Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001279.1 Hibiscus syriacus cultivar Beakdansim tig00002511_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: 6984689
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 29
Found at i:495199 original size:20 final size:19
Alignment explanation
Indices: 495176--495220 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
495166 TAACATTAAA
495176 TAGTTTAAGTTAAAACTCAT
1 TAGTTTAA-TTAAAACTCAT
*
495196 TAGTGTTTATTAAAACTCAT
1 TAGT-TTAATTAAAACTCAT
495216 TAGTT
1 TAGTT
495221 GACATGATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 19 0.83
21 3 0.13
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (19 bp):
TAGTTTAATTAAAACTCAT
Found at i:497914 original size:20 final size:19
Alignment explanation
Indices: 497891--497935 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
497881 TAACATTAAA
497891 TAGTTTAAGTTAAAACTCAT
1 TAGTTTAA-TTAAAACTCAT
*
497911 TAGTGTTTATTAAAACTCAT
1 TAGT-TTAATTAAAACTCAT
497931 TAGTT
1 TAGTT
497936 GACATGATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 19 0.83
21 3 0.13
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (19 bp):
TAGTTTAATTAAAACTCAT
Found at i:504391 original size:54 final size:54
Alignment explanation
Indices: 504304--504584 Score: 402
Period size: 54 Copynumber: 5.2 Consensus size: 54
504294 GTGTACTACA
504304 GGCACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
1 GGCACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
* * * *
504358 AGCATTATGTGTGCAACTCACGAAATTTATCATATGTTGATGAACAACCGTTTC
1 GGCACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
* * *
504412 GGCACTATGTTTGCAACTCACGGAATTCATC-TATGTTAATAAACAACCGTTTC
1 GGCACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
* *
504465 GGCACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACTGTTTT
1 GGCACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
* * * * * * *
504519 GTCACTATGTGTGCAACCCACAGAATTCATCATGTGTTGATGAACGACCGTATA
1 GGCACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
*
504573 GGCACTACGTGT
1 GGCACTATGTGT
504585 TCATCTTAAT
Statistics
Matches: 200, Mismatches: 26, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
53 50 0.25
54 150 0.75
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (54 bp):
GGCACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
Found at i:504497 original size:107 final size:107
Alignment explanation
Indices: 504304--504553 Score: 376
Period size: 107 Copynumber: 2.3 Consensus size: 107
504294 GTGTACTACA
* * *
504304 GGCACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTCAGCATTATGTG
1 GGCACTATGTGTGCAACTCACGGAATTCATC-TATGTTAATAAACAACCGTTTCAGCACTATGTG
*
504369 TGCAACTCACGAAATTTATCATATGTTGATGAACAACCGTTTC
65 TGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTC
* *
504412 GGCACTATGTTTGCAACTCACGGAATTCATCTATGTTAATAAACAACCGTTTCGGCACTATGTGT
1 GGCACTATGTGTGCAACTCACGGAATTCATCTATGTTAATAAACAACCGTTTCAGCACTATGTGT
* * *
504477 GCAACTCACGGAATTCATCATATGTTGATGAACAACTGTTTT
66 GCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTC
* * *
504519 GTCACTATGTGTGCAACCCACAGAATTCATC-ATGT
1 GGCACTATGTGTGCAACTCACGGAATTCATCTATGT
504554 GTTGATGAAC
Statistics
Matches: 129, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
106 4 0.03
107 95 0.74
108 30 0.23
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (107 bp):
GGCACTATGTGTGCAACTCACGGAATTCATCTATGTTAATAAACAACCGTTTCAGCACTATGTGT
GCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTC
Found at i:504800 original size:81 final size:81
Alignment explanation
Indices: 504695--504918 Score: 324
Period size: 81 Copynumber: 2.7 Consensus size: 81
504685 ACTGTTCTAA
*
504695 AATAAAAGACTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGTCAATAATGCAAGTTAGAAGAA
1 AATAAAAGACT-AATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGAAGAA
504760 A-TGTTAAATGCCTTTAG
65 AGT-TTAAATGCCTTTAG
* * *
504777 AATAAAAGACTAATGCCTAACTGTGTATTTGGCAAAAAGGTACCAATAATGCAAGTTAGAAGAAA
1 AATAAAAGACTAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGAAGAAA
504842 GTTTAAATGCCTTTAG
66 GTTTAAATGCCTTTAG
* * * * * *
504858 GATAAAAGACTAATGCCTAACGGTGCATTTTTGTAGAAAGGTGCCACTAATACAAGTTAGA
1 AATAAAAGACTAATGCCTAACTGTGCA-TTTGGCAGAAAGGTGCCAATAATGCAAGTTAGA
504919 TGAAGAACAA
Statistics
Matches: 127, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
81 88 0.69
82 39 0.31
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (81 bp):
AATAAAAGACTAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGAAGAAA
GTTTAAATGCCTTTAG
Found at i:518122 original size:20 final size:20
Alignment explanation
Indices: 518077--518123 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
518067 AACCAACAAA
* * *
518077 ATCGAAACGCGATCTCGAAT
1 ATCGCAACGCGAACTCCAAT
518097 -TCGCAACGCGAACTCCAAT
1 ATCGCAACGCGAACTCCAAT
518116 ATCGCAAC
1 ATCGCAAC
518124 TCAGTTTCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAACTCCAAT
Found at i:518334 original size:22 final size:22
Alignment explanation
Indices: 518309--518377 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
518299 TCTCTACGGT
518309 GACATCCGTCCCCATCTCCGGC
1 GACATCCGTCCCCATCTCCGGC
* *
518331 GACATTCGTCCTCATCTCCGGC
1 GACATCCGTCCCCATCTCCGGC
*
518353 GACATCCGTCCCCATATCCGGC
1 GACATCCGTCCCCATCTCCGGC
518375 GAC
1 GAC
518378 CCCCCTCTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.16, C:0.45, G:0.19, T:0.20
Consensus pattern (22 bp):
GACATCCGTCCCCATCTCCGGC
Found at i:518716 original size:20 final size:20
Alignment explanation
Indices: 518670--518730 Score: 97
Period size: 20 Copynumber: 3.1 Consensus size: 20
518660 AAGACTATTT
* *
518670 GAAACTGAAAATTGCAACGC
1 GAAAATGAAAATCGCAACGC
518690 G-AAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACGC
518709 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACGC
518729 GA
1 GA
518731 TTTTAGTTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 17 0.45
20 21 0.55
ACGTcount: A:0.48, C:0.20, G:0.21, T:0.11
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:520978 original size:13 final size:13
Alignment explanation
Indices: 520960--520985 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
520950 TCATTTCTAT
520960 CTCACTTTTAAAA
1 CTCACTTTTAAAA
520973 CTCACTTTTAAAA
1 CTCACTTTTAAAA
520986 GATATACCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (13 bp):
CTCACTTTTAAAA
Found at i:521855 original size:19 final size:18
Alignment explanation
Indices: 521812--521864 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
521802 CATGACCATA
*
521812 ATGCATCGGTGCATCAGT
1 ATGCATCGGTGCATAAGT
*
521830 GTGCATCGGTGCACTAAGT
1 ATGCATCGGTGCA-TAAGT
*
521849 ATGCATCGATGCATAA
1 ATGCATCGGTGCATAA
521865 AATGCATTCG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 15 0.50
19 15 0.50
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (18 bp):
ATGCATCGGTGCATAAGT
Found at i:521915 original size:64 final size:62
Alignment explanation
Indices: 521847--522009 Score: 184
Period size: 66 Copynumber: 2.5 Consensus size: 62
521837 GGTGCACTAA
* *
521847 GTATGCATCGATGCATAAAATGCATTCGATGTTTTGA-AAAAGCCTGAATGCATCGATGCATGGT
1 GTATGCATC-ATGCATAAAATGCATTCGATGTTTTCATAAAAGCAT-AATGCATCGATGCAT-GT
* * *
521911 GTATGCATCAATGCATCAAATGCATTCGATGTTTTCATTTAAAATCATAGTGCATCGATGCATGT
1 GTATGCATC-ATGCATAAAATGCATTCGATGTTTTCA--TAAAAGCATAATGCATCGATGCATGT
* *
521976 ATAGTGCATCAGTGCATGAAATGCATTCGATGTT
1 GTA-TGCATCA-TGCATAAAATGCATTCGATGTT
522010 CAATTTTTTT
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
64 34 0.40
65 5 0.06
66 41 0.48
67 6 0.07
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.33
Consensus pattern (62 bp):
GTATGCATCATGCATAAAATGCATTCGATGTTTTCATAAAAGCATAATGCATCGATGCATGT
Found at i:522044 original size:20 final size:20
Alignment explanation
Indices: 522021--522059 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
522011 AATTTTTTTC
522021 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
*
522041 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
522060 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:522050 original size:66 final size:67
Alignment explanation
Indices: 521894--522059 Score: 182
Period size: 66 Copynumber: 2.5 Consensus size: 67
521884 AAAAGCCTGA
* *
521894 ATGCATCGATGCATGG--TGTATGCATCAATGCATCAAATGCATTCGATGTTTTCATTTAAAATC
1 ATGCATCGATGCATGGATTG-ATGCATCAGTGCATGAAATGCATTCGATG-TTTCATTTAAAATC
521957 ATAG
64 ATAG
* * ***
521961 -TGCATCGATGCATGTATAG-TGCATCAGTGCATGAAATGCATTCGATG-TTCAATTT-TTTTCA
1 ATGCATCGATGCATGGATTGATGCATCAGTGCATGAAATGCATTCGATGTTTC-ATTTAAAATCA
*
522022 TTG
65 TAG
*
522025 ATGCATCGATGCATGGATTGATGCATCGGTGCATG
1 ATGCATCGATGCATGGATTGATGCATCAGTGCATG
522060 CCTTTGAAAA
Statistics
Matches: 83, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
64 8 0.10
65 21 0.25
66 53 0.64
68 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (67 bp):
ATGCATCGATGCATGGATTGATGCATCAGTGCATGAAATGCATTCGATGTTTCATTTAAAATCAT
AG
Found at i:522404 original size:42 final size:42
Alignment explanation
Indices: 522345--522424 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
522335 TTAAGATTTT
*
522345 ATTTATCAAAAATTATTTTTGAAATCATCTTTGAAAAAATAC
1 ATTTATCAAAAATTATTTTTGAAATCAACTTTGAAAAAATAC
522387 ATTTATCAAAAATTATTTTTGAAATCAACTTTGAAAAA
1 ATTTATCAAAAATTATTTTTGAAATCAACTTTGAAAAA
522425 TTACTCCCCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (42 bp):
ATTTATCAAAAATTATTTTTGAAATCAACTTTGAAAAAATAC
Found at i:523131 original size:18 final size:20
Alignment explanation
Indices: 523110--523149 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
523100 GAGGAGGAGG
523110 AGGAGCA-C-GAGAAGAACT
1 AGGAGCAGCTGAGAAGAACT
523128 AGGAGCAGCTTGAGAAGAACT
1 AGGAGCAGC-TGAGAAGAACT
523149 A
1 A
523150 TCTCCCGGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
19 1 0.05
21 11 0.58
ACGTcount: A:0.42, C:0.15, G:0.33, T:0.10
Consensus pattern (20 bp):
AGGAGCAGCTGAGAAGAACT
Found at i:530259 original size:19 final size:19
Alignment explanation
Indices: 530235--530271 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
530225 ATTTAAAATC
530235 ATAGTGCATCGATGCATGT
1 ATAGTGCATCGATGCATGT
*
530254 ATAGTGCATCGGTGCATG
1 ATAGTGCATCGATGCATG
530272 AAATGCATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (19 bp):
ATAGTGCATCGATGCATGT
Found at i:530336 original size:20 final size:20
Alignment explanation
Indices: 530298--530336 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
530288 CAATTTATTC
*
530298 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATCCATGG
*
530318 ATTGATGCATCGGTCCATG
1 ATTGATGCATCGATCCATG
530337 CCTTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATCCATGG
Found at i:531662 original size:7 final size:7
Alignment explanation
Indices: 531660--531922 Score: 203
Period size: 7 Copynumber: 35.1 Consensus size: 7
531650 TAGTATATAG
531660 TATATTA
1 TATATTA
531667 TATATTA
1 TATATTA
531674 TAGTACATTA
1 TA-T--ATTA
531684 TATA-TA
1 TATATTA
*
531690 TTATATGA
1 -TATATTA
*
531698 TAATAGTA
1 T-ATATTA
*
531706 CATCATTA
1 TAT-ATTA
531714 TTATATTA
1 -TATATTA
*
531722 TATAGTA
1 TATATTA
531729 TATATATA
1 TATAT-TA
531737 TATATTA
1 TATATTA
531744 TAATATGTTA
1 T-ATA--TTA
531754 TATATTA
1 TATATTA
*
531761 TATTAATA
1 TA-TATTA
531769 TTATATTA
1 -TATATTA
*
531777 TTATAGTA
1 -TATATTA
531785 TATATTA
1 TATATTA
531792 TATATTA
1 TATATTA
531799 TATTATATA
1 TA-TAT-TA
*
531808 TTTATTA
1 TATATTA
531815 TATATTA
1 TATATTA
531822 TAGTA-TA
1 TA-TATTA
531829 TAT-TTA
1 TATATTA
*
531835 -AAATCATA
1 TATAT--TA
531843 TATATTA
1 TATATTA
531850 TATAGTTA
1 TATA-TTA
*
531858 TATTTTA
1 TATATTA
531865 TATATTA
1 TATATTA
531872 TATATTA
1 TATATTA
531879 TATATTA
1 TATATTA
531886 TATATTA
1 TATATTA
531893 T-TATTA
1 TATATTA
531899 TTATTATTA
1 -TA-TATTA
*
531908 TATTTTA
1 TATATTA
531915 TATATTA
1 TATATTA
531922 T
1 T
531923 TTATCTATTT
Statistics
Matches: 210, Mismatches: 20, Indels: 52
0.74 0.07 0.18
Matches are distributed among these distances:
5 1 0.00
6 11 0.05
7 113 0.54
8 56 0.27
9 19 0.09
10 10 0.05
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (7 bp):
TATATTA
Found at i:531670 original size:2 final size:2
Alignment explanation
Indices: 531653--531890 Score: 120
Period size: 2 Copynumber: 128.5 Consensus size: 2
531643 GTATATGTAG
*
531653 TA TA TA GTA TA T- TA TA TA T- TA TA GTA CA T- TA TA TA TA T- TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
*
531693 TA TGA TA -A TA GTA CA TCA T- TA T- TA TA T- TA TA TA GTA TA TA
1 TA T-A TA TA TA -TA TA T-A TA TA TA TA TA TA TA TA TA -TA TA TA
*
531733 TA TA TA TA T- TA TA -A TA TG T- TA TA TA T- TA TA T- TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
531769 T- TA TA T- TA T- TA TA GTA TA TA T- TA TA TA T- TA TA T- TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
531806 TA TT TA T- TA TA TA T- TA TA GTA TA TA TT TA -A AA TCA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA T-A TA TA TA
*
531847 T- TA TA TA GT- TA TA T- TT TA TA TA T- TA TA TA T- TA TA TA T-
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
531884 TA TA TA T
1 TA TA TA T
531891 TATTATTATT
Statistics
Matches: 186, Mismatches: 11, Indels: 78
0.68 0.04 0.28
Matches are distributed among these distances:
1 29 0.16
2 138 0.74
3 19 0.10
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (2 bp):
TA
Found at i:531814 original size:43 final size:41
Alignment explanation
Indices: 531711--531922 Score: 175
Period size: 43 Copynumber: 5.3 Consensus size: 41
531701 TAGTACATCA
* *
531711 TTATTATATTATATAGTATATATATATATATTATA-ATAT-G
1 TTATTATATTATATATTATATAT-TATATATTATATATATAT
531751 TTA-TATA-T-TATATTA-ATATTATATTATTATAGTATATA-
1 TTATTATATTATATATTATATATTATA-TATTATA-TATATAT
*
531789 TTA-TATATTATATTATATATTTATTATATATTATAGTATATAT
1 TTATTATATTATA-TAT-TATATATTATATATTATA-TATATAT
** *
531832 TTAAAATCA-TATATATTATATAGTTATATTTTATATATTATAT
1 TTATTAT-ATTATATATTATATA-TTATATATTATATA-TATAT
531875 ATTA-TATATTATATATTAT-TATTAT-TATTAT-TATAT-T
1 -TTATTATATTATATATTATATATTATATATTATATATATAT
531912 TTA-TATATTAT
1 TTATTATATTAT
531923 TTATCTATTT
Statistics
Matches: 149, Mismatches: 7, Indels: 36
0.78 0.04 0.19
Matches are distributed among these distances:
35 4 0.03
36 22 0.15
37 7 0.05
38 15 0.10
39 7 0.05
40 10 0.07
41 7 0.05
42 26 0.17
43 41 0.28
44 9 0.06
45 1 0.01
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (41 bp):
TTATTATATTATATATTATATATTATATATTATATATATAT
Found at i:531860 original size:73 final size:72
Alignment explanation
Indices: 531715--531922 Score: 229
Period size: 71 Copynumber: 2.9 Consensus size: 72
531705 ACATCATTAT
* *
531715 TATATTATATAGTATATATATATATATTATA-A-TATGTTATATATTATATTAATATTATATTAT
1 TATATTATATATTATATATATATATATTATATATTATGTTATATATTATATAAATATTATATTAT
531778 TATAGTA
66 TATAGTA
*
531785 TATATTATATATTATATTATATATTTATTATATATTATAG-TATATATT-TA-AAATCATATATA
1 TATATTATATATTATA-TATATATATATTATATATTAT-GTTATATATTATATAAAT-AT-TATA
531847 TTA-TATAGTTA
62 TTATTATAG-TA
* * * *
531858 TATTTTATATATTATATAT-TATATATTATATATTATTATTAT-TATTAT-TATATTTTATA-TA
1 TATATTATATATTATATATATATATATTATATATTA-TGTTATATATTATATAAATATTATATTA
531919 TTAT
65 TTAT
531923 TTATCTATTT
Statistics
Matches: 118, Mismatches: 8, Indels: 24
0.79 0.05 0.16
Matches are distributed among these distances:
69 2 0.02
70 22 0.19
71 37 0.31
72 21 0.18
73 35 0.30
74 1 0.01
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (72 bp):
TATATTATATATTATATATATATATATTATATATTATGTTATATATTATATAAATATTATATTAT
TATAGTA
Found at i:531912 original size:50 final size:51
Alignment explanation
Indices: 531653--531922 Score: 196
Period size: 55 Copynumber: 5.1 Consensus size: 51
531643 GTATATGTAG
* * * *
531653 TATATAG--TATATTATATATTATAGTACATTATATA-TATTATATGATAATAG
1 TATATAGTATATATTATATATTATA-TATATTATATATTA-TATTTTAT-ATAT
* * *
531704 TACATCATTATTATATTATATAGTATATATA-TATATATTATAATATGTTATATAT
1 TATAT-AGTA-TATATTATATATTATATATATTATATATTAT-AT-T-TTATATAT
* *
531759 TATATTAATATTATATTATTATAGTATATATTATATATTATATTATATATTTAT-TAT
1 TATA-TAGTA-TATATTA-TATATTATATA-TAT-TA-TATATTATAT-TTTATATAT
* *
531816 ATATTATAGTATATATT-TAAAATCATATATATTATATAGTTATATTTTATATAT
1 -TA-TATAGTATATATTAT-ATATTATATATATTATATA-TTATATTTTATATAT
*
531870 TATATATTATATATTATATATTAT-TATTATTAT-TATTATATTTTATATAT
1 TATATAGTATATATTATATATTATATA-TATTATATATTATATTTTATATAT
531920 TAT
1 TAT
531923 TTATCTATTT
Statistics
Matches: 182, Mismatches: 16, Indels: 43
0.76 0.07 0.18
Matches are distributed among these distances:
50 18 0.10
51 8 0.04
52 24 0.13
53 19 0.10
54 18 0.10
55 36 0.20
56 22 0.12
57 11 0.06
58 10 0.05
59 8 0.04
60 8 0.04
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (51 bp):
TATATAGTATATATTATATATTATATATATTATATATTATATTTTATATAT
Found at i:531931 original size:20 final size:19
Alignment explanation
Indices: 531746--531932 Score: 97
Period size: 19 Copynumber: 9.9 Consensus size: 19
531736 ATATATTATA
* * *
531746 ATATGTTATATATTATATT
1 ATATATTATTTATTATTTT
**
531765 A-ATATTATATTATTATAGT
1 ATATATTAT-TTATTATTTT
* *
531784 ATATATTATATATTATATT
1 ATATATTATTTATTATTTT
*
531803 ATATATT-TATTA-TATATT
1 ATATATTAT-TTATTATTTT
** **
531821 ATAGTATATATTTAAAATCAT
1 ATA-TAT-TATTTATTATTTT
*
531842 ATATATTATATAGTTATATTT
1 ATATATTATTTA-TTAT-TTT
*
531863 -TATA-TA-TTA-TATATT
1 ATATATTATTTATTATTTT
*
531878 ATATATTATATATTATTATT
1 ATATATTATTTATTATT-TT
531898 AT-TATTA-TTA-TATTTT
1 ATATATTATTTATTATTTT
531914 ATATATTATTTATCTATTT
1 ATATATTATTTAT-TATTT
531933 ATTCATTTAT
Statistics
Matches: 131, Mismatches: 19, Indels: 35
0.71 0.10 0.19
Matches are distributed among these distances:
15 2 0.02
16 11 0.08
17 11 0.08
18 25 0.19
19 45 0.34
20 29 0.22
21 8 0.06
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (19 bp):
ATATATTATTTATTATTTT
Found at i:531933 original size:8 final size:7
Alignment explanation
Indices: 531751--531943 Score: 72
Period size: 7 Copynumber: 26.3 Consensus size: 7
531741 TTATAATATG
*
531751 TTATATA
1 TTATTTA
531758 TTATATTA
1 TTAT-TTA
*
531766 ATATTATA
1 TTATT-TA
531774 TTATTATA
1 TTATT-TA
* *
531782 GTATATA
1 TTATTTA
*
531789 TTATATA
1 TTATTTA
531796 TTATATTA
1 TTAT-TTA
531804 TATATTTA
1 T-TATTTA
*
531812 TTATATA
1 TTATTTA
*
531819 TTATAGTA
1 TTAT-TTA
531827 TATATTTA
1 T-TATTTA
* * *
531835 -AAATCA
1 TTATTTA
*
531841 -TATATA
1 TTATTTA
*
531847 TTATATA
1 TTATTTA
531854 GTTATATT-
1 -TTAT-TTA
*
531862 TTATATA
1 TTATTTA
*
531869 TTATATA
1 TTATTTA
*
531876 TTATATA
1 TTATTTA
*
531883 TTATATA
1 TTATTTA
531890 TTA-TTA
1 TTATTTA
531896 TTA-TTA
1 TTATTTA
531902 TTATTATA
1 TTATT-TA
*
531910 TTTTATATA
1 --TTATTTA
531919 TTATTTA
1 TTATTTA
531926 TCTATTTA
1 T-TATTTA
531934 TTCATTTA
1 TT-ATTTA
531942 TT
1 TT
531944 TATTCTTTCA
Statistics
Matches: 148, Mismatches: 22, Indels: 31
0.74 0.11 0.15
Matches are distributed among these distances:
6 17 0.11
7 69 0.47
8 49 0.33
9 9 0.06
10 4 0.03
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (7 bp):
TTATTTA
Found at i:534226 original size:12 final size:11
Alignment explanation
Indices: 534184--534227 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
534174 GGGTAGGAAT
534184 TTTTATTTTTA
1 TTTTATTTTTA
*
534195 TTTTCATTATTA
1 TTTT-ATTTTTA
*
534207 TTTGATTTTTA
1 TTTTATTTTTA
534218 TTTCTATTTT
1 TTT-TATTTT
534228 ACTAAATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 13 0.48
12 14 0.52
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:538340 original size:64 final size:64
Alignment explanation
Indices: 538228--538385 Score: 178
Period size: 64 Copynumber: 2.5 Consensus size: 64
538218 GCACCAAGTT
* * ** *
538228 TGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAGCCTATGTGCATC-AGTGCATTGCT-T
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAAGCAGATGTGCATCGA-TGCA-TGCTGA
538291 C
64 C
* * * *
538292 TGCATCGATGCATGAAATGCATTCGATGTTTTAATAAAATCAGA-GTGCATCGATGCATGGTGAG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAAAGCAGATGTGCATCGATGCATGCTGAC
*
538356 TGCATCGGTGCATGAAATGCATTCGATGTT
1 TGCATCGATGCATGAAATGCATTCGATGTT
538386 CAATTTATTC
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
63 3 0.04
64 72 0.89
65 6 0.07
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.32
Consensus pattern (64 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAAGCAGATGTGCATCGATGCATGCTGAC
Found at i:538404 original size:64 final size:64
Alignment explanation
Indices: 538292--538434 Score: 175
Period size: 64 Copynumber: 2.2 Consensus size: 64
538282 GCATTGCTTC
*
538292 TGCATCGATGCATGAAATGCATTCGATGTTTTAATAAAATCAGAGTGCATCGATGCATGGTGAG
1 TGCATCGATGCATGAAATGCATTCGATGTTTCAATAAAATCAGAGTGCATCGATGCATGGTGAG
* ** *
538356 TGCATCGGTGCATGAAATGCATTCGATG-TTCAATTTATTCA-ATGGTGCATCGATGCATGGTTT
1 TGCATCGATGCATGAAATGCATTCGATGTTTCAATAAAATCAGA--GTGCATCGATGCATGG--T
538419 GA-
62 GAG
*
538421 TGCATCAATGCATG
1 TGCATCGATGCATG
538435 CTTTTGAAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
62 1 0.01
63 9 0.13
64 43 0.63
65 12 0.18
66 3 0.04
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.32
Consensus pattern (64 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTCAATAAAATCAGAGTGCATCGATGCATGGTGAG
Found at i:544809 original size:21 final size:21
Alignment explanation
Indices: 544783--544822 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
544773 AAGACTATTT
544783 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTGAAACA
**
544804 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
544823 ATACAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAACA
Found at i:545807 original size:64 final size:64
Alignment explanation
Indices: 545697--545854 Score: 156
Period size: 64 Copynumber: 2.5 Consensus size: 64
545687 TCGGTGCACC
* * * * * ** * ***
545697 TGCATCGATGCATAAAATGCATTCAATGTTTGAAAATAGCCTGAGTGCATCGGTGCATTGCTTG
1 TGCACCGATGCATGAAATGCATTCGATGTTTGAAAATAACCAGAGTGCATCAATGCATGGAGAG
* * *
545761 TTCACCGATGCATGAAATGCATTCGATGTTTTAATAA-AATCAGAGTGCATCAATGCATGGAGAG
1 TGCACCGATGCATGAAATGCATTCGATGTTTGAA-AATAACCAGAGTGCATCAATGCATGGAGAG
* *
545825 TGCATCGGTGCATGAAATGCATTCGATGTT
1 TGCACCGATGCATGAAATGCATTCGATGTT
545855 CAATTTATTC
Statistics
Matches: 76, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
64 74 0.97
65 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.30
Consensus pattern (64 bp):
TGCACCGATGCATGAAATGCATTCGATGTTTGAAAATAACCAGAGTGCATCAATGCATGGAGAG
Found at i:549857 original size:42 final size:41
Alignment explanation
Indices: 549805--549904 Score: 101
Period size: 42 Copynumber: 2.4 Consensus size: 41
549795 TCCGATTGAC
* * *
549805 AAAATATCTCACCTGGCTTTCTCACGAAGAGGAGTCACTCGA
1 AAAACATCTCACCTGGCTTTCCCACGAAGAGGAGTCA-TCCA
* * ** *
549847 AAAACATCTCACATAGCTTTCCCGTGAAGGGGAGTCATCCA
1 AAAACATCTCACCTGGCTTTCCCACGAAGAGGAGTCATCCA
*
549888 AAGATCATCTCACCTGG
1 AA-AACATCTCACCTGG
549905 TTCAGACCTG
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
41 5 0.11
42 41 0.89
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (41 bp):
AAAACATCTCACCTGGCTTTCCCACGAAGAGGAGTCATCCA
Found at i:551182 original size:22 final size:20
Alignment explanation
Indices: 551154--551204 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
551144 TACATGTGGA
551154 GGGGGTATCCATACCATAACAT
1 GGGGGTATCCATACC-T-ACAT
* *
551176 GGGGGTATCGATACCTATAT
1 GGGGGTATCCATACCTACAT
551196 GGGGGTATC
1 GGGGGTATC
551205 GGTACCATCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 12 0.44
21 1 0.04
22 14 0.52
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.25
Consensus pattern (20 bp):
GGGGGTATCCATACCTACAT
Found at i:551199 original size:20 final size:22
Alignment explanation
Indices: 551154--551212 Score: 77
Period size: 20 Copynumber: 2.8 Consensus size: 22
551144 TACATGTGGA
*
551154 GGGGGTATCCATACCATAACAT
1 GGGGGTATCGATACCATAACAT
*
551176 GGGGGTATCGATACC-T-ATAT
1 GGGGGTATCGATACCATAACAT
*
551196 GGGGGTATCGGTACCAT
1 GGGGGTATCGATACCAT
551213 CCGAGCATAC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 17 0.52
21 2 0.06
22 14 0.42
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (22 bp):
GGGGGTATCGATACCATAACAT
Found at i:553881 original size:22 final size:23
Alignment explanation
Indices: 553808--553958 Score: 165
Period size: 23 Copynumber: 6.7 Consensus size: 23
553798 AACCTGACAA
*
553808 GGGGTATCGATACC-A-T-AAGG
1 GGGGTATCGATACCTATTCAAAG
553828 GAGGGTATCGATA-CTCATTCAAAG
1 G-GGGTATCGATACCT-ATTCAAAG
* * *
553852 AGGGTATTGATACCTATTC-AGG
1 GGGGTATCGATACCTATTCAAAG
*
553874 GGGGTATTGATACCTATTCAAAG
1 GGGGTATCGATACCTATTCAAAG
553897 GGGGTATCGATACCTATTCAAAG
1 GGGGTATCGATACCTATTCAAAG
553920 GGGGTATCGATACCTATATC--A-
1 GGGGTATCGATACCTAT-TCAAAG
553941 GGGGTATCGATACTCTAT
1 GGGGTATCGATAC-CTAT
553959 GCACAAAAAT
Statistics
Matches: 115, Mismatches: 7, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
20 2 0.02
21 24 0.21
22 26 0.23
23 56 0.49
24 7 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (23 bp):
GGGGTATCGATACCTATTCAAAG
Found at i:553893 original size:45 final size:45
Alignment explanation
Indices: 553809--553958 Score: 168
Period size: 45 Copynumber: 3.4 Consensus size: 45
553799 ACCTGACAAG
*
553809 GGGTATCGATACC-A-TAAGGGAGGGTATCGATA-CTCATTCAAAGA
1 GGGTATCGATACCTATTCAGGG-GGGTATCGATACCT-ATTCAAAGA
* * *
553853 GGGTATTGATACCTATTCAGGGGGGTATTGATACCTATTCAAAGG
1 GGGTATCGATACCTATTCAGGGGGGTATCGATACCTATTCAAAGA
*
553898 GGGTATCGATACCTATTCAAAGGGGGTATCGATACCTATATC--AG-
1 GGGTATCGATACCTATTC-AGGGGGGTATCGATACCTAT-TCAAAGA
553942 GGGTATCGATACTCTAT
1 GGGTATCGATAC-CTAT
553959 GCACAAAAAT
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
44 24 0.26
45 42 0.45
46 25 0.27
47 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (45 bp):
GGGTATCGATACCTATTCAGGGGGGTATCGATACCTATTCAAAGA
Found at i:557701 original size:21 final size:21
Alignment explanation
Indices: 557677--557716 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
557667 ATTTGCAATT
*
557677 CTTTAACAACTCATTATAATC
1 CTTTAACAACTCATCATAATC
557698 CTTTAACAACTCATCATAA
1 CTTTAACAACTCATCATAA
557717 GATAATTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (21 bp):
CTTTAACAACTCATCATAATC
Found at i:559579 original size:22 final size:21
Alignment explanation
Indices: 559547--559602 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
559537 CTGTGGAGGT
*
559547 GGTATCAATACCATAGCATGGG
1 GGTATCGATACCATA-CATGGG
* *
559569 GGTATTGATACC-TATATGGG
1 GGTATCGATACCATACATGGG
*
559589 GGTATCGGTACCAT
1 GGTATCGATACCAT
559603 CCGAGCATAC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 15 0.54
21 3 0.11
22 10 0.36
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (21 bp):
GGTATCGATACCATACATGGG
Found at i:560403 original size:2 final size:2
Alignment explanation
Indices: 560396--560729 Score: 286
Period size: 2 Copynumber: 178.5 Consensus size: 2
560386 ACACATTTAG
560396 TA TA TA TA GTA TA T- TA TA TA T- TA TA TA T- TA TA TA T- TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
560435 TA T- TA TA GTA TA T- TA TA TA TA -A TA TA TA T- TA TA TGA TA -A
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
*
560474 TA GTA CA T- TA T- TA T- TA TA T- 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
560513 T- TA TA TA TA TA TA TA T- TA TA T- 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 TA TA TA TA TA TA
560551 TA TA TA TA TA TA TA T- TA TA TA T- 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
*
560591 T- TA TA TA TA T- TA TA TA TA T- TA CA TA TA T- TA TA GTA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* *
560629 T- TA CA TA TA T- TA TA TA GT- TA TA TA T- TA TA GTA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA
560669 T- TA T- TA TA TA TA T- TA TA GT- TA TA TA T- TA TA TA TCA TA GTA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA T-A TA -TA
*
560709 TA TA TT TA GTA T- TA TA TA TA T
1 TA TA TA TA -TA TA TA TA TA TA T
560730 TATTTGTTTA
Statistics
Matches: 277, Mismatches: 10, Indels: 90
0.73 0.03 0.24
Matches are distributed among these distances:
1 34 0.12
2 223 0.81
3 20 0.07
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:560415 original size:7 final size:7
Alignment explanation
Indices: 560396--560732 Score: 295
Period size: 7 Copynumber: 48.4 Consensus size: 7
560386 ACACATTTAG
560396 TATATA-
1 TATATAT
560402 TAGTATAT
1 TA-TATAT
560410 TATATAT
1 TATATAT
560417 TATATAT
1 TATATAT
560424 TATATAT
1 TATATAT
560431 TATATAT
1 TATATAT
560438 TATAGTA-
1 TATA-TAT
560445 TAT-TA-
1 TATATAT
*
560450 TATATAA
1 TATATAT
560457 TATATAT
1 TATATAT
560464 TATATGA-
1 TATAT-AT
*
560471 TA-ATAG
1 TATATAT
*
560477 TACATTAT
1 TATA-TAT
560485 TATTATAT
1 TA-TATAT
560493 TATATA-
1 TATATAT
560499 TATATAT
1 TATATAT
560506 ATATATAT
1 -TATATAT
560514 TATATAT
1 TATATAT
560521 ATATATAT
1 -TATATAT
560529 TATAT-T
1 TATATAT
560535 ATATATAT
1 -TATATAT
560543 ATATATAT
1 -TATATAT
560551 TATATAT
1 TATATAT
560558 ATATATAT
1 -TATATAT
560566 TATATAT
1 TATATAT
560573 TATATA-
1 TATATAT
560579 TATATA-
1 TATATAT
560585 TATATAT
1 TATATAT
560592 TATATA-
1 TATATAT
560598 TAT-TA-
1 TATATAT
560603 TATATAT
1 TATATAT
560610 TACATATAT
1 T--ATATAT
560619 TATAGTAT
1 TATA-TAT
560627 TAT-TA-
1 TATATAT
*
560632 CATATAT
1 TATATAT
560639 TATATAGT
1 TATATA-T
560647 TATATAT
1 TATATAT
560654 TATAGTA-
1 TATA-TAT
560661 TATAT-T
1 TATATAT
560667 TAT-TAT
1 TATATAT
560673 TATATA-
1 TATATAT
560679 TATTATAGT
1 TA-TATA-T
560688 TATATAT
1 TATATAT
560695 TATATAT
1 TATATAT
*
560702 CATAGTA-
1 TATA-TAT
560709 TATAT-T
1 TATATAT
560715 TAGTAT-T
1 TA-TATAT
560722 ATATATAT
1 -TATATAT
560730 TAT
1 TAT
560733 TTGTTTATTT
Statistics
Matches: 287, Mismatches: 7, Indels: 73
0.78 0.02 0.20
Matches are distributed among these distances:
5 14 0.05
6 49 0.17
7 146 0.51
8 68 0.24
9 10 0.03
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (7 bp):
TATATAT
Found at i:560528 original size:76 final size:76
Alignment explanation
Indices: 560405--560729 Score: 338
Period size: 78 Copynumber: 4.3 Consensus size: 76
560395 GTATATATAG
560405 TATATTA-TATATTATATAT-TATATATTATATATTATAGTATAT-TATATATAATATATATTAT
1 TATATTATTATATTATATATATATATA-TATATATTATA-TATATATATATATAATATATATTAT
560467 ATGATAATAGTACA
64 AT-ATAATAGTACA
*
560481 T-TATTATTATATTATATATATATATATATATATTATATATATATATATTATATTATATATATAT
1 TATATTATTATATTATATATATATATATATATATTATATATATATATA-TATAATATATAT-TAT
* *
560545 ATATATTA-TATA
64 ATATAATAGTACA
* *
560557 TATATATATTATA-TATTATATATATATATATATATTATATATATTATATATATTACATATATTA
1 TATAT-TATTATATTA-TATATATATATATATATATTATATATA-TATATATATAATATATATTA
*
560621 TAGTAT--TATTACA
63 TA-TATAATAGTACA
* *
560634 TATATTA-TATAGTTATATATTATAGTATATATTTATTAT-TATATATAT-TATAGTTATATATT
1 TATATTATTATA-TTATATA-TATA-TATATATATATTATATATATATATATATA-ATATATATT
*
560696 ATATATCATAGT--A
62 ATATATAATAGTACA
560709 TATA-T-TTAGTATTATATATAT
1 TATATTATTA-TATTATATATAT
560730 TATTTGTTTA
Statistics
Matches: 217, Mismatches: 12, Indels: 43
0.80 0.04 0.16
Matches are distributed among these distances:
73 3 0.01
74 10 0.05
75 27 0.12
76 55 0.25
77 52 0.24
78 64 0.29
79 6 0.03
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (76 bp):
TATATTATTATATTATATATATATATATATATATTATATATATATATATATAATATATATTATAT
ATAATAGTACA
Found at i:560743 original size:4 final size:4
Alignment explanation
Indices: 560729--560762 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
560719 ATTATATATA
* *
560729 TTAT TTGT TTAT TTAT TTAT TCAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
560763 TTTCAAGTCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:560767 original size:16 final size:16
Alignment explanation
Indices: 560736--560767 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
560726 ATATTATTTG
560736 TTTATTTATTTATTCA
1 TTTATTTATTTATTCA
*
560752 TTTATTTATTTTTTCA
1 TTTATTTATTTATTCA
560768 AGTCCAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTATTTATTTATTCA
Found at i:564412 original size:40 final size:39
Alignment explanation
Indices: 564291--564430 Score: 149
Period size: 38 Copynumber: 3.4 Consensus size: 39
564281 TAATATATAT
*
564291 AAACATATATTATATATAGTTTTTAAGATATAGTATAGTTTTTGA
1 AAACATATA-TATATATAGTTTTTAA-A-A-A--ACAGTTTTTGA
*
564336 AAACATATA-ATATATAGTTTTTAAAAAACGGTTTTTGA
1 AAACATATATATATATAGTTTTTAAAAAACAGTTTTTGA
* * *
564374 AAACATATATA-ATATAGTTTTTGAAAACATATTATTTTGA
1 AAACATATATATATATAGTTTTT-AAAAAACAGT-TTTTGA
564414 AAACATATATATATATA
1 AAACATATATATATATA
564431 TATATATATA
Statistics
Matches: 85, Mismatches: 6, Indels: 12
0.83 0.06 0.12
Matches are distributed among these distances:
38 29 0.34
39 7 0.08
40 18 0.21
41 6 0.07
42 1 0.01
43 15 0.18
45 9 0.11
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (39 bp):
AAACATATATATATATAGTTTTTAAAAAACAGTTTTTGA
Found at i:564425 original size:2 final size:2
Alignment explanation
Indices: 564418--564444 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
564408 TTTTGAAAAC
564418 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 A
564445 GTTAACTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:573162 original size:24 final size:24
Alignment explanation
Indices: 573135--573201 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
573125 TACGGTGCAT
*
573135 TTCTACTTGGTACTTCGGTACAAA
1 TTCTACGTGGTACTTCGGTACAAA
* * *
573159 TTCTACGCGGTCCTTCGGGACAAA
1 TTCTACGTGGTACTTCGGTACAAA
*
573183 TTCTACGTGGCACTTCGGT
1 TTCTACGTGGTACTTCGGT
573202 GTAAATTTAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.33
Consensus pattern (24 bp):
TTCTACGTGGTACTTCGGTACAAA
Found at i:573207 original size:24 final size:24
Alignment explanation
Indices: 573119--573208 Score: 78
Period size: 24 Copynumber: 3.8 Consensus size: 24
573109 AAATCTTATA
* * *
573119 TGGCACTACGGTGC-ATTTCTACT
1 TGGCACTTCGGTGCAAATTCTACG
* *
573142 TGGTACTTCGGTACAAATTCTACG
1 TGGCACTTCGGTGCAAATTCTACG
*
573166 CGGTC-CTTCGG-GACAAATTCTACG
1 TGG-CACTTCGGTG-CAAATTCTACG
*
573190 TGGCACTTCGGTGTAAATT
1 TGGCACTTCGGTGCAAATT
573209 TATATGAGCT
Statistics
Matches: 52, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
23 12 0.23
24 39 0.75
25 1 0.02
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.32
Consensus pattern (24 bp):
TGGCACTTCGGTGCAAATTCTACG
Found at i:579705 original size:3 final size:3
Alignment explanation
Indices: 579699--579788 Score: 62
Period size: 3 Copynumber: 31.3 Consensus size: 3
579689 AAACATAAGT
* * * * * * *
579699 TAA TAA TAT TAC TAA TAA TTA TTA TTA TAC TAA TTA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
579746 TAA TAC TAA TAA TAA -CA TAA TAA TAG TAA T-A TAA T-A TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
579789 TATCATATAA
Statistics
Matches: 68, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
2 7 0.10
3 61 0.90
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:579746 original size:14 final size:14
Alignment explanation
Indices: 579711--579807 Score: 81
Period size: 14 Copynumber: 6.9 Consensus size: 14
579701 ATAATATTAC
*
579711 TAATAATTATTATTA
1 TAATAATTA-TAATA
*
579726 TACTAATTATAATA
1 TAATAATTATAATA
* *
579740 TAATAATAATACTAA
1 TAATAATTATAAT-A
*
579755 TAATAA-CATAATAA
1 TAATAATTATAAT-A
*
579769 TAGTAA-TATAATA
1 TAATAATTATAATA
*
579782 TAATAATTATCATA
1 TAATAATTATAATA
*
579796 TAATATTTATAA
1 TAATAATTATAA
579808 CCCGGACAAA
Statistics
Matches: 67, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
13 6 0.09
14 46 0.69
15 15 0.22
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (14 bp):
TAATAATTATAATA
Found at i:579752 original size:23 final size:22
Alignment explanation
Indices: 579725--579788 Score: 80
Period size: 20 Copynumber: 3.0 Consensus size: 22
579715 AATTATTATT
579725 ATACTAATTATAATATAATAATA
1 ATACTAA-TATAATATAATAATA
579748 ATACT-A-ATAATA-ACATAATA
1 ATACTAATATAATATA-ATAATA
*
579768 ATAGTAATATAATATAATAAT
1 ATACTAATATAATATAATAAT
579789 TATCATATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
19 1 0.03
20 16 0.44
21 1 0.03
22 12 0.33
23 6 0.17
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.36
Consensus pattern (22 bp):
ATACTAATATAATATAATAATA
Found at i:579784 original size:19 final size:18
Alignment explanation
Indices: 579733--579801 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 18
579723 TTATACTAAT
579733 TATAATAT-A-ATAATAA
1 TATAATATAATATAATAA
*
579749 TACTAATAATAACATAATAA
1 TA-TAAT-ATAATATAATAA
579769 TAGTAATATAATATAATAA
1 TA-TAATATAATATAATAA
*
579788 TTATCATATAATAT
1 -TATAATATAATAT
579802 TTATAACCCG
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
16 2 0.04
17 4 0.09
18 2 0.04
19 22 0.49
20 15 0.33
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (18 bp):
TATAATATAATATAATAA
Found at i:580107 original size:55 final size:55
Alignment explanation
Indices: 580021--580848 Score: 1144
Period size: 55 Copynumber: 15.3 Consensus size: 55
580011 GGAAAATAGA
* *
580021 ACTCGAAC-ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * *
580075 ACTTGAACAATCTTCAACAAACGGGT-TCGCTCCCTATTTCTTCAGAGAGTAT-AG
1 ACTCGAACAATCTTCAACAATCGCGTCT-GCCCCCTATTTCTTCAGAGAGTATAAG
* * * *
580129 AACTCGAAAAATCTTCAACAATCGTGTCCGCCCCCTATTTCTTCAGAGAGAATAAG
1 -ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
580185 ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTTTTTCTTCACAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * *
580240 AC-C-AACAATTTTCATCAATCACGTCTGCCCCCTATTTCTTTAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * *
580293 AC-C-CACAATCATCATCAAACGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
580346 ACAC--ACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * *
580399 ACTCAAACAATCTTCAACGATCGTGTATGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
580454 AC-C-CACAATCTTCATCAATCACGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
*
580507 ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
580562 ACTCGAACAATCTTCAACGATCGCGTATG-CCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
580616 ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTGCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
*
580671 ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * * *
580726 AC-C-CACAATCATCATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATACG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
580779 ACTTGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
*
580834 ACTCGAACAGTCTTC
1 ACTCGAACAATCTTC
580849 TTTTGCTTCA
Statistics
Matches: 693, Mismatches: 68, Indels: 25
0.88 0.09 0.03
Matches are distributed among these distances:
53 232 0.33
54 68 0.10
55 391 0.56
56 2 0.00
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (55 bp):
ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
Found at i:580461 original size:108 final size:109
Alignment explanation
Indices: 580021--580848 Score: 1129
Period size: 108 Copynumber: 7.6 Consensus size: 109
580011 GGAAAATAGA
* * *
580021 ACTCGAAC-ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTTGAACAA
1 ACTC-AACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
* * * *
580085 TCTTCAACAAACGGGT-TCGCTCCCTATTTCTTCAGAGAGTAT-AG
65 TCTTCAACGATCGCGTCT-GCCCCCTATTTCTTCAGAGAGTATAAG
* * * *
580129 AACTCGAAAAATCTTCAACAATCGTGTCCGCCCCCTATTTCTTCAGAGAGAATAAGACTCGAACA
1 -ACTC-AACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACA
* *
580194 ATCTTCAACGATCGCGTCTGCCCCCTTTTTCTTCACAGAGTATAAG
64 ATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * * *
580240 AC-CAACAATTTTCATCAATCACGTCTGCCCCCTATTTCTTTAGAGAGTATAAGAC-C-CACAAT
1 ACTCAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
* * * *
580302 CATCATCAAACGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
66 CTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
580346 ACAC-ACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAAACAAT
1 ACTCAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
* *
580410 CTTCAACGATCGTGTATGCCCCCTATTTCTTCAGAGAGTATAAG
66 CTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
580454 AC-CCACAATCTTCATCAATCACGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
1 ACTCAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
580518 CTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
66 CTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
580562 ACTCGAACAATCTTCAACGATCGCGTATG-CCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
1 ACTC-AACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
*
580626 TCTTCAACGATCGCGTCTGCCCCCTATTGCTTCAGAGAGTATAAG
65 TCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
580671 ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAA
1 ACTC-AACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
* * * * *
580734 TCATCATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATACG
65 TCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
580779 ACTTGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAG
1 AC-TCAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
580844 TCTTC
65 TCTTC
580849 TTTTGCTTCA
Statistics
Matches: 640, Mismatches: 66, Indels: 25
0.88 0.09 0.03
Matches are distributed among these distances:
106 91 0.14
107 4 0.01
108 284 0.44
109 117 0.18
110 141 0.22
111 3 0.00
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (109 bp):
ACTCAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
CTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
Found at i:583652 original size:195 final size:195
Alignment explanation
Indices: 583320--583723 Score: 727
Period size: 195 Copynumber: 2.1 Consensus size: 195
583310 CTAGCTGAAA
* *
583320 TCAGCTTTATTGTAATTTGCCTTTATCGGGCTAGCTGAAGCATTCATCTCATCACAAAGTCTTTG
1 TCAGCTTTATTGTAATTTGCATTTATCGGGCTAACTGAAGCATTCATCTCATCACAAAGTCTTTG
* *
583385 ACTTGACAATCACAGTGGAGCATACACCAAATTGCCGAGTACCCGATCAAGGTCATGGTTTGAAT
66 ACTTGACAATCACAATGGAGCATACACCAAATTGCCAAGTACCCGATCAAGGTCATGGTTTGAAT
583450 ATAATCTATTCATAAAGCCAAGGATTTCGAGTTTCCTCTATAACCAATTGCCTTAGTGGAATAGC
131 ATAATCTATTCATAAAGCCAAGGATTTCGAGTTTCCTCTATAACCAATTGCCTTAGTGGAATAGC
*
583515 TCAGCTTTATTGTAATTTGCATTTATCGGGCTAACTGAAGGATTCATCTCATCACAAAGTCTTTG
1 TCAGCTTTATTGTAATTTGCATTTATCGGGCTAACTGAAGCATTCATCTCATCACAAAGTCTTTG
*
583580 ACTTGACAATCACAATGGAGCATACACCGAATTGCCAAGTACCCGATCAAGGTCATGGTTTGAAT
66 ACTTGACAATCACAATGGAGCATACACCAAATTGCCAAGTACCCGATCAAGGTCATGGTTTGAAT
* * *
583645 ATAATCTATTCATAAAGCTAGGGCTTTCGAGTTTCCTCTATAACCAATTGCCTTAGTGGAATAGC
131 ATAATCTATTCATAAAGCCAAGGATTTCGAGTTTCCTCTATAACCAATTGCCTTAGTGGAATAGC
583710 TCAGCTTTATTGTA
1 TCAGCTTTATTGTA
583724 TACACATATT
Statistics
Matches: 200, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
195 200 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (195 bp):
TCAGCTTTATTGTAATTTGCATTTATCGGGCTAACTGAAGCATTCATCTCATCACAAAGTCTTTG
ACTTGACAATCACAATGGAGCATACACCAAATTGCCAAGTACCCGATCAAGGTCATGGTTTGAAT
ATAATCTATTCATAAAGCCAAGGATTTCGAGTTTCCTCTATAACCAATTGCCTTAGTGGAATAGC
Found at i:583740 original size:2 final size:2
Alignment explanation
Indices: 583729--583761 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
583719 TTGTATACAC
583729 AT AT -T 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
583762 TTTGTTGGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:585901 original size:72 final size:72
Alignment explanation
Indices: 585784--585918 Score: 200
Period size: 72 Copynumber: 1.9 Consensus size: 72
585774 CAAGTTATTT
* * *
585784 ATCATTTTCTATCATCACATTGGATGTACCACTAACATTCAGATTCTCACTCGAAGTCTTCATCT
1 ATCATTTGCTATCATCACATTGGATGCACCACTAACATTCAGATTCTCACCCGAAGTCTTCATCT
585849 GTACTTG
66 GTACTTG
* * *
585856 ATCATTTGCTATCATCATATTGGCA-GCACTACTAACATTCGGATTCTCACCCGAAGTCTTCAT
1 ATCATTTGCTATCATCACATTGG-ATGCACCACTAACATTCAGATTCTCACCCGAAGTCTTCAT
585919 TTTTTCTTGT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
72 55 0.98
73 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.36
Consensus pattern (72 bp):
ATCATTTGCTATCATCACATTGGATGCACCACTAACATTCAGATTCTCACCCGAAGTCTTCATCT
GTACTTG
Found at i:587722 original size:39 final size:39
Alignment explanation
Indices: 587678--587760 Score: 166
Period size: 39 Copynumber: 2.1 Consensus size: 39
587668 CAAATTAGAA
587678 CGAATTTATAATTTTCAATTGCAAAGACAATTAATTAAT
1 CGAATTTATAATTTTCAATTGCAAAGACAATTAATTAAT
587717 CGAATTTATAATTTTCAATTGCAAAGACAATTAATTAAT
1 CGAATTTATAATTTTCAATTGCAAAGACAATTAATTAAT
587756 CGAAT
1 CGAAT
587761 ATCGGCCTGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.37
Consensus pattern (39 bp):
CGAATTTATAATTTTCAATTGCAAAGACAATTAATTAAT
Found at i:590864 original size:3 final size:3
Alignment explanation
Indices: 590858--590983 Score: 98
Period size: 3 Copynumber: 43.3 Consensus size: 3
590848 AAACATAAGT
* * * * * * *
590858 TAA TAA TAT TAT TAA TAA TTA TTA TTA TAC TAA TTA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
590905 TAT TAC TAA TAA TAA -CA TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
590950 TAA TTA TAA TTA TAA TAA TAA TTA CAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
590984 TATCATATAA
Statistics
Matches: 98, Mismatches: 21, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
2 7 0.07
3 91 0.93
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:590939 original size:34 final size:34
Alignment explanation
Indices: 590888--590990 Score: 113
Period size: 34 Copynumber: 3.1 Consensus size: 34
590878 ATTATTATAC
*
590888 TAATTATAAT-ATAATAATATTACTAATAATAA-CA
1 TAATTATAATAAT-ATAATA-TAATAATAATAATCA
* *
590922 TAATAATAATAATATAATATAATAATAATAATTA
1 TAATTATAATAATATAATATAATAATAATAATCA
* * *
590956 TAATTATAATAATA-ATTACAATAATAATTATCA
1 TAATTATAATAATATAATATAATAATAATAATCA
590989 TA
1 TA
590991 TAATATTTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
33 28 0.47
34 29 0.49
35 2 0.03
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (34 bp):
TAATTATAATAATATAATATAATAATAATAATCA
Found at i:590964 original size:12 final size:12
Alignment explanation
Indices: 590858--591002 Score: 102
Period size: 12 Copynumber: 12.2 Consensus size: 12
590848 AAACATAAGT
590858 TAATAAT-ATTA
1 TAATAATAATTA
*
590869 TTAATAATTATTA
1 -TAATAATAATTA
* *
590882 TTATACTAATTA
1 TAATAATAATTA
*
590894 TAAT-ATAATAA
1 TAATAATAATTA
* * *
590905 TATTACTAATAA
1 TAATAATAATTA
* *
590917 TAA-CATAATAA
1 TAATAATAATTA
*
590928 TAATAAT-ATAA
1 TAATAATAATTA
*
590939 T-ATAATAATAA
1 TAATAATAATTA
*
590950 TAATTATAATTA
1 TAATAATAATTA
590962 TAATAATAATTA
1 TAATAATAATTA
*
590974 CAATAATAATTA
1 TAATAATAATTA
*
590986 TCATATAATATTTA
1 T-A-ATAATAATTA
591000 TAA
1 TAA
591003 CCTGGATAAA
Statistics
Matches: 108, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
10 5 0.05
11 27 0.25
12 60 0.56
13 6 0.06
14 10 0.09
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATAATAATTA
Found at i:594582 original size:23 final size:24
Alignment explanation
Indices: 594546--594592 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
594536 AAATCTTATA
*
594546 TGGCACTACAGTGC-ATTTCTACG
1 TGGCACTACAGTGCAAATTCTACG
* *
594569 TGGCACTTCGGTGCAAATTCTACG
1 TGGCACTACAGTGCAAATTCTACG
594593 CAGTCCTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (24 bp):
TGGCACTACAGTGCAAATTCTACG
Found at i:595188 original size:21 final size:20
Alignment explanation
Indices: 595150--595188 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
595140 AAGGTTAAAT
**
595150 TTTTACGAATTTTATGTAAG
1 TTTTACGAAAGTTATGTAAG
595170 TTTTACGAAAGTTACTGTA
1 TTTTACGAAAGTTA-TGTA
595189 GCAGTGCATC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (20 bp):
TTTTACGAAAGTTATGTAAG
Found at i:595207 original size:21 final size:21
Alignment explanation
Indices: 595183--595222 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
595173 TACGAAAGTT
595183 ACTGTAGCAGTGCATCGATGC
1 ACTGTAGCAGTGCATCGATGC
595204 ACTGTAGCAGTGCATCGAT
1 ACTGTAGCAGTGCATCGAT
595223 ACACAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATGC
Found at i:595274 original size:21 final size:21
Alignment explanation
Indices: 595248--595288 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
595238 GATATTTTTG
* *
595248 TGCATCGATGCATTGTAGCAA
1 TGCATCGATACACTGTAGCAA
595269 TGCATCGATACACTGTAGCA
1 TGCATCGATACACTGTAGCA
595289 CTGTTCATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (21 bp):
TGCATCGATACACTGTAGCAA
Found at i:602251 original size:68 final size:68
Alignment explanation
Indices: 602167--602303 Score: 274
Period size: 68 Copynumber: 2.0 Consensus size: 68
602157 GTTTTATCTT
602167 ATGTTCAAAGTATGTGAATTAGAATTTATACAGTTAGGATTTGTTCAAGAAAATAACATGCGAGA
1 ATGTTCAAAGTATGTGAATTAGAATTTATACAGTTAGGATTTGTTCAAGAAAATAACATGCGAGA
602232 TAG
66 TAG
602235 ATGTTCAAAGTATGTGAATTAGAATTTATACAGTTAGGATTTGTTCAAGAAAATAACATGCGAGA
1 ATGTTCAAAGTATGTGAATTAGAATTTATACAGTTAGGATTTGTTCAAGAAAATAACATGCGAGA
602300 TAG
66 TAG
602303 A
1 A
602304 GATCATGTCC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.32
Consensus pattern (68 bp):
ATGTTCAAAGTATGTGAATTAGAATTTATACAGTTAGGATTTGTTCAAGAAAATAACATGCGAGA
TAG
Found at i:608708 original size:201 final size:200
Alignment explanation
Indices: 608298--608828 Score: 636
Period size: 201 Copynumber: 2.6 Consensus size: 200
608288 CTGTTCACAT
* * *
608298 CATAGCTAAAGGAGAGAAAGGATATCTATCAACGAAAACTTTTGAGTTCGATTCCATTCAGCTCG
1 CATAGCTTAAGTAGAGAAAGGATATCTATCAACGAAAACTTTCGAGTTCGATTCCATTCAGCTCG
* * * * * *
608363 AGTGCGTATTCAACCGCATGGTAGCAGCGAGGATCTACA-TTCCGGTTGAATTTTAAGCCAAGGT
66 AGGGCGTA-TCAACTGCATGGTAGCAGCGAGGAACTA-ATTTTCGGTTGAATTTTAAACCTAGGT
* * ** * *
608427 CTTTATTCCAAGAAGAATAACTAGGCTGGCTGGGATTTAGCAACAAGGAACTATCTCCTATACTA
129 CTTTATT-CAAGAACAAGAACTAGGCTGGCTGCAATTTAGCAACAAGGAACTATCTCCCAGACTA
*
608492 ATTTACAG
193 ATTTACAA
* * * *
608500 CATAGCTTAAGTAGAGAAGGGCTATCTATCAACAAAAACTTTCGAGTTCGATTCCATTTAGCTCG
1 CATAGCTTAAGTAGAGAAAGGATATCTATCAACGAAAACTTTCGAGTTCGATTCCATTCAGCTCG
* * *
608565 AGGGCGTATCAACTGCATGGTAGCAGTGAGGAACTAATTTTCTGTTGAAGTTTAAACCTAGGTCT
66 AGGGCGTATCAACTGCATGGTAGCAGCGAGGAACTAATTTTCGGTTGAATTTTAAACCTAGGTCT
* * * * *
608630 TTAAGTT-AAGAACAAGACCTAGGTTGGCTGCAATTTAGTAATAAGGAACTATCTCCCAGCCTAA
131 TT-A-TTCAAGAACAAGAACTAGGCTGGCTGCAATTTAGCAACAAGGAACTATCTCCCAGACTAA
608694 TTTACAA
194 TTTACAA
* * * * * *
608701 TATAGCTTAAGTCGAGAAAAGTTGTCTATCAACGAAAACTTTCAAGTTCGATTCCATTCAGCTCG
1 CATAGCTTAAGTAGAGAAAGGATATCTATCAACGAAAACTTTCGAGTTCGATTCCATTCAGCTCG
* * * * *
608766 AGGGTGTACCAA-TCGCATGGTAGTAGCGAGGAACTACTTTTCGGTTTAATTTTAAACCTAGGT
66 AGGGCGTATCAACT-GCATGGTAGCAGCGAGGAACTAATTTTCGGTTGAATTTTAAACCTAGGT
608829 AATTAAGCAA
Statistics
Matches: 280, Mismatches: 45, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
200 2 0.01
201 210 0.75
202 66 0.24
203 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (200 bp):
CATAGCTTAAGTAGAGAAAGGATATCTATCAACGAAAACTTTCGAGTTCGATTCCATTCAGCTCG
AGGGCGTATCAACTGCATGGTAGCAGCGAGGAACTAATTTTCGGTTGAATTTTAAACCTAGGTCT
TTATTCAAGAACAAGAACTAGGCTGGCTGCAATTTAGCAACAAGGAACTATCTCCCAGACTAATT
TACAA
Found at i:609339 original size:2 final size:2
Alignment explanation
Indices: 609334--609382 Score: 75
Period size: 2 Copynumber: 25.0 Consensus size: 2
609324 TTTTTTACAT
609334 TA TA TA -A TA TA TA TGA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
609375 TA TA TA TA
1 TA TA TA TA
609383 ATTTCAAAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.05
2 40 0.91
3 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:609429 original size:20 final size:19
Alignment explanation
Indices: 609399--609436 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
609389 AAAGCATATA
609399 ATATATATAGTTTTTGAAG
1 ATATATATAGTTTTTGAAG
609418 ATATAGTATAGTTTTTGAA
1 ATATA-TATAGTTTTTGAA
609437 AACATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (19 bp):
ATATATATAGTTTTTGAAG
Found at i:609468 original size:38 final size:38
Alignment explanation
Indices: 609424--609542 Score: 127
Period size: 36 Copynumber: 3.1 Consensus size: 38
609414 GAAGATATAG
*
609424 TATAGTTTTTGAAAACATATTTTTGACAACATATAATA
1 TATAGTTTTTGAAAACATATTTTTGAAAACATATAATA
* * ***
609462 TATAG--TTTAAAAAAACGGTTTTGAAAACATAT-ATAA
1 TATAGTTTTTGAAAACATATTTTTGAAAACATATAAT-A
609498 TATAGTTTTTGAAAACATATTATTTTGAAAACATATATATA
1 TATAGTTTTTGAAAACATA-T-TTTTGAAAACATATA-ATA
609539 TATA
1 TATA
609543 TATATATATA
Statistics
Matches: 63, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
35 2 0.03
36 27 0.43
38 13 0.21
40 14 0.22
41 5 0.08
42 2 0.03
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.40
Consensus pattern (38 bp):
TATAGTTTTTGAAAACATATTTTTGAAAACATATAATA
Found at i:609537 original size:2 final size:2
Alignment explanation
Indices: 609530--609572 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
609520 TTTTGAAAAC
609530 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
609572 A
1 A
609573 GTTTTTTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:614237 original size:20 final size:21
Alignment explanation
Indices: 614152--614237 Score: 63
Period size: 22 Copynumber: 4.0 Consensus size: 21
614142 TGTACGTTAC
614152 TAAA-ATAT-ATTTAGAGTTAAT
1 TAAATATATAATTTA-A-TTAAT
**
614173 TAAATATATGTTTTAA-TAAT
1 TAAATATATAATTTAATTAAT
* *
614193 CCTAAATATTTAATTTCACTTAAT
1 --TAAATATATAATTT-AATTAAT
614217 TAAATATAT-ATTTAATTAAT
1 TAAATATATAATTTAATTAAT
614237 T
1 T
614238 TGAAATAATA
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
20 11 0.21
21 8 0.15
22 24 0.46
23 5 0.10
24 4 0.08
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (21 bp):
TAAATATATAATTTAATTAAT
Found at i:614320 original size:90 final size:90
Alignment explanation
Indices: 614212--614375 Score: 285
Period size: 90 Copynumber: 1.8 Consensus size: 90
614202 TTAATTTCAC
* *
614212 TTAATTAAATATATATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAGGGTAACTTGG
1 TTAATTAAATATATATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAGAGTAACTTGG
614277 ATATAAAAGGATTATTAAATTCTAA
66 ATATAAAAGGATTATTAAATTCTAA
614302 TTAATTAAATAT-TGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAGAGTAACTTG
1 TTAATTAAATATAT-ATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAGAGTAACTTG
*
614366 GCTATAAAAG
65 GATATAAAAG
614376 TGTGAGTTAG
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
89 1 0.01
90 69 0.99
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (90 bp):
TTAATTAAATATATATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAGAGTAACTTGG
ATATAAAAGGATTATTAAATTCTAA
Found at i:621108 original size:89 final size:90
Alignment explanation
Indices: 620995--621170 Score: 282
Period size: 89 Copynumber: 2.0 Consensus size: 90
620985 TAATCCTGAA
* * * * *
620995 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAA-AAAATCTCTAATATGAT
1 TATTAAATTCCAATTAAATAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
621059 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
621084 TATTAAATTCCAATTAAATAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
1 TATTAAATTCCAATTAAATAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
* *
621149 TAGGTTAACTTGGCTATAAAAG
66 TAGGGTAACTTGGATATAAAAG
621171 TGTGTGTTAG
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
89 44 0.56
90 35 0.44
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (90 bp):
TATTAAATTCCAATTAAATAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
TAGGGTAACTTGGATATAAAAGGAT
Found at i:639233 original size:45 final size:45
Alignment explanation
Indices: 639177--639422 Score: 339
Period size: 45 Copynumber: 5.5 Consensus size: 45
639167 AAATCTACAA
* *
639177 ATCGACATAAAAGGTGCCACTAATGAAAATTCATAACAATGCATT
1 ATCGACATAAAAGGTGCCACTAATGAAAATGCATAACGATGCATT
* * * * *
639222 ATCGGCATAAAAGGTGCCATTAATGGAAATGTATAACGGTGCATT
1 ATCGACATAAAAGGTGCCACTAATGAAAATGCATAACGATGCATT
* *
639267 ATCGGCATGAAAGGTGCCACTAATGAAAATGCATAACGATGCATT
1 ATCGACATAAAAGGTGCCACTAATGAAAATGCATAACGATGCATT
*
639312 ATCGACATAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATT
1 ATCGACATAAAAGGTGCCACTAATGAAAATGCATAACGATGCATT
* * ** *
639357 ATTGGCATAAAATATGCCACTAATGAAAATGCATAATGATGCATT
1 ATCGACATAAAAGGTGCCACTAATGAAAATGCATAACGATGCATT
* *
639402 ATCGATATAAAAGGTTCCACT
1 ATCGACATAAAAGGTGCCACT
639423 CATGGTATTC
Statistics
Matches: 174, Mismatches: 27, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 174 1.00
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (45 bp):
ATCGACATAAAAGGTGCCACTAATGAAAATGCATAACGATGCATT
Found at i:639353 original size:25 final size:25
Alignment explanation
Indices: 639279--639353 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
639269 CGGCATGAAA
639279 GGTGCCACTAATGAAAATGCATAAC
1 GGTGCCACTAATGAAAATGCATAAC
* * * *
639304 GATG-CA-TTATCG-ACAT--A-AAA
1 GGTGCCACTAAT-GAAAATGCATAAC
639324 GGTGCCACTAATGAAAATGCATAAC
1 GGTGCCACTAATGAAAATGCATAAC
639349 GGTGC
1 GGTGC
639354 ATTATTGGCA
Statistics
Matches: 35, Mismatches: 8, Indels: 14
0.61 0.14 0.25
Matches are distributed among these distances:
20 5 0.14
21 4 0.11
22 6 0.17
23 6 0.17
24 4 0.11
25 10 0.29
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (25 bp):
GGTGCCACTAATGAAAATGCATAAC
Found at i:649622 original size:33 final size:33
Alignment explanation
Indices: 649580--649644 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
649570 TAGTACAAAA
649580 GGTGGACACGACCTTATGTGTCATACGGATTAT
1 GGTGGACACGACCTTATGTGTCATACGGATTAT
649613 GGTGGACACGACCTTATGTGTCATACGGATTA
1 GGTGGACACGACCTTATGTGTCATACGGATTA
649645 GCACTACGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (33 bp):
GGTGGACACGACCTTATGTGTCATACGGATTAT
Found at i:649741 original size:20 final size:20
Alignment explanation
Indices: 649703--649741 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
649693 GTATATTGGG
* *
649703 CTATTGTCTATTGTTTATGA
1 CTATTGTCTATGGTATATGA
649723 CTATTGTCTATGGTATATG
1 CTATTGTCTATGGTATATG
649742 GTTATGGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.10, G:0.18, T:0.51
Consensus pattern (20 bp):
CTATTGTCTATGGTATATGA
Found at i:649806 original size:44 final size:45
Alignment explanation
Indices: 649743--649898 Score: 228
Period size: 45 Copynumber: 3.5 Consensus size: 45
649733 TGGTATATGG
*
649743 TTATGGAAT-AATGGAAAGTATAATGGTAAAATAAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATAATGGTAAAATAAGCTTACGAGC
* *
649787 TTATGG-ATAAATTGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATAATGGTAAAATAAGCTTACGAGC
* * *
649831 TTTTGGAATAAATGGTAATTA-AATTTGTAAAATAAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATAA-TGGTAAAATAAGCTTACGAGC
649876 TTATGGAATAAATGGTAAGTATA
1 TTATGGAATAAATGGTAAGTATA
649899 TTGGATATGC
Statistics
Matches: 98, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
43 2 0.02
44 44 0.45
45 51 0.52
46 1 0.01
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.33
Consensus pattern (45 bp):
TTATGGAATAAATGGTAAGTATAATGGTAAAATAAGCTTACGAGC
Found at i:651888 original size:13 final size:13
Alignment explanation
Indices: 651872--651899 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
651862 TGATATCAGC
651872 AATGGTTGCGATT
1 AATGGTTGCGATT
651885 AATGGTTGCGATT
1 AATGGTTGCGATT
651898 AA
1 AA
651900 GATGATGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (13 bp):
AATGGTTGCGATT
Found at i:652653 original size:30 final size:30
Alignment explanation
Indices: 652612--652669 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
652602 ATAATTAAGG
*
652612 GTAAAACGTTATATGCCAAAATGTCAAAAT
1 GTAAAAAGTTATATGCCAAAATGTCAAAAT
652642 GTAAAAAGTTATATGCCAAAATGTCAAA
1 GTAAAAAGTTATATGCCAAAATGTCAAA
652670 CTGTTCACGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (30 bp):
GTAAAAAGTTATATGCCAAAATGTCAAAAT
Found at i:657395 original size:40 final size:42
Alignment explanation
Indices: 657351--657540 Score: 135
Period size: 40 Copynumber: 4.5 Consensus size: 42
657341 ACACGACTCT
*
657351 TACGTGATGAGGA-GATCAGGT-TGGGTGATGACATGGTTCC
1 TACGTGATGAGGACGATCAGGTATGGGTGATGACACGGTTCC
* ** * *
657391 TACGTGATGAGGATGGCATGCCATCTAAGGGTGATAACACGGTTCC
1 TACGTGATGAGGA-CG-AT--CAGGTATGGGTGATGACACGGTTCC
* * * *
657437 TACGTGATGAGGACG-GCTGGTTATCTAGGGT--TGACATGGCTCC
1 TACGTGATGAGGACGATCAGG-TA--T-GGGTGATGACACGGTTCC
* * *
657480 TACGTGATGAGGA-GATCAAGT-CGGGTGATGAAACGGTTCC
1 TACGTGATGAGGACGATCAGGTATGGGTGATGACACGGTTCC
657520 TACGTGATGAGGACGA-CAGGT
1 TACGTGATGAGGACGATCAGGT
657541 CATCTAAGGG
Statistics
Matches: 114, Mismatches: 22, Indels: 28
0.70 0.13 0.17
Matches are distributed among these distances:
38 4 0.04
40 39 0.34
41 3 0.03
42 5 0.04
43 26 0.23
45 8 0.07
46 29 0.25
ACGTcount: A:0.24, C:0.16, G:0.35, T:0.25
Consensus pattern (42 bp):
TACGTGATGAGGACGATCAGGTATGGGTGATGACACGGTTCC
Found at i:657463 original size:46 final size:45
Alignment explanation
Indices: 657373--657534 Score: 153
Period size: 46 Copynumber: 3.7 Consensus size: 45
657363 AGATCAGGTT
*
657373 GGGTGATGACATGGTTCCTACGTGATGAGGATGGCATGCCATCTAA
1 GGGTGATGACATGGTTCCTACGTGATGAGGACGGCATGCCATCT-A
* * **
657419 GGGTGATAACACGGTTCCTACGTGATGAGGACGGC-TGGTTATCTA
1 GGGTGATGACATGGTTCCTACGTGATGAGGACGGCAT-GCCATCTA
* *
657464 GGGT--TGACATGGCTCCTACGTGATGAGGA--G-AT-CAAGTC--
1 GGGTGATGACATGGTTCCTACGTGATGAGGACGGCATGCCA-TCTA
* *
657502 GGGTGATGAAACGGTTCCTACGTGATGAGGACG
1 GGGTGATGACATGGTTCCTACGTGATGAGGACG
657535 ACAGGTCATC
Statistics
Matches: 96, Mismatches: 13, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
38 4 0.04
39 1 0.01
40 24 0.25
41 2 0.02
43 22 0.23
45 6 0.06
46 37 0.39
ACGTcount: A:0.23, C:0.17, G:0.35, T:0.25
Consensus pattern (45 bp):
GGGTGATGACATGGTTCCTACGTGATGAGGACGGCATGCCATCTA
Found at i:658086 original size:43 final size:43
Alignment explanation
Indices: 658022--658132 Score: 141
Period size: 43 Copynumber: 2.6 Consensus size: 43
658012 CAATTCCCTT
* * * *
658022 CGTCGTGAAGTTGAAACCGTGGATGTGTGGGCACTATATCCTC
1 CGTCGTGGAGTTGAAATCGTGGATGCGTGGGCACGATATCCTC
* * *
658065 CGTCGTGGAGTTTAAATCGTGGATCCGTGGGTACGATATCCTC
1 CGTCGTGGAGTTGAAATCGTGGATGCGTGGGCACGATATCCTC
* *
658108 TGTCGTGGAGTTGAAATCATGGATG
1 CGTCGTGGAGTTGAAATCGTGGATG
658133 GCCCCTTCCT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.30
Consensus pattern (43 bp):
CGTCGTGGAGTTGAAATCGTGGATGCGTGGGCACGATATCCTC
Found at i:658683 original size:32 final size:32
Alignment explanation
Indices: 658646--658720 Score: 107
Period size: 32 Copynumber: 2.3 Consensus size: 32
658636 ATTGAATTCC
* *
658646 CAAAGATGCCCCGATATTCGATGTTGAATC-T
1 CAAAGATGCCCCAACATTCGATGTTGAATCTT
*
658677 CAAAAGATGCCCCAACATTTGATGTTGAATCTT
1 C-AAAGATGCCCCAACATTCGATGTTGAATCTT
658710 CAAAGATGCCC
1 CAAAGATGCCC
658721 TCTATTGCTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
31 1 0.03
32 36 0.92
33 2 0.05
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (32 bp):
CAAAGATGCCCCAACATTCGATGTTGAATCTT
Found at i:659790 original size:22 final size:22
Alignment explanation
Indices: 659765--659807 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
659755 CTTGTCTTCA
659765 TTTT-TCTTTCTTCACTTTTTTC
1 TTTTATCTTTCTTC-CTTTTTTC
* *
659787 TTTTATTTTTGTTCCTTTTTT
1 TTTTATCTTTCTTCCTTTTTT
659808 GTTCTGATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.05, C:0.16, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTTATCTTTCTTCCTTTTTTC
Found at i:662472 original size:118 final size:116
Alignment explanation
Indices: 662244--662476 Score: 385
Period size: 118 Copynumber: 2.0 Consensus size: 116
662234 TCAAAAGGAA
* * * *
662244 AACCCCTCGACAAAATTGGACAGATCTGAAAGCAAAAATCAAAATGTTAGTCTAACAAAAAATGA
1 AACCACTCGACAAAACTGGACAGATCTGAAAGAAAAAATCAAAATGTTAGTATAACAAAAAATGA
662309 AGCAATTACAAACTTCAATAAATGAATCATAAATTAACTAAAAACTCGAAC
66 AGCAATTACAAACTTCAATAAATGAATCATAAATTAACTAAAAACTCGAAC
*
662360 AACCACTCGACAAACCTGGACAGATCTGAAAGAAAAAATCAAAATGTTAGTATAACAAAAAAAAT
1 AACCACTCGACAAAACTGGACAGATCTGAAAGAAAAAATCAAAATGTTAGTATAAC--AAAAAAT
* *
662425 TAAGCAATTACAAACTTCGATAAATGAATCATAAATTAACTAAAAACTCGAA
64 GAAGCAATTACAAACTTCAATAAATGAATCATAAATTAACTAAAAACTCGAA
662477 TTCATAATTT
Statistics
Matches: 108, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
116 51 0.47
118 57 0.53
ACGTcount: A:0.52, C:0.17, G:0.10, T:0.21
Consensus pattern (116 bp):
AACCACTCGACAAAACTGGACAGATCTGAAAGAAAAAATCAAAATGTTAGTATAACAAAAAATGA
AGCAATTACAAACTTCAATAAATGAATCATAAATTAACTAAAAACTCGAAC
Found at i:663106 original size:29 final size:30
Alignment explanation
Indices: 663041--663107 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
663031 ACTCAAAAAG
*
663041 CTAAAATAGCTAAAACAGAAATTTAAATGA
1 CTAAAATAGCTAAAACAGAAACTTAAATGA
* *
663071 C-ATAAATAGC-AAAACAGAAACTTCAGTGA
1 CTA-AAATAGCTAAAACAGAAACTTAAATGA
663100 CTAAAATA
1 CTAAAATA
663108 AAATAACAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
29 23 0.72
30 9 0.28
ACGTcount: A:0.55, C:0.13, G:0.10, T:0.21
Consensus pattern (30 bp):
CTAAAATAGCTAAAACAGAAACTTAAATGA
Found at i:663809 original size:3 final size:3
Alignment explanation
Indices: 663801--663888 Score: 88
Period size: 3 Copynumber: 29.3 Consensus size: 3
663791 GTAGATTTTA
* * *
663801 AAT AAT AAT AAT AAT AAT AA- AAT AAT AAT AAT AAT AAT ATT ATT ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
663848 ATT AAT AAT AAT ACT AAT AAT GAT AAT TAT ATTT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT A
663889 TTTTTTCGAC
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.03
3 69 0.95
4 2 0.03
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:663825 original size:20 final size:20
Alignment explanation
Indices: 663800--663839 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
663790 GGTAGATTTT
663800 AAATAATAATAATAATAATA
1 AAATAATAATAATAATAATA
663820 AAATAATAATAATAATAATA
1 AAATAATAATAATAATAATA
663840 TTATTATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AAATAATAATAATAATAATA
Found at i:663826 original size:17 final size:17
Alignment explanation
Indices: 663804--663837 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
663794 GATTTTAAAT
663804 AATAATAATAATAATAA
1 AATAATAATAATAATAA
663821 AATAATAATAATAATAA
1 AATAATAATAATAATAA
663838 TATTATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AATAATAATAATAATAA
Found at i:670154 original size:3 final size:3
Alignment explanation
Indices: 670146--670196 Score: 68
Period size: 3 Copynumber: 16.7 Consensus size: 3
670136 ATTTTCATTC
*
670146 TAT TAT TAT TAT TAT TAT TA- TAT ATAT TAC TAT TAT ATAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT -TAT TAT TAT
670192 TAT TA
1 TAT TA
670197 AATGAAAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:671629 original size:11 final size:11
Alignment explanation
Indices: 671613--671639 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
671603 TATTTTGGTC
671613 ATTTTATTTCA
1 ATTTTATTTCA
671624 ATTTTATTTCA
1 ATTTTATTTCA
671635 ATTTT
1 ATTTT
671640 GTATTGTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTTTATTTCA
Found at i:674484 original size:27 final size:27
Alignment explanation
Indices: 674446--674501 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
674436 ATGAAGATCT
674446 TGATGTTGTGGACTTTCAAGTTCAAAG
1 TGATGTTGTGGACTTTCAAGTTCAAAG
*
674473 TGATGCTT-TGGAGTTTCAAGTTCAAAG
1 TGATG-TTGTGGACTTTCAAGTTCAAAG
674500 TG
1 TG
674502 GTGATGGCGG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 25 0.93
28 2 0.07
ACGTcount: A:0.25, C:0.11, G:0.27, T:0.38
Consensus pattern (27 bp):
TGATGTTGTGGACTTTCAAGTTCAAAG
Found at i:675367 original size:25 final size:25
Alignment explanation
Indices: 675339--675391 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
675329 TTCAAGGACT
*
675339 TATTTGAATTTTTAAAAAAC-ACAAA
1 TATTTGAA-ATTTAAAAAACTACAAA
* *
675364 TATTTTAAATTTAAAATACTACAAA
1 TATTTGAAATTTAAAAAACTACAAA
675389 TAT
1 TAT
675392 ATGTTGATCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.40
Consensus pattern (25 bp):
TATTTGAAATTTAAAAAACTACAAA
Found at i:675911 original size:21 final size:22
Alignment explanation
Indices: 675885--675941 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 22
675875 ATAAATGGTA
*
675885 TTTTTATATTCAACTT-AATAT
1 TTTTTATATTAAACTTAAATAT
* *
675906 TTTTTATTTTAAATTTAAAATAT
1 TTTTTATATTAAACTT-AAATAT
*
675929 TTTTTATTTTAAA
1 TTTTTATATTAAA
675942 AAAATTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 13 0.42
23 18 0.58
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTTTATATTAAACTTAAATAT
Found at i:676648 original size:13 final size:13
Alignment explanation
Indices: 676630--676656 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
676620 CATAGATTAA
676630 CAGTCTTCATATG
1 CAGTCTTCATATG
676643 CAGTCTTCATATG
1 CAGTCTTCATATG
676656 C
1 C
676657 GCGTCTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:683519 original size:24 final size:22
Alignment explanation
Indices: 683464--683515 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
683454 GAGAAAACTC
683464 ATAAAAATTAGTATATATAAAT
1 ATAAAAATTAGTATATATAAAT
*
683486 ATCAAAATTAGTATATATAAAGT
1 ATAAAAATTAGTATATATAAA-T
683509 -TAAAAAT
1 ATAAAAAT
683516 ATTAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 26 0.96
23 1 0.04
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.35
Consensus pattern (22 bp):
ATAAAAATTAGTATATATAAAT
Found at i:685285 original size:35 final size:33
Alignment explanation
Indices: 685214--685288 Score: 89
Period size: 35 Copynumber: 2.2 Consensus size: 33
685204 GTACTATCAT
* * *
685214 ATCA-ATCAGAACATATTAGCACACACAGTGCT
1 ATCATATCAGAACATAATAGCACACAAAGTGCA
*
685246 ATCATATCAGAATCATAATATGCACACAAAGTTCA
1 ATCATATCAGAA-CATAATA-GCACACAAAGTGCA
685281 ATCATATC
1 ATCATATC
685289 TAAAATATAC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 4 0.11
33 7 0.19
34 6 0.17
35 19 0.53
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.25
Consensus pattern (33 bp):
ATCATATCAGAACATAATAGCACACAAAGTGCA
Found at i:685503 original size:103 final size:103
Alignment explanation
Indices: 685231--685535 Score: 413
Period size: 101 Copynumber: 3.0 Consensus size: 103
685221 AGAACATATT
* *
685231 AGCACACACAGTGCTATCATATCAGAATCATAATATGCACACAAAGTTCAATCATATCTA-AAAT
1 AGCACACACAGTGCTATCAAATCAGAATCATAATATGCACACAAAGTGCAATCATATC-AGAAAT
* ** *
685295 ATACTAGTGTACCTACCAATAACACCATTGTATATCATA
65 ATACTAGTGTACCCACCGGTAACACCACTGTATATCATA
* *
685334 AG--CACGCAGTGCTATAAAATCTA-AATCATAATATGCACACAAAGTGCAATCATATC-GAAAT
1 AGCACACACAGTGCTATCAAATC-AGAATCATAATATGCACACAAAGTGCAATCATATCAGAAA-
685395 TATACTAGTGTACCCACCGGTAACACCACTGTATATCATA
64 TATACTAGTGTACCCACCGGTAACACCACTGTATATCATA
* * * * *
685435 AGCACACACAGTGTTATCACATCGGAATCATATTATGTACACAAAGTGCAATCATATCAGAAATA
1 AGCACACACAGTGCTATCAAATCAGAATCATAATATGCACACAAAGTGCAATCATATCAGAAATA
**
685500 TACTAGTGTACCCACCGGTAACACCACAATATATCA
66 TACTAGTGTACCCACCGGTAACACCACTGTATATCA
685536 ATCACTCCAC
Statistics
Matches: 178, Mismatches: 17, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
100 3 0.02
101 86 0.48
102 1 0.01
103 84 0.47
104 4 0.02
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.25
Consensus pattern (103 bp):
AGCACACACAGTGCTATCAAATCAGAATCATAATATGCACACAAAGTGCAATCATATCAGAAATA
TACTAGTGTACCCACCGGTAACACCACTGTATATCATA
Found at i:686638 original size:42 final size:44
Alignment explanation
Indices: 686585--686671 Score: 115
Period size: 42 Copynumber: 2.0 Consensus size: 44
686575 TAAGAACCAA
*
686585 ATATATATTCCAAAGGACCAAATATATGTCTCGAA-GACC-CGT
1 ATATATATTCCAAAGGACCAAATATATGTCCCGAAGGACCACGT
* ** *
686627 ATATATGTTCCAAAGGATTACATATATGTCCCGAAGGACCACGT
1 ATATATATTCCAAAGGACCAAATATATGTCCCGAAGGACCACGT
686671 A
1 A
686672 GAACCCTCGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
42 30 0.79
43 4 0.11
44 4 0.11
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (44 bp):
ATATATATTCCAAAGGACCAAATATATGTCCCGAAGGACCACGT
Found at i:689238 original size:15 final size:15
Alignment explanation
Indices: 689220--689277 Score: 80
Period size: 15 Copynumber: 3.9 Consensus size: 15
689210 GGCTAACGGT
*
689220 TATATGGGCAATGAC
1 TATATGGGCAACGAC
*
689235 TATATGGTCAACGAC
1 TATATGGGCAACGAC
*
689250 TATATGGTCAACGAC
1 TATATGGGCAACGAC
*
689265 TATATGGGTAACG
1 TATATGGGCAACG
689278 GTCATGGCCA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.28
Consensus pattern (15 bp):
TATATGGGCAACGAC
Found at i:692246 original size:39 final size:39
Alignment explanation
Indices: 692191--692270 Score: 124
Period size: 39 Copynumber: 2.1 Consensus size: 39
692181 GAACCAAGTA
* * *
692191 CATGTATTTGCTTTCTCTCCTGGACCAATATCGGCCTCT
1 CATGTATTTGCCTTCTCTCATGGACCAATATCCGCCTCT
*
692230 CATGTATTTGCCTTCTCTCATGGACCAGTATCCGCCTCT
1 CATGTATTTGCCTTCTCTCATGGACCAATATCCGCCTCT
692269 CA
1 CA
692271 ATCATATCCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.16, C:0.33, G:0.15, T:0.36
Consensus pattern (39 bp):
CATGTATTTGCCTTCTCTCATGGACCAATATCCGCCTCT
Found at i:692797 original size:21 final size:20
Alignment explanation
Indices: 692745--692800 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
692735 CACAAAAAAA
*
692745 TAAATAAAATAATGGGCACT
1 TAAATAGAATAATGGGCACT
*
692765 AAGAAT-GAAATAATGGGCACT
1 TA-AATAG-AATAATGGGCACT
692786 CTAAATAGAATAATG
1 -TAAATAGAATAATG
692801 TAGTGGCAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 1 0.03
21 26 0.90
22 2 0.07
ACGTcount: A:0.50, C:0.09, G:0.18, T:0.23
Consensus pattern (20 bp):
TAAATAGAATAATGGGCACT
Found at i:693499 original size:58 final size:59
Alignment explanation
Indices: 693353--693588 Score: 375
Period size: 59 Copynumber: 4.0 Consensus size: 59
693343 GAGATTGTTG
* *
693353 ATATTTTTAAAAGGGTGCATAATACGTAATTAATTTATGTTAAGGTGTTATTTTTGTAA
1 ATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTAAGGTGTTATTTTTGTAA
*
693412 ATATCTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTAAGGTGTTA-TTTTGTAA
1 ATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTAAGGTGTTATTTTTGTAA
* * *
693470 ATATTTTTAAAAGGGTGCCTAATATGTAATTAATTTTTGTTAAGGTGCTATTTTTGTAA
1 ATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTAAGGTGTTATTTTTGTAA
* * * *
693529 ATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTAGGGCGATATTTGTGTAA
1 ATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTAAGGTGTTATTTTTGTAA
693588 A
1 A
693589 AGTTGGTCGT
Statistics
Matches: 163, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
58 54 0.33
59 109 0.67
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (59 bp):
ATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTAAGGTGTTATTTTTGTAA
Found at i:693501 original size:117 final size:118
Alignment explanation
Indices: 693353--693588 Score: 393
Period size: 117 Copynumber: 2.0 Consensus size: 118
693343 GAGATTGTTG
*
693353 ATATTTTTAAAAGGGTGCATAATACGTAATTAATTTATGTTAAGGTGTTATTTTTGTAAATATCT
1 ATATTTTTAAAAGGGTGCATAATACGTAATTAATTTATGTTAAGGTGCTATTTTTGTAAATATCT
* *
693418 TTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTAAGGTGTTATTT-TGTAA
66 TTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTAAGGCGATATTTGTGTAA
* * * *
693470 ATATTTTTAAAAGGGTGCCTAATATGTAATTAATTTTTGTTAAGGTGCTATTTTTGTAAATATTT
1 ATATTTTTAAAAGGGTGCATAATACGTAATTAATTTATGTTAAGGTGCTATTTTTGTAAATATCT
*
693535 TTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTAGGGCGATATTTGTGTAA
66 TTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTAAGGCGATATTTGTGTAA
693588 A
1 A
693589 AGTTGGTCGT
Statistics
Matches: 110, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
117 104 0.95
118 6 0.05
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (118 bp):
ATATTTTTAAAAGGGTGCATAATACGTAATTAATTTATGTTAAGGTGCTATTTTTGTAAATATCT
TTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTAAGGCGATATTTGTGTAA
Found at i:695045 original size:2 final size:2
Alignment explanation
Indices: 695033--695084 Score: 95
Period size: 2 Copynumber: 25.5 Consensus size: 2
695023 GTCATTTGTA
695033 AT AT GAT 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
695076 AT AT AT AT A
1 AT AT AT AT A
695085 GAATAATATT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 47 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:696015 original size:94 final size:95
Alignment explanation
Indices: 695835--696035 Score: 287
Period size: 94 Copynumber: 2.1 Consensus size: 95
695825 ATAATGATGT
* * *
695835 GAGTATTGATACTAAGAGAAAGGTATCGATACCTTGGAATCCAGAACGTAGAAATGGTATCGATA
1 GAGTATCGATACTAAGAGAAAGGTATCGATACCATGGAATCCAGAACGTAGAAATGATATCGATA
* * * *
695900 CTGAAGGGGAGTATCGATACCATAGTATAG
66 CTAAAAGGGAGTATCGATACCACAATATAG
* * *
695930 GAGTATCGATACTAAGAGAAAGTTATCGATACCATGG-ATCCAGAATGTAGAAATGATATTGATA
1 GAGTATCGATACTAAGAGAAAGGTATCGATACCATGGAATCCAGAACGTAGAAATGATATCGATA
*
695994 CTAAAAGGGAGTATCGGTACCACAATATAG
66 CTAAAAGGGAGTATCGATACCACAATATAG
*
696024 AAGTATCGATAC
1 GAGTATCGATAC
696036 CATGTTAGGG
Statistics
Matches: 94, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
94 60 0.64
95 34 0.36
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (95 bp):
GAGTATCGATACTAAGAGAAAGGTATCGATACCATGGAATCCAGAACGTAGAAATGATATCGATA
CTAAAAGGGAGTATCGATACCACAATATAG
Found at i:696464 original size:54 final size:54
Alignment explanation
Indices: 696378--696770 Score: 588
Period size: 54 Copynumber: 7.3 Consensus size: 54
696368 TATCGGATGA
*
696378 GCACTATGTGTGCAACTTAAGAAGTTCATAATAAGTTTATGAATTTCCGTATTG
1 GCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTG
* * * * *
696432 GCATTGTGTCTGCAACTTAAGAAATTCATAATAAATTTATGAATTTTCGTATTG
1 GCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTG
*
696486 GCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTG
1 GCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTG
* * *
696540 GCACTATGTGTGCAACCTAAGAAGTTCATAATAAGTTTATGAATTTCTGTATTG
1 GCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTG
*
696594 ACACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTG
1 GCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTG
* **
696648 GCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTTTATTG
1 GCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTG
* * * * * *
696702 GCAATATATGTGCAACCTAAGAAATTTATAATAAGTTTGTGAATTTCTGTATTG
1 GCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTG
* *
696756 GCACTACGAGTGCAA
1 GCACTATGTGTGCAA
696771 ACCATAGAAT
Statistics
Matches: 308, Mismatches: 31, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 308 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (54 bp):
GCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTG
Found at i:700351 original size:142 final size:140
Alignment explanation
Indices: 700080--700354 Score: 433
Period size: 142 Copynumber: 1.9 Consensus size: 140
700070 CAACCATTCA
* *
700080 AATCATCATTTGTTAATTGACACAGACAATGAATAAGCTCCACTCAACAGTCTAAAGCAAGGAAA
1 AATCATCATTTGCTAATTGACACAGACAATGAACAAGCTCCACTCAACAGTCTAAAGCAAGGAAA
* *
700145 AAACTTGCTTAAACTAACTACTTATCTTCTTGAACCTCAACATTTTCTCAATCTAGTACCTTAAA
66 AAACTTGCTTAAACTAACTACTTATCTTCTTAAACCTCAACATTTTCTCAATCCAGTACCTTAAA
700210 GACAATGAAT
131 GACAATGAAT
* * *
700220 AATCATCATTTGCTAATTGATACGGACAATGAACAAGCTCCACTCAACCAGTCTTAAGCAAGGAA
1 AATCATCATTTGCTAATTGACACAGACAATGAACAAGCTCCACTCAA-CAGTCTAAAGCAAGGAA
* * * *
700285 AAAACTTGCTTAAATTAGGCTACTTATTTTCTTAAACCTCAACATTTTCTCAATCCAGTACGTTA
65 AAAACTTGCTTAAACTA-ACTACTTATCTTCTTAAACCTCAACATTTTCTCAATCCAGTACCTTA
700350 AAGAC
129 AAGAC
700355 GATGGAGATC
Statistics
Matches: 122, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
140 43 0.35
141 32 0.26
142 47 0.39
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (140 bp):
AATCATCATTTGCTAATTGACACAGACAATGAACAAGCTCCACTCAACAGTCTAAAGCAAGGAAA
AAACTTGCTTAAACTAACTACTTATCTTCTTAAACCTCAACATTTTCTCAATCCAGTACCTTAAA
GACAATGAAT
Found at i:705140 original size:3 final size:3
Alignment explanation
Indices: 705129--705171 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
705119 TTTTTATTTT
*
705129 TTA TT- TTA TTA TTTA CTA TTTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
705172 ATTTTGTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 28 0.80
4 5 0.14
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:706577 original size:30 final size:29
Alignment explanation
Indices: 706495--706577 Score: 87
Period size: 28 Copynumber: 2.8 Consensus size: 29
706485 GGTTTATTTG
*
706495 TAATTATTATTTTAGTCCTTTAAGTTTCTA
1 TAATTA-TATTTTAGTCCTTTAAGTGTCTA
* * * *
706525 T-TTTATTTTTTAGTTCTCTAAGTGTCTA
1 TAATTATATTTTAGTCCTTTAAGTGTCTA
*
706553 TAATTACTATTTTAGGCCTTTAAGT
1 TAATTA-TATTTTAGTCCTTTAAGT
706578 TTATGTTTTT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
28 20 0.49
29 6 0.15
30 15 0.37
ACGTcount: A:0.24, C:0.11, G:0.10, T:0.55
Consensus pattern (29 bp):
TAATTATATTTTAGTCCTTTAAGTGTCTA
Found at i:706624 original size:30 final size:30
Alignment explanation
Indices: 706559--706656 Score: 76
Period size: 30 Copynumber: 3.3 Consensus size: 30
706549 TCTATAATTA
* *
706559 CTATTTTAGGCCTTTAAGTTTATGTTTTTG
1 CTATTTTAGCCCTTTAAGTTTATGTATTTG
* * *
706589 ATATTTTAGCCCCTTT-ATTTTTTGTATTTG
1 CTATTTTAG-CCCTTTAAGTTTATGTATTTG
** * *
706619 CTA-TTTAGTCCC-TTAAGTTCCTATATTTT
1 CTATTTTAG-CCCTTTAAGTTTATGTATTTG
706648 CTATTTTAG
1 CTATTTTAG
706657 TGCATTAAGT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
28 2 0.04
29 20 0.38
30 26 0.49
31 5 0.09
ACGTcount: A:0.18, C:0.14, G:0.11, T:0.56
Consensus pattern (30 bp):
CTATTTTAGCCCTTTAAGTTTATGTATTTG
Found at i:708213 original size:14 final size:14
Alignment explanation
Indices: 708194--708222 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
708184 TTTCATTATT
708194 TAACCAAATAAGCA
1 TAACCAAATAAGCA
708208 TAACCAAATAAGCA
1 TAACCAAATAAGCA
708222 T
1 T
708223 TATGGTCTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.21, G:0.07, T:0.17
Consensus pattern (14 bp):
TAACCAAATAAGCA
Found at i:710627 original size:24 final size:24
Alignment explanation
Indices: 710598--710647 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
710588 TGGTGGTTGA
*
710598 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
710622 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
710646 TT
1 TT
710648 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:711996 original size:21 final size:21
Alignment explanation
Indices: 711954--711998 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
711944 AGACGAGCTA
* * **
711954 TGACTTTGAAGTAAGGTGCCT
1 TGACTATGAAGTAAAGCCCCT
711975 TGACTATGAAGTAAAGCCCCT
1 TGACTATGAAGTAAAGCCCCT
711996 TGA
1 TGA
711999 AGTAGAATGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (21 bp):
TGACTATGAAGTAAAGCCCCT
Found at i:713239 original size:24 final size:24
Alignment explanation
Indices: 713195--713244 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
713185 ATAAAGAACC
*
713195 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
713219 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
713243 AA
1 AA
713245 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:716562 original size:19 final size:20
Alignment explanation
Indices: 716535--716577 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
716525 GAGAAAAATT
*
716535 AAAAGTTAA-AATGAAAGAG
1 AAAAATTAATAATGAAAGAG
*
716554 AAAAATTAATAATGAAAGAT
1 AAAAATTAATAATGAAAGAG
716574 AAAA
1 AAAA
716578 GAAAAAGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.67, C:0.00, G:0.14, T:0.19
Consensus pattern (20 bp):
AAAAATTAATAATGAAAGAG
Found at i:716583 original size:26 final size:26
Alignment explanation
Indices: 716513--716588 Score: 70
Period size: 26 Copynumber: 3.0 Consensus size: 26
716503 GGAAGAAGAT
*
716513 TAATGAAAGA-AAGAG-AAAAATTAA
1 TAATGAAAGATAAAAGAAAAAATTAA
* *
716537 -AAGTTAAA-ATGAAAGAGAAAAATTAA
1 TAA-TGAAAGATAAAAGA-AAAAATTAA
*
716563 TAATGAAAGATAAAAGAAAAAGTTAA
1 TAATGAAAGATAAAAGAAAAAATTAA
716589 AAATTTGAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
23 3 0.08
24 7 0.17
26 21 0.52
27 9 0.22
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (26 bp):
TAATGAAAGATAAAAGAAAAAATTAA
Found at i:720304 original size:9 final size:9
Alignment explanation
Indices: 720290--720325 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
720280 ATTTCTTTTT
720290 AAAAAAAAC
1 AAAAAAAAC
*
720299 AAAAAAAGGC
1 AAAAAAA-AC
720309 AAAAAAAAC
1 AAAAAAAAC
720318 AAAAAAAA
1 AAAAAAAA
720326 AGTCGAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.86, C:0.08, G:0.06, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:728241 original size:19 final size:21
Alignment explanation
Indices: 728204--728246 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
728194 TAACTTTTTA
728204 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
728224 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
728244 TTT
1 TTT
728247 AATTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:731562 original size:24 final size:24
Alignment explanation
Indices: 731533--731582 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
731523 TGGTGGTTGA
*
731533 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
731557 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
731581 TT
1 TT
731583 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:736019 original size:35 final size:35
Alignment explanation
Indices: 735973--736049 Score: 145
Period size: 35 Copynumber: 2.2 Consensus size: 35
735963 TTGGCTGTTA
*
735973 ATCCCAACTGTTTTAAGTGCCTGCTCAACCATTGT
1 ATCCCAACTGTTTTAAGTGCATGCTCAACCATTGT
736008 ATCCCAACTGTTTTAAGTGCATGCTCAACCATTGT
1 ATCCCAACTGTTTTAAGTGCATGCTCAACCATTGT
736043 ATCCCAA
1 ATCCCAA
736050 TAGGTTTTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (35 bp):
ATCCCAACTGTTTTAAGTGCATGCTCAACCATTGT
Done.