Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 179 of 205
Found at i:53095456 original size:50 final size:50
Alignment explanation
Indices: 53095401--53095594 Score: 214
Period size: 50 Copynumber: 3.9 Consensus size: 50
53095391 CATTAAAGTT
* *
53095401 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
* * *
53095451 ATGAGAGGTCTCC-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGAT
1 ATGAGAGGTC-CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
** * *
53095501 ATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTAC
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AC
* * ** * *
53095550 AAGAAACATCCCATGTAAGACCATGTCTGGGACATAGCTTTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
53095595 TGTTATTATC
Statistics
Matches: 122, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
48 1 0.01
49 40 0.33
50 79 0.65
51 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
Found at i:53100887 original size:20 final size:20
Alignment explanation
Indices: 53100853--53100894 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
53100843 AACTATTTAA
** *
53100853 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
53100873 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
53100893 AT
1 AT
53100895 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:53114285 original size:35 final size:35
Alignment explanation
Indices: 53114239--53114315 Score: 154
Period size: 35 Copynumber: 2.2 Consensus size: 35
53114229 AGCGCTCCTA
53114239 CATTATACCAATAGAATGTAACCAAGAATATTGTG
1 CATTATACCAATAGAATGTAACCAAGAATATTGTG
53114274 CATTATACCAATAGAATGTAACCAAGAATATTGTG
1 CATTATACCAATAGAATGTAACCAAGAATATTGTG
53114309 CATTATA
1 CATTATA
53114316 ACAAGGAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (35 bp):
CATTATACCAATAGAATGTAACCAAGAATATTGTG
Found at i:53114341 original size:4 final size:4
Alignment explanation
Indices: 53114332--53114417 Score: 154
Period size: 4 Copynumber: 21.5 Consensus size: 4
53114322 AATAAAGATA
*
53114332 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTGT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
53114380 GTGT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
53114418 GAAGAATTGG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 78 1.00
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:53128850 original size:11 final size:11
Alignment explanation
Indices: 53128828--53128867 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
53128818 AACTAATCCT
53128828 CTCTCAAATTTC
1 CTCTC-AATTTC
53128840 CTCTCAATTTC
1 CTCTCAATTTC
53128851 CTCTCAATTTC
1 CTCTCAATTTC
53128862 CT-TCAA
1 CTCTCAA
53128868 AAATTCTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 4 0.14
11 19 0.68
12 5 0.18
ACGTcount: A:0.23, C:0.35, G:0.00, T:0.42
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:53129913 original size:21 final size:20
Alignment explanation
Indices: 53129874--53129911 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
53129864 TAACGAGGTA
53129874 AATTTTATATTAGATTTTAC
1 AATTTTATATTAGATTTTAC
53129894 AATTATTATA-TAGATTTT
1 AATT-TTATATTAGATTTT
53129912 TAAAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (20 bp):
AATTTTATATTAGATTTTAC
Found at i:53131255 original size:25 final size:25
Alignment explanation
Indices: 53131227--53131274 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
53131217 TATTTTGATA
53131227 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
53131252 TTATTTGATGTAATAAAATAGAA
1 TTATTTGATGTAATAAAATAGAA
53131275 ATTTTTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.40
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:53131352 original size:23 final size:23
Alignment explanation
Indices: 53131326--53132121 Score: 901
Period size: 23 Copynumber: 35.8 Consensus size: 23
53131316 ATTAATATCC
53131326 TTAACTT-AAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
* *
53131348 TTTAA-TTAAAAACCTTAAACC--C
1 -TTAACTTAAAAACCCT-AACCTAA
53131370 TTAACTTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
*
53131393 TTAAATTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
53131416 TTAACTT-AAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
*
53131438 TTATA-TTAAAAACCTTAACCTAA
1 TTA-ACTTAAAAACCCTAACCTAA
* *
53131461 TTAAATTAAAAACCCTAACC--C
1 TTAACTTAAAAACCCTAACCTAA
53131482 TTAACTTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
*
53131505 TTAACTTAAAAACCTTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
53131528 TTAAAAC-T-AAAACCCTAACCTAA
1 TT--AACTTAAAAACCCTAACCTAA
* *
53131551 TTTAA-TTAAAAACCTTAAACC--C
1 -TTAACTTAAAAACCCT-AACCTAA
53131573 TTAACTTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
* * *
53131596 TTAAATTAAAAACTCTAACC--C
1 TTAACTTAAAAACCCTAACCTAA
53131617 TTAACTT-AAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
* **
53131639 TTAAATTAAAAACCCTAACC-CC
1 TTAACTTAAAAACCCTAACCTAA
53131661 TTAACTTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
* *
53131684 TTAAATTAAAAACCCTAACC--C
1 TTAACTTAAAAACCCTAACCTAA
*
53131705 TTAAATTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
* **
53131728 TTAAATTAAAAACCCTAACC-CC
1 TTAACTTAAAAACCCTAACCTAA
53131750 TTAACTTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
* *
53131773 TTAAATTAAAAACCCTAACC--C
1 TTAACTTAAAAACCCTAACCTAA
* *
53131794 TTAACTTAAAATCCCGAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
* *
53131817 TTAAATTAAAAACCCTAACC--C
1 TTAACTTAAAAACCCTAACCTAA
*
53131838 TTAAATTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
* *
53131861 TTAAATTAAAAACCCTAACC--C
1 TTAACTTAAAAACCCTAACCTAA
*
53131882 TTAACTTAAAAACTCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
53131905 TTAACTTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
53131928 TTAACTTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
53131951 TTAACTTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
* *
53131974 TTAAATT-AAAACCCTAACC--C
1 TTAACTTAAAAACCCTAACCTAA
*
53131994 TTAACTTAAAAACTCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
53132017 TTTAA-TTAAAAACCCTAAACCCTAA
1 -TTAACTTAAAAACCCT-AA-CCTAA
* *
53132042 --AA-TTAAAAACACTAACCT-G
1 TTAACTTAAAAACCCTAACCTAA
*
53132061 TT-ACTTAAAAACCCTAACC--C
1 TTAACTTAAAAACCCTAACCTAA
53132081 TTAACTTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
*
53132104 TTAAATTAAAAACCCTAA
1 TTAACTTAAAAACCCTAA
53132122 ACGAAATTAA
Statistics
Matches: 664, Mismatches: 65, Indels: 88
0.81 0.08 0.11
Matches are distributed among these distances:
20 23 0.03
21 160 0.24
22 114 0.17
23 342 0.52
24 17 0.03
25 8 0.01
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.27
Consensus pattern (23 bp):
TTAACTTAAAAACCCTAACCTAA
Found at i:53131505 original size:44 final size:44
Alignment explanation
Indices: 53131370--53132121 Score: 895
Period size: 44 Copynumber: 16.9 Consensus size: 44
53131360 CCTTAAACCC
* * *
53131370 TTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACC--CTTAACTTAAAAACCCTAACCTAA
* * *
53131416 TTAACTT-AAAACCCTAACCTAATTATA-TTAAAAACCTTAACCTAA
1 TTAAATTAAAAACCCTAACC--CTTA-ACTTAAAAACCCTAACCTAA
53131461 TTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAA
* * *
53131505 TTAACTTAAAAACCTTAACCTAATTAAAAC-T-AAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACC--CTT--AACTTAAAAACCCTAACCTAA
* *
53131551 TTTAATTAAAAACCTTAAACCCTTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCT-AACCCTTAACTTAAAAACCCTAACCTAA
*
53131596 TTAAATTAAAAACTCTAACCCTTAACTT-AAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAA
53131639 TTAAATTAAAAACCCTAACCCCTTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAA-CCCTTAACTTAAAAACCCTAACCTAA
*
53131684 TTAAATTAAAAACCCTAACCCTTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAA
53131728 TTAAATTAAAAACCCTAACCCCTTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAA-CCCTTAACTTAAAAACCCTAACCTAA
* *
53131773 TTAAATTAAAAACCCTAACCCTTAACTTAAAATCCCGAACCTAA
1 TTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAA
*
53131817 TTAAATTAAAAACCCTAACCCTTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAA
*
53131861 TTAAATTAAAAACCCTAACCCTTAACTTAAAAACTCTAACCTAA
1 TTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAA
* *
53131905 TTAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACC--CTTAACTTAAAAACCCTAACCTAA
* * * *
53131951 TTAACTTAAAAACCCTAACCTAATTAAATT-AAAACCCTAACC--C
1 TTAAATTAAAAACCCTAACC--CTTAACTTAAAAACCCTAACCTAA
* * *
53131994 TTAACTTAAAAACTCTAACCTAATTTAA-TTAAAAACCCTAAACCCT-A
1 TTAAATTAAAAACCCTAACC---CTTAACTTAAAAACCCT-AA-CCTAA
* * *
53132041 --AAATTAAAAACACTAA-CCTGTTACTTAAAAACCCTAACC--C
1 TTAAATTAAAAACCCTAACCCT-TAACTTAAAAACCCTAACCTAA
* * *
53132081 TTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAA
1 TTAAATTAAAAACCCTAACC--CTTAACTTAAAAACCCTAA
53132122 ACGAAATTAA
Statistics
Matches: 637, Mismatches: 42, Indels: 56
0.87 0.06 0.08
Matches are distributed among these distances:
41 3 0.00
42 18 0.03
43 69 0.11
44 259 0.41
45 176 0.28
46 104 0.16
47 5 0.01
48 3 0.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (44 bp):
TTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAA
Found at i:53132251 original size:27 final size:26
Alignment explanation
Indices: 53132187--53132255 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 26
53132177 CTGGTACTAA
*
53132187 CAATTAATAATTTTATATAATTTGAT
1 CAATTAATAATTTTATACAATTTGAT
*
53132213 -AATTTTACTAATTATTAATACAATTT-AT
1 CAA--TTAATAATT-TT-ATACAATTTGAT
53132241 CAATTAATAATTTTA
1 CAATTAATAATTTTA
53132256 CATTCACATA
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
25 3 0.09
26 2 0.06
27 16 0.46
28 4 0.11
29 10 0.29
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.49
Consensus pattern (26 bp):
CAATTAATAATTTTATACAATTTGAT
Found at i:53132332 original size:115 final size:117
Alignment explanation
Indices: 53132126--53132369 Score: 402
Period size: 116 Copynumber: 2.1 Consensus size: 117
53132116 CCCTAAACGA
* * * **
53132126 AATTAATAATTTTACTTTCACATAATGTTGGATTTGGAAAAATATTTTTTCCTGGTACTAACAAT
1 AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATAGTTTTGACTGGTACTAACAAT
* **
53132191 TAATAATTTTATATAATTTGATAA-TTTTACTAATTATTAATACAATTTATC
66 TAATAATTTTATATAATTTGACAATTTTTACTAACCATTAATACAATTTATC
53132242 AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAAT-GTTTTGACTGGTACTAACAAT
1 AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATAGTTTTGACTGGTACTAACAAT
53132306 TAATAATTTTATATAATTTGACAATTTTTACTAACCATTAATACAATTTATC
66 TAATAATTTTATATAATTTGACAATTTTTACTAACCATTAATACAATTTATC
53132358 AATTAATAATTT
1 AATTAATAATTT
53132370 CACAAACTTA
Statistics
Matches: 119, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
115 41 0.34
116 78 0.66
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (117 bp):
AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATAGTTTTGACTGGTACTAACAAT
TAATAATTTTATATAATTTGACAATTTTTACTAACCATTAATACAATTTATC
Found at i:53134660 original size:140 final size:140
Alignment explanation
Indices: 53134436--53134716 Score: 544
Period size: 140 Copynumber: 2.0 Consensus size: 140
53134426 TCTGCAGACA
53134436 GATCGACATTATGCATGTAGGTTGGAGGTGAGTATGCTCTGAATCGTGGATTTTCTTCTTCATCT
1 GATCGACATTATGCATGTAGGTTGGAGGTGAGTATGCTCTGAATCGTGGATTTTCTTCTTCATCT
*
53134501 GAACTCCTTTCAGCATATTCAGGTTCTGTTGGAATAGGTTCCGGTTCAGAAAATAAGCCAACTTA
66 GAACTCCTTTCAGCATATTCAGGTTCTGTTGGAATAGGCTCCGGTTCAGAAAATAAGCCAACTTA
53134566 TGCACCATCC
131 TGCACCATCC
53134576 GATCGACATTATGCATGTAGGTTGGAGGTGAGTATGCTCTGAATCGTGGATTTTCTTCTTCATCT
1 GATCGACATTATGCATGTAGGTTGGAGGTGAGTATGCTCTGAATCGTGGATTTTCTTCTTCATCT
*
53134641 GAACTCCTTTCAGCATATTCAGGTTCTGTTGGAATAGGCTCCGGTTCAGAAAATAAGCCAACTTC
66 GAACTCCTTTCAGCATATTCAGGTTCTGTTGGAATAGGCTCCGGTTCAGAAAATAAGCCAACTTA
53134706 TGCACCATCC
131 TGCACCATCC
53134716 G
1 G
53134717 GCCCGGGCTC
Statistics
Matches: 139, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 139 1.00
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (140 bp):
GATCGACATTATGCATGTAGGTTGGAGGTGAGTATGCTCTGAATCGTGGATTTTCTTCTTCATCT
GAACTCCTTTCAGCATATTCAGGTTCTGTTGGAATAGGCTCCGGTTCAGAAAATAAGCCAACTTA
TGCACCATCC
Found at i:53135846 original size:124 final size:124
Alignment explanation
Indices: 53135519--53135889 Score: 571
Period size: 125 Copynumber: 3.0 Consensus size: 124
53135509 CCCAAACATG
* * * *
53135519 CTACTGTAGCAAAAGCGCATCCACGAGGGCACGGTTTTCACAAATTCTTCTCAAATAGCATCCTC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGC-CCGATTTCACAAATTCTTCTCAAATAGCATCCTG
*
53135584 CTAGAAGCGATTTTATACTATTTTCTCAGAAACGTCAAAAAAAATTATTTCTTCCATAAC
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATAAC
*
53135644 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTGTCACAAATTCTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCCCGATT-TCACAAATTCTTCTCAAATAGCATCCTG
* * *
53135709 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTTATTTCTTTCATGAC
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATAAC
* * *
53135769 CTACTGTAGTAAAAGTGCGTCCACTAGGGCCCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCCCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* ***
53135834 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAACTCGAAATTATTTCTTCCA
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA-AAAAAATTATTTCTTCCA
53135890 GGACTTAAAA
Statistics
Matches: 225, Mismatches: 19, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
124 68 0.30
125 157 0.70
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCCCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATAAC
Found at i:53136473 original size:14 final size:14
Alignment explanation
Indices: 53136454--53136485 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
53136444 TTCATTAATC
53136454 TTTTCTCTCAATTT
1 TTTTCTCTCAATTT
*
53136468 TTTTCTCTTAATTT
1 TTTTCTCTCAATTT
53136482 TTTT
1 TTTT
53136486 ATCATAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTCTCTCAATTT
Found at i:53142438 original size:714 final size:717
Alignment explanation
Indices: 53141054--53142489 Score: 2707
Period size: 714 Copynumber: 2.0 Consensus size: 717
53141044 AACTACTTAT
*
53141054 CAAATTGCATACAAATATTTATTCATCAAATAAATAAAATAACTATTCATATGGTCAATTTCCCA
1 CAAATTGCATACAAATATTTATTCATCAAATAAATAAAATAACTATTCATATGGCCAATTTCCCA
53141119 AGCTTTATTCGAATACAATTAAGCTTAAATACTTATGCTTTAACCAATGTCAAATTCATCAATAC
66 AGCTTTATTCGAATACAATTAAGCTTAAATACTTATGCTTTAACCAATGTCAAATTCATCAATAC
53141184 TCAAACAATTCCATGCATAACATACCAAGACCGATCCTATATATATATTTTTATTTATTTATTTA
131 TCAAACAATTCCATGCATAACATACCAAGACCGATCC---ATATATA---TTA-TTATTTATTTA
*
53141249 CTATGTATTATTTATCCCTCAATGTTTCAAAGGTCATTTACAAGACCAATTCCATAAACAATGCT
189 CTAAGTATTATTTATCCCTCAATGTTTCAAAGGTCATTTACAAGACCAATTCCATAAACAATGCT
53141314 CATTATGCAATTTACCAATTTCAACTACTCTATATTCATAGTAAATCAATATACAACTTTCACAT
254 CATTATGCAATTTACCAATTTCAACTACTCTATATTCATAGTAAATCAATATACAACTTTCACAT
53141379 AGTAAATGATAATTCAAATTCAATCTCAATTACCGAAAATTAAAATATTTCCATCCATGATTTCA
319 AGTAAATGATAATTCAAATTCAATCTCAATTACCGAAAATTAAAATATTTCCATCCATGATTTCA
53141444 AACATAGCTTATACTTATACCGTATCATATCAATCAACTTTACTTGTCTATCACAATCAATATTC
384 AACATAGCTTATACTTATACCGTATCATATCAATCAACTTTACTTGTCTATCACAATCAATATTC
53141509 ATAATTATCAAAATTCAAAATCCTCCAAAGCATAACATCACTTATATTAGTCTCAACCATTTAAG
449 ATAATTATCAAAATTCAAAATCCTCCAAAGCATAACATCACTTATATTAGTCTCAACCATTTAAG
53141574 AAACATAGCCAAATCATCAACCATAATATTTAATCAAAGCATGAAACCATTCATGTCAAAAATAA
514 AAACATAGCCAAATCATCAACCATAATATTTAATCAAAGCATGAAACCATTCATGTCAAAAATAA
* * *
53141639 ACAAGCCATTTTCGCATGGCTTATTATATATATACATTTCATTCAAAATATATTCAAAAAGGGGT
579 ACAAGACATTTTCGCATGGCTTATTATATATACACACTTCATTCAAAATATATTCAAAAAGGGGT
*
53141704 AGTATAGCCTATACATGCCATAGATTTTATATTTAACTTTTATAAATACCGATGACAGACGATAG
644 AGTATAGCCTATACATGCCATAGATTTTATATTTAACTTTTATAAATACCGAGGACAGACGATAG
53141769 TGTGATTGA
709 TGTGATTGA
53141778 CAAATTGCATACAAATATTTATTCATCAAATAAATAAAATAACTATTCATATGGCCAATTTCCCA
1 CAAATTGCATACAAATATTTATTCATCAAATAAATAAAATAACTATTCATATGGCCAATTTCCCA
53141843 AGCTTTATTCGAATACAATTAAGCTTAAATACTTATGCTTTAACCAATGTCAAATTCATCAATAC
66 AGCTTTATTCGAATACAATTAAGCTTAAATACTTATGCTTTAACCAATGTCAAATTCATCAATAC
*
53141908 TCAAACAATTCCATGCTTAACATACCAAGACCGATCC-TATATA-TA-TATTTATTTACTAAGTA
131 TCAAACAATTCCATGCATAACATACCAAGACCGATCCATATATATTATTATTTATTTACTAAGTA
53141970 TTATTTATCCCTCAATGTTTCAAAGGTCATTTACAAGACCAATTCCATAAACAATGCTCATTATG
196 TTATTTATCCCTCAATGTTTCAAAGGTCATTTACAAGACCAATTCCATAAACAATGCTCATTATG
53142035 CAATTTACCAATTTCAACTACTCTATATTCATAGTAAATCAATATACAACTTTCACATAGTAAAT
261 CAATTTACCAATTTCAACTACTCTATATTCATAGTAAATCAATATACAACTTTCACATAGTAAAT
53142100 GATAATTCAAATTCAATCTCAATTACCGAAAATTAAAATATTTCCATCCATGATTTCAAACATAG
326 GATAATTCAAATTCAATCTCAATTACCGAAAATTAAAATATTTCCATCCATGATTTCAAACATAG
53142165 CTTATACTTATACCGTATCATATCAATCAACTTTACTTGTCTATCACAATCAATATTCATAATTA
391 CTTATACTTATACCGTATCATATCAATCAACTTTACTTGTCTATCACAATCAATATTCATAATTA
53142230 TCAAAATTCAAAATCCTCCAAAGCATAACATCACTTATATTAGTCTCAACCATTTAAGAAACATA
456 TCAAAATTCAAAATCCTCCAAAGCATAACATCACTTATATTAGTCTCAACCATTTAAGAAACATA
53142295 GCCAAATCATCAACCATAATATTTAATCAAAGCATGAAACCATTCATGTCAAAAATAAACAAGAC
521 GCCAAATCATCAACCATAATATTTAATCAAAGCATGAAACCATTCATGTCAAAAATAAACAAGAC
*
53142360 ATTTTCGCATGGCTTATTATATATACACACTTCATTCAAAATATATTCAAAAAGGGGTAGTATAT
586 ATTTTCGCATGGCTTATTATATATACACACTTCATTCAAAATATATTCAAAAAGGGGTAGTATAG
*
53142425 CCTATAGATGCCATAGATTTTATATTTAACTTTTATAAATACCGAGGACAGACGATAGTGTGATT
651 CCTATACATGCCATAGATTTTATATTTAACTTTTATAAATACCGAGGACAGACGATAGTGTGATT
53142490 AACGTCGCTG
Statistics
Matches: 703, Mismatches: 9, Indels: 10
0.97 0.01 0.01
Matches are distributed among these distances:
714 530 0.75
716 2 0.00
720 6 0.01
724 165 0.23
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.34
Consensus pattern (717 bp):
CAAATTGCATACAAATATTTATTCATCAAATAAATAAAATAACTATTCATATGGCCAATTTCCCA
AGCTTTATTCGAATACAATTAAGCTTAAATACTTATGCTTTAACCAATGTCAAATTCATCAATAC
TCAAACAATTCCATGCATAACATACCAAGACCGATCCATATATATTATTATTTATTTACTAAGTA
TTATTTATCCCTCAATGTTTCAAAGGTCATTTACAAGACCAATTCCATAAACAATGCTCATTATG
CAATTTACCAATTTCAACTACTCTATATTCATAGTAAATCAATATACAACTTTCACATAGTAAAT
GATAATTCAAATTCAATCTCAATTACCGAAAATTAAAATATTTCCATCCATGATTTCAAACATAG
CTTATACTTATACCGTATCATATCAATCAACTTTACTTGTCTATCACAATCAATATTCATAATTA
TCAAAATTCAAAATCCTCCAAAGCATAACATCACTTATATTAGTCTCAACCATTTAAGAAACATA
GCCAAATCATCAACCATAATATTTAATCAAAGCATGAAACCATTCATGTCAAAAATAAACAAGAC
ATTTTCGCATGGCTTATTATATATACACACTTCATTCAAAATATATTCAAAAAGGGGTAGTATAG
CCTATACATGCCATAGATTTTATATTTAACTTTTATAAATACCGAGGACAGACGATAGTGTGATT
GA
Found at i:53143167 original size:45 final size:42
Alignment explanation
Indices: 53143066--53143158 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
53143056 GCTCTCGGTA
*
53143066 TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAATT
1 TCGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATT
** *
53143108 TCTTACACTTAGTGCCCATTATTCAACATCATCATTTTAGTT
1 TCGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATT
53143150 TCGCACACT
1 TCGCACACT
53143159 ATTTAGTGCT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.26, C:0.27, G:0.09, T:0.39
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATT
Found at i:53150703 original size:117 final size:117
Alignment explanation
Indices: 53150495--53150705 Score: 316
Period size: 117 Copynumber: 1.8 Consensus size: 117
53150485 TTTGATTTGT
* * * * *
53150495 TGGTTATTTGTGATTTATTATTGCAATTTCAGTGTCACAATGTAGGGTTTGTTTTATCAATTTTT
1 TGGTTAATTGTGATTTATTATTGCAATTTCAATGCCACAATGTAGGGTTTGTTTTATCAATCTGT
*
53150560 GCTACGACAGTGGTCCCGATGTTGTTGATAAAACTATTGTCAAAATTACAGA
66 GATACGACAGTGGTCCCGATGTTGTTGATAAAACTATTGTCAAAATTACAGA
* *
53150612 TGGTTAATTGTGATTTATTATTGCAATTTCAATGCCACAATGTAGGGTTTGTTTTGTCCATCTGT
1 TGGTTAATTGTGATTTATTATTGCAATTTCAATGCCACAATGTAGGGTTTGTTTTATCAATCTGT
* *
53150677 GATGCGACAGTGGTCCTGAT-TATGTTGAT
66 GATACGACAGTGGTCCCGATGT-TGTTGAT
53150706 TTCTGTTACC
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
116 1 0.01
117 82 0.99
ACGTcount: A:0.24, C:0.12, G:0.21, T:0.42
Consensus pattern (117 bp):
TGGTTAATTGTGATTTATTATTGCAATTTCAATGCCACAATGTAGGGTTTGTTTTATCAATCTGT
GATACGACAGTGGTCCCGATGTTGTTGATAAAACTATTGTCAAAATTACAGA
Found at i:53154179 original size:33 final size:32
Alignment explanation
Indices: 53154112--53154287 Score: 124
Period size: 33 Copynumber: 5.3 Consensus size: 32
53154102 TATTAACTAC
53154112 TGGGGAGGGTGATGTTGAAAG-GGT-GAAAGT-TGA
1 TGGGGAGGGTGATG-T-AAAGAGGTAG-AA-TCTGA
*
53154145 TGGGGAGGGTGATGATAAAGGGGTAGAATCTGA
1 TGGGGAGGGTGATG-TAAAGAGGTAGAATCTGA
* * * * *
53154178 TGGTGAAGGTGATCTAAAAAAGGTAGAATCTGG
1 TGGGGAGGGTGATGT-AAAGAGGTAGAATCTGA
* * * * *
53154211 TGGGGAGGGTGATGTAGGAGTGGTACAAGCTAA
1 TGGGGAGGGTGATGTA-AAGAGGTAGAATCTGA
* * * *
53154244 TGGGGAGGGCGATGTAGGAGAGGTACAAGCTGA
1 TGGGGAGGGTGATGTA-AAGAGGTAGAATCTGA
53154277 TGGGGAGGGTG
1 TGGGGAGGGTG
53154288 TGTCTGCTAC
Statistics
Matches: 117, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
32 7 0.06
33 109 0.93
34 1 0.01
ACGTcount: A:0.28, C:0.05, G:0.46, T:0.21
Consensus pattern (32 bp):
TGGGGAGGGTGATGTAAAGAGGTAGAATCTGA
Found at i:53158242 original size:32 final size:32
Alignment explanation
Indices: 53158205--53158278 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
53158195 TTTGGTTCTA
*
53158205 AGGGATTTCATAATTTCATTCCTAATAGTTTT
1 AGGGATTTCATAATTTCATTCCTAAAAGTTTT
* * * * *
53158237 AGGGATTTAATGATTTGATTCGTAAAATTTTT
1 AGGGATTTCATAATTTCATTCCTAAAAGTTTT
53158269 AGGGATTTCA
1 AGGGATTTCA
53158279 AGAATATTTC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.45
Consensus pattern (32 bp):
AGGGATTTCATAATTTCATTCCTAAAAGTTTT
Found at i:53160568 original size:27 final size:26
Alignment explanation
Indices: 53160538--53160618 Score: 67
Period size: 27 Copynumber: 3.0 Consensus size: 26
53160528 GACTTTATCT
*
53160538 TATTTTATTTTTCAATTATTTAAAATG
1 TATTTTATTTTT-AATTATTTAAAATA
* *
53160565 TA-TTTATCTTTTATAATATATAATAA-A
1 TATTTTAT-TTTTA-ATTATTTAA-AATA
53160592 TATATTTATTTTTTAATTATTTAAAAT
1 TAT-TTTA-TTTTTAATTATTTAAAAT
53160619 TTGCATCGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 13
0.70 0.08 0.22
Matches are distributed among these distances:
26 6 0.14
27 17 0.40
28 9 0.21
29 9 0.21
30 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.58
Consensus pattern (26 bp):
TATTTTATTTTTAATTATTTAAAATA
Found at i:53165273 original size:26 final size:26
Alignment explanation
Indices: 53165242--53165299 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
53165232 CAACAACAGT
53165242 GATCAAAATAGTAGCACCTCTACAAC
1 GATCAAAATAGTAGCACCTCTACAAC
*
53165268 GATCAAAGTAGTAGCACCTCTACAAC
1 GATCAAAATAGTAGCACCTCTACAAC
53165294 GATCAA
1 GATCAA
53165300 TGAACAAACG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.41, C:0.26, G:0.14, T:0.19
Consensus pattern (26 bp):
GATCAAAATAGTAGCACCTCTACAAC
Found at i:53166221 original size:21 final size:20
Alignment explanation
Indices: 53166175--53166224 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
53166165 ACCTCTATTC
53166175 ATGTTTGTTTGTTTAGTTTT
1 ATGTTTGTTTGTTTAGTTTT
*
53166195 AAGTTTGTTTGTGTTCAG-TTT
1 ATGTTTGTTTGT-TT-AGTTTT
53166216 ATGTTTGTT
1 ATGTTTGTT
53166225 AAGAATTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 11 0.42
21 13 0.50
22 2 0.08
ACGTcount: A:0.12, C:0.02, G:0.22, T:0.64
Consensus pattern (20 bp):
ATGTTTGTTTGTTTAGTTTT
Found at i:53166311 original size:12 final size:12
Alignment explanation
Indices: 53166294--53166318 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53166284 TTGTTTAATG
53166294 TTCATGAACATA
1 TTCATGAACATA
53166306 TTCATGAACATA
1 TTCATGAACATA
53166318 T
1 T
53166319 AATTGAACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TTCATGAACATA
Found at i:53167491 original size:18 final size:18
Alignment explanation
Indices: 53167464--53167500 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
53167454 GCTATCAGTT
*
53167464 TCGATTTAACCAATTTGA
1 TCGATCTAACCAATTTGA
*
53167482 TCGATCTAACCAGTTTGA
1 TCGATCTAACCAATTTGA
53167500 T
1 T
53167501 TGAATAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (18 bp):
TCGATCTAACCAATTTGA
Found at i:53170229 original size:21 final size:22
Alignment explanation
Indices: 53170188--53170230 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
53170178 TTTATTTTTA
53170188 AAAATATTTAAATTATTAATAT
1 AAAATATTTAAATTATTAATAT
* *
53170210 AAAATA-TTATATTTTTAATAT
1 AAAATATTTAAATTATTAATAT
53170231 TATTAAACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AAAATATTTAAATTATTAATAT
Found at i:53170311 original size:19 final size:18
Alignment explanation
Indices: 53170270--53170330 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
53170260 TTTAGTCATA
*
53170270 TAATAAATTATTAATATAAT
1 TAATAAATTATT--TATATT
53170290 TAATATAATT-TATTATATT
1 TAATA-AATTAT-TTATATT
53170309 TAATAAATTATTTAATATT
1 TAATAAATTATTT-ATATT
53170328 TAA
1 TAA
53170331 ATTTTATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
18 6 0.17
19 19 0.53
20 6 0.17
21 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATAAATTATTTATATT
Found at i:53171719 original size:13 final size:13
Alignment explanation
Indices: 53171682--53171722 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
53171672 TTTTGCTTTA
53171682 CTGCTTTGCTCTG
1 CTGCTTTGCTCTG
53171695 CT--TTGTGCCTCTG
1 CTGCTT-TG-CTCTG
53171708 CTGCTTTGCTCTG
1 CTGCTTTGCTCTG
53171721 CT
1 CT
53171723 TTGCTTTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
11 2 0.08
12 2 0.08
13 16 0.67
14 2 0.08
15 2 0.08
ACGTcount: A:0.00, C:0.32, G:0.22, T:0.46
Consensus pattern (13 bp):
CTGCTTTGCTCTG
Found at i:53174704 original size:18 final size:18
Alignment explanation
Indices: 53174678--53174743 Score: 114
Period size: 18 Copynumber: 3.7 Consensus size: 18
53174668 AAAATATGAG
*
53174678 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTC
*
53174696 AAATCATGTTCACATTTC
1 AAATGATGTTCACATTTC
53174714 AAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
53174732 AAATGATGTTCA
1 AAATGATGTTCA
53174744 AATTGATGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:53175231 original size:72 final size:71
Alignment explanation
Indices: 53175139--53175310 Score: 254
Period size: 72 Copynumber: 2.4 Consensus size: 71
53175129 AACAACAATG
* * * * *
53175139 CTAAACTAATTTTATCAATAGTTATTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTCCTTA
1 CTAAATTAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTGGATATTGAATTTATGTTCTACTTA
*
53175204 TTTATGT
66 TTTAT-A
* * *
53175211 GTAATTTAGTTTTATTAATAGTTGTTTATGTTTGGTCTTTGGATATTGAATTTATGTTCTACTTA
1 CTAAATTAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTGGATATTGAATTTATGTTCTACTTA
53175276 TTTATA
66 TTTATA
53175282 CTAAATTAGTTTTATCAATAGTTGTTTAT
1 CTAAATTAGTTTTATCAATAGTTGTTTAT
53175311 ATATGATTTT
Statistics
Matches: 88, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
71 26 0.30
72 62 0.70
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.55
Consensus pattern (71 bp):
CTAAATTAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTGGATATTGAATTTATGTTCTACTTA
TTTATA
Found at i:53177110 original size:19 final size:19
Alignment explanation
Indices: 53177082--53177125 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
53177072 TAATTTTTAT
53177082 ATTTAAATATT-TAAATATA
1 ATTTAAATATTCTAAATA-A
* *
53177101 ATTTATATATTCTAATTAA
1 ATTTAAATATTCTAAATAA
53177120 ATTTAA
1 ATTTAA
53177126 TAATTAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTAAATATTCTAAATAA
Found at i:53177378 original size:23 final size:23
Alignment explanation
Indices: 53177351--53177396 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
53177341 AACACTTAAA
53177351 TTTTTCAAAAGCACTTCTCAAAAT
1 TTTTTCAAAA-CACTTCTCAAAAT
* *
53177375 TTTTTCACAACACTTTTCAAAA
1 TTTTTCAAAACACTTCTCAAAA
53177397 ATACTTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.37, C:0.22, G:0.02, T:0.39
Consensus pattern (23 bp):
TTTTTCAAAACACTTCTCAAAAT
Found at i:53177402 original size:13 final size:13
Alignment explanation
Indices: 53177386--53177410 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53177376 TTTTCACAAC
53177386 ACTTTTCAAAAAT
1 ACTTTTCAAAAAT
53177399 ACTTTTCAAAAA
1 ACTTTTCAAAAA
53177411 CAACGAAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
ACTTTTCAAAAAT
Found at i:53186615 original size:21 final size:21
Alignment explanation
Indices: 53186591--53186631 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53186581 AAACACTCGT
*
53186591 TTTCCTTTTTCAATTGAACCA
1 TTTCCTTTTCCAATTGAACCA
*
53186612 TTTCCTTTTCCATTTGAACC
1 TTTCCTTTTCCAATTGAACC
53186632 CTAATATCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.27, G:0.05, T:0.49
Consensus pattern (21 bp):
TTTCCTTTTCCAATTGAACCA
Found at i:53195557 original size:41 final size:42
Alignment explanation
Indices: 53195512--53195595 Score: 143
Period size: 44 Copynumber: 2.0 Consensus size: 42
53195502 AACTGTCAGC
53195512 TAATTAACAAC-TAACAAATTAACTGACTTAATCAGTTACTT
1 TAATTAACAACATAACAAATTAACTGACTTAATCAGTTACTT
53195553 TAATTAACAACTAATAACAAATTAACTGACTTAATCAGTTACT
1 TAATTAACAAC--ATAACAAATTAACTGACTTAATCAGTTACT
53195596 CTAACATTCC
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
41 11 0.28
44 29 0.73
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (42 bp):
TAATTAACAACATAACAAATTAACTGACTTAATCAGTTACTT
Found at i:53200983 original size:31 final size:29
Alignment explanation
Indices: 53200913--53200983 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 29
53200903 ATTAATATAT
53200913 AGTA-AAATT-ATCTTTTAAAAATATAAA
1 AGTATAAATTAATCTTTTAAAAATATAAA
* * *
53200940 AGTATGATTTAATCTTTTTAAAAGTTATAAA
1 AGTATAAATTAATC-TTTTAAAA-ATATAAA
*
53200971 GGTATAAATTAAT
1 AGTATAAATTAAT
53200984 ACAATAGAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
27 4 0.12
28 3 0.09
29 3 0.09
30 8 0.24
31 16 0.47
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.41
Consensus pattern (29 bp):
AGTATAAATTAATCTTTTAAAAATATAAA
Found at i:53208001 original size:31 final size:31
Alignment explanation
Indices: 53207958--53208023 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
53207948 ATGACTTTCA
* * *
53207958 ACTTCCTGCTTCTTTCTTCACTATTAGTTTG
1 ACTTACTGCTTCTTTCTTCACTATCAGTTCG
*
53207989 ACTTACTGCTTCTTTCTTCATTATCAGTTCG
1 ACTTACTGCTTCTTTCTTCACTATCAGTTCG
53208020 ACTT
1 ACTT
53208024 TCTGATACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.15, C:0.26, G:0.09, T:0.50
Consensus pattern (31 bp):
ACTTACTGCTTCTTTCTTCACTATCAGTTCG
Found at i:53208450 original size:16 final size:16
Alignment explanation
Indices: 53208408--53208450 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
53208398 TAATTTATTA
*
53208408 AATAAAA-ATAATTTT
1 AATAAAATATTATTTT
53208423 AATTAAAATATTATTTT
1 AA-TAAAATATTATTTT
53208440 AATAAAATATT
1 AATAAAATATT
53208451 TAAATTTCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 2 0.08
16 14 0.56
17 9 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATAAAATATTATTTT
Found at i:53210305 original size:3 final size:3
Alignment explanation
Indices: 53210297--53210339 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
53210287 GTCTATAGGT
53210297 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
53210340 AATGACAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:53212039 original size:101 final size:101
Alignment explanation
Indices: 53211910--53212166 Score: 327
Period size: 101 Copynumber: 2.5 Consensus size: 101
53211900 ATTCAGTCTG
* * *
53211910 TTTAACTATAATGTCGAGG-AAACAAGATCCGCCGTCGTGGCTTCAATCTGTTTCTACTACACCA
1 TTTAACTGTAATGTCG-GGAAAACAAGATCCGCCGTCGTAGCTTCAATCTGTTCCTACTACACCA
* *
53211974 CCAAGAAAGTAAGATTCGTCATTGTAACCTCAATCTT
65 CCAAGAAAGTAAGATCCGCCATTGTAACCTCAATCTT
* * *
53212011 TTTAACTGTAATGTTGGGAAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCTACTACACCGC
1 TTTAACTGTAATGTCGGGAAAACAAGATCCGCCGTCGTAGCTTCAATCTGTTCCTACTACACCAC
* * ** *
53212076 CAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTT
66 CAAGAAAGTAAGATCCGCCATTGTAACCTCAATCTT
* * * * *
53212112 TTTAATTGCAATGTCGGGGAAAACTAGATCCGTCGCCGTAGCTTCAATCTGTTCC
1 TTTAACTGTAATGTC-GGGAAAACAAGATCCGCCGTCGTAGCTTCAATCTGTTCC
53212167 ATCAATTTTT
Statistics
Matches: 135, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
100 2 0.01
101 97 0.72
102 36 0.27
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.30
Consensus pattern (101 bp):
TTTAACTGTAATGTCGGGAAAACAAGATCCGCCGTCGTAGCTTCAATCTGTTCCTACTACACCAC
CAAGAAAGTAAGATCCGCCATTGTAACCTCAATCTT
Found at i:53212224 original size:62 final size:64
Alignment explanation
Indices: 53212104--53212229 Score: 195
Period size: 62 Copynumber: 2.0 Consensus size: 64
53212094 CGTTGTGGCT
* *
53212104 TCAATCTTTTTAATTGCAATGTCGGGGAAAACTAGATCCGTCGCCGTAGCTTCAATCTGTTCCA
1 TCAATCTTTTTAATTGCAATGTCGGGGAAAACCAGATCCGCCGCCGTAGCTTCAATCTGTTCCA
*
53212168 TCAAT-TTTTTAAATTGCAATGTCGGGG-AAACCAGAT-CGCCGTCGTAGCTTCAATCTGTTCCA
1 TCAATCTTTTT-AATTGCAATGTCGGGGAAAACCAGATCCGCCGCCGTAGCTTCAATCTGTTCCA
53212230 CTACACCGCC
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
62 24 0.41
63 13 0.22
64 21 0.36
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (64 bp):
TCAATCTTTTTAATTGCAATGTCGGGGAAAACCAGATCCGCCGCCGTAGCTTCAATCTGTTCCA
Found at i:53212270 original size:50 final size:50
Alignment explanation
Indices: 53212200--53212360 Score: 128
Period size: 50 Copynumber: 3.2 Consensus size: 50
53212190 CGGGGAAACC
*
53212200 AGAT-CGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTA
1 AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTA
* * * ** * * ** *** ***
53212249 AGATCCGCCGTTGTGGCTTCAATATTTTAAATTGCAATGTTGGGGAAACC
1 AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTA
* *
53212299 AGATCCGCC-TTCGTAGCTTCAATCTGTTCCACTACACCACCAGGAAAGTA
1 AGATCCGCCGTT-GTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTA
*
53212349 AGATCCACCGTT
1 AGATCCGCCGTT
53212361 TTCAACCTAC
Statistics
Matches: 75, Mismatches: 34, Indels: 4
0.66 0.30 0.04
Matches are distributed among these distances:
49 6 0.08
50 67 0.89
51 2 0.03
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.26
Consensus pattern (50 bp):
AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTA
Found at i:53212284 original size:163 final size:164
Alignment explanation
Indices: 53212003--53212329 Score: 507
Period size: 163 Copynumber: 2.0 Consensus size: 164
53211993 CATTGTAACC
* *
53212003 TCAATCTTTTTAACTGTAATGTTGGGAAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCTAC
1 TCAATCTTTTTAACTGCAATGTCGGGAAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCTAC
* *
53212068 TACACCGCCAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAA
66 TACACCGCCAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATATTTTAAATTGCAATGTCGGGG-A
* *
53212133 AACTAGATCCGTCGCCGTAGCTTCAATCTGTTCCA
130 AACCAGATCCGCCGCCGTAGCTTCAATCTGTTCCA
* *
53212168 TCAAT-TTTTTAAATTGCAATGTCGGGGAAACCAGAT-CGCCGTCGTAGCTTCAATCTGTTCC-A
1 TCAATCTTTTT-AACTGCAATGTCGGGAAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCTA
* *
53212230 CTACACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATATTTTAAATTGCAATGTTGGGGA
65 CTACACCGCCAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATATTTTAAATTGCAATGTCGGGGA
**
53212295 AACCAGATCCGCCTTCGTAGCTTCAATCTGTTCCA
130 AACCAGATCCGCCGCCGTAGCTTCAATCTGTTCCA
53212330 CTACACCACC
Statistics
Matches: 149, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
162 32 0.21
163 61 0.41
164 30 0.20
165 26 0.17
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.30
Consensus pattern (164 bp):
TCAATCTTTTTAACTGCAATGTCGGGAAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCTAC
TACACCGCCAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATATTTTAAATTGCAATGTCGGGGAA
ACCAGATCCGCCGCCGTAGCTTCAATCTGTTCCA
Found at i:53212348 original size:100 final size:99
Alignment explanation
Indices: 53212168--53212360 Score: 323
Period size: 100 Copynumber: 1.9 Consensus size: 99
53212158 ATCTGTTCCA
*
53212168 TCAATTTTTTAAATTGCAATGTCGGGGAAACCAGATCGCCGTCGTAGCTTCAATCTGTTCCACTA
1 TCAATATTTTAAATTGCAATGTCGGGGAAACCAGATCGCCGTCGTAGCTTCAATCTGTTCCACTA
* * *
53212233 CACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCT
66 CACCACCAGGAAAGTAAGATCCACCGTTGTGGCT
* *
53212267 TCAATATTTTAAATTGCAATGTTGGGGAAACCAGATCCGCCTTCGTAGCTTCAATCTGTTCCACT
1 TCAATATTTTAAATTGCAATGTCGGGGAAACCAGAT-CGCCGTCGTAGCTTCAATCTGTTCCACT
53212332 ACACCACCAGGAAAGTAAGATCCACCGTT
65 ACACCACCAGGAAAGTAAGATCCACCGTT
53212361 TTCAACCTAC
Statistics
Matches: 87, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
99 34 0.39
100 53 0.61
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (99 bp):
TCAATATTTTAAATTGCAATGTCGGGGAAACCAGATCGCCGTCGTAGCTTCAATCTGTTCCACTA
CACCACCAGGAAAGTAAGATCCACCGTTGTGGCT
Found at i:53212488 original size:88 final size:88
Alignment explanation
Indices: 53212360--53212577 Score: 391
Period size: 88 Copynumber: 2.5 Consensus size: 88
53212350 GATCCACCGT
* * *
53212360 TTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGGTATCTTTGATCTACTTCGCTGTCAG
1 TTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGGTATATTCGATCTACTTCGCCGTCAG
53212425 TACAGGAAGGCAAGATCTGTCAA
66 TACAGGAAGGCAAGATCTGTCAA
*
53212448 TTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGGTATATTCGATCTGCTTCGCCGTCAG
1 TTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGGTATATTCGATCTACTTCGCCGTCAG
*
53212513 TACAGGAAGGCAAGATCTGTCAT
66 TACAGGAAGGCAAGATCTGTCAA
53212536 TTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGGTA
1 TTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGGTA
53212578 GTCATTACTC
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 125 1.00
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (88 bp):
TTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGGTATATTCGATCTACTTCGCCGTCAG
TACAGGAAGGCAAGATCTGTCAA
Found at i:53213627 original size:15 final size:15
Alignment explanation
Indices: 53213609--53213659 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
53213599 TTAGGCTCTC
*
53213609 CATTTTTAC-TTTTT
1 CATTTTTCCATTTTT
53213623 CCATTTTT-CATTTTT
1 -CATTTTTCCATTTTT
53213638 CATTTTTCCATTTTT
1 CATTTTTCCATTTTT
53213653 -ATTTTTC
1 CATTTTTC
53213660 ACATCTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
14 15 0.44
15 19 0.56
ACGTcount: A:0.14, C:0.18, G:0.00, T:0.69
Consensus pattern (15 bp):
CATTTTTCCATTTTT
Found at i:53213634 original size:22 final size:22
Alignment explanation
Indices: 53213609--53213660 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
53213599 TTAGGCTCTC
53213609 CATTTTT-ACTTTTTCCATTTTT
1 CATTTTTCA-TTTTTCCATTTTT
53213631 CATTTTTCATTTTTCCATTTTT
1 CATTTTTCATTTTTCCATTTTT
53213653 -ATTTTTCA
1 CATTTTTCA
53213661 CATCTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 8 0.28
22 20 0.69
23 1 0.03
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.67
Consensus pattern (22 bp):
CATTTTTCATTTTTCCATTTTT
Found at i:53213658 original size:7 final size:7
Alignment explanation
Indices: 53213609--53213660 Score: 63
Period size: 7 Copynumber: 7.3 Consensus size: 7
53213599 TTAGGCTCTC
53213609 CATTTTT
1 CATTTTT
53213616 -ACTTTTT
1 CA-TTTTT
53213623 CCATTTTT
1 -CATTTTT
53213631 CATTTTT
1 CATTTTT
53213638 CATTTTT
1 CATTTTT
53213645 CCATTTTT
1 -CATTTTT
53213653 -ATTTTT
1 CATTTTT
53213659 CA
1 CA
53213661 CATCTTTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
6 7 0.17
7 20 0.50
8 12 0.30
9 1 0.03
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.67
Consensus pattern (7 bp):
CATTTTT
Found at i:53214175 original size:10 final size:9
Alignment explanation
Indices: 53214156--53214219 Score: 58
Period size: 9 Copynumber: 7.0 Consensus size: 9
53214146 CCCAGTAGAG
53214156 GTTTTTTTT
1 GTTTTTTTT
53214165 GTTTCTTTTT
1 GTTT-TTTTT
*
53214175 GTTTTTATT
1 GTTTTTTTT
*
53214184 -TTTGTTTT
1 GTTTTTTTT
* *
53214192 ATTTTTCTT
1 GTTTTTTTT
53214201 GTTTTTTGTT
1 GTTTTTT-TT
*
53214211 CTTTTTTTT
1 GTTTTTTTT
53214220 TGGATTGAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
8 6 0.14
9 21 0.48
10 17 0.39
ACGTcount: A:0.03, C:0.05, G:0.09, T:0.83
Consensus pattern (9 bp):
GTTTTTTTT
Found at i:53214185 original size:11 final size:10
Alignment explanation
Indices: 53214157--53214218 Score: 61
Period size: 11 Copynumber: 5.8 Consensus size: 10
53214147 CCAGTAGAGG
53214157 TTTTTTTTGT
1 TTTTTTTTGT
*
53214167 TTCTTTTTGTT
1 TTTTTTTTG-T
53214178 TTTATTTTTGT
1 TTT-TTTTTGT
*
53214189 TTTATTTTTCT
1 TTT-TTTTTGT
*
53214200 TGTTTTTTGT
1 TTTTTTTTGT
53214210 TCTTTTTTT
1 T-TTTTTTT
53214219 TTGGATTGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
10 15 0.35
11 22 0.51
12 6 0.14
ACGTcount: A:0.03, C:0.05, G:0.08, T:0.84
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:53214185 original size:12 final size:11
Alignment explanation
Indices: 53214160--53214210 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 11
53214150 GTAGAGGTTT
*
53214160 TTTTTG-TTTC
1 TTTTTGTTTTA
53214170 TTTTTGTTTTTA
1 TTTTTG-TTTTA
53214182 TTTTTGTTTTA
1 TTTTTGTTTTA
* *
53214193 TTTTTCTTGT-
1 TTTTTGTTTTA
53214203 TTTTTGTT
1 TTTTTGTT
53214211 CTTTTTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
10 13 0.37
11 13 0.37
12 9 0.26
ACGTcount: A:0.04, C:0.04, G:0.10, T:0.82
Consensus pattern (11 bp):
TTTTTGTTTTA
Found at i:53217888 original size:444 final size:442
Alignment explanation
Indices: 53217059--53217956 Score: 1733
Period size: 444 Copynumber: 2.0 Consensus size: 442
53217049 AAAATGTATT
53217059 TAAAAAATATGTTAAAAAAACAATGCAATATGAAACAAATATTTTAATTTAAATTATACATGTAT
1 TAAAAAATATGTTAAAAAAACAATGCAATATGAAACAAATATTTTAATTTAAATTATACATGTAT
53217124 ATGATATATATATAAATGATATATAAGTGAATTTTGAAAATGTGTGTATGGAAAAATATAAAAGA
66 ATGATATATATATAAATGATATATAAGTGAATTTTGAAAATGTGTGTATGGAAAAATATAAAAGA
*
53217189 TGCATACGTATTATAAAATGTTGATGCATATATATATGAATACAAAAATCATGAAAATAAAACAA
131 TGCATACGTATTATAAAATGTTGATGCATATATATACGAATACAAAAATCATGAAAATAAAACAA
53217254 TAATAACATATATTAAAATATATTCATGCATTTACACAAAAATATGTAAGCATAATATATTGGTA
196 TAATAACATATATTAAAATATATTCATGCATTTACACAAAAATATGTAAGCATAATATATTGGTA
53217319 AATAAAAGAAAATGGAAAATATATTTAATAAGTTCTTAATAGAGTATAAATATATATGTACATAT
261 AATAAAAGAAAATGGAAAATATATTTAATAAGTTCTTAATAGAGTATAAATATATATGTACATAT
53217384 TATAACGAATGTATAAACATATATATAGATTATAAAATATGGACAATGTATAAATATTATAAAAT
326 TATAACGAATGTATAAACATATATATAGATTATAAAATATGGACAATGTATAAATATTATAAAAT
* *
53217449 ATGAATGTATATACATACATATAAAAACTACGAAAATAAAATAATAAAATAATA
391 ATAAATGTATATACATACATAGAAAAACTACGAAAATAAAATAATAAAAT-A-A
53217503 TAAAAAATATGTTAAAAAAACAATGCAATATGAAACAAATATTTTAATTTAAATTATACATGTAT
1 TAAAAAATATGTTAAAAAAACAATGCAATATGAAACAAATATTTTAATTTAAATTATACATGTAT
53217568 ATGATATATATATAAATGATATATAAGTGAATTTTGAAAATGTGTGTATGGAAAAATATAAAAGA
66 ATGATATATATATAAATGATATATAAGTGAATTTTGAAAATGTGTGTATGGAAAAATATAAAAGA
53217633 TGCATACGTATTATAAAATGTTGATGCATATATATACGAATACAAAAATCATGAAAATAAAACAA
131 TGCATACGTATTATAAAATGTTGATGCATATATATACGAATACAAAAATCATGAAAATAAAACAA
53217698 TAATAACATATATTAAAATATATTCATGCATTTACACAAAAATATGTAAGCATAATATATTGGTA
196 TAATAACATATATTAAAATATATTCATGCATTTACACAAAAATATGTAAGCATAATATATTGGTA
53217763 AATAAAAGAAAATGGAAAATATATTTAATAAGTTCTTAATAGAGTATAAATATATATGTACATAT
261 AATAAAAGAAAATGGAAAATATATTTAATAAGTTCTTAATAGAGTATAAATATATATGTACATAT
53217828 TATAACGAATGTATAAACATATATATAGATTATAAAATATGGACAATGTATAAATATTATAAAAT
326 TATAACGAATGTATAAACATATATATAGATTATAAAATATGGACAATGTATAAATATTATAAAAT
* *
53217893 ATAAATGTATGTACATACATAGAAAAACTATGAAAATAAAATAATAAAATAA
391 ATAAATGTATATACATACATAGAAAAACTACGAAAATAAAATAATAAAATAA
53217945 TAAAAAATATGT
1 TAAAAAATATGT
53217957 ATATGTATTT
Statistics
Matches: 449, Mismatches: 5, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
442 13 0.03
443 1 0.00
444 435 0.97
ACGTcount: A:0.52, C:0.06, G:0.10, T:0.32
Consensus pattern (442 bp):
TAAAAAATATGTTAAAAAAACAATGCAATATGAAACAAATATTTTAATTTAAATTATACATGTAT
ATGATATATATATAAATGATATATAAGTGAATTTTGAAAATGTGTGTATGGAAAAATATAAAAGA
TGCATACGTATTATAAAATGTTGATGCATATATATACGAATACAAAAATCATGAAAATAAAACAA
TAATAACATATATTAAAATATATTCATGCATTTACACAAAAATATGTAAGCATAATATATTGGTA
AATAAAAGAAAATGGAAAATATATTTAATAAGTTCTTAATAGAGTATAAATATATATGTACATAT
TATAACGAATGTATAAACATATATATAGATTATAAAATATGGACAATGTATAAATATTATAAAAT
ATAAATGTATATACATACATAGAAAAACTACGAAAATAAAATAATAAAATAA
Found at i:53218037 original size:3 final size:3
Alignment explanation
Indices: 53218029--53218086 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
53218019 GTCTATTGGT
53218029 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
53218077 ATA ATA ATA A
1 ATA ATA ATA A
53218087 AATGACAGAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:53219822 original size:101 final size:101
Alignment explanation
Indices: 53219663--53220131 Score: 572
Period size: 101 Copynumber: 4.7 Consensus size: 101
53219653 AATGTCGGAG
* * * * *
53219663 AAACAAGATCTGCCGTCGT-GCCTTCAATCTGTTCTTACTACACCACCAA-GAAAGTAAGATTCG
1 AAACCAGATCCGCCGTCGTAG-CTTCAATCTGTTC-CACTACACCGCCAAGGAAA-TAAGATCCG
* ** * * *
53219726 CTGTTGTAACCTCAATCTTTTTAACTGCAATGT-TGGGA
63 CCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCTGGGA
* * **
53219764 AAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCTACTACACTGCCAATGAAATAAGATCTACC
1 AAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCC-ACTACACCGCCAAGGAAATAAGATCCGCC
* * *
53219829 GTTATGGCTTCAATCTTTTTAATTGCAATGTCGGGGA
65 GTTGTGGCTTCAATCTTTTAAATTGCAATGTCTGGGA
* * *
53219866 AAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTACATCGCCAGGGAAATAAAATCCGCCG
1 AAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAAGGAAATAAGATCCGCCG
* *
53219931 TTGTGGCTTCATTCTTTTAAATTGCAATGTCAGGG-
66 TTGTGGCTTCAATCTTTTAAATTGCAATGTCTGGGA
* * * * *
53219966 AAACCAGAT-CGTCGTCGTAGCTTCAATCTGTTCCACTATACAGCCAGGGAACTAAGATCCGCCG
1 AAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAAGGAAATAAGATCCGCCG
*
53220030 TTGTGGCTTCAATCTTTTAAATTGCAATGT-TGGGG
66 TTGTGGCTTCAATCTTTTAAATTGCAATGTCTGGGA
* * *
53220065 AAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATCCGTCG
1 AAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAAGGAAATAAGATCCGCCG
53220130 TT
66 TT
53220132 TTCAACCTAC
Statistics
Matches: 323, Mismatches: 39, Indels: 13
0.86 0.10 0.03
Matches are distributed among these distances:
98 3 0.01
99 87 0.27
100 61 0.19
101 128 0.40
102 44 0.14
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (101 bp):
AAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAAGGAAATAAGATCCGCCG
TTGTGGCTTCAATCTTTTAAATTGCAATGTCTGGGA
Found at i:53220116 original size:50 final size:50
Alignment explanation
Indices: 53219764--53220116 Score: 237
Period size: 50 Copynumber: 7.0 Consensus size: 50
53219754 AATGTTGGGA
* **
53219764 AAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCTACTACACTGCCAATG
1 AAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCC-ACTACAATGCCAGGG
** ** ** * * ** * * * *
53219815 AAATAAGATCTACCGTTATGGCTTCAATCTTTTTAATTGCAATGTCGGGG
1 AAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTACAATGCCAGGG
53219865 AAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTAC-ATCGCCAGGG
1 -AAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTACAAT-GCCAGGG
** * * * * * ** * * *
53219916 AAATAAAATCCGCCGTTGTGGCTTCATTCTTTTAAATTGCAATGTCAGGG
1 AAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTACAATGCCAGGG
* *
53219966 AAACCAGAT-CGTCGTCGTAGCTTCAATCTGTTCCACTATACA-GCCAGGG
1 AAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTACA-ATGCCAGGG
* * * * ** * * ***
53220015 -AACTAAGATCCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTTGGGG
1 AAAC-CAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTACAATGCCAGGG
**
53220065 AAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGG
1 AAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTACAATGCCAGGG
53220115 AA
1 AA
53220117 GTAAGATCCG
Statistics
Matches: 211, Mismatches: 83, Indels: 17
0.68 0.27 0.05
Matches are distributed among these distances:
48 3 0.01
49 32 0.15
50 113 0.54
51 63 0.30
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (50 bp):
AAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTACAATGCCAGGG
Found at i:53220240 original size:88 final size:88
Alignment explanation
Indices: 53220130--53220653 Score: 832
Period size: 88 Copynumber: 6.0 Consensus size: 88
53220120 AGATCCGTCG
* * * *
53220130 TTTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGGTATCTTTGATCTGCTTCGCTGCCA
1 TTTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGGTATATTCGATCTGCTTCACTGTCA
*
53220195 GTACAGGAAGGCAAGATCTGTCA
66 GTACAGGAAGGCAAGATCTGCCA
* * *
53220218 TTTTCAACCTACTCCACTACTGCCCAAGGATACAAGGCTGGTATATTCGATCTGCTTCACCGTCA
1 TTTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGGTATATTCGATCTGCTTCACTGTCA
*
53220283 GTACAGGAAGGCAAGATCTGTCA
66 GTACAGGAAGGCAAGATCTGCCA
* *
53220306 TTTTCAACCTACTCCACTACTGCCGAGGGAGACAAGGCTGGTATATTCGATCTGCTTCACAGTCA
1 TTTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGGTATATTCGATCTGCTTCACTGTCA
53220371 GTACAGGAAGGCAAGATCTGCCA
66 GTACAGGAAGGCAAGATCTGCCA
* *
53220394 TTTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGTTGGTATATTCGATCTGCTTCACCGTCA
1 TTTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGGTATATTCGATCTGCTTCACTGTCA
*
53220459 GTACAAGAAGGCAAGATCTGCCA
66 GTACAGGAAGGCAAGATCTGCCA
* * * *
53220482 TTTTCAACCTACTCCACTACTGCCTAAGGAGACAAGGCTAGTATCTTCGATCTGCTTCACTGTCA
1 TTTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGGTATATTCGATCTGCTTCACTGTCA
53220547 GTACAGGAAGGCAAGATCTGCCA
66 GTACAGGAAGGCAAGATCTGCCA
* * * *
53220570 TTTTCAACCTACTCCACTACTGCCCAGGGAGACAAGACTAGTATCTTCGATCTGCTTCACTGTTA
1 TTTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGGTATATTCGATCTGCTTCACTGTCA
* *
53220635 GTACAAGAAGGAAAGATCT
66 GTACAGGAAGGCAAGATCT
53220654 ACTATCTTCA
Statistics
Matches: 407, Mismatches: 29, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 407 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (88 bp):
TTTTCAACCTACTCCACTACTGCCCAGGGAGACAAGGCTGGTATATTCGATCTGCTTCACTGTCA
GTACAGGAAGGCAAGATCTGCCA
Found at i:53221392 original size:10 final size:9
Alignment explanation
Indices: 53221376--53221444 Score: 53
Period size: 8 Copynumber: 8.3 Consensus size: 9
53221366 TTTTTATGTT
53221376 TTATATATA
1 TTATATATA
53221385 -TATATATA
1 TTATATATA
*
53221393 TTAT-TTTA
1 TTATATATA
53221401 TTATATA-A
1 TTATATATA
53221409 -TATA-ATA
1 TTATATATA
53221416 TT-T-TATA
1 TTATATATA
*
53221423 TTGTATTATA
1 TTATA-TATA
*
53221433 TTATATAAA
1 TTATATATA
53221442 TTA
1 TTA
53221445 AACAGATGAC
Statistics
Matches: 48, Mismatches: 4, Indels: 16
0.71 0.06 0.24
Matches are distributed among these distances:
6 1 0.02
7 11 0.23
8 18 0.38
9 10 0.21
10 8 0.17
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (9 bp):
TTATATATA
Found at i:53221407 original size:15 final size:15
Alignment explanation
Indices: 53221376--53221439 Score: 56
Period size: 15 Copynumber: 4.0 Consensus size: 15
53221366 TTTTTATGTT
53221376 TTATATATATATATATA
1 TTAT-TATAT-TATATA
*
53221393 TTATTTTATTATATA
1 TTATTATATTATATA
* * *
53221408 ATATAATATTTTATA
1 TTATTATATTATATA
53221423 TTGTATTATATTATATA
1 -T-TATTATATTATATA
53221440 AATTAAACAG
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
15 17 0.46
16 4 0.11
17 16 0.43
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (15 bp):
TTATTATATTATATA
Found at i:53221417 original size:20 final size:22
Alignment explanation
Indices: 53221374--53221423 Score: 77
Period size: 20 Copynumber: 2.4 Consensus size: 22
53221364 GATTTTTATG
*
53221374 TTTTATATATATATATATATTA
1 TTTTATATATATATATATAATA
53221396 TTTTAT-TATATA-ATATAATA
1 TTTTATATATATATATATAATA
53221416 TTTTATAT
1 TTTTATAT
53221424 TGTATTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 13 0.50
21 7 0.27
22 6 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTATATATATATATATAATA
Found at i:53224595 original size:7 final size:7
Alignment explanation
Indices: 53224539--53224597 Score: 77
Period size: 7 Copynumber: 8.3 Consensus size: 7
53224529 TTAGGCTTTC
53224539 CATTTTT
1 CATTTTT
53224546 -ACTTTTT
1 CA-TTTTT
53224553 CCATTTTT
1 -CATTTTT
53224561 CATTTTT
1 CATTTTT
53224568 CATTTTT
1 CATTTTT
53224575 CATTTTT
1 CATTTTT
53224582 CCATTTTT
1 -CATTTTT
53224590 -ATTTTT
1 CATTTTT
53224596 CA
1 CA
53224598 CATCTTTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
6 7 0.15
7 27 0.57
8 12 0.26
9 1 0.02
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (7 bp):
CATTTTT
Found at i:53224595 original size:14 final size:15
Alignment explanation
Indices: 53224535--53224596 Score: 94
Period size: 15 Copynumber: 4.3 Consensus size: 15
53224525 CACCTTAGGC
53224535 TTTCCATTTTT-ACTT
1 TTTCCATTTTTCA-TT
53224550 TTTCCATTTTTCATT
1 TTTCCATTTTTCATT
53224565 TTT-CATTTTTCATT
1 TTTCCATTTTTCATT
53224579 TTTCCATTTTT-ATT
1 TTTCCATTTTTCATT
53224593 TTTC
1 TTTC
53224597 ACATCTTTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
14 21 0.47
15 23 0.51
16 1 0.02
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTCCATTTTTCATT
Found at i:53224608 original size:14 final size:14
Alignment explanation
Indices: 53224535--53224608 Score: 62
Period size: 15 Copynumber: 5.1 Consensus size: 14
53224525 CACCTTAGGC
*
53224535 TTTCCATTTTTACTT
1 TTTCCATCTTTA-TT
*
53224550 TTTCCATTTTTCATT
1 TTTCCATCTTT-ATT
*
53224565 TTT-CATTTTTCATT
1 TTTCCATCTTT-ATT
*
53224579 TTTCCATTTTTATT
1 TTTCCATCTTTATT
53224593 TTTCACATCTTT-TT
1 TTTC-CATCTTTATT
53224607 TT
1 TT
53224609 CTTTTTTTTT
Statistics
Matches: 55, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
14 25 0.45
15 29 0.53
16 1 0.02
ACGTcount: A:0.14, C:0.18, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTCCATCTTTATT
Found at i:53225151 original size:12 final size:12
Alignment explanation
Indices: 53225095--53225152 Score: 57
Period size: 12 Copynumber: 4.7 Consensus size: 12
53225085 CCAGTAGAGG
53225095 TTTTTTTGTTTCT
1 TTTTTTTG-TTCT
*
53225108 TTTTCTTT-TTGT
1 TTTT-TTTGTTCT
53225120 TTTTATTT-TTCT
1 TTTT-TTTGTTCT
53225132 TATTTTTTGTTCT
1 T-TTTTTTGTTCT
53225145 TTTTTTTG
1 TTTTTTTG
53225153 GATTGAATCT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
12 24 0.62
13 12 0.31
14 3 0.08
ACGTcount: A:0.03, C:0.07, G:0.07, T:0.83
Consensus pattern (12 bp):
TTTTTTTGTTCT
Found at i:53238319 original size:33 final size:33
Alignment explanation
Indices: 53238251--53238320 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
53238241 ATCTATTCTA
* * *
53238251 AAAAGAAAAGAGAAAATCTAAGCTAAAAAGGTG
1 AAAAGAAAAGAGAAAACCTAACCTAAAAAGATG
**
53238284 AAAAGAAAAGA-AAAACCCTAACCTAAAACTATG
1 AAAAGAAAAGAGAAAA-CCTAACCTAAAAAGATG
53238317 AAAA
1 AAAA
53238321 CCTAATAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 4 0.13
33 27 0.87
ACGTcount: A:0.63, C:0.11, G:0.14, T:0.11
Consensus pattern (33 bp):
AAAAGAAAAGAGAAAACCTAACCTAAAAAGATG
Found at i:53245589 original size:48 final size:48
Alignment explanation
Indices: 53245518--53245630 Score: 136
Period size: 48 Copynumber: 2.4 Consensus size: 48
53245508 TACAACCAGT
* * * * * *
53245518 GGTTCATCCACAACATATTTTAGTCGGTAGTTTATTAGCACGATCAGC
1 GGTTCATCCACAACATATTTTAGTCAGCAATTTATCAGCACGACCAAC
** * *
53245566 GGTTCATCCACAATGTATTTTAGTCAGCAATTTATCAGTACGACCAAT
1 GGTTCATCCACAACATATTTTAGTCAGCAATTTATCAGCACGACCAAC
53245614 GGTTCATCCACAACATA
1 GGTTCATCCACAACATA
53245631 CTAGCAGTTG
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (48 bp):
GGTTCATCCACAACATATTTTAGTCAGCAATTTATCAGCACGACCAAC
Found at i:53245713 original size:96 final size:96
Alignment explanation
Indices: 53245613--53245818 Score: 252
Period size: 96 Copynumber: 2.1 Consensus size: 96
53245603 GTACGACCAA
* *
53245613 TGGTTCATCCACAACATACTAGCAG-TTGTTACCTTCACCAAAGGATGGTTCATCCACCAATATT
1 TGGTTCATCCACAACATACTAGCAGCTT-TTACCTGCACCAAAGGATGATTCATCCACCAATATT
** * *
53245677 TTTATCGTTAGCAGTTCATTTGCAATGATCAG
65 TTTATCGTTAGCAGTTCAGCTACAACGATCAG
** * * * * *
53245709 TGGTTCATCCACAATGTATTAGCAGCTTTTATCTGCAGCGATGGATGATTCATCCACCAATATTT
1 TGGTTCATCCACAACATACTAGCAGCTTTTACCTGCACCAAAGGATGATTCATCCACCAATATTT
*
53245774 TTATCGTTAGCATTTCAGCTACAACGATCAG
66 TTATCGTTAGCAGTTCAGCTACAACGATCAG
* *
53245805 TGGTTTATCTACAA
1 TGGTTCATCCACAA
53245819 TGTGGTGTAA
Statistics
Matches: 93, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
96 91 0.98
97 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (96 bp):
TGGTTCATCCACAACATACTAGCAGCTTTTACCTGCACCAAAGGATGATTCATCCACCAATATTT
TTATCGTTAGCAGTTCAGCTACAACGATCAG
Found at i:53246813 original size:19 final size:21
Alignment explanation
Indices: 53246769--53246814 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
53246759 AAATAAAAAT
* *
53246769 ATATTTATATTATTTTAATTA
1 ATATTTATATAATTTTAATAA
53246790 ATATTTA-ATAATTTT-ATAA
1 ATATTTATATAATTTTAATAA
53246809 ATATTT
1 ATATTT
53246815 TATTTATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 9 0.39
20 7 0.30
21 7 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATTTATATAATTTTAATAA
Found at i:53248039 original size:39 final size:39
Alignment explanation
Indices: 53247996--53248073 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
53247986 ACATTACGCG
* * *
53247996 TATAATTACATAACGTTCAAGCACATATCGCAATACTCA
1 TATAATCACATAACATTCAACCACATATCGCAATACTCA
* *
53248035 TATAATCGCATAACATTCAACCATATATCGCAATACTCA
1 TATAATCACATAACATTCAACCACATATCGCAATACTCA
53248074 AAACAGGTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.28
Consensus pattern (39 bp):
TATAATCACATAACATTCAACCACATATCGCAATACTCA
Found at i:53250286 original size:25 final size:25
Alignment explanation
Indices: 53250250--53250300 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
53250240 TACTAGGCCA
**
53250250 TGTGTGACACACGGTTTAGGCTATT
1 TGTGTGACACACGGGCTAGGCTATT
53250275 TGTG-GACTACACGGGCTAGGCTATT
1 TGTGTGAC-ACACGGGCTAGGCTATT
53250300 T
1 T
53250301 AGGTTGTGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (25 bp):
TGTGTGACACACGGGCTAGGCTATT
Found at i:53260084 original size:61 final size:62
Alignment explanation
Indices: 53259910--53260086 Score: 186
Period size: 59 Copynumber: 2.9 Consensus size: 62
53259900 TGTATTGTTC
* * * *
53259910 ATTTTAGTAAATTATATATTATAATTATTTAATATTAAGAATTTCATTAAATTATATATTTTT
1 ATTTTAGTAAATT-TATATAATAATTATTTAATATTAAGAATTTTATTAAATTATATATTATG
** * * * *
53259973 ATTAAATTATATTTA-ATAATAATTATGTTAA-ATT-A-TATTTTA-TAGCATTATATATTATG
1 ATTTTAGTAAATTTATATAATAATTAT-TTAATATTAAGAATTTTATTA-AATTATATATTATG
*
53260032 ATTTTAGTAAATTTATATCATAA-TATTTAATATTAAGAATTTTATTAAATTATAT
1 ATTTTAGTAAATTTATATAATAATTATTTAATATTAAGAATTTTATTAAATTATAT
53260087 TTAATAATAA
Statistics
Matches: 90, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
58 6 0.07
59 33 0.37
60 8 0.09
61 26 0.29
62 8 0.09
63 9 0.10
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (62 bp):
ATTTTAGTAAATTTATATAATAATTATTTAATATTAAGAATTTTATTAAATTATATATTATG
Found at i:53260088 original size:102 final size:102
Alignment explanation
Indices: 53259969--53260188 Score: 386
Period size: 102 Copynumber: 2.2 Consensus size: 102
53259959 AATTATATAT
53259969 TTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGCATTATATATTATGAT
1 TTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGCATTATATATTATGAT
* * * *
53260034 TTTAGTAAATTTATATCATAATATTTAATATTAAGAA
66 TTTAGTAAATTCATATAAGAATATTTAATACTAAGAA
* *
53260071 TTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGAT
1 TTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGCATTATATATTATGAT
53260136 TTTAGTAAATTCATATAAGAATATTTAATACTAAGAA
66 TTTAGTAAATTCATATAAGAATATTTAATACTAAGAA
53260173 TTTTATTAAATTATAT
1 TTTTATTAAATTATAT
53260189 ATTTTTGTTA
Statistics
Matches: 112, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 112 1.00
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (102 bp):
TTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGCATTATATATTATGAT
TTTAGTAAATTCATATAAGAATATTTAATACTAAGAA
Found at i:53260194 original size:18 final size:17
Alignment explanation
Indices: 53260172--53260306 Score: 86
Period size: 18 Copynumber: 8.0 Consensus size: 17
53260162 AATACTAAGA
53260172 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
*
53260189 ATTTTTGTTAAA-T-TAT
1 A-TTTTATTAAATTATAT
* *
53260205 A-TTTAAT-AATAAT-T
1 ATTTTATTAAATTATAT
* *
53260219 ATTTTAAATTATATTTTAT
1 ATTTT--ATTAAATTATAT
* *
53260238 AATATTA-TATATTATA-
1 -ATTTTATTAAATTATAT
**
53260254 ATTTTAGAAAATTCATAT
1 ATTTTATTAAATT-ATAT
53260272 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
53260289 ATTTTTATTAAATTATAT
1 A-TTTTATTAAATTATAT
53260307 TTAATAATAA
Statistics
Matches: 90, Mismatches: 15, Indels: 25
0.69 0.12 0.19
Matches are distributed among these distances:
13 2 0.02
14 6 0.07
15 9 0.10
16 8 0.09
17 20 0.22
18 40 0.44
19 1 0.01
20 4 0.04
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:53260225 original size:26 final size:25
Alignment explanation
Indices: 53260187--53260245 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
53260177 ATTAAATTAT
*
53260187 ATATTTTTGTTAAATTATATTTAATA
1 ATATTATT-TTAAATTATATTTAATA
*
53260213 ATAATTATTTTAAATTATATTTTATA
1 AT-ATTATTTTAAATTATATTTAATA
53260239 ATATTAT
1 ATATTAT
53260246 ATATTATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 5 0.17
26 20 0.67
27 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
ATATTATTTTAAATTATATTTAATA
Found at i:53260244 original size:15 final size:15
Alignment explanation
Indices: 53260200--53260255 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
53260190 TTTTTGTTAA
*
53260200 ATTATATTTAATAAT
1 ATTATATTTTATAAT
*
53260215 AAT-TA-TTT-TAA-
1 ATTATATTTTATAAT
53260226 ATTATATTTTATAAT
1 ATTATATTTTATAAT
*
53260241 ATTATATATTATAAT
1 ATTATATTTTATAAT
53260256 TTTAGAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
11 2 0.06
12 5 0.15
13 5 0.15
14 5 0.15
15 16 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTATATTTTATAAT
Found at i:53277307 original size:23 final size:24
Alignment explanation
Indices: 53277281--53277341 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
53277271 GGTGCTTATG
*
53277281 TTTTGAATTTATTAT-TGA-TAAAA
1 TTTTGAATATATTATAT-ATTAAAA
53277304 TTTT-AATATATATATATATTAAAA
1 TTTTGAATATAT-TATATATTAAAA
*
53277328 TTTTGAATGTATTA
1 TTTTGAATATATTA
53277342 GTTTTTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 6 0.19
23 8 0.25
24 12 0.38
25 6 0.19
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (24 bp):
TTTTGAATATATTATATATTAAAA
Found at i:53278785 original size:40 final size:40
Alignment explanation
Indices: 53278730--53278813 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
53278720 TTAAAAAGCG
53278730 ATACCAATTTGTTATATTTTATGGTCTATTTATGTAGATC
1 ATACCAATTTGTTATATTTTATGGTCTATTTATGTAGATC
53278770 ATACCAATTTGTTATATTTTATGGTCTATTTATGTAGATC
1 ATACCAATTTGTTATATTTTATGGTCTATTTATGTAGATC
53278810 ATAC
1 ATAC
53278814 ATGTCAAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.49
Consensus pattern (40 bp):
ATACCAATTTGTTATATTTTATGGTCTATTTATGTAGATC
Found at i:53284035 original size:17 final size:17
Alignment explanation
Indices: 53284001--53284042 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
53283991 AAATATAGAT
*
53284001 TATTATTTA-TTAAATA
1 TATTATTAACTTAAATA
* *
53284017 TATTTTTAACTTAACTA
1 TATTATTAACTTAAATA
53284034 TATTATTAA
1 TATTATTAA
53284043 TTATATTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTATTAACTTAAATA
Found at i:53284343 original size:15 final size:15
Alignment explanation
Indices: 53284323--53284353 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
53284313 ATTTCATTCT
53284323 TCCTCTATTCCATTA
1 TCCTCTATTCCATTA
53284338 TCCTCTATTCCATTA
1 TCCTCTATTCCATTA
53284353 T
1 T
53284354 GATGAACCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.32, G:0.00, T:0.48
Consensus pattern (15 bp):
TCCTCTATTCCATTA
Found at i:53290259 original size:23 final size:21
Alignment explanation
Indices: 53290221--53290263 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
53290211 TCATTTTTCA
53290221 AATTTTATAGATATGATATATC
1 AATTTTATAGATATGA-ATATC
53290243 AATTTATATA-ATGATGAATAT
1 AATTT-TATAGAT-ATGAATAT
53290264 TTGAGATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (21 bp):
AATTTTATAGATATGAATATC
Found at i:53292413 original size:7 final size:7
Alignment explanation
Indices: 53292401--53292434 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
53292391 ATGTGAGGTT
53292401 GTTTATG
1 GTTTATG
53292408 GTTTATG
1 GTTTATG
53292415 GTTTATG
1 GTTTATG
53292422 GTTTATG
1 GTTTATG
*
53292429 ATTTAT
1 GTTTAT
53292435 TCAACTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.18, C:0.00, G:0.24, T:0.59
Consensus pattern (7 bp):
GTTTATG
Found at i:53296066 original size:55 final size:55
Alignment explanation
Indices: 53296007--53296177 Score: 129
Period size: 55 Copynumber: 3.1 Consensus size: 55
53295997 TATTTATATA
53296007 TTAATTTATAACGAATAGATGTGAAAATAAAATTACAATTTGAAGCATAACTCGG
1 TTAATTTATAACGAATAGATGTGAAAATAAAATTACAATTTGAAGCATAACTCGG
* * ** ** * * * ***
53296062 TTAATATATTA--TTTA-AT-T-ATCATAAAAATAACTAATATGACTGCTATTATTA-TATA
1 TTAATTTATAACGAATAGATGTGAAAAT-AAAATTAC-AATTTGA-AGC-A-TA--ACTCGG
53296118 TTAATTTATAACGAATAGATGTGAAAATAAAATTACAATTTGAAGCATAACTCGG
1 TTAATTTATAACGAATAGATGTGAAAATAAAATTACAATTTGAAGCATAACTCGG
53296173 TTAAT
1 TTAAT
53296178 AATCATAGTT
Statistics
Matches: 79, Mismatches: 24, Indels: 26
0.61 0.19 0.20
Matches are distributed among these distances:
50 3 0.04
51 8 0.10
52 8 0.10
53 4 0.05
54 2 0.03
55 17 0.22
56 12 0.15
57 2 0.03
58 4 0.05
59 8 0.10
60 8 0.10
61 3 0.04
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (55 bp):
TTAATTTATAACGAATAGATGTGAAAATAAAATTACAATTTGAAGCATAACTCGG
Found at i:53296593 original size:15 final size:14
Alignment explanation
Indices: 53296572--53296611 Score: 62
Period size: 16 Copynumber: 2.7 Consensus size: 14
53296562 TTTAAAATTG
53296572 ATTTAAAATTTTAA
1 ATTTAAAATTTTAA
53296586 ATTTTAAAAATTTTAA
1 A-TTT-AAAATTTTAA
53296602 ATTTAAAATT
1 ATTTAAAATT
53296612 AAAAGTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 7 0.29
15 6 0.25
16 11 0.46
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTAAAATTTTAA
Found at i:53306307 original size:63 final size:63
Alignment explanation
Indices: 53306201--53306382 Score: 204
Period size: 63 Copynumber: 2.9 Consensus size: 63
53306191 GTGACAGGCT
* * * * * * *
53306201 GTGTAACTCACTA-TTTTGAGTTAATGTCAAACAGGCTAGGGACATGAGCATGTGTCTATACC
1 GTGTAACTCACTATTTTTGAGTTAGTGTCACACGGGCCAGGGACACGAGCATCTGTCTAGACC
* * *
53306263 GTGTAACTCACTATTTTTGAGTTAGGGTCACACGGGCCAGGGACACGAGCGTCTGTCTAGGCC
1 GTGTAACTCACTATTTTTGAGTTAGTGTCACACGGGCCAGGGACACGAGCATCTGTCTAGACC
* * * * * * *
53306326 GTGTAACTTACTATTTGTGAATTAGTGTTACATGGGCCAGAGACACAAGCATCTGTC
1 GTGTAACTCACTATTTTTGAGTTAGTGTCACACGGGCCAGGGACACGAGCATCTGTC
53306383 CAAGTCGTGT
Statistics
Matches: 100, Mismatches: 19, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
62 13 0.13
63 87 0.87
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (63 bp):
GTGTAACTCACTATTTTTGAGTTAGTGTCACACGGGCCAGGGACACGAGCATCTGTCTAGACC
Found at i:53316617 original size:15 final size:15
Alignment explanation
Indices: 53316584--53316622 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
53316574 CCAAGGATAA
53316584 AAAAATGAAA-GGAGG
1 AAAAA-GAAATGGAGG
53316599 -AAAAGAAATGGAGG
1 AAAAAGAAATGGAGG
53316613 AAAAAGAAAT
1 AAAAAGAAAT
53316623 ATCATGCAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.18
14 9 0.41
15 9 0.41
ACGTcount: A:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (15 bp):
AAAAAGAAATGGAGG
Found at i:53318068 original size:28 final size:28
Alignment explanation
Indices: 53318028--53318081 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
53318018 AAAAATGTGC
53318028 TTTGTAAGAAAAAGAATTATTTGAACGT
1 TTTGTAAGAAAAAGAATTATTTGAACGT
53318056 TTTGTAAGAAAAAGAATTATTTGAAC
1 TTTGTAAGAAAAAGAATTATTTGAAC
53318082 AACTCTGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (28 bp):
TTTGTAAGAAAAAGAATTATTTGAACGT
Found at i:53335066 original size:18 final size:19
Alignment explanation
Indices: 53335045--53335082 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
53335035 TTTATACAAT
53335045 AAAAAT-AATTTAAAATTA
1 AAAAATAAATTTAAAATTA
*
53335063 AAAAATAAATTTAACATTA
1 AAAAATAAATTTAAAATTA
53335082 A
1 A
53335083 TGAAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAATAAATTTAAAATTA
Found at i:53343606 original size:13 final size:13
Alignment explanation
Indices: 53343588--53343613 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53343578 AGTAACTGCT
53343588 AAATTATAGCACA
1 AAATTATAGCACA
53343601 AAATTATAGCACA
1 AAATTATAGCACA
53343614 CCCATGATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (13 bp):
AAATTATAGCACA
Found at i:53351118 original size:45 final size:45
Alignment explanation
Indices: 53351031--53351128 Score: 108
Period size: 45 Copynumber: 2.2 Consensus size: 45
53351021 AGAACGAATA
* *
53351031 GAAATAGAGAAATGAAAAGCATTCAGAAATGATTATGATTTTCTCC
1 GAAATGGAGAAATGAAAAGCATTCAGAAATGAATATGATTTTCT-C
* ** * *
53351077 GAAATGGAGAAAT-AAAATCATTTGGAAATGAATGTGGTTTTCTC
1 GAAATGGAGAAATGAAAAGCATTCAGAAATGAATATGATTTTCTC
*
53351121 AAAATGGA
1 GAAATGGA
53351129 AATAGAAATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
44 8 0.18
45 24 0.55
46 12 0.27
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.29
Consensus pattern (45 bp):
GAAATGGAGAAATGAAAAGCATTCAGAAATGAATATGATTTTCTC
Found at i:53351139 original size:12 final size:13
Alignment explanation
Indices: 53351122--53351151 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
53351112 GGTTTTCTCA
53351122 AAATGGAAAT-AG
1 AAATGGAAATGAG
53351134 AAATGGAAATGAG
1 AAATGGAAATGAG
53351147 AAATG
1 AAATG
53351152 ATTCATTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.17
Consensus pattern (13 bp):
AAATGGAAATGAG
Found at i:53351166 original size:22 final size:22
Alignment explanation
Indices: 53351140--53351188 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
53351130 ATAGAAATGG
*
53351140 AAATGAGAAATG-ATTCATTTAC
1 AAATGAGAAATGAATT-ACTTAC
*
53351162 AAATG-TAAATGAATTACTTAC
1 AAATGAGAAATGAATTACTTAC
53351183 AAATGA
1 AAATGA
53351189 TCATGAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.31
Consensus pattern (22 bp):
AAATGAGAAATGAATTACTTAC
Found at i:53353088 original size:25 final size:25
Alignment explanation
Indices: 53353005--53353087 Score: 107
Period size: 25 Copynumber: 3.3 Consensus size: 25
53352995 TGGCGTATCA
53353005 TTTGGAAAACCTTTGTGGCAAATTC
1 TTTGGAAAACCTTTGTGGCAAATTC
* **
53353030 TCTGGAAAACCTTTGTGGCGTA-TC
1 TTTGGAAAACCTTTGTGGCAAATTC
53353054 ATTT-GAAAAGCCTTTGTGGCAAATTC
1 -TTTGGAAAA-CCTTTGTGGCAAATTC
53353080 TTTGGAAA
1 TTTGGAAA
53353088 GTTGTTATGG
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
24 7 0.15
25 35 0.73
26 6 0.12
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.35
Consensus pattern (25 bp):
TTTGGAAAACCTTTGTGGCAAATTC
Found at i:53367511 original size:21 final size:20
Alignment explanation
Indices: 53367485--53367523 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
53367475 TGACCACGGT
*
53367485 CTCTCGGTGGCTGCTGTACTA
1 CTCTCGGTGG-TGCAGTACTA
53367506 CTCTCGGTGGTGCAGTAC
1 CTCTCGGTGGTGCAGTAC
53367524 CTATGCCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.10, C:0.28, G:0.31, T:0.31
Consensus pattern (20 bp):
CTCTCGGTGGTGCAGTACTA
Found at i:53372387 original size:14 final size:13
Alignment explanation
Indices: 53372307--53372398 Score: 51
Period size: 14 Copynumber: 6.6 Consensus size: 13
53372297 GCTATATATT
* *
53372307 ATTATTTTTATTA
1 ATTATATTTAATA
53372320 ATTCATATTTTAATA
1 ATT-ATA-TTTAATA
*
53372335 ATTATTATATTAAGA
1 ATTA-TAT-TTAATA
*
53372350 ATGT-TATTAAATTA
1 AT-TATATTTAA-TA
* * *
53372364 TTTATTTTTATTAA
1 ATTATATTTAAT-A
53372378 ATTATATTTAATA
1 ATTATATTTAATA
53372391 ATTATATT
1 ATTATATT
53372399 AAAATATGAT
Statistics
Matches: 59, Mismatches: 12, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
13 17 0.29
14 23 0.39
15 18 0.31
16 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (13 bp):
ATTATATTTAATA
Found at i:53372438 original size:55 final size:53
Alignment explanation
Indices: 53372333--53372446 Score: 158
Period size: 55 Copynumber: 2.1 Consensus size: 53
53372323 CATATTTTAA
* * * *
53372333 TAATTATTATATTAAGAATGTTATTAAATTATTTATTTTTATTAAATTATATT
1 TAATAATTATATTAAGAATATGATTAAATTATTTATTATTATTAAATTATATT
53372386 TAATAATTATATTAA-AATATGATTAAATTATTTGTTATTATTATTAAATTATATT
1 TAATAATTATATTAAGAATATGATTAAATTA--T-TTATTATTATTAAATTATATT
53372441 TAATAA
1 TAATAA
53372447 CAATAATCAT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
52 13 0.24
53 14 0.26
54 1 0.02
55 26 0.48
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (53 bp):
TAATAATTATATTAAGAATATGATTAAATTATTTATTATTATTAAATTATATT
Found at i:53381749 original size:22 final size:22
Alignment explanation
Indices: 53381724--53381768 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
53381714 AGAAGTGAGC
*
53381724 AAAAAAAGAAAAAAAAGTAAAA
1 AAAAAAACAAAAAAAAGTAAAA
* *
53381746 AAAAGAACAAAAAAAAGTGAAA
1 AAAAAAACAAAAAAAAGTAAAA
53381768 A
1 A
53381769 GTCTTGTGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.82, C:0.02, G:0.11, T:0.04
Consensus pattern (22 bp):
AAAAAAACAAAAAAAAGTAAAA
Found at i:53381768 original size:10 final size:9
Alignment explanation
Indices: 53381724--53381759 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
53381714 AGAAGTGAGC
53381724 AAAAAAAGA
1 AAAAAAAGA
53381733 AAAAAAAGTA
1 AAAAAAAG-A
53381743 AAAAAAAGA
1 AAAAAAAGA
53381752 ACAAAAAA
1 A-AAAAAA
53381760 AAGTGAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 10 0.40
10 15 0.60
ACGTcount: A:0.86, C:0.03, G:0.08, T:0.03
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:53384639 original size:20 final size:20
Alignment explanation
Indices: 53384593--53384639 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
53384583 AGCTCGTTTC
*
53384593 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
53384613 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
53384633 CAGCTCA
1 CAGCTCA
53384640 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:53387851 original size:31 final size:31
Alignment explanation
Indices: 53387811--53387872 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
53387801 ATATAATTTG
*
53387811 GTCATTAAATTATTCGAAAA-TTTTCATTTAA
1 GTCACTAAATTATT-GAAAAGTTTTCATTTAA
* *
53387842 GTCACTAAATTATTTAAAAGTTTTTATTTAA
1 GTCACTAAATTATTGAAAAGTTTTCATTTAA
53387873 ATTATTGGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (31 bp):
GTCACTAAATTATTGAAAAGTTTTCATTTAA
Found at i:53399328 original size:18 final size:18
Alignment explanation
Indices: 53399305--53399340 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
53399295 GCCAGCTCAA
53399305 GTGGGTCAAATGAGCCCT
1 GTGGGTCAAATGAGCCCT
53399323 GTGGGTCAAATGAGCCCT
1 GTGGGTCAAATGAGCCCT
53399341 ATTTAATCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.22
Consensus pattern (18 bp):
GTGGGTCAAATGAGCCCT
Found at i:53403852 original size:25 final size:25
Alignment explanation
Indices: 53403822--53404002 Score: 129
Period size: 25 Copynumber: 7.3 Consensus size: 25
53403812 CTCGCCATAA
53403822 AGGCTTTCCAAATAATACACCACAT
1 AGGCTTTCCAAATAATACACCACAT
* ** * * *
53403847 ATGCTTTTTGAGATAACTA-GCCACAA
1 AGGC-TTTCCAAATAA-TACACCACAT
* * * *
53403873 ATGCTTCCCAAATAATAC-GC-TAT
1 AGGCTTTCCAAATAATACACCACAT
*
53403896 AGGCTTTCCAAATAATACGCCACAT
1 AGGCTTTCCAAATAATACACCACAT
* * * *
53403921 AGGCTTTTCAGATAACA-AGCCACAA
1 AGGCTTTCCAAATAATACA-CCACAT
* *
53403946 AGGCTTCCCAAATAATACATCACAT
1 AGGCTTTCCAAATAATACACCACAT
*
53403971 AGGC-TTCCTAAATAGTACACCACAT
1 AGGCTTTCC-AAATAATACACCACAT
53403996 AGGCTTT
1 AGGCTTT
53404003 TTGAGATAAC
Statistics
Matches: 116, Mismatches: 31, Indels: 17
0.71 0.19 0.10
Matches are distributed among these distances:
23 17 0.15
24 7 0.06
25 70 0.60
26 20 0.17
27 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.26
Consensus pattern (25 bp):
AGGCTTTCCAAATAATACACCACAT
Found at i:53413134 original size:74 final size:73
Alignment explanation
Indices: 53413013--53413173 Score: 304
Period size: 74 Copynumber: 2.2 Consensus size: 73
53413003 CCCAAAAATC
*
53413013 AAATCGAATACCCATCCACGAACCCAATACCTACCCCAAATCAACTTACCCAAATACCAAATTAC
1 AAATCCAATACCCATCCACGAACCCAATACCTACCCCAAATCAACTTA-CCAAATACCAAATTAC
53413078 CCACATAAT
65 CCACATAAT
53413087 AAATCCAATACCCATCCACGAACCCAATACCTACCCCAAATCAACTTACCAAATACCAAATTACC
1 AAATCCAATACCCATCCACGAACCCAATACCTACCCCAAATCAACTTACCAAATACCAAATTACC
53413152 CACATAAT
66 CACATAAT
53413160 AAATCCAATACCCA
1 AAATCCAATACCCA
53413174 ATGTCATGAT
Statistics
Matches: 86, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
73 39 0.45
74 47 0.55
ACGTcount: A:0.44, C:0.37, G:0.02, T:0.17
Consensus pattern (73 bp):
AAATCCAATACCCATCCACGAACCCAATACCTACCCCAAATCAACTTACCAAATACCAAATTACC
CACATAAT
Found at i:53413212 original size:73 final size:68
Alignment explanation
Indices: 53413013--53413173 Score: 196
Period size: 73 Copynumber: 2.2 Consensus size: 68
53413003 CCCAAAAATC
* *
53413013 AAATCGAATACCCATCCACGAACCCAATACCTACCCCAAATCAACTTACCCAAATACCAAATTAC
1 AAATCCAATACCCATCCACGAACCCAAAACCTACCCC--A--AA--TACCCAAATACCAAATTAC
53413078 CCACATAAT
60 CCACATAAT
*
53413087 AAATCCAATACCCATCCACGAACCCAATACCTACCCCAAATCAACTTACCAAATACCAAATTACC
1 AAATCCAATACCCATCCACGAACCCAAAACCTACCCCAAAT--AC---CCAAATACCAAATTACC
53413152 CACATAAT
61 CACATAAT
53413160 AAATCCAATACCCA
1 AAATCCAATACCCA
53413174 ATGTCATGAT
Statistics
Matches: 81, Mismatches: 1, Indels: 11
0.87 0.01 0.12
Matches are distributed among these distances:
68 1 0.01
70 4 0.05
72 1 0.01
73 39 0.48
74 36 0.44
ACGTcount: A:0.44, C:0.37, G:0.02, T:0.17
Consensus pattern (68 bp):
AAATCCAATACCCATCCACGAACCCAAAACCTACCCCAAATACCCAAATACCAAATTACCCACAT
AAT
Found at i:53413369 original size:23 final size:22
Alignment explanation
Indices: 53413331--53413390 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
53413321 GGCTACAAGG
* *
53413331 AAAAAAGAAAGAAA-AAAGAGA
1 AAAAAAGAAAAAAACAAAAAGA
*
53413352 AAACAA-AAAAAAACAAAAAGA
1 AAAAAAGAAAAAAACAAAAAGA
53413373 AAAAAAGAAAAAAACAAA
1 AAAAAAGAAAAAAACAAA
53413391 CACCTAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 6 0.18
21 16 0.48
22 11 0.33
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (22 bp):
AAAAAAGAAAAAAACAAAAAGA
Found at i:53413376 original size:22 final size:23
Alignment explanation
Indices: 53413343--53413390 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
53413333 AAAAGAAAGA
53413343 AAAAAGAGAAAACAA-AAAAAAAC
1 AAAAAGAGAAAA-AAGAAAAAAAC
53413366 AAAAAGA-AAAAAAGAAAAAAAC
1 AAAAAGAGAAAAAAGAAAAAAAC
53413388 AAA
1 AAA
53413391 CACCTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 2 0.08
22 15 0.62
23 7 0.29
ACGTcount: A:0.85, C:0.06, G:0.08, T:0.00
Consensus pattern (23 bp):
AAAAAGAGAAAAAAGAAAAAAAC
Found at i:53419845 original size:25 final size:25
Alignment explanation
Indices: 53419793--53419886 Score: 89
Period size: 25 Copynumber: 3.8 Consensus size: 25
53419783 TCATGTACAT
* * ** *
53419793 GTATGCTCATACGACCTGCGAATGG
1 GTATGCTCACACGAGCTGTAAATCG
** *
53419818 GTATGCTCACTTGAGCTGTAGATCG
1 GTATGCTCACACGAGCTGTAAATCG
* * *
53419843 GTATGCTCTCACGAGCTATAAATTG
1 GTATGCTCACACGAGCTGTAAATCG
53419868 GTATGCTCACACGAGCTGT
1 GTATGCTCACACGAGCTGT
53419887 GGGTCAGATT
Statistics
Matches: 53, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (25 bp):
GTATGCTCACACGAGCTGTAAATCG
Found at i:53425687 original size:5 final size:5
Alignment explanation
Indices: 53425679--53425748 Score: 58
Period size: 5 Copynumber: 13.8 Consensus size: 5
53425669 TTTTCTTTTC
53425679 TTTAT TTTAT TTTAT TTTAT TTT-T ATTTA- TTTA- TTTATT ATTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT -TTTAT TTTAT TTTA-T -TTTAT
*
53425724 TATTAT ATTA- TTTATT TTTAT TTTA
1 T-TTAT TTTAT TTTA-T TTTAT TTTA
53425749 CTGATCCATT
Statistics
Matches: 55, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
4 12 0.22
5 30 0.55
6 9 0.16
7 4 0.07
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:53425709 original size:4 final size:4
Alignment explanation
Indices: 53425679--53425740 Score: 53
Period size: 4 Copynumber: 15.8 Consensus size: 4
53425669 TTTTCTTTTC
53425679 TTTA TTTTA TTTTA TTT- TATT- TTTA TTTA TTTA TTTA -TTA TTTA -TTA
1 TTTA -TTTA -TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
53425726 -TTA TATTA TTTA TTT
1 TTTA T-TTA TTTA TTT
53425741 TTATTTTACT
Statistics
Matches: 52, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
3 12 0.23
4 27 0.52
5 13 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:53425947 original size:18 final size:20
Alignment explanation
Indices: 53425924--53425972 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
53425914 TTCGTTTCTT
53425924 TTTTTATTTTTA-T-CTGTA
1 TTTTTATTTTTACTACTGTA
*
53425942 TTTTTATTTTTAGCTACTTTA
1 TTTTTATTTTTA-CTACTGTA
53425963 TTTTTATTTT
1 TTTTTATTTT
53425973 CTAAGACTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 12 0.44
20 1 0.04
21 14 0.52
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.73
Consensus pattern (20 bp):
TTTTTATTTTTACTACTGTA
Found at i:53427749 original size:30 final size:30
Alignment explanation
Indices: 53427714--53427770 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
53427704 TGGGCATTTT
* *
53427714 CACACGGGCTGGGCACATGCCTGTGTGATC
1 CACACGGGCTGGACACATGCCTATGTGATC
*
53427744 CACACGGGTTGGACACATGCCTATGTG
1 CACACGGGCTGGACACATGCCTATGTG
53427771 GTAGCCCATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.19, C:0.28, G:0.32, T:0.21
Consensus pattern (30 bp):
CACACGGGCTGGACACATGCCTATGTGATC
Found at i:53441838 original size:50 final size:49
Alignment explanation
Indices: 53441757--53441918 Score: 162
Period size: 50 Copynumber: 3.3 Consensus size: 49
53441747 TAGAGGACTT
* * ** *
53441757 GCCATAAAAGCTTTCCAAATAATATGCCACATAGAATTTTCAGATAAGTA
1 GCCACAAAAGCTTCCCAAATAATACACCACATAGAA-TTTCAGATAACTA
* * *
53441807 GCCACAAAAGCTTCCCAAATAATACATCACATAGGATTTCAGGTAACTA
1 GCCACAAAAGCTTCCCAAATAATACACCACATAGAATTTCAGATAACTA
* ** * **
53441856 GCCACAAAGGCTTCCCAAATAATATGCCATATAGGCTTTTCAGATAACTA
1 GCCACAAAAGCTTCCCAAATAATACACCACATA-GAATTTCAGATAACTA
* *
53441906 GCCATAAAGGCTT
1 GCCACAAAAGCTT
53441919 ATTTTGTTTG
Statistics
Matches: 94, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
49 39 0.41
50 55 0.59
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (49 bp):
GCCACAAAAGCTTCCCAAATAATACACCACATAGAATTTCAGATAACTA
Found at i:53444843 original size:30 final size:30
Alignment explanation
Indices: 53444809--53444872 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
53444799 TCGTAAGCTC
53444809 GATTTAAGTCCAATCTTGCACGTATAACAT
1 GATTTAAGTCCAATCTTGCACGTATAACAT
53444839 GATTTAAGTCCAATCTTGCACGTATAACAT
1 GATTTAAGTCCAATCTTGCACGTATAACAT
53444869 GATT
1 GATT
53444873 GCTTTAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (30 bp):
GATTTAAGTCCAATCTTGCACGTATAACAT
Found at i:53445468 original size:24 final size:24
Alignment explanation
Indices: 53445417--53445468 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
53445407 TCCAGCTAGA
* * *
53445417 GATGAGTTCAGAGGCAAGCCAGAT
1 GATGAGTTCAGAGGCAAGACAAAC
*
53445441 GATGAGTTTAGAGGCAAGACAAAC
1 GATGAGTTCAGAGGCAAGACAAAC
53445465 GATG
1 GATG
53445469 GTCCAGCTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.13, G:0.33, T:0.17
Consensus pattern (24 bp):
GATGAGTTCAGAGGCAAGACAAAC
Found at i:53449346 original size:453 final size:452
Alignment explanation
Indices: 53448499--53449404 Score: 1794
Period size: 453 Copynumber: 2.0 Consensus size: 452
53448489 TGGCTTATAC
53448499 CAGTTTTGTTGGTTTGATCATCCAAAAAATTTTGGTTAAAGCTCCAACTTATTTAAAATACGCCA
1 CAGTTTTGTTGGTTTGATCATCCAAAAAATTTTGGTTAAAGCTCCAACTTATTTAAAATACGCCA
53448564 AAAGAAAAAAAAAGAGTTAAACTGAATGCACGTATGCTTTTTGTGTAACACCTCAGTTGTTATTG
66 AAAGAAAAAAAAAGAGTTAAACTGAATGCACGTATGCTTTTTGTGTAACACCTCAGTTGTTATTG
53448629 GGAGTTGGGGTGTTACAGGATAAGACAGACAGGTCTGGGGCTAGTGCATCTACTAGAACATGTCA
131 GGAGTTGGGGTGTTACAGGATAAGACAGACAGGTCTGGGGCTAGTGCATCTACTAGAACATGTCA
53448694 TTCGAGCTAGAGAAGAGGCTTCTGCCCCAAATGTTATAACCATTACTTTTTTCTCTCTTTGGTAT
196 TTCGAGCTAGAGAAGAGGCTTCTGCCCCAAATGTTATAACCATTACTTTTTTCTCTCTTTGGTAT
53448759 GAATGTATAAGCATTGGTAAACCTTGAGTCGACTCATTCTTACAATTGTACTATTTTCGTATCTG
261 GAATGTATAAGCATTGGTAAACCTTGAGTCGACTCATTCTTACAATTGTACTATTTTCGTATCTG
53448824 GAAAGAACATACGAGTAAAATAGATTGATTTTCATGTTAATGTAACTAACCAATTGAGTTAAAAA
326 GAAAGAACATACGAGTAAAATAGATTGATTTTCATGTTAATGTAACTAACCAATTGAGTTAAAAA
*
53448889 TGTCATAGTTAGTTCGATTTATAAAAAGTCTCCACTAAGAATTCAGGTTTGTGATTTTCCTG
391 TGTCATAGTTAGTTCGATTTATAAAAAGTCTCCACTAAGAATTCAGGTTTGTGATTATCCTG
53448951 CNAGTTTTGTTGGTTTGATCATCCAAAAAATTTTGGTTAAAGCTCCAACTTATTTAAAATACGCC
1 C-AGTTTTGTTGGTTTGATCATCCAAAAAATTTTGGTTAAAGCTCCAACTTATTTAAAATACGCC
53449016 AAAAGAAAAAAAAAGAGTTAAACTGAATGCACGTATGCTTTTTGTGTAACACCTCAGTTGTTATT
65 AAAAGAAAAAAAAAGAGTTAAACTGAATGCACGTATGCTTTTTGTGTAACACCTCAGTTGTTATT
53449081 GGGAGTTGGGGTGTTACAGGATAAGACAGACAGGTCTGGGGCTAGTGCATCTACTAGAACATGTC
130 GGGAGTTGGGGTGTTACAGGATAAGACAGACAGGTCTGGGGCTAGTGCATCTACTAGAACATGTC
53449146 ATTCGAGCTAGAGAAGAGGCTTCTGCCCCAAATGTTATAACCATTACTTTTTTCTCTCTTTGGTA
195 ATTCGAGCTAGAGAAGAGGCTTCTGCCCCAAATGTTATAACCATTACTTTTTTCTCTCTTTGGTA
53449211 TGAATGTATAAGCATTGGTAAACCTTGAGTCGACTCATTCTTACAATTGTACTATTTTCGTATCT
260 TGAATGTATAAGCATTGGTAAACCTTGAGTCGACTCATTCTTACAATTGTACTATTTTCGTATCT
53449276 GGAAAGAACATACGAGTAAAATAGATTGATTTTCATGTTAATGTAACTAACCAATTGAGTTAAAA
325 GGAAAGAACATACGAGTAAAATAGATTGATTTTCATGTTAATGTAACTAACCAATTGAGTTAAAA
53449341 ATGTCATAGTTAGTTCGATTTATAAAAAGTCTCCACTAAGAATTCAGGTTTGTGATTATCCTG
390 ATGTCATAGTTAGTTCGATTTATAAAAAGTCTCCACTAAGAATTCAGGTTTGTGATTATCCTG
53449404 C
1 C
53449405 TGACATCGTT
Statistics
Matches: 452, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
452 1 0.00
453 451 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (452 bp):
CAGTTTTGTTGGTTTGATCATCCAAAAAATTTTGGTTAAAGCTCCAACTTATTTAAAATACGCCA
AAAGAAAAAAAAAGAGTTAAACTGAATGCACGTATGCTTTTTGTGTAACACCTCAGTTGTTATTG
GGAGTTGGGGTGTTACAGGATAAGACAGACAGGTCTGGGGCTAGTGCATCTACTAGAACATGTCA
TTCGAGCTAGAGAAGAGGCTTCTGCCCCAAATGTTATAACCATTACTTTTTTCTCTCTTTGGTAT
GAATGTATAAGCATTGGTAAACCTTGAGTCGACTCATTCTTACAATTGTACTATTTTCGTATCTG
GAAAGAACATACGAGTAAAATAGATTGATTTTCATGTTAATGTAACTAACCAATTGAGTTAAAAA
TGTCATAGTTAGTTCGATTTATAAAAAGTCTCCACTAAGAATTCAGGTTTGTGATTATCCTG
Found at i:53452362 original size:23 final size:23
Alignment explanation
Indices: 53452336--53452429 Score: 127
Period size: 23 Copynumber: 4.1 Consensus size: 23
53452326 TCACCTCAAG
* *
53452336 GGCATTACAGAATATGCCGA-AAA
1 GGCATCACAGAATACGCC-ACAAA
53452359 GGCATCACAGAATACGCCACAAA
1 GGCATCACAGAATACGCCACAAA
53452382 GGCATCACAGAATACGCCACAAA
1 GGCATCACAGAATACGCCACAAA
* * *
53452405 GACATCATAGAATACACCACAAA
1 GGCATCACAGAATACGCCACAAA
53452428 GG
1 GG
53452430 TTTCTGAGAG
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
22 1 0.02
23 63 0.98
ACGTcount: A:0.45, C:0.26, G:0.18, T:0.12
Consensus pattern (23 bp):
GGCATCACAGAATACGCCACAAA
Found at i:53457089 original size:96 final size:96
Alignment explanation
Indices: 53456974--53457165 Score: 348
Period size: 96 Copynumber: 2.0 Consensus size: 96
53456964 TATTCTTAGG
53456974 ACATTATTAAAAAACAGTTTATTTATACACAGAAAAGAAACTGAAATAATAATGGTAACGCCTTA
1 ACATTATTAAAAAACAGTTTATTTATACACAGAAAAGAAACTGAAATAATAATGGTAACGCCTTA
* *
53457039 TATTAATAAAGATGATAGATCAAGTAGGTTA
66 TATTAATAAACATGATAAATCAAGTAGGTTA
*
53457070 ACATTATTAGAAAACAGTTTATTTATACACAGAAAAGAAACTGAAATAATAATGGTAACGCCTTA
1 ACATTATTAAAAAACAGTTTATTTATACACAGAAAAGAAACTGAAATAATAATGGTAACGCCTTA
*
53457135 TATTAATAAACATGATAAATCAAGTATGTTA
66 TATTAATAAACATGATAAATCAAGTAGGTTA
53457166 TTACAACCAT
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
96 92 1.00
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.30
Consensus pattern (96 bp):
ACATTATTAAAAAACAGTTTATTTATACACAGAAAAGAAACTGAAATAATAATGGTAACGCCTTA
TATTAATAAACATGATAAATCAAGTAGGTTA
Found at i:53460119 original size:15 final size:15
Alignment explanation
Indices: 53460099--53460129 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
53460089 ATTACGGAAG
*
53460099 ATCAGTCTTACTACT
1 ATCAGTCTCACTACT
53460114 ATCAGTCTCACTACT
1 ATCAGTCTCACTACT
53460129 A
1 A
53460130 GGATGGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.35
Consensus pattern (15 bp):
ATCAGTCTCACTACT
Found at i:53460275 original size:75 final size:75
Alignment explanation
Indices: 53460145--53460321 Score: 207
Period size: 75 Copynumber: 2.4 Consensus size: 75
53460135 GAATAACAAC
* ** *
53460145 TCACCACAAAGGATTTCCAGAGAATTCTCCACAAAGGCTTTCCAAATGATATGCCAC-AAGGACT
1 TCACCACAAAGGCTTTCCAGAGAATTCAACACAAAAGCTTTCCAAATGATATGCCACAAAGG-CT
53460209 TT-TCAAAGAAT
65 TTCT-AAAGAAT
* * * *
53460220 TCACCAAAAAGGCTTTCCAGAGAATTCAATATAAAAGCTTTCCAAA-GAATTTGCCACAAAGGCT
1 TCACCACAAAGGCTTTCCAGAGAATTCAACACAAAAGCTTTCCAAATG-ATATGCCACAAAGGCT
53460284 TTCTAAAGAAT
65 TTCTAAAGAAT
* * *
53460295 TTACCACAAAGGCTTTCTAGCGAATTC
1 TCACCACAAAGGCTTTCCAGAGAATTC
53460322 TCAACTTAAC
Statistics
Matches: 87, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
74 1 0.01
75 81 0.93
76 5 0.06
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (75 bp):
TCACCACAAAGGCTTTCCAGAGAATTCAACACAAAAGCTTTCCAAATGATATGCCACAAAGGCTT
TCTAAAGAAT
Found at i:53460313 original size:25 final size:25
Alignment explanation
Indices: 53460147--53460311 Score: 147
Period size: 25 Copynumber: 6.6 Consensus size: 25
53460137 ATAACAACTC
* *
53460147 ACCACAAAGGATTTCCAGAGAATTCT
1 ACCACAAAGGCTTTCCAAAGAATT-T
*
53460173 -CCACAAAGGCTTTCCAAATG-ATAT
1 ACCACAAAGGCTTTCCAAA-GAATTT
* * *
53460197 GCCAC-AAGGACTTTTCAAAGAATTC
1 ACCACAAAGG-CTTTCCAAAGAATTT
* * *
53460222 ACCAAAAAGGCTTTCCAGAGAATTC
1 ACCACAAAGGCTTTCCAAAGAATTT
** * *
53460247 AATATAAAAGCTTTCCAAAGAATTT
1 ACCACAAAGGCTTTCCAAAGAATTT
* *
53460272 GCCACAAAGGCTTTCTAAAGAATTT
1 ACCACAAAGGCTTTCCAAAGAATTT
53460297 ACCACAAAGGCTTTC
1 ACCACAAAGGCTTTC
53460312 TAGCGAATTC
Statistics
Matches: 111, Mismatches: 23, Indels: 11
0.77 0.16 0.08
Matches are distributed among these distances:
24 6 0.05
25 100 0.90
26 5 0.05
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (25 bp):
ACCACAAAGGCTTTCCAAAGAATTT
Found at i:53471610 original size:3 final size:3
Alignment explanation
Indices: 53471602--53471683 Score: 155
Period size: 3 Copynumber: 27.3 Consensus size: 3
53471592 AATTAGTTAA
*
53471602 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TTT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
53471650 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
53471684 TTTTGAATAA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:53485683 original size:18 final size:18
Alignment explanation
Indices: 53485662--53485700 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
53485652 TTAGTTGTAA
53485662 TTTAGATTTTCTTTTAGT
1 TTTAGATTTTCTTTTAGT
* *
53485680 TTTAGTTTTTCTTTTTGT
1 TTTAGATTTTCTTTTAGT
53485698 TTT
1 TTT
53485701 CTATTTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.10, C:0.05, G:0.10, T:0.74
Consensus pattern (18 bp):
TTTAGATTTTCTTTTAGT
Found at i:53485707 original size:18 final size:19
Alignment explanation
Indices: 53485667--53485713 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
53485657 TGTAATTTAG
* *
53485667 ATTTTCTTTTAGTTTTAGT
1 ATTTTCTTTTTGTTTTACT
53485686 -TTTTCTTTTTGTTTT-CT
1 ATTTTCTTTTTGTTTTACT
*
53485703 ATTTTATTTTT
1 ATTTTCTTTTT
53485714 CATGAGGATC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 1 0.04
18 23 0.96
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.77
Consensus pattern (19 bp):
ATTTTCTTTTTGTTTTACT
Done.