Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: 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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 133 of 163
Found at i:43154019 original size:52 final size:49
Alignment explanation
Indices: 43153939--43154074 Score: 137
Period size: 50 Copynumber: 2.7 Consensus size: 49
43153929 AATTCATATT
* *
43153939 CAGGAATGCTCATGTGAGCACATAAACGGGAAGCTCTCTCTCGAGCCATATAA
1 CAGGAA-GCTCATATGAGC-CATAAACGGGAAGCT-TATC-CGAGCCATATAA
* * **
43153992 CAGGAAGCTCATATGAGCCATGTAACGGGAAGCTTATCCGGGCTGTATAA
1 CAGGAAGCTCATATGAGCCAT-AAACGGGAAGCTTATCCGAGCCATATAA
* * * *
43154042 CGGGAAGCTCATAAGAGCCATAATCAGGAAGCT
1 CAGGAAGCTCATATGAGCCATAAACGGGAAGCT
43154075 CATGCTAGCC
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
49 9 0.13
50 28 0.39
51 6 0.08
52 22 0.31
53 6 0.08
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (49 bp):
CAGGAAGCTCATATGAGCCATAAACGGGAAGCTTATCCGAGCCATATAA
Found at i:43154075 original size:24 final size:24
Alignment explanation
Indices: 43154044--43154234 Score: 79
Period size: 25 Copynumber: 7.7 Consensus size: 24
43154034 CTGTATAACG
43154044 GGAAGCTCATAAGAGCCATAATCA
1 GGAAGCTCATAAGAGCCATAATCA
***
43154068 GGAAGCTCATGCTAGCCAATAAT-A
1 GGAAGCTCATAAGAGCC-ATAATCA
* *
43154092 GGTAGCTTC-GAAGAGCCATTAATC-
1 GGAAGC-TCATAAGAGCCA-TAATCA
* *
43154116 GAGAAACTC-TGAATAGCCATATATC-
1 G-GAAGCTCAT-AAGAGCCATA-ATCA
* **
43154141 GAGAAGTTCATGCGAGCCAATAATCA
1 G-GAAGCTCATAAGAGCC-ATAATCA
* * *
43154167 GGAAGCTCACAAAGAGCCTTTAATCG
1 GGAAGCTCA-TAAGAGCC-ATAATCA
* *
43154193 GGAAACTCACGAAGAGCCATATATCA
1 GGAAGCTCA-TAAGAGCCATA-ATCA
*
43154219 AGACA-CTCATAAGAGC
1 GGA-AGCTCATAAGAGC
43154235 TGCGGTGTGT
Statistics
Matches: 124, Mismatches: 30, Indels: 25
0.69 0.17 0.14
Matches are distributed among these distances:
23 1 0.01
24 33 0.27
25 49 0.40
26 40 0.32
27 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (24 bp):
GGAAGCTCATAAGAGCCATAATCA
Found at i:43154184 original size:26 final size:26
Alignment explanation
Indices: 43154154--43154211 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
43154144 AAGTTCATGC
*
43154154 GAGCCAATAATCAGGAAGCTCACAAA
1 GAGCCAATAATCAGGAAACTCACAAA
** * *
43154180 GAGCCTTTAATCGGGAAACTCACGAA
1 GAGCCAATAATCAGGAAACTCACAAA
43154206 GAGCCA
1 GAGCCA
43154212 TATATCAAGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.14
Consensus pattern (26 bp):
GAGCCAATAATCAGGAAACTCACAAA
Found at i:43158115 original size:18 final size:18
Alignment explanation
Indices: 43158092--43158126 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
43158082 CAATTCAATT
*
43158092 TCTTATTTTTAACAATAA
1 TCTTATTTTCAACAATAA
43158110 TCTTATTTTCAACAATA
1 TCTTATTTTCAACAATA
43158127 GATATGAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (18 bp):
TCTTATTTTCAACAATAA
Found at i:43169445 original size:24 final size:24
Alignment explanation
Indices: 43169418--43169469 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
43169408 TTAGTAAGTC
*
43169418 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
43169442 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
43169466 AAAT
1 AAAT
43169470 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:43171413 original size:24 final size:24
Alignment explanation
Indices: 43171385--43171436 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
43171375 TTAGTAAGTC
* *
43171385 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
43171409 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
43171433 AAAT
1 AAAT
43171437 CTTCTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:43177044 original size:100 final size:100
Alignment explanation
Indices: 43176868--43177053 Score: 309
Period size: 100 Copynumber: 1.9 Consensus size: 100
43176858 AATCACCCAG
* * *
43176868 CACTTATTACATGCTCAACTGTAACAACTGTGCATCAATGACGAGCAGTATTAAAGTTCCAAAAT
1 CACTTAATACATGCTCAACTGTAACAACTGAGCATCAATGACGAGCAGTATTAAACTTCCAAAAT
*
43176933 GTATTGCTAAATCCTAGTAAGCAAGTTAGCCAAGC
66 GTATTGATAAATCCTAGTAAGCAAGTTAGCCAAGC
* *
43176968 CACTTAATACATGCTCAACTGTAATAACTGAGCATCAGTGACGAGCAGTATTAAACTTCCAAAAT
1 CACTTAATACATGCTCAACTGTAACAACTGAGCATCAATGACGAGCAGTATTAAACTTCCAAAAT
*
43177033 GTATTGATAAATCTTAGTAAG
66 GTATTGATAAATCCTAGTAAG
43177054 TTAGCCAAGC
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 79 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (100 bp):
CACTTAATACATGCTCAACTGTAACAACTGAGCATCAATGACGAGCAGTATTAAACTTCCAAAAT
GTATTGATAAATCCTAGTAAGCAAGTTAGCCAAGC
Found at i:43181230 original size:39 final size:39
Alignment explanation
Indices: 43181206--43181455 Score: 500
Period size: 39 Copynumber: 6.4 Consensus size: 39
43181196 CATACATTAA
43181206 TCCATCAACATATTTAATTTCATAACAAAATATAAATTG
1 TCCATCAACATATTTAATTTCATAACAAAATATAAATTG
43181245 TCCATCAACATATTTAATTTCATAACAAAATATAAATTG
1 TCCATCAACATATTTAATTTCATAACAAAATATAAATTG
43181284 TCCATCAACATATTTAATTTCATAACAAAATATAAATTG
1 TCCATCAACATATTTAATTTCATAACAAAATATAAATTG
43181323 TCCATCAACATATTTAATTTCATAACAAAATATAAATTG
1 TCCATCAACATATTTAATTTCATAACAAAATATAAATTG
43181362 TCCATCAACATATTTAATTTCATAACAAAATATAAATTG
1 TCCATCAACATATTTAATTTCATAACAAAATATAAATTG
43181401 TCCATCAACATATTTAATTTCATAACAAAATATAAATTG
1 TCCATCAACATATTTAATTTCATAACAAAATATAAATTG
43181440 TCCATCAACATATTTA
1 TCCATCAACATATTTA
43181456 GAAGGAAAGC
Statistics
Matches: 211, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 211 1.00
ACGTcount: A:0.46, C:0.16, G:0.02, T:0.36
Consensus pattern (39 bp):
TCCATCAACATATTTAATTTCATAACAAAATATAAATTG
Found at i:43181509 original size:9 final size:9
Alignment explanation
Indices: 43181491--43181545 Score: 74
Period size: 9 Copynumber: 6.1 Consensus size: 9
43181481 CGAAGAAACA
*
43181491 TCATCATCC
1 TCATCGTCC
43181500 TCATCGTCC
1 TCATCGTCC
*
43181509 TCATCGTCG
1 TCATCGTCC
*
43181518 TCATCGTCG
1 TCATCGTCC
43181527 TCATCGTCC
1 TCATCGTCC
*
43181536 TCATTGTCC
1 TCATCGTCC
43181545 T
1 T
43181546 TTTTGCAACC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.13, C:0.38, G:0.13, T:0.36
Consensus pattern (9 bp):
TCATCGTCC
Found at i:43186603 original size:123 final size:123
Alignment explanation
Indices: 43186384--43186631 Score: 478
Period size: 123 Copynumber: 2.0 Consensus size: 123
43186374 TAATAATAAA
43186384 TATATATATTAATTATAACCGGGCCGGGCCGGGCCCAGGCCAAAAAAATTTTACTCGAGGCCCGG
1 TATATATATTAATTATAACCGGGCCGGGCCGGGCCCAGGCCAAAAAAATTTTACTCGAGGCCCGG
*
43186449 CCCGTTTTCTAAACGGGCTTCTTTTTCTACCCGAGCCCATATTTCGGGCTTATTTTTT
66 CCCGTTTTCTAAACGGGCCTCTTTTTCTACCCGAGCCCATATTTCGGGCTTATTTTTT
*
43186507 TATATATATTAATTATAACCGGGCTGGGCCGGGCCCAGGCCAAAAAAATTTTACTCGAGGCCCGG
1 TATATATATTAATTATAACCGGGCCGGGCCGGGCCCAGGCCAAAAAAATTTTACTCGAGGCCCGG
43186572 CCCGTTTTCTAAACGGGCCTCTTTTTCTACCCGAGCCCATATTTCGGGCTTATTTTTT
66 CCCGTTTTCTAAACGGGCCTCTTTTTCTACCCGAGCCCATATTTCGGGCTTATTTTTT
43186630 TA
1 TA
43186632 CCTGAACCCT
Statistics
Matches: 123, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 123 1.00
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (123 bp):
TATATATATTAATTATAACCGGGCCGGGCCGGGCCCAGGCCAAAAAAATTTTACTCGAGGCCCGG
CCCGTTTTCTAAACGGGCCTCTTTTTCTACCCGAGCCCATATTTCGGGCTTATTTTTT
Found at i:43190316 original size:14 final size:15
Alignment explanation
Indices: 43190283--43190314 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
43190273 TATGCATGTA
*
43190283 AAATATAAAAGACAT
1 AAATAAAAAAGACAT
43190298 AAATAAAAAAGACAT
1 AAATAAAAAAGACAT
43190313 AA
1 AA
43190315 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATAAAAAAGACAT
Found at i:43190845 original size:32 final size:32
Alignment explanation
Indices: 43190804--43190883 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
43190794 TTTTAACATT
*
43190804 ATATATCATCCACAATAGA-CTAATCATCAATC
1 ATATCTCATCCACAATAGATC-AATCATCAATC
* *
43190836 ATATCTCATCCACAAAAGATCAATCATCAATT
1 ATATCTCATCCACAATAGATCAATCATCAATC
* *
43190868 ATATCCCGTCCACAAT
1 ATATCTCATCCACAAT
43190884 GGGCTAATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 40 0.98
33 1 0.02
ACGTcount: A:0.41, C:0.28, G:0.04, T:0.28
Consensus pattern (32 bp):
ATATCTCATCCACAATAGATCAATCATCAATC
Found at i:43193592 original size:46 final size:46
Alignment explanation
Indices: 43193529--43193707 Score: 225
Period size: 46 Copynumber: 3.9 Consensus size: 46
43193519 AGTGTGGAAT
* * *
43193529 GTAGGTACGGTAATTCAGTAAAGAAAACCATACTGAGTTATGGAAC
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTATGAAAC
* * * *
43193575 GTAGGTATGGTGTTTCAGTGAAGAAAACCATATTGAGTTGTGAAAC
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTATGAAAC
** * *
43193621 GTAGGTATGGTATTTCAGTAACA-AAAGTCATACTGAGTTGTGAAAA
1 GTAGGTATGGTATTTCAGTAA-AGAAAACCATACTGAGTTATGAAAC
* *
43193667 GTAGGTATGATATTTCAGTGAAGAAAACCATACTGAGTTAT
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTAT
43193708 AGCATTGCAA
Statistics
Matches: 113, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
45 1 0.01
46 111 0.98
47 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.29
Consensus pattern (46 bp):
GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTATGAAAC
Found at i:43193686 original size:92 final size:92
Alignment explanation
Indices: 43193529--43193705 Score: 248
Period size: 92 Copynumber: 1.9 Consensus size: 92
43193519 AGTGTGGAAT
* * * *
43193529 GTAGGTACGGTAATTCAGTAAAGAAAACCATACTGAGTTATGGAACGTAGGTATGGTGTTTCAGT
1 GTAGGTACGGTAATTCAGTAAAGAAAACCATACTGAGTTATGAAAAGTAGGTATGATATTTCAGT
*
43193594 GAAGAAAACCATATTGAGTTGTGAAAC
66 GAAGAAAACCATACTGAGTTGTGAAAC
* * ** *
43193621 GTAGGTATGGTATTTCAGTAACA-AAAGTCATACTGAGTTGTGAAAAGTAGGTATGATATTTCAG
1 GTAGGTACGGTAATTCAGTAA-AGAAAACCATACTGAGTTATGAAAAGTAGGTATGATATTTCAG
43193685 TGAAGAAAACCATACTGAGTT
65 TGAAGAAAACCATACTGAGTT
43193706 ATAGCATTGC
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
92 73 0.99
93 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.29
Consensus pattern (92 bp):
GTAGGTACGGTAATTCAGTAAAGAAAACCATACTGAGTTATGAAAAGTAGGTATGATATTTCAGT
GAAGAAAACCATACTGAGTTGTGAAAC
Found at i:43198382 original size:5 final size:5
Alignment explanation
Indices: 43198372--43198400 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
43198362 TATCTTGTAA
43198372 AGATT AGATT AGATT AGATT AGATT AGAT
1 AGATT AGATT AGATT AGATT AGATT AGAT
43198401 ATGGCAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (5 bp):
AGATT
Found at i:43205224 original size:21 final size:21
Alignment explanation
Indices: 43205200--43205239 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
43205190 TGCTTGATTT
43205200 ATCATCCAATTGATACTTTAA
1 ATCATCCAATTGATACTTTAA
43205221 ATCATCCAATTGATACTTT
1 ATCATCCAATTGATACTTT
43205240 GAATATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (21 bp):
ATCATCCAATTGATACTTTAA
Found at i:43206187 original size:34 final size:34
Alignment explanation
Indices: 43206149--43206219 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
43206139 ATTTTTTATA
43206149 ATATATAGCATGTATACATAAATTAGTTATGTTC
1 ATATATAGCATGTATACATAAATTAGTTATGTTC
43206183 ATATATAGCATGTATACATAAATTAGTTATGTTC
1 ATATATAGCATGTATACATAAATTAGTTATGTTC
43206217 ATA
1 ATA
43206220 CTTCTTGGCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.41
Consensus pattern (34 bp):
ATATATAGCATGTATACATAAATTAGTTATGTTC
Found at i:43206219 original size:17 final size:17
Alignment explanation
Indices: 43206165--43206219 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
43206155 AGCATGTATA
43206165 CATAAATTAGTTATGTT
1 CATAAATTAGTTATGTT
* *
43206182 CATATA-TAG-CATGTAT
1 CATAAATTAGTTATGT-T
43206198 ACATAAATTAGTTATGTT
1 -CATAAATTAGTTATGTT
43206216 CATA
1 CATA
43206220 CTTCTTGGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
15 4 0.13
16 4 0.13
17 14 0.47
18 4 0.13
19 4 0.13
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (17 bp):
CATAAATTAGTTATGTT
Found at i:43207438 original size:31 final size:31
Alignment explanation
Indices: 43207354--43207448 Score: 100
Period size: 31 Copynumber: 2.9 Consensus size: 31
43207344 TTTAGGGTTT
** *
43207354 TTTAAAAAAATTAATTAAATTAGATTTTTAAGGT
1 TTTAAAAAAA-TAATTAAATTAG-GGTTT-AGGA
*
43207388 TTTAAATAAATTAATTAAATTAGGGTTTAGGA
1 TTTAAA-AAAATAATTAAATTAGGGTTTAGGA
* *
43207420 TTTAAAAAAACAATTAAATTATGGTTTAG
1 TTTAAAAAAATAATTAAATTAGGGTTTAG
43207449 TTTTTTTTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
31 20 0.38
32 9 0.17
33 3 0.06
34 18 0.34
35 3 0.06
ACGTcount: A:0.46, C:0.01, G:0.12, T:0.41
Consensus pattern (31 bp):
TTTAAAAAAATAATTAAATTAGGGTTTAGGA
Found at i:43207892 original size:126 final size:126
Alignment explanation
Indices: 43207511--43207907 Score: 571
Period size: 126 Copynumber: 3.2 Consensus size: 126
43207501 ACTTTTGTTT
* * * * * * ** *
43207511 TTTTTCTACAGTAGTTTTTGAAAAAGTAATTTTAAGAATACGGTTTTGAAAGGATAATGTAAAAA
1 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTAAAAAAATAGTGTAAAAA
*
43207576 ACGCTTCAAGCAGGATGCACTG-CAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCTACGTGGACGCTC
* * *
43207636 TTTTTCTACAGTAGTTCCTGAAAAAATGATTTTGAGAAGACGGTTCTAAACAAATAGTGTAAAAA
1 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTAAAAAAATAGTGTAAAAA
* * * * * *
43207701 ATGCTTCAAGCAGGATGCGCTGTTAGCAAAATTACTGAAAAAAGCTCCTACGTGGATGTTG
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCTACGTGGACGCTC
* *
43207762 TTTTTTTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTAAAAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTAAAAAAATAGTGTAAAAA
* *
43207827 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCTACGTGGACACAC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCTACGTGGACGCTC
*
43207888 TTTTTCTACAATAGTTCTTG
1 TTTTTCTACAGTAGTTCTTG
43207908 TTTGGCCTTA
Statistics
Matches: 237, Mismatches: 34, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
125 73 0.31
126 164 0.69
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTAAAAAAATAGTGTAAAAA
ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCTACGTGGACGCTC
Found at i:43210950 original size:9 final size:9
Alignment explanation
Indices: 43210927--43210957 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
43210917 ATTTCTATTT
43210927 TATTAAAAA
1 TATTAAAAA
43210936 TA-TAAAAA
1 TATTAAAAA
43210944 TATTAAAAA
1 TATTAAAAA
43210953 TATTA
1 TATTA
43210958 CCTTATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
TATTAAAAA
Found at i:43211034 original size:24 final size:24
Alignment explanation
Indices: 43210978--43211034 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
43210968 AAGAACTTCT
*
43210978 ATTTTATTAAAAATATAAAAATAA
1 ATTTTATTAAAAATATAAAAACAA
*
43211002 ATTAGTATT-AAAATATTAAAAACAA
1 ATT-TTATTAAAAATA-TAAAAACAA
43211027 ATTTTATT
1 ATTTTATT
43211035 TTTTAAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 13 0.46
25 15 0.54
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (24 bp):
ATTTTATTAAAAATATAAAAACAA
Found at i:43211798 original size:431 final size:432
Alignment explanation
Indices: 43210984--43211846 Score: 1719
Period size: 431 Copynumber: 2.0 Consensus size: 432
43210974 TTCTATTTTA
43210984 TTAAAAATATAAAAATAAATTAGTATTAAAATATTAAAAACAAATTTTATTTTTTAAAATGAAAT
1 TTAAAAATATAAAAATAAATTAGTATTAAAATATTAAAAACAAATTTTATTTTTTAAAATGAAAT
43211049 AATATAAAAACAATCTGTACAAATATATTAAATAAAATCAATGTTGGTGCTAGTCGGAATCAGTG
66 AATATAAAAACAATCTGTACAAATATATTAAATAAAATCAATGTTGGTGCTAGTCGGAATCAGTG
43211114 CTACATGGGGGTCGCCGACGGTTACGCACTGGATTCCTCCTTGGTTTAGTTTCTAGTGGGGGTTG
131 CTACATGGGGGTCGCCGACGGTTACGCACTGGATTCCTCCTTGGTTTAGTTTCTAGTGGGGGTTG
43211179 TGGAGTGGTTACTCCGGTGGGGGTTATGGTTGTGGATATTAGGAGGATGACCCACCTTGATAGAA
196 TGGAGTGGTTACTCCGGTGGGGGTTATGGTTGTGGATATTAGGAGGATGACCCACCTTGATAGAA
43211244 AAAAGAATGCAAAGGTGTTTGCATCACCCACAGCGGAGGTGTTTGAATCTCATAAGGCGAAAGGG
261 AAAAGAATGCAAAGGTGTTTGCATCACCCACAGCGGAGGTGTTTGAATCTCATAAGGCGAAAGGG
43211309 ATTGGTAATGAGAAGAGCTCCCCGACGGTGCCTCGTGCGATCCCTCCTATGATGGCGGCCTATAT
326 ATTGGTAATGAGAAGAGCTCCCCGACGGTGCCTCGTGCGATCCCTCCTATGATGGCGGCCTATAT
43211374 ATCGATGGTTGAGTTAGAGTTATCGGGAAATGATATGCACCG
391 ATCGATGGTTGAGTTAGAGTTATCGGGAAATGATATGCACCG
43211416 TTAAAAATAT-AAAATAAATTAGTATTAAAATATTAAAAACAAATTTTATTTTTTAAAATGAAAT
1 TTAAAAATATAAAAATAAATTAGTATTAAAATATTAAAAACAAATTTTATTTTTTAAAATGAAAT
43211480 AATATAAAAACAATCTGTACAAATATATTAAATAAAATCAATGTTGGTGCTAGTCGGAATCAGTG
66 AATATAAAAACAATCTGTACAAATATATTAAATAAAATCAATGTTGGTGCTAGTCGGAATCAGTG
43211545 CTACATGGGGGTCGCCGACGGTTACGCACTGGATTCCTCCTTGGTTTAGTTTCTAGTGGGGGTTG
131 CTACATGGGGGTCGCCGACGGTTACGCACTGGATTCCTCCTTGGTTTAGTTTCTAGTGGGGGTTG
43211610 TGGAGTGGTTACTCCGGTGGGGGTTATGGTTGTGGATATTAGGAGGATGACCCACCTTGATAGAA
196 TGGAGTGGTTACTCCGGTGGGGGTTATGGTTGTGGATATTAGGAGGATGACCCACCTTGATAGAA
43211675 AAAAGAATGCAAAGGTGTTTGCATCACCCACAGCGGAGGTGTTTGAATCTCATAAGGCGAAAGGG
261 AAAAGAATGCAAAGGTGTTTGCATCACCCACAGCGGAGGTGTTTGAATCTCATAAGGCGAAAGGG
43211740 ATTGGTAATGAGAAGAGCTCCCCGACGGTGCCTCGTGCGATCCCTCCTATGATGGCGGCCTATAT
326 ATTGGTAATGAGAAGAGCTCCCCGACGGTGCCTCGTGCGATCCCTCCTATGATGGCGGCCTATAT
43211805 ATCGATGGTTGAGTTAGAGTTATCGGGAAATGATATGCACCG
391 ATCGATGGTTGAGTTAGAGTTATCGGGAAATGATATGCACCG
43211847 GGCCATGCAT
Statistics
Matches: 431, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
431 421 0.98
432 10 0.02
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (432 bp):
TTAAAAATATAAAAATAAATTAGTATTAAAATATTAAAAACAAATTTTATTTTTTAAAATGAAAT
AATATAAAAACAATCTGTACAAATATATTAAATAAAATCAATGTTGGTGCTAGTCGGAATCAGTG
CTACATGGGGGTCGCCGACGGTTACGCACTGGATTCCTCCTTGGTTTAGTTTCTAGTGGGGGTTG
TGGAGTGGTTACTCCGGTGGGGGTTATGGTTGTGGATATTAGGAGGATGACCCACCTTGATAGAA
AAAAGAATGCAAAGGTGTTTGCATCACCCACAGCGGAGGTGTTTGAATCTCATAAGGCGAAAGGG
ATTGGTAATGAGAAGAGCTCCCCGACGGTGCCTCGTGCGATCCCTCCTATGATGGCGGCCTATAT
ATCGATGGTTGAGTTAGAGTTATCGGGAAATGATATGCACCG
Found at i:43213496 original size:22 final size:25
Alignment explanation
Indices: 43213462--43213511 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 25
43213452 AAAAAATTAT
* *
43213462 AAAATAAGAATTACATAA-A-TGAA
1 AAAAAAAGAATTAAATAATATTGAA
43213485 AAAAAAAG-ATTAAATAATATTGAA
1 AAAAAAAGAATTAAATAATATTGAA
43213509 AAA
1 AAA
43213512 TTAAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 8 0.35
23 8 0.35
24 7 0.30
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (25 bp):
AAAAAAAGAATTAAATAATATTGAA
Found at i:43213672 original size:21 final size:20
Alignment explanation
Indices: 43213644--43213685 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
43213634 TTCAGAAAAA
**
43213644 AAATTAAAGAGAGCTTTGAG
1 AAATTAAAGAGAAATTTGAG
43213664 AAATATAAAGAGAAATTTGAG
1 AAAT-TAAAGAGAAATTTGAG
43213685 A
1 A
43213686 GAAATTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.52, C:0.02, G:0.21, T:0.24
Consensus pattern (20 bp):
AAATTAAAGAGAAATTTGAG
Found at i:43213700 original size:10 final size:11
Alignment explanation
Indices: 43213672--43213700 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
43213662 AGAAATATAA
43213672 AGAGAAATTTG
1 AGAGAAATTTG
43213683 AGAGAAATTTG
1 AGAGAAATTTG
43213694 A-AGAAAT
1 AGAGAAAT
43213701 ACTGTGTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (11 bp):
AGAGAAATTTG
Found at i:43213924 original size:18 final size:18
Alignment explanation
Indices: 43213891--43213936 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
43213881 AATCGCTCAT
* *
43213891 CTAGGAAACTTATAAGGG
1 CTAGGATACATATAAGGG
* *
43213909 TTATGATACATATAAGGG
1 CTAGGATACATATAAGGG
43213927 CTAGGATACA
1 CTAGGATACA
43213937 CACCTGGCAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (18 bp):
CTAGGATACATATAAGGG
Found at i:43216723 original size:131 final size:127
Alignment explanation
Indices: 43216571--43216829 Score: 267
Period size: 129 Copynumber: 2.0 Consensus size: 127
43216561 AGTTTTTGAA
** * * *
43216571 TTATTCAAAAGTTCTTATTTAAATAATTGAATTGTTAAAATTGATACTATATATGGCTTT-CTTT
1 TTATTCAAAAGTTCTTATTTAAATAACCGAAGTGTTAAAATCGAT-CT-TATATGCCTTTCCTTT
*
43216635 GTTTGCACTATCTACACTAA-TCAAAAGCTTTAT-GTCCCTTTCTCTTCTACA-TTTCAACTTTT
64 -TTTGCACTATCTACACCAATTCAAAA-CTTT-TCGTCCCTTTCTCTTCTACATTTTC-A-TTTT
43216697 TTTT
124 TTTT
* * * * *
43216701 TTATGTCAAAAGTT-TTCTTTTAAGTCACCGAAGTGTTAAAATCGATGTTGTATGCCTTTCCTTT
1 TTAT-TCAAAAGTTCTT-ATTTAAATAACCGAAGTGTTAAAATCGATCTTATATGCCTTTCCTTT
* * * *
43216765 TTTGCACTGTCTGCACCAATTGAAAACTTTTCTTCCCTTTCTCTTCTACATTTTCATTTTTTTT
64 TTTGCACTATCTACACCAATTCAAAACTTTTCGTCCCTTTCTCTTCTACATTTTCATTTTTTTT
43216829 T
1 T
43216830 CATGAAACAA
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
128 10 0.09
129 47 0.44
130 20 0.19
131 31 0.29
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.48
Consensus pattern (127 bp):
TTATTCAAAAGTTCTTATTTAAATAACCGAAGTGTTAAAATCGATCTTATATGCCTTTCCTTTTT
TGCACTATCTACACCAATTCAAAACTTTTCGTCCCTTTCTCTTCTACATTTTCATTTTTTTT
Found at i:43229784 original size:17 final size:18
Alignment explanation
Indices: 43229747--43229783 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
43229737 GTATATATTC
43229747 TTTAGATTTTTTTAGAAT
1 TTTAGATTTTTTTAGAAT
43229765 TTTA-ATTTTTTTA-AAT
1 TTTAGATTTTTTTAGAAT
43229781 TTT
1 TTT
43229784 TTAAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.32
17 9 0.47
18 4 0.21
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTAGATTTTTTTAGAAT
Found at i:43230182 original size:31 final size:29
Alignment explanation
Indices: 43230112--43230183 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
43230102 TTTTAGAGGT
*
43230112 TGCTCATATAAGGGCTAAACATTTCAAAA
1 TGCTCAAATAAGGGCTAAACATTTCAAAA
* *
43230141 TGATCAAATAAGGGCCT-AACATTTGCAGAAG
1 TGCTCAAATAAGGG-CTAAACATTT-CA-AAA
43230172 TGCTCAAATAAG
1 TGCTCAAATAAG
43230184 AGTTTTTCAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 19 0.53
30 4 0.11
31 13 0.36
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (29 bp):
TGCTCAAATAAGGGCTAAACATTTCAAAA
Found at i:43236124 original size:20 final size:21
Alignment explanation
Indices: 43236075--43236131 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
43236065 TAAGTTTTAG
43236075 TTAAAAACTTATATATTAAAAA
1 TTAAAAA-TTATATATTAAAAA
** *
43236097 TTTTAAATT-TATTTTAAAAA
1 TTAAAAATTATATATTAAAAA
*
43236117 TTAAAAATAATATAT
1 TTAAAAATTATATAT
43236132 ATTAGAAGTT
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
20 16 0.59
21 6 0.22
22 5 0.19
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TTAAAAATTATATATTAAAAA
Found at i:43236957 original size:24 final size:24
Alignment explanation
Indices: 43236941--43236994 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
43236931 AATCAAAATC
43236941 AAATATATTATGTTAATAAATAAT
1 AAATATATTATGTTAATAAATAAT
** * *
43236965 AAATATATTATACTCATAAATACT
1 AAATATATTATGTTAATAAATAAT
43236989 AAATAT
1 AAATAT
43236995 TCTAGAAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.39
Consensus pattern (24 bp):
AAATATATTATGTTAATAAATAAT
Found at i:43243838 original size:12 final size:12
Alignment explanation
Indices: 43243821--43243845 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43243811 TCTAGCCCGG
43243821 ACGGGTGATCCT
1 ACGGGTGATCCT
43243833 ACGGGTGATCCT
1 ACGGGTGATCCT
43243845 A
1 A
43243846 TCCTGATATA
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:0.20, C:0.24, G:0.32, T:0.24
Consensus pattern (12 bp):
ACGGGTGATCCT
Found at i:43248215 original size:32 final size:32
Alignment explanation
Indices: 43248179--43248243 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
43248169 CACCATAAAC
* *
43248179 TTATAAATTGATTACTTGAATTT-AGTAACTCA
1 TTATAAATTAATTAATTGAATTTGA-TAACTCA
*
43248211 TTATAAATTAATTAATTTAATTTGATAACTCA
1 TTATAAATTAATTAATTGAATTTGATAACTCA
43248243 T
1 T
43248244 ATTGATTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (32 bp):
TTATAAATTAATTAATTGAATTTGATAACTCA
Found at i:43249978 original size:21 final size:21
Alignment explanation
Indices: 43249936--43249985 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
43249926 TAAATAAGTG
*
43249936 TAATAATAGCACCAATAATAA
1 TAATAATAGCAACAATAATAA
* * *
43249957 TAATAATAGTAACAGTACTAA
1 TAATAATAGCAACAATAATAA
*
43249978 TAACAATA
1 TAATAATA
43249986 ATAATGATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (21 bp):
TAATAATAGCAACAATAATAA
Found at i:43251998 original size:29 final size:29
Alignment explanation
Indices: 43251956--43252021 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
43251946 TCAATTATGT
43251956 TTAAATTTTAAAAAATAAAAATAAAAGGA
1 TTAAATTTTAAAAAATAAAAATAAAAGGA
*
43251985 TTAAATTCTT-AAAAATAAAAATAAAATGA
1 TTAAATT-TTAAAAAATAAAAATAAAAGGA
*
43252014 CTAAATTT
1 TTAAATTT
43252022 CAAATGTGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 1 0.03
29 31 0.91
30 2 0.06
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (29 bp):
TTAAATTTTAAAAAATAAAAATAAAAGGA
Found at i:43252026 original size:132 final size:133
Alignment explanation
Indices: 43251675--43252035 Score: 485
Period size: 133 Copynumber: 2.7 Consensus size: 133
43251665 AGTAGAAAAA
* * * *
43251675 AGTTACCAATTATATTTAAAATTTGAAATTTGAAAAATAAAAATATTAAATTCCTAAAAATCAAA
1 AGTTACCAATTATATTTAAATTTTAAAATTTGAAAAATAAAAAGATTAAATTCCTAAAAATAAAA
* * * * *
43251740 ATAGAATGACTAAATTTCAAACGTGTGAAGATGTCGAACCAATAAATTTAGCAGAGAAATTTAGC
66 ATAAAATGACTAAATTTCAAATGTGTGAAGATGTCAAACAAACAAATTTAGCAGAGAAATTTAGC
43251805 TAG
131 TAG
* * * *
43251808 ATTTACCAATTATATTTAAATTCTAAATTTTGAAAAATAAAAAGATTAAATTCCTAAAAGTAAAA
1 AGTTACCAATTATATTTAAATTTTAAAATTTGAAAAATAAAAAGATTAAATTCCTAAAAATAAAA
* * *
43251873 ATAAAATAACTAAATTCCAAATGTGTGAATATGTCAAACAAACAAATTTAGCAGA-AAATTTTAG
66 ATAAAATGACTAAATTTCAAATGTGTGAAGATGTCAAACAAACAAATTTAGCAGAGAAA-TTTAG
43251937 -TCAG
130 CT-AG
* * ** * *
43251941 AGTTATCAATTATGTTTAAATTTTAAAAAAT-AAAAATAAAAGGATTAAATTCTTAAAAATAAAA
1 AGTTACCAATTATATTTAAATTTTAAAATTTGAAAAATAAAAAGATTAAATTCCTAAAAATAAAA
43252005 ATAAAATGACTAAATTTCAAATGTGTGAAGA
66 ATAAAATGACTAAATTTCAAATGTGTGAAGA
43252036 GTAGTAGATT
Statistics
Matches: 197, Mismatches: 29, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
132 62 0.31
133 135 0.69
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.31
Consensus pattern (133 bp):
AGTTACCAATTATATTTAAATTTTAAAATTTGAAAAATAAAAAGATTAAATTCCTAAAAATAAAA
ATAAAATGACTAAATTTCAAATGTGTGAAGATGTCAAACAAACAAATTTAGCAGAGAAATTTAGC
TAG
Found at i:43252265 original size:90 final size:89
Alignment explanation
Indices: 43252114--43252467 Score: 358
Period size: 90 Copynumber: 4.0 Consensus size: 89
43252104 CATAAAAAGT
* * * * * *
43252114 CCTC-AATTTTTTCAAAAAAAAGTAATTAAGCCA-AAATTTTTTTTACACTCAATTGGATACTTA
1 CCTCAAATTTTTTC-AAAAAAAGCAATTAAGCCATGATTTTTTTTTACATTCAATTGGGTACTTG
* * *
43252177 AATTTTTAAAATGTATCAAGATGGC
65 AACTTTTAAAATGTATCAAAAAGGC
* * * *
43252202 CCTCAAGA-TTTTTCAAAAAAAGTAATTAAGCTCATGTTTTTTTTTTCCATTTAATTGGGTACTT
1 CCTCAA-ATTTTTTCAAAAAAAGCAATTAAGC-CATGATTTTTTTTTACATTCAATTGGGTACTT
* *
43252266 GAACTTTCAAAATATATCAAAAAGGC
64 GAACTTTTAAAATGTATCAAAAAGGC
* *
43252292 CCTCAAATTTTTTCAAAAAAAGCAATTAAGCCCCTGCTTTTTTTTTACATTCAATTGGGTACTTG
1 CCTCAAATTTTTTCAAAAAAAGCAATTAAG-CCATGATTTTTTTTTACATTCAATTGGGTACTTG
* * * *
43252357 CAGTTTTAAAATGCATCAAAAAGAC
65 AACTTTTAAAATGTATCAAAAAGGC
* * * ** *
43252382 CCTCAAATTTTTTCAAAAAAAGCAATTAAGCCTCTCA-TTTTTTTAACGCTCAATTGGATACTTG
1 CCTCAAATTTTTTCAAAAAAAGCAATTAAGCC-ATGATTTTTTTTTACATTCAATTGGGTACTTG
* *
43252446 AA-TTGTCAAAATGCATCAAAAA
65 AACTT-TTAAAATGTATCAAAAA
43252468 ACCCTTTGAC
Statistics
Matches: 226, Mismatches: 32, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
88 23 0.10
89 52 0.23
90 150 0.66
91 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.36
Consensus pattern (89 bp):
CCTCAAATTTTTTCAAAAAAAGCAATTAAGCCATGATTTTTTTTTACATTCAATTGGGTACTTGA
ACTTTTAAAATGTATCAAAAAGGC
Found at i:43252587 original size:15 final size:16
Alignment explanation
Indices: 43252567--43252603 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
43252557 TGACACGTGG
43252567 TAAAAAT-ATAAATA-A
1 TAAAAATAATAAA-AGA
43252582 TAAAAATAATAAAAGA
1 TAAAAATAATAAAAGA
43252598 TAAAAA
1 TAAAAA
43252604 AATTTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (16 bp):
TAAAAATAATAAAAGA
Found at i:43266373 original size:29 final size:28
Alignment explanation
Indices: 43266290--43266373 Score: 64
Period size: 29 Copynumber: 2.9 Consensus size: 28
43266280 ATTAACCGTT
43266290 AGACTCAAATTTTGAAATTTGA-AAAGTAAA
1 AGACT-AAATTTT-AAATTT-ACAAAGTAAA
* ** *
43266320 ATGACTAAATTTTTAA-GAACAAAAGTATAG
1 A-GACTAAATTTTAAATTTAC-AAAGTA-AA
43266350 AGACTAAATTTTAAATTTACAAAG
1 AGACTAAATTTTAAATTTACAAAG
43266374 AATGCAAAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 11
0.70 0.12 0.18
Matches are distributed among these distances:
27 1 0.02
29 25 0.60
30 12 0.29
31 4 0.10
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (28 bp):
AGACTAAATTTTAAATTTACAAAGTAAA
Found at i:43278505 original size:2 final size:2
Alignment explanation
Indices: 43278498--43278528 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
43278488 TGAATATCAC
43278498 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
43278529 AGGCTCGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:43282808 original size:35 final size:35
Alignment explanation
Indices: 43282762--43282833 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
43282752 AAACCCTAAA
43282762 ACAAAATTCAAGAGGGCAAGAACTACGAAGTACTT
1 ACAAAATTCAAGAGGGCAAGAACTACGAAGTACTT
43282797 ACAAAATTCAAGAGGGCAAGAACTACGAAGTACTT
1 ACAAAATTCAAGAGGGCAAGAACTACGAAGTACTT
43282832 AC
1 AC
43282834 TTTGTTCTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.46, C:0.18, G:0.19, T:0.17
Consensus pattern (35 bp):
ACAAAATTCAAGAGGGCAAGAACTACGAAGTACTT
Found at i:43284989 original size:18 final size:18
Alignment explanation
Indices: 43284953--43285004 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
43284943 TTATTATTTT
*
43284953 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
43284971 TAAAATTTAAATATT-AAA
1 TAAAATTT-AATATTAAAA
* *
43284989 TAATATTTTATATTAA
1 TAAAATTTAATATTAA
43285005 TATTTTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 5 0.17
18 19 0.66
19 5 0.17
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:43285032 original size:10 final size:9
Alignment explanation
Indices: 43285003--43285028 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
43284993 ATTTTATATT
43285003 AATATTTTA
1 AATATTTTA
43285012 AATATTTTA
1 AATATTTTA
43285021 AATATTTT
1 AATATTTT
43285029 TAAAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
AATATTTTA
Found at i:43292154 original size:3 final size:3
Alignment explanation
Indices: 43292146--43292183 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
43292136 CAATGAGTCT
43292146 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
43292184 TTGGTGAAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:43292752 original size:14 final size:14
Alignment explanation
Indices: 43292733--43292763 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
43292723 ATATGATAAT
*
43292733 TTAAAAAATTTTAG
1 TTAAAAAATTATAG
43292747 TTAAAAAATTATAG
1 TTAAAAAATTATAG
43292761 TTA
1 TTA
43292764 CAATTTTAAA
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:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (14 bp):
TTAAAAAATTATAG
Found at i:43295677 original size:154 final size:155
Alignment explanation
Indices: 43295381--43295706 Score: 368
Period size: 154 Copynumber: 2.1 Consensus size: 155
43295371 TTGGTTTTAA
* * * ** * *
43295381 CATGATATTTATATTTTAGTTTTATTATGCATTCTTTGTTACCTCCGTCAATTATATATCAATAC
1 CATGACATTTATATTTTAATTTTATCATGCATAATTTATTACCTCCATCAATTATATATCAATAC
* * * ** * * *
43295446 TATTATTTAACCTTGGTTGAGTTGGTGTCAAGTCAACCGGACACCAACTCAACCAAAACTAATTA
66 TATTATTTAACCTTGATTGAGTTGGTGTCAAATCAAACAAAAACCAACTCAACCAAAACCAAATA
*
43295511 AAATTTTATATATGGGATTTGAACC
131 AAATTATATATATGGGATTTGAACC
* * * *
43295536 CATGACATTTA-ATTTTAATTTTATCATGCATAATTTATTATCTCTATCAATTGTATATCTATAC
1 CATGACATTTATATTTTAATTTTATCATGCATAATTTATTACCTCCATCAATTATATATCAATAC
*
43295600 TATTATTTAACCTTGATTGAGTTGGTGTCACGAATCAAACAAAAATCAACTCAACCAAAACCAAA
66 TATTATTTAACCTTGATTGAGTTGGTGTCA--AATCAAACAAAAACCAACTCAACCAAAACCAAA
* * **
43295665 TATAA-TATTATATATGGAATTTGAGTC
129 TAAAATTA-TATATATGGGATTTGAACC
* *
43295692 CGTGACATTTGTATT
1 CATGACATTTATATT
43295707 GATAAAACTT
Statistics
Matches: 140, Mismatches: 27, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
154 72 0.51
155 11 0.08
156 54 0.39
157 3 0.02
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (155 bp):
CATGACATTTATATTTTAATTTTATCATGCATAATTTATTACCTCCATCAATTATATATCAATAC
TATTATTTAACCTTGATTGAGTTGGTGTCAAATCAAACAAAAACCAACTCAACCAAAACCAAATA
AAATTATATATATGGGATTTGAACC
Found at i:43304958 original size:16 final size:17
Alignment explanation
Indices: 43304937--43304969 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
43304927 AAAAAAGTCC
*
43304937 TCAATT-AGGGGCAAAT
1 TCAATTAAGGGGAAAAT
43304953 TCAATTAAGGGGAAAAT
1 TCAATTAAGGGGAAAAT
43304970 AATAGAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.42, C:0.09, G:0.24, T:0.24
Consensus pattern (17 bp):
TCAATTAAGGGGAAAAT
Found at i:43322152 original size:1 final size:1
Alignment explanation
Indices: 43322146--43322245 Score: 65
Period size: 1 Copynumber: 100.0 Consensus size: 1
43322136 ACAGTGGAGG
* * * * * * * * * *
43322146 AAAAAAAAACAAAAGAATAAAAAAAACAAGAAAAAACAAGAAAATAAAAAATAAAAAAAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
43322211 AAAACAAGAAAATAAAAAATAAAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
43322246 CTCTACCGGG
Statistics
Matches: 69, Mismatches: 30, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.85, C:0.06, G:0.04, T:0.05
Consensus pattern (1 bp):
A
Found at i:43322179 original size:25 final size:26
Alignment explanation
Indices: 43322146--43322238 Score: 93
Period size: 27 Copynumber: 3.5 Consensus size: 26
43322136 ACAGTGGAGG
*
43322146 AAAAAAAAACAAAAG-AATAAAAAAA
1 AAAAAAAAACAAAAGAAATAAAAAAT
*
43322171 ACAAGAAAAAACAAGA-AAATAAAAAAT
1 A-AA-AAAAAACAAAAGAAATAAAAAAT
*
43322198 AAAAAAAAACAAAA-AAACAAGAAAAT
1 AAAAAAAAACAAAAGAAATAA-AAAAT
*
43322224 AAAAAATAAAAAAAA
1 AAAAAA-AAACAAAA
43322239 CAAAAAACTC
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
25 16 0.28
26 15 0.26
27 27 0.47
ACGTcount: A:0.85, C:0.05, G:0.04, T:0.05
Consensus pattern (26 bp):
AAAAAAAAACAAAAGAAATAAAAAAT
Found at i:43322179 original size:27 final size:24
Alignment explanation
Indices: 43322146--43322245 Score: 96
Period size: 23 Copynumber: 4.1 Consensus size: 24
43322136 ACAGTGGAGG
43322146 AAAAAAAAACAAAAGAATAAAAAAA
1 AAAAAAAAACAAAA-AATAAAAAAA
*
43322171 ACAAGAAAAAACAAGAAAATAAAAAAT
1 A-AA-AAAAAACAA-AAAATAAAAAAA
* *
43322198 AAAAAAAAACAAAAAA-ACAAGAA
1 AAAAAAAAACAAAAAATAAAAAAA
* * *
43322221 AATAAAAAATAAAAAA-AACAAAA
1 AAAAAAAAACAAAAAATAAAAAAA
43322244 AA
1 AA
43322246 CTCTACCGGG
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
23 24 0.38
24 4 0.06
25 10 0.16
26 4 0.06
27 19 0.30
28 2 0.03
ACGTcount: A:0.85, C:0.06, G:0.04, T:0.05
Consensus pattern (24 bp):
AAAAAAAAACAAAAAATAAAAAAA
Found at i:43322213 original size:33 final size:32
Alignment explanation
Indices: 43322151--43322245 Score: 145
Period size: 33 Copynumber: 2.8 Consensus size: 32
43322141 GGAGGAAAAA
*
43322151 AAAACAAAAGAATAAAAAAAACAAGAAAAAACAAG
1 AAAATAAAA-AATAAAAAAAAC-A-AAAAAACAAG
43322186 AAAATAAAAAATAAAAAAAAACAAAAAAACAAG
1 AAAATAAAAAAT-AAAAAAAACAAAAAAACAAG
43322219 AAAATAAAAAATAAAAAAAACAAAAAA
1 AAAATAAAAAATAAAAAAAACAAAAAA
43322246 CTCTACCGGG
Statistics
Matches: 58, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
32 15 0.26
33 22 0.38
34 4 0.07
35 17 0.29
ACGTcount: A:0.84, C:0.06, G:0.04, T:0.05
Consensus pattern (32 bp):
AAAATAAAAAATAAAAAAAACAAAAAAACAAG
Found at i:43322243 original size:8 final size:8
Alignment explanation
Indices: 43322148--43322245 Score: 83
Period size: 8 Copynumber: 11.8 Consensus size: 8
43322138 AGTGGAGGAA
43322148 AAAAAAAC
1 AAAAAAAC
43322156 AAAAGAATA-
1 AAAA-AA-AC
43322165 AAAAAAAC
1 AAAAAAAC
43322173 AAGAAAAAAC
1 -A-AAAAAAC
* *
43322183 AAGAAAAT
1 AAAAAAAC
*
43322191 AAAAAATAA
1 AAAAAA-AC
43322200 AAAAAAAC
1 AAAAAAAC
43322208 AAAAAAAC
1 AAAAAAAC
* *
43322216 AAGAAAAT
1 AAAAAAAC
43322224 AAAAAATA-
1 AAAAAA-AC
43322232 AAAAAAAC
1 AAAAAAAC
43322240 AAAAAA
1 AAAAAA
43322246 CTCTACCGGG
Statistics
Matches: 74, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
7 2 0.03
8 48 0.65
9 16 0.22
10 8 0.11
ACGTcount: A:0.85, C:0.06, G:0.04, T:0.05
Consensus pattern (8 bp):
AAAAAAAC
Found at i:43322713 original size:17 final size:17
Alignment explanation
Indices: 43322674--43322717 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
43322664 AATAAAAATA
* *
43322674 AAAAAAGAAACGAAAAG
1 AAAAATGAAAAGAAAAG
43322691 AAAAATGAAAAGAAAAG
1 AAAAATGAAAAGAAAAG
43322708 AAAAAT-AAAA
1 AAAAATGAAAA
43322718 AAAGGAGAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 4 0.16
17 21 0.84
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.05
Consensus pattern (17 bp):
AAAAATGAAAAGAAAAG
Found at i:43342177 original size:53 final size:53
Alignment explanation
Indices: 43342097--43342202 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
43342087 GCAAGTAATT
43342097 ATCATAACCGCTCTATACTCACTATCTAAAAGAAAAAAATTCACCCTATCTCG
1 ATCATAACCGCTCTATACTCACTATCTAAAAGAAAAAAATTCACCCTATCTCG
43342150 ATCATAACCGCTCTATACTCACTATCTAAAAGAAAAAAATTCACCCTATCTCG
1 ATCATAACCGCTCTATACTCACTATCTAAAAGAAAAAAATTCACCCTATCTCG
43342203 CTCTACATCT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.40, C:0.28, G:0.06, T:0.26
Consensus pattern (53 bp):
ATCATAACCGCTCTATACTCACTATCTAAAAGAAAAAAATTCACCCTATCTCG
Found at i:43342902 original size:5 final size:5
Alignment explanation
Indices: 43342894--43342921 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
43342884 TTCTTTTAAT
43342894 AATGA AATGA AATGA AATGA AATGA AAT
1 AATGA AATGA AATGA AATGA AATGA AAT
43342922 ATTTAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.21
Consensus pattern (5 bp):
AATGA
Found at i:43345081 original size:40 final size:40
Alignment explanation
Indices: 43345036--43345116 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
43345026 ACATTAATTT
43345036 TTCTATTTTCTTATTATTATTGGCTTAGTTGATTAATACG
1 TTCTATTTTCTTATTATTATTGGCTTAGTTGATTAATACG
43345076 TTCTATTTTCTTATTATTATTGGCTTAGTTGATTAATACG
1 TTCTATTTTCTTATTATTATTGGCTTAGTTGATTAATACG
43345116 T
1 T
43345117 GAAGGTTTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.56
Consensus pattern (40 bp):
TTCTATTTTCTTATTATTATTGGCTTAGTTGATTAATACG
Found at i:43352465 original size:22 final size:22
Alignment explanation
Indices: 43352440--43352502 Score: 87
Period size: 20 Copynumber: 3.0 Consensus size: 22
43352430 TAGGGGTTTG
*
43352440 AGTTTTTTTCTATATTTTTTTA
1 AGTTTTTTTATATATTTTTTTA
*
43352462 AGTTTTTTTATATA-TTATTT-
1 AGTTTTTTTATATATTTTTTTA
43352482 AGTTTTTTTATA-ATTTTTTTA
1 AGTTTTTTTATATATTTTTTTA
43352503 GATGTAAAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.03
20 17 0.47
21 5 0.14
22 13 0.36
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (22 bp):
AGTTTTTTTATATATTTTTTTA
Found at i:43354206 original size:25 final size:26
Alignment explanation
Indices: 43354152--43354206 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
43354142 ATAATTCATG
* *
43354152 TATCTCATTTTCATGTTTCAATTCAC
1 TATCCCATTTTCATGTTTCAATTCAA
43354178 TATCCCATTTTCA-G-TTCACATTCAA
1 TATCCCATTTTCATGTTTCA-ATTCAA
43354203 TATC
1 TATC
43354207 ATCCAATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 4 0.15
25 10 0.38
26 12 0.46
ACGTcount: A:0.25, C:0.25, G:0.04, T:0.45
Consensus pattern (26 bp):
TATCCCATTTTCATGTTTCAATTCAA
Found at i:43359128 original size:9 final size:9
Alignment explanation
Indices: 43359114--43359163 Score: 82
Period size: 9 Copynumber: 5.6 Consensus size: 9
43359104 TTTGGTTAAA
43359114 AATTACCCG
1 AATTACCCG
43359123 AATTACCCG
1 AATTACCCG
43359132 AATTACCCG
1 AATTACCCG
*
43359141 AATTAACCG
1 AATTACCCG
*
43359150 AATTAACCG
1 AATTACCCG
43359159 AATTA
1 AATTA
43359164 ACTGAACCGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
9 40 1.00
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:43360855 original size:16 final size:16
Alignment explanation
Indices: 43360834--43360881 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
43360824 TCCATGTCAG
43360834 GATTTGTGTTTTAATT
1 GATTTGTGTTTTAATT
* *
43360850 GATTTGGAGTTTGAATT
1 GATTT-GTGTTTTAATT
*
43360867 AATTTGTGTTTTAAT
1 GATTTGTGTTTTAAT
43360882 GTTATAGGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.23, C:0.00, G:0.21, T:0.56
Consensus pattern (16 bp):
GATTTGTGTTTTAATT
Found at i:43364999 original size:43 final size:43
Alignment explanation
Indices: 43364938--43365022 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
43364928 TTCAAATCTG
* * * *
43364938 CATATATAAACCAACATTAATTTAATTGTTCAGATGGAATAGA
1 CATATAGAAACCAACATTAACTTAATTGCTCAAATGGAATAGA
43364981 CATATAGAAACCAACATTAACTTAATTGCTCAAATGGAATAG
1 CATATAGAAACCAACATTAACTTAATTGCTCAAATGGAATAG
43365023 GAGGAGGAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (43 bp):
CATATAGAAACCAACATTAACTTAATTGCTCAAATGGAATAGA
Found at i:43366889 original size:49 final size:49
Alignment explanation
Indices: 43366791--43366890 Score: 175
Period size: 50 Copynumber: 2.0 Consensus size: 49
43366781 ACCTCCTGGG
43366791 TTTTGCCTATAAAACGCTGTCGTTAATTAGTAGGGGAACTTTGCAGGGT
1 TTTTGCCTATAAAACGCTGTCGTTAATTAGTAGGGGAACTTTGCAGGGT
*
43366840 TTTTGCCTATAAAAACGCTGTCGTTAATTCGTAGGGGAACTTTGC-GGGT
1 TTTTGCCTAT-AAAACGCTGTCGTTAATTAGTAGGGGAACTTTGCAGGGT
43366889 TT
1 TT
43366891 GGGCCTAATA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
49 16 0.33
50 33 0.67
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (49 bp):
TTTTGCCTATAAAACGCTGTCGTTAATTAGTAGGGGAACTTTGCAGGGT
Found at i:43369993 original size:22 final size:22
Alignment explanation
Indices: 43369968--43370011 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
43369958 TCTCCAAACT
43369968 TTAAAACATTCTAA-TTATATCA
1 TTAAAACATTC-AAGTTATATCA
**
43369990 TTAAATTATTCAAGTTATATCA
1 TTAAAACATTCAAGTTATATCA
43370012 ATTTGGTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.43
Consensus pattern (22 bp):
TTAAAACATTCAAGTTATATCA
Found at i:43372125 original size:19 final size:18
Alignment explanation
Indices: 43372082--43372129 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
43372072 TAGATTCGGA
43372082 TCTTTTCTTTTTTTGCTTC
1 TCTTTT-TTTTTTTGCTTC
43372101 TCTTTTGTTTTTTTG-TT-
1 TCTTTT-TTTTTTTGCTTC
43372118 T-TTTTTTTTTTT
1 TCTTTTTTTTTTT
43372130 TTCAAAGCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 7 0.25
16 4 0.14
17 1 0.04
18 2 0.07
19 14 0.50
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.83
Consensus pattern (18 bp):
TCTTTTTTTTTTTGCTTC
Found at i:43374143 original size:16 final size:16
Alignment explanation
Indices: 43374122--43374171 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
43374112 TTTTATTTTT
43374122 ATATAAAAAATTAAAA
1 ATATAAAAAATTAAAA
* *
43374138 ATATAATAAATCAAAA
1 ATATAAAAAATTAAAA
*
43374154 ACACTAAAAATATTAAAA
1 ATA-TAAAAA-ATTAAAA
43374172 TAAATGTTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 16 0.59
17 5 0.19
18 6 0.22
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (16 bp):
ATATAAAAAATTAAAA
Found at i:43375005 original size:14 final size:13
Alignment explanation
Indices: 43374966--43375015 Score: 59
Period size: 12 Copynumber: 3.9 Consensus size: 13
43374956 TGAAGTATAT
43374966 TATTATT-TATTA
1 TATTATTATATTA
* *
43374978 TATT-GTAAATTA
1 TATTATTATATTA
43374990 TATTAATTATATTA
1 TATT-ATTATATTA
43375004 TATTATTATATT
1 TATTATTATATT
43375016 TCAAATAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
11 1 0.03
12 12 0.39
13 8 0.26
14 10 0.32
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (13 bp):
TATTATTATATTA
Found at i:43378110 original size:19 final size:20
Alignment explanation
Indices: 43378073--43378112 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
43378063 TGTTACAATA
43378073 TATTTTTAAAATAATTTTTT
1 TATTTTTAAAATAATTTTTT
43378093 TATTTTTAAAATAATTTTTT
1 TATTTTTAAAATAATTTTTT
43378113 GGTGTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TATTTTTAAAATAATTTTTT
Found at i:43378120 original size:20 final size:20
Alignment explanation
Indices: 43378077--43378120 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
43378067 ACAATATATT
* *
43378077 TTTAAAATAATTTTTTTATT
1 TTTAAAATAATTTTTTGATG
*
43378097 TTTAAAATAATTTTTTGGTG
1 TTTAAAATAATTTTTTGATG
43378117 TTTA
1 TTTA
43378121 TTAAAAAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (20 bp):
TTTAAAATAATTTTTTGATG
Found at i:43385333 original size:3 final size:3
Alignment explanation
Indices: 43385325--43385349 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
43385315 AAAAAAGGGG
43385325 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
43385350 AGAATTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:43396126 original size:15 final size:15
Alignment explanation
Indices: 43396106--43396135 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43396096 ATTCCAACCC
*
43396106 AAATTAAATATATTT
1 AAATTAAACATATTT
43396121 AAATTAAACATATTT
1 AAATTAAACATATTT
43396136 TGGACACTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
AAATTAAACATATTT
Found at i:43415831 original size:129 final size:129
Alignment explanation
Indices: 43415601--43415858 Score: 516
Period size: 129 Copynumber: 2.0 Consensus size: 129
43415591 CGAATGCTGA
43415601 CTTTTATTTTATAGCAGAAGTGTGTGTGCTTGAGGCCAATTTTAGGAAATACAATTGCTCTATCT
1 CTTTTATTTTATAGCAGAAGTGTGTGTGCTTGAGGCCAATTTTAGGAAATACAATTGCTCTATCT
43415666 TGTAGTCAAGCTGCCTAATATATTAGGTTAGCTCATTCAAGGTTATATGCGTATTCACTTTAAT
66 TGTAGTCAAGCTGCCTAATATATTAGGTTAGCTCATTCAAGGTTATATGCGTATTCACTTTAAT
43415730 CTTTTATTTTATAGCAGAAGTGTGTGTGCTTGAGGCCAATTTTAGGAAATACAATTGCTCTATCT
1 CTTTTATTTTATAGCAGAAGTGTGTGTGCTTGAGGCCAATTTTAGGAAATACAATTGCTCTATCT
43415795 TGTAGTCAAGCTGCCTAATATATTAGGTTAGCTCATTCAAGGTTATATGCGTATTCACTTTAAT
66 TGTAGTCAAGCTGCCTAATATATTAGGTTAGCTCATTCAAGGTTATATGCGTATTCACTTTAAT
43415859 TAGCTTACTG
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
129 129 1.00
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.40
Consensus pattern (129 bp):
CTTTTATTTTATAGCAGAAGTGTGTGTGCTTGAGGCCAATTTTAGGAAATACAATTGCTCTATCT
TGTAGTCAAGCTGCCTAATATATTAGGTTAGCTCATTCAAGGTTATATGCGTATTCACTTTAAT
Found at i:43430277 original size:14 final size:17
Alignment explanation
Indices: 43430244--43430280 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
43430234 ACATAATACA
43430244 TAATTAATATTAGAATT
1 TAATTAATATTAGAATT
43430261 TAATTAA-A-TAG-ATT
1 TAATTAATATTAGAATT
43430275 TAATTA
1 TAATTA
43430281 TTGTTATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.45
15 3 0.15
16 1 0.05
17 7 0.35
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (17 bp):
TAATTAATATTAGAATT
Found at i:43430709 original size:24 final size:26
Alignment explanation
Indices: 43430666--43430719 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
43430656 TGAGTTAGTG
43430666 ATTTAATATAAATATATAAT-T-ATT
1 ATTTAATATAAATATATAATATAATT
*
43430690 ATTTAATATATATA-ATTAATATAATT
1 ATTTAATATAAATATA-TAATATAATT
43430716 ATTT
1 ATTT
43430720 CTTATAACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 1 0.04
24 17 0.65
25 1 0.04
26 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
ATTTAATATAAATATATAATATAATT
Found at i:43442892 original size:166 final size:166
Alignment explanation
Indices: 43442611--43442913 Score: 493
Period size: 166 Copynumber: 1.8 Consensus size: 166
43442601 CCCAATCTAT
**
43442611 TTTTAAATTTATAATACTTTATATTATGTTGTTTTTATACATTATGTAATTTAGAACACATTAAA
1 TTTTAAATTTATAATACTTTATATTATGTAATTTTTATACATTATGTAATTTAGAACACATTAAA
* *
43442676 AAAATAAAACTTATACAAAATATATAATACTACTCTAATATAAACATTAAAAATAATGTTAAAAT
66 AAAATAAAACATATACAAAACATATAATACTACTCTAATATAAACATTAAAAATAATGTTAAAAT
43442741 GACTATATAAAAATTTTCAATAAAAGGCCTAGCCTG
131 GACTATATAAAAATTTTCAATAAAAGGCCTAGCCTG
* *
43442777 TTTTAAGTTTATAATACTTTATATTATGTAATTTTTATATATTATGTAATTTAGAACACATTAAA
1 TTTTAAATTTATAATACTTTATATTATGTAATTTTTATACATTATGTAATTTAGAACACATTAAA
* * *
43442842 AAAA-ATAAACATATACTAAACATATAATA-TCACTCTAATTTAAACATTAAAAATAATGTTAAG
66 AAAATA-AAACATATACAAAACATATAATACT-ACTCTAATATAAACATTAAAAATAATGTTAAA
43442905 ATGACTATA
129 ATGACTATA
43442914 AAATTTTTTT
Statistics
Matches: 126, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
165 2 0.02
166 124 0.98
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.39
Consensus pattern (166 bp):
TTTTAAATTTATAATACTTTATATTATGTAATTTTTATACATTATGTAATTTAGAACACATTAAA
AAAATAAAACATATACAAAACATATAATACTACTCTAATATAAACATTAAAAATAATGTTAAAAT
GACTATATAAAAATTTTCAATAAAAGGCCTAGCCTG
Found at i:43458383 original size:9 final size:10
Alignment explanation
Indices: 43458341--43458383 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
43458331 TTCATAAGTA
*
43458341 TTTATAAAAT
1 TTTATAAATT
43458351 TTTA-AATATGT
1 TTTATAA-AT-T
43458362 TTTATAAATT
1 TTTATAAATT
43458372 TTTATAAATT
1 TTTATAAATT
43458382 TT
1 TT
43458384 CATATTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
9 2 0.07
10 18 0.62
11 7 0.24
12 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (10 bp):
TTTATAAATT
Found at i:43459668 original size:86 final size:88
Alignment explanation
Indices: 43459497--43459668 Score: 287
Period size: 87 Copynumber: 2.0 Consensus size: 88
43459487 TTATACTTTG
* *
43459497 GCTCCCTTTAAAAATATAAAAATTTGATTTAATTCTTTAAAAATTATAAAAATATAATCCATTAA
1 GCTCCCTTTAAAAATATAAAAAATTGATTTAATCCTTTAAAAATTATAAAAATATAATCCATTAA
*
43459562 AATAGTGAAATTGCATTTTTTTA
66 AATAGTGAAATTACATTTTTTTA
43459585 GCTCCC-TTAAAAATATAAAAAATTGATTTAATCCTTT-AAAATTATAAAAATATAATCCATT-A
1 GCTCCCTTTAAAAATATAAAAAATTGATTTAATCCTTTAAAAATTATAAAAATATAATCCATTAA
*
43459647 AATGGTGAAATTACATTTTTTT
66 AATAGTGAAATTACATTTTTTT
43459669 GTACAAATTA
Statistics
Matches: 80, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
85 21 0.26
86 24 0.30
87 29 0.36
88 6 0.08
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (88 bp):
GCTCCCTTTAAAAATATAAAAAATTGATTTAATCCTTTAAAAATTATAAAAATATAATCCATTAA
AATAGTGAAATTACATTTTTTTA
Found at i:43461592 original size:21 final size:22
Alignment explanation
Indices: 43461568--43461617 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
43461558 TTATGTGTCC
*
43461568 ATATTATATATT-ATAAAAATA
1 ATATTATATATTCATAAAAAAA
43461589 ATA-TACT-TATTCATAAAAAAA
1 ATATTA-TATATTCATAAAAAAA
43461610 ATATTATA
1 ATATTATA
43461618 GTGTTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
20 6 0.25
21 16 0.67
22 2 0.08
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATTATATATTCATAAAAAAA
Found at i:43462793 original size:24 final size:24
Alignment explanation
Indices: 43462766--43462824 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
43462756 ATGCTCATGC
43462766 GAGCATATAATAGGTAGCTCCGAA
1 GAGCATATAATAGGTAGCTCCGAA
**
43462790 GAGCACT-TAACGGGTAGCTCCGAA
1 GAGCA-TATAATAGGTAGCTCCGAA
* *
43462814 TAGCACATAAT
1 GAGCATATAAT
43462825 CAAGAAGCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
24 27 0.96
25 1 0.04
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (24 bp):
GAGCATATAATAGGTAGCTCCGAA
Found at i:43466232 original size:124 final size:125
Alignment explanation
Indices: 43466089--43466337 Score: 491
Period size: 124 Copynumber: 2.0 Consensus size: 125
43466079 TTTTTAACAT
43466089 AATTTTTTTATGTTCTTATTTTCAATTTTTACTACGTGTCATTAATTTTTTAAAAATCTTTTTGA
1 AATTTTTTTATGTTCTTATTTTCAATTTTTACTACGTGTCATTAATTTTTTAAAAATCTTTTTGA
43466154 GTATTAAATTAAATTAAATTAAATATTATTTTAATTACATAGCGCATTGTTTATTTATGG
66 GTATTAAATTAAATTAAATTAAATATTATTTTAATTACATAGCGCATTGTTTATTTATGG
43466214 AATTTTTTTA-GTTCTTATTTTCAATTTTTACTACGTGTCATTAATTTTTTAAAAATCTTTTTGA
1 AATTTTTTTATGTTCTTATTTTCAATTTTTACTACGTGTCATTAATTTTTTAAAAATCTTTTTGA
43466278 GTATTAAATTAAATTAAATTAAATATTATTTTAATTACATAGCGCATTGTTTATTTATGG
66 GTATTAAATTAAATTAAATTAAATATTATTTTAATTACATAGCGCATTGTTTATTTATGG
43466338 TAATAAATTA
Statistics
Matches: 124, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
124 114 0.92
125 10 0.08
ACGTcount: A:0.32, C:0.07, G:0.08, T:0.53
Consensus pattern (125 bp):
AATTTTTTTATGTTCTTATTTTCAATTTTTACTACGTGTCATTAATTTTTTAAAAATCTTTTTGA
GTATTAAATTAAATTAAATTAAATATTATTTTAATTACATAGCGCATTGTTTATTTATGG
Found at i:43471363 original size:3 final size:3
Alignment explanation
Indices: 43471355--43471392 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
43471345 TGGGAAGAGT
43471355 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
43471393 GTGACAAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:43472154 original size:86 final size:86
Alignment explanation
Indices: 43472064--43472247 Score: 233
Period size: 86 Copynumber: 2.1 Consensus size: 86
43472054 CATTCCCTAC
* * * * * * * **
43472064 AAACGCCGCTAAAGGTCATGTACTTTAGCGGCGCTTTTTTCGCAAACGCCGCTAAAGATCATGTT
1 AAACGCCACTAAAGATCATGTACTTTAGCGGCGCTTTCTCCACAAACGCCACTAAAGACCATGAC
* **
43472129 CTTTAGCGGCGCTTCTTTTGG
66 CGTTAGCGGCGCTTCTTTTAA
* *
43472150 AAACGCCACTAAAGATCATGTTCTTTGGCGGCGCTTTCTCCACAAACGCCACTAAAGACCATGAC
1 AAACGCCACTAAAGATCATGTACTTTAGCGGCGCTTTCTCCACAAACGCCACTAAAGACCATGAC
*
43472215 CGTTAGCGGCGCTTTTTTTAA
66 CGTTAGCGGCGCTTCTTTTAA
43472236 AAACGCCACTAA
1 AAACGCCACTAA
43472248 TTTTGGCAGA
Statistics
Matches: 83, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
86 83 1.00
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.28
Consensus pattern (86 bp):
AAACGCCACTAAAGATCATGTACTTTAGCGGCGCTTTCTCCACAAACGCCACTAAAGACCATGAC
CGTTAGCGGCGCTTCTTTTAA
Found at i:43472229 original size:43 final size:43
Alignment explanation
Indices: 43472042--43472247 Score: 184
Period size: 43 Copynumber: 4.8 Consensus size: 43
43472032 AAGGTCAGGG
* * * *
43472042 TCTTTAGCGGCGCATTC-CCTACAAACGCCGCTAAAGGTCATG-
1 TCTTTAGCGGCGCTTTCTTC-ACAAACGCCACTAAAGATCATGA
* * * *
43472084 TACTTTAGCGGCGCTTTTTTCGCAAACGCCGCTAAAGATCATGT
1 T-CTTTAGCGGCGCTTTCTTCACAAACGCCACTAAAGATCATGA
*** *
43472128 TCTTTAGCGGCGC-TTCTTTTGGAAACGCCACTAAAGATCATGT
1 TCTTTAGCGGCGCTTTC-TTCACAAACGCCACTAAAGATCATGA
* * *
43472171 TCTTTGGCGGCGCTTTCTCCACAAACGCCACTAAAGACCATGA
1 TCTTTAGCGGCGCTTTCTTCACAAACGCCACTAAAGATCATGA
* * * * *
43472214 CCGTTAGCGGCGCTTTTTTTAAAAACGCCACTAA
1 TCTTTAGCGGCGCTTTCTTCACAAACGCCACTAA
43472248 TTTTGGCAGA
Statistics
Matches: 136, Mismatches: 23, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
42 3 0.02
43 128 0.94
44 5 0.04
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (43 bp):
TCTTTAGCGGCGCTTTCTTCACAAACGCCACTAAAGATCATGA
Found at i:43472594 original size:21 final size:21
Alignment explanation
Indices: 43472568--43472617 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
43472558 TTTTACGCTG
43472568 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
43472589 CTCTGCTTCTCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
*
43472610 ATCTGCTT
1 CTCTGCTT
43472618 TAAGCTGCAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.04, C:0.44, G:0.18, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:43474340 original size:9 final size:9
Alignment explanation
Indices: 43474326--43474495 Score: 74
Period size: 9 Copynumber: 19.7 Consensus size: 9
43474316 ATAATGTAAT
43474326 TAAGTTATG
1 TAAGTTATG
*
43474335 TAAGTTGTG
1 TAAGTTATG
43474344 T-A-TTAT-
1 TAAGTTATG
*
43474350 TAAAGTTAAG
1 T-AAGTTATG
43474360 T-A-TTATG
1 TAAGTTATG
* *
43474367 TAATTTATT
1 TAAGTTATG
43474376 TAAGTTATG
1 TAAGTTATG
**
43474385 TAAGTGGTG
1 TAAGTTATG
43474394 T-A-TTATG
1 TAAGTTATG
*
43474401 TAAGTTAAG
1 TAAGTTATG
43474410 TAAGTTATG
1 TAAGTTATG
* *
43474419 TAGGCTATG
1 TAAGTTATG
43474428 T-A-TTATG
1 TAAGTTATG
* *
43474435 CAAGTTATT
1 TAAGTTATG
* *
43474444 TATGTCAGTGG
1 TAAGTTA-T-G
* *
43474455 TGTA-TTATC
1 T-AAGTTATG
*
43474464 TAAGTT-TT
1 TAAGTTATG
*
43474472 TAAGTTATA
1 TAAGTTATG
43474481 TAAGTTATG
1 TAAGTTATG
43474490 TAAGTT
1 TAAGTT
43474496 TCTATATAAG
Statistics
Matches: 115, Mismatches: 31, Indels: 30
0.65 0.18 0.17
Matches are distributed among these distances:
6 1 0.01
7 16 0.14
8 15 0.13
9 77 0.67
10 3 0.03
11 3 0.03
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:43474355 original size:25 final size:24
Alignment explanation
Indices: 43474324--43474420 Score: 90
Period size: 25 Copynumber: 3.9 Consensus size: 24
43474314 GTATAATGTA
* *
43474324 ATTAAGTTATGTAAGTTGTGTATT
1 ATTAAGTTAAGTAAGTTATGTATT
43474348 ATTAAAGTTAAGT-A-TTATGTAATTT
1 ATT-AAGTTAAGTAAGTTATGT-A-TT
* **
43474373 ATTTAAGTTATGTAAGTGGTGTATT
1 A-TTAAGTTAAGTAAGTTATGTATT
43474398 ATGTAAGTTAAGTAAGTTATGTA
1 AT-TAAGTTAAGTAAGTTATGTA
43474421 GGCTATGTAT
Statistics
Matches: 58, Mismatches: 8, Indels: 13
0.73 0.10 0.16
Matches are distributed among these distances:
23 5 0.09
24 6 0.10
25 39 0.67
26 4 0.07
27 4 0.07
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (24 bp):
ATTAAGTTAAGTAAGTTATGTATT
Found at i:43474400 original size:34 final size:34
Alignment explanation
Indices: 43474359--43474485 Score: 115
Period size: 34 Copynumber: 3.9 Consensus size: 34
43474349 TTAAAGTTAA
*
43474359 GTATTATGTAATTTATTTAAGTTATGTAAGTGGT
1 GTATTATGTAAGTTATTTAAGTTATGTAAGTGGT
** * *
43474393 GTATTATGTAAGTTAAGTAAGTTATGTAGGCT-AT
1 GTATTATGTAAGTTATTTAAGTTATGTAAG-TGGT
* *
43474427 GTATTATGCAAGTTA--T---TTATGTCAGTGGT
1 GTATTATGTAAGTTATTTAAGTTATGTAAGTGGT
* *
43474456 GTATTATCTAAGTT-TTTAAGTTATATAAGT
1 GTATTATGTAAGTTATTTAAGTTATGTAAGT
43474486 TATGTAAGTT
Statistics
Matches: 73, Mismatches: 13, Indels: 15
0.72 0.13 0.15
Matches are distributed among these distances:
28 1 0.01
29 20 0.27
30 1 0.01
32 1 0.01
33 8 0.11
34 41 0.56
35 1 0.01
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.46
Consensus pattern (34 bp):
GTATTATGTAAGTTATTTAAGTTATGTAAGTGGT
Found at i:43474434 original size:50 final size:50
Alignment explanation
Indices: 43474326--43474429 Score: 129
Period size: 50 Copynumber: 2.0 Consensus size: 50
43474316 ATAATGTAAT
* ** *
43474326 TAAGTTATGTAAGTTGTGTATTATTAAAGTTAAGTATTATGTAATTTATT
1 TAAGTTATGTAAGTGGTGTATTATTAAAGTTAAGTATTATGTAAGCTATG
*
43474376 TAAGTTATGTAAGTGGTGTATTATGT-AAGTTAAGTAAGTTATGTAGGCTATG
1 TAAGTTATGTAAGTGGTGTATTAT-TAAAGTTAAGT-A-TTATGTAAGCTATG
43474428 TA
1 TA
43474430 TTATGCAAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
50 32 0.70
51 2 0.04
52 12 0.26
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.45
Consensus pattern (50 bp):
TAAGTTATGTAAGTGGTGTATTATTAAAGTTAAGTATTATGTAAGCTATG
Found at i:43474479 original size:17 final size:18
Alignment explanation
Indices: 43474459--43474499 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
43474449 CAGTGGTGTA
*
43474459 TTATCTAAGTT-TTTAAG
1 TTATCTAAGTTATGTAAG
*
43474476 TTATATAAGTTATGTAAG
1 TTATCTAAGTTATGTAAG
43474494 TT-TCTA
1 TTATCTA
43474500 TATAAGTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (18 bp):
TTATCTAAGTTATGTAAG
Found at i:43474507 original size:12 final size:12
Alignment explanation
Indices: 43474490--43474519 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
43474480 ATAAGTTATG
43474490 TAAGTTTCTATA
1 TAAGTTTCTATA
*
43474502 TAAGTTTCTATG
1 TAAGTTTCTATA
43474514 TAAGTT
1 TAAGTT
43474520 ATGTAGGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (12 bp):
TAAGTTTCTATA
Found at i:43476961 original size:105 final size:107
Alignment explanation
Indices: 43476840--43477063 Score: 344
Period size: 105 Copynumber: 2.1 Consensus size: 107
43476830 GCAAAATATT
* *
43476840 ATTTCATTTTGAACAAAATGACACCGTTTTGCTATGGACAAAATTTTTAATTTTGATCTTT-TAA
1 ATTTCATTTTGAACAAAATGACACCGTTTTGCTATGCACAAAATTTTTAATTTTGATATTTATAA
43476904 ATTGATTTA-TTTTTTGCGGCGTTTGTAGGAAAAACGCCGCA
66 ATTGATTTACTTTTTTGCGGCGTTTGTAGGAAAAACGCCGCA
* * * *
43476945 ATTTCAATTTGAACAAAATGACGCCGTTTTGCTATGCACAAAATTTTTTATTTTGTTATTTATAA
1 ATTTCATTTTGAACAAAATGACACCGTTTTGCTATGCACAAAATTTTTAATTTTGATATTTATAA
* ** *
43477010 ATTGATTTACTTTTTTGCGGCGTTTTTATTAAAAACGCCGCT
66 ATTGATTTACTTTTTTGCGGCGTTTGTAGGAAAAACGCCGCA
43477052 ATTTCATTTTGA
1 ATTTCATTTTGA
43477064 TCGAAAACGG
Statistics
Matches: 106, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
105 55 0.52
106 12 0.11
107 39 0.37
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.44
Consensus pattern (107 bp):
ATTTCATTTTGAACAAAATGACACCGTTTTGCTATGCACAAAATTTTTAATTTTGATATTTATAA
ATTGATTTACTTTTTTGCGGCGTTTGTAGGAAAAACGCCGCA
Found at i:43477018 original size:358 final size:356
Alignment explanation
Indices: 43476461--43477229 Score: 1184
Period size: 358 Copynumber: 2.2 Consensus size: 356
43476451 GCGTTTTTGT
*
43476461 CAAAAACGCCGCAAAATATTATTTCATTTTGAACAAAATGACGTCGTTTTGCTATGCACAAAATT
1 CAAAAACGCCGCAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCACAAAATT
* * * * *
43476526 TTTTATTTTGTTTTTTTAAAATTGATTTATTTTTTACGGCGTTTTTAGGGAAAACGCCGCAACAT
66 TTTAATTTTGATCTTTTAAAATTGATTTATTTTTTACGGCGTTTGTAGGAAAAACGCCGCAACAT
* * *
43476591 CAATTTGAACAAAATGCCATCGTTTTGCTATGCACAAAATTTTTTATTTTGTTTTTTATAAATTG
131 CAATTTGAACAAAATGACACCGTTTTGCTATGCACAAAATTTTTTATTTTGTTATTTATAAATTG
*
43476656 ATTTAC-TTTTTGCGACGTTTTTTGTTAAAAACGCCGCTATTTCATTTTGATCAAAAACAGCGCC
196 ATTTACTTTTTTGCGACG-TTTTTATTAAAAACGCCGCTATTTCATTTTGATCAAAAACAGCGCC
* * * **
43476720 GTTTTTCTATGTAAATTTTTTTTTATAATTTATTTATTCCTTTTGCGGCGTTTTTTTATATAAAA
260 ATTTTGCTACGTAAATAATTTTTTATAATTTATTTATTCCTTTTGCGGCG--TTTTTATATAAAA
43476785 GCGCCGCTATTGCCTATCTTTTACGGCATTTTTGC-
323 -CGCCGCTATTGCCTATCTTTTACGGCATTTTT-CA
* * * *
43476820 GATAAACGCCGCAAAATATTATTTCATTTTGAACAAAATGACACCGTTTTGCTATGGACAAAATT
1 CAAAAACGCCGCAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCACAAAATT
* **
43476885 TTTAATTTTGATCTTTT-AAATTGATTTATTTTTTGCGGCGTTTGTAGGAAAAACGCCGCAATTT
66 TTTAATTTTGATCTTTTAAAATTGATTTATTTTTTACGGCGTTTGTAGGAAAAACGCCGCAACAT
*
43476949 CAATTTGAACAAAATGACGCCGTTTTGCTATGCACAAAATTTTTTATTTTGTTATTTATAAATTG
131 CAATTTGAACAAAATGACACCGTTTTGCTATGCACAAAATTTTTTATTTTGTTATTTATAAATTG
* * *
43477014 ATTTACTTTTTTGCGGCGTTTTTATTAAAAACGCCGCTATTTCATTTTGATCGAAAACGGCGCCA
196 ATTTACTTTTTTGCGACGTTTTTATTAAAAACGCCGCTATTTCATTTTGATCAAAAACAGCGCCA
* *
43477079 TTTTGCTACGTAAATAATTTTTTATAATTTATTTATTTCTTTTGCGGCGTTTTTATATCAAACGC
261 TTTTGCTACGTAAATAATTTTTTATAATTTATTTATTCCTTTTGCGGCGTTTTTATATAAAACGC
* *
43477144 CGCTATTGCCTATCTTTTGCGGCGTTTTTCA
326 CGCTATTGCCTATCTTTTACGGCATTTTTCA
* *
43477175 CAAAAACGCCGCACAATATTATTTCATTTTGAACAAAATGACGCTGTTTTGCTAT
1 CAAAAACGCCGCAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTAT
43477230 TTTGTTTTCT
Statistics
Matches: 373, Mismatches: 35, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
354 1 0.00
355 80 0.21
356 12 0.03
358 196 0.53
359 84 0.23
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.43
Consensus pattern (356 bp):
CAAAAACGCCGCAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCACAAAATT
TTTAATTTTGATCTTTTAAAATTGATTTATTTTTTACGGCGTTTGTAGGAAAAACGCCGCAACAT
CAATTTGAACAAAATGACACCGTTTTGCTATGCACAAAATTTTTTATTTTGTTATTTATAAATTG
ATTTACTTTTTTGCGACGTTTTTATTAAAAACGCCGCTATTTCATTTTGATCAAAAACAGCGCCA
TTTTGCTACGTAAATAATTTTTTATAATTTATTTATTCCTTTTGCGGCGTTTTTATATAAAACGC
CGCTATTGCCTATCTTTTACGGCATTTTTCA
Found at i:43477100 original size:107 final size:105
Alignment explanation
Indices: 43476840--43477088 Score: 300
Period size: 105 Copynumber: 2.3 Consensus size: 105
43476830 GCAAAATATT
* * * * * * *
43476840 ATTTCATTTTGAACAAAATGACACCGTTTTGCTATGGACAAAATTTTTAATTTTGATCTTTTAAA
1 ATTTCAATTTGAACAAAACGACGCCATTTTGCTACGCACAAAATTTTTAATTTTGATATTTTAAA
43476905 TTGATTTATTTTTTGCGGCGTTTGTAGGAAAAACGCCGCA
66 TTGATTTATTTTTTGCGGCGTTTGTAGGAAAAACGCCGCA
* * * * *
43476945 ATTTCAATTTGAACAAAATGACGCCGTTTTGCTATGCACAAAATTTTTTATTTTGTTATTTATAA
1 ATTTCAATTTGAACAAAACGACGCCATTTTGCTACGCACAAAATTTTTAATTTTGATATTT-TAA
* ** *
43477010 ATTGATTTACTTTTTTGCGGCGTTTTTATTAAAAACGCCGCT
65 ATTGATTTA-TTTTTTGCGGCGTTTGTAGGAAAAACGCCGCA
* * *
43477052 ATTTCATTTTGATCGAAAACGGCGCCATTTTGCTACG
1 ATTTCAATTTGAAC-AAAACGACGCCATTTTGCTACG
43477089 TAAATAATTT
Statistics
Matches: 125, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
105 55 0.44
106 12 0.10
107 40 0.32
108 18 0.14
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (105 bp):
ATTTCAATTTGAACAAAACGACGCCATTTTGCTACGCACAAAATTTTTAATTTTGATATTTTAAA
TTGATTTATTTTTTGCGGCGTTTGTAGGAAAAACGCCGCA
Found at i:43477268 original size:136 final size:138
Alignment explanation
Indices: 43477096--43477351 Score: 358
Period size: 136 Copynumber: 1.9 Consensus size: 138
43477086 ACGTAAATAA
* * *
43477096 TTTTTTATAATTTATTTATTTCTTTTGCGGCGTTTTTATATCAAACGCCGCTA-TTGCCTATCTT
1 TTTTCTATAATTGATTTATTTCTTTTGCGGCGTTTTTATAGCAAACGCCGCTATTTG-CTATCTT
* * *
43477160 TTGCGGCGTTTTTCACAAAAACGCCGCACAATATTATTTCATTTTGAACAAAATGACGCTGTTTT
65 TTGCGGCGTTTTGCACAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGACGCTGTTTT
43477225 GCTATTTTG
130 GCTATTTTG
* * *
43477234 TTTTCTATAAATTGATTTA-TT-TTTTGCGGC-TTTTTATAGGAAATGCCGCTATTTGTTATCTT
1 TTTTCTAT-AATTGATTTATTTCTTTTGCGGCGTTTTTATAGCAAACGCCGCTATTTGCTATCTT
** *
43477296 TTGCGGCGTTTTGCGTATAAACGCCACAAAATATTATTTCATTTTGAACAAAATGA
65 TTGCGGCGTTTTGCACAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGA
43477352 TGTCGTTTTG
Statistics
Matches: 104, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
136 74 0.71
137 12 0.12
138 9 0.09
139 9 0.09
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (138 bp):
TTTTCTATAATTGATTTATTTCTTTTGCGGCGTTTTTATAGCAAACGCCGCTATTTGCTATCTTT
TGCGGCGTTTTGCACAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGACGCTGTTTTG
CTATTTTG
Found at i:43477493 original size:7 final size:7
Alignment explanation
Indices: 43477448--43477513 Score: 51
Period size: 7 Copynumber: 9.1 Consensus size: 7
43477438 CCTTAACTCG
43477448 ACCCCTGA
1 ACCCCT-A
43477456 ACCCCTA
1 ACCCCTA
* *
43477463 AACCTTAA
1 ACCCCT-A
*
43477471 ATCCCTA
1 ACCCCTA
* *
43477478 ACTCTTA
1 ACCCCTA
43477485 ACCCCTA
1 ACCCCTA
**
43477492 ACATCTA
1 ACCCCTA
43477499 ACCCCTA
1 ACCCCTA
43477506 ACCCCTA
1 ACCCCTA
43477513 A
1 A
43477514 ACCTTAAATC
Statistics
Matches: 44, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
7 33 0.75
8 11 0.25
ACGTcount: A:0.33, C:0.44, G:0.02, T:0.21
Consensus pattern (7 bp):
ACCCCTA
Found at i:43477574 original size:15 final size:15
Alignment explanation
Indices: 43477532--43477580 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
43477522 TCCCAAGCCT
*
43477532 TAAA-CCATAGTCCC
1 TAAACCCATAATCCC
*
43477546 T-AATCCATAATCCC
1 TAAACCCATAATCCC
*
43477560 TAAACCCATACTCCC
1 TAAACCCATAATCCC
43477575 TAAACC
1 TAAACC
43477581 TTAAAATATG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
13 2 0.07
14 11 0.37
15 17 0.57
ACGTcount: A:0.37, C:0.39, G:0.02, T:0.22
Consensus pattern (15 bp):
TAAACCCATAATCCC
Found at i:43477811 original size:15 final size:15
Alignment explanation
Indices: 43477791--43477824 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
43477781 CCCCAAATGT
43477791 CTAACCC-CTAAACCC
1 CTAACCCTCT-AACCC
43477806 CTAACCCTCTAACCC
1 CTAACCCTCTAACCC
43477821 CTAA
1 CTAA
43477825 ACCTTAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 16 0.89
16 2 0.11
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (15 bp):
CTAACCCTCTAACCC
Found at i:43477827 original size:8 final size:7
Alignment explanation
Indices: 43477791--43477824 Score: 50
Period size: 8 Copynumber: 4.6 Consensus size: 7
43477781 CCCCAAATGT
43477791 CTAACCC
1 CTAACCC
43477798 CTAAACCC
1 CT-AACCC
43477806 CTAACCC
1 CTAACCC
43477813 TCTAACCC
1 -CTAACCC
43477821 CTAA
1 CTAA
43477825 ACCTTAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 11 0.44
8 14 0.56
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (7 bp):
CTAACCC
Found at i:43477864 original size:14 final size:14
Alignment explanation
Indices: 43477847--43477873 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43477837 AACCCTTAAA
43477847 CCATAATCCCTAAT
1 CCATAATCCCTAAT
43477861 CCATAATCCCTAA
1 CCATAATCCCTAA
43477874 ACCCATACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.26
Consensus pattern (14 bp):
CCATAATCCCTAAT
Found at i:43478268 original size:115 final size:113
Alignment explanation
Indices: 43477969--43478414 Score: 486
Period size: 114 Copynumber: 3.9 Consensus size: 113
43477959 ATGTTTTTTT
* * * * *
43477969 GCGGCGCTTTCCTAAAAACCGCCGCTAAATCCCCCGAAAGCTCAGAAAACAGCGTCGTTGAGCTT
1 GCGGCGCTTTCCTAAAAA--GTCACTAAAT-CCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTT
* *
43478034 ATGTCT-TTTTGCGGCGCTTTC-TCACAAACGCCGCTAAAGCCCTGAGCATTA
63 A-GTTTATTTTGCGGCGC-TTCATCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * * *
43478085 GCGGCG-TATCCCAAAAAGTGACACTAAATCCACAAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
1 GCGGCGCTTTCCTAAAAAGT--CACTAAATCCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
* * * * *
43478149 GTTTATTTTACGGCACTTCCTTAAAAACGCCGCTAAAGCCCTCAGCATTA
64 GTTTATTTTGCGGCGCTTCATCAAAAACGCCGCTAAAGCCCTGAGCATTA
** * * * * *
43478199 GCGGCGCTTTATTAAGAAACGTCACTAAATCCGTGAAAGATAAAAAAAGGGCGTCGTTGGGCTTA
1 GCGGCGCTTTCCTAA-AAA-GTCACTAAATCCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
* * * *
43478264 GTTTATTTTGCGGCGCTTTATCAAAAATGCCGCAAAAGCCCTGGGCATTA
64 GTTTATTTTGCGGCGCTTCATCAAAAACGCCGCTAAAGCCCTGAGCATTA
* *
43478314 GCGGCGC-TTCCTAAAAAATGCCACTAAATCCGCGAAAGCTCAGAAAACAGCGTCGTTGGGCTTA
1 GCGGCGCTTTCCT-AAAAA-GTCACTAAATCCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
* *
43478378 GATTATTTTGCGGCGCTTCATCAAAAGCGCCGCTAAA
64 GTTTATTTTGCGGCGCTTCATCAAAAACGCCGCTAAA
43478415 TCCCCGAAAG
Statistics
Matches: 273, Mismatches: 49, Indels: 18
0.80 0.14 0.05
Matches are distributed among these distances:
113 7 0.03
114 149 0.55
115 106 0.39
116 9 0.03
117 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.24
Consensus pattern (113 bp):
GCGGCGCTTTCCTAAAAAGTCACTAAATCCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGT
TTATTTTGCGGCGCTTCATCAAAAACGCCGCTAAAGCCCTGAGCATTA
Found at i:43478449 original size:73 final size:73
Alignment explanation
Indices: 43478314--43478487 Score: 194
Period size: 73 Copynumber: 2.4 Consensus size: 73
43478304 CTGGGCATTA
* * * * *
43478314 GCGGCGCTTCCTAAAAAATGCCACTAAATCCGCGAAAGCTCAGAAAACAGCGTCGTTGGGCTTAG
1 GCGGCGCTTCATAAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACAGCGCCGTTAGGCTTAG
43478379 ATTATTTT
66 ATTATTTT
* * *
43478387 GCGGCGCTTCATCAAAAGCGCCGCTAAATCCCCGAAAGCTCAGAAAAC-GACGCCGTTAGGCTTA
1 GCGGCGCTTCATAAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACAG-CGCCGTTAGGCTTA
43478451 TG-TCT-TTTT
65 -GAT-TATTTT
* *
43478460 ACGGCGCTTTC-TAAAAAACGCCGCTAAA
1 GCGGCGC-TTCATAAAAAACGCCACTAAA
43478488 AGCCCTGACC
Statistics
Matches: 86, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
72 1 0.01
73 80 0.93
74 5 0.06
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.23
Consensus pattern (73 bp):
GCGGCGCTTCATAAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACAGCGCCGTTAGGCTTAG
ATTATTTT
Found at i:43478591 original size:115 final size:115
Alignment explanation
Indices: 43478387--43478597 Score: 282
Period size: 115 Copynumber: 1.8 Consensus size: 115
43478377 AGATTATTTT
* * * * *
43478387 GCGGCGCTTCATCAAAAGCGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGCCGTTAGGCTTAT
1 GCGGCGCTTCATAAAAAACGCCACTAAATCCACGAAAGCTCAGAAAACGACGCCGTTAGGCTTAG
*
43478452 GTCTTTTTACGGCGCTTTCTAAAAAACGCCGCTAAAAGCCCTGACCATTA
66 GTCTTATTACGGCGCTTTCTAAAAAACGCCGCTAAAAGCCCTGACCATTA
* * * * *
43478502 GCGGCGCTT-ACTAAAAAACGCCACTAAATCTACGAAAGCTCAGAATACGGCGTCGTTGGGCTTA
1 GCGGCGCTTCA-TAAAAAACGCCACTAAATCCACGAAAGCTCAGAAAACGACGCCGTTAGGCTTA
* *
43478566 GGT-TTATTGCGGCGCTTTTTAAAAAACGCCGC
65 GGTCTTATTACGGCGCTTTCTAAAAAACGCCGC
43478598 CAATGCTTAT
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
114 27 0.33
115 55 0.67
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (115 bp):
GCGGCGCTTCATAAAAAACGCCACTAAATCCACGAAAGCTCAGAAAACGACGCCGTTAGGCTTAG
GTCTTATTACGGCGCTTTCTAAAAAACGCCGCTAAAAGCCCTGACCATTA
Found at i:43479255 original size:36 final size:35
Alignment explanation
Indices: 43479215--43479307 Score: 98
Period size: 36 Copynumber: 2.5 Consensus size: 35
43479205 TATTTGTGTG
* *
43479215 GAATTGAAATGAATAT-TGACTTGAAAATGGAAAAGT
1 GAATTGAATTGAAT-TGTGA-TTGAAAATGAAAAAGT
*
43479251 GAATTTTGAATTGAATTGTGATTGAAAGTGAAAAAGT
1 GAA--TTGAATTGAATTGTGATTGAAAATGAAAAAGT
*
43479288 GAAATTGAATTGAAATGTGA
1 G-AATTGAATTGAATTGTGA
43479308 AATTGGAGAC
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
36 18 0.37
37 16 0.33
38 15 0.31
ACGTcount: A:0.44, C:0.01, G:0.24, T:0.31
Consensus pattern (35 bp):
GAATTGAATTGAATTGTGATTGAAAATGAAAAAGT
Found at i:43482595 original size:17 final size:18
Alignment explanation
Indices: 43482569--43482605 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
43482559 TTCTAAAATT
43482569 AAATTGAGAAAAAT-ATA
1 AAATTGAGAAAAATAATA
*
43482586 AAATTTAGAAAAATAATA
1 AAATTGAGAAAAATAATA
43482604 AA
1 AA
43482606 TTATTTTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (18 bp):
AAATTGAGAAAAATAATA
Found at i:43482606 original size:17 final size:16
Alignment explanation
Indices: 43482563--43482607 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
43482553 GCTAATTTCT
43482563 AAAAT-TAAATTGAGA
1 AAAATATAAATTGAGA
*
43482578 AAAATATAAAATTTAGA
1 AAAATAT-AAATTGAGA
43482595 AAAATAATAAATT
1 AAAAT-ATAAATT
43482608 ATTTTTGCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 5 0.19
16 1 0.04
17 18 0.69
18 2 0.08
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (16 bp):
AAAATATAAATTGAGA
Found at i:43491365 original size:7 final size:7
Alignment explanation
Indices: 43491353--43491377 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
43491343 AAATCGATTT
43491353 TGGATCC
1 TGGATCC
43491360 TGGATCC
1 TGGATCC
43491367 TGGATCC
1 TGGATCC
43491374 TGGA
1 TGGA
43491378 CCCATGTTAA
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:0.16, C:0.24, G:0.32, T:0.28
Consensus pattern (7 bp):
TGGATCC
Found at i:43495972 original size:14 final size:13
Alignment explanation
Indices: 43495934--43495973 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
43495924 GTCACTGACG
43495934 AAGGATGGGCCCC
1 AAGGATGGGCCCC
43495947 AAGGATGGGCCCC
1 AAGGATGGGCCCC
*
43495960 AAGGATGGGGCCC
1 AAGGATGGGCCCC
43495973 A
1 A
43495974 TCTTCATTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.25, C:0.28, G:0.40, T:0.07
Consensus pattern (13 bp):
AAGGATGGGCCCC
Found at i:43496857 original size:31 final size:31
Alignment explanation
Indices: 43496819--43496891 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
43496809 TGATTGGGCC
*
43496819 AAGACTAAAATTT-CAAATTTTAAAAAGTACA
1 AAGACTAAAATTTACAAA-TTCAAAAAGTACA
* *
43496850 AGGACTAAAATTTACCAATTCAAAAAGTACA
1 AAGACTAAAATTTACAAATTCAAAAAGTACA
*
43496881 AAAACTAAAAT
1 AAGACTAAAAT
43496892 CGATCAAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
31 33 0.92
32 3 0.08
ACGTcount: A:0.56, C:0.12, G:0.07, T:0.25
Consensus pattern (31 bp):
AAGACTAAAATTTACAAATTCAAAAAGTACA
Found at i:43498940 original size:20 final size:22
Alignment explanation
Indices: 43498912--43498961 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
43498902 AATTTAATAA
* *
43498912 ATTAAAAAAATAT-TTAAAATT
1 ATTATAAAAATATATAAAAATT
*
43498933 -TTATAAAAATGTATAAAAATT
1 ATTATAAAAATATATAAAAATT
43498954 ATTATAAA
1 ATTATAAA
43498962 CTTATACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 10 0.42
21 7 0.29
22 7 0.29
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
ATTATAAAAATATATAAAAATT
Found at i:43499670 original size:9 final size:9
Alignment explanation
Indices: 43499579--43499773 Score: 67
Period size: 10 Copynumber: 20.7 Consensus size: 9
43499569 TTTTATGATT
43499579 TTTTTAATAA
1 TTTTT-ATAA
43499589 TTTTTATAA
1 TTTTTATAA
* *
43499598 GTTTATACCAA
1 -TTTTTA-TAA
* *
43499609 ATTTAATAA
1 TTTTTATAA
**
43499618 AATTTATAA
1 TTTTTATAA
*
43499627 TTTTCAATAA
1 TTTT-TATAA
*
43499637 TTTGTTATGA
1 TTT-TTATAA
* *
43499647 TCTTTCAAGAA
1 T-TTT-TATAA
43499658 TTTTTATAA
1 TTTTTATAA
43499667 TTTTTTATAGAA
1 -TTTTTAT--AA
* *
43499679 TTTTAAATAT
1 TTTT-TATAA
43499689 TTTTTATTAA
1 TTTTTA-TAA
43499699 -TTTTATAAA
1 TTTTTAT-AA
43499708 TTTTTATAA
1 TTTTTATAA
*
43499717 --ATTATAA
1 TTTTTATAA
*
43499724 ATTTTAT-A
1 TTTTTATAA
43499732 TTTTTAT-A
1 TTTTTATAA
*
43499740 TGTTTATAA
1 TTTTTATAA
*
43499749 TATTTATAA
1 TTTTTATAA
* *
43499758 GTTTTCATTA
1 -TTTTTATAA
43499768 TTTTTA
1 TTTTTA
43499774 GGCTTAAAGG
Statistics
Matches: 137, Mismatches: 31, Indels: 35
0.67 0.15 0.17
Matches are distributed among these distances:
7 6 0.04
8 15 0.11
9 46 0.34
10 54 0.39
11 12 0.09
12 4 0.03
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (9 bp):
TTTTTATAA
Found at i:43499678 original size:21 final size:20
Alignment explanation
Indices: 43499654--43499728 Score: 75
Period size: 19 Copynumber: 3.8 Consensus size: 20
43499644 TGATCTTTCA
43499654 AGAATTTTTATAATTTTTTAT
1 AGAA-TTTTATAATTTTTTAT
*
43499675 AGAATTTTAAATATTTTTTAT
1 AGAATTTTATA-ATTTTTTAT
* *
43499696 -TAATTTTATAAATTTTTAT
1 AGAATTTTATAATTTTTTAT
*
43499715 A-AATTATA-AATTTT
1 AGAATTTTATAATTTT
43499729 ATATTTTTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
18 5 0.11
19 14 0.30
20 14 0.30
21 13 0.28
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
AGAATTTTATAATTTTTTAT
Found at i:43499738 original size:17 final size:17
Alignment explanation
Indices: 43499698--43499762 Score: 53
Period size: 16 Copynumber: 3.8 Consensus size: 17
43499688 TTTTTTATTA
43499698 ATTTTATAAATTTTTAT
1 ATTTTATAAATTTTTAT
**
43499715 AAATTATAAA-TTTTAT
1 ATTTTATAAATTTTTAT
* *
43499731 ATTTT-TATATGTTTAT
1 ATTTTATAAATTTTTAT
*
43499747 AATATTTATAAGTTTT
1 -AT-TTTATAAATTTT
43499763 CATTATTTTT
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
15 3 0.09
16 14 0.40
17 10 0.29
18 3 0.09
19 5 0.14
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
ATTTTATAAATTTTTAT
Found at i:43499962 original size:91 final size:88
Alignment explanation
Indices: 43499796--43499980 Score: 253
Period size: 91 Copynumber: 2.1 Consensus size: 88
43499786 CAAAAGAAAT
* * * *
43499796 TCAAACTTTTTCAAAAAAGTAATTAAACCATTGTTTTTTTTTTCACTCATTTGGATACTTGAACT
1 TCAAACCTTTTCAAAAAAGTAATTAAACCATTCTTTTTTTTTGCACTCAATTGGATACTTGAACT
* *
43499861 TTTAAAATGCATCAAAAAGGCCC
66 TTCAAAATGCATCAAAAAGACCC
* * * *
43499884 TCAAACCTTTTCAAAAAAAGTAATTAAGCCTTTACCTTTTTTTTTGCATTCAATTGGGTACTTGA
1 TCAAACCTTTTC-AAAAAAGTAATTAAACCATT--CTTTTTTTTTGCACTCAATTGGATACTTGA
43499949 ACTTTCAAAATGCATCAAAAAGACCC
63 ACTTTCAAAATGCATCAAAAAGACCC
43499975 TCAAAC
1 TCAAAC
43499981 TATATCATTA
Statistics
Matches: 84, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
88 11 0.13
89 18 0.21
91 55 0.65
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (88 bp):
TCAAACCTTTTCAAAAAAGTAATTAAACCATTCTTTTTTTTTGCACTCAATTGGATACTTGAACT
TTCAAAATGCATCAAAAAGACCC
Found at i:43500674 original size:9 final size:9
Alignment explanation
Indices: 43500583--43500776 Score: 74
Period size: 10 Copynumber: 20.7 Consensus size: 9
43500573 TTTTATGATT
43500583 TTTTTAATAA
1 TTTTT-ATAA
43500593 TTTTTATAA
1 TTTTTATAA
* *
43500602 GTTTATACCAA
1 -TTTTTA-TAA
* *
43500613 ATTTAATAA
1 TTTTTATAA
**
43500622 AATTTATAA
1 TTTTTATAA
*
43500631 TTTTCAATAA
1 TTTT-TATAA
*
43500641 TTTGTTATGA
1 TTT-TTATAA
* *
43500651 TCTTTCAAGAA
1 T-TTT-TATAA
43500662 TTTTTATAA
1 TTTTTATAA
43500671 TTTTTTATAGAA
1 -TTTTTAT--AA
* *
43500683 TTTTAAATAT
1 TTTT-TATAA
43500693 TTTTTATTAA
1 TTTTTA-TAA
43500703 TTTTTA-AA
1 TTTTTATAA
43500711 TTTTTATAA
1 TTTTTATAA
*
43500720 --ATTATAA
1 TTTTTATAA
*
43500727 ATTTTAT-A
1 TTTTTATAA
43500735 TTTTTAT-A
1 TTTTTATAA
*
43500743 TGTTTATAA
1 TTTTTATAA
*
43500752 TATTTATAA
1 TTTTTATAA
* *
43500761 GTTTTCATTA
1 -TTTTTATAA
43500771 TTTTTA
1 TTTTTA
43500777 GGCTTAAAGG
Statistics
Matches: 137, Mismatches: 31, Indels: 33
0.68 0.15 0.16
Matches are distributed among these distances:
7 6 0.04
8 22 0.16
9 39 0.28
10 54 0.39
11 12 0.09
12 4 0.03
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (9 bp):
TTTTTATAA
Found at i:43500682 original size:21 final size:20
Alignment explanation
Indices: 43500658--43500731 Score: 75
Period size: 21 Copynumber: 3.8 Consensus size: 20
43500648 TGATCTTTCA
43500658 AGAATTTTTATAATTTTTTAT
1 AGAATTTTTA-AATTTTTTAT
*
43500679 AGAATTTTAAATATTTTTTAT
1 AGAATTTTTAA-ATTTTTTAT
*
43500700 -TAATTTTTAAA-TTTTTAT
1 AGAATTTTTAAATTTTTTAT
*
43500718 A-AA-TTATAAATTTT
1 AGAATTTTTAAATTTT
43500732 ATATTTTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
17 6 0.13
18 12 0.26
19 1 0.02
20 9 0.20
21 18 0.39
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
AGAATTTTTAAATTTTTTAT
Found at i:43500749 original size:25 final size:24
Alignment explanation
Indices: 43500695--43500765 Score: 61
Period size: 24 Copynumber: 2.8 Consensus size: 24
43500685 TTAAATATTT
*
43500695 TTTATTAATTTTTAAATTTTTATAA
1 TTTA-TAAATTTTAAATTTTTATAA
* * *
43500720 ATTATAAATTTTATATTTTTATATG
1 TTTATAAATTTTAAATTTTTATA-A
*
43500745 TTTATAATATTTATAAGTTTT
1 TTTATAA-ATTT-TAAATTTT
43500766 CATTATTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
24 17 0.47
25 9 0.25
26 4 0.11
27 6 0.17
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (24 bp):
TTTATAAATTTTAAATTTTTATAA
Found at i:43500965 original size:91 final size:88
Alignment explanation
Indices: 43500799--43501004 Score: 277
Period size: 91 Copynumber: 2.3 Consensus size: 88
43500789 CAAAAGAAAT
* * *
43500799 TCAAACTTTTTCAAAAAAGTAATTAAACCATTGTTTTTTTTTTCACTCATTTGGATACTTGAACT
1 TCAAACTTTTTCAAAAAAGTAATTAAACCATTCTTTTTTTTTGCACTCAATTGGATACTTGAACT
* *
43500864 TTTAAAATGCATCAAAAAGGCCC
66 TTCAAAATGCATCAAAAAGACCC
* * * * *
43500887 TCAAACCTTTTCAAAAAAAGTAATTAAGCCTTTACCTTTTTTTTTGCATTCAATTGGGTACTTGA
1 TCAAACTTTTTC-AAAAAAGTAATTAAACCATT--CTTTTTTTTTGCACTCAATTGGATACTTGA
43500952 ACTTTCAAAATGCATCAAAAAGACCC
63 ACTTTCAAAATGCATCAAAAAGACCC
*
43500978 TCAAACTTTTTCGAAAAAAGCAATTAA
1 TCAAACTTTTTC-AAAAAAGTAATTAA
43501005 CCCCCTACAT
Statistics
Matches: 102, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
88 11 0.11
89 18 0.18
91 73 0.72
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (88 bp):
TCAAACTTTTTCAAAAAAGTAATTAAACCATTCTTTTTTTTTGCACTCAATTGGATACTTGAACT
TTCAAAATGCATCAAAAAGACCC
Found at i:43501070 original size:19 final size:18
Alignment explanation
Indices: 43501019--43501099 Score: 72
Period size: 19 Copynumber: 4.3 Consensus size: 18
43501009 CTACATTTAT
43501019 TAAAAATTAGAAAAAAATA
1 TAAAAATT-GAAAAAAATA
* *
43501038 TAATAATCGAAAAAAATA
1 TAAAAATTGAAAAAAATA
***
43501056 TGAAAAATTGTAAAATTTTA
1 T-AAAAATTG-AAAAAAATA
*
43501076 TAAAAATAGAAAAAAATTA
1 TAAAAATTGAAAAAAA-TA
43501095 TAAAA
1 TAAAA
43501100 TATATAGAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
18 15 0.31
19 26 0.54
20 7 0.15
ACGTcount: A:0.67, C:0.01, G:0.06, T:0.26
Consensus pattern (18 bp):
TAAAAATTGAAAAAAATA
Found at i:43501105 original size:28 final size:28
Alignment explanation
Indices: 43501019--43501116 Score: 76
Period size: 28 Copynumber: 3.5 Consensus size: 28
43501009 CTACATTTAT
**
43501019 TAAAAATTAGAAAAAAA-TATAATAATCGA
1 TAAAAA-TAGAAAAAAATTATAA-AATATA
* * *
43501048 AAAAAATATG--AAAAATTGTAAAATTTTA
1 TAAAAATA-GAAAAAAATTATAAAA-TATA
43501076 TAAAAATAGAAAAAAATTATAAAATATA
1 TAAAAATAGAAAAAAATTATAAAATATA
* *
43501104 TAGAAATATAAAA
1 TAAAAATAGAAAA
43501117 TTTTATAAAG
Statistics
Matches: 55, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
27 8 0.15
28 29 0.53
29 18 0.33
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.27
Consensus pattern (28 bp):
TAAAAATAGAAAAAAATTATAAAATATA
Found at i:43510022 original size:25 final size:27
Alignment explanation
Indices: 43509972--43510028 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
43509962 TATTATAGGC
*
43509972 TTTTTATACATTTTTAATTGTCTATAT
1 TTTTTATAAATTTTTAATTGTCTATAT
* *
43509999 TTTTTATAAATTTATT-ATTTTATATAT
1 TTTTTATAAATTT-TTAATTGTCTATAT
43510026 TTT
1 TTT
43510029 AAAATAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.67
Consensus pattern (27 bp):
TTTTTATAAATTTTTAATTGTCTATAT
Done.