Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 59 of 144
Found at i:12229399 original size:33 final size:32
Alignment explanation
Indices: 12229359--12229437 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 32
12229349 GTTCTAAATT
* *
12229359 TTATTTTTGATCTTT-TCATTATTTTAACTTTTA
1 TTATTTTT-AT-TTTCTAATTATTTCAACTTTTA
12229392 TTATTTTTATTTTGCTAATTATTTCAACTTTTA
1 TTATTTTTATTTT-CTAATTATTTCAACTTTTA
12229425 TTATTTTTATTTT
1 TTATTTTTATTTT
12229438 GCTTTTTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.07
32 2 0.05
33 37 0.88
ACGTcount: A:0.22, C:0.08, G:0.03, T:0.68
Consensus pattern (32 bp):
TTATTTTTATTTTCTAATTATTTCAACTTTTA
Found at i:12229438 original size:33 final size:33
Alignment explanation
Indices: 12229376--12229440 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
12229366 TGATCTTTTC
*
12229376 ATTATTTTAACTTTTATTATTTTTATTTTGCTA
1 ATTATTTCAACTTTTATTATTTTTATTTTGCTA
12229409 ATTATTTCAACTTTTATTATTTTTATTTTGCT
1 ATTATTTCAACTTTTATTATTTTTATTTTGCT
12229441 TTTTTTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.66
Consensus pattern (33 bp):
ATTATTTCAACTTTTATTATTTTTATTTTGCTA
Found at i:12230049 original size:106 final size:109
Alignment explanation
Indices: 12229841--12230050 Score: 261
Period size: 106 Copynumber: 1.9 Consensus size: 109
12229831 CAAGACAATG
* * * ** *
12229841 TTCTTTTATTTTAGGGAATTCAAGAAATTGTGTCCTAACGTGTTGGGTATAGTTTTTCCTTTGAA
1 TTCTTTTATTTTAGGGAATTCAAGAAATTATGTCCAAACATACTGGGTATAGATTTT-CTTTGAA
*
12229906 CCTAAATAATCAAGTATCCTTTTTAAAATCAATAAATGTTCGATA
65 CCTAAATAATCAAGCATCCTTTTTAAAATCAATAAATGTTCGATA
12229951 TTCTTTTA-TTTAGGGAATTCAAGAAATTATG-CTCAAACATACTGGGTAT-GATTTT-TTTGAA
1 TTCTTTTATTTTAGGGAATTCAAGAAATTATGTC-CAAACATACTGGGTATAGATTTTCTTTGAA
* *
12230012 CCTAAATAATTGAA-CAT-CTTATTTAAAATCGATAAATGT
65 CCTAAATAA-TCAAGCATCCTT-TTTAAAATCAATAAATGT
12230051 CCTTTGTCAT
Statistics
Matches: 88, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
105 3 0.03
106 34 0.39
107 3 0.03
108 6 0.07
109 34 0.39
110 8 0.09
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (109 bp):
TTCTTTTATTTTAGGGAATTCAAGAAATTATGTCCAAACATACTGGGTATAGATTTTCTTTGAAC
CTAAATAATCAAGCATCCTTTTTAAAATCAATAAATGTTCGATA
Found at i:12233331 original size:25 final size:25
Alignment explanation
Indices: 12233303--12233353 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
12233293 CTATCAACGA
* *
12233303 TCAATGGGTCGAGTCAACGGTTTGG
1 TCAACGGGTCGAGTCAACAGTTTGG
12233328 TCAACGGGTCGAGTCAACAGTTTGG
1 TCAACGGGTCGAGTCAACAGTTTGG
12233353 T
1 T
12233354 TAACAAGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.27
Consensus pattern (25 bp):
TCAACGGGTCGAGTCAACAGTTTGG
Found at i:12233381 original size:12 final size:12
Alignment explanation
Indices: 12233303--12233382 Score: 52
Period size: 13 Copynumber: 6.4 Consensus size: 12
12233293 CTATCAACGA
*
12233303 TCAATGGGTCGAG
1 TCAACGGGTCG-G
* *
12233316 TCAACGGTTTGG
1 TCAACGGGTCGG
12233328 TCAACGGGTCGAG
1 TCAACGGGTCG-G
* * *
12233341 TCAACAGTTTGG
1 TCAACGGGTCGG
* **
12233353 TTAACAAGTCAGG
1 TCAACGGGTC-GG
12233366 TCAACGGGTCGG
1 TCAACGGGTCGG
12233378 TCAAC
1 TCAAC
12233383 TAGTTGTTGG
Statistics
Matches: 50, Mismatches: 15, Indels: 5
0.71 0.21 0.07
Matches are distributed among these distances:
12 24 0.48
13 26 0.52
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (12 bp):
TCAACGGGTCGG
Found at i:12242357 original size:43 final size:43
Alignment explanation
Indices: 12242295--12242837 Score: 658
Period size: 43 Copynumber: 12.6 Consensus size: 43
12242285 TATTTTTAGC
* *
12242295 CCGATGTTCCCGCACATCCAAGGTACCAAGGTGCCGATGGTGT
1 CCGATGCTCCCGCACATCCAAGGCACCAAGGTGCCGATGGTGT
* * *
12242338 CCGATACTCCCGCATATCCAAGGCACCAAGGTGTCGATGGTGT
1 CCGATGCTCCCGCACATCCAAGGCACCAAGGTGCCGATGGTGT
* * * * * *
12242381 CCGAGGCCCCCGCACATTCAAGGCACCAAGGTACTGGTGGTGT
1 CCGATGCTCCCGCACATCCAAGGCACCAAGGTGCCGATGGTGT
* *
12242424 CCGAGGCTCCCGCACATCCAAGGCACCAAGGTGCCGACGGTGT
1 CCGATGCTCCCGCACATCCAAGGCACCAAGGTGCCGATGGTGT
* * * *
12242467 CCGATGCTACCACACATCCAAGGCACCAAGGAGCCGATGCT-T
1 CCGATGCTCCCGCACATCCAAGGCACCAAGGTGCCGATGGTGT
* * * *
12242509 CTCGATGCTCCAGCACATCCAAGGCTCCGAGGTGCCGGTGGTGT
1 C-CGATGCTCCCGCACATCCAAGGCACCAAGGTGCCGATGGTGT
* * *
12242553 CCGATTCTCCTGCACATCCAAGGCACCAAGGTGCCGGTGGTGT
1 CCGATGCTCCCGCACATCCAAGGCACCAAGGTGCCGATGGTGT
** * ** *
12242596 TTGATGCTCCCGCACATCCAAGGCACCAAGGCGTTGATGCT-T
1 CCGATGCTCCCGCACATCCAAGGCACCAAGGTGCCGATGGTGT
**
12242638 CTCGATGCTCTTGCACATCCAAGGCACCAAGGTGCCGATGGTGT
1 C-CGATGCTCCCGCACATCCAAGGCACCAAGGTGCCGATGGTGT
* * * * * *
12242682 CCAATTCTCCCTCACATTCAAGACACCAAGGTGCCGATGGTGC
1 CCGATGCTCCCGCACATCCAAGGCACCAAGGTGCCGATGGTGT
* *
12242725 CCGATGCTCCCCCACATCCAAGGCACCAAGGTGCCGATGGTGC
1 CCGATGCTCCCGCACATCCAAGGCACCAAGGTGCCGATGGTGT
*
12242768 CCGATGCTCCCGCACATCCAAGGCACCAAGGTGCCGGTGGTGT
1 CCGATGCTCCCGCACATCCAAGGCACCAAGGTGCCGATGGTGT
* * *
12242811 CCGATGCTGCTGCGCATCCAAGGCACC
1 CCGATGCTCCCGCACATCCAAGGCACC
12242838 TTGGTTCCCG
Statistics
Matches: 422, Mismatches: 74, Indels: 8
0.84 0.15 0.02
Matches are distributed among these distances:
42 3 0.01
43 415 0.98
44 4 0.01
ACGTcount: A:0.21, C:0.34, G:0.27, T:0.18
Consensus pattern (43 bp):
CCGATGCTCCCGCACATCCAAGGCACCAAGGTGCCGATGGTGT
Found at i:12244381 original size:2 final size:2
Alignment explanation
Indices: 12244374--12244417 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
12244364 TATGGATTGA
12244374 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12244416 AT
1 AT
12244418 GCTTAAATTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12254797 original size:21 final size:20
Alignment explanation
Indices: 12254746--12254798 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
12254736 GAAGTCCTAT
*
12254746 TAGTATCGGTAGTTCTATAC
1 TAGTATCGATAGTTCTATAC
*
12254766 TAGTATCGATAGTTTTATAC
1 TAGTATCGATAGTTCTATAC
*
12254786 TAGGTTTCGATAG
1 TA-GTATCGATAG
12254799 AAGTTCCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 20 0.69
21 9 0.31
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (20 bp):
TAGTATCGATAGTTCTATAC
Found at i:12258357 original size:25 final size:23
Alignment explanation
Indices: 12258320--12258403 Score: 84
Period size: 23 Copynumber: 3.6 Consensus size: 23
12258310 ACCTTAGTGC
12258320 GCTCTCC-ATTTAGCA-TGTCTCGT
1 GCTCTCCGA-TTAGCATTGTCT-GT
*
12258343 GCTCTCCGTTATTAGCATTGTGTGT
1 GCTCTCCG--ATTAGCATTGTCTGT
*
12258368 GCTCTCCGATTAGCACTT-TGTGT
1 GCTCTCCGATTAGCA-TTGTCTGT
12258391 GCTCTCCGATTAG
1 GCTCTCCGATTAG
12258404 TACTTTGTGT
Statistics
Matches: 55, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
23 32 0.58
24 2 0.04
25 16 0.29
26 5 0.09
ACGTcount: A:0.13, C:0.26, G:0.21, T:0.39
Consensus pattern (23 bp):
GCTCTCCGATTAGCATTGTCTGT
Found at i:12258446 original size:23 final size:23
Alignment explanation
Indices: 12258341--12258479 Score: 138
Period size: 23 Copynumber: 5.9 Consensus size: 23
12258331 AGCATGTCTC
12258341 GTGCTCTCCGTTATTAGCA-TTGTGT
1 GTGCTCTCCG-T-TTAGCACTT-TGT
*
12258366 GTGCTCTCCGATTAGCACTTTGT
1 GTGCTCTCCGTTTAGCACTTTGT
* *
12258389 GTGCTCTCCGATTAGTACTTTGT
1 GTGCTCTCCGTTTAGCACTTTGT
* *
12258412 GTACTCTTCGTTTAGCACTTTGT
1 GTGCTCTCCGTTTAGCACTTTGT
*
12258435 GTGCTCTCCGTTACCCAGCACTTT-T
1 GTGCTCTCCGTT---TAGCACTTTGT
* *
12258460 GTGCTCTCTGTTTAGTACTT
1 GTGCTCTCCGTTTAGCACTT
12258480 CAGTACTCTC
Statistics
Matches: 98, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
22 6 0.06
23 60 0.61
24 2 0.02
25 22 0.22
26 8 0.08
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.43
Consensus pattern (23 bp):
GTGCTCTCCGTTTAGCACTTTGT
Found at i:12258841 original size:139 final size:139
Alignment explanation
Indices: 12258536--12258824 Score: 533
Period size: 139 Copynumber: 2.1 Consensus size: 139
12258526 TTCTATTATG
* *
12258536 GGCTAAGTTGTGAAAGATGAAAGAATGTGCAAATTATGATATTGAGGTATGTGAAATGATGAACA
1 GGCTAAGTTGTGAAAGATGAAAGAATGTACAAATTATGATATTGAGGCATGTGAAATGATGAACA
* *
12258601 CATGAAAGGTGAGTACTATATGTGTATGAGTAATCAAATGTTGATAAAACTAAGTAAGCTAAAGT
66 CACGAAAGATGAGTACTATATGTGTATGAGTAATCAAATGTTGATAAAACTAAGTAAGCTAAAGT
12258666 GGCTAGAAT
131 GGCTAGAAT
12258675 GGCTAAGTTGTGAAAGATGAAAGAATGTACAAATTATGATATTGAGGCATGTGAAATGATGAACA
1 GGCTAAGTTGTGAAAGATGAAAGAATGTACAAATTATGATATTGAGGCATGTGAAATGATGAACA
*
12258740 CACGAAAGATGAGTGCTATATGTGTATGAGTAATCAAATGTTGATAAAACTAAGTAAGCTAAAGT
66 CACGAAAGATGAGTACTATATGTGTATGAGTAATCAAATGTTGATAAAACTAAGTAAGCTAAAGT
12258805 GGCTAGAAT
131 GGCTAGAAT
12258814 GGCTAAGTTGT
1 GGCTAAGTTGT
12258825 AAAAAGTGGA
Statistics
Matches: 145, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
139 145 1.00
ACGTcount: A:0.40, C:0.07, G:0.25, T:0.28
Consensus pattern (139 bp):
GGCTAAGTTGTGAAAGATGAAAGAATGTACAAATTATGATATTGAGGCATGTGAAATGATGAACA
CACGAAAGATGAGTACTATATGTGTATGAGTAATCAAATGTTGATAAAACTAAGTAAGCTAAAGT
GGCTAGAAT
Found at i:12265344 original size:17 final size:17
Alignment explanation
Indices: 12265322--12265355 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12265312 GATTTAGGTA
*
12265322 AATCACACCATGAACGT
1 AATCACACCATAAACGT
12265339 AATCACACCATAAACGT
1 AATCACACCATAAACGT
12265356 CACAAGTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.29, G:0.09, T:0.18
Consensus pattern (17 bp):
AATCACACCATAAACGT
Found at i:12265958 original size:25 final size:24
Alignment explanation
Indices: 12265930--12265982 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
12265920 AAATTATATT
* *
12265930 AATATTTATATTAATGTTAAATGAA
1 AATAATTATATTAATATTAAAT-AA
12265955 AATAATTATATTAATATTAAATAA
1 AATAATTATATTAATATTAAATAA
12265979 AATA
1 AATA
12265983 CAAAACATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 6 0.23
25 20 0.77
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
AATAATTATATTAATATTAAATAA
Found at i:12278744 original size:26 final size:25
Alignment explanation
Indices: 12278728--12278792 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
12278718 CCGGCTTAAT
12278728 GCCTACTATTTAATCACTGGCTCGAA
1 GCCTACTATTTAATCACTGGCTC-AA
* *
12278754 -CCTGCTAATTAATCACTGGCTCAA
1 GCCTACTATTTAATCACTGGCTCAA
12278778 GGCCTACTATTTAAT
1 -GCCTACTATTTAAT
12278793 TTCTTTTTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 2 0.06
25 20 0.61
26 11 0.33
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (25 bp):
GCCTACTATTTAATCACTGGCTCAA
Found at i:12280702 original size:60 final size:59
Alignment explanation
Indices: 12280586--12280702 Score: 162
Period size: 59 Copynumber: 2.0 Consensus size: 59
12280576 TCTGAACTTA
* * *
12280586 CATTTTTTTTTAATTTGGTACCTAAACTTTTTTTGACCCAATTTGGTACTTGAATTTGG
1 CATTTTTTTCTAATTTGGTACCTAAACTTTTTTTGACCCAATTTGGTACCTAAATTTGG
** **
12280645 CATTTTTTTCTAATTTGGTACCTAAGTTTTTTTTAGATTCAATTTGGTACCTAAATTT
1 CATTTTTTTCTAATTTGGTACCTAAACTTTTTTT-GACCCAATTTGGTACCTAAATTT
12280703 ATTAAATATT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
59 31 0.62
60 19 0.38
ACGTcount: A:0.23, C:0.13, G:0.12, T:0.52
Consensus pattern (59 bp):
CATTTTTTTCTAATTTGGTACCTAAACTTTTTTTGACCCAATTTGGTACCTAAATTTGG
Found at i:12280992 original size:30 final size:31
Alignment explanation
Indices: 12280938--12281007 Score: 99
Period size: 30 Copynumber: 2.3 Consensus size: 31
12280928 TCAGGTTTTG
12280938 GTACCAAATTAGAAAAAAGGGTCAAGTGT-AA
1 GTACCAAATTAGAAAAAAGGGTCAAGT-TCAA
* *
12280969 GTACCAAATTA-AGAAAAGTGTCAAGTTCAA
1 GTACCAAATTAGAAAAAAGGGTCAAGTTCAA
12280999 GTACCAAAT
1 GTACCAAAT
12281008 ATTATATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 1 0.03
30 24 0.67
31 11 0.31
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.21
Consensus pattern (31 bp):
GTACCAAATTAGAAAAAAGGGTCAAGTTCAA
Found at i:12281984 original size:89 final size:89
Alignment explanation
Indices: 12281875--12282045 Score: 227
Period size: 89 Copynumber: 1.9 Consensus size: 89
12281865 GATTAAGTAC
* * * ** * *
12281875 CAAATTAGGAAAAAGAGTCAAGTTCAAGTATCAAATTGGACCCCAAAAAGTTTAAGTACCAACTT
1 CAAATTAGGAAAAAGAGTCAAGTTCAAGCACCAAATT-GAACAAAAAAAATTTAAGTACCAAATT
12281940 AAAAAAAA-TGTCAAGTTTAGGTAA
65 AAAAAAAAGTGTCAAGTTTAGGTAA
* ** *
12281964 CAAATTAGGAAAAAGTGTCAAGTTTGAGCACCAAATTGAACAAAAAAAATTTAGGTACCAAATTA
1 CAAATTAGGAAAAAGAGTCAAGTTCAAGCACCAAATTGAACAAAAAAAATTTAAGTACCAAATTA
12282029 AAAAAAAGTGTCAAGTT
66 AAAAAAAGTGTCAAGTT
12282046 CAAATATCAA
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
88 29 0.41
89 41 0.59
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.23
Consensus pattern (89 bp):
CAAATTAGGAAAAAGAGTCAAGTTCAAGCACCAAATTGAACAAAAAAAATTTAAGTACCAAATTA
AAAAAAAGTGTCAAGTTTAGGTAA
Found at i:12293750 original size:19 final size:19
Alignment explanation
Indices: 12293713--12293750 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12293703 AAAGGTAATA
**
12293713 ACAAATTTGATTATGGTGG
1 ACAAATTTGATTACAGTGG
12293732 ACAAATTTGATTACAGTGG
1 ACAAATTTGATTACAGTGG
12293751 GTGACAGTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.34
Consensus pattern (19 bp):
ACAAATTTGATTACAGTGG
Found at i:12294285 original size:8 final size:9
Alignment explanation
Indices: 12294264--12294290 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
12294254 AAATTCAAAT
12294264 TTTTTTCGA
1 TTTTTTCGA
12294273 TTTTTTCGA
1 TTTTTTCGA
12294282 TTTTTTCGA
1 TTTTTTCGA
12294291 GTAGAATCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.67
Consensus pattern (9 bp):
TTTTTTCGA
Found at i:12294601 original size:60 final size:61
Alignment explanation
Indices: 12294524--12294651 Score: 154
Period size: 60 Copynumber: 2.1 Consensus size: 61
12294514 TTAATATAAC
* * * *
12294524 ATTTGATATTTGAACTTGTTATATTTTTTT-TAATTTAGTATCTAAA-TT-TTTTTTGATTCA
1 ATTTGATACTTGAACTTG--ACATTTTTTTCTAATTTAGTACCTAAACTTGTTTTTAGATTCA
* * *
12294584 ATTTGGTACTTGAACTTGACATTTTTTTCTAATTTGGTGCCTAAACTTGTTTTTAGATTCA
1 ATTTGATACTTGAACTTGACATTTTTTTCTAATTTAGTACCTAAACTTGTTTTTAGATTCA
12294645 ATTTGAT
1 ATTTGAT
12294652 GCCTAAATTT
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
58 9 0.16
59 13 0.23
60 18 0.32
61 17 0.30
ACGTcount: A:0.25, C:0.09, G:0.12, T:0.55
Consensus pattern (61 bp):
ATTTGATACTTGAACTTGACATTTTTTTCTAATTTAGTACCTAAACTTGTTTTTAGATTCA
Found at i:12294891 original size:31 final size:31
Alignment explanation
Indices: 12294854--12294980 Score: 108
Period size: 31 Copynumber: 4.2 Consensus size: 31
12294844 GGATACCAAA
* *
12294854 AAGTTTAAGTACCAACTTAAAAAAAATTGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAGTGTC
*
12294885 AAGTTT-AGATACCAAATTAAGAAAAAGTGTC
1 AAGTTTAAG-TACCAAATTAAAAAAAAGTGTC
*
12294916 AAGTTTGAA-TACCAAATTGGACAAAAAA-----
1 AAGTTT-AAGTACCAAATT--AAAAAAAAGTGTC
* *
12294944 AAG-TTAAATACTAAATTAAAAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAGTGTC
12294974 AAGTTTA
1 AAGTTTA
12294981 GATATCGAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 24
0.71 0.06 0.22
Matches are distributed among these distances:
25 7 0.09
26 2 0.03
27 10 0.13
28 3 0.04
30 5 0.06
31 43 0.56
33 7 0.09
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.27
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAAAAAAAAGTGTC
Found at i:12294917 original size:90 final size:89
Alignment explanation
Indices: 12294808--12294984 Score: 230
Period size: 90 Copynumber: 2.0 Consensus size: 89
12294798 GATTAGGTAT
* * ** * *
12294808 AAATTAAGAAAAAGAGTCAAATCTAG-GTACCAAATTGGATACCAAAAAGTTTAAGTACCAACTT
1 AAATTAAGAAAAAGAGTCAAAT-TAGAATACCAAATTGGACAAAAAAAAG-TTAAATACCAAATT
*
12294872 AAAAAAAATTGTCAAGTTTAGATACC
64 AAAAAAAAGTGTCAAGTTTAGATACC
* * * *
12294898 AAATTAAGAAAAAGTGTCAAGTTTGAATACCAAATTGGACAAAAAAAAGTTAAATACTAAATTAA
1 AAATTAAGAAAAAGAGTCAAATTAGAATACCAAATTGGACAAAAAAAAGTTAAATACCAAATTAA
12294963 AAAAAAGTGTCAAGTTTAGATA
66 AAAAAAGTGTCAAGTTTAGATA
12294985 TCGAATGTTA
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
89 36 0.48
90 39 0.52
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (89 bp):
AAATTAAGAAAAAGAGTCAAATTAGAATACCAAATTGGACAAAAAAAAGTTAAATACCAAATTAA
AAAAAAGTGTCAAGTTTAGATACC
Found at i:12296057 original size:55 final size:55
Alignment explanation
Indices: 12295973--12296083 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
12295963 TCTTGCATAA
12295973 CTACAAATTAAACATGAAACTTAGCAAATTTACCATACCTTGACAGCCGACCTTC
1 CTACAAATTAAACATGAAACTTAGCAAATTTACCATACCTTGACAGCCGACCTTC
*
12296028 CTACAAATTAAACATGAAACTTAGCAAATTTACCATACCTTGACTGCCGACCTTC
1 CTACAAATTAAACATGAAACTTAGCAAATTTACCATACCTTGACAGCCGACCTTC
12296083 C
1 C
12296084 ATAATTCAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.37, C:0.28, G:0.09, T:0.26
Consensus pattern (55 bp):
CTACAAATTAAACATGAAACTTAGCAAATTTACCATACCTTGACAGCCGACCTTC
Found at i:12296254 original size:31 final size:32
Alignment explanation
Indices: 12296207--12296272 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
12296197 ATAAAATGGG
* *
12296207 ATTTTAGATTTTTTTAAAAGTTGGAGAAAAAA
1 ATTTTAGAGTTTTTTAAAAGTTGGAAAAAAAA
*
12296239 ATTTTA-AGTTTTTTAAAATTTGGAAAAAAAA
1 ATTTTAGAGTTTTTTAAAAGTTGGAAAAAAAA
12296270 ATT
1 ATT
12296273 GACCTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 25 0.81
32 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (32 bp):
ATTTTAGAGTTTTTTAAAAGTTGGAAAAAAAA
Found at i:12297164 original size:12 final size:12
Alignment explanation
Indices: 12297147--12297195 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
12297137 TCTTTAGTAC
12297147 TATTTTTGCTGT
1 TATTTTTGCTGT
*
12297159 TATTTTTGTTGT
1 TATTTTTGCTGT
**
12297171 TATTTTTGCTAC
1 TATTTTTGCTGT
*
12297183 TATTTTTGTTGT
1 TATTTTTGCTGT
12297195 T
1 T
12297196 TTTGTTTTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.10, C:0.06, G:0.14, T:0.69
Consensus pattern (12 bp):
TATTTTTGCTGT
Found at i:12297175 original size:24 final size:24
Alignment explanation
Indices: 12297147--12297195 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
12297137 TCTTTAGTAC
**
12297147 TATTTTTGCTGTTATTTTTGTTGT
1 TATTTTTGCTACTATTTTTGTTGT
12297171 TATTTTTGCTACTATTTTTGTTGT
1 TATTTTTGCTACTATTTTTGTTGT
12297195 T
1 T
12297196 TTTGTTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.10, C:0.06, G:0.14, T:0.69
Consensus pattern (24 bp):
TATTTTTGCTACTATTTTTGTTGT
Found at i:12297215 original size:44 final size:47
Alignment explanation
Indices: 12297149--12297253 Score: 119
Period size: 44 Copynumber: 2.3 Consensus size: 47
12297139 TTTAGTACTA
* *
12297149 TTTTTGCTGTTAT-TTTTGTTGTTATTTTTGCTACT-ATTT-TTGTTG
1 TTTTTGTTGTT-TGTTTTATTGTTATTTTTGCTACTGATTTGTTGTTG
* * *
12297194 TTTTTGTT-TTTGTTTTATTGTTATTTTTTCTGCTGTTTTGGTTGTTG
1 TTTTTGTTGTTTGTTTTATTGTTATTTTTGCTACTGATTT-GTTGTTG
12297241 TTTTTGTTGTTTG
1 TTTTTGTTGTTTG
12297254 AATGCTATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
43 1 0.02
44 21 0.42
45 10 0.20
47 14 0.28
48 4 0.08
ACGTcount: A:0.06, C:0.05, G:0.18, T:0.71
Consensus pattern (47 bp):
TTTTTGTTGTTTGTTTTATTGTTATTTTTGCTACTGATTTGTTGTTG
Found at i:12297263 original size:44 final size:44
Alignment explanation
Indices: 12297171--12297275 Score: 106
Period size: 44 Copynumber: 2.4 Consensus size: 44
12297161 TTTTTGTTGT
* * * * * * * *
12297171 TATTTTTGCTACTATTTTTGTTGTTTTTGTTTTTGTTTTATTGT
1 TATTTTTTCTGCTGTTTTGGTTGTTGTTGTTTTTGTTTGAATGC
12297215 TATTTTTTCTGCTGTTTTGGTTGTTGTT-TTTGTTGTTTGAATGC
1 TATTTTTTCTGCTGTTTTGGTTGTTGTTGTTT-TTGTTTGAATGC
*
12297259 TATTTTTTTTG-TGTTTT
1 TATTTTTTCTGCTGTTTT
12297276 TACTATTGTT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
43 9 0.18
44 42 0.82
ACGTcount: A:0.08, C:0.05, G:0.17, T:0.70
Consensus pattern (44 bp):
TATTTTTTCTGCTGTTTTGGTTGTTGTTGTTTTTGTTTGAATGC
Found at i:12297281 original size:20 final size:22
Alignment explanation
Indices: 12297258--12297304 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
12297248 TGTTTGAATG
*
12297258 CTATT-TTTT-TTGTGTTTTTA
1 CTATTGTTTTGTTGTCTTTTTA
12297278 CTATTGTTTTGTTGTCTTTTTA
1 CTATTGTTTTGTTGTCTTTTTA
*
12297300 ATATT
1 CTATT
12297305 ATTTGAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 4 0.17
22 14 0.61
ACGTcount: A:0.13, C:0.06, G:0.11, T:0.70
Consensus pattern (22 bp):
CTATTGTTTTGTTGTCTTTTTA
Found at i:12306275 original size:2 final size:2
Alignment explanation
Indices: 12306268--12306293 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12306258 AGTTGGCTTG
12306268 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
12306294 TTAATTATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12323302 original size:352 final size:352
Alignment explanation
Indices: 12322658--12323364 Score: 1342
Period size: 352 Copynumber: 2.0 Consensus size: 352
12322648 GAATTTGTTA
12322658 TTGAAGGAGGGGAATTACTTGAAAAGAGTTATAAAGATGAAAGTATGACAAAAAAATCAAATCTC
1 TTGAAGGAGGGGAATTACTTGAAAAGAGTTATAAAGATGAAAGTATGACAAAAAAATCAAATCTC
12322723 AAAATTTGAAAAGTTTGAGGATTAAAGTGTAATTTCATCAACAAAAAACCATTGAATTATATTAT
66 AAAATTTGAAAAGTTTGAGGATTAAAGTGTAATTTCATCAACAAAAAACCATTGAATTATATTAT
*
12322788 CTTAAATCATGAAAGTATCATTGAACCCTATCACTTAATATGCGATTTATTTATTTCGTGCATAA
131 CTTAAATCATGAAAGTATCATTGAACCCTATCACTTAATATGCGACTTATTTATTTCGTGCATAA
* * *
12322853 GTATAAATATTCTCGAAACCCTAAAAAGTGAAGTCGACATCTAGACAACAATAATTGACTGAAAC
196 ATATAAATATTCTCGAAACCCCAAAAAGTGAAGTCGACATCTAGACAACAACAATTGACTGAAAC
12322918 TATGTTTGTGTAGCTCCTTTTTATTTTGTAAATGGCATGTACATAAAAATAGTTGGTCTCAATTA
261 TATGTTTGTGTAGCTCCTTTTTATTTTGTAAATGGCATGTACATAAAAATAGTTGGTCTCAATTA
12322983 TAAATGGTCAACATGGTTGTATATATG
326 TAAATGGTCAACATGGTTGTATATATG
12323010 TTGAAGGAGGGGAATTACTTGAAAAGAGTTATAAAGATGAAAGTATGACAAAAAAATCAAATCTC
1 TTGAAGGAGGGGAATTACTTGAAAAGAGTTATAAAGATGAAAGTATGACAAAAAAATCAAATCTC
12323075 AAAATTTGAAAAGTTTGAGGATTAAAGTGTAATTTCATCAACAAAAAACCATTGAATTATATTAT
66 AAAATTTGAAAAGTTTGAGGATTAAAGTGTAATTTCATCAACAAAAAACCATTGAATTATATTAT
* *
12323140 CTTAAATCATGAAAGTATCATTGAGCCCTATCACTTAATGTGCGACTTATTTATTTCGTGCATAA
131 CTTAAATCATGAAAGTATCATTGAACCCTATCACTTAATATGCGACTTATTTATTTCGTGCATAA
*
12323205 ATATAAATATTCTCGAAACCCCAAAAAGTGAAGTCGACATCTAGACAACAACAATTGACTGAACC
196 ATATAAATATTCTCGAAACCCCAAAAAGTGAAGTCGACATCTAGACAACAACAATTGACTGAAAC
*
12323270 TATGTTTGTGTAGCTCTTTTTTATTTTGTAAATGGCATGTACATAAAAATAGTTGGTCTCAATTA
261 TATGTTTGTGTAGCTCCTTTTTATTTTGTAAATGGCATGTACATAAAAATAGTTGGTCTCAATTA
12323335 TAAATGGTCAACATGGTTGTATATATG
326 TAAATGGTCAACATGGTTGTATATATG
12323362 TTG
1 TTG
12323365 TGATATATGA
Statistics
Matches: 347, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
352 347 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (352 bp):
TTGAAGGAGGGGAATTACTTGAAAAGAGTTATAAAGATGAAAGTATGACAAAAAAATCAAATCTC
AAAATTTGAAAAGTTTGAGGATTAAAGTGTAATTTCATCAACAAAAAACCATTGAATTATATTAT
CTTAAATCATGAAAGTATCATTGAACCCTATCACTTAATATGCGACTTATTTATTTCGTGCATAA
ATATAAATATTCTCGAAACCCCAAAAAGTGAAGTCGACATCTAGACAACAACAATTGACTGAAAC
TATGTTTGTGTAGCTCCTTTTTATTTTGTAAATGGCATGTACATAAAAATAGTTGGTCTCAATTA
TAAATGGTCAACATGGTTGTATATATG
Found at i:12332452 original size:68 final size:68
Alignment explanation
Indices: 12332094--12332442 Score: 342
Period size: 68 Copynumber: 5.1 Consensus size: 68
12332084 AAAGAGGTAC
* * * * ** *
12332094 AAGGTGTAAGATCATAACTCGACTATGGCAACCAATAGAGTTTGTT-GAGACATTAAACATAGGG
1 AAGGTGTAAGACCATAGCTCGACTACGACAACCAATAGAGTCCGTTAG-GACATTAAACATGGGG
12332158 TTAA
65 TTAA
* * * * * * *
12332162 AATGTGTAAGACCATAGCTCGACTATGACAACTAATAGAGTCTGCTAGGACATTAAATATGGTGT
1 AAGGTGTAAGACCATAGCTCGACTACGACAACCAATAGAGTCCGTTAGGACATTAAACATGGGGT
*
12332227 TAC
66 TAA
* * * * * * ** * *
12332230 AATGTGTAAGACCATAGCTTGGCTACGTCGACCAATAGAGCCCGCCAAGACATTAAACATGAGGT
1 AAGGTGTAAGACCATAGCTCGACTACGACAACCAATAGAGTCCGTTAGGACATTAAACATGGGGT
*
12332295 TAC
66 TAA
* * * * * * *
12332298 AAGGTGTAAGACCATATCTC-AGCTACGACAACCAATAGATTTCGTCAGGACATTAAATATGAGC
1 AAGGTGTAAGACCATAGCTCGA-CTACGACAACCAATAGAGTCCGTTAGGACATTAAACATGGGG
*
12332362 TTAT
65 TTAA
* *
12332366 AAGTTGTAAGACCATAGCTCAACTACGACAACCAATAGAGTCCGTTAGGACATTAAACATGGGGT
1 AAGGTGTAAGACCATAGCTCGACTACGACAACCAATAGAGTCCGTTAGGACATTAAACATGGGGT
12332431 TAA
66 TAA
12332434 AAGGTGTAA
1 AAGGTGTAA
12332443 AGTCATAGCT
Statistics
Matches: 230, Mismatches: 48, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
68 228 0.99
69 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.25
Consensus pattern (68 bp):
AAGGTGTAAGACCATAGCTCGACTACGACAACCAATAGAGTCCGTTAGGACATTAAACATGGGGT
TAA
Found at i:12333594 original size:2 final size:2
Alignment explanation
Indices: 12333547--12333576 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
12333537 CCAAAAAGAC
*
12333547 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12333577 GCTAATACTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12334958 original size:34 final size:34
Alignment explanation
Indices: 12334898--12334987 Score: 101
Period size: 34 Copynumber: 2.6 Consensus size: 34
12334888 TGACAATACT
* * * *
12334898 AAATGTGAGCCCAGCTCTAGTTGGATAAACCAACG
1 AAATGTGTGCCCAGCACTAGTCGGATAAACCAA-A
* * *
12334933 ATAT-TGTGCCTAGCACTAGTCGGATAAATCAAA
1 AAATGTGTGCCCAGCACTAGTCGGATAAACCAAA
12334966 AAATGTGTGCCCAGCACTAGTC
1 AAATGTGTGCCCAGCACTAGTC
12334988 AAATAAACTG
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
33 3 0.07
34 39 0.87
35 3 0.07
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.23
Consensus pattern (34 bp):
AAATGTGTGCCCAGCACTAGTCGGATAAACCAAA
Found at i:12335047 original size:109 final size:108
Alignment explanation
Indices: 12334863--12335148 Score: 283
Period size: 109 Copynumber: 2.6 Consensus size: 108
12334853 CGAAAGAGTT
* * * * * * *
12334863 TGTGCCCAGCGCTAGGCGAATAAACTGAC-AATACTAAAT-GTGAGCCCAGCTCTAGTTGGATAA
1 TGTGCCCAACACTAGTCAAATAAACTGACGAA-A-TAAATAATGAACCCAGCTCTAGTTGGATTA
* * * *
12334926 ACCAACGATATTGTGC-CTAGCACTAGTCGGATAAA-TCAAAAAATG
64 ACCAACAATATTGCGCTC-AACACTAGTAGGATAAACT-AAAAAATG
* * *
12334971 TGTGCCCAGCACTAGTCAAATAAACTGACGAAATAAATTAATGATCGCAGCTCTAGTTGGATTAA
1 TGTGCCCAACACTAGTCAAATAAACTGACGAAATAAA-TAATGAACCCAGCTCTAGTTGGATTAA
* * **
12335036 CGAACAATATTGCGCTCAACGCTAGTAGGATAAACTAACGAATG
65 CCAACAATATTGCGCTCAACACTAGTAGGATAAACTAAAAAATG
* * * * **
12335080 TGTGCCCAACACTAGTCAGATAAATTGACGATATTAATAATGAACCCATATCTAGTTGGATTAAC
1 TGTGCCCAACACTAGTCAAATAAACTGACGAAATAAATAATGAACCCAGCTCTAGTTGGATTAAC
12335145 CAAC
66 CAAC
12335149 GATGTTTGCA
Statistics
Matches: 148, Mismatches: 25, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
107 4 0.03
108 55 0.37
109 87 0.59
110 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (108 bp):
TGTGCCCAACACTAGTCAAATAAACTGACGAAATAAATAATGAACCCAGCTCTAGTTGGATTAAC
CAACAATATTGCGCTCAACACTAGTAGGATAAACTAAAAAATG
Found at i:12335177 original size:109 final size:108
Alignment explanation
Indices: 12334907--12335185 Score: 253
Period size: 109 Copynumber: 2.6 Consensus size: 108
12334897 TAAATGTGAG
* * * * **
12334907 CCCAGCTCTAGTTGGATAAACCAACGATATTGTG-CCTAGCACTAGTCGGATAAA-TCAAAAAAT
1 CCCAGATCTAGTTGGATTAACCAACGAT-TT-TGCCCCAGCACTAGTCAGATAAACT-AACGAAT
* *
12334970 GTGTGCCCAGCACTAGTCAAATAAACTGACGAAATAAATTAATGAT
63 GTGTGCCCAACACTAGTCAAATAAACTGACGAAATAAATTAATGAA
* * * * * * * *
12335016 CGCAGCTCTAGTTGGATTAACGAACAATATTGCGCTCAACGCTAGT-AGGATAAACTAACGAATG
1 CCCAGATCTAGTTGGATTAACCAACGATTTTGC-CCCAGCACTAGTCA-GATAAACTAACGAATG
* * * *
12335080 TGTGCCCAACACTAGTCAGATAAATTGACGATATTAA-TAATGAA
64 TGTGCCCAACACTAGTCAAATAAACTGACGAAATAAATTAATGAA
* * *
12335124 CCCATATCTAGTTGGATTAACCAACGATGTTTGCACCCAGTACTAGTCAGAT-AACTGACGAA
1 CCCAGATCTAGTTGGATTAACCAACGAT-TTTGC-CCCAGCACTAGTCAGATAAACTAACGAA
12335186 ATATAAATAT
Statistics
Matches: 134, Mismatches: 30, Indels: 13
0.76 0.17 0.07
Matches are distributed among these distances:
107 2 0.01
108 39 0.29
109 91 0.68
110 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (108 bp):
CCCAGATCTAGTTGGATTAACCAACGATTTTGCCCCAGCACTAGTCAGATAAACTAACGAATGTG
TGCCCAACACTAGTCAAATAAACTGACGAAATAAATTAATGAA
Found at i:12337869 original size:36 final size:36
Alignment explanation
Indices: 12337828--12337900 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
12337818 GTCATGCCAC
12337828 CCTGAACTTTTTCTCTTATTTTCATCATTCTAGCAT
1 CCTGAACTTTTTCTCTTATTTTCATCATTCTAGCAT
12337864 CCTGAACTTTTTCTCTTATTTTCATCATTCTAGCAT
1 CCTGAACTTTTTCTCTTATTTTCATCATTCTAGCAT
12337900 C
1 C
12337901 ATCTAATTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.19, C:0.26, G:0.05, T:0.49
Consensus pattern (36 bp):
CCTGAACTTTTTCTCTTATTTTCATCATTCTAGCAT
Found at i:12341553 original size:21 final size:22
Alignment explanation
Indices: 12341514--12341554 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
12341504 CATATTCACT
12341514 TTGCAAATAAACTGCCACATAA
1 TTGCAAATAAACTGCCACATAA
12341536 TTGCAAA-AAA-TGGCCACAT
1 TTGCAAATAAACT-GCCACAT
12341555 CTTCCACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.06
21 10 0.56
22 7 0.39
ACGTcount: A:0.44, C:0.22, G:0.12, T:0.22
Consensus pattern (22 bp):
TTGCAAATAAACTGCCACATAA
Found at i:12346633 original size:24 final size:25
Alignment explanation
Indices: 12346593--12346643 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
12346583 TGTTCCTAAG
*
12346593 CCCAAATCCTATTAAAACAAATTAA
1 CCCAAACCCTATTAAAACAAATTAA
**
12346618 CCCAAACCCT-TTAAAACCCATTAA
1 CCCAAACCCTATTAAAACAAATTAA
12346642 CC
1 CC
12346644 TTTTTTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.22
Consensus pattern (25 bp):
CCCAAACCCTATTAAAACAAATTAA
Found at i:12346782 original size:7 final size:7
Alignment explanation
Indices: 12346772--12346859 Score: 83
Period size: 7 Copynumber: 13.0 Consensus size: 7
12346762 ATTGACCGAT
12346772 CGTTGAC
1 CGTTGAC
12346779 CGTTGAC
1 CGTTGAC
12346786 CGTTGAC
1 CGTTGAC
*
12346793 CGTTCA-
1 CGTTGAC
*
12346799 CTTTGAC
1 CGTTGAC
*
12346806 CATTGAC
1 CGTTGAC
*
12346813 CATTGAC
1 CGTTGAC
12346820 CGTTGAC
1 CGTTGAC
*
12346827 CGTT-AA
1 CGTTGAC
* *
12346833 CTTTGAT
1 CGTTGAC
12346840 CGTTGA-
1 CGTTGAC
*
12346846 CTTTGAC
1 CGTTGAC
12346853 CGTTGAC
1 CGTTGAC
12346860 TTTTTCGAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
6 13 0.19
7 54 0.81
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (7 bp):
CGTTGAC
Found at i:12346819 original size:34 final size:34
Alignment explanation
Indices: 12346774--12346859 Score: 120
Period size: 34 Copynumber: 2.6 Consensus size: 34
12346764 TGACCGATCG
* *
12346774 TTGACCGTTGACCGTTGACCGTTCACTTTGACCA
1 TTGACCATTGACCGTTGACCGTTAACTTTGACCA
* *
12346808 TTGACCATTGACCGTTGACCGTTAACTTTGATCG
1 TTGACCATTGACCGTTGACCGTTAACTTTGACCA
*
12346842 TTGA-CTTTGACCGTTGAC
1 TTGACCATTGACCGTTGAC
12346860 TTTTTCGAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 13 0.28
34 34 0.72
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.35
Consensus pattern (34 bp):
TTGACCATTGACCGTTGACCGTTAACTTTGACCA
Found at i:12346843 original size:13 final size:13
Alignment explanation
Indices: 12346808--12346862 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
12346798 ACTTTGACCA
* *
12346808 TTGACCATTGACCG
1 TTGACCGTTGA-CT
*
12346822 TTGACCGTTAACT
1 TTGACCGTTGACT
*
12346835 TTGATCGTTGACT
1 TTGACCGTTGACT
12346848 TTGACCGTTGACT
1 TTGACCGTTGACT
12346861 TT
1 TT
12346863 TTCGAAAAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
13 26 0.74
14 9 0.26
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.40
Consensus pattern (13 bp):
TTGACCGTTGACT
Found at i:12347938 original size:15 final size:16
Alignment explanation
Indices: 12347912--12347943 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
12347902 TATTTTAATT
12347912 TATTATTTATTATTAC
1 TATTATTTATTATTAC
12347928 TATTA-TTATTATTAC
1 TATTATTTATTATTAC
12347943 T
1 T
12347944 TCAAAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATTTATTATTAC
Found at i:12360601 original size:28 final size:28
Alignment explanation
Indices: 12360548--12360601 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
12360538 GATAAATTGC
* **
12360548 CACATAATTGTCAAAAATGGTTACATAT
1 CACATAATTGCCAAAAATGGCCACATAT
12360576 CACATAATTGCCAAAAATGGCCACAT
1 CACATAATTGCCAAAAATGGCCACAT
12360602 CTTCCACCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (28 bp):
CACATAATTGCCAAAAATGGCCACATAT
Found at i:12361171 original size:25 final size:26
Alignment explanation
Indices: 12361143--12361192 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
12361133 TAAAGAGGAA
* *
12361143 TTTTTTTATACA-ACATTCAGAGACT
1 TTTTTTTAGACATACATTCAAAGACT
12361168 TTTTTTTAGACATACATTCAAAGAC
1 TTTTTTTAGACATACATTCAAAGAC
12361193 AATTCAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (26 bp):
TTTTTTTAGACATACATTCAAAGACT
Found at i:12361927 original size:29 final size:30
Alignment explanation
Indices: 12361895--12361955 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 30
12361885 TTTATTACCA
*
12361895 TTATT-CCTATGATTTTATTA-TTATTTTAT
1 TTATTACC-ATGATTATATTAGTTATTTTAT
*
12361924 TTATTACCATGATTATGTTATGTTATTTTAT
1 TTATTACCATGATTATATTA-GTTATTTTAT
12361955 T
1 T
12361956 GTGTTATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 15 0.56
30 2 0.07
31 10 0.37
ACGTcount: A:0.25, C:0.07, G:0.07, T:0.62
Consensus pattern (30 bp):
TTATTACCATGATTATATTAGTTATTTTAT
Found at i:12365557 original size:30 final size:30
Alignment explanation
Indices: 12365500--12365560 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
12365490 GACGGTCCGA
*
12365500 CACATGGCCATCTGCCCAGCCCATGTGGCT
1 CACATGGCCATCTGCCCAACCCATGTGGCT
* * * *
12365530 CACATGGCCGTGTGTCCAACCCGTGTGGCT
1 CACATGGCCATCTGCCCAACCCATGTGGCT
12365560 C
1 C
12365561 CTAAAATATG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (30 bp):
CACATGGCCATCTGCCCAACCCATGTGGCT
Found at i:12367322 original size:6 final size:6
Alignment explanation
Indices: 12367313--12367381 Score: 61
Period size: 6 Copynumber: 11.2 Consensus size: 6
12367303 TAAAGTACAT
* * *
12367313 AATAAA AATAAA AATGAA AATGAA AATAAA AATATA AAT--A AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
12367359 ATATAAATA AATAAA ATATAAA A
1 A-AT-AA-A AATAAA A-ATAAA A
12367382 CTTAATGTAC
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
4 4 0.07
6 34 0.63
7 10 0.19
8 4 0.07
9 2 0.04
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (6 bp):
AATAAA
Found at i:12367361 original size:15 final size:15
Alignment explanation
Indices: 12367336--12367380 Score: 81
Period size: 15 Copynumber: 2.9 Consensus size: 15
12367326 ATGAAAATGA
12367336 AAATAAAAATATAAAT
1 AAAT-AAAATATAAAT
12367352 AAATAAAATATAAAT
1 AAATAAAATATAAAT
12367367 AAATAAAATATAAA
1 AAATAAAATATAAA
12367381 ACTTAATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 25 0.86
16 4 0.14
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATAAAATATAAAT
Found at i:12367422 original size:12 final size:12
Alignment explanation
Indices: 12367393--12367421 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
12367383 TTAATGTACT
12367393 AATTTTCTTTCA
1 AATTTTCTTTCA
12367405 AATTTTCTTTC-
1 AATTTTCTTTCA
12367416 AATTTT
1 AATTTT
12367422 TTTTATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (12 bp):
AATTTTCTTTCA
Found at i:12372754 original size:23 final size:22
Alignment explanation
Indices: 12372688--12372767 Score: 97
Period size: 23 Copynumber: 3.5 Consensus size: 22
12372678 TTCGCACTTC
* *
12372688 GTGTGCCTACTGATTTGCGCTAT
1 GTGTGCCTACTGA-TTGCACTGT
*
12372711 GTGCGCCTACTGATTGCACTGT
1 GTGTGCCTACTGATTGCACTGT
12372733 GTGTGCCTACTGGATTGCACTGT
1 GTGTGCCTACT-GATTGCACTGT
* *
12372756 GCGTGCTTACTG
1 GTGTGCCTACTG
12372768 TTTCCCCAGC
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
22 18 0.36
23 32 0.64
ACGTcount: A:0.12, C:0.24, G:0.29, T:0.35
Consensus pattern (22 bp):
GTGTGCCTACTGATTGCACTGT
Found at i:12372767 original size:45 final size:46
Alignment explanation
Indices: 12372665--12372767 Score: 113
Period size: 45 Copynumber: 2.3 Consensus size: 46
12372655 AGGAATGCTA
* *
12372665 GCGCGCTTACTGTTTCGCACTTCGTGTGCCTACTGATTTGCGCTAT
1 GCGCGCTTACTGATTCGCACTTCGTGTGCCTACTGATTTGCACTAT
* * *
12372711 GTGCGCCTACTGATT-GCACTGT-GTGTGCCTACTGGA-TTGCACTGT
1 GCGCGCTTACTGATTCGCACT-TCGTGTGCCTACT-GATTTGCACTAT
*
12372756 GCGTGCTTACTG
1 GCGCGCTTACTG
12372768 TTTCCCCAGC
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
45 32 0.68
46 15 0.32
ACGTcount: A:0.12, C:0.26, G:0.27, T:0.35
Consensus pattern (46 bp):
GCGCGCTTACTGATTCGCACTTCGTGTGCCTACTGATTTGCACTAT
Found at i:12374977 original size:20 final size:20
Alignment explanation
Indices: 12374949--12374988 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12374939 CAAATATGTT
*
12374949 AAAATCATTAATTAAAATAA
1 AAAAGCATTAATTAAAATAA
**
12374969 AAAAGCATTTTTTAAAATAA
1 AAAAGCATTAATTAAAATAA
12374989 TACAAATGTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.33
Consensus pattern (20 bp):
AAAAGCATTAATTAAAATAA
Found at i:12375655 original size:16 final size:16
Alignment explanation
Indices: 12375623--12375656 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12375613 ATCAAAATTG
* *
12375623 CAGAACAAATAATCAA
1 CAGAACAAAGAAGCAA
12375639 CAGAACAAAGAAGCAA
1 CAGAACAAAGAAGCAA
12375655 CA
1 CA
12375657 AATATGGTCA
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:0.62, C:0.21, G:0.12, T:0.06
Consensus pattern (16 bp):
CAGAACAAAGAAGCAA
Found at i:12385349 original size:31 final size:31
Alignment explanation
Indices: 12385282--12385349 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
12385272 TATAAAATAA
* *** *
12385282 TTATTAAATTATTTAAAAGTTTTTATTTAAG
1 TTATTGAATTATTTAAAAAAATTTATTCAAG
12385313 TTATTGAATTATTTAAAAAAATTTATTCAAG
1 TTATTGAATTATTTAAAAAAATTTATTCAAG
12385344 TTATTG
1 TTATTG
12385350 GGCTGTAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.01, G:0.07, T:0.51
Consensus pattern (31 bp):
TTATTGAATTATTTAAAAAAATTTATTCAAG
Found at i:12386424 original size:14 final size:16
Alignment explanation
Indices: 12386380--12386422 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
12386370 ATGGGATGAG
*
12386380 AATATATTTTTAATTA
1 AATAAATTTTTAATTA
12386396 AATAAATTTAATTAATTA
1 AATAAATTT--TTAATTA
12386414 AA-AAATTTT
1 AATAAATTTT
12386423 AACCTAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 1 0.04
16 8 0.33
17 6 0.25
18 9 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:12386935 original size:35 final size:35
Alignment explanation
Indices: 12386896--12386965 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
12386886 TAAGGTTTAA
12386896 AAATTTTAATTAATTAAATTTATTTGATTAAAGAT
1 AAATTTTAATTAATTAAATTTATTTGATTAAAGAT
12386931 AAATTTTAATTAATTAAATTTATTTGATTAAAGAT
1 AAATTTTAATTAATTAAATTTATTTGATTAAAGAT
12386966 CTATTCTCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (35 bp):
AAATTTTAATTAATTAAATTTATTTGATTAAAGAT
Found at i:12389548 original size:28 final size:29
Alignment explanation
Indices: 12389506--12389560 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
12389496 TCCCTCGAAA
*
12389506 AAAAATTATAAAAAAGTAAAAAAAAAAAG
1 AAAAATTATAAAAAAATAAAAAAAAAAAG
* *
12389535 AAAAA-TATGAAAAAATTAAAAAAAAA
1 AAAAATTATAAAAAAATAAAAAAAAAA
12389561 TCTATGAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (29 bp):
AAAAATTATAAAAAAATAAAAAAAAAAAG
Found at i:12390585 original size:21 final size:21
Alignment explanation
Indices: 12390561--12390601 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12390551 AAAATAAAAA
*
12390561 TACTTT-TAAAGTCATATTTAT
1 TACTTTATAAAAT-ATATTTAT
12390582 TACTTTATAAAATATATTTA
1 TACTTTATAAAATATATTTA
12390602 ACTAAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.51
Consensus pattern (21 bp):
TACTTTATAAAATATATTTAT
Found at i:12394218 original size:7 final size:7
Alignment explanation
Indices: 12394206--12394237 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
12394196 TGCTTCAAAA
12394206 TCATCCT
1 TCATCCT
12394213 TCATCCT
1 TCATCCT
12394220 TCATCCT
1 TCATCCT
*
12394227 TCATCCA
1 TCATCCT
12394234 TCAT
1 TCAT
12394238 TTCTCTCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.19, C:0.41, G:0.00, T:0.41
Consensus pattern (7 bp):
TCATCCT
Found at i:12397951 original size:19 final size:19
Alignment explanation
Indices: 12397927--12397983 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 19
12397917 AAGTTAATAA
*
12397927 CAAATTTGGTTACGGTGGG
1 CAAATTTGATTACGGTGGG
*
12397946 CAAATTTGATTACGGTGGA
1 CAAATTTGATTACGGTGGG
* * *
12397965 TATATTTGATTACAGTGGG
1 CAAATTTGATTACGGTGGG
12397984 TAGTAGTGAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.26, C:0.09, G:0.30, T:0.35
Consensus pattern (19 bp):
CAAATTTGATTACGGTGGG
Found at i:12399438 original size:16 final size:16
Alignment explanation
Indices: 12399417--12399448 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12399407 GTATTATACG
*
12399417 ATATATATGCGTAAAT
1 ATATATATGCATAAAT
12399433 ATATATATGCATAAAT
1 ATATATATGCATAAAT
12399449 GGTTTTGTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (16 bp):
ATATATATGCATAAAT
Found at i:12400058 original size:120 final size:116
Alignment explanation
Indices: 12399867--12400086 Score: 314
Period size: 120 Copynumber: 1.9 Consensus size: 116
12399857 GATATTAGTG
* * * *
12399867 AATTTTCTTCTCTTCTACCGTGGTTTTCCTCGAAAGGGTTTCCACGTCAAATTTGTCTTCTTTCT
1 AATTTTCTTCTCTTCTACCGTGGTTTTCCCCGAAAAGATTTCCACGTAAAATTTGTCTTCTTTCT
12399932 CTTTTTTATTTTCTTTGCAATATTTCTTCATTGTCCATGCTCATTGCACCA
66 CTTTTTTATTTTCTTTGCAATATTTCTTCATTGTCCATGCTCATTGCACCA
* * * *
12399983 AATTTTCTTTTCTTCTGCTCGTGGTTTTCTCCCGAAAAGATTTTCACGTAAAATCTATGTGTTCT
1 AATTTTCTTCTCTTCTAC-CGTGGTTTTC-CCCGAAAAGATTTCCACGTAAAAT-T-TGTCTTCT
* *
12400048 TTCTCTTTTTTGTTTTCTTTGTAATATTTCTTCATTGTC
62 TTCTCTTTTTTATTTTCTTTGCAATATTTCTTCATTGTC
12400087 GACATTCAAT
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
116 16 0.18
117 10 0.11
118 19 0.21
119 1 0.01
120 44 0.49
ACGTcount: A:0.16, C:0.21, G:0.11, T:0.51
Consensus pattern (116 bp):
AATTTTCTTCTCTTCTACCGTGGTTTTCCCCGAAAAGATTTCCACGTAAAATTTGTCTTCTTTCT
CTTTTTTATTTTCTTTGCAATATTTCTTCATTGTCCATGCTCATTGCACCA
Found at i:12410506 original size:49 final size:49
Alignment explanation
Indices: 12410442--12411066 Score: 542
Period size: 49 Copynumber: 12.7 Consensus size: 49
12410432 CGATACCTTA
* * * * * *
12410442 GAAGATGTGATGGGAAAGGTTAAGGCTGCAACGACGAACCTGGTACAAT
1 GAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGCGAACCCGGTACCAT
* * * *
12410491 GAAGATATAAAGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGT-CCTT
1 GAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGCGAACCCGGTACCAT
* * * * * *
12410539 AGAAGATGTGATGGGAAAGGTTAAAGCCGCAACGACGAATCCGATACCAT
1 -GAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGCGAACCCGGTACCAT
* * * *
12410589 AAAGATTATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTT
1 GAAGA-TATGAAGGGAAAGGTTAAGGCCGCAACGGCGAACCCGGTACCAT
* * * * * **
12410639 AGAAGATGTGATGGGAAATGTTGAGGTCGCAACGGTAAACCCGGTACCAT
1 -GAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGCGAACCCGGTACCAT
* * * *** *
12410689 GAAGATTTGAAGGG-AAGGATTGAGGCCGCAACGGTGAATTTGGTACCTT
1 GAAGATATGAAGGGAAAGG-TTAAGGCCGCAACGGCGAACCCGGTACCAT
* * * *
12410738 AGAAGATGT-AATGGGAAAGGTTAAGGCTGCAACGGTGAACCCGGTACTAT
1 -GAAGATATGAA-GGGAAAGGTTAAGGCCGCAACGGCGAACCCGGTACCAT
* * ** * *
12410788 GAAGAGATGAAGGGAAAGGTTGAGGCCATAACGGCGAACCCAGTACCTT
1 GAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGCGAACCCGGTACCAT
* * * *
12410837 AGAAGATGTGATA-GGAAAGGTTAAGACCGCAACGGTGAACCCGATACCAT
1 -GAAGATATGA-AGGGAAAGGTTAAGGCCGCAACGGCGAACCCGGTACCAT
* * *
12410887 GAAGATATGAAGGGAAAGGTT-AGGCCGTAACGGCAAACCCGATACCAT
1 GAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGCGAACCCGGTACCAT
* * * * * * *
12410935 GAAGATTTGAAGGG-AAGGATTGAGGCCGCGATGGCTAATCCGGTACCTT
1 GAAGATATGAAGGGAAAGG-TTAAGGCCGCAACGGCGAACCCGGTACCAT
* * * * *
12410984 AAAAGATGTGATGGGAAAGGTTAAGGCCGCAACGGCAAACCCGATACCAT
1 -GAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGCGAACCCGGTACCAT
*
12411034 GAAGATATGAAGGGAAAGGTTAAGGCTGCAACG
1 GAAGATATGAAGGGAAAGGTTAAGGCCGCAACG
12411067 ACAAACCTAG
Statistics
Matches: 459, Mismatches: 101, Indels: 32
0.78 0.17 0.05
Matches are distributed among these distances:
47 4 0.01
48 44 0.10
49 216 0.47
50 182 0.40
51 13 0.03
ACGTcount: A:0.34, C:0.17, G:0.32, T:0.18
Consensus pattern (49 bp):
GAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGCGAACCCGGTACCAT
Found at i:12410701 original size:99 final size:99
Alignment explanation
Indices: 12410402--12411066 Score: 702
Period size: 99 Copynumber: 6.7 Consensus size: 99
12410392 CAAGTTTGAC
* *
12410402 AGGG-AAGGATTGAGGCCACAACGGCG-ACTTCGATACCTTAGAAGATGTGATGGGAAAGGTTAA
1 AGGGAAAGG-TTGAGGCCGCAACGGCGAAC-CCGATACCTTAGAAGATGTGATGGGAAAGGTTAA
* ** * * *
12410465 GGCTGCAACGACGAACCTGGTACAATGAAGATATAA
64 GGCCGCAACGGTGAACCCGGTACCATGAAGATATGA
* * *
12410501 AGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGT-CCTTAGAAGATGTGATGGGAAAGGTTAAAG
1 AGGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTTAGAAGATGTGATGGGAAAGGTTAAGG
** * * *
12410565 CCGCAACGACGAATCCGATACCATAAAGATTATGA
66 CCGCAACGGTGAACCCGGTACCATGAAGA-TATGA
* *
12410600 AGGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTTAGAAGATGTGATGGGAAATGTTGAGG
1 AGGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTTAGAAGATGTGATGGGAAAGGTTAAGG
* * *
12410665 TCGCAACGGTAAACCCGGTACCATGAAGATTTGA
66 CCGCAACGGTGAACCCGGTACCATGAAGATATGA
* *** * *
12410699 AGGG-AAGGATTGAGGCCGCAACGGTGAATTTGGTACCTTAGAAGATGTAATGGGAAAGGTTAAG
1 AGGGAAAGG-TTGAGGCCGCAACGGCGAACCCGATACCTTAGAAGATGTGATGGGAAAGGTTAAG
* * *
12410763 GCTGCAACGGTGAACCCGGTACTATGAAGAGATGA
65 GCCGCAACGGTGAACCCGGTACCATGAAGATATGA
** *
12410798 AGGGAAAGGTTGAGGCCATAACGGCGAACCC-AGTACCTTAGAAGATGTGATAGGAAAGGTTAAG
1 AGGGAAAGGTTGAGGCCGCAACGGCGAACCCGA-TACCTTAGAAGATGTGATGGGAAAGGTTAAG
* *
12410862 ACCGCAACGGTGAACCCGATACCATGAAGATATGA
65 GCCGCAACGGTGAACCCGGTACCATGAAGATATGA
* * * * * *
12410897 AGGGAAAGGTT-AGGCCGTAACGGCAAACCCGATACCAT-GAAGATTTGAAGGG-AAGGATTGAG
1 AGGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTTAGAAGATGTGATGGGAAAGG-TTAAG
* * * * * *
12410959 GCCGCGATGGCT-AATCCGGTACCTTAAAAGATGTGA
65 GCCGCAACGG-TGAACCCGGTACCAT-GAAGATATGA
* * * * * *
12410995 TGGGAAAGGTTAAGGCCGCAACGGCAAACCCGATACCAT-GAAGATATGAAGGGAAAGGTTAAGG
1 AGGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTTAGAAGATGTGATGGGAAAGGTTAAGG
*
12411059 CTGCAACG
66 CCGCAACG
12411067 ACAAACCTAG
Statistics
Matches: 478, Mismatches: 75, Indels: 26
0.83 0.13 0.04
Matches are distributed among these distances:
96 4 0.01
97 32 0.07
98 97 0.20
99 282 0.59
100 63 0.13
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.18
Consensus pattern (99 bp):
AGGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTTAGAAGATGTGATGGGAAAGGTTAAGG
CCGCAACGGTGAACCCGGTACCATGAAGATATGA
Found at i:12411000 original size:246 final size:248
Alignment explanation
Indices: 12410492--12411059 Score: 675
Period size: 246 Copynumber: 2.3 Consensus size: 248
12410482 TGGTACAATG
* * * * * * * *
12410492 AAGATATAAAGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGT-CCTTAGAAGATG-TGATGGGA
1 AAGATGTAATGGGAAAGGTTAAGGCCGCAACGGCAAACCCGATACCAT-GAAGA-GATGAAGGGA
* ** * * * * * *
12410555 AAGGTTAAAGCCGCAACGACGAATCC-GATACCATA-AAGATTATGA-AGGGAAAGGTTGAGGCC
64 AAGGTTAAGGCCATAACGGCGAACCCAG-TACCTTAGAAGA-TGTGATA-GGAAAGGTTAAGACC
* * * * * *
12410617 GCAACGGCGAACCCGATACCTTAGAAGATGTGATGGGAAATGTTGAGGTCGCAACGGTAAACCCG
126 GCAACGGCGAACCCGATACCATAGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCAAACCCG
* ** *
12410682 GTACCATGAAGATTTGAAGGGAAGGATTGAGGCCGCAACGGTGAATTTGGTACCTTAG
191 ATACCATGAAGATTTGAAGGGAAGGATTGAGGCCGCAACGGTGAATCCGGTACCTTAA
* ** * *
12410740 AAGATGTAATGGGAAAGGTTAAGGCTGCAACGGTGAACCCGGTACTATGAAGAGATGAAGGGAAA
1 AAGATGTAATGGGAAAGGTTAAGGCCGCAACGGCAAACCCGATACCATGAAGAGATGAAGGGAAA
*
12410805 GGTTGAGGCCATAACGGCGAACCCAGTACCTTAGAAGATGTGATAGGAAAGGTTAAGACCGCAAC
66 GGTTAAGGCCATAACGGCGAACCCAGTACCTTAGAAGATGTGATAGGAAAGGTTAAGACCGCAAC
* *
12410870 GGTGAACCCGATACCAT-GAAGATATGAAGGGAAAGGTT-AGGCCGTAACGGCAAACCCGATACC
131 GGCGAACCCGATACCATAGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCAAACCCGATACC
* *
12410933 ATGAAGATTTGAAGGGAAGGATTGAGGCCGCGATGGCT-AATCCGGTACCTTAA
196 ATGAAGATTTGAAGGGAAGGATTGAGGCCGCAACGG-TGAATCCGGTACCTTAA
* *
12410986 AAGATGTGATGGGAAAGGTTAAGGCCGCAACGGCAAACCCGATACCATGAAGATATGAAGGGAAA
1 AAGATGTAATGGGAAAGGTTAAGGCCGCAACGGCAAACCCGATACCATGAAGAGATGAAGGGAAA
12411051 GGTTAAGGC
66 GGTTAAGGC
12411060 TGCAACGACA
Statistics
Matches: 273, Mismatches: 41, Indels: 14
0.83 0.12 0.04
Matches are distributed among these distances:
246 133 0.49
247 20 0.07
248 112 0.41
249 8 0.03
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.18
Consensus pattern (248 bp):
AAGATGTAATGGGAAAGGTTAAGGCCGCAACGGCAAACCCGATACCATGAAGAGATGAAGGGAAA
GGTTAAGGCCATAACGGCGAACCCAGTACCTTAGAAGATGTGATAGGAAAGGTTAAGACCGCAAC
GGCGAACCCGATACCATAGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCAAACCCGATACC
ATGAAGATTTGAAGGGAAGGATTGAGGCCGCAACGGTGAATCCGGTACCTTAA
Found at i:12411453 original size:85 final size:85
Alignment explanation
Indices: 12411291--12411446 Score: 213
Period size: 85 Copynumber: 1.8 Consensus size: 85
12411281 ATACCCCATA
* ** ** *
12411291 TTCCTGATGAGATACAAAGAAGAGGGTTAAAGGAATAAAGCGATCATCTTCCTGATGAGATGTAG
1 TTCCTGATGAGATACAAAGAAGAGGATTAAAACAATAAAGCGATCATCTTCCTGATGAGATACAA
*
12411356 AGAAGTGAACCAAATCCGTC
66 AGAAGAGAACCAAATCCGTC
* * * *
12411376 TTCCTGATGAGATATAGAGAAGTGGATTAAAACAATGAAGCGATCATCTTCCTGATGAGATACAA
1 TTCCTGATGAGATACAAAGAAGAGGATTAAAACAATAAAGCGATCATCTTCCTGATGAGATACAA
12411441 AGAAGA
66 AGAAGA
12411447 AGACCAATTC
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
85 60 1.00
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (85 bp):
TTCCTGATGAGATACAAAGAAGAGGATTAAAACAATAAAGCGATCATCTTCCTGATGAGATACAA
AGAAGAGAACCAAATCCGTC
Found at i:12413508 original size:29 final size:29
Alignment explanation
Indices: 12413415--12413537 Score: 133
Period size: 30 Copynumber: 4.2 Consensus size: 29
12413405 GAGAATTTAC
* *
12413415 ATTTTAACCCCTAAACTTTCCAAAAATTAA
1 ATTTTAACCCCTAAACTTT-TAAAAATTGA
*
12413445 ATTTAAACCCCTAAACATTTTAAAAATTTG-
1 ATTTTAACCCCTAAAC-TTTTAAAAA-TTGA
12413475 ATTTTAACCCCTAAACTTTTAAAAATTGA
1 ATTTTAACCCCTAAACTTTTAAAAATTGA
* * * *
12413504 ATTTTGACCCC-AAAATTTTCCAAAATTGC
1 ATTTTAACCCCTAAACTTTT-AAAAATTGA
12413533 ATTTT
1 ATTTT
12413538 GACTCGAAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
28 10 0.12
29 31 0.38
30 35 0.43
31 5 0.06
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.37
Consensus pattern (29 bp):
ATTTTAACCCCTAAACTTTTAAAAATTGA
Found at i:12413553 original size:29 final size:30
Alignment explanation
Indices: 12413496--12413559 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
12413486 TAAACTTTTA
**
12413496 AAAATTGAATTTTGACCCCAAAATTTTCC-
1 AAAATTGAATTTTGACCCCAAAACCTTCCT
* * *
12413525 AAAATTGCATTTTGACTCGAAAACCTTCCT
1 AAAATTGAATTTTGACCCCAAAACCTTCCT
12413555 AAAAT
1 AAAAT
12413560 CACATTTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (30 bp):
AAAATTGAATTTTGACCCCAAAACCTTCCT
Found at i:12414476 original size:28 final size:27
Alignment explanation
Indices: 12414414--12414476 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 27
12414404 ACGTTTCGAC
* *
12414414 ATATACAATATATATTAGTGGGTGTTAT
1 ATATATAATATATATTA-TGGGTGATAT
*
12414442 ATGTATAATATATATT-TGGGTGCATAT
1 ATATATAATATATATTATGGGTG-ATAT
12414469 ATAATATA
1 AT-ATATA
12414477 TTTGTGTGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 6 0.21
27 5 0.17
28 18 0.62
ACGTcount: A:0.38, C:0.03, G:0.16, T:0.43
Consensus pattern (27 bp):
ATATATAATATATATTATGGGTGATAT
Found at i:12419067 original size:136 final size:136
Alignment explanation
Indices: 12418823--12419097 Score: 541
Period size: 136 Copynumber: 2.0 Consensus size: 136
12418813 AAGAAAGATT
*
12418823 ATTTTAAGAATAATATAAGCCTCGAAGATAAATTACGAAATGTTCCTCCGGGAATGTTCAGGTAC
1 ATTTTAAGAATAATATAAGCCTCGAAGATAAATTACGAAATGTTCCGCCGGGAATGTTCAGGTAC
12418888 CAATGGGAAGAGCAAGTTAGATTTTGGAGCTCAAAGAAAGGAGATGTATTATGTATTACTAAACT
66 CAATGGGAAGAGCAAGTTAGATTTTGGAGCTCAAAGAAAGGAGATGTATTATGTATTACTAAACT
12418953 CTTATA
131 CTTATA
12418959 ATTTTAAGAATAATATAAGCCTCGAAGATAAATTACGAAATGTTCCGCCGGGAATGTTCAGGTAC
1 ATTTTAAGAATAATATAAGCCTCGAAGATAAATTACGAAATGTTCCGCCGGGAATGTTCAGGTAC
12419024 CAATGGGAAGAGCAAGTTAGATTTTGGAGCTCAAAGAAAGGAGATGTATTATGTATTACTAAACT
66 CAATGGGAAGAGCAAGTTAGATTTTGGAGCTCAAAGAAAGGAGATGTATTATGTATTACTAAACT
12419089 CTTATA
131 CTTATA
12419095 ATT
1 ATT
12419098 ATTTCTGTTT
Statistics
Matches: 138, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 138 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.29
Consensus pattern (136 bp):
ATTTTAAGAATAATATAAGCCTCGAAGATAAATTACGAAATGTTCCGCCGGGAATGTTCAGGTAC
CAATGGGAAGAGCAAGTTAGATTTTGGAGCTCAAAGAAAGGAGATGTATTATGTATTACTAAACT
CTTATA
Found at i:12420467 original size:96 final size:96
Alignment explanation
Indices: 12420287--12420470 Score: 264
Period size: 96 Copynumber: 1.9 Consensus size: 96
12420277 TTAGTGGTGT
* * **
12420287 TTGTGGGGAAGCGCCGCTAAAGACCATGTTCTTTATCGACGTTTGTGGGGAAAAGCGTTGCTAAA
1 TTGTGGGGAAGCGCCGCTAAAGACCATGTTCTTTAGCGACGTTTGTAGGGAAAAGCGCCGCTAAA
*
12420352 GACCATGTTCTTTAGCGGCGTTTAGCAACGC
66 GACCAAGTTCTTTAGCGGCGTTTAGCAACGC
* *
12420383 TTGTGGGGAAAGCGCCGCTAAAGACCATGTTCTTTAGC-AGTGTTTGTAGGG-AAAGTGCCGCTA
1 TTGTGGGG-AAGCGCCGCTAAAGACCATGTTCTTTAGCGA-CGTTTGTAGGGAAAAGCGCCGCTA
*
12420446 AAGAGCAAGTTCTTTAGCGGCGTTT
64 AAGACCAAGTTCTTTAGCGGCGTTT
12420471 GTGGGAAAGC
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
96 41 0.53
97 37 0.47
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.28
Consensus pattern (96 bp):
TTGTGGGGAAGCGCCGCTAAAGACCATGTTCTTTAGCGACGTTTGTAGGGAAAAGCGCCGCTAAA
GACCAAGTTCTTTAGCGGCGTTTAGCAACGC
Found at i:12420490 original size:42 final size:43
Alignment explanation
Indices: 12420383--12420551 Score: 250
Period size: 43 Copynumber: 4.0 Consensus size: 43
12420373 TTAGCAACGC
* *
12420383 TTGTGGGGAAAGCGCCGCTAAAGACCATGTTCTTTAGCAGTGT
1 TTGTGGGGAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGT
* * * *
12420426 TTGTAGGGAAAGTGCCGCTAAAGAGCAAGTTCTTTAGCGGCGT
1 TTGTGGGGAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGT
* *
12420469 TTGT-GGGAAAGCACCGCTAAAGACCATGTTCTTTAACGGCGT
1 TTGTGGGGAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGT
*
12420511 TTGTGGGGAAAGCGCCGCTAATGACCATGTTCTTTAGCGGC
1 TTGTGGGGAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGC
12420552 ATTTTTTCTC
Statistics
Matches: 111, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 37 0.33
43 74 0.67
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.27
Consensus pattern (43 bp):
TTGTGGGGAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGT
Found at i:12420520 original size:85 final size:86
Alignment explanation
Indices: 12420383--12420551 Score: 250
Period size: 85 Copynumber: 2.0 Consensus size: 86
12420373 TTAGCAACGC
* * * *
12420383 TTGTGGGGAAAGCGCCGCTAAAGACCATGTTCTTTAGCAGTGTTTGTAGGGAAAGTGCCGCTAAA
1 TTGTGGGGAAAGCACCGCTAAAGACCATGTTCTTTAACAGCGTTTGTAGGGAAAGCGCCGCTAAA
*
12420448 GAGCAAGTTCTTTAGCGGCGT
66 GACCAAGTTCTTTAGCGGCGT
* * *
12420469 TTGT-GGGAAAGCACCGCTAAAGACCATGTTCTTTAACGGCGTTTGTGGGGAAAGCGCCGCTAAT
1 TTGTGGGGAAAGCACCGCTAAAGACCATGTTCTTTAACAGCGTTTGTAGGGAAAGCGCCGCTAAA
*
12420533 GACCATGTTCTTTAGCGGC
66 GACCAAGTTCTTTAGCGGC
12420552 ATTTTTTCTC
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
85 70 0.95
86 4 0.05
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.27
Consensus pattern (86 bp):
TTGTGGGGAAAGCACCGCTAAAGACCATGTTCTTTAACAGCGTTTGTAGGGAAAGCGCCGCTAAA
GACCAAGTTCTTTAGCGGCGT
Found at i:12428510 original size:23 final size:23
Alignment explanation
Indices: 12428133--12428510 Score: 459
Period size: 23 Copynumber: 16.4 Consensus size: 23
12428123 ATCTTAATTC
*
12428133 TTTAAGCACAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
12428156 TTTAAGCATAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* ** *
12428179 CTTAAATACAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
** * *
12428202 TTTAATTATTAATCATATTAATA
1 TTTAAGCATAAATCACATTAATA
*
12428225 TTTAAGCACAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* * *
12428248 TTTGAGCACAAATCATATTAATA
1 TTTAAGCATAAATCACATTAATA
* *
12428271 TTTAATCATAAATCATATTAATA
1 TTTAAGCATAAATCACATTAATA
* *
12428294 TTTAAACACAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
12428317 TTTAAGCATAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* *
12428340 TTTGAGCATAAATCATATTAATA
1 TTTAAGCATAAATCACATTAATA
* *
12428363 TTTAAGCACAAATCATATTAATA
1 TTTAAGCATAAATCACATTAATA
* * * *
12428386 TTTGAGAACAAATCATATTAATA
1 TTTAAGCATAAATCACATTAATA
12428409 TTTAAGCATAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* * * *
12428432 CTTAAGTACAAATCACAATAATA
1 TTTAAGCATAAATCACATTAATA
* *
12428455 TTTAATCATAAATCATATTAATA
1 TTTAAGCATAAATCACATTAATA
* *
12428478 TTTAATCATAAATTACATTAATA
1 TTTAAGCATAAATCACATTAATA
12428501 TTTAAGCATA
1 TTTAAGCATA
12428511 GATATAAGAA
Statistics
Matches: 307, Mismatches: 48, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 307 1.00
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.36
Consensus pattern (23 bp):
TTTAAGCATAAATCACATTAATA
Found at i:12433033 original size:23 final size:23
Alignment explanation
Indices: 12432988--12433034 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
12432978 ATGAAATGAG
*
12432988 TTAACTAAGTACGTAAATTAATT
1 TTAACTAAGTACGTAAATCAATT
*
12433011 TTAACTAAGTATGTGAAA-CAATT
1 TTAACTAAGTACGT-AAATCAATT
12433034 T
1 T
12433035 AAAACAATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.38
Consensus pattern (23 bp):
TTAACTAAGTACGTAAATCAATT
Found at i:12437117 original size:34 final size:36
Alignment explanation
Indices: 12437072--12437166 Score: 106
Period size: 38 Copynumber: 2.6 Consensus size: 36
12437062 GTACATGTTC
*
12437072 ATGCAGCGACATTCTTGGGTGCAA-TT-GAATACTT
1 ATGCAGTGACATTCTTGGGTGCAATTTAGAATACTT
* *
12437106 ATGCAGTGACATT-TCTGGATGCAATTTGAAGAATATTT
1 ATGCAGTGACATTCT-TGGGTGCAATTT--AGAATACTT
*
12437144 ATGCAGTGACAGTCTTGGGTGCA
1 ATGCAGTGACATTCTTGGGTGCA
12437167 TTCCAGGAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
33 1 0.02
34 20 0.40
35 2 0.04
38 26 0.52
39 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (36 bp):
ATGCAGTGACATTCTTGGGTGCAATTTAGAATACTT
Found at i:12437251 original size:38 final size:38
Alignment explanation
Indices: 12437201--12437285 Score: 152
Period size: 38 Copynumber: 2.2 Consensus size: 38
12437191 AGTTTTGGTG
*
12437201 AAATCTGGAAGTGCTCATGCGGTGATAGTTTTGGGCAC
1 AAATTTGGAAGTGCTCATGCGGTGATAGTTTTGGGCAC
*
12437239 AAATTTGGAAGTGCTCATGCGGTGATAGTTTTGGGCGC
1 AAATTTGGAAGTGCTCATGCGGTGATAGTTTTGGGCAC
12437277 AAATTTGGA
1 AAATTTGGA
12437286 TGTTATTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.25, C:0.13, G:0.32, T:0.31
Consensus pattern (38 bp):
AAATTTGGAAGTGCTCATGCGGTGATAGTTTTGGGCAC
Found at i:12444422 original size:16 final size:16
Alignment explanation
Indices: 12444396--12444436 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
12444386 GTATGGCGAC
12444396 TTCGA-TATACCAAGA
1 TTCGAGTATACCAAGA
12444411 TTCGAGTATACCAAGA
1 TTCGAGTATACCAAGA
12444427 TTCGAGTATA
1 TTCGAGTATA
12444437 AGGTCAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 5 0.20
16 20 0.80
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (16 bp):
TTCGAGTATACCAAGA
Found at i:12449210 original size:13 final size:13
Alignment explanation
Indices: 12449192--12449216 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12449182 GTATGTATTA
12449192 AAATTTGATTGTG
1 AAATTTGATTGTG
12449205 AAATTTGATTGT
1 AAATTTGATTGT
12449217 TTAGATAGTT
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:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (13 bp):
AAATTTGATTGTG
Found at i:12450695 original size:94 final size:94
Alignment explanation
Indices: 12450391--12450701 Score: 387
Period size: 94 Copynumber: 3.3 Consensus size: 94
12450381 TATTCTTGTT
* *
12450391 AGCTTAGTGTGAGCAGCATCGT-TA-AGG-AACAGTTATATGTACATATACCATATTGATGGCTG
1 AGCTTAGTGTGAGCAGCATCGTATACTGGTAACAGTTATATGTACATATACCATATCGATGGCTG
* * *
12450453 AGGTATCGTATATGTTGCGAATCCTCATC
66 AGGTATCGCATATGTTGCGAGTCCTCGTC
* * * * *
12450482 AGCTTAGTTTGAGCAGCATTGGATACTGGTAACAATTATATGTAC-TGATACCGTATCGATGGCT
1 AGCTTAGTGTGAGCAGCATCGTATACTGGTAACAGTTATATGTACAT-ATACCATATCGATGGCT
* * * *
12450546 AAGGTATAGCATATGTTTCGAGCCCTCGTC
65 GAGGTATCGCATATGTTGCGAGTCCTCGTC
* *
12450576 ACCTTAGTGTGAGCAGCATCGTATACTGGTAACAGTTATATGAACATATACCATATCGATGGCTG
1 AGCTTAGTGTGAGCAGCATCGTATACTGGTAACAGTTATATGTACATATACCATATCGATGGCTG
* *
12450641 AGGTACCGCATATGTTGCGAGTCCTTGTC
66 AGGTATCGCATATGTTGCGAGTCCTCGTC
* * * *
12450670 AGCTTACTGTGAGCAGTATCATATACCGGTAA
1 AGCTTAGTGTGAGCAGCATCGTATACTGGTAA
12450702 TAGAAATGAC
Statistics
Matches: 183, Mismatches: 32, Indels: 7
0.82 0.14 0.03
Matches are distributed among these distances:
91 19 0.10
92 2 0.01
93 3 0.02
94 158 0.86
95 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (94 bp):
AGCTTAGTGTGAGCAGCATCGTATACTGGTAACAGTTATATGTACATATACCATATCGATGGCTG
AGGTATCGCATATGTTGCGAGTCCTCGTC
Found at i:12455297 original size:94 final size:93
Alignment explanation
Indices: 12455144--12455437 Score: 364
Period size: 94 Copynumber: 3.2 Consensus size: 93
12455134 TTTGCATATT
* * * *
12455144 CTCGTTAGCTTAGTGTGAGCA-C--CAT-CACTAGGGAACAGTTATATGTACAGATACTGTATCG
1 CTCGTCAGCTTAGTGTGAGCAGCATCATATACTA-GTAACAGTTATATGTATAGATAC-GTATCG
* *
12455205 ATGGCTGAGGTACCGCATATGTTGCGTGTC
64 ATGGCTGAGGTACCGTATATGTTGCGAGTC
* * *
12455235 CTCATCAGATTAGTGTGAGCAGCATCATATACTAGTAACAATTATATGTATAGATACGGTATCGA
1 CTCGTCAGCTTAGTGTGAGCAGCATCATATACTAGTAACAGTTATATGTATAGATAC-GTATCGA
* *
12455300 TTGCTGAGGTACCGTATATGTTACGAGTC
65 TGGCTGAGGTACCGTATATGTTGCGAGTC
* * * *
12455329 CTTGTCAGCTTAGTGTGAGCAGCATCGTATACTAGTAA-ATGTTGTATGAATAGATATCGTATCG
1 CTCGTCAGCTTAGTGTGAGCAGCATCATATACTAGTAACA-GTTATATGTATAGATA-CGTATCG
*
12455393 ATGGCTGAGGTACCGTATACGTTGCGAGTC
64 ATGGCTGAGGTACCGTATATGTTGCGAGTC
12455423 CTCGTCAGCTTAGTG
1 CTCGTCAGCTTAGTG
12455438 ATAGCATTAG
Statistics
Matches: 174, Mismatches: 23, Indels: 9
0.84 0.11 0.04
Matches are distributed among these distances:
91 18 0.10
92 1 0.01
93 1 0.01
94 149 0.86
95 5 0.03
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (93 bp):
CTCGTCAGCTTAGTGTGAGCAGCATCATATACTAGTAACAGTTATATGTATAGATACGTATCGAT
GGCTGAGGTACCGTATATGTTGCGAGTC
Found at i:12463687 original size:21 final size:21
Alignment explanation
Indices: 12463663--12463737 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
12463653 TAGTACAGAT
* *
12463663 TTCTACCTATACAAGTGACAG
1 TTCTACCGATACAAGTGACAC
*
12463684 TTCTACCGATACAAGTGACTC
1 TTCTACCGATACAAGTGACAC
* ***
12463705 TTCTACCGAAACAAGTCTTAC
1 TTCTACCGATACAAGTGACAC
12463726 TTCTACCGATAC
1 TTCTACCGATAC
12463738 TAAAAACTCC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29
Consensus pattern (21 bp):
TTCTACCGATACAAGTGACAC
Found at i:12464450 original size:19 final size:19
Alignment explanation
Indices: 12464416--12464564 Score: 124
Period size: 19 Copynumber: 8.0 Consensus size: 19
12464406 GAAATAATTC
* *
12464416 CTTACGATCCAATATTGCT
1 CTTACGAGCCAGTATTGCT
* *
12464435 CTTACAAGCTAGTATTGCT
1 CTTACGAGCCAGTATTGCT
* * *
12464454 C-AATGAGCCAGTATTACT
1 CTTACGAGCCAGTATTGCT
12464472 CTTACGAGCCAGTATTGCT
1 CTTACGAGCCAGTATTGCT
* * *
12464491 C-AATGAGCCAATATTGCT
1 CTTACGAGCCAGTATTGCT
* * *
12464509 C-AACGAGCTAGTATTACT
1 CTTACGAGCCAGTATTGCT
* *
12464527 CTTACAAGCCAGTATTGGT
1 CTTACGAGCCAGTATTGCT
* *
12464546 CTTACGAGCTAATATTGCT
1 CTTACGAGCCAGTATTGCT
12464565 ATTCTCTTTA
Statistics
Matches: 100, Mismatches: 28, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
18 42 0.42
19 58 0.58
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (19 bp):
CTTACGAGCCAGTATTGCT
Found at i:12464468 original size:18 final size:18
Alignment explanation
Indices: 12464445--12464543 Score: 99
Period size: 18 Copynumber: 5.4 Consensus size: 18
12464435 CTTACAAGCT
*
12464445 AGTATTGCTCAATGAGCC
1 AGTATTGCTCAACGAGCC
* *
12464463 AGTATTACTCTTACGAGCC
1 AGTATTGCTC-AACGAGCC
*
12464482 AGTATTGCTCAATGAGCC
1 AGTATTGCTCAACGAGCC
* *
12464500 AATATTGCTCAACGAGCT
1 AGTATTGCTCAACGAGCC
* * *
12464518 AGTATTACTCTTACAAGCC
1 AGTATTGCTC-AACGAGCC
12464537 AGTATTG
1 AGTATTG
12464544 GTCTTACGAG
Statistics
Matches: 64, Mismatches: 15, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
18 38 0.59
19 26 0.41
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (18 bp):
AGTATTGCTCAACGAGCC
Found at i:12464486 original size:37 final size:37
Alignment explanation
Indices: 12464428--12464564 Score: 159
Period size: 37 Copynumber: 3.7 Consensus size: 37
12464418 TACGATCCAA
*
12464428 TATTGCTCTTACAAGCTAGTATTGCTCAATGAGCCAG
1 TATTGCTCTTACGAGCTAGTATTGCTCAATGAGCCAG
* * *
12464465 TATTACTCTTACGAGCCAGTATTGCTCAATGAGCCAA
1 TATTGCTCTTACGAGCTAGTATTGCTCAATGAGCCAG
* * * **
12464502 TATTGCTC-AACGAGCTAGTATTACTCTTACAAGCCAG
1 TATTGCTCTTACGAGCTAGTATTGCTC-AATGAGCCAG
* *
12464539 TATTGGTCTTACGAGCTAATATTGCT
1 TATTGCTCTTACGAGCTAGTATTGCT
12464565 ATTCTCTTTA
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
36 15 0.18
37 53 0.65
38 14 0.17
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.33
Consensus pattern (37 bp):
TATTGCTCTTACGAGCTAGTATTGCTCAATGAGCCAG
Found at i:12464537 original size:74 final size:74
Alignment explanation
Indices: 12464424--12464564 Score: 176
Period size: 74 Copynumber: 1.9 Consensus size: 74
12464414 TCCTTACGAT
* * ** *
12464424 CCAATATTGCTCTTACAAGCTAGTATTGCTCAATGAGCCAGTATTACTCTTACGAGCCAGTATTG
1 CCAATATTGCTCTAACAAGCTAGTATTACTCAACAAGCCAGTATTACTCTTACGAGCCAATATTG
12464489 CTCAATGAG
66 CTCAATGAG
* * ** *
12464498 CCAATATTGCTC-AACGAGCTAGTATTACTCTTACAAGCCAGTATTGGTCTTACGAGCTAATATT
1 CCAATATTGCTCTAACAAGCTAGTATTACTC-AACAAGCCAGTATTACTCTTACGAGCCAATATT
12464562 GCT
65 GCT
12464565 ATTCTCTTTA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
73 15 0.27
74 41 0.73
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (74 bp):
CCAATATTGCTCTAACAAGCTAGTATTACTCAACAAGCCAGTATTACTCTTACGAGCCAATATTG
CTCAATGAG
Found at i:12466049 original size:19 final size:17
Alignment explanation
Indices: 12466027--12466061 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
12466017 CTTTTAGGAA
12466027 TTTTTAAAGTTTTCTTTTC
1 TTTTTAAA--TTTCTTTTC
12466046 TTTTTAAATTTCTTTT
1 TTTTTAAATTTCTTTT
12466062 ATTGAATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.17, C:0.09, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTTAAATTTCTTTTC
Found at i:12466091 original size:15 final size:15
Alignment explanation
Indices: 12466073--12466107 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
12466063 TTGAATGTAA
12466073 TTTTATTTCAGGTGG
1 TTTTATTTCAGGTGG
12466088 TTTTATTTCAGGTGG
1 TTTTATTTCAGGTGG
12466103 TTTTA
1 TTTTA
12466108 CTTTTGTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.06, G:0.23, T:0.57
Consensus pattern (15 bp):
TTTTATTTCAGGTGG
Found at i:12475000 original size:44 final size:42
Alignment explanation
Indices: 12474859--12475024 Score: 122
Period size: 42 Copynumber: 3.9 Consensus size: 42
12474849 AGACTCATAT
* * *
12474859 CTCGGGATGAGCATGAGATTATGTTAAAAAGGAAGACTCGTGA
1 CTCGAGATGAGCATGAGATTATGTT-TAAAGGAAGACTAGTGA
* * * *
12474902 CTC-AGGAAGAGCCTGAGGTTATGATTT-ATGGAAGACTCA-TGA
1 CTCGA-GATGAGCATGAGATTATG-TTTAAAGGAAGACT-AGTGA
* * * * * *
12474944 ATCAAAAGGAGTATGAGGTTATGTTTTAAAAGGAAGACTAGTGA
1 CTCGAGATGAGCATGAGATTATG-TTT-AAAGGAAGACTAGTGA
* *
12474988 CTCGAGATGAGTATGAGATTTTGTTTAAAGGAAGACT
1 CTCGAGATGAGCATGAGATTATGTTTAAAGGAAGACT
12475025 TACGACTCGA
Statistics
Matches: 96, Mismatches: 20, Indels: 15
0.73 0.15 0.11
Matches are distributed among these distances:
42 42 0.44
43 23 0.24
44 31 0.32
ACGTcount: A:0.35, C:0.10, G:0.28, T:0.27
Consensus pattern (42 bp):
CTCGAGATGAGCATGAGATTATGTTTAAAGGAAGACTAGTGA
Found at i:12475032 original size:42 final size:44
Alignment explanation
Indices: 12474952--12475034 Score: 109
Period size: 42 Copynumber: 1.9 Consensus size: 44
12474942 GAATCAAAAG
* *
12474952 GAGTATGAGGTTATGTTTTAAAAGGAAGACTAGTGACTCGAGAT
1 GAGTATGAGATTATGTTTTAAAAGGAAGACTAGCGACTCGAGAT
*
12474996 GAGTATGAGATTTTG-TTT-AAAGGAAGACTTA-CGACTCGA
1 GAGTATGAGATTATGTTTTAAAAGGAAGAC-TAGCGACTCGA
12475035 TTGATTATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 17 0.49
43 5 0.14
44 13 0.37
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.30
Consensus pattern (44 bp):
GAGTATGAGATTATGTTTTAAAAGGAAGACTAGCGACTCGAGAT
Found at i:12477570 original size:19 final size:19
Alignment explanation
Indices: 12477548--12477591 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
12477538 TTTATTTGGT
12477548 TTTAATATTTAAGATAT-TA
1 TTTAATATTTAA-ATATGTA
* *
12477567 TTTATTATTTAAATTTGTA
1 TTTAATATTTAAATATGTA
12477586 TTTAAT
1 TTTAAT
12477592 TTATTTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTAATATTTAAATATGTA
Found at i:12478423 original size:16 final size:16
Alignment explanation
Indices: 12478397--12478436 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
12478387 TACTCCTATT
12478397 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
*
12478412 TTCTATTTTCTTTTAT
1 TTCTATTTTCTTTTAA
*
12478428 TTTTATTTT
1 TTCTATTTT
12478437 TCCCCAGATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:12479997 original size:21 final size:21
Alignment explanation
Indices: 12479980--12480043 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
12479970 AGCAGCAATT
12479980 TATAGATTTTCAAAAGCAAAC
1 TATAGATTTTCAAAAGCAAAC
* *
12480001 TACAGA-TTTCAAAATCAAAC
1 TATAGATTTTCAAAAGCAAAC
* *
12480021 TGTAGATTTTCAAAAGAAAAC
1 TATAGATTTTCAAAAGCAAAC
12480042 TA
1 TA
12480044 AGGCATCTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
20 17 0.49
21 18 0.51
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.28
Consensus pattern (21 bp):
TATAGATTTTCAAAAGCAAAC
Found at i:12480012 original size:20 final size:21
Alignment explanation
Indices: 12479983--12480043 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 21
12479973 AGCAATTTAT
12479983 AGATTTTCAAAAGCAAACTAC
1 AGATTTTCAAAAGCAAACTAC
* **
12480004 AGA-TTTCAAAATCAAACTGT
1 AGATTTTCAAAAGCAAACTAC
*
12480024 AGATTTTCAAAAGAAAACTA
1 AGATTTTCAAAAGCAAACTA
12480044 AGGCATCTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.26
Consensus pattern (21 bp):
AGATTTTCAAAAGCAAACTAC
Found at i:12484028 original size:6 final size:6
Alignment explanation
Indices: 12484017--12484053 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
12484007 GGCAACCCAA
*
12484017 TTATTT TTATTT TTATTT TTATTT TTCTATT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTAT-TT TTATTT
12484054 ATTTATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (6 bp):
TTATTT
Found at i:12484042 original size:13 final size:13
Alignment explanation
Indices: 12484017--12484062 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
12484007 GGCAACCCAA
12484017 TTATTTTTA-TTT
1 TTATTTTTATTTT
12484029 TTATTTTTATTTT
1 TTATTTTTATTTT
12484042 TCTA-TTTTATTTAT
1 T-TATTTTTATTT-T
12484056 TTATTTT
1 TTATTTT
12484063 ATTATATGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 9 0.30
13 14 0.47
14 7 0.23
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTTATTTT
Found at i:12485607 original size:19 final size:19
Alignment explanation
Indices: 12485585--12485629 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
12485575 TTTTATTAGG
12485585 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
12485604 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
12485623 ATTTAAT
1 ATTTAAT
12485630 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:12486466 original size:22 final size:22
Alignment explanation
Indices: 12486424--12486464 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
12486414 ATTTCGACAC
12486424 TCCTATTTTCTATTTCTTTTAA
1 TCCTATTTTCTATTTCTTTTAA
*
12486446 TCCTATTTTCT-TTTATTTT
1 TCCTATTTTCTATTTCTTTT
12486465 TATTTTTCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (22 bp):
TCCTATTTTCTATTTCTTTTAA
Found at i:12490445 original size:21 final size:21
Alignment explanation
Indices: 12490421--12490472 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
12490411 CGGGGAGTGT
12490421 GAAAATGTATAACGACATGAA
1 GAAAATGTATAACGACATGAA
12490442 GAAAATGTATAACGACATGAA
1 GAAAATGTATAACGACATGAA
12490463 GAAAATGTAT
1 GAAAATGTAT
12490473 TGGTGGCCAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.52, C:0.08, G:0.19, T:0.21
Consensus pattern (21 bp):
GAAAATGTATAACGACATGAA
Found at i:12492966 original size:42 final size:43
Alignment explanation
Indices: 12492807--12493030 Score: 165
Period size: 42 Copynumber: 5.3 Consensus size: 43
12492797 TTAATGTGTA
* * * * *
12492807 TTAAAGGAAGACTCAAGTCTCGGGTA-AGCATAAGGGTAT-A-
1 TTAAAGGAAGACTCATGACTCGGGAAGAGCATGAGGTTATGAT
* * * * *
12492847 TTAAATGAAGACTCATGTCTTGGGATGAGCATGAGATTATG-T
1 TTAAAGGAAGACTCATGACTCGGGAAGAGCATGAGGTTATGAT
* *
12492889 TAAAAAGGAAGACTCGTGACTCGGGAAGAGCATGAGGTTATGAT
1 T-TAAAGGAAGACTCATGACTCGGGAAGAGCATGAGGTTATGAT
** * *
12492933 TT-AAGGAAGACTCATGA-TTTGGAAGGAGTATGAGGTTATGTT
1 TTAAAGGAAGACTCATGACTCGGGAA-GAGCATGAGGTTATGAT
* ** * * *
12492975 TTAAAAGGAAGACTCGTGACTCGATATGAGCATGAGATT-TTAT
1 TT-AAAGGAAGACTCATGACTCGGGAAGAGCATGAGGTTATGAT
*
12493018 TTAAAAGAAGACT
1 TTAAAGGAAGACT
12493031 TACGACTCAG
Statistics
Matches: 143, Mismatches: 32, Indels: 16
0.75 0.17 0.08
Matches are distributed among these distances:
40 21 0.15
41 15 0.10
42 42 0.29
43 37 0.26
44 26 0.18
45 2 0.01
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.28
Consensus pattern (43 bp):
TTAAAGGAAGACTCATGACTCGGGAAGAGCATGAGGTTATGAT
Found at i:12492972 original size:85 final size:84
Alignment explanation
Indices: 12492809--12492997 Score: 220
Period size: 85 Copynumber: 2.2 Consensus size: 84
12492799 AATGTGTATT
** * * * * *
12492809 AAAGGAAGACTCAAGTCTCGGGTAAGCATAAGGGTATATTAAATGAAGACTCATGTCTTGGGATG
1 AAAGGAAGACTCGTGACTCGGGAAAGCATAAGGGTATATTAAAGGAAGACTCATGTCTTGGAAGG
12492874 AGCATGAGATTATG-TTAA
66 AGCATGAGATTATGTTTAA
* * *
12492892 AAAGGAAGACTCGTGACTCGGGAAGAGCATGAGGTTATGATTTAAGGAAGACTCATGAT-TTGGA
1 AAAGGAAGACTCGTGACTCGGGAA-AGCATAAGGGTAT-ATTAAAGGAAGACTCATG-TCTTGGA
* * *
12492956 AGGAGTATGAGGTTATGTTTTA
63 AGGAGCATGAGATTATGTTTAA
12492978 AAAGGAAGACTCGTGACTCG
1 AAAGGAAGACTCGTGACTCG
12492998 ATATGAGCAT
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
83 20 0.22
84 11 0.12
85 34 0.38
86 24 0.27
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (84 bp):
AAAGGAAGACTCGTGACTCGGGAAAGCATAAGGGTATATTAAAGGAAGACTCATGTCTTGGAAGG
AGCATGAGATTATGTTTAA
Found at i:12493028 original size:86 final size:86
Alignment explanation
Indices: 12492847--12493030 Score: 221
Period size: 86 Copynumber: 2.2 Consensus size: 86
12492837 TAAGGGTATA
* * *
12492847 TTAAATGAAGACTCATGTCTTGGGATGAGCATGAGATTATGTTAAAAAGGAAGACTCGTGACTCG
1 TTAAAAGAAGACTCATGTCTTGGAAGGAGCATGAGATTATGTTAAAAAGGAAGACTCGTGACTCG
* *
12492912 GGAAGAGCATGAGGTTATGAT
66 AGAAGAGCATGAGATTATGAT
* * * *
12492933 TT-AAGGAAGACTCATGAT-TTGGAAGGAGTATGAGGTTATGTTTTAAAAGGAAGACTCGTGACT
1 TTAAAAGAAGACTCATG-TCTTGGAAGGAGCATGAGATTATG-TTAAAAAGGAAGACTCGTGACT
* * *
12492996 CGATATGAGCATGAGATT-TTAT
64 CGAGAAGAGCATGAGATTATGAT
12493018 TTAAAAGAAGACT
1 TTAAAAGAAGACT
12493031 TACGACTCAG
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
85 36 0.43
86 47 0.57
ACGTcount: A:0.35, C:0.09, G:0.27, T:0.29
Consensus pattern (86 bp):
TTAAAAGAAGACTCATGTCTTGGAAGGAGCATGAGATTATGTTAAAAAGGAAGACTCGTGACTCG
AGAAGAGCATGAGATTATGAT
Found at i:12496632 original size:28 final size:28
Alignment explanation
Indices: 12496575--12496641 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
12496565 CTAATTTTAA
* *
12496575 AAAAATAAAAATACATAAATATTTTCAT
1 AAAAATAAAAATAAATAAATATTATCAT
12496603 AAAAATATAAAATAAATTAAATA-TAT-AT
1 AAAAATA-AAAATAAA-TAAATATTATCAT
12496631 AAAAATAAAAA
1 AAAAATAAAAA
12496642 ATTTAATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 4 0.11
28 16 0.46
29 9 0.26
30 6 0.17
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (28 bp):
AAAAATAAAAATAAATAAATATTATCAT
Found at i:12499870 original size:36 final size:35
Alignment explanation
Indices: 12499830--12499912 Score: 87
Period size: 36 Copynumber: 2.3 Consensus size: 35
12499820 AAGATGGAGA
* *
12499830 CCTTTAAGCTA-TCCAAGGACTAATGAAAAGACATAC
1 CCTTTAAGCTACT-CAAAGACAAATGAAAAGACAT-C
* * *
12499866 CCTTTCATCTACTCAAAGACAAATGAAGAGACATC
1 CCTTTAAGCTACTCAAAGACAAATGAAAAGACATC
12499901 CCTTTTAAGCTA
1 CC-TTTAAGCTA
12499913 ACCATCATGG
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
35 3 0.08
36 34 0.89
37 1 0.03
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25
Consensus pattern (35 bp):
CCTTTAAGCTACTCAAAGACAAATGAAAAGACATC
Found at i:12506984 original size:13 final size:13
Alignment explanation
Indices: 12506966--12506990 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12506956 TCAAACTTTA
12506966 TTTTATTTTTATT
1 TTTTATTTTTATT
12506979 TTTTATTTTTAT
1 TTTTATTTTTAT
12506991 GCTTTCAAAC
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTATTTTTATT
Found at i:12511413 original size:25 final size:24
Alignment explanation
Indices: 12511383--12511430 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
12511373 ACTAAACATA
*
12511383 AACAATTAAAATTAAAATTAAAAAC
1 AACAATTAAAA-TAAAAGTAAAAAC
12511408 AACAATTAAAATAAAAGTAAAAA
1 AACAATTAAAATAAAAGTAAAAA
12511431 TTTCAAGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.21
Consensus pattern (24 bp):
AACAATTAAAATAAAAGTAAAAAC
Found at i:12518611 original size:23 final size:23
Alignment explanation
Indices: 12518439--12518599 Score: 157
Period size: 23 Copynumber: 6.9 Consensus size: 23
12518429 CGAAGTACTT
12518439 AACAGTAAGCACAC-AAGTGCTGGGGA
1 AACAGTAAGCACACAAAGTGC----GA
*
12518465 AACAGTAAGCACACACAGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * * * *
12518487 ATCAGTAGGCGCACATAGCGC-A
1 AACAGTAAGCACACAAAGTGCGA
* *
12518509 AATCAGTAGGCACACGAAGTGCGA
1 AA-CAGTAAGCACACAAAGTGCGA
*
12518533 AACAGTAGGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
*
12518556 AACAGTAAGCACAGAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
*
12518579 AACAGTAAGCACACACAGTGC
1 AACAGTAAGCACACAAAGTGC
12518600 TGAACGGTAA
Statistics
Matches: 116, Mismatches: 16, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
22 19 0.16
23 75 0.65
24 3 0.03
26 14 0.12
27 5 0.04
ACGTcount: A:0.41, C:0.23, G:0.25, T:0.11
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Found at i:12520911 original size:23 final size:23
Alignment explanation
Indices: 12520885--12520937 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
12520875 TCTTCCATAT
12520885 AATGCTTCATAAGGCGCCATTTG
1 AATGCTTCATAAGGCGCCATTTG
*
12520908 AATGCTTCATAAGGTGCCATTTG
1 AATGCTTCATAAGGCGCCATTTG
12520931 AATGCTT
1 AATGCTT
12520938 GACTGATAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (23 bp):
AATGCTTCATAAGGCGCCATTTG
Found at i:12525832 original size:23 final size:24
Alignment explanation
Indices: 12525802--12525909 Score: 107
Period size: 23 Copynumber: 4.7 Consensus size: 24
12525792 CACACAGTGC
* *
12525802 AATCAGTAGGCGCACATAGCGC-A
1 AATCAGTAGGCACACAAAGCGCGA
*
12525825 AATCAGTAGGCACACAAAGTGCGA
1 AATCAGTAGGCACACAAAGCGCGA
*
12525849 AA-CAGTAGGCACACAAAGTGCGA
1 AATCAGTAGGCACACAAAGCGCGA
* * * *
12525872 AA-CAGTAAGCACAGAAAGTGTGA
1 AATCAGTAGGCACACAAAGCGCGA
*
12525895 AA-CAGTAAGCACACA
1 AATCAGTAGGCACACA
12525910 CAGTGCTGAA
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
23 74 0.96
24 3 0.04
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (24 bp):
AATCAGTAGGCACACAAAGCGCGA
Found at i:12525878 original size:46 final size:46
Alignment explanation
Indices: 12525779--12525915 Score: 152
Period size: 46 Copynumber: 3.0 Consensus size: 46
12525769 AAGTGCTGGG
* * * * * *
12525779 GAAACAATAAGCACACACAGTGC-AATCAGTAGGCGCACATAGCGC
1 GAAACAGTAAGCACACAAAGTGCGAAACAGTAGGCACACAAAGTGC
*
12525824 -AAATCAGTAGGCACACAAAGTGCGAAACAGTAGGCACACAAAGTGC
1 GAAA-CAGTAAGCACACAAAGTGCGAAACAGTAGGCACACAAAGTGC
* * * *
12525870 GAAACAGTAAGCACAGAAAGTGTGAAACAGTAAGCACACACAGTGC
1 GAAACAGTAAGCACACAAAGTGCGAAACAGTAGGCACACAAAGTGC
12525916 TGAACGGTAA
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
44 3 0.04
45 16 0.21
46 55 0.71
47 3 0.04
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.11
Consensus pattern (46 bp):
GAAACAGTAAGCACACAAAGTGCGAAACAGTAGGCACACAAAGTGC
Found at i:12525914 original size:23 final size:23
Alignment explanation
Indices: 12525828--12525927 Score: 121
Period size: 23 Copynumber: 4.3 Consensus size: 23
12525818 TAGCGCAAAT
* *
12525828 CAGTAGGCACACAAAGTGCGAAA
1 CAGTAAGCACACAAAGTGTGAAA
* *
12525851 CAGTAGGCACACAAAGTGCGAAA
1 CAGTAAGCACACAAAGTGTGAAA
*
12525874 CAGTAAGCACAGAAAGTGTGAAA
1 CAGTAAGCACACAAAGTGTGAAA
*
12525897 CAGTAAGCACACACAGTGCTG-AA
1 CAGTAAGCACACAAAGTG-TGAAA
*
12525920 CGGTAAGC
1 CAGTAAGC
12525928 GCGCTAGCGT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
23 68 0.97
24 2 0.03
ACGTcount: A:0.42, C:0.21, G:0.26, T:0.11
Consensus pattern (23 bp):
CAGTAAGCACACAAAGTGTGAAA
Found at i:12525927 original size:46 final size:46
Alignment explanation
Indices: 12525755--12525915 Score: 148
Period size: 46 Copynumber: 3.5 Consensus size: 46
12525745 CGAAGTACTT
* *
12525755 AACAGTAAGCACAC-AAGTGCTGGGGAAACAATAAGCACACACAGTGC-A
1 AACAGTAAGCACACAAAGTGC----GAAACAGTAAGCACACAAAGTGCGA
* * * * * *
12525803 ATCAGTAGGCGCACATAGCGC-AAATCAGTAGGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGAAA-CAGTAAGCACACAAAGTGCGA
* * *
12525849 AACAGTAGGCACACAAAGTGCGAAACAGTAAGCACAGAAAGTGTGA
1 AACAGTAAGCACACAAAGTGCGAAACAGTAAGCACACAAAGTGCGA
*
12525895 AACAGTAAGCACACACAGTGC
1 AACAGTAAGCACACAAAGTGC
12525916 TGAACGGTAA
Statistics
Matches: 92, Mismatches: 17, Indels: 10
0.77 0.14 0.08
Matches are distributed among these distances:
44 3 0.03
45 16 0.17
46 55 0.60
47 3 0.03
48 11 0.12
49 4 0.04
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.11
Consensus pattern (46 bp):
AACAGTAAGCACACAAAGTGCGAAACAGTAAGCACACAAAGTGCGA
Found at i:12529267 original size:14 final size:15
Alignment explanation
Indices: 12529243--12529272 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
12529233 GAGTTGTTTG
12529243 AAAGCATAAAAATAA
1 AAAGCATAAAAATAA
12529258 AAAG-ATAAAAATAA
1 AAAGCATAAAAATAA
12529272 A
1 A
12529273 TAAAAGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.13
Consensus pattern (15 bp):
AAAGCATAAAAATAA
Found at i:12537518 original size:17 final size:18
Alignment explanation
Indices: 12537481--12537518 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
12537471 TTAAGGATAC
*
12537481 ATTCACTTGTGACGTTCAT
1 ATTCACTTGTAACG-TCAT
12537500 ATTCACTTGTAAC-TCAT
1 ATTCACTTGTAACGTCAT
12537517 AT
1 AT
12537519 ACTTTGATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (18 bp):
ATTCACTTGTAACGTCAT
Found at i:12558005 original size:3 final size:3
Alignment explanation
Indices: 12557993--12558023 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
12557983 AAAGCGATCT
12557993 ACA A-A ACA ACA ACA ACA ACA ACA ACA ACA AC
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA AC
12558024 TATGGTAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:12563880 original size:21 final size:21
Alignment explanation
Indices: 12563838--12563880 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
12563828 GTCTTTGTTC
* *
12563838 TATTACTAGAGGAGGTGGAGG
1 TATTACAAGAGGAGGTGCAGG
* *
12563859 TATTACAAGAGGTGTTGCAGG
1 TATTACAAGAGGAGGTGCAGG
12563880 T
1 T
12563881 CGGGCAGTAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.07, G:0.37, T:0.28
Consensus pattern (21 bp):
TATTACAAGAGGAGGTGCAGG
Found at i:12567226 original size:15 final size:15
Alignment explanation
Indices: 12567204--12567241 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
12567194 ACATGGACAT
12567204 TACGAGCACT-AATGC
1 TACGAGCACTGAA-GC
*
12567219 TGCGAGCACTGAAGC
1 TACGAGCACTGAAGC
12567234 TACGAGCA
1 TACGAGCA
12567242 TTGATGTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 18 0.90
16 2 0.10
ACGTcount: A:0.32, C:0.26, G:0.26, T:0.16
Consensus pattern (15 bp):
TACGAGCACTGAAGC
Found at i:12570956 original size:18 final size:18
Alignment explanation
Indices: 12570933--12570972 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
12570923 GAATGGATTT
12570933 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
12570951 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
12570969 TTAA
1 TTAA
12570973 GTACACCTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:12573402 original size:25 final size:26
Alignment explanation
Indices: 12573356--12573406 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
12573346 ATTATACTTT
* *
12573356 TTTTTTAATATAAGTTGTTACTTAAA
1 TTTTTTAATAGAAGTTGATACTTAAA
*
12573382 TTTTTTATTAGAAG-TGATACTTAAA
1 TTTTTTAATAGAAGTTGATACTTAAA
12573407 CTATACTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.51
Consensus pattern (26 bp):
TTTTTTAATAGAAGTTGATACTTAAA
Done.