Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, whole genome shotgun sequence
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: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 26 of 147
Found at i:5476310 original size:23 final size:22
Alignment explanation
Indices: 5476251--5476352 Score: 88
Period size: 23 Copynumber: 4.8 Consensus size: 22
5476241 AATTATGCAA
5476251 ATAAACATGCAATT--AAATAT
1 ATAAACATGCAATTAAAAATAT
* *
5476271 ATAATCATGCAAATAAAAATAT
1 ATAAACATGCAATTAAAAATAT
5476293 ATAAACCATGCAATT--AAATAT
1 ATAAA-CATGCAATTAAAAATAT
* * * *
5476314 AT-AATATGCAACTAATAATAC
1 ATAAACATGCAATTAAAAATAT
*
5476335 ATAAATCATGCAAATAAA
1 ATAAA-CATGCAATTAAA
5476353 CATGCAATTA
Statistics
Matches: 64, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
19 7 0.11
20 14 0.22
21 14 0.22
22 12 0.19
23 17 0.27
ACGTcount: A:0.56, C:0.12, G:0.05, T:0.27
Consensus pattern (22 bp):
ATAAACATGCAATTAAAAATAT
Found at i:5476323 original size:42 final size:42
Alignment explanation
Indices: 5476251--5476352 Score: 143
Period size: 42 Copynumber: 2.4 Consensus size: 42
5476241 AATTATGCAA
*
5476251 ATAAACATGCAATTAAATATATAATCATGCAAATAAAAATAT
1 ATAAACATGCAATTAAATATATAATCATGCAAATAAAAATAC
* *
5476293 ATAAACCATGCAATTAAATATATAAT-ATGCAACTAATAATAC
1 ATAAA-CATGCAATTAAATATATAATCATGCAAATAAAAATAC
*
5476335 ATAAATCATGCAAATAAA
1 ATAAA-CATGCAATTAAA
5476353 CATGCAATTA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
42 34 0.63
43 20 0.37
ACGTcount: A:0.56, C:0.12, G:0.05, T:0.27
Consensus pattern (42 bp):
ATAAACATGCAATTAAATATATAATCATGCAAATAAAAATAC
Found at i:5476352 original size:55 final size:54
Alignment explanation
Indices: 5476293--5476432 Score: 178
Period size: 55 Copynumber: 2.6 Consensus size: 54
5476283 ATAAAAATAT
* *
5476293 ATAAACCATGCAATTAAATATATAAT-ATGCAACTAATAATACATAAATCATGCAA
1 ATAAA-CATGCAATTAAATATATAATCATGCAA-TAATAATAAATAAATCATACAA
* **
5476348 ATAAACATGCAATTAAATATATAGTCAAACGAATAATAATAAATAAATCATACAA
1 ATAAACATGCAATTAAATATATAATCATGC-AATAATAATAAATAAATCATACAA
*
5476403 A-AAA-ATGCAATTAAATATACAATCATGCAA
1 ATAAACATGCAATTAAATATATAATCATGCAA
5476433 ATAAATATAT
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
52 2 0.03
53 20 0.27
54 22 0.30
55 28 0.38
56 2 0.03
ACGTcount: A:0.56, C:0.13, G:0.06, T:0.26
Consensus pattern (54 bp):
ATAAACATGCAATTAAATATATAATCATGCAATAATAATAAATAAATCATACAA
Found at i:5476450 original size:24 final size:24
Alignment explanation
Indices: 5476423--5476561 Score: 137
Period size: 24 Copynumber: 5.9 Consensus size: 24
5476413 TTAAATATAC
5476423 AATCATGCAAATAAATATATTAAT
1 AATCATGCAAATAAATATATTAAT
* *
5476447 AATCAAGCAATTAAATATATTAAT
1 AATCATGCAAATAAATATATTAAT
* *
5476471 AATCATGC-TATCAAAT-TA-GATAT
1 AATCATGCAAAT-AAATATATTA-AT
*
5476494 AATCATACAAATAAATATATTAAT
1 AATCATGCAAATAAATATATTAAT
**
5476518 AAATCACACAAATAAATATA-T--T
1 -AATCATGCAAATAAATATATTAAT
*
5476540 AATCATGCAAACAAATATATTA
1 AATCATGCAAATAAATATATTA
5476562 GGCAAATAAA
Statistics
Matches: 94, Mismatches: 13, Indels: 17
0.76 0.10 0.14
Matches are distributed among these distances:
21 16 0.17
22 3 0.03
23 16 0.17
24 40 0.43
25 19 0.20
ACGTcount: A:0.54, C:0.11, G:0.04, T:0.32
Consensus pattern (24 bp):
AATCATGCAAATAAATATATTAAT
Found at i:5476543 original size:21 final size:21
Alignment explanation
Indices: 5476493--5476561 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 21
5476483 AAATTAGATA
5476493 TAATCATACAAATAAATATATT
1 TAATCATACAAATAAATATA-T
*
5476515 AATAAATCACACAAATAAATATAT
1 --T-AATCATACAAATAAATATAT
* *
5476539 TAATCATGCAAACAAATATAT
1 TAATCATACAAATAAATATAT
5476560 TA
1 TA
5476562 GGCAAATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
21 19 0.47
22 1 0.03
24 2 0.05
25 18 0.45
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.30
Consensus pattern (21 bp):
TAATCATACAAATAAATATAT
Found at i:5476553 original size:25 final size:24
Alignment explanation
Indices: 5476430--5476556 Score: 91
Period size: 25 Copynumber: 5.2 Consensus size: 24
5476420 TACAATCATG
* *
5476430 CAAATAAATATATTAATAATCAAG
1 CAAATAAATATATTAATCATCAAA
* * **
5476454 CAATTAAATATATTAATAATCATG
1 CAAATAAATATATTAATCATCAAA
* *
5476478 C-TATCAAATTAGATATAATCAT---A
1 CAAAT-AAA-TATAT-TAATCATCAAA
* *
5476501 CAAATAAATATATTAATAAATCACA
1 CAAATAAATATATTAAT-CATCAAA
5476526 CAAATAAATATATTAATCATGCAAA
1 CAAATAAATATATTAATCAT-CAAA
5476551 CAAATA
1 CAAATA
5476557 TATTAGGCAA
Statistics
Matches: 82, Mismatches: 12, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
21 4 0.05
22 6 0.07
23 5 0.06
24 30 0.37
25 31 0.38
26 6 0.07
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.31
Consensus pattern (24 bp):
CAAATAAATATATTAATCATCAAA
Found at i:5477866 original size:43 final size:43
Alignment explanation
Indices: 5477698--5478374 Score: 583
Period size: 43 Copynumber: 15.8 Consensus size: 43
5477688 GCTCCTTTAT
*
5477698 AACTAAGGCTTTGAAACTTTTG-AAAATAAAATGCTC-CCTCAC
1 AACTGAGGCTTTGAAACTTTTGAAAAATAAAATGCTCTCC-CAC
* * * * *
5477740 AACTAAAGTTTTGAAAC-TTTGAAAAATAAAATGCTC-CATCAG
1 AACTGAGGCTTTGAAACTTTTGAAAAATAAAATGCTCTC-CCAC
* *
5477782 AACTGAAGCTTTGAAACTTTTG-AAAATAAAATGCTCCCCCAC
1 AACTGAGGCTTTGAAACTTTTGAAAAATAAAATGCTCTCCCAC
* *
5477824 AACTCAGGCTTTGAAAC-TTTGAAAAAATAAAATGCTATCCCAC
1 AACTGAGGCTTTGAAACTTTTG-AAAAATAAAATGCTCTCCCAC
* * * **
5477867 AACTGAGGCTTTGGAACTTTGGAAAAGTAAAATATTCTCCCAC
1 AACTGAGGCTTTGAAACTTTTGAAAAATAAAATGCTCTCCCAC
***
5477910 AACTGAGGCTTTGAAACTTTTGAAAAATAAAATGCTCTCCTGT
1 AACTGAGGCTTTGAAACTTTTGAAAAATAAAATGCTCTCCCAC
* * * * * ** *
5477953 AACTAAGGCTTTGGAACATTGGAAAAGTAAAATATTCTTCCAC
1 AACTGAGGCTTTGAAACTTTTGAAAAATAAAATGCTCTCCCAC
* **
5477996 AACTGAGGCTTTGAAACTTTTGAAAAATAAAATGCTCTCTCGT
1 AACTGAGGCTTTGAAACTTTTGAAAAATAAAATGCTCTCCCAC
* * * * * *
5478039 AACTAAGGCTTTGGAACATTGGCAAAAGTAAAATGCTC-CCTCAT
1 AACTGAGGCTTTGAAACTTTTG-AAAAATAAAATGCTCTCC-CAC
* * * * * *
5478083 AACTGAGGCTTTGGAA-TGCTGGAAAAGTAACATGC-CCCCTCAC
1 AACTGAGGCTTTGAAACT-TTTGAAAAATAAAATGCTCTCC-CAC
* * *
5478126 AACTGA-G-TTTGTAGAACTTTGGAAAAATAAAATGCTCCCCCAT
1 AACTGAGGCTTTG-A-AACTTTTGAAAAATAAAATGCTCTCCCAC
* * *
5478169 AACTGAGGCTTTGAAACTTTTGGAAAATGAAATGCTC-CTTCAC
1 AACTGAGGCTTTGAAACTTTTGAAAAATAAAATGCTCTC-CCAC
* * *
5478212 AACTGAGGCTTTGAAACTTTTGAAAAATAAAATGATCCCCCAT
1 AACTGAGGCTTTGAAACTTTTGAAAAATAAAATGCTCTCCCAC
* * * * *
5478255 AATTGAGGCTTTGAAAC-TTTAAAAAATAAAATACTTACCCCCAT
1 AACTGAGGCTTTGAAACTTTTGAAAAATAAAATGC-T-CTCCCAC
* * *
5478299 AATTGAGGCTTTGAAAC-TTTGAAAAATAAAATACT-TCCCTAT
1 AACTGAGGCTTTGAAACTTTTGAAAAATAAAATGCTCTCCC-AC
* **
5478341 AACTAAAACTTTGAAACTTTTGAAAAATAAAATG
1 AACTGAGGCTTTGAAACTTTTGAAAAATAAAATG
5478375 AGATCATTCT
Statistics
Matches: 525, Mismatches: 87, Indels: 45
0.80 0.13 0.07
Matches are distributed among these distances:
41 15 0.03
42 110 0.21
43 311 0.59
44 85 0.16
45 4 0.01
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (43 bp):
AACTGAGGCTTTGAAACTTTTGAAAAATAAAATGCTCTCCCAC
Found at i:5478358 original size:129 final size:127
Alignment explanation
Indices: 5477682--5478375 Score: 650
Period size: 129 Copynumber: 5.4 Consensus size: 127
5477672 CTTTTGATCT
* * * *
5477682 TAAAATGCTCCTTTATAACTAAGGCTTTGAAACTTTTG-AAAATAAAATGCTCCCTCACAACTAA
1 TAAAATGCTCC-CTATAACTAAGGCTTTGAAACTTTTGAAAAATAAAATGATCCCCCACAACTGA
* * ** * *
5477746 AGTTTTGAAACTTTGAAAAATAAAATGCTCCATCAGAACTGAAGCTTTGAAACTTTTG-AAAA
65 GGCTTTGAAACTTTGAAAAATAAAATGCTCCCCCATAACTGAGGCTTTGAAACTTTTGAAAAA
* * * * **
5477808 TAAAATGCTCCCCCACAACTCAGGCTTTGAAAC-TTTGAAAAAATAAAATGCTATCCCACAACTG
1 TAAAATGCT-CCCTATAACTAAGGCTTTGAAACTTTTG-AAAAATAAAATGATCCCCCACAACTG
* * ** * *
5477872 AGGCTTTGGAACTTTGGAAAAGTAAAATATTCTCCCACAACTGAGGCTTTGAAACTTTTGAAAAA
64 AGGCTTTGAAACTTT-GAAAAATAAAATGCTCCCCCATAACTGAGGCTTTGAAACTTTTGAAAAA
* * * * * **
5477937 TAAAATGCTCTCCTGTAACTAAGGCTTTGGAACATTGGAAAAGTAAAAT-ATTCTTCCACAACTG
1 TAAAATGCTC-CCTATAACTAAGGCTTTGAAACTTTTGAAAAATAAAATGA-TCCCCCACAACTG
* * * * * * *
5478001 AGGCTTTGAAACTTTTGAAAAATAAAATGCTCTCTCGTAACTAAGGCTTTGGAACATTGGCAAAA
64 AGGCTTTGAAAC-TTTGAAAAATAAAATGCTCCCCCATAACTGAGGCTTTGAAACTTTTG-AAAA
*
5478066 G
127 A
* * * * * * *
5478067 TAAAATGCTCCCTCATAACTGAGGCTTTGGAA-TGCTGGAAAAGTAACATG-CCCCCTCACAACT
1 TAAAATGCTCCCT-ATAACTAAGGCTTTGAAACT-TTTGAAAAATAAAATGATCCCC-CACAACT
*
5478130 GA-G-TTTGTAGAACTTTGGAAAAATAAAATGCTCCCCCATAACTGAGGCTTTGAAACTTTTGGA
63 GAGGCTTTG-A-AACTTT-GAAAAATAAAATGCTCCCCCATAACTGAGGCTTTGAAACTTTTGAA
5478193 AAA
125 AAA
* * * * * *
5478196 TGAAATGCTCCTTCACAACTGAGGCTTTGAAACTTTTGAAAAATAAAATGATCCCCCATAATTGA
1 TAAAATGCTCCCT-ATAACTAAGGCTTTGAAACTTTTGAAAAATAAAATGATCCCCCACAACTGA
* * *
5478261 GGCTTTGAAACTTTAAAAAATAAAATACTTACCCCCATAATTGAGGCTTTGAAAC-TTTGAAAAA
65 GGCTTTGAAACTTTGAAAAATAAAATGC-T-CCCCCATAACTGAGGCTTTGAAACTTTTGAAAAA
* **
5478325 TAAAATACTTCCCTATAACTAAAACTTTGAAACTTTTGAAAAATAAAATGA
1 TAAAATGC-TCCCTATAACTAAGGCTTTGAAACTTTTGAAAAATAAAATGA
5478376 GATCATTCTT
Statistics
Matches: 464, Mismatches: 80, Indels: 45
0.79 0.14 0.08
Matches are distributed among these distances:
125 4 0.01
126 26 0.06
127 35 0.08
128 53 0.11
129 210 0.45
130 132 0.28
131 4 0.01
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (127 bp):
TAAAATGCTCCCTATAACTAAGGCTTTGAAACTTTTGAAAAATAAAATGATCCCCCACAACTGAG
GCTTTGAAACTTTGAAAAATAAAATGCTCCCCCATAACTGAGGCTTTGAAACTTTTGAAAAA
Found at i:5483240 original size:185 final size:185
Alignment explanation
Indices: 5482919--5483265 Score: 457
Period size: 185 Copynumber: 1.9 Consensus size: 185
5482909 TACTGTGACA
* *
5482919 ATAAAATCAAACGTCACCTTATGTGTTAATCTTTATGATGTTAGTTTTCGTCAGCTATTAATAAA
1 ATAAAATCAAACGTCACCTTATGTGTTAATCTTTATGATGTTAATTTCCGTCAGCTATTAATAAA
* * * *
5482984 CAAAAACATCATTAAAGGCTATAATCATCACAAAATAAATTATAAAATCTTATATATTAGTGACA
66 CAAAAACATCATTAAAGACTATAATCATCACAAAATAAATGATAAAATCTGATATATTAATGACA
* *
5483049 AAAGGTAAATTGTCACAA-TATTGGTGACATAAGTATCGTCACGAATGATTATATG
131 AAAGGTAAATCGTCA-AAGTATTGGTAACATAAGTATCGTCACGAATGATTATATG
* * * * * *
5483104 ATAATATCAAACGTCACCTTATGCT-TT-TTTTTATATGATGTTAATTTCCGTTAGTTATTTATA
1 ATAAAATCAAACGTCACCTTATG-TGTTAATCTT-TATGATGTTAATTTCCGTCAGCTATTAATA
* * * * * *
5483167 AAGAAGAGCGTCATTAAAGATTATAATCATCATAAAATAAATGATAAAATCTGATATATTAATGA
64 AACAAAAACATCATTAAAGACTATAATCATCACAAAATAAATGATAAAATCTGATATATTAATGA
*
5483232 CGAAAGGTAAATCGTCAAAGTATTGGTAACATAA
129 CAAAAGGTAAATCGTCAAAGTATTGGTAACATAA
5483266 TTTTCGTCGT
Statistics
Matches: 138, Mismatches: 21, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
184 5 0.04
185 132 0.96
186 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.35
Consensus pattern (185 bp):
ATAAAATCAAACGTCACCTTATGTGTTAATCTTTATGATGTTAATTTCCGTCAGCTATTAATAAA
CAAAAACATCATTAAAGACTATAATCATCACAAAATAAATGATAAAATCTGATATATTAATGACA
AAAGGTAAATCGTCAAAGTATTGGTAACATAAGTATCGTCACGAATGATTATATG
Found at i:5483328 original size:25 final size:25
Alignment explanation
Indices: 5483291--5483343 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
5483281 ATTGTAAGAT
5483291 AACGTCAAATGTGACAATAAAATCA
1 AACGTCAAATGTGACAATAAAATCA
*
5483316 AACGTCAATTGTGACAATAAAATCA
1 AACGTCAAATGTGACAATAAAATCA
5483341 AAC
1 AAC
5483344 TTCATATTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.51, C:0.17, G:0.11, T:0.21
Consensus pattern (25 bp):
AACGTCAAATGTGACAATAAAATCA
Found at i:5491136 original size:2 final size:2
Alignment explanation
Indices: 5491082--5491117 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5491072 TATAAGCATC
5491082 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5491118 CAGAATTACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5491185 original size:20 final size:20
Alignment explanation
Indices: 5491160--5491208 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
5491150 TTGTGGTTGC
**
5491160 AGAATTACATCTATATATGT
1 AGAATTACATCTATATATAA
*
5491180 AGAATTACTTCTATATATAA
1 AGAATTACATCTATATATAA
5491200 AGAATTACA
1 AGAATTACA
5491209 ATTCAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (20 bp):
AGAATTACATCTATATATAA
Found at i:5491327 original size:20 final size:22
Alignment explanation
Indices: 5491229--5491484 Score: 85
Period size: 20 Copynumber: 12.1 Consensus size: 22
5491219 TAATAACCAG
*
5491229 CATCTATATATATGCAAAATTA
1 CATCTATATATATGCAGAATTA
*
5491251 CAT-T-TATATATGCAAAATTA
1 CATCTATATATATGCAGAATTA
* * * * * *
5491271 CAATTTA-AAAAAT-AATAACTA
1 C-ATCTATATATATGCAGAATTA
5491292 GCATCTATATATATGCAGAATTA
1 -CATCTATATATATGCAGAATTA
5491315 CATCTATA-A-ATGCAGAATTA
1 CATCTATATATATGCAGAATTA
* * * * ***
5491335 CAATTCAAAAAATA-GTA-ACCAA
1 C-A-TCTATATATATGCAGAATTA
5491357 CATCTATATATATGCAGAATTA
1 CATCTATATATATGCAGAATTA
* * * * ***
5491379 CAATTCAAAAAATAT-TA-ACCAA
1 C-A-TCTATATATATGCAGAATTA
* * *
5491401 CATCCATGTATATGTAGAATTA
1 CATCTATATATATGCAGAATTA
5491423 CATCTATATA-A-GCAGAATTA
1 CATCTATATATATGCAGAATTA
* *
5491443 TATC--TGTATATGCAGAATTA
1 CATCTATATATATGCAGAATTA
* *
5491463 CA--TGTATATACGCAGAATTA
1 CATCTATATATATGCAGAATTA
5491483 CA
1 CA
5491485 ATTCAAAAAA
Statistics
Matches: 168, Mismatches: 46, Indels: 42
0.66 0.18 0.16
Matches are distributed among these distances:
18 3 0.02
19 1 0.01
20 80 0.48
21 21 0.12
22 44 0.26
23 10 0.06
24 9 0.05
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (22 bp):
CATCTATATATATGCAGAATTA
Found at i:5491376 original size:44 final size:44
Alignment explanation
Indices: 5491314--5491424 Score: 172
Period size: 44 Copynumber: 2.6 Consensus size: 44
5491304 ATGCAGAATT
5491314 ACATCTATA-A-ATGCAGAATTACAATTCAAAAAATAGTAACCA
1 ACATCTATATATATGCAGAATTACAATTCAAAAAATAGTAACCA
*
5491356 ACATCTATATATATGCAGAATTACAATTCAAAAAATATTAACCA
1 ACATCTATATATATGCAGAATTACAATTCAAAAAATAGTAACCA
* * *
5491400 ACATCCATGTATATGTAGAATTACA
1 ACATCTATATATATGCAGAATTACA
5491425 TCTATATAAG
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
42 9 0.14
43 1 0.02
44 53 0.84
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.28
Consensus pattern (44 bp):
ACATCTATATATATGCAGAATTACAATTCAAAAAATAGTAACCA
Found at i:5491380 original size:64 final size:64
Alignment explanation
Indices: 5491171--5491380 Score: 312
Period size: 64 Copynumber: 3.3 Consensus size: 64
5491161 GAATTACATC
* * **
5491171 TATATATGTAGAATTACTTCTATATATAAAGAATTACAATTCAAAAAATAATAACCAGCATCTA
1 TATATATGCAGAATTACATCTATATATGCAGAATTACAATTCAAAAAATAATAACCAGCATCTA
* * * * *
5491235 TATATATGCAAAATTACATTTATATATGCAAAATTACAATTTAAAAAATAATAACTAGCATCTA
1 TATATATGCAGAATTACATCTATATATGCAGAATTACAATTCAAAAAATAATAACCAGCATCTA
* * *
5491299 TATATATGCAGAATTACATCTATAAATGCAGAATTACAATTCAAAAAATAGTAACCAACATCTA
1 TATATATGCAGAATTACATCTATATATGCAGAATTACAATTCAAAAAATAATAACCAGCATCTA
5491363 TATATATGCAGAATTACA
1 TATATATGCAGAATTACA
5491381 ATTCAAAAAA
Statistics
Matches: 129, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 129 1.00
ACGTcount: A:0.49, C:0.13, G:0.07, T:0.32
Consensus pattern (64 bp):
TATATATGCAGAATTACATCTATATATGCAGAATTACAATTCAAAAAATAATAACCAGCATCTA
Found at i:5491425 original size:22 final size:20
Alignment explanation
Indices: 5491407--5491484 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
5491397 CCAACATCCA
*
5491407 TGTATATGTAGAATTACATC
1 TGTATATGCAGAATTACATC
* * *
5491427 TATATAAGCAGAATTATATC
1 TGTATATGCAGAATTACATC
*
5491447 TGTATATGCAGAATTACATG
1 TGTATATGCAGAATTACATC
* *
5491467 TATATACGCAGAATTACA
1 TGTATATGCAGAATTACA
5491485 ATTCAAAAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (20 bp):
TGTATATGCAGAATTACATC
Found at i:5491460 original size:40 final size:40
Alignment explanation
Indices: 5491407--5491482 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
5491397 CCAACATCCA
*
5491407 TGTATATGTAGAATTACATCTATATAAGCAGAATTATATC
1 TGTATATGCAGAATTACATCTATATAAGCAGAATTATATC
* *
5491447 TGTATATGCAGAATTACATGTATATACGCAGAATTA
1 TGTATATGCAGAATTACATCTATATAAGCAGAATTA
5491483 CAATTCAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (40 bp):
TGTATATGCAGAATTACATCTATATAAGCAGAATTATATC
Found at i:5491526 original size:64 final size:64
Alignment explanation
Indices: 5491449--5491612 Score: 238
Period size: 64 Copynumber: 2.6 Consensus size: 64
5491439 ATTATATCTG
* * *
5491449 TATATGCAGAATTACATGTATATACGCAGAATTACAATTCAAAAAATAATAACCAGTAGCTATA
1 TATATGCAGAATTACATCTATATACGCAAAATTACAATTCAAAAAATAATAACCAGCAGCTATA
* * * * *
5491513 TATATGCAGAATTACATCTATCTATGTAAAATTACAATTCAAAAAATAATAACCAGCATCTATC
1 TATATGCAGAATTACATCTATATACGCAAAATTACAATTCAAAAAATAATAACCAGCAGCTATA
* *
5491577 TATATGCAGAATTACATCTATATAGGCATAATTACA
1 TATATGCAGAATTACATCTATATACGCAAAATTACA
5491613 TCTATATATG
Statistics
Matches: 88, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 88 1.00
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.30
Consensus pattern (64 bp):
TATATGCAGAATTACATCTATATACGCAAAATTACAATTCAAAAAATAATAACCAGCAGCTATA
Found at i:5491643 original size:20 final size:20
Alignment explanation
Indices: 5491577--5491645 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
5491567 AGCATCTATC
*
5491577 TATATGCAGAATTACATCTA
1 TATATGCATAATTACATCTA
*
5491597 TATAGGCATAATTACATCTA
1 TATATGCATAATTACATCTA
5491617 TATATGCATAATTACATCTA
1 TATATGCATAATTACATCTA
*
5491637 TAAATGCAT
1 TATATGCAT
5491646 CTATATATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (20 bp):
TATATGCATAATTACATCTA
Found at i:5492460 original size:20 final size:20
Alignment explanation
Indices: 5492431--5492500 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 20
5492421 TATATATATA
*
5492431 TATATATATATATGCAGAAT
1 TATATCTATATATGCAGAAT
*
5492451 TACATCTATATATGC---A-
1 TATATCTATATATGCAGAAT
* *
5492467 TATATATATATATACAGAAT
1 TATATCTATATATGCAGAAT
5492487 TATATCTATATATG
1 TATATCTATATATG
5492501 GAAAATAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
16 12 0.31
17 1 0.03
19 1 0.03
20 25 0.64
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (20 bp):
TATATCTATATATGCAGAAT
Found at i:5492462 original size:2 final size:2
Alignment explanation
Indices: 5492418--5492443 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5492408 AATAACCAGC
5492418 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5492444 GCAGAATTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5492470 original size:36 final size:36
Alignment explanation
Indices: 5492421--5492500 Score: 124
Period size: 36 Copynumber: 2.2 Consensus size: 36
5492411 AACCAGCATA
** *
5492421 TATATATATATATATATATATATGCAGAATTACATC
1 TATATATGCATATATATATATATACAGAATTACATC
*
5492457 TATATATGCATATATATATATATACAGAATTATATC
1 TATATATGCATATATATATATATACAGAATTACATC
5492493 TATATATG
1 TATATATG
5492501 GAAAATAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.42
Consensus pattern (36 bp):
TATATATGCATATATATATATATACAGAATTACATC
Found at i:5492666 original size:12 final size:13
Alignment explanation
Indices: 5492637--5492669 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
5492627 GCAGCAGCTA
*
5492637 AAATTAAAATTGT
1 AAATTAAAATTAT
5492650 AAATTAAAA-TAT
1 AAATTAAAATTAT
5492662 AAATTAAA
1 AAATTAAA
5492670 GCTAATACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (13 bp):
AAATTAAAATTAT
Found at i:5494221 original size:14 final size:14
Alignment explanation
Indices: 5494204--5494231 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5494194 TTCTTTTAAC
5494204 AAAATTTTTAAATT
1 AAAATTTTTAAATT
5494218 AAAATTTTTAAATT
1 AAAATTTTTAAATT
5494232 TTAAATTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAAATTTTTAAATT
Found at i:5495307 original size:234 final size:234
Alignment explanation
Indices: 5495008--5495823 Score: 791
Period size: 236 Copynumber: 3.5 Consensus size: 234
5494998 AACATCATTC
* * * ** *
5495008 AAAAGTTTGTGACATTTATGTTATCCTCATATAACACTATACATTAACATGATGAAATAGCAATG
1 AAAAGTTTGTGACATTTATGTTATCGTCATATAACACCATACATTAACGTGACAAAATTGCAATG
* *** *
5495073 TCATTAATAGTTAACTAAAGTATTTAATTTGTGACAAAAATCCGTAACATCACCTTAAATCTATT
66 TCATTAATAGTTAACTAAAGTATTCAATTTGTGACAAAAATTAATAACGTCACCTTAAATCT-TT
* * * * *
5495138 AGAAAAAATAT-GTCACAGTTAAATTTTTAAATTGGTGATAAAATTAT-GTCACCTAAAATAAAA
130 AAAAAAAATATCATCACAGATAAAATTTTAAATTGGTGATAAAATTATAATCACCTAAAATAAAA
*
5495201 AAATATCACAAAAAAATTTTTCACCAAATAAATTTGGTAAT
195 AAATATCAAAAAAAAATTTTTCACCAAATAAATTTGGT-AT
* * * *
5495242 AAAAGTTTGTGACATTTATGTTATCGTCATATAATATCATATATTAAGGTGACAAAATTGCAATG
1 AAAAGTTTGTGACATTTATGTTATCGTCATATAACACCATACATTAACGTGACAAAATTGCAATG
* * *
5495307 TCATTAATAGTTAACCAAAGTGTTCAATTTATGA-AAAATATTAATAACGTCA-CTTAAAATCTT
66 TCATTAATAGTTAACTAAAGTATTCAATTTGTGACAAAA-ATTAATAACGTCACCTT-AAATCTT
* **
5495370 TAAAAAAAAT-TCATCATAGATAAAATTTTAAATTAATG-TCAAAATTATAACATCACCTAAAAT
129 TAAAAAAAATATCATCACAGATAAAATTTTAAATTGGTGAT-AAAATTAT-A-ATCACCTAAAAT
* *
5495433 AAAAAAGTCA-CAAAAAAAAATTTCTCACCAAATAAATTT-G---
191 AAAAAAAT-ATCAAAAAAAAATTTTTCACCAAATAAATTTGGTAT
* * * * ** * *
5495473 --ACG---GT-A-A---AAGTTATTGTCATATAACACCATACATTAATGTGATGAAATTGTAATA
1 AAAAGTTTGTGACATTTATGTTATCGTCATATAACACCATACATTAACGTGACAAAATTGCAATG
* * * **
5495528 TCATTAATAGTTAACTAAAGTATTCAAGTTGCGACAAAAATTAATAACGTTACCTGT-TCTCTTA
66 TCATTAATAGTTAACTAAAGTATTCAATTTGTGACAAAAATTAATAACGTCACCT-TAAATCTT-
* * *
5495592 TAAAAAAAAT-TCATCACAAATAAAATTTTAAATTGGTGACAAAAATTATAACATCACCAAAAAT
129 TAAAAAAAATATCATCACAGATAAAATTTTAAATTGGTGA-TAAAATTAT-A-ATCACCTAAAAT
** * *
5495656 -AAAAAACGTCATAAATAAATTTTTCACCAAATAAATTTGGTGAT
191 AAAAAAATATCAAAAAAAAATTTTTCACCAAATAAATTTGGT-AT
* * *
5495700 AAAAGTTTGTGACATTTATGTTATCATCATATAA-ACCATACAATGACGTGACAAAATTGCAATG
1 AAAAGTTTGTGACATTTATGTTATCGTCATATAACACCATACATTAACGTGACAAAATTGCAATG
* * * * * * * *
5495764 TCATTAATAATTAACTAAAGCATTTATTTTGTGACAACAATTAACAATGTCACCTAAAAT
66 TCATTAATAGTTAACTAAAGTATTCAATTTGTGACAAAAATTAATAACGTCACCTTAAAT
5495824 AAAAAATGTC
Statistics
Matches: 467, Mismatches: 84, Indels: 60
0.76 0.14 0.10
Matches are distributed among these distances:
221 83 0.18
222 71 0.15
223 24 0.05
224 1 0.00
225 1 0.00
226 2 0.00
229 4 0.01
232 4 0.01
233 46 0.10
234 101 0.22
235 1 0.00
236 114 0.24
237 15 0.03
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (234 bp):
AAAAGTTTGTGACATTTATGTTATCGTCATATAACACCATACATTAACGTGACAAAATTGCAATG
TCATTAATAGTTAACTAAAGTATTCAATTTGTGACAAAAATTAATAACGTCACCTTAAATCTTTA
AAAAAAATATCATCACAGATAAAATTTTAAATTGGTGATAAAATTATAATCACCTAAAATAAAAA
AATATCAAAAAAAAATTTTTCACCAAATAAATTTGGTAT
Found at i:5495689 original size:222 final size:220
Alignment explanation
Indices: 5495261--5495694 Score: 548
Period size: 221 Copynumber: 2.0 Consensus size: 220
5495251 TGACATTTAT
* * * *
5495261 GTTATCGTCATATAATATCATATATTAAGGTGACAAAATTGCAATGTCATTAATAGTTAACCAAA
1 GTTATCGTCATATAACACCATACATTAAGGTGACAAAATTGCAATATCATTAATAGTTAACCAAA
* * * * * *
5495326 GTGTTCAATTTATGAAAAATATTAATAACGTCACTTAAAATCTTTAAAAAAAATTCATCATAGAT
66 GTATTCAAGTTACGAAAAATATTAATAACGTCACCTAAAATCTTTAAAAAAAATTCATCACAAAT
* *
5495391 AAAATTTTAAATTAATGTCAAAATTATAACATCACCTAAAATAAAAAAGTCACAAAAAAAAATTT
131 AAAATTTTAAATTAATGACAAAATTATAACATCACCAAAAATAAAAAAGT-ACAAAAAAAAATTT
5495456 CTCACCAAATAAATTTGACGGTAAAA
195 CTCACCAAATAAATTTGACGGTAAAA
* * ** * *
5495482 GTTATTGTCATATAACACCATACATTAATGTGATGAAATTGTAATATCATTAATAGTTAACTAAA
1 GTTATCGTCATATAACACCATACATTAAGGTGACAAAATTGCAATATCATTAATAGTTAACCAAA
* * ****
5495547 GTATTCAAGTTGCGACAAAA-ATTAATAACGTTACCTGTTCTCTTATAAAAAAAATTCATCACAA
66 GTATTCAAGTTACGA-AAAATATTAATAACGTCACCTAAAATCTT-TAAAAAAAATTCATCACAA
** * *
5495611 ATAAAATTTTAAATTGGTGACAAAAATTATAACATCACCAAAAATAAAAAACGT-CATAAATAAA
129 ATAAAATTTTAAATTAATGAC-AAAATTATAACATCACCAAAAATAAAAAA-GTACAAAAAAAAA
*
5495675 TTTTTCACCAAATAAATTTG
192 TTTCTCACCAAATAAATTTG
5495695 GTGATAAAAG
Statistics
Matches: 180, Mismatches: 29, Indels: 7
0.83 0.13 0.03
Matches are distributed among these distances:
221 84 0.47
222 66 0.37
223 28 0.16
224 2 0.01
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (220 bp):
GTTATCGTCATATAACACCATACATTAAGGTGACAAAATTGCAATATCATTAATAGTTAACCAAA
GTATTCAAGTTACGAAAAATATTAATAACGTCACCTAAAATCTTTAAAAAAAATTCATCACAAAT
AAAATTTTAAATTAATGACAAAATTATAACATCACCAAAAATAAAAAAGTACAAAAAAAAATTTC
TCACCAAATAAATTTGACGGTAAAA
Found at i:5497801 original size:19 final size:19
Alignment explanation
Indices: 5497761--5497802 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
5497751 CTTTTGACTA
*
5497761 AAAAAATAAAAATTAAACT
1 AAAAAATAAAAATTAAAAT
*
5497780 AAAAAATTAAAA-TACAAAT
1 AAAAAATAAAAATTA-AAAT
5497799 AAAA
1 AAAA
5497803 TTTAAGACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAAAATAAAAATTAAAAT
Found at i:5505998 original size:21 final size:20
Alignment explanation
Indices: 5505959--5506003 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
5505949 TTCAACATAC
*
5505959 ATATATATTAAGGCATATAT
1 ATATATATTAAGACATATAT
*
5505979 ATATCTATTAAGTACATATAT
1 ATATATATTAAG-ACATATAT
5506000 ATAT
1 ATAT
5506004 GTATATTGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (20 bp):
ATATATATTAAGACATATAT
Found at i:5506989 original size:22 final size:21
Alignment explanation
Indices: 5506951--5506991 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5506941 CAAAATCAAA
*
5506951 CAAACATATGTAAAAATATTT
1 CAAACATATATAAAAATATTT
*
5506972 CAAATCATATATAGAAATAT
1 CAAA-CATATATAAAAATAT
5506992 ACCAAAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.32
Consensus pattern (21 bp):
CAAACATATATAAAAATATTT
Found at i:5507345 original size:13 final size:13
Alignment explanation
Indices: 5507327--5507358 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5507317 AATATATACA
5507327 ATCATAATAACAT
1 ATCATAATAACAT
*
5507340 ATCATAATAATAT
1 ATCATAATAACAT
5507353 ATCATA
1 ATCATA
5507359 GCAAGCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (13 bp):
ATCATAATAACAT
Found at i:5511251 original size:18 final size:20
Alignment explanation
Indices: 5511215--5511262 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 20
5511205 TTAAATCGAA
*
5511215 TTATATATATTTATTAATTT
1 TTATATATATTTATAAATTT
5511235 TTATATAT-TTTA-AAA-TT
1 TTATATATATTTATAAATTT
*
5511252 TTATAAATATT
1 TTATATATATT
5511263 CAAATCTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 9 0.36
18 4 0.16
19 4 0.16
20 8 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATATATATTTATAAATTT
Found at i:5512218 original size:13 final size:13
Alignment explanation
Indices: 5512179--5512218 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
5512169 AACTTATATG
*
5512179 TTTTTATATATTA
1 TTTTTATATATTT
*
5512192 TTTTAATATAATTT
1 TTTTTATAT-ATTT
5512206 TTTTTATATATTT
1 TTTTTATATATTT
5512219 AAATAGATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTATATATTT
Found at i:5512277 original size:18 final size:18
Alignment explanation
Indices: 5512254--5512296 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
5512244 ATTTTTATTT
5512254 TATAAAA-AATTAAAAATA
1 TATAAAACAA-TAAAAATA
5512272 TATAAAAGCTAATAAAAATA
1 TATAAAA-C-AATAAAAATA
5512292 TATAA
1 TATAA
5512297 TTTAGTTCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.32
20 13 0.59
21 2 0.09
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (18 bp):
TATAAAACAATAAAAATA
Found at i:5525676 original size:31 final size:31
Alignment explanation
Indices: 5525641--5525702 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
5525631 ATCAAATTTC
* *
5525641 ATTTGTAATTCATTAAAGAAATTTATTAGGA
1 ATTTGTAACTCATTAAAAAAATTTATTAGGA
* *
5525672 ATTTGTAGCTCATTAAAAAAATTTGTTAGGA
1 ATTTGTAACTCATTAAAAAAATTTATTAGGA
5525703 TCAGACAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (31 bp):
ATTTGTAACTCATTAAAAAAATTTATTAGGA
Found at i:5537080 original size:18 final size:18
Alignment explanation
Indices: 5537066--5537100 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5537056 TTTAATATAA
5537066 ATATAAAATTAAATAAAT
1 ATATAAAATTAAATAAAT
* *
5537084 ATATATAATTAATTAAA
1 ATATAAAATTAAATAAA
5537101 AAATAATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATATAAAATTAAATAAAT
Found at i:5538715 original size:19 final size:20
Alignment explanation
Indices: 5538678--5538718 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
5538668 TTGAAAAAAA
5538678 TTGTATTTTATAGAATTTTT
1 TTGTATTTTATAGAATTTTT
5538698 TTGTAATTTT-TA-AATTTTT
1 TTGT-ATTTTATAGAATTTTT
5538717 TT
1 TT
5538719 AAAAATTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.45
20 6 0.30
21 5 0.25
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.68
Consensus pattern (20 bp):
TTGTATTTTATAGAATTTTT
Found at i:5539631 original size:18 final size:18
Alignment explanation
Indices: 5539608--5539648 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
5539598 AAATGTAATA
5539608 TTTTATTATAATTATAAC
1 TTTTATTATAATTATAAC
* *
5539626 TTTTATTATATTTATAAT
1 TTTTATTATAATTATAAC
5539644 TTTTA
1 TTTTA
5539649 AAAAAAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTATTATAATTATAAC
Found at i:5540003 original size:29 final size:31
Alignment explanation
Indices: 5539946--5540015 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 31
5539936 ATGTCACGAA
* *
5539946 TAATTATTAAATTATAATAAAATATTTAATT
1 TAATAATTAAATTATAATAAAATATTTAATG
*
5539977 TAATAATTAAATTTTAA-AAAAT-TTTAATG
1 TAATAATTAAATTATAATAAAATATTTAATG
*
5540006 TAATACTTAA
1 TAATAATTAA
5540016 TGTAAACAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 15 0.43
30 5 0.14
31 15 0.43
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (31 bp):
TAATAATTAAATTATAATAAAATATTTAATG
Found at i:5541446 original size:33 final size:33
Alignment explanation
Indices: 5541409--5541473 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
5541399 CAAGCTCAAG
5541409 ATATCTTTTTAAAAT-GTGACAAATTTAGTTAGA
1 ATATCTTTTTAAAATAG-GACAAATTTAGTTAGA
* *
5541442 ATATCTTTTTAAATTAGGATAAATTTAGTTAG
1 ATATCTTTTTAAAATAGGACAAATTTAGTTAG
5541474 GTAATTAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (33 bp):
ATATCTTTTTAAAATAGGACAAATTTAGTTAGA
Found at i:5544052 original size:2 final size:2
Alignment explanation
Indices: 5544047--5544088 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5544037 TATGTGTGTG
5544047 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5544089 ATTGTAGATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5556866 original size:22 final size:22
Alignment explanation
Indices: 5556840--5556881 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5556830 CAGCAAATCA
*
5556840 AAAGGACAAGTGAAAAAGGACG
1 AAAGGACAAATGAAAAAGGACG
* *
5556862 AAAGGGCAAATGCAAAAGGA
1 AAAGGACAAATGAAAAAGGA
5556882 AAAGATTGGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.10, G:0.31, T:0.05
Consensus pattern (22 bp):
AAAGGACAAATGAAAAAGGACG
Found at i:5557298 original size:16 final size:16
Alignment explanation
Indices: 5557279--5557348 Score: 54
Period size: 16 Copynumber: 4.3 Consensus size: 16
5557269 ATATAAAAAT
*
5557279 TATTTATTATAATTTA
1 TATTTATTAAAATTTA
* *
5557295 TATTGATATAAAAATATA
1 TATT--TATTAAAATTTA
*
5557313 TTTTTATTAAAATTT-
1 TATTTATTAAAATTTA
*
5557328 TAATTTA-TATAATTTA
1 T-ATTTATTAAAATTTA
5557344 TATTT
1 TATTT
5557349 TTTTATCGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
15 12 0.29
16 18 0.43
18 12 0.29
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (16 bp):
TATTTATTAAAATTTA
Found at i:5557338 original size:34 final size:31
Alignment explanation
Indices: 5557266--5557339 Score: 87
Period size: 34 Copynumber: 2.3 Consensus size: 31
5557256 TATATTATGT
*
5557266 TTTATATAAAAATTATTTATTATAATTTATA
1 TTTATATAAAAATTATTTATTAAAATTTATA
*
5557297 TTGATATAAAAATATATTTTTATTAAAATTT-TAA
1 TTTATATAAAAAT-TA--TTTATTAAAATTTAT-A
5557331 TTTATATAA
1 TTTATATAA
5557340 TTTATATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
31 12 0.33
32 2 0.06
33 1 0.03
34 21 0.58
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (31 bp):
TTTATATAAAAATTATTTATTAAAATTTATA
Found at i:5557862 original size:22 final size:22
Alignment explanation
Indices: 5557834--5557890 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
5557824 AAAATTCATG
*
5557834 TAATATATATTTACGAACAAAT
1 TAATATATATTCACGAACAAAT
* *
5557856 TAGTATATATTCACGAACAAGT
1 TAATATATATTCACGAACAAAT
5557878 TAATATATATTCA
1 TAATATATATTCA
5557891 TAATTATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (22 bp):
TAATATATATTCACGAACAAAT
Found at i:5557911 original size:16 final size:16
Alignment explanation
Indices: 5557881--5557930 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
5557871 AACAAGTTAA
5557881 TATATATT-CAT-AAT
1 TATATATTACATGAAT
5557895 TATATATTACATGAAT
1 TATATATTACATGAAT
* *
5557911 TTTAATCTTACATGCAAT
1 TAT-ATATTACATG-AAT
5557929 TA
1 TA
5557931 CTTTCATGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 8 0.28
15 3 0.10
16 5 0.17
17 9 0.31
18 4 0.14
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (16 bp):
TATATATTACATGAAT
Found at i:5558114 original size:15 final size:15
Alignment explanation
Indices: 5558094--5558124 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5558084 GCTTAGTTGT
5558094 TATACGACTATTAGG
1 TATACGACTATTAGG
5558109 TATACGACTATTAGG
1 TATACGACTATTAGG
5558124 T
1 T
5558125 GTATATAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (15 bp):
TATACGACTATTAGG
Found at i:5561741 original size:56 final size:58
Alignment explanation
Indices: 5561654--5561802 Score: 187
Period size: 59 Copynumber: 2.6 Consensus size: 58
5561644 TAAAAAAATA
* * * *
5561654 AAAAGATGAATTATCAATTTT-TTTAAATAAAAAAAAATTTC-AGAAAT-GTATGAGG
1 AAAAGTTGAAGTATCAATTTTCCTTAAATAAAAAAAAATTTCAAAAAATAGTATGAGG
* * * *
5561709 AAAAGTTGAAGTATCAGTTTTCCTTAAATAAAAAAATATTTCAAAAAAATATTTTGAGG
1 AAAAGTTGAAGTATCAATTTTCCTTAAATAAAAAAAAATTTC-AAAAAATAGTATGAGG
*
5561768 AAAAGTTGAAGTATAAATTTTCCTTAAATAAAAAA
1 AAAAGTTGAAGTATCAATTTTCCTTAAATAAAAAA
5561803 CGTTTTGAGA
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
55 18 0.22
56 18 0.22
58 5 0.06
59 39 0.49
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.33
Consensus pattern (58 bp):
AAAAGTTGAAGTATCAATTTTCCTTAAATAAAAAAAAATTTCAAAAAATAGTATGAGG
Found at i:5561756 original size:13 final size:13
Alignment explanation
Indices: 5561738--5561762 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5561728 TTCCTTAAAT
5561738 AAAAAAATATTTC
1 AAAAAAATATTTC
5561751 AAAAAAATATTT
1 AAAAAAATATTT
5561763 TGAGGAAAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAAAATATTTC
Found at i:5561817 original size:104 final size:106
Alignment explanation
Indices: 5561704--5561894 Score: 280
Period size: 104 Copynumber: 1.8 Consensus size: 106
5561694 CAGAAATGTA
* * * * * *
5561704 TGAGGAAAAGTTGAAGTATCAGTTTTCCTTAAATAAAAAAATA-TTTCAAAAAAATATTTTGAGG
1 TGAGAAAAAGTTAAAGTACCAATTTTCCTTAAACAAAAAAAAATTTTCAAAAAAATA-TTTGAGG
5561768 -AAAAGTTG-AAGTATAAATTTTCCTTAAATAAAAAACGTTT
65 AAAAAGTTGAAAGTATAAATTTTCCTTAAATAAAAAACGTTT
*
5561808 TGAGAAAAAGTTAAAGTACCAATTTTTCTTAAACAAAAAAAAATTTTCAAAAAAATATTTGAGGA
1 TGAGAAAAAGTTAAAGTACCAATTTTCCTTAAACAAAAAAAAATTTTCAAAAAAATATTTGAGGA
*
5561873 AAAAGTTGAAAGTATCAATTTT
66 AAAAGTTGAAAGTATAAATTTT
5561895 TTCTTACAAG
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
104 43 0.57
105 21 0.28
106 12 0.16
ACGTcount: A:0.48, C:0.07, G:0.13, T:0.32
Consensus pattern (106 bp):
TGAGAAAAAGTTAAAGTACCAATTTTCCTTAAACAAAAAAAAATTTTCAAAAAAATATTTGAGGA
AAAAGTTGAAAGTATAAATTTTCCTTAAATAAAAAACGTTT
Found at i:5561862 original size:46 final size:46
Alignment explanation
Indices: 5561750--5561854 Score: 122
Period size: 45 Copynumber: 2.3 Consensus size: 46
5561740 AAAAATATTT
* * * *
5561750 CAAAAAAATATTTTGAGGAAAAGTTGAAGTATAAATTTTCCTTAAA
1 CAAAAAAAAATTTTGAGAAAAAGTTAAAGTACAAATTTTCCTTAAA
* ** * *
5561796 -TAAAAAACGTTTTGAGAAAAAGTTAAAGTACCAATTTTTCTTAAA
1 CAAAAAAAAATTTTGAGAAAAAGTTAAAGTACAAATTTTCCTTAAA
5561841 CAAAAAAAAATTTT
1 CAAAAAAAAATTTT
5561855 CAAAAAAATA
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
45 37 0.79
46 10 0.21
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.32
Consensus pattern (46 bp):
CAAAAAAAAATTTTGAGAAAAAGTTAAAGTACAAATTTTCCTTAAA
Found at i:5571044 original size:3 final size:3
Alignment explanation
Indices: 5571036--5571078 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
5571026 CCCTTTAACT
*
5571036 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTT TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5571079 GAAATAAGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:5574073 original size:48 final size:48
Alignment explanation
Indices: 5574007--5574104 Score: 133
Period size: 48 Copynumber: 2.0 Consensus size: 48
5573997 CTATGAAATT
* ** *
5574007 ATTAATTAATATAATATTCATCCCTAATGTGATTAATTTTAAATTATA
1 ATTAATTAATATAATATTCATCCATAACATGATTAATTTTAAATGATA
* **
5574055 ATTAATTAATATAGTATTCATTTATAACATGATTAATTTTAAATGATA
1 ATTAATTAATATAATATTCATCCATAACATGATTAATTTTAAATGATA
5574103 AT
1 AT
5574105 ACGTTACAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (48 bp):
ATTAATTAATATAATATTCATCCATAACATGATTAATTTTAAATGATA
Found at i:5576020 original size:15 final size:15
Alignment explanation
Indices: 5575997--5576042 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
5575987 TTTTAATAAA
* *
5575997 TTTTGATATATATAT
1 TTTTAATATAAATAT
5576012 TTTTAATATAAATAT
1 TTTTAATATAAATAT
5576027 TTTTAATA-AAA-AT
1 TTTTAATATAAATAT
5576040 TTT
1 TTT
5576043 GACATAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 5 0.17
14 3 0.10
15 21 0.72
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
TTTTAATATAAATAT
Found at i:5578552 original size:29 final size:29
Alignment explanation
Indices: 5578519--5578579 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
5578509 CTAAATCGAT
* * *
5578519 TTAATATACAAAAAAATTGAATCTACTTA
1 TTAATATACAAAAAAACTAAATCTACTGA
*
5578548 TTAATATATAAAAAAACTAAATCTACTGA
1 TTAATATACAAAAAAACTAAATCTACTGA
5578577 TTA
1 TTA
5578580 TTGGTATGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.52, C:0.10, G:0.03, T:0.34
Consensus pattern (29 bp):
TTAATATACAAAAAAACTAAATCTACTGA
Found at i:5580274 original size:17 final size:17
Alignment explanation
Indices: 5580249--5580286 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
5580239 ATATTATTTT
* *
5580249 TTTTTTCAATGTTCTTA
1 TTTTCTCAATGATCTTA
5580266 TTTTCTCAATGATCTTA
1 TTTTCTCAATGATCTTA
5580283 TTTT
1 TTTT
5580287 ATAAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.13, G:0.05, T:0.63
Consensus pattern (17 bp):
TTTTCTCAATGATCTTA
Found at i:5580298 original size:78 final size:75
Alignment explanation
Indices: 5580141--5580308 Score: 210
Period size: 78 Copynumber: 2.2 Consensus size: 75
5580131 CATATGAAAC
* * * * * *
5580141 AATGTAAATAGTAAGATATTCAAATATTATTCTTATTTTATTTGTTTTTTTCTCAATGTTTTTAT
1 AATGTAAATAATAAGATAATCAAATATTATTCTTATTTTATTTCTTATTTTCTCAATGATCTTAT
* *
5580206 TTTATGAAAC
66 TTTATAAAAA
* * *
5580216 AATGTAAATAATAGGATAATCAAATATTATTTTTTTTTTCAATGTTCTTATTTTCTCAATGATCT
1 AATGTAAATAATAAGATAATCAAATATTATTCTTATTTT--AT-TTCTTATTTTCTCAATGATCT
5580281 TATTTTATAAAAA
63 TATTTTATAAAAA
5580294 AATGTAAATAATAAG
1 AATGTAAATAATAAG
5580309 GTATTTGAAG
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
75 34 0.44
77 2 0.03
78 42 0.54
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.49
Consensus pattern (75 bp):
AATGTAAATAATAAGATAATCAAATATTATTCTTATTTTATTTCTTATTTTCTCAATGATCTTAT
TTTATAAAAA
Found at i:5580440 original size:92 final size:91
Alignment explanation
Indices: 5580249--5580440 Score: 244
Period size: 92 Copynumber: 2.1 Consensus size: 91
5580239 ATATTATTTT
* *
5580249 TTTTTTCAATGTTCTTATTTTCTCAATGATCTTATTTTATAAAAAAATGTAAATAATAAGGTATT
1 TTTTTTCAATGTTCTTATTTTCACAATGATCTTATTTTATAAAAAAATATAAATAATAAGGTATT
*
5580314 TGAAGGTTGTTCTTATTTTATTTGCC
66 TGAAGATTGTTCTTATTTTATTTGCC
** * * *
5580340 TTTGTTTCAATGTTCTTATTTTCACTTTGTTCTTATTTTATGAAATAATATAAATAAT-A-GTAT
1 TTT-TTTCAATGTTCTTATTTTCACAATGATCTTATTTTATAAAAAAATATAAATAATAAGGTAT
* *
5580403 ATTCGAATATTGTTCTTATTTTATTTGTC
65 -TT-GAAGATTGTTCTTATTTTATTTGCC
5580432 TTATTTTCA
1 TT-TTTTCA
5580441 TTCCTTATTT
Statistics
Matches: 87, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
90 4 0.05
91 6 0.07
92 76 0.87
93 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54
Consensus pattern (91 bp):
TTTTTTCAATGTTCTTATTTTCACAATGATCTTATTTTATAAAAAAATATAAATAATAAGGTATT
TGAAGATTGTTCTTATTTTATTTGCC
Found at i:5581943 original size:56 final size:53
Alignment explanation
Indices: 5581817--5582011 Score: 216
Period size: 59 Copynumber: 3.5 Consensus size: 53
5581807 TGCTTTTGCA
* *
5581817 TAAGAAAAATTGATACTTTCAATTTTTCCTTAAAATATTTTTTTTTTAATTT-TT
1 TAAGAAAAATTGATACTTTCAACTTTT-CTTAAAATA-TTTTTTTTAAATTTATT
*
5581871 TAA-AAAAATTGGTACTTTCAACTTTTCTTCAAAATATTTTTTTTAAATTTAATT
1 TAAGAAAAATTGATACTTTCAACTTTTCTT-AAAATATTTTTTTTAAATTT-ATT
*
5581925 TCAAGAAAAATTGATACTTTCAACTTTTCCTAAAA-ATATTTTTTTAAATCTTTTTATCT
1 T-AAGAAAAATTGATACTTTCAACTTTTCTTAAAATAT-TTTTTTTAAA----TTTAT-T
*
5581984 TAAAGGAAAATTGATACTTTCAACTTTT
1 T-AAGAAAAATTGATACTTTCAACTTTT
5582012 TCTAAATGCT
Statistics
Matches: 123, Mismatches: 7, Indels: 17
0.84 0.05 0.12
Matches are distributed among these distances:
52 16 0.13
53 27 0.22
54 8 0.07
55 16 0.13
56 24 0.20
58 2 0.02
59 30 0.24
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (53 bp):
TAAGAAAAATTGATACTTTCAACTTTTCTTAAAATATTTTTTTTAAATTTATT
Found at i:5582972 original size:3 final size:3
Alignment explanation
Indices: 5582964--5583081 Score: 118
Period size: 3 Copynumber: 38.7 Consensus size: 3
5582954 ATAAAGTCAA
5582964 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
5583012 AAT AAAT AA- AAA AATT AAT AGAT AAAT AA- AA- AAT AAT -AT ATT AAT
1 AAT -AAT AAT AAT AA-T AAT A-AT -AAT AAT AAT AAT AAT AAT AAT AAT
* *
5583057 AAAT AAT AAA AAT AAAT AAA AAT AA
1 -AAT AAT AAT AAT -AAT AAT AAT AA
5583082 AACTACAAAT
Statistics
Matches: 99, Mismatches: 7, Indels: 18
0.80 0.06 0.15
Matches are distributed among these distances:
2 8 0.08
3 75 0.76
4 15 0.15
5 1 0.01
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:5583021 original size:4 final size:4
Alignment explanation
Indices: 5583012--5583076 Score: 53
Period size: 4 Copynumber: 16.5 Consensus size: 4
5583002 TAATAATAAT
* * * * *
5583012 AATA AATA AAAA AATT AATA GATA AATA AA-A AAT- AATA TATT AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
*
5583058 AATA ATAAA AATA AATA AA
1 AATA A-ATA AATA AATA AA
5583077 AATAAAACTA
Statistics
Matches: 46, Mismatches: 12, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
3 6 0.13
4 37 0.80
5 3 0.07
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:5585190 original size:182 final size:183
Alignment explanation
Indices: 5584879--5585222 Score: 564
Period size: 182 Copynumber: 1.9 Consensus size: 183
5584869 AGTTGAAACA
* *
5584879 TACCAATTGCATCTTCTTTTTTATTGACAAACGAGCCATAATTGTTTATAAGAAGAATTTTTGTT
1 TACCAATTGCATCTTCTTTTTTATTGACAAACAAGCCATAACTGTTTATAAGAAGAATTTTTGTT
* * **
5584944 AATGTTAAAAACATGGGTTGAAAATAATAATGTGTATTTGGTAGATTGAGATCTAAGATATGTCC
66 AATGTTAAAAACATGGGTTGAAAATAATAATGTGCATTTAGTAGATCAAGATCTAAGATATGTCC
*
5585009 AACATAACACAAATAGCAAACAAAATTTGATTCATTTGCAAAATAAGCACTAT
131 AACAAAACACAAATAGCAAACAAAATTTGATTCATTTGCAAAATAAGCACTAT
* *
5585062 TACCAATTGCATCTTTTTTTTTATTGACAAA-AAGCCATAACTGTTTATAAGAAGAATTTTTTTT
1 TACCAATTGCATCTTCTTTTTTATTGACAAACAAGCCATAACTGTTTATAAGAAGAATTTTTGTT
* * * *
5585126 AATGTTGAAAACATGTGTTGAAAATAATAATGTGCATTTAGTAGATCAAGATTTAAGCTATGTCC
66 AATGTTAAAAACATGGGTTGAAAATAATAATGTGCATTTAGTAGATCAAGATCTAAGATATGTCC
5585191 AACAAAACACAAATAGCAAACAAAATTTGATT
131 AACAAAACACAAATAGCAAACAAAATTTGATT
5585223 AGATTAAGAG
Statistics
Matches: 148, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
182 118 0.80
183 30 0.20
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (183 bp):
TACCAATTGCATCTTCTTTTTTATTGACAAACAAGCCATAACTGTTTATAAGAAGAATTTTTGTT
AATGTTAAAAACATGGGTTGAAAATAATAATGTGCATTTAGTAGATCAAGATCTAAGATATGTCC
AACAAAACACAAATAGCAAACAAAATTTGATTCATTTGCAAAATAAGCACTAT
Found at i:5586060 original size:266 final size:268
Alignment explanation
Indices: 5585667--5586194 Score: 681
Period size: 267 Copynumber: 2.0 Consensus size: 268
5585657 AATTACTATA
* * * * * *
5585667 TTTATTAATGACTATGTTTCTATAACAAGAAATGTAGTTATTGGTATTGAGAAAAATTTATATTT
1 TTTATCAATGACTACGTTTCCATAACAAGAAATATAGTTATTGATATTGAAAAAAATTTATATTT
* ** *
5585732 ATTAAACACTATGTTTTTTACATAAAAAATGTAGTTAAAAATATCTTAAATATTCCATTATAAAT
66 ATCAAACACTACATTTTTTACATAAAAAACGTAGTTAAAAATATCTTAAATATTCCATTAT-AAT
* * * * *
5585797 ATTATACCTATTACTATGTTAT-CATATTAAGAAATGTCATT-G-ATTAAAAATATCAAATTTAT
130 ATTATACCTATTACTATGTT-TCCAAACTAAGAAACGGCATTGGTAATAAAAATATCAAATTTAT
* * * * * *
5585859 TTTGTTATTTTTTTAATTGATTAATTATGTTTCATATGTAAATAACATAGTGCTTGTAAAAATAA
194 TTTGTTATTATTTTAATTGATCAACTATGTTTCATATGTAAAAAACATAGTACTTATAAAAATAA
5585924 AAAATTATGG
259 AAAATTATGG
5585934 TTTATCAATGACTACGTTTCCATAACAAGAAATATAGTTATTGATATAT-AAAAAAATTT-TATT
1 TTTATCAATGACTACGTTTCCATAACAAGAAATATAGTTATTGATAT-TGAAAAAAATTTATATT
* * * * *
5585997 TATCAAATATTACATTTTTTACATAAAAAACGTAGTTAAAAGTAT-TGTCAATATTCTATTATAA
65 TATCAAACACTACATTTTTTACATAAAAAACGTAGTTAAAAATATCT-TAAATATTCCATTATAA
* * * *
5586061 TGTTATATCTATTACTATGTTTCCAAACTAAGAAACGGCATTGGTAATGAAAATATCTAATTTAT
129 TATTATACCTATTACTATGTTTCCAAACTAAGAAACGGCATTGGTAATAAAAATATCAAATTTAT
* * *
5586126 TTTGTTATTATTTTAATTGATCAACTATGTTTCATATGTAAAAAATATAGTATTTATGAAAATAA
194 TTTGTTATTATTTTAATTGATCAACTATGTTTCATATGTAAAAAACATAGTACTTATAAAAATAA
5586191 AAAA
259 AAAA
5586195 AATTCAAAAT
Statistics
Matches: 223, Mismatches: 33, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
264 1 0.00
265 37 0.17
266 56 0.25
267 128 0.57
268 1 0.00
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (268 bp):
TTTATCAATGACTACGTTTCCATAACAAGAAATATAGTTATTGATATTGAAAAAAATTTATATTT
ATCAAACACTACATTTTTTACATAAAAAACGTAGTTAAAAATATCTTAAATATTCCATTATAATA
TTATACCTATTACTATGTTTCCAAACTAAGAAACGGCATTGGTAATAAAAATATCAAATTTATTT
TGTTATTATTTTAATTGATCAACTATGTTTCATATGTAAAAAACATAGTACTTATAAAAATAAAA
AATTATGG
Found at i:5588786 original size:2 final size:2
Alignment explanation
Indices: 5588779--5588815 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5588769 AGAGAAGTGA
5588779 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5588816 TTGGTGCTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5592422 original size:15 final size:15
Alignment explanation
Indices: 5592391--5592443 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
5592381 TTGATAATAT
*
5592391 AATAAAA-AATATAA
1 AATAAAATAATTTAA
5592405 AATAAAATAATTTAA
1 AATAAAATAATTTAA
*
5592420 AATTATAAT-ATTTAA
1 AA-TAAAATAATTTAA
*
5592435 AATATAATA
1 AATAAAATA
5592444 TGATAACACG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
14 13 0.38
15 16 0.47
16 5 0.15
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AATAAAATAATTTAA
Found at i:5594821 original size:32 final size:33
Alignment explanation
Indices: 5594776--5594859 Score: 100
Period size: 32 Copynumber: 2.5 Consensus size: 33
5594766 AAAGTGGACT
* **
5594776 TTATCATATTATAAGTAATAAAGGAAATAGATC-
1 TTATCCTATTATAAAAAATAAAGGAAATAGA-CG
*
5594809 TTATCC-ATTATAAAAAATAAAGTAAATAGACG
1 TTATCCTATTATAAAAAATAAAGGAAATAGACG
5594841 TTATCCTATTATAATAAAA
1 TTATCCTATTATAA-AAAA
5594860 ATATTTTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
31 1 0.02
32 27 0.61
33 12 0.27
34 4 0.09
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.33
Consensus pattern (33 bp):
TTATCCTATTATAAAAAATAAAGGAAATAGACG
Found at i:5595728 original size:11 final size:10
Alignment explanation
Indices: 5595714--5595738 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5595704 TAAAAGGTTT
5595714 AAAAAAAAAG
1 AAAAAAAAAG
5595724 AAAAAAAAAG
1 AAAAAAAAAG
5595734 AAAAA
1 AAAAA
5595739 TTAACTGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:5596164 original size:22 final size:22
Alignment explanation
Indices: 5596138--5596194 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
5596128 ATACCTCAAT
5596138 TAAATCAATTATAATTTA-ATAA
1 TAAATCAATTATAATTTAGA-AA
5596160 TAAAT-AATTGATAATTTAGAAA
1 TAAATCAATT-ATAATTTAGAAA
*
5596182 TTAATC-ATTATAA
1 TAAATCAATTATAA
5596195 ACTTAAAAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 8 0.26
22 22 0.71
23 1 0.03
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (22 bp):
TAAATCAATTATAATTTAGAAA
Found at i:5596390 original size:3 final size:3
Alignment explanation
Indices: 5596382--5596423 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
5596372 TTATAAATGC
5596382 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5596424 TAGTATTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5596508 original size:22 final size:22
Alignment explanation
Indices: 5596430--5596544 Score: 72
Period size: 22 Copynumber: 5.2 Consensus size: 22
5596420 AATATAGTAT
*
5596430 TAAATCAAGTATAACTTAATAAA
1 TAAATCAAGGATAACTTAAT-AA
* * * *
5596453 AAAAT-AAGTGATAATTTAGT-T
1 TAAATCAAG-GATAACTTAATAA
* ** *
5596474 TTAATCATTGATAATTTAATAA
1 TAAATCAAGGATAACTTAATAA
* **
5596496 TAAATCAAGGATAACTTAGTGG
1 TAAATCAAGGATAACTTAATAA
* *
5596518 TAAATTAATGATAACTTAATAA
1 TAAATCAAGGATAACTTAATAA
5596540 TAAAT
1 TAAAT
5596545 TGTTTCGGTT
Statistics
Matches: 66, Mismatches: 23, Indels: 7
0.69 0.24 0.07
Matches are distributed among these distances:
21 13 0.20
22 41 0.62
23 12 0.18
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.36
Consensus pattern (22 bp):
TAAATCAAGGATAACTTAATAA
Found at i:5596545 original size:22 final size:22
Alignment explanation
Indices: 5596482--5596545 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
5596472 TTTTAATCAT
* *
5596482 TGATAATTTAATAATAAATCAA
1 TGATAACTTAATAATAAATTAA
* * **
5596504 GGATAACTTAGTGGTAAATTAA
1 TGATAACTTAATAATAAATTAA
5596526 TGATAACTTAATAATAAATT
1 TGATAACTTAATAATAAATT
5596546 GTTTCGGTTT
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.36
Consensus pattern (22 bp):
TGATAACTTAATAATAAATTAA
Found at i:5596602 original size:22 final size:22
Alignment explanation
Indices: 5596574--5596632 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
5596564 TTAAATGATA
*
5596574 AATTTAGTAGTAAAT-TATAAAT
1 AATTTAGTAGTAAATCAAT-AAT
* *
5596596 AATTTAGTTGTAAATCAATGAT
1 AATTTAGTAGTAAATCAATAAT
*
5596618 AACTTAGTAGTAAAT
1 AATTTAGTAGTAAAT
5596633 AATTTATGAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 29 0.94
23 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.12, T:0.39
Consensus pattern (22 bp):
AATTTAGTAGTAAATCAATAAT
Found at i:5596758 original size:22 final size:22
Alignment explanation
Indices: 5596662--5596742 Score: 85
Period size: 21 Copynumber: 3.8 Consensus size: 22
5596652 TATCATTGAA
* * *
5596662 AACTTAAAAATAAATTA-ATAT
1 AACTTAATAGTAAATTATAAAT
* **
5596683 AACTTAGTAGTAAA-TATCGAT
1 AACTTAATAGTAAATTATAAAT
*
5596704 AGCTTAATAGTAAATTATAAAT
1 AACTTAATAGTAAATTATAAAT
5596726 AACTTAATAGTAAATTA
1 AACTTAATAGTAAATTA
5596743 GTAATAATTT
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
20 2 0.04
21 25 0.52
22 21 0.44
ACGTcount: A:0.52, C:0.06, G:0.07, T:0.35
Consensus pattern (22 bp):
AACTTAATAGTAAATTATAAAT
Found at i:5596859 original size:22 final size:22
Alignment explanation
Indices: 5596822--5596881 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
5596812 AAAACTTATT
* *
5596822 AGTAAATCAATGATAACACAAC
1 AGTAAATCATTAATAACACAAC
* * *
5596844 TGTAAATGCA-TAATAATATAAC
1 AGTAAAT-CATTAATAACACAAC
5596866 AGTAAATCATTAATAA
1 AGTAAATCATTAATAA
5596882 TTTAGTAGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.53, C:0.12, G:0.08, T:0.27
Consensus pattern (22 bp):
AGTAAATCATTAATAACACAAC
Found at i:5596882 original size:22 final size:22
Alignment explanation
Indices: 5596845--5596940 Score: 95
Period size: 22 Copynumber: 4.4 Consensus size: 22
5596835 TAACACAACT
*
5596845 GTAAATGCA-TAATAATATAACA
1 GTAAAT-CATTAATAATTTAACA
**
5596867 GTAAATCATTAATAATTTAGTA
1 GTAAATCATTAATAATTTAACA
* * * **
5596889 GTATATTATTGATAATTTATTA
1 GTAAATCATTAATAATTTAACA
*
5596911 GTAAATCACTAATAATTTAACA
1 GTAAATCATTAATAATTTAACA
5596933 GTAAATCA
1 GTAAATCA
5596941 CTTATAACTG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
21 2 0.03
22 58 0.97
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.38
Consensus pattern (22 bp):
GTAAATCATTAATAATTTAACA
Found at i:5597038 original size:11 final size:11
Alignment explanation
Indices: 5597018--5597073 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
5597008 CATCATTAAT
5597018 TTAGTAATAAA
1 TTAGTAATAAA
* *
5597029 TTAGTGATAATT
1 TTAGTAATAA-A
5597041 TTA-TAATAAA
1 TTAGTAATAAA
* *
5597051 TTATTAATAAC
1 TTAGTAATAAA
*
5597062 TTAATAATAAA
1 TTAGTAATAAA
5597073 T
1 T
5597074 CATTATTAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
10 3 0.08
11 30 0.83
12 3 0.08
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (11 bp):
TTAGTAATAAA
Found at i:5597039 original size:22 final size:21
Alignment explanation
Indices: 5597014--5597073 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
5597004 AAATCATCAT
*
5597014 TAATTTAGTAATAAATTAGTGA
1 TAATTTA-TAATAAATTAGTAA
*
5597036 TAATTTTATAATAAATTATTAA
1 TAA-TTTATAATAAATTAGTAA
*
5597058 TAACTTAATAATAAAT
1 TAA-TTTATAATAAAT
5597074 CATTATTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (21 bp):
TAATTTATAATAAATTAGTAA
Found at i:5597070 original size:44 final size:43
Alignment explanation
Indices: 5596989--5597189 Score: 120
Period size: 44 Copynumber: 4.7 Consensus size: 43
5596979 AGTTAATAAT
* * * * * *
5596989 TGATAAATTTATAGTAAATCATCATTAATTTAGTAATAAATTA
1 TGATAATTTTATAATAAATCATTAATAACTTAATAATAAATTA
* *
5597032 GTGATAATTTTATAATAAATTATTAATAACTTAATAATAAATCA
1 -TGATAATTTTATAATAAATCATTAATAACTTAATAATAAATTA
* * * * * ** *
5597076 TTATTAATTTT-T-TTAGATCATCACTAA-TTTGTAGTAAATTA
1 TGA-TAATTTTATAATAAATCATTAATAACTTAATAATAAATTA
* * * ** *
5597117 TTCATAACTTAAGGATAAATCATTCATAACTTAATAATAAATTAA
1 -TGATAATTTTATAATAAATCATTAATAACTTAATAATAAATT-A
* * *
5597162 TGATAATTTAATAATAAATTATTGATAA
1 TGATAATTTTATAATAAATCATTAATAA
5597190 TATAGTGGTA
Statistics
Matches: 115, Mismatches: 36, Indels: 12
0.71 0.22 0.07
Matches are distributed among these distances:
41 15 0.13
42 12 0.10
43 13 0.11
44 74 0.64
45 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (43 bp):
TGATAATTTTATAATAAATCATTAATAACTTAATAATAAATTA
Found at i:5597078 original size:22 final size:22
Alignment explanation
Indices: 5597043--5597261 Score: 88
Period size: 22 Copynumber: 10.1 Consensus size: 22
5597033 TGATAATTTT
*
5597043 ATAATAAATTATTAATAACTTA
1 ATAATAAATCATTAATAACTTA
*
5597065 ATAATAAATCATTATTAA-TT-
1 ATAATAAATCATTAATAACTTA
* ** * * * *
5597085 TTTTTAGATCATCACTAA-TTT
1 ATAATAAATCATTAATAACTTA
* * * *
5597106 GTAGTAAATTATTCATAACTTA
1 ATAATAAATCATTAATAACTTA
** *
5597128 AGGATAAATCATTCATAACTTA
1 ATAATAAATCATTAATAACTTA
* * * *
5597150 ATAATAAATTAATGATAATTTA
1 ATAATAAATCATTAATAACTTA
* *
5597172 ATAATAAATTATTGATAA-TATA
1 ATAATAAATCATTAATAACT-TA
* ** ** * *
5597194 GTGGTAAGCCCTTGATAACTTA
1 ATAATAAATCATTAATAACTTA
* *
5597216 ATAGTAAATCATTTATAA-TATA
1 ATAATAAATCATTAATAACT-TA
* *
5597238 ATAGTAAATCAATAATAACTTA
1 ATAATAAATCATTAATAACTTA
5597260 AT
1 AT
5597262 TGTCAATCTA
Statistics
Matches: 147, Mismatches: 44, Indels: 12
0.72 0.22 0.06
Matches are distributed among these distances:
20 14 0.10
21 14 0.10
22 117 0.80
23 2 0.01
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (22 bp):
ATAATAAATCATTAATAACTTA
Found at i:5597156 original size:11 final size:11
Alignment explanation
Indices: 5597142--5597182 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
5597132 TAAATCATTC
*
5597142 ATAACTTAATA
1 ATAAATTAATA
*
5597153 ATAAATTAATG
1 ATAAATTAATA
*
5597164 ATAATTTAATA
1 ATAAATTAATA
5597175 ATAAATTA
1 ATAAATTA
5597183 TTGATAATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (11 bp):
ATAAATTAATA
Found at i:5597189 original size:11 final size:11
Alignment explanation
Indices: 5597110--5597189 Score: 52
Period size: 11 Copynumber: 7.3 Consensus size: 11
5597100 TAATTTGTAG
* *
5597110 TAAATTATTCA
1 TAAATTAATGA
* *
5597121 TAACTTAAGGA
1 TAAATTAATGA
* * *
5597132 TAAATCATTCA
1 TAAATTAATGA
* *
5597143 TAACTTAATAA
1 TAAATTAATGA
5597154 TAAATTAATGA
1 TAAATTAATGA
* *
5597165 TAATTTAATAA
1 TAAATTAATGA
*
5597176 TAAATTATTGA
1 TAAATTAATGA
5597187 TAA
1 TAA
5597190 TATAGTGGTA
Statistics
Matches: 49, Mismatches: 20, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
11 49 1.00
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.39
Consensus pattern (11 bp):
TAAATTAATGA
Found at i:5597256 original size:44 final size:44
Alignment explanation
Indices: 5597120--5597261 Score: 124
Period size: 44 Copynumber: 3.2 Consensus size: 44
5597110 TAAATTATTC
** * *
5597120 ATAACTTAAGGATAAATCATTCATAACT-TAATAATAAATTAATG
1 ATAACTTAATAATAAATCATTCATAA-TATAATAGTAAATCAATG
* * * * * ** **
5597164 ATAATTTAATAATAAATTATTGATAATATAGTGGTAAGCCCTTG
1 ATAACTTAATAATAAATCATTCATAATATAATAGTAAATCAATG
* * *
5597208 ATAACTTAATAGTAAATCATTTATAATATAATAGTAAATCAATA
1 ATAACTTAATAATAAATCATTCATAATATAATAGTAAATCAATG
5597252 ATAACTTAAT
1 ATAACTTAAT
5597262 TGTCAATCTA
Statistics
Matches: 73, Mismatches: 24, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
43 1 0.01
44 72 0.99
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.37
Consensus pattern (44 bp):
ATAACTTAATAATAAATCATTCATAATATAATAGTAAATCAATG
Found at i:5597269 original size:22 final size:22
Alignment explanation
Indices: 5597208--5597276 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
5597198 TAAGCCCTTG
* *
5597208 ATAACTTAATAGTAAATCATTT
1 ATAACTTAATAGTAAATCAATA
5597230 ATAA-TATAATAGTAAATCAATA
1 ATAACT-TAATAGTAAATCAATA
* * *
5597252 ATAACTTAATTGTCAATCTATA
1 ATAACTTAATAGTAAATCAATA
5597274 ATA
1 ATA
5597277 GCTTTGTTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
21 1 0.03
22 38 0.95
23 1 0.03
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (22 bp):
ATAACTTAATAGTAAATCAATA
Found at i:5597843 original size:21 final size:21
Alignment explanation
Indices: 5597815--5597908 Score: 93
Period size: 21 Copynumber: 4.5 Consensus size: 21
5597805 AGTAAGTATG
5597815 ATATAATTTTGGTAGCCTTTA
1 ATATAATTTTGGTAGCCTTTA
* *
5597836 ATACAATTTTGGTAG-CTTATG
1 ATATAATTTTGGTAGCCTT-TA
* * *
5597857 ATATAATTTTGATAACCATTA
1 ATATAATTTTGGTAGCCTTTA
* *
5597878 ATATAATTTTGGTA-ACTTTGG
1 ATATAATTTTGGTAGCCTTT-A
5597899 ATATAATTTT
1 ATATAATTTT
5597909 AGTAAGTTTT
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
20 6 0.10
21 51 0.86
22 2 0.03
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (21 bp):
ATATAATTTTGGTAGCCTTTA
Found at i:5597865 original size:42 final size:42
Alignment explanation
Indices: 5597811--5597908 Score: 135
Period size: 42 Copynumber: 2.3 Consensus size: 42
5597801 TTTTAGTAAG
* * * *
5597811 TATGATATAATTTTGGTAGCCTTTAATACAATTTTGGTAGCT
1 TATGATATAATTTTGATAACCATTAATACAATTTTGGTAACT
*
5597853 TATGATATAATTTTGATAACCATTAATATAATTTTGGTAACT
1 TATGATATAATTTTGATAACCATTAATACAATTTTGGTAACT
5597895 T-TGGATATAATTTT
1 TAT-GATATAATTTT
5597909 AGTAAGTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
41 1 0.02
42 49 0.98
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (42 bp):
TATGATATAATTTTGATAACCATTAATACAATTTTGGTAACT
Found at i:5597877 original size:104 final size:104
Alignment explanation
Indices: 5597716--5597938 Score: 229
Period size: 104 Copynumber: 2.1 Consensus size: 104
5597706 TTTTAATACA
* * * *
5597716 AATTTTGTAACCTTTAACACTATTTTGGTAACTTATTATATGACTTAGGTACTCATTAAGACAAA
1 AATTTTGTAACCTTTAACACAATTTTGGTAACTTATGATATAACTTAGATACTCATTAAGACAAA
* * *
5597781 TTTGGTCATTTTTAATA-AAGTTTTAGTAAG-TATGATAT
66 TTTGGTAACTTTGAATATAA-TTTTAGTAAGTTATGATAT
* * * * * * *
5597819 AATTTTGGTAGCCTTTAATACAATTTTGGTAGCTTATGATATAATTTTGATAAC-CATTAATATA
1 AATTTT-GTAACCTTTAACACAATTTTGGTAACTTATGATATAACTTAGAT-ACTCATTAAGACA
* * *
5597883 ATTTTGGTAACTTTGGATATAATTTTAGTAAGTTTTGATAT
64 AATTTGGTAACTTTGAATATAATTTTAGTAAGTTATGATAT
5597924 AA-TTTGATAACCTTT
1 AATTTTG-TAACCTTT
5597939 TATATATTAT
Statistics
Matches: 97, Mismatches: 18, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
103 7 0.07
104 77 0.79
105 13 0.13
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (104 bp):
AATTTTGTAACCTTTAACACAATTTTGGTAACTTATGATATAACTTAGATACTCATTAAGACAAA
TTTGGTAACTTTGAATATAATTTTAGTAAGTTATGATAT
Found at i:5597887 original size:63 final size:62
Alignment explanation
Indices: 5597815--5597944 Score: 156
Period size: 63 Copynumber: 2.1 Consensus size: 62
5597805 AGTAAGTATG
* *
5597815 ATATAATTTTGGTAGCCTTT-AATACAATTTTGGT-AGCTTATGATATAATTTTGATAACCATTA
1 ATATAATTTTGGTA-ACTTTGAATACAATTTTAGTAAG-TTATGATATAA-TTTGATAACCATTA
* * * * *
5597878 ATATAATTTTGGTAACTTTGGATATAATTTTAGTAAGTTTTGATATAATTTGATAACCTTTT
1 ATATAATTTTGGTAACTTTGAATACAATTTTAGTAAGTTATGATATAATTTGATAACCATTA
5597940 ATATA
1 ATATA
5597945 TTATGATGAC
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
62 21 0.36
63 35 0.60
64 2 0.03
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.47
Consensus pattern (62 bp):
ATATAATTTTGGTAACTTTGAATACAATTTTAGTAAGTTATGATATAATTTGATAACCATTA
Found at i:5597913 original size:21 final size:21
Alignment explanation
Indices: 5597878--5597928 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
5597868 ATAACCATTA
*
5597878 ATATAATTTTGGTAACTTTGG
1 ATATAATTTTAGTAACTTTGG
* *
5597899 ATATAATTTTAGTAAGTTTTG
1 ATATAATTTTAGTAACTTTGG
5597920 ATATAATTT
1 ATATAATTT
5597929 GATAACCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (21 bp):
ATATAATTTTAGTAACTTTGG
Found at i:5597951 original size:20 final size:21
Alignment explanation
Indices: 5597855--5597975 Score: 74
Period size: 21 Copynumber: 5.8 Consensus size: 21
5597845 TGGTAGCTTA
*
5597855 TGATATAATTTTGATAACC-AT
1 TGATATAA-TTTGATAACCTTT
* *
5597876 TAATATAATTTTGGTAA-CTTT
1 TGATATAA-TTTGATAACCTTT
* * *
5597897 GGATATAATTTTAGTAA-GTTT
1 TGATATAATTTGA-TAACCTTT
5597918 TGATATAATTTGATAACCTTT
1 TGATATAATTTGATAACCTTT
*
5597939 T-ATAT-ATTATGATGACC-TT
1 TGATATAATT-TGATAACCTTT
* *
5597958 TGTTAGAAATTTGATAAC
1 TGATA-TAATTTGATAAC
5597976 AGTTAATAAA
Statistics
Matches: 78, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
19 6 0.08
20 20 0.26
21 49 0.63
22 3 0.04
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (21 bp):
TGATATAATTTGATAACCTTT
Found at i:5598282 original size:21 final size:22
Alignment explanation
Indices: 5598232--5598327 Score: 67
Period size: 21 Copynumber: 4.5 Consensus size: 22
5598222 GTAAGTTTGC
* *
5598232 TATAATTTTGGTAACCTTTA-A
1 TATAATTTTGATAATCTTTAGA
* * *
5598253 TACACTTTTGGTAATC-TTAGA
1 TATAATTTTGATAATCTTTAGA
* *
5598274 TATAATTTTAATAAGT-GTT-GA
1 TATAATTTTGATAA-TCTTTAGA
* *
5598295 TATAATCTTGATAA-CTTTTGA
1 TATAATTTTGATAATCTTTAGA
5598316 TATAATTTTGAT
1 TATAATTTTGAT
5598328 TTTGATAACC
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
20 5 0.08
21 51 0.86
22 3 0.05
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.48
Consensus pattern (22 bp):
TATAATTTTGATAATCTTTAGA
Found at i:5598315 original size:101 final size:101
Alignment explanation
Indices: 5598131--5598317 Score: 218
Period size: 101 Copynumber: 1.9 Consensus size: 101
5598121 TAATCTTTAA
* * **
5598131 TATAATTTTGGTAACCTTTATTACTATTTTGATAACCTATAATATAATTAGGATAACTATTTTTA
1 TATAATTTTGGTAACCTTTAATACTATTTTGATAACCTATAATATAATTAGAATAACTATTGATA
*
5598196 TAATTTTGGAAACATTTGATAAAATAGTAAGTTTGC
66 TAATCTTGGAAACATTTGATAAAATAGTAAGTTTGC
* * ** * *
5598232 TATAATTTTGGTAACCTTTAATAC-ACTTTTGGTAATCT-TAGATATAATTTTAATAAGTGTTGA
1 TATAATTTTGGTAACCTTTAATACTA-TTTTGATAACCTATA-ATATAATTAGAATAACTATTGA
*
5598295 TATAATCTT-GATAACTTTTGATA
64 TATAATCTTGGA-AACATTTGATA
5598318 TAATTTTGAT
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
100 5 0.07
101 66 0.93
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.45
Consensus pattern (101 bp):
TATAATTTTGGTAACCTTTAATACTATTTTGATAACCTATAATATAATTAGAATAACTATTGATA
TAATCTTGGAAACATTTGATAAAATAGTAAGTTTGC
Found at i:5598317 original size:10 final size:11
Alignment explanation
Indices: 5598272--5598327 Score: 55
Period size: 11 Copynumber: 5.3 Consensus size: 11
5598262 GGTAATCTTA
5598272 GATATAATTTT
1 GATATAATTTT
*
5598283 -A-ATAAGTGTT
1 GATATAA-TTTT
*
5598293 GATATAATCTT
1 GATATAATTTT
*
5598304 GATA-ACTTTT
1 GATATAATTTT
5598314 GATATAATTTT
1 GATATAATTTT
5598325 GAT
1 GAT
5598328 TTTGATAACC
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
9 4 0.11
10 12 0.33
11 16 0.44
12 4 0.11
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.48
Consensus pattern (11 bp):
GATATAATTTT
Found at i:5598519 original size:43 final size:42
Alignment explanation
Indices: 5598465--5598564 Score: 121
Period size: 43 Copynumber: 2.4 Consensus size: 42
5598455 GTAACTATTA
*
5598465 ATATAATTTTGGTAACTTTTAATAAAACATT-GATAACTTATTG
1 ATATAATTTTGGTAACCTTTAATAAAA-ATTAGATAACTTA-TG
* * * *
5598508 ATGTAATTTTGGTAACCTTTCATATAATTTAGATAACTTATG
1 ATATAATTTTGGTAACCTTTAATAAAAATTAGATAACTTATG
*
5598550 ATATACTTTTGGTAA
1 ATATAATTTTGGTAA
5598565 TCATTGATAC
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
42 17 0.35
43 32 0.65
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (42 bp):
ATATAATTTTGGTAACCTTTAATAAAAATTAGATAACTTATG
Found at i:5598535 original size:21 final size:21
Alignment explanation
Indices: 5598442--5598637 Score: 99
Period size: 21 Copynumber: 9.3 Consensus size: 21
5598432 TTTGGTAACA
* *
5598442 TGATATAGTTTTAGTAA-CTAT
1 TGATATAATTTTGGTAACCT-T
* *
5598463 TAATATAATTTTGGTAACTTT
1 TGATATAATTTTGGTAACCTT
* * ** * *
5598484 TAATAAAACATTGATAACTTAT
1 TGATATAATTTTGGTAACCT-T
*
5598506 TGATGTAATTTTGGTAACCTT
1 TGATATAATTTTGGTAACCTT
* * *
5598527 TCATATAATTTAGATAA-CTT
1 TGATATAATTTTGGTAACCTT
* * *
5598547 ATGATATACTTTTGGTAATCAT
1 -TGATATAATTTTGGTAACCTT
* * *
5598569 TGATACAATTTTGGTAGCATT
1 TGATATAATTTTGGTAACCTT
* * * **
5598590 GGGTATAGTTTTGAAAACCTT
1 TGATATAATTTTGGTAACCTT
* **
5598611 TGATATAATTTTGATAAATTT
1 TGATATAATTTTGGTAACCTT
5598632 TGATAT
1 TGATAT
5598638 TGTTTTTATT
Statistics
Matches: 127, Mismatches: 44, Indels: 8
0.71 0.25 0.04
Matches are distributed among these distances:
20 3 0.02
21 107 0.84
22 17 0.13
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.45
Consensus pattern (21 bp):
TGATATAATTTTGGTAACCTT
Found at i:5598579 original size:42 final size:43
Alignment explanation
Indices: 5598451--5598579 Score: 113
Period size: 43 Copynumber: 3.1 Consensus size: 43
5598441 ATGATATAGT
* ** * *
5598451 TTTAG-TAAC-TATTAATATAATTTTGGTAACTTTTAATAAAA
1 TTTAGATAACTTATTGATATAATTTTGGTAACCATTCATACAA
* * * *
5598492 CATT-GATAACTTATTGATGTAATTTTGGTAACCTTTCATATAA
1 -TTTAGATAACTTATTGATATAATTTTGGTAACCATTCATACAA
* * *
5598535 TTTAGATAACTTA-TGATATACTTTTGGTAATCATTGATACAA
1 TTTAGATAACTTATTGATATAATTTTGGTAACCATTCATACAA
5598577 TTT
1 TTT
5598580 TGGTAGCATT
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
41 1 0.01
42 34 0.48
43 36 0.51
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.46
Consensus pattern (43 bp):
TTTAGATAACTTATTGATATAATTTTGGTAACCATTCATACAA
Found at i:5598630 original size:10 final size:11
Alignment explanation
Indices: 5598609--5598637 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
5598599 TTTGAAAACC
5598609 TTTGATATAAT
1 TTTGATATAAT
5598620 TTTGATA-AAT
1 TTTGATATAAT
5598630 TTTGATAT
1 TTTGATAT
5598638 TGTTTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (11 bp):
TTTGATATAAT
Found at i:5598774 original size:19 final size:19
Alignment explanation
Indices: 5598750--5598790 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5598740 AAGAAATCGT
5598750 TTTGAT-ATCTTGTATATAA
1 TTTGATAAT-TTGTATATAA
*
5598769 TTTGATAATTTTTATATAA
1 TTTGATAATTTGTATATAA
5598788 TTT
1 TTT
5598791 TGATTTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (19 bp):
TTTGATAATTTGTATATAA
Found at i:5598811 original size:48 final size:48
Alignment explanation
Indices: 5598763--5598876 Score: 160
Period size: 47 Copynumber: 2.4 Consensus size: 48
5598753 GATATCTTGT
* * *
5598763 ATATAATTTGATAA-TTTTTATATAATTTTGATTTTGATAAACTTTTG
1 ATATAATTTGATAACCTTTGATATAATTTTGATTTTGATAAAATTTTG
*
5598810 -TATAAGTTGATAACCTTTGATATAATTTTGATTTTGATAAAATTTTG
1 ATATAATTTGATAACCTTTGATATAATTTTGATTTTGATAAAATTTTG
* *
5598857 ATATAATCTGATACCCTTTG
1 ATATAATTTGATAACCTTTG
5598877 TTAAAAGTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
46 12 0.21
47 30 0.52
48 16 0.28
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (48 bp):
ATATAATTTGATAACCTTTGATATAATTTTGATTTTGATAAAATTTTG
Found at i:5598833 original size:20 final size:20
Alignment explanation
Indices: 5598796--5598834 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5598786 AATTTTGATT
*
5598796 TTGATAAACTTTTGTATAAG
1 TTGATAAACCTTTGTATAAG
5598816 TTGAT-AACCTTTGATATAA
1 TTGATAAACCTTTG-TATAA
5598835 TTTTGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.44
Consensus pattern (20 bp):
TTGATAAACCTTTGTATAAG
Found at i:5598847 original size:17 final size:17
Alignment explanation
Indices: 5598825--5598858 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5598815 GTTGATAACC
*
5598825 TTTGATATAATTTTGAT
1 TTTGATAAAATTTTGAT
5598842 TTTGATAAAATTTTGAT
1 TTTGATAAAATTTTGAT
5598859 ATAATCTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (17 bp):
TTTGATAAAATTTTGAT
Found at i:5598888 original size:48 final size:47
Alignment explanation
Indices: 5598789--5598907 Score: 132
Period size: 48 Copynumber: 2.4 Consensus size: 47
5598779 TTTATATAAT
* * *
5598789 TTTGATTTTGATAAACTTTTGTATAAGTTGATAACCTTTGATATAAT
1 TTTGATTTTGATAAAATTTTGTATAAGTTGATAACCTTTGATAAAAG
* *
5598836 TTTGATTTTGATAAAATTTTGATATAA-TCTGATACCCTTTGTTAAAAG
1 TTTGATTTTGATAAAATTTTG-TATAAGT-TGATAACCTTTGATAAAAG
5598884 TTTGATAACCTTTGATAAAATTTT
1 TTTGAT----TTTGATAAAATTTT
5598908 AGTAATCTTA
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
47 21 0.34
48 26 0.43
52 14 0.23
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.48
Consensus pattern (47 bp):
TTTGATTTTGATAAAATTTTGTATAAGTTGATAACCTTTGATAAAAG
Found at i:5599752 original size:20 final size:20
Alignment explanation
Indices: 5599691--5599757 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
5599681 GTCTTTGACA
*
5599691 AAATTTTGTTAACTTATTAAT
1 AAATTTTGGTAACTTA-TAAT
* * *
5599712 ATAAATTTGGTAAATTTTAAT
1 A-AATTTTGGTAACTTATAAT
5599733 AAATTTTGGTAACTTATAAT
1 AAATTTTGGTAACTTATAAT
*
5599753 TAATT
1 AAATT
5599758 AGTATTACGT
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
20 20 0.54
21 6 0.16
22 11 0.30
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.49
Consensus pattern (20 bp):
AAATTTTGGTAACTTATAAT
Found at i:5600300 original size:17 final size:17
Alignment explanation
Indices: 5600278--5600310 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5600268 AAGAGTCAAT
5600278 ATAGTAATAAATCAGTG
1 ATAGTAATAAATCAGTG
5600295 ATAGTAATAAATCAGT
1 ATAGTAATAAATCAGT
5600311 ATTAAATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.30
Consensus pattern (17 bp):
ATAGTAATAAATCAGTG
Found at i:5600446 original size:33 final size:32
Alignment explanation
Indices: 5600404--5600500 Score: 79
Period size: 33 Copynumber: 2.9 Consensus size: 32
5600394 ATAACATAAA
* *
5600404 TTAAGTTAGTATTAATTTAATAGTAAATTATCG
1 TTAAATTAGTA-TAATTTAATAGTAAATTATAG
* * * * *
5600437 TTAATTTAGTAGTAAATTATTAATAATTTAATAG
1 TTAAATTAGTA-TAATTTAATAGTAAATT-ATAG
*
5600471 -TAAATCAGTGATAATTTAATAGTAAATTAT
1 TTAAATTAGT-ATAATTTAATAGTAAATTAT
5600501 TCATAACTTA
Statistics
Matches: 49, Mismatches: 13, Indels: 5
0.73 0.19 0.07
Matches are distributed among these distances:
32 2 0.04
33 43 0.88
34 4 0.08
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.44
Consensus pattern (32 bp):
TTAAATTAGTATAATTTAATAGTAAATTATAG
Found at i:5600466 original size:44 final size:44
Alignment explanation
Indices: 5600416--5600717 Score: 158
Period size: 44 Copynumber: 6.9 Consensus size: 44
5600406 AAGTTAGTAT
* * *
5600416 TAATTTAATAGTAAATTA-TCGTTAATTTAGTAGTAAATTATTAA
1 TAATTTAATAGTAAATCAGT-GATAATTTAATAGTAAATTATTAA
*
5600460 TAATTTAATAGTAAATCAGTGATAATTTAATAGTAAATTATTCA
1 TAATTTAATAGTAAATCAGTGATAATTTAATAGTAAATTATTAA
* ** * * *
5600504 TAACTTAATAACAAATCAATGATAAGTGTTAATTTAGTGGTAAATCATCAA
1 TAATTTAATAGTAAATCAGTGATAA-T-TTAA--TA---GTAAATTATTAA
* * ** * * * *
5600555 TAACTTAAT-GCTAAATTAGT--T-A--TAGCAATAAATCAATGA
1 TAATTTAATAG-TAAATCAGTGATAATTTAATAGTAAATTATTAA
* *
5600594 TAATTTAGTAGTAAATCAGT-ATTAATTTAATAGTAAATTATTGA
1 TAATTTAATAGTAAATCAGTGA-TAATTTAATAGTAAATTATTAA
** * * * *
5600638 TAATTTTGTAATAAATCATTGATAACTTAATA--AAATTATTGA
1 TAATTTAATAGTAAATCAGTGATAATTTAATAGTAAATTATTAA
* * * *
5600680 CAACTTAATAGTAAATCATTTG-TAACTTAATAGTAAAT
1 TAATTTAATAGTAAATCA-GTGATAATTTAATAGTAAAT
5600718 CAATGTATAA
Statistics
Matches: 201, Mismatches: 38, Indels: 38
0.73 0.14 0.14
Matches are distributed among these distances:
39 23 0.11
40 1 0.00
41 1 0.00
42 35 0.17
43 3 0.01
44 103 0.51
45 3 0.01
46 4 0.02
48 3 0.01
49 1 0.00
51 24 0.12
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (44 bp):
TAATTTAATAGTAAATCAGTGATAATTTAATAGTAAATTATTAA
Found at i:5600506 original size:22 final size:22
Alignment explanation
Indices: 5600416--5600513 Score: 117
Period size: 22 Copynumber: 4.5 Consensus size: 22
5600406 AAGTTAGTAT
*
5600416 TAATTTAATAGTAAATTA-TCGT
1 TAATTTAATAGTAAATTATTC-A
* *
5600438 TAATTTAGTAGTAAATTATTAA
1 TAATTTAATAGTAAATTATTCA
* * *
5600460 TAATTTAATAGTAAATCAGTGA
1 TAATTTAATAGTAAATTATTCA
5600482 TAATTTAATAGTAAATTATTCA
1 TAATTTAATAGTAAATTATTCA
*
5600504 TAACTTAATA
1 TAATTTAATA
5600514 ACAAATCAAT
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
22 63 0.98
23 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (22 bp):
TAATTTAATAGTAAATTATTCA
Found at i:5600611 original size:22 final size:22
Alignment explanation
Indices: 5600583--5600739 Score: 133
Period size: 22 Copynumber: 7.2 Consensus size: 22
5600573 GTTATAGCAA
* * *
5600583 TAAATCAATGATAATTTAGTAG
1 TAAATCATTGATAACTTAATAG
* *
5600605 TAAATCAGT-ATTAATTTAATAG
1 TAAATCATTGA-TAACTTAATAG
* * ** *
5600627 TAAATTATTGATAATTTTGTAA
1 TAAATCATTGATAACTTAATAG
5600649 TAAATCATTGATAACTTAATA-
1 TAAATCATTGATAACTTAATAG
* *
5600670 -AAATTATTGACAACTTAATAG
1 TAAATCATTGATAACTTAATAG
5600691 TAAATCATTTG-TAACTTAATAG
1 TAAATCA-TTGATAACTTAATAG
* *
5600713 TAAATCAATGTATAACTTAATAA
1 TAAATCATTG-ATAACTTAATAG
5600736 TAAA
1 TAAA
5600740 CTGTTATCTA
Statistics
Matches: 111, Mismatches: 17, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
20 18 0.16
21 3 0.03
22 72 0.65
23 18 0.16
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.39
Consensus pattern (22 bp):
TAAATCATTGATAACTTAATAG
Found at i:5600952 original size:3 final size:3
Alignment explanation
Indices: 5600946--5600992 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
5600936 ATACTACTTT
5600946 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5600993 CATCAAGAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5601791 original size:60 final size:57
Alignment explanation
Indices: 5601657--5601819 Score: 220
Period size: 60 Copynumber: 2.8 Consensus size: 57
5601647 TGCTTTTGTG
5601657 CAAGAAAATTTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAAAAACTTTAATTT
1 CAAGAAAA-TTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAAAAACTTTAATTT
* * *
5601715 CGAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATCCATTTTTTGGAAAAC-TTATTTT
1 CAAG-AAAATTGATACTTTCAACTTTTTCTCAAAAAT--ATTTTTT-AAAAACTTTAATTT
*
5601775 CAAAGAAAATTGATACTTTCAACTTTTCCTCAAAAATATATTTTT
1 C-AAGAAAATTGATACTTTCAACTTTTTCTCAAAAATAT-TTTTT
5601820 TTGAATTTTA
Statistics
Matches: 94, Mismatches: 5, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
58 33 0.35
59 9 0.10
60 45 0.48
61 7 0.07
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (57 bp):
CAAGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAAAAACTTTAATTT
Found at i:5601904 original size:10 final size:10
Alignment explanation
Indices: 5601852--5601934 Score: 57
Period size: 10 Copynumber: 8.3 Consensus size: 10
5601842 AAAATAAATA
5601852 AAATAA-AAT
1 AAATAATAAT
* *
5601861 AAAAAATATT
1 AAATAATAAT
* *
5601871 AAACAATTAT
1 AAATAATAAT
*
5601881 AATCTAATTAAT
1 AA-ATAA-TAAT
5601893 AAATAATAAT
1 AAATAATAAT
5601903 -AATAATACAT
1 AAATAATA-AT
5601913 -AATAATAAAT
1 AAATAAT-AAT
5601923 AAATAA-AAT
1 AAATAATAAT
5601932 AAA
1 AAA
5601935 AAAAAAAACT
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
9 18 0.31
10 25 0.42
11 11 0.19
12 5 0.08
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (10 bp):
AAATAATAAT
Found at i:5601907 original size:13 final size:13
Alignment explanation
Indices: 5601889--5601934 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
5601879 ATAATCTAAT
5601889 TAATAAATAATAA
1 TAATAAATAATAA
5601902 TAAT-AATACATAA
1 TAATAAATA-ATAA
5601915 TAATAAATAAATAA
1 TAATAAAT-AATAA
5601929 -AATAAA
1 TAATAAA
5601935 AAAAAAAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 4 0.13
13 18 0.60
14 7 0.23
15 1 0.03
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (13 bp):
TAATAAATAATAA
Found at i:5601933 original size:19 final size:19
Alignment explanation
Indices: 5601832--5601933 Score: 58
Period size: 19 Copynumber: 5.6 Consensus size: 19
5601822 GAATTTTATT
*
5601832 TAAAGAAAATAA-AATAAA
1 TAAATAAAATAATAATAAA
5601850 TAAAATAAAATAA-AA-AATA
1 T-AAATAAAATAATAATAA-A
* * * *
5601869 TTAA-ACAATTATAATCTAA
1 TAAATAAAATAATAAT-AAA
*
5601888 TTAAT-AAATAATAAT-AA
1 TAAATAAAATAATAATAAA
*
5601905 T-AAT-ACATAATAATAAA
1 TAAATAAAATAATAATAAA
5601922 TAAATAAAATAA
1 TAAATAAAATAA
5601934 AAAAAAAAAC
Statistics
Matches: 66, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
16 12 0.18
17 11 0.17
18 10 0.15
19 32 0.48
20 1 0.02
ACGTcount: A:0.69, C:0.03, G:0.01, T:0.27
Consensus pattern (19 bp):
TAAATAAAATAATAATAAA
Found at i:5602454 original size:10 final size:10
Alignment explanation
Indices: 5602439--5602483 Score: 54
Period size: 10 Copynumber: 4.1 Consensus size: 10
5602429 ACTGAAATCT
5602439 AAAAATTTTC
1 AAAAATTTTC
5602449 AAAAATTTTC
1 AAAAATTTTC
5602459 AGAAAAAATTTTTC
1 ---AAAAA-TTTTC
5602473 AAAAATTTTC
1 AAAAATTTTC
5602483 A
1 A
5602484 CCGATTCCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 16 0.52
11 5 0.16
13 5 0.16
14 5 0.16
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.38
Consensus pattern (10 bp):
AAAAATTTTC
Found at i:5602471 original size:24 final size:23
Alignment explanation
Indices: 5602439--5602483 Score: 81
Period size: 24 Copynumber: 1.9 Consensus size: 23
5602429 ACTGAAATCT
5602439 AAAAATTTTCAAAAATTTTCAGA
1 AAAAATTTTCAAAAATTTTCAGA
5602462 AAAAATTTTTCAAAAATTTTCA
1 AAAAA-TTTTCAAAAATTTTCA
5602484 CCGATTCCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.38
Consensus pattern (23 bp):
AAAAATTTTCAAAAATTTTCAGA
Found at i:5602805 original size:17 final size:17
Alignment explanation
Indices: 5602756--5602816 Score: 79
Period size: 17 Copynumber: 3.5 Consensus size: 17
5602746 AACAATAAAA
5602756 AAATAATAATAA-AGAT
1 AAATAATAATAATAGAT
*
5602772 AATATATTAATTAATAGAT
1 AA-ATAATAA-TAATAGAT
*
5602791 AAATAATAATAATAGAC
1 AAATAATAATAATAGAT
5602808 AAATAATAA
1 AAATAATAA
5602817 AGTATATATA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
16 2 0.05
17 22 0.56
18 9 0.23
19 6 0.15
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (17 bp):
AAATAATAATAATAGAT
Found at i:5602842 original size:51 final size:48
Alignment explanation
Indices: 5602760--5602854 Score: 129
Period size: 49 Copynumber: 1.9 Consensus size: 48
5602750 ATAAAAAAAT
* *
5602760 AATAATAAAGATAATATATTAATTAATAGATAAATAATAATAATAGACA
1 AATAATAAAGATAATATATTAATTAACAGATAAAT-ATAAAAATAGACA
5602809 AATAATAAAG-TATATATATGTATATTAACAGATAAATATAAAAATA
1 AATAATAAAGATA-ATATAT-TA-ATTAACAGATAAATATAAAAATA
5602855 TATATTAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
48 2 0.05
49 16 0.39
50 10 0.24
51 13 0.32
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (48 bp):
AATAATAAAGATAATATATTAATTAACAGATAAATATAAAAATAGACA
Found at i:5602864 original size:49 final size:47
Alignment explanation
Indices: 5602743--5602866 Score: 128
Period size: 49 Copynumber: 2.6 Consensus size: 47
5602733 AAAAAATAAA
* *
5602743 ATAAACAATAAAAA-AATAATAATAAAGATAATATATTAATTAATAG
1 ATAAATAATAAAAATAATAATAATAAAGATAATATATTAATTAACAG
* *
5602789 ATAAATAATAATAATAGACAAATAATAAAG-TATATATATGTATATTAACAG
1 ATAAATAATAAAAATA-A-TAATAATAAAGATA-ATATAT-TA-ATTAACAG
*
5602840 ATAAAT-ATAAAAATATATATTAATAAA
1 ATAAATAATAAAAATA-ATAATAATAAA
5602867 TAGTATCAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
46 12 0.19
47 1 0.02
48 3 0.05
49 24 0.38
50 11 0.17
51 13 0.20
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (47 bp):
ATAAATAATAAAAATAATAATAATAAAGATAATATATTAATTAACAG
Found at i:5602927 original size:21 final size:19
Alignment explanation
Indices: 5602878--5602934 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 19
5602868 AGTATCAATA
5602878 AATAAATAAATAATAAATAAG
1 AATAAA-AAATAA-AAATAAG
*
5602899 ATACAAAAAATAAAAATACCAG
1 A-ATAAAAAATAAAAATA--AG
5602921 AATAAAAAATAAAA
1 AATAAAAAATAAAA
5602935 CGGGCCTATC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 5 0.16
21 19 0.61
22 7 0.23
ACGTcount: A:0.74, C:0.05, G:0.04, T:0.18
Consensus pattern (19 bp):
AATAAAAAATAAAAATAAG
Found at i:5603259 original size:42 final size:41
Alignment explanation
Indices: 5603124--5603400 Score: 251
Period size: 42 Copynumber: 6.5 Consensus size: 41
5603114 TCCTTTAAGT
* *
5603124 AGAGGTTCAACGACTTTGAAAAACATAAACAAT-GCTACTCTAATC
1 AGAGGCTCAACGACTTTG---AA-ATAAA-AATGGCTCCTCTAATC
* *
5603169 AGAGGCTCTACGACTTTGAAAGATAAACAA-AGCTCCTCTAATC
1 AGAGGCTCAACGACTTTG-AA-ATAAA-AATGGCTCCTCTAATC
* * *
5603212 AGAGGCTCAACGATTTTGAAATTAAATATGGCTCCTCTAAAC
1 AGAGGCTCAACGACTTTGAAA-TAAAAATGGCTCCTCTAATC
5603254 AGAGGCTCAACGACTTTTGAAA-AATAAATGGCTCCTCTAATC
1 AGAGGCTCAACGAC-TTTGAAATAA-AAATGGCTCCTCTAATC
* *
5603296 AGAGGCTTAACGACTTTGAAATTAAATAA-AGCTCCTCTAAAT-
1 AGAGGCTCAACGACTTTGAAA-TAAA-AATGGCTCCTCT-AATC
* **
5603338 AGAGGTTCAATAACTTTTGAAA-AATAAATGGCTCCTCTAATC
1 AGAGGCTCAACGAC-TTTGAAATAA-AAATGGCTCCTCTAATC
*
5603380 AGAGGTTCAACGACTTTGAAA
1 AGAGGCTCAACGACTTTGAAA
5603401 AATAAACAAC
Statistics
Matches: 198, Mismatches: 21, Indels: 30
0.80 0.08 0.12
Matches are distributed among these distances:
41 25 0.13
42 98 0.49
43 59 0.30
45 16 0.08
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (41 bp):
AGAGGCTCAACGACTTTGAAATAAAAATGGCTCCTCTAATC
Found at i:5603308 original size:84 final size:84
Alignment explanation
Indices: 5603161--5603400 Score: 322
Period size: 84 Copynumber: 2.8 Consensus size: 84
5603151 AACAATGCTA
* * * ** *
5603161 CTCTAATCAGAGGCTCTACGAC-TTTGAAAGATAAACAAAGCTCCTCTAATCAGAGGCTCAACGA
1 CTCTAAACAGAGGCTCAACGACTTTTGAAAAAT-AA-ATGGCTCCTCTAATCAGAGGCTTAACGA
* **
5603225 TTTTGAAATTAAATATGGCTC
64 CTTTGAAATTAAATAAAGCTC
5603246 CTCTAAACAGAGGCTCAACGACTTTTGAAAAATAAATGGCTCCTCTAATCAGAGGCTTAACGACT
1 CTCTAAACAGAGGCTCAACGACTTTTGAAAAATAAATGGCTCCTCTAATCAGAGGCTTAACGACT
5603311 TTGAAATTAAATAAAGCTC
66 TTGAAATTAAATAAAGCTC
* * **
5603330 CTCTAAATAGAGGTTCAATAACTTTTGAAAAATAAATGGCTCCTCTAATCAGAGG-TTCAACGAC
1 CTCTAAACAGAGGCTCAACGACTTTTGAAAAATAAATGGCTCCTCTAATCAGAGGCTT-AACGAC
5603394 TTTGAAA
65 TTTGAAA
5603401 AATAAACAAC
Statistics
Matches: 140, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
83 2 0.01
84 107 0.76
85 22 0.16
86 9 0.06
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.28
Consensus pattern (84 bp):
CTCTAAACAGAGGCTCAACGACTTTTGAAAAATAAATGGCTCCTCTAATCAGAGGCTTAACGACT
TTGAAATTAAATAAAGCTC
Found at i:5603383 original size:126 final size:125
Alignment explanation
Indices: 5603124--5603406 Score: 342
Period size: 126 Copynumber: 2.2 Consensus size: 125
5603114 TCCTTTAAGT
* *
5603124 AGAGGTTCAACGACTTTGAAAAACATAAACAAT-GCTACTCTAATCAGAGGCTCTACGACTTTGA
1 AGAGGCTCAACGACTTTG-AAAA-AT--A-AATGGCTCCTCTAATCAGAGGCTCTACGACTTTGA
* *
5603188 AAGATAAACAAAGCTCCTCTAATCAGAGGCTCAACGATTTTGAAATTAAATATGGCTCCTCTAAA
61 AAGATAAACAAAGCTCCTCTAATCAGAGGCTCAACAATTTTGAAA-TAAAAATGGCTCCTCTAAA
5603253 C
125 C
5603254 AGAGGCTCAACGACTTTTGAAAAATAAATGGCTCCTCTAATCAGAGGCT-TAACGACTTTGAAA-
1 AGAGGCTCAACGAC-TTTGAAAAATAAATGGCTCCTCTAATCAGAGGCTCT-ACGACTTTGAAAG
* * * * *
5603317 TTAAATAAAGCTCCTCTAAAT-AGAGGTTCAATAACTTTTGAAA-AATAAATGGCTCCTCTAATC
64 ATAAACAAAGCTCCTCT-AATCAGAGGCTCAACAA-TTTTGAAATAA-AAATGGCTCCTCTAAAC
*
5603380 AGAGGTTCAACGACTTTGAAAAATAAA
1 AGAGGCTCAACGACTTTGAAAAATAAA
5603407 CAACTCCTTG
Statistics
Matches: 137, Mismatches: 10, Indels: 17
0.84 0.06 0.10
Matches are distributed among these distances:
125 15 0.11
126 57 0.42
127 42 0.31
129 2 0.01
130 17 0.12
131 4 0.03
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.27
Consensus pattern (125 bp):
AGAGGCTCAACGACTTTGAAAAATAAATGGCTCCTCTAATCAGAGGCTCTACGACTTTGAAAGAT
AAACAAAGCTCCTCTAATCAGAGGCTCAACAATTTTGAAATAAAAATGGCTCCTCTAAAC
Done.