Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 132 of 210
Found at i:40144028 original size:26 final size:25
Alignment explanation
Indices: 40143968--40144030 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
40143958 TCCATGTAAT
*
40143968 CATTTCATATAACACTTCATATAAT
1 CATTTCATATAACACTTCATATAAC
* *
40143993 TATTTCCATATAACTGA-TTCATATAGC
1 CATTT-CATATAAC--ACTTCATATAAC
40144020 CATTTCATATA
1 CATTTCATATA
40144031 GTCATTTCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
25 4 0.13
26 14 0.45
27 12 0.39
28 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.03, T:0.41
Consensus pattern (25 bp):
CATTTCATATAACACTTCATATAAC
Found at i:40148745 original size:19 final size:19
Alignment explanation
Indices: 40148721--40148759 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
40148711 AAATTAGCGG
40148721 TAATTATCGACTT-AGTTAA
1 TAATTA-CGACTTCAGTTAA
*
40148740 TAATTACTACTTCAGTTAA
1 TAATTACGACTTCAGTTAA
40148759 T
1 T
40148760 TCTAGGCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.44
Consensus pattern (19 bp):
TAATTACGACTTCAGTTAA
Found at i:40162479 original size:27 final size:27
Alignment explanation
Indices: 40162449--40162538 Score: 112
Period size: 27 Copynumber: 3.3 Consensus size: 27
40162439 TATAACAGTC
40162449 ATTTTACCCTATGGGGGTATTTCGGTA
1 ATTTTACCCTATGGGGGTATTTCGGTA
**
40162476 ATTTTACCC-ATCGAAGGTATTGT-GGTA
1 ATTTTACCCTAT-GGGGGTATT-TCGGTA
* *
40162503 AATTTACCCTTTGGGGGTATTTCGGTA
1 ATTTTACCCTATGGGGGTATTTCGGTA
40162530 ATTTTACCC
1 ATTTTACCC
40162539 ATCAAGGGTA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
26 3 0.06
27 47 0.90
28 2 0.04
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (27 bp):
ATTTTACCCTATGGGGGTATTTCGGTA
Found at i:40162547 original size:27 final size:27
Alignment explanation
Indices: 40162463--40162553 Score: 105
Period size: 27 Copynumber: 3.4 Consensus size: 27
40162453 TACCCTATGG
40162463 GGGTATTTCGGTAATTTTACCCATCGAA
1 GGGTATTTCGGTAATTTTACCCATC-AA
* * ***
40162491 -GGTATTGT-GGTAAATTTACCCTTTGG
1 GGGTATT-TCGGTAATTTTACCCATCAA
40162517 GGGTATTTCGGTAATTTTACCCATCAA
1 GGGTATTTCGGTAATTTTACCCATCAA
40162544 GGGTATTTCG
1 GGGTATTTCG
40162554 ATCATTTAAC
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
26 1 0.02
27 48 0.96
28 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.38
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTACCCATCAA
Found at i:40163850 original size:18 final size:18
Alignment explanation
Indices: 40163816--40163851 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40163806 GAAATGGGAC
**
40163816 GAGAAAGGAAAGGAAATG
1 GAGAAAGGAAAAAAAATG
40163834 GAGAAAGGAAAAAAAATG
1 GAGAAAGGAAAAAAAATG
40163852 ATGAGTAGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.33, T:0.06
Consensus pattern (18 bp):
GAGAAAGGAAAAAAAATG
Found at i:40165175 original size:25 final size:25
Alignment explanation
Indices: 40165124--40165203 Score: 99
Period size: 25 Copynumber: 3.2 Consensus size: 25
40165114 TATCGATTTT
* *
40165124 AGCTCTTATTAGCTTACCGA-TAATC
1 AGCTCATATGAGCTTACC-ATTAATC
*
40165149 AGCTCATATGAGCTTACCATTATTC
1 AGCTCATATGAGCTTACCATTAATC
* *
40165174 AGCTCAGAGGAGCTTACCATTAATC
1 AGCTCATATGAGCTTACCATTAATC
40165199 AGCTC
1 AGCTC
40165204 GGAGGAGCTT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
24 1 0.02
25 47 0.98
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (25 bp):
AGCTCATATGAGCTTACCATTAATC
Found at i:40165208 original size:25 final size:25
Alignment explanation
Indices: 40165134--40165216 Score: 114
Period size: 25 Copynumber: 3.3 Consensus size: 25
40165124 AGCTCTTATT
* *
40165134 AGCTTACCGA-TAATCAGCTCATATG
1 AGCTTACC-ATTAATCAGCTCAGAGG
*
40165159 AGCTTACCATTATTCAGCTCAGAGG
1 AGCTTACCATTAATCAGCTCAGAGG
*
40165184 AGCTTACCATTAATCAGCTCGGAGG
1 AGCTTACCATTAATCAGCTCAGAGG
40165209 AGCTTACC
1 AGCTTACC
40165217 GTTTACAGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
24 1 0.02
25 51 0.98
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (25 bp):
AGCTTACCATTAATCAGCTCAGAGG
Found at i:40168877 original size:25 final size:25
Alignment explanation
Indices: 40168847--40168895 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
40168837 GTGTAAGGAT
40168847 TCAAACATTATACCAAAGGGTAAGG
1 TCAAACATTATACCAAAGGGTAAGG
40168872 TCAAACATTATACCAAAGGGTAAG
1 TCAAACATTATACCAAAGGGTAAG
40168896 TTGACTCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.20
Consensus pattern (25 bp):
TCAAACATTATACCAAAGGGTAAGG
Found at i:40172806 original size:14 final size:14
Alignment explanation
Indices: 40172787--40172826 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
40172777 GATTCAAAGA
40172787 TAAATAAAATATCC
1 TAAATAAAATATCC
40172801 TAAATAAAATATCC
1 TAAATAAAATATCC
*
40172815 CAAATAAAATAT
1 TAAATAAAATAT
40172827 ATTAATAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (14 bp):
TAAATAAAATATCC
Found at i:40174145 original size:30 final size:30
Alignment explanation
Indices: 40174111--40174172 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
40174101 CTTTACTTTA
*
40174111 AACTTCTCAATATGACCATTTAAAGAGTTG
1 AACTTCTCAATATGACCAGTTAAAGAGTTG
**
40174141 AACTTCTCAATATGACTGGTTAAAGAGTTG
1 AACTTCTCAATATGACCAGTTAAAGAGTTG
40174171 AA
1 AA
40174173 GAATCCTAGC
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:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (30 bp):
AACTTCTCAATATGACCAGTTAAAGAGTTG
Found at i:40180808 original size:21 final size:21
Alignment explanation
Indices: 40180775--40180820 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
40180765 TTTTCGATTC
* *
40180775 TTTT-CTCTCTTTCAATTTTT
1 TTTTCCTCTCTTTCAATCTCT
*
40180795 TTTTCCTCTTTTTCAATCTCT
1 TTTTCCTCTCTTTCAATCTCT
40180816 TTTTC
1 TTTTC
40180821 TTTTTCATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTCCTCTCTTTCAATCTCT
Found at i:40184898 original size:40 final size:40
Alignment explanation
Indices: 40184854--40184933 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
40184844 TGTTCGAATC
40184854 CCTTTGAGTGTTTTTTATATTTATTTGTTTTTATGTTGTT
1 CCTTTGAGTGTTTTTTATATTTATTTGTTTTTATGTTGTT
40184894 CCTTTGAGTGTTTTTTATATTTATTTGTTTTTATGTTGTT
1 CCTTTGAGTGTTTTTTATATTTATTTGTTTTTATGTTGTT
40184934 TTATTTTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.12, C:0.05, G:0.15, T:0.68
Consensus pattern (40 bp):
CCTTTGAGTGTTTTTTATATTTATTTGTTTTTATGTTGTT
Found at i:40187708 original size:48 final size:48
Alignment explanation
Indices: 40187637--40187728 Score: 184
Period size: 48 Copynumber: 1.9 Consensus size: 48
40187627 AAAATAAAAT
40187637 TAAAAGATTATAAGCATGAATTTGAGTATTATTATTATGAGATTATTA
1 TAAAAGATTATAAGCATGAATTTGAGTATTATTATTATGAGATTATTA
40187685 TAAAAGATTATAAGCATGAATTTGAGTATTATTATTATGAGATT
1 TAAAAGATTATAAGCATGAATTTGAGTATTATTATTATGAGATT
40187729 GGTATTGATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.41, C:0.02, G:0.15, T:0.41
Consensus pattern (48 bp):
TAAAAGATTATAAGCATGAATTTGAGTATTATTATTATGAGATTATTA
Found at i:40197147 original size:25 final size:26
Alignment explanation
Indices: 40197105--40197153 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
40197095 AGTTGTAAAT
40197105 TAGAAAAATATCTCTAGA-AATTTTC
1 TAGAAAAATATCTCTAGAGAATTTTC
* * *
40197130 TAGAATAATCTCTTTAGAGAATTT
1 TAGAAAAATATCTCTAGAGAATTT
40197154 CTCTTTACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (26 bp):
TAGAAAAATATCTCTAGAGAATTTTC
Found at i:40219327 original size:20 final size:18
Alignment explanation
Indices: 40219280--40219328 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
40219270 CAAGATAAAC
40219280 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
40219297 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
40219317 ATTAAATTAATA
1 ATTAAATTAATA
40219329 AAATATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:40220148 original size:35 final size:35
Alignment explanation
Indices: 40220102--40220171 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
40220092 CATTAACTCT
*
40220102 TTAATTGAGCTATGGATTCCACTGTTGCTAGTAAA
1 TTAATTGAGCTATGAATTCCACTGTTGCTAGTAAA
40220137 TTAATTGAGCTATGAATTCCACTGTTGCTAGTAAA
1 TTAATTGAGCTATGAATTCCACTGTTGCTAGTAAA
40220172 GTCATGCCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (35 bp):
TTAATTGAGCTATGAATTCCACTGTTGCTAGTAAA
Found at i:40222937 original size:51 final size:50
Alignment explanation
Indices: 40222806--40222956 Score: 196
Period size: 50 Copynumber: 3.0 Consensus size: 50
40222796 GTGAAAGTGA
* * * *
40222806 AAGTGATGGTCACGTGTGTAGTACTATGTGCATGCTACTACGTGTACCAG
1 AAGTGATGGTCACATGTGTAGTACTATGTGCAAGCTACTACGTGTATCGG
* * *
40222856 AA-TAATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGG
1 AAGTGAT-GGTCACATGTGTAGTACTATGTGCAAGCTACTACGTGTATCGG
* *
40222906 ATAGTGATGGTCACATGTGTAGTACTATGTGCAAGCTACTATGTGAATCGG
1 A-AGTGATGGTCACATGTGTAGTACTATGTGCAAGCTACTACGTGTATCGG
40222957 TATCATTAAT
Statistics
Matches: 87, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
49 3 0.03
50 41 0.47
51 40 0.46
52 3 0.03
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (50 bp):
AAGTGATGGTCACATGTGTAGTACTATGTGCAAGCTACTACGTGTATCGG
Found at i:40222950 original size:26 final size:26
Alignment explanation
Indices: 40222869--40222950 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
40222859 AATAGGTCGC
*
40222869 ATGTGTAGTACTATGTGCAGGCTACT
1 ATGTGTAGTACTATGTGCAAGCTACT
* * * *
40222895 ACGTGTA-T-CGGATAGTG-ATGGTCAC-
1 ATGTGTAGTAC-TAT-GTGCAAGCT-ACT
40222920 ATGTGTAGTACTATGTGCAAGCTACT
1 ATGTGTAGTACTATGTGCAAGCTACT
40222946 ATGTG
1 ATGTG
40222951 AATCGGTATC
Statistics
Matches: 41, Mismatches: 8, Indels: 14
0.65 0.13 0.22
Matches are distributed among these distances:
24 1 0.02
25 17 0.41
26 22 0.54
27 1 0.02
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (26 bp):
ATGTGTAGTACTATGTGCAAGCTACT
Found at i:40223195 original size:16 final size:16
Alignment explanation
Indices: 40223174--40223205 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40223164 TGATTGAAAG
*
40223174 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
40223190 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
40223206 ACAACAACAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:40230107 original size:19 final size:20
Alignment explanation
Indices: 40230063--40230107 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
40230053 ATAATATAGT
*
40230063 TATATTTAAAAATTAAAATA
1 TATATTCAAAAATTAAAATA
40230083 TATATTCAAAAATTAAAATA
1 TATATTCAAAAATTAAAATA
40230103 T-TATT
1 TATATT
40230108 ATTGTATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
TATATTCAAAAATTAAAATA
Found at i:40230807 original size:31 final size:31
Alignment explanation
Indices: 40230742--40230816 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
40230732 TACAAAATCA
*
40230742 TCACTAAATTATTTGAAAATTTTCATTTAAG
1 TCACTAAATTATTTGAAAATTTTCATTCAAG
* * *
40230773 TCACTGAATTATTTGAAAATTTTTATTCATG
1 TCACTAAATTATTTGAAAATTTTCATTCAAG
* *
40230804 TCACCAAACTATT
1 TCACTAAATTATT
40230817 AAGTTTTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (31 bp):
TCACTAAATTATTTGAAAATTTTCATTCAAG
Found at i:40231217 original size:3 final size:3
Alignment explanation
Indices: 40231209--40231250 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
40231199 AGGTTACCTC
40231209 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
40231251 TATCTGCAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:40233100 original size:56 final size:50
Alignment explanation
Indices: 40232884--40233130 Score: 183
Period size: 50 Copynumber: 4.8 Consensus size: 50
40232874 GATAATAACA
* * ** * * * *
40232884 TGCCAAAT-CCATGTCCCAAACATGGTCTTACATAGGATGTTTCTTGT-AC
1 TGCC-AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* * * ** ** * *
40232933 TGCCAATGCCATATCCCAGATATGGTCTTACACGATAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* * **
40232983 TGCCCATGCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* *
40233033 TGCCAACGCCATGTCCCAGACATGGTCTAACATGGGACCTCTCATAACCTCAATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT---CTC-A-G
* * *
40233088 ATGCCAATGCCATGTCTCATACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
40233131 TTACCCAAAT
Statistics
Matches: 153, Mismatches: 37, Indels: 9
0.77 0.19 0.05
Matches are distributed among these distances:
48 3 0.02
49 31 0.20
50 77 0.50
53 3 0.02
54 1 0.01
55 1 0.01
56 37 0.24
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
Found at i:40235953 original size:20 final size:20
Alignment explanation
Indices: 40235925--40235977 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
40235915 TTAACTTTTG
* *
40235925 GAATCATAAAAATCCAACAA
1 GAATTATAAAAATCCAAAAA
* * *
40235945 GAATTATAAGATTTCAAAAA
1 GAATTATAAAAATCCAAAAA
*
40235965 GAATTCTAAAAAT
1 GAATTATAAAAAT
40235978 AGTCAATTTT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.57, C:0.11, G:0.08, T:0.25
Consensus pattern (20 bp):
GAATTATAAAAATCCAAAAA
Found at i:40238486 original size:18 final size:18
Alignment explanation
Indices: 40238463--40238507 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
40238453 TCAATCATCT
40238463 ACACCGATGCAAGAATCA
1 ACACCGATGCAAGAATCA
*
40238481 ACACCGATGCAAGAATCG
1 ACACCGATGCAAGAATCA
*
40238499 ATACCGATG
1 ACACCGATG
40238508 GTCCCACCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.40, C:0.27, G:0.20, T:0.13
Consensus pattern (18 bp):
ACACCGATGCAAGAATCA
Found at i:40241939 original size:23 final size:23
Alignment explanation
Indices: 40241913--40241958 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
40241903 AATTGTTAAC
* * *
40241913 TTTACATCTCAAAAATTATAAAT
1 TTTACATATAAAAAATTAAAAAT
*
40241936 TTTATATATAAAAAATTAAAAAT
1 TTTACATATAAAAAATTAAAAAT
40241959 ATATATAGCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (23 bp):
TTTACATATAAAAAATTAAAAAT
Found at i:40241963 original size:22 final size:23
Alignment explanation
Indices: 40241923--40241965 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
40241913 TTTACATCTC
* *
40241923 AAAAATTATAAATTTTATATATA
1 AAAAATTATAAAATATATATATA
40241946 AAAAATTA-AAAATATATATA
1 AAAAATTATAAAATATATATA
40241966 GCAAACCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AAAAATTATAAAATATATATATA
Found at i:40242069 original size:18 final size:18
Alignment explanation
Indices: 40242029--40242074 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
40242019 CTAATTTTAA
**
40242029 AAAATAAAACCCTAACTT
1 AAAATAAAACCCTAACCC
40242047 AAAATAAAACCCTAACCC
1 AAAATAAAACCCTAACCC
*
40242065 GAAATAAAAC
1 AAAATAAAAC
40242075 TTTACACATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.59, C:0.24, G:0.02, T:0.15
Consensus pattern (18 bp):
AAAATAAAACCCTAACCC
Found at i:40245126 original size:28 final size:28
Alignment explanation
Indices: 40245081--40245458 Score: 173
Period size: 28 Copynumber: 13.6 Consensus size: 28
40245071 GGGTGTTACA
* *
40245081 GTACCCATCCACGATACAACTCCTAAAG
1 GTACCCATCCATGGTACAACTCCTAAAG
*
40245109 GTACCCATCCATGGTACAACTCCTAATG
1 GTACCCATCCATGGTACAACTCCTAAAG
* *
40245137 GTACCCATCCACGATACAACT-CTGAAAG
1 GTACCCATCCATGGTACAACTCCT-AAAG
* ** * *
40245165 GTACCTATCCATGGTATGACTTCTAACG
1 GTACCCATCCATGGTACAACTCCTAAAG
*
40245193 GTA-CCATCCA-CG-ACATGACTCCTAATA-
1 GTACCCATCCATGGTACA--ACTCCTAA-AG
* *** * *
40245220 GTAGCCATCCACAATAAAACTCCTAATG
1 GTACCCATCCATGGTACAACTCCTAAAG
* * **
40245248 GTTCCCCTCCATGGTACAACTCCTAGTG
1 GTACCCATCCATGGTACAACTCCTAAAG
* * *
40245276 GTATCCATCTA-CG-ACATGACTCCTAAAG
1 GTACCCATCCATGGTACA--ACTCCTAAAG
* ** *
40245304 GTACCTATCCATGGTATGACTCATAATA-
1 GTACCCATCCATGGTACAACTCCTAA-AG
** * ** *
40245332 GTATTCATCCATGGCATGACTCCTATAG
1 GTACCCATCCATGGTACAACTCCTAAAG
* * * **
40245360 GTACCTACCCACGGTATGACTCCTAAAG
1 GTACCCATCCATGGTACAACTCCTAAAG
* * * * *
40245388 GTACGCATCTACGGTAAAACTCCTAATG
1 GTACCCATCCATGGTACAACTCCTAAAG
* ** *
40245416 GTACCTATCCACT-ACACAACTCTTAAAG
1 GTACCCATCCA-TGGTACAACTCCTAAAG
*
40245444 GTA-TCATCCATGGTA
1 GTACCCATCCATGGTA
40245459 TGGCTCCTAA
Statistics
Matches: 256, Mismatches: 77, Indels: 35
0.70 0.21 0.10
Matches are distributed among these distances:
25 1 0.00
26 5 0.02
27 26 0.10
28 217 0.85
29 4 0.02
30 3 0.01
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (28 bp):
GTACCCATCCATGGTACAACTCCTAAAG
Found at i:40245149 original size:56 final size:56
Alignment explanation
Indices: 40245081--40245495 Score: 257
Period size: 56 Copynumber: 7.4 Consensus size: 56
40245071 GGGTGTTACA
*
40245081 GTACCCATCCACGATACAACTCCTAAAGGTACCCATCCATGGTACAACTCCTAATG
1 GTACCCATCCACGATACAACTCCTAAAGGTACCCATCCATGGTATAACTCCTAATG
* * * *
40245137 GTACCCATCCACGATACAACT-CTGAAAGGTACCTATCCATGGTATGACTTCTAACG
1 GTACCCATCCACGATACAACTCCT-AAAGGTACCCATCCATGGTATAACTCCTAATG
* ** * *** *
40245193 GTA-CCATCCACGACATGACTCCTAATA-GTAGCCATCCACAATAAAACTCCTAATG
1 GTACCCATCCACGATACAACTCCTAA-AGGTACCCATCCATGGTATAACTCCTAATG
* * * * ** * * * ** * *
40245248 GTTCCCCTCCATGGTACAACTCCTAGTGGTATCCATCTACGACATGACTCCTAAAG
1 GTACCCATCCACGATACAACTCCTAAAGGTACCCATCCATGGTATAACTCCTAATG
* * * ** * ** * *
40245304 GTACCTATCCATGGTATGACTCATAATA-GTATTCATCCATGGCATGACTCCT-ATAG
1 GTACCCATCCACGATACAACTCCTAA-AGGTACCCATCCATGGTATAACTCCTAAT-G
* * * ** * * * *
40245360 GTACCTACCCACGGTATGACTCCTAAAGGTACGCATCTACGGTAAAACTCCTAATG
1 GTACCCATCCACGATACAACTCCTAAAGGTACCCATCCATGGTATAACTCCTAATG
* * * * * ** *
40245416 GTACCTATCCACTACACAACTCTTAAAGGTA-TCATCCATGGTATGGCTCCTAATA
1 GTACCCATCCACGATACAACTCCTAAAGGTACCCATCCATGGTATAACTCCTAATG
* *
40245471 GTACCCCTCCACGATACGACTCCTA
1 GTACCCATCCACGATACAACTCCTA
40245496 TTGGCACTCA
Statistics
Matches: 274, Mismatches: 76, Indels: 19
0.74 0.21 0.05
Matches are distributed among these distances:
55 77 0.28
56 195 0.71
57 2 0.01
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (56 bp):
GTACCCATCCACGATACAACTCCTAAAGGTACCCATCCATGGTATAACTCCTAATG
Found at i:40245228 original size:83 final size:84
Alignment explanation
Indices: 40245081--40245314 Score: 217
Period size: 83 Copynumber: 2.8 Consensus size: 84
40245071 GGGTGTTACA
* * * * * *
40245081 GTACCCATCCACGATACAACTCCTAAAGGTACCCATCCATGGTACA--ACTCCTAATGGTACCCA
1 GTACCCATCCATGGTACAACTCCTAACGGTATCCATCCA-CG-ACATGACTCCTAATAGTACCCA
* *
40245144 TCCACGATACAACT-CTGAAAG
64 TCCACAATAAAACTCCT-AAAG
* ** * *
40245165 GTACCTATCCATGGTATGACTTCTAACGGTA-CCATCCACGACATGACTCCTAATAGTAGCCATC
1 GTACCCATCCATGGTACAACTCCTAACGGTATCCATCCACGACATGACTCCTAATAGTACCCATC
*
40245229 CACAATAAAACTCCTAATG
66 CACAATAAAACTCCTAAAG
* * ** * *
40245248 GTTCCCCTCCATGGTACAACTCCTAGTGGTATCCATCTACGACATGACTCCTAA-AGGTACCTAT
1 GTACCCATCCATGGTACAACTCCTAACGGTATCCATCCACGACATGACTCCTAATA-GTACCCAT
40245312 CCA
65 CCA
40245315 TGGTATGACT
Statistics
Matches: 121, Mismatches: 24, Indels: 10
0.78 0.15 0.06
Matches are distributed among these distances:
81 3 0.02
82 1 0.01
83 61 0.50
84 56 0.46
ACGTcount: A:0.31, C:0.32, G:0.14, T:0.24
Consensus pattern (84 bp):
GTACCCATCCATGGTACAACTCCTAACGGTATCCATCCACGACATGACTCCTAATAGTACCCATC
CACAATAAAACTCCTAAAG
Found at i:40245426 original size:84 final size:83
Alignment explanation
Indices: 40245127--40245426 Score: 245
Period size: 84 Copynumber: 3.6 Consensus size: 83
40245117 CCATGGTACA
* * * * *
40245127 ACTCCTAATGGTACCCATCCACGATACAACT-CTGAAAGGTACCTATCCATGGTATGACTTCTA-
1 ACTCCTAAAGGTACGCATCCACGATAAAACTCCT-AATGGTACCTATCCATGGTATGACTCCTAT
40245190 ACGGTACCATCCACGACATG
65 A-GGTACCATCCACGACATG
* * ** **
40245210 ACTCCTAATA-GTA-GCCATCCACAATAAAACTCCTAATGGTTCCCCTCCATGGTACAACTCCTA
1 ACTCCTAA-AGGTACG-CATCCACGATAAAACTCCTAATGGTACCTATCCATGGTATGACTCCTA
*
40245273 GT-GGTATCCATCTACGACATG
64 -TAGGTA-CCATCCACGACATG
* * ** * * * *
40245294 ACTCCTAAAGGTAC-CTATCCATGGTATGACTCATAATAGTA-TTCATCCATGGCATGACTCCTA
1 ACTCCTAAAGGTACGC-ATCCACGATAAAACTCCTAATGGTACCT-ATCCATGGTATGACTCCTA
* **
40245357 TAGGTACCTACCCACGGTATG
64 TAGGTACC-ATCCACGACATG
* *
40245378 ACTCCTAAAGGTACGCATCTACGGTAAAACTCCTAATGGTACCTATCCA
1 ACTCCTAAAGGTACGCATCCACGATAAAACTCCTAATGGTACCTATCCA
40245427 CTACACAACT
Statistics
Matches: 166, Mismatches: 37, Indels: 27
0.72 0.16 0.12
Matches are distributed among these distances:
83 56 0.34
84 108 0.65
85 2 0.01
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (83 bp):
ACTCCTAAAGGTACGCATCCACGATAAAACTCCTAATGGTACCTATCCATGGTATGACTCCTATA
GGTACCATCCACGACATG
Found at i:40245496 original size:139 final size:138
Alignment explanation
Indices: 40245081--40245557 Score: 458
Period size: 139 Copynumber: 3.4 Consensus size: 138
40245071 GGGTGTTACA
* **
40245081 GTACCCATCCACGATACAACTCCTAAAGGTACCCATCCATGGTACAACTCCTAATGGTACCCATC
1 GTACCTATCCACGATATGACTCCTAAAGGTACCCATCCATGGTACAACTCCTAATGGTA-CCATC
* * * **
40245146 CACGATACAACTCTGAAAGGTACCTATCCATGGTATGACTTCTAACGGTACCATCCACGACATGA
65 CACGACACAACTCTTAAAGGTACCTATCCATGGTATGACTCCTAATAGTACCATCCACGACATGA
40245211 CTCCTAATA-
130 CTCCT-ATAG
* ** * * * *
40245220 GTAGCC-ATCCACAATAAAACTCCTAATGGTTCCCCTCCATGGTACAACTCCTAGTGGTATCCAT
1 GTA-CCTATCCACGATATGACTCCTAAAGGTACCCATCCATGGTACAACTCCTAATGGTA-CCAT
* ** * * * * *
40245284 CTACGACATGACTCCTAAAGGTACCTATCCATGGTATGACTCATAATAGTATTCATCCATGGCAT
64 CCACGACACAACTCTTAAAGGTACCTATCCATGGTATGACTCCTAATAGTA-CCATCCACGACAT
40245349 GACTCCTATAG
128 GACTCCTATAG
* * * * * *
40245360 GTACCTACCCACGGTATGACTCCTAAAGGTACGCATCTACGGTAAAACTCCTAATGGTACCTATC
1 GTACCTATCCACGATATGACTCCTAAAGGTACCCATCCATGGTACAACTCCTAATGGTACC-ATC
* * * * * *
40245425 CACTACACAACTCTTAAAGGTATC-ATCCATGGTATGGCTCCTAATAGTACCCCTCCACGATACG
65 CACGACACAACTCTTAAAGGTACCTATCCATGGTATGACTCCTAATAGTA-CCATCCACGACATG
*
40245489 ACTCCTATTG
129 ACTCCTATAG
* * * * * ** *
40245499 GCA-CTCATCCACGATATGACTCTTAAAGGTATCTATCTATTATACAACTCCTACTGGTA
1 GTACCT-ATCCACGATATGACTCCTAAAGGTACCCATCCATGGTACAACTCCTAATGGTA
40245558 TTCTTTACGG
Statistics
Matches: 271, Mismatches: 61, Indels: 12
0.79 0.18 0.03
Matches are distributed among these distances:
138 2 0.01
139 186 0.69
140 83 0.31
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.26
Consensus pattern (138 bp):
GTACCTATCCACGATATGACTCCTAAAGGTACCCATCCATGGTACAACTCCTAATGGTACCATCC
ACGACACAACTCTTAAAGGTACCTATCCATGGTATGACTCCTAATAGTACCATCCACGACATGAC
TCCTATAG
Found at i:40248220 original size:30 final size:30
Alignment explanation
Indices: 40248185--40248244 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
40248175 CTAAACTTAA
40248185 ATAAACTCTAATCACTTAATTAGAAAACAT
1 ATAAACTCTAATCACTTAATTAGAAAACAT
40248215 ATAAACTCTAATCACTTAATTAGAAAACAT
1 ATAAACTCTAATCACTTAATTAGAAAACAT
40248245 GAAAGAGACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.50, C:0.17, G:0.03, T:0.30
Consensus pattern (30 bp):
ATAAACTCTAATCACTTAATTAGAAAACAT
Found at i:40256815 original size:27 final size:27
Alignment explanation
Indices: 40256760--40256816 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
40256750 ATATACAATG
*
40256760 TATTGAATGAATGTGAAAATGATTATAT
1 TATTGAATGAATGT-AAAATGATGATAT
*
40256788 TATTGAATGATATGT-ATATGATGATAT
1 TATTGAATGA-ATGTAAAATGATGATAT
40256815 TA
1 TA
40256817 CAATATTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 12 0.46
28 10 0.38
29 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (27 bp):
TATTGAATGAATGTAAAATGATGATAT
Found at i:40264516 original size:9 final size:9
Alignment explanation
Indices: 40264504--40264566 Score: 63
Period size: 9 Copynumber: 6.8 Consensus size: 9
40264494 ATATTAAAAG
40264504 TGAGAGAGT
1 TGAGAGAGT
*
40264513 TGAGAGACT
1 TGAGAGAGT
*
40264522 TGAGAGTGTT
1 TGAGAGAG-T
*
40264532 TGAGAGAATT
1 TGAGAG-AGT
* *
40264542 TGAAAGAAT
1 TGAGAGAGT
40264551 TGAGAGAGT
1 TGAGAGAGT
40264560 TGAGAGA
1 TGAGAGA
40264567 AGGATGTGAA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
9 30 0.70
10 13 0.30
ACGTcount: A:0.37, C:0.02, G:0.37, T:0.25
Consensus pattern (9 bp):
TGAGAGAGT
Found at i:40270509 original size:13 final size:13
Alignment explanation
Indices: 40270474--40270512 Score: 60
Period size: 15 Copynumber: 2.8 Consensus size: 13
40270464 AATCTCGAAA
40270474 CCAAAATACTTAC
1 CCAAAATACTTAC
40270487 CCATAAAATACTTAC
1 CC--AAAATACTTAC
40270502 CCAAAATACTT
1 CCAAAATACTT
40270513 CAAATAGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 11 0.46
15 13 0.54
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (13 bp):
CCAAAATACTTAC
Found at i:40279488 original size:114 final size:114
Alignment explanation
Indices: 40279345--40279577 Score: 394
Period size: 114 Copynumber: 2.0 Consensus size: 114
40279335 TTTGTCAAAC
* * *
40279345 ATAAAAAAAACCTTGGACAAAGATTATATAAGTTCAATTTAATCCAATCCGAATTACTATTTAAT
1 ATAAAAAAAACCTTGGACAAAGATTATATAAATTAAATTTAATCCAATCCGAATTACCATTTAAT
*
40279410 GATATTTTAATTTTTATTTAAATTTATTTATAAAATATAAAAATTTAAT
66 GATATTTTAATTTTTATTTAAATTTAATTATAAAATATAAAAATTTAAT
* *
40279459 ATAAAAAAGACCTTGGATAAAGATTATATAAATTAAATTTAATCCAATCCGAATTACCATTTAAT
1 ATAAAAAAAACCTTGGACAAAGATTATATAAATTAAATTTAATCCAATCCGAATTACCATTTAAT
* *
40279524 GATATTTTAATTTTTATTTCAATTTAATTATAAAATATATAAATTTAAT
66 GATATTTTAATTTTTATTTAAATTTAATTATAAAATATAAAAATTTAAT
40279573 ATAAA
1 ATAAA
40279578 TTTAGTTTAA
Statistics
Matches: 111, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 111 1.00
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (114 bp):
ATAAAAAAAACCTTGGACAAAGATTATATAAATTAAATTTAATCCAATCCGAATTACCATTTAAT
GATATTTTAATTTTTATTTAAATTTAATTATAAAATATAAAAATTTAAT
Found at i:40282471 original size:49 final size:49
Alignment explanation
Indices: 40282409--40282517 Score: 157
Period size: 49 Copynumber: 2.2 Consensus size: 49
40282399 TTGTAGGCCG
* * *
40282409 TGTGGGTAAGCCTTGTAGGACACACGATCC-TTTGAAATAATGCAAGCCA
1 TGTGGGTAGGCCTTGTAGGACACACG-GCCGTTTGAAATAAAGCAAGCCA
* *
40282458 TGTGGGTAGGCCTTGTAGGGCACATGGCCGTTTGAAATAAAGCAAGCCA
1 TGTGGGTAGGCCTTGTAGGACACACGGCCGTTTGAAATAAAGCAAGCCA
40282507 TGTGGGTAGGC
1 TGTGGGTAGGC
40282518 GTGTGGGGCA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
48 2 0.04
49 52 0.96
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (49 bp):
TGTGGGTAGGCCTTGTAGGACACACGGCCGTTTGAAATAAAGCAAGCCA
Found at i:40283241 original size:27 final size:28
Alignment explanation
Indices: 40283203--40283263 Score: 99
Period size: 27 Copynumber: 2.2 Consensus size: 28
40283193 TTGCATGATA
*
40283203 TGATATGTTATGATTTATAATATG-TTT
1 TGATATGGTATGATTTATAATATGCTTT
40283230 TGATATGGTATGATTTATAATATGCTTT
1 TGATATGGTATGATTTATAATATGCTTT
40283258 T-ATATG
1 TGATATG
40283264 TTAAGATATG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 28 0.88
28 4 0.12
ACGTcount: A:0.30, C:0.02, G:0.16, T:0.52
Consensus pattern (28 bp):
TGATATGGTATGATTTATAATATGCTTT
Found at i:40283731 original size:11 final size:11
Alignment explanation
Indices: 40283715--40283739 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40283705 AACCCTTAAG
40283715 TGTTTTTTTTT
1 TGTTTTTTTTT
40283726 TGTTTTTTTTT
1 TGTTTTTTTTT
40283737 TGT
1 TGT
40283740 AAATAGATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (11 bp):
TGTTTTTTTTT
Found at i:40284256 original size:87 final size:87
Alignment explanation
Indices: 40284058--40284248 Score: 229
Period size: 87 Copynumber: 2.2 Consensus size: 87
40284048 CAGACACTCC
* * * *
40284058 AATTTGTAGATGAACCACCAGTGTTTGCAGATAAACTATCAGTAGGTTATGAATACACAACGTGT
1 AATTTGTGGATGAACCACCAGTGTTTGCAGATAAACTACCAGTAGGATATGAATACACAACATGT
* **
40284123 TTGCAAATAAAAGTTTTCAGTA
66 TTGCAAATAAAAGCTGCCAGTA
* * * * * * * *
40284145 AGTTTTTGGATGAACCACCAGTGTTTGTAGATAAATTGCCAGTAGGATGTGAGTGCACAACATGT
1 AATTTGTGGATGAACCACCAGTGTTTGCAGATAAACTACCAGTAGGATATGAATACACAACATGT
*
40284210 TTGCAAATAAGAGCTGCCAGTA
66 TTGCAAATAAAAGCTGCCAGTA
*
40284232 AATTTGTGGATAAACCA
1 AATTTGTGGATGAACCA
40284249 TTAGTGTTGC
Statistics
Matches: 85, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
87 85 1.00
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (87 bp):
AATTTGTGGATGAACCACCAGTGTTTGCAGATAAACTACCAGTAGGATATGAATACACAACATGT
TTGCAAATAAAAGCTGCCAGTA
Found at i:40287560 original size:32 final size:29
Alignment explanation
Indices: 40287495--40287564 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
40287485 TTAAAACAAT
* * *
40287495 TTTAAAACATGTATATTATTATTATTTAT
1 TTTAAAATATGTATATTATTATTACTTAA
*
40287524 TTTAAAATATTTATATTATTAATAGTACTTAA
1 TTTAAAATATGTATATTATT-AT--TACTTAA
40287556 TTTAAAATA
1 TTTAAAATA
40287565 ATAAAAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 18 0.53
30 2 0.06
32 14 0.41
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (29 bp):
TTTAAAATATGTATATTATTATTACTTAA
Found at i:40295024 original size:27 final size:26
Alignment explanation
Indices: 40294971--40295024 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
40294961 AGAACAAAAG
*
40294971 AAAGAAAGAAAAAGAAATGGTAGGAA
1 AAAGAAAGAAAAAGAAATGGTAAGAA
* **
40294997 AAAGAAACGTAAAAGAAATTTTAAGAA
1 AAAGAAA-GAAAAAGAAATGGTAAGAA
40295024 A
1 A
40295025 GAAAATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.65, C:0.02, G:0.20, T:0.13
Consensus pattern (26 bp):
AAAGAAAGAAAAAGAAATGGTAAGAA
Found at i:40295903 original size:29 final size:31
Alignment explanation
Indices: 40295870--40295936 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 31
40295860 ATAGGGATTT
40295870 GATCAAATTTG-TCGC-TCTACTATT-AAATG
1 GATCAAATTTGATC-CTTCTACTATTAAAATG
*
40295899 GATC-AATTTGATCCTTGTACTATTAAAATG
1 GATCAAATTTGATCCTTCTACTATTAAAATG
*
40295929 AATCAAAT
1 GATCAAAT
40295937 AAGACAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 7 0.22
29 14 0.44
30 8 0.25
31 3 0.09
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (31 bp):
GATCAAATTTGATCCTTCTACTATTAAAATG
Found at i:40296145 original size:30 final size:30
Alignment explanation
Indices: 40296111--40296189 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 30
40296101 ATAGACTTAT
** * *
40296111 TTGATTCTTTTTAATAGTATAGGGACTAAA
1 TTGATTCCATTTAATAATAGAGGGACTAAA
*
40296141 TTGA-TCCATTTAATAATAGAGGGACTAAT
1 TTGATTCCATTTAATAATAGAGGGACTAAA
40296170 TTGA-TCCAGTTTCAATAATA
1 TTGATTCCA-TTT-AATAATA
40296190 TGGGGACCTC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 28 0.67
30 7 0.17
31 7 0.17
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.39
Consensus pattern (30 bp):
TTGATTCCATTTAATAATAGAGGGACTAAA
Found at i:40296153 original size:29 final size:30
Alignment explanation
Indices: 40296120--40296196 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 30
40296110 TTTGATTCTT
*
40296120 TTTAATAGTATAGGGACTAAATTGATCCA-
1 TTTAATAATATAGGGACTAAATTGATCCAG
* *
40296149 TTTAATAATAGAGGGACTAATTTGATCCAG
1 TTTAATAATATAGGGACTAAATTGATCCAG
*
40296179 TTTCAATAATATGGGGAC
1 TTT-AATAATATAGGGAC
40296197 CTCCTAAGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
29 26 0.63
30 3 0.07
31 12 0.29
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.34
Consensus pattern (30 bp):
TTTAATAATATAGGGACTAAATTGATCCAG
Found at i:40297691 original size:45 final size:45
Alignment explanation
Indices: 40297627--40297814 Score: 238
Period size: 45 Copynumber: 4.2 Consensus size: 45
40297617 TACTACGTGT
* * * *
40297627 ACCGGGTACCATTGATTATAAAGGCGGTTGCTGTGTACTGATTCC
1 ACCGGGTATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
* *
40297672 ACCGGGTATCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCC
1 ACCGGGTATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
* * *
40297717 ACCAGGTA-CTATTGATTATGAAGGTTGTTGCTATGTGCTGATTCC
1 ACCGGGTATC-ATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
* *
40297762 ACCGAGTATCATTGACTATAAAGGTGG-TGCTATGTGCTGA-TCC
1 ACCGGGTATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
*
40297805 ACCGTGTATC
1 ACCGGGTATC
40297815 TGTTATTCTT
Statistics
Matches: 126, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
43 12 0.10
44 14 0.11
45 99 0.79
46 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (45 bp):
ACCGGGTATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
Found at i:40299929 original size:69 final size:68
Alignment explanation
Indices: 40299819--40299953 Score: 243
Period size: 69 Copynumber: 2.0 Consensus size: 68
40299809 GTTTTTGTGA
*
40299819 AATTTGTCATAAATAAGTATCTACTTCGGTGGTTAAGTGTTCTGATTGTGTGTTTAAAGTCTTGG
1 AATTTGTCATAAATAAGTATCTACTTCGATGGTTAAGTGTTCTGATTGTGTGTTTAAAGTCTTGG
40299884 GGT
66 GGT
*
40299887 AATTTGTCATAAATAAGTAATCTACTTCGATGGTTAGGTGTTCTGATTGTGTGTTTAAAGTCTTG
1 AATTTGTCATAAATAAGT-ATCTACTTCGATGGTTAAGTGTTCTGATTGTGTGTTTAAAGTCTTG
40299952 GG
65 GG
40299954 TTCAAGTCCC
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
68 18 0.28
69 46 0.72
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.42
Consensus pattern (68 bp):
AATTTGTCATAAATAAGTATCTACTTCGATGGTTAAGTGTTCTGATTGTGTGTTTAAAGTCTTGG
GGT
Found at i:40304392 original size:18 final size:19
Alignment explanation
Indices: 40304353--40304396 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
40304343 AAATCTCTTA
*
40304353 AATTTTT-TCCTAAATTCT
1 AATTTTTATCCTAAATTAT
40304371 -ATTTTTAT-CTAAATTAT
1 AATTTTTATCCTAAATTAT
40304388 AATTTTTAT
1 AATTTTTAT
40304397 TATTTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (19 bp):
AATTTTTATCCTAAATTAT
Found at i:40304553 original size:31 final size:31
Alignment explanation
Indices: 40304518--40304576 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
40304508 TCTGTCAACT
40304518 AATTGCAAATGGTAAGAATAAATTTTAAACC
1 AATTGCAAATGGTAAGAATAAATTTTAAACC
40304549 AATTGCAAATGGTAAGAATAAATTTTAA
1 AATTGCAAATGGTAAGAATAAATTTTAA
40304577 TCTTTTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.49, C:0.07, G:0.14, T:0.31
Consensus pattern (31 bp):
AATTGCAAATGGTAAGAATAAATTTTAAACC
Found at i:40307154 original size:42 final size:44
Alignment explanation
Indices: 40307045--40307203 Score: 121
Period size: 43 Copynumber: 3.7 Consensus size: 44
40307035 AGCTCGTACA
* * * * **
40307045 ATGCCAACGTCCCAGACGTGGTCTTACATGT-AATCAAATAAT-G
1 ATGCCAATGTCCCAAACATGGTCTTACACGTAAATCTCA-AATCG
* * * * * *
40307088 ACGCCACTGTCCTAGACAGGGTCTTACACGT-AA--TCATATACG
1 ATGCCAATGTCCCAAACATGGTCTTACACGTAAATCTCAAAT-CG
* *
40307130 GTGCTAATGTCCCAAACATGGTCTTACACGTAAATCTCAAATCG
1 ATGCCAATGTCCCAAACATGGTCTTACACGTAAATCTCAAATCG
* *
40307174 ATGCCAATGTCCCAGACGTGGTCTTACACG
1 ATGCCAATGTCCCAAACATGGTCTTACACG
40307204 ATATCACATT
Statistics
Matches: 89, Mismatches: 22, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
40 2 0.02
41 1 0.01
42 25 0.28
43 28 0.31
44 28 0.31
45 5 0.06
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (44 bp):
ATGCCAATGTCCCAAACATGGTCTTACACGTAAATCTCAAATCG
Found at i:40309707 original size:3 final size:3
Alignment explanation
Indices: 40309699--40309736 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
40309689 TTCCATTTCT
40309699 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
40309737 TTAGAATTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:40316518 original size:19 final size:19
Alignment explanation
Indices: 40316490--40316526 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
40316480 TCATGTTAAT
*
40316490 TTTTAAAATTTTTTAATAC
1 TTTTAAAATTTTTAAATAC
*
40316509 TTTTATAATTTTTAAATA
1 TTTTAAAATTTTTAAATA
40316527 TTTAATGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTAAAATTTTTAAATAC
Found at i:40320360 original size:29 final size:30
Alignment explanation
Indices: 40320301--40320358 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
40320291 TCCGAGCCTT
*
40320301 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
40320331 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
40320359 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:40320588 original size:13 final size:13
Alignment explanation
Indices: 40320570--40320601 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
40320560 TTTCCAGAAA
40320570 TTATGAATTTATT
1 TTATGAATTTATT
40320583 TTATGAATTTATT
1 TTATGAATTTATT
*
40320596 TGATGA
1 TTATGA
40320602 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:40320807 original size:50 final size:50
Alignment explanation
Indices: 40320696--40320944 Score: 327
Period size: 50 Copynumber: 4.8 Consensus size: 50
40320686 ATTTGGGTAA
*
40320696 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC----GA-CATG
* *
40320752 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
* *
40320802 AGAGGTCCCATGTAAGACCATGTCTGGGTCATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
* * * *
40320852 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
** *
40320902 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
40320945 TGTTATTATC
Statistics
Matches: 175, Mismatches: 17, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
50 97 0.55
51 36 0.21
55 2 0.01
56 40 0.23
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
Found at i:40327573 original size:50 final size:51
Alignment explanation
Indices: 40327497--40327616 Score: 161
Period size: 50 Copynumber: 2.4 Consensus size: 51
40327487 NNNNNNNNNN
* * * * ** *
40327497 ACCATGTCTGGGTCATGGCATTGGCACCGAGATGAG-AGGTCCCCTATAAG
1 ACCATGTCTGGGACATGGCATGGGCACCAACATGAGAACATCCCATATAAG
*
40327547 ACCATGTCTGGGACATGGCATGGGCACCAACATGAGAACATCCCATGTAAG
1 ACCATGTCTGGGACATGGCATGGGCACCAACATGAGAACATCCCATATAAG
40327598 ACCATGTCTGGGACATGGC
1 ACCATGTCTGGGACATGGC
40327617 TTTGGCATGT
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
50 32 0.52
51 29 0.48
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (51 bp):
ACCATGTCTGGGACATGGCATGGGCACCAACATGAGAACATCCCATATAAG
Found at i:40332340 original size:140 final size:139
Alignment explanation
Indices: 40331903--40332452 Score: 687
Period size: 140 Copynumber: 3.9 Consensus size: 139
40331893 TAGTGCTTTT
* * *
40331903 ATTCTTGAGT-TCTAGGTTTGATTCCTCT-CATGCTCACATTTGTATTTTTTTTATTTCATGTTG
1 ATTCTTGAGTCTCGA-GTTGGATTCCTCTAC-TACTCACATTTGTA--TTTTTTATTTCATGTTG
* *
40331966 CTTTAAGCTTTCTAAATTTTTAATTAATGTTTTTTAACATATTAGGTT-TTTCGTTAGATGGTTA
62 CTTCAAGCTTTTTAAATTTTTAATTAAT-TTTTTTAACATATTA-GTTCTTTCGTTAGATGGTTA
40332030 GATAGTTGTAATTAC
125 GATAGTTGTAATTAC
* * * * * *
40332045 ATCCTTAAGTCTTGAGTTGGATTCATCTACTACTCACATTTGTATTTTTTGTCTCATGTTGCTTC
1 ATTCTTGAGTCTCGAGTTGGATTCCTCTACTACTCACATTTGTATTTTTTATTTCATGTTGCTTC
* * *
40332110 AATCTTTTTAAATTTTTAATTAA-TTTTTTAACATATTAATTCTTTGGTTAGATGGTTAGATAGT
66 AAGCTTTTTAAATTTTTAATTAATTTTTTTAACATATTAGTTCTTTCGTTAGATGGTTAGATAGT
* **
40332174 TATTGTTAC
131 TGTAATTAC
* * * * *
40332183 A-TCTTTGAGTCTCGAGTTTGATTTCTCTCCTACTCAAACTTGTATTTTTTATTTCATGTTGCTT
1 ATTC-TTGAGTCTCGAGTTGGATTCCTCTACTACTCACATTTGTATTTTTTATTTCATGTTGCTT
* *
40332247 CAAGCTTTTTAAATTTTTAATTAATGTTTTTTAACATATTAGTTTTTTCGTTAGATGGTTACATA
65 CAAGCTTTTTAAATTTTTAATTAAT-TTTTTTAACATATTAGTTCTTTCGTTAGATGGTTAGATA
40332312 GTTGTAATTAC
129 GTTGTAATTAC
* *
40332323 ATTCTTGAGTCTCGAGTTGGATTCCTCTACTAATCACATTTGTATTTTTCATTTCATGTTGCTTC
1 ATTCTTGAGTCTCGAGTTGGATTCCTCTACTACTCACATTTGTATTTTTTATTTCATGTTGCTTC
* * * * *
40332388 AAGCTTTTTTTATTATTTTAATTAATATTTTTAACATGTTAGCTCCTTTCGTTAGATGGTTAGAT
66 AAGC-TTTTTAAAT-TTTTAATTAATTTTTTTAACATATTAG-TTCTTTCGTTAGATGGTTAGAT
40332453 GATTGCGAAT
Statistics
Matches: 348, Mismatches: 50, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
137 3 0.01
138 116 0.33
140 141 0.41
141 23 0.07
142 62 0.18
143 3 0.01
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.51
Consensus pattern (139 bp):
ATTCTTGAGTCTCGAGTTGGATTCCTCTACTACTCACATTTGTATTTTTTATTTCATGTTGCTTC
AAGCTTTTTAAATTTTTAATTAATTTTTTTAACATATTAGTTCTTTCGTTAGATGGTTAGATAGT
TGTAATTAC
Found at i:40332608 original size:22 final size:21
Alignment explanation
Indices: 40332538--40332614 Score: 72
Period size: 22 Copynumber: 3.7 Consensus size: 21
40332528 TTCAAGCTTT
40332538 TTTTTTATTTTTAATTAATCT-
1 TTTTTTATTTTTAATTAAT-TA
* *
40332559 TTTGATGATATTTT--TTAATTA
1 TTT-TTTAT-TTTTAATTAATTA
40332580 -TTTTTATTTTTAATTAATGTA
1 TTTTTTATTTTTAATTAAT-TA
40332601 TTTTTTATTTTTAA
1 TTTTTTATTTTTAA
40332615 CCTTTTTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
18 4 0.09
19 3 0.07
20 8 0.18
21 10 0.22
22 16 0.36
23 4 0.09
ACGTcount: A:0.26, C:0.01, G:0.04, T:0.69
Consensus pattern (21 bp):
TTTTTTATTTTTAATTAATTA
Found at i:40335521 original size:18 final size:19
Alignment explanation
Indices: 40335498--40335542 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
40335488 ATATATATTG
40335498 TATATATTTTAAATGTT-T
1 TATATATTTTAAATGTTAT
* *
40335516 TATATATGTTATATGTTAT
1 TATATATTTTAAATGTTAT
40335535 TAT-TATTT
1 TATATATTT
40335543 ATTTGCAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (19 bp):
TATATATTTTAAATGTTAT
Found at i:40335899 original size:44 final size:43
Alignment explanation
Indices: 40335845--40335934 Score: 110
Period size: 44 Copynumber: 2.1 Consensus size: 43
40335835 ATATACATAC
* **
40335845 TTTGTGAATATATGTACATATACTTATACATTTT-ATTTTTCTAT
1 TTTGTAAATATATACACATATAC--ATACATTTTCATTTTTCTAT
* *
40335889 TTTGTAAATATATACGCATATACATACATTTTCATTTTTTTAT
1 TTTGTAAATATATACACATATACATACATTTTCATTTTTCTAT
40335932 TTT
1 TTT
40335935 TATTTTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
42 9 0.22
43 12 0.30
44 19 0.47
ACGTcount: A:0.30, C:0.10, G:0.06, T:0.54
Consensus pattern (43 bp):
TTTGTAAATATATACACATATACATACATTTTCATTTTTCTAT
Found at i:40337975 original size:19 final size:18
Alignment explanation
Indices: 40337951--40337996 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
40337941 ACGTCTCTTT
*
40337951 TTTGCATTCATTTCATGCA
1 TTTGCATTCATTACAT-CA
40337970 TTTGCATTTCATTACATCA
1 TTTGCA-TTCATTACATCA
*
40337989 TATGCATT
1 TTTGCATT
40337997 AGACACCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 13 0.54
20 9 0.38
ACGTcount: A:0.24, C:0.20, G:0.09, T:0.48
Consensus pattern (18 bp):
TTTGCATTCATTACATCA
Found at i:40340714 original size:52 final size:50
Alignment explanation
Indices: 40340633--40340759 Score: 152
Period size: 52 Copynumber: 2.5 Consensus size: 50
40340623 CGCTTTGAGT
*
40340633 AAAAAAAAAAGGGCCAAGGTGAAACCCTACAAAGGG-GCTCTTTGAGTCAAAA
1 AAAAAAAAAAGGACCAAGGTGAAACCCTACAAAGGGAGC-C-TTGAGT-AAAA
*
40340685 AATAAAAAAAA-GACCAGGGTGAAACCCTACAAAGGGAGCCTTGAGTAAAA
1 AA-AAAAAAAAGGACCAAGGTGAAACCCTACAAAGGGAGCCTTGAGTAAAA
*
40340735 AAAAAATAGAAAGG-CTAAGGTGAAA
1 AAAAAA-A-AAAGGACCAAGGTGAAA
40340760 ACTCGCAAAG
Statistics
Matches: 66, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
49 4 0.06
50 7 0.11
51 18 0.27
52 27 0.41
53 10 0.15
ACGTcount: A:0.50, C:0.14, G:0.23, T:0.13
Consensus pattern (50 bp):
AAAAAAAAAAGGACCAAGGTGAAACCCTACAAAGGGAGCCTTGAGTAAAA
Found at i:40340736 original size:51 final size:53
Alignment explanation
Indices: 40340635--40340759 Score: 152
Period size: 51 Copynumber: 2.4 Consensus size: 53
40340625 CTTTGAGTAA
* *
40340635 AAAAAAAAGGGCCAAGGTGAAACCCTACAAAGGGGCTCTTTGAGTCAAAAAAT
1 AAAAAAAAGGACCAAGGTGAAACCCTACAAAGGGGCTCTTTGAGTAAAAAAAT
*
40340688 AAAAAAAA-GACCAGGGTGAAACCCTACAAAGGGAGC-C-TTGAGTAAAAAAA-
1 AAAAAAAAGGACCAAGGTGAAACCCTACAAAGGG-GCTCTTTGAGTAAAAAAAT
* *
40340738 AAATAGAAAGG-CTAAGGTGAAA
1 AAA-AAAAAGGACCAAGGTGAAA
40340760 ACTCGCAAAG
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
50 3 0.05
51 25 0.40
52 25 0.40
53 10 0.16
ACGTcount: A:0.50, C:0.14, G:0.23, T:0.13
Consensus pattern (53 bp):
AAAAAAAAGGACCAAGGTGAAACCCTACAAAGGGGCTCTTTGAGTAAAAAAAT
Found at i:40342126 original size:89 final size:89
Alignment explanation
Indices: 40341996--40342171 Score: 289
Period size: 89 Copynumber: 2.0 Consensus size: 89
40341986 TGAATACAAA
* * * *
40341996 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGCAGATCTTGTCTTCATGTATT
1 AGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAACAGATCTTGTCTTCATGTATT
* *
40342061 GGCGTGGAGTAGATCGAAGATACC
66 GGCGTGAAGTAGATCAAAGATACC
*
40342085 AGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAATAGATCTTGTCTTCATGTATT
1 AGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAACAGATCTTGTCTTCATGTATT
40342150 GGCGTGAAGTAGATCAAAGATA
66 GGCGTGAAGTAGATCAAAGATA
40342172 GCAGGTCCGT
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
89 80 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (89 bp):
AGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAACAGATCTTGTCTTCATGTATT
GGCGTGAAGTAGATCAAAGATACC
Found at i:40342134 original size:45 final size:45
Alignment explanation
Indices: 40341996--40342274 Score: 183
Period size: 44 Copynumber: 6.3 Consensus size: 45
40341986 TGAATACAAA
* *
40341996 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGC
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAAC
*** * * * * *
40342041 AGATCTTGTCTTCATGTATTGGCGTG-G-AGTAGATCGAAGATACC
1 AGATCTTGTCTTCCCATACTGGTG-GCGAAGTAGATCAAAGAAAAC
* * *
40342085 AGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAAT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAAC
*** * * * * *
40342130 AGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCAAAGATAGC
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAAC
* * * * * * * * *
40342174 AGGTC-CGTCTTCCTATA-TCGGTAGCGAAATGGATCGAA-TATAC
1 AGATCTTGTCTTCCCATACT-GGTGGCGAAGTAGATCAAAGAAAAC
* * * *
40342217 AGATTTTATCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGC
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAAC
*
40342262 AGGTCTTGTCTTC
1 AGATCTTGTCTTC
40342275 ATGTATTGGC
Statistics
Matches: 169, Mismatches: 57, Indels: 16
0.70 0.24 0.07
Matches are distributed among these distances:
42 1 0.01
43 16 0.09
44 89 0.53
45 62 0.37
46 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (45 bp):
AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAAC
Found at i:40342428 original size:44 final size:44
Alignment explanation
Indices: 40342377--40342568 Score: 224
Period size: 44 Copynumber: 4.3 Consensus size: 44
40342367 GGAGCAGACG
* * * *
40342377 GTGAAGTAGATCGAAGAAAGCAAATCTTATCTTTATGTATTGGC
1 GTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACTGGC
* * *
40342421 GTGAAGTAGATTGAAGAAAACAGATCTTGGCTTCATGTACTGGC
1 GTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACTGGC
* *** *
40342465 GTGAAGTAGATCAAAGATAA-CAGATCTTGTCTTCCCATACTGGTG
1 GTGAAGTAGATCGAAGA-AAGCAGATCTTGTCTTCATGTACTGG-C
* * *
40342510 GCGAAGTAGATCGAAGAAAGCAGGTCTTGTCTTCATGTATTGGC
1 GTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACTGGC
40342554 GTGAAGTAGATCGAA
1 GTGAAGTAGATCGAA
40342569 TATCGCAGAT
Statistics
Matches: 122, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
44 87 0.71
45 35 0.29
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (44 bp):
GTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACTGGC
Found at i:40342578 original size:89 final size:89
Alignment explanation
Indices: 40342423--40342585 Score: 236
Period size: 89 Copynumber: 1.8 Consensus size: 89
40342413 GTATTGGCGT
*
40342423 GAAGTAGATTGAAGAAAACAGATCTTGGCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAG
1 GAAGTAGATCGAAGAAAACAGATCTTGGCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAG
*
40342488 ATCTTGTCTTCCCATACTGGTGGC
66 ATCTGGTCTTCCCATACTGGTGGC
* * * * * * **
40342512 GAAGTAGATCGAAGAAAGCAGGTCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAATATCGCAG
1 GAAGTAGATCGAAGAAAACAGATCTTGGCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAG
40342577 ATCTGGTCT
66 ATCTGGTCT
40342586 CTCTGAAGTT
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
89 64 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (89 bp):
GAAGTAGATCGAAGAAAACAGATCTTGGCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAG
ATCTGGTCTTCCCATACTGGTGGC
Found at i:40344241 original size:18 final size:19
Alignment explanation
Indices: 40344218--40344262 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
40344208 ATATATATTG
40344218 TATATATTTTAAATGTT-T
1 TATATATTTTAAATGTTAT
* *
40344236 TATATATGTTATATGTTAT
1 TATATATTTTAAATGTTAT
40344255 TAT-TATTT
1 TATATATTT
40344263 ATTTGCAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (19 bp):
TATATATTTTAAATGTTAT
Found at i:40344490 original size:2 final size:2
Alignment explanation
Indices: 40344431--40344479 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
40344421 TTTTACATTC
40344431 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
40344473 AT TT AT A
1 AT AT AT A
40344480 CACACATATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:40349276 original size:26 final size:26
Alignment explanation
Indices: 40349247--40349298 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
40349237 CCTGGCTGAG
40349247 TTGTCCTTTGGATATGATCAAGTAAT
1 TTGTCCTTTGGATATGATCAAGTAAT
40349273 TTGTCCTTTGGATATGATCAAGTAAT
1 TTGTCCTTTGGATATGATCAAGTAAT
40349299 ATGCATTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (26 bp):
TTGTCCTTTGGATATGATCAAGTAAT
Found at i:40349313 original size:26 final size:25
Alignment explanation
Indices: 40349254--40349306 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
40349244 GAGTTGTCCT
* *
40349254 TTGGATATGATCAAGTAATTTGTCCT
1 TTGGATATGATCAAGTAATATG-CCA
40349280 TTGGATATGATCAAGTAATATG-CA
1 TTGGATATGATCAAGTAATATGCCA
40349304 TTG
1 TTG
40349307 AAGATATCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 4 0.16
26 21 0.84
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (25 bp):
TTGGATATGATCAAGTAATATGCCA
Found at i:40360538 original size:50 final size:50
Alignment explanation
Indices: 40360401--40360541 Score: 147
Period size: 50 Copynumber: 2.8 Consensus size: 50
40360391 TTTTCTGTAC
* * * * ** **
40360401 TGCCAATGTCATATCCCAGATATGATCTTACATAAGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *** *
40360451 TGCCTATGCCATGTCCCAGACATAGTCTTATGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
*
40360501 TGTCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTC
40360542 ATTCCCTTAA
Statistics
Matches: 71, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
50 71 1.00
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:40363399 original size:20 final size:20
Alignment explanation
Indices: 40363376--40363454 Score: 63
Period size: 20 Copynumber: 4.0 Consensus size: 20
40363366 GTACAGTCAT
40363376 GGGCACCAAAGTGCGAACAG
1 GGGCACCAAAGTGCGAACAG
* * *
40363396 GGGCA-CATACGTGCAAATAG
1 GGGCACCA-AAGTGCGAACAG
* * * *
40363416 GGACACCAAAGTG-TATATAT
1 GGGCACCAAAGTGCGA-ACAG
40363436 GGGCACCAAAGTGCGAACA
1 GGGCACCAAAGTGCGAACA
40363455 ATGGCACATA
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
19 3 0.07
20 39 0.87
21 3 0.07
ACGTcount: A:0.37, C:0.22, G:0.29, T:0.13
Consensus pattern (20 bp):
GGGCACCAAAGTGCGAACAG
Found at i:40363438 original size:60 final size:60
Alignment explanation
Indices: 40363374--40363561 Score: 259
Period size: 60 Copynumber: 3.1 Consensus size: 60
40363364 ACGTACAGTC
*
40363374 ATGGGCACCAAAGTGCGAACAGGGGCACATACGTGCAAATAGGGACACCAAAGTGTATAT
1 ATGGGCACCAAAGTGCGAACAGGGGCACATACGTGCAAATAGGGACACCAGAGTGTATAT
** *
40363434 ATGGGCACCAAAGTGCGAACAATGGCACATACGTGCAAACAGGGACACCAGAGTGTATAT
1 ATGGGCACCAAAGTGCGAACAGGGGCACATACGTGCAAATAGGGACACCAGAGTGTATAT
* ** * * ** * *
40363494 AGGGGCATTAAAGTGCGAATAGGAGCACAGGCGTGCAAATAGAGACACCAGAGTGTATAC
1 ATGGGCACCAAAGTGCGAACAGGGGCACATACGTGCAAATAGGGACACCAGAGTGTATAT
40363554 ATGGGCAC
1 ATGGGCAC
40363562 GCAGGGGCAC
Statistics
Matches: 110, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 110 1.00
ACGTcount: A:0.36, C:0.20, G:0.29, T:0.15
Consensus pattern (60 bp):
ATGGGCACCAAAGTGCGAACAGGGGCACATACGTGCAAATAGGGACACCAGAGTGTATAT
Found at i:40363617 original size:57 final size:56
Alignment explanation
Indices: 40363548--40363667 Score: 204
Period size: 57 Copynumber: 2.1 Consensus size: 56
40363538 ACACCAGAGT
*
40363548 GTATACATGGGCACGCAGGGGCACAGTTGTGCAAACAAAGGGCACTTCTTCATTTCC
1 GTATACATGGGCACGCAGGGGCACAATTGTGCAAAC-AAGGGCACTTCTTCATTTCC
* *
40363605 GTATACATGGGCACGTAGGGGCACAATTGTGCAAACAAGGGCACTTCTTCATTTCT
1 GTATACATGGGCACGCAGGGGCACAATTGTGCAAACAAGGGCACTTCTTCATTTCC
40363661 GTATACA
1 GTATACA
40363668 ATGGAACTCA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
56 26 0.43
57 34 0.57
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (56 bp):
GTATACATGGGCACGCAGGGGCACAATTGTGCAAACAAGGGCACTTCTTCATTTCC
Found at i:40363750 original size:85 final size:85
Alignment explanation
Indices: 40363605--40363768 Score: 285
Period size: 85 Copynumber: 1.9 Consensus size: 85
40363595 CTTCATTTCC
*
40363605 GTATACATGGGCACGTAGGGGCACAATTGTGCAAACAAGGGCACTTCTTCATTTCTGTATACAAT
1 GTATACATGGGCACGCAGGGGCACAATTGTGCAAACAAGGGCACTTCTTCATTTCTGTATACAAT
40363670 GGAACTCATTACATCAGAGT
66 GGAACTCATTACATCAGAGT
*
40363690 GTATACATGGGCACGCAGGGGCACAGTTGTGCAAACAAGGGCACTTCTTCATTT-TCGTATACAA
1 GTATACATGGGCACGCAGGGGCACAATTGTGCAAACAAGGGCACTTCTTCATTTCT-GTATACAA
*
40363754 TGGAACTCGTTACAT
65 TGGAACTCATTACAT
40363769 TCATAGATAA
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
84 1 0.01
85 74 0.99
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (85 bp):
GTATACATGGGCACGCAGGGGCACAATTGTGCAAACAAGGGCACTTCTTCATTTCTGTATACAAT
GGAACTCATTACATCAGAGT
Found at i:40381910 original size:20 final size:18
Alignment explanation
Indices: 40381881--40381934 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
40381871 TTTTAAAAAC
40381881 AATTTAACTTTGATTGAAA
1 AATTTAAC-TTGATTGAAA
40381900 AATTCTAACTTGATTGAAA
1 AATT-TAACTTGATTGAAA
*
40381919 CCATTTTAACTTGATT
1 --AATTTAACTTGATT
40381935 TAAAGGTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 14 0.45
20 14 0.45
21 3 0.10
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (18 bp):
AATTTAACTTGATTGAAA
Found at i:40381912 original size:19 final size:19
Alignment explanation
Indices: 40381877--40381934 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 19
40381867 CTTGTTTTAA
40381877 AAACAATTTAACTTTGATTG
1 AAACAATTTAAC-TTGATTG
40381897 AAA-AATTCTAACTTGATTG
1 AAACAATT-TAACTTGATTG
*
40381916 AAACCATTTTAACTTGATT
1 AAA-CAATTTAACTTGATT
40381935 TAAAGGTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 14 0.41
20 17 0.50
21 3 0.09
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (19 bp):
AAACAATTTAACTTGATTG
Found at i:40383969 original size:22 final size:23
Alignment explanation
Indices: 40383926--40383969 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
40383916 ATTGTTGAAA
*
40383926 TGTTGAAAAACTTGAAGCAATGT
1 TGTTGAAAAACTTGAAGAAATGT
* *
40383949 TGTTG-AAATCTTGATGAAATG
1 TGTTGAAAAACTTGAAGAAATG
40383970 GAGTTAGAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.36, C:0.07, G:0.23, T:0.34
Consensus pattern (23 bp):
TGTTGAAAAACTTGAAGAAATGT
Found at i:40384200 original size:20 final size:20
Alignment explanation
Indices: 40384130--40384200 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
40384120 AAACCCGATA
* *
40384130 GGTATCGATATTTTTTAAGAT
1 GGTATCGATA-ATTTTAAAAT
*
40384151 GGTATCGATAATTTTATAA-
1 GGTATCGATAATTTTAAAAT
* *
40384170 GTATATTGATAATTTTAAAAT
1 G-GTATCGATAATTTTAAAAT
40384191 GGTATCGATA
1 GGTATCGATA
40384201 CAAAATCACA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
19 1 0.03
20 28 0.70
21 11 0.28
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.44
Consensus pattern (20 bp):
GGTATCGATAATTTTAAAAT
Found at i:40386133 original size:91 final size:91
Alignment explanation
Indices: 40385978--40386160 Score: 366
Period size: 91 Copynumber: 2.0 Consensus size: 91
40385968 CACTTTCATC
40385978 TAGCTTATCCTAAAAACCCACTTAGTACCTATAGTAGATTTTTCACTAGGCCTTTCAACTAGGGT
1 TAGCTTATCCTAAAAACCCACTTAGTACCTATAGTAGATTTTTCACTAGGCCTTTCAACTAGGGT
40386043 CCATGCATTACTTCTCTCAAATTGAT
66 CCATGCATTACTTCTCTCAAATTGAT
40386069 TAGCTTATCCTAAAAACCCACTTAGTACCTATAGTAGATTTTTCACTAGGCCTTTCAACTAGGGT
1 TAGCTTATCCTAAAAACCCACTTAGTACCTATAGTAGATTTTTCACTAGGCCTTTCAACTAGGGT
40386134 CCATGCATTACTTCTCTCAAATTGAT
66 CCATGCATTACTTCTCTCAAATTGAT
40386160 T
1 T
40386161 TAACTCATCT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 92 1.00
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (91 bp):
TAGCTTATCCTAAAAACCCACTTAGTACCTATAGTAGATTTTTCACTAGGCCTTTCAACTAGGGT
CCATGCATTACTTCTCTCAAATTGAT
Found at i:40386526 original size:20 final size:18
Alignment explanation
Indices: 40386471--40386528 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 18
40386461 CTGACTTGTT
40386471 TTGAAAATAGTTTAACTTTGA
1 TTGAAAAT--TTTAAC-TTGA
40386492 TTGAAAATTTCTAACTTGA
1 TTGAAAATTT-TAACTTGA
40386511 TTGAAACCATTTTAACTT
1 TTGAAA--ATTTTAACTT
40386529 AATTTAAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
19 12 0.35
20 10 0.29
21 12 0.35
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.43
Consensus pattern (18 bp):
TTGAAAATTTTAACTTGA
Found at i:40386660 original size:22 final size:25
Alignment explanation
Indices: 40386635--40386682 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 25
40386625 TTTGTTCAAC
40386635 TTTAATTT-TTAT-TCAAAA-ATAT
1 TTTAATTTGTTATATCAAAACATAT
40386657 TTTAATTTGTTATATCAAAACATAT
1 TTTAATTTGTTATATCAAAACATAT
40386682 T
1 T
40386683 ATCAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.35
23 4 0.17
24 6 0.26
25 5 0.22
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (25 bp):
TTTAATTTGTTATATCAAAACATAT
Found at i:40388499 original size:13 final size:13
Alignment explanation
Indices: 40388483--40388512 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
40388473 ATAAGTACTA
40388483 TATATATATAATC
1 TATATATATAATC
40388496 TATATATATAATC
1 TATATATATAATC
40388509 -ATAT
1 TATAT
40388513 GAATCTAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (13 bp):
TATATATATAATC
Found at i:40389417 original size:40 final size:44
Alignment explanation
Indices: 40389372--40389474 Score: 142
Period size: 46 Copynumber: 2.4 Consensus size: 44
40389362 TCAGAACACT
40389372 GGCATTAAGCCTGCTAGACA-T-T-AA-GTCTAAATAATTCACC
1 GGCATTAAGCCTGCTAGACATTATCAATGTCTAAATAATTCACC
* *
40389412 GGCATTAAGGCTGCTAGACATTAAGTCAATGTCTGAATAATTCACC
1 GGCATTAAGCCTGCTAGACATT-A-TCAATGTCTAAATAATTCACC
40389458 GGCATTAAGCCTGCTAG
1 GGCATTAAGCCTGCTAG
40389475 GTACAGAACT
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
40 19 0.35
41 1 0.02
44 1 0.02
45 2 0.04
46 31 0.57
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.27
Consensus pattern (44 bp):
GGCATTAAGCCTGCTAGACATTATCAATGTCTAAATAATTCACC
Found at i:40392118 original size:11 final size:12
Alignment explanation
Indices: 40392091--40392117 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
40392081 TTTGTATATA
40392091 TTTTAGAATTTT
1 TTTTAGAATTTT
40392103 TTTTAGAATTTT
1 TTTTAGAATTTT
40392115 TTT
1 TTT
40392118 AATTTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.70
Consensus pattern (12 bp):
TTTTAGAATTTT
Found at i:40392154 original size:18 final size:19
Alignment explanation
Indices: 40392131--40392168 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
40392121 TTTTTAAAAA
40392131 TATAAAT-TTTGAAATTTT
1 TATAAATATTTGAAATTTT
*
40392149 TATAAATATTTTAAATTTT
1 TATAAATATTTGAAATTTT
40392168 T
1 T
40392169 TTTTGTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (19 bp):
TATAAATATTTGAAATTTT
Found at i:40392169 original size:9 final size:9
Alignment explanation
Indices: 40392101--40392169 Score: 52
Period size: 9 Copynumber: 7.7 Consensus size: 9
40392091 TTTTAGAATT
40392101 TTTTTTAGAA
1 TTTTTTA-AA
*
40392111 TTTTTTTAA
1 TTTTTTAAA
40392120 TTTTTTAAA
1 TTTTTTAAA
** *
40392129 -AATATAAA
1 TTTTTTAAA
*
40392137 -TTTTGAAA
1 TTTTTTAAA
40392145 TTTTTATAAA
1 TTTTT-TAAA
*
40392155 TATTTTAAA
1 TTTTTTAAA
40392164 TTTTTT
1 TTTTTT
40392170 TTTGTAATTT
Statistics
Matches: 45, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
8 9 0.20
9 23 0.51
10 13 0.29
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:40392402 original size:5 final size:5
Alignment explanation
Indices: 40392392--40392417 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
40392382 TTTAATTTTT
40392392 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
40392418 TGAGTTTTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:40392655 original size:19 final size:19
Alignment explanation
Indices: 40392628--40392665 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40392618 TCCATATCAT
*
40392628 CATTAAACATGCCATTTAA
1 CATTAAACATGCCACTTAA
*
40392647 CATTCAACATGCCACTTAA
1 CATTAAACATGCCACTTAA
40392666 TCACCACATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.26, G:0.05, T:0.29
Consensus pattern (19 bp):
CATTAAACATGCCACTTAA
Found at i:40401226 original size:28 final size:27
Alignment explanation
Indices: 40401167--40401220 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 27
40401157 ACAGTTCAGT
*
40401167 TCAGTTGGGCCTTTGCCCATTACAATA
1 TCAGTTGGGCCTTAGCCCATTACAATA
40401194 TCAGTGTGGGCCTTAGCCCATTACAAT
1 TCAGT-TGGGCCTTAGCCCATTACAAT
40401221 GACAGTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.31
Consensus pattern (27 bp):
TCAGTTGGGCCTTAGCCCATTACAATA
Found at i:40401541 original size:27 final size:27
Alignment explanation
Indices: 40401499--40401570 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
40401489 ATAACATAAA
*
40401499 GCAT-ACAATCATTTTATAACAT-AGGG
1 GCATAACAGTCATTTTATAACATGA-GG
*
40401525 GCATAACAGTCATTTTACT-ACGTGAGG
1 GCATAACAGTCATTTTA-TAACATGAGG
*
40401552 GCATAAAAGTCATTTTATA
1 GCATAACAGTCATTTTATA
40401571 TTAGTTTGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
26 5 0.13
27 32 0.82
28 2 0.05
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (27 bp):
GCATAACAGTCATTTTATAACATGAGG
Found at i:40405398 original size:16 final size:16
Alignment explanation
Indices: 40405377--40405430 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
40405367 ATTAAGATCT
*
40405377 TTACTTTCTTCTTTAC
1 TTACTTACTTCTTTAC
40405393 TTACTTAC-TCATTTAC
1 TTACTTACTTC-TTTAC
* *
40405409 TTACTTGCTTGCTTAAC
1 TTACTTACTT-CTTTAC
40405426 TTACT
1 TTACT
40405431 CCTTCGTTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
15 2 0.06
16 19 0.59
17 10 0.31
18 1 0.03
ACGTcount: A:0.19, C:0.24, G:0.04, T:0.54
Consensus pattern (16 bp):
TTACTTACTTCTTTAC
Found at i:40405726 original size:50 final size:50
Alignment explanation
Indices: 40405609--40405955 Score: 365
Period size: 50 Copynumber: 6.8 Consensus size: 50
40405599 GAATATAACA
* * * ** * * * *
40405609 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTCTTGT-AC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* * * * ** *
40405658 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATAT-AGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCA-G
* * *
40405708 TGCCCATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATCTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* *
40405758 TGCCAACGCCATGTCCTAGACATCGTCTTACATGGGACCTCTCATCTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* *
40405808 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* * *
40405858 TGCCAACACCATGTCCCAAACATGGTCTTACATGAGACCTCTCATAATCTCAATG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC-A-G
* *
40405913 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
40405956 TTACCCAAAT
Statistics
Matches: 253, Mismatches: 37, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
49 37 0.15
50 172 0.68
51 1 0.00
53 5 0.02
55 1 0.00
56 37 0.15
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
Found at i:40410973 original size:19 final size:20
Alignment explanation
Indices: 40410934--40410982 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
40410924 CATCAACCAT
40410934 TCATATAT-AT-ATTCAATA
1 TCATATATCATAATTCAATA
40410952 TCATATATCATAATTC-ATA
1 TCATATATCATAATTCAATA
*
40410971 TCACATATCATA
1 TCATATATCATA
40410983 TACCAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 8 0.29
19 16 0.57
20 4 0.14
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (20 bp):
TCATATATCATAATTCAATA
Found at i:40415339 original size:44 final size:45
Alignment explanation
Indices: 40415244--40415373 Score: 174
Period size: 45 Copynumber: 2.9 Consensus size: 45
40415234 TGTTATCATA
40415244 AACATGATTAAAACGAGTAAGACCATAGCTGAAAGACGCTATGGC
1 AACATGATTAAAACGAGTAAGACCATAGCTGAAAGACGCTATGGC
* * *
40415289 AACATGATTAAAACGAGTACGACCA-AGCTGAAAGATGCTATGGT
1 AACATGATTAAAACGAGTAAGACCATAGCTGAAAGACGCTATGGC
* * * *
40415333 ATCATGA-CAAAAGTGAGTAAGACCATGGCTGAAAGACGCTA
1 AACATGATTAAAA-CGAGTAAGACCATAGCTGAAAGACGCTA
40415374 CAACATCCTT
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
43 4 0.05
44 33 0.45
45 37 0.50
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (45 bp):
AACATGATTAAAACGAGTAAGACCATAGCTGAAAGACGCTATGGC
Found at i:40417190 original size:15 final size:15
Alignment explanation
Indices: 40417170--40417198 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40417160 TATAGGGTAC
40417170 AATTGTGAAAATAAT
1 AATTGTGAAAATAAT
40417185 AATTGTGAAAATAA
1 AATTGTGAAAATAA
40417199 ATATGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (15 bp):
AATTGTGAAAATAAT
Found at i:40419048 original size:27 final size:27
Alignment explanation
Indices: 40419010--40419061 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
40419000 CTGGATGAAC
40419010 ATGGGATAGGATACAATTGACATGCCA
1 ATGGGATAGGATACAATTGACATGCCA
40419037 ATGGGATAGGATACAATTGACATGC
1 ATGGGATAGGATACAATTGACATGC
40419062 AAATAGCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.23
Consensus pattern (27 bp):
ATGGGATAGGATACAATTGACATGCCA
Found at i:40421002 original size:43 final size:42
Alignment explanation
Indices: 40420899--40421003 Score: 120
Period size: 43 Copynumber: 2.5 Consensus size: 42
40420889 GGGTGTTACA
* *
40420899 CTATTTCAAATCGCAAACGGTCAGCCACATAGCCGTGTGACC
1 CTATTTCAAATCGCACACGGTCAGCCACACAGCCGTGTGACC
** * * *
40420941 CTATTTTGAATCACACACGGTCTAGCGACACGGCCGTGTGACC
1 CTATTTCAAATCGCACACGGTC-AGCCACACAGCCGTGTGACC
* *
40420984 CTATTTCAAATTGTACACGG
1 CTATTTCAAATCGCACACGG
40421004 CCTGAAAAGA
Statistics
Matches: 50, Mismatches: 12, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
42 18 0.36
43 32 0.64
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.25
Consensus pattern (42 bp):
CTATTTCAAATCGCACACGGTCAGCCACACAGCCGTGTGACC
Found at i:40422532 original size:25 final size:25
Alignment explanation
Indices: 40422473--40422532 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
40422463 AATAAGTTAA
*
40422473 TTTTGTTA-ATGTAATTATTATTAT
1 TTTTGCTATATGTAATTATTATTAT
*
40422497 TATTTTC-ATATGTAATTATTATTAT
1 T-TTTGCTATATGTAATTATTATTAT
40422522 TTTTGCTATAT
1 TTTTGCTATAT
40422533 ATATATGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 6 0.20
25 24 0.80
ACGTcount: A:0.28, C:0.03, G:0.07, T:0.62
Consensus pattern (25 bp):
TTTTGCTATATGTAATTATTATTAT
Found at i:40423138 original size:19 final size:20
Alignment explanation
Indices: 40423092--40423138 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
40423082 ATATTATTTC
* *
40423092 TATACCATTGTAATATTTAT
1 TATAGCATTGTAATATTTAA
*
40423112 TATTGCATTGT-ATATTTAA
1 TATAGCATTGTAATATTTAA
40423131 TATAGCAT
1 TATAGCAT
40423139 CACATCATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.49
Consensus pattern (20 bp):
TATAGCATTGTAATATTTAA
Found at i:40425257 original size:29 final size:29
Alignment explanation
Indices: 40425216--40425300 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
40425206 ATTGTTCTGG
*
40425216 AAAAATAATTTTGACAAGATGGGTTTTGA
1 AAAAATAATTTTGACGAGATGGGTTTTGA
* * * *
40425245 AAAAATAAATTTGACGTGATGTGTTCTGA
1 AAAAATAATTTTGACGAGATGGGTTTTGA
* *
40425274 AAAAATTATTTTGACGAGATGGATTTT
1 AAAAATAATTTTGACGAGATGGGTTTT
40425301 TTTTTTGAAA
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (29 bp):
AAAAATAATTTTGACGAGATGGGTTTTGA
Found at i:40425516 original size:20 final size:20
Alignment explanation
Indices: 40425491--40425531 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
40425481 ATGTACTGTC
40425491 AGCAAAAGTACTGAAAAATG
1 AGCAAAAGTACTGAAAAATG
40425511 AGCAAAAGTACTGAAAAATG
1 AGCAAAAGTACTGAAAAATG
40425531 A
1 A
40425532 CAGTGCATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.10, G:0.20, T:0.15
Consensus pattern (20 bp):
AGCAAAAGTACTGAAAAATG
Found at i:40428847 original size:59 final size:59
Alignment explanation
Indices: 40428716--40428894 Score: 211
Period size: 59 Copynumber: 3.1 Consensus size: 59
40428706 GTCCACATCG
* * * * ***
40428716 AAAGAACTTCTAATTTATTAAATGAAACAATAT--TATTTGGTTTGTACAAAAATATTCA
1 AAAGAACTTATATTTTATTAAATGAAACAATATAAAAATAAATTT-TACAAAAATATTCA
* * *
40428774 AAAGAACTTCTATTTTATTAAATGAAATAATATAAAAATAAATTTTACAAAAATATTGA
1 AAAGAACTTATATTTTATTAAATGAAACAATATAAAAATAAATTTTACAAAAATATTCA
* *
40428833 AAAGAACTTATATTTTATTAAATGAAACAATATAAAAAT-AATTTGAACAAAATTATTCA
1 AAAGAACTTATATTTTATTAAATGAAACAATATAAAAATAAATTT-TACAAAAATATTCA
40428892 AAA
1 AAA
40428895 ATAAATCAAT
Statistics
Matches: 105, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
58 36 0.34
59 64 0.61
60 5 0.05
ACGTcount: A:0.52, C:0.07, G:0.06, T:0.35
Consensus pattern (59 bp):
AAAGAACTTATATTTTATTAAATGAAACAATATAAAAATAAATTTTACAAAAATATTCA
Found at i:40429263 original size:18 final size:18
Alignment explanation
Indices: 40429240--40429281 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
40429230 GAAGTGAAAA
*
40429240 AGGATACATATAAGGGTT
1 AGGATAAATATAAGGGTT
40429258 AGGATAAATATAAGGGTT
1 AGGATAAATATAAGGGTT
40429276 AGGATA
1 AGGATA
40429282 TGCACTTGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.29, T:0.26
Consensus pattern (18 bp):
AGGATAAATATAAGGGTT
Found at i:40433291 original size:21 final size:22
Alignment explanation
Indices: 40433255--40433306 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
40433245 ACATTATATT
40433255 ATTATATATTGCTATAAATTTA
1 ATTATATATTGCTATAAATTTA
*
40433277 ATTAT-TATTGTTATAAA-TTA
1 ATTATATATTGCTATAAATTTA
40433297 CATTATATAT
1 -ATTATATAT
40433307 AAAAATAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 3 0.11
21 16 0.59
22 8 0.30
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (22 bp):
ATTATATATTGCTATAAATTTA
Found at i:40435515 original size:19 final size:19
Alignment explanation
Indices: 40435493--40435530 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
40435483 AAATTCAAGT
*
40435493 AAGTATAAAAGTTATTAAA
1 AAGTATAAAAATTATTAAA
40435512 AAGTATAAAAATTATTAAA
1 AAGTATAAAAATTATTAAA
40435531 GATATTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.32
Consensus pattern (19 bp):
AAGTATAAAAATTATTAAA
Found at i:40438395 original size:2 final size:2
Alignment explanation
Indices: 40438388--40438414 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40438378 GATTTCTCCC
40438388 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
40438415 CTACATAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40448691 original size:5 final size:5
Alignment explanation
Indices: 40448681--40448706 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
40448671 AAAATAAGTG
40448681 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
40448707 TTTAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:40449430 original size:21 final size:21
Alignment explanation
Indices: 40449406--40449447 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
40449396 ATTACAACCA
*
40449406 ATCTTAGAAACTCAACACCCG
1 ATCTCAGAAACTCAACACCCG
40449427 ATCTCAGAAACTCAACACCCG
1 ATCTCAGAAACTCAACACCCG
40449448 TCGTGTCTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.36, G:0.10, T:0.17
Consensus pattern (21 bp):
ATCTCAGAAACTCAACACCCG
Found at i:40453631 original size:9 final size:9
Alignment explanation
Indices: 40453546--40453630 Score: 109
Period size: 9 Copynumber: 9.4 Consensus size: 9
40453536 GTAGTGATTC
*
40453546 AATTTGGTT
1 AATTCGGTT
40453555 AATTCGGTT
1 AATTCGGTT
* *
40453564 AATTCAGAT
1 AATTCGGTT
40453573 AATTCAGG-T
1 AATTC-GGTT
40453582 AATTCGGTT
1 AATTCGGTT
*
40453591 AATTCGGGT
1 AATTCGGTT
40453600 AATTCGGTT
1 AATTCGGTT
40453609 AATTCGGTT
1 AATTCGGTT
*
40453618 AATTTGGTT
1 AATTCGGTT
40453627 AATT
1 AATT
40453631 TTTAACCAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
8 2 0.03
9 64 0.96
10 1 0.01
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.44
Consensus pattern (9 bp):
AATTCGGTT
Found at i:40453810 original size:12 final size:12
Alignment explanation
Indices: 40453793--40453817 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40453783 TGTTATTTCG
40453793 GGTCGGTTAACC
1 GGTCGGTTAACC
40453805 GGTCGGTTAACC
1 GGTCGGTTAACC
40453817 G
1 G
40453818 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:40461617 original size:17 final size:17
Alignment explanation
Indices: 40461592--40461648 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
40461582 TTTTCTAGGG
*
40461592 CTTAGTGTTTATGTTTT
1 CTTAATGTTTATGTTTT
*
40461609 CTTAATGTTTATGCTTT
1 CTTAATGTTTATGTTTT
***
40461626 -TT-CCCTTTATGTTTT
1 CTTAATGTTTATGTTTT
40461641 CTTAATGT
1 CTTAATGT
40461649 CTATTGCGAA
Statistics
Matches: 29, Mismatches: 9, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
15 9 0.31
16 4 0.14
17 16 0.55
ACGTcount: A:0.14, C:0.12, G:0.12, T:0.61
Consensus pattern (17 bp):
CTTAATGTTTATGTTTT
Found at i:40464565 original size:4 final size:4
Alignment explanation
Indices: 40464550--40464589 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
40464540 TCAACTTAGA
*
40464550 AATT AGTT AATT AATT AATT AATT AATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT AATT AATT AATT
40464590 GAACTTCGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (4 bp):
AATT
Found at i:40469720 original size:17 final size:17
Alignment explanation
Indices: 40469700--40469736 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
40469690 AATTTTTGAA
40469700 TTAGTGAATTCTGTGAT
1 TTAGTGAATTCTGTGAT
*
40469717 TTAGTGAATTTTGTGAT
1 TTAGTGAATTCTGTGAT
40469734 TTA
1 TTA
40469737 AAAAGAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.03, G:0.22, T:0.51
Consensus pattern (17 bp):
TTAGTGAATTCTGTGAT
Found at i:40470937 original size:46 final size:46
Alignment explanation
Indices: 40470884--40471069 Score: 318
Period size: 46 Copynumber: 4.0 Consensus size: 46
40470874 TCATGGAAAA
* *
40470884 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATATTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAG
* *
40470930 TTGTGAAAAATAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAG
40470976 TTGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAG
* *
40471022 TTGTGAAAAGTAGGTATGGTATTTCAATGAAGAAAACCATATTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAG
40471068 TT
1 TT
40471070 ATAGCATTGT
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 134 1.00
ACGTcount: A:0.37, C:0.08, G:0.26, T:0.30
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAG
Found at i:40475383 original size:14 final size:12
Alignment explanation
Indices: 40475353--40475378 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40475343 TATTATTATT
40475353 TAACATTAAAAA
1 TAACATTAAAAA
40475365 TAACATTAAAAA
1 TAACATTAAAAA
40475377 TA
1 TA
40475379 TAACAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (12 bp):
TAACATTAAAAA
Found at i:40477589 original size:58 final size:61
Alignment explanation
Indices: 40477527--40477660 Score: 168
Period size: 61 Copynumber: 2.2 Consensus size: 61
40477517 AATCACTTTA
*
40477527 ATATTAAATTAATATAATACTTA-T-CAAGATAAATATTAGATTAAATTTAACATTAA-AT
1 ATATTAAATTAATATAATACTTACTACAAGATAAATATTAAATTAAATTTAACATTAAGAT
* * * *
40477585 ATATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTTAATTTAATATTAAGAT
1 ATATTAAATTAATATAATACTTA-CTACAAGATAAATATTAAATTAAATTTAACATTAAGAT
* *
40477647 A-ATCAATTTAATAT
1 ATATTAAATTAATAT
40477661 TAAATTAATA
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
58 21 0.33
60 1 0.02
61 39 0.61
62 3 0.05
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (61 bp):
ATATTAAATTAATATAATACTTACTACAAGATAAATATTAAATTAAATTTAACATTAAGAT
Done.