Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015102.1 Kokia drynarioides strain JFW-HI SEQ_130146, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 783730
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 366 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:317531 original size:215 final size:217
Alignment explanation
Indices: 317128--317531 Score: 526
Period size: 215 Copynumber: 1.9 Consensus size: 217
317118 AATTTCGACA
* * * *
317128 AGCTCACTATGCTTCTCACACAAGTTGTAGAGAATCTGTAACATATGCAGGATCTCAAGCCATCC
1 AGCTCACGATGCTGCTCACACAAGCTGTAGAGAATCTGCAACATATGCAGGATCTCAAGCCATCC
* * *
317193 CTATGGTCTGTATCATCGGTACATAGTACCTGCTAAATAATCACTGGCTCACAATACTACTTGCA
66 CTA--GCCTGTATCATCGGTACATAGTACCTGCTAAATAATCACTGGATCACAATACTACTTACA
* * * **
317258 CAAGCTGTAGAGAATCCGCAACATATGTAGGATCTCAACCATCACTATTGTATGTATCACCAGTA
129 CAACCGGTAGAGAATCCGCAACATATGCAGGATCTCAACCATCACTAAGGTATGTATCACCAGTA
317323 CATAGTACTTGCTAAATAATCACT
194 CATAGTACTTGCTAAATAATCACT
* *
317347 AGCTCACGATGCTGCTCACACAAGCTGTAGAGAATTTGCAACATATGCAGGATCTC-AGCCATCT
1 AGCTCACGATGCTGCTCACACAAGCTGTAGAGAATCTGCAACATATGCAGGATCTCAAGCCATCC
* * * ** * *
317411 CTA-CCTGTATCA-CTGGTACGTAGTACTTGCTAAATAATCACTGGATTATGATACTGCTTACGC
66 CTAGCCTGTATCATC-GGTACATAGTACCTGCTAAATAATCACTGGATCACAATACTACTTACAC
* * * * *
317474 AACCGGTAGAGAATTCGCAACATATGCAGGATCTCAGCCATTATTAAGGTCTGTATCA
130 AACCGGTAGAGAATCCGCAACATATGCAGGATCTCAACCATCACTAAGGTATGTATCA
317532 TCAAATCAAG
Statistics
Matches: 158, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
214 1 0.01
215 96 0.61
218 10 0.06
219 51 0.32
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (217 bp):
AGCTCACGATGCTGCTCACACAAGCTGTAGAGAATCTGCAACATATGCAGGATCTCAAGCCATCC
CTAGCCTGTATCATCGGTACATAGTACCTGCTAAATAATCACTGGATCACAATACTACTTACACA
ACCGGTAGAGAATCCGCAACATATGCAGGATCTCAACCATCACTAAGGTATGTATCACCAGTACA
TAGTACTTGCTAAATAATCACT
Found at i:318481 original size:3 final size:3
Alignment explanation
Indices: 318468--318513 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
318458 CCTTTTTAAC
*
318468 TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
318514 TTTTTACAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:323754 original size:21 final size:21
Alignment explanation
Indices: 323712--323759 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
323702 ATAGTTCTAT
* * **
323712 CGATACAAGTCATGCTTTTAC
1 CGATACAAGCCATGATACTAC
323733 CGATACAAGCCATGATACTAC
1 CGATACAAGCCATGATACTAC
323754 CGATAC
1 CGATAC
323760 TAAAAACTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (21 bp):
CGATACAAGCCATGATACTAC
Found at i:324434 original size:41 final size:41
Alignment explanation
Indices: 324356--324450 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 41
324346 TCGTAAAACA
* *
324356 TCCTCTTTAGACAATCTTATACTTCACCGAATCATAAGTCT
1 TCCTTTTTAAACAATCTTATACTTCACCGAATCATAAGTCT
* * * * *
324397 TCCTTTTTAAACAATCTTATGCTTTATCGAGTTATAAGTCT
1 TCCTTTTTAAACAATCTTATACTTCACCGAATCATAAGTCT
*
324438 TCCTTTTCAAACA
1 TCCTTTTTAAACA
324451 TAATCTCACG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.28, C:0.23, G:0.07, T:0.41
Consensus pattern (41 bp):
TCCTTTTTAAACAATCTTATACTTCACCGAATCATAAGTCT
Found at i:324507 original size:42 final size:43
Alignment explanation
Indices: 324430--324621 Score: 140
Period size: 42 Copynumber: 4.5 Consensus size: 43
324420 TTATCGAGTT
* *
324430 ATAAGTCTTCCTTTTCAAACATAATCTCACGCTCATCCTGAGAC
1 ATAAGTCTTCCTTTT-AAACATAATCTAACGCTCATCCCGAGAC
* * **
324474 TTAAGTCTTCC-TTTAAACATAATTTAATTCTCATCCCGAGAC
1 ATAAGTCTTCCTTTTAAACATAATCTAACGCTCATCCCGAGAC
* * * * * *
324516 ATAAGTCATCCTTTTAAACATATTC-ACATGCTTAT-TCGAGTC
1 ATAAGTCTTCCTTTTAAACATAATCTA-ACGCTCATCCCGAGAC
* ** **
324558 ATGAGTCTTCCTTTTAAACA-AATTCTAATTCTCAAACCGAGAC
1 ATAAGTCTTCCTTTTAAACATAA-TCTAACGCTCATCCCGAGAC
* * * *
324601 ATGATTCTTCCATTTATACAT
1 ATAAGTCTTCCTTTTAAACAT
324622 CAAGTTATTC
Statistics
Matches: 117, Mismatches: 25, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
41 1 0.01
42 63 0.54
43 43 0.37
44 10 0.09
ACGTcount: A:0.31, C:0.24, G:0.08, T:0.36
Consensus pattern (43 bp):
ATAAGTCTTCCTTTTAAACATAATCTAACGCTCATCCCGAGAC
Found at i:324535 original size:85 final size:86
Alignment explanation
Indices: 324430--324602 Score: 208
Period size: 85 Copynumber: 2.0 Consensus size: 86
324420 TTATCGAGTT
* * *
324430 ATAAGTCTTCCTTTTCAAACATAATCTCACGCTCATCCTGAGACTTAAGTCTTCC-TTTAAACAT
1 ATAAGTCATCCTTTTCAAACATAATCACACGCTCATCC-GAGACATAAGTCTTCCTTTTAAACA-
**
324494 AATT-TAATTCTCATCCCGAGAC
64 AATTCTAATTCTCAAACCGAGAC
* * * * * *
324516 ATAAGTCATCCTTTT-AAACATATTCACATGCTTATTCGAGTCATGAGTCTTCCTTTTAAACAAA
1 ATAAGTCATCCTTTTCAAACATAATCACACGCTCATCCGAGACATAAGTCTTCCTTTTAAACAAA
324580 TTCTAATTCTCAAACCGAGAC
66 TTCTAATTCTCAAACCGAGAC
324601 AT
1 AT
324603 GATTCTTCCA
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
84 17 0.23
85 43 0.58
86 14 0.19
ACGTcount: A:0.32, C:0.24, G:0.09, T:0.35
Consensus pattern (86 bp):
ATAAGTCATCCTTTTCAAACATAATCACACGCTCATCCGAGACATAAGTCTTCCTTTTAAACAAA
TTCTAATTCTCAAACCGAGAC
Found at i:328608 original size:122 final size:123
Alignment explanation
Indices: 328436--328794 Score: 603
Period size: 122 Copynumber: 2.9 Consensus size: 123
328426 GTTTTGCTAC
* *
328436 ATTTCCTTTTATTTAATATCTCATATTAAAATGAAAATATTCCTTTAGAGAAATATACGGAAGGT
1 ATTTCCTTTTATTTAATATCTCATATTAAAATGGAAATATTCCTTTAGAGAAATATATGGAAGGT
* *
328501 TTATTAAAACATTATATCCTTTCGAAAAGGATATTAACTTCCATGTTTTTAATATTCA
66 TTATTAAAACATTATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATAGTCA
* * *
328559 ATTTTCTTTTATATAATGTCTCATATTAAAATGGAAA-ATTCCTTTAGAGAAATATATGGAAGGT
1 ATTTCCTTTTATTTAATATCTCATATTAAAATGGAAATATTCCTTTAGAGAAATATATGGAAGGT
328623 TTATTAAAACATTATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATAGTCA
66 TTATTAAAACATTATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATAGTCA
* *
328681 ATTTCCTTTTATTTAATATCTCATATTAAAATGGAAATATTCTTTTAGAGAAATAAATGGAAGGT
1 ATTTCCTTTTATTTAATATCTCATATTAAAATGGAAATATTCCTTTAGAGAAATATATGGAAGGT
* * *
328746 TTATTAAAAAATTATATCATTTCCAAAAGGATATTAACTTTCATGTTTT
66 TTATTAAAACATTATATCCTTTCCAAAAGGATATTAACTTCCATGTTTT
328795 GATATTTAAC
Statistics
Matches: 220, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
122 116 0.53
123 104 0.47
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.42
Consensus pattern (123 bp):
ATTTCCTTTTATTTAATATCTCATATTAAAATGGAAATATTCCTTTAGAGAAATATATGGAAGGT
TTATTAAAACATTATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATAGTCA
Found at i:330890 original size:21 final size:21
Alignment explanation
Indices: 330865--330920 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
330855 AATAGTGCAG
330865 ACTTCTACCGATACAAGTGAC-T
1 ACTTCTACCGATACAAGT--CTT
**
330887 -CTTCTATTGATACAAGTCTT
1 ACTTCTACCGATACAAGTCTT
330907 ACTTCTACCGATAC
1 ACTTCTACCGATAC
330921 TAAAAACTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
19 1 0.04
20 1 0.04
21 26 0.93
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.34
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTCTT
Found at i:337636 original size:12 final size:12
Alignment explanation
Indices: 337621--337645 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
337611 ATTAAATAAT
337621 TAATAGCATTCA
1 TAATAGCATTCA
337633 TAATAGCATTCA
1 TAATAGCATTCA
337645 T
1 T
337646 CATAATAACA
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TAATAGCATTCA
Found at i:344150 original size:15 final size:15
Alignment explanation
Indices: 344120--344158 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
344110 TCCTATGTCT
* *
344120 ATGGCAACTTATCGG
1 ATGGCACCTTACCGG
*
344135 ATGTCACCTTACCGG
1 ATGGCACCTTACCGG
344150 ATGGCACCT
1 ATGGCACCT
344159 AAGGAACTCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (15 bp):
ATGGCACCTTACCGG
Found at i:347415 original size:6 final size:6
Alignment explanation
Indices: 347395--347424 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
347385 AATTATAGAC
347395 TTTATA TTATATA TTTATA TTTATA TTTAT
1 TTTATA TT-TATA TTTATA TTTATA TTTAT
347425 GAATGATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTATA
Found at i:347421 original size:12 final size:13
Alignment explanation
Indices: 347382--347424 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
347372 GTTATTTAAT
*
347382 TTTA-ATTATAGA
1 TTTATATTATATA
347394 CTTTATATTATATA
1 -TTTATATTATATA
347408 TTTATATT-TATA
1 TTTATATTATATA
347420 TTTAT
1 TTTAT
347425 GAATGATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 9 0.32
13 12 0.43
14 7 0.25
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (13 bp):
TTTATATTATATA
Found at i:351117 original size:17 final size:17
Alignment explanation
Indices: 351091--351134 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
351081 TTCTCGTTGC
*
351091 CATTATATTTTAATTGT
1 CATTACATTTTAATTGT
* *
351108 CATTGCATTTTCATTGT
1 CATTACATTTTAATTGT
351125 CATTACATTT
1 CATTACATTT
351135 CCATTTGTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.55
Consensus pattern (17 bp):
CATTACATTTTAATTGT
Found at i:351139 original size:17 final size:17
Alignment explanation
Indices: 351103--351139 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
351093 TTATATTTTA
* *
351103 ATTGTCATTGCATTTTC
1 ATTGTCATTACATTTCC
351120 ATTGTCATTACATTTCC
1 ATTGTCATTACATTTCC
351137 ATT
1 ATT
351140 TGTAATTGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.19, G:0.08, T:0.51
Consensus pattern (17 bp):
ATTGTCATTACATTTCC
Found at i:362649 original size:17 final size:17
Alignment explanation
Indices: 362629--362717 Score: 88
Period size: 17 Copynumber: 5.2 Consensus size: 17
362619 TTTGTCATCA
362629 CATTCTCATTGTCATTG
1 CATTCTCATTGTCATTG
* * *
362646 CATTTTAATTGTCACTG
1 CATTCTCATTGTCATTG
* *
362663 CATTCGCATTATCATTG
1 CATTCTCATTGTCATTG
* * *
362680 CATTTTAATTGTCACTG
1 CATTCTCATTGTCATTG
* *
362697 CATTCGCATTATCATTG
1 CATTCTCATTGTCATTG
362714 CATT
1 CATT
362718 TCCATTTGTC
Statistics
Matches: 54, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 54 1.00
ACGTcount: A:0.22, C:0.21, G:0.11, T:0.45
Consensus pattern (17 bp):
CATTCTCATTGTCATTG
Found at i:362658 original size:34 final size:34
Alignment explanation
Indices: 362629--362718 Score: 162
Period size: 34 Copynumber: 2.6 Consensus size: 34
362619 TTTGTCATCA
* *
362629 CATTCTCATTGTCATTGCATTTTAATTGTCACTG
1 CATTCGCATTATCATTGCATTTTAATTGTCACTG
362663 CATTCGCATTATCATTGCATTTTAATTGTCACTG
1 CATTCGCATTATCATTGCATTTTAATTGTCACTG
362697 CATTCGCATTATCATTGCATTT
1 CATTCGCATTATCATTGCATTT
362719 CCATTTGTCT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 54 1.00
ACGTcount: A:0.22, C:0.21, G:0.11, T:0.46
Consensus pattern (34 bp):
CATTCGCATTATCATTGCATTTTAATTGTCACTG
Found at i:363213 original size:19 final size:17
Alignment explanation
Indices: 363171--363215 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
363161 TTACACTTCA
*
363171 ATTTTGTTTTTTATTTT
1 ATTTTATTTTTTATTTT
363188 ATTTTTATTTATTTATTATT
1 A-TTTTATTT-TTTATT-TT
363208 ATTTTATT
1 ATTTTATT
363216 GATAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 1 0.04
18 7 0.29
19 13 0.54
20 3 0.12
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (17 bp):
ATTTTATTTTTTATTTT
Found at i:363307 original size:24 final size:22
Alignment explanation
Indices: 363272--363324 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 22
363262 AATTCCATTT
363272 ACCCAAAACTCAAACTAAACTA
1 ACCCAAAACTCAAACTAAACTA
*
363294 ACCCTAAAAGCTCAACCTAAACTA
1 ACCC-AAAA-CTCAAACTAAACTA
363318 AGCCCAA
1 A-CCCAA
363325 GTAGCCTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 4 0.15
23 4 0.15
24 16 0.59
25 3 0.11
ACGTcount: A:0.49, C:0.34, G:0.04, T:0.13
Consensus pattern (22 bp):
ACCCAAAACTCAAACTAAACTA
Found at i:363575 original size:10 final size:10
Alignment explanation
Indices: 363545--363586 Score: 57
Period size: 11 Copynumber: 3.9 Consensus size: 10
363535 AGGAGAGAAT
363545 TACGAAAAAATA
1 TACG-AAAAA-A
363557 TACGAAAAACA
1 TACGAAAAA-A
363568 TACGAAAAAA
1 TACGAAAAAA
363578 TACGAAAAA
1 TACGAAAAA
363587 GGAGCATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 10 0.34
11 15 0.52
12 4 0.14
ACGTcount: A:0.67, C:0.12, G:0.10, T:0.12
Consensus pattern (10 bp):
TACGAAAAAA
Found at i:363575 original size:23 final size:21
Alignment explanation
Indices: 363545--363586 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 21
363535 AGGAGAGAAT
363545 TACGAAAAAATATACGAAAAACA
1 TACG-AAAAA-ATACGAAAAACA
363568 TACGAAAAAATACGAAAAA
1 TACGAAAAAATACGAAAAA
363587 GGAGCATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.53
22 5 0.26
23 4 0.21
ACGTcount: A:0.67, C:0.12, G:0.10, T:0.12
Consensus pattern (21 bp):
TACGAAAAAATACGAAAAACA
Found at i:376520 original size:39 final size:39
Alignment explanation
Indices: 376450--376586 Score: 123
Period size: 39 Copynumber: 3.5 Consensus size: 39
376440 TACAACCCCA
* *
376450 AATCTTTTTACCCTGACTATGAGGCATATTGAGGCAATTC
1 AATC-TTTTACCCTAACTATGAGGCAGATTGAGGCAATTC
* * * *
376490 AATCTTTTACTCTAACTA-GAGGGCAGATTGAAGACCATTT
1 AATCTTTTACCCTAACTATGA-GGCAGATTG-AGGCAATTC
* * * * * *
376530 GATCTCTTACCCCAACCATGAGGCAGATTGAAGCAATCC
1 AATCTTTTACCCTAACTATGAGGCAGATTGAGGCAATTC
*
376569 AATCTTTTACCCTGACTA
1 AATCTTTTACCCTAACTA
376587 CAGGACAGAT
Statistics
Matches: 73, Mismatches: 21, Indels: 7
0.72 0.21 0.07
Matches are distributed among these distances:
38 2 0.03
39 37 0.51
40 32 0.44
41 2 0.03
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (39 bp):
AATCTTTTACCCTAACTATGAGGCAGATTGAGGCAATTC
Found at i:376551 original size:79 final size:79
Alignment explanation
Indices: 376457--376975 Score: 592
Period size: 79 Copynumber: 6.6 Consensus size: 79
376447 CCAAATCTTT
* * * * * * *
376457 TTACCCTGACTATGAGGCATATTGAGGCAATTCAATCTTTTACTCTAACTAGAGGGCAGATTGAA
1 TTACCCCGACCATGGGGCAGATTGAAGCAATTCAATCTTTTACCCTAACCAGAGGGCAGATTGAA
**
376522 GACCATTTGATCTC
66 GACCATCCGATCTC
* * * * * * * *
376536 TTACCCCAACCATGAGGCAGATTGAAGCAATCCAATCTTTTACCCTGACTACAGGACAGATTAAA
1 TTACCCCGACCATGGGGCAGATTGAAGCAATTCAATCTTTTACCCTAACCAGAGGGCAGATTGAA
*
376601 GATCATCCGATCTC
66 GACCATCCGATCTC
* * *
376615 TTACCCCGATCATGGGGTAGATTGAAGCAA-TCTAGTCTTTTACCCTAACCAGAGGGCAGATTGA
1 TTACCCCGACCATGGGGCAGATTGAAGCAATTC-AATCTTTTACCCTAACCAGAGGGCAGATTGA
*
376679 AGACCATCTGATCTC
65 AGACCATCCGATCTC
* * * * * * * * *
376694 TTACCGCGACCATGGGGTAGATTAAAGCAATCCAATCTTTTATCATAACCAGAAGACAGTTTGAA
1 TTACCCCGACCATGGGGCAGATTGAAGCAATTCAATCTTTTACCCTAACCAGAGGGCAGATTGAA
*
376759 GACCATTCGATCTC
66 GACCATCCGATCTC
** * * * * *
376773 TTACCCTAACCATGGGGGAAATTGAAG-AAATCAAACCTTTTACCCTAACCAGAGGGCAGATTAA
1 TTACCCCGACCATGGGGCAGATTGAAGCAATTC-AATCTTTTACCCTAACCAGAGGGCAGATTGA
*
376837 AGACCATCCAATCTC
65 AGACCATCCGATCTC
* *
376852 TTACCCCGACCATGGGGCAGATTAAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAA
1 TTACCCCGACCATGGGGCAGATTGAAGCAATTCAATCTTTTACCCTAACCAGAGGGCAGATTGAA
*
376917 GACCATCTGATCTC
66 GACCATCCGATCTC
* * *
376931 TTACCCCGACCATAGGGCAGATTGAAACAGTTCAATCTTTTACCC
1 TTACCCCGACCATGGGGCAGATTGAAGCAATTCAATCTTTTACCC
376976 CTAAAGCTAT
Statistics
Matches: 364, Mismatches: 72, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
78 4 0.01
79 356 0.98
80 4 0.01
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (79 bp):
TTACCCCGACCATGGGGCAGATTGAAGCAATTCAATCTTTTACCCTAACCAGAGGGCAGATTGAA
GACCATCCGATCTC
Found at i:376904 original size:237 final size:238
Alignment explanation
Indices: 376483--376973 Score: 700
Period size: 237 Copynumber: 2.1 Consensus size: 238
376473 GCATATTGAG
* * * *
376483 GCAATTCAATCTTTTACTCTAACTAGAGGGCAGATTGAAGACCATTTGATCTCTTACCCCAACCA
1 GCAATTCAATCTTTTACTCTAACCAGAAGACAGATTGAAGACCATTCGATCTCTTACCCCAACCA
* * * * * * * *
376548 TGAGGCAGATTGAAGCAATCCAATCTTTTACCCTGACTACAGGACAGATTAAAGATCATCCGATC
66 TGAGGCAAATTGAAGAAATCAAACCTTTTACCCTAACCACAGGACAGATTAAAGACCATCCAATC
* * * * *
376613 TCTTACCCCGATCATGGGGTAGATTGAAGCAATCTAGTCTTTTACCCTAACCAGAGGGCAGATTG
131 TCTTACCCCGACCATGGGGCAGATTAAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAGATTG
* * *
376678 AAGACCATCTGATCTCTTACCGCGACCATGGGGTAGATT-AAA
196 AAGACCATCTGATCTCTTACCCCGACCATAGGGCAGATTGAAA
* * *
376720 GCAATCCAATCTTTTA-TCATAACCAGAAGACAGTTTGAAGACCATTCGATCTCTTACCCTAACC
1 GCAATTCAATCTTTTACTC-TAACCAGAAGACAGATTGAAGACCATTCGATCTCTTACCCCAACC
* * * *
376784 ATGGGGGAAATTGAAGAAATCAAACCTTTTACCCTAACCAGAGGGCAGATTAAAGACCATCCAAT
65 ATGAGGCAAATTGAAGAAATCAAACCTTTTACCCTAACCACAGGACAGATTAAAGACCATCCAAT
376849 CTCTTACCCCGACCATGGGGCAGATTAAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAGATT
130 CTCTTACCCCGACCATGGGGCAGATTAAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAGATT
376914 GAAGACCATCTGATCTCTTACCCCGACCATAGGGCAGATTGAAA
195 GAAGACCATCTGATCTCTTACCCCGACCATAGGGCAGATTGAAA
*
376958 -CAGTTCAATCTTTTAC
1 GCAATTCAATCTTTTAC
376974 CCCTAAAGCT
Statistics
Matches: 222, Mismatches: 29, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
236 2 0.01
237 217 0.98
238 3 0.01
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (238 bp):
GCAATTCAATCTTTTACTCTAACCAGAAGACAGATTGAAGACCATTCGATCTCTTACCCCAACCA
TGAGGCAAATTGAAGAAATCAAACCTTTTACCCTAACCACAGGACAGATTAAAGACCATCCAATC
TCTTACCCCGACCATGGGGCAGATTAAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAGATTG
AAGACCATCTGATCTCTTACCCCGACCATAGGGCAGATTGAAA
Found at i:377584 original size:24 final size:22
Alignment explanation
Indices: 377548--377600 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 22
377538 AATTTCATTT
377548 ACCCAAAACCCAAACTAAACTA
1 ACCCAAAACCCAAACTAAACTA
*
377570 ACCCGAAAAGCCCAACCTAAACTA
1 ACCC-AAAA-CCCAAACTAAACTA
377594 AGCCCAA
1 A-CCCAA
377601 GTAGCCTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 4 0.15
23 4 0.15
24 16 0.59
25 3 0.11
ACGTcount: A:0.49, C:0.38, G:0.06, T:0.08
Consensus pattern (22 bp):
ACCCAAAACCCAAACTAAACTA
Found at i:378929 original size:22 final size:22
Alignment explanation
Indices: 378901--378947 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
378891 AACTTTGATA
378901 TATATATATATAATTTATTATG
1 TATATATATATAATTTATTATG
* * *
378923 TATATATGTATATTTTATTCTG
1 TATATATATATAATTTATTATG
378945 TAT
1 TAT
378948 GTTATATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.57
Consensus pattern (22 bp):
TATATATATATAATTTATTATG
Found at i:386388 original size:49 final size:49
Alignment explanation
Indices: 386306--386399 Score: 143
Period size: 49 Copynumber: 1.9 Consensus size: 49
386296 GGTGTAACTT
* *
386306 GAATTTAAATTACATATAAAACAATGAATATTCGTAACCATCAAGACTC
1 GAATCTAAATTACATATAAAACAATGAACATTCGTAACCATCAAGACTC
* * *
386355 GAATCTAAATTATATATGAAACAATGAACATTCGTGACCATCAAG
1 GAATCTAAATTACATATAAAACAATGAACATTCGTAACCATCAAG
386400 TTGATCAAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.28
Consensus pattern (49 bp):
GAATCTAAATTACATATAAAACAATGAACATTCGTAACCATCAAGACTC
Found at i:411673 original size:31 final size:31
Alignment explanation
Indices: 411635--411728 Score: 161
Period size: 31 Copynumber: 3.0 Consensus size: 31
411625 CTTTGATGCC
*
411635 TAATTTAAGCTTTTGTCACAATTTAAGGCCA
1 TAATTTAAGCTTTTGTTACAATTTAAGGCCA
*
411666 TAATTTAAGCTTTTGTTACAAGTTAAGGCCA
1 TAATTTAAGCTTTTGTTACAATTTAAGGCCA
*
411697 CAATTTAAGCTTTTGTTACAATTTAAGGCCA
1 TAATTTAAGCTTTTGTTACAATTTAAGGCCA
411728 T
1 T
411729 GCATTAATAA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 58 1.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (31 bp):
TAATTTAAGCTTTTGTTACAATTTAAGGCCA
Found at i:412015 original size:79 final size:78
Alignment explanation
Indices: 411870--412016 Score: 215
Period size: 79 Copynumber: 1.9 Consensus size: 78
411860 GGTTAACAAC
* *
411870 AGAAATTGAATAAATTCTGTTGAACAATAGGAATAAATCTTGAAACAAAATTATTTTAATTTATT
1 AGAAATTGAATAAATTCTGTTGAACAATAGGAATAAATCTTGAAACAAAATTACTTCAATTTATT
411935 TCTGTTTGAAAAT
66 TCTGTTTGAAAAT
* * * *
411948 AGAAATTTGAATGAATTTTGTTGAACGATATGAATAAATCTTGAAACAAAATT-CTTCAATTTAA
1 AGAAA-TTGAATAAATTCTGTTGAACAATAGGAATAAATCTTGAAACAAAATTACTTCAATTT-A
412012 TTTCT
64 TTTCT
412017 ATTTACTAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
78 12 0.20
79 49 0.80
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (78 bp):
AGAAATTGAATAAATTCTGTTGAACAATAGGAATAAATCTTGAAACAAAATTACTTCAATTTATT
TCTGTTTGAAAAT
Found at i:412446 original size:15 final size:14
Alignment explanation
Indices: 412411--412444 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
412401 AAACAAGTTT
412411 GAAAAATTTGCAAA
1 GAAAAATTTGCAAA
412425 GAAAAATTT-CAAGA
1 GAAAAATTTGCAA-A
412439 GAAAAA
1 GAAAAA
412445 ATAATTGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 3 0.16
14 16 0.84
ACGTcount: A:0.62, C:0.06, G:0.15, T:0.18
Consensus pattern (14 bp):
GAAAAATTTGCAAA
Found at i:412590 original size:15 final size:15
Alignment explanation
Indices: 412565--412611 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
412555 CCATTAAATC
412565 AATTT-AATCAATTT
1 AATTTAAATCAATTT
*
412579 AATTTAAATCAATCT
1 AATTTAAATCAATTT
*
412594 AAATTAAATCAATTT
1 AATTTAAATCAATTT
412609 AAT
1 AAT
412612 ATTTGTCCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 5 0.18
15 23 0.82
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTTAAATCAATTT
Found at i:416439 original size:12 final size:12
Alignment explanation
Indices: 416422--416450 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
416412 TGCTAACGAA
416422 TTTATGGCTATT
1 TTTATGGCTATT
416434 TTTATGGCTATT
1 TTTATGGCTATT
416446 TTTAT
1 TTTAT
416451 TTGGAAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.07, G:0.14, T:0.62
Consensus pattern (12 bp):
TTTATGGCTATT
Found at i:420501 original size:20 final size:20
Alignment explanation
Indices: 420464--420501 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
420454 CCTAAAAATC
* *
420464 TTTCACTTTTCCATTTCTCA
1 TTTCACTTTTCAAGTTCTCA
420484 TTTCACTTTTCAAGTTCT
1 TTTCACTTTTCAAGTTCT
420502 ATCGATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.26, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTCACTTTTCAAGTTCTCA
Found at i:422097 original size:17 final size:18
Alignment explanation
Indices: 422054--422091 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
422044 GTAACATTCA
422054 TTTTGTTTTATTTTTGCC
1 TTTTGTTTTATTTTTGCC
422072 TTTTGTTTTA-TTTTGCC
1 TTTTGTTTTATTTTTGCC
422089 TTT
1 TTT
422092 ATTTTTGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.05, C:0.11, G:0.11, T:0.74
Consensus pattern (18 bp):
TTTTGTTTTATTTTTGCC
Found at i:430064 original size:29 final size:29
Alignment explanation
Indices: 430030--430085 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
430020 AAACAAGACT
430030 GACCTTCTCAACAGTTGTCTGAAAACTGA
1 GACCTTCTCAACAGTTGTCTGAAAACTGA
*
430059 GACCTTCTCAACAGTTGTCTTAAAACT
1 GACCTTCTCAACAGTTGTCTGAAAACT
430086 AAGTTCATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.30
Consensus pattern (29 bp):
GACCTTCTCAACAGTTGTCTGAAAACTGA
Found at i:430205 original size:13 final size:13
Alignment explanation
Indices: 430187--430211 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
430177 TTGTCTTATG
430187 CACATCCTTATCC
1 CACATCCTTATCC
430200 CACATCCTTATC
1 CACATCCTTATC
430212 TGGTGGTAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.44, G:0.00, T:0.32
Consensus pattern (13 bp):
CACATCCTTATCC
Found at i:432394 original size:74 final size:74
Alignment explanation
Indices: 432231--432446 Score: 263
Period size: 74 Copynumber: 2.9 Consensus size: 74
432221 GGGCCCAGCA
* * * * * *
432231 CTAGTCGGATAAACCGACGATATAAAATGTGAGCCTAGCTCTAGTTAGATATACCAAAAATATTT
1 CTAGTCGGATAAACCTACGATATAAGAT-TGAGCCTAGCTCTAGTTAGATAAACCGACAA-ATGT
***
432296 TGCACCTTGTG
64 TGCACCCAATG
* **
432307 CTAGTCAGATAAACCTACGATATAAGATTGAGCCTAGCTCTAGTTAGATAAATTGACAAATGTTG
1 CTAGTCGGATAAACCTACGATATAAGATTGAGCCTAGCTCTAGTTAGATAAACCGACAAATGTTG
432372 CACCCAATG
66 CACCCAATG
* * *
432381 CTAGTCGGATAAA-CTGACAATATAAGATTGAGCCCAGCTCTAGTCAGATAAACCGACAAATGTT
1 CTAGTCGGATAAACCT-ACGATATAAGATTGAGCCTAGCTCTAGTTAGATAAACCGACAAATGTT
432445 GC
65 GC
432447 GCTAGCGCTA
Statistics
Matches: 121, Mismatches: 18, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
73 2 0.02
74 68 0.56
75 26 0.21
76 25 0.21
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (74 bp):
CTAGTCGGATAAACCTACGATATAAGATTGAGCCTAGCTCTAGTTAGATAAACCGACAAATGTTG
CACCCAATG
Found at i:432431 original size:39 final size:39
Alignment explanation
Indices: 432307--432510 Score: 146
Period size: 39 Copynumber: 5.4 Consensus size: 39
432297 GCACCTTGTG
* *
432307 CTAGTCAGATAAACCT-ACGATATAAGATTGAGCCTAGCT
1 CTAGTCAGATAAA-CTGACAATATAAGATTGAGCCCAGCT
* * *
432346 CTAGTTAGATAAATTGACAA-AT--G-TTGCA-CCCA-AT
1 CTAGTCAGATAAACTGACAATATAAGATTG-AGCCCAGCT
*
432380 GCTAGTCGGATAAACTGACAATATAAGATTGAGCCCAGCT
1 -CTAGTCAGATAAACTGACAATATAAGATTGAGCCCAGCT
* * * *
432420 CTAGTCAGATAAACCGACAA-AT--G-TTGCG-CTAGCG
1 CTAGTCAGATAAACTGACAATATAAGATTGAGCCCAGCT
* * * *
432454 CTAGTCGGAT-AACTGACGAATATAAGAAGTGTGCCCAGCA
1 CTAGTCAGATAAACTGAC-AATATAAG-ATTGAGCCCAGCT
432494 CTAGTCAGATAAACTGA
1 CTAGTCAGATAAACTGA
432511 AGAAGGTTAC
Statistics
Matches: 127, Mismatches: 21, Indels: 32
0.71 0.12 0.18
Matches are distributed among these distances:
33 6 0.05
34 16 0.13
35 29 0.23
36 5 0.04
37 1 0.01
38 7 0.06
39 43 0.34
40 14 0.11
41 6 0.05
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.24
Consensus pattern (39 bp):
CTAGTCAGATAAACTGACAATATAAGATTGAGCCCAGCT
Found at i:432490 original size:74 final size:74
Alignment explanation
Indices: 432346--432585 Score: 263
Period size: 74 Copynumber: 3.2 Consensus size: 74
432336 GAGCCTAGCT
* * * * *
432346 CTAGTTAGATAAATTGACAAATGTTGCACCCAATGCTAGTCGGATAAACTGAC-AATATAAG-AT
1 CTAGTCAGATAAACTGACAAATGTTGC-GCCAACGCTAGTCGGAT-AACTGACGAATATAAGAAG
* *
432409 TGAGCCCAGCT
64 TGTGCCCAGCA
* * *
432420 CTAGTCAGATAAACCGACAAATGTTGCGCTAGCGCTAGTCGGATAACTGACGAATATAAGAAGTG
1 CTAGTCAGATAAACTGACAAATGTTGCGCCAACGCTAGTCGGATAACTGACGAATATAAGAAGTG
432485 TGCCCAGCA
66 TGCCCAGCA
* * * *
432494 CTAGTCAGATAAACTGA-AGAAGGTTACGCCCAACGCTAGTCAGATAAC-AACGAATATAAGAAG
1 CTAGTCAGATAAACTGACA-AATGTTGCG-CCAACGCTAGTCGGATAACTGACGAATATAAGAAG
* *
432557 TGTGCCTAACA
64 TGTGCCCAGCA
*
432568 CTAGTCAGATAAATTGAC
1 CTAGTCAGATAAACTGAC
432586 GAAGATTGTG
Statistics
Matches: 141, Mismatches: 20, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
72 7 0.05
73 22 0.16
74 96 0.68
75 16 0.11
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (74 bp):
CTAGTCAGATAAACTGACAAATGTTGCGCCAACGCTAGTCGGATAACTGACGAATATAAGAAGTG
TGCCCAGCA
Found at i:432575 original size:39 final size:39
Alignment explanation
Indices: 432454--432579 Score: 113
Period size: 39 Copynumber: 3.3 Consensus size: 39
432444 TGCGCTAGCG
* * *
432454 CTAGTCGGATAACTGACGAATATAAGAAGTGTGCCCAGCA
1 CTAGTCAGATAAC-AACGAATATAAGAAGTGTGCCCAACA
* *
432494 CTAGTCAGAT-A-AAC---T-GAAGAAG-GTTACGCCCAACG
1 CTAGTCAGATAACAACGAATATAAGAAGTG-T--GCCCAACA
*
432529 CTAGTCAGATAACAACGAATATAAGAAGTGTGCCTAACA
1 CTAGTCAGATAACAACGAATATAAGAAGTGTGCCCAACA
432568 CTAGTCAGATAA
1 CTAGTCAGATAA
432580 ATTGACGAAG
Statistics
Matches: 68, Mismatches: 8, Indels: 21
0.70 0.08 0.22
Matches are distributed among these distances:
32 1 0.01
33 7 0.10
34 1 0.01
35 16 0.24
36 1 0.01
37 5 0.07
39 19 0.28
40 10 0.15
41 7 0.10
42 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (39 bp):
CTAGTCAGATAACAACGAATATAAGAAGTGTGCCCAACA
Found at i:432606 original size:74 final size:75
Alignment explanation
Indices: 432380--432608 Score: 209
Period size: 74 Copynumber: 3.1 Consensus size: 75
432370 TGCACCCAAT
* * * * * * *
432380 GCTAGTCGGATAAACTGAC-AATATAAG-ATTGAGCCCAGCTCTAGTCAGATAAACCGACA-AAT
1 GCTAGTCAGAT-AACTAACGAATATAAGAAGTGTGCCCAACACTAGTCAGATAAACTGA-AGAA-
*
432442 G-TTGCG-CTAGC
63 GATTACGCCTAGC
* * * *
432453 GCTAGTCGGATAACTGACGAATATAAGAAGTGTGCCCAGCACTAGTCAGATAAACTGAAGAAGGT
1 GCTAGTCAGATAACTAACGAATATAAGAAGTGTGCCCAACACTAGTCAGATAAACTGAAGAAGAT
* *
432518 TACGCCCAAC
66 TACGCCTAGC
* * *
432528 GCTAGTCAGATAAC-AACGAATATAAGAAGTGTGCCTAACACTAGTCAGATAAATTGACGAAGAT
1 GCTAGTCAGATAACTAACGAATATAAGAAGTGTGCCCAACACTAGTCAGATAAACTGAAGAAGAT
** *
432592 TGTGCCTAGT
66 TACGCCTAGC
432602 GCTAGTC
1 GCTAGTC
432609 GAATAATTGA
Statistics
Matches: 132, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
72 7 0.05
73 21 0.16
74 88 0.67
75 16 0.12
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (75 bp):
GCTAGTCAGATAACTAACGAATATAAGAAGTGTGCCCAACACTAGTCAGATAAACTGAAGAAGAT
TACGCCTAGC
Found at i:434562 original size:30 final size:31
Alignment explanation
Indices: 434528--434599 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
434518 GTTACATTTA
* * *
434528 ACAAAACAGTCACTCAA-CT-TTGAAAATGTG
1 ACAAAACAGTCACTAAAGATATCGAAAA-GTG
*
434558 ACAAAACAATCACTAAAGATATCGAAAAGTG
1 ACAAAACAGTCACTAAAGATATCGAAAAGTG
434589 ACAAAACAGTC
1 ACAAAACAGTC
434600 CTATTGGCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 15 0.43
31 14 0.40
32 6 0.17
ACGTcount: A:0.50, C:0.19, G:0.12, T:0.18
Consensus pattern (31 bp):
ACAAAACAGTCACTAAAGATATCGAAAAGTG
Found at i:435928 original size:12 final size:12
Alignment explanation
Indices: 435911--435935 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
435901 TGACCCTAAT
435911 AACACTCCGTAA
1 AACACTCCGTAA
435923 AACACTCCGTAA
1 AACACTCCGTAA
435935 A
1 A
435936 TATTTAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.32, G:0.08, T:0.16
Consensus pattern (12 bp):
AACACTCCGTAA
Found at i:436052 original size:166 final size:166
Alignment explanation
Indices: 435778--436089 Score: 624
Period size: 166 Copynumber: 1.9 Consensus size: 166
435768 CTCTTAATTA
435778 ATGCTTTTATATCTATTTAATTCAAATAAATCTGCAGTGAATAAGTTTTATCTCTTTTACAATTT
1 ATGCTTTTATATCTATTTAATTCAAATAAATCTGCAGTGAATAAGTTTTATCTCTTTTACAATTT
435843 AGCCATTTTTAACTAATTAAATATTTAAAAGAAAAAAGTTCTTAATCAAACTTTCATATGACCCT
66 AGCCATTTTTAACTAATTAAATATTTAAAAGAAAAAAGTTCTTAATCAAACTTTCATATGACCCT
435908 AATAACACTCCGTAAAACACTCCGTAAATATTTAAT
131 AATAACACTCCGTAAAACACTCCGTAAATATTTAAT
435944 ATGCTTTTATATCTATTTAATTCAAATAAATCTGCAGTGAATAAGTTTTATCTCTTTTACAATTT
1 ATGCTTTTATATCTATTTAATTCAAATAAATCTGCAGTGAATAAGTTTTATCTCTTTTACAATTT
436009 AGCCATTTTTAACTAATTAAATATTTAAAAGAAAAAAGTTCTTAATCAAACTTTCATATGACCCT
66 AGCCATTTTTAACTAATTAAATATTTAAAAGAAAAAAGTTCTTAATCAAACTTTCATATGACCCT
436074 AATAACACTCCGTAAA
131 AATAACACTCCGTAAA
436090 TATTTAATAA
Statistics
Matches: 146, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
166 146 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (166 bp):
ATGCTTTTATATCTATTTAATTCAAATAAATCTGCAGTGAATAAGTTTTATCTCTTTTACAATTT
AGCCATTTTTAACTAATTAAATATTTAAAAGAAAAAAGTTCTTAATCAAACTTTCATATGACCCT
AATAACACTCCGTAAAACACTCCGTAAATATTTAAT
Found at i:441501 original size:15 final size:16
Alignment explanation
Indices: 441479--441517 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
441469 TTTTCTTCTC
441479 TTTT-TTTTTCTCAA-
1 TTTTCTTTTTCTCAAT
*
441493 TTTTCTTTTTTTCAAT
1 TTTTCTTTTTCTCAAT
441509 TTTTCTTTT
1 TTTTCTTTT
441518 CGACTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.18
15 9 0.41
16 9 0.41
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTCTTTTTCTCAAT
Found at i:441501 original size:16 final size:16
Alignment explanation
Indices: 441482--441517 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
441472 TCTTCTCTTT
441482 TTTTTTCTCAA-TTTTC
1 TTTTTT-TCAATTTTTC
441498 TTTTTTTCAATTTTTC
1 TTTTTTTCAATTTTTC
441514 TTTT
1 TTTT
441518 CGACTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTTTCAATTTTTC
Found at i:442472 original size:6 final size:6
Alignment explanation
Indices: 442456--442533 Score: 59
Period size: 6 Copynumber: 12.8 Consensus size: 6
442446 GCACAATAAC
* * * * *
442456 ATAAAA TTAAAA AT-AAA ATAAAA ATGAAA ATGAAA ATGAAA ATGAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
* * *
442503 CTGGAAA ATGAAAA ATGAAA ATAAAA ATAAA
1 AT-AAAA AT-AAAA ATAAAA ATAAAA ATAAA
442534 TGTACTAATT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
5 5 0.08
6 46 0.74
7 11 0.18
ACGTcount: A:0.71, C:0.01, G:0.10, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:442476 original size:17 final size:17
Alignment explanation
Indices: 442450--442498 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
442440 AATAGTGCAC
*
442450 AATAACATAAAATTAAA
1 AATAAAATAAAATTAAA
* *
442467 AATAAAATAAAAATGAA
1 AATAAAATAAAATTAAA
442484 AATGAAAATGAAAAT
1 AAT-AAAAT-AAAAT
442499 GAAACTGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 17 0.65
18 5 0.19
19 4 0.15
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.20
Consensus pattern (17 bp):
AATAAAATAAAATTAAA
Found at i:442485 original size:7 final size:6
Alignment explanation
Indices: 442465--442530 Score: 80
Period size: 6 Copynumber: 10.8 Consensus size: 6
442455 CATAAAATTA
* *
442465 AAAAT- AAAATA AAAATG AAAATG AAAATG AAAATG AAACTGG AAAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAAT-G AAAATG
*
442513 AAAAATG AAAATA AAAAT
1 -AAAATG AAAATG AAAAT
442531 AAATGTACTA
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
5 5 0.09
6 38 0.70
7 11 0.20
ACGTcount: A:0.70, C:0.02, G:0.12, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:446320 original size:28 final size:28
Alignment explanation
Indices: 446280--446335 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
446270 CTGGTAACAG
*
446280 GCATGAACTTTGGGTCAACAGGGAGTAA
1 GCATGAACTTTGGATCAACAGGGAGTAA
*
446308 GCATGACCTTTGGATCAACAGGGAGTAA
1 GCATGAACTTTGGATCAACAGGGAGTAA
446336 ATCAGATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.32, C:0.16, G:0.30, T:0.21
Consensus pattern (28 bp):
GCATGAACTTTGGATCAACAGGGAGTAA
Found at i:447093 original size:21 final size:21
Alignment explanation
Indices: 447051--447103 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
447041 GGAGTTTTTC
* *
447051 GTAT-GGTAGAAGCATGATTT
1 GTATAGGTAGAAGCATCACTT
* * *
447071 GTTTCGGTAGAAGCTTCACTT
1 GTATAGGTAGAAGCATCACTT
447092 GTATAGGTAGAA
1 GTATAGGTAGAA
447104 CTTTCATAGG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.34
Consensus pattern (21 bp):
GTATAGGTAGAAGCATCACTT
Found at i:448789 original size:15 final size:14
Alignment explanation
Indices: 448779--448810 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
448769 TAAAAAGTGA
448779 AAAAATTAAAATAT
1 AAAAATTAAAATAT
448793 AAAAATT-AAAT-T
1 AAAAATTAAAATAT
448805 AAAAAT
1 AAAAAT
448811 GCAAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 4 0.22
14 7 0.39
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAAATTAAAATAT
Found at i:451273 original size:25 final size:23
Alignment explanation
Indices: 451245--451290 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
451235 GTTGAATCCA
451245 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
451270 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
451291 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:455314 original size:22 final size:23
Alignment explanation
Indices: 455278--455323 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
455268 TTAGCAAAAA
455278 TGAGAGAAAGAGAGAAAGA-ATT
1 TGAGAGAAAGAGAGAAAGAGATT
*
455300 TGAGAG-AAGATGAGATAGAGATT
1 TGAGAGAAAGA-GAGAAAGAGATT
455323 T
1 T
455324 AGAATTCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 13 0.62
23 4 0.19
ACGTcount: A:0.48, C:0.00, G:0.33, T:0.20
Consensus pattern (23 bp):
TGAGAGAAAGAGAGAAAGAGATT
Found at i:457613 original size:62 final size:59
Alignment explanation
Indices: 457537--457656 Score: 168
Period size: 62 Copynumber: 2.0 Consensus size: 59
457527 GTATTTTATT
* * *
457537 AATTTAATATTAAATTTAATTTAATGTTTATCTTCTAGAAAAATATTTTATTAATTTAATAA
1 AATTTAATATTAAATTTAATTTAATATTTATC-T-T-GAAAAATATTATATTAATATAATAA
* *
457599 AATTTAATATTAAATTTAATTTGATATTTATCTTGATAAATATTATATTAATATAATA
1 AATTTAATATTAAATTTAATTTAATATTTATCTTGAAAAATATTATATTAATATAATA
457657 TTAAAGTGAT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
59 21 0.40
60 1 0.02
61 1 0.02
62 30 0.57
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (59 bp):
AATTTAATATTAAATTTAATTTAATATTTATCTTGAAAAATATTATATTAATATAATAA
Found at i:459757 original size:24 final size:23
Alignment explanation
Indices: 459730--459789 Score: 84
Period size: 24 Copynumber: 2.6 Consensus size: 23
459720 TCATTAACAT
459730 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTA-A
* *
459754 TGTTCATGAACATGTTCATTTAA
1 TGTTCGTGAACATGTTCAATTAA
*
459777 TATTCGTGAACAT
1 TGTTCGTGAACAT
459790 ATGCGATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 12 0.38
24 20 0.62
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:461422 original size:21 final size:21
Alignment explanation
Indices: 461374--461426 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
461364 CTATAATTAT
*
461374 TAATTTAAAATACCCTAAACTC
1 TAATTTAAAATA-CCTAAACCC
*
461396 TTATTTAAAATA-CTAAAACCC
1 TAATTTAAAATACCT-AAACCC
461417 TAATTTAAAA
1 TAATTTAAAA
461427 ACCCCAACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.07
21 14 0.52
22 11 0.41
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (21 bp):
TAATTTAAAATACCTAAACCC
Found at i:461635 original size:38 final size:38
Alignment explanation
Indices: 461593--461676 Score: 132
Period size: 38 Copynumber: 2.2 Consensus size: 38
461583 TATAATATTC
461593 TTTAAAATTTAAATACTTCTTTAATTTTTATATAAAAT
1 TTTAAAATTTAAATACTTCTTTAATTTTTATATAAAAT
* * *
461631 TTTAAAAGTTAAATACTTTTTTAATTTTTATATAATAT
1 TTTAAAATTTAAATACTTCTTTAATTTTTATATAAAAT
*
461669 TTTGAAAT
1 TTTAAAAT
461677 CTTTAATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (38 bp):
TTTAAAATTTAAATACTTCTTTAATTTTTATATAAAAT
Found at i:461671 original size:19 final size:19
Alignment explanation
Indices: 461612--461671 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 19
461602 TAAATACTTC
*
461612 TTTAATTTTTATATAAAAT
1 TTTAATTTTTATATAATAT
*** * * *
461631 TTTAAAAGTTAAATACTTT
1 TTTAATTTTTATATAATAT
461650 TTTAATTTTTATATAATAT
1 TTTAATTTTTATATAATAT
461669 TTT
1 TTT
461672 GAAATCTTTA
Statistics
Matches: 28, Mismatches: 13, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTAATTTTTATATAATAT
Found at i:465399 original size:34 final size:34
Alignment explanation
Indices: 465361--465429 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
465351 ATTTGTTTAA
465361 AATATACCAATCAAATAAGTCAAATTATAATGCT
1 AATATACCAATCAAATAAGTCAAATTATAATGCT
465395 AATATACCAATCAAATAAGTCAAATTATAATGCT
1 AATATACCAATCAAATAAGTCAAATTATAATGCT
465429 A
1 A
465430 TGTTAGCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (34 bp):
AATATACCAATCAAATAAGTCAAATTATAATGCT
Found at i:466535 original size:12 final size:12
Alignment explanation
Indices: 466518--466542 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
466508 TTTTATTAAG
466518 AGTTATAGTTTT
1 AGTTATAGTTTT
466530 AGTTATAGTTTT
1 AGTTATAGTTTT
466542 A
1 A
466543 TTAGGACTCT
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:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (12 bp):
AGTTATAGTTTT
Found at i:478409 original size:7 final size:7
Alignment explanation
Indices: 478397--478430 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
478387 CAAGATGAAC
478397 GAACAAA
1 GAACAAA
478404 GAACAAA
1 GAACAAA
*
478411 GAACGAA
1 GAACAAA
478418 GAACAAA
1 GAACAAA
478425 G-ACAAA
1 GAACAAA
478431 AAAAACTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.68, C:0.15, G:0.18, T:0.00
Consensus pattern (7 bp):
GAACAAA
Found at i:483168 original size:7 final size:7
Alignment explanation
Indices: 483156--483185 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
483146 AAATCAAATA
483156 TGTTGAG
1 TGTTGAG
483163 TGTTGAG
1 TGTTGAG
483170 TGTTGAG
1 TGTTGAG
*
483177 TGCTGAG
1 TGTTGAG
483184 TG
1 TG
483186 CTGAATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.13, C:0.03, G:0.43, T:0.40
Consensus pattern (7 bp):
TGTTGAG
Found at i:489229 original size:17 final size:18
Alignment explanation
Indices: 489207--489245 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
489197 GTTTTCCATA
*
489207 CATTTT-TATTGTTATTG
1 CATTTTCTATTGTCATTG
*
489224 CATTTTCTTTTGTCATTG
1 CATTTTCTATTGTCATTG
489242 CATT
1 CATT
489246 CATTTTGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.15, C:0.13, G:0.10, T:0.62
Consensus pattern (18 bp):
CATTTTCTATTGTCATTG
Found at i:489850 original size:12 final size:11
Alignment explanation
Indices: 489829--489877 Score: 55
Period size: 12 Copynumber: 4.3 Consensus size: 11
489819 TAGTCACTTG
489829 AAAAAGA-AAA
1 AAAAAGAGAAA
*
489839 AAAATGAGAAA
1 AAAAAGAGAAA
489850 AAGAAAGAGAAA
1 AA-AAAGAGAAA
489862 AGAAAAGAAGAAA
1 A-AAAAG-AGAAA
489875 AAA
1 AAA
489878 GATTTTATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 6 0.18
11 5 0.15
12 15 0.45
13 7 0.21
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (11 bp):
AAAAAGAGAAA
Found at i:489860 original size:24 final size:25
Alignment explanation
Indices: 489828--489876 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
489818 TTAGTCACTT
489828 GAAAAAGAAAA-AAAATG-AGAAAAA
1 GAAAAAGAAAAGAAAA-GAAGAAAAA
*
489852 GAAAGAGAAAAGAAAAGAAGAAAAA
1 GAAAAAGAAAAGAAAAGAAGAAAAA
489877 AGATTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (25 bp):
GAAAAAGAAAAGAAAAGAAGAAAAA
Found at i:489877 original size:15 final size:16
Alignment explanation
Indices: 489830--489879 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 16
489820 AGTCACTTGA
489830 AAAAGAAA-AAAAATGAG
1 AAAAGAAAGAAAAA--AG
*
489847 AAAAAGAAAGAGAAAAG
1 -AAAAGAAAGAAAAAAG
489864 AAAAG-AAGAAAAAAG
1 AAAAGAAAGAAAAAAG
489879 A
1 A
489880 TTTTATTGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 10 0.34
16 5 0.17
17 2 0.07
18 8 0.28
19 4 0.14
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (16 bp):
AAAAGAAAGAAAAAAG
Found at i:502962 original size:60 final size:60
Alignment explanation
Indices: 502866--503045 Score: 333
Period size: 60 Copynumber: 3.0 Consensus size: 60
502856 TGATTGCGTG
502866 CAAAATTATTGTAAGAGTTGCCATAAGAATTGCTATGGATATTATTGACATAGAAGGCAT
1 CAAAATTATTGTAAGAGTTGCCATAAGAATTGCTATGGATATTATTGACATAGAAGGCAT
* *
502926 CAGAATTATTGTAAGAGTTTCCATAAGAATTGCTATGGATATTATTGACATAGAAGGCAT
1 CAAAATTATTGTAAGAGTTGCCATAAGAATTGCTATGGATATTATTGACATAGAAGGCAT
*
502986 CAAAATTATTGTAAGAGTTGCCATAAGAATTGCTATGAATATTATTGACATAGAAGGCAT
1 CAAAATTATTGTAAGAGTTGCCATAAGAATTGCTATGGATATTATTGACATAGAAGGCAT
503046 TCTCTGCATG
Statistics
Matches: 115, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 115 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.32
Consensus pattern (60 bp):
CAAAATTATTGTAAGAGTTGCCATAAGAATTGCTATGGATATTATTGACATAGAAGGCAT
Found at i:516190 original size:3 final size:3
Alignment explanation
Indices: 516182--516209 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
516172 ATAGCCTAAC
516182 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
516210 GAAAATAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:522609 original size:27 final size:27
Alignment explanation
Indices: 522556--522613 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
522546 TTGCAAGTTT
* * *
522556 GGTTTGCTAGTTTATTTGTCGAGTTGG
1 GGTTTGCCAGTTTATTTGGCGAATTGG
* *
522583 GGTTTGCCAGTTTGTTTGGGGAATTGG
1 GGTTTGCCAGTTTATTTGGCGAATTGG
522610 GGTT
1 GGTT
522614 CACCTATTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.10, C:0.07, G:0.38, T:0.45
Consensus pattern (27 bp):
GGTTTGCCAGTTTATTTGGCGAATTGG
Found at i:525156 original size:39 final size:39
Alignment explanation
Indices: 525113--525193 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
525103 TCGACATGTG
525113 ATTCCAAATAAATATTCATTATTTAATATTTACGAGATC
1 ATTCCAAATAAATATTCATTATTTAATATTTACGAGATC
525152 ATTCCAAATAAATATTCATTATTTAATATTTACGAGATC
1 ATTCCAAATAAATATTCATTATTTAATATTTACGAGATC
525191 ATT
1 ATT
525194 AGTGTCATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.42
Consensus pattern (39 bp):
ATTCCAAATAAATATTCATTATTTAATATTTACGAGATC
Found at i:527950 original size:16 final size:16
Alignment explanation
Indices: 527931--527961 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
527921 GTAATTTTGA
*
527931 TGTTTAAGGAGTAAAT
1 TGTTTAAAGAGTAAAT
527947 TGTTTAAAGAGTAAA
1 TGTTTAAAGAGTAAA
527962 ATTTTGTGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TGTTTAAAGAGTAAAT
Found at i:528927 original size:19 final size:19
Alignment explanation
Indices: 528903--528942 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
528893 ATGATTATAG
528903 TAAGTTTTGAATTGAAGTA
1 TAAGTTTTGAATTGAAGTA
528922 TAAGTTTTGAATTGAAGTA
1 TAAGTTTTGAATTGAAGTA
528941 TA
1 TA
528943 TGAGCTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.20, T:0.42
Consensus pattern (19 bp):
TAAGTTTTGAATTGAAGTA
Found at i:530331 original size:425 final size:425
Alignment explanation
Indices: 529535--530386 Score: 1616
Period size: 425 Copynumber: 2.0 Consensus size: 425
529525 CCAATATGGC
529535 AATTAAACCATGGTCAAAAAGTCCAAGCGGTGGTGGATATGATTGATTCCATTAACTTTTGGGTT
1 AATTAAACCATGGTCAAAAAGTCCAAGCGGTGGTGGATATGATTGATTCCATTAACTTTTGGGTT
* *
529600 ATTTATTCATTTAGTCCTAATTAGTTTAGGACTAAATTGAAAAAAAGTTTGTTTAATCGAAGTTT
66 ATTTATTCATTTAGTCCTAATTAGTTTAGAACTAAATTGAAAAAAAGTTTGTTTAATCAAAGTTT
529665 AATATAATTGAAGGATCAATTGTGTAATTGGACCCTCCTTAAATGGCCTAATAATAGAAATGATG
131 AATATAATTGAAGGATCAATTGTGTAATTGGACCCTCCTTAAATGGCCTAATAATAGAAATGATG
529730 TGGAAATCTTTAGATTTTTGTAAATTACTATTAAATCCTAATTAAATGAGGATTTACTAAGTAGT
196 TGGAAATCTTTAGATTTTTGTAAATTACTATTAAATCCTAATTAAATGAGGATTTACTAAGTAGT
529795 TTATTTTTTTGTACGATCGAAAATGGTGATTTTGAGGTCACGACTTTGATATGTCAGGCCCTAAA
261 TTATTTTTTTGTACGATCGAAAATGGTGATTTTGAGGTCACGACTTTGATATGTCAGGCCCTAAA
529860 TATTATTTATTAATATTTATGAGGTCATTAGTATTTTATTAAATTTGGTTATGAAATTTAATCGT
326 TATTATTTATTAATATTTATGAGGTCATTAGTATTTTATTAAATTTGGTTATGAAATTTAATCGT
*
529925 TTAGATAGTTAATTAAATGAAAAGGATTAAATTGT
391 TTAGATAGTTAATTAAATGAAAAGGATTAAATCGT
*
529960 AATTAAACCATGGTCAAAAAGTCCAAGCGGTGGTGGATATGATTGATTCCATTAACTTTTTGGTT
1 AATTAAACCATGGTCAAAAAGTCCAAGCGGTGGTGGATATGATTGATTCCATTAACTTTTGGGTT
*
530025 ATTTATTCATTTAGTCCTAATTAGTTTAGAACTAAATTGAAAACAAGTTTGTTTAATCAAAGTTT
66 ATTTATTCATTTAGTCCTAATTAGTTTAGAACTAAATTGAAAAAAAGTTTGTTTAATCAAAGTTT
530090 AATATAATTGAAGGATCAATTGTGTAATTGGACCCTCCTTAAATGGCCTAATAATAGAAATGATG
131 AATATAATTGAAGGATCAATTGTGTAATTGGACCCTCCTTAAATGGCCTAATAATAGAAATGATG
530155 TGGAAATCTTTAGATTTTTGTAAATTACTATTAAATCCTAATTAAATGAGGATTTACTAAGTAGT
196 TGGAAATCTTTAGATTTTTGTAAATTACTATTAAATCCTAATTAAATGAGGATTTACTAAGTAGT
**
530220 TTA-TTTTTTGTACGATCGGGAATGGTGATTTTGAGGTCACGACTTTGATATGTCAGGCCCTAAA
261 TTATTTTTTTGTACGATCGAAAATGGTGATTTTGAGGTCACGACTTTGATATGTCAGGCCCTAAA
*
530284 TATTATTTCTTAATATTTATGAGGTCATTAGTATTTTATTAAAATTTGGTTATGAAATTTAATCG
326 TATTATTTATTAATATTTATGAGGTCATTAGTATTTTATT-AAATTTGGTTATGAAATTTAATCG
530349 TTTAGATAGTTAATTAAATGAAAAGGATTAAATCGT
390 TTTAGATAGTTAATTAAATGAAAAGGATTAAATCGT
530385 AA
1 AA
530387 AAGGTTTAAA
Statistics
Matches: 418, Mismatches: 8, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
424 98 0.23
425 320 0.77
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.39
Consensus pattern (425 bp):
AATTAAACCATGGTCAAAAAGTCCAAGCGGTGGTGGATATGATTGATTCCATTAACTTTTGGGTT
ATTTATTCATTTAGTCCTAATTAGTTTAGAACTAAATTGAAAAAAAGTTTGTTTAATCAAAGTTT
AATATAATTGAAGGATCAATTGTGTAATTGGACCCTCCTTAAATGGCCTAATAATAGAAATGATG
TGGAAATCTTTAGATTTTTGTAAATTACTATTAAATCCTAATTAAATGAGGATTTACTAAGTAGT
TTATTTTTTTGTACGATCGAAAATGGTGATTTTGAGGTCACGACTTTGATATGTCAGGCCCTAAA
TATTATTTATTAATATTTATGAGGTCATTAGTATTTTATTAAATTTGGTTATGAAATTTAATCGT
TTAGATAGTTAATTAAATGAAAAGGATTAAATCGT
Found at i:531681 original size:24 final size:24
Alignment explanation
Indices: 531654--531717 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
531644 AACTCTGTAT
*
531654 GGCTCGAATGAGCTAACTTATCTA
1 GGCTCGAATGAGCTAACCTATCTA
* * *
531678 GGCTC-ATAAGAGCTAACCTATTTG
1 GGCTCGA-ATGAGCTAACCTATCTA
*
531702 GGCTCGTATGAGCTAA
1 GGCTCGAATGAGCTAA
531718 TTTTGTCTGG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
23 1 0.03
24 31 0.97
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (24 bp):
GGCTCGAATGAGCTAACCTATCTA
Found at i:536695 original size:24 final size:23
Alignment explanation
Indices: 536659--536712 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
536649 ATAGGTTAAG
*
536659 AATAAAAACTGTCAGTGCAAATGT
1 AATAAAAACTGTCAGAGCAAAT-T
536683 AATATAAAA-TGTCAGAGCAAATT
1 AATA-AAAACTGTCAGAGCAAATT
536706 AATAAAA
1 AATAAAA
536713 TATGAATTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 3 0.11
23 5 0.18
24 16 0.57
25 4 0.14
ACGTcount: A:0.54, C:0.09, G:0.13, T:0.24
Consensus pattern (23 bp):
AATAAAAACTGTCAGAGCAAATT
Found at i:541149 original size:25 final size:25
Alignment explanation
Indices: 541094--541149 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
541084 TTATTCTTGC
* *
541094 ATAAAACTAAAGAAAACAAATTAAA
1 ATAAAACAAAAGAAAACAAAGTAAA
* *
541119 AGAAAACAAAAGACAA-AAAGTAAA
1 ATAAAACAAAAGAAAACAAAGTAAA
541143 TATAAAA
1 -ATAAAA
541150 AATTGCAATG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.73, C:0.07, G:0.07, T:0.12
Consensus pattern (25 bp):
ATAAAACAAAAGAAAACAAAGTAAA
Found at i:547017 original size:24 final size:24
Alignment explanation
Indices: 546984--547030 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
546974 GTTAAGAGTA
*
546984 AAAACTGTCAGTGCAAATGTAATAT
1 AAAACTGTCAGAGCAAAT-TAATAT
547009 AAAA-TGTCAGAGCAAATTAATA
1 AAAACTGTCAGAGCAAATTAATA
547031 AAAGATGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.26
Consensus pattern (24 bp):
AAAACTGTCAGAGCAAATTAATAT
Found at i:549337 original size:37 final size:37
Alignment explanation
Indices: 549282--549449 Score: 176
Period size: 37 Copynumber: 4.5 Consensus size: 37
549272 CCAGAATTAT
549282 GCCTAAACATGTCGCTGCATGAGCACTTCTAGATTGC
1 GCCTAAACATGTCGCTGCATGAGCACTTCTAGATTGC
* *
549319 GCCTAAACATGTCACTGCATGAGCACTTCTAAATTGC
1 GCCTAAACATGTCGCTGCATGAGCACTTCTAGATTGC
* * * * *
549356 ACCCAAACATGTCGTTGCATGAGCACCTCTAGATTAC
1 GCCTAAACATGTCGCTGCATGAGCACTTCTAGATTGC
* * * * ** *
549393 ACCAAAAAACTATCGCCACATGAGCACTTCTAGATTAC
1 GCCTAAACA-TGTCGCTGCATGAGCACTTCTAGATTGC
* *
549431 ACCAAAAC-TGTCGCTGCAT
1 GCCTAAACATGTCGCTGCAT
549450 AAATATTCTT
Statistics
Matches: 110, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
36 8 0.07
37 72 0.65
38 30 0.27
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (37 bp):
GCCTAAACATGTCGCTGCATGAGCACTTCTAGATTGC
Found at i:549436 original size:74 final size:74
Alignment explanation
Indices: 549286--549449 Score: 195
Period size: 74 Copynumber: 2.2 Consensus size: 74
549276 AATTATGCCT
* * * * * * **
549286 AAACATGTCGCTGCATGAGCACTTCTAGATTGCGCCTAAACATGTCACTGCATGAGCACTTCTAA
1 AAACATGTCGCTGCATGAGCACCTCTAGATTACACCAAAAAATATCACCACATGAGCACTTCTAA
*
549351 ATTGCACCC
66 ATTACACCC
* *
549360 AAACATGTCGTTGCATGAGCACCTCTAGATTACACCAAAAAACTATCGCCACATGAGCACTTCTA
1 AAACATGTCGCTGCATGAGCACCTCTAGATTACACCAAAAAA-TATCACCACATGAGCACTTCTA
* *
549425 GATTACACCA
65 AATTACACCC
549435 AAAC-TGTCGCTGCAT
1 AAACATGTCGCTGCAT
549450 AAATATTCTT
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
74 46 0.61
75 29 0.39
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (74 bp):
AAACATGTCGCTGCATGAGCACCTCTAGATTACACCAAAAAATATCACCACATGAGCACTTCTAA
ATTACACCC
Found at i:557725 original size:121 final size:121
Alignment explanation
Indices: 557506--557746 Score: 419
Period size: 121 Copynumber: 2.0 Consensus size: 121
557496 AGTTAGGCGA
557506 GAGCTGCTTGAGAATGGATTCCAGTTACTTATTCTTGAATGCACAACATTACTCACACCAAGAGG
1 GAGCTGCTTGAGAATGGATTCCAGTTACTTATTCTTGAATGCACAACATTACTCACACCAAGAGG
* *
557571 TGGAGTGATTGTGGGTATTTAAGTCTGGCTTAAATAGAGAGCTGTTATTGGTAAGG
66 TGGAGTGATTATGGGTATTTAAGTCTGGATTAAATAGAGAGCTGTTATTGGTAAGG
* * * * *
557627 GAGCTGCTTGAGACTGGATTCCAGTTACTTGTTCTTGAATTCACAACATTACTCACATCGAGAGG
1 GAGCTGCTTGAGAATGGATTCCAGTTACTTATTCTTGAATGCACAACATTACTCACACCAAGAGG
557692 TGGAGTGATTATGGGTATTTAAGTCTGGATTAAATAGAGAGCTGTTATTGGTAAG
66 TGGAGTGATTATGGGTATTTAAGTCTGGATTAAATAGAGAGCTGTTATTGGTAAG
557747 AACTCAAAAG
Statistics
Matches: 113, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
121 113 1.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (121 bp):
GAGCTGCTTGAGAATGGATTCCAGTTACTTATTCTTGAATGCACAACATTACTCACACCAAGAGG
TGGAGTGATTATGGGTATTTAAGTCTGGATTAAATAGAGAGCTGTTATTGGTAAGG
Found at i:566261 original size:17 final size:18
Alignment explanation
Indices: 566239--566279 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
566229 TTAGTTTTAA
566239 TGCATTTT-TATTGTCAC
1 TGCATTTTATATTGTCAC
*
566256 TGCATTTTATTTTGTCAC
1 TGCATTTTATATTGTCAC
*
566274 TACATT
1 TGCATT
566280 CATTTTGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.20, C:0.17, G:0.10, T:0.54
Consensus pattern (18 bp):
TGCATTTTATATTGTCAC
Found at i:566286 original size:17 final size:18
Alignment explanation
Indices: 566249--566287 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
566239 TGCATTTTTA
* *
566249 TTGTCACTGCATTTTATT
1 TTGTCACTACATTTCATT
566267 TTGTCACTACA-TTCATT
1 TTGTCACTACATTTCATT
566284 TTGT
1 TTGT
566288 TAACTTAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.18, C:0.18, G:0.10, T:0.54
Consensus pattern (18 bp):
TTGTCACTACATTTCATT
Found at i:566891 original size:13 final size:13
Alignment explanation
Indices: 566873--566897 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
566863 AAAAAGAAAG
566873 AAAAATAAAAAAT
1 AAAAATAAAAAAT
566886 AAAAATAAAAAA
1 AAAAATAAAAAA
566898 ATTGTTTGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:568414 original size:45 final size:45
Alignment explanation
Indices: 568350--568443 Score: 161
Period size: 45 Copynumber: 2.1 Consensus size: 45
568340 ATCACTTTAC
* *
568350 ATTTTATGCATTTAAATATTCAGCACTCAACACTTAACACATTTT
1 ATTTTATGCATTTAAATATTCAGCACTCAACACTCAACACATTTG
*
568395 ATTTTGTGCATTTAAATATTCAGCACTCAACACTCAACACATTTG
1 ATTTTATGCATTTAAATATTCAGCACTCAACACTCAACACATTTG
568440 ATTT
1 ATTT
568444 ACTTTCAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.39
Consensus pattern (45 bp):
ATTTTATGCATTTAAATATTCAGCACTCAACACTCAACACATTTG
Found at i:579237 original size:105 final size:105
Alignment explanation
Indices: 579082--579311 Score: 336
Period size: 105 Copynumber: 2.2 Consensus size: 105
579072 AGTCCTCAAT
* * * * * *
579082 AGCTCGTGCGAGCAGTATTGTGAGTCGAAAAAAGAGATATGAATCTTAGAATGAATTATAGTCCC
1 AGCTCGTGTGAGCAGCATCGTGAGTCGAAAAAAGAGATATGAATCCTAGAATGAATTACAGGCCC
579147 TGCA-ATGGCTGAGGCTTATGCATAAGTGCATACACCCAAC
66 TG-AGATGGCTGAGGCTTATGCATAAGTGCATACACCCAAC
* * *
579187 AGCTCATGTGAGCAGCATCGTGAGTCGAAAAAAGAGATATGAATCCTAGAATGGATTACAGGCCT
1 AGCTCGTGTGAGCAGCATCGTGAGTCGAAAAAAGAGATATGAATCCTAGAATGAATTACAGGCCC
* * *
579252 TGAGATGGCTGGGGCTTATGCATAAGTGCATACACCCGAT
66 TGAGATGGCTGAGGCTTATGCATAAGTGCATACACCCAAC
579292 AGCTCGTGTGAGCAGCATCG
1 AGCTCGTGTGAGCAGCATCG
579312 AGTACTGGTA
Statistics
Matches: 111, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
104 1 0.01
105 110 0.99
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (105 bp):
AGCTCGTGTGAGCAGCATCGTGAGTCGAAAAAAGAGATATGAATCCTAGAATGAATTACAGGCCC
TGAGATGGCTGAGGCTTATGCATAAGTGCATACACCCAAC
Found at i:580096 original size:21 final size:21
Alignment explanation
Indices: 580050--580097 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
580040 TTTAGTATCA
* *
580050 ATAGAAGCATGCATTGTTTCG
1 ATAGAAGCATGCATTGTATAG
*
580071 GTAGAAGTCAT-CATTGTATAG
1 ATAGAAG-CATGCATTGTATAG
580092 ATAGAA
1 ATAGAA
580098 CCATCATCAC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.31
Consensus pattern (21 bp):
ATAGAAGCATGCATTGTATAG
Found at i:587190 original size:35 final size:35
Alignment explanation
Indices: 587131--587443 Score: 157
Period size: 35 Copynumber: 8.9 Consensus size: 35
587121 GATTAAAGCG
* * **
587131 TAAGGCTT-TGGATTGCTCAAATCTCAACTAGAGCA
1 TAAGG-TTATGGATTGCTTATATCTCAGTTAGAGCA
* * *
587166 TAAGGTTATGGATTGCTTACATCTCGGTTAGAGCG
1 TAAGGTTATGGATTGCTTATATCTCAGTTAGAGCA
* ** * * *
587201 TAAGACTT-TAAATTGCTTATGTCTCAGTTAGAACG
1 TAAG-GTTATGGATTGCTTATATCTCAGTTAGAGCA
* * *
587236 TAAGGCTATGGATTGTTTATGTCTCAGTTAGAGCA
1 TAAGGTTATGGATTGCTTATATCTCAGTTAGAGCA
* * * **
587271 TAAGGCTATGGATTGCTTATGTCTCGGTTAGAGTG
1 TAAGGTTATGGATTGCTTATATCTCAGTTAGAGCA
* * ** ** * **
587306 TAAAGCTATAAACCGCTTATGTCTTGGTTAGAGCA
1 TAAGGTTATGGATTGCTTATATCTCAGTTAGAGCA
* * **
587341 TAAGGCTATGGATTGCTTACATCTTGGTTAGAG-A
1 TAAGGTTATGGATTGCTTATATCTCAGTTAGAGCA
* * ** * *
587375 GTAAAGCTATGGACCGCTTATGTCT-TGATTAGAGCA
1 -TAAGGTTATGGATTGCTTATATCTCAG-TTAGAGCA
* * ** *
587411 TAAGGCTATGGATTGTTTACGTCTCGGTTAGAG
1 TAAGGTTATGGATTGCTTATATCTCAGTTAGAG
587444 TGTAAAGCTA
Statistics
Matches: 220, Mismatches: 51, Indels: 14
0.77 0.18 0.05
Matches are distributed among these distances:
34 5 0.02
35 211 0.96
36 4 0.02
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (35 bp):
TAAGGTTATGGATTGCTTATATCTCAGTTAGAGCA
Found at i:587314 original size:70 final size:69
Alignment explanation
Indices: 587212--587454 Score: 306
Period size: 70 Copynumber: 3.5 Consensus size: 69
587202 AAGACTTTAA
* * ** * ** *
587212 ATTGCTTATGTCTCAGTTAGAACGTAAGGCTATGGATTGTTTATGTCTCAGTTAGAGCATAAGGC
1 ATTGCTTACGTCTCGGTTAGAGTGTAAAGCTATGGACCGCTTATGTCT-AGTTAGAGCATAAGGC
587277 TATGG
65 TATGG
* ** *
587282 ATTGCTTATGTCTCGGTTAGAGTGTAAAGCTATAAACCGCTTATGTCTTGGTTAGAGCATAAGGC
1 ATTGCTTACGTCTCGGTTAGAGTGTAAAGCTATGGACCGCTTATGTC-TAGTTAGAGCATAAGGC
587347 TATGG
65 TATGG
* * * *
587352 ATTGCTTACATCTTGGTTAGAGAGTAAAGCTATGGACCGCTTATGTCTTGATTAGAGCATAAGGC
1 ATTGCTTACGTCTCGGTTAGAGTGTAAAGCTATGGACCGCTTATGTCTAG-TTAGAGCATAAGGC
587417 TATGG
65 TATGG
*
587422 ATTGTTTACGTCTCGGTTAGAGTGTAAAGCTAT
1 ATTGCTTACGTCTCGGTTAGAGTGTAAAGCTAT
587455 TTTAGCTTAG
Statistics
Matches: 150, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
69 2 0.01
70 147 0.98
71 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.35
Consensus pattern (69 bp):
ATTGCTTACGTCTCGGTTAGAGTGTAAAGCTATGGACCGCTTATGTCTAGTTAGAGCATAAGGCT
ATGG
Found at i:587324 original size:105 final size:105
Alignment explanation
Indices: 587131--587419 Score: 294
Period size: 105 Copynumber: 2.8 Consensus size: 105
587121 GATTAAAGCG
* * * ** * **
587131 TAAGGCTTTGGATTGCTCAAATCTCAACTAGAGCATAAGGTTATGGATTGCTTACATCTCGGTTA
1 TAAGGCTATGGATTGCTTACATCTCAGTTAGAGCATAAGGCTATGGATTGCTTATGTCTCGGTTA
* ** *
587196 GAGCGTAAGACTTTAAATTGCTTATGTCTCAGTTAGAACG
66 GAGCGTAAGACTATAAACCGCTTATGTCTCAGTTAGAACA
* **
587236 TAAGGCTATGGATTGTTTATGTCTCAGTTAGAGCATAAGGCTATGGATTGCTTATGTCTCGGTTA
1 TAAGGCTATGGATTGCTTACATCTCAGTTAGAGCATAAGGCTATGGATTGCTTATGTCTCGGTTA
* ** *
587301 GAGTGTAA-AGCTATAAACCGCTTATGTCTTGGTTAGAGCA
66 GAGCGTAAGA-CTATAAACCGCTTATGTCTCAGTTAGAACA
** * ** * *
587341 TAAGGCTATGGATTGCTTACATCTTGGTTAGAG-AGTAAAGCTATGGACCGCTTATGTCTTGATT
1 TAAGGCTATGGATTGCTTACATCTCAGTTAGAGCA-TAAGGCTATGGATTGCTTATGTCTCGGTT
* *
587405 AGAGCATAAGGCTAT
65 AGAGCGTAAGACTAT
587420 GGATTGTTTA
Statistics
Matches: 150, Mismatches: 31, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
104 2 0.01
105 148 0.99
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (105 bp):
TAAGGCTATGGATTGCTTACATCTCAGTTAGAGCATAAGGCTATGGATTGCTTATGTCTCGGTTA
GAGCGTAAGACTATAAACCGCTTATGTCTCAGTTAGAACA
Found at i:587454 original size:35 final size:35
Alignment explanation
Indices: 587172--587454 Score: 253
Period size: 35 Copynumber: 8.1 Consensus size: 35
587162 AGCATAAGGT
**
587172 TATGGATTGCTTACATCTCGGTTAGAGCGT-AAGAC
1 TATGGATTGCTTATGTCTCGGTTAGAGCGTAAAG-C
* ** * * *
587207 TTTAAATTGCTTATGTCTCAGTTAGAACGTAAGGC
1 TATGGATTGCTTATGTCTCGGTTAGAGCGTAAAGC
* * * *
587242 TATGGATTGTTTATGTCTCAGTTAGAGCATAAGGC
1 TATGGATTGCTTATGTCTCGGTTAGAGCGTAAAGC
*
587277 TATGGATTGCTTATGTCTCGGTTAGAGTGTAAAGC
1 TATGGATTGCTTATGTCTCGGTTAGAGCGTAAAGC
** ** * * *
587312 TATAAACCGCTTATGTCTTGGTTAGAGCATAAGGC
1 TATGGATTGCTTATGTCTCGGTTAGAGCGTAAAGC
** * *
587347 TATGGATTGCTTACATCTTGGTTAGAGAGTAAAGC
1 TATGGATTGCTTATGTCTCGGTTAGAGCGTAAAGC
** * * * *
587382 TATGGACCGCTTATGTCTTGATTAGAGCATAAGGC
1 TATGGATTGCTTATGTCTCGGTTAGAGCGTAAAGC
* * *
587417 TATGGATTGTTTACGTCTCGGTTAGAGTGTAAAGC
1 TATGGATTGCTTATGTCTCGGTTAGAGCGTAAAGC
587452 TAT
1 TAT
587455 TTTAGCTTAG
Statistics
Matches: 194, Mismatches: 53, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
35 192 0.99
36 2 0.01
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (35 bp):
TATGGATTGCTTATGTCTCGGTTAGAGCGTAAAGC
Found at i:594411 original size:15 final size:15
Alignment explanation
Indices: 594393--594455 Score: 65
Period size: 15 Copynumber: 4.2 Consensus size: 15
594383 GAGCTTGGAA
*
594393 GTTGCAAGCACTCAT
1 GTTGCAAACACTCAT
594408 GTTGCAAACACTCAT
1 GTTGCAAACACTCAT
** *
594423 GTTGTGAACACTGGA-
1 GTTGCAAACACT-CAT
*
594438 GTTGCGAACACTCAT
1 GTTGCAAACACTCAT
594453 GTT
1 GTT
594456 ACGGACACAC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
14 1 0.03
15 38 0.95
16 1 0.03
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (15 bp):
GTTGCAAACACTCAT
Found at i:600602 original size:24 final size:24
Alignment explanation
Indices: 600573--600634 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
600563 GTTGAATAGC
600573 AAGTATCGGTAGTTATGTGTTTAG
1 AAGTATCGGTAGTTATGTGTTTAG
*
600597 AAGTATCAGTAGTTATGTGTTTAG
1 AAGTATCGGTAGTTATGTGTTTAG
600621 AAGTATCGGTAGTT
1 AAGTATCGGTAGTT
600635 TGTACACTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.27, C:0.05, G:0.27, T:0.40
Consensus pattern (24 bp):
AAGTATCGGTAGTTATGTGTTTAG
Found at i:606278 original size:36 final size:36
Alignment explanation
Indices: 606238--606311 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 36
606228 TGTCACTTAG
606238 ACCAA-ATCCTTTCTTCCTTTTGAACACCCACTTGCA
1 ACCAACAT-CTTTCTTCCTTTTGAACACCCACTTGCA
*
606274 ACCAACTATCTTTTTTCCTTTTGAACACCCACTTGCA
1 ACCAAC-ATCTTTCTTCCTTTTGAACACCCACTTGCA
606311 A
1 A
606312 GATTGTATAC
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
36 5 0.14
37 28 0.80
38 2 0.06
ACGTcount: A:0.26, C:0.34, G:0.05, T:0.35
Consensus pattern (36 bp):
ACCAACATCTTTCTTCCTTTTGAACACCCACTTGCA
Found at i:628763 original size:41 final size:41
Alignment explanation
Indices: 628701--628794 Score: 161
Period size: 41 Copynumber: 2.3 Consensus size: 41
628691 GAATTTTATT
* *
628701 TTAATAAGAATTCTAGTCACCCAATTCTAACAATCTCTACC
1 TTAAAAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
*
628742 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
1 TTAAAAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
628783 TTAAAAAGAATT
1 TTAAAAAGAATT
628795 TTCTACGAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.39, C:0.26, G:0.05, T:0.30
Consensus pattern (41 bp):
TTAAAAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
Found at i:632926 original size:19 final size:20
Alignment explanation
Indices: 632902--632946 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
632892 CAAATTCTGA
632902 ATAATTAA-TATCAAAAAAT
1 ATAATTAATTATCAAAAAAT
*
632921 ATAATTTAATTATCAAATAAT
1 ATAA-TTAATTATCAAAAAAT
632942 -TAATT
1 ATAATT
632947 TGTGTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 6 0.26
20 7 0.30
21 10 0.43
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAATTAATTATCAAAAAAT
Found at i:632945 original size:20 final size:20
Alignment explanation
Indices: 632902--632947 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
632892 CAAATTCTGA
632902 ATAA-TTAATATCAAAAAAT
1 ATAATTTAATATCAAAAAAT
*
632921 ATAATTTAATTATCAAATAAT
1 ATAATTTAA-TATCAAAAAAT
632942 -TAATTT
1 ATAATTT
632948 GTGTTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 4 0.17
20 10 0.42
21 10 0.42
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (20 bp):
ATAATTTAATATCAAAAAAT
Found at i:633840 original size:12 final size:12
Alignment explanation
Indices: 633823--633847 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
633813 TGTTATCATG
633823 ATGAATGCTATT
1 ATGAATGCTATT
633835 ATGAATGCTATT
1 ATGAATGCTATT
633847 A
1 A
633848 ATTCTTTAAT
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:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:636980 original size:40 final size:40
Alignment explanation
Indices: 636913--637151 Score: 232
Period size: 40 Copynumber: 6.0 Consensus size: 40
636903 ATTATAGATG
* * *
636913 TAATTCGAGCTACGGCTTAGCAAGCTTTGAGTTGATGATA
1 TAATTCGAGCTACGACTTAGCAGGCTTTGAGCTGATGATA
* ** * *
636953 TAATTCGAGCTACAACTTATTAGGCTTTAAGCCGATGATA
1 TAATTCGAGCTACGACTTAGCAGGCTTTGAGCTGATGATA
* *
636993 TAATTTGAGCTACGACTTAGAAGGCTTTGAGCT-AGTGATA
1 TAATTCGAGCTACGACTTAGCAGGCTTTGAGCTGA-TGATA
* *
637033 TAATTCGAACTACGACTTAGCAGGCTTTGAGC-CAGTGATA
1 TAATTCGAGCTACGACTTAGCAGGCTTTGAGCTGA-TGATA
* * * *
637073 CAATTCAATCTACGACTTAGCAGGCTTTGAGC-CAGTGATA
1 TAATTCGAGCTACGACTTAGCAGGCTTTGAGCTGA-TGATA
* * * * * *
637113 CAATTCAAGCTACGTCTTAACAGGATTTGAGTTGATGAT
1 TAATTCGAGCTACGACTTAGCAGGCTTTGAGCTGATGAT
637152 GAAGTAAGAT
Statistics
Matches: 170, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
39 1 0.01
40 168 0.99
41 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (40 bp):
TAATTCGAGCTACGACTTAGCAGGCTTTGAGCTGATGATA
Found at i:637126 original size:120 final size:120
Alignment explanation
Indices: 636913--637131 Score: 262
Period size: 120 Copynumber: 1.8 Consensus size: 120
636903 ATTATAGATG
* * ** * * **
636913 TAATTCGAGCTACGGCTTAGCAAGCTTTGAGTTGATGATATAATTCGAGCTACAACTTATTAGGC
1 TAATTCGAACTACGACTTAGCAAGCTTTGAGCAGATGATACAATTCAAGCTACAACTTAGCAGGC
* **
636978 TTTAAGCCGATGATATAATTTGAGCTACGACTTAGAAGGCTTTGAGCTAGTGATA
66 TTTAAGCCGATGATACAATTCAAGCTACGACTTAGAAGGCTTTGAGCTAGTGATA
* * *
637033 TAATTCGAACTACGACTTAGCAGGCTTTGAGCCAG-TGATACAATTCAATCTACGACTTAGCAGG
1 TAATTCGAACTACGACTTAGCAAGCTTTGAG-CAGATGATACAATTCAAGCTACAACTTAGCAGG
* *
637097 CTTTGAGCC-AGTGATACAATTCAAGCTACGTCTTA
65 CTTTAAGCCGA-TGATACAATTCAAGCTACGACTTA
637132 ACAGGATTTG
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
119 1 0.01
120 79 0.98
121 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (120 bp):
TAATTCGAACTACGACTTAGCAAGCTTTGAGCAGATGATACAATTCAAGCTACAACTTAGCAGGC
TTTAAGCCGATGATACAATTCAAGCTACGACTTAGAAGGCTTTGAGCTAGTGATA
Found at i:653245 original size:23 final size:21
Alignment explanation
Indices: 653219--653262 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
653209 TTTTAAGTTG
*
653219 AAACAATTTACATATCTTAAAAA
1 AAACAATGTACAT-T-TTAAAAA
*
653242 AAACGATGTACATTTTAAAAA
1 AAACAATGTACATTTTAAAAA
653263 TATGATTTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 1 0.05
23 11 0.58
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.30
Consensus pattern (21 bp):
AAACAATGTACATTTTAAAAA
Found at i:654682 original size:13 final size:13
Alignment explanation
Indices: 654664--654702 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
654654 AAAAGAAAGG
654664 TCTTTATTTTGTT
1 TCTTTATTTTGTT
* *
654677 TCTTTAATCTGTT
1 TCTTTATTTTGTT
654690 T-TTTATTTTGTT
1 TCTTTATTTTGTT
654702 T
1 T
654703 TAAAATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.10, C:0.08, G:0.08, T:0.74
Consensus pattern (13 bp):
TCTTTATTTTGTT
Found at i:654868 original size:18 final size:18
Alignment explanation
Indices: 654841--654881 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
654831 GTTAAGGGTT
654841 TCGGGCAGAGGAA-GAGTC
1 TCGGGCAGAGGAACG-GTC
*
654859 TCGGGTAGAGGAACGGTC
1 TCGGGCAGAGGAACGGTC
654877 TCGGG
1 TCGGG
654882 AGTCGAGGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.22, C:0.17, G:0.46, T:0.15
Consensus pattern (18 bp):
TCGGGCAGAGGAACGGTC
Found at i:655628 original size:50 final size:50
Alignment explanation
Indices: 655553--656026 Score: 348
Period size: 50 Copynumber: 9.6 Consensus size: 50
655543 CCCGCCATGT
* * *
655553 TTCTAAGGTATTAGGTTCGCTGTTGCGGCCTCAACCTTTCTCTTCACATC
1 TTCTAAGGTATCAGATTCGCTGTTGCGGCCTCAACCTTTCCCTTCACATC
* * * *
655603 TTCTAAGGTATCGGGTTCGCTGTTGCGACCTCAACCTTTCTCTTCACATC
1 TTCTAAGGTATCAGATTCGCTGTTGCGGCCTCAACCTTTCCCTTCACATC
* * * *
655653 TTCTAAGGTACCA-AGTTCCCCGTTGCGGCCTCAACCTTTCCCTTCATATC
1 TTCTAAGGTATCAGA-TTCGCTGTTGCGGCCTCAACCTTTCCCTTCACATC
* * * * *
655703 TTC-ATGGTACCAGATTCGCTGTTACGGCCTTAATCC-TT-CCTCTCACGTC
1 TTCTAAGGTATCAGATTCGCTGTTGCGGCCTCAA-CCTTTCCCT-TCACATC
* * * ** * * *
655752 TTTTAAGGTATCGGGTTCATTGTTGCAGCCTCAACCTTTCCCTTCATATA
1 TTCTAAGGTATCAGATTCGCTGTTGCGGCCTCAACCTTTCCCTTCACATC
* * * * * *
655802 TTC-ATGGTACCAGATTC-ATCGTTGCGGCCTTAATCC-TT-CTTATCACGTC
1 TTCTAAGGTATCAGATTCGCT-GTTGCGGCCTCAA-CCTTTCCCT-TCACATC
* * *
655851 TTCTAAGGTA-CTGATTCGCTATTGCAGCCTCAACCTTTCCCTT--CATC
1 TTCTAAGGTATCAGATTCGCTGTTGCGGCCTCAACCTTTCCCTTCACATC
* * * * * * *
655898 TT-TATGGTATTAGATTCACCGTTACGGCCTCAATCC-TTCCCATCACGTC
1 TTCTAAGGTATCAGATTCGCTGTTGCGGCCTCAA-CCTTTCCCTTCACATC
* * * *
655947 TTCTAAGGTA-CTAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTATATC
1 TTCTAAGGTATC-AGATTCGCTGTTGCGGCCTCAACCTTTCCCTTCACATC
* * *
655997 -TCTAGGGTATTAGATTCGCTATTGCGGCCT
1 TTCTAAGGTATCAGATTCGCTGTTGCGGCCT
656027 TAATCTTCCC
Statistics
Matches: 327, Mismatches: 75, Indels: 45
0.73 0.17 0.10
Matches are distributed among these distances:
46 6 0.02
47 27 0.08
48 10 0.03
49 114 0.35
50 167 0.51
51 3 0.01
ACGTcount: A:0.18, C:0.30, G:0.17, T:0.36
Consensus pattern (50 bp):
TTCTAAGGTATCAGATTCGCTGTTGCGGCCTCAACCTTTCCCTTCACATC
Found at i:655787 original size:99 final size:99
Alignment explanation
Indices: 655553--656035 Score: 480
Period size: 99 Copynumber: 4.9 Consensus size: 99
655543 CCCGCCATGT
* * * * * *
655553 TTCTAAGGTATTAGGTTCGCTGTTGCGGCCTCAACCTTTCTCTTCACATCTTCTAAGGTATCGGG
1 TTCTAAGGTA-CAGGTTCGCTGTTGCGGCCTCAACCTTTCCCTTCATATCTTC-ATGGTATCAGA
* * * * *
655618 TTCGCTGTTGCGACCTCAA-CCTTTCTCTTCACATC
64 TTCGCTGTTGCGGCCTTAATCCTTCCTCATCACGTC
* * * *
655653 TTCTAAGGTACCAAGTTCCCCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCAGAT
1 TTCTAAGGTA-CAGGTTCGCTGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTATCAGAT
*
655718 TCGCTGTTACGGCCTTAATCCTTCCTC-TCACGTC
65 TCGCTGTTGCGGCCTTAATCCTTCCTCATCACGTC
* * ** * * *
655752 TTTTAAGGTATCGGGTTCATTGTTGCAGCCTCAACCTTTCCCTTCATATATTCATGGTACCAGAT
1 TTCTAAGGTA-CAGGTTCGCTGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTATCAGAT
* *
655817 TC-ATCGTTGCGGCCTTAATCCTT-CTTATCACGTC
65 TCGCT-GTTGCGGCCTTAATCCTTCCTCATCACGTC
* * * * * *
655851 TTCTAAGGTACTGATTCGCTATTGCAGCCTCAACCTTTCCCTTC--ATCTTTATGGTATTAGATT
1 TTCTAAGGTACAGGTTCGCTGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTATCAGATT
* * * *
655914 CACCGTTACGGCCTCAATCCTTCC-CATCACGTC
66 CGCTGTTGCGGCCTTAATCCTTCCTCATCACGTC
* * * *
655947 TTCTAAGGTACTAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTATATC-TCTAGGGTATTAGA
1 TTCTAAGGTAC-AGGTTCGCTGTTGCGGCCTCAACCTTTCCCTTCATATCTTC-ATGGTATCAGA
*
656011 TTCGCTATTGCGGCCTTAAT-CTTCC
64 TTCGCTGTTGCGGCCTTAATCCTTCC
656036 CTGTCAAACC
Statistics
Matches: 318, Mismatches: 56, Indels: 20
0.81 0.14 0.05
Matches are distributed among these distances:
96 51 0.16
97 28 0.09
98 38 0.12
99 148 0.47
100 53 0.17
ACGTcount: A:0.18, C:0.30, G:0.16, T:0.36
Consensus pattern (99 bp):
TTCTAAGGTACAGGTTCGCTGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTATCAGATT
CGCTGTTGCGGCCTTAATCCTTCCTCATCACGTC
Found at i:655861 original size:149 final size:149
Alignment explanation
Indices: 655553--656035 Score: 380
Period size: 149 Copynumber: 3.3 Consensus size: 149
655543 CCCGCCATGT
* * * *
655553 TTCTAAGGTATTAGGTTCGCTGTTGCGGCCTCAACCTTTCTCTTCACATCTTCTAAGGTATCGGG
1 TTCTAAGGTA-CAGATTCGCTGTTACGGCCTCAACCTTCCTCTTCACATCTTCTAAGGTATCGGG
* * * *
655618 TTCGCTGTTGCGACCTCAACCTTTCTCTTCACATCTTCTAAGGTACCAAGTTCCCCGTTGCGGCC
65 TTCACTGTTGCGACCTCAACCTTTCCCTTCACATATTCTAAGGTACCAAGTTCACCGTTGCGGCC
*
655683 TCAACCTTTCCCTTCATATC
130 TCAACCTTTCCCTTCACATC
* * * *
655703 TTC-ATGGTACCAGATTCGCTGTTACGGCCTTAATCCTTCCTC-TCACGTCTTTTAAGGTATCGG
1 TTCTAAGGTA-CAGATTCGCTGTTACGGCCTCAA-CCTTCCTCTTCACATCTTCTAAGGTATCGG
* * * *
655766 GTTCATTGTTGC-AGCCTCAACCTTTCCCTTCATATATTC-ATGGTACC-AGATTCATCGTTGCG
64 GTTCACTGTTGCGA-CCTCAACCTTTCCCTTCACATATTCTAAGGTACCAAG-TTCACCGTTGCG
* * *
655828 GCCTTAATCC-TT-CTTATCACGTC
127 GCCTCAA-CCTTTCCCT-TCACATC
* * * * * ** *
655851 TTCTAAGGTACTGATTCGCTATTGCAGCCTCAACCTTTCC-CTT--CATCTT-TATGGTATTAGA
1 TTCTAAGGTACAGATTCGCTGTTACGGCCTCAACC-TTCCTCTTCACATCTTCTAAGGTATCGGG
* * * * * * * * *
655912 TTCACCGTTACGGCCTCAATCC-TTCCCATCACGTCTTCTAAGGTACTAGGTTCGCCGTTGCGGC
65 TTCACTGTTGCGACCTCAA-CCTTTCCCTTCACATATTCTAAGGTACCAAGTTCACCGTTGCGGC
* *
655976 CTCAACCTTTCCCTTTATATC
129 CTCAACCTTTCCCTTCACATC
* * * * * *
655997 -TCTAGGGTATTAGATTCGCTATTGCGGCCTTAATCTTCC
1 TTCTAAGGTA-CAGATTCGCTGTTACGGCCTCAACCTTCC
656036 CTGTCAAACC
Statistics
Matches: 262, Mismatches: 56, Indels: 35
0.74 0.16 0.10
Matches are distributed among these distances:
145 48 0.18
146 55 0.21
147 10 0.04
148 57 0.22
149 82 0.31
150 10 0.04
ACGTcount: A:0.18, C:0.30, G:0.16, T:0.36
Consensus pattern (149 bp):
TTCTAAGGTACAGATTCGCTGTTACGGCCTCAACCTTCCTCTTCACATCTTCTAAGGTATCGGGT
TCACTGTTGCGACCTCAACCTTTCCCTTCACATATTCTAAGGTACCAAGTTCACCGTTGCGGCCT
CAACCTTTCCCTTCACATC
Found at i:656024 original size:195 final size:197
Alignment explanation
Indices: 655553--656031 Score: 517
Period size: 195 Copynumber: 2.4 Consensus size: 197
655543 CCCGCCATGT
* * * * *
655553 TTCTAAGGTATTAGGTTCGCTGTTGCGGCCTCAACCTTTCTCTTCACATCTTCTAAGGTATCGGG
1 TTCTAAGGTA-TAGGTTCGCTGTTGCGGCCTCAACCTTTCCCTTTATATC-TCTAAGGTATCAGA
* * * *
655618 TTCGCTGTTGCGACCTCAA-CCTTTCTCTTCACATCTTCTAAGGTACCAAGTTCCCCGTTGCGGC
64 TTCGCTGTTGCGGCCTTAATCCTTTCTCTTCACATCTTCTAAGGTACCAAGTTCCCCATTGCAGC
* * *
655682 CTCAACCTTTCCCTTCATATCTTCATGGTACCAGATTCGCTGTTACGGCCTTAATCCTTCCTCTC
129 CTCAACCTTTCCCTTCA-ATCTTCATGGTACCAGATTCACCGTTACGGCCTCAATCCTTCCTCTC
655747 ACGTC
193 ACGTC
* * ** * * *
655752 TTTTAAGGTATCGGGTTCATTGTTGCAGCCTCAACCTTTCCCTTCATATAT-TC-ATGGTACCAG
1 TTCTAAGGTAT-AGGTTCGCTGTTGCGGCCTCAACCTTTCCCTT--TATATCTCTAAGGTATCAG
* * ** * *
655815 ATTC-ATCGTTGCGGCCTTAATCC-TTCT-TATCACGTCTTCTAAGGTACTGA-TTCGCTATTGC
63 ATTCGCT-GTTGCGGCCTTAATCCTTTCTCT-TCACATCTTCTAAGGTACCAAGTTCCCCATTGC
* **
655876 AGCCTCAACCTTTCCCTTC-ATCTTTATGGTATTAGATTCACCGTTACGGCCTCAATCCTTCC-C
126 AGCCTCAACCTTTCCCTTCAATCTTCATGGTACCAGATTCACCGTTACGGCCTCAATCCTTCCTC
655939 ATCACGTC
191 -TCACGTC
* * *
655947 TTCTAAGGTACTAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTATATCTCTAGGGTATTAGAT
1 TTCTAAGGTA-TAGGTTCGCTGTTGCGGCCTCAACCTTTCCCTTTATATCTCTAAGGTATCAGAT
*
656012 TCGCTATTGCGGCCTTAATC
65 TCGCTGTTGCGGCCTTAATC
656032 TTCCCTGTCA
Statistics
Matches: 230, Mismatches: 39, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
193 5 0.02
194 3 0.01
195 105 0.46
196 2 0.01
197 28 0.12
198 44 0.19
199 40 0.17
201 3 0.01
ACGTcount: A:0.18, C:0.29, G:0.16, T:0.36
Consensus pattern (197 bp):
TTCTAAGGTATAGGTTCGCTGTTGCGGCCTCAACCTTTCCCTTTATATCTCTAAGGTATCAGATT
CGCTGTTGCGGCCTTAATCCTTTCTCTTCACATCTTCTAAGGTACCAAGTTCCCCATTGCAGCCT
CAACCTTTCCCTTCAATCTTCATGGTACCAGATTCACCGTTACGGCCTCAATCCTTCCTCTCACG
TC
Found at i:670069 original size:37 final size:36
Alignment explanation
Indices: 669965--670069 Score: 131
Period size: 36 Copynumber: 2.9 Consensus size: 36
669955 TGGTAACAAG
* **
669965 CATGACCTTTGGGTCAAC-GAGGAGAAAAATAAGCAT
1 CATGACCTTTGGGTCAACAG-GGAGTAAAACGAGCAT
* * *
670001 AATGACCTTTGGATCAATAGGGAGTAAAACGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAACGAGCAT
670037 CATGACCTTTGGGGTCAACAGGGAGTAAAACGA
1 CATGACCTTT-GGGTCAACAGGGAGTAAAACGA
670070 ATAACGATTA
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
36 37 0.64
37 21 0.36
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.20
Consensus pattern (36 bp):
CATGACCTTTGGGTCAACAGGGAGTAAAACGAGCAT
Found at i:673792 original size:24 final size:24
Alignment explanation
Indices: 673757--673822 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 24
673747 TTCTGTCTGG
673757 GCTCG-AATGAGCTAATTTATCTAA
1 GCTCGTAA-GAGCTAATTTATCTAA
* ** **
673781 GCTTGTAAGAGCTAACCTATCTGG
1 GCTCGTAAGAGCTAATTTATCTAA
*
673805 GCTCGTATGAGCTAATTT
1 GCTCGTAAGAGCTAATTT
673823 TGTCTGGGCT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
24 30 0.94
25 2 0.06
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.33
Consensus pattern (24 bp):
GCTCGTAAGAGCTAATTTATCTAA
Found at i:678300 original size:42 final size:42
Alignment explanation
Indices: 678248--678352 Score: 156
Period size: 42 Copynumber: 2.5 Consensus size: 42
678238 TGAAAATTTT
**
678248 GGGGCATCGTAGTGCAATTCAGGGGCACTATAGTGTTATTCA
1 GGGGCATCGTAGTGCAATTCAGGGGCACTATAGTGCAATTCA
* * *
678290 GGGGCATCGTAGTGCAATACAGGTGCACTGTAGTGCAATTCA
1 GGGGCATCGTAGTGCAATTCAGGGGCACTATAGTGCAATTCA
*
678332 GGGGCACCGTAGTGCAATTCA
1 GGGGCATCGTAGTGCAATTCA
678353 ACGGCATCAC
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (42 bp):
GGGGCATCGTAGTGCAATTCAGGGGCACTATAGTGCAATTCA
Found at i:678358 original size:21 final size:21
Alignment explanation
Indices: 678227--678352 Score: 135
Period size: 21 Copynumber: 6.0 Consensus size: 21
678217 GCATTCACAA
* **
678227 GGGCACCGTAGTGAAAATTTTG
1 GGGCACCGTAGTG-CAATTCAG
*
678249 GGGCATCGTAGTGCAATTCAG
1 GGGCACCGTAGTGCAATTCAG
** **
678270 GGGCACTATAGTGTTATTCAG
1 GGGCACCGTAGTGCAATTCAG
* *
678291 GGGCATCGTAGTGCAATACAG
1 GGGCACCGTAGTGCAATTCAG
* *
678312 GTGCACTGTAGTGCAATTCAG
1 GGGCACCGTAGTGCAATTCAG
678333 GGGCACCGTAGTGCAATTCA
1 GGGCACCGTAGTGCAATTCA
678353 ACGGCATCAC
Statistics
Matches: 83, Mismatches: 21, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
21 71 0.86
22 12 0.14
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.25
Consensus pattern (21 bp):
GGGCACCGTAGTGCAATTCAG
Found at i:680879 original size:13 final size:13
Alignment explanation
Indices: 680861--680886 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
680851 GGGGTTATTT
680861 TAAAAGAAATAAA
1 TAAAAGAAATAAA
680874 TAAAAGAAATAAA
1 TAAAAGAAATAAA
680887 AGAATTAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
TAAAAGAAATAAA
Found at i:686613 original size:24 final size:24
Alignment explanation
Indices: 686580--686633 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
686570 ATAATTTCAT
686580 AATACTTAAATATTACATACTTTT-G
1 AATA-TTAAATA-TACATACTTTTAG
* *
686605 AATATTAAATATATATATTTTTAG
1 AATATTAAATATACATACTTTTAG
686629 AATAT
1 AATAT
686634 GATCCTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 9 0.35
24 13 0.50
25 4 0.15
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (24 bp):
AATATTAAATATACATACTTTTAG
Found at i:686856 original size:19 final size:19
Alignment explanation
Indices: 686834--686878 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
686824 TTATATTAGG
686834 ATTTAATATTTAATATAT-T
1 ATTTAATATTTAA-ATATGT
* *
686853 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
686872 ATTTAAT
1 ATTTAAT
686879 TTATATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:687710 original size:16 final size:15
Alignment explanation
Indices: 687685--687735 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
687675 CTCTATTTTC
687685 TATTTCTTTTAATTT
1 TATTTCTTTTAATTT
*
687700 TATTATCTTTTATTTT
1 TATT-TCTTTTAATTT
* *
687716 TAATTCTGTTT-CTTT
1 TATTTCT-TTTAATTT
687731 TATTT
1 TATTT
687736 TTCCTTAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 14 0.47
16 16 0.53
ACGTcount: A:0.18, C:0.08, G:0.02, T:0.73
Consensus pattern (15 bp):
TATTTCTTTTAATTT
Found at i:687716 original size:22 final size:21
Alignment explanation
Indices: 687691--687737 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
687681 TTTCTATTTC
*
687691 TTTTAATTTTATTATCTTTTAT
1 TTTTAATTCTATT-TCTTTTAT
*
687713 TTTTAATTCTGTTTCTTTTAT
1 TTTTAATTCTATTTCTTTTAT
687734 TTTT
1 TTTT
687738 CCTTAGATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTTAATTCTATTTCTTTTAT
Found at i:691695 original size:89 final size:88
Alignment explanation
Indices: 691539--691722 Score: 305
Period size: 89 Copynumber: 2.1 Consensus size: 88
691529 TTATAGCCCA
*
691539 AGCCCCAAACTGGAAATACCCCTTTAAGATCATGTGTGATGCCAGTGACCGAAGTATAGAGGCTG
1 AGCCCCAAACTGGAAATACCCCTTTAAGATCATGTGTGATGCCAATGACCGAAGTATAGAGGCTG
*
691604 TGTTGGGGCAAAAGATAAATCGAG
66 TGTTAGGG-AAAAGATAAATCGAG
* * *
691628 AGCCTCAAACTGGAAATACCCCTTTGAGATCATGTGTGATGCCAATGACCGAAGTATAGGGGCTG
1 AGCCCCAAACTGGAAATACCCCTTTAAGATCATGTGTGATGCCAATGACCGAAGTATAGAGGCTG
*
691693 TGTTAGGGAAAAGATAGATCGAG
66 TGTTAGGGAAAAGATAAATCGAG
691716 AGCCCCA
1 AGCCCCA
691723 TGTCATTTGT
Statistics
Matches: 88, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
88 20 0.23
89 68 0.77
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.21
Consensus pattern (88 bp):
AGCCCCAAACTGGAAATACCCCTTTAAGATCATGTGTGATGCCAATGACCGAAGTATAGAGGCTG
TGTTAGGGAAAAGATAAATCGAG
Found at i:693441 original size:12 final size:11
Alignment explanation
Indices: 693427--693486 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 11
693417 AACCCAATTA
693427 TTTTTATTTTT
1 TTTTTATTTTT
693438 ATTTTTATTTTT
1 -TTTTTATTTTT
*
693450 TTTCTATCTTATT
1 TTTTTAT-TT-TT
693463 TTATTTATTTATT
1 TT-TTTATTT-TT
*
693476 TATTTATTTTT
1 TTTTTATTTTT
693487 ATCCAGGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
11 8 0.19
12 20 0.48
13 10 0.24
14 4 0.10
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTATTTTT
Found at i:693461 original size:22 final size:22
Alignment explanation
Indices: 693435--693488 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
693425 TATTTTTATT
693435 TTTATTTTTATTT-TTT-TTCTA
1 TTTATTTTTATTTATTTATT-TA
693456 TCTTA-TTTTATTTATTTATTTA
1 T-TTATTTTTATTTATTTATTTA
693478 TTTATTTTTAT
1 TTTATTTTTAT
693489 CCAGGAAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
21 12 0.41
22 15 0.52
23 2 0.07
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTATTTTTATTTATTTATTTA
Found at i:693464 original size:21 final size:21
Alignment explanation
Indices: 693435--693485 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
693425 TATTTTTATT
693435 TTTATTTTTATTT-TTT-TTCTA
1 TTTA-TTTTATTTATTTATT-TA
693456 TCTTATTTTATTTATTTATTTA
1 T-TTATTTTATTTATTTATTTA
693478 TTTATTTT
1 TTTATTTT
693486 TATCCAGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 16 0.59
22 9 0.33
23 2 0.07
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTATTTTATTTATTTATTTA
Found at i:693839 original size:20 final size:21
Alignment explanation
Indices: 693814--693852 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
693804 ATGATTCTTG
693814 TTTGCTAAG-TTAATTTTGAT
1 TTTGCTAAGATTAATTTTGAT
*
693834 TTTGCTATGATTAATTTTG
1 TTTGCTAAGATTAATTTTG
693853 TCTCCACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.23, C:0.05, G:0.15, T:0.56
Consensus pattern (21 bp):
TTTGCTAAGATTAATTTTGAT
Done.