Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 142 of 153
Found at i:44531784 original size:22 final size:21
Alignment explanation
Indices: 44531756--44531802 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
44531746 CTTAGCTGGG
*
44531756 AGGGGTGCGTTAACTCTTTATT
1 AGGGGTGCGATAACTCTTTA-T
* *
44531778 AGGGGTGTGATACCTCTTTAT
1 AGGGGTGCGATAACTCTTTAT
44531799 AGGG
1 AGGG
44531803 TGCAATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.19, C:0.13, G:0.32, T:0.36
Consensus pattern (21 bp):
AGGGGTGCGATAACTCTTTAT
Found at i:44540603 original size:43 final size:43
Alignment explanation
Indices: 44540528--44540613 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
44540518 ATCATTTTTA
* * * *
44540528 TTGATCTGTGCTTCCTTTAGTCGACAAGGCATTCCTGATGATG
1 TTGATCTATGCTTCCTTTAATCAACAAAGCATTCCTGATGATG
*
44540571 TTGATCTATGCTTCTTTTAATCAACAAAGCATTCCTGATGATG
1 TTGATCTATGCTTCCTTTAATCAACAAAGCATTCCTGATGATG
44540614 CCTTGAAGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (43 bp):
TTGATCTATGCTTCCTTTAATCAACAAAGCATTCCTGATGATG
Found at i:44547848 original size:102 final size:102
Alignment explanation
Indices: 44547667--44548587 Score: 1752
Period size: 102 Copynumber: 9.0 Consensus size: 102
44547657 TTCACTTGTC
* * * * *
44547667 TTTTCTTGCAGGGAATATTTCCTGTTCACGCATTATTCTGTTGCAGGGAATCTTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
44547732 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
66 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
44547769 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
44547834 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
66 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
44547871 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
44547936 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
66 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
44547973 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
44548038 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
66 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
44548075 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
44548140 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
66 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
44548177 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
44548242 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
66 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
44548279 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
44548344 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
66 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
44548381 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
44548446 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
66 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
**
44548483 TTTTGTTGCAGGGAATCTCTCCTGTTCACGGATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
* * *
44548548 TCATTTCTTGTAGGGAATCTCTCCTGTTCATGTATTA
66 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
44548585 TTT
1 TTT
44548588 CTTTTTAGAC
Statistics
Matches: 809, Mismatches: 10, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 809 1.00
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (102 bp):
TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
Found at i:44550918 original size:21 final size:22
Alignment explanation
Indices: 44550888--44550932 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
44550878 GAGCAAATTG
44550888 TTGATTCTATTTCCTTTTTG-AT
1 TTGATTCTA-TTCCTTTTTGTAT
*
44550910 TTGA-TCTATTCTTTTTTGTAT
1 TTGATTCTATTCCTTTTTGTAT
44550931 TT
1 TT
44550933 CTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 8 0.38
22 4 0.19
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.67
Consensus pattern (22 bp):
TTGATTCTATTCCTTTTTGTAT
Found at i:44555290 original size:14 final size:13
Alignment explanation
Indices: 44555255--44555288 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
44555245 AGAAAATAGT
44555255 TTAAGTTTGAAAAC
1 TTAA-TTTGAAAAC
44555269 TTAATTTGAAAAC
1 TTAATTTGAAAAC
44555282 TTAATTT
1 TTAATTT
44555289 TGTAAATGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (13 bp):
TTAATTTGAAAAC
Found at i:44555691 original size:67 final size:67
Alignment explanation
Indices: 44555583--44556021 Score: 824
Period size: 67 Copynumber: 6.6 Consensus size: 67
44555573 TCACTTGTCT
* * * *
44555583 TTTCTTGCAGGGAATATTTCCTGTTCACGCATTATTCTGTTGCAGGGAATCTTTCCTGTTCACAT
1 TTTCTTGCAGGGAATCTCTCCTGTTCACGGATTATTTTGTTGCAGGGAATCTTTCCTGTTCACAT
44555648 CA
66 CA
44555650 TTTCTTGCAGGGAATCTCTCCTGTTCACGGATTATTTTGTTGCAGGGAATCTTTCCTGTTCACAT
1 TTTCTTGCAGGGAATCTCTCCTGTTCACGGATTATTTTGTTGCAGGGAATCTTTCCTGTTCACAT
44555715 CA
66 CA
44555717 TTTCTTGCAGGGAATCTCTCCTGTTCACGGATTATTTTGTTGCAGGGAATCTTTCCTGTTCACAT
1 TTTCTTGCAGGGAATCTCTCCTGTTCACGGATTATTTTGTTGCAGGGAATCTTTCCTGTTCACAT
44555782 CA
66 CA
44555784 TTTCTTGCAGGGAATCTCTCCTGTTCACGGATTATTTTGTTGCAGGGAATCTTTCCTGTTCACAT
1 TTTCTTGCAGGGAATCTCTCCTGTTCACGGATTATTTTGTTGCAGGGAATCTTTCCTGTTCACAT
44555849 CA
66 CA
44555851 TTTCTTGCAGGGAATCTCTCCTGTTCACGGATTATTTTGTTGCAGGGAATCTTTCCTGTTCACAT
1 TTTCTTGCAGGGAATCTCTCCTGTTCACGGATTATTTTGTTGCAGGGAATCTTTCCTGTTCACAT
44555916 CA
66 CA
44555918 TTTCTTGCAGGGAATCTCTCCTGTTCACGGATTATTTTGTTGCAGGGAATCTTTCCTGTTCACAT
1 TTTCTTGCAGGGAATCTCTCCTGTTCACGGATTATTTTGTTGCAGGGAATCTTTCCTGTTCACAT
44555983 CA
66 CA
* *
44555985 TTTCTTGCAGGGAATCTCTCCTGTTCATGTATTATTT
1 TTTCTTGCAGGGAATCTCTCCTGTTCACGGATTATTT
44556022 CTTTTTAGAC
Statistics
Matches: 366, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 366 1.00
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.41
Consensus pattern (67 bp):
TTTCTTGCAGGGAATCTCTCCTGTTCACGGATTATTTTGTTGCAGGGAATCTTTCCTGTTCACAT
CA
Found at i:44558178 original size:21 final size:22
Alignment explanation
Indices: 44558148--44558192 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
44558138 GAGCAAATTG
44558148 TTGATTCTATTTCCTTTTTG-AT
1 TTGATTCTA-TTCCTTTTTGTAT
*
44558170 TTGA-TCTATTCTTTTTTGTAT
1 TTGATTCTATTCCTTTTTGTAT
44558191 TT
1 TT
44558193 CTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 8 0.38
22 4 0.19
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.67
Consensus pattern (22 bp):
TTGATTCTATTCCTTTTTGTAT
Found at i:44558601 original size:61 final size:62
Alignment explanation
Indices: 44558526--44558685 Score: 155
Period size: 67 Copynumber: 2.5 Consensus size: 62
44558516 CCTGCTTAGA
**
44558526 TTAATTTTAATATTAAATCTATTAAATTAATAGAAT-ATTTATCTAT-AAGATAAATATTAAAC
1 TTAA-TTTAATATTAAATCTATTAAATTAATAGAATAAAATA-CTATCAAGATAAATATTAAAC
* * *
44558588 TTAATTTAATATTAAGATAATAGCTTTAATATTAAT-TAATAAAATACTATCAAGATAAGTATTA
1 TTAATTTAATATTAA-AT-CTA---TTAA-ATTAATAGAATAAAATACTATCAAGATAAATATTA
44558652 AAC
60 AAC
* * *
44558655 TAAATTTAATATTATATCTATTAAAATAATA
1 TTAATTTAATATTAAATCTATTAAATTAATA
44558686 TTATTTTAGG
Statistics
Matches: 80, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
61 16 0.20
62 10 0.12
63 2 0.03
65 2 0.03
66 13 0.16
67 37 0.46
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (62 bp):
TTAATTTAATATTAAATCTATTAAATTAATAGAATAAAATACTATCAAGATAAATATTAAAC
Found at i:44558988 original size:18 final size:19
Alignment explanation
Indices: 44558946--44558982 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
44558936 AGTTTTGGGT
44558946 TCTCAAGCCTAATTTTCAA
1 TCTCAAGCCTAATTTTCAA
44558965 TCTCAAGCC-AATTTTCAA
1 TCTCAAGCCTAATTTTCAA
44558983 GTTCAATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.35
Consensus pattern (19 bp):
TCTCAAGCCTAATTTTCAA
Found at i:44561974 original size:19 final size:18
Alignment explanation
Indices: 44561942--44561985 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
44561932 GGTGAGAAGT
44561942 AAAATTTTAGGGGGAAAATA
1 AAAATTTTAGGGGG--AATA
*
44561962 AAAATTTT-TGGGGAATA
1 AAAATTTTAGGGGGAATA
44561979 AAAATTT
1 AAAATTT
44561986 GAGGAAAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 11 0.48
19 4 0.17
20 8 0.35
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (18 bp):
AAAATTTTAGGGGGAATA
Found at i:44562115 original size:30 final size:31
Alignment explanation
Indices: 44562076--44562135 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
44562066 AGAGGTGAGA
*
44562076 TGGGAAGGGAATAAAAGTTTT-AGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTGA-GGGAAAAG
*
44562107 TGGG-AGGGAGTAAAAATTTTGAGGGAAAA
1 TGGGAAGGGAATAAAAATTTTGAGGGAAAA
44562136 TAAAAGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTGAGGGAAAAG
Found at i:44562280 original size:30 final size:30
Alignment explanation
Indices: 44562246--44562307 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
44562236 GGAGGGGAGG
* * *
44562246 GGAGTAAAAGTTTTGGGGGGAAAGTAGAAA
1 GGAGTAAAAGTTTTGAGGGAAAAGTAAAAA
44562276 GGAGTAAAAGTTTTGAGGGAAAAGTAAAAA
1 GGAGTAAAAGTTTTGAGGGAAAAGTAAAAA
44562306 GG
1 GG
44562308 TTTGGGAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.44, C:0.00, G:0.37, T:0.19
Consensus pattern (30 bp):
GGAGTAAAAGTTTTGAGGGAAAAGTAAAAA
Found at i:44562363 original size:9 final size:9
Alignment explanation
Indices: 44562349--44562385 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
44562339 TATAGTTTGA
44562349 TATTCGAAT
1 TATTCGAAT
44562358 TATTCGAAT
1 TATTCGAAT
*
44562367 TATTCGAGT
1 TATTCGAAT
44562376 TATTCGAAT
1 TATTCGAAT
44562385 T
1 T
44562386 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:44570580 original size:46 final size:47
Alignment explanation
Indices: 44570518--44570608 Score: 132
Period size: 46 Copynumber: 2.0 Consensus size: 47
44570508 ATGTTAATTA
44570518 GGAAGAGACGTACTTGATCAATTAGCCAATT-GGATCCCACAATTCAT
1 GGAAGAGACGTACTTGATCAATTAGCC-ATTCGGATCCCACAATTCAT
* * *
44570565 GGAA-AGACGTTCTTGATCAATTAGTCATTCGGATCTCACAATTC
1 GGAAGAGACGTACTTGATCAATTAGCCATTCGGATCCCACAATTC
44570609 GGGAAGTGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
45 3 0.08
46 33 0.82
47 4 0.10
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (47 bp):
GGAAGAGACGTACTTGATCAATTAGCCATTCGGATCCCACAATTCAT
Found at i:44576366 original size:22 final size:22
Alignment explanation
Indices: 44576341--44576383 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
44576331 AATATTAAGT
44576341 TAACTTGCTATTTTAAATTGAA
1 TAACTTGCTATTTTAAATTGAA
44576363 TAACTTGCTATTTTAAATTGA
1 TAACTTGCTATTTTAAATTGA
44576384 TTTTAAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (22 bp):
TAACTTGCTATTTTAAATTGAA
Found at i:44578459 original size:26 final size:25
Alignment explanation
Indices: 44578430--44578494 Score: 103
Period size: 25 Copynumber: 2.6 Consensus size: 25
44578420 ATTCTGACCT
44578430 ACAGCTCGTGTAAGTAGGCCCATTTC
1 ACAGCTCGTGTAAGTA-GCCCATTTC
*
44578456 ACAGCTCTTGTAAGTAGCCCATTTC
1 ACAGCTCGTGTAAGTAGCCCATTTC
*
44578481 ACAGCTTGTGTAAG
1 ACAGCTCGTGTAAG
44578495 CAATGATGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
25 21 0.58
26 15 0.42
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.29
Consensus pattern (25 bp):
ACAGCTCGTGTAAGTAGCCCATTTC
Found at i:44579064 original size:6 final size:6
Alignment explanation
Indices: 44579021--44579063 Score: 59
Period size: 6 Copynumber: 6.8 Consensus size: 6
44579011 AAACTGTTTG
*
44579021 TATTCTT TATTTT TATTTT TATTTT TATTTT TCTTTT ATATTT
1 TATT-TT TATTTT TATTTT TATTTT TATTTT TATTTT -TATTT
44579064 AAAAACTACA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
6 25 0.76
7 8 0.24
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (6 bp):
TATTTT
Found at i:44580312 original size:21 final size:18
Alignment explanation
Indices: 44580281--44580320 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
44580271 TCGTTTTTGT
44580281 TCATTTTTTATTCACATTA
1 TCATTTTTTATTC-CATTA
44580300 TCATGTTTATTATTCCATTA
1 TCAT-TTT-TTATTCCATTA
44580320 T
1 T
44580321 GCATATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 9 0.47
21 6 0.32
ACGTcount: A:0.25, C:0.15, G:0.03, T:0.57
Consensus pattern (18 bp):
TCATTTTTTATTCCATTA
Found at i:44583074 original size:21 final size:21
Alignment explanation
Indices: 44583033--44583074 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
44583023 TATAGGGGTA
*
44583033 TTAAAGTTTGGTTCAAAAATT
1 TTAAAGTTTGGATCAAAAATT
*
44583054 TTAACGTTTGGAT-AAATAATT
1 TTAAAGTTTGGATCAAA-AATT
44583075 AAATAAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (21 bp):
TTAAAGTTTGGATCAAAAATT
Found at i:44584422 original size:27 final size:28
Alignment explanation
Indices: 44584392--44584446 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
44584382 GTAAAAGGGG
44584392 AGGGAAAATAAAAAAAA-TTGAAGAGAA
1 AGGGAAAATAAAAAAAATTTGAAGAGAA
* *
44584419 AGGGAAAGTAAAAAAAATTTGATGAGAA
1 AGGGAAAATAAAAAAAATTTGAAGAGAA
44584447 GAGTTGGGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.15
Consensus pattern (28 bp):
AGGGAAAATAAAAAAAATTTGAAGAGAA
Found at i:44584916 original size:15 final size:16
Alignment explanation
Indices: 44584896--44584934 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
44584886 ATGAAAAGGT
* *
44584896 TGAAAAGGATGT-ATA
1 TGAAAAGGATATCAAA
44584911 TGAAAAGGATATCAAA
1 TGAAAAGGATATCAAA
44584927 TGAAAAGG
1 TGAAAAGG
44584935 TTGAAAAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.51, C:0.03, G:0.26, T:0.21
Consensus pattern (16 bp):
TGAAAAGGATATCAAA
Found at i:44584930 original size:40 final size:40
Alignment explanation
Indices: 44584886--44585036 Score: 216
Period size: 40 Copynumber: 3.8 Consensus size: 40
44584876 TTACGAATCC
*
44584886 ATGAAAAGGTTGAAAAGGATGTATATGAAAAGGATATCAA
1 ATGAAAAGGTTGAAAAAGATGTATATGAAAAGGATATCAA
* **
44584926 ATGAAAAGGTTGAAAAGGATGTATCCGAAAAGGATATCAA
1 ATGAAAAGGTTGAAAAAGATGTATATGAAAAGGATATCAA
* *
44584966 ATGAAAAGGTTGAAAAAGATGTATCTGAAAAGGATAT-TA
1 ATGAAAAGGTTGAAAAAGATGTATATGAAAAGGATATCAA
* *
44585005 ATGAAAAGTTTGAAAAAGATATA-ATGAAAAGG
1 ATGAAAAGGTTGAAAAAGATGTATATGAAAAGG
44585037 TCGAACAGGA
Statistics
Matches: 103, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
38 8 0.08
39 22 0.21
40 73 0.71
ACGTcount: A:0.50, C:0.03, G:0.24, T:0.23
Consensus pattern (40 bp):
ATGAAAAGGTTGAAAAAGATGTATATGAAAAGGATATCAA
Found at i:44585048 original size:23 final size:24
Alignment explanation
Indices: 44584992--44585061 Score: 81
Period size: 23 Copynumber: 3.0 Consensus size: 24
44584982 AGATGTATCT
* * *
44584992 GAAAAGGATATTAATGAAAAGTTT
1 GAAAAGGATAGTAATGAAAAGGTC
*
44585016 GAAAAAGATA-TAATGAAAAGGTC
1 GAAAAGGATAGTAATGAAAAGGTC
*
44585039 GAACAGGATAGTAATG-AAAGGTC
1 GAAAAGGATAGTAATGAAAAGGTC
44585062 CGTATCTCAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
23 26 0.65
24 14 0.35
ACGTcount: A:0.50, C:0.04, G:0.24, T:0.21
Consensus pattern (24 bp):
GAAAAGGATAGTAATGAAAAGGTC
Found at i:44602601 original size:32 final size:32
Alignment explanation
Indices: 44602565--44602670 Score: 81
Period size: 32 Copynumber: 3.2 Consensus size: 32
44602555 GAGGTGAAGC
44602565 TAAAAAATCGACATATATCATTAATTGATATT
1 TAAAAAATCGACATATATCATTAATTGATATT
** * * **
44602597 TAAAAAATAAAAATA-ATTATTTAATAGGTGA-AGC
1 TAAAAAATCGACATATATCA-TTAAT---TGATATT
* * *
44602631 TAAGAAATCGTCATATATCATTAATTAATATT
1 TAAAAAATCGACATATATCATTAATTGATATT
44602663 TAAAAAAT
1 TAAAAAAT
44602671 AAAATAAATA
Statistics
Matches: 52, Mismatches: 16, Indels: 12
0.65 0.20 0.15
Matches are distributed among these distances:
31 5 0.10
32 25 0.48
34 16 0.31
35 6 0.12
ACGTcount: A:0.51, C:0.07, G:0.08, T:0.35
Consensus pattern (32 bp):
TAAAAAATCGACATATATCATTAATTGATATT
Found at i:44602651 original size:66 final size:66
Alignment explanation
Indices: 44602545--44602674 Score: 215
Period size: 66 Copynumber: 2.0 Consensus size: 66
44602535 AAAAGTTGAC
* *
44602545 AATTATTTGAGAGGTGAAGCTAAAAAATCGACATATATCATTAATTGATATTTAAAAAATAAAAA
1 AATTATTTAAGAGGTGAAGCTAAAAAATCGACATATATCATTAATTAATATTTAAAAAATAAAAA
44602610 T
66 T
* * *
44602611 AATTATTTAATAGGTGAAGCTAAGAAATCGTCATATATCATTAATTAATATTTAAAAAATAAAA
1 AATTATTTAAGAGGTGAAGCTAAAAAATCGACATATATCATTAATTAATATTTAAAAAATAAAA
44602675 TAAATAAACG
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.50, C:0.06, G:0.11, T:0.33
Consensus pattern (66 bp):
AATTATTTAAGAGGTGAAGCTAAAAAATCGACATATATCATTAATTAATATTTAAAAAATAAAAA
T
Found at i:44603811 original size:22 final size:22
Alignment explanation
Indices: 44603769--44603812 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
44603759 ATGTTAAAAT
* *
44603769 TTTTAAATTTTTATTTCAATTA
1 TTTTAAATATTTAATTCAATTA
44603791 TTTTAAATAATTTAATT-AATTA
1 TTTTAAAT-ATTTAATTCAATTA
44603813 AATTTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTAAATATTTAATTCAATTA
Found at i:44619133 original size:57 final size:56
Alignment explanation
Indices: 44619066--44619240 Score: 210
Period size: 57 Copynumber: 3.1 Consensus size: 56
44619056 AATTTTCAGG
* *
44619066 TCATTTTCATTTTGTAGAAAACCACATTCATTTTCAAATGATTCCATTTCTCTATTT
1 TCATTTTCATTTTGGAGAAAACCACAATCATTTTCAAATGATTCCATTTCTC-ATTT
* * *
44619123 TCATTATCATTTTGGACAAAACC-CTAATCA-TTTCTAAATGTTTCCATTTCTCCATTT
1 TCATTTTCATTTTGGAGAAAACCAC-AATCATTTTC-AAATGATTCCATTTCT-CATTT
* * *
44619180 TCATTTTCATTTTGGAGAAAACCATAATAATTTCCAAATGATTCCCTATTTCTCATTT
1 TCATTTTCATTTTGGAGAAAACCACAATCATTTTCAAATGATT-CC-ATTTCTCATTT
44619238 TCA
1 TCA
44619241 CCATTTCTAT
Statistics
Matches: 100, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
56 5 0.05
57 75 0.75
58 14 0.14
59 6 0.06
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.45
Consensus pattern (56 bp):
TCATTTTCATTTTGGAGAAAACCACAATCATTTTCAAATGATTCCATTTCTCATTT
Found at i:44619546 original size:27 final size:27
Alignment explanation
Indices: 44619516--44619568 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
44619506 CTCATATGAT
44619516 ATCCTTAATCTCTTTGGGATAATATTC
1 ATCCTTAATCTCTTTGGGATAATATTC
44619543 ATCCTTAATCTCTTTGGGATAATATT
1 ATCCTTAATCTCTTTGGGATAATATT
44619569 TATTCTCCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.45
Consensus pattern (27 bp):
ATCCTTAATCTCTTTGGGATAATATTC
Found at i:44628407 original size:23 final size:21
Alignment explanation
Indices: 44628347--44628419 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 21
44628337 AAAGTACTCT
44628347 ACAAAGGCCAACAGAATTAGCC
1 ACAAAGGCCAACAGAATT-GCC
*
44628369 ACAAAGGCTAAACAGAATGTGCC
1 ACAAAGGC-CAACAGAAT-TGCC
* *
44628392 ACAAAGGCCATTCAGATTATGCC
1 ACAAAGGCCA-ACAGAAT-TGCC
44628415 ACAAA
1 ACAAA
44628420 AGTCATATAG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
22 9 0.21
23 33 0.77
24 1 0.02
ACGTcount: A:0.44, C:0.25, G:0.18, T:0.14
Consensus pattern (21 bp):
ACAAAGGCCAACAGAATTGCC
Found at i:44632527 original size:7 final size:7
Alignment explanation
Indices: 44632515--44632557 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
44632505 TTTAGTTATT
44632515 AAATAAA
1 AAATAAA
44632522 AAATAAA
1 AAATAAA
*
44632529 AAATTAA
1 AAATAAA
*
44632536 AAATTAA
1 AAATAAA
*
44632543 AAATTAA
1 AAATAAA
*
44632550 AAGTAAA
1 AAATAAA
44632557 A
1 A
44632558 TAATTATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (7 bp):
AAATAAA
Found at i:44632537 original size:6 final size:7
Alignment explanation
Indices: 44632515--44632551 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
44632505 TTTAGTTATT
*
44632515 AAATAAA
1 AAATTAA
*
44632522 AAATAAA
1 AAATTAA
44632529 AAATTAA
1 AAATTAA
44632536 AAATTAA
1 AAATTAA
44632543 AAATTAA
1 AAATTAA
44632550 AA
1 AA
44632552 GTAAAATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (7 bp):
AAATTAA
Found at i:44632538 original size:15 final size:14
Alignment explanation
Indices: 44632515--44632569 Score: 65
Period size: 14 Copynumber: 3.8 Consensus size: 14
44632505 TTTAGTTATT
*
44632515 AAATAAAAAATAAA
1 AAATTAAAAATAAA
*
44632529 AAATTAAAAATTAA
1 AAATTAAAAATAAA
*
44632543 AAATTAAAAGTAAA
1 AAATTAAAAATAAA
44632557 ATAATTATAAAAT
1 A-AATTA-AAAAT
44632570 GGGAGCATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 25 0.74
15 5 0.15
16 4 0.12
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (14 bp):
AAATTAAAAATAAA
Found at i:44644321 original size:23 final size:22
Alignment explanation
Indices: 44644294--44644338 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
44644284 GGGATTGTTT
44644294 AAATCCCT-TAAGATTACTAAATA
1 AAAT-CCTGTAAGATTA-TAAATA
*
44644317 AAATCTTGTAAGATTATAAATA
1 AAATCCTGTAAGATTATAAATA
44644339 TTTTAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (22 bp):
AAATCCTGTAAGATTATAAATA
Found at i:44647824 original size:22 final size:22
Alignment explanation
Indices: 44647799--44647880 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 22
44647789 CATGTATGAT
*
44647799 GGTTCGCATATATCATATATAG
1 GGTTCGCATATAACATATATAG
* *
44647821 GGTTTGTATATAACATATGTATAG
1 GGTTCGCATATAACATA--TATAG
** * *
44647845 AATTCACATGTAACATATATAG
1 GGTTCGCATATAACATATATAG
* *
44647867 GGTTTGCATGTAAC
1 GGTTCGCATATAAC
44647881 CTAGAGTTCG
Statistics
Matches: 45, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
22 29 0.64
24 16 0.36
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (22 bp):
GGTTCGCATATAACATATATAG
Found at i:44647909 original size:20 final size:20
Alignment explanation
Indices: 44647877--44647914 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
44647867 GGTTTGCATG
*
44647877 TAACCTAGAGTTCGCATGTT
1 TAACCTAGAGTTCACATGTT
44647897 TAACCTA-AGGTTCACATG
1 TAACCTAGA-GTTCACATG
44647915 AAACAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (20 bp):
TAACCTAGAGTTCACATGTT
Found at i:44649662 original size:13 final size:13
Alignment explanation
Indices: 44649642--44649673 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
44649632 GCACCACAAT
44649642 TAACATCCAAACA
1 TAACATCCAAACA
*
44649655 TTACATCCAAACA
1 TAACATCCAAACA
44649668 TAACAT
1 TAACAT
44649674 ATCAAGACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (13 bp):
TAACATCCAAACA
Found at i:44650188 original size:20 final size:19
Alignment explanation
Indices: 44650165--44650268 Score: 84
Period size: 20 Copynumber: 5.3 Consensus size: 19
44650155 TAAGTGCAAT
44650165 CAGGGGTACTGAAGTACAAA
1 CAGGGGTAC-GAAGTACAAA
* * * *
44650185 CAGGGGCACAAAAGTGCAAT
1 CAGGGGTAC-GAAGTACAAA
*
44650205 CAAGGGTATCGAAGTACAAA
1 CAGGGGTA-CGAAGTACAAA
* * *
44650225 CA-GGGCACGTAAGTGCAAT
1 CAGGGGTACG-AAGTACAAA
*
44650244 CAGGGGTACCAAGTACAAA
1 CAGGGGTACGAAGTACAAA
44650263 CAGGGG
1 CAGGGG
44650269 CATGTAAGTG
Statistics
Matches: 64, Mismatches: 17, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
18 2 0.03
19 26 0.41
20 35 0.55
21 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.31, T:0.12
Consensus pattern (19 bp):
CAGGGGTACGAAGTACAAA
Found at i:44650238 original size:19 final size:20
Alignment explanation
Indices: 44650154--44650277 Score: 76
Period size: 20 Copynumber: 6.3 Consensus size: 20
44650144 TTCGAAGTAT
* * *
44650154 GTAAGTGCAATCAGGGGTAC
1 GTAAGTACAAACAGGGGCAC
44650174 -TGAAGTACAAACAGGGGCAC
1 GT-AAGTACAAACAGGGGCAC
** * * * *
44650194 AAAAGTGCAATCAAGGGTATC
1 GTAAGTACAAACAGGGGCA-C
44650215 G-AAGTACAAACA-GGGCAC
1 GTAAGTACAAACAGGGGCAC
* * *
44650233 GTAAGTGCAATCAGGGGTAC
1 GTAAGTACAAACAGGGGCAC
* *
44650253 -CAAGTACAAACAGGGGCAT
1 GTAAGTACAAACAGGGGCAC
44650272 GTAAGT
1 GTAAGT
44650278 GCAATTATTC
Statistics
Matches: 77, Mismatches: 21, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
18 2 0.03
19 28 0.36
20 46 0.60
21 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.30, T:0.15
Consensus pattern (20 bp):
GTAAGTACAAACAGGGGCAC
Found at i:44650242 original size:39 final size:39
Alignment explanation
Indices: 44650154--44650282 Score: 188
Period size: 39 Copynumber: 3.3 Consensus size: 39
44650144 TTCGAAGTAT
44650154 GTAAGTGCAATCAGGGGTACTGAAGTACAAACAGGGGCAC
1 GTAAGTGCAATCAGGGGTAC-GAAGTACAAACAGGGGCAC
** *
44650194 AAAAGTGCAATCAAGGGTATCGAAGTACAAACA-GGGCAC
1 GTAAGTGCAATCAGGGGTA-CGAAGTACAAACAGGGGCAC
* *
44650233 GTAAGTGCAATCAGGGGTACCAAGTACAAACAGGGGCAT
1 GTAAGTGCAATCAGGGGTACGAAGTACAAACAGGGGCAC
44650272 GTAAGTGCAAT
1 GTAAGTGCAAT
44650283 TATTCAATAA
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
38 12 0.15
39 38 0.48
40 28 0.35
41 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.29, T:0.16
Consensus pattern (39 bp):
GTAAGTGCAATCAGGGGTACGAAGTACAAACAGGGGCAC
Found at i:44652377 original size:19 final size:18
Alignment explanation
Indices: 44652346--44652383 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
44652336 ACGAAATTTT
44652346 AATAATATTTTTTATAAAA
1 AATAATATTTTTTA-AAAA
44652365 AATAA-ATTATTTTAAAAA
1 AATAATATT-TTTTAAAAA
44652383 A
1 A
44652384 CTTGTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AATAATATTTTTTAAAAA
Found at i:44653007 original size:17 final size:18
Alignment explanation
Indices: 44652985--44653018 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
44652975 GCTAAACCTT
44652985 CATTTTAATTTT-TTATA
1 CATTTTAATTTTATTATA
44653002 CATTTTAATTTTATTAT
1 CATTTTAATTTTATTAT
44653019 GCACATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (18 bp):
CATTTTAATTTTATTATA
Found at i:44653082 original size:313 final size:315
Alignment explanation
Indices: 44652552--44653188 Score: 1098
Period size: 313 Copynumber: 2.0 Consensus size: 315
44652542 ATTTTGTATA
44652552 ATTTTAAGAGATAAGCCTTTTTATTTTAAAAAAAAACAATAGAAATATGCATATAGAAAGGTTTG
1 ATTTTAAGAGATAAGCCTTTTTATTTT--AAAAAAACAATAGAAATATGCATATAGAAAGGTTTG
* *
44652617 AATTTGAATCAATTGCATTAGTAATGTCTTTAACTTACCACTCAGCTAAACCTTTATTTTAATAT
64 AATTTGAATCAATTGCAATAGTAATGTCTTTAACTTACCACTCAGCTAAACCTTCATTTTAATAT
*
44652682 TTTTATACATTTTAATTTTATTGTGCACATTATTATTTCCAATAATTGTATATCTATACTATTAT
129 TTTTATACATTTTAATTTTATTATGCACATTATTATTTCCAATAATTGTATATCTATACTATTAT
* *
44652747 TTAAGCTCCTAACTAAGTTGGTGTCACGAGTCAACCGAGTACCAACTCGATTAGGTAAATTATAG
194 TTAAGCTCCTAACTAAGTTGGTGTCACGAGTCAACCGAGTACCAACTCAATTAGGTAAATTACAG
* * * *
44652812 AACCACACTTTTATAATTAAAATAGGTTATGTTATTTGAGGATATTTTAGTCTTTTC
259 AACCACACTTTCATAATTAAAATAAGTTATGTTATTTGAGCATATTTTAGTCTTTCC
* *
44652869 ATTTTAAGAGATAAGTCTTTTTATTTT-AAAAAACAATAGAAATATGCATATAGTAAGGTTTGAA
1 ATTTTAAGAGATAAGCCTTTTTATTTTAAAAAAACAATAGAAATATGCATATAGAAAGGTTTGAA
*
44652933 TTTGAATCAATTGCAATAGTAATGTCTTTAATTTACCACTCAGCTAAACCTTCATTTTAAT-TTT
66 TTTGAATCAATTGCAATAGTAATGTCTTTAACTTACCACTCAGCTAAACCTTCATTTTAATATTT
44652997 TTATACATTTTAATTTTATTATGCACATTATTATTTCCAATAATTGTATATCTATACTATTATTT
131 TTATACATTTTAATTTTATTATGCACATTATTATTTCCAATAATTGTATATCTATACTATTATTT
* * *
44653062 AAGCTCCTAACTATGTTGGTGTCATGAGTCAACCGGGTACCAACTCAATTAGGTAAATTACAGAA
196 AAGCTCCTAACTAAGTTGGTGTCACGAGTCAACCGAGTACCAACTCAATTAGGTAAATTACAGAA
*
44653127 CCACCCTTTCATAATTAAAATAAGTTATGTTATTTGAGCATATTTTAGTCTTTCC
261 CCACACTTTCATAATTAAAATAAGTTATGTTATTTGAGCATATTTTAGTCTTTCC
44653182 ATTTTAA
1 ATTTTAA
44653189 CAATAATCAA
Statistics
Matches: 304, Mismatches: 16, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
313 184 0.61
314 94 0.31
317 26 0.09
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (315 bp):
ATTTTAAGAGATAAGCCTTTTTATTTTAAAAAAACAATAGAAATATGCATATAGAAAGGTTTGAA
TTTGAATCAATTGCAATAGTAATGTCTTTAACTTACCACTCAGCTAAACCTTCATTTTAATATTT
TTATACATTTTAATTTTATTATGCACATTATTATTTCCAATAATTGTATATCTATACTATTATTT
AAGCTCCTAACTAAGTTGGTGTCACGAGTCAACCGAGTACCAACTCAATTAGGTAAATTACAGAA
CCACACTTTCATAATTAAAATAAGTTATGTTATTTGAGCATATTTTAGTCTTTCC
Found at i:44659856 original size:22 final size:22
Alignment explanation
Indices: 44659831--44659873 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
44659821 TGTGTTTTAA
44659831 TTAAATTAA-ATTAAAATAAAAG
1 TTAAATTAAGA-TAAAATAAAAG
*
44659853 TTAAGTTAAGATAAAATAAAA
1 TTAAATTAAGATAAAATAAAA
44659874 TAAACAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (22 bp):
TTAAATTAAGATAAAATAAAAG
Found at i:44665381 original size:13 final size:14
Alignment explanation
Indices: 44665350--44665389 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
44665340 GTGAGGAAAA
44665350 AGAAAAAGAAGAAG
1 AGAAAAAGAAGAAG
*
44665364 AGAAAAATAA-AAG
1 AGAAAAAGAAGAAG
*
44665377 TGAAAAAGAAGAA
1 AGAAAAAGAAGAA
44665390 AATGAAAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (14 bp):
AGAAAAAGAAGAAG
Found at i:44665385 original size:21 final size:21
Alignment explanation
Indices: 44665345--44665405 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
44665335 AACAAGTGAG
* * *
44665345 GAAAAAGAAAAAGAAGAAG-A
1 GAAAATGAAAATGAAAAAGAA
44665365 GAAAAAT-AAAAGTGAAAAAGAA
1 G-AAAATGAAAA-TGAAAAAGAA
44665387 GAAAATGAAAATGAAAAAG
1 GAAAATGAAAATGAAAAAG
44665406 GCGAAAAGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 5 0.15
21 23 0.68
22 6 0.18
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (21 bp):
GAAAATGAAAATGAAAAAGAA
Found at i:44665397 original size:27 final size:28
Alignment explanation
Indices: 44665351--44665403 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
44665341 TGAGGAAAAA
*
44665351 GAAAAAGAAGAAGAGAAAAAT-AAAAGT
1 GAAAAAGAAGAAAAGAAAAATGAAAAGT
44665378 GAAAAAGAAGAAAATG-AAAATGAAAA
1 GAAAAAGAAGAAAA-GAAAAATGAAAA
44665404 AGGCGAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.08
Consensus pattern (28 bp):
GAAAAAGAAGAAAAGAAAAATGAAAAGT
Found at i:44665417 original size:21 final size:22
Alignment explanation
Indices: 44665372--44665417 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
44665362 AGAGAAAAAT
*
44665372 AAAAGTGAAAAAGAAGAAAATG
1 AAAAGTGAAAAAGAAGAAAAGG
**
44665394 AAAA-TGAAAAAGGCGAAAAGG
1 AAAAGTGAAAAAGAAGAAAAGG
44665415 AAA
1 AAA
44665418 GCTAGAGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.67, C:0.02, G:0.24, T:0.07
Consensus pattern (22 bp):
AAAAGTGAAAAAGAAGAAAAGG
Found at i:44673116 original size:25 final size:24
Alignment explanation
Indices: 44673088--44673144 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 24
44673078 GTACACATAA
*
44673088 GCATGTTTAACATATCCCACTCCAT
1 GCATGTTTAACATAT-CCACCCCAT
44673113 GCATG--T-A-ATATCCACCCCAT
1 GCATGTTTAACATATCCACCCCAT
44673133 GCATGTTTAACA
1 GCATGTTTAACA
44673145 AATTGTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
20 13 0.48
21 4 0.15
22 2 0.07
23 2 0.07
24 1 0.04
25 5 0.19
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.30
Consensus pattern (24 bp):
GCATGTTTAACATATCCACCCCAT
Found at i:44673531 original size:16 final size:16
Alignment explanation
Indices: 44673510--44673546 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
44673500 AAAACATAGA
44673510 CTTAATTTTGTTTGGT
1 CTTAATTTTGTTTGGT
44673526 CTTAATTTTGTTTGGT
1 CTTAATTTTGTTTGGT
*
44673542 GTTAA
1 CTTAA
44673547 AAGTCACACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.16, C:0.05, G:0.19, T:0.59
Consensus pattern (16 bp):
CTTAATTTTGTTTGGT
Found at i:44686180 original size:21 final size:21
Alignment explanation
Indices: 44686155--44686198 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
44686145 CTTCCAAACA
44686155 TGCTTTGTCAAACTCAAAAAT
1 TGCTTTGTCAAACTCAAAAAT
*
44686176 TGCTTTGTTAAACTCAAAAAT
1 TGCTTTGTCAAACTCAAAAAT
44686197 TG
1 TG
44686199 TATCTTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (21 bp):
TGCTTTGTCAAACTCAAAAAT
Found at i:44697131 original size:26 final size:26
Alignment explanation
Indices: 44697080--44697133 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
44697070 CATTTGCTTA
*
44697080 TTAAGTTACATTTATCTTAGTGTTAT
1 TTAAGTTACATTTATCTTAATGTTAT
* *
44697106 TTAAGTATACATTTTTTTTAAT-TTAT
1 TTAAGT-TACATTTATCTTAATGTTAT
44697132 TT
1 TT
44697134 TCAATTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.28, C:0.06, G:0.07, T:0.59
Consensus pattern (26 bp):
TTAAGTTACATTTATCTTAATGTTAT
Found at i:44699474 original size:12 final size:12
Alignment explanation
Indices: 44699457--44699481 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44699447 CACATATTGA
44699457 ATGGTTTGTTCG
1 ATGGTTTGTTCG
44699469 ATGGTTTGTTCG
1 ATGGTTTGTTCG
44699481 A
1 A
44699482 CACCTACTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.12, C:0.08, G:0.32, T:0.48
Consensus pattern (12 bp):
ATGGTTTGTTCG
Found at i:44705108 original size:54 final size:55
Alignment explanation
Indices: 44705025--44705133 Score: 168
Period size: 54 Copynumber: 2.0 Consensus size: 55
44705015 GATTATGATT
* *
44705025 AAAAATTATACTAGTTCAACTGTGAGACACAAGGGAAATGATGGGGGG-GAAAGA
1 AAAAATTATACCAGTTCAACTATGAGACACAAGGGAAATGATGGGGGGAGAAAGA
*
44705079 NAAAAATTAT-CCAGTTCAACTATGAGACACAAGGGAAATTATGGGGGGAGAAAGA
1 -AAAAATTATACCAGTTCAACTATGAGACACAAGGGAAATGATGGGGGGAGAAAGA
44705134 GTTTGAGTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
54 35 0.70
55 15 0.30
ACGTcount: A:0.43, C:0.10, G:0.28, T:0.18
Consensus pattern (55 bp):
AAAAATTATACCAGTTCAACTATGAGACACAAGGGAAATGATGGGGGGAGAAAGA
Found at i:44705427 original size:15 final size:14
Alignment explanation
Indices: 44705409--44705458 Score: 64
Period size: 15 Copynumber: 3.4 Consensus size: 14
44705399 AAGAAAAAAA
*
44705409 AAGAAAAGAATAGAG
1 AAGAAAAGAAGA-AG
*
44705424 AAGAAAACAAGAAG
1 AAGAAAAGAAGAAG
44705438 AAGAAGAAGAAGAAG
1 AAGAA-AAGAAGAAG
44705453 AAGAAA
1 AAGAAA
44705459 GGTAACATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 8 0.26
15 23 0.74
ACGTcount: A:0.70, C:0.02, G:0.26, T:0.02
Consensus pattern (14 bp):
AAGAAAAGAAGAAG
Found at i:44705428 original size:3 final size:3
Alignment explanation
Indices: 44705409--44705457 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
44705399 AAGAAAAAAA
* *
44705409 AAG AA- AAG AAT AGAG AAG AA- AAC AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG A-AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
44705453 AAG AA
1 AAG AA
44705458 AGGTAACATT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
2 4 0.10
3 34 0.85
4 2 0.05
ACGTcount: A:0.69, C:0.02, G:0.27, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:44705435 original size:23 final size:23
Alignment explanation
Indices: 44705399--44705451 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
44705389 GAAGTATATC
*
44705399 AAGAA-AAAAAAAGAA-AAGAAT
1 AAGAAGAAAAAAAGAAGAAGAAG
*
44705420 AGAGAAGAAAACAAGAAGAAGAAG
1 A-AGAAGAAAAAAAGAAGAAGAAG
44705444 AAGAAGAA
1 AAGAAGAA
44705452 GAAGAAAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 1 0.04
22 4 0.15
23 16 0.59
24 6 0.22
ACGTcount: A:0.74, C:0.02, G:0.23, T:0.02
Consensus pattern (23 bp):
AAGAAGAAAAAAAGAAGAAGAAG
Found at i:44713593 original size:25 final size:25
Alignment explanation
Indices: 44713560--44713778 Score: 132
Period size: 25 Copynumber: 8.8 Consensus size: 25
44713550 TGAGCATATC
*
44713560 ATTATATGGCTCTCAAGAGCTTCCCG
1 ATTA-ATGGCTCTCATGAGCTTCCCG
* *
44713586 ATTAATGGCTCTCTTGAGCTTTCCG
1 ATTAATGGCTCTCATGAGCTTCCCG
* *
44713611 -TTTATGGCTCGT-ATGAGCTTCCTG
1 ATTAATGGCTC-TCATGAGCTTCCCG
*
44713635 A-TAATTAGCTCTCCA-GAGCTTCCCG
1 ATTAA-TGGCTCT-CATGAGCTTCCCG
* * **
44713660 ATAAATGGTTCTCATGAGCTTCCAA
1 ATTAATGGCTCTCATGAGCTTCCCG
* *
44713685 ATTAATGGCTCTTC-GGATCTTCCCG
1 ATTAATGGCTC-TCATGAGCTTCCCG
* *
44713710 A-TATTGGCT-TACATGAGCTTCCTG
1 ATTAATGGCTCT-CATGAGCTTCCCG
* * * *
44713734 ATT-ATGTCTTTTATGAGCTTACCG
1 ATTAATGGCTCTCATGAGCTTCCCG
* *
44713758 -TTACATGGTTCACATGAGCTT
1 ATTA-ATGGCTCTCATGAGCTT
44713779 TCTGTGATAT
Statistics
Matches: 144, Mismatches: 35, Indels: 29
0.69 0.17 0.14
Matches are distributed among these distances:
22 1 0.01
23 3 0.02
24 53 0.37
25 78 0.54
26 9 0.06
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (25 bp):
ATTAATGGCTCTCATGAGCTTCCCG
Found at i:44719501 original size:14 final size:14
Alignment explanation
Indices: 44719482--44719521 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
44719472 TTGATTGCCA
44719482 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
44719496 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
44719510 GGAAAATGTTTT
1 GTAAAATGTTTT
44719522 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:44719530 original size:20 final size:20
Alignment explanation
Indices: 44719505--44719543 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
44719495 CGTAAAATGA
*
44719505 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
44719525 TTTCTGTAAAATGATTTAC
1 TTTCTGGAAAATGATTTAC
44719544 CAGAAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:44724152 original size:50 final size:50
Alignment explanation
Indices: 44724023--44724263 Score: 214
Period size: 50 Copynumber: 4.8 Consensus size: 50
44724013 GAATATAACA
* * ** ** * * * *
44724023 TGCCAAAGCTATGTCCCAGACATATTCTTACATGGGATGTTTCTTGTA-C
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
* * * * * * ** *
44724072 TGCCAATGCCATATCCTAGATATGGACTTACATGAGAGTTCTCATATAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
* * ** *
44724122 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
* * * *
44724172 TACCAACGCCACGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
*
44724222 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
44724264 TTACCCAAAT
Statistics
Matches: 153, Mismatches: 38, Indels: 1
0.80 0.20 0.01
Matches are distributed among these distances:
49 34 0.22
50 119 0.78
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
Found at i:44726515 original size:24 final size:24
Alignment explanation
Indices: 44726400--44726528 Score: 82
Period size: 25 Copynumber: 5.2 Consensus size: 24
44726390 TTTATATTCG
*
44726400 GGAATGCTCATACGAGCACATAAATA
1 GGAA-GCTCATACGAGC-CATTAATA
* * * *
44726426 AGAAGCTCTTTCGAGCCACATAACT-
1 GGAAGCTCATACGAGCCA-TTAA-TA
** **
44726451 GGAAGCTCATGTGAGCCATGTAACC
1 GGAAGCTCATACGAGCCAT-TAATA
**
44726476 GGAAGCTCCGGA-GAGCCATTAATA
1 GGAAGCT-CATACGAGCCATTAATA
*
44726500 GGAAGCTCATACGAGCCAATAATA
1 GGAAGCTCATACGAGCCATTAATA
44726524 GGAAG
1 GGAAG
44726529 GTTCAAATGA
Statistics
Matches: 78, Mismatches: 19, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
23 2 0.03
24 28 0.36
25 43 0.55
26 5 0.06
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.19
Consensus pattern (24 bp):
GGAAGCTCATACGAGCCATTAATA
Found at i:44728227 original size:42 final size:42
Alignment explanation
Indices: 44728155--44728239 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
44728145 CTATTACAAT
* * *
44728155 ACCCGGACATAATACCAGTTTACCTAATGTTAGCAGATCCTG
1 ACCCAGACATAATACCAGCTCACCTAATGTTAGCAGATCCTG
* * *
44728197 ACCCAGACATAATACCTGCTCACCTGATGTTAGCATATCCTG
1 ACCCAGACATAATACCAGCTCACCTAATGTTAGCAGATCCTG
44728239 A
1 A
44728240 ATCGGAAGAG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (42 bp):
ACCCAGACATAATACCAGCTCACCTAATGTTAGCAGATCCTG
Found at i:44731739 original size:20 final size:20
Alignment explanation
Indices: 44731700--44731740 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
44731690 GTAAATGATA
* * *
44731700 TATAAAAATAATTAATTAAT
1 TATAAAAACAAATAAATAAT
44731720 TATAAAAACAAATAAATAAT
1 TATAAAAACAAATAAATAAT
44731740 T
1 T
44731741 CATGATAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
TATAAAAACAAATAAATAAT
Found at i:44731849 original size:25 final size:25
Alignment explanation
Indices: 44731815--44731867 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
44731805 AAGAATACTA
* *
44731815 AGCCTATACTCCGTCACCAGCTCTT
1 AGCCTATACTCCATCAACAGCTCTT
44731840 AGCCTATACTCCATCAACAGCTCTT
1 AGCCTATACTCCATCAACAGCTCTT
44731865 AGC
1 AGC
44731868 TTCTATGTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.38, G:0.11, T:0.26
Consensus pattern (25 bp):
AGCCTATACTCCATCAACAGCTCTT
Found at i:44736951 original size:82 final size:82
Alignment explanation
Indices: 44736814--44737139 Score: 616
Period size: 82 Copynumber: 4.0 Consensus size: 82
44736804 GTTAACGAAC
* *
44736814 ATGAAACAATGAACGGATACATGAAAAATACTCGAACACTCTAAATAGTGTGCACAAGCACCAAG
1 ATGAAACAATGAACGAATACATGAAAAATACTCGAGCACTCTAAATAGTGTGCACAAGCACCAAG
44736879 TGAATAGCAGTACTCCA
66 TGAATAGCAGTACTCCA
44736896 ATGAAACAATGAACGAATACATGAAAAATACTCGAGCACTCTAAATAGTGTGCACAAGCACCAAG
1 ATGAAACAATGAACGAATACATGAAAAATACTCGAGCACTCTAAATAGTGTGCACAAGCACCAAG
44736961 TGAATAGCAGTACTCCA
66 TGAATAGCAGTACTCCA
44736978 ATGAAACAATGAACGAATACATGAAAAATACTCGAGCACTCTAAATAGTGTGCACAAGCACCAAG
1 ATGAAACAATGAACGAATACATGAAAAATACTCGAGCACTCTAAATAGTGTGCACAAGCACCAAG
44737043 TGAATAGCAGTACTCCA
66 TGAATAGCAGTACTCCA
*
44737060 ATGAAACAATGAACGAATACATGAAAAATACTCGAGCACTCTAAATAGTGTGCACAAGCACCAAC
1 ATGAAACAATGAACGAATACATGAAAAATACTCGAGCACTCTAAATAGTGTGCACAAGCACCAAG
*
44737125 TGAATAGCAATACTC
66 TGAATAGCAGTACTC
44737140 ATTTGGGTGA
Statistics
Matches: 240, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 240 1.00
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.18
Consensus pattern (82 bp):
ATGAAACAATGAACGAATACATGAAAAATACTCGAGCACTCTAAATAGTGTGCACAAGCACCAAG
TGAATAGCAGTACTCCA
Found at i:44737293 original size:7 final size:7
Alignment explanation
Indices: 44737283--44737307 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
44737273 TTAATAAATA
44737283 ATATTAT
1 ATATTAT
44737290 ATATTAT
1 ATATTAT
44737297 ATATTAT
1 ATATTAT
44737304 ATAT
1 ATAT
44737308 ATTAAGTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
ATATTAT
Found at i:44737782 original size:5 final size:5
Alignment explanation
Indices: 44737772--44737796 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
44737762 TAAAATTAGT
44737772 ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA
44737797 GGAATCCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:44738192 original size:9 final size:9
Alignment explanation
Indices: 44738178--44738208 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
44738168 GTTAAACAAA
44738178 TCGAGTTAT
1 TCGAGTTAT
*
44738187 TCGAGTTAA
1 TCGAGTTAT
44738196 TCGAGTTAT
1 TCGAGTTAT
44738205 TCGA
1 TCGA
44738209 ATTAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:44738199 original size:18 final size:18
Alignment explanation
Indices: 44738176--44738218 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
44738166 GAGTTAAACA
*
44738176 AATCGAGTTATTCGAGTT
1 AATCGAGTTATTCGAATT
44738194 AATCGAGTTATTCGAATT
1 AATCGAGTTATTCGAATT
44738212 AACTCGA
1 AA-TCGA
44738219 ATTTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.35
Consensus pattern (18 bp):
AATCGAGTTATTCGAATT
Found at i:44742039 original size:26 final size:25
Alignment explanation
Indices: 44742008--44742090 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 25
44741998 ATCTTTTCAG
44742008 TACACATAGTAGCCTTCATTTAGTA
1 TACACATAGTAGCCTTCATTTAGTA
*
44742033 TTACACAT-GT-GACCATT-ATTTATTGA
1 -TACACATAGTAG-CC-TTCATTTAGT-A
* **
44742059 TACACGTAGTAGCCTTCACATAGTA
1 TACACATAGTAGCCTTCATTTAGTA
44742084 CTACACA
1 -TACACA
44742091 CGTGTTCATC
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
24 1 0.02
25 19 0.43
26 23 0.52
27 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.34
Consensus pattern (25 bp):
TACACATAGTAGCCTTCATTTAGTA
Found at i:44742046 original size:51 final size:50
Alignment explanation
Indices: 44741907--44742090 Score: 181
Period size: 51 Copynumber: 3.6 Consensus size: 50
44741897 TATCATTCGA
* * * * * *
44741907 TACACATACTAGTCTTCACATAGTACTACACATGTGATCAAGTTTTACGG
1 TACACATAGTAGCCTTCACATAGTACTACACATGTGACCAAATTTTTCAG
* * * **
44741957 TCCACGTAGTAGCCTTCACATAGTACTACTCACATGACCAAATCTTTTCAG
1 TACACATAGTAGCCTTCACATAGTACTACACATGTGACCAAAT-TTTTCAG
** * * *
44742008 TACACATAGTAGCCTTCATTTAGTATTACACATGTGACCATTATTTATTGA-
1 TACACATAGTAGCCTTCACATAGTACTACACATGTGACCA-AATTT-TTCAG
*
44742059 TACACGTAGTAGCCTTCACATAGTACTACACA
1 TACACATAGTAGCCTTCACATAGTACTACACA
44742091 CGTGTTCATC
Statistics
Matches: 106, Mismatches: 25, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
50 34 0.32
51 67 0.63
52 5 0.05
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (50 bp):
TACACATAGTAGCCTTCACATAGTACTACACATGTGACCAAATTTTTCAG
Found at i:44745345 original size:123 final size:119
Alignment explanation
Indices: 44745061--44745358 Score: 384
Period size: 123 Copynumber: 2.5 Consensus size: 119
44745051 TTAGAAGTGT
* *
44745061 TTGAAAAACTACGATAGAATCTTTTGGTACAATCATTCAACAAATACA-GAAAAAA-GGGTAATA
1 TTGAAAAACTACGATAGAATCTTTTGGTACAATCATTCAACAAATAAAGGAAAAAATGGGTAAAA
* * *
44745124 TGTAAGGAAATGACTAAAGTAAATAGTGTAAATTTTTTTAAGGGTTTGAAAAAA
66 TGTAAGGAAAGGACTAAAGTAAACAGTGTAAATTTTTTTAAGGATTTGAAAAAA
* * **
44745178 TTGGAAAATTGTGATAGAATCTTTTGGTACAATCATTCAACAAATAAAGGGAAAAAATGGGTAAA
1 TTGAAAAACTACGATAGAATCTTTTGGTACAATCATTCAACAAATAAA-GGAAAAAATGGGTAAA
* * * **
44745243 ATGTAAGTAAAGGGCTAAAGTAAACGGTGTAAATTTTGTTTTGAATTATTTGAAAAAA
65 ATGTAAGGAAAGGACTAAAGTAAACAGTGTAAA-TTT-TTTT-AAGGATTTGAAAAAA
* * *
44745301 TTGAAAAACTACGATAAAATCTTTTAGTACAATTATTCAACAAATAAAAGGAAAAAAT
1 TTGAAAAACTACGATAGAATCTTTTGGTACAATCATTCAACAAAT-AAAGGAAAAAAT
44745359 TGAGTATGAA
Statistics
Matches: 153, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
117 43 0.28
119 7 0.05
120 34 0.22
121 3 0.02
122 4 0.03
123 59 0.39
124 3 0.02
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.30
Consensus pattern (119 bp):
TTGAAAAACTACGATAGAATCTTTTGGTACAATCATTCAACAAATAAAGGAAAAAATGGGTAAAA
TGTAAGGAAAGGACTAAAGTAAACAGTGTAAATTTTTTTAAGGATTTGAAAAAA
Found at i:44748833 original size:43 final size:42
Alignment explanation
Indices: 44748767--44748923 Score: 142
Period size: 43 Copynumber: 3.7 Consensus size: 42
44748757 AGCTCGAATA
* *
44748767 ATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCAAATAATG
1 ATGCCAATGTCCCAGACAG-GGTCTTACATGTAATCAAAT-ACG
* ** * *
44748810 ATGCCATTGTCTTAGACAGGGTCTTACACGTAATCATATACG
1 ATGCCAATGTCCCAGACAGGGTCTTACATGTAATCAAATACG
* *
44748852 ATGCCAATGTCCCAGACATGGTCTTACATGTAAATCTCAAA-CCG
1 ATGCCAATGTCCCAGACAGGGTCTTACATGT-AA--TCAAATACG
44748896 ATGCC-ATCGTCCCAGAC-GTGGTCTTACA
1 ATGCCAAT-GTCCCAGACAG-GGTCTTACA
44748924 CGAAATCACA
Statistics
Matches: 93, Mismatches: 15, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
42 28 0.30
43 35 0.38
44 26 0.28
45 4 0.04
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACAGGGTCTTACATGTAATCAAATACG
Found at i:44754831 original size:23 final size:23
Alignment explanation
Indices: 44754801--44754848 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
44754791 TTTACTCAAT
*
44754801 TAACAATTACCGTATAAAAAATA
1 TAACAATTACAGTATAAAAAATA
*
44754824 TAACAATTATAGTATAAAAAATA
1 TAACAATTACAGTATAAAAAATA
44754847 TA
1 TA
44754849 CTCAAATCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.58, C:0.08, G:0.04, T:0.29
Consensus pattern (23 bp):
TAACAATTACAGTATAAAAAATA
Found at i:44756229 original size:43 final size:41
Alignment explanation
Indices: 44756171--44756264 Score: 98
Period size: 41 Copynumber: 2.2 Consensus size: 41
44756161 TCCTAGATGT
** * *
44756171 GGTCTTACATGTAATCAAATAACGATGCCACTATCCCAGACAA
1 GGTCTTACACATAATC--ATAACGATGCCAATATACCAGACAA
* * * *
44756214 GGTCTTACACATAATCATTATGATGCCAATGTACCAGACAT
1 GGTCTTACACATAATCATAACGATGCCAATATACCAGACAA
44756255 GGTCTTACAC
1 GGTCTTACAC
44756265 GTAAATCTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 29 0.67
43 14 0.33
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (41 bp):
GGTCTTACACATAATCATAACGATGCCAATATACCAGACAA
Found at i:44762517 original size:301 final size:301
Alignment explanation
Indices: 44761970--44762571 Score: 1105
Period size: 301 Copynumber: 2.0 Consensus size: 301
44761960 GTGCTAACCC
* *
44761970 TTCCTCGTACGTAACTGATTCCCGAACTCGTTTTCTCAAAATTCGTAGACTAAAATAATTTTTAA
1 TTCCTCGTACGTAACTGACTCCCGAACTCGTTTTCTCAAAATTCGTAGACCAAAATAATTTTTAA
* * *
44762035 GGTGAGCCGATCACACCTTAATAAAGGATCGGTGGCGACTCCAGTTTTATTTTTAAAGTCGGCAA
66 GATGAGCCGATCACACCTTAATAAAGGATCGGTGGCGACTCCAATTTTATTTTTAAAGTCGACAA
*
44762100 CAAAATTTTTGTTTTCAAAAAACCGATTTCGACATATATATCAAGTGTATGTAAAAGAAAAGAGT
131 CAAAATTTTTGTTTTCAAAAAAACGATTTCGACATATATATCAAGTGTATGTAAAAGAAAAGAGT
*
44762165 GACAATAGACATGCAATTTGTTGATTTAATGTAAGTATAATGTTTAAAGTCTGTTAAATGTTCCA
196 GACAATAGACATGCAATTTGTTGATTTAATGTAAGTATAATGTTGAAAGTCTGTTAAATGTTCCA
44762230 ATGATCAAACAATTTTCATAATGTTCCAAGGATCAAACAAT
261 ATGATCAAACAATTTTCATAATGTTCCAAGGATCAAACAAT
44762271 TTCCTCGTACGTAACTGACTCCCGAACTCGTTTTCTCAAAATTCGTAGACCAAAATAATTTTTAA
1 TTCCTCGTACGTAACTGACTCCCGAACTCGTTTTCTCAAAATTCGTAGACCAAAATAATTTTTAA
44762336 GATGAGCCGATCACACCTTAATAAAGGATCGGTGGCGACTCCAATTTTATTTTTAAAGTCGACAA
66 GATGAGCCGATCACACCTTAATAAAGGATCGGTGGCGACTCCAATTTTATTTTTAAAGTCGACAA
* *
44762401 CAAAATTTTTGTTTTCAAAAAAACGGTTTCGACATATATGTCAAGTGTATGTAAAAGAAAAGAGT
131 CAAAATTTTTGTTTTCAAAAAAACGATTTCGACATATATATCAAGTGTATGTAAAAGAAAAGAGT
44762466 GACAATAGACATGCAATTTGTTGATTTAATGTAAGTATAATGTTGAAAGTCTGTTAAATGTTCCA
196 GACAATAGACATGCAATTTGTTGATTTAATGTAAGTATAATGTTGAAAGTCTGTTAAATGTTCCA
* *
44762531 ATGATTAAACAATTTTCATAATGTTTCAAGGATCAAACAAT
261 ATGATCAAACAATTTTCATAATGTTCCAAGGATCAAACAAT
44762572 GATGTTTCAT
Statistics
Matches: 290, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
301 290 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (301 bp):
TTCCTCGTACGTAACTGACTCCCGAACTCGTTTTCTCAAAATTCGTAGACCAAAATAATTTTTAA
GATGAGCCGATCACACCTTAATAAAGGATCGGTGGCGACTCCAATTTTATTTTTAAAGTCGACAA
CAAAATTTTTGTTTTCAAAAAAACGATTTCGACATATATATCAAGTGTATGTAAAAGAAAAGAGT
GACAATAGACATGCAATTTGTTGATTTAATGTAAGTATAATGTTGAAAGTCTGTTAAATGTTCCA
ATGATCAAACAATTTTCATAATGTTCCAAGGATCAAACAAT
Found at i:44770913 original size:23 final size:23
Alignment explanation
Indices: 44770851--44770913 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 23
44770841 AAAAACCAAT
*
44770851 CAAATTTCAAATTTCTATTATAAA
1 CAAATTT-AAATTTATATTATAAA
* *
44770875 CAAGTATTAAA-GTATATTCATAAA
1 CAAAT-TTAAATTTATATT-ATAAA
44770899 -AAATTTAAATTTATA
1 CAAATTTAAATTTATA
44770914 CATGAATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
22 5 0.16
23 12 0.39
24 12 0.39
25 2 0.06
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.40
Consensus pattern (23 bp):
CAAATTTAAATTTATATTATAAA
Found at i:44771179 original size:31 final size:31
Alignment explanation
Indices: 44771138--44771209 Score: 110
Period size: 31 Copynumber: 2.3 Consensus size: 31
44771128 AAAATTAAAT
*
44771138 TTCATATATAAAATTGC-ACATTAGTTCAAAG
1 TTCATGTATAAAATT-CAACATTAGTTCAAAG
*
44771169 TTCATGTATAACATTCAACATTAGTTCAAAG
1 TTCATGTATAAAATTCAACATTAGTTCAAAG
44771200 TTCATGTATA
1 TTCATGTATA
44771210 GTTTTAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 1 0.03
31 37 0.97
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.38
Consensus pattern (31 bp):
TTCATGTATAAAATTCAACATTAGTTCAAAG
Found at i:44771894 original size:128 final size:128
Alignment explanation
Indices: 44771688--44772196 Score: 964
Period size: 128 Copynumber: 4.0 Consensus size: 128
44771678 TTCCAGATTC
*
44771688 TCTAATTGTTTTAGATTGAAGAAAAAGTATAAAAGGGTGAGGCCTTCAGCTCGATAGAGTGCACC
1 TCTAATTGTTTTAGATTGAAGAAAAAATATAAAAGGGTGAGGCCTTCAGCTCGATAGAGTGCACC
44771753 ACAGTCAGGAGTGTTGAAGTTAATGTTGATGCCTCTATTGCAAAAGTGTTGGCAATTAAGTTT
66 ACAGTCAGGAGTGTTGAAGTTAATGTTGATGCCTCTATTGCAAAAGTGTTGGCAATTAAGTTT
44771816 TCTAATTGTTTTAGATTGAAGAAAAAATATAAAAGGGTGAGGCCTTCAGCTCGATAGAGTGCACC
1 TCTAATTGTTTTAGATTGAAGAAAAAATATAAAAGGGTGAGGCCTTCAGCTCGATAGAGTGCACC
44771881 ACAGTCAGGAGTGTTGAAGTTAATGTTGATGCCTCTATTGCAAAAGTGTTGGCAATTAAGTTT
66 ACAGTCAGGAGTGTTGAAGTTAATGTTGATGCCTCTATTGCAAAAGTGTTGGCAATTAAGTTT
44771944 TCTAATTGTTTTAGATTGAAGAAAAAATATAAAAGGGTGAGGCCTTCAGCTCGATAGAGTGCACC
1 TCTAATTGTTTTAGATTGAAGAAAAAATATAAAAGGGTGAGGCCTTCAGCTCGATAGAGTGCACC
44772009 ACAGTCAGGAGTGTTGAAGTTAATGTTGATGCCTCTATTGCAAAAGTGTTGGCAATTAAGTTT
66 ACAGTCAGGAGTGTTGAAGTTAATGTTGATGCCTCTATTGCAAAAGTGTTGGCAATTAAGTTT
44772072 TCTAATTGTTTTAGATTGAAGAAAAAATATAAAAGGGTGAGGCCTTCAGCTCGATAGAGTGCACC
1 TCTAATTGTTTTAGATTGAAGAAAAAATATAAAAGGGTGAGGCCTTCAGCTCGATAGAGTGCACC
* * * * *
44772137 ATATTCAGGAGTGTTGAAGTTAATGTCGATGCCTCTAGTGCAAAAGTGTTGGCGATTAAG
66 ACAGTCAGGAGTGTTGAAGTTAATGTTGATGCCTCTATTGCAAAAGTGTTGGCAATTAAG
44772197 GAAGCATGCA
Statistics
Matches: 375, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 375 1.00
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.31
Consensus pattern (128 bp):
TCTAATTGTTTTAGATTGAAGAAAAAATATAAAAGGGTGAGGCCTTCAGCTCGATAGAGTGCACC
ACAGTCAGGAGTGTTGAAGTTAATGTTGATGCCTCTATTGCAAAAGTGTTGGCAATTAAGTTT
Found at i:44782839 original size:84 final size:82
Alignment explanation
Indices: 44782740--44782909 Score: 272
Period size: 84 Copynumber: 2.1 Consensus size: 82
44782730 ATTTTAAGGC
* *
44782740 TAAAAAAGTAGTTTAGTAAATAAAAGAATAATTAAGTAAATAAAATATGAATGAAGAATCATCT-
1 TAAAAAAGTAATTTAGTAAATAAAAGAATAATTAAGTAAATAAAAAATGAATGAAGAATCATCTG
44782804 TCTTTATTTTTCTTTCCCT
66 T-TTT-TTTTTCTTTCCCT
*
44782823 NTAAAAAAGTAATTTAGTAAATAAAAGAATAATTAAGTAAATAAAAAATGAATGAAGTATCATCT
1 -TAAAAAAGTAATTTAGTAAATAAAAGAATAATTAAGTAAATAAAAAATGAATGAAGAATCATCT
44782888 GTTTTTTTTTCTTTCCC-
65 GTTTTTTTTTCTTTCCCT
44782905 TAAAA
1 TAAAA
44782910 TCAATTCCAC
Statistics
Matches: 82, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
81 5 0.06
83 12 0.15
84 64 0.78
85 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.36
Consensus pattern (82 bp):
TAAAAAAGTAATTTAGTAAATAAAAGAATAATTAAGTAAATAAAAAATGAATGAAGAATCATCTG
TTTTTTTTTCTTTCCCT
Found at i:44782880 original size:20 final size:20
Alignment explanation
Indices: 44782838--44782881 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
44782828 AAAGTAATTT
*
44782838 AGTAAATAAAAGAATAATTA
1 AGTAAATAAAAGAATAATGA
44782858 AGTAAATAAAA-AATGAATGA
1 AGTAAATAAAAGAAT-AATGA
44782878 AGTA
1 AGTA
44782882 TCATCTGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.23
Consensus pattern (20 bp):
AGTAAATAAAAGAATAATGA
Found at i:44792874 original size:31 final size:31
Alignment explanation
Indices: 44792837--44792926 Score: 180
Period size: 31 Copynumber: 2.9 Consensus size: 31
44792827 AGTAAAAATA
44792837 AAATAAAAGAAAGAACCCTATTTTTTTTTCT
1 AAATAAAAGAAAGAACCCTATTTTTTTTTCT
44792868 AAATAAAAGAAAGAACCCTATTTTTTTTTCT
1 AAATAAAAGAAAGAACCCTATTTTTTTTTCT
44792899 AAATAAAAGAAAGAACCCTATTTTTTTT
1 AAATAAAAGAAAGAACCCTATTTTTTTT
44792927 CTTTCCACAG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 59 1.00
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (31 bp):
AAATAAAAGAAAGAACCCTATTTTTTTTTCT
Found at i:44804794 original size:23 final size:22
Alignment explanation
Indices: 44804742--44804794 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
44804732 GTTCTCTTCA
* *
44804742 TTTTCTTTTTTTATTTATTTGT
1 TTTTCTTATTTTATTTATTTCT
*
44804764 TTTATCTTATTTTATTTTTTTCT
1 TTT-TCTTATTTTATTTATTTCT
44804787 TTCTTCTT
1 TT-TTCTT
44804795 TTGCAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 3 0.12
23 22 0.85
24 1 0.04
ACGTcount: A:0.09, C:0.09, G:0.02, T:0.79
Consensus pattern (22 bp):
TTTTCTTATTTTATTTATTTCT
Found at i:44805941 original size:26 final size:26
Alignment explanation
Indices: 44805912--44805963 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
44805902 TCTATATGTA
*
44805912 CATACATATTACTTTTAAAATT-TTTT
1 CATACATAGTA-TTTTAAAATTGTTTT
*
44805938 CATACGTAGTATTTTAAAATTGTTTT
1 CATACATAGTATTTTAAAATTGTTTT
44805964 TGTGTATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.33, C:0.10, G:0.06, T:0.52
Consensus pattern (26 bp):
CATACATAGTATTTTAAAATTGTTTT
Found at i:44807365 original size:19 final size:19
Alignment explanation
Indices: 44807337--44807378 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
44807327 TCATCAATTA
44807337 ATTTAATAAT-ATTACTATT
1 ATTTAATAATCA-TACTATT
* *
44807356 ATTTATTAATCATATTATT
1 ATTTAATAATCATACTATT
44807375 ATTT
1 ATTT
44807379 GTATTATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTAATAATCATACTATT
Found at i:44815161 original size:22 final size:21
Alignment explanation
Indices: 44815112--44815162 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
44815102 CTATTTTCTG
* *
44815112 AAAATTCATTAAAACTCAAGA
1 AAAATTTATTAAAACTCAAAA
* *
44815133 AATATTTATTGAAACTTCAAAA
1 AAAATTTATTAAAAC-TCAAAA
44815155 AAAATTTA
1 AAAATTTA
44815163 GAAACCTCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.55, C:0.10, G:0.04, T:0.31
Consensus pattern (21 bp):
AAAATTTATTAAAACTCAAAA
Found at i:44817364 original size:4 final size:4
Alignment explanation
Indices: 44817355--44817409 Score: 51
Period size: 4 Copynumber: 13.8 Consensus size: 4
44817345 CATGCAAATT
* * *
44817355 AAGA AAGAA AAGA AAGA AAAA AAGA AAG- AA-A AAGAA AAGA AAGG GAGA
1 AAGA AAG-A AAGA AAGA AAGA AAGA AAGA AAGA AAG-A AAGA AAGA AAGA
44817403 AAGA AAG
1 AAGA AAG
44817410 TCGCGCACGG
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
3 4 0.10
4 29 0.71
5 8 0.20
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:44817369 original size:9 final size:9
Alignment explanation
Indices: 44817355--44817397 Score: 61
Period size: 9 Copynumber: 4.8 Consensus size: 9
44817345 CATGCAAATT
44817355 AAGAAAGAA
1 AAGAAAGAA
44817364 AAGAAAGAA
1 AAGAAAGAA
44817373 AA-AAAGAA
1 AAGAAAGAA
*
44817381 AGAAAAAGAA
1 A-AGAAAGAA
44817391 AAGAAAG
1 AAGAAAG
44817398 GGAGAAAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 7 0.23
9 17 0.55
10 7 0.23
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (9 bp):
AAGAAAGAA
Found at i:44817574 original size:16 final size:16
Alignment explanation
Indices: 44817553--44817587 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
44817543 GATTAAGATT
* *
44817553 TTAAATATTTTTATTA
1 TTAAATAGTTTTAGTA
44817569 TTAAATAGTTTTAGTA
1 TTAAATAGTTTTAGTA
44817585 TTA
1 TTA
44817588 GGGATTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (16 bp):
TTAAATAGTTTTAGTA
Found at i:44821156 original size:20 final size:20
Alignment explanation
Indices: 44821128--44821191 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
44821118 GCTGATAGAA
* *
44821128 AGCTAAATTGAGCTCGAATG
1 AGCTGAATTGAGCTCAAATG
44821148 AGCTGAATTGAGCTCAAATG
1 AGCTGAATTGAGCTCAAATG
* *
44821168 AGCTG-ATTGGAGCTGAAACG
1 AGCTGAATT-GAGCTCAAATG
44821188 AGCT
1 AGCT
44821192 AAAGGAGCTG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 3 0.08
20 36 0.92
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (20 bp):
AGCTGAATTGAGCTCAAATG
Found at i:44821171 original size:30 final size:30
Alignment explanation
Indices: 44821128--44821194 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
44821118 GCTGATAGAA
44821128 AGCTAAATTGAGCTCGAAT-GAGCTGAATTG
1 AGCTAAATTGAGCT-GAATGGAGCTGAATTG
* **
44821158 AGCTCAAA-TGAGCTGATTGGAGCTGAAACG
1 AGCT-AAATTGAGCTGAATGGAGCTGAATTG
44821188 AGCTAAA
1 AGCTAAA
44821195 GGAGCTGGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
29 6 0.19
30 23 0.72
31 3 0.09
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.22
Consensus pattern (30 bp):
AGCTAAATTGAGCTGAATGGAGCTGAATTG
Found at i:44825535 original size:18 final size:18
Alignment explanation
Indices: 44825499--44825540 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
44825489 TATATAATTT
*
44825499 TTAAAAATATATAATACA
1 TTAAAAATATATAAAACA
44825517 TTAAAAATAT-TAAGAACA
1 TTAAAAATATATAA-AACA
*
44825535 TCAAAA
1 TTAAAA
44825541 TAAATATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (18 bp):
TTAAAAATATATAAAACA
Found at i:44825669 original size:30 final size:30
Alignment explanation
Indices: 44825624--44825685 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
44825614 CTTAACAAGT
44825624 AAATACTTCTAAAATAATAACAAAATTAAC
1 AAATACTTCTAAAATAATAACAAAATTAAC
* * *
44825654 AAATGCTTTTAAAATAATAATAAAATTAAC
1 AAATACTTCTAAAATAATAACAAAATTAAC
44825684 AA
1 AA
44825686 TAAAATAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.29
Consensus pattern (30 bp):
AAATACTTCTAAAATAATAACAAAATTAAC
Found at i:44825728 original size:11 final size:11
Alignment explanation
Indices: 44825714--44825761 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
44825704 ATATCCAAAC
*
44825714 AATAATAACAA
1 AATAATAGCAA
*
44825725 AATAGTAGCAA
1 AATAATAGCAA
* *
44825736 CATAATAGTAA
1 AATAATAGCAA
*
44825747 AATAGTAGCAA
1 AATAATAGCAA
44825758 AATA
1 AATA
44825762 GGGAGAAAAC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.60, C:0.08, G:0.10, T:0.21
Consensus pattern (11 bp):
AATAATAGCAA
Found at i:44825740 original size:22 final size:22
Alignment explanation
Indices: 44825715--44825757 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
44825705 TATCCAAACA
44825715 ATAATAACAAAATAGTAGCAAC
1 ATAATAACAAAATAGTAGCAAC
**
44825737 ATAATAGTAAAATAGTAGCAA
1 ATAATAACAAAATAGTAGCAA
44825758 AATAGGGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (22 bp):
ATAATAACAAAATAGTAGCAAC
Found at i:44825762 original size:11 final size:11
Alignment explanation
Indices: 44825722--44825762 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
44825712 ACAATAATAA
44825722 CAAAATAGTAG
1 CAAAATAGTAG
* *
44825733 CAACATAATAG
1 CAAAATAGTAG
*
44825744 TAAAATAGTAG
1 CAAAATAGTAG
44825755 CAAAATAG
1 CAAAATAG
44825763 GGAGAAAACA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:44834880 original size:20 final size:20
Alignment explanation
Indices: 44834855--44834892 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
44834845 TAAAAACGGT
*
44834855 GCGTATAGAAGCTTTAGTAG
1 GCGTATAAAAGCTTTAGTAG
44834875 GCGTATAAAAGCTTTAGT
1 GCGTATAAAAGCTTTAGT
44834893 GAAACGGGGC
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:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (20 bp):
GCGTATAAAAGCTTTAGTAG
Found at i:44837471 original size:13 final size:13
Alignment explanation
Indices: 44837453--44837485 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
44837443 TTGTTTTCCC
44837453 ATTTCCCTTACTG
1 ATTTCCCTTACTG
*
44837466 ATTTCCCTTGCTG
1 ATTTCCCTTACTG
44837479 ATTTCCC
1 ATTTCCC
44837486 AATTGTGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.33, G:0.09, T:0.45
Consensus pattern (13 bp):
ATTTCCCTTACTG
Found at i:44839082 original size:6 final size:6
Alignment explanation
Indices: 44839071--44839098 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
44839061 GACATATACT
44839071 AAATTA AAATTA AAATTA AAATTA AAAT
1 AAATTA AAATTA AAATTA AAATTA AAAT
44839099 ATGTGAAACT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATTA
Found at i:44843498 original size:17 final size:17
Alignment explanation
Indices: 44843459--44843492 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
44843449 CATAATTTTT
44843459 TTAAAATATTTAAATAG
1 TTAAAATATTTAAATAG
44843476 TTAAAA-ATTTAAA-AG
1 TTAAAATATTTAAATAG
44843491 TT
1 TT
44843493 CTAAAACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 7 0.41
17 6 0.35
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
TTAAAATATTTAAATAG
Found at i:44853053 original size:25 final size:22
Alignment explanation
Indices: 44853007--44853053 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
44852997 CATCTCAATT
*
44853007 CACATATTCACAAACACATAAG
1 CACATATTCACAAAAACATAAG
44853029 CACATAGTTCACAAGATAACATAAG
1 CACATA-TTCACAA-A-AACATAAG
44853054 TATGAGAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 7 0.33
24 1 0.05
25 7 0.33
ACGTcount: A:0.49, C:0.23, G:0.09, T:0.19
Consensus pattern (22 bp):
CACATATTCACAAAAACATAAG
Found at i:44853334 original size:14 final size:14
Alignment explanation
Indices: 44853315--44853345 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
44853305 CAAGCAATCC
44853315 AAAAACATAAGCCT
1 AAAAACATAAGCCT
*
44853329 AAAAACATAAGCTT
1 AAAAACATAAGCCT
44853343 AAA
1 AAA
44853346 CTAAGTTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.16, G:0.06, T:0.16
Consensus pattern (14 bp):
AAAAACATAAGCCT
Found at i:44856689 original size:188 final size:183
Alignment explanation
Indices: 44856480--44856834 Score: 557
Period size: 188 Copynumber: 1.9 Consensus size: 183
44856470 AATTTTTTCT
* * * * *
44856480 TTTTCTTTTTTTCTCTTTTTTTGTTTTGTAGTTTGGCGGGGAGTAACTTTCTAGGTAGGTTTGGT
1 TTTTCTTTTTTTCTCTTTTTTTGTTCTATAGTTTGGCGGAGAGGAACTTTCTAGGTAGGTTTGAT
**
44856545 TATAATGATTTTGAGAGCATATTGCAGAGAGAAGATTGTTGAGTTGGAATTGGGGTATGCAACTT
66 TATAATGATTTTGAGAGCATATTGCA-A-AG-AGA--GTCAAGTTGGAATTGGGGTATGCAACTT
44856610 TATTCATCTTTAAACAAACTATGGAAAGTGACATTAAAGTATAAAAGTTTTTTCAATA
126 TATTCATCTTTAAACAAACTATGGAAAGTGACATTAAAGTATAAAAGTTTTTTCAATA
* * *
44856668 TTTTCTTTTTTTCTGTTTTTTTGTTCTATAGTTTGGCGGAGAGGAACTTTCTAGTTGGGTTTGAT
1 TTTTCTTTTTTTCTCTTTTTTTGTTCTATAGTTTGGCGGAGAGGAACTTTCTAGGTAGGTTTGAT
* *
44856733 TATAATGATTTTGAGAGTATATTGCAAAGAGAGTCAATTTGGAATTGGGGTATGCAACTTTATTC
66 TATAATGATTTTGAGAGCATATTGCAAAGAGAGTCAAGTTGGAATTGGGGTATGCAACTTTATTC
44856798 ATCTTTAAACAAACTATGGAAAGTGACATTAAAGTAT
131 ATCTTTAAACAAACTATGGAAAGTGACATTAAAGTAT
44856835 CAACTCCTTC
Statistics
Matches: 155, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
183 67 0.43
185 3 0.02
186 2 0.01
187 1 0.01
188 82 0.53
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.43
Consensus pattern (183 bp):
TTTTCTTTTTTTCTCTTTTTTTGTTCTATAGTTTGGCGGAGAGGAACTTTCTAGGTAGGTTTGAT
TATAATGATTTTGAGAGCATATTGCAAAGAGAGTCAAGTTGGAATTGGGGTATGCAACTTTATTC
ATCTTTAAACAAACTATGGAAAGTGACATTAAAGTATAAAAGTTTTTTCAATA
Found at i:44864001 original size:20 final size:20
Alignment explanation
Indices: 44863964--44864001 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
44863954 GATTTTTGGA
*
44863964 AAAATTAATTTTTATAAAGT
1 AAAATTAATTTATATAAAGT
44863984 AAAATTAAATTTAT-TAAA
1 AAAATT-AATTTATATAAA
44864002 TTTATTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
AAAATTAATTTATATAAAGT
Found at i:44873254 original size:14 final size:14
Alignment explanation
Indices: 44873235--44873281 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
44873225 GTTTATAAGT
*
44873235 TTTTAAAATTTATG
1 TTTTAAAATTTATA
** *
44873249 TTTTAATGTGTA-A
1 TTTTAAAATTTATA
44873262 TTTTAAAATTTATA
1 TTTTAAAATTTATA
44873276 TTTTAA
1 TTTTAA
44873282 TGTGTAAGGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
13 9 0.36
14 16 0.64
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
TTTTAAAATTTATA
Found at i:44873265 original size:27 final size:27
Alignment explanation
Indices: 44873235--44873288 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
44873225 GTTTATAAGT
*
44873235 TTTTAAAATTTATGTTTTAATGTGTAA
1 TTTTAAAATTTATATTTTAATGTGTAA
44873262 TTTTAAAATTTATATTTTAATGTGTAA
1 TTTTAAAATTTATATTTTAATGTGTAA
44873289 GGATTGTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (27 bp):
TTTTAAAATTTATATTTTAATGTGTAA
Found at i:44875768 original size:6 final size:5
Alignment explanation
Indices: 44875755--44875835 Score: 63
Period size: 6 Copynumber: 14.2 Consensus size: 5
44875745 AAAACAATTG
*
44875755 ATTTC ATATTC ATATTC ATTTCC ATTTTC ATATC ATTCTC ATTTTC ATTCTC
1 ATTTC AT-TTC AT-TTC ATTT-C A-TTTC ATTTC ATT-TC A-TTTC ATT-TC
44875807 ATTCTC ATTTC AATTTC ATTTC ATATTC A
1 ATT-TC ATTTC -ATTTC ATTTC AT-TTC A
44875836 AATTATAAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 15
0.80 0.02 0.18
Matches are distributed among these distances:
5 20 0.30
6 41 0.62
7 5 0.08
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (5 bp):
ATTTC
Found at i:44875790 original size:17 final size:18
Alignment explanation
Indices: 44875758--44875816 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
44875748 ACAATTGATT
*
44875758 TCATATTCATATTCATT-
1 TCATTTTCATATTCATTC
44875775 TCCATTTTCATA-TCATTC
1 T-CATTTTCATATTCATTC
44875793 TCATTTTCAT-TCTCATTC
1 TCATTTTCATAT-TCATTC
44875811 TCATTT
1 TCATTT
44875817 CAATTTCATT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
17 15 0.41
18 22 0.59
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.54
Consensus pattern (18 bp):
TCATTTTCATATTCATTC
Found at i:44875809 original size:29 final size:29
Alignment explanation
Indices: 44875763--44875827 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
44875753 TGATTTCATA
* *
44875763 TTCATATTCATTTCCATTTTCATATC-AT
1 TTCATTTTCATTTCCATTCTCATATCAAT
*
44875791 TCTCATTTTCA-TTCTCATTCTCATTTCAAT
1 T-TCATTTTCATTTC-CATTCTCATATCAAT
44875821 TTCATTT
1 TTCATTT
44875828 CATATTCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 4 0.13
29 24 0.77
30 3 0.10
ACGTcount: A:0.22, C:0.23, G:0.00, T:0.55
Consensus pattern (29 bp):
TTCATTTTCATTTCCATTCTCATATCAAT
Found at i:44878337 original size:89 final size:90
Alignment explanation
Indices: 44878100--44878345 Score: 257
Period size: 90 Copynumber: 2.7 Consensus size: 90
44878090 GTTCAAAATT
* ** * * * *
44878100 TTTGTATTATTTTTGTATCTGTAAATCAAATTTAGTTTGTATTATTTGTTGTTCGAATTTTATAT
1 TTTGTATT-TTCTTGTATCTGTAAATTTAATTTAGTTCGTATTATTTTTTTTTCAAATTTTATAT
* * *
44878165 TTTCGTGTATTAATTTTACCCATCTG
65 TTTCGTGTATTAATATTACACATATG
* ** *
44878191 TTTGTATTTTGTTGGGTCTGTAAATTTAATTTAG-TCTGTATTATTTGTTGTTT-AAATTTTATA
1 TTTGTATTTTCTTGTATCTGTAAATTTAATTTAGTTC-GTATTATTT-TTTTTTCAAATTTTATA
* *
44878254 TTTTCGTGTATTAATATTATAGA-ATG
64 TTTTCGTGTATTAATATTACACATATG
* * *
44878280 TTTTTATTTTCTTGTATCTGTAAATTTCATTT-GTTGCGTATTATTTTTTTTTCAAATTATATAT
1 TTTGTATTTTCTTGTATCTGTAAATTTAATTTAGTT-CGTATTATTTTTTTTTCAAATTTTATAT
44878344 TT
65 TT
44878346 GTTTTATTAA
Statistics
Matches: 128, Mismatches: 22, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
88 6 0.05
89 52 0.41
90 59 0.46
91 11 0.09
ACGTcount: A:0.23, C:0.07, G:0.12, T:0.58
Consensus pattern (90 bp):
TTTGTATTTTCTTGTATCTGTAAATTTAATTTAGTTCGTATTATTTTTTTTTCAAATTTTATATT
TTCGTGTATTAATATTACACATATG
Found at i:44880940 original size:17 final size:15
Alignment explanation
Indices: 44880914--44880960 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 15
44880904 TCACAATTCA
44880914 TTTCATTTCAATTTTT
1 TTTCATTTC-ATTTTT
44880930 TTTCATATTCATTTTT
1 TTTCAT-TTCATTTTT
44880946 TTTCTAATTTCATTT
1 TTTC--ATTTCATTT
44880961 CAATTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 16 0.57
17 10 0.36
18 2 0.07
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTCATTTCATTTTT
Found at i:44880955 original size:56 final size:56
Alignment explanation
Indices: 44880869--44880987 Score: 161
Period size: 56 Copynumber: 2.1 Consensus size: 56
44880859 CTTGTCACTT
44880869 TTTTTTTTCATTTCAATTTAGTTTCTAATTTCATTTCACAATTCATTTC-ATTTCAA
1 TTTTTTTTCATTTCAATTTAGTTTCTAATTTCATTTCA-AATTCATTTCAATTTCAA
** * * *
44880925 TTTTTTTTCATATTC-ATTTTTTTTCTAATTTCATTTCAATTTTATTTCAATTTCAC
1 TTTTTTTTCAT-TTCAATTTAGTTTCTAATTTCATTTCAAATTCATTTCAATTTCAA
44880981 TTTTTTT
1 TTTTTTT
44880988 AGTTAAAACT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
55 8 0.14
56 45 0.80
57 3 0.05
ACGTcount: A:0.22, C:0.14, G:0.01, T:0.63
Consensus pattern (56 bp):
TTTTTTTTCATTTCAATTTAGTTTCTAATTTCATTTCAAATTCATTTCAATTTCAA
Found at i:44880956 original size:39 final size:39
Alignment explanation
Indices: 44880913--44880987 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
44880903 TTCACAATTC
* *
44880913 ATTTCATTTCAATTTTTTTTC-ATATTCATTTTTTTTCTA
1 ATTTCATTTCAATTTTATTTCAAT-TTCACTTTTTTTCTA
44880952 ATTTCATTTCAATTTTATTTCAATTTCACTTTTTTT
1 ATTTCATTTCAATTTTATTTCAATTTCACTTTTTTT
44880988 AGTTAAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 31 0.94
40 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.65
Consensus pattern (39 bp):
ATTTCATTTCAATTTTATTTCAATTTCACTTTTTTTCTA
Found at i:44880962 original size:22 final size:23
Alignment explanation
Indices: 44880930--44880979 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
44880920 TTCAATTTTT
*
44880930 TTTCATATTC-ATTTTTTTTCTAA
1 TTTCATATTCAATTTTATTTC-AA
44880953 TTTCAT-TTCAATTTTATTTCAA
1 TTTCATATTCAATTTTATTTCAA
44880975 TTTCA
1 TTTCA
44880980 CTTTTTTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTCATATTCAATTTTATTTCAA
Found at i:44880977 original size:17 final size:16
Alignment explanation
Indices: 44880896--44880984 Score: 52
Period size: 17 Copynumber: 5.0 Consensus size: 16
44880886 TTAGTTTCTA
* *
44880896 ATTTCATTTCACAATTC
1 ATTTCATTTCA-ATTTT
44880913 ATTTCATTTCAATTTT
1 ATTTCATTTCAATTTT
* *
44880929 TTTTCATATTCATTTTTTTTCT
1 ATTTCAT-TTCA----ATTT-T
44880951 AATTTCATTTCAATTTT
1 -ATTTCATTTCAATTTT
*
44880968 ATTTCAATTTCACTTTT
1 ATTTC-ATTTCAATTTT
44880985 TTTAGTTAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
16 14 0.25
17 26 0.46
18 3 0.05
21 3 0.05
22 5 0.09
23 6 0.11
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTCATTTCAATTTT
Found at i:44881149 original size:34 final size:33
Alignment explanation
Indices: 44881107--44881181 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 33
44881097 TCTTCTTCAA
* *
44881107 TTAAATTTCATTTTATTTAAATTTTTTTCTCATT
1 TTAAATTTCATTTAAGTTAAATTTTTTTCTC-TT
*
44881141 TTAAATTTCATTTAAGTTCAATTTTTTTCTCTT
1 TTAAATTTCATTTAAGTTAAATTTTTTTCTCTT
*
44881174 TAAAATTT
1 TTAAATTT
44881182 TTCAAATCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 9 0.24
34 28 0.76
ACGTcount: A:0.28, C:0.09, G:0.01, T:0.61
Consensus pattern (33 bp):
TTAAATTTCATTTAAGTTAAATTTTTTTCTCTT
Found at i:44881505 original size:6 final size:6
Alignment explanation
Indices: 44881494--44881556 Score: 53
Period size: 6 Copynumber: 11.2 Consensus size: 6
44881484 TAATTAAAAC
* * *
44881494 TTAATT TTAATT TTAATT TTAATT TT--TT CTCA-T TTAATT TGAA-T
1 TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT
* *
44881538 TTAATT TAAATT ATAATT T
1 TTAATT TTAATT TTAATT T
44881557 CATTTCACTT
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
4 3 0.07
5 7 0.16
6 34 0.77
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (6 bp):
TTAATT
Found at i:44881902 original size:22 final size:21
Alignment explanation
Indices: 44881862--44881924 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 21
44881852 TTATATTTTC
44881862 ATTTCAATTTCTATTCAATTTGA
1 ATTTC-ATTTC-ATTCAATTTGA
*
44881885 ATTTCATTTCATTCCAATTTTA
1 ATTTCATTTCATT-CAATTTGA
44881907 ATTTCATTTCATTTCAAT
1 ATTTCATTTCA-TTCAAT
44881925 AAAAAAGTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
21 3 0.08
22 27 0.73
23 7 0.19
ACGTcount: A:0.29, C:0.16, G:0.02, T:0.54
Consensus pattern (21 bp):
ATTTCATTTCATTCAATTTGA
Found at i:44881992 original size:11 final size:11
Alignment explanation
Indices: 44881976--44882033 Score: 64
Period size: 11 Copynumber: 5.1 Consensus size: 11
44881966 TTTTTAAATA
44881976 TAATTTCATTT
1 TAATTTCATTT
44881987 TAATTTCA-TT
1 TAATTTCATTT
*
44881997 TCATTTCCAATTT
1 TAATTT-C-ATTT
44882010 TAATTTCATTT
1 TAATTTCATTT
*
44882021 TCATTTCACTTT
1 TAATTTCA-TTT
44882033 T
1 T
44882034 TACTTTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
10 7 0.17
11 20 0.50
12 6 0.15
13 7 0.17
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.60
Consensus pattern (11 bp):
TAATTTCATTT
Found at i:44882033 original size:23 final size:21
Alignment explanation
Indices: 44881978--44882033 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 21
44881968 TTTAAATATA
44881978 ATTTCATTTTAATTTCATTTC
1 ATTTCATTTTAATTTCATTTC
44881999 ATTTCCAATTTTAATTTCATTTTC
1 ATTT-C-ATTTTAATTTCA-TTTC
44882023 ATTTCACTTTT
1 ATTTCA-TTTT
44882034 TACTTTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
21 4 0.13
22 2 0.06
23 17 0.55
24 8 0.26
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTCATTTTAATTTCATTTC
Done.