Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 122 of 230
Found at i:35449904 original size:27 final size:26
Alignment explanation
Indices: 35449874--35449931 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
35449864 AATTTTGAGG
*
35449874 TTTATAATTTATAATTTTTATTAATT
1 TTTATAATTTATAACTTTTATTAATT
** * *
35449900 ATTTATGTTTTCTCACTTTTATTAATT
1 -TTTATAATTTATAACTTTTATTAATT
35449927 TTTAT
1 TTTAT
35449932 TATTATTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (26 bp):
TTTATAATTTATAACTTTTATTAATT
Found at i:35450222 original size:43 final size:43
Alignment explanation
Indices: 35450118--35450449 Score: 432
Period size: 43 Copynumber: 7.7 Consensus size: 43
35450108 GATATGTTTT
* * * * * * *
35450118 TAGCGGTGTTTTTGCGAGAAGCGTCGCTAAAGGT-TTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
* * *
35450160 TAGCAGCATTTGTGGGAAAAGCGCCGCTAAAGGTCATGGCCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
* * * *
35450203 TAGCGGCGTTTGTGAGAAAAACGCCGCTAAAGATCATGGTCTT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
*
35450246 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGCCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
* *
35450289 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTCTT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
* * *
35450332 TAGCGGCGTTTGTGGGAAGAGCGCCGCTAAAGCTCATGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
* **
35450375 TAGCGACGTTTGTGGGAAAAGCGCCGCTAAAGGTTGTGGTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
* *
35450418 TAGCGGCGTTTGTGGGAAAAGTGCCGCAAAAG
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG
35450450 TTAGCGACGC
Statistics
Matches: 250, Mismatches: 39, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
42 27 0.11
43 223 0.89
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
Found at i:35453539 original size:20 final size:19
Alignment explanation
Indices: 35453507--35453545 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
35453497 AACTTCTACA
35453507 AATAAGGAAAAAAAATCTG
1 AATAAGGAAAAAAAATCTG
35453526 AATAAGGAAAAAAAATCTG
1 AATAAGGAAAAAAAATCTG
35453545 A
1 A
35453546 TTTGTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.64, C:0.05, G:0.15, T:0.15
Consensus pattern (19 bp):
AATAAGGAAAAAAAATCTG
Found at i:35454126 original size:39 final size:39
Alignment explanation
Indices: 35454070--35454145 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
35454060 AACTATTACT
35454070 AAAATTCCTATTAGAAACCCAATTTTGTAACAAAATACA
1 AAAATTCCTATTAGAAACCCAATTTTGTAACAAAATACA
* *
35454109 AAAATTCCTATTGGAAACCCAATTTTGTAACCAAATA
1 AAAATTCCTATTAGAAACCCAATTTTGTAACAAAATA
35454146 TTTCGTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.46, C:0.18, G:0.07, T:0.29
Consensus pattern (39 bp):
AAAATTCCTATTAGAAACCCAATTTTGTAACAAAATACA
Found at i:35454278 original size:20 final size:20
Alignment explanation
Indices: 35454255--35454307 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
35454245 TTTTTCAAAT
35454255 AAAAATTATAAAAATCAT-AA
1 AAAAATTATAAAAA-CATCAA
* ** *
35454275 AAAAACTATAAGTACATCAC
1 AAAAATTATAAAAACATCAA
35454295 AAAAATTATAAAA
1 AAAAATTATAAAA
35454308 TTACTTTTTG
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.66, C:0.09, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAAATTATAAAAACATCAA
Found at i:35454412 original size:38 final size:39
Alignment explanation
Indices: 35454353--35454427 Score: 91
Period size: 38 Copynumber: 1.9 Consensus size: 39
35454343 TTTTCAAAAC
*
35454353 ATTTGGTTACAAAGTATGGTTT-CAATAAAAATTTTAAT
1 ATTTGGTTACAAAATATGGTTTCCAATAAAAATTTTAAT
* * *
35454391 ATTTGGTTATAAAAT-TGGGTTTCCAATAGATATTTTA
1 ATTTGGTTACAAAATAT-GGTTTCCAATAAAAATTTTA
35454428 CTAATAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
37 1 0.03
38 18 0.58
39 12 0.39
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (39 bp):
ATTTGGTTACAAAATATGGTTTCCAATAAAAATTTTAAT
Found at i:35454695 original size:18 final size:18
Alignment explanation
Indices: 35454672--35454711 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
35454662 AAAAAAAATA
35454672 TTTTATAATGT-TTATGAT
1 TTTTATAAT-TATTATGAT
35454690 TTTTATAATTATTATGAT
1 TTTTATAATTATTATGAT
35454708 TTTT
1 TTTT
35454712 CAACATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (18 bp):
TTTTATAATTATTATGAT
Found at i:35466506 original size:22 final size:23
Alignment explanation
Indices: 35466469--35466512 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
35466459 GGGGGTAAGA
*
35466469 CAAAATTTGCATGAATTTTAAAG
1 CAAAATTTACATGAATTTTAAAG
35466492 CAAAA-TTACATGAATTTTAAA
1 CAAAATTTACATGAATTTTAAA
35466513 TTTTTTCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (23 bp):
CAAAATTTACATGAATTTTAAAG
Found at i:35466607 original size:12 final size:12
Alignment explanation
Indices: 35466590--35466631 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
35466580 AAAAGTTGTT
35466590 CATAAGTTTACA
1 CATAAGTTTACA
35466602 CATAAGTTTACA
1 CATAAGTTTACA
*
35466614 CATATGTTTACA
1 CATAAGTTTACA
35466626 CATAAG
1 CATAAG
35466632 CATGATTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (12 bp):
CATAAGTTTACA
Found at i:35477348 original size:150 final size:150
Alignment explanation
Indices: 35477072--35477368 Score: 549
Period size: 150 Copynumber: 2.0 Consensus size: 150
35477062 TACTCATTTC
35477072 GTAATTCAACATTTACAGATATATAGATATAATTAAGATATTAAAGTATTAATTAAATTATTTAA
1 GTAATTCAACATTTACAGATATATAGATATAATTAAGATATTAAAGTATTAATTAAATTATTTAA
* * *
35477137 AGTAAATACATAGAGTTCGATTTCAAGGACTACAAACTTGCCTTAATCGAAACGGTTGTAAAATA
66 AGTAAATACATAGAGTTCGATTTCAAGGACTAAAAACTTACCTTAATCGAAACGGTCGTAAAATA
35477202 ACATTGGTAACTAATCCAAA
131 ACATTGGTAACTAATCCAAA
35477222 GTAATTCAACATTTACAGATATATAGATATAATTAAGATATTAAAGTATTAATTAAATTATTTAA
1 GTAATTCAACATTTACAGATATATAGATATAATTAAGATATTAAAGTATTAATTAAATTATTTAA
*
35477287 AGTAAATACATAGAGTTCGATTTTAAGGACTAAAAACTTACCTTAATCGAAACGGTCGTAAAATA
66 AGTAAATACATAGAGTTCGATTTCAAGGACTAAAAACTTACCTTAATCGAAACGGTCGTAAAATA
*
35477352 ACGTTGGTAACTAATCC
131 ACATTGGTAACTAATCC
35477369 GAAACTTTTG
Statistics
Matches: 142, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
150 142 1.00
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (150 bp):
GTAATTCAACATTTACAGATATATAGATATAATTAAGATATTAAAGTATTAATTAAATTATTTAA
AGTAAATACATAGAGTTCGATTTCAAGGACTAAAAACTTACCTTAATCGAAACGGTCGTAAAATA
ACATTGGTAACTAATCCAAA
Found at i:35481487 original size:15 final size:15
Alignment explanation
Indices: 35481467--35481496 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
35481457 GCTCCCTCAT
35481467 ACTTGTTTTTTTCAA
1 ACTTGTTTTTTTCAA
35481482 ACTTGTTTTTTTCAA
1 ACTTGTTTTTTTCAA
35481497 GCTTACCTCT
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:0.13, G:0.07, T:0.60
Consensus pattern (15 bp):
ACTTGTTTTTTTCAA
Found at i:35481957 original size:12 final size:12
Alignment explanation
Indices: 35481940--35482037 Score: 56
Period size: 12 Copynumber: 8.1 Consensus size: 12
35481930 TTCAAAAAAG
35481940 AAGAAAAACAAA
1 AAGAAAAACAAA
35481952 AAGAAAAATCAAA
1 AAGAAAAA-CAAA
** **
35481965 ATCAAAGTCAAA
1 AAGAAAAACAAA
35481977 AAG-AAAA-AAA
1 AAGAAAAACAAA
35481987 AAGAAAAATCAAA
1 AAGAAAAA-CAAA
** *
35482000 ATCAAAATCAAA
1 AAGAAAAACAAA
* **
35482012 ATGAAAATGAAA
1 AAGAAAAACAAA
*
35482024 AAGAGAAAAGAAA
1 AAGA-AAAACAAA
35482037 A
1 A
35482038 GCAAAGAAAA
Statistics
Matches: 66, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
10 6 0.09
11 6 0.09
12 30 0.45
13 24 0.36
ACGTcount: A:0.74, C:0.07, G:0.10, T:0.08
Consensus pattern (12 bp):
AAGAAAAACAAA
Found at i:35481965 original size:6 final size:6
Alignment explanation
Indices: 35481956--35482024 Score: 59
Period size: 6 Copynumber: 11.7 Consensus size: 6
35481946 AACAAAAAGA
* ** * **
35481956 AAAATC AAAATC AAAGTC AAAAAG AAAA-A AAAAGA AAAATC AAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
* *
35482003 AAAATC AAAATG AAAATG AAAA
1 AAAATC AAAATC AAAATC AAAA
35482025 AGAGAAAAGA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
5 4 0.07
6 50 0.93
ACGTcount: A:0.72, C:0.09, G:0.07, T:0.12
Consensus pattern (6 bp):
AAAATC
Found at i:35481987 original size:29 final size:30
Alignment explanation
Indices: 35481950--35482025 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
35481940 AAGAAAAACA
** *
35481950 AAAAGAAAAATCAAAATCAAAGTCAAAAAG
1 AAAAGAAAAAGAAAAATCAAAATCAAAAAG
**
35481980 AAAA-AAAAAGAAAAATCAAAATCAAAATC
1 AAAAGAAAAAGAAAAATCAAAATCAAAAAG
*
35482009 AAAATGAAAATGAAAAA
1 AAAA-GAAAAAGAAAAA
35482026 GAGAAAAGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 24 0.63
30 4 0.11
31 10 0.26
ACGTcount: A:0.74, C:0.08, G:0.08, T:0.11
Consensus pattern (30 bp):
AAAAGAAAAAGAAAAATCAAAATCAAAAAG
Found at i:35481988 original size:35 final size:36
Alignment explanation
Indices: 35481944--35482032 Score: 126
Period size: 35 Copynumber: 2.4 Consensus size: 36
35481934 AAAAAGAAGA
*
35481944 AAAACAAAAAGAAAAATCAAAATCAAAGTCAAAAAG
1 AAAACAAAAAGAAAAATCAAAATCAAAATCAAAAAG
*
35481980 AAAA-AAAAAGAAAAATCAAAATCAAAATCAAAATG
1 AAAACAAAAAGAAAAATCAAAATCAAAATCAAAAAG
*
35482015 AAAATGAAAAAGAGAAAA
1 AAAA-CAAAAAGA-AAAA
35482033 GAAAAGCAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
35 33 0.69
36 4 0.08
37 7 0.15
38 4 0.08
ACGTcount: A:0.74, C:0.08, G:0.09, T:0.09
Consensus pattern (36 bp):
AAAACAAAAAGAAAAATCAAAATCAAAATCAAAAAG
Found at i:35481988 original size:41 final size:41
Alignment explanation
Indices: 35481934--35482025 Score: 114
Period size: 41 Copynumber: 2.3 Consensus size: 41
35481924 ACCCAATTCA
* *
35481934 AAAAAG-AAGAAAAACAAAAAGAAAAATCAAAATCAAAGTC
1 AAAAAGAAAAAAAAACAAAAAGAAAAATCAAAATCAAAATC
* ** *
35481974 AAAAAGAAAAAAAAAGAAAAATCAAAATCAAAATCAAAATG
1 AAAAAGAAAAAAAAACAAAAAGAAAAATCAAAATCAAAATC
*
35482015 AAAATGAAAAA
1 AAAAAGAAAAA
35482026 GAGAAAAGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 6 0.14
41 38 0.86
ACGTcount: A:0.75, C:0.08, G:0.09, T:0.09
Consensus pattern (41 bp):
AAAAAGAAAAAAAAACAAAAAGAAAAATCAAAATCAAAATC
Found at i:35482007 original size:47 final size:47
Alignment explanation
Indices: 35481933--35482038 Score: 124
Period size: 47 Copynumber: 2.2 Consensus size: 47
35481923 GACCCAATTC
* *
35481933 AAAAAAGAAGAAAAACAAAAAGAAAAATCAAAATCAAAGTCAAAAAG
1 AAAAAAAAAGAAAAACAAAAAGAAAAATCAAAATCAAAATCAAAAAG
** * *
35481980 AAAAAAAAAGAAAAATC-AAAATCAAAATCAAAATGAAAATGAAAAAG
1 AAAAAAAAAGAAAAA-CAAAAAGAAAAATCAAAATCAAAATCAAAAAG
35482027 AGAAAAGAAAAG
1 A-AAAA-AAAAG
35482039 CAAAGAAAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
47 40 0.80
48 5 0.10
49 5 0.10
ACGTcount: A:0.75, C:0.07, G:0.11, T:0.08
Consensus pattern (47 bp):
AAAAAAAAAGAAAAACAAAAAGAAAAATCAAAATCAAAATCAAAAAG
Found at i:35482412 original size:7 final size:7
Alignment explanation
Indices: 35482400--35482429 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
35482390 AAAAAAAGAG
35482400 ATGAAAA
1 ATGAAAA
35482407 ATG-AAA
1 ATGAAAA
35482413 ATGAAAA
1 ATGAAAA
35482420 ATGAAAA
1 ATGAAAA
35482427 ATG
1 ATG
35482430 GAGAGGCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (7 bp):
ATGAAAA
Found at i:35482416 original size:13 final size:13
Alignment explanation
Indices: 35482400--35482426 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35482390 AAAAAAAGAG
35482400 ATGAAAAATGAAA
1 ATGAAAAATGAAA
35482413 ATGAAAAATGAAA
1 ATGAAAAATGAAA
35482426 A
1 A
35482427 ATGGAGAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
ATGAAAAATGAAA
Found at i:35483970 original size:87 final size:87
Alignment explanation
Indices: 35483642--35484529 Score: 1392
Period size: 87 Copynumber: 10.3 Consensus size: 87
35483632 ATAGATTAGC
* * *
35483642 AAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATAGAAAACAAAGTCTTGCCTCC
1 AAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCC
* *
35483707 ATCGGTTGCAGTGGAGCTAGTT
66 ATCGGTTGTAGTGGAGCTGGTT
* *
35483729 AAAGA-AGCAGATCTTGCCTTCCCGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCC
1 AAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCC
*
35483793 ATCGGTTGTAGTGGAGTTGGTT
66 ATCGGTTGTAGTGGAGCTGGTT
* * *
35483815 AAAGA-AG-AAATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTCC
1 AAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCC
35483878 ATCGGTTGTAGTGGAGCTGGTT
66 ATCGGTTGTAGTGGAGCTGGTT
* * *
35483900 AAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAATAAAGTCTTGCCTCC
1 AAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCC
** *
35483965 ATCGGTTACAGTAGAGCTGGTT
66 ATCGGTTGTAGTGGAGCTGGTT
* * *
35483987 AAAGA-AGCAGATCTTGCCGTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCATTGCCTCC
1 AAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCC
35484051 ATCGGTTGTAGTGGAGCTGGTT
66 ATCGGTTGTAGTGGAGCTGGTT
* *
35484073 GAACATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCC
1 AAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCC
*
35484138 ATCGGTTATAGTGGAGCTGGTT
66 ATCGGTTGTAGTGGAGCTGGTT
* *
35484160 AAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGTCTTGCCTCC
1 AAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCC
*
35484225 ATCGGTTGTAGTGGAGCTAGTT
66 ATCGGTTGTAGTGGAGCTGGTT
* * *
35484247 AAAGA-AGCAGATCTTGCCTTCCTGCGTTAATAGCGAAGCAGATCGAAAACAAAGCTTTGCCTCC
1 AAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCC
35484311 ATCGGTTGTAGTGGAGCTGGTT
66 ATCGGTTGTAGTGGAGCTGGTT
* * * *
35484333 GAAGATAGCAGATCTTGCCTTCTTGCATTAATAGCGAAGCAGATCGAAAACAAAGCCTTGCATCC
1 AAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCC
*
35484398 ATCGGTTGTAGTAGAGCTGGTT
66 ATCGGTTGTAGTGGAGCTGGTT
* *
35484420 CAAGATAGCAGAT-TTGCCTTCCTGCATTAACAGCGAAACAGATCGAAAACAAAGCCTTGCCTCC
1 AAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCC
* *
35484484 ATCGGTTGCAGTGGAGCTGTTT
66 ATCGGTTGTAGTGGAGCTGGTT
35484506 AAAGATAGCAGATCTTGCCTTCCT
1 AAAGATAGCAGATCTTGCCTTCCT
35484530 AAGCACTAGC
Statistics
Matches: 733, Mismatches: 63, Indels: 10
0.91 0.08 0.01
Matches are distributed among these distances:
85 79 0.11
86 314 0.43
87 340 0.46
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (87 bp):
AAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCC
ATCGGTTGTAGTGGAGCTGGTT
Found at i:35484064 original size:173 final size:173
Alignment explanation
Indices: 35483642--35484529 Score: 1374
Period size: 173 Copynumber: 5.1 Consensus size: 173
35483632 ATAGATTAGC
* *
35483642 AAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATAGAAAACAAAGTCTTGCCTCC
1 AAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAG-CTTGCCTCC
* * * *
35483707 ATCGGTTGCAGTGGAGCTAGTTAAAGA-AGCAGATCTTGCCTTCCCGCGTTAACAGCGAAGCAGA
65 ATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGA
*
35483771 TCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGTTGGTT
130 TCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTT
* * *
35483815 AAAGA-AG-AAATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTCC
1 AAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAG-CTTGCCTCC
*
35483878 ATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGA
65 ATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGA
* * ** *
35483943 TCGAAAATAAAGTCTTGCCTCCATCGGTTACAGTAGAGCTGGTT
130 TCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTT
* *
35483987 AAAGA-AGCAGATCTTGCCGTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCATTGCCTCC
1 AAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGC-TTGCCTCC
* *
35484051 ATCGGTTGTAGTGGAGCTGGTTGAACATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGA
65 ATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGA
*
35484116 TCGAAAACAAAGCCTTGCCTCCATCGGTTATAGTGGAGCTGGTT
130 TCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTT
*
35484160 AAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGTCTTGCCTCC
1 AAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAG-CTTGCCTCC
* * *
35484225 ATCGGTTGTAGTGGAGCTAGTTAAAGA-AGCAGATCTTGCCTTCCTGCGTTAATAGCGAAGCAGA
65 ATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGA
*
35484289 TCGAAAACAAAGCTTTGCCTCCATCGGTTGTAGTGGAGCTGGTT
130 TCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTT
* * * *
35484333 GAAGATAGCAGATCTTGCCTTCTTGCATTAATAGCGAAGCAGATCGAAAACAAAGCCTTGCATCC
1 AAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAG-CTTGCCTCC
* * *
35484398 ATCGGTTGTAGTAGAGCTGGTTCAAGATAGCAGAT-TTGCCTTCCTGCATTAACAGCGAAACAGA
65 ATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGA
* *
35484462 TCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGTTT
130 TCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTT
35484506 AAAGATAGCAGATCTTGCCTTCCT
1 AAAGATAGCAGATCTTGCCTTCCT
35484530 AAGCACTAGC
Statistics
Matches: 655, Mismatches: 54, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
171 75 0.11
172 82 0.13
173 412 0.63
174 85 0.13
175 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (173 bp):
AAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCTTGCCTCCA
TCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGAT
CGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTT
Found at i:35484201 original size:260 final size:260
Alignment explanation
Indices: 35483642--35484529 Score: 1496
Period size: 260 Copynumber: 3.4 Consensus size: 260
35483632 ATAGATTAGC
*
35483642 AAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATAGAAAACAAAGTCTTGCCTCC
1 AAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGTCTTGCCTCC
*
35483707 ATCGGTTGCAGTGGAGCTAGTTAAAGAAGCAGATCTTGCCTTCCCGCGTTAACAGCGAAGCAGAT
66 ATCGGTTGCAGTGGAGCTAGTTAAAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGAT
* * * *
35483772 CGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGTTGGTTAAAGA-AG-AAATCTTGCCTTC
131 CGAAAACAAAGCATTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTC
* *
35483835 CTGCGTTAACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTT
196 CTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTT
*
35483900 AAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAATAAAGTCTTGCCTCC
1 AAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGTCTTGCCTCC
* * * *
35483965 ATCGGTTACAGTAGAGCTGGTTAAAGAAGCAGATCTTGCCGTCCTGCGTTAACAGCGAAGCAGAT
66 ATCGGTTGCAGTGGAGCTAGTTAAAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGAT
*
35484030 CGAAAACAAAGCATTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAACATAGCAGATCTTGCCTTC
131 CGAAAACAAAGCATTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTC
*
35484095 CTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTATAGTGGAGCTGGTT
196 CTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTT
35484160 AAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGTCTTGCCTCC
1 AAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGTCTTGCCTCC
* *
35484225 ATCGGTTGTAGTGGAGCTAGTTAAAGAAGCAGATCTTGCCTTCCTGCGTTAATAGCGAAGCAGAT
66 ATCGGTTGCAGTGGAGCTAGTTAAAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGAT
*
35484290 CGAAAACAAAGCTTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTC
131 CGAAAACAAAGCATTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTC
* * * *
35484355 TTGCATTAATAGCGAAGCAGATCGAAAACAAAGCCTTGCATCCATCGGTTGTAGTAGAGCTGGTT
196 CTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTT
* * * *
35484420 CAAGATAGCAGAT-TTGCCTTCCTGCATTAACAGCGAAACAGATCGAAAACAAAGCCTTGCCTCC
1 AAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGTCTTGCCTCC
35484484 ATCGGTTGCAGTGGAGCT-GTTTAAAGATAGCAGATCTTGCCTTCCT
66 ATCGGTTGCAGTGGAGCTAG-TTAAAGA-AGCAGATCTTGCCTTCCT
35484530 AAGCACTAGC
Statistics
Matches: 592, Mismatches: 34, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
258 168 0.28
259 74 0.12
260 350 0.59
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (260 bp):
AAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGTCTTGCCTCC
ATCGGTTGCAGTGGAGCTAGTTAAAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGAT
CGAAAACAAAGCATTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTC
CTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTT
Found at i:35484888 original size:44 final size:43
Alignment explanation
Indices: 35484776--35484934 Score: 140
Period size: 44 Copynumber: 3.6 Consensus size: 43
35484766 TCGCATCGGG
* * *
35484776 TCTTATCTCCCTGAAGTTGCAGCGAAGCAGACTGAGAAAACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGA-AAAACAAA
* *** *
35484820 TCTTATCCCCCTGAAGTCATAGTGGGGCAGACTGAAAAAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAAAA-CAAA
* * * **
35484864 TCTTATTTCCCTGAGGTTGCAGTGGAGCAGATTG-AATTCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAAAAC-A-AA
* *
35484908 TCTTATCTCCTTGAAGTTGTAGTGGAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAG
35484935 TGGATCGAAG
Statistics
Matches: 90, Mismatches: 22, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
42 1 0.01
43 7 0.08
44 82 0.91
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (43 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAAAACAAA
Found at i:35497215 original size:40 final size:40
Alignment explanation
Indices: 35497171--35497478 Score: 553
Period size: 40 Copynumber: 7.7 Consensus size: 40
35497161 GCAAACACAT
* * *
35497171 TTGCCTTCGGGTCTTAGCCCGAACATATCAACTCGCATAA
1 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
*
35497211 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
35497251 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
*
35497291 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
*
35497331 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
35497371 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
35497411 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
*
35497451 TTGCCTTCGGGTCATAGCCCGGATATAT
1 TTGCCTTCGGGTCCTAGCCCGGATATAT
35497479 TCCAATGCTC
Statistics
Matches: 261, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 261 1.00
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (40 bp):
TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
Found at i:35505838 original size:40 final size:40
Alignment explanation
Indices: 35505794--35506101 Score: 553
Period size: 40 Copynumber: 7.7 Consensus size: 40
35505784 GCAAACACAT
* * *
35505794 TTGCCTTCGGGTCTTAGCCCGAACATATCAACTCGCATAA
1 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
*
35505834 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
35505874 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
*
35505914 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
*
35505954 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
35505994 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
35506034 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
*
35506074 TTGCCTTCGGGTCATAGCCCGGATATAT
1 TTGCCTTCGGGTCCTAGCCCGGATATAT
35506102 TCCAATGCTC
Statistics
Matches: 261, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 261 1.00
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (40 bp):
TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
Found at i:35513829 original size:20 final size:20
Alignment explanation
Indices: 35513783--35513832 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
35513773 TATCATGGTC
35513783 TTTGCTT-CTTCTTTACTTA
1 TTTGCTTACTTCTTTACTTA
* *
35513802 -CTGTCTTACTTGTTTACTTA
1 TTTG-CTTACTTCTTTACTTA
35513822 TTTGCTTACTT
1 TTTGCTTACTT
35513833 AAATAACTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 2 0.08
19 3 0.12
20 18 0.72
21 2 0.08
ACGTcount: A:0.12, C:0.20, G:0.08, T:0.60
Consensus pattern (20 bp):
TTTGCTTACTTCTTTACTTA
Found at i:35514113 original size:50 final size:50
Alignment explanation
Indices: 35514036--35514180 Score: 170
Period size: 50 Copynumber: 2.9 Consensus size: 50
35514026 ATAATAAAAT
* * *
35514036 GCCAAAGCCATGTCCCAA-ACATGGTCTTACATGGGAGTTCTCATATCGGT
1 GCCAACGCCATGT-CCAAGACATGGTCTTACATGGGAGCTCTCATATCGGC
* * *
35514086 GCCCATGCCATGTCCAAGACATGGTCTTAC--GGGAGACCTCTCATCTCGGC
1 GCCAACGCCATGTCCAAGACATGGTCTTACATGGGAG--CTCTCATATCGGC
* *
35514136 GCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
1 GCCAACGCCATGTCCAAGACATGGTCTTACATGGGAGCTCTCATA
35514181 ACCTCAATAA
Statistics
Matches: 80, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
48 5 0.06
49 4 0.05
50 67 0.84
52 4 0.05
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.23
Consensus pattern (50 bp):
GCCAACGCCATGTCCAAGACATGGTCTTACATGGGAGCTCTCATATCGGC
Found at i:35514212 original size:56 final size:56
Alignment explanation
Indices: 35514137--35514288 Score: 250
Period size: 56 Copynumber: 2.7 Consensus size: 56
35514127 CATCTCGGCG
*
35514137 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATAATT
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATAATT
* **
35514193 CCAATTCCATGTCTTAGACATGGTCTTACATGGGACCTCTCATAACCTCAATAATT
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATAATT
* *
35514249 CGAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
35514289 TCCTCTTAAT
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 87 1.00
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (56 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATAATT
Found at i:35517285 original size:21 final size:21
Alignment explanation
Indices: 35517261--35517300 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
35517251 AACTTGAAAA
35517261 CATAA-TATAAAAATAGAGTGT
1 CATAACTA-AAAAATAGAGTGT
35517282 CATAACTAAAAAATAGAGT
1 CATAACTAAAAAATAGAGT
35517301 TTCAAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.55, C:0.07, G:0.12, T:0.25
Consensus pattern (21 bp):
CATAACTAAAAAATAGAGTGT
Found at i:35523886 original size:49 final size:50
Alignment explanation
Indices: 35523763--35523932 Score: 200
Period size: 50 Copynumber: 3.4 Consensus size: 50
35523753 TATCCCAAAT
** * * *
35523763 ATGGTCTTACATGGGAGTTCTCATAC-AGGTGCCCATGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCAT-CTCGGTGCCAACGCCATGTCCCAGAC
* ** *
35523813 ATGGTTTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCTC-GAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
* * *
35523862 ATGGTCTTACATGGGACCTATCATCTCGATGACAACGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
*
35523912 ATGGTCTTACATGGGATCTCT
1 ATGGTCTTACATGGGACCTCT
35523933 TTGCCCAAAT
Statistics
Matches: 100, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
49 43 0.43
50 57 0.57
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.27
Consensus pattern (50 bp):
ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
Found at i:35528324 original size:583 final size:585
Alignment explanation
Indices: 35527210--35528385 Score: 2149
Period size: 583 Copynumber: 2.0 Consensus size: 585
35527200 TGAATTCCAT
* *
35527210 TCTAGTATAGCCTAATTTTTTTTAGGATCTATCTTAATCCCATCTAGGGAGATGACATGGCCAAA
1 TCTAGCATAGCCTAAATTTTTTTAGGATCTATCTTAATCCCATCTAGGGAGATGACATGGCCAAA
*
35527275 AAAGTGAACATCCTTCAAGCAAAACTTACTATTGCTAAATTTGGTGTACAGTTTGTTTTTCTCGA
66 AAAGTGAACATCCTTCAAGCAAAACTCACTATTGCTAAATTTGGTGTACAGTTTGTTTTTCTCGA
* *
35527340 AGAACATTTAAAATTATCCGTAAGTGTTCCTCGTGCTCTGCCTCACTCTTCAAGTAAATCAAAAT
131 AGAACATTTAAAATTATCCGTAAGTGTTCCTCGTGCTCCGCCTCACTATTCAAGTAAATCAAAAT
* *
35527405 ATTATCAATGAAGATGAAAACACATCGATCGAGGTAAGGTTGGAATACTCTATTCATCAAATCTA
196 ATTATCAATGAAGACGAAAACACATCGATAGAGGTAAGGTTGGAATACTCTATTCATCAAATCTA
*
35527470 TGAACACTGCTAGCGTATTAGTCCAGCCAAAAGGCGTCCTAGAAATTCATAATGCCCGTAATGTG
261 TGAACACTGCTAGCGTATTAGTCCAGCCAAAAGGAGTCCTAGAAATTCATAATGCCCGTAATGTG
*
35527535 TGTGAAATGCAATCTTAGGAATATTATCCCCTTAGATCTTAACTTGATAATACCTCGACTATAGA
326 TGTGAAATGCAATCTTAGAAATATTATCCCCTTAGATCTTAACTTGATAATACCTCGACTATAGA
*
35527600 TCAATCTTTGAGAACACTCTGGCTCTACTCAGTTGATCAACCAAGTCCTCAATCCTAGGCAACAG
391 TCAATCTTTGAGAACACTCTGGCTCTACTCAGTTGATCAACCAAGTCCTCAATCCTAGGCAAAAG
* *
35527665 ATACTTATTCTTAATGGTAACCTTGTTCAGCTGCCTATAATCAATACACAATCGGAGGGTCTCAT
456 ATACTTATTCTTAATGGTAACCTTGTTCAGCTGCCTATAACCAATACACAATCAGAGGGTCTCAT
* *
35527730 CTTTTTTCTTAAAAGATAATATTGGCGTACCCCAAGGCGAAACACTTGGTCTAATGAACCCCTTA
521 CCTTTTTCTTAAAAAATAATATTGGCGTACCCCAAGGCGAAACACTTGGTCTAATGAACCCCTTA
35527795 TCTAGCATAGCCTAAATTTTTTTAGGATCTATCTTAATCCCATCTAGGGAGATGACATGGCCAAA
1 TCTAGCATAGCCTAAATTTTTTTAGGATCTATCTTAATCCCATCTAGGGAGATGACATGGCCAAA
*
35527860 AAGGTGAACATCCTTCAAGCAAAACTCACTATTGCTAAATTTGGTGTACAGTTTG-TTTTCTCGA
66 AAAGTGAACATCCTTCAAGCAAAACTCACTATTGCTAAATTTGGTGTACAGTTTGTTTTTCTCGA
*
35527924 AGAACATTT-AAATTATCCGTAAGTGTTCCTCGTGCTCCGCCTTACTATTCAAGTAAATCAAAAT
131 AGAACATTTAAAATTATCCGTAAGTGTTCCTCGTGCTCCGCCTCACTATTCAAGTAAATCAAAAT
*
35527988 ATTATCAATGAAGACGAAAACACATCGATAGAGGTAGGGTTGGAATACTCTATTCATCAAATCTA
196 ATTATCAATGAAGACGAAAACACATCGATAGAGGTAAGGTTGGAATACTCTATTCATCAAATCTA
35528053 TGAACACTGCTAGCGTATTAGTCCAGCCAAAAGGAGTCCTAGAAATTCATAATGCCCGTAATGTG
261 TGAACACTGCTAGCGTATTAGTCCAGCCAAAAGGAGTCCTAGAAATTCATAATGCCCGTAATGTG
*
35528118 TGTGAAATGCAGTCTTAGAAATATTATCCCCTTAGATCTTAACTTGATAATACCTCGACTATAGA
326 TGTGAAATGCAATCTTAGAAATATTATCCCCTTAGATCTTAACTTGATAATACCTCGACTATAGA
*
35528183 TCAATCTTTGAGAACACTCTGGCTCTACTTAGTTGATCAACCAAGTCCTCAATCCTAGGCAAAAG
391 TCAATCTTTGAGAACACTCTGGCTCTACTCAGTTGATCAACCAAGTCCTCAATCCTAGGCAAAAG
* *
35528248 ATACTTATTCTTAATGGTCACCTTGTTCAGTTGCCTATAACCAATACACAATCAGAGGGTCTCAT
456 ATACTTATTCTTAATGGTAACCTTGTTCAGCTGCCTATAACCAATACACAATCAGAGGGTCTCAT
35528313 CCTTTTTCTTAAAAAATAATATTGGCGTACCCCAAGGCGAAACACTTGGTCTAATGAACCCCTTA
521 CCTTTTTCTTAAAAAATAATATTGGCGTACCCCAAGGCGAAACACTTGGTCTAATGAACCCCTTA
35528378 TCTAGCAT
1 TCTAGCAT
35528386 TTTTTGCAAC
Statistics
Matches: 570, Mismatches: 21, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
583 436 0.76
584 18 0.03
585 116 0.20
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (585 bp):
TCTAGCATAGCCTAAATTTTTTTAGGATCTATCTTAATCCCATCTAGGGAGATGACATGGCCAAA
AAAGTGAACATCCTTCAAGCAAAACTCACTATTGCTAAATTTGGTGTACAGTTTGTTTTTCTCGA
AGAACATTTAAAATTATCCGTAAGTGTTCCTCGTGCTCCGCCTCACTATTCAAGTAAATCAAAAT
ATTATCAATGAAGACGAAAACACATCGATAGAGGTAAGGTTGGAATACTCTATTCATCAAATCTA
TGAACACTGCTAGCGTATTAGTCCAGCCAAAAGGAGTCCTAGAAATTCATAATGCCCGTAATGTG
TGTGAAATGCAATCTTAGAAATATTATCCCCTTAGATCTTAACTTGATAATACCTCGACTATAGA
TCAATCTTTGAGAACACTCTGGCTCTACTCAGTTGATCAACCAAGTCCTCAATCCTAGGCAAAAG
ATACTTATTCTTAATGGTAACCTTGTTCAGCTGCCTATAACCAATACACAATCAGAGGGTCTCAT
CCTTTTTCTTAAAAAATAATATTGGCGTACCCCAAGGCGAAACACTTGGTCTAATGAACCCCTTA
Found at i:35538248 original size:26 final size:25
Alignment explanation
Indices: 35538218--35538359 Score: 85
Period size: 26 Copynumber: 5.6 Consensus size: 25
35538208 AATTTAAAGC
35538218 AAATAATATGTAAAACAAATTAAAAT
1 AAATAATATGTAAAA-AAATTAAAAT
* * *
35538244 GAATAATAT-TCAAAGCAATTTAAAAAT
1 AAATAATATGT-AAA-AAAATT-AAAAT
* * * *
35538271 AAATAACATATAAAATAATT--TA-
1 AAATAATATGTAAAAAAATTAAAAT
**
35538293 AAATAATATGTAAAAAGTTTAAAAT
1 AAATAATATGTAAAAAAATTAAAAT
* *
35538318 AAATAATATGTCAAAAGAAATCTTAAGT
1 AAATAATATGT-AAAA-AAAT-TAAAAT
*
35538346 GAATAATATGTAAA
1 AAATAATATGTAAA
35538360 CAATTTTATT
Statistics
Matches: 86, Mismatches: 20, Indels: 19
0.69 0.16 0.15
Matches are distributed among these distances:
22 15 0.17
23 1 0.01
24 1 0.01
25 12 0.14
26 22 0.26
27 20 0.23
28 15 0.17
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (25 bp):
AAATAATATGTAAAAAAATTAAAAT
Found at i:35538313 original size:21 final size:22
Alignment explanation
Indices: 35538271--35538319 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
35538261 ATTTAAAAAT
35538271 AAATAACATATAAAATAATTTA
1 AAATAACATATAAAATAATTTA
* * *
35538293 AAATAATATGTAAAA-AGTTTA
1 AAATAACATATAAAATAATTTA
35538314 AAATAA
1 AAATAA
35538320 ATAATATGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (22 bp):
AAATAACATATAAAATAATTTA
Found at i:35538526 original size:26 final size:26
Alignment explanation
Indices: 35538488--35538555 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 26
35538478 TTAACATAGT
**
35538488 TTAAAATGCATAATATAT-GAAAAAAA
1 TTAAAATAAATAATATATAG-AAAAAA
* * *
35538514 TTAAAATATATAATA-ATAGAATAAT
1 TTAAAATAAATAATATATAGAAAAAA
35538539 TTAAAATAAATAATATA
1 TTAAAATAAATAATATA
35538556 AATTTTAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 20 0.57
26 15 0.43
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (26 bp):
TTAAAATAAATAATATATAGAAAAAA
Found at i:35538562 original size:21 final size:22
Alignment explanation
Indices: 35538514--35538579 Score: 82
Period size: 21 Copynumber: 3.0 Consensus size: 22
35538504 ATGAAAAAAA
*
35538514 TTAAAATATATAATAATAGAATAAT
1 TTAAAATAAATAAT-ATA-AAT-AT
35538539 TTAAAATAAATAATATAAAT-T
1 TTAAAATAAATAATATAAATAT
35538560 TTAAAATAAATAA-ATAAATA
1 TTAAAATAAATAATATAAATA
35538580 AATAAATTGC
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
20 6 0.15
21 14 0.36
23 3 0.08
24 3 0.08
25 13 0.33
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
TTAAAATAAATAATATAAATAT
Found at i:35538594 original size:29 final size:29
Alignment explanation
Indices: 35538542--35538598 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
35538532 GAATAATTTA
**
35538542 AAATAAATAATATAAATTTTAAAATAAAT
1 AAATAAATAATATAAATTCAAAAATAAAT
35538571 AAATAAATAA-ATAAATTGCAAAAATAAA
1 AAATAAATAATATAAATT-CAAAAATAAA
35538599 GTGAAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (29 bp):
AAATAAATAATATAAATTCAAAAATAAAT
Found at i:35539506 original size:43 final size:43
Alignment explanation
Indices: 35539450--35539536 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
35539440 TTTGTGGTTA
35539450 TAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTCATGATT
1 TAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTCATGATT
*
35539493 TAGTCTTCTCCACTGCAACTTCAGGGAGATAAGACTCATGATT
1 TAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTCATGATT
35539536 T
1 T
35539537 TGACCTGCCC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (43 bp):
TAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTCATGATT
Found at i:35539826 original size:89 final size:89
Alignment explanation
Indices: 35539677--35540239 Score: 729
Period size: 89 Copynumber: 6.3 Consensus size: 89
35539667 CTTCAACCTA
* * * * * * * * *
35539677 CTCCACTGCAAACTCAGAGAGG-CAAGGTTGATGTTTTTGATATGCTTCACTGCCAGTACAGGAA
1 CTCCGCTGCAAACTCAGGGAGGTC-AGGCTGGTGTCTTCGATCTGCTTCGCTGCCAATACAGGAA
* * * *
35539741 TACAAGATCTGTTGTTTTCAGTCTG
65 GACAAGATCTGCTATCTTCAGTCTG
* *
35539766 CTCCGCTGCAAACTTAGGAAGG-CGAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAATACAGGAA
1 CTCCGCTGCAAACTCAGGGAGGTC-AGGCTGGTGTCTTCGATCTGCTTCGCTGCCAATACAGGAA
*
35539830 GACAAGATCTACTATCTTCAGTCTG
65 GACAAGATCTGCTATCTTCAGTCTG
* * * *
35539855 TTTCGCTGCAAACTTAGGGAGG-CGAGGCTGGTGTCTTCGATCTGCTTCGTTGCCAATACAGGAA
1 CTCCGCTGCAAACTCAGGGAGGTC-AGGCTGGTGTCTTCGATCTGCTTCGCTGCCAATACAGGAA
*
35539919 GACAAGATTTGCTATCTTCAGTCTG
65 GACAAGATCTGCTATCTTCAGTCTG
* *
35539944 CTCCGCTGCAAACTCAGGGAGGTCAGGCTAGTGTCTTCGATCTACTTCGCTG-CAAGTACAGGAA
1 CTCCGCTGCAAACTCAGGGAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAA-TACAGGAA
*
35540008 AACAAGATCTGCTATCTTCAGTCTG
65 GACAAGATCTGCTATCTTCAGTCTG
*** * * *
35540033 CTCTATTGCAAACTCAGGGAGGTCAGGCTGATGTCCTCGATCTGCTTCGCTGCCAATATAGGAAG
1 CTCCGCTGCAAACTCAGGGAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAATACAGGAAG
*
35540098 ACAAGATCTGCTATCTTCAGTCTA
66 ACAAGATCTGCTATCTTCAGTCTG
* * *
35540122 CTCCGCTGCAAACTCAAGGAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGAAAG
1 CTCCGCTGCAAACTCAGGGAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAATACAGGAAG
*
35540187 ACAAGATCTGCTATCTTCAATCTG
66 ACAAGATCTGCTATCTTCAGTCTG
* *
35540211 CTCCCCTGCAAATTCAGGGAGGTCAGGCT
1 CTCCGCTGCAAACTCAGGGAGGTCAGGCT
35540240 AGATATGATG
Statistics
Matches: 416, Mismatches: 55, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
88 3 0.01
89 409 0.98
90 4 0.01
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.28
Consensus pattern (89 bp):
CTCCGCTGCAAACTCAGGGAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAATACAGGAAG
ACAAGATCTGCTATCTTCAGTCTG
Found at i:35539862 original size:45 final size:45
Alignment explanation
Indices: 35539719--35540212 Score: 206
Period size: 45 Copynumber: 11.1 Consensus size: 45
35539709 GTTTTTGATA
* * * * * *
35539719 TGCTTCACTGCCAGTACAGGAATACAAGATCTGTTGTTTTCAGTC
1 TGCTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTC
* * * * * *
35539764 TGCTCCGCTG-CAA-ACTTAGGAAGGCGAG-GCTGGTGTCTTC-GATC
1 TGCTTCGCTGCCAATAC--AGGAAGACAAGATCTGCTATCTTCAG-TC
*
35539808 TGCTTCGCTGCCAATACAGGAAGACAAGATCTACTATCTTCAGTC
1 TGCTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTC
* * * * * * *
35539853 TGTTTCGCTG-CAA-ACTTAGGGAGGCGAG-GCTGGTGTCTTC-GATC
1 TGCTTCGCTGCCAATAC--AGGAAGACAAGATCTGCTATCTTCAG-TC
* *
35539897 TGCTTCGTTGCCAATACAGGAAGACAAGATTTGCTATCTTCAGTC
1 TGCTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTC
* * * * * *
35539942 TGCTCCGCTGCAAACT-CAGGGAGGTC-AG-GCTAG-TGTCTTC-GATC
1 TGCTTCGCTGCCAA-TACA-GGAAGACAAGATCT-GCTATCTTCAG-TC
* *
35539986 TACTTCGCTG-CAAGTACAGGAAAACAAGATCTGCTATCTTCAGTC
1 TGCTTCGCTGCCAA-TACAGGAAGACAAGATCTGCTATCTTCAGTC
** * * * * * * *
35540031 TGC-TCTATTGCAAACT-CAGGGAGGTC-AG-GCTGATGTCCTC-GATC
1 TGCTTC-GCTGCCAA-TACA-GGAAGACAAGATCTGCTATCTTCAG-TC
*
35540075 TGCTTCGCTGCCAATATAGGAAGACAAGATCTGCTATCTTCAGTC
1 TGCTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTC
* * * * * * * *
35540120 TACTCCGCTGCAAACT-CAAGGAGGTC-AG-GCTGGTGTCTTC-GATC
1 TGCTTCGCTGCCAA-TAC-AGGAAGACAAGATCTGCTATCTTCAG-TC
* * *
35540164 TGCTTCGCTGCCAGTACAGAAAGACAAGATCTGCTATCTTCAATC
1 TGCTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTC
35540209 TGCT
1 TGCT
35540213 CCCCTGCAAA
Statistics
Matches: 318, Mismatches: 92, Indels: 78
0.65 0.19 0.16
Matches are distributed among these distances:
43 28 0.09
44 129 0.41
45 133 0.42
46 28 0.09
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.28
Consensus pattern (45 bp):
TGCTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTC
Found at i:35551893 original size:24 final size:23
Alignment explanation
Indices: 35551844--35551913 Score: 59
Period size: 24 Copynumber: 2.9 Consensus size: 23
35551834 GAAACAAAAT
* ** *
35551844 AATATATAGAACAATTTGGAGTA
1 AATATATAAAACAATTTAAAGCA
35551867 AATAGTATAAAACAATTTAAAGCA
1 AATA-TATAAAACAATTTAAAGCA
*
35551891 AATAATATGTAAAACAAATTAAA
1 AAT-ATA--TAAAACAATTTAAA
35551914 ATGAATAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
23 4 0.11
24 20 0.53
25 1 0.03
26 13 0.34
ACGTcount: A:0.57, C:0.06, G:0.10, T:0.27
Consensus pattern (23 bp):
AATATATAAAACAATTTAAAGCA
Found at i:35551967 original size:27 final size:26
Alignment explanation
Indices: 35551840--35551970 Score: 108
Period size: 26 Copynumber: 5.1 Consensus size: 26
35551830 AAACGAAACA
* ** *
35551840 AAATAATATATAGAACAATTTGGAGT
1 AAATAATATATAAAACAATTTAAAAT
* **
35551866 AAAT-A-GTATAAAACAATTTAAAGC
1 AAATAATATATAAAACAATTTAAAAT
* *
35551890 AAATAATATGTAAAACAAATTAAAAT
1 AAATAATATATAAAACAATTTAAAAT
*
35551916 GAATAATAT-TCAAAGA-AATTTAAAAAT
1 AAATAATATAT-AAA-ACAATTT-AAAAT
*
35551943 AAATAACATATAAAACAATTTAAAAT
1 AAATAATATATAAAACAATTTAAAAT
35551969 AA
1 AA
35551971 TATGTAAAAG
Statistics
Matches: 84, Mismatches: 14, Indels: 14
0.75 0.12 0.12
Matches are distributed among these distances:
24 18 0.21
25 3 0.04
26 41 0.49
27 21 0.25
28 1 0.01
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.27
Consensus pattern (26 bp):
AAATAATATATAAAACAATTTAAAAT
Found at i:35552208 original size:26 final size:26
Alignment explanation
Indices: 35552170--35552237 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 26
35552160 TTAACATAGT
**
35552170 TTAAAATGCATAATATAT-GAAAAAAC
1 TTAAAATAAATAATATATAG-AAAAAC
* *
35552196 TTAAAATAAATAATA-ATAGAATAAT
1 TTAAAATAAATAATATATAGAAAAAC
35552221 TTAAAATAAATAATATA
1 TTAAAATAAATAATATA
35552238 AAGTTTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 21 0.58
26 15 0.42
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (26 bp):
TTAAAATAAATAATATATAGAAAAAC
Found at i:35552251 original size:21 final size:21
Alignment explanation
Indices: 35552191--35552259 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 21
35552181 AATATATGAA
*
35552191 AAAACTTAAAATAAATAATAAT
1 AAAATTTAAAATAAATAAT-AT
35552213 AGAATAATTTAAAATAAATAATAT
1 --AA-AATTTAAAATAAATAATAT
*
35552237 AAAGTTTAAAATAAATAA-AT
1 AAAATTTAAAATAAATAATAT
35552257 AAA
1 AAA
35552260 TAAATAAAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.12
21 15 0.36
22 2 0.05
24 4 0.10
25 16 0.38
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (21 bp):
AAAATTTAAAATAAATAATAT
Found at i:35552267 original size:21 final size:21
Alignment explanation
Indices: 35552196--35552267 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 21
35552186 ATGAAAAAAC
35552196 TTAAAATAAATAATAATAGAATAA
1 TTAAAATAAAT-A-AATA-AATAA
35552220 TTTAAAATAAATAATATAAAGT--
1 -TTAAAATAAATAA-ATAAA-TAA
35552242 TTAAAATAAATAAATAAATAA
1 TTAAAATAAATAAATAAATAA
*
35552263 ATAAA
1 TTAAA
35552268 GTGAAATCTA
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
19 1 0.02
20 5 0.12
21 17 0.40
23 3 0.07
24 5 0.12
25 11 0.26
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (21 bp):
TTAAAATAAATAAATAAATAA
Found at i:35555657 original size:29 final size:28
Alignment explanation
Indices: 35555625--35555685 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
35555615 AAAGGCCGGT
35555625 TTTTTTCAA-AATTTACCGAAATGGGCCGA
1 TTTTTT-AATAATTTACCGAAATGGGCC-A
* * *
35555654 TTTTTTAATTATTTACTGGAATGGGCCA
1 TTTTTTAATAATTTACCGAAATGGGCCA
35555682 TTTT
1 TTTT
35555686 CCGCGAAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.25
29 21 0.75
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.44
Consensus pattern (28 bp):
TTTTTTAATAATTTACCGAAATGGGCCA
Found at i:35567562 original size:27 final size:26
Alignment explanation
Indices: 35567505--35567564 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 26
35567495 TTTTAACTTT
* *
35567505 CTTTTTTTCTTCCTTATTTTCCATTCT
1 CTTTTTTTCTCCCTTATTTTCCA-TCC
35567532 CTTTTGTTTCTCCCTCTATTTTCC-TCC
1 CTTTT-TTTCTCCCT-TATTTTCCATCC
35567559 CTTTTT
1 CTTTTT
35567565 CATTTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 1 0.03
27 12 0.41
28 8 0.28
29 8 0.28
ACGTcount: A:0.05, C:0.30, G:0.02, T:0.63
Consensus pattern (26 bp):
CTTTTTTTCTCCCTTATTTTCCATCC
Found at i:35573958 original size:22 final size:22
Alignment explanation
Indices: 35573932--35573974 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
35573922 TTTTTAATTT
* *
35573932 AAAAAAATTTATTGATTAAATCG
1 AAAAAAA-TTAATAATTAAATCG
35573955 AAAAAAATTAATAATTAAAT
1 AAAAAAATTAATAATTAAAT
35573975 TATCAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (22 bp):
AAAAAAATTAATAATTAAATCG
Found at i:35576045 original size:24 final size:24
Alignment explanation
Indices: 35576013--35576088 Score: 100
Period size: 24 Copynumber: 3.1 Consensus size: 24
35576003 TACTTTCTAA
35576013 TTAAGTGCTCTTCGGAGCTTCCCG
1 TTAAGTGCTCTTCGGAGCTTCCCG
*
35576037 TTAAGTGCTCTTCGGAGCTACCCG
1 TTAAGTGCTCTTCGGAGCTTCCCG
* *
35576061 ATATAG-GCTCTTTGTGAGCTTCCCG
1 TTA-AGTGCTCTTCG-GAGCTTCCCG
35576086 TTA
1 TTA
35576089 TTAAGCCCGA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
24 32 0.71
25 13 0.29
ACGTcount: A:0.16, C:0.26, G:0.24, T:0.34
Consensus pattern (24 bp):
TTAAGTGCTCTTCGGAGCTTCCCG
Found at i:35581573 original size:54 final size:54
Alignment explanation
Indices: 35581480--35581606 Score: 141
Period size: 54 Copynumber: 2.4 Consensus size: 54
35581470 GGTCCACATG
*
35581480 GGCACAGAGAGTTACACAGCCTGGCGACACGACCGTGTGACCCTGAGCTACAC-
1 GGCACAGAGAGTTACACAGCCTGGCGACACGACCATGTGACCCTGAGCTACACA
* * * * * * * *
35581533 GGTCACAGAGAGTTACACGGCGTGGTGTCATGGCCATGTGATCCTGAGTTACACA
1 GG-CACAGAGAGTTACACAGCCTGGCGACACGACCATGTGACCCTGAGCTACACA
35581588 GGCACAGTA-AGTTACACAG
1 GGCACAG-AGAGTTACACAG
35581607 TCTACGTACA
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
53 2 0.03
54 56 0.92
55 3 0.05
ACGTcount: A:0.27, C:0.26, G:0.29, T:0.18
Consensus pattern (54 bp):
GGCACAGAGAGTTACACAGCCTGGCGACACGACCATGTGACCCTGAGCTACACA
Found at i:35584921 original size:25 final size:25
Alignment explanation
Indices: 35584893--35584940 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
35584883 CACAGCTCAA
*
35584893 ATGAGCTTCTCGTTATTCAGCTCGC
1 ATGAGCTTCCCGTTATTCAGCTCGC
*
35584918 ATGAGCTTCCCGTTATTTAGCTC
1 ATGAGCTTCCCGTTATTCAGCTC
35584941 AGAAGAGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.38
Consensus pattern (25 bp):
ATGAGCTTCCCGTTATTCAGCTCGC
Found at i:35584948 original size:25 final size:25
Alignment explanation
Indices: 35584885--35584950 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
35584875 GGACTCACCA
*
35584885 CAGCTCA-AATGAGCTTCTCGTTATT
1 CAGCTCAGAA-GAGCTTCCCGTTATT
*
35584910 CAGCTC-GCATGAGCTTCCCGTTATT
1 CAGCTCAG-AAGAGCTTCCCGTTATT
*
35584935 TAGCTCAGAAGAGCTT
1 CAGCTCAGAAGAGCTT
35584951 ATTGTTTACA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
25 32 0.94
26 2 0.06
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.32
Consensus pattern (25 bp):
CAGCTCAGAAGAGCTTCCCGTTATT
Found at i:35586792 original size:2 final size:2
Alignment explanation
Indices: 35586785--35586822 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
35586775 TTACACCCTT
35586785 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
35586823 TATATATAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:35595070 original size:37 final size:37
Alignment explanation
Indices: 35595020--35595093 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
35595010 ATTGTCAAAG
35595020 TTAACCTTTGAGAGTAGTAAATTTCTACGCCCTAAAC
1 TTAACCTTTGAGAGTAGTAAATTTCTACGCCCTAAAC
35595057 TTAACCTTTGAGAGTAGTAAATTTCTACGCCCTAAAC
1 TTAACCTTTGAGAGTAGTAAATTTCTACGCCCTAAAC
35595094 AGTTGTCATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (37 bp):
TTAACCTTTGAGAGTAGTAAATTTCTACGCCCTAAAC
Found at i:35597422 original size:28 final size:29
Alignment explanation
Indices: 35597373--35597431 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
35597363 TTTCATGATT
35597373 ATAAATATATATTTTTATAATTATAAATA
1 ATAAATATATATTTTTATAATTATAAATA
*
35597402 ATAAAT-TATAATTTTTA-AATTTTAAATA
1 ATAAATATAT-ATTTTTATAATTATAAATA
35597430 AT
1 AT
35597432 TTTTTAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 15 0.54
29 13 0.46
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
ATAAATATATATTTTTATAATTATAAATA
Found at i:35597822 original size:17 final size:17
Alignment explanation
Indices: 35597797--35597840 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
35597787 TGAAATTTTT
35597797 ATATATAAAAAAGTAAA
1 ATATATAAAAAAGTAAA
* *
35597814 ATATTTAAAAATGTAAA
1 ATATATAAAAAAGTAAA
*
35597831 GAAATATAAA
1 -ATATATAAA
35597841 TTTCATAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (17 bp):
ATATATAAAAAAGTAAA
Found at i:35598351 original size:87 final size:83
Alignment explanation
Indices: 35598253--35598411 Score: 237
Period size: 87 Copynumber: 1.9 Consensus size: 83
35598243 TTTGAAAATT
*
35598253 TTGAAGATCTTTTTGATACATTTTGAAAGTTCAAGTACTCAATTGAGTGAAAAAAACATAGGCTT
1 TTGAAAATCTTTTTGATACATTTTGAAAGTTCAAGTACTCAATTGAGTG-AAAAAA-A-AGGCTT
35598318 AATTACTTTTTTTGAAAAAAAA
63 AATTA-TTTTTTTGAAAAAAAA
** * *
35598340 TTGAAAATCTTTTTGATGTATTTTGAAAGTTTAAGTTCTCAATTGAGTGAAAAAAAAGGCTTAAT
1 TTGAAAATCTTTTTGATACATTTTGAAAGTTCAAGTACTCAATTGAGTGAAAAAAAAGGCTTAAT
35598405 TATTTTT
66 TATTTTT
35598412 AAAAAAAATT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
83 5 0.07
84 11 0.16
85 1 0.01
86 6 0.09
87 44 0.66
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (83 bp):
TTGAAAATCTTTTTGATACATTTTGAAAGTTCAAGTACTCAATTGAGTGAAAAAAAAGGCTTAAT
TATTTTTTTGAAAAAAAA
Found at i:35599453 original size:285 final size:285
Alignment explanation
Indices: 35598943--35599512 Score: 1131
Period size: 285 Copynumber: 2.0 Consensus size: 285
35598933 ATAAAAACAA
35598943 ACAACCCGAGACCCACCCCCTCCCGGGCAACCACCACTCTCGTCACTCGTCCATCCGGCCTCTCT
1 ACAACCCGAGACCCACCCCCTCCCGGGCAACCACCACTCTCGTCACTCGTCCATCCGGCCTCTCT
35599008 GACTCTCTGACTCTCTCAACCTCTCTTCACTCTTTAGTCTCCAATCTCCCTCCACCTTCCGGCTT
66 GACTCTCTGACTCTCTCAACCTCTCTTCACTCTTTAGTCTCCAATCTCCCTCCACCTTCCGGCTT
35599073 TCAGCCTCCAGTTCACCCGCCTTTAGCCGTCTGCTTCTTCGACGACCGTCCCTGCTGAAAAATGA
131 TCAGCCTCCAGTTCACCCGCCTTTAGCCGTCTGCTTCTTCGACGACCGTCCCTGCTGAAAAATGA
35599138 GAAAGTCAGAAAGACAGGTTTGGTGGTAAAGGACAAATGAGAATTGAAAAGAGTTAACGATAATA
196 GAAAGTCAGAAAGACAGGTTTGGTGGTAAAGGACAAATGAGAATTGAAAAGAGTTAACGATAATA
35599203 ATTTTTTAGGTTTTCGTACTTTATG
261 ATTTTTTAGGTTTTCGTACTTTATG
35599228 ACAACCCGAGACCCACCCCCTCCCGGGCAACCACCACTCTCGTCACTCGTCCATCCGGCCTCTCT
1 ACAACCCGAGACCCACCCCCTCCCGGGCAACCACCACTCTCGTCACTCGTCCATCCGGCCTCTCT
*
35599293 GACTCTCTGACTCTCTCAACCTCTCTTCACTCTTTAGTCTCCAATCTTCCTCCACCTTCCGGCTT
66 GACTCTCTGACTCTCTCAACCTCTCTTCACTCTTTAGTCTCCAATCTCCCTCCACCTTCCGGCTT
35599358 TCAGCCTCCAGTTCACCCGCCTTTAGCCGTCTGCTTCTTCGACGACCGTCCCTGCTGAAAAATGA
131 TCAGCCTCCAGTTCACCCGCCTTTAGCCGTCTGCTTCTTCGACGACCGTCCCTGCTGAAAAATGA
35599423 GAAAGTCAGAAAGACAGGTTTGGTGGTAAAGGACAAATGAGAATTGAAAAGAGTTAACGATAATA
196 GAAAGTCAGAAAGACAGGTTTGGTGGTAAAGGACAAATGAGAATTGAAAAGAGTTAACGATAATA
35599488 ATTTTTTAGGTTTTCGTACTTTATG
261 ATTTTTTAGGTTTTCGTACTTTATG
35599513 TTGGGTATGG
Statistics
Matches: 284, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
285 284 1.00
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.28
Consensus pattern (285 bp):
ACAACCCGAGACCCACCCCCTCCCGGGCAACCACCACTCTCGTCACTCGTCCATCCGGCCTCTCT
GACTCTCTGACTCTCTCAACCTCTCTTCACTCTTTAGTCTCCAATCTCCCTCCACCTTCCGGCTT
TCAGCCTCCAGTTCACCCGCCTTTAGCCGTCTGCTTCTTCGACGACCGTCCCTGCTGAAAAATGA
GAAAGTCAGAAAGACAGGTTTGGTGGTAAAGGACAAATGAGAATTGAAAAGAGTTAACGATAATA
ATTTTTTAGGTTTTCGTACTTTATG
Found at i:35604002 original size:30 final size:30
Alignment explanation
Indices: 35603968--35604024 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
35603958 TCAGGAGGTA
*
35603968 TCCCATCATGAAGTAGCTCATCAAGAAGAT
1 TCCCATCACGAAGTAGCTCATCAAGAAGAT
* * *
35603998 TCCCATCACGATGTTGCTCATCGAGAA
1 TCCCATCACGAAGTAGCTCATCAAGAA
35604025 CTATCCGATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.25
Consensus pattern (30 bp):
TCCCATCACGAAGTAGCTCATCAAGAAGAT
Found at i:35605891 original size:17 final size:17
Alignment explanation
Indices: 35605869--35605903 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
35605859 TCAAATGATT
**
35605869 ATTAAAAATTAAAAAGA
1 ATTAAAAAGAAAAAAGA
35605886 ATTAAAAAGAAAAAAGA
1 ATTAAAAAGAAAAAAGA
35605903 A
1 A
35605904 AAAAATACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (17 bp):
ATTAAAAAGAAAAAAGA
Found at i:35606552 original size:18 final size:17
Alignment explanation
Indices: 35606510--35606552 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
35606500 TTTTTAAGTT
*
35606510 TGTAATATTTTATATTA
1 TGTAATTTTTTATATTA
* *
35606527 TATTATTTTTATATATTA
1 TGTAATTTTT-TATATTA
35606545 TGTAATTT
1 TGTAATTT
35606553 ATAACATATA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (17 bp):
TGTAATTTTTTATATTA
Found at i:35611348 original size:21 final size:21
Alignment explanation
Indices: 35611322--35611364 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
35611312 GTCATGAGTG
35611322 TAAGGAAATCACACATCAATA
1 TAAGGAAATCACACATCAATA
35611343 TAAGGAAATCACACATCAATA
1 TAAGGAAATCACACATCAATA
35611364 T
1 T
35611365 TTTTAACAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.51, C:0.19, G:0.09, T:0.21
Consensus pattern (21 bp):
TAAGGAAATCACACATCAATA
Found at i:35614560 original size:23 final size:23
Alignment explanation
Indices: 35614530--35614596 Score: 116
Period size: 23 Copynumber: 2.9 Consensus size: 23
35614520 CCTTTTTGAA
35614530 CCATTTCCATTTCGTACCAAATT
1 CCATTTCCATTTCGTACCAAATT
35614553 CCATTTCCATTTCGTACCAAATT
1 CCATTTCCATTTCGTACCAAATT
* *
35614576 ACATTACCATTTCGTACCAAA
1 CCATTTCCATTTCGTACCAAA
35614597 CCCAAACCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.30, C:0.30, G:0.04, T:0.36
Consensus pattern (23 bp):
CCATTTCCATTTCGTACCAAATT
Found at i:35614929 original size:15 final size:15
Alignment explanation
Indices: 35614909--35614938 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35614899 ATAGGTACGT
35614909 AAAAAAAGTTTGAAA
1 AAAAAAAGTTTGAAA
*
35614924 AAAAAAATTTTGAAA
1 AAAAAAAGTTTGAAA
35614939 TTCAAAAAAA
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:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (15 bp):
AAAAAAAGTTTGAAA
Found at i:35614961 original size:23 final size:21
Alignment explanation
Indices: 35614921--35614975 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
35614911 AAAAAGTTTG
**
35614921 AAAAAAAAAATTTTGAAATTCA
1 AAAAAAAAAATTACGAAATT-A
35614943 AAAAAAAAAATATACGAAATTA
1 AAAAAAAAAAT-TACGAAATTA
35614965 AAAAAGAAAAA
1 AAAAA-AAAAA
35614976 GTGAATTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 17 0.59
23 12 0.41
ACGTcount: A:0.73, C:0.04, G:0.05, T:0.18
Consensus pattern (21 bp):
AAAAAAAAAATTACGAAATTA
Found at i:35614982 original size:19 final size:20
Alignment explanation
Indices: 35614960--35615014 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 20
35614950 AAATATACGA
*
35614960 AATTAAAAAAGAAAAA-GTG
1 AATTAAAAAAAAAAAACGTG
35614979 AATTGAAATTAAAAAAAAATCGTG
1 AATT-AAA--AAAAAAAAA-CGTG
35615003 AATTAAAAAAAA
1 AATTAAAAAAAA
35615015 GGTGTTGTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
19 4 0.13
20 3 0.10
21 5 0.17
22 8 0.27
23 3 0.10
24 7 0.23
ACGTcount: A:0.67, C:0.02, G:0.11, T:0.20
Consensus pattern (20 bp):
AATTAAAAAAAAAAAACGTG
Found at i:35617117 original size:19 final size:21
Alignment explanation
Indices: 35617088--35617131 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
35617078 CAAATGAGAG
35617088 AAAAAGAAAAGAAAA-ATGAA
1 AAAAAGAAAAGAAAACATGAA
*
35617108 AAAAAG-AAAGAAAACTTGAA
1 AAAAAGAAAAGAAAACATGAA
35617128 AAAA
1 AAAA
35617132 GAGAGTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.77, C:0.02, G:0.14, T:0.07
Consensus pattern (21 bp):
AAAAAGAAAAGAAAACATGAA
Found at i:35621316 original size:23 final size:23
Alignment explanation
Indices: 35621286--35621352 Score: 116
Period size: 23 Copynumber: 2.9 Consensus size: 23
35621276 CCTTTTTGAA
35621286 CCATTTCCATTTCGTACCAAATT
1 CCATTTCCATTTCGTACCAAATT
35621309 CCATTTCCATTTCGTACCAAATT
1 CCATTTCCATTTCGTACCAAATT
* *
35621332 ACATTACCATTTCGTACCAAA
1 CCATTTCCATTTCGTACCAAA
35621353 CCCTAACCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.30, C:0.30, G:0.04, T:0.36
Consensus pattern (23 bp):
CCATTTCCATTTCGTACCAAATT
Found at i:35621970 original size:15 final size:15
Alignment explanation
Indices: 35621950--35621979 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35621940 GGCGAACTAA
35621950 GGGGTTCACCAAAAG
1 GGGGTTCACCAAAAG
*
35621965 GGGGTTCGCCAAAAG
1 GGGGTTCACCAAAAG
35621980 TGTATCAGTA
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:0.30, C:0.20, G:0.37, T:0.13
Consensus pattern (15 bp):
GGGGTTCACCAAAAG
Found at i:35632568 original size:17 final size:16
Alignment explanation
Indices: 35632546--35632579 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
35632536 AGGGATGACG
35632546 TTTGTTTGATGTTTATT
1 TTTGTTTG-TGTTTATT
*
35632563 TTTGTTTGTTTTTATT
1 TTTGTTTGTGTTTATT
35632579 T
1 T
35632580 CATAATGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (16 bp):
TTTGTTTGTGTTTATT
Found at i:35639552 original size:19 final size:20
Alignment explanation
Indices: 35639516--35639553 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
35639506 CTGCAGTTTG
* *
35639516 AAAATTTTCTATTTTTTCTA
1 AAAATTTTATATTATTTCTA
35639536 AAAATTTTATA-TATTTCT
1 AAAATTTTATATTATTTCT
35639554 GATTTAGCCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (20 bp):
AAAATTTTATATTATTTCTA
Found at i:35653624 original size:47 final size:47
Alignment explanation
Indices: 35653570--35653680 Score: 125
Period size: 47 Copynumber: 2.4 Consensus size: 47
35653560 ACCAGTAATA
* * * *
35653570 CAGATAAACTACCACTTAATAATATTGTGGGCAAGCCACCACTTTTG
1 CAGATAAACTACCACATAAAAATATCGTGGACAAGCCACCACTTTTG
* * * *
35653617 CATATAAACTGCCACATAAAAATATCGTTGACAAGCCACCATTTTTG
1 CAGATAAACTACCACATAAAAATATCGTGGACAAGCCACCACTTTTG
*
35653664 TAGATAAAC-AGCCACAT
1 CAGATAAACTA-CCACAT
35653681 CTTCCACCTT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (47 bp):
CAGATAAACTACCACATAAAAATATCGTGGACAAGCCACCACTTTTG
Found at i:35671419 original size:28 final size:28
Alignment explanation
Indices: 35671388--35671456 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 28
35671378 AGTAACGGTC
* *
35671388 TGGGCCTAAGCCCTAAGCAGTTTCAGTG
1 TGGGCCTAAGCCCTAAGCAGTATCAATG
* *
35671416 TGGGCCAAAGCCCTAAGTAGTATCAATG
1 TGGGCCTAAGCCCTAAGCAGTATCAATG
*
35671444 TGGGCCTTAGCCC
1 TGGGCCTAAGCCC
35671457 AATACAGTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.23
Consensus pattern (28 bp):
TGGGCCTAAGCCCTAAGCAGTATCAATG
Found at i:35671879 original size:27 final size:27
Alignment explanation
Indices: 35671806--35672011 Score: 218
Period size: 27 Copynumber: 7.6 Consensus size: 27
35671796 CATCTCTTAG
* * * *
35671806 GGGTATATCAGTCATTTAACCCTAT-AA
1 GGGTATTTCGGTCATTTTACCCT-TCGA
** * *
35671833 GGGTATTTTAGTTATTTTACCCTTTG-
1 GGGTATTTCGGTCATTTTACCCTTCGA
* *
35671859 GGCGTATTTCGGTCATCTTACCCTACGA
1 GG-GTATTTCGGTCATTTTACCCTTCGA
* * *
35671887 AGGCATTTCGGTCATTTTACCCTTTGA
1 GGGTATTTCGGTCATTTTACCCTTCGA
* * *
35671914 GGGTATTTTGATCATTTTACCCTTTGA
1 GGGTATTTCGGTCATTTTACCCTTCGA
35671941 GGGTATTTCGGTCATTTTACCCTTCGA
1 GGGTATTTCGGTCATTTTACCCTTCGA
* *
35671968 GGATATTTTGGTCATTTTACCCTTCGA
1 GGGTATTTCGGTCATTTTACCCTTCGA
35671995 GGGTATTTCGGTCATTT
1 GGGTATTTCGGTCATTT
35672012 CCCCACGAAT
Statistics
Matches: 149, Mismatches: 27, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
26 3 0.02
27 145 0.97
28 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (27 bp):
GGGTATTTCGGTCATTTTACCCTTCGA
Found at i:35671922 original size:81 final size:81
Alignment explanation
Indices: 35671816--35672011 Score: 245
Period size: 81 Copynumber: 2.4 Consensus size: 81
35671806 GGGTATATCA
* * * *
35671816 GTCATTTAACCCTATAAGGGTATTTT-AGTTATTTTACCCTTTG-GGCGTATTTCGGTCATCTTA
1 GTCATTTTACCCTTTGAGGGTATTTTGA-TCATTTTACCCTTTGAGG-GTATTTCGGTCATCTTA
35671879 CCCTACGAAGG-CATTTCG
64 CCCTACG-AGGACATTTCG
*
35671897 GTCATTTTACCCTTTGAGGGTATTTTGATCATTTTACCCTTTGAGGGTATTTCGGTCATTTTACC
1 GTCATTTTACCCTTTGAGGGTATTTTGATCATTTTACCCTTTGAGGGTATTTCGGTCATCTTACC
* * *
35671962 CTTCGAGGATATTTTG
66 CTACGAGGACATTTCG
* * *
35671978 GTCATTTTACCCTTCGAGGGTATTTCGGTCATTT
1 GTCATTTTACCCTTTGAGGGTATTTTGATCATTT
35672012 CCCCACGAAT
Statistics
Matches: 101, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
80 3 0.03
81 95 0.94
82 3 0.03
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.43
Consensus pattern (81 bp):
GTCATTTTACCCTTTGAGGGTATTTTGATCATTTTACCCTTTGAGGGTATTTCGGTCATCTTACC
CTACGAGGACATTTCG
Found at i:35672694 original size:15 final size:14
Alignment explanation
Indices: 35672670--35672700 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
35672660 TCGGCCAGTA
35672670 GAAAAGAGAAAAGG
1 GAAAAGAGAAAAGG
35672684 GAAAGAGAGAAAAGG
1 GAAA-AGAGAAAAGG
35672699 GA
1 GA
35672701 GGATTCGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (14 bp):
GAAAAGAGAAAAGG
Found at i:35677966 original size:17 final size:18
Alignment explanation
Indices: 35677933--35677966 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35677923 CAAGAGTCTC
*
35677933 CCTACAGTTTCTAGTTTT
1 CCTACAGTCTCTAGTTTT
35677951 CCTACAGTCT-TAGTTT
1 CCTACAGTCTCTAGTTT
35677967 ACTCTAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.24, G:0.12, T:0.47
Consensus pattern (18 bp):
CCTACAGTCTCTAGTTTT
Found at i:35679189 original size:27 final size:27
Alignment explanation
Indices: 35679159--35679249 Score: 119
Period size: 27 Copynumber: 3.4 Consensus size: 27
35679149 TCATCTCCTA
*
35679159 AGGGTATATCGGTCATTTTACCCTTTG
1 AGGGTATTTCGGTCATTTTACCCTTTG
*
35679186 AGGGTATTTCGGTTATTTTACCCTTTG
1 AGGGTATTTCGGTCATTTTACCCTTTG
* * * *
35679213 AGGGCATTTCAGTCATTTTATCCTTCG
1 AGGGTATTTCGGTCATTTTACCCTTTG
*
35679240 AGGATATTTC
1 AGGGTATTTC
35679250 AATTATTTTC
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.43
Consensus pattern (27 bp):
AGGGTATTTCGGTCATTTTACCCTTTG
Found at i:35679948 original size:10 final size:10
Alignment explanation
Indices: 35679933--35679967 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
35679923 AGGATTCGAC
*
35679933 AAAGAGGGAA
1 AAAGAGAGAA
35679943 AAAGAGAGAA
1 AAAGAGAGAA
*
35679953 AAAGAGAAAA
1 AAAGAGAGAA
35679963 AAAGA
1 AAAGA
35679968 AAAGTGAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (10 bp):
AAAGAGAGAA
Found at i:35682299 original size:32 final size:32
Alignment explanation
Indices: 35682263--35682326 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
35682253 AAATATGAGT
35682263 TAACTAAGAAATTGTATGGTATAGTGAGTATA
1 TAACTAAGAAATTGTATGGTATAGTGAGTATA
35682295 TAACTAAGAAATTGTATGGTATAGTGAGTATA
1 TAACTAAGAAATTGTATGGTATAGTGAGTATA
35682327 AGATTTTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.34
Consensus pattern (32 bp):
TAACTAAGAAATTGTATGGTATAGTGAGTATA
Found at i:35683769 original size:13 final size:13
Alignment explanation
Indices: 35683751--35683776 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35683741 AGATATCAAG
35683751 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
35683764 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
35683777 GCTAGTTTTG
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:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:35687105 original size:25 final size:25
Alignment explanation
Indices: 35687074--35687140 Score: 89
Period size: 25 Copynumber: 2.7 Consensus size: 25
35687064 AGCTTAGATC
*
35687074 AGTATGCTTACACGAGCTAAAAATT
1 AGTATGCTCACACGAGCTAAAAATT
* *
35687099 AGTATGCTCATACGAGCTATAAATT
1 AGTATGCTCACACGAGCTAAAAATT
* *
35687124 GGTATGCTCACAGGAGC
1 AGTATGCTCACACGAGC
35687141 GGTGGGTCAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (25 bp):
AGTATGCTCACACGAGCTAAAAATT
Found at i:35690176 original size:50 final size:50
Alignment explanation
Indices: 35690061--35690298 Score: 239
Period size: 50 Copynumber: 4.7 Consensus size: 50
35690051 ATGCCAAAAT
* * * *
35690061 CATGTCCCATACATGGTCTTACATGGGATG-TTTCATGTAC--TACCAATGC
1 CATGTCCCAGACATGGTCTTACATGGGA-GCTCTCATAT-CGGTGCCAATGC
* * * *
35690110 CATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGC
1 CATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGGTGCCAATGC
* *
35690160 CATGTCCCAGACATGGTCTTACATGGGAGCTCTCGTCTCGGTGCCAATGC
1 CATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGGTGCCAATGC
* * * *
35690210 CATGTCGCAGACATGGTCTTACATAGGACCTCTCATGATCTCAAGGATGCCAATGT
1 CATGTCCCAGACATGGTCTTACATGGGAGCTCTCAT-A--TC--GG-TGCCAATGC
* *
35690266 CATGTCCCATACATGGTCTTACATGGGATCTCT
1 CATGTCCCAGACATGGTCTTACATGGGAGCTCT
35690299 TTACCCAAAT
Statistics
Matches: 157, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
48 2 0.01
49 31 0.20
50 83 0.53
53 2 0.01
55 2 0.01
56 37 0.24
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.29
Consensus pattern (50 bp):
CATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGGTGCCAATGC
Found at i:35690244 original size:100 final size:103
Alignment explanation
Indices: 35690061--35690298 Score: 263
Period size: 100 Copynumber: 2.3 Consensus size: 103
35690051 ATGCCAAAAT
* * *
35690061 CATGTCCCATACATGGTCTTACATGGGATG-TTTCATGTACTACCAATGCCATATCCCAGATATG
1 CATGTCCCATACATGGTCTTACATGGGA-GCTCTCATCTACTACCAATGCCATATCCCAGACATG
* ** *
35690125 GTCTTACATGGGAGTTCTCAT-A-TC-GG-TGCCCATGC
65 GTCTTACATAGGACCTCTCATGACTCAGGATGCCAATGC
* * * * *
35690160 CATGTCCCAGACATGGTCTTACATGGGAGCTCTCGTCT-CGGTGCCAATGCCATGTCGCAGACAT
1 CATGTCCCATACATGGTCTTACATGGGAGCTCTCATCTAC--TACCAATGCCATATCCCAGACAT
*
35690224 GGTCTTACATAGGACCTCTCATGATCTCAAGGATGCCAATGT
64 GGTCTTACATAGGACCTCTCATGA-CTC-AGGATGCCAATGC
*
35690266 CATGTCCCATACATGGTCTTACATGGGATCTCT
1 CATGTCCCATACATGGTCTTACATGGGAGCTCT
35690299 TTACCCAAAT
Statistics
Matches: 115, Mismatches: 15, Indels: 11
0.82 0.11 0.08
Matches are distributed among these distances:
98 2 0.02
99 32 0.28
100 38 0.33
101 1 0.01
103 2 0.02
105 2 0.02
106 38 0.33
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.29
Consensus pattern (103 bp):
CATGTCCCATACATGGTCTTACATGGGAGCTCTCATCTACTACCAATGCCATATCCCAGACATGG
TCTTACATAGGACCTCTCATGACTCAGGATGCCAATGC
Found at i:35691626 original size:39 final size:39
Alignment explanation
Indices: 35691580--35691656 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
35691570 TGGAAGGATT
35691580 AGATTATTCCACTAACACTCATGATTTTTGTGATTAAGC
1 AGATTATTCCACTAACACTCATGATTTTTGTGATTAAGC
35691619 AGATTATTCCACTAACACTCATGATTTTTGTGATTAAG
1 AGATTATTCCACTAACACTCATGATTTTTGTGATTAAG
35691657 TGTGTTTATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (39 bp):
AGATTATTCCACTAACACTCATGATTTTTGTGATTAAGC
Found at i:35693021 original size:13 final size:13
Alignment explanation
Indices: 35693005--35693047 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
35692995 ATACAACCAA
35693005 TTCATATAGCCAT
1 TTCATATAGCCAT
* *
35693018 TTCATATAACAAT
1 TTCATATAGCCAT
*
35693031 TTCATATGGCCAT
1 TTCATATAGCCAT
35693044 TTCA
1 TTCA
35693048 AAGTGTTAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.40
Consensus pattern (13 bp):
TTCATATAGCCAT
Found at i:35706869 original size:30 final size:30
Alignment explanation
Indices: 35706833--35706915 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
35706823 GTGTGCTAAA
* *
35706833 CGATGGTCGAAACCATCCCTTTTCCTTAAT
1 CGATGGTCAAAACCATCCCTTTTCATTAAT
*
35706863 CGATGGTCAAAACCATCCTTTTTCATTAAT
1 CGATGGTCAAAACCATCCCTTTTCATTAAT
*
35706893 CGATGATCAAAACCATCCCTTTT
1 CGATGGTCAAAACCATCCCTTTT
35706916 TATAGATGCT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.34
Consensus pattern (30 bp):
CGATGGTCAAAACCATCCCTTTTCATTAAT
Found at i:35708398 original size:29 final size:28
Alignment explanation
Indices: 35708344--35708404 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 28
35708334 TTATTTGAAA
*
35708344 AAAATTATTGTTATTTTTGTATATA-TT
1 AAAATTATTGTTATTTTTGTAAATATTT
35708371 AAAATTAGTTGTCT-TTTTCTGTAAATATTT
1 AAAATTA-TTGT-TATTTT-TGTAAATATTT
35708401 AAAA
1 AAAA
35708405 AACGTTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 7 0.24
28 8 0.28
29 8 0.28
30 6 0.21
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.52
Consensus pattern (28 bp):
AAAATTATTGTTATTTTTGTAAATATTT
Found at i:35708715 original size:6 final size:6
Alignment explanation
Indices: 35708704--35708729 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
35708694 ACTTTAAATA
35708704 TCACCT TCACCT TCACCT TCACCT TC
1 TCACCT TCACCT TCACCT TCACCT TC
35708730 TTCCATCAAT
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:0.15, C:0.50, G:0.00, T:0.35
Consensus pattern (6 bp):
TCACCT
Found at i:35710984 original size:30 final size:30
Alignment explanation
Indices: 35710950--35711046 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
35710940 TAAACTAAAA
*
35710950 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
35710980 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
35711010 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
35711039 ATGAGCTA
1 -TGAGCTA
35711047 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:35713241 original size:12 final size:12
Alignment explanation
Indices: 35713226--35713256 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
35713216 TTCTTTTTGC
35713226 TTTTCAAAGGCT
1 TTTTCAAAGGCT
35713238 TTTTCAAAGGCT
1 TTTTCAAAGGCT
35713250 TTTTCAA
1 TTTTCAA
35713257 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:35713314 original size:5 final size:5
Alignment explanation
Indices: 35713304--35713364 Score: 65
Period size: 5 Copynumber: 12.0 Consensus size: 5
35713294 CTCTTGCCTC
35713304 TCTTT TCTTT T-TATT TCTTTT TCTTT TC--T TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
35713350 TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT
35713365 GTTTTCTCTT
Statistics
Matches: 49, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
3 3 0.06
4 1 0.02
5 34 0.69
6 6 0.12
7 5 0.10
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:35713322 original size:10 final size:9
Alignment explanation
Indices: 35713306--35713371 Score: 51
Period size: 10 Copynumber: 6.7 Consensus size: 9
35713296 CTTGCCTCTC
35713306 TTTTCTTTT
1 TTTTCTTTT
35713315 TATTTCTTTTT
1 T-TTTC-TTTT
*
35713326 CTTTTCTTCT
1 -TTTTCTTTT
*
35713336 TTTGCTTTTT
1 TTTTC-TTTT
35713346 CTTTTCTTTT
1 -TTTTCTTTT
*
35713356 CTTTTCTTTG
1 -TTTTCTTTT
35713366 TTTTCT
1 TTTTCT
35713372 CTTTACAAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
9 11 0.23
10 23 0.49
11 12 0.26
12 1 0.02
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.79
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:35713345 original size:20 final size:21
Alignment explanation
Indices: 35713304--35713353 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
35713294 CTCTTGCCTC
* *
35713304 TCTTTTCTTTTTATTTCTTTT
1 TCTTTTCTTCTTATTGCTTTT
35713325 TCTTTTCTTCTT-TTGCTTTT
1 TCTTTTCTTCTTATTGCTTTT
35713345 TCTTTTCTT
1 TCTTTTCTT
35713354 TTCTTTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (21 bp):
TCTTTTCTTCTTATTGCTTTT
Found at i:35713346 original size:26 final size:26
Alignment explanation
Indices: 35713304--35713375 Score: 78
Period size: 25 Copynumber: 2.8 Consensus size: 26
35713294 CTCTTGCCTC
*
35713304 TCTTTTCTTT-TTATTTCTTTTTCTTT
1 TCTTCTCTTTGTT-TTTCTTTTTCTTT
35713330 TCTTCT-TTTGCTTTTTC-TTTTCTTT
1 TCTTCTCTTTG-TTTTTCTTTTTCTTT
*
35713355 TCTTTTCTTTGTTTTCTCTTT
1 TCTTCTCTTTGTTTT-TCTTT
35713376 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
25 20 0.51
26 15 0.38
27 4 0.10
ACGTcount: A:0.01, C:0.18, G:0.03, T:0.78
Consensus pattern (26 bp):
TCTTCTCTTTGTTTTTCTTTTTCTTT
Found at i:35713356 original size:30 final size:29
Alignment explanation
Indices: 35713304--35713363 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 29
35713294 CTCTTGCCTC
35713304 TCTTTTCTTTTTATTTCTTTTTCTTTTCT
1 TCTTTTCTTTTTATTTCTTTTTCTTTTCT
*
35713333 TCTTTTGCTTTTTCTTT-TCTTTTCTTTTCT
1 TCTTTT-CTTTTTATTTCT-TTTTCTTTTCT
35713363 T
1 T
35713364 TGTTTTCTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (29 bp):
TCTTTTCTTTTTATTTCTTTTTCTTTTCT
Found at i:35716037 original size:30 final size:30
Alignment explanation
Indices: 35716003--35716099 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
35715993 TAAACTAAAA
*
35716003 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
35716033 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
35716063 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
35716092 ATGAGCTA
1 -TGAGCTA
35716100 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:35725204 original size:33 final size:33
Alignment explanation
Indices: 35725093--35725204 Score: 86
Period size: 33 Copynumber: 3.3 Consensus size: 33
35725083 CATAGCTTCG
*
35725093 CCATGGTCTTACT-TAAACATTGCCATTGTCCAA
1 CCATGGTCTTA-TGTAAACATTGCCATAGTCCAA
* * ** *
35725126 CCATGGTCTTGTGTCTGAAAAATCACCATAG-CC-T
1 CCATGGTCTTATG--T-AAACATTGCCATAGTCCAA
*
35725160 CGCTATGGTCTTATGTAAACATTGCCATGGTCCAA
1 C-C-ATGGTCTTATGTAAACATTGCCATAGTCCAA
35725195 CCATGGTCTT
1 CCATGGTCTT
35725205 GTACATCTTT
Statistics
Matches: 59, Mismatches: 12, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
32 1 0.02
33 28 0.47
34 5 0.08
35 5 0.08
36 20 0.34
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (33 bp):
CCATGGTCTTATGTAAACATTGCCATAGTCCAA
Found at i:35725205 original size:69 final size:69
Alignment explanation
Indices: 35725044--35725206 Score: 240
Period size: 69 Copynumber: 2.4 Consensus size: 69
35725034 ATATATACAC
** * *
35725044 TGCCATGGTCCAACCATGGTCTTACGTTTGAAAAACTACCATAGCTTCGCCATGGTCTTACTTAA
1 TGCCATGGTCCAACCATGGTCTTGTGTCTGAAAAACTACCATAGCCTCGCCATGGTCTTACTTAA
35725109 ACAT
66 ACAT
* *
35725113 TGCCATTGTCCAACCATGGTCTTGTGTCTGAAAAA-TCACCATAGCCTCGCTATGGTCTTA-TGT
1 TGCCATGGTCCAACCATGGTCTTGTGTCTGAAAAACT-ACCATAGCCTCGCCATGGTCTTACT-T
35725176 AAACAT
64 AAACAT
35725182 TGCCATGGTCCAACCATGGTCTTGT
1 TGCCATGGTCCAACCATGGTCTTGT
35725207 ACATCTTTAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
68 2 0.02
69 83 0.98
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (69 bp):
TGCCATGGTCCAACCATGGTCTTGTGTCTGAAAAACTACCATAGCCTCGCCATGGTCTTACTTAA
ACAT
Found at i:35742774 original size:17 final size:16
Alignment explanation
Indices: 35742743--35742776 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
35742733 AAATATTATG
35742743 AAATAAAAACAAACAA
1 AAATAAAAACAAACAA
*
35742759 AAATAAACATCAAACAA
1 AAATAAA-AACAAACAA
35742776 A
1 A
35742777 CGCCATCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.76, C:0.15, G:0.00, T:0.09
Consensus pattern (16 bp):
AAATAAAAACAAACAA
Found at i:35750773 original size:6 final size:6
Alignment explanation
Indices: 35750762--35750836 Score: 66
Period size: 6 Copynumber: 12.8 Consensus size: 6
35750752 AATAAATAAA
* *
35750762 TTTTAT TTTTAT GTTTAT TTTTA- TTTTA- TTTTA- TTTTAT TTTTAA
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
* * * *
35750807 TTTTAT TATATCT TTTTAA GTTTAT TTTTA
1 TTTTAT T-TTTAT TTTTAT TTTTAT TTTTA
35750837 ATTAAATTTT
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
5 15 0.27
6 36 0.65
7 4 0.07
ACGTcount: A:0.21, C:0.01, G:0.03, T:0.75
Consensus pattern (6 bp):
TTTTAT
Found at i:35750830 original size:25 final size:25
Alignment explanation
Indices: 35750802--35750849 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
35750792 TTATTTTATT
*
35750802 TTTAATTTT-ATTATATCTTTTTAAG
1 TTTAATTTTAATTAAAT-TTTTTAAG
*
35750827 TTTATTTTTAATTAAATTTTTTA
1 TTTAATTTTAATTAAATTTTTTA
35750850 GATATGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (25 bp):
TTTAATTTTAATTAAATTTTTTAAG
Found at i:35753856 original size:41 final size:41
Alignment explanation
Indices: 35753783--35753905 Score: 158
Period size: 41 Copynumber: 3.0 Consensus size: 41
35753773 AAGTGTTTTT
*
35753783 AGGGGTACTGAAGTACAAAC-GGGGCACATATGTGCAATTC
1 AGGGGTACCGAAGTACAAACAGGGGCACATATGTGCAATTC
* * ** *
35753823 AGGGGTACCGAACTATAAACAGGGGCATGTATGTGTAATTC
1 AGGGGTACCGAAGTACAAACAGGGGCACATATGTGCAATTC
* * *
35753864 AAGGGTATCAAAGTACAAACAGGGGCACATATGTGCAATTC
1 AGGGGTACCGAAGTACAAACAGGGGCACATATGTGCAATTC
35753905 A
1 A
35753906 ACGCTACTCC
Statistics
Matches: 68, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
40 17 0.25
41 51 0.75
ACGTcount: A:0.35, C:0.16, G:0.28, T:0.21
Consensus pattern (41 bp):
AGGGGTACCGAAGTACAAACAGGGGCACATATGTGCAATTC
Found at i:35756604 original size:51 final size:51
Alignment explanation
Indices: 35756482--35756673 Score: 183
Period size: 51 Copynumber: 3.8 Consensus size: 51
35756472 TTATTATCAT
* * * * * * ** *
35756482 TCGATACACGTAGTAGCCTTCACATAATGCTACACACGTTATCA-AAATTT
1 TCGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACCTA
* * *
35756532 TCGGTTCACATAGTAGCCTGCACATAGTACTACACACGTGACTA-AAGCCT-
1 TCGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCATAA-CCTA
* * *
35756582 TCCGATACACATAGTAGCCTGCACATAGTACTACACATGTGACCATTATCTA
1 T-CGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACCTA
* **
35756634 TCGATACACGTAGTAGCCTGCATTTAGTACTACACACGTG
1 TCGATACACATAGTAGCCTGCACATAGTACTACACACGTG
35756674 TTTATAGGCA
Statistics
Matches: 117, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
50 38 0.32
51 77 0.66
52 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (51 bp):
TCGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACCTA
Found at i:35766584 original size:16 final size:16
Alignment explanation
Indices: 35766563--35766617 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
35766553 GTTTGGTTCA
*
35766563 CTGTAATGGAATAGAG
1 CTGTAATAGAATAGAG
35766579 CTGTAATTA-AATAGAG
1 CTGTAA-TAGAATAGAG
* *
35766595 CAGTAATAGAATAAAG
1 CTGTAATAGAATAGAG
*
35766611 TTGTAAT
1 CTGTAAT
35766618 CAGTAATTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 2 0.06
16 29 0.91
17 1 0.03
ACGTcount: A:0.44, C:0.05, G:0.22, T:0.29
Consensus pattern (16 bp):
CTGTAATAGAATAGAG
Found at i:35770807 original size:23 final size:23
Alignment explanation
Indices: 35770743--35771154 Score: 308
Period size: 23 Copynumber: 18.0 Consensus size: 23
35770733 TTTGCAGCAC
* *
35770743 TTAAACACTTCAATTGACATCAT
1 TTAAACACTTCAATTTACAACAT
* * *
35770766 TTGAGCACCTT-AATTTACAACAA
1 TTAAACA-CTTCAATTTACAACAT
*
35770789 TTAAACACTTCAATTTACAGCAT
1 TTAAACACTTCAATTTACAACAT
* *
35770812 TTAAACACCTCAACTTACAACACT
1 TTAAACACTTCAATTTACAACA-T
* *
35770836 TT-AACA-TCTCAAGTAACAACAT
1 TTAAACACT-TCAATTTACAACAT
* *
35770858 TTATACACCTCAA-TTACAACAT
1 TTAAACACTTCAATTTACAACAT
* * *
35770880 TTAAATACTTCAATTTGCAGCACT
1 TTAAACACTTCAATTTACAACA-T
*
35770904 TT-AACACTTCAATTTACAGCAT
1 TTAAACACTTCAATTTACAACAT
*
35770926 TTAAACACTTCAATTTGCAACACT
1 TTAAACACTTCAATTTACAACA-T
35770950 TT-AACACTTCAATTTACAACAT
1 TTAAACACTTCAATTTACAACAT
** *
35770972 TTAAACACTTCAATTTGTAGCACT
1 TTAAACACTTCAATTTACAACA-T
* *
35770996 TT-AACA-TCTCTATTAACAACAT
1 TTAAACACT-TCAATTTACAACAT
* * *
35771018 TTATACACTTCAA-TTACAGCAA
1 TTAAACACTTCAATTTACAACAT
* * ** *
35771040 TAAAACA-TCTCAATTTCCAGGAA
1 TTAAACACT-TCAATTTACAACAT
* * *
35771063 CTAAACAATTCAATTTGCAGTAC-T
1 TTAAACACTTCAATTTACA--ACAT
* *
35771087 TAAAACACTTTAATTTACAACAT
1 TTAAACACTTCAATTTACAACAT
* *
35771110 TTAAACACTTCAATTTGCAGCACT
1 TTAAACACTTCAATTTACAACA-T
35771134 TT-AACACTTCAATTTACAACA
1 TTAAACACTTCAATTTACAACA
35771155 AACATGTTGG
Statistics
Matches: 305, Mismatches: 62, Indels: 44
0.74 0.15 0.11
Matches are distributed among these distances:
21 1 0.00
22 51 0.17
23 219 0.72
24 34 0.11
ACGTcount: A:0.40, C:0.23, G:0.04, T:0.33
Consensus pattern (23 bp):
TTAAACACTTCAATTTACAACAT
Found at i:35770813 original size:46 final size:46
Alignment explanation
Indices: 35770743--35771154 Score: 344
Period size: 46 Copynumber: 9.0 Consensus size: 46
35770733 TTTGCAGCAC
* * *
35770743 TTAAACACTTCAA-TTGACATCA-TTTGAGCACCTTAATTTACAACAA
1 TTAAACACTTCAATTTG-CAGCACTTT-AACACCTTAATTTACAACAT
* * *
35770789 TTAAACACTTCAATTTACAGCA-TTTAAACACCTCAACTTACAACACT
1 TTAAACACTTCAATTTGCAGCACTTT-AACACCTTAATTTACAACA-T
* ** * *
35770836 TT-AACA-TCTCAAGTAACAACA-TTTATACACCTCAA-TTACAACAT
1 TTAAACACT-TCAATTTGCAGCACTTTA-ACACCTTAATTTACAACAT
* *
35770880 TTAAATACTTCAATTTGCAGCACTTTAACA-CTTCAATTTACAGCAT
1 TTAAACACTTCAATTTGCAGCACTTTAACACCTT-AATTTACAACAT
*
35770926 TTAAACACTTCAATTTGCAACACTTTAACA-CTTCAATTTACAACAT
1 TTAAACACTTCAATTTGCAGCACTTTAACACCTT-AATTTACAACAT
* * *
35770972 TTAAACACTTCAATTTGTAGCACTTTAACATCTCT-ATTAACAACAT
1 TTAAACACTTCAATTTGCAGCACTTTAACACCT-TAATTTACAACAT
* * * ** * * * ** *
35771018 TTATACACTTCAA-TTACAGCAATAAAACATCTCAATTTCCAGGAA
1 TTAAACACTTCAATTTGCAGCACTTTAACACCTTAATTTACAACAT
* * * * *
35771063 CTAAACAATTCAATTTGCAGTACTTAAAACACTTTAATTTACAACAT
1 TTAAACACTTCAATTTGCAGCACTT-TAACACCTTAATTTACAACAT
35771110 TTAAACACTTCAATTTGCAGCACTTTAACA-CTTCAATTTACAACA
1 TTAAACACTTCAATTTGCAGCACTTTAACACCTT-AATTTACAACA
35771155 AACATGTTGG
Statistics
Matches: 297, Mismatches: 54, Indels: 30
0.78 0.14 0.08
Matches are distributed among these distances:
44 5 0.02
45 59 0.20
46 190 0.64
47 42 0.14
48 1 0.00
ACGTcount: A:0.40, C:0.23, G:0.04, T:0.33
Consensus pattern (46 bp):
TTAAACACTTCAATTTGCAGCACTTTAACACCTTAATTTACAACAT
Found at i:35770969 original size:114 final size:114
Alignment explanation
Indices: 35770743--35771151 Score: 361
Period size: 114 Copynumber: 3.6 Consensus size: 114
35770733 TTTGCAGCAC
* * * ** * * * *
35770743 TTAAACACTTCAATTGACATCATTTGAGCACCTT-AATTTACAACAATTAAACACTTCAATTTAC
1 TTAAACACTTCAATTTACAACATTTAAATA-CTTCAATTTGCAGCACTTTAACACTTCAATTTAC
* * * *
35770807 AGCATTTAAACACCTCAACTTACAACACTTTAACATCTCAAGTAACAACAT
65 AGCATTTAAACACTTCAATTTACAACACTTTAACAT-TCAATTTACAACAT
* *
35770858 TTATACACCTCAA-TTACAACATTTAAATACTTCAATTTGCAGCACTTTAACACTTCAATTTACA
1 TTAAACACTTCAATTTACAACATTTAAATACTTCAATTTGCAGCACTTTAACACTTCAATTTACA
*
35770922 GCATTTAAACACTTCAATTTGCAACACTTTAACACTTCAATTTACAACAT
66 GCATTTAAACACTTCAATTTACAACACTTTAACA-TTCAATTTACAACAT
** * * ** *
35770972 TTAAACACTTCAATTTGTAGCACTTTAACAT-C-TCTATTAACAACA-TTTATACACTTCAA-TT
1 TTAAACACTTCAATTTACAACA-TTTAA-ATACTTCAATTTGCAGCACTTTA-ACACTTCAATTT
* * * * *
35771033 ACAGCAATAAAACA-TCTCAATTTCCAGGA-AC-TAAACAATTCAATTTGCAGTAC-T
63 ACAGCATTTAAACACT-TCAATTTACA--ACACTTTAAC-ATTCAATTTACA--ACAT
* * *
35771087 TAAAACACTTTAATTTACAACATTTAAACACTTCAATTTGCAGCACTTTAACACTTCAATTTACA
1 TTAAACACTTCAATTTACAACATTTAAATACTTCAATTTGCAGCACTTTAACACTTCAATTTACA
35771152 ACAAACATGT
Statistics
Matches: 238, Mismatches: 40, Indels: 31
0.77 0.13 0.10
Matches are distributed among these distances:
113 5 0.02
114 139 0.58
115 74 0.31
116 18 0.08
117 2 0.01
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.33
Consensus pattern (114 bp):
TTAAACACTTCAATTTACAACATTTAAATACTTCAATTTGCAGCACTTTAACACTTCAATTTACA
GCATTTAAACACTTCAATTTACAACACTTTAACATTCAATTTACAACAT
Found at i:35770998 original size:160 final size:158
Alignment explanation
Indices: 35770732--35771154 Score: 494
Period size: 160 Copynumber: 2.6 Consensus size: 158
35770722 ATTATATATT
* * * * *
35770732 ATTTGCAGCACTTAAACACTTCAATTGACATCATTTGAGCACCTTAATTTACAACAATTAAACAC
1 ATTTGCAGCACTTAAACACTTCAATTTACAGCATTTAAACA-CTTAATTTACAAC-ATTTAACAC
* *
35770797 TTCAATTTACAGCATTTAAACACCTCAACTTACAACACTTTAACATCTCAAGTAACAACATTTAT
64 TTCAATTTACAGCATTTAAACACTTCAATTTACAACACTTTAACATCTCAAGTAACAACATTTAT
*
35770862 ACACCTCAATTACAACATTTAAATAC-T-TCA
129 ACACCTCAATTACAACA-ATAAA-ACATCTCA
* *
35770892 ATTTGCAGCACTTTAACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAACACTTTAACAC
1 ATTTGCAGCACTTAAACACTTCAATTTACAGCATTTAAACACTT-AATTTACAACA-TTTAACAC
* ** * * *
35770957 TTCAATTTACAACATTTAAACACTTCAATTTGTAGCACTTTAACATCTCTATTAACAACATTTAT
64 TTCAATTTACAGCATTTAAACACTTCAATTTACAACACTTTAACATCTCAAGTAACAACATTTAT
* *
35771022 ACACTTCAATTACAGCAATAAAACATCTCA
129 ACACCTCAATTACAACAATAAAACATCTCA
* * * * * *
35771052 ATTTCCAGGAAC-TAAACAATTCAATTTGCAGTACTTAAAACACTTTAATTTACAACATTTAAAC
1 ATTTGCA-GCACTTAAACACTTCAATTTACAGCA-TTTAAACAC-TTAATTTACAACATTT-AAC
*
35771116 ACTTCAATTTGCAGCACTTT-AACACTTCAATTTACAACA
62 ACTTCAATTTACAGCA-TTTAAACACTTCAATTTACAACA
35771155 AACATGTTGG
Statistics
Matches: 223, Mismatches: 31, Indels: 17
0.82 0.11 0.06
Matches are distributed among these distances:
158 2 0.01
159 9 0.04
160 153 0.69
161 54 0.24
162 5 0.02
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.33
Consensus pattern (158 bp):
ATTTGCAGCACTTAAACACTTCAATTTACAGCATTTAAACACTTAATTTACAACATTTAACACTT
CAATTTACAGCATTTAAACACTTCAATTTACAACACTTTAACATCTCAAGTAACAACATTTATAC
ACCTCAATTACAACAATAAAACATCTCA
Found at i:35775738 original size:21 final size:21
Alignment explanation
Indices: 35775689--35775728 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
35775679 TGACATGTCT
*
35775689 GGAAAGAAAAATACATAATAC
1 GGAAAAAAAAATACATAATAC
35775710 GGAAAAAAAAATACATAAT
1 GGAAAAAAAAATACATAAT
35775729 CTTAAGAAAA
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:0.65, C:0.07, G:0.12, T:0.15
Consensus pattern (21 bp):
GGAAAAAAAAATACATAATAC
Found at i:35778961 original size:16 final size:18
Alignment explanation
Indices: 35778920--35778962 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
35778910 AAAAGTTATT
* *
35778920 TTTACATATACTAATAAA
1 TTTATATATATTAATAAA
35778938 TTTATATATATTAATAAA
1 TTTATATATATTAATAAA
35778956 TTTATAT
1 TTTATAT
35778963 TTTAAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTATATATATTAATAAA
Found at i:35782657 original size:12 final size:13
Alignment explanation
Indices: 35782640--35782674 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
35782630 GATGAATAGA
35782640 TATATTATAT-AT
1 TATATTATATGAT
35782652 TATATTATATGAT
1 TATATTATATGAT
35782665 TAATATTATA
1 T-ATATTATA
35782675 GAATATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.48
13 3 0.14
14 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (13 bp):
TATATTATATGAT
Found at i:35782680 original size:19 final size:18
Alignment explanation
Indices: 35782635--35782680 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
35782625 GAACGGATGA
35782635 ATAGATATATTATATATT
1 ATAGATATATTATATATT
*
35782653 ATATTATATGATTA-ATATT
1 ATA-GATAT-ATTATATATT
35782672 ATAGA-ATAT
1 ATAGATATAT
35782681 AATAGAAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
16 2 0.08
17 2 0.08
18 4 0.17
19 12 0.50
20 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.48
Consensus pattern (18 bp):
ATAGATATATTATATATT
Found at i:35794174 original size:29 final size:28
Alignment explanation
Indices: 35794141--35794195 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
35794131 TTCCTCCTAA
35794141 AACTTTTACT-CCCTCCCACTTCCCACCAT
1 AACTTTTACTCCCCTCCCA--TCCCACCAT
*
35794170 AACTTTTGCTCCCCTCCCATCCCACC
1 AACTTTTACTCCCCTCCCATCCCACC
35794196 CCCTTTACCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 7 0.29
29 9 0.38
30 8 0.33
ACGTcount: A:0.18, C:0.51, G:0.02, T:0.29
Consensus pattern (28 bp):
AACTTTTACTCCCCTCCCATCCCACCAT
Found at i:35794743 original size:19 final size:19
Alignment explanation
Indices: 35794719--35794756 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
35794709 AAAGTTAATA
*
35794719 ACAAATTTGATTACAGTGG
1 ACAAATTTAATTACAGTGG
*
35794738 ACAAATTTAATTACGGTGG
1 ACAAATTTAATTACAGTGG
35794757 GTGATATTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (19 bp):
ACAAATTTAATTACAGTGG
Found at i:35801389 original size:4 final size:4
Alignment explanation
Indices: 35801380--35801410 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
35801370 TAATTCAATC
35801380 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATT
35801411 CATACAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
ATTA
Found at i:35802664 original size:279 final size:284
Alignment explanation
Indices: 35802163--35803008 Score: 1196
Period size: 279 Copynumber: 2.9 Consensus size: 284
35802153 ATAATTAAAA
*
35802163 ATAAATTATTTAATGTTAGAAAACCACACAAACCGTCCACCCGTCCACCATTATTGAATTATGGC
1 ATAAATTATTTAATGTTAGAAAACCACACAAACCGTCCA-CCGTCCACCATTATAGAATTATGGC
* **
35802228 ATAATTACCAATTTGAATCTTAATCACTTATTAATTAAGCC-TTTTAGTTACTAAAAATCAATTT
65 ATAATTACCAATTTGAACCTTAATCACTTATTAATTAAGCCATTTTAGTTACTAAAAATCAATAC
* *
35802292 CGATTAATTTTTACAGTTTTTATAATTTAGTCCTTTTTCCATAATTAACCATCCAAACACTAAAT
130 CGATTAATTTTTACAGTTTTTACAATTTAGTCCTTTTTCCATTATTAACCATCCAAACAC-AAAT
35802357 TTTTTT-AACCAACTTCAATTCACCTATATATCAGTTCTGTACATATTTTATTAAATATTTAC-G
194 TTTTTTGAACCAACTTCAATTCACCTATATATCAGTTCTGTA-ATATTTTATTAAATATTTACAG
35802420 GACTCGGTTTAA-C-C-A-T-TTTAATT
258 G-CTCGGTTTAACCTCTATTATTTAATT
* * * * *
35802443 -TAAATTATTTAATGTTAAAAAACCACACCAACCGTCCACTCGTCCACTACTATAGAATTACGGC
1 ATAAATTATTTAATGTTAGAAAACCACACAAACCGTCCAC-CGTCCACCATTATAGAATTATGGC
*
35802507 ATAATTATCAATTTGAACCTTAATCACTTATTAATTAAGCCATTTTAGTTACTAAAAATCAATAC
65 ATAATTACCAATTTGAACCTTAATCACTTATTAATTAAGCCATTTTAGTTACTAAAAATCAATAC
* *
35802572 CGATTAATTTTTACAATTTTTACGATTTAGTCCTTTTTCCATTATTAACCATCCAAACAC-AATT
130 CGATTAATTTTTACAGTTTTTACAATTTAGTCCTTTTTCCATTATTAACCATCCAAACACAAATT
* *
35802636 TTTTTGAACCAATTTCAATTCACCTATATATCAGTTCCGTAAGTATTTTATTAAATATTTACAGG
195 TTTTTGAACCAACTTCAATTCACCTATATATCAGTTCTGTAA-TATTTTATTAAATATTTACAGG
35802701 CTCGGTTTAACCATTTTCATTTTAATTATTTAATT
259 CTCGGTTTAACC----TC----T-ATTATTTAATT
*
35802736 AAAAATAAATTATTTAATGTTAGAAAACCACACAAACCATCCACCTGTCCACCATTATAGAATTA
1 ----ATAAATTATTTAATGTTAGAAAACCACACAAACCGTCCACC-GTCCACCATTATAGAATTA
35802801 TGGCATAATTACCAATTTGAACCTTAATCACTTATTAATTAAGCCA-TTTAGTTACTAAAAATCA
61 TGGCATAATTACCAATTTGAACCTTAATCACTTATTAATTAAGCCATTTTAGTTACTAAAAATCA
*
35802865 ATACCGATTAATTTTTACAGTTTTTACAATTTAGTCCTTTTTTCA-TAGTTAACCATCCAAACAC
126 ATACCGATTAATTTTTACAGTTTTTACAATTTAGTCCTTTTTCCATTA-TTAACCATCCAAACAC
* *
35802929 TAAACTTTTTTGGACCAACTTCAATTCACCTATATA-CTAGTTCTGTAAATATTTTATTAAATAT
190 -AAATTTTTTTGAACCAACTTCAATTCACCTATATATC-AGTTCTGT-AATATTTTATTAAATAT
*
35802993 TTACAAGCTCGGTTTA
252 TTACAGGCTCGGTTTA
35803009 TAGAAACAAG
Statistics
Matches: 505, Mismatches: 31, Indels: 41
0.88 0.05 0.07
Matches are distributed among these distances:
278 11 0.02
279 157 0.31
280 80 0.16
285 1 0.00
291 1 0.00
292 1 0.00
293 7 0.01
296 2 0.00
297 77 0.15
298 98 0.19
299 68 0.13
300 2 0.00
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.39
Consensus pattern (284 bp):
ATAAATTATTTAATGTTAGAAAACCACACAAACCGTCCACCGTCCACCATTATAGAATTATGGCA
TAATTACCAATTTGAACCTTAATCACTTATTAATTAAGCCATTTTAGTTACTAAAAATCAATACC
GATTAATTTTTACAGTTTTTACAATTTAGTCCTTTTTCCATTATTAACCATCCAAACACAAATTT
TTTTGAACCAACTTCAATTCACCTATATATCAGTTCTGTAATATTTTATTAAATATTTACAGGCT
CGGTTTAACCTCTATTATTTAATT
Found at i:35805377 original size:51 final size:51
Alignment explanation
Indices: 35805256--35805442 Score: 155
Period size: 51 Copynumber: 3.7 Consensus size: 51
35805246 GAAGTTGCTA
* * * * * * *
35805256 GATCACGTGTGTAATACTATGTGCAGGCTACTACGTGTATCAGAATG--ATA
1 GATCACATGTGTAGTACTATGTGCAGGCTACTATGCGTA-CCGGATGAAATT
* * * * * **
35805306 GGTCGCATGTGTTGTACTATGTACTGGCTACTATGCGTACCGGAT-AGCTT
1 GATCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATGAAATT
* * * *
35805356 CGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAATT
1 -GATCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATGAAATT
* *
35805408 GGTCACATGTGTAGTATTATGTGCAGGCTACTATG
1 GATCACATGTGTAGTACTATGTGCAGGCTACTATG
35805443 TGAACTGGGT
Statistics
Matches: 105, Mismatches: 28, Indels: 7
0.75 0.20 0.05
Matches are distributed among these distances:
49 4 0.04
50 31 0.30
51 67 0.64
52 3 0.03
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (51 bp):
GATCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATGAAATT
Found at i:35808336 original size:29 final size:29
Alignment explanation
Indices: 35808289--35808352 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
35808279 TAATGAGGTT
*
35808289 TGGAGATAGATTGAGACTCACCAACCATAA
1 TGGA-ATAGATTAAGACTCACCAACCATAA
35808319 TGGAATAGATTAAGACTCACCAACCATAA
1 TGGAATAGATTAAGACTCACCAACCATAA
35808348 TGGAA
1 TGGAA
35808353 CTGGAAGAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 29 0.88
30 4 0.12
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (29 bp):
TGGAATAGATTAAGACTCACCAACCATAA
Found at i:35811032 original size:20 final size:20
Alignment explanation
Indices: 35811004--35811042 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35810994 AAGGTTTCTA
35811004 TGAGCTAGTGTGAAAAAGTT
1 TGAGCTAGTGTGAAAAAGTT
* *
35811024 TGAGGTAGTGTGAGAAAGT
1 TGAGCTAGTGTGAAAAAGT
35811043 GAAGAACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.36, T:0.28
Consensus pattern (20 bp):
TGAGCTAGTGTGAAAAAGTT
Found at i:35812697 original size:50 final size:50
Alignment explanation
Indices: 35812586--35813098 Score: 397
Period size: 50 Copynumber: 9.8 Consensus size: 50
35812576 ATTTGGGTAA
* *
35812586 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC---A-A-GATG
* *
35812642 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
* *
35812692 AGAGGTCCCATGTAAGACCATGTCTGGGA-AAGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
** * * *
35812741 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
** * * * * *
35812791 AGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCAGTACATTGGCATCCT
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA--CCA--AG-AT--G
* * * *
35812848 TGAGAT--CATG-AGAGGTCCCATGTAAGACCATGTTTGGAACATGGCATTGGCACCAAGACG
1 AGAGGTCCCATGTA-A-G-ACCATGT-----C-TG---GG-ACATGGCATTGGCACCAAGATG
* *
35812908 AGAGGTCCCATGTAAGACCATGTCTGGAACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
** * *
35812958 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCAATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
** * * ** *
35813008 AGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA-GTACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
* ** * *
35813057 AAACATCCCATGTAAGACCATGTCTGAGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
35813099 TGTTATTATC
Statistics
Matches: 369, Mismatches: 64, Indels: 55
0.76 0.13 0.11
Matches are distributed among these distances:
49 83 0.22
50 182 0.49
51 2 0.01
52 2 0.01
54 3 0.01
55 10 0.03
56 40 0.11
57 8 0.02
60 10 0.03
61 1 0.00
62 7 0.02
63 4 0.01
65 2 0.01
66 2 0.01
67 13 0.04
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
Done.