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 137 of 352
Found at i:44379853 original size:20 final size:20
Alignment explanation
Indices: 44379830--44379871 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
44379820 TTTTAAAAAA
*
44379830 CAAGTAAGGTTTTTAATGTC
1 CAAGTAAGGTTCTTAATGTC
44379850 CAAGTAAGGTTCTTAATGTC
1 CAAGTAAGGTTCTTAATGTC
44379870 CA
1 CA
44379872 GTTTCAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (20 bp):
CAAGTAAGGTTCTTAATGTC
Found at i:44381588 original size:57 final size:57
Alignment explanation
Indices: 44381522--44381699 Score: 191
Period size: 57 Copynumber: 3.1 Consensus size: 57
44381512 TCATTTTCAT
* * *
44381522 TTTTC-TTTTCAGTTTGGAGAAAGCCATATTCATTTATAAATGATTCCATTTCTCCA
1 TTTTCATTTTCAGTTTGGAGAAAACCATATTCATTTACAAATGTTTCCATTTCTCCA
* * * ** *
44381578 TTTTCATTTTCAGTTTGGAGAAAACTATAATCATTTCCAAATGTTTCTGTTTCTCTA
1 TTTTCATTTTCAGTTTGGAGAAAACCATATTCATTTACAAATGTTTCCATTTCTCCA
* * *
44381635 TTTT-AATTTCATTTTGGAGAAAACCATAATT-ATTTTACAAATTGTTTCCAATTTCTACA
1 TTTTCATTTTCAGTTTGGAGAAAACCAT-ATTCA-TTTACAAA-TGTTTCC-ATTTCTCCA
44381694 TTTTCA
1 TTTTCA
44381700 CCATTTCTAT
Statistics
Matches: 98, Mismatches: 18, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
56 26 0.27
57 55 0.56
58 6 0.06
59 10 0.10
60 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.47
Consensus pattern (57 bp):
TTTTCATTTTCAGTTTGGAGAAAACCATATTCATTTACAAATGTTTCCATTTCTCCA
Found at i:44392172 original size:30 final size:30
Alignment explanation
Indices: 44392127--44392186 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
44392117 ATTTAATATG
44392127 AACTTTGGCAAAATTACA-TTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTT-CCCCTA
* *
44392157 AACTTTTGCATAATTACACTTTTTCCCCTA
1 AACTTTGGCAAAATTACACTTTTTCCCCTA
44392187 GGCTCGAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.28, C:0.25, G:0.07, T:0.40
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTTCCCCTA
Found at i:44395785 original size:39 final size:39
Alignment explanation
Indices: 44395742--44395897 Score: 156
Period size: 39 Copynumber: 4.0 Consensus size: 39
44395732 GTGTGAGATA
*
44395742 TATATCCGGGCTAATTCCCGAAGGCATTTGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTGGTGT
* * *
44395781 TATATCCGGGCTAAGTCCCAAAGGCATTCGTGCTGATGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTGGTGT
* * * *
44395820 TATATCCAGGCTAAAGTCCCGCAGGC-CTTGTGC-GGATAT
1 TATATCCGGGCT-AAGTCCCGAAGGCATTTGTGCTGG-TGT
* * *
44395859 TATATCCGGGCTTAAAGTCCCGCATGC-TTTGTGGTGGTG
1 TATATCCGGGC-T-AAGTCCCGAAGGCATTTGTGCTGGTG
44395898 ATTGGATTTG
Statistics
Matches: 97, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
38 1 0.01
39 63 0.65
40 31 0.32
41 2 0.02
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (39 bp):
TATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTGGTGT
Found at i:44404580 original size:13 final size:13
Alignment explanation
Indices: 44404562--44404588 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
44404552 CTTTCAGCCC
44404562 CGTAACAAAAGAA
1 CGTAACAAAAGAA
44404575 CGTAACAAAAGAA
1 CGTAACAAAAGAA
44404588 C
1 C
44404589 ATAGATCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.59, C:0.19, G:0.15, T:0.07
Consensus pattern (13 bp):
CGTAACAAAAGAA
Found at i:44407876 original size:18 final size:18
Alignment explanation
Indices: 44407853--44407888 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
44407843 TACATGGTTA
44407853 CTGCTGCTTCAACCATGT
1 CTGCTGCTTCAACCATGT
44407871 CTGCTGCTTCAACCATGT
1 CTGCTGCTTCAACCATGT
44407889 TGGAAAAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.33, G:0.17, T:0.33
Consensus pattern (18 bp):
CTGCTGCTTCAACCATGT
Found at i:44416515 original size:21 final size:21
Alignment explanation
Indices: 44416489--44416591 Score: 111
Period size: 21 Copynumber: 4.8 Consensus size: 21
44416479 ATACATACAC
*
44416489 ATATATATAATAGTATTAGAA
1 ATATATATAATAATATTAGAA
44416510 ATATATA-ATATAATATTAGAA
1 ATATATATA-ATAATATTAGAA
**
44416531 ATATATATAATAGTATAAAAGAA
1 ATATATATAATA--ATATTAGAA
*
44416554 AAATATAACTAATAATATTA-AA
1 ATATAT-A-TAATAATATTAGAA
44416576 ATATATATAATAATAT
1 ATATATATAATAATAT
44416592 ATGTGAAATA
Statistics
Matches: 69, Mismatches: 7, Indels: 13
0.78 0.08 0.15
Matches are distributed among these distances:
20 10 0.14
21 29 0.42
22 8 0.12
23 16 0.23
24 1 0.01
25 5 0.07
ACGTcount: A:0.58, C:0.01, G:0.05, T:0.36
Consensus pattern (21 bp):
ATATATATAATAATATTAGAA
Found at i:44416536 original size:23 final size:23
Alignment explanation
Indices: 44416489--44416603 Score: 88
Period size: 23 Copynumber: 5.2 Consensus size: 23
44416479 ATACATACAC
*
44416489 ATATATAT-A-ATAGTATTAG-A
1 ATATATATAATATAATATTAGAA
44416509 A-ATATATAATATAATATTAGAA
1 ATATATATAATATAATATTAGAA
**
44416531 ATATATATAATAGT-ATAAAAGAA
1 ATATATATAATA-TAATATTAGAA
44416554 A-A-ATATAACTAATAATATTA-AA
1 ATATATATAA-T-ATAATATTAGAA
44416576 ATATATATAATA-ATATATGT-GAA
1 ATATATATAATATA-ATAT-TAGAA
44416599 ATATA
1 ATATA
44416604 ATATTAAAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 23
0.73 0.05 0.22
Matches are distributed among these distances:
19 6 0.08
20 2 0.03
21 16 0.21
22 13 0.17
23 33 0.43
24 7 0.09
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (23 bp):
ATATATATAATATAATATTAGAA
Found at i:44419051 original size:16 final size:16
Alignment explanation
Indices: 44419018--44419067 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
44419008 TACCAACTTC
44419018 TTTTATTTATAAATTATT
1 TTTTATTT-TAAA-TATT
*
44419036 TTTTATTTTGAATATT
1 TTTTATTTTAAATATT
* *
44419052 ATTTATATTAAATATT
1 TTTTATTTTAAATATT
44419068 AAATATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 17 0.61
17 3 0.11
18 8 0.29
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (16 bp):
TTTTATTTTAAATATT
Found at i:44425382 original size:26 final size:26
Alignment explanation
Indices: 44425346--44425429 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
44425336 CATGAAATTC
44425346 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
44425372 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
44425398 TTAACATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
44425424 TTATCA
1 TTATCA
44425430 ATTTGTATCA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.38, C:0.25, G:0.05, T:0.32
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:44426384 original size:29 final size:30
Alignment explanation
Indices: 44426351--44426414 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
44426341 CACTAACAAT
44426351 TTTTC-GTTACAAACATAACGGAGCTACCA
1 TTTTCTGTTACAAACATAACGGAGCTACCA
* *
44426380 TTTTCTGTTACAAACTTAACGGAGCTGCCA
1 TTTTCTGTTACAAACATAACGGAGCTACCA
44426410 TTTTC
1 TTTTC
44426415 CATCCCACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 5 0.16
30 27 0.84
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.34
Consensus pattern (30 bp):
TTTTCTGTTACAAACATAACGGAGCTACCA
Found at i:44439429 original size:15 final size:15
Alignment explanation
Indices: 44439409--44439439 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
44439399 AACTTAGTGA
44439409 CATGAGGCCGAACAT
1 CATGAGGCCGAACAT
44439424 CATGAGGCCGAACAT
1 CATGAGGCCGAACAT
44439439 C
1 C
44439440 TCGAACAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.29, G:0.26, T:0.13
Consensus pattern (15 bp):
CATGAGGCCGAACAT
Found at i:44439876 original size:31 final size:31
Alignment explanation
Indices: 44439841--44439904 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
44439831 AATGAAAAAA
44439841 CACCTCTGACTGATTTTTCATAAAATATATC
1 CACCTCTGACTGATTTTTCATAAAATATATC
* *
44439872 CACCTTTGAGTGATTTTTCATAAAATATATC
1 CACCTCTGACTGATTTTTCATAAAATATATC
44439903 CA
1 CA
44439905 TGTTATTGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (31 bp):
CACCTCTGACTGATTTTTCATAAAATATATC
Found at i:44441525 original size:31 final size:31
Alignment explanation
Indices: 44441488--44441597 Score: 85
Period size: 31 Copynumber: 3.4 Consensus size: 31
44441478 CTTCTCCCTC
44441488 TTTTTCATTCTCACGTCTGAAGCAACTTCTT
1 TTTTTCATTCTCACGTCTGAAGCAACTTCTT
* * * ****
44441519 TTTTTCATTCTTCCCATTTCCTTCCAACCTCTCTCT
1 TTTTTCATTC-TCACGTCT-GAAGCAA-CT-TCT-T
* *
44441555 CTTTTTCATTCTCACGTCCGAAGCATCTTCTT
1 -TTTTTCATTCTCACGTCTGAAGCAACTTCTT
44441587 TTTTTCATTCT
1 TTTTTCATTCT
44441598 TCTTCCCATT
Statistics
Matches: 57, Mismatches: 16, Indels: 12
0.67 0.19 0.14
Matches are distributed among these distances:
31 21 0.37
32 6 0.11
33 6 0.11
34 4 0.07
35 5 0.09
36 5 0.09
37 10 0.18
ACGTcount: A:0.15, C:0.31, G:0.05, T:0.49
Consensus pattern (31 bp):
TTTTTCATTCTCACGTCTGAAGCAACTTCTT
Found at i:44441565 original size:68 final size:70
Alignment explanation
Indices: 44441477--44441635 Score: 250
Period size: 68 Copynumber: 2.3 Consensus size: 70
44441467 TCAACTTTAC
* *
44441477 CCTTCTCCCTCTTTTTCATTCTCACGTCTGAAGCAACTTCTTTTTTTCA-TTCTTCCCATTTCCT
1 CCTTCTCACTCTTTTTCATTCTCACGTCCGAAGCAACTTCTTTTTTTCATTTCTTCCCATTTCCT
44441541 TCCAA
66 TCCAA
* *
44441546 CC-TCTCTCTCTTTTTCATTCTCACGTCCGAAGCATCTTCTTTTTTTCATTCTTCTTCCCATTTC
1 CCTTCTCACTCTTTTTCATTCTCACGTCCGAAGCAACTTCTTTTTTTCA-T-TTCTTCCCATTTC
44441610 CTTCCAA
64 CTTCCAA
44441617 CCTTCTCACTCTTTTTCAT
1 CCTTCTCACTCTTTTTCAT
44441636 GCTTCTATCC
Statistics
Matches: 82, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
68 43 0.52
69 2 0.02
71 22 0.27
72 15 0.18
ACGTcount: A:0.13, C:0.35, G:0.04, T:0.48
Consensus pattern (70 bp):
CCTTCTCACTCTTTTTCATTCTCACGTCCGAAGCAACTTCTTTTTTTCATTTCTTCCCATTTCCT
TCCAA
Found at i:44446971 original size:43 final size:44
Alignment explanation
Indices: 44446907--44446993 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 44
44446897 ATCAGGAATT
* *
44446907 GGTTGAGTATCAAGCTAG-AAAAGACATTAAATTGGTTGCCTTA
1 GGTTGAGTATCAAGCTAGAAAAAGACATCAAATTGATTGCCTTA
* * *
44446950 GGTTGGGTATCCAAG-TTGAAAAAGGCATCAAATTGATTGCCTTA
1 GGTTGAGTAT-CAAGCTAGAAAAAGACATCAAATTGATTGCCTTA
44446994 TGTATTTATA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
43 11 0.30
44 26 0.70
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (44 bp):
GGTTGAGTATCAAGCTAGAAAAAGACATCAAATTGATTGCCTTA
Found at i:44447509 original size:57 final size:55
Alignment explanation
Indices: 44447378--44447511 Score: 164
Period size: 57 Copynumber: 2.4 Consensus size: 55
44447368 TTAATTCATA
* ** *
44447378 TAATAATAATTATATTAAGAATGTTATTAAATTATATTTTTTTATTAAATTATATT
1 TAATAATAATTATATTAA-AATATGGTTAAATTATATTATTTTATTAAATTATATT
*
44447434 TAATAATAATTATGTTAAAATATGGTTAAATTATTTATTATTTTATTAAATTAT-TT
1 TAATAATAATTATATTAAAATATGGTTAAATTA--TATTATTTTATTAAATTATATT
44447490 TCAATAATAATCT-TATTAAAAT
1 T-AATAATAAT-TATATTAAAAT
44447512 TTAATAACAA
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
55 12 0.18
56 20 0.29
57 35 0.51
58 1 0.01
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (55 bp):
TAATAATAATTATATTAAAATATGGTTAAATTATATTATTTTATTAAATTATATT
Found at i:44464044 original size:20 final size:20
Alignment explanation
Indices: 44464007--44464078 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
44463997 CTGTATACAA
*
44464007 TTTAGTGTCTCT-ATTTGCAC
1 TTTAGTGCCTCTGA-TTGCAC
44464027 TTTAGTGCCTCTGATTGCAC
1 TTTAGTGCCTCTGATTGCAC
*
44464047 ATTT-GTGCCTCTGGTTGCAC
1 -TTTAGTGCCTCTGATTGCAC
* *
44464067 TATGGTGCCTCT
1 TTTAGTGCCTCT
44464079 ATATAGCATT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.04
20 40 0.87
21 4 0.09
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (20 bp):
TTTAGTGCCTCTGATTGCAC
Found at i:44473926 original size:42 final size:42
Alignment explanation
Indices: 44473879--44473963 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 42
44473869 GAGACATGGC
*
44473879 CGTGTCTGGAGCCGTGTGAGGCAC-TCGGCCTGTTCATACGAG
1 CGTGTCTGGAGCCGTGTGAGGCACAT-GGCCTGTTCACACGAG
* *
44473921 CGTGTCTGGAGTCGTGTGAGGCACATGGCTTGTTCACACGAG
1 CGTGTCTGGAGCCGTGTGAGGCACATGGCCTGTTCACACGAG
44473963 C
1 C
44473964 ATTCGTATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
42 38 0.97
43 1 0.03
ACGTcount: A:0.15, C:0.25, G:0.35, T:0.25
Consensus pattern (42 bp):
CGTGTCTGGAGCCGTGTGAGGCACATGGCCTGTTCACACGAG
Found at i:44476672 original size:30 final size:30
Alignment explanation
Indices: 44476632--44476731 Score: 137
Period size: 30 Copynumber: 3.3 Consensus size: 30
44476622 GGTTGCTCTA
* * **
44476632 GGTGAAATGAACTCGAACCGCTTATGTTCG
1 GGTGATATGAACTTGAACCGCCAATGTTCG
* *
44476662 GGTGATATGAACTTGAACCGCCCATGTCCG
1 GGTGATATGAACTTGAACCGCCAATGTTCG
*
44476692 AGTGATATGAACTTGAACCGCCAATGTTCG
1 GGTGATATGAACTTGAACCGCCAATGTTCG
44476722 GGTGATATGA
1 GGTGATATGA
44476732 TGTGCTCTAC
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (30 bp):
GGTGATATGAACTTGAACCGCCAATGTTCG
Found at i:44479284 original size:13 final size:13
Alignment explanation
Indices: 44479266--44479290 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44479256 CTTTTAAATT
44479266 TTTAAATTTTTAA
1 TTTAAATTTTTAA
44479279 TTTAAATTTTTA
1 TTTAAATTTTTA
44479291 CTTTTTTTAA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTAAATTTTTAA
Found at i:44479332 original size:20 final size:18
Alignment explanation
Indices: 44479299--44479369 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 18
44479289 TACTTTTTTT
* *
44479299 AATATATGTATTTTAAAA
1 AATATATTTTTTTTAAAA
44479317 AAGTCATATTTTTTTTAAAA
1 AA-T-ATATTTTTTTTAAAA
* *
44479337 AATAAATCCTTTTTTAAAAA
1 AATATAT--TTTTTTTAAAA
44479357 AATATATTTTTTT
1 AATATATTTTTTT
44479370 ATTTTTTAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
18 11 0.25
19 2 0.05
20 31 0.70
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (18 bp):
AATATATTTTTTTTAAAA
Found at i:44479416 original size:25 final size:24
Alignment explanation
Indices: 44479345--44479417 Score: 58
Period size: 25 Copynumber: 3.0 Consensus size: 24
44479335 AAAATAAATC
*
44479345 CTTTTTTAAA-AAAATATATTTTT
1 CTTTTTTAAATAAAATATATTTTA
* * * * *
44479368 TTATTTTTTAATTAATTAAGATTTTA
1 CT-TTTTTAAATAAAAT-ATATTTTA
44479394 CTTTTTTAAATAAAATATCATTTT
1 CTTTTTTAAATAAAATAT-ATTTT
44479418 TTAAAATTTT
Statistics
Matches: 35, Mismatches: 11, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
23 1 0.03
24 8 0.23
25 19 0.54
26 7 0.20
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.58
Consensus pattern (24 bp):
CTTTTTTAAATAAAATATATTTTA
Found at i:44479516 original size:24 final size:25
Alignment explanation
Indices: 44479485--44479531 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
44479475 ATCATAATTT
* *
44479485 AAATAATT-ATATGTAAAATTAAAA
1 AAATAATTAAAATATAAAATTAAAA
44479509 AAATAATTAAAATATAAAATTAA
1 AAATAATTAAAATATAAAATTAA
44479532 GATATACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (25 bp):
AAATAATTAAAATATAAAATTAAAA
Found at i:44479663 original size:22 final size:22
Alignment explanation
Indices: 44479614--44479665 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 22
44479604 TATATTATTA
44479614 AAAAAAT-ATATTTAAAATTTT
1 AAAAAATAATATTTAAAATTTT
44479635 -AAAAATAATATTTAAAATTTT
1 AAAAAATAATATTTAAAATTTT
44479656 AAAAAATAAT
1 AAAAAATAAT
44479666 TTCAAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.21
21 14 0.48
22 9 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAAAATAATATTTAAAATTTT
Found at i:44479667 original size:20 final size:21
Alignment explanation
Indices: 44479614--44479672 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 21
44479604 TATATTATTA
44479614 AAAAAATATATTTAAAATTTT
1 AAAAAATATATTTAAAATTTT
44479635 -AAAAATAATATTTAAAATTTT
1 AAAAAAT-ATATTTAAAATTTT
44479656 AAAAAATA-ATTTCAAAA
1 AAAAAATATATTT-AAAA
44479673 ATATATATTC
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
20 10 0.29
21 19 0.54
22 6 0.17
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAAAATATATTTAAAATTTT
Found at i:44479736 original size:45 final size:47
Alignment explanation
Indices: 44479648--44479741 Score: 113
Period size: 47 Copynumber: 2.0 Consensus size: 47
44479638 AATAATATTT
* *
44479648 AAAATTTTAAAAAATAATTTCAAAAATATATATTCAAAATTTTTTTAA
1 AAAATATTAAAAAATAATTTCAAAAATACATATTCAAAA-TTTTTTAA
* * *
44479696 AAAATATTATAAAAT-ATTTCAAATATACAT-TTC-AAGTTTTTTAA
1 AAAATATTAAAAAATAATTTCAAAAATACATATTCAAAATTTTTTAA
44479740 AA
1 AA
44479742 TTAATAATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
44 10 0.24
45 2 0.05
46 3 0.07
47 13 0.32
48 13 0.32
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.41
Consensus pattern (47 bp):
AAAATATTAAAAAATAATTTCAAAAATACATATTCAAAATTTTTTAA
Found at i:44483075 original size:18 final size:18
Alignment explanation
Indices: 44483054--44483116 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
44483044 ATTAATATAT
*
44483054 TAATTATGATTATAATTA
1 TAATTATGATTACAATTA
44483072 TAATTATGAGTTACGAATTA
1 TAATTATGA-TTAC-AATTA
* *
44483092 TGATTGATGA-TGCAATTA
1 TAATT-ATGATTACAATTA
44483110 TAATTAT
1 TAATTAT
44483117 TAGAATTAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 2 0.05
18 18 0.47
19 5 0.13
20 9 0.24
21 4 0.11
ACGTcount: A:0.40, C:0.03, G:0.13, T:0.44
Consensus pattern (18 bp):
TAATTATGATTACAATTA
Found at i:44484293 original size:12 final size:12
Alignment explanation
Indices: 44484278--44484321 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
44484268 TATATATATG
44484278 TATATTTAATTT
1 TATATTTAATTT
*
44484290 TATA-TAAATTT
1 TATATTTAATTT
44484301 TATAATTTAATTT
1 TAT-ATTTAATTT
*
44484314 TTTATTTA
1 TATATTTA
44484322 TAATATGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 9 0.33
12 10 0.37
13 8 0.30
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TATATTTAATTT
Found at i:44491817 original size:25 final size:24
Alignment explanation
Indices: 44491770--44491817 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
44491760 TATAATAATT
* *
44491770 AATTTTTAATAGTAAAACTAAATA
1 AATTTTTAATAGAAAAACAAAATA
44491794 AATTTTTAATAGAAAAATCAAAAT
1 AATTTTTAATAGAAAAA-CAAAAT
44491818 TTTAATCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (24 bp):
AATTTTTAATAGAAAAACAAAATA
Found at i:44492948 original size:11 final size:11
Alignment explanation
Indices: 44492932--44492956 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
44492922 AATTTTACTA
44492932 TTAAAATTAGG
1 TTAAAATTAGG
44492943 TTAAAATTAGG
1 TTAAAATTAGG
44492954 TTA
1 TTA
44492957 TATTCAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (11 bp):
TTAAAATTAGG
Found at i:44493019 original size:17 final size:17
Alignment explanation
Indices: 44492991--44493050 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
44492981 AATGATTGAT
*
44492991 ATTCAGTTTTGAGTCAA
1 ATTCAATTTTGAGTCAA
* * * *
44493008 ATTTAATTTTGATTGAT
1 ATTCAATTTTGAGTCAA
*
44493025 ATTCAGTTTTGAGTCAA
1 ATTCAATTTTGAGTCAA
44493042 ATTCAATTT
1 ATTCAATTT
44493051 AAGAATCATG
Statistics
Matches: 32, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.30, C:0.08, G:0.13, T:0.48
Consensus pattern (17 bp):
ATTCAATTTTGAGTCAA
Found at i:44493023 original size:34 final size:34
Alignment explanation
Indices: 44492983--44493050 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
44492973 TGGCTAAAAA
*
44492983 TGATTGATATTCAGTTTTGAGTCAAATTTAATTT
1 TGATTGATATTCAGTTTTGAGTCAAATTCAATTT
44493017 TGATTGATATTCAGTTTTGAGTCAAATTCAATTT
1 TGATTGATATTCAGTTTTGAGTCAAATTCAATTT
44493051 AAGAATCATG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49
Consensus pattern (34 bp):
TGATTGATATTCAGTTTTGAGTCAAATTCAATTT
Found at i:44497722 original size:50 final size:50
Alignment explanation
Indices: 44497635--44497923 Score: 250
Period size: 50 Copynumber: 5.9 Consensus size: 50
44497625 CCAACCACAT
* * * *
44497635 TATGGGAGCCAATGTAAGATCATGTCTGGGACATGGCATCGGCCTCGAGA
1 TATGAGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGAGA
* * *** *
44497685 TATGAAAGCTAGTGTAAGACCATGTCTAGGACATGGCATCAATAC-CGATA
1 TATGAGAGCCAGTGTAAGACCATGTCTAGGACATGGCATC-GGCCTCGAGA
* * * *
44497735 GATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGATA
1 TATGAGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGAGA
* * **
44497785 TATGAGAGTCAGTGTAAGACCATGTCT-GAGACATGGCATC-GACT-TTGA
1 TATGAGAGCCAGTGTAAGACCATGTCTAG-GACATGGCATCGGCCTCGAGA
* * * * **
44497833 TGTGTGAGCCAGTGTAAGACCATGTCCAGGACATGGCATC-GACT-TTGA
1 TATGAGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGAGA
* * * *
44497881 TATGTGAGCCAGTGTGAGACCATGTC-CGAGACATGGCGTCGGC
1 TATGAGAGCCAGTGTAAGACCATGTCTAG-GACATGGCATCGGC
44497924 ATCTTACCCT
Statistics
Matches: 200, Mismatches: 33, Indels: 13
0.81 0.13 0.05
Matches are distributed among these distances:
47 1 0.00
48 77 0.38
49 7 0.04
50 114 0.57
51 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (50 bp):
TATGAGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGAGA
Found at i:44497760 original size:100 final size:98
Alignment explanation
Indices: 44497640--44497917 Score: 305
Period size: 100 Copynumber: 2.8 Consensus size: 98
44497630 CACATTATGG
* *
44497640 GAGCCAATGTAAGATCATGTCTGGGACATGGCATCGGCCTCGAGATATGAAAG-CTAGTGTAAGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATATGAAAGTC-AGTGTAAGA
44497704 CCATGTCT-AGGACATGGCATC-AATACCGATAGATGA
65 CCATGTCTGA-GACATGGCATCGAAT-CCGAT-G-TGA
* * *
44497740 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGATATATGAGAGTCAGTGTAAGAC
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATATGAAAGTCAGTGTAAGAC
* ** *
44497805 CATGTCTGAGACATGGCATCGACTTTGATGTGT
66 CATGTCTGAGACATGGCATCGAATCCGATGTGA
** * ** ** * *
44497838 GAGCCAGTGTAAGACCATGTCCAGGACATGGCATC-GACT-TTGATATGTGAGCCAGTGTGAGAC
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATATGAAAGTCAGTGTAAGAC
*
44497901 CATGTCCGAGACATGGC
66 CATGTCTGAGACATGGC
44497918 GTCGGCATCT
Statistics
Matches: 156, Mismatches: 19, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
96 34 0.22
97 3 0.02
98 35 0.22
99 1 0.01
100 79 0.51
101 4 0.03
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (98 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATATGAAAGTCAGTGTAAGAC
CATGTCTGAGACATGGCATCGAATCCGATGTGA
Found at i:44500085 original size:42 final size:42
Alignment explanation
Indices: 44500028--44500192 Score: 138
Period size: 42 Copynumber: 3.9 Consensus size: 42
44500018 ACATTAGGGT
* *
44500028 TATGAG-TTTACGTGTAAGACCATATCTGGGATATGTCATCGT
1 TATGAGATTT-CGTGTAAGACCATATCTGGGATATGGCATCGA
* * *
44500070 TATGAGATTTCGTGT-AGTACCATGTTTGGGACATGGCATCGA
1 TATGAGATTTCGTGTAAG-ACCATATCTGGGATATGGCATCGA
** * * * * *
44500112 TATGA-AAATCGTGTAAGACCATAGCTAGGCTATTGGCGTCAA
1 TATGAGATTTCGTGTAAGACCATATCTGGGATA-TGGCATCGA
** * *
44500154 TATGAGATCCCATGTAAGACCATATCAGGGATATGGCAT
1 TATGAGATTTCGTGTAAGACCATATCTGGGATATGGCAT
44500193 TGGTATGATT
Statistics
Matches: 94, Mismatches: 24, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
41 18 0.19
42 54 0.57
43 22 0.23
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (42 bp):
TATGAGATTTCGTGTAAGACCATATCTGGGATATGGCATCGA
Found at i:44500489 original size:25 final size:25
Alignment explanation
Indices: 44500456--44500506 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
44500446 TTGTATGTTT
44500456 AAAGTTGATTATTATTTACATGCTA
1 AAAGTTGATTATTATTTACATGCTA
44500481 AAAGTTGATTATTATTTACATGCTA
1 AAAGTTGATTATTATTTACATGCTA
44500506 A
1 A
44500507 CTTACTAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (25 bp):
AAAGTTGATTATTATTTACATGCTA
Found at i:44507265 original size:46 final size:46
Alignment explanation
Indices: 44507212--44507331 Score: 152
Period size: 46 Copynumber: 2.6 Consensus size: 46
44507202 TATGTGTGCT
* * *
44507212 AGTGTAAGACATGTCTGGGACATGCATCGGC-CACATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTCACA-GACGAAAGCC
* *** *
44507258 AGTGTAAGACATGTCTGGGACATGCATTGGCTTTGAGACGAAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTCACAGACGAAAGCC
44507304 AGTGTAAGACATGTCTGGGACATGCATC
1 AGTGTAAGACATGTCTGGGACATGCATC
44507332 AGCCTCGAGA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
46 63 0.98
47 1 0.02
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTCACAGACGAAAGCC
Found at i:44509469 original size:4 final size:4
Alignment explanation
Indices: 44509460--44509517 Score: 71
Period size: 4 Copynumber: 13.5 Consensus size: 4
44509450 AGAGAGGGAG
*
44509460 AAGA AAGA AAGA AAGAA AAGAA AATA AAGA AAGAA AAGA GAAGA AAGA
1 AAGA AAGA AAGA AAG-A AAG-A AAGA AAGA AAG-A AAGA -AAGA AAGA
44509508 AAGA AAGA AA
1 AAGA AAGA AA
44509518 ATGTATTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
4 33 0.67
5 16 0.33
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (4 bp):
AAGA
Found at i:44509490 original size:18 final size:18
Alignment explanation
Indices: 44509467--44509519 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
44509457 GAGAAGAAAG
44509467 AAAGAAAGAAAAGAAAAT
1 AAAGAAAGAAAAGAAAAT
* *
44509485 AAAGAAAGAAAAGAGAAG
1 AAAGAAAGAAAAGAAAAT
44509503 AAAGAAAG-AAAGAAAAT
1 AAAGAAAGAAAAGAAAAT
44509520 GTATTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 7 0.23
18 24 0.77
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (18 bp):
AAAGAAAGAAAAGAAAAT
Found at i:44509517 original size:22 final size:22
Alignment explanation
Indices: 44509457--44509518 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
44509447 AGAAGAGAGG
44509457 GAGAAGAAAGAAAGAAAG-AAA
1 GAGAAGAAAGAAAGAAAGAAAA
*
44509478 -AG-A-AAATAAAGAAAGAAAA
1 GAGAAGAAAGAAAGAAAGAAAA
44509497 GAGAAGAAAGAAAGAAAGAAAA
1 GAGAAGAAAGAAAGAAAGAAAA
44509519 TGTATTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
18 11 0.31
19 4 0.11
20 4 0.11
21 1 0.03
22 15 0.43
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (22 bp):
GAGAAGAAAGAAAGAAAGAAAA
Found at i:44513258 original size:62 final size:62
Alignment explanation
Indices: 44513157--44513281 Score: 223
Period size: 62 Copynumber: 2.0 Consensus size: 62
44513147 CAATGTACCT
* *
44513157 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTTTATTACAA
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATATTGTAATGTATTTAATTTATATTACAA
*
44513219 AATTTATATTACAAAGTTTGTTCTAAGTTTTAATATTGTAATGTATTTAATTTATATTACAA
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATATTGTAATGTATTTAATTTATATTACAA
44513281 A
1 A
44513282 GTTTGTTCCA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.50
Consensus pattern (62 bp):
AATTTATATTACAAAGTTTGTTCCAAGTTTTAATATTGTAATGTATTTAATTTATATTACAA
Found at i:44513272 original size:48 final size:48
Alignment explanation
Indices: 44513219--44513310 Score: 166
Period size: 48 Copynumber: 1.9 Consensus size: 48
44513209 TTTATTACAA
*
44513219 AATTTATATTACAAAGTTTGTTCTAAGTTTTAATATTGTAATGTATTT
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATATTGTAATGTATTT
*
44513267 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGT
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATATTGTAATGT
44513311 TGTAATGTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.50
Consensus pattern (48 bp):
AATTTATATTACAAAGTTTGTTCCAAGTTTTAATATTGTAATGTATTT
Found at i:44514511 original size:14 final size:14
Alignment explanation
Indices: 44514492--44514526 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
44514482 TAAATTACAT
*
44514492 GTTAGAATAGTATC
1 GTTAGAATAATATC
44514506 GTTAGAATAATATC
1 GTTAGAATAATATC
*
44514520 ATTAGAA
1 GTTAGAA
44514527 AAAATGTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.34
Consensus pattern (14 bp):
GTTAGAATAATATC
Found at i:44533621 original size:40 final size:40
Alignment explanation
Indices: 44533566--44533723 Score: 289
Period size: 40 Copynumber: 4.0 Consensus size: 40
44533556 GGAAAAAAAA
*
44533566 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAC
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
44533606 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
44533646 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
* *
44533686 TATAACCGGGTTAAGTCCCGAAGGCATTTGTGCTGGTT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTT
44533724 GTTACATCCG
Statistics
Matches: 115, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 115 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (40 bp):
TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
Found at i:44533747 original size:80 final size:80
Alignment explanation
Indices: 44533581--44533749 Score: 239
Period size: 80 Copynumber: 2.1 Consensus size: 80
44533571 CCGGGTTAAG
44533581 TCCCGAAGGCATTCGTGCGGGTTACTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
1 TCCCGAAGGCATTCGTGCGGGTTACTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
* * ** *
44533646 TATAACCGGGTTAAG
66 TACAACCGAGCCAAA
* * * *
44533661 TCCCGAAGGCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGCATTTGTGCTGGTTGT
1 TCCCGAAGGCATTCGTGCGGGTTACTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
*
44533726 TACATCCGAGCCAAA
66 TACAACCGAGCCAAA
*
44533741 TTCCGAAGG
1 TCCCGAAGG
44533750 TATTTATGTT
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (80 bp):
TCCCGAAGGCATTCGTGCGGGTTACTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
TACAACCGAGCCAAA
Found at i:44535596 original size:19 final size:20
Alignment explanation
Indices: 44535574--44535611 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
44535564 CTGTTTTGTT
44535574 ATGGG-CCAACTGTATTAAA
1 ATGGGCCCAACTGTATTAAA
*
44535593 ATGGGCCCAACTGTGTTAA
1 ATGGGCCCAACTGTATTAA
44535612 TATAGGAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (20 bp):
ATGGGCCCAACTGTATTAAA
Found at i:44541309 original size:39 final size:39
Alignment explanation
Indices: 44541262--44541347 Score: 111
Period size: 39 Copynumber: 2.2 Consensus size: 39
44541252 ACTTAATGTG
** *
44541262 TAGCAGGCCTCGTGTCGGTGATAAATTTAG-GTTTATACC
1 TAGCAGGCCTCGTACCGGTG-TAAAGTTAGAGTTTATACC
* *
44541301 TAGCAGGCCTCGTACCGGTGTTAAGTTCGAGTTTATACC
1 TAGCAGGCCTCGTACCGGTGTAAAGTTAGAGTTTATACC
44541340 TAGCAGGC
1 TAGCAGGC
44541348 AAATTGCCGG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
38 6 0.15
39 35 0.85
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (39 bp):
TAGCAGGCCTCGTACCGGTGTAAAGTTAGAGTTTATACC
Found at i:44551557 original size:3 final size:3
Alignment explanation
Indices: 44551551--44551590 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
44551541 GATGATGATG
44551551 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
44551591 GAAAGAAACA
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:44552501 original size:22 final size:22
Alignment explanation
Indices: 44552470--44552532 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 22
44552460 GCTTTTGATC
* **
44552470 TTTTTGTGTATTTGATGCTCTA
1 TTTTTTTGTATTTGATAATCTA
*
44552492 TTTTTTTGTATTCGA-AATCTA
1 TTTTTTTGTATTTGATAATCTA
44552513 TTTTTTT-TATTTGATAATCT
1 TTTTTTTGTATTTGATAATCT
44552533 CATCCGTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 6 0.17
21 16 0.46
22 13 0.37
ACGTcount: A:0.19, C:0.08, G:0.11, T:0.62
Consensus pattern (22 bp):
TTTTTTTGTATTTGATAATCTA
Found at i:44553252 original size:97 final size:96
Alignment explanation
Indices: 44553143--44553319 Score: 212
Period size: 97 Copynumber: 1.8 Consensus size: 96
44553133 GATCTGATTT
* * * * * * * *
44553143 GTAATTTCTAGCTTTAATTTGTTCCACTGCAACTTTAGGGAAATGAGATTTGCTATCTTCAATCT
1 GTAATTTCTAGCTTCAATCTGCTCCACTACAACTTCAGGGAAATAAGATCTGCTATATTCAATCT
44553208 GCTCCTACTGCAACTTAAGAGAGATAAGACTC
66 GCTCC-ACTGCAACTTAAGAGAGATAAGACTC
* * * *
44553240 GTAACTTT-TAGCTTCAATCTGCTCTACTACAACTTCAGGGGAATAAGATCTGCTATATTTAGTC
1 GTAA-TTTCTAGCTTCAATCTGCTCCACTACAACTTCAGGGAAATAAGATCTGCTATATTCAATC
*
44553304 TGCTCCGCTGCAACTT
65 TGCTCCACTGCAACTT
44553320 TAGAATGATA
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
96 9 0.14
97 54 0.82
98 3 0.05
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.35
Consensus pattern (96 bp):
GTAATTTCTAGCTTCAATCTGCTCCACTACAACTTCAGGGAAATAAGATCTGCTATATTCAATCT
GCTCCACTGCAACTTAAGAGAGATAAGACTC
Found at i:44553447 original size:143 final size:142
Alignment explanation
Indices: 44553199--44553946 Score: 726
Period size: 143 Copynumber: 5.3 Consensus size: 142
44553189 GATTTGCTAT
* * *
44553199 CTTCAATCTGCTCCTACTGCAAC-TTAAGAGAGATAAGA-CT--CGTAACTTT-TAGCTTCAATC
1 CTTCAATCTGCTCC-ACTGCAACTTTAGGA-AGATAAGATCTGCCATAA-TTTGTAGCTTTAATC
* * * * * * * * * *
44553259 TGCTCTACTACAACTTCAGGGGAATAAGA-TCTGCTATATTTAGTCTGCTCCGCTGCAACTTTAG
63 TGTTCCACTGCAACGTCAAGGAAATAAGATTC-GCTGTCTTCAGTCTGCTCCGCTGCAACTTCAG
* *
44553323 AATGATAAGGCTGATGG
127 GA-GATAAGGCTGGTGG
* * * *
44553340 CTTCAGTCTGCTCCACTGCAACTTTAGGAAGATAAGATCTGCCACAATTTGTAACTTTAATCTAT
1 CTTCAATCTGCTCCACTGCAACTTTAGGAAGATAAGATCTGCCATAATTTGTAGCTTTAATCTGT
44553405 TCCACTGCAACGTCAAGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAG
66 TCCACTGCAACGTCAAGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCA-GGAG
*
44553470 ATAAGGCTAGTGG
130 ATAAGGCTGGTGG
* * * * * *
44553483 CTTCAATCTGCTCCACTACAACTTGAGGAAGATAATATTTGCTATAATTTGTAGCTTCAATCTGT
1 CTTCAATCTGCTCCACTGCAACTTTAGGAAGATAAGATCTGCCATAATTTGTAGCTTTAATCTGT
* * * * * ** ** *
44553548 TCCATTGCAACTTTAAGGAAATAAAATTCGCTGTCTTCAGTCTACTCTTCTATAACTTTAGGGAG
66 TCCACTGCAACGTCAAGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCA-GGAG
*
44553613 ACAAGGCTGGTGG
130 ATAAGGCTGGTGG
* * * * * ** * *
44553626 ATTCAATGTGCTCCACTACAACTTCAGGGAGATAAGAT-TCGCCATGGTTTGCAGCTTGAATCTG
1 CTTCAATCTGCTCCACTGCAACTTTAGGAAGATAAGATCT-GCCATAATTTGTAGCTTTAATCTG
* ** * * *
44553690 TTCCAGTGCAATTTTAGGGAAATAAGATTCGCTGTCTTTAGTCTGCTCCGCTGCAACTTCAAGGA
65 TTCCACTGCAACGTCAAGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTC-AGGA
44553755 GATAAGGCTGGTGG
129 GATAAGGCTGGTGG
* * * * * *
44553769 CTTCAATTTGCTCCACTGCAAGTTAAGGAAGATAACATCTACTATAATTTGTAGCTTTAATCTGT
1 CTTCAATCTGCTCCACTGCAACTTTAGGAAGATAAGATCTGCCATAATTTGTAGCTTTAATCTGT
* * * * * * *
44553834 TCCACTGCAACGTC-AGGGAA-AATATT-TCTGTATTCAGTCAGCTCCACTACAACTTCAGAGAG
66 TCCACTGCAACGTCAAGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAG-GAG
44553896 ATAAGGCTGGTGG
130 ATAAGGCTGGTGG
*
44553909 CTTCAATCTGTTCCACTGCAACTTTA-GAGAGATAAGAT
1 CTTCAATCTGCTCCACTGCAACTTTAGGA-AGATAAGAT
44553947 TCGCCATGGT
Statistics
Matches: 500, Mismatches: 95, Indels: 25
0.81 0.15 0.04
Matches are distributed among these distances:
139 4 0.01
140 86 0.17
141 25 0.05
142 8 0.02
143 371 0.74
144 6 0.01
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (142 bp):
CTTCAATCTGCTCCACTGCAACTTTAGGAAGATAAGATCTGCCATAATTTGTAGCTTTAATCTGT
TCCACTGCAACGTCAAGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGAGA
TAAGGCTGGTGG
Found at i:44579932 original size:14 final size:15
Alignment explanation
Indices: 44579910--44579939 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
44579900 GAATATTAAA
44579910 ACAAGAATTAAGAAC
1 ACAAGAATTAAGAAC
44579925 ACAA-AATTAAGAAC
1 ACAAGAATTAAGAAC
44579939 A
1 A
44579940 AGTCAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.63, C:0.13, G:0.10, T:0.13
Consensus pattern (15 bp):
ACAAGAATTAAGAAC
Found at i:44598567 original size:47 final size:46
Alignment explanation
Indices: 44598450--44598572 Score: 144
Period size: 46 Copynumber: 2.6 Consensus size: 46
44598440 AGACGAGTGT
* *
44598450 TAGTGTAAGACATGTCTAGGACATGCTTCAGCCTCAAGACGTAAGC
1 TAGTGTAAGACATGTCTGGGACATGCATCAGCCTCAAGACGTAAGC
* *
44598496 TAGTGTAAGACATGTCTGGGACATGCATCAG-CTACAAG-GGGATAG-
1 TAGTGTAAGACATGTCTGGGACATGCATCAGCCT-CAAGACGTA-AGC
44598541 TCAGTGTAAGACCATGTCTGGGACATGGCATC
1 T-AGTGTAAGA-CATGTCTGGGACAT-GCATC
44598573 GACTTGAGAT
Statistics
Matches: 68, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
45 5 0.07
46 44 0.65
47 14 0.21
48 5 0.07
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.24
Consensus pattern (46 bp):
TAGTGTAAGACATGTCTGGGACATGCATCAGCCTCAAGACGTAAGC
Found at i:44604853 original size:103 final size:103
Alignment explanation
Indices: 44604731--44604940 Score: 375
Period size: 103 Copynumber: 2.0 Consensus size: 103
44604721 ACGTGACTTA
*
44604731 TATGGGTGAGGGCTTGTAAGCCTATTTAACCAAGCTATGTATTGATGCCTGGTGATGTGGTCACG
1 TATGGGTGAGGGCTTGTAAGCCTATTTAACCAAGCTATGTATTGATGCCTGGCGATGTGGTCACG
44604796 TGATTATATTTGTTTGATATGAATGGTTAGTGTTACGG
66 TGATTATATTTGTTTGATATGAATGGTTAGTGTTACGG
* * *
44604834 TATGGGTGAGGGCTTGTAAGCCTATTTAACCAAGCTATGTATTGATTCTTGGCGATGTGGTCATG
1 TATGGGTGAGGGCTTGTAAGCCTATTTAACCAAGCTATGTATTGATGCCTGGCGATGTGGTCACG
*
44604899 TGATTATATTTGTTTGATATGAATGGTTAGTGTTATGG
66 TGATTATATTTGTTTGATATGAATGGTTAGTGTTACGG
44604937 TATG
1 TATG
44604941 TATGCTTGAT
Statistics
Matches: 102, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 102 1.00
ACGTcount: A:0.22, C:0.10, G:0.29, T:0.40
Consensus pattern (103 bp):
TATGGGTGAGGGCTTGTAAGCCTATTTAACCAAGCTATGTATTGATGCCTGGCGATGTGGTCACG
TGATTATATTTGTTTGATATGAATGGTTAGTGTTACGG
Found at i:44606663 original size:3 final size:3
Alignment explanation
Indices: 44606655--44606688 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
44606645 GGATGATTTA
* *
44606655 ATT ATT ATT ATT ATC ATT ATT ATT ATT ATA ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
44606689 AGTATGTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:44608770 original size:28 final size:28
Alignment explanation
Indices: 44608733--44608822 Score: 121
Period size: 28 Copynumber: 3.3 Consensus size: 28
44608723 GGGGGAAGTG
*
44608733 TTCTGGTGGCTATGCTACCAATATCTGT
1 TTCTGGTGGCTATGCCACCAATATCTGT
* *
44608761 TTCTGGTGGCTATGCCACAAATATTTG-
1 TTCTGGTGGCTATGCCACCAATATCTGT
*
44608788 TTCTGGTGGCTCTGCCA-CAATATCTGT
1 TTCTGGTGGCTATGCCACCAATATCTGT
*
44608815 ATCTGGTG
1 TTCTGGTG
44608823 ACTCTGTCAC
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
26 7 0.13
27 23 0.43
28 24 0.44
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (28 bp):
TTCTGGTGGCTATGCCACCAATATCTGT
Found at i:44608803 original size:27 final size:26
Alignment explanation
Indices: 44608731--44608846 Score: 133
Period size: 27 Copynumber: 4.3 Consensus size: 26
44608721 ATGGGGGAAG
*
44608731 TGTTCTGGTGGCTATGCTACCAATATC
1 TGTTCTGGTGGCTATGCCA-CAATATC
*
44608758 TGTTTCTGGTGGCTATGCCACAAATATT
1 TG-TTCTGGTGGCTATGCCAC-AATATC
*
44608786 TGTTCTGGTGGCTCTGCCACAATATC
1 TGTTCTGGTGGCTATGCCACAATATC
* * * *
44608812 TGTATCTGGTGACTCTGTCACAATATT
1 TGT-TCTGGTGGCTATGCCACAATATC
44608839 TGTTCTGG
1 TGTTCTGG
44608847 CAGCCCTGCT
Statistics
Matches: 79, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
26 13 0.16
27 43 0.54
28 23 0.29
ACGTcount: A:0.18, C:0.21, G:0.22, T:0.39
Consensus pattern (26 bp):
TGTTCTGGTGGCTATGCCACAATATC
Found at i:44608820 original size:54 final size:54
Alignment explanation
Indices: 44608731--44608846 Score: 162
Period size: 54 Copynumber: 2.1 Consensus size: 54
44608721 ATGGGGGAAG
* * *
44608731 TGTTCTGGTGGCTATGCTACCAATATCTGTTTCTGGTGGCTATGCCACAAATATT
1 TGTTCTGGTGGCTATGCCACCAATATCTGTATCTGGTGACTATGCCAC-AATATT
* * *
44608786 TGTTCTGGTGGCTCTGCCA-CAATATCTGTATCTGGTGACTCTGTCACAATATT
1 TGTTCTGGTGGCTATGCCACCAATATCTGTATCTGGTGACTATGCCACAATATT
44608839 TGTTCTGG
1 TGTTCTGG
44608847 CAGCCCTGCT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
53 14 0.25
54 24 0.44
55 17 0.31
ACGTcount: A:0.18, C:0.21, G:0.22, T:0.39
Consensus pattern (54 bp):
TGTTCTGGTGGCTATGCCACCAATATCTGTATCTGGTGACTATGCCACAATATT
Found at i:44612482 original size:76 final size:76
Alignment explanation
Indices: 44612356--44612507 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
44612346 AATATCAGGT
44612356 TCAACTCTCTACGGTGACATATTAACAACAGTTTATCCCACATAAGCATCTAAGCTGGGGTTGGG
1 TCAACTCTCTACGGTGACATATTAACAACAGTTTATCCCACATAAGCATCTAAGCTGGGGTTGGG
44612421 TGCCTGCTTTC
66 TGCCTGCTTTC
44612432 TCAACTCTCTACGGTGACATATTAACAACAGTTTATCCCACATAAGCATCTAAGCTGGGGTTGGG
1 TCAACTCTCTACGGTGACATATTAACAACAGTTTATCCCACATAAGCATCTAAGCTGGGGTTGGG
44612497 TGCCTGCTTTC
66 TGCCTGCTTTC
44612508 AAAGCTTTCT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (76 bp):
TCAACTCTCTACGGTGACATATTAACAACAGTTTATCCCACATAAGCATCTAAGCTGGGGTTGGG
TGCCTGCTTTC
Found at i:44617874 original size:28 final size:28
Alignment explanation
Indices: 44617837--44617951 Score: 121
Period size: 27 Copynumber: 4.2 Consensus size: 28
44617827 GGGGGAAGTG
*
44617837 TTCTGGTGGCTATGCTACAAATATCTGT
1 TTCTGGTGGCTATGCCACAAATATCTGT
*
44617865 TTCTGCTGGCTATGCCACAAATATCTG-
1 TTCTGGTGGCTATGCCACAAATATCTGT
* *
44617892 TTCTGGTAGCTCTGCCAC-AATATCTGT
1 TTCTGGTGGCTATGCCACAAATATCTGT
* * * * *
44617919 ATCTAGTGACTCTGTCAC-AATATCTG-
1 TTCTGGTGGCTATGCCACAAATATCTGT
44617945 TTCTGGT
1 TTCTGGT
44617952 AGCCCTGCTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
26 13 0.18
27 36 0.49
28 25 0.34
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (28 bp):
TTCTGGTGGCTATGCCACAAATATCTGT
Found at i:44617950 original size:53 final size:55
Alignment explanation
Indices: 44617835--44617959 Score: 148
Period size: 53 Copynumber: 2.3 Consensus size: 55
44617825 ATGGGGGAAG
* * * * *
44617835 TGTTCTGGTGGCTATGCTACAAATATCTGTTTCTGCTGGCTATGCCACAAATATC
1 TGTTCTGGTAGCTCTGCCACAAATATCTGTATCTGCTGACTATGCCACAAATATC
* *
44617890 TGTTCTGGTAGCTCTGCCAC-AATATCTGTATCTAG-TGACTCTGTCAC-AATATC
1 TGTTCTGGTAGCTCTGCCACAAATATCTGTATCT-GCTGACTATGCCACAAATATC
*
44617943 TGTTCTGGTAGCCCTGC
1 TGTTCTGGTAGCTCTGC
44617960 TGCAAATTCT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
53 22 0.36
54 21 0.34
55 18 0.30
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (55 bp):
TGTTCTGGTAGCTCTGCCACAAATATCTGTATCTGCTGACTATGCCACAAATATC
Found at i:44634253 original size:46 final size:48
Alignment explanation
Indices: 44634149--44634268 Score: 154
Period size: 48 Copynumber: 2.5 Consensus size: 48
44634139 TGTCCTCGAC
** * *
44634149 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATATATAAT
* * *
44634197 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCCATATA-A-CTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATATATAAT
*
44634243 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
44634269 CTGTCCTGTC
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
46 27 0.43
47 1 0.02
48 35 0.56
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (48 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATATATAAT
Found at i:44645150 original size:31 final size:31
Alignment explanation
Indices: 44645107--44645185 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
44645097 TTTAACGGTT
44645107 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
* * * *
44645138 ATTGGGCTGAAGCTTTTTCATAAATCATTTC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
44645169 ACTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
44645186 ACTGTAAACG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:44645254 original size:42 final size:42
Alignment explanation
Indices: 44645207--44645300 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
44645197 TATGGCCCAT
* ** *
44645207 AAGCCCATTTCAATATCACATGTAATGTCAATGGATGTATGC
1 AAGCCCATTTCAATATCACATGAAATACCAATGAATGTATGC
* *
44645249 AAGCCCTTTTCAATATCATATGAAATACCAATGAATGTATGC
1 AAGCCCATTTCAATATCACATGAAATACCAATGAATGTATGC
44645291 AAGCCCATTT
1 AAGCCCATTT
44645301 GGGGATACTA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (42 bp):
AAGCCCATTTCAATATCACATGAAATACCAATGAATGTATGC
Found at i:44645517 original size:26 final size:26
Alignment explanation
Indices: 44645433--44645568 Score: 199
Period size: 26 Copynumber: 5.3 Consensus size: 26
44645423 CTGGAGGCCT
44645433 AGCCTCTTTT-AAT-AACTGGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATA
**
44645457 AGCCCTTTTCGGTAAACTGGGGCA-A
1 AGCCCTTTTCAATAAACTGGGGCATA
44645482 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
**
44645508 AGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
44645534 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
44645560 AGCCCTTTT
1 AGCCCTTTT
44645569 GCACTTCCTC
Statistics
Matches: 101, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
23 5 0.05
24 5 0.05
25 33 0.33
26 58 0.57
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:44645557 original size:52 final size:51
Alignment explanation
Indices: 44645433--44645568 Score: 233
Period size: 52 Copynumber: 2.7 Consensus size: 51
44645423 CTGGAGGCCT
44645433 AGCCTCTTTT-AAT-AACTGGGGCA-AAGCCCTTTTCGGTAAACTGGGGCAA
1 AGCC-CTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCAA
44645482 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCA-A
44645534 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTT
1 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTT
44645569 GCACTTCCTC
Statistics
Matches: 83, Mismatches: 0, Indels: 5
0.94 0.00 0.06
Matches are distributed among these distances:
48 5 0.06
49 7 0.08
50 10 0.12
51 25 0.30
52 36 0.43
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (51 bp):
AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCAA
Found at i:44646042 original size:20 final size:21
Alignment explanation
Indices: 44646017--44646056 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
44646007 TGGGTTCGAA
44646017 AGCCCATTG-GGCCCAATTTT
1 AGCCCATTGAGGCCCAATTTT
44646037 AGCCCATTGAGGCCCAATTT
1 AGCCCATTGAGGCCCAATTT
44646057 ACCATCGTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.28
Consensus pattern (21 bp):
AGCCCATTGAGGCCCAATTTT
Found at i:44646433 original size:27 final size:27
Alignment explanation
Indices: 44646374--44646435 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
44646364 TATATTCATT
*
44646374 ATTTTACCATATAGGGGTATTACGGTC
1 ATTTTACCATACAGGGGTATTACGGTC
* *
44646401 ACTTTACCCTACAGGGGCT-TTACGGTC
1 ATTTTACCATACAGGGG-TATTACGGTC
*
44646428 TTTTTACC
1 ATTTTACC
44646436 TAATAGGGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 28 0.97
28 1 0.03
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (27 bp):
ATTTTACCATACAGGGGTATTACGGTC
Found at i:44646443 original size:27 final size:27
Alignment explanation
Indices: 44646374--44646448 Score: 66
Period size: 27 Copynumber: 2.8 Consensus size: 27
44646364 TATATTCATT
44646374 ATTTTACC-ATATAGGGGTATTACGGTC
1 ATTTTACCTA-ATAGGGGTATTACGGTC
* *
44646401 ACTTTACCCT-ACAGGGGCT-TTACGGTC
1 ATTTTA-CCTAATAGGGG-TATTACGGTC
* *
44646428 TTTTTACCTAATAGGGATATT
1 ATTTTACCTAATAGGGGTATT
44646449 TTAGTCATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
26 4 0.11
27 30 0.81
28 3 0.08
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (27 bp):
ATTTTACCTAATAGGGGTATTACGGTC
Found at i:44646519 original size:27 final size:27
Alignment explanation
Indices: 44646468--44646768 Score: 216
Period size: 27 Copynumber: 11.0 Consensus size: 27
44646458 TCATCCTACC
* * * *
44646468 AGGGTGTTTTGGTAAATCTACAAACTA
1 AGGGTATTTCGGTAATTTTACAAACTA
* **
44646495 AGGGTATTTCAGTAATTTTGTAAACTA
1 AGGGTATTTCGGTAATTTTACAAACTA
* ** * *
44646522 ATGGTATTTCTATAATTTTTAGAAAGTCA
1 AGGGTATTTCGGTAA-TTTTACAAACT-A
** *
44646551 AGGGTATTTTTGTAACTTTGTA-AATC-A
1 AGGGTATTTCGGTAA-TTT-TACAAACTA
* * * *
44646578 GGGGTATTTTGGTAATTTTACAAATTG
1 AGGGTATTTCGGTAATTTTACAAACTA
* *
44646605 AGGGTATTTCGGTAATTTCACAAAC-C
1 AGGGTATTTCGGTAATTTTACAAACTA
*
44646631 AGTGGTATTTTGGTAATTTTACAAACTA
1 AG-GGTATTTCGGTAATTTTACAAACTA
* * * *
44646659 GGGGTATTTTGGTAATTTTACAAGTCGA
1 AGGGTATTTCGGTAATTTTACAA-ACTA
* *
44646687 A-GGTATTTCAGTAATTTTACAAA-TCG
1 AGGGTATTTCGGTAATTTTACAAACT-A
* *
44646713 AGGGTATTTCAGTATTTTTACAAACTA
1 AGGGTATTTCGGTAATTTTACAAACTA
*
44646740 AGGGTATTTCGGTAATTTTAGTAAACTA
1 AGGGTATTTCGGTAATTTTA-CAAACTA
44646768 A
1 A
44646769 AATATTCTAA
Statistics
Matches: 216, Mismatches: 46, Indels: 23
0.76 0.16 0.08
Matches are distributed among these distances:
25 2 0.01
26 8 0.04
27 167 0.77
28 19 0.09
29 18 0.08
30 2 0.01
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.40
Consensus pattern (27 bp):
AGGGTATTTCGGTAATTTTACAAACTA
Found at i:44646671 original size:81 final size:81
Alignment explanation
Indices: 44646577--44646759 Score: 251
Period size: 81 Copynumber: 2.3 Consensus size: 81
44646567 TTTGTAAATC
* * *
44646577 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAA-CCAGTGGTATTT
1 AGGGGTATTTTGGTAATTTTACAAATCGAAGGTATTTCAGTAATTTCACAAATCCAG-GGTATTT
**
44646641 TGGTAATTTTACAAACT
65 CAGTAATTTTACAAACT
* * *
44646658 AGGGGTATTTTGGTAATTTTACAAGTCGAAGGTATTTCAGTAATTTTACAAATCGAGGGTATTTC
1 AGGGGTATTTTGGTAATTTTACAAATCGAAGGTATTTCAGTAATTTCACAAATCCAGGGTATTTC
*
44646723 AGTATTTTTACAAACT
66 AGTAATTTTACAAACT
* *
44646739 AAGGGTATTTCGGTAATTTTA
1 AGGGGTATTTTGGTAATTTTA
44646760 GTAAACTAAA
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
81 87 0.97
82 3 0.03
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (81 bp):
AGGGGTATTTTGGTAATTTTACAAATCGAAGGTATTTCAGTAATTTCACAAATCCAGGGTATTTC
AGTAATTTTACAAACT
Found at i:44650105 original size:32 final size:31
Alignment explanation
Indices: 44650069--44650180 Score: 125
Period size: 32 Copynumber: 3.5 Consensus size: 31
44650059 TGGGCCAGGT
* *
44650069 CATGTGGGCCACACGGCCAAGGCCAATTTGGG
1 CATGTAGGCCACACGG-CAAGGCCAATATGGG
* *
44650101 CATGTAGGCCACAAGAGCAAGGGCAATATGGG
1 CATGTAGGCCACACG-GCAAGGCCAATATGGG
* *
44650133 CATGTAGGCCACACGGGTAAGGCCAATCTGGG
1 CATGTAGGCCACAC-GGCAAGGCCAATATGGG
* *
44650165 CTTGCAGGCCACACGG
1 CATGTAGGCCACACGG
44650181 TCATGTGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
31 2 0.03
32 64 0.94
33 2 0.03
ACGTcount: A:0.26, C:0.26, G:0.34, T:0.14
Consensus pattern (31 bp):
CATGTAGGCCACACGGCAAGGCCAATATGGG
Found at i:44650969 original size:19 final size:20
Alignment explanation
Indices: 44650918--44650969 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
44650908 AAGGGCCATT
*
44650918 TTGTAAA-GTTGTAAAATAAG
1 TTGTAAATG-TGTGAAATAAG
44650938 TTGTAAATGTGTGAAATAA-
1 TTGTAAATGTGTGAAATAAG
44650957 TTG-AAATTGTGTG
1 TTGTAAA-TGTGTG
44650970 TTGCTATAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 3 0.10
19 9 0.31
20 16 0.55
21 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (20 bp):
TTGTAAATGTGTGAAATAAG
Found at i:44651763 original size:49 final size:49
Alignment explanation
Indices: 44651650--44651882 Score: 197
Period size: 49 Copynumber: 4.8 Consensus size: 49
44651640 CGGCCACATT
* * * * *
44651650 ATGAAAGCCAGTGTAAGACATGTCTGGGACAT-GCATCGGCCTCTAGAT
1 ATGAAAGCCAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAG
* ** *
44651698 ATGCAAGATAGTGTAAGACCTATCTGGGACATGGCATCGACAC-CGATAG
1 ATGAAAGCCAGTGTAAGACCTGTCTGGGACATGGCATCGAC-CTCGATAG
* * * * *
44651747 ATGAGAGCCAGTGTAAGACCTGTCTAGGACATGGCATTGGCCTCGATAT
1 ATGAAAGCCAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAG
** * * * *
44651796 ATGAAAGTTAGTGTAAGACCTGTCTGGAACATGGCATCCACTTAGATATG
1 ATGAAAGCCAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATA-G
* * *
44651846 -TG--AGCTAGTGTAAGACCATGTTTGGAACATGGCATCG
1 ATGAAAGCCAGTGTAAGACC-TGTCTGGGACATGGCATCG
44651883 GCATCGTACT
Statistics
Matches: 148, Mismatches: 32, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
47 14 0.09
48 45 0.30
49 88 0.59
50 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (49 bp):
ATGAAAGCCAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAG
Found at i:44651771 original size:97 final size:98
Alignment explanation
Indices: 44651650--44651833 Score: 271
Period size: 98 Copynumber: 1.9 Consensus size: 98
44651640 CGGCCACATT
* * *
44651650 ATGAAAGCCAGTGTAAGACATGTCTGGGACAT-GCATCGGCCTCTAGATATGCAAGATAGTGTAA
1 ATGAAAGCCAGTGTAAGACATGTCTAGGACATGGCATCGGCCTCGAGATATGAAAGATAGTGTAA
*
44651714 GACCTATCTGGGACATGGCATCGACACCGATAG
66 GACCTATCTGGAACATGGCATCGACACCGATAG
* * * * *
44651747 ATGAGAGCCAGTGTAAGACCTGTCTAGGACATGGCATTGGCCTCGATATATGAAAGTTAGTGTAA
1 ATGAAAGCCAGTGTAAGACATGTCTAGGACATGGCATCGGCCTCGAGATATGAAAGATAGTGTAA
*
44651812 GACCTGTCTGGAACATGGCATC
66 GACCTATCTGGAACATGGCATC
44651834 CACTTAGATA
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
97 29 0.38
98 47 0.62
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (98 bp):
ATGAAAGCCAGTGTAAGACATGTCTAGGACATGGCATCGGCCTCGAGATATGAAAGATAGTGTAA
GACCTATCTGGAACATGGCATCGACACCGATAG
Found at i:44654173 original size:26 final size:26
Alignment explanation
Indices: 44654144--44654193 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
44654134 ATGGGGGTAG
*
44654144 GATTCTGTTCATTTGATT-TGTTATAT
1 GATTCTGAT-ATTTGATTCTGTTATAT
*
44654170 GATTCTGATATTTGTTTCTGTTAT
1 GATTCTGATATTTGATTCTGTTAT
44654194 GGACTTAGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.18, C:0.08, G:0.16, T:0.58
Consensus pattern (26 bp):
GATTCTGATATTTGATTCTGTTATAT
Found at i:44655510 original size:29 final size:28
Alignment explanation
Indices: 44655462--44655516 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
44655452 ACAAGATTTA
44655462 CTGATTTGGCTTCAGACCATGCATATCGG
1 CTGATTTGGCTTCAGACCATG-ATATCGG
* *
44655491 CTGATTTGGCTTCGGTCCATGATATC
1 CTGATTTGGCTTCAGACCATGATATC
44655517 AAAATTTTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.35
Consensus pattern (28 bp):
CTGATTTGGCTTCAGACCATGATATCGG
Found at i:44658909 original size:39 final size:38
Alignment explanation
Indices: 44658835--44658909 Score: 87
Period size: 39 Copynumber: 1.9 Consensus size: 38
44658825 AAATCAGACA
* ** *
44658835 AGTATAGTTTGGGCCTAAGCCCATTTCAGTGGCAGTCC
1 AGTATAGTGTGGGCCTAAGCCCATAGCAGTAGCAGTCC
* *
44658873 AGTATCAGTGTGGGCCTTAGCCTATAGCAGTAGCAGT
1 AGTAT-AGTGTGGGCCTAAGCCCATAGCAGTAGCAGT
44658910 ATCAATGTGG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
38 5 0.17
39 25 0.83
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (38 bp):
AGTATAGTGTGGGCCTAAGCCCATAGCAGTAGCAGTCC
Found at i:44666573 original size:52 final size:52
Alignment explanation
Indices: 44666514--44666618 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
44666504 TAAAGACTTA
44666514 AATTTTAGAACAGTAACAAAAACAATTGTGTAGCCTCCATCGAATTCTTCGC
1 AATTTTAGAACAGTAACAAAAACAATTGTGTAGCCTCCATCGAATTCTTCGC
44666566 AATTTTAGAACAGTAACAAAAACAATTGTGTAGCCTCCATCGAATTCTTCGC
1 AATTTTAGAACAGTAACAAAAACAATTGTGTAGCCTCCATCGAATTCTTCGC
44666618 A
1 A
44666619 GCACTGACCT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (52 bp):
AATTTTAGAACAGTAACAAAAACAATTGTGTAGCCTCCATCGAATTCTTCGC
Found at i:44668228 original size:104 final size:103
Alignment explanation
Indices: 44668049--44668271 Score: 376
Period size: 104 Copynumber: 2.2 Consensus size: 103
44668039 TGTATATAAA
** * *
44668049 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGTGGTGCTATGTGCGTGATCCACCATATCTTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGTGGTGCTAAGTGCGTGATCCACCATATCTTT
44668114 GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
44668152 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCA-TGGTGGTGCTAAGTGCG-TGATCCACCATATCT
44668216 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
64 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
44668256 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
44668272 GATATCCATT
Statistics
Matches: 113, Mismatches: 5, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
103 27 0.24
104 85 0.75
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.31, T:0.31
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGTGGTGCTAAGTGCGTGATCCACCATATCTTT
GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:44668323 original size:71 final size:72
Alignment explanation
Indices: 44668190--44668341 Score: 252
Period size: 71 Copynumber: 2.1 Consensus size: 72
44668180 TCATTGGTGG
* *
44668190 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
44668255 GAGGGGT
66 GAGGGGT
***
44668262 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
44668326 GAGGGGT
66 GAGGGGT
44668333 TGCTAAGTG
1 TGCTAAGTG
44668342 ATGATTCCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 45 0.60
72 30 0.40
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:44675780 original size:104 final size:103
Alignment explanation
Indices: 44675600--44675822 Score: 367
Period size: 104 Copynumber: 2.2 Consensus size: 103
44675590 TGTATATAAA
** * *
44675600 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
44675665 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCCG
* *
44675704 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
44675768 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
44675807 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
44675823 GATATCCATT
Statistics
Matches: 112, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
103 21 0.19
104 90 0.80
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
Found at i:44675873 original size:70 final size:72
Alignment explanation
Indices: 44675742--44675892 Score: 234
Period size: 71 Copynumber: 2.1 Consensus size: 72
44675732 TCATTGGTGG
* **
44675742 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
44675806 GAGGGGT
66 GAGGGGT
***
44675813 TGCTAAGTGCGATATCCATTGTATATTTGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
44675877 GAGGGGT
66 GAGGGGT
44675884 TGCTAAGTG
1 TGCTAAGTG
44675893 ATGATTCCCC
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
70 24 0.33
71 49 0.67
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:44677242 original size:22 final size:23
Alignment explanation
Indices: 44677205--44677247 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
44677195 GAAATTCTAC
44677205 CCATCCATCCCCTACACTCCACT
1 CCATCCATCCCCTACACTCCACT
44677228 CCATCCAT-CCCTACACTCCA
1 CCATCCATCCCCTACACTCCA
44677248 TGTGGGGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.23, C:0.56, G:0.00, T:0.21
Consensus pattern (23 bp):
CCATCCATCCCCTACACTCCACT
Found at i:44685016 original size:21 final size:21
Alignment explanation
Indices: 44684991--44685054 Score: 53
Period size: 21 Copynumber: 3.0 Consensus size: 21
44684981 TATAGTATAC
44684991 ATAAAATACAAATAATTTAAT
1 ATAAAATACAAATAATTTAAT
44685012 AT-AAATAACATAAATAA--TAAT
1 ATAAAAT-AC--AAATAATTTAAT
* * *
44685033 ATAAATTACAAGTAGTTTAAT
1 ATAAAATACAAATAATTTAAT
44685054 A
1 A
44685055 ATGATATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 12
0.69 0.06 0.24
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 17 0.50
22 3 0.09
23 6 0.18
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (21 bp):
ATAAAATACAAATAATTTAAT
Found at i:44685079 original size:30 final size:27
Alignment explanation
Indices: 44685024--44685084 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 27
44685014 AAATAACATA
* *
44685024 AATAATAATATAAATTACAAGTAGTTT
1 AATAATAATATAAAATACAAATAGTTT
44685051 AATAATGATATATAAAAATACAAATAGTTT
1 AATAAT-A-ATAT-AAAATACAAATAGTTT
44685081 AATA
1 AATA
44685085 CACAAGTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 6 0.21
28 1 0.03
29 4 0.14
30 18 0.62
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.34
Consensus pattern (27 bp):
AATAATAATATAAAATACAAATAGTTT
Found at i:44686838 original size:44 final size:43
Alignment explanation
Indices: 44686778--44687017 Score: 203
Period size: 45 Copynumber: 5.4 Consensus size: 43
44686768 TAGTCTTACA
* * * * *
44686778 GCAACTTTAGGAAGATAAGGTTTGTGACTTCAACCTGCTCCACT
1 GCAACTTCAGGGAGATAAGATTTGT-ACTTTAATCTGCTCCACT
* * *
44686822 GCATCTTCAGGGAGATAAGGATTATG-GCTTTGATCTGCTCCACT
1 GCAACTTCAGGGAGATAA-GATT-TGTACTTTAATCTGCTCCACT
* * * * *
44686866 GGAACTTCAGGGAGATAAGATCTGCCATCTTTAGTCTGCTCCATT
1 GCAACTTCAGGGAGATAAGATTTG-TA-CTTTAATCTGCTCCACT
* * *
44686911 GCAACTTTAGGGAGATAAGACTTGCTATCTTTAGTCTGCTCCACT
1 GCAACTTCAGGGAGATAAGATTTG-TA-CTTTAATCTGCTCCACT
* * ** * * *
44686956 GCAAATTCAAGGAGATAAGATTACTACTTCAACCTGCTTCACT
1 GCAACTTCAGGGAGATAAGATTTGTACTTTAATCTGCTCCACT
44686999 GCAACTTCAGGGAGATAAG
1 GCAACTTCAGGGAGATAAG
44687018 GTTTTCAATC
Statistics
Matches: 158, Mismatches: 33, Indels: 11
0.78 0.16 0.05
Matches are distributed among these distances:
42 2 0.01
43 33 0.21
44 47 0.30
45 74 0.47
46 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.30
Consensus pattern (43 bp):
GCAACTTCAGGGAGATAAGATTTGTACTTTAATCTGCTCCACT
Found at i:44687029 original size:133 final size:134
Alignment explanation
Indices: 44686812--44687065 Score: 298
Period size: 133 Copynumber: 1.9 Consensus size: 134
44686802 TGACTTCAAC
** * * ** * *
44686812 CTGCTCCACTGCATCTTCAGGGAGATAAGGATTATGGCTTTGATCTGCTCCACTGGAACTTCAGG
1 CTGCTCCACTGCAAATTCAAGGAGATAAGGATTATGACTTCAACCTGCTCCACTGCAACTTCAGG
* * * * *
44686877 GAGATAAGATCTGCCATCTTTAGTCTGC-TCCATTGCAACTTTAGGGAGATAAGACTTGCTATCT
66 GAGATAAGATCTGCAATCTTCAGTCTGCTTCC-TTGCAACATCAGGAAGATAAGACTTGCTATCT
44686941 TTAGT
130 TTAGT
*
44686946 CTGCTCCACTGCAAATTCAAGGAGATAA-GATTACT-ACTTCAACCTGCTTCACTGCAACTTCAG
1 CTGCTCCACTGCAAATTCAAGGAGATAAGGATTA-TGACTTCAACCTGCTCCACTGCAACTTCAG
* * * * *
44687009 GGAGATAAGGTTTTCAATCTTCAGTTTGCTTCCTTGCTACATCAGGAAGATAAGACT
65 GGAGATAAGATCTGCAATCTTCAGTCTGCTTCCTTGCAACATCAGGAAGATAAGACT
44687066 ACAATCTTCG
Statistics
Matches: 99, Mismatches: 19, Indels: 5
0.80 0.15 0.04
Matches are distributed among these distances:
133 70 0.71
134 29 0.29
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (134 bp):
CTGCTCCACTGCAAATTCAAGGAGATAAGGATTATGACTTCAACCTGCTCCACTGCAACTTCAGG
GAGATAAGATCTGCAATCTTCAGTCTGCTTCCTTGCAACATCAGGAAGATAAGACTTGCTATCTT
TAGT
Found at i:44687054 original size:45 final size:45
Alignment explanation
Indices: 44687005--44687107 Score: 127
Period size: 44 Copynumber: 2.3 Consensus size: 45
44686995 CACTGCAACT
** * *
44687005 TCAGGGAGATAAGGTTTTCAATCTTCAGTTTGCTTCCTTGCTACA
1 TCAGGGAGATAAGGACTACAATCTTCAGTTTGCTCCCTTGCTACA
* * *
44687050 TCAGGAAGATAA-GACTACAATCTTCGGTTTGCTCCCTTGCTACT
1 TCAGGGAGATAAGGACTACAATCTTCAGTTTGCTCCCTTGCTACA
*
44687094 TTAGGGAGATAAGG
1 TCAGGGAGATAAGG
44687108 CTAGTGGTTA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
44 36 0.75
45 12 0.25
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (45 bp):
TCAGGGAGATAAGGACTACAATCTTCAGTTTGCTCCCTTGCTACA
Found at i:44687190 original size:177 final size:177
Alignment explanation
Indices: 44687007--44687901 Score: 1097
Period size: 177 Copynumber: 5.1 Consensus size: 177
44686997 CTGCAACTTC
* * * *
44687007 AGGGAGATAAGGTTTTCAATCTTCAGTTTGCTTCCTTGCTACATCAGGAAGATAAGACTACAATC
1 AGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTACAATC
**** * * * * * * *
44687072 TTCGGTTTGCTCCCTTGCTACTTTAGGGAGATAAGGCTAGTGGTTAAAATCTGCTCCCCTACTAC
66 TTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCCCTGCTAC
* *
44687137 CTCGGGAAGATAAGATTCGCCATCTTCGATCTACTTCACTACCGCTT
131 CTCGGGAAGATAAGATTCGCCATCTTCGATCTACTCCACTACTGCTT
** * *
44687184 AGGGAGATAAGATAGTCAATCCTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACT--AGTC
1 AGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTACAATC
*
44687247 TTCAACCTGCTCTATTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCCCTGCTAC
66 TTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCCCTGCTAC
* *
44687312 CTCGGGAAGATAAGATTCGCCATCCTCGATCTACTCTACTACTGCTT
131 CTCGGGAAGATAAGATTCGCCATCTTCGATCTACTCCACTACTGCTT
* * * *
44687359 AGGGAGATAGGATCTTCAATC-TCAGTCTGCTTCCTTGCTACCTCAAGAAGGTAAGACTTCAA--
1 AGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTACAATC
* * * * * *
44687421 TTCAGCCTGCTCCCTTTCTACCTTAG-GAAGATAAGGCTAGTGGCTAAAATCTACTCCCCTGCTA
66 TTCAACCTGCTCTCTTGCTACCTCAGAG-AGATAAGGCTGGTGGCTAAAATCTGCTCCCCTGCTA
* * * * **
44687485 CCTTC-GGAGGATGAGATTCACCATCTTTGATCTACTCCACTACTATTT
130 CC-TCGGGAAGATAAGATTCGCCATCTTCGATCTACTCCACTACTGCTT
* * * *
44687533 AGGGAGATAAGATCTTC-ATCATT-AGTCTGCTTCCTTGTTACCTAAGTAATATAAGACTACAAT
1 AGGGAGATAAGATCTTCAATC-TTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTACAAT
* *
44687596 CTTCAACATGCTCTCTTGCTACTTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCCCTGCTA
65 CTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCCCTGCTA
* * * * * **
44687661 CCTCGGGAAGATAAGATTTGCAATCTTCAATTTGCTCCACTGTTGCTT
130 CCTCGGGAAGATAAGATTCGCCATCTTCGATCTACTCCACTACTGCTT
* * * *
44687709 AGGGAGATAAGATCTTCAATATTCAGTTTGCTTCCTTGTTACCTCAGGAAGATAAGACTACCATC
1 AGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTACAATC
44687774 TTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCCCTGCTAC
66 TTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCCCTGCTAC
* ** * * * * *
44687839 ATCGAAAAGATAAGATTCTCCATCTTCAATCTACTCCACTTCTATCTC
131 CTCGGGAAGATAAGATTCGCCATCTTCGATCTACTCCACTACT-GCTT
*
44687887 AGGGAGATGAGATCT
1 AGGGAGATAAGATCT
44687902 GTGAATTCAC
Statistics
Matches: 611, Mismatches: 94, Indels: 25
0.84 0.13 0.03
Matches are distributed among these distances:
173 4 0.01
174 175 0.29
175 122 0.20
176 106 0.17
177 188 0.31
178 16 0.03
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (177 bp):
AGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTACAATC
TTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCCCTGCTAC
CTCGGGAAGATAAGATTCGCCATCTTCGATCTACTCCACTACTGCTT
Found at i:44687765 original size:45 final size:45
Alignment explanation
Indices: 44687648--44687765 Score: 116
Period size: 44 Copynumber: 2.6 Consensus size: 45
44687638 GGCTAAAATC
* * * *
44687648 TGCTCCCCTGCTACCTCGGGAAGATAAGATTTGCAATCTTCAATT
1 TGCTCCACTGTTACCTCAGGAAGATAAGATTTGCAATATTCAATT
* * * *
44687693 TGCTCCACTGTT-GCTTAGGGAGATAAGATCTT-CAATATTCAGTT
1 TGCTCCACTGTTACCTCAGGAAGATAAGAT-TTGCAATATTCAATT
*
44687737 TGCTTCC-TTGTTACCTCAGGAAGATAAGA
1 TGC-TCCACTGTTACCTCAGGAAGATAAGA
44687766 CTACCATCTT
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
44 30 0.52
45 28 0.48
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.33
Consensus pattern (45 bp):
TGCTCCACTGTTACCTCAGGAAGATAAGATTTGCAATATTCAATT
Found at i:44689186 original size:14 final size:12
Alignment explanation
Indices: 44689156--44689222 Score: 62
Period size: 13 Copynumber: 5.1 Consensus size: 12
44689146 TGTTGATTGA
*
44689156 TTTTTTATTATAT
1 TTTTTTATT-TTT
44689169 TTTTTTATTTTT
1 TTTTTTATTTTT
*
44689181 CCTTTTTTCTTTCTT
1 --TTTTTTATTT-TT
44689196 TTTTTTATTTTT
1 TTTTTTATTTTT
44689208 ATTTATTTATTTTT
1 -TTT-TTTATTTTT
44689222 T
1 T
44689223 AACGTCTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
12 4 0.09
13 22 0.48
14 18 0.39
15 2 0.04
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTATTTTT
Found at i:44689186 original size:27 final size:27
Alignment explanation
Indices: 44689156--44689207 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
44689146 TGTTGATTGA
44689156 TTTTTTATTAT-ATTTTTTTATTTTTCC
1 TTTTTTATT-TCATTTTTTTATTTTTCC
* *
44689183 TTTTTTCTTTCTTTTTTTTATTTTT
1 TTTTTTATTTCATTTTTTTATTTTT
44689208 ATTTATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 1 0.05
27 21 0.95
ACGTcount: A:0.10, C:0.08, G:0.00, T:0.83
Consensus pattern (27 bp):
TTTTTTATTTCATTTTTTTATTTTTCC
Found at i:44692587 original size:19 final size:19
Alignment explanation
Indices: 44692563--44692608 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
44692553 GTGAAAAGCT
44692563 AATGCAAATG-ATGCAATG
1 AATGCAAATGCATGCAATG
*
44692581 CAATGCAAATGCATGGAATG
1 -AATGCAAATGCATGCAATG
44692601 AATGCAAA
1 AATGCAAA
44692609 AGAATGAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.46, C:0.13, G:0.22, T:0.20
Consensus pattern (19 bp):
AATGCAAATGCATGCAATG
Found at i:44699953 original size:18 final size:18
Alignment explanation
Indices: 44699916--44699954 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
44699906 TTGGAAATCA
*
44699916 AAATTATTAAAAGATGAT
1 AAATTATTAAAAGATAAT
44699934 AAATTATTAAATAGA-AAT
1 AAATTATTAAA-AGATAAT
44699952 AAA
1 AAA
44699955 AATCATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (18 bp):
AAATTATTAAAAGATAAT
Found at i:44720831 original size:34 final size:34
Alignment explanation
Indices: 44720792--44720860 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
44720782 TCAGCTACCT
* *
44720792 TAGAAGAATACATATGCACTGATTAAGTATTGCA
1 TAGAAGAATAAAAATGCACTGATTAAGTATTGCA
*
44720826 TAGAAGGATAAAAATGCACTGATTAAGTATTGCA
1 TAGAAGAATAAAAATGCACTGATTAAGTATTGCA
44720860 T
1 T
44720861 CCATTAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (34 bp):
TAGAAGAATAAAAATGCACTGATTAAGTATTGCA
Found at i:44724978 original size:30 final size:30
Alignment explanation
Indices: 44724944--44725003 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
44724934 CATTTAATCT
*
44724944 AACTTTGGA-AAAATTACATTTTTTCCCCTA
1 AACTTT-GACAAAATTACACTTTTTCCCCTA
* *
44724974 AACTTTTACATAATTACACTTTTTCCCCTA
1 AACTTTGACAAAATTACACTTTTTCCCCTA
44725004 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.32, C:0.23, G:0.03, T:0.42
Consensus pattern (30 bp):
AACTTTGACAAAATTACACTTTTTCCCCTA
Found at i:44732453 original size:30 final size:30
Alignment explanation
Indices: 44732408--44732467 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
44732398 ATTTAATACG
*
44732408 AACTTTGGCAAAATTACATTTTTTCCCCTA
1 AACTTTGGCAAAATTACACTTTTTCCCCTA
* *
44732438 AACTTTTGCATAATTACACTTTTTCCCCTA
1 AACTTTGGCAAAATTACACTTTTTCCCCTA
44732468 GGCTCGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.25, G:0.05, T:0.42
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTTCCCCTA
Found at i:44735106 original size:25 final size:25
Alignment explanation
Indices: 44735041--44735106 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
44735031 TCTCAAAAAT
* *
44735041 TTAATTAAA-TAAAAATTATTAATGA
1 TTAAATAAATTAAAAATTA-TAATAA
*
44735066 TTCAATAAATTGAAAAATTA-AATAA
1 TTAAATAAATT-AAAAATTATAATAA
44735091 TTAAATAAAATTAAAA
1 TTAAAT-AAATTAAAA
44735107 TCTAGGAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
25 20 0.59
26 6 0.18
27 8 0.24
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.35
Consensus pattern (25 bp):
TTAAATAAATTAAAAATTATAATAA
Found at i:44735745 original size:18 final size:18
Alignment explanation
Indices: 44735708--44735741 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
44735698 AAACAAATAT
44735708 ATGCATATTAAATTATTA
1 ATGCATATTAAATTATTA
*
44735726 ATGC-TATTAATTTATT
1 ATGCATATTAAATTATT
44735742 TAATCAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (18 bp):
ATGCATATTAAATTATTA
Found at i:44738491 original size:20 final size:20
Alignment explanation
Indices: 44738468--44738506 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
44738458 TAAACATGGT
44738468 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
44738488 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
44738507 TGTATTCACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:44738633 original size:48 final size:48
Alignment explanation
Indices: 44738557--44738725 Score: 232
Period size: 49 Copynumber: 3.5 Consensus size: 48
44738547 GAGGAAGTGC
* * * * *
44738557 AAAAGGGCTTACGCCCCAGTTATCAAAAGGACTTATGCCCTAGTGATT
1 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
44738605 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
* *
44738653 AAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAATTATT
1 -AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
*
44738702 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
44738726 ATGATAAAGT
Statistics
Matches: 110, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
48 53 0.48
49 57 0.52
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
Found at i:44738725 original size:25 final size:24
Alignment explanation
Indices: 44738557--44738725 Score: 232
Period size: 24 Copynumber: 7.0 Consensus size: 24
44738547 GAGGAAGTGC
* *
44738557 AAAAGGGCTTACGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
* * *
44738581 AAAAGGACTTATGCCCTAGTGATT
1 AAAAGGGCTTATGCCCCAGTTATT
44738605 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
44738629 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
44738653 AAAAAGGGCTTATGCCCCAGTTATT
1 -AAAAGGGCTTATGCCCCAGTTATT
* *
44738678 AAAAGGGCTTTTGCCCCAATTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
44738702 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
44738726 ATGATAAAGT
Statistics
Matches: 129, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
24 95 0.74
25 34 0.26
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:44746700 original size:25 final size:25
Alignment explanation
Indices: 44746666--44746715 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
44746656 CCTTATAATA
*
44746666 TGAAACTGACCGTTTTGCCCCTAGG
1 TGAAAATGACCGTTTTGCCCCTAGG
44746691 TGAAAATGACCGTTTTGCCCCTAGG
1 TGAAAATGACCGTTTTGCCCCTAGG
44746716 GTTTAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (25 bp):
TGAAAATGACCGTTTTGCCCCTAGG
Found at i:44746818 original size:20 final size:20
Alignment explanation
Indices: 44746752--44746818 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
44746742 ATTTTGATAA
*
44746752 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
* *
44746772 AAATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
44746792 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
44746812 ACATGAT
1 ACATGAT
44746819 GTATTCATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:44746894 original size:24 final size:24
Alignment explanation
Indices: 44746867--44747227 Score: 535
Period size: 24 Copynumber: 15.0 Consensus size: 24
44746857 GGAGGAAGTG
*
44746867 CAAAAGCGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
44746891 CAAAAGGGCTTATGCCCTAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
44746915 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
44746939 TAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
44746963 CAAAAGGGCTTATGCCCTAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
44746987 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
44747011 TAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
44747035 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
44747059 CAAAAGGGCTTATGCCCTAATTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
44747083 TAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
44747107 CAAAAGGGCTTATGCCCCAATTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
44747131 TAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
44747155 CAAAAGGGTTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* * * * *
44747179 TATAAGGGATTTTGCTCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
44747203 TAAAAGAGG-TTAGGCCTCCAGTTAT
1 CAAAAG-GGCTTATGCC-CCAGTTAT
44747228 ATGATAAAGC
Statistics
Matches: 306, Mismatches: 29, Indels: 3
0.91 0.09 0.01
Matches are distributed among these distances:
24 296 0.97
25 10 0.03
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.29
Consensus pattern (24 bp):
CAAAAGGGCTTATGCCCCAGTTAT
Found at i:44755297 original size:20 final size:20
Alignment explanation
Indices: 44755274--44755331 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
44755264 TAAACATGGT
44755274 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
44755294 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
*
44755314 ATGTATGATATGAACATG
1 ATGTATGATATGCACATG
44755332 GTGTATTCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:44755532 original size:24 final size:24
Alignment explanation
Indices: 44755383--44755537 Score: 229
Period size: 24 Copynumber: 6.4 Consensus size: 24
44755373 GAGGAAGTGC
* *
44755383 AAAAGGGCTTATGCCCCAATTATG
1 AAAAGGGCTTATGCCCCAGTTATT
*
44755407 AAAAGGGCTTATGCCTCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
44755431 AAAAAGGGCTTATGCCCCAGTTATT
1 -AAAAGGGCTTATGCCCCAGTTATT
*
44755456 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
44755480 AAAAGGGCTTATGCCCCAATTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
44755504 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
44755528 GAAAGCGGCT
1 AAAAG-GGCT
44755538 AGGCATCCAG
Statistics
Matches: 119, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
24 92 0.77
25 27 0.23
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:44763343 original size:47 final size:48
Alignment explanation
Indices: 44763273--44763488 Score: 232
Period size: 47 Copynumber: 4.6 Consensus size: 48
44763263 TAAGTTGCCA
*
44763273 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT-ATCTCAAGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAAGCCG
* * *
44763320 GTGCCATGTCCCAGACATGGTCTTACACTGACT-ATCATCTCGTAGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTC-AAGCCG
* * *
44763368 ATG-CATGTCCCAGACGT-ATCTTACACTGGCTTA-CATCTCAAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAA-GCCG
* * ** * *
44763414 ATG-CATGTCCCAGACAT-GTCTTACACTAGCAC-TCGCCTCAGTGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCA-AGCCG
44763460 ATGCCATGTCCCAGACATGGTCTTACACT
1 ATGCCATGTCCCAGACATGGTCTTACACT
44763489 AGCTTCTCTA
Statistics
Matches: 143, Mismatches: 18, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
45 1 0.01
46 62 0.43
47 64 0.45
48 16 0.11
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAAGCCG
Found at i:44763515 original size:47 final size:45
Alignment explanation
Indices: 44763263--44763536 Score: 220
Period size: 47 Copynumber: 5.8 Consensus size: 45
44763253 CGAATATGGG
* *
44763263 TAAGTTGCCAATGCCATGTCCCAGACATGGTCTTACACTGGC-TCATATC
1 TAAG-TGCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTTC--ATC
*
44763312 TCAAGT--CGGTGCCATGTCCCAGACATGGTCTTACACT-GACTATCATC
1 T-AAGTGCCGATG-CATGTCCCAGACAT-GTCTTACACTAG-CT-TCATC
* * * *
44763359 T-CGTAGCCGATGCATGTCCCAGACGTATCTTACACTGGCTTACATC
1 TAAGT-GCCGATGCATGTCCCAGACATGTCTTACACTAGCTT-CATC
* **
44763405 TCAAG-GCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCGCC
1 T-AAGTGCCGATGCATGTCCCAGACATGTCTTACACTAGC-TTCATC
* *
44763451 TCAGTGCTGATGCCATGTCCCAGACATGGTCTTACACTAGCTTC-TC
1 TAAGTGCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTTCATC
*
44763497 TAATGTGGCCGATGCATGTCCCATACATGTCTTACACTAG
1 TAA-GT-GCCGATGCATGTCCCAGACATGTCTTACACTAG
44763537 AAAATACAAG
Statistics
Matches: 188, Mismatches: 20, Indels: 37
0.77 0.08 0.15
Matches are distributed among these distances:
45 5 0.03
46 72 0.38
47 80 0.43
48 24 0.13
49 4 0.02
50 3 0.02
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (45 bp):
TAAGTGCCGATGCATGTCCCAGACATGTCTTACACTAGCTTCATC
Found at i:44763891 original size:30 final size:30
Alignment explanation
Indices: 44763850--44763908 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
44763840 AAATTCACAT
* * *
44763850 CCTTGGTAAAATGACCATTTTGTCCCTAGA
1 CCTTGGCAAAATAACCATTTTGCCCCTAGA
44763880 CCTTGGCAAAATAACCATTTTGCCCCTAG
1 CCTTGGCAAAATAACCATTTTGCCCCTAG
44763909 GCTCGAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (30 bp):
CCTTGGCAAAATAACCATTTTGCCCCTAGA
Found at i:44766538 original size:27 final size:27
Alignment explanation
Indices: 44766507--44766558 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
44766497 TGTAGCAATT
* *
44766507 CATACAACCCATGTAATAGTAATTTAA
1 CATACAACCCATGTAACAATAATTTAA
**
44766534 CATACAATTCATGTAACAATAATTT
1 CATACAACCCATGTAACAATAATTT
44766559 GCCATTCAAT
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:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (27 bp):
CATACAACCCATGTAACAATAATTTAA
Found at i:44780012 original size:19 final size:20
Alignment explanation
Indices: 44779973--44780012 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
44779963 CCGTCCCAAT
44779973 CCAACCAACACACCACCTGTA
1 CCAACCAACACACCA-CTGTA
44779994 CCAACCAACACACCA-TGTA
1 CCAACCAACACACCACTGTA
44780013 GGGATAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
21 15 0.79
ACGTcount: A:0.40, C:0.45, G:0.05, T:0.10
Consensus pattern (20 bp):
CCAACCAACACACCACTGTA
Found at i:44780270 original size:22 final size:21
Alignment explanation
Indices: 44780238--44780318 Score: 99
Period size: 22 Copynumber: 3.7 Consensus size: 21
44780228 ATATGATCGA
* *
44780238 CACAGAACCATGATCAAGATGG
1 CACAGAGCCATAATC-AGATGG
44780260 CACAGAGCCATAATCGAGATGG
1 CACAGAGCCATAATC-AGATGG
**
44780282 CACAGAGCCATCTTCAGAATGG
1 CACAGAGCCATAATCAG-ATGG
44780304 CACAGAGCCATAATC
1 CACAGAGCCATAATC
44780319 GGATCAAGTG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
21 2 0.04
22 49 0.96
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (21 bp):
CACAGAGCCATAATCAGATGG
Found at i:44780754 original size:27 final size:27
Alignment explanation
Indices: 44780724--44780778 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
44780714 TTTTACCCTA
** *
44780724 CAGGCGTATTTTGGTAATTTTACAAAT
1 CAGGCGTATTTCAGTAATCTTACAAAT
*
44780751 CAGGGGTATTTCAGTAATCTTACAAAT
1 CAGGCGTATTTCAGTAATCTTACAAAT
44780778 C
1 C
44780779 GAGGGTCTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (27 bp):
CAGGCGTATTTCAGTAATCTTACAAAT
Found at i:44782294 original size:24 final size:24
Alignment explanation
Indices: 44782249--44782294 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
44782239 CCTAAAATCC
*
44782249 CTCCATGATTTCCTCCCCAATCTT
1 CTCCATGATTTCCTCCACAATCTT
* * *
44782273 CTCCTTGATTTTCTCCATAATC
1 CTCCATGATTTCCTCCACAATC
44782295 CATTCCTTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.17, C:0.37, G:0.04, T:0.41
Consensus pattern (24 bp):
CTCCATGATTTCCTCCACAATCTT
Found at i:44784213 original size:22 final size:22
Alignment explanation
Indices: 44784187--44784243 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
44784177 AGATGGAAGG
*
44784187 AGCCATAATCGGGATGGCACAA
1 AGCCATAATCGGAATGGCACAA
** ** *
44784209 AGCCATCTTTAGAATGGCACAG
1 AGCCATAATCGGAATGGCACAA
44784231 AGCCATAATCGGA
1 AGCCATAATCGGA
44784244 TCAAGTAGCT
Statistics
Matches: 25, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.18
Consensus pattern (22 bp):
AGCCATAATCGGAATGGCACAA
Found at i:44784317 original size:43 final size:43
Alignment explanation
Indices: 44784269--44784351 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
44784259 CCGTCGGCAG
* **
44784269 GTCCACAGTCGTCTCGTGTGACCCGTGTAACCTTAACAGAATA
1 GTCCACAGTCGTCTCGTGCGACCCGTACAACCTTAACAGAATA
44784312 GTCCACAGTCGTCTCGTGCGACCCGTACAACCTTAACAGA
1 GTCCACAGTCGTCTCGTGCGACCCGTACAACCTTAACAGA
44784352 TCAATACTGG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.23
Consensus pattern (43 bp):
GTCCACAGTCGTCTCGTGCGACCCGTACAACCTTAACAGAATA
Found at i:44784732 original size:27 final size:27
Alignment explanation
Indices: 44784649--44784734 Score: 109
Period size: 27 Copynumber: 3.2 Consensus size: 27
44784639 TACCCTACAA
* * *
44784649 GGGGTATTTCGGTAATTTTAAAAATTA
1 GGGGTATTTTGGTAATTTTACAAATTG
* *
44784676 GAGGTATTTTGATAATTTTACAAATTG
1 GGGGTATTTTGGTAATTTTACAAATTG
* *
44784703 GGGGTATTTTGGTAATCTTACAAATCG
1 GGGGTATTTTGGTAATTTTACAAATTG
44784730 GGGGT
1 GGGGT
44784735 CTTAACTACC
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.29, C:0.06, G:0.26, T:0.40
Consensus pattern (27 bp):
GGGGTATTTTGGTAATTTTACAAATTG
Done.