Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 144 of 211
Found at i:42859457 original size:31 final size:32
Alignment explanation
Indices: 42859398--42859462 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
42859388 GGCAAATTAC
42859398 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
*
42859430 AAGAGTAATTGAATCTTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
42859461 AA
1 AA
42859463 ATTATCTAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 13 0.41
32 19 0.59
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.32
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:42865632 original size:31 final size:31
Alignment explanation
Indices: 42865594--42865657 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
42865584 GGCAAATTAC
42865594 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
42865625 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
42865656 AA
1 AA
42865658 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:42866052 original size:9 final size:9
Alignment explanation
Indices: 42866034--42866141 Score: 64
Period size: 9 Copynumber: 12.2 Consensus size: 9
42866024 CTTATATATA
*
42866034 AACTTGCAT
1 AACTTACAT
42866043 AACTTACAT
1 AACTTACAT
*
42866052 AA-TAACATAAT
1 AACTTAC---AT
42866063 AACTTACAT
1 AACTTACAT
42866072 AA--TACAT
1 AACTTACAT
* *
42866079 AGCATACAT
1 AACTTACAT
42866088 AACTTACAT
1 AACTTACAT
* * *
42866097 AA--GATAG
1 AACTTACAT
*
42866104 AACTTATAT
1 AACTTACAT
*
42866113 AACTTAAAT
1 AACTTACAT
42866122 AACTTACAT
1 AACTTACAT
*
42866131 AATTTACAT
1 AACTTACAT
42866140 AA
1 AA
42866142 AACATAACTC
Statistics
Matches: 77, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
7 10 0.13
8 3 0.04
9 57 0.74
11 4 0.05
12 3 0.04
ACGTcount: A:0.49, C:0.16, G:0.04, T:0.31
Consensus pattern (9 bp):
AACTTACAT
Found at i:42866066 original size:20 final size:19
Alignment explanation
Indices: 42866041--42866079 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
42866031 ATAAACTTGC
42866041 ATAACTTACATAATAACATA
1 ATAACTTACATAAT-ACATA
42866061 ATAACTTACATAATACATA
1 ATAACTTACATAATACATA
42866080 GCATACATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAACTTACATAATACATA
Found at i:42867801 original size:21 final size:21
Alignment explanation
Indices: 42867763--42867813 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
42867753 GCTACAACTT
42867763 AAAGCAGAGGCAGCAGCGAAGG
1 AAAGCAGAGGCAGCAGCG-AGG
*
42867785 -AAGCAGAGGC-GATAGCGAGG
1 AAAGCAGAGGCAG-CAGCGAGG
42867805 AAAGCAGAG
1 AAAGCAGAG
42867814 CAGAGCAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.41, C:0.16, G:0.41, T:0.02
Consensus pattern (21 bp):
AAAGCAGAGGCAGCAGCGAGG
Found at i:42872193 original size:17 final size:17
Alignment explanation
Indices: 42872186--42872234 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
42872176 TCGTCTGGCG
42872186 GATAGTATCGCCTAGCA
1 GATAGTATCGCCTAGCA
**
42872203 GATAGTATTACCTAGCA
1 GATAGTATCGCCTAGCA
*
42872220 GACAGTATCGCCTAG
1 GATAGTATCGCCTAG
42872235 GGAATACAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (17 bp):
GATAGTATCGCCTAGCA
Found at i:42872807 original size:19 final size:20
Alignment explanation
Indices: 42872780--42872817 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
42872770 AAATCAATAC
42872780 ATCAATT-AATATGTTGTAA
1 ATCAATTAAATATGTTGTAA
* *
42872799 ATCATTTAAATATTTTGTA
1 ATCAATTAAATATGTTGTA
42872818 TAAAAAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.47
Consensus pattern (20 bp):
ATCAATTAAATATGTTGTAA
Found at i:42876063 original size:89 final size:89
Alignment explanation
Indices: 42875884--42876073 Score: 222
Period size: 89 Copynumber: 2.1 Consensus size: 89
42875874 CACTAACTCT
* * * *
42875884 TAACCCCAAACCCCTAAGCCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCATA
1 TAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCATA
* * * *
42875949 AACCCTAGCCAGACCCCGAATCCC
66 AACCCTAACCAAACCCAGAAACCC
* *
42875973 TAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAATACACTAATTAATCTAAACCCT-
1 TAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCATA
* *
42876037 AA-CCTGACACCAAATCCATAAACCC
66 AACCCT-A-ACCAAACCCAGAAACCC
*
42876062 TAAATCCCTAAC
1 T-AACCCCTAAC
42876074 TCTTAATCTC
Statistics
Matches: 85, Mismatches: 13, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
87 3 0.04
88 3 0.04
89 70 0.82
90 9 0.11
ACGTcount: A:0.44, C:0.29, G:0.03, T:0.25
Consensus pattern (89 bp):
TAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCATA
AACCCTAACCAAACCCAGAAACCC
Found at i:42876086 original size:14 final size:14
Alignment explanation
Indices: 42876064--42876115 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
42876054 ATAAACCCTA
42876064 AATCCCTAA-CTCTT
1 AATCCCTAACCTC-T
*
42876078 AATCTCTAACCTCT
1 AATCCCTAACCTCT
*
42876092 AATCCCTAACCCCT
1 AATCCCTAACCTCT
*
42876106 AACCCCTAAC
1 AATCCCTAAC
42876116 TCATAACCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 30 0.91
15 3 0.09
ACGTcount: A:0.31, C:0.42, G:0.00, T:0.27
Consensus pattern (14 bp):
AATCCCTAACCTCT
Found at i:42876737 original size:82 final size:83
Alignment explanation
Indices: 42876599--42876788 Score: 258
Period size: 82 Copynumber: 2.3 Consensus size: 83
42876589 TTTTTGCGAC
* *
42876599 ACTTTTTCAAAAACGTCGCTAAAGCCTCGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAG
1 ACTTTTTCAAAAACGCCGCTAAAGCATCGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAG
*
42876664 ATCTGAGCATTACCAGCG
66 ATCTGAGCACTACCAGCG
* * * *
42876682 -CTTTTTCAAAAACCCCGCTAAAG-ATATGAGCATTAGCGGCGCTTTTTCAAAAACGCCTCTAAA
1 ACTTTTTCAAAAACGCCGCTAAAGCAT-CGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAA
*
42876745 GATCTGAGCACTAGCAGCG
65 GATCTGAGCACTACCAGCG
* * *
42876764 ATTTTTTTAAAAACGCCACTAAAGC
1 ACTTTTTCAAAAACGCCGCTAAAGC
42876789 CCCGAAAGGT
Statistics
Matches: 92, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
81 1 0.01
82 72 0.78
83 19 0.21
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (83 bp):
ACTTTTTCAAAAACGCCGCTAAAGCATCGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAG
ATCTGAGCACTACCAGCG
Found at i:42876786 original size:42 final size:41
Alignment explanation
Indices: 42876600--42876787 Score: 234
Period size: 41 Copynumber: 4.6 Consensus size: 41
42876590 TTTTGCGACA
* * *
42876600 CTTTTTCAAAAACGTCGCTAAAG-CCTCGAGCATTAGCGGCG
1 CTTTTTCAAAAACGCCGCTAAAGATCT-GAGCATTAGCAGCG
* *
42876641 CTTTTCCAAAAACGCCGCTAAAGATCTGAGCATTACCAGCG
1 CTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTAGCAGCG
* * *
42876682 CTTTTTCAAAAACCCCGCTAAAGATATGAGCATTAGCGGCG
1 CTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTAGCAGCG
* *
42876723 CTTTTTCAAAAACGCCTCTAAAGATCTGAGCACTAGCAGCG
1 CTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTAGCAGCG
* * *
42876764 ATTTTTTTAAAAACGCCACTAAAG
1 -CTTTTTCAAAAACGCCGCTAAAG
42876788 CCCCGAAAGG
Statistics
Matches: 127, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
41 105 0.83
42 22 0.17
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.25
Consensus pattern (41 bp):
CTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTAGCAGCG
Found at i:42884329 original size:28 final size:28
Alignment explanation
Indices: 42884292--42884356 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
42884282 TGGATACCGC
* *
42884292 TTACTTATCATACTTTTGGCGAATACCT
1 TTACTAATCATACTTTTGACGAATACCT
*
42884320 TTACTAATCATACTTTTGATGAATACCT
1 TTACTAATCATACTTTTGACGAATACCT
*
42884348 TTGCTAATC
1 TTACTAATC
42884357 TTGATAAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.43
Consensus pattern (28 bp):
TTACTAATCATACTTTTGACGAATACCT
Found at i:42884850 original size:21 final size:21
Alignment explanation
Indices: 42884826--42884898 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
42884816 GGGCTAGCAG
*
42884826 AATGCTACAAAAGCCATATCA
1 AATGCCACAAAAGCCATATCA
* * *
42884847 AATGCCA-GAAAGGC-TAACA
1 AATGCCACAAAAGCCATATCA
*
42884866 TAATGCCACAAATGCCATATCA
1 -AATGCCACAAAAGCCATATCA
*
42884888 GATGCCACAAA
1 AATGCCACAAA
42884899 GGCTAACAGA
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
19 4 0.10
20 12 0.30
21 20 0.50
22 4 0.10
ACGTcount: A:0.45, C:0.25, G:0.14, T:0.16
Consensus pattern (21 bp):
AATGCCACAAAAGCCATATCA
Found at i:42884862 original size:41 final size:41
Alignment explanation
Indices: 42884810--42884914 Score: 147
Period size: 41 Copynumber: 2.6 Consensus size: 41
42884800 ACAAATTACA
* * *
42884810 CCACAAGGGCTAGCAGAATGCTACAAAAGCCATATCAAATG
1 CCACAAAGGCTAACAGAATGCCACAAAAGCCATATCAAATG
* * * *
42884851 CCAGAAAGGCTAACATAATGCCACAAATGCCATATCAGATG
1 CCACAAAGGCTAACAGAATGCCACAAAAGCCATATCAAATG
42884892 CCACAAAGGCTAACAGAATGCCA
1 CCACAAAGGCTAACAGAATGCCA
42884915 GAAGGGCTAT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.42, C:0.26, G:0.18, T:0.14
Consensus pattern (41 bp):
CCACAAAGGCTAACAGAATGCCACAAAAGCCATATCAAATG
Found at i:42884922 original size:20 final size:20
Alignment explanation
Indices: 42884847--42884923 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
42884837 AGCCATATCA
*
42884847 AATGCCAGAAAGGCTAACAT
1 AATGCCAGAAAGGCTAACAG
* * *
42884867 AATGCCACAAATGCCATATCAG
1 AATGCCAGAAA-GGC-TAACAG
*
42884889 -ATGCCACAAAGGCTAACAG
1 AATGCCAGAAAGGCTAACAG
*
42884908 AATGCCAGAAGGGCTA
1 AATGCCAGAAAGGCTA
42884924 TATTCGAATA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
19 5 0.11
20 25 0.54
21 12 0.26
22 4 0.09
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.14
Consensus pattern (20 bp):
AATGCCAGAAAGGCTAACAG
Found at i:42886347 original size:571 final size:571
Alignment explanation
Indices: 42885205--42886924 Score: 3206
Period size: 571 Copynumber: 3.0 Consensus size: 571
42885195 GAAGCTTTAA
*
42885205 GAATTTTCTAAGTAACAGATGTCACACGCCCGTGTGAATAGCCGTGTGGACGAATATAGGCCATT
1 GAATTTTCTAAGTAACAGATGTCACACGCCCGTGTGAACAGCCGTGT-G--G-----A--CCATT
* *
42885270 TGCAAGGCCAATTCACCACCTATAAGGGTCAACCCTACACAAGCACAAAATATACCATTTTTATA
56 TGCAAGGCCAATTCACCACCCATAAGGGTCAACCCTACATAAGCACAAAATATACCATTTTTATA
*
42885335 CACAATAGGTAGCTTAAACATTGTGAATTCATGCATCAAACATGCCATACCAATTCAACCATTTC
121 CACAATAGGCAGCTTAAACATTGTGAATTCATGCATCAAACATGCCATACCAATTCAACCATTTC
42885400 ATCTATTCATACACAAACTTTTGCCTAACCACAAAAATACAATATCGATATGATTTATTATTTAG
186 ATCTATTCATACACAAACTTTTGCCTAACCACAAAAATACAATATCGATATGATTTATTATTTAG
*
42885465 CCAAACAATCATCATTTAAACCAATTTAACAAGGCATGTAAATCAATATCTTTTAGACCTAAAAT
251 CCAAACAATCATCATTTAAACCAATTTAACAAGGCATGTAAATCAATGTCTTTTAGACCTAAAAT
42885530 ACTCCATTCCTTTTTCATCATCTCAATTGCAACCTAACCTCTCAATACCAATATAAACAACTGCA
316 ACTCCATTCCTTTTTCATCATCTCAATTGCAACCTAACCTCTCAATACCAATATAAACAACTGCA
42885595 TAAATACCATTATTCATCAATTGTGAATATCAATTTGGACACTTCCATTAATGCATCAATAACTT
381 TAAATACCATTATTCATCAATTGTGAATATCAATTTGGACACTTCCATTAATGCATCAATAACTT
42885660 TACTGAAGCTTACCACATAAGCACAATCACATACCAATTATAAGGCCATCTACATATCAAACCTC
446 TACTGAAGCTTACCACATAAGCACAATCACATACCAATTATAAGGCCATCTACATATCAAACCTC
*
42885725 ACATTATAAACAAGTAAAATCTCATGGCTCAATACATTTCAAACATATAGGCATCAATTGT
511 ACATTATAAACAAGTCAAATCTCATGGCTCAATACATTTCAAACATATAGGCATCAATTGT
*
42885786 GAATTTTCTAAGTAATAGATGTCACACGCCCGTGTGAACAGCCGTGTGGACCATTTGCAAGGCCA
1 GAATTTTCTAAGTAACAGATGTCACACGCCCGTGTGAACAGCCGTGTGGACCATTTGCAAGGCCA
* *
42885851 ATTCACCACCCATAAGGGTCAACCCTATATAAGCACAAAATATACCATTTTTATACATAATAGGC
66 ATTCACCACCCATAAGGGTCAACCCTACATAAGCACAAAATATACCATTTTTATACACAATAGGC
42885916 AGCTTAAACATTGTGAATTCATGCATCAAACATGCCATACCAATTCAACCATTTCATCTATTCAT
131 AGCTTAAACATTGTGAATTCATGCATCAAACATGCCATACCAATTCAACCATTTCATCTATTCAT
* *
42885981 ACACAAACTTTTGCCTAACCACAAAAATACAAAATAGATATGATTTATTATTTAGCCAAACAATC
196 ACACAAACTTTTGCCTAACCACAAAAATACAATATCGATATGATTTATTATTTAGCCAAACAATC
*
42886046 ATCATTTAAACCAATTTAACAAGGCATGTAAATCAATGTCTTTTAGACCTAAAATACTCCATTCG
261 ATCATTTAAACCAATTTAACAAGGCATGTAAATCAATGTCTTTTAGACCTAAAATACTCCATTCC
42886111 TTTTTCATCATCTCAATTGCAACCTAACCTCTCAATACCAATATAAACAACTGCATAAATACCAT
326 TTTTTCATCATCTCAATTGCAACCTAACCTCTCAATACCAATATAAACAACTGCATAAATACCAT
42886176 TATTCATCAATTGTGAATATCAATTTGGACACTTCCATTAATGCATCAATAACTTTACTGAAGCT
391 TATTCATCAATTGTGAATATCAATTTGGACACTTCCATTAATGCATCAATAACTTTACTGAAGCT
42886241 TACCACATAAGCACAATCACATACCAATTATAAGGCCATCTACATATCAAACCTCACATTATAAA
456 TACCACATAAGCACAATCACATACCAATTATAAGGCCATCTACATATCAAACCTCACATTATAAA
42886306 CAAGTCAAATCTCATGGCTCAATACATTTCAAACATATAGGCATCAATTGT
521 CAAGTCAAATCTCATGGCTCAATACATTTCAAACATATAGGCATCAATTGT
42886357 GAATTTTCTAAGTAACAGATGTCACACGCCCGTGTGAACAGCCGTGTGGACCATTTGCAAGGCCA
1 GAATTTTCTAAGTAACAGATGTCACACGCCCGTGTGAACAGCCGTGTGGACCATTTGCAAGGCCA
42886422 ATTCACCACCCATAAGGGTCAACCCTACATAAGCACAAAATATACCATTTTTATACACAATAGGC
66 ATTCACCACCCATAAGGGTCAACCCTACATAAGCACAAAATATACCATTTTTATACACAATAGGC
42886487 AGCTTAAACATTGTGAATTCATGCATCAAACATGCCATACCAATTCAACCATTTCATCTATTCAT
131 AGCTTAAACATTGTGAATTCATGCATCAAACATGCCATACCAATTCAACCATTTCATCTATTCAT
42886552 ACACAAACTTTTGCCTAACCACAAAAATACAATATCGATATGATTTATTATTTAGCCAAACAATC
196 ACACAAACTTTTGCCTAACCACAAAAATACAATATCGATATGATTTATTATTTAGCCAAACAATC
*
42886617 ATCATTTAAACCAATTTAACAAGGTATGTAAATCAATGTCTTTTAGACCTAAAATACTCCATTCC
261 ATCATTTAAACCAATTTAACAAGGCATGTAAATCAATGTCTTTTAGACCTAAAATACTCCATTCC
*
42886682 TTTTTCATCATCTCAATTGCAACCTAACCTCTCAATACCAATATAAACAAATGCATAAATACCAT
326 TTTTTCATCATCTCAATTGCAACCTAACCTCTCAATACCAATATAAACAACTGCATAAATACCAT
42886747 TATTCATCAATTGTGAATATCAATTTGGACACTTCCATTAATGCATCAATAACTTTACTGAAGCT
391 TATTCATCAATTGTGAATATCAATTTGGACACTTCCATTAATGCATCAATAACTTTACTGAAGCT
*
42886812 TACCACATAAGCACAATCACATACCAATTATAAGGCTATCTACATATCAAACCTCACATTATAAA
456 TACCACATAAGCACAATCACATACCAATTATAAGGCCATCTACATATCAAACCTCACATTATAAA
*
42886877 CAAGTCAAATCTCATGGCTCAATACATTTCAAACATATAGGCACCAAT
521 CAAGTCAAATCTCATGGCTCAATACATTTCAAACATATAGGCATCAAT
42886925 AGCCAAAATC
Statistics
Matches: 1117, Mismatches: 22, Indels: 10
0.97 0.02 0.01
Matches are distributed among these distances:
571 1069 0.96
573 1 0.00
578 1 0.00
580 1 0.00
581 45 0.04
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (571 bp):
GAATTTTCTAAGTAACAGATGTCACACGCCCGTGTGAACAGCCGTGTGGACCATTTGCAAGGCCA
ATTCACCACCCATAAGGGTCAACCCTACATAAGCACAAAATATACCATTTTTATACACAATAGGC
AGCTTAAACATTGTGAATTCATGCATCAAACATGCCATACCAATTCAACCATTTCATCTATTCAT
ACACAAACTTTTGCCTAACCACAAAAATACAATATCGATATGATTTATTATTTAGCCAAACAATC
ATCATTTAAACCAATTTAACAAGGCATGTAAATCAATGTCTTTTAGACCTAAAATACTCCATTCC
TTTTTCATCATCTCAATTGCAACCTAACCTCTCAATACCAATATAAACAACTGCATAAATACCAT
TATTCATCAATTGTGAATATCAATTTGGACACTTCCATTAATGCATCAATAACTTTACTGAAGCT
TACCACATAAGCACAATCACATACCAATTATAAGGCCATCTACATATCAAACCTCACATTATAAA
CAAGTCAAATCTCATGGCTCAATACATTTCAAACATATAGGCATCAATTGT
Found at i:42887683 original size:43 final size:43
Alignment explanation
Indices: 42887636--42887795 Score: 225
Period size: 43 Copynumber: 3.7 Consensus size: 43
42887626 TGTAATCTTG
* *
42887636 TATCGATGCCAATAG-CCCAGCCATGATCTTACACGAAATCACA
1 TATCGATGCCAAT-GTCCCAGACATGGTCTTACACGAAATCACA
*
42887679 TATCGATGCCAATGTCCCAGACATGGTCTTACATGAAATCACA
1 TATCGATGCCAATGTCCCAGACATGGTCTTACACGAAATCACA
* * *
42887722 TATCGATGCCAATGTCCCAGACATGGTTTTACACGAAGTCTCA
1 TATCGATGCCAATGTCCCAGACATGGTCTTACACGAAATCACA
* *
42887765 TATCGATGCC-ATATCCCAGATATGGTCTTAC
1 TATCGATGCCAATGTCCCAGACATGGTCTTAC
42887796 TTGAAACACT
Statistics
Matches: 106, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
42 19 0.18
43 87 0.82
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (43 bp):
TATCGATGCCAATGTCCCAGACATGGTCTTACACGAAATCACA
Found at i:42887754 original size:86 final size:85
Alignment explanation
Indices: 42887602--42887801 Score: 258
Period size: 86 Copynumber: 2.3 Consensus size: 85
42887592 CGTAACAATA
* * *** *
42887602 CCATATCCCAGATATGGTCTTTCATGTAATCTTGTATCGATGCCAATAGCCCAGCCATGATCTTA
1 CCATATCCCAGATATGGTCTTACATGAAATCACATATCGATGCCAATAGCCCAGACATGATCTTA
42887667 CACGAAATCACATATCGATG
66 CACGAAATCACATATCGATG
* * * *
42887687 CCAATGTCCCAGACATGGTCTTACATGAAATCACATATCGATGCCAAT-GTCCCAGACATGGTTT
1 CC-ATATCCCAGATATGGTCTTACATGAAATCACATATCGATGCCAATAG-CCCAGACATGATCT
* *
42887751 TACACGAAGTCTCATATCGATG
64 TACACGAAATCACATATCGATG
*
42887773 CCATATCCCAGATATGGTCTTACTTGAAA
1 CCATATCCCAGATATGGTCTTACATGAAA
42887802 CACTGAAATT
Statistics
Matches: 98, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
85 27 0.28
86 71 0.72
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (85 bp):
CCATATCCCAGATATGGTCTTACATGAAATCACATATCGATGCCAATAGCCCAGACATGATCTTA
CACGAAATCACATATCGATG
Found at i:42894896 original size:27 final size:27
Alignment explanation
Indices: 42894849--42894902 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
42894839 TTTTTCGTGT
* *
42894849 ATTATTTTTAATTATTTTATA-CATTA
1 ATTATTTTAAATTATTATATATCATTA
42894875 ATTATTTTAAAATTATTATATATCATTA
1 ATTATTTT-AAATTATTATATATCATTA
42894903 TCTTTATCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 8 0.33
27 11 0.46
28 5 0.21
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (27 bp):
ATTATTTTAAATTATTATATATCATTA
Found at i:42898471 original size:27 final size:27
Alignment explanation
Indices: 42898427--42898629 Score: 230
Period size: 27 Copynumber: 7.5 Consensus size: 27
42898417 ACTCCAAAAT
**
42898427 AGGTAAAATGACCAAAATACCCTTATA
1 AGGTAAAATGACTGAAATACCCTTATA
* *
42898454 ACGTAAAATGACTGAAATACCCCTATA
1 AGGTAAAATGACTGAAATACCCTTATA
*
42898481 GGGTAAAATGACTGAAATACCCTTATA
1 AGGTAAAATGACTGAAATACCCTTATA
**
42898508 AGGTAAAATGAAC-GAAATACCCCCATA
1 AGGTAAAATG-ACTGAAATACCCTTATA
* * *
42898535 GGGTAAAATGACTGAAATAACCTCATA
1 AGGTAAAATGACTGAAATACCCTTATA
* * * **
42898562 CGGTAGAATGACCGAAATACCCCCATA
1 AGGTAAAATGACTGAAATACCCTTATA
*
42898589 GGGTAAAATGACTGAAATACCCTTAT-
1 AGGTAAAATGACTGAAATACCCTTATA
42898615 AGAGTAAAATGACTG
1 AG-GTAAAATGACTG
42898630 TTATACCCCT
Statistics
Matches: 149, Mismatches: 24, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
26 3 0.02
27 144 0.97
28 2 0.01
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (27 bp):
AGGTAAAATGACTGAAATACCCTTATA
Found at i:42898572 original size:81 final size:81
Alignment explanation
Indices: 42898427--42898640 Score: 254
Period size: 81 Copynumber: 2.6 Consensus size: 81
42898417 ACTCCAAAAT
* * *
42898427 AGGTAAAATGACCAAAATACCCTTATA-ACGTAAAATGACTGAAATACCCCTATAGGGTAAAATG
1 AGGTAAAATGAACGAAATACCCTTATAGA-GTAAAATGACTGAAATACCCCTATACGGTAAAATG
* **
42898491 ACTGAAATACCCTTATA
65 ACCGAAATACCCCCATA
** * * *
42898508 AGGTAAAATGAACGAAATACCCCCATAGGGTAAAATGACTGAAATA-ACCTCATACGGTAGAATG
1 AGGTAAAATGAACGAAATACCCTTATAGAGTAAAATGACTGAAATACCCCT-ATACGGTAAAATG
42898572 ACCGAAATACCCCCATA
65 ACCGAAATACCCCCATA
* **
42898589 GGGTAAAATG-ACTGAAATACCCTTATAGAGTAAAATGACTGTTATACCCCTA
1 AGGTAAAATGAAC-GAAATACCCTTATAGAGTAAAATGACTGAAATACCCCTA
42898641 GGAGATGAAA
Statistics
Matches: 111, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
80 5 0.05
81 103 0.93
82 3 0.03
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.22
Consensus pattern (81 bp):
AGGTAAAATGAACGAAATACCCTTATAGAGTAAAATGACTGAAATACCCCTATACGGTAAAATGA
CCGAAATACCCCCATA
Found at i:42898656 original size:54 final size:54
Alignment explanation
Indices: 42898428--42898638 Score: 284
Period size: 54 Copynumber: 3.9 Consensus size: 54
42898418 CTCCAAAATA
** *
42898428 GGTAAAATGACCAAAATACCCTTATAACGTAAAATGACTGAAATACCCCTATAG
1 GGTAAAATGACTGAAATACCCTTATAACGTAAAATGACTGAAATACCCCCATAG
*
42898482 GGTAAAATGACTGAAATACCCTTATAAGGTAAAATGAAC-GAAATACCCCCATAG
1 GGTAAAATGACTGAAATACCCTTATAACGTAAAATG-ACTGAAATACCCCCATAG
* * * *
42898536 GGTAAAATGACTGAAATAACCTCAT-ACGGTAGAATGACCGAAATACCCCCATAG
1 GGTAAAATGACTGAAATACCCTTATAAC-GTAAAATGACTGAAATACCCCCATAG
**
42898590 GGTAAAATGACTGAAATACCCTTATAGA-GTAAAATGACTGTTATACCCC
1 GGTAAAATGACTGAAATACCCTTATA-ACGTAAAATGACTGAAATACCCC
42898639 TAGGAGATGA
Statistics
Matches: 138, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
53 3 0.02
54 132 0.96
55 2 0.01
56 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (54 bp):
GGTAAAATGACTGAAATACCCTTATAACGTAAAATGACTGAAATACCCCCATAG
Found at i:42901065 original size:25 final size:25
Alignment explanation
Indices: 42901030--42901090 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
42901020 CTCCTAAATT
* *
42901030 TTAATTTAATTATCTACT-TTTTATA
1 TTAATTAAATTAT-TAATATTTTATA
*
42901055 TTTATTAAATTATTAATATTTTATA
1 TTAATTAAATTATTAATATTTTATA
42901080 TTAATTAAATT
1 TTAATTAAATT
42901091 TTTAGAAACT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 3 0.10
25 28 0.90
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (25 bp):
TTAATTAAATTATTAATATTTTATA
Found at i:42915113 original size:25 final size:24
Alignment explanation
Indices: 42915057--42915154 Score: 99
Period size: 25 Copynumber: 4.0 Consensus size: 24
42915047 TACGAGCCAT
* *
42915057 AATCGGTAAGCTCTTTCGAGCTGA
1 AATCGGTAAGCTCATACGAGCTGA
*
42915081 ACAACGGTAAGCTCATACGAGCTGA
1 A-ATCGGTAAGCTCATACGAGCTGA
* *
42915106 GAATCGGTAAACTC-TCACGAGTTGTA
1 -AATCGGTAAGCTCAT-ACGAGCTG-A
*
42915132 AATTGGTAAGCTCATACGAGCTG
1 AATCGGTAAGCTCATACGAGCTG
42915155 TGGTGGGTCC
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
24 2 0.03
25 55 0.92
26 3 0.05
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (24 bp):
AATCGGTAAGCTCATACGAGCTGA
Found at i:42917927 original size:11 final size:13
Alignment explanation
Indices: 42917907--42917938 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
42917897 AATAAAATAA
42917907 TAAAATATC-ATT
1 TAAAATATCAATT
42917919 TAAAA-ATCAATT
1 TAAAATATCAATT
42917931 TAAAATAT
1 TAAAATAT
42917939 TAATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.17
12 13 0.72
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCAATT
Found at i:42922034 original size:17 final size:17
Alignment explanation
Indices: 42922012--42922048 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
42922002 CCAAAAAATT
42922012 GTTGTCAATAGGGGGTC
1 GTTGTCAATAGGGGGTC
42922029 GTTGTCAATAGGGGGTC
1 GTTGTCAATAGGGGGTC
42922046 GTT
1 GTT
42922049 CTACTACCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.16, C:0.11, G:0.41, T:0.32
Consensus pattern (17 bp):
GTTGTCAATAGGGGGTC
Found at i:42928189 original size:31 final size:31
Alignment explanation
Indices: 42928154--42928215 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
42928144 CGATTTGGTT
42928154 ACTGAACTATTC-AAAAATTTCCATTTAAGTC
1 ACTGAACTATTCAAAAAATTT-CATTTAAGTC
*
42928185 ACTGAACTATTCAAAAAATTTTATTTAAGTC
1 ACTGAACTATTCAAAAAATTTCATTTAAGTC
42928216 CCTGGTCTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 21 0.72
32 8 0.28
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.37
Consensus pattern (31 bp):
ACTGAACTATTCAAAAAATTTCATTTAAGTC
Found at i:42931217 original size:104 final size:103
Alignment explanation
Indices: 42931002--42931573 Score: 979
Period size: 104 Copynumber: 5.6 Consensus size: 103
42930992 AACCGTTATT
* * * * * *
42931002 GGTGGATCTCGCACTTAGCACCACCACTTAA-TCGGGAATCAGCACTTAGCAACCCCTTGGGGAA
1 GGTGGATATCGCACATAGCACCACCAATGAACTGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
** *
42931066 TCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATAC
66 TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
*
42931103 GGTGGATATCGCACTTAGCACCACCAATGAACTGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GGTGGATATCGCACATAGCACCACCAATGAACTGGGGAATCAGCACTTAGCAACCCCTC-GGGGA
42931168 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
65 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
42931207 GGTGGATATCGCACATAGCACCACCAATGAACTGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
1 GGTGGATATCGCACATAGCACCACCAATGAACTGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
42931272 TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
66 TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
42931310 GGTGGATATCGCACATAGCACCACCAATGAACTGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GGTGGATATCGCACATAGCACCACCAATGAACTGGGGAATCAGCACTTAGCAACCCCTC-GGGGA
42931375 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
65 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
42931414 GGTGGATATCGCACATAGCACCACCAATGAACTGGGGAATCAGCACTTAGCAA-CCCTCGGGGAA
1 GGTGGATATCGCACATAGCACCACCAATGAACTGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
42931478 TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
66 TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* * **
42931516 GATGGATATCGCACATAGCACCACCAATGAATTGGGGAATCAGCACACAGCAACCCCT
1 GGTGGATATCGCACATAGCACCACCAATGAACTGGGGAATCAGCACTTAGCAACCCCT
42931574 TTATGTACAA
Statistics
Matches: 453, Mismatches: 13, Indels: 8
0.96 0.03 0.02
Matches are distributed among these distances:
101 28 0.06
102 118 0.26
103 140 0.31
104 167 0.37
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.19
Consensus pattern (103 bp):
GGTGGATATCGCACATAGCACCACCAATGAACTGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:42931270 original size:26 final size:26
Alignment explanation
Indices: 42931240--42931289 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
42931230 CCAATGAACT
*
42931240 GGGGAATCAGCACTTAGCAACCCCTC
1 GGGGAATCAGCACATAGCAACCCCTC
42931266 GGGGAATCAGCACATAGCAACCCC
1 GGGGAATCAGCACATAGCAACCCC
42931290 CTTTCACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.34, G:0.24, T:0.12
Consensus pattern (26 bp):
GGGGAATCAGCACATAGCAACCCCTC
Found at i:42931475 original size:25 final size:25
Alignment explanation
Indices: 42931447--42931494 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
42931437 CCAATGAACT
*
42931447 GGGGAATCAGCACTTAGCAACCCTC
1 GGGGAATCAGCACATAGCAACCCTC
42931472 GGGGAATCAGCACATAGCAACCC
1 GGGGAATCAGCACATAGCAACCC
42931495 CCTTTCACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.31, G:0.25, T:0.12
Consensus pattern (25 bp):
GGGGAATCAGCACATAGCAACCCTC
Found at i:42931498 original size:206 final size:207
Alignment explanation
Indices: 42931002--42931573 Score: 997
Period size: 207 Copynumber: 2.8 Consensus size: 207
42930992 AACCGTTATT
* * * * * *
42931002 GGTGGATCTCGCACTTAGCACCACCACTTAA-TCGGGAATCAGCACTTAGCAACCCCTTGGGGAA
1 GGTGGATATCGCACATAGCACCACCAATGAACTGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
** * *
42931066 TCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATACGGTGGATATCGCACTTAGCACCACCAA
66 TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACGGTGGATATCGCACATAGCACCACCAA
42931130 TGAACTGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACA
131 TGAACTGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACA
42931195 TTTCAAAGATAC
196 TTTCAAAGATAC
42931207 GGTGGATATCGCACATAGCACCACCAATGAACTGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
1 GGTGGATATCGCACATAGCACCACCAATGAACTGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
42931272 TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACGGTGGATATCGCACATAGCACCACCAA
66 TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACGGTGGATATCGCACATAGCACCACCAA
42931337 TGAACTGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACA
131 TGAACTGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACA
42931402 TTTCAAAGATAC
196 TTTCAAAGATAC
42931414 GGTGGATATCGCACATAGCACCACCAATGAACTGGGGAATCAGCACTTAGCAA-CCCTCGGGGAA
1 GGTGGATATCGCACATAGCACCACCAATGAACTGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
*
42931478 TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACGATGGATATCGCACATAGCACCACCAA
66 TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACGGTGGATATCGCACATAGCACCACCAA
* **
42931543 TGAATTGGGGAATCAGCACACAGCAACCCCT
131 TGAACTGGGGAATCAGCACTTAGCAACCCCT
42931574 TTATGTACAA
Statistics
Matches: 351, Mismatches: 14, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
205 27 0.08
206 156 0.44
207 168 0.48
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.19
Consensus pattern (207 bp):
GGTGGATATCGCACATAGCACCACCAATGAACTGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACGGTGGATATCGCACATAGCACCACCAA
TGAACTGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACA
TTTCAAAGATAC
Found at i:42931935 original size:30 final size:29
Alignment explanation
Indices: 42931901--42931965 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
42931891 TAATCCACCA
42931901 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
42931931 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
42931961 CCCAA
1 CCCAA
42931966 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:42931939 original size:31 final size:30
Alignment explanation
Indices: 42931908--42931965 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
42931898 CCACCCAACT
42931908 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
42931938 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
42931966 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:42940019 original size:18 final size:18
Alignment explanation
Indices: 42939996--42940030 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
42939986 TGATGAAATA
42939996 TGGATATGTATG-TATGTC
1 TGGATA-GTATGTTATGTC
42940014 TGGATAGTATGTTATGT
1 TGGATAGTATGTTATGT
42940031 GATGCGAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.23, C:0.03, G:0.29, T:0.46
Consensus pattern (18 bp):
TGGATAGTATGTTATGTC
Found at i:42940378 original size:27 final size:27
Alignment explanation
Indices: 42940338--42940493 Score: 125
Period size: 27 Copynumber: 5.8 Consensus size: 27
42940328 AACACATCGG
* * * *
42940338 AAAAGGATAACCTTTGTGACGAAGTCT
1 AAAAGAATAACCTTTGTGGCGTATTCT
* *
42940365 AAAAGAATAGCCTTTGTGGTGTATTAC-
1 AAAAGAATAACCTTTGTGGCGTATT-CT
* * *** *
42940392 AAAATAATAGCCTTTGTGGTAAAGTCT
1 AAAAGAATAACCTTTGTGGCGTATTCT
* * * *
42940419 AAAAGAATAAACTTTATGCCGTATTAT
1 AAAAGAATAACCTTTGTGGCGTATTCT
*
42940446 GAAAGAATAACCTTTGTGGCGTATTCT
1 AAAAGAATAACCTTTGTGGCGTATTCT
**
42940473 AAAAGAATAGGCTTTGTGGCG
1 AAAAGAATAACCTTTGTGGCG
42940494 CACTTTGAAT
Statistics
Matches: 99, Mismatches: 28, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
26 1 0.01
27 97 0.98
28 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (27 bp):
AAAAGAATAACCTTTGTGGCGTATTCT
Found at i:42940474 original size:54 final size:54
Alignment explanation
Indices: 42940338--42940481 Score: 153
Period size: 54 Copynumber: 2.7 Consensus size: 54
42940328 AACACATCGG
* * ** * **
42940338 AAAAGGATAACCTTTGTGACGAAGTCTAAAAGAATAGCCTTTGTGGTGTATTAC
1 AAAAGAATAACCTTTGTGGCGAAGTCTAAAAGAATAAACTTTATGCCGTATTAC
* * ** *
42940392 AAAATAATAGCCTTTGTGGTAAAGTCTAAAAGAATAAACTTTATGCCGTATTAT
1 AAAAGAATAACCTTTGTGGCGAAGTCTAAAAGAATAAACTTTATGCCGTATTAC
* * *
42940446 GAAAGAATAACCTTTGTGGCGTATTCTAAAAGAATA
1 AAAAGAATAACCTTTGTGGCGAAGTCTAAAAGAATA
42940482 GGCTTTGTGG
Statistics
Matches: 71, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
54 71 1.00
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.31
Consensus pattern (54 bp):
AAAAGAATAACCTTTGTGGCGAAGTCTAAAAGAATAAACTTTATGCCGTATTAC
Found at i:42941681 original size:43 final size:43
Alignment explanation
Indices: 42941621--42941705 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
42941611 TTTATCCTAT
* * * *
42941621 AAAAATAATTTAAAAAGAGGAGAATATAATA-TTGGGTTGTTGA
1 AAAAAGAATTTAAAAAGAGAAGAAGATAA-ACATGGGTTGTTGA
42941664 AAAAAGAATTTAAAAAGAGAAGAAGATAAACATGGGTTGTTG
1 AAAAAGAATTTAAAAAGAGAAGAAGATAAACATGGGTTGTTG
42941706 GATTTACCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 1 0.03
43 36 0.97
ACGTcount: A:0.51, C:0.01, G:0.22, T:0.26
Consensus pattern (43 bp):
AAAAAGAATTTAAAAAGAGAAGAAGATAAACATGGGTTGTTGA
Found at i:42942637 original size:17 final size:17
Alignment explanation
Indices: 42942593--42942631 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
42942583 GCCATAACAT
42942593 TTCCAAGTATTCATTAA
1 TTCCAAGTATTCATTAA
*
42942610 TTTCAAGTATTCATTAA
1 TTCCAAGTATTCATTAA
42942627 TTCCA
1 TTCCA
42942632 CATATTGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.18, G:0.05, T:0.44
Consensus pattern (17 bp):
TTCCAAGTATTCATTAA
Found at i:42943729 original size:36 final size:36
Alignment explanation
Indices: 42943675--42943776 Score: 141
Period size: 36 Copynumber: 2.8 Consensus size: 36
42943665 TATGATTATC
*
42943675 GATATTCTGATTTGCATGTTAAGCATGCCATATTCT
1 GATATTCTGATTTACATGTTAAGCATGCCATATTCT
* *
42943711 GATATTCTAATTTACATGTTAAGCATGTCATATTCT
1 GATATTCTGATTTACATGTTAAGCATGCCATATTCT
* * * *
42943747 AATATTCTGATTTTCGTGTAAAGCATGCCA
1 GATATTCTGATTTACATGTTAAGCATGCCA
42943777 CTAAAAATCC
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (36 bp):
GATATTCTGATTTACATGTTAAGCATGCCATATTCT
Found at i:42965463 original size:44 final size:46
Alignment explanation
Indices: 42965363--42965464 Score: 113
Period size: 44 Copynumber: 2.3 Consensus size: 46
42965353 GAATGAATAG
* *
42965363 AAAAATGGAAATGGAAAACATTTAGAAATGATTATGGTTTTCCCGA
1 AAAAATGGAAATGGAAAACATTTAGAAATGAATATGGGTTTCCCGA
* * * *
42965409 AATAAA--GAAATGG-AATCATTTGGAAATGAATGTGGGTTTCTC-A
1 AA-AAATGGAAATGGAAAACATTTAGAAATGAATATGGGTTTCCCGA
42965452 AAAAATGGAAATG
1 AAAAATGGAAATG
42965465 ATAATGGAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
42 3 0.06
43 3 0.06
44 29 0.62
45 7 0.15
46 2 0.04
47 3 0.06
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.27
Consensus pattern (46 bp):
AAAAATGGAAATGGAAAACATTTAGAAATGAATATGGGTTTCCCGA
Found at i:42965472 original size:12 final size:12
Alignment explanation
Indices: 42965455--42965489 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
42965445 TTTCTCAAAA
42965455 AATGGAAATGAT
1 AATGGAAATGAT
42965467 AATGGAAATGAT
1 AATGGAAATGAT
42965479 AATGGAAATGA
1 AATGGAAATGA
42965490 AAATAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.26, T:0.23
Consensus pattern (12 bp):
AATGGAAATGAT
Found at i:42966713 original size:27 final size:29
Alignment explanation
Indices: 42966667--42966728 Score: 92
Period size: 27 Copynumber: 2.2 Consensus size: 29
42966657 AGGTTCGCTA
42966667 ATGTGTTGACGAGCTAGGGCTTCACTAGT
1 ATGTGTTGACGAGCTAGGGCTTCACTAGT
*
42966696 ATGT-TTGGCGAGCT-GGGCTTCACTAGT
1 ATGTGTTGACGAGCTAGGGCTTCACTAGT
*
42966723 CTGTGT
1 ATGTGT
42966729 GGTGAGTTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 16 0.53
28 10 0.33
29 4 0.13
ACGTcount: A:0.16, C:0.18, G:0.32, T:0.34
Consensus pattern (29 bp):
ATGTGTTGACGAGCTAGGGCTTCACTAGT
Found at i:42966739 original size:27 final size:27
Alignment explanation
Indices: 42966667--42966739 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 27
42966657 AGGTTCGCTA
*
42966667 ATGTGTTGACGAGCTAGGGCTTCACTAGT
1 ATGTG-TGGCGAGCT-GGGCTTCACTAGT
*
42966696 ATGTTTGGCGAGCTGGGCTTCACTAGT
1 ATGTGTGGCGAGCTGGGCTTCACTAGT
* * *
42966723 CTGTGTGGTGAGTTGGG
1 ATGTGTGGCGAGCTGGG
42966740 TTGGCCAGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 26 0.68
28 8 0.21
29 4 0.11
ACGTcount: A:0.15, C:0.15, G:0.37, T:0.33
Consensus pattern (27 bp):
ATGTGTGGCGAGCTGGGCTTCACTAGT
Found at i:42967774 original size:14 final size:14
Alignment explanation
Indices: 42967755--42967781 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42967745 ATGCAAGTTC
42967755 TTTTTAAAAGAAAT
1 TTTTTAAAAGAAAT
42967769 TTTTTAAAAGAAA
1 TTTTTAAAAGAAA
42967782 GGATTTCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (14 bp):
TTTTTAAAAGAAAT
Found at i:42969327 original size:45 final size:45
Alignment explanation
Indices: 42969278--42969448 Score: 236
Period size: 45 Copynumber: 3.8 Consensus size: 45
42969268 TACTAGAAAT
*
42969278 GAGTAAGACTATGACTGAAAGACGTTATGGCATCACTATTCTATC
1 GAGTAAGACCATGACTGAAAGACGTTATGGCATCACTATTCTATC
*
42969323 GAGTAAGACCATGACTGAAAAACGTTATGGCATCACTATTCTATC
1 GAGTAAGACCATGACTGAAAGACGTTATGGCATCACTATTCTATC
* * * *
42969368 GAATAAGACCATGACTGAAAGACGTTATGACATCACGATTCTATT
1 GAGTAAGACCATGACTGAAAGACGTTATGGCATCACTATTCTATC
* * * *
42969413 GAGTAAGTCCAT-AGTTGAAAGATGCTATGGCATCAC
1 GAGTAAGACCATGA-CTGAAAGACGTTATGGCATCAC
42969449 GAATCAAAGG
Statistics
Matches: 112, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
44 1 0.01
45 111 0.99
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (45 bp):
GAGTAAGACCATGACTGAAAGACGTTATGGCATCACTATTCTATC
Found at i:42969480 original size:90 final size:90
Alignment explanation
Indices: 42969282--42969470 Score: 227
Period size: 90 Copynumber: 2.1 Consensus size: 90
42969272 AGAAATGAGT
* * *
42969282 AAGACTATGACTGAAAGACGTTATGGCATCACTATTCTATCGAGTAAGACCATGACTGAAAAACG
1 AAGACCATGACTGAAAGACGTTATGACATCACGATTCTATCGAGTAAGACCATGACTGAAAAACG
* * * * * *
42969347 TTATGGCATCACTATTCTATCGAAT
66 CTATGGCATCACGAATCAAACGAAC
* * * * *
42969372 AAGACCATGACTGAAAGACGTTATGACATCACGATTCTATTGAGTAAGTCCAT-AGTTGAAAGAT
1 AAGACCATGACTGAAAGACGTTATGACATCACGATTCTATCGAGTAAGACCATGA-CTGAAAAAC
*
42969436 GCTATGGCATCACGAATCAAAGGAAC
65 GCTATGGCATCACGAATCAAACGAAC
42969462 AAGACCATG
1 AAGACCATG
42969471 GTTTAAAGAC
Statistics
Matches: 83, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
89 1 0.01
90 82 0.99
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.25
Consensus pattern (90 bp):
AAGACCATGACTGAAAGACGTTATGACATCACGATTCTATCGAGTAAGACCATGACTGAAAAACG
CTATGGCATCACGAATCAAACGAAC
Found at i:42969527 original size:48 final size:46
Alignment explanation
Indices: 42969462--42969582 Score: 138
Period size: 45 Copynumber: 2.6 Consensus size: 46
42969452 TCAAAGGAAC
* *
42969462 AAGACCATGGTTTAAAGACACTATGGCAACGCAATGGA-AAAAATGAAT
1 AAGACCATGGTTGAAAGACACTATGGCAA-GCAA--GATAAAAATAAAT
* * * *
42969510 AAGACCATGGTTGAAAGACACTGTGGC-ATCAAGATGAGAATAAAT
1 AAGACCATGGTTGAAAGACACTATGGCAAGCAAGATAAAAATAAAT
*
42969555 AAGACCATGGTTGAAAGACACCATGGCA
1 AAGACCATGGTTGAAAGACACTATGGCA
42969583 CACTCCGATC
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
44 2 0.03
45 32 0.51
46 3 0.05
47 1 0.02
48 25 0.40
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.18
Consensus pattern (46 bp):
AAGACCATGGTTGAAAGACACTATGGCAAGCAAGATAAAAATAAAT
Found at i:42969888 original size:50 final size:50
Alignment explanation
Indices: 42969829--42969926 Score: 160
Period size: 50 Copynumber: 2.0 Consensus size: 50
42969819 ACGGGCATGA
* *
42969829 AAAGGAAAGGTATGTGTTCGAATGAACTATGTCATGAAGTTATAAAAAAG
1 AAAGGAAAGGTATGTATTCGAATGAACTATGTCATGAAATTATAAAAAAG
* *
42969879 AAAGTAAAGGTATGTATTCGAATGAACTATGTCATGAAATTATGAAAA
1 AAAGGAAAGGTATGTATTCGAATGAACTATGTCATGAAATTATAAAAA
42969927 GGATTAAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.28
Consensus pattern (50 bp):
AAAGGAAAGGTATGTATTCGAATGAACTATGTCATGAAATTATAAAAAAG
Found at i:42970687 original size:43 final size:43
Alignment explanation
Indices: 42970625--42970715 Score: 139
Period size: 43 Copynumber: 2.1 Consensus size: 43
42970615 ACATGTGCAA
* *
42970625 GGTAATAAAACATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAACATACAATGCATTTACTTAATCAAGAAAATCTT
* *
42970668 GGTAATAAAAGATATAATGCATTTACTTAATCAAGAAAATCTT
1 GGTAATAAAACATACAATGCATTTACTTAATCAAGAAAATCTT
42970711 -GTAAT
1 GGTAAT
42970716 GAACTCAAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
42 5 0.11
43 39 0.89
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (43 bp):
GGTAATAAAACATACAATGCATTTACTTAATCAAGAAAATCTT
Found at i:42977128 original size:7 final size:7
Alignment explanation
Indices: 42977116--42977177 Score: 54
Period size: 7 Copynumber: 8.7 Consensus size: 7
42977106 CCCTGGAATC
42977116 CCTAAAT
1 CCTAAAT
42977123 CCTAAAT
1 CCTAAAT
42977130 CCTAAAT
1 CCTAAAT
42977137 CCTTAAAT
1 CC-TAAAT
* **
42977145 CTTAACC
1 CCTAAAT
**
42977152 CCTAACC
1 CCTAAAT
42977159 CCTAAA-
1 CCTAAAT
42977165 CCTTAAAT
1 CC-TAAAT
42977173 CCTAA
1 CCTAA
42977178 CCCCCAAATC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
6 2 0.04
7 37 0.79
8 8 0.17
ACGTcount: A:0.39, C:0.34, G:0.00, T:0.27
Consensus pattern (7 bp):
CCTAAAT
Found at i:42977137 original size:22 final size:22
Alignment explanation
Indices: 42977112--42977177 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
42977102 CTGACCCTGG
42977112 AATCCCTAAATCCTAAATCCTA
1 AATCCCTAAATCCTAAATCCTA
* * **
42977134 AATCCTTAAATCTTAACCCCT-
1 AATCCCTAAATCCTAAATCCTA
*
42977155 AACCCCTAAA-CCTTAAATCCTA
1 AATCCCTAAATCC-TAAATCCTA
42977177 A
1 A
42977178 CCCCCAAATC
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
20 1 0.03
21 14 0.42
22 18 0.55
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.27
Consensus pattern (22 bp):
AATCCCTAAATCCTAAATCCTA
Found at i:42978982 original size:41 final size:41
Alignment explanation
Indices: 42978932--42979225 Score: 212
Period size: 41 Copynumber: 7.2 Consensus size: 41
42978922 ATATTTTTTT
* *
42978932 GCGGCGCTTTCATAAAAAAGACGCTAAAAACCCGAGCATTA
1 GCGGCGCTTTCATAAAAACGCCGCTAAAAACCCGAGCATTA
* * * *
42978973 CCGGTGCTTT-TTAAAAAACGCCGCT-AAAACCCTGAGCATTG
1 GCGGCGCTTTCAT-AAAAACGCCGCTAAAAACCC-GAGCATTA
* *
42979014 GTGGCGCTTTTC-TAAAAACGCCACT-AAAACCCTGAGCATTA
1 GCGGCGC-TTTCATAAAAACGCCGCTAAAAACCC-GAGCATTA
* * * * *
42979055 ACGGCGCTTTTC-TAAAAATGTCGGTAAAACCCCGAGCATTA
1 GCGGCGC-TTTCATAAAAACGCCGCTAAAAACCCGAGCATTA
* * * *
42979096 GCGGTGCTTAATCAT--AAACGCCCCTAAAACCCCAAGCATTA
1 GCGGCGCTT--TCATAAAAACGCCGCTAAAAACCCGAGCATTA
* *
42979137 G-GACGCTTT-ATCAAAAACGCCGCTAAAATCCCGAGCATTA
1 GCGGCGCTTTCAT-AAAAACGCCGCTAAAAACCCGAGCATTA
* ** * *
42979177 GCGGTGCTTTTTTAAAAATGCCGCT-AAAACCCACAGCATTA
1 GCGGCGCTTTCATAAAAACGCCGCTAAAAACCC-GAGCATTA
*
42979218 GTGGCGCT
1 GCGGCGCT
42979226 ACTCCAAAAA
Statistics
Matches: 201, Mismatches: 38, Indels: 28
0.75 0.14 0.10
Matches are distributed among these distances:
37 2 0.01
38 1 0.00
40 45 0.22
41 139 0.69
42 13 0.06
43 1 0.00
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (41 bp):
GCGGCGCTTTCATAAAAACGCCGCTAAAAACCCGAGCATTA
Found at i:42979072 original size:82 final size:80
Alignment explanation
Indices: 42978958--42979217 Score: 251
Period size: 81 Copynumber: 3.2 Consensus size: 80
42978948 AAAGACGCTA
* * * * *
42978958 AAAACCCGAGCATTACCGGTGCTTTT-TAAAAAACGCCGCTAAAACCCTGAGCATTGGTGGCGCT
1 AAAACCCGAGCATTAACGGCGCTTTTCT-AAAAACGCCGCTAAAACCC-GAGCATTAGCGGTGCT
42979022 TTTCTAAAAACGCCACT
64 TTTCTAAAAACGCCACT
* * *
42979039 AAAACCCTGAGCATTAACGGCGCTTTTCTAAAAATGTCGGTAAAACCCCGAGCATTAGCGGTGCT
1 AAAACCC-GAGCATTAACGGCGCTTTTCTAAAAACGCCGCTAAAA-CCCGAGCATTAGCGGTGCT
* * *
42979104 TAATC-ATAAACGCCCCT
64 T-TTCTAAAAACGCCACT
*
42979121 AAAACCCCAAGCATT-A-GGACGCTTTATC-AAAAACGCCGCTAAAATCCCGAGCATTAGCGGTG
1 AAAA-CCCGAGCATTAACGG-CGCTTT-TCTAAAAACGCCGCTAAAA-CCCGAGCATTAGCGGTG
* * *
42979183 CTTTTTTAAAAATGCCGCT
62 CTTTTCTAAAAACGCCACT
*
42979202 AAAACCCACAGCATTA
1 AAAACCC-GAGCATTA
42979218 GTGGCGCTAC
Statistics
Matches: 147, Mismatches: 22, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
80 6 0.04
81 66 0.45
82 66 0.45
83 9 0.06
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (80 bp):
AAAACCCGAGCATTAACGGCGCTTTTCTAAAAACGCCGCTAAAACCCGAGCATTAGCGGTGCTTT
TCTAAAAACGCCACT
Found at i:42979176 original size:81 final size:81
Alignment explanation
Indices: 42978955--42979217 Score: 241
Period size: 82 Copynumber: 3.2 Consensus size: 81
42978945 AAAAAAGACG
* * * * * * *
42978955 CTAAAAACCCGAGCATTACCGGTGCTTTT-TAAAAAACGCCGCTAAAACCCTGAGCATTGGTGGC
1 CTAAAACCCCAAGCATTAACGGCGCTTTTCT-AAAAACGCCGCTAAAACCC-GAGCATTAGCGGT
*
42979019 GCTTTTCTAAAAACGCCA
64 GCTTATCTAAAAACGCCA
** * * *
42979037 CTAAAACCCTGAGCATTAACGGCGCTTTTCTAAAAATGTCGGTAAAACCCCGAGCATTAGCGGTG
1 CTAAAACCCCAAGCATTAACGGCGCTTTTCTAAAAACGCCGCTAAAA-CCCGAGCATTAGCGGTG
* *
42979102 CTTAATC-ATAAACGCCC
65 CTT-ATCTAAAAACGCCA
42979119 CTAAAACCCCAAGCATT-A-GGACGCTTTATC-AAAAACGCCGCTAAAATCCCGAGCATTAGCGG
1 CTAAAACCCCAAGCATTAACGG-CGCTTT-TCTAAAAACGCCGCTAAAA-CCCGAGCATTAGCGG
* * * *
42979181 TGCTTTTTTAAAAATGCCG
63 TGCTTATCTAAAAACGCCA
42979200 CTAAAA-CCCACAGCATTA
1 CTAAAACCCCA-AGCATTA
42979218 GTGGCGCTAC
Statistics
Matches: 149, Mismatches: 24, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
80 7 0.05
81 59 0.40
82 77 0.52
83 6 0.04
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (81 bp):
CTAAAACCCCAAGCATTAACGGCGCTTTTCTAAAAACGCCGCTAAAACCCGAGCATTAGCGGTGC
TTATCTAAAAACGCCA
Found at i:42979237 original size:122 final size:123
Alignment explanation
Indices: 42978933--42979239 Score: 320
Period size: 122 Copynumber: 2.5 Consensus size: 123
42978923 TATTTTTTTG
* * * * * ** * *
42978933 CGGCGC-TTTCATAAAAAAGACGCTAAAAACCCGAGCATTACCGGTGCTTTTTAAAAAACGCCGC
1 CGGCGCTTTTC-TAAAAATGCCGCTAAAACCCCGAGCATTAGCGGCGCTTAATCAAAAACGCCCC
** * *
42978997 TAAAACCCTGAGCATTGGTGGCGCTTTTCTAAAAACGCCACTAAAACCCTGAGCATTAA
65 TAAAACCCCAAGCATTAGTGACGCTTTTCTAAAAACGCCACTAAAACCCTGAGCATTAA
* * * *
42979056 CGGCGCTTTTCTAAAAATGTCGGTAAAACCCCGAGCATTAGCGGTGCTTAATCATAAACGCCCCT
1 CGGCGCTTTTCTAAAAATGCCGCTAAAACCCCGAGCATTAGCGGCGCTTAATCAAAAACGCCCCT
* *
42979121 AAAACCCCAAGCATTAG-GACGCTTTATC-AAAAACGCCGCTAAAATCCC-GAGCATTAG
66 AAAACCCCAAGCATTAGTGACGCTTT-TCTAAAAACGCCACTAAAA-CCCTGAGCATTAA
* * * *
42979178 CGGTGCTTTTTTAAAAATGCCGCTAAAACCCAC-AGCATTAGTGGCGC-TACTCCAAAAACGCC
1 CGGCGCTTTTCTAAAAATGCCGCTAAAACCC-CGAGCATTAGCGGCGCTTAAT-CAAAAACGCC
42979240 ACTATCACCA
Statistics
Matches: 155, Mismatches: 24, Indels: 11
0.82 0.13 0.06
Matches are distributed among these distances:
121 3 0.02
122 78 0.50
123 70 0.45
124 4 0.03
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (123 bp):
CGGCGCTTTTCTAAAAATGCCGCTAAAACCCCGAGCATTAGCGGCGCTTAATCAAAAACGCCCCT
AAAACCCCAAGCATTAGTGACGCTTTTCTAAAAACGCCACTAAAACCCTGAGCATTAA
Found at i:42979314 original size:40 final size:39
Alignment explanation
Indices: 42979270--42979345 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
42979260 TTGGGTTTGG
42979270 TTTTTT-GCGGAGTTTTCCCAAAAAATGCCGCTAATGCTT
1 TTTTTTAGCGGAGTTTT-CCAAAAAATGCCGCTAATGCTT
* ** *
42979309 TTTTTTAGCGGCGTTTTCTTAAAAATGCCGGTAATGC
1 TTTTTTAGCGGAGTTTTCCAAAAAATGCCGCTAATGC
42979346 ACAATCTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 23 0.72
40 9 0.28
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (39 bp):
TTTTTTAGCGGAGTTTTCCAAAAAATGCCGCTAATGCTT
Found at i:42983110 original size:40 final size:40
Alignment explanation
Indices: 42983058--42983287 Score: 336
Period size: 40 Copynumber: 5.8 Consensus size: 40
42983048 ATAACCACAA
* * * *
42983058 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
42983098 GCACGAATGCCTTCGGGTCTTAGCCCGGATATATCATCTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
42983138 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
42983178 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
42983218 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC
* *
42983258 GCATAAATGCCTTCGGGACTTAGCCCGGAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT
42983288 GTATTCAAAT
Statistics
Matches: 176, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 172 0.98
41 4 0.02
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:42991725 original size:12 final size:12
Alignment explanation
Indices: 42991708--42991748 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
42991698 GGTTCTATAT
42991708 TTTTCTTCTCAC
1 TTTTCTTCTCAC
**
42991720 TTTTCTT-T-TT
1 TTTTCTTCTCAC
42991730 TTTTCTTCTCAC
1 TTTTCTTCTCAC
42991742 TTTTCTT
1 TTTTCTT
42991749 TTTTTTTCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
10 7 0.30
11 2 0.09
12 14 0.61
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTCTTCTCAC
Found at i:42991750 original size:21 final size:22
Alignment explanation
Indices: 42991707--42991758 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
42991697 CGGTTCTATA
42991707 TTTTTCTTCTCACTTTTCTTTT
1 TTTTTCTTCTCACTTTTCTTTT
42991729 TTTTTCTTCTCACTTTTCTTTT
1 TTTTTCTTCTCACTTTTCTTTT
42991751 TTTTTCTT
1 TTTTTCTT
42991759 ACCTAGCCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTTCTTCTCACTTTTCTTTT
Found at i:42991757 original size:19 final size:20
Alignment explanation
Indices: 42991707--42991755 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
42991697 CGGTTCTATA
*
42991707 TTTTTCTTCTCACTTTTCTTT
1 TTTTTTTTCTCACTTTTC-TT
42991728 TTTTTTCTTCTCACTTTTCTT
1 TTTTTT-TTCTCACTTTTCTT
42991749 TTTTTTT
1 TTTTTTT
42991756 CTTACCTAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 1 0.04
21 13 0.50
22 12 0.46
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTTTTCTCACTTTTCTT
Found at i:42991838 original size:16 final size:16
Alignment explanation
Indices: 42991817--42991850 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
42991807 CATACCATCA
42991817 TTCTTTTTCTC-TTTTT
1 TTCTTTTTC-CATTTTT
42991833 TTCTTTTTCCATTTTT
1 TTCTTTTTCCATTTTT
42991849 TT
1 TT
42991851 ATCCTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 16 0.94
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (16 bp):
TTCTTTTTCCATTTTT
Found at i:42992681 original size:22 final size:23
Alignment explanation
Indices: 42992628--42992683 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
42992618 CCCGTTTTTA
* * *
42992628 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
42992651 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
42992673 ATTAAAATTAA
1 ATTAAAATTAA
42992684 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:42992696 original size:16 final size:16
Alignment explanation
Indices: 42992659--42992698 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
42992649 TTAATAAAAT
* *
42992659 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
42992675 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
42992691 TAAAATTA
1 TAAAATTA
42992699 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:42992777 original size:59 final size:59
Alignment explanation
Indices: 42992709--42992848 Score: 271
Period size: 59 Copynumber: 2.4 Consensus size: 59
42992699 TCAAATTATT
*
42992709 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
42992768 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
42992827 AATTATTAATTGTATTAATTGT
1 AATTATTAATTGTATTAATTGT
42992849 ATTAATTGTA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
59 80 1.00
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.47
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:42992842 original size:9 final size:9
Alignment explanation
Indices: 42992830--42992866 Score: 74
Period size: 9 Copynumber: 4.1 Consensus size: 9
42992820 TTTATCAAAT
42992830 TATTAATTG
1 TATTAATTG
42992839 TATTAATTG
1 TATTAATTG
42992848 TATTAATTG
1 TATTAATTG
42992857 TATTAATTG
1 TATTAATTG
42992866 T
1 T
42992867 TGTAACAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:42992987 original size:23 final size:24
Alignment explanation
Indices: 42992961--42993008 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
42992951 GTAAATAAAC
*
42992961 TTAAAATTAAAA-ACTAT-TATATT
1 TTAAAAATAAAATA-TATATATATT
42992984 TTAAAAATAAAATATATATATATT
1 TTAAAAATAAAATATATATATATT
42993008 T
1 T
42993009 AATATTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
TTAAAAATAAAATATATATATATT
Found at i:43001633 original size:37 final size:37
Alignment explanation
Indices: 43001583--43001657 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
43001573 GGATTGTCTG
*
43001583 CATTATAAAAACATTATCATTCACCTTTTTTTTTTTA
1 CATTATAAAAACATTATCATTCACCTATTTTTTTTTA
43001620 CATTATAAAAACATTATCATTCACCTATTTTTTTTTA
1 CATTATAAAAACATTATCATTCACCTATTTTTTTTTA
43001657 C
1 C
43001658 TGCAAATTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.49
Consensus pattern (37 bp):
CATTATAAAAACATTATCATTCACCTATTTTTTTTTA
Found at i:43006749 original size:12 final size:13
Alignment explanation
Indices: 43006724--43006771 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
43006714 TTTTCTGAGG
43006724 TAAAAATAATTAT
1 TAAAAATAATTAT
*
43006737 TAAAAGTAA-TAT
1 TAAAAATAATTAT
*
43006749 TAAAAATAAATCAT
1 TAAAAAT-AATTAT
43006763 ATAAAAATA
1 -TAAAAATA
43006772 CAAATATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 9 0.31
13 10 0.34
14 3 0.10
15 7 0.24
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (13 bp):
TAAAAATAATTAT
Found at i:43006959 original size:20 final size:20
Alignment explanation
Indices: 43006934--43006974 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
43006924 CTTGGTTTAG
43006934 TTAGTCAATTTATGAATGCT
1 TTAGTCAATTTATGAATGCT
43006954 TTAGTCAATTTATGAATGCT
1 TTAGTCAATTTATGAATGCT
43006974 T
1 T
43006975 AAGTTCGAGA
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:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (20 bp):
TTAGTCAATTTATGAATGCT
Found at i:43010046 original size:2 final size:2
Alignment explanation
Indices: 43010039--43010087 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
43010029 GAATGGTATA
*
43010039 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TA 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
43010081 TG TG TG T
1 TG TG TG T
43010088 CTAGTTGATG
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:0.02, C:0.00, G:0.47, T:0.51
Consensus pattern (2 bp):
TG
Found at i:43012359 original size:19 final size:20
Alignment explanation
Indices: 43012337--43012374 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
43012327 CTGCTAAACC
43012337 ATTTCATTGCAT-TTAGTTT
1 ATTTCATTGCATATTAGTTT
43012356 ATTTCATTGCATATTAGTT
1 ATTTCATTGCATATTAGTT
43012375 GTTAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.55
Consensus pattern (20 bp):
ATTTCATTGCATATTAGTTT
Found at i:43046768 original size:15 final size:16
Alignment explanation
Indices: 43046742--43046772 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
43046732 CAAAGGCACC
43046742 ACAATATATAAAAACA
1 ACAATATATAAAAACA
43046758 ACAAT-TATAAAAACA
1 ACAATATATAAAAACA
43046773 TGTCAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.68, C:0.13, G:0.00, T:0.19
Consensus pattern (16 bp):
ACAATATATAAAAACA
Found at i:43048759 original size:18 final size:16
Alignment explanation
Indices: 43048725--43048760 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
43048715 TAATATAATA
43048725 TATTTTTAATAACTTT
1 TATTTTTAATAACTTT
43048741 TATTTTGTAATATACTTT
1 TATTTT-TAATA-ACTTT
43048759 TA
1 TA
43048761 AAAACCCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.61
Consensus pattern (16 bp):
TATTTTTAATAACTTT
Found at i:43052625 original size:57 final size:57
Alignment explanation
Indices: 43052532--43052643 Score: 163
Period size: 57 Copynumber: 2.0 Consensus size: 57
43052522 ACCCTAATTC
* *
43052532 AGATTACCCGTCCGGGCTAAATCCATTTTCCACATATTCTTCAGGAGGGCTATATCA
1 AGATCACCCGTCCAGGCTAAATCCATTTTCCACATATTCTTCAGGAGGGCTATATCA
* * *
43052589 AGATCACCCGTCCAGGCTAGAT-CTTTTTCACACATATTCTTCGGGAGGGCTATAT
1 AGATCACCCGTCCAGGCTAAATCCATTTTC-CACATATTCTTCAGGAGGGCTATAT
43052644 TAGGATAGGA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
56 6 0.12
57 43 0.88
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (57 bp):
AGATCACCCGTCCAGGCTAAATCCATTTTCCACATATTCTTCAGGAGGGCTATATCA
Found at i:43058243 original size:50 final size:50
Alignment explanation
Indices: 43058163--43058338 Score: 244
Period size: 50 Copynumber: 3.5 Consensus size: 50
43058153 ATTTGGGTAA
* *
43058163 AGAGGTCTCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGATG
* *
43058213 AGAGGTCCCATGTTAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGATG
** * * *
43058263 AGAGGTCCCCCGTAAGACCATGTCTAGGATATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGATG
**
43058313 AGAACATCCCATGTAAGACCATGTCT
1 AG-AGGTCCCATGTAAGACCATGTCT
43058339 GGGCAATTGC
Statistics
Matches: 110, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 91 0.83
51 19 0.17
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGATG
Found at i:43067077 original size:6 final size:6
Alignment explanation
Indices: 43067066--43067093 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
43067056 TTTGGGACGT
43067066 TAAAGG TAAAGG TAAAGG TAAAGG TAAA
1 TAAAGG TAAAGG TAAAGG TAAAGG TAAA
43067094 AACATGGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.29, T:0.18
Consensus pattern (6 bp):
TAAAGG
Found at i:43070863 original size:23 final size:23
Alignment explanation
Indices: 43070808--43070866 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
43070798 CAAGCTACCG
*
43070808 ATTTTATGGAAGCATTTGTGGTT
1 ATTTTATGGAAGCATTTGTGGCT
* * *
43070831 GTTCTATGGAAGCCTTTGTGGCT
1 ATTTTATGGAAGCATTTGTGGCT
*
43070854 ATTTTGTGGAAGC
1 ATTTTATGGAAGC
43070867 TTTTCTGACT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.19, C:0.10, G:0.29, T:0.42
Consensus pattern (23 bp):
ATTTTATGGAAGCATTTGTGGCT
Found at i:43070881 original size:23 final size:23
Alignment explanation
Indices: 43070837--43070881 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
43070827 GGTTGTTCTA
* *
43070837 TGGAAGCCTTTGTGGCTATTTTG
1 TGGAAGCCTTTCTGACTATTTTG
* *
43070860 TGGAAGCTTTTCTGACTGTTTT
1 TGGAAGCCTTTCTGACTATTTT
43070882 CTATAAAGCC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.13, C:0.13, G:0.27, T:0.47
Consensus pattern (23 bp):
TGGAAGCCTTTCTGACTATTTTG
Found at i:43078689 original size:18 final size:19
Alignment explanation
Indices: 43078663--43078700 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
43078653 ATAAATATAT
*
43078663 AATTCATTTC-CATATCAA
1 AATTAATTTCACATATCAA
*
43078681 AATTAATTTCACATTTCAA
1 AATTAATTTCACATATCAA
43078700 A
1 A
43078701 TAGTCTTCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTAATTTCACATATCAA
Found at i:43103131 original size:20 final size:20
Alignment explanation
Indices: 43103101--43103138 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
43103091 TGCTAAACCA
43103101 TTTCATTGCAT-ATAGTTTG
1 TTTCATTGCATAATAGTTTG
43103120 TTTCATTTGCATAATAGTT
1 TTTCA-TTGCATAATAGTT
43103139 GTTAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.24, C:0.11, G:0.13, T:0.53
Consensus pattern (20 bp):
TTTCATTGCATAATAGTTTG
Found at i:43115998 original size:6 final size:6
Alignment explanation
Indices: 43115987--43116026 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
43115977 AGTTTATTTG
* *
43115987 TTTTAT TTTTAT TTTTAT TTTTAT GTTTAT TGTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
43116027 TTAGACTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.15, C:0.00, G:0.05, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:43119681 original size:133 final size:134
Alignment explanation
Indices: 43119427--43119668 Score: 353
Period size: 133 Copynumber: 1.8 Consensus size: 134
43119417 GGAAAAGAAA
* *
43119427 AAATAGGGTGTTGTGATTAGGGATTAATACGATGACTTAAGATCCAACATATCTTGCGGATTCTC
1 AAATAGGGTGTTGTGATCAGGGACTAATACGATGACTTAAGATCCAACATATCTTGCGGATTCTC
** *
43119492 TGAAGCTAGTGTTACCAAACTTGATCTGAAGCTAGTGTTAGTAGTCCTAATATGTCATTTTGCAA
66 TGAAGCTAGTGTTACCAAACTTGATCCAAAGCTAGTGTTAGCAGTCCTAATATGTCATTTTGCAA
43119557 AAAC
131 AAAC
* * * * *
43119561 AAATA-GGTTTTGTGATCAGGGACTAATTCGATTACTTGAGATCCAACATATGTTGCGGATTCTC
1 AAATAGGGTGTTGTGATCAGGGACTAATACGATGACTTAAGATCCAACATATCTTGCGGATTCTC
* *
43119625 TGAAGCTAGTGTTAGC-AACTCTGATCCAAAGTTAGTGTTAGCAG
66 TGAAGCTAGTGTTACCAAACT-TGATCCAAAGCTAGTGTTAGCAG
43119669 CTCAATAATG
Statistics
Matches: 95, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
132 4 0.04
133 86 0.91
134 5 0.05
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (134 bp):
AAATAGGGTGTTGTGATCAGGGACTAATACGATGACTTAAGATCCAACATATCTTGCGGATTCTC
TGAAGCTAGTGTTACCAAACTTGATCCAAAGCTAGTGTTAGCAGTCCTAATATGTCATTTTGCAA
AAAC
Found at i:43122347 original size:15 final size:15
Alignment explanation
Indices: 43122329--43122357 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
43122319 ATAATTTATC
43122329 TTATAATAAAACATT
1 TTATAATAAAACATT
43122344 TTATAATAAAACAT
1 TTATAATAAAACAT
43122358 CACACAAAAT
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:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
TTATAATAAAACATT
Found at i:43124137 original size:12 final size:12
Alignment explanation
Indices: 43124122--43124146 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43124112 GATATGTAAT
43124122 TTACAGAATAAG
1 TTACAGAATAAG
43124134 TTACAGAATAAG
1 TTACAGAATAAG
43124146 T
1 T
43124147 AGTTTACAAT
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:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (12 bp):
TTACAGAATAAG
Found at i:43128326 original size:56 final size:56
Alignment explanation
Indices: 43128240--43128351 Score: 179
Period size: 56 Copynumber: 2.0 Consensus size: 56
43128230 CTACCCTTTG
* * * *
43128240 ACCAATGAATATTTGCATCCCCAATATTAAACCCAAATGGTTACAAATCACTCTCC
1 ACCAATGAATATTTACAACCCCAATATTAAACCCAAATGATTACAAACCACTCTCC
*
43128296 ACCAATGAATATTTACAACCCCAATATTAAACCTAAATGATTACAAACCACTCTCC
1 ACCAATGAATATTTACAACCCCAATATTAAACCCAAATGATTACAAACCACTCTCC
43128352 TAAAATCTCC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.40, C:0.29, G:0.05, T:0.26
Consensus pattern (56 bp):
ACCAATGAATATTTACAACCCCAATATTAAACCCAAATGATTACAAACCACTCTCC
Found at i:43131535 original size:21 final size:19
Alignment explanation
Indices: 43131497--43131537 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
43131487 AATAAATATA
*
43131497 AAAATATTTTTAAGTTTTT
1 AAAATATTTTTAAATTTTT
43131516 AAAATATATTTTAGAATTTTT
1 AAAATAT-TTTTA-AATTTTT
43131537 A
1 A
43131538 GAATTATAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 5 0.26
21 7 0.37
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
AAAATATTTTTAAATTTTT
Found at i:43132231 original size:23 final size:25
Alignment explanation
Indices: 43132203--43132250 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 25
43132193 CTACAAACAA
43132203 TTTTTAAAT-TTTGA-TATATTTAT
1 TTTTTAAATATTTGATTATATTTAT
*
43132226 TTTTTAAATATTTTATTATATTTAT
1 TTTTTAAATATTTGATTATATTTAT
43132251 ATAAGATACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.41
24 4 0.18
25 9 0.41
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (25 bp):
TTTTTAAATATTTGATTATATTTAT
Found at i:43132238 original size:25 final size:23
Alignment explanation
Indices: 43132203--43132250 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
43132193 CTACAAACAA
43132203 TTTTTAAATTTTGA-TATATTTAT
1 TTTTTAAATTTT-ATTATATTTAT
43132226 TTTTTAAATATTTTATTATATTTAT
1 TTTTT-AA-ATTTTATTATATTTAT
43132251 ATAAGATACT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 5 0.23
24 3 0.14
25 14 0.64
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTTAAATTTTATTATATTTAT
Found at i:43133202 original size:30 final size:30
Alignment explanation
Indices: 43133168--43133230 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
43133158 ACTTATTTTA
*
43133168 TTGTTAATTTTGTTATTATTTTAAAGATAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
*
43133198 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
43133228 TTG
1 TTG
43133231 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.27, C:0.02, G:0.13, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:43133365 original size:12 final size:12
Alignment explanation
Indices: 43133344--43133377 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
43133334 TATATATTTT
*
43133344 AAAATTATATAA
1 AAAATAATATAA
43133356 AAAATAATATAA
1 AAAATAATATAA
*
43133368 AAATTAATAT
1 AAAATAATAT
43133378 GGACGGGCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:43144240 original size:28 final size:26
Alignment explanation
Indices: 43144174--43144242 Score: 70
Period size: 28 Copynumber: 2.6 Consensus size: 26
43144164 TCCTATTTTG
43144174 ACTTTTATTT-TTTTTATTTTTAATGA
1 ACTTTT-TTTATTTTTATTTTTAATGA
* *
43144200 A-TTTTTTAAATTTGTTATTTTTTAGTGA
1 ACTTTTTT-TATTT-TTA-TTTTTAATGA
43144228 ACTTTTTTTATTTTT
1 ACTTTTTTTATTTTT
43144243 TCTTTGACAC
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
24 2 0.06
25 4 0.11
26 4 0.11
27 5 0.14
28 14 0.40
29 6 0.17
ACGTcount: A:0.22, C:0.03, G:0.06, T:0.70
Consensus pattern (26 bp):
ACTTTTTTTATTTTTATTTTTAATGA
Found at i:43154504 original size:29 final size:29
Alignment explanation
Indices: 43154411--43154536 Score: 103
Period size: 29 Copynumber: 4.3 Consensus size: 29
43154401 GATATCTTTG
* * * *
43154411 AAAGGAAGCCTTTGTGTCGATCTCTGTTA
1 AAAGGATGCATTTGTGGCTATCTCTGTTA
* * * * * *
43154440 AATGGAAGCTTTTGTGACTGTCTCTTTTA
1 AAAGGATGCATTTGTGGCTATCTCTGTTA
*
43154469 AAAGGATGCATTCGTGGCTATCTCTGTTA
1 AAAGGATGCATTTGTGGCTATCTCTGTTA
*
43154498 AAAGGATGTC-TTTGTGG-TCATCTATGTTA
1 AAAGGATG-CATTTGTGGCT-ATCTCTGTTA
*
43154527 AAAGAATGCA
1 AAAGGATGCA
43154537 CTGTGGAAAA
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
28 2 0.03
29 75 0.96
30 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (29 bp):
AAAGGATGCATTTGTGGCTATCTCTGTTA
Found at i:43156083 original size:15 final size:17
Alignment explanation
Indices: 43156063--43156094 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
43156053 GAATTAGGTT
43156063 TAGG-AAATT-ATTTAA
1 TAGGAAAATTAATTTAA
43156078 TAGGAAAATTAATTTAA
1 TAGGAAAATTAATTTAA
43156095 GATGTTTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 5 0.33
17 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (17 bp):
TAGGAAAATTAATTTAA
Found at i:43158167 original size:39 final size:39
Alignment explanation
Indices: 43158090--43158168 Score: 115
Period size: 39 Copynumber: 2.0 Consensus size: 39
43158080 TGTGCTTATC
* *
43158090 TATTGTTTTAATACTTTCGGGATATTAATTCAGGTTTAA
1 TATTGTTTTAATACTTTCGGAATATTAATTCAGATTTAA
*
43158129 TATTGTTTTAATA-TTTCTGGAATATTAATTCATATTTAA
1 TATTGTTTTAATACTTTC-GGAATATTAATTCAGATTTAA
43158168 T
1 T
43158169 GTGCTTAGTC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 4 0.11
39 32 0.89
ACGTcount: A:0.30, C:0.06, G:0.11, T:0.52
Consensus pattern (39 bp):
TATTGTTTTAATACTTTCGGAATATTAATTCAGATTTAA
Found at i:43161768 original size:15 final size:17
Alignment explanation
Indices: 43161738--43161769 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
43161728 GCCTAGCGGT
43161738 ATGGCCATGTGACACAC
1 ATGGCCATGTGACACAC
43161755 ATGGCC-TG-GACACAC
1 ATGGCCATGTGACACAC
43161770 GGGCATGTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.28, C:0.31, G:0.25, T:0.16
Consensus pattern (17 bp):
ATGGCCATGTGACACAC
Found at i:43164761 original size:10 final size:10
Alignment explanation
Indices: 43164742--43164772 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
43164732 GCTTATTTTG
43164742 TGTTTATACA
1 TGTTTATACA
*
43164752 TGTTTGTACA
1 TGTTTATACA
43164762 TGTTTATACA
1 TGTTTATACA
43164772 T
1 T
43164773 TGAGGACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.52
Consensus pattern (10 bp):
TGTTTATACA
Found at i:43165094 original size:32 final size:32
Alignment explanation
Indices: 43165052--43165161 Score: 88
Period size: 32 Copynumber: 3.6 Consensus size: 32
43165042 CTTGAAGTTG
*
43165052 TGCCATAAAGGCATTCCTTAGTATCCAGTACT
1 TGCCACAAAGGCATTCCTTAGTATCCAGTACT
* *
43165084 TGCCACAAAGGC--T--TTA-TGTCCAG-AGTT
1 TGCCACAAAGGCATTCCTTAGTATCCAGTA-CT
* * *
43165111 ATGCCACAAAGGCATTTCTTAGTATCTATTACT
1 -TGCCACAAAGGCATTCCTTAGTATCCAGTACT
* *
43165144 CGCCACAAAGGCTTTCCT
1 TGCCACAAAGGCATTCCT
43165162 ATCTAGAGTT
Statistics
Matches: 60, Mismatches: 10, Indels: 16
0.70 0.12 0.19
Matches are distributed among these distances:
26 1 0.02
27 7 0.12
28 15 0.25
30 2 0.03
32 29 0.48
33 5 0.08
34 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.31
Consensus pattern (32 bp):
TGCCACAAAGGCATTCCTTAGTATCCAGTACT
Found at i:43165205 original size:61 final size:61
Alignment explanation
Indices: 43165047--43165220 Score: 224
Period size: 61 Copynumber: 2.9 Consensus size: 61
43165037 ATTATCTTGA
* *
43165047 AGTTGTGCCATAAAGGCATTCCTTAGTATCCAGTACTTGCCACAAAGGCTTT-ATGTCCAG
1 AGTTGTGCCATAAAGGCATTCCTTAGTATCCAGTACTCGCCACAAAGGCTTTCATATCCAG
* * * * * * *
43165107 AGTTATGCCACAAAGGCATTTCTTAGTATCTATTACTCGCCACAAAGGCTTTCCTATCTAG
1 AGTTGTGCCATAAAGGCATTCCTTAGTATCCAGTACTCGCCACAAAGGCTTTCATATCCAG
* * * *
43165168 AGTTGTGTCATAAAGGCATTCCTTAATATCCAGTACTCACCACAAAGACTTTC
1 AGTTGTGCCATAAAGGCATTCCTTAGTATCCAGTACTCGCCACAAAGGCTTTC
43165221 TCTTTCCTAG
Statistics
Matches: 95, Mismatches: 18, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 46 0.48
61 49 0.52
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (61 bp):
AGTTGTGCCATAAAGGCATTCCTTAGTATCCAGTACTCGCCACAAAGGCTTTCATATCCAG
Found at i:43167166 original size:18 final size:18
Alignment explanation
Indices: 43167139--43167177 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
43167129 TTTAAACTCT
*
43167139 TTAAACTCAATTAAAAAA
1 TTAAAATCAATTAAAAAA
*
43167157 TTAAAATCAATTGAAAAA
1 TTAAAATCAATTAAAAAA
43167175 TTA
1 TTA
43167178 CTACCTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31
Consensus pattern (18 bp):
TTAAAATCAATTAAAAAA
Found at i:43169593 original size:9 final size:10
Alignment explanation
Indices: 43169570--43169594 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
43169560 GCTTTATCTA
43169570 AAAAAGTTTT
1 AAAAAGTTTT
43169580 AAAAAGTTTT
1 AAAAAGTTTT
43169590 AAAAA
1 AAAAA
43169595 TTGAGAGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (10 bp):
AAAAAGTTTT
Found at i:43174485 original size:14 final size:14
Alignment explanation
Indices: 43174466--43174496 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
43174456 AATGCTCTTT
43174466 TTTACATCTATTTC
1 TTTACATCTATTTC
43174480 TTTACATCTATTTC
1 TTTACATCTATTTC
43174494 TTT
1 TTT
43174497 CGAGTCATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTACATCTATTTC
Found at i:43176416 original size:46 final size:46
Alignment explanation
Indices: 43176349--43176524 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
43176339 TGTAACCCGC
* * *
43176349 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
* * *
43176395 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGAATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCG---GAC--GTTCGCAT
* * *
43176445 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
*
43176488 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
43176525 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 3 0.03
45 2 0.02
46 60 0.56
47 26 0.24
48 2 0.02
49 3 0.03
50 3 0.03
51 3 0.03
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
Found at i:43176470 original size:93 final size:93
Alignment explanation
Indices: 43176356--43176527 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
43176346 CGCCCATAAG
* * *
43176356 CGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
43176421 ACGAGTTCGAATGCCTAGTTACATCTCA
66 ACGAGTTCGAATGCCTAGTTACATCTCA
* *
43176449 CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
43176514 ACGAGTTCGGATGC
66 ACGAGTTCGAATGC
43176528 TCAACCATCC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCAGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGAATGCCTAGTTACATCTCA
Found at i:43176543 original size:46 final size:46
Alignment explanation
Indices: 43176398--43176536 Score: 126
Period size: 47 Copynumber: 3.0 Consensus size: 46
43176388 TTCGCATCCA
*
43176398 TAAGTGAACTCGGACTCAACTCAACGAGTTCGAATGC-CTAGTTA-CATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATC
* * * * * *
43176446 TCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCA--
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-G-GATGCTCAACCATC
43176491 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
43176537 CTAGTGACAT
Statistics
Matches: 73, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
44 8 0.11
45 3 0.04
46 26 0.36
47 28 0.38
48 3 0.04
49 4 0.05
50 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
Found at i:43183552 original size:46 final size:46
Alignment explanation
Indices: 43183485--43183659 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
43183475 TGTAACCCGC
*
43183485 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
* *
43183531 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * * *
43183581 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
43183624 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG
43183660 ATGCTCAACC
Statistics
Matches: 108, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 61 0.56
47 27 0.25
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:43183605 original size:93 final size:93
Alignment explanation
Indices: 43183492--43183663 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
43183482 CGCCCATAAG
* * *
43183492 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
43183557 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
43183585 CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
43183650 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
43183664 TCAACCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:43193825 original size:20 final size:19
Alignment explanation
Indices: 43193762--43193868 Score: 88
Period size: 20 Copynumber: 5.4 Consensus size: 19
43193752 CCAGTTTATG
43193762 GACAAGCCACCAATATTGCA
1 GACAAGCCACCAA-ATTGCA
* * * * **
43193782 GATAAACCAACAGTATTGTG
1 GACAAGCCACCA-AATTGCA
43193802 GACAAGCCACCATAATTGCA
1 GACAAGCCACCA-AATTGCA
** *
43193822 GACAAGGTACCAATATTGTA
1 GACAAGCCACCAA-ATTGCA
43193842 GACAAGCCACCAGAATTGCA
1 GACAAGCCACCA-AATTGCA
43193862 GACAAGC
1 GACAAGC
43193869 TGTTAGTATT
Statistics
Matches: 65, Mismatches: 19, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
19 1 0.02
20 63 0.97
21 1 0.02
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (19 bp):
GACAAGCCACCAAATTGCA
Found at i:43193886 original size:40 final size:39
Alignment explanation
Indices: 43193753--43193894 Score: 142
Period size: 40 Copynumber: 3.6 Consensus size: 39
43193743 AATAACACAC
* * *
43193753 CAGT-TTATGGACAAGCCACCAATATTGCAGATAAACCAA
1 CAGTATTATGGACAAGCCACCAA-ATTGCAGACAAGCTAA
* * *
43193792 CAGTATTGTGGACAAGCCACCATAATTGCAGACAAGGTAC
1 CAGTATTATGGACAAGCCACCA-AATTGCAGACAAGCTAA
* * * **
43193832 CAATATTGTAGACAAGCCACCAGAATTGCAGACAAGCTGT
1 CAGTATTATGGACAAGCCACCA-AATTGCAGACAAGCTAA
*
43193872 TAGTATTATGGACAAGCCACCAA
1 CAGTATTATGGACAAGCCACCAA
43193895 TGCTGCAAAC
Statistics
Matches: 85, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
39 5 0.06
40 79 0.93
41 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (39 bp):
CAGTATTATGGACAAGCCACCAAATTGCAGACAAGCTAA
Found at i:43193907 original size:80 final size:79
Alignment explanation
Indices: 43193793--43193947 Score: 197
Period size: 80 Copynumber: 1.9 Consensus size: 79
43193783 ATAAACCAAC
* * * *
43193793 AGTATTGTGGACAAGCCACCATAATTGCAGACAAGGTA-CCAATATTGTAGACAAGCCACCAGAA
1 AGTATTATGGACAAGCCACCA-AATTGCAAACAA-GCAGCCAATAATGTAGACAAGCCACCAGAA
43193857 TTGCAGACAAGCTGTT
64 TTGCAGACAAGCTGTT
* **
43193873 AGTATTATGGACAAGCCACC-AATGCTGCAAACAAGCAGCCAATAATGTGGACAAGCCACCAGTG
1 AGTATTATGGACAAGCCACCAAAT--TGCAAACAAGCAGCCAATAATGTAGACAAGCCACCAGAA
43193937 TTGCAGACAAG
64 TTGCAGACAAG
43193948 ATGCCAGTAC
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
78 3 0.05
79 2 0.03
80 60 0.92
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.19
Consensus pattern (79 bp):
AGTATTATGGACAAGCCACCAAATTGCAAACAAGCAGCCAATAATGTAGACAAGCCACCAGAATT
GCAGACAAGCTGTT
Found at i:43194722 original size:19 final size:19
Alignment explanation
Indices: 43194698--43194793 Score: 129
Period size: 21 Copynumber: 4.8 Consensus size: 19
43194688 AATTTTTGAG
43194698 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
43194717 GATATGCAATCCAAGATAT
1 GATATGCAATCTTAGATAT
43194736 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
43194757 GATAAATGCAATCTTAGATAT
1 GAT--ATGCAATCTTAGATAT
*
43194778 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
43194794 AGATATGATT
Statistics
Matches: 68, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
19 32 0.47
21 36 0.53
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:43194743 original size:40 final size:41
Alignment explanation
Indices: 43194699--43194782 Score: 134
Period size: 40 Copynumber: 2.0 Consensus size: 41
43194689 ATTTTTGAGG
43194699 ATATGCAATCTTAGATATGAT-ATGCAATCCAAGATATGAT
1 ATATGCAATCTTAGATATGATAATGCAATCCAAGATATGAT
**
43194739 ATATGCAATCTTAGATATGATAAATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT-AATGCAATCCAAGATATGAT
43194781 AT
1 AT
43194783 GTAATCTTAG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 21 0.52
42 19 0.47
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (41 bp):
ATATGCAATCTTAGATATGATAATGCAATCCAAGATATGAT
Found at i:43194783 original size:40 final size:38
Alignment explanation
Indices: 43194698--43194800 Score: 129
Period size: 40 Copynumber: 2.7 Consensus size: 38
43194688 AATTTTTGAG
43194698 GATATGCAATCTTAGATATGATATGCAATCCAAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCCAAGATAT
**
43194736 GATATATGCAATCTTAGATATGATAAATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATATGAT--ATGCAATCCAAGATAT
*
43194778 GATATGTAATCTTAGA-A-GATATG
1 GATATGCAATCTTAGATATGATATG
43194801 ATTTTGTAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
36 3 0.05
38 4 0.07
39 1 0.02
40 35 0.60
42 15 0.26
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.34
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATATGCAATCCAAGATAT
Found at i:43194800 original size:22 final size:23
Alignment explanation
Indices: 43194772--43194816 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
43194762 ATGCAATCTT
43194772 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
43194794 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
43194817 GATTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:43194826 original size:22 final size:23
Alignment explanation
Indices: 43194782--43194826 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
43194772 AGATATGATA
*
43194782 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
43194805 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
43194827 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:43196228 original size:98 final size:98
Alignment explanation
Indices: 43196108--43196304 Score: 376
Period size: 98 Copynumber: 2.0 Consensus size: 98
43196098 TTAAGAATAA
*
43196108 TAAAGGAAATATTCCAAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCAAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
43196173 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
43196206 TAAAGGAAATATTCCAAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCAAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
43196271 TTAAATCTTGGATGAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
43196304 T
1 T
43196305 TTTATTGTAC
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 97 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCAAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:43202005 original size:44 final size:44
Alignment explanation
Indices: 43201930--43202269 Score: 151
Period size: 44 Copynumber: 7.7 Consensus size: 44
43201920 CCAAGCCTTG
* * * * *
43201930 TCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATGGTAGATCTTA
* * * * *
43201974 TCTCCCTAGGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATGGTAGATCTTA
* * *** * *
43202018 TCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCA-CCAAG-CCTTG
1 TC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--ATGGTAGATCTTA
* * * * * *
43202062 TCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATGGTAGATCTTA
* * *
43202106 TCTCCCTAAGCAGTAGTGGAGCAAATCGAAGATGGTAAATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATGGTAGATCTTA
* * *** * *
43202150 TCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCA-CCAAG-CCTTG
1 TC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--ATGGTAGATCTTA
* * * * * * *
43202194 TTTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATGGTAGATCTTA
*
43202238 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA
43202270 CGACAAATCA
Statistics
Matches: 205, Mismatches: 71, Indels: 40
0.65 0.22 0.13
Matches are distributed among these distances:
42 10 0.05
43 16 0.08
44 159 0.78
45 14 0.07
46 6 0.03
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.24
Consensus pattern (44 bp):
TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATGGTAGATCTTA
Found at i:43202146 original size:132 final size:132
Alignment explanation
Indices: 43201904--43202308 Score: 684
Period size: 132 Copynumber: 3.1 Consensus size: 132
43201894 GCCGACAGCA
** * *
43201904 AAGCAGATCGAAGACACCAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATTGTAGA
1 AAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGA
*
43201969 TCTTATCTCCCTAGGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTG
66 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTG
43202034 GG
131 GG
43202036 AAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGA
1 AAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGA
* * *
43202101 TCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGATGGTAAATCTTATCTTTCCAAGATAGTG
66 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTG
43202166 GG
131 GG
* *
43202168 AAGCAGATTTAAGCCACCAAGCCTTGTTTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGA
1 AAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGA
* * * *
43202233 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCATATATTTCCAATATAGTG
66 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTG
43202298 GG
131 GG
43202300 AAGCAGATT
1 AAGCAGATT
43202309 AAAGTCGACA
Statistics
Matches: 256, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 256 1.00
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (132 bp):
AAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGA
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTG
GG
Found at i:43202451 original size:44 final size:45
Alignment explanation
Indices: 43202401--43202528 Score: 174
Period size: 45 Copynumber: 2.9 Consensus size: 45
43202391 AGTCGCATCT
43202401 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGGA-AGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAA-GATAGCA
*
43202445 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTGAAGATAGCA
* *
43202490 AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
43202529 CACTAATTCC
Statistics
Matches: 75, Mismatches: 3, Indels: 11
0.84 0.03 0.12
Matches are distributed among these distances:
43 3 0.04
44 32 0.43
45 37 0.49
46 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (45 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCA
Found at i:43202453 original size:83 final size:87
Alignment explanation
Indices: 43202323--43202518 Score: 208
Period size: 83 Copynumber: 2.3 Consensus size: 87
43202313 TCGACAATCC
* * * *
43202323 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCACAGATATTATCC-CTCTGAAGTTGCAGA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAGCACAGATATTATCCTC-CTGAAGTTGCAGA
* * *
43202387 GA-GTAGTC-G-CAT-CTAGTCT
65 GAGGCAGACTGACATGCAAGTCT
*
43202406 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGGAAGCA-AG-TCTTATCCTCCTGAAGTTGCAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAA--AAGCACAGATATTATCCTCCTGAAGTTGCAG
* *
43202469 TGAGGCAGACTGAAGATGGCAAGTCT
64 AGAGGCAGACTG-ACAT-GCAAGTCT
43202495 TATCTCCCTGAAGTTGCAGTGGAG
1 TATCTCCCTGAAGTTGCAGTGGAG
43202519 TAGATTGAAG
Statistics
Matches: 94, Mismatches: 10, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
83 50 0.53
84 7 0.07
85 5 0.05
87 2 0.02
89 30 0.32
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27
Consensus pattern (87 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAGCACAGATATTATCCTCCTGAAGTTGCAGAG
AGGCAGACTGACATGCAAGTCT
Found at i:43202506 original size:45 final size:44
Alignment explanation
Indices: 43202401--43202518 Score: 170
Period size: 44 Copynumber: 2.7 Consensus size: 44
43202391 AGTCGCATCT
43202401 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGGAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGGAAGCA
*
43202445 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAA-GATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGGA-AGCA
43202490 AGTCTTATCTCCCTGAAGTTGCAGTGGAG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAG
43202519 TAGATTGAAG
Statistics
Matches: 67, Mismatches: 1, Indels: 11
0.85 0.01 0.14
Matches are distributed among these distances:
43 3 0.04
44 32 0.48
45 29 0.43
46 3 0.04
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (44 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGGAAGCA
Done.