Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 116 of 120
Found at i:33826346 original size:19 final size:22
Alignment explanation
Indices: 33826319--33826362 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
33826309 TTTCTAGTTA
*
33826319 ATAATAATAATAATAAT-ATATT
1 ATAATAATCAT-ATAATAATATT
33826341 ATAATAATCATATAATAATATT
1 ATAATAATCATATAATAATATT
33826363 TTATTCACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
ATAATAATCATATAATAATATT
Found at i:33826347 original size:22 final size:24
Alignment explanation
Indices: 33826317--33826366 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
33826307 TATTTCTAGT
*
33826317 TAATAATAATAATAATAATATATTA
1 TAATAATCAT-ATAATAATATATTA
*
33826342 TAATAATCATATAATAATATTTTA
1 TAATAATCATATAATAATATATTA
33826366 T
1 T
33826367 TCACAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
TAATAATCATATAATAATATATTA
Found at i:33827497 original size:17 final size:18
Alignment explanation
Indices: 33827466--33827499 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33827456 AAATTCATAA
33827466 ATCAAAATTATAAAAATG
1 ATCAAAATTATAAAAATG
*
33827484 ATCAAATTTA-AAAAAT
1 ATCAAAATTATAAAAAT
33827500 AACCTATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (18 bp):
ATCAAAATTATAAAAATG
Found at i:33834915 original size:2 final size:2
Alignment explanation
Indices: 33834908--33834950 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
33834898 NNNNNNNNNN
33834908 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33834950 T
1 T
33834951 TCTACTCACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33836085 original size:29 final size:29
Alignment explanation
Indices: 33836031--33836086 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
33836021 AATAGGGCCT
** *
33836031 GGTGCCGCCTGACAATGTCCCTCCACCTG
1 GGTGCCGCCAAACAATGTCCCCCCACCTG
33836060 GGTGCCGCCAAACAA-GTCTCCCCCACC
1 GGTGCCGCCAAACAATGTC-CCCCCACC
33836087 CCTCCAACTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 3 0.13
29 20 0.87
ACGTcount: A:0.18, C:0.45, G:0.21, T:0.16
Consensus pattern (29 bp):
GGTGCCGCCAAACAATGTCCCCCCACCTG
Found at i:33837014 original size:13 final size:13
Alignment explanation
Indices: 33836996--33837020 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33836986 AATTCTTTAT
33836996 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
33837009 TGCTTTTGAGAA
1 TGCTTTTGAGAA
33837021 ATTTCAGTGT
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:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:33839598 original size:41 final size:41
Alignment explanation
Indices: 33839553--33839637 Score: 152
Period size: 41 Copynumber: 2.1 Consensus size: 41
33839543 GCTTCAAGGC
*
33839553 CAAAGAACCAGCAAAGGGCAGAGGGTAGGGAAATTGAAAAT
1 CAAAGAACCAGCAAAGGGCAGAGGGCAGGGAAATTGAAAAT
*
33839594 CAAAGAACCAGCAAAGGGCAGAGGGCAGGGAATTTGAAAAT
1 CAAAGAACCAGCAAAGGGCAGAGGGCAGGGAAATTGAAAAT
33839635 CAA
1 CAA
33839638 TCCCAGACAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.46, C:0.14, G:0.31, T:0.09
Consensus pattern (41 bp):
CAAAGAACCAGCAAAGGGCAGAGGGCAGGGAAATTGAAAAT
Found at i:33839744 original size:23 final size:23
Alignment explanation
Indices: 33839713--33839759 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
33839703 AGGGCAGAGA
33839713 AACAAAGAACCAGCAAAGGGCAG
1 AACAAAGAACCAGCAAAGGGCAG
* *
33839736 AACACAGAACCAGCAGAGGGCAG
1 AACAAAGAACCAGCAAAGGGCAG
33839759 A
1 A
33839760 GATGAGGGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.49, C:0.23, G:0.28, T:0.00
Consensus pattern (23 bp):
AACAAAGAACCAGCAAAGGGCAG
Found at i:33841347 original size:21 final size:21
Alignment explanation
Indices: 33841321--33841365 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
33841311 GTGGGACAAT
*
33841321 TGACGTGGCTAGCTAACTAGC
1 TGACGTGGCCAGCTAACTAGC
*
33841342 TGACGTGGCCAGTTAACTAGC
1 TGACGTGGCCAGCTAACTAGC
33841363 TGA
1 TGA
33841366 TATGATCAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (21 bp):
TGACGTGGCCAGCTAACTAGC
Found at i:33842302 original size:75 final size:76
Alignment explanation
Indices: 33842179--33842355 Score: 248
Period size: 75 Copynumber: 2.3 Consensus size: 76
33842169 TGATTCCCCC
* * * * *
33842179 AAGGGTTTGCTAAGTGCTGATTCCCCGAATCGTTGGTGGTTGTTAAGTGCTGATCCCACCGTATA
1 AAGGGGTTGCTAAGTGCTGATTCCCAGAATCATTGGTGGTTGCTAAGTGCTAATCCCACCGTATA
*
33842244 TT-AAATGTGA
66 TTAAAATGTAA
* * *
33842254 AAGGGGTTGCTAAGTGCTGATTCCCAGATTCATTGGTGGTTGCTAAGTGCTAATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCAGAATCATTGGTGGTTGCTAAGTGCTAATCCCACCGTATA
33842319 TTAAAATGTAA
66 TTAAAATGTAA
*
33842330 AAGGGGGTTGCTAAGTACTGATTCCC
1 AA-GGGGTTGCTAAGTGCTGATTCCC
33842356 CCAAAGGGTT
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
75 59 0.66
76 9 0.10
77 22 0.24
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (76 bp):
AAGGGGTTGCTAAGTGCTGATTCCCAGAATCATTGGTGGTTGCTAAGTGCTAATCCCACCGTATA
TTAAAATGTAA
Found at i:33842380 original size:104 final size:103
Alignment explanation
Indices: 33842257--33842459 Score: 325
Period size: 104 Copynumber: 2.0 Consensus size: 103
33842247 AATGTGAAAG
*
33842257 GGGTTGCTAAGTGCTGATTCCCAGATTCATTGGTGGTTGCTAAGTGCTAATTCCACCGTATCTTA
1 GGGTTGCTAAGTGCTGATTCCCAGAATCATTGGTGGTTGCTAAGTGCTAATTCCACCGTATCTTA
33842322 AAATGTAAAAGGGGGTTGCTAAGTACTGATTCCCCCAAA
66 AAATGTAAAA-GGGGTTGCTAAGTACTGATTCCCCCAAA
* * * *
33842361 GGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTTT
1 GGGTTGCTAAGTGCTGATTCCCAGAATCATTGGTGGTTGCTAAGTGCTAATTCCACCGTATCTTA
* * *
33842426 GAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
66 AAATGTAAAAGGGGTTGCTAAGTACTGATTCCCC
33842460 GAATCACTGG
Statistics
Matches: 91, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
103 23 0.25
104 68 0.75
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (103 bp):
GGGTTGCTAAGTGCTGATTCCCAGAATCATTGGTGGTTGCTAAGTGCTAATTCCACCGTATCTTA
AAATGTAAAAGGGGTTGCTAAGTACTGATTCCCCCAAA
Found at i:33842404 original size:33 final size:34
Alignment explanation
Indices: 33842362--33842495 Score: 128
Period size: 33 Copynumber: 3.7 Consensus size: 34
33842352 TCCCCCAAAG
33842362 GGTTGCTAAGTGCTGATTCC-CCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCACCGAATCATTGGT
* * *
33842395 GGTTGCTAAGTGCTGATTCCACCGTATTTTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCG-A---AT-CAT-TG---GT
*
33842438 GGTTGCTAAGTGCTGATTCC-CCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCACCGAATCATTGGT
*
33842471 GGTTGCTAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCCACCGA
33842496 TAACGGATAA
Statistics
Matches: 82, Mismatches: 8, Indels: 21
0.74 0.07 0.19
Matches are distributed among these distances:
33 40 0.49
34 7 0.09
35 1 0.01
36 2 0.02
37 1 0.01
38 2 0.02
39 2 0.02
40 2 0.02
41 1 0.01
42 3 0.04
43 21 0.26
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (34 bp):
GGTTGCTAAGTGCTGATTCCACCGAATCATTGGT
Found at i:33842481 original size:180 final size:179
Alignment explanation
Indices: 33842149--33842494 Score: 570
Period size: 179 Copynumber: 1.9 Consensus size: 179
33842139 ACATTGAATA
* *
33842149 AAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGTTTGCTAAGTGCTGATTCCCCGAATCGTTG
1 AAAAGGGGGTTGCTAAGTACTGATTCCCCCAAGGGTTTGCTAAGTGCTGATTCCCCGAATCATTG
*
33842214 GTGGTTGTTAAGTGCTGATCCCACCGTATATTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCC
66 GTGGTTGCTAAGTGCTGATCCCACCGTATATTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCC
* *
33842279 AGATTCATTGGTGGTTGCTAAGTGCT-AATTCCACCGTATCTTAAAATGT
131 AGAATCACTGGTGGTTGCTAAGTGCTGAA-TCCACCGTATCTTAAAATGT
33842328 AAAAGGGGGTTGCTAAGTACTGATTCCCCCAAAGGG-TTGCTAAGTGCTGATTCCCCGAATCATT
1 AAAAGGGGGTTGCTAAGTACTGATTCCCCC-AAGGGTTTGCTAAGTGCTGATTCCCCGAATCATT
* * *
33842392 GGTGGTTGCTAAGTGCTGATTCCACCGTATTTTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTC
65 GGTGGTTGCTAAGTGCTGATCCCACCGTA-TATTAAATGTGAAAGGGGTTGCTAAGTGCTGATTC
*
33842457 CCCGAATCACTGGTGGTTGCTAAGTGCTGAATCCACCG
129 CCAGAATCACTGGTGGTTGCTAAGTGCTGAATCCACCG
33842495 ATAACGGATA
Statistics
Matches: 155, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
179 83 0.54
180 70 0.45
181 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (179 bp):
AAAAGGGGGTTGCTAAGTACTGATTCCCCCAAGGGTTTGCTAAGTGCTGATTCCCCGAATCATTG
GTGGTTGCTAAGTGCTGATCCCACCGTATATTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCC
AGAATCACTGGTGGTTGCTAAGTGCTGAATCCACCGTATCTTAAAATGT
Found at i:33844351 original size:9 final size:9
Alignment explanation
Indices: 33844333--33844392 Score: 63
Period size: 9 Copynumber: 6.9 Consensus size: 9
33844323 CACTCTAGAA
33844333 TTTTTC-TC
1 TTTTTCTTC
33844341 TTTTTCTTC
1 TTTTTCTTC
33844350 TTTTTCTTC
1 TTTTTCTTC
**
33844359 TCCTTC-TC
1 TTTTTCTTC
*
33844367 TTCTTCTT-
1 TTTTTCTTC
33844375 TTTCTTCTTC
1 TTT-TTCTTC
33844385 TTTTTCTT
1 TTTTTCTT
33844393 TTACTAACTA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
8 15 0.34
9 26 0.59
10 3 0.07
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:33844359 original size:3 final size:3
Alignment explanation
Indices: 33844339--33844392 Score: 56
Period size: 3 Copynumber: 18.3 Consensus size: 3
33844329 AGAATTTTTC
* * * *
33844339 TCT TTT TCT TCT TTT TCT TCT CCT TC- TCT TCT TCT TTT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
33844386 TTT TCT T
1 TCT TCT T
33844393 TTACTAACTA
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TCT
Found at i:33844382 original size:12 final size:12
Alignment explanation
Indices: 33844344--33844392 Score: 73
Period size: 12 Copynumber: 4.2 Consensus size: 12
33844334 TTTTCTCTTT
33844344 TTCTTCTTTTTC
1 TTCTTCTTTTTC
* *
33844356 TTC-TCCTTCTC
1 TTCTTCTTTTTC
33844367 TTCTTCTTTTTC
1 TTCTTCTTTTTC
33844379 TTCTTCTTTTTC
1 TTCTTCTTTTTC
33844391 TT
1 TT
33844393 TTACTAACTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
11 9 0.28
12 23 0.72
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (12 bp):
TTCTTCTTTTTC
Found at i:33854609 original size:2 final size:2
Alignment explanation
Indices: 33854599--33854639 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
33854589 AAATATATAT
* *
33854599 AC AC CC AC AC AC AC AA AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
33854640 AAAGAGATGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:33861390 original size:12 final size:12
Alignment explanation
Indices: 33861375--33861399 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33861365 TAATCGAGTC
33861375 TAATTACGAGCT
1 TAATTACGAGCT
33861387 TAATTACGAGCT
1 TAATTACGAGCT
33861399 T
1 T
33861400 TCGAGCTGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TAATTACGAGCT
Found at i:33869963 original size:18 final size:18
Alignment explanation
Indices: 33869940--33869974 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
33869930 ATATTAGTAG
33869940 TATATATTTATATATGTA
1 TATATATTTATATATGTA
33869958 TATATATTTATATATGT
1 TATATATTTATATATGT
33869975 TAATGTATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (18 bp):
TATATATTTATATATGTA
Found at i:33871374 original size:16 final size:16
Alignment explanation
Indices: 33871341--33871378 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
33871331 ATTTAAGAAA
* *
33871341 TAATA-ATTTTTATGT
1 TAATATATTATTATAT
33871356 TAATATATTATTATAT
1 TAATATATTATTATAT
33871372 TAATATA
1 TAATATA
33871379 ATAAACATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TAATATATTATTATAT
Found at i:33873972 original size:16 final size:16
Alignment explanation
Indices: 33873951--33873981 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33873941 TCAACAAGCA
*
33873951 ATCGAATAGAAAAAAG
1 ATCGAATACAAAAAAG
33873967 ATCGAATACAAAAAA
1 ATCGAATACAAAAAA
33873982 AAATTAAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.10, G:0.13, T:0.13
Consensus pattern (16 bp):
ATCGAATACAAAAAAG
Found at i:33876738 original size:255 final size:255
Alignment explanation
Indices: 33876287--33876803 Score: 1007
Period size: 255 Copynumber: 2.0 Consensus size: 255
33876277 CTCCTAACTC
33876287 AAGTGCTGCAGACACCAAGTTTATTCTTAAGAAACTCAAAAACGACTTACATGAAAAATTTAGTA
1 AAGTGCTGCAGACACCAAGTTTATTCTTAAGAAACTCAAAAACGACTTACATGAAAAATTTAGTA
*
33876352 AAAATATTCGTCATCTGATCTCTGATTTGCAATAAACTAGCTTCTTCAATATTCACCTTCTATGA
66 AAAATATTCGTCATCTGATCTCTGATTTGCAATAAACCAGCTTCTTCAATATTCACCTTCTATGA
33876417 ATTCCTTATTGACTAGTGTAGCTTCAAGAGTTACCTCTAATAGTTTCCTAGCAATGCCATCTAAA
131 ATTCCTTATTGACTAGTGTAGCTTCAAGAGTTACCTCTAATAGTTTCCTAGCAATGCCATCTAAA
33876482 TCAAACTTCCATAATTCAAAATCATCACAAGCTGCTCCAGAAAAGTCATGAGAGTGGTCA
196 TCAAACTTCCATAATTCAAAATCATCACAAGCTGCTCCAGAAAAGTCATGAGAGTGGTCA
33876542 AAGTGCTGCAGACACCAAGTTTATTCTTAAGAAACTCAAAAACGACTTACATGAAAAATTTAGTA
1 AAGTGCTGCAGACACCAAGTTTATTCTTAAGAAACTCAAAAACGACTTACATGAAAAATTTAGTA
33876607 AAAATATTCGTCATCTGATCTCTGATTTGCAATAAACCAGCTTCTTCAATATTCACCTTCTATGA
66 AAAATATTCGTCATCTGATCTCTGATTTGCAATAAACCAGCTTCTTCAATATTCACCTTCTATGA
* *
33876672 ATTCCTTATTGACTAGTGTAGCTTCAAGAGTTATCTCTAATAGTTTCCTAGCAATGCTATCTAAA
131 ATTCCTTATTGACTAGTGTAGCTTCAAGAGTTACCTCTAATAGTTTCCTAGCAATGCCATCTAAA
33876737 TCAAACTTCCATAATTCAAAATCATCACAAGCTGCTCCAGAAAAGTCATGAGAGTGGTCA
196 TCAAACTTCCATAATTCAAAATCATCACAAGCTGCTCCAGAAAAGTCATGAGAGTGGTCA
33876797 AAGTGCT
1 AAGTGCT
33876804 TTCCCTTCTT
Statistics
Matches: 259, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
255 259 1.00
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (255 bp):
AAGTGCTGCAGACACCAAGTTTATTCTTAAGAAACTCAAAAACGACTTACATGAAAAATTTAGTA
AAAATATTCGTCATCTGATCTCTGATTTGCAATAAACCAGCTTCTTCAATATTCACCTTCTATGA
ATTCCTTATTGACTAGTGTAGCTTCAAGAGTTACCTCTAATAGTTTCCTAGCAATGCCATCTAAA
TCAAACTTCCATAATTCAAAATCATCACAAGCTGCTCCAGAAAAGTCATGAGAGTGGTCA
Found at i:33906711 original size:22 final size:24
Alignment explanation
Indices: 33906686--33906730 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
33906676 ATATGGCAAG
33906686 GAATTAAG-TAGAAAAG-AAGTAT
1 GAATTAAGTTAGAAAAGTAAGTAT
33906708 GAATTAAGTTAGAAAAGTAAGTA
1 GAATTAAGTTAGAAAAGTAAGTA
33906731 AACTTACTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.38
23 8 0.38
24 5 0.24
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.24
Consensus pattern (24 bp):
GAATTAAGTTAGAAAAGTAAGTAT
Found at i:33909557 original size:12 final size:12
Alignment explanation
Indices: 33909540--33909584 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
33909530 AACTAATCCT
33909540 CTCTCAAATTTC
1 CTCTCAAATTTC
*
33909552 CTCTC-AATTTG
1 CTCTCAAATTTC
33909563 CTCTCAAA-TTC
1 CTCTCAAATTTC
33909574 CT-TCCAAATTT
1 CTCT-CAAATTT
33909585 TTGTGAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 1 0.04
11 18 0.64
12 9 0.32
ACGTcount: A:0.24, C:0.31, G:0.02, T:0.42
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:33909645 original size:51 final size:51
Alignment explanation
Indices: 33909553--33909652 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
33909543 TCAAATTTCC
* * *
33909553 TCTCAATTTGCTCTCAAATTCCTTCCAAATTTTTGTGAAATCCATATTTAA
1 TCTCAATTTGCTCTCAAATTCCTTCCAAATTTCTCTCAAATCCATATTTAA
* * *
33909604 TCTCAATTTGCTCTCAATTTCC-TCTTAAATTTCTCTCAAATCCCTATTT
1 TCTCAATTTGCTCTCAAATTCCTTC-CAAATTTCTCTCAAATCCATATTT
33909653 TTTAATTATT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 2 0.05
51 40 0.95
ACGTcount: A:0.26, C:0.25, G:0.04, T:0.45
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAAATTCCTTCCAAATTTCTCTCAAATCCATATTTAA
Found at i:33910982 original size:128 final size:126
Alignment explanation
Indices: 33910696--33911135 Score: 539
Period size: 128 Copynumber: 3.5 Consensus size: 126
33910686 CCCAAACATG
* * * *
33910696 CTACTATAGCAAAAGCGCGTCCACGAGGGCACGATTTCATAAATTCTTCTCA-AATAGCATCCTA
1 CTACTGTAGTAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTA
* * * * * * *
33910760 CTAGAA--GTGTTTTTATACTATTTACTCAGAATCGTCAACTCAAAATTATTTTTTCAAGAC
65 CTTGAAGCGTTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
* * *
33910820 CTATTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATCCTG
1 CTACTGTAGTAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTA
*
33910884 CTTGAAGCGTTTTTTTAAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
65 CTTGAAGCGTTTTTTT-ATACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAGGAC
* *
33910948 CTACTGTAGTGAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTATTCTCATAAAGCATCCTAC
1 CTACTGTAGTAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTAC
* * *
33911013 TTGAAGCG-TTTTTTATACTGTTTGCTCATAAACGTCAACTCGAAATTATTTTTCTAGGAC
66 TTGAAGCGTTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
* ** * * * * * * *
33911073 CTACCGTAGTAAAAGCATGTACACGTGGGCGCGACTTCAGAAATCCATCTGATAAAGCATCCT
1 CTACTGTAGTAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCT
33911136 GCTTTGATTT
Statistics
Matches: 277, Mismatches: 34, Indels: 9
0.87 0.11 0.03
Matches are distributed among these distances:
124 64 0.23
125 59 0.21
126 41 0.15
127 39 0.14
128 72 0.26
129 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (126 bp):
CTACTGTAGTAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTAC
TTGAAGCGTTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
Found at i:33912359 original size:18 final size:18
Alignment explanation
Indices: 33912324--33912361 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
33912314 TTAAAAGATA
*
33912324 TATTATTTTTTTTAATTT
1 TATTATTTTTATTAATTT
33912342 TATTATTTTATATT-ATTT
1 TATTATTTT-TATTAATTT
33912360 TA
1 TA
33912362 ATACATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TATTATTTTTATTAATTT
Found at i:33918402 original size:10 final size:10
Alignment explanation
Indices: 33918387--33918508 Score: 79
Period size: 10 Copynumber: 11.6 Consensus size: 10
33918377 AAGAAGAAGG
33918387 AAAGAAAGAA
1 AAAGAAAGAA
33918397 AAAGAAAGAA
1 AAAGAAAGAA
*
33918407 AAGGAAAGGAGA
1 AAAGAAA-GA-A
33918419 GGAAAGAAAGAA
1 --AAAGAAAGAA
*
33918431 AAAG-AAGGA
1 AAAGAAAGAA
*
33918440 AAGGAGAAGAAA
1 AAAGA-AAG-AA
33918452 AAAGAAAGAA
1 AAAGAAAGAA
*
33918462 AAAGAAGGAA
1 AAAGAAAGAA
*
33918472 AGAA-AAGGAA
1 A-AAGAAAGAA
* *
33918482 AGGAGAAGGAA
1 A-AAGAAAGAA
33918493 AAA-AAAGAA
1 AAAGAAAGAA
33918502 AGAAGAA
1 A-AAGAA
33918509 GAAGAAGAGG
Statistics
Matches: 91, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
9 13 0.14
10 44 0.48
11 19 0.21
12 7 0.08
13 2 0.02
14 6 0.07
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:33918423 original size:34 final size:34
Alignment explanation
Indices: 33918384--33918540 Score: 141
Period size: 34 Copynumber: 4.7 Consensus size: 34
33918374 AAGAAGAAGA
33918384 AGGAAAGAAAGAAAAAGAAAGAAAAGGAAAGGAG
1 AGGAAAGAAAGAAAAAGAAAGAAAAGGAAAGGAG
*
33918418 AGGAAAGAAAGAAAAAG-AAGGAAAGGAGAA-GA-
1 AGGAAAGAAAGAAAAAGAAAGAAAAGGA-AAGGAG
* * * *
33918450 A-AAAAGAAAGAAAAAG-AAGGAAAGAAAAGGAA
1 AGGAAAGAAAGAAAAAGAAAGAAAAGGAAAGGAG
*
33918482 AGGAGAAGGAAA-AAAAAGAAAGAAGAA-G-AAGAAG
1 AGGA-AA-GAAAGAAAAAGAAAGAA-AAGGAAAGGAG
* *
33918516 AGGGAATGAAGGAAAAAGAAAGAAA
1 A-GGAAAGAAAGAAAAAGAAAGAAA
33918541 GAAAAGGTAA
Statistics
Matches: 103, Mismatches: 10, Indels: 21
0.77 0.07 0.16
Matches are distributed among these distances:
30 2 0.02
31 25 0.24
32 2 0.02
33 16 0.16
34 45 0.44
35 11 0.11
36 2 0.02
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (34 bp):
AGGAAAGAAAGAAAAAGAAAGAAAAGGAAAGGAG
Found at i:33918475 original size:69 final size:67
Alignment explanation
Indices: 33918374--33918547 Score: 210
Period size: 69 Copynumber: 2.6 Consensus size: 67
33918364 AGGAGAGGGA
*
33918374 AAGAAGAAGAAGGAAAGAAAGAA-AAAGAAAGAAAAGGAAAGGAG-AGGAAAGAAAGAA-AAAGA
1 AAGAAGAAGAAAGAAAGAAA-AAGAAAGAAAGAAAAGGAAAGGAGAAGGAAA-AAA-AAGAAAGA
33918436 AGGAAAG
63 A-G-AAG
* * *
33918443 GAGAAGAAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGGAAAAAAAAGAAAGAAGA
1 AAGAAGAAGAAAGAAAGAAAAAGAAAGAAAGAAAAGGAAAGGAGAAGGAAAAAAAAGAAAGAAGA
33918508 AG
66 AG
* * *
33918510 AAGAAGAGGGAATGAAGGAAAAAGAAAGAAAGAAAAGG
1 AAGAAGA-AGAAAGAAAGAAAAAGAAAGAAAGAAAAGG
33918548 TAATTTTTGT
Statistics
Matches: 91, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
67 9 0.10
68 30 0.33
69 46 0.51
70 6 0.07
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.01
Consensus pattern (67 bp):
AAGAAGAAGAAAGAAAGAAAAAGAAAGAAAGAAAAGGAAAGGAGAAGGAAAAAAAAGAAAGAAGA
AG
Found at i:33918494 original size:31 final size:31
Alignment explanation
Indices: 33918372--33918509 Score: 120
Period size: 31 Copynumber: 4.8 Consensus size: 31
33918362 GAAGGAGAGG
*
33918372 GAAAGAAGAAGAAGGAAA-GA-AA-GAAAAA
1 GAAAGAAAAAGAAGGAAAGGAGAAGGAAAAA
33918400 GAAAG---AA-AAGGAAAGGAG-AGG--AAA
1 GAAAGAAAAAGAAGGAAAGGAGAAGGAAAAA
*
33918424 GAAAGAAAAAGAAGGAAAGGAGAAGAAAAAA
1 GAAAGAAAAAGAAGGAAAGGAGAAGGAAAAA
* *
33918455 GAAAGAAAAAGAAGGAAA-GAAAAGGAAAGGA
1 GAAAGAAAAAGAAGGAAAGGAGAAGGAAA-AA
* * *
33918486 GAAGGAAAAA-AAAGAAAGAAGAAG
1 GAAAGAAAAAGAAGGAAAGGAGAAG
33918510 AAGAAGAGGG
Statistics
Matches: 90, Mismatches: 8, Indels: 21
0.76 0.07 0.18
Matches are distributed among these distances:
24 15 0.17
25 5 0.06
26 1 0.01
27 2 0.02
28 16 0.18
29 2 0.02
30 14 0.16
31 35 0.39
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (31 bp):
GAAAGAAAAAGAAGGAAAGGAGAAGGAAAAA
Found at i:33919117 original size:120 final size:116
Alignment explanation
Indices: 33918983--33919222 Score: 290
Period size: 120 Copynumber: 2.0 Consensus size: 116
33918973 ATGCGGAGAA
* * *
33918983 AAAAATACGAATAAATGGCCGAAGTAA-GAGTGTTTTACTAAA-TTTTTTA-AAAATTCAA-AAA
1 AAAAATACGAATAAATAGCCAAAATAAGGA-TGTTTTACTAAATTTTTTTAGAAAA---AAGAAA
* *
33919044 TAATTAATACAAATATTTCAAACAAAATGTACTGAAATAATATAAAATAAGAAAATAAG
62 TAATTAATAC----ACTTCAAACAAAATGTACTAAAATAATATAAAATAAGAAAATAAG
*
33919103 AAAAATACGAATAAATAGCCAAAATAAGGATTTTTTACTAAATTTTTTTAGAAAAAAGAAATAAT
1 AAAAATACGAATAAATAGCCAAAATAAGGATGTTTTACTAAATTTTTTTAGAAAAAAGAAATAAT
* * * *
33919168 TAATACACTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATACG
66 TAATACACTTCAAACAAAATGTACTAAAATAATATAAAATAAGAAAATAAG
33919219 AAAA
1 AAAA
33919223 TAATATATTT
Statistics
Matches: 106, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
116 43 0.41
119 2 0.02
120 48 0.45
121 9 0.08
122 4 0.04
ACGTcount: A:0.55, C:0.08, G:0.09, T:0.28
Consensus pattern (116 bp):
AAAAATACGAATAAATAGCCAAAATAAGGATGTTTTACTAAATTTTTTTAGAAAAAAGAAATAAT
TAATACACTTCAAACAAAATGTACTAAAATAATATAAAATAAGAAAATAAG
Found at i:33923341 original size:25 final size:26
Alignment explanation
Indices: 33923299--33923347 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
33923289 CTAAACCCTA
33923299 AAAACTAATAATAATAAT-ACTAACT
1 AAAACTAATAATAATAATAACTAACT
* **
33923324 AAAACTATTAATCTTAATAACTAA
1 AAAACTAATAATAATAATAACTAA
33923348 ACAACAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (26 bp):
AAAACTAATAATAATAATAACTAACT
Found at i:33923455 original size:10 final size:10
Alignment explanation
Indices: 33923427--33923463 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
33923417 AAATACCTTT
33923427 TTTTTCTCTTC
1 TTTTTCTC-TC
*
33923438 TCTTTCTCTC
1 TTTTTCTCTC
33923448 TTTTTCTCTC
1 TTTTTCTCTC
33923458 TTTTTC
1 TTTTTC
33923464 CGACAGCACC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 17 0.71
11 7 0.29
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTTCTCTC
Found at i:33923575 original size:27 final size:27
Alignment explanation
Indices: 33923537--33923631 Score: 102
Period size: 27 Copynumber: 3.5 Consensus size: 27
33923527 TAACACAAGT
* * *
33923537 GGTGCTGCCTATGGGAAAGGTACCTTC
1 GGTGCCGCCTATGGGAAAGGCACCATC
33923564 GGTGCCGCCTATGGGAAAGGCACCATC
1 GGTGCCGCCTATGGGAAAGGCACCATC
* ** * *
33923591 GGTGCCGCCTCTGACAGAGGCA-CAAC
1 GGTGCCGCCTATGGGAAAGGCACCATC
33923617 TGGTGCCGCCTATGG
1 -GGTGCCGCCTATGG
33923632 CACCCCCTCC
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
26 3 0.05
27 54 0.95
ACGTcount: A:0.19, C:0.28, G:0.34, T:0.19
Consensus pattern (27 bp):
GGTGCCGCCTATGGGAAAGGCACCATC
Found at i:33924249 original size:16 final size:16
Alignment explanation
Indices: 33924228--33924284 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
33924218 TTTGGTTCGC
*
33924228 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
33924244 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
33924260 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
33924276 TGTAATGGA
1 TGTAATGGA
33924285 AAAGCTGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:33924651 original size:14 final size:15
Alignment explanation
Indices: 33924519--33924653 Score: 61
Period size: 15 Copynumber: 8.9 Consensus size: 15
33924509 TTTAAACATA
*
33924519 ATTATTATTAAATAT
1 ATTATAATTAAATAT
*
33924534 ATTTTAATTAAA-AT
1 ATTATAATTAAATAT
*
33924548 A-TATAATTTAATAT
1 ATTATAATTAAATAT
*
33924562 GAATTTACTCAAATCATAATAT
1 --A-TTA-T--AATTA-AATAT
* *
33924584 ATGATACTGTAAA-AT
1 ATTATAAT-TAAATAT
33924599 A-TA-AATTAACATA-
1 ATTATAATTAA-ATAT
*
33924612 ATTATTATTAAATAT
1 ATTATAATTAAATAT
33924627 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
33924641 A-TATAATTTAATA
1 ATTATAATTAAATA
33924654 AAATTCTTAA
Statistics
Matches: 90, Mismatches: 14, Indels: 33
0.66 0.10 0.24
Matches are distributed among these distances:
12 3 0.03
13 21 0.23
14 16 0.18
15 29 0.32
16 5 0.06
17 1 0.01
18 3 0.03
19 3 0.03
20 1 0.01
21 3 0.03
22 5 0.06
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:33924668 original size:44 final size:43
Alignment explanation
Indices: 33924579--33924669 Score: 103
Period size: 44 Copynumber: 2.1 Consensus size: 43
33924569 CTCAAATCAT
* * *
33924579 AATATATGATACTGTAAAATATAAATTAACATAATTATTATTA
1 AATATATGATAATGTAAAATATAAATTAACAAAATTATTAATA
* * *
33924622 AATATATTATAAT-TAAAATATATAATTTAATAAAATTCTTAATA
1 AATATATGATAATGTAAAATATA-AA-TTAACAAAATTATTAATA
33924666 AATA
1 AATA
33924670 AAATTCTTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
42 9 0.22
43 13 0.32
44 18 0.45
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (43 bp):
AATATATGATAATGTAAAATATAAATTAACAAAATTATTAATA
Found at i:33924758 original size:15 final size:16
Alignment explanation
Indices: 33924738--33924773 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
33924728 AATAATTAAT
33924738 ATTAA-ATATGATTTA
1 ATTAATATATGATTTA
33924753 ATTAAATATATGATTTA
1 ATT-AATATATGATTTA
33924770 ATTA
1 ATTA
33924774 TAACTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 3 0.16
16 3 0.16
17 13 0.68
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
ATTAATATATGATTTA
Found at i:33924763 original size:17 final size:20
Alignment explanation
Indices: 33924742--33924787 Score: 71
Period size: 17 Copynumber: 2.5 Consensus size: 20
33924732 ATTAATATTA
33924742 AATATGATTTAATTA-AA-T
1 AATATGATTTAATTATAACT
33924760 -ATATGATTTAATTATAACT
1 AATATGATTTAATTATAACT
33924779 AATATGATT
1 AATATGATT
33924788 ATAGTTTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 14 0.56
18 2 0.08
19 1 0.04
20 8 0.32
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (20 bp):
AATATGATTTAATTATAACT
Found at i:33924904 original size:93 final size:92
Alignment explanation
Indices: 33924794--33924988 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
33924784 GATTATAGTT
* * *
33924794 TATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATT-TAATAATAATATATAATTTC
1 TATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTAT-ATAATAATATATAATTTC
* *
33924857 ATAAAATTCTTGATAATAAAAATTTTCTTA
64 ATAAAATTCTTAATAAT-AAAATGTTCTTA
* *
33924887 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAGTGATATATAATTTCAT
1 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
33924952 AAAATTCTTAATAATAAAATGTTCTTA
66 AAAATTCTTAATAATAAAATGTTCTTA
33924979 TATGAATTTA
1 TATGAATTTA
33924989 CTAAAATCAA
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 21 0.23
93 68 0.73
94 4 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (92 bp):
TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
AAAATTCTTAATAATAAAATGTTCTTA
Found at i:33931541 original size:43 final size:43
Alignment explanation
Indices: 33931494--33931591 Score: 160
Period size: 43 Copynumber: 2.3 Consensus size: 43
33931484 TATGTGAAAG
* * *
33931494 AACGCAGCTAAAGAACATGATCTTTAGCGGCATTTTACCCACA
1 AACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTACCCACA
*
33931537 AACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCACA
1 AACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTACCCACA
33931580 AACGCCGCTAAA
1 AACGCCGCTAAA
33931592 AGTATGGTTC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.34, C:0.30, G:0.17, T:0.19
Consensus pattern (43 bp):
AACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTACCCACA
Found at i:33933366 original size:7 final size:7
Alignment explanation
Indices: 33933356--33933510 Score: 91
Period size: 7 Copynumber: 21.7 Consensus size: 7
33933346 TCATAAAACA
33933356 TAAACCC
1 TAAACCC
33933363 TAAACCCC
1 TAAA-CCC
*
33933371 TAACCCC
1 TAAACCC
33933378 TAAACTCC
1 TAAAC-CC
*
33933386 TAAACCT
1 TAAACCC
33933393 TAAACCC
1 TAAACCC
*
33933400 -CAACCC
1 TAAACCC
*
33933406 TTAAACCG
1 -TAAACCC
*
33933414 TAAACCG
1 TAAACCC
*
33933421 TAAACCA
1 TAAACCC
*
33933428 TAAACCA
1 TAAACCC
*
33933435 TAAACCA
1 TAAACCC
*
33933442 TAAACCA
1 TAAACCC
*
33933449 TAATCCC
1 TAAACCC
* *
33933456 AAAACCT
1 TAAACCC
*
33933463 TAAA--A
1 TAAACCC
33933468 TAGTAACTCC
1 TA--AAC-CC
*
33933478 TAAACCA
1 TAAACCC
*
33933485 TATACCC
1 TAAACCC
*
33933492 TAAACCA
1 TAAACCC
33933499 TAAACCC
1 TAAACCC
33933506 TAAAC
1 TAAAC
33933511 TATAATGATA
Statistics
Matches: 117, Mismatches: 22, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
5 2 0.02
6 5 0.04
7 88 0.75
8 20 0.17
10 2 0.02
ACGTcount: A:0.45, C:0.35, G:0.02, T:0.18
Consensus pattern (7 bp):
TAAACCC
Found at i:33933373 original size:8 final size:8
Alignment explanation
Indices: 33933356--33933412 Score: 52
Period size: 8 Copynumber: 7.8 Consensus size: 8
33933346 TCATAAAACA
33933356 TAAA-CCC
1 TAAACCCC
33933363 TAAACCCC
1 TAAACCCC
33933371 T-AACCCC
1 TAAACCCC
*
33933378 TAAACTCC
1 TAAACCCC
*
33933386 TAAA-CCT
1 TAAACCCC
33933393 TAAACCCC
1 TAAACCCC
*
33933401 --AACCCT
1 TAAACCCC
33933407 TAAACC
1 TAAACC
33933413 GTAAACCGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
6 5 0.12
7 16 0.40
8 19 0.47
ACGTcount: A:0.39, C:0.44, G:0.00, T:0.18
Consensus pattern (8 bp):
TAAACCCC
Found at i:33933380 original size:15 final size:15
Alignment explanation
Indices: 33933360--33933412 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
33933350 AAAACATAAA
33933360 CCCTAAACCCCTAAC
1 CCCTAAACCCCTAAC
* *
33933375 CCCTAAACTCCTAAA
1 CCCTAAACCCCTAAC
*
33933390 CCTTAAACCCC-AAC
1 CCCTAAACCCCTAAC
*
33933404 CCTTAAACC
1 CCCTAAACC
33933413 GTAAACCGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
14 11 0.33
15 22 0.67
ACGTcount: A:0.36, C:0.47, G:0.00, T:0.17
Consensus pattern (15 bp):
CCCTAAACCCCTAAC
Found at i:33933970 original size:22 final size:21
Alignment explanation
Indices: 33933925--33933978 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
33933915 TACCTTTATT
* *
33933925 TTTAATTAAAAATAAATTAAAA
1 TTTAATT-AATATAAATAAAAA
33933947 TTTAATTAATATAAATAAACAA
1 TTTAATTAATATAAATAAA-AA
*
33933969 -TTAAATAATA
1 TTTAATTAATA
33933979 AATAGTAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 19 0.68
22 9 0.32
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
TTTAATTAATATAAATAAAAA
Found at i:33934074 original size:41 final size:40
Alignment explanation
Indices: 33933997--33934186 Score: 247
Period size: 41 Copynumber: 4.7 Consensus size: 40
33933987 ATAAAATGTT
* * **
33933997 TTTTGAAAAACGCCTCTAAAG-GTCGAGCATTAGCGGCGC
1 TTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCGC
*
33934036 TTTTACAAAAACGCCGCTAAATCCCCGAGCATTAGCGGCGC
1 TTTT-CAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCGC
* *
33934077 TTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGTGGTGC
1 -TTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCGC
* *
33934118 TTTTCCAAAAACGCCGCTAAAGCCCCGATCATTAGCGGTGC
1 TTTT-CAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCGC
*
33934159 TTTGTCAAAAACGTCGCTAAAGCCCCGA
1 TTT-TCAAAAACGCCGCTAAAGCCCCGA
33934187 AAGCTAAGAA
Statistics
Matches: 135, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
39 4 0.03
40 18 0.13
41 108 0.80
42 5 0.04
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (40 bp):
TTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCGC
Found at i:33934346 original size:40 final size:40
Alignment explanation
Indices: 33934254--33934387 Score: 146
Period size: 40 Copynumber: 3.4 Consensus size: 40
33934244 AAAATGAGCA
* * * *
33934254 TTAGCGGCATTTTTGAAATAGCGTCGCTATTGCTTGATCT
1 TTAGCGGCGTTTTTCAAATAGCGCCGCTATTGCTCGATCT
33934294 TTAGCGGCGTTTTTCAAATAGCGCCGCTATTGCTCGATCT
1 TTAGCGGCGTTTTTCAAATAGCGCCGCTATTGCTCGATCT
* * * * *
33934334 TTAGCGGTG-TTTTCTAAAAAGTGCCGCTAATT-CTCTATTT
1 TTAGCGGCGTTTTTC-AAATAGCGCCGCT-ATTGCTCGATCT
*
33934374 TTAGCGACGTTTTT
1 TTAGCGGCGTTTTT
33934388 GATCCAAACG
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
39 5 0.06
40 68 0.85
41 7 0.09
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (40 bp):
TTAGCGGCGTTTTTCAAATAGCGCCGCTATTGCTCGATCT
Found at i:33934939 original size:15 final size:14
Alignment explanation
Indices: 33934915--33934963 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
33934905 TATAATAAAT
33934915 ATTTTTATTTTTAA
1 ATTTTTATTTTTAA
33934929 ATTTTTAATTTTTAAA
1 ATTTTT-ATTTTT-AA
**
33934945 ATACTT-TTTTTAA
1 ATTTTTATTTTTAA
33934958 ATTTTT
1 ATTTTT
33934964 TTAATTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
13 6 0.21
14 11 0.38
15 6 0.21
16 6 0.21
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTTTTATTTTTAA
Found at i:33934972 original size:30 final size:30
Alignment explanation
Indices: 33934922--33935009 Score: 119
Period size: 29 Copynumber: 2.9 Consensus size: 30
33934912 AATATTTTTA
33934922 TTTTTAAA--TTTTTAATTTTTAAAATACTT
1 TTTTTAAATTTTTTTAATTTTTAAAATAC-T
33934951 TTTTTAAATTTTTTTAA-TTTTAAAATACT
1 TTTTTAAATTTTTTTAATTTTTAAAATACT
*
33934980 TTTTTAATTTTTGTTTTAATTTTTAAAATA
1 TTTTTAA-ATTT-TTTTAATTTTTAAAATA
33935010 AATTTTTGGT
Statistics
Matches: 53, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
29 16 0.30
30 14 0.26
31 13 0.25
32 10 0.19
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (30 bp):
TTTTTAAATTTTTTTAATTTTTAAAATACT
Found at i:33944548 original size:27 final size:27
Alignment explanation
Indices: 33944486--33944548 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
33944476 ACATTGTGCG
* *
33944486 TCACATGGGCCGTATGTTCAACATTCA
1 TCACATGGGCCGCATATTCAACATTCA
33944513 TCA-AGTGGGCCGCATATTCAACA-TCTA
1 TCACA-TGGGCCGCATATTCAACATTC-A
33944540 TCACATGGG
1 TCACATGGG
33944549 TCCAATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
26 3 0.10
27 27 0.87
28 1 0.03
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (27 bp):
TCACATGGGCCGCATATTCAACATTCA
Found at i:33965752 original size:24 final size:24
Alignment explanation
Indices: 33965724--33965775 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
33965714 TTAGTAAGTC
* *
33965724 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
33965748 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
33965772 AAAT
1 AAAT
33965776 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:33967181 original size:5 final size:5
Alignment explanation
Indices: 33967173--33967209 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
33967163 AAAAGGAAAC
* *
33967173 AAAAT AAAAT AAAAT AAAAT AAAAT GAAAC AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
33967210 TCACCTTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:33967181 original size:15 final size:15
Alignment explanation
Indices: 33967163--33967209 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
33967153 GAAATGAAAG
*
33967163 AAAAGGAAACAAAAT
1 AAAATGAAACAAAAT
* *
33967178 AAAATAAAATAAAAT
1 AAAATGAAACAAAAT
33967193 AAAATGAAACAAAAT
1 AAAATGAAACAAAAT
33967208 AA
1 AA
33967210 TCACCTTGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.77, C:0.04, G:0.06, T:0.13
Consensus pattern (15 bp):
AAAATGAAACAAAAT
Found at i:33968457 original size:17 final size:16
Alignment explanation
Indices: 33968431--33968470 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
33968421 AAAATCAATT
33968431 AAAATTACATAATATA
1 AAAATTACATAATATA
*
33968447 AAAAGTTACATTATATA
1 AAAA-TTACATAATATA
33968464 AAAATTA
1 AAAATTA
33968471 AATGAGTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.33
Consensus pattern (16 bp):
AAAATTACATAATATA
Found at i:33968658 original size:60 final size:60
Alignment explanation
Indices: 33968585--33968706 Score: 183
Period size: 60 Copynumber: 2.0 Consensus size: 60
33968575 ATACTAAACT
* * * * *
33968585 AAACACAATAATTTATAGCTTAATCCTAAATTACTAATAAATTAAATT-TTAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATT-AATTATAAAATAATTAC
33968645 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
33968705 AA
1 AA
33968707 TATTCATACA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 4 0.07
60 52 0.93
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.33
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
Found at i:33968725 original size:21 final size:22
Alignment explanation
Indices: 33968694--33968742 Score: 91
Period size: 21 Copynumber: 2.3 Consensus size: 22
33968684 AATTAATTAT
33968694 AAAATAATTACAATATTCATAC
1 AAAATAATTACAATATTCATAC
33968716 AAAA-AATTACAATATTCATAC
1 AAAATAATTACAATATTCATAC
33968737 AAAATA
1 AAAATA
33968743 CTAATCCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAATAATTACAATATTCATAC
Found at i:33968787 original size:61 final size:61
Alignment explanation
Indices: 33968716--33968863 Score: 253
Period size: 61 Copynumber: 2.4 Consensus size: 61
33968706 ATATTCATAC
* *
33968716 AAAA-AATTACAATATTCATACAAAATACTAATCCAAAACTATACATACAAAATTAATTAT
1 AAAATAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTAT
*
33968776 AAACTAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTAT
1 AAAATAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTAT
*
33968837 AAAATAATTACAATATTCATACGAAAT
1 AAAATAATTACAATATTCATACAAAAT
33968864 TATAATATTC
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
60 3 0.04
61 79 0.96
ACGTcount: A:0.57, C:0.14, G:0.01, T:0.29
Consensus pattern (61 bp):
AAAATAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTAT
Found at i:33968870 original size:19 final size:19
Alignment explanation
Indices: 33968842--33968964 Score: 65
Period size: 19 Copynumber: 6.2 Consensus size: 19
33968832 ATTATAAAAT
*
33968842 AATTACAATATTCATACGA
1 AATTACAATATTCATACAA
*
33968861 AATTATAATATTCATACAA
1 AATTACAATATTCATACAA
* * *
33968880 AA-TACTA-ATCCAAAACTATA
1 AATTACAATATTC-ATAC-A-A
*
33968900 AA-TACAAAATTAATT-ATAAAA
1 AATTAC--AA-T-ATTCATACAA
33968921 TAATTACAATATTCATACAAAA
1 -AATTACAATATTCATAC--AA
*
33968943 AATTACAGTATTCATACAA
1 AATTACAATATTCATACAA
33968962 AAT
1 AAT
33968965 ACTAATCAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 26
0.68 0.10 0.22
Matches are distributed among these distances:
17 3 0.04
18 6 0.08
19 28 0.35
20 10 0.13
21 19 0.24
22 6 0.08
23 5 0.06
25 2 0.03
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.31
Consensus pattern (19 bp):
AATTACAATATTCATACAA
Found at i:33968878 original size:80 final size:80
Alignment explanation
Indices: 33968781--33969028 Score: 442
Period size: 80 Copynumber: 3.1 Consensus size: 80
33968771 ATTATAAACT
33968781 AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAATAATT
1 AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAATAATT
*
33968846 ACAATATTCATACGA
66 ACAATATTCATACAA
* *
33968861 AATTATAATATTCATACAAAATACTAATCCAAAACTATAAATACAAAATTAATTATAAAATAATT
1 AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAATAATT
33968926 ACAATATTCATACAAAA
66 ACAATATTCATAC--AA
*
33968943 AATTACAGTATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAATAATT
1 AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAATAATT
33969008 ACAATATTCATACAA
66 ACAATATTCATACAA
33969023 AATTAC
1 AATTAC
33969029 CCATTGGCGC
Statistics
Matches: 160, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
80 84 0.52
82 76 0.47
ACGTcount: A:0.56, C:0.12, G:0.01, T:0.30
Consensus pattern (80 bp):
AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAATAATT
ACAATATTCATACAA
Found at i:33968893 original size:141 final size:142
Alignment explanation
Indices: 33968683--33968942 Score: 468
Period size: 141 Copynumber: 1.8 Consensus size: 142
33968673 AATTACTAAC
33968683 AAATTAATTATAAAATAATTACAATATTCATACAAAAAATTACAATATTCATACAAAATACTAAT
1 AAATTAATTATAAAATAATTACAATATTCATAC-AAAAATTACAATATTCATACAAAATACTAAT
* *
33968748 CCAAAACTATACATACAAAATTAATTATAAACTAATTACAATATTCATACAAAATACTAATCAAA
65 CCAAAACTATAAATACAAAATTAATTATAAAATAATTACAATATTCATACAAAATACTAATCAAA
33968813 AACTATAAATACA
130 AACTATAAATACA
* *
33968826 AAATTAATTATAAAATAATTACAATATTCATAC-GAAATTATAATATTCATACAAAATACTAATC
1 AAATTAATTATAAAATAATTACAATATTCATACAAAAATTACAATATTCATACAAAATACTAATC
33968890 CAAAACTATAAATACAAAATTAATTATAAAATAATTACAATATTCATACAAAA
66 CAAAACTATAAATACAAAATTAATTATAAAATAATTACAATATTCATACAAAA
33968943 AATTACAGTA
Statistics
Matches: 113, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
141 80 0.71
143 33 0.29
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (142 bp):
AAATTAATTATAAAATAATTACAATATTCATACAAAAATTACAATATTCATACAAAATACTAATC
CAAAACTATAAATACAAAATTAATTATAAAATAATTACAATATTCATACAAAATACTAATCAAAA
ACTATAAATACA
Found at i:33968948 original size:21 final size:22
Alignment explanation
Indices: 33968917--33968965 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 22
33968907 AATTAATTAT
33968917 AAAATAATTACAATATTCATAC
1 AAAATAATTACAATATTCATAC
*
33968939 AAAA-AATTACAGTATTCATAC
1 AAAATAATTACAATATTCATAC
33968960 AAAATA
1 AAAATA
33968966 CTAATCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAATAATTACAATATTCATAC
Found at i:33968993 original size:82 final size:82
Alignment explanation
Indices: 33968781--33969024 Score: 438
Period size: 82 Copynumber: 3.0 Consensus size: 82
33968771 ATTATAAACT
33968781 AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAATAATT
1 AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAATAATT
*
33968846 ACAATATTCATAC--GA
66 ACAATATTCATACAAAA
* *
33968861 AATTATAATATTCATACAAAATACTAATCCAAAACTATAAATACAAAATTAATTATAAAATAATT
1 AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAATAATT
33968926 ACAATATTCATACAAAA
66 ACAATATTCATACAAAA
*
33968943 AATTACAGTATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAATAATT
1 AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAATAATT
33969008 ACAATATTCATACAAAA
66 ACAATATTCATACAAAA
33969025 TTACCCATTG
Statistics
Matches: 156, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
80 76 0.49
82 80 0.51
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.30
Consensus pattern (82 bp):
AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAATAATT
ACAATATTCATACAAAA
Found at i:33970222 original size:13 final size:13
Alignment explanation
Indices: 33970204--33970228 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33970194 GCAATTTGTA
33970204 TTATTTTTTATTT
1 TTATTTTTTATTT
33970217 TTATTTTTTATT
1 TTATTTTTTATT
33970229 ATAAAACCTA
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTATTTTTTATTT
Found at i:33975494 original size:22 final size:21
Alignment explanation
Indices: 33975443--33975503 Score: 52
Period size: 22 Copynumber: 2.7 Consensus size: 21
33975433 ATTTAGATGG
*
33975443 TATTTAAATAGTTATATATTAAA
1 TATTTAAA-AATTA-ATATTAAA
33975466 TATTTTAAAGAATTAATA-TAAA
1 TA-TTTAAA-AATTAATATTAAA
33975488 TTATTTATAAAATTAA
1 -TATTTA-AAAATTAA
33975504 CGATACATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
22 14 0.42
23 9 0.27
24 10 0.30
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (21 bp):
TATTTAAAAATTAATATTAAA
Found at i:33980287 original size:29 final size:29
Alignment explanation
Indices: 33980232--33980286 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
33980222 CGCGGAAAAT
33980232 GGCCCATTCCGGTAAATAATTAAAAAACC
1 GGCCCATTCCGGTAAATAATTAAAAAACC
*
33980261 GGCCCATTTCGGTAAAT-ATTAAAAAA
1 GGCCCATTCCGGTAAATAATTAAAAAA
33980287 AAGGGGCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.24
Consensus pattern (29 bp):
GGCCCATTCCGGTAAATAATTAAAAAACC
Found at i:33983284 original size:23 final size:22
Alignment explanation
Indices: 33983258--33983300 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
33983248 GGTTTTGCCA
*
33983258 ATTTGTGATTTGGATTGTTTTTT
1 ATTTGGGATTTGG-TTGTTTTTT
*
33983281 ATTTGGGTTTTGGTTGTTTT
1 ATTTGGGATTTGGTTGTTTT
33983301 ATGACCAGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.09, C:0.00, G:0.26, T:0.65
Consensus pattern (22 bp):
ATTTGGGATTTGGTTGTTTTTT
Found at i:33985783 original size:19 final size:19
Alignment explanation
Indices: 33985698--33985789 Score: 66
Period size: 19 Copynumber: 4.8 Consensus size: 19
33985688 AATTCTTTTG
33985698 AAAATATCATAAAAA-TAATA
1 AAAATAT-A-AAAAATTAATA
* * *
33985718 AAATAAATAAATAA-TATTA
1 AAA-ATATAAAAAATTAATA
*
33985737 AAAATAT-AAAAATTGATA
1 AAAATATAAAAAATTAATA
*
33985755 TAAACT-TAAAAAATTAATA
1 -AAAATATAAAAAATTAATA
*
33985774 AAAATATAAAATATTA
1 AAAATATAAAAAATTA
33985790 TAAGTATTAT
Statistics
Matches: 56, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
17 4 0.07
18 11 0.20
19 34 0.61
20 4 0.07
21 3 0.05
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.29
Consensus pattern (19 bp):
AAAATATAAAAAATTAATA
Found at i:33986255 original size:19 final size:19
Alignment explanation
Indices: 33986222--33986275 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
33986212 GAGTTCAAGT
33986222 TTTTATATATTTTTAAAT-AA
1 TTTT-TATA-TTTTAAATGAA
*
33986242 TTTTTATATGTTTATATGAA
1 TTTTTATAT-TTTAAATGAA
*
33986262 TTTTAATATTTTAA
1 TTTTTATATTTTAA
33986276 TAAATTTCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 1 0.03
19 14 0.48
20 14 0.48
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (19 bp):
TTTTTATATTTTAAATGAA
Found at i:33986328 original size:48 final size:44
Alignment explanation
Indices: 33986240--33986339 Score: 114
Period size: 48 Copynumber: 2.2 Consensus size: 44
33986230 ATTTTTAAAT
*
33986240 AATTTTTATATGTTTATATGAATTTTAATATTTTAATAAATTTCTA
1 AATTTTTATATGTTTATATGAATTCTAATATTTT-ATAAATTT-TA
33986286 CAATTTATTATTATGTTT-TATGAATTCTAATACGTTTT-TAAATTTTA
1 -AATTT-TTA-TATGTTTATATGAATTCTAATA--TTTTATAAATTTTA
33986333 AATTTTT
1 AATTTTT
33986340 TAAATAATAT
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
45 2 0.04
46 5 0.10
47 7 0.15
48 23 0.48
49 7 0.15
50 4 0.08
ACGTcount: A:0.34, C:0.04, G:0.05, T:0.57
Consensus pattern (44 bp):
AATTTTTATATGTTTATATGAATTCTAATATTTTATAAATTTTA
Found at i:33986368 original size:8 final size:8
Alignment explanation
Indices: 33986357--33986447 Score: 51
Period size: 8 Copynumber: 10.6 Consensus size: 8
33986347 TATTTATTAA
33986357 TTTTATATT
1 TTTTATA-T
33986366 TTTTATAAT
1 TTTTAT-AT
33986375 TTATTATAT
1 TT-TTATAT
33986384 TTTTCAT-T
1 TTTT-ATAT
*
33986392 TTTTATAA
1 TTTTATAT
33986400 TTTTATAAGT
1 TTTTAT-A-T
* *
33986410 TTATAACAAT
1 TT-TTA-TAT
*
33986420 TTTAATAT
1 TTTTATAT
33986428 TTTTAT-T
1 TTTTATAT
*
33986435 TTATATAT
1 TTTTATAT
33986443 TTTTA
1 TTTTA
33986448 ATGATTTTCA
Statistics
Matches: 65, Mismatches: 8, Indels: 19
0.71 0.09 0.21
Matches are distributed among these distances:
7 8 0.12
8 25 0.38
9 19 0.29
10 10 0.15
11 3 0.05
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (8 bp):
TTTTATAT
Found at i:33986379 original size:29 final size:27
Alignment explanation
Indices: 33986326--33986414 Score: 80
Period size: 26 Copynumber: 3.3 Consensus size: 27
33986316 TACGTTTTTA
* *
33986326 AATTTTAAATTTTTTA-AATAATATTTATT
1 AATTTTATATTTTTTATAAT-TTA-TTA-T
33986355 AATTTTATATTTTTTATAATTTATTAT
1 AATTTTATATTTTTTATAATTTATTAT
33986382 -ATTTT-TCATTTTTTATAA-TT-TTAT
1 AATTTTAT-ATTTTTTATAATTTATTAT
*
33986406 AAGTTTATA
1 AATTTTATA
33986415 ACAATTTTAA
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
24 4 0.08
25 8 0.15
26 17 0.32
27 1 0.02
28 3 0.06
29 17 0.32
30 3 0.06
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (27 bp):
AATTTTATATTTTTTATAATTTATTAT
Found at i:33986392 original size:26 final size:25
Alignment explanation
Indices: 33986348--33986402 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 25
33986338 TTTAAATAAT
33986348 ATTTATTAATTTTATATTTTTTATA
1 ATTTATTAATTTTATATTTTTTATA
33986373 ATTTATTATATTTT-TCATTTTTTATA
1 ATTTATTA-ATTTTAT-ATTTTTTATA
33986399 ATTT
1 ATTT
33986403 TATAAGTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 9 0.32
26 19 0.68
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (25 bp):
ATTTATTAATTTTATATTTTTTATA
Found at i:33986437 original size:14 final size:15
Alignment explanation
Indices: 33986418--33986447 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
33986408 GTTTATAACA
33986418 ATTTTA-ATATTTTT
1 ATTTTATATATTTTT
33986432 ATTTTATATATTTTT
1 ATTTTATATATTTTT
33986447 A
1 A
33986448 ATGATTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTATATATTTTT
Found at i:33990583 original size:50 final size:50
Alignment explanation
Indices: 33990524--33990624 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
33990514 TAGCCAAAAA
33990524 CCTCTACTATAGTTGGAAGATTCTTCTCACCTACAGTCATACATATGCAG
1 CCTCTACTATAGTTGGAAGATTCTTCTCACCTACAGTCATACATATGCAG
33990574 CCTCTACTATAGTTGGAAGATTCTTCTCACCTACAGTCATACATATGCAG
1 CCTCTACTATAGTTGGAAGATTCTTCTCACCTACAGTCATACATATGCAG
33990624 C
1 C
33990625 ATTCTCTCTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (50 bp):
CCTCTACTATAGTTGGAAGATTCTTCTCACCTACAGTCATACATATGCAG
Found at i:34002632 original size:18 final size:19
Alignment explanation
Indices: 34002577--34002627 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
34002567 TTACAAAAAC
34002577 AAAATT-AAAATAATTT-TCA
1 AAAATTCAAAAT-ATTTAT-A
34002596 AAAATTCAAAATATTTATA
1 AAAATTCAAAATATTTATA
34002615 AAAATTTCAAAAT
1 AAAA-TTCAAAAT
34002628 TTATATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATTCAAAATATTTATA
Found at i:34011275 original size:2 final size:2
Alignment explanation
Indices: 34011270--34011294 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34011260 TGTGATAGGC
34011270 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
34011295 AGGTTAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34017324 original size:15 final size:16
Alignment explanation
Indices: 34017299--34017329 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
34017289 TATTATATGT
34017299 AATATATAATTAATTA
1 AATATATAATTAATTA
34017315 AATA-ATAATTAATTA
1 AATATATAATTAATTA
34017330 TTAAATACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATATATAATTAATTA
Found at i:34023356 original size:31 final size:29
Alignment explanation
Indices: 34023295--34023380 Score: 77
Period size: 30 Copynumber: 2.9 Consensus size: 29
34023285 GGTTGAAAAA
* *
34023295 ATAATTTATAT-AAGATTTATGGTTTAATG
1 ATAATTTATATAAAAATTT-TGATTTAATG
*
34023324 TATAATTATATATAAAAATTTTGATTTTATG
1 -ATAATT-TATATAAAAATTTTGATTTAATG
*
34023355 -TAATTTTATACATAAAATTTTGATTT
1 ATAA-TTTATATA-AAAATTTTGATTT
34023381 GATTCAATTC
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
29 8 0.17
30 21 0.44
31 13 0.27
32 6 0.12
ACGTcount: A:0.40, C:0.01, G:0.08, T:0.51
Consensus pattern (29 bp):
ATAATTTATATAAAAATTTTGATTTAATG
Found at i:34023414 original size:12 final size:12
Alignment explanation
Indices: 34023397--34023426 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
34023387 ATTCTTGTGC
34023397 ATTATTAACATA
1 ATTATTAACATA
34023409 ATTATTAACATA
1 ATTATTAACATA
34023421 A-TATTA
1 ATTATTA
34023427 TTTTATGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (12 bp):
ATTATTAACATA
Found at i:34023592 original size:30 final size:30
Alignment explanation
Indices: 34023520--34023605 Score: 84
Period size: 31 Copynumber: 2.9 Consensus size: 30
34023510 GATTAAATTA
*
34023520 AAATTAAAGTTTCAAGTATACATTTGAACC
1 AAATTAAAGTTTCAAGTATACAATTGAACC
* * * * * *
34023550 ACAATTAGAGTTTCACGTGTATAATTGTACT
1 A-AATTAAAGTTTCAAGTATACAATTGAACC
*
34023581 AAATTAAAGTTT-ATGTATACAATTG
1 AAATTAAAGTTTCAAGTATACAATTG
34023606 TATATTAAAT
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
29 10 0.23
30 11 0.25
31 23 0.52
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (30 bp):
AAATTAAAGTTTCAAGTATACAATTGAACC
Found at i:34026255 original size:18 final size:18
Alignment explanation
Indices: 34026232--34026266 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
34026222 TTTGTAAAAA
34026232 GTTTAAACTATAAAAATG
1 GTTTAAACTATAAAAATG
*
34026250 GTTTAATCTATAAAAAT
1 GTTTAAACTATAAAAAT
34026267 TTTCATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (18 bp):
GTTTAAACTATAAAAATG
Found at i:34033707 original size:2 final size:2
Alignment explanation
Indices: 34033695--34033726 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
34033685 TCAAATACAG
34033695 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34033727 CTTTTGCTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:34043326 original size:2 final size:2
Alignment explanation
Indices: 34043319--34043351 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
34043309 TAGTACATGC
34043319 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34043352 CTTACACTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34046846 original size:28 final size:29
Alignment explanation
Indices: 34046811--34046868 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
34046801 TGTCCTTAAA
* *
34046811 ATTTTTAAAAAAA-TTGATTAAATCCCTT
1 ATTTTTAAAAAAATTTCATTAAACCCCTT
34046839 ATTTTTAAAAAAATTTCATTAAACCCCTT
1 ATTTTTAAAAAAATTTCATTAAACCCCTT
34046868 A
1 A
34046869 AAATTTTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (29 bp):
ATTTTTAAAAAAATTTCATTAAACCCCTT
Found at i:34047757 original size:31 final size:30
Alignment explanation
Indices: 34047722--34047838 Score: 82
Period size: 31 Copynumber: 3.9 Consensus size: 30
34047712 AGTTTAGAAG
34047722 GGTCTAATGAAAATTTTAAAAAAATTTGGGA
1 GGTCTAATGAAAATTTT-AAAAAATTTGGGA
* * *
34047753 GGTCTAATTAAATATTTTTTAAAACTTTGAGG-
1 GGTCTAATGAAA-A-TTTTAAAAAATTTG-GGA
* * *
34047785 GGTC-AAT-AAAATTTT-TAAATTTTGAGA
1 GGTCTAATGAAAATTTTAAAAAATTTGGGA
*
34047812 GGAT-TAATGAAAATTTCCAAAAAATTT
1 GG-TCTAATGAAAATTT-TAAAAAATTT
34047839 AGAGAGCTTA
Statistics
Matches: 68, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
26 1 0.01
27 9 0.13
28 8 0.12
29 8 0.12
30 3 0.04
31 20 0.29
32 13 0.19
33 6 0.09
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (30 bp):
GGTCTAATGAAAATTTTAAAAAATTTGGGA
Found at i:34068257 original size:125 final size:125
Alignment explanation
Indices: 34067993--34068274 Score: 363
Period size: 125 Copynumber: 2.3 Consensus size: 125
34067983 CCACGAGGGC
* * *
34067993 GCGATTTGACACAATTTGCTCAGAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGC
1 GCGATTTCACACTATTTCCTCAGAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGC
* * * * * * **
34068058 GAAATCGCGTCCACGAGGGCGCAATTTCATAATTTCTTCTCATATAGCATCCTGGTATCA
66 GAAATCGCGTCCACAAGGCCACAATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
* *
34068118 GCGATTTTATACTATTTCCTCAGAAAACGTCAAAAAAAAATTATTT-CTCACATGACC-ACTGTA
1 GCGATTTCACACTATTTCCTCAG-AAACGTCAAAAAAAAATTATTTCCT-ACATGACCAACTGTA
* *
34068181 GCGAAATCGCGTCCACAAGGCCACTATTTCACAATTTCTTCTTAAATAGCATCCTAGTAGAA
64 GCGAAATCGCGTCCACAAGGCCACAATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
* *
34068243 GCGATTTCCCACTATTTAAC-CAGAAACGTCAA
1 GCGATTTCACACTATTT-CCTCAGAAACGTCAA
34068275 CTCGAAAAAA
Statistics
Matches: 136, Mismatches: 18, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
124 9 0.07
125 96 0.71
126 31 0.23
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (125 bp):
GCGATTTCACACTATTTCCTCAGAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGC
GAAATCGCGTCCACAAGGCCACAATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
Found at i:34074299 original size:15 final size:14
Alignment explanation
Indices: 34074279--34074324 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
34074269 TAAAAAGTAG
34074279 AAAAATTAAATTCAT
1 AAAAATTAAATT-AT
* *
34074294 AAAAATAAAAATAT
1 AAAAATTAAATTAT
*
34074308 AAAAACTAAATTAT
1 AAAAATTAAATTAT
34074322 AAA
1 AAA
34074325 TTTGTGAAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAAATTAAATTAT
Found at i:34074311 original size:29 final size:29
Alignment explanation
Indices: 34074269--34074324 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
34074259 TTTTAAAATT
*
34074269 TAAAAAGTAGAAAAATTAAATTCATAAAAA
1 TAAAAAGTAGAAAAACTAAATT-ATAAAAA
*
34074299 TAAAAA-TATAAAAACTAAATTATAAA
1 TAAAAAGTAGAAAAACTAAATTATAAA
34074325 TTTGTGAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.21
29 13 0.54
30 6 0.25
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (29 bp):
TAAAAAGTAGAAAAACTAAATTATAAAAA
Found at i:34075905 original size:110 final size:110
Alignment explanation
Indices: 34075763--34075970 Score: 364
Period size: 110 Copynumber: 1.9 Consensus size: 110
34075753 ATGAATTTCT
*
34075763 CCCCCCCCCTTTGTAGATGATTGAGAATTAGAGTGAAATCAACCTTGTATGGTGGGTTATATTAT
1 CCCCCCCCCTTTGTAGATGATT-AGAATTAGAGTGAAATCAACCTTGTATGGTGGATTATATTAT
*
34075828 GTTATGTTCCTCCTTTCTCAGTATGGTTACCATCTCTCCCTCCTCC
65 GTTATGTTCCTCCTTGCTCAGTATGGTTACCATCTCTCCCTCCTCC
34075874 CCCCCCCCCTTTTGTAGATGATT-GAATTAGAGTGAAATCAACCTTGTATGGTGGATTATATTAT
1 CCCCCCCCC-TTTGTAGATGATTAGAATTAGAGTGAAATCAACCTTGTATGGTGGATTATATTAT
*
34075938 GTTATTTTCCTCCTTGCTCAGTATGGTTACCAT
65 GTTATGTTCCTCCTTGCTCAGTATGGTTACCAT
34075971 GATGATGGTA
Statistics
Matches: 93, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
110 71 0.76
111 9 0.10
112 13 0.14
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (110 bp):
CCCCCCCCCTTTGTAGATGATTAGAATTAGAGTGAAATCAACCTTGTATGGTGGATTATATTATG
TTATGTTCCTCCTTGCTCAGTATGGTTACCATCTCTCCCTCCTCC
Found at i:34082520 original size:24 final size:24
Alignment explanation
Indices: 34082493--34082542 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
34082483 CTTACTAATC
34082493 GAACAATTCCAAACTACAACCGAG
1 GAACAATTCCAAACTACAACCGAG
*
34082517 GAACAATTCCAAACTACAATCGAG
1 GAACAATTCCAAACTACAACCGAG
34082541 GA
1 GA
34082543 TACGGGTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.46, C:0.26, G:0.14, T:0.14
Consensus pattern (24 bp):
GAACAATTCCAAACTACAACCGAG
Found at i:34083370 original size:26 final size:27
Alignment explanation
Indices: 34083341--34083397 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 27
34083331 GGCGAAGGAA
34083341 AATTTT-TTTTTTGGGGGTTAGAATTG
1 AATTTTATTTTTTGGGGGTTAGAATTG
*
34083367 AATTTTAATTTTTTGGGTGTTAGAATTG
1 AATTTT-ATTTTTTGGGGGTTAGAATTG
34083395 AAT
1 AAT
34083398 GGTAATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 6 0.21
28 22 0.79
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.53
Consensus pattern (27 bp):
AATTTTATTTTTTGGGGGTTAGAATTG
Found at i:34083388 original size:28 final size:28
Alignment explanation
Indices: 34083347--34083408 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
34083337 GGAAAATTTT
**
34083347 TTTTTTGGGGGTTAGAATTGAATTTTAA
1 TTTTTTGGGGGTTAGAATTGAATGGTAA
*
34083375 TTTTTTGGGTGTTAGAATTGAATGGTAA
1 TTTTTTGGGGGTTAGAATTGAATGGTAA
34083403 TTTTTT
1 TTTTTT
34083409 TAGGTCAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.24, T:0.53
Consensus pattern (28 bp):
TTTTTTGGGGGTTAGAATTGAATGGTAA
Found at i:34083799 original size:17 final size:17
Alignment explanation
Indices: 34083772--34083815 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
34083762 TAAAATGTGT
34083772 TAATATTGAACTTAAACA
1 TAAT-TTGAACTTAAACA
*
34083790 TAATTTGAACTTAATCA
1 TAATTTGAACTTAAACA
*
34083807 TAATATGAA
1 TAATTTGAA
34083816 TACATGGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 20 0.83
18 4 0.17
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (17 bp):
TAATTTGAACTTAAACA
Found at i:34088569 original size:2 final size:2
Alignment explanation
Indices: 34088562--34088593 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
34088552 GGTTTCAATT
34088562 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
34088594 CCCCCCTCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:34090851 original size:16 final size:16
Alignment explanation
Indices: 34090815--34090854 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
34090805 AAAGTCTAAA
34090815 AAAAAATATATTTAAT
1 AAAAAATATATTTAAT
* *
34090831 AAAAAGTATATTTGAT
1 AAAAAATATATTTAAT
*
34090847 TAAAAATA
1 AAAAAATA
34090855 AAAATAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (16 bp):
AAAAAATATATTTAAT
Found at i:34093261 original size:31 final size:31
Alignment explanation
Indices: 34093220--34093279 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
34093210 TTATGAAATG
34093220 GTCACTGAACTATTTGAAAGTTTTCATTTAA
1 GTCACTGAACTATTTGAAAGTTTTCATTTAA
* *
34093251 GTCATTGAACTATTTGAAAGTTTTTATTT
1 GTCACTGAACTATTTGAAAGTTTTCATTT
34093280 GAGCCACTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (31 bp):
GTCACTGAACTATTTGAAAGTTTTCATTTAA
Found at i:34094918 original size:31 final size:32
Alignment explanation
Indices: 34094883--34094963 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 32
34094873 TTGGGTTCAA
* **
34094883 AACTAAAATTTTA-AAATTTGAAAAATACAAG
1 AACTAAAATTTGACAAATTCAAAAAATACAAG
* *
34094914 AACTAAAA-TTGACCAATTCAAAAAATACAGG
1 AACTAAAATTTGACAAATTCAAAAAATACAAG
34094945 AACTAAAA-TTGATCAAATT
1 AACTAAAATTTGA-CAAATT
34094964 ACAACTTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 3 0.07
31 34 0.81
32 5 0.12
ACGTcount: A:0.56, C:0.11, G:0.07, T:0.26
Consensus pattern (32 bp):
AACTAAAATTTGACAAATTCAAAAAATACAAG
Found at i:34099226 original size:223 final size:223
Alignment explanation
Indices: 34098826--34099266 Score: 623
Period size: 223 Copynumber: 2.0 Consensus size: 223
34098816 AACATGCTAG
* * * * *
34098826 CATCACTAACTCATGAAACTCTTTCCTTAAAATATTAGTATCTTACTAAATCTTTATTTTCTCTC
1 CATCACTAACTCATGAAACTCTTACCTTAAAACATTAGTATATCACTAAATCTTAATTTTCTCTC
* ** * *
34098891 TCCTCTAACATGAACATACAACTTTTCCACTTGAATATAACCTTTCTATGTTGTTCTAAACTTAA
66 TCCTCTAACATGAACATACAACCTCGCCACTTGAATATAACATTGCTATGTTGTTCTAAACTTAA
*
34098956 TTCCACTAAGAATTTCAATGGAAATTTTGTGGTTTCTGACAAAGGTTTGATAGCTATCGTGAAAA
131 TTCCACTAAGAATTTCAATAGAAATTTTGTGGTTTCTGACAAAGGTTTGATAGCTATCGTGAAAA
*
34099021 GAGACCAAACTGTATGGAAATGAGTTAA
196 GAGACCAAACTGTAAGGAAATGAGTTAA
* * *
34099049 CATCACTAACTCATGAAAGTCTTACCTTAAACCCTTAGTATATCACTAAATCTTAATTTTCTCTC
1 CATCACTAACTCATGAAACTCTTACCTTAAAACATTAGTATATCACTAAATCTTAATTTTCTCTC
* * *
34099114 TCCTTTAACATGAACATATAACCTCGCCACTTGAATATAACATTGCTATGTTGTTGTAAACTTAA
66 TCCTCTAACATGAACATACAACCTCGCCACTTGAATATAACATTGCTATGTTGTTCTAAACTTAA
* * * * * * *
34099179 TTTCATTAAGAATTTCAATAG-AATTTTGTTGGTTTTTGGCTAAGGTTTGATGGCTATCGTGAAG
131 TTCCACTAAGAATTTCAATAGAAATTTTG-TGGTTTCTGACAAAGGTTTGATAGCTATCGTGAAA
* *
34099243 AGGGACCAAATTGTAAGGAAATGA
195 AGAGACCAAACTGTAAGGAAATGA
34099267 AATTTTCCTT
Statistics
Matches: 190, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
222 7 0.04
223 183 0.96
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.37
Consensus pattern (223 bp):
CATCACTAACTCATGAAACTCTTACCTTAAAACATTAGTATATCACTAAATCTTAATTTTCTCTC
TCCTCTAACATGAACATACAACCTCGCCACTTGAATATAACATTGCTATGTTGTTCTAAACTTAA
TTCCACTAAGAATTTCAATAGAAATTTTGTGGTTTCTGACAAAGGTTTGATAGCTATCGTGAAAA
GAGACCAAACTGTAAGGAAATGAGTTAA
Found at i:34114769 original size:36 final size:35
Alignment explanation
Indices: 34114729--34114798 Score: 113
Period size: 36 Copynumber: 2.0 Consensus size: 35
34114719 CATCTCCGGA
34114729 GCTTGGCAAATAAGGAAAGTGATCTTTTGAAGATAT
1 GCTTGGCAAATAAGGAAAGTGATCTTTTG-AGATAT
* *
34114765 GCTTGGCAAATATGGAAGGTGATCTTTTGAGATA
1 GCTTGGCAAATAAGGAAAGTGATCTTTTGAGATA
34114799 CGTGATCCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 5 0.16
36 27 0.84
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.31
Consensus pattern (35 bp):
GCTTGGCAAATAAGGAAAGTGATCTTTTGAGATAT
Found at i:34115172 original size:48 final size:48
Alignment explanation
Indices: 34115100--34115191 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 48
34115090 AGGGATTCTG
** * *
34115100 TTGAATCCTTTATTGTTGCGAGTTAAGTTGACTTAGGCATTTTTACTA
1 TTGAATCCTTTATTACTGCAAGTTAAGCTGACTTAGGCATTTTTACTA
* *
34115148 TTGAATCCTTTATTACTGCAAGTTAGGCTGACTTAGGCGTTTTT
1 TTGAATCCTTTATTACTGCAAGTTAAGCTGACTTAGGCATTTTT
34115192 GAGCAAAGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.22, C:0.14, G:0.20, T:0.45
Consensus pattern (48 bp):
TTGAATCCTTTATTACTGCAAGTTAAGCTGACTTAGGCATTTTTACTA
Found at i:34119979 original size:35 final size:35
Alignment explanation
Indices: 34119918--34119988 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 35
34119908 CATCTCCGGA
34119918 GCTTGGCAAATAAGGAAAGTGATCTTTTGAAGATAT
1 GCTTGGCAAATAAGGAAAGTGATCTTTTG-AGATAT
**
34119954 GCTTGGCAAATGTGG-AAGTGATCTTTTGAGATAT
1 GCTTGGCAAATAAGGAAAGTGATCTTTTGAGATAT
34119988 G
1 G
34119989 TGATCCTAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 7 0.21
35 13 0.39
36 13 0.39
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.32
Consensus pattern (35 bp):
GCTTGGCAAATAAGGAAAGTGATCTTTTGAGATAT
Found at i:34120361 original size:48 final size:48
Alignment explanation
Indices: 34120287--34120380 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 48
34120277 AAGGGAATTT
* ** *
34120287 TGTTGAATCCTTTATTGTTGTGAGTTAAGCTGACTTAGGCGTTTTTAC
1 TGTTGAATCCTTTATTGCTGCAAGTTAAGCTGACTTAGCCGTTTTTAC
*
34120335 TGTTGAATCCTTTATTGCTGCAAGTTAGGCTGACTTAGCCGTTTTT
1 TGTTGAATCCTTTATTGCTGCAAGTTAAGCTGACTTAGCCGTTTTT
34120381 GAGCAAAGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.18, C:0.15, G:0.22, T:0.45
Consensus pattern (48 bp):
TGTTGAATCCTTTATTGCTGCAAGTTAAGCTGACTTAGCCGTTTTTAC
Found at i:34125176 original size:43 final size:42
Alignment explanation
Indices: 34125123--34125524 Score: 414
Period size: 43 Copynumber: 9.5 Consensus size: 42
34125113 ATACTAGGCC
* *
34125123 CCAAGGTGCCGATGGTGGTCGAGGCTCCCGCACATCTAAGCA
1 CCAAGGTGCCGATGGTGCTCGAGGCTCCCGCACATCCAAGCA
** * *
34125165 GTAAGGTTGCCGATGGTG-TCCGAGGCTCCCGCACATCCCAGCCC
1 CCAAGG-TGCCGATGGTGCT-CGAGGCTCCCGCACATCCAAG-CA
* * * *
34125209 CCAAGGTGCCGATGCTGGTCGAGGCTCCCGTACATCCGAGCCA
1 CCAAGGTGCCGATGGTGCTCGAGGCTCCCGCACATCCAAG-CA
* * *
34125252 CCAAGGT-CCTGATGCTGGTCGAGGCTCCCGCACATCCCAGCA
1 CCAAGGTGCC-GATGGTGCTCGAGGCTCCCGCACATCCAAGCA
* ** * *
34125294 CCAAGGTGTCGATGCAGCTCGAGGCTCCCGCATATCCGAGCCA
1 CCAAGGTGCCGATGGTGCTCGAGGCTCCCGCACATCCAAG-CA
* * *
34125337 CCAAGGTGTCGATGGTGCACGAGGCTCCCCCACATCCAAGCA
1 CCAAGGTGCCGATGGTGCTCGAGGCTCCCGCACATCCAAGCA
* * * *
34125379 CCAAGGTACCGATGAG-GCTCGAGGCTCCTGGACATCCCAGCA
1 CCAAGGTGCCGATG-GTGCTCGAGGCTCCCGCACATCCAAGCA
* * * *
34125421 CCAAGGTGCCGATGCTCCTCGGGGCTCCCGCACATCCGAGCCA
1 CCAAGGTGCCGATGGTGCTCGAGGCTCCCGCACATCCAAG-CA
* *
34125464 CCAAGGTACCGATGGTGCTCGAGGCTCCCACACATCCAAGCA
1 CCAAGGTGCCGATGGTGCTCGAGGCTCCCGCACATCCAAGCA
* *
34125506 CCAAGGTACCGATGCTGCT
1 CCAAGGTGCCGATGGTGCT
34125525 TGAGTCTCNN
Statistics
Matches: 305, Mismatches: 45, Indels: 20
0.82 0.12 0.05
Matches are distributed among these distances:
42 129 0.42
43 170 0.56
44 6 0.02
ACGTcount: A:0.21, C:0.36, G:0.28, T:0.16
Consensus pattern (42 bp):
CCAAGGTGCCGATGGTGCTCGAGGCTCCCGCACATCCAAGCA
Found at i:34125331 original size:85 final size:85
Alignment explanation
Indices: 34125106--34125524 Score: 391
Period size: 85 Copynumber: 4.9 Consensus size: 85
34125096 TTTCCTTTAG
* * * ** * ** **
34125106 CCCGCACATACTAGGCC-CCAAGGTGCCGATGGTGGTCGAGGCTCCCGCACATCTAAGCAGTAAG
1 CCCGCACATCCCA-GCCACCAAGGTACCGATGCAGCTCGAGGCTCCCGCACATCCGAGCACCAAG
* *
34125170 GTTGCCGATGGTG-TCCGAGGCT
65 G-TACCGATGCTGCT-CGAGGCT
* * * * *
34125192 CCCGCACATCCCAGCCCCCAAGGTGCCGATGCTGGTCGAGGCTCCCGTACATCCGAGCCACCAAG
1 CCCGCACATCCCAGCCACCAAGGTACCGATGCAGCTCGAGGCTCCCGCACATCCGAG-CACCAAG
*
34125257 GT-CCTGATGCTGGTCGAGGCT
65 GTACC-GATGCTGCTCGAGGCT
** *
34125278 CCCGCACATCCCAG-CACCAAGGTGTCGATGCAGCTCGAGGCTCCCGCATATCCGAGCCACCAAG
1 CCCGCACATCCCAGCCACCAAGGTACCGATGCAGCTCGAGGCTCCCGCACATCCGAG-CACCAAG
** * *
34125342 GTGTCGATGGTGCACGAGGCT
65 GTACCGATGCTGCTCGAGGCT
* * * * *
34125363 CCCCCACATCCAAG-CACCAAGGTACCGATG-AGGCTCGAGGCTCCTGGACATCCCAGCACCAAG
1 CCCGCACATCCCAGCCACCAAGGTACCGATGCA-GCTCGAGGCTCCCGCACATCCGAGCACCAAG
* * *
34125426 GTGCCGATGCTCCTCGGGGCT
65 GTACCGATGCTGCTCGAGGCT
* ** * *
34125447 CCCGCACATCCGAGCCACCAAGGTACCGATGGTGCTCGAGGCTCCCACACATCCAAGCACCAAGG
1 CCCGCACATCCCAGCCACCAAGGTACCGATGCAGCTCGAGGCTCCCGCACATCCGAGCACCAAGG
34125512 TACCGATGCTGCT
66 TACCGATGCTGCT
34125525 TGAGTCTCNN
Statistics
Matches: 284, Mismatches: 41, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
84 36 0.13
85 165 0.58
86 76 0.27
87 7 0.02
ACGTcount: A:0.21, C:0.36, G:0.27, T:0.16
Consensus pattern (85 bp):
CCCGCACATCCCAGCCACCAAGGTACCGATGCAGCTCGAGGCTCCCGCACATCCGAGCACCAAGG
TACCGATGCTGCTCGAGGCT
Found at i:34125435 original size:127 final size:127
Alignment explanation
Indices: 34125123--34125520 Score: 469
Period size: 127 Copynumber: 3.1 Consensus size: 127
34125113 ATACTAGGCC
* ** ** ** ***
34125123 CCAAGGTGCCGATGGTGGTCGAGGCTCCCGCACATCTAAGCAGTAAGGTTGCCGATG-GTGTCCG
1 CCAAGGTACCGATGCAGGTCGAGGCTCCCGCACATCCCAGCACCAAGG-TGCCGATGCACCT-CG
* * * * ** *
34125187 AGGCTCCCGCACATCCCAGCCCCCAAGGTGCCGATGCTGGTCGAGGCTCCCGTACATCCGAGCCA
64 AGGCTCCCGCACATCCGAGCCACCAAGGTGCCGATGGTGCTCGAGGCTCCCACACATCCAAG-CA
* * *
34125252 CCAAGGT-CCTGATGCTGGTCGAGGCTCCCGCACATCCCAGCACCAAGGTGTCGATGCAGCTCGA
1 CCAAGGTACC-GATGCAGGTCGAGGCTCCCGCACATCCCAGCACCAAGGTGCCGATGCACCTCGA
* * * *
34125316 GGCTCCCGCATATCCGAGCCACCAAGGTGTCGATGGTGCACGAGGCTCCCCCACATCCAAGCA
65 GGCTCCCGCACATCCGAGCCACCAAGGTGCCGATGGTGCTCGAGGCTCCCACACATCCAAGCA
* * * *
34125379 CCAAGGTACCGATG-AGGCTCGAGGCTCCTGGACATCCCAGCACCAAGGTGCCGATGCTCCTCGG
1 CCAAGGTACCGATGCAGG-TCGAGGCTCCCGCACATCCCAGCACCAAGGTGCCGATGCACCTCGA
*
34125443 GGCTCCCGCACATCCGAGCCACCAAGGTACCGATGGTGCTCGAGGCTCCCACACATCCAAGCA
65 GGCTCCCGCACATCCGAGCCACCAAGGTGCCGATGGTGCTCGAGGCTCCCACACATCCAAGCA
34125506 CCAAGGTACCGATGC
1 CCAAGGTACCGATGC
34125521 TGCTTGAGTC
Statistics
Matches: 233, Mismatches: 31, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
126 2 0.01
127 125 0.54
128 65 0.28
129 41 0.18
ACGTcount: A:0.21, C:0.36, G:0.28, T:0.16
Consensus pattern (127 bp):
CCAAGGTACCGATGCAGGTCGAGGCTCCCGCACATCCCAGCACCAAGGTGCCGATGCACCTCGAG
GCTCCCGCACATCCGAGCCACCAAGGTGCCGATGGTGCTCGAGGCTCCCACACATCCAAGCA
Found at i:34136889 original size:193 final size:193
Alignment explanation
Indices: 34136560--34136948 Score: 751
Period size: 193 Copynumber: 2.0 Consensus size: 193
34136550 ATCTTTCCTA
34136560 TTATTTCATTATTTTATTTATTTATTGTTTAATCGAATTTATCCTCAAAATATATATAAACACCA
1 TTATTTCATTATTTTATTTATTTATTGTTTAATCGAATTTATCCTCAAAATATATATAAACACCA
34136625 AAATAAACCCAATTACTAAATTGAAAGACTAAAAACTACATTAACCCATATATATAATAATTGCG
66 AAATAAACCCAATTACTAAATTGAAAGACTAAAAACTACATTAACCCATATATATAATAATTGCG
*
34136690 ATTGTGAAATTTAAGGAGACAAGACAGGTTGGGACAATGCTGTCGATGCTTGTCATTAAAAAT
131 ATTGTGAAATTTAAGGAGACAAGACACGTTGGGACAATGCTGTCGATGCTTGTCATTAAAAAT
*
34136753 TTATTTCATTATTTTATTTATTTATTGTTTAATGGAATTTATCCTCAAAATATATATAAACACCA
1 TTATTTCATTATTTTATTTATTTATTGTTTAATCGAATTTATCCTCAAAATATATATAAACACCA
34136818 AAATAAACCCAATTACTAAATTGAAAGACTAAAAACTACATTAACCCATATATATAATAATTGCG
66 AAATAAACCCAATTACTAAATTGAAAGACTAAAAACTACATTAACCCATATATATAATAATTGCG
*
34136883 ATTGTGAAATTTAAGGAGACAAGACACGTTGGGACCATGCTGTCGATGCTTGTCATTAAAAAT
131 ATTGTGAAATTTAAGGAGACAAGACACGTTGGGACAATGCTGTCGATGCTTGTCATTAAAAAT
34136946 TTA
1 TTA
34136949 CTTAATATAT
Statistics
Matches: 193, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
193 193 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (193 bp):
TTATTTCATTATTTTATTTATTTATTGTTTAATCGAATTTATCCTCAAAATATATATAAACACCA
AAATAAACCCAATTACTAAATTGAAAGACTAAAAACTACATTAACCCATATATATAATAATTGCG
ATTGTGAAATTTAAGGAGACAAGACACGTTGGGACAATGCTGTCGATGCTTGTCATTAAAAAT
Found at i:34147793 original size:2 final size:2
Alignment explanation
Indices: 34147786--34147821 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
34147776 CCGATCTTAC
34147786 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34147822 TGTGAAAGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34149353 original size:21 final size:20
Alignment explanation
Indices: 34149337--34149375 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
34149327 ATCACCTCCT
34149337 TCACCATCACCACCACCATCA
1 TCACCATCACCACCACC-TCA
*
34149358 TCATCATCACCACCACCT
1 TCACCATCACCACCACCT
34149376 TCACCTCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.31, C:0.51, G:0.00, T:0.18
Consensus pattern (20 bp):
TCACCATCACCACCACCTCA
Found at i:34149385 original size:3 final size:3
Alignment explanation
Indices: 34149379--34149409 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
34149369 ACCACCTTCA
*
34149379 CCT CCT CCT CCT CCT TCT CCT CCT CCT CCT C
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT C
34149410 AGGAACAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
CCT
Found at i:34149520 original size:39 final size:39
Alignment explanation
Indices: 34149476--34149555 Score: 126
Period size: 39 Copynumber: 2.1 Consensus size: 39
34149466 TCACCGTCAC
34149476 CATCACCGCCACCTCCTAAG-AAACAATCATCACCACCTT
1 CATCACCGCCACCTCCTAAGCAAA-AATCATCACCACCTT
* *
34149515 CATCACCTCCTCCTCCTAAGCAAAAATCATCACCACCTT
1 CATCACCGCCACCTCCTAAGCAAAAATCATCACCACCTT
34149554 CA
1 CA
34149556 GATAGCTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 35 0.92
40 3 0.08
ACGTcount: A:0.33, C:0.44, G:0.04, T:0.20
Consensus pattern (39 bp):
CATCACCGCCACCTCCTAAGCAAAAATCATCACCACCTT
Found at i:34155075 original size:17 final size:17
Alignment explanation
Indices: 34155053--34155087 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
34155043 GAAACAATTC
* *
34155053 AAACCCTAAATAATTTA
1 AAACCCAAAATAACTTA
34155070 AAACCCAAAATAACTTA
1 AAACCCAAAATAACTTA
34155087 A
1 A
34155088 GTCTCAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.57, C:0.20, G:0.00, T:0.23
Consensus pattern (17 bp):
AAACCCAAAATAACTTA
Found at i:34158678 original size:26 final size:26
Alignment explanation
Indices: 34158647--34158697 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
34158637 ATTTCATAAG
34158647 AAATTGCATAACTTCAATCTTACCAT
1 AAATTGCATAACTTCAATCTTACCAT
34158673 AAATTGCATAACTTCAATCTTACCA
1 AAATTGCATAACTTCAATCTTACCA
34158698 CTCTTTCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.39, C:0.24, G:0.04, T:0.33
Consensus pattern (26 bp):
AAATTGCATAACTTCAATCTTACCAT
Found at i:34159139 original size:24 final size:24
Alignment explanation
Indices: 34159106--34159153 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
34159096 TTACTTGGGT
34159106 AATTTGCCGTCAATTCATCCTTTA
1 AATTTGCCGTCAATTCATCCTTTA
*
34159130 AATTTTCCGTCAATTCATCCTTTA
1 AATTTGCCGTCAATTCATCCTTTA
34159154 CATTCGTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.25, G:0.06, T:0.44
Consensus pattern (24 bp):
AATTTGCCGTCAATTCATCCTTTA
Found at i:34159339 original size:101 final size:101
Alignment explanation
Indices: 34159151--34159390 Score: 363
Period size: 101 Copynumber: 2.4 Consensus size: 101
34159141 AATTCATCCT
* * * * * * *
34159151 TTACATTCGTAGTGCCATAACCCATTTATGGTATTATCATTAGAATGCCATAGCCCAGCTATGGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAACCCAGCTATGAT
* *
34159216 CTTACATATAAACACTGTCATGGTCTAACCATGGCC
66 CTTACATATAAACACTGCCATGGTCCAACCATGGCC
* *
34159252 TTACGTTCATAGTGCCATAACCCAGTTATAGTCTTATCATCAGAATGTCATAACCCAGCTATGAT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAACCCAGCTATGAT
*
34159317 CTTACATATAAACACTGCCATGGTCCAACCATGGTC
66 CTTACATATAAACACTGCCATGGTCCAACCATGGCC
*
34159353 TCACGTTCATAGTGCCATAACCCAGTTATGGTCTTATC
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATC
34159391 CGTCAATTCA
Statistics
Matches: 125, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
101 125 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (101 bp):
TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAACCCAGCTATGAT
CTTACATATAAACACTGCCATGGTCCAACCATGGCC
Found at i:34160374 original size:16 final size:16
Alignment explanation
Indices: 34160353--34160409 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
34160343 TTTGGTTCGC
*
34160353 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
34160369 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
34160385 TGTAATGGAGTAGAGG
1 TGTAATGGATTAGAGG
34160401 TGTAATGGA
1 TGTAATGGA
34160410 AAAGCTGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.28, C:0.00, G:0.39, T:0.33
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:34160670 original size:18 final size:17
Alignment explanation
Indices: 34160649--34160683 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
34160639 TTATTATTAA
*
34160649 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
34160667 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
34160684 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:34167541 original size:33 final size:33
Alignment explanation
Indices: 34167499--34167568 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
34167489 TTCAATGTTT
* *
34167499 CCATTTCCATGGA-TTCTAAATCCTCTAAGATCC
1 CCATTTCCATGCACTT-TAAATCCTCTAACATCC
*
34167532 CCATTTCCATGCACTTTAAATCCTTTAACATCC
1 CCATTTCCATGCACTTTAAATCCTCTAACATCC
34167565 CCAT
1 CCAT
34167569 GCTTTCCGGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 31 0.94
34 2 0.06
ACGTcount: A:0.27, C:0.33, G:0.06, T:0.34
Consensus pattern (33 bp):
CCATTTCCATGCACTTTAAATCCTCTAACATCC
Found at i:34168139 original size:2 final size:2
Alignment explanation
Indices: 34168132--34168168 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
34168122 TGTTACAAAC
34168132 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34168169 GATGTATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34168332 original size:43 final size:41
Alignment explanation
Indices: 34168265--34168352 Score: 149
Period size: 43 Copynumber: 2.1 Consensus size: 41
34168255 TAGTTTTACA
*
34168265 ATTTCGATTTTTTTTGTATGATCAAAGTATCATTCATATTT
1 ATTTCGATTTTTTTTGTATAATCAAAGTATCATTCATATTT
34168306 ATTTCGATTTTTTTTTTGTATAATCAAAGTATCATTCATATTT
1 ATTTCGA--TTTTTTTTGTATAATCAAAGTATCATTCATATTT
34168349 ATTT
1 ATTT
34168353 TATGGTCAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
41 7 0.16
43 37 0.84
ACGTcount: A:0.27, C:0.09, G:0.08, T:0.56
Consensus pattern (41 bp):
ATTTCGATTTTTTTTGTATAATCAAAGTATCATTCATATTT
Done.