Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004270.1 Hibiscus syriacus cultivar Beakdansim tig00009364_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: 73112
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8863 original size:13 final size:13
Alignment explanation
Indices: 8845--8869 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8835 GACAACGTAG
8845 AAAAATAAAAAAT
1 AAAAATAAAAAAT
8858 AAAAATAAAAAA
1 AAAAATAAAAAA
8870 AACAGTCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:9089 original size:2 final size:2
Alignment explanation
Indices: 9082--9112 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
9072 CGAGCATTTA
9082 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9113 TGTACTTACC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:9194 original size:13 final size:14
Alignment explanation
Indices: 9166--9200 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
9156 ATTTGTAATG
*
9166 AACCTTAAATTCTA
1 AACCCTAAATTCTA
9180 AACCCTAAA-TCTA
1 AACCCTAAATTCTA
9193 AACCCTAA
1 AACCCTAA
9201 CCTTGAACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.26
Consensus pattern (14 bp):
AACCCTAAATTCTA
Found at i:13384 original size:53 final size:53
Alignment explanation
Indices: 13294--13533 Score: 318
Period size: 53 Copynumber: 4.5 Consensus size: 53
13284 TGATCCAACG
* *
13294 GCTTACATTAATAGGTAAACTATTTATTTATAGTTTATTATAAGGATACATCT
1 GCTTACATTCATAGGTAAGCTATTTATTTATAGTTTATTATAAGGATACATCT
* * * * *
13347 ACTTATATTCATAGGTAAGCTATTTATTTATAATTTATTATAAGGATATAGCT
1 GCTTACATTCATAGGTAAGCTATTTATTTATAGTTTATTATAAGGATACATCT
* * * *
13400 GCTTACACTCATAGGTAAGCTATATGTTTATAGTTTATTATAAGGATATATCT
1 GCTTACATTCATAGGTAAGCTATTTATTTATAGTTTATTATAAGGATACATCT
* *
13453 GCTTACACTCATAGGTAAGCTATTTATTTATAGTTTATCATAAGGATACAGCTGCAT
1 GCTTACATTCATAGGTAAGCTATTTATTTATAGTTTATTATAAGGATACA--T-C-T
*
13510 GCTTATATTCATAGGTAAGCTATT
1 GCTTACATTCATAGGTAAGCTATT
13534 ATGATTTGTT
Statistics
Matches: 163, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
53 138 0.85
55 1 0.01
56 1 0.01
57 23 0.14
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (53 bp):
GCTTACATTCATAGGTAAGCTATTTATTTATAGTTTATTATAAGGATACATCT
Found at i:20667 original size:13 final size:13
Alignment explanation
Indices: 20651--20684 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
20641 ACCTTAAAAG
20651 ATAAAAACATAA-A
1 ATAAAAA-ATAATA
20664 ATAAAAAATAATA
1 ATAAAAAATAATA
20677 ATAAAAAA
1 ATAAAAAA
20685 CATCGACCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (13 bp):
ATAAAAAATAATA
Found at i:22130 original size:14 final size:14
Alignment explanation
Indices: 22111--22137 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22101 TTACATCTTT
22111 TGAAAAATATTTTC
1 TGAAAAATATTTTC
22125 TGAAAAATATTTT
1 TGAAAAATATTTT
22138 ACGGTGCTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (14 bp):
TGAAAAATATTTTC
Found at i:22268 original size:22 final size:22
Alignment explanation
Indices: 22227--22267 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
22217 ATATAATAAA
22227 TAATATTATTTATTATAAAACT
1 TAATATTATTTATTATAAAACT
*
22249 TAATATTA-TTATTTTAAAA
1 TAATATTATTTATTATAAAA
22268 ATATTAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TAATATTATTTATTATAAAACT
Found at i:22298 original size:14 final size:14
Alignment explanation
Indices: 22279--22325 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
22269 TATTAGAATA
22279 ATTTATTTAATATT
1 ATTTATTTAATATT
*
22293 ATTTATGCTAATATT
1 ATTTAT-TTAATATT
*
22308 A-TTATTAAAATATT
1 ATTTATT-TAATATT
22322 ATTT
1 ATTT
22326 CTAAAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 17 0.63
15 10 0.37
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (14 bp):
ATTTATTTAATATT
Found at i:28264 original size:20 final size:20
Alignment explanation
Indices: 28241--28280 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28231 TATTGCTTTA
*
28241 ATTAAATATAT-ATTTTTAAT
1 ATTAAA-ATATCATTATTAAT
28261 ATTAAAATATCATTATTAAT
1 ATTAAAATATCATTATTAAT
28281 GTTGATACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTAAAATATCATTATTAAT
Found at i:32649 original size:18 final size:19
Alignment explanation
Indices: 32626--32664 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
32616 CCAAGCTTCA
32626 CGTGCTCCCCT-CTGCTCC
1 CGTGCTCCCCTCCTGCTCC
32644 CGTGCTCCCCTCCTGCTCC
1 CGTGCTCCCCTCCTGCTCC
32663 CG
1 CG
32665 CTGCATGCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.00, C:0.56, G:0.18, T:0.26
Consensus pattern (19 bp):
CGTGCTCCCCTCCTGCTCC
Found at i:32821 original size:33 final size:33
Alignment explanation
Indices: 32784--32850 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
32774 CAATTGCACA
32784 ATTATTGGTGAAATAATTGAGGCAGCCGATGAC
1 ATTATTGGTGAAATAATTGAGGCAGCCGATGAC
32817 ATTATTGGTGAAATAATTGAGGCAGCCGATGAC
1 ATTATTGGTGAAATAATTGAGGCAGCCGATGAC
32850 A
1 A
32851 CCTAAATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.27
Consensus pattern (33 bp):
ATTATTGGTGAAATAATTGAGGCAGCCGATGAC
Found at i:32956 original size:29 final size:27
Alignment explanation
Indices: 32896--32958 Score: 92
Period size: 26 Copynumber: 2.3 Consensus size: 27
32886 ACATAAAAGA
*
32896 AAAGAAAGGGAGAAGAGATTGCAGCAG
1 AAAGAAAGGGAGAAGAAATTGCAGCAG
32923 -AAGAAAGGGAGAAGAAATTGCAGCCGAG
1 AAAGAAAGGGAGAAGAAATTGCAG-C-AG
32951 AAAGAAAG
1 AAAGAAAG
32959 AAATGGAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 22 0.69
27 1 0.03
28 2 0.06
29 7 0.22
ACGTcount: A:0.51, C:0.08, G:0.35, T:0.06
Consensus pattern (27 bp):
AAAGAAAGGGAGAAGAAATTGCAGCAG
Found at i:33132 original size:22 final size:21
Alignment explanation
Indices: 33100--33140 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
33090 ATTAATTAGT
*
33100 TTGTTAATTTAGGGTTATATGA
1 TTGTTAATTTA-AGTTATATGA
*
33122 TTGTTAGTTTAAGTTATAT
1 TTGTTAATTTAAGTTATAT
33141 TATACATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.54
Consensus pattern (21 bp):
TTGTTAATTTAAGTTATATGA
Found at i:33472 original size:16 final size:16
Alignment explanation
Indices: 33440--33486 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
33430 TTTAAAAAGT
*
33440 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
33456 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
33472 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
33487 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:33481 original size:15 final size:14
Alignment explanation
Indices: 33461--33491 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
33451 GTTTATTAGT
33461 TTATTATATTATAAG
1 TTATTATATTA-AAG
33476 TTATTATATTAAAG
1 TTATTATATTAAAG
33490 TT
1 TT
33492 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:35739 original size:21 final size:22
Alignment explanation
Indices: 35708--35789 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 22
35698 AAATCATTAC
35708 TAAATCATTAATATCAAATCAT
1 TAAATCATTAATATCAAATCAT
* *
35730 TAAAT-ATTAATAATAAATTATTAT
1 TAAATCATTAAT-ATCAA--ATCAT
*
35754 TACTAATCATTACTATCAAATCAT
1 TA--AATCATTAATATCAAATCAT
*
35778 TAAA-AATTAATA
1 TAAATCATTAATA
35790 ATAATTTCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 13
0.70 0.10 0.19
Matches are distributed among these distances:
21 12 0.26
22 11 0.23
24 12 0.26
26 7 0.15
27 5 0.11
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATCATTAATATCAAATCAT
Found at i:35756 original size:49 final size:48
Alignment explanation
Indices: 35703--35860 Score: 223
Period size: 46 Copynumber: 3.3 Consensus size: 48
35693 GTCGTAAATC
*
35703 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATT
1 ATTACT-AATCATTAATATCAAATCATTAAATATTAATAATAATTTATT
* *
35752 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAATTT-ATT
*
35801 ATTACTAATCATT-A-CT-AAATCATTAAATATTAATAATAATTTTATT
1 ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAA-TTTATT
*
35847 ATTACTAATTATTA
1 ATTACTAATCATTA
35861 CTAAATCATT
Statistics
Matches: 99, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
46 37 0.37
47 4 0.04
48 36 0.36
49 22 0.22
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.43
Consensus pattern (48 bp):
ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAATTTATT
Found at i:35823 original size:11 final size:10
Alignment explanation
Indices: 35801--35874 Score: 50
Period size: 10 Copynumber: 7.7 Consensus size: 10
35791 TAATTTCATT
35801 ATTACTAATC
1 ATTACTAATC
35811 ATTACTAAATC
1 ATTACT-AATC
35822 ATTA--AAT-
1 ATTACTAATC
* *
35829 ATTAATAATA
1 ATTACTAATC
* *
35839 ATT--TTATT
1 ATTACTAATC
*
35847 ATTACTAATT
1 ATTACTAATC
35857 ATTACTAAATC
1 ATTACT-AATC
35868 ATTACTA
1 ATTACTA
35875 TCAAATCATT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
7 4 0.08
8 9 0.17
9 3 0.06
10 20 0.38
11 17 0.32
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.45
Consensus pattern (10 bp):
ATTACTAATC
Found at i:35832 original size:28 final size:28
Alignment explanation
Indices: 35800--35892 Score: 71
Period size: 28 Copynumber: 3.2 Consensus size: 28
35790 ATAATTTCAT
35800 TATTACTAATCATTACTAAATCATTAAA
1 TATTACTAATCATTACTAAATCATTAAA
* * * * * * *
35828 TATTAATAATAATT-TTATTATTACTAAT
1 TATTACTAATCATTACTA-AATCATTAAA
35856 TATTACTAAATCATTACTATCAAATCATTAAA
1 TATTACT-AATCATTAC--T-AAATCATTAAA
35888 TATTA
1 TATTA
35893 ATAACAATTT
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
27 2 0.04
28 24 0.53
29 6 0.13
32 12 0.27
33 1 0.02
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.44
Consensus pattern (28 bp):
TATTACTAATCATTACTAAATCATTAAA
Found at i:35837 original size:46 final size:45
Alignment explanation
Indices: 35723--35871 Score: 226
Period size: 46 Copynumber: 3.2 Consensus size: 45
35713 CATTAATATC
*
35723 AAATCATTAAATATTAATAATAAATTATTATTACTAATCATTACTAT
1 AAATCATTAAATATTAATAATAATTTATTATTACTAATCATTAC--T
*
35770 CAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
1 -AAATCATTAAATATTAATAATAATTT-ATTATTACTAATCATTACT
*
35817 AAATCATTAAATATTAATAATAATTTTATTATTACTAATTATTACT
1 AAATCATTAAATATTAATAATAA-TTTATTATTACTAATCATTACT
35863 AAATCATTA
1 AAATCATTA
35872 CTATCAAATC
Statistics
Matches: 95, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
46 49 0.52
47 4 0.04
48 24 0.25
49 18 0.19
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (45 bp):
AAATCATTAAATATTAATAATAATTTATTATTACTAATCATTACT
Found at i:35881 original size:60 final size:60
Alignment explanation
Indices: 35817--35983 Score: 280
Period size: 60 Copynumber: 2.8 Consensus size: 60
35807 AATCATTACT
* * *
35817 AAATCATTAAATATTAATAATAATTTTATTATTACTAATTATTACTAAATCATTACTATC
1 AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATC
* *
35877 AAATCATTAAATATTAATAACAATTTCACTATTACTAATCATTACTAAATCATTAATATC
1 AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATC
*
35937 AAATCATTAAATATTAATAATAATTTCATTATTATTAATCATTACTA
1 AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTA
35984 TCAAATCATT
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 99 1.00
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (60 bp):
AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATC
Found at i:35944 original size:120 final size:120
Alignment explanation
Indices: 35817--36619 Score: 575
Period size: 120 Copynumber: 6.8 Consensus size: 120
35807 AATCATTACT
35817 AAATCATTAAATATTAATAATAATTTTATTATTACTAATTATTACTAAATCATTACTATCAAATC
1 AAATCATTAAATATTAATAATAATTTTATTATTACTAATTATTACTAAATCATTACTATCAAATC
*
35882 ATTAAATATTAATAACAATTTCACTATTACTAATCATTACTAAATCATTAATATC
66 ATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAATCATTAATATC
*
35937 AAATCATTAAATATTAATAAT-A----A-T-TT-C--ATTATTA-TTAATCATTACTATCAAATC
1 AAATCATTAAATATTAATAATAATTTTATTATTACTAATTATTACTAAATCATTACTATCAAATC
* * *
35991 ATTAAAAATTAATAATAATTTCATTATTATTAATCATTACTAAATCATTAATATC
66 ATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAATCATTAATATC
* *
36046 AAATCATTAAATATTAATAATAATTTCATTATTATTAATTATTACTAAATCATTACTATCAAATC
1 AAATCATTAAATATTAATAATAATTTTATTATTACTAATTATTACTAAATCATTACTATCAAATC
*
36111 ATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAATCATT-A-CT-
66 ATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAATCATTAATATC
* * * * * * * * *
36163 AAATCATTACTAATCATTACTAAATCATTATTATCAAATCATTAAATATTAATAACAAT-TTTAT
1 AAATCATTA--AAT-ATTAAT-AATAATT-TTAT--TATTACTAATTATTACT-A-AATCATTAC
* * * * * *
36227 TATTACTAATCATTACTAAATCATTAATATCAA-ATCATTAAATATTAAT-A--A-TAATTTCAT
57 TA-T-CAAATCA-T--TAAAT-ATTAATAACAATTTCATT-ATTACTAATCATTACTAA-ATCAT
*
36287 TATTA-C
114 TAATATC
* * * * *
36293 TAATCATTACTAAATCATT-ATTATAA--TT-TCATTACTAATTATGTAACGAAA--A-TA-TGG
1 AAATCA-T--TAAAT-ATTAATAATAATTTTATTATTACTAATTAT-T-ACTAAATCATTACT-A
* * * ** * * * * *
36350 TTAATTGAACCAAACATT-GT-TCATTGTTCA--AGT-CGTAAATCATTACTATCAAATCATTAA
59 TCAAAT-CATTAAATATTAATAACAAT-TTCATTATTAC-T-AATCATTAC--T-AAATCATTAA
*
36410 TATT
117 TATC
36414 AAATCATTAAATATTAATAAT-A----A--A-T--T-ATTATTACT-AATCATTACTATCAAATC
1 AAATCATTAAATATTAATAATAATTTTATTATTACTAATTATTACTAAATCATTACTATCAAATC
* *
36467 ATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATC
66 ATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAATCATTAATATC
* *
36522 AAATCATTAAATATTAATAATAATTTCATTATTA-TTATTCATTACTAAATCATTACTATCAAAT
1 AAATCATTAAATATTAATAATAATTTTATTATTACTAATT-ATTACTAAATCATTACTATCAAAT
* *
36586 CATTAAATATTAATAATAATTTCATCATTACTAA
65 CATTAAATATTAATAACAATTTCATTATTACTAA
36620 ATCTTATAAA
Statistics
Matches: 537, Mismatches: 73, Indels: 146
0.71 0.10 0.19
Matches are distributed among these distances:
107 2 0.00
108 36 0.07
109 102 0.19
110 24 0.04
111 13 0.02
112 4 0.01
113 8 0.01
114 9 0.02
115 5 0.01
116 9 0.02
117 18 0.03
118 13 0.02
119 20 0.04
120 153 0.28
121 15 0.03
122 3 0.01
123 11 0.02
124 15 0.03
125 8 0.01
126 6 0.01
127 9 0.02
128 7 0.01
129 3 0.01
130 17 0.03
131 25 0.05
133 2 0.00
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.42
Consensus pattern (120 bp):
AAATCATTAAATATTAATAATAATTTTATTATTACTAATTATTACTAAATCATTACTATCAAATC
ATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAATCATTAATATC
Found at i:35978 original size:49 final size:49
Alignment explanation
Indices: 35924--36241 Score: 204
Period size: 49 Copynumber: 6.2 Consensus size: 49
35914 ATCATTACTA
35924 AATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTATT
1 AATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTATT
* *
35973 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTATT
1 AATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTATT
* *
36022 AATCATTACTAAATCATTAAT-ATCAAATCATTAAATATTAATAATAATTTCATTATTATTAATT
1 AATCATTA--ATATCA--AATCATTAAAT-ATT--A-A-TAA---TAATTTC------ATT-ATT
36086 ATTACT
47 A-T--T
* * *
36092 AAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACT
1 -AATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTATT
* * * * *
36142 AATCATT-A-CT-AAATCATTACTAA-ATCATTACTAA--TCATTACTA--
1 AATCATTAATATCAAATCATTA--AATATTAATAATAATTTCATTATTATT
* * * *
36185 AATCATTATTATCAAATCATTAAATATTAATAACAATTTTATTATTACT
1 AATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTATT
36234 AATCATTA
1 AATCATTA
36242 CTAAATCATT
Statistics
Matches: 209, Mismatches: 26, Indels: 68
0.69 0.09 0.22
Matches are distributed among these distances:
43 7 0.03
44 2 0.01
45 16 0.08
46 18 0.09
47 15 0.07
48 2 0.01
49 70 0.33
50 1 0.00
51 4 0.02
52 5 0.02
53 10 0.05
54 3 0.01
55 1 0.00
56 1 0.00
57 3 0.01
60 13 0.06
63 3 0.01
64 1 0.00
65 1 0.00
66 3 0.01
67 10 0.05
68 7 0.03
69 4 0.02
70 1 0.00
71 8 0.04
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (49 bp):
AATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTATT
Found at i:36011 original size:109 final size:108
Alignment explanation
Indices: 35699--36304 Score: 689
Period size: 109 Copynumber: 5.6 Consensus size: 108
35689 TCAAGTCGTA
* *
35699 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCAT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTATTATTATTAATCAT
*
35764 TACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
66 TACTATCAAATCATTAAAAATTAATAACAATTTCATTATTACT
* * * * * *
35807 AATCATTACTAAATCATTAAATAT-TAAT-AATAATTTTATTATTACTAA-TTATTACTA--AAT
1 AATCATTACTAAATCATT-AATATCAAATCATTAA--ATATTAATAATAATTTATTATTATTAAT
* *
35867 CATTACTATCAAATCATTAAATATTAATAACAATTTCACTATTACT
63 CATTACTATCAAATCATTAAAAATTAATAACAATTTCATTATTACT
35913 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTATTAATCA
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTT-ATTATTATTAATCA
* *
35978 TTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTATT
65 TTACTATCAAATCATTAAAAATTAATAACAATTTCATTATTACT
36022 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTATTAATTA
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAAT-A----A-T-TTATT-ATTA
*
36087 TTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACT
58 -T--T-AATCATTACTATCAAATCATTAAAAATTAATAACAATTTCATTATTACT
* * * * * *
36142 AATCATTACTAAATCATT-A-CT-AAATCATT-ACTAATCATTACTAA---ATCATTATT-ATCA
1 AATCATTACTAAATCATTAATATCAAATCATTAAAT-ATTAATAATAATTTATTATTATTAATCA
* *
36199 --A--ATC--AT---TAAATATTAATAACAATTTTATTATTACT
65 TTACTATCAAATCATTAAAAATTAATAACAATTTCATTATTACT
*
36234 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTT-ATTATTATTAATCA
36299 TTACTA
65 TTACTA
36305 AATCATTATT
Statistics
Matches: 427, Mismatches: 36, Indels: 74
0.80 0.07 0.14
Matches are distributed among these distances:
92 46 0.11
93 1 0.00
94 1 0.00
95 18 0.04
96 2 0.00
97 3 0.01
99 8 0.02
100 4 0.01
101 4 0.01
102 1 0.00
103 1 0.00
104 1 0.00
105 16 0.04
106 73 0.17
107 16 0.04
108 29 0.07
109 105 0.25
110 1 0.00
112 1 0.00
114 1 0.00
115 4 0.01
116 9 0.02
117 15 0.04
118 1 0.00
119 2 0.00
120 64 0.15
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (108 bp):
AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTATTATTATTAATCAT
TACTATCAAATCATTAAAAATTAATAACAATTTCATTATTACT
Found at i:36037 original size:60 final size:60
Alignment explanation
Indices: 35973--36615 Score: 412
Period size: 60 Copynumber: 10.8 Consensus size: 60
35963 CATTATTATT
*
35973 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTATTAATCATTACTA
1 AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTATTAATCATTACTA
* *
36033 AATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTATTAATTATTACTA
1 AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTATTAATCATTACTA
* *
36093 AATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTA
1 AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTATTAATCATTACTA
* *
36153 AATCATTAC--T-AAATCATTACTAATCATTACT-A-AA--TCATTATTATCAAATCA-T--TA
1 AATCATTACTATCAAATCATTA--AAT-ATTAATAATAATTTCATTATTAT-TAATCATTACTA
* * * * * * * * *
36207 AAT-ATTAATAAC-AAT--TTTATTATTACTAATCATTAC-TAAATCATTAAT-A-T-C-A
1 AATCATTACTATCAAATCATTAAATATTAATAATAATTTCAT-TATTATTAATCATTACTA
* * * * * * * *
36259 AATCATTAAATAT-TAAT-AATAATTTCATTATTACTAA--TCATTACTA--AATCATTATTA
1 AATCATT-ACTATCAAATCATTAA-AT-ATTAATAATAATTTCATTATTATTAATCATTACTA
* ** * ** * * * **
36316 TAATTTCATTACTAATTATGTAACGAAAATATGGTTAATTGAACCAA--ACATTGTTCATTGTTC
1 -AA--TCATTACT-ATCAAATCA-TTAAATA---TTAA-T-AA-TAATTTCATTATT-ATTAATC
*
36379 AAGT-CGTA
54 -ATTAC-TA
* * * * *
36387 AATCATTACTATCAAATCATT-AATATTAAATCATTAAATATTAATAATAAATT-ATTATTACT-
1 AATCATTACTATCAAATCATTAAATATT-AAT-AAT-AAT-TTCATTAT-TATTAATCATTACTA
* *
36449 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTA
1 AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTATTAATCATTACTA
* *
36509 AATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTATTATTCATTACTA
1 AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTATTAATCATTACTA
*
36569 AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTA
1 AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTA
36616 CTAAATCTTA
Statistics
Matches: 454, Mismatches: 77, Indels: 104
0.71 0.12 0.16
Matches are distributed among these distances:
50 6 0.01
51 3 0.01
52 7 0.02
53 16 0.04
54 18 0.04
55 9 0.02
56 13 0.03
57 23 0.05
58 7 0.02
59 20 0.04
60 238 0.52
61 4 0.01
62 32 0.07
63 12 0.03
64 5 0.01
65 11 0.02
66 1 0.00
67 12 0.03
68 9 0.02
70 4 0.01
71 4 0.01
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.42
Consensus pattern (60 bp):
AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTATTAATCATTACTA
Found at i:36186 original size:92 final size:92
Alignment explanation
Indices: 36076--36252 Score: 318
Period size: 92 Copynumber: 1.9 Consensus size: 92
36066 TAATTTCATT
* *
36076 ATTATTAATTATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTAC
1 ATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTAC
36141 TAATCATTACTAAATCATTACTAAATC
66 TAATCATTACTAAATCATTACTAAATC
* *
36168 ATTACTAATCATTACTAAATCATTATTATCAAATCATTAAATATTAATAACAATTTTATTATTAC
1 ATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTAC
36233 TAATCATTACTAAATCATTA
66 TAATCATTACTAAATCATTA
36253 ATATCAAATC
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 81 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.42
Consensus pattern (92 bp):
ATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTAC
TAATCATTACTAAATCATTACTAAATC
Found at i:36200 original size:321 final size:313
Alignment explanation
Indices: 35699--36619 Score: 946
Period size: 321 Copynumber: 2.8 Consensus size: 313
35689 TCAAGTCGTA
35699 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCAT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCAT
*
35764 TACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAAAT
66 TACTATCAAATCATTAAAAATTAATAACAATTTCATTATTACTAATCATTACTAAATC-----A-
* *
35829 ATTAATAATAATTTTATTATTACTAATTATTACTAAATCATTACTATCAAATCATTAAATATTAA
125 ATT-ATAATAA---TATCATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAA
35894 TAACAATTTCACTATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATA
186 TAACAATTTCACTATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATA
*
35959 ATTTCATTATTATTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTATT
251 ATTTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTATT
36022 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTATTAATTA
1 AATCATTACTAAATCATTAATATCAAATCATTAAATA-T--TAATAA--T-A--A--ATT-ATTA
*
36087 TTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACT
55 TTACT-AATCATTACTATCAAATCATTAAAAATTAATAACAATTTCATTATTACTAATCATTACT
* *
36152 AAATC-A-T-TACTAA-ATCATTACTAATCATTACTAAATCATTATTATCAAATCATTAAATATT
119 AAATCAATTATAATAATATCATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATT
* *
36213 AATAACAATTTTATTATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAA
184 AATAACAATTTCACTATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAA
*
36278 TAATTTCATTATTACTAATCATTAC--T-AAATCATT----A-T--T-ATAATTTCATTACTAAT
249 TAATTTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTA-TTAT
36332 T
313 T
* * * * * * * ** *
36333 -AT-GTAACGAAAAT-ATGGTTAATTGAACCAAA-CATTGTTCATTGTTCAAGTCGTAAATCATT
1 AATCATTAC-TAAATCA---TTAA-T--ATCAAATCA---TTAAATATT-AA-TAATAAATTATT
* * * * * * *
36394 ACTATCAAATCATTAATATTAAATCATTAAATATTAATAATAAATT-ATTATTACTAATCATTAC
54 ATTA-CTAATCATTACTATCAAATCATTAAAAATTAATAACAATTTCATTATTACTAATCATTAC
* *
36458 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATCA
118 --T-AAATC------AATT-ATAATAA--T-ATCATTACTAATCATTACTAAATCATTACTATCA
* * * * *
36523 AATCATTAAATATTAATAATAATTTCATTATTATTATTCATTACTAAATCATTACTATCAAATCA
170 AATCATTAAATATTAATAACAATTTCACTATTACTAATCATTACTAAATCATTAATATCAAATCA
*
36588 TTAAATATTAATAATAATTTCATCATTACTAA
235 TTAAATATTAATAATAATTTCATTATTACTAA
36620 ATCTTATAAA
Statistics
Matches: 520, Mismatches: 35, Indels: 85
0.81 0.05 0.13
Matches are distributed among these distances:
307 18 0.03
308 41 0.08
309 8 0.02
310 23 0.04
311 6 0.01
312 4 0.01
313 3 0.01
314 5 0.01
315 7 0.01
316 2 0.00
317 5 0.01
318 9 0.02
319 1 0.00
320 5 0.01
321 132 0.25
323 37 0.07
324 124 0.24
325 5 0.01
326 6 0.01
327 1 0.00
328 2 0.00
329 1 0.00
331 1 0.00
333 3 0.01
334 9 0.02
335 62 0.12
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.42
Consensus pattern (313 bp):
AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCAT
TACTATCAAATCATTAAAAATTAATAACAATTTCATTATTACTAATCATTACTAAATCAATTATA
ATAATATCATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTC
ACTATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTAT
TACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTATT
Found at i:36206 original size:11 final size:11
Alignment explanation
Indices: 36136--36192 Score: 100
Period size: 11 Copynumber: 5.4 Consensus size: 11
36126 CAATTTCATT
36136 ATTACT-AATC
1 ATTACTAAATC
36146 ATTACTAAATC
1 ATTACTAAATC
36157 ATTACTAAATC
1 ATTACTAAATC
36168 ATTACT-AATC
1 ATTACTAAATC
36178 ATTACTAAATC
1 ATTACTAAATC
36189 ATTA
1 ATTA
36193 TTATCAAATC
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
10 16 0.36
11 29 0.64
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.39
Consensus pattern (11 bp):
ATTACTAAATC
Found at i:36312 original size:21 final size:21
Alignment explanation
Indices: 36136--36312 Score: 99
Period size: 21 Copynumber: 8.7 Consensus size: 21
36126 CAATTTCATT
36136 ATTACT-AATCATTACTAAATC
1 ATTACTAAATCATTACT-AATC
36157 ATTACTAAATCATTACTAATC
1 ATTACTAAATCATTACTAATC
*
36178 ATTACTAAATCATTA-TTATC
1 ATTACTAAATCATTACTAATC
* * *
36198 AAATCATTAAAT-ATTAATAA-C
1 --ATTACTAAATCATTACTAATC
* *
36219 AATT--T-TATTATTACTAATC
1 -ATTACTAAATCATTACTAATC
*
36238 ATTACTAAATCATTAAT-ATC
1 ATTACTAAATCATTACTAATC
* * * *
36258 AAATCATTAAAT-ATTAATAATA
1 --ATTACTAAATCATTACTAATC
* *
36280 ATT--T-CATTATTACTAATC
1 ATTACTAAATCATTACTAATC
36298 ATTACTAAATCATTA
1 ATTACTAAATCATTA
36313 TTATAATTTC
Statistics
Matches: 121, Mismatches: 19, Indels: 32
0.70 0.11 0.19
Matches are distributed among these distances:
17 4 0.03
18 23 0.19
19 1 0.01
20 14 0.12
21 49 0.40
22 30 0.25
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTACTAAATCATTACTAATC
Found at i:36329 original size:25 final size:24
Alignment explanation
Indices: 36283--36330 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
36273 AATAATAATT
36283 TCATTATTACTAATCATTACTAAA
1 TCATTATTACTAATCATTACTAAA
36307 TCATTATTA-TAATTTCATTACTAA
1 TCATTATTACTAA--TCATTACTAA
36331 TTATGTAACG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 3 0.14
24 9 0.41
25 10 0.45
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.46
Consensus pattern (24 bp):
TCATTATTACTAATCATTACTAAA
Found at i:36428 original size:15 final size:14
Alignment explanation
Indices: 36385--36471 Score: 66
Period size: 14 Copynumber: 5.8 Consensus size: 14
36375 GTTCAAGTCG
*
36385 TAAATCATTACTAT
1 TAAATCATTAATAT
*
36399 CAAATCATTAATAT
1 TAAATCATTAATAT
36413 TAAATCATTAAATAT
1 TAAATCATT-AATAT
* *
36428 TAATAATAAATTATTAT
1 T-A-AAT-CATTAATAT
*
36445 TACTAATCATTACTAT
1 TA--AATCATTAATAT
*
36461 CAAATCATTAA
1 TAAATCATTAA
36472 AAATTAATAA
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
14 28 0.47
15 6 0.10
16 10 0.17
17 12 0.20
18 3 0.05
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAATCATTAATAT
Found at i:36429 original size:21 final size:21
Alignment explanation
Indices: 36400--36600 Score: 62
Period size: 21 Copynumber: 9.5 Consensus size: 21
36390 CATTACTATC
36400 AAATCATTAATATTAAATCATT
1 AAAT-ATTAATATTAAATCATT
* *
36422 AAATATTAATAATAAATTATTATT
1 AAATATTAAT-ATTAA--ATCATT
* *
36446 ACTAATCATTACTATCAAATCATT
1 A--AAT-ATTAATATTAAATCATT
* * *
36470 AAAAATTAATAATAATTTCATT
1 AAATATTAATATTAA-ATCATT
* *
36492 -ATTACTAATCATT--A-C--T
1 AAATATTAAT-ATTAAATCATT
*
36508 AAATCATTAATATCAAATCATT
1 AAAT-ATTAATATTAAATCATT
*
36530 AAATATTAATAAT-AAT--TT
1 AAATATTAATATTAAATCATT
* * * * * *
36548 CATTATTATTATT-CATTACT
1 AAATATTAATATTAAATCATT
* *
36568 AAATCATTACTATCAAATCATT
1 AAAT-ATTAATATTAAATCATT
36590 AAATATTAATA
1 AAATATTAATA
36601 ATAATTTCAT
Statistics
Matches: 126, Mismatches: 34, Indels: 39
0.63 0.17 0.20
Matches are distributed among these distances:
16 1 0.01
17 4 0.03
18 19 0.15
19 1 0.01
20 7 0.06
21 40 0.32
22 30 0.24
24 12 0.10
26 7 0.06
27 5 0.04
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATATTAATATTAAATCATT
Found at i:36455 original size:48 final size:49
Alignment explanation
Indices: 36401--36505 Score: 167
Period size: 48 Copynumber: 2.2 Consensus size: 49
36391 ATTACTATCA
* *
36401 AATCATTAATATTAAATCATTAAATATTAATAATAAATT-ATTATTACT
1 AATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATTATTACT
* *
36449 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
1 AATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATTATTACT
36498 AATCATTA
1 AATCATTA
36506 CTAAATCATT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
48 35 0.67
49 17 0.33
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.42
Consensus pattern (49 bp):
AATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATTATTACT
Found at i:39312 original size:29 final size:29
Alignment explanation
Indices: 39270--39328 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
39260 TTTCCATAAT
39270 ATGTCCATTATAATGGACAATCGTGAAAA
1 ATGTCCATTATAATGGACAATCGTGAAAA
39299 ATGTCCATTATAATGGACAATCGTGAAAA
1 ATGTCCATTATAATGGACAATCGTGAAAA
39328 A
1 A
39329 GCTGTTGCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (29 bp):
ATGTCCATTATAATGGACAATCGTGAAAA
Found at i:40190 original size:28 final size:30
Alignment explanation
Indices: 40142--40203 Score: 110
Period size: 28 Copynumber: 2.1 Consensus size: 30
40132 ATTTTTTATA
40142 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
40172 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
40200 TAAT
1 TAAT
40204 TAACTAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:40658 original size:23 final size:23
Alignment explanation
Indices: 40628--40671 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
40618 GCTTGGCTAC
40628 AATCTCCCAGCTATGGATGCAGT
1 AATCTCCCAGCTATGGATGCAGT
40651 AATCTCCCAGCTATGGATGCA
1 AATCTCCCAGCTATGGATGCA
40672 AACCCATGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (23 bp):
AATCTCCCAGCTATGGATGCAGT
Found at i:40728 original size:45 final size:46
Alignment explanation
Indices: 40661--40751 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 46
40651 AATCTCCCAG
40661 CTATGGATGCAAACCCATGCACGAGGGAGCAAGGTTAAGTTTGGTC
1 CTATGGATGCAAACCCATGCACGAGGGAGCAAGGTTAAGTTTGGTC
*
40707 CTATGGATGC-AACCCATGCACGAGGGAGCAGGGTTAAGTTTGGTC
1 CTATGGATGCAAACCCATGCACGAGGGAGCAAGGTTAAGTTTGGTC
40752 GCCAATAGAG
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 34 0.77
46 10 0.23
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22
Consensus pattern (46 bp):
CTATGGATGCAAACCCATGCACGAGGGAGCAAGGTTAAGTTTGGTC
Found at i:40859 original size:29 final size:29
Alignment explanation
Indices: 40776--40864 Score: 124
Period size: 29 Copynumber: 3.1 Consensus size: 29
40766 GTCGAGGCTT
* * ***
40776 GGTCGCCGGGACTGCTTGGCGACCTACAA
1 GGTCGCTGGGAGTGCTTGGCGACCTTGTA
*
40805 GGTCGCTGGGAGTGCATGGCGACCTTGTA
1 GGTCGCTGGGAGTGCTTGGCGACCTTGTA
40834 GGTCGCTGGGAGTGCTTGGCGACCTTGTA
1 GGTCGCTGGGAGTGCTTGGCGACCTTGTA
40863 GG
1 GG
40865 GGTGTTGGGG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.13, C:0.24, G:0.40, T:0.22
Consensus pattern (29 bp):
GGTCGCTGGGAGTGCTTGGCGACCTTGTA
Found at i:44024 original size:21 final size:20
Alignment explanation
Indices: 43994--44033 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
43984 CTTCATGTTA
43994 TAATTAATTTTAAAATATTT
1 TAATTAATTTTAAAATATTT
*
44014 TAATTGAATTTTAAATTATT
1 TAATT-AATTTTAAAATATT
44034 AATATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TAATTAATTTTAAAATATTT
Found at i:44747 original size:3 final size:3
Alignment explanation
Indices: 44739--44778 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
44729 CAACCTCACT
* *
44739 TTC TTC TTC TTC TTC TTC TTC TTC TTC -AC TTC TCC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
44779 AACAACAGTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 1 0.03
3 31 0.97
ACGTcount: A:0.03, C:0.35, G:0.00, T:0.62
Consensus pattern (3 bp):
TTC
Found at i:52466 original size:21 final size:21
Alignment explanation
Indices: 52450--52503 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
52440 GCATTGCATT
52450 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
*
52471 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAA
52492 TCGCGTTGCGAT
1 TCGCGTTGCGAT
52504 TTTTCAGTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Found at i:52523 original size:41 final size:41
Alignment explanation
Indices: 52471--52639 Score: 187
Period size: 41 Copynumber: 4.3 Consensus size: 41
52461 TAATTGAAAA
*
52471 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTTCAGT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGT
* * * *
52512 TCGCGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-AGT
52555 T--CGTTGC-------GAAAATCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGT
*
52587 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGT
52628 TCGCGTTGCGAT
1 TCGCGTTGCGAT
52640 TTTCCAGTTG
Statistics
Matches: 105, Mismatches: 10, Indels: 26
0.74 0.07 0.18
Matches are distributed among these distances:
32 3 0.03
33 14 0.13
34 10 0.10
41 61 0.58
42 14 0.13
43 3 0.03
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.36
Consensus pattern (41 bp):
TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGT
Found at i:52592 original size:20 final size:20
Alignment explanation
Indices: 52567--52648 Score: 101
Period size: 20 Copynumber: 4.0 Consensus size: 20
52557 GTTGCGAAAA
52567 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* ** **
52587 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCAGT
*
52608 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
52628 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
52648 T
1 T
52649 GCGATAGTCT
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
20 35 0.70
21 15 0.30
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAGT
Found at i:52653 original size:75 final size:75
Alignment explanation
Indices: 52487--52625 Score: 219
Period size: 75 Copynumber: 1.9 Consensus size: 75
52477 TGCGATAGTT
* * * *
52487 GAAAATCGCGTTGCGATTTTTCAGTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCA
1 GAAAATCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTCTAAAATCGTCGTTGCGATTTTCCA
52552 AATTCGTTGC
66 AATTCGTTGC
52562 GAAAATCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC
1 GAAAATCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTCT-AAAATCGTCGTTGCGATTTTCC
52625 A
65 A
52626 TTTCGCGTTG
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
74 16 0.27
75 43 0.73
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.35
Consensus pattern (75 bp):
GAAAATCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTCTAAAATCGTCGTTGCGATTTTCCA
AATTCGTTGC
Found at i:53321 original size:6 final size:6
Alignment explanation
Indices: 53310--53337 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
53300 GTCCGTCTCG
53310 GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTC
53338 AGATAAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.18, G:0.50, T:0.32
Consensus pattern (6 bp):
GGTCGT
Done.