Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold82
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: 2626005
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.31
Warning! 196346 characters in sequence are not A, C, G, or T
File 3 of 17
Found at i:251953 original size:22 final size:23
Alignment explanation
Indices: 251905--251960 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
251895 ATGTTTTTTA
*
251905 ATATAAATATAAAAATATAATTT
1 ATATAAATATATAAATATAATTT
251928 -TATAAATATATAAA-A-AATTAT
1 ATATAAATATATAAATATAATT-T
*
251949 ATATAATTATAT
1 ATATAAATATAT
251961 TTAATATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 4 0.14
21 2 0.07
22 23 0.79
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
ATATAAATATATAAATATAATTT
Found at i:253196 original size:34 final size:34
Alignment explanation
Indices: 253129--253344 Score: 283
Period size: 34 Copynumber: 6.4 Consensus size: 34
253119 ATAAACTTGC
* * *
253129 TGTTGATTAAAT-GGTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
253162 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
253196 TGTTGACTAAAT-GAAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
253229 TGTTGATTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
253263 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
253297 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
253331 TGTTGATTAAATGG
1 TGTTGATTAAATGG
253345 TGGTTTTTAC
Statistics
Matches: 160, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
33 39 0.24
34 121 0.76
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:253310 original size:68 final size:67
Alignment explanation
Indices: 253129--253346 Score: 310
Period size: 67 Copynumber: 3.2 Consensus size: 67
253119 ATAAACTTGC
* * * * *
253129 TGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
253194 AT
66 AT
* ** * *
253196 TGTTGACTAAATGAAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
253261 AT
66 AT
* * *
253263 TGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGC
253328 CAT
65 CAT
253331 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
253347 GTTTTTACCA
Statistics
Matches: 132, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
67 72 0.55
68 60 0.45
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
AT
Found at i:257827 original size:34 final size:34
Alignment explanation
Indices: 257758--257975 Score: 287
Period size: 34 Copynumber: 6.5 Consensus size: 34
257748 AAGTGGGAGA
* * *
257758 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
257791 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
257825 ATTGTTGACTAAAT-GAAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
257858 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
257892 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
257926 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
257960 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
257976 TGGTTTTTAC
Statistics
Matches: 162, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
33 41 0.25
34 121 0.75
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:257941 original size:68 final size:67
Alignment explanation
Indices: 257758--257977 Score: 314
Period size: 67 Copynumber: 3.3 Consensus size: 67
257748 AAGTGGGAGA
* * * * *
257758 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
257823 CC
66 CC
* ** * *
257825 ATTGTTGACTAAATGAAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
257890 CC
66 CC
* * *
257892 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
257957 GCC
65 GCC
257960 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
257978 GTTTTTACCA
Statistics
Matches: 134, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
67 74 0.55
68 60 0.45
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
CC
Found at i:265982 original size:3 final size:3
Alignment explanation
Indices: 265974--266006 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
265964 ATATATTTAT
265974 TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TA
266007 TATTTTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:266016 original size:53 final size:49
Alignment explanation
Indices: 265953--266056 Score: 147
Period size: 50 Copynumber: 2.0 Consensus size: 49
265943 AAGGTGACAG
265953 ATATTTTTATAATATATTTATTAATAATAATAA-TAATAATAATAAATAATAAT
1 ATATTTTTATAATATATTTA--AA-AATAATAACTAA-AATAATAAATAA-AAT
*
266006 ATATTTTTATAATATATTTAAAAATAATAACTTAAATAATAAATAAAAT
1 ATATTTTTATAATATATTTAAAAATAATAACTAAAATAATAAATAAAAT
266055 AT
1 AT
266057 GTGATATTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
49 5 0.10
50 20 0.41
51 4 0.08
53 20 0.41
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (49 bp):
ATATTTTTATAATATATTTAAAAATAATAACTAAAATAATAAATAAAAT
Found at i:266918 original size:14 final size:14
Alignment explanation
Indices: 266899--266925 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
266889 TTAATTATAA
266899 AATATAAAAATATT
1 AATATAAAAATATT
266913 AATATAAAAATAT
1 AATATAAAAATAT
266926 ATTTTAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATATAAAAATATT
Found at i:269859 original size:28 final size:28
Alignment explanation
Indices: 269795--269859 Score: 64
Period size: 28 Copynumber: 2.3 Consensus size: 28
269785 AAAAATAAAC
*
269795 CATTAAACTAAATATATATTTTTATTAA
1 CATTAAACTAAATATATATTATTATTAA
*
269823 CTATT-AACTATAT-TAATATTCATTA-TAA
1 C-ATTAAACTAAATAT-ATATT-ATTATTAA
269851 CATTAAACT
1 CATTAAACT
269860 TAGTTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
27 4 0.13
28 21 0.68
29 6 0.19
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.45
Consensus pattern (28 bp):
CATTAAACTAAATATATATTATTATTAA
Found at i:270168 original size:20 final size:20
Alignment explanation
Indices: 270124--270178 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 20
270114 ATTCAAGTCT
270124 ATTTATATTTATAAATAAATA
1 ATTTATATTTAT-AATAAATA
*
270145 ATTTATATTTAT-TTAAATTA
1 ATTTATATTTATAATAAA-TA
270165 ATTTATATTATATA
1 ATTTATATT-TATA
270179 TATTTTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 4 0.13
20 11 0.37
21 15 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTTATATTTATAATAAATA
Found at i:271287 original size:25 final size:26
Alignment explanation
Indices: 271249--271302 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
271239 TTTTGATATT
* **
271249 AATATATTATATTATTTTTATTTAAA
1 AATAAATTATATTATCATTATTTAAA
271275 AATAAATTA-ATTATCATTATTTAAA
1 AATAAATTATATTATCATTATTTAAA
271300 AAT
1 AAT
271303 TTAAAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 17 0.68
26 8 0.32
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
AATAAATTATATTATCATTATTTAAA
Found at i:271550 original size:17 final size:17
Alignment explanation
Indices: 271514--271546 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
271504 ATTTATTTAA
*
271514 AAATTTAATATATAATT
1 AAATTTAAAATATAATT
271531 AAATTTAAAATA-AATT
1 AAATTTAAAATATAATT
271547 TAAAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATTTAAAATATAATT
Found at i:271685 original size:16 final size:17
Alignment explanation
Indices: 271664--271695 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
271654 AAAATATTTT
271664 AAATAAAAA-TAATAAA
1 AAATAAAAATTAATAAA
271680 AAATAAAAATTAATAA
1 AAATAAAAATTAATAA
271696 TTGATAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (17 bp):
AAATAAAAATTAATAAA
Found at i:271823 original size:28 final size:27
Alignment explanation
Indices: 271751--271838 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 27
271741 TAAAAATAAT
*
271751 AATTTAAAATAAAT-ATATTTTTAATTAAA
1 AATTAAAAATAAATAATA-TTTT--TTAAA
*
271780 ATTTTAAAAATAAATAAATATTTTTTAAA
1 A-ATTAAAAATAAAT-AATATTTTTTAAA
271809 AATTAAAAATAAAT-ATATTTTTTAATA
1 AATTAAAAATAAATAATATTTTTTAA-A
271836 AAT
1 AAT
271839 GCTTTTCTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
26 11 0.21
27 4 0.08
28 12 0.23
29 7 0.13
30 11 0.21
31 4 0.08
32 3 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
AATTAAAAATAAATAATATTTTTTAAA
Found at i:278448 original size:20 final size:20
Alignment explanation
Indices: 278423--278461 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
278413 AAATGTAATT
278423 TAATTTAATAA-TAATTAAAA
1 TAATTTAA-AATTAATTAAAA
278443 TAATTTAAAATTAATTAAA
1 TAATTTAAAATTAATTAAA
278462 TTTTTATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAATTTAAAATTAATTAAAA
Found at i:287602 original size:20 final size:20
Alignment explanation
Indices: 287577--287649 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
287567 ACAACAAATT
287577 AATATATCGATACATAAGTG
1 AATATATCGATACATAAGTG
287597 AATATATCGATACATAAGTG
1 AATATATCGATACATAAGTG
* * *
287617 AATATATCGATACACAGGTA
1 AATATATCGATACATAAGTG
*
287637 AATGTATCGATAC
1 AATATATCGATAC
287650 TGGACTATGT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (20 bp):
AATATATCGATACATAAGTG
Found at i:295609 original size:17 final size:17
Alignment explanation
Indices: 295584--295640 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 17
295574 AATACACTTG
* *
295584 AAATATATTTAAATTTT
1 AAATTTATTTATATTTT
295601 AAATTTATTTTATATATTT
1 AAATTTA-TTTATAT-TTT
295620 AAATTTTATTTATA-TTT
1 AAA-TTTATTTATATTTT
295637 AAAT
1 AAAT
295641 GTATATCGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
16 1 0.03
17 12 0.34
18 6 0.17
19 12 0.34
20 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AAATTTATTTATATTTT
Found at i:295627 original size:20 final size:18
Alignment explanation
Indices: 295584--295634 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
295574 AATACACTTG
* *
295584 AAATATATTTAAAT-TTT
1 AAATTTATTTATATATTT
295601 AAATTTATTTTATATATTT
1 AAATTTA-TTTATATATTT
295620 AAATTTTATTTATAT
1 AAA-TTTATTTATAT
295635 TTAAATGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 6 0.21
18 6 0.21
19 13 0.45
20 4 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
AAATTTATTTATATATTT
Found at i:295850 original size:23 final size:23
Alignment explanation
Indices: 295807--295869 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 23
295797 AATCAATTTT
295807 AATTATTCATATTATTTTATAAA
1 AATTATTCATATTATTTTATAAA
* *
295830 AATTATT-ATA-TATTATATATA
1 AATTATTCATATTATTTTATAAA
* *
295851 AATGA-T-ATATTATGTTATA
1 AATTATTCATATTATTTTATA
295870 TTATTTTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 4 0.12
21 20 0.59
22 3 0.09
23 7 0.21
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (23 bp):
AATTATTCATATTATTTTATAAA
Found at i:295918 original size:26 final size:30
Alignment explanation
Indices: 295865--295920 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
295855 ATATATTATG
295865 TTATATTATTTTAAATTATTATATAAATATT
1 TTATATTATTTTAAA-TATTATATAAATATT
295896 TTAT-TTATTTTAAA-A-TATA-AAATAT
1 TTATATTATTTTAAATATTATATAAATAT
295921 AATTAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 6 0.24
27 4 0.16
28 1 0.04
30 10 0.40
31 4 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
TTATATTATTTTAAATATTATATAAATATT
Found at i:303190 original size:29 final size:29
Alignment explanation
Indices: 303157--303215 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
303147 AAATGATTGA
303157 ACCACTTATCAACAATCACAAGCACAAAT
1 ACCACTTATCAACAATCACAAGCACAAAT
303186 ACCACTTATCAACAATCACAAGCACAAAT
1 ACCACTTATCAACAATCACAAGCACAAAT
303215 A
1 A
303216 GCTTCTTTAA
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:0.49, C:0.31, G:0.03, T:0.17
Consensus pattern (29 bp):
ACCACTTATCAACAATCACAAGCACAAAT
Found at i:304876 original size:5 final size:5
Alignment explanation
Indices: 304866--304890 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
304856 AATTATATGA
304866 AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT
304891 TATAATCACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:304957 original size:18 final size:18
Alignment explanation
Indices: 304934--304973 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
304924 TATTTTAATT
304934 TTAAAAAATAATTATTTA
1 TTAAAAAATAATTATTTA
* *
304952 TTAAAAATTATTTATTTA
1 TTAAAAAATAATTATTTA
304970 TTAA
1 TTAA
304974 TATATTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAAAAAATAATTATTTA
Found at i:304959 original size:17 final size:17
Alignment explanation
Indices: 304937--305014 Score: 63
Period size: 17 Copynumber: 4.6 Consensus size: 17
304927 TTTAATTTTA
304937 AAAAATAATTATTTATT
1 AAAAATAATTATTTATT
*
304954 AAAAATTATTTATTTATT
1 AAAAA-TAATTATTTATT
* *
304972 -AATAT-ATT-TTATTTT
1 AAAAATAATTATT-TATT
* *
304987 AAAAATATTTTTTTATT
1 AAAAATAATTATTTATT
*
305004 AAAAATCATTA
1 AAAAATAATTA
305015 CATTTTTAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
14 2 0.04
15 5 0.11
16 5 0.11
17 21 0.46
18 13 0.28
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (17 bp):
AAAAATAATTATTTATT
Found at i:304993 original size:18 final size:18
Alignment explanation
Indices: 304924--305009 Score: 60
Period size: 18 Copynumber: 4.9 Consensus size: 18
304914 GTTATCTAAG
304924 TATTTTAATTTTAAAAA-A
1 TATTTT-ATTTTAAAAATA
*
304942 TAATTATT-TATTAAAAAT-
1 T-ATT-TTATTTTAAAAATA
**
304960 TA-TTTA-TTTATTAATA
1 TATTTTATTTTAAAAATA
304976 TATTTTATTTTAAAAATA
1 TATTTTATTTTAAAAATA
304994 T-TTTT-TTATTAAAAAT
1 TATTTTATT-TTAAAAAT
305010 CATTACATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 17
0.70 0.08 0.22
Matches are distributed among these distances:
15 8 0.15
16 5 0.09
17 17 0.31
18 19 0.35
19 3 0.06
20 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTTTATTTTAAAAATA
Found at i:305053 original size:50 final size:49
Alignment explanation
Indices: 304924--305053 Score: 122
Period size: 50 Copynumber: 2.6 Consensus size: 49
304914 GTTATCTAAG
* *
304924 TATTTTAATTTTAAAAAATAATTATTTATTAAAAATTATTTATTTATTAATA
1 TATTTT-ATTTT-AAAAAT-ATTATTTATTAAAAATCATTCATTTATTAATA
*
304976 TATTTTATTTTAAAAATATTTTTTTATTAAAAATCATTACATTT-TTAA-A
1 TATTTTATTTTAAAAATA-TTATTTATTAAAAATCATT-CATTTATTAATA
**
305025 T-TTATTATCTTTTGAAATATTATATTATT
1 TATT-TTAT-TTTAAAAATATTAT-TTATT
305054 CTTTAAAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
48 2 0.03
49 10 0.15
50 40 0.60
51 9 0.13
52 6 0.09
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (49 bp):
TATTTTATTTTAAAAATATTATTTATTAAAAATCATTCATTTATTAATA
Found at i:305303 original size:18 final size:18
Alignment explanation
Indices: 305280--305322 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
305270 TAAAATTTTA
305280 TTTTTAAATATTATATAT
1 TTTTTAAATATTATATAT
*
305298 TTTTTAAAATATTCTATAT
1 TTTTT-AAATATTATATAT
305317 TTTTTA
1 TTTTTA
305323 TAAAATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTAAATATTATATAT
Found at i:305321 original size:21 final size:19
Alignment explanation
Indices: 305274--305328 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
305264 TTAAGTTAAA
*
305274 ATTTTATTTTTAAATATTAT
1 ATTTT-TTTTAAAATATTAT
*
305294 ATATTTTTTAAAATATTCTAT
1 ATTTTTTTTAAAATA-T-TAT
*
305315 ATTTTTTATAAAAT
1 ATTTTTTTTAAAAT
305329 TTAATAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 9 0.31
20 5 0.17
21 15 0.52
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTTTTTTAAAATATTAT
Found at i:305373 original size:19 final size:19
Alignment explanation
Indices: 305349--305388 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
305339 AATAATTTAA
*
305349 TTATATACATTTATTATAT
1 TTATATACATTTATCATAT
**
305368 TTATATATTTTTATCATAT
1 TTATATACATTTATCATAT
305387 TT
1 TT
305389 TTTATATTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATATACATTTATCATAT
Found at i:305474 original size:14 final size:14
Alignment explanation
Indices: 305457--305502 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 14
305447 AAAAAATTAA
305457 AAATTTTTAAATTT
1 AAATTTTTAAATTT
305471 AAA-TTTTAAATTTT
1 AAATTTTTAAA-TTT
305485 AAATTTTTTAAATATT
1 AAA-TTTTTAAAT-TT
305501 AA
1 AA
305503 TTAATTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 7 0.25
14 9 0.32
15 1 0.04
16 11 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AAATTTTTAAATTT
Found at i:305502 original size:7 final size:7
Alignment explanation
Indices: 305461--305491 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
305451 AATTAAAAAT
305461 TTTTAAA
1 TTTTAAA
305468 -TTTAAA
1 TTTTAAA
305474 TTTTAAA
1 TTTTAAA
305481 TTTTAAA
1 TTTTAAA
305488 TTTT
1 TTTT
305492 TTAAATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
TTTTAAA
Found at i:306352 original size:30 final size:30
Alignment explanation
Indices: 306318--306374 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
306308 TTTTAGTGAA
*
306318 TATAAATTTTTGTATTTTACAATAAATGAT
1 TATAAATTTTTATATTTTACAATAAATGAT
*
306348 TATAAATTTTTATATTTTATAATAAAT
1 TATAAATTTTTATATTTTACAATAAAT
306375 AGATCCAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (30 bp):
TATAAATTTTTATATTTTACAATAAATGAT
Found at i:306423 original size:13 final size:13
Alignment explanation
Indices: 306405--306430 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
306395 CATAAATAAT
306405 ACAAATTTAAATA
1 ACAAATTTAAATA
306418 ACAAATTTAAATA
1 ACAAATTTAAATA
306431 TTTAAATCTA
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:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
ACAAATTTAAATA
Found at i:306844 original size:15 final size:15
Alignment explanation
Indices: 306810--306864 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
306800 ATTAAAATAT
*
306810 TTATTATTATTTATTA
1 TTATTATTAATT-TTA
306826 -TATTATTAATTTTA
1 TTATTATTAATTTTA
*
306840 TTATT-TAAAATTTT-
1 TTATTAT-TAATTTTA
306854 TTATTATTAAT
1 TTATTATTAAT
306865 AAAATTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
14 12 0.36
15 21 0.64
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATTATTAATTTTA
Found at i:306854 original size:16 final size:18
Alignment explanation
Indices: 306835--306884 Score: 68
Period size: 17 Copynumber: 2.8 Consensus size: 18
306825 ATATTATTAA
306835 TTTTATTATT-TAAAATT
1 TTTTATTATTATAAAATT
306852 TTTTATTATTAATAAAATT
1 TTTTATTATT-ATAAAATT
*
306871 TATTA-TATTATAAA
1 TTTTATTATTATAAA
306885 TAAAAATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 15 0.50
18 4 0.13
19 11 0.37
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTATTATTATAAAATT
Found at i:306881 original size:21 final size:20
Alignment explanation
Indices: 306813--306881 Score: 65
Period size: 19 Copynumber: 3.6 Consensus size: 20
306803 AAAATATTTA
**
306813 TTATTAT-TTATTATATTAT
1 TTATTATATTATTATAAAAT
* *
306832 TAATTTTATTATT-TAAAAT
1 TTATTATATTATTATAAAAT
306851 TT-TT-TATTATTAATAAAAT
1 TTATTATATTATT-ATAAAAT
306870 TTATTATATTAT
1 TTATTATATTAT
306882 AAATAAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
17 7 0.17
18 2 0.05
19 18 0.45
20 7 0.17
21 6 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTATATTATTATAAAAT
Found at i:306886 original size:21 final size:19
Alignment explanation
Indices: 306845--306894 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
306835 TTTTATTATT
*
306845 TAAAATTTTTTATTATTAA
1 TAAAATTTTTTATTATAAA
306864 TAAAATTTATTATATTATAAA
1 TAAAATTT-TT-TATTATAAA
306885 TAAAAATTTT
1 T-AAAATTTT
306895 AAAATAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 8 0.30
20 2 0.07
21 10 0.37
22 7 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAAAATTTTTTATTATAAA
Found at i:307595 original size:18 final size:18
Alignment explanation
Indices: 307572--307627 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
307562 TTTTTGTCAC
*
307572 ATATTTTTATATAATATA
1 ATATTTTTTTATAATATA
* *
307590 ATATTTGTTTTTTAACATA
1 ATATTT-TTTTATAATATA
307609 AT-TTTTTTTATAAATATA
1 ATATTTTTTTAT-AATATA
307627 A
1 A
307628 AATAATTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
17 5 0.16
18 15 0.48
19 11 0.35
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
ATATTTTTTTATAATATA
Found at i:309093 original size:40 final size:43
Alignment explanation
Indices: 309012--309101 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 43
309002 GTTCACTATA
* *
309012 TTTTTAAATTATAATTATAAATCATTTTTATTCTTAATAAAATT
1 TTTTTAAATTATAA-TATAAATAATTTTAATTCTTAATAAAATT
* *
309056 TTTTTAATTTATAA-ATAAA-AATTTTAATT-TTATTAAAATT
1 TTTTTAAATTATAATATAAATAATTTTAATTCTTAATAAAATT
*
309096 ATTTTA
1 TTTTTA
309102 TTAAATATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
40 15 0.37
41 8 0.20
42 5 0.12
44 13 0.32
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (43 bp):
TTTTTAAATTATAATATAAATAATTTTAATTCTTAATAAAATT
Found at i:309099 original size:20 final size:20
Alignment explanation
Indices: 309030--309101 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
309020 TTATAATTAT
* *
309030 AAATCATTTTTATTCTTAATA
1 AAATTATTTTAATT-TTAATA
*
309051 AAATTTTTTTAATTTATAAATA
1 AAATTATTTTAATTT-T-AATA
*
309073 AAA--ATTTTAATTTTATTA
1 AAATTATTTTAATTTTAATA
309091 AAATTATTTTA
1 AAATTATTTTA
309102 TTAAATATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
18 6 0.14
19 1 0.02
20 16 0.38
21 12 0.29
22 7 0.17
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (20 bp):
AAATTATTTTAATTTTAATA
Found at i:321417 original size:19 final size:21
Alignment explanation
Indices: 321383--321425 Score: 72
Period size: 19 Copynumber: 2.1 Consensus size: 21
321373 GTGCAACTGT
321383 AAAGAGAAAGGCAAAAGGGAA
1 AAAGAGAAAGGCAAAAGGGAA
321404 AAAGA-AAAGG-AAAAGGGAA
1 AAAGAGAAAGGCAAAAGGGAA
321423 AAA
1 AAA
321426 ATGCAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 12 0.55
20 5 0.23
21 5 0.23
ACGTcount: A:0.67, C:0.02, G:0.30, T:0.00
Consensus pattern (21 bp):
AAAGAGAAAGGCAAAAGGGAA
Found at i:325534 original size:31 final size:31
Alignment explanation
Indices: 325476--325534 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
325466 AATTTAAATA
* *
325476 TAAAAAATAAATAAAACTAATTTAAAATATC
1 TAAAAAATAAATAAAACTAAATAAAAATATC
* * *
325507 TAAAAATTAATTAAATCTAAATAAAAAT
1 TAAAAAATAAATAAAACTAAATAAAAAT
325535 TTTTAAGACT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (31 bp):
TAAAAAATAAATAAAACTAAATAAAAATATC
Found at i:331503 original size:22 final size:21
Alignment explanation
Indices: 331474--331517 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
331464 AATAAACTTA
*
331474 TAAATTTATA-TTTAATAGATT
1 TAAATTTAAATTTTAATA-ATT
331495 TAAAGTTTAAATTTTAATAATT
1 TAAA-TTTAAATTTTAATAATT
331517 T
1 T
331518 TTTTTCATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 9 0.45
23 7 0.35
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (21 bp):
TAAATTTAAATTTTAATAATT
Found at i:332044 original size:10 final size:10
Alignment explanation
Indices: 332024--332057 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
332014 TTAGGCCTTA
332024 ATAATTAAAAT
1 ATAA-TAAAAT
332035 ATAATAAAAT
1 ATAATAAAAT
332045 ATAA-AAAAT
1 ATAATAAAAT
332054 ATAA
1 ATAA
332058 ACACTCGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.39
10 10 0.43
11 4 0.17
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
ATAATAAAAT
Found at i:332111 original size:34 final size:33
Alignment explanation
Indices: 332065--332138 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 33
332055 TAAACACTCG
*
332065 TATATATTAAAATATATATATAATATAAATTAT-T
1 TATATATCAAAATATATATA-AAT-TAAATTATCT
* *
332099 TATATATCAAAATTTATATAAATTATATTATCT
1 TATATATCAAAATATATATAAATTAAATTATCT
332132 TATATAT
1 TATATAT
332139 AATTATAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 7 0.19
33 11 0.31
34 18 0.50
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (33 bp):
TATATATCAAAATATATATAAATTAAATTATCT
Found at i:332115 original size:18 final size:17
Alignment explanation
Indices: 332065--332118 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 17
332055 TAAACACTCG
*
332065 TATATAT-TAAAATATA
1 TATATATATAAAATTTA
332081 TATATA-ATATAAA-TTA
1 TATATATATA-AAATTTA
*
332097 TTTATATATCAAAATTTA
1 TATATATAT-AAAATTTA
332115 TATA
1 TATA
332119 AATTATATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
16 15 0.50
17 8 0.27
18 7 0.23
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TATATATATAAAATTTA
Found at i:332150 original size:32 final size:28
Alignment explanation
Indices: 332076--332150 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 28
332066 ATATATTAAA
332076 ATATAT-A-TATAATATAAATTATTTAT
1 ATATATAATTATAATATAAATTATTTAT
*
332102 ATATCAAAATT-T-ATATAAATTATATTATCTT
1 ATAT-ATAATTATAATATAAATTAT-TTA---T
332133 ATATATAATTATAATATA
1 ATATATAATTATAATATA
332151 TAAAAATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
26 4 0.11
27 12 0.32
28 5 0.13
29 1 0.03
30 5 0.13
31 6 0.16
32 5 0.13
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (28 bp):
ATATATAATTATAATATAAATTATTTAT
Found at i:335427 original size:2 final size:2
Alignment explanation
Indices: 335420--335448 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
335410 TTTACTTCCT
335420 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
335449 CCAGACTCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:337618 original size:16 final size:16
Alignment explanation
Indices: 337583--337615 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
337573 TTGAGTTGAG
*
337583 TTGAGTTATTTTGGGT
1 TTGAGTTATTTCGGGT
337599 TTGA-TTATTTCGGGT
1 TTGAGTTATTTCGGGT
337614 TT
1 TT
337616 TGAATTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.12, C:0.03, G:0.27, T:0.58
Consensus pattern (16 bp):
TTGAGTTATTTCGGGT
Found at i:341653 original size:16 final size:18
Alignment explanation
Indices: 341632--341669 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
341622 ATATAAATAA
341632 TTTTTTG-TCAT-AATTT
1 TTTTTTGTTCATAAATTT
341648 TTTTTTGTTCATAAATTT
1 TTTTTTGTTCATAAATTT
341666 TTTT
1 TTTT
341670 ATCGTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.35
17 4 0.20
18 9 0.45
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (18 bp):
TTTTTTGTTCATAAATTT
Found at i:344325 original size:14 final size:14
Alignment explanation
Indices: 344274--344325 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
344264 TACTTTTTTT
*
344274 TATTATATAATATA
1 TATTATATAATTTA
344288 TATT-TATATATTTA
1 TATTATATA-ATTTA
*
344302 TATTGTATAATTTA
1 TATTATATAATTTA
*
344316 TATTACATAA
1 TATTATATAA
344326 AGAAGAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
13 4 0.12
14 25 0.76
15 4 0.12
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (14 bp):
TATTATATAATTTA
Found at i:344395 original size:15 final size:15
Alignment explanation
Indices: 344375--344415 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
344365 TATGTTAAGT
*
344375 TATTTAAATATTAAA
1 TATTTAAAAATTAAA
344390 TATTTAAAAATTAAA
1 TATTTAAAAATTAAA
344405 T-TTATAAAAAT
1 TATT-TAAAAAT
344416 AAAAATATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 22 0.92
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TATTTAAAAATTAAA
Found at i:345925 original size:20 final size:20
Alignment explanation
Indices: 345896--345935 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
345886 AATTAATATT
*
345896 TTTTATTAATATAAAAAATA
1 TTTTAATAATATAAAAAATA
*
345916 TTTTAATAATATAATAAATA
1 TTTTAATAATATAAAAAATA
345936 GTCAAATTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTTAATAATATAAAAAATA
Found at i:347691 original size:3 final size:3
Alignment explanation
Indices: 347683--347709 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
347673 GAGTAAAATG
347683 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
347710 TTCCCTCTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:351079 original size:2 final size:2
Alignment explanation
Indices: 351067--351106 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
351057 AAAGTGTTAT
351067 TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
351107 CAATAGCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:358968 original size:22 final size:22
Alignment explanation
Indices: 358927--358968 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
358917 AAATTTAAAT
*
358927 TATTATTTATTTAATAAAATAA
1 TATTATTTATTTAAAAAAATAA
358949 TATT-TTTATTTAAAATAAAT
1 TATTATTTATTTAAAA-AAAT
358969 TGTTAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TATTATTTATTTAAAAAAATAA
Found at i:358995 original size:12 final size:12
Alignment explanation
Indices: 358978--359017 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
358968 TTGTTAAAAT
358978 ATATAAATTTTA
1 ATATAAATTTTA
358990 ATATAAAATTTTA
1 ATAT-AAATTTTA
* *
359003 AAATATATTTTA
1 ATATAAATTTTA
359015 ATA
1 ATA
359018 AATATTCAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATAAATTTTA
Found at i:359000 original size:13 final size:13
Alignment explanation
Indices: 358975--359017 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
358965 AAATTGTTAA
358975 AATATATAAATTTT
1 AATATA-AAATTTT
358989 AATATAAAATTTT
1 AATATAAAATTTT
* *
359002 AAAAT-ATATTTT
1 AATATAAAATTTT
359014 AATA
1 AATA
359018 AATATTCAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 9 0.35
13 11 0.42
14 6 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATAAAATTTT
Found at i:360109 original size:17 final size:17
Alignment explanation
Indices: 360057--360111 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
360047 AATAAATTTT
360057 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
*
360073 T-AAA-TTAT-TAATGTA
1 TAAAATTTATATAA-ATA
360088 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
360106 TAAAAT
1 TAAAAT
360112 ATTTTAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
13 1 0.03
14 5 0.16
15 5 0.16
16 2 0.06
17 9 0.29
18 6 0.19
19 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:361284 original size:6 final size:6
Alignment explanation
Indices: 361275--361363 Score: 52
Period size: 6 Copynumber: 14.3 Consensus size: 6
361265 AATCATAATG
* ** ** *
361275 ATGATA ATGATA ATGATA ATGATG ATGACG ATGATA ACAACTA TGGTGATA
1 ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA ATGA-TA --ATGATA
* * * * *
361326 ATGATA ATAATA ATAATA ATAATA ATAATA ATAATA AT
1 ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA AT
361364 TTTTTAAAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
6 64 0.93
7 2 0.03
8 2 0.03
9 1 0.01
ACGTcount: A:0.52, C:0.03, G:0.13, T:0.31
Consensus pattern (6 bp):
ATGATA
Found at i:361337 original size:3 final size:3
Alignment explanation
Indices: 361323--361363 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
361313 AACTATGGTG
*
361323 ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
361364 TTTTTAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:361537 original size:9 final size:9
Alignment explanation
Indices: 361507--361549 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
361497 TGATCTAATT
361507 TTAAAAATA
1 TTAAAAATA
*
361516 TTATAAATAA
1 TTAAAAAT-A
361526 TTAAAAATA
1 TTAAAAATA
* *
361535 TTAACATTA
1 TTAAAAATA
361544 TTAAAA
1 TTAAAA
361550 TAATAATATT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (9 bp):
TTAAAAATA
Found at i:361551 original size:17 final size:17
Alignment explanation
Indices: 361510--361597 Score: 54
Period size: 17 Copynumber: 5.1 Consensus size: 17
361500 TCTAATTTTA
*
361510 AAAATATTATAAATAATT
1 AAAATATTA-AAATTATT
*
361528 AAAAATATTAACATTATT
1 -AAAATATTAAAATTATT
* * *
361546 AAAATAATAATATTGTT
1 AAAATATTAAAATTATT
*
361563 ATAAATATT--TATTATT
1 A-AAATATTAAAATTATT
* *
361579 TAAATAATAAAATATATT
1 AAAATATTAAAAT-TATT
361597 A
1 A
361598 TTTTTTGTTT
Statistics
Matches: 54, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
15 6 0.11
16 6 0.11
17 17 0.31
18 16 0.30
19 9 0.17
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (17 bp):
AAAATATTAAAATTATT
Found at i:364811 original size:16 final size:15
Alignment explanation
Indices: 364790--364883 Score: 82
Period size: 16 Copynumber: 6.0 Consensus size: 15
364780 TTTTGATTTA
364790 GGTCATTTCGGGTTC
1 GGTCATTTCGGGTTC
* *
364805 GGTTCATTT-AGATTC
1 GG-TCATTTCGGGTTC
*
364820 GGGTCATTTTGGGTTC
1 -GGTCATTTCGGGTTC
*
364836 AGGTCATTTCGGATTCC
1 -GGTCATTTCGGGTT-C
* *
364853 AGTCATTTCGGGTTTG
1 GGTCATTTCGGG-TTC
364869 GGTCATTTCGGGTTC
1 GGTCATTTCGGGTTC
364884 AGGTTGTTTT
Statistics
Matches: 62, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
15 14 0.23
16 45 0.73
17 3 0.05
ACGTcount: A:0.12, C:0.17, G:0.30, T:0.41
Consensus pattern (15 bp):
GGTCATTTCGGGTTC
Found at i:364812 original size:32 final size:31
Alignment explanation
Indices: 364776--364876 Score: 89
Period size: 32 Copynumber: 3.2 Consensus size: 31
364766 CGGGTTTAGA
* *
364776 TCATTTTTGATTTAGGTCATTTCGGGTTCGG
1 TCATTTTAGATTCAGGTCATTTCGGGTTCGG
* *
364807 TTCA-TTTAGATTCGGGTCATTTTGGGTTCAGG
1 -TCATTTTAGATTCAGGTCATTTCGGGTTC-GG
** *
364839 TCATTTCGGATTCCA-GTCATTTCGGGTTTGGG
1 TCATTTTAGATT-CAGGTCATTTCGGG-TTCGG
364871 TCATTT
1 TCATTT
364877 CGGGTTCAGG
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
31 24 0.43
32 29 0.52
33 3 0.05
ACGTcount: A:0.14, C:0.15, G:0.26, T:0.46
Consensus pattern (31 bp):
TCATTTTAGATTCAGGTCATTTCGGGTTCGG
Found at i:364877 original size:32 final size:32
Alignment explanation
Indices: 364791--364879 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 32
364781 TTTGATTTAG
* * **
364791 GTCATTTCGGGTTCGGTTCATTT-AGATTCGG
1 GTCATTTCGGGTTCGGGTCATTTCGGATTCCA
* *
364822 GTCATTTTGGGTTCAGGTCATTTCGGATTCCA
1 GTCATTTCGGGTTCGGGTCATTTCGGATTCCA
*
364854 GTCATTTCGGGTTTGGGTCATTTCGG
1 GTCATTTCGGGTTCGGGTCATTTCGG
364880 GTTCAGGTTG
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
31 20 0.42
32 28 0.58
ACGTcount: A:0.12, C:0.17, G:0.29, T:0.42
Consensus pattern (32 bp):
GTCATTTCGGGTTCGGGTCATTTCGGATTCCA
Found at i:365557 original size:167 final size:166
Alignment explanation
Indices: 365267--365586 Score: 428
Period size: 167 Copynumber: 1.9 Consensus size: 166
365257 AATTTTTTAA
* *
365267 TTTTTTTTGAAATACGATGTTTTCTACTACATAAATTTTTCTGAAGGGATTTTTCTCGGTTTTTA
1 TTTTTTTTAAAATACGATGTGTTCTACTACATAAATTTTTCTGAAGGGATTTTTCTC-GTTTTTA
* * * * * *
365332 ATTTTTAAAATTCATCAAATATTATCATTTATTTCATATTAATTCAGTTTTCAAAAATTTATTCA
65 ATTTTTAAAATTCATCAAACATCATCATTTATTTCATATTAATTCAATTTTAAAAAATTAATTAA
**
365397 TTTTCATGAGTTTTTTATTTTTTTCCTTGAAATTCTT
130 TTTTCATGAGTTTTGAATTTTTTTCCTTGAAATTCTT
* * * * *
365434 TTTTTTTTCAAAATACGGTGTGTTCTACTCCGTAAATTTTTTTGAGGGGATTTTTCTC-TATTTT
1 TTTTTTTT-AAAATACGATGTGTTCTACTACATAAATTTTTCTGAAGGGATTTTTCTCGT-TTTT
* * *
365498 AATTTTTAAATTTTATCAAACATCATTATTTGA-TTCATATTAATTCAATTTTAAAAAATTAATT
64 AATTTTTAAAATTCATCAAACATCATCATTT-ATTTCATATTAATTCAATTTTAAAAAATTAATT
365562 AATTTTCATGAGTTTTGAATTTTTT
128 AATTTTCATGAGTTTTGAATTTTTT
365587 GTTAAAATTT
Statistics
Matches: 132, Mismatches: 18, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
166 1 0.01
167 88 0.67
168 43 0.33
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.53
Consensus pattern (166 bp):
TTTTTTTTAAAATACGATGTGTTCTACTACATAAATTTTTCTGAAGGGATTTTTCTCGTTTTTAA
TTTTTAAAATTCATCAAACATCATCATTTATTTCATATTAATTCAATTTTAAAAAATTAATTAAT
TTTCATGAGTTTTGAATTTTTTTCCTTGAAATTCTT
Found at i:366216 original size:21 final size:20
Alignment explanation
Indices: 366171--366216 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 20
366161 GGCAAAAAGT
*
366171 TGAAAAAACAAGTAAAAAAA
1 TGAAAAAACAAATAAAAAAA
366191 T-AAAAAA-AAATAATAATAAA
1 TGAAAAAACAAATAA-AA-AAA
366211 TGAAAA
1 TGAAAA
366217 GGCATGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 5 0.23
19 8 0.36
20 5 0.23
21 4 0.18
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (20 bp):
TGAAAAAACAAATAAAAAAA
Found at i:367525 original size:30 final size:30
Alignment explanation
Indices: 367491--367549 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
367481 AATAAATAAA
*
367491 CATATTACCAATTAATCTATATAATTACAG
1 CATATTACCAATTAATCTATAGAATTACAG
367521 CATATTACCAATTAATCTATAGAATTACA
1 CATATTACCAATTAATCTATAGAATTACA
367550 ACTTTAATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.44, C:0.17, G:0.03, T:0.36
Consensus pattern (30 bp):
CATATTACCAATTAATCTATAGAATTACAG
Found at i:370259 original size:334 final size:333
Alignment explanation
Indices: 369728--370349 Score: 876
Period size: 334 Copynumber: 1.9 Consensus size: 333
369718 AAATTTCAAC
** * * * * *
369728 AAAAAAATCCAAAACTTATAAAAATTAATCAATTTTTTAAAACTGAATTAATATGAATCAAATAA
1 AAAAAAATAAAAAACTCATAAAAATGAATAAATTTTTGAAAACTAAATTAATATGAATCAAATAA
* * *
369793 TGATGTTTGATGAAATTTAAAATTGAAAATCGAGAAAAATCCCTTCAAAAAAATTTACGGAGTAA
66 TAATATTTGATGAAATTTAAAATTGAAAACCGAGAAAAATCCCTTCAAAAAAATTTACGGAGTAA
* * * *
369858 AAAATGCCGTATTTCGAAAAAAGAAAGTTTCAAGGAAAAAAATAAAAAACTCATGAAAATGAATA
131 AAAATACCATATTTCGAAAAAAGAAAGTTTCAAGGAAAAAAATAAAAAACTCATAAAAATAAATA
* *
369923 AATTTTTGAAAACTGAATTAATATAAAATAAATGATAATATTTGATGAATTTGAAAAATTAAAAA
196 AATTTTTGAAAAATGAATTAATATAAAATAAATGATAATATTTGATAAATTTGAAAAATTAAAAA
*
369988 CCGAGAAAAATACTCTCAAAAAAATTTAAAGAGTAGAAAATACCGTATTTCGAAAAAATGAGAGT
261 CCGAGAAAAATACCCTCAAAAAAATTTAAAGAGTAGAAAATACCGTATTTCGAAAAAATGAGAGT
370053 TTCGAGGG
326 TTCGAGGG
* *
370061 AAAAAAATAAAAAACTCATGAAAATGAATAAATTTTTGAAAACTAAATTAATATGAAAT-AAATG
1 AAAAAAATAAAAAACTCATAAAAATGAATAAATTTTTGAAAACTAAATTAATATG-AATCAAATA
* *
370125 ATAATATTTGATGAATTTTAAAAATTGAAAACCGAGAAAAAAAT-CCTCTC-GAAAAATTTACGG
65 ATAATATTTGATGAAATTT-AAAATTGAAAACCGAG--AAAAATCCCT-TCAAAAAAATTTACGG
* * * * *
370188 AGTAGAAAATATCATATTTTGAAAAAA-AATAGTTTCAA-GAGAAAAATTAAAAACTCATAAAAA
126 AGTAAAAAATACCATATTTCGAAAAAAGAA-AGTTTCAAGGAAAAAAATAAAAAACTCATAAAAA
* *
370251 TAAATAAATTTTTGAAAAATGAATTAATATAAAATAAGTGATAATATTTGATAAATTTTAAAAAT
190 TAAATAAATTTTTGAAAAATGAATTAATATAAAATAAATGATAATATTTGATAAATTTGAAAAAT
* * *
370316 TAAAAATCTAGAAAAATCCCCTCAAAAAAATTTA
255 TAAAAACCGAGAAAAATACCCTCAAAAAAATTTA
370350 CGGTATTTCG
Statistics
Matches: 252, Mismatches: 31, Indels: 11
0.86 0.11 0.04
Matches are distributed among these distances:
333 67 0.27
334 132 0.52
335 45 0.18
336 8 0.03
ACGTcount: A:0.54, C:0.08, G:0.11, T:0.28
Consensus pattern (333 bp):
AAAAAAATAAAAAACTCATAAAAATGAATAAATTTTTGAAAACTAAATTAATATGAATCAAATAA
TAATATTTGATGAAATTTAAAATTGAAAACCGAGAAAAATCCCTTCAAAAAAATTTACGGAGTAA
AAAATACCATATTTCGAAAAAAGAAAGTTTCAAGGAAAAAAATAAAAAACTCATAAAAATAAATA
AATTTTTGAAAAATGAATTAATATAAAATAAATGATAATATTTGATAAATTTGAAAAATTAAAAA
CCGAGAAAAATACCCTCAAAAAAATTTAAAGAGTAGAAAATACCGTATTTCGAAAAAATGAGAGT
TTCGAGGG
Found at i:370301 original size:166 final size:165
Alignment explanation
Indices: 369634--370352 Score: 817
Period size: 166 Copynumber: 4.4 Consensus size: 165
369624 TTTGTAATAG
* * ** ** * * *
369634 TATTAGATGAGTTTTAAAAATTCTAAACTAAGAAAAATCCTCCCAAAAAAATTTACAGAGAAGAA
1 TATTTGATGAATTTTAAAAATTAAAAACCGAGAAAAATCCTCTCAAAAAAATTTACGGAGTAGAA
* * * ** * * *
369699 AACT-CGATTTTTCG-AAAAA-AAA-TTTCAACAAAAAAATCCAAAACTTATAAAAATTAATCAA
66 AA-TACCATATTTCGAAAAAAGAAAGTTTCAAGAAAAAAATAAAAAACTCATAAAAATGAATAAA
* * * *
369760 TTTTTTAAAACTGAATTAATAT-GAATCAAATAATGA
130 TTTTTGAAAACTGAATTAATATAAAAT-AAATGATAA
* * * * *
369796 TGTTTGATGAAATTT-AAAATTGAAAATCGAGAAAAATCC-CTTCAAAAAAATTTACGGAGTAAA
1 TATTTGATGAATTTTAAAAATTAAAAACCGAGAAAAATCCTC-TCAAAAAAATTTACGGAGTAGA
* * *
369859 AAATGCCGTATTTCGAAAAAAGAAAGTTTCAAGGAAAAAAATAAAAAACTCATGAAAATGAATAA
65 AAATACCATATTTCGAAAAAAGAAAGTTTCAA-GAAAAAAATAAAAAACTCATAAAAATGAATAA
369924 ATTTTTGAAAACTGAATTAATATAAAATAAATGATAA
129 ATTTTTGAAAACTGAATTAATATAAAATAAATGATAA
* * **
369961 TATTTGATGAATTTGAAAAATTAAAAACCGAGAAAAATACTCTCAAAAAAATTTAAAGAGTAGAA
1 TATTTGATGAATTTTAAAAATTAAAAACCGAGAAAAATCCTCTCAAAAAAATTTACGGAGTAGAA
* * * *
370026 AATACCGTATTTCGAAAAAATGAGAGTTTCGAGGGAAAAAAATAAAAAACTCATGAAAATGAATA
66 AATACCATATTTCGAAAAAA-GAAAGTTTC-A-AGAAAAAAATAAAAAACTCATAAAAATGAATA
* *
370091 AATTTTTGAAAACTAAATTAATATGAAATAAATGATAA
128 AATTTTTGAAAACTGAATTAATATAAAATAAATGATAA
* *
370129 TATTTGATGAATTTTAAAAATTGAAAACCGAGAAAAAAATCCTCTC-GAAAAATTTACGGAGTAG
1 TATTTGATGAATTTTAAAAATTAAAAACCGAG--AAAAATCCTCTCAAAAAAATTTACGGAGTAG
* * * * *
370193 AAAATATCATATTTTGAAAAAA-AATAGTTTCAAGAGAAAAATTAAAAACTCATAAAAATAAATA
64 AAAATACCATATTTCGAAAAAAGAA-AGTTTCAAGAAAAAAATAAAAAACTCATAAAAATGAATA
* *
370257 AATTTTTGAAAAATGAATTAATATAAAATAAGTGATAA
128 AATTTTTGAAAACTGAATTAATATAAAATAAATGATAA
* * * *
370295 TATTTGATAAATTTTAAAAATTAAAAATCTAGAAAAATCCCCTCAAAAAAATTTACGG
1 TATTTGATGAATTTTAAAAATTAAAAACCGAGAAAAATCCTCTCAAAAAAATTTACGG
370353 TATTTCGAAA
Statistics
Matches: 475, Mismatches: 66, Indels: 29
0.83 0.12 0.05
Matches are distributed among these distances:
160 2 0.00
161 47 0.10
162 16 0.03
163 3 0.01
164 17 0.04
165 78 0.16
166 152 0.32
167 11 0.02
168 104 0.22
169 34 0.07
170 11 0.02
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.28
Consensus pattern (165 bp):
TATTTGATGAATTTTAAAAATTAAAAACCGAGAAAAATCCTCTCAAAAAAATTTACGGAGTAGAA
AATACCATATTTCGAAAAAAGAAAGTTTCAAGAAAAAAATAAAAAACTCATAAAAATGAATAAAT
TTTTGAAAACTGAATTAATATAAAATAAATGATAA
Found at i:370669 original size:22 final size:23
Alignment explanation
Indices: 370626--370669 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
370616 CTAAAATGAC
370626 TTAAACCCAATTTAACCCGAATG
1 TTAAACCCAATTTAACCCGAATG
*
370649 TTAAACCCAA-TTAACCGGAAT
1 TTAAACCCAATTTAACCCGAAT
370670 TCAGAATGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.41, C:0.25, G:0.09, T:0.25
Consensus pattern (23 bp):
TTAAACCCAATTTAACCCGAATG
Found at i:370777 original size:16 final size:16
Alignment explanation
Indices: 370756--370793 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
370746 AACCGGAACA
370756 CGAAATGACCTAAACC
1 CGAAATGACCTAAACC
* *
370772 CGAAATGACTTAAATC
1 CGAAATGACCTAAACC
370788 CGAAAT
1 CGAAAT
370794 AACTCGAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.45, C:0.24, G:0.13, T:0.18
Consensus pattern (16 bp):
CGAAATGACCTAAACC
Found at i:370817 original size:16 final size:15
Alignment explanation
Indices: 370798--370861 Score: 74
Period size: 16 Copynumber: 4.0 Consensus size: 15
370788 CGAAATAACT
370798 CGAACCAGAAATGATC
1 CGAACCA-AAATGATC
*
370814 CGAATCCAAAGTGATC
1 CGAA-CCAAAATGATC
*
370830 CGAACCCGAAATGATC
1 CGAA-CCAAAATGATC
370846 CGAACCTAAAATGATC
1 CGAACC-AAAATGATC
370862 TAAACTTGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
15 2 0.05
16 36 0.88
17 3 0.07
ACGTcount: A:0.41, C:0.27, G:0.17, T:0.16
Consensus pattern (15 bp):
CGAACCAAAATGATC
Found at i:370861 original size:32 final size:32
Alignment explanation
Indices: 370798--370861 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
370788 CGAAATAACT
*
370798 CGAACCAGAAATGATCCGAATCCAAAGTGATC
1 CGAACCAGAAATGATCCGAATCCAAAATGATC
*
370830 CGAACCCGAAATGATCCGAA-CCTAAAATGATC
1 CGAACCAGAAATGATCCGAATCC-AAAATGATC
370862 TAAACTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 2 0.07
32 27 0.93
ACGTcount: A:0.41, C:0.27, G:0.17, T:0.16
Consensus pattern (32 bp):
CGAACCAGAAATGATCCGAATCCAAAATGATC
Found at i:373598 original size:2 final size:2
Alignment explanation
Indices: 373552--373586 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
373542 TGCATATAAC
* *
373552 AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
373587 AAGGTGATAT
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:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:374086 original size:29 final size:28
Alignment explanation
Indices: 374054--374113 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
374044 TACACGTGGC
** *
374054 TTTATGTTGTAAGAACAAAAAAATTTATT
1 TTTATGTTAAAAGAA-AAAAAAATATATT
* *
374083 TTTATTTTAAAAGTAAAAAAAATATATT
1 TTTATGTTAAAAGAAAAAAAAATATATT
374111 TTT
1 TTT
374114 TGAAAAGTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 15 0.58
29 11 0.42
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.45
Consensus pattern (28 bp):
TTTATGTTAAAAGAAAAAAAAATATATT
Found at i:374101 original size:25 final size:25
Alignment explanation
Indices: 374071--374126 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
374061 TGTAAGAACA
* * *
374071 AAAAAATTTATTTTTATTTTAAAAGT
1 AAAAAATATATATTT-TTTGAAAAGT
*
374097 AAAAAAAATATATTTTTTGAAAAGT
1 AAAAAATATATATTTTTTGAAAAGT
374122 AAAAA
1 AAAAA
374127 TAAACATCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (25 bp):
AAAAAATATATATTTTTTGAAAAGT
Found at i:375009 original size:21 final size:21
Alignment explanation
Indices: 374969--375010 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
374959 GTATTGGTTG
* **
374969 GATGAAAAAATGTATTTTTTA
1 GATGAAAAAATATAACTTTTA
374990 GATGAAAAAATATAACTTTTA
1 GATGAAAAAATATAACTTTTA
375011 ATAACGACAA
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:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (21 bp):
GATGAAAAAATATAACTTTTA
Found at i:378373 original size:21 final size:21
Alignment explanation
Indices: 378349--378393 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
378339 GAATGAATTG
*
378349 ATGCATTGGTTGGATGAAAGA
1 ATGCATTGGTTGGATGAAAAA
**
378370 ATGCATTTTTTGGATGAAAAA
1 ATGCATTGGTTGGATGAAAAA
378391 ATG
1 ATG
378394 TAACTTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (21 bp):
ATGCATTGGTTGGATGAAAAA
Found at i:378401 original size:21 final size:21
Alignment explanation
Indices: 378358--378401 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
378348 GATGCATTGG
* **
378358 TTGGATGAAAGAATGCATTTT
1 TTGGATGAAAAAATGCAACTT
*
378379 TTGGATGAAAAAATGTAACTT
1 TTGGATGAAAAAATGCAACTT
378400 TT
1 TT
378402 AATAACCAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (21 bp):
TTGGATGAAAAAATGCAACTT
Found at i:380065 original size:20 final size:20
Alignment explanation
Indices: 380040--380082 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
380030 AAAAGTTATC
*
380040 TAATAATTATTAA-ATAATAT
1 TAATAATT-CTAATATAATAT
380060 TAATAATTCTAATATAATAT
1 TAATAATTCTAATATAATAT
380080 TAA
1 TAA
380083 AAATATTGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
TAATAATTCTAATATAATAT
Found at i:380806 original size:17 final size:17
Alignment explanation
Indices: 380784--380816 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
380774 ATGCTTGCCT
380784 GAAATAGCCATTCAAGG
1 GAAATAGCCATTCAAGG
380801 GAAATAGCCATTCAAG
1 GAAATAGCCATTCAAG
380817 TGCGAGCCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.18
Consensus pattern (17 bp):
GAAATAGCCATTCAAGG
Found at i:381333 original size:2 final size:2
Alignment explanation
Indices: 381326--381360 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
381316 TAGGAAGACG
381326 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
381361 TAATTTACCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:381470 original size:19 final size:19
Alignment explanation
Indices: 381448--381487 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
381438 TTATTTAAAT
381448 TTAAATTTTGAA-AAGTTTA
1 TTAAATTTTGAATAA-TTTA
381467 TTAAATTTTGAATAATTTA
1 TTAAATTTTGAATAATTTA
381486 TT
1 TT
381488 TTGAGTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (19 bp):
TTAAATTTTGAATAATTTA
Found at i:385951 original size:24 final size:23
Alignment explanation
Indices: 385898--386001 Score: 75
Period size: 24 Copynumber: 4.3 Consensus size: 23
385888 ATATAATACA
* *
385898 AATAAAATTTATTTAATATATAT
1 AATATAATATATTTAATATATAT
*
385921 AAAATAATATATTTAA-ATATGATT
1 AATATAATATATTTAATATAT-A-T
* * *
385945 AATATAAATTTATATTAATATTTAAA
1 AATAT-AATATAT-TTAATATAT-AT
*
385971 AATTTAATATATTTAATAATATAT
1 AATATAATATATTTAAT-ATATAT
*
385995 AAAATAA
1 AATATAA
386002 AAAATACGAA
Statistics
Matches: 61, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
22 4 0.07
23 14 0.23
24 16 0.26
25 15 0.25
26 8 0.13
27 4 0.07
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (23 bp):
AATATAATATATTTAATATATAT
Found at i:387306 original size:2 final size:2
Alignment explanation
Indices: 387299--387323 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
387289 AGGAGTTTCA
387299 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 A
387324 ATACATCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:390132 original size:5 final size:5
Alignment explanation
Indices: 390110--390178 Score: 51
Period size: 5 Copynumber: 14.6 Consensus size: 5
390100 AATAATTTTA
* *
390110 AATAT AATAT --TAT TATAT AATAT AAATAT AATAT AA-A- AA-AT AATTAA
1 AATAT AATAT AATAT AATAT AATAT -AATAT AATAT AATAT AATAT AA-TAT
*
390157 AATAT AATAT -ATAT AAAAT AAT
1 AATAT AATAT AATAT AATAT AAT
390179 TTTATTGTGA
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
3 6 0.12
4 7 0.13
5 31 0.60
6 8 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:390138 original size:11 final size:11
Alignment explanation
Indices: 390108--390167 Score: 59
Period size: 11 Copynumber: 5.2 Consensus size: 11
390098 TTAATAATTT
390108 TAAATATAATA
1 TAAATATAATA
*
390119 TTATTATATAATA
1 -TA-AATATAATA
390132 TAAATATAATA
1 TAAATATAATA
*
390143 TAAAAAATAAT-
1 T-AAATATAATA
390154 TAAAATATAATA
1 T-AAATATAATA
390166 TA
1 TA
390168 TATAAAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
11 20 0.49
12 13 0.32
13 8 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TAAATATAATA
Found at i:390144 original size:18 final size:18
Alignment explanation
Indices: 390110--390178 Score: 52
Period size: 18 Copynumber: 3.8 Consensus size: 18
390100 AATAATTTTA
*
390110 AATAT-AATATTATTATAT
1 AATATAAATA-TAATATAT
*
390128 AATATAAATATAATATAA
1 AATATAAATATAATATAT
* * *
390146 AAAATAATTAAAATATAAT
1 AATATAAATATAATAT-AT
390165 ATATATAAA-ATAAT
1 A-ATATAAATATAAT
390179 TTTATTGTGA
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
18 24 0.62
19 10 0.26
20 5 0.13
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATATAAATATAATATAT
Found at i:390159 original size:23 final size:25
Alignment explanation
Indices: 390100--390179 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 25
390090 TCATAAATTT
* *
390100 AATAATTTTAAATATAATAT-TATTA
1 AATAA-TTAAAATATAATATATATAA
*
390125 TATAA-TATAAATATAATATA-A-AA
1 AATAATTA-AAATATAATATATATAA
390148 AATAATTAAAATATAATATATATAA
1 AATAATTAAAATATAATATATATAA
390173 AATAATT
1 AATAATT
390180 TTATTGTGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
23 18 0.39
24 15 0.33
25 13 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
AATAATTAAAATATAATATATATAA
Found at i:390230 original size:21 final size:21
Alignment explanation
Indices: 390197--390238 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
390187 GATAAAAATA
390197 TTTAAATAAAAATTA-TAATT
1 TTTAAATAAAAATTATTAATT
*
390217 TTTATAATATAAATTATTAATT
1 TTTA-AATAAAAATTATTAATT
390239 ATAAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 10 0.53
22 5 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTAAATAAAAATTATTAATT
Found at i:390722 original size:3 final size:3
Alignment explanation
Indices: 390714--390751 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
390704 CTAAAAAGAA
390714 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
390752 AGGTTTAGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:394114 original size:19 final size:20
Alignment explanation
Indices: 394092--394130 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
394082 TTGATTTATA
*
394092 TTATATTAAATA-TTAAATT
1 TTATATTAAAAATTTAAATT
*
394111 TTATTTTAAAAATTTAAATT
1 TTATATTAAAAATTTAAATT
394131 AATCTGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTATATTAAAAATTTAAATT
Found at i:395600 original size:2 final size:2
Alignment explanation
Indices: 395593--395622 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
395583 TTCTTAATGG
*
395593 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
395623 TTAAAGAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:398329 original size:2 final size:2
Alignment explanation
Indices: 398322--398352 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
398312 TCATACAAAG
398322 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
398353 GTAATATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:407144 original size:18 final size:17
Alignment explanation
Indices: 407113--407148 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
407103 CATAAATAAT
407113 TTAAAAATATAATTTTA
1 TTAAAAATATAATTTTA
407130 TTAAAAATATAAATTTTA
1 TTAAAAATAT-AATTTTA
407148 T
1 T
407149 ATTTTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAAAATATAATTTTA
Found at i:407315 original size:17 final size:17
Alignment explanation
Indices: 407279--407330 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
407269 AATATAATTT
407279 TATTTAAA-ATATA-AA
1 TATTTAAATATATATAA
* * *
407294 T-TTTATATATTTATAT
1 TATTTAAATATATATAA
407310 TATTTAAATATATATAA
1 TATTTAAATATATATAA
407327 TATT
1 TATT
407331 AATAGTTTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
14 5 0.18
15 5 0.18
16 2 0.07
17 16 0.57
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATTTAAATATATATAA
Found at i:407357 original size:149 final size:152
Alignment explanation
Indices: 407118--407416 Score: 462
Period size: 151 Copynumber: 2.0 Consensus size: 152
407108 ATAATTTAAA
* * **
407118 AATATAATTTTATTAAAAATATAAATTTTATATTTTTTTATTATTCATATTTACATATAATATTA
1 AATATAATTTTATTAAAAATATAAATTTTATATATTTATATTATT-ATAAATACATATAATATTA
407183 ATAATTTAATAATACGACTTAATTTAAAATAAAAATTTTAT-TTTTTTAAATTTAATAAATTAAA
65 ATAATTTAATAATACGACTTAATTTAAAATAAAAATTTTATATTTTTTAAATTTAATAAATTAAA
407247 -TTACGTATAATATTAATAACAT
130 TTTACGTATAATATTAATAACAT
* *
407269 AATATAATTTTATTTAAAATATAAATTTTATATATTTATATTATT-TAAATATATATAATATTAA
1 AATATAATTTTATTAAAAATATAAATTTTATATATTTATATTATTATAAATACATATAATATTAA
* * *
407333 TAGTTTAATAATACTG-CTTAATTTAAAATATAAATTTTATATTTTTTAAATTTAATAATTTAAA
66 TAATTTAATAATAC-GACTTAATTTAAAATAAAAATTTTATATTTTTTAAATTTAATAAATTAAA
*
407397 TTTATGTATAATATTAATAA
130 TTTACGTATAATATTAATAA
407417 TTTAATAATG
Statistics
Matches: 135, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
149 52 0.39
150 23 0.17
151 60 0.44
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (152 bp):
AATATAATTTTATTAAAAATATAAATTTTATATATTTATATTATTATAAATACATATAATATTAA
TAATTTAATAATACGACTTAATTTAAAATAAAAATTTTATATTTTTTAAATTTAATAAATTAAAT
TTACGTATAATATTAATAACAT
Found at i:407369 original size:73 final size:73
Alignment explanation
Indices: 407133--407378 Score: 250
Period size: 76 Copynumber: 3.3 Consensus size: 73
407123 AATTTTATTA
* ** *
407133 AAAATATAAATTTTATATTTTTTTATTATTCATATTTACATATAATATTAATAATTTAATAATAC
1 AAAATATAAATTTTATATTTTTATATTATT--TAAATATATATAATATTAATAATTTAATAATAC
407198 -GACTTAATTT
64 TG-CTTAATTT
* * * **
407208 AAAATAAAAATTTTATTTTTTTAAATTTAATAAATTAAAT-TACGTATAATATTAATAACATAAT
1 AAAATATAAATTTTATATTTTTATA-TT-AT---TTAAATATA--TATAATATTAATAATTTAAT
* *
407272 -ATAAT--TTTATTT
59 AATACTGCTTAATTT
* *
407284 AAAATATAAATTTTATATATTTATATTATTTAAATATATATAATATTAATAGTTTAATAATACTG
1 AAAATATAAATTTTATATTTTTATATTATTTAAATATATATAATATTAATAATTTAATAATACTG
407349 CTTAATTT
66 CTTAATTT
407357 AAAATATAAATTTTATATTTTT
1 AAAATATAAATTTTATATTTTT
407379 TAAATTTAAT
Statistics
Matches: 138, Mismatches: 21, Indels: 26
0.75 0.11 0.14
Matches are distributed among these distances:
70 17 0.12
71 10 0.07
72 2 0.01
73 27 0.20
74 2 0.01
75 23 0.17
76 29 0.21
77 3 0.02
78 6 0.04
79 18 0.13
80 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.50
Consensus pattern (73 bp):
AAAATATAAATTTTATATTTTTATATTATTTAAATATATATAATATTAATAATTTAATAATACTG
CTTAATTT
Found at i:407414 original size:73 final size:72
Alignment explanation
Indices: 407280--407417 Score: 149
Period size: 73 Copynumber: 1.9 Consensus size: 72
407270 ATATAATTTT
* * * * *
407280 ATTTAAAATATAAATTTTATATATTTATATTATTTAA-ATATATATAA-TATTAATAGTTTAATA
1 ATTTAAAATATAAATTTTATAT-TTTTTA-AATTTAATA-ATTTACAATTATTAATAATTTAATA
407343 ATACTGCTTA
63 ATACTGCTTA
407353 ATTTAAAATATAAATTTTATATTTTTTAAATTTAATAATTTA-AATTTATGT-ATAATATTAATA
1 ATTTAAAATATAAATTTTATATTTTTTAAATTTAATAATTTACAA-TTAT-TAATAAT-TTAATA
407416 AT
63 AT
407418 TTAATAATGA
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
70 2 0.04
71 10 0.18
72 13 0.23
73 31 0.55
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (72 bp):
ATTTAAAATATAAATTTTATATTTTTTAAATTTAATAATTTACAATTATTAATAATTTAATAATA
CTGCTTA
Found at i:407595 original size:12 final size:12
Alignment explanation
Indices: 407574--407608 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
407564 TTTAATTAAA
407574 ATTTTAAATATAT
1 ATTTT-AATATAT
407587 ATTTTAATATAT
1 ATTTTAATATAT
*
407599 TTTTTAATAT
1 ATTTTAATAT
407609 TTAAATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
ATTTTAATATAT
Found at i:414215 original size:51 final size:51
Alignment explanation
Indices: 414151--414247 Score: 131
Period size: 51 Copynumber: 1.9 Consensus size: 51
414141 TACATTGAAG
* * **
414151 AATGTATCAATACAGTCATACATGTATCGATACATCTGGGTAAAAAAATAA
1 AATGTATCAATACAGTCAAAAATGTATCGATACATCTAAGTAAAAAAATAA
* * *
414202 AATGTATCGATACATTGAAAAATGTATCGATACATCTAAGTAAAAA
1 AATGTATCAATACAGTCAAAAATGTATCGATACATCTAAGTAAAAA
414248 TGTGACTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 39 1.00
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.28
Consensus pattern (51 bp):
AATGTATCAATACAGTCAAAAATGTATCGATACATCTAAGTAAAAAAATAA
Found at i:414229 original size:71 final size:72
Alignment explanation
Indices: 414100--414235 Score: 229
Period size: 71 Copynumber: 1.9 Consensus size: 72
414090 ATATTGAAAA
* *
414100 ATGTATCGATACATCTGGGAAAAAAAGATAGAATGTATCGATACATTGAAGAATGTATCAATACA
1 ATGTATCGATACATCTGGGAAAAAAAGATAAAATGTATCGATACATTGAAAAATGTATCAATACA
414165 GTCATAC
66 GTCATAC
* *
414172 ATGTATCGATACATCTGGGTAAAAAA-ATAAAATGTATCGATACATTGAAAAATGTATCGATACA
1 ATGTATCGATACATCTGGGAAAAAAAGATAAAATGTATCGATACATTGAAAAATGTATCAATACA
414236 TCTAAGTAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
71 35 0.58
72 25 0.42
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (72 bp):
ATGTATCGATACATCTGGGAAAAAAAGATAAAATGTATCGATACATTGAAAAATGTATCAATACA
GTCATAC
Found at i:416507 original size:13 final size:13
Alignment explanation
Indices: 416489--416518 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
416479 CGACACATGC
416489 ACATTGTATCAAT
1 ACATTGTATCAAT
416502 ACATTGTATCAAT
1 ACATTGTATCAAT
416515 ACAT
1 ACAT
416519 GAAAAATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.37
Consensus pattern (13 bp):
ACATTGTATCAAT
Found at i:419420 original size:2 final size:2
Alignment explanation
Indices: 419413--419457 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
419403 TTAAGTTAGA
* *
419413 AT AT AT AT AT AC AT AT AT AT AT AT AT AC 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
419455 AT A
1 AT A
419458 AACTCAAATC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:419434 original size:16 final size:16
Alignment explanation
Indices: 419413--419455 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
419403 TTAAGTTAGA
419413 ATATATATATACATAT
1 ATATATATATACATAT
419429 ATATATATATACATAT
1 ATATATATATACATAT
419445 ATATATATATA
1 ATATATATATA
419456 TAAACTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATATATATACATAT
Found at i:419942 original size:13 final size:13
Alignment explanation
Indices: 419924--419950 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
419914 TAAATACATG
419924 ATTTATAATAATT
1 ATTTATAATAATT
419937 ATTTATAATAATT
1 ATTTATAATAATT
419950 A
1 A
419951 AAACTGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTATAATAATT
Found at i:420862 original size:21 final size:21
Alignment explanation
Indices: 420837--420876 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
420827 GACTTTACTC
420837 AAAATAGAATTAAGTTAACTT
1 AAAATAGAATTAAGTTAACTT
420858 AAAATAGAATTAAGTTAAC
1 AAAATAGAATTAAGTTAAC
420877 GACGTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAATAGAATTAAGTTAACTT
Found at i:422478 original size:13 final size:13
Alignment explanation
Indices: 422460--422497 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
422450 TGTAAAATAA
*
422460 AAAAAATTAATTT
1 AAAAAATAAATTT
422473 AAAAAATAAATTT
1 AAAAAATAAATTT
*
422486 AAATAA-AAATTT
1 AAAAAATAAATTT
422498 TATTTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AAAAAATAAATTT
Found at i:422492 original size:17 final size:17
Alignment explanation
Indices: 422472--422530 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
422462 AAAATTAATT
422472 TAAAAAATAAATTTAAA
1 TAAAAAATAAATTTAAA
* **
422489 TAAAAATTTTATTTAAA
1 TAAAAAATAAATTTAAA
422506 -AAATAAATAAATTTTAAA
1 TAAA-AAATAAA-TTTAAA
422524 TTAAAAA
1 -TAAAAA
422531 CTTTAAACTC
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
16 3 0.09
17 18 0.56
18 6 0.19
19 2 0.06
20 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAAAATAAATTTAAA
Found at i:422503 original size:30 final size:28
Alignment explanation
Indices: 422457--422513 Score: 87
Period size: 30 Copynumber: 2.0 Consensus size: 28
422447 AGATGTAAAA
422457 TAAAAAAAATTAATTTAAAAAATAAATT
1 TAAAAAAAATTAATTTAAAAAATAAATT
*
422485 TAAATAAAAATTTTATTTAAAAAATAAAT
1 TAAA-AAAAA-TTAATTTAAAAAATAAAT
422514 AAATTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 4 0.15
29 5 0.19
30 17 0.65
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (28 bp):
TAAAAAAAATTAATTTAAAAAATAAATT
Found at i:422635 original size:23 final size:23
Alignment explanation
Indices: 422587--422647 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
422577 AATTTATATT
* * *
422587 TTATAAT-ATAGTTATATATTTT
1 TTATAATAATAGTTATAGAGTTA
*
422609 TTATAATAATAGTTATAGCGTTA
1 TTATAATAATAGTTATAGAGTTA
* *
422632 TTATACTAATTGTTAT
1 TTATAATAATAGTTAT
422648 TTATTGAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 7 0.22
23 25 0.78
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.52
Consensus pattern (23 bp):
TTATAATAATAGTTATAGAGTTA
Found at i:423074 original size:17 final size:17
Alignment explanation
Indices: 423052--423090 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
423042 TAAGAACATG
423052 AAGGAAAA-AAAAAAAGA
1 AAGGAAAAGAAAAAAA-A
*
423069 AAGGAAAAGAAAAGAAA
1 AAGGAAAAGAAAAAAAA
423086 AAGGA
1 AAGGA
423091 GAGAATGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (17 bp):
AAGGAAAAGAAAAAAAA
Found at i:424413 original size:19 final size:20
Alignment explanation
Indices: 424386--424438 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
424376 ATAAAATATA
424386 ATTATATATTTATAAATTAAT
1 ATTA-ATATTTATAAATTAAT
* * *
424407 A-TAATATTAATTATTTAAT
1 ATTAATATTTATAAATTAAT
*
424426 ATTAAAATTTATA
1 ATTAATATTTATA
424439 TAAATATAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
19 14 0.56
20 10 0.40
21 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTAATATTTATAAATTAAT
Found at i:424446 original size:6 final size:6
Alignment explanation
Indices: 424436--424502 Score: 57
Period size: 6 Copynumber: 11.2 Consensus size: 6
424426 ATTAAAATTT
* * * *
424436 ATATAA ATATAA AT-T-A TTTTAA ATATAA TTATGAA ATAAAA ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATAT-AA ATATAA ATATAA
*
424483 AAATATA ATATAA ATATAA A
1 ATATA-A ATATAA ATATAA A
424503 AATTATAAAG
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
4 2 0.04
5 2 0.04
6 35 0.73
7 9 0.19
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (6 bp):
ATATAA
Found at i:424449 original size:16 final size:15
Alignment explanation
Indices: 424379--424490 Score: 65
Period size: 15 Copynumber: 7.5 Consensus size: 15
424369 AAATATAATA
424379 AAATAT-AATTATAT
1 AAATATAAATTATAT
**
424393 ATTTATAAATTA-AT
1 AAATATAAATTATAT
*
424407 ATAATATTAATTAT-T
1 A-AATATAAATTATAT
*
424422 TAATATTAAAATTTATAT
1 AAATA-T-AAA-TTATAT
*
424440 AAATATAAATTATTTT
1 AAATATAAATTA-TAT
*
424456 AAATAT-AATTAT-G
1 AAATATAAATTATAT
* *
424469 AAATA-AAAATATAA
1 AAATATAAATTATAT
424483 AAATATAA
1 AAATATAA
424491 TATAAATATA
Statistics
Matches: 75, Mismatches: 12, Indels: 21
0.69 0.11 0.19
Matches are distributed among these distances:
13 10 0.13
14 17 0.23
15 25 0.33
16 13 0.17
17 5 0.07
18 5 0.07
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (15 bp):
AAATATAAATTATAT
Found at i:424451 original size:32 final size:30
Alignment explanation
Indices: 424369--424454 Score: 88
Period size: 32 Copynumber: 2.8 Consensus size: 30
424359 AAAATAAGTA
*
424369 AAATATAATA-AAATATAATTATATATTTAT
1 AAAT-TAATATAAATATAATTATTTATTTAT
424399 AAATTAATAT-AATATTAATTATTTAATATTA-
1 AAATTAATATAAATA-TAATTATTT-AT-TTAT
*
424430 AAATTTATATAAATATAAATTATTT
1 AAATTAATATAAATAT-AATTATTT
424455 TAAATATAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
29 9 0.19
30 12 0.25
31 12 0.25
32 15 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
AAATTAATATAAATATAATTATTTATTTAT
Found at i:424486 original size:27 final size:28
Alignment explanation
Indices: 424456--424524 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
424446 AAATTATTTT
*
424456 AAATATAATTATGAA-ATAAAAA-TATAA
1 AAATATAA-TATAAATATAAAAATTATAA
424483 AAATATAATATAAATATAAAAATTATAA
1 AAATATAATATAAATATAAAAATTATAA
*
424511 AGCATAT-ATATAAA
1 A-AATATAATATAAA
424525 AATTTAGAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
26 5 0.14
27 15 0.41
28 13 0.35
29 4 0.11
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.30
Consensus pattern (28 bp):
AAATATAATATAAATATAAAAATTATAA
Found at i:424492 original size:19 final size:20
Alignment explanation
Indices: 424470--424510 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
424460 ATAATTATGA
424470 AATAAAAATATAAAAA-TAT
1 AATAAAAATATAAAAATTAT
*
424489 AATATAAATATAAAAATTAT
1 AATAAAAATATAAAAATTAT
424509 AA
1 AA
424511 AGCATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
AATAAAAATATAAAAATTAT
Done.