Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 48 of 438
Found at i:12090197 original size:122 final size:122
Alignment explanation
Indices: 12090049--12090337 Score: 474
Period size: 122 Copynumber: 2.4 Consensus size: 122
12090039 AAACACCTCT
*
12090049 AAAAACAGAGCAATAGCGGCGTTTTTGGTCAAACGCCGCTAAAAACAAAGCAATAGCGGCGTTTT
1 AAAAACAGAGCAATAGCGGCGTTTTTGGTCAAACGCCGCTAAAAACAAAGCAATAGCGGCATTTT
*
12090114 TGGCCAAATGCCGCTAAAAAACAGAGCAATAGCGGCGTTTTT-GTCCAAACGCCGCTA
66 TGGCCAAACGCCGCTAAAAAACAGAGCAATAGCGGCGTTTTTGGT-CAAACGCCGCTA
* *
12090171 AAAAACAGAGCAATAGCGGCGTTTTTGGTCAAACGCCGCTAAAAATAGAGCAATAGCGGCATTTT
1 AAAAACAGAGCAATAGCGGCGTTTTTGGTCAAACGCCGCTAAAAACAAAGCAATAGCGGCATTTT
*
12090236 TGTCCAAACGCCGCTAAAAAACAGAGCAATAGCGGCGTTTTTGGTCAAACGCCGCTA
66 TGGCCAAACGCCGCTAAAAAACAGAGCAATAGCGGCGTTTTTGGTCAAACGCCGCTA
* * *
12090293 AAAAACTGAGCAATAGCGGCGTTTTTGCTTAAAACGCCGC-AAAAA
1 AAAAACAGAGCAATAGCGGCGTTTTTG-GTCAAACGCCGCTAAAAA
12090338 GTCATATAAC
Statistics
Matches: 157, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
122 145 0.92
123 12 0.08
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.20
Consensus pattern (122 bp):
AAAAACAGAGCAATAGCGGCGTTTTTGGTCAAACGCCGCTAAAAACAAAGCAATAGCGGCATTTT
TGGCCAAACGCCGCTAAAAAACAGAGCAATAGCGGCGTTTTTGGTCAAACGCCGCTA
Found at i:12090337 original size:41 final size:41
Alignment explanation
Indices: 12090049--12090337 Score: 444
Period size: 41 Copynumber: 7.1 Consensus size: 41
12090039 AAACACCTCT
12090049 AAAAACAGAGCAATAGCGGCGTTTTTGGTCAAACGCCGCT-
1 AAAAACAGAGCAATAGCGGCGTTTTTGGTCAAACGCCGCTA
* * *
12090089 AAAAACAAAGCAATAGCGGCGTTTTTGGCCAAATGCCGCTA
1 AAAAACAGAGCAATAGCGGCGTTTTTGGTCAAACGCCGCTA
12090130 AAAAACAGAGCAATAGCGGCGTTTTT-GTCCAAACGCCGCTA
1 AAAAACAGAGCAATAGCGGCGTTTTTGGT-CAAACGCCGCTA
12090171 AAAAACAGAGCAATAGCGGCGTTTTTGGTCAAACGCCGCT-
1 AAAAACAGAGCAATAGCGGCGTTTTTGGTCAAACGCCGCTA
* *
12090211 AAAAATAGAGCAATAGCGGCATTTTT-GTCCAAACGCCGCTA
1 AAAAACAGAGCAATAGCGGCGTTTTTGGT-CAAACGCCGCTA
12090252 AAAAACAGAGCAATAGCGGCGTTTTTGGTCAAACGCCGCTA
1 AAAAACAGAGCAATAGCGGCGTTTTTGGTCAAACGCCGCTA
* * *
12090293 AAAAACTGAGCAATAGCGGCGTTTTTGCTTAAAACGCCGC-A
1 AAAAACAGAGCAATAGCGGCGTTTTTG-GTCAAACGCCGCTA
12090334 AAAA
1 AAAA
12090338 GTCATATAAC
Statistics
Matches: 229, Mismatches: 13, Indels: 13
0.90 0.05 0.05
Matches are distributed among these distances:
39 2 0.01
40 73 0.32
41 140 0.61
42 14 0.06
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.20
Consensus pattern (41 bp):
AAAAACAGAGCAATAGCGGCGTTTTTGGTCAAACGCCGCTA
Found at i:12090411 original size:46 final size:47
Alignment explanation
Indices: 12090342--12090465 Score: 155
Period size: 47 Copynumber: 2.7 Consensus size: 47
12090332 CAAAAAGTCA
12090342 TATAACCCCTAAAATCCTAAA-CCCAAAAAAATCA-TAAACACTAATC
1 TATAACCCCTAAAATCCTAAACCCCAAAAAAA-CACTAAACACTAATC
**
12090388 TATAACCCCTAAAATCCCT-AACCCCTTAAAAACACTAAACACTAATC
1 TATAACCCCTAAAAT-CCTAAACCCCAAAAAAACACTAAACACTAATC
*** *
12090435 TATAACTTTTAAAACCCTAAACCCCAAAAAA
1 TATAACCCCTAAAATCCTAAACCCCAAAAAA
12090466 CACCATATGG
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
46 22 0.33
47 44 0.67
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.21
Consensus pattern (47 bp):
TATAACCCCTAAAATCCTAAACCCCAAAAAAACACTAAACACTAATC
Found at i:12090630 original size:21 final size:21
Alignment explanation
Indices: 12090589--12090630 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
12090579 GGGTTTAATA
*
12090589 TTTAAGATTTAAGGTCTATGG
1 TTTAAGATTTAAGGTCCATGG
*
12090610 TTTAAGGTTTAATGG-CCATGG
1 TTTAAGATTTAA-GGTCCATGG
12090631 GTAGTATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.40
Consensus pattern (21 bp):
TTTAAGATTTAAGGTCCATGG
Found at i:12090781 original size:36 final size:37
Alignment explanation
Indices: 12090716--12090808 Score: 152
Period size: 36 Copynumber: 2.5 Consensus size: 37
12090706 TTTTCGTTTG
12090716 TCGCCTTCGCCCCGTGCATCGCAACCCATCCCCTCCA
1 TCGCCTTCGCCCCGTGCATCGCAACCCATCCCCTCCA
* *
12090753 TCGCCTTCGCCCC-TGCGTCGCAACCCATCTCCTCCA
1 TCGCCTTCGCCCCGTGCATCGCAACCCATCCCCTCCA
*
12090789 TCGCCTTCGCCCTGTGCATC
1 TCGCCTTCGCCCCGTGCATC
12090809 TGCTGCATAG
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
36 33 0.65
37 18 0.35
ACGTcount: A:0.11, C:0.52, G:0.15, T:0.23
Consensus pattern (37 bp):
TCGCCTTCGCCCCGTGCATCGCAACCCATCCCCTCCA
Found at i:12091145 original size:15 final size:15
Alignment explanation
Indices: 12091120--12091170 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
12091110 AATCTTCAAA
12091120 AAAAATT-AAAATTT
1 AAAAATTAAAAATTT
*
12091134 AAAAATTAAAAATTA
1 AAAAATTAAAAATTT
* *
12091149 AAAAATAAAAAACTT
1 AAAAATTAAAAATTT
12091164 AAAAATT
1 AAAAATT
12091171 TAATATTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
14 7 0.23
15 24 0.77
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAAATTAAAAATTT
Found at i:12091173 original size:8 final size:7
Alignment explanation
Indices: 12091120--12091170 Score: 66
Period size: 7 Copynumber: 7.0 Consensus size: 7
12091110 AATCTTCAAA
12091120 AAAAATT
1 AAAAATT
*
12091127 AAAATTT
1 AAAAATT
12091134 AAAAATT
1 AAAAATT
12091141 AAAAATT
1 AAAAATT
*
12091148 AAAAAATA
1 -AAAAATT
12091156 AAAAACTT
1 AAAAA-TT
12091164 AAAAATT
1 AAAAATT
12091171 TAATATTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 26 0.68
8 12 0.32
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAAATT
Found at i:12091550 original size:17 final size:17
Alignment explanation
Indices: 12091525--12091557 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12091515 AAAATTTAGC
12091525 TACTCTTTTTCTCTCGT
1 TACTCTTTTTCTCTCGT
*
12091542 TACTGTTTTTCTCTCG
1 TACTCTTTTTCTCTCG
12091558 ATCCTTCGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.27, G:0.09, T:0.58
Consensus pattern (17 bp):
TACTCTTTTTCTCTCGT
Found at i:12094243 original size:12 final size:12
Alignment explanation
Indices: 12094226--12094250 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12094216 TCAGTTCAAA
12094226 TTAGTGTTAAAT
1 TTAGTGTTAAAT
12094238 TTAGTGTTAAAT
1 TTAGTGTTAAAT
12094250 T
1 T
12094251 GTTATTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TTAGTGTTAAAT
Found at i:12095524 original size:15 final size:15
Alignment explanation
Indices: 12095504--12095532 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12095494 AATTCAATTT
12095504 ATAATTTGTTGCTAC
1 ATAATTTGTTGCTAC
12095519 ATAATTTGTTGCTA
1 ATAATTTGTTGCTA
12095533 ATATTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.10, G:0.14, T:0.48
Consensus pattern (15 bp):
ATAATTTGTTGCTAC
Found at i:12096310 original size:31 final size:31
Alignment explanation
Indices: 12096272--12096352 Score: 98
Period size: 31 Copynumber: 2.6 Consensus size: 31
12096262 TTGTTGTATT
12096272 TTATTTATATTTATATTTAATCTA-ATTTTTA
1 TTATTTAT-TTTATATTTAATCTATATTTTTA
*
12096303 TTATTTATTTTAGT-TTTGATTCTATATTTTTA
1 TTATTTATTTTA-TATTT-AATCTATATTTTTA
12096335 TT-TTTATTTT-TATTTAAT
1 TTATTTATTTTATATTTAAT
12096353 AATGAATTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
29 3 0.07
30 10 0.23
31 22 0.50
32 9 0.20
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (31 bp):
TTATTTATTTTATATTTAATCTATATTTTTA
Found at i:12096489 original size:17 final size:17
Alignment explanation
Indices: 12096459--12096492 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12096449 CTTTATAATA
*
12096459 TTTTTATAATATTTTAT
1 TTTTTATAAAATTTTAT
*
12096476 TTTTTTTAAAATTTTAT
1 TTTTTATAAAATTTTAT
12096493 GACCTTTAGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTATAAAATTTTAT
Found at i:12096495 original size:46 final size:49
Alignment explanation
Indices: 12096406--12096500 Score: 124
Period size: 47 Copynumber: 2.0 Consensus size: 49
12096396 TATTCTTCTC
* *
12096406 AATATTTTGATAATAAATTTTAATTTTTTTATATTTTTCATGA-CTTTAT
1 AATATTTTGATAAT-AATTTTAATTTTTTTAAAATTTTCATGACCTTTAT
* *
12096455 AATATTTTTATAAT-ATTTTATTTTTTTTAAAATTTT-ATGACCTTTA
1 AATATTTTGATAATAATTTTAATTTTTTTAAAATTTTCATGACCTTTA
12096501 GCGGCGTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
46 4 0.10
47 24 0.59
49 13 0.32
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.60
Consensus pattern (49 bp):
AATATTTTGATAATAATTTTAATTTTTTTAAAATTTTCATGACCTTTAT
Found at i:12096538 original size:43 final size:43
Alignment explanation
Indices: 12096491--12096724 Score: 258
Period size: 43 Copynumber: 5.4 Consensus size: 43
12096481 TTAAAATTTT
* **
12096491 ATGACCTTTAGCGGCGTTTTTGGGAAAAGTGCCGCTAAAGGCC
1 ATGACCTTTAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGATC
* * * * *
12096534 ATGACTTTTAGCGGCATTTGTGGGAAAAGCGTCGCTAAAGACC
1 ATGACCTTTAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGATC
** * * *
12096577 ATGGTCTTTAGCGGCGTTTGTAGAAAAAGCGCCGCTAAA-AGTC
1 ATGACCTTTAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGA-TC
* *
12096620 ATGGCCTTTAACGGCGTTTGT-GGATAAAGTGCCGCTAAAGATC
1 ATGACCTTTAGCGGCGTTTGTGGGA-AAAGTGCCGCTAAAGATC
* *
12096663 ATGACCTTTAGCGGCGTTTGTGGGGAAAGCT-TCGCTAAAGATC
1 ATGACCTTTAGCGGCGTTTGTGGGAAAAG-TGCCGCTAAAGATC
*
12096706 ATGACTTTTAGCGGCGTTT
1 ATGACCTTTAGCGGCGTTT
12096725 TTTTTCTATA
Statistics
Matches: 163, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
42 3 0.02
43 156 0.96
44 4 0.02
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.28
Consensus pattern (43 bp):
ATGACCTTTAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGATC
Found at i:12100284 original size:21 final size:21
Alignment explanation
Indices: 12100258--12100300 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
12100248 CTACGTGACA
12100258 AATTAACTGGCCACATCAGCT
1 AATTAACTGGCCACATCAGCT
**
12100279 AATTAACTGGCCATGTCAGCT
1 AATTAACTGGCCACATCAGCT
12100300 A
1 A
12100301 TTCCGTTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (21 bp):
AATTAACTGGCCACATCAGCT
Found at i:12109613 original size:38 final size:38
Alignment explanation
Indices: 12109571--12109643 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
12109561 GAAACTTAAT
*
12109571 TTTTATATTTGTTTTTGAATTTT-TTATAAGTTTAAGGA
1 TTTTAGATTTGTTTTTGAATTTTGTTATAA-TTTAAGGA
* *
12109609 TTTTAGATTTTTTTTTGTATTTTGTTATAATTTAA
1 TTTTAGATTTGTTTTTGAATTTTGTTATAATTTAA
12109644 AAGTGTATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
38 25 0.81
39 6 0.19
ACGTcount: A:0.25, C:0.00, G:0.11, T:0.64
Consensus pattern (38 bp):
TTTTAGATTTGTTTTTGAATTTTGTTATAATTTAAGGA
Found at i:12110856 original size:30 final size:30
Alignment explanation
Indices: 12110822--12110904 Score: 76
Period size: 33 Copynumber: 2.7 Consensus size: 30
12110812 ATGGGGTGGT
*
12110822 GGTGGAGGAGGAGACTTGTAAACGGGAGGA
1 GGTGGAGGAGGAGACTTGTAAACCGGAGGA
* * * *
12110852 GGTGGTGGAGACTTATACTTGTAAACCGGAGGT
1 GGTGGAGGAG---GAGACTTGTAAACCGGAGGA
* *
12110885 GGTGGGGGTGGAGACTTGTA
1 GGTGGAGGAGGAGACTTGTA
12110905 CTTGTAAGGG
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
30 17 0.41
33 24 0.59
ACGTcount: A:0.24, C:0.08, G:0.46, T:0.22
Consensus pattern (30 bp):
GGTGGAGGAGGAGACTTGTAAACCGGAGGA
Found at i:12110872 original size:33 final size:34
Alignment explanation
Indices: 12110835--12110911 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 34
12110825 GGAGGAGGAG
*
12110835 ACTTGTAAACGGGAGGAGGT-GGTGGAGACTTAT
1 ACTTGTAAACCGGAGGAGGTGGGTGGAGACTTAT
* *
12110868 ACTTGTAAACCGGAGGTGGTGGGGGTGGAGACTTGT
1 ACTTGTAAACCGGAGGAGGT--GGGTGGAGACTTAT
12110904 ACTTGTAA
1 ACTTGTAA
12110912 GGGTGCTTGG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 18 0.47
36 20 0.53
ACGTcount: A:0.25, C:0.10, G:0.39, T:0.26
Consensus pattern (34 bp):
ACTTGTAAACCGGAGGAGGTGGGTGGAGACTTAT
Found at i:12110985 original size:99 final size:98
Alignment explanation
Indices: 12110882--12111393 Score: 543
Period size: 99 Copynumber: 5.2 Consensus size: 98
12110872 GTAAACCGGA
* * *
12110882 GGTGGTGGGGGTGGAGACTTGTACTTGTAAGGGTGCTTGGGTGGGGATGGAGGTGGTGGTGGGGG
1 GGTGGTGGGGGTGGAGACTTGTACTTGTAAGGGTGCTTGGGTGGTGATGGTGGTGGAGGTGGGGG
12110947 AGACTTGTACTTGTAGGAATGCTTGGGTGGTGAT
66 AGACTTGTACTTGTAGG-ATGCTTGGGTGGTGAT
* * *
12110981 GGTGGTGGTGGTGGAGACTTGTACTTATAAGGATGCTTTGGG-GGTGATGGTGGTGGAGGT--GG
1 GGTGGTGGGGGTGGAGACTTGTACTTGTAAGGGTGC-TTGGGTGGTGATGGTGGTGGAGGTGGGG
*
12111043 G-GACTTGTACTTGTAAGGGTGCTTGGGTGGTGAT
65 GAGACTTGTACTTGT-AGGATGCTTGGGTGGTGAT
* *
12111077 GGTGGTGGAGGTGGTGGGGACTTGTACTTGTAAGGGTGCTTGGGTGGTGATGGCGGTGGAGGTGG
1 GGTGGT-G-GG-GGTGGAGACTTGTACTTGTAAGGGTGCTTGGGTGGTGATGGTGGTGGAGGTGG
* * *
12111142 TGGAGACTTATACTTGTA--A-AC-----T-G-GA-
63 GGGAGACTTGTACTTGTAGGATGCTTGGGTGGTGAT
* * * *
12111167 GATGGTGGGGGTGGAGACTTGTACTTGTAAGGGTGCTTAGGTGGTGATGGTGGGGGTGG-GGGTG
1 GGTGGTGGGGGTGGAGACTTGTACTTGTAAGGGTGCTTGGGTGGTGATGGTGGTGGAGGTGGG-G
* * *
12111231 GGGACTTGTACTTGTAGGGGTGTTTGGGTGGTGAGGGT
65 GAGACTTGTACTTGTA-GGATGCTTGGGTGGTGA---T
* *
12111269 GGTGGTGGTGGTGGTGGGGACTTGTACTTGTAAGGATGCTTGGGTGGTGATGGTGGTGGAGGTGG
1 GGTGGT-G-GG-GGTGGAGACTTGTACTTGTAAGGGTGCTTGGGTGGTGATGGTGGTGGAGGTGG
*
12111334 AGGAGACTTGTACTTGTAAGGATGCTTGGGTGGTGAT
63 GGGAGACTTGTACTTGT-AGGATGCTTGGGTGGTGAT
* * * *
12111371 GGAGGAGGTGGTGGGGACTTGTA
1 GGTGGTGGGGGTGGAGACTTGTA
12111394 AACAGGAGTT
Statistics
Matches: 342, Mismatches: 41, Indels: 60
0.77 0.09 0.14
Matches are distributed among these distances:
86 2 0.01
87 60 0.18
88 2 0.01
89 1 0.00
90 5 0.01
91 2 0.01
92 1 0.00
93 1 0.00
96 35 0.10
97 8 0.02
98 9 0.03
99 103 0.30
100 6 0.02
101 4 0.01
102 22 0.06
103 1 0.00
104 2 0.01
105 75 0.22
106 3 0.01
ACGTcount: A:0.14, C:0.06, G:0.49, T:0.30
Consensus pattern (98 bp):
GGTGGTGGGGGTGGAGACTTGTACTTGTAAGGGTGCTTGGGTGGTGATGGTGGTGGAGGTGGGGG
AGACTTGTACTTGTAGGATGCTTGGGTGGTGAT
Found at i:12110989 original size:48 final size:48
Alignment explanation
Indices: 12110882--12111393 Score: 448
Period size: 51 Copynumber: 10.5 Consensus size: 48
12110872 GTAAACCGGA
* *
12110882 GGTGGTGG-GGGTGGAGACTTGTACTTGTAAGGGTGCTTGGGTGGGGAT
1 GGTGGTGGTGGG-GGAGACTTGTACTTGTAAGGATGCTTGGGTGGTGAT
12110930 GGAGGTGGTGGTGGGGGAGACTTGTACTTGT-AGGAATGCTTGGGTGGTGAT
1 ---GGTGGTGGTGGGGGAGACTTGTACTTGTAAGG-ATGCTTGGGTGGTGAT
* *
12110981 GGTGGTGGTGGTGGAGACTTGTACTTATAAGGATGCTTTGGG-GGTGAT
1 GGTGGTGGTGGGGGAGACTTGTACTTGTAAGGATGC-TTGGGTGGTGAT
* *
12111029 GGTGGTGGAGGTGGG-GACTTGTACTTGTAAGGGTGCTTGGGTGGTGAT
1 GGTGGTGGTGG-GGGAGACTTGTACTTGTAAGGATGCTTGGGTGGTGAT
*
12111077 GGTGGTGGAGGTGGTGGG-GACTTGTACTTGTAAGGGTGCTTGGGTGGTGAT
1 GGTGGT---GGTGG-GGGAGACTTGTACTTGTAAGGATGCTTGGGTGGTGAT
* * * *
12111128 GGCGGTGGAGGTGGTGGAGACTTATACTTGTAA--A--C-----TGGAGAT
1 ---GGTGGTGGTGGGGGAGACTTGTACTTGTAAGGATGCTTGGGTGGTGAT
* * *
12111170 GGT-G-GG-GGTGGAGACTTGTACTTGTAAGGGTGCTTAGGTGGTGAT
1 GGTGGTGGTGGGGGAGACTTGTACTTGTAAGGATGCTTGGGTGGTGAT
* * * * *
12111215 GGTGGGGGTGGGGGTGGGGACTTGTACTTGTAGGGGTGTTTGGGTGGTGAGGGT
1 GGTGGTGGT--GGG-GGAGACTTGTACTTGTAAGGATGCTTGGGTGGTGA---T
*
12111269 GGTGGTGGTGGTGGTGGGGACTTGTACTTGTAAGGATGCTTGGGTGGTGAT
1 GGTGGTGGT-G-GG-GGAGACTTGTACTTGTAAGGATGCTTGGGTGGTGAT
*
12111320 GGTGGTGGAGGTGGAGGAGACTTGTACTTGTAAGGATGCTTGGGTGGTGAT
1 GGTGGT---GGTGGGGGAGACTTGTACTTGTAAGGATGCTTGGGTGGTGAT
* *
12111371 GGAGGAGGTGGTGGG-GACTTGTA
1 GGTGGTGGTGG-GGGAGACTTGTA
12111394 AACAGGAGTT
Statistics
Matches: 394, Mismatches: 31, Indels: 75
0.79 0.06 0.15
Matches are distributed among these distances:
36 20 0.05
37 2 0.01
38 1 0.00
39 3 0.01
40 1 0.00
42 6 0.02
45 9 0.02
46 1 0.00
47 8 0.02
48 90 0.23
49 12 0.03
50 7 0.02
51 175 0.44
52 4 0.01
53 3 0.01
54 52 0.13
ACGTcount: A:0.14, C:0.06, G:0.49, T:0.30
Consensus pattern (48 bp):
GGTGGTGGTGGGGGAGACTTGTACTTGTAAGGATGCTTGGGTGGTGAT
Found at i:12111032 original size:42 final size:42
Alignment explanation
Indices: 12110933--12111086 Score: 123
Period size: 48 Copynumber: 3.4 Consensus size: 42
12110923 TGGGGATGGA
* * *
12110933 GGTGGTGGTGGGGGAGACTTGTACTTGT-AGGAATGCTTGGGT
1 GGTGATGGTGGTGGAGACTTGTACTTATAAGG-ATGCTTGGGT
12110975 GGTGATGGTGGTGGTGGTGGAGACTTGTACTTATAAGGATGCTTTGGG-
1 GGTGA------TGGTGGTGGAGACTTGTACTTATAAGGATGC-TTGGGT
* *
12111023 GGTGATGGTGGTGGAGGTGGGGACTTGTACTTGTAAGGGTGCTTGGGT
1 GGTGATGGTGGTGGA------GACTTGTACTTATAAGGATGCTTGGGT
12111071 GGTGATGGTGGTGGAG
1 GGTGATGGTGGTGGAG
12111087 GTGGTGGGGA
Statistics
Matches: 92, Mismatches: 5, Indels: 30
0.72 0.04 0.24
Matches are distributed among these distances:
42 15 0.16
47 5 0.05
48 64 0.70
49 8 0.09
ACGTcount: A:0.14, C:0.06, G:0.49, T:0.31
Consensus pattern (42 bp):
GGTGATGGTGGTGGAGACTTGTACTTATAAGGATGCTTGGGT
Found at i:12111297 original size:105 final size:105
Alignment explanation
Indices: 12111164--12111386 Score: 302
Period size: 105 Copynumber: 2.1 Consensus size: 105
12111154 CTTGTAAACT
* * *
12111164 GGAGATGGTGGGGGTGGAGACTTGTACTTGTAAGGGTGCTTAGGTGGTGATGGTGGGGGTGGGGG
1 GGAGGTGGTGGGGGTGGAGACTTGTACTTGTAAGGATGCTTAGGTGGTGATGGTGGGGGAGGGGG
* * * * * *
12111229 TGGGGACTTGTACTTGTAGGGGTGTTTGGGTGGTGAGGGT
66 AGGAGACTTGTACTTGTAAGGATGCTTGGGTGGTGAGGGA
* * * * * *
12111269 GGTGGTGGTGGTGGTGGGGACTTGTACTTGTAAGGATGCTTGGGTGGTGATGGTGGTGGAGGTGG
1 GGAGGTGGTGGGGGTGGAGACTTGTACTTGTAAGGATGCTTAGGTGGTGATGGTGGGGGAGGGGG
*
12111334 AGGAGACTTGTACTTGTAAGGATGCTTGGGTGGTGATGGA
66 AGGAGACTTGTACTTGTAAGGATGCTTGGGTGGTGAGGGA
12111374 GGAGGTGGTGGGG
1 GGAGGTGGTGGGG
12111387 ACTTGTAAAC
Statistics
Matches: 100, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
105 100 1.00
ACGTcount: A:0.13, C:0.05, G:0.52, T:0.29
Consensus pattern (105 bp):
GGAGGTGGTGGGGGTGGAGACTTGTACTTGTAAGGATGCTTAGGTGGTGATGGTGGGGGAGGGGG
AGGAGACTTGTACTTGTAAGGATGCTTGGGTGGTGAGGGA
Found at i:12111394 original size:285 final size:280
Alignment explanation
Indices: 12110849--12111386 Score: 785
Period size: 285 Copynumber: 1.9 Consensus size: 280
12110839 GTAAACGGGA
*
12110849 GGAGGTGGTGGAGACTTATACTTGTAAACCGGAGGTGGTGGGGGTGGAGACTTGTACTTGTAAGG
1 GGAGGTGGTGGAGACTTATACTTGTAAACCGGAGATGGTGGGGGTGGAGACTTGTACTTGTAAGG
* *
12110914 GTGCTTGGGTGGGGATGGAGGTGGTGGTGGGGGAGACTTGTACTTGTAGGAATGCTTGGGTGGTG
66 GTGCTTAGGTGGGGATGGAGGGGGTGGTGGGGGAGACTTGTACTTGTAGGAATGCTTGGGTGGTG
12110979 ATGGTGGTGGTGGTGGAGACTTGTACTTATAAGGATGCTTTGGGGGTGATGGTGGTGGAGGTGGG
131 ATGGTGGTGGTGGTGGAGACTTGTACTTATAAGGATGCTTTGGGGGTGATGGTGGTGGAGGTGGG
* *
12111044 GACTTGTACTTGTAAGGGTGCTTGGGTGGTGATGGTGGTGGAGGTGGTGGGGACTTGTACTTGTA
196 GACTTGTACTTGTAAGGATGCTTGGGTGGTGA--GTGGAGGAGGTGGTGGGG---TGTACTTGTA
12111109 AGGGTGCTTGGGTGGTGATGGCGGT
256 AGGGTGCTTGGGTGGTGATGGCGGT
*
12111134 GGAGGTGGTGGAGACTTATACTTGTAAACTGGAGATGGTGGGGGTGGAGACTTGTACTTGTAAGG
1 GGAGGTGGTGGAGACTTATACTTGTAAACCGGAGATGGTGGGGGTGGAGACTTGTACTTGTAAGG
* * * ** *
12111199 GTGCTTAGGTGGTGATGGTGGGGGTGG-GGGTGGGGACTTGTACTTGTAGGGGTGTTTGGGTGGT
66 GTGCTTAGGTGGGGATGGAGGGGGTGGTGGG-GGAGACTTGTACTTGTAGGAATGCTTGGGTGGT
* *
12111263 GAGGGTGGTGGTGGTGGTGGTGGGGACTTGTACTTGTAAGGATGC-TTGGGTGGTGATGGTGGTG
130 GA------TGGTGGTGGTGGTGGAGACTTGTACTTATAAGGATGCTTTGGG-GGTGATGGTGGTG
12111327 GAGGTGGAGGAGACTTGTACTTGTAAGGATGCTTGGGTGGTGA-TGGAGGAGGTGGTGGGG
188 GAGGT-G-GG-GACTTGTACTTGTAAGGATGCTTGGGTGGTGAGTGGAGGAGGTGGTGGGG
12111387 ACTTGTAAAC
Statistics
Matches: 228, Mismatches: 14, Indels: 16
0.88 0.05 0.06
Matches are distributed among these distances:
284 3 0.01
285 117 0.51
290 5 0.02
291 69 0.30
292 1 0.00
293 2 0.01
294 31 0.14
ACGTcount: A:0.15, C:0.06, G:0.49, T:0.30
Consensus pattern (280 bp):
GGAGGTGGTGGAGACTTATACTTGTAAACCGGAGATGGTGGGGGTGGAGACTTGTACTTGTAAGG
GTGCTTAGGTGGGGATGGAGGGGGTGGTGGGGGAGACTTGTACTTGTAGGAATGCTTGGGTGGTG
ATGGTGGTGGTGGTGGAGACTTGTACTTATAAGGATGCTTTGGGGGTGATGGTGGTGGAGGTGGG
GACTTGTACTTGTAAGGATGCTTGGGTGGTGAGTGGAGGAGGTGGTGGGGTGTACTTGTAAGGGT
GCTTGGGTGGTGATGGCGGT
Found at i:12114568 original size:21 final size:21
Alignment explanation
Indices: 12114539--12114580 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
12114529 AGAGTATAGA
*
12114539 CTCTGTTAGTCTGTTACCATT
1 CTCTATTAGTCTGTTACCATT
12114560 CTCTATTAGTCTGTTACCATT
1 CTCTATTAGTCTGTTACCATT
12114581 TTGTTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.17, C:0.24, G:0.12, T:0.48
Consensus pattern (21 bp):
CTCTATTAGTCTGTTACCATT
Found at i:12126297 original size:12 final size:13
Alignment explanation
Indices: 12126261--12126298 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
12126251 AAATATTTGA
12126261 CTTGTTCTTAATT
1 CTTGTTCTTAATT
*
12126274 ATGTGTTCTTAATT
1 CT-TGTTCTTAATT
12126288 CTTG-TCTTAAT
1 CTTGTTCTTAAT
12126299 ATTCCAGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 7 0.32
13 3 0.14
14 12 0.55
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (13 bp):
CTTGTTCTTAATT
Found at i:12131500 original size:17 final size:17
Alignment explanation
Indices: 12131470--12131508 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
12131460 AAAAAGCCCT
*
12131470 CCAAATCCTAGAGTTCA
1 CCAAAACCTAGAGTTCA
* *
12131487 CCAAAACCTGGAGTTCG
1 CCAAAACCTAGAGTTCA
12131504 CCAAA
1 CCAAA
12131509 TAGAGATTCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.31, G:0.15, T:0.18
Consensus pattern (17 bp):
CCAAAACCTAGAGTTCA
Found at i:12140637 original size:17 final size:18
Alignment explanation
Indices: 12140617--12140650 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12140607 AAGGGAATTG
12140617 AAATTGT-GAAATTAAAT
1 AAATTGTCGAAATTAAAT
12140634 AAATTGTCGAAATTAAA
1 AAATTGTCGAAATTAAA
12140651 ATGAGGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.32
Consensus pattern (18 bp):
AAATTGTCGAAATTAAAT
Found at i:12145793 original size:38 final size:38
Alignment explanation
Indices: 12145742--12145818 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
12145732 AAAAATTAAC
*
12145742 TAAGTTTTCAAAAAAAAAAGTCACTGTGATGAGAAGAA
1 TAAGTTTTCAAAAAAAAAAGTCACCGTGATGAGAAGAA
*
12145780 TAAGTTTTCAAAAACAAAAGTCACCGTGATGAGAAGAA
1 TAAGTTTTCAAAAAAAAAAGTCACCGTGATGAGAAGAA
12145818 T
1 T
12145819 GTCAAAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.48, C:0.10, G:0.18, T:0.23
Consensus pattern (38 bp):
TAAGTTTTCAAAAAAAAAAGTCACCGTGATGAGAAGAA
Found at i:12148260 original size:20 final size:20
Alignment explanation
Indices: 12148230--12148317 Score: 61
Period size: 20 Copynumber: 4.3 Consensus size: 20
12148220 TACTCAATGA
*
12148230 TGCATAACAGAGGCACCAAAG
1 TGCA-AACAAAGGCACCAAAG
* * **
12148251 TGCAAACAGAGGAAGGAATA-
1 TGCAAACAAAGGCACCAA-AG
* ***
12148271 TGCAATCAAAGGCATTGAAG
1 TGCAAACAAAGGCACCAAAG
*
12148291 TGCAAACAAATGCACCAAAG
1 TGCAAACAAAGGCACCAAAG
12148311 TGCAAAC
1 TGCAAAC
12148318 CCGTACAAGC
Statistics
Matches: 51, Mismatches: 14, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
19 1 0.02
20 45 0.88
21 5 0.10
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.12
Consensus pattern (20 bp):
TGCAAACAAAGGCACCAAAG
Found at i:12149607 original size:11 final size:11
Alignment explanation
Indices: 12149593--12149617 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12149583 ATATAACTCT
12149593 ATAAACATAAA
1 ATAAACATAAA
12149604 ATAAACATAAA
1 ATAAACATAAA
12149615 ATA
1 ATA
12149618 CTGACTCACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (11 bp):
ATAAACATAAA
Found at i:12150556 original size:32 final size:33
Alignment explanation
Indices: 12150501--12150563 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
12150491 CAACACAATT
*
12150501 ATATGAAAAGGTATCTTATTAAAAGATACATTC
1 ATATGAAAAGGTATCTCATTAAAAGATACATTC
* *
12150534 ATATTAAAGGGTATCTCA-TAAAAGATACAT
1 ATATGAAAAGGTATCTCATTAAAAGATACAT
12150564 CTATTGGATG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.32
Consensus pattern (33 bp):
ATATGAAAAGGTATCTCATTAAAAGATACATTC
Found at i:12151194 original size:31 final size:32
Alignment explanation
Indices: 12151150--12151214 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 32
12151140 TATATAAAAA
* * *
12151150 ATTAGATTAATTTATATTTTATATATCATTAT
1 ATTAAATTAATTTAAATATTATATATCATTAT
* *
12151182 ATTAAATT-ATTTAAATATTATTTATTATTAT
1 ATTAAATTAATTTAAATATTATATATCATTAT
12151213 AT
1 AT
12151215 CTTTTAATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 21 0.75
32 7 0.25
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (32 bp):
ATTAAATTAATTTAAATATTATATATCATTAT
Found at i:12158864 original size:33 final size:33
Alignment explanation
Indices: 12158822--12158888 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
12158812 AATCAACACT
12158822 TTGCACTAAAACTGTTTTGGACAGTAGCAGTAG
1 TTGCACTAAAACTGTTTTGGACAGTAGCAGTAG
12158855 TTGCACTAAAACTGTTTTGGACAGTAGCAGTAG
1 TTGCACTAAAACTGTTTTGGACAGTAGCAGTAG
12158888 T
1 T
12158889 CTAACTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (33 bp):
TTGCACTAAAACTGTTTTGGACAGTAGCAGTAG
Found at i:12159927 original size:50 final size:50
Alignment explanation
Indices: 12159852--12160128 Score: 437
Period size: 50 Copynumber: 5.5 Consensus size: 50
12159842 CCATGGCAAC
* * *
12159852 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTAATCAATGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
12159902 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * * *
12159952 AAGTGATAAGTGATAGCTTCAGCTACACTTATTTGATCAAGGATAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
12160002 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
12160052 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGACAAATGGC
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAAT-GA
* * *
12160103 AAGTAAAAAGTGGTAGCTTCGGCTAC
1 AAGTGATAAGTGATAGCTTCGGCTAC
12160129 CTGATCAATG
Statistics
Matches: 209, Mismatches: 17, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
50 186 0.89
51 23 0.11
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.27
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:12160146 original size:31 final size:31
Alignment explanation
Indices: 12160108--12160166 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
12160098 ATGGCAAGTA
12160108 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
12160139 AAAAGTGGTAGCTTCGGCTACCTGATCA
1 AAAAGTGGTAGCTTCGGCTACCTGATCA
12160167 TCGGCTACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (31 bp):
AAAAGTGGTAGCTTCGGCTACCTGATCAATG
Found at i:12160174 original size:46 final size:46
Alignment explanation
Indices: 12160121--12160212 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
12160111 AGTGGTAGCT
* *
12160121 TCGGCTACCTGATCAATGAAAAGTGGTAGCTTCGGCTACCTGATCA
1 TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
* * *
12160167 TCGGCTACTTGATTAGTGAAAAATGGTAGCTCCGGCTACCTGATCA
1 TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
12160213 GTGAATAGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (46 bp):
TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
Found at i:12160216 original size:31 final size:31
Alignment explanation
Indices: 12160168--12160236 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
12160158 ACCTGATCAT
* * *
12160168 CGGCTACTTGATTAGTGAAAAATGGTAGCTC
1 CGGCTACCTGATCAGTGAAAAATGATAGCTC
* * *
12160199 CGGCTACCTGATCAGTGAATAGTGATAGCTT
1 CGGCTACCTGATCAGTGAAAAATGATAGCTC
12160230 CGGCTAC
1 CGGCTAC
12160237 AAGTGACAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (31 bp):
CGGCTACCTGATCAGTGAAAAATGATAGCTC
Found at i:12163447 original size:87 final size:86
Alignment explanation
Indices: 12163257--12163485 Score: 257
Period size: 87 Copynumber: 2.7 Consensus size: 86
12163247 GTGAATTCAC
* * * * * * *
12163257 AAGCTTTAACCCCCTAAGCAGGAGGGTAACAAGCT-GAAAAATACATATC-TTATCCCTAAATAG
1 AAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAG-AAATTACAGATCTTTCTCCCTAAACAG
* * * *
12163320 TAGTGGACAGATCGAAGTCAGT
65 TAGCGGACAAATCAAAGACAGT
* *
12163342 AAGCCTTAACCTCCTAAGCAGTAGGGTAACAGGCTAGAAATTACAGATCTTTCTCCCTAAGCAGT
1 AAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAGAAATTACAGATCTTTCTCCCTAAACAGT
*
12163407 AGCGGAGCAAATCAAAGACGGT
66 AGCGGA-CAAATCAAAGACAGT
* *
12163429 GAA-CCTTAACCCCCTAAGCAGTAGGGTAGCAGGCTAAAAATTACAGATCTTATCTCC
1 -AAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAGAAATTACAGATCTT-TCTCC
12163486 ATGTATCGGC
Statistics
Matches: 122, Mismatches: 17, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
85 41 0.34
86 18 0.15
87 56 0.46
88 7 0.06
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (86 bp):
AAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAGAAATTACAGATCTTTCTCCCTAAACAGT
AGCGGACAAATCAAAGACAGT
Found at i:12163525 original size:45 final size:45
Alignment explanation
Indices: 12163476--12163686 Score: 153
Period size: 45 Copynumber: 4.7 Consensus size: 45
12163466 AAATTACAGA
12163476 TCTTATCTCCATGTATCGGCTATGGAGCAGATAAAAAATCGCGAG
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATAAAAAATCGCGAG
* * *** ** * *
12163521 TCTTATCTCCATGTATCGACTATGGAGTAGAT-TTTAGCCACAAG
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATAAAAAATCGCGAG
* * * * * ** ***
12163565 TCTTATCTTCTTG-AGGT-AGC-AAGGAAGCAGACTGAAAGTTATAGA-
1 TCTTATCTCCATGTA--TCGGCTATGG-AGCAGA-TAAAAAATCGCGAG
* *
12163610 TCTTATCTCCATGTATTGGCTATGGAGCAGATAAAAAATGGCGAG
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATAAAAAATCGCGAG
*
12163655 TCTTATCTCCATGAATCGGCTATGGAGCAGAT
1 TCTTATCTCCATGTATCGGCTATGGAGCAGAT
12163687 TTTAGCCACA
Statistics
Matches: 120, Mismatches: 37, Indels: 18
0.69 0.21 0.10
Matches are distributed among these distances:
43 4 0.03
44 30 0.25
45 81 0.68
46 5 0.04
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (45 bp):
TCTTATCTCCATGTATCGGCTATGGAGCAGATAAAAAATCGCGAG
Found at i:12163874 original size:196 final size:196
Alignment explanation
Indices: 12163535--12163899 Score: 579
Period size: 196 Copynumber: 1.9 Consensus size: 196
12163525 ATCTCCATGT
* * *
12163535 ATCGACTATGGAGTAGATTTTAGCCACAAGTCTTATCTTCTTGAGGTAGCAAGGAAGCAGACTGA
1 ATCGACTATGGAGCAGATTTTAGCCACAAGTCTTATATTCTTGAGGTAGCAAGGAAGCAGACTAA
* * * *
12163600 AAGTTATAGATCTTATCTCCATGTATTGGCTATGGAGCAGATAAAAAATGGCGAGTCTTATCTCC
66 AAGTTACAGATCTTATCTCCATGAATCGGCTATGGAGCAAATAAAAAATGGCGAGTCTTATCTCC
* *
12163665 ATGAATCGGCTATGGAGCAGATTTTAGCCACAAGTCTTACCCCCTAAGCAGTAGGTTAACAAGCA
131 ATGAATAGGCTATGGAGCAGATTTTAGCCACAAATCTTACCCCCTAAGCAGTAGGTTAACAAGCA
12163730 G
196 G
*
12163731 ATCGGCTATGGAGCAGATTTTAGCCACAAGTCTTATATT-TATGAGGTAGCAAGGAAGCAGACTA
1 ATCGACTATGGAGCAGATTTTAGCCACAAGTCTTATATTCT-TGAGGTAGCAAGGAAGCAGACTA
* * *
12163795 AAAGTTACAGATCTTATCTCCATGAATCGGCTATGGAGCAAATCAGAAATGGTGAGTCTTATCTC
65 AAAGTTACAGATCTTATCTCCATGAATCGGCTATGGAGCAAATAAAAAATGGCGAGTCTTATCTC
* *
12163860 CATGTATAGGCTATGGAGCAGATTTTAGCCATAAATCTTA
130 CATGAATAGGCTATGGAGCAGATTTTAGCCACAAATCTTA
12163900 TCTTCCTAAG
Statistics
Matches: 153, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
195 1 0.01
196 152 0.99
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (196 bp):
ATCGACTATGGAGCAGATTTTAGCCACAAGTCTTATATTCTTGAGGTAGCAAGGAAGCAGACTAA
AAGTTACAGATCTTATCTCCATGAATCGGCTATGGAGCAAATAAAAAATGGCGAGTCTTATCTCC
ATGAATAGGCTATGGAGCAGATTTTAGCCACAAATCTTACCCCCTAAGCAGTAGGTTAACAAGCA
G
Found at i:12165223 original size:36 final size:39
Alignment explanation
Indices: 12165133--12165223 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 39
12165123 TTTTTTCCAT
*
12165133 AAAATAAGAATATATTATTTTAACATATAGTTTTGTTTAAC
1 AAAATAAGAATATATTATTTT-A-ATATAGTTATGTTTAAC
*
12165174 AAAAT-TGATATATATT-TTTGT-ATATA-TTAT-TTTAAC
1 AAAATAAGA-ATATATTATTT-TAATATAGTTATGTTTAAC
12165210 AAAATAAGAATATA
1 AAAATAAGAATATA
12165224 ATGTTTTCTT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
36 16 0.36
37 5 0.11
38 5 0.11
40 5 0.11
41 13 0.30
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (39 bp):
AAAATAAGAATATATTATTTTAATATAGTTATGTTTAAC
Found at i:12165416 original size:28 final size:28
Alignment explanation
Indices: 12165385--12165452 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
12165375 ATTGACTTCC
*
12165385 TTTTATTTTATGTAAA-TATTTCCTTTTA
1 TTTTATTTTATGTAAATTA-TTCATTTTA
* * *
12165413 TTTTTTTTTATGTATATTATTGATTTTA
1 TTTTATTTTATGTAAATTATTCATTTTA
*
12165441 TGTTATTTTATG
1 TTTTATTTTATG
12165453 CTTGTTTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 31 0.94
29 2 0.06
ACGTcount: A:0.22, C:0.03, G:0.07, T:0.68
Consensus pattern (28 bp):
TTTTATTTTATGTAAATTATTCATTTTA
Found at i:12169753 original size:15 final size:15
Alignment explanation
Indices: 12169733--12169763 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12169723 TTTAAAGTTG
*
12169733 TACATGGATTTTGGT
1 TACATGAATTTTGGT
12169748 TACATGAATTTTGGT
1 TACATGAATTTTGGT
12169763 T
1 T
12169764 TAATGTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.06, G:0.23, T:0.48
Consensus pattern (15 bp):
TACATGAATTTTGGT
Found at i:12170413 original size:19 final size:20
Alignment explanation
Indices: 12170391--12170429 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
12170381 AAAATTTTCT
*
12170391 AAAATTTTAAATAT-ATTAA
1 AAAATGTTAAATATAATTAA
*
12170410 AAAATGTTAAGTATAATTAA
1 AAAATGTTAAATATAATTAA
12170430 TTTTAAAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAATGTTAAATATAATTAA
Found at i:12170453 original size:17 final size:17
Alignment explanation
Indices: 12170431--12170469 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
12170421 TATAATTAAT
*
12170431 TTTAAAAGTTTAATATA
1 TTTAAAAATTTAATATA
12170448 TTTAAAAATTTAATATA
1 TTTAAAAATTTAATATA
*
12170465 CTTAA
1 TTTAA
12170470 TATATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (17 bp):
TTTAAAAATTTAATATA
Found at i:12170528 original size:9 final size:9
Alignment explanation
Indices: 12170512--12170562 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
12170502 TTTTTAATAT
12170512 ATTT-AAAA
1 ATTTAAAAA
*
12170520 TTTTAAAAA
1 ATTTAAAAA
*
12170529 ACTTAAAAA
1 ATTTAAAAA
*
12170538 ATTTAAATA
1 ATTTAAAAA
*
12170547 TTTTAAAAA
1 ATTTAAAAA
12170556 ATATTAA
1 AT-TTAA
12170563 GTATAACTAA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
8 3 0.09
9 26 0.79
10 4 0.12
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (9 bp):
ATTTAAAAA
Found at i:12170552 original size:18 final size:18
Alignment explanation
Indices: 12170531--12170645 Score: 60
Period size: 18 Copynumber: 6.3 Consensus size: 18
12170521 TTTAAAAAAC
12170531 TTAAAAAATTTAAATATT
1 TTAAAAAATTTAAATATT
*
12170549 TTAAAAAATATTAAGTA--
1 TTAAAAAAT-TTAAATATT
* *
12170566 -TAACTAATTTTAAA-ATT
1 TTAA-AAAATTTAAATATT
* *
12170583 TTAATATATTTAATATATTT
1 TTAAAAAATTTAA-ATA-TT
12170603 TTAAAATATATTTTAAA-ATT
1 TTAAAA-A-A-TTTAAATATT
* * *
12170623 TTAATATATTTAAATTTT
1 TTAAAAAATTTAAATATT
12170641 TTAAA
1 TTAAA
12170646 GTTTTTTAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 24
0.67 0.11 0.22
Matches are distributed among these distances:
15 1 0.01
16 7 0.10
17 16 0.22
18 20 0.27
19 7 0.10
20 14 0.19
21 1 0.01
22 2 0.03
23 5 0.07
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (18 bp):
TTAAAAAATTTAAATATT
Found at i:12170612 original size:13 final size:12
Alignment explanation
Indices: 12170585--12170621 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
12170575 TTAAAATTTT
12170585 AATATA-TTTAA
1 AATATATTTTAA
*
12170596 TATAT-TTTTAA
1 AATATATTTTAA
12170607 AATATATTTTAA
1 AATATATTTTAA
12170619 AAT
1 AAT
12170622 TTTAATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 13 0.59
12 9 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
AATATATTTTAA
Found at i:12170623 original size:40 final size:37
Alignment explanation
Indices: 12170572--12170669 Score: 135
Period size: 40 Copynumber: 2.6 Consensus size: 37
12170562 AGTATAACTA
12170572 ATTTTAAAATTTTAATATATTTAATATATTTTTAAAATAT
1 ATTTTAAAATTTTAATATATTTAA-AT-TTTTTAAAAT-T
*
12170612 ATTTTAAAATTTTAATATATTTAAATTTTTTAAAGTT
1 ATTTTAAAATTTTAATATATTTAAATTTTTTAAAATT
*
12170649 -TTTTAAAATTTCAAATATATT
1 ATTTTAAAATTT-TAATATATT
12170670 AAAAAAAATT
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
36 11 0.20
37 9 0.16
38 9 0.16
39 2 0.04
40 24 0.44
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (37 bp):
ATTTTAAAATTTTAATATATTTAAATTTTTTAAAATT
Found at i:12170908 original size:18 final size:17
Alignment explanation
Indices: 12170874--12170912 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
12170864 AAAATATATA
*
12170874 TTAAGTATATTAAATTT
1 TTAAATATATTAAATTT
*
12170891 TTAAATATATTAAAATT
1 TTAAATATATTAAATTT
12170908 TTAAA
1 TTAAA
12170913 AATAATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
TTAAATATATTAAATTT
Found at i:12170920 original size:18 final size:17
Alignment explanation
Indices: 12170880--12170916 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
12170870 TATATTAAGT
* *
12170880 ATATTAAATTTTTAAAT
1 ATATTAAAATTTTAAAA
12170897 ATATTAAAATTTTAAAA
1 ATATTAAAATTTTAAAA
12170914 ATA
1 ATA
12170917 ATTATACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATTAAAATTTTAAAA
Found at i:12170940 original size:42 final size:42
Alignment explanation
Indices: 12170879--12170958 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
12170869 ATATATTAAG
12170879 TATATTAAATTTTTAAATATA-TTAAAATTTTA-AAAATAAT
1 TATATTAAATTTTTAAATATATTTAAAATTTTAGAAAATAAT
* *
12170919 TATACTTAACATTTTTTAATATATTTAAACTTTTAGAAAA
1 TATA-TTAA-ATTTTTAAATATATTTAAAATTTTAGAAAA
12170959 CTTTAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 4 0.12
41 4 0.12
42 12 0.35
43 10 0.29
44 4 0.12
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (42 bp):
TATATTAAATTTTTAAATATATTTAAAATTTTAGAAAATAAT
Found at i:12173662 original size:95 final size:99
Alignment explanation
Indices: 12173554--12173973 Score: 550
Period size: 95 Copynumber: 4.2 Consensus size: 99
12173544 TGGAGGAGGA
*
12173554 GGTGGTGGAGACTTGTACTTGTAAGGGTGC-TTGGGGGTGATGGTGGGGGTGGTGG-GGGTGACT
1 GGTGGTGGAGACTTGTACTTGTAAGGGTGCTTTGGGGGTGATGGTGGTGGTGGTGGTGGG-GACT
12173617 TGTACTTGTAGGGGTGCTTAGGTGGTGACGGT-G-
65 TGTACTTGTAGGGGTGCTTAGGTGGTGACGGTGGT
* * *
12173650 GG-GGTGGGGACTTGTACTTGTAAGGGTGC-TTGGGGGTGATGGTGGTGGTGGTGGAGGTGACTT
1 GGTGGTGGAGACTTGTACTTGTAAGGGTGCTTTGGGGGTGATGGTGGTGGTGGTGGTGGGGACTT
*
12173713 GTACTTGTAGGGGTGCTTGGGTGGTGACGGTGGT
66 GTACTTGTAGGGGTGCTTAGGTGGTGACGGTGGT
*
12173747 GGTGGTGGGGGGACTTGTACTTGT-AGGGATGCTTTGGTGGG-GATGGTGGTGGTGGTGGTGGGG
1 GGTGGT--GGAGACTTGTACTTGTAAGGG-TGCTTTGG-GGGTGATGGTGGTGGTGGTGGTGGGG
* * *
12173810 ACTTGTACTTGTAGGGATGCTTAGGTGGGGATGGTGGT
62 ACTTGTACTTGTAGGGGTGCTTAGGTGGTGACGGTGGT
* * * *
12173848 GGTGGTGGAGACTTGTATTTGTAAGGATGCTTTGGTGGTGATGGTGGTGGAGGTGGTGGGGACTT
1 GGTGGTGGAGACTTGTACTTGTAAGGGTGCTTTGGGGGTGATGGTGGTGGTGGTGGTGGGGACTT
* * * *
12173913 GTACTTGTAAGGGTGCTTGGGTGGTGATGGAGGTGGA
66 GTACTTGTAGGGGTGCTTAGGTGGTGA---CGGTGGT
*
12173950 GGTGGTGGAGACTTATACTTGTAA
1 GGTGGTGGAGACTTGTACTTGTAA
12173974 ACTGGAGGTG
Statistics
Matches: 287, Mismatches: 23, Indels: 22
0.86 0.07 0.07
Matches are distributed among these distances:
95 85 0.30
96 5 0.02
97 2 0.01
98 5 0.02
99 74 0.26
100 22 0.08
101 64 0.22
102 30 0.10
ACGTcount: A:0.13, C:0.06, G:0.50, T:0.31
Consensus pattern (99 bp):
GGTGGTGGAGACTTGTACTTGTAAGGGTGCTTTGGGGGTGATGGTGGTGGTGGTGGTGGGGACTT
GTACTTGTAGGGGTGCTTAGGTGGTGACGGTGGT
Found at i:12173893 original size:87 final size:87
Alignment explanation
Indices: 12173790--12174266 Score: 391
Period size: 87 Copynumber: 5.2 Consensus size: 87
12173780 TTGGTGGGGA
* * *
12173790 TGGTGGTGGTGGTGGTGGGGACTTGTACTTGTAGGGATGCTTAGGTGGGGATGGTGGTGGTGGTG
1 TGGTGGTGGTGGTGGTGGGGACTTGTACTTGTAGGG-TGCTTGGGTGGTGATGGTGGAGGTGGTG
*
12173855 GAGACTTGTATTTGTAAGGATGC
65 GAGACTTGTACTTGTAAGGATGC
12173878 TTTGGTGGTGATGGTGGTGGAGGTGGTGGGGACTTGTACTTGTAAGGGTGCTTGGGTGGTGATGG
1 -----T-G-G-TGGTGGT---GGTGGTGGGGACTTGTACTTGT-AGGGTGCTTGGGTGGTGAT--
*
12173943 AGGTGGAGGTGGTGGAGACTTATACTTGTAA--A--C
52 -GGTGGAGGTGGTGGAGACTTGTACTTGTAAGGATGC
* * *
12173976 TGGAGGTGGTGGGGGTGGAGACTTGTACTTGTAGGGGTGCTTGGGTGGTGATGGAGGTGGAGGTG
1 TGGTGGTGGTGGTGGTGGGGACTTGTACTTGTA-GGGTGCTTGGGTGGTGAT---GGTGGAGGTG
*
12174041 GTGGAGACTTATACTTGTAA--A--C
62 GTGGAGACTTGTACTTGTAAGGATGC
* * *
12174063 TGGAGGTGGTGGGGGTGGAGACTTGTACTTGTAAGGGTGCTTGGGTGGTGATGGT-G-GG-GGTG
1 TGGTGGTGGTGGTGGTGGGGACTTGTACTTGT-AGGGTGCTTGGGTGGTGATGGTGGAGGTGGTG
* * *
12174125 GGGACTTGTACTTGTAGGGGTGTTTAGGTGG
65 GAGACTTGTACTTGTA--AG-G---A--TGC
* *
12174156 TGATGGTGGTGGTGGTGGGGACTTGTACTTGTAAGGATGCTTGGGTGGTGATGGTGGTGGAGGTG
1 TGGTGGTGGTGGTGGTGGGGACTTGTACTTGT-AGGGTGCTTGGGTGGTGA---TGGTGGAGGTG
*
12174221 GAGGAGACTTGTACTTGTAAGGATGC
62 GTGGAGACTTGTACTTGTAAGGATGC
*
12174247 TTGGGTGGTGATGGTGGTGG
1 -T-GGTGGTGGTGGTGGTGG
12174267 AGGTGGTGGA
Statistics
Matches: 329, Mismatches: 23, Indels: 64
0.79 0.06 0.15
Matches are distributed among these distances:
81 18 0.05
82 2 0.01
83 1 0.00
84 3 0.01
86 1 0.00
87 123 0.37
88 1 0.00
89 1 0.00
90 6 0.02
91 3 0.01
92 2 0.01
93 64 0.19
94 1 0.00
95 1 0.00
96 12 0.04
97 2 0.01
98 3 0.01
99 53 0.16
100 5 0.02
102 27 0.08
ACGTcount: A:0.15, C:0.06, G:0.48, T:0.31
Consensus pattern (87 bp):
TGGTGGTGGTGGTGGTGGGGACTTGTACTTGTAGGGTGCTTGGGTGGTGATGGTGGAGGTGGTGG
AGACTTGTACTTGTAAGGATGC
Found at i:12173973 original size:51 final size:51
Alignment explanation
Indices: 12173554--12174291 Score: 537
Period size: 51 Copynumber: 14.5 Consensus size: 51
12173544 TGGAGGAGGA
* *
12173554 GGTGGTGGAGACTTGTACTTGTAAGGGTGCTTGGG-GGTGATGGTGGGGGT
1 GGTGGTGGGGACTTGTACTTGTAAGGGTGCTTGGGTGGTGATGGTGGTGGT
* * *
12173604 GGTGG-GGGTGACTTGTACTTGTAGGGGTGCTTAGGTGGTGA---CGGT-G-
1 GGTGGTGGG-GACTTGTACTTGTAAGGGTGCTTGGGTGGTGATGGTGGTGGT
12173650 GG-GGTGGGGACTTGTACTTGTAAGGGTGCTTGGG-GGTGATGGTGGTGGT
1 GGTGGTGGGGACTTGTACTTGTAAGGGTGCTTGGGTGGTGATGGTGGTGGT
* * * *
12173699 GGTGGAGGTGACTTGTACTTGTAGGGGTGCTTGGGTGGTGACGGTGGTGGT
1 GGTGGTGGGGACTTGTACTTGTAAGGGTGCTTGGGTGGTGATGGTGGTGGT
* *
12173750 GGTGG-GGGGACTTGTACTTGT-AGGGATGCTTTGGTGGGGATGGTGGTGGT
1 GGTGGTGGGGACTTGTACTTGTAAGGG-TGCTTGGGTGGTGATGGTGGTGGT
* *
12173800 GGTGGTGGGGACTTGTACTTGT-AGGGATGCTTAGGTGG-G--GATGGTGGT
1 GGTGGTGGGGACTTGTACTTGTAAGGG-TGCTTGGGTGGTGATGGTGGTGGT
* * * * *
12173848 GGTGGTGGAGACTTGTATTTGTAAGGATGCTTTGGTGGTGATGGTGGTGGA
1 GGTGGTGGGGACTTGTACTTGTAAGGGTGCTTGGGTGGTGATGGTGGTGGT
* *
12173899 GGTGGTGGGGACTTGTACTTGTAAGGGTGCTTGGGTGGTGATGGAGGTGGA
1 GGTGGTGGGGACTTGTACTTGTAAGGGTGCTTGGGTGGTGATGGTGGTGGT
* * * * * * *
12173950 GGTGGTGGAGACTTATACTTGTAAACTGGAGGTGGTGGGGGTGGAGACTTGTACTTGTAGG-
1 GGTGGTGGGGACTTGTACTTGT-AA---G-GGTGCT-TGGGTGGTGA--TG--GTGGT-GGT
* * * ** * * ** * ** *
12174011 GGTGCTTGGGTG-GTGATGGAGGTG-GA-GGTG-GTGGAGACTTAT-ACTTGTAAACTGGA
1 GGTG-GTGGG-GACT--TGTACTTGTAAGGGTGCTTGG-G--TGGTGA-TGGT--GGTGGT
12174067 GGTGGTGGGGGTGGAGACTTGTACTTGTAAGGGTGCTTGGGTGGTGA---TGGT-G-
1 GGTGGTGGG------GACTTGTACTTGTAAGGGTGCTTGGGTGGTGATGGTGGTGGT
* * *
12174119 GG-GGTGGGGACTTGTACTTGTAGGGGTGTTTAGGTGGTGA---TGGTGGT
1 GGTGGTGGGGACTTGTACTTGTAAGGGTGCTTGGGTGGTGATGGTGGTGGT
* *
12174166 GGTGGTGGGGACTTGTACTTGTAAGGATGCTTGGGTGGTGATGGTGGTGGA
1 GGTGGTGGGGACTTGTACTTGTAAGGGTGCTTGGGTGGTGATGGTGGTGGT
* * * *
12174217 GGTGGAGGAGACTTGTACTTGTAAGGATGCTTGGGTGGTGATGGTGGTGGA
1 GGTGGTGGGGACTTGTACTTGTAAGGGTGCTTGGGTGGTGATGGTGGTGGT
* *
12174268 GGTGGTGGAGACTTATACTTGTAA
1 GGTGGTGGGGACTTGTACTTGTAA
12174292 ACAGGAGTTG
Statistics
Matches: 555, Mismatches: 80, Indels: 105
0.75 0.11 0.14
Matches are distributed among these distances:
44 5 0.01
45 59 0.11
46 6 0.01
47 6 0.01
48 75 0.14
49 11 0.02
50 100 0.18
51 211 0.38
52 4 0.01
53 1 0.00
54 2 0.00
55 9 0.02
56 13 0.02
57 13 0.02
58 1 0.00
59 9 0.02
60 3 0.01
61 12 0.02
62 10 0.02
63 1 0.00
64 4 0.01
ACGTcount: A:0.14, C:0.06, G:0.49, T:0.31
Consensus pattern (51 bp):
GGTGGTGGGGACTTGTACTTGTAAGGGTGCTTGGGTGGTGATGGTGGTGGT
Found at i:12173993 original size:36 final size:36
Alignment explanation
Indices: 12173940--12174008 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
12173930 TGGGTGGTGA
*
12173940 TGGAGGTGGAGGTGGTGGAGACTTATACTTGTAAAC
1 TGGAGGTGGAGGGGGTGGAGACTTATACTTGTAAAC
* *
12173976 TGGAGGTGGTGGGGGTGGAGACTTGTACTTGTA
1 TGGAGGTGGAGGGGGTGGAGACTTATACTTGTA
12174009 GGGGTGCTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.20, C:0.07, G:0.43, T:0.29
Consensus pattern (36 bp):
TGGAGGTGGAGGGGGTGGAGACTTATACTTGTAAAC
Found at i:12174080 original size:36 final size:36
Alignment explanation
Indices: 12174027--12174096 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
12174017 TGGGTGGTGA
*
12174027 TGGAGGTGGAGGTGGTGGAGACTTATACTTGTAAAC
1 TGGAGGTGGAGGGGGTGGAGACTTATACTTGTAAAC
* *
12174063 TGGAGGTGGTGGGGGTGGAGACTTGTACTTGTAA
1 TGGAGGTGGAGGGGGTGGAGACTTATACTTGTAA
12174097 GGGTGCTTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.07, G:0.43, T:0.29
Consensus pattern (36 bp):
TGGAGGTGGAGGGGGTGGAGACTTATACTTGTAAAC
Found at i:12174164 original size:39 final size:39
Alignment explanation
Indices: 12174066--12174164 Score: 90
Period size: 45 Copynumber: 2.4 Consensus size: 39
12174056 TGTAAACTGG
**
12174066 AGGTGGTGGGGGTGGAGACTTGTACTTGTAAGGGTGCTT
1 AGGTGGTGATGGTGGAGACTTGTACTTGTAAGGGTGCTT
* * * *
12174105 GGGTGGTGATGGTGGGGGTGGGGACTTGTACTTGTAGGGGTGTTT
1 AGGTGGTGA---T---GGTGGAGACTTGTACTTGTAAGGGTGCTT
12174150 AGGTGGTGATGGTGG
1 AGGTGGTGATGGTGG
12174165 TGGTGGTGGG
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
39 12 0.26
42 1 0.02
45 34 0.72
ACGTcount: A:0.12, C:0.05, G:0.52, T:0.31
Consensus pattern (39 bp):
AGGTGGTGATGGTGGAGACTTGTACTTGTAAGGGTGCTT
Found at i:12180815 original size:24 final size:23
Alignment explanation
Indices: 12180767--12180816 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
12180757 AAAGTAATTA
*
12180767 ATTTTTCTGTTAAAAATTGTATCT
1 ATTTTTCTATTAAAAATTG-ATCT
12180791 ATTTTTACTATTAAAAACTTG-TCT
1 ATTTTT-CTATTAAAAA-TTGATCT
12180815 AT
1 AT
12180817 GTACGTCAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 11 0.48
25 9 0.39
26 3 0.13
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.52
Consensus pattern (23 bp):
ATTTTTCTATTAAAAATTGATCT
Found at i:12185762 original size:26 final size:26
Alignment explanation
Indices: 12185731--12185838 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
12185721 TGAAATGCCC
*
12185731 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
12185757 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
12185783 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
12185809 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
12185835 ATCA
1 ATCA
12185839 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:12192820 original size:26 final size:26
Alignment explanation
Indices: 12192789--12192896 Score: 164
Period size: 26 Copynumber: 4.2 Consensus size: 26
12192779 TGAAATGCCC
*
12192789 ATCATGGAACATTTACCAAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
12192815 ATCATGGAACATTTACCT-AACCTATT
1 ATCATGGAACATTTACCTAAACC-ATT
* *
12192841 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
*
12192867 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
12192893 ATCA
1 ATCA
12192897 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
25 4 0.05
26 68 0.91
27 3 0.04
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:12194850 original size:122 final size:122
Alignment explanation
Indices: 12194633--12194874 Score: 403
Period size: 122 Copynumber: 2.0 Consensus size: 122
12194623 AAATGTCTGT
* * *
12194633 CAATTAAGCACAAGTAGACAAGAATAAACTTGAGCAAAAGAAAGACAATAAGACCTCACAAGTGT
1 CAATTAAGCACAAATAGACAAGAACAAACTTAAGCAAAAGAAAGACAATAAGACCTCACAAGTGT
* *
12194698 GTACAAGAGAATTGTGGAAGTATTGAGTACAAAGGTTGTTTGATTGATAATTTTTTC
66 GTACAAGAGAAGTATGGAAGTATTGAGTACAAAGGTTGTTTGATTGATAATTTTTTC
* * * *
12194755 CAATTAAGCACAAATAGACAAGAACACACTTAAGCAAAAGAAAGACGATAAGAGCTCATAAGTGT
1 CAATTAAGCACAAATAGACAAGAACAAACTTAAGCAAAAGAAAGACAATAAGACCTCACAAGTGT
12194820 GTACAAGAGAAGTATGGAAGTATTGAGTACAAAGGTTGTTTGATTGATAATTTTT
66 GTACAAGAGAAGTATGGAAGTATTGAGTACAAAGGTTGTTTGATTGATAATTTTT
12194875 GCTCCAATAT
Statistics
Matches: 111, Mismatches: 9, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
122 111 1.00
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.26
Consensus pattern (122 bp):
CAATTAAGCACAAATAGACAAGAACAAACTTAAGCAAAAGAAAGACAATAAGACCTCACAAGTGT
GTACAAGAGAAGTATGGAAGTATTGAGTACAAAGGTTGTTTGATTGATAATTTTTTC
Found at i:12196039 original size:13 final size:13
Alignment explanation
Indices: 12196021--12196046 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12196011 TATTTTTAGG
12196021 TCATTTTCATTTT
1 TCATTTTCATTTT
12196034 TCATTTTCATTTT
1 TCATTTTCATTTT
12196047 GAATAAAACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (13 bp):
TCATTTTCATTTT
Found at i:12198732 original size:36 final size:36
Alignment explanation
Indices: 12198685--12198756 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
12198675 TTTGGAATGT
*
12198685 GACATTCCAAGAAATAATAATCTTATGTTCAAACTC
1 GACATTCCAAGAAATAATAATATTATGTTCAAACTC
*
12198721 GACATTCCAAGAGATAATAATATTATGTTCAAACTC
1 GACATTCCAAGAAATAATAATATTATGTTCAAACTC
12198757 TACTAAATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.31
Consensus pattern (36 bp):
GACATTCCAAGAAATAATAATATTATGTTCAAACTC
Found at i:12198847 original size:7 final size:7
Alignment explanation
Indices: 12198835--12198875 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
12198825 TTTCATTTTA
12198835 TTAATTT
1 TTAATTT
12198842 TTAATTT
1 TTAATTT
12198849 TTAATTT
1 TTAATTT
12198856 TTAATTT
1 TTAATTT
12198863 TTAATTT
1 TTAATTT
12198870 TTAATT
1 TTAATT
12198876 ATTTTAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTAATTT
Found at i:12209967 original size:140 final size:140
Alignment explanation
Indices: 12209708--12209970 Score: 393
Period size: 140 Copynumber: 1.9 Consensus size: 140
12209698 CTTCTGGGTC
* * *
12209708 GACAGTTTCCTAAGTGTTGGGATAGACTTGTCAATATATGCTTTGGCCAACTCTTTGTATAAGGG
1 GACAGTTTCCTAAGTGTTGGGATAAACTTGTCAACATACGCTTTGGCCAACTCTTTGTATAAGGG
* * **
12209773 TTGCGATATGCATGTCTAAGGCAAAACTTAAATAACAGTCGGCTTTGTCCAACACTATACCGGTA
66 TTGCGATATGCATGCCTAAGGCAAAACTTAAATAAAAGTCACCTTTGTCCAACACTATACCGGTA
12209838 CTTTTGGGCT
131 CTTTTGGGCT
* * *
12209848 GACATTTTCCTAAGTGTTGGGATAAACTTG-CAGACATACGCTTTGGCCAACTTTTTGTATAATG
1 GACAGTTTCCTAAGTGTTGGGATAAACTTGTCA-ACATACGCTTTGGCCAACTCTTTGTATAAGG
* * *
12209912 GTTGGGATATGCATGCCTAAGGCAACACTTAAATAAAAGTCACCTTTGTCTAACACTAT
65 GTTGCGATATGCATGCCTAAGGCAAAACTTAAATAAAAGTCACCTTTGTCCAACACTAT
12209971 GCCGACTTTT
Statistics
Matches: 109, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
139 2 0.02
140 107 0.98
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (140 bp):
GACAGTTTCCTAAGTGTTGGGATAAACTTGTCAACATACGCTTTGGCCAACTCTTTGTATAAGGG
TTGCGATATGCATGCCTAAGGCAAAACTTAAATAAAAGTCACCTTTGTCCAACACTATACCGGTA
CTTTTGGGCT
Found at i:12210059 original size:16 final size:16
Alignment explanation
Indices: 12210038--12210088 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
12210028 ACACAAATGG
12210038 TATGAAATGGCATGTT
1 TATGAAATGGCATGTT
12210054 TATGAATTATGG--TG-T
1 TATGAA--ATGGCATGTT
12210069 T-TGAAATGGCATGTT
1 TATGAAATGGCATGTT
12210084 TATGA
1 TATGA
12210089 GTGTTTGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
12 4 0.14
14 6 0.21
15 4 0.14
16 11 0.38
18 4 0.14
ACGTcount: A:0.29, C:0.04, G:0.25, T:0.41
Consensus pattern (16 bp):
TATGAAATGGCATGTT
Found at i:12210793 original size:3 final size:3
Alignment explanation
Indices: 12210785--12210817 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
12210775 AGCACAGCTA
*
12210785 AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
12210818 TAATGGATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:12214314 original size:35 final size:35
Alignment explanation
Indices: 12214275--12214434 Score: 212
Period size: 35 Copynumber: 4.6 Consensus size: 35
12214265 CATTAGACAT
*
12214275 GTCTATCCCAACATTTTTAAGGTTGCCTTAGACGG
1 GTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGG
** *
12214310 GTCTATCCCAACCTTTTTAAAATTTCCTTAGACGG
1 GTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGG
* *
12214345 ATCTATCTCAACCTTTTTAAGGTTGCCTTAGACGG
1 GTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGG
* * * * *
12214380 GTGTATCCCAACTTTTTTAAGGTTGACTTAAACGA
1 GTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGG
*
12214415 GTTTATCCCAACCTTTTTAA
1 GTCTATCCCAACCTTTTTAA
12214435 AGTCACATTT
Statistics
Matches: 107, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 107 1.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.38
Consensus pattern (35 bp):
GTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGG
Found at i:12216234 original size:3 final size:3
Alignment explanation
Indices: 12216226--12216251 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12216216 TTTTTATGAC
12216226 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
12216252 GTGTTTTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:12218431 original size:2 final size:2
Alignment explanation
Indices: 12218426--12218464 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
12218416 AGTCTTTTGT
12218426 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12218465 GTACGTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12220200 original size:101 final size:101
Alignment explanation
Indices: 12220025--12220228 Score: 338
Period size: 101 Copynumber: 2.0 Consensus size: 101
12220015 TTAGTTTATA
** *
12220025 AGTTAAACTCATTCAATTAATGTTAAGAATGAGTCTGCTGATTCAATGGTTAAGTTTCTGTATGC
1 AGTTAAACTCATTCAATTAATGCCAAGAATGAGTCTGCTGATTCAATGGTTAAGTTTCTGTATAC
12220090 TATTGGGTCTTATGTTCAAATCCCGATGAAAGCAAT
66 TATTGGGTCTTATGTTCAAATCCCGATGAAAGCAAT
* * *
12220126 AGTTAAACTCATTCAATTAATGCCAAGAATGAG-CTTGTTGGTTCAATGGTTAAGTTTTTGTATA
1 AGTTAAACTCATTCAATTAATGCCAAGAATGAGTC-TGCTGATTCAATGGTTAAGTTTCTGTATA
12220190 CTATTGGGTCTTATGTTCAAATCCCGATGAAAGCAAT
65 CTATTGGGTCTTATGTTCAAATCCCGATGAAAGCAAT
12220227 AG
1 AG
12220229 GAAATGTTTT
Statistics
Matches: 96, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
100 1 0.01
101 95 0.99
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (101 bp):
AGTTAAACTCATTCAATTAATGCCAAGAATGAGTCTGCTGATTCAATGGTTAAGTTTCTGTATAC
TATTGGGTCTTATGTTCAAATCCCGATGAAAGCAAT
Found at i:12222261 original size:2 final size:2
Alignment explanation
Indices: 12222256--12222289 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12222246 TTTTTTATTT
12222256 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12222290 ATCCCGTCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12222945 original size:18 final size:16
Alignment explanation
Indices: 12222887--12222946 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
12222877 TTTTTAATCA
*
12222887 TAAAATTTTAAAATA-
1 TAAAAATTTAAAATAT
* *
12222902 TAAAAA--GAAATTAT
1 TAAAAATTTAAAATAT
12222916 TAAAAATTTAAAATAT
1 TAAAAATTTAAAATAT
12222932 TATAAAATTATAAAA
1 TA-AAAATT-TAAAA
12222947 AGAAGGAGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
13 5 0.14
14 6 0.17
15 5 0.14
16 8 0.23
17 6 0.17
18 5 0.14
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (16 bp):
TAAAAATTTAAAATAT
Found at i:12225314 original size:25 final size:26
Alignment explanation
Indices: 12225284--12225340 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
12225274 TCTTTCTCAA
*
12225284 TAAAAATTATAATATTTA-AAATATT
1 TAAAAATTATAAAATTTATAAATATT
* *
12225309 TAAAAATTCTAAAATTTATATATATT
1 TAAAAATTATAAAATTTATAAATATT
12225335 TAAAAA
1 TAAAAA
12225341 ATCATAACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 16 0.57
26 12 0.43
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (26 bp):
TAAAAATTATAAAATTTATAAATATT
Found at i:12236885 original size:27 final size:27
Alignment explanation
Indices: 12236855--12236916 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 27
12236845 TTAGAGCAGT
* *
12236855 AATATATGTAAAAA-CACATTTAAAATA
1 AATATATGCAAAAAGCA-ATTCAAAATA
*
12236882 AATAT-TACAAAAAGCAATTCAAAATA
1 AATATATGCAAAAAGCAATTCAAAATA
12236908 AATAATATG
1 AAT-ATATG
12236917 AAACAATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
26 18 0.64
27 9 0.32
28 1 0.04
ACGTcount: A:0.60, C:0.08, G:0.05, T:0.27
Consensus pattern (27 bp):
AATATATGCAAAAAGCAATTCAAAATA
Found at i:12236893 original size:25 final size:25
Alignment explanation
Indices: 12236865--12236928 Score: 60
Period size: 26 Copynumber: 2.6 Consensus size: 25
12236855 AATATATGTA
*
12236865 AAAACACATTTAAAATAAATATTAC
1 AAAACACATTTAAAATAAATAATAC
* *
12236890 AAAA-AGCAATTCAAAATAAATAATAT
1 AAAACA-C-ATTTAAAATAAATAATAC
*
12236916 GAAACA-ATTTAAA
1 AAAACACATTTAAA
12236929 GTCATCAATG
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
24 7 0.23
25 5 0.16
26 18 0.58
27 1 0.03
ACGTcount: A:0.62, C:0.09, G:0.03, T:0.25
Consensus pattern (25 bp):
AAAACACATTTAAAATAAATAATAC
Found at i:12238533 original size:44 final size:44
Alignment explanation
Indices: 12238449--12238642 Score: 271
Period size: 44 Copynumber: 4.4 Consensus size: 44
12238439 CGATACCTAC
* ** *
12238449 TATCTTTGATCTGCTCCCCGTCCAATACAGAGACACCAAATCTGT
1 TATCTTTGATCTGCTCTCCG-CCGCTACAGAGACGCCAAATCTGT
*
12238494 CATCTTTGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGT
1 TATCTTTGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGT
* * * *
12238538 TATATTTGATCTGCTCTCTGCCGCTACAGAAACGTCAAATCTGT
1 TATCTTTGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGT
* *
12238582 TATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAAATCTGT
1 TATCTTTGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGT
*
12238626 TATCTTCGATCTGCTCT
1 TATCTTTGATCTGCTCT
12238643 ACTGTAAGCA
Statistics
Matches: 135, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
44 117 0.87
45 18 0.13
ACGTcount: A:0.22, C:0.30, G:0.16, T:0.31
Consensus pattern (44 bp):
TATCTTTGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGT
Found at i:12238785 original size:88 final size:88
Alignment explanation
Indices: 12238672--12238927 Score: 390
Period size: 88 Copynumber: 2.9 Consensus size: 88
12238662 CAGATCTGCT
* * * * * * *
12238672 ATCTTCGATCTG-TTCCCTATAAGCACAGGGATGCCAAATCTGCTATTTTTAACTTGCTCCCTAT
1 ATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATTTTCAACTTGTTCCCTAT
*
12238736 AAGCACAGGGATGCCATGCTGAA
66 AAGCACAGGGATGCCATGCTAAA
12238759 ATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATTTTCAACTTGTTCCCTAT
1 ATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATTTTCAACTTGTTCCCTAT
*
12238824 AAGTACAGGGATGCCATGCTAAA
66 AAGCACAGGGATGCCATGCTAAA
* *
12238847 ATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGTTATCTTCAA-TCTGTTCCCTA
1 ATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATTTTCAACT-TGTTCCCTA
12238911 TAAGCACAGGGATGCCA
65 TAAGCACAGGGATGCCA
12238928 AATCTACTGT
Statistics
Matches: 155, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
87 13 0.08
88 142 0.92
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (88 bp):
ATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATTTTCAACTTGTTCCCTAT
AAGCACAGGGATGCCATGCTAAA
Found at i:12238871 original size:132 final size:132
Alignment explanation
Indices: 12238627--12239018 Score: 429
Period size: 132 Copynumber: 3.0 Consensus size: 132
12238617 CAAATCTGTT
* * *
12238627 ATCTTCGATCTGC-TCTACTGTAAGCACAAGAATGTCAGATCTGCTATCTTCGA-TCTGTTCCCT
1 ATCTTCGATCTGCTTC-ACTGTAAGCACAGGAATGTCAGATCTGCTATTTTCAACT-TGTTCCCT
** ** * * *
12238690 ATAAGCACAGGGATGCCAAAT-CTGCTAT-TTTTAACTTGC-TCCCTATAAGCACAGGGATGCCA
64 ATAAGCACAGGGATGCC--ATGCTGAAATCTTCGAAC-TGCTTCACTGTAAGCACAGGAATGCCA
12238752 TG-CTGAA
126 -GACTGAA
12238759 ATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATTTTCAACTTGTTCCCTAT
1 ATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATTTTCAACTTGTTCCCTAT
* * * *
12238824 AAGTACAGGGATGCCATGCTAAAATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCT
66 AAGCACAGGGATGCCATGCTGAAATCTTCGAACTGCTTCACTGTAAGCACAGGAATGCCAGA-CT
**
12238889 GTT
130 GAA
* * * * * * * *
12238892 ATCTTCAATCTG-TTCCCTATAAGCACAGGGATGCCAAATCTACTGTTTTCAACTTGTTCCCTAT
1 ATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATTTTCAACTTGTTCCCTAT
* * *
12238956 AAGCACAGGGATGCCATGCTGAAATCTTCGACCTGTTTCACTGTAAGCACAGGAATGTCAGAC
66 AAGCACAGGGATGCCATGCTGAAATCTTCGAACTGCTTCACTGTAAGCACAGGAATGCCAGAC
12239019 CTGCTATCTT
Statistics
Matches: 225, Mismatches: 28, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
130 2 0.01
131 9 0.04
132 197 0.88
133 17 0.08
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (132 bp):
ATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATTTTCAACTTGTTCCCTAT
AAGCACAGGGATGCCATGCTGAAATCTTCGAACTGCTTCACTGTAAGCACAGGAATGCCAGACTG
AA
Found at i:12238927 original size:220 final size:220
Alignment explanation
Indices: 12238627--12239030 Score: 693
Period size: 220 Copynumber: 1.8 Consensus size: 220
12238617 CAAATCTGTT
*
12238627 ATCTTCGATCTGCTCTACTGTAAGCACAAGAATGTCAGATCTGCTATCTTCGATCTGTTCCCTAT
1 ATCTTCGATCTGCTCTACTGTAAGCACAAGAATGTCAGATCTGCTATCTTCAATCTGTTCCCTAT
* *
12238692 AAGCACAGGGATGCCAAATCTGCTATTTTTAACTTGCTCCCTATAAGCACAGGGATGCCATGCTG
66 AAGCACAGGGATGCCAAATCTACTATTTTCAACTTGCTCCCTATAAGCACAGGGATGCCATGCTG
* * *
12238757 AAATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATTTTCAACTTGTTCCCT
131 AAATCTTCGACCTGCTTCACTGTAAGCACAGGAATGTCAGACCTGCTATCTTCAACTTGTTCCCT
12238822 ATAAGTACAGGGATGCCATGCTAAA
196 ATAAGTACAGGGATGCCATGCTAAA
* *
12238847 ATCTTCGATCTGCT-TCACTGTAAGCACAGGAATGTCAGATCTGTTATCTTCAATCTGTTCCCTA
1 ATCTTCGATCTGCTCT-ACTGTAAGCACAAGAATGTCAGATCTGCTATCTTCAATCTGTTCCCTA
* *
12238911 TAAGCACAGGGATGCCAAATCTACTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCT
65 TAAGCACAGGGATGCCAAATCTACTATTTTCAACTTGCTCCCTATAAGCACAGGGATGCCATGCT
*
12238976 GAAATCTTCGACCTGTTTCACTGTAAGCACAGGAATGTCAGACCTGCTATCTTCA
130 GAAATCTTCGACCTGCTTCACTGTAAGCACAGGAATGTCAGACCTGCTATCTTCA
12239031 GTCTGCTCCT
Statistics
Matches: 172, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
219 1 0.01
220 171 0.99
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (220 bp):
ATCTTCGATCTGCTCTACTGTAAGCACAAGAATGTCAGATCTGCTATCTTCAATCTGTTCCCTAT
AAGCACAGGGATGCCAAATCTACTATTTTCAACTTGCTCCCTATAAGCACAGGGATGCCATGCTG
AAATCTTCGACCTGCTTCACTGTAAGCACAGGAATGTCAGACCTGCTATCTTCAACTTGTTCCCT
ATAAGTACAGGGATGCCATGCTAAA
Found at i:12239165 original size:68 final size:68
Alignment explanation
Indices: 12239083--12239351 Score: 335
Period size: 68 Copynumber: 4.0 Consensus size: 68
12239073 TCTTCTTCTG
* * ** * * *
12239083 CTGAAACTTTAAGGAAATCTGCTGTAACTTTTAGTCGTTCCAACGCCATTTCAGGGAGAAGAGAT
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAAAAGAGAT
12239148 CTA
66 CTA
* * * * *
12239151 CTGAAACTTCAAGGAGATTTGCTGTGGGTTTTAACAGCTCCAACGCCATTTCA-GGAAGAAGAGG
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAA-AAGAGA
*
12239215 T-TCG
65 TCT-A
* *
12239219 CTGAAACTTCAAGGAGATCTGCTATGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAAAAGAGAC
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAAAAGAGAT
*
12239284 CCA
66 CTA
* * *
12239287 CTGAAACTTTAAGGAGATTTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTTAGGGAAAAGAGAT
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAAAAGAGAT
12239352 TTGATTTCTA
Statistics
Matches: 170, Mismatches: 27, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
67 4 0.02
68 162 0.95
69 4 0.02
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (68 bp):
CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAAAAGAGAT
CTA
Found at i:12239349 original size:136 final size:136
Alignment explanation
Indices: 12239082--12239337 Score: 386
Period size: 136 Copynumber: 1.9 Consensus size: 136
12239072 ATCTTCTTCT
* * * * *
12239082 GCTGAAACTTTAAGGAAATCTGCTGTAACTTTTAGTCGTTCCAACGCCATTTCAGGGAGAAGAGA
1 GCTGAAACTTCAAGGAAATCTGCTATAACTTTTAGCCGCTCCAACGCCATTTCAGGGAAAAGAGA
* * *
12239147 TCTACTGAAACTTCAAGGAGATTTGCTGTGGGTTTTAACAGCTCCAACGCCATTTCAGGAAGAAG
66 CCCACTGAAACTTCAAGGAGATTTGCTGTGGCTTTTAACAGCTCCAACGCCATTTCAGGAAGAAG
12239212 AGGTTC
131 AGGTTC
* **
12239218 GCTGAAACTTCAAGGAGATCTGCTATGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAAAAGAGA
1 GCTGAAACTTCAAGGAAATCTGCTATAACTTTTAGCCGCTCCAACGCCATTTCAGGGAAAAGAGA
* * *
12239283 CCCACTGAAACTTTAAGGAGATTTGCTGTGGCTTTTAGCCGCTCCAACGCCATTT
66 CCCACTGAAACTTCAAGGAGATTTGCTGTGGCTTTTAACAGCTCCAACGCCATTT
12239338 TAGGGAAAAG
Statistics
Matches: 106, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
136 106 1.00
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (136 bp):
GCTGAAACTTCAAGGAAATCTGCTATAACTTTTAGCCGCTCCAACGCCATTTCAGGGAAAAGAGA
CCCACTGAAACTTCAAGGAGATTTGCTGTGGCTTTTAACAGCTCCAACGCCATTTCAGGAAGAAG
AGGTTC
Found at i:12239493 original size:87 final size:86
Alignment explanation
Indices: 12239363--12239745 Score: 304
Period size: 87 Copynumber: 4.4 Consensus size: 86
12239353 TGATTTCTAG
* ** * *
12239363 CCTGTTACCCTACTACTTAGGGGGTTAAGGCCCATCGTATTCGATCTGTTTCCCTACTACTTAGG
1 CCTGTTACCCTACTGCTTAGGGGGTTAAGGTTCATCATCTTCGATCTGTTTCCCTACTACTTAGG
* * *
12239428 GTGATAAGATATGTGAATTTAA
66 G-GATAAGATCTGTAAATTCAA
* * * * * * *
12239450 CCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGAT-TATCTCCACTAATGCTTAG
1 CCTGTTACCCTACTGCTTAGGGGGTTAAGGTTCATCATCTTCGATCTGTTTCC-CTACTACTTAG
*
12239514 GGAGACAAGATCTGTAAATTCAA
65 GG-GATAAGATCTGTAAATTCAA
* * ** * * * * *
12239537 CCTGTTACCCTA-TAGGTTAGGGGGTTAAGATTTGTAAATCTT-TAGCCTGTTACCCTACTGCTT
1 CCTGTTACCCTACT-GCTTAGGGGGTTAAGGTTCAT-CATCTTCGA-TCTGTTTCCCTACTACTT
* * * * **
12239600 AGGGGTTTAAGGTTTGTAGATTCGG
63 AGGGG-ATAAGATCTGTAAATTCAA
* * * *
12239625 CTTGTTACCCTACTGCTTAGGGGGTTAAAGCTCATCATCTTTGATCTGTTTCCCTACTACTTAGG
1 CCTGTTACCCTACTGCTTAGGGGGTTAAGGTTCATCATCTTCGATCTGTTTCCCTACTACTTA-G
* *
12239690 GGGTTAAGATCTGTAAATCTTCAG
65 GGGATAAGATCTGTAAA--TTCAA
* *
12239714 CCTGTTACCCTACTGCTTAAGGGTTTAAGGTT
1 CCTGTTACCCTACTGCTTAGGGGGTTAAGGTT
12239746 TGTAGATTCG
Statistics
Matches: 229, Mismatches: 56, Indels: 20
0.75 0.18 0.07
Matches are distributed among these distances:
86 6 0.03
87 128 0.56
88 59 0.26
89 36 0.16
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (86 bp):
CCTGTTACCCTACTGCTTAGGGGGTTAAGGTTCATCATCTTCGATCTGTTTCCCTACTACTTAGG
GGATAAGATCTGTAAATTCAA
Found at i:12239674 original size:132 final size:132
Alignment explanation
Indices: 12239365--12240002 Score: 683
Period size: 132 Copynumber: 4.9 Consensus size: 132
12239355 ATTTCTAGCC
* * * * * * *
12239365 TGTTACCCTACTACTTAGGGGGTTAAGGCCCATCGTATTCGATCTGTTTCCCTACTACTTAGGGT
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCTCATCATCTTTGATCTGTTTCCCTACTACTTAGGGG
* * * * * *
12239430 GATAAGATATGTGAAT-TT-AACCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCT-TCGTCTTC
66 GTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGTT-TGTAG-ATTC
*
12239492 -GAT
129 GGCT
* * * * * ** ** * * *
12239495 TATCT-CCACTAATGCTTAGGGAG--ACAAGATC-TGTAAATTCAACCTGTTACCCTA-TAGGTT
1 TGT-TACC-CTACTGCTTAGGGGGTTA-AAGCTCAT-CATCTTTGATCTGTTTCCCTACTA-CTT
* *
12239555 AGGGGGTTAAGATTTGTAAATCTTTAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGTTTGTAGA
61 AGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGTTTGTAGA
12239620 TTCGGCT
126 TTCGGCT
12239627 TGTTACCCTACTGCTTAGGGGGTTAAAGCTCATCATCTTTGATCTGTTTCCCTACTACTTAGGGG
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCTCATCATCTTTGATCTGTTTCCCTACTACTTAGGGG
*
12239692 GTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAAGGGTTTAAGGTTTGTAGATTCGG
66 GTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGTTTGTAGATTCGG
12239757 CT
131 CT
*
12239759 TGTTACCCTACTACTTAGGGGGTTAAAGCTCATCATCTTTGATCTGTTTCCCTACTACTTAGGGG
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCTCATCATCTTTGATCTGTTTCCCTACTACTTAGGGG
* * * *
12239824 GTTAAGATCTGTAAATCTTCAGCCTGTTACTCTACTGCTTAGGGGGTTAAGGCTTGTAAATTCGG
66 GTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGTTTGTAGATTCGG
12239889 CT
131 CT
** ** * * *
12239891 TGTTACCCTACTGCTTAGGGGGTTAAAGCTTGT-AAATTTG-GCTTGTTACCCTACTGCTTAGGG
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCTCATCATCTTTGATC-TGTTTCCCTACTACTTAGGG
* * * * *
12239954 GGTTAA-AGCTTGTAAAT-TT-GGCTTGTTACCCTACTACTTAGGGGGTTAA
65 GGTTAAGATC-TGTAAATCTTCAGCCTGTTACCCTACTGCTTAGGGGTTTAA
12240003 AGCCCATCAT
Statistics
Matches: 436, Mismatches: 56, Indels: 33
0.83 0.11 0.06
Matches are distributed among these distances:
129 30 0.07
130 46 0.11
131 69 0.16
132 287 0.66
133 4 0.01
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (132 bp):
TGTTACCCTACTGCTTAGGGGGTTAAAGCTCATCATCTTTGATCTGTTTCCCTACTACTTAGGGG
GTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGTTTGTAGATTCGG
CT
Found at i:12239690 original size:175 final size:173
Alignment explanation
Indices: 12239452--12240090 Score: 619
Period size: 175 Copynumber: 3.7 Consensus size: 173
12239442 GAATTTAACC
* * * * * * * * * *
12239452 TGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGAT-TATCTCCACTAATGCTTAGGG
1 TGTTACCCTACTACTTAGGGGGTTAAAGCTCATCATCTTTGATCTGTTTCC-CTACTGCTTAGGG
* ** * *
12239516 AGACAAGATCTGTAAATTCAACCTGTTACCCTA-TAGGTTAGGGGGTTAAGATTTGTAAATCTTT
65 GGTTAAGATCTGTAAATTCAGCCTGTTACCCTACT-GCTTAGGGGGTTAAGATTTGTAAA--TTT
* * * * * * *
12239580 AGCCTGTTACCCTACTGCTTAGGGGTTTAAGGTTTGTAGATTCGGCT
127 GGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCTTGTAAATTTGGCT
* *
12239627 TGTTACCCTACTGCTTAGGGGGTTAAAGCTCATCATCTTTGATCTGTTTCCCTACTACTTAGGGG
1 TGTTACCCTACTACTTAGGGGGTTAAAGCTCATCATCTTTGATCTGTTTCCCTACTGCTTAGGGG
* * * * *
12239692 GTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAAGGGTTTAAGGTTTGTAGATTCGG
66 GTTAAGATCTGTAAA--TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGATTTGTAAATTTGG
* ** * * *
12239757 CTTGTTACCCTACTACTTAGGGGGTTAAAGCTCAT-CATCTTTGAT
129 CTTGTTACCCTACTGCTTAGGGGGTTAAAGCTTGTAAAT-TTGGCT
* * * * * * * *
12239802 CTGTTTCCCTACTACTTAGGGGGTT-AAGATCTGTAAATC-TTCAGCCTGTTACTCTACTGCTTA
1 -TGTTACCCTACTACTTAGGGGGTTAAAGCTC-AT-CATCTTTGA-TCTGTTTCCCTACTGCTTA
* * * *
12239865 GGGGGTTAAG-GCTTGTAAATTCGGCTTGTTACCCTACTGCTTAGGGGGTTAA-AGCTTGTAAAT
62 GGGGGTTAAGATC-TGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGA-TTTGTAAAT
12239928 TTGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCTTGTAAATTTGGCT
125 TTGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCTTGTAAATTTGGCT
* *
12239977 TGTTACCCTACTACTTAGGGGGTTAAAGCCCATCATCTTTGATCTGTTTCCCTACTGCTTAGGAG
1 TGTTACCCTACTACTTAGGGGGTTAAAGCTCATCATCTTTGATCTGTTTCCCTACTGCTTAGGGG
* * * * *
12240042 GTTAAGATCTGT-AATTCGGTCTGTTACCCTACCGATTAGGGGTTTAAGA
66 GTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGA
12240091 CCCTCAGTAG
Statistics
Matches: 375, Mismatches: 73, Indels: 34
0.78 0.15 0.07
Matches are distributed among these distances:
172 30 0.08
173 32 0.09
174 30 0.08
175 179 0.48
176 34 0.09
177 69 0.18
178 1 0.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (173 bp):
TGTTACCCTACTACTTAGGGGGTTAAAGCTCATCATCTTTGATCTGTTTCCCTACTGCTTAGGGG
GTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGATTTGTAAATTTGGCT
TGTTACCCTACTGCTTAGGGGGTTAAAGCTTGTAAATTTGGCT
Found at i:12240003 original size:43 final size:43
Alignment explanation
Indices: 12239539--12240005 Score: 406
Period size: 43 Copynumber: 10.7 Consensus size: 43
12239529 AAATTCAACC
* * * *
12239539 TGTTACCCTA-TAGGTTAGGGGGTT-AAGATTTGTAAATCTTTAGCC
1 TGTTACCCTACT-GCTTAGGGGGTTAAAG-CTTGTAAA--TTTGGCT
* * * * *
12239584 TGTTACCCTACTGCTTAGGGGTTTAAGGTTTGTAGATTCGGCT
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCTTGTAAATTTGGCT
** * * *
12239627 TGTTACCCTACTGCTTAGGGGGTTAAAGCTCAT-CATCTTTGAT
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCTTGTAAAT-TTGGCT
* * * * *
12239670 CTGTTTCCCTACTACTTAGGGGGTT-AAGATCTGTAAATCTTCAGCC
1 -TGTTACCCTACTGCTTAGGGGGTTAAAGCT-TGTAAAT-TT-GGCT
* * * * * *
12239716 TGTTACCCTACTGCTTAAGGGTTTAAGGTTTGTAGATTCGGCT
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCTTGTAAATTTGGCT
* ** * * *
12239759 TGTTACCCTACTACTTAGGGGGTTAAAGCTCAT-CATCTTTGAT
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCTTGTAAAT-TTGGCT
* * * * *
12239802 CTGTTTCCCTACTACTTAGGGGGTT-AAGATCTGTAAATCTTCAGCC
1 -TGTTACCCTACTGCTTAGGGGGTTAAAGCT-TGTAAAT-TT-GGCT
* * *
12239848 TGTTACTCTACTGCTTAGGGGGTTAAGGCTTGTAAATTCGGCT
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCTTGTAAATTTGGCT
12239891 TGTTACCCTACTGCTTAGGGGGTTAAAGCTTGTAAATTTGGCT
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCTTGTAAATTTGGCT
12239934 TGTTACCCTACTGCTTAGGGGGTTAAAGCTTGTAAATTTGGCT
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCTTGTAAATTTGGCT
*
12239977 TGTTACCCTACTACTTAGGGGGTTAAAGC
1 TGTTACCCTACTGCTTAGGGGGTTAAAGC
12240006 CCATCATCTT
Statistics
Matches: 342, Mismatches: 66, Indels: 30
0.78 0.15 0.07
Matches are distributed among these distances:
42 4 0.01
43 187 0.55
44 49 0.14
45 91 0.27
46 11 0.03
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.37
Consensus pattern (43 bp):
TGTTACCCTACTGCTTAGGGGGTTAAAGCTTGTAAATTTGGCT
Found at i:12240081 original size:86 final size:87
Alignment explanation
Indices: 12239584--12240088 Score: 300
Period size: 86 Copynumber: 5.8 Consensus size: 87
12239574 ATCTTTAGCC
* * * * *
12239584 TGTTACCCTACTGCTTAGGGGTTTAAG-GTTTGTAGATTCGGCTTGTTACCCTACTGCTTAGGGG
1 TGTTACCCTACTGCTTAGGGGGTTAAGAGCTTGTAAATTCGGCTTGTTACCCTACCGATTAGGGG
* * * *
12239648 GTTAAAGCTCAT-CATCTTTGAT
66 GTTAAAGCCCATAAAT-TTGGCT
* * * * * * * *
12239670 CTGTTTCCCTACTACTTAGGGGGTTAAGATC-TGTAAATCTTCAGCCTGTTACCCTACTGCTTAA
1 -TGTTACCCTACTGCTTAGGGGGTTAAGAGCTTGTAAA--TTCGGCTTGTTACCCTACCGATTAG
* * **** * *
12239734 GGGTTTAAGGTTTGTAGATTCGGCT
63 GGGGTTAAAGCCCATAAATTTGGCT
* ** * ** * * *
12239759 TGTTACCCTACTACTTAGGGGGTTAA-AGCTCAT-CATCTTTGATCTGTTTCCCTA-CTACTTAG
1 TGTTACCCTACTGCTTAGGGGGTTAAGAGCTTGTAAAT-TCGGCT-TGTTACCCTACCGA-TTAG
* ** * *
12239821 GGGGTT-AAGATCTGTAAATCTTCAGCC
63 GGGGTTAAAG-CCCATAAAT-TT-GGCT
* * *
12239848 TGTTACTCTACTGCTTAGGGGGTTAAG-GCTTGTAAATTCGGCTTGTTACCCTACTGCTTAGGGG
1 TGTTACCCTACTGCTTAGGGGGTTAAGAGCTTGTAAATTCGGCTTGTTACCCTACCGATTAGGGG
***
12239912 GTTAAAGCTTGTAAATTTGGCT
66 GTTAAAGCCCATAAATTTGGCT
* *
12239934 TGTTACCCTACTGCTTAGGGGGTTAA-AGCTTGTAAATTTGGCTTGTTACCCTA-CTACTTAGGG
1 TGTTACCCTACTGCTTAGGGGGTTAAGAGCTTGTAAATTCGGCTTGTTACCCTACCGA-TTAGGG
* * *
12239997 GGTTAAAGCCCAT-CATCTTTGAT
65 GGTTAAAGCCCATAAAT-TTGGCT
* * *
12240020 CTGTTTCCCTACTGCTTAGGAGGTTAAGATC-TGT-AATTCGG-TCTGTTACCCTACCGATTAGG
1 -TGTTACCCTACTGCTTAGGGGGTTAAGAGCTTGTAAATTCGGCT-TGTTACCCTACCGATTAGG
*
12240082 GGTTTAA
64 GGGTTAA
12240089 GACCCTCAGT
Statistics
Matches: 324, Mismatches: 72, Indels: 45
0.73 0.16 0.10
Matches are distributed among these distances:
85 4 0.01
86 103 0.32
87 87 0.27
88 55 0.17
89 71 0.22
90 4 0.01
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.37
Consensus pattern (87 bp):
TGTTACCCTACTGCTTAGGGGGTTAAGAGCTTGTAAATTCGGCTTGTTACCCTACCGATTAGGGG
GTTAAAGCCCATAAATTTGGCT
Found at i:12240154 original size:44 final size:43
Alignment explanation
Indices: 12240106--12240405 Score: 234
Period size: 42 Copynumber: 7.0 Consensus size: 43
12240096 AGTAGGGGTT
*
12240106 TAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGAGA
1 TAAGACCCTTCGACTTCGATCTGTTTCCCTACTGCTTAGGG-GA
* * * * * * * *
12240150 TAAGA-TCTGC-AATTCGGTCTGTTACCCTACCGATTAGGGGTT
1 TAAGACCCTTCGACTTCGATCTGTTTCCCTACTGCTTAGGGG-A
*
12240192 TAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGAGA
1 TAAGACCCTTCGACTTCGATCTGTTTCCCTACTGCTTAGGG-GA
* * * * * * * *
12240236 TAAGA-TCTGC-AATTCGGTCTGTTACCCTACCGATTAGGGGTT
1 TAAGACCCTTCGACTTCGATCTGTTTCCCTACTGCTTAGGGG-A
* *
12240278 TAAGACCCTTCGTCTTCGATCTATTTCCCTACTGCTTAGGGAGA
1 TAAGACCCTTCGACTTCGATCTGTTTCCCTACTGCTTAGGG-GA
* * * * * * * **
12240322 TAAGA-TCTGC-AATTCGGTCTGTTACCCTACCGATTAAGGGTT
1 TAAGACCCTTCGACTTCGATCTGTTTCCCTACTGCTT-AGGGGA
*
12240364 TAAGACCCTTCGCCTTCGATCTGTTTCCCTACTGCTTAGGGG
1 TAAGACCCTTCGACTTCGATCTGTTTCCCTACTGCTTAGGGG
12240406 GTTAAGATCT
Statistics
Matches: 188, Mismatches: 57, Indels: 23
0.70 0.21 0.09
Matches are distributed among these distances:
41 2 0.01
42 79 0.42
43 26 0.14
44 79 0.42
45 2 0.01
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (43 bp):
TAAGACCCTTCGACTTCGATCTGTTTCCCTACTGCTTAGGGGA
Found at i:12240177 original size:106 final size:105
Alignment explanation
Indices: 12239995--12240200 Score: 333
Period size: 106 Copynumber: 2.0 Consensus size: 105
12239985 TACTACTTAG
* * *
12239995 GGGGTTAAAGCCCATCATCTTTGATCTGTTTCCCTACTGCTTAGGAGGTTAAGATCTGTAATTCG
1 GGGGTTAAAGCCCATCATCTTCGATCTGTTTCCCTACTGCTTAGGAGGATAAGATCTGCAATTCG
12240060 GTCTGTTACCCTACCGATTAGGGGTTTAAGACCCTCAGTA
66 GTCTGTTACCCTACCGATTAGGGGTTTAAGACCCTCAGTA
* * *
12240100 GGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGG-GAGATAAGATCTGCAATT
1 GGGGTTAAAG-CCCATCATCTTCGATCTGTTTCCCTACTGCTTAGGAG-GATAAGATCTGCAATT
12240164 CGGTCTGTTACCCTACCGATTAGGGGTTTAAGACCCT
64 CGGTCTGTTACCCTACCGATTAGGGGTTTAAGACCCT
12240201 TCGTCTTCGA
Statistics
Matches: 93, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
105 10 0.11
106 83 0.89
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (105 bp):
GGGGTTAAAGCCCATCATCTTCGATCTGTTTCCCTACTGCTTAGGAGGATAAGATCTGCAATTCG
GTCTGTTACCCTACCGATTAGGGGTTTAAGACCCTCAGTA
Found at i:12240243 original size:86 final size:86
Alignment explanation
Indices: 12240098--12240416 Score: 593
Period size: 86 Copynumber: 3.7 Consensus size: 86
12240088 AGACCCTCAG
12240098 TAGGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGAGATAAGATCTGCAAT
1 TAGGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGAGATAAGATCTGCAAT
12240163 TCGGTCTGTTACCCTACCGAT
66 TCGGTCTGTTACCCTACCGAT
12240184 TAGGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGAGATAAGATCTGCAAT
1 TAGGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGAGATAAGATCTGCAAT
12240249 TCGGTCTGTTACCCTACCGAT
66 TCGGTCTGTTACCCTACCGAT
*
12240270 TAGGGGTTTAAGACCCTTCGTCTTCGATCTATTTCCCTACTGCTTAGGGAGATAAGATCTGCAAT
1 TAGGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGAGATAAGATCTGCAAT
12240335 TCGGTCTGTTACCCTACCGAT
66 TCGGTCTGTTACCCTACCGAT
* * * *
12240356 TAAGGGTTTAAGACCCTTCGCCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTG
1 TAGGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGAGATAAGATCTG
12240417 TAAATCTTCA
Statistics
Matches: 227, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
86 227 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (86 bp):
TAGGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGAGATAAGATCTGCAAT
TCGGTCTGTTACCCTACCGAT
Found at i:12240411 original size:44 final size:44
Alignment explanation
Indices: 12240098--12240412 Score: 243
Period size: 44 Copynumber: 7.3 Consensus size: 44
12240088 AGACCCTCAG
* *
12240098 TAGGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCT
1 TAGGGGGTTAAGACCCTTCGCCTTCGATCTGTTTCCCTACTGCT
* * * * * * * *
12240142 TAGGGAGATAAGA-TC-T-GCAATTCGGTCTGTTACCCTACCGAT
1 TAGGGGGTTAAGACCCTTCGC-CTTCGATCTGTTTCCCTACTGCT
* *
12240184 TAGGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCT
1 TAGGGGGTTAAGACCCTTCGCCTTCGATCTGTTTCCCTACTGCT
* * * * * * * *
12240228 TAGGGAGATAAGA-TC-T-GCAATTCGGTCTGTTACCCTACCGAT
1 TAGGGGGTTAAGACCCTTCGC-CTTCGATCTGTTTCCCTACTGCT
* * *
12240270 TAGGGGTTTAAGACCCTTCGTCTTCGATCTATTTCCCTACTGCT
1 TAGGGGGTTAAGACCCTTCGCCTTCGATCTGTTTCCCTACTGCT
* * * * * * * *
12240314 TAGGGAGATAAGA-TC-T-GCAATTCGGTCTGTTACCCTACCGAT
1 TAGGGGGTTAAGACCCTTCGC-CTTCGATCTGTTTCCCTACTGCT
* *
12240356 TAAGGGTTTAAGACCCTTCGCCTTCGATCTGTTTCCCTACTGCT
1 TAGGGGGTTAAGACCCTTCGCCTTCGATCTGTTTCCCTACTGCT
12240400 TAGGGGGTTAAGA
1 TAGGGGGTTAAGA
12240413 TCTGTAAATC
Statistics
Matches: 195, Mismatches: 64, Indels: 24
0.69 0.23 0.08
Matches are distributed among these distances:
41 3 0.02
42 85 0.44
43 6 0.03
44 97 0.50
45 4 0.02
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (44 bp):
TAGGGGGTTAAGACCCTTCGCCTTCGATCTGTTTCCCTACTGCT
Found at i:12240602 original size:66 final size:66
Alignment explanation
Indices: 12240520--12240646 Score: 227
Period size: 66 Copynumber: 1.9 Consensus size: 66
12240510 TCTATGCTTA
* *
12240520 TGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTTCTAGCTAGATGTGTTATGAAT
1 TGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTATGAAT
12240585 G
66 G
*
12240586 TGTCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGCTCCTAACTAGATGTGTTAT
1 TGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTAT
12240647 TATATGAATG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (66 bp):
TGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTATGAAT
G
Found at i:12240625 original size:32 final size:32
Alignment explanation
Indices: 12240522--12240625 Score: 79
Period size: 32 Copynumber: 3.2 Consensus size: 32
12240512 TATGCTTATG
*
12240522 TCAAATAATTAGGATGCTATGATCGAAATGAA
1 TCAAATAATTAGGATGCTATGATTGAAATGAA
** ** **
12240554 TCAAATGCTT-CTA-GCTA-GATGTGTTATGAATGTG
1 TCAAATAATTAGGATGCTATGAT-TG--A--AATGAA
12240588 TCAAATAATTAGGATGCTATGATTGAAATGAA
1 TCAAATAATTAGGATGCTATGATTGAAATGAA
12240620 TCAAAT
1 TCAAAT
12240626 GCTCCTAACT
Statistics
Matches: 51, Mismatches: 13, Indels: 16
0.64 0.16 0.20
Matches are distributed among these distances:
29 3 0.06
30 5 0.10
31 1 0.02
32 19 0.37
34 13 0.25
35 1 0.02
36 6 0.12
37 3 0.06
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (32 bp):
TCAAATAATTAGGATGCTATGATTGAAATGAA
Found at i:12242352 original size:1 final size:1
Alignment explanation
Indices: 12242341--12242410 Score: 77
Period size: 1 Copynumber: 70.0 Consensus size: 1
12242331 GTTGGGTCCC
* * * * * * *
12242341 TTTTTTGTTTTTGTTTTTTTTTTATTTTTTTTTGTTTTTTATTTTTTGTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12242406 TTTTT
1 TTTTT
12242411 GCCTTTGCCA
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.03, C:0.00, G:0.07, T:0.90
Consensus pattern (1 bp):
T
Found at i:12242363 original size:17 final size:16
Alignment explanation
Indices: 12242341--12242410 Score: 95
Period size: 17 Copynumber: 4.2 Consensus size: 16
12242331 GTTGGGTCCC
*
12242341 TTTTTTGTTTTTGTTTT
1 TTTTTTATTTTT-TTTT
12242358 TTTTTTATTTTTTTTT
1 TTTTTTATTTTTTTTT
12242374 GTTTTTTATTTTTTGTTT
1 -TTTTTTATTTTTT-TTT
*
12242392 TTTTTTGTTTTTTTTT
1 TTTTTTATTTTTTTTT
12242408 TTT
1 TTT
12242411 GCCTTTGCCA
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
16 10 0.20
17 36 0.73
18 3 0.06
ACGTcount: A:0.03, C:0.00, G:0.07, T:0.90
Consensus pattern (16 bp):
TTTTTTATTTTTTTTT
Found at i:12242385 original size:24 final size:23
Alignment explanation
Indices: 12242341--12242410 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 23
12242331 GTTGGGTCCC
12242341 TTTTTTGTTT-TTGTTTTTTTTTTA
1 TTTTTT-TTTGTT-TTTTTTTTTTA
*
12242365 TTTTTTTTTGTTTTTTATTTTTTG
1 TTTTTTTTTGTTTTTT-TTTTTTA
12242389 TTTTTTTTTGTTTTTTTTTTTT
1 TTTTTTTTTGTTTTTTTTTTTT
12242411 GCCTTTGCCA
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
23 13 0.30
24 30 0.70
ACGTcount: A:0.03, C:0.00, G:0.07, T:0.90
Consensus pattern (23 bp):
TTTTTTTTTGTTTTTTTTTTTTA
Found at i:12245210 original size:6 final size:6
Alignment explanation
Indices: 12245197--12245230 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
12245187 AATGCAAATG
12245197 ATGC-A ATGCAA ATGCAA ATGCAA ATGCAA ATGCA
1 ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA ATGCA
12245231 TGGAATGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (6 bp):
ATGCAA
Found at i:12248147 original size:27 final size:27
Alignment explanation
Indices: 12248117--12248178 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 27
12248107 TTAGAGCAGT
* *
12248117 AATATATGTAAAAA-CACATTTAAAATA
1 AATATATGCAAAAAGCA-ATTCAAAATA
*
12248144 AATAT-TACAAAAAGCAATTCAAAATA
1 AATATATGCAAAAAGCAATTCAAAATA
12248170 AATAATATG
1 AAT-ATATG
12248179 AAACAATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
26 18 0.64
27 9 0.32
28 1 0.04
ACGTcount: A:0.60, C:0.08, G:0.05, T:0.27
Consensus pattern (27 bp):
AATATATGCAAAAAGCAATTCAAAATA
Found at i:12248155 original size:25 final size:25
Alignment explanation
Indices: 12248127--12248190 Score: 60
Period size: 26 Copynumber: 2.6 Consensus size: 25
12248117 AATATATGTA
*
12248127 AAAACACATTTAAAATAAATATTAC
1 AAAACACATTTAAAATAAATAATAC
* *
12248152 AAAA-AGCAATTCAAAATAAATAATAT
1 AAAACA-C-ATTTAAAATAAATAATAC
*
12248178 GAAACA-ATTTAAA
1 AAAACACATTTAAA
12248191 GTCATCAATG
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
24 7 0.23
25 5 0.16
26 18 0.58
27 1 0.03
ACGTcount: A:0.62, C:0.09, G:0.03, T:0.25
Consensus pattern (25 bp):
AAAACACATTTAAAATAAATAATAC
Found at i:12248264 original size:22 final size:21
Alignment explanation
Indices: 12248239--12248288 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
12248229 CAAATAAAAT
12248239 AAATAATTAATAAAGAAATTTA
1 AAATAATTAAT-AAGAAATTTA
* * **
12248261 AAATAAATAGTAAGAGGTTTA
1 AAATAATTAATAAGAAATTTA
12248282 AAATAAT
1 AAATAAT
12248289 AACAGATGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (21 bp):
AAATAATTAATAAGAAATTTA
Found at i:12248326 original size:2 final size:2
Alignment explanation
Indices: 12248319--12248362 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
12248309 GAAACAAGTA
*
12248319 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12248361 AT
1 AT
12248363 TTAAACAAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12248367 original size:8 final size:8
Alignment explanation
Indices: 12248318--12248367 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
12248308 TGAAACAAGT
12248318 AATATATA
1 AATATATA
*
12248326 TATATATA
1 AATATATA
*
12248334 TATATATA
1 AATATATA
*
12248342 TATATATA
1 AATATATA
*
12248350 TATATATA
1 AATATATA
*
12248358 AATATTTA
1 AATATATA
12248366 AA
1 AA
12248368 CAAGGTGTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 39 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AATATATA
Found at i:12254657 original size:45 final size:43
Alignment explanation
Indices: 12254585--12254671 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 43
12254575 TATATATAGG
12254585 GTTAGAAGTTGTTACCTAAATTCATGTTAAACATAAAATACAT
1 GTTAGAAGTTGTTACCTAAATTCATGTTAAACATAAAATACAT
*
12254628 GTTAGAAGTTGTGTAACTTAAATTCATGTTAAACATAAAATACA
1 GTTAGAAGTTGT-T-ACCTAAATTCATGTTAAACATAAAATACA
12254672 AGTGGCAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
43 12 0.29
44 1 0.02
45 28 0.68
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (43 bp):
GTTAGAAGTTGTTACCTAAATTCATGTTAAACATAAAATACAT
Found at i:12256240 original size:34 final size:34
Alignment explanation
Indices: 12256154--12256223 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
12256144 TACAAATGGG
*
12256154 GTAACATAATATATAAAAAAATCATATATTTTAT
1 GTAACTTAATATATAAAAAAATCATATATTTTAT
12256188 GTAACTTAATATATAAAAAAATCATATATTTTAT
1 GTAACTTAATATATAAAAAAATCATATATTTTAT
12256222 GT
1 GT
12256224 TTACATTACT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (34 bp):
GTAACTTAATATATAAAAAAATCATATATTTTAT
Found at i:12257568 original size:2 final size:2
Alignment explanation
Indices: 12257561--12257590 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12257551 TCACAGTTTA
12257561 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
12257591 GTTAAATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12260653 original size:19 final size:20
Alignment explanation
Indices: 12260616--12260656 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
12260606 TACAACACAA
*
12260616 TTCAATTTCATATTGAATAT
1 TTCAATTTCATATTCAATAT
*
12260636 TTCAATTT-TTATTCAATAT
1 TTCAATTTCATATTCAATAT
12260655 TT
1 TT
12260657 GCCTAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (20 bp):
TTCAATTTCATATTCAATAT
Found at i:12263330 original size:29 final size:30
Alignment explanation
Indices: 12263273--12263330 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
12263263 CACCCTTAAA
* * * *
12263273 ATATTTGCACTCTTAGTCCTTCAACTTTTC
1 ATATTTACACTCTTAATCCCTCAAATTTTC
12263303 ATATTTACACT-TTAATCCCTCAAATTTT
1 ATATTTACACTCTTAATCCCTCAAATTTT
12263331 GAGTAGTTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.26, C:0.24, G:0.03, T:0.47
Consensus pattern (30 bp):
ATATTTACACTCTTAATCCCTCAAATTTTC
Found at i:12269909 original size:2 final size:2
Alignment explanation
Indices: 12269904--12269941 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
12269894 TATATTCATA
12269904 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
12269942 CAATTCAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12270227 original size:19 final size:20
Alignment explanation
Indices: 12270190--12270230 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
12270180 TACAACACAA
*
12270190 TTCAATTTCATATTGAATAT
1 TTCAATTTCATATTCAATAT
*
12270210 TTCAATTT-TTATTCAATAT
1 TTCAATTTCATATTCAATAT
12270229 TT
1 TT
12270231 GCCTAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (20 bp):
TTCAATTTCATATTCAATAT
Found at i:12272470 original size:5 final size:5
Alignment explanation
Indices: 12272460--12272493 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
12272450 TATCACCGCG
*
12272460 TATCA TATCA TATCA TATAA TATCA TA-CA TATCA
1 TATCA TATCA TATCA TATCA TATCA TATCA TATCA
12272494 AAAGAAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (5 bp):
TATCA
Found at i:12275210 original size:7 final size:7
Alignment explanation
Indices: 12275198--12275222 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12275188 GAAAATACTC
12275198 AAAATTG
1 AAAATTG
12275205 AAAATTG
1 AAAATTG
12275212 AAAATTG
1 AAAATTG
12275219 AAAA
1 AAAA
12275223 AGTTGGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (7 bp):
AAAATTG
Found at i:12282555 original size:42 final size:42
Alignment explanation
Indices: 12282496--12282580 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
12282486 TGTGGAGTGA
*
12282496 AAATAGGTTTGGTTAAAGCTGCATTTCTCACCCTCCACAAGC
1 AAATAGGCTTGGTTAAAGCTGCATTTCTCACCCTCCACAAGC
12282538 AAATAGGCTTGGTTAAAGCTGCATTTCTCACCCTCCACAAGC
1 AAATAGGCTTGGTTAAAGCTGCATTTCTCACCCTCCACAAGC
12282580 A
1 A
12282581 TACTTAAACA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.27
Consensus pattern (42 bp):
AAATAGGCTTGGTTAAAGCTGCATTTCTCACCCTCCACAAGC
Found at i:12285079 original size:33 final size:29
Alignment explanation
Indices: 12285019--12285077 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
12285009 TGTACGTACC
*
12285019 TGCATTGCTTAATTTATTTACACTTTCTT
1 TGCATTGCTTAATTCATTTACACTTTCTT
12285048 TGCATTGCTTAATTCATTTACACTTTCTT
1 TGCATTGCTTAATTCATTTACACTTTCTT
12285077 T
1 T
12285078 CTCGACTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.20, C:0.19, G:0.07, T:0.54
Consensus pattern (29 bp):
TGCATTGCTTAATTCATTTACACTTTCTT
Found at i:12285295 original size:43 final size:43
Alignment explanation
Indices: 12285248--12285358 Score: 159
Period size: 43 Copynumber: 2.6 Consensus size: 43
12285238 TCGATGTCCC
* *
12285248 ACACATGGTCTTACACGTAATCGCAATACAATGCCACTATCCA
1 ACACAAGGTCTTACACGTAATCACAATACAATGCCACTATCCA
* * * *
12285291 ACACAGGGTCTTTCACGTAATCACAATACAATGCCACTGTCCC
1 ACACAAGGTCTTACACGTAATCACAATACAATGCCACTATCCA
*
12285334 ACACAAGGTCTTACATGTAATCACA
1 ACACAAGGTCTTACACGTAATCACA
12285359 TCTCGATAAC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.34, C:0.30, G:0.13, T:0.23
Consensus pattern (43 bp):
ACACAAGGTCTTACACGTAATCACAATACAATGCCACTATCCA
Found at i:12291356 original size:24 final size:24
Alignment explanation
Indices: 12291324--12291372 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
12291314 GTAGTGTTTG
12291324 TGATGTTAACCACAGAATCGATCT
1 TGATGTTAACCACAGAATCGATCT
12291348 TGATGTTAACCACAGAATCGATCT
1 TGATGTTAACCACAGAATCGATCT
12291372 T
1 T
12291373 CCACCAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (24 bp):
TGATGTTAACCACAGAATCGATCT
Found at i:12295482 original size:22 final size:21
Alignment explanation
Indices: 12295444--12295484 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
12295434 AGTTTAAATC
12295444 GTAAAATAAATAAATATATCG
1 GTAAAATAAATAAATATATCG
12295465 GTAAATATAAA-AATATATAT
1 GTAAA-ATAAATAA-ATATAT
12295485 AATTATAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (21 bp):
GTAAAATAAATAAATATATCG
Found at i:12296753 original size:16 final size:16
Alignment explanation
Indices: 12296729--12296765 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
12296719 TTATTTCATC
*
12296729 AACCACGTCAATTTTT
1 AACCTCGTCAATTTTT
*
12296745 AACCTCGTCAGTTTTT
1 AACCTCGTCAATTTTT
12296761 AACCT
1 AACCT
12296766 ACAAATTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.38
Consensus pattern (16 bp):
AACCTCGTCAATTTTT
Found at i:12302330 original size:19 final size:20
Alignment explanation
Indices: 12302289--12302331 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
12302279 CTACTTTTTG
* *
12302289 CATT-CATTTCATTCATCTG
1 CATTACATTTCATTCATATA
12302308 CATTACATTTCA-TCATATA
1 CATTACATTTCATTCATATA
12302327 CATTA
1 CATTA
12302332 AGTTTCATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.30, C:0.23, G:0.02, T:0.44
Consensus pattern (20 bp):
CATTACATTTCATTCATATA
Found at i:12305307 original size:40 final size:40
Alignment explanation
Indices: 12305252--12305478 Score: 332
Period size: 40 Copynumber: 5.7 Consensus size: 40
12305242 TGAATGATAC
* * * *
12305252 CCGGGCTAAGCCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATAT
12305292 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
* *
12305332 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
12305372 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
* * *
12305412 CTGGGTTAAGACCCGAAAGCATTTGTGCGAGTTGCTATA-
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
* *
12305451 CCGGGTTAAGACCCGAAGGCAATTGTGC
1 CCGGGCTAAGACCCGAAGGCATTTGTGC
12305479 TTGTGGTTAT
Statistics
Matches: 172, Mismatches: 14, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
39 25 0.15
40 145 0.84
41 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
Done.