATTACTTTAAACTTCTTAATA
41307327 TGACTAGTTAAAGAGATGAAAAGTCCTACAAAACTCCATTGAATAAACATGATATTTATCACTAA
196 TGACTAGTTAAAGAGATGAAAAGTCCTACAAAACTCCATTGAATAAACATGATATTTATCACTAA
41307392 AACAATATTTTTATCATCTAGAGCTAATAAAACTTTCATGTTTACTTTTAAAATCTTTTTAGTTT
261 AACAATATTTTTATCATCTAGAGCTAATAAAACTTTCATGTTTACTTTTAAAATCTTTTTAGTTT
41307457 CAAAGCTGAAAAATAATTAGCCTAAAAATACGATAAATCAACAATTAGAACAAAAGCATATAATG
326 CAAAGCTGAAAAATAATTAGCCTAAAAATACGATAAATCAACAATTAGAACAAAAGCATATAATG
41307522 TAAAAAATAAGAGCAGAAAAGAACCAACACAAACGTTATTTGTTAATGCAATTCAAACACAAGGA
391 TAAAAAATAAGAGCAGAAAAGAACCAACACAAACGTTATTTGTTAATGCAATTCAAACACAAGGA
41307587 TTTTATATCTGCAGAGTCTTGACTTAAGCTCAATTCACCC
456 TTTTATATCTGCAGAGTCTTGACTTAAGCTCAATTCACCC
41307627 TAATATAAATAAGCAATTGCAACTCAAATCTCGATCTCAGTTGTCACAAATCACTCACCCAAGTT
1 TAATATAAATAAGCAATTGCAACTCAAATCTCGATCTCAGTTGTCACAAATCACTCACCCAAGTT
41307692 TAAAAAAATGAAATTATCCCATTAATGATCTTGAGTATTTATCAACTAAAAATCATCATAAATTA
66 TAAAAAAATGAAATTATCCCATTAATGATCTTGAGTATTTATCAACTAAAAATCATCATAAATTA
41307757 GTCTTTTAACGATACCAAAACTCTCTCAAAAGATAAACATTATCATTACTTTAAACTTCTTAATA
131 GTCTTTTAACGATACCAAAACTCTCTCAAAAGATAAACATTATCATTACTTTAAACTTCTTAATA
41307822 TGACTAGTTAAAGAGATGAAAAGTCCTACAAAACTCCATTGAATAAACATGATATTTATCACTAA
196 TGACTAGTTAAAGAGATGAAAAGTCCTACAAAACTCCATTGAATAAACATGATATTTATCACTAA
41307887 AACAATATTTTTATCATCTAGAGCTAATAAAACTTTCATGTTTACTTTTAAAATCTTTTTAGTTT
261 AACAATATTTTTATCATCTAGAGCTAATAAAACTTTCATGTTTACTTTTAAAATCTTTTTAGTTT
41307952 CAAAGCTGAAAAATAATTAGCCTAAAAATACGATAAATCAACAATTAGAACAAAAGCATATAATG
326 CAAAGCTGAAAAATAATTAGCCTAAAAATACGATAAATCAACAATTAGAACAAAAGCATATAATG
41308017 TAAAAAATAAGAGCAGAAAAGAACCAACACAAACGTTATTTGTTAATGCAATTCAAACACAAGGA
391 TAAAAAATAAGAGCAGAAAAGAACCAACACAAACGTTATTTGTTAATGCAATTCAAACACAAGGA
41308082 TTTTATATCTGCAGAGTCTTGACTTAAGCTCAATTCACCC
456 TTTTATATCTGCAGAGTCTTGACTTAAGCTCAATTCACCC
41308122 TAATATAAATAAGCAATTGCAACTCAAATCTCGATCTCAGTTGTCACAAATCACTCACCCAAGTT
1 TAATATAAATAAGCAATTGCAACTCAAATCTCGATCTCAGTTGTCACAAATCACTCACCCAAGTT
41308187 TAAAAAAATGAAATTATCCCATTAATGATCTTGAGTATTTATCAACTAAAAATCATCATAAATTA
66 TAAAAAAATGAAATTATCCCATTAATGATCTTGAGTATTTATCAACTAAAAATCATCATAAATTA
41308252 GTCTTTTAACGATACCAAAACTCTCTCAAAAGATAAACATTATCATTACTTTAAACTTCTTAATA
131 GTCTTTTAACGATACCAAAACTCTCTCAAAAGATAAACATTATCATTACTTTAAACTTCTTAATA
41308317 TGACTAGTTAAAGAGATGAAAAGTCCTACAAAACTCCATTGAATAAACATGATATTTATCACTAA
196 TGACTAGTTAAAGAGATGAAAAGTCCTACAAAACTCCATTGAATAAACATGATATTTATCACTAA
41308382 AACAATATTTTTATCATCTAGAGCTAATAAAACTTTCATGTTTACTTTTAAAATCTTTTTAGTTT
261 AACAATATTTTTATCATCTAGAGCTAATAAAACTTTCATGTTTACTTTTAAAATCTTTTTAGTTT
*
41308447 CAAAGCTGAAAAATAATTAGCCTACAAATACGATAAATCAACAATTAGAACAAAAGCATATAATG
326 CAAAGCTGAAAAATAATTAGCCTAAAAATACGATAAATCAACAATTAGAACAAAAGCATATAATG
41308512 TAAAAAATAAGAGCAGAAAAGAACCAACACAAACGTTATTTGTTAATGCAATTCAAACACAAGGA
391 TAAAAAATAAGAGCAGAAAAGAACCAACACAAACGTTATTTGTTAATGCAATTCAAACACAAGGA
41308577 TTTTATATCTGCAGAGTCTTGACTTAAGCTCAATTCACCC
456 TTTTATATCTGCAGAGTCTTGACTTAAGCTCAATTCACCC
41308617 TAATATAAATAAGCAATTGCAACTCAAATCTCGATCTCAGTTGTCACAAATCACTCACCCAAGTT
1 TAATATAAATAAGCAATTGCAACTCAAATCTCGATCTCAGTTGTCACAAATCACTCACCCAAGTT
41308682 TAAAAAAATGAAATTATCCCATTAATGATCTTGAGTATTTATCAACTAAAAATCATCATAAATTA
66 TAAAAAAATGAAATTATCCCATTAATGATCTTGAGTATTTATCAACTAAAAATCATCATAAATTA
41308747 GTCTTTTAACGATACCAAAACTCTCTCAAAAGATAAACATTATCATTACTTTAAACTTCTTAATA
131 GTCTTTTAACGATACCAAAACTCTCTCAAAAGATAAACATTATCATTACTTTAAACTTCTTAATA
41308812 TGACTAGTTAAAGAGATGAAAAGTCCTACAAAACTCCATTGAATAAACATGATATTTATCACTAA
196 TGACTAGTTAAAGAGATGAAAAGTCCTACAAAACTCCATTGAATAAACATGATATTTATCACTAA
41308877 AACAATATTTTTATCATCTAGAGCTAATAAAACTTTCATGTTTACTTTTAAAATCTTTTTAGTTT
261 AACAATATTTTTATCATCTAGAGCTAATAAAACTTTCATGTTTACTTTTAAAATCTTTTTAGTTT
*
41308942 CAAAGCTGAAAAATAATTAGCCTACAAATACGATAAATCAACAATTAGAACAAAAGCATATAATG
326 CAAAGCTGAAAAATAATTAGCCTAAAAATACGATAAATCAACAATTAGAACAAAAGCATATAATG
*
41309007 TAAAAAATAAGAGCAGAAAAGAACCAACACAAACGTTATTTGTTAACGCAATTCAAACACAAGGA
391 TAAAAAATAAGAGCAGAAAAGAACCAACACAAACGTTATTTGTTAATGCAATTCAAACACAAGGA
41309072 TTTTATATCTGCAGAGTCTTGACTTAAGCTCAATTCACCC
456 TTTTATATCTGCAGAGTCTTGACTTAAGCTCAATTCACCC
41309112 TAATATAAATAAGCAATTGCAACTCAAATCTCGATCTCAGTTGTCACAAATCACTCACCCAAGTT
1 TAATATAAATAAGCAATTGCAACTCAAATCTCGATCTCAGTTGTCACAAATCACTCACCCAAGTT
41309177 TAAAAAAATGAAATTATCCCATTAATGATCTTGAGTATTTATCAACTAAAAATCATCATAAATTA
66 TAAAAAAATGAAATTATCCCATTAATGATCTTGAGTATTTATCAACTAAAAATCATCATAAATTA
41309242 GTCTTTTAACGATACCAAAACTCTCTCAAAAGATAAACATTATCATTACTTTAAACTTCTTAATA
131 GTCTTTTAACGATACCAAAACTCTCTCAAAAGATAAACATTATCATTACTTTAAACTTCTTAATA
41309307 TGACTAGTTAAAGAGATGAAAAGTCCTACAAAACTCCATTGAATAAACATGATATTTATCACTAA
196 TGACTAGTTAAAGAGATGAAAAGTCCTACAAAACTCCATTGAATAAACATGATATTTATCACTAA
41309372 AACAATATTTTTATCATCTAGAGCTAATAAAACTTTCATGTTTACTTTTAAAATCTTTTTAGTTT
261 AACAATATTTTTATCATCTAGAGCTAATAAAACTTTCATGTTTACTTTTAAAATCTTTTTAGTTT
*
41309437 CAAAGCTGAAAAATAATTAGCCTACAAATACGATAAATCAACAATTAGAACAAAAGCATATAATG
326 CAAAGCTGAAAAATAATTAGCCTAAAAATACGATAAATCAACAATTAGAACAAAAGCATATAATG
*
41309502 TAAAAAATAAGAGCAGAAAAGAACCAACACAAACGTTATTTGTTAACGCAATTCAAACACAAGGA
391 TAAAAAATAAGAGCAGAAAAGAACCAACACAAACGTTATTTGTTAATGCAATTCAAACACAAGGA
41309567 TTTTATATCTGCAGAGTCTTGACTTAAGCTCAATTCACCC
456 TTTTATATCTGCAGAGTCTTGACTTAAGCTCAATTCACCC
41309607 TAATATAAATAAGCAATTGCAACTCAAATCTCGATCTCAGTTGTCACAAATCACTCACCCAAGTT
1 TAATATAAATAAGCAATTGCAACTCAAATCTCGATCTCAGTTGTCACAAATCACTCACCCAAGTT
41309672 TAAAAAAATGAAATTATCCCATTAATGATCTTGAGTATTTATCAACTAAAAATCATCATAAATTA
66 TAAAAAAATGAAATTATCCCATTAATGATCTTGAGTATTTATCAACTAAAAATCATCATAAATTA
41309737 GTCTTTTAACGATACCAAAACTCTCTCAAAAGATAAACATTATCATTACTTTAAACTTCTTAATA
131 GTCTTTTAACGATACCAAAACTCTCTCAAAAGATAAACATTATCATTACTTTAAACTTCTTAATA
41309802 TGACTAGTTAAAGAGATGAAAAGTCCTACAAAACTCCATTGAATAAACATGATATTTATCACTAA
196 TGACTAGTTAAAGAGATGAAAAGTCCTACAAAACTCCATTGAATAAACATGATATTTATCACTAA
41309867 AACAATATTTTTATCATCTAGAGCTAATAAAACTTTCATGTTTACTTTTAAAATCTTTTTAGTTT
261 AACAATATTTTTATCATCTAGAGCTAATAAAACTTTCATGTTTACTTTTAAAATCTTTTTAGTTT
*
41309932 CAAAGCTGAAAAATAATTAGCCTACAAATACGATAAATCAACAATTAGAACAAAAGCATATAATG
326 CAAAGCTGAAAAATAATTAGCCTAAAAATACGATAAATCAACAATTAGAACAAAAGCATATAATG
*
41309997 TAAAAAATAAGAGCAGAAAAGAACCAACACAAACGTTATTTGTTAACGCAATTCAAACACAAGGA
391 TAAAAAATAAGAGCAGAAAAGAACCAACACAAACGTTATTTGTTAATGCAATTCAAACACAAGGA
41310062 TTTTATATCTGCAGAGTCTTGACTTAAGCTCAATTCACCC
456 TTTTATATCTGCAGAGTCTTGACTTAAGCTCAATTCACCC
41310102 TAATATAAATAAGCAATTGCAACTCAAATCTCGATCTCAGTTGTCACAAATCACTCACCCAAGTT
1 TAATATAAATAAGCAATTGCAACTCAAATCTCGATCTCAGTTGTCACAAATCACTCACCCAAGTT
*
41310167 TAAAAAAATGAAATTATCCCATTAATGATCCTGAGTATTTATCAACTAAAAATCATCATAAATTA
66 TAAAAAAATGAAATTATCCCATTAATGATCTTGAGTATTTATCAACTAAAAATCATCATAAATTA
41310232 GTCTTTTAACGATACCAAAACTCTCTCAAAAGATAAACATTATCATTACTTTAAACTTCTTAATA
131 GTCTTTTAACGATACCAAAACTCTCTCAAAAGATAAACATTATCATTACTTTAAACTTCTTAATA
41310297 TGACTAGTTAAAGAGATGAAAAGTCCTACAAAACTCCATTGAATAAACATGATATTTATCACTAA
196 TGACTAGTTAAAGAGATGAAAAGTCCTACAAAACTCCATTGAATAAACATGATATTTATCACTAA
41310362 AACAATATTTTTATCATCTAGAGCTAATAAAACTTTCATGTTTA
261 AACAATATTTTTATCATCTAGAGCTAATAAAACTTTCATGTTTA
41310406 TCCAATCACC
Statistics
Matches: 5251, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
495 5251 1.00
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (495 bp):
TAATATAAATAAGCAATTGCAACTCAAATCTCGATCTCAGTTGTCACAAATCACTCACCCAAGTT
TAAAAAAATGAAATTATCCCATTAATGATCTTGAGTATTTATCAACTAAAAATCATCATAAATTA
GTCTTTTAACGATACCAAAACTCTCTCAAAAGATAAACATTATCATTACTTTAAACTTCTTAATA
TGACTAGTTAAAGAGATGAAAAGTCCTACAAAACTCCATTGAATAAACATGATATTTATCACTAA
AACAATATTTTTATCATCTAGAGCTAATAAAACTTTCATGTTTACTTTTAAAATCTTTTTAGTTT
CAAAGCTGAAAAATAATTAGCCTAAAAATACGATAAATCAACAATTAGAACAAAAGCATATAATG
TAAAAAATAAGAGCAGAAAAGAACCAACACAAACGTTATTTGTTAATGCAATTCAAACACAAGGA
TTTTATATCTGCAGAGTCTTGACTTAAGCTCAATTCACCC
Found at i:41310863 original size:14 final size:15
Alignment explanation
Indices: 41310829--41310869 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
41310819 TTTTTAATGA
41310829 ATTTGTATATATTTT
1 ATTTGTATATATTTT
*
41310844 -TATGTATA-ATTTT
1 ATTTGTATATATTTT
41310857 ATTTGTAATATAT
1 ATTTGT-ATATAT
41310870 ATATAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
13 5 0.24
14 11 0.52
15 3 0.14
16 2 0.10
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (15 bp):
ATTTGTATATATTTT
Found at i:41314318 original size:47 final size:47
Alignment explanation
Indices: 41314265--41314358 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
41314255 AAATGCTGAT
* *
41314265 TCATATCCAATCGCCTGTTTGCTTTTATAGCAATGTTCGGGGAAAGA
1 TCATATCCAATCGCCTGTTTGCTTTAATAGCAATGTTCGGGCAAAGA
*
41314312 TCATATCCAATCGCCTGTTTGCTTTAATAGCATTGTTCGGGCAAAGA
1 TCATATCCAATCGCCTGTTTGCTTTAATAGCAATGTTCGGGCAAAGA
41314359 GTGAGTTGGG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (47 bp):
TCATATCCAATCGCCTGTTTGCTTTAATAGCAATGTTCGGGCAAAGA
Found at i:41317506 original size:2 final size:2
Alignment explanation
Indices: 41317499--41317523 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41317489 GCCTGCTATT
41317499 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
41317524 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:41321477 original size:2 final size:2
Alignment explanation
Indices: 41321470--41321500 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
41321460 TACCTACCTC
41321470 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
41321501 TTACTTCTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:41325069 original size:31 final size:31
Alignment explanation
Indices: 41325028--41325090 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
41325018 TTTGAAAATT
* *
41325028 AGGGGCTTAAT-ATGAACTTTCAAAAATTTTG
1 AGGGGATTAATGA-GAACTTTCAAAAAATTTG
*
41325059 AGGGGATTAATGAGAATTTTCAAAAAATTTG
1 AGGGGATTAATGAGAACTTTCAAAAAATTTG
41325090 A
1 A
41325091 AAGGTTCAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (31 bp):
AGGGGATTAATGAGAACTTTCAAAAAATTTG
Found at i:41325975 original size:11 final size:11
Alignment explanation
Indices: 41325961--41325991 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
41325951 TTTTTTGCTA
41325961 TTTTTTTATTG
1 TTTTTTTATTG
41325972 TTTTTTTATTG
1 TTTTTTTATTG
*
41325983 TTTTGTTAT
1 TTTTTTTAT
41325992 CATTTCGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.81
Consensus pattern (11 bp):
TTTTTTTATTG
Found at i:41335107 original size:30 final size:30
Alignment explanation
Indices: 41335073--41335134 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
41335063 ACTTATTTTC
41335073 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
* * *
41335103 TTGTTATTTTTTTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
41335133 TT
1 TT
41335135 ACTTGTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.23, C:0.03, G:0.13, T:0.61
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:41335285 original size:10 final size:11
Alignment explanation
Indices: 41335259--41335292 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
41335249 TATATATATT
41335259 TAAAAATAATA
1 TAAAAATAATA
*
41335270 TAAAAATAGTA
1 TAAAAATAATA
41335281 TAAAAATTAATA
1 TAAAAA-TAATA
41335293 CAGGCCCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:41340469 original size:30 final size:30
Alignment explanation
Indices: 41340435--41340521 Score: 75
Period size: 31 Copynumber: 2.8 Consensus size: 30
41340425 ATACATATTA
* * *
41340435 TTTGATTTGGTGCAATTATACGCATGAAAC
1 TTTGATTTGATGCAAATATACACATGAAAC
* *
41340465 TTTGATTGTGATTCAAATATATACATGAAAC
1 TTTGATT-TGATGCAAATATACACATGAAAC
* * * *
41340496 TTTCATTTTGATTCAATTACACACAT
1 TTTGA-TTTGATGCAAATATACACAT
41340522 TTAAAGAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
30 7 0.15
31 37 0.80
32 2 0.04
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (30 bp):
TTTGATTTGATGCAAATATACACATGAAAC
Found at i:41341329 original size:26 final size:25
Alignment explanation
Indices: 41341300--41341352 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
41341290 CTCTTTTGAG
*
41341300 TTTATAAA-TTCTCTTTGAGTTTTCTT
1 TTTAAAAATTTCTC-TTGAG-TTTCTT
41341326 TTTAAAAATTTCTCTTGAGTTTCTT
1 TTTAAAAATTTCTCTTGAGTTTCTT
41341351 TT
1 TT
41341353 AGAAGAGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 8 0.32
26 12 0.48
27 5 0.20
ACGTcount: A:0.21, C:0.11, G:0.08, T:0.60
Consensus pattern (25 bp):
TTTAAAAATTTCTCTTGAGTTTCTT
Found at i:41348830 original size:19 final size:20
Alignment explanation
Indices: 41348783--41348832 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
41348773 CTCAAAAAAA
**
41348783 TTATAAAAAAATAAAATAAT
1 TTATAAAAATTTAAAATAAT
*
41348803 TT-TTAAAATTTAAAAT-AT
1 TTATAAAAATTTAAAATAAT
41348821 TTATAAAAATTT
1 TTATAAAAATTT
41348833 GAATATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 4 0.16
19 19 0.76
20 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TTATAAAAATTTAAAATAAT
Found at i:41348845 original size:20 final size:19
Alignment explanation
Indices: 41348807--41348845 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
41348797 AATAATTTTT
*
41348807 AAAATTTAAAATATTTATA
1 AAAATTTAAAATATATATA
*
41348826 AAAATTTGAATATATATATA
1 AAAATTT-AAAATATATATA
41348846 TTTAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
AAAATTTAAAATATATATA
Found at i:41348867 original size:25 final size:26
Alignment explanation
Indices: 41348817--41348870 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
41348807 AAAATTTAAA
* *
41348817 ATATTTATAAAAATTTGAATATATAT
1 ATATTTATAAAAATTTAAAGATATAT
41348843 ATATTTA-AAAAATTCTAAAGA-ATAT
1 ATATTTATAAAAATT-TAAAGATATAT
41348868 ATA
1 ATA
41348871 AAGAAGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (26 bp):
ATATTTATAAAAATTTAAAGATATAT
Found at i:41356633 original size:18 final size:18
Alignment explanation
Indices: 41356610--41356666 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
41356600 CCCAACTACT
*
41356610 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
41356628 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
41356646 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
41356664 GTA
1 GTA
41356667 AACGGTCGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:41363584 original size:5 final size:5
Alignment explanation
Indices: 41363574--41363600 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
41363564 ATTATATATG
41363574 TTCTT TTCTT TTCTT TTCTT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TT
41363601 TTGATTTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTCTT
Found at i:41364381 original size:12 final size:12
Alignment explanation
Indices: 41364366--41364400 Score: 61
Period size: 13 Copynumber: 2.8 Consensus size: 12
41364356 TGAGACAATA
41364366 TATTCTTTAAAT
1 TATTCTTTAAAT
41364378 TATTCTTTTAAAT
1 TATTC-TTTAAAT
41364391 TATTCTTTAA
1 TATTCTTTAA
41364401 GTAACATAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTCTTTAAAT
Found at i:41364549 original size:19 final size:22
Alignment explanation
Indices: 41364503--41364548 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
41364493 AAGTAGGTTG
41364503 TATATTATTTTTTGTAATATTA
1 TATATTATTTTTTGTAATATTA
41364525 TATATTATTTTTAT-TAAT-TTA
1 TATATTATTTTT-TGTAATATTA
41364546 TAT
1 TAT
41364549 TTTAATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.26
22 16 0.70
23 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TATATTATTTTTTGTAATATTA
Found at i:41364601 original size:21 final size:20
Alignment explanation
Indices: 41364572--41364611 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
41364562 ATATTAAGAA
41364572 TATTATTAAATTATATATTAT
1 TATTATTAAATTATA-ATTAT
*
41364593 TATTGTTAAATTATAATTA
1 TATTATTAAATTATAATTA
41364612 ATAATAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TATTATTAAATTATAATTAT
Found at i:41364675 original size:58 final size:60
Alignment explanation
Indices: 41364523--41364676 Score: 140
Period size: 58 Copynumber: 2.5 Consensus size: 60
41364513 TTTGTAATAT
* * **
41364523 TATA-TATTATTTTTATTAATTTATATTTTAATAATTGCTATATTAAGAATATTATTAAATTA
1 TATATTATTATTTTTATTAAATTATA--TTAATAAAT-CTATATTAAGAATAGGATTAAATTA
* *
41364585 TATATTATTATTGTTAAATTATAATTA-A-TAATAAAT-T-TATTAA-AATAGGGTTAAATTA
1 TATATTATTATT-TT-TATTA-AATTATATTAATAAATCTATATTAAGAATAGGATTAAATTA
*
41364643 TGTATTATTATTTTTATTAAATTATATCTAATAA
1 TATATTATTATTTTTATTAAATTATAT-TAATAA
41364677 TAATCCTATT
Statistics
Matches: 77, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
55 5 0.06
56 5 0.06
57 2 0.03
58 29 0.38
59 6 0.08
60 1 0.01
62 11 0.14
63 7 0.09
64 2 0.03
65 5 0.06
66 4 0.05
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (60 bp):
TATATTATTATTTTTATTAAATTATATTAATAAATCTATATTAAGAATAGGATTAAATTA
Found at i:41364870 original size:16 final size:16
Alignment explanation
Indices: 41364851--41364920 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
41364841 TTGAATTGCT
*
41364851 ATTACAGTTCTATTCT
1 ATTACAGTTCTATTCC
*
41364867 ATTACAATTCTATTCC
1 ATTACAGTTCTATTCC
41364883 ATTACAGTTCTATTCC
1 ATTACAGTTCTATTCC
***
41364899 ATTACAACCCTATTCC
1 ATTACAGTTCTATTCC
41364915 ATTACA
1 ATTACA
41364921 CTGAACCAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.30, C:0.26, G:0.03, T:0.41
Consensus pattern (16 bp):
ATTACAGTTCTATTCC
Found at i:41364888 original size:32 final size:32
Alignment explanation
Indices: 41364851--41364920 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
41364841 TTGAATTGCT
* **
41364851 ATTACAGTTCTATTCTATTACAATTCTATTCC
1 ATTACAGTTCTATTCCATTACAACCCTATTCC
41364883 ATTACAGTTCTATTCCATTACAACCCTATTCC
1 ATTACAGTTCTATTCCATTACAACCCTATTCC
41364915 ATTACA
1 ATTACA
41364921 CTGAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.30, C:0.26, G:0.03, T:0.41
Consensus pattern (32 bp):
ATTACAGTTCTATTCCATTACAACCCTATTCC
Found at i:41366833 original size:18 final size:18
Alignment explanation
Indices: 41366810--41367092 Score: 151
Period size: 18 Copynumber: 15.3 Consensus size: 18
41366800 GAATAATTAT
41366810 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAGTCAG
* * *
41366828 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAGTCAG
* * **
41366846 TTATTCAATAATAACCAG
1 TTATTCAGTAACAGTCAG
* *
41366864 TTATTCAATATCGATCAATTGATCGG
1 TTATTCAGTA---A-C-A--G-TCAG
* *
41366890 TTATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
*
41366908 TTATTCAGTAA-AATCAG
1 TTATTCAGTAACAGTCAG
* * *
41366925 ATATTCAGTAACTATTAAG
1 TTATTCAGTAAC-AGTCAG
*
41366944 TTATTCAGTAGCAGTCA-
1 TTATTCAGTAACAGTCAG
* *
41366961 TTCATTCAGTGACAATCAG
1 TT-ATTCAGTAACAGTCAG
* * *
41366980 TTATTCAGCAA-TGATCAA
1 TTATTCAGTAACAG-TCAG
* *
41366998 TTATTCAGTAATATTCAG
1 TTATTCAGTAACAGTCAG
41367016 TTATTCAGTAACAGTCTA-
1 TTATTCAGTAACAGTC-AG
* * *
41367034 ATATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* * *
41367052 TTATCCGGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* *
41367070 TTATTCAGTAATAATCAG
1 TTATTCAGTAACAGTCAG
41367088 TTATT
1 TTATT
41367093 TTATACCTTT
Statistics
Matches: 200, Mismatches: 49, Indels: 32
0.71 0.17 0.11
Matches are distributed among these distances:
17 17 0.09
18 150 0.75
19 18 0.09
21 2 0.01
22 1 0.00
23 2 0.01
26 10 0.05
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAG
Found at i:41366852 original size:36 final size:36
Alignment explanation
Indices: 41366810--41367092 Score: 178
Period size: 36 Copynumber: 7.6 Consensus size: 36
41366800 GAATAATTAT
* *
41366810 TTATTCAGTAACAGTCAGTTATTCGGTAACAATCAA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
* * * * * *
41366846 TTATTCAATAATAACCAGTTATTCAATATCGATCAA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
* *
41366882 TTGATCGGTTATCCAGTAACAGTCAATTATTCAGTAA-AATCAGA
1 TT-A-----T-T-CAGTAACAATCAGTTATTCAGTAACAATCA-A
* * * *
41366926 -TATTCAGTAACTATTAAGTTATTCAGTAGCAGTC-A
1 TTATTCAGTAAC-AATCAGTTATTCAGTAACAATCAA
* * **
41366961 TTCATTCAGTGACAATCAGTTATTCAGCAATGATCAA
1 TT-ATTCAGTAACAATCAGTTATTCAGTAACAATCAA
* * *
41366998 TTATTCAGTAATATTCAGTTATTCAGTAACAGTCTAA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATC-AA
* * * * * *
41367035 -TATCCAGTAACAGTCAATTATCCGGTAACAGTCAA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
*
41367070 TTATTCAGTAATAATCAGTTATT
1 TTATTCAGTAACAATCAGTTATT
41367093 TTATACCTTT
Statistics
Matches: 184, Mismatches: 47, Indels: 32
0.70 0.18 0.12
Matches are distributed among these distances:
35 10 0.05
36 129 0.70
37 19 0.10
42 2 0.01
43 6 0.03
44 18 0.10
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.35
Consensus pattern (36 bp):
TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
Found at i:41367025 original size:72 final size:72
Alignment explanation
Indices: 41366891--41367092 Score: 196
Period size: 72 Copynumber: 2.8 Consensus size: 72
41366881 ATTGATCGGT
* * * * *
41366891 TATCCAGTAACAGTCAATTATTCAGTAA-AATCAGA-TATTCAGTAACTATTAAGTTATTCAGTA
1 TATCCAGTAACAATCAATTATCCAGCAACAGTCA-ATTATTCAGTAA-TATTCAGTTATTCAGTA
* *
41366954 GCAGTC-AT
64 ACAGTCTAA
* * * * *
41366962 TCATTCAGTGACAATCAGTTATTCAGCAA-TGATCAATTATTCAGTAATATTCAGTTATTCAGTA
1 T-ATCCAGTAACAATCAATTATCCAGCAACAG-TCAATTATTCAGTAATATTCAGTTATTCAGTA
41367026 ACAGTCTAA
64 ACAGTCTAA
* * * *
41367035 TATCCAGTAACAGTCAATTATCCGGTAACAGTCAATTATTCAGTAATAATCAGTTATT
1 TATCCAGTAACAATCAATTATCCAGCAACAGTCAATTATTCAGTAATATTCAGTTATT
41367093 TTATACCTTT
Statistics
Matches: 107, Mismatches: 19, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
71 1 0.01
72 90 0.84
73 16 0.15
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (72 bp):
TATCCAGTAACAATCAATTATCCAGCAACAGTCAATTATTCAGTAATATTCAGTTATTCAGTAAC
AGTCTAA
Found at i:41367261 original size:6 final size:6
Alignment explanation
Indices: 41367250--41367274 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
41367240 ACAAATCCGG
41367250 AACAGT AACAGT AACAGT AACAGT A
1 AACAGT AACAGT AACAGT AACAGT A
41367275 TTCAACACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
AACAGT
Found at i:41367322 original size:45 final size:45
Alignment explanation
Indices: 41367254--41367493 Score: 318
Period size: 45 Copynumber: 5.3 Consensus size: 45
41367244 ATCCGGAACA
* * * * *
41367254 GTAACAGTAACAGTAACAGTATTCAACACACGAAGTACTGAATCG
1 GTAACAGTAGCAGTAACAATATTCGACACACAAAGTACCGAATCG
* * *
41367299 GTAACGGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
1 GTAACAGTAGCAGTAACAATATTCGACACACAAAGTACCGAATCG
* * * **
41367344 ATAACGGTAGCAGTAACAATATTCGACACACACAGTGTCGAATCG
1 GTAACAGTAGCAGTAACAATATTCGACACACAAAGTACCGAATCG
* *
41367389 GTAATAGTAGCAGTAACAATATTCGACACATAAAGTACCGAATCG
1 GTAACAGTAGCAGTAACAATATTCGACACACAAAGTACCGAATCG
* *
41367434 GTAACAGTAGCAGTAACAATATTCGACACACAAAGTGCCGAATCA
1 GTAACAGTAGCAGTAACAATATTCGACACACAAAGTACCGAATCG
*
41367479 GTAACAGTAGTAGTA
1 GTAACAGTAGCAGTA
41367494 GCAGTAACAG
Statistics
Matches: 173, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 173 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (45 bp):
GTAACAGTAGCAGTAACAATATTCGACACACAAAGTACCGAATCG
Found at i:41368113 original size:33 final size:34
Alignment explanation
Indices: 41368050--41368113 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 34
41368040 CATATTCATA
* *
41368050 ATTTATTTTATTTTTATTCAATTCATATTTATTT
1 ATTTATTTTATTTTTATCCAATTCAAATTTATTT
*
41368084 ATTTA-TTTATTTATTGTCCAA-TCAAATTTA
1 ATTTATTTTATTT-TTATCCAATTCAAATTTA
41368114 AAATCACTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
33 15 0.58
34 11 0.42
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.61
Consensus pattern (34 bp):
ATTTATTTTATTTTTATCCAATTCAAATTTATTT
Found at i:41368295 original size:5 final size:6
Alignment explanation
Indices: 41368250--41368295 Score: 60
Period size: 6 Copynumber: 7.8 Consensus size: 6
41368240 ACTTTTCCAA
*
41368250 TCAATT T-ACATT TTAATT TCAATT TCAATT TCAATT TCAA-T TCAAT
1 TCAATT TCA-ATT TCAATT TCAATT TCAATT TCAATT TCAATT TCAAT
41368296 AACAATTCAC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
5 6 0.17
6 29 0.81
7 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (6 bp):
TCAATT
Found at i:41371299 original size:3 final size:3
Alignment explanation
Indices: 41371291--41371315 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
41371281 ATGAGCTTCT
41371291 CAC CAC CAC CAC CAC CAC CAC CAC C
1 CAC CAC CAC CAC CAC CAC CAC CAC C
41371316 TGTTTTTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:41375422 original size:15 final size:15
Alignment explanation
Indices: 41375379--41375426 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
41375369 GAAAATTAAT
41375379 ATAAAATCTAAAAT-A
1 ATAAAAT-TAAAATAA
*
41375394 ATAGTAATTAAAAATAA
1 ATA-AAATT-AAAATAA
41375411 ATAAAATTAAAATAA
1 ATAAAATTAAAATAA
41375426 A
1 A
41375427 CTTAAAATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 12 0.43
16 12 0.43
17 4 0.14
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (15 bp):
ATAAAATTAAAATAA
Found at i:41375425 original size:11 final size:11
Alignment explanation
Indices: 41375370--41375440 Score: 56
Period size: 11 Copynumber: 6.5 Consensus size: 11
41375360 ATAGCTTAAG
*
41375370 AAAATTAATAT
1 AAAATTAAAAT
41375381 AAAATCTAAAAT
1 AAAAT-TAAAAT
* * *
41375393 AATAGT-AATT
1 AAAATTAAAAT
*
41375403 AAAAAT-AAAT
1 AAAATTAAAAT
41375413 AAAATTAAAAT
1 AAAATTAAAAT
*
41375424 AAACTTAAAAT
1 AAAATTAAAAT
*
41375435 AGAATT
1 AAAATT
41375441 TCCTATTTTT
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
10 15 0.32
11 24 0.51
12 8 0.17
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:41377406 original size:46 final size:46
Alignment explanation
Indices: 41377300--41377620 Score: 426
Period size: 46 Copynumber: 7.0 Consensus size: 46
41377290 TTTGACATGA
* * * * ** * * *
41377300 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTTTTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGC
** * *
41377347 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
*** *** * *
41377393 TGCCATGGTATCTTTCAACCATGGTCTTATTTATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
41377439 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
*
41377485 TGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
*
41377531 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
41377577 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
41377621 AGAGCACACT
Statistics
Matches: 250, Mismatches: 24, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
46 221 0.88
47 29 0.12
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
Found at i:41384200 original size:16 final size:16
Alignment explanation
Indices: 41384170--41384217 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
41384160 GAAAATTAAT
41384170 ATAAAATCT-AAAAT-A
1 ATAAAAT-TAAAAATAA
41384185 ATAATAATTAAAAATAA
1 ATAA-AATTAAAAATAA
41384202 ATAAAATT-AAAATAA
1 ATAAAATTAAAAATAA
41384217 A
1 A
41384218 CTTAAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.43
16 12 0.40
17 5 0.17
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAAATAA
Found at i:41384216 original size:11 final size:11
Alignment explanation
Indices: 41384161--41384231 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
41384151 ATAGCTTAAG
*
41384161 AAAATTAATAT
1 AAAATTAAAAT
41384172 AAAATCTAAAAT
1 AAAAT-TAAAAT
*
41384184 AATAA-T-AATT
1 AA-AATTAAAAT
*
41384194 AAAAAT-AAAT
1 AAAATTAAAAT
41384204 AAAATTAAAAT
1 AAAATTAAAAT
*
41384215 AAACTTAAAAT
1 AAAATTAAAAT
*
41384226 AGAATT
1 AAAATT
41384232 TCCTATTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
9 2 0.04
10 14 0.29
11 24 0.49
12 7 0.14
13 2 0.04
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:41390103 original size:25 final size:25
Alignment explanation
Indices: 41390069--41390120 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
41390059 CGTGGATGAC
*
41390069 ATGCCAGCCAGTATTTAATTAATTT
1 ATGCCAGCCAATATTTAATTAATTT
41390094 ATGCCAGCCAATATTTAATTAATTT
1 ATGCCAGCCAATATTTAATTAATTT
41390119 AT
1 AT
41390121 TAAAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (25 bp):
ATGCCAGCCAATATTTAATTAATTT
Found at i:41390363 original size:22 final size:22
Alignment explanation
Indices: 41390338--41390389 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
41390328 AAAAAATACA
41390338 AATTTAAAAAGTAAAAAATTTT
1 AATTTAAAAAGTAAAAAATTTT
* *
41390360 AA-TTAGAAAATTAAAATATTTT
1 AATTTA-AAAAGTAAAAAATTTT
*
41390382 -TTTTAAAA
1 AATTTAAAA
41390390 TTAAAGAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (22 bp):
AATTTAAAAAGTAAAAAATTTT
Found at i:41396659 original size:30 final size:30
Alignment explanation
Indices: 41396623--41396684 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
41396613 TTTTGAAAAA
41396623 CAGAAATT-AAAAGACTCAACTCAACTCTCG
1 CAGAAATTAAAAAG-CTCAACTCAACTCTCG
*
41396653 CAGAAATTAAAAAGCTCAACTCACCTCTCG
1 CAGAAATTAAAAAGCTCAACTCAACTCTCG
41396683 CA
1 CA
41396685 ATATGAGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.42, C:0.29, G:0.10, T:0.19
Consensus pattern (30 bp):
CAGAAATTAAAAAGCTCAACTCAACTCTCG
Found at i:41396804 original size:14 final size:14
Alignment explanation
Indices: 41396781--41396815 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
41396771 TGAGTTGATT
41396781 TTTG-AAAACAGAA
1 TTTGAAAAACAGAA
*
41396794 TTTGAAAAACAGAT
1 TTTGAAAAACAGAA
41396808 TTTGAAAA
1 TTTGAAAA
41396816 TACCTCGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (14 bp):
TTTGAAAAACAGAA
Found at i:41397003 original size:77 final size:75
Alignment explanation
Indices: 41396794--41397174 Score: 373
Period size: 72 Copynumber: 5.0 Consensus size: 75
41396784 GAAAACAGAA
** * * * * *
41396794 TTTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCCGAGGCTCAACTCACATCTCGCAATG
1 TTTGAAAAACAGAAATTGAAAATACCTC-A-ACGTGATCCAAGGCTCAACTCACCTCTCGCAATA
41396859 TGAGTTGATTTT
64 TGAGTTGATTTT
* * ** **
41396871 TTTGAAAAATATAAATTGAAAAAATACCTCAGTGTGTGATTTGAA-GCTCAACTCACCTCTCGCA
1 TTTGAAAAACAGAAATTG--AAAATACCTCA--ACGTGA-TCCAAGGCTCAACTCACCTCTCGCA
41396935 ATATGAGTTGATTTT
61 ATATGAGTTGATTTT
* * * * *
41396950 TTTGAAAGATAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATA
1 TTTGAAAAACAGAAATTGAAAATACCTCA--ACGTGATCCAAGGCTCAACTCACCTCTCGCAATA
*
41397015 TAAGTTGA-TTT
64 TGAGTTGATTTT
** **
41397026 TTT-AAAAACAGAAATTGAAAATACCTCAACGTG-TCTTGAGGCTCAACTCATTTCTCGCAATAT
1 TTTGAAAAACAGAAATTGAAAATACCTCAACGTGATC-CAAGGCTCAACTCACCTCTCGCAATAT
*
41397089 GAGTTGA--AT
65 GAGTTGATTTT
* *
41397098 TTTG-AAAACAGAAATTGAAATTACCTCAACGTG-TCCCGAGGCTCAACTCACCTCTCGCAATAT
1 TTTGAAAAACAGAAATTGAAAATACCTCAACGTGAT-CCAAGGCTCAACTCACCTCTCGCAATAT
41397161 GAGTTGATTTT
65 GAGTTGATTTT
41397172 TTT
1 TTT
41397175 TTGAAAGGCA
Statistics
Matches: 257, Mismatches: 37, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
72 65 0.25
73 34 0.13
74 4 0.02
75 22 0.09
76 8 0.03
77 59 0.23
78 1 0.00
79 63 0.25
80 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (75 bp):
TTTGAAAAACAGAAATTGAAAATACCTCAACGTGATCCAAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTTT
Found at i:41397131 original size:72 final size:73
Alignment explanation
Indices: 41396834--41397538 Score: 563
Period size: 77 Copynumber: 9.2 Consensus size: 73
41396824 CATGTGACCC
* * * *
41396834 GAGGCTCAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATACC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTG-AAAACAGAAATTG--AAAATACC
* *
41396899 TCAGTGTGTGATTT
62 TCAGCGTGT--CTT
* * *
41396913 GAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGATAGAAATTGAAAATAGCTC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAAAATACCTC
* *
41396978 AGCGCGTGAGC-C
64 A--GCGTG-TCTT
* * * *
41396990 AAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTAAAAACAGAAATTGAAAATACCTCAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAG
41397055 CGTGTCTT
66 CGTGTCTT
** * * *
41397063 GAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTCAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAG
**
41397127 CGTGTCCC
66 CGTGTCTT
* *
41397135 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGGCAAAAATTGAAAAATGG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTGAAA-ACAGAAATTG-AAAAT--
** * * * *
41397200 AAATTGAAAATACCTCGGCGTGT
59 -ACCT---CA-GCGT-GTC-T-T
* * * ** * *
41397223 GA-TCTGAGGCTCAACTCACCTCTCGCAATACAAGTTGACTTTTTTGACAACAGAAATTGAAATT
1 GAGGCTCA-ACTC-----ACCTCTCGCAATATGAGTTGA-TTTTTTGAAAACAGAAATTGAAAAT
* *
41397287 ACCTCAGCATGTCCT
59 ACCTCAGCGTGTCTT
41397302 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTG-AAAACAGAAATTGAAAATACCTC
*
41397367 AGCATGTCTT
64 AGCGTGTCTT
** *
41397377 GAGGCTCAACTCATTTCTCACAATATGAGTTGATTTTTTTTTGAAAAACAGAAATTGAAAATACC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTG-AAAACAGAAATTGAAAATACC
**
41397442 TCAGCAAGTCTT
62 TCAGCGTGTCTT
* * ** * * *
41397454 AAGGCTCAACTAATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTCCG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAG
41397518 CGTGTCTT
66 CGTGTCTT
41397526 GAGGCTCAACTCA
1 GAGGCTCAACTCA
41397539 TTTTGAACAG
Statistics
Matches: 515, Mismatches: 80, Indels: 69
0.78 0.12 0.10
Matches are distributed among these distances:
72 106 0.21
73 38 0.07
74 26 0.05
75 79 0.15
76 17 0.03
77 119 0.23
78 7 0.01
79 57 0.11
80 3 0.01
81 4 0.01
82 2 0.00
83 1 0.00
84 1 0.00
85 3 0.01
86 4 0.01
87 3 0.01
88 5 0.01
89 4 0.01
90 8 0.02
91 9 0.02
93 19 0.04
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (73 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAG
CGTGTCTT
Found at i:41397308 original size:167 final size:163
Alignment explanation
Indices: 41397036--41397341 Score: 468
Period size: 167 Copynumber: 1.9 Consensus size: 163
41397026 TTTAAAAACA
* ** **
41397036 GAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTT
1 GAAATTGAAAATACCTCAACGTGTATTGAGGCTCAACTCACCTCTCGCAATACAAGTTGAATTTT
*
41397101 GAAAACAGAAATTGAAATTACCTCAACGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
66 GAAAACAGAAATTGAAATTACCTCAACATGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
41397166 GATTTTTTTTTGAAAGGCAAAAATTGAAAAATG
131 GATTTTTTTTTGAAAGGCAAAAATTGAAAAATG
** *
41397199 GAAATTGAAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACAAGTTGACTT
1 GAAATTGAAAATACCTCAACGTGT-AT-TGAGGCTCAACTCACCTCTCGCAATACAAGTTGA--A
* * *
41397264 TTTTGACAACAGAAATTGAAATTACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATG
62 TTTTGAAAACAGAAATTGAAATTACCTCAACATGTCCCGAGGCTCAACTCACCTCTCGCAATATG
41397329 AGTTGATTTTTTT
127 AGTTGATTTTTTT
41397342 GAAAAACAGA
Statistics
Matches: 127, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
163 22 0.17
164 1 0.01
165 30 0.24
167 74 0.58
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (163 bp):
GAAATTGAAAATACCTCAACGTGTATTGAGGCTCAACTCACCTCTCGCAATACAAGTTGAATTTT
GAAAACAGAAATTGAAATTACCTCAACATGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTTTTTTTTGAAAGGCAAAAATTGAAAAATG
Found at i:41397413 original size:242 final size:238
Alignment explanation
Indices: 41396951--41397437 Score: 677
Period size: 242 Copynumber: 2.0 Consensus size: 238
41396941 GTTGATTTTT
* * *
41396951 TTGAAAGATAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAATAGAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATAC
* * **
41397016 AAGTTGATTTTTTAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCT
66 AAGTTGATTTTTTAAAAACAGAAATTGAAAATACCTCAACATGTCCTGAGGCTCAACTCACCTCT
* *
41397081 CGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCCCGAGGCTCAACT
131 CGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAACATGTCCCGAGGCTCAACT
* **
41397146 CACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGGCAAAAA
196 CACCTCTCACAATATGAGTTGATTTTTTTTTGAAAAACAAAAA
* * * * **
41397189 TTGAAAAATGGAAATTGAAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATAC
1 TTGAAAAATAGAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATAC
* * * *
41397254 AAGTTGACTTTTTTGACAACAGAAATTGAAATTACCTCAGCATGTCCTGAGGCTCAACTCACCTC
66 AAGTTGA-TTTTTTAAAAACAGAAATTGAAAATACCTCAACATGTCCTGAGGCTCAACTCACCTC
* * **
41397319 TCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTC
130 TCGCAATATGAGTTGA--ATTTTG-AAAACAGAAATTGAAAATACCTCAACATGTCCCGAGGCTC
** *
41397384 AACTCATTTCTCACAATATGAGTTGATTTTTTTTTGAAAAACAGAAA
192 AACTCACCTCTCACAATATGAGTTGATTTTTTTTTGAAAAACAAAAA
41397431 TTGAAAA
1 TTGAAAA
41397438 TACCTCAGCA
Statistics
Matches: 216, Mismatches: 29, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
238 63 0.29
239 65 0.30
241 5 0.02
242 83 0.38
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (238 bp):
TTGAAAAATAGAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATAC
AAGTTGATTTTTTAAAAACAGAAATTGAAAATACCTCAACATGTCCTGAGGCTCAACTCACCTCT
CGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAACATGTCCCGAGGCTCAACT
CACCTCTCACAATATGAGTTGATTTTTTTTTGAAAAACAAAAA
Found at i:41397497 original size:391 final size:386
Alignment explanation
Indices: 41396711--41397538 Score: 1027
Period size: 391 Copynumber: 2.1 Consensus size: 386
41396701 TTTGAAAAAA
* * ** * *
41396711 AAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAGT
1 AAAACAGAAATTGAAATTACCTCA--ACGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGT
* * **
41396776 TGATTTTTGAAAACAGAATTTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCCGAGGCTC
64 TGATTTTTGAAAACAAAAATTGAAAAACAGAAATTGAAAATACCTCGACATGTGACCCGAGGCTC
*** * * * **
41396841 AACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATACCTCAGTGT
129 AACTCACATCTCGCAATACAAGTTGACTTTTTTGAAAAACAGAAATTG-AAAAATACCTCAGCAT
** * *
41396906 GTGATTTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGATAGAAATTGAAA
193 GT-ACCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAA
* * *
41396971 ATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTAAAAACA
257 ATACCTCA-CGCATGAGCCAAGGCTCAACTCACCTCTCACAATATAAGTTGATTTTTTAAAAACA
** * *
41397036 GAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTT
321 GAAATTGAAAATACCTCAACAAGTCTTAAGGCTCAACTAATTTCTCGCAATATGAGTTGAATTTT
41397101 G
386 G
41397102 AAAACAGAAATTGAAATTACCTCAACGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAATTACCTCAACGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
* ** * * * *
41397167 ATTTTTTTTTGAAAGGCAAAAATTGAAAAATGGAAATTGAAAATACCTCGGCGTGTGATCTGAGG
66 A----TTTTTGAAA-ACAAAAATTGAAAAACAGAAATTGAAAATACCTCGACATGTGACCCGAGG
* * *
41397232 CTCAACTCACCTCTCGCAATACAAGTTGACTTTTTTG-ACAACAGAAATTG-AAATTACCTCAGC
126 CTCAACTCACATCTCGCAATACAAGTTGACTTTTTTGAAAAACAGAAATTGAAAAATACCTCAGC
*
41397295 ATGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAA
191 ATGTACCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAA
* ** ** *
41397359 AATACCTCA-GCATG-TCTTGAGGCTCAACTCATTTCTCACAATATGAGTTGATTTTTTTTTGAA
256 AATACCTCACGCATGAGC-CAAGGCTCAACTCACCTCTCACAATATAAGTTGA---TTTTTT-AA
*
41397422 AAACAGAAATTGAAAATACCTCAGCAAGTCTTAAGGCTCAACTAATTTCTCGCAATATGAGTTGA
316 AAACAGAAATTGAAAATACCTCAACAAGTCTTAAGGCTCAACTAATTTCTCGCAATATGAGTTGA
41397487 ATTTTG
381 ATTTTG
** **
41397493 AAAACAGAAATTGAAATTACCTCCGCGTGTCTTGAGGCTCAACTCA
1 AAAACAGAAATTGAAATTACCTCAACGTGTCCCGAGGCTCAACTCA
41397539 TTTTGAACAG
Statistics
Matches: 376, Mismatches: 51, Indels: 20
0.84 0.11 0.04
Matches are distributed among these distances:
386 1 0.00
387 32 0.09
389 101 0.27
390 6 0.02
391 146 0.39
393 19 0.05
394 71 0.19
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29
Consensus pattern (386 bp):
AAAACAGAAATTGAAATTACCTCAACGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTTTGAAAACAAAAATTGAAAAACAGAAATTGAAAATACCTCGACATGTGACCCGAGGCTCAA
CTCACATCTCGCAATACAAGTTGACTTTTTTGAAAAACAGAAATTGAAAAATACCTCAGCATGTA
CCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATAC
CTCACGCATGAGCCAAGGCTCAACTCACCTCTCACAATATAAGTTGATTTTTTAAAAACAGAAAT
TGAAAATACCTCAACAAGTCTTAAGGCTCAACTAATTTCTCGCAATATGAGTTGAATTTTG
Found at i:41397524 original size:149 final size:148
Alignment explanation
Indices: 41397189--41397541 Score: 440
Period size: 149 Copynumber: 2.4 Consensus size: 148
41397179 AAGGCAAAAA
** * * ** *
41397189 TTGAAAAATGGAAATTGAAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATAC
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGT-CT-TGAGGCTCAACTCATTTCTCACAATAC
* * * * *
41397254 AAGTTGACTTTTTTGACAACAGAAATTGAAATTACCTCAGCATGTCCTGAGGCTCAACTCACCTC
64 AAGTTGACTTTTTTGAAAACAGAAATTGAAAATACCTCAGCAAGTCCTAAGGCTCAACTAACCTC
*
41397319 TCGCAATATGAGTTGATTTTT
129 TCGCAATATGAGTTGA-TATT
* **
41397340 TTGAAAAACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCACAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCACAATACAA
* * **
41397405 GTTGATTTTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCAAGTCTTAAGGCTCAACTAATTT
66 GTTGA--CTTTTTTG-AAAACAGAAATTGAAAATACCTCAGCAAGTCCTAAGGCTCAACTAACCT
41397470 CTCGCAATATGAGTTGA-ATT
128 CTCGCAATATGAGTTGATATT
* *
41397490 TTG-AAAACAGAAATTGAAATTACCTCCGCGTGTCTTGAGGCTCAACTCATTT
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTT
41397542 TGAACAGAAA
Statistics
Matches: 176, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
149 75 0.43
150 6 0.03
151 37 0.21
152 58 0.33
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (148 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCACAATACAA
GTTGACTTTTTTGAAAACAGAAATTGAAAATACCTCAGCAAGTCCTAAGGCTCAACTAACCTCTC
GCAATATGAGTTGATATT
Found at i:41397561 original size:49 final size:49
Alignment explanation
Indices: 41397495--41397590 Score: 174
Period size: 49 Copynumber: 2.0 Consensus size: 49
41397485 GAATTTTGAA
**
41397495 AACAGAAATTGAAATTACCTCCGCGTGTCTTGAGGCTCAACTCATTTTG
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
41397544 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
41397591 CTCGCAATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (49 bp):
AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
Found at i:41397580 original size:121 final size:121
Alignment explanation
Indices: 41397423--41397662 Score: 408
Period size: 121 Copynumber: 2.0 Consensus size: 121
41397413 TTTTTTGAAA
*
41397423 AACAGAAATTGAAAATACCTCAGCAAGTCTTAAGGCTCAACTAATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAAATACCTCAACAAGTCTTAAGGCTCAACTAATTTCTCGCAATATGAGTTGAA
**
41397488 TTTTGAAAACAGAAATTGAAATTACCTCCGCGTGTCTTGAGGCTCAACTCATTTTG
66 TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
* ** * *
41397544 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAAATACCTCAACAAGTCTTAAGGCTCAACTAATTTCTCGCAATATGAGTTGAA
41397609 TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
66 TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
41397663 CTCGCAATAT
Statistics
Matches: 111, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
121 111 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (121 bp):
AACAGAAATTGAAAATACCTCAACAAGTCTTAAGGCTCAACTAATTTCTCGCAATATGAGTTGAA
TTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
Found at i:41397624 original size:72 final size:72
Alignment explanation
Indices: 41397544--41397841 Score: 429
Period size: 72 Copynumber: 4.0 Consensus size: 72
41397534 ACTCATTTTG
41397544 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
41397609 TTTTGAA
66 TTTTGAA
41397616 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
41397681 TTTTGAA
66 TTTTGAA
41397688 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
41397753 TTTTTTTTTTGAA
66 ------TTTTGAA
* * * * ** *
41397766 AGACAGAAATTGAAAATACCTCAGCATGTGAAC-CGAGGCTCAACTCACCTCTCGCAATATGAGC
1 A-ACAGAAATTGAAATTACCTCA--ACGTG-TCTTGAGGCTCAACTCATTTCTCGCAATATGAGT
41397830 TG-ATTTTGAA
62 TGAATTTTGAA
41397840 AA
1 AA
41397842 AGTAGAAATT
Statistics
Matches: 209, Mismatches: 7, Indels: 19
0.89 0.03 0.08
Matches are distributed among these distances:
72 137 0.66
73 1 0.00
74 8 0.04
78 8 0.04
79 20 0.10
80 1 0.00
81 33 0.16
82 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Consensus pattern (72 bp):
AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
TTTTGAA
Found at i:41397684 original size:193 final size:195
Alignment explanation
Indices: 41397346--41397734 Score: 620
Period size: 193 Copynumber: 2.0 Consensus size: 195
41397336 TTTTTTGAAA
*
41397346 AACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCACAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTCATTTCTCACAATATGAGTTGA-
* *
41397411 TTTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCAAGTCTTAAGGCTCAACTAATTTCTCGCA
65 --TATTTTGAAAAACAGAAATTGAAAATACCTCAACAAGTCTTAAGGCTCAACTAATTTCTCGCA
**
41397476 ATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCCGCGTGTCTTGAGGCTCAACTCATT
128 ATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATT
41397541 TTG
193 TTG
* * *
41397544 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-
1 AACAGAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTCATTTCTCACAATATGAGTTGAT
* ** * *
41397608 ATTTTG-AAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATA
66 ATTTTGAAAAACAGAAATTGAAAATACCTCAACAAGTCTTAAGGCTCAACTAATTTCTCGCAATA
41397672 TGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
131 TGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
41397735 CTCGCAATAT
Statistics
Matches: 178, Mismatches: 13, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
193 113 0.63
194 5 0.03
198 60 0.34
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.32
Consensus pattern (195 bp):
AACAGAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTCATTTCTCACAATATGAGTTGAT
ATTTTGAAAAACAGAAATTGAAAATACCTCAACAAGTCTTAAGGCTCAACTAATTTCTCGCAATA
TGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
Found at i:41397905 original size:54 final size:55
Alignment explanation
Indices: 41397805--41397910 Score: 144
Period size: 54 Copynumber: 1.9 Consensus size: 55
41397795 GAACCGAGGC
* *
41397805 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGCAGAAATTGAAAAGGT
* * *
41397859 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAA-CATAAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAAAAAGCAGAAATTGAAAA
41397911 CAGAAATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
54 34 0.76
55 11 0.24
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (55 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGCAGAAATTGAAAAGGT
Found at i:41397917 original size:13 final size:13
Alignment explanation
Indices: 41397890--41397923 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
41397880 GAGTTGATTC
*
41397890 TTGAACAACATAAA
1 TTGAA-AACAGAAA
41397904 TTGAAAACAGAAA
1 TTGAAAACAGAAA
41397917 TTGAAAA
1 TTGAAAA
41397924 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (13 bp):
TTGAAAACAGAAA
Found at i:41397971 original size:140 final size:140
Alignment explanation
Indices: 41397761--41398248 Score: 888
Period size: 140 Copynumber: 3.5 Consensus size: 140
41397751 AATTTTTTTT
41397761 TTGAAAGACAGAAATTGAAAATACCTCAGCATGTGAACC-GAGGCTCAACTCACCTCTCGCAATA
1 TTGAAA-ACAGAAATTGAAAATACCTCAGC--GTG-ACCTGAGGCTCAACTCACCTCTCGCAATA
41397825 TGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTC
62 TGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTC
*
41397890 TTGAACAACATAAA
127 TTGAACAACGTAAA
41397904 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
*
41397969 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACTTCTCGCAATATGAGTTGATTCTTGA
66 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
41398034 ACAACGTAAA
131 ACAACGTAAA
* * *
41398044 TTGAAAACAGAAATTGAAAATACCTTAGCATGACCTGAGGCTCAACTCACCTCTCGCAGTATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
41398109 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
66 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
41398174 ACAACGTAAA
131 ACAACGTAAA
41398184 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
41398249 TTGAAATTAA
Statistics
Matches: 335, Mismatches: 9, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
139 3 0.01
140 303 0.90
142 23 0.07
143 6 0.02
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (140 bp):
TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
ACAACGTAAA
Found at i:41398045 original size:54 final size:54
Alignment explanation
Indices: 41397945--41398050 Score: 135
Period size: 54 Copynumber: 1.9 Consensus size: 54
41397935 GACCTGAGGC
*
41397945 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTA-AAATTGAAAAGGT
* * *
41397999 TCAACCCACTTCTCGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTGAAAA
41398051 CAGAAATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
54 32 0.71
55 9 0.20
56 4 0.09
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAAAATTGAAAAGGT
Found at i:41398185 original size:54 final size:54
Alignment explanation
Indices: 41398085--41398190 Score: 135
Period size: 54 Copynumber: 1.9 Consensus size: 54
41398075 GACCTGAGGC
* *
41398085 TCAACTCACCTCTCGCAGTATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTA-AAATTGAAAAGGT
* *
41398139 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTGAAAA
41398191 CAGAAATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
54 32 0.71
55 9 0.20
56 4 0.09
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAAAATTGAAAAGGT
Found at i:41398311 original size:72 final size:71
Alignment explanation
Indices: 41398181--41398346 Score: 253
Period size: 72 Copynumber: 2.3 Consensus size: 71
41398171 TGAACAACGT
* * *
41398181 AAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
1 AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATAT
41398246 GAGTTG
66 GAGTTG
*
41398252 AAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATA
1 AAATTAAAA-ACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATA
41398317 TGAGTTG
65 TGAGTTG
**
41398324 ATTTTGAAAAACAAAAATT-AAAA
1 AAATT-AAAAACAAAAATTGAAAA
41398347 GGCTTAACTC
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
71 12 0.14
72 71 0.82
73 4 0.05
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (71 bp):
AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATAT
GAGTTG
Found at i:41398441 original size:122 final size:124
Alignment explanation
Indices: 41398221--41398467 Score: 401
Period size: 122 Copynumber: 2.0 Consensus size: 124
41398211 GCGTGACCTG
* *
41398221 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
41398286 TGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
66 TGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTG-AAAACAAAAATTAAA
* * * *
41398346 AGGCTTAACTCACCTCTCGCAATATGAG-T-CAATTTAAA-ACATAAACTAAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
*
41398408 TGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAA
66 TGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAA
41398467 A
1 A
41398468 ATACCTCAAC
Statistics
Matches: 115, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
121 16 0.14
122 64 0.56
123 7 0.06
124 1 0.01
125 27 0.23
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (124 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
TGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAA
Found at i:41398489 original size:71 final size:69
Alignment explanation
Indices: 41398346--41398497 Score: 196
Period size: 71 Copynumber: 2.2 Consensus size: 69
41398336 AAAAATTAAA
* * *
41398346 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCAGCGTGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTCAATTTAAAACAAAAACTAAAAATACCTCAACGTGC
41398411 CCCG
66 CCCG
* * * *
41398415 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACCTCTCGCAATATGAG-TCAATTT-AAAACAAAAACTAAAAATACCTCAACGT
* **
41398480 GTCTTG
64 GCCCCG
41398486 AGGCTCAACTCA
1 AGGCTCAACTCA
41398498 TGTGACAGCC
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
69 26 0.37
70 5 0.07
71 40 0.56
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (69 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTCAATTTAAAACAAAAACTAAAAATACCTCAACGTGC
CCCG
Found at i:41400505 original size:40 final size:40
Alignment explanation
Indices: 41400297--41400558 Score: 289
Period size: 41 Copynumber: 6.5 Consensus size: 40
41400287 TGGATGATAA
* **
41400297 CCGGGCTAAGTCCCGAAGGCATTT-TGCGCTAGTGACTAGTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG--AGTTACTACAT
* *
41400338 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTATTACATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACA-T
* * *
41400379 TCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTATTACATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACA-T
*
41400420 CCGGGCTAAGTCCCGAAGGCATTTGTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCA-TT-TGTGCGAGTTACTACAT
* *
41400462 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACAT
* * *
41400502 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTACAT
* *
41400541 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
41400559 TACTTGGCTT
Statistics
Matches: 199, Mismatches: 17, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
38 15 0.08
39 15 0.08
40 40 0.20
41 87 0.44
42 27 0.14
43 15 0.08
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACAT
Found at i:41412285 original size:24 final size:25
Alignment explanation
Indices: 41412248--41412307 Score: 86
Period size: 24 Copynumber: 2.4 Consensus size: 25
41412238 GGTTTCTTGG
**
41412248 TTTTTTTTGGGGGTTAGG-TTTTTC
1 TTTTTTTTTTGGGTTAGGTTTTTTC
41412272 TTTTTTTTTTGGGTTAGGTTTTTTC
1 TTTTTTTTTTGGGTTAGGTTTTTTC
41412297 TTTTTTCTTTT
1 TTTTTT-TTTT
41412308 TTTTTTTGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 16 0.50
25 12 0.38
26 4 0.12
ACGTcount: A:0.03, C:0.05, G:0.20, T:0.72
Consensus pattern (25 bp):
TTTTTTTTTTGGGTTAGGTTTTTTC
Found at i:41412328 original size:33 final size:32
Alignment explanation
Indices: 41412266--41412327 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
41412256 GGGGGTTAGG
41412266 TTTTTCTTTTTTTTTTGGGTTAGGTTTTTTCT
1 TTTTTCTTTTTTTTTTGGGTTAGGTTTTTTCT
*
41412298 TTTTTCTTTTTTTTTTTGGTTAGGTTTTTT
1 TTTTTCTTTTTTTTTTGGGTTAGGTTTTTT
41412328 TTTGGAGGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.03, C:0.05, G:0.15, T:0.77
Consensus pattern (32 bp):
TTTTTCTTTTTTTTTTGGGTTAGGTTTTTTCT
Found at i:41413041 original size:40 final size:40
Alignment explanation
Indices: 41412996--41413129 Score: 139
Period size: 41 Copynumber: 3.4 Consensus size: 40
41412986 ACCAGTTTGG
41412996 CACCCAGTGCCTCATCGGATAATTCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGGATAATTCGAAGTAGTAAATTGA
* * *
41413036 CACCCAGTGTCTCATCGAATAAATTCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGGAT-AATTCGAAGTAGTAAATTGA
* ** * ** *
41413077 CACTCAGTGTATCATCGGTTAAACCG-A--AGTAAATTGG
1 CACCCAGTGCCTCATCGGATAATTCGAAGTAGTAAATTGA
*
41413114 CACCTAGTGCCTCATC
1 CACCCAGTGCCTCATC
41413130 AAATCCTATG
Statistics
Matches: 78, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
37 20 0.26
39 1 0.01
40 22 0.28
41 35 0.45
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGGATAATTCGAAGTAGTAAATTGA
Found at i:41413073 original size:41 final size:40
Alignment explanation
Indices: 41412996--41413093 Score: 142
Period size: 41 Copynumber: 2.4 Consensus size: 40
41412986 ACCAGTTTGG
* * *
41412996 CACCCAGTGCCTCATCGGATAATTCGAAGTAGTAAATTGA
1 CACCCAGTGTCTCATCGAATAATTCGAAGTAATAAATTGA
41413036 CACCCAGTGTCTCATCGAATAAATTCGAAGTAATAAATTGA
1 CACCCAGTGTCTCATCGAAT-AATTCGAAGTAATAAATTGA
* *
41413077 CACTCAGTGTATCATCG
1 CACCCAGTGTCTCATCG
41413094 GTTAAACCGA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
40 18 0.35
41 34 0.65
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (40 bp):
CACCCAGTGTCTCATCGAATAATTCGAAGTAATAAATTGA
Found at i:41413995 original size:6 final size:6
Alignment explanation
Indices: 41413969--41414044 Score: 55
Period size: 6 Copynumber: 12.2 Consensus size: 6
41413959 TTCGCATTTG
* * *
41413969 TTTCTT TCTTCGT TCTCTT TTTCTT TTTCTT TCTT-TT CTTTCTG TTTCGTT
1 TTTCTT T-TTCTT TTTCTT TTTCTT TTTCTT T-TTCTT -TTTCTT TTTC-TT
* * *
41414020 TTACTT TCTCTC TTTCTT TTTCTT T
1 TTTCTT TTTCTT TTTCTT TTTCTT T
41414045 ATTTCATTTA
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
6 40 0.75
7 13 0.25
ACGTcount: A:0.01, C:0.22, G:0.04, T:0.72
Consensus pattern (6 bp):
TTTCTT
Found at i:41413997 original size:25 final size:24
Alignment explanation
Indices: 41413969--41414044 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 24
41413959 TTCGCATTTG
41413969 TTTCTTTCTTCGTTCTCTTTTTCTT
1 TTTCTTTCTTC-TTCTCTTTTTCTT
*
41413994 TTTCTTTCTT-TTCTTTCTGTTTCGTT
1 TTTCTTTCTTCTTC--TCTTTTTC-TT
*
41414020 TTACTTTCTCTCTT-TCTTTTTCTT
1 TTTCTTTCT-TCTTCTCTTTTTCTT
41414044 T
1 T
41414045 ATTTCATTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
23 3 0.07
24 3 0.07
25 24 0.56
26 10 0.23
27 1 0.02
28 2 0.05
ACGTcount: A:0.01, C:0.22, G:0.04, T:0.72
Consensus pattern (24 bp):
TTTCTTTCTTCTTCTCTTTTTCTT
Found at i:41420012 original size:18 final size:19
Alignment explanation
Indices: 41419973--41420014 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
41419963 AAAACACGAT
41419973 TTATTTTTTAATTAACACAAC
1 TTATTTTTTAATT-A-ACAAC
41419994 TTATTTTTTAATT-ACAAC
1 TTATTTTTTAATTAACAAC
41420012 TTA
1 TTA
41420015 ACCTATGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (19 bp):
TTATTTTTTAATTAACAAC
Found at i:41421025 original size:19 final size:19
Alignment explanation
Indices: 41421001--41421038 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
41420991 GACAACTTTG
41421001 TCATTATTATTTCAATTAA
1 TCATTATTATTTCAATTAA
41421020 TCATTATTATTTCAATTAA
1 TCATTATTATTTCAATTAA
41421039 CTCTTTACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.53
Consensus pattern (19 bp):
TCATTATTATTTCAATTAA
Found at i:41421215 original size:90 final size:90
Alignment explanation
Indices: 41421057--41421221 Score: 213
Period size: 90 Copynumber: 1.8 Consensus size: 90
41421047 TAAACCGCAA
* * ** **
41421057 GCCTTGTTCCATCATCAAGTTTCCATCAACTCATCCAGAAACTTGTTATATTGTCTCAATCTTTC
1 GCCTTGTTCCATCATCAAGCTTCCATCAACTCATCCAGAAACTTATTATATCATCTCAATCTCCC
41421122 ATCTACTCAACCAAAAGCGTTCAGT
66 ATCTACTCAACCAAAAGCGTTCAGT
* * * * * *
41421147 GCCTTTTTCTATCATCAGGCTTCCATCAACTCATCTAGAGACTTATTTTATCATCTCAATCTCCC
1 GCCTTGTTCCATCATCAAGCTTCCATCAACTCATCCAGAAACTTATTATATCATCTCAATCTCCC
*
41421212 ATCTGCTCAA
66 ATCTACTCAA
41421222 TCAGAAGCCT
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
90 62 1.00
ACGTcount: A:0.26, C:0.29, G:0.09, T:0.36
Consensus pattern (90 bp):
GCCTTGTTCCATCATCAAGCTTCCATCAACTCATCCAGAAACTTATTATATCATCTCAATCTCCC
ATCTACTCAACCAAAAGCGTTCAGT
Found at i:41423813 original size:18 final size:18
Alignment explanation
Indices: 41423777--41423815 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
41423767 TCGGAAATAA
* *
41423777 TTATAAATTTTTTAATTT
1 TTATAAATATTATAATTT
*
41423795 TTATAAATATTATATTTT
1 TTATAAATATTATAATTT
41423813 TTA
1 TTA
41423816 CATTTTTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTATAAATATTATAATTT
Found at i:41425269 original size:131 final size:132
Alignment explanation
Indices: 41425117--41425368 Score: 326
Period size: 131 Copynumber: 1.9 Consensus size: 132
41425107 AAGAGAAGGG
* * *
41425117 TGAAATTCCAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGG
1 TGAAATTCCAAAGGAACATTCGATTATTTTGAACAAACGAAAAATCACAACCCAGCACGATAGGG
* *** ** *
41425182 CACAATTCC-CGAATTGCCAAACATCGTGTATTACTTTCGTTTTAAAGAATTTTTAGAAAACATG
66 CACAATCCCGCGAATTGCCAAACATCGAACACCACCTTCGTTTTAAAGAATTTTTAGAAAACATG
41425246 AA
131 AA
* * ** ** *
41425248 TGAAATTCTAAAGGGACATTCGATTATTTTGAGTAAACGAAAAATTGCAACCCAGCACGTTAGGG
1 TGAAATTCCAAAGGAACATTCGATTATTTTGAACAAACGAAAAATCACAACCCAGCACGATAGGG
* *
41425313 CACGATCCCGCGAATTGCCAAATATCGAACACCACCTTCGTTTTAAAGAATTTTTA
66 CACAATCCCGCGAATTGCCAAACATCGAACACCACCTTCGTTTTAAAGAATTTTTA
41425369 AATGAATAAT
Statistics
Matches: 101, Mismatches: 19, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
131 62 0.61
132 39 0.39
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (132 bp):
TGAAATTCCAAAGGAACATTCGATTATTTTGAACAAACGAAAAATCACAACCCAGCACGATAGGG
CACAATCCCGCGAATTGCCAAACATCGAACACCACCTTCGTTTTAAAGAATTTTTAGAAAACATG
AA
Found at i:41428352 original size:19 final size:19
Alignment explanation
Indices: 41428328--41428369 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
41428318 TGAATATTTT
*
41428328 ATTTTTTAAAA-AAAATATA
1 ATTTTTAAAAATAAAAT-TA
41428347 ATTTTTAAAAATAAAATTA
1 ATTTTTAAAAATAAAATTA
41428366 ATTT
1 ATTT
41428370 AACAATTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTTTAAAAATAAAATTA
Found at i:41452258 original size:216 final size:216
Alignment explanation
Indices: 41451949--41453034 Score: 1368
Period size: 216 Copynumber: 5.0 Consensus size: 216
41451939 ATGGTATCAG
* * * * * * * *
41451949 AGATGGATTTAGCTCCTGATATAGAAAAGGTTTCTCCCCCACTGGGAGCTTCTGATATTGGAAGT
1 AGATGGCTTTAGTTCCTGATACAGAAAAGGCTTCTCCTCCACTGGAAGCTTCTGCTATTGAAAGT
** ** ***
41452014 GAAATTACAACTGAATCGGCTCCTTCAGAGTCTGGTTTGGAAAGTGAAGTTCCCCACAGTGTTAA
66 GAAATTACAACTGAATTAGCTCCTTCAGAGTCCAGTTCCAAAAGTGAAGTTCCCCACAGTGTTAA
* * **
41452079 GTTGGAAGAAGAAGAAAACGCTGGTGCTGAGGAAAATGGTGAGGGGTTTGGTAAAATTGAGTGTA
131 GTTGGAAGAGGAAGAAAACGCTGGTGCTGAGGAAAAAGGTGAGGGAATTGGTAAAATTGAGTGTA
*
41452144 CTATTTTGAATACAGAGTCTA
196 CTATTTTGAATACGGAGTCTA
* * * * * *
41452165 AGATGGCTTTAGTTCTTGATACAGAAAAGGCTGCGCTTCCACTTGAAGTTTCTGCTATTGAAAGT
1 AGATGGCTTTAGTTCCTGATACAGAAAAGGCTTCTCCTCCACTGGAAGCTTCTGCTATTGAAAGT
41452230 GAAATTACAACTGAATTAGCTCCTTCAGAGTCCAGTTCCAAAAGTGAAGTTCCCCACAGTGTTAA
66 GAAATTACAACTGAATTAGCTCCTTCAGAGTCCAGTTCCAAAAGTGAAGTTCCCCACAGTGTTAA
* * * *
41452295 GTTGGAAGAGGATGAAAATGCTGGTGCTGAGGAAAAAGGTGAGGGAATTGGTAAAATTGAATGTT
131 GTTGGAAGAGGAAGAAAACGCTGGTGCTGAGGAAAAAGGTGAGGGAATTGGTAAAATTGAGTGTA
*
41452360 CTATTTTGAATACAGAGTCTA
196 CTATTTTGAATACGGAGTCTA
*
41452381 AGATGGCTTTAGTTCCTGATACAGAAAAGGCTTCTCCTCCACTGGAAGCTTTTGCTATTGAAAGT
1 AGATGGCTTTAGTTCCTGATACAGAAAAGGCTTCTCCTCCACTGGAAGCTTCTGCTATTGAAAGT
* * * *
41452446 GAAACTACAACTGCATTAGCTCCTTCAGAGTCCAGTTCCAAAAGTAAAGTTCCCCAGAGTGTTAA
66 GAAATTACAACTGAATTAGCTCCTTCAGAGTCCAGTTCCAAAAGTGAAGTTCCCCACAGTGTTAA
* ** *
41452511 GTTGGAAAAGGAAGAAAATACTGGTGCTGAGGAAGAAGGTGAGGGAATTGGTAAAATTGAGTGTA
131 GTTGGAAGAGGAAGAAAACGCTGGTGCTGAGGAAAAAGGTGAGGGAATTGGTAAAATTGAGTGTA
*
41452576 CAATTTTGAATACGGAGTCTA
196 CTATTTTGAATACGGAGTCTA
* * *
41452597 AGATAGCTTTAGTTGCTGATACAGAAAAGGCTTCTCCTCCACTGGAAGCTTCTGCCATTGAAAGT
1 AGATGGCTTTAGTTCCTGATACAGAAAAGGCTTCTCCTCCACTGGAAGCTTCTGCTATTGAAAGT
* * * * *
41452662 GAAATTACAACTGAATCAGCTCCTTTAGAGTCCGGTTCCAAAAGTGAAGATCCCCAGAGTGTTAA
66 GAAATTACAACTGAATTAGCTCCTTCAGAGTCCAGTTCCAAAAGTGAAGTTCCCCACAGTGTTAA
* * * ** *
41452727 GTTGGAAGAGGAAGAAGACACTAGTGCTGAGGAAAAAGGTGAAAGAATTGGTAAATTTGAGTGTA
131 GTTGGAAGAGGAAGAAAACGCTGGTGCTGAGGAAAAAGGTGAGGGAATTGGTAAAATTGAGTGTA
* * *
41452792 CTACTTCGAATATGGAGTCTA
196 CTATTTTGAATACGGAGTCTA
** * * * *
41452813 AGATGGCTTTAGTTCCTGATTTAGAAAAGGCTTCTCCTCCATTGGAAGCTCCTGCTAGTGGAAGT
1 AGATGGCTTTAGTTCCTGATACAGAAAAGGCTTCTCCTCCACTGGAAGCTTCTGCTATTGAAAGT
* * * * * * * *
41452878 GAAACTAGAACTGAATTAGCTTCTTTAGAG-CTTAGTTCCAAAAGCGAAGTTTCTCACAGTGTTA
66 GAAATTACAACTGAATTAGCTCCTTCAGAGTC-CAGTTCCAAAAGTGAAGTTCCCCACAGTGTTA
* * * * * * **
41452942 A-TCTGGAGGAGGAAGAAAATAG-TGGTGCCGGGGAAAATGGTGAGAGAATTGGTAAAATTGAAA
130 AGT-TGGAAGAGGAAGAAAA-CGCTGGTGCTGAGGAAAAAGGTGAGGGAATTGGTAAAATTGAGT
* * * *
41453005 GTATTACTTTGAATATGGAATCTA
193 GTACTATTTTGAATACGGAGTCTA
41453029 AGATGG
1 AGATGG
41453035 ACTTAGCAGT
Statistics
Matches: 761, Mismatches: 106, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
215 2 0.00
216 759 1.00
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (216 bp):
AGATGGCTTTAGTTCCTGATACAGAAAAGGCTTCTCCTCCACTGGAAGCTTCTGCTATTGAAAGT
GAAATTACAACTGAATTAGCTCCTTCAGAGTCCAGTTCCAAAAGTGAAGTTCCCCACAGTGTTAA
GTTGGAAGAGGAAGAAAACGCTGGTGCTGAGGAAAAAGGTGAGGGAATTGGTAAAATTGAGTGTA
CTATTTTGAATACGGAGTCTA
Found at i:41456481 original size:30 final size:30
Alignment explanation
Indices: 41456447--41456507 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
41456437 ATACAAAAGA
41456447 TAAAAATATATTTGTAATTGCCTCCTGCAC
1 TAAAAATATATTTGTAATTGCCTCCTGCAC
41456477 TAAAAATATATTTGTAATTGCCTCCTGCAC
1 TAAAAATATATTTGTAATTGCCTCCTGCAC
41456507 T
1 T
41456508 TTGAAAGCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.38
Consensus pattern (30 bp):
TAAAAATATATTTGTAATTGCCTCCTGCAC
Found at i:41460629 original size:24 final size:24
Alignment explanation
Indices: 41460596--41460641 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
41460586 TACCTCATTC
* *
41460596 TAATATATATAGATTAAATTTTAA
1 TAATAAATATAGATGAAATTTTAA
*
41460620 TAATAAATATGGATGAAATTTT
1 TAATAAATATAGATGAAATTTT
41460642 TTAAAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (24 bp):
TAATAAATATAGATGAAATTTTAA
Found at i:41461522 original size:41 final size:42
Alignment explanation
Indices: 41461452--41461545 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 42
41461442 TTCCAACCCA
*
41461452 AAACCTTAAACTTGAACACCAAACACGTAACTC-TAAATCGTT
1 AAACCTTAAACCTGAACACCAAACACGTAACTCGTAAATCG-T
* *
41461494 AAACCTTAAACCT-AA-ATCCAAACTCGTAACTCGTAACTCGT
1 AAACCTTAAACCTGAACA-CCAAACACGTAACTCGTAAATCGT
41461535 -AACCTTAAACC
1 AAACCTTAAACC
41461546 ATTAAACCTA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
40 12 0.26
41 17 0.36
42 18 0.38
ACGTcount: A:0.41, C:0.29, G:0.06, T:0.23
Consensus pattern (42 bp):
AAACCTTAAACCTGAACACCAAACACGTAACTCGTAAATCGT
Found at i:41461830 original size:20 final size:20
Alignment explanation
Indices: 41461788--41461830 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
41461778 GCAAAAAAAT
* * *
41461788 AAAAAAAGATTAACTTATGA
1 AAAAAAAGATAAAATGATGA
*
41461808 AAAAAAAGATAAAATGATTA
1 AAAAAAAGATAAAATGATGA
41461828 AAA
1 AAA
41461831 TTTGTAAAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.21
Consensus pattern (20 bp):
AAAAAAAGATAAAATGATGA
Found at i:41470263 original size:40 final size:40
Alignment explanation
Indices: 41470180--41470522 Score: 485
Period size: 40 Copynumber: 8.6 Consensus size: 40
41470170 TTGAATGCTG
* * * * * *
41470180 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
41470220 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
41470260 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
41470300 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
41470340 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
41470380 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
41470420 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
41470460 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
41470499 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
41470523 TGAACGAGGA
Statistics
Matches: 281, Mismatches: 19, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
39 35 0.12
40 238 0.85
41 8 0.03
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:41472387 original size:42 final size:43
Alignment explanation
Indices: 41472308--41472401 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 43
41472298 TCCTGGACGT
* * **
41472308 GGTCTTACATGTAATTCAGTTTCGATGCCTTTATCCCAGACAG
1 GGTCTTACATGTAATTCAGATACGATGCCGATATCCCAGACAG
* * *
41472351 GGTCTTACATG-AATTCAGATACGATGTCGATGTCCCAGACAT
1 GGTCTTACATGTAATTCAGATACGATGCCGATATCCCAGACAG
41472393 GGTCTTACA
1 GGTCTTACA
41472402 CATAAATCTC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 33 0.75
43 11 0.25
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (43 bp):
GGTCTTACATGTAATTCAGATACGATGCCGATATCCCAGACAG
Found at i:41474595 original size:14 final size:14
Alignment explanation
Indices: 41474576--41474603 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
41474566 AAAGGTCGTT
41474576 TTGCATATGTTTGA
1 TTGCATATGTTTGA
41474590 TTGCATATGTTTGA
1 TTGCATATGTTTGA
41474604 ATGACTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.50
Consensus pattern (14 bp):
TTGCATATGTTTGA
Found at i:41474778 original size:42 final size:42
Alignment explanation
Indices: 41474719--41474860 Score: 221
Period size: 42 Copynumber: 3.4 Consensus size: 42
41474709 GGGTGTTACA
*
41474719 CTCTAAATGTAATGAAAAGTAAATGGACCTCCACACCTAGGC
1 CTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGGC
* * *
41474761 CTCTAAATGCGATGAAAAGTAAATGGACCTCCACCCCTGGGC
1 CTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGGC
* *
41474803 CTCTAACTGCAATCAAAAGTAAATGGACCTCCACACCTAGGC
1 CTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGGC
*
41474845 CTTTAAATGCAATGAA
1 CTCTAAATGCAATGAA
41474861 TGCTTTCCTT
Statistics
Matches: 88, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 88 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (42 bp):
CTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGGC
Found at i:41484088 original size:39 final size:38
Alignment explanation
Indices: 41484045--41484126 Score: 92
Period size: 38 Copynumber: 2.1 Consensus size: 38
41484035 TAGGTTTCAA
* *
41484045 AACCCAAATCCAGTCACCAGCACAAAACCTACGGGATTT
1 AACCCAAATACAAT-ACCAGCACAAAACCTACGGGATTT
** * * *
41484084 AACCCGGATATAATACCAGCACGAAGCCTACGGGATTT
1 AACCCAAATACAATACCAGCACAAAACCTACGGGATTT
41484122 AACCC
1 AACCC
41484127 GGATATAATA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
38 27 0.75
39 9 0.25
ACGTcount: A:0.37, C:0.32, G:0.16, T:0.16
Consensus pattern (38 bp):
AACCCAAATACAATACCAGCACAAAACCTACGGGATTT
Found at i:41484102 original size:38 final size:38
Alignment explanation
Indices: 41484060--41484139 Score: 142
Period size: 38 Copynumber: 2.1 Consensus size: 38
41484050 AAATCCAGTC
41484060 ACCAGCACAAAACCTACGGGATTTAACCCGGATATAAT
1 ACCAGCACAAAACCTACGGGATTTAACCCGGATATAAT
* *
41484098 ACCAGCACGAAGCCTACGGGATTTAACCCGGATATAAT
1 ACCAGCACAAAACCTACGGGATTTAACCCGGATATAAT
41484136 ACCA
1 ACCA
41484140 ACACGAAGCC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (38 bp):
ACCAGCACAAAACCTACGGGATTTAACCCGGATATAAT
Found at i:41484145 original size:38 final size:38
Alignment explanation
Indices: 41484072--41484150 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
41484062 CAGCACAAAA
*
41484072 CCTACGGGATTTAACCCGGATATAATACCAGCACGAAG
1 CCTACGGGATTTAACCCGGATATAATACCAACACGAAG
41484110 CCTACGGGATTTAACCCGGATATAATACCAACACGAAG
1 CCTACGGGATTTAACCCGGATATAATACCAACACGAAG
41484148 CCT
1 CCT
41484151 GCGGACCTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (38 bp):
CCTACGGGATTTAACCCGGATATAATACCAACACGAAG
Found at i:41500094 original size:33 final size:34
Alignment explanation
Indices: 41500057--41500121 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
41500047 GTCTCAATTA
* **
41500057 GGGCCTTAGCCC-TTTCAGTAGTAGTATCAGTGT
1 GGGCCTTAGCCCAATTCAGTAACAGTATCAGTGT
41500090 GGGCCTTAGCCCAATTCAGTAACAGTATCAGT
1 GGGCCTTAGCCCAATTCAGTAACAGTATCAGT
41500122 ATAAAATGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 12 0.43
34 16 0.57
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (34 bp):
GGGCCTTAGCCCAATTCAGTAACAGTATCAGTGT
Found at i:41500729 original size:17 final size:17
Alignment explanation
Indices: 41500680--41500722 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
41500670 TACCCGTATA
*
41500680 GGGCCCACAAGCCCGTG
1 GGGCCCACAAGCCCATG
41500697 GGGCCCACAAGCCCATG
1 GGGCCCACAAGCCCATG
41500714 GGGCCCACA
1 GGGCCCACA
41500723 CACCCATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.21, C:0.42, G:0.33, T:0.05
Consensus pattern (17 bp):
GGGCCCACAAGCCCATG
Found at i:41507996 original size:13 final size:12
Alignment explanation
Indices: 41507980--41508047 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 12
41507970 ATATGTAAGG
41507980 ATAATATATATAA
1 ATAATATA-ATAA
41507993 ATAAT-TAATAA
1 ATAATATAATAA
41508004 AT-ATATAATACA
1 ATAATATAATA-A
41508016 AGTAAAATATAAT-A
1 A-T--AATATAATAA
*
41508030 ATAATATAGAAAA
1 ATAATATA-ATAA
41508043 ATAAT
1 ATAAT
41508048 GATGGAAAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 16
0.73 0.02 0.25
Matches are distributed among these distances:
10 2 0.04
11 17 0.37
12 5 0.11
13 13 0.28
14 2 0.04
16 7 0.15
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.32
Consensus pattern (12 bp):
ATAATATAATAA
Found at i:41508047 original size:35 final size:35
Alignment explanation
Indices: 41508008--41508123 Score: 92
Period size: 35 Copynumber: 3.1 Consensus size: 35
41507998 TAATAAATAT
41508008 ATAATACAAGTAAAAT-ATAATAATAATATAGAAAA
1 ATAATACAAG-AAAATAATAATAATAATATAGAAAA
** * *
41508043 ATAATGA-TGGAAAATAATAATAATAATTTGTGAAAAA
1 ATAAT-ACAAGAAAATAATAATAATAATAT-AG-AAAA
* *
41508080 ATAATATACGATAAATAATAATAATATATATATGATAAA
1 ATAATACAAGA-AAATAATAATAATA-ATATA-GA-AAA
41508119 ATAAT
1 ATAAT
41508124 CTTATAGTGT
Statistics
Matches: 64, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
34 5 0.08
35 18 0.28
36 3 0.05
37 11 0.17
38 15 0.23
39 12 0.19
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (35 bp):
ATAATACAAGAAAATAATAATAATAATATAGAAAA
Found at i:41508069 original size:22 final size:21
Alignment explanation
Indices: 41508042--41508085 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
41508032 AATATAGAAA
41508042 AATAATGATG-GAAAATAATAAT
1 AATAAT-ATGTGAAAA-AATAAT
*
41508064 AATAATTTGTGAAAAAATAAT
1 AATAATATGTGAAAAAATAAT
41508085 A
1 A
41508086 TACGATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (21 bp):
AATAATATGTGAAAAAATAAT
Found at i:41510234 original size:206 final size:206
Alignment explanation
Indices: 41509862--41510545 Score: 987
Period size: 206 Copynumber: 3.3 Consensus size: 206
41509852 TCACAAAGAC
* ** * * *
41509862 GCCAAATCATCTTGGATCTTGCTTCAGTC-TAATTATC-TGAAGGCCAGATCTGCTATGTCTTCG
1 GCCAAATCATCTTAGAT-TTGCTTCA-TCGTAAACA-CGTGAAAGCCAAATCAGCTATGTCTTCG
*
41509925 ATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGATCTTGCTTCAGTCTAATCATCTGA
63 ATTTGTTCCTTATAAGCACAAGGATGCCAAATCATCTTGGATCTTGCTTCAGTCTAATCATCTGA
* *
41509990 AGGCCAGATCTGCTATGTGTTTGCCCTCCGTCGAAGTGGAGATGCCAGACTTCGATTTGCTCTCC
128 AGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAAGTGGAGATGCCAGACTTCGATTTGCTCTCA
41510055 GCAAATACAGAGAT
193 GCAAATACAGAGAT
* *
41510069 GCCAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAGCTATGTATTCAATT
1 GCCAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAGCTATGTCTTCGATT
* *
41510134 TGTTCCTTATAAGCACAAGGATGCCAAATCATCTTGGATCTTACTTCAGTCTAATCATCTGATGG
66 TGTTCCTTATAAGCACAAGGATGCCAAATCATCTTGGATCTTGCTTCAGTCTAATCATCTGAAGG
* * *
41510199 CCAAATCTACTATGTGTCTGCCCTCCGTCGAAGTGGAGATGCCAGACTTCGATTTGCTCTCAGCC
131 CCAGATCTGCTATGTGTCTGCCCTCCGTCGAAGTGGAGATGCCAGACTTCGATTTGCTCTCAGCA
41510264 AATACAGAGAT
196 AATACAGAGAT
* * *
41510275 GCCAAATTATCTTAGATTTGCTTCATCGTAAACACGTGAAATCCAAATCAACTATGTCTTCGATT
1 GCCAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAGCTATGTCTTCGATT
* *
41510340 TGTTCCTTATAAGCAGAAGGATGCCAAATCATCTTGGATCTTGCTTCAGTCTAATCACCTGAAGG
66 TGTTCCTTATAAGCACAAGGATGCCAAATCATCTTGGATCTTGCTTCAGTCTAATCATCTGAAGG
* * * * * * * * *
41510405 TCAGATCTGCTATGTATCTGCTCTCCATTGAATTGGAGATGCCAAACTTCGATTTGTTCTCTG-A
131 CCAGATCTGCTATGTGTCTGCCCTCCGTCGAAGTGGAGATGCCAGACTTCGATTTGCTCTCAGCA
*
41510469 CAATACAGAGAC
196 -AATACAGAGAT
** **
41510481 AACAAATCATCTTAGATTTTGCTTCATCGTAAACAATTGAAAGCCAAATCAGCTATGTCTTCGAT
1 GCCAAATCATCTTAGA-TTTGCTTCATCGTAAACACGTGAAAGCCAAATCAGCTATGTCTTCGAT
41510546 CTACTCCCCA
Statistics
Matches: 428, Mismatches: 45, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
205 3 0.01
206 365 0.85
207 60 0.14
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (206 bp):
GCCAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAGCTATGTCTTCGATT
TGTTCCTTATAAGCACAAGGATGCCAAATCATCTTGGATCTTGCTTCAGTCTAATCATCTGAAGG
CCAGATCTGCTATGTGTCTGCCCTCCGTCGAAGTGGAGATGCCAGACTTCGATTTGCTCTCAGCA
AATACAGAGAT
Found at i:41518576 original size:15 final size:15
Alignment explanation
Indices: 41518534--41518576 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
41518524 ATAACTTTAA
*
41518534 ATGCAAATG-ATGTG
1 ATGCAAATGCATGAG
41518548 ATG-AAATGCTATGAG
1 ATGCAAATGC-ATGAG
41518563 ATGCAAATGCATGA
1 ATGCAAATGCATGA
41518577 ATGAAAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 5 0.20
14 3 0.12
15 11 0.44
16 6 0.24
ACGTcount: A:0.40, C:0.09, G:0.26, T:0.26
Consensus pattern (15 bp):
ATGCAAATGCATGAG
Found at i:41522136 original size:35 final size:35
Alignment explanation
Indices: 41522097--41522212 Score: 92
Period size: 35 Copynumber: 3.1 Consensus size: 35
41522087 TAATAAATAT
41522097 ATAATACAAGTAAAAT-ATAATAATAATATAGAAAA
1 ATAATACAAG-AAAATAATAATAATAATATAGAAAA
** * *
41522132 ATAATGA-TGGAAAATAATAATAATAATTTGTGAAAAA
1 ATAAT-ACAAGAAAATAATAATAATAATAT-AG-AAAA
* *
41522169 ATAATATACGATAAATAATAATAATATATATATGATAAA
1 ATAATACAAGA-AAATAATAATAATA-ATATA-GA-AAA
41522208 ATAAT
1 ATAAT
41522213 CTTATAGTGT
Statistics
Matches: 64, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
34 5 0.08
35 18 0.28
36 3 0.05
37 11 0.17
38 15 0.23
39 12 0.19
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (35 bp):
ATAATACAAGAAAATAATAATAATAATATAGAAAA
Found at i:41522158 original size:22 final size:21
Alignment explanation
Indices: 41522131--41522174 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
41522121 AATATAGAAA
41522131 AATAATGATG-GAAAATAATAAT
1 AATAAT-ATGTGAAAA-AATAAT
*
41522153 AATAATTTGTGAAAAAATAAT
1 AATAATATGTGAAAAAATAAT
41522174 A
1 A
41522175 TACGATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (21 bp):
AATAATATGTGAAAAAATAAT
Found at i:41525676 original size:232 final size:232
Alignment explanation
Indices: 41525263--41525726 Score: 883
Period size: 232 Copynumber: 2.0 Consensus size: 232
41525253 AAATATCATA
* *
41525263 ATGAGAGGAGAAATTAGCTTTGGTAAACCGACTAATTTAGACACGATGTTGAAAGAATGTGGTAA
1 ATGAGAAGAGAAATTAACTTTGGTAAACCGACTAATTTAGACACGATGTTGAAAGAATGTGGTAA
*
41525328 CCAGAATTCTTTTGAACTTATTTTCTTCAGTGAAAGAAATAATACGAGATTATTGATGACAAAAA
66 CCAGAATTCTTTTGAACTTATTTTCTTCAGTGAAAGAAATAATACGAGATTAGTGATGACAAAAA
41525393 TAATTGAAGGAATAATATTTGAAATGTATGACATTTGAGTGTAACAGCTTACAGTGAGTGGATTA
131 TAATTGAAGGAATAATATTTGAAATGTATGACATTTGAGTGTAACAGCTTACAGTGAGTGGATTA
41525458 TGACTGTCTCTCTTGAGGTACCCTAAGGATTTATTTG
196 TGACTGTCTCTCTTGAGGTACCCTAAGGATTTATTTG
*
41525495 ATGAGAAGAGAAATTAACTTTGGTAAACCGACTGATTTAGACACGATGTTGAAAGAATGTGGTAA
1 ATGAGAAGAGAAATTAACTTTGGTAAACCGACTAATTTAGACACGATGTTGAAAGAATGTGGTAA
*
41525560 CCAGAATTCTTTTGAACTTATTTTTTTCAGTGAAAGAAATAATACGAGATTAGTGATGACAAAAA
66 CCAGAATTCTTTTGAACTTATTTTCTTCAGTGAAAGAAATAATACGAGATTAGTGATGACAAAAA
41525625 TAATTGAAGGAATAATATTTGAAATGTATGACATTTGAGTGTAACAGCTTACAGTGAGTGGATTA
131 TAATTGAAGGAATAATATTTGAAATGTATGACATTTGAGTGTAACAGCTTACAGTGAGTGGATTA
41525690 TGACTGTCTCTCTTGAGGTACCCTAAGGATTTATTTG
196 TGACTGTCTCTCTTGAGGTACCCTAAGGATTTATTTG
41525727 TTCTAGGAAG
Statistics
Matches: 227, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
232 227 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.33
Consensus pattern (232 bp):
ATGAGAAGAGAAATTAACTTTGGTAAACCGACTAATTTAGACACGATGTTGAAAGAATGTGGTAA
CCAGAATTCTTTTGAACTTATTTTCTTCAGTGAAAGAAATAATACGAGATTAGTGATGACAAAAA
TAATTGAAGGAATAATATTTGAAATGTATGACATTTGAGTGTAACAGCTTACAGTGAGTGGATTA
TGACTGTCTCTCTTGAGGTACCCTAAGGATTTATTTG
Found at i:41530266 original size:39 final size:40
Alignment explanation
Indices: 41530221--41530405 Score: 178
Period size: 40 Copynumber: 4.7 Consensus size: 40
41530211 GCTCCTCGTT
* * *
41530221 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
**
41530261 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
41530300 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * * * * *
41530340 CAAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CATAACCCGGATTTAGTAAC-TCGCA
* *
41530381 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACATAACCCGGA
41530406 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 37 0.30
40 74 0.61
41 11 0.09
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:41530321 original size:40 final size:39
Alignment explanation
Indices: 41530188--41530405 Score: 165
Period size: 40 Copynumber: 5.5 Consensus size: 39
41530178 AAATCACGTA
* * **
41530188 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCA-AATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCG--CACAATG
* * * * *
41530227 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
* *
41530266 CCTTCGGGACATAACCCGGATTTAACAACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * *
41530306 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * * * *
41530346 CCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCACAAAG
1 CCTTCGGGA-CTTAACCCGGATTTA-GCAAC-TCGCACAATG
*
41530386 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
41530406 CAGCATTCAA
Statistics
Matches: 143, Mismatches: 29, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
38 2 0.01
39 48 0.34
40 85 0.59
41 8 0.06
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
Found at i:41535931 original size:7 final size:7
Alignment explanation
Indices: 41535904--41535998 Score: 66
Period size: 7 Copynumber: 13.4 Consensus size: 7
41535894 AAAACATAAT
*
41535904 CCCTTAA
1 CCCTAAA
*
41535911 CCCTAAC
1 CCCTAAA
41535918 CCCTAAA
1 CCCTAAA
*
41535925 CCTTAAA
1 CCCTAAA
*
41535932 CCCCAATA
1 CCCTAA-A
41535940 CCCTAAA
1 CCCTAAA
* *
41535947 ACTTAAA
1 CCCTAAA
41535954 CCCT-AA
1 CCCTAAA
* *
41535960 CCTTTAA
1 CCCTAAA
41535967 CCCATAAA
1 CCC-TAAA
*
41535975 CCATAAA
1 CCCTAAA
* *
41535982 CCATAAT
1 CCCTAAA
41535989 CCCTAAA
1 CCCTAAA
41535996 CCC
1 CCC
41535999 AGAATACATA
Statistics
Matches: 67, Mismatches: 18, Indels: 6
0.74 0.20 0.07
Matches are distributed among these distances:
6 5 0.07
7 51 0.76
8 11 0.16
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (7 bp):
CCCTAAA
Found at i:41536429 original size:40 final size:39
Alignment explanation
Indices: 41536361--41536512 Score: 146
Period size: 40 Copynumber: 3.8 Consensus size: 39
41536351 TTTACAAAAT
* *
41536361 TCTTTAGCGGCGCTTTTTAGAGAA-CGCCGCTAATGCTTGA
1 TCTTTAGCGGCG-TTTTTA-AAAAGCGCCGCTAATGCTCGA
* * * *
41536401 TCTTTAGCGGCGTTTTCAAAAAGGCGCCGCTAAAGGTGGA
1 TCTTTAGCGGCGTTTTTAAAAA-GCGCCGCTAATGCTCGA
* *
41536441 -CATATAGCGGCGTTTTTAGAAAAGCGCCGCTAATACTCGA
1 TC-TTTAGCGGCGTTTTTA-AAAAGCGCCGCTAATGCTCGA
** *
41536481 TCTTTAGTAGCGTTTTTAGAAAGCGCCGCTAA
1 TCTTTAGCGGCGTTTTTAAAAAGCGCCGCTAA
41536513 AGCCACCAAC
Statistics
Matches: 92, Mismatches: 15, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
38 3 0.03
39 19 0.21
40 65 0.71
41 5 0.05
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (39 bp):
TCTTTAGCGGCGTTTTTAAAAAGCGCCGCTAATGCTCGA
Found at i:41536471 original size:80 final size:79
Alignment explanation
Indices: 41536365--41536514 Score: 212
Period size: 80 Copynumber: 1.9 Consensus size: 79
41536355 CAAAATTCTT
* * * *
41536365 TAGCGGCGCTTTTTAGAGAACGCCGCTAATGCTTGATCTTTAGCGGCGTTTTCAAAAAGGCGCCG
1 TAGCGGCGCTTTTTAGAAAACGCCGCTAATACTCGATCTTTAGCAGCGTTTTCAAAAA-GCGCCG
41536430 CTAAAGGTGGACATA
65 CTAAAGGTGGACATA
* * *
41536445 TAGCGGCG-TTTTTAGAAAAGCGCCGCTAATACTCGATCTTTAGTAGCGTTTTTAGAAAGCGCCG
1 TAGCGGCGCTTTTTAGAAAA-CGCCGCTAATACTCGATCTTTAGCAGCGTTTTCAAAAAGCGCCG
41536509 CTAAAG
65 CTAAAG
41536515 CCACCAACGT
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
79 22 0.35
80 40 0.65
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (79 bp):
TAGCGGCGCTTTTTAGAAAACGCCGCTAATACTCGATCTTTAGCAGCGTTTTCAAAAAGCGCCGC
TAAAGGTGGACATA
Found at i:41540603 original size:7 final size:7
Alignment explanation
Indices: 41540576--41540670 Score: 66
Period size: 7 Copynumber: 13.4 Consensus size: 7
41540566 AAAACATAAT
*
41540576 CCCTTAA
1 CCCTAAA
*
41540583 CCCTAAC
1 CCCTAAA
41540590 CCCTAAA
1 CCCTAAA
*
41540597 CCTTAAA
1 CCCTAAA
*
41540604 CCCCAATA
1 CCCTAA-A
41540612 CCCTAAA
1 CCCTAAA
* *
41540619 ACTTAAA
1 CCCTAAA
41540626 CCCT-AA
1 CCCTAAA
* *
41540632 CCTTTAA
1 CCCTAAA
41540639 CCCATAAA
1 CCC-TAAA
*
41540647 CCATAAA
1 CCCTAAA
* *
41540654 CCATAAT
1 CCCTAAA
41540661 CCCTAAA
1 CCCTAAA
41540668 CCC
1 CCC
41540671 ATGATACATA
Statistics
Matches: 67, Mismatches: 18, Indels: 6
0.74 0.20 0.07
Matches are distributed among these distances:
6 5 0.07
7 51 0.76
8 11 0.16
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (7 bp):
CCCTAAA
Found at i:41541373 original size:12 final size:12
Alignment explanation
Indices: 41541356--41541383 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
41541346 TTTTTTATTC
41541356 AAACGCCGCTAA
1 AAACGCCGCTAA
41541368 AAACGCCGCTAA
1 AAACGCCGCTAA
41541380 AAAC
1 AAAC
41541384 CAGTTTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.32, G:0.14, T:0.07
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:41553560 original size:13 final size:13
Alignment explanation
Indices: 41553542--41553568 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41553532 GAAGTAATTG
41553542 CACACGGGCATGT
1 CACACGGGCATGT
41553555 CACACGGGCATGT
1 CACACGGGCATGT
41553568 C
1 C
41553569 CCTGCCAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.33, G:0.30, T:0.15
Consensus pattern (13 bp):
CACACGGGCATGT
Found at i:41557614 original size:47 final size:45
Alignment explanation
Indices: 41557499--41557767 Score: 199
Period size: 47 Copynumber: 5.8 Consensus size: 45
41557489 TTTCTTGTGT
* * * *
41557499 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATAAGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCTAGA-TATGAGA
* *
41557545 GCCAATGTAAGACCATGCCTGGGACATGACATCGGCGTAGATATGAGA
1 GCCAGTGTAAGA-CATGTCTGGGACATG-CATCGGC-TAGATATGAGA
* *
41557593 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTTGATGATGATA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGG-CTAGAT-ATGAGA
* * * *
41557640 GCCAGTGTAAGA-AGTGTCTAGGACATGCACCGGCTAAGAGTCT---C
1 GCCAGTGTAAGACA-TGTCTGGGACATGCATCGGCT-AGA-TATGAGA
* **
41557684 GCTAGTGTAAGACATGT-TCGGGACATGCATCAAC-ACGTATATACGAGA
1 GCCAGTGTAAGACATGTCT-GGGACATGCATCGGCTA-G-ATAT--GAGA
* *
41557732 GCTAGTATAAGACCATGTCTGGGACATGGCATCGGC
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
41557768 AACGAGAAGT
Statistics
Matches: 178, Mismatches: 25, Indels: 36
0.74 0.10 0.15
Matches are distributed among these distances:
42 1 0.01
43 4 0.02
44 26 0.15
45 1 0.01
46 24 0.13
47 66 0.37
48 35 0.20
49 14 0.08
50 7 0.04
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (45 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCTAGATATGAGA
Found at i:41563724 original size:2 final size:2
Alignment explanation
Indices: 41563717--41563860 Score: 288
Period size: 2 Copynumber: 72.0 Consensus size: 2
41563707 GAGATGTATA
41563717 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
41563759 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
41563801 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
41563843 TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG
41563861 AGTGCTAATG
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 142 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:41569922 original size:15 final size:15
Alignment explanation
Indices: 41569889--41569927 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
41569879 TTTCAAGCAT
* *
41569889 ATTTAATGA-AAATA
1 ATTTAATCATAAAAA
41569903 ATTTAATCATAAAAA
1 ATTTAATCATAAAAA
41569918 ATTTAATCAT
1 ATTTAATCAT
41569928 CCAAATATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (15 bp):
ATTTAATCATAAAAA
Found at i:41570648 original size:9 final size:9
Alignment explanation
Indices: 41570623--41570648 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
41570613 TATTAATTAT
41570623 TAAAATTTA
1 TAAAATTTA
41570632 TAAAATTTA
1 TAAAATTTA
41570641 TAAAATTT
1 TAAAATTT
41570649 GAATTTAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
TAAAATTTA
Found at i:41570816 original size:19 final size:18
Alignment explanation
Indices: 41570787--41570836 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
41570777 TTTAGTTTTT
*
41570787 TATTGATTAATATTTAATG
1 TATT-ATTAATATTTAATC
*
41570806 TTTCTATTAATA-TTAATC
1 TAT-TATTAATATTTAATC
41570824 TATTATTAATATT
1 TATTATTAATATT
41570837 ATTATATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 8 0.31
18 8 0.31
19 9 0.35
20 1 0.04
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (18 bp):
TATTATTAATATTTAATC
Found at i:41570844 original size:14 final size:17
Alignment explanation
Indices: 41570787--41570837 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 17
41570777 TTTAGTTTTT
*
41570787 TATTGATTAATATTTAATG
1 TATT-ATTAATA-TTAATC
*
41570806 TTTCTATTAATATTAATC
1 TAT-TATTAATATTAATC
41570824 TATTATTAATATTA
1 TATTATTAATATTA
41570838 TTATATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 11 0.39
18 7 0.25
19 9 0.32
20 1 0.04
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (17 bp):
TATTATTAATATTAATC
Done.