Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 63 of 352
Found at i:19745910 original size:15 final size:15
Alignment explanation
Indices: 19745890--19745930 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 15
19745880 TTTATATTTG
19745890 GTTTTATATGTTAAA
1 GTTTTATATGTTAAA
*
19745905 GTTTTATAT-TT--G
1 GTTTTATATGTTAAA
19745917 GTTTTATATGTTAA
1 GTTTTATATGTTAA
19745931 TGGCATGCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
12 9 0.41
13 2 0.09
14 2 0.09
15 9 0.41
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.59
Consensus pattern (15 bp):
GTTTTATATGTTAAA
Found at i:19745911 original size:27 final size:27
Alignment explanation
Indices: 19745879--19745930 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
19745869 TAGCGGGAGA
19745879 TTTTATATTTGGTTTTATATGTTAAAG
1 TTTTATATTTGGTTTTATATGTTAAAG
19745906 TTTTATATTTGGTTTTATATGTTAA
1 TTTTATATTTGGTTTTATATGTTAA
19745931 TGGCATGCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.00, G:0.13, T:0.62
Consensus pattern (27 bp):
TTTTATATTTGGTTTTATATGTTAAAG
Found at i:19747828 original size:128 final size:127
Alignment explanation
Indices: 19747656--19747985 Score: 421
Period size: 128 Copynumber: 2.6 Consensus size: 127
19747646 AAAAATTCCT
*
19747656 TAAAACGAAGGCAATGTTTGATGTTTGGAAATTCGAGAAATCGTGCCCTACCGTGTTGGGTTTCG
1 TAAAAC-AAGGCAATGTTTGATGTTTGGAAATTCGAGGAATCGTGCCCTACCGTGTTGGGTTTCG
* * * * * *
19747721 ATTTTCCGTTTGTTCGAAATAATCGAATTTTCCTTTAGAATTTCACTT-GTGTTTTTCTAAATTC
65 ATTTTCCGTTTGTTCAAAATAATCAAATATTCCTTTAGAATTTCA-TTCATATTCTT-TAAATTC
* * * * *
19747785 TAAAACAAGGCAATGTTTGCTGCTTGGAAATTCGGGGAATCGTGCCCTATCGTGCTGGGTTTCGA
1 TAAAACAAGGCAATGTTTGATGTTTGGAAATTCGAGGAATCGTGCCCTACCGTGTTGGGTTTCGA
* *
19747850 -TTTCTCATTTGTTCAAAATAATTAAATATTCCTTTAGAATTTCATTCATATTCTTTAAATTC
66 TTTTC-CGTTTGTTCAAAATAATCAAATATTCCTTTAGAATTTCATTCATATTCTTTAAATTC
** * * ** *
19747912 TAAAACAAGGCAATGTTCAATGTTTGGAAGTTCGAGGAATTGTTTCCTACCATGTTGGGTTTCGA
1 TAAAACAAGGCAATGTTTGATGTTTGGAAATTCGAGGAATCGTGCCCTACCGTGTTGGGTTTCGA
19747977 TTTTCCGTT
66 TTTTCCGTT
19747986 GGACTAAATA
Statistics
Matches: 171, Mismatches: 27, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
127 69 0.40
128 96 0.56
129 6 0.04
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (127 bp):
TAAAACAAGGCAATGTTTGATGTTTGGAAATTCGAGGAATCGTGCCCTACCGTGTTGGGTTTCGA
TTTTCCGTTTGTTCAAAATAATCAAATATTCCTTTAGAATTTCATTCATATTCTTTAAATTC
Found at i:19752997 original size:17 final size:17
Alignment explanation
Indices: 19752966--19753023 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
19752956 TAATAAATTT
*
19752966 AAAATATAATATATAATA
1 AAAATAT-ATTTATAATA
*
19752984 AAAATATATTTATAAGA
1 AAAATATATTTATAATA
*
19753001 ATAATA-A-TTAT-AT-
1 AAAATATATTTATAATA
19753014 AAAATATATT
1 AAAATATATT
19753024 GGTTTAGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
13 5 0.15
14 2 0.06
15 5 0.15
16 1 0.03
17 13 0.39
18 7 0.21
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
AAAATATATTTATAATA
Found at i:19753533 original size:17 final size:18
Alignment explanation
Indices: 19753499--19753542 Score: 72
Period size: 17 Copynumber: 2.5 Consensus size: 18
19753489 AATCATATCT
19753499 TCTAAGATTGCAATCATA
1 TCTAAGATTGCAATCATA
*
19753517 TCTAAGATTG-TATCATA
1 TCTAAGATTGCAATCATA
19753534 TCTAAGATT
1 TCTAAGATT
19753543 ATATTTCCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (18 bp):
TCTAAGATTGCAATCATA
Found at i:19754171 original size:5 final size:5
Alignment explanation
Indices: 19754147--19754191 Score: 65
Period size: 5 Copynumber: 9.0 Consensus size: 5
19754137 TCGAAATAGT
*
19754147 AATT- AATTA TAATTA GATTA AATTA AATTA AATTA AATTA AATTA
1 AATTA AATTA -AATTA AATTA AATTA AATTA AATTA AATTA AATTA
19754192 TTTTCTTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
4 4 0.11
5 28 0.76
6 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (5 bp):
AATTA
Found at i:19762301 original size:24 final size:24
Alignment explanation
Indices: 19762274--19762344 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
19762264 ATACTTTTAA
19762274 ACATGGCAACTCACGTAACAATTC
1 ACATGGCAACTCACGTAACAATTC
19762298 ACATGGCAACT-ACCGTAACAATTC
1 ACATGGCAACTCA-CGTAACAATTC
* *
19762322 ACATGGTAACTCACATAACAATT
1 ACATGGCAACTCACGTAACAATT
19762345 TAATTTTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.02
24 41 0.95
25 1 0.02
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.23
Consensus pattern (24 bp):
ACATGGCAACTCACGTAACAATTC
Found at i:19762621 original size:17 final size:20
Alignment explanation
Indices: 19762590--19762628 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
19762580 TTTAATTTAA
19762590 AAAAAATAATAGTAAAT-TT
1 AAAAAATAATAGTAAATATT
19762609 AAAAAA-AAT-GTAAATATT
1 AAAAAATAATAGTAAATATT
19762627 AA
1 AA
19762629 TAACTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 7 0.37
19 6 0.32
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (20 bp):
AAAAAATAATAGTAAATATT
Found at i:19763117 original size:22 final size:24
Alignment explanation
Indices: 19763092--19763138 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
19763082 CTACAAGCAG
*
19763092 AGAAGAGAAA-ACATT-AAAAAAA
1 AGAAGAGAAATAAATTGAAAAAAA
*
19763114 AGAAGGGAAATAAATTGAAAAAAA
1 AGAAGAGAAATAAATTGAAAAAAA
19763138 A
1 A
19763139 AAGGAGACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 9 0.43
23 4 0.19
24 8 0.38
ACGTcount: A:0.70, C:0.02, G:0.17, T:0.11
Consensus pattern (24 bp):
AGAAGAGAAATAAATTGAAAAAAA
Found at i:19764158 original size:16 final size:16
Alignment explanation
Indices: 19764122--19764160 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
19764112 AAAAATTTAT
19764122 ATTTTCTATTCTTCTA
1 ATTTTCTATTCTTCTA
*
19764138 TTTTTCTATTCTT-TCA
1 ATTTTCTATTCTTCT-A
19764154 ATTTTCT
1 ATTTTCT
19764161 TTCCATTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 1 0.05
16 19 0.95
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTTCTATTCTTCTA
Found at i:19766823 original size:27 final size:28
Alignment explanation
Indices: 19766762--19766837 Score: 91
Period size: 27 Copynumber: 2.7 Consensus size: 28
19766752 GGGACTATAG
*
19766762 TGCTCACACAAGCTGACAGTGATCAAGGT
1 TGCTCACACAAGCTGACA-TTATCAAGGT
* * *
19766791 TACTCACACAAGCTGACATTATGAA-TT
1 TGCTCACACAAGCTGACATTATCAAGGT
*
19766818 TGCTCACACAAGCTAACATT
1 TGCTCACACAAGCTGACATT
19766838 GTATCGAGGT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 19 0.46
28 5 0.12
29 17 0.41
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (28 bp):
TGCTCACACAAGCTGACATTATCAAGGT
Found at i:19771143 original size:16 final size:16
Alignment explanation
Indices: 19771122--19771152 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19771112 TGTTTTAACT
*
19771122 ATAATAATATAATATA
1 ATAATAAAATAATATA
19771138 ATAATAAAATAATAT
1 ATAATAAAATAATAT
19771153 TTACTTAAAT
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:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAATAAAATAATATA
Found at i:19785348 original size:24 final size:23
Alignment explanation
Indices: 19785289--19785348 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 23
19785279 TTCAAATTAA
*
19785289 TATAATATTTATTTATATATTTT
1 TATAATATATATTTATATATTTT
*
19785312 TA-AAAATTAATATTTATATATTTT
1 TATAATA-T-ATATTTATATATTTT
19785336 TATAATATGATAT
1 TATAATAT-ATAT
19785349 AAATTTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
22 3 0.10
23 3 0.10
24 21 0.70
25 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TATAATATATATTTATATATTTT
Found at i:19785379 original size:28 final size:29
Alignment explanation
Indices: 19785317--19785381 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
19785307 ATTTTTAAAA
19785317 ATTAATATTTATATATTTTTATAATATGAT
1 ATTAA-ATTTATATATTTTTATAATATGAT
* * *
19785347 A-TAAATTTATTTATTTTTATTAT-TTAT
1 ATTAAATTTATATATTTTTATAATATGAT
19785374 ATTAAATT
1 ATTAAATT
19785382 AGAATTGAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 4 0.13
28 23 0.74
29 3 0.10
30 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (29 bp):
ATTAAATTTATATATTTTTATAATATGAT
Found at i:19787128 original size:21 final size:21
Alignment explanation
Indices: 19787078--19787133 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
19787068 TAAAACAACG
*
19787078 GTAATGATAAGATTAATTATC
1 GTAATGATGAGATTAATTATC
19787099 GTAATGATGAGATTGAA-TATC
1 GTAATGATGAGATT-AATTATC
*
19787120 GTAATGATGTGATT
1 GTAATGATGAGATT
19787134 TAAAACAGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.38
Consensus pattern (21 bp):
GTAATGATGAGATTAATTATC
Found at i:19787307 original size:22 final size:20
Alignment explanation
Indices: 19787280--19787331 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
19787270 TTTAATAAAG
19787280 TATTAAAAGTATTTATTATGTT
1 TATTAAAA-TATTTATTAT-TT
*
19787302 TATTAAAATGTTTATT-TTT
1 TATTAAAATATTTATTATTT
*
19787321 AATTAAAATAT
1 TATTAAAATAT
19787332 ATTTATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 11 0.41
20 1 0.04
21 7 0.26
22 8 0.30
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (20 bp):
TATTAAAATATTTATTATTT
Found at i:19788223 original size:58 final size:58
Alignment explanation
Indices: 19788152--19788267 Score: 196
Period size: 58 Copynumber: 2.0 Consensus size: 58
19788142 GACCTATCAA
* **
19788152 AATGGTTTAAAGACTACCTGTGATATTGCAGATCAATCTTTAAAAATTGGAGATTCAT
1 AATGGTCTAAAGACTACCTGTGATATTGCAGATCAATCTTTAAAAATTAAAGATTCAT
*
19788210 AATGGTCTAAAGACTACCTGTGATATTGCAGATCAATCTTTCAAAATTAAAGATTCAT
1 AATGGTCTAAAGACTACCTGTGATATTGCAGATCAATCTTTAAAAATTAAAGATTCAT
19788268 GATGAAGAGG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.34
Consensus pattern (58 bp):
AATGGTCTAAAGACTACCTGTGATATTGCAGATCAATCTTTAAAAATTAAAGATTCAT
Found at i:19789076 original size:9 final size:9
Alignment explanation
Indices: 19789062--19789107 Score: 92
Period size: 9 Copynumber: 5.1 Consensus size: 9
19789052 TGAGTTTTTG
19789062 AATTCGAAT
1 AATTCGAAT
19789071 AATTCGAAT
1 AATTCGAAT
19789080 AATTCGAAT
1 AATTCGAAT
19789089 AATTCGAAT
1 AATTCGAAT
19789098 AATTCGAAT
1 AATTCGAAT
19789107 A
1 A
19789108 TTAAACTATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (9 bp):
AATTCGAAT
Found at i:19790921 original size:23 final size:25
Alignment explanation
Indices: 19790885--19790936 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 25
19790875 AAAATAGTAA
*
19790885 TTTTAGTTTATTTATTTTTCAC-TTT
1 TTTTAGTTTATTTATATTT-ACGTTT
19790910 TTTTAG-TT-TTTATATTTACGTTT
1 TTTTAGTTTATTTATATTTACGTTT
19790933 TTTT
1 TTTT
19790937 TAAATTACCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 2 0.08
23 15 0.60
24 2 0.08
25 6 0.24
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.73
Consensus pattern (25 bp):
TTTTAGTTTATTTATATTTACGTTT
Found at i:19791110 original size:20 final size:19
Alignment explanation
Indices: 19791085--19791150 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
19791075 TTTTTAAAAA
19791085 TTAAAAATCATTAAAATTAT
1 TTAAAAAT-ATTAAAATTAT
*
19791105 TTAAAAAGTATAAAAATTAT
1 TTAAAAA-TATTAAAATTAT
** *
19791125 AAAAAAATTATTAAATATTTT
1 TTAAAAA-TATTAAA-ATTAT
19791146 TTAAA
1 TTAAA
19791151 TTTTAAAAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
20 28 0.78
21 8 0.22
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (19 bp):
TTAAAAATATTAAAATTAT
Found at i:19792404 original size:11 final size:10
Alignment explanation
Indices: 19792387--19792412 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
19792377 GTATTCAGAG
19792387 ATTTTTTTTT
1 ATTTTTTTTT
19792397 ATTTTTTTTT
1 ATTTTTTTTT
19792407 ATTTTT
1 ATTTTT
19792413 ATAAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (10 bp):
ATTTTTTTTT
Found at i:19793348 original size:23 final size:22
Alignment explanation
Indices: 19793321--19793370 Score: 84
Period size: 21 Copynumber: 2.3 Consensus size: 22
19793311 TGCCTAAAAT
19793321 GACACACGAGGTGCCTG-ATAC
1 GACACACGAGGTGCCTGAATAC
19793342 GACACACGAGGTGCCTGAAATAC
1 GACACACGAGGTGCCTG-AATAC
19793365 GACACA
1 GACACA
19793371 TAAAGTGCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 17 0.63
23 10 0.37
ACGTcount: A:0.34, C:0.28, G:0.26, T:0.12
Consensus pattern (22 bp):
GACACACGAGGTGCCTGAATAC
Found at i:19793378 original size:23 final size:23
Alignment explanation
Indices: 19793296--19793382 Score: 83
Period size: 21 Copynumber: 4.0 Consensus size: 23
19793286 CCTGATCAGT
*
19793296 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* * *
19793318 A-ATGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
19793338 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
19793361 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
19793383 TCAGTAAAGC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
20 1 0.02
21 32 0.60
22 1 0.02
23 19 0.36
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:19801622 original size:32 final size:32
Alignment explanation
Indices: 19801581--19801649 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
19801571 TTTTTTTTTT
* *
19801581 TTAAAAAAAAGTGTTTAAGTT-CAAATACTAAA
1 TTAAAAAAAAAT-TTCAAGTTCCAAATACTAAA
* * *
19801613 TTAAGAAAAAATTTCAAGTTCCAAATATTACA
1 TTAAAAAAAAATTTCAAGTTCCAAATACTAAA
19801645 TTAAA
1 TTAAA
19801650 CCTTAAATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
31 7 0.23
32 23 0.77
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.32
Consensus pattern (32 bp):
TTAAAAAAAAATTTCAAGTTCCAAATACTAAA
Found at i:19818627 original size:14 final size:14
Alignment explanation
Indices: 19818608--19818635 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19818598 ATTTACAAAT
19818608 GGAATTTCAATCTA
1 GGAATTTCAATCTA
19818622 GGAATTTCAATCTA
1 GGAATTTCAATCTA
19818636 CTCTTATAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
GGAATTTCAATCTA
Found at i:19821148 original size:20 final size:20
Alignment explanation
Indices: 19821123--19821164 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
19821113 CATGTGTTAG
19821123 TTGAATTAGCAGTTCTTCCA
1 TTGAATTAGCAGTTCTTCCA
19821143 TTGAATTAGCAGTTCTTCCA
1 TTGAATTAGCAGTTCTTCCA
19821163 TT
1 TT
19821165 TAACTTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (20 bp):
TTGAATTAGCAGTTCTTCCA
Found at i:19826670 original size:11 final size:11
Alignment explanation
Indices: 19826652--19826705 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
19826642 CCGGAAACCC
19826652 TATTTTATTTT
1 TATTTTATTTT
*
19826663 TCTTTTATTTT
1 TATTTTATTTT
*
19826674 TATTTTATGTT
1 TATTTTATTTT
* *
19826685 TAATTTAATTT
1 TATTTTATTTT
* *
19826696 AATTTAATTT
1 TATTTTATTT
19826706 GTTGATCTTT
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
11 33 1.00
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (11 bp):
TATTTTATTTT
Found at i:19827145 original size:16 final size:16
Alignment explanation
Indices: 19827124--19827154 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19827114 CATATTAGAG
19827124 CATATAAATTTGAAAC
1 CATATAAATTTGAAAC
*
19827140 CATATATATTTGAAA
1 CATATAAATTTGAAA
19827155 ACTTATTTAG
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:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (16 bp):
CATATAAATTTGAAAC
Found at i:19827226 original size:12 final size:11
Alignment explanation
Indices: 19827209--19827243 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
19827199 TTTAACTTTC
19827209 TTTATATATTTT
1 TTTATA-ATTTT
19827221 TTTATAA-TTT
1 TTTATAATTTT
19827231 TTTATAATTTT
1 TTTATAATTTT
19827242 TT
1 TT
19827244 AAAGATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 6 0.27
12 6 0.27
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTATAATTTT
Found at i:19827241 original size:9 final size:10
Alignment explanation
Indices: 19827213--19827244 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
19827203 ACTTTCTTTA
*
19827213 TATATTTTTT
1 TATAATTTTT
19827223 TATAATTTTT
1 TATAATTTTT
19827233 TATAATTTTT
1 TATAATTTTT
19827243 TA
1 TA
19827245 AAGATATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TATAATTTTT
Found at i:19827284 original size:19 final size:19
Alignment explanation
Indices: 19827249--19827304 Score: 71
Period size: 18 Copynumber: 3.0 Consensus size: 19
19827239 TTTTTAAAGA
*
19827249 TATAAAT-TTTGAAATTTT
1 TATAAATATTTTAAATTTT
19827267 TATAAATATTTTAAA-TTT
1 TATAAATATTTTAAATTTT
*
19827285 TAAAAATAATTTTAAATTTT
1 TATAAAT-ATTTTAAATTTT
19827305 ATTTTTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 16 0.48
19 14 0.42
20 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
TATAAATATTTTAAATTTT
Found at i:19827305 original size:19 final size:19
Alignment explanation
Indices: 19827253--19827305 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 19
19827243 TAAAGATATA
*
19827253 AATTTTGAAATTTTTATAAAT
1 AATTTT-AAA-TTTTAAAAAT
19827274 -ATTTTAAATTTTAAAAAT
1 AATTTTAAATTTTAAAAAT
19827292 AATTTTAAATTTTA
1 AATTTTAAATTTTA
19827306 TTTTTTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 9 0.30
19 16 0.53
20 5 0.17
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
AATTTTAAATTTTAAAAAT
Found at i:19833854 original size:57 final size:57
Alignment explanation
Indices: 19833788--19834009 Score: 192
Period size: 57 Copynumber: 3.9 Consensus size: 57
19833778 AAAATACAAG
* *
19833788 TTTTCAAAAAAAAAAGAATTTTTTTTTGTGCTGGTCTGTCAATGGCCGGCACCA-A-TAA
1 TTTT-AAAAAAAAAA-AA-TTTTTTTTGTGCTGGCCTATCAATGGCCGGCACCAGAGTAA
** *
19833846 TTTT-AAAAAAATTAATTTTTTTTGTGCTGGCCTATCAATAGCCGGCACCAGTAGTAA
1 TTTTAAAAAAAAAAAATTTTTTTTGTGCTGGCCTATCAATGGCCGGCACCAG-AGTAA
*** * *
19833903 -TTTAAAAAATTTAAATTTTTTTGGTGCTGGCCTATCAATGGCCGGCACCAGAATACGA
1 TTTTAAAAAAAAAAAATTTTTTTTGTGCTGGCCTATCAATGGCCGGCACCAGAGTA--A
* * * *
19833961 GTTTT-TAAAAAAAAAA----TTTGGTGCTGGCCTGTCAATGGCTGGCACCAGA
1 -TTTTAAAAAAAAAAAATTTTTTTTGTGCTGGCCTATCAATGGCCGGCACCAGA
19834010 ATACAAGTTT
Statistics
Matches: 139, Mismatches: 17, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
54 32 0.23
55 33 0.24
56 14 0.10
57 45 0.32
58 5 0.04
59 7 0.05
60 3 0.02
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (57 bp):
TTTTAAAAAAAAAAAATTTTTTTTGTGCTGGCCTATCAATGGCCGGCACCAGAGTAA
Found at i:19833870 original size:54 final size:56
Alignment explanation
Indices: 19833807--19833954 Score: 212
Period size: 57 Copynumber: 2.7 Consensus size: 56
19833797 AAAAAAGAAT
* *
19833807 TTTTTTTTGTGCTGGTCTGTCAATGGCCGGCACCA-A-TAATTTTAAAAAAATT-AA
1 TTTTTTTTGTGCTGGCCTATCAATGGCCGGCACCAGAGTAA-TTTAAAAAAATTAAA
* *
19833861 TTTTTTTTGTGCTGGCCTATCAATAGCCGGCACCAGTAGTAATTTAAAAAATTTAAA
1 TTTTTTTTGTGCTGGCCTATCAATGGCCGGCACCAG-AGTAATTTAAAAAAATTAAA
*
19833918 TTTTTTTGGTGCTGGCCTATCAATGGCCGGCACCAGA
1 TTTTTTTTGTGCTGGCCTATCAATGGCCGGCACCAGA
19833955 ATACGAGTTT
Statistics
Matches: 84, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
54 32 0.38
56 13 0.15
57 39 0.46
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (56 bp):
TTTTTTTTGTGCTGGCCTATCAATGGCCGGCACCAGAGTAATTTAAAAAAATTAAA
Found at i:19834050 original size:54 final size:55
Alignment explanation
Indices: 19833921--19834061 Score: 221
Period size: 54 Copynumber: 2.6 Consensus size: 55
19833911 ATTTAAATTT
* *
19833921 TTTTGGTGCTGGCCTATCAATGGCCGGCACCAGAATACGAGTTTTTAAAAAAAAA
1 TTTTGGTGCTGGCCTATCAATGGCTGGCACCAGAATACAAGTTTTTAAAAAAAAA
* * *
19833976 ATTTGGTGCTGGCCTGTCAATGGCTGGCACCAGAATACAAG-TTTTCAAAAAAAA
1 TTTTGGTGCTGGCCTATCAATGGCTGGCACCAGAATACAAGTTTTTAAAAAAAAA
*
19834030 TTTTGGTGTTGGCCTATCAATGGCTGGCACCA
1 TTTTGGTGCTGGCCTATCAATGGCTGGCACCA
19834062 ATATTAAAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
54 41 0.53
55 37 0.47
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (55 bp):
TTTTGGTGCTGGCCTATCAATGGCTGGCACCAGAATACAAGTTTTTAAAAAAAAA
Found at i:19836062 original size:11 final size:12
Alignment explanation
Indices: 19836037--19836069 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
19836027 TTATCAACCC
19836037 TTTTATTTTTCA
1 TTTTATTTTTCA
19836049 TTTTATTTTT-A
1 TTTTATTTTTCA
19836060 TTTTATTTTT
1 TTTTATTTTT
19836070 TTTCAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTATTTTTCA
Found at i:19836079 original size:14 final size:14
Alignment explanation
Indices: 19836062--19836142 Score: 60
Period size: 14 Copynumber: 5.5 Consensus size: 14
19836052 TATTTTTATT
19836062 TTATTTTTTTTCAA
1 TTATTTTTTTTCAA
19836076 TTATTTTTTTTTCAA
1 TTA-TTTTTTTTCAA
* *
19836091 TTCATTTCATATT--A
1 TT-ATTT-TTTTTCAA
19836105 TTATTTTCTTTTTCATA
1 TTA-TTT-TTTTTCA-A
19836122 TTA-TTTTTTTCAA
1 TTATTTTTTTTCAA
19836135 TTCATTTT
1 TT-ATTTT
19836143 ATATTATTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
13 4 0.07
14 21 0.39
15 21 0.39
16 4 0.07
17 4 0.07
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATTTTTTTTCAA
Found at i:19836119 original size:25 final size:25
Alignment explanation
Indices: 19836037--19836120 Score: 74
Period size: 23 Copynumber: 3.5 Consensus size: 25
19836027 TTATCAACCC
*
19836037 TTTTATTTTTCATTT--TATTTTTA
1 TTTTATTTTTCATTTCATATTATTA
19836060 TTTTATTTTT--TTTCA-ATTATT-
1 TTTTATTTTTCATTTCATATTATTA
19836081 TTTT-TTTCAATTCATTTCATATTATTA
1 TTTTATTT---TTCATTTCATATTATTA
*
19836108 TTTTCTTTTTCAT
1 TTTTATTTTTCAT
19836121 ATTATTTTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 18
0.72 0.01 0.26
Matches are distributed among these distances:
20 3 0.06
21 7 0.14
22 5 0.10
23 12 0.24
25 10 0.20
26 6 0.12
27 4 0.08
28 3 0.06
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (25 bp):
TTTTATTTTTCATTTCATATTATTA
Found at i:19836120 original size:20 final size:20
Alignment explanation
Indices: 19836095--19836132 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
19836085 TTTCAATTCA
19836095 TTTCATATTATTATTTTCTT
1 TTTCATATTATTATTTTCTT
*
19836115 TTTCATATTATTTTTTTC
1 TTTCATATTATTATTTTC
19836133 AATTCATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTCATATTATTATTTTCTT
Found at i:19836146 original size:24 final size:24
Alignment explanation
Indices: 19836077--19836158 Score: 111
Period size: 24 Copynumber: 3.6 Consensus size: 24
19836067 TTTTTTCAAT
19836077 TATT-TTTTTTTCAATTCATTTCA
1 TATTATTTTTTTCAATTCATTTCA
*
19836100 TATTATTATTTTC--TT--TTTCA
1 TATTATTTTTTTCAATTCATTTCA
*
19836120 TATTATTTTTTTCAATTCATTTTA
1 TATTATTTTTTTCAATTCATTTCA
19836144 TATTATTTTTTTCAA
1 TATTATTTTTTTCAA
19836159 ATTAATTAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
20 17 0.33
22 4 0.08
23 4 0.08
24 26 0.51
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (24 bp):
TATTATTTTTTTCAATTCATTTCA
Found at i:19836156 original size:44 final size:44
Alignment explanation
Indices: 19836045--19836156 Score: 147
Period size: 44 Copynumber: 2.5 Consensus size: 44
19836035 CCTTTTATTT
*
19836045 TTCATTTTATTTTTATTTTATTT-TTTTTCAATTATTTTTTTTTCAA
1 TTCATTTTA-TATTATTTT-TTTCTTTTTCAATTA-TTTTTTTTCAA
* *
19836091 TTCATTTCATATTATTATTTTCTTTTTCATATTA-TTTTTTTCAA
1 TTCATTTTATATTATTTTTTTCTTTTTCA-ATTATTTTTTTTCAA
19836135 TTCATTTTATATTATTTTTTTC
1 TTCATTTTATATTATTTTTTTC
19836157 AAATTAATTA
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
44 33 0.56
45 14 0.24
46 12 0.20
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.71
Consensus pattern (44 bp):
TTCATTTTATATTATTTTTTTCTTTTTCAATTATTTTTTTTCAA
Found at i:19836464 original size:5 final size:5
Alignment explanation
Indices: 19836456--19836532 Score: 82
Period size: 5 Copynumber: 14.6 Consensus size: 5
19836446 ACTCTTTTTT
* *
19836456 TTTCA TTTCT TTTCA TTTTCA TTTCA TCTTCA TTTTA TTTCA TTTCAA
1 TTTCA TTTCA TTTCA -TTTCA TTTCA T-TTCA TTTCA TTTCA TTTC-A
* *
19836504 CTTCA TTTCA TTCTAA TTTCA TTTCA TTT
1 TTTCA TTTCA TT-TCA TTTCA TTTCA TTT
19836533 AAAATTTTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
5 42 0.70
6 18 0.30
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (5 bp):
TTTCA
Found at i:19836513 original size:16 final size:16
Alignment explanation
Indices: 19836456--19836532 Score: 86
Period size: 16 Copynumber: 4.8 Consensus size: 16
19836446 ACTCTTTTTT
* *
19836456 TTTCATTTCTTTTCAT
1 TTTCATTTCATTTCAA
19836472 TTTCATTTCATCTTC-A
1 TTTCATTTCAT-TTCAA
*
19836488 TTTTATTTCATTTCAA
1 TTTCATTTCATTTCAA
*
19836504 CTTCATTTCA-TTCTAA
1 TTTCATTTCATTTC-AA
19836520 TTTCATTTCATTT
1 TTTCATTTCATTT
19836533 AAAATTTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
15 6 0.12
16 40 0.78
17 5 0.10
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTCATTTCATTTCAA
Found at i:19836545 original size:17 final size:18
Alignment explanation
Indices: 19836525--19836562 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
19836515 TCTAATTTCA
19836525 TTTC-ATTTAAAATTT-TT
1 TTTCAATTT-AAATTTATT
19836542 TTTCAATTTAAATTTATT
1 TTTCAATTTAAATTTATT
19836560 TTT
1 TTT
19836563 TTCTCAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTCAATTTAAATTTATT
Found at i:19836604 original size:41 final size:41
Alignment explanation
Indices: 19836539--19836632 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 41
19836529 ATTTAAAATT
* * *
19836539 TTTTTTCAA-TTTAAATTTATTTTTTTCTCAATTCATTTATA
1 TTTTTT-AATTTTAAATTTAATTTTTCCTCAATTCATTTAAA
* * *
19836580 TTTTTTAATTTTAATTTTAATTTTTCCTTATTTCATTTAAA
1 TTTTTTAATTTTAAATTTAATTTTTCCTCAATTCATTTAAA
*
19836621 TTTTTTATTTTT
1 TTTTTTAATTTT
19836633 CATTGCAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 2 0.04
41 43 0.96
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.68
Consensus pattern (41 bp):
TTTTTTAATTTTAAATTTAATTTTTCCTCAATTCATTTAAA
Found at i:19836633 original size:20 final size:20
Alignment explanation
Indices: 19836570--19836636 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
19836560 TTTTTCTCAA
* *
19836570 TTCATTTATATTTTTTAATT
1 TTCATTTAAATTTTTTATTT
* * **
19836590 TTAATTTTAATTTTTCCTTAT
1 TTCATTTAAATTTTTTATT-T
19836611 TTCATTTAAATTTTTTATTT
1 TTCATTTAAATTTTTTATTT
19836631 TTCATT
1 TTCATT
19836637 GCAATTTTAA
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 20 0.56
21 16 0.44
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (20 bp):
TTCATTTAAATTTTTTATTT
Found at i:19836783 original size:27 final size:28
Alignment explanation
Indices: 19836765--19836817 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
19836755 TTAATTTCAT
*
19836765 TTTTTTTCTCATTTCATTTCAA-TTAAA
1 TTTTTTCCTCATTTCATTTCAATTTAAA
* *
19836792 TTTTTTCCTCATTTCTTTTGAATTTA
1 TTTTTTCCTCATTTCATTTCAATTTA
19836818 TCTTTCTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 19 0.86
28 3 0.14
ACGTcount: A:0.21, C:0.15, G:0.02, T:0.62
Consensus pattern (28 bp):
TTTTTTCCTCATTTCATTTCAATTTAAA
Found at i:19836795 original size:26 final size:26
Alignment explanation
Indices: 19836766--19836900 Score: 75
Period size: 26 Copynumber: 5.2 Consensus size: 26
19836756 TAATTTCATT
19836766 TTTTTTCTCATTTCATTTCAATTAAA
1 TTTTTTCTCATTTCATTTCAATTAAA
* *
19836792 TTTTTTCCTCATTTCTTTTGAATT---
1 TTTTTT-CTCATTTCATTTCAATTAAA
* * *
19836816 TATCTT-TC-TTTCAATTTTCATTTAAA
1 TTTTTTCTCATTTC-A-TTTCAATTAAA
* ** * *
19836842 TTTTGTAC-CGCTTCATTTCAATTTAT
1 TTTT-TTCTCATTTCATTTCAATTAAA
*
19836868 TTTTTTCTCATTTCATTTAAATTATCAA
1 TTTTTTCTCATTTCATTTCAATTA--AA
19836896 TTTTT
1 TTTTT
19836901 CCATGTAATT
Statistics
Matches: 77, Mismatches: 20, Indels: 22
0.65 0.17 0.18
Matches are distributed among these distances:
21 4 0.05
22 2 0.03
23 6 0.08
24 4 0.05
25 2 0.03
26 32 0.42
27 18 0.23
28 9 0.12
ACGTcount: A:0.22, C:0.16, G:0.02, T:0.60
Consensus pattern (26 bp):
TTTTTTCTCATTTCATTTCAATTAAA
Found at i:19836832 original size:76 final size:76
Alignment explanation
Indices: 19836689--19836838 Score: 178
Period size: 77 Copynumber: 2.0 Consensus size: 76
19836679 TTTCCATTTA
*
19836689 TTTTTTTCTCATCTTATTTAAATTAAAAGTTTCTCCCATTCATTTAAATTTGTATTTCTTTCAAA
1 TTTTTTTCTCATCTTATTTAAATTAAAAGTTTCTCCCATTCATTTAAATTTATATTTCTTTCAAA
19836754 TTTAATTTCAT
66 TTTAATTTCAT
* * * * * *
19836765 TTTTTTTCTCAT-TTCATTTCAATT-AAATTTTTTCCTCATTTCTTTTGAATTTATCTTTCTTTC
1 TTTTTTTCTCATCTT-ATTTAAATTAAAAGTTTCTCC-CA-TTCATTTAAATTTATATTTCTTTC
* *
19836828 AATTTTCATTT
63 AAATTTAATTT
19836839 AAATTTTGTA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
75 11 0.18
76 22 0.35
77 29 0.47
ACGTcount: A:0.23, C:0.15, G:0.02, T:0.59
Consensus pattern (76 bp):
TTTTTTTCTCATCTTATTTAAATTAAAAGTTTCTCCCATTCATTTAAATTTATATTTCTTTCAAA
TTTAATTTCAT
Found at i:19838712 original size:20 final size:20
Alignment explanation
Indices: 19838687--19838740 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
19838677 AGGGGCACAC
*
19838687 GCCCGTGTGGCCTGGGACAT
1 GCCCGTGTGGCCTGGAACAT
19838707 GCCCGTGTGGCCTGGAACAT
1 GCCCGTGTGGCCTGGAACAT
19838727 GCCCGTGTGGCCTG
1 GCCCGTGTGGCCTG
19838741 CCCGTAGGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.09, C:0.31, G:0.39, T:0.20
Consensus pattern (20 bp):
GCCCGTGTGGCCTGGAACAT
Found at i:19840904 original size:3 final size:3
Alignment explanation
Indices: 19840883--19840923 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
19840873 TTATCTCAAT
*
19840883 TAA TAGA TAA -AA T-A TAA TAA TAA TAA TAA TAG TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19840924 GTAAATATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 4 0.12
3 26 0.79
4 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:19842765 original size:53 final size:52
Alignment explanation
Indices: 19842701--19842882 Score: 206
Period size: 54 Copynumber: 3.3 Consensus size: 52
19842691 GATAAATTTA
*
19842701 GTGCCGGCCATTGATAGGCCAACAACAAAAAAATTTAATTTTTTTTAATACTG
1 GTGCC-GCCATTGACAGGCCAACAACAAAAAAATTTAATTTTTTTTAATACTG
* * *
19842754 GTGCCTGCCATTGACAAGCTACCACAA-AAAAAAATTCAATTTTTTTTAATACTG
1 GTGCC-GCCATTGACAGGC--CAACAACAAAAAAATTTAATTTTTTTTAATACTG
* *
19842808 GTGCCGACCATTGATAGGCCAGC-ACTAAAAAAATTTCAAATTTTTTTTTAAATACTG
1 GTGCCG-CCATTGACAGGCCAACAAC-AAAAAAATTT--AA-TTTTTTTT-AATACTG
19842865 GTGCCGCCATTGACAGGC
1 GTGCCGCCATTGACAGGC
19842883 AAGCACCAAT
Statistics
Matches: 109, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
51 1 0.01
52 2 0.02
53 26 0.24
54 41 0.38
55 7 0.06
56 19 0.17
57 13 0.12
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (52 bp):
GTGCCGCCATTGACAGGCCAACAACAAAAAAATTTAATTTTTTTTAATACTG
Found at i:19844412 original size:24 final size:25
Alignment explanation
Indices: 19844385--19844433 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
19844375 TTAATTCAAG
19844385 CCAAAA-ATTTTAACTTTTTTCTTT
1 CCAAAATATTTTAACTTTTTTCTTT
*
19844409 CCAAAATTTTTTAACTTTTTTCTTT
1 CCAAAATATTTTAACTTTTTTCTTT
19844434 TTTGGAATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.27, C:0.16, G:0.00, T:0.57
Consensus pattern (25 bp):
CCAAAATATTTTAACTTTTTTCTTT
Found at i:19847315 original size:36 final size:36
Alignment explanation
Indices: 19847275--19847392 Score: 200
Period size: 36 Copynumber: 3.3 Consensus size: 36
19847265 ACTGCCACCA
19847275 CCAGCTCCACTTATTCCAAACCCATTTCAGCCTCCT
1 CCAGCTCCACTTATTCCAAACCCATTTCAGCCTCCT
*
19847311 CCAGCTCCACTTATTCCAAACCCCTTTCAGCCTCCT
1 CCAGCTCCACTTATTCCAAACCCATTTCAGCCTCCT
* *
19847347 CCAGCTCCTCTTATTCCAAACCCTTTTCAGCCTCCT
1 CCAGCTCCACTTATTCCAAACCCATTTCAGCCTCCT
*
19847383 CCAGCCCCAC
1 CCAGCTCCAC
19847393 CGGCTCCACT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 77 1.00
ACGTcount: A:0.19, C:0.47, G:0.06, T:0.27
Consensus pattern (36 bp):
CCAGCTCCACTTATTCCAAACCCATTTCAGCCTCCT
Found at i:19847525 original size:45 final size:45
Alignment explanation
Indices: 19847344--19847531 Score: 250
Period size: 45 Copynumber: 4.2 Consensus size: 45
19847334 CTTTCAGCCT
* * * *
19847344 CCTCCAGCTCCTCTTATTCCAAACCCTTTTCAGCCTCCTCCAGCC
1 CCTCCAGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA
* * *
19847389 CCACCGGCTCCACTTATTCCAAACCCTTTTCAGCCTCCTCCCGCA
1 CCTCCAGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA
* *
19847434 CCACCGGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA
1 CCTCCAGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA
* * * * *
19847479 CCTCCAGCTCCATTTATCCCAAACCCCTTCCAGCCTCCTTCGGCA
1 CCTCCAGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA
19847524 CCTCCAGC
1 CCTCCAGC
19847532 ACCTCCAGCA
Statistics
Matches: 130, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 130 1.00
ACGTcount: A:0.17, C:0.50, G:0.09, T:0.24
Consensus pattern (45 bp):
CCTCCAGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA
Found at i:19856552 original size:13 final size:13
Alignment explanation
Indices: 19856534--19856575 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
19856524 ATATGACGTG
19856534 ATTTTTTTGGTTC
1 ATTTTTTTGGTTC
* *
19856547 ATTTTTTT-ATGC
1 ATTTTTTTGGTTC
19856559 ACTTTTTTTGGTTC
1 A-TTTTTTTGGTTC
19856573 ATT
1 ATT
19856576 AATGTGACGT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 3 0.13
13 17 0.74
14 3 0.13
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.67
Consensus pattern (13 bp):
ATTTTTTTGGTTC
Found at i:19860728 original size:33 final size:33
Alignment explanation
Indices: 19860691--19860769 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 33
19860681 TAGCCTTGCC
* *
19860691 ATGGTCTTACACTC-GTAATGTCATAACCCAGTT
1 ATGGTCTTACACTCAG-AATGCCATAACCCAATT
* *
19860724 ATGGTCTTATCA-TCAGGATGCCATAGCCCAATT
1 ATGGTCTTA-CACTCAGAATGCCATAACCCAATT
19860757 ATGGTCTTACACT
1 ATGGTCTTACACT
19860770 TATACATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
32 2 0.05
33 34 0.87
34 3 0.08
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (33 bp):
ATGGTCTTACACTCAGAATGCCATAACCCAATT
Found at i:19860825 original size:105 final size:101
Alignment explanation
Indices: 19860709--19860906 Score: 272
Period size: 105 Copynumber: 1.9 Consensus size: 101
19860699 ACACTCGTAA
* **
19860709 TGTCATAACCCAGTTATGGTCTTATCA-TCAGGATGCCATAGCCCAATTATGGTCTTACACTTAT
1 TGTCATAACCCAGTTATAGTCTTATCACT-AAAATGCCATAGCCCAATTATGGTCTTACA-TT-T
*
19860773 ACATATACTACCATGGTCTAACCATGGTCTTATGTTCATGG
63 A-A-ACACTACCATGGTCTAACCATGGTCTTATGTTCATGG
* *
19860814 TGTCATAACCCAGTTATAGTCTTTTCACTAAAATGCCATAGCCCAGTTATGGTCTTACATTTAAA
1 TGTCATAACCCAGTTATAGTCTTATCACTAAAATGCCATAGCCCAATTATGGTCTTACATTTAAA
* *
19860879 CATTACCATGGTCTAACCATTGTCTTAT
66 CACTACCATGGTCTAACCATGGTCTTAT
19860907 CCATCAATTC
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
101 26 0.31
102 1 0.01
103 2 0.02
104 2 0.02
105 52 0.62
106 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (101 bp):
TGTCATAACCCAGTTATAGTCTTATCACTAAAATGCCATAGCCCAATTATGGTCTTACATTTAAA
CACTACCATGGTCTAACCATGGTCTTATGTTCATGG
Found at i:19862099 original size:34 final size:34
Alignment explanation
Indices: 19862056--19862124 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
19862046 ATGCATAGGA
19862056 CTTAGTTTTCGCTTTGACTTGAAGGTTATAAATT
1 CTTAGTTTTCGCTTTGACTTGAAGGTTATAAATT
19862090 CTTAGTTTTCGCTTTGACTTGAAGGTTATAAATT
1 CTTAGTTTTCGCTTTGACTTGAAGGTTATAAATT
19862124 C
1 C
19862125 GCTTGAGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.46
Consensus pattern (34 bp):
CTTAGTTTTCGCTTTGACTTGAAGGTTATAAATT
Found at i:19865023 original size:21 final size:21
Alignment explanation
Indices: 19864999--19865040 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
19864989 CTTTTCTAAA
** *
19864999 GTTAAAATTCAAAATTATTAT
1 GTTAAAAGGCAAAACTATTAT
19865020 GTTAAAAGGCAAAACTATTAT
1 GTTAAAAGGCAAAACTATTAT
19865041 TGTTTATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.36
Consensus pattern (21 bp):
GTTAAAAGGCAAAACTATTAT
Found at i:19865464 original size:60 final size:60
Alignment explanation
Indices: 19865392--19865515 Score: 230
Period size: 60 Copynumber: 2.1 Consensus size: 60
19865382 TCTTTTAGAT
19865392 ATATCAATATTAGCTCTTCTAGAGCTTTAAACTAAATTTGTACACCCAAATATTGCATTA
1 ATATCAATATTAGCTCTTCTAGAGCTTTAAACTAAATTTGTACACCCAAATATTGCATTA
* *
19865452 ATATCAATATTAGCTCTTCTAGAGCTTTAAACTGAATTTGTACACCCAGATATTGCATTA
1 ATATCAATATTAGCTCTTCTAGAGCTTTAAACTAAATTTGTACACCCAAATATTGCATTA
19865512 ATAT
1 ATAT
19865516 TGGTTTATTT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (60 bp):
ATATCAATATTAGCTCTTCTAGAGCTTTAAACTAAATTTGTACACCCAAATATTGCATTA
Found at i:19865847 original size:3 final size:3
Alignment explanation
Indices: 19865837--19865875 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
19865827 TATGTCCATA
19865837 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
19865876 GTTTACATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:19867236 original size:27 final size:27
Alignment explanation
Indices: 19867181--19867238 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
19867171 CAAGTGCGAC
* * **
19867181 TGGTTGAGCCTGTCAGATAGGCGTGAT
1 TGGTTAAGCCTGTCAGATAAGCGCAAT
*
19867208 TGGTTAAGCTTGTCAGATAAGCGCAAT
1 TGGTTAAGCCTGTCAGATAAGCGCAAT
19867235 TGGT
1 TGGT
19867239 GAGGCCCACA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.22, C:0.14, G:0.33, T:0.31
Consensus pattern (27 bp):
TGGTTAAGCCTGTCAGATAAGCGCAAT
Found at i:19867704 original size:54 final size:54
Alignment explanation
Indices: 19867645--19867749 Score: 210
Period size: 54 Copynumber: 1.9 Consensus size: 54
19867635 AAAAAATTTG
19867645 CATTACTAAAAACTCACAAAACACAACAATTTATAATAAATTACTAACAAATTA
1 CATTACTAAAAACTCACAAAACACAACAATTTATAATAAATTACTAACAAATTA
19867699 CATTACTAAAAACTCACAAAACACAACAATTTATAATAAATTACTAACAAA
1 CATTACTAAAAACTCACAAAACACAACAATTTATAATAAATTACTAACAAA
19867750 ATATTTAATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.25
Consensus pattern (54 bp):
CATTACTAAAAACTCACAAAACACAACAATTTATAATAAATTACTAACAAATTA
Found at i:19867877 original size:60 final size:60
Alignment explanation
Indices: 19867805--19867919 Score: 185
Period size: 60 Copynumber: 1.9 Consensus size: 60
19867795 TAAACTAAAT
* * *
19867805 ACAATAATTTATAACATAGTCCTAAATTACTAATAAAATAATTTTAAAATAATTACAAAC
1 ACAACAATTTATAACATAGTCCTAAATTACAAACAAAATAATTTTAAAATAATTACAAAC
* *
19867865 ACAACAATTTATAACATATTCCTAAATTACAAACAAATTAATTTTAAAATAATTA
1 ACAACAATTTATAACATAGTCCTAAATTACAAACAAAATAATTTTAAAATAATTA
19867920 TAAAAATATT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (60 bp):
ACAACAATTTATAACATAGTCCTAAATTACAAACAAAATAATTTTAAAATAATTACAAAC
Found at i:19868078 original size:25 final size:25
Alignment explanation
Indices: 19868024--19868079 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
19868014 ATATAAATTT
19868024 AAATATTTTTATAAAAATAAAATAA
1 AAATATTTTTATAAAAATAAAATAA
* *
19868049 TAATATTTTATTTAAAAA-ACAAA-AA
1 AAATATTTT-TATAAAAATA-AAATAA
19868074 AAATAT
1 AAATAT
19868080 GTAATGTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (25 bp):
AAATATTTTTATAAAAATAAAATAA
Found at i:19869695 original size:15 final size:15
Alignment explanation
Indices: 19869675--19869731 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
19869665 ATTCAATATT
19869675 AATATTTTAATAATA
1 AATATTTTAATAATA
*
19869690 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
19869709 AATATATTAATAATA
1 AATATTTTAATAATA
*
19869724 AATGTTTT
1 AATATTTT
19869732 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:19877343 original size:52 final size:52
Alignment explanation
Indices: 19877269--19877476 Score: 193
Period size: 53 Copynumber: 3.9 Consensus size: 52
19877259 ATATATCATA
* * * * *
19877269 CCGATGCCATATCCCAGATATGGTCTTACACGGGAGCACTTATCACTTTTCT
1 CCGATGCCATAGCCCAGCTATGGTCTTATACGGGATCACTTATCACTTTTAT
* *
19877321 CCGATGCCATAGCCTAGCTATGGTCTTATAC-GGATCACTTGTATCACTTTAAT
1 CCGATGCCATAGCCCAGCTATGGTCTTATACGGGATCAC-T-TATCACTTTTAT
* * * ** *
19877374 CCGAAGCTATAGCCTAGCTATGGTCTTATACAGAAATCACTTATCACTTGTTTT
1 CCGATGCCATAGCCCAGCTATGGTCTTATAC-GGGATCACTTATCACTT-TTAT
* * * * **
19877428 TCGATTCTATAGCCCAGCTATGGTCTTGTACGAATATCACTTATCACTT
1 CCGATGCCATAGCCCAGCTATGGTCTTATACG-GGATCACTTATCACTT
19877477 GTTTCCATGG
Statistics
Matches: 131, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
51 6 0.05
52 28 0.21
53 48 0.37
54 44 0.34
55 5 0.04
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (52 bp):
CCGATGCCATAGCCCAGCTATGGTCTTATACGGGATCACTTATCACTTTTAT
Found at i:19885059 original size:54 final size:52
Alignment explanation
Indices: 19884898--19885087 Score: 215
Period size: 54 Copynumber: 3.6 Consensus size: 52
19884888 ATATCCTGAA
* * * * * *
19884898 TATGGTCTTACACGGGAGCACTTATCACTTTTCTCCGATGCCATAGCCCAGC
1 TATGGTCTTATACGGAATCACTTATCACTTTTATCCAATGCCATAGCCCAGT
19884950 TATGGTCTTATACGG-ATCACTTGTATCA-TTTTAATCCGAA-GCCATAGCCCAGT
1 TATGGTCTTATACGGAATCAC-T-TATCACTTTT-ATCC-AATGCCATAGCCCAGT
* * *
19885003 TATGGTATTATATGGAAATCACTTATCACTTGTTTTCCAATGCCATAGCCCAGT
1 TATGGTCTTATACGG-AATCACTTATCACTT-TTATCCAATGCCATAGCCCAGT
19885057 TATGGTCTTATACGGATATCACTTATCACTT
1 TATGGTCTTATACGGA-ATCACTTATCACTT
19885088 GTTGCCATGG
Statistics
Matches: 118, Mismatches: 10, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
51 4 0.03
52 19 0.16
53 41 0.35
54 47 0.40
55 7 0.06
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (52 bp):
TATGGTCTTATACGGAATCACTTATCACTTTTATCCAATGCCATAGCCCAGT
Found at i:19896518 original size:19 final size:18
Alignment explanation
Indices: 19896479--19896518 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
19896469 TATAAGAAAG
* *
19896479 TATTTTAATTTTAGAATA
1 TATTTTAATTTTAAAAAA
19896497 TATTTTAATTTTTAAAAAA
1 TATTTTAA-TTTTAAAAAA
19896516 TAT
1 TAT
19896519 AATTATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
TATTTTAATTTTAAAAAA
Found at i:19898735 original size:2 final size:2
Alignment explanation
Indices: 19898680--19898716 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
19898670 AAAAAAGCAA
19898680 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
19898717 AATGGGAGGA
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19902027 original size:21 final size:23
Alignment explanation
Indices: 19901991--19902040 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
19901981 AAGAAAAGAA
* *
19901991 AAAGGGAAGGGAAAAAGTAGA-G
1 AAAGGGAAGAGAAAAAGGAGATG
19902013 AAAGGGAA-AGAAAAAGGAGATG
1 AAAGGGAAGAGAAAAAGGAGATG
19902035 AAAGGG
1 AAAGGG
19902041 TGGAAGGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.56, C:0.00, G:0.40, T:0.04
Consensus pattern (23 bp):
AAAGGGAAGAGAAAAAGGAGATG
Found at i:19912221 original size:18 final size:18
Alignment explanation
Indices: 19912189--19912224 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19912179 AAAACCCTAA
**
19912189 ATTTTCTTTTTCTTTTTC
1 ATTTTCTTTCCCTTTTTC
19912207 ATTTTCTTTCCCTTTTTC
1 ATTTTCTTTCCCTTTTTC
19912225 CCTCCTTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (18 bp):
ATTTTCTTTCCCTTTTTC
Found at i:19912295 original size:16 final size:15
Alignment explanation
Indices: 19912252--19912298 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
19912242 TATTCATGCC
* *
19912252 TTTCTTTCTCTTTT-
1 TTTCTTTATGTTTTA
19912266 TTTCTTTATGTTTTA
1 TTTCTTTATGTTTTA
*
19912281 TTTCTTTTATTTTTTA
1 TTTC-TTTATGTTTTA
19912297 TT
1 TT
19912299 CATTCTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 12 0.43
15 4 0.14
16 12 0.43
ACGTcount: A:0.09, C:0.11, G:0.02, T:0.79
Consensus pattern (15 bp):
TTTCTTTATGTTTTA
Found at i:19912360 original size:17 final size:16
Alignment explanation
Indices: 19912330--19912382 Score: 63
Period size: 17 Copynumber: 3.3 Consensus size: 16
19912320 ATTATAATTA
*
19912330 TATAATATAC-TATAT
1 TATAATTTACTTATAT
19912345 TATAATTTACTTTATAT
1 TATAATTTAC-TTATAT
*
19912362 TATTATTTACTTATAT
1 TATAATTTACTTATAT
*
19912378 AATAA
1 TATAA
19912383 GTAAATACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 9 0.28
16 9 0.28
17 14 0.44
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (16 bp):
TATAATTTACTTATAT
Found at i:19913701 original size:6 final size:6
Alignment explanation
Indices: 19913692--19913719 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
19913682 ATAAAGCGAA
19913692 GGGGAG GGGGAG GGGGAG GGGGAG GGGG
1 GGGGAG GGGGAG GGGGAG GGGGAG GGGG
19913720 GTTTAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.86, T:0.00
Consensus pattern (6 bp):
GGGGAG
Found at i:19925291 original size:25 final size:23
Alignment explanation
Indices: 19925245--19925291 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
19925235 TGTTTAGAAA
*
19925245 TTAAATAATTGAAACAACATTAT
1 TTAAATAATTGAAACAAAATTAT
*
19925268 TTAAATAAATTGGAAATAAAATTA
1 TTAAAT-AATT-GAAACAAAATTA
19925292 AATTGGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 4 0.20
25 10 0.50
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.34
Consensus pattern (23 bp):
TTAAATAATTGAAACAAAATTAT
Found at i:19925306 original size:17 final size:16
Alignment explanation
Indices: 19925269--19925307 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
19925259 CAACATTATT
19925269 TAAA-TAAATTGGAAA
1 TAAATTAAATTGGAAA
19925284 TAAAATTAAATTGGGAAA
1 T-AAATTAAATT-GGAAA
19925302 TAAATT
1 TAAATT
19925308 TGGATTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.05
16 3 0.14
17 11 0.52
18 6 0.29
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (16 bp):
TAAATTAAATTGGAAA
Found at i:19928060 original size:66 final size:66
Alignment explanation
Indices: 19927985--19928111 Score: 220
Period size: 66 Copynumber: 1.9 Consensus size: 66
19927975 TACCTAAGAT
19927985 ACTAAGCCAGGTCTAGTGTATTATGCATACAGGGCTAACTCTAATTTAACTG-TCAGGGATCGAC
1 ACTAAGCCAGGTCTAGTGTATTATGCATACAGGGCTAACTCTAATTTAACTGCT-AGGGATCGAC
19928049 TG
65 TG
* *
19928051 ACTAAGCCAGGTCTGGTGTATTATGCATACAGGGCTGACTCTAATTTAACTGCTAGGGATC
1 ACTAAGCCAGGTCTAGTGTATTATGCATACAGGGCTAACTCTAATTTAACTGCTAGGGATC
19928112 TGCTAAATTG
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
66 57 0.98
67 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.29
Consensus pattern (66 bp):
ACTAAGCCAGGTCTAGTGTATTATGCATACAGGGCTAACTCTAATTTAACTGCTAGGGATCGACT
G
Found at i:19928995 original size:17 final size:18
Alignment explanation
Indices: 19928965--19928998 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19928955 AATAAAATTA
19928965 AAAATGGTGTAAATTGAT
1 AAAATGGTGTAAATTGAT
*
19928983 AAAATTGTG-AAATTGA
1 AAAATGGTGTAAATTGA
19928999 CCTTGAATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (18 bp):
AAAATGGTGTAAATTGAT
Found at i:19933124 original size:33 final size:33
Alignment explanation
Indices: 19933071--19933140 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
19933061 ATTATTTAAA
* *
19933071 TATGATTTGAAAATGCTTTTGAGTATGTTTAGG
1 TATGATTTGAAAATACTTTTGAGAATGTTTAGG
* * * *
19933104 TATGATTTGAACATATTTTTGGGAATGTTTTGG
1 TATGATTTGAAAATACTTTTGAGAATGTTTAGG
19933137 TATG
1 TATG
19933141 GTTGATAGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.26, C:0.03, G:0.24, T:0.47
Consensus pattern (33 bp):
TATGATTTGAAAATACTTTTGAGAATGTTTAGG
Found at i:19945449 original size:15 final size:14
Alignment explanation
Indices: 19945429--19945467 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
19945419 TCTTGCTCTT
19945429 TCATATTATATCATA
1 TCATATTATAT-ATA
19945444 TCATATTATATATA
1 TCATATTATATATA
19945458 T-ATA-TATATA
1 TCATATTATATA
19945468 ATATTATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 6 0.25
13 3 0.12
14 4 0.17
15 11 0.46
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.49
Consensus pattern (14 bp):
TCATATTATATATA
Found at i:19946145 original size:118 final size:118
Alignment explanation
Indices: 19945937--19946172 Score: 472
Period size: 118 Copynumber: 2.0 Consensus size: 118
19945927 ATGGACTTGA
19945937 ATGGAAAAGTTTGGACAAAAATATAACCTCGAAAAATGAATTTAGAAACGAACCAAGCCTCAAGT
1 ATGGAAAAGTTTGGACAAAAATATAACCTCGAAAAATGAATTTAGAAACGAACCAAGCCTCAAGT
19946002 AAGATTTTTTGGTCTGGGTTACTGCTGTTTTGTTGTCGTTTTGCTGTTATTTT
66 AAGATTTTTTGGTCTGGGTTACTGCTGTTTTGTTGTCGTTTTGCTGTTATTTT
19946055 ATGGAAAAGTTTGGACAAAAATATAACCTCGAAAAATGAATTTAGAAACGAACCAAGCCTCAAGT
1 ATGGAAAAGTTTGGACAAAAATATAACCTCGAAAAATGAATTTAGAAACGAACCAAGCCTCAAGT
19946120 AAGATTTTTTGGTCTGGGTTACTGCTGTTTTGTTGTCGTTTTGCTGTTATTTT
66 AAGATTTTTTGGTCTGGGTTACTGCTGTTTTGTTGTCGTTTTGCTGTTATTTT
19946173 GTTATTTAAT
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 118 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (118 bp):
ATGGAAAAGTTTGGACAAAAATATAACCTCGAAAAATGAATTTAGAAACGAACCAAGCCTCAAGT
AAGATTTTTTGGTCTGGGTTACTGCTGTTTTGTTGTCGTTTTGCTGTTATTTT
Found at i:19963219 original size:11 final size:11
Alignment explanation
Indices: 19963199--19963231 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
19963189 TCCCAAAATT
19963199 GAAAAGAAAAA
1 GAAAAGAAAAA
*
19963210 GAAGAGAAAAA
1 GAAAAGAAAAA
19963221 GAAAAGAAAAA
1 GAAAAGAAAAA
19963232 TGTTGTTGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
GAAAAGAAAAA
Found at i:19965426 original size:52 final size:48
Alignment explanation
Indices: 19965235--19965423 Score: 213
Period size: 48 Copynumber: 3.9 Consensus size: 48
19965225 GAGAGTTTTT
* * *
19965235 CACCTTAAGTGCCAATATCATAGCCCGAAGCCAACTCAATAAATCATG
1 CACCTGAAGTGCAAATATCATGGCCCGAAGCCAACTCAATAAATCATG
*
19965283 CA-CTCGAAGTGCAAATATCATGGCCCGTAGCCAACTCAATAAATCATG
1 CACCT-GAAGTGCAAATATCATGGCCCGAAGCCAACTCAATAAATCATG
** *
19965331 CACCCAAAGTGCAAATATCATGGCCC-ATAGCTAACTCAATATATAT-ATCTCG
1 CACCTGAAGTGCAAATATCATGGCCCGA-AGCCAACTCAATA-A-ATCA--T-G
* *
19965383 CACCTGAAGTGCCAATATCATGGCCTGAAGCCAACTCAATA
1 CACCTGAAGTGCAAATATCATGGCCCGAAGCCAACTCAATA
19965424 TATCCCTAAT
Statistics
Matches: 119, Mismatches: 13, Indels: 14
0.82 0.09 0.10
Matches are distributed among these distances:
47 2 0.02
48 75 0.63
49 3 0.03
50 2 0.02
51 1 0.01
52 35 0.29
53 1 0.01
ACGTcount: A:0.36, C:0.28, G:0.14, T:0.22
Consensus pattern (48 bp):
CACCTGAAGTGCAAATATCATGGCCCGAAGCCAACTCAATAAATCATG
Found at i:19966002 original size:21 final size:20
Alignment explanation
Indices: 19965974--19966012 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
19965964 CAAAACTTGT
19965974 ATAACTATCATCAAACATTC
1 ATAACTATCATCAAACATTC
*
19965994 ATAATCTATCATTAAACAT
1 ATAA-CTATCATCAAACAT
19966013 CAAAATACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAACTATCATCAAACATTC
Found at i:19966964 original size:96 final size:95
Alignment explanation
Indices: 19966793--19966981 Score: 288
Period size: 96 Copynumber: 2.0 Consensus size: 95
19966783 TAAGATGATT
*
19966793 AAATATCTCATGACTTGATTCGCGATTGTTGATATGGAATATCGAGAATTGGACTGAAATGAATA
1 AAATATCTCATGACTTGATTCGCGATTGTTGATATGAAATATCGAGAATTGGACTGAAATGAATA
*
19966858 AAATATAAATAAGCATGATAACAAATTGAAA
66 AAATAGAAATAAGCATGAT-ACAAATTGAAA
* * * * * *
19966889 AAATGTCTCATGACTTGATTCGTGATTGTTGATATTAAATGTTGAGAATTGGATTGAAATGAATA
1 AAATATCTCATGACTTGATTCGCGATTGTTGATATGAAATATCGAGAATTGGACTGAAATGAATA
*
19966954 AAATAGAAATAAGCATGATATAAATTGA
66 AAATAGAAATAAGCATGATACAAATTGA
19966982 TAAGTGTCTT
Statistics
Matches: 84, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
95 8 0.10
96 76 0.90
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (95 bp):
AAATATCTCATGACTTGATTCGCGATTGTTGATATGAAATATCGAGAATTGGACTGAAATGAATA
AAATAGAAATAAGCATGATACAAATTGAAA
Found at i:19967235 original size:19 final size:19
Alignment explanation
Indices: 19967212--19967266 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
19967202 GTGTGGGTTT
*
19967212 ATGCACTTCGTGTGCCAGT
1 ATGCACTTCGTGTGCCAGG
* *
19967231 TTGCACTTTGTGTGCCAGG
1 ATGCACTTCGTGTGCCAGG
*
19967250 ATGCATTTCG-GTGCCAG
1 ATGCACTTCGTGTGCCAG
19967267 ATTGGTGTCG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 7 0.23
19 23 0.77
ACGTcount: A:0.15, C:0.24, G:0.29, T:0.33
Consensus pattern (19 bp):
ATGCACTTCGTGTGCCAGG
Found at i:19968332 original size:44 final size:45
Alignment explanation
Indices: 19968258--19968351 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 45
19968248 TTTAAATATT
* * *
19968258 AATATATTAACTCTTTTGGAGCTTTCAACTAATTTTGTACTACCC
1 AATATATTAACTCTTTTGGAGCTTTAAACTAAATTTGTACTACCA
* *
19968303 AATA-ATTAGCTCTTTTGGAGCTTTAAACTAAATTTGTAGTACCA
1 AATATATTAACTCTTTTGGAGCTTTAAACTAAATTTGTACTACCA
19968347 AATAT
1 AATAT
19968352 TGCATTAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 39 0.91
45 4 0.09
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (45 bp):
AATATATTAACTCTTTTGGAGCTTTAAACTAAATTTGTACTACCA
Found at i:19972527 original size:16 final size:17
Alignment explanation
Indices: 19972496--19972528 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
19972486 TTCATAAGTA
19972496 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
19972513 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
19972529 GCTCTATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:19973087 original size:46 final size:46
Alignment explanation
Indices: 19972809--19973086 Score: 396
Period size: 46 Copynumber: 6.0 Consensus size: 46
19972799 TTATCTTTGA
* * * * *
19972809 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATAT
*
19972855 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
* * * ***
19972901 CACGTTGCCATGGTATCTTCCAACCATGGTCTTATTCATTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
*
19972947 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
*
19972993 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
* *
19973039 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
19973085 CA
1 CA
19973087 GAGAACACAC
Statistics
Matches: 212, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 4 0.02
46 208 0.98
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.40
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
Found at i:19975282 original size:29 final size:30
Alignment explanation
Indices: 19975230--19975298 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
19975220 CCACCCTTAA
* * *
19975230 CATATTTTCACTATTAGTCCTTCAACTTTT
1 CATATTTACACTATTAATCCTTCAAATTTT
19975260 CATATTTACACT-TTAATCCTTCAAATTTT
1 CATATTTACACTATTAATCCTTCAAATTTT
*
19975289 GAGTATTTAC
1 CA-TATTTAC
19975299 TCTTGGACCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.47
30 18 0.53
ACGTcount: A:0.28, C:0.20, G:0.04, T:0.48
Consensus pattern (30 bp):
CATATTTACACTATTAATCCTTCAAATTTT
Found at i:19978965 original size:27 final size:27
Alignment explanation
Indices: 19978935--19978988 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
19978925 GAGTGGTTAA
19978935 TTAGAGTTTAATTAAGTGAACTAGCTT
1 TTAGAGTTTAATTAAGTGAACTAGCTT
19978962 TTAGAGTTTAATTAAGTGAACTAGCTT
1 TTAGAGTTTAATTAAGTGAACTAGCTT
19978989 AAGTTAAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.41
Consensus pattern (27 bp):
TTAGAGTTTAATTAAGTGAACTAGCTT
Found at i:19980159 original size:27 final size:27
Alignment explanation
Indices: 19980128--19980231 Score: 131
Period size: 27 Copynumber: 3.8 Consensus size: 27
19980118 CTGCCAGAAA
* *
19980128 AGATAATGTGACAGAGTCACCAGATAC
1 AGATAATGTGGCAGAGCCACCAGATAC
19980155 AGATAATCGTGGCAGAGCCACCAGA-AC
1 AGATAAT-GTGGCAGAGCCACCAGATAC
19980182 AGATATATGTGGCAGAGCCACCAGAT-C
1 AGATA-ATGTGGCAGAGCCACCAGATAC
* *
19980209 AGATATTTGTGGCATAGCCACCA
1 AGATA-ATGTGGCAGAGCCACCA
19980232 AAACACTTCC
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
27 53 0.76
28 17 0.24
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (27 bp):
AGATAATGTGGCAGAGCCACCAGATAC
Found at i:19980180 original size:54 final size:54
Alignment explanation
Indices: 19980121--19980231 Score: 152
Period size: 54 Copynumber: 2.1 Consensus size: 54
19980111 AGCATGGCTG
*
19980121 CCAGAAAAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAAAAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * * *
19980175 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAAAAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
19980229 CCA
1 CCA
19980232 AAACACTTCC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 32 0.64
55 18 0.36
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAAAAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:19981888 original size:26 final size:26
Alignment explanation
Indices: 19981852--19981961 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
19981842 CATGAAATTC
19981852 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
19981878 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
19981904 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
19981930 TTATCATTG-AACATTTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCCA
19981956 TTATCA
1 TTATCA
19981962 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
26 79 0.98
27 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:19981972 original size:10 final size:10
Alignment explanation
Indices: 19981957--19981981 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
19981947 CCTAACCTAT
19981957 TATCAATTTG
1 TATCAATTTG
19981967 TATCAATTTG
1 TATCAATTTG
19981977 TATCA
1 TATCA
19981982 TAAATTATGG
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:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (10 bp):
TATCAATTTG
Found at i:19982652 original size:20 final size:18
Alignment explanation
Indices: 19982623--19982667 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
19982613 AACGAAAAGC
19982623 AGGG-AAAGAAAGAAAGAA
1 AGGGAAAAGAAAG-AAGAA
19982641 AGGAGAAAAGAAAGAAGAA
1 AGG-GAAAAGAAAGAAGAA
19982660 AGGGAAAA
1 AGGGAAAA
19982668 TTTAAGGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.32
19 9 0.36
20 8 0.32
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
AGGGAAAAGAAAGAAGAA
Found at i:19985900 original size:27 final size:28
Alignment explanation
Indices: 19985865--19985921 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
19985855 ATATAAAAAG
* *
19985865 TATAAATAATATAAAGCTCTAC-TTTAA
1 TATAAATAATATAAAACTATACTTTTAA
*
19985892 TATACATAATATAAAACTATACTTTTAA
1 TATAAATAATATAAAACTATACTTTTAA
19985920 TA
1 TA
19985922 AATATTAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.39
Consensus pattern (28 bp):
TATAAATAATATAAAACTATACTTTTAA
Found at i:19995305 original size:24 final size:23
Alignment explanation
Indices: 19995261--19995305 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
19995251 GGTACTGTAG
*
19995261 TTCATTTCATGTTATTTTGGTAT
1 TTCATTTCATGTTATTATGGTAT
* *
19995284 TTCATTTTCTTGTTCTTATGGT
1 TTCA-TTTCATGTTATTATGGT
19995306 CAATTTCAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 4 0.22
24 14 0.78
ACGTcount: A:0.13, C:0.11, G:0.13, T:0.62
Consensus pattern (23 bp):
TTCATTTCATGTTATTATGGTAT
Found at i:20004671 original size:30 final size:30
Alignment explanation
Indices: 20004637--20004695 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
20004627 AGTTCATACC
20004637 CCAAATATGCCATTCAAGTGCCATACATAA
1 CCAAATATGCCATTCAAGTGCCATACATAA
*
20004667 CCAAATATGCCATTCAAGTTCCATACATA
1 CCAAATATGCCATTCAAGTGCCATACATA
20004696 TAGCTTAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.27, G:0.08, T:0.25
Consensus pattern (30 bp):
CCAAATATGCCATTCAAGTGCCATACATAA
Found at i:20008665 original size:51 final size:51
Alignment explanation
Indices: 20008582--20008700 Score: 143
Period size: 51 Copynumber: 2.3 Consensus size: 51
20008572 TAAAAAATAT
* * *
20008582 TTTTTATTTGGTGTTGGCTTTCCTGAATCCAGCACCAGTTTTTTTATTGAAA
1 TTTTT-TTTGGTGTTGGCTTTCCTGAATCCAGCACCAGTGTTGTTAATGAAA
* * *
20008634 TTTTTTTTGGTGTTGGCTTTCTTG-TTGCCAGCACCAGTGTTGTTAATGCAA
1 TTTTTTTTGGTGTTGGCTTTCCTGAAT-CCAGCACCAGTGTTGTTAATGAAA
20008685 TTTTCTTTT-GTGTTGG
1 TTTT-TTTTGGTGTTGG
20008701 TGTTCTCGTT
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
50 1 0.02
51 49 0.83
52 9 0.15
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.50
Consensus pattern (51 bp):
TTTTTTTTGGTGTTGGCTTTCCTGAATCCAGCACCAGTGTTGTTAATGAAA
Found at i:20008719 original size:51 final size:51
Alignment explanation
Indices: 20008582--20008720 Score: 133
Period size: 51 Copynumber: 2.7 Consensus size: 51
20008572 TAAAAAATAT
* * * *
20008582 TTTTTATTTGGTGTTGGCTTTC-CTGAAT-CCAGCACCAGTTTTTTTATTGAAA
1 TTTTT-TTTGGTGTTGGCTTTCTC-G-TTGCCAGCACCAGTGTTGTTAATGAAA
* *
20008634 TTTTTTTTGGTGTTGGCTTTCTTGTTGCCAGCACCAGTGTTGTTAATGCAA
1 TTTTTTTTGGTGTTGGCTTTCTCGTTGCCAGCACCAGTGTTGTTAATGAAA
* *
20008685 TTTTCTTTT-GTGTTGG-TGTTCTCGTTGTCGGCACCA
1 TTTT-TTTTGGTGTTGGCT-TTCTCGTTGCCAGCACCA
20008721 CCAGGCTATA
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
50 2 0.03
51 63 0.85
52 9 0.12
ACGTcount: A:0.14, C:0.17, G:0.22, T:0.48
Consensus pattern (51 bp):
TTTTTTTTGGTGTTGGCTTTCTCGTTGCCAGCACCAGTGTTGTTAATGAAA
Found at i:20015966 original size:2 final size:2
Alignment explanation
Indices: 20015959--20016001 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
20015949 TTATTTCTTG
20015959 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
20016001 A
1 A
20016002 TATATATATA
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:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:20016479 original size:21 final size:21
Alignment explanation
Indices: 20016453--20016492 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
20016443 GAACAAAAAT
*
20016453 GACATGTTGAACAGGTTTCGG
1 GACATGTTGAACAAGTTTCGG
20016474 GACATGTTGAACAAGTTTC
1 GACATGTTGAACAAGTTTC
20016493 TAGGTAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (21 bp):
GACATGTTGAACAAGTTTCGG
Found at i:20017974 original size:10 final size:10
Alignment explanation
Indices: 20017947--20018006 Score: 70
Period size: 10 Copynumber: 6.0 Consensus size: 10
20017937 TGAAATTCTA
20017947 AAAGATAAAT
1 AAAGATAAAT
20017957 ACAA-ATAAAT
1 A-AAGATAAAT
*
20017967 AAAGATAATT
1 AAAGATAAAT
20017977 AAAGATAAAT
1 AAAGATAAAT
*
20017987 AACGATAAAT
1 AAAGATAAAT
20017997 GAAA-ATAAAT
1 -AAAGATAAAT
20018007 CCTAAAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
9 2 0.05
10 37 0.86
11 4 0.09
ACGTcount: A:0.67, C:0.03, G:0.08, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:20019006 original size:29 final size:30
Alignment explanation
Indices: 20018942--20019008 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
20018932 TAAATTGGCC
20018942 CTAAATTTTTAAAATTAAGAAGTAGAGGAA
1 CTAAATTTTTAAAATTAAGAAGTAGAGGAA
*
20018972 CTAAATTCTTTAAAA-TAA-AATTAG-GGAAA
1 CTAAATT-TTTAAAATTAAGAAGTAGAGG-AA
20019001 CTAAATTT
1 CTAAATTT
20019009 CAACTGTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
28 3 0.09
29 14 0.41
30 10 0.29
31 7 0.21
ACGTcount: A:0.49, C:0.06, G:0.12, T:0.33
Consensus pattern (30 bp):
CTAAATTTTTAAAATTAAGAAGTAGAGGAA
Found at i:20019468 original size:4 final size:4
Alignment explanation
Indices: 20019461--20019606 Score: 274
Period size: 4 Copynumber: 36.5 Consensus size: 4
20019451 TAAATAAATA
*
20019461 ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
20019509 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
20019557 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
20019605 AT
1 AT
20019607 TGTTTAGATA
Statistics
Matches: 138, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 138 1.00
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:20020154 original size:17 final size:16
Alignment explanation
Indices: 20020130--20020167 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
20020120 TTATAAAAGT
*
20020130 ATAAAAT-ATCTTA-A
1 ATAAAATAATATTATA
20020144 ATAAAATAATATTATA
1 ATAAAATAATATTATA
20020160 ATAAAATA
1 ATAAAATA
20020168 TACAAATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.33
15 5 0.24
16 9 0.43
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (16 bp):
ATAAAATAATATTATA
Found at i:20020869 original size:29 final size:28
Alignment explanation
Indices: 20020805--20020878 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 28
20020795 TTTATATTTG
* *
20020805 AATATTTATTATGATTTTAAATATTTTT
1 AATAATTATTATAATTTTAAATATTTTT
20020833 AATAAATTATTATAATTCTTAAA-ATTTTT
1 AAT-AATTATTATAATT-TTAAATATTTTT
*
20020862 AAATAATTTTTATAATT
1 -AATAATTATTATAATT
20020879 AAATCGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
28 3 0.08
29 29 0.73
30 8 0.20
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (28 bp):
AATAATTATTATAATTTTAAATATTTTT
Found at i:20021035 original size:12 final size:12
Alignment explanation
Indices: 20020995--20021037 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
20020985 ATGTCATCAC
20020995 TTAATTATAAAAA
1 TTAATTA-AAAAA
* **
20021008 TAAATTAAAATT
1 TTAATTAAAAAA
20021020 TTAATTAAAAAA
1 TTAATTAAAAAA
20021032 TTAATT
1 TTAATT
20021038 TATTTTTTAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
12 18 0.75
13 6 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TTAATTAAAAAA
Found at i:20024310 original size:20 final size:20
Alignment explanation
Indices: 20024285--20024351 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
20024275 TCCAAGGGTC
20024285 AGTTTTACTATTAATTTCAT
1 AGTTTTACTATTAATTTCAT
* * **
20024305 AGTTTTACCTCTTGAGGTC--
1 AGTTTTA-CTATTAATTTCAT
20024324 AGTTTTACTATTAATTTCAT
1 AGTTTTACTATTAATTTCAT
*
20024344 GGTTTTAC
1 AGTTTTAC
20024352 CTCTTGAGGG
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
18 7 0.20
19 7 0.20
20 14 0.40
21 7 0.20
ACGTcount: A:0.24, C:0.13, G:0.12, T:0.51
Consensus pattern (20 bp):
AGTTTTACTATTAATTTCAT
Found at i:20024335 original size:39 final size:39
Alignment explanation
Indices: 20024281--20024360 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
20024271 AAGGTCCAAG
20024281 GGTCAGTTTTACTATTAATTTCATAGTTTTACCTCTTGA
1 GGTCAGTTTTACTATTAATTTCATAGTTTTACCTCTTGA
*
20024320 GGTCAGTTTTACTATTAATTTCATGGTTTTACCTCTTGA
1 GGTCAGTTTTACTATTAATTTCATAGTTTTACCTCTTGA
20024359 GG
1 GG
20024361 GGTGTGATGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.21, C:0.15, G:0.16, T:0.47
Consensus pattern (39 bp):
GGTCAGTTTTACTATTAATTTCATAGTTTTACCTCTTGA
Found at i:20027756 original size:39 final size:40
Alignment explanation
Indices: 20027713--20027821 Score: 125
Period size: 39 Copynumber: 2.8 Consensus size: 40
20027703 ACCAGCTCGA
* *
20027713 AGCCTGCGGGA-CTTTAGCCCGAACGTAATTCCAGCATAT
1 AGCCTGCGGGACCTTAAGCCCGAACATAATTCCAGCATAT
* * *
20027752 AGCCTGC-GGACCTTAAGTCCGGATATAATTCCAGCATAT
1 AGCCTGCGGGACCTTAAGCCCGAACATAATTCCAGCATAT
* * *
20027791 AGCCTGC-GGACCTTAAGTCCGGATATAATTC
1 AGCCTGCGGGACCTTAAGCCCGAACATAATTC
20027822 ATCACTGAGT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
38 3 0.05
39 61 0.95
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
AGCCTGCGGGACCTTAAGCCCGAACATAATTCCAGCATAT
Found at i:20031424 original size:118 final size:118
Alignment explanation
Indices: 20031210--20031456 Score: 440
Period size: 118 Copynumber: 2.1 Consensus size: 118
20031200 TTTTCCTTAA
*
20031210 TTTAACTTACATTCTAACTTTTTACTAAATTACCCTTTAATATAACTTATAAAATTACTAAATCA
1 TTTAA-TTACATTCTAACTTTTCACTAAATTACCCTTTAATATAACTTATAAAATTACTAAATCA
20031275 TGTCCATAAATGTCCATAATATAAGTATATGGTATAATTACCATCTAAGGAAGG
65 TGTCCATAAATGTCCATAATATAAGTATATGGTATAATTACCATCTAAGGAAGG
* *
20031329 TTTAATTACATTCTAACTTTTCACTAAATTTCCCTTTAATATAACTTATAAAATTACTAACTCAT
1 TTTAATTACATTCTAACTTTTCACTAAATTACCCTTTAATATAACTTATAAAATTACTAAATCAT
* *
20031394 GTCGATAAATGTCCATAATATAAGTATATGGTATAATTACCCTCTAAGGAAGG
66 GTCCATAAATGTCCATAATATAAGTATATGGTATAATTACCATCTAAGGAAGG
20031447 TTTAATTACA
1 TTTAATTACA
20031457 CAATTGGTCT
Statistics
Matches: 123, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
118 118 0.96
119 5 0.04
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (118 bp):
TTTAATTACATTCTAACTTTTCACTAAATTACCCTTTAATATAACTTATAAAATTACTAAATCAT
GTCCATAAATGTCCATAATATAAGTATATGGTATAATTACCATCTAAGGAAGG
Found at i:20037201 original size:15 final size:14
Alignment explanation
Indices: 20037133--20037261 Score: 70
Period size: 15 Copynumber: 8.9 Consensus size: 14
20037123 TTATTGCTAT
20037133 TATTTTTATGTT-TC
1 TATTTTTAT-TTATC
*
20037147 TATTTATATTTAT-
1 TATTTTTATTTATC
*
20037160 T-TTGTTATTCTAATAC
1 TATTTTTATT-T-AT-C
*
20037176 TATTATTATTTATC
1 TATTTTTATTTATC
20037190 TAATTTTTATTTATC
1 T-ATTTTTATTTATC
* *
20037205 TATTTATATTTCTAC
1 TATTTTTATTTAT-C
*
20037220 TATTATTATATT-TC
1 TATTTTTAT-TTATC
*
20037234 TATTTATTATATT-TT
1 TATTT-TTAT-TTATC
*
20037249 TATTTCTATTTAT
1 TATTTTTATTTAT
20037262 ATACTAATAT
Statistics
Matches: 92, Mismatches: 12, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
12 6 0.07
13 6 0.07
14 32 0.35
15 37 0.40
16 4 0.04
17 7 0.08
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.66
Consensus pattern (14 bp):
TATTTTTATTTATC
Found at i:20037214 original size:29 final size:28
Alignment explanation
Indices: 20037133--20037240 Score: 78
Period size: 29 Copynumber: 3.8 Consensus size: 28
20037123 TTATTGCTAT
*
20037133 TATTTTTATGTTTCTATTTATATTTAT-
1 TATTTTTATATTTCTATTTATATTTATC
* * * *
20037160 TTTGTTATTCTAATACTA-TTATTATTTATC
1 TAT-TT-TTATATTTCTATTTA-TATTTATC
*
20037190 TAATTTTTAT-TTATCTATTTATATTTCTAC
1 T-ATTTTTATATT-TCTATTTATATTTAT-C
*
20037220 TATTATTATATTTCTATTTAT
1 TATTTTTATATTTCTATTTAT
20037241 TATATTTTTA
Statistics
Matches: 61, Mismatches: 11, Indels: 16
0.69 0.12 0.18
Matches are distributed among these distances:
27 2 0.03
28 6 0.10
29 42 0.69
30 10 0.16
31 1 0.02
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.65
Consensus pattern (28 bp):
TATTTTTATATTTCTATTTATATTTATC
Found at i:20037246 original size:23 final size:24
Alignment explanation
Indices: 20037173--20037287 Score: 83
Period size: 21 Copynumber: 5.2 Consensus size: 24
20037163 GTTATTCTAA
20037173 TACTATTATTAT-TTATCTAATTT-T
1 TACTATTATTATATT-TCT-ATTTAT
* * *
20037197 TA-T-TTA-TCTATTTATATTT-C
1 TACTATTATTATATTTCTATTTAT
20037217 TACTATTATTATATTTCTATTTAT
1 TACTATTATTATATTTCTATTTAT
20037241 TA-TATT-TT-TATTTCTATTTAT
1 TACTATTATTATATTTCTATTTAT
*
20037262 ATACTAATATTAT-TTTC-A-TTAT
1 -TACTATTATTATATTTCTATTTAT
20037284 TACT
1 TACT
20037288 TTTTTCCTTA
Statistics
Matches: 75, Mismatches: 7, Indels: 21
0.73 0.07 0.20
Matches are distributed among these distances:
20 6 0.08
21 22 0.29
22 16 0.21
23 20 0.27
24 10 0.13
25 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.63
Consensus pattern (24 bp):
TACTATTATTATATTTCTATTTAT
Found at i:20039331 original size:17 final size:21
Alignment explanation
Indices: 20039309--20039351 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
20039299 ACCTAAAAAT
20039309 TTTCAA-CC-AAACAA-T-TA
1 TTTCAAGCCAAAACAAGTATA
20039326 TTTCAAGCCAAAACAAGTATA
1 TTTCAAGCCAAAACAAGTATA
20039347 TTTCA
1 TTTCA
20039352 TTTTCCAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.27
18 2 0.09
19 6 0.27
20 1 0.05
21 7 0.32
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.30
Consensus pattern (21 bp):
TTTCAAGCCAAAACAAGTATA
Found at i:20041207 original size:17 final size:18
Alignment explanation
Indices: 20041174--20041207 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20041164 TTTTATCTTA
20041174 TTTAATCTATAAATTTCT
1 TTTAATCTATAAATTTCT
*
20041192 TTTAATTTAT-AATTTC
1 TTTAATCTATAAATTTC
20041208 ACTAATTCCA
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:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTAATCTATAAATTTCT
Done.