Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 113 of 204
Found at i:34494368 original size:85 final size:85
Alignment explanation
Indices: 34494241--34494398 Score: 208
Period size: 85 Copynumber: 1.9 Consensus size: 85
34494231 AGAAGAAACC
* * * * * * *
34494241 AATCCTATCTCCCTGAAGTTATAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAGTTG
1 AATCCTATCTCCCTGAAGATATAGTAGAGCGGACTAAAACCACAAATCTCATCCCCCTAAAGTTG
*
34494306 CAGTAGAGCAGATCGCGTCT
66 CAGCAGAGCAGATCGCGTCT
* * * *
34494326 AATCCTATCTCTCTGAAGATGTAGTAGAGTGGACTAAAACCACAAATCTCGTCCCCCTAAAGTTG
1 AATCCTATCTCCCTGAAGATATAGTAGAGCGGACTAAAACCACAAATCTCATCCCCCTAAAGTTG
34494391 CAGCAGAG
66 CAGCAGAG
34494399 TGGATTGAAG
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
85 61 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (85 bp):
AATCCTATCTCCCTGAAGATATAGTAGAGCGGACTAAAACCACAAATCTCATCCCCCTAAAGTTG
CAGCAGAGCAGATCGCGTCT
Found at i:34501260 original size:22 final size:22
Alignment explanation
Indices: 34501232--34501276 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
34501222 ATTATGATGA
34501232 TTGATATG-ATGTGATTGATATT
1 TTGATATGTATGTGATTG-TATT
34501254 TTGATATGTATGTGATTGTATT
1 TTGATATGTATGTGATTGTATT
34501276 T
1 T
34501277 GTGTTGATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.53
Consensus pattern (22 bp):
TTGATATGTATGTGATTGTATT
Found at i:34502176 original size:15 final size:15
Alignment explanation
Indices: 34502158--34502208 Score: 61
Period size: 16 Copynumber: 3.5 Consensus size: 15
34502148 CTATATACTA
*
34502158 TGAAACTATAGATTC
1 TGAAACTATAGATAC
34502173 TGAAAACTATAGATAC
1 TG-AAACTATAGATAC
*
34502189 TGATACTATAG-TAC
1 TGAAACTATAGATAC
34502203 -GAAACT
1 TGAAACT
34502209 TTTAAAACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
13 5 0.16
14 3 0.09
15 10 0.31
16 14 0.44
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (15 bp):
TGAAACTATAGATAC
Found at i:34506575 original size:12 final size:12
Alignment explanation
Indices: 34506547--34506577 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
34506537 CTCAGGTTGT
*
34506547 CACACGGCCTAG
1 CACATGGCCTAG
34506559 CACATGGCCTAG
1 CACATGGCCTAG
34506571 CACATGG
1 CACATGG
34506578 GCGTGTGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.35, G:0.26, T:0.13
Consensus pattern (12 bp):
CACATGGCCTAG
Found at i:34508834 original size:14 final size:15
Alignment explanation
Indices: 34508805--34508837 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
34508795 GAACTTGTGA
*
34508805 ATATTATGATGATTG
1 ATATGATGATGATTG
34508820 ATATGATGA-GATTG
1 ATATGATGATGATTG
34508834 ATAT
1 ATAT
34508838 TTTGATATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.42
Consensus pattern (15 bp):
ATATGATGATGATTG
Found at i:34508842 original size:22 final size:22
Alignment explanation
Indices: 34508817--34508861 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
34508807 ATTATGATGA
34508817 TTGATATG-ATGAGATTGATATT
1 TTGATATGTATGAGA-TGATATT
*
34508839 TTGATATGTATGTGATGATATT
1 TTGATATGTATGAGATGATATT
34508861 T
1 T
34508862 GTGTTGATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (22 bp):
TTGATATGTATGAGATGATATT
Found at i:34509595 original size:12 final size:12
Alignment explanation
Indices: 34509576--34509605 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
34509566 CCTCACACGC
34509576 CCGTGTGCTAGG
1 CCGTGTGCTAGG
*
34509588 CTGTGTGCTAGG
1 CCGTGTGCTAGG
34509600 CCGTGT
1 CCGTGT
34509606 AACTGCTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.23, G:0.40, T:0.30
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:34514939 original size:91 final size:91
Alignment explanation
Indices: 34514790--34514997 Score: 335
Period size: 91 Copynumber: 2.3 Consensus size: 91
34514780 TTGATTTTAG
* * *
34514790 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
* * *
34514855 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
*
34514882 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTACTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTATA
34514947 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
*
34514973 CAAATTCATATAAGAAAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
34514998 GTTATAATTA
Statistics
Matches: 108, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 92 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:34514972 original size:44 final size:43
Alignment explanation
Indices: 34514830--34514972 Score: 105
Period size: 44 Copynumber: 3.2 Consensus size: 43
34514820 GAATTTTATG
* * *
34514830 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATTACTATTAAATTATA-TTAATAATAATTATTTT
* * * *
34514874 AAATTGTATAAATT-CATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATTAC-TAT---TAAATTATATTAAT-AATAATTATT-TT
34514921 AAATTATATATTACTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTACTATTAAATTATAT-TAATAATAATTATTTT
34514965 AAATTATA
1 AAATTATA
34514973 CAAATTCATA
Statistics
Matches: 75, Mismatches: 11, Indels: 26
0.67 0.10 0.23
Matches are distributed among these distances:
42 5 0.07
43 3 0.04
44 19 0.25
45 15 0.20
46 15 0.20
47 11 0.15
48 2 0.03
49 5 0.07
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (43 bp):
AAATTATATATTACTATTAAATTATATTAATAATAATTATTTT
Found at i:34515090 original size:59 final size:57
Alignment explanation
Indices: 34515002--34515452 Score: 198
Period size: 54 Copynumber: 7.6 Consensus size: 57
34514992 TTATTAGTTA
* *
34515002 TAATTATTTTAAATT-TTATTAA--ATCATATATTTTAATTAAAATATAATTAATAT
1 TAATTATTTAAAATTATTTTTAAGTATCATATATTTTAATTAAAATATAATTAATAT
* * * **
34515056 TAATTATTTCAAATTATGTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATA
1 TAATTATTTAAAATTAT-TTTTA-AGTATCATATATT-TTAATT-A--AAA-T-ATA-ATTAATA
34515121 T
57 T
* * *
34515122 TAATTA-TTAAGAATT-TTATTAA--ATTATATATTTTAATTAAAATATATTTAATAT
1 TAATTATTTAA-AATTATTTTTAAGTATCATATATTTTAATTAAAATATAATTAATAT
* * * **
34515176 TAATTATTTCAAATTATCTTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATA
1 TAATTATTTAAAATTAT-TTTTA-AGTATCATATATT-TTAATT-A--AAA-T-ATA-ATTAATA
34515241 T
57 T
* * ** *
34515242 TAATTA-TTAAGAATT-TTATTAA--ATTATATATTTTAATTAAAATATGTTTAATAA
1 TAATTATTTAA-AATTATTTTTAAGTATCATATATTTTAATTAAAATATAATTAATAT
* * **
34515296 TAATTATGTT-AAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAAT
1 TAATTAT-TTAAAATTAT-TTTTA-AGTATCATATATT-TTAATT-A--AAA-T-ATA-ATTAAT
34515360 AT
56 AT
* * * * * *
34515362 TAGTTA-TTAAGAATT-TTATTAA--ATTATATATTTTAATTATAATATATTTAATAA
1 TAATTATTTAA-AATTATTTTTAAGTATCATATATTTTAATTAAAATATAATTAATAT
*
34515416 TAATTATGTT-AATTTATATTTTATAGTATCATATATT
1 TAATTAT-TTAAAATTAT-TTTTA-AGTATCATATATT
34515453 ATGATTTGAG
Statistics
Matches: 292, Mismatches: 55, Indels: 95
0.66 0.12 0.21
Matches are distributed among these distances:
54 55 0.19
55 17 0.06
56 23 0.08
57 12 0.04
59 40 0.14
60 24 0.08
61 30 0.10
63 12 0.04
64 17 0.06
65 18 0.06
66 44 0.15
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (57 bp):
TAATTATTTAAAATTATTTTTAAGTATCATATATTTTAATTAAAATATAATTAATAT
Found at i:34515137 original size:120 final size:120
Alignment explanation
Indices: 34515013--34515550 Score: 918
Period size: 120 Copynumber: 4.5 Consensus size: 120
34515003 AATTATTTTA
* * * *
34515013 AATTTTATTAAATCATATATTTTAATTAAAATATAATTAATATTAATTAT-TTCAAATTATGTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATCTTT
34515077 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
34515133 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATCTTT
*
34515197 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
34515253 AATTTTATTAAATTATATATTTTAATTAAAATATGTTTAATAATAATTATGTTAAATTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
*
34515318 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAGTTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* * *
34515373 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
*
34515438 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
34515493 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
34515551 ATGATTAAAT
Statistics
Matches: 401, Mismatches: 15, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
120 394 0.98
121 7 0.02
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:34515162 original size:18 final size:17
Alignment explanation
Indices: 34515134--34515168 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
34515124 ATTATTAAGA
*
34515134 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
34515151 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
34515169 TTAATATTAA
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:34515413 original size:15 final size:15
Alignment explanation
Indices: 34515378--34515429 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
34515368 TTAAGAATTT
*
34515378 TATTAAATTAT-ATA
1 TATTTAATTATAATA
34515392 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
34515406 TATTTAATAATAAT-
1 TATTTAATTATAATA
34515420 TATGTTAATT
1 TAT-TTAATT
34515430 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:34515528 original size:16 final size:16
Alignment explanation
Indices: 34515507--34515548 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
34515497 TTATTAAATT
*
34515507 ATATATTTTAATTATA
1 ATATATTTTAATAATA
34515523 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
34515538 AT-TATGTTTAA
1 ATATAT-TTTAA
34515549 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:34515533 original size:15 final size:15
Alignment explanation
Indices: 34515498--34515539 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
34515488 TTAAGAATTT
*
34515498 TATTAAATTAT-ATA
1 TATTTAATTATAATA
34515512 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
34515526 TATTTAATAATAAT
1 TATTTAATTATAAT
34515540 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:34515780 original size:16 final size:16
Alignment explanation
Indices: 34515759--34515791 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
34515749 TTGTTTTGCT
34515759 ATTACGCCTATATTCC
1 ATTACGCCTATATTCC
*
34515775 ATTACGCCTCTATTCC
1 ATTACGCCTATATTCC
34515791 A
1 A
34515792 ATACAGCGAA
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:0.24, C:0.33, G:0.06, T:0.36
Consensus pattern (16 bp):
ATTACGCCTATATTCC
Found at i:34522661 original size:110 final size:109
Alignment explanation
Indices: 34522468--34522718 Score: 335
Period size: 110 Copynumber: 2.3 Consensus size: 109
34522458 GTTTCTCTTT
* * *
34522468 CATGGTCTTATACATAGCTTTATGTCGTGATATGCTAGTTCAGTCTATACTTCACTGGAGGCATC
1 CATGGTCTTATACATA-CTTCATGTCGTGATATGCTAGTTCAATCTATACTTCACTAGAGGCATC
* *
34522533 ACCATGAGTATTTTCATTATCATACAATGCCATGGGTCTCAGCCA
65 ACCATGAGTATTTTCATTAGCATACAATGCCATGAGTCTCAGCCA
*
34522578 CATGGTCTTATACATACTCTCATGTCGTGATATGCTAG-TCAAATCTTTA-TCTCACTAGAGGCA
1 CATGGTCTTATACATACT-TCATGTCGTGATATGCTAGTTC-AATCTATACT-TCACTAGAGGCA
* * *
34522641 TCAGCATGAGTATTTTCATTAGCATACGATGCCATGAGTCTCATCCA
63 TCACCATGAGTATTTTCATTAGCATACAATGCCATGAGTCTCAGCCA
* * *
34522688 TATGGTTTTATACATACTTTCATGTCATGAT
1 CATGGTCTTATACATAC-TTCATGTCGTGAT
34522719 TTGCCTGTCT
Statistics
Matches: 125, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
109 5 0.04
110 119 0.95
111 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (109 bp):
CATGGTCTTATACATACTTCATGTCGTGATATGCTAGTTCAATCTATACTTCACTAGAGGCATCA
CCATGAGTATTTTCATTAGCATACAATGCCATGAGTCTCAGCCA
Found at i:34528039 original size:27 final size:27
Alignment explanation
Indices: 34527974--34528045 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
34527964 TTACAATTCA
* *
34527974 CCAGGCCCACTAGCAAACCCCAGCTCG
1 CCAGGCCCACTGGCGAACCCCAGCTCG
* **
34528001 CTAGGCCCACTGGCGAACCTTAGCTCG
1 CCAGGCCCACTGGCGAACCCCAGCTCG
34528028 CCAGGCCCACTGGCGAAC
1 CCAGGCCCACTGGCGAAC
34528046 ACCATCTTGC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.22, C:0.43, G:0.24, T:0.11
Consensus pattern (27 bp):
CCAGGCCCACTGGCGAACCCCAGCTCG
Found at i:34528326 original size:35 final size:35
Alignment explanation
Indices: 34528279--34528351 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
34528269 TGAGATGTTA
*
34528279 CATAAACGAAATCACCAAGATTAACATTTCAATAC
1 CATAAACCAAATCACCAAGATTAACATTTCAATAC
34528314 CATAAACCAAATCACCAAGATTAACATTTCAATAC
1 CATAAACCAAATCACCAAGATTAACATTTCAATAC
34528349 CAT
1 CAT
34528352 TCTCAAAACC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.48, C:0.25, G:0.04, T:0.23
Consensus pattern (35 bp):
CATAAACCAAATCACCAAGATTAACATTTCAATAC
Found at i:34530279 original size:20 final size:20
Alignment explanation
Indices: 34530255--34530312 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
34530245 CCAGTGCTGC
*
34530255 AGACAAGCTACTAGTAATGT
1 AGACAAGCTACCAGTAATGT
* * *
34530275 TGACAAGCCACCAGTATTGT
1 AGACAAGCTACCAGTAATGT
*
34530295 AGACAAGCTATCAGTAAT
1 AGACAAGCTACCAGTAAT
34530313 TCCACCTTAC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (20 bp):
AGACAAGCTACCAGTAATGT
Found at i:34534232 original size:23 final size:21
Alignment explanation
Indices: 34534205--34534246 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
34534195 ATGTTTATCT
34534205 TGTGAATTATGTACATATGTGAA
1 TGTGAA-TATGT-CATATGTGAA
*
34534228 TGTGAATATGTGATATGTG
1 TGTGAATATGTCATATGTG
34534247 GATATGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 5 0.28
23 6 0.33
ACGTcount: A:0.31, C:0.02, G:0.26, T:0.40
Consensus pattern (21 bp):
TGTGAATATGTCATATGTGAA
Found at i:34558792 original size:42 final size:41
Alignment explanation
Indices: 34558706--34558795 Score: 101
Period size: 42 Copynumber: 2.2 Consensus size: 41
34558696 AAAATTCCAT
* * *
34558706 TATTGCTCGACTTTTAGCGGCGTTTGGACAAAAAATGACAC
1 TATTGCTCAACTTTTAGCGGCGTTTGAACAAAAAACGACAC
* * *
34558747 TATTGCTCAACATTTTTGCGGCGTTTGCAAC-AAAAACGCCGC
1 TATTGCTCAAC-TTTTAGCGGCGTTTG-AACAAAAAACGACAC
34558789 TATTGCT
1 TATTGCT
34558796 TACCTTTTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
41 10 0.24
42 29 0.71
43 2 0.05
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (41 bp):
TATTGCTCAACTTTTAGCGGCGTTTGAACAAAAAACGACAC
Found at i:34559376 original size:7 final size:7
Alignment explanation
Indices: 34559324--34559498 Score: 75
Period size: 7 Copynumber: 24.7 Consensus size: 7
34559314 AATTAATCTA
34559324 AAACC-T
1 AAACCAT
34559330 AAACCATT
1 AAACCA-T
* *
34559338 AACCCCT
1 AAACCAT
34559345 AAATCC-T
1 AAA-CCAT
*
34559352 AAATCAT
1 AAACCAT
*
34559359 AAAACAT
1 AAACCAT
34559366 AAACCAT
1 AAACCAT
*
34559373 AAACTCTT
1 AAAC-CAT
* *
34559381 AACCCCT
1 AAACCAT
* *
34559388 AACCCCT
1 AAACCAT
* *
34559395 AACCCCT
1 AAACCAT
*
34559402 AAACCTT
1 AAACCAT
**
34559409 AAACCCC
1 AAACCAT
* *
34559416 AACCCTT
1 AAACCAT
34559423 AAACCAT
1 AAACCAT
34559430 AAACCAT
1 AAACCAT
* *
34559437 AATCCCT
1 AAACCAT
*
34559444 AAACTCTT
1 AAAC-CAT
*
34559452 AATCCAT
1 AAACCAT
* *
34559459 AAATCTT
1 AAACCAT
*
34559466 AAACCCT
1 AAACCAT
34559473 AAACCAT
1 AAACCAT
* *
34559480 ATACCCT
1 AAACCAT
34559487 AAACCAT
1 AAACCAT
34559494 AAACC
1 AAACC
34559499 CTGAACTATA
Statistics
Matches: 129, Mismatches: 34, Indels: 11
0.74 0.20 0.06
Matches are distributed among these distances:
6 6 0.05
7 106 0.82
8 17 0.13
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (7 bp):
AAACCAT
Found at i:34559467 original size:57 final size:56
Alignment explanation
Indices: 34559363--34559505 Score: 142
Period size: 57 Copynumber: 2.5 Consensus size: 56
34559353 AATCATAAAA
* * * * *
34559363 CATAAACCATAAACTCTTAACCCCTAACCCCTAACCCCTAAACCTTAAACCCCAACC
1 CATAAACCATAAAC-CATAAACCCTAACTCCTAACCCATAAACCTTAAACCCCAAAC
* * * * * *
34559420 CTTAAACCATAAACCATAATCCCTAAACTCTTAATCCATAAATCTTAAACCCTAAAC
1 CATAAACCATAAACCATAAACCCT-AACTCCTAACCCATAAACCTTAAACCCCAAAC
* *
34559477 CATATACCCTAAACCATAAACCCTGAACT
1 CATAAACCATAAACCATAAACCCT-AACT
34559506 ATAATGATAA
Statistics
Matches: 70, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
56 8 0.11
57 62 0.89
ACGTcount: A:0.41, C:0.36, G:0.01, T:0.22
Consensus pattern (56 bp):
CATAAACCATAAACCATAAACCCTAACTCCTAACCCATAAACCTTAAACCCCAAAC
Found at i:34559489 original size:21 final size:20
Alignment explanation
Indices: 34559398--34559498 Score: 85
Period size: 21 Copynumber: 4.8 Consensus size: 20
34559388 AACCCCTAAC
* **
34559398 CCCTAAACCTTAAACCCCAA
1 CCCTAAACCATAAACCATAA
34559418 CCCTTAAACCATAAACCATAA
1 CCC-TAAACCATAAACCATAA
* *
34559439 TCCCTAAACTCTTAATCCATAAA
1 -CCCTAAAC-CATAAACCAT-AA
* * *
34559462 TCTTAAACCCTAAACCATATA
1 CCCTAAACCATAAACCATA-A
34559483 CCCTAAACCATAAACC
1 CCCTAAACCATAAACC
34559499 CTGAACTATA
Statistics
Matches: 64, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
20 4 0.06
21 41 0.64
22 17 0.27
23 2 0.03
ACGTcount: A:0.43, C:0.36, G:0.00, T:0.22
Consensus pattern (20 bp):
CCCTAAACCATAAACCATAA
Found at i:34559509 original size:14 final size:14
Alignment explanation
Indices: 34559322--34559500 Score: 108
Period size: 14 Copynumber: 12.6 Consensus size: 14
34559312 CTAATTAATC
*
34559322 TAAAACCTAAACCA
1 TAAACCCTAAACCA
*
34559336 TTAACCCCTAAATCC-
1 -TAAACCCTAAA-CCA
* * *
34559351 TAAATCATAAAACA
1 TAAACCCTAAACCA
* *
34559365 TAAACCATAAACTCT
1 TAAACCCTAAAC-CA
* * *
34559380 TAACCCCTAACCCC
1 TAAACCCTAAACCA
* *
34559394 TAACCCCTAAACCT
1 TAAACCCTAAACCA
* * *
34559408 TAAACCCCAACCCT
1 TAAACCCTAAACCA
*
34559422 TAAACCATAAACCA
1 TAAACCCTAAACCA
* *
34559436 TAATCCCTAAACTCT
1 TAAACCCTAAAC-CA
* * * *
34559451 TAATCCATAAATCT
1 TAAACCCTAAACCA
34559465 TAAACCCTAAACCA
1 TAAACCCTAAACCA
*
34559479 TATACCCTAAACCA
1 TAAACCCTAAACCA
34559493 TAAACCCT
1 TAAACCCT
34559501 GAACTATAAT
Statistics
Matches: 127, Mismatches: 33, Indels: 9
0.75 0.20 0.05
Matches are distributed among these distances:
13 1 0.01
14 94 0.74
15 30 0.24
16 2 0.02
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:34559981 original size:40 final size:40
Alignment explanation
Indices: 34559926--34560035 Score: 139
Period size: 40 Copynumber: 2.8 Consensus size: 40
34559916 TAATTTTTTT
* * *
34559926 GCGGCATTTTTCAAAAAGTGCCGCTCATGGTCGACCTATA
1 GCGGCATTTTTCAAAAAGCGCCGCTAATGCTCGACCTATA
** * *
34559966 GCGGCATTTTTCAAAAAGCGCCATTAATGCTTGATCTATA
1 GCGGCATTTTTCAAAAAGCGCCGCTAATGCTCGACCTATA
* *
34560006 GCAGCGTTTTTCAAAAAGCGCCGCTAATGC
1 GCGGCATTTTTCAAAAAGCGCCGCTAATGC
34560036 CACTAAAGCT
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (40 bp):
GCGGCATTTTTCAAAAAGCGCCGCTAATGCTCGACCTATA
Found at i:34560136 original size:40 final size:40
Alignment explanation
Indices: 34560081--34560202 Score: 147
Period size: 40 Copynumber: 3.0 Consensus size: 40
34560071 TAATTTTTTT
* * *
34560081 GCGGCGTTTCTCAAAAAGCGATGCTAATGGTCGACCTATA
1 GCGGCGTTTTTCAAAAAGCGATGCTAATGCTCGATCTATA
*
34560121 GCGGCGTTTTTCAAAAAGC-ACCGCTAATGCTCGATCTATA
1 GCGGCGTTTTTCAAAAAGCGA-TGCTAATGCTCGATCTATA
* * * * *
34560161 GCGGCATTTTTTAAAAAACGTTGTTAATGCTCGATCTATA
1 GCGGCGTTTTTCAAAAAGCGATGCTAATGCTCGATCTATA
34560201 GC
1 GC
34560203 ACCATATTTT
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
39 1 0.01
40 69 0.99
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (40 bp):
GCGGCGTTTTTCAAAAAGCGATGCTAATGCTCGATCTATA
Found at i:34560137 original size:155 final size:153
Alignment explanation
Indices: 34559835--34560177 Score: 461
Period size: 155 Copynumber: 2.2 Consensus size: 153
34559825 CAAAGAGTCG
* * * *
34559835 CTAAAGCTTTATCTATAGCGATGTTTTTCAAAAAGTGCCGCTAATACCACTAAAACTCAACATAA
1 CTAATGCTTGATCTATAGCG-CGTTTTTCAAAAAGCGCCGCTAATACCACTAAAACTCAACATAA
* * * * *
34559900 AACGACGCGTTGTGCTTAATTTTTTTGCGGCATTTTTCAAAAAGTGCCGCTCATGGTCGACCTAT
65 AACGACACGTTGTGCTTAATTTTTTTGCGGCATTTCTCAAAAAGCGACGCTAATGGTCGACCTAT
*
34559965 AGCGGCATTTTTCAAAAAGCGCCA
130 AGCGGCATTTTTCAAAAAGCACCA
* * *
34559989 TTAATGCTTGATCTATAGCAGCGTTTTTCAAAAAGCGCCGCTAATGCCACTAAAGCTCAACATAA
1 CTAATGCTTGATCTATAGC-GCGTTTTTCAAAAAGCGCCGCTAATACCACTAAAACTCAACATAA
* * *
34560054 AACGACAACGTTGTGGTTAATTTTTTTGCGGCGTTTCTCAAAAAGCGATGCTAATGGTCGACCTA
65 AACGAC-ACGTTGTGCTTAATTTTTTTGCGGCATTTCTCAAAAAGCGACGCTAATGGTCGACCTA
* *
34560119 TAGCGGCGTTTTTCAAAAAGCACCG
129 TAGCGGCATTTTTCAAAAAGCACCA
* * *
34560144 CTAATGCTCGATCTATAGCGGCATTTTTTAAAAA
1 CTAATGCTTGATCTATAGC-GCGTTTTTCAAAAA
34560178 ACGTTGTTAA
Statistics
Matches: 164, Mismatches: 23, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
154 62 0.38
155 102 0.62
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (153 bp):
CTAATGCTTGATCTATAGCGCGTTTTTCAAAAAGCGCCGCTAATACCACTAAAACTCAACATAAA
ACGACACGTTGTGCTTAATTTTTTTGCGGCATTTCTCAAAAAGCGACGCTAATGGTCGACCTATA
GCGGCATTTTTCAAAAAGCACCA
Found at i:34563015 original size:25 final size:26
Alignment explanation
Indices: 34562978--34563030 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
34562968 GTAACAGTCA
*
34562978 CATAAATATCATAAAG-CAAAACAGT
1 CATAAATAGCATAAAGCCAAAACAGT
* * *
34563003 CATACATAGCATAAGGCCATAACAGT
1 CATAAATAGCATAAAGCCAAAACAGT
34563029 CA
1 CA
34563031 GTTTATCCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.49, C:0.21, G:0.11, T:0.19
Consensus pattern (26 bp):
CATAAATAGCATAAAGCCAAAACAGT
Found at i:34563075 original size:22 final size:23
Alignment explanation
Indices: 34563046--34563118 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 23
34563036 TCCTATGGAG
*
34563046 GTATTTCGGTAATTTTACCCATC
1 GTATTTCGATAATTTTACCCATC
*
34563069 -TATTTCGTTAATTTTACCCATC
1 GTATTTCGATAATTTTACCCATC
34563091 AGGGGTATTTCGATAATTTTACCCATC
1 ----GTATTTCGATAATTTTACCCATC
34563118 G
1 G
34563119 CGATATTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
22 21 0.49
23 1 0.02
27 21 0.49
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (23 bp):
GTATTTCGATAATTTTACCCATC
Found at i:34563107 original size:27 final size:26
Alignment explanation
Indices: 34563045--34563162 Score: 102
Period size: 27 Copynumber: 4.6 Consensus size: 26
34563035 ATCCTATGGA
*
34563045 GGTATTTCGGTAATTTTACCCATC--
1 GGTATTTCGATAATTTTACCCATCGG
*
34563069 --TATTTCGTTAATTTTACCCATCAGG
1 GGTATTTCGATAATTTTACCCATC-GG
*
34563094 GGTATTTCGATAATTTTACCCATCGC
1 GGTATTTCGATAATTTTACCCATCGG
* * *
34563120 GATATTT-TAGTAATTTTACCCATTAGG
1 GGTATTTCGA-TAATTTTACCCA-TCGG
* *
34563147 GGTATTTTGGTAATTT
1 GGTATTTCGATAATTT
34563163 AATAAACTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
22 21 0.28
25 1 0.01
26 19 0.25
27 35 0.46
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (26 bp):
GGTATTTCGATAATTTTACCCATCGG
Found at i:34563148 original size:53 final size:49
Alignment explanation
Indices: 34563045--34563162 Score: 148
Period size: 53 Copynumber: 2.3 Consensus size: 49
34563035 ATCCTATGGA
*
34563045 GGTATTTCGGTAATTTTACCCATCTATTTCGTTAATTTTACCCATCAGG
1 GGTATTTCGGTAATTTTACCCATCTATTTAGTTAATTTTACCCATCAGG
* *
34563094 GGTATTTCGATAATTTTACCCATCGCGATATTTTAG-TAATTTTACCCATTAGG
1 GGTATTTCGGTAATTTTACCCAT--C--TA-TTTAGTTAATTTTACCCATCAGG
*
34563147 GGTATTTTGGTAATTT
1 GGTATTTCGGTAATTT
34563163 AATAAACTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
49 22 0.37
51 1 0.02
53 32 0.54
54 4 0.07
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (49 bp):
GGTATTTCGGTAATTTTACCCATCTATTTAGTTAATTTTACCCATCAGG
Found at i:34574399 original size:225 final size:225
Alignment explanation
Indices: 34574008--34574450 Score: 787
Period size: 225 Copynumber: 2.0 Consensus size: 225
34573998 ACGTACATGG
* *
34574008 TAAAGAATGATGCTTTGATTTAAAGCCAAGCAGCAACACTGAAAAATTTAGAAAACCAAATGGGT
1 TAAAGAATGATGCTTTGAGTTAAAGCCAAGCAGCAAAACTGAAAAATTTAGAAAACCAAATGGGT
* *
34574073 TAGATAGCTACAGAGCTACGTAATAGACCACAATGAACCTTGCCGAGCGATACTGAGAATCCAAG
66 TAGATAGCTACAGAGCTACGTAATAGACCACAATGAACCTTACCGAGCGATACTGAAAATCCAAG
* *
34574138 AAATTTTGGTAAAGAACATATCAAAGCAGTGGCATTATAGAGTGGTAAAATTCTAGAACCCCGAT
131 AAATTTGGGTAAAGAACATATCAAAGCAGTGGCATTATAGAGTGGTAAAATTCTAGAACCCCAAT
34574203 TGATTGGTGTCGAAGATAAGCCCGATAATT
196 TGATTGGTGTCGAAGATAAGCCCGATAATT
*
34574233 TAAAGAATGATGCTTTGAGTTAAAGCCAAGCAGCAAAACTGAAAAATTTGGAAAACCAAATGGGT
1 TAAAGAATGATGCTTTGAGTTAAAGCCAAGCAGCAAAACTGAAAAATTTAGAAAACCAAATGGGT
* *
34574298 TAGATAGCTACGGAGCTACGTAATAGACCACAATGAACCTTACCGAGCGATACTGAAAATCCATG
66 TAGATAGCTACAGAGCTACGTAATAGACCACAATGAACCTTACCGAGCGATACTGAAAATCCAAG
* *
34574363 AAATTTGGGTAAAGAACATATCAAGGCAGTGGCATTATAGAGTGGTAAAATTCTAGAACCCTAAT
131 AAATTTGGGTAAAGAACATATCAAAGCAGTGGCATTATAGAGTGGTAAAATTCTAGAACCCCAAT
34574428 TGATTGGTGTCGAAGATAAGCCC
196 TGATTGGTGTCGAAGATAAGCCC
34574451 ATTGAGAAGA
Statistics
Matches: 207, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
225 207 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.23
Consensus pattern (225 bp):
TAAAGAATGATGCTTTGAGTTAAAGCCAAGCAGCAAAACTGAAAAATTTAGAAAACCAAATGGGT
TAGATAGCTACAGAGCTACGTAATAGACCACAATGAACCTTACCGAGCGATACTGAAAATCCAAG
AAATTTGGGTAAAGAACATATCAAAGCAGTGGCATTATAGAGTGGTAAAATTCTAGAACCCCAAT
TGATTGGTGTCGAAGATAAGCCCGATAATT
Found at i:34583956 original size:30 final size:32
Alignment explanation
Indices: 34583917--34583985 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
34583907 TGGCCTAATA
34583917 CCCACACG-CCAATATGGCAT-GCCTGTGTGG
1 CCCACACGCCCAATATGGCATAGCCTGTGTGG
* * *
34583947 CCCATACGCCCAATCTGGCCTAGCCTGTGTGG
1 CCCACACGCCCAATATGGCATAGCCTGTGTGG
*
34583979 CCTACAC
1 CCCACAC
34583986 TGCCACACTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 7 0.22
31 10 0.31
32 15 0.47
ACGTcount: A:0.19, C:0.38, G:0.23, T:0.20
Consensus pattern (32 bp):
CCCACACGCCCAATATGGCATAGCCTGTGTGG
Found at i:34590576 original size:50 final size:50
Alignment explanation
Indices: 34590471--34590658 Score: 144
Period size: 50 Copynumber: 3.8 Consensus size: 50
34590461 TTATTGAGGT
* * * * *
34590471 TATGAGAGGTTCCATGTAAGACCATGTCTGGGACATGGCCTTGGTACCCA
1 TATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCACCCA
* * * *
34590521 GATGAGAGGTCCCCCGTAAGACTATGTCTGGGACATGGCATGGGCACCGA
1 TATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCACCCA
** * * * * * ** **
34590571 TATGAGAACTCCCATGTAAGTCCATATCTGGGATATGACATTTGCA-GTA
1 TATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCACCCA
* * ** *
34590620 TAGGAAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 TATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGC
34590659 TTTGGCATGT
Statistics
Matches: 107, Mismatches: 31, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
49 32 0.30
50 75 0.70
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (50 bp):
TATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCACCCA
Found at i:34590901 original size:16 final size:16
Alignment explanation
Indices: 34590879--34590917 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
34590869 GTAAGCAAGT
*
34590879 AAGTAAACAAATAAGA
1 AAGTAAACAAAGAAGA
* *
34590895 GAGTAAATAAAGAAGA
1 AAGTAAACAAAGAAGA
34590911 AAGTAAA
1 AAGTAAA
34590918 GATCATGATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.67, C:0.03, G:0.18, T:0.13
Consensus pattern (16 bp):
AAGTAAACAAAGAAGA
Found at i:34600216 original size:6 final size:6
Alignment explanation
Indices: 34600205--34600232 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
34600195 TTGAAAAAAT
34600205 AATAAA AATAAA AATAAA AATAAA AATA
1 AATAAA AATAAA AATAAA AATAAA AATA
34600233 TTATGTATTC
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:0.00, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:34600542 original size:88 final size:87
Alignment explanation
Indices: 34600368--34600552 Score: 226
Period size: 88 Copynumber: 2.1 Consensus size: 87
34600358 AGTGAAGATA
* *
34600368 ACAGATCTTGCCTTCCTACACCGACTGCAAAGAAGATTGAAGACACCAGCCTTGCCTCCCTGGGT
1 ACAGATCTTGCCTTCCTACACCGACAGCAAAGAAGATCGAAGACACCAGCCTTGCCTCCCTGGGT
* ** *
34600433 TGCCGCGGTTCAGGCTAAAAAT
66 TGCAGCGGAGCAGGCTGAAAAT
* * ** *
34600455 AGCAGATCTTGCCTTTCTGCACCGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGG
1 A-CAGATCTTGCCTTCCTACACCGACAGCAAAGAAGATCGAAGACACCAGCCTTGCCTCCCTGGG
* * *
34600520 TTGTAGTGGAGCAGGTTGAAAATT
65 TTGCAGCGGAGCAGGCTGAAAA-T
34600544 ACAGATCTT
1 ACAGATCTT
34600553 ACCTCCATAA
Statistics
Matches: 82, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
87 1 0.01
88 79 0.96
89 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.23
Consensus pattern (87 bp):
ACAGATCTTGCCTTCCTACACCGACAGCAAAGAAGATCGAAGACACCAGCCTTGCCTCCCTGGGT
TGCAGCGGAGCAGGCTGAAAAT
Found at i:34600570 original size:44 final size:43
Alignment explanation
Indices: 34600522--34600664 Score: 126
Period size: 44 Copynumber: 3.3 Consensus size: 43
34600512 TCCCTGGGTT
* *
34600522 GTAGTGGAGCAGGTTGAAAATTACAGATCTTACCTCCATAAGCA
1 GTAGTGGAGCAGGTTG-AAATTACAGATCTTATCTCCCTAAGCA
* * * * ** * * **
34600566 GTAGTGGAGAAGATCGAAGTCCCTAG-GCTTGTCTCCCGGAGCA
1 GTAGTGGAGCAGGTTGAAATTAC-AGATCTTATCTCCCTAAGCA
* *
34600609 GTAGTGGAGTAGGTTGGAAATTACAGATATTATCTCCCTAAGCA
1 GTAGTGGAGCAGGTT-GAAATTACAGATCTTATCTCCCTAAGCA
34600653 GTAGTGGAGCAG
1 GTAGTGGAGCAG
34600665 ATCGAAGTCC
Statistics
Matches: 72, Mismatches: 24, Indels: 6
0.71 0.24 0.06
Matches are distributed among these distances:
43 29 0.40
44 43 0.60
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.24
Consensus pattern (43 bp):
GTAGTGGAGCAGGTTGAAATTACAGATCTTATCTCCCTAAGCA
Found at i:34600729 original size:87 final size:86
Alignment explanation
Indices: 34600481--34600736 Score: 291
Period size: 87 Copynumber: 2.9 Consensus size: 86
34600471 CTGCACCGAC
* * * * *
34600481 AGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAAATTAC
1 AGTGGAGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGTTGTAGTGGAGCAGGTTG-AAATTAC
* *
34600546 AGATCTTACCTCCATAAGCAGT
65 AGATCTTATCTCCCTAAGCAGT
* * * * ** *
34600568 AGTGGAGAAGATCGAAGTCCCTAGGCTTGTCTCCCGGAGCAGTAGTGGAGTAGGTTGGAAATTAC
1 AGTGGAGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGTTGTAGTGGAGCAGGTT-GAAATTAC
*
34600633 AGATATTATCTCCCTAAGCAGT
65 AGATCTTATCTCCCTAAGCAGT
* *
34600655 AGTGGAGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAAGTTGCAGTGGAGCAGGTT-AAAGCCT
1 AGTGGAGCAGATCGAAGTCCCCAGCCTTGTCTCCCTG-AGTTGTAGTGGAGCAGGTTGAAA--TT
*
34600719 ATA-ATCTTATCTCCCTAA
63 ACAGATCTTATCTCCCTAA
34600737 AGTTGCAGTG
Statistics
Matches: 139, Mismatches: 26, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
86 3 0.02
87 117 0.84
88 19 0.14
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (86 bp):
AGTGGAGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGTTGTAGTGGAGCAGGTTGAAATTACA
GATCTTATCTCCCTAAGCAGT
Found at i:34600732 original size:44 final size:44
Alignment explanation
Indices: 34600684--34601486 Score: 371
Period size: 44 Copynumber: 18.6 Consensus size: 44
34600674 CCCAGCCTTG
*
34600684 TCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAGCCTATAATCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCTATAATCTTA
* ** ** *
34600728 TCTCCCTAAAGTTGCAGTGGAGTGGATTAAAATCT-TGGATCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCTAT-AATCTTA
* * * * * * *
34600772 TCTCTCTAAAGTTGCAG-AGAGCAGA-T--CGCATCTAGTCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCTATAATCTTA
* * * **
34600812 TCTCCCTGAAGTTGCAATCGAGCAGACTAAGGAAG-C-A-GGTCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGA-TTA--AAGCCTATAATCTTA
* *
34600856 TC-CTCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGC-A-AATCTTA
1 TCTC-CCTGAAGTTGCAGTGGAGCAGA-TTAA-A-GCCTATAATCTTA
* * **
34600901 TCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCAA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCTATAATCTTA
*
34600945 TCTCCCTGAAGTTGCAGTGGAGC-GTATTAAAACCT-TAGATCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCAG-ATTAAAGCCTATA-ATCTTA
* ** * * * *
34600989 TCTCTCTGAAGTTGCAG-AAAGCAGA-T--CGCATCTAGTCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCTATAATCTTA
* * *
34601029 TCTCCCTGAAGTTGTAGTGGAGCAGACTAAGTAAG-C-A-AGTCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGA-TTA--AAGCCTATAATCTTA
* *
34601073 TC-CTCCTGAAGTTGCTA-T-GAGGCAGACTAAAG-ATGGCA-AATCTTA
1 TCTC-CCTGAAGTTGC-AGTGGA-GCAGATTAAAGCCT---ATAATCTTA
* * *
34601118 TCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCGATAATCCTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCTATAATCTTA
* *
34601162 TCTCCCTGAAGTTGCAGTGGATCAGATTAAAACCT-TAGATCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCTATA-ATCTTA
* * * * * * *
34601206 TCTCTCTGAAGTTGCAG-AGAGTAGA-T--CGCATCTAGTCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCTATAATCTTA
* * * *
34601246 TCTCCCTAAAGTTGCAGTGGAGCAGACTAAGTAAG-C-A-AGTCTTG
1 TCTCCCTGAAGTTGCAGTGGAGCAGA-TTA--AAGCCTATAATCTTA
* * * *
34601290 TC-CTCCTGAATTTGCAG-AGAGGCAGACTGAAGATGGC-A-AATCTTA
1 TCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-GCCTATAATCTTA
* * * *
34601335 TCTCCCTGAAGTTACAGTGGAGCAGATTAGAGCCGATAATC--C
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCTATAATCTTA
* ** * *
34601377 TCTCCCTGAAGTTACAGTGGAGTGGATTAAAACCT-TAAACCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCTAT-AATCTTA
* * * * * *
34601421 TCTCTCTGAAGTTGCAG-AGATCAGATT---GCATCTAGTCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCTATAATCTTA
*
34601461 TCTCCCTGAAGTTGCACTGGAGCAGA
1 TCTCCCTGAAGTTGCAGTGGAGCAGA
34601487 CTAAGTAAGC
Statistics
Matches: 575, Mismatches: 122, Indels: 127
0.70 0.15 0.15
Matches are distributed among these distances:
40 86 0.15
41 35 0.06
42 42 0.07
43 41 0.07
44 275 0.48
45 86 0.15
46 7 0.01
47 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (44 bp):
TCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCTATAATCTTA
Found at i:34601059 original size:217 final size:217
Alignment explanation
Indices: 34600684--34601570 Score: 1377
Period size: 217 Copynumber: 4.1 Consensus size: 217
34600674 CCCAGCCTTG
* * * *
34600684 TCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAGCCTATAATCTTATCTCCCTAAAGTTGCAGTGGA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGA
* * * *
34600749 GTGGATTAAAATCTTGGATCTTATCTCTCTAAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATC
66 GCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATC
* * * *
34600814 TCCCTGAAGTTGCAATCGAGCAGACTAAGGAAGCAGGTCTTATCCTCCTGAAGTTGCAGTG-GAG
131 TCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAG-G
34600878 CAGACTGAAGATGGCAAATCTTA
195 CAGACTGAAGATGGCAAATCTTA
* * *
34600901 TCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCAATCTCCCTGAAGTTGCAGTGGA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGA
* *
34600966 GCGTATTAAAACCTTAGATCTTATCTCTCTGAAGTTGCAGAAAGCAGATCGCATCTAGTCTTATC
66 GCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATC
*
34601031 TCCCTGAAGTTGTAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCTA-TGAGG
131 TCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGC-AGTGAGG
*
34601095 CAGACTAAAGATGGCAAATCTTA
195 CAGACTGAAGATGGCAAATCTTA
*
34601118 TCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGA
* * *
34601183 TCAGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGCAGAGAGTAGATCGCATCTAGTCTTATC
66 GCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATC
* * * *
34601248 TCCCTAAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTGTCCTCCTGAATTTGCAGAGAGGC
131 TCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGC
34601313 AGACTGAAGATGGCAAATCTTA
196 AGACTGAAGATGGCAAATCTTA
* * *
34601335 TCTCCCTGAAGTTACAGTGGAGCAGATTAGAGCCGATAATCC--TCTCCCTGAAGTTACAGTGGA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGA
* * * * *
34601398 GTGGATTAAAACCTTAAACCTTATCTCTCTGAAGTTGCAGAGATCAGATTGCATCTAGTCTTATC
66 GCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATC
* *
34601463 TCCCTGAAGTTGCACTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGAAGTGAGGC
131 TCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGC
* *
34601528 AGCCTGAAGATGGCGAATCTTA
196 AGACTGAAGATGGCAAATCTTA
34601550 TCTCCCTGAAGTTGCAGTGGA
1 TCTCCCTGAAGTTGCAGTGGA
34601571 ATAGATTGAA
Statistics
Matches: 615, Mismatches: 52, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
215 176 0.29
216 1 0.00
217 436 0.71
218 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (217 bp):
TCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGA
GCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATC
TCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGC
AGACTGAAGATGGCAAATCTTA
Found at i:34607835 original size:49 final size:50
Alignment explanation
Indices: 34607731--34607862 Score: 122
Period size: 49 Copynumber: 2.7 Consensus size: 50
34607721 TTATTGAGGT
* * * * *
34607731 TATGAGAGGTCTCACATAAGACCATGTCTGGGACATGGCATTCGTACCTA
1 TATGAGAGGTCTCACATAAGACCATATCTGGGACATAGCATGCGCACCGA
* * * * *
34607781 GATGAGAGGTC-CCCGTAAGACCATATTTGGGACATAGCATGGGCACCGA
1 TATGAGAGGTCTCACATAAGACCATATCTGGGACATAGCATGCGCACCGA
** ** *
34607830 TATGAGAACTCTCATGTAAGACCATTTCTGGGA
1 TATGAGAGGTCTCACATAAGACCATATCTGGGA
34607863 TATGACATTT
Statistics
Matches: 64, Mismatches: 17, Indels: 2
0.77 0.20 0.02
Matches are distributed among these distances:
49 37 0.58
50 27 0.42
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (50 bp):
TATGAGAGGTCTCACATAAGACCATATCTGGGACATAGCATGCGCACCGA
Found at i:34615746 original size:40 final size:40
Alignment explanation
Indices: 34615666--34615746 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
34615656 CTAACATCTG
* *
34615666 TAAACGGTGTTAGGAGCTTTTTGGGCCACACCGATTTTTA
1 TAAACGGTGTTAGCAGCTTTTTGGGCCACACCGATGTTTA
* * * *
34615706 TAAAGGGTGTTAGCAGCTTTTTGGTCCATACCGGTGTTTA
1 TAAACGGTGTTAGCAGCTTTTTGGGCCACACCGATGTTTA
34615746 T
1 T
34615747 CGAAGCTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.37
Consensus pattern (40 bp):
TAAACGGTGTTAGCAGCTTTTTGGGCCACACCGATGTTTA
Found at i:34617999 original size:22 final size:21
Alignment explanation
Indices: 34617974--34618017 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
34617964 TGATAAACTT
34617974 TAATCTATA-ATTATATTATTTA
1 TAATCTATATATTA-ATT-TTTA
*
34617996 TAATTTATATATTAATTTTTA
1 TAATCTATATATTAATTTTTA
34618017 T
1 T
34618018 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATCTATATATTAATTTTTA
Found at i:34626298 original size:30 final size:30
Alignment explanation
Indices: 34626248--34626545 Score: 197
Period size: 30 Copynumber: 9.9 Consensus size: 30
34626238 CGGCGTATCG
* * *
34626248 ACGGCCATCGATCTAAGAAAAGGGATAGCT
1 ACGGCCATCAAACTATGAAAAGGGATAGCT
* * *
34626278 TCGGCTATCGAACTATGAAAAGGGATAGCT
1 ACGGCCATCAAACTATGAAAAGGGATAGCT
* * * * * *
34626308 CCAGCTATCAAATTATGAAATGGGAT-GGT
1 ACGGCCATCAAACTATGAAAAGGGATAGCT
* * *
34626337 GACGACCATCAAACAATGAAAAGGGAT-GGT
1 -ACGGCCATCAAACTATGAAAAGGGATAGCT
* * *
34626367 GACGACCATAAAAATTATGAAAAGGGATAGCT
1 -ACGGCCAT-CAAACTATGAAAAGGGATAGCT
* * *
34626399 TCAGCTATCAAACTATGAAAAGGGATAGCT
1 ACGGCCATCAAACTATGAAAAGGGATAGCT
* * * * * *
34626429 TCAGCTATCAAATTATGAAAATGGATGGCT
1 ACGGCCATCAAACTATGAAAAGGGATAGCT
* * *
34626459 ACGACCATCAAACAATGAAAAGGGAT-GGT
1 ACGGCCATCAAACTATGAAAAGGGATAGCT
* *
34626488 GACGACCATCAAAATTATGAAAAGGGATAGCT
1 -ACGGCCATC-AAACTATGAAAAGGGATAGCT
* * * * *
34626520 TCGGCTATCGAATTATGGAAAGGGAT
1 ACGGCCATCAAACTATGAAAAGGGAT
34626546 GGTATCAACC
Statistics
Matches: 216, Mismatches: 46, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
29 4 0.02
30 168 0.78
31 40 0.19
32 4 0.02
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.21
Consensus pattern (30 bp):
ACGGCCATCAAACTATGAAAAGGGATAGCT
Found at i:34626447 original size:91 final size:90
Alignment explanation
Indices: 34626291--34626558 Score: 260
Period size: 91 Copynumber: 2.9 Consensus size: 90
34626281 GCTATCGAAC
* * * * * **
34626291 TATGAAAAGGGATAGCTCCAGCTATCAAATTATGAAATGGGAT-G-GTGACGACCATCAAACAAT
1 TATGAAAAGGGATAGCTTCAGCTATCAAATTATGAAAAGGGATAGCTTCA-G-CTATCAAATTAT
34626354 GAAAAGGGATGGTGACGACCAT-AAAAA
64 GAAAAGGGATGGT-ACGACCATCAAAAA
*
34626381 TTATGAAAAGGGATAGCTTCAGCTATCAAACTATGAAAAGGGATAGCTTCAGCTATCAAATTATG
1 -TATGAAAAGGGATAGCTTCAGCTATCAAATTATGAAAAGGGATAGCTTCAGCTATCAAATTATG
* *
34626446 AAAATGGATGGCTACGACCATCAAACA
65 AAAAGGGATGG-TACGACCATCAAAAA
* * * * *
34626473 -ATGAAAAGGGAT-G-GTGACGACCATCAAAATTATGAAAAGGGATAGCTTCGGCTATCGAATTA
1 TATGAAAAGGGATAGCTTCA-G-CTATC-AAATTATGAAAAGGGATAGCTTCAGCTATCAAATTA
* *
34626535 TGGAAAGGGATGGTATCAACCATC
63 TGAAAAGGGATGGTA-CGACCATC
34626559 CTATTATCAC
Statistics
Matches: 150, Mismatches: 19, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
88 2 0.01
89 2 0.01
90 18 0.12
91 119 0.79
92 7 0.05
93 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.22
Consensus pattern (90 bp):
TATGAAAAGGGATAGCTTCAGCTATCAAATTATGAAAAGGGATAGCTTCAGCTATCAAATTATGA
AAAGGGATGGTACGACCATCAAAAA
Found at i:34626565 original size:121 final size:121
Alignment explanation
Indices: 34626264--34626545 Score: 478
Period size: 121 Copynumber: 2.3 Consensus size: 121
34626254 ATCGATCTAA
*
34626264 GAAAAGGGATAGCTTCGGCTATCGAACTATGAAAAGGGATAGCTCCAGCTATCAAATTATGAAAT
1 GAAAAGGGATAGCTTCGGCTATCGAACTATGAAAAGGGATAGCTTCAGCTATCAAATTATGAAAT
34626329 GGGATGGTGACGACCATCAAACAATGAAAAGGGATGGTGACGACCATAAAAATTAT
66 GGGATGGTGACGACCATCAAACAATGAAAAGGGATGGTGACGACCATAAAAATTAT
* *
34626385 GAAAAGGGATAGCTTCAGCTATCAAACTATGAAAAGGGATAGCTTCAGCTATCAAATTATGAAAA
1 GAAAAGGGATAGCTTCGGCTATCGAACTATGAAAAGGGATAGCTTCAGCTATCAAATTATG-AAA
*
34626450 T-GGATGGCT-ACGACCATCAAACAATGAAAAGGGATGGTGACGACCATCAAAATTAT
65 TGGGATGG-TGACGACCATCAAACAATGAAAAGGGATGGTGACGACCATAAAAATTAT
* *
34626506 GAAAAGGGATAGCTTCGGCTATCGAATTATGGAAAGGGAT
1 GAAAAGGGATAGCTTCGGCTATCGAACTATGAAAAGGGAT
34626546 GGTATCAACC
Statistics
Matches: 151, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
121 146 0.97
122 5 0.03
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (121 bp):
GAAAAGGGATAGCTTCGGCTATCGAACTATGAAAAGGGATAGCTTCAGCTATCAAATTATGAAAT
GGGATGGTGACGACCATCAAACAATGAAAAGGGATGGTGACGACCATAAAAATTAT
Found at i:34631489 original size:30 final size:31
Alignment explanation
Indices: 34631455--34631516 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 31
34631445 ATGAAATTAT
34631455 TATTTAGGGAT-TAAATTGAAAAATAA-GAAA
1 TATTTAGGG-TGTAAATTGAAAAATAATGAAA
* **
34631485 TATTTATGGTGTAAATTGTGAAATAATGAAA
1 TATTTAGGGTGTAAATTGAAAAATAATGAAA
34631516 T
1 T
34631517 GTGTGGGCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 1 0.04
30 21 0.78
31 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (31 bp):
TATTTAGGGTGTAAATTGAAAAATAATGAAA
Found at i:34631970 original size:30 final size:30
Alignment explanation
Indices: 34631929--34632122 Score: 135
Period size: 30 Copynumber: 6.4 Consensus size: 30
34631919 GAATCAAAAT
*
34631929 TATGAAAAGGGATAGCTTCAGCTATCGAAC
1 TATGAAAAGGGATAGCTTCAGCTATCAAAC
* * * *
34631959 TATGGAAAGGGATAGCTCCGGCTATCAAAT
1 TATGAAAAGGGATAGCTTCAGCTATCAAAC
* * * *
34631989 TATGAAAATGGATGGCTAC-GACTATTAAAC
1 TATGAAAAGGGATAGCTTCAG-CTATCAAAC
* * * *
34632019 AATGAAAAGGGAT-G-GTGACGACCATCAAAAC
1 TATGAAAAGGGATAGCTTCA-G-CTATC-AAAC
* *
34632050 TATGAAAAGGGATATCTTCAGCTATCGAA-
1 TATGAAAAGGGATAGCTTCAGCTATCAAAC
* * * *
34632079 TCACGAAAAGGGATAGCTTCGGCTATCGAAT
1 T-ATGAAAAGGGATAGCTTCAGCTATCAAAC
*
34632110 TATGGAAAGGGAT
1 TATGAAAAGGGAT
34632123 GGTATCAACC
Statistics
Matches: 127, Mismatches: 29, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
29 3 0.02
30 100 0.79
31 21 0.17
32 1 0.01
33 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.23
Consensus pattern (30 bp):
TATGAAAAGGGATAGCTTCAGCTATCAAAC
Found at i:34632089 original size:121 final size:121
Alignment explanation
Indices: 34631903--34632124 Score: 329
Period size: 121 Copynumber: 1.8 Consensus size: 121
34631893 TACATTGTGG
* * * *
34631903 AAAGGGATAGTGACGAGAATCAAAATTATGAAAAGGGATAGCTTCAGCTATCGAACTATGGAAAG
1 AAAGGGATAGTGACGACAATCAAAACTATGAAAAGGGATAGCTTCAGCTATCGAACTACGAAAAG
*
34631968 GGATAGCTCCGGCTATCAAATTATGAAAATGGATGGCTACGACTATTAAACAATGA
66 GGATAGCTCCGGCTATCAAATTATGAAAAGGGATGGCTACGACTATTAAACAATGA
* * *
34632024 AAAGGGATGGTGACGACCATCAAAACTATGAAAAGGGATATCTTCAGCTATCGAA-TCACGAAAA
1 AAAGGGATAGTGACGACAATCAAAACTATGAAAAGGGATAGCTTCAGCTATCGAACT-ACGAAAA
* * *
34632088 GGGATAGCTTCGGCTATCGAATTATGGAAAGGGATGG
65 GGGATAGCTCCGGCTATCAAATTATGAAAAGGGATGG
34632125 TATCAACCAT
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
120 1 0.01
121 88 0.99
ACGTcount: A:0.39, C:0.14, G:0.26, T:0.22
Consensus pattern (121 bp):
AAAGGGATAGTGACGACAATCAAAACTATGAAAAGGGATAGCTTCAGCTATCGAACTACGAAAAG
GGATAGCTCCGGCTATCAAATTATGAAAAGGGATGGCTACGACTATTAAACAATGA
Found at i:34646854 original size:13 final size:13
Alignment explanation
Indices: 34646798--34646855 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
34646788 TATTTTAAAA
34646798 TTATTTTCTGTGT
1 TTATTTTCTGTGT
*
34646811 TTA--TTATGTGT
1 TTATTTTCTGTGT
** *
34646822 GAATTTACTTGTGT
1 TTATTTTC-TGTGT
34646836 TTATTTTCTGTGT
1 TTATTTTCTGTGT
34646849 TTATTTT
1 TTATTTT
34646856 AAAGCCAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
11 8 0.24
13 16 0.47
14 10 0.29
ACGTcount: A:0.14, C:0.05, G:0.16, T:0.66
Consensus pattern (13 bp):
TTATTTTCTGTGT
Found at i:34650193 original size:12 final size:12
Alignment explanation
Indices: 34650176--34650200 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34650166 GAAAATTAGG
34650176 TAAATTGATTGT
1 TAAATTGATTGT
34650188 TAAATTGATTGT
1 TAAATTGATTGT
34650200 T
1 T
34650201 TATGTGCTAA
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:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TAAATTGATTGT
Found at i:34654807 original size:348 final size:348
Alignment explanation
Indices: 34654170--34654866 Score: 1304
Period size: 348 Copynumber: 2.0 Consensus size: 348
34654160 AGCTTGAGAC
*
34654170 TTTACAATAACATATATGTGTTTTTGTTGATTATTGTGAATATATAAATAGGAAGTAAATAAGGT
1 TTTACAATAACATATATGTGTTTTTGTTGATTATTATGAATATATAAATAGGAAGTAAATAAGGT
* *
34654235 TTCCTATATGACCGAATAGGTAATTAAATGTATCGGTTAAGTATATGTATTTTAGCTATGATATT
66 TTCCTATATGACCAAATAGGTAATTAAATGTATCGGTTAAGTATATGTATTTTAACTATGATATT
* *
34654300 TGGGCATGTGAAATAGGTGTAATATTAGTCATTATTTGTGTTCAAGATGATTTAAATTATTATGG
131 TGGGCATGTGAAATAAGTGTAATATTAGTCATTATTTGTGTTCAAGATAATTTAAATTATTATGG
34654365 TCCATGCGCATAATCTTGAAATAAATTATAATGGCTAAGTATTTGATAAATTTGGTAATAGTTAA
196 TCCATGCGCATAATCTTGAAATAAATTATAATGGCTAAGTATTTGATAAATTTGGTAATAGTTAA
34654430 GCAAACAAAATTGAATAATGGATGTTTAATGCATATTAGGTATGAGATGATTATATGTTCAAATA
261 GCAAACAAAATTGAATAATGGATGTTTAATGCATATTAGGTATGAGATGATTATATGTTCAAATA
34654495 TACTTTGAATATTTTGATTTGGT
326 TACTTTGAATATTTTGATTTGGT
34654518 TTTACAATAACATATATGTGTTTTTGTTGATTATTATGAATATATAAATAGGAAGTAAATAAGGT
1 TTTACAATAACATATATGTGTTTTTGTTGATTATTATGAATATATAAATAGGAAGTAAATAAGGT
34654583 TTCCTATATGACCAAATAGGTAATTAAATGTATCGGTTAAGTATATGTATTTTAACTATGATATT
66 TTCCTATATGACCAAATAGGTAATTAAATGTATCGGTTAAGTATATGTATTTTAACTATGATATT
34654648 TGGGCATGTGAAATAAGTGTAATATTAGTCATTATTTGTGTTCAAGATAATTTAAATTATTATGG
131 TGGGCATGTGAAATAAGTGTAATATTAGTCATTATTTGTGTTCAAGATAATTTAAATTATTATGG
34654713 TCCATGCGCATAATCTTGAAATAAATTATAATGGCTAAGTATTTGATAAATTTGGTAATAGTTAA
196 TCCATGCGCATAATCTTGAAATAAATTATAATGGCTAAGTATTTGATAAATTTGGTAATAGTTAA
* * *
34654778 GCAAACGAAATTGAATAGTGGATGTTTAATGCATATTAGGTATGAGATGATTATATGTTCAAATG
261 GCAAACAAAATTGAATAATGGATGTTTAATGCATATTAGGTATGAGATGATTATATGTTCAAATA
**
34654843 TACTTTGGTTATTTTGATTTGGT
326 TACTTTGAATATTTTGATTTGGT
34654866 T
1 T
34654867 GTAATAGCAA
Statistics
Matches: 339, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
348 339 1.00
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.40
Consensus pattern (348 bp):
TTTACAATAACATATATGTGTTTTTGTTGATTATTATGAATATATAAATAGGAAGTAAATAAGGT
TTCCTATATGACCAAATAGGTAATTAAATGTATCGGTTAAGTATATGTATTTTAACTATGATATT
TGGGCATGTGAAATAAGTGTAATATTAGTCATTATTTGTGTTCAAGATAATTTAAATTATTATGG
TCCATGCGCATAATCTTGAAATAAATTATAATGGCTAAGTATTTGATAAATTTGGTAATAGTTAA
GCAAACAAAATTGAATAATGGATGTTTAATGCATATTAGGTATGAGATGATTATATGTTCAAATA
TACTTTGAATATTTTGATTTGGT
Found at i:34655222 original size:10 final size:11
Alignment explanation
Indices: 34655200--34655224 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
34655190 TAGAAAATGT
34655200 AAAAATACAAA
1 AAAAATACAAA
34655211 AAAAATACAAA
1 AAAAATACAAA
34655222 AAA
1 AAA
34655225 TAGAAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAATACAAA
Found at i:34656718 original size:32 final size:32
Alignment explanation
Indices: 34656680--34656743 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
34656670 ACAAAATGTG
34656680 AAAAACAACCTTAAAAACACTCTTTCATTGAA
1 AAAAACAACCTTAAAAACACTCTTTCATTGAA
*
34656712 AAAAACAACCTTAGAAACACTCTTTCATTGAA
1 AAAAACAACCTTAAAAACACTCTTTCATTGAA
34656744 GCATTACCTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.48, C:0.22, G:0.05, T:0.25
Consensus pattern (32 bp):
AAAAACAACCTTAAAAACACTCTTTCATTGAA
Found at i:34660479 original size:37 final size:37
Alignment explanation
Indices: 34660399--34660483 Score: 93
Period size: 37 Copynumber: 2.3 Consensus size: 37
34660389 CCAAACACTT
* * *
34660399 ATAAGAGCTAATCCAACTGATAACACGTCGAATCCTC
1 ATAAGAGCTAATCCAACCGATAACACCTAGAATCCTC
* *
34660436 AAAAGAGCTAATCCAACCG-TAAACACACTAG-ATGCTC
1 ATAAGAGCTAATCCAACCGAT-AACAC-CTAGAATCCTC
34660473 ATAAGAGCTAA
1 ATAAGAGCTAA
34660484 ACATCTGCTC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
36 1 0.03
37 37 0.93
38 2 0.05
ACGTcount: A:0.42, C:0.25, G:0.14, T:0.19
Consensus pattern (37 bp):
ATAAGAGCTAATCCAACCGATAACACCTAGAATCCTC
Found at i:34663040 original size:26 final size:26
Alignment explanation
Indices: 34663010--34663077 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
34663000 CCTGTACATA
* *
34663010 TATGCTCACACGATCTGTTAAATGAG
1 TATGCTCACACGAGCTGTGAAATGAG
** *
34663036 TATGCTTTCACAAGCTGTGAAATGAG
1 TATGCTCACACGAGCTGTGAAATGAG
34663062 TATGCTCACACGAGCT
1 TATGCTCACACGAGCT
34663078 ATAGGTCAGA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (26 bp):
TATGCTCACACGAGCTGTGAAATGAG
Found at i:34663788 original size:28 final size:29
Alignment explanation
Indices: 34663756--34663812 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
34663746 TACTTTTAAA
* *
34663756 TAACAACTAATATCTCAA-ATTCATCAAT
1 TAACAACTAAAATCACAAGATTCATCAAT
* *
34663784 TAACATCTAAAATCACAAGGTTCATCAAT
1 TAACAACTAAAATCACAAGATTCATCAAT
34663813 GGAAACATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.46, C:0.21, G:0.04, T:0.30
Consensus pattern (29 bp):
TAACAACTAAAATCACAAGATTCATCAAT
Found at i:34672828 original size:54 final size:55
Alignment explanation
Indices: 34672765--34672891 Score: 161
Period size: 54 Copynumber: 2.3 Consensus size: 55
34672755 GAATATCATA
* * *
34672765 CCCCCATAGGGTAAAATGACT-GAAAAACCC-CAATTGGGTAAAATGACCGTAATG
1 CCCCTATAGGGTAAAATGAATCGAAAAACCCTC-ATAGGGTAAAATGACCGTAATG
*
34672819 CCCCTATAGGGTAAAAT-AATCGAAAAACCCTCATAGGGTAAAATGATCGTAATG
1 CCCCTATAGGGTAAAATGAATCGAAAAACCCTCATAGGGTAAAATGACCGTAATG
* * *
34672873 CCCTTATAGTGCAAAATGA
1 CCCCTATAGGGTAAAATGA
34672892 TCATAATACC
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
53 2 0.03
54 59 0.94
55 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.21
Consensus pattern (55 bp):
CCCCTATAGGGTAAAATGAATCGAAAAACCCTCATAGGGTAAAATGACCGTAATG
Found at i:34672867 original size:27 final size:26
Alignment explanation
Indices: 34672766--34672945 Score: 121
Period size: 27 Copynumber: 6.7 Consensus size: 26
34672756 AATATCATAC
*
34672766 CCCCATAGGGTAAAATGA-CTGAAAAA
1 CCCCATAGGGTAAAATGATC-GAAATA
* * * *
34672792 CCCCAATTGGGTAAAATGACCGTAATG
1 CCCC-ATAGGGTAAAATGATCGAAATA
* *
34672819 CCCCTATAGGGTAAAATAATCGAAAAA
1 CCCC-ATAGGGTAAAATGATCGAAATA
* *
34672846 CCCTCATAGGGTAAAATGATCGTAATG
1 CCC-CATAGGGTAAAATGATCGAAATA
* * *
34672873 CCCTTATAGTGCAAAATGATC-ATAATA
1 CCC-CATAGGGTAAAATGATCGA-AATA
* * *
34672900 CCCCCATAGGTTTAAATGATTGAAATA
1 -CCCCATAGGGTAAAATGATCGAAATA
* *
34672927 CCCCTGTAAGGTAAAATGA
1 CCCC-ATAGGGTAAAATGA
34672946 CCATAATGCC
Statistics
Matches: 117, Mismatches: 30, Indels: 13
0.73 0.19 0.08
Matches are distributed among these distances:
26 8 0.07
27 103 0.88
28 6 0.05
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.23
Consensus pattern (26 bp):
CCCCATAGGGTAAAATGATCGAAATA
Found at i:34672908 original size:54 final size:54
Alignment explanation
Indices: 34672786--34672919 Score: 153
Period size: 54 Copynumber: 2.5 Consensus size: 54
34672776 TAAAATGACT
* * * *
34672786 GAAAAACCCCAATTGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATAATC
1 GAAAAACCCCCATAGGGTAAAATGATCGTAATGCCCCTATAGGGCAAAATAATC
* * * *
34672840 GAAAAACCCTCATAGGGTAAAATGATCGTAATGCCCTTATAGTGCAAAATGATC
1 GAAAAACCCCCATAGGGTAAAATGATCGTAATGCCCCTATAGGGCAAAATAATC
* * *
34672894 -ATAATACCCCCATAGGTTTAAATGAT
1 GA-AAAACCCCCATAGGGTAAAATGAT
34672920 TGAAATACCC
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
53 1 0.01
54 66 0.99
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (54 bp):
GAAAAACCCCCATAGGGTAAAATGATCGTAATGCCCCTATAGGGCAAAATAATC
Found at i:34673015 original size:11 final size:11
Alignment explanation
Indices: 34672999--34673068 Score: 50
Period size: 11 Copynumber: 6.0 Consensus size: 11
34672989 TGTAAATGAT
*
34672999 TGATTTGTCTG
1 TGATTTGTATG
**
34673010 TGATTTAAATG
1 TGATTTGTATG
*
34673021 ACTGATTTGTCTG
1 --TGATTTGTATG
*
34673034 TGATTGGTATG
1 TGATTTGTATG
*
34673045 ACTGATTTGTTTG
1 --TGATTTGTATG
34673058 TGATTTGTATG
1 TGATTTGTATG
34673069 ACTGATTCTA
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
11 27 0.61
13 17 0.39
ACGTcount: A:0.19, C:0.06, G:0.26, T:0.50
Consensus pattern (11 bp):
TGATTTGTATG
Found at i:34673026 original size:24 final size:24
Alignment explanation
Indices: 34672991--34673075 Score: 107
Period size: 24 Copynumber: 3.5 Consensus size: 24
34672981 CCCTCGAGTG
*
34672991 TAAATGATTGATTTGTCTGTGATT
1 TAAATGACTGATTTGTCTGTGATT
34673015 TAAATGACTGATTTGTCTGTGATT
1 TAAATGACTGATTTGTCTGTGATT
*** *
34673039 GGTATGACTGATTTGTTTGTGATT
1 TAAATGACTGATTTGTCTGTGATT
**
34673063 TGTATGACTGATT
1 TAAATGACTGATT
34673076 CTAAGGAAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.22, C:0.06, G:0.24, T:0.48
Consensus pattern (24 bp):
TAAATGACTGATTTGTCTGTGATT
Found at i:34673347 original size:32 final size:31
Alignment explanation
Indices: 34673250--34673356 Score: 99
Period size: 32 Copynumber: 3.4 Consensus size: 31
34673240 GCAATGCTAT
* * *
34673250 TGATGGCTTTTTACTGATCATATTACTGTTAC
1 TGATGGCTTTGTGCCGATCATA-TACTGTTAC
*
34673282 TGATGGCTTTGTGCCGATCATAATACCGTTAC
1 TGATGGCTTTGTGCCGATCAT-ATACTGTTAC
* * *
34673314 TGAT-GTTTGTGTGCCGGTCATATCACTGCTAC
1 TGATGGCTT-TGTGCCGATCATAT-ACTGTTAC
*
34673346 TGGTGGCTTTG
1 TGATGGCTTTG
34673357 CTCCAATCAT
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
31 5 0.08
32 52 0.85
33 4 0.07
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.40
Consensus pattern (31 bp):
TGATGGCTTTGTGCCGATCATATACTGTTAC
Found at i:34673412 original size:22 final size:20
Alignment explanation
Indices: 34673382--34673441 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 20
34673372 TATACTTTTG
34673382 GCTTGTAGCCATTTTGTTTAT
1 GCTT-TAGCCATTTTGTTTAT
* *
34673403 AGCTTATAGCTATCTTGTTTAT
1 -GCTT-TAGCCATTTTGTTTAT
34673425 GACTCTTAGCCATTTTG
1 G-CT-TTAGCCATTTTG
34673442 GTTACTGGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
21 1 0.03
22 29 0.94
23 1 0.03
ACGTcount: A:0.18, C:0.17, G:0.17, T:0.48
Consensus pattern (20 bp):
GCTTTAGCCATTTTGTTTAT
Found at i:34675889 original size:110 final size:110
Alignment explanation
Indices: 34675692--34675908 Score: 371
Period size: 110 Copynumber: 2.0 Consensus size: 110
34675682 TTGTGGAAAC
34675692 TCCACAAATCATGTGAGCAACATCATGTAGCTTACATTCCGACCCAAAACTCATGTGAGTAGGCC
1 TCCACAAATCATGTGAGCAACATCATGTAGCTTACATTCCGACCCAAAACTCATGTGAGTAGGCC
* * *
34675757 CATTTCACAGCTTGTGTGAGCAATAATATGAAGGAAAGGTTACAT
66 CATTTCACAGCTTATGTAAGCAACAATATGAAGGAAAGGTTACAT
* * *
34675802 TCCACAACTCATGTGAGCAACATCGTGTAGCTTACATTCCGACCCACAACTCATGTGAGTAGGCC
1 TCCACAAATCATGTGAGCAACATCATGTAGCTTACATTCCGACCCAAAACTCATGTGAGTAGGCC
*
34675867 CATTTCAGAGCTTATGTAAGCAACAATATGAAGGAAAGGTTA
66 CATTTCACAGCTTATGTAAGCAACAATATGAAGGAAAGGTTA
34675909 GAATTATATG
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
110 100 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (110 bp):
TCCACAAATCATGTGAGCAACATCATGTAGCTTACATTCCGACCCAAAACTCATGTGAGTAGGCC
CATTTCACAGCTTATGTAAGCAACAATATGAAGGAAAGGTTACAT
Found at i:34679294 original size:50 final size:50
Alignment explanation
Indices: 34679227--34679472 Score: 233
Period size: 50 Copynumber: 4.7 Consensus size: 50
34679217 TTTTTTGTAC
* * ** *
34679227 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTTATA-TCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCA-ACTCGG
* ***
34679277 TGCCCATGCCATGTCCCAGACATGGTCTTATGGGGGACCTCTCAACTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAACTCGG
* *
34679327 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAACTCGG
** * * * *
34679377 TGTTAACGCCATGTCCCAGACATTGTCTTACATGGCACCTCTCATAATCTCAATAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC--AA-CTC------GG
*
34679436 TGCCAATTCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
34679473 TCTCATTCCC
Statistics
Matches: 159, Mismatches: 27, Indels: 11
0.81 0.14 0.06
Matches are distributed among these distances:
49 1 0.01
50 121 0.76
52 1 0.01
53 3 0.02
59 33 0.21
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAACTCGG
Found at i:34686580 original size:12 final size:12
Alignment explanation
Indices: 34686555--34686593 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
34686545 ACTCGCTTCT
* *
34686555 TTACTTACTCAC
1 TTACTTGCTTAC
*
34686567 TTACTTGTTTAC
1 TTACTTGCTTAC
34686579 TTACTTGCTTAC
1 TTACTTGCTTAC
34686591 TTA
1 TTA
34686594 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:34686910 original size:50 final size:50
Alignment explanation
Indices: 34686846--34687087 Score: 216
Period size: 50 Copynumber: 4.7 Consensus size: 50
34686836 CTATACTACT
* * * **
34686846 AATGCCATATCCCAGATATGGCCTTACATGGGAGTTCTCATATCGGTGCC
1 AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCC
* ***
34686896 CATGCCATGTCCCAGACATGGTCTTATGGGGGACCTCTCA-ACTCGGTGCC
1 AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA-TCGGTGCC
* * * * **
34686946 AACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGATGTT
1 AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCC
* * *
34686996 AATGCCATGTCCCAGACATTGTCTTACATGGCACCTCTCATAATCTAAATAATGATGCC
1 AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-ATC--------GGTGCC
*
34687055 AATGCCATGTCCCAGACATGGTCTTAGATGGGA
1 AATGCCATGTCCCAGACATGGTCTTACATGGGA
34687088 TCTCATTCCC
Statistics
Matches: 152, Mismatches: 29, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
49 1 0.01
50 115 0.76
51 2 0.01
59 34 0.22
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.27
Consensus pattern (50 bp):
AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCC
Found at i:34691041 original size:21 final size:22
Alignment explanation
Indices: 34690995--34691041 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
34690985 TCCTGATTGG
34690995 TTTTATTGACTTGATTAGTTTA
1 TTTTATTGACTTGATTAGTTTA
** *
34691017 -TTTATTTTCTTGTTTA-TTTA
1 TTTTATTGACTTGATTAGTTTA
34691037 TTTTA
1 TTTTA
34691042 CTTATTTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.19, C:0.04, G:0.09, T:0.68
Consensus pattern (22 bp):
TTTTATTGACTTGATTAGTTTA
Found at i:34698415 original size:28 final size:28
Alignment explanation
Indices: 34698371--34698424 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
34698361 GTAACTGTAC
*
34698371 AGTGTGGGCCTTGGCCCAATACAGTAAA
1 AGTGTGGGCCTTAGCCCAATACAGTAAA
34698399 AGTGTGGGCCTTAGCCCAATACAGTA
1 AGTGTGGGCCTTAGCCCAATACAGTA
34698425 TCAGTAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (28 bp):
AGTGTGGGCCTTAGCCCAATACAGTAAA
Found at i:34698561 original size:26 final size:26
Alignment explanation
Indices: 34698532--34698602 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 26
34698522 AACACACCAA
* *
34698532 TATCGCAGTAAAGCTGCCAGTAATAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
*
34698558 TATCGCAGCAAAGCTTG-TAGTAACAG
1 TATCGCAGCAAAGC-TGCCAGTAACAG
*
34698584 TATCGCAACAAAGCTGCCA
1 TATCGCAGCAAAGCTGCCA
34698603 ATATAATGTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
25 2 0.05
26 34 0.89
27 2 0.05
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTAACAG
Found at i:34702296 original size:33 final size:33
Alignment explanation
Indices: 34702259--34702326 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
34702249 ATTTATCATG
34702259 TTTAACAATGTTCTAGAAGAATTCCATGTCAAC
1 TTTAACAATGTTCTAGAAGAATTCCATGTCAAC
34702292 TTTAACAATGTTCTAGAAGAATTCCATGTCAAC
1 TTTAACAATGTTCTAGAAGAATTCCATGTCAAC
34702325 TT
1 TT
34702327 GATCATTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (33 bp):
TTTAACAATGTTCTAGAAGAATTCCATGTCAAC
Found at i:34718687 original size:50 final size:50
Alignment explanation
Indices: 34718584--34718776 Score: 188
Period size: 50 Copynumber: 3.7 Consensus size: 50
34718574 GGGAATGAGA
* *
34718584 TCCCATGTAAGACCATGTCTGGGACATGGCATTTGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGG
* *
34718640 TCCAATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
** * * * * **
34718690 TCCCCCGTAAGACTATGTCTGGGACATGGCATGGGCACCTATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * *
34718740 TCCCATGTAAAACCATATCTAGGATATGGCATTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
34718777 GTACAAGAAA
Statistics
Matches: 115, Mismatches: 22, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
50 77 0.67
53 3 0.03
55 1 0.01
56 34 0.30
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:34724950 original size:50 final size:50
Alignment explanation
Indices: 34724883--34725069 Score: 248
Period size: 50 Copynumber: 3.7 Consensus size: 50
34724873 GGGAATGAGA
*
34724883 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATGAGAGG
* * *
34724933 TCCCATTTAAGACCATGTCTGGAACATGGCGTTGGCACCAAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATGAGAGG
** * * * **
34724983 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCTATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATGAGAGG
* * *
34725033 TCCCATGTAAGACCATATCTAGGATATGGCATTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
34725070 GTACAAGAAA
Statistics
Matches: 117, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 117 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATGAGAGG
Found at i:34729486 original size:37 final size:38
Alignment explanation
Indices: 34729436--34729509 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 38
34729426 ACACATGGTC
34729436 ACCCTATTTTATCATTAACAAAGATT-AATTGCAGGCT
1 ACCCTATTTTATCATTAACAAAGATTCAATTGCAGGCT
* * *
34729473 ACCCTCTTTTATCATTAACAAAGGTTCAATTGTAGGC
1 ACCCTATTTTATCATTAACAAAGATTCAATTGCAGGC
34729510 ATAATAAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 24 0.73
38 9 0.27
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.35
Consensus pattern (38 bp):
ACCCTATTTTATCATTAACAAAGATTCAATTGCAGGCT
Found at i:34736235 original size:22 final size:24
Alignment explanation
Indices: 34736203--34736251 Score: 75
Period size: 22 Copynumber: 2.1 Consensus size: 24
34736193 AAGAGCCAAA
*
34736203 CAAGCATAAAC-AAAAAA-AATAG
1 CAAGCAAAAACAAAAAAAGAATAG
34736225 CAAGCAAAAACAAAAAAAGAATAG
1 CAAGCAAAAACAAAAAAAGAATAG
34736249 CAA
1 CAA
34736252 AGAAGAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 10 0.42
23 6 0.25
24 8 0.33
ACGTcount: A:0.69, C:0.14, G:0.10, T:0.06
Consensus pattern (24 bp):
CAAGCAAAAACAAAAAAAGAATAG
Found at i:34736266 original size:21 final size:20
Alignment explanation
Indices: 34736227--34736266 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
34736217 AAAAATAGCA
34736227 AGCAAAAACAAAAAAAGAAT
1 AGCAAAAACAAAAAAAGAAT
* *
34736247 AGCAAAGAAGAAAGAAAGAA
1 AGCAAA-AACAAAAAAAGAA
34736267 GGAGAGGAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.72, C:0.07, G:0.17, T:0.03
Consensus pattern (20 bp):
AGCAAAAACAAAAAAAGAAT
Found at i:34736448 original size:25 final size:25
Alignment explanation
Indices: 34736380--34736448 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
34736370 GGAGAAAAAG
34736380 AAAAATGAAAG-AAAAAAAGATAGA
1 AAAAATGAAAGAAAAAAAAGATAGA
**
34736404 AGAAAGGGAAAGAAAAAAAAGA-AGA
1 A-AAAATGAAAGAAAAAAAAGATAGA
*
34736429 AAAAATGAACGAAAAGAAAA
1 AAAAATGAAAGAAAA-AAAA
34736449 AAATTCAAGC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
24 12 0.32
25 16 0.43
26 9 0.24
ACGTcount: A:0.74, C:0.01, G:0.20, T:0.04
Consensus pattern (25 bp):
AAAAATGAAAGAAAAAAAAGATAGA
Found at i:34736777 original size:18 final size:18
Alignment explanation
Indices: 34736756--34736818 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
34736746 GAAAGGAACG
*
34736756 GAGAAGAAGAAGAAAAAA
1 GAGAAAAAGAAGAAAAAA
34736774 GAGAAAAAGAA-AGAAAAA
1 GAGAAAAAGAAGA-AAAAA
* *
34736792 GAGGAAAAAAAAGGAAAAA
1 GA-GAAAAAGAAGAAAAAA
34736811 GAGGAAAA
1 GA-GAAAA
34736819 TTAATATATA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
17 1 0.03
18 17 0.44
19 21 0.54
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (18 bp):
GAGAAAAAGAAGAAAAAA
Found at i:34736789 original size:19 final size:19
Alignment explanation
Indices: 34736769--34736818 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
34736759 AAGAAGAAGA
34736769 AAAAAGA-GAAAAAGAAAG
1 AAAAAGAGGAAAAAGAAAG
34736787 AAAAAGAGGAAAAA-AAAGG
1 AAAAAGAGGAAAAAGAAA-G
34736806 AAAAAGAGGAAAA
1 AAAAAGAGGAAAA
34736819 TTAATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.33
19 20 0.67
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (19 bp):
AAAAAGAGGAAAAAGAAAG
Found at i:34736809 original size:8 final size:9
Alignment explanation
Indices: 34736769--34736818 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
34736759 AAGAAGAAGA
34736769 AAAAAGA-G
1 AAAAAGAGG
*
34736777 AAAAAGAAAG
1 AAAAAG-AGG
34736787 AAAAAGAGG
1 AAAAAGAGG
*
34736796 AAAAAAAAGG
1 -AAAAAGAGG
34736806 AAAAAGAGG
1 AAAAAGAGG
34736815 AAAA
1 AAAA
34736819 TTAATATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
8 6 0.17
9 15 0.42
10 15 0.42
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (9 bp):
AAAAAGAGG
Found at i:34736936 original size:20 final size:20
Alignment explanation
Indices: 34736894--34736942 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
34736884 CAGCAGCAAC
34736894 ACAGCAGG-CCAAGTCTCCA
1 ACAGCAGGCCCAAGTCTCCA
* * *
34736913 ACAGCAGGCCCAATTTTCCT
1 ACAGCAGGCCCAAGTCTCCA
34736933 ACAGCAGGCC
1 ACAGCAGGCC
34736943 TGTCCTAGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.29, C:0.37, G:0.20, T:0.14
Consensus pattern (20 bp):
ACAGCAGGCCCAAGTCTCCA
Found at i:34738807 original size:12 final size:12
Alignment explanation
Indices: 34738790--34738821 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
34738780 TAGGAAGGTG
34738790 TTATTAGGCATT
1 TTATTAGGCATT
*
34738802 TTATTAGACATT
1 TTATTAGGCATT
34738814 TTATTAGG
1 TTATTAGG
34738822 AAGGTGTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.16, T:0.50
Consensus pattern (12 bp):
TTATTAGGCATT
Found at i:34742458 original size:32 final size:32
Alignment explanation
Indices: 34742417--34742482 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
34742407 TCTCGATTTA
34742417 TTGCTCAACTTACCAACAAATGTGACCAAATT
1 TTGCTCAACTTACCAACAAATGTGACCAAATT
* *
34742449 TTGCTCAACTTAGCAACAAATGTGACCCAATT
1 TTGCTCAACTTACCAACAAATGTGACCAAATT
34742481 TT
1 TT
34742483 CTAACTCCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (32 bp):
TTGCTCAACTTACCAACAAATGTGACCAAATT
Found at i:34745809 original size:75 final size:75
Alignment explanation
Indices: 34745686--34746238 Score: 589
Period size: 75 Copynumber: 7.3 Consensus size: 75
34745676 CAAGAATTAT
* * *
34745686 TTTTCAATTTCTGCTTTTT-TAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCATTGGGTCAC
1 TTTTCAATTTCTG-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
34745750 ACGCCGAGGTA
65 ACGCCGAGGTA
* * *
34745761 TTTTCAATTTTTGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC-GGACATA
1 TTTTCAATTTCTGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
* *
34745825 TGCCAAGGTA
66 CGCCGAGGTA
* * *
34745835 TTTTTCAATTGCAT-TTTAAAAAATAATAATAATCAACTCATAATGCGAGAGGTGAGTTGAGCCT
1 -TTTTCAATTTC-TGTTT-----TTCA-AA-AATCAACTCATAATGCGAGAGGTGAGTTGAGCCT
* * *
34745899 CAGG-CACACGTCGAGATA
57 CGGGTCACACGCCGAGGTA
* *
34745917 TTTTCAATTTCTGTTTTTTCAAAAATCAACTCATAATGCGAGAGATGAGTTGAGCCTCGGGTCGC
1 TTTTCAATTTCTG-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
* *
34745982 ACGCTGAGGTG
65 ACGCCGAGGTA
* ** ** * *
34745993 TTTTCAATTTTTGTTTTTCAAAAATCAACTCATAATGTAAGAGGTGAGTTGAGCCT-TAGACCCA
1 TTTTCAATTTCTGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
*
34746057 TGCCGAGGTA
66 CGCCGAGGTA
* * * *
34746067 TTTTTCAATTTCAT-TTTTTAAAAAATAAACTCATAATGCG-GTGGTGAGTTGAGCCTCGGGTCG
1 -TTTTCAATTTC-TGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
* * *
34746130 CATGCTGGGGTA
64 CACGCCGAGGTA
* * * * *
34746142 TTTCCAATTTATGTTTTTCAAACATCAACTCATAATCCAAGAGGTGAGTTGAGCCTCGGGTCACA
1 TTTTCAATTTCTGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
*
34746207 CGCTGAGGTA
66 CGCCGAGGTA
34746217 TTTTCAATTTCTGTTTTTCAAA
1 TTTTCAATTTCTGTTTTTCAAA
34746239 TAAATAATAA
Statistics
Matches: 396, Mismatches: 63, Indels: 38
0.80 0.13 0.08
Matches are distributed among these distances:
73 1 0.00
74 74 0.19
75 230 0.58
76 25 0.06
77 2 0.01
80 3 0.01
81 12 0.03
82 47 0.12
83 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (75 bp):
TTTTCAATTTCTGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
CGCCGAGGTA
Found at i:34746184 original size:149 final size:150
Alignment explanation
Indices: 34745706--34746245 Score: 507
Period size: 149 Copynumber: 3.5 Consensus size: 150
34745696 CTGCTTTTTT
* * ** * *
34745706 AAAATCAACTCATAATGCGAGAGGTGAGTTGAGCATTGGGTCACACGCCGAGGTATTTTCAATTT
1 AAAATCAACTCATAATGCAAGAGGTGAGTTGAGC-CTCAGACACACGCCGAGATATTTTCAATTT
* * * * ** * **
34745771 -T-TGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC-GGACATATGCCAAGG
65 CTAT-TTTTTAAAAAATAAACTCATAATGCGAGAGATGAGTTGAGCCTCGGGTCGCACGCTGAGG
* * * *
34745833 TATTTTTCAATTGCAT-TTTAAAAAATAA
129 TA-TTTCCAATT-TATGTTT-----TTCA
* * *
34745861 TAATAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGCACACGTCGAGATATTTTCAATT
1 -AA-AATCAACTCATAATGCAAGAGGTGAGTTGAGCCTCAGACACACGCCGAGATATTTTCAATT
* * *
34745926 TCTGTTTTTTCAAAAATCAACTCATAATGCGAGAGATGAGTTGAGCCTCGGGTCGCACGCTGAGG
64 TCTATTTTTTAAAAAATAAACTCATAATGCGAGAGATGAGTTGAGCCTCGGGTCGCACGCTGAGG
* * *
34745991 TGTTTTCAATTTTTGTTTTTCA
129 TATTTCCAATTTATGTTTTTCA
* * * * *
34746013 AAAATCAACTCATAATGTAAGAGGTGAGTTGAGCCTTAGACCCATGCCGAGGTATTTTTCAATTT
1 AAAATCAACTCATAATGCAAGAGGTGAGTTGAGCCTCAGACACACGCCGAGATA-TTTTCAATTT
* * * *
34746078 C-ATTTTTTAAAAAATAAACTCATAATGCG-GTGGTGAGTTGAGCCTCGGGTCGCATGCTGGGGT
65 CTATTTTTTAAAAAATAAACTCATAATGCGAGAGATGAGTTGAGCCTCGGGTCGCACGCTGAGGT
34746141 ATTTCCAATTTATGTTTTTCA
130 ATTTCCAATTTATGTTTTTCA
* * * * * *
34746162 AACATCAACTCATAATCCAAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCAATTT
1 AAAATCAACTCATAATGCAAGAGGTGAGTTGAGCCTC-AGACACACGCCGAGATATTTTCAATTT
* *
34746227 CTGTTTTTCAAATAAATAA
65 CTATTTTTTAAA-AAATAA
34746246 TAATAATTTT
Statistics
Matches: 328, Mismatches: 47, Indels: 23
0.82 0.12 0.06
Matches are distributed among these distances:
149 92 0.28
150 89 0.27
151 19 0.06
152 2 0.01
156 27 0.08
157 88 0.27
158 11 0.03
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (150 bp):
AAAATCAACTCATAATGCAAGAGGTGAGTTGAGCCTCAGACACACGCCGAGATATTTTCAATTTC
TATTTTTTAAAAAATAAACTCATAATGCGAGAGATGAGTTGAGCCTCGGGTCGCACGCTGAGGTA
TTTCCAATTTATGTTTTTCA
Found at i:34746620 original size:29 final size:29
Alignment explanation
Indices: 34746564--34746634 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 29
34746554 AAAAAAAAAA
*
34746564 TAAATTACATTTTGACCCTTAAATTTTTC
1 TAAATTACATTTTGACCCTCAAATTTTTC
*
34746593 TAAATTTACATTTTGACCC-CAACA-TTTTG
1 TAAA-TTACATTTTGACCCTCAA-ATTTTTC
34746622 TAAATTACATTTT
1 TAAATTACATTTT
34746635 AGCCTCTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
28 9 0.24
29 14 0.37
30 15 0.39
ACGTcount: A:0.32, C:0.17, G:0.04, T:0.46
Consensus pattern (29 bp):
TAAATTACATTTTGACCCTCAAATTTTTC
Found at i:34746649 original size:29 final size:30
Alignment explanation
Indices: 34746564--34746668 Score: 78
Period size: 30 Copynumber: 3.6 Consensus size: 30
34746554 AAAAAAAAAA
* * *
34746564 TAAATTACATTTTGACCCT-TAAA-TTTTTC
1 TAAATTACATTTT-AGCCTCTAAACATTTTG
*
34746593 TAAATTTACATTTT-GACC-C-CAACATTTTG
1 TAAA-TTACATTTTAG-CCTCTAAACATTTTG
*
34746622 TAAATTACATTTTAGCCTCTAAACTTTTTG
1 TAAATTACATTTTAGCCTCTAAACATTTTG
*
34746652 AAAATT-CTATTTTAGCC
1 TAAATTAC-ATTTTAGCC
34746669 CCAAATTTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 15
0.73 0.08 0.18
Matches are distributed among these distances:
28 13 0.21
29 17 0.28
30 31 0.51
ACGTcount: A:0.31, C:0.18, G:0.06, T:0.45
Consensus pattern (30 bp):
TAAATTACATTTTAGCCTCTAAACATTTTG
Found at i:34746657 original size:30 final size:28
Alignment explanation
Indices: 34746609--34746685 Score: 77
Period size: 30 Copynumber: 2.7 Consensus size: 28
34746599 TACATTTTGA
*
34746609 CCCCAACA-TTTTGTAAATTAC-ATTTTAG
1 CCCCAA-ATTTTTGAAAATT-CTATTTTAG
*
34746637 CCTCTAAACTTTTTGAAAATTCTATTTTAG
1 CC-CCAAA-TTTTTGAAAATTCTATTTTAG
*
34746667 CCCCAAATTTTTTAAAATT
1 CCCCAAATTTTTGAAAATT
34746686 GCACTGTTGC
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
28 14 0.34
29 8 0.20
30 19 0.46
ACGTcount: A:0.32, C:0.19, G:0.05, T:0.43
Consensus pattern (28 bp):
CCCCAAATTTTTGAAAATTCTATTTTAG
Found at i:34746664 original size:58 final size:56
Alignment explanation
Indices: 34746564--34746682 Score: 127
Period size: 58 Copynumber: 2.1 Consensus size: 56
34746554 AAAAAAAAAA
*
34746564 TAAATTACATTTTGACCCTTAAATTTTTCTAAATTTACATTTT-GACCCCAACATTTTG
1 TAAATTACATTTTGACCCTTAAATTTTTCAAAATTTA-ATTTTAG-CCCCAA-ATTTTG
* * *
34746622 TAAATTACATTTT-AGCCTCTAAACTTTTTGAAAATTCT-ATTTTAGCCCCAAATTTTT
1 TAAATTACATTTTGACCCT-TAAA-TTTTTCAAAATT-TAATTTTAGCCCCAAATTTTG
34746679 TAAA
1 TAAA
34746683 ATTGCACTGT
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
57 13 0.25
58 28 0.53
59 11 0.21
60 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.05, T:0.45
Consensus pattern (56 bp):
TAAATTACATTTTGACCCTTAAATTTTTCAAAATTTAATTTTAGCCCCAAATTTTG
Found at i:34747234 original size:27 final size:27
Alignment explanation
Indices: 34747204--34747265 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
34747194 AGAAGAAAGG
34747204 AGAAAAAGAAAAGGGAAAGAAAAAAAA
1 AGAAAAAGAAAAGGGAAAGAAAAAAAA
* * * *
34747231 AGAAAGATG-AACGGGAAGGAAAAAAAG
1 AGAAA-AAGAAAAGGGAAAGAAAAAAAA
34747258 A-AAAAAGA
1 AGAAAAAGA
34747266 TGAAAAAAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
25 2 0.07
26 3 0.11
27 21 0.75
28 2 0.07
ACGTcount: A:0.71, C:0.02, G:0.26, T:0.02
Consensus pattern (27 bp):
AGAAAAAGAAAAGGGAAAGAAAAAAAA
Found at i:34747264 original size:28 final size:27
Alignment explanation
Indices: 34747216--34747269 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
34747206 AAAAAGAAAA
*
34747216 GGGAAAGAAAAAAAAAGAAAGATGAAC
1 GGGAAAGAAAAAAAAAAAAAGATGAAC
*
34747243 GGGAAGGAAAAAAAGAAAAAAGATGAA
1 GGGAAAGAAAAAAA-AAAAAAGATGAA
34747270 AAAAAGGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.67, C:0.02, G:0.28, T:0.04
Consensus pattern (27 bp):
GGGAAAGAAAAAAAAAAAAAGATGAAC
Found at i:34747430 original size:18 final size:19
Alignment explanation
Indices: 34747396--34747431 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
34747386 CTACTAATAC
*
34747396 CAAAAGAAAGCAAATCAAG
1 CAAAAGAAAGAAAATCAAG
34747415 CAAAAGAAA-AAAATCAA
1 CAAAAGAAAGAAAATCAA
34747432 AATAAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.69, C:0.14, G:0.11, T:0.06
Consensus pattern (19 bp):
CAAAAGAAAGAAAATCAAG
Found at i:34747639 original size:26 final size:25
Alignment explanation
Indices: 34747601--34747661 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
34747591 CGAGAAGAAG
*
34747601 AAGAAAAAGGGGAAAAAGAAAGAAAA
1 AAGAAAAAAGGGAAAAA-AAAGAAAA
*
34747627 AAGAAAAAAGGGAAAAAAATGAAAA
1 AAGAAAAAAGGGAAAAAAAAGAAAA
*
34747652 AGAGGAAAAA
1 A-AGAAAAAA
34747662 TAATATATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 8 0.26
26 23 0.74
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.02
Consensus pattern (25 bp):
AAGAAAAAAGGGAAAAAAAAGAAAA
Found at i:34747659 original size:9 final size:9
Alignment explanation
Indices: 34747598--34747661 Score: 51
Period size: 9 Copynumber: 7.2 Consensus size: 9
34747588 GAACGAGAAG
*
34747598 AAGAAGAAA
1 AAGAGGAAA
*
34747607 AAGGGGAAA
1 AAGAGGAAA
*
34747616 AAGAAAGAAA
1 AAG-AGGAAA
*
34747626 AA-AGAAAA
1 AAGAGGAAA
34747634 AAG-GGAAA
1 AAGAGGAAA
* *
34747642 AAAATGAAA
1 AAGAGGAAA
34747651 AAGAGGAAA
1 AAGAGGAAA
34747660 AA
1 AA
34747662 TAATATATAA
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
8 12 0.29
9 23 0.56
10 6 0.15
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (9 bp):
AAGAGGAAA
Found at i:34749103 original size:37 final size:37
Alignment explanation
Indices: 34749002--34749108 Score: 110
Period size: 37 Copynumber: 2.9 Consensus size: 37
34748992 GGCCAACTGA
* * * * *
34749002 TCATAAGAGCTCATCGACCCGATAACACGCCAATTGC
1 TCATAAGAGCTAATCCACCCGATAACATGTCAAATGC
* *
34749039 T-TTGAAGAGCTAATCCAACCGGA-AACATGTCAAATGC
1 TCAT-AAGAGCTAATCC-ACCCGATAACATGTCAAATGC
*
34749076 TCATAAGAGCTAATCCACCCAATAACATGTCAA
1 TCATAAGAGCTAATCCACCCGATAACATGTCAA
34749109 TTTCTCCGTA
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
36 5 0.09
37 45 0.80
38 6 0.11
ACGTcount: A:0.37, C:0.27, G:0.15, T:0.21
Consensus pattern (37 bp):
TCATAAGAGCTAATCCACCCGATAACATGTCAAATGC
Found at i:34749373 original size:10 final size:10
Alignment explanation
Indices: 34749349--34749378 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
34749339 ATAATAAAAC
34749349 TATTATATC-
1 TATTATATCA
34749358 TATTATATCA
1 TATTATATCA
34749368 TATTATATCA
1 TATTATATCA
34749378 T
1 T
34749379 CAAACATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (10 bp):
TATTATATCA
Found at i:34750109 original size:21 final size:22
Alignment explanation
Indices: 34750070--34750112 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
34750060 GAAGATGAAA
* *
34750070 TGTTTTATTCTTTCTTTAATTT
1 TGTTTTAATCTTTCATTAATTT
34750092 TGTTTTAAT-TTTCATTAATTT
1 TGTTTTAATCTTTCATTAATTT
34750113 ACAAAATTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.70
Consensus pattern (22 bp):
TGTTTTAATCTTTCATTAATTT
Found at i:34751995 original size:33 final size:33
Alignment explanation
Indices: 34751953--34752105 Score: 120
Period size: 33 Copynumber: 4.5 Consensus size: 33
34751943 ATACAGTGGG
34751953 ATCAGCACTTAGCAACCACCAATGAATCGGGGA
1 ATCAGCACTTAGCAACCACCAATGAATCGGGGA
*
34751986 ATCAGCACTTAGCAACC-CC--T---TGGGGGA
1 ATCAGCACTTAGCAACCACCAATGAATCGGGGA
* *
34752013 ATCAGCACTTAGCAACCCCCTTTATATTCAAAGATACGGTGGA
1 ATCAGCACTTAGCAACCACC---A-A-T--GA-AT-CGG-GGA
* *
34752056 ATCAGCACTTGGCAACCACCAATGAGTCGGGGA
1 ATCAGCACTTAGCAACCACCAATGAATCGGGGA
*
34752089 ATCAGCAGTTAGCAACC
1 ATCAGCACTTAGCAACC
34752106 CCTTGGGGGA
Statistics
Matches: 96, Mismatches: 8, Indels: 32
0.71 0.06 0.24
Matches are distributed among these distances:
27 23 0.24
28 2 0.02
30 1 0.01
32 2 0.02
33 35 0.36
34 3 0.03
35 2 0.02
36 1 0.01
38 1 0.01
39 1 0.01
40 1 0.01
41 1 0.01
42 2 0.02
43 21 0.22
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.19
Consensus pattern (33 bp):
ATCAGCACTTAGCAACCACCAATGAATCGGGGA
Found at i:34752101 original size:103 final size:103
Alignment explanation
Indices: 34751803--34752146 Score: 530
Period size: 103 Copynumber: 3.3 Consensus size: 103
34751793 CTAGTGATTC
*
34751803 GGGGAATCAGCACTTAGCAA-CCCCTTTCACATTCAAAGATATGGTGGAATCAGCACTTAGCAAC
1 GGGGAATCAGCACTTAGCAACCCCCTTT-ACATTCAAAGATACGGTGGAATCAGCACTTAGCAAC
* * *
34751867 CACCAATGATTCGGGGAATCAACACTTAGCAGCCCCTTG
65 CACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
* * * * *
34751906 GGGGAATTAGCACTTAGCAACCCCCTTCACATTTAAA-ATACAGTGGGATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTTACATTCAAAGATACGGTGGAATCAGCACTTAGCAACC
34751970 ACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
66 ACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
* *
34752008 GGGGAATCAGCACTTAGCAACCCCCTTTATATTCAAAGATACGGTGGAATCAGCACTTGGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTTACATTCAAAGATACGGTGGAATCAGCACTTAGCAACC
* *
34752073 ACCAATGAGTCGGGGAATCAGCAGTTAGCAACCCCTTG
66 ACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
* *
34752111 GGGGAATCAACACTTAGCAACCCCCTTTATATTCAA
1 GGGGAATCAGCACTTAGCAACCCCCTTTACATTCAA
34752147 TGTACTCCGG
Statistics
Matches: 220, Mismatches: 19, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
102 92 0.42
103 122 0.55
104 6 0.03
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.21
Consensus pattern (103 bp):
GGGGAATCAGCACTTAGCAACCCCCTTTACATTCAAAGATACGGTGGAATCAGCACTTAGCAACC
ACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
Found at i:34759603 original size:102 final size:103
Alignment explanation
Indices: 34759417--34759749 Score: 479
Period size: 103 Copynumber: 3.2 Consensus size: 103
34759407 AGTGATTCGA
* * *
34759417 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAAGATATGGTGGAATCAGCACTTAGCAACCAC
1 GGAATCAACACTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTAGCAACCAC
* * * * ** *
34759482 GAATGATTCAGGGAATCAGCATTTAGCAGGCCTTTGGG
66 CAATGAATCGGGGAATCAGCACTTAGCAACCCCTTGGG
* * *
34759520 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAA-ATACAGTGGGATCAGCACTTAGCAACCAC
1 GGAATCAACACTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTAGCAACCAC
34759584 CAATGAATCGGGGAATCAGCACTTAGCAACCCCTTGGG
66 CAATGAATCGGGGAATCAGCACTTAGCAACCCCTTGGG
* * * * *
34759622 GGAATCAACATTTAGCAACCCCCTTTATATTCAAAGATACGGTGGAATCAGCACTTGGCAACCAC
1 GGAATCAACACTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTAGCAACCAC
* *
34759687 CAATGAGTCGGGGAATCAGCAGTTAGCAACCCCTTGGG
66 CAATGAATCGGGGAATCAGCACTTAGCAACCCCTTGGG
34759725 GGAATCAACACTTAGCAACCCCCTT
1 GGAATCAACACTTAGCAACCCCCTT
34759750 TATATTCAAT
Statistics
Matches: 207, Mismatches: 22, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
102 87 0.42
103 120 0.58
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.22
Consensus pattern (103 bp):
GGAATCAACACTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTAGCAACCAC
CAATGAATCGGGGAATCAGCACTTAGCAACCCCTTGGG
Found at i:34759607 original size:33 final size:33
Alignment explanation
Indices: 34759565--34759717 Score: 102
Period size: 33 Copynumber: 4.5 Consensus size: 33
34759555 ATACAGTGGG
34759565 ATCAGCACTTAGCAACCACCAATGAATCGGGGA
1 ATCAGCACTTAGCAACCACCAATGAATCGGGGA
*
34759598 ATCAGCACTTAGCAACC-CC--T---TGGGGGA
1 ATCAGCACTTAGCAACCACCAATGAATCGGGGA
* * * *
34759625 ATCAACATTTAGCAACCCCCTTTATATTCAAAGATACGGTGGA
1 ATCAGCACTTAGCAACCACC---A-A-T--GA-AT-CGG-GGA
* *
34759668 ATCAGCACTTGGCAACCACCAATGAGTCGGGGA
1 ATCAGCACTTAGCAACCACCAATGAATCGGGGA
*
34759701 ATCAGCAGTTAGCAACC
1 ATCAGCACTTAGCAACC
34759718 CCTTGGGGGA
Statistics
Matches: 92, Mismatches: 12, Indels: 32
0.68 0.09 0.24
Matches are distributed among these distances:
27 21 0.23
28 2 0.02
30 1 0.01
32 2 0.02
33 35 0.38
34 3 0.03
35 2 0.02
36 1 0.01
38 1 0.01
39 1 0.01
40 1 0.01
41 1 0.01
42 2 0.02
43 19 0.21
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.20
Consensus pattern (33 bp):
ATCAGCACTTAGCAACCACCAATGAATCGGGGA
Found at i:34763053 original size:20 final size:20
Alignment explanation
Indices: 34763028--34763067 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
34763018 TAAGACGTAC
*
34763028 TAAAAAAATGCTCAGATTAT
1 TAAAAAAATACTCAGATTAT
34763048 TAAAAAAATACTCAGATTAT
1 TAAAAAAATACTCAGATTAT
34763068 AACATACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (20 bp):
TAAAAAAATACTCAGATTAT
Found at i:34764616 original size:20 final size:20
Alignment explanation
Indices: 34764591--34764629 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
34764581 TACTTTCTTC
34764591 TTTACTTACTCTCTTACTTG
1 TTTACTTACTCTCTTACTTG
34764611 TTTACTTACTCTCTTACTT
1 TTTACTTACTCTCTTACTT
34764630 AAATAACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.26, G:0.03, T:0.56
Consensus pattern (20 bp):
TTTACTTACTCTCTTACTTG
Found at i:34764955 original size:50 final size:50
Alignment explanation
Indices: 34764882--34765122 Score: 234
Period size: 50 Copynumber: 4.7 Consensus size: 50
34764872 CCCTGTACTA
* * **
34764882 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCAGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAGTG
* ** *
34764932 CCAATGCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTC-GATG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAG-TG
* ** *
34764982 CCAACGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTC-GATG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAG-TG
* * * * *
34765032 CCAACGCCATGTCCCTGACATGGTTTTACGTGGGACCTCTCATAACCTCAATAATG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---AGTG
*
34765088 CCAATGCCATGTCCTAGACATGGTCTTACATGGGA
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGA
34765123 TCTCATCCCC
Statistics
Matches: 163, Mismatches: 20, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 128 0.79
53 2 0.01
56 32 0.20
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAGTG
Found at i:34765023 original size:100 final size:102
Alignment explanation
Indices: 34764882--34765122 Score: 274
Period size: 100 Copynumber: 2.3 Consensus size: 102
34764872 CCCTGTACTA
* * * ** *
34764882 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATC-AGTGCCAATGCCATGT-C
1 CCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGA-TGCCAACGCCATGTCC
*
34764945 CTAGACATGGTCTTACGGGGGACCTCTCAT-CTC-GATG
65 CT-GACATGGTCTTACGGGGGACCTCTCATACTCAAATG
* * *
34764982 CCAACGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGATGCCAACGCCATGTCCC
1 CCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGATGCCAACGCCATGTCCC
* *
34765047 TGACATGGTTTTACGTGGGACCTCTCATAACCTCAATAATG
66 TGACATGGTCTTACGGGGGACCTCTCAT-A-CTC-A-AATG
* *
34765088 CCAATGCCATGTCCTAGACATGGTCTTACATGGGA
1 CCAATGCCATGTCCCAGACATGGTCTTACAGGGGA
34765123 TCTCATCCCC
Statistics
Matches: 117, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
100 76 0.65
101 4 0.03
103 3 0.03
106 34 0.29
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (102 bp):
CCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGATGCCAACGCCATGTCCC
TGACATGGTCTTACGGGGGACCTCTCATACTCAAATG
Found at i:34767008 original size:24 final size:24
Alignment explanation
Indices: 34766980--34767026 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
34766970 GTCCATACAA
34766980 AGCTTCATAAGGGGCCATCTTCAG
1 AGCTTCATAAGGGGCCATCTTCAG
34767004 AGCTTCATAAGGGGCCATCTTCA
1 AGCTTCATAAGGGGCCATCTTCA
34767027 AACTCGACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (24 bp):
AGCTTCATAAGGGGCCATCTTCAG
Found at i:34770063 original size:13 final size:13
Alignment explanation
Indices: 34770045--34770108 Score: 110
Period size: 13 Copynumber: 4.9 Consensus size: 13
34770035 AGTTCTTCAT
34770045 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
34770058 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
* *
34770071 TACTTTTCAGAAG
1 TGCTTTTGAGAAG
34770084 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
34770097 TGCTTTTGAGAA
1 TGCTTTTGAGAA
34770109 ATTTGAGTGT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 47 1.00
ACGTcount: A:0.25, C:0.09, G:0.27, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:34770758 original size:44 final size:44
Alignment explanation
Indices: 34770710--34770803 Score: 170
Period size: 44 Copynumber: 2.1 Consensus size: 44
34770700 TATATTCAAT
*
34770710 AAATGATTTGGTTAATACAGTACTTATATTTGATAAGCATATGA
1 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
34770754 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
1 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
*
34770798 CAATGA
1 AAATGA
34770804 AAGTCGAGAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.37
Consensus pattern (44 bp):
AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
Found at i:34775034 original size:80 final size:81
Alignment explanation
Indices: 34774912--34775084 Score: 235
Period size: 80 Copynumber: 2.1 Consensus size: 81
34774902 GGTACTACAG
* *
34774912 TCATTCTACCCTAAAGGGGTATTTCAGTTATTGTACCCTATGGGGGTATTTCGGTCATTTTACCC
1 TCATTTTACCCTAAAGGGGTATTTCAGTTATTGTACCCTATGGGGGTATTTCGATCATTTTACCC
* *
34774977 TAT-GGGGTATTTCGT
66 AATGGGGGTATTTCGA
* * *
34774992 TCATTTTACCCTATAA-GGGTATTTC-GTTCATTTTACCTTATGGGGGTATTTCGATCATTTTAT
1 TCATTTTACCCTA-AAGGGGTATTTCAGTT-ATTGTACCCTATGGGGGTATTTCGATCATTTTAC
34775055 CCAATGGGGGTATTTCGA
64 CCAATGGGGGTATTTCGA
*
34775073 TCATTTGACCCT
1 TCATTTTACCCT
34775085 CTTGAAAGAT
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
79 3 0.04
80 55 0.67
81 24 0.29
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (81 bp):
TCATTTTACCCTAAAGGGGTATTTCAGTTATTGTACCCTATGGGGGTATTTCGATCATTTTACCC
AATGGGGGTATTTCGA
Found at i:34775044 original size:27 final size:27
Alignment explanation
Indices: 34774912--34775084 Score: 206
Period size: 27 Copynumber: 6.4 Consensus size: 27
34774902 GGTACTACAG
* **
34774912 TCATTCTACCCTAAAGGGGTATTTCAGT
1 TCATTTTACCCTATGGGGGTATTTC-GT
* *
34774940 T-ATTGTACCCTATGGGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGT
34774966 TCATTTTACCCTAT-GGGGTATTTCGT
1 TCATTTTACCCTATGGGGGTATTTCGT
**
34774992 TCATTTTACCCTATAAGGGTATTTCGT
1 TCATTTTACCCTATGGGGGTATTTCGT
* *
34775019 TCATTTTACCTTATGGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGT
* * *
34775046 TCATTTTATCCAATGGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGT
*
34775073 TCATTTGACCCT
1 TCATTTTACCCT
34775085 CTTGAAAGAT
Statistics
Matches: 126, Mismatches: 17, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
26 27 0.21
27 98 0.78
28 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCGT
Found at i:34778898 original size:65 final size:65
Alignment explanation
Indices: 34778794--34778923 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
34778784 TTATCTGATG
34778794 GTTTTGACCCCTATTCACTAGAAATAAATTATCTCATTGTACAAAATTTCTTATAATGTTCTTGT
1 GTTTTGACCCCTATTCACTAGAAATAAATTATCTCATTGTACAAAATTTCTTATAATGTTCTTGT
34778859 GTTTTGACCCCTATTCACTAGAAATAAATTATCTCATTGTACAAAATTTCTTATAATGTTCTTGT
1 GTTTTGACCCCTATTCACTAGAAATAAATTATCTCATTGTACAAAATTTCTTATAATGTTCTTGT
34778924 TTATTATTTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.43
Consensus pattern (65 bp):
GTTTTGACCCCTATTCACTAGAAATAAATTATCTCATTGTACAAAATTTCTTATAATGTTCTTGT
Found at i:34779965 original size:49 final size:50
Alignment explanation
Indices: 34779892--34780014 Score: 151
Period size: 49 Copynumber: 2.5 Consensus size: 50
34779882 ACATGCGAAA
* * *
34779892 GCCATGTCTCAGACATGGTTTTACATGGGATGTT-TCCTATA-CTACCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATATAGCTACCAAT
* * * * *
34779941 GCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATAGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATAGCTACCAAT
34779991 GCCATGTCCCAGACATGGTCTTAC
1 GCCATGTCCCAGACATGGTCTTAC
34780015 GGGGGACCTC
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
48 3 0.05
49 32 0.52
50 27 0.44
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATAGCTACCAAT
Found at i:34780009 original size:50 final size:50
Alignment explanation
Indices: 34779892--34780123 Score: 166
Period size: 50 Copynumber: 4.5 Consensus size: 50
34779882 ACATGCGAAA
* * * * *
34779892 GCCATGTCTCAGACATGGTTTTACATGGGATGTT-TCCTATA-CTACCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATATAGGTGCCAAT
* * *
34779941 GCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATAGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATAGGTGCCAAT
** ** * * * *
34779991 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTTATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATAGGTGCCAAT
* * * * *
34780041 GCCATGTCTCTGACATGGTCTTACGTGGAACCGCTCATAACCTCA-ATA-ATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGA--G-T--T---CTCATATAGGTGCCAAT
34780097 GCCATGTCCCAGACATGGTCTTACATG
1 GCCATGTCCCAGACATGGTCTTACATG
34780124 TGATCTCATC
Statistics
Matches: 140, Mismatches: 33, Indels: 13
0.75 0.18 0.07
Matches are distributed among these distances:
48 3 0.02
49 32 0.23
50 70 0.50
55 1 0.01
56 30 0.21
57 1 0.01
58 3 0.02
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.28
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATAGGTGCCAAT
Found at i:34785825 original size:43 final size:43
Alignment explanation
Indices: 34785733--34785828 Score: 131
Period size: 43 Copynumber: 2.2 Consensus size: 43
34785723 GGTGTGATTT
*
34785733 CATGTAAGACCATGTCTAGGACATTGGCATCGATATGAGACTA
1 CATGTAAGACCATGTCTAGGACAATGGCATCGATATGAGACTA
* * * *
34785776 CGTGTAAGACCTTGTGTAGGACAATGGCATCGATATGTGA-TAA
1 CATGTAAGACCATGTCTAGGACAATGGCATCGATATGAGACT-A
34785819 CATGTAAGAC
1 CATGTAAGAC
34785829 TATATCTGGG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 1 0.02
43 45 0.98
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (43 bp):
CATGTAAGACCATGTCTAGGACAATGGCATCGATATGAGACTA
Found at i:34791364 original size:15 final size:15
Alignment explanation
Indices: 34791344--34791373 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
34791334 TATGACAAAA
34791344 TTGCTAAAGTGTTTT
1 TTGCTAAAGTGTTTT
34791359 TTGCTAAAGTGTTTT
1 TTGCTAAAGTGTTTT
34791374 GGCATGAATG
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:0.20, C:0.07, G:0.20, T:0.53
Consensus pattern (15 bp):
TTGCTAAAGTGTTTT
Found at i:34793608 original size:19 final size:19
Alignment explanation
Indices: 34793584--34793620 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
34793574 TTTATAACTG
*
34793584 AAAAAATAATGTTGTTATA
1 AAAAAATAATGTTATTATA
34793603 AAAAAATAATGTTATTAT
1 AAAAAATAATGTTATTAT
34793621 TATGTGCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (19 bp):
AAAAAATAATGTTATTATA
Done.