Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 152 of 279
Found at i:49471539 original size:15 final size:16
Alignment explanation
Indices: 49471511--49471544 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
49471501 TAATAAATTG
49471511 AAAAATAAAGTATTAA
1 AAAAATAAAGTATTAA
49471527 AAAAATAAA-TATTAA
1 AAAAATAAAGTATTAA
49471542 AAA
1 AAA
49471545 TTTAAGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
AAAAATAAAGTATTAA
Found at i:49471554 original size:15 final size:15
Alignment explanation
Indices: 49471511--49471555 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
49471501 TAATAAATTG
49471511 AAAAATAAAGTATTAA
1 AAAAAT-AAGTATTAA
*
49471527 AAAAATAAATATTAA
1 AAAAATAAGTATTAA
**
49471542 AAATTTAAGTATTA
1 AAAAATAAGTATTA
49471556 GATTTAAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 19 0.76
16 6 0.24
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (15 bp):
AAAAATAAGTATTAA
Found at i:49472034 original size:18 final size:19
Alignment explanation
Indices: 49472013--49472057 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
49472003 TTAGATTAAT
*
49472013 AAAATTTTAATAAT-ATTA
1 AAAATTTAAATAATAATTA
*
49472031 AAAATTTAAATCATAATTA
1 AAAATTTAAATAATAATTA
49472050 AAACATTT
1 AAA-ATTT
49472058 GTACTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 12 0.52
19 7 0.30
20 4 0.17
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATTTAAATAATAATTA
Found at i:49477332 original size:46 final size:46
Alignment explanation
Indices: 49477282--49478193 Score: 1686
Period size: 46 Copynumber: 19.8 Consensus size: 46
49477272 TGGTTGAGCA
49477282 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
49477328 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
49477374 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
49477420 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
49477466 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
49477512 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
49477558 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
49477604 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
49477650 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
49477696 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
49477742 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
49477788 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
49477834 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
49477880 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
49477926 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
49477972 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
49478018 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*** * *
49478064 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA--
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAATG
* *
49478111 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
49478157 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
49478194 GCGGGTTACA
Statistics
Matches: 847, Mismatches: 12, Indels: 14
0.97 0.01 0.02
Matches are distributed among these distances:
43 1 0.00
44 3 0.00
45 1 0.00
46 805 0.95
47 32 0.04
48 1 0.00
49 3 0.00
50 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:49490236 original size:39 final size:39
Alignment explanation
Indices: 49490182--49490372 Score: 208
Period size: 39 Copynumber: 4.9 Consensus size: 39
49490172 TTCAGTGATG
* *
49490182 TATATCCGGACTTAGGGTCCGCAGGCTATGTGTTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
*
49490221 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* *
49490260 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* * * * * *
49490299 TATGTCCGGGCTAAAGTTCCGCAGGCT-TCGAGCTGGTAT
1 TATATCCGGACTTAAGGTCCGCAGGCTAT-GTGCTGGAAT
** **
49490338 TATA-CCGGGTTTAAATTCCCGCAGGCT-TGTGCTGG
1 TATATCCGGACTTAAGGT-CCGCAGGCTATGTGCTGG
49490373 TATTTGGATT
Statistics
Matches: 133, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
38 16 0.12
39 117 0.88
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.28
Consensus pattern (39 bp):
TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
Found at i:49493013 original size:21 final size:21
Alignment explanation
Indices: 49492987--49493114 Score: 114
Period size: 21 Copynumber: 6.0 Consensus size: 21
49492977 ATAAAAATAT
49492987 TCAGGCACCTCGTGTGTCGTA
1 TCAGGCACCTCGTGTGTCGTA
* *
49493008 TCAGGCACTTCGTGTGTCGTT
1 TCAGGCACCTCGTGTGTCGTA
* ** **
49493029 TTAGGCATTTTATGTGTCGTA
1 TCAGGCACCTCGTGTGTCGTA
* *
49493050 TTTCAGGCACCTTGTGTGTTGTA
1 --TCAGGCACCTCGTGTGTCGTA
*
49493073 TCAGGCACCTCGTGTGTCGTT
1 TCAGGCACCTCGTGTGTCGTA
* **
49493094 TCAAGCA-CTTATGTGTCGTA
1 TCAGGCACCTCGTGTGTCGTA
49493114 T
1 T
49493115 ACTGATCAGG
Statistics
Matches: 86, Mismatches: 19, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
20 11 0.13
21 59 0.69
23 16 0.19
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (21 bp):
TCAGGCACCTCGTGTGTCGTA
Found at i:49493076 original size:65 final size:64
Alignment explanation
Indices: 49492986--49493114 Score: 195
Period size: 65 Copynumber: 2.0 Consensus size: 64
49492976 TATAAAAATA
* * * *
49492986 TTCAGGCACCTCGTGTGTCGTATCAGGCACTTCGTGTGTCGTTTTAGGCATTTTATGTGTCGTAT
1 TTCAGGCACCTCGTGTGTCGTATCAGGCACCTCGTGTGTCGTTTCAAGCA-CTTATGTGTCGTAT
* *
49493051 TTCAGGCACCTTGTGTGTTGTATCAGGCACCTCGTGTGTCGTTTCAAGCACTTATGTGTCGTAT
1 TTCAGGCACCTCGTGTGTCGTATCAGGCACCTCGTGTGTCGTTTCAAGCACTTATGTGTCGTAT
49493115 ACTGATCAGG
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
64 13 0.22
65 45 0.78
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.39
Consensus pattern (64 bp):
TTCAGGCACCTCGTGTGTCGTATCAGGCACCTCGTGTGTCGTTTCAAGCACTTATGTGTCGTAT
Found at i:49493089 original size:44 final size:42
Alignment explanation
Indices: 49492987--49493114 Score: 125
Period size: 44 Copynumber: 3.0 Consensus size: 42
49492977 ATAAAAATAT
*
49492987 TCAGGCACCTCGTGTGTCGTATCAGGCACTTCGTGTGTCGTT
1 TCAGGCACCTCGTGTGTCGTATCAGGCACTTCGTGTGTCGTA
* ** ** *
49493029 TTAGGCATTTTATGTGTCGTATTTCAGGCACCTT-GTGTGTTGTA
1 TCAGGCACCTCGTGTGTCGTA--TCAGGCA-CTTCGTGTGTCGTA
* * *
49493073 TCAGGCACCTCGTGTGTCGTTTCAAGCACTT-ATGTGTCGTA
1 TCAGGCACCTCGTGTGTCGTATCAGGCACTTCGTGTGTCGTA
49493114 T
1 T
49493115 ACTGATCAGG
Statistics
Matches: 67, Mismatches: 16, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
41 12 0.18
42 22 0.33
44 30 0.45
45 3 0.04
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (42 bp):
TCAGGCACCTCGTGTGTCGTATCAGGCACTTCGTGTGTCGTA
Found at i:49495785 original size:34 final size:34
Alignment explanation
Indices: 49495707--49495787 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
49495697 TTTATATAAA
* * *
49495707 AATATATATTATATACTATATTAACTTAATATTT
1 AATATATAATATATAATATATTAACTTAATATAT
*
49495741 AAGTAT-TAATATATAATATATTATA-TTATTATAT
1 AA-TATATAATATATAATATATTA-ACTTAATATAT
49495775 AATATATAATATA
1 AATATATAATATA
49495788 ATATATAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
33 3 0.08
34 33 0.82
35 4 0.10
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (34 bp):
AATATATAATATATAATATATTAACTTAATATAT
Found at i:49495793 original size:7 final size:7
Alignment explanation
Indices: 49495707--49495795 Score: 64
Period size: 7 Copynumber: 13.3 Consensus size: 7
49495697 TTTATATAAA
49495707 AATATAT
1 AATATAT
*
49495714 ATTATAT
1 AATATAT
*
49495721 ACTATATT
1 AATATA-T
*
49495729 AA-CT-T
1 AATATAT
*
49495734 AATATTT
1 AATATAT
49495741 AAGTAT-T
1 AA-TATAT
49495748 AATATAT
1 AATATAT
49495755 AATATAT
1 AATATAT
*
49495762 TATAT-T
1 AATATAT
*
49495768 ATTATAT
1 AATATAT
49495775 AATATAT
1 AATATAT
49495782 -A-ATAT
1 AATATAT
49495787 AATATAT
1 AATATAT
49495794 AA
1 AA
49495796 AACATAAAGT
Statistics
Matches: 65, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
5 7 0.11
6 10 0.15
7 43 0.66
8 5 0.08
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (7 bp):
AATATAT
Found at i:49496959 original size:29 final size:31
Alignment explanation
Indices: 49496922--49496979 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
49496912 CTAGCGCGCT
49496922 TTCTGATTATTAGCACATT-AGTGCTCTCCG
1 TTCTGATTATTAGCACATTAAGTGCTCTCCG
*
49496952 TTCT-ATTATTAGCACGTTAAGTGCTCTC
1 TTCTGATTATTAGCACATTAAGTGCTCTC
49496980 TGTTTAGCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (31 bp):
TTCTGATTATTAGCACATTAAGTGCTCTCCG
Found at i:49499508 original size:47 final size:47
Alignment explanation
Indices: 49499392--49499524 Score: 162
Period size: 46 Copynumber: 2.9 Consensus size: 47
49499382 ATAATCTCAC
* * *
49499392 CCATAATGAACTCGGAACGCAACTCAATGAGCTCGGGTG-TTCGCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTCGCAT
* * * *
49499438 TCATAATAAACTTGGAACACAACTCAACGAGTTCGGATGCTT-GCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTCGCAT
* *
49499484 CCATAGGTGAACTCGGAACGCAACTCAACGTGTTCGGATGC
1 CCATA-ATGAACTCGGAACGCAACTCAACGAGTTCGGATGC
49499525 CTCATAATTC
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
46 40 0.56
47 32 0.44
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (47 bp):
CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTCGCAT
Found at i:49507721 original size:19 final size:21
Alignment explanation
Indices: 49507683--49507723 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
49507673 ATGGAGGTCT
49507683 TCAATCTTTGAATATATAAAA
1 TCAATCTTTGAATATATAAAA
*
49507704 TCAA-CTTT-AATGTATAAAA
1 TCAATCTTTGAATATATAAAA
49507723 T
1 T
49507724 TTTGATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 4 0.21
21 4 0.21
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (21 bp):
TCAATCTTTGAATATATAAAA
Found at i:49511362 original size:24 final size:25
Alignment explanation
Indices: 49511333--49511388 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
49511323 TGTGTCATAC
* *
49511333 TATTATTCATTGATGGTGCATTAAA
1 TATTATTCAGTGATAGTGCATTAAA
*
49511358 T-TTATGCAGTGATAGTGCATTAAA
1 TATTATTCAGTGATAGTGCATTAAA
49511382 TATTATT
1 TATTATT
49511389 TCTATTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.45
Consensus pattern (25 bp):
TATTATTCAGTGATAGTGCATTAAA
Found at i:49514560 original size:12 final size:12
Alignment explanation
Indices: 49514543--49514567 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49514533 TGCTGATAGT
49514543 AAAAAACAAAAA
1 AAAAAACAAAAA
49514555 AAAAAACAAAAA
1 AAAAAACAAAAA
49514567 A
1 A
49514568 TTAAGACGAA
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:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAACAAAAA
Found at i:49515420 original size:18 final size:18
Alignment explanation
Indices: 49515399--49515440 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
49515389 CATACATGAC
49515399 ATGCAAAACATAATAAAA
1 ATGCAAAACATAATAAAA
* *
49515417 ATGCAGAACATAATAGAA
1 ATGCAAAACATAATAAAA
49515435 ATGCAA
1 ATGCAA
49515441 CAATTGAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.17
Consensus pattern (18 bp):
ATGCAAAACATAATAAAA
Found at i:49530354 original size:29 final size:28
Alignment explanation
Indices: 49530321--49530390 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 28
49530311 TATTTGAAAT
49530321 TTTTTATTTAAATAATTGAA-CTATTAAAG
1 TTTTTATTTAAATAATT-AAGCTATT-AAG
* * *
49530350 TTTTTATTTAAGTCATTAAGCTATTAAT
1 TTTTTATTTAAATAATTAAGCTATTAAG
*
49530378 TTTTTTTTTAAAT
1 TTTTTATTTAAAT
49530391 CTAGCTAGCA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 15 0.43
29 20 0.57
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (28 bp):
TTTTTATTTAAATAATTAAGCTATTAAG
Found at i:49530704 original size:29 final size:29
Alignment explanation
Indices: 49530633--49530697 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
49530623 ACAAATAGAG
*
49530633 AATGTCATAAAATATCGATTTTTACAATT
1 AATGACATAAAATATCGATTTTTACAATT
* *
49530662 AATGTCATAAAATATCGATTTTTACAGTT
1 AATGACATAAAATATCGATTTTTACAATT
49530691 CAATGAC
1 -AATGAC
49530698 TTGAATAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
29 28 0.85
30 5 0.15
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.38
Consensus pattern (29 bp):
AATGACATAAAATATCGATTTTTACAATT
Found at i:49539946 original size:29 final size:28
Alignment explanation
Indices: 49539913--49539969 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
49539903 TTAAGGGACT
*
49539913 CCCAAGTTGCATCTTTAGGGAAAGAGTC
1 CCCAAGTTGCATCTTCAGGGAAAGAGTC
*
49539941 NCCCAAGTTGCGTCTTCAGGGAAAGAGTC
1 -CCCAAGTTGCATCTTCAGGGAAAGAGTC
49539970 TACCCATTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.23
Consensus pattern (28 bp):
CCCAAGTTGCATCTTCAGGGAAAGAGTC
Found at i:49543563 original size:8 final size:9
Alignment explanation
Indices: 49543530--49543562 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
49543520 ATAGAAGATA
49543530 TTTTTTTAT
1 TTTTTTTAT
49543539 TTTTTTTAT
1 TTTTTTTAT
49543548 TTTTTTTAT
1 TTTTTTTAT
49543557 TATTTT
1 T-TTTT
49543563 AGGATTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 19 0.83
10 4 0.17
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:49562768 original size:59 final size:59
Alignment explanation
Indices: 49562699--49562817 Score: 220
Period size: 59 Copynumber: 2.0 Consensus size: 59
49562689 AAACGCAACA
*
49562699 TATACTTATTCCATTACTTCAATTCCTTTATTTTATCTACCTTTCAATTTTTCTATAGT
1 TATACATATTCCATTACTTCAATTCCTTTATTTTATCTACCTTTCAATTTTTCTATAGT
*
49562758 TATACATATTCCATTACTTCAATTCCTTTATTTTATCTGCCTTTCAATTTTTCTATAGT
1 TATACATATTCCATTACTTCAATTCCTTTATTTTATCTACCTTTCAATTTTTCTATAGT
49562817 T
1 T
49562818 TTACTCTCAG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.24, C:0.20, G:0.03, T:0.54
Consensus pattern (59 bp):
TATACATATTCCATTACTTCAATTCCTTTATTTTATCTACCTTTCAATTTTTCTATAGT
Found at i:49565409 original size:30 final size:30
Alignment explanation
Indices: 49565373--49565429 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
49565363 CCCAGTTGTC
*
49565373 TTTTTTTTTTTTTTTTTTGTGGGGGGGTTT
1 TTTTTTTTTTTTTTTTTTGGGGGGGGGTTT
49565403 TTTTTTTTTTTTTTTTTTGGGGGGGGG
1 TTTTTTTTTTTTTTTTTTGGGGGGGGG
49565430 GAGGGGGGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.30, T:0.70
Consensus pattern (30 bp):
TTTTTTTTTTTTTTTTTTGGGGGGGGGTTT
Found at i:49565413 original size:28 final size:28
Alignment explanation
Indices: 49565373--49565427 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
49565363 CCCAGTTGTC
49565373 TTTTTTTTTTTTTTTTTTGTGGGGGGGT
1 TTTTTTTTTTTTTTTTTTGTGGGGGGGT
*
49565401 TTTTTTTTTTTTTTTTTTTTGGGGGGG
1 TTTTTTTTTTTTTTTTTTGTGGGGGGG
49565428 GGGAGGGGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.27, T:0.73
Consensus pattern (28 bp):
TTTTTTTTTTTTTTTTTTGTGGGGGGGT
Found at i:49571236 original size:16 final size:16
Alignment explanation
Indices: 49571215--49571266 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
49571205 TTTGGTTCGC
49571215 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
49571231 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
49571247 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
49571263 TGTA
1 TGTA
49571267 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:49571524 original size:18 final size:17
Alignment explanation
Indices: 49571503--49571537 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
49571493 TTATTATTTA
*
49571503 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
49571521 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
49571538 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:49571531 original size:28 final size:27
Alignment explanation
Indices: 49571461--49571533 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
49571451 TTTATTATCA
*
49571461 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
49571489 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
49571516 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
49571534 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:49573143 original size:19 final size:19
Alignment explanation
Indices: 49573114--49573179 Score: 123
Period size: 19 Copynumber: 3.4 Consensus size: 19
49573104 CAACTACACA
49573114 AATTCACAATGTAACCTACT
1 AATT-ACAATGTAACCTACT
49573134 AATTACAATGTAACCTACT
1 AATTACAATGTAACCTACT
49573153 AATTACAATGTAACCTACT
1 AATTACAATGTAACCTACT
49573172 AATTACAA
1 AATTACAA
49573180 CTTCGACCTA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
19 42 0.91
20 4 0.09
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.30
Consensus pattern (19 bp):
AATTACAATGTAACCTACT
Found at i:49573892 original size:14 final size:14
Alignment explanation
Indices: 49573867--49573901 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
49573857 AAGAAGAAGC
49573867 AGAAATATGGAGAAA
1 AGAAA-ATGGAGAAA
49573882 AGAAAATGGAGAAA
1 AGAAAATGGAGAAA
49573896 AGAAAA
1 AGAAAA
49573902 GAAATGTGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.66, C:0.00, G:0.26, T:0.09
Consensus pattern (14 bp):
AGAAAATGGAGAAA
Found at i:49573899 original size:19 final size:18
Alignment explanation
Indices: 49573877--49573921 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
49573867 AGAAATATGG
49573877 AGAAAAGAAAATG-GAGAAA
1 AGAAAAGAAAATGTGAG--A
49573896 AGAAAAG-AAATGTGAGA
1 AGAAAAGAAAATGTGAGA
49573913 AGAAAAGAA
1 AGAAAAGAA
49573922 GCGTACCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.33
18 6 0.25
19 10 0.42
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (18 bp):
AGAAAAGAAAATGTGAGA
Found at i:49578170 original size:48 final size:48
Alignment explanation
Indices: 49578114--49578211 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
49578104 CACAGGCGAT
49578114 GAAGAACAATCAAATCAATTGTTGGCGAATGGACATTGTGGCGAAGAG
1 GAAGAACAATCAAATCAATTGTTGGCGAATGGACATTGTGGCGAAGAG
49578162 GAAGAACAATCAAATCAATTGTTGGCGAATGGACATTGTGGCGAAGAG
1 GAAGAACAATCAAATCAATTGTTGGCGAATGGACATTGTGGCGAAGAG
49578210 GA
1 GA
49578212 TTCTCTCATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.38, C:0.12, G:0.30, T:0.20
Consensus pattern (48 bp):
GAAGAACAATCAAATCAATTGTTGGCGAATGGACATTGTGGCGAAGAG
Found at i:49582370 original size:39 final size:39
Alignment explanation
Indices: 49582316--49582390 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
49582306 GGCATGTTCA
49582316 TTCAAGGTCAACATTTTTACTCTCCTCTCAATTTAATAT
1 TTCAAGGTCAACATTTTTACTCTCCTCTCAATTTAATAT
*
49582355 TTCAAGGTCAACATTTTTACTCTCTTCTCAATTTAA
1 TTCAAGGTCAACATTTTTACTCTCCTCTCAATTTAA
49582391 CATTCTTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.44
Consensus pattern (39 bp):
TTCAAGGTCAACATTTTTACTCTCCTCTCAATTTAATAT
Found at i:49591528 original size:20 final size:20
Alignment explanation
Indices: 49591503--49591542 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
49591493 CGTAAAATGA
*
49591503 TTTCTGTAAAATGTTTTACT
1 TTTCTGTAAAATGATTTACT
49591523 TTTCTGTAAAATGATTTACT
1 TTTCTGTAAAATGATTTACT
49591543 GAAAAATATT
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:0.28, C:0.10, G:0.10, T:0.53
Consensus pattern (20 bp):
TTTCTGTAAAATGATTTACT
Found at i:49591532 original size:34 final size:35
Alignment explanation
Indices: 49591488--49591554 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
49591478 CAGTAAAATA
* *
49591488 TTTTCCGTAAAATGATTT-CTGTAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
*
49591522 TTTTCTGTAAAATGATTTACTGAAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
49591555 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.10, T:0.48
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:49591773 original size:25 final size:25
Alignment explanation
Indices: 49591745--49591838 Score: 75
Period size: 26 Copynumber: 3.7 Consensus size: 25
49591735 ATATTAATCG
49591745 TTATAAATTGAAAAAAAATACATTC
1 TTATAAATTGAAAAAAAATACATTC
* * * * *
49591770 TTAT-TATT-AAACTACAATATTAATC
1 TTATAAATTGAAA-AAAAATA-CATTC
49591795 GTTATAAATTGAAAAAAAATACATTC
1 -TTATAAATTGAAAAAAAATACATTC
* *
49591821 TTATTAGTTAGAAAAAAA
1 TTATAAATT-GAAAAAAA
49591839 GTGAAGAGAA
Statistics
Matches: 51, Mismatches: 12, Indels: 11
0.69 0.16 0.15
Matches are distributed among these distances:
23 3 0.06
24 8 0.16
25 14 0.27
26 15 0.29
27 8 0.16
28 3 0.06
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.35
Consensus pattern (25 bp):
TTATAAATTGAAAAAAAATACATTC
Found at i:49591782 original size:51 final size:51
Alignment explanation
Indices: 49591721--49591826 Score: 212
Period size: 51 Copynumber: 2.1 Consensus size: 51
49591711 ATAATACTCA
49591721 ATTATTAAACTACAATATTAATCGTTATAAATTGAAAAAAAATACATTCTT
1 ATTATTAAACTACAATATTAATCGTTATAAATTGAAAAAAAATACATTCTT
49591772 ATTATTAAACTACAATATTAATCGTTATAAATTGAAAAAAAATACATTCTT
1 ATTATTAAACTACAATATTAATCGTTATAAATTGAAAAAAAATACATTCTT
49591823 ATTA
1 ATTA
49591827 GTTAGAAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (51 bp):
ATTATTAAACTACAATATTAATCGTTATAAATTGAAAAAAAATACATTCTT
Found at i:49592445 original size:109 final size:111
Alignment explanation
Indices: 49592132--49592461 Score: 637
Period size: 111 Copynumber: 3.0 Consensus size: 111
49592122 GATGAAGTAT
49592132 TGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAAT
1 TGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAAT
49592197 GTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATGA
66 GTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATGA
49592243 TGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAAT
1 TGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAAT
49592308 GTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATGA
66 GTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATGA
*
49592354 TGTTGTCT-A-AGAGAGAGCAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAAT
1 TGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAAT
49592417 GTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
66 GTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
49592462 CATGGTATTG
Statistics
Matches: 218, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
109 98 0.45
110 1 0.00
111 119 0.55
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (111 bp):
TGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAAT
GTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATGA
Found at i:49609216 original size:23 final size:22
Alignment explanation
Indices: 49609175--49609218 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
49609165 TACTCAATTA
49609175 AATAAAGAATAATTATTTAAAT
1 AATAAAGAATAATTATTTAAAT
49609197 AATAAA-AATATATATATTTAAA
1 AATAAAGAATA-AT-TATTTAAA
49609219 AGTTGAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 8 0.40
23 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
AATAAAGAATAATTATTTAAAT
Found at i:49610285 original size:52 final size:52
Alignment explanation
Indices: 49610205--49610304 Score: 191
Period size: 52 Copynumber: 1.9 Consensus size: 52
49610195 TACTATATTG
49610205 TTCAATCTTATTTGTCGAATTTAGTGATCTCAAATCACCATTTCCGACCTTT
1 TTCAATCTTATTTGTCGAATTTAGTGATCTCAAATCACCATTTCCGACCTTT
*
49610257 TTCAATCTTATTTGTCGAATTTATTGATCTCAAATCACCATTTCCGAC
1 TTCAATCTTATTTGTCGAATTTAGTGATCTCAAATCACCATTTCCGAC
49610305 ACCACTGAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (52 bp):
TTCAATCTTATTTGTCGAATTTAGTGATCTCAAATCACCATTTCCGACCTTT
Found at i:49616131 original size:40 final size:40
Alignment explanation
Indices: 49615934--49616117 Score: 198
Period size: 40 Copynumber: 4.6 Consensus size: 40
49615924 CGAATGATGT
* * * * *
49615934 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAATGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
49615974 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
49616014 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
49616052 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
49616093 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
49616118 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 14, Indels: 14
0.81 0.09 0.09
Matches are distributed among these distances:
39 34 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:49616139 original size:79 final size:79
Alignment explanation
Indices: 49615986--49616150 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
49615976 GGACTAAGAT
* **
49615986 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
49616051 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
49616065 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
49616128 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
49616144 CCGAAGG
1 CCGAAGG
49616151 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.65
80 24 0.32
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:49617574 original size:4 final size:4
Alignment explanation
Indices: 49617565--49617593 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
49617555 AGCAAACGTG
49617565 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
49617594 TAGAAAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:49620348 original size:52 final size:53
Alignment explanation
Indices: 49620255--49620404 Score: 187
Period size: 52 Copynumber: 2.8 Consensus size: 53
49620245 CTTACACGGT
* * *
49620255 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTTTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
49620310 TCACATTATACCGATGCCATA-CCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** * *
49620362 TCACATTGCACCGATGCCATAGCCAAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
49620405 GCACACTTAT
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
51 1 0.01
52 46 0.53
53 32 0.37
54 1 0.01
55 6 0.07
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.27
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:49620415 original size:52 final size:52
Alignment explanation
Indices: 49620286--49620419 Score: 173
Period size: 52 Copynumber: 2.6 Consensus size: 52
49620276 TATCCCAGAC
* * * * *
49620286 ATGGTTTTATACGGAATCACATTATCACATTATACCGATGCCATACCCAGCT
1 ATGGTCTTAAACGGAGTCACATTATCACATTACACCGATGCCATACCAAGCT
* *
49620338 ATGGTCTTATACGGAGTCACATTATCACATTGCACCGATGCCATAGCCAAGCT
1 ATGGTCTTAAACGGAGTCACATTATCACATTACACCGATGCCATA-CCAAGCT
49620391 ATGGTCTTAAACGG-G-CACACTTATCACAT
1 ATGGTCTTAAACGGAGTCACA-TTATCACAT
49620420 ATTTTTCGTC
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
51 4 0.05
52 51 0.69
53 19 0.26
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28
Consensus pattern (52 bp):
ATGGTCTTAAACGGAGTCACATTATCACATTACACCGATGCCATACCAAGCT
Found at i:49627854 original size:53 final size:53
Alignment explanation
Indices: 49627773--49627923 Score: 205
Period size: 53 Copynumber: 2.8 Consensus size: 53
49627763 CTTACACGGT
* * *
49627773 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTTTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
49627828 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
49627881 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
49627924 GCACACTTAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
52 1 0.01
53 80 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:49633778 original size:56 final size:56
Alignment explanation
Indices: 49633692--49633811 Score: 240
Period size: 56 Copynumber: 2.1 Consensus size: 56
49633682 ACAAGGGATG
49633692 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
49633748 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
49633804 ATGGGCAA
1 ATGGGCAA
49633812 TAAACTAATA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 64 1.00
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
Found at i:49635179 original size:40 final size:40
Alignment explanation
Indices: 49634941--49635165 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
49634931 TCGAATGATG
* * * * *
49634941 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAATGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
49634981 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
49635021 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
49635060 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
49635100 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
49635141 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
49635166 AACGAGTAGC
Statistics
Matches: 164, Mismatches: 16, Indels: 10
0.86 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 120 0.73
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:49636622 original size:4 final size:4
Alignment explanation
Indices: 49636613--49637393 Score: 1562
Period size: 4 Copynumber: 195.2 Consensus size: 4
49636603 AGCAAACGTG
49636613 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
49636661 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
49636709 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
49636757 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
49636805 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
49636853 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
49636901 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
49636949 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
49636997 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
49637045 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
49637093 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
49637141 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
49637189 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
49637237 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
49637285 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
49637333 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
49637381 AGAA AGAA AGAA A
1 AGAA AGAA AGAA A
49637394 TAGAAAAGGG
Statistics
Matches: 777, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 777 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:49637870 original size:27 final size:27
Alignment explanation
Indices: 49637839--49637892 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
49637829 ACAATTCAAA
*
49637839 CATACCTGAATTAGATATATATTCATT
1 CATACCTGAATCAGATATATATTCATT
49637866 CATACCTGAATCAGATATATATTCATT
1 CATACCTGAATCAGATATATATTCATT
49637893 TATTCATTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (27 bp):
CATACCTGAATCAGATATATATTCATT
Found at i:49638081 original size:42 final size:42
Alignment explanation
Indices: 49637973--49638132 Score: 142
Period size: 43 Copynumber: 3.7 Consensus size: 42
49637963 AGCATATACA
* *** * * *
49637973 ATGCCAACGTCCCAGGTGTGGTCTTACATGTAATCAAACATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGAAATCAGA-ATCG
* *
49638016 ATGCCACTGTCCCAGACAGGGTCTTACACGAAATCAG-ATACG
1 ATGCCAATGTCCCAGACATGGTCTTACACGAAATCAGAAT-CG
* **
49638058 ATGCCAATGTCCCAAACATGGTCTTACACGTAAAAAAGAAGTCG
1 ATGCCAATGTCCCAGACATGGTCTTACACG-AAATCAGAA-TCG
* **
49638102 ATGCCAACGTCCCAGATGTGGTCTTACACGA
1 ATGCCAATGTCCCAGACATGGTCTTACACGA
49638133 TAACACATAC
Statistics
Matches: 95, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
41 2 0.02
42 29 0.31
43 34 0.36
44 29 0.31
45 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGAAATCAGAATCG
Found at i:49638114 original size:44 final size:41
Alignment explanation
Indices: 49637973--49638132 Score: 133
Period size: 42 Copynumber: 3.8 Consensus size: 41
49637963 AGCATATACA
*** * * *
49637973 ATGCCAACGTCCCAGGTGTGGTCTTACATGTAATCAAACATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACG-AA-AAAAGATCG
* **
49638016 ATGCC-ACTGTCCCAGACAGGGTCTTACACGAAATCAGATACG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGAAAAAAGAT-CG
* *
49638058 ATGCCAATGTCCCAAACATGGTCTTACACGTAAAAAAGAAGTCG
1 ATGCCAACGTCCCAGACATGGTCTTACACG-AAAAAAG-A-TCG
**
49638102 ATGCCAACGTCCCAGATGTGGTCTTACACGA
1 ATGCCAACGTCCCAGACATGGTCTTACACGA
49638133 TAACACATAC
Statistics
Matches: 93, Mismatches: 18, Indels: 12
0.76 0.15 0.10
Matches are distributed among these distances:
41 3 0.03
42 31 0.33
43 29 0.31
44 29 0.31
45 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (41 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGAAAAAAGATCG
Found at i:49639251 original size:24 final size:24
Alignment explanation
Indices: 49639223--49639274 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
49639213 TTCGTAGGTC
* * *
49639223 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTATACTAACAAATACT
*
49639247 AAATATATTATACTAACAAATACT
1 AAATAAATTATACTAACAAATACT
49639271 AAAT
1 AAAT
49639275 CTTTTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAACAAATACT
Found at i:49649085 original size:18 final size:18
Alignment explanation
Indices: 49649041--49649087 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
49649031 TGTTTTTCAC
* *
49649041 TGTGAACACTACTCTAAG
1 TGTGAACACTCCTCCAAG
*
49649059 TAT-AGACACTCCTCCAAG
1 TGTGA-ACACTCCTCCAAG
49649077 TGTGAACACTC
1 TGTGAACACTC
49649088 TTTTTGAGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
17 1 0.04
18 21 0.91
19 1 0.04
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (18 bp):
TGTGAACACTCCTCCAAG
Found at i:49653292 original size:5 final size:5
Alignment explanation
Indices: 49653282--49653309 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
49653272 CACTTATTGC
49653282 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
49653310 TACTTAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:49653316 original size:15 final size:15
Alignment explanation
Indices: 49653283--49653316 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
49653273 ACTTATTGCT
*
49653283 TTAATTTAATTTAAT
1 TTAATTTAATTTAAC
*
49653298 TTAATTTAATTTTAC
1 TTAATTTAATTTAAC
49653313 TTAA
1 TTAA
49653317 AACACTTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
TTAATTTAATTTAAC
Found at i:49654483 original size:131 final size:132
Alignment explanation
Indices: 49654272--49654517 Score: 282
Period size: 131 Copynumber: 1.9 Consensus size: 132
49654262 GATACTTGGT
* * * ** *
49654272 AATTCGCGGAATCGTACCCTAACGTGTTGGGTTGCAATTTCTCGTTTGCTCAAAGTAATCGAAGG
1 AATTCGCGGAATCATACCCTAACGAGCTGGGTTGCAATTTCTCGTTTGCTCAAAACAATCGAAGA
*
49654337 TCCCTTTAGAATTTCACCCGTGTCTT-CTAAAAATCCTTT-AAAACGAAGGCAATATTCGGTGTT
66 TCCCTTTAGAATTTCACCCATGT-TTACTAAAAA-CCTTTCAAAACGAAGGCAATATTCGGTGTT
49654400 TAAC
129 TAAC
* * ** * *
49654404 AATTCG-GGAATCATGCCCTATCGAGCTGGGTTGTGATTTCTCGTTTGCTCAAAACAATCTAATA
1 AATTCGCGGAATCATACCCTAACGAGCTGGGTTGCAATTTCTCGTTTGCTCAAAACAATCGAAGA
* ** ** *
49654468 TTCCTTTAGGTTTTCATTCATGTTTATTAAAAACCTTTCAAAACGAAGGC
66 TCCCTTTAGAATTTCACCCATGTTTACTAAAAACCTTTCAAAACGAAGGC
49654518 GATGTCCGAT
Statistics
Matches: 93, Mismatches: 19, Indels: 5
0.79 0.16 0.04
Matches are distributed among these distances:
130 7 0.08
131 80 0.86
132 6 0.06
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (132 bp):
AATTCGCGGAATCATACCCTAACGAGCTGGGTTGCAATTTCTCGTTTGCTCAAAACAATCGAAGA
TCCCTTTAGAATTTCACCCATGTTTACTAAAAACCTTTCAAAACGAAGGCAATATTCGGTGTTTA
AC
Found at i:49656147 original size:5 final size:5
Alignment explanation
Indices: 49656137--49656188 Score: 72
Period size: 5 Copynumber: 10.6 Consensus size: 5
49656127 CATGCATTTA
*
49656137 CATTG CATTG CATTG CATTG CATTG CA-T- CATTTG CATAG CATTG CATTG
1 CATTG CATTG CATTG CATTG CATTG CATTG CA-TTG CATTG CATTG CATTG
49656186 CAT
1 CAT
49656189 CATTTGCATT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
3 2 0.05
4 1 0.02
5 37 0.88
6 2 0.05
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.38
Consensus pattern (5 bp):
CATTG
Found at i:49656173 original size:24 final size:24
Alignment explanation
Indices: 49656144--49656198 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
49656134 TTACATTGCA
49656144 TTGCATTGCATTGCATTGCATCAT
1 TTGCATTGCATTGCATTGCATCAT
*
49656168 TTGCATAGCATTGCATTGCATCAT
1 TTGCATTGCATTGCATTGCATCAT
49656192 TTGCATT
1 TTGCATT
49656199 AAATTTCCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (24 bp):
TTGCATTGCATTGCATTGCATCAT
Found at i:49656600 original size:14 final size:14
Alignment explanation
Indices: 49656581--49656625 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
49656571 TTCAAGTGCA
49656581 TTGCATTGCATCAT
1 TTGCATTGCATCAT
*
49656595 TTGCA-T--AGCA-
1 TTGCATTGCATCAT
49656605 TTGCATTGCATCAT
1 TTGCATTGCATCAT
49656619 TTGCATT
1 TTGCATT
49656626 AAATTTCCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
10 5 0.20
11 4 0.16
13 4 0.16
14 12 0.48
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (14 bp):
TTGCATTGCATCAT
Found at i:49656610 original size:24 final size:24
Alignment explanation
Indices: 49656578--49656624 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
49656568 GGGTTCAAGT
49656578 GCATTGCATTGCATCATTTGCATA
1 GCATTGCATTGCATCATTTGCATA
49656602 GCATTGCATTGCATCATTTGCAT
1 GCATTGCATTGCATCATTTGCAT
49656625 TAAATTTCCC
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:0.23, C:0.21, G:0.17, T:0.38
Consensus pattern (24 bp):
GCATTGCATTGCATCATTTGCATA
Found at i:49656945 original size:427 final size:427
Alignment explanation
Indices: 49656150--49657001 Score: 1677
Period size: 427 Copynumber: 2.0 Consensus size: 427
49656140 TGCATTGCAT
49656150 TGCATTGCATTGCATCATTTGCATAGCATTGCATTGCATCATTTGCATTAAATTTCCCAAAAGGA
1 TGCATTGCATTGCATCATTTGCATAGCATTGCATTGCATCATTTGCATTAAATTTCCCAAAAGGA
49656215 CCCTAATTAGGTAAAGTTATTTCAGAACCGACAAAAGATATGGACCAAAGGTTGGAGAGAATGGA
66 CCCTAATTAGGTAAAGTTATTTCAGAACCGACAAAAGATATGGACCAAAGGTTGGAGAGAATGGA
49656280 GCAAAGGCAAATACAGATGCAAGAGCAGTTGATCGAAATTCAACAAGATATGCGAGAAATGCTAG
131 GCAAAGGCAAATACAGATGCAAGAGCAGTTGATCGAAATTCAACAAGATATGCGAGAAATGCTAG
49656345 AACTCCAAAGAAATATGATGGGCCAGGTAACCCATTTACTGGCCGGAGAATTCAAAAAAAGGAGT
196 AACTCCAAAGAAATATGATGGGCCAGGTAACCCATTTACTGGCCGGAGAATTCAAAAAAAGGAGT
*
49656410 GGCCCAGTGGTCAATGGTGGGGATGATGTTGAAGAGATCATTTACTCCCCAGGCTTTACCCTAAT
261 GGCCCAGTGGTCAATGGTGGGGATGATGTTGAAGAGATCATTTACTCCCCAAGCTTTACCCTAAT
49656475 AAGCGTCCCGACCCAACCAGACATGCAAGGGGTACCCGCTGTTATCAGACACCAATATCAGACGG
326 AAGCGTCCCGACCCAACCAGACATGCAAGGGGTACCCGCTGTTATCAGACACCAATATCAGACGG
49656540 ATACATCAACACTGATGAGTTTCTCGATGGGTTCAAG
391 ATACATCAACACTGATGAGTTTCTCGATGGGTTCAAG
49656577 TGCATTGCATTGCATCATTTGCATAGCATTGCATTGCATCATTTGCATTAAATTTCCCAAAAGGA
1 TGCATTGCATTGCATCATTTGCATAGCATTGCATTGCATCATTTGCATTAAATTTCCCAAAAGGA
49656642 CCCTAATTAGGTAAAGTTATTTCAGAACCGACAAAAGATATGGACCAAAGGTTGGAGAGAATGGA
66 CCCTAATTAGGTAAAGTTATTTCAGAACCGACAAAAGATATGGACCAAAGGTTGGAGAGAATGGA
49656707 GCAAAGGCAAATACAGATGCAAGAGCAGTTGATCGAAATTCAACAAGATATGCGAGAAATGCTAG
131 GCAAAGGCAAATACAGATGCAAGAGCAGTTGATCGAAATTCAACAAGATATGCGAGAAATGCTAG
49656772 AACTCCAAAGAAATATGATGGGCCAGGTAACCCATTTACTGGCCGGAGAATTCAAAAAAAGGAGT
196 AACTCCAAAGAAATATGATGGGCCAGGTAACCCATTTACTGGCCGGAGAATTCAAAAAAAGGAGT
49656837 GGCCCAGTGGTCAATGGTGGGGATGATGTTGAAGAGATCATTTACTCCCCAAGCTTTACCCTAAT
261 GGCCCAGTGGTCAATGGTGGGGATGATGTTGAAGAGATCATTTACTCCCCAAGCTTTACCCTAAT
* *
49656902 AAGCGTTCCGACCCAACCAGACATGCAAGGGGTACCCGCTGTTATCGGACACCAATATCAGACGG
326 AAGCGTCCCGACCCAACCAGACATGCAAGGGGTACCCGCTGTTATCAGACACCAATATCAGACGG
49656967 ATACATCAACACTGATGAGTTTCTCGATGGGTTCA
391 ATACATCAACACTGATGAGTTTCTCGATGGGTTCA
49657002 GGTTTTAACC
Statistics
Matches: 422, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
427 422 1.00
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (427 bp):
TGCATTGCATTGCATCATTTGCATAGCATTGCATTGCATCATTTGCATTAAATTTCCCAAAAGGA
CCCTAATTAGGTAAAGTTATTTCAGAACCGACAAAAGATATGGACCAAAGGTTGGAGAGAATGGA
GCAAAGGCAAATACAGATGCAAGAGCAGTTGATCGAAATTCAACAAGATATGCGAGAAATGCTAG
AACTCCAAAGAAATATGATGGGCCAGGTAACCCATTTACTGGCCGGAGAATTCAAAAAAAGGAGT
GGCCCAGTGGTCAATGGTGGGGATGATGTTGAAGAGATCATTTACTCCCCAAGCTTTACCCTAAT
AAGCGTCCCGACCCAACCAGACATGCAAGGGGTACCCGCTGTTATCAGACACCAATATCAGACGG
ATACATCAACACTGATGAGTTTCTCGATGGGTTCAAG
Found at i:49660516 original size:45 final size:43
Alignment explanation
Indices: 49660451--49660919 Score: 124
Period size: 45 Copynumber: 10.6 Consensus size: 43
49660441 TAGATCTTGT
* *
49660451 TTCCTTGAAATTGAAGTGAAGCAGATCAAAGACGACGAATCTGAGC
1 TTCC-TGAAGTTGCAGTGAAGCAGATCAAAGACGAC-AATCT-AGC
** * *
49660497 TTCCTGAAGTTGCAGTGAAGCAGATTTAAG-CCACCAACCTAGC
1 TTCCTGAAGTTGCAGTGAAGCAGATCAAAGACGA-CAATCTAGC
* * * * * * *** * *
49660540 TCCCTAAAGTTGTAGTGGAGTAG-GCTAAA-ATTTCAGATCTTGT
1 TTCCTGAAGTTGCAGTGAAGCAGATC-AAAGACGACA-ATCTAGC
* * *
49660583 TTCCCTGAAGTTGCAGTGAAGCAGATCGAAGATGGCAAATCTGAGC
1 TT-CCTGAAGTTGCAGTGAAGCAGATCAAAGACGAC-AATCT-AGC
** * * * *
49660629 TTCCTGAAGTTGCAGTGAAGCAGATTTAAGCCGCCAACCCAGC
1 TTCCTGAAGTTGCAGTGAAGCAGATCAAAGACGACAATCTAGC
* * * * * * *** * *
49660672 TCCCTAAAGTTGTAGTGGAGTAG-GCTAAA-ATTTCAAGATCTTGT
1 TTCCTGAAGTTGCAGTGAAGCAGATC-AAAGACGAC-A-ATCTAGC
* * * *
49660716 TTCCCTGAAGTTGCAGTGAAACAGATCGAAGATGGCGAATCTGAGC
1 TT-CCTGAAGTTGCAGTGAAGCAGATCAAAGACGAC-AATCT-AGC
* ** * * * *
49660762 TTCCTAAAGTTGCAGTGAAGCAGATTTAAGCCGCCAACCCAGC
1 TTCCTGAAGTTGCAGTGAAGCAGATCAAAGACGACAATCTAGC
* * * * * * *** * *
49660805 TCCCTAAAGTTGTAGTGGAGTAG-GCTAAA-ATTTCAAGATCTTGT
1 TTCCTGAAGTTGCAGTGAAGCAGATC-AAAGACGAC-A-ATCTAGC
* * * *
49660849 TTCCCTGAAGTTGCAGTGAAACAGATCGAAGATGGCGAATCTGAGC
1 TT-CCTGAAGTTGCAGTGAAGCAGATCAAAGACGAC-AATCT-AGC
*
49660895 TTCCTAAAGTTGCAGTGAAGCAGAT
1 TTCCTGAAGTTGCAGTGAAGCAGAT
49660920 TCAAGCCACC
Statistics
Matches: 294, Mismatches: 106, Indels: 47
0.66 0.24 0.11
Matches are distributed among these distances:
42 4 0.01
43 77 0.26
44 39 0.13
45 150 0.51
46 24 0.08
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (43 bp):
TTCCTGAAGTTGCAGTGAAGCAGATCAAAGACGACAATCTAGC
Found at i:49661118 original size:131 final size:128
Alignment explanation
Indices: 49660430--49661606 Score: 1343
Period size: 131 Copynumber: 9.0 Consensus size: 128
49660420 GGGCCTATGG
* * * * * *
49660430 GGCTGAA-ATTTTAGATCTTGTTTCCTTGAAATTGAAGTGAAGCAGATCAAAGACGACGAATCTG
1 GGCTGAAGATTATAGATCTTGTTTCCCTG-AATTGCAGTGAGGCAGATCGAAGACGGCGAATCTG
*
49660494 AGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGA
65 -GCTTCCTGAAGTTGCAGTGAAGCAGATTTAAG-CA--ATCCTAGCTCCCTAAAGTTGTAGTGGA
49660559 GTA
126 GTA
* * * *
49660562 GGCT-AAAATT-TCAGATCTTGTTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGATGGCAAATCT
1 GGCTGAAGATTAT-AGATCTTGTTTCCCTGAA-TTGCAGTGAGGCAGATCGAAGACGGCGAATCT
*
49660625 GAGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCCGCCAA-CCCAGCTCCCTAAAGTTGTAGTG
64 G-GCTTCCTGAAGTTGCAGTGAAGCAGATTTAA---G-CAATCCTAGCTCCCTAAAGTTGTAGTG
49660689 GAGTA
124 GAGTA
* ** *
49660694 GGCT-AAAATT-TCAAGATCTTGTTTCCCTGAAGTTGCAGTGAAACAGATCGAAGATGGCGAATC
1 GGCTGAAGATTAT--AGATCTTGTTTCCCTGAA-TTGCAGTGAGGCAGATCGAAGACGGCGAATC
* *
49660757 TGAGCTTCCTAAAGTTGCAGTGAAGCAGATTTAAGCCGCCAA-CCCAGCTCCCTAAAGTTGTAGT
63 TG-GCTTCCTGAAGTTGCAGTGAAGCAGATTTAA---G-CAATCCTAGCTCCCTAAAGTTGTAGT
49660821 GGAGTA
123 GGAGTA
* ** *
49660827 GGCT-AAAATT-TCAAGATCTTGTTTCCCTGAAGTTGCAGTGAAACAGATCGAAGATGGCGAATC
1 GGCTGAAGATTAT--AGATCTTGTTTCCCTGAA-TTGCAGTGAGGCAGATCGAAGACGGCGAATC
* * *
49660890 TGAGCTTCCTAAAGTTGCAGTGAAGCAGATTCAAGCCACCATCCTAGCTCCCTAAGGTTGTAGTG
63 TG-GCTTCCTGAAGTTGCAGTGAAGCAGATTTAAG-CA--ATCCTAGCTCCCTAAAGTTGTAGTG
49660955 GAGTA
124 GAGTA
*
49660960 GGCTGAAGATTATAGATCTTGTTTCCTTGAGATTGCAGT-AGGGCAGATCGAAGACGGCGAATCT
1 GGCTGAAGATTATAGATCTTGTTTCCCTGA-ATTGCAGTGA-GGCAGATCGAAGACGGCGAATCT
* * *
49661024 AGGCTTTCTGATGTTGCAGTGAAGCAGATTTAAGCAAGTCCTAGCTCTCTAAAGTTGTAGTGGAG
64 -GGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCAA-TCCTAGCTCCCTAAAGTTGTAGTGGAG
49661089 TA
127 TA
*
49661091 GGCTGAAGATTATAGATCTTGTTTCCTTGAGATTGCAGT-AGGGCAGATCGAAGACGGCGAATCT
1 GGCTGAAGATTATAGATCTTGTTTCCCTGA-ATTGCAGTGA-GGCAGATCGAAGACGGCGAATCT
* * *
49661155 AGGCTTTCTGATGTTGCAGTGAAGCAGATTTAAGCAAGTCCTAGCTCTCTAAAGTTGTAGTGGAG
64 -GGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCAA-TCCTAGCTCCCTAAAGTTGTAGTGGAG
49661220 TA
127 TA
* * *
49661222 GGCTGAAGATTATGGATCTTGCTTCCCTGAGATTGCAGTGGGGCAGATCGAAGACGGCGAATCTA
1 GGCTGAAGATTATAGATCTTGTTTCCCTGA-ATTGCAGTGAGGCAGATCGAAGACGGCGAATCT-
* * *
49661287 GGCTTTCTGATGTTGCAGTGAAGCAGATTTAAGC-ATCCTAGCTCCCTAAGGTTGTAGTGGAGTA
64 GGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCAATCCTAGCTCCCTAAAGTTGTAGTGGAGTA
* * * *
49661351 GGCTGAAGATTATGGATCTTGCTTCCCTGAGATTGCAGTGGGGCAGATCGAAGACTGCGAATCTA
1 GGCTGAAGATTATAGATCTTGTTTCCCTGA-ATTGCAGTGAGGCAGATCGAAGACGGCGAATCT-
* * * * *
49661416 GGCTTCCTGATGTTGTAGTAAAGCAGATTTAAGCAAGTTCTAGCTCTCTAAAGTTGTAGTGGAGT
64 GGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCAA-TCCTAGCTCCCTAAAGTTGTAGTGGAGT
49661481 A
128 A
* * * * * * ***
49661482 GGCTGAGGATTGTAGATCTCGTCTCCCTGAAGTTGCAGTGAGGCAAATCAAAGACGATAAATCTT
1 GGCTGAAGATTATAGATCTTGTTTCCCTGAA-TTGCAGTGAGGCAGATCGAAGACGGCGAATC-T
* * *
49661547 GGCTTCCTGAAGATGCAGCGAAGCAGATTTAAGCAAGTCCTAGCTCCCTAAGGTTGTAGT
64 GGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCAA-TCCTAGCTCCCTAAAGTTGTAGT
49661607 AAATTGGGCT
Statistics
Matches: 965, Mismatches: 59, Indels: 43
0.90 0.06 0.04
Matches are distributed among these distances:
129 122 0.13
130 8 0.01
131 383 0.40
132 125 0.13
133 315 0.33
134 7 0.01
135 5 0.01
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (128 bp):
GGCTGAAGATTATAGATCTTGTTTCCCTGAATTGCAGTGAGGCAGATCGAAGACGGCGAATCTGG
CTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCAATCCTAGCTCCCTAAAGTTGTAGTGGAGTA
Found at i:49661875 original size:44 final size:44
Alignment explanation
Indices: 49661812--49662785 Score: 1161
Period size: 44 Copynumber: 22.1 Consensus size: 44
49661802 CAAGACCAGA
* *
49661812 CAGATTTGGCGTCTCTGTAGTAGCGGAGAGCAAATCGAAGATAG
1 CAGATTTGGCGTCTCTGTAGTGGCGGAGAGCAGATCGAAGATAG
* * *
49661856 CAGATTTGGCATCTCTGTAGTGGTGGAGAGCAAATCGAAGATAG
1 CAGATTTGGCGTCTCTGTAGTGGCGGAGAGCAGATCGAAGATAG
* * *
49661900 CAGATTTGGCGTCTCTTTATTGGCGGAGAGCAGATCGAAAATAG
1 CAGATTTGGCGTCTCTGTAGTGGCGGAGAGCAGATCGAAGATAG
* * * * * *
49661944 CAGATTTGGCATTTCTGTATTGGCAGAGAGCAGATCAAAAATAG
1 CAGATTTGGCGTCTCTGTAGTGGCGGAGAGCAGATCGAAGATAG
49661988 CAGATTTGGCGTCTCTGT-GTTGGCGGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTAG-TGGCGGAGAGCAGATCGAAGATAG
* *
49662032 CAGATTTGGCGTCTCTGTAGTGGCAGAGAGCAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTAGTGGCGGAGAGCAGATCGAAGATAG
* * * *
49662076 CATATTTGGCATCTCTGT-GTTGACAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTAG-TGGCGGAGAGCAGATCGAAGATAG
* *
49662120 CAGATTTGGCGTCTCTGTAGTGGCAGAGAGCAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTAGTGGCGGAGAGCAGATCGAAGATAG
* * * *
49662164 CATATTTGGCATCTCTGT-GTTGACAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTAG-TGGCGGAGAGCAGATCGAAGATAG
* * * *
49662208 CAGATTTGGCATCTCTGTAGTGGCGGTGTGCAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTAGTGGCGGAGAGCAGATCGAAGATAG
* *
49662252 CAGATTTGGCATCTCTGTAGTAGCGGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTAGTGGCGGAGAGCAGATCGAAGATAG
** * *
49662296 CAGATTTGGCGTCTCCCTATTGGCGGAGAGTAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTAGTGGCGGAGAGCAGATCGAAGATAG
* * *
49662340 CAGATTTGGCGTCTCTGAAGTGGCAGAGAGCAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTAGTGGCGGAGAGCAGATCGAAGATAG
* * *
49662384 CAGATTTGGCATCTCTGT-GTTGACAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTAG-TGGCGGAGAGCAGATCGAAGATAG
* * *
49662428 CAGATTTGGCATCTCTGTAGTGGCGGAGCGCAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTAGTGGCGGAGAGCAGATCGAAGATAG
* *
49662472 CAGATTTGGCATCTCTGTAGTTGCGGAGAGCAGATCGAAGAT-G
1 CAGATTTGGCGTCTCTGTAGTGGCGGAGAGCAGATCGAAGATAG
* * * *
49662515 ACAGATTCGGCTTCTCTGT-GTTGGTGGAGAGCAGATCAAAGATAG
1 -CAGATTTGGCGTCTCTGTAG-TGGCGGAGAGCAGATCGAAGATAG
* *
49662560 CAGATTTAGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTAGTGGCGGAGAGCAGATCGAAGATAG
* * * *
49662604 CAAATTTGGCGTCTCTATAATGGCGGAGAGCAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTAGTGGCGGAGAGCAGATCGAAGATAG
* * *
49662648 CAGATTTGGCGTCTCTGTAGTGGCGGAGAGCAAATCGAATATAA
1 CAGATTTGGCGTCTCTGTAGTGGCGGAGAGCAGATCGAAGATAG
* * * * * * *
49662692 TAGATTTGGTGTCTCTGTATTGTCAGAGGGCAGATCGAAAAT-G
1 CAGATTTGGCGTCTCTGTAGTGGCGGAGAGCAGATCGAAGATAG
* * * ** * * *
49662735 ACAGATTTGGCGTATCTATATTGGTAGAGAGCAGATTGAAAATAA
1 -CAGATTTGGCGTCTCTGTAGTGGCGGAGAGCAGATCGAAGATAG
49662780 CAGATT
1 CAGATT
49662786 GGTGTTCCCG
Statistics
Matches: 809, Mismatches: 107, Indels: 28
0.86 0.11 0.03
Matches are distributed among these distances:
43 4 0.00
44 800 0.99
45 5 0.01
ACGTcount: A:0.29, C:0.15, G:0.30, T:0.25
Consensus pattern (44 bp):
CAGATTTGGCGTCTCTGTAGTGGCGGAGAGCAGATCGAAGATAG
Found at i:49664633 original size:5 final size:5
Alignment explanation
Indices: 49664623--49664650 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
49664613 CACTTATTGC
49664623 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
49664651 TACTTAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:49664657 original size:15 final size:15
Alignment explanation
Indices: 49664624--49664657 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
49664614 ACTTATTGCT
*
49664624 TTAATTTAATTTAAT
1 TTAATTTAATTTAAC
*
49664639 TTAATTTAATTTTAC
1 TTAATTTAATTTAAC
49664654 TTAA
1 TTAA
49664658 AACACTTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
TTAATTTAATTTAAC
Found at i:49687598 original size:18 final size:19
Alignment explanation
Indices: 49687577--49687619 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
49687567 TAAGTTTGCA
49687577 AGCTCAATCAAAAG-TACG
1 AGCTCAATCAAAAGATACG
49687595 AGCTC-ATCAAAAGATACG
1 AGCTCAATCAAAAGATACG
49687613 AGCTCAA
1 AGCTCAA
49687620 CTCATGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.35
18 14 0.61
19 1 0.04
ACGTcount: A:0.44, C:0.23, G:0.16, T:0.16
Consensus pattern (19 bp):
AGCTCAATCAAAAGATACG
Found at i:49692786 original size:29 final size:29
Alignment explanation
Indices: 49692744--49692800 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
49692734 GCCTAAACCC
49692744 CTATCCTAAAGTTCTGAGTGTAAGCTTTT
1 CTATCCTAAAGTTCTGAGTGTAAGCTTTT
49692773 CTATCCTAAAGTTCTGAGTGTAAGCTTT
1 CTATCCTAAAGTTCTGAGTGTAAGCTTT
49692801 CTTATACCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.40
Consensus pattern (29 bp):
CTATCCTAAAGTTCTGAGTGTAAGCTTTT
Found at i:49704879 original size:46 final size:46
Alignment explanation
Indices: 49704812--49704948 Score: 204
Period size: 46 Copynumber: 3.0 Consensus size: 46
49704802 GAGTGTGTTC
49704812 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
49704858 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
* * * * * *
49704904 CATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CCTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
49704949 TCATGTTAAA
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
45 1 0.01
46 83 0.99
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.22
Consensus pattern (46 bp):
CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
Found at i:49716214 original size:7 final size:7
Alignment explanation
Indices: 49716204--49716240 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
49716194 GGGAAAGGTA
49716204 AGAGAGG
1 AGAGAGG
49716211 AGAGAGG
1 AGAGAGG
49716218 AGAGAGG
1 AGAGAGG
49716225 AGAGAGG
1 AGAGAGG
49716232 AGAGAGG
1 AGAGAGG
49716239 AG
1 AG
49716241 GGTGAGGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (7 bp):
AGAGAGG
Found at i:49718990 original size:22 final size:22
Alignment explanation
Indices: 49718965--49719010 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
49718955 CTTAAATTGC
*
49718965 TTAAATTACTAAGTAGTTCAAT
1 TTAAATTACTAAGTAGCTCAAT
*
49718987 TTAAATTACTAAGTGGCTCAAT
1 TTAAATTACTAAGTAGCTCAAT
49719009 TT
1 TT
49719011 TATCTTTCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (22 bp):
TTAAATTACTAAGTAGCTCAAT
Found at i:49720766 original size:20 final size:20
Alignment explanation
Indices: 49720729--49720766 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
49720719 TGATGGGGAG
*
49720729 CAAGAATATCAAGTTGGATT
1 CAAGAATATCAAGCTGGATT
49720749 CAAGAA-ATCGAAGCTGGA
1 CAAGAATATC-AAGCTGGA
49720767 GGAGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (20 bp):
CAAGAATATCAAGCTGGATT
Found at i:49722715 original size:46 final size:46
Alignment explanation
Indices: 49722663--49722833 Score: 245
Period size: 46 Copynumber: 3.7 Consensus size: 46
49722653 GTGTGCTCTC
***
49722663 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACG
49722709 TGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACG
* *
49722755 TGATATGAAATGAACAAGACTATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACG
* ** *
49722801 TGACA-GAAAATGAGTAAGACCATAGTTGAAAGA
1 TGATATG-AAATGAACAAGACCATGGTTGAAAGA
49722834 CACTATGGAT
Statistics
Matches: 114, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
45 1 0.01
46 113 0.99
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (46 bp):
TGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACG
Found at i:49731827 original size:15 final size:15
Alignment explanation
Indices: 49731804--49731833 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
49731794 TTTATATAAT
49731804 TTATGCAAAACAATA
1 TTATGCAAAACAATA
*
49731819 TTATTCAAAACAATA
1 TTATGCAAAACAATA
49731834 ACTAATTAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.30
Consensus pattern (15 bp):
TTATGCAAAACAATA
Found at i:49731995 original size:6 final size:6
Alignment explanation
Indices: 49731984--49732024 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
49731974 TTTTAACTAA
*
49731984 TAATTG TAATTG TAATTG TAATTG TAATTG TAATCG TAATT
1 TAATTG TAATTG TAATTG TAATTG TAATTG TAATTG TAATT
49732025 ATCACAACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.34, C:0.02, G:0.15, T:0.49
Consensus pattern (6 bp):
TAATTG
Found at i:49732182 original size:44 final size:44
Alignment explanation
Indices: 49732119--49732204 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 44
49732109 ATAATTGTAA
* * *
49732119 ATTAAATTATAATTATTTTTAAATATGTAATTATCACAACTTCT
1 ATTAAATTACAATTATTTTTAAATATATAATTATAACAACTTCT
* *
49732163 ATTAAATTACAATTATTTTTAAATGTATACTTATAACAACTT
1 ATTAAATTACAATTATTTTTAAATATATAATTATAACAACTT
49732205 TTGTTTTGCT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (44 bp):
ATTAAATTACAATTATTTTTAAATATATAATTATAACAACTTCT
Found at i:49732273 original size:6 final size:6
Alignment explanation
Indices: 49732262--49732288 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
49732252 GATTGAAAAT
49732262 ATTATA ATTATA ATTATA ATTATA ATT
1 ATTATA ATTATA ATTATA ATTATA ATT
49732289 GACGTTTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
ATTATA
Found at i:49732442 original size:17 final size:17
Alignment explanation
Indices: 49732431--49732462 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
49732421 CAATTTTTAA
49732431 TAAAT-TATAATTATTT
1 TAAATGTATAATTATTT
49732447 TAAATGTATAATTATT
1 TAAATGTATAATTATT
49732463 GCAACTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TAAATGTATAATTATTT
Found at i:49737842 original size:21 final size:21
Alignment explanation
Indices: 49737818--49737857 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
49737808 ACCTTTTCTA
*
49737818 AAGTTAAAAGTCAAAACTATT
1 AAGTTAAAAGGCAAAACTATT
49737839 AAGTTAAAAGGCAAAACTA
1 AAGTTAAAAGGCAAAACTA
49737858 CGTCGTTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.23
Consensus pattern (21 bp):
AAGTTAAAAGGCAAAACTATT
Found at i:49742695 original size:13 final size:13
Alignment explanation
Indices: 49742677--49742702 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49742667 AGACATCTCC
49742677 GCATTAACCATCT
1 GCATTAACCATCT
49742690 GCATTAACCATCT
1 GCATTAACCATCT
49742703 CAGCTAACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.31
Consensus pattern (13 bp):
GCATTAACCATCT
Found at i:49743781 original size:32 final size:32
Alignment explanation
Indices: 49743745--49743809 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
49743735 GCATGGAAGC
49743745 AAAAGTGACACACAGCATAATGACGCGAACTA
1 AAAAGTGACACACAGCATAATGACGCGAACTA
* *
49743777 AAAAGTGACACACCGCATAATGACGTGAACTA
1 AAAAGTGACACACAGCATAATGACGCGAACTA
49743809 A
1 A
49743810 CCTCTTAGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.46, C:0.22, G:0.18, T:0.14
Consensus pattern (32 bp):
AAAAGTGACACACAGCATAATGACGCGAACTA
Found at i:49746001 original size:11 final size:11
Alignment explanation
Indices: 49745985--49746012 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
49745975 CTTAATCACA
49745985 TTCCGAAGAAG
1 TTCCGAAGAAG
49745996 TTCCGAAGAAG
1 TTCCGAAGAAG
49746007 TTCCGA
1 TTCCGA
49746013 GATGCAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.21
Consensus pattern (11 bp):
TTCCGAAGAAG
Found at i:49753690 original size:15 final size:15
Alignment explanation
Indices: 49753672--49753703 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
49753662 ATGTTTTGTA
*
49753672 AAGTGAATTTTTGGT
1 AAGTGAAATTTTGGT
49753687 AAGTGAAATTTTGGT
1 AAGTGAAATTTTGGT
49753702 AA
1 AA
49753704 AAATGTCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.25, T:0.41
Consensus pattern (15 bp):
AAGTGAAATTTTGGT
Found at i:49754452 original size:43 final size:43
Alignment explanation
Indices: 49754388--49754534 Score: 140
Period size: 43 Copynumber: 3.4 Consensus size: 43
49754378 ATTGAGATGT
* *
49754388 GATTACATGTAAGACCCTGTGTGGGATAGTGGCATTGTATTGC
1 GATTACATGTAAGACCATGTGTGGGACAGTGGCATTGTATTGC
* * *
49754431 GATTACGTGTAAGACCATGTGTGGGACA-TCGGCATCGTTAAT-C
1 GATTACATGTAAGACCATGTGTGGGACAGT-GGCATTG-TATTGC
* * * *
49754474 GACTT-CGTGTAAGACCCTATGTGGGACAGTGGCATTG-ATATGT
1 GA-TTACATGTAAGACCATGTGTGGGACAGTGGCATTGTAT-TGC
*
49754517 GATAACATGTAAGACCAT
1 GATTACATGTAAGACCAT
49754535 ACCGAGTATC
Statistics
Matches: 84, Mismatches: 13, Indels: 14
0.76 0.12 0.13
Matches are distributed among these distances:
41 1 0.01
42 3 0.04
43 74 0.88
44 6 0.07
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (43 bp):
GATTACATGTAAGACCATGTGTGGGACAGTGGCATTGTATTGC
Found at i:49763107 original size:18 final size:18
Alignment explanation
Indices: 49763078--49763115 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
49763068 AAGAGAATTG
49763078 AAATTGAGAAATT-AAAT
1 AAATTGAGAAATTGAAAT
49763095 AAATTGCAGAAATTGAAAT
1 AAATTG-AGAAATTGAAAT
49763114 AA
1 AA
49763116 GGAAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
18 7 0.37
19 6 0.32
ACGTcount: A:0.58, C:0.03, G:0.13, T:0.26
Consensus pattern (18 bp):
AAATTGAGAAATTGAAAT
Found at i:49763204 original size:35 final size:35
Alignment explanation
Indices: 49763136--49763204 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
49763126 ATAGAGTTGG
*
49763136 GAAAAGAGAAAGTTTCTTATGTCGTGAGATTCCAA
1 GAAAAGAGAAAGTTTCTTATGTCGCGAGATTCCAA
* *
49763171 GAAAAGAGAAAGTTTCTTATGTGGCGAGGTTCCA
1 GAAAAGAGAAAGTTTCTTATGTCGCGAGATTCCA
49763205 GCCTCTGGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.28
Consensus pattern (35 bp):
GAAAAGAGAAAGTTTCTTATGTCGCGAGATTCCAA
Found at i:49763898 original size:28 final size:27
Alignment explanation
Indices: 49763867--49763931 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
49763857 AGATAATTAA
49763867 AATAAAATCCTAAAATTTAAATAATCCT
1 AATAAAATCCTAAAATTT-AATAATCCT
* * * *
49763895 AATAATTATCTTAATATTTAATTATCCT
1 AATAA-AATCCTAAAATTTAATAATCCT
49763923 AATATAAAT
1 AATA-AAAT
49763932 AAAATGGAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
28 19 0.63
29 11 0.37
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (27 bp):
AATAAAATCCTAAAATTTAATAATCCT
Found at i:49763918 original size:16 final size:16
Alignment explanation
Indices: 49763897--49763927 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49763887 ATAATCCTAA
*
49763897 TAATTATCTTAATATT
1 TAATTATCCTAATATT
49763913 TAATTATCCTAATAT
1 TAATTATCCTAATAT
49763928 AAATAAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATTATCCTAATATT
Found at i:49765802 original size:15 final size:14
Alignment explanation
Indices: 49765782--49765849 Score: 66
Period size: 15 Copynumber: 4.7 Consensus size: 14
49765772 TTATTAATAT
49765782 AATAAAATAATTAAA
1 AATAAAATAA-TAAA
* **
49765797 AATAAAACAAATTGA
1 AATAAAA-TAATAAA
49765812 AATAAAATAATAAA
1 AATAAAATAATAAA
*
49765826 AA-AAAATAATAAC
1 AATAAAATAATAAA
49765839 AATAGAAATAA
1 AATA-AAATAA
49765850 AATTTAAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
13 12 0.28
14 7 0.16
15 22 0.51
16 2 0.05
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (14 bp):
AATAAAATAATAAA
Found at i:49771510 original size:17 final size:19
Alignment explanation
Indices: 49771490--49771527 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
49771480 AAGTGAATTG
49771490 AAATTGC-GAAATT-AAAT
1 AAATTGCAGAAATTGAAAT
49771507 AAATTGCAGAAATTGAAAT
1 AAATTGCAGAAATTGAAAT
49771526 AA
1 AA
49771528 GGAAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 6 0.32
19 6 0.32
ACGTcount: A:0.55, C:0.05, G:0.13, T:0.26
Consensus pattern (19 bp):
AAATTGCAGAAATTGAAAT
Found at i:49772297 original size:28 final size:27
Alignment explanation
Indices: 49772265--49772329 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
49772255 AGAGAATTAA
49772265 AATAAAATCCTAAAATTTAAATAATCCT
1 AATAAAATCCTAAAATTT-AATAATCCT
* * * *
49772293 AATAATTATCTTAATATTTAATTATCCT
1 AATAA-AATCCTAAAATTTAATAATCCT
49772321 AATATAAAT
1 AATA-AAAT
49772330 AAAATGGAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
28 19 0.63
29 11 0.37
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (27 bp):
AATAAAATCCTAAAATTTAATAATCCT
Found at i:49772316 original size:16 final size:16
Alignment explanation
Indices: 49772295--49772325 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49772285 ATAATCCTAA
*
49772295 TAATTATCTTAATATT
1 TAATTATCCTAATATT
49772311 TAATTATCCTAATAT
1 TAATTATCCTAATAT
49772326 AAATAAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATTATCCTAATATT
Found at i:49776611 original size:6 final size:6
Alignment explanation
Indices: 49776600--49776625 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
49776590 ATACATTAAA
49776600 AATTTT AATTTT AATTTT AATTTT AA
1 AATTTT AATTTT AATTTT AATTTT AA
49776626 AATTAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
AATTTT
Found at i:49777907 original size:22 final size:22
Alignment explanation
Indices: 49777881--49777925 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
49777871 TTATTAATAC
49777881 ATTTATAATATAATTTT-ATAAT
1 ATTTATAATAT-ATTTTCATAAT
49777903 ATTTATAATATATTTTCATAAT
1 ATTTATAATATATTTTCATAAT
49777925 A
1 A
49777926 ATAAAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTTATAATATATTTTCATAAT
Found at i:49782288 original size:25 final size:25
Alignment explanation
Indices: 49782258--49782313 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
49782248 AACCCTCTTG
49782258 AGCATCCTATTAAATAGATCTTCCA
1 AGCATCCTATTAAATAGATCTTCCA
* * *
49782283 AGCATCCTATTAAATAGTTCTTGCG
1 AGCATCCTATTAAATAGATCTTCCA
49782308 AGCATC
1 AGCATC
49782314 TTGATCGGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.32
Consensus pattern (25 bp):
AGCATCCTATTAAATAGATCTTCCA
Found at i:49786179 original size:24 final size:23
Alignment explanation
Indices: 49786150--49786212 Score: 81
Period size: 24 Copynumber: 2.7 Consensus size: 23
49786140 AACCGAATTT
* * *
49786150 GCACACATAGTGCTTATTACACTC
1 GCACACATAGTGCATAGTAAAC-C
49786174 GCACACATAGTGCCATAGTAAACC
1 GCACACATAGTG-CATAGTAAACC
49786198 GCACACATAGTGCAT
1 GCACACATAGTGCAT
49786213 TGGATTTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
23 3 0.09
24 25 0.71
25 7 0.20
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (23 bp):
GCACACATAGTGCATAGTAAACC
Found at i:49793325 original size:24 final size:24
Alignment explanation
Indices: 49793297--49793357 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
49793287 AACCGTATTT
* * *
49793297 GCACACATAGTGCTA-ATTACACTC
1 GCACACATAGTGCCATAGTAAAC-C
49793321 GCACACATAGTGCCATAGTAAACC
1 GCACACATAGTGCCATAGTAAACC
49793345 GCACACATAGTGC
1 GCACACATAGTGC
49793358 ATTGGATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 28 0.85
25 5 0.15
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.20
Consensus pattern (24 bp):
GCACACATAGTGCCATAGTAAACC
Found at i:49799435 original size:47 final size:47
Alignment explanation
Indices: 49799339--49799515 Score: 164
Period size: 47 Copynumber: 3.8 Consensus size: 47
49799329 GGAAATTGAG
* * * * * * *
49799339 ATCCGAACCCGTTGAGTTGCGTTCCGAGTTCGTGA-GAATTATGAGGC
1 ATCCGAACTCGTTGAGTTGCGTTCCGAGTTCATTATGGA-TGTCAAGC
* *
49799386 ATCTGAACTCATTGAGTTGCGTTCCGAGTTCACTTATGGATG-CAAGC
1 ATCCGAACTCGTTGAGTTGCGTTCCGAGTTCA-TTATGGATGTCAAGC
* * * *
49799433 ATCCAAACTCGTTGAGTTGTGTTCCGAGTTTATTATGGATGTGAA-C
1 ATCCGAACTCGTTGAGTTGCGTTCCGAGTTCATTATGGATGTCAAGC
* * *
49799479 ACCCGAGCTCGTTGAGTTGCGTTCTG-GTTCATTATGG
1 ATCCGAACTCGTTGAGTTGCGTTCCGAGTTCATTATGG
49799516 GTGAAATTAT
Statistics
Matches: 106, Mismatches: 21, Indels: 8
0.79 0.16 0.06
Matches are distributed among these distances:
45 10 0.09
46 31 0.29
47 60 0.57
48 3 0.03
49 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.33
Consensus pattern (47 bp):
ATCCGAACTCGTTGAGTTGCGTTCCGAGTTCATTATGGATGTCAAGC
Found at i:49799490 original size:46 final size:46
Alignment explanation
Indices: 49799391--49799515 Score: 146
Period size: 46 Copynumber: 2.7 Consensus size: 46
49799381 GAGGCATCTG
* *
49799391 AACTCATTGAGTTGCGTTCCGAGTTCACTTATGGATGCAAGCATCCA
1 AACTCGTTGAGTTGCGTTCCGAGTTCA-TTATGGATGCAAGCACCCA
* * * *
49799438 AACTCGTTGAGTTGTGTTCCGAGTTTATTATGGATGTGAA-CACCCG
1 AACTCGTTGAGTTGCGTTCCGAGTTCATTATGGATG-CAAGCACCCA
* *
49799484 AGCTCGTTGAGTTGCGTTCTG-GTTCATTATGG
1 AACTCGTTGAGTTGCGTTCCGAGTTCATTATGG
49799516 GTGAAATTAT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
45 10 0.15
46 31 0.46
47 26 0.39
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (46 bp):
AACTCGTTGAGTTGCGTTCCGAGTTCATTATGGATGCAAGCACCCA
Found at i:49800782 original size:17 final size:16
Alignment explanation
Indices: 49800738--49800797 Score: 59
Period size: 17 Copynumber: 3.7 Consensus size: 16
49800728 TTAATCACTT
*
49800738 TAATATTAAATTAATA
1 TAATATTAAATTAAAA
*
49800754 TAATATT-TATTAAAA
1 TAATATTAAATTAAAA
* *
49800769 TAAATATTAGATTAAATT
1 T-AATATTAAATTAAA-A
49800787 TAATATTAAAT
1 TAATATTAAAT
49800798 CTTATTAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
15 7 0.19
16 13 0.36
17 15 0.42
18 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
TAATATTAAATTAAAA
Found at i:49800883 original size:20 final size:19
Alignment explanation
Indices: 49800833--49800885 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
49800823 CTTGTACATA
49800833 AACATTAAATT-A-AATTT
1 AACATTAAATTAATAATTT
* **
49800850 AATATTAAGGTAATCAATTT
1 AACATTAAATTAAT-AATTT
49800870 AACATTAAATTAATAA
1 AACATTAAATTAATAA
49800886 AATATTATTA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 2 0.07
20 16 0.59
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.38
Consensus pattern (19 bp):
AACATTAAATTAATAATTT
Found at i:49806366 original size:27 final size:27
Alignment explanation
Indices: 49806328--49806382 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
49806318 GCAAAATTAG
49806328 ATAACCAATCTCTATGGATTTGACCCT
1 ATAACCAATCTCTATGGATTTGACCCT
49806355 ATAACCAATCTCTATGGATTTGACCCT
1 ATAACCAATCTCTATGGATTTGACCCT
49806382 A
1 A
49806383 CTGCTCTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (27 bp):
ATAACCAATCTCTATGGATTTGACCCT
Found at i:49808342 original size:41 final size:41
Alignment explanation
Indices: 49808284--49808405 Score: 199
Period size: 41 Copynumber: 3.0 Consensus size: 41
49808274 GTTGGAATTA
* *
49808284 AAAAGGTCATGTTCGACTTAGGTGCATCTATTAATGTTATAC
1 AAAA-GTCATGTGCGACTTAGGTGCATCTATTAACGTTATAC
*
49808326 AAAAGTCATGTGCGACTTAGGTGCATCTATTAACATTATAC
1 AAAAGTCATGTGCGACTTAGGTGCATCTATTAACGTTATAC
*
49808367 AAAAGTCACGTGCGACTTAGGTGCATCTATTAACGTTAT
1 AAAAGTCATGTGCGACTTAGGTGCATCTATTAACGTTAT
49808406 GCCTTTTTCT
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
41 71 0.95
42 4 0.05
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (41 bp):
AAAAGTCATGTGCGACTTAGGTGCATCTATTAACGTTATAC
Found at i:49816233 original size:53 final size:53
Alignment explanation
Indices: 49816077--49816242 Score: 221
Period size: 53 Copynumber: 3.1 Consensus size: 53
49816067 GACGAAAAAT
* **
49816077 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
49816129 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
* * *
49816182 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGA
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A
49816236 TATGTGA
1 -ATGTGA
49816243 ACCGTGTAAG
Statistics
Matches: 103, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
51 4 0.04
52 11 0.11
53 81 0.79
54 1 0.01
55 6 0.06
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
Found at i:49818967 original size:46 final size:44
Alignment explanation
Indices: 49818863--49818970 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
49818853 TGTCTTTGAC
** * * *
49818863 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
49818907 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
49818953 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
49818971 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:49821037 original size:13 final size:13
Alignment explanation
Indices: 49821019--49821043 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49821009 AGTGCCAGAA
49821019 GAGAAATTTTCTT
1 GAGAAATTTTCTT
49821032 GAGAAATTTTCT
1 GAGAAATTTTCT
49821044 AGAAAGAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
GAGAAATTTTCTT
Found at i:49822813 original size:47 final size:47
Alignment explanation
Indices: 49822704--49822814 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
49822694 CCGGGATAAG
* *
49822704 CACATAGTGCTTCATCGGAATAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
49822751 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
49822798 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
49822815 ACTCAATGTC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 1 0.02
47 52 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:49823587 original size:4 final size:4
Alignment explanation
Indices: 49823578--49823658 Score: 72
Period size: 4 Copynumber: 19.8 Consensus size: 4
49823568 CCCTTTTCTA
** * * *
49823578 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TCAC GTTTGC TCTC TGTA
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTT-C TTTC TTTC
** *
49823628 ACTC TTTC TATC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
49823659 TTTTTTAACT
Statistics
Matches: 61, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
4 57 0.93
5 3 0.05
6 1 0.02
ACGTcount: A:0.05, C:0.26, G:0.04, T:0.65
Consensus pattern (4 bp):
TTTC
Found at i:49829806 original size:29 final size:29
Alignment explanation
Indices: 49829773--49829830 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
49829763 TAGCCTGCGC
49829773 ACGGAAACAAACCGTACGCTGAGAATACT
1 ACGGAAACAAACCGTACGCTGAGAATACT
* *
49829802 ACGGAAACAAATCGTACGTTGAGAATACT
1 ACGGAAACAAACCGTACGCTGAGAATACT
49829831 TTCAGTGGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (29 bp):
ACGGAAACAAACCGTACGCTGAGAATACT
Found at i:49836226 original size:43 final size:43
Alignment explanation
Indices: 49836173--49836305 Score: 207
Period size: 43 Copynumber: 3.1 Consensus size: 43
49836163 CCGGCATTAC
* *
49836173 GCCTGTTAGGCACGAAGGCCCGAATACACATCACCAGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACTAA
*
49836216 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACTAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACTAA
* *
49836259 GCCTGCTAGGCACGAAGGCCCGAATATA-AT-ACCAGCACTAG
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACTAA
49836300 GCCTGC
1 GCCTGC
49836306 GGGATTTATC
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
41 15 0.18
42 2 0.02
43 67 0.80
ACGTcount: A:0.30, C:0.33, G:0.24, T:0.13
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACTAA
Found at i:49836342 original size:38 final size:37
Alignment explanation
Indices: 49836277--49836359 Score: 114
Period size: 38 Copynumber: 2.2 Consensus size: 37
49836267 GGCACGAAGG
* *
49836277 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTA
1 CCCGAATATAATACCAACACTAAGCCTGCGGGATTTA
*
49836314 TCCCGGATATAATACCAACA-TGAAGCCTGCGGGATTTA
1 -CCCGAATATAATACCAACACT-AAGCCTGCGGGATTTA
49836352 CCCGAATA
1 CCCGAATA
49836360 CACATCAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
37 8 0.20
38 32 0.80
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (37 bp):
CCCGAATATAATACCAACACTAAGCCTGCGGGATTTA
Found at i:49853477 original size:20 final size:21
Alignment explanation
Indices: 49853448--49853488 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
49853438 ACATCTTGGA
49853448 TTTTCCCTTTTT-TTTCTTTC
1 TTTTCCCTTTTTCTTTCTTTC
*
49853468 TTTTCTCTTTTTCTTTCTTTC
1 TTTTCCCTTTTTCTTTCTTTC
49853489 CTTCCCCTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTCCCTTTTTCTTTCTTTC
Found at i:49875113 original size:31 final size:30
Alignment explanation
Indices: 49875056--49875113 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
49875046 GTCAACAAAT
*
49875056 AAATTAAAATTTATAAAATATTCAAAATAG
1 AAATTAAAATTCATAAAATATTCAAAATAG
49875086 AAATTAAAAAGTTCATAAAA-ATTCAAAA
1 AAATT-AAAA-TTCATAAAATATTCAAAA
49875114 ATTTAGAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 5 0.20
31 12 0.48
32 8 0.32
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.29
Consensus pattern (30 bp):
AAATTAAAATTCATAAAATATTCAAAATAG
Found at i:49875285 original size:27 final size:29
Alignment explanation
Indices: 49875220--49875285 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 29
49875210 CTTGTTTTTG
*
49875220 AAAAGAT-TAGGGAACAAATTTAACTAAA
1 AAAAGATATAAGGAACAAATTTAACTAAA
* *
49875248 AAAAGGA-ATAAGGAATAAATTTGA-T-AA
1 AAAA-GATATAAGGAACAAATTTAACTAAA
49875275 AAAAGATATAA
1 AAAAGATATAA
49875286 ACATTGGGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
26 2 0.06
27 10 0.31
28 5 0.16
29 15 0.47
ACGTcount: A:0.61, C:0.03, G:0.15, T:0.21
Consensus pattern (29 bp):
AAAAGATATAAGGAACAAATTTAACTAAA
Found at i:49876384 original size:31 final size:29
Alignment explanation
Indices: 49876344--49876444 Score: 73
Period size: 31 Copynumber: 3.4 Consensus size: 29
49876334 AAAATGGTTT
* *
49876344 AGGTGCCAAATTAGGAAAAATTGTCAAGTTG
1 AGGTACCAAATTAGGAAAAA-TGT-AAGTTA
*
49876375 AGGTACCAAATTGGGCCAAAAA---AAGTTA
1 AGGTACCAAATTAGG--AAAAATGTAAGTTA
* *
49876403 AGGTACAAAATTAGGAAAAAGTGTGAAGTTC
1 AGGTACCAAATTAGGAAAAA-TGT-AAGTTA
*
49876434 AGGTAGCAAAT
1 AGGTACCAAAT
49876445 GTTATATTAA
Statistics
Matches: 55, Mismatches: 8, Indels: 14
0.71 0.10 0.18
Matches are distributed among these distances:
26 5 0.09
28 18 0.33
31 27 0.49
33 5 0.09
ACGTcount: A:0.44, C:0.10, G:0.25, T:0.22
Consensus pattern (29 bp):
AGGTACCAAATTAGGAAAAATGTAAGTTA
Found at i:49876396 original size:59 final size:59
Alignment explanation
Indices: 49876273--49876444 Score: 193
Period size: 60 Copynumber: 2.9 Consensus size: 59
49876263 AATGAACCTA
* * * **
49876273 AAAAAATGCTTAGGTACTAAATTAGGAAAAAATGGCAAGTTG-GTGTATAAAATTGGGCC
1 AAAAAATGTTTAGGTACAAAATTAGGAAAAAATGTCAAGTTGAG-GTACCAAATTGGGCC
* * *
49876332 AAAAAATGGTTTAGGTGCCAAATTAGGAAAAATTGTCAAGTTGAGGTACCAAATTGGGCC
1 AAAAAAT-GTTTAGGTACAAAATTAGGAAAAAATGTCAAGTTGAGGTACCAAATTGGGCC
* * * * * *
49876392 AAAAAAAGTTAAGGTACAAAATTAGGAAAAAGTGTGAAGTTCAGGTAGCAAAT
1 AAAAAATGTTTAGGTACAAAATTAGGAAAAAATGTCAAGTTGAGGTACCAAAT
49876445 GTTATATTAA
Statistics
Matches: 96, Mismatches: 15, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
59 46 0.48
60 49 0.51
61 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.24
Consensus pattern (59 bp):
AAAAAATGTTTAGGTACAAAATTAGGAAAAAATGTCAAGTTGAGGTACCAAATTGGGCC
Found at i:49876731 original size:22 final size:23
Alignment explanation
Indices: 49876679--49876731 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 23
49876669 TAAATTAAAG
49876679 TTTTATTTTAATATGTTTTACACAT
1 TTTTATTTTAATATG--TTACACAT
49876704 TTTTATTTTAATATG-TACA-AT
1 TTTTATTTTAATATGTTACACAT
49876725 TTATTAT
1 TT-TTAT
49876732 CTTCATCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 4 0.15
22 8 0.30
25 15 0.56
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTTATTTTAATATGTTACACAT
Found at i:49883219 original size:6 final size:6
Alignment explanation
Indices: 49883208--49883249 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
49883198 AGTCGAAGAC
49883208 CCTACA CCTACA CCTACA CCTACA CCTACA CCTACA CCTACA
1 CCTACA CCTACA CCTACA CCTACA CCTACA CCTACA CCTACA
49883250 TGGACTCATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.33, C:0.50, G:0.00, T:0.17
Consensus pattern (6 bp):
CCTACA
Found at i:49886138 original size:18 final size:18
Alignment explanation
Indices: 49886112--49886153 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
49886102 ATTGGGCTTG
* *
49886112 TATAATATATATTTATTT
1 TATAATATAGATATATTT
*
49886130 TATATTATAGATATATTT
1 TATAATATAGATATATTT
49886148 TA-AATA
1 TATAATA
49886154 ATTAAAAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
TATAATATAGATATATTT
Found at i:49899326 original size:19 final size:19
Alignment explanation
Indices: 49899280--49899327 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
49899270 AAAGTTTAGT
49899280 TTCATTAATTCTATTTATTA
1 TTCA-TAATTCTATTTATTA
*
49899300 TTCA-AATTTTATCTTATTA
1 TTCATAATTCTAT-TTATTA
49899319 TT-ATAATTC
1 TTCATAATTC
49899328 ATAAAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 8 0.33
19 12 0.50
20 4 0.17
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.58
Consensus pattern (19 bp):
TTCATAATTCTATTTATTA
Found at i:49918678 original size:17 final size:15
Alignment explanation
Indices: 49918656--49918691 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
49918646 AAGCTCTAAG
49918656 CCCAATACACCCAATAA
1 CCCAATAC-CCCAA-AA
49918673 CCCAATACCCCAAAA
1 CCCAATACCCCAAAA
49918688 CCCA
1 CCCA
49918692 CCTAAACCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 5 0.26
17 8 0.42
ACGTcount: A:0.44, C:0.47, G:0.00, T:0.08
Consensus pattern (15 bp):
CCCAATACCCCAAAA
Done.