Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 100 of 235
Found at i:34546177 original size:16 final size:15
Alignment explanation
Indices: 34546156--34546185 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
34546146 AATAGGCAAA
34546156 TAAATTATTAAATTAT
1 TAAATTA-TAAATTAT
34546172 TAAATTATAAATTA
1 TAAATTATAAATTA
34546186 AATAATGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAAATTATAAATTAT
Found at i:34547390 original size:21 final size:23
Alignment explanation
Indices: 34547361--34547404 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
34547351 TCTACAGAAA
34547361 CAATATAACACA-AATATA-AATT
1 CAATATAACA-ATAATATAGAATT
34547383 CAAT-TAACAATAATATAGAATT
1 CAATATAACAATAATATAGAATT
34547405 AATCAAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 1 0.05
21 11 0.55
22 8 0.40
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (23 bp):
CAATATAACAATAATATAGAATT
Found at i:34548349 original size:20 final size:21
Alignment explanation
Indices: 34548326--34548364 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
34548316 ATTTTTATAT
34548326 TTTTCATAATAT-TTAATACC
1 TTTTCATAATATATTAATACC
*
34548346 TTTTTATAATATATTAATA
1 TTTTCATAATATATTAATA
34548365 ATATTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTTCATAATATATTAATACC
Found at i:34548362 original size:21 final size:21
Alignment explanation
Indices: 34548325--34548364 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
34548315 TATTTTTATA
34548325 TTTTTCATAATATTTAATACC
1 TTTTTCATAATATTTAATACC
34548346 TTTTT-ATAATATATTAATA
1 TTTTTCATAATAT-TTAATA
34548365 ATATTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTTCATAATATTTAATACC
Found at i:34548447 original size:18 final size:19
Alignment explanation
Indices: 34548411--34548451 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
34548401 TTTTTATTAT
*
34548411 ATTTTATACTTTTTAATAA
1 ATTTTATACTTTTCAATAA
*
34548430 ATTTTATA-TTTTCCATAA
1 ATTTTATACTTTTCAATAA
34548448 ATTT
1 ATTT
34548452 ATTATAGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTTATACTTTTCAATAA
Found at i:34548535 original size:33 final size:33
Alignment explanation
Indices: 34548480--34548543 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 33
34548470 ATTTAAGCTT
* *
34548480 AAATAATTAAAAATATTTAATT-AGTCCCTCATA
1 AAATAATTAAAAATAGTCAATTAAG-CCCTCATA
34548513 AAATAATTTAAAAA-AGTCAATTAAGCCCTCA
1 AAATAA-TTAAAAATAGTCAATTAAGCCCTCA
34548544 AATTATATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 18 0.67
34 9 0.33
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.31
Consensus pattern (33 bp):
AAATAATTAAAAATAGTCAATTAAGCCCTCATA
Found at i:34550404 original size:6 final size:6
Alignment explanation
Indices: 34550397--34550433 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
34550387 CATCTAAAAA
*
34550397 TGAAAA TGAAAT TGAAAT TGAAAT TG-AAT TG-AAT TGA
1 TGAAAT TGAAAT TGAAAT TGAAAT TGAAAT TGAAAT TGA
34550434 TATATGTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 10 0.34
6 19 0.66
ACGTcount: A:0.49, C:0.00, G:0.19, T:0.32
Consensus pattern (6 bp):
TGAAAT
Found at i:34550513 original size:34 final size:34
Alignment explanation
Indices: 34550470--34550574 Score: 192
Period size: 34 Copynumber: 3.1 Consensus size: 34
34550460 GATGTTTAGA
34550470 ATTGATGAATTGAAATGAATTATTATAAATCGGG
1 ATTGATGAATTGAAATGAATTATTATAAATCGGG
**
34550504 ATTGATGAATTGAAATGAATTATTATAAATTTGG
1 ATTGATGAATTGAAATGAATTATTATAAATCGGG
34550538 ATTGATGAATTGAAATGAATTATTATAAATCGGG
1 ATTGATGAATTGAAATGAATTATTATAAATCGGG
34550572 ATT
1 ATT
34550575 TAAATCAATT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 67 1.00
ACGTcount: A:0.41, C:0.02, G:0.19, T:0.38
Consensus pattern (34 bp):
ATTGATGAATTGAAATGAATTATTATAAATCGGG
Found at i:34551178 original size:28 final size:28
Alignment explanation
Indices: 34551133--34551213 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 28
34551123 AAGCAACCCA
* **
34551133 AATATCACAACTTTTGTGAGCAAATTCA-
1 AATATCACAGCTCGTGTGAGCAAATT-AG
*
34551161 AATATCATAGCTCGTGTGAGCAAATTAG
1 AATATCACAGCTCGTGTGAGCAAATTAG
* * *
34551189 AATATTACAGCTTGTATGAGCAAAT
1 AATATCACAGCTCGTGTGAGCAAAT
34551214 CAATCTTGTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.98
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (28 bp):
AATATCACAGCTCGTGTGAGCAAATTAG
Found at i:34551830 original size:20 final size:20
Alignment explanation
Indices: 34551805--34551850 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
34551795 AAATAAGAAG
34551805 AAAGAAACTAAGTAAGTTCA
1 AAAGAAACTAAGTAAGTTCA
* * *
34551825 AAAG-AACTTAGTGAGTTCC
1 AAAGAAACTAAGTAAGTTCA
34551844 AAAGAAA
1 AAAGAAA
34551851 TGTAATCCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.52, C:0.11, G:0.17, T:0.20
Consensus pattern (20 bp):
AAAGAAACTAAGTAAGTTCA
Found at i:34554637 original size:352 final size:352
Alignment explanation
Indices: 34554074--34555047 Score: 1849
Period size: 352 Copynumber: 2.8 Consensus size: 352
34554064 TGTGCAAAAC
34554074 ACAAAAATGGTATGCTTAAATGTTGATTTTGAATGGTTTAAAAACATGAATAAATGTTGGTTCAT
1 ACAAAAATGGTATGCTTAAATGTTGATTTTGAATGGTTTAAAAACATGAATAAATGTTGGTTCAT
34554139 TAACTTGAAAGTGTATAAGTTCAATTGGAGTGGTTTAGTGTCAAATGGGGCATGTTGGTTGAATT
66 TAACTTGAAAGTGTATAAGTTCAATTGGAGTGGTTTAGTGTCAAATGGGGCATGTTGGTTGAATT
*
34554204 GATTGTGATTGACTTAATGTTATATTTAATCATGTTTGTTATATGTTTAAAAGGGATTTTTATGC
131 GATTGTGATTGACTTAATGTTATGTTTAATCATGTTTGTTATATGTTTAAAAGGGATTTTTATGC
*
34554269 AAGTCTCAAATGTGCCTTAAAGTGCTTTGAGAATAAAACTTTTTGTTTGGCATGAAATGGTTTCA
196 AAGTCTCAAATGTGCCTTAAAGTGCTTTGAGAATAAAACTTTTTGTTGGGCATGAAATGGTTTCA
34554334 AATGAAGGTTAAGGTATGTTTTGGTCATGTTTTGGGATCATTTGTATAGTGATTGAATGGTTCAT
261 AATGAAGGTTAAGGTATGTTTTGGTCATGTTTTGGGATCATTTGTATAGTGATTGAATGGTTCAT
34554399 TGAATGTGCAAATGGTATGAATTGAAA
326 TGAATGTGCAAATGGTATGAATTGAAA
34554426 ACAAAAATGGTATGCTTAAATGTTGATTTTGAATGGTTTAAAAACATGAATAAATGTTGGTTCAT
1 ACAAAAATGGTATGCTTAAATGTTGATTTTGAATGGTTTAAAAACATGAATAAATGTTGGTTCAT
34554491 TAACTTGAAAGTGTATAAGTTCAATTGGAGTGGTTTAGTGTCAAATGGGGCATGTTGGTTGAATT
66 TAACTTGAAAGTGTATAAGTTCAATTGGAGTGGTTTAGTGTCAAATGGGGCATGTTGGTTGAATT
34554556 GATTGTGATTGACTTAATGTTATGTTTAATCATGTTTGTTATATGTTTAAAAGGGATTTTTATGC
131 GATTGTGATTGACTTAATGTTATGTTTAATCATGTTTGTTATATGTTTAAAAGGGATTTTTATGC
** *
34554621 AAGTCTCATTTGTGCCTTAAAGTGCTTTGGGAATAAAACTTTTTGTTGGGCATGAAATGGTTTCA
196 AAGTCTCAAATGTGCCTTAAAGTGCTTTGAGAATAAAACTTTTTGTTGGGCATGAAATGGTTTCA
*
34554686 AATGAAGGTTAATGTATGTTTTGGTCATGTTTTGGGATCATTTGTATAGTGATTGAATGGTTCAT
261 AATGAAGGTTAAGGTATGTTTTGGTCATGTTTTGGGATCATTTGTATAGTGATTGAATGGTTCAT
*
34554751 TGAATGTGCAAATGGTATGAATTGAAC
326 TGAATGTGCAAATGGTATGAATTGAAA
*
34554778 ACAAAAATGGTATGCTTAAATGTTGATTTTGAATGGTTTAAAAACATAAATAAATGTTGGTTCAT
1 ACAAAAATGGTATGCTTAAATGTTGATTTTGAATGGTTTAAAAACATGAATAAATGTTGGTTCAT
*
34554843 TAACGTGAAAGTGTATAAGTTCAATTGGAGTGGTTTAGTGTCAAATGGGGCATGTTGGTTGAATT
66 TAACTTGAAAGTGTATAAGTTCAATTGGAGTGGTTTAGTGTCAAATGGGGCATGTTGGTTGAATT
*
34554908 GATTGTGATTGACTTAATGTTATGTTTAATCATGTTTGTTATATGTTTAAAAGGAATTTTTATGC
131 GATTGTGATTGACTTAATGTTATGTTTAATCATGTTTGTTATATGTTTAAAAGGGATTTTTATGC
*
34554973 AAGCCTCAAATGTGCCTTAAAGTGCTTTGAGAATAAAACTTTTTGTTGGGCATGAAATGGTTTCA
196 AAGTCTCAAATGTGCCTTAAAGTGCTTTGAGAATAAAACTTTTTGTTGGGCATGAAATGGTTTCA
34555038 AATGAAGGTT
261 AATGAAGGTT
34555048 TTTAACATTT
Statistics
Matches: 608, Mismatches: 14, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
352 608 1.00
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (352 bp):
ACAAAAATGGTATGCTTAAATGTTGATTTTGAATGGTTTAAAAACATGAATAAATGTTGGTTCAT
TAACTTGAAAGTGTATAAGTTCAATTGGAGTGGTTTAGTGTCAAATGGGGCATGTTGGTTGAATT
GATTGTGATTGACTTAATGTTATGTTTAATCATGTTTGTTATATGTTTAAAAGGGATTTTTATGC
AAGTCTCAAATGTGCCTTAAAGTGCTTTGAGAATAAAACTTTTTGTTGGGCATGAAATGGTTTCA
AATGAAGGTTAAGGTATGTTTTGGTCATGTTTTGGGATCATTTGTATAGTGATTGAATGGTTCAT
TGAATGTGCAAATGGTATGAATTGAAA
Found at i:34555962 original size:49 final size:48
Alignment explanation
Indices: 34555882--34556015 Score: 117
Period size: 49 Copynumber: 2.7 Consensus size: 48
34555872 TCAACTTGGA
* * *
34555882 CCTTGAGTTATACTTAAACCCACGACCGTATAACTATCGTCAACTAAG-AG
1 CCTT-AGTTATACTTAAA-CCACGACCGTATAACCACCGT-AAATAAGAAG
** * **
34555932 CCTTAGTTATACTTAAACCTGGTACTGTATAACCACCGTAAATTGGAAG
1 CCTTAGTTATACTTAAACCACG-ACCGTATAACCACCGTAAATAAGAAG
* * *
34555981 CCTTAGTTATACTTGAACCCATGATCGTATAACCA
1 CCTTAGTTATACTT-AAACCACGACCGTATAACCA
34556016 AAATAAACTA
Statistics
Matches: 68, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
48 7 0.10
49 52 0.76
50 9 0.13
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (48 bp):
CCTTAGTTATACTTAAACCACGACCGTATAACCACCGTAAATAAGAAG
Found at i:34558372 original size:30 final size:30
Alignment explanation
Indices: 34558306--34558373 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
34558296 GATAGGGGAT
*
34558306 GGAAAATGGTAGCTCCGTTAAGTATCTAAC
1 GGAAAATGGTAGCTCCGTTAAGTATATAAC
** * * *
34558336 AAAAAATGGTAGCTTCGTTATGTCTATAAC
1 GGAAAATGGTAGCTCCGTTAAGTATATAAC
34558366 GGAAAATG
1 GGAAAATG
34558374 ATTAGTGGTG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (30 bp):
GGAAAATGGTAGCTCCGTTAAGTATATAAC
Found at i:34562612 original size:13 final size:13
Alignment explanation
Indices: 34562594--34562618 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34562584 CAAACTCCTT
34562594 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
34562607 TTTTTTCTTTTT
1 TTTTTTCTTTTT
34562619 ATCATTTGCT
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:34563308 original size:5 final size:5
Alignment explanation
Indices: 34563300--34563328 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
34563290 ATAAAAGTAA
34563300 AAATT AAATT AAATT AAATT AAATT AAAT
1 AAATT AAATT AAATT AAATT AAATT AAAT
34563329 CAATTGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AAATT
Found at i:34565891 original size:12 final size:12
Alignment explanation
Indices: 34565874--34565901 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
34565864 ATATGTGTGA
34565874 AAAAAATAAAAT
1 AAAAAATAAAAT
34565886 AAAAAATAAAAT
1 AAAAAATAAAAT
34565898 AAAA
1 AAAA
34565902 TAAAGAACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAATAAAAT
Found at i:34565986 original size:28 final size:28
Alignment explanation
Indices: 34565944--34566000 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
34565934 TTTTGGGAAA
34565944 AAACCACGGGCAGAGGAGAAGAAAATTC
1 AAACCACGGGCAGAGGAGAAGAAAATTC
*
34565972 AAACCACGGGTAGAGGAGAAGAAAATTC
1 AAACCACGGGCAGAGGAGAAGAAAATTC
34566000 A
1 A
34566001 CTATGTCGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.47, C:0.16, G:0.28, T:0.09
Consensus pattern (28 bp):
AAACCACGGGCAGAGGAGAAGAAAATTC
Found at i:34570999 original size:6 final size:6
Alignment explanation
Indices: 34570988--34571022 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
34570978 GATTTTTTCC
34570988 AAAATG AAAATG AAAATG AAAATGG AGAAATG AAA
1 AAAATG AAAATG AAAATG AAAAT-G A-AAATG AAA
34571023 CCATTTGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 19 0.70
7 4 0.15
8 4 0.15
ACGTcount: A:0.66, C:0.00, G:0.20, T:0.14
Consensus pattern (6 bp):
AAAATG
Found at i:34573320 original size:89 final size:89
Alignment explanation
Indices: 34573153--34573317 Score: 226
Period size: 89 Copynumber: 1.8 Consensus size: 89
34573143 ATGGATGTGT
* * * *
34573153 GCTAGTGTAAGACATGTTTGGGACATACATCGGCCACATTATGAGAGCAAGTGTAAGACCATGTC
1 GCTAGTGCAAGACATGTCTAGGACATACATCGGCCACAATATGAGAGCAAGTGTAAGACCATGTC
34573218 TGGGACATGGGCATTAAGACGAGA
66 TGGGACATGGGCATTAAGACGAGA
* * *
34573242 GCTAGTGCAAGACATGTCTAGGACATGCATCGGCCTCGAGATATGCA-AGCTAGTGTAAGA-CAT
1 GCTAGTGCAAGACATGTCTAGGACATACATCGGCCAC-A-ATATG-AGAGCAAGTGTAAGACCAT
34573305 GTCTGGGACATGG
63 GTCTGGGACATGG
34573318 CATCGGCTGC
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
89 32 0.48
90 17 0.26
91 16 0.24
92 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.22
Consensus pattern (89 bp):
GCTAGTGCAAGACATGTCTAGGACATACATCGGCCACAATATGAGAGCAAGTGTAAGACCATGTC
TGGGACATGGGCATTAAGACGAGA
Found at i:34580720 original size:28 final size:28
Alignment explanation
Indices: 34580688--34580814 Score: 150
Period size: 28 Copynumber: 4.5 Consensus size: 28
34580678 CGATACCTTG
* * * *
34580688 CACACTAAGTGCCGTTTTGGATGTTTCG
1 CACACTAAGTGCCATTCTGGATGTATCA
* * *
34580716 TACACTAAGTGCCATCCTCG-T-TACTTCA
1 CACACTAAGTGCCATTCTGGATGTA--TCA
34580744 CACACTAAGTGCCATTCTGGATGTATCA
1 CACACTAAGTGCCATTCTGGATGTATCA
*
34580772 CACACTAAGTGCCATTCTGGATGTATCG
1 CACACTAAGTGCCATTCTGGATGTATCA
34580800 CACACTAAGTGCCAT
1 CACACTAAGTGCCAT
34580815 CCCCATTATT
Statistics
Matches: 84, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
26 1 0.01
27 1 0.01
28 79 0.94
29 1 0.01
30 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (28 bp):
CACACTAAGTGCCATTCTGGATGTATCA
Found at i:34580730 original size:56 final size:56
Alignment explanation
Indices: 34580652--34580814 Score: 154
Period size: 56 Copynumber: 2.9 Consensus size: 56
34580642 TGAATATTCA
* * * *
34580652 ATGTATCGCACACT-AGATGCCATAGC-CGATACCTT-GCACACTAAGTGCCGTTTTGG
1 ATGTATCGCACACTAAG-TGCCAT-CCTCGATA-CTTCACACACTAAGTGCCATTCTGG
* * *
34580708 ATGTTTCGTACACTAAGTGCCATCCTCGTTACTTCACACACTAAGTGCCATTCTGG
1 ATGTATCGCACACTAAGTGCCATCCTCGATACTTCACACACTAAGTGCCATTCTGG
* * * * *
34580764 ATGTATCACACACTAAGTGCCATTCTGGAT-GTATCGCACACTAAGTGCCAT
1 ATGTATCGCACACTAAGTGCCATCCTCGATACT-TCACACACTAAGTGCCAT
34580815 CCCCATTATT
Statistics
Matches: 88, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
55 5 0.06
56 81 0.92
57 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (56 bp):
ATGTATCGCACACTAAGTGCCATCCTCGATACTTCACACACTAAGTGCCATTCTGG
Found at i:34585052 original size:43 final size:43
Alignment explanation
Indices: 34584990--34585077 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
34584980 TTCGCAACTC
34584990 CTTCACTTCACGAGCTAGGATACGAATCGGTTCTTCTTCATAA
1 CTTCACTTCACGAGCTAGGATACGAATCGGTTCTTCTTCATAA
*
34585033 CTTCACTTCACGAGTTAGGATACGAATCGGTTCTTCTTCATAA
1 CTTCACTTCACGAGCTAGGATACGAATCGGTTCTTCTTCATAA
34585076 CT
1 CT
34585078 CAAGTCAGAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (43 bp):
CTTCACTTCACGAGCTAGGATACGAATCGGTTCTTCTTCATAA
Found at i:34585500 original size:44 final size:44
Alignment explanation
Indices: 34585452--34585541 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
34585442 AAATCAACTC
34585452 CGAAAATTTTACTTTCACCGAGCTCGGTCCAAAACAATGGTGTA
1 CGAAAATTTTACTTTCACCGAGCTCGGTCCAAAACAATGGTGTA
*
34585496 CGAAAATTTTACTTTCACTGAGCTCGGTCCAAAACAATGGTGTA
1 CGAAAATTTTACTTTCACCGAGCTCGGTCCAAAACAATGGTGTA
34585540 CG
1 CG
34585542 GCATTTACGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (44 bp):
CGAAAATTTTACTTTCACCGAGCTCGGTCCAAAACAATGGTGTA
Found at i:34591239 original size:119 final size:120
Alignment explanation
Indices: 34591063--34591285 Score: 303
Period size: 119 Copynumber: 1.9 Consensus size: 120
34591053 TACTCGTTCA
* *
34591063 AATGCCTTCGGGACATAGCCCGGTTATAGTGACTCGCACAAATGCCTTCGGGACTTAG-CCCGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGTCCCGA-
*
34591127 TATAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
65 TATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* *
34591183 AATGCCTTC-GGACTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGTCCCG
* * *
34591245 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
34591286 CATCATTCAA
Statistics
Matches: 91, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
118 4 0.04
119 66 0.73
120 21 0.23
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGTCCCGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:34591285 original size:40 final size:40
Alignment explanation
Indices: 34591042--34591285 Score: 293
Period size: 40 Copynumber: 6.1 Consensus size: 40
34591032 CGGAATTTAA
** *
34591042 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
34591082 CCGGTTATAGTGACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
34591122 CC-GATTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGA-TATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
34591162 CCGGATTTAGTAACTCGCACCAATGCCTTC-GGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
34591201 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
34591241 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
34591281 CCGGA
1 CCGGA
34591286 CATCATTCAA
Statistics
Matches: 179, Mismatches: 17, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
39 40 0.22
40 125 0.70
41 14 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:34597519 original size:28 final size:28
Alignment explanation
Indices: 34597488--34597589 Score: 100
Period size: 28 Copynumber: 3.6 Consensus size: 28
34597478 TTTTGGATGT
*
34597488 TTCGCACACTAAGTACCATCCTCGTTAA
1 TTCGCACACTAAGTGCCATCCTCGTTAA
* *
34597516 TTCGCACACTAAGTGCCATTCTGGATGT-A
1 TTCGCACACTAAGTGCCATCCTCG-T-TAA
* * *
34597545 -TCGCACACTAAGTGCCATCCCCGATAC
1 TTCGCACACTAAGTGCCATCCTCGTTAA
**
34597572 TTCGCACGTTAAGTGCCA
1 TTCGCACACTAAGTGCCA
34597590 CATATAATAT
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
26 1 0.02
28 56 0.93
29 2 0.03
30 1 0.02
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.26
Consensus pattern (28 bp):
TTCGCACACTAAGTGCCATCCTCGTTAA
Found at i:34597525 original size:56 final size:56
Alignment explanation
Indices: 34597428--34597589 Score: 175
Period size: 56 Copynumber: 2.9 Consensus size: 56
34597418 TGAATATTCA
* * * * * *
34597428 ATGTATCGCACACT-AGATGCCATACCCGATACCTT-GCACACTAAGTGTCGTTTTGG
1 ATGTATCGCACACTAAG-TACCATCCCCGATA-ATTCGCACACTAAGTGCCATTCTGG
* * *
34597484 ATGTTTCGCACACTAAGTACCATCCTCGTTAATTCGCACACTAAGTGCCATTCTGG
1 ATGTATCGCACACTAAGTACCATCCCCGATAATTCGCACACTAAGTGCCATTCTGG
* * **
34597540 ATGTATCGCACACTAAGTGCCATCCCCGATACTTCGCACGTTAAGTGCCA
1 ATGTATCGCACACTAAGTACCATCCCCGATAATTCGCACACTAAGTGCCA
34597590 CATATAATAT
Statistics
Matches: 88, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
55 2 0.02
56 84 0.95
57 2 0.02
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (56 bp):
ATGTATCGCACACTAAGTACCATCCCCGATAATTCGCACACTAAGTGCCATTCTGG
Found at i:34600909 original size:29 final size:29
Alignment explanation
Indices: 34600864--34600923 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
34600854 TCAAGTGGGA
34600864 GATAGAGTATTCCTAAAAGTATCTCCATG
1 GATAGAGTATTCCTAAAAGTATCTCCATG
*
34600893 GATAGAGTATTCTTAAAAGTATCTCCATG
1 GATAGAGTATTCCTAAAAGTATCTCCATG
34600922 GA
1 GA
34600924 AAAAAGTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (29 bp):
GATAGAGTATTCCTAAAAGTATCTCCATG
Found at i:34607497 original size:6 final size:6
Alignment explanation
Indices: 34607486--34607532 Score: 60
Period size: 6 Copynumber: 7.5 Consensus size: 6
34607476 AGTGTAGAAG
34607486 AAAAGA AAAAGA AAAAGA AAAAGA ATAAA-A GAAAAGA AAAATGA AAA
1 AAAAGA AAAAGA AAAAGA AAAAGA A-AAAGA -AAAAGA AAAA-GA AAA
34607533 GAATGAGGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
6 27 0.73
7 10 0.27
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (6 bp):
AAAAGA
Found at i:34607533 original size:12 final size:11
Alignment explanation
Indices: 34607483--34607535 Score: 58
Period size: 12 Copynumber: 4.9 Consensus size: 11
34607473 AGAAGTGTAG
34607483 AAGAAAAGAAA
1 AAGAAAAGAAA
34607494 AAGAAAAAGAAA
1 AAG-AAAAGAAA
*
34607506 AAG--AA-TAA
1 AAGAAAAGAAA
34607514 AAGAAAAGAAA
1 AAGAAAAGAAA
34607525 AATGAAAAGAA
1 AA-GAAAAGAA
34607536 TGAGGGAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
8 5 0.14
9 2 0.06
10 2 0.06
11 7 0.20
12 19 0.54
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (11 bp):
AAGAAAAGAAA
Found at i:34607544 original size:25 final size:25
Alignment explanation
Indices: 34607481--34607536 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
34607471 GAAGAAGTGT
*
34607481 AGAAGAAAAGAAAAAGAAAAA-GAAAA
1 AGAATAAAAG-AAAAGAAAAATG-AAA
34607507 AGAATAAAAGAAAAGAAAAATGAAA
1 AGAATAAAAGAAAAGAAAAATGAAA
34607532 AGAAT
1 AGAAT
34607537 GAGGGAAAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 18 0.64
26 10 0.36
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (25 bp):
AGAATAAAAGAAAAGAAAAATGAAA
Found at i:34607958 original size:13 final size:13
Alignment explanation
Indices: 34607940--34607965 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34607930 TCATATATAA
34607940 TAAAAATTACATC
1 TAAAAATTACATC
34607953 TAAAAATTACATC
1 TAAAAATTACATC
34607966 ATAATAATCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAAAATTACATC
Found at i:34618609 original size:27 final size:26
Alignment explanation
Indices: 34618551--34618688 Score: 147
Period size: 27 Copynumber: 5.3 Consensus size: 26
34618541 AGCTGCCAGA
* * *
34618551 AACAGTAAATGTGGCA-AGCCACCAGT
1 AACAGT-AATGTGACATAGTCACCAAT
* * * *
34618577 ATCAGTAATTGTGGCACAGCCACCAAT
1 AACAGTAA-TGTGACATAGTCACCAAT
34618604 AACAGTTAATGTGACATAGTCACCAAT
1 AACAG-TAATGTGACATAGTCACCAAT
*
34618631 AACAGTTAATGTGACATAGTCACCAGT
1 AACAG-TAATGTGACATAGTCACCAAT
34618658 -ACAGTAATGTGACATAGTCACCAAT
1 AACAGTAATGTGACATAGTCACCAAT
34618683 -ACAGTA
1 AACAGTA
34618689 CTTCCTCCAT
Statistics
Matches: 101, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
25 28 0.28
26 16 0.16
27 54 0.53
28 3 0.03
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.22
Consensus pattern (26 bp):
AACAGTAATGTGACATAGTCACCAAT
Found at i:34619038 original size:27 final size:27
Alignment explanation
Indices: 34618827--34619044 Score: 265
Period size: 27 Copynumber: 8.1 Consensus size: 27
34618817 TATAATTGTT
* * *
34618827 ATTTTACCATACAAGGGTATTACGATC
1 ATTTTACCCTACAGGGGTATTACGGTC
* ** *
34618854 ATTTTACCCTACAAGGGTATTACTATT
1 ATTTTACCCTACAGGGGTATTACGGTC
* * * *
34618881 ATTTTACCCCACAGGGGCATTATGGCC
1 ATTTTACCCTACAGGGGTATTACGGTC
*
34618908 ATTTTACCCTACAGGGGTATTACAGTC
1 ATTTTACCCTACAGGGGTATTACGGTC
* *
34618935 ATTTTACCCTACAGAGATATTACGGTC
1 ATTTTACCCTACAGGGGTATTACGGTC
* *
34618962 ATTTTACCCTACAGGGGCATTATGGTC
1 ATTTTACCCTACAGGGGTATTACGGTC
* *
34618989 ATCTTACCCTACAGTGGTATTACGGTC
1 ATTTTACCCTACAGGGGTATTACGGTC
*
34619016 ATTTTACCCTACAGGGGTATTACAGTC
1 ATTTTACCCTACAGGGGTATTACGGTC
34619043 AT
1 AT
34619045 ATTATAAATT
Statistics
Matches: 161, Mismatches: 30, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 161 1.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.33
Consensus pattern (27 bp):
ATTTTACCCTACAGGGGTATTACGGTC
Found at i:34619135 original size:27 final size:27
Alignment explanation
Indices: 34619060--34619136 Score: 100
Period size: 27 Copynumber: 2.9 Consensus size: 27
34619050 AAATTTAGGG
* **
34619060 TATTTTGGTAATTTCACAAATTAGGGG
1 TATTTTGGTAATTTCACAAATCAGGAA
*
34619087 TATTTTGGTAACTTCACAAATCAGGAA
1 TATTTTGGTAATTTCACAAATCAGGAA
* *
34619114 TATTTCGGTAATTTTACAAATCA
1 TATTTTGGTAATTTCACAAATCA
34619137 AGGTCTTAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.39
Consensus pattern (27 bp):
TATTTTGGTAATTTCACAAATCAGGAA
Found at i:34619610 original size:17 final size:18
Alignment explanation
Indices: 34619585--34619618 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
34619575 TTTATTCGTG
*
34619585 TGGGCCCATAA-GCCCAT
1 TGGGACCATAAGGCCCAT
34619602 TGGGACCATAAGGCCCA
1 TGGGACCATAAGGCCCA
34619619 GTACAGCCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.15
Consensus pattern (18 bp):
TGGGACCATAAGGCCCAT
Found at i:34623121 original size:32 final size:33
Alignment explanation
Indices: 34623085--34623169 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
34623075 TCTGGGCTTG
* * * *
34623085 AGCCCTATCCAGTATCAGTACATTTTG-GCCTT
1 AGCCCTATACAGTAACAGTACAGTCTGAGCCTT
* *
34623117 AGCCCTATACAGTAACAGAACAGTCTGAGCTTT
1 AGCCCTATACAGTAACAGTACAGTCTGAGCCTT
34623150 AGCCCTATACAGTAACAGTA
1 AGCCCTATACAGTAACAGTA
34623170 TGGGCCTAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 22 0.49
33 23 0.51
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (33 bp):
AGCCCTATACAGTAACAGTACAGTCTGAGCCTT
Found at i:34623156 original size:33 final size:32
Alignment explanation
Indices: 34623070--34623167 Score: 106
Period size: 33 Copynumber: 3.0 Consensus size: 32
34623060 TGCATGCAGT
* * *
34623070 AACAATCTGGGCTTGAGCCCTATCCAGTATCAG
1 AACAATCT-GGCTTTAGCCCTATACAGTAACAG
* * * *
34623103 TACATTTTGGCCTTAGCCCTATACAGTAACAG
1 AACAATCTGGCTTTAGCCCTATACAGTAACAG
*
34623135 AACAGTCTGAGCTTTAGCCCTATACAGTAACAG
1 AACAATCTG-GCTTTAGCCCTATACAGTAACAG
34623168 TATGGGCCTA
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
32 26 0.49
33 27 0.51
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (32 bp):
AACAATCTGGCTTTAGCCCTATACAGTAACAG
Found at i:34623384 original size:26 final size:27
Alignment explanation
Indices: 34623355--34623463 Score: 134
Period size: 26 Copynumber: 4.1 Consensus size: 27
34623345 TGCTAAAAAT
*
34623355 AGTAAATGTGGCA-AGCCACCAGTATC
1 AGTAAATGTGACATAGCCACCAGTATC
* *
34623381 AGTAATTGTGGCATAGCCACCAGTATC
1 AGTAAATGTGACATAGCCACCAGTATC
* *
34623408 AGTAATTGTGACATAGCCACC-GTAAC
1 AGTAAATGTGACATAGCCACCAGTATC
* *
34623434 AGTGAATGTGACATAGTCACCAGTA-C
1 AGTAAATGTGACATAGCCACCAGTATC
34623460 AGTA
1 AGTA
34623464 CTTCCTCTAT
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
26 38 0.51
27 36 0.49
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (27 bp):
AGTAAATGTGACATAGCCACCAGTATC
Found at i:34623406 original size:27 final size:27
Alignment explanation
Indices: 34623355--34623463 Score: 136
Period size: 27 Copynumber: 4.1 Consensus size: 27
34623345 TGCTAAAAAT
* *
34623355 AGTAAATGTGGCA-AGCCACCAGTATC
1 AGTAATTGTGACATAGCCACCAGTATC
*
34623381 AGTAATTGTGGCATAGCCACCAGTATC
1 AGTAATTGTGACATAGCCACCAGTATC
*
34623408 AGTAATTGTGACATAGCCACC-GTAAC
1 AGTAATTGTGACATAGCCACCAGTATC
*
34623434 AGTGAA-TGTGACATAGTCACCAGTA-C
1 AGT-AATTGTGACATAGCCACCAGTATC
34623460 AGTA
1 AGTA
34623464 CTTCCTCTAT
Statistics
Matches: 76, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
25 1 0.01
26 37 0.49
27 38 0.50
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (27 bp):
AGTAATTGTGACATAGCCACCAGTATC
Found at i:34623412 original size:53 final size:52
Alignment explanation
Indices: 34623355--34623463 Score: 132
Period size: 53 Copynumber: 2.1 Consensus size: 52
34623345 TGCTAAAAAT
* * *
34623355 AGTAAATGTGGCA-AGCCACCAGTATCAGT-AATTGTGGCATAGCCACCAGTATC
1 AGTAAATGTGACATAGCCACC-GTAACAGTGAA-TGTGACATAGCCACCAGTA-C
* *
34623408 AGTAATTGTGACATAGCCACCGTAACAGTGAATGTGACATAGTCACCAGTAC
1 AGTAAATGTGACATAGCCACCGTAACAGTGAATGTGACATAGCCACCAGTAC
34623460 AGTA
1 AGTA
34623464 CTTCCTCTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
52 5 0.10
53 35 0.71
54 9 0.18
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (52 bp):
AGTAAATGTGACATAGCCACCGTAACAGTGAATGTGACATAGCCACCAGTAC
Found at i:34623677 original size:27 final size:27
Alignment explanation
Indices: 34623600--34623678 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
34623590 GGCATAATTA
* ** * *
34623600 TCATTTTACCATACAGATGTATCACTG
1 TCATTTTACCCTACAGGGGTATTACAG
**
34623627 TCATTTTACCCTACAGGGACATTACAG
1 TCATTTTACCCTACAGGGGTATTACAG
34623654 TCATTTTACCCTACAGGGGTATTAC
1 TCATTTTACCCTACAGGGGTATTAC
34623679 GATTATTTTA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (27 bp):
TCATTTTACCCTACAGGGGTATTACAG
Found at i:34623713 original size:27 final size:26
Alignment explanation
Indices: 34623696--34623774 Score: 86
Period size: 27 Copynumber: 3.0 Consensus size: 26
34623686 TTACAAACCG
34623696 AAGGTATTTTGGTAATTTCACAAATC
1 AAGGTATTTTGGTAATTTCACAAATC
* *
34623722 AAGAGTATTTTAGTAACTTCACAAATC
1 AAG-GTATTTTGGTAATTTCACAAATC
* * * *
34623749 AGGGGTATTTCGATAATTTTACAAAT
1 A-AGGTATTTTGGTAATTTCACAAAT
34623775 TGGGGTCTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
26 3 0.07
27 39 0.91
28 1 0.02
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (26 bp):
AAGGTATTTTGGTAATTTCACAAATC
Found at i:34628352 original size:19 final size:19
Alignment explanation
Indices: 34628321--34628366 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
34628311 CGAAAAATGA
34628321 TTTCTGAGAAATGATTTACT
1 TTTCTG-GAAATGATTTACT
34628341 TTTCTGGAAATGATTTACT
1 TTTCTGGAAATGATTTACT
34628360 TTTCTGG
1 TTTCTGG
34628367 TATTTGGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.48
Consensus pattern (19 bp):
TTTCTGGAAATGATTTACT
Found at i:34628467 original size:18 final size:18
Alignment explanation
Indices: 34628441--34628483 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
34628431 AAAAGTTATT
*
34628441 TTTACATATATTAATAAA
1 TTTATATATATTAATAAA
34628459 TTTATATATATTAATAAA
1 TTTATATATATTAATAAA
34628477 TTTATAT
1 TTTATAT
34628484 TTTAAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATATATATTAATAAA
Found at i:34628543 original size:54 final size:54
Alignment explanation
Indices: 34628436--34628544 Score: 125
Period size: 54 Copynumber: 2.0 Consensus size: 54
34628426 TCCAGAAAAG
* ** **
34628436 TTATTTTTACATATATTAATAAATTTATATATATTAATAAATTTATATTTTAAA
1 TTATTTTTACATATATTAATAAATTTATATATATAAATAAATAAATAAATTAAA
34628490 TTATTTTTACATATATTGCAAT-AATTTAT-T-TATAAATAAATAAATCAAATTAAA
1 TTATTTTTACATATATT--AATAAATTTATATATATAAATAAATAAAT-AAATTAAA
34628544 T
1 T
34628545 ATATAATAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
53 12 0.26
54 25 0.53
55 7 0.15
56 3 0.06
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.50
Consensus pattern (54 bp):
TTATTTTTACATATATTAATAAATTTATATATATAAATAAATAAATAAATTAAA
Found at i:34629828 original size:15 final size:15
Alignment explanation
Indices: 34629808--34629837 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
34629798 TCCAAACTAG
34629808 TTAAATTGCATATGT
1 TTAAATTGCATATGT
34629823 TTAAATTGCATATGT
1 TTAAATTGCATATGT
34629838 AGCATGTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (15 bp):
TTAAATTGCATATGT
Found at i:34630522 original size:168 final size:169
Alignment explanation
Indices: 34630195--34630557 Score: 502
Period size: 168 Copynumber: 2.2 Consensus size: 169
34630185 AAGATATAAT
* * * *
34630195 TTTAAGCAAATCAGTTTCCTAAAAT-AAAATTTTAAGACCAAGGTTTTATTACTATTTACGTATA
1 TTTAAACAAATCTGTTTCCTAAAATCAAAATTGTAAGACCAAGGTTTCATTACTATTTACGTATA
**
34630259 TTCCATTGTGAAATTGGAAAACCATATAAATAAAGGACAAGAAAGCACTCATGTGAATGTCATCA
66 TTCCATTGTGAAATTGGAAAACCATATAAATAAAGGACAAGAAAGCACTCAAATGAATGTCATCA
*
34630324 CAAAATCTAATTTATCATGCTGTAAAATTGAAGTCTT-A
131 CAAAATCTAATTTATCAAGCTGTAAAATTGAAGTCTTAA
* *
34630362 TTTAAACAAATCTGTTTCCTAGAATCAAAA-TGTAAGACCCAAGGTTTCATTACTATTTACTTAT
1 TTTAAACAAATCTGTTTCCTAAAATCAAAATTGTAAGA-CCAAGGTTTCATTACTATTTACGTAT
* ** * * *
34630426 ATTCCTTTGTGTGATTGGAAAACCATATAAATCAAGGACAAGAAAGCATTCAAATTACATGTCAT
65 ATTCCATTGTGAAATTGGAAAACCATATAAATAAAGGACAAGAAAGCACTCAAATGA-ATGTCAT
* * *
34630491 CACAAAGTCTAATTTATTAAGTTGT-AAATTGAAGTCTTAA
129 CACAAAATCTAATTTATCAAGCTGTAAAATTGAAGTCTTAA
34630531 TTTAAACAAA-CGTGTTTCCTAAAATCA
1 TTTAAACAAATC-TGTTTCCTAAAATCA
34630558 TTCAAGACCA
Statistics
Matches: 172, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
167 28 0.16
168 91 0.53
169 53 0.31
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.34
Consensus pattern (169 bp):
TTTAAACAAATCTGTTTCCTAAAATCAAAATTGTAAGACCAAGGTTTCATTACTATTTACGTATA
TTCCATTGTGAAATTGGAAAACCATATAAATAAAGGACAAGAAAGCACTCAAATGAATGTCATCA
CAAAATCTAATTTATCAAGCTGTAAAATTGAAGTCTTAA
Found at i:34632974 original size:53 final size:53
Alignment explanation
Indices: 34632915--34633018 Score: 199
Period size: 53 Copynumber: 2.0 Consensus size: 53
34632905 TTCTTATGGC
34632915 TTCTTTTGATGATTTTAGATAGTTGTTTCCTCTTTTTTTTTTTTTTTGGGGGT
1 TTCTTTTGATGATTTTAGATAGTTGTTTCCTCTTTTTTTTTTTTTTTGGGGGT
*
34632968 TTCTTTTGATGATTTTAGATAGTTTTTTCCTCTTTTTTTTTTTTTTTGGGG
1 TTCTTTTGATGATTTTAGATAGTTGTTTCCTCTTTTTTTTTTTTTTTGGGG
34633019 ATGTACTTCT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.10, C:0.08, G:0.17, T:0.65
Consensus pattern (53 bp):
TTCTTTTGATGATTTTAGATAGTTGTTTCCTCTTTTTTTTTTTTTTTGGGGGT
Found at i:34636605 original size:27 final size:27
Alignment explanation
Indices: 34636575--34636629 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
34636565 TGTTATAAGT
* *
34636575 GGCACCAGTGGTGCCAATTTTGTAGGC
1 GGCACCACTGGTGCCAATCTTGTAGGC
*
34636602 GGCACTACTGGTGCCAATCTTGTAGGC
1 GGCACCACTGGTGCCAATCTTGTAGGC
34636629 G
1 G
34636630 ACATCAGTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.18, C:0.24, G:0.33, T:0.25
Consensus pattern (27 bp):
GGCACCACTGGTGCCAATCTTGTAGGC
Found at i:34638789 original size:314 final size:314
Alignment explanation
Indices: 34638220--34638847 Score: 1229
Period size: 314 Copynumber: 2.0 Consensus size: 314
34638210 AGACTCATTA
34638220 GCTTTAATCTCATTTTTTTTCCAGCCCTTAACTCAATTTCCACAATTTATGGTGAATTTTCAAAT
1 GCTTTAATCTCATTTTTTTTCCAGCCCTTAACTCAATTTCCACAATTTATGGTGAATTTTCAAAT
34638285 TCAAACTACTGCTACTTACCAAAAACTGTTTTAGTACAAATATTGTTAACTAGTTCATAACATCT
66 TCAAACTACTGCTACTTACCAAAAACTGTTTTAGTACAAATATTGTTAACTAGTTCATAACATCT
34638350 TTACTTCAATTCATTCAAACTCTATACATGCCATATAAATCTTTAAACATAAAACAAAAACTACC
131 TTACTTCAATTCATTCAAACTCTATACATGCCATATAAATCTTTAAACATAAAACAAAAACTACC
*
34638415 AGAATTGATCTGAATAGTGTGCCCTGTTGTGTTGATCCAATCTACCCACTTCACTTCAAGTCAAT
196 AGAATTGATCTGAATAGTGTGCCCTATTGTGTTGATCCAATCTACCCACTTCACTTCAAGTCAAT
34638480 CTACATAAAAATATTAAACACACACAAGTAAGCTTATTGAAGCTTAGTAAGCTC
261 CTACATAAAAATATTAAACACACACAAGTAAGCTTATTGAAGCTTAGTAAGCTC
34638534 GCTTTAATCTCATTTTTTTTCCAGCCCTTAACTCAATTTCCACAATTTATGGTGAATTTTCAAAT
1 GCTTTAATCTCATTTTTTTTCCAGCCCTTAACTCAATTTCCACAATTTATGGTGAATTTTCAAAT
34638599 TCAAACTACTGCTACTTACCAAAAACTGTTTTAGTACAAATATTGTTAACTAGTTCATAACATCT
66 TCAAACTACTGCTACTTACCAAAAACTGTTTTAGTACAAATATTGTTAACTAGTTCATAACATCT
34638664 TTACTTCAATTCATTCAAACTCTATACATGCCATATAAATCTTTAAACATAAAACAAAAACTACC
131 TTACTTCAATTCATTCAAACTCTATACATGCCATATAAATCTTTAAACATAAAACAAAAACTACC
* *
34638729 AGAATTGATTTGAATAGTGTGCCCTATTGTGTTGATCCGATCTACCCACTTCACTTCAAGTCAAT
196 AGAATTGATCTGAATAGTGTGCCCTATTGTGTTGATCCAATCTACCCACTTCACTTCAAGTCAAT
34638794 CTACATAAAAATATTAAACACACACAAGTAAGCTTATTGAAGCTTAGTAAGCTC
261 CTACATAAAAATATTAAACACACACAAGTAAGCTTATTGAAGCTTAGTAAGCTC
34638848 ATAGGCATAT
Statistics
Matches: 311, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
314 311 1.00
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (314 bp):
GCTTTAATCTCATTTTTTTTCCAGCCCTTAACTCAATTTCCACAATTTATGGTGAATTTTCAAAT
TCAAACTACTGCTACTTACCAAAAACTGTTTTAGTACAAATATTGTTAACTAGTTCATAACATCT
TTACTTCAATTCATTCAAACTCTATACATGCCATATAAATCTTTAAACATAAAACAAAAACTACC
AGAATTGATCTGAATAGTGTGCCCTATTGTGTTGATCCAATCTACCCACTTCACTTCAAGTCAAT
CTACATAAAAATATTAAACACACACAAGTAAGCTTATTGAAGCTTAGTAAGCTC
Found at i:34639218 original size:53 final size:53
Alignment explanation
Indices: 34639148--34639461 Score: 535
Period size: 53 Copynumber: 5.9 Consensus size: 53
34639138 CACATATCAT
* * * **
34639148 ACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTATCACATTAT
1 ACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAGTCACATTATCACATTGC
34639201 ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTATCACATTGC
1 ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTATCACATTGC
34639254 ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTATCACATTGC
1 ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTATCACATTGC
34639307 ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTATCACATTGC
1 ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTATCACATTGC
34639360 ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTATCACATTGC
1 ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTATCACATTGC
*
34639413 ACCGATGCCATAGCCCAGCTATGGTCTTAAACGG-G-CACACTTATCACAT
1 ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACA-TTATCACAT
34639462 ATTTTTCGTC
Statistics
Matches: 253, Mismatches: 6, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
51 4 0.02
52 11 0.04
53 238 0.94
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (53 bp):
ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTATCACATTGC
Found at i:34650433 original size:5 final size:6
Alignment explanation
Indices: 34650415--34650442 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
34650405 CGCTTTTGGC
34650415 AAGAAA AAGAAA AAGAAA AAGAAA AAGA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGA
34650443 GTCTAGAGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:34650739 original size:32 final size:31
Alignment explanation
Indices: 34650681--34650754 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 31
34650671 GTCACAAACC
*
34650681 TTAAATATAAAAAAATTATTTATTATTAAAT
1 TTAAATATAAAAAAATGATTTATTATTAAAT
*
34650712 TTAAATATAATTAAAATAGATTT-TTATTAAA-
1 TTAAATATAA-AAAAAT-GATTTATTATTAAAT
*
34650743 AT-AATATAAAAA
1 TTAAATATAAAAA
34650755 TATAAAATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
29 2 0.05
30 7 0.19
31 11 0.30
32 13 0.35
33 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (31 bp):
TTAAATATAAAAAAATGATTTATTATTAAAT
Found at i:34650797 original size:29 final size:32
Alignment explanation
Indices: 34650733--34650809 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 32
34650723 TAAAATAGAT
34650733 TTTTATTAAAATAATATAAAAATATAAAATTAA
1 TTTT-TTAAAATAATATAAAAATATAAAATTAA
* *
34650766 TTTTTTAAAATATTAT-AAATTAT-AAATT-A
1 TTTTTTAAAATAATATAAAAATATAAAATTAA
* *
34650795 TTTATCAAAATAATA
1 TTTTTTAAAATAATA
34650810 CAAGAACTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
29 13 0.33
30 5 0.13
31 6 0.15
32 11 0.28
33 4 0.10
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (32 bp):
TTTTTTAAAATAATATAAAAATATAAAATTAA
Found at i:34651051 original size:29 final size:29
Alignment explanation
Indices: 34651001--34651068 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
34650991 ATAAAATATT
34651001 AAAATAATATAAAAATAGAATTAATTT-TC
1 AAAATAATATAAAAATAGAATT-ATTTATC
* *
34651030 AAAATGATATAAATTATA-AATTATTTATC
1 AAAATAATATAAA-AATAGAATTATTTATC
34651059 AAAATAATAT
1 AAAATAATAT
34651069 GAAAGTTACA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.12
29 27 0.79
30 3 0.09
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (29 bp):
AAAATAATATAAAAATAGAATTATTTATC
Found at i:34651189 original size:29 final size:31
Alignment explanation
Indices: 34651132--34651202 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 31
34651122 TAATTATTAT
*
34651132 TAAATAATTATATAAGTTTCATATTATTTGAG
1 TAAATAATT-TATAAGCTTCATATTATTTGAG
*
34651164 TAAATAATTTATAA-CTT-ATATTATTTTAG
1 TAAATAATTTATAAGCTTCATATTATTTGAG
34651193 -AAATTAATTT
1 TAAA-TAATTT
34651203 TATTGTTACA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
28 3 0.08
29 17 0.47
30 2 0.06
31 5 0.14
32 9 0.25
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (31 bp):
TAAATAATTTATAAGCTTCATATTATTTGAG
Found at i:34652082 original size:5 final size:6
Alignment explanation
Indices: 34652069--34652127 Score: 73
Period size: 6 Copynumber: 9.5 Consensus size: 6
34652059 ATAATTTAAT
* * *
34652069 AAATAA AAATAA AAATCTAA AACTAA AACTAA AACTAA AAATAA AAATAA
1 AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAATAA AAATAA
34652119 AAATAA AAA
1 AAATAA AAA
34652128 AACATATAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
6 44 0.90
8 5 0.10
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:34652162 original size:9 final size:9
Alignment explanation
Indices: 34652148--34652215 Score: 91
Period size: 9 Copynumber: 7.6 Consensus size: 9
34652138 TTTATACAAA
34652148 TAATTCGGT
1 TAATTCGGT
34652157 TAATTCGGT
1 TAATTCGGT
* *
34652166 TAATTTGGG
1 TAATTCGGT
*
34652175 TAATTCGGG
1 TAATTCGGT
*
34652184 TAATTCGAT
1 TAATTCGGT
34652193 TAATTCGGT
1 TAATTCGGT
*
34652202 TAATTCAGT
1 TAATTCGGT
34652211 TAATT
1 TAATT
34652216 TTATACTTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 52 1.00
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (9 bp):
TAATTCGGT
Found at i:34653750 original size:19 final size:19
Alignment explanation
Indices: 34653709--34653751 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
34653699 TCATGCTTTT
*
34653709 TATTCACATTTTCATATTC
1 TATTCACATTTTCATAATC
34653728 TATTCACATTTTCA-AATC
1 TATTCACATTTTCATAATC
34653746 ATATTC
1 -TATTC
34653752 CACAGATTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.49
Consensus pattern (19 bp):
TATTCACATTTTCATAATC
Found at i:34666113 original size:47 final size:44
Alignment explanation
Indices: 34666040--34666254 Score: 148
Period size: 46 Copynumber: 4.6 Consensus size: 44
34666030 TTATTTGTGT
* * *
34666040 GCCAGTGTAAGATATGTCTGGAACATGCATCGGCCGCATTATGACA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGG--GCATTATGAGA
*
34666086 GCCAGTGTAAGACCATGTCTGGGACATGGCAT-TGGCATTGAGATGAGA
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGGCATT---ATGAGA
* * ** **
34666134 ACCAGTGTAAGACATGTCTGGGACATGTATCGACCTCAAAATGTA-A
1 GCCAGTGTAAGACATGTCTGGGACATGCATCG--GGCATTATG-AGA
* * *
34666180 ACCAGTGTAAGACATGTTTGGGACATGGAATC-GGCATGTATAGAGA
1 GCCAGTGTAAGACATGTCTGGGACAT-GCATCGGGCAT-TAT-GAGA
*
34666226 TGCCAGTGTAAGACCATGTCTAGGACATG
1 -GCCAGTGTAAGA-CATGTCTGGGACATG
34666255 ACATTGGCAC
Statistics
Matches: 134, Mismatches: 20, Indels: 29
0.73 0.11 0.16
Matches are distributed among these distances:
44 2 0.01
45 8 0.06
46 46 0.34
47 44 0.33
48 32 0.24
49 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (44 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGGCATTATGAGA
Found at i:34666246 original size:94 final size:95
Alignment explanation
Indices: 34666039--34666254 Score: 244
Period size: 94 Copynumber: 2.3 Consensus size: 95
34666029 GTTATTTGTG
* * * ** *
34666039 TGCCAGTGTAAGATATGTCTGGAACATGCATCGGCCGCATTATGACAGCCAGTGTAAGACCATGT
1 TGCCAGTGTAAGACATGTCTGGGACATGCATCGACCGCAAAATGACAACCAGTGTAAGACCATGT
* *
34666104 CTGGGACATGGCATTGGCATTGAGATGAGA
66 CTGGGACATGGAATCGGCATTGAGATGAGA
* * *
34666134 -ACCAGTGTAAGACATGTCTGGGACATGTATCGACCTCAAAATGTA-AACCAGTGTAAGA-CATG
1 TGCCAGTGTAAGACATGTCTGGGACATGCATCGACCGCAAAATG-ACAACCAGTGTAAGACCATG
* *
34666196 TTTGGGACATGGAATCGGCA-TG-TATAGAGA
65 TCTGGGACATGGAATCGGCATTGAGAT-GAGA
*
34666226 TGCCAGTGTAAGACCATGTCTAGGACATG
1 TGCCAGTGTAAGA-CATGTCTGGGACATG
34666255 ACATTGGCAC
Statistics
Matches: 102, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
91 2 0.02
92 6 0.06
93 32 0.31
94 61 0.60
95 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (95 bp):
TGCCAGTGTAAGACATGTCTGGGACATGCATCGACCGCAAAATGACAACCAGTGTAAGACCATGT
CTGGGACATGGAATCGGCATTGAGATGAGA
Found at i:34669376 original size:63 final size:63
Alignment explanation
Indices: 34669303--34669431 Score: 249
Period size: 63 Copynumber: 2.0 Consensus size: 63
34669293 CAATCATTAT
*
34669303 AATATCTAAGTTTATAATTAAATTTGTGTTACGAATTAAATGGTCATTAATTCAATTGAAAAA
1 AATATCTAAGTTTATAATTAAATTTGTGTTACGAATTAAATAGTCATTAATTCAATTGAAAAA
34669366 AATATCTAAGTTTATAATTAAATTTGTGTTACGAATTAAATAGTCATTAATTCAATTGAAAAA
1 AATATCTAAGTTTATAATTAAATTTGTGTTACGAATTAAATAGTCATTAATTCAATTGAAAAA
34669429 AAT
1 AAT
34669432 TTAAAAATAA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (63 bp):
AATATCTAAGTTTATAATTAAATTTGTGTTACGAATTAAATAGTCATTAATTCAATTGAAAAA
Found at i:34683393 original size:27 final size:27
Alignment explanation
Indices: 34683355--34683407 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
34683345 AAGAGTAAGC
*
34683355 TCACAAAAGAACTAGATAATCTAATGT
1 TCACAAAAGAACTAGAAAATCTAATGT
*
34683382 TCACAAAGGAACTAGAAAATCTAATG
1 TCACAAAAGAACTAGAAAATCTAATG
34683408 GAAAGGGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.49, C:0.15, G:0.13, T:0.23
Consensus pattern (27 bp):
TCACAAAAGAACTAGAAAATCTAATGT
Found at i:34690407 original size:22 final size:24
Alignment explanation
Indices: 34690373--34690418 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
34690363 AAAAAAGTTC
34690373 TATATCGATATT-GAAATGGCAAAA
1 TATATCGATATTGGAAATGG-AAAA
34690397 TATAT-GA-ATTGGAAATGGAAAA
1 TATATCGATATTGGAAATGGAAAA
34690419 GTGGATTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 7 0.33
23 9 0.43
24 5 0.24
ACGTcount: A:0.48, C:0.04, G:0.20, T:0.28
Consensus pattern (24 bp):
TATATCGATATTGGAAATGGAAAA
Found at i:34691604 original size:83 final size:83
Alignment explanation
Indices: 34691465--34691792 Score: 611
Period size: 83 Copynumber: 4.0 Consensus size: 83
34691455 TTACATGGGC
* * ** *
34691465 ACGGAAACAGGCTGGGACACGGCCGTGTGTATCAGCCGTGTGACACCTGCAGTTGAATTTTTCTA
1 ACGGACACGGGCTGGGACACGGCTATGTGTATCAGCCGTGTGACCCCTGCAGTTGAATTTTTCTA
34691530 ACTTTTTCCTTAAATTTT
66 ACTTTTTCCTTAAATTTT
34691548 ACGGACACGGGCTGGGACACGGCTATGTGTATCAGCCGTGTGACCCCTGCAGTTGAATTTTTCTA
1 ACGGACACGGGCTGGGACACGGCTATGTGTATCAGCCGTGTGACCCCTGCAGTTGAATTTTTCTA
34691613 ACTTTTTCCTTAAATTTT
66 ACTTTTTCCTTAAATTTT
34691631 ACGGACACGGGCTGGGACACGGCTATGTGTATCAGCCGTGTGACCCCTGCAGTTGAATTTTTCTA
1 ACGGACACGGGCTGGGACACGGCTATGTGTATCAGCCGTGTGACCCCTGCAGTTGAATTTTTCTA
34691696 ACTTTTTCCTTAAATTTT
66 ACTTTTTCCTTAAATTTT
34691714 ACGGACACGGGCTGGGACACGGCTATGTGTATCAGCCGTGTGACCCCTGCAGTTGAATTTTTCTA
1 ACGGACACGGGCTGGGACACGGCTATGTGTATCAGCCGTGTGACCCCTGCAGTTGAATTTTTCTA
34691779 ACTTTTTCCTTAAA
66 ACTTTTTCCTTAAA
34691793 ATTTCAAATG
Statistics
Matches: 240, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 240 1.00
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (83 bp):
ACGGACACGGGCTGGGACACGGCTATGTGTATCAGCCGTGTGACCCCTGCAGTTGAATTTTTCTA
ACTTTTTCCTTAAATTTT
Found at i:34692319 original size:18 final size:19
Alignment explanation
Indices: 34692296--34692331 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
34692286 AACTCAATCA
*
34692296 ATTTTC-TTTTTCTTTTTC
1 ATTTTCATTTTCCTTTTTC
34692314 ATTTTCATTTTCCTTTTT
1 ATTTTCATTTTCCTTTTT
34692332 TTTAAGAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (19 bp):
ATTTTCATTTTCCTTTTTC
Found at i:34698503 original size:20 final size:20
Alignment explanation
Indices: 34698472--34698529 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
34698462 TTTTTATGTG
* *
34698472 TTAAAATGATTTTAACTTGG
1 TTAAAATAATTTTAACTTGA
* * *
34698492 TTGAAATCATTTTGACTTGA
1 TTAAAATAATTTTAACTTGA
34698512 TTAAAATAATTTTAACTT
1 TTAAAATAATTTTAACTT
34698530 TATTTTAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.47
Consensus pattern (20 bp):
TTAAAATAATTTTAACTTGA
Found at i:34698516 original size:40 final size:40
Alignment explanation
Indices: 34698447--34698529 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 40
34698437 TACTTTTTGG
* * *
34698447 CTTGTTTGAAAATCATTTTTATGTGTTAAAATGATTTTAA
1 CTTGGTTGAAAATCATTTTGATGTGTTAAAATAATTTTAA
34698487 CTTGGTTG-AAATCATTTTGACT-TGATTAAAATAATTTTAA
1 CTTGGTTGAAAATCATTTTGA-TGTG-TTAAAATAATTTTAA
34698527 CTT
1 CTT
34698530 TATTTTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
39 13 0.34
40 25 0.66
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.48
Consensus pattern (40 bp):
CTTGGTTGAAAATCATTTTGATGTGTTAAAATAATTTTAA
Found at i:34700718 original size:49 final size:49
Alignment explanation
Indices: 34700646--34700823 Score: 227
Period size: 49 Copynumber: 3.7 Consensus size: 49
34700636 AAGGCATAAT
*
34700646 GTCGATGCCATGTCCCAAACATGGTCTTACACTGACTATCGAAATTGAG
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTGACTATCGAAATTGAG
* ** * *
34700695 GTCGATGCCATGTCCCAGACATGGTCTTACACTGGC--TC-ACCTATCAA
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTGACTATCGAAAT-TGAG
* * *
34700742 GTTGATGCCATGTTCCAGACATGGTCTTACACTGACTATCGAAATCGAG
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTGACTATCGAAATTGAG
* *
34700791 GTCGACGCCATGTACCAGACATGGTCTTACACT
1 GTCGATGCCATGTCCCAGACATGGTCTTACACT
34700824 AGCTCTCACA
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
46 2 0.02
47 37 0.34
49 67 0.62
50 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (49 bp):
GTCGATGCCATGTCCCAGACATGGTCTTACACTGACTATCGAAATTGAG
Found at i:34700813 original size:96 final size:96
Alignment explanation
Indices: 34700649--34700828 Score: 306
Period size: 96 Copynumber: 1.9 Consensus size: 96
34700639 GCATAATGTC
* * *
34700649 GATGCCATGTCCCAAACATGGTCTTACACTGACTATCGAAATTGAGGTCGATGCCATGTCCCAGA
1 GATGCCATGTCCCAAACATGGTCTTACACTGACTATCGAAATCGAGGTCGACGCCATGTACCAGA
*
34700714 CATGGTCTTACACTGGCTCACCTATCAAGTT
66 CATGGTCTTACACTAGCTCACCTATCAAGTT
* *
34700745 GATGCCATGTTCCAGACATGGTCTTACACTGACTATCGAAATCGAGGTCGACGCCATGTACCAGA
1 GATGCCATGTCCCAAACATGGTCTTACACTGACTATCGAAATCGAGGTCGACGCCATGTACCAGA
34700810 CATGGTCTTACACTAGCTC
66 CATGGTCTTACACTAGCTC
34700829 TCACATATCC
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
96 78 1.00
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (96 bp):
GATGCCATGTCCCAAACATGGTCTTACACTGACTATCGAAATCGAGGTCGACGCCATGTACCAGA
CATGGTCTTACACTAGCTCACCTATCAAGTT
Found at i:34701010 original size:46 final size:46
Alignment explanation
Indices: 34700697--34701105 Score: 233
Period size: 46 Copynumber: 8.7 Consensus size: 46
34700687 AAATTGAGGT
* * * * *
34700697 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACCTATCAA-GT
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCGTCTCAATGC
* * * ** * * *
34700744 TGATGCCATGTTCCAGACATGGTCTTACACT-GACTATCGAAATCGAGGT
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAG-CTCTCG-TCTCAATGC
* * * * **
34700793 CGACGCCATGTACCAGACATGGTCTTACACTAGCTCTCACATATCCTTGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCT--CGTCTCAATGC
* * * * * *
34700843 CAATGCAATGTCACAGACATGGTCTTACACT-G-ACACATCTC-GTAGC
1 CGATGC-ATGTCCCAGACAT-GTCTTACACTAGCTCTCGTCTCAAT-GC
* * * * * *
34700889 CGATGCATGTGCCACACATGTCTTACACTGGCT-TACATCTCGAGGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTCT-CGTCTCAATGC
* * *
34700935 CAATGCATGTCCTAAACATGTCTTACACTAGCTCTCGTCTCAATGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGC
34700981 CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGC
* * *
34701027 TGATGCCATGTCCCAGATAGGTCTTACACTAGCTCTCG--T-AATGTGGC
1 CGATG-CATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAA--T-GC
* **
34701074 CAATGCATGTCTTAGACATGTCTTACACTAGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGC
34701106 ATACAATTAA
Statistics
Matches: 292, Mismatches: 53, Indels: 35
0.77 0.14 0.09
Matches are distributed among these distances:
44 12 0.04
45 13 0.04
46 128 0.44
47 68 0.23
48 5 0.02
49 35 0.12
50 30 0.10
51 1 0.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.28
Consensus pattern (46 bp):
CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGC
Found at i:34701065 original size:93 final size:91
Alignment explanation
Indices: 34700799--34701110 Score: 233
Period size: 93 Copynumber: 3.4 Consensus size: 91
34700789 AGGTCGACGC
* * *** * *
34700799 CATGTACCAGACATGGTCTTACACTAGCTCTCACATATCCTTGCCAATGCAATGTCACAGACATG
1 CATGTCCCAGACAT-GTCTTACACTAGCT-T-ACATCTCAAGGCCAATGC-ATGTCCCAAACA-G
*
34700864 GTCTTACACTGACACATCTCGT-A---GCCGATG
61 GTCTTACACT-A-GC-TCTCGTAAGTGGCCGATG
* * * * * *
34700894 CATGTGCCACACATGTCTTACACTGGCTTACATCTCGAGGCCAATGCATGTCCTAAACATGTCTT
1 CATGTCCCAGACATGTCTTACACTAGCTTACATCTCAAGGCCAATGCATGTCCCAAACAGGTCTT
34700959 ACACTAGCTCTCGTCTCAA-T-GCCGATG
66 ACACTAGCTCTCG--T-AAGTGGCCGATG
* * ** * *
34700986 CATGTCCCAGACATGTCTTACACTAGCTCT-CGTCTCAATGCTGATGCCATGTCCCAGATAGGTC
1 CATGTCCCAGACATGTCTTACACTAGCT-TACATCTCAAGGCCAATG-CATGTCCCAAACAGGTC
*
34701050 TTACACTAGCTCTCGTAATGTGGCCAATG
64 TTACACTAGCTCTCGTAA-GTGGCCGATG
** *
34701079 CATGTCTTAGACATGTCTTACACTAGCATACA
1 CATGTCCCAGACATGTCTTACACTAGCTTACA
34701111 ATTAACCCGA
Statistics
Matches: 177, Mismatches: 29, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
87 5 0.03
88 1 0.01
89 2 0.01
90 12 0.07
91 11 0.06
92 59 0.33
93 62 0.35
94 13 0.07
95 12 0.07
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.28
Consensus pattern (91 bp):
CATGTCCCAGACATGTCTTACACTAGCTTACATCTCAAGGCCAATGCATGTCCCAAACAGGTCTT
ACACTAGCTCTCGTAAGTGGCCGATG
Found at i:34701816 original size:13 final size:13
Alignment explanation
Indices: 34701798--34701822 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34701788 CTAAAAGTGC
34701798 AAAAATCATCAAG
1 AAAAATCATCAAG
34701811 AAAAATCATCAA
1 AAAAATCATCAA
34701823 AATCACTTAC
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:0.64, C:0.16, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAAATCATCAAG
Found at i:34711050 original size:160 final size:160
Alignment explanation
Indices: 34710868--34711180 Score: 617
Period size: 160 Copynumber: 2.0 Consensus size: 160
34710858 TTAGTAGTAA
*
34710868 GGGCATTTTGGTCATTTAGGGGTAAAATGAATTAAAATACAAAATTAAAAGTCAATTTTGCTCAT
1 GGGCATTTTGGTCATTTAGGGGTAAAATGAATTAAAATACAAAATTAAAAGCCAATTTTGCTCAT
34710933 CTTCAACCCCATGGCCGAATATAGCAAGGAGAAACCATGGCTAGGGTTTTTCAAGCTTCCAAGCT
66 CTTCAACCCCATGGCCGAATATAGCAAGGAGAAACCATGGCTAGGGTTTTTCAAGCTTCCAAGCT
34710998 CGATTGTAAGTCCGTTCTAGCCTAGTTTAG
131 CGATTGTAAGTCCGTTCTAGCCTAGTTTAG
34711028 GGGCATTTTGGTCATTTAGGGGTAAAATGAATTAAAATACAAAATTAAAAGCCAATTTTGCTCAT
1 GGGCATTTTGGTCATTTAGGGGTAAAATGAATTAAAATACAAAATTAAAAGCCAATTTTGCTCAT
34711093 CTTCAACCCCATGGCCGAATATAGCAAGGAGAAACCATGGCTAGGGTTTTTCAAGCTTCCAAGCT
66 CTTCAACCCCATGGCCGAATATAGCAAGGAGAAACCATGGCTAGGGTTTTTCAAGCTTCCAAGCT
34711158 CGATTGTAAGTCCGTTCTAGCCT
131 CGATTGTAAGTCCGTTCTAGCCT
34711181 CATTTTTAAT
Statistics
Matches: 152, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 152 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.29
Consensus pattern (160 bp):
GGGCATTTTGGTCATTTAGGGGTAAAATGAATTAAAATACAAAATTAAAAGCCAATTTTGCTCAT
CTTCAACCCCATGGCCGAATATAGCAAGGAGAAACCATGGCTAGGGTTTTTCAAGCTTCCAAGCT
CGATTGTAAGTCCGTTCTAGCCTAGTTTAG
Found at i:34712047 original size:46 final size:46
Alignment explanation
Indices: 34711997--34712172 Score: 201
Period size: 46 Copynumber: 3.8 Consensus size: 46
34711987 TGTTTGGGCA
*
34711997 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
*** * * ** *
34712043 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGC-AAACG
* * *
34712090 TCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
34712136 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
34712173 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 22, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
46 71 0.68
47 34 0.32
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:34712152 original size:93 final size:93
Alignment explanation
Indices: 34711993--34712164 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
34711983 AGGATGTTTG
* *
34711993 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAG
34712058 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * * *
34712086 GGCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAG
34712151 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
34712165 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:34715301 original size:46 final size:48
Alignment explanation
Indices: 34715170--34715428 Score: 231
Period size: 46 Copynumber: 5.5 Consensus size: 48
34715160 AAGTCGATCC
* * * **
34715170 CATGTCCCAGACATGGTCTTACACTAGCTCTCAGATATCCGT--GCTAATG
1 CATGTCCCAGACATGGTCTTACACTGGCT-T-ACATCT-CGTAGGCCGATG
* *
34715219 CAATGTCACAGACATGGTCTTACACTGAC--ACATCTCGTA-GCCGATG
1 C-ATGTCCCAGACATGGTCTTACACTGGCTTACATCTCGTAGGCCGATG
34715265 CATGTCCCAGACAT-GTCTTACACTGGCTTACATCTCG-AGGCCGATG
1 CATGTCCCAGACATGGTCTTACACTGGCTTACATCTCGTAGGCCGATG
* * * *
34715311 CATGTCCCAGACAT-GTCTTACACTAGCTCT-CATCTC-AATGCTGATG
1 CATGTCCCAGACATGGTCTTACACTGGCT-TACATCTCGTAGGCCGATG
**
34715357 TCATGTCCCAGACATGGTCTTACACTGGC-T-C-TCGTAATATGGCCGATG
1 -CATGTCCCAGACATGGTCTTACACTGGCTTACATC-TCGTA-GGCCGATG
34715405 CATGTCCCAGACAT-GTCTTACACT
1 CATGTCCCAGACATGGTCTTACACT
34715429 AGCACACAAT
Statistics
Matches: 181, Mismatches: 17, Indels: 27
0.80 0.08 0.12
Matches are distributed among these distances:
44 12 0.07
45 18 0.10
46 78 0.43
47 30 0.17
48 18 0.10
49 1 0.01
50 24 0.13
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (48 bp):
CATGTCCCAGACATGGTCTTACACTGGCTTACATCTCGTAGGCCGATG
Found at i:34715377 original size:94 final size:94
Alignment explanation
Indices: 34715170--34715436 Score: 273
Period size: 94 Copynumber: 2.9 Consensus size: 94
34715160 AAGTCGATCC
* * * * * ** *
34715170 CATGTCCCAGACATGGTCTTACACTAGCTCTCAGATATCCG-TGCTAATGCAATGTCACAGACAT
1 CATGTCCCAGACATGGTCTTACACTGGCT-T-ACATCTACGAGGCCGATGC-ATGTCCCAGACAT
*
34715234 GGTCTTACACT-G-ACACATCTCGTAGCCGATG
63 -GTCTTACACTAGCACACATCTCATAGCCGATG
34715265 CATGTCCCAGACAT-GTCTTACACTGGCTTACATCT-CGAGGCCGATGCATGTCCCAGACATGTC
1 CATGTCCCAGACATGGTCTTACACTGGCTTACATCTACGAGGCCGATGCATGTCCCAGACATGTC
* * *
34715328 TTACACTAGCTCTCATCTCA-ATGCTGATG
66 TTACACTAGCACACATCTCATA-GCCGATG
**
34715357 TCATGTCCCAGACATGGTCTTACACTGGC-T-C-TCGTAATATGGCCGATGCATGTCCCAGACAT
1 -CATGTCCCAGACATGGTCTTACACTGGCTTACATC-TACGA-GGCCGATGCATGTCCCAGACAT
34715419 GTCTTACACTAGCACACA
63 GTCTTACACTAGCACACA
34715437 ATTAACTCGA
Statistics
Matches: 148, Mismatches: 15, Indels: 19
0.81 0.08 0.10
Matches are distributed among these distances:
90 10 0.07
91 18 0.12
92 25 0.17
93 17 0.11
94 64 0.43
95 14 0.09
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.27
Consensus pattern (94 bp):
CATGTCCCAGACATGGTCTTACACTGGCTTACATCTACGAGGCCGATGCATGTCCCAGACATGTC
TTACACTAGCACACATCTCATAGCCGATG
Found at i:34715406 original size:140 final size:140
Alignment explanation
Indices: 34715170--34715428 Score: 364
Period size: 140 Copynumber: 1.8 Consensus size: 140
34715160 AAGTCGATCC
**
34715170 CATGTCCCAGACATGGTCTTACACTAGCTCTCAGATATCCGTGCTAATGCAATGTCACAGACATG
1 CATGTCCCAGACATGGTCTTACACTAGCTCTCA-ATATCAATGCTAATGCAATGTCACAGACATG
**
34715235 GTCTTACACTGACACATCTCGTAGCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCT
65 GTCTTACACTGACACATCTAATAGCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCT
34715300 CGAGGCCGATG
130 CGAGGCCGATG
* * *
34715311 CATGTCCCAGACAT-GTCTTACACTAGCTCTC-ATCTCAATGCTGATGTC-ATGTCCCAGACATG
1 CATGTCCCAGACATGGTCTTACACTAGCTCTCAATATCAATGCTAATG-CAATGTCACAGACATG
* *
34715373 GTCTTACACTGGCTC-TCGTAATATGGCCGATGCATGTCCCAGACATGTCTTACACT
65 GTCTTACACTGACACATC-TAATA--GCCGATGCATGTCCCAGACATGTCTTACACT
34715429 AGCACACAAT
Statistics
Matches: 105, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
137 2 0.02
138 40 0.38
139 1 0.01
140 48 0.46
141 14 0.13
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (140 bp):
CATGTCCCAGACATGGTCTTACACTAGCTCTCAATATCAATGCTAATGCAATGTCACAGACATGG
TCTTACACTGACACATCTAATAGCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTC
GAGGCCGATG
Found at i:34716155 original size:13 final size:13
Alignment explanation
Indices: 34716137--34716161 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34716127 CTAAAAGTGC
34716137 AAAAATCATCAAG
1 AAAAATCATCAAG
34716150 AAAAATCATCAA
1 AAAAATCATCAA
34716162 AATCACTTAC
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:0.64, C:0.16, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAAATCATCAAG
Found at i:34718033 original size:12 final size:14
Alignment explanation
Indices: 34718003--34718034 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
34717993 AAATAAAAGA
34718003 AAAAATTAGAATGT
1 AAAAATTAGAATGT
34718017 AAAAATTA-AAT-T
1 AAAAATTAGAATGT
34718029 AAAAAT
1 AAAAAT
34718035 AAAAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 3 0.17
14 8 0.44
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (14 bp):
AAAAATTAGAATGT
Found at i:34718039 original size:6 final size:6
Alignment explanation
Indices: 34718016--34718059 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
34718006 AATTAGAATG
* *
34718016 TAAAAA TTAAAT TAAAAA TAAAAA TATTAAAA TAAAAA TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TA--AAAA TAAAAA TAAAAA
34718060 AGGGTAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 26 0.81
8 6 0.19
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (6 bp):
TAAAAA
Found at i:34718046 original size:20 final size:19
Alignment explanation
Indices: 34718017--34718060 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
34718007 ATTAGAATGT
*
34718017 AAAAATTAAATTAAAAATA
1 AAAAATTAAAATAAAAATA
34718036 AAAATATTAAAATAAAAATA
1 AAAA-ATTAAAATAAAAATA
34718056 AAAAA
1 AAAAA
34718061 GGGTAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAAATTAAAATAAAAATA
Found at i:34720284 original size:28 final size:28
Alignment explanation
Indices: 34720252--34720311 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
34720242 GAATGGAGAG
*
34720252 ATTCAAGTCAAGATTGTGTAGGAATAGT
1 ATTCAAGTCAAGATTGTCTAGGAATAGT
34720280 ATTCAAGTCAAGATTGTCTAGGAATAGT
1 ATTCAAGTCAAGATTGTCTAGGAATAGT
34720308 ATTC
1 ATTC
34720312 TCCACTTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33
Consensus pattern (28 bp):
ATTCAAGTCAAGATTGTCTAGGAATAGT
Found at i:34732759 original size:23 final size:24
Alignment explanation
Indices: 34732732--34732778 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
34732722 TTTGTACAAG
34732732 AAATTATAAAAAT-AT-TTTTATTT
1 AAATTA-AAAAATAATATTTTATTT
*
34732755 AAATTAAAATATAATATTTTATTT
1 AAATTAAAAAATAATATTTTATTT
34732779 CTTTTGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 8 0.38
24 8 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
AAATTAAAAAATAATATTTTATTT
Found at i:34742089 original size:57 final size:56
Alignment explanation
Indices: 34742000--34742115 Score: 182
Period size: 57 Copynumber: 2.1 Consensus size: 56
34741990 TCGGAACAGG
34742000 ATTACGAAGTATTACTGGTCACTACAGTTCGATTGCAATTAATAGAGAAAGAAATACA
1 ATTACGAAGTATTACTGGTCACTACAGTTCGATTGCAATTAATAGAG--AGAAATACA
*
34742058 ATTACGAA-TATTA-TCGGTCACTACATTTCGATTGCAATTAATAGAGAGAAATACA
1 ATTACGAAGTATTACT-GGTCACTACAGTTCGATTGCAATTAATAGAGAGAAATACA
34742113 ATT
1 ATT
34742116 CAGTTCATAA
Statistics
Matches: 56, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
55 12 0.21
56 1 0.02
57 35 0.62
58 8 0.14
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.30
Consensus pattern (56 bp):
ATTACGAAGTATTACTGGTCACTACAGTTCGATTGCAATTAATAGAGAGAAATACA
Found at i:34742230 original size:11 final size:12
Alignment explanation
Indices: 34742205--34742229 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34742195 AATCGGAAGC
34742205 TTATAAAATTTT
1 TTATAAAATTTT
34742217 TTATAAAATTTT
1 TTATAAAATTTT
34742229 T
1 T
34742230 AAATTTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTATAAAATTTT
Found at i:34743419 original size:18 final size:19
Alignment explanation
Indices: 34743382--34743425 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
34743372 AGAGTCGGAA
* *
34743382 TACACTGTAACGGTAACAG
1 TACACAGTAACAGTAACAG
*
34743401 TA-ACAGTAACAGTATCAG
1 TACACAGTAACAGTAACAG
34743419 TACACAG
1 TACACAG
34743426 CGTACCTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.20
Consensus pattern (19 bp):
TACACAGTAACAGTAACAG
Found at i:34744000 original size:19 final size:18
Alignment explanation
Indices: 34743960--34744009 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 18
34743950 TAATATTAAT
34743960 TTAATAATAAA--AATCA
1 TTAATAATAAATTAATCA
34743976 -TAATAATAAATTAATCAA
1 TTAATAATAAATTAATC-A
*
34743994 TTAATAATAATTTAAT
1 TTAATAATAAATTAAT
34744010 ATATTTTAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 10 0.34
17 4 0.14
18 1 0.03
19 14 0.48
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
TTAATAATAAATTAATCA
Found at i:34753766 original size:19 final size:19
Alignment explanation
Indices: 34753719--34753756 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
34753709 AAATGATGTT
34753719 ATATCAATAATTGTATTAA
1 ATATCAATAATTGTATTAA
34753738 ATATCAATAATTGTATTAA
1 ATATCAATAATTGTATTAA
34753757 TAATGTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (19 bp):
ATATCAATAATTGTATTAA
Found at i:34755642 original size:180 final size:177
Alignment explanation
Indices: 34755319--34755644 Score: 474
Period size: 180 Copynumber: 1.8 Consensus size: 177
34755309 GCATATGTGG
* * *
34755319 CATGCGAAACTTCATCTCCATGCGAGATTAATTCTGCAGCCTTATCTTTAATAATCCTAGCTACA
1 CATGCGAAACTTCATCTCCACGCGAGATTAATTCTGCAGCCTTACCTTTAAGAATCCTAGCTACA
** * * *
34755384 TTATTAGCTATAACATGGCACACCGTCTCTGTCAAAGCCTCAAACTTAGCTATAACATCTTCACT
66 CCATCAGCTATAACATGGCACACCGTCTCTGTCAAAGCCTCAAACTTAGCCATAACATCTTCACC
*
34755449 CGTGATCTTATCACCAGATACATATGTTTCCTCTACCTCATTATAGA
131 CATGATCTTATCACCAGATACATATGTTTCCTCTACCTCATTATAGA
* * *
34755496 CATGGGAAACTTCATTTCTTCCACGCGAGATTGATTCTGCAGCCTTACCTTTAAGGATCCTAGCT
1 CATGCGAAACTTCA--TC-TCCACGCGAGATTAATTCTGCAGCCTTACCTTTAAGAATCCTAGCT
* * *
34755561 ACACCATCAGCTATAATATGGGA-AGCCTTCTCTGTCAAAGCCTCAAACTTAGCCATAACATCTT
63 ACACCATCAGCTATAACATGGCACA-CCGTCTCTGTCAAAGCCTCAAACTTAGCCATAACATCTT
34755625 CACCCATGATCTTATCACCA
127 CACCCATGATCTTATCACCA
34755645 AACTTAGCCA
Statistics
Matches: 130, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
177 13 0.10
179 3 0.02
180 114 0.88
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.31
Consensus pattern (177 bp):
CATGCGAAACTTCATCTCCACGCGAGATTAATTCTGCAGCCTTACCTTTAAGAATCCTAGCTACA
CCATCAGCTATAACATGGCACACCGTCTCTGTCAAAGCCTCAAACTTAGCCATAACATCTTCACC
CATGATCTTATCACCAGATACATATGTTTCCTCTACCTCATTATAGA
Found at i:34755663 original size:39 final size:39
Alignment explanation
Indices: 34755604--34755683 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
34755594 GTCAAAGCCT
*
34755604 CAAACTTAGCCATAACATCTTCACCCATGATCTTATCAC
1 CAAACTTAGCCATAAAATCTTCACCCATGATCTTATCAC
*
34755643 CAAACTTAGCCATAAAATCTTCACTCATGATCTTATCAC
1 CAAACTTAGCCATAAAATCTTCACCCATGATCTTATCAC
34755682 CA
1 CA
34755684 GATGCATATG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.35, C:0.31, G:0.05, T:0.29
Consensus pattern (39 bp):
CAAACTTAGCCATAAAATCTTCACCCATGATCTTATCAC
Found at i:34756134 original size:54 final size:54
Alignment explanation
Indices: 34756048--34756205 Score: 203
Period size: 54 Copynumber: 2.9 Consensus size: 54
34756038 GCTTTATCTG
* * *
34756048 TTCCATGCTCCTTCGCATCTGCAATTTCATCTTTCGCATGATGGGCTTCATCTC
1 TTCCATGCTCCATCGCATCTGCAATTTCATCTTTCGCATGATGAGCTTCACCTC
* * * * *
34756102 TTCTATGCTGCATTGCATCTGCAGTTTCATCTTTCGTATGATGAGCTTCACCTC
1 TTCCATGCTCCATCGCATCTGCAATTTCATCTTTCGCATGATGAGCTTCACCTC
*
34756156 TTCCATGCTCCATCGCATCTGCAACTTT-TTC-TTCTGCATGATGAGCTTCA
1 TTCCATGCTCCATCGCATCTGCAA-TTTCATCTTTC-GCATGATGAGCTTCA
34756206 TGCCGAGCTT
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
53 3 0.03
54 82 0.93
55 3 0.03
ACGTcount: A:0.16, C:0.29, G:0.15, T:0.39
Consensus pattern (54 bp):
TTCCATGCTCCATCGCATCTGCAATTTCATCTTTCGCATGATGAGCTTCACCTC
Found at i:34757672 original size:16 final size:16
Alignment explanation
Indices: 34757610--34757674 Score: 51
Period size: 16 Copynumber: 3.9 Consensus size: 16
34757600 TATAATGTAC
34757610 ATTTTATTTTTTTAAT
1 ATTTTATTTTTTTAAT
**
34757626 -TTATTATAATTTTAGAAT
1 ATT-TTAT--TTTTTTAAT
* * *
34757644 ATTTGAGTATTTTAAT
1 ATTTTATTTTTTTAAT
34757660 ATTTTATTTTTTTAA
1 ATTTTATTTTTTTAA
34757675 AGAAATTTGA
Statistics
Matches: 35, Mismatches: 10, Indels: 8
0.66 0.19 0.15
Matches are distributed among these distances:
15 2 0.06
16 22 0.63
18 9 0.26
19 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.65
Consensus pattern (16 bp):
ATTTTATTTTTTTAAT
Found at i:34758283 original size:2 final size:2
Alignment explanation
Indices: 34758276--34758317 Score: 59
Period size: 2 Copynumber: 21.0 Consensus size: 2
34758266 TAAAATACCG
*
34758276 AT AT AT AT AT AT AT AT AT AT GA- AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT
34758318 TAAACTGTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 34 0.94
3 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34758746 original size:19 final size:19
Alignment explanation
Indices: 34758699--34758736 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
34758689 AAATGATGTT
34758699 ATATCAATAATTGTATTAA
1 ATATCAATAATTGTATTAA
34758718 ATATCAATAATTGTATTAA
1 ATATCAATAATTGTATTAA
34758737 TAATGTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (19 bp):
ATATCAATAATTGTATTAA
Found at i:34759474 original size:49 final size:49
Alignment explanation
Indices: 34759402--34759500 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
34759392 GCCAAACAGT
34759402 AAGCTACCTTGTCACTTCCTCGCAGGATATGCCTAAACTTCACTTTCCA
1 AAGCTACCTTGTCACTTCCTCGCAGGATATGCCTAAACTTCACTTTCCA
34759451 AAGCTACCTTGTCACTTCCTCGCAGGATATGCCTAAACTTCACTTTCCA
1 AAGCTACCTTGTCACTTCCTCGCAGGATATGCCTAAACTTCACTTTCCA
34759500 A
1 A
34759501 TCCTTATTGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.25, C:0.32, G:0.12, T:0.30
Consensus pattern (49 bp):
AAGCTACCTTGTCACTTCCTCGCAGGATATGCCTAAACTTCACTTTCCA
Found at i:34760332 original size:27 final size:27
Alignment explanation
Indices: 34760302--34760354 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
34760292 AATTTGATAA
*
34760302 AATAAATCATTA-AAAAAACATAAAAAT
1 AATAAAT-ATTATAAAAAAAATAAAAAT
*
34760329 AATATATATTATAAAAAAAATAAAAA
1 AATAAATATTATAAAAAAAATAAAAA
34760355 AATTCAGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.25
Consensus pattern (27 bp):
AATAAATATTATAAAAAAAATAAAAAT
Found at i:34761803 original size:17 final size:17
Alignment explanation
Indices: 34761777--34761811 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
34761767 AATATTTGCA
* *
34761777 CCAAATTTAGAACCATT
1 CCAAAATTAGAACAATT
34761794 CCAAAATTAGAACAATT
1 CCAAAATTAGAACAATT
34761811 C
1 C
34761812 ATATCTAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.23, G:0.06, T:0.26
Consensus pattern (17 bp):
CCAAAATTAGAACAATT
Found at i:34765036 original size:46 final size:45
Alignment explanation
Indices: 34764972--34765187 Score: 274
Period size: 46 Copynumber: 4.7 Consensus size: 45
34764962 TCTCGAGGCT
* * * * *
34764972 GATGTATGTCCCAGACATGTCTTACACTAGCTCTCGTTTCAA-T-GAC
1 GATGCATGTCCCAGACATGTCTTACACTGGCTTTC--AT-AAGTGGCC
*
34765018 GATGCATGTCCCAGACATGTCTTACACTGGCTTTCATAACATGGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCTTTCATAA-GTGGCC
* *
34765064 GATGCATGTCCCAGGCATGTCTTACACTAGCTTTCATAATGTGGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCTTTCATAA-GTGGCC
*
34765110 AATGCATGTCCCAGACATGTCTTACACTGGCTTTCATAATGTGGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCTTTCATAA-GTGGCC
*
34765156 GATGCATGTCCCAAACATGTCTTACACTGGCT
1 GATGCATGTCCCAGACATGTCTTACACTGGCT
34765188 CACATACCAC
Statistics
Matches: 153, Mismatches: 14, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
43 2 0.01
44 1 0.01
45 1 0.01
46 149 0.97
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTTTCATAAGTGGCC
Found at i:34766668 original size:3 final size:3
Alignment explanation
Indices: 34766660--34766701 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
34766650 AATTCAAAGA
*
34766660 AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
34766702 CAAAGCCTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:34768989 original size:22 final size:22
Alignment explanation
Indices: 34768964--34769008 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
34768954 ATAGTTTTAC
*
34768964 TTTA-TTTCAAATTGGTTTTTTT
1 TTTACTTTC-AATTGATTTTTTT
*
34768986 TTTACTTTCATTTGATTTTTTT
1 TTTACTTTCAATTGATTTTTTT
34769008 T
1 T
34769009 GTTTAATTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.71
Consensus pattern (22 bp):
TTTACTTTCAATTGATTTTTTT
Found at i:34769156 original size:31 final size:32
Alignment explanation
Indices: 34769097--34769157 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
34769087 TTTATGGCTA
* * *
34769097 TATTTTCTTTTAAATTTATTCATATATATACG
1 TATTTCCTTTCAAACTTATTCATATATATACG
34769129 TATTTCCTTTCAAACTTATT-ATATATATA
1 TATTTCCTTTCAAACTTATTCATATATATA
34769158 GTTTATTCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 9 0.35
32 17 0.65
ACGTcount: A:0.33, C:0.11, G:0.02, T:0.54
Consensus pattern (32 bp):
TATTTCCTTTCAAACTTATTCATATATATACG
Found at i:34779958 original size:44 final size:44
Alignment explanation
Indices: 34779905--34779993 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
34779895 CTAAAGAAAA
34779905 GAACATGAACCTTTCTTCCTCAGTGAAAGCTATGAGAAAGAAGG
1 GAACATGAACCTTTCTTCCTCAGTGAAAGCTATGAGAAAGAAGG
34779949 GAACATGAACCTTTCTTCCTCAGTGAAAGCTATGAGAAAGAAGG
1 GAACATGAACCTTTCTTCCTCAGTGAAAGCTATGAGAAAGAAGG
34779993 G
1 G
34779994 TCAAATGGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (44 bp):
GAACATGAACCTTTCTTCCTCAGTGAAAGCTATGAGAAAGAAGG
Found at i:34784007 original size:31 final size:32
Alignment explanation
Indices: 34783966--34784025 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
34783956 TAAGTAAGAG
34783966 ATGAGAATTGAAAGTAT-TTTGAATGATTACTT
1 ATGAGAATTGAAA-TATCTTTGAATGATTACTT
* *
34783998 ATGA-AATTGATATTTCTTTGAATGATTA
1 ATGAGAATTGAAATATCTTTGAATGATTA
34784026 TTGTTATGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 2 0.08
31 19 0.76
32 4 0.16
ACGTcount: A:0.37, C:0.03, G:0.17, T:0.43
Consensus pattern (32 bp):
ATGAGAATTGAAATATCTTTGAATGATTACTT
Found at i:34790172 original size:61 final size:61
Alignment explanation
Indices: 34790105--34790252 Score: 173
Period size: 60 Copynumber: 2.5 Consensus size: 61
34790095 TAGTGTTAAC
* * *
34790105 TGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCGCT-TTAC-AGTATC-AGAGTATAT
1 TGGGCCTTAGCCCATATCAATATCAATCTGGGCCATAACCCTATTACAAG--TCGAGA-TATAT
* *
34790166 TGGGCC-TAGCCCATATCAGTATCAATCTGGGCCGTAACCCTATTACAAGTCGAGATATAT
1 TGGGCCTTAGCCCATATCAATATCAATCTGGGCCATAACCCTATTACAAGTCGAGATATAT
*
34790226 TGGGCCTTA-CCCATTTCAATA-CAATCT
1 TGGGCCTTAGCCCATATCAATATCAATCT
34790253 CATATGATTA
Statistics
Matches: 76, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
59 6 0.08
60 53 0.70
61 15 0.20
62 2 0.03
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (61 bp):
TGGGCCTTAGCCCATATCAATATCAATCTGGGCCATAACCCTATTACAAGTCGAGATATAT
Found at i:34790872 original size:16 final size:16
Alignment explanation
Indices: 34790851--34790883 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
34790841 ACAAAATGCT
34790851 GGCTTTTCGACATTTC
1 GGCTTTTCGACATTTC
*
34790867 GGCTTTTCGACTTTTC
1 GGCTTTTCGACATTTC
34790883 G
1 G
34790884 CCGATCTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.45
Consensus pattern (16 bp):
GGCTTTTCGACATTTC
Found at i:34793436 original size:13 final size:13
Alignment explanation
Indices: 34793418--34793442 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34793408 TTTAAGAAAA
34793418 TATTATATTATAT
1 TATTATATTATAT
34793431 TATTATATTATA
1 TATTATATTATA
34793443 ACTAAAGTAA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTATATTATAT
Found at i:34797762 original size:56 final size:55
Alignment explanation
Indices: 34797676--34797784 Score: 173
Period size: 56 Copynumber: 2.0 Consensus size: 55
34797666 CATGGGTTAC
*
34797676 CACTTTGGCTACAGGTTCAGACGTTTTACAACGGTGTGAACAGCTCAACGAGGGA
1 CACTTTGGCTACAGGTTCAGACGTTTTACAACGGTGGGAACAGCTCAACGAGGGA
* * *
34797731 NCACTTTGGCTATAGGTTCAGATGTTTTACAACGGTGGGAACCGCTCAACGAGG
1 -CACTTTGGCTACAGGTTCAGACGTTTTACAACGGTGGGAACAGCTCAACGAGG
34797785 CAACTCATCA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (55 bp):
CACTTTGGCTACAGGTTCAGACGTTTTACAACGGTGGGAACAGCTCAACGAGGGA
Found at i:34800701 original size:50 final size:49
Alignment explanation
Indices: 34800626--34800724 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 49
34800616 TCACCATGGG
*
34800626 TTACCACTTTGGCTATAGGTTCAGATGTTTTACAACGGTGTGAACCGCT
1 TTACCACTTTGGCTATAGGTTCAGATGTTTTACAACGGTGGGAACCGCT
34800675 NTTACCACTTTGGCTATAGGTTCAGATGTTTTACAACGGTGGGAACCGCT
1 -TTACCACTTTGGCTATAGGTTCAGATGTTTTACAACGGTGGGAACCGCT
34800725 CAACGAGGCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.33
Consensus pattern (49 bp):
TTACCACTTTGGCTATAGGTTCAGATGTTTTACAACGGTGGGAACCGCT
Found at i:34810186 original size:19 final size:22
Alignment explanation
Indices: 34810147--34810186 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
34810137 AGAAACCCAA
34810147 CCATATCCAACCGTATACACCC
1 CCATATCCAACCGTATACACCC
34810169 CCATA-CCAACC-T-TACACC
1 CCATATCCAACCGTATACACC
34810187 GTGTGGGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 6 0.33
22 5 0.28
ACGTcount: A:0.33, C:0.47, G:0.03, T:0.17
Consensus pattern (22 bp):
CCATATCCAACCGTATACACCC
Found at i:34810285 original size:27 final size:26
Alignment explanation
Indices: 34810248--34810362 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
34810238 AGCATGGCTG
* *
34810248 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
34810274 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
34810302 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
34810329 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
34810356 CCAGAAC
1 CCAGAAC
34810363 GCTTCCTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:34810307 original size:54 final size:54
Alignment explanation
Indices: 34810248--34810362 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
34810238 AGCATGGCTG
*
34810248 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
34810302 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
34810356 CCAGAAC
1 CCAGAAC
34810363 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:34812018 original size:26 final size:26
Alignment explanation
Indices: 34811981--34812090 Score: 168
Period size: 26 Copynumber: 4.2 Consensus size: 26
34811971 CATGAAATTC
34811981 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
34812007 CTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
34812033 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
34812059 TTATCATTG-AACATTTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCCA
34812085 TTATCA
1 TTATCA
34812091 ATTTGTATCA
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
26 77 0.97
27 2 0.03
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:34815298 original size:26 final size:26
Alignment explanation
Indices: 34815269--34815324 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
34815259 TGATACAAAT
34815269 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
34815295 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
34815321 TGAT
1 TGAT
34815325 GGGAATTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.27, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:34815952 original size:253 final size:253
Alignment explanation
Indices: 34815504--34816008 Score: 983
Period size: 253 Copynumber: 2.0 Consensus size: 253
34815494 GAAATTGAAG
34815504 GTAAGTTCATGGTAGTTTGCTTCTATCTTGAGGTTCATGAGTTCTTCTTGATTCTACCTTAACTC
1 GTAAGTTCATGGTAGTTTGCTTCTATCTTGAGGTTCATGAGTTCTTCTTGATTCTACCTTAACTC
34815569 TTGAAGCATATTTTGGTTTTTAGTTGTGTTGTGAACATTTAGTCATGAATTAAAATGAAGGAAAT
66 TTGAAGCATATTTTGGTTTTTAGTTGTGTTGTGAACATTTAGTCATGAATTAAAATGAAGGAAAT
*
34815634 GGTTGTTGTTTCATGTTCTTTTGATGAAAAATGGAAGATAGGTGAAGTTGAGCCAAACAAATGAG
131 GGTTGTTGTTTCATGTTCTTTTGATGAAAAATGGAAGATAGGTGAAGTTGAGACAAACAAATGAG
34815699 CATGCATGTGCCTTAGATGCTAAAGGGAAAAATCGGCTAACACGTTGTGCTTTAAAAT
196 CATGCATGTGCCTTAGATGCTAAAGGGAAAAATCGGCTAACACGTTGTGCTTTAAAAT
34815757 GTAAGTTCATGGTAGTTTGCTTCTATCTTGAGGTTCATGAGTTCTTCTTGATTCTACCTTAACTC
1 GTAAGTTCATGGTAGTTTGCTTCTATCTTGAGGTTCATGAGTTCTTCTTGATTCTACCTTAACTC
34815822 TTGAAGCATATTTTGGTTTTTAGTTGTGTTGTGAACATTTAGTCATGAATTAAAATGAAGGAAAT
66 TTGAAGCATATTTTGGTTTTTAGTTGTGTTGTGAACATTTAGTCATGAATTAAAATGAAGGAAAT
*
34815887 GGTTGTTGTTTCATGTTCTTTTGATGAAAAATGGAAGATAGGTGAAGTTGATACAAACAAATGAG
131 GGTTGTTGTTTCATGTTCTTTTGATGAAAAATGGAAGATAGGTGAAGTTGAGACAAACAAATGAG
*
34815952 CATGCATGTGCCTTAGATGCTAAAGGGAAAAATCGGCTAACATGTTGTGCTTTAAAA
196 CATGCATGTGCCTTAGATGCTAAAGGGAAAAATCGGCTAACACGTTGTGCTTTAAAA
34816009 AGATGAAATG
Statistics
Matches: 249, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
253 249 1.00
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.37
Consensus pattern (253 bp):
GTAAGTTCATGGTAGTTTGCTTCTATCTTGAGGTTCATGAGTTCTTCTTGATTCTACCTTAACTC
TTGAAGCATATTTTGGTTTTTAGTTGTGTTGTGAACATTTAGTCATGAATTAAAATGAAGGAAAT
GGTTGTTGTTTCATGTTCTTTTGATGAAAAATGGAAGATAGGTGAAGTTGAGACAAACAAATGAG
CATGCATGTGCCTTAGATGCTAAAGGGAAAAATCGGCTAACACGTTGTGCTTTAAAAT
Found at i:34822593 original size:26 final size:26
Alignment explanation
Indices: 34822564--34822619 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
34822554 TGATACAAAT
*
34822564 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAACGGGTTAGGTAAATGTTCCA
*
34822590 TGATAACGGGTTAGGTAAATGTTTCA
1 TGATAACGGGTTAGGTAAATGTTCCA
34822616 TGAT
1 TGAT
34822620 GGGAATTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAACGGGTTAGGTAAATGTTCCA
Found at i:34825389 original size:24 final size:23
Alignment explanation
Indices: 34825314--34825391 Score: 81
Period size: 24 Copynumber: 3.4 Consensus size: 23
34825304 ACAGAATACA
*
34825314 CCACAAAGG-CTAATAGAA-T-G
1 CCACAAAGGCCAAATAGAAGTAG
*
34825334 CCACAAAGGCCAAACAGAAGTACG
1 CCACAAAGGCCAAATAGAAGTA-G
* *
34825358 TCAAAAAGGCCAAATAGAAGTAAG
1 CCACAAAGGCCAAATAGAAGT-AG
34825382 CCACAAAGGC
1 CCACAAAGGC
34825392 TAACCAAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
20 9 0.20
21 7 0.15
22 1 0.02
24 28 0.61
25 1 0.02
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (23 bp):
CCACAAAGGCCAAATAGAAGTAG
Found at i:34826515 original size:15 final size:15
Alignment explanation
Indices: 34826492--34826526 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
34826482 TGAAGGGGAA
* *
34826492 AATGGAAGGTTTATG
1 AATGAAAGGTTAATG
34826507 AATGAAAGGTTAATG
1 AATGAAAGGTTAATG
34826522 AATGA
1 AATGA
34826527 TGAAAGGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (15 bp):
AATGAAAGGTTAATG
Done.