Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 137 of 211
Found at i:40597343 original size:23 final size:23
Alignment explanation
Indices: 40597317--40597386 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
40597307 AATTTAGTTA
* *
40597317 AAATTTTCCTAAATATTATCTCT
1 AAATATTCCTAAATATTATCACT
**
40597340 AAATAACCCTAAATATTATCACT
1 AAATATTCCTAAATATTATCACT
*
40597363 AAAGAATT-CTAAATATTATCACT
1 AAA-TATTCCTAAATATTATCACT
40597386 A
1 A
40597387 CCATTAATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
23 38 0.97
24 1 0.03
ACGTcount: A:0.44, C:0.17, G:0.01, T:0.37
Consensus pattern (23 bp):
AAATATTCCTAAATATTATCACT
Found at i:40606622 original size:20 final size:20
Alignment explanation
Indices: 40606597--40606652 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
40606587 CCTTAAGTGA
40606597 CAACTAAACATCAATTACAT
1 CAACTAAACATCAATTACAT
* *
40606617 CAACTAAAAATTAATTACAT
1 CAACTAAACATCAATTACAT
40606637 CAACTAAACATCAATT
1 CAACTAAACATCAATT
40606653 TGCAGGTTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (20 bp):
CAACTAAACATCAATTACAT
Found at i:40620933 original size:20 final size:19
Alignment explanation
Indices: 40620894--40620931 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40620884 ATGATACCAC
* *
40620894 TTCAAAATAATATCATAAA
1 TTCAAAAAAAAATCATAAA
40620913 TTCAAAAAAAAATCATAAA
1 TTCAAAAAAAAATCATAAA
40620932 ATCCAAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (19 bp):
TTCAAAAAAAAATCATAAA
Found at i:40622975 original size:11 final size:11
Alignment explanation
Indices: 40622959--40622992 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
40622949 TCAATTATTT
40622959 TCTCAATTTCC
1 TCTCAATTTCC
*
40622970 TCTCAATTTGC
1 TCTCAATTTCC
40622981 TCTCAATTTCC
1 TCTCAATTTCC
40622992 T
1 T
40622993 TCCAAATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.18, C:0.32, G:0.03, T:0.47
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:40622987 original size:22 final size:22
Alignment explanation
Indices: 40622955--40623008 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
40622945 TCTCTCAATT
40622955 ATTT-TCTCAATTTCC-TCTC-A
1 ATTTCTCTCAATTTCCTTC-CAA
40622975 ATTTGCTCTCAATTTCCTTCCAA
1 ATTT-CTCTCAATTTCCTTCCAA
40622998 ATTTCTCTCAA
1 ATTTCTCTCAA
40623009 ATCCATATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.13
22 19 0.63
23 7 0.23
ACGTcount: A:0.22, C:0.30, G:0.02, T:0.46
Consensus pattern (22 bp):
ATTTCTCTCAATTTCCTTCCAA
Found at i:40625505 original size:126 final size:125
Alignment explanation
Indices: 40625106--40625543 Score: 698
Period size: 125 Copynumber: 3.5 Consensus size: 125
40625096 CAAACATGCT
* * * *
40625106 ACTGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCATAAATTCTTCTGATAAAGCATCCTGCTT
1 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTACTT
*
40625171 GAAGCGTTTTTTATTCTATTTTCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGA-CA
66 GAAGCGTTTTTTATACTATTTTCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCA
* * * *
40625230 TACTGTAGCAAAAGCGCGTCCACGTGGGGGCAATTTCAGAAATTCTTCTAATAAAGCATCCTGCT
1 -ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTACT
* ** *
40625295 TGAAGCATTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACTA
65 TGAAGCGTTTTTTATACTATTTTCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCA
*
40625356 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTTAGAAATTCTTCTGATAAAGCATCCTACTT
1 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTACTT
*
40625421 GAAGCGTTTTTTTATACTATTTTCTCACAAACGTCAACTCGAAATTATTTTTTCAGGACCA
66 GAAGCG-TTTTTTATACTATTTTCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCA
* *
40625482 ACTGTAGCAAAAGCGCGTCCACGTGGGTGCCATTTCAGAAATTCTTCTGATAAAGCATCCTA
1 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTA
40625544 AACCATAAAC
Statistics
Matches: 287, Mismatches: 24, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
125 177 0.62
126 110 0.38
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (125 bp):
ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTACTT
GAAGCGTTTTTTATACTATTTTCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCA
Found at i:40634802 original size:19 final size:19
Alignment explanation
Indices: 40634778--40634817 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
40634768 ATGAGAGTTT
40634778 GTCTCTGCCATAAATTAGG
1 GTCTCTGCCATAAATTAGG
40634797 GTCTCTGCCATAAATTAGG
1 GTCTCTGCCATAAATTAGG
40634816 GT
1 GT
40634818 TTCCTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (19 bp):
GTCTCTGCCATAAATTAGG
Found at i:40637391 original size:28 final size:28
Alignment explanation
Indices: 40637324--40637392 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
40637314 AATATATAAT
*
40637324 AAATATATTTTTTATTTTTTTAATTTTA
1 AAATATATTTTTTACTTTTTTAATTTTA
*
40637352 AAATACTTTTTTTTACTTTTTT-ATTTGTA
1 AAATA-TATTTTTTACTTTTTTAATTT-TA
*
40637381 AAATAAATTTTT
1 AAATATATTTTT
40637393 GGTGTTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 14 0.40
29 21 0.60
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (28 bp):
AAATATATTTTTTACTTTTTTAATTTTA
Found at i:40643230 original size:23 final size:23
Alignment explanation
Indices: 40643204--40643249 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
40643194 GGCACACGAG
*
40643204 GTGCCTAAAATACGACACATAAA
1 GTGCCCAAAATACGACACATAAA
* *
40643227 GTGCCCGATATACGACACATAAA
1 GTGCCCAAAATACGACACATAAA
40643250 ATACCTGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.24, G:0.15, T:0.17
Consensus pattern (23 bp):
GTGCCCAAAATACGACACATAAA
Found at i:40643402 original size:27 final size:23
Alignment explanation
Indices: 40643363--40643421 Score: 57
Period size: 27 Copynumber: 2.4 Consensus size: 23
40643353 CAATTAAAAC
*
40643363 TCAATTCAGTCATAATTTCTCACATTT
1 TCAATTCAATCAT--TTTC-CAC-TTT
*
40643390 TCAATTGAATCATTTTCCACTTT
1 TCAATTCAATCATTTTCCACTTT
40643413 TCAA-TCAAT
1 TCAATTCAAT
40643422 TTTAAATTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 4 0.14
23 7 0.24
24 3 0.10
25 4 0.14
27 11 0.38
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.44
Consensus pattern (23 bp):
TCAATTCAATCATTTTCCACTTT
Found at i:40644394 original size:17 final size:16
Alignment explanation
Indices: 40644369--40644404 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
40644359 AACCCTAGTT
* *
40644369 TTTCCCTTTTCTTTTC
1 TTTCCCCTTTCCTTTC
40644385 TTTCCCCTTTCCTTTC
1 TTTCCCCTTTCCTTTC
40644401 TTTC
1 TTTC
40644405 TTTTTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTCCCCTTTCCTTTC
Found at i:40644642 original size:5 final size:5
Alignment explanation
Indices: 40644640--40644671 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
40644630 TTAAAATATA
40644640 ATAAT ATAAT ATAAT -TAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
40644672 TTTTCTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:40644660 original size:14 final size:14
Alignment explanation
Indices: 40644634--40644668 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
40644624 GTTTATTTAA
40644634 AATATAA-TAATAT
1 AATATAATTAATAT
40644647 AATATAATTAATAT
1 AATATAATTAATAT
40644661 AATATAAT
1 AATATAAT
40644669 ATATTTTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATTAATAT
Found at i:40644660 original size:22 final size:20
Alignment explanation
Indices: 40644635--40644699 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
40644625 TTTATTTAAA
40644635 ATATAATAATATAATATAATT
1 ATATAATAATATAATAT-ATT
40644656 A-AT-ATAATATAATATATT
1 ATATAATAATATAATATATT
* * *
40644674 TTCTAATAAAATAATATATT
1 ATATAATAATATAATATATT
40644694 AATATA
1 -ATATA
40644700 TTTAAAACAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
18 3 0.08
19 13 0.36
20 16 0.44
21 4 0.11
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATAATAATATAATATATT
Found at i:40644664 original size:19 final size:19
Alignment explanation
Indices: 40644640--40644699 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
40644630 TTAAAATATA
40644640 ATAATATAATATAATTAAT
1 ATAATATAATATAATTAAT
* **
40644659 ATAATATAATATATTTTCT
1 ATAATATAATATAATTAAT
*
40644678 AATAAAATAATAT-ATTAAT
1 -ATAATATAATATAATTAAT
40644697 ATA
1 ATA
40644700 TTTAAAACAT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
18 3 0.09
19 19 0.58
20 11 0.33
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
ATAATATAATATAATTAAT
Found at i:40646317 original size:33 final size:33
Alignment explanation
Indices: 40646280--40646387 Score: 137
Period size: 33 Copynumber: 3.3 Consensus size: 33
40646270 TGGCCCTGCC
*
40646280 ATGGTCTTCCATTTGTAGTGCCATAACCCAGTT
1 ATGGTCTTACATTTGTAGTGCCATAACCCAGTT
** * * * *
40646313 ATGGTCTTATCATCAG-AATGCCATAGCCTAGAT
1 ATGGTCTTA-CATTTGTAGTGCCATAACCCAGTT
40646346 ATGGTCTTACATTTGTAGTGCCATAACCCAGTT
1 ATGGTCTTACATTTGTAGTGCCATAACCCAGTT
40646379 ATGGTCTTA
1 ATGGTCTTA
40646388 TCATCAGAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
32 4 0.07
33 52 0.87
34 4 0.07
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (33 bp):
ATGGTCTTACATTTGTAGTGCCATAACCCAGTT
Found at i:40646320 original size:66 final size:66
Alignment explanation
Indices: 40646279--40646422 Score: 229
Period size: 66 Copynumber: 2.2 Consensus size: 66
40646269 ATGGCCCTGC
*
40646279 CATGGTCTTCCATTTGTAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCTAG
1 CATGGTCTTACATTTGTAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCTAG
40646344 A
66 A
* *
40646345 TATGGTCTTACATTTGTAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGTCATAG-CTCA
1 CATGGTCTTACATTTGTAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCT-A
40646409 G-
65 GA
40646410 CTATGGTCTTACA
1 C-ATGGTCTTACA
40646423 CATGTATTTA
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
65 2 0.03
66 70 0.97
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (66 bp):
CATGGTCTTACATTTGTAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCTAG
A
Found at i:40646415 original size:33 final size:32
Alignment explanation
Indices: 40646298--40646420 Score: 113
Period size: 33 Copynumber: 3.7 Consensus size: 32
40646288 CCATTTGTAG
* *
40646298 TGCCATAACCCAGTTATGGTCTTATCATCAGAA
1 TGCCAT-AGCCAGATATGGTCTTATCATCAGAA
** *
40646331 TGCCATAGCCTAGATATGGTCTTA-CATTTGTAG
1 TGCCATAGCC-AGATATGGTCTTATCATCAG-AA
* *
40646364 TGCCATAACCCAGTTATGGTCTTATCATCAGAA
1 TGCCAT-AGCCAGATATGGTCTTATCATCAGAA
* *
40646397 TGTCATAGCTCAGCTATGGTCTTA
1 TGCCATAGC-CAGATATGGTCTTA
40646421 CACATGTATT
Statistics
Matches: 72, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
32 9 0.12
33 56 0.78
34 7 0.10
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (32 bp):
TGCCATAGCCAGATATGGTCTTATCATCAGAA
Found at i:40651913 original size:7 final size:7
Alignment explanation
Indices: 40651901--40651932 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
40651891 ATAAATAAAT
40651901 AAAAAAG
1 AAAAAAG
40651908 AAAAAAG
1 AAAAAAG
40651915 AAAAAAG
1 AAAAAAG
40651922 AAAAAGAG
1 AAAAA-AG
40651930 AAA
1 AAA
40651933 TCAATCAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.79
8 5 0.21
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:40652348 original size:7 final size:7
Alignment explanation
Indices: 40652336--40652368 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
40652326 AAAAGGAGTG
40652336 ATGAAAA
1 ATGAAAA
40652343 ATG-AAA
1 ATGAAAA
40652349 ATG-AAA
1 ATGAAAA
40652355 ATGAAAA
1 ATGAAAA
40652362 ATGAAAA
1 ATGAAAA
40652369 GTAAAATGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (7 bp):
ATGAAAA
Found at i:40653746 original size:87 final size:87
Alignment explanation
Indices: 40653594--40654186 Score: 936
Period size: 87 Copynumber: 6.8 Consensus size: 87
40653584 AGATCAGTGA
*
40653594 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
*
40653659 CTTCCTGCGTTAATAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
* * *
40653681 AGACCAAAAACAAAGCATTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTTGC
1 AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
40653746 CTTCCTGCGTTAACAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
* *
40653768 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* * * *
40653833 CTTCCTACGTTAATAGTGAAGT
66 CTTCCTGCGTTAACAGCGAAGC
* * *
40653855 AGA-CAAAAAATAAAGCCTTGCCTCCATCAGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTTG
1 AGATC-AAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTG
* * * *
40653919 CCTTCTTGCGTTAACACCAAAGT
65 CCTTCCTGCGTTAACAGCGAAGC
* * *
40653942 AGATCAAAAACAAAGCCTTGTCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAAATCTTGC
1 AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
40654007 CTTCCTGCGTTAACAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
* *
40654029 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
40654094 CTTCCTGCGTTAACAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
* * *
40654116 AGATCGAAAACAATGCCTTGCCTCCATCAGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
40654181 CTTCCT
66 CTTCCT
40654187 AAGTACTAGC
Statistics
Matches: 463, Mismatches: 41, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
86 1 0.00
87 461 1.00
88 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (87 bp):
AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
CTTCCTGCGTTAACAGCGAAGC
Found at i:40654042 original size:42 final size:42
Alignment explanation
Indices: 40653995--40654128 Score: 103
Period size: 42 Copynumber: 3.1 Consensus size: 42
40653985 GGTTAAAGAT
40653995 AACAAATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAA
1 AACAAATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAA
* * ** * * * **
40654037 AACAAAGCCTTGCC-TCCAT-CGGTT-GCAATGGAGCTGGTTAAA
1 AACAAA-TCTTGCCTTCC-TGC-GTTAACAGCGAAGCAGATCGAA
*
40654079 GATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAA
1 -A-A-CAAATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAA
40654124 AACAA
1 AACAA
40654129 TGCCTTGCCT
Statistics
Matches: 63, Mismatches: 20, Indels: 18
0.62 0.20 0.18
Matches are distributed among these distances:
42 22 0.35
43 12 0.19
44 12 0.19
45 17 0.27
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.22
Consensus pattern (42 bp):
AACAAATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAA
Found at i:40654138 original size:43 final size:43
Alignment explanation
Indices: 40654002--40654138 Score: 104
Period size: 43 Copynumber: 3.2 Consensus size: 43
40653992 GATAACAAAT
*
40654002 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAATGC
* ** * * * **
40654045 CTTGCC-TCCAT-CGGTT-GCAATGGAGCTGGTTAAAGATAGCAGAT--
1 CTTGCCTTCC-TGC-GTTAACAGCGAAGCAGATCGAA-A-A-CA-ATGC
40654089 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAATGC
1 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAATGC
40654132 CTTGCCT
1 CTTGCCT
40654139 CCATCAGTTG
Statistics
Matches: 66, Mismatches: 17, Indels: 22
0.63 0.16 0.21
Matches are distributed among these distances:
41 2 0.03
42 16 0.24
43 19 0.29
44 12 0.18
45 16 0.24
46 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (43 bp):
CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAATGC
Found at i:40656073 original size:3 final size:3
Alignment explanation
Indices: 40655996--40656053 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
40655986 GGGTCTGTTA
40655996 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40656044 TAT TAT TAT T
1 TAT TAT TAT T
40656054 GCTACTTATC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:40657323 original size:43 final size:42
Alignment explanation
Indices: 40657197--40657401 Score: 116
Period size: 43 Copynumber: 5.1 Consensus size: 42
40657187 TAAAATGGTA
*
40657197 AAAAAATTATTACATAAATACAAAGTTGACTATTTAAATTGC
1 AAAAAATTATTACATTAATACAAAGTTGACTATTTAAATTGC
* * * * * ** *
40657239 AAAAAA--A-AAAACTCATA-AGA-TTGA-TAAATAAAATGAC
1 AAAAAATTATTACATTAATACAAAGTTGACTATTTAAATTG-C
40657276 AAAAAATTCATTACATTAATACAAAGTTGACTATTTAAATTGC
1 AAAAAATT-ATTACATTAATACAAAGTTGACTATTTAAATTGC
** * * * *
40657319 AAAAAA--A--A-A-CCATA-AAA-TTGA-TAAATAAAATGGA
1 AAAAAATTATTACATTAATACAAAGTTGACT-ATTTAAATTGC
* *
40657353 AAAAAATTTATTACATAAATACAAAGTTGACTATTAAAATTGC
1 AAAAAA-TTATTACATTAATACAAAGTTGACTATTTAAATTGC
40657396 AAAAAA
1 AAAAAA
40657402 CCCATAAAAT
Statistics
Matches: 116, Mismatches: 28, Indels: 37
0.64 0.15 0.20
Matches are distributed among these distances:
33 1 0.01
34 17 0.15
35 3 0.03
36 11 0.09
37 13 0.11
38 3 0.03
39 6 0.05
40 4 0.03
41 9 0.08
42 11 0.09
43 29 0.25
44 9 0.08
ACGTcount: A:0.57, C:0.09, G:0.07, T:0.27
Consensus pattern (42 bp):
AAAAAATTATTACATTAATACAAAGTTGACTATTTAAATTGC
Found at i:40657366 original size:77 final size:77
Alignment explanation
Indices: 40657178--40657526 Score: 517
Period size: 75 Copynumber: 4.5 Consensus size: 77
40657168 TGGTGTCAAC
*
40657178 ATTGATAATTAAAATGGTAAAAAAATT-ATTACATAAATACAAAGTTGACTATTTAAATTGCAAA
1 ATTGATAAATAAAATGG-AAAAAAATTCATTACATAAATACAAAGTTGACTATTTAAATTGC--A
*
40657242 AAAAAAAACTCATAAG
63 AAAAAAAAC-CATAAA
*
40657258 ATTGATAAATAAAAT-GACAAAAAATTCATTACATTAATACAAAGTTGACTATTTAAATTGCAAA
1 ATTGATAAATAAAATGGA-AAAAAATTCATTACATAAATACAAAGTTGACTATTTAAATTGCAAA
40657322 AAAAAACCATAAA
65 AAAAAACCATAAA
* *
40657335 ATTGATAAATAAAATGGAAAAAAATTTATTACATAAATACAAAGTTGACTATTAAAATTGC--AA
1 ATTGATAAATAAAATGGAAAAAAATTCATTACATAAATACAAAGTTGACTATTTAAATTGCAAAA
*
40657398 AAAACCCATAAA
66 AAAAACCATAAA
* * **
40657410 ATTGATAAATAAAATGGCAACAAATTCATTACATAAATATGAAGTTGACTATTTAAATTGCAAAA
1 ATTGATAAATAAAATGGAAAAAAATTCATTACATAAATACAAAGTTGACTATTTAAATTGCAAAA
40657475 AAAAATCCATAAA
66 AAAAA-CCATAAA
*
40657488 ATTGATAAATAAAATGGAAAAAAATCCATTACATAAATA
1 ATTGATAAATAAAATGGAAAAAAATTCATTACATAAATA
40657527 TGAAGTTATT
Statistics
Matches: 246, Mismatches: 17, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
75 68 0.28
77 66 0.27
78 56 0.23
79 9 0.04
80 47 0.19
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (77 bp):
ATTGATAAATAAAATGGAAAAAAATTCATTACATAAATACAAAGTTGACTATTTAAATTGCAAAA
AAAAACCATAAA
Found at i:40657478 original size:152 final size:154
Alignment explanation
Indices: 40657178--40657526 Score: 533
Period size: 152 Copynumber: 2.3 Consensus size: 154
40657168 TGGTGTCAAC
* *
40657178 ATTGATAATTAAAATGGTAAAAAAA-TTATTACATAAATACAAAGTTGACTATTTAAATTGCAAA
1 ATTGATAAATAAAATGG-AAAAAAATTTATTACATAAATACAAAGTTGACTATTAAAATTGC---
* * *
40657242 AAAAAAAACTCATAAGATTGATAAATAAAATGACAAAAAATTCATTACATTAATACAAAGTTGAC
62 -AAAAAAACCCATAAAATTGATAAATAAAATGACAAAAAATTCATTACATAAATACAAAGTTGAC
40657307 TATTTAAATTGCAAAAAAAAA-CCATAAA
126 TATTTAAATTGCAAAAAAAAATCCATAAA
40657335 ATTGATAAATAAAATGGAAAAAAATTTATTACATAAATACAAAGTTGACTATTAAAATTGC-AAA
1 ATTGATAAATAAAATGGAAAAAAATTTATTACATAAATACAAAGTTGACTATTAAAATTGCAAAA
* * **
40657399 AAACCCATAAAATTGATAAATAAAATGGCAACAAATTCATTACATAAATATGAAGTTGACTATTT
66 AAACCCATAAAATTGATAAATAAAATGACAAAAAATTCATTACATAAATACAAAGTTGACTATTT
40657464 AAATTGCAAAAAAAAATCCATAAA
131 AAATTGCAAAAAAAAATCCATAAA
**
40657488 ATTGATAAATAAAATGGAAAAAAATCCATTACATAAATA
1 ATTGATAAATAAAATGGAAAAAAATTTATTACATAAATA
40657527 TGAAGTTATT
Statistics
Matches: 179, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
152 77 0.43
153 44 0.25
156 7 0.04
157 51 0.28
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (154 bp):
ATTGATAAATAAAATGGAAAAAAATTTATTACATAAATACAAAGTTGACTATTAAAATTGCAAAA
AAACCCATAAAATTGATAAATAAAATGACAAAAAATTCATTACATAAATACAAAGTTGACTATTT
AAATTGCAAAAAAAAATCCATAAA
Found at i:40657763 original size:33 final size:33
Alignment explanation
Indices: 40657721--40657863 Score: 130
Period size: 33 Copynumber: 4.3 Consensus size: 33
40657711 GAGCTGGGAG
*
40657721 GAGTGGAGTACGACAGTGGATACGGGCCAGGAT
1 GAGTGGAGTACGACAGTGGATACGAGCCAGGAT
* * * *
40657754 GAGTGGAGTAC-AGCGGTGGATACGGGCCGGGAA
1 GAGTGGAGTACGA-CAGTGGATACGAGCCAGGAT
* * * *
40657787 GAGTGGAGTACGGCAGTAGATACGAGCC-GAAAG
1 GAGTGGAGTACGACAGTGGATACGAGCCAG-GAT
* *
40657820 GAGCGGAGTACTGA-GGTGGATACGAGCCAGGAT
1 GAGTGGAGTAC-GACAGTGGATACGAGCCAGGAT
*
40657853 GACTGGAGTAC
1 GAGTGGAGTAC
40657864 TGAGGTGGTA
Statistics
Matches: 88, Mismatches: 17, Indels: 10
0.77 0.15 0.09
Matches are distributed among these distances:
32 2 0.02
33 84 0.95
34 2 0.02
ACGTcount: A:0.28, C:0.15, G:0.43, T:0.14
Consensus pattern (33 bp):
GAGTGGAGTACGACAGTGGATACGAGCCAGGAT
Found at i:40657828 original size:66 final size:66
Alignment explanation
Indices: 40657711--40657863 Score: 164
Period size: 66 Copynumber: 2.3 Consensus size: 66
40657701 CAATGAACTT
* * * * * * * *
40657711 GAGCTGGGAGGAGTGGAGTACGACAGTGGATACGGGCCAGGATGAGTGGAGTACAGCGGTGGATA
1 GAGCCGGGAAGAGTGGAGTACGACAGTAGATACGAGCCAGAAGGAGCGGAGTACAGAGGTGGATA
40657776 C
66 C
* * *
40657777 GGGCCGGGAAGAGTGGAGTACGGCAGTAGATACGAGCC-GAAAGGAGCGGAGTACTGAGGTGGAT
1 GAGCCGGGAAGAGTGGAGTACGACAGTAGATACGAGCCAG-AAGGAGCGGAGTACAGAGGTGGAT
40657841 AC
65 AC
* * *
40657843 GAGCCAGGATGACTGGAGTAC
1 GAGCCGGGAAGAGTGGAGTAC
40657864 TGAGGTGGTA
Statistics
Matches: 71, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
65 1 0.01
66 70 0.99
ACGTcount: A:0.27, C:0.15, G:0.44, T:0.14
Consensus pattern (66 bp):
GAGCCGGGAAGAGTGGAGTACGACAGTAGATACGAGCCAGAAGGAGCGGAGTACAGAGGTGGATA
C
Found at i:40660061 original size:75 final size:79
Alignment explanation
Indices: 40659982--40660133 Score: 240
Period size: 77 Copynumber: 2.0 Consensus size: 79
40659972 TACTAACAAA
*
40659982 ATAACTATAAAATTA-TTTTTTTTAAAA-TACATTACTAAAAAATCACAAAAA-CATA-ACTAAA
1 ATAACTATAAAATTACTTTTTTTAAAAATTACATTACTAAAAAATCACAAAAACCATATACTAAA
40660043 CACTAAAAATTTAT
66 CACTAAAAATTTAT
* *
40660057 ATAACTATAAATTTACTTTTTTTAAAAATTACATTACTAAAAAATCACAAAAACCCTATACTAAA
1 ATAACTATAAAATTACTTTTTTTAAAAATTACATTACTAAAAAATCACAAAAACCATATACTAAA
*
40660122 CACTAACAATTT
66 CACTAAAAATTT
40660134 GTAACCTAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
75 14 0.20
76 11 0.16
77 24 0.35
78 3 0.04
79 17 0.25
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (79 bp):
ATAACTATAAAATTACTTTTTTTAAAAATTACATTACTAAAAAATCACAAAAACCATATACTAAA
CACTAAAAATTTAT
Found at i:40660422 original size:60 final size:60
Alignment explanation
Indices: 40660358--40660476 Score: 211
Period size: 60 Copynumber: 2.0 Consensus size: 60
40660348 ATACTAAACT
* *
40660358 AAACACAACAATTTATAACATAGTCCTAAATGACTAATAAATTAATTTTAAAATAATTAC
1 AAACACAACAATTTATAACATAATCCTAAATGACTAACAAATTAATTTTAAAATAATTAC
*
40660418 AAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 AAACACAACAATTTATAACATAATCCTAAATGACTAACAAATTAATTTTAAAATAATTA
40660477 TAAAAAAAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.32
Consensus pattern (60 bp):
AAACACAACAATTTATAACATAATCCTAAATGACTAACAAATTAATTTTAAAATAATTAC
Found at i:40661830 original size:51 final size:52
Alignment explanation
Indices: 40661735--40661832 Score: 119
Period size: 52 Copynumber: 1.9 Consensus size: 52
40661725 TATAAATATA
* * * *
40661735 CGTTCATAACAATTTGTATCAATTGTTCATAATTATTATAATAATTAATTTG
1 CGTTCATAACAACTCGTATCAATTGTTCATAATAAATATAATAATTAATTTG
* *
40661787 CGTTGATAACAACTCGTATCTA-TGTTCATAAATAAATAT-ATAATTA
1 CGTTCATAACAACTCGTATCAATTGTTCAT-AATAAATATAATAATTA
40661833 TATTAAGATA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
51 14 0.36
52 25 0.64
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (52 bp):
CGTTCATAACAACTCGTATCAATTGTTCATAATAAATATAATAATTAATTTG
Found at i:40661913 original size:23 final size:23
Alignment explanation
Indices: 40661887--40661942 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
40661877 TGAATTAATT
40661887 TTAATTTTAAT-TTAAAAAGAAAG
1 TTAATTTTAATCTTAAAAA-AAAG
* *
40661910 TTAA-TTTAATCTTCAAAATAAG
1 TTAATTTTAATCTTAAAAAAAAG
40661932 TTAAATTTTAA
1 TT-AATTTTAA
40661943 ATAATTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 11 0.39
23 12 0.43
24 5 0.18
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (23 bp):
TTAATTTTAATCTTAAAAAAAAG
Found at i:40661995 original size:18 final size:18
Alignment explanation
Indices: 40661946--40661996 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
40661936 ATTTTAAATA
40661946 ATTAAAAATAA-AATATT
1 ATTAAAAATAATAATATT
* * *
40661963 ATCTTATAAT-TTAATATT
1 AT-TAAAAATAATAATATT
40661981 ATTAAAAATAATAATA
1 ATTAAAAATAATAATA
40661997 GTGAATATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 5
0.69 0.17 0.14
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTAAAAATAATAATATT
Found at i:40664467 original size:10 final size:10
Alignment explanation
Indices: 40664435--40664490 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
40664425 TAATATATAA
40664435 TTATAAAAAT
1 TTATAAAAAT
* *
40664445 TTTTAAGAA-
1 TTATAAAAAT
40664454 TTATAAAAAT
1 TTATAAAAAT
40664464 TTATCAAAAA-
1 TTAT-AAAAAT
* *
40664474 GTATTAAAAT
1 TTATAAAAAT
40664484 TTATAAA
1 TTATAAA
40664491 TAAAAGAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
9 11 0.31
10 19 0.54
11 5 0.14
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (10 bp):
TTATAAAAAT
Found at i:40666804 original size:11 final size:11
Alignment explanation
Indices: 40666788--40666812 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40666778 GTAGTGCCGT
40666788 TTTTATTTTTA
1 TTTTATTTTTA
40666799 TTTTATTTTTA
1 TTTTATTTTTA
40666810 TTT
1 TTT
40666813 ACATTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:40668862 original size:6 final size:6
Alignment explanation
Indices: 40668851--40668882 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
40668841 AAATTTCTAC
40668851 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA AT
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA AT
40668883 GAATTGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:40680645 original size:18 final size:18
Alignment explanation
Indices: 40680622--40680658 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
40680612 ATCCCAACTT
*
40680622 ATAAATATGAACGATAAA
1 ATAAATATAAACGATAAA
*
40680640 ATAAATATAAAGGATAAA
1 ATAAATATAAACGATAAA
40680658 A
1 A
40680659 AATACATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.65, C:0.03, G:0.11, T:0.22
Consensus pattern (18 bp):
ATAAATATAAACGATAAA
Found at i:40698742 original size:6 final size:6
Alignment explanation
Indices: 40698731--40698776 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
40698721 TAAAAAGAAC
** *
40698731 TAAAAA TAAAAA TAAAAA TAAACG T-AAAA TAAATA -AAAAA TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
40698777 AAATAAACTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
5 7 0.22
6 25 0.78
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:40698779 original size:11 final size:11
Alignment explanation
Indices: 40698732--40698779 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
40698722 AAAAAGAACT
40698732 AAAAATAAAAA
1 AAAAATAAAAA
**
40698743 TAAAAATAAACG
1 -AAAAATAAAAA
* *
40698755 TAAAATAAATA
1 AAAAATAAAAA
40698766 AAAAATAAAAA
1 AAAAATAAAAA
40698777 AAA
1 AAA
40698780 TAAACTTAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
11 20 0.69
12 9 0.31
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.15
Consensus pattern (11 bp):
AAAAATAAAAA
Found at i:40700258 original size:16 final size:15
Alignment explanation
Indices: 40700237--40700268 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
40700227 GCAAACTAAG
40700237 AAATAATAATGAAGAA
1 AAATAATAAT-AAGAA
40700253 AAATAATAATAAGAA
1 AAATAATAATAAGAA
40700268 A
1 A
40700269 TAAAGTGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (15 bp):
AAATAATAATAAGAA
Found at i:40700259 original size:13 final size:14
Alignment explanation
Indices: 40700234--40700271 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
40700224 CATGCAAACT
40700234 AAGAAATAATAATG
1 AAGAAATAATAATG
40700248 AAGAAAAATAATAAT-
1 AAG--AAATAATAATG
40700263 AAGAAATAA
1 AAGAAATAA
40700272 AGTGAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 6 0.27
14 3 0.14
15 3 0.14
16 10 0.45
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.18
Consensus pattern (14 bp):
AAGAAATAATAATG
Found at i:40700519 original size:23 final size:23
Alignment explanation
Indices: 40700487--40700538 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
40700477 GACAGTAAGG
*
40700487 ATAA-AAAACAACTAGAACTAGAA
1 ATAATAAAACAA-TAGAACTAAAA
*
40700510 A-AATAAAACAATATAACTAAAA
1 ATAATAAAACAATAGAACTAAAA
40700532 ATAATAA
1 ATAATAA
40700539 TATTAAGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.69, C:0.10, G:0.04, T:0.17
Consensus pattern (23 bp):
ATAATAAAACAATAGAACTAAAA
Found at i:40710670 original size:20 final size:20
Alignment explanation
Indices: 40710624--40710670 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
40710614 TAGTAAAGTT
*
40710624 ATAAAATTAATTTTAGAATA
1 ATAAAATTAATTTTAAAATA
*
40710644 ATTAAATTAA-TTTAAAATAA
1 ATAAAATTAATTTTAAAAT-A
40710664 ATAAAAT
1 ATAAAAT
40710671 AAAACAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
ATAAAATTAATTTTAAAATA
Found at i:40711061 original size:20 final size:19
Alignment explanation
Indices: 40711029--40711068 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
40711019 AAGTTAACAG
*
40711029 TAATATTTTAAAAAATAAT
1 TAATATTTAAAAAAATAAT
40711048 TAATGATTTAAAAAAATAAT
1 TAAT-ATTTAAAAAAATAAT
40711068 T
1 T
40711069 CGAGTATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (19 bp):
TAATATTTAAAAAAATAAT
Found at i:40712805 original size:16 final size:16
Alignment explanation
Indices: 40712784--40712843 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
40712774 TTAACATTTT
40712784 TTTTTCTTTTTTTCTC
1 TTTTTCTTTTTTTCTC
* *
40712800 TTTTTCTCTTTTCCTC
1 TTTTTCTTTTTTTCTC
*
40712816 TGTTCTTCTTCCTTTT-TC
1 T-TT-TTCTT-TTTTTCTC
*
40712834 TTTCTCTTTT
1 TTTTTCTTTT
40712844 CTCTTCCATA
Statistics
Matches: 34, Mismatches: 7, Indels: 7
0.71 0.15 0.15
Matches are distributed among these distances:
15 1 0.03
16 19 0.56
17 4 0.12
18 7 0.21
19 3 0.09
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.73
Consensus pattern (16 bp):
TTTTTCTTTTTTTCTC
Found at i:40719877 original size:28 final size:29
Alignment explanation
Indices: 40719846--40719911 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
40719836 TTTAAGTGGT
* *
40719846 TTTTATTAATT-TTTAATTTTTTAAAAAA
1 TTTTATAAATTATTTAATATTTTAAAAAA
* *
40719874 TTTTA-AAATTATTTAATATTTTATAAAT
1 TTTTATAAATTATTTAATATTTTAAAAAA
40719902 TTTTATAAAT
1 TTTTATAAAT
40719912 ATATAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 4 0.12
28 24 0.75
29 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (29 bp):
TTTTATAAATTATTTAATATTTTAAAAAA
Found at i:40720477 original size:27 final size:27
Alignment explanation
Indices: 40720439--40720494 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
40720429 TCGAATCACC
40720439 TTACAATTCAATTGTTTTAATAAAACG
1 TTACAATTCAATTGTTTTAATAAAACG
40720466 TTACAATTCAATTGTTTTAATAAAACG
1 TTACAATTCAATTGTTTTAATAAAACG
40720493 TT
1 TT
40720495 TCGATTTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (27 bp):
TTACAATTCAATTGTTTTAATAAAACG
Found at i:40724329 original size:85 final size:85
Alignment explanation
Indices: 40724186--40724436 Score: 322
Period size: 85 Copynumber: 3.0 Consensus size: 85
40724176 ACCATCACTG
* * *
40724186 ATTTGCAGTTATTGCCACTTGTTGTAGGTGCACAACATATTTGTAAATTAAATGAACTGCCACTT
1 ATTTGCAGTTACTGCCACTTGTTGTGGGTGCACAACATATTTGTAGATTAAATGAACTGCCACTT
** *
40724251 GGTTTGTGATCGAACTGCAT
66 GGTTCATGATCGAACCGCAT
* * * * *
40724271 ATTTGCAATTAGTGCCACTTGTTGTGGGTGCACAACAAATTTGTAGATTAAACGAACTGCTACTT
1 ATTTGCAGTTACTGCCACTTGTTGTGGGTGCACAACATATTTGTAGATTAAATGAACTGCCACTT
*
40724336 GGTTCATGATCGAACCGTAT
66 GGTTCATGATCGAACCGCAT
*** ** * * *
40724356 ATTTTTTGTTACTATCACTTGTTATGGGTGCACAACATATTTGAAGATTAAATGAACTGTCACTT
1 ATTTGCAGTTACTGCCACTTGTTGTGGGTGCACAACATATTTGTAGATTAAATGAACTGCCACTT
40724421 GGTTCATGATCGAACC
66 GGTTCATGATCGAACC
40724437 ACACTGTTTG
Statistics
Matches: 142, Mismatches: 24, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
85 142 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.36
Consensus pattern (85 bp):
ATTTGCAGTTACTGCCACTTGTTGTGGGTGCACAACATATTTGTAGATTAAATGAACTGCCACTT
GGTTCATGATCGAACCGCAT
Found at i:40727833 original size:12 final size:12
Alignment explanation
Indices: 40727799--40727836 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
40727789 ATTTTTAATT
40727799 AAGTAAATGTTAA
1 AAGTAAA-GTTAA
*
40727812 AA-TTAAGTTAA
1 AAGTAAAGTTAA
40727823 AAGTAAAGTTAA
1 AAGTAAAGTTAA
40727835 AA
1 AA
40727837 TATAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 7 0.32
12 13 0.59
13 2 0.09
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (12 bp):
AAGTAAAGTTAA
Found at i:40728996 original size:4 final size:4
Alignment explanation
Indices: 40728987--40729102 Score: 205
Period size: 4 Copynumber: 29.0 Consensus size: 4
40728977 TTTATTATAG
*
40728987 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TATA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
40729035 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA GGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
40729083 CGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA
40729103 AATATGTAAC
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 106 1.00
ACGTcount: A:0.26, C:0.01, G:0.25, T:0.48
Consensus pattern (4 bp):
TGTA
Found at i:40730708 original size:25 final size:24
Alignment explanation
Indices: 40730648--40730710 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 24
40730638 GTACATCTAT
40730648 GCTCATACGAGCTATAAACGGTAA
1 GCTCATACGAGCTATAAACGGTAA
* ** *
40730672 GCTCTTTTGAGCTGA-ATAATGGTAA
1 GCTCATACGAGCT-ATA-AACGGTAA
40730697 GCTCATACGAGCTA
1 GCTCATACGAGCTA
40730711 AGAGCCGAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
24 12 0.40
25 18 0.60
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (24 bp):
GCTCATACGAGCTATAAACGGTAA
Found at i:40738357 original size:25 final size:26
Alignment explanation
Indices: 40738315--40738368 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
40738305 TTCTCCTAAA
*
40738315 TTTCAATTTTATTTAATTATTTAAT-T
1 TTTCAATTTTATTGAATTA-TTAATAT
40738341 TTTCAA-TTTATTGAATTATTAATAT
1 TTTCAATTTTATTGAATTATTAATAT
40738366 TTT
1 TTT
40738369 ATACTAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 15 0.58
26 6 0.23
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTCAATTTTATTGAATTATTAATAT
Found at i:40740568 original size:14 final size:14
Alignment explanation
Indices: 40740551--40740596 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
40740541 TGCTCATGAA
*
40740551 AAAATAAAAGAAAG
1 AAAAGAAAAGAAAG
40740565 AAAAGAAAAGAAA-
1 AAAAGAAAAGAAAG
*
40740578 AAGAGAAAA-AAAG
1 AAAAGAAAAGAAAG
*
40740591 AGAAGA
1 AAAAGA
40740597 GCTTATGTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 3 0.11
13 12 0.44
14 12 0.44
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:40743431 original size:10 final size:10
Alignment explanation
Indices: 40743408--40743455 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
40743398 GAATCTGTCG
*
40743408 AAAATAAATT
1 AAAATTAATT
*
40743418 AAAATTAATC
1 AAAATTAATT
*
40743428 AAAATTTATTAT
1 AAAA-TTAAT-T
40743440 AAAATTAATT
1 AAAATTAATT
40743450 AAAATT
1 AAAATT
40743456 CAACACGTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
10 19 0.61
11 8 0.26
12 4 0.13
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (10 bp):
AAAATTAATT
Found at i:40744299 original size:11 final size:11
Alignment explanation
Indices: 40744285--40744357 Score: 57
Period size: 11 Copynumber: 6.9 Consensus size: 11
40744275 TAAATTTATC
40744285 ATATTTTTAAA
1 ATATTTTTAAA
40744296 ATATTTTT-AA
1 ATATTTTTAAA
*
40744306 A-A-TTTT-CA
1 ATATTTTTAAA
*
40744314 AT-TTCTTAAA
1 ATATTTTTAAA
*
40744324 ATATTTTTTAA
1 ATATTTTTAAA
*
40744335 TTATTTTTTAAA
1 ATA-TTTTTAAA
40744347 ATATATTTTAA
1 ATAT-TTTTAA
40744358 TATTTAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
8 6 0.12
9 4 0.08
10 6 0.12
11 17 0.35
12 15 0.31
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.58
Consensus pattern (11 bp):
ATATTTTTAAA
Found at i:40744334 original size:12 final size:12
Alignment explanation
Indices: 40744314--40744357 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
40744304 AAAATTTTCA
*
40744314 ATTTCTTAAAAT
1 ATTTTTTAAAAT
*
40744326 ATTTTTT-AATT
1 ATTTTTTAAAAT
40744337 ATTTTTTAAAAT
1 ATTTTTTAAAAT
*
40744349 ATATTTTAA
1 ATTTTTTAA
40744358 TATTTAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTTTTTAAAAT
Found at i:40744345 original size:23 final size:22
Alignment explanation
Indices: 40744314--40744362 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
40744304 AAAATTTTCA
*
40744314 ATTTCTTAAAATATTTTTTAATT
1 ATTTCTTAAAATATATTTTAA-T
*
40744337 ATTTTTTAAAATATATTTTAAT
1 ATTTCTTAAAATATATTTTAAT
40744359 ATTT
1 ATTT
40744363 AAAAATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTCTTAAAATATATTTTAAT
Found at i:40745952 original size:16 final size:16
Alignment explanation
Indices: 40745928--40745981 Score: 72
Period size: 16 Copynumber: 3.3 Consensus size: 16
40745918 CAAATCGAGT
*
40745928 TATTCAAATTATTTTA
1 TATTTAAATTATTTTA
**
40745944 TATTTAAATTATTAAA
1 TATTTAAATTATTTTA
40745960 TATATTAAATTATTTTA
1 TAT-TTAAATTATTTTA
40745977 TATTT
1 TATTT
40745982 TTAATAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 18 0.56
17 14 0.44
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTTAAATTATTTTA
Found at i:40745979 original size:17 final size:17
Alignment explanation
Indices: 40745928--40745979 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
40745918 CAAATCGAGT
40745928 TATTCAAATTATTTTATA
1 TATT-AAATTATTTTATA
**
40745946 T-TTAAATTATTAAATA
1 TATTAAATTATTTTATA
40745962 TATTAAATTATTTTATA
1 TATTAAATTATTTTATA
40745979 T
1 T
40745980 TTTTAATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 12 0.41
17 16 0.55
18 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTAAATTATTTTATA
Found at i:40747129 original size:2 final size:2
Alignment explanation
Indices: 40747122--40747154 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
40747112 ACCTAAGTGT
40747122 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 T
40747155 TTGAGATGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40748701 original size:1 final size:1
Alignment explanation
Indices: 40748695--40748730 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
40748685 CCATCTTTGC
* *
40748695 AAAAAAAAAAAAAAAAAAAAAAAAAACAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
40748731 CACACGGAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:40749583 original size:21 final size:21
Alignment explanation
Indices: 40749558--40749612 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
40749548 TAACTTCATT
40749558 TATTTTAATAAAAAACATT-AA
1 TATTTTAATAAAAAA-ATTGAA
* * *
40749579 TATTTTTATATAAAATTTGAA
1 TATTTTAATAAAAAAATTGAA
*
40749600 CATTTTAATAAAA
1 TATTTTAATAAAA
40749613 TAATATCTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (21 bp):
TATTTTAATAAAAAAATTGAA
Found at i:40761319 original size:9 final size:9
Alignment explanation
Indices: 40761305--40761335 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
40761295 GATAAAGTAA
40761305 AATTAAATT
1 AATTAAATT
40761314 AATTAAATT
1 AATTAAATT
40761323 AATTAAAATT
1 AATT-AAATT
40761333 AAT
1 AAT
40761336 GTTATTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AATTAAATT
Found at i:40761879 original size:11 final size:11
Alignment explanation
Indices: 40761851--40761915 Score: 52
Period size: 11 Copynumber: 6.3 Consensus size: 11
40761841 AATATTCTAC
40761851 TAATTTAATA-
1 TAATTTAATAT
40761861 -AGATTTAATAT
1 TA-ATTTAATAT
40761872 TAATTTAATA-
1 TAATTTAATAT
*
40761882 TAATATTTATAT
1 TAAT-TTAATAT
*
40761894 T--GTT-ATAT
1 TAATTTAATAT
40761902 TAATTTAATAT
1 TAATTTAATAT
40761913 TAA
1 TAA
40761916 AGTGGTTAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 15
0.71 0.05 0.24
Matches are distributed among these distances:
8 5 0.11
9 3 0.07
10 14 0.32
11 20 0.45
12 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (11 bp):
TAATTTAATAT
Found at i:40765408 original size:3 final size:3
Alignment explanation
Indices: 40765389--40765422 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
40765379 ATTAGTTTAA
* *
40765389 TAT TTT TAT TAT CAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
40765423 GTTTTTAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:40767438 original size:26 final size:26
Alignment explanation
Indices: 40767407--40767457 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
40767397 CCTTCCTTTT
40767407 ATATTTCACCACAAAGGCTTTTCTTC
1 ATATTTCACCACAAAGGCTTTTCTTC
* *
40767433 ATATTTCGCCATAAAGGCTTTTCTT
1 ATATTTCACCACAAAGGCTTTTCTT
40767458 TCTCGACGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.25, C:0.24, G:0.10, T:0.41
Consensus pattern (26 bp):
ATATTTCACCACAAAGGCTTTTCTTC
Found at i:40770670 original size:41 final size:41
Alignment explanation
Indices: 40770625--40770742 Score: 182
Period size: 41 Copynumber: 2.9 Consensus size: 41
40770615 TACTGAAGTA
* * *
40770625 CACCAGCATGAAGCCTGTTAGACAATAAGTCTGAAGTAATT
1 CACCAGCATCAAGCCTGTTAGACATTAAGTCTGAAATAATT
*
40770666 CACCAGCATCAAGCCTGCTAGACATTAAGTCTGAAATAATT
1 CACCAGCATCAAGCCTGTTAGACATTAAGTCTGAAATAATT
* *
40770707 CACCAGCATCAAGCCTGTTAGGCATTAAGCCTGAAA
1 CACCAGCATCAAGCCTGTTAGACATTAAGTCTGAAA
40770743 ACCAATTATA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 70 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.23
Consensus pattern (41 bp):
CACCAGCATCAAGCCTGTTAGACATTAAGTCTGAAATAATT
Found at i:40772102 original size:13 final size:13
Alignment explanation
Indices: 40772084--40772109 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40772074 TCAAACTATC
40772084 AAATTTTCACACA
1 AAATTTTCACACA
40772097 AAATTTTCACACA
1 AAATTTTCACACA
40772110 TATAACTTAA
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:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATTTTCACACA
Found at i:40773103 original size:32 final size:32
Alignment explanation
Indices: 40773062--40773159 Score: 95
Period size: 32 Copynumber: 3.3 Consensus size: 32
40773052 AAAGAAAGGG
40773062 AAAAAAAGAATGATAGTGGATGCATACAAATT
1 AAAAAAAGAATGATAGTGGATGCATACAAATT
* * ***
40773094 AAAAAAAGAA--A-A--GAAAG-A-A-AAGGG
1 AAAAAAAGAATGATAGTGGATGCATACAAATT
40773118 AAAAAAAGAATGATAGTGGATGCATACAAATT
1 AAAAAAAGAATGATAGTGGATGCATACAAATT
40773150 AAAAAAAGAA
1 AAAAAAAGAA
40773160 AAGAAAGAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 16
0.65 0.14 0.22
Matches are distributed among these distances:
24 12 0.25
25 1 0.02
26 2 0.04
27 4 0.08
29 4 0.08
30 2 0.04
31 1 0.02
32 22 0.46
ACGTcount: A:0.62, C:0.04, G:0.19, T:0.14
Consensus pattern (32 bp):
AAAAAAAGAATGATAGTGGATGCATACAAATT
Found at i:40773132 original size:56 final size:56
Alignment explanation
Indices: 40773052--40773170 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
40773042 ATTTATAATA
40773052 AAAG-AAAGGGAAAAAAAGAATGATAGTGGATGCATACAAATTAAAAAAAGAAAAG
1 AAAGAAAAGGGAAAAAAAGAATGATAGTGGATGCATACAAATTAAAAAAAGAAAAG
40773107 AAAGAAAAGGGAAAAAAAGAATGATAGTGGATGCATACAAATTAAAAAAAGAAAAG
1 AAAGAAAAGGGAAAAAAAGAATGATAGTGGATGCATACAAATTAAAAAAAGAAAAG
40773163 AAAGAAAA
1 AAAGAAAA
40773171 AAGAAAGAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 4 0.06
56 59 0.94
ACGTcount: A:0.64, C:0.03, G:0.21, T:0.12
Consensus pattern (56 bp):
AAAGAAAAGGGAAAAAAAGAATGATAGTGGATGCATACAAATTAAAAAAAGAAAAG
Found at i:40773177 original size:15 final size:16
Alignment explanation
Indices: 40773151--40773185 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
40773141 ATACAAATTA
40773151 AAAAAAGAAAAGAAAG
1 AAAAAAGAAAAGAAAG
*
40773167 AAAAAAG-AAAGAAAT
1 AAAAAAGAAAAGAAAG
40773182 AAAA
1 AAAA
40773186 TGAGAAGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (16 bp):
AAAAAAGAAAAGAAAG
Found at i:40773637 original size:12 final size:12
Alignment explanation
Indices: 40773620--40773645 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40773610 GTGTGAAAAT
40773620 TGAAATTTTATG
1 TGAAATTTTATG
40773632 TGAAATTTTATG
1 TGAAATTTTATG
40773644 TG
1 TG
40773646 TAATATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (12 bp):
TGAAATTTTATG
Found at i:40781211 original size:36 final size:36
Alignment explanation
Indices: 40781133--40781213 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 36
40781123 TTATTGCTAT
* *
40781133 TATTTTTTTTCTTTTTATATTTTTGTTTTATTAGTA
1 TATTTTTTTTCTTTTTATATTTATGTTTCATTAGTA
40781169 TAATTTTCTTTTCTTTTTAT-TTGTAT-TTTCATTAGTA
1 T-ATTTT-TTTTCTTTTTATATT-TATGTTTCATTAGTA
40781206 TATTTTTT
1 TATTTTTT
40781214 AGTACATAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
35 2 0.05
36 6 0.15
37 18 0.45
38 14 0.35
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.73
Consensus pattern (36 bp):
TATTTTTTTTCTTTTTATATTTATGTTTCATTAGTA
Found at i:40788795 original size:230 final size:230
Alignment explanation
Indices: 40788379--40788796 Score: 613
Period size: 230 Copynumber: 1.8 Consensus size: 230
40788369 GACGGATGAG
* * *
40788379 TGAACACCACTCACCGTTATTGTAGGATTACTCTTGTAAGATAGTTCGACTGAACCTTCCCTCAT
1 TGAACACCAATCACCCTTATTGTAGGATTACTCTTGTAAGATAGTTCAACTGAACCTTCCCTCAT
* *
40788444 CAGGTAGTTTGAATGGATATTTCTAGAGGTAGATAGTCCCTGACGAACTATCTAACCCCTAGATT
66 AAGGTAGTTTGAATGGATATTTCTAGAGGTAGATAATCCCTGACGAACTATCTAACCCCTAGATT
* * *
40788509 GTATAAGGTATACTTTTCATTTATAAGAAAATCCTTAATGGATTTTACAGCACTAGATATTTGAC
131 GTATAAGGTATACTTCTCATTTATAAGAAAATCCTTAATGGATTTCACAACACTAGATATTTGAC
40788574 GTATTAGGCCTTCAATTAGAGATTTGATGAATGGA
196 GTATTAGGCCTTCAATTAGAGATTTGATGAATGGA
* * *
40788609 TGAACACCAATCACCCTTATTGTTGGATTACTCTTGTAAGATATTTCAACTGAACCTT-CTTCCA
1 TGAACACCAATCACCCTTATTGTAGGATTACTCTTGTAAGATAGTTCAACTGAACCTTCCCT-CA
* * * * * * **
40788673 TAAGGTAGTTTGAATTGATATTTCTAGAGGTGGATAATCCTTGGCGAACTATCTCATCTTTAGAT
65 TAAGGTAGTTTGAATGGATATTTCTAGAGGTAGATAATCCCTGACGAACTATCTAACCCCTAGAT
* * * *
40788738 TTTATAAGGTGTACTTCTCATTTATAAGAAAATCCTTACTGTATTTCACAACACTAGAT
130 TGTATAAGGTATACTTCTCATTTATAAGAAAATCCTTAATGGATTTCACAACACTAGAT
40788797 GCTCCAAATA
Statistics
Matches: 164, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
229 2 0.01
230 162 0.99
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.36
Consensus pattern (230 bp):
TGAACACCAATCACCCTTATTGTAGGATTACTCTTGTAAGATAGTTCAACTGAACCTTCCCTCAT
AAGGTAGTTTGAATGGATATTTCTAGAGGTAGATAATCCCTGACGAACTATCTAACCCCTAGATT
GTATAAGGTATACTTCTCATTTATAAGAAAATCCTTAATGGATTTCACAACACTAGATATTTGAC
GTATTAGGCCTTCAATTAGAGATTTGATGAATGGA
Found at i:40790137 original size:27 final size:27
Alignment explanation
Indices: 40790102--40790158 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
40790092 AAATATATAT
40790102 ATATGGCAAACTCTAAAGGAATGGAAC
1 ATATGGCAAACTCTAAAGGAATGGAAC
*
40790129 ATATGGCAAACTCTGAAGGAATGGAAC
1 ATATGGCAAACTCTAAAGGAATGGAAC
40790156 ATA
1 ATA
40790159 ATGGTTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.44, C:0.14, G:0.23, T:0.19
Consensus pattern (27 bp):
ATATGGCAAACTCTAAAGGAATGGAAC
Found at i:40795063 original size:47 final size:47
Alignment explanation
Indices: 40795009--40795102 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
40794999 GAAAAGGGAC
40795009 TGGTAACCAAGTGGCTAATCAGTTGTCGAGATTGGAAGTTTGACTTG
1 TGGTAACCAAGTGGCTAATCAGTTGTCGAGATTGGAAGTTTGACTTG
40795056 TGGTAACCAAGTGGCTAATCAGTTGTCGAGATTGGAAGTTTGACTTG
1 TGGTAACCAAGTGGCTAATCAGTTGTCGAGATTGGAAGTTTGACTTG
40795103 AAGATGGAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.26, C:0.13, G:0.30, T:0.32
Consensus pattern (47 bp):
TGGTAACCAAGTGGCTAATCAGTTGTCGAGATTGGAAGTTTGACTTG
Found at i:40796944 original size:40 final size:40
Alignment explanation
Indices: 40796898--40797082 Score: 257
Period size: 40 Copynumber: 4.6 Consensus size: 40
40796888 GCTACTCGTT
* * *
40796898 CAAATGCCTTCGGGACATAGCCCGGTCATAGTACCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
40796938 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
40796978 CAAATGCCTTCGGGACTTAACCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * * * *
40797018 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCA
40797059 CAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
40797083 ACATCATTCA
Statistics
Matches: 131, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
39 3 0.02
40 117 0.89
41 11 0.08
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:40804941 original size:40 final size:40
Alignment explanation
Indices: 40804895--40805077 Score: 253
Period size: 40 Copynumber: 4.6 Consensus size: 40
40804885 GCTACTCGTT
* * *
40804895 CAAATGCCTTCGGGACATAGCCCGGTCATAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
40804935 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
40804975 CAAATGCCTTCGGGACTTAACCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * * * *
40805015 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCA
40805056 CAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCC
40805078 AGACATCATT
Statistics
Matches: 129, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
39 3 0.02
40 115 0.89
41 11 0.09
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:40812176 original size:35 final size:35
Alignment explanation
Indices: 40812039--40812177 Score: 99
Period size: 35 Copynumber: 3.9 Consensus size: 35
40812029 ATGTAAAGCC
*
40812039 TATATA-T-TTTCCATGGTGTCACTCCCTAGAGCCT
1 TATATACTGTTTCCATGGTGTCACTCCGTAGAG-CT
* * *
40812073 T-TATACCGTTTCCATGAT-TACACTCTAGTA-AGCTT
1 TATATACTGTTTCCATGGTGT-CACTC-CGTAGAGC-T
* ** * **
40812108 GTAGATAACAATTTTCATGGTGTCACTTTGTAGAGCT
1 -TATAT-ACTGTTTCCATGGTGTCACTCCGTAGAGCT
40812145 TATATACTGTTTCCATGGTGTCACTCCGTAGAG
1 TATATACTGTTTCCATGGTGTCACTCCGTAGAG
40812178 GCAATGGATA
Statistics
Matches: 78, Mismatches: 17, Indels: 19
0.68 0.15 0.17
Matches are distributed among these distances:
33 4 0.05
34 3 0.04
35 40 0.51
36 7 0.09
37 6 0.08
38 17 0.22
39 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (35 bp):
TATATACTGTTTCCATGGTGTCACTCCGTAGAGCT
Found at i:40821808 original size:81 final size:81
Alignment explanation
Indices: 40821712--40821868 Score: 217
Period size: 81 Copynumber: 1.9 Consensus size: 81
40821702 AAAATTACCG
** * *
40821712 AAATACCCTTGAAGGGTAAAATTACT-AGAACACCCTCGAAGGGTAAAATGATCGAAACACCTCT
1 AAATACCCTCAAAGGGTAAAATGACTGA-AACACCCTCGAAGGGTAAAATGATCGAAACACCCCT
40821776 AAAGGGTAAAATTATTT
65 AAAGGGTAAAATTATTT
* * * *
40821793 AAATACCCTCAAAGGGTAAAATGACTGAAATACCCTCGATGGGTAAAATGATCGTAACACCCCTT
1 AAATACCCTCAAAGGGTAAAATGACTGAAACACCCTCGAAGGGTAAAATGATCGAAACACCCCTA
*
40821858 TAGGGTAAAAT
66 AAGGGTAAAAT
40821869 GACTGTAATG
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
81 65 0.98
82 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (81 bp):
AAATACCCTCAAAGGGTAAAATGACTGAAACACCCTCGAAGGGTAAAATGATCGAAACACCCCTA
AAGGGTAAAATTATTT
Found at i:40821843 original size:27 final size:27
Alignment explanation
Indices: 40821673--40821841 Score: 182
Period size: 27 Copynumber: 6.3 Consensus size: 27
40821663 CGAAAAGGTT
*
40821673 GTAAAATTACTGAAATACCCTCGAAGA
1 GTAAAATTACTGAAATACCCTCGAAGG
* *
40821700 GTAAAATTACCGAAATACCCTTGAAGG
1 GTAAAATTACTGAAATACCCTCGAAGG
*
40821727 GTAAAATTACT-AGAACACCCTCGAAGG
1 GTAAAATTACTGA-AATACCCTCGAAGG
* * *
40821754 GTAAAATGA-TCGAAACA-CCTCTAAAGG
1 GTAAAATTACT-GAAATACCCTC-GAAGG
* * *
40821781 GTAAAATTATTTAAATACCCTCAAAGG
1 GTAAAATTACTGAAATACCCTCGAAGG
* *
40821808 GTAAAATGACTGAAATACCCTCGATGG
1 GTAAAATTACTGAAATACCCTCGAAGG
40821835 GTAAAAT
1 GTAAAAT
40821842 GATCGTAACA
Statistics
Matches: 120, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
26 6 0.05
27 108 0.90
28 6 0.05
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.22
Consensus pattern (27 bp):
GTAAAATTACTGAAATACCCTCGAAGG
Found at i:40821876 original size:27 final size:26
Alignment explanation
Indices: 40821673--40821876 Score: 92
Period size: 27 Copynumber: 7.6 Consensus size: 26
40821663 CGAAAAGGTT
* * * *
40821673 GTAAAATTACTGAAATACCCTCGAAGA
1 GTAAAATGACTGTAACACCCTCG-AGG
* * * * *
40821700 GTAAAATTACCGAAATACCCTTGAAGG
1 GTAAAATGACTGTAACACCCTCG-AGG
*
40821727 GTAAAATTACTAG-AACACCCTCGAAGG
1 GTAAAATGACT-GTAACACCCTCG-AGG
* **
40821754 GTAAAATGA-TCGAAACACCTCTAAAGG
1 GTAAAATGACT-GTAACACC-CTCGAGG
* * * *
40821781 GTAAAATTA-TTTAAATACCCTCAAAGG
1 GTAAAATGACTGT-AACACCCTC-GAGG
* *
40821808 GTAAAATGACTGAAATACCCTCGATGG
1 GTAAAATGACTGTAACACCCTCGA-GG
**
40821835 GTAAAATGA-TCGTAACACCCCTTTAGG
1 GTAAAATGACT-GTAACA-CCCTCGAGG
40821862 GTAAAATGACTGTAA
1 GTAAAATGACTGTAA
40821877 TGCCCTAATA
Statistics
Matches: 144, Mismatches: 23, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
26 6 0.04
27 128 0.89
28 10 0.07
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (26 bp):
GTAAAATGACTGTAACACCCTCGAGG
Found at i:40821888 original size:27 final size:26
Alignment explanation
Indices: 40821751--40821897 Score: 95
Period size: 27 Copynumber: 5.5 Consensus size: 26
40821741 ACACCCTCGA
* * *
40821751 AGGGTAAAATGA-TCGAAACACCTCTAA
1 AGGGTAAAATGACT-GTAATACC-CTAT
* * *
40821778 AGGGTAAAATTA-TTTAAATACCCTCAA
1 AGGGTAAAATGACTGT-AATACCCT-AT
*
40821805 AGGGTAAAATGACTGAAATACCCTCGAT
1 AGGGTAAAATGACTGTAATACCCT--AT
* *
40821833 -GGGTAAAATGA-TCGTAACACCCCTTT
1 AGGGTAAAATGACT-GTAATA-CCCTAT
*
40821859 AGGGTAAAATGACTGTAATGCCCTAAT
1 AGGGTAAAATGACTGTAATACCCT-AT
40821886 AGGGTAAAATGA
1 AGGGTAAAATGA
40821898 TTGATTTGCC
Statistics
Matches: 96, Mismatches: 15, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
26 8 0.08
27 81 0.84
28 7 0.07
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (26 bp):
AGGGTAAAATGACTGTAATACCCTAT
Found at i:40821890 original size:81 final size:81
Alignment explanation
Indices: 40821712--40821897 Score: 216
Period size: 81 Copynumber: 2.3 Consensus size: 81
40821702 AAAATTACCG
** * *
40821712 AAATACCCTTGAAGGGTAAAATTACTAGAACACCCTCGAAGGGTAAAATGATCGAAACACCTCTA
1 AAATACCCTCAAAGGGTAAAATGACTAGAACACCCTCGAAGGGTAAAATGATCGAAACACCCCTA
* *
40821777 AAGGGTAAAATTATTT
66 AAGGGTAAAATGATGT
* * *
40821793 AAATACCCTCAAAGGGTAAAATGACT-GAAATACCCTCGATGGGTAAAATGATCGTAACACCCCT
1 AAATACCCTCAAAGGGTAAAATGACTAG-AACACCCTCGAAGGGTAAAATGATCGAAACACCCCT
**
40821857 TTAGGGTAAAATGACTGT
65 AAAGGGTAAAATGA-TGT
*
40821875 -AATGCCCT-AATAGGGTAAAATGA
1 AAATACCCTCAA-AGGGTAAAATGA
40821898 TTGATTTGCC
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
80 3 0.03
81 85 0.94
82 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (81 bp):
AAATACCCTCAAAGGGTAAAATGACTAGAACACCCTCGAAGGGTAAAATGATCGAAACACCCCTA
AAGGGTAAAATGATGT
Found at i:40821924 original size:24 final size:24
Alignment explanation
Indices: 40821892--40821945 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
40821882 TAATAGGGTA
*
40821892 AAATGATTGATTT-GCCTGTGATGT
1 AAATGATTGATTTAGCC-GAGATGT
*
40821916 AAATGATTGATTTATCCGAGATGT
1 AAATGATTGATTTAGCCGAGATGT
40821940 AAATGA
1 AAATGA
40821946 ATAATTTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.37
Consensus pattern (24 bp):
AAATGATTGATTTAGCCGAGATGT
Found at i:40822079 original size:27 final size:27
Alignment explanation
Indices: 40822039--40822104 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
40822029 ATGAAGGAAG
*
40822039 TACTG-TACTGGTGGCTTTGCCACA-A
1 TACTGTTACTGGTGGCTTGGCCACATA
*
40822064 TCACTGTTACTTGTGGCTTGGCCACATA
1 T-ACTGTTACTGGTGGCTTGGCCACATA
40822092 TACTGTTACTGGT
1 TACTGTTACTGGT
40822105 AGATTTCCTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 1 0.03
26 4 0.11
27 28 0.80
28 2 0.06
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (27 bp):
TACTGTTACTGGTGGCTTGGCCACATA
Found at i:40822201 original size:32 final size:32
Alignment explanation
Indices: 40822150--40822336 Score: 230
Period size: 32 Copynumber: 5.8 Consensus size: 32
40822140 GCGATACTAT
* * * * *
40822150 TGATGACTTTGTGCTGATCATATTACCATTAT
1 TGATGGCTGTGTGCCGATCATATTACTATTAC
* *
40822182 TGATGGCTGTGTGTCGATCATATTACCATTAC
1 TGATGGCTGTGTGCCGATCATATTACTATTAC
* * *
40822214 TGATGGCTGTATGACGATCATATTACTACTAC
1 TGATGGCTGTGTGCCGATCATATTACTATTAC
* * *
40822246 TGATGGCTTTGTGTCGATCATACTACTATTAC
1 TGATGGCTGTGTGCCGATCATATTACTATTAC
*
40822278 TGATGGCTGTGTGCCGATCATATTACTACTAC
1 TGATGGCTGTGTGCCGATCATATTACTATTAC
* *
40822310 TGATGGCTTTGTGCCAATCATATTACT
1 TGATGGCTGTGTGCCGATCATATTACT
40822337 GTACTTATTG
Statistics
Matches: 135, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 135 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.39
Consensus pattern (32 bp):
TGATGGCTGTGTGCCGATCATATTACTATTAC
Found at i:40822311 original size:96 final size:96
Alignment explanation
Indices: 40822144--40822336 Score: 262
Period size: 96 Copynumber: 2.0 Consensus size: 96
40822134 TTTGCTGCGA
* * * *
40822144 TACTATTGATGACTTTGTGCTGATCATATTACCATTATTGATGGCTGTGTGTCGATCATATTACC
1 TACTACTGATGACTTTGTGCTGATCATACTACCATTACTGATGGCTGTGTGCCGATCATATTACC
* *
40822209 ATTACTGATGGCTGTATGACGATCATATTAC
66 ACTACTGATGGCTGTATGACAATCATATTAC
* *
40822240 TACTACTGATGGCTTTGTG-TCGATCATACTACTATTACTGATGGCTGTGTGCCGATCATATTAC
1 TACTACTGATGACTTTGTGCT-GATCATACTACCATTACTGATGGCTGTGTGCCGATCATATTAC
* * * *
40822304 TACTACTGATGGCTTTGTGCCAATCATATTAC
65 CACTACTGATGGCTGTATGACAATCATATTAC
40822336 T
1 T
40822337 GTACTTATTG
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
95 1 0.01
96 83 0.99
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.39
Consensus pattern (96 bp):
TACTACTGATGACTTTGTGCTGATCATACTACCATTACTGATGGCTGTGTGCCGATCATATTACC
ACTACTGATGGCTGTATGACAATCATATTAC
Found at i:40824153 original size:30 final size:27
Alignment explanation
Indices: 40824100--40824155 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 27
40824090 CTTTTAGGTT
*
40824100 CACACAGGCTGGCACACGGTCGTGTGA
1 CACACAGGCTGGCACACGATCGTGTGA
40824127 CACACAAGGCCTGGCGACACGATCGTGTG
1 CACAC-AGG-CTGGC-ACACGATCGTGTG
40824156 TCATTTAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 5 0.20
28 3 0.12
29 5 0.20
30 12 0.48
ACGTcount: A:0.23, C:0.30, G:0.32, T:0.14
Consensus pattern (27 bp):
CACACAGGCTGGCACACGATCGTGTGA
Found at i:40826563 original size:70 final size:70
Alignment explanation
Indices: 40826488--40826637 Score: 246
Period size: 70 Copynumber: 2.1 Consensus size: 70
40826478 ACCATAGCGA
*
40826488 GGCTATGGCAATTATTCAAACGTAAGACCATGGTTGGACCATGGTAGTGTTTATATGTAAGATAT
1 GGCTATGGCAATTATTCAAACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGATAT
40826553 AGCTG
66 AGCTG
* * * *
40826558 GGCTATGCCATTTATTCAAACGTAAGACCATGGTTGGACTATGGCAGTGTTTATATGTAATATAT
1 GGCTATGGCAATTATTCAAACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGATAT
*
40826623 AGTTG
66 AGCTG
40826628 GGCTATGGCA
1 GGCTATGGCA
40826638 TTCTGATAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 73 1.00
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (70 bp):
GGCTATGGCAATTATTCAAACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGATAT
AGCTG
Found at i:40828391 original size:25 final size:25
Alignment explanation
Indices: 40828337--40828418 Score: 80
Period size: 25 Copynumber: 3.3 Consensus size: 25
40828327 ATGCTCATAT
*
40828337 GAGCTGTAAATCGGTATGCTAACTCA-
1 GAGCTATAAATCGGTATGCT--CTCAC
*
40828363 -AGCTATAGATCGGTATGCTCTCAC
1 GAGCTATAAATCGGTATGCTCTCAC
* *
40828387 GAGCTATACATCAGTATGCT-TACAC
1 GAGCTATAAATCGGTATGCTCT-CAC
40828412 GAGCTAT
1 GAGCTAT
40828419 GGGTCAGAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
23 4 0.08
24 1 0.02
25 44 0.90
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (25 bp):
GAGCTATAAATCGGTATGCTCTCAC
Found at i:40831202 original size:40 final size:40
Alignment explanation
Indices: 40831106--40831217 Score: 127
Period size: 40 Copynumber: 2.8 Consensus size: 40
40831096 CAACATTGAA
* * *
40831106 GGGTACCAAAGTACAAAC-GGGGCATGTATGTGCATTTTG
1 GGGTACCGAAGTACAAACAGGGGCACGTATGTGCATTTAG
* * * *
40831145 GGGTACTGAACTGCAAACAGGGGCACGTATTTGCATTTAG
1 GGGTACCGAAGTACAAACAGGGGCACGTATGTGCATTTAG
** *
40831185 GGGTACCGAAGTACAAACAATGGCACATATGTG
1 GGGTACCGAAGTACAAACAGGGGCACGTATGTG
40831218 TATTCATACA
Statistics
Matches: 58, Mismatches: 14, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
39 14 0.24
40 44 0.76
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.23
Consensus pattern (40 bp):
GGGTACCGAAGTACAAACAGGGGCACGTATGTGCATTTAG
Found at i:40831520 original size:26 final size:26
Alignment explanation
Indices: 40831431--40831535 Score: 129
Period size: 27 Copynumber: 4.0 Consensus size: 26
40831421 CGAAAAGGTT
*
40831431 GTAAAATTACTGAAATAGCCTCGAAG
1 GTAAAATTACTGAAATACCCTCGAAG
** *
40831457 AGTAAAATTACCAAAAGACCCTCGAATG
1 -GTAAAATTACTGAAATACCCTCGAA-G
* *
40831485 GTAATATTACTGAAATACCCTTGAAG
1 GTAAAATTACTGAAATACCCTCGAAG
*
40831511 GTAAAATTACTGGAATACCCTCGAA
1 GTAAAATTACTGAAATACCCTCGAA
40831536 AAATACCCTC
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
26 23 0.35
27 41 0.63
28 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (26 bp):
GTAAAATTACTGAAATACCCTCGAAG
Found at i:40831634 original size:54 final size:53
Alignment explanation
Indices: 40831548--40831667 Score: 145
Period size: 54 Copynumber: 2.2 Consensus size: 53
40831538 ATACCCTCAA
* *
40831548 AGGGTAAAATGGA-CGAAATACCCTCGTTGGGTAAAATGAACGCAACGCCTCTGT
1 AGGGTAAAAT-GACCGAAATACCCTCGTAGGGTAAAATG-ACGCAACGCCCCTGT
* * *
40831602 AGGGTAAAATGACCGTAATGACCCT-GTAGGGTAAAATGACGTAATGCCCCTGT
1 AGGGTAAAATGACCGAAAT-ACCCTCGTAGGGTAAAATGACGCAACGCCCCTGT
*
40831655 AGGATAAAATGAC
1 AGGGTAAAATGAC
40831668 TATTTTACCT
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
53 26 0.45
54 27 0.47
55 5 0.09
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (53 bp):
AGGGTAAAATGACCGAAATACCCTCGTAGGGTAAAATGACGCAACGCCCCTGT
Found at i:40831652 original size:26 final size:26
Alignment explanation
Indices: 40831548--40831667 Score: 127
Period size: 27 Copynumber: 4.5 Consensus size: 26
40831538 ATACCCTCAA
*
40831548 AGGGTAAAATGGACGAAAT-ACCCTCGT
1 AGGGTAAAAT-GACGTAATGACCCT-GT
* * *
40831575 TGGGTAAAATGAACGCAACG-CCTCTGT
1 AGGGTAAAATG-ACGTAATGACC-CTGT
40831602 AGGGTAAAATGACCGTAATGACCCTGT
1 AGGGTAAAATGA-CGTAATGACCCTGT
*
40831629 AGGGTAAAATGACGTAATGCCCCTGT
1 AGGGTAAAATGACGTAATGACCCTGT
*
40831655 AGGATAAAATGAC
1 AGGGTAAAATGAC
40831668 TATTTTACCT
Statistics
Matches: 80, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
26 27 0.34
27 49 0.61
28 4 0.05
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (26 bp):
AGGGTAAAATGACGTAATGACCCTGT
Found at i:40831819 original size:24 final size:24
Alignment explanation
Indices: 40831685--40831806 Score: 154
Period size: 24 Copynumber: 5.1 Consensus size: 24
40831675 CCTCTCAGAG
* *
40831685 TTAAATGATTGATTTGCCTGTGAT
1 TTAAATGACTGATTTGTCTGTGAT
* * * *
40831709 GTAAATGATTGATTTGTCCGAGAT
1 TTAAATGACTGATTTGTCTGTGAT
* * *
40831733 GTAAATGACTAATTTGTCTATGAT
1 TTAAATGACTGATTTGTCTGTGAT
*
40831757 TTAAATGACTGATTTGTGTGTGAT
1 TTAAATGACTGATTTGTCTGTGAT
40831781 TTAAATGACTGATTTGTCTGTGAT
1 TTAAATGACTGATTTGTCTGTGAT
40831805 TT
1 TT
40831807 GTATGATTGA
Statistics
Matches: 84, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 84 1.00
ACGTcount: A:0.27, C:0.07, G:0.21, T:0.44
Consensus pattern (24 bp):
TTAAATGACTGATTTGTCTGTGAT
Found at i:40831920 original size:27 final size:27
Alignment explanation
Indices: 40831882--40831946 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
40831872 ATGGGGGAAG
* *
40831882 TACTG-TACTGGTGGCTTTGCCATA-A
1 TACTGTTACTGGTGGCTTGGCCACATA
40831907 TCACTGTTACTGGTGGCTTGGCCACATA
1 T-ACTGTTACTGGTGGCTTGGCCACATA
40831935 TACTGTTACTGG
1 TACTGTTACTGG
40831947 GAGCTTTACT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 1 0.03
26 4 0.11
27 28 0.80
28 2 0.06
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (27 bp):
TACTGTTACTGGTGGCTTGGCCACATA
Found at i:40832059 original size:32 final size:32
Alignment explanation
Indices: 40831995--40832147 Score: 157
Period size: 32 Copynumber: 4.8 Consensus size: 32
40831985 AATGCTATTA
* * *
40831995 ATGGCTTTGTGCTGATCATATTACCATTACTG
1 ATGGCTTTGTGCCGATCATATTACTACTACTG
*
40832027 ATGG-TTGTGTGCCGATCATATTACTACCACTG
1 ATGGCTT-TGTGCCGATCATATTACTACTACTG
* * * *
40832059 ATGGCTTTGTGCCG-GCTACACTACTATTACTG
1 ATGGCTTTGTGCCGATC-ATATTACTACTACTG
* * *
40832091 ATGGCTGTGTGTCGATCATCTTACTACTACTG
1 ATGGCTTTGTGCCGATCATATTACTACTACTG
* *
40832123 ATGGCTTTGTGCCAATCGTATTACT
1 ATGGCTTTGTGCCGATCATATTACT
40832148 GTACTTATGG
Statistics
Matches: 96, Mismatches: 21, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
31 3 0.03
32 90 0.94
33 3 0.03
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.37
Consensus pattern (32 bp):
ATGGCTTTGTGCCGATCATATTACTACTACTG
Found at i:40846580 original size:50 final size:50
Alignment explanation
Indices: 40846456--40846702 Score: 273
Period size: 50 Copynumber: 4.8 Consensus size: 50
40846446 GATAATAACA
* ** * *
40846456 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * **
40846505 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* ** * *
40846555 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCTTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
*
40846605 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC--GG
*
40846660 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
40846703 TTACCTAAAT
Statistics
Matches: 166, Mismatches: 24, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
48 1 0.01
49 40 0.24
50 81 0.49
53 2 0.01
55 2 0.01
56 40 0.24
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:40853914 original size:11 final size:11
Alignment explanation
Indices: 40853900--40853930 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
40853890 ATCATATAAT
40853900 AATAAAATATG
1 AATAAAATATG
40853911 AATAAAATATG
1 AATAAAATATG
*
40853922 AATTAAATA
1 AATAAAATA
40853931 ACATTTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (11 bp):
AATAAAATATG
Found at i:40856880 original size:28 final size:28
Alignment explanation
Indices: 40856848--40856980 Score: 77
Period size: 30 Copynumber: 4.6 Consensus size: 28
40856838 TGGTATCCAC
*
40856848 CACCAGTACATAGTACATGGAAACATAG
1 CACCAGTACATAGTACATGGAAACATAA
* * * * *
40856876 CACCAGCACAGAGTGCCTGGAAATAATAA
1 CACCAGTACATAGTACATGGAAA-CATAA
* * * *
40856905 CACCGGTACATAGTTCTTGGAAACTGTAA
1 CACCAGTACATAGTACATGGAAAC-ATAA
** * **
40856934 TCACTGGTACATAGTACCTAAAAACTATAA
1 -CACCAGTACATAGTACATGGAAAC-ATAA
*
40856964 TCACCAGTGCATAGTAC
1 -CACCAGTACATAGTAC
40856981 CTAGAAACTG
Statistics
Matches: 80, Mismatches: 22, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
28 19 0.24
29 24 0.30
30 37 0.46
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (28 bp):
CACCAGTACATAGTACATGGAAACATAA
Found at i:40856959 original size:30 final size:30
Alignment explanation
Indices: 40856925--40856999 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
40856915 TAGTTCTTGG
40856925 AAACTGTAATCACTGGTACATAGTACCTAA
1 AAACTGTAATCACTGGTACATAGTACCTAA
* ** * *
40856955 AAACTATAATCACCAGTGCATAGTACCTAG
1 AAACTGTAATCACTGGTACATAGTACCTAA
* *
40856985 AAACTGAAACCACTG
1 AAACTGTAATCACTG
40857000 ACACCTAGTG
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.41, C:0.23, G:0.13, T:0.23
Consensus pattern (30 bp):
AAACTGTAATCACTGGTACATAGTACCTAA
Found at i:40860484 original size:18 final size:19
Alignment explanation
Indices: 40860449--40860484 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
40860439 ATTTTAGGGT
*
40860449 TTTCATTCTTAGGTTTTTC
1 TTTCATTCTTAAGTTTTTC
40860468 TTTCATTC-TAAGTTTTT
1 TTTCATTCTTAAGTTTTT
40860485 ACTTAGGTTA
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:0.14, G:0.08, T:0.64
Consensus pattern (19 bp):
TTTCATTCTTAAGTTTTTC
Found at i:40875901 original size:12 final size:13
Alignment explanation
Indices: 40875884--40875922 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 13
40875874 AACACACTTA
40875884 TTTTC-TCTCTTT
1 TTTTCTTCTCTTT
40875896 TTTTCTTCTTCATTT
1 TTTTCTTC-TC-TTT
40875911 TTTTCTTCTCTT
1 TTTTCTTCTCTT
40875923 GCTTTGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 5 0.21
13 4 0.17
14 4 0.17
15 11 0.46
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTCTTCTCTTT
Found at i:40887910 original size:48 final size:48
Alignment explanation
Indices: 40887810--40887913 Score: 154
Period size: 48 Copynumber: 2.2 Consensus size: 48
40887800 CTGCGTCGCA
* **
40887810 ACATCGAAGGCACTCTCAAATTTTCTCCATTTTGCTTCCTATGCTGCC
1 ACATCGAAGGCACTCTCAAATTTTCTCCATTTTGCTCCCTATGCTAAC
* * *
40887858 ACATCGAAGGCAGTCTCAAATTTTCTCCATTTTGCTCCCTATGTTAAG
1 ACATCGAAGGCACTCTCAAATTTTCTCCATTTTGCTCCCTATGCTAAC
40887906 ACATCGAA
1 ACATCGAA
40887914 CCCTCCATGT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.34
Consensus pattern (48 bp):
ACATCGAAGGCACTCTCAAATTTTCTCCATTTTGCTCCCTATGCTAAC
Found at i:40888797 original size:13 final size:12
Alignment explanation
Indices: 40888772--40888809 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
40888762 AATGAATGAG
*
40888772 TTTTTCTTACTT
1 TTTTTCTTTCTT
40888784 TTTTTACTTTCTT
1 TTTTT-CTTTCTT
40888797 TTTTTCTTT-TT
1 TTTTTCTTTCTT
40888808 TT
1 TT
40888810 CAATATGTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 4 0.17
12 9 0.38
13 11 0.46
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTCTTTCTT
Found at i:40893292 original size:50 final size:50
Alignment explanation
Indices: 40893233--40893353 Score: 152
Period size: 50 Copynumber: 2.4 Consensus size: 50
40893223 TATCCCTGAT
** * * *
40893233 ATGGTCTTACATGAGAGTTCTCATATAGGTGCCCATGCCATGTCCTAGAC
1 ATGGTCTTACATGAGACCTCTCATATAGGTGCCAACGCCATGTCCCAGAC
* * * *
40893283 ATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGAGACCTCTCATATAGGTGCCAACGCCATGTCCCAGAC
*
40893333 ATGGTCTTACATGGGACCTCT
1 ATGGTCTTACATGAGACCTCT
40893354 TTACCCAAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.27
Consensus pattern (50 bp):
ATGGTCTTACATGAGACCTCTCATATAGGTGCCAACGCCATGTCCCAGAC
Found at i:40896956 original size:26 final size:26
Alignment explanation
Indices: 40896927--40896981 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
40896917 TTACTTTTTT
*
40896927 TTTCATATAAGCATTTCATCTAAACA
1 TTTCATATAACCATTTCATCTAAACA
* * * *
40896953 TTTCATCTTACCATTTCATTTACACA
1 TTTCATATAACCATTTCATCTAAACA
40896979 TTT
1 TTT
40896982 AACTCATAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.22, G:0.02, T:0.45
Consensus pattern (26 bp):
TTTCATATAACCATTTCATCTAAACA
Found at i:40899702 original size:57 final size:58
Alignment explanation
Indices: 40899636--40899750 Score: 160
Period size: 57 Copynumber: 2.0 Consensus size: 58
40899626 CATTTCCAAG
* * * * *
40899636 TCATTTTCATTTTGGAGAAAACCACATTCATTTTCAAATGATT-TCATTTCTCTATTT
1 TCATTTTCATTTAGGAGAAAACCACAATAATTTCCAAATGATTCTCATTTCTCCATTT
* *
40899693 TCATTTTCATTTAGGAGAAAACCATAATAATTTCCAAATGTTTCTCATTTCTCCATTT
1 TCATTTTCATTTAGGAGAAAACCACAATAATTTCCAAATGATTCTCATTTCTCCATTT
40899751 CTATTTATAT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
57 37 0.74
58 13 0.26
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.45
Consensus pattern (58 bp):
TCATTTTCATTTAGGAGAAAACCACAATAATTTCCAAATGATTCTCATTTCTCCATTT
Found at i:40904736 original size:27 final size:27
Alignment explanation
Indices: 40904664--40904757 Score: 84
Period size: 27 Copynumber: 3.5 Consensus size: 27
40904654 TATGGAGCCA
* *
40904664 TTCCTTTACAGTTTACCATACATATCT
1 TTCCTTCAGAGTTTACCATACATATCT
* **
40904691 TTCCTTTAGAGTTCGCCATACATAT-T
1 TTCCTTCAGAGTTTACCATACATATCT
* *
40904717 ATT-CTTCCAGAGTTTACCATATATACCT
1 -TTCCTT-CAGAGTTTACCATACATATCT
*
40904745 ATCCTTCAGAGTT
1 TTCCTTCAGAGTT
40904758 CTCCGGGAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
26 4 0.07
27 46 0.85
28 4 0.07
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (27 bp):
TTCCTTCAGAGTTTACCATACATATCT
Found at i:40904895 original size:27 final size:27
Alignment explanation
Indices: 40904850--40904912 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
40904840 ATATACCAAG
* *
40904850 AAGGCATTCGTTTTTATAGATTGCCACA
1 AAGGC-TTCATTTTCATAGATTGCCACA
40904878 AAGGCTTCATTTTCATAGATTGCCACA
1 AAGGCTTCATTTTCATAGATTGCCACA
*
40904905 AAGACTTC
1 AAGGCTTC
40904913 TTGTAACACC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 27 0.84
28 5 0.16
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (27 bp):
AAGGCTTCATTTTCATAGATTGCCACA
Found at i:40906392 original size:30 final size:30
Alignment explanation
Indices: 40906329--40906544 Score: 129
Period size: 30 Copynumber: 7.2 Consensus size: 30
40906319 CTATTACCAC
* * * * **
40906329 CCCTTTTCATAGTTCGATAGTCAAAGCTGT
1 CCCTTTTCATAATTTGATAGCCGAAGCCAT
* *
40906359 CCCTTTTCATATTTTGATCGCCGAAGCCAT
1 CCCTTTTCATAATTTGATAGCCGAAGCCAT
* * * *
40906389 CCCTTCTCAT--TGTTGATGGTCGTCA-CCAT
1 CCCTTTTCATAAT-TTGATAGCCG-AAGCCAT
* * * **
40906418 CCCTTTTCAT--TGTTGATGGTCGTCA-TTAT
1 CCCTTTTCATAAT-TTGATAGCCG-AAGCCAT
* *
40906447 CCCTTTTCATAATTCGATAGCTGAAGCCCTAT
1 CCCTTTTCATAATTTGATAGCCGAAG-CC-AT
* *
40906479 CCCTTTTCATAATTCGATAGCTGAAGCCAT
1 CCCTTTTCATAATTTGATAGCCGAAGCCAT
* *
40906509 CCCTTTTCATAATTTGATAGTCGAAGCTAT
1 CCCTTTTCATAATTTGATAGCCGAAGCCAT
40906539 CCCTTT
1 CCCTTT
40906545 CCATTGGTCA
Statistics
Matches: 154, Mismatches: 25, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
28 1 0.01
29 49 0.32
30 73 0.47
31 3 0.02
32 28 0.18
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.38
Consensus pattern (30 bp):
CCCTTTTCATAATTTGATAGCCGAAGCCAT
Found at i:40906417 original size:29 final size:29
Alignment explanation
Indices: 40906385--40906456 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
40906375 ATCGCCGAAG
*
40906385 CCATCCCTTCTCATTGTTGATGGTCGTCA
1 CCATCCCTTTTCATTGTTGATGGTCGTCA
40906414 CCATCCCTTTTCATTGTTGATGGTCGTCA
1 CCATCCCTTTTCATTGTTGATGGTCGTCA
**
40906443 TTATCCCTTTTCAT
1 CCATCCCTTTTCAT
40906457 AATTCGATAG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.14, C:0.29, G:0.14, T:0.43
Consensus pattern (29 bp):
CCATCCCTTTTCATTGTTGATGGTCGTCA
Found at i:40906485 original size:32 final size:31
Alignment explanation
Indices: 40906444--40906544 Score: 154
Period size: 30 Copynumber: 3.3 Consensus size: 31
40906434 TGGTCGTCAT
40906444 TATCCCTTTTCATAATTCGATAGCTGAAGCCC
1 TATCCCTTTTCATAATTCGATAGCTGAAG-CC
40906476 TATCCCTTTTCATAATTCGATAGCTGAAGCC
1 TATCCCTTTTCATAATTCGATAGCTGAAGCC
*
40906507 -ATCCCTTTTCATAATTTGATAG-TCGAAG-C
1 TATCCCTTTTCATAATTCGATAGCT-GAAGCC
40906536 TATCCCTTT
1 TATCCCTTT
40906545 CCATTGGTCA
Statistics
Matches: 66, Mismatches: 1, Indels: 6
0.90 0.01 0.08
Matches are distributed among these distances:
29 2 0.03
30 33 0.50
31 2 0.03
32 29 0.44
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.38
Consensus pattern (31 bp):
TATCCCTTTTCATAATTCGATAGCTGAAGCC
Found at i:40909401 original size:30 final size:31
Alignment explanation
Indices: 40909351--40909413 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
40909341 TACTCCTTTG
*
40909351 GTCTTTTTCAATTTCAAAAATGAAAAAAAAATA
1 GTCTTTTTCAA--TCAAAAATCAAAAAAAAATA
*
40909384 GTCTTTTTCAA-CAAAAATCACAAAAAAATA
1 GTCTTTTTCAATCAAAAATCAAAAAAAAATA
40909414 ATAATTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 17 0.61
33 11 0.39
ACGTcount: A:0.52, C:0.13, G:0.05, T:0.30
Consensus pattern (31 bp):
GTCTTTTTCAATCAAAAATCAAAAAAAAATA
Found at i:40909455 original size:19 final size:20
Alignment explanation
Indices: 40909411--40909456 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
40909401 TCACAAAAAA
* *
40909411 ATAATAATTTAAAATGATTT
1 ATAAAAATTCAAAATGATTT
40909431 -TCAAAAATTCAAAAT-ATTT
1 AT-AAAAATTCAAAATGATTT
40909450 ATAAAAA
1 ATAAAAA
40909457 AAAGTCTACA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (20 bp):
ATAAAAATTCAAAATGATTT
Found at i:40920307 original size:136 final size:136
Alignment explanation
Indices: 40920063--40920335 Score: 415
Period size: 136 Copynumber: 2.0 Consensus size: 136
40920053 TAGTATATGA
* *
40920063 ACAATGGTTATGTGGCCTCTAGTAAGGCAGGTACATTGCAAACCAGACTAGCTAGCATGGCAAAG
1 ACAATGGTTATGTGGCCTCTAGTAAGGCAGGTACATTACAAACCAGACTAGCTAGCATGACAAAG
* *
40920128 GAAATGAAAGGAATTGTTGATCTCTGAATACAAAACCGGGTTTGGCCAACACAAAAAAGGTTGTC
66 GAAATGAAAGGAATTGTTGATCTCTGAACACAAAACCAGGTTTGGCCAACACAAAAAAGGTTGTC
40920193 TGCATG
131 TGCATG
40920199 ACAATGGTTATGTGGCCTC-AGGTAAGGCAGGTACATTACAAACCAGACTAGCTAGCATGACAAA
1 ACAATGGTTATGTGGCCTCTA-GTAAGGCAGGTACATTACAAACCAGACTAGCTAGCATGACAAA
* ** * * * *
40920263 GGAAATGAAAGGAA-TGATTGATCTTTGAACACGGACCCATGTTTGGCTAACACAAAGAAGGTTG
65 GGAAATGAAAGGAATTG-TTGATCTCTGAACACAAAACCAGGTTTGGCCAACACAAAAAAGGTTG
40920327 TCTGCATG
129 TCTGCATG
40920335 A
1 A
40920336 ATGTATGGGC
Statistics
Matches: 124, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
135 3 0.02
136 121 0.98
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.23
Consensus pattern (136 bp):
ACAATGGTTATGTGGCCTCTAGTAAGGCAGGTACATTACAAACCAGACTAGCTAGCATGACAAAG
GAAATGAAAGGAATTGTTGATCTCTGAACACAAAACCAGGTTTGGCCAACACAAAAAAGGTTGTC
TGCATG
Found at i:40922954 original size:18 final size:19
Alignment explanation
Indices: 40922928--40922963 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
40922918 ACTCTATATC
40922928 CTTCAGGGA-TTTTAAATT
1 CTTCAGGGATTTTTAAATT
*
40922946 CTTCTGGGATTTTTAAAT
1 CTTCAGGGATTTTTAAAT
40922964 AAATTTCACT
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:0.25, C:0.11, G:0.17, T:0.47
Consensus pattern (19 bp):
CTTCAGGGATTTTTAAATT
Found at i:40923294 original size:37 final size:37
Alignment explanation
Indices: 40923253--40923327 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
40923243 TCCAAAAACA
40923253 TTACGTTTAGAAAGTGAATTTAATTCTTCTTGAATTG
1 TTACGTTTAGAAAGTGAATTTAATTCTTCTTGAATTG
40923290 TTACGTTTAGAAAGTGAATTTAATTCTTCTTGAATTG
1 TTACGTTTAGAAAGTGAATTTAATTCTTCTTGAATTG
40923327 T
1 T
40923328 GTCTTTCCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.29, C:0.08, G:0.16, T:0.47
Consensus pattern (37 bp):
TTACGTTTAGAAAGTGAATTTAATTCTTCTTGAATTG
Done.