Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold215
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2124891
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 3 of 16
Found at i:379595 original size:12 final size:12
Alignment explanation
Indices: 379578--379628 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
379568 TTTATTCTTA
379578 TATTTTTATTAT
1 TATTTTTATTAT
*
379590 TA-TTTTATTTTT
1 TATTTTTA-TTAT
* *
379602 TATTTTTTTTGT
1 TATTTTTATTAT
379614 TATTTTT-TTAT
1 TATTTTTATTAT
379625 TATT
1 TATT
379629 CATGTTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
11 12 0.36
12 17 0.52
13 4 0.12
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (12 bp):
TATTTTTATTAT
Found at i:380026 original size:36 final size:33
Alignment explanation
Indices: 379940--380037 Score: 112
Period size: 36 Copynumber: 3.0 Consensus size: 33
379930 CCTTACAACA
* *
379940 CTATC-TTTC-AAGGCTAAGATAGAAAC-CACC
1 CTATCTTTTCAAAGGCTAAGATAGAATCTCTCC
* *
379970 CTATCTTTTCACAGGTTAAGATAGAATCTCTCTC
1 CTATCTTTTCAAAGGCTAAGATAGAATCTCTC-C
380004 CTTATCTTTTTCAAAGGCTAAGATAGAATCTCTC
1 C-TATC-TTTTCAAAGGCTAAGATAGAATCTCTC
380038 AATTACTTAG
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
30 5 0.09
31 4 0.07
32 14 0.25
33 2 0.04
34 2 0.04
35 4 0.07
36 25 0.45
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (33 bp):
CTATCTTTTCAAAGGCTAAGATAGAATCTCTCC
Found at i:381165 original size:217 final size:217
Alignment explanation
Indices: 380790--381223 Score: 850
Period size: 217 Copynumber: 2.0 Consensus size: 217
380780 ACTCAAAACA
380790 TCGATCCCGTGGTCTACGTAATTTAGAGATTCACCGGTTGGGTTCGGGAGTTGGTTATACGCAAA
1 TCGATCCCGTGGTCTACGTAATTTAGAGATTCACCGGTTGGGTTCGGGAGTTGGTTATACGCAAA
380855 GAGGTACGAACCTCCTCGTGACGCCCGAAATTAGTACACTATTAACAATGTTTTGACTCGATATT
66 GAGGTACGAACCTCCTCGTGACGCCCGAAATTAGTACACTATTAACAATGTTTTGACTCGATATT
*
380920 GGTTACATTGGTTTCGATTCAATATTATTTCGACATGATCCCTTTTGAATGCATGAATCTTGTAT
131 GGTTACATTGGTTTCGATTCAATATTATTTCGACATGATCCCCTTTGAATGCATGAATCTTGTAT
380985 TAAAAACAAATCCAGGTTTTTG
196 TAAAAACAAATCCAGGTTTTTG
*
381007 TCGATCCCGTGGTCTACGTAATTTAGAGATTCATCGGTTGGGTTCGGGAGTTGGTTATACGCAAA
1 TCGATCCCGTGGTCTACGTAATTTAGAGATTCACCGGTTGGGTTCGGGAGTTGGTTATACGCAAA
381072 GAGGTACGAACCTCCTCGTGACGCCCGAAATTAGTACACTATTAACAATGTTTTGACTCGATATT
66 GAGGTACGAACCTCCTCGTGACGCCCGAAATTAGTACACTATTAACAATGTTTTGACTCGATATT
381137 GGTTACATTGGTTTCGATTCAATATTATTTCGACATGATCCCCTTTGAATGCATGAATCTTGTAT
131 GGTTACATTGGTTTCGATTCAATATTATTTCGACATGATCCCCTTTGAATGCATGAATCTTGTAT
381202 TAAAAACAAATCCAGGTTTTTG
196 TAAAAACAAATCCAGGTTTTTG
381224 AAAAATGTTT
Statistics
Matches: 215, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
217 215 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (217 bp):
TCGATCCCGTGGTCTACGTAATTTAGAGATTCACCGGTTGGGTTCGGGAGTTGGTTATACGCAAA
GAGGTACGAACCTCCTCGTGACGCCCGAAATTAGTACACTATTAACAATGTTTTGACTCGATATT
GGTTACATTGGTTTCGATTCAATATTATTTCGACATGATCCCCTTTGAATGCATGAATCTTGTAT
TAAAAACAAATCCAGGTTTTTG
Found at i:383847 original size:13 final size:13
Alignment explanation
Indices: 383829--383854 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
383819 ATTTGCCTGC
383829 ATGTATCGATACA
1 ATGTATCGATACA
383842 ATGTATCGATACA
1 ATGTATCGATACA
383855 TTGAATAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:384115 original size:33 final size:32
Alignment explanation
Indices: 384055--384119 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
384045 CAATTCATGA
384055 TGTATCGATATAATGAACATGTATCGATACAT
1 TGTATCGATATAATGAACATGTATCGATACAT
*
384087 TGTATCGATACTAA-GCAATATGTATCGATACAT
1 TGTATCGATA-TAATG-AACATGTATCGATACAT
384120 CTGGGTGTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 11 0.37
33 19 0.63
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (32 bp):
TGTATCGATATAATGAACATGTATCGATACAT
Found at i:384693 original size:3 final size:3
Alignment explanation
Indices: 384685--384744 Score: 102
Period size: 3 Copynumber: 20.0 Consensus size: 3
384675 CGAGTCAACT
*
384685 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA CCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
*
384733 TCT TCA TCA TCA
1 TCA TCA TCA TCA
384745 ATAATGGTTG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:386421 original size:20 final size:20
Alignment explanation
Indices: 386392--386442 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
386382 GCCAGTTTCA
* * *
386392 TGTATTGATACTTTTCAAGG
1 TGTATCGATACTTATCAACG
*
386412 TGTATCGATAC-TATGAACG
1 TGTATCGATACTTATCAACG
386431 TGTATCGATACT
1 TGTATCGATACT
386443 AAGCAATATG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (20 bp):
TGTATCGATACTTATCAACG
Found at i:390594 original size:13 final size:13
Alignment explanation
Indices: 390576--390601 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
390566 AATTTCTTTG
390576 TGTATCGATACAT
1 TGTATCGATACAT
390589 TGTATCGATACAT
1 TGTATCGATACAT
390602 ACTTTGGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:390617 original size:33 final size:34
Alignment explanation
Indices: 390555--390620 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 34
390545 TACAAGCCAA
*
390555 TGTATCGATACAATTTCTTTGTGTATCGATACAT
1 TGTATCGATACAATTACTTTGTGTATCGATACAT
390589 TGTATCGATAC-A-TACTTTGGTGTATCGATACA
1 TGTATCGATACAATTACTTT-GTGTATCGATACA
390621 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 5 0.17
33 14 0.47
34 11 0.37
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (34 bp):
TGTATCGATACAATTACTTTGTGTATCGATACAT
Found at i:393206 original size:13 final size:13
Alignment explanation
Indices: 393188--393226 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
393178 ATAATCCCCT
*
393188 TGTATCGATACAG
1 TGTATCGATACAA
393201 TGTATCGATACAA
1 TGTATCGATACAA
*
393214 TGTATCAATACAA
1 TGTATCGATACAA
393227 AGAAAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:399421 original size:33 final size:34
Alignment explanation
Indices: 399359--399424 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 34
399349 TACAACCCAA
*
399359 TGTATCGATACAATTTCTTTGTGTATCGATACAT
1 TGTATCGATACAATTACTTTGTGTATCGATACAT
399393 TGTATCGATA-AA-TACTTTGGTGTATCGATACA
1 TGTATCGATACAATTACTTT-GTGTATCGATACA
399425 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 5 0.17
33 15 0.50
34 10 0.33
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.41
Consensus pattern (34 bp):
TGTATCGATACAATTACTTTGTGTATCGATACAT
Found at i:400311 original size:21 final size:22
Alignment explanation
Indices: 400287--400336 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
400277 ATCAAATCAT
* *
400287 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
400308 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
400330 --TCAAAAT
1 CTTCAAAAT
400337 CATCACCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:402413 original size:13 final size:13
Alignment explanation
Indices: 402395--402419 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
402385 ACATTATGCT
402395 TTGTATCGATACG
1 TTGTATCGATACG
402408 TTGTATCGATAC
1 TTGTATCGATAC
402420 ATGATCATTG
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:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACG
Found at i:402418 original size:33 final size:32
Alignment explanation
Indices: 402376--402438 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
402366 CACACCCAGA
* *
402376 TGTATCGATACATTATGCTTTGTATCGATACGT
1 TGTATCGATACATGAT-CATTGTATCGATACGT
402409 TGTATCGATACATGATCATTGTATCGATAC
1 TGTATCGATACATGATCATTGTATCGATAC
402439 ATGGACAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATGATCATTGTATCGATACGT
Found at i:402451 original size:20 final size:20
Alignment explanation
Indices: 402408--402460 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
402398 TATCGATACG
402408 TTGTATCGATACAT-GATCA
1 TTGTATCGATACATGGATCA
402427 TTGTATCGATACATGGA-CAA
1 TTGTATCGATACATGGATC-A
402447 TTGTATC-ATACATG
1 TTGTATCGATACATG
402461 AAACTGGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 22 0.69
20 10 0.31
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (20 bp):
TTGTATCGATACATGGATCA
Found at i:402517 original size:20 final size:20
Alignment explanation
Indices: 402492--402542 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
402482 TCACTGTTTG
*
402492 TATCGATACATGGT-ACATTA
1 TATCGATACATGATGA-ATTA
*
402512 TATCGATACATGATGAATTG
1 TATCGATACATGATGAATTA
402532 TATCGATACAT
1 TATCGATACAT
402543 TGCTTGTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (20 bp):
TATCGATACATGATGAATTA
Found at i:403086 original size:14 final size:14
Alignment explanation
Indices: 403067--403098 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
403057 TAAAAGTAAT
403067 CAATTCTAGTAGTG
1 CAATTCTAGTAGTG
403081 CAATTCTAGTAGTG
1 CAATTCTAGTAGTG
403095 -AATT
1 CAATT
403099 GGATGACCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (14 bp):
CAATTCTAGTAGTG
Found at i:411272 original size:13 final size:13
Alignment explanation
Indices: 411254--411278 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
411244 ATTATGCTTC
411254 GTATCGATACATT
1 GTATCGATACATT
411267 GTATCGATACAT
1 GTATCGATACAT
411279 AGACAATTGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:411353 original size:20 final size:20
Alignment explanation
Indices: 411328--411381 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
411318 CTACCACTGT
* *
411328 TTGTATCAATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
*
411348 TTGTATCGATAGATGATGAA
1 TTGTATCGATACATGATGAA
411368 TTGTATCGATACAT
1 TTGTATCGATACAT
411382 TGCTTGTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:412718 original size:19 final size:20
Alignment explanation
Indices: 412694--412746 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
412684 ATCGATATAA
**
412694 TGTATCGATACATGTTC-AT
1 TGTATCGATACATGGACAAT
412713 TGTATCGATACATGGACAAT
1 TGTATCGATACATGGACAAT
*
412733 TTTATCGATACATG
1 TGTATCGATACATG
412747 AAACTTGGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATGGACAAT
Found at i:412721 original size:32 final size:33
Alignment explanation
Indices: 412660--412722 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
412650 ACACACCCAG
*
412660 ATGTATCGATACATTATGCTTTGTATCGATATA
1 ATGTATCGATACATTATGCATTGTATCGATATA
412693 ATGTATCGATACATGT-T-CATTGTATCGATA
1 ATGTATCGATACAT-TATGCATTGTATCGATA
412723 CATGGACAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 12 0.43
33 15 0.54
34 1 0.04
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (33 bp):
ATGTATCGATACATTATGCATTGTATCGATATA
Found at i:412801 original size:20 final size:19
Alignment explanation
Indices: 412776--412829 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
412766 CTACCACTGT
412776 TTGTATCGATACATG-GCACA
1 TTGTATCGATACATGAG-A-A
*
412796 TTGTATCCATACATGATGAA
1 TTGTATCGATACATGA-GAA
412816 TTGTATCGATACAT
1 TTGTATCGATACAT
412830 TACTTTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 28 0.93
21 1 0.03
22 1 0.03
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATGAGAA
Found at i:414335 original size:20 final size:20
Alignment explanation
Indices: 414312--414377 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
414302 CACACCCAGA
414312 TGTATCGATACATATTGCTT
1 TGTATCGATACATATTGCTT
414332 TGTATCGATAC--A-----T
1 TGTATCGATACATATTGCTT
*
414345 TGTATCGATATATATTGCTT
1 TGTATCGATACATATTGCTT
414365 TGTATCGATACAT
1 TGTATCGATACAT
414378 TGTATCGATA
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
13 11 0.30
15 1 0.03
18 1 0.03
20 24 0.65
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (20 bp):
TGTATCGATACATATTGCTT
Found at i:414354 original size:33 final size:33
Alignment explanation
Indices: 414312--414390 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
414302 CACACCCAGA
414312 TGTATCGATACATATTGCTTTGTATCGATACAT
1 TGTATCGATACATATTGCTTTGTATCGATACAT
*
414345 TGTATCGATATATATTGCTTTGTATCGATACAT
1 TGTATCGATACATATTGCTTTGTATCGATACAT
414378 TGTATCGATACAT
1 TGTATCGATACAT
414391 GTTCATTATA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATATTGCTTTGTATCGATACAT
Found at i:414382 original size:13 final size:13
Alignment explanation
Indices: 414364--414390 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
414354 ATATATTGCT
414364 TTGTATCGATACA
1 TTGTATCGATACA
414377 TTGTATCGATACA
1 TTGTATCGATACA
414390 T
1 T
414391 GTTCATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:419614 original size:20 final size:19
Alignment explanation
Indices: 419585--419659 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
419575 AAAAAGACAT
419585 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
* *
419604 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
* *
419625 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTG-AA
419645 AATGTATCGATACAT
1 AATGTATCGATACAT
419660 CTGGGAAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:419642 original size:40 final size:39
Alignment explanation
Indices: 419582--419659 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
419572 GGTAAAAAGA
*
419582 CATAATGTATCGATACATTGAAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
419621 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
419660 CTGGGAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:420281 original size:28 final size:28
Alignment explanation
Indices: 420197--421995 Score: 1419
Period size: 28 Copynumber: 62.2 Consensus size: 28
420187 CACTAACTTG
* **
420197 TGTGGGCTTTGAAAAGAGTTGCCACCAACT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT
* * *
420227 CGTGTGGGATTTGAAAAGAGTACCACTGACT
1 --TGTGGGCTTTG-AAAGGGTGCCACTGACT
420258 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * **
420286 TGTGGGCTTTGAAAAGATGCCACCAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
** * * *
420314 CATGGGCTTTGAAAGGATACCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
420342 TATAGGCTTTGAAAAGGGTTACCACTGACT
1 TGTGGGCTTTG-AAAGGG-TGCCACTGACT
*
420372 CGTGTGGGCTTTGAAAGGATGCCACTGACT
1 --TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
420402 TGTGGGCTTTGAAAGGGTGCTATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* **
420430 TGTGGGCTTTGAAAAGAGTTGCCACCAACT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT
* * *
420460 CGTGTGGGCTTTAAAAAGAGTACCACTGACT
1 --TGTGGGCTTT-GAAAGGGTGCCACTGACT
*
420491 TGGGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * **
420519 TGTGGGCTTTGAAAATGTTGCCACCAACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
** * * *
420548 CATGGGCTTTGAAAGGATACCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
420576 TATAGGCTTTGAAAAGGGTTACCACCGACT
1 TGTGGGCTTTG-AAAGGG-TGCCACTGACT
*
420606 CGTGTGGGCTTTGAAAGGATGCCACTGACT
1 --TGTGGGCTTTGAAAGGGTGCCACTGACT
*
420636 TGTGGGCTTTGAAAGTGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
420664 TGTGGGCTTTGAAAAGTGCTGCCACTGACT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT
* * *
420694 CGTGAGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
420722 TGTGGGCTTTAAAAAGGGTTGCCACCGACT
1 TGTGGGCTTT-GAAAGGG-TGCCACTGACT
*
420752 CGTGTGGGCTTTGAAAAGAGTGCCACTGACT
1 --TGTGGGCTTTG-AAAGGGTGCCACTGACT
*
420783 TGTGGGCTTTGAAAGGGTGACACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
420811 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
420839 TGTGGGCTTTGAAAAAGTGTTACCACTCACT
1 TGTGGGCTTTG--AAAG-GGTGCCACTGACT
* * *
420870 CGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
420898 TGTGGGCTTTGAAAAGGGTTGCCACCGACT
1 TGTGGGCTTTG-AAAGGG-TGCCACTGACT
*
420928 CGTGTGGGCTTTGAAAAGAGTGCCACTGACT
1 --TGTGGGCTTTG-AAAGGGTGCCACTGACT
*
420959 TGTGGGCTTTGAAAGGGTGCCACTGATT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
420987 TGTGGGCTTTAAAAGGGTGCCACTGATT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
421015 TGTGGGCTTTGAAAATGTTGCCACCGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* * * *
421044 CGTGGGCTTTGAAAGGATACCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
421072 TGTGGGCTTTGAAAAGGGTTGCCACCGACT
1 TGTGGGCTTTG-AAAGGG-TGCCACTGACT
*
421102 CGTGTGGGCTTTGAAAGGATGCCACTGACT
1 --TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
421132 TGTGGGCTTTGAAAAGTGTTGCCACCGACT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT
* *
421162 CGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
421190 TGTGGGCTTTGAAAAGGGTTGCCACCGACTT
1 TGTGGGCTTTG-AAAGGG-TGCCACTGAC-T
*
421221 GTGTGGGCTTTGAAAAGAGTGCCACTGACT
1 -TGTGGGCTTTG-AAAGGGTGCCACTGACT
421251 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
** *
421279 TGTGGGCTTTGAAAGTATGACACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
421307 TGTGGGCTTTGAAAAGTGTTGCCACTGACT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT
* * *
421337 CGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
421365 TGTGGGCTTTGAAAAGGGTTGCCACCGACT
1 TGTGGGCTTTG-AAAGGG-TGCCACTGACT
*
421395 CGTGTGGGCTTTGAAAAGAGTGCCACTGACT
1 --TGTGGGCTTTG-AAAGGGTGCCACTGACT
*
421426 TGTGGGCTTTGAAAGGGTGCCACTGATT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
421454 TGTGGGCTTTGAAATGGGTTGCCACCGACTT
1 TGTGGGCTTTGAAA-GGG-TGCCACTGAC-T
* *
421485 GTGTGGGCTTTCAAATGGGTTGCCACCGACTT
1 -TGTGGGCTTTGAAA-GGG-TGCCACTGAC-T
*
421517 GTGTGGGCTTTGAAATAGGTTGCCA-TCGACTT
1 -TGTGGGCTTTG-AA-AGGGTGCCACT-GAC-T
*
421549 GTGTGGGCTTTAAAAGGGTGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
** * *
421578 TGTGGGCTTAAAAAGGATGCCAC-GAAGT
1 TGTGGGCTTTGAAAGGGTGCCACTG-ACT
** * * *
421606 TGTGAAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
421633 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
421661 TGTGGACTTT-AAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
421688 TGTGGAC-TT-AAACCGATGCCACGGAGT
1 TGTGGGCTTTGAAA-GGGTGCCACTGACT
* * * * *
421715 TGTAGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * * *
421743 TATGGACTTT-AAATGGTACCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * * *
421770 TGTGGAC-TTAAAACGATGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
421797 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
421825 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
421853 TGTGGACTTT-AAAGGGTACCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * * *
421880 TGTGGAC-TTAAAACGATGTCAC-GAAAT
1 TGTGGGCTTTGAAAGGGTGCCACTG-ACT
* * *
421907 TGTGGACTTTAAAAGGGTGCCAC-GAAGT
1 TGTGGGCTTTGAAAGGGTGCCACTG-ACT
* * * *
421935 TGTGGACTTTAAAAGGATGCCA-TGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACT-GACT
* * * * *
421963 TGTGGACTTTAAAAGGATGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
421991 TGTGG
1 TGTGG
421996 ACTTAAAAGG
Statistics
Matches: 1511, Mismatches: 189, Indels: 138
0.82 0.10 0.08
Matches are distributed among these distances:
26 10 0.01
27 147 0.10
28 699 0.46
29 183 0.12
30 186 0.12
31 95 0.06
32 186 0.12
33 4 0.00
34 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.28
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:420745 original size:292 final size:289
Alignment explanation
Indices: 420186--421600 Score: 1631
Period size: 292 Copynumber: 4.8 Consensus size: 289
420176 AAAAATAGGG
* * * * *
420186 CCACTAACTTGTGTGGGCTTTGAAAAGAGTTGCCACCAACTCGTGTGGGATTTGAAAAGAGTACC
1 CCACTAAC-T-TGTGGGCTTTGAAAAGGGTTGCCACCGACTC-TGTGGGCTTTGAAAGGA-TGCC
* *
420251 ACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAA-GATGCCACCAACTC
62 ACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACCGACTT
* * * ** * * * *
420315 ATGGGCTTTGAAA-GGATACCACTAACT-TATAGGCTTTGAAAAGGGTTACCACTGACTCGTGTG
127 GTGGGCTTTGAAAGGGTTGCCACCGACTGTGTGGGCTTTGAAAAGAG-TGCCACTGACT--TGTG
* * * *
420378 GGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCTATTGACTTGTGGGCTTTGAA
189 GGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAA
* * *
420443 AAGAGTTGCCACCAACTCGTGTGGGCTTTAAAAAGAGTA
254 AAGTGTTGCCACCGACTC--GTGGGCTTTGAAAAGA-TA
* * * * * *
420482 CCACTGACTTGGGGGCTTTG-AAAGGG-TGCCACTGACT-TGTGGGCTTTGAAAATGTTGCCACC
1 CCACTAACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTCTGTGGGCTTTG-AAAGGATGCCACT
* ** * * * * * * *
420544 AACTCATGGGCTTTGAAAGGATACCACTAACTTATAGGCTTTGAAAAGGGTTACCACCGACTCGT
65 GACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAA-GGATGCCACCGACT--T
* * *
420609 GTGGGCTTTGAAA-GGATGCCACTGACT-TGTGGGCTTTG-AAAGTGTGCCACTGACTTGTGGGC
127 GTGGGCTTTGAAAGGGTTGCCACCGACTGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* * * *
420671 TTTGAAAAGTGCTGCCACTGACTCGTGAGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTAAAA
192 TTTG-AAAG-GGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAA
* *
420736 AGGGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAGTG
255 AGTGTTGCCACCGACTC--GTGGGCTTTGAAAAGA-TA
* * *
420774 CCACTGACTTGTGGGCTTTG-AAAGGG-TGACACTGACT-TGTGGGCTTTGAAAGGATGCCACTG
1 CCACTAACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTCTGTGGGCTTTGAAAGGATGCCACTG
* * * * **
420836 ACTTGTGGGCTTTGAAAAAGTGTTACCACTCACTCGTGGGCTTTG-AAAGGATGCCACTAACTTG
66 ACTTGTGGGCTTTG--AAAG-GGTGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACCGACTTG
420900 TGGGCTTTGAAAAGGGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGG
128 TGGGCTTTG-AAAGGGTTGCCACCGACT-GTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGG
* * * *
420965 CTTTGAAAGGGTGCCACTGATTTGTGGGCTTTAAAAGGGTGCCACTGATTTGTGGGCTTTGAAAA
191 CTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAA
*
421030 -TGTTGCCACCGACTCGTGGGCTTTGAAAGGATA
256 GTGTTGCCACCGACTCGTGGGCTTTGAAAAGATA
421063 CCACTAACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTCGTGTGGGCTTTGAAAGGATGCCACT
1 CCACTAACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTC-TGTGGGCTTTGAAAGGATGCCACT
* * * *
421128 GACTTGTGGGCTTTGAAAAGTGTTGCCACCGACTCGTGGGCTTTG-AAAGGATGCCACTGACTTG
65 GACTTGTGGGCTTTG-AAAG-GGTGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACCGACTTG
421192 TGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGG
128 TGGGCTTTG-AAAGGGTTGCCACCGAC-TGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGG
* *
421257 CTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGTATGACACTGACTTGTGGGCTTTGAAAA
191 CTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAA
* * *
421322 GTGTTGCCACTGACTCGTGGGCTTTGAAAGGATG
256 GTGTTGCCACCGACTCGTGGGCTTTGAAAAGATA
*
421356 CCACTAACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAGTGCCAC
1 CCACTAACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTC-TGTGGGCTTTGAAAGGA-TGCCAC
* * *
421421 TGACTTGTGGGCTTTGAAAGGGTGCCACTGATTTGTGGGCTTTGAAATGGGTTGCCACCGACTTG
64 TGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAA-AGGATGCCACCGAC-T-
*
421486 TGTGGGCTTTCAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATAG-GTTGCCA-TCGACTT
126 TGTGGGCTTTGAAA-GGGTTGCCACCGAC-TGTGTGGGCTTTGAAA-AGAG-TGCCACT-GAC-T
* **
421549 GTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTAAAAAGGATGCCAC
185 -TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCAC
421601 GAAGTTGTGA
Statistics
Matches: 987, Mismatches: 100, Indels: 61
0.86 0.09 0.05
Matches are distributed among these distances:
289 20 0.02
290 97 0.10
291 42 0.04
292 380 0.39
293 199 0.20
294 110 0.11
295 32 0.03
296 50 0.05
297 10 0.01
298 1 0.00
299 46 0.05
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (289 bp):
CCACTAACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTCTGTGGGCTTTGAAAGGATGCCACTG
ACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACCGACTTGTGG
GCTTTGAAAGGGTTGCCACCGACTGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGTGTT
GCCACCGACTCGTGGGCTTTGAAAAGATA
Found at i:421164 original size:468 final size:464
Alignment explanation
Indices: 420197--421600 Score: 1889
Period size: 468 Copynumber: 3.0 Consensus size: 464
420187 CACTAACTTG
* * * * *
420197 TGTGGGCTTTGAAAAGAGTTGCCACCAACTCGTGTGGGATTTGAAAAGAGTACCACTGACTTGTG
1 TGTGGGCTTTGAAAAGTGTTGCCACCGACTC--GTGGGCTTTGAAAGGA-TGCCACTGACTTGTG
* * ** **
420262 GGCTTTGAAAGGG-TGCCACTGACT-TGTGGGCTTTGAAAAGA-TGCCACCAACTCATGGGCTTT
63 GGCTTTAAAAGGGTTGCCACCGACTGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTT
* * * * * *
420324 GAAAGGAT-ACCACTAACTTATAGGCTTTGAAAAGGGTTACCACTGACTCGTGTGGGCTTTG-AA
128 GAAAGGGTGA-CACTGACTTGTGGGCTTTG-AAA-GGATGCCACTGACT--TGTGGGCTTTGAAA
* * * * * * *
420387 AG-GATGCCACTGACTTGTGGGCTTTGAAAGGGTGCTATTGACTTGTGGGCTTTGAAAAGAGTTG
188 AGTGTTGCCACTGACTCGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGGTTG
* * * *
420451 CCACCAACTCGTGTGGGCTTTAAAAAGAGTACCACTGACTTGGGGGCTTTGAAAGGGTGCCACTG
253 CCACCGACTCGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
* * * * * ** * * * ** * *
420516 ACTTGTGGGCTTTGAAAATGTTGCCACCAACTCATGGGCTTTGAAAGGATACCACTAACTTATAG
318 ATTTGTGGGCTTTGAAAAGGGTGCCACCGATTTGTGGGCTTTGAAATGTTGCCACCGACTTGTGG
* *
420581 GCTTTGAAAAGGGTTACCACCGACTCGTGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTT
383 GCTTTGAAAA-GGTTACCACTGACT-GTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTT
420645 TGAAAGTG-TGCCACTGACT
446 TGAAAG-GATGCCACTGACT
* * *
420664 TGTGGGCTTTGAAAAGTGCTGCCACTGACTCGTGAGCTTTGAAAGGATGCCACTGACTTGTGGGC
1 TGTGGGCTTTGAAAAGTGTTGCCACCGACTCGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGC
420729 TTTAAAAAGGGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
66 TTT-AAAAGGGTTGCCACCGACT-GTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
420794 AAAGGGTGACACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAAGTGT
129 AAAGGGTGACACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG-AAAAGTGT
* *
420859 TACCACTCACTCGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGGTTGCCACC
193 TGCCACTGACTCGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGGTTGCCACC
420924 GACTCGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGATTTG
258 GACTCGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGATTTG
* *
420989 TGGGCTTT-AAAAGGGTGCCACTGATTTGTGGGCTTTGAAAATGTTGCCACCGACTCGTGGGCTT
323 TGGGCTTTGAAAAGGGTGCCACCGATTTGTGGGCTTTG-AAATGTTGCCACCGACTTGTGGGCTT
* * *
421053 TG-AAAGGATACCACTAACT-TGTGGGCTTTGAAAAGGGTTGCCACCGACTCGTGTGGGCTTTGA
387 TGAAAAGGTTACCACTGACTGTGTGGGCTTTGAAAAGGG-TGCCACTGACT--TGTGGGCTTTGA
421116 AAGGATGCCACTGACT
449 AAGGATGCCACTGACT
421132 TGTGGGCTTTGAAAAGTGTTGCCACCGACTCGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGC
1 TGTGGGCTTTGAAAAGTGTTGCCACCGACTCGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGC
421197 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
66 TTT-AAAAGGGTTGCCACCGAC-TGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * *
421262 AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGTATGACACTGACTTGTGGGCTTTGAAAAGTGTT
129 AAAGGGTGACACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGTGTT
421327 GCCACTGACTCGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGGTTGCCACCG
194 GCCACTGACTCGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGGTTGCCACCG
421392 ACTCGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGATTTGT
259 ACTCGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGATTTGT
* *
421457 GGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTCAAATGGGTTGCCACCGACTTGTGTG
324 GGGCTTTGAAAAGGG-TGCCACCGA-TT-TGTGGGCTTTGAAAT--GTTGCCACCGAC-T-TGTG
*
421522 GGCTTTGAAATAGGTTGCCA-TCGACTTGTGTGGGCTTT-AAAAGGGTGCCACTGACTTGTGGGC
382 GGCTTTGAAA-AGGTTACCACT-GAC-TGTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGC
**
421585 TTAAAAAGGATGCCAC
444 TTTGAAAGGATGCCAC
421601 GAAGTTGTGA
Statistics
Matches: 835, Mismatches: 73, Indels: 51
0.87 0.08 0.05
Matches are distributed among these distances:
464 31 0.04
465 35 0.04
466 31 0.04
467 213 0.26
468 375 0.45
469 49 0.06
470 7 0.01
471 10 0.01
472 12 0.01
473 1 0.00
474 31 0.04
475 3 0.00
476 19 0.02
477 8 0.01
478 10 0.01
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (464 bp):
TGTGGGCTTTGAAAAGTGTTGCCACCGACTCGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGC
TTTAAAAGGGTTGCCACCGACTGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAA
AGGGTGACACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGTGTTGC
CACTGACTCGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGGTTGCCACCGAC
TCGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGATTTGTGG
GCTTTGAAAAGGGTGCCACCGATTTGTGGGCTTTGAAATGTTGCCACCGACTTGTGGGCTTTGAA
AAGGTTACCACTGACTGTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATG
CCACTGACT
Found at i:422027 original size:55 final size:55
Alignment explanation
Indices: 420700--422056 Score: 642
Period size: 55 Copynumber: 23.6 Consensus size: 55
420690 GACTCGTGAG
* * * * * * *
420700 CTTTGAAAGGATGCCACTGACTTGTGGGCTTTAAAAAGGGTTGCCACCGACTCGTGTGGG
1 CTTTAAAAGGATGCCACGGAGTTGTGGAC-TT-AAAAGGG-TGCCACGGAGT--TGTGGA
* * * * * * * *
420760 CTTTGAAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGACACTGACTTGTGGG
1 CTTT-AAAAGGA-TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGA
* * * * * * ** * * *
420817 CTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAAGTGTTACCACTCACTCGTGGG
1 CTTTAAAAGGATGCCACGGAGTTGTGGAC-TT--AAAAG-GGTGCCACGGAGTTGTGGA
* ** * * * * *
420876 CTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTCGTGTGGG
1 CTTTAAAAGGATGCCACGGAGTTGTGGAC-TT-AAAAGGG-TGCCACGGAGT--TGTGGA
* * * * * * *
420936 CTTTGAAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGATTTGTGGG
1 CTTT-AAAAGGA-TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGA
* * * * * * * * * *
420993 CTTTAAAAGGGTGCCACTGATTTGTGGGCTTTGAAAATGTTGCCACCGACTCGTGGG
1 CTTTAAAAGGATGCCACGGAGTTGTGGAC-TT-AAAAGGGTGCCACGGAGTTGTGGA
* * ** * * * * *
421050 CTTTGAAAGGATACCACTAACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTCGTGTGGG
1 CTTTAAAAGGATGCCACGGAGTTGTGGAC-TT-AAAAGGG-TGCCACGGAGT--TGTGGA
* * * * * * * * *
421110 CTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGTGTTGCCACCGACTCGTGGG
1 CTTTAAAAGGATGCCACGGAGTTGTGGAC-TT-AAAAG-GGTGCCACGGAGTTGTGGA
* * * * * * *
421168 CTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGG
1 CTTTAAAAGGATGCCACGGAGTTGTGGAC-TT-AAAAGGG-TGCCACGGA-GT-TGTGGA
* * * * * * *
421228 CTTTGAAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGG
1 CTTT-AAAAGGA-TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGA
* * * * * * * * * * *
421285 CTTTGAAAGTATGACACTGACTTGTGGGCTTTGAAAAGTGTTGCCACTGACTCGTGGG
1 CTTTAAAAGGATGCCACGGAGTTGTGGAC-TT-AAAAG-GGTGCCACGGAGTTGTGGA
* ** * * * * *
421343 CTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTCGTGTGGG
1 CTTTAAAAGGATGCCACGGAGTTGTGGAC-TT-AAAAGGG-TGCCACGGAGT--TGTGGA
* * * * * * *
421403 CTTTGAAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGATTTGTGGG
1 CTTT-AAAAGGA-TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGA
* * * * * * * * *
421460 CTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTCAAATGGGTTGCCACCGACTTGTGTGGG
1 CTTT-AAA-AGGATGCCACGGA-GT-TGTGGAC-TT-AAAAGGG-TGCCACGGA-GT-TGTGGA
* * * * * *
421524 CTTTGAAATAGGTTGCCATC-GACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGG
1 CTTT-AAA-AGGATGCCA-CGGA-GT-TGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGA
* * *
421584 CTTAAAAAGGATGCCACGAAGTTGTGAACTTAAAAGGGTGCCACGGAGTTGTGGA
1 CTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGA
* *
421639 CTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGA
1 CTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGA
** * *
421694 C-TTAAACCGATGCCACGGAGTTGTAGACTTTAAAAGGGTGCCACGGAGTTATGGA
1 CTTTAAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGA
* * * *
421749 CTTTAAATGG-TACCACGGAGTTGTGGACTTAAAACGATGCCACGGAGTTGTGGA
1 CTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGA
*
421803 CTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGA
1 CTTTAAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGA
* * * * * * *
421859 CTTT-AAAGGGTACCACGGAGTTGTGGACTTAAAACGATGTCACGAAATTGTGGA
1 CTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGA
* * * *
421913 CTTTAAAAGGGTGCCACGAAGTTGTGGACTTTAAAAGGATGCCATGGAGTTGTGGA
1 CTTTAAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGA
* **
421969 CTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCATAGAGTTGTGGA
1 CTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGA
* * *
422024 CTTTAAAAGAAAATGCCACTGAGTCGTGGACTT
1 CTTTAAAAG--GATGCCACGGAGTTGTGGACTT
422057 TGAAAAGGTC
Statistics
Matches: 1121, Mismatches: 128, Indels: 99
0.83 0.09 0.07
Matches are distributed among these distances:
54 80 0.07
55 211 0.19
56 158 0.14
57 127 0.11
58 160 0.14
59 86 0.08
60 134 0.12
61 101 0.09
62 16 0.01
63 8 0.01
64 39 0.03
65 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.27
Consensus pattern (55 bp):
CTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGA
Found at i:423113 original size:10 final size:9
Alignment explanation
Indices: 423077--423112 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
423067 GAAAAGGTTT
423077 TTTTTTTTGG
1 TTTTTTTT-G
423087 TTTTTTTTG
1 TTTTTTTTG
*
423096 TTTTTTTTC
1 TTTTTTTTG
423105 TTTTTTTT
1 TTTTTTTT
423113 TAGGATTAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.00, C:0.03, G:0.08, T:0.89
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:430497 original size:20 final size:19
Alignment explanation
Indices: 430468--430542 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
430458 AAAAAGACAT
430468 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
* *
430487 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
* *
430508 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTG-AA
430528 AATGTATCGATACAT
1 AATGTATCGATACAT
430543 CTGGGAAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:430525 original size:40 final size:39
Alignment explanation
Indices: 430465--430542 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
430455 GGTAAAAAGA
*
430465 CATAATGTATCGATACATTGAAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
430504 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
430543 CTGGGAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:431683 original size:80 final size:80
Alignment explanation
Indices: 431550--431712 Score: 317
Period size: 80 Copynumber: 2.0 Consensus size: 80
431540 AATCAGCACC
431550 ATTGGTAACAACTCTTCATTTTATGTTGAAAATGTTTTGTATGTCAATGGTCTTAAGCACAACCT
1 ATTGGTAACAACTCTTCATTTTATGTTGAAAATGTTTTGTATGTCAATGGTCTTAAGCACAACCT
431615 CTTAAGCATTAGTCA
66 CTTAAGCATTAGTCA
*
431630 ATTGGTAACAACTCTTCATTTTATGTTGAAAATGTTTTGTATGTCAATGGTCTTAAGCATAACCT
1 ATTGGTAACAACTCTTCATTTTATGTTGAAAATGTTTTGTATGTCAATGGTCTTAAGCACAACCT
431695 CTTAAGCATTAGTCA
66 CTTAAGCATTAGTCA
431710 ATT
1 ATT
431713 ATGTGACAAG
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (80 bp):
ATTGGTAACAACTCTTCATTTTATGTTGAAAATGTTTTGTATGTCAATGGTCTTAAGCACAACCT
CTTAAGCATTAGTCA
Found at i:435174 original size:28 final size:27
Alignment explanation
Indices: 435137--435209 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
435127 AAATAAAACT
*
435137 GGGTTGGAGTATCCCCTCAGAAATAAC
1 GGGTTGGAGTATCCCCTCAAAAATAAC
* ** *
435164 AGGGTTAGAGTATCTACTTAAAAATAAC
1 -GGGTTGGAGTATCCCCTCAAAAATAAC
435192 GAGGTTGGAGTATCCCCT
1 G-GGTTGGAGTATCCCCT
435210 ATTGTGGAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
27 1 0.03
28 35 0.97
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (27 bp):
GGGTTGGAGTATCCCCTCAAAAATAAC
Found at i:435280 original size:28 final size:28
Alignment explanation
Indices: 435244--435316 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
435234 AATAAAAACG
* *
435244 GGGGCTGGAGTATCCCCTCGAAAATAAT
1 GGGGTTGGAGTATCCCCTCGAAAATAAC
*
435272 GGGGTTGGAGTATCTCCTCGAAAATAAC
1 GGGGTTGGAGTATCCCCTCGAAAATAAC
* *
435300 AGGGTTAGAGTATCCCC
1 GGGGTTGGAGTATCCCC
435317 GATTATAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCTCGAAAATAAC
Found at i:435345 original size:108 final size:106
Alignment explanation
Indices: 435087--435393 Score: 339
Period size: 108 Copynumber: 2.9 Consensus size: 106
435077 GGAAATAATG
435087 GGGTTGGAGTATCCCCGATTGTGAAAAATCGATATTTTGAAAATAAAAC-TGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCGATTGTGAAAAATCGATATTTTGAAAATAAAACGTGGGTTGGAGTATCC
* *
435151 CCTC-AGAAATAACAGGGTTAGAGTATCTACTTAAAAATAAC
66 CCTCGA-AAATAACAGGGTTGGAGTATCTACTCAAAAATAAC
* * * * * *** * *
435192 GAGGTTGGAGTATCCCCTATTGTGGAAAATTGGTGTTGCAAAAATAAAAACGGGGGCTGGAGTAT
1 G-GGTTGGAGTATCCCCGATTGTGAAAAATCGATATTTTGAAAAT-AAAACGTGGGTTGGAGTAT
** * *
435257 CCCCTCGAAAATAATGGGGTTGGAGTATCTCCTCGAAAATAAC
64 CCCCTCGAAAATAACAGGGTTGGAGTATCTACTCAAAAATAAC
* * * * * *
435300 AGGGTTAGAGTATCCCCGATTATAAAAAATCAATATTTTGGAAATAAAACTGTGGGTTAGAGTAT
1 -GGGTTGGAGTATCCCCGATTGTGAAAAATCGATATTTTGAAAATAAAAC-GTGGGTTGGAGTAT
* *
435365 CTCCACGAAAATAACAGGGTTGGAGTATC
64 CCCCTCGAAAATAACAGGGTTGGAGTATC
435394 CCCGATTGTG
Statistics
Matches: 160, Mismatches: 36, Indels: 9
0.78 0.18 0.04
Matches are distributed among these distances:
105 1 0.01
106 35 0.22
107 10 0.06
108 112 0.70
109 2 0.01
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (106 bp):
GGGTTGGAGTATCCCCGATTGTGAAAAATCGATATTTTGAAAATAAAACGTGGGTTGGAGTATCC
CCTCGAAAATAACAGGGTTGGAGTATCTACTCAAAAATAAC
Found at i:435357 original size:80 final size:78
Alignment explanation
Indices: 435272--435694 Score: 436
Period size: 79 Copynumber: 5.3 Consensus size: 78
435262 CGAAAATAAT
* * * * * *
435272 GGGGTTGGAGTATCTCCTCGAAAATAACAGGGTTAGAGTATCCCCGATTATAAAAAATCAATATT
1 GGGGTTGGAGTATCCCCTCGAAAATAAC-GGGTTGGAGTATCCCCGATTGTAAAAAATTAGTGTT
435337 TTGGAAATAAAA-C
65 TTGGAAATAAAATC
* * * * *
435350 TGTGGGTTAGAGTATCTCCACGAAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTG
1 -G-GGGTTGGAGTATCCCCTCGAAAATAAC-GGGTTGGAGTATCCCCGATTGTAAAAAATTAGTG
*
435415 TTGTGGAAATAAAATC
63 TTTTGGAAATAAAATC
* * * * * * *
435431 GAGATTGAAGTATCCCCTTGGAAATAACGGTGTTGGAGTATCCCCAATTGTAAAAAATTGGTGTT
1 GGGGTTGGAGTATCCCCTCGAAAATAACGG-GTTGGAGTATCCCCGATTGTAAAAAATTAGTGTT
*
435496 TTGGAAATAAAATT
65 TTGGAAATAAAATC
** * *
435510 GGGGTTAAAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATTAGTGTT
1 GGGGTTGGAGTATCCCCTCGAAAATAAC-GGGTTGGAGTATCCCCGATTGTAAAAAATTAGTGTT
*
435575 TTGAAAATAAAATC
65 TTGGAAATAAAATC
* * ** ** *
435589 GGCGTTGGAGTATCCCTTC-AGAAATAACGGGATTGGAGTATCCCTAATTGTGGAAAATTGGTGT
1 GGGGTTGGAGTATCCCCTCGA-AAATAACGGG-TTGGAGTATCCCCGATTGTAAAAAATTAGTGT
*
435653 TTTGGAAATAAAACC
64 TTTGGAAATAAAATC
* * *
435668 AGGGTTGGTGTATCCCCTCAAAAATAA
1 GGGGTTGGAGTATCCCCTCGAAAATAA
435695 AAACATGAAT
Statistics
Matches: 289, Mismatches: 48, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
78 6 0.02
79 212 0.73
80 70 0.24
81 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (78 bp):
GGGGTTGGAGTATCCCCTCGAAAATAACGGGTTGGAGTATCCCCGATTGTAAAAAATTAGTGTTT
TGGAAATAAAATC
Found at i:435574 original size:158 final size:158
Alignment explanation
Indices: 435293--435666 Score: 484
Period size: 158 Copynumber: 2.4 Consensus size: 158
435283 ATCTCCTCGA
* * * *** *
435293 AAATAACAGGGTTAGAGTATCCCCGATTATAAAAAATCAATATTTTGGAAATAAAACTGTGGGTT
1 AAATAAC-GGGTTGGAGTATCCCCAATTGTAAAAAATTGGTGTTTTGGAAATAAAACTGTGGGTT
* * * *
435358 AGAGTATCTCCACGAAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTGTGGAA
65 AAAGTATCCCCACGAAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTGTGAAA
*
435423 ATAAAATCGAG-ATTGAAGTATCCCCTT-GG
130 ATAAAATCG-GCATTGAAGTAT-CCCTTCAG
*
435452 AAATAACGGTGTTGGAGTATCCCCAATTGTAAAAAATTGGTGTTTTGGAAATAAAATTG-GGGTT
1 AAATAACGG-GTTGGAGTATCCCCAATTGTAAAAAATTGGTGTTTTGGAAATAAAACTGTGGGTT
* * * *
435516 AAAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTTGAAA
65 AAAGTATCCCCACGAAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTGTGAAA
* *
435581 ATAAAATCGGCGTTGGAGTATCCCTTCAG
130 ATAAAATCGGCATTGAAGTATCCCTTCAG
* **
435610 AAATAACGGGATTGGAGTATCCCTAATTGTGGAAAATTGGTGTTTTGGAAATAAAAC
1 AAATAACGGG-TTGGAGTATCCCCAATTGTAAAAAATTGGTGTTTTGGAAATAAAAC
435667 CAGGGTTGGT
Statistics
Matches: 188, Mismatches: 23, Indels: 9
0.85 0.10 0.04
Matches are distributed among these distances:
157 7 0.04
158 133 0.71
159 48 0.26
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (158 bp):
AAATAACGGGTTGGAGTATCCCCAATTGTAAAAAATTGGTGTTTTGGAAATAAAACTGTGGGTTA
AAGTATCCCCACGAAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTGTGAAAA
TAAAATCGGCATTGAAGTATCCCTTCAG
Found at i:437996 original size:20 final size:19
Alignment explanation
Indices: 437971--438025 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
437961 AAAATGCCTG
437971 AATGTATCGATACATTGAAA
1 AATGTAT-GATACATTGAAA
* *
437991 AATGTATTGATACAATGAAT
1 AATGTA-TGATACATTGAAA
438011 AATGTATGATACATT
1 AATGTATGATACATT
438026 TGGGTAAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.26
20 22 0.71
21 1 0.03
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.35
Consensus pattern (19 bp):
AATGTATGATACATTGAAA
Found at i:438818 original size:42 final size:41
Alignment explanation
Indices: 438772--438862 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 41
438762 GTCTTGCTTC
* *
438772 TTGAGGACAAAGTGAAAAAAAGAG-CGAAATGCGTCCTGCTCT
1 TTGAGGACAAA--GAAAAAAAGAGACAAAATGCATCCTGCTCT
*
438814 TTGAGGACAAAGAAAAAAAGAGAATAAAATGCATCCTGCTCT
1 TTGAGGACAAAGAAAAAAAGAG-ACAAAATGCATCCTGCTCT
*
438856 TTTAGGA
1 TTGAGGA
438863 TGAAAGCTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 11 0.26
42 32 0.74
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (41 bp):
TTGAGGACAAAGAAAAAAAGAGACAAAATGCATCCTGCTCT
Found at i:439641 original size:13 final size:13
Alignment explanation
Indices: 439623--439648 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
439613 CAATTTTTTG
439623 TGTATCGATACAT
1 TGTATCGATACAT
439636 TGTATCGATACAT
1 TGTATCGATACAT
439649 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:440001 original size:21 final size:21
Alignment explanation
Indices: 439960--440003 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
439950 CTCTCCTTTA
* *
439960 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
439981 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
440002 TC
1 TC
440004 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:441831 original size:13 final size:13
Alignment explanation
Indices: 441813--441851 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
441803 ATAATCACCC
441813 TGTATCGATACAA
1 TGTATCGATACAA
441826 TGTATCGATACAA
1 TGTATCGATACAA
441839 TGTATCGATACAA
1 TGTATCGATACAA
441852 AGAAAGATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:441863 original size:20 final size:20
Alignment explanation
Indices: 441838--441915 Score: 75
Period size: 20 Copynumber: 3.6 Consensus size: 20
441828 TATCGATACA
441838 ATGTATCGATACAAAGAAAG
1 ATGTATCGATACAAAGAAAG
**
441858 ATGTATCGATACATTGAATTTCCAG
1 ATGTATCGATACAAAGAA-----AG
* *
441883 ATGTATCGATACACAGAAAC
1 ATGTATCGATACAAAGAAAG
441903 ATGTATCGATACA
1 ATGTATCGATACA
441916 TTTTGGACAT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
20 30 0.62
25 18 0.38
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (20 bp):
ATGTATCGATACAAAGAAAG
Found at i:443437 original size:13 final size:13
Alignment explanation
Indices: 443419--443443 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
443409 AAAACCATTT
443419 AATATTTCTTTTG
1 AATATTTCTTTTG
443432 AATATTTCTTTT
1 AATATTTCTTTT
443444 CGGCTTGAGT
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:0.24, C:0.08, G:0.04, T:0.64
Consensus pattern (13 bp):
AATATTTCTTTTG
Found at i:443500 original size:15 final size:15
Alignment explanation
Indices: 443480--443510 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
443470 ATTTCGTTTG
*
443480 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
443495 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
443510 G
1 G
443511 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:445343 original size:21 final size:21
Alignment explanation
Indices: 445314--445358 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
445304 AAGTTTTCAT
*
445314 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
445334 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
445356 TTT
1 TTT
445359 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:447592 original size:13 final size:13
Alignment explanation
Indices: 447574--447599 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
447564 CAATTTTTTG
447574 TGTATCGATACAT
1 TGTATCGATACAT
447587 TGTATCGATACAT
1 TGTATCGATACAT
447600 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:448426 original size:122 final size:121
Alignment explanation
Indices: 448178--449427 Score: 1356
Period size: 123 Copynumber: 10.2 Consensus size: 121
448168 AAAGGAGAAT
* * *
448178 AAAGTGCGTCATGCTTTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAA
1 AAAG-GCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
* * * *
448243 GGCGTCCTACAT-TTTGAGCACTGAAAAGTGCCACCAACTTATGTGGGCTTTAAAAGGA
64 GGCGTCCTGC-TCTTTGAGGACTGAAAGGTGCCACCAACTCATGTGGGCTTTAAAAGGA
* * *
448301 AAAGGCGTCCTGGTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTAGGCTTTAAAAGGAAAA
1 AAAGGCGTCCTGCTCTTTGAGGACT--AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
* * * * * * * *
448365 GGTGTCATGCTCTTCG-GGATTGAAATGTGCCACCAACTCGTGTGGGTTTTAAAAGAA
64 GGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTCATGTGGGCTTTAAAAGGA
* ** * **
448422 AAAAGCGT-CTGCTCTTTGAGGACTAAAATATGCCACCAACTCGTGTAAGCTTTAAAAGGAAAAA
1 AAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AAAA
* * * *
448486 GGTGTCCTACTCTTTGAGCACTGAAGGGTGCCACCAACTCATGTGGGCTTTGAAATA-GA
64 GGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTCATGTGGGCTTT-AAA-AGGA
* * * *
448545 AAAGGCATCCTGCTCTTTGAGGACTAAAGGTGCTACCAACTCGTGTGGGCTTTGAAAAGAAAAAG
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAG
* *
448610 GCATCCTACTCTTTGAGGACT-AAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGGA
65 GCGTCCTGCTCTTTGAGGACTGAAA-GGTGCCACCAACTCATGTGGGCTTT-AAAAGGA
* * * * * * *
448668 AAAGGCATCCTACTCTTTGAGGACTAAAGGTGACACCAACTAGTATAGGCTTTAAAAGAAGAAAG
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAG
* *
448733 GAGTCCTGCTCTTTGAGGACT-AAAGGGTGCCACCAACTCCTGTGGGCTTTGAAAAGGA
65 GCGTCCTGCTCTTTGAGGACTGAAA-GGTGCCACCAACTCATGTGGGCTTT-AAAAGGA
* * * * * * *
448791 AAAAGCATCCTCCTCTTTAAGGACTAAAGGTGCCACCAACTCGTGTGGTCTTTGAAAAGAAAAAG
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAG
* * *
448856 GCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAGCTCGTGT-GG-TTGAAAAGGA
65 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTCATGTGGGCTTTAAAAGGA
* * **
448910 AAAGACGTCCTGCTCTTTAAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAA-GGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAA
*** * * * * * *
448975 AATGCCCTACTCTTTAAGGA-TTAGAAGGTGCCACCAACTTATGTGTGCTTTGAAAA-GA
64 GGCGTCCTGCTCTTTGAGGACTGA-AAGGTGCCACCAACTCATGTGGGCTTT-AAAAGGA
* * *
449033 GAAGGCGTCCTGCTCTTTGAGGACTAGATGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAG
1 AAAGGCGTCCTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
* ** *
449098 GCGTCCTG-TACTTTGAGGACCGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
65 GCGTCCTGCT-CTTTGAGGACTGAAAGGTGCCACCAACTCATGTGGGCTTTAAAAGGA
* * * *
449155 AAAGGCATCCTACTCTTTGAAGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 AAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
* * *
449220 GCGTCCTGCTCTTTGAGGACTGAAAAGTGTCACCAACTTATGTGGGCTTTAAAAGGA
65 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTCATGTGGGCTTTAAAAGGA
** *
449277 AAATACGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAA
1 AAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAA
* * * * * ** *
449342 GGTGTTCTGCTTTTTAAGGACTAAAAGGTGCCACCAACTTGTGTGAGCTTTAAAAGGA
64 GGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTCATGTGGGCTTTAAAAGGA
*
449400 AAAGGTGTCCTGCTCTTTGAGGACTAAA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAA
449428 AGGGCTAAAA
Statistics
Matches: 967, Mismatches: 134, Indels: 53
0.84 0.12 0.05
Matches are distributed among these distances:
119 35 0.04
120 93 0.10
121 83 0.09
122 318 0.33
123 404 0.42
124 34 0.04
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (121 bp):
AAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
CGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTCATGTGGGCTTTAAAAGGA
Found at i:449428 original size:61 final size:61
Alignment explanation
Indices: 448178--449430 Score: 1343
Period size: 61 Copynumber: 20.5 Consensus size: 61
448168 AAAGGAGAAT
* *
448178 AAAGTGCGTCATGCTTTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
1 AAAG-GCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* * * *
448240 GAAGGCGTCCTACAT-TTTGAGCACTGAAAA-GTGCCACCAACTTATGTGGGCTTTAAAAGGA
1 AAAGGCGTCCTGC-TCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* *
448301 AAAGGCGTCCTGGTCTTTGAGGACTGGAAAA--TGCCACCAACTTGTGTAGGCTTTAAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACT--AAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* * * * * * * * *
448362 AAAGGTGTCATGCTCTTCG-GGATTGAAATGTGCCACCAACTCGTGTGGGTTTTAAAAGAA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* ** * **
448422 AAAAGCGT-CTGCTCTTTGAGGACTAAAATATGCCACCAACTCGTGTAAGCTTTAAAAGGAA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG-A
* * * * * **
448483 AAAGGTGTCCTACTCTTTGAGCACTGAAGGGTGCCACCAACTCATGTGGGCTTTGAAATA-GA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAA-AGGA
* * * *
448545 AAAGGCATCCTGCTCTTTGAGGACT-AAAGGTGCTACCAACTCGTGTGGGCTTTGAAAAGAA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGA
* * * **
448606 AAAGGCATCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGA
* * * * * * *
448668 AAAGGCATCCTACTCTTTGAGGACT-AAAGGTGACACCAACTAGTATAGGCTTTAAAAGAA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* * **
448728 GAAAGGAGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCCTGTGGGCTTTGAAAAGGA
1 -AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGA
* * * * * * *
448791 AAAAGCATCCTCCTCTTTAAGGACT-AAAGGTGCCACCAACTCGTGTGGTCTTTGAAAAGAA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGA
* * *
448852 AAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAGCTCGTGT-GG-TTGAAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* * * **
448910 AAAGACGTCCTGCTCTTTAAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGA
*** * * * * * * *
448972 AAAAATGCCCTACTCTTTAAGGATTAGAAGGTGCCACCAACTTATGTGTGCTTTGAAAA-GA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGA
* * *
449033 GAAGGCGTCCTGCTCTTTGAGGACTAGATGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* ** *
449094 GAAGGCGTCCTG-TACTTTGAGGACCGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
1 AAAGGCGTCCTGCT-CTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* * *
449155 AAAGGCATCCTACTCTTTGAAGACTGAAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* *
449216 AAAGGCGTCCTGCTCTTTGAGGACTGAAAA-GTGTCACCAACTTATGTGGGCTTTAAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
** * *
449277 AAATACGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGA
* * * * *
449339 AAAGGTGTTCTGCTTTTTAAGGACTAAAAGGTGCCACCAACTTGTGTGAGCTTTAAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
*
449400 AAAGGTGTCCTGCTCTTTGAGGACTAAAAGG
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAAGG
449431 GCTAAAATGG
Statistics
Matches: 1014, Mismatches: 151, Indels: 53
0.83 0.12 0.04
Matches are distributed among these distances:
58 32 0.03
59 28 0.03
60 88 0.09
61 572 0.56
62 283 0.28
63 10 0.01
64 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (61 bp):
AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
Found at i:453714 original size:39 final size:39
Alignment explanation
Indices: 453628--453714 Score: 120
Period size: 39 Copynumber: 2.2 Consensus size: 39
453618 TGATACATTG
* * * *
453628 TATCGATGCATGTTCTTGGTATCGATACACACTGAATTG
1 TATCGATACATGTTCTTGGTATAGATACACACTAAATTA
* *
453667 TATTGATACATGTTCTTGGTATAGATACACATTAAATTA
1 TATCGATACATGTTCTTGGTATAGATACACACTAAATTA
453706 TATCGATAC
1 TATCGATAC
453715 GTAAAACTGG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (39 bp):
TATCGATACATGTTCTTGGTATAGATACACACTAAATTA
Found at i:453802 original size:20 final size:20
Alignment explanation
Indices: 453755--453810 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 20
453745 ATATCAATAC
* *
453755 ATTGTATCGACACATACTTT
1 ATTGTATCGATACATACTGT
*
453775 ATTTGTATCGATACATAGTGT
1 A-TTGTATCGATACATACTGT
453796 ATTGTATCGATACAT
1 ATTGTATCGATACAT
453811 TGAGCCCAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.41
Consensus pattern (20 bp):
ATTGTATCGATACATACTGT
Found at i:454310 original size:35 final size:36
Alignment explanation
Indices: 454243--454311 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
454233 AGTGATTAAG
**
454243 AGGTTTTATCTTAGCCTTTGAAAAAGATAGGGAGAA
1 AGGTTTTATCTTAGCCCGTGAAAAAGATAGGGAGAA
454279 AGGTTTTATCTTAGCCCGTG-AAAAGATAGGGAG
1 AGGTTTTATCTTAGCCCGTGAAAAAGATAGGGAG
454312 GTTTCTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 13 0.42
36 18 0.58
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.29
Consensus pattern (36 bp):
AGGTTTTATCTTAGCCCGTGAAAAAGATAGGGAGAA
Found at i:455829 original size:13 final size:13
Alignment explanation
Indices: 455811--455847 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
455801 ATATTGATTA
455811 GTATCGATACATT
1 GTATCGATACATT
455824 GTATCGATACATT
1 GTATCGATACATT
455837 GTATCGATACA
1 GTATCGATACA
455848 CCTTGAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:456027 original size:29 final size:28
Alignment explanation
Indices: 455994--456050 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 28
455984 TATCAATACA
455994 TAAGAGCATATTTATGTAGAAACAAGCGT
1 TAAGAGCATATTTATGTAGAAA-AAGCGT
456023 TAAGAGCATATTTATGTAGAAAAAGCGT
1 TAAGAGCATATTTATGTAGAAAAAGCGT
456051 GAAACAAGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.28
Consensus pattern (28 bp):
TAAGAGCATATTTATGTAGAAAAAGCGT
Found at i:456967 original size:12 final size:12
Alignment explanation
Indices: 456950--456974 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
456940 GGATAGTAAA
456950 ATAATAATAATT
1 ATAATAATAATT
456962 ATAATAATAATT
1 ATAATAATAATT
456974 A
1 A
456975 AAATTCCAAA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATAATAATT
Found at i:457207 original size:17 final size:17
Alignment explanation
Indices: 457187--457221 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
457177 ATTTCATGCC
*
457187 TTCATGCCTCCATGCAT
1 TTCATACCTCCATGCAT
*
457204 TTCATACCTTCATGCAT
1 TTCATACCTCCATGCAT
457221 T
1 T
457222 GATTCTTTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.31, G:0.09, T:0.40
Consensus pattern (17 bp):
TTCATACCTCCATGCAT
Found at i:459225 original size:159 final size:157
Alignment explanation
Indices: 459018--459420 Score: 433
Period size: 161 Copynumber: 2.5 Consensus size: 157
459008 TTCCTATACA
* ** * *
459018 TAGGGGTTTAAGGATCTTAAAAACTTTTCGTTTCTTTTTGAGTTTCCATTATGGTATAAAATGAT
1 TAGGGGTTAAAGGATCTTAAAAACTTTTCGAATCTTTTTGAGTTTCCATTAAGGTACAAAATGAT
* * * * *
459083 ATTTTTCAAAAATAAATAAAAATTAAATTAATACTT-TCATAATTAAAATAAATATTAATTGTTT
66 ATTTTTCAAAAATAAATAAAAATAAAATTAATACTTAT-ACAACTAAAAGAAACATTAATT-TTT
* *
459147 TTAATCTTTTATATTCCTATGGGTGTCCG
129 TGAATCTTTTATATTCCTATGGGGGTCCG
* *
459176 TAGGGGTCTAAAGGATCTTAAAAACTTTTCGAATCTTTTTGGGTCTCCATTAAGGTACGAAAA-G
1 TAGGGGT-TAAAGGATCTTAAAAACTTTTCGAATCTTTTTGAGTTTCCATTAAGGTAC-AAAATG
** * * *
459240 GCATTTCTCAAAAATGAATAAATAAAATAAAATTAATACTTATACAACTGAAAGAAACATTAATT
64 ATATTTTTCAAAAAT-AA-ATA-AAAATAAAATTAATACTTATACAACTAAAAGAAACATTAATT
* *
459305 TTTTGAATCTTTTATATTCTTATGGGGGTTCG
126 TTTTGAATCTTTTATATTCCTATGGGGGTCCG
* * * *
459337 TAGGGGTATAAAAGAT-TTCAAAAA-TATTTC-ATATCTTTTCGAGTTTCCATTAAGATACGAAA
1 TAGGGGT-TAAAGGATCTT-AAAAACT-TTTCGA-ATCTTTTTGAGTTTCCATTAAGGTACAAAA
459399 TGATA-TTTTCAAAAA-AAATAAA
62 TGATATTTTTCAAAAATAAATAAA
459421 TAAAGTAATG
Statistics
Matches: 203, Mismatches: 32, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
156 2 0.01
157 2 0.01
158 9 0.04
159 56 0.28
160 22 0.11
161 77 0.38
162 34 0.17
163 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (157 bp):
TAGGGGTTAAAGGATCTTAAAAACTTTTCGAATCTTTTTGAGTTTCCATTAAGGTACAAAATGAT
ATTTTTCAAAAATAAATAAAAATAAAATTAATACTTATACAACTAAAAGAAACATTAATTTTTTG
AATCTTTTATATTCCTATGGGGGTCCG
Found at i:460678 original size:8 final size:9
Alignment explanation
Indices: 460657--460692 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
460647 GATTTATTTG
460657 AAAAAATAC
1 AAAAAATAC
460666 AAAAAATAC
1 AAAAAATAC
*
460675 AAAAAATAA
1 AAAAAATAC
460684 ATAAAAATA
1 A-AAAAATA
460693 AATAAGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 18 0.72
10 7 0.28
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.14
Consensus pattern (9 bp):
AAAAAATAC
Found at i:460686 original size:22 final size:22
Alignment explanation
Indices: 460660--460716 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
460650 TTATTTGAAA
*
460660 AAATACAAA-AAATACAAAAAAT
1 AAATAAAAATAAATA-AAAAAAT
*
460682 AAATAAAAATAAATAAGAAAAT
1 AAATAAAAATAAATAAAAAAAT
*
460704 AAAGAAAGAATAA
1 AAATAAA-AATAA
460717 GTGGCCTAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 20 0.67
23 10 0.33
ACGTcount: A:0.77, C:0.04, G:0.05, T:0.14
Consensus pattern (22 bp):
AAATAAAAATAAATAAAAAAAT
Found at i:470767 original size:23 final size:23
Alignment explanation
Indices: 470734--470791 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
470724 TGTTCACATC
*
470734 AATTTTCTTTATAAAAAAATTAA
1 AATTTTATTTATAAAAAAATTAA
470757 AATTTTATTTATAAAAAAATTAA
1 AATTTTATTTATAAAAAAATTAA
470780 AATTTTATTTAT
1 AATTTTATTTAT
470792 CGAGGATACT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
AATTTTATTTATAAAAAAATTAA
Found at i:470950 original size:97 final size:97
Alignment explanation
Indices: 470790--471026 Score: 316
Period size: 97 Copynumber: 2.4 Consensus size: 97
470780 AATTTTATTT
* * * *
470790 ATCGAGGATACTCCAACTCTATTCCTCCG-AGAGGATACTCCAACCCCGCTTTTAAACACATCAA
1 ATCGAGGACACTCCAACCCCATTCCTCCGAAG-GGATACTCCAAACCCGCTTTTAAACACATCAA
*
470854 AGTTTAAATCTTATT-TGCACTTAAATTGTCATC
65 AGTTTAAATCTTATTCT-CACTTAAATTATCATC
* * * **
470887 ATCGAGGACACTTCAACCCCATTCCTCCGAAGGGACACTCCAAACCTGCTTTTAAACGTATCAAA
1 ATCGAGGACACTCCAACCCCATTCCTCCGAAGGGATACTCCAAACCCGCTTTTAAACACATCAAA
*
470952 GTTTAAATTTTATTCTCACTTAAATTATCATC
66 GTTTAAATCTTATTCTCACTTAAATTATCATC
* * *
470984 ATCGGGGACACTCCAACCCCATTCCTCAGAGGGGATACTCCAA
1 ATCGAGGACACTCCAACCCCATTCCTCCGAAGGGATACTCCAA
471027 TCTCGTTTTT
Statistics
Matches: 122, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
97 119 0.98
98 3 0.02
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (97 bp):
ATCGAGGACACTCCAACCCCATTCCTCCGAAGGGATACTCCAAACCCGCTTTTAAACACATCAAA
GTTTAAATCTTATTCTCACTTAAATTATCATC
Found at i:474500 original size:12 final size:11
Alignment explanation
Indices: 474483--474546 Score: 60
Period size: 12 Copynumber: 5.6 Consensus size: 11
474473 GAAAGAAGAT
474483 ATAGGAGGGATG
1 ATAGGAGGGA-G
474495 ATAGGAGGAGAG
1 ATAGGAGG-GAG
*
474507 ATAGTA--GAG
1 ATAGGAGGGAG
*
474516 ATAGGAGGGATA
1 ATAGGAGGGA-G
474528 ATAGGAGGAGAG
1 ATAGGAGG-GAG
474540 ATAGGAG
1 ATAGGAG
474547 AGATAATAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
9 8 0.19
11 2 0.05
12 29 0.67
13 4 0.09
ACGTcount: A:0.41, C:0.00, G:0.45, T:0.14
Consensus pattern (11 bp):
ATAGGAGGGAG
Found at i:474520 original size:33 final size:33
Alignment explanation
Indices: 474483--474551 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
474473 GAAAGAAGAT
* *
474483 ATAGGAGGGATGATAGGAGGAGAGATAGTAGAG
1 ATAGGAGGGATAATAGGAGGAGAGATAGGAGAG
474516 ATAGGAGGGATAATAGGAGGAGAGATAGGAGAG
1 ATAGGAGGGATAATAGGAGGAGAGATAGGAGAG
474549 ATA
1 ATA
474552 ATAGAGAGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.42, C:0.00, G:0.43, T:0.14
Consensus pattern (33 bp):
ATAGGAGGGATAATAGGAGGAGAGATAGGAGAG
Found at i:474542 original size:15 final size:15
Alignment explanation
Indices: 474485--474542 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
474475 AAGAAGATAT
* *
474485 AGGAGGGATGATAGG
1 AGGAGAGATAATAGG
*
474500 AGGAGAGATAGTAGAG
1 AGGAGAGATAATAG-G
*
474516 ATAGGAGGGATAATAGG
1 --AGGAGAGATAATAGG
474533 AGGAGAGATA
1 AGGAGAGATA
474543 GGAGAGATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
15 20 0.59
16 1 0.03
17 1 0.03
18 12 0.35
ACGTcount: A:0.41, C:0.00, G:0.45, T:0.14
Consensus pattern (15 bp):
AGGAGAGATAATAGG
Found at i:474547 original size:42 final size:42
Alignment explanation
Indices: 474500--474580 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
474490 GGATGATAGG
* * *
474500 AGGAGAGATAGTAGAGATAGGAGGGATAATAGGAGGAGAGAT
1 AGGAGAGATAATAGAGAGAGGAAGGATAATAGGAGGAGAGAT
*
474542 AGGAGAGATAATAGAGAGAGGAAGGATGATAGGAGGAGA
1 AGGAGAGATAATAGAGAGAGGAAGGATAATAGGAGGAGA
474581 AGAGAAGAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.43, T:0.12
Consensus pattern (42 bp):
AGGAGAGATAATAGAGAGAGGAAGGATAATAGGAGGAGAGAT
Found at i:476347 original size:51 final size:51
Alignment explanation
Indices: 476271--476373 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
476261 CAAGAAAGTG
476271 CCTTATGACTTACCTCCAATTAGAGGGATAGAACACCAAATTGACTTAATT
1 CCTTATGACTTACCTCCAATTAGAGGGATAGAACACCAAATTGACTTAATT
476322 CCTTATGACTTACCTCCAATTAGAGGGATAGAACACCAAATTGACTTAATT
1 CCTTATGACTTACCTCCAATTAGAGGGATAGAACACCAAATTGACTTAATT
476373 C
1 C
476374 TAGAGCAACA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (51 bp):
CCTTATGACTTACCTCCAATTAGAGGGATAGAACACCAAATTGACTTAATT
Found at i:477887 original size:52 final size:52
Alignment explanation
Indices: 477809--477908 Score: 182
Period size: 52 Copynumber: 1.9 Consensus size: 52
477799 TGCAAGAACC
*
477809 CACTGTTCATCACTGTTCATGTATCGATACATTGTGAATAGTATCGATGCAT
1 CACTGTTCATCACTGTTCATATATCGATACATTGTGAATAGTATCGATGCAT
*
477861 CACTGTTCATCACTTTTCATATATCGATACATTGTGAATAGTATCGAT
1 CACTGTTCATCACTGTTCATATATCGATACATTGTGAATAGTATCGAT
477909 ACATTGAGTC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (52 bp):
CACTGTTCATCACTGTTCATATATCGATACATTGTGAATAGTATCGATGCAT
Found at i:479713 original size:34 final size:34
Alignment explanation
Indices: 479665--479734 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
479655 AAAGGGAAAG
* *
479665 AGAAAGAAGTTAATGCTATCAACATAGATAGCCC
1 AGAAAGAAGCTAATGCTATCAACAGAGATAGCCC
479699 AGAAAGAAGCTAATGCTATCAACAGAGATAGCCC
1 AGAAAGAAGCTAATGCTATCAACAGAGATAGCCC
479733 AG
1 AG
479735 CAAAATTTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.44, C:0.19, G:0.20, T:0.17
Consensus pattern (34 bp):
AGAAAGAAGCTAATGCTATCAACAGAGATAGCCC
Found at i:487696 original size:16 final size:16
Alignment explanation
Indices: 487654--487696 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
487644 TGATTACATC
487654 TTTATAGATTTACTCA
1 TTTATAGATTTACTCA
* * *
487670 TTTGTATATTTACTTA
1 TTTATAGATTTACTCA
487686 TTTATAGATTT
1 TTTATAGATTT
487697 GTTCATAAAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.58
Consensus pattern (16 bp):
TTTATAGATTTACTCA
Found at i:488106 original size:24 final size:23
Alignment explanation
Indices: 488057--488107 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
488047 TTTTTTTTTA
*
488057 GTTTAAATTTTTTGGCCAAATGG
1 GTTTAAATTTTTTGGCCAAATAG
* *
488080 GTTTAAATTTTTTAGGTCGAATAG
1 GTTTAAATTTTTT-GGCCAAATAG
488104 GTTT
1 GTTT
488108 TTATAGTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.25, C:0.06, G:0.22, T:0.47
Consensus pattern (23 bp):
GTTTAAATTTTTTGGCCAAATAG
Found at i:488425 original size:42 final size:42
Alignment explanation
Indices: 488379--488480 Score: 118
Period size: 42 Copynumber: 2.4 Consensus size: 42
488369 TGGAAGGTTT
* * *
488379 AAATTCAAAAGTTGAAATTTATA-AAGAAATGATGGAAAATTG
1 AAATT-AAAAATTGAAATTTAAAGAAGAAATGATGGAAAAGTG
**
488421 AAATTAAATAATTGAAA-TTAAAGAAGAAATGATGGAGGAGTG
1 AAATTAAA-AATTGAAATTTAAAGAAGAAATGATGGAAAAGTG
488463 AAATTGAAAAATTGAAAT
1 AAATT-AAAAATTGAAAT
488481 GATGGAATTG
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
41 7 0.14
42 41 0.80
43 3 0.06
ACGTcount: A:0.54, C:0.01, G:0.19, T:0.26
Consensus pattern (42 bp):
AAATTAAAAATTGAAATTTAAAGAAGAAATGATGGAAAAGTG
Found at i:488435 original size:14 final size:14
Alignment explanation
Indices: 488416--488442 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
488406 AATGATGGAA
488416 AATTGAAATTAAAT
1 AATTGAAATTAAAT
488430 AATTGAAATTAAA
1 AATTGAAATTAAA
488443 GAAGAAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.33
Consensus pattern (14 bp):
AATTGAAATTAAAT
Found at i:488865 original size:9 final size:9
Alignment explanation
Indices: 488848--488905 Score: 57
Period size: 9 Copynumber: 6.4 Consensus size: 9
488838 GCCTAACAAG
488848 AAAGAGAAA
1 AAAGAGAAA
*
488857 AAAGGGAAA
1 AAAGAGAAA
*
488866 AGAGAGAAA
1 AAAGAGAAA
488875 AAATGA-AAA
1 AAA-GAGAAA
*
488884 AAAAATGAAA
1 AAAGA-GAAA
488894 AAAGA-AAA
1 AAAGAGAAA
488902 AAAG
1 AAAG
488906 GGTTTTTTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
8 8 0.20
9 23 0.57
10 9 0.22
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (9 bp):
AAAGAGAAA
Found at i:488904 original size:10 final size:11
Alignment explanation
Indices: 488872--488896 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
488862 GAAAAGAGAG
488872 AAAAAATGAAA
1 AAAAAATGAAA
488883 AAAAAATGAAA
1 AAAAAATGAAA
488894 AAA
1 AAA
488897 GAAAAAAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAAATGAAA
Found at i:489642 original size:28 final size:30
Alignment explanation
Indices: 489604--489664 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 30
489594 AATCAAAATG
*
489604 AAAAAGTCAACTTCT-AT-AAATTGGTAGA
1 AAAAAATCAACTTCTAATCAAATTGGTAGA
* *
489632 AAAAAATCAACTTTTAATCAAATTGGTTGA
1 AAAAAATCAACTTCTAATCAAATTGGTAGA
489662 AAA
1 AAA
489665 GTCAAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 13 0.46
29 2 0.07
30 13 0.46
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (30 bp):
AAAAAATCAACTTCTAATCAAATTGGTAGA
Found at i:490058 original size:29 final size:27
Alignment explanation
Indices: 489969--490123 Score: 106
Period size: 28 Copynumber: 5.6 Consensus size: 27
489959 AAGAATTGTC
* **
489969 AATTAAACTTTT-CATATACAAAATTTCC
1 AATTAAACTTTTACATAT--AAATTTTTT
* * * *
489997 AATTAAAC-TTTGCAAACAAAATTTTT
1 AATTAAACTTTTACATATAAATTTTTT
490023 AGA-TAAACTTGTTACATATACAATTTTTT
1 A-ATTAAACTT-TTACATATA-AATTTTTT
490052 AATTAAACTTTTTACACT-TAAAGTTTTTT
1 AATTAAAC-TTTTACA-TATAAA-TTTTTT
* *
490081 -ATTAGACTTTTACATATTGAA-TTTTT
1 AATTAAACTTTTACATA-TAAATTTTTT
490107 AATTAAACTTTTACATA
1 AATTAAACTTTTACATA
490124 CGTAATTTTC
Statistics
Matches: 104, Mismatches: 11, Indels: 25
0.74 0.08 0.18
Matches are distributed among these distances:
26 19 0.18
27 27 0.26
28 29 0.28
29 26 0.25
30 3 0.03
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.45
Consensus pattern (27 bp):
AATTAAACTTTTACATATAAATTTTTT
Found at i:490130 original size:27 final size:28
Alignment explanation
Indices: 490015--490146 Score: 107
Period size: 27 Copynumber: 4.8 Consensus size: 28
490005 TTTGCAAACA
490015 AAATTTTTAGA-TAAACTTGTTACATA--T
1 AAATTTTTA-ATTAAACTT-TTACATACTT
490042 ACAATTTTTTAATTAAACTTTTTAC--ACTT
1 A-AA-TTTTTAATTAAAC-TTTTACATACTT
* *
490071 AAAGTTTTTTATTAGACTTTTACATA-TT
1 AAA-TTTTTAATTAAACTTTTACATACTT
* *
490099 GAATTTTTAATTAAACTTTTACATACGT
1 AAATTTTTAATTAAACTTTTACATACTT
* *
490127 -AATTTTCAATTAGACTTTTA
1 AAATTTTTAATTAAACTTTTA
490147 ATTAAACTTT
Statistics
Matches: 87, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
27 46 0.53
28 21 0.24
29 18 0.21
30 2 0.02
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (28 bp):
AAATTTTTAATTAAACTTTTACATACTT
Found at i:490143 original size:54 final size:56
Alignment explanation
Indices: 490029--490146 Score: 136
Period size: 54 Copynumber: 2.1 Consensus size: 56
490019 TTTTAGATAA
* **
490029 ACTTGTTACATATACAATTTTTTAATTAAACTTTTTACACTTAAAGTTTTTTATTAG
1 ACTT-TTACATATACAATTTTTTAATTAAACTTTTTACACGTAAAGTTTTCAATTAG
**
490086 ACTTTTACATATTGAA-TTTTTAATTAAAC-TTTTACATACGT-AA-TTTTCAATTAG
1 ACTTTTACATATACAATTTTTTAATTAAACTTTTTAC--ACGTAAAGTTTTCAATTAG
490140 ACTTTTA
1 ACTTTTA
490147 ATTAAACTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
54 22 0.41
55 15 0.28
56 13 0.24
57 4 0.07
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (56 bp):
ACTTTTACATATACAATTTTTTAATTAAACTTTTTACACGTAAAGTTTTCAATTAG
Found at i:490183 original size:14 final size:14
Alignment explanation
Indices: 490166--490207 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
490156 TTTACCTGTG
490166 AAATTTTTAAATAA
1 AAATTTTTAAATAA
* *
490180 AAATTTTCACAT-A
1 AAATTTTTAAATAA
*
490193 AAATTTTTAATTAA
1 AAATTTTTAAATAA
490207 A
1 A
490208 CTTGTATATA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATTTTTAAATAA
Found at i:490249 original size:55 final size:54
Alignment explanation
Indices: 490190--490342 Score: 180
Period size: 54 Copynumber: 2.8 Consensus size: 54
490180 AAATTTTCAC
* *
490190 ATAAAATTTTTAATTAAACTTGTATATATAAAACTTTTAGTTAGAATTTTCATAT
1 ATAAAATTTTTAATTAAACTTGTACATAT-AAACTTTTAATTAGAATTTTCATAT
** * *
490245 ATAAAATGATTAATTAAACTTGTACATATAAACTTTTAATTAGACTTTTCGTAT
1 ATAAAATTTTTAATTAAACTTGTACATATAAACTTTTAATTAGAATTTTCATAT
* * * * *
490299 GTAAAATTTTTAATTTAACTTTTTACATAAAAAATTTTTAATTA
1 ATAAAATTTTTAATTAAAC-TTGTACAT-ATAAACTTTTAATTA
490343 AACAATTTGT
Statistics
Matches: 83, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
54 37 0.45
55 33 0.40
56 13 0.16
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (54 bp):
ATAAAATTTTTAATTAAACTTGTACATATAAACTTTTAATTAGAATTTTCATAT
Found at i:490313 original size:28 final size:27
Alignment explanation
Indices: 490142--490345 Score: 137
Period size: 28 Copynumber: 7.4 Consensus size: 27
490132 TCAATTAGAC
* *
490142 TTTTAATTAAACTTTT-TACCTGTGAAAT
1 TTTTAATTAAACTTTTATA--TATAAAAT
* * * *
490170 TTTTAAATAAAAATTTT-CACATAAAAT
1 TTTT-AATTAAACTTTTATATATAAAAT
* *
490197 TTTTAATTAAACTTGTATATATAAAAC
1 TTTTAATTAAACTTTTATATATAAAAT
*
490224 TTTTAGTTAGAA-TTTTCATATATAAAAT
1 TTTTAATTA-AACTTTT-ATATATAAAAT
** * * *
490252 GATTAATTAAACTTGTACATAT-AAAC
1 TTTTAATTAAACTTTTATATATAAAAT
* * *
490278 TTTTAATTAGACTTTTCGTATGTAAAAT
1 TTTTAATTAAACTTTT-ATATATAAAAT
* * *
490306 TTTTAATTTAACTTTTTACATAAAAAAT
1 TTTTAATTAAAC-TTTTATATATAAAAT
490334 TTTTAATTAAAC
1 TTTTAATTAAAC
490346 AATTTGTTAC
Statistics
Matches: 132, Mismatches: 36, Indels: 16
0.72 0.20 0.09
Matches are distributed among these distances:
26 24 0.18
27 37 0.28
28 56 0.42
29 15 0.11
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (27 bp):
TTTTAATTAAACTTTTATATATAAAAT
Found at i:495951 original size:19 final size:17
Alignment explanation
Indices: 495906--495955 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 17
495896 AGGTCAACTT
*
495906 ATTT-TTTTATATTAAA
1 ATTTATTTTAAATTAAA
*
495922 ATTTATATTAAATTAAA
1 ATTTATTTTAAATTAAA
495939 GAGTTTATTTTAAATTA
1 -A-TTTATTTTAAATTA
495956 TTTGATAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 4 0.14
17 10 0.36
18 1 0.04
19 13 0.46
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
ATTTATTTTAAATTAAA
Found at i:497124 original size:3 final size:3
Alignment explanation
Indices: 497113--497145 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
497103 AAACCTAAAT
497113 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
497146 AAAGCTATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:499582 original size:14 final size:13
Alignment explanation
Indices: 499563--499596 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
499553 TTTTATAGGA
*
499563 ATTTTTTTAGTTT
1 ATTTTTTTAGATT
499576 ATGTTTTTTAGATT
1 AT-TTTTTTAGATT
499590 ATTTTTT
1 ATTTTTT
499597 AAAATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.74
Consensus pattern (13 bp):
ATTTTTTTAGATT
Found at i:500367 original size:22 final size:21
Alignment explanation
Indices: 500316--500367 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
500306 TTTTAAATTG
500316 AATTTTAATTTTTAAAAGATT
1 AATTTTAATTTTTAAAAGATT
* *
500337 AGATATTAAGTTTTTGAAA-ATAT
1 A-ATTTTAA-TTTTTAAAAGAT-T
500360 AATTTTAA
1 AATTTTAA
500368 ATATTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 1 0.04
22 14 0.56
23 10 0.40
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (21 bp):
AATTTTAATTTTTAAAAGATT
Found at i:500430 original size:25 final size:25
Alignment explanation
Indices: 500380--500434 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
500370 ATTTTTATAT
* * *
500380 TTTTAAAATGATTTTATCTTTTATA
1 TTTTAAAATGATGTTATATTTCATA
500405 TTTTAAAAGTGATGTTA-ATTTCATA
1 TTTTAAAA-TGATGTTATATTTCATA
500430 TTTTA
1 TTTTA
500435 TATATTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (25 bp):
TTTTAAAATGATGTTATATTTCATA
Found at i:501722 original size:11 final size:11
Alignment explanation
Indices: 501706--501730 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
501696 GATAAAAATA
501706 TATATTTATAT
1 TATATTTATAT
501717 TATATTTATAT
1 TATATTTATAT
501728 TAT
1 TAT
501731 TTTTTGTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATTTATAT
Found at i:502146 original size:50 final size:50
Alignment explanation
Indices: 502065--502287 Score: 261
Period size: 50 Copynumber: 4.5 Consensus size: 50
502055 AGATGTTTAG
* * * *
502065 AGTCAACAATTACGGTCACCT-TC-CGTTATTGTTAAAGGTTGGTGAATAAT
1 AGTCAACAATTACGATCACCTCTCTCG--ATTGTCAAATGTTGGTGAAGAAT
* ** * *
502115 AGTCAACAATTACGGTCACCTCTCTTAATTGTCAAATGTTAGTGAGGAAT
1 AGTCAACAATTACGATCACCTCTCTCGATTGTCAAATGTTGGTGAAGAAT
* * * *
502165 AGTTAACAATTATGATCACTTCTCTCGATTGTCAAAAGTTGGTGAAGAAT
1 AGTCAACAATTACGATCACCTCTCTCGATTGTCAAATGTTGGTGAAGAAT
*
502215 AGTCAACAATTACGACCACCTCTCTCGATTGTCAAATGTTGGTGAAGAAT
1 AGTCAACAATTACGATCACCTCTCTCGATTGTCAAATGTTGGTGAAGAAT
* * *
502265 AATCAACAATTACAACCACCTCT
1 AGTCAACAATTACGATCACCTCT
502288 TTTACACCAA
Statistics
Matches: 148, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
50 146 0.99
51 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (50 bp):
AGTCAACAATTACGATCACCTCTCTCGATTGTCAAATGTTGGTGAAGAAT
Found at i:506744 original size:50 final size:50
Alignment explanation
Indices: 506663--506773 Score: 123
Period size: 50 Copynumber: 2.2 Consensus size: 50
506653 GCTTAGAGTT
* * * * *
506663 AACAATTATGGTCATTTTTTTCTATTATCAAATGTTAGTAAAAAATAGTC
1 AACAATTATAGACATTTTTCTCAATTATCAAAGGTTAGTAAAAAATAGTC
* * * * *
506713 AACAATTATAGACATTTTTCTCAATTGTCAAAGGTTGGTGAGAAATAGTT
1 AACAATTATAGACATTTTTCTCAATTATCAAAGGTTAGTAAAAAATAGTC
*
506763 AATAATTATAG
1 AACAATTATAG
506774 CTACCTCTCT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (50 bp):
AACAATTATAGACATTTTTCTCAATTATCAAAGGTTAGTAAAAAATAGTC
Found at i:508213 original size:19 final size:19
Alignment explanation
Indices: 508161--508217 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
508151 TATTCTAATT
* *
508161 AAAAT-TTATTAAATTTATA
1 AAAATATTA-TAATTTTAAA
508180 AAAATATGTAT--TTTTAAA
1 AAAATAT-TATAATTTTAAA
508198 AAAATATTATAATTTTAAA
1 AAAATATTATAATTTTAAA
508217 A
1 A
508218 GGATGTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
17 3 0.09
18 12 0.38
19 13 0.41
20 2 0.06
21 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
AAAATATTATAATTTTAAA
Found at i:508422 original size:23 final size:24
Alignment explanation
Indices: 508378--508424 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
508368 AATATCTCAA
508378 AATTTATTTTAATAGTATAATTTT
1 AATTTATTTTAATAGTATAATTTT
*
508402 AATTATATTTTTATA-TA-AATTTT
1 AATT-TATTTTAATAGTATAATTTT
508425 TTAATTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 6 0.29
25 9 0.43
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
AATTTATTTTAATAGTATAATTTT
Found at i:508663 original size:15 final size:16
Alignment explanation
Indices: 508634--508674 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
508624 TTTGTTGTTT
508634 ATATGTAA-A-TATAA
1 ATATGTAATATTATAA
508648 AT-TGTAATATTATAA
1 ATATGTAATATTATAA
*
508663 ATATTTAATATT
1 ATATGTAATATT
508675 TAGAGTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 5 0.22
14 3 0.13
15 7 0.30
16 8 0.35
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (16 bp):
ATATGTAATATTATAA
Found at i:509724 original size:2 final size:2
Alignment explanation
Indices: 509717--509741 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
509707 TTCTAGTAAG
509717 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
509742 GATAAAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:509814 original size:2 final size:2
Alignment explanation
Indices: 509807--509831 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
509797 ACCATCTACT
509807 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
509832 GTACATTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:513158 original size:18 final size:20
Alignment explanation
Indices: 513135--513177 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
513125 TTGATTTGAT
513135 TTAAAAT-A-ATATTTTTAA
1 TTAAAATAATATATTTTTAA
513153 TTAAAATAATATATTTTTAA
1 TTAAAATAATATATTTTTAA
513173 TTAAA
1 TTAAA
513178 TTTAATTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 7 0.30
19 1 0.04
20 15 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAAAATAATATATTTTTAA
Found at i:513196 original size:19 final size:17
Alignment explanation
Indices: 513174--513228 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 17
513164 TATTTTTAAT
513174 TAAATTTAATTATAAAATA
1 TAAATTTAA-TATAAAA-A
513193 TAAATTTAATATAAAAA
1 TAAATTTAATATAAAAA
*
513210 T-AATTT-TTA-AAAAA
1 TAAATTTAATATAAAAA
513224 TAAAT
1 TAAAT
513229 AATAATTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
14 6 0.18
15 5 0.15
16 5 0.15
17 2 0.06
18 7 0.21
19 9 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATTTAATATAAAAA
Found at i:513219 original size:18 final size:19
Alignment explanation
Indices: 513174--513212 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
513164 TATTTTTAAT
513174 TAAATTTAATTATAAAATA
1 TAAATTTAATTATAAAATA
513193 TAAATTTAA-TATAAAA-A
1 TAAATTTAATTATAAAATA
513210 TAA
1 TAA
513213 TTTTTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.20
18 7 0.35
19 9 0.45
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAATTTAATTATAAAATA
Found at i:516356 original size:2 final size:2
Alignment explanation
Indices: 516351--516379 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
516341 AAATACACAC
516351 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
516380 AAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:516784 original size:18 final size:18
Alignment explanation
Indices: 516758--516800 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
516748 AAATACATTT
*
516758 ATTTATTAAAATTTTTTGA
1 ATTT-TTAAAATTGTTTGA
516777 ATTTTTAAAATTGTTTGA
1 ATTTTTAAAATTGTTTGA
516795 ATTTTT
1 ATTTTT
516801 TATTTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (18 bp):
ATTTTTAAAATTGTTTGA
Found at i:519791 original size:22 final size:22
Alignment explanation
Indices: 519763--519807 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
519753 AATATTTGGC
519763 AGCTTATGGTGTTGGTAAGAAT
1 AGCTTATGGTGTTGGTAAGAAT
*
519785 AGCTTATGGTGTTGTTAAGAAT
1 AGCTTATGGTGTTGGTAAGAAT
519807 A
1 A
519808 AGATGTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.38
Consensus pattern (22 bp):
AGCTTATGGTGTTGGTAAGAAT
Found at i:523260 original size:13 final size:13
Alignment explanation
Indices: 523242--523268 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
523232 CATTTTGGGA
523242 TGTATCGATACAT
1 TGTATCGATACAT
523255 TGTATCGATACAT
1 TGTATCGATACAT
523268 T
1 T
523269 TTGTGTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:523264 original size:33 final size:32
Alignment explanation
Indices: 523222--523283 Score: 106
Period size: 33 Copynumber: 1.9 Consensus size: 32
523212 TACAAGCCAA
523222 TGTATCGATACATTTTGGGATGTATCGATACAT
1 TGTATCGATACATTTTGGG-TGTATCGATACAT
*
523255 TGTATCGATACATTTTGTGTGTATCGATA
1 TGTATCGATACATTTTGGGTGTATCGATA
523284 TAAACAGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 10 0.36
33 18 0.64
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (32 bp):
TGTATCGATACATTTTGGGTGTATCGATACAT
Found at i:523374 original size:20 final size:21
Alignment explanation
Indices: 523327--523379 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
523317 GCCAATGACC
*
523327 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
523348 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
523368 TGTATCGATACA
1 TGTATCGATACA
523380 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:523385 original size:13 final size:13
Alignment explanation
Indices: 523367--523391 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
523357 ACATTTGGTC
523367 ATGTATCGATACA
1 ATGTATCGATACA
523380 ATGTATCGATAC
1 ATGTATCGATAC
523392 TGTGCAATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:524017 original size:21 final size:21
Alignment explanation
Indices: 523993--524034 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
523983 GGCAATTTAA
523993 CAATAATTTTTAATCACATAT
1 CAATAATTTTTAATCACATAT
524014 CAATAATTTTTAATCACATAT
1 CAATAATTTTTAATCACATAT
524035 TTCTTTCTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (21 bp):
CAATAATTTTTAATCACATAT
Found at i:525409 original size:20 final size:22
Alignment explanation
Indices: 525370--525414 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
525360 GCTGCTAGAG
*
525370 TGGGGGTTGCCCGGTTGCGACC
1 TGGGGGTTGCCCGGTCGCGACC
525392 TGGGGG-TG-CCGGTCGCGACC
1 TGGGGGTTGCCCGGTCGCGACC
525412 TGG
1 TGG
525415 TAGGTGCTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.64
21 2 0.09
22 6 0.27
ACGTcount: A:0.04, C:0.27, G:0.49, T:0.20
Consensus pattern (22 bp):
TGGGGGTTGCCCGGTCGCGACC
Found at i:525420 original size:21 final size:20
Alignment explanation
Indices: 525380--525421 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
525370 TGGGGGTTGC
* *
525380 CCGGTTGCGACCTGGGGGTG
1 CCGGTCGCGACCTGGAGGTG
525400 CCGGTCGCGACCTGGTAGGTG
1 CCGGTCGCGACCTGG-AGGTG
525421 C
1 C
525422 TGCCTAGAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.07, C:0.29, G:0.45, T:0.19
Consensus pattern (20 bp):
CCGGTCGCGACCTGGAGGTG
Found at i:530667 original size:52 final size:52
Alignment explanation
Indices: 530597--530717 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
530587 GAAAATTTAT
*
530597 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
530649 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
530701 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
530718 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:530730 original size:52 final size:51
Alignment explanation
Indices: 530597--530737 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
530587 GAAAATTTAT
530597 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
530649 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
530701 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
530738 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:530744 original size:13 final size:13
Alignment explanation
Indices: 530726--530750 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
530716 CAAAGATCAG
530726 TGTATCGATACAA
1 TGTATCGATACAA
530739 TGTATCGATACA
1 TGTATCGATACA
530751 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:530833 original size:13 final size:13
Alignment explanation
Indices: 530815--530839 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
530805 CAAAAAAATA
530815 TGTATCGATACAT
1 TGTATCGATACAT
530828 TGTATCGATACA
1 TGTATCGATACA
530840 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:530835 original size:33 final size:33
Alignment explanation
Indices: 530793--530859 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
530783 AGTAGCTTAA
530793 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
530826 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
530859 A
1 A
530860 GATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:531825 original size:55 final size:55
Alignment explanation
Indices: 531728--532049 Score: 266
Period size: 55 Copynumber: 5.8 Consensus size: 55
531718 AAGTGATAAA
* * * * * *
531728 GATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAG
1 GATGTCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAGAAAAAG
** * *
531783 GATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAT--G---AA-
1 GATGTCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAGAAAAAG
* *
531832 GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAAG
1 GATGTCAATATGCTGATTCAAGGCCAGCTATATTGGACTT--AAA-GATGA-GA-AAAAG
* * * * *
531892 TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAG
1 -GAT---G-T--CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAGAAAAAG
** * * *
531954 GATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG-G-AAAAT
1 GATGTCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAGAAAAAG
*
532007 G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 GATGTCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
532050 GTGCCAATGT
Statistics
Matches: 213, Mismatches: 36, Indels: 39
0.74 0.12 0.14
Matches are distributed among these distances:
49 34 0.16
50 2 0.01
51 3 0.01
52 40 0.19
53 6 0.03
54 1 0.00
55 70 0.33
57 1 0.00
58 1 0.00
59 2 0.01
61 6 0.03
62 5 0.02
63 2 0.01
64 6 0.03
65 3 0.01
67 31 0.15
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (55 bp):
GATGTCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAGAAAAAG
Found at i:531872 original size:49 final size:49
Alignment explanation
Indices: 531726--531884 Score: 156
Period size: 49 Copynumber: 3.1 Consensus size: 49
531716 AAAAGTGATA
* * * *
531726 AAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--G
* ** * * *
531777 AAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG
1 ---AA-GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
*
531830 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
*
531879 ATGATG
1 AAGATG
531885 AGAAAAGTGA
Statistics
Matches: 86, Mismatches: 18, Indels: 7
0.77 0.16 0.06
Matches are distributed among these distances:
49 45 0.52
50 2 0.02
53 1 0.01
54 2 0.02
55 36 0.42
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (49 bp):
AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
Found at i:531906 original size:171 final size:173
Alignment explanation
Indices: 531664--532048 Score: 711
Period size: 171 Copynumber: 2.2 Consensus size: 173
531654 GAGATGATAA
*
531664 GCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGATGATGAGAAAAGTGATAAAG
1 GCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAAATGATGATGAGAAAAGTGATAAAG
531729 ATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGT
66 ATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGT
*
531794 GCTGATTCAAGGCCAGCTACATTGAACTTAAAGAT-GAAGA-T
131 GCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGT
*
531835 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAAGTGATAAAG
1 GCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAAATGATGATGAGAAAAGTGATAAAG
531900 ATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGT
66 ATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGT
531965 GCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGT
131 GCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAA-GT
*
532009 GCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
1 GCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAA
532049 GGTGCCAATG
Statistics
Matches: 207, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
171 163 0.79
172 4 0.02
174 40 0.19
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.25
Consensus pattern (173 bp):
GCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAAATGATGATGAGAAAAGTGATAAAG
ATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGT
GCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGT
Found at i:532106 original size:49 final size:49
Alignment explanation
Indices: 531964--532334 Score: 460
Period size: 49 Copynumber: 7.7 Consensus size: 49
531954 GATGTCAACG
* *
531964 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAGA--TGCCAATA
* *
532016 TGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G--G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
532059 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * *
532108 TGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G--G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
*
532151 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * * *
532200 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* *
532249 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGATGCCAATA
* *
532301 TGCTGATTCAAGGCCAGCTATATTGGGCTTAAAG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
532335 GGGTTGCCAC
Statistics
Matches: 279, Mismatches: 25, Indels: 30
0.84 0.07 0.09
Matches are distributed among these distances:
43 70 0.25
44 5 0.02
45 2 0.01
46 3 0.01
47 1 0.00
48 5 0.02
49 119 0.43
50 2 0.01
51 2 0.01
52 70 0.25
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (49 bp):
TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
Found at i:532137 original size:92 final size:93
Alignment explanation
Indices: 531963--532335 Score: 570
Period size: 92 Copynumber: 3.9 Consensus size: 93
531953 GGATGTCAAC
* * *
531963 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAG
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAGA--TGCCAATATGCTGATTCAAG
*
532028 GCCAGCTATATTGGACTTAAAGGTGCCAAT
64 GCCAGCGATATTGGACTTAAAGGTGCCAAT
*
532058 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAGATGCCAATATGCTGATTCAAGGC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAGATGCCAATATGCTGATTCAAGGC
532122 CAGCGATATTGGACTTAAAGGTGCCAAT
66 CAGCGATATTGGACTTAAAGGTGCCAAT
532150 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAGATGCCAATATGCTGATTCAAGGC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAGATGCCAATATGCTGATTCAAGGC
532214 CAGCGATATTGGACTTAAAGATGAAGGTGCCAAT
66 CAGCGATATTGGACTT----A--AAGGTGCCAAT
*
532248 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAG
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGG--AAGATGCCAATATGCTGATTCAAG
* *
532313 GCCAGCTATATTGGGCTTAAAGG
64 GCCAGCGATATTGGACTTAAAGG
532336 GGTTGCCACC
Statistics
Matches: 262, Mismatches: 7, Indels: 18
0.91 0.02 0.06
Matches are distributed among these distances:
92 128 0.49
94 4 0.02
95 40 0.15
96 1 0.00
97 1 0.00
98 48 0.18
99 1 0.00
101 39 0.15
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (93 bp):
GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAGATGCCAATATGCTGATTCAAGGC
CAGCGATATTGGACTTAAAGGTGCCAAT
Done.