Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 142 of 185
Found at i:43941749 original size:32 final size:32
Alignment explanation
Indices: 43941691--43941780 Score: 96
Period size: 32 Copynumber: 2.8 Consensus size: 32
43941681 AAAAGCATAA
*
43941691 CAAAAAATGCATAACAAAATAAAATATATAAAT-
1 CAAAAAA--CATAAAAAAATAAAATATATAAATC
*
43941724 C-GAAAACATAAAAAATATATAAATATATAAATC
1 CAAAAAACATAAAAAA-ATA-AAATATATAAATC
43941757 CAAAAAACATAAAAATAA-AAAATA
1 CAAAAAACATAAAAA-AATAAAATA
43941781 AAAATAAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
30 8 0.16
31 3 0.06
32 21 0.43
33 3 0.06
34 13 0.27
35 1 0.02
ACGTcount: A:0.69, C:0.09, G:0.02, T:0.20
Consensus pattern (32 bp):
CAAAAAACATAAAAAAATAAAATATATAAATC
Found at i:43941781 original size:13 final size:14
Alignment explanation
Indices: 43941759--43941790 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
43941749 TATAAATCCA
43941759 AAAAACATAAAAAT
1 AAAAACATAAAAAT
43941773 AAAAA-ATAAAAAT
1 AAAAACATAAAAAT
43941786 AAAAA
1 AAAAA
43941791 TATGGTTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.12
Consensus pattern (14 bp):
AAAAACATAAAAAT
Found at i:43942391 original size:44 final size:46
Alignment explanation
Indices: 43942289--43942391 Score: 106
Period size: 44 Copynumber: 2.3 Consensus size: 46
43942279 AATGTCAAAT
*
43942289 TTCTTCTTCTCCTTAAAAAAAACCCCCCTAAATTAAACCCCAAATCAA
1 TTCTTCTTCTTCTTAAAAAAAA-CCCCCTAAATTAAACCCCAAATC-A
* * * *
43942337 TTATTC-TCTTCTT-AAAAAAA-CCCTTAAATTAAACTCCCCATTC-
1 TTCTTCTTCTTCTTAAAAAAAACCCCCTAAATTAAAC-CCCAAATCA
43942380 TTCTTCTTCTTC
1 TTCTTCTTCTTC
43942392 CTCATCAGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
43 5 0.11
44 18 0.38
45 6 0.13
46 7 0.15
47 6 0.13
48 5 0.11
ACGTcount: A:0.33, C:0.31, G:0.00, T:0.36
Consensus pattern (46 bp):
TTCTTCTTCTTCTTAAAAAAAACCCCCTAAATTAAACCCCAAATCA
Found at i:43949847 original size:7 final size:7
Alignment explanation
Indices: 43949791--43949846 Score: 69
Period size: 7 Copynumber: 8.0 Consensus size: 7
43949781 TAAAAATAAT
43949791 AATTGAG
1 AATTGAG
43949798 AATTGAG
1 AATTGAG
43949805 AATTGAG
1 AATTGAG
43949812 AATTGAG
1 AATTGAG
*
43949819 AATTTAG
1 AATTGAG
*
43949826 GATTGA-
1 AATTGAG
43949832 AGATTGAG
1 A-ATTGAG
*
43949840 TATTGAG
1 AATTGAG
43949847 TTAAAAATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (7 bp):
AATTGAG
Found at i:43964839 original size:24 final size:24
Alignment explanation
Indices: 43964808--43964877 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 24
43964798 GATATGCTCT
*
43964808 TACGAGCTGTAAT-TGGTAA-TCTCA
1 TACGAGCTG-AATACGGTAAGT-TCA
43964832 TACGAGCTGAATAACGGTAAGTTCA
1 TACGAGCTGAAT-ACGGTAAGTTCA
43964857 TACGAGCTGAATATCGGTAAG
1 TACGAGCTGAATA-CGGTAAG
43964878 CTCTCTCGAG
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
23 3 0.07
24 10 0.24
25 27 0.66
26 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (24 bp):
TACGAGCTGAATACGGTAAGTTCA
Found at i:43964887 original size:25 final size:25
Alignment explanation
Indices: 43964829--43964877 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
43964819 ATTGGTAATC
43964829 TCATACGAGCTGAATAACGGTAAGT
1 TCATACGAGCTGAATAACGGTAAGT
*
43964854 TCATACGAGCTGAATATCGGTAAG
1 TCATACGAGCTGAATAACGGTAAG
43964878 CTCTCTCGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.24
Consensus pattern (25 bp):
TCATACGAGCTGAATAACGGTAAGT
Found at i:43967065 original size:11 final size:11
Alignment explanation
Indices: 43967049--43967075 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
43967039 TGCATATCTC
43967049 TATAAGCAGCT
1 TATAAGCAGCT
43967060 TATAAGCAGCT
1 TATAAGCAGCT
43967071 TATAA
1 TATAA
43967076 AGCACCTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (11 bp):
TATAAGCAGCT
Found at i:43968570 original size:313 final size:308
Alignment explanation
Indices: 43967952--43968549 Score: 822
Period size: 313 Copynumber: 1.9 Consensus size: 308
43967942 TATTTGTGTA
* * **
43967952 TAATAAAAATTAGTATTCGAGCTATTAATTTTTTATTACACTTCCAACAAGTGGTATCCGAGCTA
1 TAATAAAAATTAGTATTCAAGCTATTAATTTTTCATTACACTTCCAACAAGTAATATCCGAGCTA
* * *
43968017 GGTTTGTGTCAACGTCACAATGGTAAACATGATTCATAGATCCCGAAATTAACAAAGACAAAATA
66 GGTTCGTGTCAACGTCACAATGGCAAACATGATTCATAGATCCCAAAATTAACAAAGACAAAATA
* * * * * * *
43968082 TAGCAATTGGAGCACCCAGATGAAGGCTTTGCTCGGTTCTCAAGATTGTTGGGACGTTGTCAAAG
131 GAACAATTAGAACACCCAGATAAAGACTTTGCTCGATTCTCAAGATTGTTGGGACGTTGTCAAAG
* ** *
43968147 AAGGATATGTCAAGCCCTAAAATGTAGCTGCCAAAACAGCTTTGACAAACGAAGAAAAAAGAGTA
196 AAGGATATGTCAAGCCCTAAAATGCAGCTGCCAAAACAGC-TTGACAAAAAAAGAAAAAAAAGTA
* *** * *
43968212 TTGAAATAAGCTCGTAAAAAGGATATTTGTATTATGTGTTATTTTTATG
260 TTGAAAAAAGCTCGTAAAAAGGATAAGGGCATTATCTGTTATTTTTATG
* *
43968261 TAATAAAAATTAGTATTTAAGCTATTAATTTTTCATTACGCTTCCAACAAGTAATATCCGAGCTA
1 TAATAAAAATTAGTATTCAAGCTATTAATTTTTCATTACACTTCCAACAAGTAATATCCGAGCTA
43968326 GGTTCGTGTCAACGTCACAATGGCAAACATGATTCAATCGTAGATCCCAAAATTAACAAAGACAA
66 GGTTCGTGTCAACGTCACAATGGCAAACATGATTC-A---TAGATCCCAAAATTAACAAAGACAA
* * *
43968391 ATTAGAACAATTAGAACATCCGGATAAAGACTTTGCTCGATTCTCAAGATTGTTGGGACGTTGTC
127 AATAGAACAATTAGAACACCCAGATAAAGACTTTGCTCGATTCTCAAGATTGTTGGGACGTTGTC
* * ***
43968456 AAAGAATGATATGTCAA-CCCTTAAGATGCAGCTGCCAAAGTGGC-TGACAAAAAAAGAAAAAAA
192 AAAGAAGGATATGTCAAGCCC-TAAAATGCAGCTGCCAAAACAGCTTGACAAAAAAAGAAAAAAA
43968519 AGTATTGAAAAAAGCTCGTAAAAAGGATAAG
256 AGTATTGAAAAAAGCTCGTAAAAAGGATAAG
43968550 AGGGCGTTGA
Statistics
Matches: 253, Mismatches: 31, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
309 92 0.36
310 1 0.00
311 44 0.17
312 3 0.01
313 113 0.45
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (308 bp):
TAATAAAAATTAGTATTCAAGCTATTAATTTTTCATTACACTTCCAACAAGTAATATCCGAGCTA
GGTTCGTGTCAACGTCACAATGGCAAACATGATTCATAGATCCCAAAATTAACAAAGACAAAATA
GAACAATTAGAACACCCAGATAAAGACTTTGCTCGATTCTCAAGATTGTTGGGACGTTGTCAAAG
AAGGATATGTCAAGCCCTAAAATGCAGCTGCCAAAACAGCTTGACAAAAAAAGAAAAAAAAGTAT
TGAAAAAAGCTCGTAAAAAGGATAAGGGCATTATCTGTTATTTTTATG
Found at i:43969068 original size:12 final size:12
Alignment explanation
Indices: 43969051--43969076 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
43969041 GGTATAAGCA
43969051 ATCGTGGAGGAT
1 ATCGTGGAGGAT
43969063 ATCGTGGAGGAT
1 ATCGTGGAGGAT
43969075 AT
1 AT
43969077 AGAGGTGGAC
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:0.27, C:0.08, G:0.38, T:0.27
Consensus pattern (12 bp):
ATCGTGGAGGAT
Found at i:43971372 original size:21 final size:21
Alignment explanation
Indices: 43971347--43971386 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
43971337 GAAGATAAAG
*
43971347 TATATCGCTTGAAGAAAGCTT
1 TATATCGATTGAAGAAAGCTT
* *
43971368 TATATGGATTGAAGCAAGC
1 TATATCGATTGAAGAAAGC
43971387 CTCAAGAGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (21 bp):
TATATCGATTGAAGAAAGCTT
Found at i:43979172 original size:13 final size:13
Alignment explanation
Indices: 43979154--43979179 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43979144 CATATTCCCA
43979154 TAATTTTATGTAT
1 TAATTTTATGTAT
43979167 TAATTTTATGTAT
1 TAATTTTATGTAT
43979180 ATACATACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TAATTTTATGTAT
Found at i:43979418 original size:21 final size:18
Alignment explanation
Indices: 43979387--43979426 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
43979377 TTGTTTTAGT
43979387 TCATTTTTTATTCATATTA
1 TCATTTTTTATTC-TATTA
43979406 TCATGTTTATTATTCTATTA
1 TCAT-TTT-TTATTCTATTA
43979426 T
1 T
43979427 GCATATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 9 0.47
21 6 0.32
ACGTcount: A:0.25, C:0.10, G:0.03, T:0.62
Consensus pattern (18 bp):
TCATTTTTTATTCTATTA
Found at i:43979670 original size:110 final size:109
Alignment explanation
Indices: 43979472--43979782 Score: 421
Period size: 110 Copynumber: 2.9 Consensus size: 109
43979462 TTTCTAATTG
*
43979472 AGGCAATATTTAGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTC
1 AGGCAATATTTTGCGTTT-GGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTC
* * *
43979537 TCGTTCAACCAAATGGCTTAATATCCTTTTAAAATTTTTTAAAATA
65 TCGTTCAACCAAATGGCTAAATATCCTTTTAAAA-ATTCTAAAATA
* * *
43979583 AGGCAATATTTTGCGTTTGGAAATTAGAGAAAACATGTCCAAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* *
43979648 CATTCAACCAAATGGCTAAATATCCTTTTAAAAATTCTCAAATA
66 CGTTCAACCAAATGGCTAAATATCCTTTTAAAAATTCTAAAATA
* * * * *
43979692 AGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAATGTGCTGGGTTTCGA--TTTCT
1 AGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* * * *
43979754 CGTTTAACCAAATAGCCATATATCCTTTT
66 CGTTCAACCAAATGGCTAAATATCCTTTT
43979783 GAATTTCAAT
Statistics
Matches: 178, Mismatches: 22, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
106 29 0.16
108 22 0.12
109 35 0.20
110 75 0.42
111 17 0.10
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (109 bp):
AGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
CGTTCAACCAAATGGCTAAATATCCTTTTAAAAATTCTAAAATA
Found at i:43983852 original size:23 final size:23
Alignment explanation
Indices: 43983826--43983881 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 23
43983816 CAAAATAAAA
43983826 AAAAGAAGAAAAA-AATCAAAGTC
1 AAAAGAA-AAAAACAATCAAAGTC
43983849 AAAAGAAAAAAATCAATCAAAGTC
1 AAAAGAAAAAAA-CAATCAAAGTC
*
43983873 AAAATAAAA
1 AAAAGAAAA
43983882 TATGAAAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 5 0.17
23 7 0.23
24 18 0.60
ACGTcount: A:0.71, C:0.09, G:0.09, T:0.11
Consensus pattern (23 bp):
AAAAGAAAAAAACAATCAAAGTC
Found at i:43984766 original size:13 final size:13
Alignment explanation
Indices: 43984748--43984773 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43984738 AGTCGGGGAA
43984748 AAAAATGAAAATG
1 AAAAATGAAAATG
43984761 AAAAATGAAAATG
1 AAAAATGAAAATG
43984774 GAGAGGCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAAATGAAAATG
Found at i:43986110 original size:87 final size:87
Alignment explanation
Indices: 43985957--43986615 Score: 973
Period size: 87 Copynumber: 7.6 Consensus size: 87
43985947 AGATCAGTGA
* * *
43985957 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTCAAGATAGTAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAAAGATAGCAGATCTTGC
* *
43986022 CTTTCTGCATTGACAGCGAAGC
66 CTTCCTGCATTAACAGCGAAGC
* * * *
43986044 AGGTC-AGAAACAAAGCCTTACCTCCATCAGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTG
1 AGATCGA-AAACAAAGCCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAAAGATAGCAGATCTTG
43986108 CCTTCCTGCATTAACAGCGAAGC
65 CCTTCCTGCATTAACAGCGAAGC
*
43986131 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAAAGATAGCAGATCTTGT
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAAAGATAGCAGATCTTGC
* *
43986196 CTTCTTGCATTAACAGCGAAAC
66 CTTCCTGCATTAACAGCGAAGC
* *
43986218 ATATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAAAGATAGTAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAAAGATAGCAGATCTTGC
* * *
43986283 CTTTCTGTATTGACAGCGAAGC
66 CTTCCTGCATTAACAGCGAAGC
* * *
43986305 AGATC-AGAAACAAAGCCTTGCCTCCATCAGTTCCAGTGGAGCTGGTTAAAGATAGCAGATCTTG
1 AGATCGA-AAACAAAGCCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAAAGATAGCAGATCTTG
*
43986369 CCTTCCTGCATTAACAGTGAAGC
65 CCTTCCTGCATTAACAGCGAAGC
*
43986392 AGATCGAAAACAAAGCATTGCCTCCATCGGTTGCAATGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAAAGATAGCAGATCTTGC
*
43986457 CTTCCTACATTAACAGCGAAGC
66 CTTCCTGCATTAACAGCGAAGC
* * *
43986479 AGATCGAAAACAAAGCCTTGCATCCATCGGTTGCAATAGAGCTGGTTAAAGATAACAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAAAGATAGCAGATCTTGC
*
43986544 CTTCCTGCGTTAACAGCGAAGC
66 CTTCCTGCATTAACAGCGAAGC
* * * * * *
43986566 AGATC-AAGAACAAAGTCTTGCCTCTATCGATTACAGTGGAGCGGGTTAAA
1 AGATCGAA-AACAAAGCCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAAA
43986616 ATAAAAGATC
Statistics
Matches: 516, Mismatches: 51, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
86 4 0.01
87 510 0.99
88 2 0.00
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.24
Consensus pattern (87 bp):
AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAAAGATAGCAGATCTTGC
CTTCCTGCATTAACAGCGAAGC
Found at i:43986729 original size:44 final size:44
Alignment explanation
Indices: 43986661--43986921 Score: 206
Period size: 44 Copynumber: 5.7 Consensus size: 44
43986651 TAGATCGCAT
43986661 CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGCGGAG
1 CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGCGGAG
* * * *
43986705 CAGATTGAAGCTAGTAATCCTATCTCCCTAAGATTACAGTGGAG
1 CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGCGGAG
* * ** * *
43986749 CGGGTT-AAAATAAAAGATCTTATCTCTCTGA-AGTTACAGCAGAGTAG
1 CAGATTGAAGCTAGAA-ATCTTATCTCCCTGAGA-TTACAGC-G-G-AG
*
43986796 ATCACATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
1 -------CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGCGGAG
* * * *
43986847 CATATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGCGGAG
* * *
43986891 CGGATTAAAG-TA-ATAGATCTTATCTCTCTGA
1 CAGATTGAAGCTAGA-A-ATCTTATCTCCCTGA
43986922 AGTTGCAGTA
Statistics
Matches: 169, Mismatches: 32, Indels: 32
0.73 0.14 0.14
Matches are distributed among these distances:
43 9 0.05
44 121 0.72
45 1 0.01
46 1 0.01
47 2 0.01
51 2 0.01
52 1 0.01
53 1 0.01
54 25 0.15
55 6 0.04
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (44 bp):
CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGCGGAG
Found at i:43986762 original size:142 final size:142
Alignment explanation
Indices: 43986594--43986948 Score: 620
Period size: 142 Copynumber: 2.5 Consensus size: 142
43986584 TGCCTCTATC
43986594 GATTACAGTGGAGCGGGTTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGC
1 GATTACAGTGGAGCGGGTTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGC
*
43986659 ATCAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATC
66 ATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATC
43986724 CTATCTCCCTAA
131 CTATCTCCCTAA
*
43986736 GATTACAGTGGAGCGGGTTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCAC
1 GATTACAGTGGAGCGGGTTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGC
*
43986801 ATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCATATTGAAGCTAGTAATC
66 ATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATC
*
43986866 CTATCTCCCTGA
131 CTATCTCCCTAA
* * * * * *
43986878 GATTACAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGC
1 GATTACAGTGGAGCGGGTTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGC
43986943 ATCAGA
66 ATCAGA
43986949 CCTTATTCCC
Statistics
Matches: 202, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
142 202 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.27
Consensus pattern (142 bp):
GATTACAGTGGAGCGGGTTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGC
ATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATC
CTATCTCCCTAA
Found at i:43988912 original size:13 final size:13
Alignment explanation
Indices: 43988894--43988919 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43988884 CTTATTCCCA
43988894 TAATTTTATGTAT
1 TAATTTTATGTAT
43988907 TAATTTTATGTAT
1 TAATTTTATGTAT
43988920 ATACATACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TAATTTTATGTAT
Found at i:43989143 original size:21 final size:18
Alignment explanation
Indices: 43989112--43989151 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
43989102 TTGTTTTAGT
43989112 TCATTTTTTATTCATATTA
1 TCATTTTTTATTC-TATTA
43989131 TCATGTTTATTATTCTATTA
1 TCAT-TTT-TTATTCTATTA
43989151 T
1 T
43989152 GCATATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 9 0.47
21 6 0.32
ACGTcount: A:0.25, C:0.10, G:0.03, T:0.62
Consensus pattern (18 bp):
TCATTTTTTATTCTATTA
Found at i:43989395 original size:110 final size:109
Alignment explanation
Indices: 43989197--43989507 Score: 430
Period size: 110 Copynumber: 2.9 Consensus size: 109
43989187 TTTCTAATTG
* * *
43989197 AGGCAATATTTAGCGTTTGGGAAATTCGAGAAAACATGTCCTAAGGTGCTGGGTGTCGATTTTTC
1 AGGCAATGTTTTGCGTTT-GGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTC
* *
43989262 TCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTTAAAATA
65 TCGTTCAACCAAATGGCTAAATATCCTTTTAAAAA-TTCTAAAATA
*
43989308 AGGCAATGTTTTGCGTTTGGAAATTAGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* *
43989373 CATTCAACCAAATGGCTAAATATCCTTTTAAAAATTCTCAAATA
66 CGTTCAACCAAATGGCTAAATATCCTTTTAAAAATTCTAAAATA
* * * * * *
43989417 AGGCAATGTTTTGAGTTTGGAAATTCGAG-GAACGTGCCCTAATGTGTTGGGTTTCGA--TTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* * *
43989479 CGTTTAACCAAATAGCCAAATATCCTTTT
66 CGTTCAACCAAATGGCTAAATATCCTTTT
43989508 GAATTTCAAT
Statistics
Matches: 181, Mismatches: 19, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
106 30 0.17
108 23 0.13
109 35 0.19
110 77 0.43
111 16 0.09
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.35
Consensus pattern (109 bp):
AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
CGTTCAACCAAATGGCTAAATATCCTTTTAAAAATTCTAAAATA
Found at i:44006600 original size:11 final size:11
Alignment explanation
Indices: 44006586--44006635 Score: 82
Period size: 11 Copynumber: 4.5 Consensus size: 11
44006576 TAGCAATGCC
*
44006586 TATTTTAATCC
1 TATTTTAATCA
*
44006597 TATTTTAATTA
1 TATTTTAATCA
44006608 TATTTTAATCA
1 TATTTTAATCA
44006619 TATTTTAATCA
1 TATTTTAATCA
44006630 TATTTT
1 TATTTT
44006636 TTTAAATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 36 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTTAATCA
Found at i:44009069 original size:3 final size:3
Alignment explanation
Indices: 44009061--44009134 Score: 148
Period size: 3 Copynumber: 24.7 Consensus size: 3
44009051 GAGAATGCTT
44009061 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
44009109 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
44009135 TTATTATTAT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:44013627 original size:20 final size:20
Alignment explanation
Indices: 44013590--44013632 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
44013580 CTTTTAAAGG
** *
44013590 ATAATATAATTTATTTAAAA
1 ATAATATAAAATAATTAAAA
*
44013610 ATAATATAAAATAATTAATA
1 ATAATATAAAATAATTAAAA
44013630 ATA
1 ATA
44013633 TTCTACTTGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAATATAAAATAATTAAAA
Found at i:44015884 original size:22 final size:20
Alignment explanation
Indices: 44015850--44015890 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
44015840 AATTGTTGAT
*
44015850 AAATTGATGAATTAGGCTTG
1 AAATTGATGAATTAAGCTTG
44015870 AAATTGATAGAAATTAAGCTT
1 AAATTGAT-G-AATTAAGCTT
44015891 AGATTATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (20 bp):
AAATTGATGAATTAAGCTTG
Found at i:44017233 original size:43 final size:43
Alignment explanation
Indices: 44017185--44017368 Score: 208
Period size: 43 Copynumber: 4.1 Consensus size: 43
44017175 AGAAATAAAT
* *
44017185 GCCGCTATAGATCATGACCTTTAGCGGCGTTTTTCCCACAAAC
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCACAAAC
* * * *
44017228 GCCGCTATAGATCAGTACCTTTAGTGGTTAGTGGTGCTTTT-ACACAAAC
1 GCCGCTATAGATCAGGACC-----T--TTAGCGGCGCTTTTCCCACAAAC
* *
44017277 GCCGCTATAGCTCAGGACCTTTAGCGACGCTTTTCCCACAAAC
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCACAAAC
* *
44017320 GCCGCTATAGCTCAGGACCTTTAGCGGCGCTTTTCCCACAAGC
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCACAAAC
44017363 GCCGCT
1 GCCGCT
44017369 GTCTGCTTTC
Statistics
Matches: 119, Mismatches: 14, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
42 11 0.09
43 71 0.60
44 1 0.01
48 1 0.01
49 24 0.20
50 11 0.09
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (43 bp):
GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCACAAAC
Found at i:44017842 original size:43 final size:43
Alignment explanation
Indices: 44017781--44017883 Score: 179
Period size: 43 Copynumber: 2.4 Consensus size: 43
44017771 ATGGGTCCCC
*
44017781 CTATAGATTAAGACCTTTAACGGCGCTTTTTCCACAAACGACG
1 CTATAGATCAAGACCTTTAACGGCGCTTTTTCCACAAACGACG
* *
44017824 CTATAGATCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCCG
1 CTATAGATCAAGACCTTTAACGGCGCTTTTTCCACAAACGACG
44017867 CTATAGATCAAGACCTT
1 CTATAGATCAAGACCTT
44017884 AGTATTAAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (43 bp):
CTATAGATCAAGACCTTTAACGGCGCTTTTTCCACAAACGACG
Found at i:44017921 original size:16 final size:16
Alignment explanation
Indices: 44017900--44017933 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
44017890 AAATATTAAA
*
44017900 TATTAAAATCAAACAT
1 TATTAAAATCAAAAAT
*
44017916 TATTAATATCAAAAAT
1 TATTAAAATCAAAAAT
44017932 TA
1 TA
44017934 ATTAGTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (16 bp):
TATTAAAATCAAAAAT
Found at i:44019119 original size:192 final size:191
Alignment explanation
Indices: 44018869--44019242 Score: 459
Period size: 192 Copynumber: 2.0 Consensus size: 191
44018859 AAAGGTCCCA
* * * *
44018869 AACTTGGTCTATTATGTTCATTAACATCATAAAAAATCATCAATTACATCCTAATAACAATTTCA
1 AACTTAGTCTATTATATTCATTAACATCATAAAAAAACATCAATTACATCCTAATAACAATTCCA
* * * * * * * *
44018934 ACTCCAAAGTT-GACTAAAGAAGCTTTGCAGGATATGA-AAACACAAGTGCATTTCCATTCAAGT
66 ACCCCAAAGTTCAACTAAA-AAACATTCCAGGATA-CACAAACACAAATGCATTTCCATTAAAGT
** * * *
44018997 AAATTGTTGTGTTGTAATCACAAAG-TTCAAATGAAAACCATGACTCGAACCCATAAAAAATTC
129 -AATAATAGTGTTGTAATCACAAAGCTCCAAATGAAAACCATGACTCAAACCCATAAAAAATTC
* *
44019060 AACTTAGTCTATTGTATTCATTAACATCA-ACATAAAAACATCAATTACTTCCTAATAACAATTC
1 AACTTAGTCTATTATATTCATTAACATCATA-A-AAAAACATCAATTACATCCTAATAACAATTC
* **
44019124 CAACCCCAAAGTTCAATTAAAAAACATTCCAGGATACACAAATGCAAATGCATTTCCATTAAAGT
64 CAACCCCAAAGTTCAACTAAAAAACATTCCAGGATACACAAACACAAATGCATTTCCATTAAAGT
* *
44019189 AATAATAGTGTTTTAATCACAAAGCTCCAAATGAAAACCATGACTTAAACCCAT
129 AATAATAGTGTTGTAATCACAAAGCTCCAAATGAAAACCATGACTCAAACCCAT
44019243 TATAGATTAC
Statistics
Matches: 154, Mismatches: 24, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
190 1 0.01
191 48 0.31
192 100 0.65
193 5 0.03
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.29
Consensus pattern (191 bp):
AACTTAGTCTATTATATTCATTAACATCATAAAAAAACATCAATTACATCCTAATAACAATTCCA
ACCCCAAAGTTCAACTAAAAAACATTCCAGGATACACAAACACAAATGCATTTCCATTAAAGTAA
TAATAGTGTTGTAATCACAAAGCTCCAAATGAAAACCATGACTCAAACCCATAAAAAATTC
Found at i:44019770 original size:18 final size:18
Alignment explanation
Indices: 44019747--44019782 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
44019737 CTGCTGTTGA
44019747 AGATCTGGAACAAAATCC
1 AGATCTGGAACAAAATCC
44019765 AGATCTGGAACAAAATCC
1 AGATCTGGAACAAAATCC
44019783 GACGTAGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.17
Consensus pattern (18 bp):
AGATCTGGAACAAAATCC
Found at i:44021386 original size:20 final size:20
Alignment explanation
Indices: 44021361--44021400 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
44021351 AAGTATGGTT
44021361 AGTTTAGCAGTTAGCAGTAA
1 AGTTTAGCAGTTAGCAGTAA
44021381 AGTTTAGCAGTTAGCAGTAA
1 AGTTTAGCAGTTAGCAGTAA
44021401 GTGCAGTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (20 bp):
AGTTTAGCAGTTAGCAGTAA
Found at i:44025887 original size:20 final size:20
Alignment explanation
Indices: 44025862--44025901 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
44025852 AAGTATGGTT
*
44025862 AGTTTAGTAGTTAGCAGTAA
1 AGTTTAGCAGTTAGCAGTAA
44025882 AGTTTAGCAGTTAGCAGTAA
1 AGTTTAGCAGTTAGCAGTAA
44025902 GTGCAGTCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.25, T:0.33
Consensus pattern (20 bp):
AGTTTAGCAGTTAGCAGTAA
Found at i:44025912 original size:20 final size:20
Alignment explanation
Indices: 44025870--44025914 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
44025860 TTAGTTTAGT
**
44025870 AGTTAGCAGTAAAGTTTAGC
1 AGTTAGCAGTAAAGTGCAGC
44025890 AGTTAGCAGT-AAGTGCAGTC
1 AGTTAGCAGTAAAGTGCAG-C
44025910 AGTTA
1 AGTTA
44025915 AACTGTTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.29
Consensus pattern (20 bp):
AGTTAGCAGTAAAGTGCAGC
Found at i:44031174 original size:9 final size:9
Alignment explanation
Indices: 44031152--44031190 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
44031142 TATAAAATTT
*
44031152 ATTATTCGA
1 ATTATTTGA
*
44031161 GTTATTTGA
1 ATTATTTGA
44031170 ATTATTTGA
1 ATTATTTGA
*
44031179 GTTATTTGA
1 ATTATTTGA
44031188 ATT
1 ATT
44031191 GCAATATTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.28, C:0.03, G:0.15, T:0.54
Consensus pattern (9 bp):
ATTATTTGA
Found at i:44031175 original size:18 final size:18
Alignment explanation
Indices: 44031152--44031190 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
44031142 TATAAAATTT
44031152 ATTATTCGAGTTATTTGA
1 ATTATTCGAGTTATTTGA
*
44031170 ATTATTTGAGTTATTTGA
1 ATTATTCGAGTTATTTGA
44031188 ATT
1 ATT
44031191 GCAATATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.03, G:0.15, T:0.54
Consensus pattern (18 bp):
ATTATTCGAGTTATTTGA
Found at i:44032676 original size:19 final size:19
Alignment explanation
Indices: 44032652--44032698 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
44032642 GTGATTTCAA
*
44032652 CTTTTATTTCTCTGTTTCT
1 CTTTTATTTCTCAGTTTCT
*
44032671 CTTTTATTTTTCAGTTTCT
1 CTTTTATTTCTCAGTTTCT
44032690 -TTTGTATTT
1 CTTT-TATTT
44032699 ATTTCGACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 3 0.12
19 22 0.88
ACGTcount: A:0.09, C:0.15, G:0.06, T:0.70
Consensus pattern (19 bp):
CTTTTATTTCTCAGTTTCT
Found at i:44033453 original size:3 final size:3
Alignment explanation
Indices: 44033447--44033485 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
44033437 CTTTTAATAA
* *
44033447 TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
44033486 AATTGCCCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:44034285 original size:111 final size:111
Alignment explanation
Indices: 44034000--44034548 Score: 843
Period size: 110 Copynumber: 5.0 Consensus size: 111
44033990 TATCAAAAAT
* ** * *
44034000 AAAATTTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTTGAGAAAAAATGTCCTAAGGTACT
1 AAAATTTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
* *
44034065 GGGTGTCGATTTTTCTCATTCAACCAAATGACTAAATATTCTTTTA
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTA
* *
44034111 AAAA-TTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCT
1 AAAATTTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
*
44034175 GGTTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTA
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTA
* *
44034221 AAAATTTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAGAACGTGCCCTAAAGTGCT
1 AAAATTTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
*
44034286 GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAA
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT-A
** *
44034333 AAAATTTTCGAAATAAGGCAATGTTTTGCATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
1 AAAATTTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
*
44034398 GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTT-
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTA
** * *
44034443 AAAATTTTTAAAATAAGGCAATGTTTTATGTTT-GAAAATTCGAGAAAACGTACCCTAAGGTGCT
1 AAAATTTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
* * * *
44034507 GGGTGTCGATTTTTCTCATTTAACCGAATAGCCAAATATCCT
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCT
44034549 CTTGAATTTC
Statistics
Matches: 405, Mismatches: 31, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
109 66 0.16
110 130 0.32
111 103 0.25
112 106 0.26
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.35
Consensus pattern (111 bp):
AAAATTTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTA
Found at i:44034508 original size:221 final size:220
Alignment explanation
Indices: 44033999--44034548 Score: 868
Period size: 221 Copynumber: 2.5 Consensus size: 220
44033989 TTATCAAAAA
* ** * *
44033999 TAAAATTTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTTGAGAAAAAATGTCCTAAGGTAC
1 TAAAATTTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGC
* *
44034064 TGGGTGTCGATTTTTCTCATTCAACCAAATGACTAAATATTCTTTTAAAAATTTTCAAATAAGGC
66 TGGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAATTTTCAAATAAGGC
* *
44034129 AATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGTTGTCGATTTTTCTCAT
131 AATGTTTTGCATTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCAT
44034194 TCAACCAAATGGCTAAATATCCTTT
196 TCAACCAAATGGCTAAATATCCTTT
* *
44034219 TAAAAATTTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAGAACGTGCCCTAAAGTG
1 T-AAAATTTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTG
*
44034284 CTGGGTGTCGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAAAAAATTTTCGAAATAA
65 CTGGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT-AAAAATTTTC-AAATAA
*
44034349 GGCAATGTTTTGCATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
128 GGCAATGTTTTGCATTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
*
44034414 CGTTCAACCAAATGGCTAAATATCCTTT
193 CATTCAACCAAATGGCTAAATATCCTTT
** * *
44034442 TAAAATTTTTAAAATAAGGCAATGTTTTATGTTT-GAAAATTCGAGAAAACGTACCCTAAGGTGC
1 TAAAATTTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGC
* * * *
44034506 TGGGTGTCGATTTTTCTCATTTAACCGAATAGCCAAATATCCT
66 TGGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCT
44034549 CTTGAATTTC
Statistics
Matches: 302, Mismatches: 25, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
220 1 0.00
221 164 0.54
222 41 0.14
223 96 0.32
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.35
Consensus pattern (220 bp):
TAAAATTTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGC
TGGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAATTTTCAAATAAGGC
AATGTTTTGCATTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCAT
TCAACCAAATGGCTAAATATCCTTT
Found at i:44037903 original size:6 final size:6
Alignment explanation
Indices: 44037894--44037961 Score: 52
Period size: 6 Copynumber: 11.7 Consensus size: 6
44037884 AAGAAAAAGA
* * * *
44037894 AAAATC AAAATC AAAGTC AAAATG AAAATG AAAAT- GAAA-- AAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
* *
44037939 AAAAATC AAAATA AAAAAC AAAA
1 -AAAATC AAAATC AAAATC AAAA
44037962 AAAAAGAGAA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
4 3 0.06
5 3 0.06
6 39 0.76
7 6 0.12
ACGTcount: A:0.72, C:0.09, G:0.06, T:0.13
Consensus pattern (6 bp):
AAAATC
Found at i:44038015 original size:51 final size:52
Alignment explanation
Indices: 44037933--44038033 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 52
44037923 GAAAATGAAA
44037933 AAAATCAAAAATCAAAATAAAAAACAAAAAAA-AAGAGAAAGAA-GAAAAAATC
1 AAAATCAAAAATCAAAATAAAAAACAAAAAAAGAA-AG-AAGAATGAAAAAATC
* ** *
44037985 AAAATC-AAGATCAAAATAAAAATGAGAAAAAGAAAGAAGAATGAAAAAA
1 AAAATCAAAAATCAAAATAAAAAACAAAAAAAGAAAGAAGAATGAAAAAA
44038034 GAGAAATCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
50 5 0.12
51 30 0.70
52 8 0.19
ACGTcount: A:0.74, C:0.06, G:0.11, T:0.09
Consensus pattern (52 bp):
AAAATCAAAAATCAAAATAAAAAACAAAAAAAGAAAGAAGAATGAAAAAATC
Found at i:44038018 original size:40 final size:40
Alignment explanation
Indices: 44037900--44038019 Score: 136
Period size: 40 Copynumber: 3.0 Consensus size: 40
44037890 AAGAAAAATC
* * * * **
44037900 AAAATCAAAGTCAAAATGAAAATGAAAATGAAAAAAATCA
1 AAAATCAAAATCAAAATCAAAATAAAAATGAGAAAAAGAA
* *
44037940 AAAATCAAAATAAAAAACAAAA-AAAAA-GAGAAAGAAGAA
1 AAAATCAAAATCAAAATCAAAATAAAAATGAGAAA-AAGAA
*
44037979 AAAATCAAAATCAAGATCAAAATAAAAATGAGAAAAAGAA
1 AAAATCAAAATCAAAATCAAAATAAAAATGAGAAAAAGAA
44038019 A
1 A
44038020 GAAGAATGAA
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
38 5 0.08
39 26 0.39
40 29 0.44
41 6 0.09
ACGTcount: A:0.72, C:0.07, G:0.10, T:0.11
Consensus pattern (40 bp):
AAAATCAAAATCAAAATCAAAATAAAAATGAGAAAAAGAA
Found at i:44038952 original size:10 final size:10
Alignment explanation
Indices: 44038937--44038974 Score: 67
Period size: 10 Copynumber: 3.7 Consensus size: 10
44038927 CTCTTTGAGT
44038937 AAAAAAAACA
1 AAAAAAAACA
44038947 AAAAAAAACA
1 AAAAAAAACA
44038957 ACAAAAAAACA
1 A-AAAAAAACA
44038968 AAAAAAA
1 AAAAAAA
44038975 TGAAAATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 17 0.63
11 10 0.37
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:44038953 original size:11 final size:11
Alignment explanation
Indices: 44038937--44038974 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
44038927 CTCTTTGAGT
44038937 AAAAAAAAC-A
1 AAAAAAAACAA
44038947 AAAAAAAACAA
1 AAAAAAAACAA
*
44038958 CAAAAAAACAA
1 AAAAAAAACAA
44038969 AAAAAA
1 AAAAAA
44038975 TGAAAATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:44038959 original size:13 final size:12
Alignment explanation
Indices: 44038937--44038974 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
44038927 CTCTTTGAGT
44038937 AAAAAAAACAAA
1 AAAAAAAACAAA
44038949 AAAAAACAACAAA
1 AAAAAA-AACAAA
44038962 AAAACAAAA-AAA
1 AAAA-AAAACAAA
44038974 A
1 A
44038975 TGAAAATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 10 0.42
13 12 0.50
14 2 0.08
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAACAAA
Found at i:44040480 original size:100 final size:100
Alignment explanation
Indices: 44040287--44040468 Score: 260
Period size: 100 Copynumber: 1.8 Consensus size: 100
44040277 CTTTACTTCC
* *
44040287 CAGGCGGTGCAGTAAAAAAGATTAAAGCCACAACGGTGAATATTGCCTCCCTGACATTGCGATTA
1 CAGGCGGTGCAGTAAAAAAGATTAAAACCACAACGGTGAATATTGCCTCCCTGACATTACGATTA
*
44040352 AAAAGATTAAAGCTACAGCAGCGAATCTTACCTCT
66 AAAAGATTAAAGCCACAGCAGCGAATCTTACCTCT
** * * *
44040387 CAGGCGGTGCAGTGGAACAGATTAAAACCACATCGGTGAATCTTGCCTCCCCT-ACATTAC-AGT
1 CAGGCGGTGCAGTAAAAAAGATTAAAACCACAACGGTGAATATTGCCT-CCCTGACATTACGA-T
44040450 TAAAAAGATTAAAGCCACA
64 TAAAAAGATTAAAGCCACA
44040469 TCGGTGAATC
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
99 1 0.01
100 67 0.93
101 4 0.06
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (100 bp):
CAGGCGGTGCAGTAAAAAAGATTAAAACCACAACGGTGAATATTGCCTCCCTGACATTACGATTA
AAAAGATTAAAGCCACAGCAGCGAATCTTACCTCT
Found at i:44040502 original size:25 final size:25
Alignment explanation
Indices: 44040456--44040505 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
44040446 CAGTTAAAAA
* * *
44040456 GATTAAAGCCACATCGGTGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
*
44040481 GATTAAAGCTACAACAGCGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
44040506 ACTCCCCAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (25 bp):
GATTAAAGCCACAACAGCGAATCTT
Found at i:44040628 original size:44 final size:42
Alignment explanation
Indices: 44040573--44041329 Score: 455
Period size: 44 Copynumber: 17.7 Consensus size: 42
44040563 CCCAAAATCC
* *
44040573 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGA-TAAAA-CACAGATCT
* * * *
44040617 TATCTCTCTGAAGTTGCAGTAGAGCAGGTCACATC-CAG-TCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGAT-AAAACACAGATCT
* * * *
44040658 TATCTCCCTGAA-TTGCAGTGGAGCAGACGAAAGAAATCA-ATCC
1 TATCTCTCTGAAGTTGCAGTGGAGCAGA-TAAA-ACA-CAGATCT
*
44040701 TATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGA-TAAAA-CACAGATCT
* * * * * *
44040745 TATCTCTCTAAAGTTGCTGTAGAGCAGATCACATACAG-TCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATAAAACACAGATCT
* * * *
44040786 TATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAATCA-ATCC
1 TATCTCTCTGAAGTTGCAGTGGAGCAGA-TAAA-ACA-CAGATCT
* *
44040830 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGA-TAAAA-CACAGATCT
* * * * * *
44040874 TATCTCTCTAAAGTTGCAATAGAGCAGGTCACATC-CAG-TCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGAT-AAAACACAGATCT
* * * * * *
44040915 TATTTCCCTGAAGTTGTAGTGGAGCAGACAACAGAAATCA-ATCC
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATAA-A-ACA-CAGATCT
* ** * *
44040959 TATCTCCCTGAAGTTGCAAAGGAGCGGATTAAAACCCTAGATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGA-TAAAACAC-AGATCT
* * * * * *
44041003 TATCTCTCTAAAGTTGCAATAGAGCAGATCACATACAG-TCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATAAAACACAGATCT
* * * *
44041044 TATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAATCA-ATCC
1 TATCTCTCTGAAGTTGCAGTGGAGCAGA-TAAA-ACA-CAGATCT
* * * *
44041088 TATCTCTCTGAAGTTGCTGAGGAGCGGATTAAAACCCTAGATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGA-TAAAACAC-AGATCT
* * *
44041132 TATCTCTCTGAAGTTGCAGTAGAGCAGATCACATC-CAG-TCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGAT-AAAACACAGATCT
* * * * * * *
44041173 TATCCCCCAGAAGTTGCAGTGGAGCAAACGAAAGAAATC-GATCC
1 TATCTCTCTGAAGTTGCAGTGGAGCAGA-TAAA-ACA-CAGATCT
* * *
44041217 TATCTCTCTAAAGTTACAGTGGAGCGGATTAAAACCACAGATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGA-TAAAA-CACAGATCT
* * *** **
44041261 TATCTCTCTGAAGTTGTAGTAGAGCAGATCGCATTCAG-TCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATAAAACACAGATCT
* *
44041302 TATCTCCCAGAAGTTGCAGTGGAGCAGA
1 TATCTCTCTGAAGTTGCAGTGGAGCAGA
44041330 CGAAAAAAAT
Statistics
Matches: 537, Mismatches: 138, Indels: 79
0.71 0.18 0.10
Matches are distributed among these distances:
40 16 0.03
41 148 0.28
42 21 0.04
43 47 0.09
44 303 0.56
45 2 0.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (42 bp):
TATCTCTCTGAAGTTGCAGTGGAGCAGATAAAACACAGATCT
Found at i:44040881 original size:129 final size:129
Alignment explanation
Indices: 44040568--44041379 Score: 1263
Period size: 129 Copynumber: 6.3 Consensus size: 129
44040558 GAAGACCCAA
*
44040568 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAGTTG
*
44040633 CAGTAGAGCAGGTCACATCCAGTCTTATCTCCCTGAA-TTGCAGTGGAGCAGACGAAAGAAATC
66 CAGTAGAGCAGATCACATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAATC
*
44040696 AATCCTATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAGTTG
* *
44040761 CTGTAGAGCAGATCACATACAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAATC
66 CAGTAGAGCAGATCACATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAATC
44040825 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAGTTG
* * * *
44040890 CAATAGAGCAGGTCACATCCAGTCTTATTTCCCTGAAGTTGTAGTGGAGCAGAC-AACAGAAATC
66 CAGTAGAGCAGATCACATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAA-AGAAATC
**
44040954 AATCCTATCTCCCTGAAGTTGCAAAGGAGCGGATTAAAACC-CTAGATCTTATCTCTCTAAAGTT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCAC-AGATCTTATCTCTCTAAAGTT
* *
44041018 GCAATAGAGCAGATCACATACAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAATC
65 GCAGTAGAGCAGATCACATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAATC
* * * *
44041083 AATCCTATCTCTCTGAAGTTGCTGAGGAGCGGATTAAAACC-CTAGATCTTATCTCTCTGAAGTT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCAC-AGATCTTATCTCTCTAAAGTT
* * *
44041147 GCAGTAGAGCAGATCACATCCAGTCTTATCCCCCAGAAGTTGCAGTGGAGCAAACGAAAGAAATC
65 GCAGTAGAGCAGATCACATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAATC
* * * * *
44041212 GATCCTATCTCTCTAAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAGTTG
* * * * * *
44041277 TAGTAGAGCAGATCGCATTCAGTCTTATCTCCCAGAAGTTGCAGTGGAGCAGACGAAAAAAATT
66 CAGTAGAGCAGATCACATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAATC
* * *
44041341 AATCCTATCTTCCTGAAGTTGTAGTGAAGCGGATTAAAA
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAA
44041380 TGATGGATCC
Statistics
Matches: 633, Mismatches: 46, Indels: 9
0.92 0.07 0.01
Matches are distributed among these distances:
128 100 0.16
129 530 0.84
130 3 0.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (129 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAGTTG
CAGTAGAGCAGATCACATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAATC
Found at i:44042401 original size:19 final size:19
Alignment explanation
Indices: 44042377--44042423 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
44042367 GTGATTTCAA
*
44042377 CTTTTATTTCTCTGTTTCT
1 CTTTTATTTCTCAGTTTCT
*
44042396 CTTTTATTTTTCAGTTTCT
1 CTTTTATTTCTCAGTTTCT
44042415 -TTTGTATTT
1 CTTT-TATTT
44042424 ATTTCAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 3 0.12
19 22 0.88
ACGTcount: A:0.09, C:0.15, G:0.06, T:0.70
Consensus pattern (19 bp):
CTTTTATTTCTCAGTTTCT
Found at i:44043179 original size:3 final size:3
Alignment explanation
Indices: 44043173--44043222 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
44043163 CTTTTAATAA
* * * *
44043173 TAT TAT TAT TAT TGT TAT TAT TAT TAT TAA TAT TAT CAT TAT TAT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
44043221 TA
1 TA
44043223 CCCTTATATA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:44043269 original size:24 final size:25
Alignment explanation
Indices: 44043237--44043304 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 25
44043227 TATATATACG
*
44043237 TTTTT-TATATATATACATATA-TT
1 TTTTTATATATATATACACATACTT
*
44043260 TTTTTATATACT-TACACACATACTT
1 TTTTTATATA-TATATACACATACTT
*
44043285 TTTGTAATATATATATACAC
1 TTT-TTATATATATATACAC
44043305 TTACATATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
23 5 0.14
24 12 0.33
25 7 0.19
26 12 0.33
ACGTcount: A:0.35, C:0.12, G:0.01, T:0.51
Consensus pattern (25 bp):
TTTTTATATATATATACACATACTT
Found at i:44043411 original size:39 final size:39
Alignment explanation
Indices: 44043349--44043426 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 39
44043339 TATATGTGTT
* * *
44043349 CTTTATATTTTATGATTCATACATATATCTATATATATA
1 CTTTATATTTTATGATACATACATACATATATATATATA
* ** *
44043388 CTTTTTATTTTATGATAGTTACATACATATATATGTATA
1 CTTTATATTTTATGATACATACATACATATATATATATA
44043427 TGCTTACTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.51
Consensus pattern (39 bp):
CTTTATATTTTATGATACATACATACATATATATATATA
Found at i:44044013 original size:111 final size:111
Alignment explanation
Indices: 44043722--44044270 Score: 888
Period size: 110 Copynumber: 5.0 Consensus size: 111
44043712 TATCAAAAAC
* ** *
44043722 AAAATTTTTAAAATAAGACAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTATCCTAAGGTGTT
1 AAAATTTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
44043787 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTA
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTA
* * *
44043833 AAAA-TTTTCAAATAAGGCAATGTTTTGCATTTGGGAAATTCGAGAAAATGTGCCCTAAGGTGCT
1 AAAATTTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
44043897 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTA
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTA
* *
44043943 AAAATTTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAGAACGTGCCCTAAAGTGCT
1 AAAATTTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
*
44044008 GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAA
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT-A
** *
44044055 AAAATTTTCGAAATAAGGCAATGTTTTGCATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
1 AAAATTTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
**
44044120 GGGTGTCGATTTTTCTTGTTCAACCAAATGGCTAAATATCCTTTT-
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTA
*
44044165 AAAATTTTTAAAATAAGGCAATGTTTTGCGTTT-GAAAATTCGAGAAAACGTGCCCTAAGGTGCT
1 AAAATTTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
* * * *
44044229 GGGTGTCGATTTTTCTCATTTAACCGAATAGCCAAATATCCT
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCT
44044271 CTTGAATTTC
Statistics
Matches: 407, Mismatches: 29, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
109 66 0.16
110 133 0.33
111 103 0.25
112 105 0.26
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.34
Consensus pattern (111 bp):
AAAATTTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTA
Found at i:44044206 original size:221 final size:221
Alignment explanation
Indices: 44043722--44044270 Score: 931
Period size: 221 Copynumber: 2.5 Consensus size: 221
44043712 TATCAAAAAC
* ** *
44043722 AAAATTTTTAAAATAAGACAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTATCCTAAGGTGTT
1 AAAATTTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
44043787 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAATTTTCAAATAAGGCA
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAATTTTCAAATAAGGCA
*
44043852 ATGTTTTGCATTTGGGAAATTCGAGAAAATGTGCCCTAAGGTGCTGGGTGTCGATTTTTCTCATT
131 ATGTTTTGCATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCTCATT
44043917 CAACCAAATGGCTAAATATCCTTTTA
196 CAACCAAATGGCTAAATATCCTTTTA
* *
44043943 AAAATTTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAGAACGTGCCCTAAAGTGCT
1 AAAATTTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
*
44044008 GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAAAAAATTTTCGAAATAAGG
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT-AAAAATTTTC-AAATAAGG
**
44044073 CAATGTTTTGCATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCTTG
129 CAATGTTTTGCATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCTCA
44044138 TTCAACCAAATGGCTAAATATCCTTTT-
194 TTCAACCAAATGGCTAAATATCCTTTTA
*
44044165 AAAATTTTTAAAATAAGGCAATGTTTTGCGTTT-GAAAATTCGAGAAAACGTGCCCTAAGGTGCT
1 AAAATTTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
* * * *
44044229 GGGTGTCGATTTTTCTCATTTAACCGAATAGCCAAATATCCT
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCT
44044271 CTTGAATTTC
Statistics
Matches: 308, Mismatches: 18, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
221 168 0.55
222 43 0.14
223 97 0.31
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.34
Consensus pattern (221 bp):
AAAATTTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAATTTTCAAATAAGGCA
ATGTTTTGCATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCTCATT
CAACCAAATGGCTAAATATCCTTTTA
Found at i:44046148 original size:15 final size:14
Alignment explanation
Indices: 44046115--44046165 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
44046105 AATTTATAAG
**
44046115 AAAAGAATAAAATCA
1 AAAA-AATAAAATTT
44046130 AAAAGAATAAAATTT
1 AAAA-AATAAAATTT
44046145 AAAAAAT--AATTT
1 AAAAAATAAAATTT
44046157 AAAAAATAA
1 AAAAAATAA
44046166 TTTAGGATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 12 0.38
14 3 0.09
15 17 0.53
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.22
Consensus pattern (14 bp):
AAAAAATAAAATTT
Found at i:44046157 original size:12 final size:12
Alignment explanation
Indices: 44046140--44046169 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
44046130 AAAAGAATAA
44046140 AATTTAAAAAAT
1 AATTTAAAAAAT
44046152 AATTTAAAAAAT
1 AATTTAAAAAAT
44046164 AATTTA
1 AATTTA
44046170 GGATTGAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AATTTAAAAAAT
Found at i:44048300 original size:29 final size:29
Alignment explanation
Indices: 44048262--44048321 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
44048252 TGAATGTTTA
44048262 TTTTTAATAGAAATTAAGGAAAACATTAT
1 TTTTTAATAGAAATTAAGGAAAACATTAT
44048291 TTTTTAATAGAAATTAAGGAAAACATTAT
1 TTTTTAATAGAAATTAAGGAAAACATTAT
44048320 TT
1 TT
44048322 CAATGTAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (29 bp):
TTTTTAATAGAAATTAAGGAAAACATTAT
Found at i:44053311 original size:18 final size:18
Alignment explanation
Indices: 44053274--44053307 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
44053264 AATAAAGGGG
44053274 AAGAAGAAAAAGAAAATA
1 AAGAAGAAAAAGAAAATA
*
44053292 AAGAAGTAAAA-AAAAT
1 AAGAAGAAAAAGAAAAT
44053308 TAAATTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (18 bp):
AAGAAGAAAAAGAAAATA
Found at i:44055321 original size:17 final size:17
Alignment explanation
Indices: 44055299--44055340 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
44055289 GGCCTGAGGT
* *
44055299 GGCCCAAACCCAACTGA
1 GGCCCAAACCAAACAGA
44055316 GGCCCAAACCAAACAGA
1 GGCCCAAACCAAACAGA
*
44055333 AGCCCAAA
1 GGCCCAAA
44055341 GCAGATTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.43, C:0.38, G:0.17, T:0.02
Consensus pattern (17 bp):
GGCCCAAACCAAACAGA
Found at i:44056704 original size:22 final size:21
Alignment explanation
Indices: 44056676--44056735 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
44056666 CTTCGTAATT
44056676 TCATTTATTATAT-TTATATTG
1 TCATTTATTATATATTATA-TG
44056697 CTCATTTATTTGATATATTATATG
1 -TCATTTA-TT-ATATATTATATG
*
44056721 TCA-TTATTATTTATT
1 TCATTTATTATATATT
44056736 TTTCATATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 6 0.18
21 2 0.06
22 10 0.29
23 5 0.15
24 6 0.18
25 5 0.15
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (21 bp):
TCATTTATTATATATTATATG
Found at i:44057095 original size:97 final size:97
Alignment explanation
Indices: 44056963--44057157 Score: 338
Period size: 97 Copynumber: 2.0 Consensus size: 97
44056953 TTAAAAATAA
* * * *
44056963 TAAAGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCT
1 TAAAGAAATATTCCAAATTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCT
44057028 TAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TAAATCTTGGATAAGTGGATGTTCTTTTAAAG
44057060 TAAAGGAAATATT-CAAATTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAA-GAAATATTCCAAATTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
44057124 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
65 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
44057157 T
1 T
44057158 TTTATTGTAC
Statistics
Matches: 93, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
97 85 0.91
98 8 0.09
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.37
Consensus pattern (97 bp):
TAAAGAAATATTCCAAATTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCT
TAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:44060252 original size:19 final size:20
Alignment explanation
Indices: 44060228--44060265 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
44060218 TCTTATTTGT
44060228 AATTT-ATTT-TATGTAAAGG
1 AATTTAATTTCTA-GTAAAGG
44060247 AATTTAATTTCTAGTAAAG
1 AATTTAATTTCTAGTAAAG
44060266 TTTTCTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 10 0.59
21 2 0.12
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.45
Consensus pattern (20 bp):
AATTTAATTTCTAGTAAAGG
Found at i:44069550 original size:44 final size:43
Alignment explanation
Indices: 44069486--44070471 Score: 399
Period size: 44 Copynumber: 22.7 Consensus size: 43
44069476 AAATTGAGTT
44069486 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-ATAATC
* * *
44069530 CTATCTCCCTGAACTTGCAGTGGAG-AGAATTAAAACC-TCAGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAG-ATTAAAGCCAT-A-ATC
* * *** * *
44069574 TTATCTCTCTGAAGTTGCAG-AGAGCAGATCGCA-TC-TAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCATAATC
* * * *
44069614 ATATCTCCCTGAGGTTGCAGTGGAGCAGAATATGTAAG-CA-AGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAG-AT-T-AAAGCCATAATC
* *
44069658 TTATC-CTCCTGAAGTTGCAGT-GAGACAGACTGAAGATGTCA-AATC
1 TTATCTC-CCTGAAGTTGCAGTGGAG-CAGA-TTAA-A-GCCATAATC
*
44069703 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-ATAATC
* * * ** * *
44069747 CTATCTCCCTAAAGTTACAGTGGAGTGGATTAAAATCTCA-GATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGC-CATAATC
* * * ** *** * *
44069791 TTATCTCTCTGAAGATGCAG-AGAATAGATCGCA-TC-TAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCATAATC
* * *
44069831 TTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGCAAAGCAAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC-CA-TAA-TC
* * *
44069876 TTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGGTGGCA-AATC
1 TTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA--AGCCATAATC
* * *
44069921 TTATCTCCCTGAAGTTGTAGTAGAGCAGATTAAAGCCGACAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-ATAATC
* * * *
44069965 CTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTAGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCATA-ATC
* * * *** * *
44070009 TTATCTCTCTGAAGTTGCAG-AGAACAGATCGCATCC--AGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCATAATC
* * * *
44070049 ATATCTCCCTGAGGTTGCAGTGGAGCCA-AATACGTAAG-CA-AGTC
1 TTATCTCCCTGAAGTTGCAGTGGAG-CAGATTA---AAGCCATAATC
* * *
44070093 TTATC-CTCCTGAAGTTACAGT-GAGGCAGACTGAAGATGGCA-AATC
1 TTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-GCCATAATC
*
44070138 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-ATAATC
* * * * ** * *
44070182 CTATTTCCGTGAAGTTACAGTGGAGTGGATTAAAATCTCA-GATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGC-CATAATC
* * * * *** * *
44070226 TTATCTCTCTGAAGATGCAG-AGAGTAGATCGCA-TC-TAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCATAATC
* * * *
44070266 TTATCTCCCTGAGGTTGCAGTGGAGCAGACT-AAGCAAAGCAAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC-CA-TAA-TC
* * * *
44070311 TTATC-CTCCTGAAGTTGCAGT-AAGGCAGACTGAAGGTGGCA-AATC
1 TTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA--AGCCATAATC
* * * *
44070356 TTATCTCCCTGAAGTTGTAGTAGAGCAGA-TAAAGTCGACAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CCATAATC
* * * * *
44070399 CTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTCTGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-ATAATC
*
44070443 TTATC-CCTCTGAAGTTGTAGTGGAGCAGA
1 TTATCTCC-CTGAAGTTGCAGTGGAGCAGA
44070472 CTGGTGGATC
Statistics
Matches: 700, Mismatches: 163, Indels: 158
0.69 0.16 0.15
Matches are distributed among these distances:
40 81 0.12
41 23 0.03
42 18 0.03
43 84 0.12
44 302 0.43
45 168 0.24
46 18 0.03
47 2 0.00
48 2 0.00
49 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (43 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCATAATC
Found at i:44070197 original size:217 final size:218
Alignment explanation
Indices: 44069486--44070459 Score: 1515
Period size: 217 Copynumber: 4.5 Consensus size: 218
44069476 AAATTGAGTT
* * *
44069486 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAACTTGCAGT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGT
* * *
44069551 GGAGAGAATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCAT
66 GGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAACAGATCGCATCTAGTCAT
* *
44069616 ATCTCCCTGAGGTTGCAGTGGAGCAGAATATG-TAAGCAAGTCTTATCCTCCTGAAGTTGCAGTG
131 ATCTCCCTGAGGTTGCAGTGGAGCAGAATAAGCAAAGCAAGTCTTATCCTCCTGAAGTTGCAGTG
* *
44069680 AGACAGACTGAAGATGTCAAATC
196 AGGCAGACTGAAGATGGCAAATC
* *
44069703 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATCCTATCTCCCTAAAGTTACAGT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGT
* * * * *
44069768 GGAGTGGATTAAAATCTCAGATCTTATCTCTCTGAAGATGCAGAGAATAGATCGCATCTAGTCTT
66 GGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAACAGATCGCATCTAGTCAT
* *
44069833 ATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAAGCAAGTCTTATCCTCCTGAAGTTGCAGTG
131 ATCTCCCTGAGGTTGCAGTGGAGCAGAATAAGCAAAGCAAGTCTTATCCTCCTGAAGTTGCAGTG
*
44069898 AGGCAGACTGAAGGTGGCAAATC
196 AGGCAGACTGAAGATGGCAAATC
* *
44069921 TTATCTCCCTGAAGTTGTAGTAGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGT
* *
44069986 GGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGCAGAGAACAGATCGCATCCAGTCAT
66 GGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAACAGATCGCATCTAGTCAT
* * *
44070051 ATCTCCCTGAGGTTGCAGTGGAGCCA-AATACG-TAAGCAAGTCTTATCCTCCTGAAGTTACAGT
131 ATCTCCCTGAGGTTGCAGTGGAG-CAGAATAAGCAAAGCAAGTCTTATCCTCCTGAAGTTGCAGT
44070114 GAGGCAGACTGAAGATGGCAAATC
195 GAGGCAGACTGAAGATGGCAAATC
* * *
44070138 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATCCTATTTCCGTGAAGTTACAGT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGT
* * * ** *
44070203 GGAGTGGATTAAAATCTCAGATCTTATCTCTCTGAAGATGCAGAGAGTAGATCGCATCTAGTCTT
66 GGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAACAGATCGCATCTAGTCAT
* *
44070268 ATCTCCCTGAGGTTGCAGTGGAGCAGACTAAGCAAAGCAAGTCTTATCCTCCTGAAGTTGCAGTA
131 ATCTCCCTGAGGTTGCAGTGGAGCAGAATAAGCAAAGCAAGTCTTATCCTCCTGAAGTTGCAGTG
*
44070333 AGGCAGACTGAAGGTGGCAAATC
196 AGGCAGACTGAAGATGGCAAATC
* * *
44070356 TTATCTCCCTGAAGTTGTAGTAGAGCAGA-TAAAGTCGACAATCCTATCTCCCTGAAGTTGCAGT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGT
* *
44070420 GGAGCGGATTAAAACCTCTGATCTTATCCCTCTGAAGTTG
66 GGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTG
44070460 TAGTGGAGCA
Statistics
Matches: 687, Mismatches: 66, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
216 2 0.00
217 409 0.60
218 274 0.40
219 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (218 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGT
GGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAACAGATCGCATCTAGTCAT
ATCTCCCTGAGGTTGCAGTGGAGCAGAATAAGCAAAGCAAGTCTTATCCTCCTGAAGTTGCAGTG
AGGCAGACTGAAGATGGCAAATC
Found at i:44070296 original size:435 final size:435
Alignment explanation
Indices: 44069486--44070459 Score: 1711
Period size: 435 Copynumber: 2.2 Consensus size: 435
44069476 AAATTGAGTT
* * * * *
44069486 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAACTTGCAGT
1 TTATCTCCCTGAAGTTGTAGTAGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGT
* * * * *
44069551 GGAGAGAATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCAT
66 GGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGCAGAGAACAGATCGCATCCAGTCAT
* *
44069616 ATCTCCCTGAGGTTGCAGTGGAGCAGAATATGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGA
131 ATCTCCCTGAGGTTGCAGTGGAGCAGAATACGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTGA
*
44069681 GACAGACTGAAGATGTCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAAT
196 GACAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAAT
44069746 CCTATCTCCCTAAAGTTACAGTGGAGTGGATTAAAATCTCAGATCTTATCTCTCTGAAGATGCAG
261 CCTATCTCCCTAAAGTTACAGTGGAGTGGATTAAAATCTCAGATCTTATCTCTCTGAAGATGCAG
44069811 AGAATAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAAGCAAGTC
326 AGAATAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAAGCAAGTC
*
44069876 TTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGGTGGCAAATC
391 TTATCCTCCTGAAGTTGCAGTAAGGCAGACTGAAGGTGGCAAATC
44069921 TTATCTCCCTGAAGTTGTAGTAGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGT
1 TTATCTCCCTGAAGTTGTAGTAGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGT
44069986 GGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGCAGAGAACAGATCGCATCCAGTCAT
66 GGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGCAGAGAACAGATCGCATCCAGTCAT
44070051 ATCTCCCTGAGGTTGCAGTGGAGCCA-AATACGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTG
131 ATCTCCCTGAGGTTGCAGTGGAG-CAGAATACGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTG
*
44070115 AGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAA
195 AGACAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAA
* * *
44070180 TCCTATTTCCGTGAAGTTACAGTGGAGTGGATTAAAATCTCAGATCTTATCTCTCTGAAGATGCA
260 TCCTATCTCCCTAAAGTTACAGTGGAGTGGATTAAAATCTCAGATCTTATCTCTCTGAAGATGCA
* *
44070245 GAGAGTAGATCGCATCTAGTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTAAGCAAAGCAAGT
325 GAGAATAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAAGCAAGT
44070310 CTTATCCTCCTGAAGTTGCAGTAAGGCAGACTGAAGGTGGCAAATC
390 CTTATCCTCCTGAAGTTGCAGTAAGGCAGACTGAAGGTGGCAAATC
*
44070356 TTATCTCCCTGAAGTTGTAGTAGAGCAGA-TAAAGTCGACAATCCTATCTCCCTGAAGTTGCAGT
1 TTATCTCCCTGAAGTTGTAGTAGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGT
*
44070420 GGAGCGGATTAAAACCTCT-GATCTTATCCCTCTGAAGTTG
66 GGAGCGGATTAAAACCT-TAGATCTTATCTCTCTGAAGTTG
44070460 TAGTGGAGCA
Statistics
Matches: 515, Mismatches: 22, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
434 71 0.14
435 442 0.86
436 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (435 bp):
TTATCTCCCTGAAGTTGTAGTAGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGT
GGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGCAGAGAACAGATCGCATCCAGTCAT
ATCTCCCTGAGGTTGCAGTGGAGCAGAATACGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTGA
GACAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAAT
CCTATCTCCCTAAAGTTACAGTGGAGTGGATTAAAATCTCAGATCTTATCTCTCTGAAGATGCAG
AGAATAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAAGCAAGTC
TTATCCTCCTGAAGTTGCAGTAAGGCAGACTGAAGGTGGCAAATC
Found at i:44070750 original size:17 final size:17
Alignment explanation
Indices: 44070728--44070769 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
44070718 GGCCCGAGAT
* *
44070728 GGCCCAAACCCAACTGA
1 GGCCCAAACCAAACAGA
44070745 GGCCCAAACCAAACAGA
1 GGCCCAAACCAAACAGA
*
44070762 AGCCCAAA
1 GGCCCAAA
44070770 GCAGATTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.43, C:0.38, G:0.17, T:0.02
Consensus pattern (17 bp):
GGCCCAAACCAAACAGA
Found at i:44072144 original size:22 final size:21
Alignment explanation
Indices: 44072116--44072176 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
44072106 CTTCGTAATT
44072116 TCATTTATTATAT-TTATATTG
1 TCATTTATTATATATTATA-TG
44072137 CTCATTTATTTGATATATTATATG
1 -TCATTTA-TT-ATATATTATATG
* *
44072161 TCATTCATTATTTATT
1 TCATTTATTATATATT
44072177 TGTTCATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 6 0.18
22 9 0.26
23 8 0.24
24 6 0.18
25 5 0.15
ACGTcount: A:0.28, C:0.08, G:0.05, T:0.59
Consensus pattern (21 bp):
TCATTTATTATATATTATATG
Found at i:44072537 original size:98 final size:98
Alignment explanation
Indices: 44072407--44072603 Score: 340
Period size: 98 Copynumber: 2.0 Consensus size: 98
44072397 TAAAAAATAA
* * * *
44072407 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGAAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCAAATTTGGGATTCTAAAGAAATCGTGCCCTAACGTATTGGGTGTGATTTC
44072472 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
* *
44072505 TAAAGGAAATATTTCAAATTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCAAATTTGGGATTCTAAAGAAATCGTGCCCTAACGTATTGGGTGTGATTTC
44072570 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
44072603 T
1 T
44072604 TTTATTGTAC
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCAAATTTGGGATTCTAAAGAAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:44078633 original size:24 final size:24
Alignment explanation
Indices: 44078603--44078661 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
44078593 ACATATCTAA
44078603 AATAATATTAA-TTTTTGCTTCAAT
1 AATAATATTAACTTTTT-CTTCAAT
*
44078627 AATAATATTAACTTTTTTTTCAAT
1 AATAATATTAACTTTTTCTTCAAT
44078651 AATAATATTAA
1 AATAATATTAA
44078662 ATTTCTGATT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
24 28 0.85
25 5 0.15
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (24 bp):
AATAATATTAACTTTTTCTTCAAT
Found at i:44082097 original size:14 final size:14
Alignment explanation
Indices: 44082078--44082104 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44082068 ACTATATTCC
44082078 CACTTTTACTGGTT
1 CACTTTTACTGGTT
44082092 CACTTTTACTGGT
1 CACTTTTACTGGT
44082105 CCATGATTAT
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:0.15, C:0.22, G:0.15, T:0.48
Consensus pattern (14 bp):
CACTTTTACTGGTT
Found at i:44084932 original size:64 final size:64
Alignment explanation
Indices: 44084823--44084963 Score: 264
Period size: 64 Copynumber: 2.2 Consensus size: 64
44084813 GACTAATGGC
*
44084823 ACGCTCTATAATTGACACATGTGCACTAAAATGAGTTAATTTATTAATCCTAAACATATTATAT
1 ACGCTCTATAATTGACACATGTGCACTAAAATGAGTTAATGTATTAATCCTAAACATATTATAT
*
44084887 ACGCTCTATAATTGACACATGTGCACTAAAATGAGTTGATGTATTAATCCTAAACATATTATAT
1 ACGCTCTATAATTGACACATGTGCACTAAAATGAGTTAATGTATTAATCCTAAACATATTATAT
44084951 ACGCTCTATAATT
1 ACGCTCTATAATT
44084964 AGTCAAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 75 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (64 bp):
ACGCTCTATAATTGACACATGTGCACTAAAATGAGTTAATGTATTAATCCTAAACATATTATAT
Found at i:44093055 original size:16 final size:16
Alignment explanation
Indices: 44093036--44093078 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 16
44093026 TAAAAATAAT
*
44093036 TTAAGATATAAATTTA
1 TTAATATATAAATTTA
44093052 TTAATATATATAAATTTA
1 TT-A-ATATATAAATTTA
44093070 TTAATATAT
1 TTAATATAT
44093079 GTAAAAATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 8 0.33
17 2 0.08
18 14 0.58
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
TTAATATATAAATTTA
Found at i:44093062 original size:18 final size:18
Alignment explanation
Indices: 44093041--44093083 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
44093031 ATAATTTAAG
44093041 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
44093059 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
*
44093077 ATGTAAA
1 ATATAAA
44093084 AATAGCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
ATATAAATTTATTAATAT
Found at i:44108123 original size:56 final size:56
Alignment explanation
Indices: 44108037--44108149 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
44108027 TTGGTGTGGA
44108037 TGGTGTGGTTGTCCTAAGGAGTGATCCACGAAAGACTCGTTTATTCTCGTAGGTTT
1 TGGTGTGGTTGTCCTAAGGAGTGATCCACGAAAGACTCGTTTATTCTCGTAGGTTT
44108093 TGGTGTGGTTGTCCTAAGGAGTGATCCACGAAAGACTCGTTTATTCTCGTAGGTTT
1 TGGTGTGGTTGTCCTAAGGAGTGATCCACGAAAGACTCGTTTATTCTCGTAGGTTT
44108149 T
1 T
44108150 CTTTCACTTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.19, C:0.16, G:0.28, T:0.36
Consensus pattern (56 bp):
TGGTGTGGTTGTCCTAAGGAGTGATCCACGAAAGACTCGTTTATTCTCGTAGGTTT
Found at i:44110130 original size:162 final size:162
Alignment explanation
Indices: 44109862--44110175 Score: 583
Period size: 162 Copynumber: 1.9 Consensus size: 162
44109852 GGAGGTTGAA
44109862 TTTTGTGACTGTAAAACCATGAAAGAAGAGATGATTCGATTCTTAAGAGCCTGGAGCCTTCAAAC
1 TTTTGTGACTGTAAAACCATGAAAGAAGAGATGATTCGATTCTTAAGAGCCTGGAGCCTTCAAAC
* * * *
44109927 CCCAAACTTTACCTATGATTTCTAGTTTCCCAATTGGTGTCATCTTAGCTATAGTTCCTTGAGTT
66 CCCAAACTTTACCTATGATTTCCAGTTTCCCAATCGGTGTCATCTTAACAATAGTTCCTTGAGTT
44109992 TCATCTTGCCTCTCGTCTTATTGGGGGCTGAC
131 TCATCTTGCCTCTCGTCTTATTGGGGGCTGAC
*
44110024 TTTTGTGACTGTAAAACCATGAAAGAAGAGATGATTTGATTCTTAAGAGCCTGGAGCCTTCAAAC
1 TTTTGTGACTGTAAAACCATGAAAGAAGAGATGATTCGATTCTTAAGAGCCTGGAGCCTTCAAAC
44110089 CCCAAACTTTACCTATGATTTCCAGTTTCCCAATCGGTGTCATCTTAACAATAGTTCCTTGAGTT
66 CCCAAACTTTACCTATGATTTCCAGTTTCCCAATCGGTGTCATCTTAACAATAGTTCCTTGAGTT
44110154 TCATCTTGCCTCTCGTCTTATT
131 TCATCTTGCCTCTCGTCTTATT
44110176 AGAGGCGGGA
Statistics
Matches: 147, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
162 147 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (162 bp):
TTTTGTGACTGTAAAACCATGAAAGAAGAGATGATTCGATTCTTAAGAGCCTGGAGCCTTCAAAC
CCCAAACTTTACCTATGATTTCCAGTTTCCCAATCGGTGTCATCTTAACAATAGTTCCTTGAGTT
TCATCTTGCCTCTCGTCTTATTGGGGGCTGAC
Found at i:44115737 original size:16 final size:16
Alignment explanation
Indices: 44115716--44115785 Score: 113
Period size: 16 Copynumber: 4.4 Consensus size: 16
44115706 TTTGGTTCGC
*
44115716 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
44115732 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
44115748 TGTAATGGATTAGAGG
1 TGTAATGGATTAGAGG
*
44115764 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
44115780 TGTAAT
1 TGTAAT
44115786 AGCAAATCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.30, C:0.00, G:0.36, T:0.34
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:44115870 original size:39 final size:40
Alignment explanation
Indices: 44115767--44115873 Score: 110
Period size: 44 Copynumber: 2.6 Consensus size: 40
44115757 TTAGAGGTGT
44115767 AATGGAATAGAGGTGTAATAGCAAATCAACTATTTGGTTG
1 AATGGAATAGAGGTGTAATAGCAAATCAACTATTTGGTTG
* * * *
44115807 AATGTAATAGAATAGAGGCGTAATAG-TAATCTTA-TGTTTGGTTG
1 AATG-----GAATAGAGGTGTAATAGCAAATC-AACTATTTGGTTG
44115851 AATGGAATAGAGGTGTAATAGCA
1 AATGGAATAGAGGTGTAATAGCA
44115874 TAATGAAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
39 16 0.30
40 4 0.07
44 17 0.31
45 17 0.31
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (40 bp):
AATGGAATAGAGGTGTAATAGCAAATCAACTATTTGGTTG
Found at i:44116040 original size:18 final size:17
Alignment explanation
Indices: 44116019--44116053 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
44116009 TTATTATTAA
*
44116019 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
44116037 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
44116054 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:44116107 original size:157 final size:157
Alignment explanation
Indices: 44115906--44116222 Score: 589
Period size: 157 Copynumber: 2.0 Consensus size: 157
44115896 TAGAATACCC
*
44115906 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
*
44115971 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
44116036 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
*
44116063 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* *
44116128 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATCTTTTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
44116193 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
44116220 TTA
1 TTA
44116223 ATATTCTTAT
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:44116527 original size:75 final size:75
Alignment explanation
Indices: 44116404--44116554 Score: 302
Period size: 75 Copynumber: 2.0 Consensus size: 75
44116394 ATCCAATGGA
44116404 AGCAAACTAGACTAAAAGCAGATAATAGCCAAATGTTTCCATTTTTTCTTTTTCATGTTTTTAAG
1 AGCAAACTAGACTAAAAGCAGATAATAGCCAAATGTTTCCATTTTTTCTTTTTCATGTTTTTAAG
44116469 ATACAGGCAT
66 ATACAGGCAT
44116479 AGCAAACTAGACTAAAAGCAGATAATAGCCAAATGTTTCCATTTTTTCTTTTTCATGTTTTTAAG
1 AGCAAACTAGACTAAAAGCAGATAATAGCCAAATGTTTCCATTTTTTCTTTTTCATGTTTTTAAG
44116544 ATACAGGCAT
66 ATACAGGCAT
44116554 A
1 A
44116555 CATTGAAAGC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (75 bp):
AGCAAACTAGACTAAAAGCAGATAATAGCCAAATGTTTCCATTTTTTCTTTTTCATGTTTTTAAG
ATACAGGCAT
Found at i:44118178 original size:15 final size:15
Alignment explanation
Indices: 44118158--44118273 Score: 53
Period size: 15 Copynumber: 7.5 Consensus size: 15
44118148 AACATGGTAC
44118158 AGAAACAGAAAATAG
1 AGAAACAGAAAATAG
*
44118173 AGAAACA-AAAA-ACC
1 AGAAACAGAAAATA-G
**
44118187 A-CTACAGAAAATAG
1 AGAAACAGAAAATAG
* *
44118201 AGGAACA-AAACATGGTAC
1 AGAAACAGAAA-A---TAG
44118219 AGAAACAGAAAATAG
1 AGAAACAGAAAATAG
*
44118234 AGAAACA-AAACATGGTAC
1 AGAAACAGAAA-A---TAG
*
44118252 AAAAACAGAAAATAG
1 AGAAACAGAAAATAG
44118267 AGAAACA
1 AGAAACA
44118274 TAAAGCAGAC
Statistics
Matches: 74, Mismatches: 13, Indels: 28
0.64 0.11 0.24
Matches are distributed among these distances:
13 4 0.05
14 16 0.22
15 30 0.41
18 18 0.24
19 6 0.08
ACGTcount: A:0.63, C:0.13, G:0.16, T:0.08
Consensus pattern (15 bp):
AGAAACAGAAAATAG
Found at i:44118180 original size:33 final size:33
Alignment explanation
Indices: 44118138--44118273 Score: 176
Period size: 33 Copynumber: 4.3 Consensus size: 33
44118128 AAAAATGGCA
*
44118138 AGAGGAACAAAACATGGTACAGAAACAGAAAAT
1 AGAGAAACAAAACATGGTACAGAAACAGAAAAT
**
44118171 AGAGAAACAAAA-A----ACCA-CTACAGAAAAT
1 AGAGAAACAAAACATGGTA-CAGAAACAGAAAAT
*
44118199 AGAGGAACAAAACATGGTACAGAAACAGAAAAT
1 AGAGAAACAAAACATGGTACAGAAACAGAAAAT
*
44118232 AGAGAAACAAAACATGGTACAAAAACAGAAAAT
1 AGAGAAACAAAACATGGTACAGAAACAGAAAAT
44118265 AGAGAAACA
1 AGAGAAACA
44118274 TAAAGCAGAC
Statistics
Matches: 88, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
28 21 0.24
29 3 0.03
32 3 0.03
33 61 0.69
ACGTcount: A:0.61, C:0.13, G:0.18, T:0.08
Consensus pattern (33 bp):
AGAGAAACAAAACATGGTACAGAAACAGAAAAT
Found at i:44119212 original size:37 final size:38
Alignment explanation
Indices: 44119137--44119212 Score: 93
Period size: 37 Copynumber: 2.0 Consensus size: 38
44119127 ATAATATTAT
* *
44119137 AATTTTAGTATTAAAAATATATTAAATTATTTATATTTAG
1 AATTTTAG-ATTAAAAATATA-TAAATTATTAAAATTTAG
44119177 AATTTTA-ATTAAAACATATA-AAATTATTAAAATTTA
1 AATTTTAGATTAAAA-ATATATAAATTATTAAAATTTA
44119213 AGTTAAAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
37 14 0.42
38 7 0.21
39 5 0.15
40 7 0.21
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (38 bp):
AATTTTAGATTAAAAATATATAAATTATTAAAATTTAG
Found at i:44119344 original size:10 final size:10
Alignment explanation
Indices: 44119300--44119352 Score: 52
Period size: 10 Copynumber: 5.0 Consensus size: 10
44119290 ATCAACTATT
44119300 TTTTATTCAA
1 TTTTATTCAA
**
44119310 TTTTAAACAAA
1 TTTTATTC-AA
*
44119321 TTATTTTGTCAA
1 TT-TTAT-TCAA
44119333 TTTTATTCAA
1 TTTTATTCAA
44119343 TTTTATTCAA
1 TTTTATTCAA
44119353 AACATTTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
10 20 0.59
11 7 0.21
12 6 0.18
13 1 0.03
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (10 bp):
TTTTATTCAA
Found at i:44121215 original size:9 final size:9
Alignment explanation
Indices: 44121201--44121242 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
44121191 ACAGATCAAA
44121201 AATTAACCG
1 AATTAACCG
*
44121210 AATTAACCA
1 AATTAACCG
**
44121219 AATTAATTG
1 AATTAACCG
44121228 AATTAACCG
1 AATTAACCG
44121237 AATTAA
1 AATTAA
44121243 ACAAACAATC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:44121294 original size:45 final size:45
Alignment explanation
Indices: 44121243--44121330 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
44121233 ACCGAATTAA
*
44121243 ACAAACAATCCTACCGTAATACCTACATTAAATGCACATAATTCT
1 ACAAACAATCCTACCATAATACCTACATTAAATGCACATAATTCT
*
44121288 ACAAACAATCCTATCATAATACCTACATTAAATGCACATAATT
1 ACAAACAATCCTACCATAATACCTACATTAAATGCACATAATT
44121331 AATTTACTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.44, C:0.25, G:0.03, T:0.27
Consensus pattern (45 bp):
ACAAACAATCCTACCATAATACCTACATTAAATGCACATAATTCT
Found at i:44130450 original size:30 final size:29
Alignment explanation
Indices: 44130404--44130482 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 29
44130394 AATTATTTAT
* * *
44130404 ATTTAGAATTTTAATTAAAACATATAAAA
1 ATTTAAAATTTAAATTAAAACAGATAAAA
*
44130433 TTATTAAAATTTAAATTAAAAACAGATAAAA
1 AT-TTAAAATTTAAATT-AAAACAGATAAAA
*
44130464 ATTTAAAA-ATAAATTAAAA
1 ATTTAAAATTTAAATTAAAA
44130483 TTTAAACTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
28 4 0.10
29 7 0.17
30 18 0.43
31 13 0.31
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (29 bp):
ATTTAAAATTTAAATTAAAACAGATAAAA
Found at i:44130471 original size:18 final size:18
Alignment explanation
Indices: 44130448--44130488 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
44130438 AAAATTTAAA
*
44130448 TTAAAAACAGATAAAAAT
1 TTAAAAACAAATAAAAAT
* *
44130466 TTAAAAATAAATTAAAAT
1 TTAAAAACAAATAAAAAT
44130484 TTAAA
1 TTAAA
44130489 CTTAAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
TTAAAAACAAATAAAAAT
Found at i:44132149 original size:178 final size:178
Alignment explanation
Indices: 44131850--44132212 Score: 656
Period size: 178 Copynumber: 2.0 Consensus size: 178
44131840 AGCATGGTAG
* *
44131850 TTGGTACTGTTCTGATAGTAAACCAAAACAACAAATTTTAGGTTCCATTCAAGTGCAAATTCTAG
1 TTGGTACCGTTCTGATAGTAAACCAAAACAACAAATTTTAGGTTCCATTCAAGTGCAAATTCCAG
*
44131915 TTGGTACCTGTCGTGCCAATACATATCAGTTAATTTCACCTGTACTAGCCAAAATATGGTGTACC
66 TTGGTACCTGTCGTGCCAATACATATCAGTTAATTTCACCTGTACTAGCCAAAATATGCTGTACC
*
44131980 GGTACCGAAAAATAATTTTAAAATTAAAATTAAATTTTTATTATTTAT
131 GGTACCGAAAAATAATTTTAAAATTAAAATTAAAATTTTATTATTTAT
* * *
44132028 TTGGTACCGTTTTGATAGTAAACCGAAACAACAAATTTTAGGTTCCATTCAAGTGCAAATTCCGG
1 TTGGTACCGTTCTGATAGTAAACCAAAACAACAAATTTTAGGTTCCATTCAAGTGCAAATTCCAG
44132093 TTGGTACCTGTCGTGCCAATACATATCAGTTAATTTCACCTGTACTAGCCAAAATATGCTGTACC
66 TTGGTACCTGTCGTGCCAATACATATCAGTTAATTTCACCTGTACTAGCCAAAATATGCTGTACC
44132158 GGTACCGAAAAATAATTTTAAAATTAAAATTAAAATTTTATTATTTAT
131 GGTACCGAAAAATAATTTTAAAATTAAAATTAAAATTTTATTATTTAT
44132206 TT-GTACC
1 TTGGTACC
44132213 AAAAAATAAT
Statistics
Matches: 178, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
177 5 0.03
178 173 0.97
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (178 bp):
TTGGTACCGTTCTGATAGTAAACCAAAACAACAAATTTTAGGTTCCATTCAAGTGCAAATTCCAG
TTGGTACCTGTCGTGCCAATACATATCAGTTAATTTCACCTGTACTAGCCAAAATATGCTGTACC
GGTACCGAAAAATAATTTTAAAATTAAAATTAAAATTTTATTATTTAT
Found at i:44144301 original size:13 final size:13
Alignment explanation
Indices: 44144268--44144302 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
44144258 TATTTAAATG
* *
44144268 TTATTATCATTTA
1 TTATTATTATTAA
44144281 TTATTATTATTAA
1 TTATTATTATTAA
44144294 TTATTATTA
1 TTATTATTA
44144303 GTTTTATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATTATTATTAA
Found at i:44144484 original size:35 final size:33
Alignment explanation
Indices: 44144411--44144491 Score: 83
Period size: 35 Copynumber: 2.4 Consensus size: 33
44144401 TATACCCATG
* * * *
44144411 TATAT-TTTTATATATGCGTACACATATATGTT
1 TATATATTTTATTTATGCATACACATACATGTC
*
44144443 TCTATATTTTATTTATGCATACCTACATACATGTC
1 TATATATTTTATTTATGCATA-C-ACATACATGTC
*
44144478 TATATATTTCATTT
1 TATATATTTTATTT
44144492 TCATAATGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
32 4 0.10
33 13 0.33
34 1 0.03
35 21 0.54
ACGTcount: A:0.30, C:0.14, G:0.06, T:0.51
Consensus pattern (33 bp):
TATATATTTTATTTATGCATACACATACATGTC
Found at i:44157043 original size:45 final size:45
Alignment explanation
Indices: 44156979--44157256 Score: 366
Period size: 45 Copynumber: 6.2 Consensus size: 45
44156969 CTCAAAGAAC
* * *
44156979 AGATCGAAGATAGCAGATCTTGTCTGCCTGAATTGGCAGCGAAGT
1 AGATCGAAGATAGAAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
44157024 AGATCGAAGATAGAAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
1 AGATCGAAGATAGAAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* * *
44157069 AGATCAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAACGAAGT
1 AGATCGAAGATAGAAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* *
44157114 AGATCAAAGATAGAA-AGTCTTGTCTTCCTGTATTGGCAGCGGAGT
1 AGATCGAAGATAGAAGA-TCTTGTCTTCCTGTATTGGCAGCGAAGT
* *
44157159 AGATCGAAGATAGCAAG-TCTTGTCTTCCTATATTGGTAGCGAAGT
1 AGATCGAAGATAG-AAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* * * *
44157204 AGA-CTGAAGATA-ACAGATCTTGTCTTTCTGTACTGGCAACGAAGC
1 AGATC-GAAGATAGA-AGATCTTGTCTTCCTGTATTGGCAGCGAAGT
44157249 AGATCGAA
1 AGATCGAA
44157257 AAACAAGTCT
Statistics
Matches: 207, Mismatches: 19, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
43 1 0.00
44 4 0.02
45 199 0.96
46 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (45 bp):
AGATCGAAGATAGAAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
Found at i:44158770 original size:3 final size:3
Alignment explanation
Indices: 44158754--44158797 Score: 61
Period size: 3 Copynumber: 14.0 Consensus size: 3
44158744 TATTTAAATG
*
44158754 TTA TTA TCA TTTA TTA TTA TTA TTA TTA TTA TTAA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
44158798 GTTTTATTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 32 0.86
4 5 0.14
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:44158782 original size:22 final size:22
Alignment explanation
Indices: 44158754--44158797 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
44158744 TATTTAAATG
*
44158754 TTATTATCATTTATTATTATTA
1 TTATTATCATTAATTATTATTA
*
44158776 TTATTATTATTAATTATTATTA
1 TTATTATCATTAATTATTATTA
44158798 GTTTTATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (22 bp):
TTATTATCATTAATTATTATTA
Found at i:44158804 original size:22 final size:22
Alignment explanation
Indices: 44158755--44158805 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
44158745 ATTTAAATGT
* * *
44158755 TATTATCATTTATTATTATTAT
1 TATTATTATTAATTATTATTAG
44158777 TATTATTATTAATTATTATTAG
1 TATTATTATTAATTATTATTAG
*
44158799 TTTTATT
1 TATTATT
44158806 TCCCTTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (22 bp):
TATTATTATTAATTATTATTAG
Found at i:44158805 original size:9 final size:9
Alignment explanation
Indices: 44158754--44158797 Score: 61
Period size: 10 Copynumber: 4.7 Consensus size: 9
44158744 TATTTAAATG
*
44158754 TTATTATCA
1 TTATTATTA
44158763 TTTATTATTA
1 -TTATTATTA
44158773 TTATTATTA
1 TTATTATTA
44158782 TTATTAATTA
1 TTATT-ATTA
44158792 TTATTA
1 TTATTA
44158798 GTTTTATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
9 15 0.47
10 17 0.53
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (9 bp):
TTATTATTA
Found at i:44160265 original size:6 final size:6
Alignment explanation
Indices: 44160255--44160284 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
44160245 GGTTTTCTTG
*
44160255 AAATGG AAATGA AAATGA AAATGA AAATGA
1 AAATGA AAATGA AAATGA AAATGA AAATGA
44160285 GAAACAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (6 bp):
AAATGA
Found at i:44164118 original size:7 final size:7
Alignment explanation
Indices: 44164106--44164139 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
44164096 TTTATTTATA
44164106 TTTATTT
1 TTTATTT
44164113 TTTATTT
1 TTTATTT
44164120 TTTATTT
1 TTTATTT
44164127 TTTATTT
1 TTTATTT
*
44164134 ATTATT
1 TTTATT
44164140 ATTATATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTATTT
Found at i:44175212 original size:16 final size:16
Alignment explanation
Indices: 44175182--44175219 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
44175172 CAAAAATCTA
44175182 TAAGACAAAATAAACAG
1 TAAG-CAAAATAAACAG
44175199 -AAGCAAACATAAACAG
1 TAAGCAAA-ATAAACAG
44175215 TAAGC
1 TAAGC
44175220 CATTAATAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.21
16 11 0.58
17 4 0.21
ACGTcount: A:0.61, C:0.16, G:0.13, T:0.11
Consensus pattern (16 bp):
TAAGCAAAATAAACAG
Found at i:44175415 original size:31 final size:31
Alignment explanation
Indices: 44175380--44175455 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
44175370 CTCGTCGAAT
44175380 GCATATAACCGAATATTGATATACATCAAGA
1 GCATATAACCGAATATTGATATACATCAAGA
* *
44175411 GCATATAACCGAGTATTTATATACATCAAGA
1 GCATATAACCGAATATTGATATACATCAAGA
*
44175442 GCATATACCCGAAT
1 GCATATAACCGAAT
44175456 GTATGTATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.26
Consensus pattern (31 bp):
GCATATAACCGAATATTGATATACATCAAGA
Found at i:44195429 original size:44 final size:44
Alignment explanation
Indices: 44195097--44195415 Score: 444
Period size: 44 Copynumber: 7.2 Consensus size: 44
44195087 AACAAACCGG
* * *
44195097 TGAAGACTATAAGCCCTATCTCCCTGACCAGCAGTGGAATAGGT
1 TGAAGATTGTAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGT
*
44195141 TGAAGATTGCAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGT
1 TGAAGATTGTAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGT
*
44195185 TGAA-AGTTGCAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGT
1 TGAAGA-TTGTAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGT
* *
44195229 AGAAGATTGTAAGCCCTATCTCCCTGACCAGCAGTGGAATAGGT
1 TGAAGATTGTAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGT
*
44195273 TGAAGATTGCAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGT
1 TGAAGATTGTAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGT
** * * *
44195317 AAAAGATTATAAGTCTTATCTCCCTGAACAGCAGTGGAATAGG-
1 TGAAGATTGTAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGT
* * * * *
44195360 TGAAATATTGTACGTCCTATTTCCCTGAACAGAAGTGGAATAGGT
1 TG-AAGATTGTAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGT
44195405 TGAAGATTGTA
1 TGAAGATTGTA
44195416 GATCCAGTCT
Statistics
Matches: 246, Mismatches: 25, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
43 1 0.00
44 242 0.98
45 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (44 bp):
TGAAGATTGTAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGT
Found at i:44196068 original size:19 final size:19
Alignment explanation
Indices: 44196023--44196069 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 19
44196013 AAAACCAGGC
* *
44196023 CTCCTCCTCGCGCATGTTG
1 CTCCTCCGCGCGCATGTAG
*
44196042 --CGTCCGCGCGCATGTAG
1 CTCCTCCGCGCGCATGTAG
44196059 CTCCTCCGCGC
1 CTCCTCCGCGC
44196070 CAAATCCACG
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
17 14 0.64
19 8 0.36
ACGTcount: A:0.06, C:0.45, G:0.26, T:0.23
Consensus pattern (19 bp):
CTCCTCCGCGCGCATGTAG
Found at i:44199515 original size:41 final size:41
Alignment explanation
Indices: 44199453--44199565 Score: 160
Period size: 41 Copynumber: 2.8 Consensus size: 41
44199443 GTGTGCCAAT
44199453 TTACTTC-AATTTAATT-GATGAGACACTGGGTGTCAATTTA
1 TTACTTCGAATTT-ATTCGATGAGACACTGGGTGTCAATTTA
* *
44199493 TTACTTCGAATTTATTCAATGAGATACTGGGTGTCAATTTA
1 TTACTTCGAATTTATTCGATGAGACACTGGGTGTCAATTTA
* *
44199534 CTACTTCGAA-TTATCCGATGAGACACTGGGTG
1 TTACTTCGAATTTATTCGATGAGACACTGGGTG
44199566 CCAAATTGGT
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
40 29 0.45
41 36 0.55
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.37
Consensus pattern (41 bp):
TTACTTCGAATTTATTCGATGAGACACTGGGTGTCAATTTA
Found at i:44203567 original size:41 final size:41
Alignment explanation
Indices: 44203501--44203607 Score: 137
Period size: 41 Copynumber: 2.7 Consensus size: 41
44203491 AATTTCTAAT
* *
44203501 TTACTTCGG-TTTAACCAATGAGACACAGGGTGTCAATTTA
1 TTACTTCGGATTTATCCGATGAGACACAGGGTGTCAATTTA
* * *
44203541 TTACTTCGGATTTATTCGATGAGACACTGGGTGTTAATTTA
1 TTACTTCGGATTTATCCGATGAGACACAGGGTGTCAATTTA
* *
44203582 CTACTTC-GAATTATCCGATGAGACAC
1 TTACTTCGGATTTATCCGATGAGACAC
44203608 TATGTGCCAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 26 0.45
41 32 0.55
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.35
Consensus pattern (41 bp):
TTACTTCGGATTTATCCGATGAGACACAGGGTGTCAATTTA
Found at i:44206253 original size:4 final size:4
Alignment explanation
Indices: 44206244--44206322 Score: 51
Period size: 4 Copynumber: 20.0 Consensus size: 4
44206234 TGTCTTTCTC
*
44206244 CTTT CTTT CTTT CCCTT -TTT C-TT -TTT CTTT CTTT CTTT C-TT CTTT
1 CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
* * *
44206289 CAGTTT CATTT -TAT CATT CTTT CTTT ATTT CTTT
1 C--TTT C-TTT CTTT CTTT CTTT CTTT CTTT CTTT
44206323 TTATTACTTA
Statistics
Matches: 58, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
3 11 0.19
4 37 0.64
5 6 0.10
6 4 0.07
ACGTcount: A:0.06, C:0.23, G:0.01, T:0.70
Consensus pattern (4 bp):
CTTT
Found at i:44208015 original size:42 final size:42
Alignment explanation
Indices: 44207964--44208381 Score: 206
Period size: 42 Copynumber: 9.9 Consensus size: 42
44207954 GTTTACAACC
* * *
44207964 AAAAACGCCGTTAAAGATCATGTTCTTTAGCGGCGCTTATAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
*
44208006 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
* * * * ** ** *
44208048 AAAAACGCCACTGAAGAACATGGTCTTTAGTGGCATTTTTAT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
** * * * ****
44208090 CTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
** * * * * * ****
44208132 CTAAGCGCCGCTGAAGAACATGTTCTCTAGCGGAGTTTTTTT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
* * * * * ****
44208174 ATAAGCGCCGCTGAAGAACATGTTCTTTAGCGGAGTTTTTTT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
* * * * * ***
44208216 ATAAGCGCCGCTAAAGAACATGATCTTTAGTGGCGTTTTTTA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
** * * * * *
44208258 TTAAGCGCCGCTAAAGAACATGTTCTTTAACGGCGTTTTGTAT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG-AA
* * * ** * ****
44208301 AAAAACACCGCTAGAGATCATAATCTTTAGCGGCTCTTTTTTT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGC-TTAGAA
*
44208344 ACAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTT
44208382 TTGTACAAAA
Statistics
Matches: 315, Mismatches: 59, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
42 257 0.82
43 55 0.17
44 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
Found at i:44208105 original size:84 final size:85
Alignment explanation
Indices: 44208011--44208396 Score: 377
Period size: 84 Copynumber: 4.5 Consensus size: 85
44208001 TATAAAAAAA
* * * * *
44208011 CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAGAAAAACGCCACTGAAGAACATGGTCTTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTGATAAAAACGCCGCTGAAGAACATGATCTTT
*
44208076 AGTGGC-ATTTTTATCTAAG
66 AGCGGCGATTTTTATCTAAG
* ** ** * * *
44208095 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTGAAGAACATGTTCTCT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTGATAAAAACGCCGCTGAAGAACATGATCTTT
* * *
44208160 AGCGGAG-TTTTTTTATAAG
66 AGCGGCGATTTTTATCTAAG
* * ** * * *
44208179 CGCCGCTGAAGAACATGTTCTTTAGCGGAGTTTTTTTATAAGCGCCGCTAAAGAACATGATCTTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTGATAAAAACGCCGCTGAAGAACATGATCTTT
* *
44208244 AGTGGCGTTTTTTAT-TAAG
66 AGCGGCGATTTTTATCTAAG
* * * *
44208263 CGCCGCTAAAGAACATGTTCTTTAACGGCGTTTTGTATAAAAACACCGCT-AGAGATCATAATCT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTG-ATAAAAACGCCGCTGA-AGAACATGATCT
** * *
44208327 TTAGCGGCTCTTTTTTTAC-AAA
64 TTAGCGGCGATTTTTAT-CTAAG
*
44208349 CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTTGTACAAAAACGCC
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTTG-ATAAAAACGCC
44208397 ACTATTTTTG
Statistics
Matches: 251, Mismatches: 44, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
84 166 0.66
85 39 0.16
86 31 0.12
87 15 0.06
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (85 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTGATAAAAACGCCGCTGAAGAACATGATCTTT
AGCGGCGATTTTTATCTAAG
Found at i:44208194 original size:126 final size:127
Alignment explanation
Indices: 44207969--44208383 Score: 410
Period size: 126 Copynumber: 3.3 Consensus size: 127
44207959 CAACCAAAAA
* * * * * * ** * *
44207969 CGCCGTTAAAGATCATGTTCTTTAGCGGCGCTTATAAAAAAACGCCGCTAAAGAACATGTTCTTT
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTATTAAGCGCCGCTAAAGAACATGTTCTCT
* * * * * * * * *
44208034 AGCGGCGCTTAG-AGAAAAACGCCACTGAAGAACATGGTCTTTAGTGGCATTTTTATCTAAG
66 AACGGAGTTTTGTATAAAAACGCCGCTGAAGAACATGATCTTTAGCGGCATTTTTTTCTAAG
* *
44208095 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTT-TCTAAGCGCCGCTGAAGAACATGTTCTC
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTAT-TAAGCGCCGCTAAAGAACATGTTCTC
* * * * * *
44208159 TAGCGGAGTTTT-TTTATAAGCGCCGCTGAAGAACATGTTCTTTAGCGG-AGTTTTTTTATAAG
65 TAACGGAGTTTTGTATAAAAACGCCGCTGAAGAACATGATCTTTAGCGGCA-TTTTTTTCTAAG
* *
44208221 CGCCGCTAAAGAACATGATCTTTAGTGGCGTTTTTTATTAAGCGCCGCTAAAGAACATGTTCTTT
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTATTAAGCGCCGCTAAAGAACATGTTCTCT
* * * * * *
44208286 AACGGCGTTTTGTATAAAAACACCGCT-AGAGATCATAATCTTTAGCGGCTCTTTTTTTAC-AAA
66 AACGGAGTTTTGTATAAAAACGCCGCTGA-AGAACATGATCTTTAGCGGC-ATTTTTTT-CTAAG
* *
44208349 CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTT
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT
44208384 GTACAAAAAC
Statistics
Matches: 238, Mismatches: 42, Indels: 16
0.80 0.14 0.05
Matches are distributed among these distances:
125 1 0.00
126 168 0.71
127 28 0.12
128 41 0.17
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (127 bp):
CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTATTAAGCGCCGCTAAAGAACATGTTCTCT
AACGGAGTTTTGTATAAAAACGCCGCTGAAGAACATGATCTTTAGCGGCATTTTTTTCTAAG
Found at i:44210598 original size:44 final size:44
Alignment explanation
Indices: 44210536--44210622 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
44210526 AAGAATGAAG
* * *
44210536 GAGGCGATTTAGGGATTTGGGATTTCAAGAAATTCGGCAAGAAT
1 GAGGCGATTTACGAATTTGGGAATTCAAGAAATTCGGCAAGAAT
*
44210580 GAGGCGATTTACGAATTTGGGAATTCAAGAAATTGGGCAAGAA
1 GAGGCGATTTACGAATTTGGGAATTCAAGAAATTCGGCAAGAA
44210623 GGACGCAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.25
Consensus pattern (44 bp):
GAGGCGATTTACGAATTTGGGAATTCAAGAAATTCGGCAAGAAT
Found at i:44211450 original size:22 final size:23
Alignment explanation
Indices: 44211424--44211468 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
44211414 TATATTATTC
*
44211424 AATTA-ATGTACTATAATTTTAA
1 AATTATATATACTATAATTTTAA
* *
44211446 AATTATATATACTCTATTTTTAA
1 AATTATATATACTATAATTTTAA
44211469 GTGCATATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (23 bp):
AATTATATATACTATAATTTTAA
Found at i:44211808 original size:7 final size:7
Alignment explanation
Indices: 44211796--44211852 Score: 51
Period size: 7 Copynumber: 8.0 Consensus size: 7
44211786 ACTAAAGTAG
44211796 CCTAAAC
1 CCTAAAC
44211803 CCTAAAC
1 CCTAAAC
* *
44211810 CCCAAAT
1 CCTAAAC
*
44211817 CTTAAAC
1 CCTAAAC
*
44211824 CCCAAAC
1 CCTAAAC
*
44211831 TTCTAAAC
1 -CCTAAAC
44211839 CCTAAAC
1 CCTAAAC
*
44211846 CCAAAAC
1 CCTAAAC
44211853 ACCATAACCC
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
7 33 0.87
8 5 0.13
ACGTcount: A:0.44, C:0.40, G:0.00, T:0.16
Consensus pattern (7 bp):
CCTAAAC
Found at i:44212799 original size:55 final size:55
Alignment explanation
Indices: 44212712--44212819 Score: 135
Period size: 55 Copynumber: 2.0 Consensus size: 55
44212702 CAAATTGTAT
* * * *
44212712 TATACATCGAGACCAAATCGCTGTGTTTTGGTTAACATTTTTTGCGACGCTTTAA
1 TATACATCAAGACCAAAACGCTGCGTTTTGGTTAACATATTTTGCGACGCTTTAA
* * * * *
44212767 TATACATCAAGATCAAAACTCTGCGTTTTGGTTATCATATTTTGTGGCGCTTT
1 TATACATCAAGACCAAAACGCTGCGTTTTGGTTAACATATTTTGCGACGCTTT
44212820 TCGTAAGCGC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.40
Consensus pattern (55 bp):
TATACATCAAGACCAAAACGCTGCGTTTTGGTTAACATATTTTGCGACGCTTTAA
Found at i:44214048 original size:40 final size:39
Alignment explanation
Indices: 44213990--44214127 Score: 111
Period size: 40 Copynumber: 3.5 Consensus size: 39
44213980 ACACACCAAT
* *
44213990 TTGACACCAAGTGCCTCATTAGATAATTTGAAGTAGTAAA
1 TTGACACCTAGTGCCTCATTAGATAATCTGAAGTA-TAAA
* ** * *
44214030 TTGACACCTAGTGTCTCATCGGATAAACCGAAGTA-AAA
1 TTGACACCTAGTGCCTCATTAGATAATCTGAAGTATAAA
* *
44214068 TTGGCA-CTCAGTGCCTCA-TCGAATAAATCTGAAGTAATAAA
1 TTGACACCT-AGTGCCTCATTAG-AT-AATCTGAAGT-ATAAA
* *
44214109 TTGACACCCAGTGTCTCAT
1 TTGACACCTAGTGCCTCAT
44214128 CGACTCAAAG
Statistics
Matches: 75, Mismatches: 16, Indels: 12
0.73 0.16 0.12
Matches are distributed among these distances:
37 3 0.04
38 18 0.24
39 8 0.11
40 29 0.39
41 16 0.21
42 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (39 bp):
TTGACACCTAGTGCCTCATTAGATAATCTGAAGTATAAA
Found at i:44214086 original size:38 final size:41
Alignment explanation
Indices: 44214019--44214130 Score: 140
Period size: 38 Copynumber: 2.8 Consensus size: 41
44214009 TAGATAATTT
* * *
44214019 GAAGTAGTAAATTGACACCTAGTGTCTCATCGGATAAA-CC
1 GAAGTAATAAATTGACACCCAGTGTCTCATCGAATAAATCC
* * * *
44214059 GAAGT-A-AAATTGGCACTCAGTGCCTCATCGAATAAATCT
1 GAAGTAATAAATTGACACCCAGTGTCTCATCGAATAAATCC
44214098 GAAGTAATAAATTGACACCCAGTGTCTCATCGA
1 GAAGTAATAAATTGACACCCAGTGTCTCATCGA
44214131 CTCAAAGTCG
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
38 25 0.42
39 6 0.10
40 6 0.10
41 22 0.37
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.25
Consensus pattern (41 bp):
GAAGTAATAAATTGACACCCAGTGTCTCATCGAATAAATCC
Found at i:44214969 original size:4 final size:4
Alignment explanation
Indices: 44214960--44215038 Score: 60
Period size: 4 Copynumber: 19.8 Consensus size: 4
44214950 GTCTTTCTCG
*
44214960 TTTC TTTC TTTCC CTT- TTTC -TT- TTTC TTTC TTTC TTTC -TTC TTTC
1 TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
*
44215005 TGTTTC GTTT- TTATC TTTC TTTC TTTA TTTC TTT
1 --TTTC -TTTC TT-TC TTTC TTTC TTTC TTTC TTT
44215039 TTATTACTTA
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
3 11 0.18
4 38 0.61
5 9 0.15
6 4 0.06
ACGTcount: A:0.03, C:0.22, G:0.03, T:0.73
Consensus pattern (4 bp):
TTTC
Found at i:44214996 original size:30 final size:29
Alignment explanation
Indices: 44214960--44215030 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
44214950 GTCTTTCTCG
* * *
44214960 TTTCTTTCTTTCCCTTTTTCTTTTTCTTTC
1 TTTCTTTCTTTCCCTGTTTCGTTTT-TATC
**
44214990 TTTCTTTCTTCTTTCTGTTTCGTTTTTATC
1 TTTCTTTCTT-TCCCTGTTTCGTTTTTATC
44215020 TTTCTTTCTTT
1 TTTCTTTCTTT
44215031 ATTTCTTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 1 0.03
30 23 0.66
31 11 0.31
ACGTcount: A:0.01, C:0.23, G:0.03, T:0.73
Consensus pattern (29 bp):
TTTCTTTCTTTCCCTGTTTCGTTTTTATC
Found at i:44217244 original size:21 final size:22
Alignment explanation
Indices: 44217220--44217260 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
44217210 CCACAAGGCT
*
44217220 ATGTGACC-CTCTCACACGATC
1 ATGTGACCTATCTCACACGATC
*
44217241 ATGTGGCCTATCTCACACGA
1 ATGTGACCTATCTCACACGA
44217261 GCACGACTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.24, C:0.34, G:0.17, T:0.24
Consensus pattern (22 bp):
ATGTGACCTATCTCACACGATC
Found at i:44220326 original size:47 final size:47
Alignment explanation
Indices: 44220172--44220324 Score: 243
Period size: 47 Copynumber: 3.3 Consensus size: 47
44220162 GTCATAGTAA
*
44220172 TGCAAATAAACTACCAATAATCAAAATTGTGGACAAACCACCAAAAT
1 TGCAAATAAACTACCAATAATCAAAATTGTGGACAAGCCACCAAAAT
*
44220219 TGCAAATAAACTACCAATAATCAAAATTGTGGATAAGCCACCAAAAT
1 TGCAAATAAACTACCAATAATCAAAATTGTGGACAAGCCACCAAAAT
* * * *
44220266 TACAGATAAACTGCCAATAATCAAAATCGTGGACAAGCCACCAAAAT
1 TGCAAATAAACTACCAATAATCAAAATTGTGGACAAGCCACCAAAAT
*
44220313 TGTAAATAAACT
1 TGCAAATAAACT
44220325 GCTAAAAACT
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 96 1.00
ACGTcount: A:0.49, C:0.20, G:0.10, T:0.20
Consensus pattern (47 bp):
TGCAAATAAACTACCAATAATCAAAATTGTGGACAAGCCACCAAAAT
Found at i:44221901 original size:13 final size:13
Alignment explanation
Indices: 44221883--44221907 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44221873 CAAAAAATTA
44221883 AAAAAATATTTTC
1 AAAAAATATTTTC
44221896 AAAAAATATTTT
1 AAAAAATATTTT
44221908 TAAAGATTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAAAATATTTTC
Done.