Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008086.1 Hibiscus syriacus cultivar Beakdansim tig00110596_pilon, 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: 756749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:316902 original size:61 final size:61
Alignment explanation
Indices: 316835--316985 Score: 293
Period size: 61 Copynumber: 2.5 Consensus size: 61
316825 CTATCGCAAC
316835 GCGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATTTGAGATAGTGGAGATCGCGTT
1 GCGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATTTGAGATAGTGGAGATCGCGTT
*
316896 GCGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATTTGCGATAGTGGAGATCGCGTT
1 GCGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATTTGAGATAGTGGAGATCGCGTT
316957 GCGATTTTCAACTATCGCAACGCGAAATG
1 GCGATTTTCAACTATCGCAACGCGAAATG
316986 GAAAATCGCA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 89 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (61 bp):
GCGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATTTGAGATAGTGGAGATCGCGTT
Found at i:316981 original size:21 final size:21
Alignment explanation
Indices: 316957--317022 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
316947 AGATCGCGTT
316957 GCGATTTTCAACTATCGCAAC
1 GCGATTTTCAACTATCGCAAC
** ** * *
316978 GCGAAATGGAA-AATCGCAAT
1 GCGATTTTCAACTATCGCAAC
*
316998 GCGATTTTCAACTATTGCAAC
1 GCGATTTTCAACTATCGCAAC
317019 GCGA
1 GCGA
317023 AATGCAACGC
Statistics
Matches: 31, Mismatches: 13, Indels: 2
0.67 0.28 0.04
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (21 bp):
GCGATTTTCAACTATCGCAAC
Found at i:317030 original size:21 final size:21
Alignment explanation
Indices: 316965--317030 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
316955 TTGCGATTTT
316965 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * * ** *
316986 GAA-AATCGCAATGCGATTTT
1 CAACTATCGCAACGCGAAATG
*
317006 CAACTATTGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
317027 CAAC
1 CAAC
317031 GCGAATTTGC
Statistics
Matches: 31, Mismatches: 13, Indels: 2
0.67 0.28 0.04
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:318292 original size:2 final size:2
Alignment explanation
Indices: 318285--318339 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
318275 GTTAAAAGAG
318285 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
318327 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
318340 TTAAATTCTC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:320000 original size:3 final size:3
Alignment explanation
Indices: 319992--320018 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
319982 GACCTTCAAA
319992 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
320019 CTCTCTGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:321019 original size:25 final size:25
Alignment explanation
Indices: 320985--321036 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
320975 ACAAGGAAAG
320985 GTAGAAATAAGATTGACTCAAATAC
1 GTAGAAATAAGATTGACTCAAATAC
321010 GTAGAAATAAGATTGACTCAAATAC
1 GTAGAAATAAGATTGACTCAAATAC
321035 GT
1 GT
321037 GAACCCTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (25 bp):
GTAGAAATAAGATTGACTCAAATAC
Found at i:328336 original size:2 final size:2
Alignment explanation
Indices: 328329--328361 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
328319 ACCCTTCTCC
328329 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
328362 AAGCAGCCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:336102 original size:2 final size:2
Alignment explanation
Indices: 336095--336119 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
336085 TTTCTCATTC
336095 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
336120 CACACACGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:338258 original size:21 final size:21
Alignment explanation
Indices: 338233--338273 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
338223 GTAGTATAAT
338233 TATATTGTTATGTTCGTATAC
1 TATATTGTTATGTTCGTATAC
338254 TATATTGTTATGTTCGTATA
1 TATATTGTTATGTTCGTATA
338274 TGTCCATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.07, G:0.15, T:0.54
Consensus pattern (21 bp):
TATATTGTTATGTTCGTATAC
Found at i:339054 original size:28 final size:26
Alignment explanation
Indices: 339000--339058 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
338990 GTAAAAATAA
* * *
339000 TAATTTTTTTTTTATTTTTAGTAATT
1 TAATTTTTTTTTTAGTATTACTAATT
339026 TAATTTTTATTTTTAGTATTACTATATT
1 TAATTTTT-TTTTTAGTATTACTA-ATT
339054 TAATT
1 TAATT
339059 CTTTGAACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 8 0.29
27 12 0.43
28 8 0.29
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (26 bp):
TAATTTTTTTTTTAGTATTACTAATT
Found at i:339115 original size:24 final size:23
Alignment explanation
Indices: 339060--339115 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
339050 TATTTAATTC
*
339060 TTTGAACATTTTTATATTTTAAA
1 TTTGAATATTTTTATATTTTAAA
*
339083 TTTATAATATTTTT-TATTTTAAAAA
1 TTT-GAATATTTTTATATTTT--AAA
339108 TTTGAATA
1 TTTGAATA
339116 AGCTCTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
23 9 0.33
24 12 0.44
25 6 0.22
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (23 bp):
TTTGAATATTTTTATATTTTAAA
Found at i:342467 original size:18 final size:18
Alignment explanation
Indices: 342444--342483 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
342434 TTTCTGAATC
342444 AAAAATTAAAATAAATTT
1 AAAAATTAAAATAAATTT
* *
342462 AAAAATTATAATAAGTTT
1 AAAAATTAAAATAAATTT
342480 AAAA
1 AAAA
342484 CTAATTACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (18 bp):
AAAAATTAAAATAAATTT
Found at i:347869 original size:20 final size:20
Alignment explanation
Indices: 347833--347870 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
347823 ATCCTATTCC
**
347833 CTGATAATCTTTTATTCCCA
1 CTGATAATCTTACATTCCCA
347853 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
347871 GTGAACCAGA
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:0.26, C:0.26, G:0.05, T:0.42
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:350658 original size:16 final size:15
Alignment explanation
Indices: 350627--350682 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
350617 CTATTTAATA
350627 TAAATCCTAAACAAAT
1 TAAA-CCTAAACAAAT
350643 TAAACCTAAACTAAAT
1 TAAACCTAAAC-AAAT
**
350659 TAAATATAAACAAAT
1 TAAACCTAAACAAAT
*
350674 TTAACCTAA
1 TAAACCTAA
350683 TGCGTGGAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 17 0.50
16 17 0.50
ACGTcount: A:0.57, C:0.16, G:0.00, T:0.27
Consensus pattern (15 bp):
TAAACCTAAACAAAT
Found at i:352467 original size:64 final size:64
Alignment explanation
Indices: 352368--352491 Score: 212
Period size: 64 Copynumber: 1.9 Consensus size: 64
352358 AATTAATTCA
**
352368 TTTTTTAAAATTATTATCTTTTTATTTCTTATTGTTAATCTCAATTGTCTATTTAATTTTTTAT
1 TTTTTTAAAATTATTATCTTCCTATTTCTTATTGTTAATCTCAATTGTCTATTTAATTTTTTAT
* *
352432 TTTTTTTAAATTATTATCTTCCTATTTCTTATTGTTAATCTCAGTTGTCTATTTAATTTT
1 TTTTTTAAAATTATTATCTTCCTATTTCTTATTGTTAATCTCAATTGTCTATTTAATTTT
352492 ATTCTTCCAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.23, C:0.10, G:0.04, T:0.63
Consensus pattern (64 bp):
TTTTTTAAAATTATTATCTTCCTATTTCTTATTGTTAATCTCAATTGTCTATTTAATTTTTTAT
Found at i:365897 original size:18 final size:19
Alignment explanation
Indices: 365865--365900 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
365855 TTTTATTATG
365865 AAATAAAGAAAATAAAAAA
1 AAATAAAGAAAATAAAAAA
*
365884 AAAT-AAGAATATAAAAA
1 AAATAAAGAAAATAAAAA
365901 TAAGAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.14
Consensus pattern (19 bp):
AAATAAAGAAAATAAAAAA
Found at i:365901 original size:14 final size:13
Alignment explanation
Indices: 365864--365910 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
365854 TTTTTATTAT
365864 GAAATAAAGAA-AA
1 GAAATAAA-AATAA
* *
365877 TAAAAAAAAATAA
1 GAAATAAAAATAA
365890 GAATATAAAAATAA
1 GAA-ATAAAAATAA
365904 GAAATAA
1 GAAATAA
365911 GAGAAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 2 0.07
13 14 0.50
14 12 0.43
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.15
Consensus pattern (13 bp):
GAAATAAAAATAA
Found at i:366065 original size:10 final size:10
Alignment explanation
Indices: 366052--366092 Score: 50
Period size: 9 Copynumber: 4.3 Consensus size: 10
366042 AATTTGTAAA
366052 TATTTTATAT
1 TATTTTATAT
366062 TATTTTATA-
1 TATTTTATAT
366071 TATTTTA-AT
1 TATTTTATAT
* *
366080 GATTTTAAAT
1 TATTTTATAT
366090 TAT
1 TAT
366093 CAGTTTAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 1 0.04
9 13 0.48
10 13 0.48
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (10 bp):
TATTTTATAT
Found at i:385013 original size:15 final size:16
Alignment explanation
Indices: 384977--385016 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
384967 CAGATGGTTC
*
384977 TCTTGTAAGGATTTTT
1 TCTTGTAAGGATGTTT
*
384993 TTTTGTAAGG-TGTTT
1 TCTTGTAAGGATGTTT
385008 TCTTGTAAG
1 TCTTGTAAG
385017 TTGATTAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.17, C:0.05, G:0.23, T:0.55
Consensus pattern (16 bp):
TCTTGTAAGGATGTTT
Found at i:427703 original size:2 final size:2
Alignment explanation
Indices: 427696--427742 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
427686 TTTTGAATCA
427696 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
427738 A- AT AT
1 AT AT AT
427743 TATCAATAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:429014 original size:43 final size:44
Alignment explanation
Indices: 428967--429123 Score: 152
Period size: 43 Copynumber: 3.7 Consensus size: 44
428957 TTACAACATA
* *
428967 TAGCGGCGATTGT-TCA-ACAAACGCCGCAAAAGGTATTGATATT
1 TAGCGGCGATT-TATCATACAAACGCCGCAATAGGTGTTGATATT
429010 TAGCGGCG-TTTATCATTA-AAACGCCGCAATAGGTGTTGATATT
1 TAGCGGCGATTTATCA-TACAAACGCCGCAATAGGTGTTGATATT
* ** *
429053 TAACGGC-ATTTGGCATACAAACGCCGCAATA-GTCGTTGATGTT
1 TAGCGGCGATTTATCATACAAACGCCGCAATAGGT-GTTGATATT
429096 TAGCGGCG-TTT-TC-TACAAAAACGCCGCA
1 TAGCGGCGATTTATCATAC--AAACGCCGCA
429124 GTATATTTTT
Statistics
Matches: 97, Mismatches: 8, Indels: 18
0.79 0.07 0.15
Matches are distributed among these distances:
41 4 0.04
42 10 0.10
43 82 0.85
44 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (44 bp):
TAGCGGCGATTTATCATACAAACGCCGCAATAGGTGTTGATATT
Found at i:429594 original size:42 final size:42
Alignment explanation
Indices: 429546--429641 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
429536 TGATATATTA
*
429546 CTTCTCTCTGTTCTGCCGCTGCCT-CTCTCTG-TGCTGCCGCTG
1 CTTCTCTCTGTTCTGCCGCTG-CTGCTCT-AGCTGCTGCCGCTG
* * * *
429588 CTTCTCTCTCTGCTTCCGCTGCTGCTCTAGCTGCTTCCGCTG
1 CTTCTCTCTGTTCTGCCGCTGCTGCTCTAGCTGCTGCCGCTG
*
429630 CTGCTCTCTGTT
1 CTTCTCTCTGTT
429642 TCCCTTGCTT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
41 3 0.07
42 41 0.93
ACGTcount: A:0.01, C:0.40, G:0.20, T:0.40
Consensus pattern (42 bp):
CTTCTCTCTGTTCTGCCGCTGCTGCTCTAGCTGCTGCCGCTG
Found at i:429610 original size:21 final size:21
Alignment explanation
Indices: 429546--429638 Score: 96
Period size: 21 Copynumber: 4.4 Consensus size: 21
429536 TGATATATTA
* *
429546 CTTCTCTCTGTTCTGCCGCTG
1 CTTCTCTCTCTGCTGCCGCTG
* *
429567 CCTCTCTCTGTGCTGCCGCTG
1 CTTCTCTCTCTGCTGCCGCTG
*
429588 CTTCTCTCTCTGCTTCCGCTG
1 CTTCTCTCTCTGCTGCCGCTG
* ** *
429609 CTGCTCTAGCTGCTTCCGCTG
1 CTTCTCTCTCTGCTGCCGCTG
*
429630 CTGCTCTCT
1 CTTCTCTCT
429639 GTTTCCCTTG
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.01, C:0.41, G:0.19, T:0.39
Consensus pattern (21 bp):
CTTCTCTCTCTGCTGCCGCTG
Found at i:437880 original size:83 final size:83
Alignment explanation
Indices: 437772--438014 Score: 281
Period size: 83 Copynumber: 2.9 Consensus size: 83
437762 ACTTTATGTG
* * * * *
437772 TAATATATTGCGGCGTTTTTTGTAAAAACGCCGCCAATTTACCGCTCTATTGCGGCGTTTTTACT
1 TAATCTATTGAGGCGTTTGTGGTAAAAACGCCGCCAATTTACCACTCTATTGCGGCGTTTTTACT
* *
437837 CAATCGCTGCAAAATTTA
66 AAATCGCCGCAAAATTTA
* * * * * **
437855 TATTCTATTGTGGCGTTTGTGGTAAAAACGCTGCCAGTTTACCACTATATTGCGGCGTTTTGGCT
1 TAATCTATTGAGGCGTTTGTGGTAAAAACGCCGCCAATTTACCACTCTATTGCGGCGTTTTTACT
437920 AAATCGCCGCAAAATTTA
66 AAATCGCCGCAAAATTTA
* * * * * *
437938 TAATCTATTGAAGCGTTTGTGATATAAACGCCGCTAATTTATCACCCTATTGCGGCGTTTTTA-T
1 TAATCTATTGAGGCGTTTGTGGTAAAAACGCCGCCAATTTACCACTCTATTGCGGCGTTTTTACT
*
438002 AAAAACGCCGCAA
66 -AAATCGCCGCAA
438015 TATGTCAATT
Statistics
Matches: 132, Mismatches: 27, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
82 1 0.01
83 131 0.99
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (83 bp):
TAATCTATTGAGGCGTTTGTGGTAAAAACGCCGCCAATTTACCACTCTATTGCGGCGTTTTTACT
AAATCGCCGCAAAATTTA
Found at i:437887 original size:42 final size:42
Alignment explanation
Indices: 437841--437968 Score: 100
Period size: 42 Copynumber: 3.1 Consensus size: 42
437831 TTTACTCAAT
* *
437841 CGCTGCAAAATTTATATTCTATTGTGGCGTTTGTGGTAAAAA
1 CGCTGCAAAATTTATAATCTATTGAGGCGTTTGTGGTAAAAA
* * * * * * *
437883 CGCTGC-CAGTTTACCACTATATTGCGGCGTTT-TGGCT-AAAT
1 CGCTGCAAAATTTA-TAATCTATTGAGGCGTTTGTGG-TAAAAA
* * * *
437924 CGCCGCAAAATTTATAATCTATTGAAGCGTTTGTGATATAAA
1 CGCTGCAAAATTTATAATCTATTGAGGCGTTTGTGGTAAAAA
437966 CGC
1 CGC
437969 CGCTAATTTA
Statistics
Matches: 63, Mismatches: 18, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
41 30 0.48
42 33 0.52
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (42 bp):
CGCTGCAAAATTTATAATCTATTGAGGCGTTTGTGGTAAAAA
Found at i:438008 original size:41 final size:41
Alignment explanation
Indices: 437777--438054 Score: 161
Period size: 41 Copynumber: 6.7 Consensus size: 41
437767 ATGTGTAATA
* * * *
437777 TATTGCGGCGTTTTTTGTAAAAACGCCGCCAATTTACCGCTC
1 TATTGCGGCG-TTTTTATAAAAACGCCGCAAATTTATCACTC
* * * *
437819 TATTGCGGCGTTTTTACT-CAATCGCTGCAAAATTTAT-ATTC
1 TATTGCGGCGTTTTTA-TAAAAACGCCGC-AAATTTATCACTC
* ** * * * * *
437860 TATTGTGGCGTTTGTGGTAAAAACGCTGCCAGTTTACCACTA
1 TATTGCGGCGTTT-TTATAAAAACGCCGCAAATTTATCACTC
** * *
437902 TATTGCGGCGTTTTGGCT-AAATCGCCGCAAAATTTAT-AATC
1 TATTGCGGCGTTTT-TATAAAAACGCCGC-AAATTTATCACTC
** * * * *
437943 TATTGAAGCGTTTGTGATATAAACGCCGCTAATTTATCACCC
1 TATTGCGGCGTTT-TTATAAAAACGCCGCAAATTTATCACTC
* * * *
437985 TATTGCGGCGTTTTTATAAAAACGCCGC-AATATGTCAATTA
1 TATTGCGGCGTTTTTATAAAAACGCCGCAAATTTATC-ACTC
*
438026 TATTGCAGCGTTTTTACTAAAAACGCCGC
1 TATTGCGGCGTTTTTA-TAAAAACGCCGC
438055 TAAAGTATCA
Statistics
Matches: 179, Mismatches: 45, Indels: 24
0.72 0.18 0.10
Matches are distributed among these distances:
40 6 0.03
41 92 0.51
42 81 0.45
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (41 bp):
TATTGCGGCGTTTTTATAAAAACGCCGCAAATTTATCACTC
Found at i:439417 original size:25 final size:25
Alignment explanation
Indices: 439384--439432 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
439374 AATTTTTTTG
*
439384 TGTCTATATATCATGTGAAGGTGAT
1 TGTCTATATATCACGTGAAGGTGAT
*
439409 TGTCTATATATTACGTGAAGGTGA
1 TGTCTATATATCACGTGAAGGTGA
439433 CATCGTCTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.08, G:0.24, T:0.39
Consensus pattern (25 bp):
TGTCTATATATCACGTGAAGGTGAT
Found at i:444171 original size:23 final size:23
Alignment explanation
Indices: 444145--444189 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
444135 CACCACAGCT
*
444145 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
444168 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
444190 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:444427 original size:149 final size:149
Alignment explanation
Indices: 444168--444471 Score: 590
Period size: 149 Copynumber: 2.0 Consensus size: 149
444158 CGAAGTGCCC
444168 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTATTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTATTTAAGAAT
*
444233 CATATACATATGCTATGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
444298 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
*
444317 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTATTTAAGAAT
444382 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
444447 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
444466 CGTAGA
1 CGTAGA
444472 CCCTCGACTC
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTATTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCG
Found at i:445013 original size:2 final size:2
Alignment explanation
Indices: 445006--445045 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
444996 TCTCTTAGAC
445006 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
445046 CACATGTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:445395 original size:18 final size:18
Alignment explanation
Indices: 445374--445408 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
445364 TCCCATCTAG
445374 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
445392 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
445409 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:445999 original size:46 final size:46
Alignment explanation
Indices: 445948--446054 Score: 196
Period size: 46 Copynumber: 2.3 Consensus size: 46
445938 CCCTACTGAG
445948 GGGGTATCGATTCCCTCATGACATTCTGGAAATTTTGTCGTTTGAA
1 GGGGTATCGATTCCCTCATGACATTCTGGAAATTTTGTCGTTTGAA
*
445994 GGGGTATCGATTCCCTCATGACATTCTGGAAATTTTGTCGTTTGAT
1 GGGGTATCGATTCCCTCATGACATTCTGGAAATTTTGTCGTTTGAA
*
446040 GGGGTATCGGTTCCC
1 GGGGTATCGATTCCC
446055 CTTGAATGGG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (46 bp):
GGGGTATCGATTCCCTCATGACATTCTGGAAATTTTGTCGTTTGAA
Found at i:448411 original size:16 final size:16
Alignment explanation
Indices: 448387--448420 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
448377 TATCACCGAC
*
448387 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
448403 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
448419 CG
1 CG
448421 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:454672 original size:2 final size:2
Alignment explanation
Indices: 454665--454695 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
454655 AAGGGTTTAT
454665 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
454696 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:456539 original size:229 final size:227
Alignment explanation
Indices: 456134--456582 Score: 783
Period size: 229 Copynumber: 2.0 Consensus size: 227
456124 GTAAATTATC
* * * *
456134 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATAATATTTAGT
*
456199 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
456264 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
456329 AAACATAAATTACATAACTTTCAAAAAAATATA
196 AAACATAAATTACATAACTTT-AAAAAAATATA
*
456362 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATAATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATAATATTTAG
*
456427 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAAT-ATAAT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAT-AT
* *
456491 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
129 TTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAT
456556 TGAAACATAAATTACATAACTTTAAAA
194 TGAAACATAAATTACATAACTTTAAAA
456583 GCAGTTTTAA
Statistics
Matches: 210, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
228 42 0.20
229 168 0.80
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATAATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAATATA
Found at i:456671 original size:20 final size:19
Alignment explanation
Indices: 456648--456693 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
456638 CGATATACCA
456648 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
456668 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
456688 GGTAAA
1 GGTAAA
456694 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:456837 original size:20 final size:19
Alignment explanation
Indices: 456814--456860 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
456804 CGATATAACA
*
456814 GGTAAAAATATGATAAAACT
1 GGTAAAAA-ATGATAAAACC
456834 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
456854 GGTAAAA
1 GGTAAAA
456861 TGATACCGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:459136 original size:21 final size:21
Alignment explanation
Indices: 459089--459153 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
459079 AAGACAATCA
* *
459089 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
459111 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
459131 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
459152 AG
1 AG
459154 GAATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:459228 original size:33 final size:33
Alignment explanation
Indices: 459186--459251 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
459176 AAATAGATGG
*
459186 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
459219 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
459252 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:461079 original size:18 final size:19
Alignment explanation
Indices: 461035--461082 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
461025 AATGTCGAGT
461035 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
461054 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
461073 T-ATTTTGTAT
1 TAATTTTGTAT
461083 GTGAATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:461559 original size:193 final size:198
Alignment explanation
Indices: 461200--462345 Score: 2018
Period size: 193 Copynumber: 5.9 Consensus size: 198
461190 CAATATGGCC
* * *
461200 AACAGGGTGCACCCATAAAGTGTCGATCCATATAAAAAAAGTGTCAATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
461265 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGATTTTATGAGAG
66 CAAAAG-ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
461330 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
130 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
461395 GGAA
195 GGAA
*
461399 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
461464 C-AAA-ATAATGT-ATATGT-ATTTTTCAATCTAA-CGGTACAATTATACCGGTTTTATGAGAGA
66 CAAAAGATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
461524 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATG
131 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATG
461589 GAA
196 GAA
461592 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
461657 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAG-ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
461722 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTT-CCATAATGAAT
130 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
461786 GG-A
195 GGAA
461789 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
461854 CAAAAG-T-ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
66 CAAAAGATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
461917 ATATGTCTAAAT-ATGT-TCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATG
131 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATG
461980 G-A
196 GAA
461982 AAC-AGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCC-AAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
462044 CAAAAGTATAATGTAATATGTAATTTTTCAATC---CCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAG-ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
462106 AATATGTCTAAATAATGTGTCGACACTAATAT--TTTGTGTCGATAC-TTTTTCCCAGAATGAAT
130 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
462168 GGAA
195 GGAA
*
462172 AACAAGGTGCA-CCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCCAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
462235 CAAAAGTATAATGTAATATGT-ATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAG-ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
462299 AATATGTCTAAATAATGTGTCGACACT-ATATAGTTTGTGTCGATACT
130 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
462346 AATTTAAATA
Statistics
Matches: 919, Mismatches: 7, Indels: 46
0.95 0.01 0.05
Matches are distributed among these distances:
189 19 0.02
190 127 0.14
191 59 0.06
192 83 0.09
193 260 0.28
194 98 0.11
195 7 0.01
196 14 0.02
197 78 0.08
198 29 0.03
199 145 0.16
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (198 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATG
GAA
Found at i:463805 original size:3 final size:3
Alignment explanation
Indices: 463797--463868 Score: 72
Period size: 3 Copynumber: 24.0 Consensus size: 3
463787 TGAAGCTGAC
* * * ** * *
463797 GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT GAC GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
463845 GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT
463869 CCAAACAAGT
Statistics
Matches: 54, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.35, C:0.06, G:0.35, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:465383 original size:178 final size:182
Alignment explanation
Indices: 465045--465725 Score: 1132
Period size: 178 Copynumber: 3.8 Consensus size: 182
465035 ACAAAGTTTT
* * * *
465045 CACTTTTTAATA-TGTGTCTGTACTTTATGTCCAGAATGAAAGAAAAATGTGTCGATACCATTTA
1 CACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTA
* *** *
465109 AAAAAGTGTCGATTGAAAAAAACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATA
66 AAAAAGTGTCGA--CATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATA
*
465174 TAACCGGTATAAATATACCGG-TTTATGAGCGAATAGGTCTACAACCTATATCGA
129 TAACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCT-TATCGA
465228 CACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAG-AAAATGTGTCGATA-CATTT-
1 CACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTA
*
465290 AAAAAGTGTCGACATTTACACATCGGAACCCATA-TTATAATGTAATAGATAA-TTTGTAATATA
66 AAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATA
465353 ACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCGA
131 ACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACC-TTATCGA
*
465406 CACTTTCTAATATTGTGTCGGTACTTTATGTTCAGATT-GAAG-AAAATGTGTCGATACCATTTA
1 CACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTA
465469 AAAAAGTGTCGACA-TTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATA
66 AAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATA
465533 ACCGGTATAAAAATACCGGTTTTATGAGCGAATA-GTCTACAACCTTATCGA
131 ACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTATCGA
*
465584 CACTTTCTAATATTGTGTCGGTACTTTATGTTCAGATTGGAAGAAAAATGTGTCGATACCATTTA
1 CACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTA
465649 AAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATA
66 AAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATA
465714 ACCGGTATAAAA
131 ACCGGTATAAAA
465726 TGTGTCGATA
Statistics
Matches: 475, Mismatches: 13, Indels: 22
0.93 0.03 0.04
Matches are distributed among these distances:
177 47 0.10
178 154 0.32
179 63 0.13
180 80 0.17
181 74 0.16
182 5 0.01
183 25 0.05
184 27 0.06
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (182 bp):
CACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTA
AAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATA
ACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTATCGA
Found at i:465764 original size:23 final size:23
Alignment explanation
Indices: 465719--465764 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
465709 ATATAACCGG
465719 TATAAAATGTGTCGATACCTTTT
1 TATAAAATGTGTCGATACCTTTT
*
465742 TATAAAA-GTGTCGATACTTTTT
1 TATAAAATGTGTCGATACCTTTT
465764 T
1 T
465765 CACTGTGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (23 bp):
TATAAAATGTGTCGATACCTTTT
Found at i:468861 original size:21 final size:20
Alignment explanation
Indices: 468835--468887 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
468825 TAAACATATG
468835 ATGTAATAGGTAGCCCTTAT
1 ATGTAATAGGTAGCCCTTAT
* *
468855 AATGTAATAGGTA-TCGTTAT
1 -ATGTAATAGGTAGCCCTTAT
468875 ATGTAATAGGTAG
1 ATGTAATAGGTAG
468888 GGTTATATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 12 0.41
20 5 0.17
21 12 0.41
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.36
Consensus pattern (20 bp):
ATGTAATAGGTAGCCCTTAT
Found at i:468880 original size:19 final size:19
Alignment explanation
Indices: 468835--468900 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
468825 TAAACATATG
*
468835 ATGTAATAGGTAGCCCTTAT
1 ATGTAATAGGTA-CCGTTAT
*
468855 AATGTAATAGGTATCGTTAT
1 -ATGTAATAGGTACCGTTAT
**
468875 ATGTAATAGGTAGGGTTAT
1 ATGTAATAGGTACCGTTAT
468894 ATTGTAA
1 A-TGTAA
468901 AGTGTCTATC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
19 18 0.45
20 10 0.25
21 12 0.30
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.38
Consensus pattern (19 bp):
ATGTAATAGGTACCGTTAT
Found at i:469311 original size:23 final size:23
Alignment explanation
Indices: 469263--469311 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
469253 TAGGTAGCCC
*
469263 TATATAATGTAATAGGTATCGTT
1 TATATAATGTAATAGGTATCGGT
469286 TATATAATGTAATAGGTAGT-GGT
1 TATATAATGTAATAGGTA-TCGGT
469309 TAT
1 TAT
469312 TGTAAAGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.20, T:0.43
Consensus pattern (23 bp):
TATATAATGTAATAGGTATCGGT
Found at i:469522 original size:416 final size:413
Alignment explanation
Indices: 468738--469546 Score: 1393
Period size: 416 Copynumber: 1.9 Consensus size: 413
468728 TCGCAGTACA
468738 TGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAGTATCGATCCTTTTATAAAAAGT
1 TGTTAAAAAAATTGAAACATAAA-TACATAAGTTTTAAAAAAGTATCGATCCTTTTATAAAAAGT
468803 ATGGACACTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATAATGTAATAGGTA
65 ATGGACACTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATAATGTAATAGGTA
468868 TCGTTATATGTAATAGGTAGGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATAC
130 TCGTTATATGTAATAGGTAGGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATAC
468933 TTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGGTTTTAAGATATTAATTTAG
195 TTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGGTTTTAAGATATTAATTTAG
* *
468998 TAATTATAGGCGTCTAATGATTTATTTTTACGTTACGGTTATATTATTATTAAATTAAAAATTCT
260 TAATTATAGGCGTATAATGATTTATTTTTACGTTACGATTATATTATTATTAAATTAAAAATTCT
*
469063 AAATAATATTTTATAAAATATAAAAACAATCAAATATTTTTTGTGCAAATGAAATTATTAAATCA
325 AAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTGTGCAAATGAAATTATTAAATCA
469128 AATTGTAGGTGGAAAACATGAAAC
390 AATTGTAGGTGGAAAACATGAAAC
469152 TGTT-AAAAAATTGAAACATAAA-ACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAG
1 TGTTAAAAAAATTGAAACATAAATACATAAGTTTT-AAAAAAGTATCGATCC-TTTTATAAAAAG
469215 TATGGACACTTTCAATATAA-AGGTAAACATATGATGT-ATAGGTAGCCCTATATAATGTAATAG
64 TATGGACAC-TTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCT-TATAATGTAATAG
469278 GTATCGTTTATATAATGTAATAGGTAGTGG-T-TATTGTAAAGTGTCTATCCTTTTTATAAAAGT
127 GTATCG--T-TAT-ATGTAATAGGTAG-GGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGT
469341 GTCCATACTTTTTTCAC-GTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATA
187 GTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTG-GTTTTAAGATA
469405 TTAATTTAGTAATTATAGG-GTATAATGATTTATTTTTTACGTTACGATATATATTATTATTAAA
251 TTAATTTAGTAATTATAGGCGTATAATGATTTA-TTTTTACGTTACGAT-TATATTATTATTAAA
* *
469469 TTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATC-AATAATTTTTGTGCAAATGAAA
314 TTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTGTGCAAATGAAA
469533 TTATTAAATCAAAT
379 TTATTAAATCAAAT
469547 AATTCAAATT
Statistics
Matches: 378, Mismatches: 5, Indels: 22
0.93 0.01 0.05
Matches are distributed among these distances:
411 11 0.03
412 28 0.07
413 75 0.20
414 14 0.04
415 48 0.13
416 131 0.35
417 69 0.18
418 2 0.01
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (413 bp):
TGTTAAAAAAATTGAAACATAAATACATAAGTTTTAAAAAAGTATCGATCCTTTTATAAAAAGTA
TGGACACTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATAATGTAATAGGTAT
CGTTATATGTAATAGGTAGGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACT
TTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGGTTTTAAGATATTAATTTAGT
AATTATAGGCGTATAATGATTTATTTTTACGTTACGATTATATTATTATTAAATTAAAAATTCTA
AATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTGTGCAAATGAAATTATTAAATCAA
ATTGTAGGTGGAAAACATGAAAC
Found at i:469610 original size:25 final size:25
Alignment explanation
Indices: 469576--469626 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
469566 ACAACAAATC
*
469576 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
469601 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
469626 A
1 A
469627 TTTGGATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:469892 original size:18 final size:18
Alignment explanation
Indices: 469871--469907 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
469861 GTAATTGGAG
469871 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
469889 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
469907 T
1 T
469908 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:469915 original size:24 final size:24
Alignment explanation
Indices: 469863--469909 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
469853 ATTTATATGT
* *
469863 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
469887 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
469910 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:470226 original size:38 final size:38
Alignment explanation
Indices: 470160--470282 Score: 196
Period size: 37 Copynumber: 3.2 Consensus size: 38
470150 TCCGATGCTC
* *
470160 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAA-TTCATATGATGCCAAGCAAAAGGAA
470199 ATCAAAATCCAAATTCATATGATGCCAAGC-AAAGGAA
1 ATCAAAATCCAAATTCATATGATGCCAAGCAAAAGGAA
470236 ATC-AAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAT-TCATATGATGCCAAGCAAAAGGAA
470274 ATCAAAATC
1 ATCAAAATC
470283 TACAACTTGA
Statistics
Matches: 79, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
36 10 0.13
37 26 0.33
38 25 0.32
39 18 0.23
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (38 bp):
ATCAAAATCCAAATTCATATGATGCCAAGCAAAAGGAA
Found at i:470254 original size:37 final size:38
Alignment explanation
Indices: 470164--470279 Score: 191
Period size: 38 Copynumber: 3.1 Consensus size: 38
470154 ATGCTCATCA
* *
470164 AAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAAATC
1 AAATCCAAATCTCATATGATGCCAAGCAAAAGGAAATC
470202 AAAATCCAAAT-TCATATGATGCCAAGC-AAAGGAAATC
1 -AAATCCAAATCTCATATGATGCCAAGCAAAAGGAAATC
470239 AAATCCAAATCTCATATGATGCCAAGCAAAAGGAAATC
1 AAATCCAAATCTCATATGATGCCAAGCAAAAGGAAATC
470277 AAA
1 AAA
470280 ATCTACAACT
Statistics
Matches: 73, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
36 10 0.14
37 26 0.36
38 28 0.38
39 9 0.12
ACGTcount: A:0.48, C:0.20, G:0.15, T:0.17
Consensus pattern (38 bp):
AAATCCAAATCTCATATGATGCCAAGCAAAAGGAAATC
Found at i:470704 original size:23 final size:23
Alignment explanation
Indices: 470673--470736 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
470663 ATAGGTAAAC
*
470673 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
470696 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
470719 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
470737 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:470743 original size:23 final size:23
Alignment explanation
Indices: 470673--470745 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
470663 ATAGGTAAAC
* **
470673 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
470696 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
470719 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
470742 ATAT
1 ATAT
470746 TGTAAACTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:472056 original size:23 final size:23
Alignment explanation
Indices: 472024--472097 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
472014 GTGTTCATTT
* *
472024 ATTTATTGTTCGCGAACGTGTTC
1 ATTTAGTGTTCACGAACGTGTTC
* *
472047 GTTTAGTGTTCACGAAAGTGTTC
1 ATTTAGTGTTCACGAACGTGTTC
* *
472070 ATTTAGTGTCCACGAACGTGTTT
1 ATTTAGTGTTCACGAACGTGTTC
472093 ATTTA
1 ATTTA
472098 ACATTTACGA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.42
Consensus pattern (23 bp):
ATTTAGTGTTCACGAACGTGTTC
Found at i:474232 original size:23 final size:24
Alignment explanation
Indices: 474206--474254 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
474196 AACTGAACAA
*
474206 AATTTAAATATAAAATA-ACATCT
1 AATTCAAATATAAAATATACATCT
* *
474229 AATTCAAATATAGAATATATATCT
1 AATTCAAATATAAAATATACATCT
474253 AA
1 AA
474255 ATCTATTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (24 bp):
AATTCAAATATAAAATATACATCT
Found at i:475031 original size:21 final size:20
Alignment explanation
Indices: 474945--475102 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
474935 AAATGACCAA
**
474945 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
474964 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
474984 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
475004 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
475025 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
475046 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
475066 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
475087 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
475103 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:475196 original size:20 final size:20
Alignment explanation
Indices: 475070--475274 Score: 201
Period size: 20 Copynumber: 10.5 Consensus size: 20
475060 GATTTTCAAT
* ** *
475070 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
475090 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
475110 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
475130 AATCGCAACGTGTAT-CGTA
1 AATCGCAACGCGTATCCGTA
**
475149 AATCGCAACGCGTATGGGGTA
1 AATCGCAACGCGTAT-CCGTA
*
475170 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
475190 TATCGCAA--CGTAT-C--A
1 AATCGCAACGCGTATCCGTA
475205 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
475225 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
475245 AATCGCAACG-ATAATCTGTA
1 AATCGCAACGCGT-ATCCGTA
475265 AATCGCAACG
1 AATCGCAACG
475275 ATAATCTAAA
Statistics
Matches: 157, Mismatches: 18, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
15 8 0.05
17 6 0.04
18 6 0.04
19 20 0.13
20 98 0.62
21 19 0.12
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:475209 original size:35 final size:35
Alignment explanation
Indices: 475089--475235 Score: 118
Period size: 35 Copynumber: 3.9 Consensus size: 35
475079 GCGAATATGA
* *
475089 AAATCGCAACGCG-AACACATAAATCGCAACGCGTATCC
1 AAATCGCAACGCGTATC-CGTAAATCGCAA--CGTAT-C
* *
475127 GTAAATCGCAACGTGTAT-CGTAAATCGCAACGCGTATGGGGT
1 --AAATCGCAACGCGTATCCGTAAATCGCAA--CGTAT----C
* *
475169 AAATCGCAATGCGTATCCGTATATCGCAACGTATC
1 AAATCGCAACGCGTATCCGTAAATCGCAACGTATC
475204 AAATCGCAACGCGTATCCGTAAATCGCAACGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGT
475236 GTATCCGTAA
Statistics
Matches: 91, Mismatches: 11, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
35 30 0.33
39 23 0.25
40 26 0.29
41 12 0.13
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.20
Consensus pattern (35 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGTATC
Found at i:475270 original size:75 final size:74
Alignment explanation
Indices: 475129--475274 Score: 188
Period size: 75 Copynumber: 1.9 Consensus size: 74
475119 GCGTATCCGT
* ** *
475129 AAATCGCAACGTGTATCGTAAATCGCAACGCGTATGGGGTAAATCGCAATGCGTATCCGTATATC
1 AAATCGCAACGCGTATCGTAAATCGCAACGCGTATGCCGTAAATCGCAA-GCGTATCCGTAAATC
475194 GCAACGTATC
65 GCAACGTATC
* *
475204 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT-CCGTAAATCGCAA-CGATAATCTGTAAA
1 AAATCGCAACGCGTAT-CGTAAATCGCAACGCGTATGCCGTAAATCGCAAGCG-T-ATCCGTAAA
475267 TCGCAACG
63 TCGCAACG
475275 ATAATCTAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
73 2 0.03
74 1 0.02
75 41 0.66
76 18 0.29
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.23
Consensus pattern (74 bp):
AAATCGCAACGCGTATCGTAAATCGCAACGCGTATGCCGTAAATCGCAAGCGTATCCGTAAATCG
CAACGTATC
Found at i:475275 original size:20 final size:20
Alignment explanation
Indices: 475204--475301 Score: 110
Period size: 20 Copynumber: 4.9 Consensus size: 20
475194 GCAACGTATC
* *
475204 AAATCGCAACGCGT-ATCCGT
1 AAATCGCAACG-ATAATCTGT
* *
475224 AAATCGCAACG-TGTATCCGT
1 AAATCGCAACGAT-AATCTGT
475244 AAATCGCAACGATAATCTGT
1 AAATCGCAACGATAATCTGT
**
475264 AAATCGCAACGATAATCTAA
1 AAATCGCAACGATAATCTGT
475284 AAATCGCAACGATAATCT
1 AAATCGCAACGATAATCT
475302 AATCGTAAAT
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
18 1 0.01
20 69 0.97
21 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.22
Consensus pattern (20 bp):
AAATCGCAACGATAATCTGT
Found at i:475290 original size:95 final size:94
Alignment explanation
Indices: 475109--475294 Score: 243
Period size: 95 Copynumber: 2.0 Consensus size: 94
475099 GCGAACACAT
* *
475109 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCGTAAATCGCAACGCGTATGGGGTAAATC
1 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCGTAAATCGCAACGCATATGCGGTAAATC
** *
475174 GCAATGCGTATCCGTATATCGCAACGTATC
66 GCAA-GCGTATCCAAAAATCGCAACGTATC
*
475204 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTAAATCGCAACG-ATAAT-CTGTAAA
1 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT-CGTAAATCGCAACGCAT-ATGCGGTAAA
*
475267 TCGCAA-CGATAATCTAAAAATCGCAACG
64 TCGCAAGCG-T-ATCCAAAAATCGCAACG
475295 ATAATCTAAT
Statistics
Matches: 80, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
93 2 0.03
94 1 0.01
95 61 0.76
96 16 0.20
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.22
Consensus pattern (94 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCGTAAATCGCAACGCATATGCGGTAAATC
GCAAGCGTATCCAAAAATCGCAACGTATC
Found at i:476040 original size:24 final size:24
Alignment explanation
Indices: 476001--476047 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
475991 AAATTTGGTC
476001 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
476025 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
476048 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:476238 original size:12 final size:12
Alignment explanation
Indices: 476221--476245 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
476211 ATATAATCCT
476221 GAAGAAGAAAAA
1 GAAGAAGAAAAA
476233 GAAGAAGAAAAA
1 GAAGAAGAAAAA
476245 G
1 G
476246 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:478580 original size:18 final size:19
Alignment explanation
Indices: 478547--478582 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
478537 ACTCAGATTT
478547 AAAACTTTTAAGGGAAAAA
1 AAAACTTTTAAGGGAAAAA
478566 AAAACTTTTAA-GGAAAA
1 AAAACTTTTAAGGGAAAA
478583 TAATACACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.58, C:0.06, G:0.14, T:0.22
Consensus pattern (19 bp):
AAAACTTTTAAGGGAAAAA
Found at i:479589 original size:2 final size:2
Alignment explanation
Indices: 479582--479619 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
479572 TAAGAAAATC
479582 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
479620 TATTAATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:479873 original size:13 final size:14
Alignment explanation
Indices: 479855--479887 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
479845 AAAAATATTT
479855 TATATTTA-AAAAA
1 TATATTTATAAAAA
479868 TATATTTATAAAAA
1 TATATTTATAAAAA
479882 T-TATTT
1 TATATTT
479888 TAATAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TATATTTATAAAAA
Found at i:481465 original size:18 final size:18
Alignment explanation
Indices: 481444--481479 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
481434 ATTTTTATAC
481444 ATTATATATTTCATATCA
1 ATTATATATTTCATATCA
481462 ATTATATATTTCATATCA
1 ATTATATATTTCATATCA
481480 TATAGAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTATATATTTCATATCA
Found at i:483512 original size:16 final size:16
Alignment explanation
Indices: 483491--483522 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
483481 AATAAATAAG
483491 CGAACATAAACGAACA
1 CGAACATAAACGAACA
483507 CGAACATAAACGAACA
1 CGAACATAAACGAACA
483523 AATTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.25, G:0.12, T:0.06
Consensus pattern (16 bp):
CGAACATAAACGAACA
Found at i:483616 original size:16 final size:16
Alignment explanation
Indices: 483595--483663 Score: 111
Period size: 16 Copynumber: 4.3 Consensus size: 16
483585 TAAATAAACG
483595 AACATAAACGAACACA
1 AACATAAACGAACACA
*
483611 AACATAAACGAACACG
1 AACATAAACGAACACA
*
483627 AACATAAATGAACACA
1 AACATAAACGAACACA
*
483643 AACATAAACGAACATA
1 AACATAAACGAACACA
483659 AACAT
1 AACAT
483664 TGGAGACCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.61, C:0.22, G:0.07, T:0.10
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:485234 original size:24 final size:24
Alignment explanation
Indices: 485173--485234 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
485163 TATTAGGTTA
*
485173 AACATAAATGAACGCACATAAACG
1 AACATAACTGAACGCACATAAACG
* *
485197 AACATAACTAAACGCATATAAACG
1 AACATAACTGAACGCACATAAACG
*
485221 AACATAACCGAACG
1 AACATAACTGAACG
485235 TTCACGAACG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.53, C:0.23, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAACTGAACGCACATAAACG
Found at i:488710 original size:60 final size:60
Alignment explanation
Indices: 488645--488787 Score: 268
Period size: 60 Copynumber: 2.4 Consensus size: 60
488635 TTGGGATGTG
488645 TTGGTGGTGGTGGGGATTTGTAGACATAATGAGGAGGTGGCGCTTTGTAGGGTTTTGGGT
1 TTGGTGGTGGTGGGGATTTGTAGACATAATGAGGAGGTGGCGCTTTGTAGGGTTTTGGGT
*
488705 TTGGTGGTGGTGGGGATTTGTAGACATAATGAGGAGGTGGTGCTTTGTAGGGTTTTGGGT
1 TTGGTGGTGGTGGGGATTTGTAGACATAATGAGGAGGTGGCGCTTTGTAGGGTTTTGGGT
*
488765 GTGGTGGTGGTGGGGATTTGTAG
1 TTGGTGGTGGTGGGGATTTGTAG
488788 TGATATGGTG
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 81 1.00
ACGTcount: A:0.14, C:0.03, G:0.47, T:0.36
Consensus pattern (60 bp):
TTGGTGGTGGTGGGGATTTGTAGACATAATGAGGAGGTGGCGCTTTGTAGGGTTTTGGGT
Found at i:488831 original size:48 final size:48
Alignment explanation
Indices: 488773--488959 Score: 225
Period size: 48 Copynumber: 3.9 Consensus size: 48
488763 GTGTGGTGGT
* *
488773 GGTGGGGATTTGTAGTGATATGGTGGCTGG-GAAGATTTTACTGGAGGA
1 GGTGGAGATTTGTAGTGATATGGTGG-TGGTGGAGATTTTACTGGAGGA
* * * * *
488821 GGTGGAGATTTATAGTGATATGTTGGTGGTGGATATTTCACTGGAGGT
1 GGTGGAGATTTGTAGTGATATGGTGGTGGTGGAGATTTTACTGGAGGA
* * *
488869 GGTGGAGATTTGTATTTG-TATGGTGGAGGGGGAGATTTTACTGGAGGA
1 GGTGGAGATTTGTA-GTGATATGGTGGTGGTGGAGATTTTACTGGAGGA
* *
488917 GGTGGAGATTTGTAATGATACGGTGGTGGTGGAGATTTGTACT
1 GGTGGAGATTTGTAGTGATATGGTGGTGGTGGAGATTT-TACT
488960 TGTATGGTGG
Statistics
Matches: 116, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
47 5 0.04
48 105 0.91
49 6 0.05
ACGTcount: A:0.21, C:0.04, G:0.41, T:0.34
Consensus pattern (48 bp):
GGTGGAGATTTGTAGTGATATGGTGGTGGTGGAGATTTTACTGGAGGA
Found at i:488902 original size:27 final size:26
Alignment explanation
Indices: 488872--488981 Score: 86
Period size: 27 Copynumber: 4.3 Consensus size: 26
488862 TGGAGGTGGT
488872 GGAGATTTGTATTTGTATGGTGGAGGG
1 GGAGATTTGTA-TTGTATGGTGGAGGG
* * *
488899 GGAGATTT-TA----CTGGAGGAGGT
1 GGAGATTTGTATTGTATGGTGGAGGG
* * * *
488920 GGAGATTTGTAATGATACGGTGGTGGT
1 GGAGATTTGTATTG-TATGGTGGAGGG
*
488947 GGAGATTTGTACTTGTATGGTGGCGGG
1 GGAGATTTGTA-TTGTATGGTGGAGGG
488974 GGAGATTT
1 GGAGATTT
488982 CACTGGAGGT
Statistics
Matches: 65, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
21 16 0.25
22 2 0.03
26 2 0.03
27 43 0.66
28 2 0.03
ACGTcount: A:0.20, C:0.04, G:0.43, T:0.34
Consensus pattern (26 bp):
GGAGATTTGTATTGTATGGTGGAGGG
Found at i:488906 original size:21 final size:22
Alignment explanation
Indices: 488882--488930 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
488872 GGAGATTTGT
*
488882 ATTTGTA-TGGTGGAGGGGGAG
1 ATTTGTACTGGAGGAGGGGGAG
*
488903 ATTT-TACTGGAGGAGGTGGAG
1 ATTTGTACTGGAGGAGGGGGAG
488924 ATTTGTA
1 ATTTGTA
488931 ATGATACGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 20 0.83
22 2 0.08
ACGTcount: A:0.22, C:0.02, G:0.43, T:0.33
Consensus pattern (22 bp):
ATTTGTACTGGAGGAGGGGGAG
Found at i:488912 original size:96 final size:96
Alignment explanation
Indices: 488770--488954 Score: 264
Period size: 96 Copynumber: 1.9 Consensus size: 96
488760 TGGGTGTGGT
* **
488770 GGTGGTGGGGATTTGTAGTGATATGGTGGCTGGGAAGATTTTACTGGAGGAGGTGGAGATTTATA
1 GGTGGTGGAGATTTGTAGTGATATGGTGGAGGGGAAGATTTTACTGGAGGAGGTGGAGATTTATA
* * * *
488835 GTGATATGTTGGTGGTGGATATTTCACTGGA
66 ATGATACGGTGGTGGTGGAGATTTCACTGGA
* * *
488866 GGTGGTGGAGATTTGTATTTG-TATGGTGGAGGGGGAGATTTTACTGGAGGAGGTGGAGATTTGT
1 GGTGGTGGAGATTTGTA-GTGATATGGTGGAGGGGAAGATTTTACTGGAGGAGGTGGAGATTTAT
488930 AATGATACGGTGGTGGTGGAGATTT
65 AATGATACGGTGGTGGTGGAGATTT
488955 GTACTTGTAT
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
96 76 0.97
97 2 0.03
ACGTcount: A:0.21, C:0.03, G:0.42, T:0.34
Consensus pattern (96 bp):
GGTGGTGGAGATTTGTAGTGATATGGTGGAGGGGAAGATTTTACTGGAGGAGGTGGAGATTTATA
ATGATACGGTGGTGGTGGAGATTTCACTGGA
Found at i:488945 original size:75 final size:75
Alignment explanation
Indices: 488866--489029 Score: 256
Period size: 75 Copynumber: 2.2 Consensus size: 75
488856 TTTCACTGGA
* * *
488866 GGTGGTGGAGATTTGTATTTGTATGGTGGAGGGGGAGATTTTACTGGAGGAGGTGGAGATTTGTA
1 GGTGGTGGAGATTTGTACTTGTATGGTGGAGGGGGAGATTTCACTGGAGGAGGTGGAGATGTGTA
488931 ATGATACGGT
66 ATGATACGGT
* *
488941 GGTGGTGGAGATTTGTACTTGTATGGTGGCGGGGGAGATTTCACTGGAGGTGGTGGAGATGTGTA
1 GGTGGTGGAGATTTGTACTTGTATGGTGGAGGGGGAGATTTCACTGGAGGAGGTGGAGATGTGTA
* *
489006 GTGATATGGT
66 ATGATACGGT
*
489016 GGTGGTGGATATTT
1 GGTGGTGGAGATTT
489030 CACTAGAGGC
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 81 1.00
ACGTcount: A:0.19, C:0.04, G:0.44, T:0.34
Consensus pattern (75 bp):
GGTGGTGGAGATTTGTACTTGTATGGTGGAGGGGGAGATTTCACTGGAGGAGGTGGAGATGTGTA
ATGATACGGT
Found at i:488993 original size:48 final size:48
Alignment explanation
Indices: 488941--489325 Score: 470
Period size: 48 Copynumber: 8.0 Consensus size: 48
488931 ATGATACGGT
* * *
488941 GGTGGTGGAGATTTGTACTTG-TATGGTGGCGGGGGAGATTTCACTGGA
1 GGTGGTGGAGATGTGTA-GTGATATGGTGGTGGGGGAGATTTCACTGGA
* * *
488989 GGTGGTGGAGATGTGTAGTGATATGGTGGTGGTGGATATTTCACTAGA
1 GGTGGTGGAGATGTGTAGTGATATGGTGGTGGGGGAGATTTCACTGGA
* * * * * * *
489037 GGCGGTGGAGATTTATACTTG-TATGGTGGCGGGGAAGATTTCACCGGA
1 GGTGGTGGAGATGTGTA-GTGATATGGTGGTGGGGGAGATTTCACTGGA
* *
489085 GGCGGTGGAGATGTGTAGTGATATGGTGGTGGGGGATATTTCACTGGA
1 GGTGGTGGAGATGTGTAGTGATATGGTGGTGGGGGAGATTTCACTGGA
* * *
489133 GGTGGTGGAGATTTGTACTTG-TATGGTGGTGGGGGAGATTTCACGGGA
1 GGTGGTGGAGATGTGTA-GTGATATGGTGGTGGGGGAGATTTCACTGGA
*
489181 GGTGGTGGAGATGTGTAGTGATATGGTGGTGGGGGATATTTCACTGGA
1 GGTGGTGGAGATGTGTAGTGATATGGTGGTGGGGGAGATTTCACTGGA
* * * * * * *
489229 GGCGGTGGAGATTTATAGTTATATGGTGATGGGGGAGATTTTACTGGT
1 GGTGGTGGAGATGTGTAGTGATATGGTGGTGGGGGAGATTTCACTGGA
* *
489277 GGTGGTGGAGATGTGTAGTGATATGGTGGCGGGGGAGATTTTACTGGA
1 GGTGGTGGAGATGTGTAGTGATATGGTGGTGGGGGAGATTTCACTGGA
489325 G
1 G
489326 AAGGCGGAAC
Statistics
Matches: 285, Mismatches: 47, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
47 6 0.02
48 275 0.96
49 4 0.01
ACGTcount: A:0.19, C:0.06, G:0.44, T:0.31
Consensus pattern (48 bp):
GGTGGTGGAGATGTGTAGTGATATGGTGGTGGGGGAGATTTCACTGGA
Found at i:489026 original size:171 final size:171
Alignment explanation
Indices: 488767--489125 Score: 495
Period size: 171 Copynumber: 2.1 Consensus size: 171
488757 TTTTGGGTGT
* * * *
488767 GGTGGTGGTGGGGATTTGTAGTGATATGGTGGCTGGGAAGATTTTACTGGAGGAGGTGGAGATTT
1 GGTGGTGGTGGAGATTTGTAGTGATATGGTGGCGGGGAAGATTTCACTGGAGGAGGTGGAGATGT
* * * * *
488832 ATAGTGATATGTTGGTGGTGGATATTTCACTGGAGGTGGTGGAGATTTGTATTTGTATGGTGGAG
66 ATAGTGATATGGTGGTGGTGGATATTTCACTAGAGGCGGTGGAGATTTATACTTGTATGGTGGAG
* * * *
488897 GGGGAGATTTTACTGGAGGAGGTGGAGATTTGTAATGATAC
131 GGGAAGATTTCACCGGAGGAGGTGGAGATGTGTAATGATAC
* * *
488938 GGTGGTGGTGGAGATTTGTACTTG-TATGGTGGCGGGGGAGATTTCACTGGAGGTGGTGGAGATG
1 GGTGGTGGTGGAGATTTGTA-GTGATATGGTGGCGGGGAAGATTTCACTGGAGGAGGTGGAGATG
* *
489002 TGTAGTGATATGGTGGTGGTGGATATTTCACTAGAGGCGGTGGAGATTTATACTTGTATGGTGGC
65 TATAGTGATATGGTGGTGGTGGATATTTCACTAGAGGCGGTGGAGATTTATACTTGTATGGTGGA
* * *
489067 GGGGAAGATTTCACCGGAGGCGGTGGAGATGTGTAGTGATAT
130 GGGGAAGATTTCACCGGAGGAGGTGGAGATGTGTAATGATAC
* *
489109 GGTGGTGGGGGATATTT
1 GGTGGTGGTGGAGATTT
489126 CACTGGAGGT
Statistics
Matches: 164, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
171 162 0.99
172 2 0.01
ACGTcount: A:0.20, C:0.05, G:0.43, T:0.32
Consensus pattern (171 bp):
GGTGGTGGTGGAGATTTGTAGTGATATGGTGGCGGGGAAGATTTCACTGGAGGAGGTGGAGATGT
ATAGTGATATGGTGGTGGTGGATATTTCACTAGAGGCGGTGGAGATTTATACTTGTATGGTGGAG
GGGAAGATTTCACCGGAGGAGGTGGAGATGTGTAATGATAC
Found at i:489047 original size:144 final size:140
Alignment explanation
Indices: 488899--489317 Score: 391
Period size: 144 Copynumber: 2.9 Consensus size: 140
488889 TGGTGGAGGG
* * * * *
488899 GGAGATTTTACTGGA-GGAGGTGGAGATTTGTAATGATACGGTGGTGGTGGAGATTTGTACTTGT
1 GGAGATTTTACTGTATGGTGGTGGGGA-TTGT-AT--TACGGAGGCGGTGGAGATTTGTA-TTGT
* * *
488963 ATGGTGGCGGGGGAGATTTCACTGGAGGTGGTGGAGATGTGTAGTGATATGGTGGTGGTGGATAT
61 ATGGTGGTGGGGGAGATTTCACTGGAGGTGGTGGAGATGTGTAGTGATATGGTGGTGGGGGAGAT
*
489028 TTCACTAGAGGCGGT
126 TTCACGAGAGGCGGT
* * * *
489043 GGAGATTTATACTTGTATGGTGGCGGGGA-AG-ATTTCACCGGAGGCGGTGGAGATGTGTAGTGA
1 GGAGATTT-TAC-TGTATGGTGGTGGGGATTGTA-TT-A-CGGAGGCGGTGGAGATTTGTATTG-
* * *
489106 TATGGTGGTGGGGGATATTTCACTGGAGGTGGTGGAGATTTGTACTTG-TATGGTGGTGGGGGAG
60 TATGGTGGTGGGGGAGATTTCACTGGAGGTGGTGGAGATGTGTA-GTGATATGGTGGTGGGGGAG
* *
489170 ATTTCACGGGAGGTGGT
124 ATTTCACGAGAGGCGGT
* * * * *
489187 GGAGATGTGTAGTGATATGGTGGTGGGGGATAT-T-TCACTGGAGGCGGTGGAGATTTATAGTTA
1 GGAGAT-TTTACTG-TATGGTGGT-GGGGAT-TGTATTAC-GGAGGCGGTGGAGATTTGTA-TTG
* * * *
489250 TATGGTGATGGGGGAGATTTTACTGGTGGTGGTGGAGATGTGTAGTGATATGGTGGCGGGGGAGA
60 TATGGTGGTGGGGGAGATTTCACTGGAGGTGGTGGAGATGTGTAGTGATATGGTGGTGGGGGAGA
489315 TTT
125 TTT
489318 TACTGGAGAA
Statistics
Matches: 224, Mismatches: 34, Indels: 34
0.77 0.12 0.12
Matches are distributed among these distances:
142 1 0.00
143 9 0.04
144 189 0.84
145 14 0.06
146 3 0.01
147 8 0.04
ACGTcount: A:0.20, C:0.06, G:0.43, T:0.31
Consensus pattern (140 bp):
GGAGATTTTACTGTATGGTGGTGGGGATTGTATTACGGAGGCGGTGGAGATTTGTATTGTATGGT
GGTGGGGGAGATTTCACTGGAGGTGGTGGAGATGTGTAGTGATATGGTGGTGGGGGAGATTTCAC
GAGAGGCGGT
Found at i:489146 original size:21 final size:21
Alignment explanation
Indices: 489112--489192 Score: 63
Period size: 21 Copynumber: 3.6 Consensus size: 21
489102 GTGATATGGT
* *
489112 GGTGGGGGATATTTCACTGGA
1 GGTGGTGGAGATTTCACTGGA
* *
489133 GGTGGTGGAGATTTGTACTTGTA
1 GGTGGTGGAGATTT-CAC-TGGA
*
489156 TGGTGGTGGGGGAGATTTCACGGGA
1 -GGTGGT---GGAGATTTCACTGGA
489181 GGTGGTGGAGAT
1 GGTGGTGGAGAT
489193 GTGTAGTGAT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
21 18 0.38
22 2 0.04
23 3 0.06
24 12 0.26
25 2 0.04
26 2 0.04
27 8 0.17
ACGTcount: A:0.17, C:0.06, G:0.47, T:0.30
Consensus pattern (21 bp):
GGTGGTGGAGATTTCACTGGA
Found at i:489211 original size:27 final size:26
Alignment explanation
Indices: 489181--489315 Score: 65
Period size: 27 Copynumber: 5.5 Consensus size: 26
489171 TTTCACGGGA
489181 GGTGGTGGAGATGTGTAGTGATATGGT
1 GGTGGTGGAGATGT-TAGTGATATGGT
* * * *
489208 GGTGG-GG-GATATT--TCA-CTGGA
1 GGTGGTGGAGATGTTAGTGATATGGT
* * *
489229 GGCGGTGGAGATTTATAGTTATATGGT
1 GGTGGTGGAGATGT-TAGTGATATGGT
* * *
489256 GATGGGGGAGAT-TT--T-A-CTGGT
1 GGTGGTGGAGATGTTAGTGATATGGT
489277 GGTGGTGGAGATGTGTAGTGATATGGT
1 GGTGGTGGAGATGT-TAGTGATATGGT
* *
489304 GGCGGGGGAGAT
1 GGTGGTGGAGAT
489316 TTTACTGGAG
Statistics
Matches: 78, Mismatches: 18, Indels: 24
0.65 0.15 0.20
Matches are distributed among these distances:
21 21 0.27
22 6 0.08
23 6 0.08
24 2 0.03
25 6 0.08
26 6 0.08
27 31 0.40
ACGTcount: A:0.19, C:0.04, G:0.46, T:0.31
Consensus pattern (26 bp):
GGTGGTGGAGATGTTAGTGATATGGT
Found at i:489311 original size:96 final size:96
Alignment explanation
Indices: 488944--489325 Score: 593
Period size: 96 Copynumber: 4.0 Consensus size: 96
488934 ATACGGTGGT
*
488944 GGTGGAGATTTGTACTTGTATGGTGGCGGGGGAGATTTCACTGGAGGTGGTGGAGATGTGTAGTG
1 GGTGGAGATTTATACTTGTATGGTGGCGGGGGAGATTTCACTGGAGGTGGTGGAGATGTGTAGTG
* *
489009 ATATGGTGGTGGTGGATATTTCACTAGAGGC
66 ATATGGTGGTGGGGGATATTTCACTGGAGGC
* * *
489040 GGTGGAGATTTATACTTGTATGGTGGCGGGGAAGATTTCACCGGAGGCGGTGGAGATGTGTAGTG
1 GGTGGAGATTTATACTTGTATGGTGGCGGGGGAGATTTCACTGGAGGTGGTGGAGATGTGTAGTG
*
489105 ATATGGTGGTGGGGGATATTTCACTGGAGGT
66 ATATGGTGGTGGGGGATATTTCACTGGAGGC
* * *
489136 GGTGGAGATTTGTACTTGTATGGTGGTGGGGGAGATTTCACGGGAGGTGGTGGAGATGTGTAGTG
1 GGTGGAGATTTATACTTGTATGGTGGCGGGGGAGATTTCACTGGAGGTGGTGGAGATGTGTAGTG
489201 ATATGGTGGTGGGGGATATTTCACTGGAGGC
66 ATATGGTGGTGGGGGATATTTCACTGGAGGC
* * ** * *
489232 GGTGGAGATTTATAGTTATATGGTGATGGGGGAGATTTTACTGGTGGTGGTGGAGATGTGTAGTG
1 GGTGGAGATTTATACTTGTATGGTGGCGGGGGAGATTTCACTGGAGGTGGTGGAGATGTGTAGTG
* * *
489297 ATATGGTGGCGGGGGAGATTTTACTGGAG
66 ATATGGTGGTGGGGGATATTTCACTGGAG
489326 AAGGCGGAAC
Statistics
Matches: 263, Mismatches: 23, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 263 1.00
ACGTcount: A:0.19, C:0.06, G:0.44, T:0.31
Consensus pattern (96 bp):
GGTGGAGATTTATACTTGTATGGTGGCGGGGGAGATTTCACTGGAGGTGGTGGAGATGTGTAGTG
ATATGGTGGTGGGGGATATTTCACTGGAGGC
Found at i:505200 original size:20 final size:20
Alignment explanation
Indices: 505175--505267 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
505165 TTTTCCCAAT
505175 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
505195 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
505215 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
505236 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
505257 TCGCAATGCGA
1 TCGCAATGCGA
505268 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:505217 original size:41 final size:41
Alignment explanation
Indices: 505172--505267 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
505162 CGATTTTCCC
505172 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
505213 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
505254 AAATCGCAATGCGA
1 AATTCGCAATGCGA
505268 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:505221 original size:21 final size:20
Alignment explanation
Indices: 505175--505267 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
505165 TTTTCCCAAT
*
505175 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
505195 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
505215 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
505236 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
505257 TCGCAATGCGA
1 TCGCAATGCGA
505268 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:505280 original size:41 final size:41
Alignment explanation
Indices: 505194--505328 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
505184 GAATAAGTAA
* * *
505194 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
505235 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
505276 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
505317 TTCGCAACGCGA
1 ATCGCAACGCGA
505329 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:505281 original size:20 final size:20
Alignment explanation
Indices: 505256--505349 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
505246 AATTGGGAAA
*
505256 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
505276 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
505297 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
505317 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
505337 TTCGCAACGCGAT
1 ATCGCAACGCGAT
505350 TTACTTAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:505917 original size:19 final size:19
Alignment explanation
Indices: 505895--505938 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
505885 GGAAATGACT
505895 ATCGCAACGCGAAATA-AAA
1 ATCGCAACGCGAAA-ACAAA
505914 ATCGCAACGCGAAAACAAA
1 ATCGCAACGCGAAAACAAA
505933 ATCGCA
1 ATCGCA
505939 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 1 0.04
19 23 0.96
ACGTcount: A:0.50, C:0.25, G:0.16, T:0.09
Consensus pattern (19 bp):
ATCGCAACGCGAAAACAAA
Found at i:505956 original size:19 final size:19
Alignment explanation
Indices: 505934--506118 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
505924 GAAAACAAAA
*
505934 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
505953 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
505972 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
505991 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
506011 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
506027 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
506044 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
506058 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
506077 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
506097 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
506117 TC
1 TC
506119 AACCAAAAGA
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 20 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 60 0.43
20 49 0.36
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:506012 original size:39 final size:38
Alignment explanation
Indices: 505934--506023 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 38
505924 GAAAACAAAA
* *
505934 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGCATTGCGATTTTCATT
*
505972 TCGCGTTGCGATTTTAATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGC-ATTGCGATTTTCATT
506011 TCGCGTTGCGATT
1 TCGCGTTGCGATT
506024 GTCTGGTCGC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 21 0.44
39 27 0.56
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTAATTTCGCATTGCGATTTTCATT
Found at i:506043 original size:33 final size:33
Alignment explanation
Indices: 506006--506093 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
505996 GTTGCGATTT
* *
506006 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
506039 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
506072 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
506094 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:506095 original size:20 final size:20
Alignment explanation
Indices: 506061--506118 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
506051 GCGATTCTCT
**
506061 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
506081 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
506101 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
506119 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:508181 original size:42 final size:42
Alignment explanation
Indices: 508120--508242 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 42
508110 GCCCGACTCG
* * *
508120 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * * *
508162 CCTATTATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
508204 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
508243 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
42 60 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.24
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:508200 original size:21 final size:21
Alignment explanation
Indices: 508176--508242 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
508166 TTATTCCTCG
508176 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
508197 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
508218 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
508239 AGAG
1 AGAG
508243 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:509617 original size:14 final size:14
Alignment explanation
Indices: 509598--509633 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
509588 ATTGTTTAAT
509598 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
509612 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
509626 TGATTTGT
1 TGATTTGT
509634 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:509834 original size:19 final size:19
Alignment explanation
Indices: 509812--509931 Score: 71
Period size: 19 Copynumber: 6.7 Consensus size: 19
509802 CGAAATTAAA
509812 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
509831 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
509846 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
509864 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
509879 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * *
509897 TTCGCATTGTGATTTTGTCGT
1 TTCGCGTTGCGA-TTT-TCAT
509918 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
509932 GGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 24
0.65 0.13 0.21
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 27 0.37
20 3 0.04
21 6 0.08
22 8 0.11
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:509918 original size:33 final size:33
Alignment explanation
Indices: 509816--509910 Score: 172
Period size: 33 Copynumber: 2.9 Consensus size: 33
509806 ATTAAATTCG
*
509816 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
509849 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
509882 CGTTGCGATTTTCATTTCGCATTGTGATT
1 CGTTGCGATTTTCATTTCGCATTGCGATT
509911 TTGTCGTTTC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:512221 original size:12 final size:12
Alignment explanation
Indices: 512204--512228 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
512194 TCTTCGGGGA
512204 CTTTTTCTTCTT
1 CTTTTTCTTCTT
512216 CTTTTTCTTCTT
1 CTTTTTCTTCTT
512228 C
1 C
512229 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:513726 original size:14 final size:14
Alignment explanation
Indices: 513707--513743 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
513697 CATCAATTAA
513707 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
513721 ACAAATCATCTTTT
1 ACAAATCAACATTT
513735 ACAAATCAA
1 ACAAATCAA
513744 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:514315 original size:14 final size:14
Alignment explanation
Indices: 514296--514332 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
514286 CATCAATTAA
514296 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
514310 ACAAATCATCTTTT
1 ACAAATCAACATTT
514324 ACAAATCAA
1 ACAAATCAA
514333 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:514446 original size:589 final size:590
Alignment explanation
Indices: 513330--515169 Score: 3587
Period size: 589 Copynumber: 3.1 Consensus size: 590
513320 TTTAACAATT
513330 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
513395 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
513460 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
513525 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATTTCATTTCGCATTGCGATTTT
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATTTCATTTCGCATTGCGATTTT
513590 CTCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAA
261 CTCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAA
513655 ATCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATT
326 ATCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATT
513720 TACAAATCATCTTTTACAAATCAATTAAACAATC-AAAAATAATAATAATTCTTATTTCTTCATC
391 TACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATC
513784 AATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAG
456 AATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAG
513849 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
521 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
*
513914 AGCAA
586 AACAA
513919 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
513984 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
*
514049 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTCACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
514114 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATTTCATTTCGCATTGCGATTTT
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATTTCATTTCGCATTGCGATTTT
514179 CTCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAA
261 CTCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAA
514244 ATCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATT
326 ATCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATT
514309 TACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATC
391 TACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATC
514374 AATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAA-
456 AATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAG
514438 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
521 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
514503 AACAA
586 AACAA
514508 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
514573 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
514638 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
** **
514703 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAA-TGAAAATCGCATTGCGATTTT
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATTTCATTTCGCATTGCGATTTT
* *
514767 CTCGTTGCGATAACCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCATATTGAAA
261 CTCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAA
514832 ATCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATT
326 ATCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATT
514897 TACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATC
391 TACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATC
514962 AATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAG
456 AATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAG
515027 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
521 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
515092 AACAA
586 AACAA
515097 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
515162 CTTGCATT
66 CTTGCATT
515170 TGACTTACCA
Statistics
Matches: 1240, Mismatches: 9, Indels: 4
0.99 0.01 0.00
Matches are distributed among these distances:
588 274 0.22
589 872 0.70
590 94 0.08
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (590 bp):
ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATTTCATTTCGCATTGCGATTTT
CTCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAA
ATCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATT
TACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATC
AATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAG
GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
AACAA
Found at i:514903 original size:14 final size:14
Alignment explanation
Indices: 514884--514920 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
514874 CATCAATTAA
514884 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
514898 ACAAATCATCTTTT
1 ACAAATCAACATTT
514912 ACAAATCAA
1 ACAAATCAA
514921 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:516823 original size:20 final size:19
Alignment explanation
Indices: 516788--516854 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
516778 GAAACTTAAA
516788 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
516807 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
516827 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
516846 ATCGCAACG
1 ATCGCAACG
516855 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:516862 original size:14 final size:14
Alignment explanation
Indices: 516843--516900 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
516833 ATGCGAAATG
516843 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
516857 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
516873 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
516889 AAAATCGCAACG
1 AAAATCGCAACG
516901 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:516885 original size:32 final size:33
Alignment explanation
Indices: 516827--516905 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
516817 GGAAATGGCT
*
516827 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
516860 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
516892 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
516906 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:516934 original size:19 final size:19
Alignment explanation
Indices: 516912--516993 Score: 95
Period size: 18 Copynumber: 4.6 Consensus size: 19
516902 GAAACACAAA
516912 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
516931 TCGCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
* *
516949 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
516965 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
516982 TCGCATTGCGAT
1 TCGCATTGCGAT
516994 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
14 6 0.11
15 3 0.05
16 4 0.07
17 4 0.07
18 21 0.38
19 17 0.31
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:517009 original size:39 final size:35
Alignment explanation
Indices: 516912--517023 Score: 97
Period size: 33 Copynumber: 3.1 Consensus size: 35
516902 GAAACACAAA
516912 TCGCATTGCGATTTTCATTTCGCGTTGCGA-TTTCATT
1 TCGCATTGCGA---TCATTTCGCGTTGCGATTTTCATT
*
516949 TCGCGTTGCGAT--TTT-GTCGTTGCGATTTTCATT
1 TCGCATTGCGATCATTTCG-CGTTGCGATTTTCATT
**
516982 TCGCATTGCGATAGCCATTTCCGCGTTGCGATAGTCATT
1 TCGCATTGCGAT---CATTT-CGCGTTGCGATTTTCATT
517021 TCG
1 TCG
517024 TGTTGCGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 16
0.76 0.05 0.20
Matches are distributed among these distances:
31 1 0.02
32 11 0.18
33 18 0.29
34 1 0.02
37 10 0.16
38 3 0.05
39 17 0.27
40 1 0.02
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.42
Consensus pattern (35 bp):
TCGCATTGCGATCATTTCGCGTTGCGATTTTCATT
Found at i:517012 original size:20 final size:19
Alignment explanation
Indices: 516978--517031 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
516968 TTGCGATTTT
*
516978 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
516997 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
517017 CATTTCGTGTTGCGA
1 CATTTCGCGTTGCGA
517032 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:517030 original size:19 final size:19
Alignment explanation
Indices: 516912--517031 Score: 92
Period size: 19 Copynumber: 6.6 Consensus size: 19
516902 GAAACACAAA
* **
516912 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATAGTCATT
*
516931 TCGCGTTGCGAT-TTCATT
1 TCGCGTTGCGATAGTCATT
516949 TCGCGTTGCG--A-T--TT
1 TCGCGTTGCGATAGTCATT
**
516963 T-GTCGTTGCGATTTTCATT
1 TCG-CGTTGCGATAGTCATT
* *
516982 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGATAGTCATT
517001 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATAGTCATT
*
517021 TCGTGTTGCGA
1 TCGCGTTGCGA
517032 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 9, Indels: 18
0.75 0.08 0.16
Matches are distributed among these distances:
13 1 0.01
14 10 0.12
16 1 0.01
17 1 0.01
18 16 0.19
19 36 0.43
20 18 0.22
ACGTcount: A:0.13, C:0.22, G:0.23, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATAGTCATT
Found at i:517529 original size:18 final size:18
Alignment explanation
Indices: 517503--517547 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
517493 GTCGATCAGA
*
517503 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
517521 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
517539 TGATGGCTC
1 TGATGGCTC
517548 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:518892 original size:20 final size:20
Alignment explanation
Indices: 518867--518920 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
518857 AATAGTTTCT
518867 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
518887 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
*
518907 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
518921 GTTGCGATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:519179 original size:22 final size:22
Alignment explanation
Indices: 519154--519197 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
519144 GATTTAGATA
519154 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
519176 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
519198 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:519410 original size:20 final size:20
Alignment explanation
Indices: 519385--519478 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
519375 GATTATGTAT
519385 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
519405 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
519425 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
519446 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
519466 TATCGCATTGCGA
1 TATCGCGTTGCGA
519479 TTTTCTCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:519450 original size:41 final size:42
Alignment explanation
Indices: 519405--519540 Score: 118
Period size: 41 Copynumber: 3.3 Consensus size: 42
519395 CGAAAGTCAG
* * * *
519405 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTAT
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
* * *
519446 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAA
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
** ** * *
519488 T-TCGCGTTGCG-ATTTACTTATTCGCATTGCGAATTTCCCAA
1 TATCGCGTTGCGAAAGTAAGTA-TCGCATTGCGATTTTCTCAA
519529 T-TCGCGTTGCGA
1 TATCGCGTTGCGA
519541 TTTACTTATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
40 3 0.04
41 70 0.92
42 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (42 bp):
TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
Found at i:519479 original size:20 final size:20
Alignment explanation
Indices: 519365--519479 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
519355 CGCTTTGAAA
*
519365 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
519386 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
519406 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
519426 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
519447 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
519467 ATCGCATTGCGAT
1 ATCGCATTGCGAT
519480 TTTCTCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:519512 original size:20 final size:20
Alignment explanation
Indices: 519468--519560 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
519458 ATAGTCAGTA
*
519468 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
519489 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
519509 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
519530 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
519550 TCGCATTGCGA
1 TCGCATTGCGA
519561 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.47
21 31 0.53
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:519541 original size:41 final size:41
Alignment explanation
Indices: 519468--519563 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
519458 ATAGTCAGTA
* *
519468 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
519509 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
519550 TCGCATTGCGAATT
1 TCGCATTGCGAATT
519564 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:520541 original size:20 final size:21
Alignment explanation
Indices: 520516--520556 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
520506 CCCTAAATTG
520516 ATAACCT-TAAATTTTAAACT
1 ATAACCTCTAAATTTTAAACT
*
520536 ATAACCTCGTAACTTTTAAAC
1 ATAACCTC-TAAATTTTAAAC
520557 CCTAAACCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.41, C:0.20, G:0.02, T:0.37
Consensus pattern (21 bp):
ATAACCTCTAAATTTTAAACT
Done.