Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000186.1 Hibiscus syriacus cultivar Beakdansim tig00000329_pilon, whole genome shotgun sequence
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: 3152351
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 16 of 17
Found at i:2858020 original size:41 final size:41
Alignment explanation
Indices: 2857970--2858052 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
2857960 ACTCGTTTTT
2857970 CTCGATCCATCTCTGTTGAACCCGACTCCACTTCTCTAATG
1 CTCGATCCATCTCTGTTGAACCCGACTCCACTTCTCTAATG
2858011 CTCGATCCATCTCTGTTGAACCCGACTCCACTTCTCTAATG
1 CTCGATCCATCTCTGTTGAACCCGACTCCACTTCTCTAATG
2858052 C
1 C
2858053 GTTTGTATGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.19, C:0.37, G:0.12, T:0.31
Consensus pattern (41 bp):
CTCGATCCATCTCTGTTGAACCCGACTCCACTTCTCTAATG
Found at i:2866981 original size:276 final size:275
Alignment explanation
Indices: 2866424--2867010 Score: 994
Period size: 276 Copynumber: 2.1 Consensus size: 275
2866414 TTGTCCGAAG
* * * *
2866424 CTGAAGAAGAAAGGAAAAGCTGCTCTAGATGTATGTATTGCAGAGCATGATGCAAATGACTTTGA
1 CTGAAGAAGAAAGGAAAAGCTGCTCCATATGTATGTATTGCAGAGCATGATGAAAATGACTCTGA
2866489 CATATCATTGGTTGCTTCATCAACAAAATTCCATTCAGATGAATGGATATTAGATTCGGGTTGCA
66 CATATCATTGGTTGCTTCATCAACAAAATTCCATTCAGATGAATGGATATTAGATTCGGGTTGCA
*
2866554 CATATCATATGCCCCTAATCGGGAGTGGTTCTCCGATTTAGTAGAACTAAATGTAGGAGTTGTTT
131 CATATCATATGCCCCTAATCGGGAGTGGTTCTCCGATTTAGTAGAACTAAATGCAGGAGTTGTTT
2866619 ATATGGGCAATGACAATGCCTGTAAAACTGTTGGGATAGGTTCAATTCGATTGAAGAATCAAGAT
196 ATATGGGCAATGACAATGCCTGTAAAACTGTTGGGATAGGTTCAATTCGATTGAAGAATCAAGAT
2866684 GGATCAACTAGAGTC
261 GGATCAACTAGAGTC
*
2866699 CTGAAGAAGAAAGGAAAAGCTGCTCCATATGTATGTATTGCAGATCATGATGAAAATGACTCTGA
1 CTGAAGAAGAAAGGAAAAGCTGCTCCATATGTATGTATTGCAGAGCATGATGAAAATGACTCTGA
* * *
2866764 CATATCATTGGTTGCTTCATCAATAACATTCCATTCAGATGAATGTATATTAGATTCGGGTTGCA
66 CATATCATTGGTTGCTTCATCAACAAAATTCCATTCAGATGAATGGATATTAGATTCGGGTTGCA
* *
2866829 CCTATCATATGTCCCCTAATCGGGAGTGGTTCTCTGATTTAGTAGAACTAAATGCAGGAGTTGTT
131 CATATCATATG-CCCCTAATCGGGAGTGGTTCTCCGATTTAGTAGAACTAAATGCAGGAGTTGTT
* * * *
2866894 TATATGGGCAATGACAATGCCTGTAAAACTGTTGGTATAGGTTTAATTCGATTGAAGAATCGATA
195 TATATGGGCAATGACAATGCCTGTAAAACTGTTGGGATAGGTTCAATTCGATTGAAGAATCAAGA
*
2866959 TGGATCAACTAGAGTT
260 TGGATCAACTAGAGTC
* * *
2866975 CTGAAGAAGAAAGAAAAAGCTACTCCATATGCATGT
1 CTGAAGAAGAAAGGAAAAGCTGCTCCATATGTATGT
2867011 TGTTAGGATT
Statistics
Matches: 292, Mismatches: 19, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
275 132 0.45
276 160 0.55
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (275 bp):
CTGAAGAAGAAAGGAAAAGCTGCTCCATATGTATGTATTGCAGAGCATGATGAAAATGACTCTGA
CATATCATTGGTTGCTTCATCAACAAAATTCCATTCAGATGAATGGATATTAGATTCGGGTTGCA
CATATCATATGCCCCTAATCGGGAGTGGTTCTCCGATTTAGTAGAACTAAATGCAGGAGTTGTTT
ATATGGGCAATGACAATGCCTGTAAAACTGTTGGGATAGGTTCAATTCGATTGAAGAATCAAGAT
GGATCAACTAGAGTC
Found at i:2867625 original size:21 final size:21
Alignment explanation
Indices: 2867599--2867640 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2867589 CCAGAATGGG
*
2867599 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
2867620 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
2867641 ATATTCAAAT
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:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:2867770 original size:19 final size:19
Alignment explanation
Indices: 2867746--2867812 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
2867736 GAGCCTCGGG
*
2867746 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAACAGTAAT
*
2867765 TTACTGTTCAAATAGTAAT
1 TTACTGTTCAAACAGTAAT
* *
2867784 TTACTGTTCAAATAGTAAA
1 TTACTGTTCAAACAGTAAT
*
2867803 TTACTATTCA
1 TTACTGTTCA
2867813 TAAAAACATT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.40
Consensus pattern (19 bp):
TTACTGTTCAAACAGTAAT
Found at i:2867888 original size:31 final size:31
Alignment explanation
Indices: 2867814--2867888 Score: 125
Period size: 31 Copynumber: 2.4 Consensus size: 31
2867804 TACTATTCAT
*
2867814 AAAAA-CATTTTTGTGAATTCAATTCAAGTCC
1 AAAAACCA-TTTTGTAAATTCAATTCAAGTCC
2867845 AAAAACCATTTTGTAAATTCAATTCAAGTCC
1 AAAAACCATTTTGTAAATTCAATTCAAGTCC
2867876 AAAAACCATTTTG
1 AAAAACCATTTTG
2867889 CCTTAAATTG
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
31 40 0.95
32 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.33
Consensus pattern (31 bp):
AAAAACCATTTTGTAAATTCAATTCAAGTCC
Found at i:2868084 original size:24 final size:24
Alignment explanation
Indices: 2868051--2868099 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2868041 AAGCTCCCCC
2868051 TTTTTCATTAAGAAATTGAATTTT
1 TTTTTCATTAAGAAATTGAATTTT
*
2868075 TTTTTTATTAAGAAATTGAATTTT
1 TTTTTCATTAAGAAATTGAATTTT
2868099 T
1 T
2868100 CAAACCAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (24 bp):
TTTTTCATTAAGAAATTGAATTTT
Found at i:2871512 original size:21 final size:20
Alignment explanation
Indices: 2871444--2871525 Score: 67
Period size: 21 Copynumber: 3.9 Consensus size: 20
2871434 TTGGTGCAGA
*
2871444 GGGAATCGA-TCCCCCCAATG
1 GGGAACCGATTCCCCCCAA-G
*
2871464 AGGGAACCGATTCCCCCTTTGAAG
1 -GGGAACCGATTCCCCC---CAAG
2871488 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCA-AG
* *
2871509 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
2871526 TGGGGTTCTG
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
20 1 0.02
21 25 0.49
22 6 0.12
23 16 0.31
24 1 0.02
25 2 0.04
ACGTcount: A:0.24, C:0.37, G:0.24, T:0.15
Consensus pattern (20 bp):
GGGAACCGATTCCCCCCAAG
Found at i:2879786 original size:4 final size:4
Alignment explanation
Indices: 2879777--2879809 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
2879767 TAAACATTCT
2879777 CATA CATA CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA CATA CATA C
2879810 GAAAATCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:2883720 original size:24 final size:24
Alignment explanation
Indices: 2883693--2883764 Score: 78
Period size: 23 Copynumber: 3.0 Consensus size: 24
2883683 TATCAGTTCT
2883693 TAAACATGTCTATTTATATATTCA
1 TAAACATGTCTATTTATATATTCA
* *
2883717 TAAACATG-CTAGTTTAAAT-TTTA
1 TAAACATGTCTA-TTTATATATTCA
*
2883740 TGAACATGATC-ATTTATATATTCA
1 TAAACATG-TCTATTTATATATTCA
2883764 T
1 T
2883765 TTAATGTTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
23 19 0.49
24 19 0.49
25 1 0.03
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (24 bp):
TAAACATGTCTATTTATATATTCA
Found at i:2889387 original size:24 final size:24
Alignment explanation
Indices: 2889359--2889471 Score: 74
Period size: 24 Copynumber: 5.3 Consensus size: 24
2889349 AGACAAAGCC
2889359 ATGGAATTTAATAATTAAAGCACT
1 ATGGAATTTAATAATTAAAGCACT
* * *
2889383 ATGGAA--T-A-GA-CAAATC-C-
1 ATGGAATTTAATAATTAAAGCACT
2889400 ATGGAATTTAATAATTAAAGCACT
1 ATGGAATTTAATAATTAAAGCACT
* * *
2889424 ATGGAA--T-A-GA-CAAATC-C-
1 ATGGAATTTAATAATTAAAGCACT
2889441 ATGGAATTTAATAATTAAAGCACT
1 ATGGAATTTAATAATTAAAGCACT
2889465 ATGGAAT
1 ATGGAAT
2889472 AAGACAAAGC
Statistics
Matches: 63, Mismatches: 12, Indels: 28
0.61 0.12 0.27
Matches are distributed among these distances:
17 12 0.19
18 2 0.03
19 10 0.16
20 4 0.06
21 4 0.06
22 10 0.16
23 2 0.03
24 19 0.30
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.28
Consensus pattern (24 bp):
ATGGAATTTAATAATTAAAGCACT
Found at i:2889406 original size:41 final size:41
Alignment explanation
Indices: 2889349--2889485 Score: 247
Period size: 41 Copynumber: 3.3 Consensus size: 41
2889339 TGAAGGTAGA
2889349 AGACAAAGCCATGGAATTTAATAATTAAAGCACTATGGAAT
1 AGACAAAGCCATGGAATTTAATAATTAAAGCACTATGGAAT
*
2889390 AGACAAATCCATGGAATTTAATAATTAAAGCACTATGGAAT
1 AGACAAAGCCATGGAATTTAATAATTAAAGCACTATGGAAT
*
2889431 AGACAAATCCATGGAATTTAATAATTAAAGCACTATGGAAT
1 AGACAAAGCCATGGAATTTAATAATTAAAGCACTATGGAAT
2889472 AAGACAAAGCCATG
1 -AGACAAAGCCATG
2889486 AAACTCCATT
Statistics
Matches: 93, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
41 81 0.87
42 12 0.13
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (41 bp):
AGACAAAGCCATGGAATTTAATAATTAAAGCACTATGGAAT
Found at i:2890612 original size:18 final size:19
Alignment explanation
Indices: 2890591--2890626 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
2890581 TCTAATTCAC
2890591 TTATCAAAATTAA-TTTTT
1 TTATCAAAATTAACTTTTT
2890609 TTATCAAAATTAACTTTT
1 TTATCAAAATTAACTTTT
2890627 AACTATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATCAAAATTAACTTTTT
Found at i:2890842 original size:17 final size:17
Alignment explanation
Indices: 2890810--2890843 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2890800 TAACTTTAAC
* *
2890810 TTATTATTATTTAAAAT
1 TTATTATTAATAAAAAT
2890827 TTATTATTAATAAAAAT
1 TTATTATTAATAAAAAT
2890844 ATGAAAAAAC
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATTATTAATAAAAAT
Found at i:2890907 original size:16 final size:15
Alignment explanation
Indices: 2890878--2890911 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
2890868 CAATCGAGTA
2890878 TTTTTAATAAATATT
1 TTTTTAATAAATATT
*
2890893 TTTTTATATATATATT
1 TTTTTA-ATAAATATT
2890909 TTT
1 TTT
2890912 AAAATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTTAATAAATATT
Found at i:2897478 original size:38 final size:38
Alignment explanation
Indices: 2897436--2897580 Score: 229
Period size: 38 Copynumber: 3.8 Consensus size: 38
2897426 GATTTGTTTC
* *
2897436 CTTAAAATAACTATGCTTTTAAATTACGGATGCGGTTA
1 CTTAAAATAACTATGCTTTTAAATTGCGGATGTGGTTA
*
2897474 CTTAAAATAACTATGCTTTTAAATTGCGGACGTGGTTA
1 CTTAAAATAACTATGCTTTTAAATTGCGGATGTGGTTA
*
2897512 CTTAAAATAAATATGCTTTTAAATTGCGGATGTGGTTA
1 CTTAAAATAACTATGCTTTTAAATTGCGGATGTGGTTA
*
2897550 CTTAAAATAA-TAATGATTTTAAATTGCGGAT
1 CTTAAAATAACT-ATGCTTTTAAATTGCGGAT
2897581 TCGAGCACGA
Statistics
Matches: 100, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
37 1 0.01
38 99 0.99
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (38 bp):
CTTAAAATAACTATGCTTTTAAATTGCGGATGTGGTTA
Found at i:2897739 original size:14 final size:14
Alignment explanation
Indices: 2897704--2897733 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2897694 TATCTTTGAA
*
2897704 TATATACTCTATTG
1 TATATACTATATTG
2897718 TATATACTATATTG
1 TATATACTATATTG
2897732 TA
1 TA
2897734 CTTACTTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (14 bp):
TATATACTATATTG
Found at i:2902106 original size:24 final size:24
Alignment explanation
Indices: 2902074--2902122 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2902064 AGTCTTCCTG
2902074 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
2902098 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
2902122 A
1 A
2902123 ATATCATGTA
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:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:2903622 original size:26 final size:26
Alignment explanation
Indices: 2903593--2903651 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
2903583 TTATTCATCT
2903593 TTCATTATAATTTAATGAATTTTTAA
1 TTCATTATAATTTAATGAATTTTTAA
2903619 TTCATTATAATTTAATGAATTTTTAA
1 TTCATTATAATTTAATGAATTTTTAA
2903645 TTCATTA
1 TTCATTA
2903652 AATGCTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.54
Consensus pattern (26 bp):
TTCATTATAATTTAATGAATTTTTAA
Found at i:2918637 original size:112 final size:112
Alignment explanation
Indices: 2918309--2918881 Score: 918
Period size: 112 Copynumber: 5.1 Consensus size: 112
2918299 TTGTCGGTTT
** *
2918309 GTGTCGATACTTTATAAAAATATATTAATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
2918374 GGTATATAAATAACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
* *
2918421 GTGTCAATACTTTATAAAAATATATTGATCCATAACAATAT-ACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
2918485 GGTCTATAAATGACAAAACAAGTAAAGCGCTACC-GAATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAG-ATATATTGAAA
*
2918532 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAATAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
2918597 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
* * *
2918644 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAAAATAACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
2918709 GGTCTATAAATGACAAAACAGGTAAAACGCTACCAGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
** *
2918756 GTGTCGATACTTTATAAAAATGCATCGATCCATAACAATATAACAGGT-AAAAATTGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* ** * *
2918820 GGTCTATAAATGACAAAACAGATAAAGCGCTACTGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
2918867 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
2918882 TATAAGTATA
Statistics
Matches: 433, Mismatches: 25, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
110 1 0.00
111 173 0.40
112 258 0.60
113 1 0.00
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
Found at i:2918816 original size:223 final size:223
Alignment explanation
Indices: 2918309--2918881 Score: 925
Period size: 223 Copynumber: 2.6 Consensus size: 223
2918299 TTGTCGGTTT
** *
2918309 GTGTCGATACTTTATAAAAATATATTAATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
2918374 GGTATATAAATAACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCAATACTTTATAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
* *
2918439 AATATATTGATCCATAACAATATACAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAAAC
131 AATATATCGATCCATAACAATATACAGGTAAAAAAATAACAAAACCGGTCTATAAATGACAAAAC
*
2918504 AAGTAAAGCGCTACCGAATATATTGAAA
196 AAGTAAAACGCTACCGAATATATTGAAA
*
2918532 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAATAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
2918597 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTATAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
* *
2918662 AATGTATCGATCCATAACAATATAACATGTAAAAAAATAACAAAACCGGTCTATAAATGACAAAA
131 AATATATCGATCCATAACAATAT-ACAGGTAAAAAAATAACAAAACCGGTCTATAAATGACAAAA
*
2918727 CAGGTAAAACGCTACC-AGATATATTGAAA
195 CAAGTAAAACGCTACCGA-ATATATTGAAA
** *
2918756 GTGTCGATACTTTATAAAAATGCATCGATCCATAACAATATAACAGGT-AAAAATTGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * * *
2918820 GGTCTATAAATGACAAAACAGATAAAGCGCTACTGGATATGTTGATAGTGTCGATACTTTAT
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAT
2918882 TATAAGTATA
Statistics
Matches: 325, Mismatches: 23, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
223 216 0.66
224 109 0.34
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (223 bp):
GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
AATATATCGATCCATAACAATATACAGGTAAAAAAATAACAAAACCGGTCTATAAATGACAAAAC
AAGTAAAACGCTACCGAATATATTGAAA
Found at i:2919063 original size:182 final size:182
Alignment explanation
Indices: 2918753--2919207 Score: 741
Period size: 182 Copynumber: 2.5 Consensus size: 182
2918743 AGATATATTG
* *
2918753 AAAGTGTCGATACTTTATAAAAATGCATCGATCCATAACAATATAACAGGTAAAAAT-TGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAA
** * * ** * *
2918817 ACCGGTCTATAAATGACAAAACAGATAAAGCGCTACTGGATATGTTGATAGTGTCGATACTTTAT
66 ACCGGTCTCGAAATGACAAAACCGGTAAAGAACTACCGGATATGTTGAAAGTGTCGATACTTTAT
* * *
2918882 TATAAGTATAGACACTTTTGGAATTTAAAAGAGAATAAGTTATAACGCTAAT
131 TATAAGTATAGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAACGCCAAT
*
2918934 AAAGTGTTGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAA
2918999 ACCGGTCTCGAAATGACAAAACCGGTAAAGAACTACCGGATATGTTGAAAGTGTCGATACTTTAT
66 ACCGGTCTCGAAATGACAAAACCGGTAAAGAACTACCGGATATGTTGAAAGTGTCGATACTTTAT
* *
2919064 TATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
131 TATAAGTATAGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAACGCCAAT
2919116 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAA
* *
2919181 ATCGATCTCGAAATGACAAAACCGGTA
66 ACCGGTCTCGAAATGACAAAACCGGTA
2919208 GTAAAAAAGT
Statistics
Matches: 254, Mismatches: 19, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
181 54 0.21
182 200 0.79
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (182 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAA
ACCGGTCTCGAAATGACAAAACCGGTAAAGAACTACCGGATATGTTGAAAGTGTCGATACTTTAT
TATAAGTATAGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAACGCCAAT
Found at i:2920434 original size:29 final size:28
Alignment explanation
Indices: 2920401--2920476 Score: 95
Period size: 29 Copynumber: 2.8 Consensus size: 28
2920391 TCATTTGAAT
2920401 ATTATTTATATTTTATTATTATTATTATA
1 ATTATTTATATTTTATTATTATTATTA-A
*
2920430 ATTA-TTATTATATTATTATTATTATTAA
1 ATTATTTA-TATTTTATTATTATTATTAA
*
2920458 ATAATTT-TA-TTTATTATTA
1 ATTATTTATATTTTATTATTA
2920477 AAGACCCAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
26 9 0.21
27 2 0.05
28 7 0.17
29 24 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (28 bp):
ATTATTTATATTTTATTATTATTATTAA
Found at i:2920438 original size:26 final size:25
Alignment explanation
Indices: 2920409--2920476 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 25
2920399 ATATTATTTA
2920409 TATTTTATTATTATTATTA-TAATTAT
1 TATTTTATTATTATTATTATTAA--AT
*
2920435 TATTATATTATTATTATTATTAAAT
1 TATTTTATTATTATTATTATTAAAT
*
2920460 AATTTTATTTATTATTA
1 TATTTTA-TTATTATTA
2920477 AAGACCCAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 7 0.19
26 27 0.73
27 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TATTTTATTATTATTATTATTAAAT
Found at i:2920476 original size:3 final size:3
Alignment explanation
Indices: 2920400--2920456 Score: 75
Period size: 3 Copynumber: 19.7 Consensus size: 3
2920390 TTCATTTGAA
*
2920400 TAT TAT T-T ATAT T-T TAT TAT TAT TAT TAT AAT TAT TAT TA- TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2920443 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
2920457 AATAATTTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
2 5 0.10
3 42 0.88
4 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2920939 original size:28 final size:27
Alignment explanation
Indices: 2920887--2920940 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
2920877 AGAGAGGAAG
*
2920887 AATCCAAGAGACAACACCAGCAACCAA
1 AATCCAAGAGACAACACCAGAAACCAA
*
2920914 AATCCGAGAGAACAACAACCA-AAACCA
1 AATCCAAGAG-ACAAC-ACCAGAAACCA
2920941 CCAAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 9 0.39
28 10 0.43
29 4 0.17
ACGTcount: A:0.54, C:0.31, G:0.11, T:0.04
Consensus pattern (27 bp):
AATCCAAGAGACAACACCAGAAACCAA
Found at i:2921783 original size:25 final size:25
Alignment explanation
Indices: 2921713--2921783 Score: 62
Period size: 25 Copynumber: 2.9 Consensus size: 25
2921703 AGTCATTAAC
*
2921713 TTTAAATTAT-TA-GTTTATTA-TT
1 TTTAATTTATATATGTTTATTATTT
*
2921735 TTTAATTTCATTTAT-TTTAGTTATTGT
1 TTTAATTT-ATATATGTTTA-TTATT-T
2921762 TTTAATTT-TATATGTTTATTAT
1 TTTAATTTATATATGTTTATTAT
2921784 CAATATATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
22 7 0.17
23 2 0.05
24 6 0.15
25 11 0.28
26 5 0.12
27 9 0.22
ACGTcount: A:0.27, C:0.01, G:0.06, T:0.66
Consensus pattern (25 bp):
TTTAATTTATATATGTTTATTATTT
Found at i:2933708 original size:18 final size:18
Alignment explanation
Indices: 2933685--2933719 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2933675 CAAGTTTATC
2933685 TTTTTGAAATTCAATTTA
1 TTTTTGAAATTCAATTTA
2933703 TTTTTGAAATTCAATTT
1 TTTTTGAAATTCAATTT
2933720 GTTTCATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (18 bp):
TTTTTGAAATTCAATTTA
Found at i:2935075 original size:123 final size:123
Alignment explanation
Indices: 2934895--2935541 Score: 685
Period size: 123 Copynumber: 5.5 Consensus size: 123
2934885 TATTCGATGG
* *
2934895 ATCAACTTTTCC-G-GAATAATTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCA
1 ATCAACTTTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
*
2934958 TAATGAGAAGAGCTTGTTCAACCTTTCGCATGACTCTATCACAGAATGAGATAGATCAAC
65 TAATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAG-ATGAGATAGATCAAC
2935018 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT-AAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * * * * * * *
2935082 TATGTGAAGAACTTGTTTAACCTTTTGC-TCAAAT-TCATCAC---T-TGATGGAT---C
66 AATGAGAAGAGCTTGTTCAACCTTTTGCAT-GACTCT-ATCACAGATGAGATAGATCAAC
* * *
2935133 AGC-A--TTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
** ** * * *
2935195 AATGAGAAGAATTTGTTCAAACCTTTTGTTTGA--AT-TCATC--AT----TCGAT--AG
66 AATGAGAAGAGCTTGTTC-AACCTTTTGCATGACTCTATCA-CAGATGAGATAGATCAAC
*
2935244 ATCAACTTTTCCAGAG-AAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * * *
2935307 AATGAGAAGAGCTTGTTCAACCTTTTGTATGACTCTATCACAGAAGGAGATAAATCAGC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAG-ATGAGATAGATCAAC
* * *
2935366 ATCAACTTTTCCAAAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAATAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * *
2935431 AATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCATAG--GAGATAGAACATC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGATGAGATAGATCAAC
**
2935487 ATCAACATTTT-CAGA-AGTGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAG
1 ATCAAC-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
2935542 CAGAACGTAT
Statistics
Matches: 446, Mismatches: 49, Indels: 62
0.80 0.09 0.11
Matches are distributed among these distances:
110 4 0.01
111 18 0.04
112 69 0.15
113 66 0.15
114 23 0.05
115 4 0.01
116 1 0.00
118 6 0.01
119 9 0.02
120 31 0.07
121 19 0.04
122 21 0.05
123 91 0.20
124 81 0.18
125 3 0.01
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (123 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGATGAGATAGATCAAC
Found at i:2935154 original size:112 final size:112
Alignment explanation
Indices: 2935018--2935458 Score: 451
Period size: 112 Copynumber: 3.8 Consensus size: 112
2935008 ATAGATCAAC
*
2935018 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT-AAGAAGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * * *
2935082 TATGTGAAGAACTTGTTTAACCTTTTGCTCAAATTCATCACTT-GATGG
65 AATGAGAAGAACTTGTTAAACCTTTTGCTCAAATTCATCA-TTCGATAG
* *
2935130 ATCAGCATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCAT
1 ATCAACATTTCCAGAGA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * **
2935195 AATGAGAAGAATTTGTTCAAACCTTTTGTTTGAATTCATCATTCGATAG
65 AATGAGAAGAACTTGTT-AAACCTTTTGCTCAAATTCATCATTCGATAG
* *
2935244 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
* * * * * **
2935308 ATGAGAAGAGCTTGTTCAACCTTTTG-T-ATGACTCTATCACAGAAGGAGATAAATCAG
66 ATGAGAAGAACTTGTTAAACCTTTTGCTCA-AATTC-AT--C------A-TTCGAT-AG
* * * *
2935365 CATCAACTTTTCCAAAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAATAAGAAGTTCA
1 -ATCAACATTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* *
2935430 TAATGAGAAGAGCTTGTTCAACCTTTTGC
64 TAATGAGAAGAACTTGTTAAACCTTTTGC
2935459 ATGACTCTAT
Statistics
Matches: 281, Mismatches: 28, Indels: 27
0.84 0.08 0.08
Matches are distributed among these distances:
110 4 0.01
111 12 0.04
112 70 0.25
113 65 0.23
114 38 0.14
119 1 0.00
120 3 0.01
121 2 0.01
122 15 0.05
123 28 0.10
124 43 0.15
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.28
Consensus pattern (112 bp):
ATCAACATTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTAAACCTTTTGCTCAAATTCATCATTCGATAG
Found at i:2935435 original size:124 final size:119
Alignment explanation
Indices: 2935244--2935541 Score: 424
Period size: 124 Copynumber: 2.5 Consensus size: 119
2935234 CATTCGATAG
*
2935244 ATCAACTTTTCC-AGAGAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAAGA-AAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
*
2935308 ATGAGAAGAGCTTGTTCAACCTTTTGTATGACTCTATCACAGAAGGAGATA-AATCAGC
65 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTAT--CA-AAGGAGATAGAA-CAGC
* *
2935366 ATCAACTTTTCCAAAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAATAAGAAGTTCAT
1 ATCAACTTTTCC-AAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCAT
* *
2935431 AATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCATAGGAGATAGAACATC
64 AATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCAAAGGAGATAGAACAGC
*
2935487 ATCAACATTTT-C-AGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAG
1 ATCAAC-TTTTCCAAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAG
2935542 CAGAACGTAT
Statistics
Matches: 161, Mismatches: 9, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
119 12 0.07
120 27 0.17
121 18 0.11
122 20 0.12
123 28 0.17
124 56 0.35
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (119 bp):
ATCAACTTTTCCAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCAAAGGAGATAGAACAGC
Found at i:2935787 original size:3 final size:3
Alignment explanation
Indices: 2935781--2935848 Score: 99
Period size: 3 Copynumber: 23.7 Consensus size: 3
2935771 TTCATTTGAA
2935781 TAT TAT T-T ATAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2935825 TAT TA- TAT TA- TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
2935849 AATAATTTTA
Statistics
Matches: 60, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
2 7 0.12
3 52 0.87
4 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2935859 original size:16 final size:19
Alignment explanation
Indices: 2935798--2935866 Score: 83
Period size: 18 Copynumber: 3.8 Consensus size: 19
2935788 TATATTTTAT
*
2935798 TATTATTATTATTATTAT-
1 TATTATTATTATTATAATA
*
2935816 TATTATTATTATTATATTA
1 TATTATTATTATTATAATA
2935835 TATTATTATTATTA-AATA
1 TATTATTATTATTATAATA
2935853 -ATT-TTATTCATTAT
1 TATTATTATT-ATTAT
2935867 TACAGACCCA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
16 5 0.11
17 7 0.16
18 19 0.42
19 14 0.31
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTATTATTATTATAATA
Found at i:2937175 original size:25 final size:25
Alignment explanation
Indices: 2937105--2937175 Score: 62
Period size: 25 Copynumber: 2.9 Consensus size: 25
2937095 AGTCCTTAAC
*
2937105 TTTAAATTAT-TA-GTTTATTA-TT
1 TTTAATTTATATATGTTTATTATTT
*
2937127 TTTAATTTCATTTAT-TTTAGTTATTGT
1 TTTAATTT-ATATATGTTTA-TTATT-T
2937154 TTTAATTT-TATATGTTTATTAT
1 TTTAATTTATATATGTTTATTAT
2937176 CAATATATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
22 7 0.17
23 2 0.05
24 6 0.15
25 11 0.28
26 5 0.12
27 9 0.22
ACGTcount: A:0.27, C:0.01, G:0.06, T:0.66
Consensus pattern (25 bp):
TTTAATTTATATATGTTTATTATTT
Found at i:2940015 original size:3 final size:3
Alignment explanation
Indices: 2940007--2940094 Score: 176
Period size: 3 Copynumber: 29.3 Consensus size: 3
2939997 TATTTATTTT
2940007 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2940055 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2940095 GCCATAGATG
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2945118 original size:29 final size:29
Alignment explanation
Indices: 2945084--2945142 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2945074 CCTAAATTAA
2945084 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
2945113 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
2945142 T
1 T
2945143 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:2949775 original size:29 final size:29
Alignment explanation
Indices: 2949741--2949799 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2949731 CCTAAATTAA
2949741 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
2949770 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
2949799 T
1 T
2949800 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:2950389 original size:29 final size:29
Alignment explanation
Indices: 2950344--2950399 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
2950334 TTAAGGGCCC
2950344 CATTTTTTATATCTTTATAATTAAGGTCTT
1 CATTTTTTATATCTTTATAATT-AGGTCTT
*
2950374 CATTTTTTCAT-T-TTTATAGTTAGGTC
1 CATTTTTT-ATATCTTTATAATTAGGTC
2950400 CCTATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 5 0.21
29 8 0.33
30 9 0.38
31 2 0.08
ACGTcount: A:0.23, C:0.11, G:0.09, T:0.57
Consensus pattern (29 bp):
CATTTTTTATATCTTTATAATTAGGTCTT
Found at i:2950449 original size:42 final size:42
Alignment explanation
Indices: 2950403--2950493 Score: 94
Period size: 42 Copynumber: 2.1 Consensus size: 42
2950393 TTAGGTCCCT
* * * * *
2950403 ATTTTTTAAATATTATTTTTTGTCTTTATAATTGAGGT-TCTA
1 ATTTTTTAAATATCA-CTTTTATCGTTATAATTGAAGTATCTA
* *
2950445 ATTTTATTCAATCTCACTTTTATCGTTATAATTGAAGTATCTA
1 ATTTT-TTAAATATCACTTTTATCGTTATAATTGAAGTATCTA
2950488 ATTTTT
1 ATTTTT
2950494 CAATCCCTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
42 24 0.60
43 16 0.40
ACGTcount: A:0.27, C:0.09, G:0.08, T:0.56
Consensus pattern (42 bp):
ATTTTTTAAATATCACTTTTATCGTTATAATTGAAGTATCTA
Found at i:2950621 original size:43 final size:42
Alignment explanation
Indices: 2950425--2950621 Score: 170
Period size: 42 Copynumber: 4.6 Consensus size: 42
2950415 TTATTTTTTG
2950425 TCTTTATAATTGAGGT-TCTAATTTTATTCAATCTCACTTT-TA
1 TCTTTATAATTGAGGTCTCTAA-TTT-TTCAATCTCACTTTCTA
* * * * ** *
2950467 TCGTTATAATTGAAGTATCTAATTTTTCAATCCCTTTTTTTA
1 TCTTTATAATTGAGGTCTCTAATTTTTCAATCTCACTTTCTA
* * * *
2950509 TCTTTATAATCGATGCCTCTAATTTTGT-AATCTTACTTTCTA
1 TCTTTATAATTGAGGTCTCTAATTTT-TCAATCTCACTTTCTA
* *
2950551 ACTTT-TAATTGAGG-CCCTTAAGTTTTTTCAATCTCACTTTCTA
1 TCTTTATAATTGAGGTCTC-TAA--TTTTTCAATCTCACTTTCTA
*
2950594 TCTTTACAATTGAGGTCTCTAAGTTTTT
1 TCTTTATAATTGAGGTCTCTAA-TTTTT
2950622 TCTACCTCTA
Statistics
Matches: 122, Mismatches: 24, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
40 2 0.02
41 21 0.17
42 54 0.44
43 32 0.26
44 11 0.09
45 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.09, T:0.50
Consensus pattern (42 bp):
TCTTTATAATTGAGGTCTCTAATTTTTCAATCTCACTTTCTA
Found at i:2950675 original size:76 final size:75
Alignment explanation
Indices: 2950556--2950697 Score: 164
Period size: 76 Copynumber: 1.9 Consensus size: 75
2950546 TTCTAACTTT
* * * * *
2950556 TAATTGAGGCCCTTAAGTTTTTTCAATCTCACTTTCTATCTTTACAATTGAGG-TCTCTAAGTTT
1 TAATTGAAGCCCCTAAGTTTTTTCAATCCCACTTTCTAACTTTACAA-TGAGGCCCT-TAAGTTT
2950620 TTTCTACCTCTA
64 TTTCTACCTCTA
* *
2950632 TAATTGAAGCCCCTAA-TTTTTT-AATCCCACTTTTTTTAACTTTATAATGAGGCCCTTAAGTTT
1 TAATTGAAGCCCCTAAGTTTTTTCAATCCCAC--TTTCTAACTTTACAATGAGGCCCTTAAGTTT
2950695 TTT
64 TTT
2950698 TTCCCTTAAG
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
74 7 0.12
75 21 0.38
76 28 0.50
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (75 bp):
TAATTGAAGCCCCTAAGTTTTTTCAATCCCACTTTCTAACTTTACAATGAGGCCCTTAAGTTTTT
TCTACCTCTA
Found at i:2950713 original size:15 final size:16
Alignment explanation
Indices: 2950684--2950714 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2950674 TATAATGAGG
2950684 CCCTTAAGTTTTTTTT
1 CCCTTAAGTTTTTTTT
2950700 CCCTTAAGTTTTTTT
1 CCCTTAAGTTTTTTT
2950715 AATTTCACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.19, G:0.06, T:0.61
Consensus pattern (16 bp):
CCCTTAAGTTTTTTTT
Found at i:2950752 original size:44 final size:44
Alignment explanation
Indices: 2950704--2950871 Score: 200
Period size: 44 Copynumber: 3.9 Consensus size: 44
2950694 TTTTTTCCCT
2950704 TAAGTTTTTTTAATTTCACTTTTTACCTTTATAATTGAGGTCCA
1 TAAGTTTTTTTAATTTCACTTTTTACCTTTATAATTGAGGTCCA
2950748 TAAG--TTTTTAATTTCACTTTTTACCTTTATAATTGAGGTCCA
1 TAAGTTTTTTTAATTTCACTTTTTACCTTTATAATTGAGGTCCA
** ** * * * *
2950790 TAAGTTTTTCCAAACTCAATTTTTATCTTTATAATTGAGGCCCC
1 TAAGTTTTTTTAATTTCACTTTTTACCTTTATAATTGAGGTCCA
* * *
2950834 TAAGTTTTTTTAGTCTTGA--TTATACCTTTATAATTGAG
1 TAAGTTTTTTTAAT-TTCACTTTTTACCTTTATAATTGAG
2950872 ACTCCTATTT
Statistics
Matches: 105, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
42 42 0.40
43 17 0.16
44 44 0.42
45 2 0.02
ACGTcount: A:0.26, C:0.14, G:0.10, T:0.49
Consensus pattern (44 bp):
TAAGTTTTTTTAATTTCACTTTTTACCTTTATAATTGAGGTCCA
Found at i:2950760 original size:42 final size:42
Alignment explanation
Indices: 2950710--2950842 Score: 194
Period size: 42 Copynumber: 3.1 Consensus size: 42
2950700 CCCTTAAGTT
2950710 TTTTTAATTTCACTTTTTACCTTTATAATTGAGGTCCATAAG
1 TTTTTAATTTCACTTTTTACCTTTATAATTGAGGTCCATAAG
2950752 TTTTTAATTTCACTTTTTACCTTTATAATTGAGGTCCATAAG
1 TTTTTAATTTCACTTTTTACCTTTATAATTGAGGTCCATAAG
** * * * *
2950794 TTTTTCCAAACTCAATTTTTATCTTTATAATTGAGGCCCCTAAG
1 TTTTT--AATTTCACTTTTTACCTTTATAATTGAGGTCCATAAG
2950838 TTTTT
1 TTTTT
2950843 TTAGTCTTGA
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
42 47 0.57
44 36 0.43
ACGTcount: A:0.26, C:0.16, G:0.09, T:0.50
Consensus pattern (42 bp):
TTTTTAATTTCACTTTTTACCTTTATAATTGAGGTCCATAAG
Found at i:2950931 original size:89 final size:87
Alignment explanation
Indices: 2950769--2950932 Score: 202
Period size: 89 Copynumber: 1.9 Consensus size: 87
2950759 TTTCACTTTT
* ** * *
2950769 TACCTTTATAATTGAGGTCCATAAGTTTTTCCAAACTCAATTTTTATCTTTATAATTGAGGCCCC
1 TACCTTTATAATTGAGCTCCATAAGTTTTTCCAAACTCAATTCCTATCTTTATAATTAAGACCCC
*
2950834 TAAGTTTTTTTAGTCTTGATTA
66 TAAATTTTTTTAGTCTTGATTA
*** * *
2950856 TACCTTTATAATTGAGACTCCTATTTTTTTTTTCAATCTCAATTCCTATCTTTATAATTAAGACC
1 TACCTTTATAATTGAG-CTCC-ATAAGTTTTTCCAAACTCAATTCCTATCTTTATAATTAAGACC
*
2950921 TCTAAATTTTTT
64 CCTAAATTTTTT
2950933 CAATTTAATA
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
87 16 0.25
88 3 0.05
89 44 0.70
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (87 bp):
TACCTTTATAATTGAGCTCCATAAGTTTTTCCAAACTCAATTCCTATCTTTATAATTAAGACCCC
TAAATTTTTTTAGTCTTGATTA
Found at i:2956152 original size:16 final size:16
Alignment explanation
Indices: 2956131--2956163 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2956121 CGTATCGCCG
*
2956131 ACAAAATTTACTATTC
1 ACAAAATATACTATTC
2956147 ACAAAATATACTATTC
1 ACAAAATATACTATTC
2956163 A
1 A
2956164 TGTGAATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.33
Consensus pattern (16 bp):
ACAAAATATACTATTC
Found at i:2957523 original size:13 final size:14
Alignment explanation
Indices: 2957498--2957527 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2957488 CAAAGCATGT
2957498 TTAATGTGATGACA
1 TTAATGTGATGACA
2957512 TTAATG-GATGACA
1 TTAATGTGATGACA
2957525 TTA
1 TTA
2957528 TGCTTTGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.37
Consensus pattern (14 bp):
TTAATGTGATGACA
Found at i:2960944 original size:5 final size:5
Alignment explanation
Indices: 2960891--2960938 Score: 87
Period size: 5 Copynumber: 9.6 Consensus size: 5
2960881 CTTCACCCCT
*
2960891 CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC ATCTC CTC
1 CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTC
2960939 GTCTCGCCTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.02, C:0.58, G:0.00, T:0.40
Consensus pattern (5 bp):
CTCTC
Found at i:2966893 original size:495 final size:495
Alignment explanation
Indices: 2965963--2966954 Score: 1921
Period size: 495 Copynumber: 2.0 Consensus size: 495
2965953 TAACTCACGA
2965963 TCTGTCTCGTCTTATTTACAACCCTACTAGATGGTACAACTGAGTGTAGAAGGTCGCATATCGTA
1 TCTGTCTCGTCTTATTTACAACCCTACTAGATGGTACAACTGAGTGTAGAAGGTCGCATATCGTA
2966028 TTAAGATATCATTTCCATTTTCAAAATGTAATTGAAATCAATTTCAATGAATAAAATACTTATAA
66 TTAAGATATCATTTCCATTTTCAAAATGTAATTGAAATCAATTTCAATGAATAAAATACTTATAA
2966093 TGGTAAAATACAAATATATATATATATATCAACATTAGAAATATGTATGAAAACATGTTCAAAAT
131 TGGTAAAATACAAATATATATATATATATCAACATTAGAAATATGTATGAAAACATGTTCAAAAT
*
2966158 AAAATATCGGTAATATAGATACATACAAACATACATACATACAATAGTAAAAATATGAGTCACCA
196 AAAATATCAGTAATATAGATACATACAAACATACATACATACAATAGTAAAAATATGAGTCACCA
*
2966223 AAATATAATAGAGATGAGCATAAGAGAATATACAGTGGTATACAAATGGAGAACAATTGATCCTC
261 AAATATAATAGAGATGAGCATAAGAGAATATACAGTGGTATACAAATGAAGAACAATTGATCCTC
2966288 TTGATGCCAAGTCTACTAGCGTACTTTCGGGTAATATCTGAAAAGTTAAAAATTAAAGAATAAGC
326 TTGATGCCAAGTCTACTAGCGTACTTTCGGGTAATATCTGAAAAGTTAAAAATTAAAGAATAAGC
*
2966353 TAAAAAGCTCAGTGTGCTCATTGTGGTGCATAAAAACATACAGATAAATAATTAGGCAAAAATCA
391 TAAAAAGCTCAATGTGCTCATTGTGGTGCATAAAAACATACAGATAAATAATTAGGCAAAAATCA
2966418 TTTTATAAAACATGCTTTTAAAACATGAACACTAGCCCCT
456 TTTTATAAAACATGCTTTTAAAACATGAACACTAGCCCCT
2966458 TCTGTCTCGTCTTATTTACAACCCTACTAGATGGTACAACTGAGTGTAGAAGGTCGCATATCGTA
1 TCTGTCTCGTCTTATTTACAACCCTACTAGATGGTACAACTGAGTGTAGAAGGTCGCATATCGTA
2966523 TTAAGATATCATTTCCATTTTCAAAATGTAATTGAAATCAATTTCAATGAATAAAATACTTATAA
66 TTAAGATATCATTTCCATTTTCAAAATGTAATTGAAATCAATTTCAATGAATAAAATACTTATAA
2966588 TGGTAAAATACAAATATATATATATATATCAACATTAGAAATATGTATGAAAACATGTTCAAAAT
131 TGGTAAAATACAAATATATATATATATATCAACATTAGAAATATGTATGAAAACATGTTCAAAAT
2966653 AAAATATCAGTAATATAGATACATACAAACATACATACATACAATAGTAAAAATATGAGTCACCA
196 AAAATATCAGTAATATAGATACATACAAACATACATACATACAATAGTAAAAATATGAGTCACCA
2966718 AAATATAATAGAGATGAGCATAAGAGAATATACAGTGGTATACAAATGAAGAACAATTGATCCTC
261 AAATATAATAGAGATGAGCATAAGAGAATATACAGTGGTATACAAATGAAGAACAATTGATCCTC
2966783 TTGATGCCAAGTCTACTAGCGTACTTTCGGGTAATATCTGAAAAGTTAAAAATTAAAGAATAAGC
326 TTGATGCCAAGTCTACTAGCGTACTTTCGGGTAATATCTGAAAAGTTAAAAATTAAAGAATAAGC
* * *
2966848 TAAAAAGCTCAATGTGCTCCTTGTGGTGTATAAAAACATACAGATAAATAATTAGGTAAAAATCA
391 TAAAAAGCTCAATGTGCTCATTGTGGTGCATAAAAACATACAGATAAATAATTAGGCAAAAATCA
*
2966913 TTTTTTAAAACATGCTTTTAAAACATGAACACTAGCCCCT
456 TTTTATAAAACATGCTTTTAAAACATGAACACTAGCCCCT
2966953 TC
1 TC
2966955 CGAACACCAG
Statistics
Matches: 490, Mismatches: 7, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
495 490 1.00
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (495 bp):
TCTGTCTCGTCTTATTTACAACCCTACTAGATGGTACAACTGAGTGTAGAAGGTCGCATATCGTA
TTAAGATATCATTTCCATTTTCAAAATGTAATTGAAATCAATTTCAATGAATAAAATACTTATAA
TGGTAAAATACAAATATATATATATATATCAACATTAGAAATATGTATGAAAACATGTTCAAAAT
AAAATATCAGTAATATAGATACATACAAACATACATACATACAATAGTAAAAATATGAGTCACCA
AAATATAATAGAGATGAGCATAAGAGAATATACAGTGGTATACAAATGAAGAACAATTGATCCTC
TTGATGCCAAGTCTACTAGCGTACTTTCGGGTAATATCTGAAAAGTTAAAAATTAAAGAATAAGC
TAAAAAGCTCAATGTGCTCATTGTGGTGCATAAAAACATACAGATAAATAATTAGGCAAAAATCA
TTTTATAAAACATGCTTTTAAAACATGAACACTAGCCCCT
Found at i:2966931 original size:14 final size:13
Alignment explanation
Indices: 2966915--2966939 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2966905 AAAAATCATT
2966915 TTTTAAAACATGC
1 TTTTAAAACATGC
2966928 TTTTAAAACATG
1 TTTTAAAACATG
2966940 AACACTAGCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (13 bp):
TTTTAAAACATGC
Found at i:2969533 original size:18 final size:18
Alignment explanation
Indices: 2969493--2969526 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2969483 TATCATGCAG
*
2969493 TCAGAATATTTAATATAA
1 TCAGAATATTTAAAATAA
2969511 TCAGAAT-TTTAAAATA
1 TCAGAATATTTAAAATA
2969527 GTTCAGAGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (18 bp):
TCAGAATATTTAAAATAA
Found at i:2971169 original size:31 final size:31
Alignment explanation
Indices: 2971133--2971191 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2971123 AACATAAAAG
* *
2971133 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
2971164 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
2971192 AAATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:2971242 original size:22 final size:22
Alignment explanation
Indices: 2971216--2971258 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2971206 TAATAAATTA
*
2971216 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAACCAATCCATAT
*
2971238 TTTAAAATAAACCAATTCATA
1 TTTAAAATAAACCAATCCATA
2971259 CTAATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAACCAATCCATAT
Found at i:2971264 original size:54 final size:54
Alignment explanation
Indices: 2971206--2972337 Score: 819
Period size: 54 Copynumber: 20.6 Consensus size: 54
2971196 ACAACTACAA
* *
2971206 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAACCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *
2971260 TAATAAATTATTTAAAATAAATCAATCCATACAACTATAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * ** ** *
2971317 TTTTAAAATAAAT-CAATCCATACAAATAAAT-TATTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
*
2971372 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATGC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* **
2971426 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
2971484 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * **
2971538 TAATAAATTATTTATAATAAATCAATCCATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * ** ** *
2971595 TTTTAAAATAAAT-CAATCCATACTAATAAAT-TATTTAAAATAAATCAATCCATATTT
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATA--C
* ** * * * *
2971652 TAAAATAAATTAATCCATACAAATAAAT---TA-TTTAAAATAAATCAATCTATAC
1 T--AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
2971704 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT-CATGC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* **
2971757 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
*
2971815 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCATTCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * **
2971869 TAATAAATTATTTAAAATAAATCAATTCATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * ** ** *
2971926 TTTTAAAATAAAT-CAATCCATACTAATAAAT-TATTTATAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
*
2971981 -AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* ** *
2972029 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCTATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * * **
2972086 TTTTAAAATAAAT-CAATACATACAAATAAAT-TATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
*
2972141 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * **
2972195 TAATAAATTATTTAAAATAAATCAATCTATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** ** *
2972252 TTTTAAA--A-TAAACCAATCCATACAAATAAAT-TATTTAAAATAAATCATTCCATAC
1 TAATAAATTATTTAA--AATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
2972307 TAATAAATTATTTAAAATAAATCAATCCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
2972338 CAACTACAAT
Statistics
Matches: 840, Mismatches: 160, Indels: 155
0.73 0.14 0.13
Matches are distributed among these distances:
48 29 0.03
49 4 0.00
50 25 0.03
51 1 0.00
52 2 0.00
53 36 0.04
54 367 0.44
55 54 0.06
56 46 0.05
57 80 0.10
58 186 0.22
59 7 0.01
60 3 0.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.33
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:2971347 original size:22 final size:23
Alignment explanation
Indices: 2971272--2971346 Score: 89
Period size: 22 Copynumber: 3.2 Consensus size: 23
2971262 ATAAATTATT
2971272 TAAAATAAATCAATCCATACAACTA
1 TAAAATAAATCAATCCATACAA--A
***
2971297 TAATAATAAATCAATCCATA-TTT
1 TAA-AATAAATCAATCCATACAAA
2971320 TAAAATAAATCAATCCATACAAA
1 TAAAATAAATCAATCCATACAAA
2971343 TAAA
1 TAAA
2971347 TTATTTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
22 16 0.38
23 7 0.17
25 3 0.07
26 16 0.38
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACAAA
Found at i:2971357 original size:14 final size:14
Alignment explanation
Indices: 2971340--2971393 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
2971330 CAATCCATAC
2971340 AAATAAATTATTTA
1 AAATAAATTATTTA
*
2971354 AAATAAATCAATCTATA
1 AAATAAAT-TAT-T-TA
*
2971371 CTAATAAATTATTTA
1 -AAATAAATTATTTA
2971386 AAATAAAT
1 AAATAAAT
2971394 CAATCCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.47
15 4 0.12
16 2 0.06
17 4 0.12
18 7 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:2971372 original size:112 final size:111
Alignment explanation
Indices: 2971238--2972471 Score: 733
Period size: 112 Copynumber: 11.2 Consensus size: 111
2971228 CAATCCATAT
* * *
2971238 TTTAAAATAAACCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTATAATAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA-AATTATAATAA
*
2971303 TAAATCAATCCATA-T-TTTAAAATAAATCAATCCATACAAATAAATTA
65 TAAATCAATCCATATTATTTAAAATAAATCAATCCATACAAATACA--A
* ** *
2971350 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAAATTATAAT-AA
* * * *
2971415 TCAATCCATGCTAATAAATTATTTAAAATAAATCAATCCATACAACTACAA
65 TAAATCAAT-C-CAT--ATTATTTAAAATAAATCAATCCATACAAATACAA
** *
2971466 --T--AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAAATTATAAT-AA
* * * * *
2971527 TCAATCCATACTAATAAATTATTTATAATAAATCAATCCATACAACTACAA
65 TAAATCAAT-C-CAT--ATTATTTAAAATAAATCAATCCATACAAATACAA
** * * *
2971578 --T--AATAAATCAATCCATA-TTTTAAA--A--T-AAATCAATCCATACTAATAAATTATTTAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT-C-CATAAATTA--TAA
* *
2971633 -AATAAATCAATCCATA-T-TTTAAAATAAATTAATCCATACAAATAAATTA
62 TAATAAATCAATCCATATTATTTAAAATAAATCAATCCATACAAATACA--A
* *
2971682 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCAT--ATTTTAA-AAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAAATTATAATAAT
*
2971744 AAATCAATCATGCTAATAAATTATTTAAAATAAATCAATCCATACAACTACAA
66 AAATCAATC---C--AT--ATTATTTAAAATAAATCAATCCATACAAATACAA
** *
2971797 --T--AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAAATTATAAT-AA
* * * * * *
2971858 TCATTCCATACTAATAAATTATTTAAAATAAATCAATTCATACAACTACAA
65 TAAATCAAT-C-CAT--ATTATTTAAAATAAATCAATCCATACAAATACAA
** * * * *
2971909 --T--AATAAATCAATCCATA-TTTTAAA--A--T-AAATCAATCCATACTAATAAATTATTTAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT-C-CATAAATTA-TAAT
** **
2971964 AATAAATCAATCCATACAACTACAATAATAAATCAATCCAT----AT----
63 AATAAATCAATCCATATTA-TTTAA-AATAAATCAATCCATACAAATACAA
* *
2972007 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA-AATTATAATAA
* * *
2972072 TAAATCAATCTATA-T-TTTAAAATAAATCAATACATACAAATAAATTA
65 TAAATCAATCCATATTATTTAAAATAAATCAATCCATACAAATACA--A
*
2972119 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCAT--ATTTTAA-AAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAAATTATAATAAT
* *
2972181 AAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCTATACAACTACAA
66 AAATCAA-TC---C--AT--ATTATTTAAAATAAATCAATCCATACAAATACAA
** ** * *
2972235 --T--AATAAATCAATCCATA-TTTTAAA--A--T-AAACCAATCCATACAAATAAATTATTTAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT-C-CATAAATTA--TAA
* *
2972290 -AATAAATCATTCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAA
62 TAATAAATCA----AT-C-CAT--ATTATTTAAAATAAATCAATCCATACAAATACAA
** * *
2972347 --T--AATAAATCAATCCATA-TTTTAAA--A--T-AAATAAATCCATACTAATAAATTATTTAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT-C-CATAAATTA--TAA
* *
2972402 -AATAAATCAATCCATA-T-TTTAAAATAAATCAATCCATACTAATAAATTA
62 TAATAAATCAATCCATATTATTTAAAATAAATCAATCCATACAAATACA--A
2972451 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
2972472 TTTTAAAATA
Statistics
Matches: 925, Mismatches: 107, Indels: 184
0.76 0.09 0.15
Matches are distributed among these distances:
100 1 0.00
102 82 0.09
103 10 0.01
104 6 0.01
105 4 0.00
106 73 0.08
107 15 0.02
108 99 0.11
109 16 0.02
110 8 0.01
111 68 0.07
112 418 0.45
113 10 0.01
114 16 0.02
115 11 0.01
116 8 0.01
117 28 0.03
118 52 0.06
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (111 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAAATTATAATAAT
AAATCAATCCATATTATTTAAAATAAATCAATCCATACAAATACAA
Found at i:2971391 original size:166 final size:163
Alignment explanation
Indices: 2971189--2972221 Score: 903
Period size: 166 Copynumber: 6.3 Consensus size: 163
2971179 AAATTTAAAT
* * *
2971189 AATAAATACAA-CTACAATAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAACCAA
1 AATAAAT-CAATCTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAA
*
2971253 TTCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTATAATAATAAATCAATCCATAT
65 -TCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATA-
* * * *
2971318 TTTAAAATAAATCAATCCATACAAATAAAT-TA-TTTAA
128 -CT--AATAAATTAATCAAAACAAATAAATCTATTTTAA
2971355 AATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT
1 AATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT
*
2971420 CCATGCTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATACT
66 -CATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATACT
* * * *
2971485 AATAAATTATTTAAAATAAATCAATCCATATTTTAA
130 AATAAATTAATCAAAACAAATAAAT-C-TATTTTAA
* * *** *
2971521 AATAAATCAATCCATACTAATAAATTATTTATAATAAATCAATCCATACAACTACAAT-AAT-AA
1 AATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAA
** *
2971584 --AT-C-AATCCA-TATTTTAAAATAAATCAATCCATACTAA-TAAATTATTTAAAATAAATCAA
65 TCATACTAATAAATTA-TTTAAAATAAATCAATCCATAC-AACTACA--A--T--AATAAATCAA
* * *
2971643 TCCATATTTTAAAATAAATTAATCCATACAAATAAAT-TA-TTTAA
122 TCCATA--CT--AATAAATTAATCAAAACAAATAAATCTATTTTAA
2971687 AATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT
1 AATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT
*
2971752 CATGCTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATACTA
66 CATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATACTA
* * * *
2971817 ATAAATTATTTAAAATAAATCAATCCATATTTTAA
131 ATAAATTAATCAAAACAAATAAAT-C-TATTTTAA
* * * *** *
2971852 AATAAATCATTCCATACTAATAAATTATTTAAAATAAATCAATTCATACAACTACAAT-AAT-AA
1 AATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAA
** *
2971915 --AT-C-AATCCA-TATTTTAAAATAAATCAATCCATACTAA-TAAATTATTTATAATAAATCAA
65 TCATACTAATAAATTA-TTTAAAATAAATCAATCCATAC-AACT--A-CA---ATAATAAATCAA
* **
2971974 TCCATAC-AACTACAA-TAAT-AAATC-AATCCA--TATTTTAA
122 TCCATACTAA-TA-AATTAATCAAAACAAATAAATCTATTTTAA
* *** * *
2972012 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT-AATAAA
1 AATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAA
* * *
2972076 TCA-ATCT-AT--A-T-TTTAAAATAAATCAATACATACAAATAAATTATTTAAAATAAATCAAT
65 TCATA-CTAATAAATTATTTAAAATAAATCAATCCATACAACTACA--A--T--AATAAATCAAT
* * * *
2972135 CCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAA
123 CCATACTAATAAATTAATCAAAACAAATAAAT-C-TATTTTAA
2972178 AATAAATCAAT-TCATACTAATAAATTATTTAAAATAAATCAATC
1 AATAAATCAATCT-ATACTAATAAATTATTTAAAATAAATCAATC
2972222 TATACAACTA
Statistics
Matches: 737, Mismatches: 68, Indels: 124
0.79 0.07 0.13
Matches are distributed among these distances:
156 3 0.00
157 1 0.00
158 2 0.00
159 8 0.01
160 167 0.23
161 32 0.04
162 31 0.04
163 3 0.00
164 14 0.02
165 87 0.12
166 320 0.43
167 12 0.02
168 1 0.00
169 3 0.00
170 22 0.03
171 29 0.04
172 2 0.00
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (163 bp):
AATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT
CATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATACTA
ATAAATTAATCAAAACAAATAAATCTATTTTAA
Found at i:2971408 original size:22 final size:22
Alignment explanation
Indices: 2971382--2971423 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
2971372 TAATAAATTA
2971382 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
2971404 TTTAAAATAAATCAATCCAT
1 TTTAAAATAAATCAATCCAT
2971424 GCTAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:2971433 original size:22 final size:22
Alignment explanation
Indices: 2971384--2971432 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2971374 ATAAATTATT
**
2971384 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
2971406 TAAAATAAATCAATCCATGCTAA
1 TAAAATAAATCAATCCAT-ATAA
2971429 TAAA
1 TAAA
2971433 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:2971520 original size:22 final size:22
Alignment explanation
Indices: 2971494--2971536 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2971484 TAATAAATTA
2971494 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
2971516 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
2971537 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:2971545 original size:22 final size:22
Alignment explanation
Indices: 2971496--2971544 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2971486 ATAAATTATT
**
2971496 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
2971518 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
2971541 TAAA
1 TAAA
2971545 TTATTTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:2971625 original size:22 final size:23
Alignment explanation
Indices: 2971553--2971624 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 23
2971543 AATTATTTAT
2971553 AATAAATCAATCCATAC-AACTACAA
1 AATAAATCAATCCATACTAA-T--AA
**
2971578 TAATAAATCAATCCATA-TTTTAA
1 -AATAAATCAATCCATACTAATAA
2971601 AATAAATCAATCCATACTAATAA
1 AATAAATCAATCCATACTAATAA
2971624 A
1 A
2971625 TTATTTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
22 16 0.40
23 7 0.17
25 1 0.03
26 16 0.40
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.28
Consensus pattern (23 bp):
AATAAATCAATCCATACTAATAA
Found at i:2971654 original size:22 final size:22
Alignment explanation
Indices: 2971628--2971670 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2971618 TAATAAATTA
2971628 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
2971650 TTTAAAATAAATTAATCCATA
1 TTTAAAATAAATCAATCCATA
2971671 CAAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:2971689 original size:14 final size:14
Alignment explanation
Indices: 2971672--2971725 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
2971662 TAATCCATAC
2971672 AAATAAATTATTTA
1 AAATAAATTATTTA
*
2971686 AAATAAATCAATCTATA
1 AAATAAAT-TAT-T-TA
*
2971703 CTAATAAATTATTTA
1 -AAATAAATTATTTA
2971718 AAATAAAT
1 AAATAAAT
2971726 CAATCCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.47
15 4 0.12
16 2 0.06
17 4 0.12
18 7 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:2971851 original size:22 final size:22
Alignment explanation
Indices: 2971825--2971867 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2971815 TAATAAATTA
2971825 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
2971847 TTTAAAATAAATCATTCCATA
1 TTTAAAATAAATCAATCCATA
2971868 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:2971868 original size:80 final size:82
Alignment explanation
Indices: 2971436--2972471 Score: 810
Period size: 80 Copynumber: 12.6 Consensus size: 82
2971426 TAATAAATTA
*
2971436 TTTAAAATAAATCAATCCATAC-AACTACA-A-TAATAAATCAATCCATACTAATAAATTATTTA
1 TTTAAAATAAATCAATCCATACTAA-TAAATATTAATAAATCAATCCATACTAATAAATTATTTA
2971498 AAATAAATCAATCCATAT
65 AAATAAATCAATCCATAT
*
2971516 TTTAAAATAAATCAATCCATACTAATAAATTATTTATAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAATAAA-TA--T-TAATAAATCAATCCATACTAA-TAAATTA
2971578 --T--AATAAATCAATCCATAT
61 TTTAAAATAAATCAATCCATAT
*
2971596 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA-TT--AATAAATCAATCCATA--CT--AATAAA
* ** * * *
2971661 TTAATCCATACAAATAAAT---TA-
58 TTATTTAAAATAAATCAATCCATAT
* ** * *
2971682 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA-TT--AATAAATCAATCCATACTAATAAATTAT
* * * **
2971746 AT-CAAT-CATGCTAATAAAT-T
62 TTAAAATAAAT-C-AATCCATAT
*
2971766 ATTTAAAATAAATCAATCCATAC-AACTACA-A-TAATAAATCAATCCATACTAATAAATTATTT
1 -TTTAAAATAAATCAATCCATACTAA-TAAATATTAATAAATCAATCCATACTAATAAATTATTT
2971828 AAAATAAATCAATCCATAT
64 AAAATAAATCAATCCATAT
* * *
2971847 TTTAAAATAAATCATTCCATACTAATAAATTATTTAAAATAAATCAATTCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAATAAA-TA-TT--AATAAATCAATCCATACTAA-TAAATTA
2971909 --T--AATAAATCAATCCATAT
61 TTTAAAATAAATCAATCCATAT
*
2971927 TTTAAAATAAATCAATCCATACTAATAAATTATTTATAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAATAAA-TA--T-TAATAAATCAATCCATACTAA-TAAATTA
2971989 --T--AATAAATCAATCCATAT
61 TTTAAAATAAATCAATCCATAT
*
2972007 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAATAAA-TA-TT--AATAAATCAATCCATACTAA-TAAATTA
*
2972069 --T--AATAAATCAATCTATAT
61 TTTAAAATAAATCAATCCATAT
* *
2972087 TTTAAAATAAATCAATACATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTAT
1 TTTAAAATAAATCAATCCATACTAATAAA-TA-TT--AATAAATCAATCCATACTAATAAATTAT
2972152 TTAAAATAAATCAATCCATAT
62 TTAAAATAAATCAATCCATAT
* * * * * *
2972173 TTTAAAATAAATCAATTCATACTAATAAATTATTTA-AAATAAATCAAT-CT-ATACAACTA--C
1 TTTAAAATAAATCAATCCATACTAATAAA-TATTAATAAATCAATCCATACTAATA-AATTATTT
2972233 AATAATAAATCAATCCATAT
64 AA-AATAAATCAATCCATAT
* * *
2972253 TTTAAAATAAACCAATCCATACAAATAAATTATTTAAAATAAATCATTCCATACTAATAAATTAT
1 TTTAAAATAAATCAATCCATACTAATAAA-TA-TT--AATAAATCAATCCATACTAATAAATTAT
*
2972318 TTAAAATAAATCAATCCATACAAC
62 TTAAAATAAATCAATCCAT---AT
** * * *
2972342 TACAATAATAAATCAATCCATA-T--T--TTA-AAATAAATAAATCCATACTAATAAATTATTTA
1 TTTAA-AATAAATCAATCCATACTAATAAATATTAATAAATCAATCCATACTAATAAATTATTTA
2972401 AAATAAATCAATCCATAT
65 AAATAAATCAATCCATAT
2972419 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA-TT--AATAAATCAATCCATA
2972472 TTTTAAAATA
Statistics
Matches: 808, Mismatches: 72, Indels: 146
0.79 0.07 0.14
Matches are distributed among these distances:
76 16 0.02
77 5 0.01
78 2 0.00
79 25 0.03
80 441 0.55
81 32 0.04
82 20 0.02
83 4 0.00
84 21 0.03
85 38 0.05
86 172 0.21
87 5 0.01
89 4 0.00
90 23 0.03
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (82 bp):
TTTAAAATAAATCAATCCATACTAATAAATATTAATAAATCAATCCATACTAATAAATTATTTAA
AATAAATCAATCCATAT
Found at i:2971876 original size:22 final size:22
Alignment explanation
Indices: 2971827--2971875 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2971817 ATAAATTATT
**
2971827 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
2971849 TAAAATAAATCATTCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
2971872 TAAA
1 TAAA
2971876 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:2971956 original size:22 final size:22
Alignment explanation
Indices: 2971881--2971955 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 22
2971871 ATAAATTATT
* *
2971881 TAAAATAAATCAATTCATACAA
1 TAAAATAAATCAATCCATATAA
**
2971903 CTACAATAATAAATCAATCCATATTT
1 -T--AA-AATAAATCAATCCATATAA
2971929 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
2971952 TAAA
1 TAAA
2971956 TTATTTATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 16 0.38
23 8 0.19
25 3 0.07
26 15 0.36
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:2972036 original size:22 final size:23
Alignment explanation
Indices: 2971964--2972035 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 23
2971954 AATTATTTAT
2971964 AATAAATCAATCCATAC-AACTACAA
1 AATAAATCAATCCATACTAA-T--AA
**
2971989 TAATAAATCAATCCATA-TTTTAA
1 -AATAAATCAATCCATACTAATAA
2972012 AATAAATCAATCCATACTAATAA
1 AATAAATCAATCCATACTAATAA
2972035 A
1 A
2972036 TTATTTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
22 16 0.40
23 7 0.17
25 1 0.03
26 16 0.40
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.28
Consensus pattern (23 bp):
AATAAATCAATCCATACTAATAA
Found at i:2972177 original size:22 final size:22
Alignment explanation
Indices: 2972151--2972193 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2972141 TAATAAATTA
2972151 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
2972173 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
2972194 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:2972202 original size:22 final size:22
Alignment explanation
Indices: 2972153--2972201 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2972143 ATAAATTATT
**
2972153 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
2972175 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
2972198 TAAA
1 TAAA
2972202 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:2972294 original size:14 final size:14
Alignment explanation
Indices: 2972275--2972328 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
2972265 CAATCCATAC
2972275 AAATAAATTATTTA
1 AAATAAATTATTTA
*
2972289 AAATAAATCATTCCATA
1 AAATAAATTATT---TA
*
2972306 CTAATAAATTATTTA
1 -AAATAAATTATTTA
2972321 AAATAAAT
1 AAATAAAT
2972329 CAATCCATAC
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 18 0.56
15 2 0.06
17 2 0.06
18 10 0.31
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:2972414 original size:54 final size:54
Alignment explanation
Indices: 2972348--2972563 Score: 374
Period size: 54 Copynumber: 4.1 Consensus size: 54
2972338 CAACTACAAT
*
2972348 AATAAATCAATCCATATTTTAAAATAAATAAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
2972402 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
2972456 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
2972510 AAT--A--AAT---TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
2972557 AATAAAT
1 AATAAAT
2972564 TATTTTAAAA
Statistics
Matches: 158, Mismatches: 1, Indels: 10
0.93 0.01 0.06
Matches are distributed among these distances:
47 43 0.27
49 1 0.01
50 3 0.02
52 1 0.01
54 110 0.70
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:2972423 original size:22 final size:22
Alignment explanation
Indices: 2972397--2972439 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2972387 TAATAAATTA
2972397 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
2972419 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
2972440 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:2972448 original size:22 final size:22
Alignment explanation
Indices: 2972399--2972447 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2972389 ATAAATTATT
**
2972399 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
2972421 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
2972444 TAAA
1 TAAA
2972448 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:2972525 original size:15 final size:15
Alignment explanation
Indices: 2972496--2972645 Score: 133
Period size: 15 Copynumber: 9.5 Consensus size: 15
2972486 AATCCATACT
2972496 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
2972510 AATAAATTATTTTAA
1 AATAAATTATTTTAA
* ** *
2972525 AATAAATCAATCCATACT
1 AATAAAT-TAT-TTTA-A
2972543 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
2972557 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
2972572 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
2972594 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
2972609 AATAAATTATTTTAT
1 AATAAATTATTTTAA
2972624 AATAAATTATTTTAA
1 AATAAATTATTTTAA
2972639 AATAAAT
1 AATAAAT
2972646 AACCTTATTA
Statistics
Matches: 110, Mismatches: 14, Indels: 23
0.75 0.10 0.16
Matches are distributed among these distances:
14 18 0.16
15 63 0.57
16 2 0.02
17 4 0.04
18 9 0.08
19 3 0.03
20 1 0.01
22 10 0.09
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:2972563 original size:32 final size:32
Alignment explanation
Indices: 2972419--2972516 Score: 126
Period size: 32 Copynumber: 3.4 Consensus size: 32
2972409 CAATCCATAT
2972419 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
2972451 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
2972473 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
2972505 TTTAAAATAAAT
1 TTTAAAATAAAT
2972517 TATTTTAAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 20
0.74 0.00 0.26
Matches are distributed among these distances:
22 16 0.29
23 2 0.04
24 1 0.02
26 3 0.05
28 3 0.05
30 1 0.02
31 2 0.04
32 28 0.50
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:2976246 original size:21 final size:21
Alignment explanation
Indices: 2976206--2976248 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2976196 TGTTCCCCCT
*
2976206 GTATCGATACCCTCCACATAG
1 GTATCGATACCCTACACATAG
2976227 GTATCGATACCTCTAC-CATAG
1 GTATCGATACC-CTACACATAG
2976248 G
1 G
2976249 GTATTGACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (21 bp):
GTATCGATACCCTACACATAG
Found at i:2981308 original size:14 final size:14
Alignment explanation
Indices: 2981289--2981319 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2981279 CCTATTTGCA
2981289 TATGATCATGAACT
1 TATGATCATGAACT
2981303 TATGATCATGAACT
1 TATGATCATGAACT
2981317 TAT
1 TAT
2981320 CATTTACACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (14 bp):
TATGATCATGAACT
Found at i:2981530 original size:18 final size:18
Alignment explanation
Indices: 2981507--2981565 Score: 100
Period size: 18 Copynumber: 3.3 Consensus size: 18
2981497 GCGTAGAATT
2981507 TGTCCCGAATGACCACTA
1 TGTCCCGAATGACCACTA
2981525 TGTCCCGAATGACCACTA
1 TGTCCCGAATGACCACTA
* *
2981543 TATCCCGAAGGACCACTA
1 TGTCCCGAATGACCACTA
2981561 TGTCC
1 TGTCC
2981566 TAAAGGACCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.27, C:0.34, G:0.17, T:0.22
Consensus pattern (18 bp):
TGTCCCGAATGACCACTA
Found at i:2981571 original size:18 final size:18
Alignment explanation
Indices: 2981507--2981576 Score: 95
Period size: 18 Copynumber: 3.9 Consensus size: 18
2981497 GCGTAGAATT
*
2981507 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
2981525 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
2981543 TATCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
**
2981561 TGTCCTAAAGGACCAC
1 TGTCCCGAAGGACCAC
2981577 ATAGAACAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:2982337 original size:22 final size:22
Alignment explanation
Indices: 2982311--2982366 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
2982301 CCACCCTCAC
2982311 GGTATCGATACCTCTATGCTAG
1 GGTATCGATACCTCTATGCTAG
2982333 GGTATCGATACCTCTATGCTAG
1 GGTATCGATACCTCTATGCTAG
2982355 GGTATCGATACC
1 GGTATCGATACC
2982367 CTACCCAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (22 bp):
GGTATCGATACCTCTATGCTAG
Found at i:2982440 original size:21 final size:22
Alignment explanation
Indices: 2982410--2982462 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2982400 TGTTCCCCCT
2982410 GTATCGATACC-C-TCCATATAG
1 GTATCGATACCTCTTCCATAT-G
*
2982431 GTATCAATACCTCTTCCATATG
1 GTATCGATACCTCTTCCATATG
2982453 GTATCGATAC
1 GTATCGATAC
2982463 TATTCATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 10 0.36
22 11 0.39
23 7 0.25
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.32
Consensus pattern (22 bp):
GTATCGATACCTCTTCCATATG
Found at i:2982462 original size:22 final size:21
Alignment explanation
Indices: 2982410--2982485 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
2982400 TGTTCCCCCT
2982410 GTATCGATACCCTCCATATAG
1 GTATCGATACCCTCCATATAG
*
2982431 GTATCAATACCTCTTCCATAT-G
1 GTATCGATACC-C-TCCATATAG
** * *
2982453 GTATCGATACTATTCATACAG
1 GTATCGATACCCTCCATATAG
*
2982474 GTACCGATACCC
1 GTATCGATACCC
2982486 CTTGCATCAT
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
20 5 0.12
21 20 0.47
22 11 0.26
23 7 0.16
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.30
Consensus pattern (21 bp):
GTATCGATACCCTCCATATAG
Found at i:2983790 original size:18 final size:18
Alignment explanation
Indices: 2983763--2983797 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2983753 ATTCAGAGTT
*
2983763 AAATTTTGCTCATGCAGA
1 AAATTGTGCTCATGCAGA
2983781 AAATTGTGCTCATGCAG
1 AAATTGTGCTCATGCAG
2983798 CCATTTCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (18 bp):
AAATTGTGCTCATGCAGA
Found at i:2994381 original size:31 final size:32
Alignment explanation
Indices: 2994333--2994398 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
2994323 GTAAAATCAA
* * *
2994333 ATCAATTGGCTTTTGGGTTGGGTTAATATTGG
1 ATCAATTGGCTTTTGGGTCGGGTCAATATTAG
2994365 ATCAATTGG-TTTTGGGTCGGGTCAATATTAG
1 ATCAATTGGCTTTTGGGTCGGGTCAATATTAG
2994396 ATC
1 ATC
2994399 GAATGATTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 22 0.71
32 9 0.29
ACGTcount: A:0.21, C:0.09, G:0.29, T:0.41
Consensus pattern (32 bp):
ATCAATTGGCTTTTGGGTCGGGTCAATATTAG
Found at i:2998410 original size:15 final size:16
Alignment explanation
Indices: 2998383--2998412 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2998373 TTCTTTTATA
2998383 AATTTTATTAAAAATC
1 AATTTTATTAAAAATC
2998399 AATTTT-TTAAAAAT
1 AATTTTATTAAAAAT
2998413 ATAACTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTTTATTAAAAATC
Found at i:2999877 original size:29 final size:30
Alignment explanation
Indices: 2999845--2999913 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 30
2999835 ATTAGACTCT
*
2999845 ATTTAAATTTTATAT-TTATTATATTA-TTA
1 ATTTAAATTTTATATATTA-AATATTATTTA
*
2999874 ATTT-AATTGATATATATTAAATATTATTTA
1 ATTTAAATT-TTATATATTAAATATTATTTA
*
2999904 ATTCAAATTT
1 ATTTAAATTT
2999914 GCAACTGTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
28 4 0.12
29 15 0.47
30 9 0.28
31 4 0.12
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (30 bp):
ATTTAAATTTTATATATTAAATATTATTTA
Found at i:3001811 original size:2 final size:2
Alignment explanation
Indices: 3001748--3001802 Score: 74
Period size: 2 Copynumber: 27.5 Consensus size: 2
3001738 AAGATATAAG
* * **
3001748 AT AT AT GT AT GT AT AT AT GC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3001790 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
3001803 GACATATATG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3001819 original size:12 final size:12
Alignment explanation
Indices: 3001759--3001825 Score: 62
Period size: 12 Copynumber: 5.4 Consensus size: 12
3001749 TATATGTATG
*
3001759 TATATATGCATA
1 TATATATACATA
*
3001771 TATATATATATA
1 TATATATACATA
*
3001783 TATATATATATA
1 TATATATACATA
3001795 TATATATAGACATA
1 TATATAT--ACATA
**
3001809 TATGCATACATA
1 TATATATACATA
*
3001821 CATAT
1 TATAT
3001826 GTTGAAATGC
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
12 36 0.80
14 9 0.20
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.42
Consensus pattern (12 bp):
TATATATACATA
Found at i:3002693 original size:17 final size:15
Alignment explanation
Indices: 3002655--3002685 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3002645 AAATTTTAAA
*
3002655 TATTTAAATAAAAAT
1 TATTTATATAAAAAT
3002670 TATTTATATAAAAAT
1 TATTTATATAAAAAT
3002685 T
1 T
3002686 TTATTTATTG
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTATATAAAAAT
Found at i:3010513 original size:2 final size:2
Alignment explanation
Indices: 3010506--3010541 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3010496 ATATTCTTTA
3010506 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
3010542 TCCAATAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3010733 original size:53 final size:53
Alignment explanation
Indices: 3010642--3010743 Score: 141
Period size: 53 Copynumber: 1.9 Consensus size: 53
3010632 TTTTTAGGTA
* * *
3010642 CTAAGATATTGAGAGATGTATATACTTACACCGGTGTAAATATATGTTAATTG
1 CTAAGATATTGAGAAATGTACATACTTACACCGATGTAAATATATGTTAATTG
* * * *
3010695 CTAAGATGTTGAGAAATGTACATGCTTAGACCGATGTAAATATTTGTTA
1 CTAAGATATTGAGAAATGTACATACTTACACCGATGTAAATATATGTTA
3010744 TTGTTACACA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (53 bp):
CTAAGATATTGAGAAATGTACATACTTACACCGATGTAAATATATGTTAATTG
Found at i:3011767 original size:14 final size:15
Alignment explanation
Indices: 3011748--3011776 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3011738 AATGTTCCTA
3011748 TTTATA-ACAAAATT
1 TTTATAGACAAAATT
3011762 TTTATAGACAAAATT
1 TTTATAGACAAAATT
3011777 ACTTGGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (15 bp):
TTTATAGACAAAATT
Found at i:3025401 original size:23 final size:23
Alignment explanation
Indices: 3025375--3025422 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
3025365 ATAAAGTACA
* *
3025375 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGATAGCGCTTAT
**
3025398 ATAATGTAATAGATAGCGCTTAT
1 ATAACATAATAGATAGCGCTTAT
3025421 AT
1 AT
3025423 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGATAGCGCTTAT
Found at i:3025837 original size:20 final size:21
Alignment explanation
Indices: 3025798--3025840 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3025788 TCCACAGTGA
* *
3025798 AAAAAGTATGGACACTTTTAT
1 AAAAAGGATAGACACTTTTAT
3025819 AAAAAGGATAGACAC-TTTAT
1 AAAAAGGATAGACACTTTTAT
3025839 AA
1 AA
3025841 TATAACTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (21 bp):
AAAAAGGATAGACACTTTTAT
Found at i:3025867 original size:23 final size:22
Alignment explanation
Indices: 3025840--3025912 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 22
3025830 ACACTTTATA
3025840 ATATAACTACTACCTATTACATT
1 ATATAAC-ACTACCTATTACATT
3025863 ATATAA-ACGATACCTATTACATT
1 ATATAACAC--TACCTATTACATT
* *
3025886 ATATAAGCGCTACCTATTACATC
1 ATATAA-CACTACCTATTACATT
3025909 ATAT
1 ATAT
3025913 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
21 2 0.05
23 41 0.93
25 1 0.02
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.36
Consensus pattern (22 bp):
ATATAACACTACCTATTACATT
Found at i:3026266 original size:20 final size:21
Alignment explanation
Indices: 3026228--3026267 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3026218 TCCACAGTGA
* *
3026228 AAAAAGTATGGACACTTTTAT
1 AAAAAGGATAGACACTTTTAT
3026249 AAAAAGGATAGACA-TTTTA
1 AAAAAGGATAGACACTTTTA
3026268 CAATATAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
AAAAAGGATAGACACTTTTAT
Found at i:3026290 original size:430 final size:430
Alignment explanation
Indices: 3025489--3026549 Score: 1989
Period size: 430 Copynumber: 2.5 Consensus size: 430
3025479 TATTACATTA
*
3025489 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATATTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
3025554 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
3025619 ATTTGCACAAAAAATTATTTGATTTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
131 ATTTGCACAAAAAATTATTTGA-TTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
3025684 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
195 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
3025749 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
260 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
* *
3025814 TTTATAAAAAGGATAGACACTTTATAATATAACTACTACCTATTACATTATATAAACGATACCTA
325 TTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
3025879 TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
390 TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
3025920 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
*
3025985 TTATGTTTCAATTTTTTATAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
*
3026050 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
131 ATTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
3026115 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
196 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
3026180 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
261 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
* *
3026245 TTATAAAAAGGATAGACATTTTACAATATAACCACTACCTATTACATTATATAAACGATATCTAT
326 TTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTAT
3026310 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
391 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
*
3026350 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
* * *
3026415 TTATGTTTTAATTTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATGATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
*
3026480 ATTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAA-TTTAAATTTA
131 ATTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
*
3026544 ACAATA
196 ATAATA
3026550 TTAACCAAAG
Statistics
Matches: 615, Mismatches: 15, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
429 14 0.02
430 451 0.73
431 150 0.24
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (430 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
ATTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
TTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTAT
TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
Found at i:3026309 original size:23 final size:23
Alignment explanation
Indices: 3026280--3026342 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
3026270 ATATAACCAC
3026280 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* * *
3026303 TATCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
3026326 TACCTATTACATCATAT
1 TACCTATTACATTATAT
3026343 TTTTACCTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:3027670 original size:183 final size:183
Alignment explanation
Indices: 3027336--3027670 Score: 537
Period size: 183 Copynumber: 1.8 Consensus size: 183
3027326 TTACCGACAC
* * * *
3027336 TTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATATTATAA
1 TTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAGATTAAAA
* * *
3027401 AGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTATATTAC
66 AGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGATACATTAC
*
3027466 AAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGTCGATACT
131 AAAATTACCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGTCGATACT
*
3027519 TTTTTAAATCGTATTGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAGATTAAAA
1 TTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAGATTAAAA
*
3027584 AGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACC-GATAGCATTG
66 AGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGATA-CATTA
* **
3027648 CAAATTTACCTATTTTATTATAA
130 CAAAATTACCTATTACATTATAA
3027671 TATGTTGAAA
Statistics
Matches: 138, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
182 3 0.02
183 135 0.98
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (183 bp):
TTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAGATTAAAA
AGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGATACATTAC
AAAATTACCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGTCGATACT
Found at i:3028866 original size:199 final size:199
Alignment explanation
Indices: 3028526--3029915 Score: 2166
Period size: 199 Copynumber: 7.1 Consensus size: 199
3028516 GTAGGAATCA
3028526 TATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTT
1 TATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTT
*
3028591 GCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAATTAAATTAGTGTCGACACAT
66 GCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACAT
*
3028656 TATTTAGACATATTCTCTCATAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTAAATATT
131 TATTTAGACATATTCTCTCATAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTACATATT
3028721 ACAT
196 ACAT
*
3028725 TATACTTTTGGGTTCGATGATTTTGGGATCGACATTTTTTATATATGGATCGACACTTTATGGTT
1 TATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTT
*
3028790 GCACCCTGTTTTCCATTCATTATGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACAT
66 GCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACAT
*
3028855 TATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTACATATT
131 TATTTAGACATATTCTCTCATAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTACATATT
3028920 ACAT
196 ACAT
3028924 TATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTT
1 TATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTT
* *
3028989 GCGCCCTGTTTTCCATTCATTATGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACAT
66 GCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACAT
*
3029054 TATTTAGACATATTCTCTCATAAAACCGGTAAATTTGTACCGGTTAGATTGAAAAATTACATATT
131 TATTTAGACATATTCTCTCATAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTACATATT
3029119 ACAT
196 ACAT
* * *
3029123 TATACTTTTGGTTTTCGATGTTTTTGGGATCGACAC-TTTTATATATGGATCGACACTTTATGGG
1 TATACTTTTGG-GTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGT
3029187 TGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACA
65 TGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACA
*
3029252 TTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTACATAT
130 TTATTTAGACATATTCTCTCATAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTACATAT
3029317 TACAT
195 TACAT
*
3029322 TATACTTTTGGGTTCGTTGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTT
1 TATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTT
* *
3029387 GCACCCTGTTTTCCATTCATTCTGTAACAAAAATATCGACACAAACTAAATTAGTGTCGACATAT
66 GCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACAT
* *
3029452 TATTTAGACATATTCTCTCATAAAATCGGTAAAAGTGTACCGGTTAGATTGAAAAATTACATATT
131 TATTTAGACATATTCTCTCATAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTACATATT
3029517 ACAT
196 ACAT
3029521 TATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTT
1 TATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTT
* * *
3029586 GCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCG--AC--AC---ATTA-TTTAGACATAT
66 GCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACAT
* * * ** ** * *** * * * * * *
3029643 TCTCTCATA-A-AACCGGTAAACTTGTACCGGTTAGATTG-A-----AAAATT-ACATATTACAT
131 TAT-TTAGACATATTCTCT-CA-TAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTACAT
3029699 -TATAC-T
193 AT-TACAT
* * *
3029705 T-T--TGGTT---TTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGG
1 TATACT-TTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGT
3029764 TGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACA
65 TGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACA
*
3029829 TTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTACATAT
130 TTATTTAGACATATTCTCTCATAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTACATAT
3029894 TACAT
195 TACAT
*
3029899 TATACTTTTGGGATCGA
1 TATACTTTTGGGTTCGA
3029916 CACTTTTTAT
Statistics
Matches: 1087, Mismatches: 72, Indels: 64
0.89 0.06 0.05
Matches are distributed among these distances:
179 89 0.08
181 3 0.00
182 2 0.00
183 3 0.00
184 3 0.00
185 12 0.01
186 22 0.02
187 13 0.01
188 3 0.00
190 3 0.00
191 14 0.01
192 21 0.02
193 12 0.01
194 3 0.00
195 3 0.00
196 2 0.00
197 3 0.00
198 21 0.02
199 833 0.77
200 22 0.02
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (199 bp):
TATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTT
GCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACAT
TATTTAGACATATTCTCTCATAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTACATATT
ACAT
Found at i:3029262 original size:398 final size:398
Alignment explanation
Indices: 3028526--3030288 Score: 3051
Period size: 398 Copynumber: 4.5 Consensus size: 398
3028516 GTAGGAATCA
3028526 TATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTT
1 TATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTT
*
3028591 GCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAATTAAATTAGTGTCGACACAT
66 GCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACAT
*
3028656 TATTTAGACATATTCTCTCATAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTAAATATT
131 TATTTAGACATATTCTCTCATAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTACATATT
*
3028721 ACATTATACTTTTGGGTTCGATGATTTTGGGATCGACATTTTTTATATATGGATCGACACTTTAT
196 ACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTAT
*
3028786 GGTTGCACCCTGTTTTCCATTCATTATGGAACAAAAATATCGACACAAACTAAATTAGTGTCGAC
261 GGTTGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGAC
3028851 ACATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTACA
326 ACATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTACA
3028916 TATTACAT
391 TATTACAT
3028924 TATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTT
1 TATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTT
* *
3028989 GCGCCCTGTTTTCCATTCATTATGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACAT
66 GCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACAT
*
3029054 TATTTAGACATATTCTCTCATAAAACCGGTAAATTTGTACCGGTTAGATTGAAAAATTACATATT
131 TATTTAGACATATTCTCTCATAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTACATATT
* *
3029119 ACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACAC-TTTTATATATGGATCGACACTTTA
196 ACATTATACTTTTGG-GTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTA
*
3029183 TGGGTGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGA
260 TGGTTGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGA
3029248 CACATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTAC
325 CACATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTAC
3029313 ATATTACAT
390 ATATTACAT
*
3029322 TATACTTTTGGGTTCGTTGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTT
1 TATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTT
* *
3029387 GCACCCTGTTTTCCATTCATTCTGTAACAAAAATATCGACACAAACTAAATTAGTGTCGACATAT
66 GCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACAT
* *
3029452 TATTTAGACATATTCTCTCATAAAATCGGTAAAAGTGTACCGGTTAGATTGAAAAATTACATATT
131 TATTTAGACATATTCTCTCATAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTACATATT
3029517 ACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTAT
196 ACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTAT
3029582 GGTTGCACCCTGTTTTCCATTCATTCT-G------------GA-AC-AA--AAA-TA---TCGAC
261 GGTTGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGAC
3029626 ACATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTACA
326 ACATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTACA
3029691 TATTACAT
391 TATTACAT
* * *
3029699 TATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGG
1 TATACTTTTGG-GTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGT
3029764 TGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACA
65 TGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACA
*
3029829 TTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTACATAT
130 TTATTTAGACATATTCTCTCATAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTACATAT
3029894 TACATTATA----------C-----TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTA
195 TACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTA
*
3029944 TGGTTGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACATAAACTAAATTAGTGTCGA
260 TGGTTGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGA
*
3030009 CACATTATTTAGACATATTCTCTCATAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTAC
325 CACATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTAC
3030074 ATATTACAT
390 ATATTACAT
3030083 TATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTT
1 TATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTT
3030148 GCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACAT
66 GCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACAT
*
3030213 TATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTACATATT
131 TATTTAGACATATTCTCTCATAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTACATATT
3030278 ACATTATACTT
196 ACATTATACTT
3030289 GTACCGGTAA
Statistics
Matches: 1303, Mismatches: 35, Indels: 66
0.93 0.02 0.05
Matches are distributed among these distances:
363 68 0.05
364 1 0.00
368 1 0.00
376 2 0.00
377 90 0.07
378 185 0.14
380 5 0.00
381 5 0.00
383 191 0.15
384 90 0.07
385 2 0.00
397 23 0.02
398 619 0.48
399 21 0.02
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (398 bp):
TATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTT
GCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACAT
TATTTAGACATATTCTCTCATAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTACATATT
ACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTAT
GGTTGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGAC
ACATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTACA
TATTACAT
Found at i:3029752 original size:597 final size:580
Alignment explanation
Indices: 3028526--3030288 Score: 2909
Period size: 597 Copynumber: 3.0 Consensus size: 580
3028516 GTAGGAATCA
* * *
3028526 TATACTTTTGG-GTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGT
1 TATACTTTTGGTTTTCGATGTTTTTGGGATCGACAC-TTTTATATATGGATCGACACTTTATGGG
*
3028590 TGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAATTAAATTAGTGTCGACACA
65 TGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACA
* *
3028655 TTATTTAGACATATTCTCTCATAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTAAATAT
130 TTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTACATAT
*
3028720 TACATTATACTTTTGGGTTCGATGATTTTGGGATCGACATTTTTTATATATGGATCGACACTTTA
195 TACATTATACTTTTGGGTTCG-TGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTA
*
3028785 TGGTTGCACCCTGTTTTCCATTCATTATGGAACAAAAATATCGACACAAACTAAATTAGTGTCGA
259 TGGTTGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGA
*
3028850 CACATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTAC
324 CACATTATTTAGACATATTCTCTCATAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTAC
3028915 ATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACAC
389 ATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACAC
* *
3028980 TTTATGGTTGCGCCCTGTTTTCCATTCATTATGGAACAAAAATATCGACACAAACTAAATTAGTG
454 TTTATGGTTGCACCCTGTTTTCCATTCA-T-T----C-------TGGACACAAAC-AAATTA--G
*
3029045 TCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAATTTGTACCGGTTAGATTGAAAAA
503 TCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAA
3029110 TTACATATTACAT
568 TTACATATTACAT
3029123 TATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTATATATGGATCGACACTTTATGGGT
1 TATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTATATATGGATCGACACTTTATGGGT
3029188 GCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACAT
66 GCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACAT
3029253 TATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTACATATT
131 TATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTACATATT
3029318 ACATTATACTTTTGGGTTCGTTGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTAT
196 ACATTATACTTTTGGGTTCG-TGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTAT
*
3029383 GGTTGCACCCTGTTTTCCATTCATTCTGTAACAAAAATATCGACACAAACTAAATTAGTGTCGAC
260 GGTTGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGAC
* * *
3029448 ATATTATTTAGACATATTCTCTCATAAAATCGGTAAAAGTGTACCGGTTAGATTGAAAAATTACA
325 ACATTATTTAGACATATTCTCTCATAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTACA
3029513 TATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACT
390 TATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACT
3029578 TTATGGTTGCACCCTGTTTTCCATTCATTCTGGA-AC-AA-AAA-TA-TCGACACATTATTTAGA
455 TTATGGTTGCACCCTGTTTTCCATTCATTCTGGACACAAACAAATTAGTCGACACATTATTTAGA
3029638 CATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTACATATTACAT
520 CATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTACATATTACAT
3029699 TATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGG
1 TATACTTTTGGTTTTCGATGTTTTTGGGATCGACAC-TTTTATATATGGATCGACACTTTATGGG
3029764 TGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACA
65 TGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACA
3029829 TTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTACATAT
130 TTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTACATAT
3029894 TACATTATA----------C----TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTAT
195 TACATTATACTTTTGGGTTCGTGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTAT
*
3029945 GGTTGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACATAAACTAAATTAGTGTCGAC
260 GGTTGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGAC
3030010 ACATTATTTAGACATATTCTCTCATAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTACA
325 ACATTATTTAGACATATTCTCTCATAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTACA
3030075 TATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACT
390 TATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACT
3030140 TTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGT
455 TTATGGTTGCACCCTGTTTTCCATTCATTCT-G------------GACACAAAC-AAATTA--GT
3030205 CGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAAT
504 CGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAAT
3030270 TACATATTACAT
569 TACATATTACAT
3030282 TATACTT
1 TATACTT
3030289 GTACCGGTAA
Statistics
Matches: 1121, Mismatches: 22, Indels: 60
0.93 0.02 0.05
Matches are distributed among these distances:
562 262 0.23
563 1 0.00
567 1 0.00
575 2 0.00
576 115 0.10
577 169 0.15
579 5 0.00
580 5 0.00
582 2 0.00
583 87 0.08
584 3 0.00
591 1 0.00
595 1 0.00
596 1 0.00
597 444 0.40
598 22 0.02
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (580 bp):
TATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTATATATGGATCGACACTTTATGGGT
GCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACAT
TATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTACATATT
ACATTATACTTTTGGGTTCGTGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATG
GTTGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACA
CATTATTTAGACATATTCTCTCATAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTACAT
ATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTT
TATGGTTGCACCCTGTTTTCCATTCATTCTGGACACAAACAAATTAGTCGACACATTATTTAGAC
ATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTACATATTACAT
Found at i:3029954 original size:184 final size:184
Alignment explanation
Indices: 3029720--3030288 Score: 729
Period size: 184 Copynumber: 3.0 Consensus size: 184
3029710 TTTTCGATGT
*
3029720 TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCAT
1 TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCAT
3029785 TCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCA
66 TCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCA
3029850 TAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC
131 TAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC
3029904 TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCAT
1 TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCAT
*
3029969 TCTGGAACAAAAATATCGACATAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCA
66 TCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCA
*
3030034 TAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC
131 TAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC
* ** * * * *
3030088 TTTTGGGTTCG--A-TGATT-T-T-GGGATCGACACTTTTTAT-ATATGGATCGACACTTTATGG
1 TTTTGGGATCGACACTTTTTATATATGGATCGACAC--TTTATGGT-T-G--C-ACCCTGT-T--
* ***** * *
3030146 TTGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACAC
56 TT----CC---ATT-CATTC-TGGAACAAAAAT---ATCGACACAAACTAAATTAGTGTCGACAC
3030211 ATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTACATA
109 ATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTACATA
3030276 TTACATTATAC
174 TTACATTATAC
3030287 TT
1 TT
3030289 GTACCGGTAA
Statistics
Matches: 343, Mismatches: 20, Indels: 29
0.88 0.05 0.07
Matches are distributed among these distances:
178 10 0.03
179 2 0.01
180 7 0.02
181 4 0.01
182 1 0.00
183 1 0.00
184 196 0.57
185 1 0.00
187 2 0.01
191 2 0.01
194 2 0.01
195 5 0.01
196 5 0.01
199 105 0.31
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (184 bp):
TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCAT
TCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCA
TAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC
Found at i:3030138 original size:199 final size:199
Alignment explanation
Indices: 3029904--3030288 Score: 752
Period size: 199 Copynumber: 1.9 Consensus size: 199
3029894 TACATTATAC
3029904 TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCAT
1 TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCAT
*
3029969 TCTGGAACAAAAATATCGACATAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCA
66 TCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCA
3030034 TAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCG
131 TAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCG
3030099 ATGA
196 ATGA
3030103 TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCAT
1 TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCAT
3030168 TCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCA
66 TCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCA
*
3030233 TAAAACCGGTAAACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
131 TAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
3030289 GTACCGGTAA
Statistics
Matches: 184, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
199 184 1.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.36
Consensus pattern (199 bp):
TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCAT
TCTGGAACAAAAATATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCA
TAAAACCGGTAAAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCG
ATGA
Found at i:3030997 original size:21 final size:21
Alignment explanation
Indices: 3030972--3031015 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3030962 CCCCTTATGC
3030972 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
3030993 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
3031014 CT
1 CT
3031016 TGATTGTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:3033150 original size:22 final size:23
Alignment explanation
Indices: 3033122--3033179 Score: 88
Period size: 19 Copynumber: 2.7 Consensus size: 23
3033112 TTTTATGTCA
3033122 GGTTTTATCATATTTTTGATACC
1 GGTTTTATCATATTTTTGATACC
3033145 GG-TTTATC--A-TTTTGATACC
1 GGTTTTATCATATTTTTGATACC
3033164 GGTTTTATCATATTTT
1 GGTTTTATCATATTTT
3033180 ACCTGTTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
19 12 0.39
20 7 0.23
22 7 0.23
23 5 0.16
ACGTcount: A:0.21, C:0.12, G:0.14, T:0.53
Consensus pattern (23 bp):
GGTTTTATCATATTTTTGATACC
Found at i:3033344 original size:20 final size:20
Alignment explanation
Indices: 3033317--3033363 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
3033307 TCCGGTAACG
3033317 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
3033336 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
3033357 TTTTACC
1 TTTTACC
3033364 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:3034051 original size:228 final size:229
Alignment explanation
Indices: 3033412--3034130 Score: 1345
Period size: 228 Copynumber: 3.1 Consensus size: 229
3033402 ACTTTTATAC
3033412 GTATGAACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAA-TT
1 GTATGAACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
3033476 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
66 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
3033541 TTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
131 TTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
3033606 GATAATAATAAATATGTTTTCCACAGTGAAATAA
196 GATAATAATAAATATGTTTTCCACAGTGAAATAA
3033640 GTATGAACACTTTTATAAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATT
1 GTATGAACACTTTTAT-AAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATT
*
3033705 TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTATTAATTTCATTTACACAAAAA
65 TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAA
3033770 ATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAA
130 ATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAA
3033835 AGATAATAATAAATATGTTTTCCACAGTGAAATAA
195 AGATAATAATAAATATGTTTTCCACAGTGAAATAA
3033870 GTATGAACACTTTTATAAAAATGATATATA-TTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
1 GTATGAACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
* *
3033934 TTTTTAATAGTGTTTCATGTTTTACACCTACAATATTAATTTAATAATTTCATTTACACACAAAA
66 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
3033999 TTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
131 TTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
*
3034064 GATAATAATAAATATATTTT-CACAGTGAAATAA
196 GATAATAATAAATATGTTTTCCACAGTGAAATAA
* * *
3034097 GTATGGACACTTTTATAAAAAGGATAGATACTTT
1 GTATGAACACTTTTATAAAAATGATATATACTTT
3034131 ACAATATAAC
Statistics
Matches: 480, Mismatches: 8, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
227 40 0.08
228 199 0.41
229 60 0.12
230 181 0.38
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (229 bp):
GTATGAACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
TTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA
GATAATAATAAATATGTTTTCCACAGTGAAATAA
Found at i:3034373 original size:11 final size:11
Alignment explanation
Indices: 3034352--3034381 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3034342 AATGTATCCG
3034352 ATATT-ACCGT
1 ATATTAACCGT
3034362 ATATTAACCGT
1 ATATTAACCGT
3034373 ATATTAACC
1 ATATTAACC
3034382 CGCCTTTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.37
Consensus pattern (11 bp):
ATATTAACCGT
Found at i:3034963 original size:16 final size:16
Alignment explanation
Indices: 3034939--3034994 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
3034929 TTTGAATTGT
* *
3034939 TATTGACCTAATTTGA
1 TATTTACCTAACTTGA
3034955 TATTTACCTAACTTGA
1 TATTTACCTAACTTGA
**
3034971 TATTTATTTAACTT-A
1 TATTTACCTAACTTGA
3034986 TATATTACC
1 TAT-TTACC
3034995 ATTAATGAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
15 4 0.12
16 29 0.88
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.48
Consensus pattern (16 bp):
TATTTACCTAACTTGA
Found at i:3035024 original size:19 final size:19
Alignment explanation
Indices: 3034996--3035038 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
3034986 TATATTACCA
*
3034996 TTAATGAAATTATAAGATT
1 TTAATAAAATTATAAGATT
* *
3035015 TTAATAAAATTGTGAGATT
1 TTAATAAAATTATAAGATT
3035034 TTAAT
1 TTAAT
3035039 TTGTATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (19 bp):
TTAATAAAATTATAAGATT
Found at i:3035717 original size:18 final size:18
Alignment explanation
Indices: 3035672--3035718 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
3035662 TGGGCATGAT
*
3035672 TATAATATATAGTATGTA
1 TATAAGATATAGTATGTA
*
3035690 TATAATATATAGT-TGTCA
1 TATAAGATATAGTATGT-A
*
3035708 TATTAGATATA
1 TATAAGATATA
3035719 TCATATATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 3 0.12
18 23 0.88
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.45
Consensus pattern (18 bp):
TATAAGATATAGTATGTA
Found at i:3035855 original size:17 final size:17
Alignment explanation
Indices: 3035810--3035858 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 17
3035800 TAATAGTTGC
*
3035810 ATTGCATATCAT-AA-A
1 ATTGCATATTATAAATA
*
3035825 ATTTCATA-TA-AAATA
1 ATTGCATATTATAAATA
3035840 ATTGCATATTATAAATA
1 ATTGCATATTATAAATA
3035857 AT
1 AT
3035859 ATTACATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
14 3 0.11
15 15 0.56
16 2 0.07
17 7 0.26
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (17 bp):
ATTGCATATTATAAATA
Found at i:3035897 original size:16 final size:16
Alignment explanation
Indices: 3035871--3035925 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
3035861 TACATATTAT
*
3035871 ATTAG-ATATTAAATA
1 ATTAGTATATTATATA
3035886 ATTAGTATATTATATA
1 ATTAGTATATTATATA
*
3035902 GTT--TATATTATATA
1 ATTAGTATATTATATA
*
3035916 GTTAGTATAT
1 ATTAGTATAT
3035926 ACTATAAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
14 14 0.40
15 5 0.14
16 16 0.46
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (16 bp):
ATTAGTATATTATATA
Found at i:3035931 original size:16 final size:16
Alignment explanation
Indices: 3035868--3035925 Score: 70
Period size: 14 Copynumber: 3.9 Consensus size: 16
3035858 TATTACATAT
3035868 TATA-TTAG-ATATTA
1 TATAGTTAGTATATTA
* *
3035882 AATAATTAGTATATTA
1 TATAGTTAGTATATTA
3035898 TATAGTT--TATATTA
1 TATAGTTAGTATATTA
3035912 TATAGTTAGTATAT
1 TATAGTTAGTATAT
3035926 ACTATAAAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
14 17 0.46
15 4 0.11
16 16 0.43
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (16 bp):
TATAGTTAGTATATTA
Found at i:3037032 original size:27 final size:27
Alignment explanation
Indices: 3037000--3037108 Score: 114
Period size: 27 Copynumber: 3.9 Consensus size: 27
3036990 TAGTATAAAT
3037000 TATATAAATATAAACTATATTATATAGA
1 TATATAAATATAAACTATATTATATA-A
* * * *
3037028 -GTATAAATATCATCTATAGTATATAA
1 TATATAAATATAAACTATATTATATAA
3037054 TATATAAATATAAACTATAGGTTATATAA
1 TATATAAATATAAACTATA--TTATATAA
3037083 TATATATATATATAATA-TATATTATA
1 TATATA-A-ATATAA-ACTATATTATA
3037109 CAAATAGTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
26 1 0.01
27 36 0.54
29 18 0.27
30 1 0.01
31 10 0.15
32 1 0.01
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (27 bp):
TATATAAATATAAACTATATTATATAA
Found at i:3037057 original size:7 final size:7
Alignment explanation
Indices: 3036986--3037108 Score: 62
Period size: 7 Copynumber: 17.6 Consensus size: 7
3036976 TTTTTGAATT
*
3036986 TATATAG
1 TATATAA
3036993 TATA-AA
1 TATATAA
3036999 TTATATAA
1 -TATATAA
3037007 -ATATAA
1 TATATAA
*
3037013 -ACTATAT
1 TA-TATAA
3037020 TATATAGA
1 TATATA-A
*
3037028 -GTATAA
1 TATATAA
*
3037034 -ATATCA
1 TATATAA
* *
3037040 TCTATAG
1 TATATAA
3037047 TATATAA
1 TATATAA
3037054 TATATAA
1 TATATAA
3037061 -ATATAA
1 TATATAA
*
3037067 -ACTATAGGT
1 TA-TATA--A
3037076 TATATAA
1 TATATAA
3037083 TATATATA
1 TATATA-A
3037091 TATATAA
1 TATATAA
*
3037098 TATATAT
1 TATATAA
3037105 TATA
1 TATA
3037109 CAAATAGTTT
Statistics
Matches: 91, Mismatches: 14, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
6 20 0.22
7 56 0.62
8 10 0.11
9 4 0.04
10 1 0.01
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.41
Consensus pattern (7 bp):
TATATAA
Found at i:3037108 original size:20 final size:20
Alignment explanation
Indices: 3036986--3037371 Score: 82
Period size: 20 Copynumber: 19.0 Consensus size: 20
3036976 TTTTTGAATT
* *
3036986 TATATAGTATAAATTATATA
1 TATATAATATATATTATATA
*
3037006 AATATAA-ACTATATTATATA
1 TATATAATA-TATATTATATA
* *
3037026 GAGTATAA-ATATCATCTATA-G
1 TA-TATAATATAT-AT-TATATA
*
3037047 TATATAATATATA-AATATA
1 TATATAATATATATTATATA
* *
3037066 AACTATAGGTTATATAATATATATA
1 TA-TATA--ATATAT-AT-TATATA
*
3037091 TATATAATATATATTATACA
1 TATATAATATATATTATATA
* *
3037111 AATAGT-TTATATATT-TCAT-
1 TATA-TAATATATATTAT-ATA
3037130 TA-ATAA-ACTATA-TATATA
1 TATATAATA-TATATTATATA
* *
3037148 -AT-TCATATGTAAATTATATA
1 TATAT-A-ATATATATTATATA
* *
3037168 GTTTATACACATA-ATTCATATA
1 -TATATA-ATATATATT-ATATA
* * *
3037190 TA-ATAATGTAAACTATATA
1 TATATAATATATATTATATA
* *
3037209 TTATACAATATATA-AATATCA
1 -TATATAATATATATTATAT-A
* *
3037230 AATATAGTATATAGTT-TATA
1 TATATAATATATA-TTATATA
*
3037250 TATA-AAT-TATAGT-T-TA
1 TATATAATATATATTATATA
*
3037266 TATATAATATATAATAATATA
1 TATATAATATAT-ATTATATA
*
3037287 AATATAAACTATATAGTTTATATA
1 TATAT-AA-TATATA--TTATATA
*
3037311 TATATAATACATATACTT-TGTA
1 TATATAAT--ATATA-TTATATA
3037333 TATA-AACTATATAGTT-TATA
1 TATATAA-TATATA-TTATATA
* *
3037353 TATGTTATAT-TATTATATA
1 TATATAATATATATTATATA
3037372 GTTTATTTAT
Statistics
Matches: 268, Mismatches: 51, Indels: 95
0.65 0.12 0.23
Matches are distributed among these distances:
16 6 0.02
17 12 0.04
18 19 0.07
19 25 0.09
20 94 0.35
21 40 0.15
22 36 0.13
23 11 0.04
24 19 0.07
25 6 0.02
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (20 bp):
TATATAATATATATTATATA
Done.