Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 2 of 126
Found at i:287665 original size:26 final size:26
Alignment explanation
Indices: 287636--287688 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
287626 TAAAAAAAGT
287636 TCCACGTCATTTACGAAAATAAATTA
1 TCCACGTCATTTACGAAAATAAATTA
*
287662 TCCACGTCATTTACGAAACTAAATTA
1 TCCACGTCATTTACGAAAATAAATTA
287688 T
1 T
287689 GTTATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.32
Consensus pattern (26 bp):
TCCACGTCATTTACGAAAATAAATTA
Found at i:288487 original size:14 final size:14
Alignment explanation
Indices: 288468--288501 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
288458 TGACTTTTTT
288468 TTCTAATGATACTA
1 TTCTAATGATACTA
288482 TTCTAATGATACTA
1 TTCTAATGATACTA
288496 TTCTAA
1 TTCTAA
288502 CATGTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (14 bp):
TTCTAATGATACTA
Found at i:289348 original size:33 final size:33
Alignment explanation
Indices: 289311--289385 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 33
289301 CATAGTACAT
* * *
289311 CACTCCTTCAAGCCCGTATCTACCGCATTACTC
1 CACTCCTCCAAGCCCGTATCCACCGCAATACTC
** *
289344 CACTCCTCCTCGCTCGTATCCACCGCAATACTC
1 CACTCCTCCAAGCCCGTATCCACCGCAATACTC
289377 CACTCCTCC
1 CACTCCTCC
289386 CGGCTCAAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.19, C:0.48, G:0.08, T:0.25
Consensus pattern (33 bp):
CACTCCTCCAAGCCCGTATCCACCGCAATACTC
Found at i:289865 original size:48 final size:48
Alignment explanation
Indices: 289650--290822 Score: 2062
Period size: 48 Copynumber: 24.3 Consensus size: 48
289640 GTATTTATTT
* * **
289650 AATTAGATTA-ATTGCAATATTAAAACTTGGAACAAACTTTGTGGTCATA
1 AATTAGA-TACATTACAACATTAAAACTTGGAACAAACTTTGTAAT-ATA
* * **
289699 AATTAGATACATTACAAGATTAAAACTTAGAA-AACACTTTGTGACCATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAA-ACTTTGT-AATATA
289748 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATCATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAAT-ATA
289797 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
289845 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
289893 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
289941 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
289989 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
290037 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
290085 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
290133 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
290181 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
290229 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
290277 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
290325 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
290373 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
*
290421 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAACATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
290469 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATCATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAAT-ATA
290518 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATCATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAAT-ATA
* *
290567 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTGATCGTA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAAT-ATA
**
290616 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTGCTCATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAAT-ATA
*
290665 AATTAGATACATTACAACATTAAAACTTGAAACAAACTTTGTAATATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
*
290713 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTGATCATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAAT-ATA
* ** *
290762 AATTAGATACATTGCAACATTAAAACGAGGAACAAACTTTGTAATTTA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
*
290810 AATTAGGTACATT
1 AATTAGATACATT
290823 GGATTACATA
Statistics
Matches: 1090, Mismatches: 27, Indels: 15
0.96 0.02 0.01
Matches are distributed among these distances:
48 735 0.67
49 353 0.32
50 2 0.00
ACGTcount: A:0.47, C:0.13, G:0.09, T:0.31
Consensus pattern (48 bp):
AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
Found at i:295370 original size:11 final size:11
Alignment explanation
Indices: 295347--295375 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
295337 TATGGTTTTG
295347 TTCTTGA-TTA
1 TTCTTGATTTA
295357 TTCTTGATTTA
1 TTCTTGATTTA
295368 TTCTTGAT
1 TTCTTGAT
295376 GATTTGACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.17, C:0.10, G:0.10, T:0.62
Consensus pattern (11 bp):
TTCTTGATTTA
Found at i:295629 original size:28 final size:25
Alignment explanation
Indices: 295577--295629 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
295567 GAATCTGTGA
*
295577 GATTCTTAAAAAAATTTTGGGTTTT
1 GATTCTTAAAAAAATTTTGGATTTT
295602 GATTCTTTAAATAAAATTTTAGGATTTT
1 GATTC-TTAAA-AAAATTTT-GGATTTT
295630 ATAAATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 5 0.21
26 5 0.21
27 8 0.33
28 6 0.25
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.49
Consensus pattern (25 bp):
GATTCTTAAAAAAATTTTGGATTTT
Found at i:299441 original size:26 final size:26
Alignment explanation
Indices: 299405--299461 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
299395 TTGTCTACAT
299405 TAACAACCCTGGTTTGGACCATTGGA
1 TAACAACCCTGGTTTGGACCATTGGA
299431 TAACAACCCTGGTTTGGACCATTGGA
1 TAACAACCCTGGTTTGGACCATTGGA
299457 TAACA
1 TAACA
299462 TCTAAGAGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (26 bp):
TAACAACCCTGGTTTGGACCATTGGA
Found at i:305964 original size:1 final size:1
Alignment explanation
Indices: 305958--306010 Score: 88
Period size: 1 Copynumber: 53.0 Consensus size: 1
305948 GCCTTGCTGC
**
305958 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACCAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
306011 GAAGAAGCCA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.96, C:0.04, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:307409 original size:30 final size:31
Alignment explanation
Indices: 307366--307431 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 31
307356 TCTAAACTTT
* * *
307366 AATTTGATTAATTT-TAGTTTTGTATTTTTTA
1 AATTTGATCAATTTATA-TTTTATAGTTTTTA
*
307397 AATTTG-TCAATTTATATTTTATAGTTTTTG
1 AATTTGATCAATTTATATTTTATAGTTTTTA
307427 AATTT
1 AATTT
307432 TAAAATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
30 22 0.73
31 8 0.27
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.62
Consensus pattern (31 bp):
AATTTGATCAATTTATATTTTATAGTTTTTA
Found at i:322847 original size:16 final size:16
Alignment explanation
Indices: 322826--322858 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
322816 TTCGCTGTAT
322826 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
322842 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
322858 T
1 T
322859 AACAAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.36, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:323113 original size:18 final size:17
Alignment explanation
Indices: 323092--323126 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
323082 TTATTATTAA
*
323092 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
323110 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
323127 TCTTAATACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:323241 original size:56 final size:59
Alignment explanation
Indices: 323084--323243 Score: 139
Period size: 56 Copynumber: 2.7 Consensus size: 59
323074 TAACATAATT
* * *
323084 ATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATACTCAATATT
1 ATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAA-TCATAATACTCAATATA
* * * * ** * * * * *
323144 CTTATATGAATTTACTAAAATCATAATATATGATAGT-ATAAAAT-ATAAT-TTGAA-ATA
1 ATTAT-TAAATATATTTTAATTAAAATATATGAT-TTAATAAAATCATAATACTCAATATA
323201 ATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAAT
1 ATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAAT
323244 TTAAAATAAT
Statistics
Matches: 74, Mismatches: 23, Indels: 10
0.69 0.21 0.09
Matches are distributed among these distances:
55 1 0.01
56 28 0.38
57 6 0.08
58 3 0.04
59 4 0.05
60 5 0.07
61 26 0.35
62 1 0.01
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (59 bp):
ATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATCATAATACTCAATATA
Found at i:323315 original size:26 final size:26
Alignment explanation
Indices: 323285--323400 Score: 80
Period size: 26 Copynumber: 4.5 Consensus size: 26
323275 TATGAATTTG
*
323285 TATAATTTAATATAATTATTATTAAA
1 TATAATTTAATATAATTATAATTAAA
**
323311 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAAT-ATAAT-TATAATTAAA
* * * *
323339 TAAAAATTT--TCTTA-TATGAATT-TA
1 T-ATAATTTAATATAATTAT-AATTAAA
*
323363 TATAATTTAAAATAATTA-ATATTAAA
1 TATAATTTAATATAATTATA-ATTAAA
323389 TATAATTTAATA
1 TATAATTTAATA
323401 ATGATATATA
Statistics
Matches: 68, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
23 6 0.09
24 6 0.09
25 9 0.13
26 27 0.40
27 6 0.09
28 8 0.12
29 6 0.09
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (26 bp):
TATAATTTAATATAATTATAATTAAA
Found at i:323335 original size:44 final size:43
Alignment explanation
Indices: 323285--323423 Score: 116
Period size: 44 Copynumber: 3.4 Consensus size: 43
323275 TATGAATTTG
323285 TATAATTTAATATAATTATTATTAAATATAATTTAATAATAATA
1 TATAATTTAATATAATTATTATTAAATATAATTTAATAAT-ATA
* * ** *
323329 TATAATTTCATA-AA-AATT-TT-CTTAT-A-TGAAT--T-TA
1 TATAATTTAATATAATTATTATTAAATATAATTTAATAATATA
* *
323363 TATAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAATATAATTATTATTAAATATAATTTAATAAT-ATA
* *
323407 TATAATTTCATAAAATT
1 TATAATTTAATATAATT
323424 CTTGATAATA
Statistics
Matches: 70, Mismatches: 15, Indels: 20
0.67 0.14 0.19
Matches are distributed among these distances:
34 12 0.17
35 2 0.03
36 3 0.04
37 2 0.03
38 7 0.10
39 2 0.03
40 7 0.10
41 2 0.03
42 4 0.06
43 2 0.03
44 27 0.39
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (43 bp):
TATAATTTAATATAATTATTATTAAATATAATTTAATAATATA
Found at i:323350 original size:78 final size:78
Alignment explanation
Indices: 323264--323421 Score: 280
Period size: 78 Copynumber: 2.0 Consensus size: 78
323254 TATTAGTAAT
* * *
323264 AAATTTTCTTATATGAATTTGTATAATTTAATATAATTATTATTAAATATAATTTAATAATAATA
1 AAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATA
323329 TATAATTTCATAA
66 TATAATTTCATAA
*
323342 AAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 AAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATA
323407 TATAATTTCATAA
66 TATAATTTCATAA
323420 AA
1 AA
323422 TTCTTGATAA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (78 bp):
AAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATA
TATAATTTCATAA
Found at i:325052 original size:23 final size:24
Alignment explanation
Indices: 324992--325054 Score: 87
Period size: 23 Copynumber: 2.7 Consensus size: 24
324982 TCTACTCACT
324992 AACAAATCAAGAACAATTTCCAGC
1 AACAAATCAAGAACAATTTCCAGC
*
325016 AGAC-TATCAA-AACAATTTCCAG-
1 A-ACAAATCAAGAACAATTTCCAGC
325038 AACAAATCAAGAACAAT
1 AACAAATCAAGAACAAT
325055 ATCAAAACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 2 0.06
22 6 0.18
23 18 0.53
24 6 0.18
25 2 0.06
ACGTcount: A:0.52, C:0.22, G:0.08, T:0.17
Consensus pattern (24 bp):
AACAAATCAAGAACAATTTCCAGC
Found at i:325063 original size:22 final size:22
Alignment explanation
Indices: 325021--325066 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
325011 CCAGCAGACT
* *
325021 ATCAAAACAATTTCCAGAACAA
1 ATCAAAACAATATCCAAAACAA
325043 ATCAAGAACAATAT-CAAAACAA
1 ATCAA-AACAATATCCAAAACAA
325065 AT
1 AT
325067 GCAACAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.59, C:0.20, G:0.04, T:0.17
Consensus pattern (22 bp):
ATCAAAACAATATCCAAAACAA
Found at i:325081 original size:107 final size:107
Alignment explanation
Indices: 324964--325193 Score: 433
Period size: 107 Copynumber: 2.1 Consensus size: 107
324954 ACTATACTTG
*
324964 CAATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAAC
1 CAATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAACAGACTATCAAAAC
325029 AATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAA
66 AATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAA
*
325071 CAATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCTAACAGACTATCAAAAC
1 CAATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAACAGACTATCAAAAC
325136 AATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAA
66 AATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAA
*
325178 CAATTTCTAGTTTCAT
1 CAATTTCCAGTTTCAT
325194 TGAAAACAGC
Statistics
Matches: 120, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 120 1.00
ACGTcount: A:0.45, C:0.23, G:0.06, T:0.26
Consensus pattern (107 bp):
CAATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAACAGACTATCAAAAC
AATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAA
Found at i:325159 original size:23 final size:24
Alignment explanation
Indices: 325099--325173 Score: 72
Period size: 23 Copynumber: 3.3 Consensus size: 24
325089 TCTACTCACT
325099 AACAAATCAAGAACAATTTCTAACAG
1 AACAAATCAAGAACAATTTC--ACAG
*
325125 -AC-TATCAA-AACAATTTC-CAG
1 AACAAATCAAGAACAATTTCACAG
*
325145 AACAAATCAAGAACAATATCA-A-
1 AACAAATCAAGAACAATTTCACAG
325167 AACAAAT
1 AACAAAT
325174 GCAACAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
20 3 0.07
21 2 0.05
22 12 0.29
23 18 0.43
24 5 0.12
25 2 0.05
ACGTcount: A:0.56, C:0.20, G:0.05, T:0.19
Consensus pattern (24 bp):
AACAAATCAAGAACAATTTCACAG
Found at i:335871 original size:28 final size:27
Alignment explanation
Indices: 335840--335901 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
335830 GAAATAAAGG
335840 AAATTATATATTAAA-ATAAATTTAAAAT
1 AAATTATATA-TAAATA-AAATTTAAAAT
* *
335868 AAATAATATATAAATGAAAATTTGAAAT
1 AAATTATATATAAAT-AAAATTTAAAAT
335896 AAATTA
1 AAATTA
335902 AATAATACGG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 4 0.14
28 24 0.83
29 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (27 bp):
AAATTATATATAAATAAAATTTAAAAT
Found at i:337160 original size:13 final size:11
Alignment explanation
Indices: 337135--337177 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
337125 CTCTCTGTTC
337135 TTTTTTTTCT-
1 TTTTTTTTCTA
*
337145 TTTTTTTGGCTA
1 TTTTTTT-TCTA
337157 TTTTTTTTCTA
1 TTTTTTTTCTA
*
337168 TTTTTCTTCT
1 TTTTTTTTCT
337178 CGTTTTGCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 7 0.25
11 14 0.50
12 7 0.25
ACGTcount: A:0.05, C:0.12, G:0.05, T:0.79
Consensus pattern (11 bp):
TTTTTTTTCTA
Found at i:338128 original size:87 final size:87
Alignment explanation
Indices: 338002--339100 Score: 1658
Period size: 87 Copynumber: 12.7 Consensus size: 87
337992 TCATGGAGAT
* * * * *
338002 AAGACCTGTTATCTTTAACCAGCTCCACTACAACTGATGGAGGCAAGGCTTTGTTTTTGATCTGC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
*
338067 TTCGCTGTTAATGCAAGAAGGC
66 TTCGCTGTCAATGCAAGAAGGC
*
338089 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCCGC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
* *
338154 TTCGTTGTTAATGC-AGAAAGGC
66 TTCGCTGTCAATGCAAG-AAGGC
*
338176 AAGATCTGCTATCTTTAACCAGCTCCAATGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
338241 TTCGCTGTCAATGCAAGAAGGC
66 TTCGCTGTCAATGCAAGAAGGC
* * * * *
338263 AAGATCTGCTATCTTTAACCAGCTCTATTGCAACCGATGGTGGAAAGGCTTTGTTTTTGATCTGC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
* *
338328 TTCGCTGTTAATGCAGGAAGGC
66 TTCGCTGTCAATGCAAGAAGGC
* *
338350 AAGA-CTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTATTTTCGATTTGC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
* * *
338414 TTTGCTGTTAATGCAGGAAGGC
66 TTCGCTGTCAATGCAAGAAGGC
* *
338436 AAGATCTGCTATCTTTAACTAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
338501 TTCGCTGTCAATGCAAGAAGGC
66 TTCGCTGTCAATGCAAGAAGGC
* *
338523 AAGATCTGCTATCTTTAACTAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
338588 TTCGCTGTCAATGCAAGAAGGC
66 TTCGCTGTCAATGCAAGAAGGC
* *
338610 AAGATCTGCTATCTTTAACTAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
338675 TTCGCTGTCAATGCAAGAAGGC
66 TTCGCTGTCAATGCAAGAAGGC
* * * *
338697 AAGATCTGCTATCTTTAACTAGCTCCACTACAACCGAT----G---TGTTTTGTTTTCGATCTGC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
* * *
338755 TTCTCTGTTAATGCAGGAAGGC
66 TTCGCTGTCAATGCAAGAAGGC
* *
338777 AAGATCTACTATCTTTAACCAGTTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
**
338842 TTCGCTGTCAATGCGGGAAGGC
66 TTCGCTGTCAATGCAAGAAGGC
* *
338864 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTATTTTCGATTTGC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
* * *
338929 TTTGCTGTTAATGCAGGAAGGC
66 TTCGCTGTCAATGCAAGAAGGC
* * *
338951 AAGATCTGCTATCTTTAACTAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTTGATCTGC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
* ** *
339016 TTCGTTGTCAATGCGGGAAGGA
66 TTCGCTGTCAATGCAAGAAGGC
*
339038 AAGATCTGCTATCTTTAACTAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCT
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCT
339101 TCACTGATCT
Statistics
Matches: 936, Mismatches: 66, Indels: 20
0.92 0.06 0.02
Matches are distributed among these distances:
80 70 0.07
83 1 0.00
84 1 0.00
86 80 0.09
87 782 0.84
88 2 0.00
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.30
Consensus pattern (87 bp):
AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
TTCGCTGTCAATGCAAGAAGGC
Found at i:338900 original size:341 final size:342
Alignment explanation
Indices: 338047--339081 Score: 1626
Period size: 341 Copynumber: 3.0 Consensus size: 342
338037 GATGGAGGCA
* * *
338047 AGGCTTTGTTTTTGATCTGCTTCGCTGTTAATGCAAGAAGGCAAGATCTGCTATCTTTAACCAGC
1 AGGCTTTGTTTTCGATCTGCTTCTCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGC
* * * *
338112 TCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCCGCTTCGTTGTTAATGCAGAAAGGCA
66 TCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCA
*
338177 AGATCTGCTATCTTTAACCAGCTCCAATGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCT
131 AGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCT
* * * * * *
338242 TCGCTGTCAATGCAAGAAGGCAAGATCTGCTATCTTTAACCAGCTCTATTGCAACCGATGGTGGA
196 TCGCTGTCAATGCAAGAAGGCAAGATCTGCTATCTTTAACTAGCTCCACTACAACCGATGGAGGC
* *
338307 AAGGCTTTGTTTTTGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGA-CTGCTATCTTTAACCAG
261 AAGGCTTTGTTTTTGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAACTAG
338371 CTCCACTGCAACCGATGGAGG
326 CTCCACTGCAACCGAT----G
* * *
338392 CAAGGCTTTATTTTCGATTTGCTT-TGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACT
1 --AGGCTTTGTTTTCGATCTGCTTCT-CTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACC
* *
338456 AGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTCAATGCAAGAAG
63 AGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTCAATGCAGGAAG
* *
338521 GCAAGATCTGCTATCTTTAACTAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCT
128 GCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCT
338586 GCTTCGCTGTCAATGCAAGAAGGCAAGATCTGCTATCTTTAACTAGCTCCACTACAACCGATGGA
193 GCTTCGCTGTCAATGCAAGAAGGCAAGATCTGCTATCTTTAACTAGCTCCACTACAACCGATGGA
* *
338651 GGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTCAATGCAAGAAGGCAAGATCTGCTATCTTTAAC
258 GGCAAGGCTTTGTTTTTGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAAC
*
338716 TAGCTCCACTACAACCGATG
323 TAGCTCCACTGCAACCGATG
* * * *
338736 -TGTTTTGTTTTCGATCTGCTTCTCTGTTAATGCAGGAAGGCAAGATCTACTATCTTTAACCAGT
1 AGGCTTTGTTTTCGATCTGCTTCTCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGC
*
338800 TCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTCAATGCGGGAAGGCA
66 TCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCA
* *
338865 AGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTATTTTCGATTTGCT
131 AGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCT
* * *
338930 TTGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACTAGCTCCACTACAACCGATGGAGGC
196 TCGCTGTCAATGCAAGAAGGCAAGATCTGCTATCTTTAACTAGCTCCACTACAACCGATGGAGGC
* * *
338995 AAGGCTTTGTTTTTGATCTGCTTCGTTGTCAATGCGGGAAGGAAAGATCTGCTATCTTTAACTAG
261 AAGGCTTTGTTTTTGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAACTAG
339060 CTCCACTGCAACCGATGG
326 CTCCACTGCAACCGAT-G
339078 AGGC
1 AGGC
339082 AAGGCTTTGT
Statistics
Matches: 632, Mismatches: 51, Indels: 14
0.91 0.07 0.02
Matches are distributed among these distances:
341 315 0.50
342 2 0.00
343 1 0.00
344 1 0.00
347 282 0.45
348 31 0.05
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (342 bp):
AGGCTTTGTTTTCGATCTGCTTCTCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGC
TCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCA
AGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCT
TCGCTGTCAATGCAAGAAGGCAAGATCTGCTATCTTTAACTAGCTCCACTACAACCGATGGAGGC
AAGGCTTTGTTTTTGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAACTAG
CTCCACTGCAACCGATG
Found at i:340304 original size:7 final size:7
Alignment explanation
Indices: 340292--340352 Score: 99
Period size: 7 Copynumber: 9.0 Consensus size: 7
340282 TTAGCCTCTC
340292 CATTTTT
1 CATTTTT
340299 CATTTTT
1 CATTTTT
340306 CATTTTT
1 CATTTTT
340313 CA-TTTT
1 CATTTTT
340319 CATTTTT
1 CATTTTT
340326 CATTTTT
1 CATTTTT
*
340333 CA-TTCT
1 CATTTTT
340339 CATTTTT
1 CATTTTT
340346 CATTTTT
1 CATTTTT
340353 TTGACTTAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
6 11 0.22
7 39 0.78
ACGTcount: A:0.15, C:0.16, G:0.00, T:0.69
Consensus pattern (7 bp):
CATTTTT
Found at i:340318 original size:13 final size:14
Alignment explanation
Indices: 340292--340352 Score: 99
Period size: 13 Copynumber: 4.5 Consensus size: 14
340282 TTAGCCTCTC
340292 CATTTTTCATTTTT
1 CATTTTTCATTTTT
340306 CATTTTTCA-TTTT
1 CATTTTTCATTTTT
340319 CATTTTTCATTTTT
1 CATTTTTCATTTTT
*
340333 CA-TTCTCATTTTT
1 CATTTTTCATTTTT
340346 CATTTTT
1 CATTTTT
340353 TTGACTTAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
13 25 0.58
14 18 0.42
ACGTcount: A:0.15, C:0.16, G:0.00, T:0.69
Consensus pattern (14 bp):
CATTTTTCATTTTT
Found at i:340320 original size:20 final size:20
Alignment explanation
Indices: 340295--340352 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
340285 GCCTCTCCAT
340295 TTTTCATTTTTCATTTTTCA
1 TTTTCATTTTTCATTTTTCA
340315 TTTTCATTTTTCATTTTTCA
1 TTTTCATTTTTCATTTTTCA
*
340335 TTCTCATTTTTCATTTTT
1 TTTTCATTTTTCATTTTT
340353 TTGACTTAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTCATTTTTCATTTTTCA
Found at i:340322 original size:27 final size:27
Alignment explanation
Indices: 340292--340352 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
340282 TTAGCCTCTC
*
340292 CATTTTTCATTTTTCATTTTTCA-TTTT
1 CATTTTTCATTTTTCA-TTCTCATTTTT
340319 CATTTTTCATTTTTCATTCTCATTTTT
1 CATTTTTCATTTTTCATTCTCATTTTT
340346 CATTTTT
1 CATTTTT
340353 TTGACTTAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 5 0.16
27 27 0.84
ACGTcount: A:0.15, C:0.16, G:0.00, T:0.69
Consensus pattern (27 bp):
CATTTTTCATTTTTCATTCTCATTTTT
Found at i:341996 original size:35 final size:35
Alignment explanation
Indices: 341954--342032 Score: 131
Period size: 35 Copynumber: 2.3 Consensus size: 35
341944 GTATAAATTC
* * *
341954 ATGAATAATTATTTGTATCATATGATTATGAATGA
1 ATGAATAATAATTTGTATCATATGATAATGAACGA
341989 ATGAATAATAATTTGTATCATATGATAATGAACGA
1 ATGAATAATAATTTGTATCATATGATAATGAACGA
342024 ATGAATAAT
1 ATGAATAAT
342033 GAATGAATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.44, C:0.04, G:0.14, T:0.38
Consensus pattern (35 bp):
ATGAATAATAATTTGTATCATATGATAATGAACGA
Found at i:342033 original size:15 final size:14
Alignment explanation
Indices: 342013--342046 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
342003 GTATCATATG
342013 ATAATGAACGAATGA
1 ATAATGAACGAAT-A
*
342028 ATAATGAATGAATA
1 ATAATGAACGAATA
342042 ATAAT
1 ATAAT
342047 TTGGAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.56, C:0.03, G:0.15, T:0.26
Consensus pattern (14 bp):
ATAATGAACGAATA
Found at i:354475 original size:16 final size:17
Alignment explanation
Indices: 354435--354478 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
354425 GTTTTCATGT
354435 TGATACATTGGAAGAAC
1 TGATACATTGGAAGAAC
354452 T-ACT-CATTGGAAGAA-
1 TGA-TACATTGGAAGAAC
354467 TGATACATTGGA
1 TGATACATTGGA
354479 CTGGACCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
15 2 0.08
16 20 0.83
17 2 0.08
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (17 bp):
TGATACATTGGAAGAAC
Found at i:355912 original size:26 final size:26
Alignment explanation
Indices: 355883--355937 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
355873 ATATGTATAT
*
355883 TATAGATAAATATTATA-TTAATTTAA
1 TATA-ATAAATATTAAATTTAATTTAA
*
355909 TATAATTAATATTAAATTTAATTTAA
1 TATAATAAATATTAAATTTAATTTAA
355935 TAT
1 TAT
355938 TTAAGTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (26 bp):
TATAATAAATATTAAATTTAATTTAA
Found at i:355928 original size:21 final size:20
Alignment explanation
Indices: 355897--355935 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
355887 GATAAATATT
355897 ATATTAATTTAATATAATTA
1 ATATTAATTTAATATAATTA
*
355917 ATATTAAATTTAATTTAAT
1 ATATT-AATTTAATATAAT
355936 ATTTAAGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATTAATTTAATATAATTA
Found at i:355963 original size:28 final size:28
Alignment explanation
Indices: 355891--355971 Score: 96
Period size: 28 Copynumber: 3.0 Consensus size: 28
355881 ATTATAGATA
*
355891 AATATTATATTAATTTAATA--TAA-TT
1 AATATTATTTTAATTTAATATTTAAGTT
*
355916 AATATTAAATTTAATTTAATATTTAAGTT
1 AATATT-ATTTTAATTTAATATTTAAGTT
* *
355945 GATATTATTTTAATTTAATATTAAAGT
1 AATATTATTTTAATTTAATATTTAAGT
355972 GATTAAGTCT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
25 6 0.13
26 12 0.26
28 22 0.47
29 7 0.15
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (28 bp):
AATATTATTTTAATTTAATATTTAAGTT
Found at i:355965 original size:16 final size:17
Alignment explanation
Indices: 355891--355967 Score: 61
Period size: 17 Copynumber: 4.4 Consensus size: 17
355881 ATTATAGATA
355891 AATATTATA-TTAATTT
1 AATATTATATTTAATTT
*
355907 AATATAATTAATATTAAATTT
1 -A-AT-ATT-ATATTTAATTT
*
355928 AAT-TTAATATTTAAGTT
1 AATATT-ATATTTAATTT
*
355945 GATATTAT-TTTAATTT
1 AATATTATATTTAATTT
355961 AATATTA
1 AATATTA
355968 AAGTGATTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
16 13 0.27
17 17 0.35
18 4 0.08
19 5 0.10
20 4 0.08
21 6 0.12
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
AATATTATATTTAATTT
Found at i:358328 original size:68 final size:68
Alignment explanation
Indices: 358256--358896 Score: 381
Period size: 68 Copynumber: 9.4 Consensus size: 68
358246 ACGACTTACC
* * *
358256 TACATAGCATGCCGATTTAAGATCACGCTCCTATCTTACAACCTACTAATTTAACATCACAACTA
1 TACATAGCACGCCGATTTAAGATCACGCTCCTATCTTACAACCTACTGATTTAAGATCACAACTA
358321 ATT
66 ATT
* * * ** * * * * *
358324 TACATAGCACACCAATTTAATATTGCGCCCCTATTTTA-TA-GTTCGTTGATTTAAGATCACAAC
1 TACATAGCACGCCGATTTAAGATCACGCTCCTATCTTACAACCTAC--TGATTTAAGATCACAAC
**
358387 TAACC
64 TAATT
* * * * *
358392 TACATAGCACACTGATTTAAGATCGCGCTCCTATCTTACAATCC-ACTGATTTAAGATCGCGACT
1 TACATAGCACGCCGATTTAAGATCACGCTCCTATCTTACAA-CCTACTGATTTAAGATCACAACT
358456 AATT
65 AATT
** * * * * ** * * *
358460 T-CTATAGCACATCAATTTAAGATCGCAC-CT-TTATTTTATAGTCTGCTGATTGAAGATCACAG
1 TAC-ATAGCACGCCGATTTAAGAT--CACGCTCCTATCTTACAACCTACTGATTTAAGATCACAA
358522 CTAATT
63 CTAATT
* * ** * ****
358528 TACATAGCACGCTGATTTAAGAT-ATCGCTCCTATATTAC-AGTTCACTGATTTAATATCATGGT
1 TACATAGCACGCCGATTTAAGATCA-CGCTCCTATCTTACAACCT-ACTGATTTAAGATCACAAC
**
358591 TAACC
64 TAATT
* * * * * * * * * *
358596 TATATAGCACGCCAATTTAAGATCGCACTCTTATCTTATAGCCCACCGATTTAAGATCATAACTA
1 TACATAGCACGCCGATTTAAGATCACGCTCCTATCTTACAACCTACTGATTTAAGATCACAACTA
358661 ATT
66 ATT
* * * * * **
358664 TACATAGCACGTCGATTTAAGATTTCAC-C-CCTATTTTATAGATC-GCTGATTTAAGATCACGG
1 TACATAGCACGCCGATTTAAGA--TCACGCTCCTATCTTACA-ACCTACTGATTTAAGATCACAA
*
358726 CTAATC
63 CTAATT
* * * ***
358732 TACATAGCACGCCAATTTAAGATCACACTCATATCTTACAATCCGT--TGATTTAAGATCACGGT
1 TACATAGCACGCCGATTTAAGATCACGCTCCTATCTTACAA-CC-TACTGATTTAAGATCACAAC
**
358795 TAACC
64 TAATT
* * * * ** *
358800 TACATAGGATGCTGATTTAAGATCACGCTCCTATCTTACAACATGTTGTTTTAAGATCACAACTA
1 TACATAGCACGCCGATTTAAGATCACGCTCCTATCTTACAACCTACTGATTTAAGATCACAACTA
358865 ATT
66 ATT
**
358868 TACATAGCACGGTGATTTAAGATCACGCT
1 TACATAGCACGCCGATTTAAGATCACGCT
358897 TTTATTTATA
Statistics
Matches: 430, Mismatches: 117, Indels: 52
0.72 0.20 0.09
Matches are distributed among these distances:
65 1 0.00
66 8 0.02
67 9 0.02
68 400 0.93
69 6 0.01
70 6 0.01
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (68 bp):
TACATAGCACGCCGATTTAAGATCACGCTCCTATCTTACAACCTACTGATTTAAGATCACAACTA
ATT
Found at i:358457 original size:136 final size:135
Alignment explanation
Indices: 358202--358877 Score: 601
Period size: 136 Copynumber: 5.0 Consensus size: 135
358192 AGAGTTAGCG
* * * * * *
358202 ATTTAAGATCACACCCTTATTTTATAGTTTGTTGATTTAATATCACGACTTACCTACATAGCATG
1 ATTTAAGATCGCACCCTTATTTTATAGTTCGTTGATTTAAGATCACAACTAACCTACATAGCACG
* * * * *
358267 CCGATTTAAGATCACGCTCCTATCTTACAACCTACTAATTTAACATCACAACTAATTTACATAGC
66 CTGATTTAAGATCACGCTCCTATCTTACAATC-ACTGATTTAAGATCACGACTAATTTACATAGC
358332 ACACCA
130 ACACCA
* * * * *
358338 ATTTAATATTGCGCCCCTATTTTATAGTTCGTTGATTTAAGATCACAACTAACCTACATAGCACA
1 ATTTAAGATCGCACCCTTATTTTATAGTTCGTTGATTTAAGATCACAACTAACCTACATAGCACG
* *
358403 CTGATTTAAGATCGCGCTCCTATCTTACAATCCACTGATTTAAGATCGCGACTAATTT-CTATAG
66 CTGATTTAAGATCACGCTCCTATCTTACAAT-CACTGATTTAAGATCACGACTAATTTAC-ATAG
*
358467 CACATCA
129 CACACCA
* * * * **
358474 ATTTAAGATCGCACCTTTATTTTATAG-TCTGCTGATTGAAGATCACAGCTAATTTACATAGCAC
1 ATTTAAGATCGCACCCTTATTTTATAGTTC-GTTGATTTAAGATCACAACTAACCTACATAGCAC
* * * * ** ** *
358538 GCTGATTTAAGAT-ATCGCTCCTATATTACAGTTCACTGATTTAATATCATGGTTAACCTATATA
65 GCTGATTTAAGATCA-CGCTCCTATCTTACA-ATCACTGATTTAAGATCACGACTAATTTACATA
*
358602 GCACGCCA
128 GCACACCA
* * ** *** * **
358610 ATTTAAGATCGCACTCTTATCTTATAGCCCACCGATTTAAGATCATAACTAATTTACATAGCACG
1 ATTTAAGATCGCACCCTTATTTTATAGTTCGTTGATTTAAGATCACAACTAACCTACATAGCACG
* * * * *
358675 -TCGATTTAAGATTTCAC-C-CCTATTTTATAGATCGCTGATTTAAGATCACGGCTAATCTACAT
66 CT-GATTTAAGA--TCACGCTCCTATCTTACA-ATCACTGATTTAAGATCACGACTAATTTACAT
*
358737 AGCACGCCA
127 AGCACACCA
* * * * * * * *** * *
358746 ATTTAAGATCACACTCATATCTTACAATCCGTTGATTTAAGATCACGGTTAACCTACATAGGATG
1 ATTTAAGATCGCACCCTTATTTTATAGTTCGTTGATTTAAGATCACAACTAACCTACATAGCACG
* * *
358811 CTGATTTAAGATCACGCTCCTATCTTACAA-CATGTTGTTTTAAGATCACAACTAATTTACATAG
66 CTGATTTAAGATCACGCTCCTATCTTACAATCA--CTGATTTAAGATCACGACTAATTTACATAG
358875 CAC
129 CAC
358878 GGTGATTTAA
Statistics
Matches: 439, Mismatches: 85, Indels: 32
0.79 0.15 0.06
Matches are distributed among these distances:
134 5 0.01
135 6 0.01
136 420 0.96
137 5 0.01
138 2 0.00
139 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (135 bp):
ATTTAAGATCGCACCCTTATTTTATAGTTCGTTGATTTAAGATCACAACTAACCTACATAGCACG
CTGATTTAAGATCACGCTCCTATCTTACAATCACTGATTTAAGATCACGACTAATTTACATAGCA
CACCA
Found at i:358597 original size:204 final size:204
Alignment explanation
Indices: 358311--358877 Score: 611
Period size: 204 Copynumber: 2.8 Consensus size: 204
358301 CTAATTTAAC
* * * * * *
358311 ATCACAACTAATTTACATAGCACACCAATTTAATAT-TGCGCCCCTATTTTATAGTTCGTTGATT
1 ATCACAGCTAATTTACATAGCACGCCAATTTAAGATAT-CGCTCCTATATTACAGTTCGTTGATT
*** * * *
358375 TAAGATCACAACTAACCTACATAGCACACTGATTTAAGATCGCGCTCCTATCTTACAATCCACTG
65 TAAGATCACGGTTAACCTACATAGCACGCTGATTTAAGATCGCGCTCCTATCTTACAACCCACCG
* * **
358440 ATTTAAGATCGCGACTAATTT-CTATAGCACATCAATTTAAGATCGCACCTTTATTTTATAG-TC
130 ATTTAAGATCACAACTAATTTAC-ATAGCACATCAATTTAAGATCGCACCCCTATTTTATAGATC
358503 TGCTGATTGAAG
194 -GCTGATTGAAG
** **
358515 ATCACAGCTAATTTACATAGCACGCTGATTTAAGATATCGCTCCTATATTACAGTTCACTGATTT
1 ATCACAGCTAATTTACATAGCACGCCAATTTAAGATATCGCTCCTATATTACAGTTCGTTGATTT
* * * ** * * * *
358580 AATATCATGGTTAACCTATATAGCACGCCAATTTAAGATCGCACTCTTATCTTATAGCCCACCGA
66 AAGATCACGGTTAACCTACATAGCACGCTGATTTAAGATCGCGCTCCTATCTTACAACCCACCGA
* * * **
358645 TTTAAGATCATAACTAATTTACATAGCACGTCGATTTAAGATTTCACCCCTATTTTATAGATCGC
131 TTTAAGATCACAACTAATTTACATAGCACATCAATTTAAGATCGCACCCCTATTTTATAGATCGC
*
358710 TGATTTAAG
196 TGATTGAAG
* * * * * * *
358719 ATCACGGCTAATCTACATAGCACGCCAATTTAAGATCA-CACTCATATCTTACAATCCGTTGATT
1 ATCACAGCTAATTTACATAGCACGCCAATTTAAGAT-ATCGCTCCTATATTACAGTTCGTTGATT
* * * *****
358783 TAAGATCACGGTTAACCTACATAGGATGCTGATTTAAGATCACGCTCCTATCTTACAACATGTTG
65 TAAGATCACGGTTAACCTACATAGCACGCTGATTTAAGATCGCGCTCCTATCTTACAACCCACCG
*
358848 TTTTAAGATCACAACTAATTTACATAGCAC
130 ATTTAAGATCACAACTAATTTACATAGCAC
358878 GGTGATTTAA
Statistics
Matches: 294, Mismatches: 65, Indels: 8
0.80 0.18 0.02
Matches are distributed among these distances:
204 289 0.98
205 5 0.02
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.33
Consensus pattern (204 bp):
ATCACAGCTAATTTACATAGCACGCCAATTTAAGATATCGCTCCTATATTACAGTTCGTTGATTT
AAGATCACGGTTAACCTACATAGCACGCTGATTTAAGATCGCGCTCCTATCTTACAACCCACCGA
TTTAAGATCACAACTAATTTACATAGCACATCAATTTAAGATCGCACCCCTATTTTATAGATCGC
TGATTGAAG
Found at i:358887 original size:34 final size:33
Alignment explanation
Indices: 358643--358893 Score: 122
Period size: 34 Copynumber: 7.4 Consensus size: 33
358633 ATAGCCCACC
*
358643 GATTTAAGATCATAACTAATTTACATAGCACG-T
1 GATTTAAGATCA-CACTAATTTACATAGCACGCT
* *
358676 CGATTTAAGATTTCACCCCT-ATTT-TATAG-ATCGCT
1 -GATTTAAGA--TCA-CACTAATTTACATAGCA-CGCT
* * *
358711 GATTTAAGATCACGGCTAATCTACATAGCACGCC
1 GATTTAAGATCAC-ACTAATTTACATAGCACGCT
* * *
358745 AATTTAAGATCACACTCATATCTTACA-ATC-CGTT
1 GATTTAAGATCACACT-A-AT-TTACATAGCACGCT
** ** * *
358779 GATTTAAGATCACGGTTAACCTACATAGGATGCT
1 GATTTAAGATCAC-ACTAATTTACATAGCACGCT
* * * *
358813 GATTTAAGATCACGCTCCTATCTTACA-A-CATGTT
1 GATTTAAGATCACACT--AAT-TTACATAGCACGCT
* *
358847 GTTTTAAGATCACAACTAATTTACATAGCACGGT
1 GATTTAAGATCAC-ACTAATTTACATAGCACGCT
358881 GATTTAAGATCAC
1 GATTTAAGATCAC
358894 GCTTTTATTT
Statistics
Matches: 162, Mismatches: 35, Indels: 40
0.68 0.15 0.17
Matches are distributed among these distances:
31 1 0.01
32 14 0.09
33 13 0.08
34 106 0.65
35 15 0.09
36 13 0.08
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.33
Consensus pattern (33 bp):
GATTTAAGATCACACTAATTTACATAGCACGCT
Found at i:363938 original size:19 final size:19
Alignment explanation
Indices: 363914--363956 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
363904 TTTATTTGCA
*
363914 CCACTCCGCTCCTCGCTCG
1 CCACTCCGCTCCTAGCTCG
363933 CCACTCCGCTCCTAGCTCG
1 CCACTCCGCTCCTAGCTCG
363952 CCACT
1 CCACT
363957 TTCCCCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.09, C:0.56, G:0.14, T:0.21
Consensus pattern (19 bp):
CCACTCCGCTCCTAGCTCG
Found at i:368542 original size:19 final size:19
Alignment explanation
Indices: 368515--368553 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
368505 TTATAAAGGT
*
368515 TATATTTTA-ATATTTAAAA
1 TATAGTTTATATA-TTAAAA
368534 TATAGTTTATATATTAAAA
1 TATAGTTTATATATTAAAA
368553 T
1 T
368554 TAAATTTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
TATAGTTTATATATTAAAA
Found at i:374859 original size:21 final size:21
Alignment explanation
Indices: 374835--374876 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
374825 TTAACGGGAC
* * *
374835 AGCTGATGTGGCTAGTTAACT
1 AGCTGACGTGGCCAATTAACT
374856 AGCTGACGTGGCCAATTAACT
1 AGCTGACGTGGCCAATTAACT
374877 TGCCACATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (21 bp):
AGCTGACGTGGCCAATTAACT
Found at i:377106 original size:34 final size:34
Alignment explanation
Indices: 377059--377128 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
377049 TAACAATTAG
* *
377059 TTGAGGTTCAAAAAAGGTCCTCATCTTCAAAATT
1 TTGAGGTTAAAAAAAGGTCCTCACCTTCAAAATT
* *
377093 TTGAGGTTAAAAAAATGTCTTCACCTTCAAAATT
1 TTGAGGTTAAAAAAAGGTCCTCACCTTCAAAATT
377127 TT
1 TT
377129 CAAGTCTCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (34 bp):
TTGAGGTTAAAAAAAGGTCCTCACCTTCAAAATT
Found at i:382223 original size:27 final size:27
Alignment explanation
Indices: 382192--382269 Score: 129
Period size: 27 Copynumber: 2.9 Consensus size: 27
382182 GGGTGTGGTG
382192 CCTATCTGATAGGCGGCACTAGTGACC
1 CCTATCTGATAGGCGGCACTAGTGACC
*
382219 CCTATCTGATAGGCGGCACTGGTGACC
1 CCTATCTGATAGGCGGCACTAGTGACC
* *
382246 TCTATCTGATAGGCGACACTAGTG
1 CCTATCTGATAGGCGGCACTAGTG
382270 CATTAATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (27 bp):
CCTATCTGATAGGCGGCACTAGTGACC
Found at i:382367 original size:4 final size:4
Alignment explanation
Indices: 382358--382421 Score: 69
Period size: 4 Copynumber: 15.5 Consensus size: 4
382348 AGAGAGGGAG
*
382358 AAGA AAGA AAGA AAGA AAGGA GAAGA AATA AAGA AAGA AAGGA GAAG-
1 AAGA AAGA AAGA AAGA AA-GA -AAGA AAGA AAGA AAGA AA-GA -AAGA
382405 AA-A AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AA
382422 ATGTATTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
3 4 0.08
4 37 0.71
5 7 0.13
6 4 0.08
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.02
Consensus pattern (4 bp):
AAGA
Found at i:382369 original size:22 final size:22
Alignment explanation
Indices: 382354--382421 Score: 109
Period size: 22 Copynumber: 3.0 Consensus size: 22
382344 AAGAAGAGAG
382354 GGAGAAGAAAGAAAGAAAGAAA
1 GGAGAAGAAAGAAAGAAAGAAA
*
382376 GGAGAAGAAATAAAGAAAGAAA
1 GGAGAAGAAAGAAAGAAAGAAA
382398 GGAGAAGAAAAAGAAAGAAAGAAA
1 GGAGAAG--AAAGAAAGAAAGAAA
382422 ATGTATTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
22 28 0.67
24 14 0.33
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.01
Consensus pattern (22 bp):
GGAGAAGAAAGAAAGAAAGAAA
Found at i:382419 original size:14 final size:14
Alignment explanation
Indices: 382365--382422 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
382355 GAGAAGAAAG
*
382365 AAAGAAAGAAAGGA
1 AAAGAAAGAAAGAA
* *
382379 GAAGAAATAAAG--
1 AAAGAAAGAAAGAA
382391 AAAGAAAGGAGAAGAA
1 AAAGAAA-GA-AAGAA
382407 AAAGAAAGAAAGAA
1 AAAGAAAGAAAGAA
382421 AA
1 AA
382423 TGTATTTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
12 6 0.17
13 1 0.03
14 20 0.56
15 2 0.06
16 7 0.19
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (14 bp):
AAAGAAAGAAAGAA
Found at i:382649 original size:10 final size:11
Alignment explanation
Indices: 382623--382649 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
382613 ATATATATTA
382623 ATTTTTAAGTT
1 ATTTTTAAGTT
382634 ATTTTTAAGTT
1 ATTTTTAAGTT
382645 ATTTT
1 ATTTT
382650 GTTAGTAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (11 bp):
ATTTTTAAGTT
Found at i:386444 original size:48 final size:48
Alignment explanation
Indices: 386382--386520 Score: 172
Period size: 48 Copynumber: 2.9 Consensus size: 48
386372 AATGTAATCT
* * *
386382 AATGTACCTAATTTATATAATAAAGTATGTTCATCGTTTTAATGTTGC
1 AATGTATCTAATTTATATAACAAAGTATGTTCATCATTTTAATGTTGC
* * * *
386430 AATGTATCTAATTTATATTACAAAGTTTGTTCCTCATTTTAATGTTGT
1 AATGTATCTAATTTATATAACAAAGTATGTTCATCATTTTAATGTTGC
* * *
386478 AATGTATCTAATCTATATTACAAAGT-TCGTTCCTCATTTTAAT
1 AATGTATCTAATTTATATAACAAAGTAT-GTTCATCATTTTAAT
386521 TTACAAAGTT
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
47 1 0.01
48 81 0.99
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (48 bp):
AATGTATCTAATTTATATAACAAAGTATGTTCATCATTTTAATGTTGC
Found at i:386535 original size:26 final size:26
Alignment explanation
Indices: 386495--386546 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
386485 CTAATCTATA
386495 TTACAAAGTTCGTTCCTCATTTTAAT
1 TTACAAAGTTCGTTCCTCATTTTAAT
* *
386521 TTACAAAGTTTGTTCCTCGTTTTAAT
1 TTACAAAGTTCGTTCCTCATTTTAAT
386547 GTAGTAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.48
Consensus pattern (26 bp):
TTACAAAGTTCGTTCCTCATTTTAAT
Found at i:386592 original size:74 final size:74
Alignment explanation
Indices: 386447--386594 Score: 217
Period size: 74 Copynumber: 2.0 Consensus size: 74
386437 CTAATTTATA
* **
386447 TTACAAAGTTTGTTCCTCATTTTAATGTTGTAATGTATCTAATCTATATTACAAAGTTCGTTCCT
1 TTACAAAGTTTGTTCCTCATTTTAATGTAGTAATGTATCTAATCTATATTACAAAGTTCACTCCT
*
386512 CATTTTAAT
66 AATTTTAAT
* * *
386521 TTACAAAGTTTGTTCCTCGTTTTAATGTAGTAATGTATCTAATTTATATTACAAAGTTTACTCC-
1 TTACAAAGTTTGTTCCTCATTTTAATGTAGTAATGTATCTAATCTATATTACAAAGTTCACTCCT
386585 AAGTTTTAAT
66 AA-TTTTAAT
386595 GTTGCAATTA
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
73 1 0.02
74 65 0.98
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.47
Consensus pattern (74 bp):
TTACAAAGTTTGTTCCTCATTTTAATGTAGTAATGTATCTAATCTATATTACAAAGTTCACTCCT
AATTTTAAT
Found at i:386911 original size:33 final size:33
Alignment explanation
Indices: 386864--386944 Score: 126
Period size: 33 Copynumber: 2.5 Consensus size: 33
386854 TGATGAATTT
* * *
386864 GAGCTGGGAGGAGTGGAGTATTACGGTGGATAC
1 GAGCCGGGAGGAGTGGAGTAATACGGTGGATAA
*
386897 GAGCCGGGAGGAGTGGAGTAATGCGGTGGATAA
1 GAGCCGGGAGGAGTGGAGTAATACGGTGGATAA
386930 GAGCCGGGAGGAGTG
1 GAGCCGGGAGGAGTG
386945 CTATACTGCA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.25, C:0.10, G:0.49, T:0.16
Consensus pattern (33 bp):
GAGCCGGGAGGAGTGGAGTAATACGGTGGATAA
Found at i:387113 original size:12 final size:12
Alignment explanation
Indices: 387075--387114 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
387065 GTATGAGACT
*
387075 GCTCGGGCTCTG
1 GCTCAGGCTCTG
*
387087 GCTCAGGTTCTG
1 GCTCAGGCTCTG
*
387099 GCTCAGGCTCAG
1 GCTCAGGCTCTG
387111 GCTC
1 GCTC
387115 GTATGCCCCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.07, C:0.33, G:0.35, T:0.25
Consensus pattern (12 bp):
GCTCAGGCTCTG
Found at i:388769 original size:12 final size:12
Alignment explanation
Indices: 388752--388776 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
388742 CTAAATGTGA
388752 TACAATAAATTT
1 TACAATAAATTT
388764 TACAATAAATTT
1 TACAATAAATTT
388776 T
1 T
388777 CATTACAAAA
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TACAATAAATTT
Found at i:389747 original size:32 final size:31
Alignment explanation
Indices: 389700--389788 Score: 90
Period size: 31 Copynumber: 2.8 Consensus size: 31
389690 CTTTTATGAT
* *
389700 TTTTTTCTTCTAACCCCAAATACAATCTCTCAA
1 TTTTTT-TTCAAACCCCAAACACAA-CTCTCAA
* *
389733 TTTTTTTTCAAACCCTAAACACAAC-CTTAA
1 TTTTTTTTCAAACCCCAAACACAACTCTCAA
* *
389763 TTCTTTTCTCAAATCCCAAACACAAC
1 TT-TTTTTTCAAACCCCAAACACAAC
389789 CTCTTCTCCT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
30 6 0.12
31 21 0.44
32 15 0.31
33 6 0.12
ACGTcount: A:0.34, C:0.30, G:0.00, T:0.36
Consensus pattern (31 bp):
TTTTTTTTCAAACCCCAAACACAACTCTCAA
Found at i:390775 original size:73 final size:73
Alignment explanation
Indices: 390696--390852 Score: 296
Period size: 73 Copynumber: 2.2 Consensus size: 73
390686 ATTATTAATA
*
390696 AAATTATATAATATAAATTTAATTGTCGAAATTATGCATATTTATTAAAATAATTAATTATTGTA
1 AAATTATAAAATATAAATTTAATTGTCGAAATTATGCATATTTATTAAAATAATTAATTATTGTA
390761 CTCTATAG
66 CTCTATAG
390769 AAATTATAAAATATAAATTTAATTGTCGAAATTATGCATATTTATTAAAATAATTAATTATTGTA
1 AAATTATAAAATATAAATTTAATTGTCGAAATTATGCATATTTATTAAAATAATTAATTATTGTA
*
390834 CTTTATAG
66 CTCTATAG
390842 AAATTATAAAA
1 AAATTATAAAA
390853 ATGATCAACA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 82 1.00
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.43
Consensus pattern (73 bp):
AAATTATAAAATATAAATTTAATTGTCGAAATTATGCATATTTATTAAAATAATTAATTATTGTA
CTCTATAG
Found at i:393652 original size:46 final size:46
Alignment explanation
Indices: 393595--393713 Score: 143
Period size: 46 Copynumber: 2.6 Consensus size: 46
393585 TGCTAGCATA
*
393595 TGTTGCAGACTCGAGAATA-TAGATATAGGTTTCGAGCTACAACAAT-
1 TGTTGCAGACTCGAGAATACAAG-TATAGGTTTCGAGCTACAAC-ATG
** * * *
393641 TGTTGTGGACTCAAGAATACAAGTATAGGTTTCGAGCTCCAGCATG
1 TGTTGCAGACTCGAGAATACAAGTATAGGTTTCGAGCTACAACATG
*
393687 TGTTGCAGACTCGAGAATACAGGTATA
1 TGTTGCAGACTCGAGAATACAAGTATA
393714 ATAAGACCTG
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
45 2 0.03
46 57 0.93
47 2 0.03
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (46 bp):
TGTTGCAGACTCGAGAATACAAGTATAGGTTTCGAGCTACAACATG
Found at i:394243 original size:31 final size:31
Alignment explanation
Indices: 394183--394244 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 31
394173 TTTAAATTAG
394183 AGTTTAGGGTTTTTTTAGATTATAAGTGTTTA
1 AGTTTAGGGTTTTTTTA-ATTATAAGTGTTTA
*
394215 AGTTTAGGGTTTTATTT-ATTTTAAGTGTTT
1 AGTTTAGGGTTTT-TTTAATTATAAGTGTTT
394245 TTTAATTATG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 12 0.43
32 13 0.46
33 3 0.11
ACGTcount: A:0.23, C:0.00, G:0.21, T:0.56
Consensus pattern (31 bp):
AGTTTAGGGTTTTTTTAATTATAAGTGTTTA
Found at i:397660 original size:15 final size:15
Alignment explanation
Indices: 397640--397668 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
397630 GACTCACACG
397640 GCTGAGACACATGCA
1 GCTGAGACACATGCA
397655 GCTGAGACACATGC
1 GCTGAGACACATGC
397669 CCGTGTCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.28, G:0.28, T:0.14
Consensus pattern (15 bp):
GCTGAGACACATGCA
Found at i:398958 original size:26 final size:26
Alignment explanation
Indices: 398918--398987 Score: 113
Period size: 26 Copynumber: 2.7 Consensus size: 26
398908 TTTTACATCG
* *
398918 TTGCTCACACAAGCTGTGAAATGAGT
1 TTGCTCACACGAGCTGTGAAATGAGC
*
398944 TTGCTCACACGAGCTGTGAAATGGGC
1 TTGCTCACACGAGCTGTGAAATGAGC
398970 TTGCTCACACGAGCTGTG
1 TTGCTCACACGAGCTGTG
398988 GGTCAGAATG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (26 bp):
TTGCTCACACGAGCTGTGAAATGAGC
Found at i:401784 original size:26 final size:26
Alignment explanation
Indices: 401747--401818 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 26
401737 TGGAGGAAGT
*
401747 ATACTG-TACTGGCAGTTTTGCTGCA
1 ATACTGATACTGGCAGCTTTGCTGCA
401772 ATACTGATACTGGCAGCTTTGCTGCA
1 ATACTGATACTGGCAGCTTTGCTGCA
* *
401798 TTACT-ATTACTGGCAACTTTG
1 ATACTGA-TACTGGCAGCTTTG
401819 TTGCTATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
25 7 0.17
26 35 0.83
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (26 bp):
ATACTGATACTGGCAGCTTTGCTGCA
Found at i:401998 original size:32 final size:31
Alignment explanation
Indices: 401923--402007 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 31
401913 TACATTATTG
* * * *
401923 CACTGTATTGATACTATAATGGGCTAAGGCC
1 CACTGTACTGTTACTGTATTGGGCTAAGGCC
401954 CAC---ACTGTTACTGTATTGGGCTAAGGCC
1 CACTGTACTGTTACTGTATTGGGCTAAGGCC
* *
401982 ACACTGTACTGTTACTGAATAGGGCT
1 -CACTGTACTGTTACTGTATTGGGCT
402008 CCAGCCCAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
28 21 0.48
29 3 0.07
31 3 0.07
32 17 0.39
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (31 bp):
CACTGTACTGTTACTGTATTGGGCTAAGGCC
Found at i:417811 original size:43 final size:43
Alignment explanation
Indices: 417750--417836 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
417740 AAATGCATAG
*
417750 ATAATTTAAAAAATTAAGGCATGATCACTCTCTCTCGATTCAC
1 ATAATTTAAAAAATTAAGGCATGACCACTCTCTCTCGATTCAC
417793 ATAATTTAAAAAATTAAGGCATGACCACTCTCTCTCGATTCAC
1 ATAATTTAAAAAATTAAGGCATGACCACTCTCTCTCGATTCAC
417836 A
1 A
417837 AACCCAATTC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (43 bp):
ATAATTTAAAAAATTAAGGCATGACCACTCTCTCTCGATTCAC
Found at i:422098 original size:21 final size:21
Alignment explanation
Indices: 422050--422090 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
422040 AATTCTCATA
*
422050 TTATTTAGATTATTATTGATT
1 TTATTTTGATTATTATTGATT
*
422071 TTATTTTGATTCTTA-TGATT
1 TTATTTTGATTATTATTGATT
422091 CTTGTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.63
Consensus pattern (21 bp):
TTATTTTGATTATTATTGATT
Found at i:422493 original size:15 final size:15
Alignment explanation
Indices: 422469--422501 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
422459 TTTTTAATTG
422469 ATTGTGTTCTTTTCA
1 ATTGTGTTCTTTTCA
*
422484 ATTGTTTTCTTTTCA
1 ATTGTGTTCTTTTCA
422499 ATT
1 ATT
422502 TCCTCTCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.09, T:0.64
Consensus pattern (15 bp):
ATTGTGTTCTTTTCA
Found at i:423740 original size:34 final size:32
Alignment explanation
Indices: 423664--423747 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 32
423654 TATAACTGTC
*
423664 ACTGTTACTGTACTGTGATGGGCTAAGGCCTTA
1 ACTGTTACTGTACTG-GATGGGCTAAGGCCTAA
*
423697 A-TGCTTACTGTTACTGGAATGGGCTAAGGTCTAA
1 ACTG-TTACTG-TACTGG-ATGGGCTAAGGCCTAA
*
423731 ACTGGTACTGATACTGG
1 ACTGTTACTG-TACTGG
423748 TATTGAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
32 2 0.05
33 8 0.19
34 31 0.72
35 2 0.05
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (32 bp):
ACTGTTACTGTACTGGATGGGCTAAGGCCTAA
Found at i:432194 original size:34 final size:34
Alignment explanation
Indices: 432155--432220 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
432145 CGATCTCAAA
* * *
432155 AAAAAAGAAGCAAAAGCAAAATCAAGATCAAAAT
1 AAAAAAGAAGAAAAAGAAAAATCAAAATCAAAAT
432189 AAAAAAGAAGAAAAAGAAAAATCAAAATCAAA
1 AAAAAAGAAGAAAAAGAAAAATCAAAATCAAA
432221 GTCAAAATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.73, C:0.09, G:0.11, T:0.08
Consensus pattern (34 bp):
AAAAAAGAAGAAAAAGAAAAATCAAAATCAAAAT
Found at i:432226 original size:40 final size:39
Alignment explanation
Indices: 432152--432241 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 39
432142 ATCCGATCTC
* *
432152 AAAAA-AAAAGAAGCAAAAGCAAAATCAAGATCAAAATA
1 AAAAAGAAAAAAAGAAAAAGCAAAATCAAGATCAAAATA
* *
432190 AAAAAGAAGAAAAAGAAAAATCAAAATCAA-AGTCAAAATG
1 AAAAAGAA-AAAAAGAAAAAGCAAAATCAAGA-TCAAAATA
*
432230 AAAATGAAAAAA
1 AAAAAGAAAAAA
432242 GAGAGAAGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
38 5 0.11
39 7 0.16
40 32 0.73
ACGTcount: A:0.72, C:0.08, G:0.11, T:0.09
Consensus pattern (39 bp):
AAAAAGAAAAAAAGAAAAAGCAAAATCAAGATCAAAATA
Found at i:432234 original size:46 final size:49
Alignment explanation
Indices: 432154--432258 Score: 126
Period size: 46 Copynumber: 2.2 Consensus size: 49
432144 CCGATCTCAA
* *
432154 AAAAAAAGAAGCAAAAGCAAAATCAAGATCAAAAT-AAAAAAGA-AGAA-
1 AAAAAAA-AATCAAAAGCAAAATCAAAATCAAAATGAAAAAAGAGAGAAG
* * * *
432201 AAAGAAAAATCAAAATCAAAGTCAAAATGAAAATGAAAAAAGAGAGAAG
1 AAAAAAAAATCAAAAGCAAAATCAAAATCAAAATGAAAAAAGAGAGAAG
432250 AAAAAAAAA
1 AAAAAAAAA
432259 GGAAAAAGAA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
46 22 0.46
47 14 0.29
48 4 0.08
49 8 0.17
ACGTcount: A:0.72, C:0.07, G:0.13, T:0.08
Consensus pattern (49 bp):
AAAAAAAAATCAAAAGCAAAATCAAAATCAAAATGAAAAAAGAGAGAAG
Found at i:433086 original size:14 final size:14
Alignment explanation
Indices: 433069--433127 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
433059 GAAAAAAAGA
*
433069 AAAAAAGAAAAATC
1 AAAAAAGAAAAATG
433083 AAAAAAGAGAAAATG
1 AAAAAAGA-AAAATG
* *
433098 GAAAAATAAAAATG
1 AAAAAAGAAAAATG
433112 -AAAAAGTAAAAATG
1 AAAAAAG-AAAAATG
433126 AA
1 AA
433128 GAGGTTGAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
13 5 0.13
14 21 0.55
15 12 0.32
ACGTcount: A:0.75, C:0.02, G:0.14, T:0.10
Consensus pattern (14 bp):
AAAAAAGAAAAATG
Found at i:434499 original size:44 final size:44
Alignment explanation
Indices: 434438--434822 Score: 235
Period size: 44 Copynumber: 8.3 Consensus size: 44
434428 TTTAAGCCAC
*
434438 AGTGGAGCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTAC
1 AGTGGAGCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTAT
* * *
434482 AGTGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAT
1 AGTGGAGCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTAT
*** * *
434526 AGTGGAGC-GAATT-AAAATA-AAGGATCTTATCTCTCT-AAAGTTACAAT
1 AGTGGAGCAG-ATTGAAGCCAGAA--ATCTTATCTCCCTGAGA-TT---AT
*
434573 AGAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTAT
1 --AGT-G---G-AGCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTAT
** * *
434624 AGCAGAGCAGATTGAAGCCAGTAATCTTATTTCCCTGAGATTAT
1 AGTGGAGCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTAT
* *** * * *
434668 AGTGGAGC-GAATTAAAATAACG-GATCTTATCTCTCT-AAAGTTACAAT
1 AGTGGAGCAG-ATTGAAGCCA-GAAATCTTATCTCCCTGAGA-TT---AT
*
434715 AGAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTAT
1 --AGT-G---G-AGCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTAT
** * *
434766 AGCAGAGCAGATTGAAGCCAGTAATCTTATTTCCCTGAGATTAT
1 AGTGGAGCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTAT
*
434810 AGTGGAGCGGATT
1 AGTGGAGCAGATT
434823 AGAATAAAGG
Statistics
Matches: 260, Mismatches: 47, Indels: 68
0.69 0.13 0.18
Matches are distributed among these distances:
42 1 0.00
43 10 0.04
44 171 0.66
45 3 0.01
47 4 0.02
49 10 0.04
50 2 0.01
51 4 0.02
53 3 0.01
54 41 0.16
55 9 0.03
56 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (44 bp):
AGTGGAGCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTAT
Found at i:434701 original size:142 final size:142
Alignment explanation
Indices: 434445--434866 Score: 745
Period size: 142 Copynumber: 3.0 Consensus size: 142
434435 CACAGTGGAG
* ** * *
434445 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTATAGCAGAGCAGATTGAAGCCAGTAATCTT
*
434510 ATCTCCCTGAGATTATAGTGGAGCGAATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAATAG
66 ATTTCCCTGAGATTATAGTGGAGCGAATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAATAG
434575 AGTAGATCGCAT
131 AGTAGATCGCAT
434587 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTATAGCAGAGCAGATTGAAGCCAGTAATCTT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTATAGCAGAGCAGATTGAAGCCAGTAATCTT
*
434652 ATTTCCCTGAGATTATAGTGGAGCGAATTAAAATAACGGATCTTATCTCTCTAAAGTTACAATAG
66 ATTTCCCTGAGATTATAGTGGAGCGAATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAATAG
434717 AGTAGATCGCAT
131 AGTAGATCGCAT
434729 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTATAGCAGAGCAGATTGAAGCCAGTAATCTT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTATAGCAGAGCAGATTGAAGCCAGTAATCTT
* * * *
434794 ATTTCCCTGAGATTATAGTGGAGCGGATTAGAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
66 ATTTCCCTGAGATTATAGTGGAGCGAATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAATAG
434859 AGTAGATC
131 AGTAGATC
434867 ATAACAGGTC
Statistics
Matches: 268, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
142 268 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (142 bp):
CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTATAGCAGAGCAGATTGAAGCCAGTAATCTT
ATTTCCCTGAGATTATAGTGGAGCGAATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAATAG
AGTAGATCGCAT
Found at i:434837 original size:44 final size:44
Alignment explanation
Indices: 434729--434847 Score: 114
Period size: 44 Copynumber: 2.7 Consensus size: 44
434719 TAGATCGCAT
** *
434729 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTATAGCAGAG
1 CAGATTGAAGAAAGTAATCTTATCTCCCTGAGATTATAGCAGAG
** * **
434773 CAGATTGAAGCCAGTAATCTTATTTCCCTGAGATTATAGTGGAG
1 CAGATTGAAGAAAGTAATCTTATCTCCCTGAGATTATAGCAGAG
* * * *
434817 CGGATTAGAATAAAG-GATCTTATCTCTCTGA
1 CAGATT-GAAGAAAGTAATCTTATCTCCCTGA
434848 AGTTACAGTA
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 58 0.92
45 5 0.08
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (44 bp):
CAGATTGAAGAAAGTAATCTTATCTCCCTGAGATTATAGCAGAG
Found at i:435005 original size:50 final size:49
Alignment explanation
Indices: 434950--435531 Score: 364
Period size: 50 Copynumber: 11.6 Consensus size: 49
434940 GCAGTGGAAC
* *
434950 AGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGACATTGCAGTTAAA
1 AGATTAAAGCCACAACGGTGAATCTTACTTCCCTGACATTGCAGTTAAA
* *** ** ** * *
434999 AGGATTAAAGCTACAGTAGTGAATCTTACCCCCCCAAGCGA-TGCAGTGGAAC
1 A-GATTAAAGCCACAACGGTGAATCTTACTTCCCTGA-C-ATTGCAGT-TAAA
* * *
435051 AGATTAAAGCCACAACGGTGAATCTTACCTCCCAGGCATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTACTTCCCTGACATTGCAGTT-AAA
* * * * * ** * *
435101 AGATTAAAGCTACAGCAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
1 AGATTAAAGCCACAACGGTGAATCTTACTTCCCTGACATTGCAGT-TAAA
* *
435151 AGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTACTTCCCTGACATTGCAGTT-AAA
* * * ** * * *
435201 AGATTAAA-CCTACAGCAGCGAATCTTACTTCCCT-AGCGGTACAGTGGAAC
1 AGATTAAAGCC-ACAACGGTGAATCTTACTTCCCTGA-CATTGCAGT-TAAA
* ** ** *
435251 AGATTAATGCCACAACGACGAATCTTGTTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTACTTCCCTGACATTGCAGTT-AAA
* * * ** * ** * * *
435301 AGATTAAAGCTAGAACAGCAAATCTTACTTCCCAGGA-GGTACAGTGGAAC
1 AGATTAAAGCCACAACGGTGAATCTTACTTCCC-TGACATTGCAGT-TAAA
* *
435351 AGATTAAAGCCACAACGGTGAATCTTACTTCCCAGGCATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTACTTCCCTGACATTGCAGTT-AAA
* * * * * * * *
435401 AGATTAAAGCTACAGCAGCGAATCTTACTTCCCTGGCGGTT-CAGTGGAAC
1 AGATTAAAGCCACAACGGTGAATCTTACTTCCCTGAC-ATTGCAGT-TAAA
* * *
435451 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTACTTCCCTGACATTGCAGTT-AAA
* * * *
435501 AGATTAAAGCTACCACAGCGAATCTTACTTC
1 AGATTAAAGCCACAACGGTGAATCTTACTTC
435532 TCAAGCGGTG
Statistics
Matches: 398, Mismatches: 113, Indels: 43
0.72 0.20 0.08
Matches are distributed among these distances:
49 8 0.02
50 345 0.87
51 41 0.10
52 4 0.01
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (49 bp):
AGATTAAAGCCACAACGGTGAATCTTACTTCCCTGACATTGCAGTTAAA
Found at i:435183 original size:100 final size:100
Alignment explanation
Indices: 434928--435551 Score: 892
Period size: 100 Copynumber: 6.2 Consensus size: 100
434918 AGATCTTATT
*
434928 TTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGACATTGCA
1 TTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCCAGACATTGCA
* * *
434993 GTTAAAAGGATTAAAGCTACAGTAGTGAATCTTACC
66 GTTAAAAAGATTAAAGCTACAGCAGCGAATCTTA-C
** * * * *
435029 CCCCCAAGCGATGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTACCTCCCAGGCATTGCA
1 TTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCCAGACATTGCA
435094 GTTAAAAAGATTAAAGCTACAGCAGCGAATCTTAC
66 GTTAAAAAGATTAAAGCTACAGCAGCGAATCTTAC
* *
435129 TTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGACATTGCA
1 TTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCCAGACATTGCA
*
435194 GTTAAAAAGATTAAACCTACAGCAGCGAATCTTAC
66 GTTAAAAAGATTAAAGCTACAGCAGCGAATCTTAC
* * ** ** *
435229 TTCCCTA-GCGGTACAGTGGAACAGATTAATGCCACAACGACGAATCTTGTTTCCCCGACATTGC
1 TTCCC-AGGCGGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCCAGACATTGC
* * *
435293 AGTTAAAAAGATTAAAGCTAGAACAGCAAATCTTAC
65 AGTTAAAAAGATTAAAGCTACAGCAGCGAATCTTAC
* * * * *
435329 TTCCCAGGAGGTACAGTGGAACAGATTAAAGCCACAACGGTGAATCTTACTTCCCAGGCATTGCA
1 TTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCCAGACATTGCA
435394 GTTAAAAAGATTAAAGCTACAGCAGCGAATCTTAC
66 GTTAAAAAGATTAAAGCTACAGCAGCGAATCTTAC
* * * * *
435429 TTCCCTGGCGGTTCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCA
1 TTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCCAGACATTGCA
435494 GTTAAAAAGATTAAAGCTACCA-CAGCGAATCTTAC
66 GTTAAAAAGATTAAAGCTA-CAGCAGCGAATCTTAC
* *
435529 TTCTCAAGCGGTGCAGTGGAACA
1 TTCCCAGGCGGTGCAGTGGAACA
435552 ACAAATCTTG
Statistics
Matches: 467, Mismatches: 53, Indels: 7
0.89 0.10 0.01
Matches are distributed among these distances:
99 1 0.00
100 375 0.80
101 91 0.19
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.23
Consensus pattern (100 bp):
TTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCCAGACATTGCA
GTTAAAAAGATTAAAGCTACAGCAGCGAATCTTAC
Found at i:436957 original size:5 final size:6
Alignment explanation
Indices: 436906--436962 Score: 60
Period size: 6 Copynumber: 9.2 Consensus size: 6
436896 ACCAACTTAG
* * * *
436906 TTTATC TTTATT TTTCTT TTTATT TCTATT TGTAGTGT TTTATT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTA-T-T TTTATT TTTATT
436956 TTTATT T
1 TTTATT T
436963 GAATTCCAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
6 37 0.86
7 2 0.05
8 4 0.09
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.75
Consensus pattern (6 bp):
TTTATT
Found at i:436995 original size:3 final size:3
Alignment explanation
Indices: 436987--437011 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
436977 TTTTTAATCC
436987 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
437012 TCTTCTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:437083 original size:23 final size:23
Alignment explanation
Indices: 437056--437115 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
437046 TGACATTACC
*
437056 TTTAAACTTATTATTATTATAAT
1 TTTAAACTTATTATTACTATAAT
* * *
437079 TTTAAAACGTAATA-TACTATTAT
1 TTT-AAACTTATTATTACTATAAT
437102 TTTAAA-TTATTATT
1 TTTAAACTTATTATT
437116 GACATGTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
21 4 0.14
22 4 0.14
23 13 0.45
24 8 0.28
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (23 bp):
TTTAAACTTATTATTACTATAAT
Found at i:444609 original size:14 final size:13
Alignment explanation
Indices: 444590--444619 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
444580 CCCTCTTGGC
444590 GAAAAAAGAAAACA
1 GAAAAAAGAAAA-A
444604 GAAAAAAGAAAAA
1 GAAAAAAGAAAAA
444617 GAA
1 GAA
444620 TTTGTAGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (13 bp):
GAAAAAAGAAAAA
Found at i:448531 original size:51 final size:50
Alignment explanation
Indices: 448451--448675 Score: 144
Period size: 50 Copynumber: 4.5 Consensus size: 50
448441 CAAAACTTTG
* ** *
448451 TTTTAAAAAATTTAAACTTTTTCCATTAAAATGACTAAAAAACATATTTTTA
1 TTTT-AAAAATTTAAACTTTCTCTTTTAAAATGA-TAAAAAACATAATTTTA
448503 TTTTAAAAATTTAAACTTTCTCTTTTAAAA--AT---AAACATAATTTT-
1 TTTTAAAAATTTAAACTTTCTCTTTTAAAATGATAAAAAACATAATTTTA
* * ** * * * *
448547 TCTTAAAGATCAAAACTTT-TATTTTGAAATAGTTGAAAAAAAATTCAAAATTTTG
1 TTTTAAAAATTTAAACTTTCTCTTTT-AAA-A--TGATAAAAAA--CATAATTTTA
* * *
448602 TTTTAAAAATTTTAACTTTC-C-TTTAAAATGGCTAAAAAAACATATTTTTA
1 TTTTAAAAATTTAAACTTTCTCTTTTAAAAT-GAT-AAAAAACATAATTTTA
* *
448652 TTTTAAAAATCTAAACTTTTTCTT
1 TTTTAAAAATTTAAACTTTCTCTT
448676 CTTTTTTTTT
Statistics
Matches: 131, Mismatches: 25, Indels: 34
0.69 0.13 0.18
Matches are distributed among these distances:
43 5 0.04
44 18 0.14
45 12 0.09
48 1 0.01
49 2 0.02
50 25 0.19
51 25 0.19
52 15 0.11
53 3 0.02
54 11 0.08
55 14 0.11
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (50 bp):
TTTTAAAAATTTAAACTTTCTCTTTTAAAATGATAAAAAACATAATTTTA
Found at i:448629 original size:148 final size:148
Alignment explanation
Indices: 448394--448675 Score: 426
Period size: 149 Copynumber: 1.9 Consensus size: 148
448384 AAAAATCACT
*
448394 ATTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGAAAAAGATCAAAACTTTGTTTTAAAA
1 ATTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGAAAAAAATCAAAACTTTGTTTTAAAA
*
448459 AATTTAAACTTTTTCCATTAAAATGACT-AAAAAACATATTTTTATTTTAAAAATTTAAACTTTC
66 AATTTAAAC-TTTTCCATTAAAATGACTAAAAAAACATATTTTTATTTTAAAAATCTAAACTTTC
448523 TCTTTTAAAAATAAACATA
130 TCTTTTAAAAATAAACATA
* * *
448542 ATTTTTCTTAAAGATCAAAACTTTTATTTTGAAATAGTTGAAAAAAAATTCAAAATTTTGTTTT-
1 ATTTTTCTTAAAAATCAAAAC-TTTATTTCGAAATAGTTG-AAAAAAA-TCAAAACTTTGTTTTA
* * *
448606 AAAAATTTTAAC-TTTCCTTTAAAATGGCTAAAAAAACATATTTTTATTTTAAAAATCTAAACTT
63 AAAAATTTAAACTTTTCCATTAAAATGACTAAAAAAACATATTTTTATTTTAAAAATCTAAACTT
*
448670 TTTCTT
128 TCTCTT
448676 CTTTTTTTTT
Statistics
Matches: 121, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
148 35 0.29
149 55 0.45
150 17 0.14
151 14 0.12
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.43
Consensus pattern (148 bp):
ATTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGAAAAAAATCAAAACTTTGTTTTAAAA
AATTTAAACTTTTCCATTAAAATGACTAAAAAAACATATTTTTATTTTAAAAATCTAAACTTTCT
CTTTTAAAAATAAACATA
Found at i:449568 original size:42 final size:42
Alignment explanation
Indices: 449521--449783 Score: 373
Period size: 42 Copynumber: 6.3 Consensus size: 42
449511 CTTCATATAG
* * * *
449521 AATGCAATGAAAAGTAAATGGATCTCTAAACCTGGGCCTTTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* ** *
449563 AATGCAAGGAAAAGTAAACAGACCTCCATACCTGGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * **
449605 GATGCAATGAAAAGTAAATGGACCCCCACACCTGGGTATCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
*
449647 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTTTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * *
449689 AATGTAATGAAAAGTAAATGGACCTCCACACGTGAGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
*
449731 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCTTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
449773 AATGCAATGAA
1 AATGCAATGAA
449784 TGCTTTCCTT
Statistics
Matches: 193, Mismatches: 28, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 193 1.00
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (42 bp):
AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
Found at i:461083 original size:23 final size:20
Alignment explanation
Indices: 461034--461083 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
461024 ATGACATTAG
*
461034 ACAATTAAATAAATTAATGC
1 ACAAATAAATAAATTAATGC
*
461054 ACGAATAAATAAATCTAATATGC
1 ACAAATAAATAAAT-T-A-ATGC
461077 ACAAATA
1 ACAAATA
461084 CTAGAAAACC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 12 0.50
21 1 0.04
22 1 0.04
23 10 0.42
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (20 bp):
ACAAATAAATAAATTAATGC
Found at i:484557 original size:20 final size:21
Alignment explanation
Indices: 484519--484557 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
484509 CAACAAATCA
*
484519 ATTTTACTTGCACACCTAACC
1 ATTTTACTTCCACACCTAACC
*
484540 ATTTTA-TTCCACATCTAA
1 ATTTTACTTCCACACCTAA
484558 ACTACTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.31, C:0.28, G:0.03, T:0.38
Consensus pattern (21 bp):
ATTTTACTTCCACACCTAACC
Found at i:486812 original size:39 final size:40
Alignment explanation
Indices: 486608--486830 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
486598 TTGAATGCTG
* * * * * *
486608 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
** * * *
486648 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
486688 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
**
486728 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
486768 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
486807 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
486831 TGAACGAGGA
Statistics
Matches: 161, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 35 0.22
40 118 0.73
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:486850 original size:79 final size:80
Alignment explanation
Indices: 486683--486865 Score: 226
Period size: 79 Copynumber: 2.3 Consensus size: 80
486673 GTGCGAGATA
* * *
486683 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
486748 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
486763 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
486827 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
486842 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
486866 TACGTGATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:492526 original size:43 final size:43
Alignment explanation
Indices: 492476--492678 Score: 270
Period size: 43 Copynumber: 4.8 Consensus size: 43
492466 AAAGTCAGGG
492476 TCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGATCATGT
1 TCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGATCATGT
* *
492519 TCCTTAGCGGCGTTTTTTCCACAAACGCCGCTAAAGATCATGT
1 TCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGATCATGT
*
492562 TCTTTAGCGGCGCTTTTTCCACAAATC-CTGCTAAAGATCATG-
1 TCTTTAGCGGCGCTTTTTCCACAAA-CGCCGCTAAAGATCATGT
* * * * *
492604 T-TTTAGCGGTGCTTCTTCCGCAAACGCCACTAAAGGTCATGT
1 TCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGATCATGT
* *
492646 TCTTTTAGCAGCG-TTTTTACACAAACGCCGCTA
1 TC-TTTAGCGGCGCTTTTTCCACAAACGCCGCTA
492679 TTTGTTTGGT
Statistics
Matches: 138, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
40 1 0.01
41 32 0.23
42 2 0.01
43 94 0.68
44 9 0.07
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (43 bp):
TCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGATCATGT
Found at i:492663 original size:84 final size:85
Alignment explanation
Indices: 492476--492678 Score: 277
Period size: 84 Copynumber: 2.4 Consensus size: 85
492466 AAAGTCAGGG
* *
492476 TCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGATCATGTTCCTTAGCGGCGTTTTTTCCAC
1 TCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGATCATGTT-CTTAGCGGCGCTTCTTCCAC
*
492541 AAACGCCGCTAAAGATCATGT
65 AAACGCCACTAAAGATCATGT
* * *
492562 TCTTTAGCGGCGCTTTTTCCACAAATC-CTGCTAAAGATCATGTT-TTAGCGGTGCTTCTTCCGC
1 TCTTTAGCGGCGCTTTTTCCACAAA-CGCCGCTAAAGATCATGTTCTTAGCGGCGCTTCTTCCAC
*
492625 AAACGCCACTAAAGGTCATGT
65 AAACGCCACTAAAGATCATGT
* *
492646 TCTTTTAGCAGCG-TTTTTACACAAACGCCGCTA
1 TC-TTTAGCGGCGCTTTTTCCACAAACGCCGCTA
492679 TTTGTTTGGT
Statistics
Matches: 104, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
83 1 0.01
84 52 0.50
85 9 0.09
86 41 0.39
87 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (85 bp):
TCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGATCATGTTCTTAGCGGCGCTTCTTCCACA
AACGCCACTAAAGATCATGT
Found at i:498607 original size:9 final size:9
Alignment explanation
Indices: 498593--499234 Score: 281
Period size: 9 Copynumber: 75.2 Consensus size: 9
498583 CATCATATAT
498593 TTATGTAAG
1 TTATGTAAG
498602 TTATGTAAG
1 TTATGTAAG
498611 TTATGT-A-
1 TTATGTAAG
* *
498618 TTAAGTAAA
1 TTATGTAAG
498627 TTATGTAAG
1 TTATGTAAG
498636 TTATGT-A-
1 TTATGTAAG
498643 TTATGTAAG
1 TTATGTAAG
498652 TTATGTAAG
1 TTATGTAAG
*
498661 TTGTGT-A-
1 TTATGTAAG
* *
498668 TTATGAAAC
1 TTATGTAAG
498677 TTATGTAAG
1 TTATGTAAG
*
498686 TTATGT--C
1 TTATGTAAG
*
498693 TTATGTAGG
1 TTATGTAAG
498702 TTATGTAAG
1 TTATGTAAG
498711 TTATGT-A-
1 TTATGTAAG
498718 TTATGTAAG
1 TTATGTAAG
498727 TTATGT-A-
1 TTATGTAAG
*
498734 TTAAGTAAG
1 TTATGTAAG
498743 TTATGTAAG
1 TTATGTAAG
*
498752 -T-TGT--C
1 TTATGTAAG
*
498757 TTATATAAG
1 TTATGTAAG
498766 TTATGTAAG
1 TTATGTAAG
498775 TTATGT-A-
1 TTATGTAAG
498782 TTATGTAAG
1 TTATGTAAG
498791 TTATGTAAG
1 TTATGTAAG
498800 TTATGT-A-
1 TTATGTAAG
* *
498807 TTAAGTAGG
1 TTATGTAAG
498816 TTATGTAAG
1 TTATGTAAG
498825 TTATGT-A-
1 TTATGTAAG
498832 TTATGTAAG
1 TTATGTAAG
498841 TTATGTAAG
1 TTATGTAAG
*
498850 TTTTTGT--G
1 -TTATGTAAG
*
498858 TT-TGTGTA-
1 TTATGT-AAG
* *
498866 TTATATAAC
1 TTATGTAAG
* *
498875 TTATTTAAT
1 TTATGTAAG
*
498884 TTATGTAGG
1 TTATGTAAG
498893 TTATGTATTA-
1 TTATGTA--AG
498903 TTATGTAAG
1 TTATGTAAG
*
498912 TTAT-TATG
1 TTATGTAAG
*
498920 -TA-GGATA-
1 TTATGTA-AG
498927 TTATGTAAG
1 TTATGTAAG
498936 TTATGTAAG
1 TTATGTAAG
* ***
498945 TTTTTGTTTT
1 -TTATGTAAG
*
498955 TTGTGT-A-
1 TTATGTAAG
*
498962 TTATGTAAC
1 TTATGTAAG
* *
498971 TTATTTAAT
1 TTATGTAAG
*
498980 TTATGTAGG
1 TTATGTAAG
498989 TTATGTATTA-
1 TTATGTA--AG
498999 TTATGTAAG
1 TTATGTAAG
*
499008 TTAT-TATG
1 TTATGTAAG
*
499016 -TA-GGATA-
1 TTATGTA-AG
499023 TTATGTAAG
1 TTATGTAAG
499032 TTATGTAAG
1 TTATGTAAG
* ***
499041 TTTTTGTTTT
1 -TTATGTAAG
*
499051 TTGTGT-A-
1 TTATGTAAG
*
499058 TTATGTAAC
1 TTATGTAAG
* *
499067 TTATTTAAT
1 TTATGTAAG
*
499076 TTATGTAGG
1 TTATGTAAG
499085 TTATGTATTA-
1 TTATGTA--AG
499095 TTATGTAAG
1 TTATGTAAG
*
499104 TTAT-TATG
1 TTATGTAAG
*
499112 -TA-GGATA-
1 TTATGTA-AG
499119 TTATGTAAG
1 TTATGTAAG
499128 TTATGTAAG
1 TTATGTAAG
* ***
499137 TTTTTGTTTT
1 -TTATGTAAG
*
499147 TTGTGT-A-
1 TTATGTAAG
*
499154 TTATGTAAC
1 TTATGTAAG
* *
499163 TTATTTAAT
1 TTATGTAAG
*
499172 TTATGTAGG
1 TTATGTAAG
499181 TTATGTATTA-
1 TTATGTA--AG
499191 TTATGTAAG
1 TTATGTAAG
*
499200 TTAT-TATG
1 TTATGTAAG
*
499208 -TA-GGATA-
1 TTATGTA-AG
499215 TTATGTAAG
1 TTATGTAAG
499224 TTATGTAAG
1 TTATGTAAG
499233 TT
1 TT
499235 TTTGTTTTTT
Statistics
Matches: 479, Mismatches: 85, Indels: 138
0.68 0.12 0.20
Matches are distributed among these distances:
6 4 0.01
7 83 0.17
8 51 0.11
9 293 0.61
10 48 0.10
ACGTcount: A:0.29, C:0.01, G:0.19, T:0.51
Consensus pattern (9 bp):
TTATGTAAG
Found at i:498630 original size:16 final size:17
Alignment explanation
Indices: 498593--498847 Score: 227
Period size: 16 Copynumber: 15.4 Consensus size: 17
498583 CATCATATAT
498593 TTATGTAAGTTATGTAAG
1 TTATGT-AGTTATGTAAG
* *
498611 TTATGTA-TTAAGTAAA
1 TTATGTAGTTATGTAAG
498627 TTATGTAAGTTATGT-A-
1 TTATGT-AGTTATGTAAG
498643 TTATGTAAGTTATGTAAG
1 TTATGT-AGTTATGTAAG
* * *
498661 TTGTGTA-TTATGAAAC
1 TTATGTAGTTATGTAAG
*
498677 TTATGTAAGTTATGT--C
1 TTATGT-AGTTATGTAAG
498693 TTATGTAGGTTATGTAAG
1 TTATGTA-GTTATGTAAG
498711 TTATGTA-TTATGTAAG
1 TTATGTAGTTATGTAAG
*
498727 TTATGTA-TTAAGTAAG
1 TTATGTAGTTATGTAAG
*
498743 TTATGTAAG-T-TGT--C
1 TTATGT-AGTTATGTAAG
*
498757 TTATATAAGTTATGTAAG
1 TTATGT-AGTTATGTAAG
498775 TTATGTA-TTATGTAAG
1 TTATGTAGTTATGTAAG
498791 TTATGTAAGTTATGT-A-
1 TTATGT-AGTTATGTAAG
*
498807 TTAAGTAGGTTATGTAAG
1 TTATGTA-GTTATGTAAG
498825 TTATGTA-TTATGTAAG
1 TTATGTAGTTATGTAAG
498841 TTATGTA
1 TTATGTA
498848 AGTTTTTGTG
Statistics
Matches: 200, Mismatches: 17, Indels: 42
0.77 0.07 0.16
Matches are distributed among these distances:
14 8 0.04
15 3 0.01
16 132 0.66
17 12 0.06
18 45 0.22
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (17 bp):
TTATGTAGTTATGTAAG
Found at i:498630 original size:25 final size:25
Alignment explanation
Indices: 498593--498942 Score: 250
Period size: 25 Copynumber: 14.0 Consensus size: 25
498583 CATCATATAT
498593 TTATGTAAGTTATGTAAGTTATGTA
1 TTATGTAAGTTATGTAAGTTATGTA
* *
498618 TTAAGTAAATTATGTAAGTTATGTA
1 TTATGTAAGTTATGTAAGTTATGTA
*
498643 TTATGTAAGTTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTAAGTTATGTA
* * *
498668 TTATGAAACTTATGTAAGTTATGTC
1 TTATGTAAGTTATGTAAGTTATGTA
*
498693 TTATGTAGGTTATGTAAGTTATGTA
1 TTATGTAAGTTATGTAAGTTATGTA
*
498718 TTATGTAAGTTATGT-A-TTAAGTAA
1 TTATGTAAGTTATGTAAGTTATGT-A
* *
498742 GTTATGTAAG-T-TGT--CTTATATAA
1 -TTATGTAAGTTATGTAAGTTATGT-A
498765 GTTATGTAAGTTATGT-A-TTATGTAA
1 -TTATGTAAGTTATGTAAGTTATGT-A
*
498790 GTTATGTAAGTTATGT-A-TTAAGTA
1 -TTATGTAAGTTATGTAAGTTATGTA
498814 GGTTATGTAAGTTATGT-A-TTATGTAA
1 --TTATGTAAGTTATGTAAGTTATGT-A
* *
498840 GTTATGTAAGTTTTTGT--GTTTGTGTA
1 -TTATGTAAG-TTATGTAAG-TTATGTA
* * * *
498866 TTATATAACTTATTTAATTTATGTA
1 TTATGTAAGTTATGTAAGTTATGTA
498891 GGTTATGTATTA-TTATGTAAGTTAT-TA
1 --TTATGTA--AGTTATGTAAGTTATGTA
*
498918 TGTA-GGATA-TTATGTAAGTTATGTA
1 T-TATGTA-AGTTATGTAAGTTATGTA
498943 AGTTTTTGTT
Statistics
Matches: 274, Mismatches: 32, Indels: 38
0.80 0.09 0.11
Matches are distributed among these distances:
23 24 0.09
24 24 0.09
25 192 0.70
26 9 0.03
27 13 0.05
28 11 0.04
29 1 0.00
ACGTcount: A:0.31, C:0.01, G:0.19, T:0.48
Consensus pattern (25 bp):
TTATGTAAGTTATGTAAGTTATGTA
Found at i:498652 original size:50 final size:50
Alignment explanation
Indices: 498593--499364 Score: 266
Period size: 50 Copynumber: 15.3 Consensus size: 50
498583 CATCATATAT
* *
498593 TTATGTAAGTTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTA
1 TTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTATGTA
* * * *
498643 TTATGTAAGTTATGTAAGTTGTGTATTATGAAACTTATGTAAGTTATGTC
1 TTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTATGTA
* *
498693 TTATGTAGGTTATGTAAGTTATGTATTATGTAAGTTATGT-A-TTAAGTAA
1 TTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTATGT-A
* *
498742 GTTATGTAAG-T-TGT--CTTATATAAGTTATGTAAGTTATGT-A-TTATGTAA
1 -TTATGTAAGTTATGTAAGTTATGT-A-TTATGTAAGTTATGTAAGTTATGT-A
*
498790 GTTATGTAAGTTATGT-A-TTAAGTAGGTTATGTAAGTTATGT-A-TTATGTAA
1 -TTATGTAAGTTATGTAAGTTATGTA--TTATGTAAGTTATGTAAGTTATGT-A
* * * * * *
498840 GTTATGTAAGTTTTTGT--GTTTGTGTATTATATAACTTATTTAATTTATGTA
1 -TTATGTAAG-TTATGTAAG-TTATGTATTATGTAAGTTATGTAAGTTATGTA
*
498891 GGTTATGTATTA-TTATGTAAGTTAT-TATGTA-GGATA-TTATGTAAGTTATGTAA
1 --TTATGTA--AGTTATGTAAGTTATGTAT-TATGTA-AGTTATGTAAGTTATGT-A
* *** * * * *
498944 GTTTTTGTTTTTTGTGT-A-TTATGTAACTTATTTAATTTATGTAGGTTATGTATTA
1 --TTATGTAAGTTATGTAAGTTATGT-A-TTATGTAAGTTATGTAAGTTATG---TA
* * * *
498999 TTATGTAAGTTAT-TATG-TAGGATATTATGTAAGTTATGTAAGTTTTTGTT
1 TTATGTAAGTTATGTAAGTTATG-TATTATGTAAGTTATGTAAG-TTATGTA
* * * * *
499049 TTTTGTGTA-TTATGTAACTTATTTAATTTATGTAGGTTA--T--G-TAT-TA
1 TTATGT-AAGTTATGTAAGTTATGT-A-TTATGTAAGTTATGTAAGTTATGTA
* * * *
499095 TTATGTAAGTTAT-TATG-TAGGATATTATGTAAGTTATGTAAGTTTTTGTT
1 TTATGTAAGTTATGTAAGTTATG-TATTATGTAAGTTATGTAAG-TTATGTA
* * * * *
499145 TTTTGTGTA-TTATGTAACTTATTTAATTTATGTAGGTTA--T--G-TAT-TA
1 TTATGT-AAGTTATGTAAGTTATGT-A-TTATGTAAGTTATGTAAGTTATGTA
* * * *
499191 TTATGTAAGTTAT-TATG-TAGGATATTATGTAAGTTATGTAAGTTTTTGTT
1 TTATGTAAGTTATGTAAGTTATG-TATTATGTAAGTTATGTAAG-TTATGTA
* * * * *
499241 TTTTGTGTA-TTATGTAACTTATTTAATTTATGTAGGTTATGTATTA-TTATGTA
1 TTATGT-AAGTTATGTAAGTTATGT-A-TTATGTAAGTTATGTA--AGTTATGTA
* * * *
499294 TTATAAATTTAAGTTATATAAGTTATGTATTATGTGTAAGCTTATGTATG-TA-G-G
1 -T-T--ATGTAAGTTATGTAAGTTATGTATTA--TGTAAG-TTATGTAAGTTATGTA
499348 TTATGTAAGTTATGTAA
1 TTATGTAAGTTATGTAA
499365 AGTATCAATT
Statistics
Matches: 539, Mismatches: 105, Indels: 156
0.67 0.13 0.19
Matches are distributed among these distances:
43 22 0.04
44 6 0.01
45 10 0.02
46 25 0.05
47 7 0.01
48 41 0.08
49 10 0.02
50 190 0.35
51 23 0.04
52 76 0.14
53 87 0.16
54 4 0.01
55 7 0.01
56 5 0.01
57 19 0.04
58 7 0.01
ACGTcount: A:0.29, C:0.01, G:0.18, T:0.51
Consensus pattern (50 bp):
TTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTATGTA
Found at i:498975 original size:96 final size:96
Alignment explanation
Indices: 498830--499293 Score: 903
Period size: 96 Copynumber: 4.8 Consensus size: 96
498820 GTAAGTTATG
* *
498830 TATTATGTAAGTTATGTAAGTTTTTG-TGTTTGTGTATTATATAACTTATTTAATTTATGTAGGT
1 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
498894 TATGTATTATTATGTAAGTTATTATGTAGGA
66 TATGTATTATTATGTAAGTTATTATGTAGGA
498925 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
1 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
498990 TATGTATTATTATGTAAGTTATTATGTAGGA
66 TATGTATTATTATGTAAGTTATTATGTAGGA
499021 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
1 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
499086 TATGTATTATTATGTAAGTTATTATGTAGGA
66 TATGTATTATTATGTAAGTTATTATGTAGGA
499117 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
1 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
499182 TATGTATTATTATGTAAGTTATTATGTAGGA
66 TATGTATTATTATGTAAGTTATTATGTAGGA
499213 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
1 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
499278 TATGTATTATTATGTA
66 TATGTATTATTATGTA
499294 TTATAAATTT
Statistics
Matches: 366, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
95 26 0.07
96 340 0.93
ACGTcount: A:0.27, C:0.01, G:0.17, T:0.54
Consensus pattern (96 bp):
TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
TATGTATTATTATGTAAGTTATTATGTAGGA
Found at i:499429 original size:19 final size:18
Alignment explanation
Indices: 499379--499432 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 18
499369 TCAATTTTTA
*
499379 AAAATATATATAAATTTT
1 AAAATATATATAAATATT
*
499397 AAAA-ATAT-T-TATATT
1 AAAATATATATAAATATT
499412 AAAACTATATATAAATATT
1 AAAA-TATATATAAATATT
499431 AA
1 AA
499433 TAAGTTATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
15 8 0.28
16 1 0.03
17 8 0.28
18 5 0.17
19 7 0.24
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATATATATAAATATT
Found at i:499485 original size:18 final size:18
Alignment explanation
Indices: 499462--499502 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
499452 ATTATAAATT
499462 TAAATTA-TGTAAGTTATG
1 TAAATTACT-TAAGTTATG
499480 TAAATTACTTAAGTTATG
1 TAAATTACTTAAGTTATG
499498 -AAATT
1 TAAATT
499503 TGAACTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.23
18 16 0.73
19 1 0.05
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.44
Consensus pattern (18 bp):
TAAATTACTTAAGTTATG
Found at i:500526 original size:32 final size:31
Alignment explanation
Indices: 500464--500526 Score: 74
Period size: 33 Copynumber: 2.0 Consensus size: 31
500454 CATTAACCAA
* *
500464 ATACCAAATTAAAACAATCCCAACTACAAAT
1 ATACCAAATTAAAACAATCCAAAATACAAAT
*
500495 ATACCAAATATAAAAACAGTCCAAAAT-CAAAT
1 ATACCAAAT-T-AAAACAATCCAAAATACAAAT
500527 GTAAATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 9 0.33
32 6 0.22
33 12 0.44
ACGTcount: A:0.57, C:0.22, G:0.02, T:0.19
Consensus pattern (31 bp):
ATACCAAATTAAAACAATCCAAAATACAAAT
Found at i:502189 original size:22 final size:22
Alignment explanation
Indices: 502164--502209 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
502154 AAACTTTATT
*
502164 CCTTAGACCC-TAAATCTTAAAC
1 CCTTA-ACCCTTAAACCTTAAAC
502186 CCTTAACCCTTAAACCTTAAAC
1 CCTTAACCCTTAAACCTTAAAC
502208 CC
1 CC
502210 ACGAACCCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.35, C:0.37, G:0.02, T:0.26
Consensus pattern (22 bp):
CCTTAACCCTTAAACCTTAAAC
Found at i:502568 original size:14 final size:14
Alignment explanation
Indices: 502549--502581 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
502539 TAGAACATAT
502549 ATAAA-CCTAAAATC
1 ATAAACCCT-AAATC
502563 ATAAACCCTAAATC
1 ATAAACCCTAAATC
502577 ATAAA
1 ATAAA
502582 ACATATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 15 0.83
15 3 0.17
ACGTcount: A:0.58, C:0.21, G:0.00, T:0.21
Consensus pattern (14 bp):
ATAAACCCTAAATC
Found at i:502620 original size:7 final size:7
Alignment explanation
Indices: 502610--502640 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
502600 CCTCAACCCT
502610 TAAACAA
1 TAAACAA
502617 TAAACAA
1 TAAACAA
502624 TAAACAA
1 TAAACAA
*
502631 TAAACCA
1 TAAACAA
502638 TAA
1 TAA
502641 GGCCTAAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAACAA
Found at i:503291 original size:208 final size:208
Alignment explanation
Indices: 502997--503654 Score: 938
Period size: 208 Copynumber: 3.2 Consensus size: 208
502987 TTTTGGCAAT
* * * * * * * *
502997 GCGCCACTAATGTCTCTAAATCTGAAAAAGAAAATGCTGTCATTTGCCTAAAACTATTATCAATA
1 GCGCCACTATTGTGTCTAAAACTCAACAAGAAAACGTTGTCATTTGCCTAAAACTATTACCAATA
* *
503062 ATGCTTGAATTTTGCGGCGTTTTTCGCGAAGCGCCACTAATTTCCCTAAGCACAATAGAAAATGA
66 ATGCTTGAATTTTGCGGCGTTTTTCGCGAAGCGCCACTAATGTCCCTAAGCACAACAGAAAATGA
* ** * **
503127 TGGCGTATGCTTAAAACTTTTTGCGGTGCTTCCTCTAAAGCGGGGCTAATGATTGACTTCGGCAA
131 TGGCGTATGCTTAAAACTTTTTGCGGCGCTTCCTCTAAAGCGCCGCTAATGATTGACTTCAGCGG
*
503192 CGATTTCTTCGAA
196 CGATTTCTTTGAA
** *
503205 GCGCCACTATTGTGTCTAAAACTCAACAAGAAAACGTTGTTGTTTGTCTAAAACTATTACCAATA
1 GCGCCACTATTGTGTCTAAAACTCAACAAGAAAACGTTGTCATTTGCCTAAAACTATTACCAATA
** * * *
503270 ATGCTTGAATTTTATGGCGTTTTTCGCGAAGCACCACTAATGTCCCTAAGCACAACAGAGAACGA
66 ATGCTTGAATTTTGCGGCGTTTTTCGCGAAGCGCCACTAATGTCCCTAAGCACAACAGAAAATGA
* ** *
503335 TGGTGTATGCTTAAAACTTTTTGCGGCGCTTCCTCTAAAGCGCCAATAGTGATTGACTTCAGCGG
131 TGGCGTATGCTTAAAACTTTTTGCGGCGCTTCCTCTAAAGCGCCGCTAATGATTGACTTCAGCGG
*
503400 CAATTTCTTTGAA
196 CGATTTCTTTGAA
* * * *
503413 GTGCCATTATTGTGTCTAAAACTGAACAAGAAAACGTTGTCATTTGCCTAAAACTATTACCGATA
1 GCGCCACTATTGTGTCTAAAACTCAACAAGAAAACGTTGTCATTTGCCTAAAACTATTACCAATA
* * * *
503478 ATCCTTGACTTTTGCGGCGTTTTTCGCGACGCGTCACTAATGTCCCTAAGCACAACAGAAAATGA
66 ATGCTTGAATTTTGCGGCGTTTTTCGCGAAGCGCCACTAATGTCCCTAAGCACAACAGAAAATGA
* **
503543 CGGCGTATGCTTAAAACTTTTTGTAGCGCTTCCTCTAAAGCGCCGCTAATGATTGACTTCAGCGG
131 TGGCGTATGCTTAAAACTTTTTGCGGCGCTTCCTCTAAAGCGCCGCTAATGATTGACTTCAGCGG
*
503608 CGATTTCTTTGAG
196 CGATTTCTTTGAA
503621 GCGCCACTATTGTGTCTAAAACTCAACAAGAAAA
1 GCGCCACTATTGTGTCTAAAACTCAACAAGAAAA
503655 AGACGTCGTT
Statistics
Matches: 392, Mismatches: 58, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
208 392 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (208 bp):
GCGCCACTATTGTGTCTAAAACTCAACAAGAAAACGTTGTCATTTGCCTAAAACTATTACCAATA
ATGCTTGAATTTTGCGGCGTTTTTCGCGAAGCGCCACTAATGTCCCTAAGCACAACAGAAAATGA
TGGCGTATGCTTAAAACTTTTTGCGGCGCTTCCTCTAAAGCGCCGCTAATGATTGACTTCAGCGG
CGATTTCTTTGAA
Found at i:508058 original size:17 final size:17
Alignment explanation
Indices: 508036--508070 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
508026 TTGAGAAACA
*
508036 TATATTGTCATTGCATT
1 TATATTGTCATTACATT
508053 TATATTGTCATTACATT
1 TATATTGTCATTACATT
508070 T
1 T
508071 TCATGTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.54
Consensus pattern (17 bp):
TATATTGTCATTACATT
Found at i:519695 original size:29 final size:26
Alignment explanation
Indices: 519628--519696 Score: 66
Period size: 29 Copynumber: 2.5 Consensus size: 26
519618 CTATTTTAAG
* *
519628 ATTTTATACTTTTGCCCTATTTTTCAA
1 ATTTTATA-TTTTGCCCTACTTTACAA
*
519655 ATTTTACAATTTTGTCCCTTACTTTACAA
1 ATTTTA-TATTTTG-CCC-TACTTTACAA
519684 ATTTTATTATTTT
1 ATTTTA-TATTTT
519697 AACCCAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
27 11 0.32
28 4 0.12
29 19 0.56
ACGTcount: A:0.25, C:0.16, G:0.03, T:0.57
Consensus pattern (26 bp):
ATTTTATATTTTGCCCTACTTTACAA
Found at i:526515 original size:18 final size:18
Alignment explanation
Indices: 526491--526530 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
526481 GAAAGGGAAG
526491 GAGAGAATGATATAATGAAA
1 GAGA-AATGATA-AATGAAA
*
526511 GAGAAATGTTAAATGAAA
1 GAGAAATGATAAATGAAA
526529 GA
1 GA
526531 TTAATGAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 6 0.32
20 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.25, T:0.20
Consensus pattern (18 bp):
GAGAAATGATAAATGAAA
Found at i:530262 original size:42 final size:42
Alignment explanation
Indices: 530203--530287 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
530193 TTAAATGAGT
530203 TAATTTTGAATACATATAGATCAAGAAAAAAGGAATCTAAAA
1 TAATTTTGAATACATATAGATCAAGAAAAAAGGAATCTAAAA
* *
530245 TAATTTTGAATACATATAGATCAAGAAAAAAGGACTCTGAAA
1 TAATTTTGAATACATATAGATCAAGAAAAAAGGAATCTAAAA
530287 T
1 T
530288 TAGATCGGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.52, C:0.08, G:0.13, T:0.27
Consensus pattern (42 bp):
TAATTTTGAATACATATAGATCAAGAAAAAAGGAATCTAAAA
Found at i:538540 original size:50 final size:50
Alignment explanation
Indices: 538465--538660 Score: 230
Period size: 50 Copynumber: 3.9 Consensus size: 50
538455 CATTAAGATT
*
538465 ATGAGAGGTCCCACGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
** *
538515 ATGAGAGGTCCCGTGTAAGACCATGTCTGGGACATGGCGTTGACACCGAG
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
* * * * ** *
538565 ATGAGAGGTCCCCCATAAGACCATGTCTGGAACATGGCATAAGCACCGAT
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
** * * * * *
538615 ATGAGAACTCCCATGTAAGACCATATCTGGGATATGACATTGGCAC
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCGTTGGCAC
538661 TACAGTAAAC
Statistics
Matches: 122, Mismatches: 24, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 122 1.00
ACGTcount: A:0.28, C:0.23, G:0.29, T:0.20
Consensus pattern (50 bp):
ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
Found at i:538601 original size:100 final size:100
Alignment explanation
Indices: 538465--538646 Score: 256
Period size: 100 Copynumber: 1.8 Consensus size: 100
538455 CATTAAGATT
* * * * ** ** *
538465 ATGAGAGGTCCCACGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCGTG
1 ATGAGAGGTCCCACATAAGACCATGTCTGGAACATGGCATAAGCACCGAGATGAGAACTCCCATG
*
538530 TAAGACCATGTCTGGGACATGGCGTTGACACCGAG
66 TAAGACCATATCTGGGACATGGCGTTGACACCGAG
* *
538565 ATGAGAGGTCCCCCATAAGACCATGTCTGGAACATGGCATAAGCACCGATATGAGAACTCCCATG
1 ATGAGAGGTCCCACATAAGACCATGTCTGGAACATGGCATAAGCACCGAGATGAGAACTCCCATG
538630 TAAGACCATATCTGGGA
66 TAAGACCATATCTGGGA
538647 TATGACATTG
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
100 70 1.00
ACGTcount: A:0.28, C:0.23, G:0.29, T:0.20
Consensus pattern (100 bp):
ATGAGAGGTCCCACATAAGACCATGTCTGGAACATGGCATAAGCACCGAGATGAGAACTCCCATG
TAAGACCATATCTGGGACATGGCGTTGACACCGAG
Found at i:558888 original size:20 final size:20
Alignment explanation
Indices: 558863--558900 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
558853 ACCCCTTTTA
558863 TTAACATAAA-AATTTAAAAT
1 TTAACA-AAATAATTTAAAAT
558883 TTAACAAAATAATTTAAA
1 TTAACAAAATAATTTAAA
558901 CTAGAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
TTAACAAAATAATTTAAAAT
Found at i:563813 original size:27 final size:27
Alignment explanation
Indices: 563782--563959 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
563772 TAAATTGTAC
563782 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
563809 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
563835 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
563863 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
563891 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
563918 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
563945 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
563960 GGCTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:563896 original size:82 final size:81
Alignment explanation
Indices: 563783--563938 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
563773 AAATTGTACA
* *
563783 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
563847 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
563864 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
563929 TGCGAGTTGA
65 TGCGAATTGA
563939 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:563950 original size:82 final size:81
Alignment explanation
Indices: 563779--563959 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
563769 GATTAAATTG
* *
563779 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
563844 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
563860 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
563924 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
563942 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
563960 GGCTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:563970 original size:27 final size:27
Alignment explanation
Indices: 563864--563970 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
563854 TGACCATGCG
* * * *
563864 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
563892 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
563919 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
563946 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
563971 CATTCGTGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 53 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:571806 original size:27 final size:27
Alignment explanation
Indices: 571747--571898 Score: 223
Period size: 27 Copynumber: 5.6 Consensus size: 27
571737 TAAATTGTAC
*
571747 AGCACTAAGTGTGCGAGTTGGACTATGT
1 AGCACTAAGTGTGCGAATT-GACTATGT
571775 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
571802 TGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
571829 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* *
571857 AGCACTAAGTGTGCGAGTTGACTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
571884 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
571899 GACTTAATAT
Statistics
Matches: 114, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
27 71 0.62
28 43 0.38
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:571813 original size:55 final size:55
Alignment explanation
Indices: 571747--571898 Score: 234
Period size: 55 Copynumber: 2.8 Consensus size: 55
571737 TAAATTGTAC
571747 AGCACTAAGTGTGCGAGTTGGACTATGTAGCACTAAGTGTGCGA-ATTGACTATGT
1 AGCACTAAGTGTGCGAGTT-GACTATGTAGCACTAAGTGTGCGAGATTGACTATGT
* * * *
571802 TGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGATTGACTATGT
* *
571857 AGCACTAAGTGTGCGAGTTGACTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
571899 GACTTAATAT
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 24 0.27
55 64 0.73
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGATTGACTATGT
Found at i:571861 original size:82 final size:82
Alignment explanation
Indices: 571747--571898 Score: 250
Period size: 82 Copynumber: 1.9 Consensus size: 82
571737 TAAATTGTAC
* *
571747 AGCACTAAGTGTGCGAGTTGGACTATGTAGCACTAAGTGTGCGAATTGACTATGTTGCACTAAGT
1 AGCACTAAGTGTGCGAGTTGGACTATGTAGCACTAAGTGTGCGAATTGACTATATAGCACTAAGT
571812 GTGCGAATTGACTATGT
66 GTGCGAATTGACTATGT
* * * *
571829 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTGACTATATAGCACTGAGT
1 AGCACTAAGTGTGCGAGTTGGACTATGTAGCACTAAGTGTGCGAATTGACTATATAGCACTAAGT
571894 GTGCG
66 GTGCG
571899 GACTTAATAT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 64 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.30
Consensus pattern (82 bp):
AGCACTAAGTGTGCGAGTTGGACTATGTAGCACTAAGTGTGCGAATTGACTATATAGCACTAAGT
GTGCGAATTGACTATGT
Found at i:579965 original size:17 final size:18
Alignment explanation
Indices: 579936--579973 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
579926 GCCCAGCCAC
*
579936 AAAGAGAAAAAAAAATAA
1 AAAGAGAAAAAAAAAGAA
579954 AAAGAG-AAAAAAAAGAA
1 AAAGAGAAAAAAAAAGAA
579971 AAA
1 AAA
579974 ATTAAACCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (18 bp):
AAAGAGAAAAAAAAAGAA
Found at i:583281 original size:5 final size:5
Alignment explanation
Indices: 583271--583314 Score: 56
Period size: 5 Copynumber: 8.8 Consensus size: 5
583261 GAAAAAAATC
583271 TTATT TTATT TT-TAT TTA-T TTATT TTATT TTATT TTGATT TTAT
1 TTATT TTATT TTAT-T TTATT TTATT TTATT TTATT TT-ATT TTAT
583315 GTTAAATTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
4 5 0.14
5 25 0.71
6 5 0.14
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:583294 original size:14 final size:14
Alignment explanation
Indices: 583271--583314 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 14
583261 GAAAAAAATC
583271 TTATTTTATTTTTAT
1 TTATTTTA-TTTTAT
583286 TTA-TTTATTTTATT
1 TTATTTTATTTTA-T
583300 TTATTTTGATTTTAT
1 TTATTTT-ATTTTAT
583315 GTTAAATTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 5 0.19
14 8 0.31
15 7 0.27
16 6 0.23
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.77
Consensus pattern (14 bp):
TTATTTTATTTTAT
Found at i:584980 original size:54 final size:54
Alignment explanation
Indices: 584898--585018 Score: 206
Period size: 54 Copynumber: 2.2 Consensus size: 54
584888 CAAGCCAAGT
* * *
584898 AGTTACACGGCCTAGCACATGGCTTGACACACTAGTATGTGAGGCCATTTTGAA
1 AGTTACACGGCCTAGCACATAGCTTGACACACTAGTATGTAAGGCCATTTCGAA
*
584952 AGTTACACGGCCTAGCACATAGCTTGACACACTGGTATGTAAGGCCATTTCGAA
1 AGTTACACGGCCTAGCACATAGCTTGACACACTAGTATGTAAGGCCATTTCGAA
585006 AGTTACACGGCCT
1 AGTTACACGGCCT
585019 GGTACATGGG
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 63 1.00
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (54 bp):
AGTTACACGGCCTAGCACATAGCTTGACACACTAGTATGTAAGGCCATTTCGAA
Found at i:590928 original size:31 final size:31
Alignment explanation
Indices: 590893--590963 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
590883 TATTAGTTGG
590893 TATATTAGTATGAATATCATGTACATTATGA
1 TATATTAGTATGAATATCATGTACATTATGA
* * * **
590924 TATATTAGTGTGTATATTATGTATGTTATGA
1 TATATTAGTATGAATATCATGTACATTATGA
*
590955 TATTTTAGT
1 TATATTAGT
590964 GTATATATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.32, C:0.03, G:0.15, T:0.49
Consensus pattern (31 bp):
TATATTAGTATGAATATCATGTACATTATGA
Found at i:590964 original size:31 final size:31
Alignment explanation
Indices: 590918--590984 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
590908 ATCATGTACA
*
590918 TTATGATATATTAGTGTGTATATTATGTATG
1 TTATGATATATTAGTGTATATATTATGTATG
*
590949 TTATGATATTTTAGTGTATATATTATGTATG
1 TTATGATATATTAGTGTATATATTATGTATG
590980 TTATG
1 TTATG
590985 TGTCAGACCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.28, C:0.00, G:0.18, T:0.54
Consensus pattern (31 bp):
TTATGATATATTAGTGTATATATTATGTATG
Found at i:598076 original size:19 final size:19
Alignment explanation
Indices: 598054--598106 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
598044 AAAAATTAGA
*
598054 AAAAAAATATAAAAATCGT
1 AAAAAATTATAAAAATCGT
** *
598073 AAAATTTTATAAAAATTGT
1 AAAAAATTATAAAAATCGT
598092 AAAACAATTATAAAA
1 AAAA-AATTATAAAA
598107 TATATAGAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (19 bp):
AAAAAATTATAAAAATCGT
Done.