Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007951.1 Hibiscus syriacus cultivar Beakdansim tig00110374_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: 657610
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:387549 original size:29 final size:30
Alignment explanation
Indices: 387479--387551 Score: 139
Period size: 30 Copynumber: 2.5 Consensus size: 30
387469 TTGATTTTCC
387479 GGAAAATGAATTACTGGAATTTGAATTACT
1 GGAAAATGAATTACTGGAATTTGAATTACT
387509 GGAAAATGAATTACTGGAATTTGAATT-CT
1 GGAAAATGAATTACTGGAATTTGAATTACT
387538 GGAAAATGAATTAC
1 GGAAAATGAATTAC
387552 ATTTCTGGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 16 0.37
30 27 0.63
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.32
Consensus pattern (30 bp):
GGAAAATGAATTACTGGAATTTGAATTACT
Found at i:387557 original size:20 final size:20
Alignment explanation
Indices: 387534--387583 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
387524 GGAATTTGAA
387534 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
387554 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
387574 TTCTGGAAAA
1 TTCTGGAAAA
387584 CGTTTTATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:387765 original size:49 final size:50
Alignment explanation
Indices: 387668--387766 Score: 114
Period size: 49 Copynumber: 2.0 Consensus size: 50
387658 TACAAATATT
*
387668 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATTATTTTA
1 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
* * * *
387718 AAATATTA-AAATAATA-TATTTATTATTAAATA-TTATTTTTATAATTTTA
1 AAATATAATAAATAATATTATTTATCA-TAAA-ACTTAATATTATAATTTTA
387767 TTAATAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
48 8 0.19
49 26 0.62
50 8 0.19
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (50 bp):
AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
Found at i:387952 original size:26 final size:25
Alignment explanation
Indices: 387903--387974 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 25
387893 TTTACTAAAA
387903 TATTATTTAAATATATAAATAAAATTAT
1 TATTA-TTAAATATAT-AA-AAAATTAT
387931 TCATTATTAAATATATAAAAAATTAT
1 T-ATTATTAAATATATAAAAAATTAT
387957 TATATATTAAA-ATA-AAAA
1 TAT-TATTAAATATATAAAA
387975 TATAATATCT
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
24 4 0.10
25 5 0.12
26 16 0.38
27 2 0.05
28 11 0.26
29 4 0.10
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (25 bp):
TATTATTAAATATATAAAAAATTAT
Found at i:387957 original size:19 final size:18
Alignment explanation
Indices: 387933--387968 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
387923 AAAATTATTC
387933 ATTATTAAATATATAAAAA
1 ATTATTAAATAT-TAAAAA
*
387952 ATTATTATATATTAAAA
1 ATTATTAAATATTAAAA
387969 TAAAAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTATTAAATATTAAAAA
Found at i:388057 original size:30 final size:29
Alignment explanation
Indices: 387986--388083 Score: 78
Period size: 30 Copynumber: 3.3 Consensus size: 29
387976 ATAATATCTT
*
387986 ATATTATTATAATATA-ATTGAT-TATTTTATA
1 ATATTAATA-AATATATATT-ATATA-TTTA-A
388017 ATATT-A-AAATATATATTATATATTATAA
1 ATATTAATAAATATATATTATATATT-TAA
* * *
388045 ATATTAATAAATATATTTTAAATATTTTA
1 ATATTAATAAATATATATTATATATTTAA
388074 ATAATTAATA
1 AT-ATTAATA
388084 TTTTGATGAA
Statistics
Matches: 57, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
28 16 0.28
29 13 0.23
30 23 0.40
31 5 0.09
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (29 bp):
ATATTAATAAATATATATTATATATTTAA
Found at i:388058 original size:19 final size:19
Alignment explanation
Indices: 388016--388058 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
388006 ATTATTTTAT
*
388016 AATATTAAAATATATATTA
1 AATATTAAAATATATAATA
*
388035 TATATTATAAATAT-TAATA
1 AATATTA-AAATATATAATA
388054 AATAT
1 AATAT
388059 ATTTTAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATATTAAAATATATAATA
Found at i:388058 original size:26 final size:26
Alignment explanation
Indices: 387906--388058 Score: 74
Period size: 26 Copynumber: 5.8 Consensus size: 26
387896 ACTAAAATAT
387906 TATT-TAAATATATAAATAAA-ATTAT-
1 TATTATAAATAT-T-AATAAATATTATA
*
387931 TCATTATTAAATATATAAAAAATTATTATA
1 T-ATTA-TAAATAT-TAATAAA-TATTATA
**
387961 TATTA-AAATAAAAATATAATATCT-TA
1 TATTATAAATATTAATA-AATAT-TATA
* * *
387987 TATTAT-TATAAT-ATAATTGATTAT-
1 TATTATAAATATTAATAAAT-ATTATA
*
388011 T-TTAT-AATATTAAAATATATATTATA
1 TATTATAAATATT--AATAAATATTATA
388037 TATTATAAATATTAATAAATAT
1 TATTATAAATATTAATAAATAT
388059 ATTTTAAATA
Statistics
Matches: 99, Mismatches: 12, Indels: 33
0.69 0.08 0.23
Matches are distributed among these distances:
23 8 0.08
24 4 0.04
25 12 0.12
26 33 0.33
27 17 0.17
28 15 0.15
29 9 0.09
30 1 0.01
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (26 bp):
TATTATAAATATTAATAAATATTATA
Found at i:388066 original size:11 final size:11
Alignment explanation
Indices: 388017--388069 Score: 51
Period size: 10 Copynumber: 5.2 Consensus size: 11
388007 TTATTTTATA
388017 ATATTA-AAAT
1 ATATTATAAAT
*
388027 ATA-TAT-TAT
1 ATATTATAAAT
388036 ATATTATAAAT
1 ATATTATAAAT
*
388047 AT-TAATAAAT
1 ATATTATAAAT
*
388057 ATATTTTAAAT
1 ATATTATAAAT
388068 AT
1 AT
388070 TTTAATAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
9 7 0.21
10 15 0.44
11 12 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATATTATAAAT
Found at i:388324 original size:42 final size:42
Alignment explanation
Indices: 388263--388377 Score: 194
Period size: 42 Copynumber: 2.7 Consensus size: 42
388253 ATTACGTTCT
* *
388263 GGAAAACGAATTACGTGAAACAAACACGGTAAAACATTTTCC
1 GGAAAACGAATTACATGAAACAAACACGGGAAAACATTTTCC
* *
388305 GGAAAATGAATTACATGAAACAAACACGGGAAAATATTTTCC
1 GGAAAACGAATTACATGAAACAAACACGGGAAAACATTTTCC
388347 GGAAAACGAATTACATGAAACAAACACGGGA
1 GGAAAACGAATTACATGAAACAAACACGGGA
388378 TTTCGGGGAA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.48, C:0.17, G:0.18, T:0.17
Consensus pattern (42 bp):
GGAAAACGAATTACATGAAACAAACACGGGAAAACATTTTCC
Found at i:393166 original size:138 final size:138
Alignment explanation
Indices: 392918--393688 Score: 1036
Period size: 138 Copynumber: 5.6 Consensus size: 138
392908 TACTATTCAC
* * * *
392918 GTGAAGGCGCGTTTCAGGGGGCGTGCTTTCCCTTTTTTTGTCAGAGAATATGTTATAATTGCCCT
1 GTGAAAGCGCGTTTCAGGGGGCGTGCCTTCCATTATTTTGTCAGAGAATATGTTATAATTGCCCT
* * * * * * *
392983 ATTATGTGAGTCATGTCCTCGAGTGCACTATTTATGTCAGTACCTATCATATTTGAGGGGACACA
66 ATTATGTGACTCATGTCCCCGAGCGCACTATTCATGTCGGTACCTATCATGTTTGAGGGGACGCA
393048 ACAAAGTG
131 ACAAAGTG
* ** * *
393056 GTGAAAGCGCATTTCAGGGGGCGCACCTTCCATTATTTTATTAGAGAATATGTTATAATTGCCCT
1 GTGAAAGCGCGTTTCAGGGGGCGTGCCTTCCATTATTTTGTCAGAGAATATGTTATAATTGCCCT
* * * ***
393121 ATTATGTGAGTCATGTCCTCGAGCGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGATATA
66 ATTATGTGACTCATGTCCCCGAGCGCACTATTCATGTCGGTACCTATCATGTTTGAGGGGACGCA
393186 ACAAAGTG
131 ACAAAGTG
* * * * ** * *
393194 GTGAAAGTGCGTCTCATGGGTCGTTTCTTTCATTATTTTTTCAGAGAATATGTTATAATTGCCCT
1 GTGAAAGCGCGTTTCAGGGGGCGTGCCTTCCATTATTTTGTCAGAGAATATGTTATAATTGCCCT
* *
393259 ATTATGTGACTCATGTCCCC-AGGGCACTATTCATGTCGGTACTTATCATGTTTGAGGGGACGCA
66 ATTATGTGACTCATGTCCCCGAGCGCACTATTCATGTCGGTACCTATCATGTTTGAGGGGACGCA
*
393323 ATAAAGTG
131 ACAAAGTG
* * * * *
393331 GTGAAAGTGCATTTCAGGGGGAGCGCC-TCCTTTATTTTGTCAGAGAATATGTTATAATTGCCCT
1 GTGAAAGCGCGTTTCAGGGGGCGTGCCTTCCATTATTTTGTCAGAGAATATGTTATAATTGCCCT
** *
393395 ATTATGTGACTCATGTCCCCCTG-GCACTATTCATGTCGGTACCTATCATGTTTGAGAGGACGCA
66 ATTATGTGACTCATGTCCCCGAGCGCACTATTCATGTCGGTACCTATCATGTTTGAGGGGACGCA
393459 ACAAAGTG
131 ACAAAGTG
* * *
393467 GTGAAAGCGCGTTTCAGGGGGCGTGCCTTCTATTATTTTTTTCAGAGAATATGTTATAATTTCCC
1 GTGAAAGCGCGTTTCAGGGGGCGTGCCTTCCATTA-TTTTGTCAGAGAATATGTTATAATTGCCC
*
393532 TATTATGTGACTCATGTCCCCCGAGC-CACTATTCATGTCGGTGCCTATCATGTTTGAGGGGACG
65 TATTATGTGACTCATGT-CCCCGAGCGCACTATTCATGTCGGTACCTATCATGTTTGAGGGGACG
393596 CAACAAAGTG
129 CAACAAAGTG
* *
393606 GTGAAAGTGCGTATT-A-GGGG-G-GCCTTCCATTATTTTGTCAGAGAATATGTTATGATTGCCC
1 GTGAAAGCGCGT-TTCAGGGGGCGTGCCTTCCATTATTTTGTCAGAGAATATGTTATAATTGCCC
393667 TATTATGTGACTCATGTCCCCG
65 TATTATGTGACTCATGTCCCCG
393689 GGGTCACAAC
Statistics
Matches: 561, Mismatches: 66, Indels: 16
0.87 0.10 0.02
Matches are distributed among these distances:
134 5 0.01
135 43 0.08
136 133 0.24
137 71 0.13
138 244 0.43
139 63 0.11
140 2 0.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (138 bp):
GTGAAAGCGCGTTTCAGGGGGCGTGCCTTCCATTATTTTGTCAGAGAATATGTTATAATTGCCCT
ATTATGTGACTCATGTCCCCGAGCGCACTATTCATGTCGGTACCTATCATGTTTGAGGGGACGCA
ACAAAGTG
Found at i:394269 original size:15 final size:14
Alignment explanation
Indices: 394235--394281 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
394225 GAATTTGAAT
394235 AAAATATAACTTTA
1 AAAATATAACTTTA
394249 AAAATATAACTTTA
1 AAAATATAACTTTA
* *
394263 CAAA-ATAACATTA
1 AAAATATAACTTTA
394276 AAAATA
1 AAAATA
394282 ATTCACGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 11 0.38
14 18 0.62
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAATATAACTTTA
Found at i:394791 original size:21 final size:21
Alignment explanation
Indices: 394767--394812 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
394757 ATAAAACTTG
*
394767 GCGGGCTAGGAATATAACCCT
1 GCGGGCTAAGAATATAACCCT
* *
394788 GCGGGCTAAGAATGTAATCCT
1 GCGGGCTAAGAATATAACCCT
394809 GCGG
1 GCGG
394813 AGATGGCATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.22, G:0.33, T:0.20
Consensus pattern (21 bp):
GCGGGCTAAGAATATAACCCT
Found at i:396598 original size:15 final size:16
Alignment explanation
Indices: 396578--396607 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
396568 AACTGTAGAC
396578 AAAAAAT-ATAATTAG
1 AAAAAATAATAATTAG
396593 AAAAAATAATAATTA
1 AAAAAATAATAATTA
396608 ATTAATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (16 bp):
AAAAAATAATAATTAG
Found at i:401764 original size:17 final size:16
Alignment explanation
Indices: 401738--401771 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
401728 TTTCACTAAT
*
401738 AGAGGAAATATTACAA
1 AGAGGAAATAATACAA
401754 AGAGAGAAATAATACAA
1 AGAG-GAAATAATACAA
401771 A
1 A
401772 TAGCCTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.62, C:0.06, G:0.18, T:0.15
Consensus pattern (16 bp):
AGAGGAAATAATACAA
Found at i:402629 original size:50 final size:52
Alignment explanation
Indices: 402571--402710 Score: 149
Period size: 59 Copynumber: 2.6 Consensus size: 52
402561 CTTCACACTC
* *
402571 AATTTGTCTTTTCATCGTGACTAGGAGGGTT-GG-TTAGAGCCATATTATCG
1 AATTTGTCTTTTCATTGAGACTAGGAGGGTTAGGATTAGAGCCATATTATCG
* * *
402621 AATTTGTCTTTTCATTGCGATTAAGAGGGTTCAATAGGACACTTAGAGCCATATTATCG
1 AATTTGTCTTTTCATTGAGACTAGGAGGG-T---TAGG--A-TTAGAGCCATATTATCG
*
402680 AGTTTGTCTTTTCATTGAGACTAGGAGGGTT
1 AATTTGTCTTTTCATTGAGACTAGGAGGGTT
402711 CGATAGGACA
Statistics
Matches: 73, Mismatches: 8, Indels: 13
0.78 0.09 0.14
Matches are distributed among these distances:
50 25 0.34
51 1 0.01
54 1 0.01
55 3 0.04
58 1 0.01
59 42 0.58
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (52 bp):
AATTTGTCTTTTCATTGAGACTAGGAGGGTTAGGATTAGAGCCATATTATCG
Found at i:402696 original size:59 final size:59
Alignment explanation
Indices: 402604--402724 Score: 197
Period size: 59 Copynumber: 2.1 Consensus size: 59
402594 GGAGGGTTGG
* *
402604 TTAGAGCCATATTATCGAATTTGTCTTTTCATTGCGATTAAGAGGGTTCAATAGGACAC
1 TTAGAGCCATATTATCGAATTTGTCTTTTCATTGAGACTAAGAGGGTTCAATAGGACAC
* * *
402663 TTAGAGCCATATTATCGAGTTTGTCTTTTCATTGAGACTAGGAGGGTTCGATAGGACAC
1 TTAGAGCCATATTATCGAATTTGTCTTTTCATTGAGACTAAGAGGGTTCAATAGGACAC
402722 TTA
1 TTA
402725 TCCATCTATT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (59 bp):
TTAGAGCCATATTATCGAATTTGTCTTTTCATTGAGACTAAGAGGGTTCAATAGGACAC
Found at i:402923 original size:62 final size:62
Alignment explanation
Indices: 402847--402975 Score: 231
Period size: 62 Copynumber: 2.1 Consensus size: 62
402837 TTCTAGGTTT
*
402847 GATTCTTCAACAAGATCAACGTTCATTAATCTGCAGATTCTTTTTTATTTAATTTTAATTTA
1 GATTCTTCAACAAGATCAACGTTCATTAATCTGCAGACTCTTTTTTATTTAATTTTAATTTA
* *
402909 GATTCTTCAACAAGATCAACTTTCATTAATCTGCAGGCTCTTTTTTATTTAATTTTAATTTA
1 GATTCTTCAACAAGATCAACGTTCATTAATCTGCAGACTCTTTTTTATTTAATTTTAATTTA
402971 GATTC
1 GATTC
402976 AAATCCTTCT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.47
Consensus pattern (62 bp):
GATTCTTCAACAAGATCAACGTTCATTAATCTGCAGACTCTTTTTTATTTAATTTTAATTTA
Found at i:419996 original size:6 final size:6
Alignment explanation
Indices: 419979--420162 Score: 160
Period size: 6 Copynumber: 31.5 Consensus size: 6
419969 CTCATCCATA
* *
419979 AAAAAG AGAAAG AAAAAGG AAAAA- AAAAA- AAAAAA AAAAAG AAAAA-
1 AAAAAG AAAAAG AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
*
420025 AAAGAA- AAGAAAG AGAAAG AAAAAG --AAAG AAAAAG AAAAAG AAAAATG
1 AAA-AAG AA-AAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA-G
* *
420073 -AAAAG AAAAAGG AAAAGG AAAAGG AAAAAG AAAAAG -AAAAG -AAAA-
1 AAAAAG AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
420118 AAAAAG AAAAAAG AAAAA- AGAAAAG -AAAAG AAGAAA- AAAAAG AAA
1 AAAAAG -AAAAAG AAAAAG A-AAAAG AAAAAG AA-AAAG AAAAAG AAA
420163 TTGAAACAAG
Statistics
Matches: 153, Mismatches: 7, Indels: 36
0.78 0.04 0.18
Matches are distributed among these distances:
4 4 0.03
5 36 0.24
6 90 0.59
7 23 0.15
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.01
Consensus pattern (6 bp):
AAAAAG
Found at i:420002 original size:1 final size:1
Alignment explanation
Indices: 419998--420158 Score: 70
Period size: 1 Copynumber: 161.0 Consensus size: 1
419988 AAGAAAAAGG
* * * * * * * * *
419998 AAAAAAAAAAAAAAAAAAAAAGAAAAAAAAGAAAAGAAAGAGAAAGAAAAAGAAAGAAAAAGAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* ** * ** ** ** * * * *
420063 AAGAAAAATGAAAAGAAAAAGGAAAAGGAAAAGGAAAAAGAAAAAGAAAAGAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
420128 AAGAAAAAAGAAAAGAAAAGAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
420159 GAAATTGAAA
Statistics
Matches: 111, Mismatches: 49, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 111 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.01
Consensus pattern (1 bp):
A
Found at i:420038 original size:53 final size:52
Alignment explanation
Indices: 419981--420162 Score: 208
Period size: 53 Copynumber: 3.4 Consensus size: 52
419971 CATCCATAAA
*
419981 AAAGAGAAAGAAAAAGGAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAGAAAAG
1 AAAGAGAAAGAAAAA-GAAAAAAAAAAAAAAGAAAAAAGAAAAAAAAGAAAAG
* *
420034 AAAGAGAAAGAAAAAGAAAGAAAAAGAAAAAGAAAAATGAAAAGAAAAAGGAAAAGG
1 AAAGAGAAAGAAAAAGAAA-AAAAAAAAAAAGAAAAAAG-AAA-AAAAA-GAAAA-G
* *
420091 AAAAGGAAAAAGAAAAAGAAAAGAAAAAAAAAGAAAAAAG--AAAAAAGAAAAG
1 -AAA-GAGAAAGAAAAAGAAAAAAAAAAAAAAGAAAAAAGAAAAAAAAGAAAAG
420143 AAAAGAAGAAA-AAAAAGAAA
1 -AAAG-AGAAAGAAAAAGAAA
420163 TTGAAACAAG
Statistics
Matches: 113, Mismatches: 8, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
51 10 0.09
52 13 0.12
53 36 0.32
54 8 0.07
55 6 0.05
56 5 0.04
57 1 0.01
58 19 0.17
59 15 0.13
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (52 bp):
AAAGAGAAAGAAAAAGAAAAAAAAAAAAAAGAAAAAAGAAAAAAAAGAAAAG
Found at i:420168 original size:93 final size:93
Alignment explanation
Indices: 419980--420162 Score: 239
Period size: 94 Copynumber: 2.0 Consensus size: 93
419970 TCATCCATAA
* *
419980 AAAAGAGAAAGAAAAAGGAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAGAAAAGAAAGAGAAAGA
1 AAAAGAAAAAGAAAAAGGAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAGAAAAGAAAGAAAAAGA
420045 AAAAGAAAGAAAAAGAAAAAGAAAAATG
66 AAAAGAAAGAAAAAGAAAAAGAAAAATG
* * * *
420073 AAAAGAAAAAGGAAAAGGAAAAGGAAAAAGAAAAAGAAAAGAAAAAAAA-AGAAA-AAAGAAAAA
1 AAAAGAAAAAGAAAAAGGAAAA-AAAAAAAAAAAAAAAAAGAAAAAAAAGA-AAAGAAAGAAAAA
420136 -AGAAAAGAAAAGAAGAAA-AAAAAGAAA
64 GA-AAAAG-AAAGAA-AAAGAAAAAGAAA
420163 TTGAAACAAG
Statistics
Matches: 79, Mismatches: 6, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
92 1 0.01
93 34 0.43
94 41 0.52
95 3 0.04
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (93 bp):
AAAAGAAAAAGAAAAAGGAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAGAAAAGAAAGAAAAAGA
AAAAGAAAGAAAAAGAAAAAGAAAAATG
Found at i:420173 original size:22 final size:22
Alignment explanation
Indices: 419978--420162 Score: 122
Period size: 22 Copynumber: 8.5 Consensus size: 22
419968 ACTCATCCAT
*
419978 AAAAAAGAGAAAGAAAA-AGGAA
1 AAAAAAGA-AAAGAAAACAAGAA
* * *
420000 AAAAAAAAAAAAAAAAAAAGAA
1 AAAAAAGAAAAGAAAACAAGAA
*
420022 AAAAAAGAAAAGAAAGAGAAAGAA
1 AAAAAAGAAAAGAAA-A-CAAGAA
420046 AAAGAAAGAAAA-AGAAA-AAG--
1 AAA-AAAGAAAAGA-AAACAAGAA
* *
420066 AAAAATGAAAAGAAAA-AGGAA
1 AAAAAAGAAAAGAAAACAAGAA
420087 AAGGAAAAGGAAAA-AGAAA-AAGAA
1 AA--AAAA-GAAAAGA-AAACAAGAA
*
420111 AAGAAAAAAAAAGAAAA-AAG--
1 AA-AAAAGAAAAGAAAACAAGAA
*
420131 AAAAAAGAAAAGAAAAGAAGAA
1 AAAAAAGAAAAGAAAACAAGAA
420153 AAAAAAGAAA
1 AAAAAAGAAA
420163 TTGAAACAAG
Statistics
Matches: 136, Mismatches: 11, Indels: 32
0.76 0.06 0.18
Matches are distributed among these distances:
19 25 0.18
20 9 0.07
21 9 0.07
22 47 0.35
23 11 0.08
24 25 0.18
25 10 0.07
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.01
Consensus pattern (22 bp):
AAAAAAGAAAAGAAAACAAGAA
Found at i:421308 original size:23 final size:23
Alignment explanation
Indices: 421282--421342 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
421272 CTCGTATAAA
*
421282 TGTATCGAAGTGCCACGTAGAAT
1 TGTACCGAAGTGCCACGTAGAAT
* * *
421305 TGTACCTAAGTGCCGCGTAGAAA
1 TGTACCGAAGTGCCACGTAGAAT
* *
421328 TGCACCAAAGTGCCA
1 TGTACCGAAGTGCCA
421343 TATGAGATGT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.21
Consensus pattern (23 bp):
TGTACCGAAGTGCCACGTAGAAT
Found at i:421819 original size:18 final size:19
Alignment explanation
Indices: 421786--421821 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
421776 ACTTATTTTG
421786 CTTTCTCATATCATATATA
1 CTTTCTCATATCATATATA
*
421805 CTTTCTC-TTTCATATAT
1 CTTTCTCATATCATATAT
421822 CTAATGTCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (19 bp):
CTTTCTCATATCATATATA
Found at i:424665 original size:52 final size:52
Alignment explanation
Indices: 424545--424787 Score: 384
Period size: 51 Copynumber: 4.7 Consensus size: 52
424535 TATATTATCT
*
424545 ATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAAGACA-AAGTAATCC
1 ATGTGAGGCATCTTGAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCC
424596 ATGTGAGGCATCTTGAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCC
1 ATGTGAGGCATCTTGAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCC
*
424648 ATGTGAGGCATCTTGAAGGCTCACATCAGCAT-AAAAAGATAGAAGTAATCC
1 ATGTGAGGCATCTTGAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCC
* * *
424699 ATGTGAGACATCTTGAAGGTTCACATCAGCATGAAAAAGACAGATA-TTATCC
1 ATGTGAGGCATCTTGAAGGCTCACATCAGCATGAAAAAGACAGA-AGTAATCC
* * *
424751 ATGTGGGGCATCTTGAAGGCTCACACCAACATGAAAA
1 ATGTGAGGCATCTTGAAGGCTCACATCAGCATGAAAA
424788 GGTTGGGATA
Statistics
Matches: 178, Mismatches: 11, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
51 89 0.50
52 88 0.49
53 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (52 bp):
ATGTGAGGCATCTTGAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCC
Found at i:424788 original size:103 final size:102
Alignment explanation
Indices: 424536--424788 Score: 391
Period size: 103 Copynumber: 2.5 Consensus size: 102
424526 TTATAGGTCT
*
424536 ATATTATCTATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAAGACAAAGTAATCCATGTG
1 ATATTATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATG-AAAAGACAAAGTAATCCATGTG
*
424601 AGGCATCTTGAAGGCTCACATCAGCATGAAAAAGACAG
65 AGACATCTTGAAGGCTCACATCAGCATGAAAAAGACAG
* * * *
424639 A-AGTAATCCATGTGAGGCATCTTGAAGGCTCACATCAGCATAAAAAGATAGAAGTAATCCATGT
1 ATA-TTATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAGACA-AAGTAATCCATGT
*
424703 GAGACATCTTGAAGGTTCACATCAGCATGAAAAAGACAG
64 GAGACATCTTGAAGGCTCACATCAGCATGAAAAAGACAG
* *
424742 ATATTATCCATGTGGGGCATCTTGAAGGCTCACACCAACATGAAAAG
1 ATATTATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAG
424789 GTTGGGATAT
Statistics
Matches: 135, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
102 8 0.06
103 126 0.93
104 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.22
Consensus pattern (102 bp):
ATATTATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAGACAAAGTAATCCATGTGA
GACATCTTGAAGGCTCACATCAGCATGAAAAAGACAG
Found at i:426110 original size:10 final size:10
Alignment explanation
Indices: 426095--426130 Score: 54
Period size: 10 Copynumber: 3.4 Consensus size: 10
426085 GGAATTCTAG
426095 AGATTAGCAA
1 AGATTAGCAA
426105 AGATTAGCAA
1 AGATTAGCAA
426115 AGATTTCAGCAA
1 AGA-TT-AGCAA
426127 AGAT
1 AGAT
426131 CATGATCCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 13 0.54
11 3 0.12
12 8 0.33
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.22
Consensus pattern (10 bp):
AGATTAGCAA
Found at i:426425 original size:117 final size:115
Alignment explanation
Indices: 426136--426581 Score: 549
Period size: 117 Copynumber: 3.9 Consensus size: 115
426126 AAGATCATGA
* *
426136 TCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCTAA
1 TCCACCACAGAAAGAGGTGAACCAACATTTCAAGAAGAGTTCATAATGAGAAGAACTCATCC-AA
* ** *
426201 --AGG-AG-A-AAGTTCATAATGAGATGAACTTGTT---CC-T--TTCAAG
65 TGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTTGAT
* * * *
426241 TCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCGAT
1 TCCACCACAGAAAGAGGTGAACCAACATTTCAAGAAGAGTTCATAATGAGAAGAACTCATCCAAT
426306 GAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTTGAT
66 GAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTTGAT
* * * *
426356 TCCATCACAGAAAGAGGTGGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCA
1 TCCACCACAGAAAGAGGTGAACCAACA-TTTCAA-GAAGAGTTCATAATGAGAAGAACTCATCCA
426421 ATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTTGAT
64 ATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTTGAT
* * * * * *
426473 TCCATCAAAGAAAGAGGTGGATCAACATTTTCAGTGGAA-AGTTCATAATGAGAAGAACTCATCT
1 TCCACCACAGAAAGAGGTGAACCAACA-TTTCA--AGAAGAGTTCATAATGAGAAGAACTCATCC
* *
426537 AACGA-GAAGAAGAAGTTCATAATGAGAAGAACTCGTTCAACCTTG
63 AATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTG
426582 CATTAACATT
Statistics
Matches: 306, Mismatches: 20, Indels: 19
0.89 0.06 0.06
Matches are distributed among these distances:
104 1 0.00
105 61 0.20
106 3 0.01
107 2 0.01
108 1 0.00
109 24 0.08
112 2 0.01
113 1 0.00
115 25 0.08
116 44 0.14
117 140 0.46
118 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.24
Consensus pattern (115 bp):
TCCACCACAGAAAGAGGTGAACCAACATTTCAAGAAGAGTTCATAATGAGAAGAACTCATCCAAT
GAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTTGAT
Found at i:426565 original size:20 final size:21
Alignment explanation
Indices: 426511--426568 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 21
426501 TTTCAGTGGA
*
426511 AAGTTCATAATGAGAAGAACT
1 AAGTTCATAATGAGAAGAACG
* *
426532 CA--TC-TAACGAGAAGAA-G
1 AAGTTCATAATGAGAAGAACG
426549 AAGTTCATAATGAGAAGAAC
1 AAGTTCATAATGAGAAGAAC
426569 TCGTTCAACC
Statistics
Matches: 28, Mismatches: 5, Indels: 8
0.68 0.12 0.20
Matches are distributed among these distances:
17 1 0.04
18 11 0.39
19 4 0.14
20 11 0.39
21 1 0.04
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.19
Consensus pattern (21 bp):
AAGTTCATAATGAGAAGAACG
Found at i:426574 original size:20 final size:20
Alignment explanation
Indices: 426513--426575 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
426503 TCAGTGGAAA
426513 GTTCATAATGAGAAGAACTC
1 GTTCATAATGAGAAGAACTC
* * ***
426533 -ATC-TAACGAGAAGAAGAA
1 GTTCATAATGAGAAGAACTC
426551 GTTCATAATGAGAAGAACTC
1 GTTCATAATGAGAAGAACTC
426571 GTTCA
1 GTTCA
426576 ACCTTGCATT
Statistics
Matches: 31, Mismatches: 10, Indels: 4
0.69 0.22 0.09
Matches are distributed among these distances:
18 11 0.35
19 4 0.13
20 16 0.52
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.22
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTC
Found at i:426609 original size:90 final size:91
Alignment explanation
Indices: 426496--426667 Score: 267
Period size: 90 Copynumber: 1.9 Consensus size: 91
426486 GAGGTGGATC
* * * * *
426496 AACATTTTCAGTGGAAAGTTCATAATGAGAAGAACTCATCTAACGAGA-AGAAGAAGTTCATAAT
1 AACATTTCCAGTAGAAAGTTCATAATGAGAAAAACTCATCCAACAAGAGAGAAGAAGTTCATAAT
426560 GAGAAGAACTCGTTCAACCTTGCATT
66 GAGAAGAACTCGTTCAACCTTGCATT
426586 AACATTTCCAGTAGAGAA-TTCATAATGAGAAAAACTCATCCAACAAGAGAGAAGAAGTTCATAA
1 AACATTTCCAGTAGA-AAGTTCATAATGAGAAAAACTCATCCAACAAGAGAGAAGAAGTTCATAA
*
426650 TGAGAAGAACTTGTTCAA
65 TGAGAAGAACTCGTTCAA
426668 TTCAACACTT
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
90 40 0.54
91 34 0.46
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.24
Consensus pattern (91 bp):
AACATTTCCAGTAGAAAGTTCATAATGAGAAAAACTCATCCAACAAGAGAGAAGAAGTTCATAAT
GAGAAGAACTCGTTCAACCTTGCATT
Found at i:427086 original size:129 final size:133
Alignment explanation
Indices: 426920--427269 Score: 337
Period size: 134 Copynumber: 2.7 Consensus size: 133
426910 ACGTAGGAAT
* *
426920 GTGTCATCACCCGACCT-GATCTCCTCATTATGTAGGAGTCGTGTCAATCCTTGATAACCAGAAC
1 GTGTCATCACCCGA-CTAGATTTCCTCATTATGTAGGAGTCATGTCAATCCTTGATAACCAGAAC
* * * *
426984 TCTTCATCATGTATGAGCCGTGTTATCA-CCTT-T-AGATTGCCAA-AACTCTTCATCACGTATA
65 TCTTCATCACGTATGAGCCGTGTTATCACCCTTCTAAGATGGCAAAGAACTCTTCATAACGTATA
427045 AGTC-
130 AG-CA
* *
427049 GTGTCATCACCCGACTAGATTTCCTCATTATGTAGGAG-CTATGTCAA-CCTAGATAAACAG-AC
1 GTGTCATCACCCGACTAGATTTCCTCATTATGTAGGAGTC-ATGTCAATCCTTGATAACCAGAAC
* * * *
427111 GTCCTCATCACGTAGGAACCGAGTTATCACCCTTCCTAAAGATGGCAAAGAACTCTTCATAACGT
65 -TCTTCATCACGTATGAGCCGTGTTATCACCCTT-CT-AAGATGGCAAAGAACTCTTCATAACGT
*
427176 ATGAGCA
127 ATAAGCA
* * * * ** *
427183 GTGTCATC-CCATGACTAAATCTT-CTCATTATGTAGGAGTCTTGTCACT-CTTAGACGACTAGA
1 GTGTCATCACC-CGACTAGAT-TTCCTCATTATGTAGGAGTCATGTCAATCCTT-GATAACCAGA
* *
427245 ACTCTTCAGCACGTATGAGTCGTGT
63 ACTCTTCATCACGTATGAGCCGTGT
427270 CGTCTCCCAA
Statistics
Matches: 177, Mismatches: 28, Indels: 26
0.77 0.12 0.11
Matches are distributed among these distances:
127 2 0.01
128 37 0.21
129 44 0.25
131 1 0.01
133 11 0.06
134 55 0.31
135 25 0.14
136 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (133 bp):
GTGTCATCACCCGACTAGATTTCCTCATTATGTAGGAGTCATGTCAATCCTTGATAACCAGAACT
CTTCATCACGTATGAGCCGTGTTATCACCCTTCTAAGATGGCAAAGAACTCTTCATAACGTATAA
GCA
Found at i:427448 original size:20 final size:22
Alignment explanation
Indices: 427423--427478 Score: 75
Period size: 20 Copynumber: 2.7 Consensus size: 22
427413 CGAAAAAACG
427423 TTATTAAT-TATATTAGTATT-
1 TTATTAATCTATATTAGTATTA
*
427443 TTATT-ATCTATATTATTATTA
1 TTATTAATCTATATTAGTATTA
427464 TTATTAATCT-TATTA
1 TTATTAATCTATATTA
427479 CTAATTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 2 0.06
20 16 0.50
21 10 0.31
22 4 0.12
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.61
Consensus pattern (22 bp):
TTATTAATCTATATTAGTATTA
Found at i:429897 original size:16 final size:17
Alignment explanation
Indices: 429860--429897 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
429850 CACATACCAA
429860 TTTTTGTCTTAAAAATG
1 TTTTTGTCTTAAAAATG
* *
429877 ATTTT-TCTTAAAATTG
1 TTTTTGTCTTAAAAATG
429893 TTTTT
1 TTTTT
429898 AAAAGAAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.61
Consensus pattern (17 bp):
TTTTTGTCTTAAAAATG
Found at i:432085 original size:22 final size:22
Alignment explanation
Indices: 432057--432099 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
432047 TATGAGCAGA
432057 AGAAGGGAATCAATCATTCTGG
1 AGAAGGGAATCAATCATTCTGG
432079 AGAAGGGAATCAATCATTCTG
1 AGAAGGGAATCAATCATTCTG
432100 TATAAGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AGAAGGGAATCAATCATTCTGG
Found at i:441873 original size:11 final size:11
Alignment explanation
Indices: 441844--441885 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
441834 TGAACTCGTT
441844 GACCGTTGACC
1 GACCGTTGACC
441855 GA-CGTTGACC
1 GACCGTTGACC
*
441865 GACCGTTGAAC
1 GACCGTTGACC
*
441876 GACCTTTGAC
1 GACCGTTGAC
441886 TTTGACCGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 10 0.37
11 17 0.63
ACGTcount: A:0.21, C:0.31, G:0.26, T:0.21
Consensus pattern (11 bp):
GACCGTTGACC
Found at i:447092 original size:2 final size:2
Alignment explanation
Indices: 447085--447116 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
447075 TCAATCTACA
447085 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
447117 TTACGAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:457883 original size:6 final size:6
Alignment explanation
Indices: 457874--457900 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
457864 TTCTTCTTTG
457874 TTTTAT TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTT
457901 CAAAAATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:458590 original size:8 final size:8
Alignment explanation
Indices: 458577--458616 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
458567 ACCTCACCTT
458577 TATTTTTA
1 TATTTTTA
458585 TATTTTTA
1 TATTTTTA
458593 TATTTTTA
1 TATTTTTA
*
458601 T-TTTTATT
1 TATTTT-TA
458609 TATTTTTA
1 TATTTTTA
458617 ATCTTGAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 4 0.14
8 20 0.71
9 4 0.14
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TATTTTTA
Found at i:458602 original size:14 final size:13
Alignment explanation
Indices: 458575--458609 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
458565 TAACCTCACC
458575 TTTATTTTTATATT
1 TTTATTTTT-TATT
458589 TTTATATTTTTATT
1 TTTAT-TTTTTATT
458603 TTTATTT
1 TTTATTT
458610 ATTTTTAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.10
14 14 0.70
15 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTATTTTTTATT
Found at i:459376 original size:23 final size:24
Alignment explanation
Indices: 459348--459393 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
459338 TCTACCTTTA
459348 TGGCATGTTTATCTCTGT-TTTTG
1 TGGCATGTTTATCTCTGTCTTTTG
*
459371 TGGCATGTTTTTCTCTGTCTTTT
1 TGGCATGTTTATCTCTGTCTTTT
459394 TGTAGCTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.07, C:0.15, G:0.20, T:0.59
Consensus pattern (24 bp):
TGGCATGTTTATCTCTGTCTTTTG
Found at i:462857 original size:3 final size:3
Alignment explanation
Indices: 462851--462908 Score: 66
Period size: 3 Copynumber: 19.0 Consensus size: 3
462841 CTGTGTCTTT
*
462851 TTA TTA TTA TTA -TA TATA TTA TTA TTA TTA CTA TTA CTT- TTA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
462896 TTAA TTA TTA TTA
1 TT-A TTA TTA TTA
462909 CATTTTGTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
2 4 0.08
3 36 0.75
4 8 0.17
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:466054 original size:2 final size:2
Alignment explanation
Indices: 466047--466078 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
466037 CGTGTAGCTA
466047 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
466079 CTTCTTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:472894 original size:2 final size:2
Alignment explanation
Indices: 472887--472920 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
472877 CGTGTAGCTA
472887 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
472921 CTATTCTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:474416 original size:22 final size:22
Alignment explanation
Indices: 474384--474443 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
474374 ATAAAAATCA
474384 TAATTATTTTTAAAATAATATT
1 TAATTATTTTTAAAATAATATT
*
474406 TAATTACTTTTAAAATAATATT
1 TAATTATTTTTAAAATAATATT
474428 TAATTATTTTTCAAAA
1 TAATTATTTTT-AAAA
474444 AAAATGGTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 31 0.89
23 4 0.11
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (22 bp):
TAATTATTTTTAAAATAATATT
Found at i:475034 original size:2 final size:2
Alignment explanation
Indices: 475027--475054 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
475017 CTTAAATCAT
475027 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
475055 ATTGATGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:476661 original size:18 final size:18
Alignment explanation
Indices: 476638--476672 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
476628 GAGTTCCGTC
* *
476638 TCATCTTGGTCTTCATCT
1 TCATCTTCGTCGTCATCT
476656 TCATCTTCGTCGTCATC
1 TCATCTTCGTCGTCATC
476673 CACATCTTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.31, G:0.11, T:0.46
Consensus pattern (18 bp):
TCATCTTCGTCGTCATCT
Found at i:482105 original size:12 final size:12
Alignment explanation
Indices: 482088--482112 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
482078 ATATTTATAA
482088 TATAACAAATTT
1 TATAACAAATTT
482100 TATAACAAATTT
1 TATAACAAATTT
482112 T
1 T
482113 TTTTTCTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TATAACAAATTT
Found at i:483293 original size:28 final size:26
Alignment explanation
Indices: 483258--483328 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 26
483248 CAAGAAATGA
* *
483258 AAAATAAATAAAAACATGGGGCTAAATT
1 AAAATAAATAAAAACAT--AGCCAAATT
*
483286 AAAATAAATTAAAGCTACATAGCCAAATT
1 AAAATAAA-TAAA--AACATAGCCAAATT
483315 AAAATAAATAAAAA
1 AAAATAAATAAAAA
483329 ATAAAATCGG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
26 1 0.03
28 12 0.33
29 19 0.53
31 4 0.11
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.21
Consensus pattern (26 bp):
AAAATAAATAAAAACATAGCCAAATT
Found at i:485336 original size:3 final size:3
Alignment explanation
Indices: 485328--485406 Score: 77
Period size: 3 Copynumber: 25.7 Consensus size: 3
485318 TTCATTTAAA
* * * * *
485328 TAT TAT TAT AAT TAT TAT TAT TAT AAT TAT AAT TAC TAA TAT TAT TATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
* *
485377 TAT TAC TAA TAT TAT TAT TAAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
485407 CAAACGGGCC
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
3 56 0.90
4 6 0.10
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:485348 original size:15 final size:15
Alignment explanation
Indices: 485328--485406 Score: 85
Period size: 15 Copynumber: 5.3 Consensus size: 15
485318 TTCATTTAAA
485328 TATTATTATAATTAT
1 TATTATTATAATTAT
485343 TATTATTATAATTAT
1 TATTATTATAATTAT
* *
485358 AATTACTA-ATATTAT
1 TATTATTATA-ATTAT
485373 TATTTATTACTAA-TAT
1 TA-TTATTA-TAATTAT
485389 TATTA-T-TAATTAT
1 TATTATTATAATTAT
485402 TATTA
1 TATTA
485407 CAAACGGGCC
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
12 3 0.05
13 8 0.15
14 2 0.04
15 30 0.55
16 10 0.18
17 1 0.02
18 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTATTATAATTAT
Found at i:486823 original size:13 final size:13
Alignment explanation
Indices: 486805--486843 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
486795 GTAATTAAAT
486805 TTTTAAATATTTA
1 TTTTAAATATTTA
*
486818 TTTTAAATGAATTA
1 TTTTAAAT-ATTTA
486832 TTTT-AATATTTA
1 TTTTAAATATTTA
486844 GCTTCAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 4 0.17
13 11 0.48
14 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
TTTTAAATATTTA
Found at i:487490 original size:20 final size:21
Alignment explanation
Indices: 487467--487518 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
487457 AGAAATTAAA
487467 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
487487 AATTCTTTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
487509 -ATT-ATTTATT
1 AATTCATTTATT
487519 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:494658 original size:83 final size:83
Alignment explanation
Indices: 494557--494904 Score: 599
Period size: 83 Copynumber: 4.2 Consensus size: 83
494547 AATGGAACAA
*
494557 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
*
494622 AATCATTGAATTTGGAAG
66 AATCATTGAATTTAGAAG
*
494640 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
494705 AATCATTGAATTTAGAAG
66 AATCATTGAATTTAGAAG
*
494723 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
494788 AATCATTGAATTTAGAAG
66 AATCATTGAATTTAGAAG
* * *
494806 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGG-TTGGACAGAAC
1 ATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAAAAC
*
494870 CAATCATTGAATTTGGAAG
65 CAATCATTGAATTTAGAAG
*
494889 ATTAATTTGCTCATAG
1 ATGAATTTGCTCATAG
494905 TAGAAATAAG
Statistics
Matches: 256, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
82 4 0.02
83 252 0.98
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (83 bp):
ATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
AATCATTGAATTTAGAAG
Found at i:497524 original size:22 final size:22
Alignment explanation
Indices: 497493--497547 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
497483 ATCTACACTC
*
497493 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
497515 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
497537 TTCAAAGATGA
1 TTCAAAGATGA
497548 AAGCTTTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:498147 original size:113 final size:113
Alignment explanation
Indices: 497977--499199 Score: 1784
Period size: 113 Copynumber: 10.7 Consensus size: 113
497967 ATCAGCATTA
497977 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
* *
498042 ATTTGTTCAACCTTTTGCTCAAA-TCTATCACTTGATGGATTATTTTTG
66 ATTTGTTCAACCTTTTGCTTAAATTC-ATCACTTGATGGATCATTTTTG
498090 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
* *
498155 ATTTGTTCAACCTTTTG-TCTGAATTCATCACTTGATGGATTATTTTTG
66 ATTTGTTCAACCTTTTGCT-TAAATTCATCACTTGATGGATCATTTTTG
498203 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
* *
498268 ATTTGTTCAACCTTTTG-TCTGAATTCATCACTTGATGGATTATTTTTG
66 ATTTGTTCAACCTTTTGCT-TAAATTCATCACTTGATGGATCATTTTTG
*
498316 CCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
* *
498381 ATTTGTTCAACCTTTTGCTCAAA-TCTATCACTTGATGGATTATTTTTG
66 ATTTGTTCAACCTTTTGCTTAAATTC-ATCACTTGATGGATCATTTTTG
498429 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
* *
498494 ATTTGTTCAACCTTTTG-TCTGAATTCATCACTTGATGGATTATTTTTG
66 ATTTGTTCAACCTTTTGCT-TAAATTCATCACTTGATGGATCATTTTTG
*
498542 CCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
* *
498607 ATTTGTTCAACCTTTTGTTTAAATTCATCACTTGATGGATCAGCTTTT-
66 ATTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCA-TTTTTG
* *
498655 CCAGAAAAAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
* * ***
498720 ATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTG
66 ATTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCATTTTTG
**
498768 CCAG-GAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAG
1 CCAGAGAA-AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* * ***
498832 AAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTG
62 AAGAATTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCATTTTTG
498884 CCAG-GAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 CCAGAGAA-AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* * ***
498948 AAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTG
62 AAGAATTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCATTTTTG
499000 CCAG-GAAGAGTTCATAATGAGAAGAACTCATCATTTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 CCAGAGAA-AGTTCATAATGAGAAGAACTCATC---TGAAGAAGGAAGAAGAAGTTCATAATGAG
* * * ***
499064 AAGAATTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAACATTG
62 AAGAATTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCATTTTTG
*
499116 CCAG-GAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA-AAAGAAGAAGTTCATAATGAG
1 CCAGAGAA-AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
** *
499179 AAGAGCTTATTCAACCTTTTG
62 AAGAATTTGTTCAACCTTTTG
499200 AATGACTCTA
Statistics
Matches: 1060, Mismatches: 31, Indels: 36
0.94 0.03 0.03
Matches are distributed among these distances:
112 8 0.01
113 661 0.62
114 11 0.01
115 37 0.03
116 337 0.32
118 1 0.00
119 5 0.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (113 bp):
CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
ATTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCATTTTTG
Found at i:498717 original size:24 final size:23
Alignment explanation
Indices: 498674--498718 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
498664 GTTCATAATG
*
498674 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
498697 AGAAGAAGTTCATAATG-AGAAG
1 AGAAGAA-TTCAT-ATGAAGAAG
498719 AATTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:499430 original size:3 final size:3
Alignment explanation
Indices: 499422--499512 Score: 92
Period size: 3 Copynumber: 29.7 Consensus size: 3
499412 TTCATTTAAA
* * * * *
499422 TAT TAT TAT AAT TAT TAT TAT AAT TAT TAT TAT TAT AAT TAT AAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
499470 TAA TAT TAT TATT TAT TAC TAA TAT TAT TAT TAAT TAT TAT TA
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
499513 CAAACGGGCC
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
3 66 0.92
4 6 0.08
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:500820 original size:19 final size:19
Alignment explanation
Indices: 500782--500819 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
500772 TATAATTTAG
500782 TCATTTATTTTATATGTTT
1 TCATTTATTTTATATGTTT
500801 TCATTTATTTTAT-TGTTT
1 TCATTTATTTTATATGTTT
500819 T
1 T
500820 TAAAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (19 bp):
TCATTTATTTTATATGTTT
Found at i:505438 original size:140 final size:137
Alignment explanation
Indices: 505264--505621 Score: 511
Period size: 140 Copynumber: 2.6 Consensus size: 137
505254 TGAAAGCACG
* * *
505264 TTTCAGGG-GGCGCATTCCCTTTTTTTGTCAGAGAATAGGTTATAATTGCCCTATTATGTGTTAT
1 TTTCAGGGAGGCACCTT-CCTTTTTTTGTCAGAGAATAGGTTATAATTGCCCTATTATGTGTCAT
* * * * *
505328 GTCCCTCGGTGGGGCACTATTCATGTCAGTACCTATAATGTTTGAGGGGACGCAATAATGTGGTT
65 GTCCCCCGGCGGGGCACTATTCATGTCAGTACCTATAATGTTTGAGAGGACGCAACAATATGGTT
505393 AAAGCGCA
130 AAAGCGCA
* * * * *
505401 TTTTAGGGGGGGCATCTTTCCTTTTTTTTGTCAGAGAATAGGTTATAATTACCTTATTATGTGTC
1 TTTCA-GGGAGGCA-CCTTCC-TTTTTTTGTCAGAGAATAGGTTATAATTGCCCTATTATGTGTC
*
505466 ATGTCCCCCGGCGGGGAACTATTCATGTCAGTACCTATAATGTTTGAGAGGACGCAACAATATGG
63 ATGTCCCCCGGCGGGGCACTATTCATGTCAGTACCTATAATGTTTGAGAGGACGCAACAATATGG
*
505531 TTAAAGCGCG
128 TTAAAGCGCA
* * *
505541 TTTCAGGGAGGCACCTACCCTTTTTTGTCAGAAAATAGGTTATAATTGCCCTATTATGTGTCATG
1 TTTCAGGGAGGCACCTTCCTTTTTTTGTCAGAGAATAGGTTATAATTGCCCTATTATGTGTCATG
505606 TCCCCCGGCGGGGCAC
66 TCCCCCGGCGGGGCAC
505622 ATTGTTACGT
Statistics
Matches: 195, Mismatches: 22, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
137 61 0.31
138 7 0.04
139 12 0.06
140 115 0.59
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (137 bp):
TTTCAGGGAGGCACCTTCCTTTTTTTGTCAGAGAATAGGTTATAATTGCCCTATTATGTGTCATG
TCCCCCGGCGGGGCACTATTCATGTCAGTACCTATAATGTTTGAGAGGACGCAACAATATGGTTA
AAGCGCA
Found at i:505983 original size:137 final size:137
Alignment explanation
Indices: 505732--506173 Score: 572
Period size: 140 Copynumber: 3.2 Consensus size: 137
505722 GTTGGGCATG
* * * * * * *
505732 TAACCTATTTTCTAACAAAAAAGGGAATATGCGCCCCCTAAAATGCACTTTAACCACATTGTTGC
1 TAACCTATTTTCTAACAAAAAAAGGAA-AGGCACCCCCTGAAATACGCTTTAACCACATTGTTAC
*
505797 ATCCCCTCAAAC---ATAGGTACTGACATGAATAGTGCCCCGTCGGGGGACATGACACATAATAG
65 GTCCCCTCAAACATTATAGGTACTGACATGAATAGTGCCCCGTCGGGGGACATGACACATAATAG
505859 GGCAATTA
130 GGCAATTA
*
505867 TAACCTATTTTCTAACAAGAAAAGGAAAGGCACCCCCTGAAATACGCTTTAACCACATTGTTACG
1 TAACCTATTTTCTAACAAAAAAAGGAAAGGCACCCCCTGAAATACGCTTTAACCACATTGTTACG
* * **
505932 TCTCCTCAAACATTATAGGTACTGACATGAATAGTGTCCCACCGGGGGACATGACACATAATAGG
66 TCCCCTCAAACATTATAGGTACTGACATGAATAGTGCCCCGTCGGGGGACATGACACATAATAGG
505997 GCAATTA
131 GCAATTA
* * * * *
506004 TAACCAATTATCTGATA-AAAAAAAGGGAAGGCACACCCCCTGAAATGA-GATTTAACCATATTG
1 TAACCTATTTTCT-A-ACAAAAAAAGGAAAGG--CACCCCCTGAAAT-ACGCTTTAACCACATTG
* * *
506067 TTACGTCCCCTCAAACATTATAAGTACTGATATAAATAGTGCCCCGTCGGGGGACATGACACATA
61 TTACGTCCCCTCAAACATTATAGGTACTGACATGAATAGTGCCCCGTCGGGGGACATGACACATA
506132 ATA-GGCAATTA
126 ATAGGGCAATTA
* * *
506143 TAACCTATTCTCTGACAAAAAAAGGGAAGGC
1 TAACCTATTTTCTAACAAAAAAAGGAAAGGC
506174 GCGTCCTCTG
Statistics
Matches: 269, Mismatches: 29, Indels: 17
0.85 0.09 0.05
Matches are distributed among these distances:
134 41 0.15
135 25 0.09
136 1 0.00
137 67 0.25
138 27 0.10
139 20 0.07
140 87 0.32
141 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.24
Consensus pattern (137 bp):
TAACCTATTTTCTAACAAAAAAAGGAAAGGCACCCCCTGAAATACGCTTTAACCACATTGTTACG
TCCCCTCAAACATTATAGGTACTGACATGAATAGTGCCCCGTCGGGGGACATGACACATAATAGG
GCAATTA
Found at i:510140 original size:13 final size:14
Alignment explanation
Indices: 510111--510137 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
510101 ATAATTTTAA
510111 AAATTTTATTTTTT
1 AAATTTTATTTTTT
510125 AAATTTTATTTTT
1 AAATTTTATTTTT
510138 AAAAGTGTAA
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
AAATTTTATTTTTT
Found at i:517390 original size:7 final size:7
Alignment explanation
Indices: 517378--517409 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
517368 AATCGGTTGG
517378 AGGCTGA
1 AGGCTGA
517385 AGGCTGA
1 AGGCTGA
517392 AGGCTGA
1 AGGCTGA
517399 AGGCTGA
1 AGGCTGA
517406 AGGC
1 AGGC
517410 CAAAGCTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.44, T:0.12
Consensus pattern (7 bp):
AGGCTGA
Found at i:518622 original size:6 final size:6
Alignment explanation
Indices: 518611--518646 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
518601 AAAATATAAA
518611 AATTAT AATTAT AA-TAT AA-T-T AATTAT AATTAT AAT
1 AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT AAT
518647 AAAATCATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 3 0.11
5 7 0.25
6 18 0.64
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
AATTAT
Found at i:518634 original size:15 final size:16
Alignment explanation
Indices: 518616--518646 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
518606 ATAAAAATTA
518616 TAATTATAA-TATAAT
1 TAATTATAATTATAAT
518631 TAATTATAATTATAAT
1 TAATTATAATTATAAT
518647 AAAATCATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATTATAATTATAAT
Found at i:518637 original size:21 final size:20
Alignment explanation
Indices: 518603--518647 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 20
518593 ACCATAATAA
518603 AATATAAAAATTATAATTAT
1 AATATAAAAATTATAATTAT
*
518623 AATATAATTAATTATAATTAT
1 AATATAA-AAATTATAATTAT
518644 AATA
1 AATA
518648 AAATCATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AATATAAAAATTATAATTAT
Found at i:518664 original size:24 final size:21
Alignment explanation
Indices: 518611--518651 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
518601 AAAATATAAA
*
518611 AATTATAATTATAATATAATT
1 AATTATAATTATAATAAAATT
518632 AATTATAATTATAATAAAAT
1 AATTATAATTATAATAAAAT
518652 CATATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTATAATTATAATAAAATT
Found at i:518666 original size:27 final size:27
Alignment explanation
Indices: 518605--518666 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
518595 CATAATAAAA
* *
518605 TATAAAAATTATAATTATAATATAATT
1 TATAATAATTATAATTAAAATATAATT
* * *
518632 AATTATAATTATAA-TAAAATCATATTT
1 TATAATAATTATAATTAAAAT-ATAATT
518659 TATAATAA
1 TATAATAA
518667 CTCATTATTA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
26 5 0.19
27 22 0.81
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (27 bp):
TATAATAATTATAATTAAAATATAATT
Found at i:521943 original size:109 final size:109
Alignment explanation
Indices: 521830--522057 Score: 230
Period size: 109 Copynumber: 2.1 Consensus size: 109
521820 TAAACAGTTA
* * *
521830 CTACATATGACCAAAATG-TAAAACACGCATAAA-TATACAAGTACTAAACAAAAAAT-AACTTT
1 CTACATATGACCAAAATGCAAAAACACGC-TAAAGT-TACAAGGACTAAACAAAAAATAAAC--C
* * *
521892 AAAAATATATAACATGCATAA-AAGTGGGTAAATTACAAAAACAATCG
62 AAAAATATATAACATGCATAAGAAATAGGTAAATTACAAAAACAATCC
** * * *** * *
521939 CTACAGGTGACTAATATGCAAAAACACGCTAAAGTTATGGGGACTAAACAATAATTAAACCAAAA
1 CTACATATGACCAAAATGCAAAAACACGCTAAAGTTACAAGGACTAAACAAAAAATAAACCAAAA
* * *
522004 ATATATAATATGCATAAGAAATAGGTAAATTATAAAATCAATCC
66 ATATATAACATGCATAAGAAATAGGTAAATTACAAAAACAATCC
522048 CTACATATGA
1 CTACATATGA
522058 TCATTTTGCA
Statistics
Matches: 95, Mismatches: 20, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
108 20 0.21
109 62 0.65
110 13 0.14
ACGTcount: A:0.51, C:0.14, G:0.11, T:0.23
Consensus pattern (109 bp):
CTACATATGACCAAAATGCAAAAACACGCTAAAGTTACAAGGACTAAACAAAAAATAAACCAAAA
ATATATAACATGCATAAGAAATAGGTAAATTACAAAAACAATCC
Found at i:525142 original size:18 final size:18
Alignment explanation
Indices: 525111--525159 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
525101 ACTGAAGGTT
* * *
525111 TGTCCTGAATGACCATTA
1 TGTCCCGAAGGACCACTA
525129 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
525147 TCTCTCGAAGGAC
1 TGTCCCGAAGGAC
525160 TACTCCTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:528657 original size:21 final size:21
Alignment explanation
Indices: 528619--528708 Score: 65
Period size: 21 Copynumber: 4.3 Consensus size: 21
528609 GTTAACCTGC
* *
528619 CACCTTGGACAGTCATGTCAG
1 CACCGTGGACTGTCATGTCAG
* *
528640 TACCGTGGACTGTTATGTCAG
1 CACCGTGGACTGTCATGTCAG
* *
528661 CACCGTGAACTG-CAATGCCAG
1 CACCGTGGACTGTC-ATGTCAG
*** * *
528682 CATTATGAACTGTCATATCAG
1 CACCGTGGACTGTCATGTCAG
528703 CACCGT
1 CACCGT
528709 AACGGTTAAT
Statistics
Matches: 51, Mismatches: 16, Indels: 4
0.72 0.23 0.06
Matches are distributed among these distances:
21 50 0.98
22 1 0.02
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (21 bp):
CACCGTGGACTGTCATGTCAG
Found at i:531350 original size:20 final size:19
Alignment explanation
Indices: 531327--531373 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
531317 CGATATACCA
531327 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
531347 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
531367 GGTAAAA
1 GGTAAAA
531374 CGTTACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:531474 original size:181 final size:183
Alignment explanation
Indices: 531123--531586 Score: 702
Period size: 182 Copynumber: 2.6 Consensus size: 183
531113 TCGGTTCGTG
* **
531123 TCGATCCAAAACGATATAACAGGTAAAACTATGATAAAAACCGGTATTGAAATGATAAAACCGGT
1 TCGATCCAAAACGATATAACAGGTAAAAATATGAT-AAAACCGGTATCAAAATGATAAAACCGGT
* * * * *
531188 AAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTCGTGAATTT
65 AAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTCGTGAATTT
* * *
531253 AAAAGAGAAGCAGTTTTAAATCATATAAAGTGTCGATACTTT-TAAAAAATGTA
130 AAAAGAGAAGCAGTTTTAAAGCATATAAAGTGTCGATACTTTAAAAAAAATATA
*
531306 TCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTATCAAAATGATAAAACCGGTA
1 TCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATAAAACCGGTA
* *
531371 AAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTTGTGAATTTA
66 AAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTCGTGAATTTA
* ** * *
531435 AAAGAGAAGTAGTTTTAGCGCCTATAATGTGTCGATACTTTAAAAAAAATATA
131 AAAGAGAAGCAGTTTTAAAGCATATAAAGTGTCGATACTTTAAAAAAAATATA
*
531488 TCGATCCACAACGATATAACA-GT-AAAATATGATAAAACCGGTATCAAAATGATAAAACCGGTA
1 TCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATAAAACCGGTA
*
531551 AAACGATACCAGATATATTGAAAGTGTCGATACTTT
66 AAACGATACCGGATATATTGAAAGTGTCGATACTTT
531587 CGTAAGTACG
Statistics
Matches: 258, Mismatches: 22, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
180 74 0.29
181 64 0.25
182 87 0.34
183 33 0.13
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (183 bp):
TCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATAAAACCGGTA
AAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTCGTGAATTTA
AAAGAGAAGCAGTTTTAAAGCATATAAAGTGTCGATACTTTAAAAAAAATATA
Found at i:531558 original size:17 final size:19
Alignment explanation
Indices: 531518--531558 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
531508 AGTAAAATAT
*
531518 GATAAAACCGGTATCAAAAT
1 GATAAAACCGG-ATCAAAAC
531538 GATAAAACCGG-T-AAAAC
1 GATAAAACCGGATCAAAAC
531555 GATA
1 GATA
531559 CCAGATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 8 0.40
18 1 0.05
20 11 0.55
ACGTcount: A:0.51, C:0.15, G:0.17, T:0.17
Consensus pattern (19 bp):
GATAAAACCGGATCAAAAC
Found at i:533777 original size:21 final size:21
Alignment explanation
Indices: 533751--533815 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
533741 AAGACAATCA
*
533751 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
533772 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
533793 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
533814 AG
1 AG
533816 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:535701 original size:19 final size:19
Alignment explanation
Indices: 535679--535723 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
535669 GTAGGGTTAA
535679 TTTGTATAAGATTTATAAT
1 TTTGTATAAGATTTATAAT
*
535698 TTTGTATACGATTTATAAT
1 TTTGTATAAGATTTATAAT
535717 TTTGTAT
1 TTTGTAT
535724 GTGAATATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56
Consensus pattern (19 bp):
TTTGTATAAGATTTATAAT
Found at i:536314 original size:198 final size:200
Alignment explanation
Indices: 535950--536575 Score: 1126
Period size: 196 Copynumber: 3.2 Consensus size: 200
535940 AATTTACAAT
*
535950 ATGGCAAACA-GGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
536014 CGAAACCCA-AAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTACAAGTATACC-ATTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
536077 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
536142 AATGA
196 AATGA
*
536147 ATGGCAAACA-GGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
536211 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
536276 ATGAGAGAATAGGTCT-AATAATGTATCGACACTTTTGTAGTTTGTGTCGATA-TTTTGGT-CAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
536338 AATGA
196 AATGA
536343 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
536407 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
536472 ATGAGAG-ATAGGTTTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
536536 AATGA
196 AATGA
*
536541 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCC
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCC
536576 CATAAACATC
Statistics
Matches: 415, Mismatches: 8, Indels: 11
0.96 0.02 0.03
Matches are distributed among these distances:
195 7 0.02
196 147 0.35
197 115 0.28
198 126 0.30
199 20 0.05
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.30
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
AATGA
Found at i:538148 original size:6 final size:6
Alignment explanation
Indices: 538137--538176 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
538127 CAAGCGGTCA
* * *
538137 ATGAAG ATGAAG CTGACG ATGAAG ATGACG ATGAAG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGA
538177 CAACGATGAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.42, C:0.07, G:0.33, T:0.17
Consensus pattern (6 bp):
ATGAAG
Found at i:538159 original size:12 final size:12
Alignment explanation
Indices: 538137--538177 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
538127 CAAGCGGTCA
*
538137 ATGAAGATGAAG
1 ATGACGATGAAG
*
538149 CTGACGATGAAG
1 ATGACGATGAAG
538161 ATGACGATGAAG
1 ATGACGATGAAG
538173 ATGAC
1 ATGAC
538178 AACGATGATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.41, C:0.10, G:0.32, T:0.17
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:539740 original size:176 final size:178
Alignment explanation
Indices: 539398--540127 Score: 1020
Period size: 176 Copynumber: 4.1 Consensus size: 178
539388 CTTTTTAATA
* * *
539398 TTGTGTCGGTACTTTATGTCCAGAATAGAAG-AAAATGTGTCGATACCTTTTCAAAAAATGTCG-
1 TTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGA
* * *
539461 -ATTGAAAAAACATCGGAACCC---ATTATAATGTAATAGATAATTTTGTAATATAATCGGTAAA
66 CATT---TACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTAAA
*
539522 TATACCGGTTTTATGAGAGAAAAAATAGGTCTACAA-CTATATCGACAC-TT-TT
128 TATACCGGTTTTATGAGCG----AATAGGTCTACAACCTATATCGACACTTTATT
539574 TTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAAATGTGTCGATACCTTGTCAAAAAGTGTCG
1 TTGTGTCGGTACTTTATGTCCAGAATGGAAG-AAAAATGTGTCGATACCTTGTCAAAAAGTGTCG
539639 ACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAA-TTT-TAATATAACCGGTATAAT
65 ACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTA-AAT
*
539702 ATGCCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTT-TT
129 ATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATT
* *
539751 AATAT-TGTCGGTACTTTATGTCTAGAAT-GAA-AAAAAAGTGTCGATACCTTGTCAAAAAGTGT
1 --T-TGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGT
* *
539813 --ACATTTACACATCGGAACCCATAATTATAA-GTAATAGATAATTTTGTAATATAACCGGTATA
63 CGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTAAA
*
539875 TATATCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATT
128 TATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACAC--TTT-ATT
539929 TTGTGTC-GTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGA
1 TTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGA
539993 CATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGT-A-ATAACCGGTAAATAT
66 CATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTAAATAT
*
540056 ACCGGTTTTATGAGCGAATAGGTTTACAACC--TATCGACACTTTTAATT
131 ACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACAC-TTT-ATT
540104 TTGTGTCGGTACTTTATGTCCAGA
1 TTGTGTCGGTACTTTATGTCCAGA
540128 TTATAATGTA
Statistics
Matches: 508, Mismatches: 20, Indels: 52
0.88 0.03 0.09
Matches are distributed among these distances:
173 11 0.02
174 76 0.15
175 60 0.12
176 108 0.21
177 47 0.09
178 91 0.18
179 75 0.15
180 40 0.08
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (178 bp):
TTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGA
CATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTAAATAT
ACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATT
Found at i:540223 original size:115 final size:112
Alignment explanation
Indices: 540010--540242 Score: 319
Period size: 115 Copynumber: 2.0 Consensus size: 112
540000 ACATCGGAAC
*
540010 CCAGAATTATAATGTAATAGATAATTTTGTAATAACCGGTAAATATACCGGTTTTATGAGCGAAT
1 CCAG-ATTATAATGTAATAGATAATTTTATAATAACCGGTAAATATACCGGTTTTATGAGCGAAT
* *
540075 AGGTTTACAACCTATCGACACTTTTAATTTTGTGTCGGTACTTTATGT
65 AGGTCTACAACCTATCGACACTTTTAATATTGTGTCGGTACTTTATGT
* * * *
540123 CCAGATTATAATGTACTA-CTAATTTTATAATATAACCGGTATAAGTATACCGG-TTTATTAGTG
1 CCAGATTATAATGTAATAGATAATTTTAT-A-ATAACCGGTA-AA-TATACCGGTTTTATGAGCG
540186 AATAGGTCTACAACCTATGTCG-CACTTTTAATATTGTGTCGGTACTTTATGT
62 AATAGGTCTACAACCTA--TCGACACTTTTAATATTGTGTCGGTACTTTATGT
540238 CCAGA
1 CCAGA
540243 ATGGAAGAAA
Statistics
Matches: 107, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
111 8 0.07
112 14 0.13
113 14 0.13
114 26 0.24
115 42 0.39
116 3 0.03
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (112 bp):
CCAGATTATAATGTAATAGATAATTTTATAATAACCGGTAAATATACCGGTTTTATGAGCGAATA
GGTCTACAACCTATCGACACTTTTAATATTGTGTCGGTACTTTATGT
Found at i:540241 original size:291 final size:296
Alignment explanation
Indices: 539851--540425 Score: 941
Period size: 291 Copynumber: 2.0 Consensus size: 296
539841 AAGTAATAGA
* *
539851 TAATTTTGTAATATAACCGGTATATATATCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
1 TAATTTTATAATATAACCGGTATATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
539916 ACACTTTTTAATTTTGTGTCGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTC
66 ACACTTTTTAATATTGTGTCGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTC
*
539981 AAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGT-A-ATA
131 AAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATACATAATTTTGTAATATA
*
540044 ACCGG-TAAATATACCGGTTTTATGAGCGAATAGGTTTACAACC-TATCGACACTTTT-AATTTT
196 ACCGGATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCATATCGACACTTTTAAATTTT
540106 GTGTCGGTACTTTATGTCCAGATTATAATGTACTAC
261 GTGTCGGTACTTTATGTCCAGATTATAATGTACTAC
* * *
540142 TAATTTTATAATATAACCGGTATAAGTATACCGG-TTTATTAGTGAATAGGTCTACAACCTATGT
1 TAATTTTATAATATAACCGGTAT-A-TATACCGGTTTTATGAGCGAATAGGTCTACAACCTATAT
540206 CG-CAC-TTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTT
64 CGACACTTTTTAATATTGTGTC-GTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTT
*
540269 GTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATTTAATACATAATTTTGTAAT
128 GTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATACATAATTTTGTAAT
* * *
540334 ATAACCGGTATAAATATACTGGTTTTATGAGCGAATAGGTCTACAACCTATATTGATACTTTTAA
193 ATAACCGG-ATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACC-ATATCGACACTTTTAA
540399 ATTTTGTGTCGGTACTTTATGTCCAGA
256 ATTTTGTGTCGGTACTTTATGTCCAGA
540426 ATGGAAGAAA
Statistics
Matches: 262, Mismatches: 12, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
290 14 0.05
291 127 0.48
292 31 0.12
293 15 0.06
295 36 0.14
297 11 0.04
298 28 0.11
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (296 bp):
TAATTTTATAATATAACCGGTATATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
ACACTTTTTAATATTGTGTCGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTC
AAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATACATAATTTTGTAATATA
ACCGGATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCATATCGACACTTTTAAATTTT
GTGTCGGTACTTTATGTCCAGATTATAATGTACTAC
Found at i:540447 original size:183 final size:182
Alignment explanation
Indices: 540123--540609 Score: 770
Period size: 183 Copynumber: 2.7 Consensus size: 182
540113 TACTTTATGT
* * * * * *
540123 CCAG-ATTATAATGTACTAC-TAATTTTATAATATAACCGGTATAAGTATACCGG-TTTATTAGT
1 CCAGAATTATAATGTAATACATAATTTTGTAATATAACCGGTATAAATATACTGGTTTTATGAGC
* * *
540185 GAATAGGTCTACAACCTATGTCG-CACTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAA
66 GAATAGGTCTACAACCTATATCGATACTTTTAATTTTGTGTCGGTACTTTATGTCCAGAATGGAA
540249 GAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAAC
131 GAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAAC
*
540301 CCAGAATTATAATTTAATACATAATTTTGTAATATAACCGGTATAAATATACTGGTTTTATGAGC
1 CCAGAATTATAATGTAATACATAATTTTGTAATATAACCGGTATAAATATACTGGTTTTATGAGC
*
540366 GAATAGGTCTACAACCTATATTGATACTTTTAAATTTTGTGTCGGTACTTTATGTCCAGAATGGA
66 GAATAGGTCTACAACCTATATCGATACTTTT-AATTTTGTGTCGGTACTTTATGTCCAGAATGGA
*
540431 AGAAAATTGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAAC
130 AGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAAC
* *
540484 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACTGGTATAAATATA-TCGGTTTTATGAG
1 CCAGAATTATAATGTAATACATAATTTTGTAATATAACCGGTATAAATATACT-GGTTTTATGAG
*
540548 CGAATAGGTCTACAACCTATATCGATACTTTTTAATTTTGTATCGGTAC-TTATGTCCAGAAT
65 CGAATAGGTCTACAACCTATATCGATAC-TTTTAATTTTGTGTCGGTACTTTATGTCCAGAAT
540610 TATAATGTAC
Statistics
Matches: 285, Mismatches: 17, Indels: 10
0.91 0.05 0.03
Matches are distributed among these distances:
178 4 0.01
179 13 0.05
180 31 0.11
181 28 0.10
182 20 0.07
183 185 0.65
184 4 0.01
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (182 bp):
CCAGAATTATAATGTAATACATAATTTTGTAATATAACCGGTATAAATATACTGGTTTTATGAGC
GAATAGGTCTACAACCTATATCGATACTTTTAATTTTGTGTCGGTACTTTATGTCCAGAATGGAA
GAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAAC
Found at i:540671 original size:299 final size:297
Alignment explanation
Indices: 540301--540877 Score: 935
Period size: 299 Copynumber: 1.9 Consensus size: 297
540291 ACATCGGAAC
* *
540301 CCAGAATTATAATTTAATACATAATTTTGTAATATAACCGGTATAAATATACTGGTTTTATGAGC
1 CCAGAATTATAATGTAATACATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
* * *
540366 GAATAGGTCTACAACCTATATTGATACTTTTAAATTTTGTGTCGGTACTTTATGTCCAGAATGGA
66 GAATAGGTCTACAACCTATATCGACACTTTTAAATATTGTGTCGGTACTTTATGTCCAGAATGGA
*
540431 AGAAAATTGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAA
131 AGAAAAATGTGTCGATACC-TGTCAAAAAG-GTCGACATTTACACATCGGAACCCAGAATTATAA
** *
540496 TGTAATAGATAATTTTGTAATATAACTGGTATAAATATATCGGTTTTATGAGCGAATAGGTCTAC
194 TGTAATAGATAATTTT-TAATATAAC--CAATAAATATACCGGTTTTATGAGCGAATAGGTCTAC
*
540561 AACCTATATCGATACTTTTTAATTTTGTATCGGTACTTATGT
256 AACCTATATCGACACTTTTTAATTTTGTATCGGTACTTATGT
* * * *
540603 CCAGAATTATAATGTACTAGAT-A-TTTGTAATAT-ACCGGTATAAGTATACCGGTTTTATTAGC
1 CCAGAATTATAATGTAATACATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
* *
540665 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGA
66 GAATAGGTCTACAACCTATATCGACACTTTTAAATATTGTGTCGGTACTTTATGTCCAGAATGGA
540730 AGAAAAATGTGTCGATACCTGTCAAAAAGGTCGACATTTACACATCGGAACCCAGAATTATAATG
131 AGAAAAATGTGTCGATACCTGTCAAAAAGGTCGACATTTACACATCGGAACCCAGAATTATAATG
540795 TAATAGATAATTTTTAATATAACCAATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCT
196 TAATAGATAATTTTTAATATAACCAATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCT
*
540860 ATATCGACATTTTTTAAT
261 ATATCGACACTTTTTAAT
540878 AATGTGTCGC
Statistics
Matches: 258, Mismatches: 17, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
294 55 0.21
296 9 0.03
297 50 0.19
298 10 0.04
299 104 0.40
300 10 0.04
301 1 0.00
302 19 0.07
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (297 bp):
CCAGAATTATAATGTAATACATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
GAATAGGTCTACAACCTATATCGACACTTTTAAATATTGTGTCGGTACTTTATGTCCAGAATGGA
AGAAAAATGTGTCGATACCTGTCAAAAAGGTCGACATTTACACATCGGAACCCAGAATTATAATG
TAATAGATAATTTTTAATATAACCAATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCT
ATATCGACACTTTTTAATTTTGTATCGGTACTTATGT
Found at i:540694 original size:116 final size:120
Alignment explanation
Indices: 540484--540726 Score: 377
Period size: 116 Copynumber: 2.1 Consensus size: 120
540474 ACATCGGAAC
* *
540484 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACTGGTATAAATATATCGGTTTTATGAGC
1 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
* *
540549 GAATAGGTCTACAACCTATATCGATACTTTTTAATTTTGTATCGGTAC-TTATGT
66 GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTATCGGTACTTTATGT
* * *
540603 CCAGAATTATAATGTACTAGAT-A-TTTGTAATAT-ACCGGTATAAGTATACCGGTTTTATTAGC
1 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
* *
540665 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGT
66 GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTATCGGTACTTTATGT
540720 CCAGAAT
1 CCAGAAT
540727 GGAAGAAAAA
Statistics
Matches: 114, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
116 69 0.61
117 23 0.20
118 1 0.01
119 21 0.18
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (120 bp):
CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTATCGGTACTTTATGT
Found at i:544322 original size:87 final size:85
Alignment explanation
Indices: 544177--544337 Score: 243
Period size: 87 Copynumber: 1.9 Consensus size: 85
544167 AATAGGTTCA
*
544177 ATATAAACGCTACCTATACCATTAATAAGCGCTACCTAATATGTTATGTACTTGATAATATTTCC
1 ATATAAACGCTACCTATACCATTAATAAGCGCTACCTAATATGATATGTACTTGATAATATTTCC
544242 CGTTAAATACCTATTTTATT
66 CGTTAAATACCTATTTTATT
* * *
544262 ATATAAGCGCTATCTATTA-CATTATATAAGCGTTACCTAATATGATATTGTACTTGATAATATT
1 ATATAAACGCTACCTA-TACCATTA-ATAAGCGCTACCTAATATGATA-TGTACTTGATAATATT
*
544326 TCCGGTTAAATA
63 TCCCGTTAAATA
544338 ATATAATATA
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
85 19 0.28
86 22 0.32
87 27 0.40
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (85 bp):
ATATAAACGCTACCTATACCATTAATAAGCGCTACCTAATATGATATGTACTTGATAATATTTCC
CGTTAAATACCTATTTTATT
Found at i:545622 original size:78 final size:77
Alignment explanation
Indices: 545527--545681 Score: 283
Period size: 78 Copynumber: 2.0 Consensus size: 77
545517 AAAGTTTAGT
545527 AATTAAAATAAACTTTAAAAAATTTAGAGGTCGAAAATGTAATTTCTAAATAAAATAAAATTTTA
1 AATTAAAATAAACTTTAAAAAATTTAGAGGTCGAAAATGTAATTTCTAAATAAAATAAAATTTTA
545592 AATAACTGTGAA
66 AATAACTGTGAA
* *
545604 AATTAAATGTAAACTTTAAAAAATTTAGAGGTCGAAAATGTAATTTCTAAATTAAATAAAATTTT
1 AATTAAA-ATAAACTTTAAAAAATTTAGAGGTCGAAAATGTAATTTCTAAATAAAATAAAATTTT
545669 AAATAACTGTGAA
65 AAATAACTGTGAA
545682 TAGTGATCAT
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
77 7 0.09
78 68 0.91
ACGTcount: A:0.52, C:0.05, G:0.10, T:0.34
Consensus pattern (77 bp):
AATTAAAATAAACTTTAAAAAATTTAGAGGTCGAAAATGTAATTTCTAAATAAAATAAAATTTTA
AATAACTGTGAA
Found at i:552304 original size:44 final size:44
Alignment explanation
Indices: 552180--552311 Score: 162
Period size: 43 Copynumber: 3.0 Consensus size: 44
552170 TTAAGACCTC
* * *
552180 TAAGTTTTTTCAATCTCAATTTCT-ACATTTATAATTGAGGCCCT
1 TAAGTTTTTTTAATCTCATTTTTTAAC-TTTATAATTGAGGCCCT
* *
552224 TAA--TTTTCTAATCTCACTTTTTTAATTTTATAATTGAGGCCCT
1 TAAGTTTTTTTAATCTCA-TTTTTTAACTTTATAATTGAGGCCCT
*
552267 TAAGTTTTTTTAATCTCATTTTTTAACTTTCTAATTGAGGTCCCT
1 TAAGTTTTTTTAATCTCATTTTTTAACTTTATAATTGAGG-CCCT
552312 AAGAATTTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
42 11 0.15
43 24 0.32
44 24 0.32
45 16 0.21
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (44 bp):
TAAGTTTTTTTAATCTCATTTTTTAACTTTATAATTGAGGCCCT
Found at i:552321 original size:44 final size:45
Alignment explanation
Indices: 552207--552321 Score: 141
Period size: 44 Copynumber: 2.6 Consensus size: 45
552197 AATTTCTACA
*
552207 TTTATAATTGAGGCCCTT---AATTTTCTAATCTCACTTTTTTAAT
1 TTTATAATTGAGGCCCTTAAGAATTTT-TAATCTCACTTTTTTAAC
**
552250 TTTATAATTGAGGCCCTTAAGTTTTTTTAATCTCA-TTTTTTAAC
1 TTTATAATTGAGGCCCTTAAGAATTTTTAATCTCACTTTTTTAAC
*
552294 TTTCTAATTGAGGTCCC-TAAGAATTTTT
1 TTTATAATTGAGG-CCCTTAAGAATTTTT
552322 TATCATTTAT
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
43 18 0.29
44 29 0.47
45 11 0.18
46 4 0.06
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.50
Consensus pattern (45 bp):
TTTATAATTGAGGCCCTTAAGAATTTTTAATCTCACTTTTTTAAC
Found at i:554505 original size:21 final size:21
Alignment explanation
Indices: 554476--554519 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
554466 CGATAAAAAA
* * *
554476 TTATTTAAAATATTATTATTT
1 TTATCTAAAACATTAATATTT
554497 TTATCTAAAACATTAATATTT
1 TTATCTAAAACATTAATATTT
554518 TT
1 TT
554520 TAATATTTCC
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:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATCTAAAACATTAATATTT
Found at i:562320 original size:323 final size:324
Alignment explanation
Indices: 561732--562378 Score: 1226
Period size: 323 Copynumber: 2.0 Consensus size: 324
561722 ATATACTTTG
*
561732 AAAGAAAAATAGAAAACACAAATTCATTTTAATTCCCTCTAAAAATCAAGGGATACATACCTGAA
1 AAAGAAAAATAGAAAACACAAATTCATTTTAATTCCCTCTAAAAATCAAAGGATACATACCTGAA
561797 GGCCAATCTGGGATTGGAGAAGGCAAAGAAAAAGGCCAAGGTAGAGTCAAAGGTAAGAACTCGTC
66 GGCCAATCTGGGATTGGAGAAGGCAAAGAAAAAGGCCAAGGTAGAGTCAAAGGTAAGAACTCGTC
*
561862 ATCATCTGTGTGTTTATTATGCCAACAAAAACATTCACACCCCAACATATCTTTAAATCTTTGAA
131 ATCATCAGTGTGTTTATTATGCCAACAAAAACATTCACACCCCAACATATCTTTAAATCTTTGAA
561927 ACTCAAAAGACCCACCAAAACCCAGAATTTATCTTCCCCAACCCTCCTTTTCAACTTCATTTCCA
196 ACTCAAAAGACCCACCAAAACCCAGAATTTATCTTCCCCAACCCTCCTTTTCAACTTCATTTCCA
561992 AAGAAACCCTCGAAAAGAAAGAGAGGAAATCAAAAGAA-GG-TGTTTAAAAACAATCCCATCTAT
261 AAGAAACCCTCGAAAAGAAAGAGAGGAAATCAAAAGAAGGGATGTTT-AAAACAATCCCATCTAT
*
562055 AAAGAAAAATAGAAAACACAAATTCATTTTAATTCCCTCTAAAAATCAAAGGATGCATACCTGAA
1 AAAGAAAAATAGAAAACACAAATTCATTTTAATTCCCTCTAAAAATCAAAGGATACATACCTGAA
*
562120 GGCCAATCTGGGATTGGAGAAGGCAAAGAAAAAGGCTAAGGTAGAGTCAAAGGTAAGAACTCGTC
66 GGCCAATCTGGGATTGGAGAAGGCAAAGAAAAAGGCCAAGGTAGAGTCAAAGGTAAGAACTCGTC
562185 ATCATCAGTGTGTTTATTATGCCAACAAAAACATTCACACCCCAACATATCTTTAAATCTTTGAA
131 ATCATCAGTGTGTTTATTATGCCAACAAAAACATTCACACCCCAACATATCTTTAAATCTTTGAA
562250 ACTCAAAAGACCCACCAAAACCCAGAATTTATCTTCCCCAACCCTCCTTTTCAACTTCATTTCCA
196 ACTCAAAAGACCCACCAAAACCCAGAATTTATCTTCCCCAACCCTCCTTTTCAACTTCATTTCCA
*
562315 AAGAAACCCTCGAAAAGAAAGAGAGGCAATCAAAAGAAGGGATGTTTAAAACAATCCCATCTAT
261 AAGAAACCCTCGAAAAGAAAGAGAGGAAATCAAAAGAAGGGATGTTTAAAACAATCCCATCTAT
562379 CCCTCTTTCT
Statistics
Matches: 317, Mismatches: 5, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
323 293 0.92
324 19 0.06
325 5 0.02
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.23
Consensus pattern (324 bp):
AAAGAAAAATAGAAAACACAAATTCATTTTAATTCCCTCTAAAAATCAAAGGATACATACCTGAA
GGCCAATCTGGGATTGGAGAAGGCAAAGAAAAAGGCCAAGGTAGAGTCAAAGGTAAGAACTCGTC
ATCATCAGTGTGTTTATTATGCCAACAAAAACATTCACACCCCAACATATCTTTAAATCTTTGAA
ACTCAAAAGACCCACCAAAACCCAGAATTTATCTTCCCCAACCCTCCTTTTCAACTTCATTTCCA
AAGAAACCCTCGAAAAGAAAGAGAGGAAATCAAAAGAAGGGATGTTTAAAACAATCCCATCTAT
Found at i:563117 original size:3 final size:3
Alignment explanation
Indices: 563109--563169 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
563099 TCGAGTTCAC
563109 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
563156 ATT ATT ATT ATT AT
1 ATT ATT ATT ATT AT
563170 GTGTTGCGGG
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.04
3 55 0.96
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:570886 original size:42 final size:40
Alignment explanation
Indices: 570840--570927 Score: 97
Period size: 40 Copynumber: 2.1 Consensus size: 40
570830 GTCGAATTCA
*
570840 CAACTCGAATTTGACATTTTCGCAACAAGAATTTCT-TTTTCG
1 CAACTCGAATTTGA-A-ATTCGCAACAAGAATTT-TGTTTTCG
* * * *
570882 CAACTCGATTTTTAAATTCGCAACACGAGTTTTGTTTTCG
1 CAACTCGAATTTGAAATTCGCAACAAGAATTTTGTTTTCG
570922 CAACTC
1 CAACTC
570928 AAAAATAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 1 0.03
40 26 0.65
41 1 0.03
42 12 0.30
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (40 bp):
CAACTCGAATTTGAAATTCGCAACAAGAATTTTGTTTTCG
Found at i:570921 original size:20 final size:19
Alignment explanation
Indices: 570856--570925 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 19
570846 GAATTTGACA
*
570856 TTTTCGCAACAAGAATTTCT
1 TTTTCGCAACACGAATTT-T
*
570876 TTTTCGCAACTCG-ATTTT
1 TTTTCGCAACACGAATTTT
* *
570894 TAAATTCGCAACACGAGTTTT
1 T--TTTCGCAACACGAATTTT
570915 GTTTTCGCAAC
1 -TTTTCGCAAC
570926 TCAAAAATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 2 0.05
19 4 0.10
20 29 0.73
21 4 0.10
22 1 0.03
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (19 bp):
TTTTCGCAACACGAATTTT
Found at i:570994 original size:20 final size:20
Alignment explanation
Indices: 570947--570986 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
570937 ATCCGCAACT
* *
570947 CGAATTTCATTTTTGAGTTG
1 CGAATTTCATTTTCGAATTG
570967 CGAATTTCATTTTCGAATTG
1 CGAATTTCATTTTCGAATTG
570987 TGATTTTCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.47
Consensus pattern (20 bp):
CGAATTTCATTTTCGAATTG
Found at i:571482 original size:12 final size:12
Alignment explanation
Indices: 571461--571494 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
571451 ACCACATTTC
*
571461 CAATACCAAACA
1 CAATATCAAACA
571473 CAATATCAAACA
1 CAATATCAAACA
*
571485 CAATCTCAAA
1 CAATATCAAA
571495 ATCCACAACT
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:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:571632 original size:24 final size:24
Alignment explanation
Indices: 571614--571660 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
571604 AGTCAGTATT
571614 CGAAATTTGATCTTGGTCAATACA
1 CGAAATTTGATCTTGGTCAATACA
* *
571638 CGGACTTTGATCTTGGTCAATAC
1 CGAAATTTGATCTTGGTCAATAC
571661 TCGGATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (24 bp):
CGAAATTTGATCTTGGTCAATACA
Found at i:571665 original size:24 final size:24
Alignment explanation
Indices: 571619--571672 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
571609 GTATTCGAAA
571619 TTTGATCTTGGTCAATACACGGAC
1 TTTGATCTTGGTCAATACACGGAC
* *
571643 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACACGGAC
571667 TTTGAT
1 TTTGAT
571673 GATGTTTCAG
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:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACACGGAC
Found at i:574240 original size:14 final size:11
Alignment explanation
Indices: 574207--574239 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
574197 TCTGAAAACT
574207 CTTTCTTCTTC
1 CTTTCTTCTTC
574218 CTTTCTTCTTC
1 CTTTCTTCTTC
574229 CTTTCTTCTTC
1 CTTTCTTCTTC
574240 TCCCAACCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (11 bp):
CTTTCTTCTTC
Found at i:575433 original size:38 final size:36
Alignment explanation
Indices: 575383--575459 Score: 118
Period size: 38 Copynumber: 2.1 Consensus size: 36
575373 GATTACCTAC
*
575383 ACACAGATCATCCTTCGGGATGACAGGTCCTTCGGG
1 ACACAGATCATCCTTCGGGATGACAGGTCATTCGGG
*
575419 ACACAGATGACATCCTTCGGGATGATAGGTCATTCGGG
1 ACACAGAT--CATCCTTCGGGATGACAGGTCATTCGGG
575457 ACA
1 ACA
575460 TTTATACGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 8 0.22
38 29 0.78
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.22
Consensus pattern (36 bp):
ACACAGATCATCCTTCGGGATGACAGGTCATTCGGG
Found at i:577381 original size:33 final size:33
Alignment explanation
Indices: 577344--577433 Score: 101
Period size: 33 Copynumber: 2.7 Consensus size: 33
577334 TCGAAAATCG
*
577344 AATTCGCAATTCGAAACTCAAATTCGCAACTC-A
1 AATTCG-AATTCGAAACTCAAATTCACAACTCGA
* *
577377 AATTCGTAACTCGAAATTCAAATTCACAACTCGA
1 AATTCG-AATTCGAAACTCAAATTCACAACTCGA
* * *
577411 AAATCGAATTCGCAACTCGAATT
1 AATTCGAATTCGAAACTCAAATT
577434 TCGAATTCGC
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
33 41 0.87
34 6 0.13
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (33 bp):
AATTCGAATTCGAAACTCAAATTCACAACTCGA
Found at i:577388 original size:53 final size:53
Alignment explanation
Indices: 577324--577433 Score: 148
Period size: 53 Copynumber: 2.1 Consensus size: 53
577314 TCGAAAATCG
* * * *
577324 AATTCGCAACTCGAAAATCGAATTCGCAATTCGAAACTCAAATTCGCAACTCA
1 AATTCGCAACTCGAAAATCAAATTCACAACTCGAAAATCAAATTCGCAACTCA
* * * *
577377 AATTCGTAACTCGAAATTCAAATTCACAACTCGAAAATCGAATTCGCAACTCG
1 AATTCGCAACTCGAAAATCAAATTCACAACTCGAAAATCAAATTCGCAACTCA
577430 AATT
1 AATT
577434 TCGAATTCGC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.40, C:0.25, G:0.11, T:0.25
Consensus pattern (53 bp):
AATTCGCAACTCGAAAATCAAATTCACAACTCGAAAATCAAATTCGCAACTCA
Found at i:577422 original size:73 final size:73
Alignment explanation
Indices: 577303--577453 Score: 221
Period size: 73 Copynumber: 2.1 Consensus size: 73
577293 TACCTAGTGA
* * *
577303 AAATTCGCAACTCGAAAATCGAATTCGCAACTCGAAAATCGAATTCGCAATTCGAAACTCAAATT
1 AAATTCGCAACTCGAAAATCAAATTCACAACTCGAAAATCGAATTCGCAACTCGAAACTCAAATT
577368 CGCAACTC
66 CGCAACTC
* * ** *
577376 AAATTCGTAACTCGAAATTCAAATTCACAACTCGAAAATCGAATTCGCAACTCGAATTTCGAATT
1 AAATTCGCAACTCGAAAATCAAATTCACAACTCGAAAATCGAATTCGCAACTCGAAACTCAAATT
577441 CGCAACTC
66 CGCAACTC
*
577449 GAATT
1 AAATT
577454 TCATTTTCGA
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.25
Consensus pattern (73 bp):
AAATTCGCAACTCGAAAATCAAATTCACAACTCGAAAATCGAATTCGCAACTCGAAACTCAAATT
CGCAACTC
Found at i:577453 original size:13 final size:13
Alignment explanation
Indices: 577314--577438 Score: 74
Period size: 13 Copynumber: 9.4 Consensus size: 13
577304 AATTCGCAAC
*
577314 TCGAAAATCGAAT
1 TCGAAACTCGAAT
* *
577327 TCGCAACTCGAAAA
1 TCGAAACTCG-AAT
*
577341 TCG-AATTCGCAAT
1 TCGAAACTCG-AAT
*
577354 TCGAAACTCAAAT
1 TCGAAACTCGAAT
* *
577367 TCGCAACTCAAAT
1 TCGAAACTCGAAT
*
577380 TCGTAACTCGAAAT
1 TCGAAACTCG-AAT
* * *
577394 TC-AAATTCACAAC
1 TCGAAACTC-GAAT
*
577407 TCGAAAATCGAAT
1 TCGAAACTCGAAT
*
577420 TCGCAACTCGAATT
1 TCGAAACTCGAA-T
577434 TCGAA
1 TCGAA
577439 TTCGCAACTC
Statistics
Matches: 85, Mismatches: 21, Indels: 11
0.73 0.18 0.09
Matches are distributed among these distances:
13 61 0.72
14 24 0.28
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (13 bp):
TCGAAACTCGAAT
Found at i:577455 original size:20 final size:20
Alignment explanation
Indices: 577304--577451 Score: 166
Period size: 20 Copynumber: 7.8 Consensus size: 20
577294 ACCTAGTGAA
577304 AATTCGCAACTCGAAAATCG
1 AATTCGCAACTCGAAAATCG
577324 AATTCGCAACTCGAAAATCG
1 AATTCGCAACTCGAAAATCG
* * *
577344 AATTCGCAATTCGAAACTCA
1 AATTCGCAACTCGAAAATCG
577364 AATTCGCAACTC----A---
1 AATTCGCAACTCGAAAATCG
* * *
577377 AATTCGTAACTCGAAATTCA
1 AATTCGCAACTCGAAAATCG
*
577397 AATTCACAACTCGAAAATCG
1 AATTCGCAACTCGAAAATCG
**
577417 AATTCGCAACTCGAATTTCG
1 AATTCGCAACTCGAAAATCG
577437 AATTCGCAACTCGAA
1 AATTCGCAACTCGAA
577452 TTTCATTTTC
Statistics
Matches: 107, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
13 11 0.10
20 96 0.90
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.24
Consensus pattern (20 bp):
AATTCGCAACTCGAAAATCG
Found at i:577475 original size:20 final size:20
Alignment explanation
Indices: 577452--577515 Score: 110
Period size: 20 Copynumber: 3.2 Consensus size: 20
577442 GCAACTCGAA
577452 TTTCATTTTCGAGTTGCGAT
1 TTTCATTTTCGAGTTGCGAT
* *
577472 TTTCATTTTCAAGTTGCGAA
1 TTTCATTTTCGAGTTGCGAT
577492 TTTCATTTTCGAGTTGCGAT
1 TTTCATTTTCGAGTTGCGAT
577512 TTTC
1 TTTC
577516 GTGTTACGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.17, C:0.16, G:0.17, T:0.50
Consensus pattern (20 bp):
TTTCATTTTCGAGTTGCGAT
Found at i:577526 original size:34 final size:36
Alignment explanation
Indices: 577448--577542 Score: 106
Period size: 40 Copynumber: 2.6 Consensus size: 36
577438 ATTCGCAACT
* *
577448 CGAATTTCATTTTCGAGTTGCGATTTTCATTTTCAAGTTG
1 CGAATTTCATTTTCGAGTTGCGATTTTC--TGT--AGTTA
577488 CGAATTTCATTTTCGAGTTGCGATTTTC-GT-GTTA
1 CGAATTTCATTTTCGAGTTGCGATTTTCTGTAGTTA
577522 CGAA-TTCGATTTTCGAGTTGC
1 CGAATTTC-ATTTTCGAGTTGC
577543 AAAGAATTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
33 3 0.06
34 20 0.38
37 1 0.02
40 28 0.54
ACGTcount: A:0.19, C:0.16, G:0.20, T:0.45
Consensus pattern (36 bp):
CGAATTTCATTTTCGAGTTGCGATTTTCTGTAGTTA
Found at i:580931 original size:21 final size:21
Alignment explanation
Indices: 580887--580991 Score: 79
Period size: 21 Copynumber: 5.0 Consensus size: 21
580877 AGTATGGAAT
*
580887 GTGAATTTTGAACGATGCGG-G
1 GTGAATCTTGAACGATG-GGAG
*
580908 GTGAATCTTGAATGATGGGAG
1 GTGAATCTTGAACGATGGGAG
* *
580929 GTGGATCCTGAACGATGGGAG
1 GTGAATCTTGAACGATGGGAG
* ** * * *
580950 GGGCCTCTTGAACAATGAGAA
1 GTGAATCTTGAACGATGGGAG
*
580971 GTGAATCCTGAA-GAATGGGAG
1 GTGAATCTTGAACG-ATGGGAG
580992 ATAGACCCTG
Statistics
Matches: 63, Mismatches: 19, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
20 2 0.03
21 61 0.97
ACGTcount: A:0.29, C:0.11, G:0.37, T:0.23
Consensus pattern (21 bp):
GTGAATCTTGAACGATGGGAG
Found at i:581375 original size:21 final size:21
Alignment explanation
Indices: 581359--581436 Score: 104
Period size: 21 Copynumber: 3.7 Consensus size: 21
581349 TCTCACATAG
581359 AGCACCTACCTCATCACGTAA
1 AGCACCTACCTCATCACGTAA
* **
581380 AGAACC-ATTGTCATCACGTAA
1 AGCACCTA-CCTCATCACGTAA
581401 AGCACCTACCTCATCACGTAA
1 AGCACCTACCTCATCACGTAA
*
581422 AGCACCTAACTCATC
1 AGCACCTACCTCATC
581437 TCGTGGAGGT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 1 0.02
21 46 0.96
22 1 0.02
ACGTcount: A:0.35, C:0.35, G:0.10, T:0.21
Consensus pattern (21 bp):
AGCACCTACCTCATCACGTAA
Found at i:581630 original size:42 final size:42
Alignment explanation
Indices: 581536--581659 Score: 173
Period size: 42 Copynumber: 3.0 Consensus size: 42
581526 GTGATGGAAT
* * *
581536 AGGTGATGGATCTCGGTGTCGAGGTGTAGAGTCTACT--A-G
1 AGGTGATGGATCTCAGTGTCGAGGTGTAGAATCGACTCGATG
*
581575 AGGTGATGGATCTCAGTGTCGAGGTGTAGAATCGGCTCGATG
1 AGGTGATGGATCTCAGTGTCGAGGTGTAGAATCGACTCGATG
* *
581617 AGGTGATGGATCTCAGTGTCGAAGTGAAGAATCGACTCGATG
1 AGGTGATGGATCTCAGTGTCGAGGTGTAGAATCGACTCGATG
581659 A
1 A
581660 AAAAGTAGGG
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
39 33 0.44
41 1 0.01
42 41 0.55
ACGTcount: A:0.24, C:0.14, G:0.36, T:0.26
Consensus pattern (42 bp):
AGGTGATGGATCTCAGTGTCGAGGTGTAGAATCGACTCGATG
Found at i:582643 original size:17 final size:16
Alignment explanation
Indices: 582621--582686 Score: 64
Period size: 15 Copynumber: 4.1 Consensus size: 16
582611 CCGTGTCCCG
*
582621 ACCCGGATGTTACGGGT
1 ACCCGGATATT-CGGGT
*
582638 ACCCGG-TAATCGGGT
1 ACCCGGATATTCGGGT
*
582653 ACCCGGATTTTGCGGGT
1 ACCCGGATATT-CGGGT
*
582670 ACCC-GATAATCGGGT
1 ACCCGGATATTCGGGT
582685 AC
1 AC
582687 TCGATACCCA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
15 18 0.44
16 8 0.20
17 15 0.37
ACGTcount: A:0.20, C:0.26, G:0.32, T:0.23
Consensus pattern (16 bp):
ACCCGGATATTCGGGT
Found at i:582657 original size:32 final size:32
Alignment explanation
Indices: 582621--582686 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
582611 CCGTGTCCCG
*
582621 ACCCGGATGTTACGGGTACCCGGTAATCGGGT
1 ACCCGGATGTTACGGGTACCCGATAATCGGGT
* *
582653 ACCCGGATTTTGCGGGTACCCGATAATCGGGT
1 ACCCGGATGTTACGGGTACCCGATAATCGGGT
582685 AC
1 AC
582687 TCGATACCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.20, C:0.26, G:0.32, T:0.23
Consensus pattern (32 bp):
ACCCGGATGTTACGGGTACCCGATAATCGGGT
Found at i:582691 original size:15 final size:15
Alignment explanation
Indices: 582633--582692 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
582623 CCGGATGTTA
*
582633 CGGGTACCCGGTAAT
1 CGGGTACCCGATAAT
**
582648 CGGGTACCCGGATTTT
1 CGGGTACCC-GATAAT
582664 GCGGGTACCCGATAAT
1 -CGGGTACCCGATAAT
*
582680 CGGGTACTCGATA
1 CGGGTACCCGATA
582693 CCCAGTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
15 21 0.57
16 7 0.19
17 9 0.24
ACGTcount: A:0.20, C:0.25, G:0.32, T:0.23
Consensus pattern (15 bp):
CGGGTACCCGATAAT
Found at i:584175 original size:22 final size:22
Alignment explanation
Indices: 584095--584189 Score: 113
Period size: 22 Copynumber: 4.3 Consensus size: 22
584085 GAGGGGGTAT
* *
584095 TCGGAGATGGGGA-TGAATGTCG
1 TCGGAGATGGGGACAG-GTGTCG
584117 TCGGAGATGGGGAC-GGATGTCG
1 TCGGAGATGGGGACAGG-TGTCG
584139 TCGGAGATGGGGACAGGTGTCG
1 TCGGAGATGGGGACAGGTGTCG
* *
584161 ACGAAGATGGGGACAGGTGTCG
1 TCGGAGATGGGGACAGGTGTCG
*
584183 CCGGAGA
1 TCGGAGA
584190 GAGTGAGAGA
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
22 63 0.97
23 2 0.03
ACGTcount: A:0.22, C:0.14, G:0.47, T:0.17
Consensus pattern (22 bp):
TCGGAGATGGGGACAGGTGTCG
Found at i:584309 original size:20 final size:20
Alignment explanation
Indices: 584286--584373 Score: 63
Period size: 20 Copynumber: 4.4 Consensus size: 20
584276 AATTAAAAGC
584286 TGAGTTGCGAATTCGAAAAT
1 TGAGTTGCGAATTCGAAAAT
* **
584306 TGAGTTGTGAAAACG-AAAT
1 TGAGTTGCGAATTCGAAAAT
* *
584325 TCGTGTTGCGAAATT-GAAACT
1 T-GAGTTGCG-AATTCGAAAAT
* * *
584346 CGCGTTGCGAATTAGAAAAT
1 TGAGTTGCGAATTCGAAAAT
*
584366 CGAGTTGC
1 TGAGTTGC
584374 AAAAACGAAA
Statistics
Matches: 52, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
19 9 0.17
20 38 0.73
21 5 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.28
Consensus pattern (20 bp):
TGAGTTGCGAATTCGAAAAT
Found at i:584373 original size:40 final size:40
Alignment explanation
Indices: 584320--584458 Score: 138
Period size: 40 Copynumber: 3.4 Consensus size: 40
584310 TTGTGAAAAC
* * * * *
584320 GAAATTCGTGTTGCGAAATTGAAACTCGCGTTGCGAATTA
1 GAAAATCGAGTTGCGAAAATGAAATTCGTGTTGCGAATTA
* *
584360 GAAAATCGAGTTGCAAAAACGAAATTCGTGTTGCGAATTTA
1 GAAAATCGAGTTGCGAAAATGAAATTCGTGTTGCGAA-TTA
* *
584401 -AAAATCGAGTAGCGAAAAAGAAATTCGTGTTGCGAAATT-
1 GAAAATCGAGTTGCGAAAATGAAATTCGTGTTGCG-AATTA
*
584440 GTCAAATTCGAGTTGCGAA
1 G--AAAATCGAGTTGCGAA
584459 TTTGACTTCT
Statistics
Matches: 82, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
40 63 0.77
41 5 0.06
42 14 0.17
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.27
Consensus pattern (40 bp):
GAAAATCGAGTTGCGAAAATGAAATTCGTGTTGCGAATTA
Found at i:584416 original size:60 final size:59
Alignment explanation
Indices: 584267--584437 Score: 198
Period size: 60 Copynumber: 2.8 Consensus size: 59
584257 GTTTATATAT
* * * *
584267 GTGTTGCGAAATTAAAAGCTGAGTTGCGAATTCGAAAATTGAGTTGTGAAAACGAAATTC
1 GTGTTGCGAAATTAAAATC-GAGTTGCGAATTAGAAAATCGAGTTGCGAAAACGAAATTC
* * *
584327 GTGTTGCGAAATTGAAACTCGCGTTGCGAATTAGAAAATCGAGTTGCAAAAACGAAATTC
1 GTGTTGCGAAATT-AAAATCGAGTTGCGAATTAGAAAATCGAGTTGCGAAAACGAAATTC
* * ** * *
584387 GTGTTGCGAATTTAAAAATCGAGTAGCGAAAAAGAAATTCGTGTTGCGAAA
1 GTGTTGCGAAATT-AAAATCGAGTTGCGAATTAGAAAATCGAGTTGCGAAA
584438 TTGTCAAATT
Statistics
Matches: 93, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
60 89 0.96
61 4 0.04
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26
Consensus pattern (59 bp):
GTGTTGCGAAATTAAAATCGAGTTGCGAATTAGAAAATCGAGTTGCGAAAACGAAATTC
Found at i:584435 original size:20 final size:20
Alignment explanation
Indices: 584309--584437 Score: 93
Period size: 20 Copynumber: 6.5 Consensus size: 20
584299 CGAAAATTGA
* *
584309 GTTGTGAAAACGAAATTCGT
1 GTTGCGAAAAAGAAATTCGT
** * *
584329 GTTGCGAAATTGAAACTCGC
1 GTTGCGAAAAAGAAATTCGT
** * *
584349 GTTGCGAATTAGAAAATCGA
1 GTTGCGAAAAAGAAATTCGT
584369 GTTGC-AAAAACGAAATTCGT
1 GTTGCGAAAAA-GAAATTCGT
* *
584389 GTTGCGAATTTAA-AAA-TCGA
1 GTTGCGAA--AAAGAAATTCGT
*
584409 GTAGCGAAAAAGAAATTCGT
1 GTTGCGAAAAAGAAATTCGT
584429 GTTGCGAAA
1 GTTGCGAAA
584438 TTGTCAAATT
Statistics
Matches: 84, Mismatches: 19, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
18 2 0.02
19 6 0.07
20 69 0.82
21 5 0.06
23 2 0.02
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (20 bp):
GTTGCGAAAAAGAAATTCGT
Found at i:586676 original size:5 final size:5
Alignment explanation
Indices: 586666--586699 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
586656 ATTTATTTAT
*
586666 ATATA ATATA ATATA ATATA ATATT ATATA ATAT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATAT
586700 GAAAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
ATATA
Done.