Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 164 of 204
Found at i:49084101 original size:21 final size:20
Alignment explanation
Indices: 49084057--49084111 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
49084047 ATAATCTTGC
**
49084057 ATAACTTAATAACAACTTCC
1 ATAACTTAATAACAACTTAA
*
49084077 ATAACTTAATACACCACTTAA
1 ATAACTTAATA-ACAACTTAA
49084098 ATAACTTACATAAC
1 ATAACTTA-ATAAC
49084112 TTACATAGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 11 0.37
21 16 0.53
22 3 0.10
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (20 bp):
ATAACTTAATAACAACTTAA
Found at i:49084110 original size:9 final size:9
Alignment explanation
Indices: 49084092--49084301 Score: 91
Period size: 9 Copynumber: 23.7 Consensus size: 9
49084082 TTAATACACC
*
49084092 ACTTAAATA
1 ACTTACATA
49084101 ACTTACATA
1 ACTTACATA
49084110 ACTTACATA
1 ACTTACATA
*
49084119 GCTTACATA
1 ACTTACATA
* *
49084128 AC-T-CGTT
1 ACTTACATA
*
49084135 A-TAAGCATA
1 ACTTA-CATA
*
49084144 ACTTGCATA
1 ACTTACATA
49084153 ACTTACGTAATA
1 ACTTAC---ATA
*
49084165 ACATAGCATA
1 ACTTA-CATA
49084175 ACTTACATA
1 ACTTACATA
* *
49084184 GTAC--AAAAA
1 --ACTTACATA
49084193 ACTTACATA
1 ACTTACATA
*
49084202 ACTTAAATA
1 ACTTACATA
* * *
49084211 TCTGACACA
1 ACTTACATA
*
49084220 ACTTATATA
1 ACTTACATA
*
49084229 A--TACACA
1 ACTTACATA
49084236 ACTTACATA
1 ACTTACATA
* *
49084245 GCTTACTTA
1 ACTTACATA
49084254 A--TACATA
1 ACTTACATA
49084261 ACTTACATA
1 ACTTACATA
49084270 ACTT--ATA
1 ACTTACATA
* *
49084277 CACGTACCTA
1 -ACTTACATA
49084287 ACTTACATA
1 ACTTACATA
*
49084296 ATTTAC
1 ACTTAC
49084302 TTAATACATA
Statistics
Matches: 144, Mismatches: 38, Indels: 38
0.65 0.17 0.17
Matches are distributed among these distances:
7 19 0.13
8 4 0.03
9 101 0.70
10 10 0.07
11 2 0.01
12 7 0.05
13 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.31
Consensus pattern (9 bp):
ACTTACATA
Found at i:49084255 original size:25 final size:25
Alignment explanation
Indices: 49084219--49084309 Score: 82
Period size: 25 Copynumber: 3.6 Consensus size: 25
49084209 TATCTGACAC
49084219 AACTTA-TATAATACACAACTTACAT
1 AACTTACT-TAATACACAACTTACAT
* *
49084244 AGCTTACTTAATACATAACTTACAT
1 AACTTACTTAATACACAACTTACAT
49084269 AACTTA--TACACGTAC-CTAACTTACAT
1 AACTTACTTA-A--TACAC-AACTTACAT
*
49084295 AATTTACTTAATACA
1 AACTTACTTAATACA
49084310 TAAATATATA
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
23 2 0.04
24 1 0.02
25 29 0.55
26 18 0.34
27 1 0.02
28 2 0.04
ACGTcount: A:0.43, C:0.21, G:0.02, T:0.34
Consensus pattern (25 bp):
AACTTACTTAATACACAACTTACAT
Found at i:49089473 original size:21 final size:21
Alignment explanation
Indices: 49089447--49089518 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
49089437 CTACAACTTA
* * *
49089447 AAGCAGACGCGGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGAG
*
49089468 AAGCAGAGGCTGCAACGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
*
49089489 AAGCAGAGGCTACAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
49089510 AAGCAGAGG
1 AAGCAGAGG
49089519 TTCAAAAGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.36, C:0.19, G:0.42, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGAG
Found at i:49089963 original size:42 final size:42
Alignment explanation
Indices: 49089899--49090017 Score: 166
Period size: 42 Copynumber: 2.8 Consensus size: 42
49089889 GTTTTTGTAC
* * *
49089899 AAAAGCGCCGCTAAAGAACATGTTCTTCAGCGGTGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTCAGCGGCGCTTAGAA
* * *
49089941 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTATAT
1 AAAAACGCCGCTAAAGACCATGTTCTTCAGCGGCGCTTAGAA
* *
49089983 AAAAACGCCGCTAAAGACAATGTTCTTCAGTGGCG
1 AAAAACGCCGCTAAAGACCATGTTCTTCAGCGGCG
49090018 TTTTTCTCAA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.23
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGACCATGTTCTTCAGCGGCGCTTAGAA
Found at i:49090034 original size:42 final size:42
Alignment explanation
Indices: 49089899--49090051 Score: 164
Period size: 42 Copynumber: 3.6 Consensus size: 42
49089889 GTTTTTGTAC
* * * *
49089899 AAAAGCGCCGCTAAAGAACATGTTCTTCAGCGGTGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTCAGCGGCGCTTATAT
* *
49089941 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTATAT
1 AAAAACGCCGCTAAAGAACATGTTCTTCAGCGGCGCTTATAT
* * * *
49089983 AAAAACGCCGCTAAAG-ACAATGTTCTTCAGTGGCGTTTTTCT
1 AAAAACGCCGCTAAAGAAC-ATGTTCTTCAGCGGCGCTTATAT
* * * *
49090025 CAAAGCGCCGCTAAGGAATATGTTCTT
1 AAAAACGCCGCTAAAGAACATGTTCTT
49090052 TAGCAGCGTT
Statistics
Matches: 93, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
41 1 0.01
42 91 0.98
43 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGTTCTTCAGCGGCGCTTATAT
Found at i:49090061 original size:42 final size:41
Alignment explanation
Indices: 49089886--49090064 Score: 151
Period size: 42 Copynumber: 4.2 Consensus size: 41
49089876 CAAAAATAGT
* *
49089886 GGCGTTTTTGTACAAAAGCGCCGCTAAAGAACATGTTCTTCAGC
1 GGCGTTTTTATA-AAAA-CGCCGCTAAAGAA-ATGTTCTTTAGC
* * ** * *
49089930 GGTGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGC
1 GGCGTTTTTATAAAAACGCCGCTAAAGA-AATGTTCTTTAGC
* * * *
49089972 GGCGCTTATATAAAAACGCCGCTAAAGACAATGTTCTTCAGT
1 GGCGTTTTTATAAAAACGCCGCTAAAGA-AATGTTCTTTAGC
* * * *
49090014 GGCGTTTTTCTCAAAGCGCCGCTAAGGAATATGTTCTTTAGC
1 GGCGTTTTTATAAAAACGCCGCTAAAGAA-ATGTTCTTTAGC
*
49090056 AGCGTTTTT
1 GGCGTTTTT
49090065 GGTTGTAAAC
Statistics
Matches: 110, Mismatches: 23, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
41 1 0.01
42 99 0.90
43 4 0.04
44 6 0.05
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (41 bp):
GGCGTTTTTATAAAAACGCCGCTAAAGAAATGTTCTTTAGC
Found at i:49090145 original size:22 final size:21
Alignment explanation
Indices: 49090120--49090167 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
49090110 TTTTGCGGCG
49090120 CTTTAGGAAGCGCCGCAAATAA
1 CTTTA-GAAGCGCCGCAAATAA
49090142 CTTTA-AAGCGCCGCAAATAA
1 CTTTAGAAGCGCCGCAAATAA
49090162 CTTTAG
1 CTTTAG
49090168 TGGCGTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 20 0.80
22 5 0.20
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (21 bp):
CTTTAGAAGCGCCGCAAATAA
Found at i:49096167 original size:17 final size:18
Alignment explanation
Indices: 49096134--49096170 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
49096124 ATATTATTAT
49096134 AATAATTAAAATGAAAGA
1 AATAATTAAAATGAAAGA
49096152 AATAA-TAAAA-GAAAAGA
1 AATAATTAAAATG-AAAGA
49096169 AA
1 AA
49096171 GTGGAGACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 1 0.06
17 12 0.67
18 5 0.28
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (18 bp):
AATAATTAAAATGAAAGA
Found at i:49096206 original size:4 final size:4
Alignment explanation
Indices: 49096192--49096223 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
49096182 CAAATTAAAC
49096192 AAAG TAAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG -AAAG AAAG AAAG AAAG AAAG AAAG AAA
49096224 AGGAGAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:49097403 original size:43 final size:43
Alignment explanation
Indices: 49097355--49097456 Score: 107
Period size: 43 Copynumber: 2.3 Consensus size: 43
49097345 TTATGTGATT
*
49097355 GATATTGAAATGACAAATAAGAGAAATAAATATAAGATGAGAAA
1 GATATTGAAATGA-AAATAAGAGAAAGAAATATAAGATGAGAAA
* * * * *
49097399 -ATATTAAAATGGAAAATATGAGAAAGGATTATGAGATGAGAAA
1 GATATTGAAAT-GAAAATAAGAGAAAGAAATATAAGATGAGAAA
49097442 TGATATATGAAATGA
1 -GATAT-TGAAATGA
49097457 TGAATTGAGA
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
43 34 0.72
44 2 0.04
45 6 0.13
46 5 0.11
ACGTcount: A:0.55, C:0.01, G:0.21, T:0.24
Consensus pattern (43 bp):
GATATTGAAATGAAAATAAGAGAAAGAAATATAAGATGAGAAA
Found at i:49097439 original size:18 final size:19
Alignment explanation
Indices: 49097416--49097456 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
49097406 AATGGAAAAT
*
49097416 ATGAGAAAGGAT-TATGAG
1 ATGAGAAAGGATATATGAA
*
49097434 ATGAGAAATGATATATGAA
1 ATGAGAAAGGATATATGAA
49097453 ATGA
1 ATGA
49097457 TGAATTGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (19 bp):
ATGAGAAAGGATATATGAA
Found at i:49099556 original size:22 final size:22
Alignment explanation
Indices: 49099531--49099579 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
49099521 TTTTGCTGTT
* *
49099531 ATTTTACTGTTGTTTTACTACC
1 ATTTCACTGTTGTGTTACTACC
49099553 ATTTCACTGTTGTGTTACTACC
1 ATTTCACTGTTGTGTTACTACC
49099575 ATTTC
1 ATTTC
49099580 GTTATTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.18, C:0.20, G:0.10, T:0.51
Consensus pattern (22 bp):
ATTTCACTGTTGTGTTACTACC
Found at i:49102865 original size:125 final size:125
Alignment explanation
Indices: 49102669--49103104 Score: 640
Period size: 125 Copynumber: 3.5 Consensus size: 125
49102659 TTAGGGTTTT
* * *
49102669 GGATGCTTTATTAGAAGAATTTCTGAACTCGCGCCCACGTGGACGCGCTTGTGCTACAGTTGGTC
1 GGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTTGGTC
* * * * ** * *
49102734 CTGAAAAAATAATTTTGAGATGATGTTTTTGAGAAAATAGTATAAAAAACGCATCAAGCA
66 CTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCGAATAGTATAAAAAATGCTTCAAGCA
* * *
49102794 GGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGTGGACTCGCTTTTG-TAAGAGTTGGT
1 GGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCT-ACAGTTGGT
*
49102858 CCTGAAAAAATAATTTCGAGTTGACATTTCTGAGCGAATAGTATAAAAAATGCTTCAAGCA
65 CCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCGAATAGTATAAAAAATGCTTCAAGCA
* * * *
49102919 GGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTAGACGCACTCTTGCTACAGTAGGTC
1 GGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTTGGTC
*
49102984 CTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCGAATAGTATAAAAAAATACTTCAAGCA
66 CTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCGAATAGTAT-AAAAAATGCTTCAAGCA
* * *
49103045 GGATGCTTCATCAGAAGAATTTATGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
1 GGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
49103105 AGCATGTTTG
Statistics
Matches: 278, Mismatches: 30, Indels: 5
0.89 0.10 0.02
Matches are distributed among these distances:
124 1 0.00
125 206 0.74
126 71 0.26
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (125 bp):
GGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTTGGTC
CTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCGAATAGTATAAAAAATGCTTCAAGCA
Found at i:49106192 original size:12 final size:14
Alignment explanation
Indices: 49106175--49106208 Score: 54
Period size: 12 Copynumber: 2.6 Consensus size: 14
49106165 TTATATCATA
49106175 TTAGGGTTA-GG-T
1 TTAGGGTTAGGGTT
49106187 TTAGGGTTAGGGTT
1 TTAGGGTTAGGGTT
49106201 TTAGGGTT
1 TTAGGGTT
49106209 TAGAGTAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.45
13 2 0.10
14 9 0.45
ACGTcount: A:0.15, C:0.00, G:0.41, T:0.44
Consensus pattern (14 bp):
TTAGGGTTAGGGTT
Found at i:49106217 original size:20 final size:21
Alignment explanation
Indices: 49106184--49106229 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
49106174 ATTAGGGTTA
*
49106184 GGTTTAGGGTTAGGGTTTTAG
1 GGTTTAGAGTTAGGGTTTTAG
49106205 GGTTTAGAG-TAGGGTTTTAG
1 GGTTTAGAGTTAGGGTTTTAG
49106225 GGTTT
1 GGTTT
49106230 TAAGTTAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.15, C:0.00, G:0.41, T:0.43
Consensus pattern (21 bp):
GGTTTAGAGTTAGGGTTTTAG
Found at i:49106247 original size:28 final size:28
Alignment explanation
Indices: 49106193--49106250 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
49106183 AGGTTTAGGG
* *
49106193 TTAGGGTTTTAGGGTTTAGAGTAGGGTT
1 TTAGGGTTTTAGAGTTAAGAGTAGGGTT
*
49106221 TTAGGGTTTTA-AGTTAAGAGTTGGGGTT
1 TTAGGGTTTTAGAGTTAAGAG-TAGGGTT
49106249 TT
1 TT
49106251 TAAGTTAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 7 0.27
28 19 0.73
ACGTcount: A:0.19, C:0.00, G:0.36, T:0.45
Consensus pattern (28 bp):
TTAGGGTTTTAGAGTTAAGAGTAGGGTT
Found at i:49106251 original size:21 final size:21
Alignment explanation
Indices: 49106221--49106460 Score: 227
Period size: 21 Copynumber: 11.4 Consensus size: 21
49106211 GAGTAGGGTT
*
49106221 TTAGGG-TTTTAAGTTAAGAG
1 TTAGGGTTTTTAAGTTAAGGG
*
49106241 TTGGGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAAGTTAAGGG
*
49106262 TTATGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAAGTTAAGGG
* *
49106283 TTAGGATTTTTAAGTTAATGG
1 TTAGGGTTTTTAAGTTAAGGG
49106304 TTAGGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAAGTTAAGGG
49106325 TTTAGGGTTTTTAAGTTAAGGG
1 -TTAGGGTTTTTAAGTTAAGGG
*** * * * ***
49106347 TTATAATTATAAATTATAAATT
1 TTAGGGTTTTTAAGT-TAAGGG
*** * *
49106369 TATAAATTTTTATTAAATT-A-GT
1 T-T-AGGGTTT-TTAAGTTAAGGG
49106391 TTAGGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAAGTTAAGGG
*
49106412 TTAGGGTTTTTAGGTTAA-GG
1 TTAGGGTTTTTAAGTTAAGGG
49106432 TTAGGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAAGTTAAGGG
49106453 TTAGGGTT
1 TTAGGGTT
49106461 AGGGTTAGGA
Statistics
Matches: 179, Mismatches: 32, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
19 6 0.03
20 29 0.16
21 107 0.60
22 27 0.15
23 2 0.01
24 4 0.02
25 4 0.02
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.46
Consensus pattern (21 bp):
TTAGGGTTTTTAAGTTAAGGG
Found at i:49106294 original size:63 final size:64
Alignment explanation
Indices: 49106227--49106460 Score: 232
Period size: 64 Copynumber: 3.7 Consensus size: 64
49106217 GGTTTTAGGG
* *
49106227 TTTTAAGTTAA-GAGTTGGGGTTTTTAAGTTAAGGG-TTATGGTTTTTAAGTTAAGGGTTAGGAT
1 TTTTAAGTTAATG-GTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGAT
**
49106290 TTTTAAGTTAATGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTATAAT
1 TTTTAAGTTAATGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGAT
* * * *** **
49106354 TATAAATTATAAAT--TTATAAATTTTT-A-TTAAATTAGTTTAGGGTTTTTAAGTTAAGGGTTA
1 TTTTAAGT-T-AATGGTTA-GGGTTTTTAAGTT-AA-GGGTTTAGGGTTTTTAAGTTAAGGGTTA
*
49106415 GGGT
61 GGAT
*
49106419 TTTTAGGTTAA-GGTTAGGGTTTTTAAGTTAAGGG-TTAGGGTT
1 TTTTAAGTTAATGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
49106461 AGGGTTAGGA
Statistics
Matches: 136, Mismatches: 24, Indels: 23
0.74 0.13 0.13
Matches are distributed among these distances:
62 8 0.06
63 42 0.31
64 44 0.32
65 39 0.29
66 3 0.02
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (64 bp):
TTTTAAGTTAATGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGAT
Found at i:49106467 original size:33 final size:31
Alignment explanation
Indices: 49106411--49106491 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 31
49106401 TAAGTTAAGG
*
49106411 GTTAGGGTTTTTA-GGTTAAGGTTAGGGTTTTT
1 GTTAGGG--TTTAGGGTTAAGGTTAGGATTTTT
*
49106443 AAGTTAAGGG-TTAGGGTTAGGGTTAGGATTTTT
1 --GTT-AGGGTTTAGGGTTAAGGTTAGGATTTTT
49106476 GTTAGGGTTTAGGGTT
1 GTTAGGGTTTAGGGTT
49106492 TAAATTATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
30 4 0.10
31 11 0.26
32 3 0.07
33 17 0.40
34 3 0.07
35 4 0.10
ACGTcount: A:0.19, C:0.00, G:0.37, T:0.44
Consensus pattern (31 bp):
GTTAGGGTTTAGGGTTAAGGTTAGGATTTTT
Found at i:49106502 original size:7 final size:7
Alignment explanation
Indices: 49106492--49106523 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
49106482 GTTTAGGGTT
49106492 TAAATTA
1 TAAATTA
49106499 TAAATT-
1 TAAATTA
49106505 T-AATTA
1 TAAATTA
49106511 TAAATTA
1 TAAATTA
49106518 TAAATT
1 TAAATT
49106524 TTTAAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
5 4 0.17
6 2 0.09
7 17 0.74
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TAAATTA
Found at i:49106518 original size:155 final size:162
Alignment explanation
Indices: 49106220--49106574 Score: 458
Period size: 155 Copynumber: 2.2 Consensus size: 162
49106210 AGAGTAGGGT
* * *
49106220 TTTAGGG-TTTTAAGTTAAGAGTTGGGGTTTTTAAGTTAAGGGTTATGGTTTTTAAGTTAAGGGT
1 TTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGT
* * * **
49106284 TAGGATTTTTAAGTTAATGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTT
66 TAGG-----T--GTTAAGGGTTAGGATTTTT-AGTTAAGGGTTTAGGG-TTTTAAATTAAGAATT
*
49106349 ATAATTATAAATTATAAATTTATAAATTTTTATTAAATTAG
122 ATAATTATAAATTATAAATTTATAAATTTTTAATAAATTAG
*
49106390 TTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAGGTTAA-GGTTAGGGTTTTTAAGTTAAGGGT
1 TTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGT
49106454 TAGG-GTT-AGGGTTAGGATTTTT-GTT-AGGGTTTAGGG-TTTAAATTATA-AATT-TAATTAT
66 TAGGTGTTAAGGGTTAGGATTTTTAGTTAAGGGTTTAGGGTTTTAAATTA-AGAATTATAATTAT
*
49106512 AAATTATAAATTTTTAAATTTTTAATAAATTAG
130 AAATTATAAATTTATAAATTTTTAATAAATTAG
49106545 TTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
1 TTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
49106575 AGGGTTAGGG
Statistics
Matches: 172, Mismatches: 11, Indels: 19
0.85 0.05 0.09
Matches are distributed among these distances:
155 68 0.40
156 10 0.06
157 1 0.01
158 11 0.06
159 3 0.02
161 13 0.08
162 3 0.02
170 34 0.20
171 29 0.17
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (162 bp):
TTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGT
TAGGTGTTAAGGGTTAGGATTTTTAGTTAAGGGTTTAGGGTTTTAAATTAAGAATTATAATTATA
AATTATAAATTTATAAATTTTTAATAAATTAG
Found at i:49106661 original size:110 final size:112
Alignment explanation
Indices: 49106432--49106670 Score: 392
Period size: 110 Copynumber: 2.1 Consensus size: 112
49106422 TAGGTTAAGG
*
49106432 TTAGGGTTTTTAAGTTAAGGGTTAGGGTTAGGGTTAGGATTTTTGTTAGGGTTTAGGGTTTAAAT
1 TTAGGGTTTTTAAGTTAAGGGTTAGGGTTAGGGTTAGGATTTTTGTTAGGGTTT--GGTTCAAAT
* *
49106497 TATAAATTTAATTATAAATTATAAATTTTTAAATTTTTAATAAATTAGT
64 TATAAATTTAATTATAAACTATAAATTTATAAATTTTTAATAAATTAGT
* *
49106546 TTAGGGTTTTTAAGTTAAGGGTTAGGGTTAGGGTTAGGGTTTTTGTTAGGGTTT-G-TCAATTTA
1 TTAGGGTTTTTAAGTTAAGGGTTAGGGTTAGGGTTAGGATTTTTGTTAGGGTTTGGTTCAAATTA
*
49106609 TAAATTTAGTTATAAACTATAAATTTATAAATTTTTAATAAATTAGT
66 TAAATTTAATTATAAACTATAAATTTATAAATTTTTAATAAATTAGT
49106656 TTAGGGTTTTTAAGT
1 TTAGGGTTTTTAAGT
49106671 AGTACCTCAA
Statistics
Matches: 119, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
110 65 0.55
111 1 0.01
114 53 0.45
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (112 bp):
TTAGGGTTTTTAAGTTAAGGGTTAGGGTTAGGGTTAGGATTTTTGTTAGGGTTTGGTTCAAATTA
TAAATTTAATTATAAACTATAAATTTATAAATTTTTAATAAATTAGT
Found at i:49108998 original size:27 final size:28
Alignment explanation
Indices: 49108945--49108998 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 28
49108935 ATTTTTACGA
**
49108945 TTTAAAAAAATTTAAAAATATTAATTTT
1 TTTAAAAAAATTTAAAAATAAGAATTTT
* *
49108973 TTTAAAATAA-TTAAAAATAAGGATTT
1 TTTAAAAAAATTTAAAAATAAGAATTT
49108999 AAGAGAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 13 0.59
28 9 0.41
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (28 bp):
TTTAAAAAAATTTAAAAATAAGAATTTT
Found at i:49109062 original size:11 final size:10
Alignment explanation
Indices: 49109048--49109112 Score: 69
Period size: 11 Copynumber: 6.1 Consensus size: 10
49109038 AAATATGGAT
49109048 TTGAGAGAAA
1 TTGAGAGAAA
*
49109058 TTTGAAAGGAAA
1 -TTGAGA-GAAA
49109070 TTGAGAGCAAA
1 TTGAGAG-AAA
49109081 TTGAGAGCAAA
1 TTGAGAG-AAA
49109092 TTGAGAGGAAA
1 TTGAGA-GAAA
49109103 TTGAGA-AAA
1 TTGAGAGAAA
49109112 T
1 T
49109113 AATTGAGAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
9 4 0.08
10 1 0.02
11 39 0.80
12 5 0.10
ACGTcount: A:0.48, C:0.03, G:0.28, T:0.22
Consensus pattern (10 bp):
TTGAGAGAAA
Found at i:49109085 original size:33 final size:33
Alignment explanation
Indices: 49109048--49109122 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 33
49109038 AAATATGGAT
**
49109048 TTGAGAGAAATTTGAAAGGAAATTGAGAGCA-AA
1 TTGAGAGAAA-TTGAAAGGAAATTGAGAAAATAA
*
49109081 TTGAGAGCAAATTGAGAGGAAATTGAGAAAATAA
1 TTGAGAG-AAATTGAAAGGAAATTGAGAAAATAA
49109115 TTGAGAGA
1 TTGAGAGA
49109123 GTATTAGTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 25 0.68
34 12 0.32
ACGTcount: A:0.48, C:0.03, G:0.28, T:0.21
Consensus pattern (33 bp):
TTGAGAGAAATTGAAAGGAAATTGAGAAAATAA
Found at i:49109105 original size:22 final size:22
Alignment explanation
Indices: 49109048--49109108 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
49109038 AAATATGGAT
* *
49109048 TTGAGA-GAAATTTGAAAGGAAA
1 TTGAGAGGAAA-TTGAGAGCAAA
*
49109070 TTGAGAGCAAATTGAGAGCAAA
1 TTGAGAGGAAATTGAGAGCAAA
49109092 TTGAGAGGAAATTGAGA
1 TTGAGAGGAAATTGAGA
49109109 AAATAATTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 31 0.91
23 3 0.09
ACGTcount: A:0.46, C:0.03, G:0.30, T:0.21
Consensus pattern (22 bp):
TTGAGAGGAAATTGAGAGCAAA
Found at i:49109635 original size:15 final size:17
Alignment explanation
Indices: 49109634--49109670 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
49109624 ATATAAAAAA
49109634 ATAAAAAGAAGTAATAT
1 ATAAAAAGAAGTAATAT
*
49109651 AT-AAAATAA-TAATAT
1 ATAAAAAGAAGTAATAT
49109666 ATAAA
1 ATAAA
49109671 TGAGTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 8 0.44
16 8 0.44
17 2 0.11
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (17 bp):
ATAAAAAGAAGTAATAT
Found at i:49111084 original size:131 final size:132
Alignment explanation
Indices: 49110844--49111261 Score: 601
Period size: 131 Copynumber: 3.2 Consensus size: 132
49110834 TAGGAATTGG
** **
49110844 TAAT-TTCAACCTGTTCCACTGCAACTTCAGGGAGATAAGG-CTGGTGGCTTAAATCTGCTTCCC
1 TAATCTTCAACCTACTCCACTGCTGC-TCAGGGAGAT-AGGACTGGTGGCTTAAATCTGCTTCCC
* * * *
49110907 TACTACCTCGGGAAGATAAGACTCACCGTCTTTGATCTGCTCCACTACTGCTTTGGGAGACAAGA
64 TACTACCTCGGGAAGATAAGATTCACCATATTTGATCTGCTCCACTACTGCTTAGGGAGACAAGA
*
49110972 TATA
129 TCTA
* *
49110976 TAATCTTCAACCTATTCCACTACTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTT-CCTA
1 TAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTA
* *
49111040 CTATCTCGGGAAGATAAGATTCACCAT-TTTCGATCTGCTCCACTACTGCTTAGGGAGACAGGAT
66 CTACCTCGGGAAGATAAGATTCACCATATTT-GATCTGCTCCACTACTGCTTAGGGAGACAAGAT
49111104 CTA
130 CTA
*
49111107 GAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTA
1 TAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTA
* ** * *
49111172 CTACCTTGAAAAGATAAGATTCACCATATTTGATTTGCTCCACTACTGCTTAGGGAGACAAAATC
66 CTACCTCGGGAAGATAAGATTCACCATATTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATC
49111237 TA
131 TA
*
49111239 CAATCTTCAACCTACTCCACTGC
1 TAATCTTCAACCTACTCCACTGC
49111262 AAACTCAGAG
Statistics
Matches: 260, Mismatches: 21, Indels: 10
0.89 0.07 0.03
Matches are distributed among these distances:
130 3 0.01
131 121 0.47
132 116 0.45
133 20 0.08
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.29
Consensus pattern (132 bp):
TAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTA
CTACCTCGGGAAGATAAGATTCACCATATTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATC
TA
Found at i:49111381 original size:89 final size:89
Alignment explanation
Indices: 49111258--49111635 Score: 474
Period size: 89 Copynumber: 4.2 Consensus size: 89
49111248 ACCTACTCCA
* * * * *
49111258 CTGCAAACTC-AGAGAGGCAAGACTAGTGTTTTCGATCTGCTTCACTACCAGTACAGGAAGACAA
1 CTGCAAACTCAAG-GAGGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGCCAATACAGGAAGACAA
* * * *
49111322 GATCTGTTGTTTTCAGTTTGTTCTG
65 GATCTGCTATCTTCAGTCTGTTCTG
49111347 CTGCAAACTCAAGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGCCAATACAGGAAGACAAG
1 CTGCAAACTCAAGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGCCAATACAGGAAGACAAG
* *
49111412 ATATGCTATCTTTAGTCTGTT-TCG
66 ATCTGCTATCTTCAGTCTGTTCT-G
* * * *
49111436 CTGCAAACTC-AGAGAGGTAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAATACAGAAAGACAA
1 CTGCAAACTCAAG-GAGGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGCCAATACAGGAAGACAA
* *
49111500 GATCTGCTATCTTCAATCTGCTCTG
65 GATCTGCTATCTTCAGTCTGTTCTG
* * * * *
49111525 CTGCAAACTCAGGGAGGAAAGGCTGGTGTCTTTGATCTGCTTCGCTGCCAATATAGGAAGACAAG
1 CTGCAAACTCAAGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGCCAATACAGGAAGACAAG
* * *
49111590 ATCTGTTATCTTCAGTCAGTTCCG
66 ATCTGCTATCTTCAGTCTGTTCTG
*
49111614 CTGCAAACTCAGGGAGGCAAGG
1 CTGCAAACTCAAGGAGGCAAGG
49111636 ATTTGTAGCT
Statistics
Matches: 253, Mismatches: 31, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
88 3 0.01
89 246 0.97
90 4 0.02
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (89 bp):
CTGCAAACTCAAGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGCCAATACAGGAAGACAAG
ATCTGCTATCTTCAGTCTGTTCTG
Found at i:49111519 original size:45 final size:44
Alignment explanation
Indices: 49111375--49111530 Score: 129
Period size: 45 Copynumber: 3.5 Consensus size: 44
49111365 AAGGCTAGTG
* * *
49111375 TCTTCGATCTGCTTCGCTGCCAATACAGGAAGACAAGATATGCTA
1 TCTTCAATCTGCTTCGCTG-CAATACAGAAAGACAAGATCTGCTA
* * * * ** * * *
49111420 TCTTTAGTCTGTTTCGCTGCAA-ACTCAGAGAGGTAAG-GCTGGTG
1 TCTTCAATCTGCTTCGCTGCAATA--CAGAAAGACAAGATCTGCTA
*
49111464 TCTTCGATCTGCTTCGCTGTCAATACAGAAAGACAAGATCTGCTA
1 TCTTCAATCTGCTTCGCTG-CAATACAGAAAGACAAGATCTGCTA
49111509 TCTTCAATCTGC-TCTGCTGCAA
1 TCTTCAATCTGCTTC-GCTGCAA
49111531 ACTCAGGGAG
Statistics
Matches: 82, Mismatches: 23, Indels: 13
0.69 0.19 0.11
Matches are distributed among these distances:
43 1 0.01
44 35 0.43
45 45 0.55
46 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (44 bp):
TCTTCAATCTGCTTCGCTGCAATACAGAAAGACAAGATCTGCTA
Found at i:49111564 original size:178 final size:178
Alignment explanation
Indices: 49111258--49111635 Score: 522
Period size: 178 Copynumber: 2.1 Consensus size: 178
49111248 ACCTACTCCA
* * * *
49111258 CTGCAAACTCAGAGAGGCAAGACTAGTGTTTTCGATCTGCTTCACTACCAGTACAGGAAGACAAG
1 CTGCAAACTCAGAGAGGCAAGGCTAGTGTCTTCGATCTGCTTCACTACCAATACAGAAAGACAAG
* * * * * * *
49111323 ATCTGTTGTTTTCAGTTTGTTCTGCTGCAAACTCAAGGAGGCAAGGCTAGTGTCTTCGATCTGCT
66 ATCTGCTATCTTCAATCTGCTCTGCTGCAAACTCAAGGAGGAAAGGCTAGTGTCTTCGATCTGCT
* * *
49111388 TCGCTGCCAATACAGGAAGACAAGATATGCTATCTTTAGTCTGTTTCG
131 TCGCTGCCAATACAGGAAGACAAGATATGCTATCTTCAGTCAGTTCCG
* * * **
49111436 CTGCAAACTCAGAGAGGTAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAATACAGAAAGACAAG
1 CTGCAAACTCAGAGAGGCAAGGCTAGTGTCTTCGATCTGCTTCACTACCAATACAGAAAGACAAG
* * *
49111501 ATCTGCTATCTTCAATCTGCTCTGCTGCAAACTCAGGGAGGAAAGGCTGGTGTCTTTGATCTGCT
66 ATCTGCTATCTTCAATCTGCTCTGCTGCAAACTCAAGGAGGAAAGGCTAGTGTCTTCGATCTGCT
* * *
49111566 TCGCTGCCAATATAGGAAGACAAGATCTGTTATCTTCAGTCAGTTCCG
131 TCGCTGCCAATACAGGAAGACAAGATATGCTATCTTCAGTCAGTTCCG
*
49111614 CTGCAAACTCAGGGAGGCAAGG
1 CTGCAAACTCAGAGAGGCAAGG
49111636 ATTTGTAGCT
Statistics
Matches: 173, Mismatches: 27, Indels: 0
0.87 0.14 0.00
Matches are distributed among these distances:
178 173 1.00
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (178 bp):
CTGCAAACTCAGAGAGGCAAGGCTAGTGTCTTCGATCTGCTTCACTACCAATACAGAAAGACAAG
ATCTGCTATCTTCAATCTGCTCTGCTGCAAACTCAAGGAGGAAAGGCTAGTGTCTTCGATCTGCT
TCGCTGCCAATACAGGAAGACAAGATATGCTATCTTCAGTCAGTTCCG
Found at i:49111755 original size:44 final size:43
Alignment explanation
Indices: 49111638--49112037 Score: 186
Period size: 44 Copynumber: 9.0 Consensus size: 43
49111628 AGGCAAGGAT
* * *
49111638 TTGTAGCTTCAATCTGCTCTACTGCAACTTCATGGAGATAAGA
1 TTGTAACTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGA
* * *
49111681 TTCGCTATCTTCAGTTTGCTCCACTGCAACTTCAAGGAGATAAGA
1 TT-G-TAACTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGA
* *
49111726 CTTGTAACTTCAATCTACTCCACTACAACTTC-AGAGAGATAAGA
1 -TTGTAACTTCAATCTGCTCCACTGCAACTTCAAG-GAGATAAGA
* ** * * * * * *
49111770 TTATTGGCTTTAATCTCCTCCACTGCATCTTTAGGGAGATTAGA
1 TT-GTAACTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGA
* * * * *
49111814 TTCGT--CAT-GATTTGCTCTACTGCAACTTCAAAGAGATAAGATCA
1 TT-GTAACTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAG---A
* * * * * *
49111858 GTAATTTATAGCTTTAATCTGTTCCACTGCAA-TTTAGGGAAATAAGA
1 -T--TGTA-A-CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGA
* * *
49111905 TTTTCTATCTTCAGTCTGCTCCACTGCAACTTC-AGAGAGATAAGA
1 --TTGTAACTTCAATCTGCTCCACTGCAACTTCAAG-GAGATAAGA
* * * *
49111950 CT-TCACTTCAATCCGCTCCACTGCAACTTC-AGAGAGATAGGA
1 TTGTAACTTCAATCTGCTCCACTGCAACTTCAAG-GAGATAAGA
* *** * * * *
49111992 TTATTGGTTTTAATCTACTCCACTACAACTTCAGGGAGATAAGA
1 TT-GTAACTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGA
49112036 TT
1 TT
49112038 TGTCATCTTC
Statistics
Matches: 267, Mismatches: 67, Indels: 45
0.70 0.18 0.12
Matches are distributed among these distances:
41 23 0.09
42 38 0.14
43 7 0.03
44 116 0.43
45 49 0.18
46 6 0.02
47 2 0.01
48 1 0.00
50 12 0.04
51 13 0.05
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (43 bp):
TTGTAACTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGA
Found at i:49116577 original size:19 final size:20
Alignment explanation
Indices: 49116553--49116597 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
49116543 TGTGAAAATC
* *
49116553 TAATGCATATG-ATGTAATG
1 TAATGCAGATGCATGGAATG
49116572 TAATGCAGATGCATGGAATG
1 TAATGCAGATGCATGGAATG
49116592 -AATGCA
1 TAATGCA
49116598 AAAAGAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (20 bp):
TAATGCAGATGCATGGAATG
Found at i:49118535 original size:15 final size:14
Alignment explanation
Indices: 49118497--49118549 Score: 60
Period size: 15 Copynumber: 3.9 Consensus size: 14
49118487 GTTTGGAATA
49118497 AATAATATATAAA-
1 AATAATATATAAAG
49118510 AA-AATA-A-AAAG
1 AATAATATATAAAG
49118521 AAGTAATATATAAAG
1 AA-TAATATATAAAG
49118536 TAATAATATATAAA
1 -AATAATATATAAA
49118550 TGAGTTTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
10 3 0.09
11 3 0.09
12 4 0.12
13 6 0.18
14 1 0.03
15 15 0.44
16 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (14 bp):
AATAATATATAAAG
Found at i:49129796 original size:18 final size:19
Alignment explanation
Indices: 49129757--49129797 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
49129747 TAATATTAGA
*
49129757 ATATTTTAATTTTAGTACAT
1 ATATTTTAATTTTAG-AAAT
49129777 ATATTTTAATTTTA-AAAT
1 ATATTTTAATTTTAGAAAT
49129795 ATA
1 ATA
49129798 ATTATATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
20 14 0.70
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (19 bp):
ATATTTTAATTTTAGAAAT
Found at i:49129972 original size:22 final size:22
Alignment explanation
Indices: 49129947--49130017 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 22
49129937 ATTACATGGA
49129947 ACTATTTTTTATTAATTATTAT
1 ACTATTTTTTATTAATTATTAT
* *
49129969 ACTAATTTTAATTAAATTA-TAT
1 ACTATTTTTTATT-AATTATTAT
* *
49129991 AGTATTTATTATTTAATTATATAT
1 ACTATTTTTTA-TTAATTAT-TAT
49130015 ACT
1 ACT
49130018 TAGTTAAGGA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
22 26 0.68
23 7 0.18
24 5 0.13
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.56
Consensus pattern (22 bp):
ACTATTTTTTATTAATTATTAT
Found at i:49130562 original size:55 final size:55
Alignment explanation
Indices: 49130503--49130621 Score: 229
Period size: 55 Copynumber: 2.2 Consensus size: 55
49130493 ACTATTTGAT
49130503 AAATAAAATTTTAAAAAATTAAAAACAAAGTATTTGGATAATGTTTAAAGAAATA
1 AAATAAAATTTTAAAAAATTAAAAACAAAGTATTTGGATAATGTTTAAAGAAATA
*
49130558 AAATAAAATTTTAAAAATTTAAAAACAAAGTATTTGGATAATGTTTAAAGAAATA
1 AAATAAAATTTTAAAAAATTAAAAACAAAGTATTTGGATAATGTTTAAAGAAATA
49130613 AAATAAAAT
1 AAATAAAAT
49130622 AAAATAAAAA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 63 1.00
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.31
Consensus pattern (55 bp):
AAATAAAATTTTAAAAAATTAAAAACAAAGTATTTGGATAATGTTTAAAGAAATA
Found at i:49131340 original size:13 final size:13
Alignment explanation
Indices: 49131322--49131346 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49131312 AAAGTATAAA
49131322 AAATTAAAATATC
1 AAATTAAAATATC
49131335 AAATTAAAATAT
1 AAATTAAAATAT
49131347 AACAAATAAA
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATTAAAATATC
Found at i:49131797 original size:22 final size:22
Alignment explanation
Indices: 49131769--49131814 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
49131759 CAAAACTCAA
49131769 TGCCAGCGTGTCATATTTCCAT
1 TGCCAGCGTGTCATATTTCCAT
49131791 TGCCAGCGTGTCATATTTCCAT
1 TGCCAGCGTGTCATATTTCCAT
49131813 TG
1 TG
49131815 GTTTCCTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.26, G:0.20, T:0.37
Consensus pattern (22 bp):
TGCCAGCGTGTCATATTTCCAT
Found at i:49132511 original size:6 final size:6
Alignment explanation
Indices: 49132500--49132533 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
49132490 TGGGTAAGTG
*
49132500 TTTTGT TTTTGT TTTTGT TTTTTT TTTTGT TTTT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTT
49132534 TGTGTTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (6 bp):
TTTTGT
Found at i:49132541 original size:18 final size:18
Alignment explanation
Indices: 49132505--49132542 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
49132495 AAGTGTTTTG
*
49132505 TTTTTGTTTTTGTTTTTT
1 TTTTTGTTTTTGTTGTTT
49132523 TTTTTGTTTTT-TGTGTTT
1 TTTTTGTTTTTGT-TGTTT
49132541 TT
1 TT
49132543 CAAGAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (18 bp):
TTTTTGTTTTTGTTGTTT
Found at i:49139000 original size:26 final size:27
Alignment explanation
Indices: 49138960--49139012 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
49138950 GAAAATCAAT
49138960 CTTTTCAAGTCAGAAGGTTGAAAATGA
1 CTTTTCAAGTCAGAAGGTTGAAAATGA
* *
49138987 CTTTT-AAGTTAGAATGTTGAAAATGA
1 CTTTTCAAGTCAGAAGGTTGAAAATGA
49139013 GAGACAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.34
Consensus pattern (27 bp):
CTTTTCAAGTCAGAAGGTTGAAAATGA
Found at i:49142132 original size:5 final size:5
Alignment explanation
Indices: 49142122--49142147 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
49142112 ATGTCATTTA
49142122 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
49142148 CTTGAATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:49142313 original size:48 final size:46
Alignment explanation
Indices: 49142240--49142330 Score: 155
Period size: 48 Copynumber: 1.9 Consensus size: 46
49142230 TACGATATCC
*
49142240 TAACAATTTTATTAAATACATCATTTTAAAAAAAATAAAAAATAATTT
1 TAACAATTTTATTAAATACACCATTTT--AAAAAATAAAAAATAATTT
49142288 TAACAATTTTATTAAATACACCATTTTAAAAAATAAAAAATAA
1 TAACAATTTTATTAAATACACCATTTTAAAAAATAAAAAATAA
49142331 AAAATAAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
46 16 0.38
48 26 0.62
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (46 bp):
TAACAATTTTATTAAATACACCATTTTAAAAAATAAAAAATAATTT
Found at i:49142332 original size:6 final size:7
Alignment explanation
Indices: 49142314--49142338 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
49142304 TACACCATTT
49142314 TAAAAAA
1 TAAAAAA
49142321 TAAAAAA
1 TAAAAAA
49142328 TAAAAAA
1 TAAAAAA
49142335 TAAA
1 TAAA
49142339 TTTTATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAAAAA
Found at i:49144192 original size:12 final size:13
Alignment explanation
Indices: 49144175--49144203 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
49144165 TTCTGTCAAG
49144175 AGAATGAATAA-A
1 AGAATGAATAATA
49144187 AGAATGAATAATA
1 AGAATGAATAATA
49144200 AGAA
1 AGAA
49144204 AAGCCCATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (13 bp):
AGAATGAATAATA
Found at i:49144355 original size:28 final size:27
Alignment explanation
Indices: 49144270--49144363 Score: 100
Period size: 28 Copynumber: 3.4 Consensus size: 27
49144260 AAAATTAGCA
*
49144270 TGCTTATCGTATTATTTCGCACTTCGG
1 TGCTTATCGTATTATTTTGCACTTCGG
* * * *
49144297 TGCTTATTGT-TGTAAAATTTGAACTTTGG
1 TGCTTATCGTAT-T--ATTTTGCACTTCGG
49144326 TGCTTATCGTAATTATTTTGCACTTCGG
1 TGCTTATCGT-ATTATTTTGCACTTCGG
49144354 TGCTTATCGT
1 TGCTTATCGT
49144364 TATTTGTAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 9
0.75 0.13 0.13
Matches are distributed among these distances:
26 1 0.02
27 10 0.19
28 21 0.40
29 19 0.36
30 1 0.02
31 1 0.02
ACGTcount: A:0.18, C:0.16, G:0.19, T:0.47
Consensus pattern (27 bp):
TGCTTATCGTATTATTTTGCACTTCGG
Found at i:49153988 original size:37 final size:37
Alignment explanation
Indices: 49153945--49154084 Score: 246
Period size: 37 Copynumber: 3.8 Consensus size: 37
49153935 TTTGAGTACT
*
49153945 TCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
49153982 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
49154019 TCTGATCAAGAAGCAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
49154056 TCTGATC-AGAAACAAAGTGATAGGTGGCT
1 TCTGATCAAGAAACAAAGTGATAAGTGGCT
49154085 NNNNNNNNNN
Statistics
Matches: 99, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 20 0.20
37 79 0.80
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (37 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
Found at i:49155822 original size:2 final size:2
Alignment explanation
Indices: 49155815--49155847 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
49155805 TATGAAATTA
49155815 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
49155848 ATAAGAGTTT
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:49162371 original size:2 final size:2
Alignment explanation
Indices: 49162364--49162388 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
49162354 ATTTTTCTGT
49162364 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 T
49162389 TTATGAATAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49164136 original size:18 final size:19
Alignment explanation
Indices: 49164108--49164151 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
49164098 GTCTTGATTC
*
49164108 AAAATATTATAAAATTATT
1 AAAATATTATAAAATTATG
49164127 AAAA-ATTATAAAATTATG
1 AAAATATTATAAAATTATG
49164145 AAAATAT
1 AAAATAT
49164152 AATTTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
AAAATATTATAAAATTATG
Found at i:49166521 original size:14 final size:14
Alignment explanation
Indices: 49166502--49166531 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
49166492 AAGGATGTCA
49166502 TTTTGAAATTTAGG
1 TTTTGAAATTTAGG
49166516 TTTTGAAATTTAGG
1 TTTTGAAATTTAGG
49166530 TT
1 TT
49166532 GTCTATGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (14 bp):
TTTTGAAATTTAGG
Found at i:49167716 original size:31 final size:31
Alignment explanation
Indices: 49167681--49167744 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
49167671 CCTGGGCTCG
49167681 ACCCAACCCGAATTTTCAATAAAAAAACCTT
1 ACCCAACCCGAATTTTCAATAAAAAAACCTT
49167712 ACCCAACCCGAATTTTCAATAAAAAAACCTT
1 ACCCAACCCGAATTTTCAATAAAAAAACCTT
49167743 AC
1 AC
49167745 TATTTTTGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.45, C:0.30, G:0.03, T:0.22
Consensus pattern (31 bp):
ACCCAACCCGAATTTTCAATAAAAAAACCTT
Found at i:49177771 original size:22 final size:19
Alignment explanation
Indices: 49177732--49177773 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
49177722 TACAAAGTTG
49177732 ATAATAATTAATATATATT
1 ATAATAATTAATATATATT
49177751 ATAATAGATATAATTATATATT
1 ATAATA-AT-TAA-TATATATT
49177773 A
1 A
49177774 ATGATTGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 3 0.15
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
ATAATAATTAATATATATT
Found at i:49196982 original size:3 final size:3
Alignment explanation
Indices: 49196974--49197035 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
49196964 CACTTTTAGA
*
49196974 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTT TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
*
49197022 TTG TTT TTG TTG TT
1 TTG TTG TTG TTG TT
49197036 AAAAATTAGA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.00, C:0.00, G:0.29, T:0.71
Consensus pattern (3 bp):
TTG
Found at i:49205695 original size:27 final size:27
Alignment explanation
Indices: 49205665--49205716 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
49205655 AATGACCGAA
* *
49205665 ATACCCCCATCAGGTAAAATGACTGTT
1 ATACCCCCAGCAGATAAAATGACTGTT
* *
49205692 ATACCCCTAGGAGATAAAATGACTG
1 ATACCCCCAGCAGATAAAATGACTG
49205717 ATATGGCCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (27 bp):
ATACCCCCAGCAGATAAAATGACTGTT
Found at i:49206006 original size:28 final size:28
Alignment explanation
Indices: 49205961--49206015 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
49205951 CATTGTACTA
*
49205961 TTACTGTATTAGGCTAAGGCCCACACTG
1 TTACTGTATTAGGATAAGGCCCACACTG
*
49205989 TTACTGTATTGGGATAAGGCCCACACT
1 TTACTGTATTAGGATAAGGCCCACACT
49206016 ATACTGTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (28 bp):
TTACTGTATTAGGATAAGGCCCACACTG
Found at i:49218359 original size:49 final size:49
Alignment explanation
Indices: 49218306--49218405 Score: 155
Period size: 49 Copynumber: 2.0 Consensus size: 49
49218296 AGTAGAAGAG
* * *
49218306 AATTAAACATGAAGTAATTCATATATAAAATAAAACGAAACGAAATGAC
1 AATTAAACATGAAATAATTCATATAAAAAATAAAACAAAACGAAATGAC
* *
49218355 AATTAAACATGAAATAATTCATATAAAAAATAAGACAAAACGAATTGAC
1 AATTAAACATGAAATAATTCATATAAAAAATAAAACAAAACGAAATGAC
49218404 AA
1 AA
49218406 GTAGTAAAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.59, C:0.10, G:0.09, T:0.22
Consensus pattern (49 bp):
AATTAAACATGAAATAATTCATATAAAAAATAAAACAAAACGAAATGAC
Found at i:49219084 original size:28 final size:28
Alignment explanation
Indices: 49219051--49219108 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
49219041 TTAATTTAAT
49219051 TATAAA-TATATATAATTATTATT-TAACA
1 TATAAATTA-ATATAA-TATTATTATAACA
*
49219079 TATAAATTAATATAATATTTTTATAACA
1 TATAAATTAATATAATATTATTATAACA
49219107 TA
1 TA
49219109 ATATATTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 6 0.22
28 19 0.70
29 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (28 bp):
TATAAATTAATATAATATTATTATAACA
Found at i:49223066 original size:21 final size:22
Alignment explanation
Indices: 49223040--49223081 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
49223030 AAGGGACTTT
*
49223040 ATGATGATGTTTGAC-TATGAG
1 ATGATGATGTATGACTTATGAG
49223061 ATGATGATGTATGACTTATGA
1 ATGATGATGTATGACTTATGA
49223082 TTGTGAAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.31, C:0.05, G:0.26, T:0.38
Consensus pattern (22 bp):
ATGATGATGTATGACTTATGAG
Found at i:49224651 original size:42 final size:42
Alignment explanation
Indices: 49224546--49224695 Score: 133
Period size: 43 Copynumber: 3.5 Consensus size: 42
49224536 CAAAAAGCTC
* ** * *
49224546 ATACAATGCCAACGTCCCTTAC-GTGGTCTTACATGTAATCAA
1 ATACAATGCCAATGTCCCAGACAG-GGTCTTACACGTAACCAA
* * * *
49224588 ATAACGATGTCATTGTCCCAGACAGGGTCTTACACGTAACCAT
1 AT-ACAATGCCAATGTCCCAGACAGGGTCTTACACGTAACCAA
*
49224631 ATACAATGCCAATGTCCCAGACATGGTCTTACACGTAAATCACAA
1 ATACAATGCCAATGTCCCAGACAGGGTCTTACACGT-AA-C-CAA
* *
49224676 AT-CGATGCCAACGTCCCAGA
1 ATACAATGCCAATGTCCCAGA
49224696 TGTGCTCTTA
Statistics
Matches: 87, Mismatches: 16, Indels: 8
0.78 0.14 0.07
Matches are distributed among these distances:
42 32 0.37
43 33 0.38
44 18 0.21
45 4 0.05
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (42 bp):
ATACAATGCCAATGTCCCAGACAGGGTCTTACACGTAACCAA
Found at i:49225815 original size:13 final size:13
Alignment explanation
Indices: 49225797--49225821 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49225787 ACAAACGATA
49225797 AAATTTTCACACG
1 AAATTTTCACACG
49225810 AAATTTTCACAC
1 AAATTTTCACAC
49225822 TTATAAATTA
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:49228601 original size:52 final size:52
Alignment explanation
Indices: 49228505--49228604 Score: 130
Period size: 52 Copynumber: 1.9 Consensus size: 52
49228495 TTAGAAATGG
* * * **
49228505 TAAGAAAATATTATTTAATTATTTAATTTTATTCTTTTAATTATTATGATTT
1 TAAGAAAATATTAATAAATTATTTAATTTTAATCAGTTAATTATTATGATTT
*
49228557 TAAGAAAATATTAATAAATTATTTAATTTTAAAT-AGTTAGTTATTATG
1 TAAGAAAATATTAATAAATTATTTAATTTT-AATCAGTTAATTATTATG
49228605 TTGTTCAGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
52 39 0.95
53 2 0.05
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (52 bp):
TAAGAAAATATTAATAAATTATTTAATTTTAATCAGTTAATTATTATGATTT
Found at i:49230506 original size:3 final size:3
Alignment explanation
Indices: 49230452--49230491 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
49230442 AAGCAAATGT
49230452 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 A
49230492 ATTAAAGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:49231268 original size:2 final size:2
Alignment explanation
Indices: 49231261--49231352 Score: 63
Period size: 2 Copynumber: 47.0 Consensus size: 2
49231251 GATTGAATTG
*
49231261 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT GA- AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
* *
49231302 -T GAT -T AT TT GA- AT -T GAA AT GA- 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 AT AT
49231341 AT AT AT AT AT AT
1 AT AT AT AT AT AT
49231353 GTGTAAATGT
Statistics
Matches: 72, Mismatches: 6, Indels: 24
0.71 0.06 0.24
Matches are distributed among these distances:
1 7 0.10
2 62 0.86
3 3 0.04
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49231436 original size:16 final size:16
Alignment explanation
Indices: 49231402--49231444 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
49231392 AATTGAAATG
*
49231402 AATAT-ATATATGTGTA
1 AATATGATA-ATGTGCA
*
49231418 AATGTGATAATGTGCA
1 AATATGATAATGTGCA
49231434 AATATGATAAT
1 AATATGATAAT
49231445 TGGATATTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 20 0.87
17 3 0.13
ACGTcount: A:0.44, C:0.02, G:0.16, T:0.37
Consensus pattern (16 bp):
AATATGATAATGTGCA
Found at i:49236668 original size:3 final size:3
Alignment explanation
Indices: 49236660--49236685 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
49236650 AAATTAGTTA
49236660 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
49236686 AAGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:49242008 original size:3 final size:3
Alignment explanation
Indices: 49242000--49242034 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
49241990 ATATATCCTT
49242000 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
49242035 TAACTAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:49247377 original size:37 final size:37
Alignment explanation
Indices: 49247336--49247484 Score: 235
Period size: 37 Copynumber: 4.0 Consensus size: 37
49247326 GCTGAAGCTA
*
49247336 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
49247373 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
** *
49247410 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
***
49247447 CCACTTATCACTTTGTTTTTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
49247484 C
1 C
49247485 TAAAACTACC
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 106 1.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (37 bp):
CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
Found at i:49249527 original size:13 final size:13
Alignment explanation
Indices: 49249509--49249538 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
49249499 AGCCCAAACT
49249509 CAATTACCCAACC
1 CAATTACCCAACC
49249522 CAATTACCCAACC
1 CAATTACCCAACC
49249535 CAAT
1 CAAT
49249539 AAAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:49249737 original size:9 final size:9
Alignment explanation
Indices: 49249678--49249736 Score: 66
Period size: 9 Copynumber: 6.4 Consensus size: 9
49249668 AAAATAAAAA
49249678 AATTCGGGT
1 AATTCGGGT
49249687 AATTCGGGT
1 AATTCGGGT
*
49249696 ATTTTTC-GGT
1 A--ATTCGGGT
*
49249706 AATTCGGTT
1 AATTCGGGT
49249715 AATTCGGGT
1 AATTCGGGT
*
49249724 AATTTGGGT
1 AATTCGGGT
49249733 AATT
1 AATT
49249737 TTTAACCAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
8 3 0.07
9 32 0.76
10 4 0.10
11 3 0.07
ACGTcount: A:0.22, C:0.08, G:0.27, T:0.42
Consensus pattern (9 bp):
AATTCGGGT
Found at i:49250506 original size:12 final size:13
Alignment explanation
Indices: 49250466--49250504 Score: 69
Period size: 13 Copynumber: 2.9 Consensus size: 13
49250456 AAAAAATTAA
49250466 AAAAAGTATTTTTT
1 AAAAA-TATTTTTT
49250480 AAAAATATTTTTT
1 AAAAATATTTTTT
49250493 AAAAATATTTTT
1 AAAAATATTTTT
49250505 AACCCCTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 20 0.80
14 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (13 bp):
AAAAATATTTTTT
Found at i:49250552 original size:12 final size:11
Alignment explanation
Indices: 49250531--49250557 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
49250521 GGCAGTCTCA
49250531 AAAATATTTTT
1 AAAATATTTTT
49250542 AAAATATTTTT
1 AAAATATTTTT
49250553 AAAAT
1 AAAAT
49250558 TAACAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
AAAATATTTTT
Found at i:49250572 original size:18 final size:18
Alignment explanation
Indices: 49250539--49250694 Score: 101
Period size: 19 Copynumber: 8.6 Consensus size: 18
49250529 CAAAAATATT
* *
49250539 TTTAAAATATTTTTAAAA
1 TTTAAAAAAATTTTAAAA
49250557 -TTAACAAAAATTTT-AAA
1 TTTAA-AAAAATTTTAAAA
**
49250574 ---AAAAAAATTAACAAAA
1 TTTAAAAAAATT-TTAAAA
*
49250590 TTTAAAAATATTTTAAAA
1 TTTAAAAAAATTTTAAAA
*
49250608 -TTAAAAAATATTTAAAATA
1 TTTAAAAAA-ATTTTAAA-A
*
49250627 TTTAAAAATATTTTAAAA
1 TTTAAAAAAATTTTAAAA
**
49250645 TTTAAAAAAAATTAAAAAA
1 TTT-AAAAAAATTTTAAAA
*
49250664 GTATGTAAAAATATTTTAAAA
1 -T-T-TAAAAAAATTTTAAAA
49250685 -TTAAAAAAAT
1 TTTAAAAAAAT
49250695 AAATATATTT
Statistics
Matches: 107, Mismatches: 18, Indels: 27
0.70 0.12 0.18
Matches are distributed among these distances:
14 7 0.07
15 2 0.02
16 3 0.03
17 22 0.21
18 23 0.21
19 28 0.26
20 8 0.07
21 13 0.12
22 1 0.01
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (18 bp):
TTTAAAAAAATTTTAAAA
Found at i:49250585 original size:24 final size:22
Alignment explanation
Indices: 49250553--49250597 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 22
49250543 AAATATTTTT
49250553 AAAATTAACAAAAATTTTAAAAAA
1 AAAATTAAC-AAAA-TTTAAAAAA
49250577 AAAATTAACAAAATTTAAAAA
1 AAAATTAACAAAATTTAAAAA
49250598 TATTTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.38
23 4 0.19
24 9 0.43
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (22 bp):
AAAATTAACAAAATTTAAAAAA
Found at i:49250630 original size:37 final size:39
Alignment explanation
Indices: 49250573--49250693 Score: 169
Period size: 37 Copynumber: 3.2 Consensus size: 39
49250563 AAAATTTTAA
*
49250573 AAAAAAAATTAACAAA--ATTTAAAAATATTTTAAAATT
1 AAAAAAAATTAAAAAAGTATTTAAAAATATTTTAAAATT
* *
49250610 AAAAAATATT-TAAAA-TATTTAAAAATATTTTAAAATTT
1 AAAAAAAATTAAAAAAGTATTTAAAAATATTTTAAAA-TT
*
49250648 AAAAAAAATTAAAAAAGTATGTAAAAATATTTTAAAATT
1 AAAAAAAATTAAAAAAGTATTTAAAAATATTTTAAAATT
49250687 AAAAAAA
1 AAAAAAA
49250694 TAAATATATT
Statistics
Matches: 74, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
36 3 0.04
37 28 0.38
38 11 0.15
39 13 0.18
40 19 0.26
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (39 bp):
AAAAAAAATTAAAAAAGTATTTAAAAATATTTTAAAATT
Found at i:49250685 original size:10 final size:10
Alignment explanation
Indices: 49250589--49250685 Score: 85
Period size: 10 Copynumber: 10.0 Consensus size: 10
49250579 AATTAACAAA
49250589 ATTTAAAAAT
1 ATTTAAAAAT
*
49250599 ATTT-TAAA-
1 ATTTAAAAAT
*
49250607 ATTAAAAAAT
1 ATTTAAAAAT
49250617 ATTT-AAAAT
1 ATTTAAAAAT
49250626 ATTTAAAAAT
1 ATTTAAAAAT
*
49250636 ATTTTAAAAT
1 ATTTAAAAAT
* *
49250646 -TTAAAAAAA
1 ATTTAAAAAT
*
49250655 ATTAAAAAAGT
1 ATTTAAAAA-T
*
49250666 ATGTAAAAAT
1 ATTTAAAAAT
*
49250676 ATTTTAAAAT
1 ATTTAAAAAT
49250686 TAAAAAAATA
Statistics
Matches: 69, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
8 3 0.04
9 21 0.30
10 38 0.55
11 7 0.10
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (10 bp):
ATTTAAAAAT
Found at i:49255285 original size:67 final size:67
Alignment explanation
Indices: 49255177--49255311 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
49255167 TAGTAGAGTT
49255177 AGAAATTTAATTCTTTTAGGTTTAATATATCAAAAAGTCCCTGTAAAATAATTTTATAATCAATT
1 AGAAATTTAATTCTTTTAGGTTTAATATATCAAAAAGTCCCTGTAAAATAATTTTATAATCAATT
49255242 GA
66 GA
49255244 AGAAATTTAATTCTTTTAGGTTTAATATATCAAAAAGTCCCTGTAAAATAATTTTATAATCAATT
1 AGAAATTTAATTCTTTTAGGTTTAATATATCAAAAAGTCCCTGTAAAATAATTTTATAATCAATT
49255309 GA
66 GA
49255311 A
1 A
49255312 CCATCAATTA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (67 bp):
AGAAATTTAATTCTTTTAGGTTTAATATATCAAAAAGTCCCTGTAAAATAATTTTATAATCAATT
GA
Found at i:49255939 original size:13 final size:13
Alignment explanation
Indices: 49255920--49255952 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
49255910 GGCCTGTGGC
49255920 AAAAAATAAAA-A
1 AAAAAATAAAATA
49255932 ATAAAAATAAAATA
1 A-AAAAATAAAATA
49255946 AAAAAAT
1 AAAAAAT
49255953 TTATTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.05
13 16 0.84
14 2 0.11
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAAATAAAATA
Found at i:49259774 original size:17 final size:18
Alignment explanation
Indices: 49259742--49259775 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
49259732 AAAAATTCAG
*
49259742 AAAATTATACATAAAAAT
1 AAAATTATACAAAAAAAT
49259760 AAAATT-TACAAAAAAA
1 AAAATTATACAAAAAAA
49259776 ATACAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAATTATACAAAAAAAT
Found at i:49259838 original size:32 final size:33
Alignment explanation
Indices: 49259802--49259869 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 33
49259792 ATATTAGTTG
* * *
49259802 AAATTAATAATATTATTACA-AAATATGTAAAA
1 AAATTAATAAAATTATAAAACAAATATGTAAAA
* *
49259834 AAATTTATAAAATTATAAAACAAATATTTAAAA
1 AAATTAATAAAATTATAAAACAAATATGTAAAA
49259867 AAA
1 AAA
49259870 AGCTTAAAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
32 16 0.53
33 14 0.47
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.32
Consensus pattern (33 bp):
AAATTAATAAAATTATAAAACAAATATGTAAAA
Found at i:49259994 original size:20 final size:21
Alignment explanation
Indices: 49259950--49260004 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
49259940 GAAATTTAAA
49259950 TATTTTTAATTTTT-TATAAC
1 TATTTTTAATTTTTATATAAC
* *
49259970 AATTTTTAATTTTTATAT-AT
1 TATTTTTAATTTTTATATAAC
*
49259990 TATTTTGAATTTTTA
1 TATTTTTAATTTTTA
49260005 AAATTTATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 27 0.90
21 3 0.10
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (21 bp):
TATTTTTAATTTTTATATAAC
Found at i:49260329 original size:22 final size:21
Alignment explanation
Indices: 49260294--49260352 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
49260284 TCTAATAGTG
*
49260294 TCAAGTGGTAGGTCAATGCCCGA
1 TCAA-TGGTTGGTCAATG-CCGA
* * *
49260317 TTAATGGTTGGTCAATGCTGG
1 TCAATGGTTGGTCAATGCCGA
49260338 TCAATGGTTGGTCAA
1 TCAATGGTTGGTCAA
49260353 CATTGATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 16 0.52
22 12 0.39
23 3 0.10
ACGTcount: A:0.24, C:0.15, G:0.31, T:0.31
Consensus pattern (21 bp):
TCAATGGTTGGTCAATGCCGA
Found at i:49260333 original size:11 final size:11
Alignment explanation
Indices: 49260319--49260352 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
49260309 ATGCCCGATT
49260319 AATGGTTGGTC
1 AATGGTTGGTC
*
49260330 AAT-GCTGGTC
1 AATGGTTGGTC
49260340 AATGGTTGGTC
1 AATGGTTGGTC
49260351 AA
1 AA
49260353 CATTGATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.24, C:0.12, G:0.32, T:0.32
Consensus pattern (11 bp):
AATGGTTGGTC
Found at i:49260424 original size:13 final size:13
Alignment explanation
Indices: 49260408--49260432 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49260398 AAATATTTAA
49260408 TATTTTAATTTTC
1 TATTTTAATTTTC
49260421 TATTTTAATTTT
1 TATTTTAATTTT
49260433 AATTTAATAA
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:0.04, G:0.00, T:0.72
Consensus pattern (13 bp):
TATTTTAATTTTC
Found at i:49260445 original size:14 final size:15
Alignment explanation
Indices: 49260426--49260464 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
49260416 TTTTCTATTT
49260426 TAATTTTAATTT-AA
1 TAATTTTAATTTAAA
49260440 TAATTTT-ATTTAAA
1 TAATTTTAATTTAAA
*
49260454 TAAATTTAATT
1 TAATTTTAATT
49260465 GACATGTGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 4 0.18
14 15 0.68
15 3 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TAATTTTAATTTAAA
Found at i:49260450 original size:19 final size:18
Alignment explanation
Indices: 49260394--49260450 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 18
49260384 ATTTTTTAAT
49260394 ATTTAAATATTTAATATTTTA
1 ATTT-AATATTT--TATTTTA
**
49260415 ATTTTCTATTTTAATTTTA
1 ATTTAATATTTT-ATTTTA
49260434 ATTTAATAATTTTATTT
1 ATTTAAT-ATTTTATTT
49260451 AAATAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
18 1 0.03
19 15 0.50
20 10 0.33
21 4 0.13
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTAATATTTTATTTTA
Found at i:49262087 original size:39 final size:40
Alignment explanation
Indices: 49261995--49262129 Score: 150
Period size: 39 Copynumber: 3.4 Consensus size: 40
49261985 TTTGGATAAA
* *
49261995 AAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTACAT
1 AAAACGCCGCTAAAAATCGAGCATTAGTGGCGCTTTACAG
* *
49262035 AAAACGCCACTAAAGATCGAGCA-TAGTGGCGCTTTA-AGG
1 AAAACGCCGCTAAAAATCGAGCATTAGTGGCGCTTTACA-G
** * *
49262074 AAAGTGCCGCTAAAAAT-GAGCATTAGTGGCGTTTTTCTAG
1 AAAACGCCGCTAAAAATCGAGCATTAGTGGCGCTTTAC-AG
*
49262114 AAAACGCCGCAAAAAA
1 AAAACGCCGCTAAAAA
49262130 CGTAAGCCCA
Statistics
Matches: 78, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
38 6 0.08
39 36 0.46
40 35 0.45
41 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (40 bp):
AAAACGCCGCTAAAAATCGAGCATTAGTGGCGCTTTACAG
Found at i:49262269 original size:41 final size:41
Alignment explanation
Indices: 49262167--49262488 Score: 486
Period size: 41 Copynumber: 7.9 Consensus size: 41
49262157 CCTTTCGGGG
* * *
49262167 CTTTAGCGGCGTTTTTGAAAAAGCGCCACTAATGCTCGGGA
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGT
49262208 CTTT-GCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGT
* * *
49262248 CTTTAGCGGCGTCTTTGAAAAAGCGCCACTAATGCTCTAGT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGT
49262289 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGT
** * *
49262330 CTTTAGCGGCG-TTTTGAAAAAGCGCCATTAATGCTCGGGA
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGT
* *
49262370 CTTTAGTGGCGTTTTTAAAAAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGT
*
49262411 CTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGT
* * *
49262452 CTTTAGTGGCATTTTCGAAAAAGCGCCGCTAATGCTC
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
49262489 AAAAATATTT
Statistics
Matches: 255, Mismatches: 24, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
40 72 0.28
41 183 0.72
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.30
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGT
Found at i:49262346 original size:81 final size:82
Alignment explanation
Indices: 49262167--49262488 Score: 504
Period size: 81 Copynumber: 4.0 Consensus size: 82
49262157 CCTTTCGGGG
49262167 CTTTAGCGGCGTTTTTGAAAAAGCGCCACTAATGCTCGGGACTTT-GCGGCGTTTTTGAAAAAGC
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCACTAATGCTCGGGACTTTAGCGGCGTTTTTGAAAAAGC
49262231 GCCGCTAATGCTCTGGT
66 GCCGCTAATGCTCTGGT
* ** *
49262248 CTTTAGCGGCGTCTTTGAAAAAGCGCCACTAATGCTCTAGTCTTTAGCGGCGTTTTTGAAAAAGC
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCACTAATGCTCGGGACTTTAGCGGCGTTTTTGAAAAAGC
49262313 GCCGCTAATGCTCTGGT
66 GCCGCTAATGCTCTGGT
* * *
49262330 CTTTAGCGGCG-TTTTGAAAAAGCGCCATTAATGCTCGGGACTTTAGTGGCGTTTTTAAAAAAGC
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCACTAATGCTCGGGACTTTAGCGGCGTTTTTGAAAAAGC
49262394 GCCGCTAATGCTCTGGT
66 GCCGCTAATGCTCTGGT
* * * * * * *
49262411 CTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCTGGTCTTTAGTGGCATTTTCGAAAAAGC
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCACTAATGCTCGGGACTTTAGCGGCGTTTTTGAAAAAGC
49262476 GCCGCTAATGCTC
66 GCCGCTAATGCTC
49262489 AAAAATATTT
Statistics
Matches: 220, Mismatches: 19, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
81 115 0.52
82 105 0.48
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.30
Consensus pattern (82 bp):
CTTTAGCGGCGTTTTTGAAAAAGCGCCACTAATGCTCGGGACTTTAGCGGCGTTTTTGAAAAAGC
GCCGCTAATGCTCTGGT
Found at i:49262391 original size:122 final size:122
Alignment explanation
Indices: 49262167--49262488 Score: 484
Period size: 122 Copynumber: 2.6 Consensus size: 122
49262157 CCTTTCGGGG
* * *
49262167 CTTTAGCGGCGTTTTTGAAAAAGCGCCACTAATGCTCGGGACTTT-GCGGCGTTTTTGAAAAAGC
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCG-TTTTGAAAAAGC
* * *
49262231 GCCGCTAATGCTCTGGTCTTTAGCGGCGTCTTTGAAAAAGCGCCACTAATGCTCTAGT
65 GCCGCTAATGCTCGGGACTTTAGCGGCGTCTTTAAAAAAGCGCCACTAATGCTCTAGT
49262289 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTGAAAAAGCG
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTGAAAAAGCG
** * * * *
49262354 CCATTAATGCTCGGGACTTTAGTGGCGTTTTTAAAAAAGCGCCGCTAATGCTCTGGT
66 CCGCTAATGCTCGGGACTTTAGCGGCGTCTTTAAAAAAGCGCCACTAATGCTCTAGT
* * *
49262411 CTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCTGGTCTTTAGTGGCATTTTCGAAAAAGC
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTT-GAAAAAGC
49262476 GCCGCTAATGCTC
65 GCCGCTAATGCTC
49262489 AAAAATATTT
Statistics
Matches: 181, Mismatches: 17, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
122 156 0.86
123 25 0.14
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.30
Consensus pattern (122 bp):
CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTGAAAAAGCG
CCGCTAATGCTCGGGACTTTAGCGGCGTCTTTAAAAAAGCGCCACTAATGCTCTAGT
Found at i:49262914 original size:14 final size:15
Alignment explanation
Indices: 49262886--49262918 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
49262876 AAGGTTTATA
49262886 GATTATGGAATTAGG
1 GATTATGGAATTAGG
49262901 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
49262915 GATT
1 GATT
49262919 CTGGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:49263169 original size:14 final size:14
Alignment explanation
Indices: 49263152--49263218 Score: 64
Period size: 14 Copynumber: 4.8 Consensus size: 14
49263142 TTAGGGATTT
49263152 GGGTTAGAGTTTAG
1 GGGTTAGAGTTTAG
* *
49263166 GGGTTAGAGATT-C
1 GGGTTAGAGTTTAG
* *
49263179 GGTTTAGGGTTTAG
1 GGGTTAGAGTTTAG
* *
49263193 GGGTTAGACTTTAT
1 GGGTTAGAGTTTAG
49263207 GGGTTAAGAGTT
1 GGGTT-AGAGTT
49263219 AGAGATTTAG
Statistics
Matches: 40, Mismatches: 11, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
13 9 0.22
14 26 0.65
15 5 0.12
ACGTcount: A:0.21, C:0.03, G:0.39, T:0.37
Consensus pattern (14 bp):
GGGTTAGAGTTTAG
Found at i:49263172 original size:27 final size:27
Alignment explanation
Indices: 49263142--49263200 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
49263132 TTTAATTGGT
* *
49263142 TTAGGGATTTGGGTTAGAGTTTAGGGG
1 TTAGAGATTCGGGTTAGAGTTTAGGGG
* *
49263169 TTAGAGATTCGGTTTAGGGTTTAGGGG
1 TTAGAGATTCGGGTTAGAGTTTAGGGG
49263196 TTAGA
1 TTAGA
49263201 CTTTATGGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.20, C:0.02, G:0.41, T:0.37
Consensus pattern (27 bp):
TTAGAGATTCGGGTTAGAGTTTAGGGG
Found at i:49263571 original size:23 final size:23
Alignment explanation
Indices: 49263536--49263721 Score: 178
Period size: 23 Copynumber: 7.6 Consensus size: 23
49263526 AGATTTAAAT
*
49263536 AATAA-TTTAAATATAATTAATA
1 AATAAGTTTAAATAGAATTAATA
* *
49263558 AATAAGTTTAAATAAAATATATTTA
1 AATAAGTTTAAATAGAAT-TA-ATA
49263583 AATATTAGTTTAAATAGAATTAATA
1 AATA--AGTTTAAATAGAATTAATA
* *
49263608 AATAAGTTTAAATAAAATATATTTA
1 AATAAGTTTAAATAGAAT-TA-ATA
49263633 AATATTAGTTTAAATAGAATTAATA
1 AATA--AGTTTAAATAGAATTAATA
*
49263658 AATAAGTTTAAAT-GAAATATATTTA
1 AATAAGTTTAAATAG-AAT-TA-ATA
49263683 AATATTAGTTTAAATAGAATTAATA
1 AATA--AGTTTAAATAGAATTAATA
*
49263708 ATTAAGTTTAAATA
1 AATAAGTTTAAATA
49263722 AAATATATTT
Statistics
Matches: 138, Mismatches: 11, Indels: 29
0.78 0.06 0.16
Matches are distributed among these distances:
22 6 0.04
23 46 0.33
24 6 0.04
25 35 0.25
26 6 0.04
27 38 0.28
28 1 0.01
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (23 bp):
AATAAGTTTAAATAGAATTAATA
Found at i:49263595 original size:50 final size:50
Alignment explanation
Indices: 49263528--49263738 Score: 377
Period size: 50 Copynumber: 4.2 Consensus size: 50
49263518 CATTTGATAG
* * *
49263528 ATTTAAATAATAATTTAAATATAATTAATAAATAAGTTTAAATAAAATAT
1 ATTTAAATATTAGTTTAAATAGAATTAATAAATAAGTTTAAATAAAATAT
49263578 ATTTAAATATTAGTTTAAATAGAATTAATAAATAAGTTTAAATAAAATAT
1 ATTTAAATATTAGTTTAAATAGAATTAATAAATAAGTTTAAATAAAATAT
*
49263628 ATTTAAATATTAGTTTAAATAGAATTAATAAATAAGTTTAAATGAAATAT
1 ATTTAAATATTAGTTTAAATAGAATTAATAAATAAGTTTAAATAAAATAT
*
49263678 ATTTAAATATTAGTTTAAATAGAATTAATAATTAAGTTTAAATAAAATAT
1 ATTTAAATATTAGTTTAAATAGAATTAATAAATAAGTTTAAATAAAATAT
49263728 ATTTAAATATT
1 ATTTAAATATT
49263739 TAAATATTAG
Statistics
Matches: 155, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 155 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (50 bp):
ATTTAAATATTAGTTTAAATAGAATTAATAAATAAGTTTAAATAAAATAT
Found at i:49263604 original size:15 final size:14
Alignment explanation
Indices: 49263554--49263704 Score: 61
Period size: 15 Copynumber: 11.6 Consensus size: 14
49263544 AAATATAATT
*
49263554 AATAAATAAGTTTA
1 AATAAATTAGTTTA
49263568 AATAAAATATA-TTTA
1 AAT-AAAT-TAGTTTA
49263583 AAT--ATTAGTTTA
1 AATAAATTAGTTTA
*
49263595 AATAGA--A--TT-
1 AATAAATTAGTTTA
*
49263604 AATAAATAAGTTTA
1 AATAAATTAGTTTA
49263618 AATAAAATATA-TTTA
1 AAT-AAAT-TAGTTTA
49263633 AAT--ATTAGTTTA
1 AATAAATTAGTTTA
*
49263645 AATAGA--A--TT-
1 AATAAATTAGTTTA
*
49263654 AATAAATAAGTTTA
1 AATAAATTAGTTTA
49263668 AATGAAATATA-TTTA
1 AAT-AAAT-TAGTTTA
49263683 AAT--ATTAGTTTA
1 AATAAATTAGTTTA
49263695 AATAGAATTA
1 AATA-AATTA
49263705 ATAATTAAGT
Statistics
Matches: 106, Mismatches: 5, Indels: 51
0.65 0.03 0.31
Matches are distributed among these distances:
9 10 0.09
10 4 0.04
11 8 0.08
12 29 0.27
13 4 0.04
14 11 0.10
15 37 0.35
16 3 0.03
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.40
Consensus pattern (14 bp):
AATAAATTAGTTTA
Found at i:49263740 original size:23 final size:24
Alignment explanation
Indices: 49263556--49263800 Score: 149
Period size: 23 Copynumber: 10.0 Consensus size: 24
49263546 ATATAATTAA
49263556 TAAATAAGTTTAAATAAAATATATT
1 TAAAT-AGTTTAAATAAAATATATT
* *
49263581 TAAATATTAGTTTAAATAGAAT-TA-A
1 T-AA-A-TAGTTTAAATAAAATATATT
49263606 TAAATAAGTTTAAATAAAATATATT
1 TAAAT-AGTTTAAATAAAATATATT
* *
49263631 TAAATATTAGTTTAAATAGAAT-TA-A
1 T-AA-A-TAGTTTAAATAAAATATATT
*
49263656 TAAATAAGTTTAAATGAAATATATT
1 TAAAT-AGTTTAAATAAAATATATT
* *
49263681 TAAATATTAGTTTAAATAGAAT-TA-A
1 T-AA-A-TAGTTTAAATAAAATATATT
*
49263706 TAATTAAGTTTAAATAAAATATATT
1 TAAAT-AGTTTAAATAAAATATATT
49263731 TAAATA-TTTAAAT---AT-TAGTT
1 TAAATAGTTTAAATAAAATATA-TT
*
49263751 TAAATAGAATT-AAT-AAATATATT
1 TAAATAG-TTTAAATAAAATATATT
49263774 TAAATATTAGTTTAAATAAAATA-ATT
1 T-AA-A-TAGTTTAAATAAAATATATT
49263800 T
1 T
49263801 TTGCTCAAAA
Statistics
Matches: 173, Mismatches: 18, Indels: 57
0.70 0.07 0.23
Matches are distributed among these distances:
19 2 0.01
20 10 0.06
21 3 0.02
22 5 0.03
23 52 0.30
24 17 0.10
25 13 0.08
26 22 0.13
27 46 0.27
28 3 0.02
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (24 bp):
TAAATAGTTTAAATAAAATATATT
Found at i:49263751 original size:35 final size:36
Alignment explanation
Indices: 49263712--49263800 Score: 130
Period size: 35 Copynumber: 2.6 Consensus size: 36
49263702 TTAATAATTA
49263712 AGTTTAAATAAAATATATTTAA-ATATTTAAATATT
1 AGTTTAAATAAAATATATTTAATATATTTAAATATT
* * *
49263747 AGTTTAAATAGAAT-TAATAAATATATTTAAATATT
1 AGTTTAAATAAAATATATTTAATATATTTAAATATT
49263782 AGTTTAAATAAAATA-ATTT
1 AGTTTAAATAAAATATATTT
49263801 TTGCTCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
34 5 0.11
35 41 0.89
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (36 bp):
AGTTTAAATAAAATATATTTAATATATTTAAATATT
Found at i:49268205 original size:43 final size:43
Alignment explanation
Indices: 49268147--49268278 Score: 149
Period size: 43 Copynumber: 3.1 Consensus size: 43
49268137 TTATAATGGT
* * ** * *
49268147 GTTTGTAATAGAAGCGCCGCTAAAGGTCATGATTTTTAGCAGC
1 GTTTGTAAAAAAAGCGCCGCTAAAGACCATGATCTTTAGCGGC
*** *
49268190 GTTTGTGTGAAAAGCGCCTCTAAAGACCATGATCTTTAGCGGC
1 GTTTGTAAAAAAAGCGCCGCTAAAGACCATGATCTTTAGCGGC
* *
49268233 ATTTGTAAAAAAAGCACCGCT-AAGACCATGATCTTTAGCGGC
1 GTTTGTAAAAAAAGCGCCGCTAAAGACCATGATCTTTAGCGGC
49268275 GTTT
1 GTTT
49268279 TTTCACATAA
Statistics
Matches: 73, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
42 24 0.33
43 49 0.67
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (43 bp):
GTTTGTAAAAAAAGCGCCGCTAAAGACCATGATCTTTAGCGGC
Found at i:49271829 original size:46 final size:46
Alignment explanation
Indices: 49271722--49271889 Score: 288
Period size: 46 Copynumber: 3.7 Consensus size: 46
49271712 TACGTATGAT
* *
49271722 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
49271765 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
49271811 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
49271857 CACTTATCACTTTGTCACTTGATCAGATAAGTG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTG
49271890 ATAAGTGATC
Statistics
Matches: 118, Mismatches: 4, Indels: 3
0.94 0.03 0.02
Matches are distributed among these distances:
43 10 0.08
44 5 0.04
45 20 0.17
46 83 0.70
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:49272865 original size:49 final size:47
Alignment explanation
Indices: 49272766--49272884 Score: 141
Period size: 49 Copynumber: 2.5 Consensus size: 47
49272756 TCCGTATAAT
* * *
49272766 ACCATATCTGGGATATGGCATCAGTGTGATATGTGCTACAGTGTAAG
1 ACCATAGCTGGGCTATGGCATCAGTATGATATGTGCTACAGTGTAAG
* *
49272813 ACCATAGCTGGGCTATGGCATCAGTATGTATTATGTGATTA-TGTGTAAG
1 ACCATAGCTGGGCTATGGCATCAGTATG-A-TATGTG-CTACAGTGTAAG
* *
49272862 ACCATAGTTGGACTATGGCATCA
1 ACCATAGCTGGGCTATGGCATCA
49272885 ACAAAACGAA
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
47 25 0.40
48 1 0.02
49 34 0.55
50 2 0.03
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (47 bp):
ACCATAGCTGGGCTATGGCATCAGTATGATATGTGCTACAGTGTAAG
Found at i:49276934 original size:46 final size:46
Alignment explanation
Indices: 49276868--49277166 Score: 489
Period size: 46 Copynumber: 6.6 Consensus size: 46
49276858 TTTGAGTACT
49276868 TCTGATC-AGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
49276913 TCTGATCAAGTGACAAAGTGATAGGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
49276959 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
49277005 TCTGATCAAGTGGCAAAATGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
49277051 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
49277097 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
49277142 TCTGATC-AGGGAC-AAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
49277167 ATCATACGTA
Statistics
Matches: 240, Mismatches: 13, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
43 11 0.05
44 5 0.02
45 26 0.11
46 198 0.82
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.29
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:49281338 original size:21 final size:21
Alignment explanation
Indices: 49281254--49281421 Score: 101
Period size: 21 Copynumber: 8.0 Consensus size: 21
49281244 TATTTTCTTA
*
49281254 CAGTTTAGCTCTTATGAGCTT
1 CAGTTTAACTCTTATGAGCTT
*
49281275 CAG-TTAACT-TATATGAGTTT
1 CAGTTTAACTCT-TATGAGCTT
* * *
49281295 CAATTTAACTCTTCT-AGGTTT
1 CAGTTTAACTCTTATGA-GCTT
* *
49281316 CAGTTTAGCTCTTTTGAGCTT
1 CAGTTTAACTCTTATGAGCTT
* * *
49281337 CAGTTTAACCCTTATGGGTTT
1 CAGTTTAACTCTTATGAGCTT
* * *
49281358 CCGTTCAGCTCTTATGAGCTT
1 CAGTTTAACTCTTATGAGCTT
* * *
49281379 CCA-TTTAACCCTTATGGGTTT
1 -CAGTTTAACTCTTATGAGCTT
* * * *
49281400 CCGTTTAGCACTTATGTGCTT
1 CAGTTTAACTCTTATGAGCTT
49281421 C
1 C
49281422 TGTGCAGCCT
Statistics
Matches: 110, Mismatches: 30, Indels: 14
0.71 0.19 0.09
Matches are distributed among these distances:
19 1 0.01
20 17 0.15
21 89 0.81
22 3 0.03
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.43
Consensus pattern (21 bp):
CAGTTTAACTCTTATGAGCTT
Found at i:49281357 original size:42 final size:41
Alignment explanation
Indices: 49281286--49281421 Score: 164
Period size: 42 Copynumber: 3.2 Consensus size: 41
49281276 AGTTAACTTA
* * * * *
49281286 TATGAGTTTCAATTTAACTCTTCTAGGTTTCAGTTTAGCTCT
1 TATGAGCTTC-ATTTAACCCTTATGGGTTTCCGTTTAGCTCT
* *
49281328 TTTGAGCTTCAGTTTAACCCTTATGGGTTTCCGTTCAGCTCT
1 TATGAGCTTCA-TTTAACCCTTATGGGTTTCCGTTTAGCTCT
*
49281370 TATGAGCTTCCATTTAACCCTTATGGGTTTCCGTTTAGCACT
1 TATGAGCTT-CATTTAACCCTTATGGGTTTCCGTTTAGCTCT
*
49281412 TATGTGCTTC
1 TATGAGCTTC
49281422 TGTGCAGCCT
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
41 2 0.02
42 77 0.95
43 2 0.02
ACGTcount: A:0.18, C:0.21, G:0.17, T:0.44
Consensus pattern (41 bp):
TATGAGCTTCATTTAACCCTTATGGGTTTCCGTTTAGCTCT
Found at i:49289271 original size:11 final size:12
Alignment explanation
Indices: 49289243--49289271 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
49289233 AATATATATA
49289243 TGAGAGAAAACT
1 TGAGAGAAAACT
49289255 TGAGAGAAAAC-
1 TGAGAGAAAACT
49289266 TGAGAG
1 TGAGAG
49289272 CATATGGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.48, C:0.07, G:0.31, T:0.14
Consensus pattern (12 bp):
TGAGAGAAAACT
Found at i:49295376 original size:18 final size:18
Alignment explanation
Indices: 49295355--49295392 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
49295345 TTTAAAAATA
49295355 TATAAAT-TTTGAAATTTT
1 TATAAATATTTG-AATTTT
49295373 TATAAATAATTTGAATTTT
1 TATAAAT-ATTTGAATTTT
49295392 T
1 T
49295393 TGAAACTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 7 0.39
20 4 0.22
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
TATAAATATTTGAATTTT
Found at i:49295393 original size:21 final size:22
Alignment explanation
Indices: 49295369--49295419 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
49295359 AATTTTGAAA
49295369 TTTTTATAA-ATAATTTGAATT
1 TTTTTATAACATAATTTGAATT
* * *
49295390 TTTTGA-AACTTATTTTGAATT
1 TTTTTATAACATAATTTGAATT
*
49295411 ATTTTATAA
1 TTTTTATAA
49295420 TTTTTGTTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 2 0.09
21 19 0.83
22 2 0.09
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (22 bp):
TTTTTATAACATAATTTGAATT
Found at i:49300333 original size:82 final size:82
Alignment explanation
Indices: 49300231--49300389 Score: 273
Period size: 82 Copynumber: 1.9 Consensus size: 82
49300221 GTAGTTAAGC
* * *
49300231 TATCCTCTACTCTTAGGACTATGTAAGTCACATAACTTGTCTTATTTGAAGTTGGTAATCTTTTC
1 TATCCTCTACTCTTAGGACTATGTAAGTCAAATAACTTGTCCTATTTGAAGTTGATAATCTTTTC
49300296 ATCAAAATCAGTCGTAA
66 ATCAAAATCAGTCGTAA
* *
49300313 TATCCTCTGCTCTTAGGACTATGTGAGTCAAATAACTTGTCCTATTTGAAGTTGATAATCTTTTC
1 TATCCTCTACTCTTAGGACTATGTAAGTCAAATAACTTGTCCTATTTGAAGTTGATAATCTTTTC
49300378 ATCAAAATCAGT
66 ATCAAAATCAGT
49300390 TGACAATGAA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 72 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (82 bp):
TATCCTCTACTCTTAGGACTATGTAAGTCAAATAACTTGTCCTATTTGAAGTTGATAATCTTTTC
ATCAAAATCAGTCGTAA
Found at i:49307723 original size:14 final size:14
Alignment explanation
Indices: 49307676--49307724 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
49307666 TGCACATGTA
*
49307676 AGGTTCACACATGT
1 AGGTTCACACATAT
*
49307690 AGGATTCACATATAT
1 AGG-TTCACACATAT
* *
49307705 GGGTTCACACATCT
1 AGGTTCACACATAT
49307719 AGGTTC
1 AGGTTC
49307725 GCACTTGTGG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (14 bp):
AGGTTCACACATAT
Found at i:49310841 original size:37 final size:35
Alignment explanation
Indices: 49310735--49310842 Score: 105
Period size: 37 Copynumber: 3.0 Consensus size: 35
49310725 ATTCCAAAAA
*
49310735 TAAT-ATTATTTTAATAATTTAATATTAAATTTAATT
1 TAATAATTATCTTAATAATTTAAT-TT-AATTTAATT
* *
49310771 TAATACTTATCTTAATAGTATTTTA-TTAATTTAATAT
1 TAATAATTATCTTAATA--ATTTAATTTAATTTAAT-T
49310808 TAAAATAATTATCTTAA-AATTTAATTTAATTTAAT
1 T--AATAATTATCTTAATAATTTAATTTAATTTAAT
49310843 GCTTATCTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
36 17 0.28
37 24 0.40
38 1 0.02
39 18 0.30
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.53
Consensus pattern (35 bp):
TAATAATTATCTTAATAATTTAATTTAATTTAATT
Found at i:49311712 original size:2 final size:2
Alignment explanation
Indices: 49311705--49311742 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
49311695 TAAGGATTCG
*
49311705 TA TA TA TA TA -A AA 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 TA TA TA T
49311743 TTCCTCCTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:49316197 original size:37 final size:37
Alignment explanation
Indices: 49316156--49316231 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
49316146 AAAGATGATT
*
49316156 TTCACCTTTTGAATTATATAAATAAATTATTTTTGTC
1 TTCACCTTTTGAATTATATAAATAAACTATTTTTGTC
*
49316193 TTCACCTTTTGAATTATATAAATAAGCTATTTTTGTC
1 TTCACCTTTTGAATTATATAAATAAACTATTTTTGTC
49316230 TT
1 TT
49316232 TCATATATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.51
Consensus pattern (37 bp):
TTCACCTTTTGAATTATATAAATAAACTATTTTTGTC
Found at i:49318851 original size:24 final size:25
Alignment explanation
Indices: 49318819--49318870 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
49318809 GCTATTATTA
49318819 TTGTATAAAAATAA-AA-TTTAAAAC
1 TTGTATAAAAA-AATAACTTTAAAAC
*
49318843 TTGTTTAAAAAAATAACTTTTAAAAC
1 TTGTATAAAAAAATAAC-TTTAAAAC
49318869 TT
1 TT
49318871 AAATCATGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 2 0.08
24 12 0.50
26 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (25 bp):
TTGTATAAAAAAATAACTTTAAAAC
Found at i:49319154 original size:2 final size:2
Alignment explanation
Indices: 49319142--49319170 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
49319132 TATACGTCAA
49319142 AT AT A- 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
49319171 CATTGCATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49323732 original size:2 final size:2
Alignment explanation
Indices: 49323725--49323755 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
49323715 AGGATTTCTT
49323725 TA TA 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 T
49323756 TTAAAATTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49334745 original size:10 final size:10
Alignment explanation
Indices: 49334732--49334756 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
49334722 GTTTTTTAAT
49334732 TTTTAAAATA
1 TTTTAAAATA
49334742 TTTTAAAATA
1 TTTTAAAATA
49334752 TTTTA
1 TTTTA
49334757 TTTTGTCGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTTAAAATA
Found at i:49335247 original size:26 final size:26
Alignment explanation
Indices: 49335218--49335273 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
49335208 TCCTGAGGTT
49335218 AATCGGAGGAATTCTAATGCCCGATA
1 AATCGGAGGAATTCTAATGCCCGATA
49335244 AATCGGAGGAATTCTAATGCCCGATA
1 AATCGGAGGAATTCTAATGCCCGATA
49335270 AATC
1 AATC
49335274 TCAAATTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (26 bp):
AATCGGAGGAATTCTAATGCCCGATA
Found at i:49337033 original size:52 final size:52
Alignment explanation
Indices: 49336950--49337055 Score: 194
Period size: 52 Copynumber: 2.0 Consensus size: 52
49336940 GAATTACTAC
*
49336950 AAAATAGGGAAAATAAAACAGAGTAAACATTTAATGCTTAGTAAGTTCGTAT
1 AAAACAGGGAAAATAAAACAGAGTAAACATTTAATGCTTAGTAAGTTCGTAT
*
49337002 AAAACAGGGAAAATAAAACAGAGTAAGCATTTAATGCTTAGTAAGTTCGTAT
1 AAAACAGGGAAAATAAAACAGAGTAAACATTTAATGCTTAGTAAGTTCGTAT
49337054 AA
1 AA
49337056 CATGGAATCT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.48, C:0.08, G:0.18, T:0.25
Consensus pattern (52 bp):
AAAACAGGGAAAATAAAACAGAGTAAACATTTAATGCTTAGTAAGTTCGTAT
Done.