Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 73 of 120
Found at i:22041231 original size:27 final size:27
Alignment explanation
Indices: 22041201--22041517 Score: 294
Period size: 27 Copynumber: 11.9 Consensus size: 27
22041191 GGTATAAAAA
* *
22041201 TCATTTTACACTATAGGGGTATTTCGG
1 TCATTTTACCCTATAGGGGTATTTCAG
* *
22041228 TCATTTTACCCT-TTGAGGGTATTTCAA
1 TCATTTTACCCTATAG-GGGTATTTCAG
* * *
22041255 TCA--TT--CCTTTGGGGGTATTTCGG
1 TCATTTTACCCTATAGGGGTATTTCAG
* * *
22041278 TCAATTTACCCT-TCGAGGGTATTTCGG
1 TCATTTTACCCTATAG-GGGTATTTCAG
*
22041305 TCATTTTACCCT-TCAAGGGTATTTCAG
1 TCATTTTACCCTAT-AGGGGTATTTCAG
*
22041332 TCATTTTACCCTTTTA-GGGTATTTCAG
1 TCATTTTACCC-TATAGGGGTATTTCAG
* **
22041359 TCATTTTACCCT-TCGAGGGTATTTTGG
1 TCATTTTACCCTATAG-GGGTATTTCAG
* *
22041386 TCATTTTACCTTTCTA-GGGTATTTCAG
1 TCATTTTACC-CTATAGGGGTATTTCAG
* * *
22041413 TTATTTTATCCTATGGGGGTATTTCAG
1 TCATTTTACCCTATAGGGGTATTTCAG
* *
22041440 TCATTTTACCCTATGGGGGTATTTTAG
1 TCATTTTACCCTATAGGGGTATTTCAG
* *
22041467 TTATTTTACCCTATAGGGGTATTTCGG
1 TCATTTTACCCTATAGGGGTATTTCAG
22041494 TCATTTTACCCTATAGGGGTATTT
1 TCATTTTACCCTATAGGGGTATTT
22041518 TGATGATTTA
Statistics
Matches: 243, Mismatches: 32, Indels: 30
0.80 0.10 0.10
Matches are distributed among these distances:
23 15 0.06
24 2 0.01
25 5 0.02
26 7 0.03
27 209 0.86
28 3 0.01
29 2 0.01
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.44
Consensus pattern (27 bp):
TCATTTTACCCTATAGGGGTATTTCAG
Found at i:22041389 original size:81 final size:81
Alignment explanation
Indices: 22041217--22041517 Score: 353
Period size: 81 Copynumber: 3.8 Consensus size: 81
22041207 TACACTATAG
** * *
22041217 GGGTATTTCGGTCATTTTACCCTTTGAGGGTATTTCAATCA--TT--CCTTTGGGGGTATTTCGG
1 GGGTATTTCGGTCATTTTACCCTTCAAGGGTATTTCAGTCATTTTACCCTTTGGGGGTATTTCAG
*
22041278 TCAATTTACCCTTCGA
66 TCATTTTACCCTTCGA
**
22041294 GGGTATTTCGGTCATTTTACCCTTCAAGGGTATTTCAGTCATTTTACCCTTTTAGGGTATTTCAG
1 GGGTATTTCGGTCATTTTACCCTTCAAGGGTATTTCAGTCATTTTACCCTTTGGGGGTATTTCAG
22041359 TCATTTTACCCTTCGA
66 TCATTTTACCCTTCGA
* * * * * *
22041375 GGGTATTTTGGTCATTTTACCTTTCTAGGGTATTTCAGTTATTTTATCCTATGGGGGTATTTCAG
1 GGGTATTTCGGTCATTTTACCCTTCAAGGGTATTTCAGTCATTTTACCCTTTGGGGGTATTTCAG
*
22041440 TCATTTTACCCTAT-GG
66 TCATTTTACCCT-TCGA
** * * * * *
22041456 GGGTATTTTAGTTATTTTACCCTAT-AGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTT
1 GGGTATTTCGGTCATTTTACCCT-TCAAGGGTATTTCAGTCATTTTACCCTTTGGGGGTATTT
22041518 TGATGATTTA
Statistics
Matches: 193, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
77 38 0.20
79 2 0.01
81 151 0.78
82 2 0.01
ACGTcount: A:0.18, C:0.17, G:0.21, T:0.44
Consensus pattern (81 bp):
GGGTATTTCGGTCATTTTACCCTTCAAGGGTATTTCAGTCATTTTACCCTTTGGGGGTATTTCAG
TCATTTTACCCTTCGA
Found at i:22041507 original size:54 final size:54
Alignment explanation
Indices: 22041201--22041505 Score: 345
Period size: 54 Copynumber: 5.7 Consensus size: 54
22041191 GGTATAAAAA
* *
22041201 TCATTTTACACTATAGGGGTATTTCGGTCATTTTACCCTTTGAGGGTATTTCAA
1 TCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTTTGAGGGTATTTCAG
* * * * *
22041255 TCA--TT--CCTTTGGGGGTATTTCGGTCAATTTACCCTTCGAGGGTATTTCGG
1 TCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTTTGAGGGTATTTCAG
* * *
22041305 TCATTTTACCCT-TCAAGGGTATTTCAGTCATTTTACCCTTTTAGGGTATTTCAG
1 TCATTTTACCCTAT-AGGGGTATTTCGGTCATTTTACCCTTTGAGGGTATTTCAG
* * *
22041359 TCATTTTACCCT-TCGAGGGTATTTTGGTCATTTTA-CCTTTCTAGGGTATTTCAG
1 TCATTTTACCCTATAG-GGGTATTTCGGTCATTTTACCCTTT-GAGGGTATTTCAG
* * * * * * *
22041413 TTATTTTATCCTATGGGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTTAG
1 TCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTTTGAGGGTATTTCAG
*
22041467 TTATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCT
1 TCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCT
22041506 ATAGGGGTAT
Statistics
Matches: 212, Mismatches: 30, Indels: 18
0.82 0.12 0.07
Matches are distributed among these distances:
50 41 0.19
52 4 0.02
53 6 0.03
54 155 0.73
55 6 0.03
ACGTcount: A:0.18, C:0.18, G:0.19, T:0.44
Consensus pattern (54 bp):
TCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTTTGAGGGTATTTCAG
Found at i:22042547 original size:5 final size:5
Alignment explanation
Indices: 22042526--22042560 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
22042516 ATTAAAAACT
* *
22042526 ATAAA ACAAA GTAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
22042561 GTTCTAATGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (5 bp):
ATAAA
Found at i:22043537 original size:14 final size:14
Alignment explanation
Indices: 22043518--22043548 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
22043508 AAGTGAGAGA
*
22043518 TGAGAGAAGAGTTG
1 TGAGAGAAGAGATG
22043532 TGAGAGAAGAGATG
1 TGAGAGAAGAGATG
22043546 TGA
1 TGA
22043549 ATGAGGGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.42, T:0.19
Consensus pattern (14 bp):
TGAGAGAAGAGATG
Found at i:22051759 original size:17 final size:17
Alignment explanation
Indices: 22051720--22051760 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
22051710 AAATGTTTTT
22051720 TCTTTTTCTTTTTTTCA
1 TCTTTTTCTTTTTTTCA
*
22051737 TATTTTTCTTTTTTTGCA
1 TCTTTTTCTTTTTTT-CA
22051755 -CTTTTT
1 TCTTTTT
22051761 GATCACTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 19 0.90
18 2 0.10
ACGTcount: A:0.07, C:0.15, G:0.02, T:0.76
Consensus pattern (17 bp):
TCTTTTTCTTTTTTTCA
Found at i:22056220 original size:18 final size:19
Alignment explanation
Indices: 22056183--22056225 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
22056173 TTTAGTTTGG
*
22056183 TTATTTTACTTAG-TAGTT
1 TTATTTAACTTAGTTAGTT
**
22056201 TTATTTAACTTAGTTTTTT
1 TTATTTAACTTAGTTAGTT
22056220 TTATTT
1 TTATTT
22056226 TTTACAGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.21, C:0.05, G:0.07, T:0.67
Consensus pattern (19 bp):
TTATTTAACTTAGTTAGTT
Found at i:22059559 original size:23 final size:23
Alignment explanation
Indices: 22059529--22059582 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
22059519 ATACCCTATT
22059529 TGGTGTGTTGGGTTGGTCAGAGA
1 TGGTGTGTTGGGTTGGTCAGAGA
22059552 TGGTGTGTTGGGTTGGTCAGAGA
1 TGGTGTGTTGGGTTGGTCAGAGA
*
22059575 TAGTGTGT
1 TGGTGTGT
22059583 AGCGGCTGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.13, C:0.04, G:0.46, T:0.37
Consensus pattern (23 bp):
TGGTGTGTTGGGTTGGTCAGAGA
Found at i:22065821 original size:15 final size:15
Alignment explanation
Indices: 22065798--22065828 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
22065788 GGTGGTAAAA
22065798 TGACAAAAATACCCT
1 TGACAAAAATACCCT
*
22065813 TGACGAAAATACCCT
1 TGACAAAAATACCCT
22065828 T
1 T
22065829 AGGTTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.23
Consensus pattern (15 bp):
TGACAAAAATACCCT
Found at i:22069495 original size:247 final size:244
Alignment explanation
Indices: 22069031--22069521 Score: 757
Period size: 247 Copynumber: 2.0 Consensus size: 244
22069021 CTTCAGCTAG
* *
22069031 ATTTTGTGTGAATCAGTGTTGAGAATGAGCCTATTGGTTCAATGGTTAAGTGTCTGGCCCACTAC
1 ATTTTGTGTAAATCAGTGTTGAGAATGAGCCTATTGGTTCAATGGTTAAGTGTCTGCCCCACTAC
*
22069096 TAGTCCTGTGTTCGAGTCGCGATGTGCGCGATATGGAAATTTTTTTTCTTGTCTAAATTTTGAAT
66 TAGTCCTGTGTTCGAGTCGCGATGTGCGCAATATGGAAATTTTTTTTCTTGTCTAAATTTTGAAT
* *
22069161 CGATAGTTTCTAAAGGAATTAAACATCTTATTTCATGTCACTTTTCCTTTTTCGTACTTTTTCTT
131 CGATAGTTTCTAAAGGAATTAAACATCTTATTTCATGTCACTTTTCCCTTTTCATACTTTTTCTT
*
22069226 CTTTTTTTCTTTTTCATTTTTATTATTCTTCTCTTCCTTTCTTTTCTTT
196 CTTTTTTTCTCTTTCATTTTTATTATTCTTCTCTTCCTTTCTTTTCTTT
* * * * *
22069275 ATTTTGTGTAAATTAGTGTTGAGAATGAGCCTGTTGGTTCAATGGTTACGTTTCTGCCCCATTAC
1 ATTTTGTGTAAATCAGTGTTGAGAATGAGCCTATTGGTTCAATGGTTAAGTGTCTGCCCCACTAC
* * * * *
22069340 TAGTCTTGTGTTCGAGTCGCGTTGTGCGCAATATGGAAATATTTTTGTTACTTGTCTGACTTTTT
66 TAGTCCTGTGTTCGAGTCGCGATGTGCGCAATATGGAAAT-TTTTT-TT-CTTGTCTAAATTTTG
* * *
22069405 AATCGATAGTTTCTAAAGGAATTAAACGTCTTATTTCCTGTCTCTTTTCCCTTTTCATACTTTTT
128 AATCGATAGTTTCTAAAGGAATTAAACATCTTATTTCATGTCACTTTTCCCTTTTCATACTTTTT
* * *
22069470 TTTCTTTTTTTCTCTTTCATTTTTATTCTTCTTCTCTTTCTTTCTTTTCTTT
193 CTTCTTTTTTTCTCTTTCATTTTTATTATTCTTCTCTTCCTTTCTTTTCTTT
22069522 CCATTTTGGG
Statistics
Matches: 222, Mismatches: 22, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
244 95 0.43
245 5 0.02
246 2 0.01
247 120 0.54
ACGTcount: A:0.18, C:0.17, G:0.15, T:0.50
Consensus pattern (244 bp):
ATTTTGTGTAAATCAGTGTTGAGAATGAGCCTATTGGTTCAATGGTTAAGTGTCTGCCCCACTAC
TAGTCCTGTGTTCGAGTCGCGATGTGCGCAATATGGAAATTTTTTTTCTTGTCTAAATTTTGAAT
CGATAGTTTCTAAAGGAATTAAACATCTTATTTCATGTCACTTTTCCCTTTTCATACTTTTTCTT
CTTTTTTTCTCTTTCATTTTTATTATTCTTCTCTTCCTTTCTTTTCTTT
Found at i:22069498 original size:16 final size:14
Alignment explanation
Indices: 22069470--22069521 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 14
22069460 CATACTTTTT
22069470 TTTCTTTTTTTCTC
1 TTTCTTTTTTTCTC
22069484 TTTCATTTTTATTCTTC
1 TTTC-TTTTT-TTC-TC
*
22069501 TTCTCTTTCTTTCT-
1 TT-TCTTTTTTTCTC
22069515 TTTCTTT
1 TTTCTTT
22069522 CCATTTTGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
13 5 0.15
14 6 0.18
15 6 0.18
16 6 0.18
17 8 0.24
18 2 0.06
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTCTTTTTTTCTC
Found at i:22077899 original size:26 final size:26
Alignment explanation
Indices: 22077865--22077924 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
22077855 ATAAGTGAGC
*
22077865 CTTTGTGGCTATCTCTAAATAAACAT
1 CTTTATGGCTATCTCTAAATAAACAT
* ** *
22077891 CTTTATGGCTATCTCTGAATGGACGT
1 CTTTATGGCTATCTCTAAATAAACAT
22077917 CTTTATGG
1 CTTTATGG
22077925 TGATCTATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.40
Consensus pattern (26 bp):
CTTTATGGCTATCTCTAAATAAACAT
Found at i:22077976 original size:29 final size:29
Alignment explanation
Indices: 22077944--22078155 Score: 110
Period size: 29 Copynumber: 7.3 Consensus size: 29
22077934 TTATAAGGAA
* *
22077944 GCCTTTATGGCTATCTCAATTAAATGAAT
1 GCCTTTGTGGCTATCTCAGTTAAATGAAT
* ** * *
22077973 GCCTATGTGGAAATCTCTGTAAAAATG-AT
1 GCCTTTGTGGCTATCTCAGT-TAAATGAAT
*
22078002 GCCTTTGTGGCTATCTTAGTTAAATGAAT
1 GCCTTTGTGGCTATCTCAGTTAAATGAAT
* * * * * *
22078031 GCCTTTGAGGCTCTCTTAGGTAAAAGGAT
1 GCCTTTGTGGCTATCTCAGTTAAATGAAT
* * ** * *
22078060 TCCTTTATTTCTATCTCTATTTAAA-GGAT
1 GCCTTTGTGGCTATCTC-AGTTAAATGAAT
* * *
22078089 GTCTTTGTGGCTATCTTC-GTTAAAAGGAT
1 GCCTTTGTGGCTATC-TCAGTTAAATGAAT
* * *
22078118 GTCTTTGTGG-TCATCTCTGTTAAACGAAT
1 GCCTTTGTGGCT-ATCTCAGTTAAATGAAT
*
22078147 GTC-TTGTGG
1 GCCTTTGTGG
22078156 AAACCTCTGC
Statistics
Matches: 141, Mismatches: 35, Indels: 15
0.74 0.18 0.08
Matches are distributed among these distances:
28 19 0.13
29 110 0.78
30 12 0.09
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.40
Consensus pattern (29 bp):
GCCTTTGTGGCTATCTCAGTTAAATGAAT
Found at i:22078065 original size:58 final size:58
Alignment explanation
Indices: 22077994--22078147 Score: 136
Period size: 58 Copynumber: 2.7 Consensus size: 58
22077984 AATCTCTGTA
* * *
22077994 AAAATGATGCCTTTGTGGCTATCT-TAGTTAAATGAATGCCTTTGAGGCTCTCTTAGGT
1 AAAAGGATTCCTTTGTGGCTATCTCTAGTTAAA-GAATGCCTTTGAGGCTATCTTAGGT
* ** * * * * * *
22078052 AAAAGGATTCCTTTATTTCTATCTCTATTTAAAGGATGTCTTTGTGGCTATCTTCGTT
1 AAAAGGATTCCTTTGTGGCTATCTCTAGTTAAAGAATGCCTTTGAGGCTATCTTAGGT
22078110 AAAAGGATGT-CTTTGTGG-TCATCTCT-GTTAAACGAATG
1 AAAAGGAT-TCCTTTGTGGCT-ATCTCTAGTTAAA-GAATG
22078148 TCTTGTGGAA
Statistics
Matches: 75, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
57 6 0.08
58 61 0.81
59 8 0.11
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (58 bp):
AAAAGGATTCCTTTGTGGCTATCTCTAGTTAAAGAATGCCTTTGAGGCTATCTTAGGT
Found at i:22080469 original size:21 final size:22
Alignment explanation
Indices: 22080440--22080481 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
22080430 TATTTTCTTT
22080440 TAGGATA-TTTTAAGTTTATTA
1 TAGGATATTTTTAAGTTTATTA
* *
22080461 TAGGTTATTTTTAATTTTATT
1 TAGGATATTTTTAAGTTTATT
22080482 TTTATTTCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.60
Consensus pattern (22 bp):
TAGGATATTTTTAAGTTTATTA
Found at i:22081058 original size:16 final size:16
Alignment explanation
Indices: 22081033--22081063 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22081023 TTTAGAACTG
*
22081033 AAAACTTTCAAGTAAT
1 AAAACCTTCAAGTAAT
22081049 AAAACCTTCAAGTAA
1 AAAACCTTCAAGTAA
22081064 ATGTTGGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.16, G:0.06, T:0.26
Consensus pattern (16 bp):
AAAACCTTCAAGTAAT
Found at i:22081425 original size:43 final size:43
Alignment explanation
Indices: 22081364--22081450 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
22081354 CTGATATTTC
22081364 TGTAGATAGTTCCTTGAGACAATCCATGATAGTGAATAGGAAG
1 TGTAGATAGTTCCTTGAGACAATCCATGATAGTGAATAGGAAG
22081407 TGTAGATAGTTCCTTGAGACAATCCATGATAGTGAATAGGAAG
1 TGTAGATAGTTCCTTGAGACAATCCATGATAGTGAATAGGAAG
22081450 T
1 T
22081451 CTGTTTGTAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.29
Consensus pattern (43 bp):
TGTAGATAGTTCCTTGAGACAATCCATGATAGTGAATAGGAAG
Found at i:22082255 original size:11 final size:11
Alignment explanation
Indices: 22082218--22082279 Score: 54
Period size: 11 Copynumber: 5.6 Consensus size: 11
22082208 ACAACCAAAA
* *
22082218 CACCACTATAT
1 CACCACCATAG
*
22082229 CACCACAATA-
1 CACCACCATAG
*
22082239 CAACCACCATGG
1 C-ACCACCATAG
* *
22082251 CACCACCACAC
1 CACCACCATAG
22082262 CACCACCATAG
1 CACCACCATAG
22082273 CACCACC
1 CACCACC
22082280 GTATCTGTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
10 1 0.02
11 39 0.95
12 1 0.02
ACGTcount: A:0.37, C:0.48, G:0.05, T:0.10
Consensus pattern (11 bp):
CACCACCATAG
Found at i:22082279 original size:22 final size:22
Alignment explanation
Indices: 22082218--22082279 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
22082208 ACAACCAAAA
* * * *
22082218 CACCACTATATCACCACAATAC
1 CACCACCATAGCACCACCACAC
* *
22082240 AACCACCATGGCACCACCACAC
1 CACCACCATAGCACCACCACAC
22082262 CACCACCATAGCACCACC
1 CACCACCATAGCACCACC
22082280 GTATCTGTAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.37, C:0.48, G:0.05, T:0.10
Consensus pattern (22 bp):
CACCACCATAGCACCACCACAC
Found at i:22108415 original size:17 final size:17
Alignment explanation
Indices: 22108393--22108451 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
22108383 ATTCTTTAGA
22108393 ATTTTTATAATTTTTTT
1 ATTTTTATAATTTTTTT
*
22108410 ATTTTTATAAATATTTTGT
1 ATTTTTAT-AAT-TTTTTT
* *
22108429 A-TTTTAGAAATTATTTT
1 ATTTTTA-TAATTTTTTT
22108446 ATTTTT
1 ATTTTT
22108452 TTGTAATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
17 13 0.38
18 15 0.44
19 6 0.18
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
ATTTTTATAATTTTTTT
Found at i:22108431 original size:19 final size:17
Alignment explanation
Indices: 22108374--22108433 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 17
22108364 ATTTTTAACT
*
22108374 TTTTTATATATTCTTTAGAA
1 TTTTTATA-ATT-TTT-GTA
*
22108394 TTTTTATAATTTTTTTA
1 TTTTTATAATTTTTGTA
22108411 TTTTTATAAATATTTTGTA
1 TTTTTAT-AAT-TTTTGTA
22108430 TTTT
1 TTTT
22108434 AGAAATTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
17 8 0.23
18 6 0.17
19 13 0.37
20 8 0.23
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTTTATAATTTTTGTA
Found at i:22108452 original size:19 final size:19
Alignment explanation
Indices: 22108401--22108452 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
22108391 GAATTTTTAT
* *
22108401 AATTTTTTTA-TTTTTATA
1 AATTATTTTATTTTTTAGA
* *
22108419 AA-TATTTTGTATTTTAGA
1 AATTATTTTATTTTTTAGA
22108437 AATTATTTTATTTTTT
1 AATTATTTTATTTTTT
22108453 TGTAATTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
17 5 0.19
18 10 0.38
19 11 0.42
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (19 bp):
AATTATTTTATTTTTTAGA
Found at i:22109853 original size:40 final size:40
Alignment explanation
Indices: 22109809--22109899 Score: 94
Period size: 42 Copynumber: 2.2 Consensus size: 40
22109799 TCCTCGTAGG
* * *
22109809 CGCGATTTGTGTCAACGTAAGC-AAATCGCGCTGACGTGGA
1 CGCGATTTCTGAC-ACGTAACCGAAATCGCGCTGACGTGGA
* * *
22109849 CGCGATGTCCTGACACGTACCCTGATATCGCGCTGACGTGGA
1 CGCGAT-TTCTGACACGTAACC-GAAATCGCGCTGACGTGGA
22109891 CGCGATTTC
1 CGCGATTTC
22109900 GCGGAAAATG
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
40 12 0.29
41 6 0.15
42 23 0.56
ACGTcount: A:0.21, C:0.27, G:0.29, T:0.23
Consensus pattern (40 bp):
CGCGATTTCTGACACGTAACCGAAATCGCGCTGACGTGGA
Found at i:22110096 original size:3 final size:3
Alignment explanation
Indices: 22110088--22110112 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
22110078 AAATTCACAT
22110088 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
22110113 AGTTGATATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:22120924 original size:2 final size:2
Alignment explanation
Indices: 22120917--22120973 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
22120907 CTAATGCATC
22120917 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
22120959 CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT C
22120974 CAGCCAATTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:22127350 original size:29 final size:29
Alignment explanation
Indices: 22127257--22127479 Score: 114
Period size: 29 Copynumber: 7.7 Consensus size: 29
22127247 TCAGATCCTG
* * * * *
22127257 CCACGAAGGCATCCTTTTAA-AAAAATAG
1 CCACAAAGGCTTCCTTTTAACAGAGATAA
* *
22127285 CCACAAA-GCATTCCTTTTAACAAAGATAG
1 CCACAAAGGC-TTCCTTTTAACAGAGATAA
* * *
22127314 CTGA-AAAGGCTTCCTTTTAGCAGATATAA
1 C-CACAAAGGCTTCCTTTTAACAGAGATAA
* *
22127343 CCATAAAGGCATT-CTTTTAACAGAGATCA
1 CCACAAAGGC-TTCCTTTTAACAGAGATAA
* * * *
22127372 CCACAAAGGCTTCATTATAACAAAGATAG
1 CCACAAAGGCTTCCTTTTAACAGAGATAA
* * * *
22127401 CCATAAAGACATT-CATTTAACAGAGATAG
1 CCACAAAGGC-TTCCTTTTAACAGAGATAA
* * ** * *
22127430 CTATAAAAACATCCTTTTAACAGAGATAG
1 CCACAAAGGCTTCCTTTTAACAGAGATAA
* * *
22127459 CCACAGAGGCATCATTTTAAC
1 CCACAAAGGCTTCCTTTTAAC
22127480 TGATATAGCC
Statistics
Matches: 152, Mismatches: 34, Indels: 17
0.75 0.17 0.08
Matches are distributed among these distances:
27 2 0.01
28 19 0.12
29 124 0.82
30 7 0.05
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.25
Consensus pattern (29 bp):
CCACAAAGGCTTCCTTTTAACAGAGATAA
Found at i:22127451 original size:58 final size:56
Alignment explanation
Indices: 22127262--22127461 Score: 179
Period size: 58 Copynumber: 3.5 Consensus size: 56
22127252 TCCTGCCACG
* * *
22127262 AAGGCATCCTTTTAA-AAAAATAGCCACAAAGCATTCCTTTTAACAAAGATAGCTGAA
1 AAGGCATCCTTTTAACAAAGATAGCCATAAAGCATT-CTTTTAACAGAGATAGCT-AA
* * * * * *
22127319 AAGGCTTCCTTTTAGCAGATATAACCATAAAGGCATTCTTTTAACAGAGATCA-CCACA
1 AAGGCATCCTTTTAACAAAGATAGCCATAAA-GCATTCTTTTAACAGAGAT-AGCTA-A
* * * *
22127377 AAGGCTTCATTATAACAAAGATAGCCATAAAGACATTCATTTAACAGAGATAGCTATA
1 AAGGCATCCTTTTAACAAAGATAGCCATAAAG-CATTCTTTTAACAGAGATAGCTA-A
** *
22127435 AAAACATCCTTTTAACAGAGATAGCCA
1 AAGGCATCCTTTTAACAAAGATAGCCA
22127462 CAGAGGCATC
Statistics
Matches: 114, Mismatches: 23, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
57 16 0.14
58 92 0.81
59 6 0.05
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.26
Consensus pattern (56 bp):
AAGGCATCCTTTTAACAAAGATAGCCATAAAGCATTCTTTTAACAGAGATAGCTAA
Found at i:22131274 original size:14 final size:15
Alignment explanation
Indices: 22131249--22131277 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
22131239 AATTAATCAA
22131249 ATTTTAATAAAAAAT
1 ATTTTAATAAAAAAT
22131264 ATTTT-ATAAAAAAT
1 ATTTTAATAAAAAAT
22131278 TCTTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTTTAATAAAAAAT
Found at i:22134530 original size:24 final size:24
Alignment explanation
Indices: 22134486--22134532 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
22134476 TTTATTTTTA
*
22134486 AAATAATTAATTTTATTTAATATT
1 AAATAATTAATTTTATCTAATATT
22134510 AAATAATTATATTTTA-CTAATAT
1 AAATAATTA-ATTTTATCTAATAT
22134533 CATATTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
AAATAATTAATTTTATCTAATATT
Found at i:22137773 original size:41 final size:41
Alignment explanation
Indices: 22137711--22137830 Score: 150
Period size: 41 Copynumber: 2.9 Consensus size: 41
22137701 TGATCGAATG
* *
22137711 TAATACAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAA
1 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
*
22137752 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGATA
1 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
* * * * * * *
22137793 CATTTCGGACTATAGGTCTAGCAGGCTAAAAGCCGGTG
1 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTG
22137831 TACTAAATCA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (41 bp):
TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
Found at i:22138140 original size:2 final size:2
Alignment explanation
Indices: 22138133--22138159 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
22138123 TGCAATTGGG
22138133 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
22138160 AATGTACTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22140520 original size:26 final size:25
Alignment explanation
Indices: 22140491--22140649 Score: 72
Period size: 26 Copynumber: 6.5 Consensus size: 25
22140481 TACATTTTTA
22140491 TTAAATTATATTTAATAATAATTATT
1 TTAAATTATATTT-ATAATAATTATT
*
22140517 TTAAATTATATTT-T-AT-ACTATT
1 TTAAATTATATTTATAATAATTATT
* * *
22140539 ATATATTATGATTT-TAGTAAATTCA-T
1 TTAAATTAT-ATTTATAAT-AATT-ATT
* * **
22140565 ATAAGA--ATATTTAATATTAAGAATT
1 TTAA-ATTATATTT-ATAATAATTATT
*
22140590 TT--ATTA-AATTAT-ATATATT-TT
1 TTAAATTATATTTATAATA-ATTATT
*
22140611 TTAAATTATATTTAATAATAATTATG
1 TTAAATTATATTT-ATAATAATTATT
22140637 TTAAATTATATTT
1 TTAAATTATATTT
22140650 TATACTATTA
Statistics
Matches: 99, Mismatches: 16, Indels: 36
0.66 0.11 0.24
Matches are distributed among these distances:
21 6 0.06
22 16 0.16
23 14 0.14
24 11 0.11
25 11 0.11
26 39 0.39
27 2 0.02
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (25 bp):
TTAAATTATATTTATAATAATTATT
Found at i:22140631 original size:120 final size:120
Alignment explanation
Indices: 22140476--22141003 Score: 810
Period size: 120 Copynumber: 4.4 Consensus size: 120
22140466 AAAATCAGAA
* * * * *
22140476 AAAT-ATACATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATACTATTA
1 AAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATACTATCA
* *
22140540 TATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATT
66 TATATTATAATTTTAGTAAATTCATATAAGAATATTGAATATTAAGAATTTTATT
* * *
22140595 AAATTATATATATTT-TTTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATACTATT
1 AAATCATATAT-TTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATACTA-T
* * *
22140659 ATATATATTATAATTTTAGTAAATTCATATAAGAATATTTAATACTAAGAATTTTATT
64 -CATATATTATAATTTTAGTAAATTCATATAAGAATATTGAATATTAAGAATTTTATT
22140717 AAATCATATATTTTAATTAAAATATATTTAATAATAATTAT-TTCAAATTATATTTTATACTATC
1 AAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTTTATACTATC
*
22140781 ATATATTATAATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATT
65 ATATATTATAATTTTAGTAAATTCATATAAGAATATTGAATATTAAGAATTTTATT
*
22140837 AAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTATCA
1 AAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATACTATCA
* * * * *
22140902 TATATTATGATTTGAGTAAAATAATATAAGAATATTGATTATTAAGAATTTTATT
66 TATATTATAATTTTAGTAAATTCATATAAGAATATTGAATATTAAGAATTTTATT
*
22140957 AAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
1 AAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
22141004 ATATGATTAA
Statistics
Matches: 384, Mismatches: 18, Indels: 13
0.93 0.04 0.03
Matches are distributed among these distances:
119 4 0.01
120 261 0.68
121 12 0.03
122 107 0.28
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (120 bp):
AAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATACTATCA
TATATTATAATTTTAGTAAATTCATATAAGAATATTGAATATTAAGAATTTTATT
Found at i:22140977 original size:18 final size:17
Alignment explanation
Indices: 22140949--22140983 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
22140939 ATTATTAAGA
*
22140949 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
22140966 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
22140984 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:22141205 original size:44 final size:44
Alignment explanation
Indices: 22141142--22141238 Score: 133
Period size: 44 Copynumber: 2.2 Consensus size: 44
22141132 CTATTACTCC
*
22141142 TCCATTCCATTCAACCAAACACA-AGAATACTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACA-ATAGAATACTATTACGCCTCTAT
** * *
22141186 TCCATTACATTCAACCAAACAATTTATTGCTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACAATAGAATACTATTACGCCTCTAT
22141230 TCCATTACA
1 TCCATTACA
22141239 GCGAACCAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 1 0.02
44 46 0.98
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (44 bp):
TCCATTACATTCAACCAAACAATAGAATACTATTACGCCTCTAT
Found at i:22145435 original size:8 final size:8
Alignment explanation
Indices: 22145410--22145452 Score: 59
Period size: 8 Copynumber: 5.1 Consensus size: 8
22145400 TTATTTATTC
22145410 TCTTTTCTT
1 TCTTTT-TT
22145419 TCTTTTTTT
1 TC-TTTTTT
22145428 TCTTTTTT
1 TCTTTTTT
*
22145436 TCGTTTTT
1 TCTTTTTT
22145444 TCTTTTTT
1 TCTTTTTT
22145452 T
1 T
22145453 TCAGCTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
8 21 0.68
9 6 0.19
10 4 0.13
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (8 bp):
TCTTTTTT
Found at i:22145453 original size:9 final size:9
Alignment explanation
Indices: 22145410--22145454 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
22145400 TTATTTATTC
*
22145410 TCTTTTCTT
1 TCTTTTTTT
22145419 TCTTTTTTT
1 TCTTTTTTT
22145428 TC-TTTTTT
1 TCTTTTTTT
*
22145436 TC-GTTTTT
1 TCTTTTTTT
22145444 TCTTTTTTT
1 TCTTTTTTT
22145453 TC
1 TC
22145455 AGCTAAATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
8 15 0.47
9 17 0.53
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:22147648 original size:22 final size:22
Alignment explanation
Indices: 22147623--22147670 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
22147613 AAAAGATGGC
22147623 TAGGATGTGATAGGCGAAAGCT
1 TAGGATGTGATAGGCGAAAGCT
* * * *
22147645 TAGGATTTGATGGGTGAAAGGT
1 TAGGATGTGATAGGCGAAAGCT
22147667 TAGG
1 TAGG
22147671 TTTTTTTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.04, G:0.40, T:0.27
Consensus pattern (22 bp):
TAGGATGTGATAGGCGAAAGCT
Found at i:22147879 original size:6 final size:6
Alignment explanation
Indices: 22147868--22147930 Score: 94
Period size: 6 Copynumber: 10.8 Consensus size: 6
22147858 ATAAAAATAG
22147868 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT --AATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT
* *
22147914 AGAATA AAAATT AAAAT
1 AAAATT AAAATT AAAAT
22147931 CTGTAATTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
4 4 0.08
6 48 0.92
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:22147923 original size:16 final size:16
Alignment explanation
Indices: 22147861--22147927 Score: 62
Period size: 18 Copynumber: 3.9 Consensus size: 16
22147851 GCAAAATATA
22147861 AAAATAGAAAATTAAAATT
1 AAAATA-AAAATT--AATT
*
22147880 AAAATTAAAATTAAAATT
1 AAAATAAAAATT--AATT
*
22147898 AAAATTAAAATTAATT
1 AAAATAAAAATTAATT
*
22147914 AGAATAAAAATTAA
1 AAAATAAAAATTAA
22147928 AATCTGTAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
16 16 0.36
18 24 0.53
19 5 0.11
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
AAAATAAAAATTAATT
Found at i:22153924 original size:21 final size:21
Alignment explanation
Indices: 22153900--22153943 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
22153890 AAACAAATAA
*
22153900 TAAAAACAG-TTAAATAAATCT
1 TAAAAAAAGATTAAATAAA-CT
*
22153921 TAAAAAAAGATTAATTAAACT
1 TAAAAAAAGATTAAATAAACT
22153942 TA
1 TA
22153944 GCTCAGCTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.30
Consensus pattern (21 bp):
TAAAAAAAGATTAAATAAACT
Found at i:22156848 original size:37 final size:37
Alignment explanation
Indices: 22156779--22156850 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
22156769 GTTTTAAATT
* **
22156779 ATTATGTCTTGTTTAATTACATGTTTAATATGTGTTA
1 ATTATGTCTAGTTTAATTACATCATTAATATGTGTTA
*
22156816 ATTATGTCCTAGTTT-ATTACATCATTATTATGTGT
1 ATTATGT-CTAGTTTAATTACATCATTAATATGTGT
22156851 CTTAAGCATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 24 0.80
38 6 0.20
ACGTcount: A:0.26, C:0.08, G:0.12, T:0.53
Consensus pattern (37 bp):
ATTATGTCTAGTTTAATTACATCATTAATATGTGTTA
Found at i:22161481 original size:9 final size:9
Alignment explanation
Indices: 22161463--22161500 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
22161453 GTTTCCCACG
*
22161463 TTAGGTTTT
1 TTAGGGTTT
22161472 TTAGGGTTT
1 TTAGGGTTT
*
22161481 TTAGGATTT
1 TTAGGGTTT
22161490 TTAGGGTTT
1 TTAGGGTTT
22161499 TT
1 TT
22161501 GGAGAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.13, C:0.00, G:0.26, T:0.61
Consensus pattern (9 bp):
TTAGGGTTT
Found at i:22161490 original size:18 final size:18
Alignment explanation
Indices: 22161463--22161500 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
22161453 GTTTCCCACG
*
22161463 TTAGGTTTTTTAGGGTTT
1 TTAGGATTTTTAGGGTTT
22161481 TTAGGATTTTTAGGGTTT
1 TTAGGATTTTTAGGGTTT
22161499 TT
1 TT
22161501 GGAGAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.26, T:0.61
Consensus pattern (18 bp):
TTAGGATTTTTAGGGTTT
Found at i:22161840 original size:126 final size:126
Alignment explanation
Indices: 22161615--22162057 Score: 617
Period size: 126 Copynumber: 3.5 Consensus size: 126
22161605 GATAAAATTA
* * * * * * * *
22161615 AAGCAGGATGAT-TTATCAGAAGGATTTTTGAAGTCGCGCTCACATGAACGCGCTTTTGCTACAG
1 AAGCAGGATGCTATT-TGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAG
*
22161679 TAGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGTAAATAGTATAAAACAACGCTGC
65 TAGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAACAACGCTGC
*
22161741 AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * *
22161806 AGGTCCTAAAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAATAACGCTGC
66 AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAACAACGCTGC
* * * *
22161867 AAGCAGGATGCTATTTGAGAAGAATTTATGAAATCGCGCCCTCGTGGATGCGCTTTTGTTACAGT
1 AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * *
22161932 AGGTCCTGGAAAAATAATTTTGACTTGACGTTTCTGAGCAAATAGTATAAAATC-A--CTTC
66 AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAA-CAACGCTGC
* *
22161991 TAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACACGCTTTTGCTACAG
1 AAGCAGGATGCTATT-TGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAG
22162055 TAG
65 TAG
22162058 CATGTTTGGG
Statistics
Matches: 283, Mismatches: 31, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
123 2 0.01
124 61 0.22
126 218 0.77
127 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (126 bp):
AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAACAACGCTGC
Found at i:22165132 original size:53 final size:53
Alignment explanation
Indices: 22165065--22165168 Score: 172
Period size: 53 Copynumber: 2.0 Consensus size: 53
22165055 ATATTTTTTC
* ** *
22165065 AATTATTAATTGATAATTGTATTAATTTTTAGTAAAATTATCAAATTATATCA
1 AATTATTAACTGATAATTGTATTAATGGTTAGTAAAATTAGCAAATTATATCA
22165118 AATTATTAACTGATAATTGTATTAATGGTTAGTAAAATTAGCAAATTATAT
1 AATTATTAACTGATAATTGTATTAATGGTTAGTAAAATTAGCAAATTATAT
22165169 TTAAGTTAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (53 bp):
AATTATTAACTGATAATTGTATTAATGGTTAGTAAAATTAGCAAATTATATCA
Found at i:22165247 original size:43 final size:43
Alignment explanation
Indices: 22165168--22165531 Score: 437
Period size: 43 Copynumber: 8.5 Consensus size: 43
22165158 GCAAATTATA
* *
22165168 TTTAAGTTAAGGG-TTAGGGTTTTTTATTTAAGGGTTACGGTT
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTACGGTT
* * ** *
22165210 TTAAAGTTAAGGGTTTAGGATTTTTATTTTAATGGTTACGGTT
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTACGGTT
* * *
22165253 TTTAAGTTAAGGGTTTAGGGATTTTAGGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTACGGTT
** **
22165296 TTTAAGTTAAGGGTTTAGGGTTTTTATTTTAAGGGTTACATTT
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTACGGTT
* *
22165339 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAATGGTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTACGGTT
* * * * *
22165382 TTTCAGTTAAGGATTTATGATTTTTAAGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGG-TTACGGTT
* *
22165426 TTTAAGTTAAGGG-TTAGGGTTTTTAGGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGG-TTACGGTT
* * *
22165469 TTTAAGTTAATGATTTAGGGTTTTTAATTTAAGGGTTA-GTGTT
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTACG-GTT
*
22165512 TTTAATTTAAGGGTTTAGGG
1 TTTAAGTTAAGGGTTTAGGG
22165532 GTAGGGTTTT
Statistics
Matches: 275, Mismatches: 43, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
42 13 0.05
43 225 0.82
44 37 0.13
ACGTcount: A:0.24, C:0.01, G:0.27, T:0.48
Consensus pattern (43 bp):
TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTACGGTT
Found at i:22165328 original size:65 final size:65
Alignment explanation
Indices: 22165168--22165528 Score: 417
Period size: 65 Copynumber: 5.6 Consensus size: 65
22165158 GCAAATTATA
* * *
22165168 TTTAAGTTAAGGGTTAGGGTTTTTTATTTAAGGG-TTACGG-TTTTAAAGTTAAGGGTTTAGGAT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTACGGATTTT-AAGTTAAGGGTTTAGGGT
22165231 T
65 T
** * * * *
22165232 TTTATTTTAATGGTTACGGTTTTTAAGTTAAGGGTTTAGGGATTTTAGGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTACGGATTTTAAGTTAAGGGTTTAGGGTT
** ***
22165296 TTTAAGTTAAGGGTTTAGGGTTTTTATTTTAAGGG-TTACATTTTTTAAGTTAAGGGTTTAGGGT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTACGGATTTTAAGTTAAGGGTTTAGGGT
22165360 T
65 T
* * * * *
22165361 TTTAAGTTAATGGTTAGGGTTTTTCAGTTAAGGATTTA-TGATTTTTAAGTTAAGGGTTTAAGGT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTACGGA-TTTTAAGTTAAGGGTTTAGGGT
22165425 T
65 T
* * * * *
22165426 TTTAAGTTAAGGGTTAGGGTTTTTAGGTTAAGGGTTTATGGTTTTTAAGTTAATGATTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTACGGATTTTAAGTTAAGGGTTTAGGGTT
* * *
22165491 TTTAATTTAAGGGTTAGTGTTTTTAATTTAAGGGTTTA
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTA
22165529 GGGGTAGGGT
Statistics
Matches: 248, Mismatches: 42, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
64 78 0.31
65 165 0.67
66 5 0.02
ACGTcount: A:0.24, C:0.01, G:0.27, T:0.48
Consensus pattern (65 bp):
TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTACGGATTTTAAGTTAAGGGTTTAGGGTT
Found at i:22165830 original size:21 final size:21
Alignment explanation
Indices: 22165806--22165849 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
22165796 TCCAGCTTCT
22165806 GGCGGCGG-TTGTGGTTCCTCC
1 GGCGG-GGATTGTGGTTCCTCC
* *
22165827 GGCGGGGATTTTGGTTCTTCC
1 GGCGGGGATTGTGGTTCCTCC
22165848 GG
1 GG
22165850 TAGGACATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.02, C:0.23, G:0.43, T:0.32
Consensus pattern (21 bp):
GGCGGGGATTGTGGTTCCTCC
Found at i:22166803 original size:7 final size:7
Alignment explanation
Indices: 22166788--22166819 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
22166778 TATTAGTTAT
*
22166788 ATACAAA
1 ATACTAA
22166795 ATACTAA
1 ATACTAA
22166802 ATACTAA
1 ATACTAA
22166809 ATACTAA
1 ATACTAA
22166816 ATAC
1 ATAC
22166820 CAATTGACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.59, C:0.16, G:0.00, T:0.25
Consensus pattern (7 bp):
ATACTAA
Found at i:22167021 original size:20 final size:20
Alignment explanation
Indices: 22166984--22167021 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
22166974 TTAATTTTTA
*
22166984 AAAATCTACATAATAATTGT
1 AAAATCTACATAAGAATTGT
22167004 AAAATCTA-ATATAGAATT
1 AAAATCTACATA-AGAATT
22167022 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAGAATTGT
Found at i:22168033 original size:11 final size:11
Alignment explanation
Indices: 22168019--22168095 Score: 63
Period size: 11 Copynumber: 6.9 Consensus size: 11
22168009 TTATATATGG
22168019 ATTTGAGAGAA
1 ATTTGAGAGAA
*
22168030 ATTTG-GAAGGA
1 ATTTGAG-AGAA
22168041 ATTTGAGAGTAA
1 ATTTGAGAG-AA
22168053 A-TTGAGAGGAA
1 ATTTGAGA-GAA
22168064 ATTT-AGAGGAA
1 ATTTGAGA-GAA
*
22168075 A-ATGAGATGAA
1 ATTTGAGA-GAA
22168086 ATTTGAGAGA
1 ATTTGAGAGA
22168096 GGATTAATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
10 2 0.04
11 41 0.76
12 11 0.20
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:22168081 original size:33 final size:35
Alignment explanation
Indices: 22168019--22168094 Score: 88
Period size: 33 Copynumber: 2.3 Consensus size: 35
22168009 TTATATATGG
* **
22168019 ATTTGAGA-GAAATTTGGAAGGAATTTGAGA-GTAA
1 ATTTGAGAGGAAATTTAGAAGGAAAATGAGATG-AA
22168053 A-TTGAGAGGAAATTTAG-AGGAAAATGAGATGAA
1 ATTTGAGAGGAAATTTAGAAGGAAAATGAGATGAA
22168086 ATTTGAGAG
1 ATTTGAGAG
22168095 AGGATTAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
33 19 0.53
34 17 0.47
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.26
Consensus pattern (35 bp):
ATTTGAGAGGAAATTTAGAAGGAAAATGAGATGAA
Found at i:22168349 original size:40 final size:40
Alignment explanation
Indices: 22168274--22168350 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
22168264 ACGTGGACAC
* * * * **
22168274 AAATCGCGCTTACGTGGATGCTATTTGCTGCCACGTCAGA
1 AAATCACGCTGACGTGAACGCTATTTGCTAACACGTCAGA
22168314 AAATCACGCTGACGTGAACGCTATTTGCTAACACGTC
1 AAATCACGCTGACGTGAACGCTATTTGCTAACACGTC
22168351 CCCTGACATC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
AAATCACGCTGACGTGAACGCTATTTGCTAACACGTCAGA
Found at i:22169114 original size:12 final size:12
Alignment explanation
Indices: 22169093--22169126 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
22169083 TATATATTTT
*
22169093 AAAATTATATAA
1 AAAATAATATAA
22169105 AAAATAATATAA
1 AAAATAATATAA
*
22169117 AAATTAATAT
1 AAAATAATAT
22169127 GGGTAGGCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:22169482 original size:20 final size:21
Alignment explanation
Indices: 22169451--22169493 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
22169441 AATTCATTTG
*
22169451 AAGAATATATAAAAAAAACTT
1 AAGAATATATAAAAAAAAATT
22169472 AAGAA-ATATAAAAAAAAATT
1 AAGAATATATAAAAAAAAATT
22169492 AA
1 AA
22169494 AAACCCTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (21 bp):
AAGAATATATAAAAAAAAATT
Found at i:22170526 original size:25 final size:24
Alignment explanation
Indices: 22170492--22170545 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 24
22170482 ATTTTATATC
*
22170492 AATATTTATAATAATATTAAATAA
1 AATAATTATAATAATATTAAATAA
22170516 ATATAATTATAATAATATTAAATAA
1 A-ATAATTATAATAATATTAAATAA
22170541 AATAA
1 AATAA
22170546 AAATCCGCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 5 0.18
25 23 0.82
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
AATAATTATAATAATATTAAATAA
Found at i:22172002 original size:32 final size:32
Alignment explanation
Indices: 22171966--22172034 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
22171956 GCCTTGTTGT
* * *
22171966 TAGGCGACACCACTTTGGTGAAGCCTCTCTAA
1 TAGGCGACACCACTCTAGTGAAGCCTCCCTAA
** *
22171998 TAGGCGGTACCACTCTAGTGAAGCCTCCCTGA
1 TAGGCGACACCACTCTAGTGAAGCCTCCCTAA
22172030 TAGGC
1 TAGGC
22172035 AGCACCGGTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.23
Consensus pattern (32 bp):
TAGGCGACACCACTCTAGTGAAGCCTCCCTAA
Found at i:22172291 original size:11 final size:11
Alignment explanation
Indices: 22172263--22172316 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
22172253 AGATTAGTAT
*
22172263 AGAAGATAG-A
1 AGAAGAAAGAA
22172273 AG-AGAAAGAA
1 AGAAGAAAGAA
22172283 AGAAGAAAGAA
1 AGAAGAAAGAA
* *
22172294 AGGAGAAGGAA
1 AGAAGAAAGAA
22172305 A-AAGAAAAGAA
1 AGAAG-AAAGAA
22172316 A
1 A
22172317 AACACATAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
9 5 0.14
10 7 0.19
11 24 0.67
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.02
Consensus pattern (11 bp):
AGAAGAAAGAA
Found at i:22172305 original size:22 final size:22
Alignment explanation
Indices: 22172274--22172316 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
22172264 GAAGATAGAA
22172274 GAGAAAGAAAGAAG-AAAGAAAG
1 GAGAAAGAAA-AAGAAAAGAAAG
*
22172296 GAGAAGGAAAAAGAAAAGAAA
1 GAGAAAGAAAAAGAAAAGAAA
22172317 AACACATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (22 bp):
GAGAAAGAAAAAGAAAAGAAAG
Found at i:22172630 original size:13 final size:13
Alignment explanation
Indices: 22172614--22172638 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22172604 TTTTTTTATT
22172614 TATTTTTGTAAGG
1 TATTTTTGTAAGG
22172627 TATTTTTGTAAG
1 TATTTTTGTAAG
22172639 AAATATAGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (13 bp):
TATTTTTGTAAGG
Found at i:22173091 original size:11 final size:11
Alignment explanation
Indices: 22173074--22173108 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
22173064 TTTTTAATCA
22173074 AATATATATTT
1 AATATATATTT
* *
22173085 TATATATATTA
1 AATATATATTT
22173096 AATATATATTT
1 AATATATATTT
22173107 AA
1 AA
22173109 AATGGGTCGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
AATATATATTT
Found at i:22173096 original size:26 final size:25
Alignment explanation
Indices: 22173023--22173085 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 25
22173013 ATTATATATT
22173023 AAATATAT-TTTTTTATTTTTAATC
1 AAATATATATTTTTTATTTTTAATC
22173047 AAATATATATATTTTTATTTTTAATC
1 AAATATATAT-TTTTTATTTTTAATC
22173073 AAATATATATTTT
1 AAATATATATTTT
22173086 ATATATATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
24 8 0.22
25 4 0.11
26 25 0.68
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (25 bp):
AAATATATATTTTTTATTTTTAATC
Found at i:22173104 original size:26 final size:25
Alignment explanation
Indices: 22173015--22173104 Score: 80
Period size: 24 Copynumber: 3.7 Consensus size: 25
22173005 CGACTCGAAT
22173015 TATATATTAAATATAT-T-TTTTTA
1 TATATATTAAATATATATATTTTTA
* * *
22173038 TTTTTAATCAAATATATATATTTTTA
1 TATAT-ATTAAATATATATATTTTTA
* * * *
22173064 TTTTTAATCAA-ATATATA-TTTTA
1 TATATATTAAATATATATATTTTTA
22173087 TATATATTAAATATATAT
1 TATATATTAAATATATAT
22173105 TTAAAATGGG
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
23 15 0.28
24 23 0.43
25 4 0.08
26 11 0.21
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
TATATATTAAATATATATATTTTTA
Found at i:22174591 original size:41 final size:41
Alignment explanation
Indices: 22174530--22174891 Score: 383
Period size: 41 Copynumber: 8.9 Consensus size: 41
22174520 TTCTTACCTT
* * * *
22174530 TCGGGGCTTTAGCGGTGTTTTCGAAAAAGCGCCGCTAATAC
1 TCGGGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
* * *
22174571 TCGGGGTTTTAGCGGCGTTTTTTAAAATGCGTCGCTAATGC
1 TCGGGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
* * ** * *
22174612 TCGGGGTTTTAGTGGCGTTTTTGGAAAATTGCTGCTAATTC
1 TCGGGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
* * *
22174653 TCGGTGTTTTAGCGGCATTTTT-CAAAAGCGCCGCTAATGC
1 TCGGGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
* **
22174693 TTGGGGTTTTAGCGGCGTTTTTGAAAATTCGCCGCT-ATGC
1 TCGGGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
* * * * *
22174733 TGGGGGCTTTAACGGCATTTTTGATAAAGCGCCGCTAATGC
1 TCGGGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
* *
22174774 TC--GGTGTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGC
1 TCGGGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
* * * *
22174813 TGGGGGTATTAGCAGCGTTTTTGAAAAAGCGCCGCTAATAC
1 TCGGGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
* * *
22174854 T-GGAGGCTTTAGCGGTGTTTTTGAAAATGCGCCGCTAA
1 TCGG-GGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAA
22174892 AAACATTTTA
Statistics
Matches: 262, Mismatches: 54, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
39 32 0.12
40 67 0.26
41 163 0.62
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (41 bp):
TCGGGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
Found at i:22174712 original size:81 final size:79
Alignment explanation
Indices: 22174532--22174891 Score: 328
Period size: 80 Copynumber: 4.4 Consensus size: 79
22174522 CTTACCTTTC
* * * ** * *
22174532 GGGGCTTTAGCGGTGTTTTCGAAAAAGCGCCGCTAATACTCGGGGTTTTAGCGGCGTTTTTTAAA
1 GGGGTTTTAGCGGCGTTTTTG-AAAATTGCCGCTAATGCTCGGGGTTTTAGCGGC-ATTTTTAAA
* *
22174597 ATGCGTCGCTAATGCT
64 AAGCGCCGCTAATGCT
* * * * *
22174613 CGGGGTTTTAGTGGCGTTTTTGGAAAATTGCTGCTAATTCTCGGTGTTTTAGCGGCATTTTTCAA
1 -GGGGTTTTAGCGGCGTTTTT-GAAAATTGCCGCTAATGCTCGGGGTTTTAGCGGCATTTTTAAA
22174678 AAGCGCCGCTAATGCTT
64 AAGCGCCGCTAATGC-T
* * * *
22174695 GGGGTTTTAGCGGCGTTTTTGAAAATTCGCCGCT-ATGCTGGGGGCTTTAACGGCATTTTTGATA
1 GGGGTTTTAGCGGCGTTTTTGAAAATT-GCCGCTAATGCTCGGGGTTTTAGCGGCATTTTT-AAA
22174759 AAGCGCCGCTAATGCT
64 AAGCGCCGCTAATGCT
* * * ** * * * *
22174775 -CGGTGTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTGGGGGTATTAGCAGCGTTTTTGAAA
1 GGGGTTTTAGCGGCG-TTTTTGAAAATTGCCGCTAATGCTCGGGGTTTTAGCGGCATTTTT-AAA
*
22174839 AAGCGCCGCTAATACT
64 AAGCGCCGCTAATGCT
* * *
22174855 GGAGGCTTTAGCGGTGTTTTTGAAAATGCGCCGCTAA
1 GG-GGTTTTAGCGGCGTTTTTGAAAAT-TGCCGCTAA
22174892 AAACATTTTA
Statistics
Matches: 229, Mismatches: 40, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
79 18 0.08
80 77 0.34
81 69 0.30
82 64 0.28
83 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (79 bp):
GGGGTTTTAGCGGCGTTTTTGAAAATTGCCGCTAATGCTCGGGGTTTTAGCGGCATTTTTAAAAA
GCGCCGCTAATGCT
Found at i:22175275 original size:14 final size:15
Alignment explanation
Indices: 22175240--22175280 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
22175230 TATTTTAAGT
*
22175240 TTTAGGGAGTATGGA
1 TTTAGGGATTATGGA
22175255 TTTAGGGATTATGGA
1 TTTAGGGATTATGGA
22175270 -TTAGGGATTAT
1 TTTAGGGATTAT
22175281 TGTTTAAGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (15 bp):
TTTAGGGATTATGGA
Found at i:22175566 original size:15 final size:15
Alignment explanation
Indices: 22175543--22175621 Score: 67
Period size: 15 Copynumber: 5.5 Consensus size: 15
22175533 TATTTTAAGG
*
22175543 TTTAGGGAGTATGGA
1 TTTAAGGAGTATGGA
*
22175558 TTTAAGGAGTATGAA
1 TTTAAGGAGTATGGA
* *
22175573 TTTAGGGATTATGGA
1 TTTAAGGAGTATGGA
* *
22175588 -TTATGGATTATGG-
1 TTTAAGGAGTATGGA
22175601 TTTAAGG-GT-TGGGA
1 TTTAAGGAGTAT-GGA
22175615 TTTAAGG
1 TTTAAGG
22175622 TTTAAGGGTT
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
12 1 0.02
13 3 0.06
14 24 0.45
15 25 0.47
ACGTcount: A:0.28, C:0.00, G:0.34, T:0.38
Consensus pattern (15 bp):
TTTAAGGAGTATGGA
Found at i:22175624 original size:21 final size:22
Alignment explanation
Indices: 22175599--22175681 Score: 91
Period size: 21 Copynumber: 3.8 Consensus size: 22
22175589 TATGGATTAT
22175599 GGTTTAAGGGTT-GGGATTTAA
1 GGTTTAAGGGTTAGGGATTTAA
* *
22175620 GGTTTAAGGGTTAGGG-GTTAG
1 GGTTTAAGGGTTAGGGATTTAA
* *
22175641 GGGTTAAGAGTTAGGGATTTAA
1 GGTTTAAGGGTTAGGGATTTAA
22175663 GGTTT-AGGGATTCAGGGAT
1 GGTTTAAGGG-TT-AGGGAT
22175682 CGGGTTAGGG
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
21 32 0.64
22 12 0.24
23 6 0.12
ACGTcount: A:0.24, C:0.01, G:0.41, T:0.34
Consensus pattern (22 bp):
GGTTTAAGGGTTAGGGATTTAA
Found at i:22177676 original size:47 final size:47
Alignment explanation
Indices: 22177601--22177691 Score: 157
Period size: 47 Copynumber: 1.9 Consensus size: 47
22177591 TACTAGCTCG
22177601 TTTTAGCTCACTGAAGCAAAGAGAAGAAGTGTGTATGGAAAATATTC
1 TTTTAGCTCACTGAAGCAAAGAGAAGAAGTGTGTATGGAAAATATTC
*
22177648 TTTTTGCTCACTGAAGCAAAGA-ATAGAAGTGTGTATGGAAAATA
1 TTTTAGCTCACTGAAGCAAAGAGA-AGAAGTGTGTATGGAAAATA
22177692 AGTTTAAATC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
46 1 0.02
47 41 0.98
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (47 bp):
TTTTAGCTCACTGAAGCAAAGAGAAGAAGTGTGTATGGAAAATATTC
Found at i:22180845 original size:43 final size:43
Alignment explanation
Indices: 22180798--22181024 Score: 323
Period size: 43 Copynumber: 5.3 Consensus size: 43
22180788 GAACAGTACT
* **
22180798 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGATCATATTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGCTC
* * *
22180841 TTTAGTGGCGTCTGTAATAAAAGCGCCGCTAAAGGTCATGCTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGCTC
* *
22180884 TTTAGCGGCATTTGTGATAAAAGCGCAGCTAAAGGTCATGCTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGCTC
* *
22180927 TTTAGCGGCGTTTGTGATAAAAGTGCCGCTAAAGATCATG-TC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGCTC
*
22180969 TTTAGCGGCGTTTGTGGAT-AAAGCGCCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGT-GATAAAAGCGCCGCTAAAGGTCATGCTC
*
22181012 TATAGCGGCGTTT
1 TTTAGCGGCGTTT
22181025 TTTCACATTA
Statistics
Matches: 164, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
42 36 0.22
43 128 0.78
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGCTC
Found at i:22182609 original size:44 final size:44
Alignment explanation
Indices: 22182481--22182609 Score: 159
Period size: 44 Copynumber: 2.9 Consensus size: 44
22182471 ATACATGCAA
* * *
22182481 AAATTAGATGCATTGAAAGAAATTTGGAACAAACTTTATAATTT
1 AAATTAGATGCATTGAAACAAAATTGGAACAAACTTTGTAATTT
* * ***
22182525 AAATGAGATGTATTGCTCCAAAATTGGAACAAACTTTGTAATTT
1 AAATTAGATGCATTGAAACAAAATTGGAACAAACTTTGTAATTT
* * *
22182569 AAATTAGATGCATTGGAACAAACTTGGAACAAACTCTGTAA
1 AAATTAGATGCATTGAAACAAAATTGGAACAAACTTTGTAA
22182610 AATATATATA
Statistics
Matches: 70, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 70 1.00
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.31
Consensus pattern (44 bp):
AAATTAGATGCATTGAAACAAAATTGGAACAAACTTTGTAATTT
Found at i:22186037 original size:22 final size:22
Alignment explanation
Indices: 22186009--22186053 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
22185999 TGGATTATAT
22186009 ACCAAAATGGTATACCCATGCA
1 ACCAAAATGGTATACCCATGCA
22186031 ACCAAAATGGTATACCCATGCA
1 ACCAAAATGGTATACCCATGCA
22186053 A
1 A
22186054 GTGGAGAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.27, G:0.13, T:0.18
Consensus pattern (22 bp):
ACCAAAATGGTATACCCATGCA
Found at i:22187528 original size:25 final size:25
Alignment explanation
Indices: 22187500--22187557 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
22187490 CTCAGCTCAT
22187500 ATGAGCTTCCCGTTATTCATCTCGC
1 ATGAGCTTCCCGTTATTCATCTCGC
* *
22187525 ATGAGCTTTCCGTTATTCATCTCGG
1 ATGAGCTTCCCGTTATTCATCTCGC
*
22187550 AAGAGCTT
1 ATGAGCTT
22187558 ATTGTTTACA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (25 bp):
ATGAGCTTCCCGTTATTCATCTCGC
Found at i:22195641 original size:25 final size:25
Alignment explanation
Indices: 22195601--22195669 Score: 93
Period size: 25 Copynumber: 2.8 Consensus size: 25
22195591 GACACACCAT
*
22195601 AGCTCTTATGAGCTTCCCGATACTC
1 AGCTCGTATGAGCTTCCCGATACTC
* * *
22195626 AGGTCGTATGAGCTTCCCGTTATTC
1 AGCTCGTATGAGCTTCCCGATACTC
*
22195651 AGCTCGCATGAGCTTCCCG
1 AGCTCGTATGAGCTTCCCG
22195670 TTATTCATCT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.17, C:0.30, G:0.22, T:0.30
Consensus pattern (25 bp):
AGCTCGTATGAGCTTCCCGATACTC
Found at i:22195670 original size:25 final size:25
Alignment explanation
Indices: 22195608--22195690 Score: 103
Period size: 25 Copynumber: 3.3 Consensus size: 25
22195598 CATAGCTCTT
* * * *
22195608 ATGAGCTTCCCGATACTCAGGTCGT
1 ATGAGCTTCCCGTTATTCAGCTCGA
*
22195633 ATGAGCTTCCCGTTATTCAGCTCGC
1 ATGAGCTTCCCGTTATTCAGCTCGA
*
22195658 ATGAGCTTCCCGTTATTCATCTCGA
1 ATGAGCTTCCCGTTATTCAGCTCGA
*
22195683 AAGAGCTT
1 ATGAGCTT
22195691 ACTGTTTACA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.31
Consensus pattern (25 bp):
ATGAGCTTCCCGTTATTCAGCTCGA
Found at i:22196980 original size:27 final size:27
Alignment explanation
Indices: 22196938--22197016 Score: 140
Period size: 27 Copynumber: 2.9 Consensus size: 27
22196928 GGGTGTTATA
* *
22196938 GCACTAGTGACCCCTATCTGATAGGTG
1 GCACTGGTGACTCCTATCTGATAGGTG
22196965 GCACTGGTGACTCCTATCTGATAGGTG
1 GCACTGGTGACTCCTATCTGATAGGTG
22196992 GCACTGGTGACTCCTATCTGATAGG
1 GCACTGGTGACTCCTATCTGATAGG
22197017 CGCCACCAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTGGTGACTCCTATCTGATAGGTG
Found at i:22197124 original size:26 final size:27
Alignment explanation
Indices: 22197095--22197152 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
22197085 AAAAGATAGC
* *
22197095 AGAAAAT-AAGGAAG-AAGAGAGGGAGA
1 AGAAAATAAAGAAAGAAAGA-AAGGAGA
22197121 AG-AAATAAAGAAAGAAAGAAAGGAGA
1 AGAAAATAAAGAAAGAAAGAAAGGAGA
22197147 AGAAAA
1 AGAAAA
22197153 AGAAGGATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 4 0.15
26 16 0.59
27 7 0.26
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (27 bp):
AGAAAATAAAGAAAGAAAGAAAGGAGA
Found at i:22197306 original size:25 final size:26
Alignment explanation
Indices: 22197260--22197308 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
22197250 GTTTTTAATT
*
22197260 TATTTTAAAGTTATTTTGTTAGTTAC
1 TATTATAAAGTTATTTTGTTAGTTAC
22197286 TATTATAAA-TTA-TTTGTTTAGTT
1 TATTATAAAGTTATTTTG-TTAGTT
22197309 TAATGTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 9 0.43
26 8 0.38
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (26 bp):
TATTATAAAGTTATTTTGTTAGTTAC
Found at i:22197394 original size:16 final size:16
Alignment explanation
Indices: 22197375--22197405 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22197365 ATTTATTTTA
*
22197375 AAGTTTTTTTATTAGT
1 AAGTTTTTTGATTAGT
22197391 AAGTTTTTTGATTAG
1 AAGTTTTTTGATTAG
22197406 GTTAATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (16 bp):
AAGTTTTTTGATTAGT
Found at i:22199503 original size:3 final size:3
Alignment explanation
Indices: 22199495--22199525 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
22199485 TATATTTTAC
*
22199495 TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
22199526 TGCTTATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:22202732 original size:14 final size:15
Alignment explanation
Indices: 22202706--22202738 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
22202696 TGCCAAACTG
*
22202706 GGAAGGACCTTATGT
1 GGAAGGACCTTATCT
22202721 GGAAGG-CCTTATCT
1 GGAAGGACCTTATCT
22202735 GGAA
1 GGAA
22202739 AAGCGTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.24
Consensus pattern (15 bp):
GGAAGGACCTTATCT
Found at i:22202868 original size:15 final size:15
Alignment explanation
Indices: 22202822--22202868 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
22202812 ATTTCATAAA
*
22202822 AAAAAGAGAAAAGAAA
1 AAAAAGA-AAAAGAAG
22202838 AGAAAAGAAAAAGAAG
1 A-AAAAGAAAAAGAAG
*
22202854 AAAAAGAAAAGGAAG
1 AAAAAGAAAAAGAAG
22202869 GCCAAGGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 13 0.46
16 9 0.32
17 6 0.21
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAGAAG
Found at i:22204070 original size:45 final size:46
Alignment explanation
Indices: 22203958--22204071 Score: 140
Period size: 46 Copynumber: 2.5 Consensus size: 46
22203948 GAAGATCATA
* *
22203958 ACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAGGATAAAAATAC
1 ACAATCCTTATCTCCTTGAAGTTGCAGTGGAACAGGATAAAAATAC
* * * * **
22204004 ACAAACCTTATCTTCTTGAAGTTGCAGTGGAACAGGTTGAAGTTAC
1 ACAATCCTTATCTCCTTGAAGTTGCAGTGGAACAGGATAAAAATAC
*
22204050 -CAATTCTTATCTCCTTGAAGTT
1 ACAATCCTTATCTCCTTGAAGTT
22204072 CCAGCGGAGT
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
45 19 0.33
46 38 0.67
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (46 bp):
ACAATCCTTATCTCCTTGAAGTTGCAGTGGAACAGGATAAAAATAC
Found at i:22204184 original size:179 final size:179
Alignment explanation
Indices: 22203958--22204562 Score: 908
Period size: 179 Copynumber: 3.4 Consensus size: 179
22203948 GAAGATCATA
* * *
22203958 ACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAGGATAAAAATACACAAACCTTATCTTCTTGA
1 ACAATCCTTATCTCCCTGAAATTGCAGTGGAGCAGGATAAAAATACACAAACCTTATCTCCCTGA
*
22204023 AGTTGCAGTGGAACAGGTTGAAGTTACCAATTCTTATCTCCTTGAAGTTCCAGCGGAGTAGATCG
66 AGTTGCAGTGGAGCAGGTTGAAGTTACCAATTCTTATCTCCTTGAAGTTCCAGCGGAGTAGATCG
* * *
22204088 AAGCTACAAATCTCTTCTCCCTAAAATTAAATTGGAGTAGATCAAAGCC
131 AAGCTACAAATCTCTTCTCCCTAAAATTACATTGGAGCAGATCGAAGCC
* ** * *
22204137 ATAATCCTTATCTCATTGAAATTGAAGTGAAGCAGGATAAAAATACACAAACCTTATCTCCCTGA
1 ACAATCCTTATCTCCCTGAAATTGCAGTGGAGCAGGATAAAAATACACAAACCTTATCTCCCTGA
* * * *
22204202 AGTTACAGTGGAGCAGGTTGAAGTTACCAATTCTTATCCCCTTGAAGTTCCAACGGAGTATATCG
66 AGTTGCAGTGGAGCAGGTTGAAGTTACCAATTCTTATCTCCTTGAAGTTCCAGCGGAGTAGATCG
*
22204267 AAGCTACAAATCTCTTCTCCCTAAAATTACATTGAAGCAGATCGAAGCC
131 AAGCTACAAATCTCTTCTCCCTAAAATTACATTGGAGCAGATCGAAGCC
* * * *
22204316 ACAATCCTTATCTCCTTAAAATTTTC-GTTGAGCAGGATAAAAATACACAAACCTTATCTCCCTG
1 ACAATCCTTATCTCCCTGAAA-TTGCAGTGGAGCAGGATAAAAATACACAAACCTTATCTCCCTG
22204380 AAGTTGCAGTGGAGCAGGTTGAAGTTACCAATTCTTATCTCCTTGAAGTTCCAGCGGAGTAGATC
65 AAGTTGCAGTGGAGCAGGTTGAAGTTACCAATTCTTATCTCCTTGAAGTTCCAGCGGAGTAGATC
* *
22204445 GAAGCTACAAATCTCTTCTCCCTGAAATTACATTAGAGCAGATCGAAGCC
130 GAAGCTACAAATCTCTTCTCCCTAAAATTACATTGGAGCAGATCGAAGCC
* * * * * ** *
22204495 ACAATCCTTTTCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATTAC-CAATTCTTATCTCCTTGA
1 ACAATCCTTATCTCCCTGAAATTGCAGTGGAGCAGGATAAAAATACACAAACCTTATCTCCCTGA
22204559 AGTT
66 AGTT
22204563 ACAACGGAGT
Statistics
Matches: 381, Mismatches: 43, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
178 22 0.06
179 357 0.94
180 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (179 bp):
ACAATCCTTATCTCCCTGAAATTGCAGTGGAGCAGGATAAAAATACACAAACCTTATCTCCCTGA
AGTTGCAGTGGAGCAGGTTGAAGTTACCAATTCTTATCTCCTTGAAGTTCCAGCGGAGTAGATCG
AAGCTACAAATCTCTTCTCCCTAAAATTACATTGGAGCAGATCGAAGCC
Found at i:22204528 original size:44 final size:44
Alignment explanation
Indices: 22203958--22204529 Score: 233
Period size: 44 Copynumber: 12.8 Consensus size: 44
22203948 GAAGATCATA
** **
22203958 ACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAGGATAAAAATAC
1 ACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCA-GAT-CGAAGCC
* * * * * * **
22204004 ACAAACCTTATCTTCTTGAAGTTGCAGTGGAACAGGTTGAAGTT
1 ACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCC
* * * * * *
22204048 ACCAATTCTTATCTCCTTGAAGTTCCAGCGGAGTAGATCGAAGCT
1 A-CAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCC
* * ** * * *
22204093 ACAAAT-CTCT-TCTCCCTAAAATTAAATTGGAGTAGATCAAAGCC
1 AC-AATCCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCC
* ** * * * ** **
22204137 ATAATCCTTATCTCATTGAAATTGAAGTGAAGCAGGATAAAAATAC
1 ACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCA-GAT-CGAAGCC
* * * * **
22204183 ACAAACCTTATCTCCCTGAAGTTACAGTGGAGCAGGTTGAAGTT
1 ACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCC
* * ** * * *
22204227 ACCAATTCTTATC-CCCTTGAAGTTCCAACGGAGTATATCGAAGCT
1 A-CAATCCTTATCTCCC-TGAAGTTGCAGTGGAGCAGATCGAAGCC
* * * * *
22204272 ACAAAT-CTCT-TCTCCCTAAAATTACATTGAAGCAGATCGAAGCC
1 AC-AATCCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCC
* * * * * ** **
22204316 ACAATCCTTATCTCCTTAAAATTTTC-GTTGAGCAGGATAAAAATAC
1 ACAATCCTTATCTCCCT-GAAGTTGCAGTGGAGCA-GAT-CGAAGCC
* * * **
22204362 ACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTT
1 ACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCC
* * * * * *
22204406 ACCAATTCTTATCTCCTTGAAGTTCCAGCGGAGTAGATCGAAGCT
1 A-CAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCC
* * * *
22204451 ACAAAT-CTCT-TCTCCCTGAAATTACATTAGAGCAGATCGAAGCC
1 AC-AATCCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCC
*
22204495 ACAATCCTTTTCTCCCTGAAGTTGCAGTGGAGCAG
1 ACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAG
22204530 GTTGAAATTA
Statistics
Matches: 387, Mismatches: 116, Indels: 48
0.70 0.21 0.09
Matches are distributed among these distances:
43 12 0.03
44 153 0.40
45 137 0.35
46 85 0.22
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (44 bp):
ACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCC
Found at i:22204530 original size:133 final size:133
Alignment explanation
Indices: 22204361--22204624 Score: 438
Period size: 133 Copynumber: 2.0 Consensus size: 133
22204351 GATAAAAATA
*
22204361 CACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACCAATTCTTATCTCCTTGA
1 CACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATTACCAATTCTTATCTCCTTGA
* *
22204426 AGTTCCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATTACATTAGAGCAGATCGA
66 AGTTACAACGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATTACATTAGAGCAGATCGA
22204491 AGC
131 AGC
* *
22204494 CACAATCCTTTTCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATTACCAATTCTTATCTCCTTGA
1 CACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATTACCAATTCTTATCTCCTTGA
* * * * *
22204559 AGTTACAACGGAGTAGATCGAAGCTGCAAGTCTCTTCTCCCTGGAATTACATTGGAGCGGATCGA
66 AGTTACAACGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATTACATTAGAGCAGATCGA
22204624 A
131 A
22204625 ACACCAATTC
Statistics
Matches: 121, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
133 121 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.28
Consensus pattern (133 bp):
CACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATTACCAATTCTTATCTCCTTGA
AGTTACAACGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATTACATTAGAGCAGATCGA
AGC
Found at i:22206213 original size:21 final size:21
Alignment explanation
Indices: 22206187--22206226 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
22206177 TGCAAATTGT
22206187 TTTATTCATT-AGTTTATTTTA
1 TTTATTCATTCA-TTTATTTTA
*
22206208 TTTATTTATTCATTTATTT
1 TTTATTCATTCATTTATTT
22206227 ATTATTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.70
Consensus pattern (21 bp):
TTTATTCATTCATTTATTTTA
Found at i:22206222 original size:12 final size:12
Alignment explanation
Indices: 22206187--22206233 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
22206177 TGCAAATTGT
22206187 TTTATTCA-TTA
1 TTTATTCATTTA
*
22206198 GTTTATTTTATTTA
1 -TTTA-TTCATTTA
22206212 TTTATTCATTTA
1 TTTATTCATTTA
22206224 TTTATT-ATTT
1 TTTATTCATTT
22206234 CTTCAACCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 4 0.13
12 17 0.55
13 7 0.23
14 3 0.10
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.70
Consensus pattern (12 bp):
TTTATTCATTTA
Found at i:22208394 original size:29 final size:27
Alignment explanation
Indices: 22208361--22208415 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 27
22208351 GTGATTAAAT
22208361 AAAATTGACA-CAAGCAGAATTTAAAAGAA
1 AAAATTGACAGCAAG-A-AA-TTAAAAGAA
22208390 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATTGACAGCAAGAAATTAAAAGA
22208416 TAAGTCCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 8 0.32
28 2 0.08
29 11 0.44
30 4 0.16
ACGTcount: A:0.60, C:0.09, G:0.15, T:0.16
Consensus pattern (27 bp):
AAAATTGACAGCAAGAAATTAAAAGAA
Found at i:22211461 original size:48 final size:48
Alignment explanation
Indices: 22211397--22211507 Score: 159
Period size: 48 Copynumber: 2.3 Consensus size: 48
22211387 TAATGTAATC
* * *
22211397 CAATGTATGTAATTTATATTACAAAGTTTGTTCCTTATTTTAATGTTG
1 CAATGAATCTAATTTATATTACAAAGTTTGTTCCTCATTTTAATGTTG
* *
22211445 CAATTAATCTAATTTATATTACAAAGTTTGTTCCTCGTTTTAATGTTG
1 CAATGAATCTAATTTATATTACAAAGTTTGTTCCTCATTTTAATGTTG
*
22211493 TAATGAATCTCAATT
1 CAATGAATCT-AATT
22211508 AAATAAATAT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 51 0.93
49 4 0.07
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.48
Consensus pattern (48 bp):
CAATGAATCTAATTTATATTACAAAGTTTGTTCCTCATTTTAATGTTG
Found at i:22215421 original size:43 final size:43
Alignment explanation
Indices: 22215359--22215476 Score: 141
Period size: 43 Copynumber: 2.8 Consensus size: 43
22215349 TGTAATCTCG
*
22215359 TATTGATGCCAATAGCCCAGCCATGGTCTTACACGAAATCACA
1 TATTGATGCCAATAGCCCAGACATGGTCTTACACGAAATCACA
* * *
22215402 TATTGATGCCAAT-GTCCCAGACATGGTCTTACATGAATTCTCA
1 TATTGATGCCAATAG-CCCAGACATGGTCTTACACGAAATCACA
* * * *
22215445 TATCGATGCC-ATATCCCAAATATGGTCTTACA
1 TATTGATGCCAATAGCCCAGACATGGTCTTACA
22215477 TGTAATCTCG
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
42 19 0.29
43 46 0.71
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (43 bp):
TATTGATGCCAATAGCCCAGACATGGTCTTACACGAAATCACA
Found at i:22222402 original size:21 final size:23
Alignment explanation
Indices: 22222377--22222424 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
22222367 AAATTTATCA
*
22222377 ATTTAA-GTTTTAAAA-CCAATG
1 ATTTAAGGTTTTAAAATCCAAAG
22222398 ATTTAAGTGTTTTAAAATCCAAAG
1 ATTTAAG-GTTTTAAAATCCAAAG
22222422 ATT
1 ATT
22222425 ATGCATGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 6 0.26
23 9 0.39
24 8 0.35
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (23 bp):
ATTTAAGGTTTTAAAATCCAAAG
Found at i:22222755 original size:199 final size:198
Alignment explanation
Indices: 22222515--22222913 Score: 674
Period size: 199 Copynumber: 2.0 Consensus size: 198
22222505 ACAATCCCAA
* *
22222515 AAGAGTTTTAAAAACTTTATTTTAAAATGAATCTGAGAATCTCCTCCAATTGT-TGCATCCAAGT
1 AAGAGTTTTAAAAACTTTATTTTAAAATAAATCTGAGAATCTCCTCAAATT-TATGCATCCAAGT
* *
22222579 TCTATCCTTGAGTGTTATCTGAAAAGTTTTAAGAAAACTAAAAGAGTGAGCTAATATGCCCAGTG
65 CCTATCATTGAGTGTTATCTGAAAAGTTTTAAGAAAACTAAAAGAGTGAGCTAATATGCCCAGTG
* * *
22222644 TGAGTTTTATATCAAGCTTAAATAAAATAAGAAATTAGTTTAGATGAAACAAAAATATTATTAAG
130 CGAATTTTACATCAAGCTTAAATAAAATAAGAAATTAGTTTAGAT-AAACAAAAATATTATTAAG
22222709 CACAT
194 CACAT
* * *
22222714 AAGAGTTTTAAATACTTTATTTTAAAATAAATTTGAGAATCTCCTCAAATTTATGTATCCAAGTC
1 AAGAGTTTTAAAAACTTTATTTTAAAATAAATCTGAGAATCTCCTCAAATTTATGCATCCAAGTC
*
22222779 CTATCATTGAGTGTTATCTGAAAAGTTTTAAGAAAACTAAAAGAGTGAGCTAATATGCCTAGTGC
66 CTATCATTGAGTGTTATCTGAAAAGTTTTAAGAAAACTAAAAGAGTGAGCTAATATGCCCAGTGC
22222844 GAATTTTACATCAAGCTTAAATAAAATAAGAAATTAGTTTAGATAAACAAAAATATTATTAAGCA
131 GAATTTTACATCAAGCTTAAATAAAATAAGAAATTAGTTTAGATAAACAAAAATATTATTAAGCA
22222909 CAT
196 CAT
22222912 AA
1 AA
22222914 TAATCAAACA
Statistics
Matches: 188, Mismatches: 11, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
198 27 0.14
199 161 0.86
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.33
Consensus pattern (198 bp):
AAGAGTTTTAAAAACTTTATTTTAAAATAAATCTGAGAATCTCCTCAAATTTATGCATCCAAGTC
CTATCATTGAGTGTTATCTGAAAAGTTTTAAGAAAACTAAAAGAGTGAGCTAATATGCCCAGTGC
GAATTTTACATCAAGCTTAAATAAAATAAGAAATTAGTTTAGATAAACAAAAATATTATTAAGCA
CAT
Found at i:22227456 original size:27 final size:27
Alignment explanation
Indices: 22227385--22227456 Score: 62
Period size: 27 Copynumber: 2.7 Consensus size: 27
22227375 TTCTCGAGAA
* *
22227385 TCATGAATATCAAGTA-TTTTGACAATT
1 TCATGAA-ATCAAATATTTTTAACAATT
22227412 TGCA--AAAT-AAGATGATTTTTAACAATT
1 T-CATGAAATCAA-AT-ATTTTTAACAATT
22227439 TCATGAAATCAAATATTT
1 TCATGAAATCAAATATTT
22227457 AAAAAATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
24 2 0.06
25 3 0.08
26 5 0.14
27 16 0.44
28 8 0.22
29 2 0.06
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.39
Consensus pattern (27 bp):
TCATGAAATCAAATATTTTTAACAATT
Found at i:22227855 original size:16 final size:17
Alignment explanation
Indices: 22227836--22227873 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
22227826 AATTAAGATT
22227836 AGAA-AAAATTATAAAA
1 AGAATAAAATTATAAAA
*
22227852 AGAATAATATTATAAAA
1 AGAATAAAATTATAAAA
22227869 AGAAT
1 AGAAT
22227874 GTTATAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (17 bp):
AGAATAAAATTATAAAA
Found at i:22229722 original size:50 final size:49
Alignment explanation
Indices: 22229663--22230142 Score: 294
Period size: 50 Copynumber: 9.6 Consensus size: 49
22229653 AACTTTTGGA
* * *
22229663 AAGTAAGATTCGCCCTTGTAGCTTCAATCTTATTAACTGCATTGTCGGGG
1 AAGTAAGATTCGCCGTTGTAGCTTTAATCTT-TTAACTGCAATGTCGGGG
* * * ** ** * *
22229713 AAGTAAGATTTGTCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGG
1 AAGTAAGATTCGCCGTTGTAGCTTTAATCT-TTTAACTGCAATGTCGGGG
* * *
22229763 AAGTAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTGCAATGTCGGGG
1 AAGTAAGATTCGCCGTTGTAGCTTTAATC-TTTTAACTGCAATGTCGGGG
* * * * * * ** * * * *
22229813 AAGCATGATTTGCCATTGTGGCTTCAATCTGTTCCACTACACTGCCTGGG
1 AAGTAAGATTCGCCGTTGTAGCTTTAATCT-TTTAACTGCAATGTCGGGG
* **
22229863 AAGTAAGATTCACTATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGG
1 AAGTAAGATTCGCCGTTGTAGCTTTAATC-TTTTAACTGCAATGTCGGGG
* * * ** * ** * *
22229913 AAGCAAGATTCGTCGTTGTGGCTTTAATCTGTTCCACCGCACCGCCTGGG
1 AAGTAAGATTCGCCGTTGTAGCTTTAATCT-TTTAACTGCAATGTCGGGG
* * * *
22229963 AAGTAAGATTCACTGTTGTAGTTTTAATCTTTTTAACTGCAATGTCGAGG
1 AAGTAAGATTCGCCGTTGTAGCTTTAATC-TTTTAACTGCAATGTCGGGG
* * * * ** * ** * *
22230013 AAGCAAGATTCGCCGTTTTGGCTTTAGTCTGTTCCACTACACCGCCTGGG
1 AAGTAAGATTCGCCGTTGTAGCTTTAATCT-TTTAACTGCAATGTCGGGG
* ** * *
22230063 AAGTAAGATACGTTGTTGTAGCTTTAATCTTTTTAACTGTAATGTTGGGG
1 AAGTAAGATTCGCCGTTGTAGCTTTAATC-TTTTAACTGCAATGTCGGGG
* *** *
22230113 AAGCAAGATTCATTGTTGTGGCTTTAATCT
1 AAGTAAGATTCGCCGTTGTAGCTTTAATCT
22230143 GTTCCATCGC
Statistics
Matches: 311, Mismatches: 111, Indels: 17
0.71 0.25 0.04
Matches are distributed among these distances:
49 4 0.01
50 302 0.97
51 5 0.02
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (49 bp):
AAGTAAGATTCGCCGTTGTAGCTTTAATCTTTTAACTGCAATGTCGGGG
Found at i:22229836 original size:100 final size:100
Alignment explanation
Indices: 22229663--22230171 Score: 696
Period size: 100 Copynumber: 5.1 Consensus size: 100
22229653 AACTTTTGGA
* ** * * * * *
22229663 AAGTAAGATTCGCCCTTGTAGCTTCAATCTTATTAACTGCATTGTCGGGGAAGTAAGATTTGTCG
1 AAGTAAGATTCACTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGTCG
22229728 TTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGG
66 TTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGG
* * * * * * *
22229763 AAGTAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCATGATTTGCCA
1 AAGTAAGATTCACTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGTCG
* * *
22229828 TTGTGGCTTCAATCTGTTCCACTACACTGCCTGGG
66 TTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGG
*
22229863 AAGTAAGATTCACTATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGTCG
1 AAGTAAGATTCACTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGTCG
*
22229928 TTGTGGCTTTAATCTGTTCCACCGCACCGCCTGGG
66 TTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGG
* * *
22229963 AAGTAAGATTCACTGTTGTAGTTTTAATCTTTTTAACTGCAATGTCGAGGAAGCAAGATTCGCCG
1 AAGTAAGATTCACTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGTCG
* * *
22230028 TTTTGGCTTTAGTCTGTTCCACTACACCGCCTGGG
66 TTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGG
* ** * * * *
22230063 AAGTAAGATACGTTGTTGTAGCTTTAATCTTTTTAACTGTAATGTTGGGGAAGCAAGATTCATTG
1 AAGTAAGATTCACTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGTCG
*
22230128 TTGTGGCTTTAATCTGTTCCA-TCGCATCGCCTGGG
66 TTGTGGCTTTAATCTGTTCCACT-GCACCGCCTGGG
22230163 AAGTAAGAT
1 AAGTAAGAT
22230172 CTGTAATTTT
Statistics
Matches: 362, Mismatches: 46, Indels: 2
0.88 0.11 0.00
Matches are distributed among these distances:
99 1 0.00
100 361 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (100 bp):
AAGTAAGATTCACTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGTCG
TTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGG
Found at i:22230379 original size:131 final size:131
Alignment explanation
Indices: 22230237--22231062 Score: 1377
Period size: 131 Copynumber: 6.3 Consensus size: 131
22230227 AACTTATTTT
* * * * * *
22230237 ACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAATCTTCTTCCCTATTCTTGGGAAAGATATGA
1 ACTGCTGACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGA
* ** *
22230302 TTTG-CTGTCTTCGATCTATTCCACTACTGCTTAGGGAGATAAAATCTGTAATTTCCAACCTATT
66 TTCGTC-GTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTATT
22230366 CC
130 CC
* *
22230368 ACT-CTTGACCAGGGAGATAGGACTTGTGGCTTAAATTTGCTTCCCTATTCCTGGGGAAGATAAG
1 ACTGC-TGACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAG
* *
22230432 ATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTATT
65 ATTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTATT
22230497 CC
130 CC
*
22230499 ATTGCTGACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGA
1 ACTGCTGACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGA
* *
22230564 TTCGCCGTCTTCGATCTGCTCTACTACTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTATTC
66 TTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTATTC
22230629 C
131 C
* * * *
22230630 ACCGCTGACCAGGGAGATAGGACTAGTGGCTTAAATCTGTTTCCCTACTCCTGAGGAAGATAAGA
1 ACTGCTGACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGA
* *
22230695 TTTGTCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTAATTTCCAACCTATTC
66 TTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTATTC
22230760 C
131 C
22230761 ACTGCTGACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGA
1 ACTGCTGACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGA
*
22230826 TTCGTCGTCTTGGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTATTC
66 TTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTATTC
22230891 C
131 C
* * *
22230892 ACTGCTTACCAGGGAGATAGGACTTGTAGCTTAAATCTGCTTCCCTACTCCTGGGGGAGATAAGA
1 ACTGCTGACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGA
22230957 TTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTATTC
66 TTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTATTC
22231022 C
131 C
22231023 ACTGCTGACCAGGGAGATAGGACTTGTGGCTTAAATCTGC
1 ACTGCTGACCAGGGAGATAGGACTTGTGGCTTAAATCTGC
22231063 CCCAGATATC
Statistics
Matches: 654, Mismatches: 38, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
130 1 0.00
131 651 1.00
132 2 0.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.31
Consensus pattern (131 bp):
ACTGCTGACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGA
TTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTATTC
C
Found at i:22230722 original size:44 final size:44
Alignment explanation
Indices: 22230440--22231006 Score: 179
Period size: 44 Copynumber: 13.0 Consensus size: 44
22230430 AGATTCGCCA
* * * * *
22230440 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA
1 TCTTCAATCTGCTCCACTACTCCTGAGGGAGATAAGATTTGTAG
* ** * * * *
22230484 T-TTCCAACCTATTCCATTGCTGACC--AGGGAGATAGGACTTGT-G
1 TCTT-CAATCTGCTCCACTACT--CCTGAGGGAGATAAGATTTGTAG
* * * **
22230527 GCTTAAATCTGCTTCC-CTACTCCTG-GGGAAGATAAGATTCGCCG
1 TCTTCAATCTGC-TCCACTACTCCTGAGGG-AGATAAGATTTGTAG
* * * * * *
22230571 TCTTCGATCTGCTCTACTACTGCTTAGGGAGATAAGATCTGTAA
1 TCTTCAATCTGCTCCACTACTCCTGAGGGAGATAAGATTTGTAG
* ** ** * * *
22230615 T-TTCCAACCTATTCCACCGCTGACC--AGGGAGATAGGACTAGT-G
1 TCTT-CAATCTGCTCCACTACT--CCTGAGGGAGATAAGATTTGTAG
* * * * *
22230658 GCTTAAATCTGTTTCC-CTACTCCTGAGGAAGATAAGATTTGTCG
1 TCTTCAATCTG-CTCCACTACTCCTGAGGGAGATAAGATTTGTAG
* * * * *
22230702 TCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTAA
1 TCTTCAATCTGCTCCACTACTCCTGAGGGAGATAAGATTTGTAG
* ** * * *
22230746 T-TTCCAACCTATTCCACTGCTGACC--AGGGAGATAGGACTTGT-G
1 TCTT-CAATCTGCTCCACTACT--CCTGAGGGAGATAAGATTTGTAG
* * * *
22230789 GCTTAAATCTGCTTCC-CTACTCCTG-GGGAAGATAAGATTCGTCG
1 TCTTCAATCTGC-TCCACTACTCCTGAGGG-AGATAAGATTTGTAG
** * * * *
22230833 TCTTGGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA
1 TCTTCAATCTGCTCCACTACTCCTGAGGGAGATAAGATTTGTAG
* ** * * *
22230877 T-TTCCAACCTATTCCACTGCTTACC--AGGGAGATAGGACTTGTAG
1 TCTT-CAATCTGCTCCACTAC-T-CCTGAGGGAGATAAGATTTGTAG
* * * *
22230921 -CTTAAATCTGCTTCC-CTACTCCTGGGGGAGATAAGATTCGTCG
1 TCTTCAATCTGC-TCCACTACTCCTGAGGGAGATAAGATTTGTAG
* * * *
22230964 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTA
1 TCTTCAATCTGCTCCACTACTCCTGAGGGAGATAAGATTTGTA
22231007 ATTTCCAACC
Statistics
Matches: 360, Mismatches: 123, Indels: 80
0.64 0.22 0.14
Matches are distributed among these distances:
41 8 0.02
42 7 0.02
43 94 0.26
44 240 0.67
45 7 0.02
46 4 0.01
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (44 bp):
TCTTCAATCTGCTCCACTACTCCTGAGGGAGATAAGATTTGTAG
Found at i:22232270 original size:27 final size:25
Alignment explanation
Indices: 22232240--22232314 Score: 60
Period size: 27 Copynumber: 2.8 Consensus size: 25
22232230 CGCCTTGGCC
22232240 TTTCCTTTTCTTTTTTCTTTTTGTCAT
1 TTTCCTTTT-TTTTTTCTTTTTGTC-T
* * ** *
22232267 TTTCATTTTGATTTTGATTTTTTTCT
1 TTTCCTTTT-TTTTTTCTTTTTGTCT
*
22232293 TTTTCTTTTTTTCTTTCTTTTT
1 TTTCCTTTTTTT-TTTCTTTTT
22232315 TTGATTTTTG
Statistics
Matches: 36, Mismatches: 11, Indels: 3
0.72 0.22 0.06
Matches are distributed among these distances:
25 2 0.06
26 15 0.42
27 19 0.53
ACGTcount: A:0.05, C:0.13, G:0.04, T:0.77
Consensus pattern (25 bp):
TTTCCTTTTTTTTTTCTTTTTGTCT
Found at i:22232301 original size:41 final size:43
Alignment explanation
Indices: 22232245--22232331 Score: 117
Period size: 41 Copynumber: 2.1 Consensus size: 43
22232235 TGGCCTTTCC
22232245 TTTTCTTTTTTCTTTTTGTCATTT-TCATTTTGA-TTTTGATTT
1 TTTTCTTTTTTCTTTTTGTC-TTTCTCATTTTGATTTTTGATTT
* **
22232287 TTTTC-TTTTTCTTTTTTTCTTTCTTTTTTTGATTTTTGATTT
1 TTTTCTTTTTTCTTTTTGTCTTTCTCATTTTGATTTTTGATTT
22232329 TTT
1 TTT
22232332 GATTTTGTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
40 3 0.08
41 20 0.50
42 17 0.43
ACGTcount: A:0.07, C:0.09, G:0.06, T:0.78
Consensus pattern (43 bp):
TTTTCTTTTTTCTTTTTGTCTTTCTCATTTTGATTTTTGATTT
Found at i:22232305 original size:35 final size:35
Alignment explanation
Indices: 22232250--22232323 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 35
22232240 TTTCCTTTTC
*
22232250 TTTTTTCTTTTTGTCATTTTCATTT-TGATTTTGAT
1 TTTTTTCTTTTTCTCATTTTC-TTTCTGATTTTGAT
** **
22232285 TTTTTTCTTTTTCTTTTTTTCTTTCTTTTTTTGAT
1 TTTTTTCTTTTTCTCATTTTCTTTCTGATTTTGAT
22232320 TTTT
1 TTTT
22232324 GATTTTTTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
34 3 0.09
35 30 0.91
ACGTcount: A:0.07, C:0.09, G:0.05, T:0.78
Consensus pattern (35 bp):
TTTTTTCTTTTTCTCATTTTCTTTCTGATTTTGAT
Found at i:22232322 original size:8 final size:8
Alignment explanation
Indices: 22232311--22232356 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
22232301 TTTTCTTTCT
22232311 TTTTTTGA
1 TTTTTTGA
22232319 -TTTTTGA
1 TTTTTTGA
22232326 TTTTTTGA
1 TTTTTTGA
*
22232334 TTTTGTT-T
1 TTTT-TTGA
22232342 TTTTATTGA
1 TTTT-TTGA
22232351 TTTTTT
1 TTTTTT
22232357 ATTCCGATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
7 7 0.22
8 19 0.59
9 6 0.19
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.78
Consensus pattern (8 bp):
TTTTTTGA
Found at i:22232355 original size:41 final size:41
Alignment explanation
Indices: 22232272--22232356 Score: 100
Period size: 41 Copynumber: 2.1 Consensus size: 41
22232262 GTCATTTTCA
* * **
22232272 TTTTGATTTTGATTTTTTTCTTTTTCTTTTTTTCTTTCTTT
1 TTTTGATTTTGATTTTTTTCATTTTCTTTTTTTATTGATTT
* *
22232313 TTTTGATTTTTGA-TTTTTTGATTTTGTTTTTTTATTGATTT
1 TTTTGA-TTTTGATTTTTTTCATTTTCTTTTTTTATTGATTT
22232354 TTT
1 TTT
22232357 ATTCCGATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
41 31 0.84
42 6 0.16
ACGTcount: A:0.08, C:0.05, G:0.08, T:0.79
Consensus pattern (41 bp):
TTTTGATTTTGATTTTTTTCATTTTCTTTTTTTATTGATTT
Found at i:22232367 original size:25 final size:25
Alignment explanation
Indices: 22232322--22232370 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
22232312 TTTTTGATTT
**
22232322 TTGATTTTTTGATTTTGTTTTTTTA
1 TTGATTTTTTGATTCCGTTTTTTTA
22232347 TTGATTTTTT-ATTCCGATTTTTTT
1 TTGATTTTTTGATTCCG-TTTTTTT
22232371 TATTTCGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.12, C:0.04, G:0.10, T:0.73
Consensus pattern (25 bp):
TTGATTTTTTGATTCCGTTTTTTTA
Found at i:22232371 original size:15 final size:15
Alignment explanation
Indices: 22232351--22232380 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
22232341 TTTTTATTGA
22232351 TTTTTTATTCCGATT
1 TTTTTTATTCCGATT
*
22232366 TTTTTTATTTCGATT
1 TTTTTTATTCCGATT
22232381 GTGAATTTTT
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:0.07, T:0.70
Consensus pattern (15 bp):
TTTTTTATTCCGATT
Found at i:22236294 original size:27 final size:27
Alignment explanation
Indices: 22236242--22236294 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
22236232 ATTTTTCCCC
* *
22236242 TATTTTTCTTTTCTGTTGCTATTTTGT
1 TATTTTTCTTTTCTCTTGCTAGTTTGT
*
22236269 TATTTTTCCTTTTCTCTTTCT-GTTTG
1 TATTTTT-CTTTTCTCTTGCTAGTTTG
22236295 CTGCTTGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.06, C:0.15, G:0.09, T:0.70
Consensus pattern (27 bp):
TATTTTTCTTTTCTCTTGCTAGTTTGT
Found at i:22236634 original size:2 final size:2
Alignment explanation
Indices: 22236627--22236657 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
22236617 GGACTTTTAT
*
22236627 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22236658 GTGGGTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:22240674 original size:15 final size:16
Alignment explanation
Indices: 22240650--22240690 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
22240640 AACTTTCGGA
22240650 TCAAGCCCAAGCT-GG
1 TCAAGCCCAAGCTAGG
* *
22240665 TCATGCCCAAGTTAGG
1 TCAAGCCCAAGCTAGG
22240681 TCAAGCCCAA
1 TCAAGCCCAA
22240691 TACCTATGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.29, C:0.32, G:0.22, T:0.17
Consensus pattern (16 bp):
TCAAGCCCAAGCTAGG
Found at i:22244533 original size:21 final size:21
Alignment explanation
Indices: 22244499--22244538 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
22244489 TGAAGTTGAT
* * *
22244499 TTAATGCTTTGTGTGAACATG
1 TTAATGCCTAGTGTAAACATG
22244520 TTAATGCCTAGTGTAAACA
1 TTAATGCCTAGTGTAAACA
22244539 CCATTAGGGC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (21 bp):
TTAATGCCTAGTGTAAACATG
Found at i:22246191 original size:18 final size:18
Alignment explanation
Indices: 22246168--22246202 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
22246158 GAAATTGTGA
22246168 AAAGAGAAAAATGAAAAG
1 AAAGAGAAAAATGAAAAG
* *
22246186 AAAGAGGAAATTGAAAA
1 AAAGAGAAAAATGAAAA
22246203 AAAAAAAGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.23, T:0.09
Consensus pattern (18 bp):
AAAGAGAAAAATGAAAAG
Found at i:22249700 original size:30 final size:28
Alignment explanation
Indices: 22249633--22249700 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 28
22249623 TAAAATCTGT
*
22249633 AAAAATAAAAAATTCAAAATTTTAAAAA
1 AAAAATAAAAAATTCAAAAATTTAAAAA
* *
22249661 AATATATAAAAAGTTCATAAAATTTAAAAA
1 AA-AAATAAAAAATTCA-AAAATTTAAAAA
22249691 AAAACATAAA
1 AAAA-ATAAA
22249701 GTACACTTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 2 0.06
29 13 0.39
30 18 0.55
ACGTcount: A:0.69, C:0.04, G:0.01, T:0.25
Consensus pattern (28 bp):
AAAAATAAAAAATTCAAAAATTTAAAAA
Found at i:22266996 original size:17 final size:18
Alignment explanation
Indices: 22266968--22267003 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
22266958 ATATAGTGTT
22266968 AAAAATATTATTTTTAAA
1 AAAAATATTATTTTTAAA
22266986 AAAAATA-TATTTTTAAA
1 AAAAATATTATTTTTAAA
22267003 A
1 A
22267004 TTTTTAGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAAATATTATTTTTAAA
Found at i:22267864 original size:31 final size:32
Alignment explanation
Indices: 22267829--22267889 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 32
22267819 AAAATGAATC
22267829 TAGACAATAATTTG-TCCTG-TTCATTTTAATT
1 TAGACAATAATTTGTTCC-GATTCATTTTAATT
*
22267860 TAGACAATCATTTGTTCCGATTCATTTTAA
1 TAGACAATAATTTGTTCCGATTCATTTTAA
22267890 ATGCATTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 14 0.52
32 13 0.48
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.46
Consensus pattern (32 bp):
TAGACAATAATTTGTTCCGATTCATTTTAATT
Found at i:22268182 original size:19 final size:18
Alignment explanation
Indices: 22268158--22268396 Score: 87
Period size: 19 Copynumber: 13.3 Consensus size: 18
22268148 ATTTTTCCCT
22268158 TAAAAATCATAAAAAATTA
1 TAAAAAT-ATAAAAAATTA
*
22268177 TAAAAAAATCAAAAAA-TA
1 TAAAAATAT-AAAAAATTA
* * *
22268195 T-TAAATATTAAATATTA
1 TAAAAATATAAAAAATTA
22268212 -AAAAATA-AAAGAAA-T-
1 TAAAAATATAAA-AAATTA
* * * *
22268227 TAAAATTGACAGAAACTTA
1 TAAAAAT-ATAAAAAATTA
*
22268246 TTAAAATTATAAAAAATTA
1 -TAAAAATATAAAAAATTA
* *
22268265 TAAATAT-TATAAAATTA
1 TAAAAATATAAAAAATTA
22268282 TAAAGTAATAT-AAAAATTA
1 TAAA--AATATAAAAAATTA
22268301 T-AAAAT-TAATAAAATTTA
1 TAAAAATATAA-AAAA-TTA
*
22268319 TTTAAAAT-TAAAAAA--A
1 -TAAAAATATAAAAAATTA
22268335 TAAAAATTATTAAAAAA-TA
1 TAAAAA-TA-TAAAAAATTA
* *
22268354 -AAAAATTTATTAAAATTGA
1 TAAAAATATA-AAAAATT-A
* *
22268373 TATAAACT-TAGAAAATTA
1 TA-AAAATATAAAAAATTA
22268391 TAAAAA
1 TAAAAA
22268397 AAAGATCAAA
Statistics
Matches: 168, Mismatches: 25, Indels: 56
0.67 0.10 0.22
Matches are distributed among these distances:
15 6 0.04
16 20 0.12
17 42 0.25
18 34 0.20
19 43 0.26
20 19 0.11
21 4 0.02
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (18 bp):
TAAAAATATAAAAAATTA
Found at i:22268263 original size:10 final size:9
Alignment explanation
Indices: 22268243--22268396 Score: 99
Period size: 10 Copynumber: 17.0 Consensus size: 9
22268233 TGACAGAAAC
*
22268243 TTATTAAAA
1 TTATAAAAA
22268252 TTATAAAAAA
1 TTAT-AAAAA
*
22268262 TTATAAATA
1 TTATAAAAA
22268271 TTAT-AAAA
1 TTATAAAAA
22268279 TTATAAAGTAA
1 TTATAAA--AA
22268290 -TATAAAAA
1 TTATAAAAA
22268298 TTAT-AAAA
1 TTATAAAAA
*
22268306 TTAATAAAAT
1 TT-ATAAAAA
*
22268316 TTATTTAAAA
1 TTA-TAAAAA
22268326 TTA-AAAAA
1 TTATAAAAA
22268334 --ATAAAAA
1 TTATAAAAA
22268341 TTATTAAAAA
1 TTA-TAAAAA
*
22268351 ATA-AAAAA
1 TTATAAAAA
*
22268359 TTTATTAAAA
1 -TTATAAAAA
*
22268369 TTGATATAAAC
1 TT-ATA-AAAA
*
22268380 TTA-GAAAA
1 TTATAAAAA
22268388 TTATAAAAA
1 TTATAAAAA
22268397 AAAGATCAAA
Statistics
Matches: 113, Mismatches: 15, Indels: 34
0.70 0.09 0.21
Matches are distributed among these distances:
6 1 0.01
7 5 0.04
8 30 0.27
9 29 0.26
10 41 0.36
11 7 0.06
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (9 bp):
TTATAAAAA
Found at i:22268278 original size:18 final size:18
Alignment explanation
Indices: 22268247--22268370 Score: 82
Period size: 18 Copynumber: 6.9 Consensus size: 18
22268237 AGAAACTTAT
22268247 TAAA-ATTATAAAAAATTA
1 TAAATATTAT-AAAAATTA
22268265 TAAATATTAT-AAAATTA
1 TAAATATTATAAAAATTA
*
22268282 TAAAGTAATATAAAAATTA
1 TAAA-TATTATAAAAATTA
*
22268301 TAAA-ATTAATAAAATTTA
1 TAAATATT-ATAAAAATTA
*
22268319 TTTAAA-ATTA-AAAAAATA
1 --TAAATATTATAAAAATTA
* *
22268337 AAAATTATTA-AAAAATAA
1 TAAA-TATTATAAAAATTA
* *
22268355 AAAAT-TTATTAAAATT
1 TAAATATTATAAAAATT
22268371 GATATAAACT
Statistics
Matches: 87, Mismatches: 10, Indels: 19
0.75 0.09 0.16
Matches are distributed among these distances:
16 6 0.07
17 19 0.22
18 38 0.44
19 17 0.20
20 7 0.08
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (18 bp):
TAAATATTATAAAAATTA
Found at i:22268282 original size:27 final size:26
Alignment explanation
Indices: 22268247--22268397 Score: 99
Period size: 27 Copynumber: 5.6 Consensus size: 26
22268237 AGAAACTTAT
*
22268247 TAAAATTATAAAAAATTATAAATATTA
1 TAAAATTATAAAAAA-TATAAAAATTA
*
22268274 TAAAATTATAAAGTAATATAAAAATTA
1 TAAAATTATAAA-AAATATAAAAATTA
** *
22268301 TAAAATTAATAAAATTTATTTAAAATTA
1 TAAAATT-ATAAAAAATA-TAAAAATTA
* * *
22268329 -AAAA-AATAAAAATTATTAAAAAATA
1 TAAAATTATAAAAAATA-TAAAAATTA
* * * *
22268354 AAAAATTTATTAAAATTGATATAAACTTA
1 TAAAA-TTATAAAAAAT-ATA-AAAATTA
*
22268383 GAAAATTATAAAAAA
1 TAAAATTATAAAAAA
22268398 AAGATCAAAA
Statistics
Matches: 99, Mismatches: 17, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
25 17 0.17
26 4 0.04
27 35 0.35
28 33 0.33
29 10 0.10
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.34
Consensus pattern (26 bp):
TAAAATTATAAAAAATATAAAAATTA
Found at i:22268325 original size:28 final size:27
Alignment explanation
Indices: 22268294--22268395 Score: 84
Period size: 28 Copynumber: 3.7 Consensus size: 27
22268284 AAGTAATATA
22268294 AAAATTATAAAATTAATAAAATTTATTT
1 AAAATTA-AAAATTAATAAAATTTATTT
* *
22268322 AAAATTAAAAA--AATAAAAATTATTAA
1 AAAATTAAAAATTAATAAAATTTATT-T
* * * *
22268348 AAAATAAAAAATTTATTAAAATTGATAT
1 AAAATTAAAAA-TTAATAAAATTTATTT
*
22268376 AAACTTAGAAAATT-ATAAAA
1 AAAATTA-AAAATTAATAAAA
22268396 AAAAGATCAA
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
25 12 0.21
26 10 0.17
27 9 0.16
28 14 0.24
29 13 0.22
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (27 bp):
AAAATTAAAAATTAATAAAATTTATTT
Done.