Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 153 of 211
Found at i:48163654 original size:25 final size:23
Alignment explanation
Indices: 48163596--48163657 Score: 88
Period size: 23 Copynumber: 2.6 Consensus size: 23
48163586 AAATATATAT
*
48163596 AATATATATTAAATTAAAAATAA
1 AATATATATTTAATTAAAAATAA
*
48163619 AATATATATTTGATTAAAAATAAAA
1 AATATATATTTAATTAAAAAT--AA
48163644 AATATATATTTAAT
1 AATATATATTTAAT
48163658 ATATAAATCG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 19 0.56
25 15 0.44
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
AATATATATTTAATTAAAAATAA
Found at i:48165897 original size:20 final size:20
Alignment explanation
Indices: 48165872--48165911 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
48165862 CGTAAAATGA
*
48165872 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
48165892 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
48165912 GGAAAATATT
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:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:48165901 original size:34 final size:35
Alignment explanation
Indices: 48165857--48165923 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
48165847 CAGTAAAATA
*
48165857 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
48165891 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
48165924 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:48165927 original size:14 final size:15
Alignment explanation
Indices: 48165851--48165927 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
48165841 GATTGCCAGT
* *
48165851 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
48165865 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
48165879 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
48165899 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
48165914 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
48165928 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:48165988 original size:32 final size:32
Alignment explanation
Indices: 48165913--48165991 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 32
48165903 TGATTTACTG
* ** **
48165913 GAAAATATTTTCTGGTGTTTGATTGAATCTGT
1 GAAAATATTTTCTGCTGTTTGACAGAATCCCT
*
48165945 GTAAAATATTTTCTGCTGTTTGACAGATTCCCT
1 G-AAAATATTTTCTGCTGTTTGACAGAATCCCT
48165978 GAAAATATTTTCTG
1 GAAAATATTTTCTG
48165992 AAAAAGTTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
32 14 0.35
33 26 0.65
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.44
Consensus pattern (32 bp):
GAAAATATTTTCTGCTGTTTGACAGAATCCCT
Found at i:48166680 original size:64 final size:66
Alignment explanation
Indices: 48166555--48166683 Score: 167
Period size: 64 Copynumber: 2.0 Consensus size: 66
48166545 TCTGAAGCTG
* * ***
48166555 TAGCTGGAGTTTATCATATTTTCTTATTGCCTCTGCTTCTCTCGTTGCTGCCTCTGTTTTAAGTT
1 TAGCTGGAGTTCATCATATTTTCTTATAGCCTCTGCTTCTCTCGTTGCTGCCTCCACTTTAAGTT
48166620 A
66 A
48166621 TAGCTGGAGTTCATCAT-TTTT-TT-TGAGCCTCTGCTTCTCTCGATT-CTGCCTCCACTTTAAG
1 TAGCTGGAGTTCATCATATTTTCTTAT-AGCCTCTGCTTCTCTCG-TTGCTGCCTCCACTTTAAG
48166682 TT
64 TT
48166684 GAGCAATTTG
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.02
64 33 0.59
65 6 0.11
66 16 0.29
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.47
Consensus pattern (66 bp):
TAGCTGGAGTTCATCATATTTTCTTATAGCCTCTGCTTCTCTCGTTGCTGCCTCCACTTTAAGTT
A
Found at i:48198770 original size:26 final size:27
Alignment explanation
Indices: 48198713--48198770 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
48198703 AGGTTACGTT
*
48198713 ATTATCAATAAATGAATAATTTATTTA
1 ATTATCAATAAATGAATAATTTATTAA
* * * *
48198740 TTTATCAGTAAATTAA-CATTTATTAA
1 ATTATCAATAAATGAATAATTTATTAA
48198766 ATTAT
1 ATTAT
48198771 AAAAAATTGT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (27 bp):
ATTATCAATAAATGAATAATTTATTAA
Found at i:48200117 original size:89 final size:89
Alignment explanation
Indices: 48199956--48200122 Score: 282
Period size: 88 Copynumber: 1.9 Consensus size: 89
48199946 ACAGTACACT
* *
48199956 GGAGGTGATCAAATTCAGTTAAAAACTGGCAAATTTGCACTAATGACATTCCTCTGGAGTGAGGT
1 GGAGGTGATCAAATTCAGTTAAAAAATAGCAAATTTGCACTAATGACATTCCTCTGGAGTGAGGT
48200021 TGAGCAAGTCAACTTCAAAGACTC
66 TGAGCAAGTCAACTTCAAAGACTC
* *
48200045 GGAGGTGAT-AAATTCAGTTAAAAAATAGCAATTTTGCACTAATGGCATTCCTCTTGGAGTGAGG
1 GGAGGTGATCAAATTCAGTTAAAAAATAGCAAATTTGCACTAATGACATTCCTC-TGGAGTGAGG
48200109 TTGAGCAAGTCAAC
65 TTGAGCAAGTCAAC
48200123 CATTCATTAC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
88 40 0.55
89 33 0.45
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (89 bp):
GGAGGTGATCAAATTCAGTTAAAAAATAGCAAATTTGCACTAATGACATTCCTCTGGAGTGAGGT
TGAGCAAGTCAACTTCAAAGACTC
Found at i:48208229 original size:19 final size:17
Alignment explanation
Indices: 48208193--48208226 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
48208183 TATTTTTTTA
48208193 TTTTTAATCAAATATAT
1 TTTTTAATCAAATATAT
48208210 TTTTTAATCAAATATAT
1 TTTTTAATCAAATATAT
48208227 ATTAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTTTAATCAAATATAT
Found at i:48209335 original size:22 final size:22
Alignment explanation
Indices: 48209307--48209351 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
48209297 AATGGGATAA
**
48209307 AGAAAAACTCAAGTGTCAAACT
1 AGAAAAACTCAAGTACCAAACT
*
48209329 AGAAAAACTTAAGTACCAAACT
1 AGAAAAACTCAAGTACCAAACT
48209351 A
1 A
48209352 AACATTGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.18, G:0.11, T:0.18
Consensus pattern (22 bp):
AGAAAAACTCAAGTACCAAACT
Found at i:48211722 original size:16 final size:16
Alignment explanation
Indices: 48211682--48211723 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
48211672 AATGAGTGAA
*
48211682 ATTAAAGAA-GAACAT
1 ATTAAAGAATGAAAAT
**
48211697 ATTATGGAATGAAAAT
1 ATTAAAGAATGAAAAT
48211713 ATTAAAGAATG
1 ATTAAAGAATG
48211724 TATGTGACAT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.55, C:0.02, G:0.17, T:0.26
Consensus pattern (16 bp):
ATTAAAGAATGAAAAT
Found at i:48213163 original size:15 final size:15
Alignment explanation
Indices: 48213103--48213165 Score: 76
Period size: 15 Copynumber: 4.3 Consensus size: 15
48213093 GCTGATTTCT
48213103 GGTTTAGGCTAGTTG
1 GGTTTAGGCTAGTTG
* *
48213118 GG-CTAGGGTA-TTG
1 GGTTTAGGCTAGTTG
* *
48213131 GGCTTAGGCTAATTG
1 GGTTTAGGCTAGTTG
48213146 GGTTTAGGCTAGTTG
1 GGTTTAGGCTAGTTG
48213161 GGTTT
1 GGTTT
48213166 CTGTAACTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
13 5 0.12
14 12 0.30
15 23 0.57
ACGTcount: A:0.14, C:0.08, G:0.40, T:0.38
Consensus pattern (15 bp):
GGTTTAGGCTAGTTG
Found at i:48214092 original size:34 final size:34
Alignment explanation
Indices: 48214042--48214109 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
48214032 GATGCAGCAT
48214042 GTACAGTCAACCGTCATTAGAGATTTAACACTTG
1 GTACAGTCAACCGTCATTAGAGATTTAACACTTG
* * *
48214076 GTACAGTCCACTGTCATTAGAGATTTAACGCTTG
1 GTACAGTCAACCGTCATTAGAGATTTAACACTTG
48214110 AGTGACTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (34 bp):
GTACAGTCAACCGTCATTAGAGATTTAACACTTG
Found at i:48215798 original size:25 final size:24
Alignment explanation
Indices: 48215760--48215812 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
48215750 AAGTTCAAGT
*
48215760 GAGCCATATTAGGAAGCTCACAAA
1 GAGCCATATCAGGAAGCTCACAAA
* *
48215784 GAGCCTATATCAGGACGCTCATAAA
1 GAGCC-ATATCAGGAAGCTCACAAA
48215809 GAGC
1 GAGC
48215813 TGCGATATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.17
Consensus pattern (24 bp):
GAGCCATATCAGGAAGCTCACAAA
Found at i:48215900 original size:64 final size:64
Alignment explanation
Indices: 48215789--48215914 Score: 153
Period size: 64 Copynumber: 2.0 Consensus size: 64
48215779 ACAAAGAGCC
* * *** ** * *
48215789 TATATCAGGACGCTCATAAAGAGCTGCGATATGTTTGCATTATATGCAGGATCCATACCGATCA
1 TATAACAGGACGCTCACAAAGAGCTGCGATATGACCGCAACACATGCAGGATCAATACCGATCA
* *
48215853 TATAACAGGATGCTCACAAAGAGCTGCGATATGACCGCAACACATGCAGGGTCAATACCGAT
1 TATAACAGGACGCTCACAAAGAGCTGCGATATGACCGCAACACATGCAGGATCAATACCGAT
48215915 TGGGATGCTC
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
64 51 1.00
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.23
Consensus pattern (64 bp):
TATAACAGGACGCTCACAAAGAGCTGCGATATGACCGCAACACATGCAGGATCAATACCGATCA
Found at i:48217390 original size:31 final size:31
Alignment explanation
Indices: 48217355--48217414 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
48217345 CATATAATTT
*
48217355 AAATTGATAAATTTTAATCCCTGTACTTTTC
1 AAATTGATAAAATTTAATCCCTGTACTTTTC
* * *
48217386 AAATTGGTAAAATTTAGTCTCTGTACTTT
1 AAATTGATAAAATTTAATCCCTGTACTTT
48217415 CCAAGTTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (31 bp):
AAATTGATAAAATTTAATCCCTGTACTTTTC
Found at i:48218415 original size:34 final size:34
Alignment explanation
Indices: 48218372--48218440 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
48218362 AATCTAAATA
48218372 TATTCCTCCTTGGGCAACATTTCTTTTATTTAAG
1 TATTCCTCCTTGGGCAACATTTCTTTTATTTAAG
48218406 TATTCCTCCTTGGGCAACATTTCTTTTATTTAAG
1 TATTCCTCCTTGGGCAACATTTCTTTTATTTAAG
48218440 T
1 T
48218441 CATCTATTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.48
Consensus pattern (34 bp):
TATTCCTCCTTGGGCAACATTTCTTTTATTTAAG
Found at i:48219639 original size:18 final size:18
Alignment explanation
Indices: 48219603--48219636 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
48219593 AAATGTTTAC
48219603 AAATATCAAATACTAAAT
1 AAATATCAAATACTAAAT
*
48219621 AAATTTCAAATA-TAAA
1 AAATATCAAATACTAAA
48219637 ATATCCATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATATCAAATACTAAAT
Found at i:48222406 original size:154 final size:151
Alignment explanation
Indices: 48222128--48222822 Score: 901
Period size: 154 Copynumber: 4.6 Consensus size: 151
48222118 AACATGTTCG
* * *
48222128 TATTTCAGCCCTTTGTTCGTATTTTTTTCCGGATTTTATTACTTTAAAAAAATATACTATTTTCT
1 TATTTCGGCCATTTGTTCGTATTTTTTCCCGGATTTTATTACTTTAAAAAAATATACTATTTTCT
* * *
48222193 AATTTTATTATTTTACATTATTTTAATACACTATGTTTGAAATGTATTCATTTAGTGTGTTTTTT
66 AATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTGTTTTTT
**
48222258 ATTTAAATTTAAAAAAACCCT
131 AAATAAATTTAAAAAAACCCT
* * *
48222279 TATTTCGGCCCTTTATTCGTATTTTTTCCCAGGATTTTATTACTTTTAATAAAAATATATTATTT
1 TATTTCGGCCATTTGTTCGTATTTTTTCCC-GGATTTTATTAC-TTTAA-AAAAATATACTATTT
*
48222344 TCGT-ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTT
63 TC-TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTGTT
*
48222408 TTTTAAATAACTTTTTAAAAAAACCCT
127 TTTTAAATAA--ATTTAAAAAAACCCT
* * * * *
48222435 TATTTTGACCATTTGTTCGTATTTTGTCCCCAGATTTTATTACTTTAAAAAAATATACTACTTTC
1 TATTTCGGCCATTTGTTCGTATTTT-TTCCCGGATTTTATTACTTTAAAAAAATATACTATTTTC
**
48222500 TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATCCATTTAGTGTGTTTTT
65 TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTG-TTTT
* *
48222565 TTAAATAAAATTAAAAAAACTCT
129 TTAAATAAATTTAAAAAAACCCT
* * *
48222588 TATTTCAGCCTTTTGTTCGTATTTTTTTCCCGGATTTTATTACTTTCAATAAAAATATATTATTT
1 TATTTCGGCCATTTGTTCGTA-TTTTTTCCCGGATTTTATTACTTT-AA-AAAAATATACTATTT
* * *
48222653 T-TGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAATGTGGT
63 TCT-AATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTGTT
48222717 TTTTAAATAAATTTAGTAAAAAACCCT
127 TTTTAAATAAATTTA--AAAAAACCCT
* * *
48222744 TATTTCGGCCATTTGTTCGTA---TTT------TTTTATTAATTT-AAAAAATATACAATTTTTT
1 TATTTCGGCCATTTGTTCGTATTTTTTCCCGGATTTTATTACTTTAAAAAAATATACTATTTTCT
48222799 AATTTTATTATTTTACATTATTTT
66 AATTTTATTATTTTACATTATTTT
48222823 TGTAGCAGGC
Statistics
Matches: 482, Mismatches: 46, Indels: 40
0.85 0.08 0.07
Matches are distributed among these distances:
143 37 0.08
144 2 0.00
146 11 0.02
151 27 0.06
152 15 0.03
153 53 0.11
154 172 0.36
155 87 0.18
156 74 0.15
157 4 0.01
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (151 bp):
TATTTCGGCCATTTGTTCGTATTTTTTCCCGGATTTTATTACTTTAAAAAAATATACTATTTTCT
AATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTGTTTTTT
AAATAAATTTAAAAAAACCCT
Found at i:48222722 original size:309 final size:307
Alignment explanation
Indices: 48222139--48222822 Score: 1014
Period size: 309 Copynumber: 2.3 Consensus size: 307
48222129 ATTTCAGCCC
** * *
48222139 TTTGTTCGTATTTTTTTCCGGATTTTATTACTTTAAAAAAATATACTATTTTCTAATTTTATTAT
1 TTTGTTCGTATTTTTCCCCAGATTTTATTACTTTAAAAAAATATACTACTTTCTAATTTTATTAT
* ** *
48222204 TTTACATTATTTTAATACACTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTATTTAAATTTA
66 TTTACATTATTTTAATACACTATGTTTGAAATGTATCCATTTAGTGTGTTTTTTAAATAAAATTA
* *
48222269 AAAAAACCCTTATTTCGGCCCTTTATTCGTATTTTTTCCCAGGATTTTATTACTTTTAATAAAAA
131 AAAAAACCCTTATTTCAGCCCTTTATTCGTATTTTTTCCCAGGATTTTATTACTTTCAATAAAAA
48222334 TATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATT
196 TATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATT
* * * * *
48222399 TACTGTGTTTTTTAAATAACTTT-TTAAAAAAACCCTTATTTTGACCA
261 TAATGTGGTTTTTAAATAAATTTAGT-AAAAAACCCTTATTTCGACCA
48222446 TTTGTTCGTATTTTGTCCCCAGATTTTATTACTTTAAAAAAATATACTACTTTCTAATTTTATTA
1 TTTGTTCGTATTTT-TCCCCAGATTTTATTACTTTAAAAAAATATACTACTTTCTAATTTTATTA
* *
48222511 TTTTACATTATTTTAGTACATTATGTTTGAAATGTATCCATTTAGTGTGTTTTTTTAAATAAAAT
65 TTTTACATTATTTTAATACACTATGTTTGAAATGTATCCATTTAGTGTG-TTTTTTAAATAAAAT
* * *
48222576 TAAAAAAACTCTTATTTCAGCCTTTTGTTCGTATTTTTTTCCC-GGATTTTATTACTTTCAATAA
129 TAAAAAAACCCTTATTTCAGCCCTTTATTCGTA-TTTTTTCCCAGGATTTTATTACTTTCAATAA
*
48222640 AAATATATTATTTTTGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTA
193 AAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTA
*
48222705 ATTTAATGTGGTTTTTAAATAAATTTAGTAAAAAACCCTTATTTCGGCCA
258 ATTTAATGTGGTTTTTAAATAAATTTAGTAAAAAACCCTTATTTCGACCA
* * * *
48222755 TTTGTTCGTA--TTT-------TTTTATTAATTT-AAAAAATATACAATTTTTTAATTTTATTAT
1 TTTGTTCGTATTTTTCCCCAGATTTTATTACTTTAAAAAAATATACTACTTTCTAATTTTATTAT
48222810 TTTACATTATTTT
66 TTTACATTATTTT
48222823 TGTAGCAGGC
Statistics
Matches: 347, Mismatches: 26, Indels: 17
0.89 0.07 0.04
Matches are distributed among these distances:
298 40 0.12
299 11 0.03
306 1 0.00
307 16 0.05
308 92 0.27
309 177 0.51
310 10 0.03
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (307 bp):
TTTGTTCGTATTTTTCCCCAGATTTTATTACTTTAAAAAAATATACTACTTTCTAATTTTATTAT
TTTACATTATTTTAATACACTATGTTTGAAATGTATCCATTTAGTGTGTTTTTTAAATAAAATTA
AAAAAACCCTTATTTCAGCCCTTTATTCGTATTTTTTCCCAGGATTTTATTACTTTCAATAAAAA
TATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATT
TAATGTGGTTTTTAAATAAATTTAGTAAAAAACCCTTATTTCGACCA
Found at i:48223270 original size:15 final size:15
Alignment explanation
Indices: 48223259--48223288 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
48223249 CTATTTTGTT
48223259 TTATTTTATTTTATC
1 TTATTTTATTTTATC
*
48223274 TTATTTTCTTTTATC
1 TTATTTTATTTTATC
48223289 AAAAACAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (15 bp):
TTATTTTATTTTATC
Found at i:48226423 original size:16 final size:17
Alignment explanation
Indices: 48226387--48226423 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
48226377 ATGAAACAGT
48226387 TAAA-AAAATAATAGTA
1 TAAATAAAATAATAGTA
48226403 T-AATAAAATAATA-TA
1 TAAATAAAATAATAGTA
48226418 TAAATA
1 TAAATA
48226424 GGTACATAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (17 bp):
TAAATAAAATAATAGTA
Found at i:48230498 original size:21 final size:21
Alignment explanation
Indices: 48230472--48230512 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
48230462 TGCAGACTTT
*
48230472 GGCAATATAGGCTGATATTAG
1 GGCAATATAGGCTGACATTAG
48230493 GGCAATATAGGCTGACATTA
1 GGCAATATAGGCTGACATTA
48230513 TGGGAGAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.27
Consensus pattern (21 bp):
GGCAATATAGGCTGACATTAG
Found at i:48230749 original size:20 final size:20
Alignment explanation
Indices: 48230724--48230763 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
48230714 TTCATCTCAT
48230724 GCATCGCATCATATGCATTA
1 GCATCGCATCATATGCATTA
* *
48230744 GCATCGTATTATATGCATTA
1 GCATCGCATCATATGCATTA
48230764 AATACCTTTA
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:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (20 bp):
GCATCGCATCATATGCATTA
Found at i:48239096 original size:89 final size:89
Alignment explanation
Indices: 48238872--48239810 Score: 1190
Period size: 89 Copynumber: 10.5 Consensus size: 89
48238862 GGGGCGAAGG
* *
48238872 AGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGCCTTCC
1 AGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCC
*
48238937 AATACTGGTGGCGAAGCAGATCGAA
66 CATACTGGTGGCGAAGCAGATC-AA
* * * *
48238962 GGAAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATACCAGATCTTGCCTTC
1 AG-AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTC
48239027 CCATACTGGTGGCGAAGCAGATCAA
65 CCATACTGGTGGCGAAGCAGATCAA
* *
48239052 AGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGCCTTCC
1 AGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCC
*
48239117 TATACTGGTGGCGAAGCAGATCGAA
66 CATACTGGTGGCGAAGCAGATC-AA
* * * * *
48239142 GGAAAAAGTAAATTTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGA-AAGTAGATCTTGTCT
1 --AGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAA-CAGATCTTGTCT
* *
48239206 TCCCATACTGGTGGTGAAGCAGATCGA
63 TCCCATACTGGTGGCGAAGCAGATCAA
* * * * *
48239233 AGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACATATCTTGCCTCCC
1 AGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCC
* * **
48239298 CATACTGGTGGTGGAGCAGATTGA
66 CATACTGGTGGCGAAGCAGATCAA
* * *
48239322 AGAAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAAATACCAGATCTTGTC-TC
1 AG-AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTC
* * *
48239386 CCTATACTGGTGGTGGAGTAGATCAA
65 CC-ATACTGGTGGCGAAGCAGATCAA
* * * * *
48239412 AGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAAATCAAAGACAACAGATTTTGTCTCCC
1 AGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCC
* *
48239477 CATACTGGTGGCGAAACAGATCGA
66 CATACTGGTGGCGAAGCAGATCAA
* *
48239501 AGAAAGTAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGTCTTCC
1 AGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCC
* * **
48239566 CATACTCGTGGCGAAACAGATTGA
66 CATACTGGTGGCGAAGCAGATCAA
* * *
48239590 AGAAAGTAGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGATAATAGATCTTGTCTTCC
1 AGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCC
*
48239655 CATACTGGTGGCGAAGTAGATCGAA
66 CATACTGGTGGCGAAGCAGATC-AA
* * *
48239680 GGGAAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGACAACAGATCTTGTC-T
1 -AG-AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTT
* * * *
48239744 CCCTATACTGGTGGGGGAGTAGATCGA
64 CCC-ATACTGGTGGCGAAGCAGATCAA
* * *
48239771 AGAAAACAGACCTTGTTTTCA--T--TGGCGTGAAGTAGATCAA
1 AGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAA
48239811 GCGCAGCAGA
Statistics
Matches: 756, Mismatches: 80, Indels: 31
0.87 0.09 0.04
Matches are distributed among these distances:
85 18 0.02
87 1 0.00
89 410 0.54
90 89 0.12
91 90 0.12
92 148 0.20
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (89 bp):
AGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCC
CATACTGGTGGCGAAGCAGATCAA
Found at i:48239718 original size:449 final size:449
Alignment explanation
Indices: 48238872--48239810 Score: 1365
Period size: 449 Copynumber: 2.1 Consensus size: 449
48238862 GGGGCGAAGG
* ** *
48238872 AGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGCCTTCC
1 AGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAAATAACAGATCTTGCCTCCC
* *
48238937 AATACTGGTGGCGAAGCAGATCGAAGGAAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAG
66 AATACTGGTGGCGAAGCAGATCGAAAGAAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAA
* * * * *
48239002 ATCAGAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAGCAGATCTTG
131 ATCAAAGACAACAGATCTTGCCTCCCCATACTGGTGGCGAAACAGATCAAAGAAAGCAGATCTTG
* * *
48239067 TCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGCCTTCCTATACTGGTGGCGAA
196 TCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCTTCCCATACTCGTGGCGAA
* * *
48239132 GCAGATCGAAGGAAAAAGTAAATTTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAGTAG
261 ACAGATCGAAGG-AAAAGTAAATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAGTAG
*
48239197 ATCTTGTCTTCCCATACTGGTGGTGAAGCAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGG
325 ATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGG
** * * *
48239262 CGTGAAGTAGATCAAAGGTAACATATCTTGCCTCCCCATACTGGTGGTGGAGCAGATTGA
390 CGTGAAGTAGATCAAAGACAACAGATCTTGCCTCCCCATACTGGTGGGGGAGCAGATCGA
* *
48239322 AGAAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAAATACCAGATCTTGTCTCC
1 AG-AAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAAATAACAGATCTTGCCTCC
* * * *
48239387 CTATACTGGTGGTGGAGTAGATC-AAAGAAAA-CAGATCTTGTCTTCATGTACTGGCGTGAAGTA
65 CAATACTGGTGGCGAAGCAGATCGAAAGAAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTA
* * * *
48239450 AATCAAAGACAACAGATTTTGTCTCCCCATACTGGTGGCGAAACAGATCGAAGAAAGTAGATCTT
130 AATCAAAGACAACAGATCTTGCCTCCCCATACTGGTGGCGAAACAGATCAAAGAAAGCAGATCTT
* *
48239515 GTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGTCTTCCCATACTCGTGGCGA
195 GTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCTTCCCATACTCGTGGCGA
* *
48239580 AACAGATTGAA-G-AAAGTAGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGATAA-TA
260 AACAGATCGAAGGAAAAGTAAATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGA-AAGTA
*
48239642 GATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGGGAAAAGCAGATCTTGTCTTCATGTA
324 GATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAA--GAAAA-CAGATCTTGTCTTCATGTA
* * * *
48239707 TTGGCGTGAAGTAGATCAAAGACAACAGATCTTGTCTCCCTATACTGGTGGGGGAGTAGATCGA
386 CTGGCGTGAAGTAGATCAAAGACAACAGATCTTGCCTCCCCATACTGGTGGGGGAGCAGATCGA
* *
48239771 AGAAAACAGACCTTGTTTTCA--T--TGGCGTGAAGTAGATCAA
1 AGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAA
48239811 GCGCAGCAGA
Statistics
Matches: 440, Mismatches: 44, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
444 18 0.04
446 81 0.18
447 2 0.00
448 23 0.05
449 232 0.53
450 9 0.02
451 75 0.17
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (449 bp):
AGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAAATAACAGATCTTGCCTCCC
AATACTGGTGGCGAAGCAGATCGAAAGAAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAA
ATCAAAGACAACAGATCTTGCCTCCCCATACTGGTGGCGAAACAGATCAAAGAAAGCAGATCTTG
TCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCTTCCCATACTCGTGGCGAA
ACAGATCGAAGGAAAAGTAAATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAGTAGA
TCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGC
GTGAAGTAGATCAAAGACAACAGATCTTGCCTCCCCATACTGGTGGGGGAGCAGATCGA
Found at i:48239786 original size:45 final size:45
Alignment explanation
Indices: 48238872--48239786 Score: 593
Period size: 44 Copynumber: 20.4 Consensus size: 45
48238862 GGGGCGAAGG
* * * * *
48238872 AGAAAGCAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAA
1 AGAAAACAGATCTTGTCTCCCTATACTGGTGGTGAAGTAGATCAA
** * * * * *
48238916 AGGTAACAGATCTTGCCTTCCAATACTGGTGGCGAAGCAGATCGAA
1 AGAAAACAGATCTTGTCTCCCTATACTGGTGGTGAAGTAGATC-AA
* * * * * *
48238962 GGAAAAGCAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAG
1 AGAAAA-CAGATCTTGTCTCCCTATACTGGTGGTGAAGTAGATCAA
* * * * *
48239007 AGATACCAGATCTTGCCTTCCC-ATACTGGTGGCGAAGCAGATCAA
1 AGAAAACAGATCTTGTC-TCCCTATACTGGTGGTGAAGTAGATCAA
* * * * * *
48239052 AGAAAGCAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAG
1 AGAAAACAGATCTTGTCTCCCTATACTGGTGGTGAAGTAGATCAA
* * * * *
48239096 AGATAACAGATCTTGCCTTCCTATACTGGTGGCGAAGCAGATCGAA
1 AGAAAACAGATCTTGTCTCCCTATACTGGTGGTGAAGTAGATC-AA
* * * * * *
48239142 GGAAAA-AGTAAATTTTGTCTTCATGTACTGG-CGTGAAGTAGATCAA
1 AGAAAACAG---ATCTTGTCTCCCTATACTGGTGGTGAAGTAGATCAA
** * *
48239188 AGAAAGTAGATCTTGTCTTCCC-ATACTGGTGGTGAAGCAGATCGA
1 AGAAAACAGATCTTGTC-TCCCTATACTGGTGGTGAAGTAGATCAA
* * * *
48239233 AGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAA
1 AGAAAACAGATCTTGTCTCCCTATACTGGTGGTGAAGTAGATCAA
** * * * * * **
48239277 AGGTAACATATCTTGCCTCCCCATACTGGTGGTGGAGCAGATTGA
1 AGAAAACAGATCTTGTCTCCCTATACTGGTGGTGAAGTAGATCAA
* * * *
48239322 AGAAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAA
1 AG-AAAACAGATCTTGTCTCCCTATACTGGTGGTGAAGTAGATCAA
* *
48239367 A-AATACCAGATCTTGTCTCCCTATACTGGTGGTGGAGTAGATCAA
1 AGAA-AACAGATCTTGTCTCCCTATACTGGTGGTGAAGTAGATCAA
* * * * *
48239412 AGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAAATCAA
1 AGAAAACAGATCTTGTCTCCCTATACTGGTGGTGAAGTAGATCAA
* * * * ** *
48239456 AGACAACAGATTTTGTCTCCCCATACTGGTGGCGAAACAGATCGA
1 AGAAAACAGATCTTGTCTCCCTATACTGGTGGTGAAGTAGATCAA
** * * * *
48239501 AGAAAGTAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAA
1 AGAAAACAGATCTTGTCTCCCTATACTGGTGGTGAAGTAGATCAA
** * * ** **
48239545 AGGTAACAGATCTTGTCTTCCC-ATACTCGTGGCGAAACAGATTGA
1 AGAAAACAGATCTTGTC-TCCCTATACTGGTGGTGAAGTAGATCAA
** * * * * *
48239590 AGAAAGTAGATCTTATCTTCATGTACTGG-CGTGAAGTAGATCAA
1 AGAAAACAGATCTTGTCTCCCTATACTGGTGGTGAAGTAGATCAA
* * *
48239634 AGATAATAGATCTTGTCTTCCC-ATACTGGTGGCGAAGTAGATCGAA
1 AGAAAACAGATCTTGTC-TCCCTATACTGGTGGTGAAGTAGATC-AA
* * * * * *
48239680 GGGAAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCAA
1 -AGAAAA-CAGATCTTGTCTCCCTATACTGGTGGTGAAGTAGATCAA
* * * *
48239726 AGACAACAGATCTTGTCTCCCTATACTGGTGGGGGAGTAGATCGA
1 AGAAAACAGATCTTGTCTCCCTATACTGGTGGTGAAGTAGATCAA
*
48239771 AGAAAACAGACCTTGT
1 AGAAAACAGATCTTGT
48239787 TTTCATTGGC
Statistics
Matches: 641, Mismatches: 199, Indels: 61
0.71 0.22 0.07
Matches are distributed among these distances:
43 2 0.00
44 257 0.40
45 252 0.39
46 51 0.08
47 48 0.07
48 31 0.05
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.26
Consensus pattern (45 bp):
AGAAAACAGATCTTGTCTCCCTATACTGGTGGTGAAGTAGATCAA
Found at i:48240757 original size:15 final size:15
Alignment explanation
Indices: 48240739--48240768 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
48240729 CTATTTTGTT
*
48240739 TTATTTTGTTTTATC
1 TTATTTTCTTTTATC
48240754 TTATTTTCTTTTATC
1 TTATTTTCTTTTATC
48240769 AAAAACAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.03, T:0.73
Consensus pattern (15 bp):
TTATTTTCTTTTATC
Found at i:48267982 original size:14 final size:14
Alignment explanation
Indices: 48267963--48268002 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
48267953 TTGATTGGCA
48267963 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
48267977 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
48267991 GGAAAATGTTTT
1 GTAAAATGTTTT
48268003 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:48268015 original size:34 final size:35
Alignment explanation
Indices: 48267971--48268037 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
48267961 CAGTAAAATG
* *
48267971 TTTTCCGTAAAATGA-TTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
*
48268005 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTT
48268038 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 14 0.48
35 15 0.52
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
Found at i:48268024 original size:20 final size:20
Alignment explanation
Indices: 48267986--48268025 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
48267976 CGTAAAATGA
**
48267986 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGACTTACT
*
48268006 TTTCTGTAAAATGACTTACT
1 TTTCTGGAAAATGACTTACT
48268026 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:48269406 original size:27 final size:27
Alignment explanation
Indices: 48269376--48269443 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
48269366 AATAATCAAT
*
48269376 TCAATATCCAACAATGTTAAAACATA-A
1 TCAATATCCAACAAT-TCAAAACATATA
* *
48269403 TCAATATCTAACAAATTCAAGACATATA
1 TCAATATCCAAC-AATTCAAAACATATA
*
48269431 TCAAAATCCAACA
1 TCAATATCCAACA
48269444 GTCTAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
27 20 0.59
28 14 0.41
ACGTcount: A:0.51, C:0.21, G:0.03, T:0.25
Consensus pattern (27 bp):
TCAATATCCAACAATTCAAAACATATA
Found at i:48274232 original size:42 final size:42
Alignment explanation
Indices: 48274173--48274254 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
48274163 GGTTCGATTT
* *
48274173 CCGGCTGGTGCATACCTGGAGCTTGGATCTTTTATTCAATTC
1 CCGGCTGGTGCATACCTGGAGCCTGGATCCTTTATTCAATTC
48274215 CCGGCTGGTGCATACCTGGAGCCTGGATCCTTTATTCAAT
1 CCGGCTGGTGCATACCTGGAGCCTGGATCCTTTATTCAAT
48274255 CTGATTTCAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (42 bp):
CCGGCTGGTGCATACCTGGAGCCTGGATCCTTTATTCAATTC
Found at i:48277544 original size:7 final size:7
Alignment explanation
Indices: 48277532--48277556 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
48277522 TCTGCAATTG
48277532 GATCTCC
1 GATCTCC
48277539 GATCTCC
1 GATCTCC
48277546 GATCTCC
1 GATCTCC
48277553 GATC
1 GATC
48277557 ATCAATCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.40, G:0.16, T:0.28
Consensus pattern (7 bp):
GATCTCC
Found at i:48284047 original size:17 final size:17
Alignment explanation
Indices: 48284022--48284056 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
48284012 ATAAGTTAAT
48284022 TTAAATAAATAAATTTC
1 TTAAATAAATAAATTTC
* *
48284039 TTAAGTAAATAATTTTC
1 TTAAATAAATAAATTTC
48284056 T
1 T
48284057 GAACCCGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (17 bp):
TTAAATAAATAAATTTC
Found at i:48295538 original size:76 final size:76
Alignment explanation
Indices: 48295411--48295557 Score: 215
Period size: 76 Copynumber: 1.9 Consensus size: 76
48295401 CTACACTCAG
* * * * *
48295411 GTTTGATACTTTTGAAAACTTCAGTTTCTCTCTCGATGTCCATAGTTAATTCTCCCCGTCTTACG
1 GTTTGACACATTTGAAAACTTCAGTTTCTCTCTCGATATCCATAGTCAATTCTCCCCGTCCTACG
48295476 TCTATGATCTA
66 TCTATGATCTA
* *
48295487 GTTTGACACATTTGAAAACTTTAGTTTCTC-CTTCGATATCCATAGTCAATTCTCGCCGTCCTAC
1 GTTTGACACATTTGAAAACTTCAGTTTCTCTC-TCGATATCCATAGTCAATTCTCCCCGTCCTAC
48295551 GTCTATG
65 GTCTATG
48295558 GTGGTCCGAG
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
75 1 0.02
76 62 0.98
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.40
Consensus pattern (76 bp):
GTTTGACACATTTGAAAACTTCAGTTTCTCTCTCGATATCCATAGTCAATTCTCCCCGTCCTACG
TCTATGATCTA
Found at i:48300171 original size:47 final size:48
Alignment explanation
Indices: 48300112--48300297 Score: 223
Period size: 47 Copynumber: 3.8 Consensus size: 48
48300102 TCACATATTG
*
48300112 GTGCCGATGCCATGTCCTAGACATGGTCTTACACTGGCACTCATC-TC
1 GTGCCGATGCCATGTCCTAGACATGGTCTTACACTGGCACTCCTCGTC
* * * * *
48300159 GAGCCGATGCCATGTCCTAGACATGGTCTTATACTGACTCTCCTCTTCC
1 GTGCCGATGCCATGTCCTAGACATGGTCTTACACTGGCACTCCTCGT-C
* * * *
48300208 GTGCCGATGCCATGTCCCAGACATGGTCATACACTAGCAGTCCTCGGTC
1 GTGCCGATGCCATGTCCTAGACATGGTCTTACACTGGCACTCCTC-GTC
*
48300257 TGTGCCGATGCCATGT-CTCAGACATGGTCTTACATTGGCAC
1 -GTGCCGATGCCATGTCCT-AGACATGGTCTTACACTGGCAC
48300298 ACTCACTGCC
Statistics
Matches: 115, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
47 40 0.35
48 1 0.01
49 40 0.35
50 34 0.30
ACGTcount: A:0.19, C:0.31, G:0.22, T:0.27
Consensus pattern (48 bp):
GTGCCGATGCCATGTCCTAGACATGGTCTTACACTGGCACTCCTCGTC
Found at i:48305586 original size:45 final size:45
Alignment explanation
Indices: 48305517--48305675 Score: 121
Period size: 45 Copynumber: 3.6 Consensus size: 45
48305507 TACACGGTGG
* * * * *
48305517 ATCAGCACACAGC-ACCACCCTTATAGTCAATAGTACTC-AGTGAA
1 ATCAACACATAGCAACCACCTTTATAATCAAT-GTACTCGGGTGAA
*
48305561 ATCAACACATAGCAACCACCTTTATACTCAATGATAC-CGGGTGAA
1 ATCAACACATAGCAACCACCTTTATAATCAATG-TACTCGGGTGAA
* * * * * *
48305606 TTCAGCACATAGCAATCA-CTTATATAACCATTGGTA-TCTGGTGAA
1 ATCAACACATAGCAACCACCTT-TATAATCAAT-GTACTCGGGTGAA
* *
48305651 ATCAACACATAGCAATCACTTTTAT
1 ATCAACACATAGCAACCACCTTTAT
48305676 TTTCATTAAT
Statistics
Matches: 93, Mismatches: 15, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
44 16 0.17
45 74 0.80
46 3 0.03
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (45 bp):
ATCAACACATAGCAACCACCTTTATAATCAATGTACTCGGGTGAA
Found at i:48305699 original size:45 final size:45
Alignment explanation
Indices: 48305560--48305706 Score: 136
Period size: 45 Copynumber: 3.3 Consensus size: 45
48305550 TACTCAGTGA
* * * *
48305560 AATCAACACATAGCAACCACCTTTATACTCAATGATA-CCGG-GTG
1 AATCAACACATAGCAATCACTTTTATAATCATTGATATCCGGTG-G
* * * * * *
48305604 AATTCAGCACATAGCAATCACTTATATAACCATTGGTATCTGGTGA
1 AA-TCAACACATAGCAATCACTTTTATAATCATTGATATCCGGTGG
** *
48305650 AATCAACACATAGCAATCACTTTTATTTTCATTAATATCCGGTGG
1 AATCAACACATAGCAATCACTTTTATAATCATTGATATCCGGTGG
*
48305695 AATCAGCACATA
1 AATCAACACATA
48305707 ACATCCACCT
Statistics
Matches: 80, Mismatches: 20, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
44 2 0.03
45 72 0.90
46 5 0.06
47 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (45 bp):
AATCAACACATAGCAATCACTTTTATAATCATTGATATCCGGTGG
Found at i:48305720 original size:90 final size:90
Alignment explanation
Indices: 48305556--48305720 Score: 210
Period size: 90 Copynumber: 1.8 Consensus size: 90
48305546 ATAGTACTCA
* *
48305556 GTGAAATCAACACATAGCAACCACCTTTATACTCAATGATACCGGGTGAATTCAGCACATAGCAA
1 GTGAAATCAACACATAGCAACCACCTTTATACTCAATAATACCGGGTGAATTCAGCACATAACAA
*
48305621 TCACTTATATAACCATTGGTATCTG
66 TCACCTATATAACCATTGGTATCTG
* * ** *
48305646 GTGAAATCAACACATAGCAATCACTTTTATTTTCATTAATATCC-GGTGGAA-TCAGCACATAAC
1 GTGAAATCAACACATAGCAACCACCTTTATACTCAATAATA-CCGGGT-GAATTCAGCACATAAC
48305709 -ATCCACCTATAT
64 AAT-CACCTATAT
48305721 TTCCAACGAT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
89 2 0.03
90 57 0.89
91 5 0.08
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (90 bp):
GTGAAATCAACACATAGCAACCACCTTTATACTCAATAATACCGGGTGAATTCAGCACATAACAA
TCACCTATATAACCATTGGTATCTG
Found at i:48307435 original size:23 final size:23
Alignment explanation
Indices: 48307409--48307453 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
48307399 TTGAAGATTC
48307409 GTAATCTAAAAAGATTTGATTTT
1 GTAATCTAAAAAGATTTGATTTT
*
48307432 GTAATCTTAAAAGATTTGATTT
1 GTAATCTAAAAAGATTTGATTT
48307454 GTAGATTGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.44
Consensus pattern (23 bp):
GTAATCTAAAAAGATTTGATTTT
Found at i:48307629 original size:16 final size:16
Alignment explanation
Indices: 48307605--48307639 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
48307595 TCAAACTCTT
*
48307605 TGTGCTTTTTCTTTTC
1 TGTGCTTTTTCTATTC
*
48307621 TGTGGTTTTTCTATTC
1 TGTGCTTTTTCTATTC
48307637 TGT
1 TGT
48307640 TGAACATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.03, C:0.14, G:0.17, T:0.66
Consensus pattern (16 bp):
TGTGCTTTTTCTATTC
Found at i:48309377 original size:90 final size:87
Alignment explanation
Indices: 48309270--48309494 Score: 317
Period size: 90 Copynumber: 2.5 Consensus size: 87
48309260 TTAAGGGTGC
* *
48309270 AAAA-GCCCTCAAACTTTTTTAAAAAAAGCAATTAAGCCCCTACTTTTTTTTGCACTCATTTGGG
1 AAAAGGCCCTCAAAC-TTTTTAAAAAAA-AAATTAAGCCCCTACTTTTTTTTGCACTCAATTGGG
48309334 TACTTAAACTTTCAAAATGCATCA
64 TACTTAAACTTTCAAAATGCATCA
*
48309358 AAAAGGCCCTCAAATCTTTTCAAAAAAAAAATTAAGCCCCTACTATTTTTTTTGCACTCAATTGG
1 AAAAGGCCCTCAAA-CTTTTTAAAAAAAAAATTAAGCCCCTAC--TTTTTTTTGCACTCAATTGG
* *
48309423 GTACTTGAACTTTTAAAATGCATCA
63 GTACTTAAACTTTCAAAATGCATCA
* * *
48309448 AAAAGACTCTCAAACTTTTTAAAAAAAATAATTAAGCCCCTTCTTTT
1 AAAAGGCCCTCAAACTTTTTAAAAAAAA-AATTAAGCCCCTACTTTT
48309495 ATTAAAAATT
Statistics
Matches: 123, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
88 22 0.18
89 33 0.27
90 68 0.55
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.34
Consensus pattern (87 bp):
AAAAGGCCCTCAAACTTTTTAAAAAAAAAATTAAGCCCCTACTTTTTTTTGCACTCAATTGGGTA
CTTAAACTTTCAAAATGCATCA
Found at i:48309595 original size:28 final size:27
Alignment explanation
Indices: 48309557--48309705 Score: 131
Period size: 28 Copynumber: 5.4 Consensus size: 27
48309547 ATTTTAATAT
*
48309557 AAAAATT-TAAAATATTAAAAATTAGA
1 AAAAATTATAAAATATTAAAAATTATA
** *
48309583 AAAAATATATAAAATCGTAAAAAATATA
1 AAAAAT-TATAAAATATTAAAAATTATA
* *
48309611 TAAAAATTGTAAAATTTTATAAAATTATA
1 -AAAAATTATAAAATATTA-AAAATTATA
* *
48309640 AAATATTATAAAATATGTAGAAA-TATA
1 AAAAATTATAAAATAT-TAAAAATTATA
* * *
48309667 AAAAATTATAAAATTTTATAAAGTTGTA
1 AAAAATTATAAAATATTA-AAAATTATA
48309695 AGAAAATTATA
1 A-AAAATTATA
48309706 CAAAATGTAA
Statistics
Matches: 98, Mismatches: 17, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
26 8 0.08
27 21 0.21
28 44 0.45
29 25 0.26
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.34
Consensus pattern (27 bp):
AAAAATTATAAAATATTAAAAATTATA
Found at i:48309596 original size:10 final size:10
Alignment explanation
Indices: 48309553--48309679 Score: 66
Period size: 9 Copynumber: 13.8 Consensus size: 10
48309543 TTAAATTTTA
48309553 ATATAAAAAT
1 ATATAAAAAT
48309563 -T-T-AAAAT
1 ATATAAAAAT
48309570 AT-TAAAAAT
1 ATATAAAAAT
*
48309579 -TAGAAAAA-
1 ATATAAAAAT
48309587 ATATATAAAAT
1 ATATA-AAAAT
*
48309598 CGTA-AAAAAT
1 -ATATAAAAAT
48309608 ATATAAAAAT
1 ATATAAAAAT
* *
48309618 -TGTAAAATT
1 ATATAAAAAT
*
48309627 TTAT-AAAAT
1 ATATAAAAAT
48309636 -TAT-AAAAT
1 ATATAAAAAT
48309644 AT-TATAAAAT
1 ATATA-AAAAT
* *
48309654 ATGTAGAAAT
1 ATATAAAAAT
48309664 ATA-AAAAAT
1 ATATAAAAAT
48309673 -TATAAAA
1 ATATAAAA
48309680 TTTTATAAAG
Statistics
Matches: 92, Mismatches: 11, Indels: 29
0.70 0.08 0.22
Matches are distributed among these distances:
7 5 0.05
8 15 0.16
9 37 0.40
10 30 0.33
11 3 0.03
12 2 0.02
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (10 bp):
ATATAAAAAT
Found at i:48309604 original size:18 final size:18
Alignment explanation
Indices: 48309552--48309726 Score: 103
Period size: 19 Copynumber: 9.6 Consensus size: 18
48309542 ATTAAATTTT
48309552 AATATA-AAAATT-T-AA
1 AATATATAAAATTGTAAA
*
48309567 AATAT-TAAAAATTAGAAAA
1 AATATAT-AAAATT-GTAAA
*
48309586 AATATATAAAATCGTAAAA
1 AATATATAAAATTGT-AAA
48309605 AATATATAAAAATTGTAAA
1 AATATAT-AAAATTGTAAA
* * *
48309624 ATTTTATAAAATTAT-AA
1 AATATATAAAATTGTAAA
*
48309641 AATATTATAAAATATGTAGA
1 AATA-TATAAAAT-TGTAAA
* *
48309661 AATATAAAAAATTATAAA
1 AATATATAAAATTGTAAA
* * *
48309679 ATTTTATAAAGTTGTAAGA
1 AATATATAAAATTGTAA-A
*
48309698 AA-ATTATACAAAATGTAAA
1 AATA-TATA-AAATTGTAAA
48309717 GAA-ATATAAA
1 -AATATATAAA
48309727 TTTCATAAAA
Statistics
Matches: 122, Mismatches: 23, Indels: 27
0.71 0.13 0.16
Matches are distributed among these distances:
15 5 0.04
16 6 0.05
17 4 0.03
18 34 0.28
19 50 0.41
20 23 0.19
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.32
Consensus pattern (18 bp):
AATATATAAAATTGTAAA
Found at i:48309624 original size:56 final size:55
Alignment explanation
Indices: 48309553--48309724 Score: 174
Period size: 55 Copynumber: 3.1 Consensus size: 55
48309543 TTAAATTTTA
*
48309553 ATATAAAAATTTAAAATATTA-AAAATTAGAAAAAATATATAAAATCGTAAAAAAT
1 ATATAAAAATTTAAAATTTTATAAAATTAGAAAAAATATATAAAAT-GTAAAAAAT
* * *
48309608 ATATAAAAATTGTAAAATTTTATAAAATTATAAAATAT-TATAAAATATGT-AGAAAT
1 ATATAAAAATT-TAAAATTTTATAAAATTAGAAAAAATATAT-AAA-ATGTAAAAAAT
* *
48309664 ATA-AAAAATTATAAAATTTTATAAAGTT-GTAAGAAAATTATACAAAATGTAAAGAAAT
1 ATATAAAAATT-TAAAATTTTATAAAATTAG-AA-AAAA-TATATAAAATGTAAA-AAAT
48309722 ATA
1 ATA
48309725 AATTTCATAA
Statistics
Matches: 97, Mismatches: 10, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
55 36 0.37
56 27 0.28
57 23 0.24
58 11 0.11
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.33
Consensus pattern (55 bp):
ATATAAAAATTTAAAATTTTATAAAATTAGAAAAAATATATAAAATGTAAAAAAT
Found at i:48309638 original size:8 final size:8
Alignment explanation
Indices: 48309584--48309681 Score: 52
Period size: 10 Copynumber: 10.8 Consensus size: 8
48309574 AAAATTAGAA
48309584 AAAATATAT
1 AAAAT-TAT
*
48309593 AAAATCGTAA
1 AAAAT--TAT
48309603 AAAATATAT
1 AAAAT-TAT
*
48309612 AAAAATTGT
1 -AAAATTAT
48309621 AAAATTTTAT
1 AAAA--TTAT
48309631 AAAATTAT
1 AAAATTAT
48309639 AAAATATTAT
1 -AAA-ATTAT
*
48309649 AAAATATGT
1 AAAAT-TAT
*
48309658 AGAAATATAA
1 A-AAAT-TAT
48309668 AAAATTAT
1 AAAATTAT
48309676 AAAATT
1 AAAATT
48309682 TTATAAAGTT
Statistics
Matches: 71, Mismatches: 10, Indels: 17
0.72 0.10 0.17
Matches are distributed among these distances:
8 18 0.25
9 22 0.31
10 31 0.44
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (8 bp):
AAAATTAT
Found at i:48309650 original size:37 final size:35
Alignment explanation
Indices: 48309552--48309680 Score: 122
Period size: 37 Copynumber: 3.6 Consensus size: 35
48309542 ATTAAATTTT
*
48309552 AATATA-AAAATT-TAAAATAT-TAAAAATTAGAAAA
1 AATATATAAAATTATAAAATATATAAAAATT-G-TAA
*
48309586 AATATATAAAATCGTAAAAAATATATAAAAATTGTAA
1 AATATATAAAAT--TATAAAATATATAAAAATTGTAA
*
48309623 AATTTTATAAAATTATAAAATAT-TATAAAATATGTAGA
1 AA-TATATAAAATTATAAAATATATA-AAAAT-TGTA-A
*
48309661 AATATAAAAAATTATAAAAT
1 AATATATAAAATTATAAAAT
48309681 TTTATAAAGT
Statistics
Matches: 80, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
34 6 0.08
35 7 0.09
36 14 0.17
37 25 0.31
38 20 0.25
39 8 0.10
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.33
Consensus pattern (35 bp):
AATATATAAAATTATAAAATATATAAAAATTGTAA
Found at i:48310021 original size:36 final size:36
Alignment explanation
Indices: 48309955--48310023 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
48309945 AATTATAATC
** *
48309955 TTTAATAAATTTTTAATTTTTATATTTTTATTAAAA
1 TTTAATAAATTTTTAAAATTTATATATTTATTAAAA
48309991 TTTAATAAATTTTCTAAAATTTAT-TATTTATTA
1 TTTAATAAATTTT-TAAAATTTATATATTTATTA
48310024 TTTATTTTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 21 0.72
37 8 0.28
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (36 bp):
TTTAATAAATTTTTAAAATTTATATATTTATTAAAA
Found at i:48310149 original size:88 final size:88
Alignment explanation
Indices: 48310050--48310268 Score: 271
Period size: 88 Copynumber: 2.5 Consensus size: 88
48310040 TAATAAGAGT
48310050 AGGGGCTTAATTGTTTTTTTGAAAAATTTTAAGGGTCTTTTTGATGCATTTTAAAAGTTCAAGTA
1 AGGGGCTTAATTGTTTTTTTGAAAAATTTTAAGGGT-TTTTTGATGCATTTTAAAAGTTCAAGTA
48310115 CCCAATTGAATG-AAAAAAAAGAC
65 CCCAATTGAATGAAAAAAAAAGAC
* * * * *
48310138 AGGGGCTTAATTGCTTTTTTTGAAGAAGTTTGAGGGTTTTTTTATGCATTTTGAAAGTTCAAGTA
1 AGGGGCTTAATTG-TTTTTTTGAAAAATTTTAAGGGTTTTTTGATGCATTTTAAAAGTTCAAGTA
* * *
48310203 CTCAATTGAGTGCAAAAAAAAAGAG
65 CCCAATTGAATG-AAAAAAAAAGAC
* * * * *
48310228 AGAGACTTAATTATTTCTTTTGAAAAGTTTGAA-GGTTTTTT
1 AGGGGCTTAATTGTTT-TTTTGAAAAATTTTAAGGGTTTTTT
48310269 ATGGCCTTAA
Statistics
Matches: 111, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
88 49 0.44
89 31 0.28
90 31 0.28
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (88 bp):
AGGGGCTTAATTGTTTTTTTGAAAAATTTTAAGGGTTTTTTGATGCATTTTAAAAGTTCAAGTAC
CCAATTGAATGAAAAAAAAAGAC
Found at i:48312299 original size:18 final size:18
Alignment explanation
Indices: 48312276--48312313 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
48312266 AGATCAGCAG
48312276 TGGTTTAACACCAGTCGA
1 TGGTTTAACACCAGTCGA
48312294 TGGTTTAACACCAGTCGA
1 TGGTTTAACACCAGTCGA
48312312 TG
1 TG
48312314 TTCCGGCAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (18 bp):
TGGTTTAACACCAGTCGA
Found at i:48315782 original size:2 final size:2
Alignment explanation
Indices: 48315735--48315767 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
48315725 TTATCACTTT
48315735 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48315768 AAACTATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48315783 original size:8 final size:8
Alignment explanation
Indices: 48315736--48315786 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
48315726 TATCACTTTT
*
48315736 ATATATAT
1 ATATATAA
*
48315744 ATATATAT
1 ATATATAA
*
48315752 ATATATAT
1 ATATATAA
48315760 ATATTATAA
1 ATA-TATAA
48315769 A-ACTATAA
1 ATA-TATAA
48315777 ATATATAA
1 ATATATAA
48315785 AT
1 AT
48315787 TATTTAGATT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
8 33 0.85
9 6 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (8 bp):
ATATATAA
Found at i:48316854 original size:31 final size:29
Alignment explanation
Indices: 48316790--48316858 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 29
48316780 ACGATAACGT
** *
48316790 AAGTGACTAAAACGTAACGTTTCAAACAT
1 AAGTGACTAAAACGTAACGAGTCAAACAA
*
48316819 AAGTGACTAAAATGTAACCTGAGTCAAACAA
1 AAGTGACTAAAACGTAA-C-GAGTCAAACAA
48316850 AAGTGACTA
1 AAGTGACTA
48316859 TTTTGGTAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.47
30 1 0.03
31 17 0.50
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (29 bp):
AAGTGACTAAAACGTAACGAGTCAAACAA
Found at i:48318255 original size:15 final size:16
Alignment explanation
Indices: 48318235--48318270 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
48318225 TTAAGTTTTT
*
48318235 TTTAAAA-AAATTAAA
1 TTTAAAACAAATCAAA
48318250 TTTAAAACAAATCAAA
1 TTTAAAACAAATCAAA
48318266 TTTAA
1 TTTAA
48318271 GTTTTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (16 bp):
TTTAAAACAAATCAAA
Found at i:48318292 original size:14 final size:14
Alignment explanation
Indices: 48318273--48318306 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
48318263 AAATTTAAGT
48318273 TTTTCAAATT-TTAA
1 TTTTCAAATTATT-A
48318287 TTTTCAAATTATTA
1 TTTTCAAATTATTA
48318301 TTTTCA
1 TTTTCA
48318307 TACACTTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.89
15 2 0.11
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTTCAAATTATTA
Found at i:48324469 original size:6 final size:6
Alignment explanation
Indices: 48324458--48324486 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
48324448 CCTTTACAGT
48324458 AAGTTA AAGTTA AAGTTA AAGTTA AAGTT
1 AAGTTA AAGTTA AAGTTA AAGTTA AAGTT
48324487 TAATACAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.34
Consensus pattern (6 bp):
AAGTTA
Found at i:48328574 original size:15 final size:15
Alignment explanation
Indices: 48328554--48328585 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
48328544 CTTAGACAAG
48328554 TGACCACACCAATTT
1 TGACCACACCAATTT
48328569 TGACCACACCAATTT
1 TGACCACACCAATTT
48328584 TG
1 TG
48328586 TTACCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.31, G:0.09, T:0.28
Consensus pattern (15 bp):
TGACCACACCAATTT
Found at i:48337931 original size:25 final size:24
Alignment explanation
Indices: 48337895--48337951 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
48337885 AACTCTTCAA
*
48337895 AGCTACCC-ATTATTGGCTCACATG
1 AGCTTCCCGATTA-TGGCTCACATG
**
48337919 AGCTTCCCGATTATGGCTCTTATG
1 AGCTTCCCGATTATGGCTCACATG
48337943 AGCTTCCCG
1 AGCTTCCCG
48337952 TAGTTGTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.32
Consensus pattern (24 bp):
AGCTTCCCGATTATGGCTCACATG
Found at i:48347078 original size:9 final size:9
Alignment explanation
Indices: 48347051--48347087 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
48347041 TGAGTTTTTG
48347051 AATTCGAAT
1 AATTCGAAT
* *
48347060 AACTCAAAT
1 AATTCGAAT
48347069 AATTCGAAT
1 AATTCGAAT
48347078 AATTCGAAT
1 AATTCGAAT
48347087 A
1 A
48347088 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:48355752 original size:49 final size:50
Alignment explanation
Indices: 48355677--48355774 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 50
48355667 ACAATATGAA
**
48355677 CATATTGAAAGATAGCAAATAAGCTTTAGCACTAGTGAGTGAAATCACAG
1 CATATTGAAAGATAGCAAATAAGCTTTAGCACTACCGAGTGAAATCACAG
48355727 CATATTGAAAGAT-GCAAATAAGCTTTAGCACTACCGAGTGAAATCACA
1 CATATTGAAAGATAGCAAATAAGCTTTAGCACTACCGAGTGAAATCACA
48355775 TGCCTTGTGC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 33 0.72
50 13 0.28
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.23
Consensus pattern (50 bp):
CATATTGAAAGATAGCAAATAAGCTTTAGCACTACCGAGTGAAATCACAG
Found at i:48366575 original size:44 final size:43
Alignment explanation
Indices: 48366524--48366639 Score: 139
Period size: 44 Copynumber: 2.7 Consensus size: 43
48366514 ATGAATTATT
48366524 GTGTAAGACCACGTCTGGGATGTTGGCATCGAT-TTGAGATTTAC
1 GTGTAAGACCACGTCTGGGATGTTGGCATCGATGTT-AGA-TTAC
* * *
48366568 GTGTAAGACC-CTGTTTGGGACAG-TGGCATCGATGTTTGATTAC
1 GTGTAAGACCAC-GTCTGGGA-TGTTGGCATCGATGTTAGATTAC
*
48366611 ATGTAAGACCACGTCTGGGATGTTGGCAT
1 GTGTAAGACCACGTCTGGGATGTTGGCAT
48366640 TGTACGAGCT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
42 1 0.02
43 27 0.44
44 30 0.49
45 3 0.05
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.31
Consensus pattern (43 bp):
GTGTAAGACCACGTCTGGGATGTTGGCATCGATGTTAGATTAC
Found at i:48368538 original size:16 final size:17
Alignment explanation
Indices: 48368513--48368545 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
48368503 TTTTTTATGG
48368513 TTTTTAAT-AAATTTAT
1 TTTTTAATAAAATTTAT
*
48368529 TTTTTTATAAAATTTAT
1 TTTTTAATAAAATTTAT
48368546 AAAAAAATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTTAATAAAATTTAT
Found at i:48383065 original size:30 final size:30
Alignment explanation
Indices: 48383031--48383091 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
48383021 GGGGTTATTT
48383031 TAGTTTCCTTATTAGGAACTCTATTCAATA
1 TAGTTTCCTTATTAGGAACTCTATTCAATA
48383061 TAGTTTCCTTATTAGGAACTCTATTCAATA
1 TAGTTTCCTTATTAGGAACTCTATTCAATA
48383091 T
1 T
48383092 GTGACAAGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (30 bp):
TAGTTTCCTTATTAGGAACTCTATTCAATA
Found at i:48391470 original size:3 final size:3
Alignment explanation
Indices: 48391444--48391506 Score: 62
Period size: 3 Copynumber: 21.3 Consensus size: 3
48391434 GTTTTTTAGT
*
48391444 TTA TT- TTA TTA GTA TTGA -TA TTA TTA TT- TTCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TT-A TTA TTA TTA TTA
48391488 TTA -TA TTA TATA TTA TTA T
1 TTA TTA TTA T-TA TTA TTA T
48391507 ACCTATATAT
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
2 7 0.14
3 38 0.75
4 6 0.12
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:48392083 original size:12 final size:12
Alignment explanation
Indices: 48392064--48392101 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
48392054 CATTGATTTA
48392064 TTTTTATTT-TT
1 TTTTTATTTATT
48392075 TTGTTTATTTATT
1 TT-TTTATTTATT
48392088 TTTTTATGTTATT
1 TTTTTAT-TTATT
48392101 T
1 T
48392102 CTATACAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 12 0.50
13 10 0.42
ACGTcount: A:0.13, C:0.00, G:0.05, T:0.82
Consensus pattern (12 bp):
TTTTTATTTATT
Found at i:48392092 original size:17 final size:19
Alignment explanation
Indices: 48392060--48392101 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
48392050 ATGTCATTGA
*
48392060 TTTATTTTTATTTTTT-TG
1 TTTATTTATATTTTTTATG
48392078 TTTATTTAT-TTTTTTATG
1 TTTATTTATATTTTTTATG
48392096 -TTATTT
1 TTTATTT
48392102 CTATACAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (19 bp):
TTTATTTATATTTTTTATG
Found at i:48392097 original size:18 final size:18
Alignment explanation
Indices: 48392060--48392101 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
48392050 ATGTCATTGA
*
48392060 TTTATTTTTATTTTTTTG
1 TTTATTTTTATTTTTATG
48392078 TTTATTTATT-TTTTTATG
1 TTTATTT-TTATTTTTATG
48392096 -TTATTT
1 TTTATTT
48392102 CTATACAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 6 0.27
18 14 0.64
19 2 0.09
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (18 bp):
TTTATTTTTATTTTTATG
Found at i:48398212 original size:34 final size:34
Alignment explanation
Indices: 48398169--48398242 Score: 139
Period size: 34 Copynumber: 2.2 Consensus size: 34
48398159 TTTTTTAGTT
*
48398169 TTTGACTTAGTCCCTATTTGTTTCTAAAACATAA
1 TTTGGCTTAGTCCCTATTTGTTTCTAAAACATAA
48398203 TTTGGCTTAGTCCCTATTTGTTTCTAAAACATAA
1 TTTGGCTTAGTCCCTATTTGTTTCTAAAACATAA
48398237 TTTGGC
1 TTTGGC
48398243 CCTCGAGGGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.45
Consensus pattern (34 bp):
TTTGGCTTAGTCCCTATTTGTTTCTAAAACATAA
Found at i:48401947 original size:17 final size:17
Alignment explanation
Indices: 48401908--48401950 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
48401898 ATATAAATGA
48401908 ATAGAAATGGTGAAAAT
1 ATAGAAATGGTGAAAAT
*
48401925 AGAGAAATGG-GAAACAT
1 ATAGAAATGGTGAAA-AT
*
48401942 TTAGAAATG
1 ATAGAAATG
48401951 ATTATTGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.51, C:0.02, G:0.26, T:0.21
Consensus pattern (17 bp):
ATAGAAATGGTGAAAAT
Found at i:48402217 original size:34 final size:34
Alignment explanation
Indices: 48402179--48402278 Score: 95
Period size: 34 Copynumber: 3.1 Consensus size: 34
48402169 AGTCGTCATG
48402179 ATTTTAACAAAACTAGAACTGAGTTGAGAAGATT
1 ATTTTAACAAAACTAGAACTGAGTTGAGAAGATT
*** * * *
48402213 ATTTTATGGAAA--A-AA-T-A-TTAAGATGTTT
1 ATTTTAACAAAACTAGAACTGAGTTGAGAAGATT
*
48402241 ATTTTGACAAAACTAGAACTGAGTTGAGAAGATT
1 ATTTTAACAAAACTAGAACTGAGTTGAGAAGATT
48402275 ATTT
1 ATTT
48402279 AATGGAAAAA
Statistics
Matches: 47, Mismatches: 13, Indels: 12
0.65 0.18 0.17
Matches are distributed among these distances:
28 16 0.34
29 1 0.02
30 2 0.04
31 4 0.09
32 2 0.04
33 1 0.02
34 21 0.45
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (34 bp):
ATTTTAACAAAACTAGAACTGAGTTGAGAAGATT
Found at i:48402276 original size:62 final size:61
Alignment explanation
Indices: 48402179--48402307 Score: 222
Period size: 62 Copynumber: 2.1 Consensus size: 61
48402169 AGTCGTCATG
* *
48402179 ATTTTAACAAAACTAGAACTGAGTTGAGAAGATTATTTTATGGAAAAAATATTAAGATGTTT
1 ATTTTGACAAAACTAGAACTGAGTTGAGAAGATTATTTAATGG-AAAAATATTAAGATGTTT
48402241 ATTTTGACAAAACTAGAACTGAGTTGAGAAGATTATTTAATGGAAAAATATTAAGATGTTT
1 ATTTTGACAAAACTAGAACTGAGTTGAGAAGATTATTTAATGGAAAAATATTAAGATGTTT
*
48402302 GTTTTG
1 ATTTTG
48402308 GGAAATAGAA
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
61 23 0.36
62 41 0.64
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.36
Consensus pattern (61 bp):
ATTTTGACAAAACTAGAACTGAGTTGAGAAGATTATTTAATGGAAAAATATTAAGATGTTT
Found at i:48411954 original size:13 final size:13
Alignment explanation
Indices: 48411936--48411962 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
48411926 ATCATGGAAA
48411936 ATCATCTCCAAGT
1 ATCATCTCCAAGT
48411949 ATCATCTCCAAGT
1 ATCATCTCCAAGT
48411962 A
1 A
48411963 GAGTTTTATT
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:0.33, C:0.30, G:0.07, T:0.30
Consensus pattern (13 bp):
ATCATCTCCAAGT
Found at i:48414713 original size:19 final size:18
Alignment explanation
Indices: 48414684--48414719 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
48414674 GGTTTCGAAG
*
48414684 TTGTTAAATTTGAAGTTC
1 TTGTTAAATTTAAAGTTC
48414702 TTGTTGAAATTTAAAGTT
1 TTGTT-AAATTTAAAGTT
48414720 GTATATAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.50
Consensus pattern (18 bp):
TTGTTAAATTTAAAGTTC
Found at i:48415893 original size:22 final size:22
Alignment explanation
Indices: 48415866--48415916 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
48415856 CAACAAGAAA
48415866 CAAAGAAACTCATAATAATCTC
1 CAAAGAAACTCATAATAATCTC
48415888 CAAAGAAACTCATAATAATCTC
1 CAAAGAAACTCATAATAATCTC
48415910 CAAAGAA
1 CAAAGAA
48415917 GTGAAAAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.53, C:0.22, G:0.06, T:0.20
Consensus pattern (22 bp):
CAAAGAAACTCATAATAATCTC
Found at i:48419920 original size:20 final size:19
Alignment explanation
Indices: 48419895--48419946 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
48419885 TTTAATTAGC
*
48419895 CTTAATTAATCATATTTTAT
1 CTTAATTAATCATAATTT-T
48419915 CTTAATTAAAT-ATAATTTT
1 CTTAATT-AATCATAATTTT
48419934 CTTAATTAATCAT
1 CTTAATTAATCAT
48419947 TAGGAACCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 3 0.10
19 10 0.34
20 13 0.45
21 3 0.10
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (19 bp):
CTTAATTAATCATAATTTT
Found at i:48420576 original size:33 final size:34
Alignment explanation
Indices: 48420520--48420596 Score: 111
Period size: 33 Copynumber: 2.3 Consensus size: 34
48420510 CATTATCAAC
*
48420520 CATACCAAAACATCCTCGAAAAACATGTTCAAAT
1 CATACCTAAACATCCTCGAAAAACATGTTCAAAT
* * *
48420554 CATGCCTAAACATGCTC-AAAAACATGTTCCAAT
1 CATACCTAAACATCCTCGAAAAACATGTTCAAAT
48420587 CATACCTAAA
1 CATACCTAAA
48420597 TAATAACTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
33 24 0.63
34 14 0.37
ACGTcount: A:0.44, C:0.27, G:0.06, T:0.22
Consensus pattern (34 bp):
CATACCTAAACATCCTCGAAAAACATGTTCAAAT
Found at i:48425594 original size:22 final size:22
Alignment explanation
Indices: 48425552--48425597 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
48425542 TAATTTATAT
*
48425552 ATTTTACATTTTAATTAATTTA
1 ATTTTACATATTAATTAATTTA
*
48425574 ATTTTA-ATATTAATATTATTTA
1 ATTTTACATATTAAT-TAATTTA
48425596 AT
1 AT
48425598 CAAAACCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTTTACATATTAATTAATTTA
Found at i:48431762 original size:14 final size:14
Alignment explanation
Indices: 48431743--48431769 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
48431733 AATGAGTAAT
48431743 TCCACTATATTTAA
1 TCCACTATATTTAA
48431757 TCCACTATATTTA
1 TCCACTATATTTA
48431770 CACAGTTTGG
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:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (14 bp):
TCCACTATATTTAA
Found at i:48443667 original size:2 final size:2
Alignment explanation
Indices: 48443660--48443686 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
48443650 ATACATAAGA
48443660 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
48443687 TTTAAAGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:48450115 original size:42 final size:42
Alignment explanation
Indices: 48450068--48450225 Score: 183
Period size: 42 Copynumber: 3.8 Consensus size: 42
48450058 GCACATAAGT
* * **
48450068 GCTAAACAGAAACCCATAAGGGTTGAACGGAAGCTTGTAAGA
1 GCTAAACGGAAACCCATAAGGGTTAAACGGAAGCTTAAAAGA
* *
48450110 GCTAAACGGAAACCCATAAGGGTTAAACTGAAGCTCAAAAGA
1 GCTAAACGGAAACCCATAAGGGTTAAACGGAAGCTTAAAAGA
* * * * * *
48450152 GCTGAACGGGAACCTATTAGGGTTGAACTGAAGCTTAAAAGA
1 GCTAAACGGAAACCCATAAGGGTTAAACGGAAGCTTAAAAGA
*
48450194 GCTGAACGGAAACCCATTAA-GGTTAAACGGAA
1 GCTAAACGGAAACCCA-TAAGGGTTAAACGGAA
48450226 ACTCATATAA
Statistics
Matches: 98, Mismatches: 17, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
42 96 0.98
43 2 0.02
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.17
Consensus pattern (42 bp):
GCTAAACGGAAACCCATAAGGGTTAAACGGAAGCTTAAAAGA
Found at i:48450129 original size:21 final size:21
Alignment explanation
Indices: 48450061--48450232 Score: 58
Period size: 21 Copynumber: 8.2 Consensus size: 21
48450051 CACATAAGCA
* *
48450061 CATAAGTGCTAAACAGAAACC
1 CATAAGAGCTAAACGGAAACC
* * * * *
48450082 CATAAGGGTTGAACGGAAGCT
1 CATAAGAGCTAAACGGAAACC
**
48450103 TGTAAGAGCTAAACGGAAACC
1 CATAAGAGCTAAACGGAAACC
* * * * *
48450124 CATAAGGGTTAAACTGAAGCT
1 CATAAGAGCTAAACGGAAACC
* * *
48450145 CAAAAGAGCTGAACGGGAACC
1 CATAAGAGCTAAACGGAAACC
* * * * * * * *
48450166 TATTAGGGTTGAACTGAAGCT
1 CATAAGAGCTAAACGGAAACC
* * *
48450187 TAAAAGAGCTGAACGGAAACC
1 CATAAGAGCTAAACGGAAACC
* *
48450208 CATTAAG-GTTAAACGGAAACT
1 CA-TAAGAGCTAAACGGAAACC
48450229 CATA
1 CATA
48450233 TAAGTTAACA
Statistics
Matches: 101, Mismatches: 49, Indels: 3
0.66 0.32 0.02
Matches are distributed among these distances:
20 2 0.02
21 96 0.95
22 3 0.03
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (21 bp):
CATAAGAGCTAAACGGAAACC
Found at i:48450239 original size:21 final size:21
Alignment explanation
Indices: 48450198--48450240 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
48450188 AAAAGAGCTG
48450198 AACGGAAACCCATTAAGGTTA
1 AACGGAAACCCATTAAGGTTA
*
48450219 AACGGAAACTCATATAA-GTTA
1 AACGGAAACCCAT-TAAGGTTA
48450240 A
1 A
48450241 CAGAACCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (21 bp):
AACGGAAACCCATTAAGGTTA
Found at i:48455540 original size:32 final size:32
Alignment explanation
Indices: 48455504--48455567 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
48455494 TGATAATTTG
48455504 TTACATTACATGGTATTGAAATTTAAGGTACT
1 TTACATTACATGGTATTGAAATTTAAGGTACT
48455536 TTACATTACATGGTATTGAAATTTAAGGTACT
1 TTACATTACATGGTATTGAAATTTAAGGTACT
48455568 AAGGAGCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (32 bp):
TTACATTACATGGTATTGAAATTTAAGGTACT
Found at i:48455988 original size:13 final size:13
Alignment explanation
Indices: 48455970--48456040 Score: 88
Period size: 13 Copynumber: 5.5 Consensus size: 13
48455960 CTCAAAATTT
48455970 TCAAAAGCACTTC
1 TCAAAAGCACTTC
*
48455983 TCAAAATCACTTC
1 TCAAAAGCACTTC
*
48455996 TCAAAAGCACTTT
1 TCAAAAGCACTTC
* *
48456009 TCCACAGCACTTC
1 TCAAAAGCACTTC
* *
48456022 TCAAAAGTACTTT
1 TCAAAAGCACTTC
48456035 TCAAAA
1 TCAAAA
48456041 ACAATGAAGA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 48 1.00
ACGTcount: A:0.38, C:0.28, G:0.06, T:0.28
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:48455999 original size:26 final size:26
Alignment explanation
Indices: 48455970--48456040 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 26
48455960 CTCAAAATTT
* *
48455970 TCAAAAGCACTTCTCAAAATCACTTC
1 TCAAAAGCACTTTTCAAAAGCACTTC
* *
48455996 TCAAAAGCACTTTTCCACAGCACTTC
1 TCAAAAGCACTTTTCAAAAGCACTTC
*
48456022 TCAAAAGTACTTTTCAAAA
1 TCAAAAGCACTTTTCAAAA
48456041 ACAATGAAGA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.38, C:0.28, G:0.06, T:0.28
Consensus pattern (26 bp):
TCAAAAGCACTTTTCAAAAGCACTTC
Found at i:48469530 original size:27 final size:27
Alignment explanation
Indices: 48469492--48469546 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
48469482 TTTATTTAAT
*
48469492 CATCCAACTTACTCAAATGATCTTATA
1 CATCCAACTTACTCAAATGATCATATA
48469519 CATCCAACTTACTCAAATGATCATATA
1 CATCCAACTTACTCAAATGATCATATA
48469546 C
1 C
48469547 TTACTTAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.27, G:0.04, T:0.31
Consensus pattern (27 bp):
CATCCAACTTACTCAAATGATCATATA
Found at i:48470286 original size:25 final size:25
Alignment explanation
Indices: 48470257--48470317 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
48470247 GCACTCTTTC
*
48470257 GAGCCATATAACAAGAAGCTCATGT
1 GAGCCATATAACAAGAAGCTCATCT
* * *
48470282 GAGCCATGTAACAGGAAGCTTATCT
1 GAGCCATATAACAAGAAGCTCATCT
48470307 GAG-C-TATAACA
1 GAGCCATATAACA
48470318 GAAAACTCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 6 0.19
24 1 0.03
25 24 0.77
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (25 bp):
GAGCCATATAACAAGAAGCTCATCT
Found at i:48475760 original size:13 final size:13
Alignment explanation
Indices: 48475742--48475784 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
48475732 TAGATTTTTC
48475742 CTAAATATTATCA
1 CTAAATATTATCA
48475755 CTAAATA--ATC-
1 CTAAATATTATCA
48475765 CTAAATATTATCA
1 CTAAATATTATCA
48475778 CTAAATA
1 CTAAATA
48475785 AATCAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 7 0.26
11 3 0.11
12 3 0.11
13 14 0.52
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:48475767 original size:23 final size:23
Alignment explanation
Indices: 48475740--48475785 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
48475730 GTTAGATTTT
48475740 TCCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
48475763 TCCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
48475786 ATCAAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (23 bp):
TCCTAAATATTATCACTAAATAA
Found at i:48475793 original size:23 final size:23
Alignment explanation
Indices: 48475744--48475793 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
48475734 GATTTTTCCT
*
48475744 AAATATTATCACTAAATAATCCT
1 AAATATTATCACTAAATAATCCA
48475767 AAATATTATCACTAAATAAAT-CA
1 AAATATTATCACTAAAT-AATCCA
48475790 AAAT
1 AAAT
48475794 TTAAAAATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 22 0.88
24 3 0.12
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (23 bp):
AAATATTATCACTAAATAATCCA
Found at i:48476915 original size:18 final size:17
Alignment explanation
Indices: 48476873--48476915 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
48476863 ATTTCAAATT
*
48476873 TATAATATTTTATATTA
1 TATAATTTTTTATATTA
* *
48476890 TGTTATTTTTATATATTA
1 TATAATTTTT-TATATTA
48476908 TATAATTT
1 TATAATTT
48476916 ATAACACAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:48479654 original size:42 final size:44
Alignment explanation
Indices: 48479595--48479676 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
48479585 CTGTTTAAGG
*
48479595 TCGTGATTTGTTTTTG-TT-ATAATTGTGTTTAAGGTATTATGA
1 TCGTGATTTGTTTTTGTTTCATAATTGCGTTTAAGGTATTATGA
*
48479637 TCGTG-TTGTGTTTTTGTTTCATAATTGCGTTTGAGGTATT
1 TCGTGATT-TGTTTTTGTTTCATAATTGCGTTTAAGGTATT
48479677 CATGTTAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 2 0.06
42 13 0.37
43 2 0.06
44 18 0.51
ACGTcount: A:0.17, C:0.05, G:0.23, T:0.55
Consensus pattern (44 bp):
TCGTGATTTGTTTTTGTTTCATAATTGCGTTTAAGGTATTATGA
Found at i:48488775 original size:2 final size:2
Alignment explanation
Indices: 48488768--48488797 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
48488758 AATTAAAAGA
48488768 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48488798 GCAGTCACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48491019 original size:30 final size:30
Alignment explanation
Indices: 48490968--48491052 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
48490958 GAAAAAGTAA
48490968 AAAAG-TGATGGAGTCAAAGTGTGAATATTT-
1 AAAAGTTGATGGAGTCAAAGTGT-AA-ATTTG
* *
48490998 AAAAGTTGATGG-GTTATAGTGTAAATTTG
1 AAAAGTTGATGGAGTCAAAGTGTAAATTTG
* * *
48491027 AAAAGTTGAAGGACTAAAAGTGTAAA
1 AAAAGTTGATGGAGTCAAAGTGTAAA
48491053 AAACCAAAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
28 4 0.09
29 13 0.28
30 23 0.50
31 6 0.13
ACGTcount: A:0.42, C:0.02, G:0.26, T:0.29
Consensus pattern (30 bp):
AAAAGTTGATGGAGTCAAAGTGTAAATTTG
Found at i:48494223 original size:35 final size:35
Alignment explanation
Indices: 48494167--48494269 Score: 120
Period size: 34 Copynumber: 3.0 Consensus size: 35
48494157 TTCACTATTT
*
48494167 ATTCGTCGGTTTATCTTACTAGCGCTGGGCGCAAC
1 ATTCGTCGGTTTATCTGACTAGCGCTGGGCGCAAC
* * * *
48494202 -TTCCGTCAGTTTATCTGACTAGTGCTGGACAC-AC
1 ATT-CGTCGGTTTATCTGACTAGCGCTGGGCGCAAC
* *
48494236 ATTTGTCGGTTTATCTGACTAGCGCAGGGCGCAA
1 ATTCGTCGGTTTATCTGACTAGCGCTGGGCGCAA
48494270 ACTCTTTCAT
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
34 27 0.50
35 27 0.50
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.31
Consensus pattern (35 bp):
ATTCGTCGGTTTATCTGACTAGCGCTGGGCGCAAC
Found at i:48497239 original size:21 final size:21
Alignment explanation
Indices: 48497215--48497256 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
48497205 GAAATTAAAA
48497215 TGTTTTAATTT-CACTTTAATT
1 TGTTTTAATTTCCA-TTTAATT
48497236 TGTTTTAATTTCCATTTAATT
1 TGTTTTAATTTCCATTTAATT
48497257 AAAAAATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.24, C:0.10, G:0.05, T:0.62
Consensus pattern (21 bp):
TGTTTTAATTTCCATTTAATT
Found at i:48498147 original size:22 final size:22
Alignment explanation
Indices: 48498117--48498200 Score: 69
Period size: 22 Copynumber: 3.5 Consensus size: 22
48498107 TTGGTAAATG
48498117 ATGTATATATTTTGATATAATT
1 ATGTATATATTTTGATATAATT
* * * *
48498139 ATGTTTATATTTAGAATCTTGGTAAATG
1 ATGTATATATTTTG-A---T-AT-AATT
48498167 ATGTATATATTTTGATATAATT
1 ATGTATATATTTTGATATAATT
*
48498189 ATGTTTATATTT
1 ATGTATATATTT
48498201 GTAAATGTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
22 26 0.55
23 2 0.04
24 1 0.02
26 1 0.02
27 2 0.04
28 15 0.32
ACGTcount: A:0.33, C:0.01, G:0.12, T:0.54
Consensus pattern (22 bp):
ATGTATATATTTTGATATAATT
Found at i:48498158 original size:50 final size:50
Alignment explanation
Indices: 48498099--48498200 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
48498089 GATATATAAG
48498099 TTAGAATCTTGGTAAATGATGTATATATTTTGATATAATTATGTTTATAT
1 TTAGAATCTTGGTAAATGATGTATATATTTTGATATAATTATGTTTATAT
48498149 TTAGAATCTTGGTAAATGATGTATATATTTTGATATAATTATGTTTATAT
1 TTAGAATCTTGGTAAATGATGTATATATTTTGATATAATTATGTTTATAT
48498199 TT
1 TT
48498201 GTAAATGTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (50 bp):
TTAGAATCTTGGTAAATGATGTATATATTTTGATATAATTATGTTTATAT
Found at i:48505667 original size:25 final size:24
Alignment explanation
Indices: 48505613--48505685 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 24
48505603 TATGCCCATA
*
48505613 TGAG-CATGTAATCAGGAAGCTCTT
1 TGAGCCATGTAA-CAGGAAGCTCTG
48505637 TCGAGCCATGTAACAGGAAGCTCATG
1 T-GAGCCATGTAACAGGAAGCTC-TG
* **
48505663 TGAGCCATATAATGGGAAGCTCT
1 TGAGCCATGTAACAGGAAGCTCT
48505686 TGCAAGCCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
24 2 0.05
25 31 0.74
26 9 0.21
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (24 bp):
TGAGCCATGTAACAGGAAGCTCTG
Found at i:48505693 original size:25 final size:25
Alignment explanation
Indices: 48505625--48505694 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
48505615 AGCATGTAAT
* *
48505625 CAGGAAGCTCTTTCGAGCCATGTAA
1 CAGGAAGCTCTTGCGAGCCATATAA
* *
48505650 CAGGAAGCTCATGTGAGCCATATAA
1 CAGGAAGCTCTTGCGAGCCATATAA
** *
48505675 TGGGAAGCTCTTGCAAGCCA
1 CAGGAAGCTCTTGCGAGCCA
48505695 ATTATCAGGA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (25 bp):
CAGGAAGCTCTTGCGAGCCATATAA
Found at i:48505705 original size:25 final size:25
Alignment explanation
Indices: 48505623--48505734 Score: 63
Period size: 25 Copynumber: 4.5 Consensus size: 25
48505613 TGAGCATGTA
* *
48505623 ATCAGGAAGCTCTTTCGAGCC-ATGT
1 ATCAGGAAGCTCTTGCAAGCCAAT-T
* * ** *
48505648 AACAGGAAGCTCATGTGAGCCATATA
1 ATCAGGAAGCTCTTGCAAGCCA-ATT
*
48505674 AT-GGGAAGCTCTTGCAAGCCAATT
1 ATCAGGAAGCTCTTGCAAGCCAATT
*
48505698 ATCAGGAA--TCTTAAGACAA-CCAAAT
1 ATCAGGAAGCTCTT--G-CAAGCCAATT
48505723 ATCAGGAAGCTC
1 ATCAGGAAGCTC
48505735 CATAGAGCCA
Statistics
Matches: 66, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
23 4 0.06
24 4 0.06
25 50 0.76
26 4 0.06
27 4 0.06
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.22
Consensus pattern (25 bp):
ATCAGGAAGCTCTTGCAAGCCAATT
Found at i:48505825 original size:24 final size:25
Alignment explanation
Indices: 48505727--48505833 Score: 91
Period size: 24 Copynumber: 4.4 Consensus size: 25
48505717 CCAAATATCA
*
48505727 GGAAGCTCCATAGAGCCAT-TAATCG
1 GGAAGCT-CATGGAGCCATGTAATCG
* * *
48505752 GGAAGCTCAT-AAGATC-TGTAATTG
1 GGAAGCTCATGGAG-CCATGTAATCG
*
48505776 GGAAGCTCATGCGAGCCA-AT-ATCG
1 GGAAGCTCATG-GAGCCATGTAATCG
48505800 GGAAGCTCATGGAGCCATGTAA-CG
1 GGAAGCTCATGGAGCCATGTAATCG
*
48505824 GGATGCTCAT
1 GGAAGCTCAT
48505834 AAGAGCTAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
23 9 0.14
24 45 0.68
25 10 0.15
26 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (25 bp):
GGAAGCTCATGGAGCCATGTAATCG
Found at i:48512537 original size:15 final size:15
Alignment explanation
Indices: 48512517--48512545 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
48512507 TTATTATAAT
48512517 TGTGTATATATATTG
1 TGTGTATATATATTG
48512532 TGTGTATATATATT
1 TGTGTATATATATT
48512546 ATATGCATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (15 bp):
TGTGTATATATATTG
Found at i:48513631 original size:110 final size:110
Alignment explanation
Indices: 48513438--48513658 Score: 415
Period size: 110 Copynumber: 2.0 Consensus size: 110
48513428 GCCAAATGAA
*
48513438 GGTTAATAATATCTACTAATATAAATTCTATACTTATGCTTAATGGGACTAATTTCAATGAATGA
1 GGTTAATAATATCTACTAATATAAATTCTATACTAATGCTTAATGGGACTAATTTCAATGAATGA
*
48513503 AAAAGGCACTTACTTATAGTGTTTGGTTGTATGAACATAGACATT
66 AAAAGGCACTTACTTATAGTGTTTGGTTGTATGAACACAGACATT
*
48513548 GGTTAATAATATCTGCTAATATAAATTCTATACTAATGCTTAATGGGACTAATTTCAATGAATGA
1 GGTTAATAATATCTACTAATATAAATTCTATACTAATGCTTAATGGGACTAATTTCAATGAATGA
48513613 AAAAGGCACTTACTTATAGTGTTTGGTTGTATGAACACAGACATT
66 AAAAGGCACTTACTTATAGTGTTTGGTTGTATGAACACAGACATT
48513658 G
1 G
48513659 CACTAAGGGA
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 108 1.00
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (110 bp):
GGTTAATAATATCTACTAATATAAATTCTATACTAATGCTTAATGGGACTAATTTCAATGAATGA
AAAAGGCACTTACTTATAGTGTTTGGTTGTATGAACACAGACATT
Found at i:48525230 original size:25 final size:26
Alignment explanation
Indices: 48525187--48525238 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
48525177 TGCTATAATT
48525187 TTTTTTATTTACCAAAAAATATATAAA
1 TTTTTTATTTACC-AAAAATATATAAA
*
48525214 TTTTTTATTTATC-AAAATATATAAA
1 TTTTTTATTTACCAAAAATATATAAA
48525239 AAACTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 12 0.50
27 12 0.50
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (26 bp):
TTTTTTATTTACCAAAAATATATAAA
Found at i:48525256 original size:17 final size:17
Alignment explanation
Indices: 48525236--48525268 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
48525226 CAAAATATAT
*
48525236 AAAAAACTAAAA-AACA
1 AAAAAAATAAAAGAACA
48525252 AAAAAAATAAAAGAACA
1 AAAAAAATAAAAGAACA
48525269 GGAAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.82, C:0.09, G:0.03, T:0.06
Consensus pattern (17 bp):
AAAAAAATAAAAGAACA
Found at i:48525697 original size:3 final size:3
Alignment explanation
Indices: 48525689--48525735 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
48525679 AATTTTATAG
48525689 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
48525736 AGATGTTACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:48525762 original size:12 final size:12
Alignment explanation
Indices: 48525686--48525762 Score: 77
Period size: 12 Copynumber: 6.4 Consensus size: 12
48525676 AAAAATTTTA
48525686 TAGTATTATTAT
1 TAGTATTATTAT
*
48525698 TATTATTATTAT
1 TAGTATTATTAT
*
48525710 TATTATTATTAT
1 TAGTATTATTAT
*
48525722 TATTATTATTAT
1 TAGTATTATTAT
*
48525734 TAAG-A-TGTTACT
1 T-AGTATTATTA-T
*
48525746 TAGTATTATTGT
1 TAGTATTATTAT
48525758 TAGTA
1 TAGTA
48525763 AAAAACTAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
11 6 0.11
12 46 0.82
13 4 0.07
ACGTcount: A:0.32, C:0.01, G:0.08, T:0.58
Consensus pattern (12 bp):
TAGTATTATTAT
Found at i:48526501 original size:18 final size:18
Alignment explanation
Indices: 48526473--48526517 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
48526463 TTGATATGGT
* *
48526473 TGGTGGTGAAGAAGAATG
1 TGGTGGCGAAGAAGAAGG
*
48526491 TGGTTGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
48526509 TGGTGGCGA
1 TGGTGGCGA
48526518 TCATTGGGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.04, G:0.47, T:0.20
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:48531264 original size:24 final size:23
Alignment explanation
Indices: 48531237--48531365 Score: 87
Period size: 25 Copynumber: 5.0 Consensus size: 23
48531227 AGTTTTTTTG
48531237 ATATTTTGGTAAATAAACAAAATTATAT
1 ATATTTTGGTAAAT-AA-AAAA--AT-T
*
48531265 ATATTTTGGTAAATAAAAAAAAAT
1 ATATTTTGGTAAAT-AAAAAAATT
* * *
48531289 ATATTTCGGTAAATAAAAATTTTTTTATA
1 ATATTTTGGTAAATAAAAA------AATT
48531318 ATATTTTGGTAAATAAAAAATATAT
1 ATATTTTGGTAAATAAAAAA-AT-T
*
48531343 ATATTTCGGTAAATAAAAAAATT
1 ATATTTTGGTAAATAAAAAAATT
48531366 TATAATATTT
Statistics
Matches: 84, Mismatches: 9, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
23 6 0.07
24 18 0.21
25 20 0.24
27 4 0.05
28 17 0.20
29 19 0.23
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (23 bp):
ATATTTTGGTAAATAAAAAAATT
Found at i:48531269 original size:28 final size:27
Alignment explanation
Indices: 48531237--48531381 Score: 167
Period size: 28 Copynumber: 5.4 Consensus size: 27
48531227 AGTTTTTTTG
48531237 ATATTTTGGTAAATAAACAAAATTATAT
1 ATATTTTGGTAAATAAA-AAAATTATAT
48531265 ATATTTTGGTAAATAAAAAAA--A-AT
1 ATATTTTGGTAAATAAAAAAATTATAT
* ** *
48531289 ATATTTCGGTAAATAAAAATTTTTTTAT
1 ATATTTTGGTAAATAAAAA-AATTATAT
48531317 AATATTTTGGTAAAT-AAAAAA-TATAT
1 -ATATTTTGGTAAATAAAAAAATTATAT
*
48531343 ATATTTCGGTAAATAAAAAAATT-TAT
1 ATATTTTGGTAAATAAAAAAATTATAT
48531369 AATATTTTGGTAA
1 -ATATTTTGGTAA
48531382 TTTTTTATTT
Statistics
Matches: 99, Mismatches: 10, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
24 20 0.20
25 14 0.14
26 13 0.13
27 16 0.16
28 23 0.23
29 13 0.13
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.41
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAATTATAT
Found at i:48531300 original size:52 final size:52
Alignment explanation
Indices: 48531237--48531381 Score: 204
Period size: 52 Copynumber: 2.8 Consensus size: 52
48531227 AGTTTTTTTG
*
48531237 ATATTTTGGTAAATAAACAAAA-TTATATATATTTTGGTAAATAAAAAA-AAAT
1 ATATTTCGGTAAATAAA-AAAATTTATA-ATATTTTGGTAAATAAAAAATAAAT
** *
48531289 ATATTTCGGTAAATAAAAATTTTTTTATAATATTTTGGTAAATAAAAAATATAT
1 ATATTTCGGTAAATAAAAA--AATTTATAATATTTTGGTAAATAAAAAATAAAT
48531343 ATATTTCGGTAAATAAAAAAATTTATAATATTTTGGTAA
1 ATATTTCGGTAAATAAAAAAATTTATAATATTTTGGTAA
48531382 TTTTTTATTT
Statistics
Matches: 83, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
51 2 0.02
52 34 0.41
53 20 0.24
54 27 0.33
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.41
Consensus pattern (52 bp):
ATATTTCGGTAAATAAAAAAATTTATAATATTTTGGTAAATAAAAAATAAAT
Found at i:48531321 original size:29 final size:25
Alignment explanation
Indices: 48531237--48531381 Score: 130
Period size: 24 Copynumber: 5.5 Consensus size: 25
48531227 AGTTTTTTTG
*
48531237 ATATTTTGGTAAATAAACAAAATTATAT
1 ATATTTCGGTAAAT-AA-AAAA-TATAT
* *
48531265 ATATTTTGGTAAATAAAAAA-AAAT
1 ATATTTCGGTAAATAAAAAATATAT
* *
48531289 ATATTTCGGTAAATAAAAATTTTTTTAT
1 ATATTTCGGTAAATAAAAA---ATATAT
*
48531317 AATATTTTGGTAAATAAAAAATATAT
1 -ATATTTCGGTAAATAAAAAATATAT
*
48531343 ATATTTCGGTAAATAAAAAAATTTAT
1 ATATTTCGGTAAAT-AAAAAATATAT
*
48531369 AATATTTTGGTAA
1 -ATATTTCGGTAA
48531382 TTTTTTATTT
Statistics
Matches: 99, Mismatches: 11, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
24 21 0.21
25 13 0.13
26 18 0.18
27 13 0.13
28 16 0.16
29 18 0.18
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.41
Consensus pattern (25 bp):
ATATTTCGGTAAATAAAAAATATAT
Found at i:48531461 original size:18 final size:18
Alignment explanation
Indices: 48531422--48531466 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
48531412 AACCCATAAT
* *
48531422 AAAACATTACAAAAAAAT
1 AAAATATTACAAAAAAAC
48531440 AAAATATTA-AAAAAAACC
1 AAAATATTACAAAAAAA-C
48531458 AAAATATTA
1 AAAATATTA
48531467 TATATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAATATTACAAAAAAAC
Found at i:48532259 original size:4 final size:4
Alignment explanation
Indices: 48532250--48532319 Score: 51
Period size: 4 Copynumber: 17.5 Consensus size: 4
48532240 CCCCTTTCCT
*
48532250 TTTC TTTC TTTC -TT- TTTC TTTC TTTCC TCTTC TTTCC TTTTC CTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT-C T-TTC TTT-C -TTTC TTTC
48532296 -TT- TTTC TTTC -TTC ATTTC TTTC TT
1 TTTC TTTC TTTC TTTC -TTTC TTTC TT
48532320 CTTCTTCCCC
Statistics
Matches: 55, Mismatches: 1, Indels: 20
0.72 0.01 0.26
Matches are distributed among these distances:
3 11 0.20
4 30 0.55
5 9 0.16
6 5 0.09
ACGTcount: A:0.01, C:0.27, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTC
Found at i:48532266 original size:14 final size:14
Alignment explanation
Indices: 48532243--48532319 Score: 66
Period size: 14 Copynumber: 5.2 Consensus size: 14
48532233 TTTTCTTCCC
*
48532243 CTTTCCTTTTCTTT
1 CTTTCTTTTTCTTT
48532257 CTTTCTTTTTCTTT
1 CTTTCTTTTTCTTT
* *
48532271 CTTTCCTCTTCTTT
1 CTTTCTTTTTCTTT
*
48532285 CCTTTTCCTTCTT-TTT
1 -C-TTT-CTTTTTCTTT
48532301 CTTTCTTCATTTCTTT
1 CTTTCTT--TTTCTTT
48532317 CTT
1 CTT
48532320 CTTCTTCCCC
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
13 3 0.06
14 28 0.54
15 4 0.08
16 12 0.23
17 5 0.10
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (14 bp):
CTTTCTTTTTCTTT
Found at i:48532272 original size:34 final size:35
Alignment explanation
Indices: 48532227--48532308 Score: 98
Period size: 34 Copynumber: 2.4 Consensus size: 35
48532217 TTATAAACTG
* * *
48532227 CTTTTTTTTTCTTCCCCT-TTCCTTTTC-TTTCTTT
1 CTTTTTCTTTCTTCCCCTCTT-CTTTCCTTTTCCTT
*
48532261 CTTTTTCTTTCTT-TCCTCTTCTTTCCTTTTCCTT
1 CTTTTTCTTTCTTCCCCTCTTCTTTCCTTTTCCTT
48532295 CTTTTTCTTTCTTC
1 CTTTTTCTTTCTTC
48532309 ATTTCTTTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
33 8 0.20
34 33 0.80
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (35 bp):
CTTTTTCTTTCTTCCCCTCTTCTTTCCTTTTCCTT
Found at i:48532297 original size:42 final size:43
Alignment explanation
Indices: 48532235--48532339 Score: 117
Period size: 42 Copynumber: 2.4 Consensus size: 43
48532225 TGCTTTTTTT
*
48532235 TTCTTCCCCTTTCCTTTTCTTTCTTTCTTT-TTC-TTTCTTTCCTC
1 TTCTTCCCCTCTCC--TTCTTT-TTTCTTTCTTCATTTCTTTCCTC
* * * *
48532279 TTCTTTCCTTTTCCTTC-TTTTTCTTTCTTCATTTCTTTCTTC
1 TTCTTCCCCTCTCCTTCTTTTTTCTTTCTTCATTTCTTTCCTC
48532321 TTCTTCCCCTCTCCTTCTT
1 TTCTTCCCCTCTCCTTCTT
48532340 CCCCCCACCA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
40 7 0.13
41 5 0.10
42 27 0.52
43 1 0.02
44 12 0.23
ACGTcount: A:0.01, C:0.34, G:0.00, T:0.65
Consensus pattern (43 bp):
TTCTTCCCCTCTCCTTCTTTTTTCTTTCTTCATTTCTTTCCTC
Done.