Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold295
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: 644316
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 33643 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:364699 original size:42 final size:42
Alignment explanation
Indices: 364619--364700 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
364609 CATTTTCTCT
* **
364619 ATGCCATAGTCCAACTATGGTCTTACACATATTTACATATTG
1 ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
*
364661 ATGCCATAGCCCAGCTATGGTCTTACACA-ATAGCACATAT
1 ATGCCATAGCCCAACTATGGTCTTACACATAT-GCACATAT
364701 CACACCGATG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 2 0.06
42 33 0.94
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.30
Consensus pattern (42 bp):
ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
Found at i:379004 original size:37 final size:37
Alignment explanation
Indices: 378963--379073 Score: 213
Period size: 37 Copynumber: 3.0 Consensus size: 37
378953 ATATATATGT
378963 ATGTGTGTGATTTAATATGGTTATAGCTTGTGGAGCA
1 ATGTGTGTGATTTAATATGGTTATAGCTTGTGGAGCA
*
379000 ATGTGTGTGATTTAATATGGTTATAGCTTGTGGTGCA
1 ATGTGTGTGATTTAATATGGTTATAGCTTGTGGAGCA
379037 ATGTGTGTGATTTAATATGGTTATAGCTTGTGGAGCA
1 ATGTGTGTGATTTAATATGGTTATAGCTTGTGGAGCA
379074 TTATGTTTGC
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 72 1.00
ACGTcount: A:0.23, C:0.05, G:0.30, T:0.41
Consensus pattern (37 bp):
ATGTGTGTGATTTAATATGGTTATAGCTTGTGGAGCA
Found at i:386590 original size:66 final size:66
Alignment explanation
Indices: 386499--386628 Score: 233
Period size: 66 Copynumber: 2.0 Consensus size: 66
386489 TCACACAAGA
386499 AATTTAGAGAATATTTGCTCTCTCTTTCCCAAGGATGAGATATTAGAAAAGTTATCATGTGTATA
1 AATTTAGAGAATATTTGCTCTCTCTTTCCCAAGGATGAGATATTAGAAAAGTTATCATGTGTATA
386564 T
66 T
* * *
386565 AATTTAGAGAATATTTGCTCTCTCTTTCCTAAGGATGGGATATTAGAAAAGTTATCTTGTGTAT
1 AATTTAGAGAATATTTGCTCTCTCTTTCCCAAGGATGAGATATTAGAAAAGTTATCATGTGTAT
386629 GATTTGGGGA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.39
Consensus pattern (66 bp):
AATTTAGAGAATATTTGCTCTCTCTTTCCCAAGGATGAGATATTAGAAAAGTTATCATGTGTATA
T
Found at i:387849 original size:30 final size:30
Alignment explanation
Indices: 387804--387864 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
387794 GTACATAAAG
*
387804 CTTAGCTATAGTGTTAACCAACTTAACTAA
1 CTTAGCTATACTGTTAACCAACTTAACTAA
*
387834 CTTATCTATACTGTTAACCAACTTAACTAA
1 CTTAGCTATACTGTTAACCAACTTAACTAA
387864 C
1 C
387865 ATGAAGAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.34
Consensus pattern (30 bp):
CTTAGCTATACTGTTAACCAACTTAACTAA
Found at i:388675 original size:27 final size:27
Alignment explanation
Indices: 388645--388704 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
388635 CGCCTGATTT
* *
388645 CTGGTGAAC-CTAAGCTCGTCAGGCCTA
1 CTGGTGAACTCCAA-CTCGACAGGCCTA
* *
388672 CTGGCGTACTCCAACTCGACAGGCCTA
1 CTGGTGAACTCCAACTCGACAGGCCTA
388699 CTGGTG
1 CTGGTG
388705 TACACCAGCC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 24 0.89
28 3 0.11
ACGTcount: A:0.20, C:0.32, G:0.27, T:0.22
Consensus pattern (27 bp):
CTGGTGAACTCCAACTCGACAGGCCTA
Found at i:392792 original size:16 final size:16
Alignment explanation
Indices: 392771--392803 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
392761 AATCAAAAGA
392771 TTGTTAAAACAACTTC
1 TTGTTAAAACAACTTC
392787 TTGTTAAAACAACTTC
1 TTGTTAAAACAACTTC
392803 T
1 T
392804 AAAGAAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.39
Consensus pattern (16 bp):
TTGTTAAAACAACTTC
Found at i:393845 original size:20 final size:20
Alignment explanation
Indices: 393820--393862 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
393810 ACCACTCCAT
393820 TTACTTATC-ATTCCATTTAC
1 TTACTT-TCTATTCCATTTAC
*
393840 TTACTTTCTATTTCATTTAC
1 TTACTTTCTATTCCATTTAC
393860 TTA
1 TTA
393863 GCATAAGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.23, C:0.21, G:0.00, T:0.56
Consensus pattern (20 bp):
TTACTTTCTATTCCATTTAC
Found at i:394607 original size:6 final size:6
Alignment explanation
Indices: 394596--394645 Score: 100
Period size: 6 Copynumber: 8.3 Consensus size: 6
394586 AGTCGTAACC
394596 TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT
1 TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT
394644 TT
1 TT
394646 ACATCATAGC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTCCT
Found at i:401055 original size:18 final size:18
Alignment explanation
Indices: 401032--401066 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
401022 ACGATATGCC
401032 AAACTATTTTCATGCTTG
1 AAACTATTTTCATGCTTG
*
401050 AAACTATTTTGATGCTT
1 AAACTATTTTCATGCTT
401067 CCTATTCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (18 bp):
AAACTATTTTCATGCTTG
Found at i:406896 original size:27 final size:27
Alignment explanation
Indices: 406866--406917 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
406856 CCTATTGGCG
*
406866 TACTACAACTCTCCAGGCCTACTGGTT
1 TACTACAACTCGCCAGGCCTACTGGTT
* *
406893 TACTTCAACTCGCCATGCCTACTGG
1 TACTACAACTCGCCAGGCCTACTGG
406918 CGTACACCAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.21, C:0.35, G:0.15, T:0.29
Consensus pattern (27 bp):
TACTACAACTCGCCAGGCCTACTGGTT
Found at i:408986 original size:126 final size:126
Alignment explanation
Indices: 408757--409173 Score: 708
Period size: 126 Copynumber: 3.3 Consensus size: 126
408747 CCAAACATGC
408757 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
* * * *
408822 GTTTAAAGCGTTTTTGACACTATTTTCTCAGAATCGTCTACTCGAAATTATTTTTTCAAGA
66 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
* *
408883 GCTACTGTAGCAAAAGCACGTCCGCGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
*
408948 GCTTAAAGCGTTTTTGACACCATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
66 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
* * *
409009 GTTACTGTAGCAAAAGCGCGTCCACGTGCGAGCTTCTTTCAGTACTTCTACTGACAAAGCATCCT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
* * *
409074 ACTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTTGAAACTATTTTTTCAGGA
66 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
*
409135 GCTACTGTAGCAAAAGTGCGTCCACGTGGGAGCTTCTTT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTT
409174 AAATTAACAA
Statistics
Matches: 272, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
126 272 1.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.32
Consensus pattern (126 bp):
GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
Found at i:409432 original size:95 final size:95
Alignment explanation
Indices: 409218--409481 Score: 275
Period size: 95 Copynumber: 2.8 Consensus size: 95
409208 CCCCAAACAT
409218 TAATTTATTTGAGTTCTTACTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTATAAAAATT
1 TAATTTATTTGA-TTCTTACTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTATAAAAA-T
* *
409283 TATAATTAATTTACTCAAGTAACCCTGAACCC
64 TATAATTAAATTACTCAAGTAACCCTAAACCC
* * * * * * **
409315 TAATTTATTTAATTCTTCCTTAAAAACCCTTAACTCTAAACCTTAATCTAATTTTTTTTTTAAA-
1 TAATTTATTTGATTCTTACTTAAAAACCCTAAACACTAAACCCTAATCTAA--TTTTATAAAAAT
*
409379 T-TAATTAAATTACTCAAGTAACCTTAAACCC
64 TATAATTAAATTACTCAAGTAACCCTAAACCC
* * * ** * * *
409410 TAATTTAATTGATTTTTTCTTAAAAAACAATAAACACGAAA-CCTAATCCAATTTTGA-AAAATT
1 TAATTTATTTGATTCTTACTT-AAAAACCCTAAACACTAAACCCTAATCTAATTTT-ATAAAAAT
409473 TATAATTAA
64 TATAATTAA
409482 TTTAATTGAC
Statistics
Matches: 135, Mismatches: 26, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
93 6 0.04
94 1 0.01
95 59 0.44
96 50 0.37
97 11 0.08
98 8 0.06
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.39
Consensus pattern (95 bp):
TAATTTATTTGATTCTTACTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTATAAAAATTA
TAATTAAATTACTCAAGTAACCCTAAACCC
Found at i:410915 original size:43 final size:43
Alignment explanation
Indices: 410867--411260 Score: 427
Period size: 43 Copynumber: 9.2 Consensus size: 43
410857 TTATAGAAAA
* *
410867 AAACGCCGCTAAAGACCAAGACCTTTAGTGGCGCTTCTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCTCAC
* *
410910 AAACGCCGCTAAAGACCAAGACCTTTAGTGGCGCTTCTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCTCAC
*
410953 AAACGCCGCTAAAGACCAATACCTTTAGCGGCGCTTCTCTCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCTCAC
* * *
410996 GAACGCTGCTAAAGACCAATACCTTTAGCGGCGCTTCTCTCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCTCAC
* * * *
411039 AAACGCCGCTAAAGACCAATACCTTTAGCAGCGCTTTTCTTAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCTCAC
* * * * * *
411082 AGACGCCGCTAAAAACTAGGACCTTTAGCGGCGCTTCTATTAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCTCAC
*** * * * *
411125 AAACGCCGCTATAA-A-TTTGACTTTTAGCGACACTT-TTTCAC
1 AAACGCCGCTA-AAGACCAAGACCTTTAGCGGCGCTTCTCTCAC
* * * * *
411166 AAACGCCGCTAAA-AACAATACCTTTAGCAGCGCTTTTCTTAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCTCAC
* * * * * *
411208 AGACGCCGCTAAAAACTAGGACCTTTAGCGGCGCTTCTATTAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCTCAC
411251 AAACGCCGCT
1 AAACGCCGCT
411261 TAAAATTTGA
Statistics
Matches: 302, Mismatches: 45, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
40 3 0.01
41 27 0.09
42 31 0.10
43 239 0.79
44 2 0.01
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCTCAC
Found at i:411214 original size:126 final size:126
Alignment explanation
Indices: 411035--411308 Score: 514
Period size: 126 Copynumber: 2.2 Consensus size: 126
411025 GGCGCTTCTC
*
411035 TCACAAACGCCGCTAAAGACCAATACCTTTAGCAGCGCTTTTCTTACAGACGCCGCTAAAAACTA
1 TCACAAACGCCGCTAAA-AACAATACCTTTAGCAGCGCTTTTCTTACAGACGCCGCTAAAAACTA
411100 GGACCTTTAGCGGCGCTTCTATTACAAACGCCGC-TATAAATTTGACTTTTAGCGACACTTTT
65 GGACCTTTAGCGGCGCTTCTATTACAAACGCCGCTTA-AAATTTGACTTTTAGCGACACTTTT
411162 TCACAAACGCCGCTAAAAACAATACCTTTAGCAGCGCTTTTCTTACAGACGCCGCTAAAAACTAG
1 TCACAAACGCCGCTAAAAACAATACCTTTAGCAGCGCTTTTCTTACAGACGCCGCTAAAAACTAG
411227 GACCTTTAGCGGCGCTTCTATTACAAACGCCGCTTAAAATTTGACTTTTAGCGACACTTTT
66 GACCTTTAGCGGCGCTTCTATTACAAACGCCGCTTAAAATTTGACTTTTAGCGACACTTTT
411288 TCACAAACGCCGCTAAAAACA
1 TCACAAACGCCGCTAAAAACA
411309 TAACTTTTAA
Statistics
Matches: 145, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
126 126 0.87
127 19 0.13
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (126 bp):
TCACAAACGCCGCTAAAAACAATACCTTTAGCAGCGCTTTTCTTACAGACGCCGCTAAAAACTAG
GACCTTTAGCGGCGCTTCTATTACAAACGCCGCTTAAAATTTGACTTTTAGCGACACTTTT
Found at i:411317 original size:41 final size:42
Alignment explanation
Indices: 410867--411310 Score: 268
Period size: 43 Copynumber: 10.5 Consensus size: 42
410857 TTATAGAAAA
* * * **
410867 AAACGCCGCTAAAGACCA-AGACCTTTAGTGGCGCTTCTCCCAC
1 AAACGCCGCTAAA-AACATAGACCTTTAGCGACGCTT-TTTCAC
* * * **
410910 AAACGCCGCTAAAGACCA-AGACCTTTAGTGGCGCTTCTCCCAC
1 AAACGCCGCTAAA-AACATAGACCTTTAGCGACGCTT-TTTCAC
* * * *
410953 AAACGCCGCTAAAGACCA-ATACCTTTAGCGGCGCTTCTCTCAC
1 AAACGCCGCTAAA-AACATAGACCTTTAGCGACGCTT-TTTCAC
* * * * * *
410996 GAACGCTGCTAAAGACCA-ATACCTTTAGCGGCGCTTCTCTCAC
1 AAACGCCGCTAAA-AACATAGACCTTTAGCGACGCTT-TTTCAC
* * *
411039 AAACGCCGCTAAAGACCA-ATACCTTTAGC-AGCGCTTTTCTTAC
1 AAACGCCGCTAAA-AACATAGACCTTTAGCGA-CGCTTTT-TCAC
* *
411082 AGACGCCGCTAAAAAC-TAGGACCTTTAGCGGCGCTTCTATT-AC
1 AAACGCCGCTAAAAACATA-GACCTTTAGCGACGCTT-T-TTCAC
* * * * *
411125 AAACGCCGCTATAAA-TTTGACTTTTAGCGACACTTTTTCAC
1 AAACGCCGCTAAAAACATAGACCTTTAGCGACGCTTTTTCAC
* *
411166 AAACGCCGCTAAAAACA-ATACCTTTAGC-AGCGCTTTTCTTAC
1 AAACGCCGCTAAAAACATAGACCTTTAGCGA-CGCTTTT-TCAC
* *
411208 AGACGCCGCTAAAAAC-TAGGACCTTTAGCGGCGCTTCTATT-AC
1 AAACGCCGCTAAAAACATA-GACCTTTAGCGACGCTT-T-TTCAC
* * * * *
411251 AAACGCCGCTTAAAA-TTTGACTTTTAGCGACACTTTTTCAC
1 AAACGCCGCTAAAAACATAGACCTTTAGCGACGCTTTTTCAC
411292 AAACGCCGCTAAAAACATA
1 AAACGCCGCTAAAAACATA
411311 ACTTTTAAAA
Statistics
Matches: 342, Mismatches: 39, Indels: 41
0.81 0.09 0.10
Matches are distributed among these distances:
40 5 0.01
41 48 0.14
42 52 0.15
43 231 0.68
44 4 0.01
45 2 0.01
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (42 bp):
AAACGCCGCTAAAAACATAGACCTTTAGCGACGCTTTTTCAC
Found at i:417673 original size:7 final size:7
Alignment explanation
Indices: 417661--417793 Score: 74
Period size: 7 Copynumber: 18.7 Consensus size: 7
417651 ACTAGTTAAT
417661 CTAAACC
1 CTAAACC
417668 CTAAACC
1 CTAAACC
*
417675 ATAAA-C
1 CTAAACC
417681 CTAAACC
1 CTAAACC
417688 CTAAAACC
1 CT-AAACC
417696 CTAAACC
1 CTAAACC
* *
417703 CTTAACA
1 CTAAACC
417710 C-ATAACC
1 CTA-AACC
417717 TCTAAACC
1 -CTAAACC
*
417725 TTAAACC
1 CTAAACC
*
417732 C-CAACC
1 CTAAACC
*
417738 TTTAAACC
1 -CTAAACC
*
417746 ATAAACC
1 CTAAACC
* *
417753 ATAAATC
1 CTAAACC
* *
417760 ATAACCC
1 CTAAACC
417767 CTAAACC
1 CTAAACC
*
417774 CATAATCC
1 C-TAAACC
*
417782 ATAAACC
1 CTAAACC
*
417789 TTAAA
1 CTAAA
417794 ATAGTAACTC
Statistics
Matches: 97, Mismatches: 21, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
6 9 0.09
7 66 0.68
8 21 0.22
9 1 0.01
ACGTcount: A:0.46, C:0.35, G:0.00, T:0.20
Consensus pattern (7 bp):
CTAAACC
Found at i:417681 original size:14 final size:14
Alignment explanation
Indices: 417661--417851 Score: 95
Period size: 14 Copynumber: 13.4 Consensus size: 14
417651 ACTAGTTAAT
*
417661 CTAAACCCTAAACC
1 CTAAACCATAAACC
*
417675 ATAAACC-TAAACC
1 CTAAACCATAAACC
*
417688 CTAAAACCCTAAACC
1 CT-AAACCATAAACC
*
417703 CTTAACACAT-AACC
1 CTAAAC-CATAAACC
*
417717 TCTAAACCTTAAACC
1 -CTAAACCATAAACC
* *
417732 C-CAACCTTTAAACC
1 CTAAACC-ATAAACC
* *
417746 ATAAACCATAAATC
1 CTAAACCATAAACC
* * *
417760 ATAACCCCTAAACC
1 CTAAACCATAAACC
*
417774 CATAATCCATAAACC
1 C-TAAACCATAAACC
*
417789 TTAAA--ATAGTAACTC
1 CTAAACCATA--AAC-C
** *
417804 CTAAACTTTAAACT
1 CTAAACCATAAACC
*
417818 CTAAACCATATACC
1 CTAAACCATAAACC
*
417832 CTAAACCAAAAACC
1 CTAAACCATAAACC
*
417846 TTAAAC
1 CTAAAC
417852 TATAGTGATA
Statistics
Matches: 135, Mismatches: 29, Indels: 26
0.71 0.15 0.14
Matches are distributed among these distances:
12 3 0.02
13 11 0.08
14 77 0.57
15 42 0.31
17 2 0.01
ACGTcount: A:0.46, C:0.32, G:0.01, T:0.21
Consensus pattern (14 bp):
CTAAACCATAAACC
Found at i:418213 original size:41 final size:40
Alignment explanation
Indices: 418148--418386 Score: 345
Period size: 41 Copynumber: 5.8 Consensus size: 40
418138 ATATTTTTTT
* *
418148 CGGCGCTT-TTCCAAAAACGACGCTAAAGACCCAAGAATTAG
1 CGGCGCTTCTT-C-AAAACGCCGCTAAAGACCCAAGCATTAG
*
418189 CGGCGCTTCTTCAAAAGCGCCGCTAAAGACCTAAGCATTAG
1 CGGCGCTTCTTCAAAA-CGCCGCTAAAGACCCAAGCATTAG
*
418230 CGGCGCTTCTTCAGAAGCGCCGCTAAAGACCCAAGCATTAG
1 CGGCGCTTCTTCA-AAACGCCGCTAAAGACCCAAGCATTAG
418271 CGGCGCTTCTTCAGAAACGCCGCTAAAGACCCAAGCATTAG
1 CGGCGCTTCTTCA-AAACGCCGCTAAAGACCCAAGCATTAG
418312 CGGCGCTTCTTCAAAAACGCCGCTAAAGACCCAAGCATTAG
1 CGGCGCTTCTTC-AAAACGCCGCTAAAGACCCAAGCATTAG
* * *
418353 CGGCGCTTTTTGGAAAACGCCGCTAAAGTCCCAA
1 CGGCGCTTCTT-CAAAACGCCGCTAAAGACCCAA
418387 ACTAACAAAA
Statistics
Matches: 184, Mismatches: 9, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
40 4 0.02
41 175 0.95
42 5 0.03
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.18
Consensus pattern (40 bp):
CGGCGCTTCTTCAAAACGCCGCTAAAGACCCAAGCATTAG
Found at i:418466 original size:39 final size:40
Alignment explanation
Indices: 418417--418544 Score: 124
Period size: 40 Copynumber: 3.2 Consensus size: 40
418407 TGGGCTTCGG
*
418417 TTTTT-GCGGCGCTTTTTGGAAAA-CGCCGCTAATTC-TCA
1 TTTTTAGCGGCGCTTTTT-GAAAAGCGCCGCTAATACTTCA
** *
418455 TTTTTAGCGGCG-TTTTTAGAAAAGCGCCGAGAATACTTGA
1 TTTTTAGCGGCGCTTTTT-GAAAAGCGCCGCTAATACTTCA
* *
418495 TCTTTAGCGGCGCTTTTCT-AAAAGCGCCGCTAATGA-TTGA
1 TTTTTAGCGGCGCTTTT-TGAAAAGCGCCGCTAAT-ACTTCA
418535 TTTTTAGCGG
1 TTTTTAGCGG
418545 TGTTTTTTAT
Statistics
Matches: 75, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
38 15 0.20
39 15 0.20
40 39 0.52
41 5 0.07
42 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (40 bp):
TTTTTAGCGGCGCTTTTTGAAAAGCGCCGCTAATACTTCA
Found at i:418911 original size:40 final size:40
Alignment explanation
Indices: 418870--418944 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
418860 GTAAATTGAT
* *
418870 TTTTTTAAAA-AGTGATTAATTGCGATATGTATATATAGA
1 TTTTTCAAAAGAGTGATTAATTACGATATGTATATATAGA
* * *
418909 TTTTTCAAAAGAGTGGTTAATTATGATATTTATATA
1 TTTTTCAAAAGAGTGATTAATTACGATATGTATATA
418945 AGCACTTTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
39 9 0.30
40 21 0.70
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.45
Consensus pattern (40 bp):
TTTTTCAAAAGAGTGATTAATTACGATATGTATATATAGA
Found at i:425510 original size:48 final size:48
Alignment explanation
Indices: 425436--425531 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
425426 TGGAAAATAA
* *
425436 ATTTGTCTGCAACTCTGCATTGGTCAACTTGGAATTACAGTTAGGATT
1 ATTTGTCTGCAACTCTGCATTAGTCAACTTGGAATTACAATTAGGATT
*
425484 ATTTGTCTGCAACTCTGCATTAGTCAACTTGGGATTACAATTAGGATT
1 ATTTGTCTGCAACTCTGCATTAGTCAACTTGGAATTACAATTAGGATT
425532 GGTAAATTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.38
Consensus pattern (48 bp):
ATTTGTCTGCAACTCTGCATTAGTCAACTTGGAATTACAATTAGGATT
Found at i:437888 original size:45 final size:45
Alignment explanation
Indices: 437824--437917 Score: 161
Period size: 45 Copynumber: 2.1 Consensus size: 45
437814 AACAGATACT
* *
437824 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
*
437869 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
437914 CGGT
1 CGGT
437918 TCACATAGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:438029 original size:51 final size:50
Alignment explanation
Indices: 437919--438106 Score: 164
Period size: 51 Copynumber: 3.7 Consensus size: 50
437909 ATGTTCGGTT
* * ** * *
437919 CACATAGTAGCCTGCATATAGTACTACATATATGACCAGTACCATTCGA-TA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCA--AACATTCCAGTA
** * *
437970 CATGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAAC-TATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCAAACAT-TCCAGTA
* * ** * * *
438021 CGCATAGTAGCCTACACATAGTACTACACTTGCGACCTATCATTCCAGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCAAACATTCCAGTA
*
438071 CACGTAGTAGCCTGCACATAGTACTACACACGTGAC
1 CACATAGTAGCCTGCACATAGTACTACACACGTGAC
438107 TATCACTTTC
Statistics
Matches: 106, Mismatches: 27, Indels: 9
0.75 0.19 0.06
Matches are distributed among these distances:
49 1 0.01
50 43 0.41
51 60 0.57
52 2 0.02
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCAAACATTCCAGTA
Found at i:438129 original size:101 final size:99
Alignment explanation
Indices: 437920--438105 Score: 250
Period size: 101 Copynumber: 1.8 Consensus size: 99
437910 TGTTCGGTTC
* * * * *
437920 ACATAGTAGCCTGCATATAGTACTACATATATGACCAGTACCATTCGATACATGTAGTAGCCTGC
1 ACATAGTAGCCTACACATAGTACTACATATACGACCA-TACCATTCCATACACGTAGTAGCCTGC
437985 ACATAGTACTACACACGTGATCGAAACTATCCGGT
65 ACATAGTACTACACACGTGATCGAAACTATCCGGT
* *
438020 ACGCATAGTAGCCTACACATAGTACTACACT-TGCGACC-TATCATTCCAGTACACGTAGTAGCC
1 A--CATAGTAGCCTACACATAGTACTACA-TATACGACCATACCATTCCA-TACACGTAGTAGCC
438083 TGCACATAGTACTACACACGTGA
62 TGCACATAGTACTACACACGTGA
438106 CTATCACTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
100 9 0.12
101 36 0.48
102 29 0.39
103 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (99 bp):
ACATAGTAGCCTACACATAGTACTACATATACGACCATACCATTCCATACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCGAAACTATCCGGT
Found at i:440180 original size:21 final size:21
Alignment explanation
Indices: 440154--440193 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
440144 TAATCATAAT
440154 AAAATACAG-ATAAAATGAATA
1 AAAATA-AGAATAAAATGAATA
*
440175 AAAATAAGAATAATATGAA
1 AAAATAAGAATAAAATGAA
440194 AAACAACCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.68, C:0.03, G:0.10, T:0.20
Consensus pattern (21 bp):
AAAATAAGAATAAAATGAATA
Found at i:447344 original size:19 final size:19
Alignment explanation
Indices: 447320--447421 Score: 177
Period size: 19 Copynumber: 5.3 Consensus size: 19
447310 AATTTTTGAG
447320 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
447339 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
447358 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
447377 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
447398 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
447417 GATAT
1 GATAT
447422 ATNNNNNNNN
Statistics
Matches: 79, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
19 60 0.76
21 19 0.24
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:447395 original size:40 final size:40
Alignment explanation
Indices: 447320--447423 Score: 185
Period size: 40 Copynumber: 2.6 Consensus size: 40
447310 AATTTTTGAG
447320 GATATGCAATCTTAGATATG--ATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATATGATATATGCAATCCTAGATAT
*
447358 GATATGCAATCTTAGATATGATATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATGATATATGCAATCCTAGATAT
447398 GATATGCAATCTTAGATATGATATAT
1 GATATGCAATCTTAGATATGATATAT
447424 NNNNNNNNNN
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
38 20 0.32
40 43 0.68
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.37
Consensus pattern (40 bp):
GATATGCAATCTTAGATATGATATATGCAATCCTAGATAT
Found at i:447532 original size:19 final size:19
Alignment explanation
Indices: 447508--447562 Score: 92
Period size: 19 Copynumber: 2.9 Consensus size: 19
447498 NNNNNNNNNN
447508 TGATATGCAATCTTAGATA
1 TGATATGCAATCTTAGATA
**
447527 TGATATATAATCTTAGATA
1 TGATATGCAATCTTAGATA
447546 TGATATGCAATCTTAGA
1 TGATATGCAATCTTAGA
447563 ATATATGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (19 bp):
TGATATGCAATCTTAGATA
Found at i:465473 original size:56 final size:57
Alignment explanation
Indices: 465411--465523 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 57
465401 AGGATGTCAG
465411 GCTGGTGCCGCCTGACTGCGACCAAACCGGTCACGGCTCA-CCCCAACCTTTTTTTT
1 GCTGGTGCCGCCTGACTGCGACCAAACCGGTCACGGCTCACCCCCAACCTTTTTTTT
465467 GCTGGTGCCGCCTGACTGCGACCAAACCGGTCACGGCTCACCCCCAACCTTTTTTTT
1 GCTGGTGCCGCCTGACTGCGACCAAACCGGTCACGGCTCACCCCCAACCTTTTTTTT
465524 CTCCATCCTT
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 40 0.71
57 16 0.29
ACGTcount: A:0.16, C:0.38, G:0.21, T:0.25
Consensus pattern (57 bp):
GCTGGTGCCGCCTGACTGCGACCAAACCGGTCACGGCTCACCCCCAACCTTTTTTTT
Found at i:466916 original size:21 final size:21
Alignment explanation
Indices: 466890--466933 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
466880 GGGTATTTTA
*
466890 GGAATTTTAGCCTTAGTGTTC
1 GGAATTTTAGCCTTAATGTTC
466911 GGAATTTTAGCCTTAATGTTC
1 GGAATTTTAGCCTTAATGTTC
466932 GG
1 GG
466934 TTTATAAGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.14, G:0.25, T:0.41
Consensus pattern (21 bp):
GGAATTTTAGCCTTAATGTTC
Found at i:472431 original size:48 final size:48
Alignment explanation
Indices: 472301--472507 Score: 245
Period size: 48 Copynumber: 4.3 Consensus size: 48
472291 CTACTATGCG
* *
472301 CACCGATATTCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGC
1 CACCGATAATCTGTTATGACACAAGGGTGGCACGGACTATGTGCAGGC
* * * * *
472349 CACCGAT-ATTTGTTATGATATAAGGATGGCACGGACTGTGTGCAGGC
1 CACCGATAATCTGTTATGACACAAGGGTGGCACGGACTATGTGCAGGC
* * * * *
472396 CATCAATAACCTGTTAAGATACAAGGGTGGCACGGACTATGTGCAGGC
1 CACCGATAATCTGTTATGACACAAGGGTGGCACGGACTATGTGCAGGC
* * * *
472444 CACCGAGAATCTGTTATTACACAAAGGTGGTACGGACTATGTGCAGGC
1 CACCGATAATCTGTTATGACACAAGGGTGGCACGGACTATGTGCAGGC
*
472492 CACCGAGAAATCTGTT
1 CACCGA-TAATCTGTT
472508 TTTATTCTGA
Statistics
Matches: 134, Mismatches: 23, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
47 40 0.30
48 86 0.64
49 8 0.06
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (48 bp):
CACCGATAATCTGTTATGACACAAGGGTGGCACGGACTATGTGCAGGC
Found at i:482383 original size:14 final size:14
Alignment explanation
Indices: 482364--482425 Score: 56
Period size: 13 Copynumber: 4.6 Consensus size: 14
482354 ATGTTATTAT
482364 ATTTTTTTATTTTG
1 ATTTTTTTATTTTG
*
482378 ATTTTTTTATCTT-
1 ATTTTTTTATTTTG
* ** *
482391 AATTAGTTGTTTTG
1 ATTTTTTTATTTTG
*
482405 ATTTTTTT-TTTGG
1 ATTTTTTTATTTTG
482418 ATTTTTTT
1 ATTTTTTT
482426 TTGTTGGTGC
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
13 20 0.54
14 17 0.46
ACGTcount: A:0.15, C:0.02, G:0.10, T:0.74
Consensus pattern (14 bp):
ATTTTTTTATTTTG
Found at i:489424 original size:60 final size:60
Alignment explanation
Indices: 489357--489477 Score: 224
Period size: 60 Copynumber: 2.0 Consensus size: 60
489347 AAGTGGAGAA
*
489357 AACCGAATTTGTACATGTTGAATCTAATAAGGATGAAGCTGATGTGACTCAAGCTACTAC
1 AACCGAATTTGTACATGTTGAATCTAATAAGGATGAAGCTGATGTGACCCAAGCTACTAC
*
489417 AACCGAATTTGTACATGTTGAATCTAATAAGGATGAAGCTGATGTGGCCCAAGCTACTAC
1 AACCGAATTTGTACATGTTGAATCTAATAAGGATGAAGCTGATGTGACCCAAGCTACTAC
489477 A
1 A
489478 CCTGCTGACA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (60 bp):
AACCGAATTTGTACATGTTGAATCTAATAAGGATGAAGCTGATGTGACCCAAGCTACTAC
Found at i:494998 original size:23 final size:22
Alignment explanation
Indices: 494967--495051 Score: 91
Period size: 23 Copynumber: 3.6 Consensus size: 22
494957 AGTATAAGAG
494967 TAATAAAAATAAAAATAAATAGAT
1 TAAT-AAAATAAAAATAAATA-AT
*
494991 TAGTAAAATAAAAATAAATAAT
1 TAATAAAATAAAAATAAATAAT
*
495013 ATAAT-AAATAATAATAAATAAAT
1 -TAATAAAATAAAAATAAAT-AAT
495036 TAAATTAAAATAAAAA
1 T-AA-TAAAATAAAAA
495052 AGGGTAAAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
22 16 0.31
23 24 0.46
24 4 0.08
25 8 0.15
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (22 bp):
TAATAAAATAAAAATAAATAAT
Found at i:496102 original size:23 final size:22
Alignment explanation
Indices: 496071--496155 Score: 91
Period size: 23 Copynumber: 3.6 Consensus size: 22
496061 AGTATAAGAG
496071 TAATAAAAATAAAAATAAATAGAT
1 TAAT-AAAATAAAAATAAATA-AT
*
496095 TAGTAAAATAAAAATAAATAAT
1 TAATAAAATAAAAATAAATAAT
*
496117 ATAAT-AAATAATAATAAATAAAT
1 -TAATAAAATAAAAATAAAT-AAT
496140 TAAATTAAAATAAAAA
1 T-AA-TAAAATAAAAA
496156 AGGGTAAAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
22 16 0.31
23 24 0.46
24 4 0.08
25 8 0.15
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (22 bp):
TAATAAAATAAAAATAAATAAT
Found at i:499559 original size:25 final size:25
Alignment explanation
Indices: 499524--499571 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
499514 TGAAGCAACT
*
499524 GCAGGAGGTAGCTGAGATCTAGGTA
1 GCAGGAAGTAGCTGAGATCTAGGTA
499549 GCAGGAAGTAGCTGAGATCTAGG
1 GCAGGAAGTAGCTGAGATCTAGG
499572 ACAATGCTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.12, G:0.40, T:0.19
Consensus pattern (25 bp):
GCAGGAAGTAGCTGAGATCTAGGTA
Found at i:502929 original size:23 final size:23
Alignment explanation
Indices: 502902--502946 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
502892 TTATATATAT
* *
502902 TTTTTCTTTTTTCTTTTTTTTTCC
1 TTTTT-TTATTTCTCTTTTTTTCC
502926 TTTTTTTATTTCTCTTTTTTT
1 TTTTTTTATTTCTCTTTTTTT
502947 AATTTTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.84
Consensus pattern (23 bp):
TTTTTTTATTTCTCTTTTTTTCC
Found at i:502932 original size:14 final size:14
Alignment explanation
Indices: 502915--502947 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
502905 TTCTTTTTTC
502915 TTTTTT-TTTC-CT
1 TTTTTTATTTCTCT
502927 TTTTTTATTTCTCT
1 TTTTTTATTTCTCT
502941 TTTTTTA
1 TTTTTTA
502948 ATTTTTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 4 0.21
14 9 0.47
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTTATTTCTCT
Found at i:502952 original size:23 final size:23
Alignment explanation
Indices: 502902--502954 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
502892 TTATATATAT
* * **
502902 TTTTTCTTTTTTCTTTTTTTTTCC
1 TTTTT-TTATTTCTCTTTTTTTAA
502926 TTTTTTTATTTCTCTTTTTTTAA
1 TTTTTTTATTTCTCTTTTTTTAA
502949 TTTTTT
1 TTTTTT
502955 CAAACAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (23 bp):
TTTTTTTATTTCTCTTTTTTTAA
Found at i:503917 original size:6 final size:6
Alignment explanation
Indices: 503903--504002 Score: 65
Period size: 6 Copynumber: 16.7 Consensus size: 6
503893 TAAAATGAAT
* * * * * * *
503903 AAAAAC AAAAGC AAACAC AAACAC AAACAC AAACAC AAAATC AAAACC
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
* * * * * * * *
503951 AAAACC AAAACC AAAACC AAAACC AAAATC AAAATC AAAATC AAAATC
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
503999 AAAA
1 AAAA
504003 TAAAATATAA
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 87 1.00
ACGTcount: A:0.69, C:0.25, G:0.01, T:0.05
Consensus pattern (6 bp):
AAAAAC
Found at i:504003 original size:6 final size:6
Alignment explanation
Indices: 503938--504008 Score: 90
Period size: 6 Copynumber: 12.0 Consensus size: 6
503928 AACACAAACA
* * * * *
503938 CAAAAT CAAAAC CAAAAC CAAAAC CAAAAC CAAAAC CAAAAT CAAAAT
1 CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT
503986 CAAAAT CAAAAT CAAAAT -AAAAT
1 CAAAAT CAAAAT CAAAAT CAAAAT
504009 ATAAAATATA
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
5 5 0.08
6 58 0.92
ACGTcount: A:0.68, C:0.23, G:0.00, T:0.10
Consensus pattern (6 bp):
CAAAAT
Found at i:504003 original size:18 final size:18
Alignment explanation
Indices: 503933--504002 Score: 104
Period size: 18 Copynumber: 3.8 Consensus size: 18
503923 ACACAAACAC
503933 AAACACAAAATCAAAACCA
1 AAAC-CAAAATCAAAACCA
*
503952 AAACCAAAACCAAAACCA
1 AAACCAAAATCAAAACCA
*
503970 AAACCAAAATCAAAATCA
1 AAACCAAAATCAAAACCA
*
503988 AAATCAAAATCAAAA
1 AAACCAAAATCAAAA
504003 TAAAATATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
18 43 0.91
19 4 0.09
ACGTcount: A:0.69, C:0.24, G:0.00, T:0.07
Consensus pattern (18 bp):
AAACCAAAATCAAAACCA
Found at i:504014 original size:7 final size:7
Alignment explanation
Indices: 504002--504045 Score: 61
Period size: 7 Copynumber: 5.9 Consensus size: 7
503992 CAAAATCAAA
504002 ATAAAAT
1 ATAAAAT
504009 ATAAAAT
1 ATAAAAT
504016 ATAAAAT
1 ATAAAAT
504023 ATAAAAAT
1 AT-AAAAT
504031 AAATAAAAT
1 --ATAAAAT
504040 ATAAAA
1 ATAAAA
504046 CTAAATGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
7 22 0.65
8 5 0.15
9 5 0.15
10 2 0.06
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (7 bp):
ATAAAAT
Found at i:504038 original size:17 final size:17
Alignment explanation
Indices: 504000--504056 Score: 75
Period size: 17 Copynumber: 3.5 Consensus size: 17
503990 ATCAAAATCA
504000 AAATAAAATAT-AAAAT
1 AAATAAAATATAAAAAT
504016 --ATAAAATATAAAAAT
1 AAATAAAATATAAAAAT
*
504031 AAATAAAATATAAAACT
1 AAATAAAATATAAAAAT
*
504048 AAATGAAAT
1 AAATAAAAT
504057 CACTTTGGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
14 9 0.25
15 5 0.14
17 22 0.61
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (17 bp):
AAATAAAATATAAAAAT
Found at i:504621 original size:14 final size:16
Alignment explanation
Indices: 504584--504623 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
504574 TTTAATTTTT
504584 TAAAAATAATATGAAAG
1 TAAAAATAA-ATGAAAG
504601 T-AAAATAAAT-AAA-
1 TAAAAATAAATGAAAG
504614 TAAAAATAAA
1 TAAAAATAAA
504624 AACACTCGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.05
14 11 0.50
15 2 0.09
16 7 0.32
17 1 0.05
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (16 bp):
TAAAAATAAATGAAAG
Found at i:519080 original size:22 final size:22
Alignment explanation
Indices: 519052--519120 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
519042 TCTCTAATTA
*
519052 TTAGCACATTAGTGCTATCTGT
1 TTAGCACATTAGTGCTCTCTGT
* *
519074 TTAGCACATTTGTGCTCTCTAT
1 TTAGCACATTAGTGCTCTCTGT
* *
519096 ATAGCACTTTAGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
519118 TTA
1 TTA
519121 ATAGTGTATA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.43
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTCTGT
Found at i:520296 original size:23 final size:23
Alignment explanation
Indices: 520262--520308 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
520252 AATGCAGTGG
520262 CATTTTAGTATAATAAAGTAATT
1 CATTTTAGTATAATAAAGTAATT
* *
520285 CATTTTATTATAATCAAGTAATT
1 CATTTTAGTATAATAAAGTAATT
520308 C
1 C
520309 GTTAGCATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (23 bp):
CATTTTAGTATAATAAAGTAATT
Found at i:524848 original size:24 final size:24
Alignment explanation
Indices: 524821--524962 Score: 139
Period size: 24 Copynumber: 5.9 Consensus size: 24
524811 AGCTCCCGTT
524821 ATATGGCTCTTTATGAGCTTCCCG
1 ATATGGCTCTTTATGAGCTTCCCG
* *
524845 ATATGGTTCTTTATGAACTTCCTC-
1 ATATGGCTCTTTATGAGCTTCC-CG
524869 ATTATGGCTC-TTATGAGCTTCCCG
1 A-TATGGCTCTTTATGAGCTTCCCG
* * * * *
524893 TTATATAGC-CCTGATAAGCTTCTCG
1 --ATATGGCTCTTTATGAGCTTCCCG
*
524918 ATAT-GCTCTTTGTGAGCTTCCCG
1 ATATGGCTCTTTATGAGCTTCCCG
*
524941 ATATGGCTCTTTGTGAGCTTCC
1 ATATGGCTCTTTATGAGCTTCC
524963 TGTTATATAG
Statistics
Matches: 97, Mismatches: 13, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
22 2 0.02
23 20 0.21
24 50 0.52
25 24 0.25
26 1 0.01
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.39
Consensus pattern (24 bp):
ATATGGCTCTTTATGAGCTTCCCG
Found at i:524875 original size:73 final size:74
Alignment explanation
Indices: 524751--524975 Score: 169
Period size: 73 Copynumber: 3.1 Consensus size: 74
524741 CCTATTAAAT
* * *
524751 TGGCTCTTTGTGAGCTTCCCGATAGTGCTCGCTTGAACTTCCCGATGTATGGTTATTCGGAGC-T
1 TGGCTCTTTATGAGCTTCCCGATAGTGCTCGCTTGAACTTCCCGATGTATGGCTATTAGGAGCTT
524815 CCCGTTATA
66 CCCGTTATA
* ** * *
524824 TGGCTCTTTATGAGCTTCCCGATA-TGGTTCTTTATGAACTTCCTC-AT-TATGGCTCTTATGAG
1 TGGCTCTTTATGAGCTTCCCGATAGT-GCTCGCT-TGAACTTCC-CGATGTATGGCTATTAGGAG
524886 CTTCCCGTTATA
63 CTTCCCGTTATA
* * * * * ** * * *
524898 TAGC-CCTGATAAGCTTCTCGATA-TGCTCTTTGTGAGCTTCCCGA--TATGGCTCTTTGTGAGC
1 TGGCTCTTTATGAGCTTCCCGATAGTGCTCGCT-TGAACTTCCCGATGTATGGCTATTAG-GAGC
*
524959 TTCCTGTTATA
64 TTCCCGTTATA
*
524970 TAGCTC
1 TGGCTC
524976 GAGAAAGGGT
Statistics
Matches: 126, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
71 11 0.09
72 34 0.27
73 56 0.44
74 24 0.19
75 1 0.01
ACGTcount: A:0.16, C:0.24, G:0.21, T:0.39
Consensus pattern (74 bp):
TGGCTCTTTATGAGCTTCCCGATAGTGCTCGCTTGAACTTCCCGATGTATGGCTATTAGGAGCTT
CCCGTTATA
Found at i:524935 original size:23 final size:24
Alignment explanation
Indices: 524751--524962 Score: 136
Period size: 24 Copynumber: 8.8 Consensus size: 24
524741 CCTATTAAAT
524751 TGGCTCTTTGTGAGCTTCCCGATA
1 TGGCTCTTTGTGAGCTTCCCGATA
** *
524775 -GTGCTCGCT-TGAACTTCCCGATGTA
1 TG-GCTCTTTGTGAGCTTCCCGA--TA
* * *
524800 TGGTTATTCG-GAGC-TCCCGTTATA
1 TGGCTCTTTGTGAGCTTCCCG--ATA
*
524824 TGGCTCTTTATGAGCTTCCCGATA
1 TGGCTCTTTGTGAGCTTCCCGATA
* * *
524848 TGGTTCTTTATGAACTTCCTC-ATTA
1 TGGCTCTTTGTGAGCTTCC-CGA-TA
*
524873 TGGCTC-TTATGAGCTTCCCGTTATA
1 TGGCTCTTTGTGAGCTTCCCG--ATA
* * * *
524898 TAGC-C-CTGATAAGCTTCTCGATA
1 TGGCTCTTTG-TGAGCTTCCCGATA
524921 T-GCTCTTTGTGAGCTTCCCGATA
1 TGGCTCTTTGTGAGCTTCCCGATA
524944 TGGCTCTTTGTGAGCTTCC
1 TGGCTCTTTGTGAGCTTCC
524963 TGTTATATAG
Statistics
Matches: 145, Mismatches: 25, Indels: 36
0.70 0.12 0.17
Matches are distributed among these distances:
22 2 0.01
23 31 0.21
24 71 0.49
25 33 0.23
26 8 0.06
ACGTcount: A:0.16, C:0.25, G:0.21, T:0.38
Consensus pattern (24 bp):
TGGCTCTTTGTGAGCTTCCCGATA
Found at i:529045 original size:14 final size:14
Alignment explanation
Indices: 529008--529065 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
528998 GGAATTTAGG
*
529008 ATAATAAATTGAGA
1 ATAACAAATTGAGA
*
529022 ATTGAC-AATTGAGA
1 A-TAACAAATTGAGA
*
529036 ATAACAAATTCAGA
1 ATAACAAATTGAGA
*
529050 ACAACAAATTGAGA
1 ATAACAAATTGAGA
529064 AT
1 AT
529066 CAAATTGTGA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
13 3 0.09
14 30 0.86
15 2 0.06
ACGTcount: A:0.53, C:0.09, G:0.14, T:0.24
Consensus pattern (14 bp):
ATAACAAATTGAGA
Found at i:545318 original size:7 final size:7
Alignment explanation
Indices: 545300--545352 Score: 83
Period size: 7 Copynumber: 7.9 Consensus size: 7
545290 CACTACATTT
545300 AGTTTT-
1 AGTTTTA
545306 AGTTTTA
1 AGTTTTA
545313 AGTTTTA
1 AGTTTTA
545320 AGTTTTA
1 AGTTTTA
545327 A-TTTTA
1 AGTTTTA
*
545333 TGTTTTA
1 AGTTTTA
545340 AGTTTTA
1 AGTTTTA
545347 AGTTTT
1 AGTTTT
545353 GTTTTACTGC
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
6 11 0.26
7 32 0.74
ACGTcount: A:0.25, C:0.00, G:0.13, T:0.62
Consensus pattern (7 bp):
AGTTTTA
Found at i:545323 original size:20 final size:20
Alignment explanation
Indices: 545300--545352 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
545290 CACTACATTT
545300 AGTTTTAGTTTTAAGTTTTA
1 AGTTTTAGTTTTAAGTTTTA
* *
545320 AGTTTTAATTTTATGTTTTA
1 AGTTTTAGTTTTAAGTTTTA
545340 AGTTTTAAGTTTT
1 AGTTTT-AGTTTT
545353 GTTTTACTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 24 0.83
21 5 0.17
ACGTcount: A:0.25, C:0.00, G:0.13, T:0.62
Consensus pattern (20 bp):
AGTTTTAGTTTTAAGTTTTA
Found at i:545337 original size:27 final size:26
Alignment explanation
Indices: 545297--545352 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 26
545287 ATACACTACA
*
545297 TTTAGTTTTAGTTTTAAGTTTTAAGT
1 TTTAATTTTAGTTTTAAGTTTTAAGT
545323 TTTAATTTTATGTTTTAAGTTTTAAGT
1 TTTAATTTTA-GTTTTAAGTTTTAAGT
545350 TTT
1 TTT
545353 GTTTTACTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 9 0.32
27 19 0.68
ACGTcount: A:0.23, C:0.00, G:0.12, T:0.64
Consensus pattern (26 bp):
TTTAATTTTAGTTTTAAGTTTTAAGT
Found at i:545459 original size:14 final size:14
Alignment explanation
Indices: 545440--545473 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
545430 GCATCAAGCT
545440 ACCTCCACCGATCC
1 ACCTCCACCGATCC
* *
545454 ACCTCCACTGGTCC
1 ACCTCCACCGATCC
545468 ACCTCC
1 ACCTCC
545474 GGTCCTCTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.56, G:0.09, T:0.18
Consensus pattern (14 bp):
ACCTCCACCGATCC
Found at i:545966 original size:44 final size:44
Alignment explanation
Indices: 545912--546058 Score: 269
Period size: 44 Copynumber: 3.4 Consensus size: 44
545902 AAGTAGAGAT
545912 ATTT-AGCATGTTTTGGGATGACTCAGTATTTTGAGTTTAGGTG
1 ATTTGAGCATGTTTTGGGATGACTCAGTATTTTGAGTTTAGGTG
*
545955 ATTTGAGCATGTTTTGGGATGACTCAGTGTTTTGAGTTTAGGTG
1 ATTTGAGCATGTTTTGGGATGACTCAGTATTTTGAGTTTAGGTG
545999 ATTTGAGCATGTTTTGGGATGACTCAGTATTTTGAGTTTAGGTG
1 ATTTGAGCATGTTTTGGGATGACTCAGTATTTTGAGTTTAGGTG
*
546043 ATTTGAGCATTTTTTG
1 ATTTGAGCATGTTTTG
546059 AAAGCCTACA
Statistics
Matches: 100, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
43 4 0.04
44 96 0.96
ACGTcount: A:0.20, C:0.07, G:0.29, T:0.45
Consensus pattern (44 bp):
ATTTGAGCATGTTTTGGGATGACTCAGTATTTTGAGTTTAGGTG
Found at i:546268 original size:21 final size:21
Alignment explanation
Indices: 546244--546296 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 21
546234 TTTTAATTTA
546244 CTTAATTGTT-GTTGTATTTTG
1 CTTAATT-TTCGTTGTATTTTG
546265 CTTAATTTTCGCGTTGTATTTTG
1 CTTAATTTT--CGTTGTATTTTG
546288 CTTAATTTT
1 CTTAATTTT
546297 TGCGTTTGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 2 0.07
21 7 0.24
23 20 0.69
ACGTcount: A:0.15, C:0.09, G:0.15, T:0.60
Consensus pattern (21 bp):
CTTAATTTTCGTTGTATTTTG
Found at i:546284 original size:23 final size:23
Alignment explanation
Indices: 546254--546302 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
546244 CTTAATTGTT
546254 GTTGTATTTTGCTTAATTTTCGC
1 GTTGTATTTTGCTTAATTTTCGC
*
546277 GTTGTATTTTGCTTAATTTTTGC
1 GTTGTATTTTGCTTAATTTTCGC
546300 GTT
1 GTT
546303 TGAGTCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.12, C:0.10, G:0.18, T:0.59
Consensus pattern (23 bp):
GTTGTATTTTGCTTAATTTTCGC
Found at i:546751 original size:5 final size:5
Alignment explanation
Indices: 546720--546749 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
546710 TTCTTTTTAG
*
546720 AATTT AATTT AATTT AATTT AATTT TATTT
1 AATTT AATTT AATTT AATTT AATTT AATTT
546750 TACTTTGTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
AATTT
Found at i:570662 original size:21 final size:19
Alignment explanation
Indices: 570638--570680 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
570628 GTTCCTGAGC
*
570638 CACACGGCCTGGGCTCTGT
1 CACACAGCCTGGGCTCTGT
570657 CACACAGCCTGGGCTCTGT
1 CACACAGCCTGGGCTCTGT
570676 CACAC
1 CACAC
570681 CGCCCTGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.16, C:0.40, G:0.26, T:0.19
Consensus pattern (19 bp):
CACACAGCCTGGGCTCTGT
Found at i:572247 original size:17 final size:18
Alignment explanation
Indices: 572222--572262 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
572212 TTGTTTTCTT
*
572222 TTTACTCTTTTA-GTTTC
1 TTTACTCTTTTATGTTTA
*
572239 TTTATTCTTTTATGTTTA
1 TTTACTCTTTTATGTTTA
572257 TTTACT
1 TTTACT
572263 TTATTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.15, C:0.12, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTACTCTTTTATGTTTA
Found at i:572264 original size:23 final size:23
Alignment explanation
Indices: 572230--572273 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
572220 TTTTTACTCT
*
572230 TTTAGTTTCTTTATTCTTTTATG
1 TTTAGTTTCTTTATTATTTTATG
572253 TTTA-TTTACTTTATTATTTTA
1 TTTAGTTT-CTTTATTATTTTA
572274 ATGATAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.18, C:0.07, G:0.05, T:0.70
Consensus pattern (23 bp):
TTTAGTTTCTTTATTATTTTATG
Found at i:572617 original size:9 final size:9
Alignment explanation
Indices: 572603--572651 Score: 66
Period size: 9 Copynumber: 5.6 Consensus size: 9
572593 AATTTGAATA
572603 AATAATTAT
1 AATAATTAT
572612 AATAATTAT
1 AATAATTAT
572621 AATAATTAT
1 AATAATTAT
572630 -ATAGA-TAT
1 AATA-ATTAT
*
572638 AATATTTAT
1 AATAATTAT
572647 AATAA
1 AATAA
572652 CTTGAATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 6 0.17
9 29 0.83
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (9 bp):
AATAATTAT
Found at i:573069 original size:165 final size:167
Alignment explanation
Indices: 572765--573072 Score: 383
Period size: 165 Copynumber: 1.9 Consensus size: 167
572755 CTTTCACTCT
* * ** * *
572765 TTATTCGATTTGATCCTTTTTTCCTAATTATTCTTAATTAGACTAAATTCACCTAATTGATACCT
1 TTATTCAATTTAATCCTTTTTTCCTAATTACCCTTAATTAGACTAAATTCACCTAATTAAAACCT
* * * * *
572830 AATTAAACATACAACTAGTCTCGTAAATATTTCTAATAATTATTTTCAAACTCAGTTTACTAAGA
66 AATTAAACATACAACTAGACTCATAAATATTTCTAATAATTATTATCAAACTAAATTTACTAAGA
*
572895 TGGAGGCCCGATATTATACTTTTCCGATGCCCGTAAA
131 CGGAGGCCCGATATTATACTTTTCCGATGCCCGTAAA
*
572932 TTATTCAATTTAATCC-TTTTTCC-AATTACCCTTAATTA-AGCTAAATTCACTTAATTAAAACC
1 TTATTCAATTTAATCCTTTTTTCCTAATTACCCTTAATTAGA-CTAAATTCACCTAATTAAAACC
* * *** *
572994 TAATTAAGC-TCACTACTAGACTCATAAATATTTCTAATAATTATCTAT-AGGTTAAATTTTCTA
65 TAATTAAACAT-ACAACTAGACTCATAAATATTTCTAATAATTAT-TATCAAACTAAATTTACTA
573057 AGACGGAGGCCCGATA
128 AGACGGAGGCCCGATA
573073 CTACAATTTT
Statistics
Matches: 119, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
164 2 0.02
165 94 0.79
166 9 0.08
167 14 0.12
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.39
Consensus pattern (167 bp):
TTATTCAATTTAATCCTTTTTTCCTAATTACCCTTAATTAGACTAAATTCACCTAATTAAAACCT
AATTAAACATACAACTAGACTCATAAATATTTCTAATAATTATTATCAAACTAAATTTACTAAGA
CGGAGGCCCGATATTATACTTTTCCGATGCCCGTAAA
Found at i:584768 original size:214 final size:215
Alignment explanation
Indices: 584527--584959 Score: 850
Period size: 214 Copynumber: 2.0 Consensus size: 215
584517 TTCAATAAAC
584527 TATTAAGATATAATTTTTTTCATCTTGGATTTAATTGCTAAATAATTTTTTTTAATTTTTTATTT
1 TATTAAGATAT-ATTTTTTTCATCTTGGATTTAATTGCTAAATAATTTTTTTTAATTTTTTATTT
584592 AAAGATTATATAAAAATATAAAAATACAAAAATATCTTTACAACAATATTAATTACTTTTTAAAA
65 AAAGATTATATAAAAATATAAAAATACAAAAATATCTTTACAACAATATTAATTACTTTTTAAAA
584657 TAAGAATATTTTAGTAGATTTACAATTAAATTGATATTGAGTTGACTTGTGACCCCAACTCAGTC
130 TAAGAATATTTTAGTAGATTTACAATTAAATTGATATTGAGTTGACTTGTGACCCCAACTCAGTC
584722 AACTATTTTATATATAGTATA
195 AACTATTTTATATATAGTATA
584743 TATTAAGATAT-TTTTTTTCATCTTGGATTTAATTGCTAAATAATTTTTTTTAATTTTTTATTTA
1 TATTAAGATATATTTTTTTCATCTTGGATTTAATTGCTAAATAATTTTTTTTAATTTTTTATTTA
584807 AAGATTATATAAAAATATAAAAATACAAAAATATCTTTACAACAATATTAATTACTTTTTAAAAT
66 AAGATTATATAAAAATATAAAAATACAAAAATATCTTTACAACAATATTAATTACTTTTTAAAAT
584872 AAGAATATTTTAGTAGATTTACAATTAAATTGATATTGAGTTGACTTGTGACCCCAACTCAGTCA
131 AAGAATATTTTAGTAGATTTACAATTAAATTGATATTGAGTTGACTTGTGACCCCAACTCAGTCA
584937 ACTATTTTATATATAGTATA
196 ACTATTTTATATATAGTATA
584957 TAT
1 TAT
584960 AAAAGTCACA
Statistics
Matches: 217, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
214 206 0.95
216 11 0.05
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.44
Consensus pattern (215 bp):
TATTAAGATATATTTTTTTCATCTTGGATTTAATTGCTAAATAATTTTTTTTAATTTTTTATTTA
AAGATTATATAAAAATATAAAAATACAAAAATATCTTTACAACAATATTAATTACTTTTTAAAAT
AAGAATATTTTAGTAGATTTACAATTAAATTGATATTGAGTTGACTTGTGACCCCAACTCAGTCA
ACTATTTTATATATAGTATA
Found at i:585538 original size:17 final size:17
Alignment explanation
Indices: 585516--585550 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
585506 TATGTCTCTT
585516 TTTTTAAGTA-TTTATTA
1 TTTTTAA-TATTTTATTA
585533 TTTTTAATATTTTATTA
1 TTTTTAATATTTTATTA
585550 T
1 T
585551 ATCTCTATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTTAATATTTTATTA
Found at i:590657 original size:26 final size:26
Alignment explanation
Indices: 590606--590659 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
590596 TTCTTAGAAG
* *
590606 ATTTAGTATTTATGAGTATATAATAT
1 ATTTAGCATTTATGAGCATATAATAT
*
590632 ATTTAGCATTTATTAGC--ATAATAT
1 ATTTAGCATTTATGAGCATATAATAT
590656 ATTT
1 ATTT
590660 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 11 0.44
26 14 0.56
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (26 bp):
ATTTAGCATTTATGAGCATATAATAT
Found at i:596213 original size:17 final size:18
Alignment explanation
Indices: 596191--596229 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
596181 AGATATTTGT
*
596191 TATATA-TTATTTTTTAA
1 TATATATTTATATTTTAA
596208 TATATATTTATATTTTAA
1 TATATATTTATATTTTAA
596226 -ATAT
1 TATAT
596230 GTGATATTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATATATTTATATTTTAA
Found at i:596223 original size:19 final size:17
Alignment explanation
Indices: 596191--596229 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
596181 AGATATTTGT
*
596191 TATATATTATTTTTTAA
1 TATATATTATTTTTAAA
596208 TATATATTTATATTTTAAA
1 TATATA-TTAT-TTTTAAA
596227 TAT
1 TAT
596230 GTGATATTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATATTATTTTTAAA
Found at i:596713 original size:48 final size:50
Alignment explanation
Indices: 596659--596767 Score: 145
Period size: 51 Copynumber: 2.2 Consensus size: 50
596649 TATTTCTTCA
*
596659 CCATCGTCTTCAACATTTTTC-CTTG-CTACTTTCTCTTTCGTTTTCCCTG
1 CCATCGTCTTCAACATTTTTCTCTTGTCT-CTTTCTCTTTCCTTTTCCCTG
*
596708 -CATCGTCTTCAACATTTTTCATTCTTGTCTCTTTCTCTTTCCTTTTCTCTG
1 CCATCGTCTTCAACATTTTTC--TCTTGTCTCTTTCTCTTTCCTTTTCCCTG
596759 CCATC-TCTT
1 CCATCGTCTT
596768 TCATTTTTCC
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
48 20 0.38
51 27 0.51
52 6 0.11
ACGTcount: A:0.10, C:0.32, G:0.06, T:0.51
Consensus pattern (50 bp):
CCATCGTCTTCAACATTTTTCTCTTGTCTCTTTCTCTTTCCTTTTCCCTG
Found at i:597614 original size:14 final size:14
Alignment explanation
Indices: 597595--597642 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
597585 ATAAACTGTA
*
597595 CATCAAAATACAAC
1 CATCAAAATAAAAC
* *
597609 CATCAAAAT-GATC
1 CATCAAAATAAAAC
*
597622 CAACAAAATAAAAC
1 CATCAAAATAAAAC
597636 CATCAAA
1 CATCAAA
597643 TTATCTACAG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.58, C:0.25, G:0.02, T:0.15
Consensus pattern (14 bp):
CATCAAAATAAAAC
Found at i:597670 original size:36 final size:34
Alignment explanation
Indices: 597623--597747 Score: 107
Period size: 36 Copynumber: 3.6 Consensus size: 34
597613 AAAATGATCC
597623 AACAAAATAAAACCATCAAATTATCTACAGTATGTT
1 AACAAAATAAAACCATCAAATTATC-A-AGTATGTT
* * *
597659 AACAAAATAAAACCATC----CATCAA-AATGATCC
1 AACAAAATAAAACCATCAAATTATCAAGTATG-T-T
* *
597690 AACAAAATCAAACCATCTAATTATCCATAGTATGTT
1 AACAAAATAAAACCATCAAATTAT-CA-AGTATGTT
*
597726 AACAAAATCAAACCATCAAATT
1 AACAAAATAAAACCATCAAATT
597748 TTCCATCAAT
Statistics
Matches: 72, Mismatches: 8, Indels: 18
0.73 0.08 0.18
Matches are distributed among these distances:
29 3 0.04
30 2 0.03
31 17 0.24
32 3 0.04
35 2 0.03
36 40 0.56
37 2 0.03
38 3 0.04
ACGTcount: A:0.51, C:0.21, G:0.04, T:0.24
Consensus pattern (34 bp):
AACAAAATAAAACCATCAAATTATCAAGTATGTT
Found at i:597683 original size:67 final size:67
Alignment explanation
Indices: 597608--597742 Score: 225
Period size: 67 Copynumber: 2.0 Consensus size: 67
597598 CAAAATACAA
*
597608 CCATCAAAATGATCCAACAAAATAAAACCATCAAATTATCTACAGTATGTTAACAAAATAAAACC
1 CCATCAAAATGATCCAACAAAATAAAACCATCAAATTATCCACAGTATGTTAACAAAATAAAACC
597673 AT
66 AT
* * * *
597675 CCATCAAAATGATCCAACAAAATCAAACCATCTAATTATCCATAGTATGTTAACAAAATCAAACC
1 CCATCAAAATGATCCAACAAAATAAAACCATCAAATTATCCACAGTATGTTAACAAAATAAAACC
597740 AT
66 AT
597742 C
1 C
597743 AAATTTTCCA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.50, C:0.23, G:0.04, T:0.23
Consensus pattern (67 bp):
CCATCAAAATGATCCAACAAAATAAAACCATCAAATTATCCACAGTATGTTAACAAAATAAAACC
AT
Found at i:598686 original size:26 final size:26
Alignment explanation
Indices: 598650--598701 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
598640 CTACTAAAGC
598650 ATGTGGATATGGGATGCCAGTGAGAT
1 ATGTGGATATGGGATGCCAGTGAGAT
598676 ATGTGGATATGGGATGCCAGTGAGAT
1 ATGTGGATATGGGATGCCAGTGAGAT
598702 CCTATCTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.08, G:0.38, T:0.27
Consensus pattern (26 bp):
ATGTGGATATGGGATGCCAGTGAGAT
Found at i:601123 original size:14 final size:14
Alignment explanation
Indices: 601104--601134 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
601094 TGAAAATATA
601104 AACCAAGTGAACCG
1 AACCAAGTGAACCG
601118 AACCAAGTGAACCG
1 AACCAAGTGAACCG
601132 AAC
1 AAC
601135 TGACTAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.29, G:0.19, T:0.06
Consensus pattern (14 bp):
AACCAAGTGAACCG
Found at i:608722 original size:10 final size:9
Alignment explanation
Indices: 608709--608851 Score: 65
Period size: 9 Copynumber: 14.9 Consensus size: 9
608699 ATACATATTT
608709 TAAACAGTAA
1 TAAACA-TAA
608719 TAAACATAA
1 TAAACATAA
* *
608728 CATACATACA
1 TAAACATA-A
608738 TAAACAGTAA
1 TAAACA-TAA
608748 TAAACATAA
1 TAAACATAA
* *
608757 CATACATAA
1 TAAACATAA
*
608766 TATACATACA
1 TAAACATA-A
*
608776 T-AACATAC
1 TAAACATAA
608784 TAACAGACATACA
1 T-A-A-ACATA-A
*
608797 TAAATAGTAA
1 TAAACA-TAA
*
608807 TATACATAA
1 TAAACATAA
* *
608816 CATACATAA
1 TAAACATAA
*
608825 TATACATACA
1 TAAACATA-A
608835 T-AACAATAA
1 TAAAC-ATAA
*
608844 TATACATA
1 TAAACATA
608852 CATACATACA
Statistics
Matches: 104, Mismatches: 17, Indels: 25
0.71 0.12 0.17
Matches are distributed among these distances:
8 1 0.01
9 56 0.54
10 34 0.33
11 6 0.06
12 6 0.06
13 1 0.01
ACGTcount: A:0.57, C:0.16, G:0.03, T:0.24
Consensus pattern (9 bp):
TAAACATAA
Found at i:608736 original size:4 final size:4
Alignment explanation
Indices: 608722--608931 Score: 186
Period size: 4 Copynumber: 51.8 Consensus size: 4
608712 ACAGTAATAA
*
608722 ACAT AACAT ACAT ACAT A-A- ACAGT A-AT A-A- ACAT AACAT ACAT AATAT
1 ACAT -ACAT ACAT ACAT ACAT ACA-T ACAT ACAT ACAT -ACAT ACAT -ACAT
* * * *
608769 ACAT ACAT AACAT AC-T AACAG ACAT ACAT AAAT A-GT AATAT ACAT AACAT
1 ACAT ACAT -ACAT ACAT -ACAT ACAT ACAT ACAT ACAT -ACAT ACAT -ACAT
* *
608819 ACAT AATAT ACAT ACAT AACAAT AATAT ACAT ACAT ACAT ACAT ACAT
1 ACAT -ACAT ACAT ACAT -AC-AT -ACAT ACAT ACAT ACAT ACAT ACAT
608867 ACAT ACAT ACAT ACAT --AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
608913 ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACA
608932 CAGTAATATT
Statistics
Matches: 175, Mismatches: 12, Indels: 37
0.78 0.05 0.17
Matches are distributed among these distances:
2 4 0.02
3 8 0.05
4 131 0.75
5 28 0.16
6 4 0.02
ACGTcount: A:0.54, C:0.20, G:0.01, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:608737 original size:34 final size:32
Alignment explanation
Indices: 608695--608827 Score: 108
Period size: 29 Copynumber: 4.4 Consensus size: 32
608685 AAATTGTAAT
608695 ATACATACATATTTTAAACAGTAATAAACATAAC
1 ATACATACATA--TTAAACAGTAATAAACATAAC
608729 ATACATAC--A-TAAACAGTAATAAACATAAC
1 ATACATACATATTAAACAGTAATAAACATAAC
* *
608758 ATACATA-ATA-TACATACA-TAACATAC-TAAC
1 ATACATACATATTA-A-ACAGTAATAAACATAAC
* * *
608788 AGACATAC--A-TAAATAGTAATATACATAAC
1 ATACATACATATTAAACAGTAATAAACATAAC
608817 ATACATA-ATAT
1 ATACATACATAT
608828 ACATACATAA
Statistics
Matches: 83, Mismatches: 6, Indels: 23
0.74 0.05 0.21
Matches are distributed among these distances:
27 2 0.02
28 8 0.10
29 40 0.48
30 14 0.17
31 7 0.08
32 4 0.05
34 8 0.10
ACGTcount: A:0.55, C:0.16, G:0.03, T:0.26
Consensus pattern (32 bp):
ATACATACATATTAAACAGTAATAAACATAAC
Found at i:608763 original size:59 final size:59
Alignment explanation
Indices: 608720--608893 Score: 207
Period size: 59 Copynumber: 3.0 Consensus size: 59
608710 AAACAGTAAT
*
608720 AAACATAACATACATACATAAACAGTAATAAACATAACATACATAATATACATACATAAC
1 AAAC-TAACAGACATACATAAACAGTAATAAACATAACATACATAATATACATACATAAC
* * *
608780 ATACTAACAGACATACATAAATAGTAATATACATAACATACATAATATACATACATAAC
1 AAACTAACAGACATACATAAACAGTAATAAACATAACATACATAATATACATACATAAC
* *
608839 -AA-TAATATACATACAT--ACA-TACATACATACAT-ACATACATACATATACATACATA
1 AAACTAACAGACATACATAAACAGTA-ATA-A-ACATAACATACATA-ATATACATACATA
608894 CATACATACA
Statistics
Matches: 101, Mismatches: 9, Indels: 11
0.83 0.07 0.09
Matches are distributed among these distances:
54 2 0.02
55 5 0.05
56 9 0.09
57 29 0.29
58 1 0.01
59 52 0.51
60 3 0.03
ACGTcount: A:0.55, C:0.18, G:0.02, T:0.25
Consensus pattern (59 bp):
AAACTAACAGACATACATAAACAGTAATAAACATAACATACATAATATACATACATAAC
Found at i:608764 original size:38 final size:37
Alignment explanation
Indices: 608722--608997 Score: 177
Period size: 38 Copynumber: 7.5 Consensus size: 37
608712 ACAGTAATAA
608722 ACATAACATACATACATAAACAGTAATAAACATAACAT
1 ACATAACATACATACATAAACA-TAATAAACATAACAT
* * *
608760 ACATAATATACATACAT-AACATACT-AACA-GACAT
1 ACATAACATACATACATAAACATAATAAACATAACAT
* * * * *
608794 ACATAA-ATA-GTA-ATATACATAACATACATAATAT
1 ACATAACATACATACATAAACATAATAAACATAACAT
*
608828 ACAT-ACATAACAATA-ATATACATACATACATACAT-ACAT
1 ACATAACAT-AC-ATACATAAACATA-ATA-A-ACATAACAT
*
608867 ACAT-ACATACATACATATACATACAT--ACAT-ACAT
1 ACATAACATACATACATAAACATA-ATAAACATAACAT
* *
608901 ACAT-ACATACATACATACATACATACATACACAGTAATAT
1 ACATAACATACATACATA-A-ACATA-ATAAACA-TAACAT
* * * *
608941 TCATAACAGACATA-ATAGACATACATAAACAATAATAT
1 ACATAACATACATACATAAACATA-ATAAAC-ATAACAT
*
608979 ACATAACATACAAACATAA
1 ACATAACATACATACATAA
608998 CAGATCGACC
Statistics
Matches: 194, Mismatches: 24, Indels: 39
0.75 0.09 0.15
Matches are distributed among these distances:
31 2 0.01
32 7 0.04
33 7 0.04
34 44 0.23
35 5 0.03
36 11 0.06
37 18 0.09
38 63 0.32
39 16 0.08
40 13 0.07
41 8 0.04
ACGTcount: A:0.54, C:0.19, G:0.02, T:0.24
Consensus pattern (37 bp):
ACATAACATACATACATAAACATAATAAACATAACAT
Found at i:608996 original size:8 final size:9
Alignment explanation
Indices: 608722--608996 Score: 165
Period size: 8 Copynumber: 31.1 Consensus size: 9
608712 ACAGTAATAA
608722 ACATAACAT
1 ACATAACAT
608731 ACAT-ACAT
1 ACATAACAT
* *
608739 AAACAGTAATAA
1 --ACA-TAACAT
608751 ACATAACAT
1 ACATAACAT
*
608760 ACATAATAT
1 ACATAACAT
608769 ACAT-ACAT
1 ACATAACAT
608777 AACAT-AC-T
1 -ACATAACAT
*
608785 AACA-GACAT
1 -ACATAACAT
608794 ACATAA-AT
1 ACATAACAT
* *
608802 A-GTAATAT
1 ACATAACAT
608810 ACATAACAT
1 ACATAACAT
*
608819 ACATAATAT
1 ACATAACAT
608828 ACAT-ACAT
1 ACATAACAT
*
608836 AACAATAATAT
1 -AC-ATAACAT
608847 ACAT-ACAT
1 ACATAACAT
608855 ACAT-ACAT
1 ACATAACAT
608863 ACAT-ACAT
1 ACATAACAT
608871 ACAT-ACAT
1 ACATAACAT
608879 ACATATACAT
1 ACATA-ACAT
608889 ACAT-ACAT
1 ACATAACAT
608897 ACAT-ACAT
1 ACATAACAT
608905 ACAT-ACAT
1 ACATAACAT
608913 ACAT-ACAT
1 ACATAACAT
608921 ACAT-ACAT
1 ACATAACAT
*
608929 ACACAGTAATAT
1 --ACA-TAACAT
* *
608941 TCATAACAG
1 ACATAACAT
* *
608950 ACATAATAG
1 ACATAACAT
608959 ACAT-ACAT
1 ACATAACAT
*
608967 AAACAATAATAT
1 --AC-ATAACAT
608979 ACATAACAT
1 ACATAACAT
608988 ACA-AACAT
1 ACATAACAT
608996 A
1 A
608997 ACAGATCGAC
Statistics
Matches: 219, Mismatches: 24, Indels: 47
0.76 0.08 0.16
Matches are distributed among these distances:
7 3 0.01
8 101 0.46
9 73 0.33
10 27 0.12
11 7 0.03
12 8 0.04
ACGTcount: A:0.54, C:0.19, G:0.02, T:0.24
Consensus pattern (9 bp):
ACATAACAT
Found at i:611984 original size:24 final size:24
Alignment explanation
Indices: 611948--611998 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
611938 ATCTTTGTTA
* *
611948 ATGCAATTTAGACACAATGGTTTT
1 ATGCAATTCAGACACAATGGTTCT
611972 ATGCAATTCAGACACAATGGTTCT
1 ATGCAATTCAGACACAATGGTTCT
611996 ATG
1 ATG
611999 TCTACGTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (24 bp):
ATGCAATTCAGACACAATGGTTCT
Found at i:612583 original size:21 final size:21
Alignment explanation
Indices: 612557--612598 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
612547 CAAACAATGA
* *
612557 CAAAAAGTATCGATATCTTTT
1 CAAAAAGTAACGATACCTTTT
612578 CAAAAAGTAACGATACCTTTT
1 CAAAAAGTAACGATACCTTTT
612599 ATCAGGTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (21 bp):
CAAAAAGTAACGATACCTTTT
Found at i:614614 original size:27 final size:27
Alignment explanation
Indices: 614558--614616 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
614548 TTAGGAAATG
* *
614558 AAAGCCTTTGTGGTGAATCATGAAAGA
1 AAAGCCTTTGTGGTAAAACATGAAAGA
614585 AAAGCCTTTGTGGTAAAACATGAAAGA
1 AAAGCCTTTGTGGTAAAACATGAAAGA
614612 AAAGC
1 AAAGC
614617 ATGTGTGGCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.22
Consensus pattern (27 bp):
AAAGCCTTTGTGGTAAAACATGAAAGA
Found at i:614623 original size:27 final size:27
Alignment explanation
Indices: 614566--614624 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
614556 TGAAAGCCTT
* * * *
614566 TGTGGTGAATCATGAAAGAAAAGCCTT
1 TGTGGTAAAACATGAAAGAAAAGCATG
614593 TGTGGTAAAACATGAAAGAAAAGCATG
1 TGTGGTAAAACATGAAAGAAAAGCATG
614620 TGTGG
1 TGTGG
614625 CGAATTATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.39, C:0.08, G:0.29, T:0.24
Consensus pattern (27 bp):
TGTGGTAAAACATGAAAGAAAAGCATG
Found at i:615894 original size:22 final size:22
Alignment explanation
Indices: 615869--615913 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
615859 TTTCATGTTT
*
615869 ATCTAATCTCCTCAAACAATTC
1 ATCTAATCACCTCAAACAATTC
615891 ATCTAATCACCTCAAACAATTC
1 ATCTAATCACCTCAAACAATTC
615913 A
1 A
615914 GTTGGGGTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.31, G:0.00, T:0.29
Consensus pattern (22 bp):
ATCTAATCACCTCAAACAATTC
Found at i:616423 original size:32 final size:32
Alignment explanation
Indices: 616387--616453 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 32
616377 ATTTTAAATC
616387 AAATAAAT-TATTAAAAAATCA-TAAAAAAATAA
1 AAATAAATAT-TTAAAAAA-CATTAAAAAAATAA
* * *
616419 AAATATATATTTAAAAAACATTAGAAAATTAA
1 AAATAAATATTTAAAAAACATTAAAAAAATAA
616451 AAA
1 AAA
616454 CTGTCAGTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
31 2 0.07
32 27 0.90
33 1 0.03
ACGTcount: A:0.69, C:0.03, G:0.01, T:0.27
Consensus pattern (32 bp):
AAATAAATATTTAAAAAACATTAAAAAAATAA
Found at i:629696 original size:23 final size:22
Alignment explanation
Indices: 629655--629700 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
629645 GTTATTTCAC
**
629655 TAAAGTACATTAAAGTTGAATAA
1 TAAAGTACAAGAAAGTTG-ATAA
*
629678 TAAAGTACAAGAAATTTGATAA
1 TAAAGTACAAGAAAGTTGATAA
629700 T
1 T
629701 TAGTGAAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.52, C:0.04, G:0.13, T:0.30
Consensus pattern (22 bp):
TAAAGTACAAGAAAGTTGATAA
Found at i:637580 original size:18 final size:18
Alignment explanation
Indices: 637557--637594 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
637547 GAAAAATATA
637557 TAGATCCATATATGGACT
1 TAGATCCATATATGGACT
637575 TAGATCCATATATGGACT
1 TAGATCCATATATGGACT
637593 TA
1 TA
637595 AGCAATCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (18 bp):
TAGATCCATATATGGACT
Found at i:643359 original size:29 final size:28
Alignment explanation
Indices: 643327--643388 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
643317 AAAAAGCCAT
*
643327 TTTTTTCAAAATTTACCGAAATGGGTCGA
1 TTTTTTCAAAATTTACCGAAAT-GGTCCA
* ** *
643356 TTTTTTGATTATTTACCGGAATGGTCCA
1 TTTTTTCAAAATTTACCGAAATGGTCCA
643384 TTTTT
1 TTTTT
643389 CGGGAAATCG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 10 0.36
29 18 0.64
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (28 bp):
TTTTTTCAAAATTTACCGAAATGGTCCA
Found at i:643666 original size:22 final size:22
Alignment explanation
Indices: 643640--643989 Score: 700
Period size: 22 Copynumber: 15.9 Consensus size: 22
643630 CTCTCTAATC
643640 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
643662 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
643684 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
643706 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
643728 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
643750 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
643772 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
643794 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
643816 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
643838 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
643860 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
643882 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
643904 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
643926 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
643948 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
643970 CTCTCAATTTCCTTCCAAAA
1 CTCTCAATTTCCTTCCAAAA
643990 ACTACCTGCG
Statistics
Matches: 328, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 328 1.00
ACGTcount: A:0.27, C:0.32, G:0.00, T:0.41
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:644224 original size:29 final size:29
Alignment explanation
Indices: 644179--644274 Score: 156
Period size: 29 Copynumber: 3.3 Consensus size: 29
644169 GTGGACGGGC
644179 ACCCTAACCTAAATTAACTAAAAACCCTA
1 ACCCTAACCTAAATTAACTAAAAACCCTA
* *
644208 ACTCTAACCTAAATTAATTAAAAACCCTA
1 ACCCTAACCTAAATTAACTAAAAACCCTA
* *
644237 ACCCTAACCTAAATTACCTAAAAACTCTA
1 ACCCTAACCTAAATTAACTAAAAACCCTA
644266 ACCCTAACC
1 ACCCTAACC
644275 GTAACCATTA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 61 1.00
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (29 bp):
ACCCTAACCTAAATTAACTAAAAACCCTA
Done.