Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold393
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1263635
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 115792 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:300633 original size:16 final size:17
Alignment explanation
Indices: 300594--300631 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
300584 CAATTTTAAT
**
300594 AAAAATGAGGTTTTTGA
1 AAAAATGAAATTTTTGA
300611 AAAAATGAAATTTTTGA
1 AAAAATGAAATTTTTGA
300628 AAAA
1 AAAA
300632 TGCTTTTTCG
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:0.53, C:0.00, G:0.16, T:0.32
Consensus pattern (17 bp):
AAAAATGAAATTTTTGA
Found at i:301200 original size:21 final size:21
Alignment explanation
Indices: 301176--301371 Score: 114
Period size: 21 Copynumber: 9.1 Consensus size: 21
301166 ATGCGATTTG
* * *
301176 ATTATGTGAAAATGCAAGTTA
1 ATTATGTCAACATGCAAGATA
*
301197 ATTATGTTAACATGCAAGATA
1 ATTATGTCAACATGCAAGATA
*
301218 TTTATGTCAACATGCAATGAT-
1 ATTATGTCAACATGCAA-GATA
301239 -TTATGTCAACATGCAAGA-A
1 ATTATGTCAACATGCAAGATA
* *
301258 ATGTATGTCAACTTGCTAGATA
1 AT-TATGTCAACATGCAAGATA
* ** * * *
301280 ATTAAGTTTACATGCGACATT
1 ATTATGTCAACATGCAAGATA
* *
301301 ATT-TGGTCAACATGC-GGTTTA
1 ATTAT-GTCAACATGCAAG-ATA
* *
301322 ATTATGTTGAACTAACGTACAAGATA
1 ATTATG-T---C-AACATGCAAGATA
*
301348 TTTATGTCAACATGCAAGATA
1 ATTATGTCAACATGCAAGATA
301369 ATT
1 ATT
301372 CTGGTTATCA
Statistics
Matches: 132, Mismatches: 29, Indels: 28
0.70 0.15 0.15
Matches are distributed among these distances:
19 2 0.02
20 17 0.13
21 89 0.67
22 9 0.07
25 2 0.02
26 12 0.09
27 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (21 bp):
ATTATGTCAACATGCAAGATA
Found at i:301545 original size:42 final size:42
Alignment explanation
Indices: 301407--301545 Score: 125
Period size: 42 Copynumber: 3.3 Consensus size: 42
301397 GAGAAAACGT
* * *
301407 GCATATTGACATAAATATCTTGCATGTTAACATAATTGACTT
1 GCATGTTGACATAAATATCTTGCATGTTAACATAATTAACTC
* * * ** * ** * *
301449 ACGTGTTGATATAAATAAGTCGCATGTCGACATACTTAAATC
1 GCATGTTGACATAAATATCTTGCATGTTAACATAATTAACTC
* ** *
301491 GTATGTCAACATAAATATCTTGCATGTTTACATAATTAACTC
1 GCATGTTGACATAAATATCTTGCATGTTAACATAATTAACTC
301533 GCATGTTGACATA
1 GCATGTTGACATA
301546 CTTAGTCGCA
Statistics
Matches: 68, Mismatches: 29, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (42 bp):
GCATGTTGACATAAATATCTTGCATGTTAACATAATTAACTC
Found at i:301556 original size:20 final size:21
Alignment explanation
Indices: 301407--301564 Score: 84
Period size: 21 Copynumber: 7.6 Consensus size: 21
301397 GAGAAAACGT
* * * *
301407 GCATATTGACATAAATATCTT
1 GCATGTTGACATAATTAACTC
* * *
301428 GCATGTTAACATAATTGACTT
1 GCATGTTGACATAATTAACTC
* * * * *
301449 ACGTGTTGATATAAATAAGTC
1 GCATGTTGACATAATTAACTC
* * *
301470 GCATGTCGACATACTTAAATC
1 GCATGTTGACATAATTAACTC
* ** * * *
301491 GTATGTCAACATAAATATCTT
1 GCATGTTGACATAATTAACTC
*
301512 GCATGTTTACATAATTAACTC
1 GCATGTTGACATAATTAACTC
* *
301533 GCATGTTGACATACTT-AGTC
1 GCATGTTGACATAATTAACTC
*
301553 GCATGTCGACAT
1 GCATGTTGACAT
301565 CAATATGTTG
Statistics
Matches: 100, Mismatches: 37, Indels: 1
0.72 0.27 0.01
Matches are distributed among these distances:
20 14 0.14
21 86 0.86
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (21 bp):
GCATGTTGACATAATTAACTC
Found at i:304327 original size:23 final size:23
Alignment explanation
Indices: 304297--304393 Score: 185
Period size: 23 Copynumber: 4.2 Consensus size: 23
304287 GTCTTGCATG
304297 CTTTCACTATATTAAGTAAGGTC
1 CTTTCACTATATTAAGTAAGGTC
*
304320 CTTTCACTATATCAAGTAAGGTC
1 CTTTCACTATATTAAGTAAGGTC
304343 CTTTCACTATATTAAGTAAGGTC
1 CTTTCACTATATTAAGTAAGGTC
304366 CTTTCACTATATTAAGTAAGGTC
1 CTTTCACTATATTAAGTAAGGTC
304389 CTTTC
1 CTTTC
304394 CGTACTTTTG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 72 1.00
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (23 bp):
CTTTCACTATATTAAGTAAGGTC
Found at i:313534 original size:3 final size:3
Alignment explanation
Indices: 313526--313571 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
313516 ACACTGTCAG
* * * *
313526 CAA CAA CAA CAA CAA TAA CAA CAA CAT CAG CGA CAA CAA CAA CAA C
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA C
313572 TGTGTCATCA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.59, C:0.33, G:0.04, T:0.04
Consensus pattern (3 bp):
CAA
Found at i:320655 original size:12 final size:11
Alignment explanation
Indices: 320626--320676 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
320616 CAAAGATTTG
320626 TTTTTGTTGTTT
1 TTTTTG-TGTTT
320638 TGTTTTGTGTTT
1 T-TTTTGTGTTT
*
320650 GTTTTTG-CTTT
1 -TTTTTGTGTTT
*
320661 TTTTGGTGTTT
1 TTTTTGTGTTT
320672 TTTTT
1 TTTTT
320677 TGGAGGGGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
10 5 0.16
11 10 0.31
12 11 0.34
13 6 0.19
ACGTcount: A:0.00, C:0.02, G:0.20, T:0.78
Consensus pattern (11 bp):
TTTTTGTGTTT
Found at i:320676 original size:22 final size:22
Alignment explanation
Indices: 320626--320678 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
320616 CAAAGATTTG
* *
320626 TTTTTGTTGTTTTGTTTTGTGT
1 TTTTTTTTGTTTTGTTTGGTGT
*
320648 TTGTTTTTGCTTTT-TTTGGTGT
1 TTTTTTTTG-TTTTGTTTGGTGT
320670 TTTTTTTTG
1 TTTTTTTTG
320679 GAGGGGGGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.00, C:0.02, G:0.21, T:0.77
Consensus pattern (22 bp):
TTTTTTTTGTTTTGTTTGGTGT
Found at i:322035 original size:18 final size:18
Alignment explanation
Indices: 322012--322047 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
322002 CCCAATGTCA
* *
322012 TATCGGTAAAATTGTCGT
1 TATCGGGAAAAATGTCGT
322030 TATCGGGAAAAATGTCGT
1 TATCGGGAAAAATGTCGT
322048 AATTTGGGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (18 bp):
TATCGGGAAAAATGTCGT
Found at i:323649 original size:16 final size:16
Alignment explanation
Indices: 323628--323660 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
323618 CACCCTCTAC
323628 GCTACGCTATGGATGT
1 GCTACGCTATGGATGT
323644 GCTACGCTATGGATGT
1 GCTACGCTATGGATGT
323660 G
1 G
323661 GAATCTGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.33, T:0.30
Consensus pattern (16 bp):
GCTACGCTATGGATGT
Found at i:325568 original size:166 final size:165
Alignment explanation
Indices: 325315--325760 Score: 585
Period size: 166 Copynumber: 2.7 Consensus size: 165
325305 TAAACTTGTG
* * * *
325315 TGGAGGCATCCTCAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGAGGGTAGGGAGG
1 TGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCGGA-GGTAGGGTGG
* * * *
325380 GGCAACAA-GAGGGGGTTCAAGTTTTACATAGGAATATATAGAGAAAATATTTGAAGATCTTCTT
65 GGCCACAATG-GGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATATTTAAAAATCTTCTT
*
325444 CTCAAAAACTATCAGGCCAGA-AAAGCTCAAATTAAAA
129 CTAAAAAACTATCAGGCCA-ACAAAGCTCAAATTAAAA
*
325481 TGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCTGGAGGTAGGGTGG
1 TGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCC-GGAGGTAGGGTGG
* *
325546 GGCCACAATGGGGGGATCAAGTTTTACATAGGAACATATAGAGAAAATCTTTAAAAATCTTCTTC
65 GGCCACAATGGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATATTTAAAAATCTTCTTC
* * ** *
325611 TAAAAAAGTATTAGGCCAACAAAGCTCAAATTTGAG
130 TAAAAAACTATCAGGCCAACAAAGCTCAAATTAAAA
*
325647 TGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAACCATGGTCCCCAGG-GGTAGGGTG
1 TGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGT-CCC-GGAGGTAGGGTG
** * * *
325711 GGGCCACAATTAGGGGAT-AATTTTTTTAAACAGGAATATATAGAGAAAAT
64 GGGCCACAATGGGGGGATCAA--GTTTTACATAGGAATATATAGAGAAAAT
325761 CATTNGCCAC
Statistics
Matches: 248, Mismatches: 26, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
165 3 0.01
166 213 0.86
167 32 0.13
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.26
Consensus pattern (165 bp):
TGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCGGAGGTAGGGTGGG
GCCACAATGGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATATTTAAAAATCTTCTTCT
AAAAAACTATCAGGCCAACAAAGCTCAAATTAAAA
Found at i:328390 original size:16 final size:16
Alignment explanation
Indices: 328369--328403 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
328359 GCTGTTTTCA
*
328369 AGAAGTGAGGGATAAT
1 AGAAGTGAGGAATAAT
*
328385 AGAAGTTAGGAATAAT
1 AGAAGTGAGGAATAAT
328401 AGA
1 AGA
328404 TAAATATTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.31, T:0.20
Consensus pattern (16 bp):
AGAAGTGAGGAATAAT
Found at i:338276 original size:2 final size:2
Alignment explanation
Indices: 338269--338310 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
338259 NNNNNNNNNN
338269 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
338311 GTTGTAATGT
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:356325 original size:26 final size:26
Alignment explanation
Indices: 356289--356359 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 26
356279 TTATACTATA
* *
356289 TATACATAAGATACATATGTTTTGTC
1 TATACATAAGATACATAAGTTGTGTC
* *
356315 TATACTTAAGATATATAAGTTGTGTC
1 TATACATAAGATACATAAGTTGTGTC
* *
356341 TATACATAACATATATAAG
1 TATACATAAGATACATAAG
356360 ATGTAAGATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.39
Consensus pattern (26 bp):
TATACATAAGATACATAAGTTGTGTC
Found at i:357126 original size:26 final size:26
Alignment explanation
Indices: 357018--357202 Score: 244
Period size: 26 Copynumber: 7.0 Consensus size: 26
357008 AGATGGTAAC
*
357018 ATACATAAGATGTGTCTCTACGTACTAAG
1 ATACATAAGATGTGTCTATAC--A-TAAG
357047 ATACATAAGATGTGTCTATACATAAG
1 ATACATAAGATGTGTCTATACATAAG
* * *
357073 ATACAAAAGGTTGTTTCTATACATAAG
1 ATACATAA-GATGTGTCTATACATAAG
*
357100 ATACATAAGATGTGTCTATACACAAG
1 ATACATAAGATGTGTCTATACATAAG
357126 ATACATAAGATGTGTCTATACATAAG
1 ATACATAAGATGTGTCTATACATAAG
* * *
357152 AAACATGAGATGTGTCCATACATAAG
1 ATACATAAGATGTGTCTATACATAAG
* *
357178 ATACATAAGGTGTATCTATACATAA
1 ATACATAAGATGTGTCTATACATAA
357203 ATAAAATGTG
Statistics
Matches: 138, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
26 94 0.68
27 24 0.17
29 20 0.14
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.30
Consensus pattern (26 bp):
ATACATAAGATGTGTCTATACATAAG
Found at i:357166 original size:52 final size:52
Alignment explanation
Indices: 357018--357581 Score: 365
Period size: 52 Copynumber: 10.9 Consensus size: 52
357008 AGATGGTAAC
*
357018 ATACATAAGATGTGTCTCTACGTACTAAGATACATAAGATGTGTCTATACATAAG
1 ATACATAAGATGTGTCTATAC--A-TAAGATACATAAGATGTGTCTATACATAAG
* * * *
357073 ATACAAAAGGTTGTTTCTATACATAAGATACATAAGATGTGTCTATACACAAG
1 ATACATAA-GATGTGTCTATACATAAGATACATAAGATGTGTCTATACATAAG
* * *
357126 ATACATAAGATGTGTCTATACATAAGAAACATGAGATGTGTCCATACATAAG
1 ATACATAAGATGTGTCTATACATAAGATACATAAGATGTGTCTATACATAAG
* * **
357178 ATACATAAGGTGTATCTATACATAA-AT--A-AA-ATGTGTCCCTACATAAG
1 ATACATAAGATGTGTCTATACATAAGATACATAAGATGTGTCTATACATAAG
* **** * * *
357225 AATTGCCTATCCACAAGAAAAATTTATACATACA-AT--GTAGGATGTGTC---A-AT--G
1 -A-----TA--CATAAGATGTGTCTATACATA-AGATACATAAGATGTGTCTATACATAAG
* * * * *
357277 ---CATTAGAAGTGTTTATACATTAGATACATAAGGTGTGTCTATACATAAG
1 ATACATAAGATGTGTCTATACATAAGATACATAAGATGTGTCTATACATAAG
* * * *
357326 ATACATTAA-ATGTGTTTTTACATAAGATACAAAAGATGTGTCTATACGTAAG
1 ATACA-TAAGATGTGTCTATACATAAGATACATAAGATGTGTCTATACATAAG
* * * * * * * *
357378 ATGCATTACATGTGTCTATACATAAGATACATTACATATATCTATACGTAAG
1 ATACATAAGATGTGTCTATACATAAGATACATAAGATGTGTCTATACATAAG
* * * * *
357430 ATACATGAGA-ATCTCTATACATAAGATGCATTAGATGTGTCTATACATAAG
1 ATACATAAGATGTGTCTATACATAAGATACATAAGATGTGTCTATACATAAG
* * * * * * *
357481 GTACATTAGATTTGCCTATACATAAGATACATTAGATGTATCTATACGTAAG
1 ATACATAAGATGTGTCTATACATAAGATACATAAGATGTGTCTATACATAAG
* * *
357533 ATTCATACATGAGATGTGTCTATACATAAGATACATAAGAGGTGCCTAT
1 ----ATACATAAGATGTGTCTATACATAAGATACATAAGATGTGTCTAT
357582 CCACAAGAGG
Statistics
Matches: 402, Mismatches: 76, Indels: 61
0.75 0.14 0.11
Matches are distributed among these distances:
40 1 0.00
41 17 0.04
43 9 0.02
46 1 0.00
47 18 0.04
48 2 0.00
49 2 0.00
51 45 0.11
52 183 0.46
53 40 0.10
54 3 0.01
55 23 0.06
56 50 0.12
57 1 0.00
58 7 0.02
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (52 bp):
ATACATAAGATGTGTCTATACATAAGATACATAAGATGTGTCTATACATAAG
Found at i:357319 original size:26 final size:26
Alignment explanation
Indices: 357285--357581 Score: 265
Period size: 26 Copynumber: 11.3 Consensus size: 26
357275 TGCATTAGAA
* * *
357285 GTGTTTATACATTAGATACATAAGGT
1 GTGTCTATACATAAGATACATAAGAT
357311 GTGTCTATACATAAGATACATTAA-AT
1 GTGTCTATACATAAGATACA-TAAGAT
* * *
357337 GTGTTTTTACATAAGATACAAAAGAT
1 GTGTCTATACATAAGATACATAAGAT
* * * *
357363 GTGTCTATACGTAAGATGCATTACAT
1 GTGTCTATACATAAGATACATAAGAT
* *
357389 GTGTCTATACATAAGATACATTACAT
1 GTGTCTATACATAAGATACATAAGAT
* * * *
357415 ATATCTATACGTAAGATACATGAGA-
1 GTGTCTATACATAAGATACATAAGAT
* * * *
357440 ATCTCTATACATAAGATGCATTAGAT
1 GTGTCTATACATAAGATACATAAGAT
* *
357466 GTGTCTATACATAAGGTACATTAGAT
1 GTGTCTATACATAAGATACATAAGAT
* * *
357492 TTGCCTATACATAAGATACATTAGAT
1 GTGTCTATACATAAGATACATAAGAT
* * *
357518 GTATCTATACGTAAGATTCATACATGAGAT
1 GTGTCTATACATAAG----ATACATAAGAT
*
357548 GTGTCTATACATAAGATACATAAGAG
1 GTGTCTATACATAAGATACATAAGAT
*
357574 GTGCCTAT
1 GTGTCTAT
357582 CCACAAGAGG
Statistics
Matches: 223, Mismatches: 41, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
25 23 0.10
26 174 0.78
27 3 0.01
30 23 0.10
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.34
Consensus pattern (26 bp):
GTGTCTATACATAAGATACATAAGAT
Found at i:357500 original size:103 final size:103
Alignment explanation
Indices: 357344--357581 Score: 287
Period size: 103 Copynumber: 2.3 Consensus size: 103
357334 AATGTGTTTT
* * *
357344 TACATAAGATACAAAAGATGTGTCTATACGTAAGATGCATTACATGTGTCTATACATAAGATACA
1 TACATAAGATACAAAAGATGTGTCTATACATAAGATACATTACATGTGCCTATACATAAGATACA
357409 TTACATATATCTATACGTAAGATACATGAGAATCTCTA
66 TTACATATATCTATACGTAAGATACATGAGAATCTCTA
* ** * * *
357447 TACATAAGATGCATTAGATGTGTCTATACATAAGGTACATTAGATTTGCCTATACATAAGATACA
1 TACATAAGATACAAAAGATGTGTCTATACATAAGATACATTACATGTGCCTATACATAAGATACA
* * * *
357512 TTAGATGTATCTATACGTAAGATTCATACATGAGATGTGTCTA
66 TTACATATATCTATACGTAAG----ATACATGAGA-ATCTCTA
* * *
357555 TACATAAGATACATAAGAGGTGCCTAT
1 TACATAAGATACAAAAGATGTGTCTAT
357582 CCACAAGAGG
Statistics
Matches: 113, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
103 75 0.66
107 10 0.09
108 28 0.25
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (103 bp):
TACATAAGATACAAAAGATGTGTCTATACATAAGATACATTACATGTGCCTATACATAAGATACA
TTACATATATCTATACGTAAGATACATGAGAATCTCTA
Found at i:357527 original size:17 final size:16
Alignment explanation
Indices: 357507--357564 Score: 50
Period size: 17 Copynumber: 3.7 Consensus size: 16
357497 TATACATAAG
*
357507 ATACATTAGATGTATCT
1 ATACATAAGATGT-TCT
*
357524 ATACGTAAGA--TTC-
1 ATACATAAGATGTTCT
*
357537 ATACATGAGATGTGTCT
1 ATACATAAGATGT-TCT
357554 ATACATAAGAT
1 ATACATAAGAT
357565 ACATAAGAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
13 8 0.25
14 2 0.06
15 2 0.06
16 2 0.06
17 18 0.56
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (16 bp):
ATACATAAGATGTTCT
Found at i:357548 original size:30 final size:30
Alignment explanation
Indices: 357496--357569 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 30
357486 TTAGATTTGC
357496 CTATACATAAGATACAT---T-AGATGTAT
1 CTATACATAAGATACATACATGAGATGTAT
* * *
357522 CTATACGTAAGATTCATACATGAGATGTGT
1 CTATACATAAGATACATACATGAGATGTAT
357552 CTATACATAAGATACATA
1 CTATACATAAGATACATA
357570 AGAGGTGCCT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
26 15 0.38
29 1 0.03
30 23 0.59
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (30 bp):
CTATACATAAGATACATACATGAGATGTAT
Found at i:357634 original size:17 final size:17
Alignment explanation
Indices: 357596--357628 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
357586 AAGAGGAATT
357596 AATACATTAGATGTGTC
1 AATACATTAGATGTGTC
*
357613 AATACGTTAGATGTGT
1 AATACATTAGATGTGT
357629 TTATACATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.36
Consensus pattern (17 bp):
AATACATTAGATGTGTC
Found at i:370092 original size:22 final size:22
Alignment explanation
Indices: 370053--370099 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
370043 ATTTTTTGTA
* *
370053 TCCAGTAATTATAAGAAAATAC
1 TCCAGTAATGATAAGAAAAAAC
* *
370075 TCCAGTTATGATACGAAAAAAC
1 TCCAGTAATGATAAGAAAAAAC
370097 TCC
1 TCC
370100 TTTTATATGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (22 bp):
TCCAGTAATGATAAGAAAAAAC
Found at i:376466 original size:10 final size:10
Alignment explanation
Indices: 376451--376480 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
376441 ATGTTACAAT
376451 GCAAACCAAA
1 GCAAACCAAA
376461 GCAAACCAAA
1 GCAAACCAAA
*
376471 CCAAACCAAA
1 GCAAACCAAA
376481 TCAGTATGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.60, C:0.33, G:0.07, T:0.00
Consensus pattern (10 bp):
GCAAACCAAA
Found at i:378311 original size:32 final size:32
Alignment explanation
Indices: 378270--378363 Score: 136
Period size: 32 Copynumber: 2.9 Consensus size: 32
378260 AATGACCGGG
* *
378270 GGTCATTTTTCGACGTAGAATAATGACCCCCC
1 GGTCATTTTTCTACGTAGAAAAATGACCCCCC
*
378302 GGTCATTTTTTTACGCT-GAAAAATGACCCCCC
1 GGTCATTTTTCTACG-TAGAAAAATGACCCCCC
*
378334 GGTCATTATTCTACGTAGAAAAATGACCCC
1 GGTCATTTTTCTACGTAGAAAAATGACCCC
378364 TTTGCCTGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
31 1 0.02
32 53 0.96
33 1 0.02
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.29
Consensus pattern (32 bp):
GGTCATTTTTCTACGTAGAAAAATGACCCCCC
Found at i:379876 original size:18 final size:19
Alignment explanation
Indices: 379855--379893 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
379845 GCACCTGCAA
* *
379855 CAAAAA-CTTTACCTGCTC
1 CAAAAATCTTAACCTCCTC
379873 CAAAAATCTTAACCTCCTC
1 CAAAAATCTTAACCTCCTC
379892 CA
1 CA
379894 GCATCTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.36, C:0.36, G:0.03, T:0.26
Consensus pattern (19 bp):
CAAAAATCTTAACCTCCTC
Found at i:401097 original size:25 final size:24
Alignment explanation
Indices: 401013--401095 Score: 121
Period size: 24 Copynumber: 3.4 Consensus size: 24
401003 TGTGGATGTG
* * *
401013 AAACGGTCTCTCTCTATACATATA
1 AAACGGTCCCTCTCTATACAGACA
401037 AAACGGTCCCTCTCTATACAGACA
1 AAACGGTCCCTCTCTATACAGACA
*
401061 AAACGGGTCCCTCTCTATATAGACA
1 AAAC-GGTCCCTCTCTATACAGACA
401086 AAACGGTCCC
1 AAACGGTCCC
401096 CTTTAACCAT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
24 31 0.57
25 23 0.43
ACGTcount: A:0.33, C:0.30, G:0.13, T:0.24
Consensus pattern (24 bp):
AAACGGTCCCTCTCTATACAGACA
Found at i:405453 original size:209 final size:204
Alignment explanation
Indices: 405055--405467 Score: 718
Period size: 209 Copynumber: 2.0 Consensus size: 204
405045 AATAGTGTTT
405055 ACCCATCTGTTCCTCGCAGATTATACTATGTACCCGGCCAGCTTATCGGTGCTTTACTGGATTTT
1 ACCCATCTGTTCCTCGCAGATTATACTATGTACCCGGCCAGCTTATCGGTGCTTTACTGGATTTT
* *
405120 ACGAGCCTCGATATATATTGTCCGTAAACAACATTGAATCGACACAACAAAAGGGGCGGCTCTAT
66 ACGAGCCTCGATATATACTGTCCGTAAACAACATTGAATCGACACAACAAAAGGGGCGGCTCTAA
405185 CTTATCCCTCAAAGATAATTTTGCTGAATGAAATCATTGTCGATGATTATATCTTCGTCACACGA
131 CTTATCCCTCAAAGATAATTTTGCTGAATGAAATCATTGTCGATGATTATATCTTCGTCACACGA
405250 TAAATTACC
196 TAAATTACC
**
405259 NACCCATCTGTTCCTCGCAGATTATACTATGTACCCGGCCAGCTTATCGGTGCTTTACTTTATTT
1 -ACCCATCTGTTCCTCGCAGATTATACTATGTACCCGGCCAGCTTATCGGTGCTTTACTGGATTT
** *
405324 TACGAGCCTCGATATATACTGTCCGTAATGAGCATTGCAAGAATCGACACAACAAAAGGGGCGGC
65 TACGAGCCTCGATATATACTGTCCGTAAACAACATT----GAATCGACACAACAAAAGGGGCGGC
405389 TCTAACTTATCCCTCAAAGATAATTTTGCTGAATGAAATCATTGTCGATGATTATATCTTCGTCA
126 TCTAACTTATCCCTCAAAGATAATTTTGCTGAATGAAATCATTGTCGATGATTATATCTTCGTCA
405454 CACGATAAATTACC
191 CACGATAAATTACC
405468 TCAAGGCAAA
Statistics
Matches: 197, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
205 94 0.48
209 103 0.52
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (204 bp):
ACCCATCTGTTCCTCGCAGATTATACTATGTACCCGGCCAGCTTATCGGTGCTTTACTGGATTTT
ACGAGCCTCGATATATACTGTCCGTAAACAACATTGAATCGACACAACAAAAGGGGCGGCTCTAA
CTTATCCCTCAAAGATAATTTTGCTGAATGAAATCATTGTCGATGATTATATCTTCGTCACACGA
TAAATTACC
Found at i:417263 original size:32 final size:32
Alignment explanation
Indices: 417200--417264 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
417190 ATTCCATCTG
* *
417200 CCTGAGACCCACCTTAATCCACTATTTATCCA
1 CCTGAGACCCACCTTAATCCACTACTCATCCA
*
417232 CCTGAGACCCACCTTAATGTCACT-CTCATCCA
1 CCTGAGACCCACCTTAAT-CCACTACTCATCCA
417264 C
1 C
417265 TATTTATCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 25 0.86
33 4 0.14
ACGTcount: A:0.26, C:0.40, G:0.08, T:0.26
Consensus pattern (32 bp):
CCTGAGACCCACCTTAATCCACTACTCATCCA
Found at i:417282 original size:43 final size:44
Alignment explanation
Indices: 417216--417674 Score: 638
Period size: 44 Copynumber: 10.3 Consensus size: 44
417206 ACCCACCTTA
* *
417216 ATCCACTATT-TATCCACCTGAGACCCACCTTAATGTCACTCTC
1 ATCCACTATTCCATCCACCTGAGACCCACCTTAATGACACTCTC
* * *
417259 ATCCACTATTTATCCACCCGAGACCTACCTGAGACCCACCTTAATGTCAATCTC
1 ATCCACTA--T-T----CC-A-TCC-ACCTGAGACCCACCTTAATGACACTCTC
**
417313 ATCCACT-TTTTATCCACCTGAGACCCACCTTAATGACACTCTC
1 ATCCACTATTCCATCCACCTGAGACCCACCTTAATGACACTCTC
* * *
417356 ATCCACTATT-TACCCACCTGAGACCCACCTTAATGACCCTCTC
1 ATCCACTATTCCATCCACCTGAGACCCACCTTAATGACACTCTC
*
417399 ATCCACTATTCCATCCACCTGAGACCCACCTTAATGACCCTCTC
1 ATCCACTATTCCATCCACCTGAGACCCACCTTAATGACACTCTC
* *
417443 ATCCCCTATTCCATCCACCTGAGACCCACCTTAATGACCCTCTC
1 ATCCACTATTCCATCCACCTGAGACCCACCTTAATGACACTCTC
*
417487 ATCCACTATTCCATCCACCTGAGACCCACCTTAATGACTCTCTC
1 ATCCACTATTCCATCCACCTGAGACCCACCTTAATGACACTCTC
*
417531 ATCCACTATTCCATCCACCTGAGACCCACCTTAATGACCCTCTC
1 ATCCACTATTCCATCCACCTGAGACCCACCTTAATGACACTCTC
*
417575 ATCCACTATTCCATCCACCTGAGACCCACCTTAATGACAATCTC
1 ATCCACTATTCCATCCACCTGAGACCCACCTTAATGACACTCTC
* *
417619 ATCCACTATT-TATCCACCTGAGACCCACCTTAATGACACTTTC
1 ATCCACTATTCCATCCACCTGAGACCCACCTTAATGACACTCTC
417662 ATCCACTATTCCA
1 ATCCACTATTCCA
417675 CCTATAACAT
Statistics
Matches: 380, Mismatches: 22, Indels: 27
0.89 0.05 0.06
Matches are distributed among these distances:
43 122 0.32
44 216 0.57
45 2 0.01
46 1 0.00
50 1 0.00
51 1 0.00
52 1 0.00
53 2 0.01
54 34 0.09
ACGTcount: A:0.26, C:0.40, G:0.07, T:0.27
Consensus pattern (44 bp):
ATCCACTATTCCATCCACCTGAGACCCACCTTAATGACACTCTC
Found at i:417298 original size:54 final size:54
Alignment explanation
Indices: 417229--417342 Score: 192
Period size: 54 Copynumber: 2.1 Consensus size: 54
417219 CACTATTTAT
*
417229 CCACCTGAGACCCACCTTAATGTCACTCTCATCCACTATTTATCCACCCGAGAC
1 CCACCTGAGACCCACCTTAATGTCAATCTCATCCACTATTTATCCACCCGAGAC
* * *
417283 CTACCTGAGACCCACCTTAATGTCAATCTCATCCACTTTTTATCCACCTGAGAC
1 CCACCTGAGACCCACCTTAATGTCAATCTCATCCACTATTTATCCACCCGAGAC
417337 CCACCT
1 CCACCT
417343 TAATGACACT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.25, C:0.39, G:0.09, T:0.26
Consensus pattern (54 bp):
CCACCTGAGACCCACCTTAATGTCAATCTCATCCACTATTTATCCACCCGAGAC
Found at i:421464 original size:23 final size:23
Alignment explanation
Indices: 421428--422334 Score: 1331
Period size: 23 Copynumber: 39.6 Consensus size: 23
421418 TAACCTAATA
421428 TACTCCCTGATGTCCATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
** *
421451 TACTTGCTGGTGTCCATGTG-TG
1 TACTCCCTGATGTCCATGTGTTG
* * * **
421473 TATTCCTTGGTGTCCACATGTTG
1 TACTCCCTGATGTCCATGTGTTG
* *
421496 TACT--CAG-TGTACATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
421516 TACTCCCTCG-TGTCCATGTGTTG
1 TACTCCCT-GATGTCCATGTGTTG
* **
421539 TAATCCCTGATGTTGATGT-TATG
1 TACTCCCTGATGTCCATGTGT-TG
421562 TACTCCCTGATGTCCATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
*
421585 TACTCCCTGGTGTCCATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
421608 TACTCCCTGATGTCCATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
*
421631 TACTCCCTGATGTCAATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
421654 TACTCCCTGATGTCCATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
*
421677 TACTCCCTGGTGTCCATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
421700 TACTCCCTGATGTCCATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
421723 TACTCCCTGATGTCCATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
421746 TACTCCCTGATGTCCATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
421769 TACTCCCTGATGTCCATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
421792 TACTCCCTGATGTCCATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
* * *
421815 TACTCCCAGGTGACCATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
*
421838 TACTCCCTGGTGTCCATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
* *
421861 TACTCCCTGATATCTATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
421884 TACTCCCTGATGTCCATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
*
421907 TACTCCCTGATGACCATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
*
421930 TACTCCCTGATGTCTATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
*
421953 TACTCCCTGGTGTCCATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
421976 TACTCCCTGATGTCCATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
* *
421999 TACTCCCTGGTGACCATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
* *
422022 TACTCCCTGATATCTATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
422045 TACTCCCTGATGTCCATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
*
422068 TACTCCCTGATGTCCACGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
422091 TACTCCCTGATGTCCATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
* *
422114 TACTCCCTGGTGACCATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
* * *
422137 TACTCCCTGATATCTATGTCTTG
1 TACTCCCTGATGTCCATGTGTTG
422160 TACTCCCTGATGTCCATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
422183 TACTCCCTGATGTCCATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
*
422206 TACTCCCTGGTGTCCATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
* *
422229 TACTCCCTGGTGACCATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
* * *
422252 TACTCCCTGATATCTATTTGTTG
1 TACTCCCTGATGTCCATGTGTTG
*
422275 TACTCCCTGATGACCATGTGTTG
1 TACTCCCTGATGTCCATGTGTTG
* * * *
422298 TACTCTCTGGTGTCCATGTTTTA
1 TACTCCCTGATGTCCATGTGTTG
*
422321 TACTCCCTGGTGTC
1 TACTCCCTGATGTC
422335 TAAGAAATTC
Statistics
Matches: 795, Mismatches: 82, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
20 14 0.02
21 1 0.00
22 19 0.02
23 760 0.96
24 1 0.00
ACGTcount: A:0.13, C:0.25, G:0.22, T:0.39
Consensus pattern (23 bp):
TACTCCCTGATGTCCATGTGTTG
Found at i:427427 original size:41 final size:41
Alignment explanation
Indices: 427382--427464 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
427372 AAAATCAAAG
**
427382 GGACAAGATTACATAAATGATGGCATGTGATACGAATGTGT
1 GGACAAGATTACATAAATGACAGCATGTGATACGAATGTGT
427423 GGACAAGATTACATAAATGACAGCATGTGATACGAATGTGT
1 GGACAAGATTACATAAATGACAGCATGTGATACGAATGTGT
427464 G
1 G
427465 TTCGTGTGAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.37, C:0.11, G:0.27, T:0.25
Consensus pattern (41 bp):
GGACAAGATTACATAAATGACAGCATGTGATACGAATGTGT
Found at i:433627 original size:2 final size:2
Alignment explanation
Indices: 433620--433663 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
433610 ACCTCTATAT
433620 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
433662 TC
1 TC
433664 AGAGACCTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:441337 original size:26 final size:26
Alignment explanation
Indices: 441308--441358 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
441298 AACACTAAAT
441308 ACATGTATACCAGTATTCTATAATAA
1 ACATGTATACCAGTATTCTATAATAA
441334 ACATGTATACCAGTATTCTATAATA
1 ACATGTATACCAGTATTCTATAATA
441359 TTAAACTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.35
Consensus pattern (26 bp):
ACATGTATACCAGTATTCTATAATAA
Found at i:441564 original size:37 final size:37
Alignment explanation
Indices: 441515--441985 Score: 754
Period size: 37 Copynumber: 12.6 Consensus size: 37
441505 GCGAAGTTTG
* *
441515 ACTTACAGGATGTTGGCTTACTTACATGGTGTTGGCTT
1 ACTTACATGATGTTGGCTTACTTA-ATGATGTTGGCTT
441553 ACTTA-ATGATGTTGGCTTACTTAATGATGATGTTGGCTT
1 ACTTACATGATGTTGGCTTACTT-A--ATGATGTTGGCTT
*
441592 ACTTA-ATGATGTTGGCTTACTTACATGGTGTTGGCTT
1 ACTTACATGATGTTGGCTTACTTA-ATGATGTTGGCTT
441629 ACTTA-ATGATGTTGGCTTACTTAATGATGTTGGCTT
1 ACTTACATGATGTTGGCTTACTTAATGATGTTGGCTT
441665 ACTTACATGATGTTGGCTTACTTAATGATGTTGGCTT
1 ACTTACATGATGTTGGCTTACTTAATGATGTTGGCTT
441702 ACTTACATGATGTTGGCTTACTTAATGATGTTGGCTT
1 ACTTACATGATGTTGGCTTACTTAATGATGTTGGCTT
*
441739 ACTTA-ATAATGTTGGCTTACTTACATGATGTTGGCTT
1 ACTTACATGATGTTGGCTTACTTA-ATGATGTTGGCTT
441776 ACTTA-ATGATGTTGGCTTACTTAATGATGTTGGCTT
1 ACTTACATGATGTTGGCTTACTTAATGATGTTGGCTT
441812 ACTTACATGATGTTGGCTTACTTAATGATGTTGGCTT
1 ACTTACATGATGTTGGCTTACTTAATGATGTTGGCTT
*
441849 ACTTACATGATGTTGGCTTACTTAATAATGTTGGCTT
1 ACTTACATGATGTTGGCTTACTTAATGATGTTGGCTT
** *
441886 ACTTACACAATGTTGGCTTACTTACCTGATGTTGGCTT
1 ACTTACATGATGTTGGCTTACTTA-ATGATGTTGGCTT
*
441924 ACTTACATGATGTTGGCTTCCTTACATGATGTTGGCTT
1 ACTTACATGATGTTGGCTTACTTA-ATGATGTTGGCTT
441962 ACTTACATGATGTTGGCTTACTTA
1 ACTTACATGATGTTGGCTTACTTA
441986 NNNNNNNNNN
Statistics
Matches: 409, Mismatches: 18, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
36 52 0.13
37 248 0.61
38 75 0.18
39 34 0.08
ACGTcount: A:0.22, C:0.14, G:0.21, T:0.43
Consensus pattern (37 bp):
ACTTACATGATGTTGGCTTACTTAATGATGTTGGCTT
Found at i:441654 original size:55 final size:56
Alignment explanation
Indices: 441515--441985 Score: 749
Period size: 55 Copynumber: 8.4 Consensus size: 56
441505 GCGAAGTTTG
* *
441515 ACTTACAGGATGTTGGCTTACTTACATGGTGTTGGCTTACTTAATGATGTTGGCTT
1 ACTTACATGATGTTGGCTTACTTACATGATGTTGGCTTACTTAATGATGTTGGCTT
* *
441571 ACTTAATGATGATGTTGGCTTACTTA-ATGATGTTGGCTTACTTACATGGTGTTGGCTT
1 ACTT-A-CATGATGTTGGCTTACTTACATGATGTTGGCTTACTTA-ATGATGTTGGCTT
441629 ACTTA-ATGATGTTGGCTTACTTA-ATGATGTTGGCTTACTTACATGATGTTGGCTT
1 ACTTACATGATGTTGGCTTACTTACATGATGTTGGCTTACTTA-ATGATGTTGGCTT
441684 ACTTA-ATGATGTTGGCTTACTTACATGATGTTGGCTTACTTAATGATGTTGGCTT
1 ACTTACATGATGTTGGCTTACTTACATGATGTTGGCTTACTTAATGATGTTGGCTT
*
441739 ACTTA-ATAATGTTGGCTTACTTACATGATGTTGGCTTACTTAATGATGTTGGCTT
1 ACTTACATGATGTTGGCTTACTTACATGATGTTGGCTTACTTAATGATGTTGGCTT
441794 ACTTA-ATGATGTTGGCTTACTTACATGATGTTGGCTTACTTAATGATGTTGGCTT
1 ACTTACATGATGTTGGCTTACTTACATGATGTTGGCTTACTTAATGATGTTGGCTT
* **
441849 ACTTACATGATGTTGGCTTACTTA-ATAATGTTGGCTTACTTACACAATGTTGGCTT
1 ACTTACATGATGTTGGCTTACTTACATGATGTTGGCTTACTTA-ATGATGTTGGCTT
* *
441905 ACTTACCTGATGTTGGCTTACTTACATGATGTTGGCTTCCTTACATGATGTTGGCTT
1 ACTTACATGATGTTGGCTTACTTACATGATGTTGGCTTACTTA-ATGATGTTGGCTT
441962 ACTTACATGATGTTGGCTTACTTA
1 ACTTACATGATGTTGGCTTACTTA
441986 NNNNNNNNNN
Statistics
Matches: 392, Mismatches: 16, Indels: 13
0.93 0.04 0.03
Matches are distributed among these distances:
55 215 0.55
56 74 0.19
57 70 0.18
58 33 0.08
ACGTcount: A:0.22, C:0.14, G:0.21, T:0.43
Consensus pattern (56 bp):
ACTTACATGATGTTGGCTTACTTACATGATGTTGGCTTACTTAATGATGTTGGCTT
Found at i:441702 original size:92 final size:93
Alignment explanation
Indices: 441515--441985 Score: 795
Period size: 92 Copynumber: 5.1 Consensus size: 93
441505 GCGAAGTTTG
* * *
441515 ACTTACAGGATGTTGGCTTACTTACATGGTGTTGGCTTACTTAATGATGTTGGCTTACTTAATGA
1 ACTTACATGATGTTGGCTTACTTACATGATGTTGGCTTACTTAATGATGTTGGCTTACTT-A-CA
441580 TGATGTTGGCTTACTTAATGATGTTGGCTT
64 TGATGTTGGCTTACTTAATGATGTTGGCTT
*
441610 ACTTACATGGTGTTGGCTTACTTA-ATGATGTTGGCTTACTTAATGATGTTGGCTTACTTACATG
1 ACTTACATGATGTTGGCTTACTTACATGATGTTGGCTTACTTAATGATGTTGGCTTACTTACATG
441674 ATGTTGGCTTACTTAATGATGTTGGCTT
66 ATGTTGGCTTACTTAATGATGTTGGCTT
*
441702 ACTTACATGATGTTGGCTTACTTA-ATGATGTTGGCTTACTTAATAATGTTGGCTTACTTACATG
1 ACTTACATGATGTTGGCTTACTTACATGATGTTGGCTTACTTAATGATGTTGGCTTACTTACATG
441766 ATGTTGGCTTACTTAATGATGTTGGCTT
66 ATGTTGGCTTACTTAATGATGTTGGCTT
441794 ACTTA-ATGATGTTGGCTTACTTACATGATGTTGGCTTACTTAATGATGTTGGCTTACTTACATG
1 ACTTACATGATGTTGGCTTACTTACATGATGTTGGCTTACTTAATGATGTTGGCTTACTTACATG
*
441858 ATGTTGGCTTACTTAATAATGTTGGCTT
66 ATGTTGGCTTACTTAATGATGTTGGCTT
** * *
441886 ACTTACACAATGTTGGCTTACTTACCTGATGTTGGCTTACTTACATGATGTTGGCTTCCTTACAT
1 ACTTACATGATGTTGGCTTACTTACATGATGTTGGCTTACTTA-ATGATGTTGGCTTACTTACAT
441951 GATGTTGGCTTACTTACATGATGTTGGCTT
65 GATGTTGGCTTACTTA-ATGATGTTGGCTT
441981 ACTTA
1 ACTTA
441986 NNNNNNNNNN
Statistics
Matches: 359, Mismatches: 13, Indels: 8
0.94 0.03 0.02
Matches are distributed among these distances:
91 18 0.05
92 197 0.55
93 35 0.10
94 70 0.19
95 39 0.11
ACGTcount: A:0.22, C:0.14, G:0.21, T:0.43
Consensus pattern (93 bp):
ACTTACATGATGTTGGCTTACTTACATGATGTTGGCTTACTTAATGATGTTGGCTTACTTACATG
ATGTTGGCTTACTTAATGATGTTGGCTT
Found at i:441981 original size:15 final size:16
Alignment explanation
Indices: 441579--441982 Score: 110
Period size: 19 Copynumber: 22.0 Consensus size: 16
441569 TTACTTAATG
441579 ATGATGTTGG-CTTAC
1 ATGATGTTGGTCTTAC
441594 TTAATGATGTTGGCTTACTTAC
1 ---ATGATGTTGG--T-CTTAC
*
441616 ATGGTGTTGG-CTTAC
1 ATGATGTTGGTCTTAC
441631 TTAATGATGTTGG-CTTAC
1 ---ATGATGTTGGTCTTAC
441649 TTAATGATGTTGGCTTACTTAC
1 ---ATGATGTTGG--T-CTTAC
441671 ATGATGTTGG-CTTAC
1 ATGATGTTGGTCTTAC
441686 TTAATGATGTTGGCTTACTTAC
1 ---ATGATGTTGG--T-CTTAC
441708 ATGATGTTGG-CTTAC
1 ATGATGTTGGTCTTAC
441723 TTAATGATGTTGG-CTTAC
1 ---ATGATGTTGGTCTTAC
*
441741 TTAATAATGTTGGCTTACTTAC
1 ---ATGATGTTGG--T-CTTAC
441763 ATGATGTTGG-CTTAC
1 ATGATGTTGGTCTTAC
441778 TTAATGATGTTGG-CTTAC
1 ---ATGATGTTGGTCTTAC
441796 TTAATGATGTTGGCTTACTTAC
1 ---ATGATGTTGG--T-CTTAC
441818 ATGATGTTGG-CTTAC
1 ATGATGTTGGTCTTAC
441833 TTAATGATGTTGGCTTACTTAC
1 ---ATGATGTTGG--T-CTTAC
441855 ATGATGTTGG-CTTAC
1 ATGATGTTGGTCTTAC
*
441870 TTAATAATGTTGGCTTACTTAC
1 ---ATGATGTTGG--T-CTTAC
**
441892 ACAATGTTGGCTTACTTAC
1 ATGATGTTGG--T-CTTAC
*
441911 CTGATGTTGGCTTACTTAC
1 ATGATGTTGG--T-CTTAC
441930 ATGATGTTGGCTTCCTTAC
1 ATGATGTTGG--T-CTTAC
441949 ATGATGTTGGCTTACTTAC
1 ATGATGTTGG--T-CTTAC
441968 ATGATGTTGG-CTTAC
1 ATGATGTTGGTCTTAC
441983 TTANNNNNNN
Statistics
Matches: 328, Mismatches: 12, Indels: 95
0.75 0.03 0.22
Matches are distributed among these distances:
15 35 0.11
18 121 0.37
19 137 0.42
22 35 0.11
ACGTcount: A:0.22, C:0.14, G:0.21, T:0.43
Consensus pattern (16 bp):
ATGATGTTGGTCTTAC
Found at i:442560 original size:18 final size:19
Alignment explanation
Indices: 442523--442644 Score: 139
Period size: 18 Copynumber: 6.5 Consensus size: 19
442513 NNNNNNNTAC
442523 ATGATGGTT-GGCTTACTTA
1 ATGAT-GTTGGGCTTACTTA
* *
442542 ATTATGTTGGGTTTA-TTAA
1 ATGATGTTGGGCTTACTT-A
442561 ATGATGTT-GGCTTACTTA
1 ATGATGTTGGGCTTACTTA
442579 ATGATGTT-GGCTTACTTA
1 ATGATGTTGGGCTTACTTA
*
442597 GTGATGTT-GGCTTACTTA
1 ATGATGTTGGGCTTACTTA
442615 CATGATGTT-GGCTTACTTA
1 -ATGATGTTGGGCTTACTTA
442634 CATGATGTTGG
1 -ATGATGTTGG
442645 CTTTGTGAAC
Statistics
Matches: 92, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
18 46 0.50
19 45 0.49
20 1 0.01
ACGTcount: A:0.21, C:0.10, G:0.25, T:0.44
Consensus pattern (19 bp):
ATGATGTTGGGCTTACTTA
Found at i:442569 original size:19 final size:19
Alignment explanation
Indices: 442523--442647 Score: 159
Period size: 19 Copynumber: 6.7 Consensus size: 19
442513 NNNNNNNTAC
442523 ATGATGGTTGGCTTACTT-A
1 ATGAT-GTTGGCTTACTTAA
* *
442542 ATTATGTTGGGTTTA-TTAA
1 ATGATGTT-GGCTTACTTAA
442561 ATGATGTTGGCTTACTT-A
1 ATGATGTTGGCTTACTTAA
442579 ATGATGTTGGCTTACTT-A
1 ATGATGTTGGCTTACTTAA
* *
442597 GTGATGTTGGCTTACTTAC
1 ATGATGTTGGCTTACTTAA
*
442616 ATGATGTTGGCTTACTTAC
1 ATGATGTTGGCTTACTTAA
442635 ATGATGTTGGCTT
1 ATGATGTTGGCTT
442648 TGTGAACTGC
Statistics
Matches: 95, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
18 45 0.47
19 50 0.53
ACGTcount: A:0.21, C:0.10, G:0.24, T:0.45
Consensus pattern (19 bp):
ATGATGTTGGCTTACTTAA
Found at i:442574 original size:37 final size:37
Alignment explanation
Indices: 442523--442647 Score: 173
Period size: 37 Copynumber: 3.4 Consensus size: 37
442513 NNNNNNNTAC
* *
442523 ATGATGGTTGGCTTACTTAATTATGTTGGGTTTA-TTAA
1 ATGAT-GTTGGCTTACTTAATGATGTT-GGCTTACTTAA
442561 ATGATGTTGGCTTACTTAATGATGTTGGCTTACTT-A
1 ATGATGTTGGCTTACTTAATGATGTTGGCTTACTTAA
* *
442597 GTGATGTTGGCTTACTTACATGATGTTGGCTTACTTAC
1 ATGATGTTGGCTTACTTA-ATGATGTTGGCTTACTTAA
442635 ATGATGTTGGCTT
1 ATGATGTTGGCTT
442648 TGTGAACTGC
Statistics
Matches: 79, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
36 23 0.29
37 39 0.49
38 17 0.22
ACGTcount: A:0.21, C:0.10, G:0.24, T:0.45
Consensus pattern (37 bp):
ATGATGTTGGCTTACTTAATGATGTTGGCTTACTTAA
Found at i:445307 original size:4 final size:4
Alignment explanation
Indices: 445308--445377 Score: 122
Period size: 4 Copynumber: 17.5 Consensus size: 4
445298 CTGTCTGTCT
*
445308 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCT GTCC GTCC GTCC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC
*
445356 GTCC GTCC GTCT GTCC GTCC GT
1 GTCC GTCC GTCC GTCC GTCC GT
445378 AACAAAAATT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 62 1.00
ACGTcount: A:0.00, C:0.46, G:0.26, T:0.29
Consensus pattern (4 bp):
GTCC
Found at i:445796 original size:166 final size:166
Alignment explanation
Indices: 445401--446360 Score: 1363
Period size: 166 Copynumber: 5.8 Consensus size: 166
445391 GTCGCATTTA
* * * *
445401 TCTCAGCAACTTTTTATCGCAGATGCTTGAAATTTTTACACAGTGTTGGT-TAAGGCATGCCATA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAAATTTTACACAGTATTTGTAT-AGGCATGCCATA
*
445465 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTT
65 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTA-TT
* *
445530 TTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
129 TTTAGCCAAAATTTTCAAACAAATTTTTGTCAAAGATT
* * *
445568 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAATATTTGTATAGGTATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAAATTTTACACAGTATTTGTATAGGCATGCCATAT
* *
445633 CGTGGGATATATTTTTGTACCAATTGGACATCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
* *
445698 TAGCAAAAATTTTCAAACAAATTTTTGTCAAAGAAT
131 TAGCCAAAATTTTCAAACAAATTTTTGTCAAAGATT
* * *
445734 TCTCAGCAACTGTTAATCGCAGATGCATGAAAATTTTACACAGTATTTGTATAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAAATTTTACACAGTATTTGTATAGGCATGCCATAT
* *
445799 TGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTG-TAAATGACGACTTTGTTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
* *
445863 TAGCAAAAATTTTCAAACAAATTTTTGTCAAAGAAT
131 TAGCCAAAATTTTCAAACAAATTTTTGTCAAAGATT
* * *
445899 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCTATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAAATTTTACACAGTATTTGTATAGGCATGCCATAT
* * *
445964 CGTGGGATGTATTTTTGTACTAATCGGACGTCAACTTCCTGTTTAATGA-GTACTTTGTTTATTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACG-ACTTTGTTTATTT
** *
446028 TTAGCCAAAATTTTCAAACAAATTTCCGTCAATGATT
130 TTAGCCAAAATTTTCAAACAAATTTTTGTCAAAGATT
*
446065 TCTCAGCAACCATTTATCGCAGATGCTTG-AAATTTTAACACAGTATTTGTATAGGCATGCCATA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAAATTTT-ACACAGTATTTGTATAGGCATGCCATA
* * * * * *
446129 TTGTGGGATAAATTTTTGTATCAATCGGACGTCAACTTCCTGTGAAATAACGACTTTGTTTATAT
65 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTT
* *
446194 TTAGCCAAAATTTTCAAACCAATTTTTGTTAAAGATT
130 TTAGCCAAAATTTTCAAACAAATTTTTGTCAAAGATT
* * * *
446231 TCTCAGCAGCTATTTATCGCAGATGCTTG-AAATTTTAACACACTATTTGTTTAGGCATACCATA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAAATTTT-ACACAGTATTTGTATAGGCATGCCATA
* * * * * * * * * *
446295 TTGTGAGATATATTTCTGTACCAATTGGATGCCAGCTTTCTGTTAAATGTCGACTTTGCTTATTT
65 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTT
446360 T
130 T
446361 GCATATTCAC
Statistics
Matches: 715, Mismatches: 73, Indels: 11
0.89 0.09 0.01
Matches are distributed among these distances:
165 164 0.23
166 433 0.61
167 117 0.16
168 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (166 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAAATTTTACACAGTATTTGTATAGGCATGCCATAT
CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
TAGCCAAAATTTTCAAACAAATTTTTGTCAAAGATT
Found at i:446005 original size:331 final size:331
Alignment explanation
Indices: 445401--446360 Score: 1404
Period size: 331 Copynumber: 2.9 Consensus size: 331
445391 GTCGCATTTA
* * * *
445401 TCTCAGCAACTTTTTATCGCAGATGCTTGAAATTTTTACACAGTGTTGGT-TAAGGCATGCCATA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAAATTTTACACAGTATTTGTAT-AGGCATGCCATA
* *
445465 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTT
65 TTGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTG-TAAATGACGACTTTGTTTA-TT
* *
445530 TTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCT
128 TTTAGCCAAAATTTTCAAACAAATTTTTGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCT
*
445595 TGAAATTTTTACACAATATTTGTATAGGTATGCCATATCGTGGGATATATTTTTGTACCAATTGG
193 TGAAATTTTTACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATTGG
* **
445660 ACATCAACTTCCTGTTAAATGACGACTTTGTTTATTTTTAGCAAAAATTTTCAAACAAATTTTTG
258 ACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTTTAGCAAAAATTTTCAAACAAATTTCCG
445725 TCAAAGAAT
323 TCAAAGAAT
* * *
445734 TCTCAGCAACTGTTAATCGCAGATGCATGAAAATTTTACACAGTATTTGTATAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAAATTTTACACAGTATTTGTATAGGCATGCCATAT
*
445799 TGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTAAATGACGACTTTGTTTATTTTT
66 TGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTAAATGACGACTTTGTTTATTTTT
* * *
445864 AGCAAAAATTTTCAAACAAATTTTTGTCAAAGAATTCTCAGCAACTGTTTATCGCAGATGCTTGA
131 AGCCAAAATTTTCAAACAAATTTTTGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTTGA
* * * * *
445929 AATTTTTACACAGTATTTGTATAGGCATGCTATATCGTGGGATGTATTTTTGTACTAATCGGACG
196 AATTTTTACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATTGGACG
* *
445994 TCAACTTCCTGTTTAATGA-GTACTTTGTTTATTTTTAGCCAAAATTTTCAAACAAATTTCCGTC
261 TCAACTTCCTGTTAAATGACG-ACTTTGTTTATTTTTAGCAAAAATTTTCAAACAAATTTCCGTC
* *
446058 AATGATT
325 AAAGAAT
*
446065 TCTCAGCAACCATTTATCGCAGATGCTTG-AAATTTTAACACAGTATTTGTATAGGCATGCCATA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAAATTTT-ACACAGTATTTGTATAGGCATGCCATA
* * * *
446129 TTGTGGGATAAATTTTTGTATCAATCGGACGTCAACTTCCTGTGAAATAACGACTTTGTTTATAT
65 TTGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGT-AAATGACGACTTTGTTTATTT
* * *
446194 TTAGCCAAAATTTTCAAACCAATTTTTGTTAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTT
129 TTAGCCAAAATTTTCAAACAAATTTTTGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTT
* * * * * * *
446259 GAAATTTTAACACACTATTTGTTTAGGCATACCATATTGTGAGATATATTTCTGTACCAATTGGA
194 GAAATTTTTACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATTGGA
* * * * * *
446324 TGCCAGCTTTCTGTTAAATGTCGACTTTGCTTATTTT
259 CGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
446361 GCATATTCAC
Statistics
Matches: 562, Mismatches: 60, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
330 8 0.01
331 278 0.49
332 178 0.32
333 97 0.17
334 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (331 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAAATTTTACACAGTATTTGTATAGGCATGCCATAT
TGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTAAATGACGACTTTGTTTATTTTT
AGCCAAAATTTTCAAACAAATTTTTGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTTGA
AATTTTTACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATTGGACG
TCAACTTCCTGTTAAATGACGACTTTGTTTATTTTTAGCAAAAATTTTCAAACAAATTTCCGTCA
AAGAAT
Found at i:448682 original size:14 final size:14
Alignment explanation
Indices: 448663--448693 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
448653 GGGTGATGAC
448663 ACCAATGAGACATT
1 ACCAATGAGACATT
448677 ACCAATGAGACATT
1 ACCAATGAGACATT
448691 ACC
1 ACC
448694 TGTGTGTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.26, G:0.13, T:0.19
Consensus pattern (14 bp):
ACCAATGAGACATT
Found at i:448724 original size:36 final size:36
Alignment explanation
Indices: 448677--448776 Score: 191
Period size: 36 Copynumber: 2.8 Consensus size: 36
448667 ATGAGACATT
448677 ACCAATGAGACATTACCTGTGTGTATGGGTGATGAC
1 ACCAATGAGACATTACCTGTGTGTATGGGTGATGAC
*
448713 ACCAACGAGACATTACCTGTGTGTATGGGTGATGAC
1 ACCAATGAGACATTACCTGTGTGTATGGGTGATGAC
448749 ACCAATGAGACATTACCTGTGTGTATGG
1 ACCAATGAGACATTACCTGTGTGTATGG
448777 AGAGTCGCAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 62 1.00
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (36 bp):
ACCAATGAGACATTACCTGTGTGTATGGGTGATGAC
Found at i:449450 original size:25 final size:25
Alignment explanation
Indices: 449430--449532 Score: 143
Period size: 25 Copynumber: 4.1 Consensus size: 25
449420 TGCTTTGGAT
449430 TGTGCATTATTATCTCCCTTTAGAG
1 TGTGCATTATTATCTCCCTTTAGAG
* *
449455 TGTGCATCATCATCTCCCTTTAGAG
1 TGTGCATTATTATCTCCCTTTAGAG
449480 TGTGCATTATTATCTCCCTTTAGAG
1 TGTGCATTATTATCTCCCTTTAGAG
* * * * *
449505 TGTTCGTTCTTCTCTCCCTTGAGAG
1 TGTGCATTATTATCTCCCTTTAGAG
449530 TGT
1 TGT
449533 AGTCTCGCTT
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 69 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (25 bp):
TGTGCATTATTATCTCCCTTTAGAG
Found at i:449623 original size:25 final size:25
Alignment explanation
Indices: 449593--449822 Score: 270
Period size: 25 Copynumber: 9.1 Consensus size: 25
449583 AGCGAGACTA
449593 TTGAGAGTGTGCATTATTACTTCCC
1 TTGAGAGTGTGCATTATTACTTCCC
*
449618 TTGAGAGTGTGCATTATTATCTTCCT
1 TTGAGAGTGTGCATTATTA-CTTCCC
* * *
449644 TGATGAGAGTGTGGATTTTTACCTCCC
1 T--TGAGAGTGTGCATTATTACTTCCC
449671 TTGAGAGTGTGCATTATTA-TCTCCC
1 TTGAGAGTGTGCATTATTACT-TCCC
* * *
449696 TTGAGAGTGTGGATCT-TAACTTCCT
1 TTGAGAGTGTGCAT-TATTACTTCCC
449721 TTGAGAGTGTGCATTATTA-TCTCCC
1 TTGAGAGTGTGCATTATTACT-TCCC
* * *
449746 TTGAGAGTGTGGATTTTTACCTCCC
1 TTGAGAGTGTGCATTATTACTTCCC
*
449771 TTGAGAGTGTGCATTATTACCTCCC
1 TTGAGAGTGTGCATTATTACTTCCC
449796 TTGAGAGTGTGCATTATTA-TCTCCC
1 TTGAGAGTGTGCATTATTACT-TCCC
449821 TT
1 TT
449823 TAAAGATTAT
Statistics
Matches: 175, Mismatches: 20, Indels: 20
0.81 0.09 0.09
Matches are distributed among these distances:
24 2 0.01
25 144 0.82
26 8 0.05
27 5 0.03
28 16 0.09
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (25 bp):
TTGAGAGTGTGCATTATTACTTCCC
Found at i:449708 original size:50 final size:50
Alignment explanation
Indices: 449593--449822 Score: 325
Period size: 50 Copynumber: 4.5 Consensus size: 50
449583 AGCGAGACTA
* * * *
449593 TTGAGAGTGTGCATTATTACTTCCCTTGAGAGTGTGCATTATTATCTTCCT
1 TTGAGAGTGTGGATTTTTACCTCCCTTGAGAGTGTGCATTATTATC-TCCC
449644 TGATGAGAGTGTGGATTTTTACCTCCCTTGAGAGTGTGCATTATTATCTCCC
1 T--TGAGAGTGTGGATTTTTACCTCCCTTGAGAGTGTGCATTATTATCTCCC
* * * *
449696 TTGAGAGTGTGGATCTTAACTTCCTTTGAGAGTGTGCATTATTATCTCCC
1 TTGAGAGTGTGGATTTTTACCTCCCTTGAGAGTGTGCATTATTATCTCCC
*
449746 TTGAGAGTGTGGATTTTTACCTCCCTTGAGAGTGTGCATTATTACCTCCC
1 TTGAGAGTGTGGATTTTTACCTCCCTTGAGAGTGTGCATTATTATCTCCC
* * *
449796 TTGAGAGTGTGCATTATTATCTCCCTT
1 TTGAGAGTGTGGATTTTTACCTCCCTT
449823 TAAAGATTAT
Statistics
Matches: 161, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
50 114 0.71
51 1 0.01
52 4 0.02
53 42 0.26
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (50 bp):
TTGAGAGTGTGGATTTTTACCTCCCTTGAGAGTGTGCATTATTATCTCCC
Found at i:449770 original size:75 final size:74
Alignment explanation
Indices: 449593--449822 Score: 298
Period size: 75 Copynumber: 3.0 Consensus size: 74
449583 AGCGAGACTA
* * *
449593 TTGAGAGTGTGCATTATTACTTCCCTTGAGAGTGTGCATTATTATCTTCCTTGATGAGAGTGTGG
1 TTGAGAGTGTGCATTATTACCTCCCTTGAGAGTGTGCA-T-TTAACTTCCTT--TGAGAGTGTGC
* *
449658 ATTTTTACCTCCC
62 ATTATTATCTCCC
* *
449671 TTGAGAGTGTGCATTATTATCTCCCTTGAGAGTGTGGATCTTAACTTCCTTTGAGAGTGTGCATT
1 TTGAGAGTGTGCATTATTACCTCCCTTGAGAGTGTGCAT-TTAACTTCCTTTGAGAGTGTGCATT
449736 ATTATCTCCC
65 ATTATCTCCC
* * * * *
449746 TTGAGAGTGTGGATTTTTACCTCCCTTGAGAGTGTGCATTATTACCTCCCTTGAGAGTGTGCATT
1 TTGAGAGTGTGCATTATTACCTCCCTTGAGAGTGTGCATT-TAACTTCCTTTGAGAGTGTGCATT
449811 ATTATCTCCC
65 ATTATCTCCC
449821 TT
1 TT
449823 TAAAGATTAT
Statistics
Matches: 136, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
74 1 0.01
75 89 0.65
77 11 0.08
78 35 0.26
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (74 bp):
TTGAGAGTGTGCATTATTACCTCCCTTGAGAGTGTGCATTTAACTTCCTTTGAGAGTGTGCATTA
TTATCTCCC
Found at i:452527 original size:40 final size:40
Alignment explanation
Indices: 452339--452527 Score: 369
Period size: 40 Copynumber: 4.7 Consensus size: 40
452329 GAGGCACTTA
452339 CCTTGTATCCATGATAGTCCACCTCTACTAAAGACACCTG
1 CCTTGTATCCATGATAGTCCACCTCTACTAAAGACACCTG
452379 CCTTGTATCCATGATAGTCCACCTCTACTAAAGACACCTG
1 CCTTGTATCCATGATAGTCCACCTCTACTAAAGACACCTG
452419 CCTTGTATCCATGATAGTCCACCTCTACTAAAGACACCTG
1 CCTTGTATCCATGATAGTCCACCTCTACTAAAGACACCTG
452459 CCTTGTATCCATGATAGTCCACCTCTACTAAAGACACCTG
1 CCTTGTATCCATGATAGTCCACCTCTACTAAAGACACCTG
*
452499 CCTTGTATCCATGATAGTCCAACTCTACT
1 CCTTGTATCCATGATAGTCCACCTCTACT
452528 TGAGTCATTC
Statistics
Matches: 148, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 148 1.00
ACGTcount: A:0.27, C:0.32, G:0.12, T:0.29
Consensus pattern (40 bp):
CCTTGTATCCATGATAGTCCACCTCTACTAAAGACACCTG
Found at i:462817 original size:2 final size:2
Alignment explanation
Indices: 462810--462870 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
462800 AACATGTGAG
462810 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* *
462852 TC TA GC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC T
462871 AAGTTTGAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.02, C:0.48, G:0.02, T:0.49
Consensus pattern (2 bp):
TC
Found at i:467813 original size:20 final size:20
Alignment explanation
Indices: 467774--467961 Score: 103
Period size: 20 Copynumber: 9.4 Consensus size: 20
467764 TAACCATCAA
* * *
467774 TGTTTACAGCTTTCTATCAC
1 TGTTTACAGATTACTGTCAC
*
467794 TGTTTACATATTACTGTCAC
1 TGTTTACAGATTACTGTCAC
* * * *
467814 TGTTGACAGCTTCAC-ATAAC
1 TGTTTACAGATT-ACTGTCAC
*
467834 TGTTTACAGTTTACTGTCAC
1 TGTTTACAGATTACTGTCAC
*
467854 AGTTTACAGATTACTGTCA-
1 TGTTTACAGATTACTGTCAC
* *
467873 TGATTTACAGGTTACTGCCAC
1 TG-TTTACAGATTACTGTCAC
* * * * *
467894 AGTTTGA-AGCTTGCAGTAAC
1 TGTTT-ACAGATTACTGTCAC
* *
467914 TGTTTACAGCTCACTGTCAC
1 TGTTTACAGATTACTGTCAC
* ** * **
467934 AGTAAACAGTTTTTTGTCAC
1 TGTTTACAGATTACTGTCAC
467954 TGTTTACA
1 TGTTTACA
467962 TATATATAAC
Statistics
Matches: 123, Mismatches: 39, Indels: 12
0.71 0.22 0.07
Matches are distributed among these distances:
19 4 0.03
20 115 0.93
21 4 0.03
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (20 bp):
TGTTTACAGATTACTGTCAC
Found at i:467920 original size:40 final size:40
Alignment explanation
Indices: 467792--467936 Score: 125
Period size: 40 Copynumber: 3.6 Consensus size: 40
467782 GCTTTCTATC
** * * *
467792 ACTGTTTACATATTACTGTCACTGTTGACAGCTTCACA-TA
1 ACTGTTTACAGCTTACTGTCACAGTTTACAGATT-ACAGTA
* * *
467832 ACTGTTTACAGTTTACTGTCACAGTTTACAGATTACTGTC
1 ACTGTTTACAGCTTACTGTCACAGTTTACAGATTACAGTA
* * * *
467872 A-TGATTTACAGGTTACTGCCACAGTTTGA-AGCTTGCAGTA
1 ACTG-TTTACAGCTTACTGTCACAGTTT-ACAGATTACAGTA
*
467912 ACTGTTTACAGCTCACTGTCACAGT
1 ACTGTTTACAGCTTACTGTCACAGT
467937 AAACAGTTTT
Statistics
Matches: 85, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
39 4 0.05
40 78 0.92
41 3 0.04
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (40 bp):
ACTGTTTACAGCTTACTGTCACAGTTTACAGATTACAGTA
Found at i:468002 original size:20 final size:20
Alignment explanation
Indices: 467971--468044 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 20
467961 ATATATATAA
*
467971 CTATCACCGTTTACAGCTTT
1 CTATCACTGTTTACAGCTTT
* * * * *
467991 CTCTCACAGTTTATAACTTA
1 CTATCACTGTTTACAGCTTT
* * *
468011 ATGTCACTGTTTACAGCTAT
1 CTATCACTGTTTACAGCTTT
468031 CTATCACTGTTTAC
1 CTATCACTGTTTAC
468045 TCCTTCTCGT
Statistics
Matches: 40, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.24, C:0.26, G:0.09, T:0.41
Consensus pattern (20 bp):
CTATCACTGTTTACAGCTTT
Found at i:474572 original size:39 final size:39
Alignment explanation
Indices: 474516--475569 Score: 1268
Period size: 39 Copynumber: 26.0 Consensus size: 39
474506 GGTACCCTCG
*
474516 AGAACTTGAACAGGGGACTAGGTTTGAGAAAGAGGTAAA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAA
*
474555 AGAACTTGAACATG-GGACTAGGTTTGAGAATGAGGTAAA
1 AGAACTTGAACA-GAGGACTAGGTTTGAGAAAGAGGTAAA
*
474594 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAGA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAA
*
474633 AGAACTTGAACAGAGGACTAGGTTTGAGAGAGAGGTAAACAAAAAAAA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGT---------AAA
* *
474681 AGAACTTGAACAGGGGACTAGGTTTGAGAAAGAGGTAGA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAA
*
474720 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAGA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAA
*
474759 AGAACTTGAACAGAGGACTAGGTTTGAGAGAGAGGTAAACAAAAAAAA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGT---------AAA
* *
474807 AGAACTTGAACAGGGGACTAGGTTTGAGAAAGAGGTAGA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAA
*
474846 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAGA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAA
* * *
474885 AGAACTTGAACAGAGGACTTGGTTTAATAAAGAGGTAAAAAA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGT---AAA
* * *
474927 AAAACTTGAAGAGAGAACTAGGTTTGAGAAAGAGGT-AA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAA
* *
474965 AGAACTTGAACAGGGGACGAGGTTTGAGAAAGAGGTGGAAAAA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGT----AAA
* *
475008 AAAACTTGAACAGAGGACTAGATTTGAGAAAGAGGTAAA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAA
*
475047 AGAACTTGAACAGGGGACTAGGTTTGAGAAAGAGGTAAA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAA
*
475086 AGAACTTGAACAGAGGATTAGGTTTGAGAAAGAGGTAAAAAAAA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGT-----AAA
* * * *
475130 ATAACTTGAACACAGGACTTGGTTTGAGAAAGAAGTAAA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAA
*
475169 AGAACTTGAACAGAGGAGGACTAGATTTGAGAAAGAGGTGGAAAA
1 AGAACTTGAAC--A-GAGGACTAGGTTTGAGAAAGAGGT---AAA
* *
475214 AAAACTTGAACAGAGGACTAGATTTGAGAAAGAGGTAAA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAA
* *
475253 AGAACTTGAACAGGGGACGAGGTTTGAGAAAGAGGTAAAAA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGT--AAA
* ** **
475294 AAAACTTGAACAGATAACTAAATTTGAGAAAGAGGTAAA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAA
*
475333 AGAACTTGAACAGAGGACTAGATTTGAGAAAGAGGTAAA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAA
*
475372 AGAACTTGAACAGAGGACTAGATTTGAGAAAGAGGTAAAAA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGT--AAA
* *
475413 AAAACTTGAACATG-GGACTAGGTTTGAGAAAGAGGTTAA
1 AGAACTTGAACA-GAGGACTAGGTTTGAGAAAGAGGTAAA
* * *
475452 AGAACTCGAACAGAGAAGTAGGTTTGAGAAAGAGGTAAA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAA
** * *
475491 AGAACTTGAACAGAGGACTATATTTGAGAAAGGGGCAAA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAA
*
475530 AGAACTTGAACAGAGGACTAGATTTGAGAAAGAGGTAAA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAA
475569 A
1 A
475570 AAAAAAAAAG
Statistics
Matches: 887, Mismatches: 83, Indels: 90
0.84 0.08 0.08
Matches are distributed among these distances:
38 35 0.04
39 552 0.62
40 1 0.00
41 68 0.08
42 77 0.09
43 35 0.04
44 34 0.04
45 13 0.01
48 72 0.08
ACGTcount: A:0.45, C:0.08, G:0.30, T:0.18
Consensus pattern (39 bp):
AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAA
Found at i:474777 original size:126 final size:121
Alignment explanation
Indices: 474516--475569 Score: 1297
Period size: 126 Copynumber: 8.7 Consensus size: 121
474506 GGTACCCTCG
* *
474516 AGAACTTGAACAGGGGACTAGGTTTGAGAAAGAGGT----AAAAGAACTTGAACATGGGACTAGG
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAAAAAAAGAACTTGAACAGGGGACTAGG
* *
474577 TTTGAGAATGAGGTAAAAGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAGA
66 TTTGAGAAAGAGGTAAAAGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAA
*
474633 AGAACTTGAACAGAGGACTAGGTTTGAGAGAGAGGTAAACAAAAAAAAAGAACTTGAACAGGGGA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGT-----AAAAAAAAGAACTTGAACAGGGGA
* *
474698 CTAGGTTTGAGAAAGAGGTAGAAGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAGA
61 CTAGGTTTGAGAAAGAGGTAAAAGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAA
*
474759 AGAACTTGAACAGAGGACTAGGTTTGAGAGAGAGGTAAACAAAAAAAAAGAACTTGAACAGGGGA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGT-----AAAAAAAAGAACTTGAACAGGGGA
* *
474824 CTAGGTTTGAGAAAGAGGTAGAAGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAGA
61 CTAGGTTTGAGAAAGAGGTAAAAGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAA
* * * * * *
474885 AGAACTTGAACAGAGGACTTGGTTTAATAAAGAGGTAAAAAAAA-AACTTGAAGAGAGAACTAGG
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAAAAAAAGAACTTGAACAGGGGACTAGG
* *
474949 TTTGAGAAAGAGGT-AAAGAACTTGAACAGGGGACGAGGTTTGAGAAAGAGGTGGAAAAA
66 TTTGAGAAAGAGGTAAAAGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGT----AAA
* *
475008 AAAACTTGAACAGAGGACTAGATTTGAGAAAGAGGT----AAAAGAACTTGAACAGGGGACTAGG
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAAAAAAAGAACTTGAACAGGGGACTAGG
*
475069 TTTGAGAAAGAGGTAAAAGAACTTGAACAGAGGATTAGGTTTGAGAAAGAGGTAAAAAAAA
66 TTTGAGAAAGAGGTAAAAGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGT-----AAA
* * * *
475130 ATAACTTGAACACAGGACTTGGTTTGAGAAAGAAGT----AAAAGAACTTGAACAGAGGAGGACT
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAAAAAAAGAACTTGAAC--AGG-GGACT
* * *
475191 AGATTTGAGAAAGAGGTGGAAAAAAAACTTGAACAGAGGACTAGATTTGAGAAAGAGGTAAA
63 AGGTTTGAGAAAGAGGT---AAAAGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAA
* * *** **
475253 AGAACTTGAACAGGGGACGAGGTTTGAGAAAGAGGT-AAAAAAA-AACTTGAACAGATAACTAAA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAAAAAAAGAACTTGAACAGGGGACTAGG
*
475316 TTTGAGAAAGAGGTAAAAGAACTTGAACAGAGGACTAGATTTGAGAAAGAGGTAAA
66 TTTGAGAAAGAGGTAAAAGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAA
* *
475372 AGAACTTGAACAGAGGACTAGATTTGAGAAAGAGGT-AAAAAAA-AACTTGAACATGGGACTAGG
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAAAAAAAGAACTTGAACAGGGGACTAGG
* * * *
475435 TTTGAGAAAGAGGTTAAAGAACTCGAACAGAGAAGTAGGTTTGAGAAAGAGGTAAA
66 TTTGAGAAAGAGGTAAAAGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAA
** ** * *
475491 AGAACTTGAACAGAGGACTATATTTGAGAAAG-GG---GCAAAAGAACTTGAACAGAGGACTAGA
1 AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAAAAAAAGAACTTGAACAGGGGACTAGG
475552 TTTGAGAAAGAGGTAAAA
66 TTTGAGAAAGAGGTAAAA
475570 AAAAAAAAAG
Statistics
Matches: 841, Mismatches: 70, Indels: 52
0.87 0.07 0.05
Matches are distributed among these distances:
116 4 0.00
117 68 0.08
118 2 0.00
119 216 0.26
120 62 0.07
121 43 0.05
122 69 0.08
123 68 0.08
124 3 0.00
125 30 0.04
126 240 0.29
128 36 0.04
ACGTcount: A:0.45, C:0.08, G:0.30, T:0.18
Consensus pattern (121 bp):
AGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAAAAAAAGAACTTGAACAGGGGACTAGG
TTTGAGAAAGAGGTAAAAGAACTTGAACAGAGGACTAGGTTTGAGAAAGAGGTAAA
Found at i:478242 original size:31 final size:31
Alignment explanation
Indices: 478205--478389 Score: 334
Period size: 31 Copynumber: 6.0 Consensus size: 31
478195 GGTGTCCTGA
*
478205 TAGATATACAATGGATATCTCATACTTCACG
1 TAGATATACAATAGATATCTCATACTTCACG
* *
478236 TAGATATACAATGGATATCTCATACTTCACA
1 TAGATATACAATAGATATCTCATACTTCACG
478267 TAGATATACAATAGATATCTCATACTTCACG
1 TAGATATACAATAGATATCTCATACTTCACG
478298 TAGATATACAATAGATATCTCATACTTCACG
1 TAGATATACAATAGATATCTCATACTTCACG
*
478329 TAGATATACAATGGATATCTCATACTTCACG
1 TAGATATACAATAGATATCTCATACTTCACG
478360 TAGATATACAATAGATATCTCATACTTCAC
1 TAGATATACAATAGATATCTCATACTTCAC
478390 TTCAGTGGAA
Statistics
Matches: 149, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 149 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.32
Consensus pattern (31 bp):
TAGATATACAATAGATATCTCATACTTCACG
Found at i:485836 original size:14 final size:14
Alignment explanation
Indices: 485817--485849 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
485807 GGAAAAAAAT
485817 CTGGAAAAGGTCAG
1 CTGGAAAAGGTCAG
485831 CTGGAAAAGGTCAG
1 CTGGAAAAGGTCAG
485845 CTGGA
1 CTGGA
485850 TCAGAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.36, T:0.15
Consensus pattern (14 bp):
CTGGAAAAGGTCAG
Found at i:486853 original size:12 final size:12
Alignment explanation
Indices: 486836--486860 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
486826 AGAAAGAGTG
486836 AAGTCAAGGTCA
1 AAGTCAAGGTCA
486848 AAGTCAAGGTCA
1 AAGTCAAGGTCA
486860 A
1 A
486861 GATCAGATAA
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:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (12 bp):
AAGTCAAGGTCA
Found at i:494340 original size:17 final size:17
Alignment explanation
Indices: 494302--494361 Score: 95
Period size: 17 Copynumber: 3.6 Consensus size: 17
494292 TTCTCTCTCT
* *
494302 CTCTCTCTCTCGTTCT-
1 CTCTCTCTCTTGTTATG
494318 CTCTCTCTCTTGTTATG
1 CTCTCTCTCTTGTTATG
494335 CTCTCTCTCTTGTTATG
1 CTCTCTCTCTTGTTATG
494352 CTCTCTCTCT
1 CTCTCTCTCT
494362 CTTTCTCTCC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
16 14 0.34
17 27 0.66
ACGTcount: A:0.03, C:0.37, G:0.08, T:0.52
Consensus pattern (17 bp):
CTCTCTCTCTTGTTATG
Found at i:494344 original size:2 final size:2
Alignment explanation
Indices: 494281--494327 Score: 69
Period size: 2 Copynumber: 23.5 Consensus size: 2
494271 TATCAGTGTA
*
494281 TC TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC GT- TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC -TC TC TC TC TC
494323 TC TC T
1 TC TC T
494328 TGTTATGCTC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 1 0.02
2 39 0.95
3 1 0.02
ACGTcount: A:0.00, C:0.45, G:0.02, T:0.53
Consensus pattern (2 bp):
TC
Found at i:497109 original size:16 final size:16
Alignment explanation
Indices: 497088--497138 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
497078 AAAAGGGACG
497088 TACTAAAGACCTGAAA
1 TACTAAAGACCTGAAA
*
497104 TACTAATGACCTGAAA
1 TACTAAAGACCTGAAA
* *
497120 GACCAGAAAGACCTGAAA
1 TA-C-TAAAGACCTGAAA
497138 T
1 T
497139 TTTATATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
16 16 0.57
17 1 0.04
18 11 0.39
ACGTcount: A:0.47, C:0.20, G:0.16, T:0.18
Consensus pattern (16 bp):
TACTAAAGACCTGAAA
Found at i:497128 original size:9 final size:9
Alignment explanation
Indices: 497092--497137 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
497082 GGGACGTACT
497092 AAAGACCTG
1 AAAGACCTG
*
497101 AAATA-CT-
1 AAAGACCTG
*
497108 AATGACCTG
1 AAAGACCTG
*
497117 AAAGACCAG
1 AAAGACCTG
497126 AAAGACCTG
1 AAAGACCTG
497135 AAA
1 AAA
497138 TTTTATATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
7 3 0.10
8 4 0.14
9 22 0.76
ACGTcount: A:0.50, C:0.20, G:0.17, T:0.13
Consensus pattern (9 bp):
AAAGACCTG
Found at i:497298 original size:17 final size:17
Alignment explanation
Indices: 497270--497324 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
497260 AAATATGAAA
* *
497270 GACCTGAGAATTTGAATT
1 GACCTGA-AATTTCAAAT
497288 GACCTGAAATTTTCAAAT
1 GACCTGAAA-TTTCAAAT
*
497306 GACCTGAAATTTTAAAT
1 GACCTGAAATTTCAAAT
497323 GA
1 GA
497325 TTGATACATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 11 0.33
18 22 0.67
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (17 bp):
GACCTGAAATTTCAAAT
Found at i:497473 original size:18 final size:18
Alignment explanation
Indices: 497446--497490 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
497436 GAGTACGAAA
* *
497446 GACCTTAAAATTTGAATT
1 GACCTGAAAATTTGAACT
*
497464 GACCTGAAAATTTGAGCT
1 GACCTGAAAATTTGAACT
497482 GACCTGAAA
1 GACCTGAAA
497491 TTATATATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (18 bp):
GACCTGAAAATTTGAACT
Found at i:497635 original size:177 final size:176
Alignment explanation
Indices: 497200--497810 Score: 920
Period size: 176 Copynumber: 3.5 Consensus size: 176
497190 GGGGGTTTAA
** * * * * * * * *
497200 ATCATATTTCCAGGTATAATTTTGTTTTAAAAAATATCATAATGACCAGTTATTCATGCA-AAAT
1 ATCATATTTCCAGGTAT-A-TAAGTGTTAAAATATATCATACTGATCAATTATTTATGCAGGAGT
* * * * * *
497264 ATGAAAGACCTGAGAATTTGAATTGACCTGAAATTTTCAAATGACCTGAAATTTTAAATGATTGA
64 ACGAAAGACCTTAAAATTTGAATTGACCTGAAAATTTCAAATGACCTGAAATTTTATATAATTGA
497329 TACATTTCTATGTTCTGTGTCAATATTAATGTCTATTTGTAAGTTTTT
129 TACATTTCTATGTTCTGTGTCAATATTAATGTCTATTTGTAAGTTTTT
*
497377 ATCATATTTCCAGGTGTATAAGTGTTAAAATATATCATACTGATCAATTATTTATGCAGGAGTAC
1 ATCATATTTCCAGGTATATAAGTGTTAAAATATATCATACTGATCAATTATTTATGCAGGAGTAC
* ** * *
497442 GAAAGACCTTAAAATTTGAATTGACCTGAAAATTTGAGCTGACCTGAAATTATATATAATTGAAA
66 GAAAGACCTTAAAATTTGAATTGACCTGAAAATTTCAAATGACCTGAAATTTTATATAATTGATA
* * * *
497507 CATTTCTAAGTTCTGTGTCAGTTTTAATGTCTATTTGTGAGTTTTT
131 CATTTCTATGTTCTGTGTCAATATTAATGTCTATTTGTAAGTTTTT
* *
497553 AATCATATTTCCAGGTATATAAGTGTTAAAATATATCATATTGATCAATTATTTACGCAGGAGTA
1 -ATCATATTTCCAGGTATATAAGTGTTAAAATATATCATACTGATCAATTATTTATGCAGGAGTA
497618 CGAAAGA-CTTGAAAATTTGAATTGACCTGAAAATTTCAAATGACCTGAAATTTTATATAATTGA
65 CGAAAGACCTT-AAAATTTGAATTGACCTGAAAATTTCAAATGACCTGAAATTTTATATAATTGA
497682 TACATTTCTATGTTCTGTGTCAATATTAATGTCTATTTGTAAGTTTTT
129 TACATTTCTATGTTCTGTGTCAATATTAATGTCTATTTGTAAGTTTTT
497730 ATCATATTTCCAGGTATATAAGTGTTAAAATATATCATACTGATCAATTATTTATGCAGGAGTAC
1 ATCATATTTCCAGGTATATAAGTGTTAAAATATATCATACTGATCAATTATTTATGCAGGAGTAC
497795 GAAAGACCTTAAAATT
66 GAAAGACCTTAAAATT
497811 ATAAAAGTAT
Statistics
Matches: 390, Mismatches: 40, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
175 32 0.08
176 179 0.46
177 179 0.46
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.39
Consensus pattern (176 bp):
ATCATATTTCCAGGTATATAAGTGTTAAAATATATCATACTGATCAATTATTTATGCAGGAGTAC
GAAAGACCTTAAAATTTGAATTGACCTGAAAATTTCAAATGACCTGAAATTTTATATAATTGATA
CATTTCTATGTTCTGTGTCAATATTAATGTCTATTTGTAAGTTTTT
Found at i:497670 original size:17 final size:18
Alignment explanation
Indices: 497627--497667 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
497617 ACGAAAGACT
* *
497627 TGAAAATTTGAATTGACC
1 TGAAAATTTCAAATGACC
497645 TGAAAATTTCAAATGACC
1 TGAAAATTTCAAATGACC
497663 TGAAA
1 TGAAA
497668 TTTTATATAA
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:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (18 bp):
TGAAAATTTCAAATGACC
Found at i:497872 original size:17 final size:18
Alignment explanation
Indices: 497847--497895 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
497837 TCAATTGATA
*
497847 TAAAATTTCAGGTC-ATT
1 TAAATTTTCAGGTCAATT
497864 TAAATTTTCAGGTCAATT
1 TAAATTTTCAGGTCAATT
*
497882 CAAATTTTCAGGTC
1 TAAATTTTCAGGTC
497896 TTTCATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 13 0.45
18 16 0.55
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (18 bp):
TAAATTTTCAGGTCAATT
Found at i:497905 original size:17 final size:18
Alignment explanation
Indices: 497852--497905 Score: 76
Period size: 17 Copynumber: 3.1 Consensus size: 18
497842 TGATATAAAA
497852 TTTCAGGTCATTT-AAAT
1 TTTCAGGTCATTTCAAAT
*
497869 TTTCAGGTCAATTCAAAT
1 TTTCAGGTCATTTCAAAT
*
497887 TTTCAGGTC-TTTCATAT
1 TTTCAGGTCATTTCAAAT
497904 TT
1 TT
497906 CTGCTTGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
17 20 0.61
18 13 0.39
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.48
Consensus pattern (18 bp):
TTTCAGGTCATTTCAAAT
Found at i:498059 original size:16 final size:16
Alignment explanation
Indices: 498038--498070 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
498028 ATTTCAGGTC
498038 TTTCAGGTCATTAGTA
1 TTTCAGGTCATTAGTA
*
498054 TTTCAGGTCTTTAGTA
1 TTTCAGGTCATTAGTA
498070 T
1 T
498071 GTTCCGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.48
Consensus pattern (16 bp):
TTTCAGGTCATTAGTA
Found at i:504522 original size:35 final size:34
Alignment explanation
Indices: 504472--504655 Score: 89
Period size: 35 Copynumber: 5.8 Consensus size: 34
504462 GCTGCAGACT
*
504472 CTGTATATTTGCTACAGCTGTAAAGGTAAACCAC
1 CTGTATATTTACTACAGCTGTAAAGGTAAACCAC
* *
504506 CTGTAATATTTACTACAACT-TCAAAGGTAATCCA-
1 CTGT-ATATTTACTACAGCTGT-AAAGGTAAACCAC
* * *
504540 -T-T-CA-GT-GT--A-CTGTAAAGGTAAACCAC
1 CTGTATATTTACTACAGCTGTAAAGGTAAACCAC
*
504566 CTGTAATAGTTACTACAGCTGTAAAGGT-AA-CA-
1 CTGT-ATATTTACTACAGCTGTAAAGGTAAACCAC
* *
504598 CTGAATATGTGACATACA--TGTAAAGGT-AA-CA-
1 CTGTATAT-TTAC-TACAGCTGTAAAGGTAAACCAC
* * *
504629 GTGTATACTTGCTACAGCTGTAAAGGT
1 CTGTATATTTACTACAGCTGTAAAGGT
504656 TACACTATAT
Statistics
Matches: 115, Mismatches: 18, Indels: 37
0.68 0.11 0.22
Matches are distributed among these distances:
25 13 0.11
26 2 0.02
27 1 0.01
28 2 0.02
29 5 0.04
30 4 0.03
31 31 0.27
32 8 0.07
33 7 0.06
34 8 0.07
35 34 0.30
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29
Consensus pattern (34 bp):
CTGTATATTTACTACAGCTGTAAAGGTAAACCAC
Found at i:504651 original size:31 final size:32
Alignment explanation
Indices: 504549--504661 Score: 101
Period size: 31 Copynumber: 3.5 Consensus size: 32
504539 ATTCAGTGTA
*
504549 CTGTAAAGGTAAACCACCTGTAATA-GTTACTACAG
1 CTGTAAAGGT-AA-CA-CTG-AATATGTGACTACAG
504584 CTGTAAAGGTAACACTGAATATGTGACATACA-
1 CTGTAAAGGTAACACTGAATATGTGAC-TACAG
* *
504616 -TGTAAAGGTAACAGTGTATACT-TG-CTACAG
1 CTGTAAAGGTAACACTGAATA-TGTGACTACAG
*
504646 CTGTAAAGGTTACACT
1 CTGTAAAGGTAACACT
504662 ATATTTTAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
29 4 0.06
30 1 0.01
31 37 0.54
32 8 0.12
33 6 0.09
34 2 0.03
35 10 0.15
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.27
Consensus pattern (32 bp):
CTGTAAAGGTAACACTGAATATGTGACTACAG
Found at i:511184 original size:35 final size:34
Alignment explanation
Indices: 511134--511257 Score: 88
Period size: 35 Copynumber: 3.9 Consensus size: 34
511124 GCTGCAGACT
*
511134 CTGTATATTTGCTACAGCTGTAAAGGTAAACCAC
1 CTGTATATTTACTACAGCTGTAAAGGTAAACCAC
* *
511168 CTGTAATATTTACTACAACT-TCAAAGGTAATCCA-
1 CTGT-ATATTTACTACAGCTGT-AAAGGTAAACCAC
* * *
511202 -T-T-CA-GT-GT--A-CTGTAAAGGTAAACCAC
1 CTGTATATTTACTACAGCTGTAAAGGTAAACCAC
*
511228 CTGTAATAGTTACTACAGCTGTAAAGGTAA
1 CTGT-ATATTTACTACAGCTGTAAAGGTAA
511258 CACTGAATAT
Statistics
Matches: 67, Mismatches: 10, Indels: 25
0.66 0.10 0.25
Matches are distributed among these distances:
25 13 0.19
26 2 0.03
27 1 0.01
28 2 0.03
29 1 0.01
30 2 0.03
31 1 0.01
32 2 0.03
33 1 0.01
34 6 0.09
35 36 0.54
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (34 bp):
CTGTATATTTACTACAGCTGTAAAGGTAAACCAC
Found at i:511313 original size:31 final size:32
Alignment explanation
Indices: 511211--511323 Score: 101
Period size: 31 Copynumber: 3.5 Consensus size: 32
511201 ATTCAGTGTA
*
511211 CTGTAAAGGTAAACCACCTGTAATA-GTTACTACAG
1 CTGTAAAGGT-AA-CA-CTG-AATATGTGACTACAG
511246 CTGTAAAGGTAACACTGAATATGTGACATACA-
1 CTGTAAAGGTAACACTGAATATGTGAC-TACAG
* *
511278 -TGTAAAGGTAACAGTGCATACT-TG-CTACAG
1 CTGTAAAGGTAACACTGAATA-TGTGACTACAG
*
511308 CTGTAAAGGTTACACT
1 CTGTAAAGGTAACACT
511324 ATATTTTAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
29 4 0.06
30 1 0.01
31 37 0.54
32 8 0.12
33 6 0.09
34 2 0.03
35 10 0.15
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (32 bp):
CTGTAAAGGTAACACTGAATATGTGACTACAG
Found at i:513087 original size:37 final size:37
Alignment explanation
Indices: 513037--513150 Score: 210
Period size: 37 Copynumber: 3.1 Consensus size: 37
513027 GATTGTGACA
*
513037 TGCATTGTTTTGTTTACAGGGCTGACCTAACACACCT
1 TGCATTGTTTTGTTTACAGGGCCGACCTAACACACCT
*
513074 TGCATTGTTTTGTTTACAGGGCCGACCTAACACACTT
1 TGCATTGTTTTGTTTACAGGGCCGACCTAACACACCT
513111 TGCATTGTTTTGTTTACAGGGCCGACCTAACACACCT
1 TGCATTGTTTTGTTTACAGGGCCGACCTAACACACCT
513148 TGC
1 TGC
513151 TCTCTTCAAT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 74 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.34
Consensus pattern (37 bp):
TGCATTGTTTTGTTTACAGGGCCGACCTAACACACCT
Found at i:513354 original size:53 final size:52
Alignment explanation
Indices: 513274--513373 Score: 164
Period size: 53 Copynumber: 1.9 Consensus size: 52
513264 AGGCCCGGTC
* *
513274 AAGTCCGAGTTCTCTCTGTATCATTAGAATTAAGATGATATTCAGGTCCAATT
1 AAGTCCGAGTTCTCTCTGTATCATTAG-ATTAAGACGATATACAGGTCCAATT
*
513327 AAGTCCGAGTTCTCTCTGTATCATTAGATTAATACGATATACAGGTC
1 AAGTCCGAGTTCTCTCTGTATCATTAGATTAAGACGATATACAGGTC
513374 TGATCAAGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 17 0.39
53 27 0.61
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
AAGTCCGAGTTCTCTCTGTATCATTAGATTAAGACGATATACAGGTCCAATT
Found at i:528467 original size:22 final size:22
Alignment explanation
Indices: 528444--528528 Score: 134
Period size: 22 Copynumber: 3.9 Consensus size: 22
528434 CCAGAACAAG
* *
528444 TCAGAAGTTTACCTTCAGTCAG
1 TCAGAAGTTTACCTTCAGCCAA
*
528466 TCAGAAGTTTACCTTCAACCAA
1 TCAGAAGTTTACCTTCAGCCAA
*
528488 TCAGAAATTTACCTTCAGCCAA
1 TCAGAAGTTTACCTTCAGCCAA
528510 TCAGAAGTTTACCTTCAGC
1 TCAGAAGTTTACCTTCAGC
528529 TTATTAAAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 57 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (22 bp):
TCAGAAGTTTACCTTCAGCCAA
Found at i:528979 original size:12 final size:12
Alignment explanation
Indices: 528955--528995 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
528945 ATCACATTTT
528955 GTCTGTC-GTCC
1 GTCTGTCTGTCC
528966 GTCTGTCTGTCC
1 GTCTGTCTGTCC
528978 GTCCT-TCTGTCC
1 GT-CTGTCTGTCC
528990 GTCTGT
1 GTCTGT
528996 AAACTTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.33
12 16 0.59
13 2 0.07
ACGTcount: A:0.00, C:0.34, G:0.24, T:0.41
Consensus pattern (12 bp):
GTCTGTCTGTCC
Found at i:528986 original size:16 final size:15
Alignment explanation
Indices: 528954--528988 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
528944 GATCACATTT
528954 TGTCTGTCGTCCGTC
1 TGTCTGTCGTCCGTC
*
528969 TGTCTGTCCGTCCTTC
1 TGTCTGT-CGTCCGTC
528985 TGTC
1 TGTC
528989 CGTCTGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.00, C:0.34, G:0.23, T:0.43
Consensus pattern (15 bp):
TGTCTGTCGTCCGTC
Found at i:529460 original size:166 final size:165
Alignment explanation
Indices: 529165--530861 Score: 2526
Period size: 166 Copynumber: 10.2 Consensus size: 165
529155 AGAAATTTTC
* *
529165 AAAAATCTTGTTCTCAAGAACCATAAT--GCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
1 AAAAATCTTCTTCTC-AGAAAC-TAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
529228 GGTAGTGTAGATTCCAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGG
64 GGTAGTGTAGATTCCAAGTTGTGAAAATCATGACCCCC-GGGGTAGGGTGGGGCCACAATGGGGG
*
529293 GTCGAAGTTTTACATAGGATTATATAGAGTAAATCTTT
128 GTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
*
529331 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGACACTTGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* ** *
529396 TAGTGTAGATTCAAAGTTGTGAATTTCATGACCCCCGGGGTAGGTTGGGGCCACAATGGGGGGGT
66 TAGTGTAGATTCCAAGTTGTGAAAATCATGACCCCCGGGGTAGGGTGGGGCCACAAT-GGGGGGT
*
529461 TGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
130 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* *
529497 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGCGTGGAAGCATCCTCAAG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* * ** * * *
529562 AAGTGTAGATTCAAAGTTGTGAATTTCATGACCCCCGGGGTAGGTTGGGGCCACAATGGGAGCTC
66 TAGTGTAGATTCCAAGTTGTGAAAATCATGACCCCCGGGGTAGGGTGGGGCCACAATGGGGGGTC
529627 GAAGTTTTACATAGGAATATATAGAGTAAATCTTT
131 GAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* * *
529662 AAAAATCTTCTTCTCAGAAACTTATCAGCCAGGAAAGCTGACACTTGTGTGGAAGCATGCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
*
529727 TAGTGTAGATTCCAAGTTGTGAAAATCATGACCCCCGCGGGTAGGGTGGGGCCATAATGGGGGGT
66 TAGTGTAGATTCCAAGTTGTGAAAATCATGACCCCCG-GGGTAGGGTGGGGCCACAATGGGGGGT
*
529792 CGAAGTTTTACATAGGAATATAAAAGAGTAAATCTTT
130 CGAAGTTTTACATAGGAATAT-ATAGAGTAAATCTTT
* *
529829 AAAAATCTTCTTCTCAGACACTAATCAGCCAGGAAAGCTGAAACTTGTGGGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
*
529894 TAGTGTAGATTCCAAGTTGTGAAAATCATGACCCCTGGGGGTAGGGTGGGGCCACAATGGGGGGT
66 TAGTGTAGATTCCAAGTTGTGAAAATCATGACCCC-CGGGGTAGGGTGGGGCCACAATGGGGGGT
529959 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
130 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
*
529995 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATGCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* * *
530060 TAGTGTAGATTCCAAGTTATGAAAATCATGACCCCCAGGTGTAGGGTGGGGCAACAATGGGGGGT
66 TAGTGTAGATTCCAAGTTGTGAAAATCATGACCCCC-GGGGTAGGGTGGGGCCACAATGGGGGGT
* * *
530125 CGAAATTTTACATAGGAATTTACAGAGTAAATCTTT
130 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* * * *
530161 AAAAATCTTGTTCTCATG-AAC-CATAAGACCAGGAAAGCTGAAACTTGCGTGGAAGCATCCTCA
1 AAAAATCTTCTTCTCA-GAAACTAATCAG-CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
* * * * **
530224 AGAAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGCGGGTAGGATGGGGCCACAATGAAGG
64 GGTAGTGTAGATTCCAAGTTGTGAAAATCATGACCCCCG-GGGTAGGGTGGGGCCACAATGGGGG
530289 GTCGAAGTTTTACATAGGAATATATAGAGTAAATCTATAT
128 GTCGAAGTTTTACATAGGAATATATAGAGTAAATCT-T-T
* * * * *
530329 AAAAA---TCTTCTCAGAAACTAATCAGCCAGCAAAGCTGACACTTGTATGAAAGCATCCTCAGT
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
** *
530391 TAGTGTAGATTATAAGTTGTGAAAATCATGACCCCCGGGGATAGGTTGGGGCCACAATGGGGTGG
66 TAGTGTAGATTCCAAGTTGTGAAAATCATGACCCCCGGGG-TAGGGTGGGGCCACAA-----TGG
*
530456 GGGGTCGAAGTTTTACATAGGAATATATAGGGTAAATCTTT
125 GGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* *
530497 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGCAAAGCTGACACTTGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
*
530562 TAGTGTAGATTCCAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGT
66 TAGTGTAGATTCCAAGTTGTGAAAATCATGACCCCC-GGGGTAGGGTGGGGCCACAATGGGGGGT
* * * *
530627 TGAAGTTTAACATATGAATATCTAGAGTAAATCTTT
130 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
*
530663 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACATGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* * * *
530728 TAGTGTAGATTCCAAGTTGTGAAAATCATGACCCCTGGGGGGTAGGTTTGGGCCACTATGGGGGG
66 TAGTGTAGATTCCAAGTTGTGAAAATCATGACCCC--CGGGGTAGGGTGGGGCCACAATGGGGGG
* * * * *
530793 TCAAAGTTTAACAAAGGAATGTATAGGGTAAATCTTT
129 TCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
530830 AAAAATCTTCTTCTCAGAAACTAATCAGCCAG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAG
530862 ATGATTCTTT
Statistics
Matches: 1396, Mismatches: 109, Indels: 51
0.90 0.07 0.03
Matches are distributed among these distances:
164 8 0.01
165 252 0.18
166 733 0.53
167 243 0.17
168 13 0.01
169 1 0.00
170 39 0.03
171 103 0.07
172 4 0.00
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (165 bp):
AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
TAGTGTAGATTCCAAGTTGTGAAAATCATGACCCCCGGGGTAGGGTGGGGCCACAATGGGGGGTC
GAAGTTTTACATAGGAATATATAGAGTAAATCTTT
Found at i:535616 original size:23 final size:24
Alignment explanation
Indices: 535572--535634 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
535562 TGATCATTGG
* *
535572 GATATTCCTAGTGTGA-CGTTTTA
1 GATATCCCTAATGTGATCGTTTTA
*
535595 GATATCCCTAATGTGATC-TTTTT
1 GATATCCCTAATGTGATCGTTTTA
535618 GATATACCC-AATGTGAT
1 GATAT-CCCTAATGTGAT
535635 ATTCCTAGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 31 0.89
24 4 0.11
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.41
Consensus pattern (24 bp):
GATATCCCTAATGTGATCGTTTTA
Found at i:535741 original size:23 final size:23
Alignment explanation
Indices: 535686--535741 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
535676 GTAATATTTC
* *
535686 AGATATTCCTTGTGTGATCTTTT
1 AGATATCCCTGGTGTGATCTTTT
* *
535709 AGATACCCCTGGTGTGGTCTTCTT
1 AGATATCCCTGGTGTGATCTT-TT
535733 -GATATCCCT
1 AGATATCCCT
535742 ATTGTGATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 25 0.93
24 2 0.07
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.43
Consensus pattern (23 bp):
AGATATCCCTGGTGTGATCTTTT
Found at i:536104 original size:23 final size:23
Alignment explanation
Indices: 536037--536106 Score: 61
Period size: 23 Copynumber: 3.1 Consensus size: 23
536027 ATTAATTTTG
* * *
536037 TATCTGTAGTGTGATCATCCTGA
1 TATCCGTAGTGTGATCTTACTGA
* * * *
536060 TA-CCCTAGTGTTATTTTTCTGA
1 TATCCGTAGTGTGATCTTACTGA
*
536082 TATCCGTAGTGTGATGTTACTGA
1 TATCCGTAGTGTGATCTTACTGA
536105 TA
1 TA
536107 CAATATCTGT
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
22 16 0.44
23 20 0.56
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.43
Consensus pattern (23 bp):
TATCCGTAGTGTGATCTTACTGA
Found at i:548102 original size:37 final size:37
Alignment explanation
Indices: 548061--548207 Score: 213
Period size: 37 Copynumber: 4.0 Consensus size: 37
548051 GTCTGTTGCA
548061 TTTGTCTGTCTGTGTCTATGTCACTGACAGCTGTGGG
1 TTTGTCTGTCTGTGTCTATGTCACTGACAGCTGTGGG
*
548098 TTTGTCTGTCTGTGTCTTTGTCACTGACAGCTGTGGG
1 TTTGTCTGTCTGTGTCTATGTCACTGACAGCTGTGGG
* * ***
548135 TTTGTCTGTCTGTATCTATGTCAATGACAGCTGTTAA
1 TTTGTCTGTCTGTGTCTATGTCACTGACAGCTGTGGG
* * *
548172 TTTGTCCGTCTGTTTATATGTCACTGACAGCTGTGG
1 TTTGTCTGTCTGTGTCTATGTCACTGACAGCTGTGG
548208 ATATACCAGT
Statistics
Matches: 97, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 97 1.00
ACGTcount: A:0.14, C:0.18, G:0.26, T:0.42
Consensus pattern (37 bp):
TTTGTCTGTCTGTGTCTATGTCACTGACAGCTGTGGG
Found at i:548103 original size:21 final size:21
Alignment explanation
Indices: 548079--548140 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
548069 TCTGTGTCTA
548079 TGTCACTGACAGCTGTGGGTT
1 TGTCACTGACAGCTGTGGGTT
* **
548100 TGT--CTG---TCTGTGTCTT
1 TGTCACTGACAGCTGTGGGTT
548116 TGTCACTGACAGCTGTGGGTT
1 TGTCACTGACAGCTGTGGGTT
548137 TGTC
1 TGTC
548141 TGTCTGTATC
Statistics
Matches: 30, Mismatches: 6, Indels: 10
0.65 0.13 0.22
Matches are distributed among these distances:
16 10 0.33
18 3 0.10
19 3 0.10
21 14 0.47
ACGTcount: A:0.10, C:0.19, G:0.31, T:0.40
Consensus pattern (21 bp):
TGTCACTGACAGCTGTGGGTT
Found at i:548759 original size:2 final size:2
Alignment explanation
Indices: 548752--548792 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
548742 AACTGCAGAG
*
548752 CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
548793 ACACACAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:553664 original size:35 final size:37
Alignment explanation
Indices: 553582--553686 Score: 119
Period size: 35 Copynumber: 2.9 Consensus size: 37
553572 AACTATTGTA
* * *
553582 TGATGTATTTTGGGGTTTGTTCAGTTACCT-T-TGCG
1 TGATGTATTTTGGGATATGTTCAGTTACCTATGTGAG
* *
553617 TGATGTAATTTGGGATGTGTTCAGTTACCTATGTGAG
1 TGATGTATTTTGGGATATGTTCAGTTACCTATGTGAG
* *
553654 T-A-GTATTTTGGGATATATTCAGTAACCTATGTG
1 TGATGTATTTTGGGATATGTTCAGTTACCTATGTG
553687 CTTTTCAGAC
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
35 54 0.90
36 2 0.03
37 4 0.07
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.44
Consensus pattern (37 bp):
TGATGTATTTTGGGATATGTTCAGTTACCTATGTGAG
Found at i:555170 original size:47 final size:47
Alignment explanation
Indices: 555116--555639 Score: 785
Period size: 47 Copynumber: 11.5 Consensus size: 47
555106 GTATAAGATG
*
555116 AGTGCCCCTCTGACTTGCTCTGTGTTTACTGTTATAGATGACTTAAA
1 AGTGCCCCTCTGACTTGCTCTGTGTTTACTGTTATAGATGACTTACA
* * *
555163 AGTGCCCCTCTGAC-T--T-AGTGTTTAATGTTATAGATGACTTAAA
1 AGTGCCCCTCTGACTTGCTCTGTGTTTACTGTTATAGATGACTTACA
* *
555206 AGTGCCCCTCTGAC-T--T-AGTGTTTACTGTTTTAGATGACTTACA
1 AGTGCCCCTCTGACTTGCTCTGTGTTTACTGTTATAGATGACTTACA
*
555249 AGTGCCCATCTGACTTGCTCTGTGTTTACTGTTATAGATGACTTACA
1 AGTGCCCCTCTGACTTGCTCTGTGTTTACTGTTATAGATGACTTACA
*
555296 AGTGCCCCTTTGACTTGCTCTGTGTTTACTGTTATAGATGACTTACA
1 AGTGCCCCTCTGACTTGCTCTGTGTTTACTGTTATAGATGACTTACA
*
555343 AGTGCCCCTCTGACTTGCTTTGTGTTTACTGTTATAGATGACTTACA
1 AGTGCCCCTCTGACTTGCTCTGTGTTTACTGTTATAGATGACTTACA
555390 AGTGCCCCTCTGACTTGCTCTGTGTTTACTG-T-T--AT-A--TACA
1 AGTGCCCCTCTGACTTGCTCTGTGTTTACTGTTATAGATGACTTACA
* * *
555430 AGTGCCCCTCTGACTTACACTGTGTTTATTG-TATAGATGACTTACA
1 AGTGCCCCTCTGACTTGCTCTGTGTTTACTGTTATAGATGACTTACA
* *
555476 AGTGCCCCTCTGACTTACTCTGTGTTTATTG-TATAGATGACTTACA
1 AGTGCCCCTCTGACTTGCTCTGTGTTTACTGTTATAGATGACTTACA
*
555522 AGTGCCCCTCTGACTTGCTTTGTGTTTACTGTTATAGATGACTTACA
1 AGTGCCCCTCTGACTTGCTCTGTGTTTACTGTTATAGATGACTTACA
*
555569 AGTGCCCCTCTGACTTGCTTTGTGTTTACTGTTATAGATGACTTACA
1 AGTGCCCCTCTGACTTGCTCTGTGTTTACTGTTATAGATGACTTACA
555616 AGTGCCCCTCTGACTTGCTCTGTG
1 AGTGCCCCTCTGACTTGCTCTGTG
555640 CCTGTATGGA
Statistics
Matches: 445, Mismatches: 21, Indels: 22
0.91 0.04 0.05
Matches are distributed among these distances:
40 33 0.07
41 1 0.00
42 1 0.00
43 82 0.18
44 3 0.01
45 1 0.00
46 80 0.18
47 244 0.55
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (47 bp):
AGTGCCCCTCTGACTTGCTCTGTGTTTACTGTTATAGATGACTTACA
Found at i:555546 original size:179 final size:181
Alignment explanation
Indices: 555116--555604 Score: 728
Period size: 180 Copynumber: 2.7 Consensus size: 181
555106 GTATAAGATG
*
555116 AGTGCCCCTCTGACTTGCTCTGTGTTTACTGTTATAGATGACTTAAAAGTGCCCCTCTGA----C
1 AGTGCCCCTCTGACTTGCTCTGTGTTTACTGTTATAGATGACTTACAAGTGCCCCTCTGACTTGC
* * * *
555177 TTAGTGTTTAATGTTATAGATGACTTAAAAGTGCCCCTCTGAC-T--TAGTGTTTACTGTTTTAG
66 TTTGTGTTTACTGTTATAGATGACTTACAAGTGCCCCTCTGACTTGCTTGTGTTTACTG--TT--
* *
555239 ATGACTTACAAGTGCCCATCTGACTTGCTCTGTGTTTACTGTTATAGATGACTTACA
127 AT-AC-TACAAGTGCCCATCTGACTTACACTGTGTTTACTGTTATAGATGACTTACA
*
555296 AGTGCCCCTTTGACTTGCTCTGTGTTTACTGTTATAGATGACTTACAAGTGCCCCTCTGACTTGC
1 AGTGCCCCTCTGACTTGCTCTGTGTTTACTGTTATAGATGACTTACAAGTGCCCCTCTGACTTGC
555361 TTTGTGTTTACTGTTATAGATGACTTACAAGTGCCCCTCTGACTTGCTCTGTGTTTACTGTTATA
66 TTTGTGTTTACTGTTATAGATGACTTACAAGTGCCCCTCTGACTTGCT-TGTGTTTACTGTTATA
* *
555426 -TACAAGTGCCCCTCTGACTTACACTGTGTTTATTG-TATAGATGACTTACA
130 CTACAAGTGCCCATCTGACTTACACTGTGTTTACTGTTATAGATGACTTACA
* *
555476 AGTGCCCCTCTGACTTACTCTGTGTTTATTG-TATAGATGACTTACAAGTGCCCCTCTGACTTGC
1 AGTGCCCCTCTGACTTGCTCTGTGTTTACTGTTATAGATGACTTACAAGTGCCCCTCTGACTTGC
555540 TTTGTGTTTACTGTTATAGATGACTTACAAGTGCCCCTCTGACTTGCTTTGTGTTTACTGTTATA
66 TTTGTGTTTACTGTTATAGATGACTTACAAGTGCCCCTCTGACTTGC-TTGTGTTTACTGTTATA
555605 GATGACTTAC
Statistics
Matches: 287, Mismatches: 13, Indels: 19
0.90 0.04 0.06
Matches are distributed among these distances:
179 96 0.33
180 102 0.36
181 31 0.11
183 1 0.00
184 43 0.15
185 1 0.00
186 2 0.01
187 1 0.00
188 10 0.03
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (181 bp):
AGTGCCCCTCTGACTTGCTCTGTGTTTACTGTTATAGATGACTTACAAGTGCCCCTCTGACTTGC
TTTGTGTTTACTGTTATAGATGACTTACAAGTGCCCCTCTGACTTGCTTGTGTTTACTGTTATAC
TACAAGTGCCCATCTGACTTACACTGTGTTTACTGTTATAGATGACTTACA
Found at i:555589 original size:226 final size:227
Alignment explanation
Indices: 555054--555639 Score: 819
Period size: 226 Copynumber: 2.6 Consensus size: 227
555044 TATACATATC
* * * * * *
555054 TTTACTGCTATAGATGACCTACAAGTGCACCTTTGACTTGATCTGTG-TTAATG-TATA-A-GA-
1 TTTACTGTTATAGATGACTTACAAGTGCCCCTCTGACTTGCTCTGTGTTTACTGTTATAGATGAC
* * *
555114 -T--GAGTGCCCCTCTGACTTGCTCTGTGTTTACTGTTATAGATGACTTAAAAGTGCCCCTCTGA
66 TTACAAGTGCCCCTCTGACTTGCTTTGTGTTTACTGTTATAGATGACTTACAAGTGCCCCTCTGA
* *
555176 C-T--T-AGTGTTTAATGTTATAGATGACTTAAAAGTGCCCCTCTGACTTAGTGTTTACTGTTTT
131 CTTGCTCTGTGTTTAATGTTATA-ATGAC---AAAGTGCCCCTCTGACTTAGTGTTTACTGTTAT
*
555237 AGATGACTTACAAGTGCCCATCTGACTTGCTCTGTG
192 AGATGACTTACAAGTGCCCATCTGACTTACTCTGTG
*
555273 TTTACTGTTATAGATGACTTACAAGTGCCCCTTTGACTTGCTCTGTGTTTACTGTTATAGATGAC
1 TTTACTGTTATAGATGACTTACAAGTGCCCCTCTGACTTGCTCTGTGTTTACTGTTATAGATGAC
555338 TTACAAGTGCCCCTCTGACTTGCTTTGTGTTTACTGTTATAGATGACTTACAAGTGCCCCTCTGA
66 TTACAAGTGCCCCTCTGACTTGCTTTGTGTTTACTGTTATAGATGACTTACAAGTGCCCCTCTGA
* *
555403 CTTGCTCTGTGTTTACTGTTAT-AT-AC-AAGTGCCCCTCTGACTTACACTGTGTTTATTG-TAT
131 CTTGCTCTGTGTTTAATGTTATAATGACAAAGTGCCCCTCTGACTT--A--GTGTTTACTGTTAT
*
555464 AGATGACTTACAAGTGCCCCTCTGACTTACTCTGTG
192 AGATGACTTACAAGTGCCCATCTGACTTACTCTGTG
* *
555500 TTTATTG-TATAGATGACTTACAAGTGCCCCTCTGACTTGCTTTGTGTTTACTGTTATAGATGAC
1 TTTACTGTTATAGATGACTTACAAGTGCCCCTCTGACTTGCTCTGTGTTTACTGTTATAGATGAC
555564 TTACAAGTGCCCCTCTGACTTGCTTTGTGTTTACTGTTATAGATGACTTACAAGTGCCCCTCTGA
66 TTACAAGTGCCCCTCTGACTTGCTTTGTGTTTACTGTTATAGATGACTTACAAGTGCCCCTCTGA
555629 CTTGCTCTGTG
131 CTTGCTCTGTG
555640 CCTGTATGGA
Statistics
Matches: 334, Mismatches: 17, Indels: 25
0.89 0.05 0.07
Matches are distributed among these distances:
219 43 0.13
220 5 0.01
221 4 0.01
222 1 0.00
223 2 0.01
224 17 0.05
225 1 0.00
226 132 0.40
227 101 0.30
228 12 0.04
229 2 0.01
230 1 0.00
231 13 0.04
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (227 bp):
TTTACTGTTATAGATGACTTACAAGTGCCCCTCTGACTTGCTCTGTGTTTACTGTTATAGATGAC
TTACAAGTGCCCCTCTGACTTGCTTTGTGTTTACTGTTATAGATGACTTACAAGTGCCCCTCTGA
CTTGCTCTGTGTTTAATGTTATAATGACAAAGTGCCCCTCTGACTTAGTGTTTACTGTTATAGAT
GACTTACAAGTGCCCATCTGACTTACTCTGTG
Found at i:556939 original size:2 final size:2
Alignment explanation
Indices: 556932--556989 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
556922 AACATTCATA
*
556932 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
556974 TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC
556990 CAGTAACACA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:558147 original size:440 final size:434
Alignment explanation
Indices: 557326--558391 Score: 1577
Period size: 440 Copynumber: 2.4 Consensus size: 434
557316 TGTCCAGGCC
557326 GTAACTTAAATACCCTTTGACATTAAGACTTCAAACTTGGAATATAGGTAGATGGTATTGAGAAG
1 GTAACTTAAATACCCTTTGACATTAAGACTTCAAACTTGGAATATAGGTAGATGGTATTGAGAAG
* *
557391 GAGTGCACGCCACCAAAATCTTTGACCTTGACGTA-TTTTGTTCTTCAAGGTCAAGCATTTTATA
66 GAGTGCACGCCACC-AAATATTTGACCTTGACCTATTTTTG-TCTTCAAGGTCAAGCATTTTATA
* * * * *
557455 AAAAATATTGTCCAGACCATAACACAAGAC-CTCTTCAACATACAGACTTTAAACTTCTATCATA
129 AAAAATATTGTCCGGACCATAACATAAGACTC-CTTCAACATACAGGCTTTTAACTTGTATCATA
557519 GATAGATGGTATATAACCAAGCTGAACCCCACCAAAATGTTTGACCTTGACCTTAATTTTTAATT
193 GATAGATGGTATATAACCAAGCTGAACCCCACCAAAATGTTTGACCTTGACCTTAATTTTTAATT
557584 TCAAGGTCAAATTGGAAAAAACGTCATTGTTCAACTCCTAAATATACTTCGACAGAAGGACTTCA
258 TCAAGGTCAAATTGGAAAAAACGTCATTGTTCAACTCCTAAATATACTTCGACAGAAGGACTTCA
* *
557649 AACTTTAAACAAAGAACAATTATAATACACTGAGGTGTTCTATTGATTAATATTTGACCTTTACC
323 AACTTTAAACAAAGAACAATAATAATACACTGAGGTGTTCTATTGATTAATATTTGACCTTGACC
557714 TTGTTTTACTCAAGGTCAAATTAAGAAAAAATAATAAAATTTTGTCTGGGTT
388 TTGTTTTACTCAAGGTCAAATTAAGAAAAAA-AAT----TTTTGTCTGGGTT
* * *
557766 GTAACTTGAATACCCTTTGACATTAAGACTTCAAACTTGAAATATAGGTCGATGGTATTGAGAAG
1 GTAACTTAAATACCCTTTGACATTAAGACTTCAAACTTGGAATATAGGTAGATGGTATTGAGAAG
* *
557831 GAGTGCACGCCACCAAACTATTTGACCTTGACTTATTTTTGTCTTCAAGGTCAAGCGTTTTATAA
66 GAGTGCACGCCACCAAA-TATTTGACCTTGACCTATTTTTGTCTTCAAGGTCAAGCATTTTATAA
*
557896 AATATATTGTCCGGACCATAACATAAGACTCCTTCAACATACAGGCTTTTAACTTGTATCATAGA
130 AAAATATTGTCCGGACCATAACATAAGACTCCTTCAACATACAGGCTTTTAACTTGTATCATAGA
* ** * *
557961 TAGATGGTATATAACCAAGTTGAACCTTACCAAAATGTTTGACCTTGACCTTATTTTTTTATTTC
195 TAGATGGTATATAACCAAGCTGAACCCCACCAAAATGTTTGACCTTGACCTTAATTTTTAATTTC
* *
558026 AAGGTCAAATTGGAAAAAACGTCATTGTTCAACTCCTAAATATACTTTGACAGAAGGACTTTAAA
260 AAGGTCAAATTGGAAAAAACGTCATTGTTCAACTCCTAAATATACTTCGACAGAAGGACTTCAAA
* *
558091 CTTTAAACAAAGAATAATAATAATACACTGAGGTGTTCTATTGATTAATATTTGACCTTGCCCTT
325 CTTTAAACAAAGAACAATAATAATACACTGAGGTGTTCTATTGATTAATATTTGACCTTGACCTT
*
558156 GTTTTACTCAAGGTCAAATTAAGAAGAAAAATTTTTGTCTGGGTT
390 GTTTTACTCAAGGTCAAATTAAGAAAAAAAATTTTTGTCTGGGTT
* *
558201 GTAACTTAAATACCATTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTGAGTAA
1 GTAACTTAAATACCCTTTGACATTAAGACTTCAAACTTGGAATATAGGTAGATGGTATTGAG-AA
* * * * * ** *
558266 -GAGTGCACAG-CACCATAATTTTTTACCTTGACCAATCTTTTGTC-TCAAGTTGATTCATTTTC
65 GGAGTGCAC-GCCACCA-AATATTTGACCTTGACCTAT-TTTTGTCTTCAAGGTCAAGCATTTTA
** * * * * * *
558328 TAAAAAATATTGTATGAATCATAACATGAGATTCCTTAAACATACATG-TTTTAAACTTGTATCA
127 TAAAAAATATTGTCCGGACCATAACATAAGACTCCTTCAACATACAGGCTTTT-AACTTGTATCA
558392 CATATGAATA
Statistics
Matches: 570, Mismatches: 48, Indels: 21
0.89 0.08 0.03
Matches are distributed among these distances:
434 4 0.01
435 159 0.28
436 12 0.02
439 6 0.01
440 383 0.67
441 6 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (434 bp):
GTAACTTAAATACCCTTTGACATTAAGACTTCAAACTTGGAATATAGGTAGATGGTATTGAGAAG
GAGTGCACGCCACCAAATATTTGACCTTGACCTATTTTTGTCTTCAAGGTCAAGCATTTTATAAA
AAATATTGTCCGGACCATAACATAAGACTCCTTCAACATACAGGCTTTTAACTTGTATCATAGAT
AGATGGTATATAACCAAGCTGAACCCCACCAAAATGTTTGACCTTGACCTTAATTTTTAATTTCA
AGGTCAAATTGGAAAAAACGTCATTGTTCAACTCCTAAATATACTTCGACAGAAGGACTTCAAAC
TTTAAACAAAGAACAATAATAATACACTGAGGTGTTCTATTGATTAATATTTGACCTTGACCTTG
TTTTACTCAAGGTCAAATTAAGAAAAAAAATTTTTGTCTGGGTT
Found at i:558935 original size:14 final size:14
Alignment explanation
Indices: 558901--558961 Score: 79
Period size: 14 Copynumber: 4.4 Consensus size: 14
558891 AACTACAAGG
*
558901 AACAAACTTTA-GT
1 AACAAACTTCAGGT
* *
558914 AACTAACTTCAGTT
1 AACAAACTTCAGGT
*
558928 AACAAACTACAGGT
1 AACAAACTTCAGGT
558942 AACAAACTTCAGGT
1 AACAAACTTCAGGT
558956 AACAAA
1 AACAAA
558962 TAAACTATAT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
13 9 0.22
14 31 0.77
ACGTcount: A:0.48, C:0.20, G:0.10, T:0.23
Consensus pattern (14 bp):
AACAAACTTCAGGT
Found at i:558993 original size:18 final size:18
Alignment explanation
Indices: 558942--558997 Score: 78
Period size: 18 Copynumber: 3.1 Consensus size: 18
558932 AACTACAGGT
558942 AACAAACTTCAGGTAACA
1 AACAAACTTCAGGTAACA
* *
558960 AATAAACTAT-ATGTAACA
1 AACAAACT-TCAGGTAACA
558978 AACAAACTTCAGGTAACA
1 AACAAACTTCAGGTAACA
558996 AA
1 AA
558998 AACTAAGCTG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 1 0.03
18 30 0.94
19 1 0.03
ACGTcount: A:0.54, C:0.18, G:0.09, T:0.20
Consensus pattern (18 bp):
AACAAACTTCAGGTAACA
Found at i:562460 original size:1 final size:1
Alignment explanation
Indices: 562456--562480 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
562446 ACTTAAAAAT
562456 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
562481 CTGCTGATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:562780 original size:34 final size:34
Alignment explanation
Indices: 562737--562977 Score: 376
Period size: 34 Copynumber: 7.1 Consensus size: 34
562727 AGACGTCTGT
* * * *
562737 GTCAGACTGTTGACTAAGGTAAGACCTTTGTTTG
1 GTCAGACTGTTGGCCAAGGTAAGACTTTTGATTG
* *
562771 GTCAGACTGTTTGCCAAGGTAAGACTTTTGATCG
1 GTCAGACTGTTGGCCAAGGTAAGACTTTTGATTG
*
562805 GTCAGACTGTTGGCCACGGTAAGACTTTTGATTG
1 GTCAGACTGTTGGCCAAGGTAAGACTTTTGATTG
562839 GTCAGACTGTTGGCCAAGGTAAGA-TTTTGATTG
1 GTCAGACTGTTGGCCAAGGTAAGACTTTTGATTG
562872 GTCAGACTGTTGGCCAAGGTAAGACTTTTGATTG
1 GTCAGACTGTTGGCCAAGGTAAGACTTTTGATTG
*
562906 GTCAGACTGTTGGCCATGGTAAGACTTTTGATTG
1 GTCAGACTGTTGGCCAAGGTAAGACTTTTGATTG
* * *
562940 GTCAGACTATTGGCCAAGGTAAGACCTTTGTTTG
1 GTCAGACTGTTGGCCAAGGTAAGACTTTTGATTG
562974 GTCA
1 GTCA
562978 TCTTTTCTCC
Statistics
Matches: 191, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
33 33 0.17
34 158 0.83
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (34 bp):
GTCAGACTGTTGGCCAAGGTAAGACTTTTGATTG
Found at i:562829 original size:18 final size:18
Alignment explanation
Indices: 562774--562834 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
562764 TTGTTTGGTC
*
562774 AGACTGTTTGCCAAGGTA
1 AGACTGTTTGCCACGGTA
*
562792 AGACT-TTTG--ATCGGTC
1 AGACTGTTTGCCA-CGGTA
*
562808 AGACTGTTGGCCACGGTA
1 AGACTGTTTGCCACGGTA
562826 AGACT-TTTG
1 AGACTGTTTG
562835 ATTGGTCAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
15 1 0.03
16 8 0.24
17 10 0.29
18 14 0.41
19 1 0.03
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (18 bp):
AGACTGTTTGCCACGGTA
Found at i:562913 original size:101 final size:102
Alignment explanation
Indices: 562737--562977 Score: 403
Period size: 101 Copynumber: 2.4 Consensus size: 102
562727 AGACGTCTGT
* * *
562737 GTCAGACTGTTGACTAAGGTAAGACCTTTGTTTGGTCAGACTGTTTGCCAAGGTAAGACTTTTGA
1 GTCAGACTGTTGGCCAAGGTAAGACCTTTGTTTGGTCAGACTGTTGGCCAAGGTAAGACTTTTGA
562802 TCGGTCAGACTGTTGGCCACGGTAAGACTTTTGATTG
66 TCGGTCAGACTGTTGGCCACGGTAAGACTTTTGATTG
* *
562839 GTCAGACTGTTGGCCAAGGTAAGA-TTTTGATTGGTCAGACTGTTGGCCAAGGTAAGACTTTTGA
1 GTCAGACTGTTGGCCAAGGTAAGACCTTTGTTTGGTCAGACTGTTGGCCAAGGTAAGACTTTTGA
* *
562903 TTGGTCAGACTGTTGGCCATGGTAAGACTTTTGATTG
66 TCGGTCAGACTGTTGGCCACGGTAAGACTTTTGATTG
*
562940 GTCAGACTATTGGCCAAGGTAAGACCTTTGTTTGGTCA
1 GTCAGACTGTTGGCCAAGGTAAGACCTTTGTTTGGTCA
562978 TCTTTTCTCC
Statistics
Matches: 128, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
101 95 0.74
102 33 0.26
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (102 bp):
GTCAGACTGTTGGCCAAGGTAAGACCTTTGTTTGGTCAGACTGTTGGCCAAGGTAAGACTTTTGA
TCGGTCAGACTGTTGGCCACGGTAAGACTTTTGATTG
Found at i:573320 original size:62 final size:62
Alignment explanation
Indices: 573223--573434 Score: 415
Period size: 62 Copynumber: 3.4 Consensus size: 62
573213 GCGGTGGGAG
*
573223 TGGTAATCACTGCAAGAACCACACATTGCATATTATTACTCTATACCATGAAAAGGGAAACA
1 TGGTAGTCACTGCAAGAACCACACATTGCATATTATTACTCTATACCATGAAAAGGGAAACA
573285 TGGTAGTCACTGCAAGAACCACACATTGCATATTATTACTCTATACCATGAAAAGGGAAACA
1 TGGTAGTCACTGCAAGAACCACACATTGCATATTATTACTCTATACCATGAAAAGGGAAACA
573347 TGGTAGTCACTGCAAGAACCACACATTGCATATTATTACTCTATACCATGAAAAGGGAAACA
1 TGGTAGTCACTGCAAGAACCACACATTGCATATTATTACTCTATACCATGAAAAGGGAAACA
573409 TGGTAGTCACTGCAAGAACCACACAT
1 TGGTAGTCACTGCAAGAACCACACAT
573435 ACTATTTACT
Statistics
Matches: 149, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 149 1.00
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.24
Consensus pattern (62 bp):
TGGTAGTCACTGCAAGAACCACACATTGCATATTATTACTCTATACCATGAAAAGGGAAACA
Found at i:573472 original size:37 final size:37
Alignment explanation
Indices: 573422--573496 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
573412 TAGTCACTGC
* * *
573422 AAGAACCACACATACTATTTACTCATTGACCATGAAA
1 AAGAACCACACATACTAGTGACTCACTGACCATGAAA
*
573459 AAGAACCACACATATTAGTGACTCACTGACCATGAAA
1 AAGAACCACACATACTAGTGACTCACTGACCATGAAA
573496 A
1 A
573497 GGGAAACATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.44, C:0.24, G:0.11, T:0.21
Consensus pattern (37 bp):
AAGAACCACACATACTAGTGACTCACTGACCATGAAA
Found at i:576649 original size:2 final size:2
Alignment explanation
Indices: 576642--576697 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
576632 TTAAAAGCAT
576642 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
576684 GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA
576698 TTTTATTTCA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:578709 original size:26 final size:26
Alignment explanation
Indices: 578673--578857 Score: 298
Period size: 26 Copynumber: 7.1 Consensus size: 26
578663 TGGAAGAAAA
*
578673 ATTCAGGTAAATAATTACGGTATATC
1 ATTCAGGTAAATAATTACGGTAAATC
578699 ATTCAGGTAAATAATTACGGTAAATC
1 ATTCAGGTAAATAATTACGGTAAATC
* * *
578725 ATTCAGGTAAATAAATATGGTAATTC
1 ATTCAGGTAAATAATTACGGTAAATC
*
578751 ATTCAGGTAAATAATTACGGTAATTC
1 ATTCAGGTAAATAATTACGGTAAATC
*
578777 ATTCAGGTAAATAATTACGGTAAAAC
1 ATTCAGGTAAATAATTACGGTAAATC
*
578803 ATTCAGGTAAAAAATTACGGTAAATC
1 ATTCAGGTAAATAATTACGGTAAATC
*
578829 ATTCAGGTAAATAATTACGGAAAATC
1 ATTCAGGTAAATAATTACGGTAAATC
578855 ATT
1 ATT
578858 GGCTGAAATG
Statistics
Matches: 147, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 147 1.00
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (26 bp):
ATTCAGGTAAATAATTACGGTAAATC
Found at i:585165 original size:2 final size:2
Alignment explanation
Indices: 585160--585192 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
585150 TATGTGGATA
585160 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
585193 CACTAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:585790 original size:1 final size:1
Alignment explanation
Indices: 585786--585810 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
585776 TTTAGTTTAG
585786 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
585811 GGGGGGGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:592410 original size:127 final size:128
Alignment explanation
Indices: 592246--592506 Score: 488
Period size: 128 Copynumber: 2.0 Consensus size: 128
592236 TTTACTTGTC
*
592246 ATTTTGTCTAAGAAATGGTAATTCTTACATTATA-TTTTTGTAAACAACTATAAGACTCGAGCTT
1 ATTTTGTCTAAGAAATGGTAATTCTTACATTACATTTTTTGTAAACAACTATAAGACTCGAGCTT
*
592310 TGTTTACATAACAACAAATTCTTACCTCTGTATCTCACTCGTAACTTGACTTTAACATTCAAT
66 TGTTTACATAACAACAAATTCTTACCTCTGTATCTCAATCGTAACTTGACTTTAACATTCAAT
592373 ATTTTGTCTAAGAAATGGTAATTCTTACATTACATTTTTTGTAAACAACTATAAGACTCGAGCTT
1 ATTTTGTCTAAGAAATGGTAATTCTTACATTACATTTTTTGTAAACAACTATAAGACTCGAGCTT
*
592438 TGTTTACATAACAACTAATTCTTACCTCTGTATCTCAATCGTAACTTGACTTTAACATTCAAT
66 TGTTTACATAACAACAAATTCTTACCTCTGTATCTCAATCGTAACTTGACTTTAACATTCAAT
592501 ATTTTG
1 ATTTTG
592507 GTCAATCATT
Statistics
Matches: 130, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
127 33 0.25
128 97 0.75
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.40
Consensus pattern (128 bp):
ATTTTGTCTAAGAAATGGTAATTCTTACATTACATTTTTTGTAAACAACTATAAGACTCGAGCTT
TGTTTACATAACAACAAATTCTTACCTCTGTATCTCAATCGTAACTTGACTTTAACATTCAAT
Found at i:596871 original size:1 final size:1
Alignment explanation
Indices: 596865--596894 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
596855 TCAAAACTGT
596865 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
596895 GGGGGGGGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:603668 original size:29 final size:29
Alignment explanation
Indices: 603626--603682 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
603616 TACATGTACA
603626 TCTCTCTCTCTGCATGTTGCCATTTTTTG
1 TCTCTCTCTCTGCATGTTGCCATTTTTTG
603655 TCTCTCTCTCTGCATGTTGCCATTTTTT
1 TCTCTCTCTCTGCATGTTGCCATTTTTT
603683 AAAGGTTCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.07, C:0.28, G:0.12, T:0.53
Consensus pattern (29 bp):
TCTCTCTCTCTGCATGTTGCCATTTTTTG
Found at i:610442 original size:2 final size:2
Alignment explanation
Indices: 610437--610522 Score: 140
Period size: 2 Copynumber: 43.5 Consensus size: 2
610427 CCCCCTCCCC
610437 CT CT CT CT AC- CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT -CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
610479 CT CT CT CT C- CT CT CT CT CT CT CT CT CT CT CG CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
610520 CT C
1 CT C
610523 AAATATTTTA
Statistics
Matches: 79, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
1 2 0.03
2 76 0.96
3 1 0.01
ACGTcount: A:0.01, C:0.51, G:0.01, T:0.47
Consensus pattern (2 bp):
CT
Found at i:614355 original size:14 final size:14
Alignment explanation
Indices: 614336--614377 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
614326 ATATCAACTG
*
614336 ATATAGTTACAAAC
1 ATATAGATACAAAC
614350 ATATAGATACAAAC
1 ATATAGATACAAAC
614364 ATATAGATACAAAC
1 ATATAGATACAAAC
614378 TTCTATACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.55, C:0.14, G:0.07, T:0.24
Consensus pattern (14 bp):
ATATAGATACAAAC
Found at i:618196 original size:2 final size:2
Alignment explanation
Indices: 618191--618217 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
618181 CCCCCCCCCC
618191 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
618218 GTAATATCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:630933 original size:2 final size:2
Alignment explanation
Indices: 630926--631010 Score: 143
Period size: 2 Copynumber: 42.5 Consensus size: 2
630916 GTTGACAAAA
*
630926 TC TC TC TC TC TC TC TC TC TC TC TC TC AC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* *
630968 TC TC TC TT TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
631010 T
1 T
631011 TTTATAAATA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.01, C:0.47, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:634068 original size:13 final size:13
Alignment explanation
Indices: 634050--634074 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
634040 AACAACGGCG
634050 AAAAATTAAAAAA
1 AAAAATTAAAAAA
634063 AAAAATTAAAAA
1 AAAAATTAAAAA
634075 GTTAAAGTTC
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAATTAAAAAA
Found at i:636216 original size:21 final size:21
Alignment explanation
Indices: 636176--636216 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
636166 AAAAACAAGG
* *
636176 ATCAAAATATTGCGCAAAACA
1 ATCAAAATATGGCACAAAACA
*
636197 ATCAAAATATGGCACCAAAC
1 ATCAAAATATGGCACAAAAC
636217 CAGATGCAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.22, G:0.10, T:0.17
Consensus pattern (21 bp):
ATCAAAATATGGCACAAAACA
Found at i:644680 original size:55 final size:52
Alignment explanation
Indices: 644577--644686 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 52
644567 CAAACACAAC
*
644577 GCGACCTATTATGAACTTTTAATATTTTTTAAATTGTGATTTTGTACATTTT
1 GCGACCTAATATGAACTTTTAATATTTTTTAAATTGTGATTTTGTACATTTT
*
644629 GCGACCTAATATGAAC-TTTAATATTTTTTTTTTGAATTGTGATTTTGTACATTTT
1 GCGACCTAATATGAACTTTTAATA----TTTTTTAAATTGTGATTTTGTACATTTT
644684 GCG
1 GCG
644687 GCCCGGAGTA
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
51 7 0.13
52 15 0.29
55 30 0.58
ACGTcount: A:0.25, C:0.10, G:0.14, T:0.51
Consensus pattern (52 bp):
GCGACCTAATATGAACTTTTAATATTTTTTAAATTGTGATTTTGTACATTTT
Found at i:645381 original size:2 final size:2
Alignment explanation
Indices: 645374--645410 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
645364 GATGAGTGAT
*
645374 AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
645411 TCCTTATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:646263 original size:29 final size:29
Alignment explanation
Indices: 646231--646470 Score: 335
Period size: 29 Copynumber: 8.3 Consensus size: 29
646221 AGAATTGGTT
**
646231 GTTCCTTTGTTGTATCGTCCTTTTGATTG
1 GTTCCTTTGTCCTATCGTCCTTTTGATTG
646260 GTTCCTTTGTCCTATCGTCCTTTTGATTG
1 GTTCCTTTGTCCTATCGTCCTTTTGATTG
* *
646289 GTTCCTTTGTCTTTTCG-CCATTTTGATTG
1 GTTCCTTTGTCCTATCGTCC-TTTTGATTG
* *
646318 GTTCCTTTGTCCCATCGTCCTTTGGATTG
1 GTTCCTTTGTCCTATCGTCCTTTTGATTG
*
646347 GTTCCTTTGTCCTATC-ACCATTTTGATTG
1 GTTCCTTTGTCCTATCGTCC-TTTTGATTG
646376 GTTCCTTTGTCC-ATCGTCCTTTTGATTG
1 GTTCCTTTGTCCTATCGTCCTTTTGATTG
* *
646404 GTTCCTATGTCATATCGTCCTTTTGATTG
1 GTTCCTTTGTCCTATCGTCCTTTTGATTG
* *
646433 GTT-CTTTGTCCTATAGTACTTTTGATTG
1 GTTCCTTTGTCCTATCGTCCTTTTGATTG
646461 GTTCCTTTGT
1 GTTCCTTTGT
646471 ATATTCGTCT
Statistics
Matches: 187, Mismatches: 18, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
28 50 0.27
29 135 0.72
30 2 0.01
ACGTcount: A:0.09, C:0.22, G:0.18, T:0.51
Consensus pattern (29 bp):
GTTCCTTTGTCCTATCGTCCTTTTGATTG
Found at i:658991 original size:13 final size:13
Alignment explanation
Indices: 658973--659077 Score: 156
Period size: 13 Copynumber: 8.1 Consensus size: 13
658963 AATATAGTTA
* *
658973 TATATTTGCATGT
1 TATATTGGCATAT
658986 TATATTGGCATAT
1 TATATTGGCATAT
**
658999 TATATTTCCATAT
1 TATATTGGCATAT
659012 TATATTGGCATAT
1 TATATTGGCATAT
* *
659025 TATATTTGCATTT
1 TATATTGGCATAT
659038 TATATTGGCATAT
1 TATATTGGCATAT
659051 TATATTGGCATAT
1 TATATTGGCATAT
659064 TATATTGGCATAT
1 TATATTGGCATAT
659077 T
1 T
659078 TTCCATGATG
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 82 1.00
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.50
Consensus pattern (13 bp):
TATATTGGCATAT
Found at i:659014 original size:26 final size:26
Alignment explanation
Indices: 658973--659077 Score: 174
Period size: 26 Copynumber: 4.0 Consensus size: 26
658963 AATATAGTTA
*
658973 TATATTTGCATGTTATATTGGCATAT
1 TATATTTGCATATTATATTGGCATAT
*
658999 TATATTTCCATATTATATTGGCATAT
1 TATATTTGCATATTATATTGGCATAT
*
659025 TATATTTGCATTTTATATTGGCATAT
1 TATATTTGCATATTATATTGGCATAT
*
659051 TATATTGGCATATTATATTGGCATAT
1 TATATTTGCATATTATATTGGCATAT
659077 T
1 T
659078 TTCCATGATG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.50
Consensus pattern (26 bp):
TATATTTGCATATTATATTGGCATAT
Found at i:665653 original size:27 final size:27
Alignment explanation
Indices: 665618--665674 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
665608 TTAATCATTA
*
665618 CGTTTATTTTAAATAAAAAGCATTTAC
1 CGTTAATTTTAAATAAAAAGCATTTAC
*
665645 CGTTAATTTTAAATAAAGAGCATTTAC
1 CGTTAATTTTAAATAAAAAGCATTTAC
665672 CGT
1 CGT
665675 AACATTCACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.39
Consensus pattern (27 bp):
CGTTAATTTTAAATAAAAAGCATTTAC
Done.