Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008750.1 Hibiscus syriacus cultivar Beakdansim tig00111841_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: 3719443
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 18
Found at i:251779 original size:82 final size:80
Alignment explanation
Indices: 251503--251780 Score: 227
Period size: 82 Copynumber: 3.4 Consensus size: 80
251493 TGGTAAACGC
** * * ** * **
251503 CGTAATAGG-TCTATCTATAGTGTTGCTTTTTCAACAAACACCGTAAGGGAATAGTTTTTTAGCG
1 CGTAATAGGTTC-A-CTATAGTGACGTTTTTTCAACAAACGCCGTAAAAGAATACTACTTTAGCG
251567 GCGTTTTTTATACAAACT
64 GCG-TTTTTATACAAACT
* * * * * * *
251585 CCGCAATAGGTCCA-TCTAGTGTCGTTTTTTTCAACAAATGCCGTAAAAGAGTACTACTTTAGCA
1 -CGTAATAGGTTCACTATAGTGACG-TTTTTTCAACAAACGCCGTAAAAGAATACTACTTTAGCG
* *
251649 GCGTATTTATACAAACG
64 GCGTTTTTATACAAACT
* * * * * *
251666 CAGTGATATGATTAACTATAGTGACGTTTTTTCAATAAACGCTGTAAAGGAATACTACTTTAGCG
1 C-GTAATA-GGTTCACTATAGTGACGTTTTTTCAACAAACGCCGTAAAAGAATACTACTTTAGCG
251731 GCGTTTTTATACAAACAT
64 GCGTTTTTATACAAAC-T
*
251749 CGTAATAGGGTTCACTTATAGTGGCGTTTTTT
1 CGTAATA-GGTTCAC-TATAGTGACGTTTTTT
251781 TTCCTCACAA
Statistics
Matches: 152, Mismatches: 36, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
80 1 0.01
81 24 0.16
82 93 0.61
83 33 0.22
84 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (80 bp):
CGTAATAGGTTCACTATAGTGACGTTTTTTCAACAAACGCCGTAAAAGAATACTACTTTAGCGGC
GTTTTTATACAAACT
Found at i:253513 original size:22 final size:20
Alignment explanation
Indices: 253487--253529 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
253477 AAAAACCGAA
253487 CCGAACCGAACCGTTAAAAAAC
1 CCGAACCGAACCG--AAAAAAC
*
253509 CCGAATCGAACCGAAAAAAC
1 CCGAACCGAACCGAAAAAAC
253529 C
1 C
253530 GGTTTCGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
22 12 0.60
ACGTcount: A:0.47, C:0.33, G:0.14, T:0.07
Consensus pattern (20 bp):
CCGAACCGAACCGAAAAAAC
Found at i:254000 original size:21 final size:21
Alignment explanation
Indices: 253976--254019 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
253966 ATTTATTATA
*
253976 ATGGATTTAAAGTTGGTTGTT
1 ATGGAATTAAAGTTGGTTGTT
**
253997 ATGGAATTAAAGTTTTTTGTT
1 ATGGAATTAAAGTTGGTTGTT
254018 AT
1 AT
254020 AGATGTCATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (21 bp):
ATGGAATTAAAGTTGGTTGTT
Found at i:255884 original size:2 final size:2
Alignment explanation
Indices: 255877--255916 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
255867 AAATCTATCA
*
255877 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC 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
255917 TATGTAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:257881 original size:14 final size:14
Alignment explanation
Indices: 257862--257917 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
257852 CGTTCGTGAA
257862 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
257876 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
257890 CG-T---TTATGTT
1 CGTTCGGTTATGTT
257900 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
257914 CGTT
1 CGTT
257918 TATGTTCATT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.09, C:0.14, G:0.25, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:257890 original size:24 final size:24
Alignment explanation
Indices: 257863--257937 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 24
257853 GTTCGTGAAC
*
257863 GTTCGGTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
*
257887 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGATTAT
*
257911 GTTCGTTTATGTTCATTC-ATTTAT
1 GTTCGTTTATGTTCGTTCGA-TTAT
257935 GTT
1 GTT
257938 TAACCCAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.55
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGATTAT
Found at i:258977 original size:16 final size:16
Alignment explanation
Indices: 258956--259022 Score: 102
Period size: 16 Copynumber: 4.3 Consensus size: 16
258946 GTCTCCAACG
258956 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
258972 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
258988 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
259004 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
259018 TTTAT
1 TTTAT
259023 TAAATGAACG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 42 0.86
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:258995 original size:32 final size:32
Alignment explanation
Indices: 258954--259014 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
258944 AGGTCTCCAA
258954 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
*
258986 CGTTTATGTTCGTGTTCGTTTATGTTCGT
1 CGTTTATGTTCGTGTTCATTTATGTTCGT
259015 TTATTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.08, C:0.13, G:0.23, T:0.56
Consensus pattern (32 bp):
CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
Found at i:259105 original size:16 final size:16
Alignment explanation
Indices: 259084--259116 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
259074 AAAAAAAAAT
259084 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
259100 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
259116 T
1 T
259117 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:260379 original size:2 final size:2
Alignment explanation
Indices: 260331--260361 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
260321 TTAGTCTTAA
260331 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
260362 ATTATTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:261825 original size:22 final size:22
Alignment explanation
Indices: 261793--261855 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 22
261783 TTTAAATTTG
*
261793 AATCTTCAAAT-TATAAACCTTA
1 AATCTTAAAATATAT-AACCTTA
261815 AATCTTAAAATATATAACCTTAA
1 AATCTTAAAATATATAACCTT-A
261838 AATC-TAAATCATATATAA
1 AATCTTAAA--ATATATAA
261856 AACAAATCAC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
22 20 0.56
23 8 0.22
24 8 0.22
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
AATCTTAAAATATATAACCTTA
Found at i:262819 original size:14 final size:14
Alignment explanation
Indices: 262800--262826 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
262790 GTTCCTTCAA
262800 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
262814 AAAAGAAAAGAAA
1 AAAAGAAAAGAAA
262827 TGTGGGAATT
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:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:263280 original size:20 final size:20
Alignment explanation
Indices: 263234--263285 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
263224 TGCGATCTCG
* * *
263234 AATTCGGAACGCGAATATGT
1 AATTCGCAACACGAATATAT
* *
263254 AAATCGCAACACGAATTTAT
1 AATTCGCAACACGAATATAT
263274 AATTCGCAACAC
1 AATTCGCAACAC
263286 ATAAGTCAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.23
Consensus pattern (20 bp):
AATTCGCAACACGAATATAT
Found at i:263476 original size:22 final size:22
Alignment explanation
Indices: 263451--263501 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
263441 CTATGCTGAC
*
263451 ATCCGTCCCCATCTCCGATGAA
1 ATCCGTCCCCATCTCCGACGAA
263473 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
263495 ATCCGTC
1 ATCCGTC
263502 TATCTCCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.22, C:0.43, G:0.14, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:265451 original size:21 final size:21
Alignment explanation
Indices: 265411--265451 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
265401 AGGGGAGTTA
*
265411 CGTGATGAGGACAGTGCTTTG
1 CGTGATGAGGACAGTACTTTG
* *
265432 CGTGATGAGGTCGGTACTTT
1 CGTGATGAGGACAGTACTTT
265452 ACGTCACGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.15, G:0.37, T:0.32
Consensus pattern (21 bp):
CGTGATGAGGACAGTACTTTG
Found at i:265523 original size:42 final size:43
Alignment explanation
Indices: 265477--265569 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 43
265467 TGCATGGTGT
*
265477 GATGAGGTACGGT-CTTTACGTGGTGAGGTAGATATTTTACGC
1 GATGAGGTACGGTGCTTTACGTGGTGAGGTAGATACTTTACGC
** * ** *
265519 GATGA-AAATGGTGCTTTACGTGGTGAGGTATCTACTTTACGT
1 GATGAGGTACGGTGCTTTACGTGGTGAGGTAGATACTTTACGC
265561 GATGAGGTA
1 GATGAGGTA
265570 GCCGCTCTAC
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
41 4 0.10
42 35 0.88
43 1 0.03
ACGTcount: A:0.24, C:0.11, G:0.32, T:0.33
Consensus pattern (43 bp):
GATGAGGTACGGTGCTTTACGTGGTGAGGTAGATACTTTACGC
Found at i:265689 original size:4 final size:4
Alignment explanation
Indices: 265680--265725 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
265670 TTTTTTGGCA
* * * *
265680 TTAT TTAT TTAT TTAT TTAT TTAC TGAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
265726 TTAGTGGCCC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (4 bp):
TTAT
Found at i:265896 original size:21 final size:21
Alignment explanation
Indices: 265872--266012 Score: 162
Period size: 21 Copynumber: 6.8 Consensus size: 21
265862 TTCACCTGTC
*
265872 ATCGTTCAAGAGGCACCTCCT
1 ATCGTTCAAGAGGCCCCTCCT
265893 ATCGTTCAAGAGGCCCCTCCT
1 ATCGTTCAAGAGGCCCCTCCT
* *
265914 ATCGTTCAAGACGCCTCT-CT
1 ATCGTTCAAGAGGCCCCTCCT
*
265934 CATCGTTCAAGAGGCCCCTCCC
1 -ATCGTTCAAGAGGCCCCTCCT
* *
265956 ACCGTTCAAGAGGCCCCT-AT
1 ATCGTTCAAGAGGCCCCTCCT
* *
265976 CATCGTTCAAGAGGTCCCTCCC
1 -ATCGTTCAAGAGGCCCCTCCT
*
265998 ACCGTTCAAG-GGCCC
1 ATCGTTCAAGAGGCCC
266013 GATTCACGTG
Statistics
Matches: 101, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
20 6 0.06
21 94 0.93
22 1 0.01
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.22
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCCT
Found at i:270055 original size:24 final size:24
Alignment explanation
Indices: 270021--270074 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
270011 CTGAAACATC
270021 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
270045 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
270069 ATCAAA
1 ATCAAA
270075 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:270088 original size:24 final size:24
Alignment explanation
Indices: 270021--270088 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
270011 CTGAAACATC
* * *
270021 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
270045 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
270069 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
270089 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:270221 original size:12 final size:12
Alignment explanation
Indices: 270200--270233 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
270190 GGTTGTGGGT
*
270200 TTTGAGATTGTG
1 TTTGATATTGTG
270212 TTTGATATTGTG
1 TTTGATATTGTG
*
270224 TTTGGTATTG
1 TTTGATATTG
270234 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:270852 original size:16 final size:16
Alignment explanation
Indices: 270830--270869 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
270820 GAAATCATTG
*
270830 AAAAATTATATAGAAA
1 AAAAATTATATAAAAA
* *
270846 TAAAATTATGTAAAAA
1 AAAAATTATATAAAAA
270862 AAAAATTA
1 AAAAATTA
270870 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (16 bp):
AAAAATTATATAAAAA
Found at i:271072 original size:40 final size:40
Alignment explanation
Indices: 271028--271123 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
271018 TAAAACCTGG
* *
271028 TGCGAAATTAAAATTCGTGTTTCGAATTC-GAAAATCGAGT
1 TGCGAAATTAAAATTCGCGTTGCGAATTCAG-AAATCGAGT
**
271068 TGCGAAAACAAAATTCGCGTTGCGAATTCAGAAATCGAGT
1 TGCGAAATTAAAATTCGCGTTGCGAATTCAGAAATCGAGT
* * *
271108 TGTGAATTTGAAATTC
1 TGCGAAATTAAAATTC
271124 AATGTTGCAA
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
40 45 0.98
41 1 0.02
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (40 bp):
TGCGAAATTAAAATTCGCGTTGCGAATTCAGAAATCGAGT
Found at i:271109 original size:20 final size:20
Alignment explanation
Indices: 271050--271156 Score: 67
Period size: 20 Copynumber: 5.3 Consensus size: 20
271040 ATTCGTGTTT
271050 CGAATTC-GAAAATCGAGTTG
1 CGAATTCAG-AAATCGAGTTG
** *
271070 CGAAAACA-AAATTCGCGTTG
1 CGAATTCAGAAA-TCGAGTTG
271090 CGAATTCAGAAATCGAGTTG
1 CGAATTCAGAAATCGAGTTG
* * *
271110 TGAATT-TGAAATTCAATGTTG
1 CGAATTCAGAAA-TCGA-GTTG
* ** *
271131 CAAATTTGGAAATCGCGTTG
1 CGAATTCAGAAATCGAGTTG
271151 CGAATT
1 CGAATT
271157 TGGAAACTGT
Statistics
Matches: 66, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
19 7 0.11
20 42 0.64
21 13 0.20
22 4 0.06
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (20 bp):
CGAATTCAGAAATCGAGTTG
Found at i:271157 original size:20 final size:20
Alignment explanation
Indices: 271082--271180 Score: 76
Period size: 20 Copynumber: 4.9 Consensus size: 20
271072 AAAACAAAAT
**
271082 TCGCGTTGCGAATTCAGAAA
1 TCGCGTTGCGAATTTGGAAA
* *
271102 TCGAGTTGTGAATTT-GAAA
1 TCGCGTTGCGAATTTGGAAA
** *
271121 TTCAATGTTGCAAATTTGGAAA
1 -TC-GCGTTGCGAATTTGGAAA
271143 TCGCGTTGCGAATTTGGAAA
1 TCGCGTTGCGAATTTGGAAA
* *
271163 -CTGTGTTGCGAAATTGGA
1 TC-GCGTTGCGAATTTGGA
271181 GTTTGCGTTA
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
19 5 0.08
20 43 0.68
21 11 0.17
22 4 0.06
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.32
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGGAAA
Found at i:274745 original size:47 final size:45
Alignment explanation
Indices: 274647--274772 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
274637 GTAACCATGC
* * * *
274647 AAATAAGCTTATGAGCTTACGGAAT-AATAGCAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGAA
* *
274691 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATTGGAA
*
274738 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
274773 AGATTTTATA
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 22 0.31
45 11 0.15
46 1 0.01
47 38 0.53
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGAA
Found at i:275186 original size:30 final size:30
Alignment explanation
Indices: 275152--275211 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
275142 TAGCAGTTAA
* *
275152 TGTAGCGGTTACTGTAGTGTATCGATGCAT
1 TGTAGCAGTTACTGTAGCGTATCGATGCAT
275182 TGTAGCAGTTACTGTAGCGTATCGATGCAT
1 TGTAGCAGTTACTGTAGCGTATCGATGCAT
275212 AATATTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (30 bp):
TGTAGCAGTTACTGTAGCGTATCGATGCAT
Found at i:278429 original size:25 final size:25
Alignment explanation
Indices: 278375--278429 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
278365 AATTTTCAAG
278375 CTCGACTCGAAATAAAAAATTGAAA
1 CTCGACTCGAAATAAAAAATTGAAA
* ** * *
278400 TTCGACTCGAGCTCAAAAATTGGAA
1 CTCGACTCGAAATAAAAAATTGAAA
278425 CTCGA
1 CTCGA
278430 AATATTCTCA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (25 bp):
CTCGACTCGAAATAAAAAATTGAAA
Found at i:282302 original size:12 final size:12
Alignment explanation
Indices: 282285--282310 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
282275 TAATATTGTG
282285 TTCATTTATTTA
1 TTCATTTATTTA
282297 TTCATTTATTTA
1 TTCATTTATTTA
282309 TT
1 TT
282311 TTTGAAGGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (12 bp):
TTCATTTATTTA
Found at i:285165 original size:20 final size:21
Alignment explanation
Indices: 285112--285168 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
285102 ACTTGTACTG
*
285112 CTTGTTGAGTATCCATACTCC
1 CTTGTTGAGTATTCATACTCC
** *
285133 CTAATTGAGTATTCATA-TTC
1 CTTGTTGAGTATTCATACTCC
285153 CTTGTTGAGTATTCAT
1 CTTGTTGAGTATTCAT
285169 GCTCTGTAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (21 bp):
CTTGTTGAGTATTCATACTCC
Found at i:285944 original size:19 final size:19
Alignment explanation
Indices: 285920--285957 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
285910 CAATCCTAAC
285920 AATTAGGCTATAATTTAGG
1 AATTAGGCTATAATTTAGG
285939 AATTAGGCTATAATTTAGG
1 AATTAGGCTATAATTTAGG
285958 CAACTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (19 bp):
AATTAGGCTATAATTTAGG
Found at i:289457 original size:25 final size:24
Alignment explanation
Indices: 289429--289486 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
289419 CAGTCGAAAC
* * *
289429 TGCCGCTTAGAATTTTGCACTGAAG
1 TGCCACTTAG-ATTATGCACCGAAG
*
289454 TGCCACGTAGATTATGCACCGAAG
1 TGCCACTTAGATTATGCACCGAAG
289478 TGCCACTTA
1 TGCCACTTA
289487 TATTTGTCCT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 20 0.71
25 8 0.29
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (24 bp):
TGCCACTTAGATTATGCACCGAAG
Found at i:291217 original size:13 final size:14
Alignment explanation
Indices: 291190--291238 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
291180 TATATTTTGT
291190 AAATCTTTTTAAAA
1 AAATCTTTTTAAAA
291204 AAATCTTTTT-AAA
1 AAATCTTTTTAAAA
*
291217 AAGTCTTTTTTAAACA
1 AAATC-TTTTTAAA-A
291233 AAATCT
1 AAATCT
291239 AAACATGACA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 7 0.23
14 15 0.50
15 3 0.10
16 5 0.17
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (14 bp):
AAATCTTTTTAAAA
Found at i:292036 original size:259 final size:259
Alignment explanation
Indices: 291577--292096 Score: 950
Period size: 259 Copynumber: 2.0 Consensus size: 259
291567 TCCCTCAATA
291577 TTAAAAGTTCCAAAATGATAATTTGACTATTCATATGTTATAAATTCGTCCTTTTCGTTAAAAAG
1 TTAAAAGTTCCAAAATGATAATTTGACTATTCATATGTTATAAATTCGTCCTTTTCGTTAAAAAG
* * * *
291642 TTAACATACGTCTAAGTTGGATGTTAACTTACTGTTAAGATATGATAAAATCTTACCCCATAACT
66 TTAACAGACATCTAAGTTGGATGTTAACTTACTGCTAAGACATGATAAAATCTTACCCCATAACT
291707 ATTTGAGTTGTATTTTGTGGATCAAATTTTATCATATCGCACTTAACAAGTTAATGTCCAATTCA
131 ATTTGAGTTGTATTTTGTGGATCAAATTTTATCATATCGCACTTAACAAGTTAATGTCCAATTCA
* **
291772 GATGACTATCAATTTTTGACCGAAAAGGACGAGTTTGAAATTTATAAATAGTCAAATAATCATT
196 GATGACTATCAAATTTTGACCGAAAAGGACGAGTTTGAAACGTATAAATAGTCAAATAATCATT
*
291836 TTAAAAGTTCCAAAATGATAATTTGACTATTCATATGTTCTAAATTCGTCCTTTTCGTTAAAAAG
1 TTAAAAGTTCCAAAATGATAATTTGACTATTCATATGTTATAAATTCGTCCTTTTCGTTAAAAAG
* *
291901 TTAACAGACATCTAAGTTGGATGTTAACTTACTGCTAAGACATGATAAAATCTTATCTCATAACT
66 TTAACAGACATCTAAGTTGGATGTTAACTTACTGCTAAGACATGATAAAATCTTACCCCATAACT
291966 ATTTGAGTTGTATTTTGTGGATCAAATTTTATCATATCGCACTTAACAAGTTAATGTCCAATTCA
131 ATTTGAGTTGTATTTTGTGGATCAAATTTTATCATATCGCACTTAACAAGTTAATGTCCAATTCA
292031 GATGACTATCAAATTTTGACCGAAAAGGACGAGTTTGAAACGTATAAATAGTCAAATAATCATT
196 GATGACTATCAAATTTTGACCGAAAAGGACGAGTTTGAAACGTATAAATAGTCAAATAATCATT
292095 TT
1 TT
292097 TCTAACTTTT
Statistics
Matches: 251, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
259 251 1.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (259 bp):
TTAAAAGTTCCAAAATGATAATTTGACTATTCATATGTTATAAATTCGTCCTTTTCGTTAAAAAG
TTAACAGACATCTAAGTTGGATGTTAACTTACTGCTAAGACATGATAAAATCTTACCCCATAACT
ATTTGAGTTGTATTTTGTGGATCAAATTTTATCATATCGCACTTAACAAGTTAATGTCCAATTCA
GATGACTATCAAATTTTGACCGAAAAGGACGAGTTTGAAACGTATAAATAGTCAAATAATCATT
Found at i:293493 original size:21 final size:21
Alignment explanation
Indices: 293462--293518 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
293452 GATTCTAACT
**
293462 ATCGCATTGCGATTTTCCAAA
1 ATCGCATTGCGATAGTCCAAA
* *
293483 TTCGCAATGCGATAGTCCAAA
1 ATCGCATTGCGATAGTCCAAA
293504 ATCGCATTGCGATAG
1 ATCGCATTGCGATAG
293519 CACTGTTCAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (21 bp):
ATCGCATTGCGATAGTCCAAA
Found at i:293534 original size:21 final size:21
Alignment explanation
Indices: 293508--293560 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
293498 TCCAAAATCG
293508 CATTGCGATAGCACTGTTCAC
1 CATTGCGATAGCACTGTTCAC
*
293529 CGTTGCGATAGCACTGTTCAC
1 CATTGCGATAGCACTGTTCAC
*
293550 TATTGCGATAG
1 CATTGCGATAG
293561 TGATCAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (21 bp):
CATTGCGATAGCACTGTTCAC
Found at i:294264 original size:21 final size:21
Alignment explanation
Indices: 294238--294361 Score: 221
Period size: 21 Copynumber: 5.9 Consensus size: 21
294228 AATTCGTAAT
294238 GTGAACAGTGCTATCGCAACG
1 GTGAACAGTGCTATCGCAACG
294259 GTGAACAGTGCTATCGCAACG
1 GTGAACAGTGCTATCGCAACG
*
294280 GTGAACAGTGTTATCGCAACG
1 GTGAACAGTGCTATCGCAACG
*
294301 GTGAACAGTGTTATCGCAACG
1 GTGAACAGTGCTATCGCAACG
*
294322 GTGAACACTGCTATCGCAACG
1 GTGAACAGTGCTATCGCAACG
294343 GTGAACAGTGCTATCGCAA
1 GTGAACAGTGCTATCGCAA
294362 TGCGATTTTG
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 99 1.00
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (21 bp):
GTGAACAGTGCTATCGCAACG
Found at i:294377 original size:21 final size:21
Alignment explanation
Indices: 294355--294429 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
294345 GAACAGTGCT
* **
294355 ATCGCAATGCGATTTTGGACT
1 ATCGCAATGCGAATTTGGAAA
* *
294376 ATCGCATTGCGAATTCGGAAA
1 ATCGCAATGCGAATTTGGAAA
**
294397 ATCGCAACACGAATTTGGAAA
1 ATCGCAATGCGAATTTGGAAA
294418 ATCGCAATGCGA
1 ATCGCAATGCGA
294430 TAGTCAGAAT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (21 bp):
ATCGCAATGCGAATTTGGAAA
Found at i:300779 original size:20 final size:20
Alignment explanation
Indices: 300756--300903 Score: 215
Period size: 20 Copynumber: 7.3 Consensus size: 20
300746 AATTTATAAA
*
300756 TCGCAACACCGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
300776 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
300796 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
300816 TTGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
300836 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
300856 TCGCAACACATAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* * *
300876 TTGCAACACTGAATTTCAAAT
1 TCGCAACACAGAA-GTCAAAT
300897 TCGCAAC
1 TCGCAAC
300904 TGAATTTCAA
Statistics
Matches: 115, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
20 103 0.90
21 12 0.10
ACGTcount: A:0.44, C:0.25, G:0.12, T:0.19
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:300795 original size:60 final size:60
Alignment explanation
Indices: 300731--300903 Score: 213
Period size: 60 Copynumber: 2.9 Consensus size: 60
300721 ACACAGTTTC
* * * * *
300731 CAAATTCGCAACA-TAAATTTATAAATCGCAACACCGAAGTCAAATTCGCAACACAGAAGT
1 CAAATTCGCAACACAAAAGTCA-AAATCGCAACACAGAAGTCAAATTCGCAACACAAAAGT
* *
300791 CAAATTCGCAACACAAAAGTCAAATTTGCAACACAGAAGTCAAATTCGCAACACAAAAGT
1 CAAATTCGCAACACAAAAGTCAAAATCGCAACACAGAAGTCAAATTCGCAACACAAAAGT
* * * * *
300851 CAAATTCGCAACACATAAGTCAAATTTGCAACACTGAATTTCAAATTCGCAAC
1 CAAATTCGCAACACAAAAGTCAAAATCGCAACACAGAA-GTCAAATTCGCAAC
300904 TGAATTTCAA
Statistics
Matches: 101, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
60 83 0.82
61 18 0.18
ACGTcount: A:0.45, C:0.24, G:0.11, T:0.20
Consensus pattern (60 bp):
CAAATTCGCAACACAAAAGTCAAAATCGCAACACAGAAGTCAAATTCGCAACACAAAAGT
Found at i:300907 original size:19 final size:19
Alignment explanation
Indices: 300883--300980 Score: 126
Period size: 19 Copynumber: 5.1 Consensus size: 19
300873 AATTTGCAAC
300883 ACTGAATTTCAAATTCGCA
1 ACTGAATTTCAAATTCGCA
300902 ACTGAATTTCAAATTCGCA
1 ACTGAATTTCAAATTCGCA
*
300921 ACTGAATTTTAAATTCGCA
1 ACTGAATTTCAAATTCGCA
* *
300940 ACTCGATTTTCGAATTCGCA
1 ACT-GAATTTCAAATTCGCA
* *
300960 ACACGAATTT-AATTTCGCA
1 AC-TGAATTTCAAATTCGCA
300979 AC
1 AC
300981 ATGTTTTAGT
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
19 49 0.71
20 20 0.29
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (19 bp):
ACTGAATTTCAAATTCGCA
Found at i:300922 original size:60 final size:60
Alignment explanation
Indices: 300758--300903 Score: 238
Period size: 60 Copynumber: 2.4 Consensus size: 60
300748 TTTATAAATC
* *
300758 GCAACACCGAAGTCAAATTCGCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAATTT
1 GCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACACAAAAGTCAAATTT
*
300818 GCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACACATAAGTCAAATTT
1 GCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACACAAAAGTCAAATTT
* *
300878 GCAACACTGAATTTCAAATTCGCAAC
1 GCAACACAGAA-GTCAAATTCGCAAC
300904 TGAATTTCAA
Statistics
Matches: 80, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
60 67 0.84
61 13 0.16
ACGTcount: A:0.45, C:0.25, G:0.12, T:0.18
Consensus pattern (60 bp):
GCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACACAAAAGTCAAATTT
Found at i:300971 original size:39 final size:38
Alignment explanation
Indices: 300870--300980 Score: 134
Period size: 39 Copynumber: 2.8 Consensus size: 38
300860 AACACATAAG
*
300870 TCAAATTTGCAACACTGAATTTCAAATTCGCAACTGAATT
1 TCAAATTCGCAACAC-GAATTT-AAATTCGCAACTGAATT
* *
300910 TCAAATTCGCAAC-TGAATTTTAAATTCGCAACTCGATTT
1 TCAAATTCGCAACACGAA-TTTAAATTCGCAACT-GAATT
* *
300949 TCGAATTCGCAACACGAATTTAATTTCGCAAC
1 TCAAATTCGCAACACGAATTTAAATTCGCAAC
300981 ATGTTTTAGT
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
38 15 0.24
39 32 0.52
40 15 0.24
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (38 bp):
TCAAATTCGCAACACGAATTTAAATTCGCAACTGAATT
Found at i:300981 original size:19 final size:20
Alignment explanation
Indices: 300715--300981 Score: 192
Period size: 20 Copynumber: 13.4 Consensus size: 20
300705 GATCTCCTAT
*
300715 TTCGCAACAC-AGTTTCCAAA
1 TTCGCAACACGAATTT-CAAA
**
300735 TTCGCAACATAAATTT-ATAA
1 TTCGCAACACGAATTTCA-AA
* *
300755 ATCGCAACACCGAA-GTCAAA
1 TTCGCAACA-CGAATTTCAAA
*
300775 TTCGCAACACAGAA-GTCAAA
1 TTCGCAACAC-GAATTTCAAA
* **
300795 TTCGCAACACAAAAGTCAAA
1 TTCGCAACACGAATTTCAAA
* *
300815 TTTGCAACACAGAA-GTCAAA
1 TTCGCAACAC-GAATTTCAAA
* **
300835 TTCGCAACACAAAAGTCAAA
1 TTCGCAACACGAATTTCAAA
**
300855 TTCGCAACAC-ATAAGTCAAA
1 TTCGCAACACGA-ATTTCAAA
*
300875 TTTGCAACACTGAATTTCAAA
1 TTCGCAACAC-GAATTTCAAA
*
300896 TTCGCAAC-TGAATTTCAAA
1 TTCGCAACACGAATTTCAAA
* *
300915 TTCGCAAC-TGAATTTTAAA
1 TTCGCAACACGAATTTCAAA
* * *
300934 TTCGCAACTCGATTTTCGAA
1 TTCGCAACACGAATTTCAAA
*
300954 TTCGCAACACGAATTT-AAT
1 TTCGCAACACGAATTTCAAA
300973 TTCGCAACA
1 TTCGCAACA
300982 TGTTTTAGTT
Statistics
Matches: 209, Mismatches: 26, Indels: 25
0.80 0.10 0.10
Matches are distributed among these distances:
19 53 0.25
20 133 0.64
21 22 0.11
22 1 0.00
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.25
Consensus pattern (20 bp):
TTCGCAACACGAATTTCAAA
Found at i:304250 original size:18 final size:18
Alignment explanation
Indices: 304227--304262 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
304217 AAGCAAAAGG
*
304227 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
304245 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
304263 CAACCGGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:304487 original size:20 final size:20
Alignment explanation
Indices: 304462--304510 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
304452 GTTTTCCTTG
*
304462 AATTCGCAACGCGAAAGTCA
1 AATTCGCAACGCGAAAATCA
*
304482 AATTCGTAACGCGAAAATCA
1 AATTCGCAACGCGAAAATCA
*
304502 AAATCGCAA
1 AATTCGCAA
304511 ACCGGAAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.45, C:0.22, G:0.16, T:0.16
Consensus pattern (20 bp):
AATTCGCAACGCGAAAATCA
Found at i:304552 original size:20 final size:20
Alignment explanation
Indices: 304529--304570 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
304519 TCGCAATGCG
304529 AATTTGACTTTCGCGTTACA
1 AATTTGACTTTCGCGTTACA
* *
304549 AATTTGATTTTCGCGTTGCA
1 AATTTGACTTTCGCGTTACA
304569 AA
1 AA
304571 AGTGTACCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (20 bp):
AATTTGACTTTCGCGTTACA
Found at i:306169 original size:21 final size:20
Alignment explanation
Indices: 306145--306220 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 20
306135 GCGGGCGAGA
306145 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAACGATGA-AGGGG
*
306166 CCTCTTGAACGGTGGAAGGGG
1 CCTCTTGAACGAT-GAAGGGG
* *
306187 CCTGTTCG-ATGATGAGAGGGG
1 CCTCTT-GAACGATGA-AGGGG
306208 CCTCTTGAACGAT
1 CCTCTTGAACGAT
306221 AGGAAGTGCC
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
20 3 0.07
21 39 0.87
22 3 0.07
ACGTcount: A:0.21, C:0.21, G:0.36, T:0.22
Consensus pattern (20 bp):
CCTCTTGAACGATGAAGGGG
Found at i:306241 original size:42 final size:42
Alignment explanation
Indices: 306145--306241 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
306135 GCGGGCGAGA
* *
306145 CCTCTTGAACGATGACAGGGGCCTCTTGAACGGTGGAAGGGG
1 CCTCTTGAATGATGACAGGGGCCTCTTGAACGATGGAAGGGG
* * *
306187 CCTGTTCG-ATGATGAGAGGGGCCTCTTGAACGATAGGAA-GTG
1 CCTCTT-GAATGATGACAGGGGCCTCTTGAACGAT-GGAAGGGG
306229 CCTCTTGAATGAT
1 CCTCTTGAATGAT
306242 AATAGGTGCA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
41 1 0.02
42 40 0.87
43 5 0.11
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.24
Consensus pattern (42 bp):
CCTCTTGAATGATGACAGGGGCCTCTTGAACGATGGAAGGGG
Found at i:306413 original size:20 final size:20
Alignment explanation
Indices: 306388--306426 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
306378 GGCCGCTAAA
* *
306388 AGTAAATTAATACATAAATC
1 AGTAAATAAATAAATAAATC
306408 AGTAAATAAATAAATAAAT
1 AGTAAATAAATAAATAAAT
306427 AATGTCGAAA
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:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (20 bp):
AGTAAATAAATAAATAAATC
Found at i:308372 original size:19 final size:20
Alignment explanation
Indices: 308323--308361 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
308313 TAACTTGAAA
*
308323 ATGAAAATCGCAACGCGAAC
1 ATGAAAATCGCAACGCAAAC
308343 ATGAAAATCGCAACGCAAA
1 ATGAAAATCGCAACGCAAA
308362 ACTAAAATCG
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:0.49, C:0.23, G:0.18, T:0.10
Consensus pattern (20 bp):
ATGAAAATCGCAACGCAAAC
Found at i:308416 original size:20 final size:20
Alignment explanation
Indices: 308369--308419 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
308359 AAAACTAAAA
* *
308369 TCGCGTTACGATTTTTATTT
1 TCGCGTTGCGATTTTCATTT
308389 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCATTT
*
308409 TCGTGTTGCGA
1 TCGCGTTGCGA
308420 ATTTATGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.49
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATTT
Found at i:308430 original size:20 final size:19
Alignment explanation
Indices: 308382--308430 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
308372 CGTTACGATT
*
308382 TTTATTTTCGCGTTGCGAT
1 TTTATTTTCGCGTTGCGAA
*
308401 TTTCATTTTCGTGTTGCGAA
1 TTT-ATTTTCGCGTTGCGAA
308421 TTTATGTTTC
1 TTTAT-TTTC
308431 AAAAACTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.12, C:0.14, G:0.18, T:0.55
Consensus pattern (19 bp):
TTTATTTTCGCGTTGCGAA
Found at i:308769 original size:22 final size:22
Alignment explanation
Indices: 308739--308782 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
308729 GATGGAGATA
*
308739 GACGGATTTCGCCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
*
308761 GACGAATTTCGTCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
308783 AACAGATGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGAATTTCGCCGGAGATGGG
Found at i:308969 original size:20 final size:20
Alignment explanation
Indices: 308944--309069 Score: 198
Period size: 20 Copynumber: 6.3 Consensus size: 20
308934 TAAACGCGCT
308944 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTTTGTG
308964 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTTTGTG
* *
308984 TTGCAAATTTGACTTATGTG
1 TTGCGAATTTGACTTTTGTG
309004 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTTTGTG
* *
309024 TTGCAAATTTGACTTCTGTG
1 TTGCGAATTTGACTTTTGTG
* *
309044 TTGTGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTTTGTG
309064 TTGCGA
1 TTGCGA
309070 TTTACATAAT
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 97 1.00
ACGTcount: A:0.17, C:0.11, G:0.24, T:0.48
Consensus pattern (20 bp):
TTGCGAATTTGACTTTTGTG
Found at i:309087 original size:60 final size:60
Alignment explanation
Indices: 308944--309094 Score: 171
Period size: 60 Copynumber: 2.5 Consensus size: 60
308934 TAAACGCGCT
* * * * *
308944 TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTTTGTGTTGCAAATTTGACTTATGTG
1 TTGCGAATTTGACTATCGCGTTGCAAATTTGACTTCTGTGTTGCAAATTTGACTTATGTG
* * * ** *
309004 TTGCGAATTTGACTTTTGTGTTGCAAATTTGACTTCTGTGTTGTGAATTTGACTTCTGTG
1 TTGCGAATTTGACTATCGCGTTGCAAATTTGACTTCTGTGTTGCAAATTTGACTTATGTG
309064 TTGCG-ATTT-ACATAATCGCGTTGCAAATTTG
1 TTGCGAATTTGAC-T-ATCGCGTTGCAAATTTG
309095 GAAACTGGGT
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
58 2 0.02
59 5 0.06
60 74 0.91
ACGTcount: A:0.19, C:0.12, G:0.23, T:0.46
Consensus pattern (60 bp):
TTGCGAATTTGACTATCGCGTTGCAAATTTGACTTCTGTGTTGCAAATTTGACTTATGTG
Found at i:310185 original size:21 final size:21
Alignment explanation
Indices: 310137--310194 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
310127 CAGGGACCAT
* *
310137 CATGTCTATCAACAAATATTGT
1 CATG-CTATCAGCAAATATTGA
* *
310159 CGTGCTATCAGCAAATCTTGA
1 CATGCTATCAGCAAATATTGA
*
310180 CATGCTAACAGCAAA
1 CATGCTATCAGCAAA
310195 ACTGATGGCC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 27 0.90
22 3 0.10
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (21 bp):
CATGCTATCAGCAAATATTGA
Found at i:316261 original size:65 final size:65
Alignment explanation
Indices: 316135--316286 Score: 193
Period size: 65 Copynumber: 2.4 Consensus size: 65
316125 AGAGTGCACC
*
316135 GATGCATCAAGTGCATTCGAT-TTTTCAAAATAGCCAAAGTGCATCGATGCATGGCTGGTGCATT
1 GATGCATCAAATGCATTCGATGTTTTCAAAATAGCCAAAGTGCATCGATGCATGGCTGGTGCATT
* ** * *
316199 GATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-TATGTGCA
1 GATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCAAAGTGCATCGATGCATGGCT-GGTGCA
316262 TT
64 TT
* *
316264 GATGCATGAAATGCATTCAATGT
1 GATGCATCAAATGCATTCGATGT
316287 CCAATTTAAT
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
64 21 0.27
65 53 0.69
66 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (65 bp):
GATGCATCAAATGCATTCGATGTTTTCAAAATAGCCAAAGTGCATCGATGCATGGCTGGTGCATT
Found at i:316326 original size:65 final size:63
Alignment explanation
Indices: 316172--316337 Score: 167
Period size: 65 Copynumber: 2.6 Consensus size: 63
316162 AAATAGCCAA
* * *
316172 AGTGCATCGATGCATGGCTGGTGCATTGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTC
1 AGTGCATCGATGCATGGTTGGTGCATTGATGCATCAAATGCATTCAATG-TTCCATAAAAT-CTC
* * **
316237 AGTGCATCGGTGCATGGTAT-GTGCATTGATGCATGAAATGCATTCAATG-TCCAATTTAAT-TC
1 AGTGCATCGATGCATGGT-TGGTGCATTGATGCATCAAATGCATTCAATGTTCC-ATAAAATCTC
* *
316299 ATGGTGCATCGATGCATGGATTGGTGCATCGGTGCATCA
1 A--GTGCATCGATGCATGG-TTGGTGCATTGATGCATCA
316338 CTTTGATAAA
Statistics
Matches: 84, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
62 3 0.04
63 2 0.02
64 21 0.25
65 57 0.68
66 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (63 bp):
AGTGCATCGATGCATGGTTGGTGCATTGATGCATCAAATGCATTCAATGTTCCATAAAATCTC
Found at i:316610 original size:92 final size:89
Alignment explanation
Indices: 316451--316636 Score: 338
Period size: 92 Copynumber: 2.1 Consensus size: 89
316441 TTTGACTTTG
316451 AACTT-GAAAGACTTGGTAATAATTTGATATTCGATTAATAAATCGAATATACTTAGAAAATCAT
1 AACTTAGAAAGACTTGGTAATAATTTGATATTCGATTAATAAATCGAATATACTTAGAAAATCAT
316515 TTGTAAAATCTTAAAATTCATTTA
66 TTGTAAAATCTTAAAATTCATTTA
316539 AACTTAGAAAGACTTGGAGTAATAATTTGATATTCGATTAATTAAATCGAATATACTTAGAAAAT
1 AACTTAGAAAGACTT-G-GTAATAATTTGATATTCGATTAA-TAAATCGAATATACTTAGAAAAT
316604 CATTTGTAAAATCTTAAAATTCATTTA
63 CATTTGTAAAATCTTAAAATTCATTTA
316631 AACTTA
1 AACTTA
316637 ATTTGTTATA
Statistics
Matches: 94, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
88 5 0.05
89 9 0.10
90 1 0.01
91 23 0.24
92 56 0.60
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (89 bp):
AACTTAGAAAGACTTGGTAATAATTTGATATTCGATTAATAAATCGAATATACTTAGAAAATCAT
TTGTAAAATCTTAAAATTCATTTA
Found at i:317490 original size:21 final size:21
Alignment explanation
Indices: 317466--317509 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
317456 CCAGAGGAGG
*
317466 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
* *
317487 AGGAGCAGCTCGTGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
317508 AG
1 AG
317510 CTCCCGGGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.16, G:0.41, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAGCT
Found at i:318898 original size:23 final size:23
Alignment explanation
Indices: 318868--318948 Score: 105
Period size: 23 Copynumber: 3.7 Consensus size: 23
318858 TGCATGACCC
318868 TGTGCATCGATGCACATTCAAGG
1 TGTGCATCGATGCACATTCAAGG
* * *
318891 TGTGCATCGGTGCACCTTCATGG
1 TGTGCATCGATGCACATTCAAGG
318914 TGT--ATCGATGCACATTCAAGG
1 TGTGCATCGATGCACATTCAAGG
*
318935 -ATGCATCGATGCAC
1 TGTGCATCGATGCAC
318949 TGTTAGGTGC
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
20 1 0.02
21 15 0.31
22 10 0.20
23 23 0.47
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.27
Consensus pattern (23 bp):
TGTGCATCGATGCACATTCAAGG
Found at i:322002 original size:24 final size:24
Alignment explanation
Indices: 321934--322003 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
321924 GAACTAGGCA
321934 TAAATTACTCATATCAATAGAGTC
1 TAAATTACTCATATCAATAGAGTC
* * *
321958 TAAA-TGCACA-ATC-AT----TA
1 TAAATTACTCATATCAATAGAGTC
321975 TAAATTACTCATATCAATAGAGTC
1 TAAATTACTCATATCAATAGAGTC
321999 TAAAT
1 TAAAT
322004 GCACCATGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 14
0.62 0.11 0.26
Matches are distributed among these distances:
17 5 0.15
18 4 0.12
19 3 0.09
20 2 0.06
21 2 0.06
22 3 0.09
23 4 0.12
24 10 0.30
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (24 bp):
TAAATTACTCATATCAATAGAGTC
Found at i:324800 original size:64 final size:63
Alignment explanation
Indices: 324728--324907 Score: 168
Period size: 65 Copynumber: 2.8 Consensus size: 63
324718 TTGGGCCCTT
* *
324728 AGTGCATCGGTGCA-CTAAGAGTGCATCGATGCATCAAGTGCATTTGATG-TTTCA-AAATAGCC
1 AGTGCATCGGTGCAGCT--G-GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-AGCC
324790 AA
62 AA
* * **
324792 AGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTC
1 AGTGCATCGGTGCA--GCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCAA
* * * * *
324857 AGTGCATCGGTGCATGGTATGCGCATCAATGCATGAAATGCATTCGATGTT
1 AGTGCATCGGTGCA-GCT-GGTGCATCGATGCATCAAATGCATTCGATGTT
324908 CAATTTAATT
Statistics
Matches: 97, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
64 42 0.43
65 50 0.52
66 3 0.03
67 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (63 bp):
AGTGCATCGGTGCAGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCAA
Found at i:324948 original size:65 final size:63
Alignment explanation
Indices: 324748--324957 Score: 187
Period size: 65 Copynumber: 3.3 Consensus size: 63
324738 TGCACTAAGA
* * * * *
324748 GTGCATCGATGCATCAAGTGCATTTGATGTTTCA-AAATAGC-CAAAGTGCATCGATGCATGGCT
1 GTGCATCAATGCATCAAATGCATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGTT
324811 G
63 G
* *
324812 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCAATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-T
324877 -
63 G
* * **
324877 GCGCATCAATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATCAATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-T
324940 TG
62 TG
*
324942 GTGCATCAGTGCATCA
1 GTGCATCAATGCATCA
324958 CTTTGATAAA
Statistics
Matches: 122, Mismatches: 14, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 48 0.39
65 62 0.51
66 5 0.04
67 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.30
Consensus pattern (63 bp):
GTGCATCAATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:326202 original size:19 final size:19
Alignment explanation
Indices: 326166--326241 Score: 53
Period size: 19 Copynumber: 3.7 Consensus size: 19
326156 AATGATTTTG
**
326166 TTTTAAAAATTAAATTAGA
1 TTTTAAAAAAGAAATTAGA
*
326185 TTTTAAAAAAGAATTTAGA
1 TTTTAAAAAAGAAATTAGA
* * *
326204 GCTTTCAAAAATGAGAAATGAAAA
1 --TTTTAAAAA--AGAAAT-TAGA
326228 TTTTAAAAAAGAAA
1 TTTTAAAAAAGAAA
326242 ATTTTGATTT
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
19 16 0.36
20 5 0.11
21 8 0.18
22 8 0.18
23 5 0.11
24 2 0.05
ACGTcount: A:0.55, C:0.03, G:0.11, T:0.32
Consensus pattern (19 bp):
TTTTAAAAAAGAAATTAGA
Found at i:328031 original size:20 final size:20
Alignment explanation
Indices: 327986--328035 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
327976 TTTCAGTTAA
*
327986 TTAAAATATTTTTAAAGTGT
1 TTAAAATATGTTTAAAGTGT
* *
328006 TAAAAATGTGTTTAAAGCT-T
1 TTAAAATATGTTTAAAG-TGT
328026 TTAAAATATG
1 TTAAAATATG
328036 AAAAACACTA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (20 bp):
TTAAAATATGTTTAAAGTGT
Found at i:331391 original size:21 final size:21
Alignment explanation
Indices: 331361--331416 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
331351 CGGGTCGAGT
*
331361 CGGGTCAACGGGTCAGGTAAA
1 CGGGTAAACGGGTCAGGTAAA
331382 CGGGTAAACGGGTCAGGTAAA
1 CGGGTAAACGGGTCAGGTAAA
331403 CGGGTAAACGGGTC
1 CGGGTAAACGGGTC
331417 GTGACCGGTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.29, C:0.18, G:0.39, T:0.14
Consensus pattern (21 bp):
CGGGTAAACGGGTCAGGTAAA
Found at i:331445 original size:20 final size:19
Alignment explanation
Indices: 331420--331464 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
331410 ACGGGTCGTG
331420 ACCGGTCAAACCGGTTCAAA
1 ACCGGTCAAACCGG-TCAAA
* *
331440 ACCGGTTACACCGGTCAAA
1 ACCGGTCAAACCGGTCAAA
331459 ACCGGT
1 ACCGGT
331465 TTTCAGCGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAACCGGTCAAA
Found at i:338671 original size:9 final size:9
Alignment explanation
Indices: 338657--338714 Score: 71
Period size: 9 Copynumber: 6.1 Consensus size: 9
338647 ACGGGTCGTG
338657 ACCGGTCAA
1 ACCGGTCAA
338666 ACCGGTCAA
1 ACCGGTCAA
338675 ACCGGTCAAA
1 ACCGGTC-AA
*
338685 ATCGGTTCAAA
1 ACCGG-TC-AA
*
338696 ACCGGTTAA
1 ACCGGTCAA
338705 ACCGGTCAA
1 ACCGGTCAA
338714 A
1 A
338715 ATCGGTTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
9 27 0.63
10 7 0.16
11 9 0.21
ACGTcount: A:0.36, C:0.28, G:0.21, T:0.16
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:338696 original size:11 final size:11
Alignment explanation
Indices: 338664--338721 Score: 56
Period size: 9 Copynumber: 5.8 Consensus size: 11
338654 GTGACCGGTC
338664 AAACCGG-TC-
1 AAACCGGTTCA
338673 AAACCGG-TCA
1 AAACCGGTTCA
*
338683 AAATCGGTTCA
1 AAACCGGTTCA
338694 AAACCGGTT--
1 AAACCGGTTCA
338703 AAACCGG-TCA
1 AAACCGGTTCA
*
338713 AAATCGGTT
1 AAACCGGTT
338722 TTCAGCGTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
8 1 0.02
9 16 0.39
10 12 0.29
11 12 0.29
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (11 bp):
AAACCGGTTCA
Found at i:338700 original size:30 final size:30
Alignment explanation
Indices: 338664--338721 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
338654 GTGACCGGTC
338664 AAACCGGTCAAACCGGTCAAAATCGGTTCA
1 AAACCGGTCAAACCGGTCAAAATCGGTTCA
*
338694 AAACCGGTTAAACCGGTCAAAATCGGTT
1 AAACCGGTCAAACCGGTCAAAATCGGTT
338722 TTCAGCGTTC
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:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (30 bp):
AAACCGGTCAAACCGGTCAAAATCGGTTCA
Found at i:338721 original size:19 final size:19
Alignment explanation
Indices: 338657--338721 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
338647 ACGGGTCGTG
*
338657 ACCGGTCAAACCGGTC-AA
1 ACCGGTTAAACCGGTCAAA
* *
338675 ACCGGTCAAAATCGGTTCAAA
1 ACCGGT-TAAACCGG-TCAAA
338696 ACCGGTTAAACCGGTCAAA
1 ACCGGTTAAACCGGTCAAA
*
338715 ATCGGTT
1 ACCGGTT
338722 TTCAGCGTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
18 6 0.15
19 17 0.44
20 8 0.21
21 8 0.21
ACGTcount: A:0.34, C:0.26, G:0.22, T:0.18
Consensus pattern (19 bp):
ACCGGTTAAACCGGTCAAA
Found at i:344124 original size:60 final size:60
Alignment explanation
Indices: 344010--344142 Score: 137
Period size: 60 Copynumber: 2.2 Consensus size: 60
344000 GAAAAGTTTC
* * * * * *
344010 ATTTCGTA-ACTTTTAATAGTCGAGGGATTTAAAAAAGTAATATTATGTAGTCGGAGGACA
1 ATTT-GTATACTTTTAATAGTCGAGGAACTTAAAAAAGCAATACTATATAATCGGAGGACA
* * *
344070 ATTT-TATAGCTTTTAATAGTCGAGGAACTTAATAAAA-CAATACTCTATAATCGGATGACC
1 ATTTGTATA-CTTTTAATAGTCGAGGAACTTAA-AAAAGCAATACTATATAATCGGAGGACA
344130 ATTTGTATACTTT
1 ATTTGTATACTTT
344143 ACCCTTTAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
58 2 0.03
59 1 0.02
60 49 0.82
61 8 0.13
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (60 bp):
ATTTGTATACTTTTAATAGTCGAGGAACTTAAAAAAGCAATACTATATAATCGGAGGACA
Found at i:346824 original size:27 final size:26
Alignment explanation
Indices: 346766--346824 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
346756 ATTCATTATT
*
346766 TATTAAAATAACAATATTATAATATA
1 TATTAAAATAAAAATATTATAATATA
*
346792 TAATTAAAATAAAAAATTTTATTAA-ATA
1 T-ATTAAAAT-AAAAATATTA-TAATATA
346820 TATTA
1 TATTA
346825 GTTACTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
26 1 0.04
27 12 0.43
28 12 0.43
29 3 0.11
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (26 bp):
TATTAAAATAAAAATATTATAATATA
Found at i:347023 original size:28 final size:28
Alignment explanation
Indices: 346992--347054 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
346982 ATTAATAATT
346992 TATTATTAGAATAAAATGTAA-TATCA-TA
1 TATTATTAGAATAAAAT-TAAGTAT-ATTA
* *
347020 TATTATTATAATATAATTAAGTATATTA
1 TATTATTAGAATAAAATTAAGTATATTA
347048 TATTATT
1 TATTATT
347055 GAAAATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 4 0.13
28 27 0.87
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (28 bp):
TATTATTAGAATAAAATTAAGTATATTA
Found at i:347897 original size:2 final size:2
Alignment explanation
Indices: 347890--347916 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
347880 AAATTACCGT
347890 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
347917 TCTCGTATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:348075 original size:26 final size:26
Alignment explanation
Indices: 348029--348078 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
348019 TTCTCTCTAA
*
348029 AAGAAAATATTTTGATCTTTGAAGTG
1 AAGAAAATATTTCGATCTTTGAAGTG
*
348055 AAGAAAAT-TTATCGATTTTTGAAG
1 AAGAAAATATT-TCGATCTTTGAAG
348079 GTTTATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.10
26 19 0.90
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (26 bp):
AAGAAAATATTTCGATCTTTGAAGTG
Found at i:350593 original size:2 final size:2
Alignment explanation
Indices: 350586--350612 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
350576 AAATAAATAA
350586 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
350613 ATTTTTAATA
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:354299 original size:101 final size:100
Alignment explanation
Indices: 353657--354533 Score: 436
Period size: 102 Copynumber: 8.7 Consensus size: 100
353647 TGCGATTTTA
* * ** * * * * *
353657 TATAACAATAAAGGTAGCGTCTTTTTATATTGTCAACCGTGTAAGTTATATGCGTGAAA-CATGT
1 TATAACAATACATGTAGCACCTTTTTATATTGTCAACTGTTTAAGTTATATG-TTGAAACCTTTT
* * * *
353721 TTCATTAATAACATGTAAGACAAAA-AGAGTTT-TATT
65 TTTATTAA-AAAATGTAAGACAAAACA-TGTTTAAATT
* * * ** * * * * *
353757 TATAAAAATA-TTGGTAGTAAATTTTTATAGTGTCCACCGTTTACGTGATATGATTGAAACC-TT
1 TATAACAATACAT-GTAGCACCTTTTTATATTGTCAACTGTTTAAGTTATATG-TTGAAACCTTT
* * * *
353820 TATTATTACAAAATTGTAAGAGATAACATGTTTAAATT
64 TTTTATTA-AAAAATGTAAGACAAAACATGTTTAAATT
* * ** * * * *
353858 TATAACAATACAAGTAGCGCCTTTTATATATTGTCAACCATGTAAGTTACACGTATGAAA-CTTG
1 TATAACAATACATGTAGCACCTTTT-TATATTGTCAACTGTTTAAGTTATATGT-TGAAACCTTT
* * ** * * *
353922 TGTCATTATGGACATGTAAGACAAAACATGGTTATATT
64 TTTTATTA-AAAAATGTAAGACAAAACATGTTTAAATT
* ** * *
353960 TATAACAATGA-AGGTAGTGCCTTTTTTATAGTGTCAA-TCGTTTACA-TGATATGTTTGAAACC
1 TATAACAAT-ACATGTAGCACC-TTTTTATATTGTCAACT-GTTTA-AGTTATATG-TTGAAACC
* * * *
354022 -TTTATTATTAACAAACTGTAACACAAAACAGGTTTAAATT
61 TTTTTTTATTAA-AAAATGTAAGACAAAACATGTTTAAATT
* ** * * ** * * ** * * * * *
354062 TTTAACAATTTAGGTTGTGCCATTTTATAATGGAAATTGTGTGAGTTATATGTGTGAAA-CATGT
1 TATAACAATACATGTAGCACCTTTTTATATTGTCAACTGTTTAAGTTATATGT-TGAAACCTTTT
* * * ** * * *
354126 TTCATTATGAACATGTATTACAAAACAAGCTTATATT
65 TTTATTA-AAAAATGTAAGACAAAACATGTTTAAATT
* * *
354163 TATAAACAATACATGTAGCACCTTTTTATAGTGTCAACTGTTTACGTTATATGTTCAAAACCTTT
1 TAT-AACAATACATGTAGCACCTTTTTATATTGTCAACTGTTTAAGTTATATGTT-GAAACCTTT
354228 TTTTATTAAAATAATGTAAGA-AAAACATGTTTAAATT
64 TTTTATTAAAA-AATGTAAGACAAAACATGTTTAAATT
*** * * *
354265 TATAACAATACATGTAGCGTTTTTTTATATTGTCAACCGTGTAAGTTATATATATGAAA-CTTTT
1 TATAACAATACATGTAGCACCTTTTTATATTGTCAACTGTTTAAGTTATATGT-TGAAACCTTTT
* * * * * **
354329 TTCATTATGAACATGTAAGACTAAAC-TAGGTTATGTT
65 TTTATTA-AAAAATGTAAGACAAAACAT-GTTTAAATT
* * * * * * *
354366 TATAACAATACAGGTAACA-CTATTTTTTAATGTCAA-TCGTTTAAATGATAAGTTTGAAACCTT
1 TATAACAATACATGTAGCACCT-TTTTATATTGTCAACT-GTTTAAGTTATATG-TTGAAACCTT
* * * * *
354429 ATTTTATTAATAAACTATAAGAGAAAACATGTTAAAATT
63 TTTTTATTAA-AAAATGTAAGACAAAACATGTTTAAATT
* * *
354468 TATAACAATACAAGTAGCACCTTTTTATATTGTCAACAGTTTAAGTTATATGTCTGAAACATTTT
1 TATAACAATACATGTAGCACCTTTTTATATTGTCAACTGTTTAAGTTATATGT-TGAAACCTTTT
354533 T
65 T
354534 CGTTATGGTT
Statistics
Matches: 571, Mismatches: 167, Indels: 76
0.70 0.21 0.09
Matches are distributed among these distances:
100 91 0.16
101 181 0.32
102 273 0.48
103 26 0.05
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.38
Consensus pattern (100 bp):
TATAACAATACATGTAGCACCTTTTTATATTGTCAACTGTTTAAGTTATATGTTGAAACCTTTTT
TTATTAAAAAATGTAAGACAAAACATGTTTAAATT
Found at i:354517 original size:406 final size:403
Alignment explanation
Indices: 353657--354540 Score: 1025
Period size: 406 Copynumber: 2.2 Consensus size: 403
353647 TGCGATTTTA
* * *
353657 TATAACAATAAAGGTAGCGTCTTTTTATATTGTCAACCGTGTAAGTTATATGCGTGAAACATGTT
1 TATAACAATAAA-GTAGCGCCTTTTTATATTGTCAACAGTGTAAGTTATATGTGTGAAACATGTT
* * *
353722 TCATTAAT-AACATGTAAGACAAAAAGAGTTTTATTTATAAAAATATTGGTAGTAAATTTTTATA
65 TCATT-ATGAACATGTAAGACAAAAAGAGTTATATTTATAAAAATAATGGTAGCAAATTTTTATA
* * * *
353786 GTGTCCACCGTTTACGTGATATGATTGAAACCTTTATTATTACAAAATTGTAAGAGATAACATGT
129 GTGTCAACCGTTTACGTGATATGATTAAAACCTTTATTATTACAAAAATGTAAGAGAAAACATGT
*
353851 TTAAATTTATAACAATACAAGTAGCGCCTTTTATATATTGTCAACCATGTAAGTTACACGTATGA
194 TTAAATTTATAACAATACAAGTAGCGCCTTTTATATATTGTCAACCATGTAAGTTACACATATGA
* *
353916 AACTTGTGTCATTATGGACATGTAAGACAAAACATGGTTATATTTATAACAATGAAGGTAGTGCC
259 AACTTGTGTCATTATGAACATGTAAGACAAAACATGGTTATATTTATAACAATGAAGGTAG-ACC
* * * *
353981 TTTTTTATAGTGTCAATCGTTTACATGATATGTTTGAAACCTTTATTATTAACAAACTGTAACAC
323 TTTTTTATAATGTCAATCGTTTAAATGATAAGTTTGAAACCTTTATTATTAACAAACTATAACAC
*
354046 AAAACAGGTTTAAATT
388 AAAACAGGTTAAAATT
* * * * * * * ** ** *
354062 TTTAACAATTTAGGTTGTGCCATTTTATAATGGAAATTGTGTGAGTTATATGTGTGAAACATGTT
1 TATAACAA-TAAAGTAGCGCCTTTTTATATTGTCAACAGTGTAAGTTATATGTGTGAAACATGTT
** **
354127 TCATTATGAACATGTATTACAAAACA-AGCTTATATTTATAAACAATACAT-GTAGCACCTTTTT
65 TCATTATGAACATGTAAGACAAAA-AGAG-TTATATTTATAAA-AATA-ATGGTAGCAAATTTTT
* * *
354190 ATAGTGTCAACTGTTTACGTTATATG-TTCAAAACCTTTTTTTATTA-AAATAATGTAAGA-AAA
126 ATAGTGTCAACCGTTTACGTGATATGATT-AAAACC-TTTATTATTACAAA-AATGTAAGAGAAA
* * * * * *
354252 ACATGTTTAAATTTATAACAATACATGTAGCG-TTTTTTTATATTGTCAACCGTGTAAGTTATAT
188 ACATGTTTAAATTTATAACAATACAAGTAGCGCCTTTTATATATTGTCAACCATGTAAGTTACAC
* * * *
354316 ATATGAAACTTTTTTCATTATGAACATGTAAGACTAAAC-TAGGTTATGTTTATAACAAT-ACAG
253 ATATGAAACTTGTGTCATTATGAACATGTAAGACAAAACAT-GGTTATATTTATAACAATGA-AG
* *
354379 GTA-ACACTATTTTT-TAATGTCAATCGTTTAAATGATAAGTTTGAAACCTTATTTTATTAATAA
316 GTAGAC-CT-TTTTTATAATGTCAATCGTTTAAATGATAAGTTTGAAACCTT-TATTATTAACAA
* * *
354442 ACTATAAGAGAAAACATGTTAAAATT
378 ACTATAACACAAAACAGGTTAAAATT
* * * *
354468 TATAACAATACAAGTAGCACCTTTTTATATTGTCAACAGTTTAAGTTATATGTCTGAAACATTTT
1 TATAACAATA-AAGTAGCGCCTTTTTATATTGTCAACAGTGTAAGTTATATGTGTGAAACATGTT
*
354533 TCGTTATG
65 TCATTATG
354541 GTTATTTATG
Statistics
Matches: 396, Mismatches: 68, Indels: 29
0.80 0.14 0.06
Matches are distributed among these distances:
404 3 0.01
405 107 0.27
406 190 0.48
407 78 0.20
408 18 0.05
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (403 bp):
TATAACAATAAAGTAGCGCCTTTTTATATTGTCAACAGTGTAAGTTATATGTGTGAAACATGTTT
CATTATGAACATGTAAGACAAAAAGAGTTATATTTATAAAAATAATGGTAGCAAATTTTTATAGT
GTCAACCGTTTACGTGATATGATTAAAACCTTTATTATTACAAAAATGTAAGAGAAAACATGTTT
AAATTTATAACAATACAAGTAGCGCCTTTTATATATTGTCAACCATGTAAGTTACACATATGAAA
CTTGTGTCATTATGAACATGTAAGACAAAACATGGTTATATTTATAACAATGAAGGTAGACCTTT
TTTATAATGTCAATCGTTTAAATGATAAGTTTGAAACCTTTATTATTAACAAACTATAACACAAA
ACAGGTTAAAATT
Found at i:354577 original size:203 final size:200
Alignment explanation
Indices: 353657--354585 Score: 881
Period size: 203 Copynumber: 4.6 Consensus size: 200
353647 TGCGATTTTA
* * ** *
353657 TATAACAATA-AAGGTAGCGTCTTTTTATATTGTCAACCGTGTAAGTTATATGCGTGAAACATGT
1 TATAACAATACAA-GTAGCGCCTTTTTATATTGTCAACAGTGTAAGTTATATGTATGAAACATTT
* * ** * *
353721 TTCATTAAT-AACATGTAAGACAAAA-A-GAGTTTTATTTATAAAAATATTGGTAGTAAATTTTT
65 TTCATT-ATGAACATGTAAGACAAAACATG-GTTATATTTATAACAATACAGGTAG-CACTTTTT
* * * * * * *
353783 ATAGTGTCCACCGTTTACGTGATATGATTGAAACCTTTATTATTACAAAATTGTAAGAGATAACA
127 TTAGTGTCAATCGTTTACATGATATGTTTGAAACCTTTATTATTA-AAAACTGTAAGAGAAAACA
353848 TGTTTAAATT
191 TGTTTAAATT
* *
353858 TATAACAATACAAGTAGCGCCTTTTATATATTGTCAACCA-TGTAAGTTACACGTATGAAAC-TT
1 TATAACAATACAAGTAGCGCCTTTT-TATATTGTCAA-CAGTGTAAGTTATATGTATGAAACATT
* *
353921 GTGTCATTATGGACATGTAAGACAAAACATGGTTATATTTATAACAATGA-AGGTAGTGC-CTTT
64 -TTTCATTATGAACATGTAAGACAAAACATGGTTATATTTATAACAAT-ACAGGTA--GCACTTT
* *
353984 TTTATAGTGTCAATCGTTTACATGATATGTTTGAAACCTTTATTATTAACAAACTGTAACACAAA
125 TTT-TAGTGTCAATCGTTTACATGATATGTTTGAAACCTTTATTATTAA-AAACTGTAAGAGAAA
*
354049 ACAGGTTTAAATT
188 ACATGTTTAAATT
* ** * * * * * ** ** * * *
354062 TTTAACAATTTAGGTTGTGCCATTTTATAATGGAAATTGTGTGAGTTATATGTGTGAAACATGTT
1 TATAACAATACAAGTAGCGCCTTTTTATATTGTCAACAGTGTAAGTTATATGTATGAAACATTTT
** * * * *
354127 TCATTATGAACATGTATTACAAAACAAGCTTATATTTATAAACAATACATGTAGCACCTTTTTAT
66 TCATTATGAACATGTAAGACAAAACATGGTTATATTTAT-AACAATACAGGTAGCA-CTTTTTTT
* * ** * *
354192 AGTGTCAA-CTGTTTACGTTATATGTTCAAAACCTTTTTTTATTAAAATAATGTAAGA-AAAACA
129 AGTGTCAATC-GTTTACATGATATGTTTGAAACC-TTTATTATTAAAA-ACTGTAAGAGAAAACA
354255 TGTTTAAATT
191 TGTTTAAATT
* ** * * *
354265 TATAACAATACATGTAGCGTTTTTTTATATTGTCAACCGTGTAAGTTATATATATGAAACTTTTT
1 TATAACAATACAAGTAGCGCCTTTTTATATTGTCAACAGTGTAAGTTATATGTATGAAACATTTT
* * *
354330 TCATTATGAACATGTAAGACTAAAC-TAGGTTATGTTTATAACAATACAGGTAACACTATTTTTT
66 TCATTATGAACATGTAAGACAAAACAT-GGTTATATTTATAACAATACAGGTAGCACT-TTTTTT
* * * * *
354394 AATGTCAATCGTTTAAATGATAAGTTTGAAACCTTATTTTATTAATAAACTATAAGAGAAAACAT
129 AGTGTCAATCGTTTACATGATATGTTTGAAACCTT-TATTATTAA-AAACTGTAAGAGAAAACAT
*
354459 GTTAAAATT
192 GTTTAAATT
* * *
354468 TATAACAATACAAGTAGCACCTTTTTATATTGTCAACAGTTTAAGTTATATGTCTGAAACATTTT
1 TATAACAATACAAGTAGCGCCTTTTTATATTGTCAACAGTGTAAGTTATATGTATGAAACATTTT
* *** * * * *
354533 TCGTTATGGTTATTTATGACAAAATATGGTTATATTTTTAACAATACAGGTAG
66 TCATTATGAACATGTAAGACAAAACATGGTTATATTTATAACAATACAGGTAG
354586 TGCCTTTTTA
Statistics
Matches: 585, Mismatches: 115, Indels: 54
0.78 0.15 0.07
Matches are distributed among these distances:
201 28 0.05
202 113 0.19
203 325 0.56
204 118 0.20
205 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.39
Consensus pattern (200 bp):
TATAACAATACAAGTAGCGCCTTTTTATATTGTCAACAGTGTAAGTTATATGTATGAAACATTTT
TCATTATGAACATGTAAGACAAAACATGGTTATATTTATAACAATACAGGTAGCACTTTTTTTAG
TGTCAATCGTTTACATGATATGTTTGAAACCTTTATTATTAAAAACTGTAAGAGAAAACATGTTT
AAATT
Found at i:355488 original size:205 final size:208
Alignment explanation
Indices: 355079--355587 Score: 618
Period size: 205 Copynumber: 2.5 Consensus size: 208
355069 ACCCGATAGT
* * ** * * *
355079 GCCTTTTTATATTGTCAACCCTGTAAGTTATATGTGAAAAACATGTTTCATTATGGATATGGAAG
1 GCCTTTTTATATTGTCAACCATTTAAGTTATATGTGTGAAACATGTTTTATTATGGTTATGTAAG
* *
355144 ACAAAACATGGTTATATTTATAACAATACA---AGTAATGCCTTCATATAGTGTCAACTGTTTAC
66 ACAAAACATGGTTATATTTATAACAATACAGGTAGTAACGCCTTCATATAGTGTCAACTATTTAC
* * *
355206 TTGATATGTTTGAAACCTTTATTATTAAGAAACTGTAACAGAAAATAGGTTTAAATTTATAATAA
131 GTGATATGTTTGAAACCTTTATTATTAAGAAACTGTAACAAAAAACAGGTTTAAATTTATAATAA
* *
355271 TAATATAGGTAGC
196 CAATACAGGTAGC
* * *
355284 GTCTTTTTATATTGTTAACCATTTAAGTTATATGCGTGAAACATGTTTTATTATGGTTATGTAAG
1 GCCTTTTTATATTGTCAACCATTTAAGTTATATGTGTGAAACATGTTTTATTATGGTTATGTAAG
* * * * * **
355349 GCAAAACAGGGATATGTTTATAACAATACAGGTAGTAGCGCCTTTTTATAGTGTCAACTATTTAC
66 ACAAAACATGGTTATATTTATAACAATACAGGTAGTAACGCCTTCATATAGTGTCAACTATTTAC
* * * * * *
355414 GTGATATGTTTGAAACCTTTTTTATTAATACATTGTAAGAAAAAACATGTTTAAA-TT-T-ATAA
131 GTGATATGTTTGAAACCTTTATTATTAAGAAACTGTAACAAAAAACAGGTTTAAATTTATAATAA
355476 CAATACAGGTAGC
196 CAATACAGGTAGC
* * * * *
355489 GCCTTCTTATATTGTGAACCGTTTAAGTTATATGTGTGAAACCT-TTTTCATTATGATTATGTAA
1 GCCTTTTTATATTGTCAACCATTTAAGTTATATGTGTGAAACATGTTTT-ATTATGGTTATGTAA
* * *
355553 GACGAAACATAGTTATATTTATAACAATATAGGTA
65 GACAAAACATGGTTATATTTATAACAATACAGGTA
355588 TCGCCTTCTT
Statistics
Matches: 256, Mismatches: 44, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
204 4 0.02
205 176 0.69
206 1 0.00
207 2 0.01
208 73 0.29
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.38
Consensus pattern (208 bp):
GCCTTTTTATATTGTCAACCATTTAAGTTATATGTGTGAAACATGTTTTATTATGGTTATGTAAG
ACAAAACATGGTTATATTTATAACAATACAGGTAGTAACGCCTTCATATAGTGTCAACTATTTAC
GTGATATGTTTGAAACCTTTATTATTAAGAAACTGTAACAAAAAACAGGTTTAAATTTATAATAA
CAATACAGGTAGC
Found at i:355552 original size:101 final size:100
Alignment explanation
Indices: 355079--355621 Score: 414
Period size: 101 Copynumber: 5.3 Consensus size: 100
355069 ACCCGATAGT
* * * ** * * *
355079 GCCTTTTTATATTGTCAACCCTGTAAGTTATATGTGAAAAACATGTTTCATTATGGA-TATGGAA
1 GCCTTCTTATATTGTCAACCGTTTAAGTTATATGTGTGAAACCT-TTTTATTAT-GATTATGTAA
* **
355143 GACAAAACATGGTTATATTTATAACAATACAAGTAAT
64 GACAAAACATGGTTATATTTATAACAATACAGGTAGC
* * * * * * *
355180 GCCTTCATATAGTGTCAACTGTTT-ACTTGATATGTTTGAAACCTTTATTATTAAGA-AACTGTA
1 GCCTTCTTATATTGTCAACCGTTTAAGTT-ATATGTGTGAAACCTTT-TTATTATGATTA-TGTA
* * * * * *
355243 ACAGAAAATA-GGTTTAAATTTATAATAATAATATAGGTAGC
63 AGACAAAACATGG-TTATA-TT-T-ATAACAATACAGGTAGC
* * * * * * *
355284 GTCTTTTTATATTGTTAACCATTTAAGTTATATGCGTGAAACATGTTTTATTATGGTTATGTAAG
1 GCCTTCTTATATTGTCAACCGTTTAAGTTATATGTGTGAAACCT-TTTTATTATGATTATGTAAG
* * * *
355349 GCAAAACAGGGATATGTTTATAACAATACAGGTAGTAGC
65 ACAAAACATGGTTATATTTATAACAATACA-G--GTAGC
* * ** * * * *
355388 GCCTTTTTATAGTGTCAACTATTTACGTGATATGTTTGAAACCTTTTTTATTA--ATACATTGTA
1 GCCTTCTTATATTGTCAACCGTTTAAGTTATATGTGTGAAACC-TTTTTATTATGAT-TA-TGTA
* * *
355451 AGAAAAAACATGTTTAAATTTATAACAATACAGGTAGC
63 AGACAAAACATGGTTATATTTATAACAATACAGGTAGC
*
355489 GCCTTCTTATATTGTGAACCGTTTAAGTTATATGTGTGAAACCTTTTTCATTATGATTATGTAAG
1 GCCTTCTTATATTGTCAACCGTTTAAGTTATATGTGTGAAACCTTTTT-ATTATGATTATGTAAG
* * * *
355554 ACGAAACATAGTTATATTTATAACAATATAGGTATC
65 ACAAAACATGGTTATATTTATAACAATACAGGTAGC
* *
355590 GCCTTCTTATATTATCAACCGTTTAGGTTATA
1 GCCTTCTTATATTGTCAACCGTTTAAGTTATA
355622 GGGAACAAAT
Statistics
Matches: 338, Mismatches: 84, Indels: 40
0.73 0.18 0.09
Matches are distributed among these distances:
100 15 0.04
101 165 0.49
102 6 0.02
103 7 0.02
104 136 0.40
105 9 0.03
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.39
Consensus pattern (100 bp):
GCCTTCTTATATTGTCAACCGTTTAAGTTATATGTGTGAAACCTTTTTATTATGATTATGTAAGA
CAAAACATGGTTATATTTATAACAATACAGGTAGC
Found at i:355676 original size:23 final size:21
Alignment explanation
Indices: 355650--355692 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
355640 TTATTAAATT
355650 TAATATAAATATGGTTTTTATTG
1 TAATAT-AATA-GGTTTTTATTG
*
355673 TAATGTAATAGGTTTTTATT
1 TAATATAATAGGTTTTTATT
355693 CAGTACATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 4 0.21
23 5 0.26
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (21 bp):
TAATATAATAGGTTTTTATTG
Found at i:356898 original size:99 final size:99
Alignment explanation
Indices: 356705--356916 Score: 221
Period size: 99 Copynumber: 2.2 Consensus size: 99
356695 GTTGCCACCA
* * ** * *
356705 TGTATATTATG-AAACATTACACAAACCTTCTTTTTTGGCTAAAATTATAGGTTGCACCTTGTTC
1 TGTATATTATGAAAACATAAAACAAACCTAATTTTTGGGCTAAAATTATAGGTTGCACCTTCTTC
* *
356769 TTGTGATAACTGATTAACTTATAGGTTGAAAACC
66 TTATGATAACTGATTAACTTATAGGCTGAAAACC
* * *
356803 TGTATATTATGAAAACGTAAAACAAACCTAATTTCTTGGGC-AACATTATAGGTTGCGCCTTCTT
1 TGTATATTATGAAAACATAAAACAAACCTAATTT-TTGGGCTAAAATTATAGGTTGCACCTTCTT
* * * * * * *
356867 GTTATGTTAACTGGTTAAGTTATATGCTGAAATCG
65 CTTATGATAACTGATTAACTTATAGGCTGAAAACC
* *
356902 TATACATTATGAAAA
1 TGTATATTATGAAAA
356917 GATTAATAGA
Statistics
Matches: 92, Mismatches: 20, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
98 11 0.12
99 76 0.83
100 5 0.05
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (99 bp):
TGTATATTATGAAAACATAAAACAAACCTAATTTTTGGGCTAAAATTATAGGTTGCACCTTCTTC
TTATGATAACTGATTAACTTATAGGCTGAAAACC
Found at i:360695 original size:185 final size:185
Alignment explanation
Indices: 360208--360860 Score: 717
Period size: 186 Copynumber: 3.5 Consensus size: 185
360198 GATGCAACCA
* **
360208 TATTTCTTATATATGTTCATAATATTTTCAGTTTTAAACTTATTTTCTTATACTTTGATAATCGA
1 TATTTCTTATATATGTTCATAACATTTTCAGTTTTAAACTTATTTTCTTATACTGGGATAATCGA
* * * **
360273 AGGCTCCATC-CGCTTAAA-TCTGCTAACATTTTCGGCACAACCTACTTTATTATTAAAA-AAGT
66 AAGCTCCATCACACTTAAACTCTGATAACATTTTCGGGTCAACCTACTTTATTATTAAAAGAA-T
* * *
360335 TAACATTCCAGATTACAACTTTTTCTATTATTGAATCATGACATTATTTGA-CACAACTG
130 TAACATTCCAAATTAC-A-TCTTT-TATTATTGAATCATAACATTA-TTGAGCACAACTG
* * * *
360394 TAATTCTTATATATGTTCATAATATTTTCAGTTTTAAACTTATTTTCTTATATTGGGATAA-C-C
1 TATTTCTTATATATGTTCATAACATTTTCAGTTTTAAACTTATTTTCTTATACTGGGATAATCGA
* * *
360457 AAGAATCCATC-GACTTAAACTCTGATAACATTTTTGGCGT-AACCTACTTTATTATTAAAAGAA
66 AAG-CTCCATCACACTTAAACTCTGATAACATTTTCGG-GTCAACCTACTTTATTATTAAAAGAA
* * * * * *
360520 TTAA-ATTCTATATTACGTCTTTTATTATTGAATCGTCACATTATTGAGCACAATTG
129 TTAACATTCCAAATTACATCTTTTATTATTGAATCATAACATTATTGAGCACAACTG
* * * *
360576 TATTTCTTATGTATGGTCATAACATTTTTAG-TTTAAGCTTATTTTCTTATACTGGGATAATC-A
1 TATTTCTTATATATGTTCATAACATTTTCAGTTTTAAACTTATTTTCTTATACTGGGATAATCGA
* *
360639 AAGCTCCATCCATCACCTTAAACTCTGATAACATTTTCGGGTCAACCTATTTTATTATTAAAAGT
66 AAGCTCCAT-CA-CA-CTTAAACTCTGATAACATTTTCGGGTCAACCTACTTTATTATTAAAAGA
* *
360704 ATTAACATTCCAAATTACAACATCTTTTATTATTGAA-CTATAACATTATT-AGACGCAACCG
128 ATTAACATTCCAAATT---ACATCTTTTATTATTGAATC-ATAACATTATTGAG-CACAACTG
* * *
360765 TATTTCTTATATA--TTCATAACATTTCCAGTTTTAAACTTATTTTCTTATATTGGGATAATCTA
1 TATTTCTTATATATGTTCATAACATTTTCAGTTTTAAACTTATTTTCTTATACTGGGATAATCGA
* * *
360828 ACGCTCCATCA-ACTTAAACTATAATAACATTTT
66 AAGCTCCATCACACTTAAACTCTGATAACATTTT
360861 TGGCGCAATC
Statistics
Matches: 398, Mismatches: 50, Indels: 39
0.82 0.10 0.08
Matches are distributed among these distances:
181 36 0.09
182 57 0.14
183 4 0.01
184 5 0.01
185 90 0.23
186 105 0.26
187 15 0.04
188 34 0.09
189 52 0.13
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.42
Consensus pattern (185 bp):
TATTTCTTATATATGTTCATAACATTTTCAGTTTTAAACTTATTTTCTTATACTGGGATAATCGA
AAGCTCCATCACACTTAAACTCTGATAACATTTTCGGGTCAACCTACTTTATTATTAAAAGAATT
AACATTCCAAATTACATCTTTTATTATTGAATCATAACATTATTGAGCACAACTG
Found at i:362280 original size:12 final size:12
Alignment explanation
Indices: 362263--362296 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
362253 TTATCGCAAA
362263 TTCGCGTTGCAT
1 TTCGCGTTGCAT
362275 TTCGCGTTGCAT
1 TTCGCGTTGCAT
362287 TTCGCGTTGC
1 TTCGCGTTGC
362297 GATAGTTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.06, C:0.26, G:0.26, T:0.41
Consensus pattern (12 bp):
TTCGCGTTGCAT
Found at i:362376 original size:20 final size:21
Alignment explanation
Indices: 362351--362402 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
362341 TTTTCCCAAT
*
362351 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
362371 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
362392 TCGCAATGCGA
1 TCGCAATGCGA
362403 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:362416 original size:20 final size:20
Alignment explanation
Indices: 362391--362504 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
362381 AATTGGGAAA
*
362391 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
362411 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
362431 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
362452 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
362472 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
362492 TTCGCAACGCGAT
1 ATCGCAACGCGAT
362505 TTACATAGCG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:362435 original size:61 final size:61
Alignment explanation
Indices: 362388--362504 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
362378 GCGAATTGGG
* * * * *
362388 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
362449 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
362505 TTACATAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:363080 original size:18 final size:19
Alignment explanation
Indices: 363057--363099 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
363047 GCAACGAGAG
*
363057 AATCGCAACGCGAAA-TAA
1 AATCGCAACGCGAAACCAA
363075 AATCGC-ACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
363093 AATCGCA
1 AATCGCA
363100 TTGCGATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.47, C:0.28, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:363117 original size:19 final size:19
Alignment explanation
Indices: 363095--363240 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
363085 GAAACCAAAA
*
363095 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
363114 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
363133 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
363147 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
363166 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
363180 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
363199 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
363219 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
363239 TC
1 TC
363241 AACCAAAAGA
Statistics
Matches: 101, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
14 19 0.19
16 4 0.04
17 5 0.05
19 41 0.41
20 31 0.31
21 1 0.01
ACGTcount: A:0.12, C:0.25, G:0.21, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:363165 original size:33 final size:33
Alignment explanation
Indices: 363128--363215 Score: 158
Period size: 33 Copynumber: 2.6 Consensus size: 33
363118 GTTGCGATTT
363128 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
363161 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
363194 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
363216 ATTATCTCGT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 38 0.72
34 15 0.28
ACGTcount: A:0.11, C:0.27, G:0.23, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:365385 original size:42 final size:42
Alignment explanation
Indices: 365325--365501 Score: 194
Period size: 42 Copynumber: 4.2 Consensus size: 42
365315 GCCCGACTCG
* *
365325 CCTATCATCCCTCAAGAGTCAACTCCTATCATTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
* * * * *
365367 CCTATCATTCCTCGAGAGTCCCCT-CTCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCT-ATCGTTGAAGAGGCC
*
365409 ACTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
* * * * * *
365451 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
* *
365493 ACTGTCATC
1 CCTATCATC
365502 GTTGAAGAGG
Statistics
Matches: 110, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
41 2 0.02
42 106 0.96
43 2 0.02
ACGTcount: A:0.23, C:0.37, G:0.16, T:0.24
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
Found at i:365389 original size:21 final size:21
Alignment explanation
Indices: 365360--365474 Score: 58
Period size: 21 Copynumber: 5.5 Consensus size: 21
365350 CTATCATTGA
365360 AGAGGCCCCTATCATTCCTCG
1 AGAGGCCCCTATCATTCCTCG
* * *
365381 AGAGTCCCCTCTCA--CCGTTCA
1 AGAGGCCCCTATCATTCC--TCG
* * *
365402 AGAGGCCACTATCATCCCTCA
1 AGAGGCCCCTATCATTCCTCG
* * * * *
365423 AGAGTCCAC--TCCTATCGTTG
1 AGAGGCCCCTATCAT-TCCTCG
365443 AAGAGGCCCCTATCATTCCTCG
1 -AGAGGCCCCTATCATTCCTCG
*
365465 AGAGTCCCCT
1 AGAGGCCCCT
365475 CCCACCGTTC
Statistics
Matches: 68, Mismatches: 18, Indels: 16
0.67 0.18 0.16
Matches are distributed among these distances:
19 5 0.07
20 2 0.03
21 52 0.76
22 4 0.06
23 5 0.07
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.23
Consensus pattern (21 bp):
AGAGGCCCCTATCATTCCTCG
Found at i:365489 original size:21 final size:21
Alignment explanation
Indices: 365465--365531 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
365455 TCATTCCTCG
365465 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
365486 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
365507 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
365528 AGAG
1 AGAG
365532 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:365510 original size:84 final size:84
Alignment explanation
Indices: 365326--365501 Score: 316
Period size: 84 Copynumber: 2.1 Consensus size: 84
365316 CCCGACTCGC
*
365326 CTATCATCCCTCAAGAGTCAACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTATCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
*
365391 CTCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
*
365410 CTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTATCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
365475 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
*
365494 CTGTCATC
1 CTATCATC
365502 GTTGAAGAGG
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 88 1.00
ACGTcount: A:0.23, C:0.37, G:0.16, T:0.24
Consensus pattern (84 bp):
CTATCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:365517 original size:42 final size:41
Alignment explanation
Indices: 365359--365531 Score: 161
Period size: 42 Copynumber: 4.1 Consensus size: 41
365349 CCTATCATTG
* * *
365359 AAGAGGCCCCTATCATTCCTCG-AGAGTCCCCTCTCACCGTTC
1 AAGAGGCCACTATCA-TCCTTGAAGAGT-CCCTCCCACCGTTC
* * * * *
365401 AAGAGGCCACTATCATCCCTCAAGAGTCCACTCCTATCGTTG
1 AAGAGGCCACTATCATCCTTGAAGAGTCC-CTCCCACCGTTC
* *
365443 AAGAGGCCCCTATCATTCCTCG-AGAGTCCCCTCCCACCGTTC
1 AAGAGGCCACTATCA-TCCTTGAAGAGT-CCCTCCCACCGTTC
* * *
365485 AAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCACCATTC
1 AAGAGGCCACTATCATCCTTGAAGA-GTCCCTCCCACCGTTC
365527 AAGAG
1 AAGAG
365532 CCCGATTCAC
Statistics
Matches: 105, Mismatches: 20, Indels: 12
0.77 0.15 0.09
Matches are distributed among these distances:
41 9 0.09
42 89 0.85
43 7 0.07
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.22
Consensus pattern (41 bp):
AAGAGGCCACTATCATCCTTGAAGAGTCCCTCCCACCGTTC
Found at i:365531 original size:84 final size:84
Alignment explanation
Indices: 365326--365531 Score: 288
Period size: 84 Copynumber: 2.5 Consensus size: 84
365316 CCCGACTCGC
* * *
365326 CTATCATCCCTCAAGAGTCAACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTATCATCCCTCAAGAGTCCACTCCCACCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
*
365391 CTCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* * *
365410 CTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTATCATCCCTCAAGAGTCCACTCCCACCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
365475 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* ** * *
365494 CTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CTATCATCCCTCAAGA-GTCCACTCCCACCATTGAAGAG
365532 CCCGATTCAC
Statistics
Matches: 110, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
84 106 0.96
85 4 0.04
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.23
Consensus pattern (84 bp):
CTATCATCCCTCAAGAGTCCACTCCCACCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:366908 original size:14 final size:14
Alignment explanation
Indices: 366889--366924 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
366879 ATTGTTTAAT
366889 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
366903 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
366917 TGATTTGT
1 TGATTTGT
366925 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:367071 original size:14 final size:14
Alignment explanation
Indices: 367049--367105 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
367039 GCAAAATGAA
*
367049 AATCACAACGAGAG
1 AATCGCAACGAGAG
*
367063 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
367082 AATCGCAACGAGAG
1 AATCGCAACGAGAG
367096 AATCGCAACG
1 AATCGCAACG
367106 CGAAATTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:367079 original size:33 final size:33
Alignment explanation
Indices: 367031--367111 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
367021 AAAAAGTACT
* *
367031 ATCGCAATGCAAAATGAAAATCACAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCACAACGAGAGA
*
367064 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCACAACGAGAGA
367097 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
367112 TAAATTCGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCACAACGAGAGA
Found at i:367162 original size:33 final size:31
Alignment explanation
Indices: 367119--367279 Score: 187
Period size: 33 Copynumber: 4.9 Consensus size: 31
367109 AATTAAATTC
*
367119 GCGTTGCGATTTTCATTTCGCATTGCGATTCCC
1 GCGTTGCGATTTTCATTTCGCATTGCGATT--A
* *
367152 TCGTTGCGATTTTCATTTCGCATTGTGAAATTA
1 GCGTTGCGATTTTCATTTCGCATTGCG--ATTA
*
367185 GCGTTGCAATTTTCATTTCGCATTGCGAAATTA
1 GCGTTGCGATTTTCATTTCGCATTGCG--ATTA
* *
367218 GCGTTGCGATTTTCATTTCACATTGCGATTCTC
1 GCGTTGCGATTTTCATTTCGCATTGCGA-T-TA
*
367251 TCGTTGCGATTTTCATTTCGCATTGCGAT
1 GCGTTGCGATTTTCATTTCGCATTGCGAT
367280 AGTAATTTCC
Statistics
Matches: 113, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
31 1 0.01
32 2 0.02
33 107 0.95
35 3 0.03
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.42
Consensus pattern (31 bp):
GCGTTGCGATTTTCATTTCGCATTGCGATTA
Found at i:367197 original size:66 final size:64
Alignment explanation
Indices: 367113--367279 Score: 210
Period size: 66 Copynumber: 2.5 Consensus size: 64
367103 ACGCGAAATT
** * *
367113 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGT
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATT--AGCGTTGCGATTTTCATTTCACATTGC
367178 G
64 G
* *
367179 AAATTAGCGTTGCAATTTTCATTTCGCATTGCGAAATTAGCGTTGCGATTTTCATTTCACATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCG--ATTAGCGTTGCGATTTTCATTTCACATTGC
367244 G
64 G
* *
367245 -ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 AAAT-TCGCGTTGCGATTTTCATTTCGCATTGCGAT
367280 AGTAATTTCC
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
64 2 0.02
65 2 0.02
66 81 0.92
68 3 0.03
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.42
Consensus pattern (64 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTAGCGTTGCGATTTTCATTTCACATTGCG
Found at i:367245 original size:19 final size:19
Alignment explanation
Indices: 367221--367279 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
367211 GAAATTAGCG
367221 TTGCGATTTTCATTTCACA
1 TTGCGATTTTCATTTCACA
* *
367240 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCACA
*
367254 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCACA
367273 TTGCGAT
1 TTGCGAT
367280 AGTAATTTCC
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 9 0.29
16 3 0.10
17 3 0.10
19 16 0.52
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCACA
Found at i:369792 original size:24 final size:24
Alignment explanation
Indices: 369758--369811 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
369748 CTGAAACATC
*
369758 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
369782 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
369806 ATCAAA
1 ATCAAA
369812 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:370644 original size:21 final size:20
Alignment explanation
Indices: 370598--370649 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
370588 TTTTTCTAAT
*
370598 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
370618 TAGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
370639 TCGCAATGCGA
1 TCGCAATGCGA
370650 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:370671 original size:20 final size:20
Alignment explanation
Indices: 370638--370716 Score: 61
Period size: 20 Copynumber: 3.9 Consensus size: 20
370628 AATTTGGAAA
* *
370638 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
370658 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
*
370679 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* * *
370699 TTCACAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
370717 AAATTGCAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
19 2 0.04
20 29 0.62
21 14 0.30
22 2 0.04
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:371074 original size:19 final size:19
Alignment explanation
Indices: 371033--371100 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
371023 GAAATGAAAA
371033 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
371049 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
371066 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
371085 TTGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
371101 TCGTTGCGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
19 29 0.63
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:373194 original size:19 final size:20
Alignment explanation
Indices: 373143--373206 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
373133 CTTAAAATCA
*
373143 CAACGCGAAAATGACTATCG
1 CAACGCGGAAATGACTATCG
*
373163 CAACGCGGAAATGGCTATCG
1 CAACGCGGAAATGACTATCG
* * **
373183 TAATGC-GAAATGAAAATCG
1 CAACGCGGAAATGACTATCG
373202 CAACG
1 CAACG
373207 ACAAAATCGC
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
19 13 0.37
20 22 0.63
ACGTcount: A:0.39, C:0.22, G:0.23, T:0.16
Consensus pattern (20 bp):
CAACGCGGAAATGACTATCG
Found at i:373214 original size:14 final size:14
Alignment explanation
Indices: 373195--373285 Score: 74
Period size: 14 Copynumber: 5.9 Consensus size: 14
373185 ATGCGAAATG
373195 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
373209 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
373228 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
373242 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
373258 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
373274 AAAATAGCAACG
1 AAAATCGCAACG
373286 CGAAACACAA
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 10 0.16
17 2 0.03
18 10 0.16
19 10 0.16
ACGTcount: A:0.49, C:0.22, G:0.18, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:373270 original size:32 final size:33
Alignment explanation
Indices: 373179--373290 Score: 190
Period size: 33 Copynumber: 3.4 Consensus size: 33
373169 GGAAATGGCT
*
373179 ATCGTAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
373212 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
373245 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
373277 ATAGCAACGCGAAA
1 ATCGCAATGCGAAA
373291 CACAAATCGC
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 28 0.37
33 48 0.63
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:373298 original size:65 final size:66
Alignment explanation
Indices: 373179--373301 Score: 187
Period size: 65 Copynumber: 1.9 Consensus size: 66
373169 GGAAATGGCT
* * * *
373179 ATCGTAATGCGAAATGAAAATCGCAACGACAAAATCGCAATGCGAAATGAAAATCGCAACGACAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATAGCAACGCGAAATCAAAATCGCAACGACAA
373244 A
66 A
373245 ATCGCAATGCGAAATG-AAATCGCAACGACAAAATAGCAACGCGAAA-CACAAATCGCA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATAGCAACGCGAAATCA-AAATCGCA
373302 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
64 1 0.02
65 36 0.69
66 15 0.29
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (66 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAAATAGCAACGCGAAATCAAAATCGCAACGACAA
A
Found at i:373319 original size:19 final size:19
Alignment explanation
Indices: 373297--373378 Score: 104
Period size: 18 Copynumber: 4.6 Consensus size: 19
373287 GAAACACAAA
373297 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
373316 TCGCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
373334 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
373350 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
373367 TCGCATTGCGAT
1 TCGCATTGCGAT
373379 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.11
15 3 0.06
16 4 0.07
17 4 0.07
18 20 0.37
19 17 0.31
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:373405 original size:20 final size:19
Alignment explanation
Indices: 373297--373417 Score: 76
Period size: 19 Copynumber: 6.6 Consensus size: 19
373287 GAAACACAAA
**
373297 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATAGTCATT
* *
373316 TCGCGTTGCGAT-TTCATT
1 TCGCATTGCGATAGTCATT
373334 TCGCATTGCGAT--T--TT
1 TCGCATTGCGATAGTCATT
**
373349 GTCG--TTGCGATTTTCATT
1 -TCGCATTGCGATAGTCATT
*
373367 TCGCATTGCGATAGCCATT
1 TCGCATTGCGATAGTCATT
* *
373386 TCCGCGTTGCGGTAGTCATTT
1 T-CGCATTGCGATAGTCA-TT
*
373407 TCGTATTGCGA
1 TCGCATTGCGA
373418 AAGTAAACTA
Statistics
Matches: 82, Mismatches: 11, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
14 7 0.09
15 2 0.02
16 4 0.05
17 4 0.05
18 19 0.23
19 23 0.28
20 20 0.24
21 3 0.04
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.42
Consensus pattern (19 bp):
TCGCATTGCGATAGTCATT
Found at i:375311 original size:20 final size:20
Alignment explanation
Indices: 375263--375326 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
375253 AATAGTTTCT
** *
375263 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
375283 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
** *
375303 GAATTTGACTATCGCAACGT
1 GAAAATGACTATCGCAACGC
375323 GAAA
1 GAAA
375327 CTAAAATCGC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.44, C:0.20, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:375597 original size:22 final size:22
Alignment explanation
Indices: 375570--375635 Score: 123
Period size: 22 Copynumber: 3.0 Consensus size: 22
375560 GATGGAGATA
*
375570 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTTGGAGATGGG
375592 GACGGATTTCGTTGGAGATGGG
1 GACGGATTTCGTTGGAGATGGG
375614 GACGGATTTCGTTGGAGATGGG
1 GACGGATTTCGTTGGAGATGGG
375636 TGAGAGAGTG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.11, G:0.45, T:0.26
Consensus pattern (22 bp):
GACGGATTTCGTTGGAGATGGG
Found at i:375909 original size:20 final size:20
Alignment explanation
Indices: 375823--375917 Score: 93
Period size: 20 Copynumber: 4.7 Consensus size: 20
375813 GATTATGTAT
*
375823 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
375843 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
375863 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
*
375884 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
375904 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
375918 TTTCCCAATT
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 3 0.05
20 45 0.73
21 12 0.19
22 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:375936 original size:41 final size:41
Alignment explanation
Indices: 375844--375938 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 41
375834 GAAAGTCAGA
* * * ** *
375844 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
*
375885 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT-CCAAT
375927 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
375939 TTACTTATTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
Done.