Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold341
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: 1349338
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 4 of 9
Found at i:485122 original size:34 final size:35
Alignment explanation
Indices: 485083--485155 Score: 121
Period size: 34 Copynumber: 2.1 Consensus size: 35
485073 AATTTTTAAT
485083 ATATTCTATTAAAAATAGCAATTAA-TTTAAAAAA
1 ATATTCTATTAAAAATAGCAATTAATTTTAAAAAA
* *
485117 ATATTCTATTAAAAATAGCTATTAATTTTTAAAAA
1 ATATTCTATTAAAAATAGCAATTAATTTTAAAAAA
485152 ATAT
1 ATAT
485156 AATTTGAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 24 0.67
35 12 0.33
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (35 bp):
ATATTCTATTAAAAATAGCAATTAATTTTAAAAAA
Found at i:493624 original size:18 final size:19
Alignment explanation
Indices: 493592--493630 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
493582 ATATATTTAT
493592 AAAATAAATTAAAAAATAA
1 AAAATAAATTAAAAAATAA
*
493611 AAAATTAATT-AAAAATAA
1 AAAATAAATTAAAAAATAA
493629 AA
1 AA
493631 TGTGATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAATAAATTAAAAAATAA
Found at i:494061 original size:34 final size:34
Alignment explanation
Indices: 494023--494092 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
494013 AATTTAGAAG
494023 TTAAT-TTTATTATATATTATTAA-A-ATATTTTATA
1 TTAATATTTA-TATATATTA-TAATATATATTTT-TA
*
494057 TTAATATTTATATATTTTATAATATATATTTTTA
1 TTAATATTTATATATATTATAATATATATTTTTA
494091 TT
1 TT
494093 GTTTAATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
33 3 0.09
34 18 0.56
35 11 0.34
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (34 bp):
TTAATATTTATATATATTATAATATATATTTTTA
Found at i:496422 original size:17 final size:17
Alignment explanation
Indices: 496382--496427 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
496372 TTTAGATAAT
*
496382 AATTTATTAGATATTTAA
1 AATTT-TTAAATATTTAA
*
496400 ATTTTTTAAATATTTAA
1 AATTTTTAAATATTTAA
*
496417 AATTTTAAAAT
1 AATTTTTAAAT
496428 TAACTTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 20 0.83
18 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
AATTTTTAAATATTTAA
Found at i:496978 original size:14 final size:14
Alignment explanation
Indices: 496955--496984 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
496945 CATGTCCCTC
496955 TTTTTCTCTTCTTT
1 TTTTTCTCTTCTTT
*
496969 TTTTTTTCTTCTTT
1 TTTTTCTCTTCTTT
496983 TT
1 TT
496985 ATTATTATGT
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:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTCTCTTCTTT
Found at i:497103 original size:13 final size:13
Alignment explanation
Indices: 497085--497110 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
497075 ATAATTAAAA
497085 AAATTTAATTTAT
1 AAATTTAATTTAT
497098 AAATTTAATTTAT
1 AAATTTAATTTAT
497111 TATTTATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AAATTTAATTTAT
Found at i:497204 original size:20 final size:19
Alignment explanation
Indices: 497175--497223 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 19
497165 TATAATTAAA
*
497175 TTTAAATAAAAATATATTAT
1 TTTAATTAAAAA-ATATTAT
497195 TTTAATT-AAAAATATTAT
1 TTTAATTAAAAAATATTAT
497213 TTTAAATTAAA
1 TTT-AATTAAA
497224 TTAAAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 10 0.38
19 8 0.31
20 8 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTAATTAAAAAATATTAT
Found at i:497220 original size:19 final size:20
Alignment explanation
Indices: 497175--497223 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
497165 TATAATTAAA
*
497175 TTTAAATAAAAATATATTAT
1 TTTAAATTAAAATATATTAT
497195 TTT-AATTAAAA-ATATTAT
1 TTTAAATTAAAATATATTAT
497213 TTTAAATTAAA
1 TTTAAATTAAA
497224 TTAAAATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 10 0.37
19 14 0.52
20 3 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAAATTAAAATATATTAT
Found at i:497225 original size:24 final size:26
Alignment explanation
Indices: 497198--497263 Score: 77
Period size: 24 Copynumber: 2.7 Consensus size: 26
497188 ATATTATTTT
* *
497198 AATTAAAAAT-ATTATTTTAAATT-A
1 AATTAAAAATAATAAATTTAAATTCA
497222 AATT-AAAATAATAAATTTAAATTCA
1 AATTAAAAATAATAAATTTAAATTCA
497247 AATTAAATAA-AATAAAT
1 AATTAAA-AATAATAAAT
497264 AATTAGATCG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
23 5 0.14
24 15 0.42
25 5 0.14
26 9 0.25
27 2 0.06
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (26 bp):
AATTAAAAATAATAAATTTAAATTCA
Found at i:497297 original size:11 final size:11
Alignment explanation
Indices: 497275--497315 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 11
497265 ATTAGATCGA
497275 TAAATA-AATT
1 TAAATATAATT
497285 TAAATATAATT
1 TAAATATAATT
*
497296 TAAATTATTATT
1 TAAA-TATAATT
497308 TAAA-ATAA
1 TAAATATAA
497316 AAATATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.33
11 8 0.30
12 10 0.37
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TAAATATAATT
Found at i:497362 original size:33 final size:32
Alignment explanation
Indices: 497285--497364 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 32
497275 TAAATAAATT
* *
497285 TAAATA-TAATTTAAATTATTATTTAAAATAA
1 TAAATATTAATATAAATTATTATATAAAATAA
*
497316 -AAATATTTTATATAAATTTATT-TATAAAATTAA
1 TAAATA-TTAATATAAA-TTATTATATAAAA-TAA
497349 TAAATATTAATATAAA
1 TAAATATTAATATAAA
497365 AATACTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
30 5 0.12
32 13 0.32
33 17 0.43
34 5 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
TAAATATTAATATAAATTATTATATAAAATAA
Found at i:503828 original size:5 final size:5
Alignment explanation
Indices: 503805--503864 Score: 52
Period size: 5 Copynumber: 11.6 Consensus size: 5
503795 TAGAATTTAA
* *
503805 TATAT T-TAT T-TATT TATAT TATATT TATAT TATTTT TATAT CATAT
1 TATAT TATAT TATA-T TATAT TATA-T TATAT TA-TAT TATAT TATAT
503851 TATAT TATAGT TAT
1 TATAT TATA-T TAT
503865 TTTTTTTGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
4 6 0.13
5 25 0.54
6 15 0.33
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (5 bp):
TATAT
Found at i:503831 original size:11 final size:11
Alignment explanation
Indices: 503811--503889 Score: 71
Period size: 11 Copynumber: 7.7 Consensus size: 11
503801 TTAATATATT
503811 TATT-TATTTA
1 TATTATATTTA
503821 TATTATATTTA
1 TATTATATTTA
*
503832 TATTATTTTTA
1 TATTATATTTA
*
503843 TATCATA-TTA
1 TATTATATTTA
*
503853 TATTATAGTTA
1 TATTATATTTA
503864 T-TT-T-TTT-
1 TATTATATTTA
* *
503871 TGTTATATTTG
1 TATTATATTTA
503882 TATTATAT
1 TATTATAT
503890 CTAAAATTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
7 1 0.02
8 4 0.07
9 2 0.04
10 18 0.32
11 32 0.56
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.66
Consensus pattern (11 bp):
TATTATATTTA
Found at i:503834 original size:27 final size:28
Alignment explanation
Indices: 503799--503868 Score: 69
Period size: 27 Copynumber: 2.6 Consensus size: 28
503789 GTATTATAGA
*
503799 ATTTAATA-TATTTATT-TATTTATATTAT
1 ATTTAATATTATTT-TTATA-TCATATTAT
503827 ATTT-ATATTATTTTTATATCATATTAT
1 ATTTAATATTATTTTTATATCATATTAT
503854 A-TT-ATAGTTATTTTT
1 ATTTAATA-TTATTTTT
503869 TTTGTTATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
26 5 0.13
27 22 0.58
28 11 0.29
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (28 bp):
ATTTAATATTATTTTTATATCATATTAT
Found at i:503864 original size:21 final size:21
Alignment explanation
Indices: 503799--503864 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
503789 GTATTATAGA
503799 ATTTA-AT-ATATT-TATT-T
1 ATTTATATCATATTATATTAT
*
503816 ATTTATATTATATTTATATTAT
1 ATTTATATCATA-TTATATTAT
*
503838 TTTTATATCATATTATATTAT
1 ATTTATATCATATTATATTAT
*
503859 AGTTAT
1 ATTTAT
503865 TTTTTTTGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
17 5 0.12
18 2 0.05
19 3 0.08
20 2 0.05
21 17 0.43
22 11 0.28
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (21 bp):
ATTTATATCATATTATATTAT
Found at i:504978 original size:13 final size:13
Alignment explanation
Indices: 504960--504989 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
504950 ACTAGATTCC
504960 TTTTTTTTC-TTT
1 TTTTTTTTCATTT
504972 TTTTTTTTCATTT
1 TTTTTTTTCATTT
504985 TTTTT
1 TTTTT
504990 CCTTTCCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.03, C:0.07, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTTTTCATTT
Found at i:506293 original size:15 final size:15
Alignment explanation
Indices: 506247--506294 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
506237 TAAACTAATT
*
506247 TTTTTAAATA-ATTAA
1 TTTTAAAATATATT-A
506262 TTATTAAAATAATATTA
1 TT-TTAAAAT-ATATTA
506279 TTTTAAAATATATTA
1 TTTTAAAATATATTA
506294 T
1 T
506295 CAAAATATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 9 0.31
16 13 0.45
17 4 0.14
18 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTTAAAATATATTA
Found at i:506683 original size:18 final size:18
Alignment explanation
Indices: 506661--506709 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
506651 AAATGAATAT
506661 ATAAAAAAATAACATGAC
1 ATAAAAAAATAACATGAC
* * *
506679 TTAAAATACT-ACATGAC
1 ATAAAAAAATAACATGAC
*
506696 ATGAAAAAATAACA
1 ATAAAAAAATAACA
506710 CCAATATGAA
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.61, C:0.12, G:0.06, T:0.20
Consensus pattern (18 bp):
ATAAAAAAATAACATGAC
Found at i:506804 original size:22 final size:23
Alignment explanation
Indices: 506760--506809 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
506750 AAATTATTGT
506760 ATACAACATAAAAAAATAAAACAA
1 ATACAACATAAAAAAAT-AAACAA
*
506784 ATACAACATGAAAAAAT-AACAA
1 ATACAACATAAAAAAATAAACAA
506806 ATAC
1 ATAC
506810 GAATTATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 9 0.36
24 16 0.64
ACGTcount: A:0.70, C:0.14, G:0.02, T:0.14
Consensus pattern (23 bp):
ATACAACATAAAAAAATAAACAA
Found at i:507245 original size:20 final size:21
Alignment explanation
Indices: 507222--507277 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 21
507212 ATTTTCAATT
507222 ATGTTATTTTTTGT-ATATTC
1 ATGTTATTTTTTGTCATATTC
*
507242 ATGTTATTTTTCATATCATATTC
1 ATGTTATTTTT--TGTCATATTC
*
507265 ATTTTATTTTTTG
1 ATGTTATTTTTTG
507278 CATTGTGTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 11 0.37
21 1 0.03
22 2 0.07
23 16 0.53
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.64
Consensus pattern (21 bp):
ATGTTATTTTTTGTCATATTC
Found at i:507310 original size:17 final size:17
Alignment explanation
Indices: 507268--507310 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
507258 CATATTCATT
507268 TTATTTTTTGCATTGTG
1 TTATTTTTTGCATTGTG
* *
507285 TCATATTTT-CGATTGTG
1 TTATTTTTTGC-ATTGTG
507302 TTATTTTTT
1 TTATTTTTT
507311 TCATATCATG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 1 0.05
17 20 0.95
ACGTcount: A:0.14, C:0.07, G:0.14, T:0.65
Consensus pattern (17 bp):
TTATTTTTTGCATTGTG
Found at i:507350 original size:59 final size:59
Alignment explanation
Indices: 507248--507362 Score: 149
Period size: 59 Copynumber: 1.9 Consensus size: 59
507238 ATTCATGTTA
* * * *
507248 TTTTTCATATCATATTCATTTTATTTTTTGCATTGTGTCATATTTTCGATTGTGTTATT
1 TTTTTCATATCATATTCATTTTATTTTTCGCATCGTATCATATTTTCGATTATGTTATT
* * * * *
507307 TTTTTCATATCATGTTCCTTTTATTTTTCGTATCGTATTATATTTTTGATTATGTT
1 TTTTTCATATCATATTCATTTTATTTTTCGCATCGTATCATATTTTCGATTATGTT
507363 TTAATTGTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 47 1.00
ACGTcount: A:0.18, C:0.10, G:0.10, T:0.62
Consensus pattern (59 bp):
TTTTTCATATCATATTCATTTTATTTTTCGCATCGTATCATATTTTCGATTATGTTATT
Found at i:509931 original size:19 final size:18
Alignment explanation
Indices: 509891--509932 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
509881 TTAATTTGTT
*
509891 ATTTTATTTAAATTATCA
1 ATTTTATTTAAAATATCA
509909 ATTTTAATTTAAAAT-TCA
1 ATTTT-ATTTAAAATATCA
509927 CATTTT
1 -ATTTT
509933 TATCAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTATTTAAAATATCA
Found at i:512873 original size:14 final size:16
Alignment explanation
Indices: 512843--512874 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
512833 TTATTTTAGA
512843 TAAAAAGAACGAATTT
1 TAAAAAGAACGAATTT
512859 TAAAAAG-AC-AATTT
1 TAAAAAGAACGAATTT
512873 TA
1 TA
512875 TTTTTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 2 0.12
16 7 0.44
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.28
Consensus pattern (16 bp):
TAAAAAGAACGAATTT
Found at i:513741 original size:167 final size:167
Alignment explanation
Indices: 513464--513765 Score: 416
Period size: 166 Copynumber: 1.8 Consensus size: 167
513454 CCTGTTTCCA
* * * *
513464 AAATACGAGATTTTCTTCTCTGTAAATTTTTTGGGGGAGGATTTTCATTGGTTCAAAATTTTTAA
1 AAATACGAGATTTTCTTCTCCGTAAATATTTTCGGGGAGGATTTTCATTGGTTCAAAATTTATAA
* * *
513529 AATTAATCAAATATTATTATTTAACTCATATTAAATCAGTTTTAAAAAATTCATTTATTTTCATG
66 AATTAATCAAATATCATCATTTAACTCATATTAAATCAGTTTT-AAAAATTAATTTATTTTCATG
513594 AGTTTTTCATTTTTTTCCTTAAACTTTTTCTATTTTTG
130 AGTTTTTCATTTTTTTCCTTAAACTTTTTCTATTTTTG
*
513632 AAATAC-AGAGTTTTCTAT-TCCGTAAATATTTTCGGGG-GGATTTTTC-TTGGTTCATAA-TTA
1 AAATACGAGA-TTTTCT-TCTCCGTAAATATTTTCGGGGAGGA-TTTTCATTGGTTCAAAATTTA
* * * *
513692 TAAAATTCATGAAATATCATCATTTAATTCATATTAAATTAGTTTTTAAAAATTAATTTATTTTC
63 TAAAATTAATCAAATATCATCATTTAACTCATATTAAATCAG-TTTTAAAAATTAATTTATTTTC
513757 ATGAGTTTT
127 ATGAGTTTT
513766 GAATTTTTCT
Statistics
Matches: 118, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
166 64 0.54
167 20 0.17
168 33 0.28
169 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (167 bp):
AAATACGAGATTTTCTTCTCCGTAAATATTTTCGGGGAGGATTTTCATTGGTTCAAAATTTATAA
AATTAATCAAATATCATCATTTAACTCATATTAAATCAGTTTTAAAAATTAATTTATTTTCATGA
GTTTTTCATTTTTTTCCTTAAACTTTTTCTATTTTTG
Found at i:513758 original size:166 final size:168
Alignment explanation
Indices: 513390--513765 Score: 426
Period size: 168 Copynumber: 2.2 Consensus size: 168
513380 TCTAATCACC
* * * * *
513390 ATTAAATCAATTTCAAAAAATTTATTCATTTTCATGAGCTTTTTCA-TTTTTT-CTTAGAA-TAC
1 ATTAAATCAGTTTTAAAAAATTAATTTATTTTCATGAG-TTTTTCATTTTTTTCCTTA-AACT-T
* * * *** * * *
513452 CTCCTGTTTCCAAAATACGAGATTTTCTTCTCTGTAAATTTTTTGGGGGAGGATTTTCATTGGTT
63 TTTCTATTTTTGAAATACGAGATTTTCTTCTCCGTAAATATTTTCGGGGAGGATTTTCATTGGTT
* * *
513517 CAAAATTTTTAAAATTAATCAAATATTATTATTTAACTCAT
128 CAAAATTTATAAAATTAATCAAATATCATCATTTAACTCAT
*
513558 ATTAAATCAGTTTTAAAAAATTCATTTATTTTCATGAGTTTTTCATTTTTTTCCTTAAACTTTTT
1 ATTAAATCAGTTTTAAAAAATTAATTTATTTTCATGAGTTTTTCATTTTTTTCCTTAAACTTTTT
513623 CTATTTTTGAAATAC-AGAGTTTTCTAT-TCCGTAAATATTTTCGGGG-GGATTTTTC-TTGGTT
66 CTATTTTTGAAATACGAGA-TTTTCT-TCTCCGTAAATATTTTCGGGGAGGA-TTTTCATTGGTT
* * * *
513684 CATAA-TTATAAAATTCATGAAATATCATCATTTAATTCAT
128 CAAAATTTATAAAATTAATCAAATATCATCATTTAACTCAT
* *
513724 ATTAAATTAGTTTTTAAAAATTAATTTATTTTCATGAGTTTT
1 ATTAAATCAGTTTTAAAAAATTAATTTATTTTCATGAGTTTT
513766 GAATTTTTCT
Statistics
Matches: 178, Mismatches: 24, Indels: 14
0.82 0.11 0.06
Matches are distributed among these distances:
166 68 0.38
167 23 0.13
168 81 0.46
169 6 0.03
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.48
Consensus pattern (168 bp):
ATTAAATCAGTTTTAAAAAATTAATTTATTTTCATGAGTTTTTCATTTTTTTCCTTAAACTTTTT
CTATTTTTGAAATACGAGATTTTCTTCTCCGTAAATATTTTCGGGGAGGATTTTCATTGGTTCAA
AATTTATAAAATTAATCAAATATCATCATTTAACTCAT
Found at i:514148 original size:98 final size:99
Alignment explanation
Indices: 514044--514242 Score: 364
Period size: 98 Copynumber: 2.0 Consensus size: 99
514034 TGAAAATTGA
*
514044 TCATATAAAATTTTATTTTAATTTTCAAGTTTTAATTTTTACAATTTAAT-ATTTTTATTATTTT
1 TCATATAAAATTTTATCTTAATTTTCAAGTTTTAATTTTTACAATTTAATCATTTTTATTATTTT
*
514108 TTATGGTATAATTTTACAAATTTATATAAATGTC
66 TTATGATATAATTTTACAAATTTATATAAATGTC
*
514142 TCATATAAAATTTTATCTTAATTTTCAAGTTTTAATTTTTACAATTTAATCTTTTTTATTATTTT
1 TCATATAAAATTTTATCTTAATTTTCAAGTTTTAATTTTTACAATTTAATCATTTTTATTATTTT
514207 TTATGATATAATTTTACAAATTTATATAAATGTC
66 TTATGATATAATTTTACAAATTTATATAAATGTC
514241 TC
1 TC
514243 TCAAAATCTA
Statistics
Matches: 97, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
98 49 0.51
99 48 0.49
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.56
Consensus pattern (99 bp):
TCATATAAAATTTTATCTTAATTTTCAAGTTTTAATTTTTACAATTTAATCATTTTTATTATTTT
TTATGATATAATTTTACAAATTTATATAAATGTC
Found at i:521132 original size:2 final size:2
Alignment explanation
Indices: 521125--521159 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
521115 GAGGATTTTC
* *
521125 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
521160 ACAAACAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:522339 original size:8 final size:8
Alignment explanation
Indices: 522318--522360 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
522308 CCTAAGCCAC
*
522318 TTATTTTC
1 TTATTTTT
*
522326 TCATTTTT
1 TTATTTTT
522334 TTATTTTT
1 TTATTTTT
522342 TTAATTTTTT
1 TT-A-TTTTT
522352 TTATTTTT
1 TTATTTTT
522360 T
1 T
522361 CAAATACGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 21 0.70
9 2 0.07
10 7 0.23
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (8 bp):
TTATTTTT
Found at i:522341 original size:9 final size:9
Alignment explanation
Indices: 522329--522360 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
522319 TATTTTCTCA
522329 TTTTTTTAT
1 TTTTTTTAT
*
522338 TTTTTTAAT
1 TTTTTTTAT
522347 TTTTTTTAT
1 TTTTTTTAT
522356 TTTTT
1 TTTTT
522361 CAAATACGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:522982 original size:65 final size:65
Alignment explanation
Indices: 522895--523297 Score: 163
Period size: 62 Copynumber: 6.5 Consensus size: 65
522885 GACATTGGGC
* * * * * * ** *
522895 TTAGAAAGAGATGCCACCAACTTGTGCGGGCTTTTG-AGAATGTTGCCATTGACTTGTGTCGGCT
1 TTAGAAAGGGTTGCCACAAACTTGTGCGGGCTTTAGAAAAAGGTTGCCACCGACTTATGTCGGC-
522959 T
65 T
* * *
522960 TTAGAAAGGGTTGTCACAAACTTGTGTGGGCTTTAGAAAAAGGTTGCCACCGACTTATGTGGGCT
1 TTAGAAAGGGTTGCCACAAACTTGTGCGGGCTTTAGAAAAAGGTTGCCACCGACTTATGTCGGCT
* ** ** ** * * *
523025 TTAG-AAGGGTTGCTACCGACTTGTGTAGGCTTTA-ACTAGGGTTGCCATCGAC-T-TGTGGGCT
1 TTAGAAAGGGTTGCCACAAACTTGTGCGGGCTTTAGAAAAAGGTTGCCACCGACTTATGTCGGCT
* ** * * * * * *
523086 TTA-AAAGGGGTGCCACTGA-TT-TGTGGGCTTT-G-AAAGGGGTGTCACTGAC-T-TGTGGGCT
1 TTAGAAAGGGTTGCCACAAACTTGTGCGGGCTTTAGAAAAAGGTTGCCACCGACTTATGTCGGCT
** * * * *
523144 TTAG-AAGGG-TGCCATTAACATGT--GGACTTT--AAAAAGGGTGCCACTC-AC-T-TGTGGGC
1 TTAGAAAGGGTTGCCACAAACTTGTGCGGGCTTTAGAAAAAGGTTGCCAC-CGACTTATGTCGGC
523200 T
65 T
* * ** * * * * *
523201 TTCGAAAAAGGTTGCCACCGACTTTTGTGGGCTTTAG--AAGGGTTGCCACCGACTTGTGTGGGC
1 TTAG-AAAGGGTTGCCACAAACTTGTGCGGGCTTTAGAAAAAGGTTGCCACCGACTTATGTCGGC
523264 T
65 T
* *
523265 TTAG-AAGGGTTGCCATC-GACTTGTGTGGGCTTT
1 TTAGAAAGGGTTGCCA-CAAACTTGTGCGGGCTTT
523298 GGCTAGGGTT
Statistics
Matches: 268, Mismatches: 51, Indels: 41
0.74 0.14 0.11
Matches are distributed among these distances:
57 38 0.14
58 29 0.11
59 14 0.05
60 11 0.04
61 24 0.09
62 44 0.16
63 16 0.06
64 36 0.13
65 35 0.13
66 21 0.08
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (65 bp):
TTAGAAAGGGTTGCCACAAACTTGTGCGGGCTTTAGAAAAAGGTTGCCACCGACTTATGTCGGCT
Found at i:523005 original size:33 final size:33
Alignment explanation
Indices: 522890--523297 Score: 106
Period size: 31 Copynumber: 13.2 Consensus size: 33
522880 CCAACGACAT
* * *
522890 TGGGC-TTAGAAAGA-GATGCCACCAACTTGTG
1 TGGGCTTTAGAAAAAGGTTGCCACAAACTTGTG
* * * * ***
522921 CGGGCTTTTG-AGAATGTTGCCATTGACTTGTG
1 TGGGCTTTAGAAAAAGGTTGCCACAAACTTGTG
* * *
522953 TCGGCTTTTAG-AAAGGGTTGTCACAAACTTGTG
1 TGGGC-TTTAGAAAAAGGTTGCCACAAACTTGTG
** *
522986 TGGGCTTTAGAAAAAGGTTGCCACCGACTTATG
1 TGGGCTTTAGAAAAAGGTTGCCACAAACTTGTG
* * **
523019 TGGGCTTTAG--AAGGGTTGCTACCGACTTGTG
1 TGGGCTTTAGAAAAAGGTTGCCACAAACTTGTG
* ** * *
523050 TAGGCTTTA-ACTAGGGTTGCCATC-GAC-T-TG
1 TGGGCTTTAGAAAAAGGTTGCCA-CAAACTTGTG
* * **
523080 TGGGCTTT--AAAAGGGGTGCCACTGA-TT-TG
1 TGGGCTTTAGAAAAAGGTTGCCACAAACTTGTG
* * * **
523109 TGGGCTTT-G-AAAGGGGTGTCACTGAC-T-TG
1 TGGGCTTTAGAAAAAGGTTGCCACAAACTTGTG
* ** *
523138 TGGGCTTTAG---AAGGGTGCCATTAAC--ATG
1 TGGGCTTTAGAAAAAGGTTGCCACAAACTTGTG
* * **
523166 TGGACTTT--AAAAAGGGTGCCACTCAC-T-TG
1 TGGGCTTTAGAAAAAGGTTGCCACAAACTTGTG
* ** *
523195 TGGGCTTTCGAAAAAGGTTGCCACCGACTTTTG
1 TGGGCTTTAGAAAAAGGTTGCCACAAACTTGTG
* **
523228 TGGGCTTTAG--AAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAAAAAGGTTGCCACAAACTTGTG
* *
523259 TGGGCTTTAG--AAGGGTTGCCATC-GACTTGTG
1 TGGGCTTTAGAAAAAGGTTGCCA-CAAACTTGTG
523290 TGGGCTTT
1 TGGGCTTT
523298 GGCTAGGGTT
Statistics
Matches: 306, Mismatches: 49, Indels: 44
0.77 0.12 0.11
Matches are distributed among these distances:
28 21 0.07
29 71 0.23
30 10 0.03
31 104 0.34
32 38 0.12
33 62 0.20
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (33 bp):
TGGGCTTTAGAAAAAGGTTGCCACAAACTTGTG
Found at i:523109 original size:29 final size:29
Alignment explanation
Indices: 522984--523621 Score: 425
Period size: 29 Copynumber: 21.6 Consensus size: 29
522974 CACAAACTTG
* * *
522984 TGTGGGCTTTAGAAAAAGGTTGCCACCGACTT
1 TGTGGGCTTT--AAAAGGGGTGCCACTGAC-T
* * * *
523016 ATGTGGGCTTTAGAAGGGTTGCTACCGACT
1 -TGTGGGCTTTAAAAGGGGTGCCACTGACT
* *
523046 TGTGTAGGCTTTAACTAGGGTTGCCA-TCGACT
1 TGTG--GGCTTTAA-AAGGGGTGCCACT-GACT
*
523078 TGTGGGCTTTAAAAGGGGTGCCACTGATT
1 TGTGGGCTTTAAAAGGGGTGCCACTGACT
* *
523107 TGTGGGCTTTGAAAGGGGTGTCACTGACT
1 TGTGGGCTTTAAAAGGGGTGCCACTGACT
* * * *
523136 TGTGGGCTTTAGAA-GGGTGCCATTAACA
1 TGTGGGCTTTAAAAGGGGTGCCACTGACT
* * *
523164 TGTGGACTTTAAAAAGGGTGCCACTCACT
1 TGTGGGCTTTAAAAGGGGTGCCACTGACT
* * *
523193 TGTGGGCTTTCGAAAAAGGTTGCCACCGACTTT
1 TGTGGGCTTT--AAAAGGGGTGCCACTGAC--T
* * *
523226 TGTGGGCTTTAGAAGGGTTGCCACCGACTT
1 TGTGGGCTTTAAAAGGGGTGCCACTGAC-T
* *
523256 GTGTGGGCTTTAGAAGGGTTGCCA-TCGACTT
1 -TGTGGGCTTTAAAAGGGGTGCCACT-GAC-T
*** *
523287 GTGTGGGCTTTGGCTAGGGTTGCCA-TCGACT
1 -TGTGGGCTTT-AAAAGGGGTGCCACT-GACT
**
523318 TGTGGGCTTTAAAAGGGGTGTTACTGACT
1 TGTGGGCTTTAAAAGGGGTGCCACTGACT
* * * *
523347 TGTAGGCTTTGAAAGGGGTGTCATTGACT
1 TGTGGGCTTTAAAAGGGGTGCCACTGACT
* ** * * *
523376 GGTGGGCTTTGGAA-GGGTGCCATTAACA
1 TGTGGGCTTTAAAAGGGGTGCCACTGACT
*
523404 TGTGGGCTTTGGAAA-GGGTGCCACTGACT
1 TGTGGGCTTT-AAAAGGGGTGCCACTGACT
* **
523433 TGTAGGCTTTGGAA-GGGTGCCACTGACT
1 TGTGGGCTTTAAAAGGGGTGCCACTGACT
* * *
523461 TGTAGGCTTTGAAAGGGGTGACACTGACT
1 TGTGGGCTTTAAAAGGGGTGCCACTGACT
* * *
523490 TATAGGCTTTGAAAA-AGGTGCCACTGACT
1 TGTGGGCTTT-AAAAGGGGTGCCACTGACT
* * *
523519 TGTGGGTTTTGAAAA-AGGTGCCGCTGACT
1 TGTGGGCTTT-AAAAGGGGTGCCACTGACT
* *
523548 TGTGGGCTTTGAAAA-GGGTGCCATTGACA
1 TGTGGGCTTT-AAAAGGGGTGCCACTGACT
* * * *
523577 TGTAGACTTTAAAAGGGATGCCACTGAGT
1 TGTGGGCTTTAAAAGGGGTGCCACTGACT
*
523606 TGTGGAC-TTAAAAGGG
1 TGTGGGCTTTAAAAGGG
523622 TGTCACGAAG
Statistics
Matches: 508, Mismatches: 79, Indels: 41
0.81 0.13 0.07
Matches are distributed among these distances:
28 85 0.17
29 251 0.49
30 26 0.05
31 93 0.18
32 32 0.06
33 21 0.04
ACGTcount: A:0.21, C:0.16, G:0.33, T:0.30
Consensus pattern (29 bp):
TGTGGGCTTTAAAAGGGGTGCCACTGACT
Found at i:523183 original size:57 final size:57
Alignment explanation
Indices: 522984--523623 Score: 475
Period size: 57 Copynumber: 10.8 Consensus size: 57
522974 CACAAACTTG
* * * * *
522984 TGTGGGCTTTAGAAAAAGGTTGCCACCGACTTATGTGGGCTTTAGAAGGGTTGCTACCGACT
1 TGTGGGCTTT-G-AAAAGGGTGCCACTGAC-T-TGTGGGCTTTAAAAGGG-TGCCACTGACT
* *
523046 TGTGTAGGCTTT-AACTAGGGTTGCCA-TCGACTTGTGGGCTTTAAAAGGGGTGCCACTGATT
1 TGTG--GGCTTTGAA-AAGGG-TGCCACT-GACTTGTGGGCTTTAAAA-GGGTGCCACTGACT
* * * * * *
523107 TGTGGGCTTTGAAAGGGGTGTCACTGACTTGTGGGCTTTAGAAGGGTGCCATTAACA
1 TGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACT
* * * * *
523164 TGTGGACTTTAAAAAGGGTGCCACTCACTTGTGGGCTTTCGAAAAAGGTTGCCACCGACTTT
1 TGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTT---AAAAGGGTGCCACTGAC--T
* * *
523226 TGTGGGCTTT-AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAAGGGTTGCCA-TCGACTT
1 TGTGGGCTTTGAAAAGGG-TGCCACTGAC-T-TGTGGGCTTTAAAAGGG-TGCCACT-GAC-T
*** **
523287 GTGTGGGCTTTGGCTAGGGTTGCCA-TCGACTTGTGGGCTTTAAAAGGGGTGTTACTGACT
1 -TGTGGGCTTTGAAAAGGG-TGCCACT-GACTTGTGGGCTTTAAAA-GGGTGCCACTGACT
* * * * * ** * * *
523347 TGTAGGCTTTGAAAGGGGTGTCATTGACTGGTGGGCTTTGGAAGGGTGCCATTAACA
1 TGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACT
* * **
523404 TGTGGGCTTTGGAAAGGGTGCCACTGACTTGTAGGCTTTGGAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACT
* * * * * *
523461 TGTAGGCTTTGAAAGGGGTGACACTGACTTATAGGCTTTGAAAAAGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTT-AAAAGGGTGCCACTGACT
* * * * *
523519 TGTGGGTTTTGAAAAAGGTGCCGCTGACTTGTGGGCTTTGAAAAGGGTGCCATTGACA
1 TGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTT-AAAAGGGTGCCACTGACT
* * * *
523577 TGTAGACTTT-AAAAGGGATGCCACTGAGTTGTGGAC-TTAAAAGGGTG
1 TGTGGGCTTTGAAAAGGG-TGCCACTGACTTGTGGGCTTTAAAAGGGTG
523624 TCACGAAGTT
Statistics
Matches: 462, Mismatches: 90, Indels: 58
0.76 0.15 0.10
Matches are distributed among these distances:
56 9 0.02
57 142 0.31
58 124 0.27
59 24 0.05
60 15 0.03
61 59 0.13
62 51 0.11
63 22 0.05
64 16 0.03
ACGTcount: A:0.21, C:0.16, G:0.33, T:0.30
Consensus pattern (57 bp):
TGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACT
Found at i:523424 original size:240 final size:241
Alignment explanation
Indices: 522979--523442 Score: 732
Period size: 240 Copynumber: 1.9 Consensus size: 241
522969 GTTGTCACAA
*
522979 ACTTGTGTGGGCTTTAGAAAAAGGTTGCCACCGACTTATGTGGGCTTTAGAAGGGTTGCTACCGA
1 ACTTGTGTGGGCTTTAG-AAAAGGTTGCCACCGACTTATGTGGGCTTTAGAAGGGTTGCCACCGA
*
523044 CTTGTGTAGGCTTTAACTAGGGTTGCCATCGACTTGTGGGCTTTAAAAGGGGTGCCACTGATTTG
65 CTTGTGTAGGCTTTAACTAGGGTTGCCATCGACTTGTGGGCTTTAAAAGGGGTGCCACTGACTTG
* *
523109 TGGGCTTTGAAAGGGGTGTCACTGACTTGTGGGCTTTAGAAGGGTGCCATTAACATGTGGACTTT
130 TAGGCTTTGAAAGGGGTGTCACTGACTGGTGGGCTTTAGAAGGGTGCCATTAACATGTGGACTTT
*
523174 AAAAAGGGTGCCACTCACTTGTGGGCTTTCGAAAAAGGTTGCCACCG
195 AAAAAGGGTGCCACTCACTTGTAGGCTTTCGAAAAAGGTTGCCACCG
* * * *
523221 ACTTTTGTGGGCTTTAG-AAGGGTTGCCACCGACTTGTGTGGGCTTTAGAAGGGTTGCCATCGAC
1 ACTTGTGTGGGCTTTAGAAAAGGTTGCCACCGACTTATGTGGGCTTTAGAAGGGTTGCCACCGAC
* ** **
523285 TTGTGTGGGCTTTGGCTAGGGTTGCCATCGACTTGTGGGCTTTAAAAGGGGTGTTACTGACTTGT
66 TTGTGTAGGCTTTAACTAGGGTTGCCATCGACTTGTGGGCTTTAAAAGGGGTGCCACTGACTTGT
* * * *
523350 AGGCTTTGAAAGGGGTGTCATTGACTGGTGGGCTTTGGAAGGGTGCCATTAACATGTGGGCTTTG
131 AGGCTTTGAAAGGGGTGTCACTGACTGGTGGGCTTTAGAAGGGTGCCATTAACATGTGGACTTTA
* *
523415 GAAAGGGTGCCACTGACTTGTAGGCTTT
196 AAAAGGGTGCCACTCACTTGTAGGCTTT
523443 GGAAGGGTGC
Statistics
Matches: 202, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
240 186 0.92
242 16 0.08
ACGTcount: A:0.20, C:0.16, G:0.33, T:0.31
Consensus pattern (241 bp):
ACTTGTGTGGGCTTTAGAAAAGGTTGCCACCGACTTATGTGGGCTTTAGAAGGGTTGCCACCGAC
TTGTGTAGGCTTTAACTAGGGTTGCCATCGACTTGTGGGCTTTAAAAGGGGTGCCACTGACTTGT
AGGCTTTGAAAGGGGTGTCACTGACTGGTGGGCTTTAGAAGGGTGCCATTAACATGTGGACTTTA
AAAAGGGTGCCACTCACTTGTAGGCTTTCGAAAAAGGTTGCCACCG
Found at i:523550 original size:87 final size:86
Alignment explanation
Indices: 523074--523610 Score: 273
Period size: 86 Copynumber: 6.1 Consensus size: 86
523064 GGTTGCCATC
* * * * * *
523074 GACTTGTGGGCTTT-AAAAGGGGTGCCACTGATTTGTGGGCTTTGAAAGGGGTGTCACTGACTTG
1 GACTTGTGGGCTTTGAAAA--GGTGCCACTGACTTGTAGGCTTTGAAAAGGGTGACACTGACATA
* * *
523138 TGGGCTTT-AGAAGGGTGCCATT
64 TAGGCTTTGAAAAGGGTGCCACT
* * * * * * * * *
523160 AACATGTGGACTTTAAAAAGGGTGCCACTCACTTGTGGGCTTTCGAAAAAGGTTGCCACCGACTT
1 GACTTGTGGGCTTTGAAAA-GGTGCCACTGACTTGTAGGCTTT-G-AAAAGGGTGACACTGAC--
* * * * *
523225 TTGTGGGCTTT-AGAAGGGTTGCCACC
61 ATATAGGCTTTGAAAAGGG-TGCCACT
* * *** *
523251 GACTTGTGTGGGCTTT-AGAAGGGTTGCCA-TCGACTTGTGTGGGCTTTGGCTAGGGTTGCCA-T
1 GAC-T-TGTGGGCTTTGA-AAAGG-TGCCACT-GAC-T-TGTAGGCTTTGAAAAGGG-TGACACT
* * * **
523313 CGACTTGTGGGCTTT-AAAAGGGGTGTTACT
58 -GACATATAGGCTTTGAAAA-GGGTGCCACT
* * * * * * * * * * *
523343 GACTTGTAGGCTTTGAAAGGGGTGTCATTGACTGGTGGGCTTTG-GAAGGGTGCCATTAACATGT
1 GACTTGTGGGCTTTGAAA-AGGTGCCACTGACTTGTAGGCTTTGAAAAGGGTGACACTGACATAT
* *
523407 GGGCTTTGGAAAGGGTGCCACT
65 AGGCTTTGAAAAGGGTGCCACT
* * * * *
523429 GACTTGTAGGCTTTGGAAGGGTGCCACTGACTTGTAGGCTTTGAAAGGGGTGACACTGACTTATA
1 GACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTAGGCTTTGAAAAGGGTGACACTGACATATA
*
523494 GGCTTTGAAAAAGGTGCCACT
66 GGCTTTGAAAAGGGTGCCACT
* * * * * *
523515 GACTTGTGGGTTTTGAAAAAGGTGCCGCTGACTTGTGGGCTTTGAAAAGGGTGCCATTGACATGT
1 GACTTGTGGGCTTTG-AAAAGGTGCCACTGACTTGTAGGCTTTGAAAAGGGTGACACTGACATAT
*
523580 AGACTTT-AAAAGGGATGCCACT
65 AGGCTTTGAAAAGGG-TGCCACT
*
523602 GAGTTGTGG
1 GACTTGTGG
523611 ACTTAAAAGG
Statistics
Matches: 363, Mismatches: 64, Indels: 47
0.77 0.14 0.10
Matches are distributed among these distances:
85 21 0.06
86 126 0.35
87 74 0.20
88 23 0.06
89 1 0.00
90 36 0.10
91 13 0.04
92 25 0.07
93 24 0.07
94 10 0.03
95 10 0.03
ACGTcount: A:0.21, C:0.16, G:0.34, T:0.30
Consensus pattern (86 bp):
GACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTAGGCTTTGAAAAGGGTGACACTGACATATA
GGCTTTGAAAAGGGTGCCACT
Found at i:523638 original size:27 final size:26
Alignment explanation
Indices: 523585--523672 Score: 122
Period size: 27 Copynumber: 3.3 Consensus size: 26
523575 CATGTAGACT
523585 TTAAAAGGGATGCCACTGAGTTGTGGAC
1 TTAAAAGGG-TGCCAC-GAGTTGTGGAC
*
523613 TTAAAAGGGTGTCACGAAGTTGTGGAC
1 TTAAAAGGGTGCCACG-AGTTGTGGAC
* *
523640 TTAAAAGTGTACCACGAGTTGTGGAC
1 TTAAAAGGGTGCCACGAGTTGTGGAC
523666 TTAAAAG
1 TTAAAAG
523673 AAATGCCACT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
26 18 0.33
27 28 0.51
28 9 0.16
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.26
Consensus pattern (26 bp):
TTAAAAGGGTGCCACGAGTTGTGGAC
Found at i:525076 original size:24 final size:23
Alignment explanation
Indices: 525049--525120 Score: 83
Period size: 24 Copynumber: 3.1 Consensus size: 23
525039 TTGTTCTCTC
525049 TTTTTATTTTTCTTTTGCACTTTT
1 TTTTTATTTTTCTTTTGCA-TTTT
* *
525073 TTTTTGTTTTTCTTTT-CATCTT
1 TTTTTATTTTTCTTTTGCATTTT
* *
525095 TTTTTACTTTTGCTTTTGAATTTT
1 TTTTTA-TTTTTCTTTTGCATTTT
525119 TT
1 TT
525121 GTCATTTTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
22 8 0.20
23 11 0.28
24 21 0.52
ACGTcount: A:0.08, C:0.11, G:0.06, T:0.75
Consensus pattern (23 bp):
TTTTTATTTTTCTTTTGCATTTT
Found at i:525099 original size:46 final size:46
Alignment explanation
Indices: 525025--525120 Score: 115
Period size: 46 Copynumber: 2.1 Consensus size: 46
525015 CATGTCTTTG
* * *
525025 TTTTTTTATTTTTGTTGTTCTCTCTTTTTA-TTTTTCTTTTGCACTT
1 TTTTTTTATTTTTCTTGTTCTCTCTTTTTACTTTTGCTTTTG-AATT
* *
525071 TTTTTTTGTTTTTCTT-TTCATCTTTTTTTACTTTTGCTTTTGAATT
1 TTTTTTTATTTTTCTTGTTC-TCTCTTTTTACTTTTGCTTTTGAATT
525117 TTTT
1 TTTT
525121 GTCATTTTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
45 3 0.07
46 30 0.70
47 10 0.23
ACGTcount: A:0.07, C:0.11, G:0.06, T:0.75
Consensus pattern (46 bp):
TTTTTTTATTTTTCTTGTTCTCTCTTTTTACTTTTGCTTTTGAATT
Found at i:528768 original size:14 final size:15
Alignment explanation
Indices: 528738--528768 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
528728 TTTCTTTGCC
528738 ATATTTATTGAAATG
1 ATATTTATTGAAATG
528753 ATATTTATTG-AATG
1 ATATTTATTGAAATG
528767 AT
1 AT
528769 GAGATGATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (15 bp):
ATATTTATTGAAATG
Found at i:531113 original size:28 final size:27
Alignment explanation
Indices: 531060--531114 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
531050 GATTATAGTT
* * *
531060 AGCTTGATAACAATCGTAAATTCGTGC
1 AGCTTGATAAAAACCGTAAATCCGTGC
531087 AGCTTGATGAAAAACCGTAAATCCGTGC
1 AGCTTGAT-AAAAACCGTAAATCCGTGC
531115 TAATCTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (27 bp):
AGCTTGATAAAAACCGTAAATCCGTGC
Found at i:532171 original size:18 final size:19
Alignment explanation
Indices: 532140--532175 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
532130 GAAAGTTACC
*
532140 TTATTTTTATTATTTTTTT
1 TTATTTTTACTATTTTTTT
532159 TTATTTTT-CTATTTTTT
1 TTATTTTTACTATTTTTT
532176 CATAACTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (19 bp):
TTATTTTTACTATTTTTTT
Found at i:532477 original size:176 final size:175
Alignment explanation
Indices: 532284--532634 Score: 648
Period size: 176 Copynumber: 2.0 Consensus size: 175
532274 AACCCAGGTC
532284 ACTCGGTTTTTTTTTTTTTGGTGCATGTGTCACAATGATCATTTTCTATTCTTTTGTTAATTTAT
1 ACTCGGTTTTTTTTTTTTTGGTGCATGTGTCACAATGATCATTTTCTATTCTTTTGTTAATTTAT
* *
532349 GATCAAAGCTTAACTTTAGTACTCAAAGTAGCCTGGGTTCGAAACCTAGGTCACTCATTTTCTCC
66 GATCAAAGCTTAACTTTAGTACTCAAAGTAGCCTGGGTTCGAAACCCAAGTCACTCATTTTCTCC
532414 TTTTTTTGGTGCATGTGTCACAATGATTATTTTTTATTCTTTTGT
131 TTTTTTTGGTGCATGTGTCACAATGATTATTTTTTATTCTTTTGT
* *
532459 ACTCGTTTTTCTTTTTTTTTTGTGCATGTGTCACAATGATCATTTTCTATTCTTTTGTTAATTTA
1 ACTCGGTTTT-TTTTTTTTTGGTGCATGTGTCACAATGATCATTTTCTATTCTTTTGTTAATTTA
*
532524 TGATCAAAGCTTAACTTTAGTACTCAAAGTAGTCTGGGTTCGAAACCCAAGTCACTCATTTTCTC
65 TGATCAAAGCTTAACTTTAGTACTCAAAGTAGCCTGGGTTCGAAACCCAAGTCACTCATTTTCTC
532589 CTTTTTTTGGTGCATGTGTCACAATGATTATTTTTTATTCTTTTGT
130 CTTTTTTTGGTGCATGTGTCACAATGATTATTTTTTATTCTTTTGT
532635 TAATTTATGA
Statistics
Matches: 170, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
175 9 0.05
176 161 0.95
ACGTcount: A:0.21, C:0.16, G:0.15, T:0.48
Consensus pattern (175 bp):
ACTCGGTTTTTTTTTTTTTGGTGCATGTGTCACAATGATCATTTTCTATTCTTTTGTTAATTTAT
GATCAAAGCTTAACTTTAGTACTCAAAGTAGCCTGGGTTCGAAACCCAAGTCACTCATTTTCTCC
TTTTTTTGGTGCATGTGTCACAATGATTATTTTTTATTCTTTTGT
Found at i:534374 original size:2 final size:2
Alignment explanation
Indices: 534369--534417 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
534359 ATTAAAAAAG
* * *
534369 AT AT AT AT AG AA AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
534411 A- AT AT AT
1 AT AT AT AT
534418 TGTGTAGACA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:534382 original size:16 final size:16
Alignment explanation
Indices: 534363--534393 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
534353 ATACAGATTA
534363 AAAAAGATATATATAG
1 AAAAAGATATATATAG
*
534379 AAAAATATATATATA
1 AAAAAGATATATATA
534394 TATATATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (16 bp):
AAAAAGATATATATAG
Found at i:535429 original size:12 final size:13
Alignment explanation
Indices: 535401--535428 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
535391 GCATCGCCTC
535401 TTTCTTTTTTTTT
1 TTTCTTTTTTTTT
535414 TTTCTTTTTTTTT
1 TTTCTTTTTTTTT
535427 TT
1 TT
535429 CCCTTTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (13 bp):
TTTCTTTTTTTTT
Found at i:536556 original size:21 final size:22
Alignment explanation
Indices: 536536--536577 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
536526 TTTATAATTA
536536 AATTT-ATATAAAAATA-TATT
1 AATTTAATATAAAAATACTATT
*
536556 ATTTTAATATAAAAATACTATT
1 AATTTAATATAAAAATACTATT
536578 TTAAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTTAATATAAAAATACTATT
Found at i:536578 original size:19 final size:21
Alignment explanation
Indices: 536541--536581 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
536531 AATTAAATTT
*
536541 ATATAAAAATATATTATTTTA
1 ATATAAAAATATACTATTTTA
536562 ATAT-AAAA-ATACTATTTTA
1 ATATAAAAATATACTATTTTA
536581 A
1 A
536582 ATTAAACTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 4 0.21
21 4 0.21
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATAAAAATATACTATTTTA
Found at i:538291 original size:20 final size:21
Alignment explanation
Indices: 538268--538311 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
538258 TATTTAATAC
538268 TTATTAAATA-TTAAAATTAT
1 TTATTAAATATTTAAAATTAT
* *
538288 TTATTTAATATTTAAAATTTT
1 TTATTAAATATTTAAAATTAT
538309 TTA
1 TTA
538312 ATATAACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATTAAATATTTAAAATTAT
Found at i:538625 original size:40 final size:40
Alignment explanation
Indices: 538577--538654 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 40
538567 ACAAATCAAT
*
538577 AAATTAAATCTCAAGAACACAAAATCTT-TTGACATCAACA
1 AAATTAAATCTAAAGAACACAAAAT-TTGTTGACATCAACA
*
538617 AAATTAAATCTAAAGAACCCAAAATTTGTTGACATCAA
1 AAATTAAATCTAAAGAACACAAAATTTGTTGACATCAA
538655 GAACTTAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 2 0.06
40 33 0.94
ACGTcount: A:0.50, C:0.18, G:0.06, T:0.26
Consensus pattern (40 bp):
AAATTAAATCTAAAGAACACAAAATTTGTTGACATCAACA
Found at i:539451 original size:2 final size:2
Alignment explanation
Indices: 539446--539473 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
539436 ACACACACAC
539446 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
539474 GTATGTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:541892 original size:18 final size:18
Alignment explanation
Indices: 541869--541906 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
541859 CTACCAGCAT
541869 ATATAAAGTATCATTTTG
1 ATATAAAGTATCATTTTG
541887 ATATAAAGTATCATTTTG
1 ATATAAAGTATCATTTTG
541905 AT
1 AT
541907 CAACAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (18 bp):
ATATAAAGTATCATTTTG
Found at i:543039 original size:51 final size:51
Alignment explanation
Indices: 542977--543077 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 51
542967 TACTGTTGTT
*
542977 AAAAAAATTCAGAACATAG-AAAGAAAAATAAACTTCAAATTCCTAAGGCAA
1 AAAAAAATTCAGAACATAGAAAAGAAAAAT-AACTTCAAATTCCAAAGGCAA
543028 AAAAAAATTCAGAACATAGAAAAGAAAAATAACTTCAAATTCCAAAGGCA
1 AAAAAAATTCAGAACATAGAAAAGAAAAATAACTTCAAATTCCAAAGGCA
543078 GAGAAAATTA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 38 0.79
52 10 0.21
ACGTcount: A:0.59, C:0.14, G:0.10, T:0.17
Consensus pattern (51 bp):
AAAAAAATTCAGAACATAGAAAAGAAAAATAACTTCAAATTCCAAAGGCAA
Found at i:543055 original size:26 final size:25
Alignment explanation
Indices: 542977--543056 Score: 67
Period size: 26 Copynumber: 3.1 Consensus size: 25
542967 TACTGTTGTT
542977 AAAAAAATTCAGAACATAGAAAGAA
1 AAAAAAATTCAGAACATAGAAAGAA
* * *
543002 AAATAAACTTCA-AATTCCT--AAGGCAA
1 AAA-AAAATTCAGAA--CATAGAAAG-AA
543028 AAAAAAATTCAGAACATAGAAAAGAA
1 AAAAAAATTCAGAACATAG-AAAGAA
543054 AAA
1 AAA
543057 TAACTTCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 15
0.66 0.10 0.24
Matches are distributed among these distances:
24 2 0.05
25 15 0.37
26 19 0.46
27 5 0.12
ACGTcount: A:0.64, C:0.11, G:0.10, T:0.15
Consensus pattern (25 bp):
AAAAAAATTCAGAACATAGAAAGAA
Found at i:543064 original size:26 final size:23
Alignment explanation
Indices: 542977--543056 Score: 56
Period size: 24 Copynumber: 3.2 Consensus size: 23
542967 TACTGTTGTT
542977 AAAAAAATTCAGAACATAGAAAG
1 AAAAAAATTCAGAACATAGAAAG
* *
543000 AAAAATAAACTTCA-AATTCCTAAGGCAA-
1 -AAAA-AAA-TTCAGAA--CAT-A-GAAAG
543028 AAAAAAATTCAGAACATAGAAAAG
1 AAAAAAATTCAGAACATAG-AAAG
543052 AAAAA
1 AAAAA
543057 TAACTTCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
22 1 0.02
23 3 0.07
24 11 0.26
25 9 0.21
26 9 0.21
27 6 0.14
28 1 0.02
29 3 0.07
ACGTcount: A:0.64, C:0.11, G:0.10, T:0.15
Consensus pattern (23 bp):
AAAAAAATTCAGAACATAGAAAG
Found at i:544150 original size:3 final size:3
Alignment explanation
Indices: 544142--544191 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
544132 GATTTTCCTT
544142 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
544190 TT
1 TT
544192 TGGTATTGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:544403 original size:2 final size:2
Alignment explanation
Indices: 544396--544434 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
544386 AACCCATCCA
544396 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
544435 CAGAGTTGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:544588 original size:16 final size:18
Alignment explanation
Indices: 544562--544594 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
544552 TTTTATATCA
544562 TTTATTTTTAAT-TATTT
1 TTTATTTTTAATATATTT
544579 TTTA-TTTTAATATATT
1 TTTATTTTTAATATATT
544595 ATAAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTATTTTTAATATATTT
Found at i:546305 original size:11 final size:12
Alignment explanation
Indices: 546291--546333 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
546281 AAATTATCAA
546291 AAAATA-AAATT
1 AAAATATAAATT
* *
546302 AAAATATTAATA
1 AAAATATAAATT
546314 AAAATATAAATT
1 AAAATATAAATT
546326 AAAGATAT
1 AAA-ATAT
546334 TTATATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 6 0.23
12 16 0.62
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (12 bp):
AAAATATAAATT
Found at i:548932 original size:2 final size:2
Alignment explanation
Indices: 548925--548951 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
548915 AGGTTAAAGT
548925 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
548952 TCTTGGGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:549363 original size:17 final size:18
Alignment explanation
Indices: 549343--549376 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
549333 AAATCTCTTA
549343 TAAATTAATT-TTTATTC
1 TAAATTAATTATTTATTC
*
549360 TAAATTTATTATTTATT
1 TAAATTAATTATTTATT
549377 TATAACTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TAAATTAATTATTTATTC
Found at i:549890 original size:16 final size:17
Alignment explanation
Indices: 549859--549890 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
549849 TGAATATGTA
549859 TAAATAATATAATTTTT
1 TAAATAATATAATTTTT
549876 TAAAT-ATAT-ATTTTT
1 TAAATAATATAATTTTT
549891 ATTTGATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAAATAATATAATTTTT
Found at i:550927 original size:17 final size:17
Alignment explanation
Indices: 550905--550982 Score: 88
Period size: 16 Copynumber: 4.6 Consensus size: 17
550895 TATAAAAATC
*
550905 AAATTAAAAATTTAAAA
1 AAATTAAAAATTTTAAA
*
550922 AAATT-AAAATTTTATA
1 AAATTAAAAATTTTAAA
550938 AAATTAAAATATTTGTAAA
1 AAATTAAAA-ATTT-TAAA
*
550957 AAA-TAAAAAATTTAAA
1 AAATTAAAAATTTTAAA
*
550973 ACATTAAAAA
1 AAATTAAAAA
550983 ATTATTAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
16 20 0.38
17 17 0.33
18 9 0.17
19 6 0.12
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (17 bp):
AAATTAAAAATTTTAAA
Found at i:550983 original size:17 final size:16
Alignment explanation
Indices: 550905--550985 Score: 67
Period size: 17 Copynumber: 4.8 Consensus size: 16
550895 TATAAAAATC
550905 AAATT-AAAAATTTAAAA
1 AAATTAAAAAATTT--AA
*
550922 AAATT-AAAATTTTATA
1 AAATTAAAAAATTTA-A
*
550938 AAATTAAAATATTTGTAA
1 AAATTAAAA-AATT-TAA
*
550956 AAAATAAAAAATTTAA
1 AAATTAAAAAATTTAA
550972 AACATTAAAAAATT
1 AA-ATTAAAAAATT
550986 ATTAATTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
15 1 0.02
16 11 0.20
17 28 0.51
18 13 0.24
19 2 0.04
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (16 bp):
AAATTAAAAAATTTAA
Found at i:550986 original size:8 final size:8
Alignment explanation
Indices: 550905--550986 Score: 58
Period size: 8 Copynumber: 9.8 Consensus size: 8
550895 TATAAAAATC
550905 AAATTAAA
1 AAATTAAA
*
550913 AATTTAAAA
1 AAATT-AAA
550922 AAATTAAA
1 AAATTAAA
** *
550930 ATTTTATA
1 AAATTAAA
550938 AAATTAAA
1 AAATTAAA
*
550946 ATATTTGTAAA
1 A-A-AT-TAAA
550957 AAA-TAAA
1 AAATTAAA
550964 AAATTTAAA
1 AAA-TTAAA
*
550973 ACATTAAA
1 AAATTAAA
550981 AAATTA
1 AAATTA
550987 TTAATTTTTA
Statistics
Matches: 56, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
7 7 0.12
8 28 0.50
9 14 0.25
10 2 0.04
11 5 0.09
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (8 bp):
AAATTAAA
Found at i:551072 original size:17 final size:17
Alignment explanation
Indices: 551050--551086 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
551040 AAAAAAAAAG
551050 AAAGACTTTTGAATTAA
1 AAAGACTTTTGAATTAA
551067 AAAGACTTTTGAATTAA
1 AAAGACTTTTGAATTAA
551084 AAA
1 AAA
551087 ATTTTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.32
Consensus pattern (17 bp):
AAAGACTTTTGAATTAA
Found at i:551472 original size:30 final size:30
Alignment explanation
Indices: 551437--551548 Score: 75
Period size: 30 Copynumber: 3.5 Consensus size: 30
551427 CAATTTTCAG
551437 ATATTTTTTAAAAATTATTTTGAATTTTTT
1 ATATTTTTTAAAAATTATTTTGAATTTTTT
* *
551467 ATA-TTTTCATAAAATTAATTTGAAGTTTATGAATTT
1 ATATTTTTTA-AAAATTATTTTGAA--TT-T---TTT
* ** **
551503 ATAATTTTTTTAATTTTATTTACAA-TTTTT
1 AT-ATTTTTTAAAAATTATTTTGAATTTTTT
551533 ATATTTTTTAAAAATT
1 ATATTTTTTAAAAATT
551549 TTGATGACAG
Statistics
Matches: 61, Mismatches: 12, Indels: 19
0.66 0.13 0.21
Matches are distributed among these distances:
29 16 0.26
30 21 0.34
32 2 0.03
33 2 0.03
34 1 0.02
36 5 0.08
37 10 0.16
38 4 0.07
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.59
Consensus pattern (30 bp):
ATATTTTTTAAAAATTATTTTGAATTTTTT
Found at i:551540 original size:21 final size:21
Alignment explanation
Indices: 551499--551540 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
551489 AAGTTTATGA
* *
551499 ATTTATAATTTTTTTAATTTT
1 ATTTACAATTTTTATAATTTT
*
551520 ATTTACAATTTTTATATTTTT
1 ATTTACAATTTTTATAATTTT
551541 TAAAAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (21 bp):
ATTTACAATTTTTATAATTTT
Found at i:552074 original size:22 final size:21
Alignment explanation
Indices: 552034--552082 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
552024 AATGTATTTA
*
552034 ATTTATGAATATATTTAATATT
1 ATTTATGAATATATTTAAT-TC
*
552056 ATTTATGTATAT-TTATAATTC
1 ATTTATGAATATATT-TAATTC
552077 ATTTAT
1 ATTTAT
552083 ATTCAAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (21 bp):
ATTTATGAATATATTTAATTC
Found at i:552924 original size:18 final size:19
Alignment explanation
Indices: 552901--553017 Score: 59
Period size: 20 Copynumber: 6.3 Consensus size: 19
552891 GCTTATTTAA
552901 AAATTAA-ATAATTT-ATTT
1 AAATTAATA-AATTTAATTT
552919 AAATTAATAAATTTAAATTT
1 AAATTAATAAATTT-AATTT
* *
552939 AAATT--T-TA-TTATTTT
1 AAATTAATAAATTTAATTT
* * *
552954 AAATTTATTTAATTTTATTT
1 AAA-TTAATAAATTTAATTT
* *
552974 AAAATAATAATTTTTAA-TT
1 AAATTAATAA-ATTTAATTT
* *
552993 AAAATAATATATTTATATTT
1 AAATTAATAAATTTA-ATTT
553013 AAATT
1 AAATT
553018 TAATTAAAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
15 7 0.09
16 4 0.05
17 1 0.01
18 18 0.24
19 18 0.24
20 27 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATTAATAAATTTAATTT
Found at i:552982 original size:55 final size:58
Alignment explanation
Indices: 552894--553024 Score: 144
Period size: 55 Copynumber: 2.3 Consensus size: 58
552884 TAACGAGGCT
* * * * *
552894 TATTTAAAAATTAAATAA-TTTATTTAAATTAATAAATTTAAATTTAAAT-TTTA-TTA
1 TATTT-AAATTTAATTAATTTTATTTAAAATAATAAATTTAAATTAAAATATATATTTA
* * *
552950 T-TTTAAATTTATTTAATTTTATTTAAAATAATAATTTTTAATTAAAATAATATATTTA
1 TATTTAAATTTAATTAATTTTATTTAAAATAATAAATTTAAATTAAAAT-ATATATTTA
553008 TATTTAAATTTAATTAA
1 TATTTAAATTTAATTAA
553025 AAATATATAA
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
54 9 0.15
55 30 0.49
56 1 0.02
57 3 0.05
58 4 0.07
59 14 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (58 bp):
TATTTAAATTTAATTAATTTTATTTAAAATAATAAATTTAAATTAAAATATATATTTA
Found at i:553014 original size:20 final size:18
Alignment explanation
Indices: 552963--553015 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 18
552953 TAAATTTATT
552963 TAATTTTATTTAAAATAA
1 TAATTTTATTTAAAATAA
*
552981 TAATTTTTAATTAAAATAA
1 TAA-TTTTATTTAAAATAA
553000 TATATTTATATTTAAA
1 TA-ATTT-TATTTAAA
553016 TTTAATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 3 0.10
19 19 0.63
20 8 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTTTATTTAAAATAA
Found at i:553030 original size:20 final size:21
Alignment explanation
Indices: 553007--553050 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
552997 TAATATATTT
* *
553007 ATATTTAAAT-TTAATTAAAA
1 ATATATAAATATTAATAAAAA
553027 ATATATAAATATTAATAAAAA
1 ATATATAAATATTAATAAAAA
553048 ATA
1 ATA
553051 ATTTTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATATATAAATATTAATAAAAA
Found at i:553079 original size:21 final size:20
Alignment explanation
Indices: 553041--553080 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
553031 ATAAATATTA
**
553041 ATAAAAAATAATTTTTTAAT
1 ATAAAAAATAATAATTTAAT
553061 ATAAATAAATAATAATTTAA
1 ATAAA-AAATAATAATTTAA
553081 GATTATAGCT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAAAAAATAATAATTTAAT
Found at i:556086 original size:2 final size:2
Alignment explanation
Indices: 556079--556105 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
556069 CTTTGTAGCA
556079 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
556106 GGTGCATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:558097 original size:2 final size:2
Alignment explanation
Indices: 558090--558121 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
558080 AAATGCAAAC
558090 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
558122 TGAGATTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:560696 original size:107 final size:107
Alignment explanation
Indices: 560510--560721 Score: 388
Period size: 107 Copynumber: 2.0 Consensus size: 107
560500 CTTCCTTACA
* *
560510 TCTCTATAGAACCTTCTCCCATATAGAGACCTTGTAAGGATTATATCTCTCATAATTTTAAAAGT
1 TCTCTATAGAACCCTCTCCCATATAGAGACCTTGTAAGGATTATATCTCTCATAATTCTAAAAGT
560575 TAATACTCATTTCATATTTATAGAACCTATTACGTAATCACC
66 TAATACTCATTTCATATTTATAGAACCTATTACGTAATCACC
*
560617 TCTCTATAGATCCCTCTCCCATATAGAGACCTTGTAAGGATTATATCTCTCATAATTCTAAAAGT
1 TCTCTATAGAACCCTCTCCCATATAGAGACCTTGTAAGGATTATATCTCTCATAATTCTAAAAGT
*
560682 TAATACTCATTTCATATTTATAGAGCCTATTACGTAATCA
66 TAATACTCATTTCATATTTATAGAACCTATTACGTAATCA
560722 TCGAGAAATC
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
107 101 1.00
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.37
Consensus pattern (107 bp):
TCTCTATAGAACCCTCTCCCATATAGAGACCTTGTAAGGATTATATCTCTCATAATTCTAAAAGT
TAATACTCATTTCATATTTATAGAACCTATTACGTAATCACC
Found at i:563832 original size:22 final size:21
Alignment explanation
Indices: 563805--563857 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
563795 TATTAATTTT
563805 AAAAATATAAATTGTAAAA-TA
1 AAAAATATAAATT-TAAAAGTA
563826 AATAAAT-TAAAATTTAAAAGTA
1 AA-AAATAT-AAATTTAAAAGTA
*
563848 AAAAAAATAA
1 AAAAATATAA
563858 TTAAAACACA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (21 bp):
AAAAATATAAATTTAAAAGTA
Found at i:564296 original size:16 final size:16
Alignment explanation
Indices: 564265--564370 Score: 53
Period size: 15 Copynumber: 6.6 Consensus size: 16
564255 CCCTTTTTAT
*
564265 TTAT-TTTTATTA-AA
1 TTATATTTTAATATAA
*
564279 TTATATTTTACTATAA
1 TTATATTTTAATATAA
564295 TTA-ATATTTAATATAA
1 TTATAT-TTTAATATAA
*
564311 TTTTTAATTTTTAATATAAA
1 -TTAT-A-TTTTAATAT-AA
* *
564331 TAAAATTTT-A-ATAA
1 TTATATTTTAATATAA
*
564345 TT-TATTTTTATATAA
1 TTATATTTTAATATAA
*
564360 ATATAATTTTA
1 TTAT-ATTTTA
564371 TTTATATTTT
Statistics
Matches: 70, Mismatches: 10, Indels: 21
0.69 0.10 0.21
Matches are distributed among these distances:
13 5 0.07
14 8 0.11
15 16 0.23
16 16 0.23
17 11 0.16
18 1 0.01
19 10 0.14
20 3 0.04
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATATTTTAATATAA
Found at i:564371 original size:16 final size:16
Alignment explanation
Indices: 564319--564371 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
564309 AATTTTTAAT
*
564319 TTTTAATATAAATAAAA
1 TTTT-ATATAAATATAA
* *
564336 TTTTA-AT-AATTTAT
1 TTTTATATAAATATAA
564350 TTTTATATAAATATAA
1 TTTTATATAAATATAA
564366 TTTTAT
1 TTTTAT
564372 TTATATTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
14 9 0.31
15 4 0.14
16 12 0.41
17 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTTATATAAATATAA
Found at i:564373 original size:26 final size:26
Alignment explanation
Indices: 564259--564380 Score: 74
Period size: 25 Copynumber: 4.5 Consensus size: 26
564249 CTCTAACCCT
564259 TTTTATTTATTTTTAT-TAAAT-TATA
1 TTTTATTTATTTTTATATAAATATA-A
* * * *
564284 TTTTA-CTATAATTAATATTTAATATAA
1 TTTTATTTAT-TTTTATA-TAAATATAA
* *
564311 -TTT-TTAATTTTTAATATAAATAAAA
1 TTTTATTTATTTTT-ATATAAATATAA
564336 TTTTAATAATTTATTTTTATATAAATATAA
1 -TTT--T-ATTTATTTTTATATAAATATAA
564366 TTTTATTTATATTTT
1 TTTTATTTAT-TTTT
564381 TTATTTTATT
Statistics
Matches: 72, Mismatches: 12, Indels: 24
0.67 0.11 0.22
Matches are distributed among these distances:
24 3 0.04
25 18 0.25
26 14 0.19
27 12 0.17
28 2 0.03
29 4 0.06
30 11 0.15
31 8 0.11
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (26 bp):
TTTTATTTATTTTTATATAAATATAA
Found at i:564431 original size:42 final size:41
Alignment explanation
Indices: 564329--564431 Score: 104
Period size: 42 Copynumber: 2.5 Consensus size: 41
564319 TTTTAATATA
* * *
564329 AATAAAATTTTAATAATTTATTTTTATATAAATATAATTTT
1 AATAATATTTTAATTATTTATTTTAATATAAATATAATTTT
* * *
564370 ATTTATATTTT--TTATTTTATTAATTAATATAAATATATTTTT
1 AATAATATTTTAATTA-TTTATT--TTAATATAAATATAATTTT
564412 AATAAT-TTTTAATTATTTAT
1 AATAATATTTTAATTATTTAT
564432 CATATATATA
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
39 2 0.04
40 6 0.12
41 12 0.24
42 26 0.53
43 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (41 bp):
AATAATATTTTAATTATTTATTTTAATATAAATATAATTTT
Found at i:564812 original size:24 final size:26
Alignment explanation
Indices: 564778--564836 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 26
564768 TAATTTTCTC
*
564778 AAAAATA-TATACTAA-TAAAA-AAT
1 AAAAATATTATAATAATTAAAATAAT
564801 AAAAATATTATAATAATTTAAAATTAAT
1 AAAAATATTATAATAA-TTAAAA-TAAT
564829 AAAAATAT
1 AAAAATAT
564837 ATGTTAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 7 0.23
24 7 0.23
26 5 0.17
28 11 0.37
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (26 bp):
AAAAATATTATAATAATTAAAATAAT
Found at i:564856 original size:19 final size:18
Alignment explanation
Indices: 564803--564869 Score: 50
Period size: 19 Copynumber: 3.6 Consensus size: 18
564793 TAAAAAATAA
564803 AAATATTATAATA-ATTT
1 AAATATTATAATATATTT
564820 AAA-ATTAATAAAAATATATGTT
1 AAATATT-AT---AATATAT-TT
*
564842 AAATATTATAATATAAATT
1 AAATATTATAATAT-ATTT
564861 AAAT-TTATA
1 AAATATTATA
564870 TTAACATTAC
Statistics
Matches: 41, Mismatches: 1, Indels: 15
0.72 0.02 0.26
Matches are distributed among these distances:
16 3 0.07
17 5 0.12
18 5 0.12
19 11 0.27
20 5 0.12
21 2 0.05
22 7 0.17
23 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (18 bp):
AAATATTATAATATATTT
Found at i:565315 original size:18 final size:18
Alignment explanation
Indices: 565259--565321 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 18
565249 TTAAATATAT
565259 ATTTTATTATAAATT-TTA
1 ATTTTATTAT-AATTATTA
565277 ATTTTATTATAATAATAATTA
1 ATTTTATTATAAT--T-ATTA
*
565298 ATTTCATTATAATTATTA
1 ATTTTATTATAATTATTA
*
565316 TTTTTA
1 ATTTTA
565322 ATAACATCGT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
17 3 0.08
18 18 0.47
19 2 0.05
21 15 0.39
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTTATTATAATTATTA
Found at i:565969 original size:71 final size:74
Alignment explanation
Indices: 565881--566019 Score: 212
Period size: 75 Copynumber: 1.9 Consensus size: 74
565871 ACACTTTTGT
* * *
565881 TTTTGTTTCTATGTTTGGGTT-GCT-TTCCTTT-TCTCTTTTTATCACCACATTTAGTGATTGCA
1 TTTTGTTTCTATCTTTGGGTTGGCTCTTCCTTTCTCTCTTCTTATCACCACATTTAGTGATTACA
565943 ATGCAATAA
66 ATGCAATAA
*
565952 TTTTGTTTCTATCTTTGGGTTGGTTGCTTCCTTTCTCTCTTCTTATCACCACATTTAGTGATTAC
1 TTTTGTTTCTATCTTTGGGTTGGCT-CTTCCTTTCTCTCTTCTTATCACCACATTTAGTGATTAC
566017 AAT
65 AAT
566020 ATAATGCTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
71 20 0.33
72 2 0.03
74 7 0.12
75 31 0.52
ACGTcount: A:0.17, C:0.19, G:0.14, T:0.51
Consensus pattern (74 bp):
TTTTGTTTCTATCTTTGGGTTGGCTCTTCCTTTCTCTCTTCTTATCACCACATTTAGTGATTACA
ATGCAATAA
Found at i:566260 original size:15 final size:15
Alignment explanation
Indices: 566240--566269 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
566230 ATATTATTAA
566240 AATATTAATATAATT
1 AATATTAATATAATT
*
566255 AATATTTATATAATT
1 AATATTAATATAATT
566270 TTATAATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATATTAATATAATT
Found at i:566295 original size:23 final size:23
Alignment explanation
Indices: 566248--566296 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
566238 AAAATATTAA
* *
566248 TATAATTAATATTTATATAATTT
1 TATAATTAATATTTAAATAAATT
566271 TATAATTAA-ATTTAAATAAAATT
1 TATAATTAATATTTAAAT-AAATT
566294 TAT
1 TAT
566297 TTTTATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATAATTAATATTTAAATAAATT
Found at i:566782 original size:22 final size:22
Alignment explanation
Indices: 566757--566800 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
566747 TAATAGTACG
566757 TTTAATTCACT-AAAATAAAATA
1 TTTAATTCA-TAAAAATAAAATA
* *
566779 TTTATTTTATAAAAATAAAATA
1 TTTAATTCATAAAAATAAAATA
566801 AAGTTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTAATTCATAAAAATAAAATA
Found at i:567474 original size:2 final size:2
Alignment explanation
Indices: 567467--567540 Score: 68
Period size: 2 Copynumber: 39.0 Consensus size: 2
567457 AATTATGTAG
* *
567467 TA TA TA TA -A TA TA CA TA TA TA AA GTA TA TA TA -A TA T- TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* *
567506 TA TA TA CA TC TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
567541 CTAAAAATAT
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
1 5 0.09
2 52 0.90
3 1 0.02
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (2 bp):
TA
Found at i:567486 original size:13 final size:12
Alignment explanation
Indices: 567468--567538 Score: 56
Period size: 13 Copynumber: 5.6 Consensus size: 12
567458 ATTATGTAGT
567468 ATATATAATATA
1 ATATATAATATA
567480 CATATATAA-AGT-
1 -ATATATAATA-TA
567492 ATATATAATATTA
1 ATATATAATA-TA
* *
567505 TTATATACATCTA
1 ATATATA-ATATA
567518 ATATATATATATA
1 ATATATA-ATATA
567531 TATATATA
1 -ATATATA
567539 TACTAAAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
11 8 0.17
12 3 0.06
13 27 0.57
14 9 0.19
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (12 bp):
ATATATAATATA
Found at i:568846 original size:157 final size:157
Alignment explanation
Indices: 568521--568909 Score: 453
Period size: 157 Copynumber: 2.5 Consensus size: 157
568511 AAAAAACAGT
* * * *
568521 GTTGGAGTATCTCTT-TAGAAATAACGGGGTTGGAGTATCCTCGATGGTGGAAAATC-AGTGTTT
1 GTTGGAGTATCCCTTCGA-AAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGA-TGTTT
* * **
568584 TAGAAATAAAAACGGGGTTGGAGTATCTCCTCGAAAATAACAGGGTTGGAGTATCCTCAATGGTA
64 TAAAAAT-AAAACGGGGTTGGAGTATCTCCTCGAAAATAACAGGGTTGGAATATCCTCAATAATA
* *
568649 AAAAATCAGTATTTTAGAAATCAAACCGAT
128 AAAAATCAGTATTTTAGAAATAAAACCGAG
* * *
568679 GTTGTAGTATCCCTTCGAAAATAACGGGATTGGAGTATCCCCGATGGTAAAAAATCGATGTTTTA
1 GTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTTA
* * * * *
568744 AAAATAAAACTGGGTTGGAGTAT-TCCCTTGAAAATAACGGGGTTGGAATATCCCTGAA-AATGA
66 AAAATAAAACGGGGTTGGAGTATCT-CCTCGAAAATAACAGGGTTGGAATAT-CCTCAATAATAA
* * * ** *
568807 AAAATCGGTGTTTTAGAAGTAAAATTGGG
129 AAAATCAGTATTTTAGAAATAAAACCGAG
* * * *
568836 GTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATACCCGATGGTGAAAAATCGGTATTTTA
1 GTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTTA
568901 AAAATAAAA
66 AAAATAAAA
568910 ACATCAATGA
Statistics
Matches: 196, Mismatches: 31, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
156 1 0.01
157 130 0.66
158 63 0.32
159 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (157 bp):
GTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTTA
AAAATAAAACGGGGTTGGAGTATCTCCTCGAAAATAACAGGGTTGGAATATCCTCAATAATAAAA
AATCAGTATTTTAGAAATAAAACCGAG
Found at i:568909 original size:79 final size:78
Alignment explanation
Indices: 568539--568909 Score: 420
Period size: 79 Copynumber: 4.7 Consensus size: 78
568529 ATCTCTTTAG
* * *
568539 AAATAACGGGGTTGGAGTATCCTCGATGGTGGAAAATCAGTGTTTTAGAAATAAAAACGGGGTTG
1 AAATAACGGGGTTGGAGTATCC-CGATGGTGAAAAATCGGTGTTTTAGAAATAAAACCGGGGTTG
*
568604 GAGTATCTCCTCGA
65 GAGTATCCCCTCGA
* * * * * * **
568618 AAATAACAGGGTTGGAGTATCCTCAATGGTAAAAAATCAGTATTTTAGAAATCAAACCGATGTTG
1 AAATAACGGGGTTGGAGTATCC-CGATGGTGAAAAATCGGTGTTTTAGAAATAAAACCGGGGTTG
* *
568683 TAGTATCCCTTCGA
65 GAGTATCCCCTCGA
* * * * *
568697 AAATAACGGGATTGGAGTATCCCCGATGGTAAAAAATCGATGTTTTAAAAATAAAA-CTGGGTTG
1 AAATAACGGGGTTGGAGTAT-CCCGATGGTGAAAAATCGGTGTTTTAGAAATAAAACCGGGGTTG
* *
568761 GAGTATTCCCTTGA
65 GAGTATCCCCTCGA
* *** * **
568775 AAATAACGGGGTTGGAATATCCCTGAAAATGAAAAATCGGTGTTTTAGAAGTAAAATTGGGGTTG
1 AAATAACGGGGTTGGAGTATCCC-GATGGTGAAAAATCGGTGTTTTAGAAATAAAACCGGGGTTG
568840 GAGTATCCCCTCGA
65 GAGTATCCCCTCGA
* *
568854 AAATAACGGGGTTGGAGTATACCCGATGGTGAAAAATCGGTATTTTAAAAATAAAA
1 AAATAACGGGGTTGGAGTAT-CCCGATGGTGAAAAATCGGTGTTTTAGAAATAAAA
568910 ACATCAATGA
Statistics
Matches: 241, Mismatches: 47, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
77 3 0.01
78 58 0.24
79 175 0.73
80 5 0.02
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (78 bp):
AAATAACGGGGTTGGAGTATCCCGATGGTGAAAAATCGGTGTTTTAGAAATAAAACCGGGGTTGG
AGTATCCCCTCGA
Found at i:571034 original size:51 final size:51
Alignment explanation
Indices: 570958--571091 Score: 178
Period size: 51 Copynumber: 2.6 Consensus size: 51
570948 AAAATGCCTG
* * * * **
570958 AATGTATCGATACATTGAGAAATGTATCGATACATCTGGGTTAGAACCCCT
1 AATGTATCGATACAATGAAAAATGTATCGATACATCTAGGTTAAAACCCAA
* * *
571009 AATGTATCGATACAATAAAAAATGTATCGAGACATTTAGGTTAAAACCCAA
1 AATGTATCGATACAATGAAAAATGTATCGATACATCTAGGTTAAAACCCAA
*
571060 AATATATCGATACAATGAAAAATGTATCGATA
1 AATGTATCGATACAATGAAAAATGTATCGATA
571092 TATTTACTTA
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 71 1.00
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.28
Consensus pattern (51 bp):
AATGTATCGATACAATGAAAAATGTATCGATACATCTAGGTTAAAACCCAA
Found at i:572186 original size:4 final size:4
Alignment explanation
Indices: 572177--572251 Score: 75
Period size: 4 Copynumber: 18.8 Consensus size: 4
572167 CCTTTTTACT
* * *
572177 TTTA TTTA TTTA TTTA TTTA TTTA TTTTAA ATTA -TTA ATT- TTTA GTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTT-A TTTA TTTA TTTA TTTA TTTA
572225 TTTA -TTA TTTA TTTA TTTAA TTTA TTT
1 TTTA TTTA TTTA TTTA TTT-A TTTA TTT
572252 TTAATATAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
3 8 0.13
4 43 0.70
5 9 0.15
6 1 0.02
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:572283 original size:34 final size:33
Alignment explanation
Indices: 572245--572315 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 33
572235 ATTTATTTAA
*
572245 TTTATTTTTAATATAAATATA-ATTTAAATAATTT
1 TTTATTTTTAAAATAAATATACATTT-AAT-ATTT
*
572279 TTTATTTTTAAAATAATTATACATTTAATATTT
1 TTTATTTTTAAAATAAATATACATTTAATATTT
572312 TTTA
1 TTTA
572316 ATTATTAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 8 0.24
34 22 0.65
35 4 0.12
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (33 bp):
TTTATTTTTAAAATAAATATACATTTAATATTT
Found at i:573533 original size:18 final size:19
Alignment explanation
Indices: 573498--573535 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
573488 TGTTGATGAA
573498 AATAAAATTTAAAATTATT
1 AATAAAATTTAAAATTATT
*
573517 AATAAAA-TTATAATTATT
1 AATAAAATTTAAAATTATT
573535 A
1 A
573536 TATTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATAAAATTTAAAATTATT
Found at i:577258 original size:2 final size:2
Alignment explanation
Indices: 577251--577276 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
577241 TATTAGCTAT
577251 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
577277 GAATGTCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:580199 original size:2 final size:2
Alignment explanation
Indices: 580192--580230 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
580182 TGACACATGC
580192 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
580231 GCTTATTGCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:580315 original size:29 final size:29
Alignment explanation
Indices: 580273--580332 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
580263 GCTGCCATGG
580273 AAGCTTGAAGTACTATTATATGCACAAGA
1 AAGCTTGAAGTACTATTATATGCACAAGA
* *
580302 AAGCTTGAAGTACTATTATGTGCATAAGA
1 AAGCTTGAAGTACTATTATATGCACAAGA
580331 AA
1 AA
580333 TTCTTACTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (29 bp):
AAGCTTGAAGTACTATTATATGCACAAGA
Found at i:582416 original size:15 final size:15
Alignment explanation
Indices: 582393--582440 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
582383 TTTCGATTAC
582393 TTATATTATTTATTT
1 TTATATTATTTATTT
* *
582408 TTATGTTATTTATAT
1 TTATATTATTTATTT
* * *
582423 ATATTTTATTAATTT
1 TTATATTATTTATTT
582438 TTA
1 TTA
582441 AAATTTTTCT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (15 bp):
TTATATTATTTATTT
Found at i:582509 original size:18 final size:19
Alignment explanation
Indices: 582473--582514 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
582463 TTTTTAAAAA
*
582473 ATTTATAATTATTTTTATT
1 ATTTATAATTATTTATATT
*
582492 ATTT-TAATTCTTTATATT
1 ATTTATAATTATTTATATT
582510 ATTTA
1 ATTTA
582515 ATAGTTGAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTATAATTATTTATATT
Found at i:583462 original size:34 final size:34
Alignment explanation
Indices: 583413--583523 Score: 127
Period size: 34 Copynumber: 3.3 Consensus size: 34
583403 GTCACTTATG
* *
583413 TTGATTAAATAGGTGATTTGGTAGTTTG-CTATTA
1 TTGACTAAATAGGTGATTTGGTGGTTTGTC-ATTA
* * *
583447 TTGACTAAATTGGTGATTTGATGGTTTGTCATTG
1 TTGACTAAATAGGTGATTTGGTGGTTTGTCATTA
* * *
583481 TTGA-TTAATGGGTGGTTTGGTGGTTTGTCATTA
1 TTGACTAAATAGGTGATTTGGTGGTTTGTCATTA
583514 TTGACTAAAT
1 TTGACTAAAT
583524 GACTAAAAGA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
33 28 0.44
34 35 0.55
35 1 0.02
ACGTcount: A:0.23, C:0.05, G:0.26, T:0.47
Consensus pattern (34 bp):
TTGACTAAATAGGTGATTTGGTGGTTTGTCATTA
Found at i:583906 original size:19 final size:19
Alignment explanation
Indices: 583882--583918 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
583872 TTAGTTGTCG
* *
583882 AGGCACTGTTCACGTATAC
1 AGGCACTCTTCACATATAC
583901 AGGCACTCTTCACATATA
1 AGGCACTCTTCACATATA
583919 TAGTTACTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (19 bp):
AGGCACTCTTCACATATAC
Found at i:588033 original size:34 final size:34
Alignment explanation
Indices: 587990--588071 Score: 128
Period size: 34 Copynumber: 2.4 Consensus size: 34
587980 AAGTGAGAGA
* *
587990 ATTGTTGACTAAATGGGTGATTTGGTAGTTTGTC
1 ATTGTTGACTAAATGGGTGATTTAGTAGTTTATC
*
588024 ATTGTTGACTAAATGGGTGATTTAGTGGTTTATC
1 ATTGTTGACTAAATGGGTGATTTAGTAGTTTATC
*
588058 ATTATTGACTAAAT
1 ATTGTTGACTAAAT
588072 AGTTAAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.26, C:0.06, G:0.24, T:0.44
Consensus pattern (34 bp):
ATTGTTGACTAAATGGGTGATTTAGTAGTTTATC
Found at i:593001 original size:12 final size:11
Alignment explanation
Indices: 592974--593038 Score: 51
Period size: 12 Copynumber: 5.7 Consensus size: 11
592964 AAATATTATA
*
592974 AAAATAAAAAT
1 AAAATAATAAT
592985 AAAATTAATAAT
1 AAAA-TAATAAT
*
592997 AAAATATATATT
1 AAAATA-ATAAT
* *
593009 TAAATTA-AAT
1 AAAATAATAAT
*
593019 ATAATAATAAT
1 AAAATAATAAT
593030 AAAAGTAAT
1 AAAA-TAAT
593039 TATTAAAAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
10 6 0.15
11 13 0.32
12 22 0.54
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:593082 original size:23 final size:23
Alignment explanation
Indices: 593056--593115 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 23
593046 AATATTTGAT
593056 TAAAATATATTTATATATATAAATAA
1 TAAAATATA-TT-TATAT-TAAATAA
593082 -AAAAGTTATATTTATATTAAATAA
1 TAAAA--TATATTTATATTAAATAA
593106 TAAAATATAT
1 TAAAATATAT
593116 ATTAAAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
23 5 0.16
24 7 0.23
25 13 0.42
26 2 0.06
27 4 0.13
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
TAAAATATATTTATATTAAATAA
Found at i:593085 original size:25 final size:25
Alignment explanation
Indices: 593057--593118 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 25
593047 ATATTTGATT
*
593057 AAAATATATTTATA-TATATAAATAA
1 AAAATATATTTATATTAAAT-AATAA
593082 AAAAGTTATATTTATATTAAATAATAA
1 AAAA--TATATTTATATTAAATAATAA
*
593109 AATATATATT
1 AAAATATATT
593119 AAAAATTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 10 0.31
27 18 0.56
28 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
AAAATATATTTATATTAAATAATAA
Found at i:593090 original size:21 final size:21
Alignment explanation
Indices: 593066--593121 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 21
593056 TAAAATATAT
593066 TTATATATATAAATAA-AAAA
1 TTATATATATAAATAATAAAA
593086 GTTATATTTATATTAAATAATAAAA
1 -TTATA--TATA-TAAATAATAAAA
593111 -TATATAT-TAAA
1 TTATATATATAAA
593122 AATTTTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
19 4 0.13
21 8 0.26
23 8 0.26
24 7 0.23
25 4 0.13
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
TTATATATATAAATAATAAAA
Found at i:593474 original size:34 final size:34
Alignment explanation
Indices: 593414--593478 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
593404 TATTATTATA
*
593414 ATTAATTATAATAAAATAAATATATAAAATAGAT
1 ATTAATAATAATAAAATAAATATATAAAATAGAT
593448 ATTAATAATAA-AAAATTAAA-ATTATAAAATA
1 ATTAATAATAATAAAA-TAAATA-TATAAAATA
593479 ACGAATATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 5 0.18
34 23 0.82
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (34 bp):
ATTAATAATAATAAAATAAATATATAAAATAGAT
Found at i:593826 original size:13 final size:13
Alignment explanation
Indices: 593798--593840 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
593788 ATCTTACATT
*
593798 TATATCTAAT-TA
1 TATATCAAATATA
593810 TATATCAAATATA
1 TATATCAAATATA
593823 TATATCAAATATA
1 TATATCAAATATA
*
593836 AATAT
1 TATAT
593841 TTAAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (13 bp):
TATATCAAATATA
Found at i:594952 original size:17 final size:16
Alignment explanation
Indices: 594913--594953 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
594903 TATATAGAGT
* *
594913 TTATTTTGAATTTACA
1 TTATTTTAAATTTAAA
594929 TTATTTTAAATTTAAA
1 TTATTTTAAATTTAAA
594945 TATATTTTA
1 T-TATTTTA
594954 TTTAAGTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (16 bp):
TTATTTTAAATTTAAA
Found at i:598788 original size:16 final size:15
Alignment explanation
Indices: 598769--598833 Score: 62
Period size: 16 Copynumber: 4.3 Consensus size: 15
598759 AAATACTACA
598769 AATTTAAATTATTTTG
1 AATTTAAA-TATTTTG
*
598785 AATTTAAA-ATTTTC
1 AATTTAAATATTTTG
**
598799 AAGTCCAAATATTTTG
1 AA-TTTAAATATTTTG
*
598815 AATTTAGATATTTT-
1 AATTTAAATATTTTG
598829 AATTT
1 AATTT
598834 TGAGCTATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
14 12 0.30
15 13 0.32
16 15 0.38
ACGTcount: A:0.38, C:0.05, G:0.06, T:0.51
Consensus pattern (15 bp):
AATTTAAATATTTTG
Found at i:602067 original size:13 final size:14
Alignment explanation
Indices: 602049--602103 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 14
602039 TTTTATTTTT
602049 AAATAA-ATTATTA
1 AAATAATATTATTA
*
602062 AAATAATATTATTTTT
1 AAATAATATTA--TTA
*
602078 AAAT-ATATTATCA
1 AAATAATATTATTA
*
602091 AAATATTATTATT
1 AAATAATATTATT
602104 GAGATTTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
13 11 0.33
14 10 0.30
15 6 0.18
16 6 0.18
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATAATATTATTA
Found at i:602077 original size:29 final size:29
Alignment explanation
Indices: 602041--602103 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
602031 AATTATTTTT
*
602041 TTATTTTTAAATAAATTATTAAAATAATA
1 TTATTTTTAAATAAATTATCAAAATAATA
* *
602070 TTATTTTTAAATATATTATCAAAATATTA
1 TTATTTTTAAATAAATTATCAAAATAATA
602099 TTATT
1 TTATT
602104 GAGATTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (29 bp):
TTATTTTTAAATAAATTATCAAAATAATA
Found at i:602463 original size:17 final size:18
Alignment explanation
Indices: 602419--602467 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
602409 TTTAAAAAGA
* *
602419 TATATTCTTATGAATATT
1 TATATTCTTATTAATACT
*
602437 TA-ATTTTTATTAA-ACT
1 TATATTCTTATTAATACT
602453 TATATTCTTATTAAT
1 TATATTCTTATTAAT
602468 TTATAATGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 4 0.16
17 19 0.76
18 2 0.08
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (18 bp):
TATATTCTTATTAATACT
Found at i:602504 original size:14 final size:15
Alignment explanation
Indices: 602485--602513 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
602475 GATATTATTG
602485 TTATTA-ATTTTTAA
1 TTATTATATTTTTAA
602499 TTATTATATTTTTAA
1 TTATTATATTTTTAA
602514 AAAATTAATA
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATTATATTTTTAA
Found at i:602508 original size:25 final size:25
Alignment explanation
Indices: 602452--602508 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
602442 TTTATTAAAC
602452 TTATATTCTTATTAATTTATAATGA
1 TTATATTCTTATTAATTTATAATGA
* * *
602477 -TATTATTGTTATTAATTTTTAATTA
1 TTA-TATTCTTATTAATTTATAATGA
602502 TTATATT
1 TTATATT
602509 TTTAAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 2 0.07
25 23 0.85
26 2 0.07
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (25 bp):
TTATATTCTTATTAATTTATAATGA
Found at i:602801 original size:21 final size:23
Alignment explanation
Indices: 602777--602840 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 23
602767 AGATTAATGT
602777 AAAATATCTAAAAACAT-AA-TC
1 AAAATATCTAAAAACATCAATTC
* *
602798 AAAATCAATCATAAAAAAATCAATTT
1 AAAAT--ATC-TAAAAACATCAATTC
*
602824 AAAATATCCAAAAACAT
1 AAAATATCTAAAAACAT
602841 GTGCAATACA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
21 5 0.15
23 10 0.29
24 11 0.32
25 2 0.06
26 6 0.18
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.23
Consensus pattern (23 bp):
AAAATATCTAAAAACATCAATTC
Found at i:604704 original size:209 final size:209
Alignment explanation
Indices: 604344--604728 Score: 549
Period size: 209 Copynumber: 1.8 Consensus size: 209
604334 TCATAATTAG
** * *
604344 TTACCTTACATAATTTTTGTATAGATATGAAATGCATACAGATCCCCAACTATAGTTTCGAAGCT
1 TTACCTTACATAATTTTAATATAGATATGAAAGGCATACAGATCCCCAACTATAGTTTCGAACCT
* * * *
604409 TTTCGAAGTCCATTAATAGAGGGAGGTTCATTAAATGTATATATCTACTCAAATTATCGATAAAT
66 CTTCGAAGTCCATTAATAGAGGGAGGTACATTAAATGTACATATCTACTCAAATGATCGATAAAT
* * *
604474 AACAACCTTTGGCTCAATCTAAGAAAATACGCTTGCGTATATCGCTGTACATACAGATCCCTAAC
131 AACAACCTTTCGATCAATCTAAGAAAATACGCTTGCGCATATCGCTGTACATACAGATCCCTAAC
604539 TGTAAGGCATATAA
196 TGTAAGGCATATAA
* **
604553 TTACCTTACATAATTCTTAATATAGATATGAGAGGCATACAGATTTCCAACTATAGTTTTC-AAC
1 TTACCTTACATAATT-TTAATATAGATATGAAAGGCATACAGATCCCCAACTATAG-TTTCGAAC
* *
604617 CTCTTCGAA-TCTATTAATAGAGGGAGGTACATTAAATGTACATATCTACTTAAATGATCGATAA
64 CTCTTCGAAGTCCATTAATAGAGGGAGGTACATTAAATGTACATATCTACTCAAATGATCGATAA
* * * * *
604681 ATTACAACTTTTCGATCAATCTAAGACAATATGCTTGTGCATATCGCT
129 ATAACAACCTTTCGATCAATCTAAGAAAATACGCTTGCGCATATCGCT
604729 AAAATGTGAT
Statistics
Matches: 153, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
209 105 0.69
210 44 0.29
211 4 0.03
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (209 bp):
TTACCTTACATAATTTTAATATAGATATGAAAGGCATACAGATCCCCAACTATAGTTTCGAACCT
CTTCGAAGTCCATTAATAGAGGGAGGTACATTAAATGTACATATCTACTCAAATGATCGATAAAT
AACAACCTTTCGATCAATCTAAGAAAATACGCTTGCGCATATCGCTGTACATACAGATCCCTAAC
TGTAAGGCATATAA
Done.