Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008082.1 Hibiscus syriacus cultivar Beakdansim tig00110584_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: 6025995
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 28
Found at i:3526908 original size:30 final size:31
Alignment explanation
Indices: 3526853--3526924 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
3526843 TAACATGGGC
* *
3526853 GTCCATAGGTCCTGAAGAACCTAGGTA-AGTT
1 GTCCATATGTCCTGAAGAACATAGGTATA-TT
*
3526884 GTCCATATGTCCT-TAGAACATAGGTATATT
1 GTCCATATGTCCTGAAGAACATAGGTATATT
3526914 GTCCATATGTC
1 GTCCATATGTC
3526925 TCAAAAGACA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 24 0.65
31 13 0.35
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (31 bp):
GTCCATATGTCCTGAAGAACATAGGTATATT
Found at i:3526999 original size:32 final size:30
Alignment explanation
Indices: 3526853--3526999 Score: 94
Period size: 31 Copynumber: 4.9 Consensus size: 30
3526843 TAACATGGGC
* * * *
3526853 GTCCATAGGTCCTGAAGAACCTAGGTAAGTT
1 GTCCATATGTCC-GTAGAACATAGGTAATTT
*
3526884 GTCCATATGTCCTTAGAACATAGGT-ATATT
1 GTCCATATGTCCGTAGAACATAGGTAAT-TT
* *
3526914 GTCCATATGTCTC-AAAAGACATAGGTAATTCT
1 GTCCATATGTC-CGTAGA-ACATAGGTAATT-T
*
3526946 GT-CATA---ACG-A-ATACATAGGTAATTCT
1 GTCCATATGTCCGTAGA-ACATAGGTAATT-T
3526972 GTCCATATGTTCCGTAGAACATAGGTAA
1 GTCCATATG-TCCGTAGAACATAGGTAA
3527000 ACCTTCGACT
Statistics
Matches: 93, Mismatches: 10, Indels: 25
0.73 0.08 0.20
Matches are distributed among these distances:
26 17 0.18
27 6 0.06
29 1 0.01
30 25 0.27
31 27 0.29
32 16 0.17
33 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (30 bp):
GTCCATATGTCCGTAGAACATAGGTAATTT
Found at i:3527010 original size:202 final size:208
Alignment explanation
Indices: 3526644--3527057 Score: 741
Period size: 202 Copynumber: 2.0 Consensus size: 208
3526634 CTCGAAAACT
3526644 GTCCATAGGTCCTGAAGAACCTAGGTAAGTTGTCCATATGTTCCTTAGAACATAGGTATATTGTC
1 GTCCATAGGTCCTGAAGAACCTAGGTAAGTTGTCCATATGTTCCTTAGAACATAGGTATATTGTC
*
3526709 CATATGTCTCAAAAGACATAGGTAATTCTGTCCATATGTCCCGAAATACATAGGTAATTCTGTCC
66 CATATGTCTCAAAAGACATAGGTAATTCTGTCCATA--T-ACGAAATACATAGGTAATTCTGTCC
3526774 ATATGTTCCGTAGAACATAGGTAAACCTTCGACTCTTGGCATGTCAACT-TACCACTAG-CTCAT
128 ATATGTTCCGTAGAACATAGGTAAACCTTCGACTCTTGGCATGTCAACTATACCACTAGCCTCAT
3526837 ATTACATAACATGGGC
193 ATTACATAACATGGGC
3526853 GTCCATAGGTCCTGAAGAACCTAGGTAAGTTGTCCATATG-TCCTTAGAACATAGGTATATTGTC
1 GTCCATAGGTCCTGAAGAACCTAGGTAAGTTGTCCATATGTTCCTTAGAACATAGGTATATTGTC
3526917 CATATGTCTCAAAAGACATAGGTAATTCTGT-CATA-ACG-AATACATAGGTAATTCTGTCCATA
66 CATATGTCTCAAAAGACATAGGTAATTCTGTCCATATACGAAATACATAGGTAATTCTGTCCATA
3526979 TGTTCCGTAGAACATAGGTAAACCTTCGACTCTTGGCATGTCAACTATACCACTAGCTCTCATAT
131 TGTTCCGTAGAACATAGGTAAACCTTCGACTCTTGGCATGTCAACTATACCACTAGC-CTCATAT
3527044 TACATAACATGGGC
195 TACATAACATGGGC
3527058 ATTATCATTT
Statistics
Matches: 201, Mismatches: 1, Indels: 10
0.95 0.00 0.05
Matches are distributed among these distances:
202 70 0.35
203 11 0.05
205 21 0.10
207 4 0.02
208 55 0.27
209 40 0.20
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (208 bp):
GTCCATAGGTCCTGAAGAACCTAGGTAAGTTGTCCATATGTTCCTTAGAACATAGGTATATTGTC
CATATGTCTCAAAAGACATAGGTAATTCTGTCCATATACGAAATACATAGGTAATTCTGTCCATA
TGTTCCGTAGAACATAGGTAAACCTTCGACTCTTGGCATGTCAACTATACCACTAGCCTCATATT
ACATAACATGGGC
Found at i:3528945 original size:30 final size:30
Alignment explanation
Indices: 3528879--3528945 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
3528869 ATGAATTTTT
*
3528879 AATTTGACCCCTAAAATTAGGAAAAATATT
1 AATTTGACCCCTAAAATTAGGAAAAATATC
*
3528909 ATTTTGA-CCCTAAAATTTA-GATAAAATATC
1 AATTTGACCCCTAAAA-TTAGGA-AAAATATC
3528939 AATTTGA
1 AATTTGA
3528946 TCAAATTCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 10 0.31
30 22 0.69
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (30 bp):
AATTTGACCCCTAAAATTAGGAAAAATATC
Found at i:3529609 original size:18 final size:19
Alignment explanation
Indices: 3529572--3529651 Score: 56
Period size: 20 Copynumber: 4.1 Consensus size: 19
3529562 TTTTAAAGAT
* *
3529572 TAAAAAATTAAAAATAATA
1 TAAAATATTATAAATAATA
3529591 TTAAAAT-TTATAAAT-ATA
1 -TAAAATATTATAAATAATA
* *
3529609 TAAAATATTATTATTATAAACA
1 TAAAATATTA-TA-AAT-AATA
*
3529631 TAAAAAATTATAACATAATA
1 TAAAATATTATAA-ATAATA
3529651 T
1 T
3529652 TTTATAAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
17 6 0.13
18 6 0.13
19 9 0.19
20 11 0.23
21 4 0.09
22 11 0.23
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAATATTATAAATAATA
Found at i:3529640 original size:22 final size:24
Alignment explanation
Indices: 3529598--3529641 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3529588 ATATTAAAAT
*
3529598 TTATAAATATATAAAATATTATTA
1 TTATAAACATATAAAATATTATTA
3529622 TTATAAACATA-AAAA-ATTAT
1 TTATAAACATATAAAATATTAT
3529642 AACATAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 4 0.21
24 10 0.53
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
TTATAAACATATAAAATATTATTA
Found at i:3530361 original size:43 final size:43
Alignment explanation
Indices: 3530274--3530602 Score: 347
Period size: 43 Copynumber: 7.7 Consensus size: 43
3530264 GCCGCTAAAG
* * * *
3530274 TTAGCGGCGTTT-TAAACAAAAAACACTGCAATAGGTTTTTTTAT
1 TTAGCGGCGTTTGT-CAC-AAAAACGCCGCAATAGGTTTTGTTAT
* *
3530318 TTAGCGGCGTTTGTCACAAAAACGCCGCAATATGTGTTGTTAT
1 TTAGCGGCGTTTGTCACAAAAACGCCGCAATAGGTTTTGTTAT
* * *
3530361 TTAACAGCGTTTGTCACAAAAACGCCGCAATAGGTGTTGTTAT
1 TTAGCGGCGTTTGTCACAAAAACGCCGCAATAGGTTTTGTTAT
*
3530404 TTAGCGGCGTTTGTCAAAAAAACGCCGCAATAGGTTTTGTTAT
1 TTAGCGGCGTTTGTCACAAAAACGCCGCAATAGGTTTTGTTAT
* * * *
3530447 TTAGCGGCGTTTATCACAAAAATGTCGTAATAGGTTTTGTTAT
1 TTAGCGGCGTTTGTCACAAAAACGCCGCAATAGGTTTTGTTAT
* * * ***
3530490 TTAGCGACGTTTGTCACAAAAATGCCGCAGTAGGTTTTAAGAT
1 TTAGCGGCGTTTGTCACAAAAACGCCGCAATAGGTTTTGTTAT
* * * * ** * *
3530533 TTAGCGGTGTTT-TCCCACAAACGCCGCAAAAGGTGGTGATGT
1 TTAGCGGCGTTTGTCACAAAAACGCCGCAATAGGTTTTGTTAT
* * *
3530575 TTAGCGGCGTTTTTCGCACAAACGCCGC
1 TTAGCGGCGTTTGTCACAAAAACGCCGC
3530603 TAAAGTTGGG
Statistics
Matches: 243, Mismatches: 40, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
42 31 0.13
43 197 0.81
44 14 0.06
45 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (43 bp):
TTAGCGGCGTTTGTCACAAAAACGCCGCAATAGGTTTTGTTAT
Found at i:3531045 original size:21 final size:21
Alignment explanation
Indices: 3531027--3531069 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3531017 TATGTGCTGT
* *
3531027 CGCTGCTTCTTTCTCTGCTTC
1 CGCTGCTACTCTCTCTGCTTC
3531048 CGCTGCTACTCTCTCTGCTTC
1 CGCTGCTACTCTCTCTGCTTC
3531069 C
1 C
3531070 CTTGTTTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.02, C:0.42, G:0.14, T:0.42
Consensus pattern (21 bp):
CGCTGCTACTCTCTCTGCTTC
Found at i:3539661 original size:41 final size:41
Alignment explanation
Indices: 3539616--3539761 Score: 129
Period size: 41 Copynumber: 3.5 Consensus size: 41
3539606 CATATTTATT
*
3539616 GGCGTTT-TCATAAAATCGCCGTTAAAGTTCTATTATATTGC
1 GGCGTTTGTCATAAAA-CGCCGCTAAAGTTCTATTATATTGC
* * * *
3539657 GGCGTTTGT-ATAAAAACGCCGCTATAGAT-TATATCTACTGC
1 GGCGTTTGTCAT-AAAACGCCGCTAAAGTTCTAT-TATATTGC
* *
3539698 GGCATTTGTACA-AAAACGCCACTAAAGTTCTATTATATTGC
1 GGCGTTTGT-CATAAAACGCCGCTAAAGTTCTATTATATTGC
* *
3539739 GGCAGTTTTTGATACAAACGCCG
1 GGC-GTTTGTCATA-AAACGCCG
3539762 TAACAAGTCA
Statistics
Matches: 81, Mismatches: 15, Indels: 16
0.72 0.13 0.14
Matches are distributed among these distances:
40 3 0.04
41 57 0.70
42 13 0.16
43 8 0.10
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Consensus pattern (41 bp):
GGCGTTTGTCATAAAACGCCGCTAAAGTTCTATTATATTGC
Found at i:3539756 original size:45 final size:42
Alignment explanation
Indices: 3539638--3539746 Score: 134
Period size: 41 Copynumber: 2.6 Consensus size: 42
3539628 AAATCGCCGT
* *
3539638 TAAAGTTCTATTATATTGCGGC-GTTTGTATAAAAACGCCGC
1 TAAAGTTCTATTATATTGCGGCAGTTTGTACAAAAACGCCAC
* * * *
3539679 TATAGAT-TATATCTACTGCGGCA-TTTGTACAAAAACGCCAC
1 TAAAGTTCTAT-TATATTGCGGCAGTTTGTACAAAAACGCCAC
3539720 TAAAGTTCTATTATATTGCGGCAGTTT
1 TAAAGTTCTATTATATTGCGGCAGTTT
3539747 TTGATACAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
40 3 0.06
41 45 0.83
42 6 0.11
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (42 bp):
TAAAGTTCTATTATATTGCGGCAGTTTGTACAAAAACGCCAC
Found at i:3540057 original size:146 final size:146
Alignment explanation
Indices: 3539810--3540101 Score: 566
Period size: 146 Copynumber: 2.0 Consensus size: 146
3539800 CGCCGCTAAT
3539810 TTCATTAAACTGTATAAGATTAATTGATTTTCCATATTTTATTTTTTCTCTACATAAACTTAATT
1 TTCATTAAACTGTATAAGATTAATTGATTTTCCATATTTTATTTTTTCTCTACATAAACTTAATT
3539875 TACTATCATATAGCTTTATTTAATTAAAAACAACCATAGACTTTAATTAAGACACACATTATGCA
66 TACTATCATATAGCTTTATTTAATTAAAAACAACCATAGACTTTAATTAAGACACACATTATGCA
3539940 TACAAATACTTAACAA
131 TACAAATACTTAACAA
3539956 TTCATTAAACTGTATAAGATTAATTGATTTTCCATATTTTATTTTTTCTCTACATAAACTTAATT
1 TTCATTAAACTGTATAAGATTAATTGATTTTCCATATTTTATTTTTTCTCTACATAAACTTAATT
* *
3540021 TACTATCATATAGCTTTATTTAATTAAAAACAACCATAGATTTTAATTAAGACACACGTTATGCA
66 TACTATCATATAGCTTTATTTAATTAAAAACAACCATAGACTTTAATTAAGACACACATTATGCA
3540086 TACAAATACTTAACAA
131 TACAAATACTTAACAA
3540102 CAAAATACAT
Statistics
Matches: 144, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
146 144 1.00
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.41
Consensus pattern (146 bp):
TTCATTAAACTGTATAAGATTAATTGATTTTCCATATTTTATTTTTTCTCTACATAAACTTAATT
TACTATCATATAGCTTTATTTAATTAAAAACAACCATAGACTTTAATTAAGACACACATTATGCA
TACAAATACTTAACAA
Found at i:3540925 original size:22 final size:22
Alignment explanation
Indices: 3540877--3540925 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
3540867 TCATGTTTCA
*
3540877 AAAGCTATTATTTTCCTATTCG
1 AAAGCTATTATTTTCCTATTAG
*
3540899 GAAGCTATTATTCTT-CTATTAG
1 AAAGCTATTATT-TTCCTATTAG
3540921 AAAGC
1 AAAGC
3540926 AGAAAAACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (22 bp):
AAAGCTATTATTTTCCTATTAG
Found at i:3541417 original size:42 final size:42
Alignment explanation
Indices: 3541370--3541489 Score: 136
Period size: 42 Copynumber: 2.9 Consensus size: 42
3541360 ATAAACAAAC
3541370 ATATTGCGGCATTTGTACTATAAACGCCGCTAAATTATTACT
1 ATATTGCGGCATTTGTACTATAAACGCCGCTAAATTATTACT
* * *
3541412 ATATTGCGGCATTTTTAC-ACAAACGCCACTAAATTATTACT
1 ATATTGCGGCATTTGTACTATAAACGCCGCTAAATTATTACT
* ** * * *
3541453 CTACAGCAGCGTTTGT-TTGATAAACGCCGCTAAATTA
1 ATATTGCGGCATTTGTACT-ATAAACGCCGCTAAATTA
3541490 CATCTCTGTT
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
41 31 0.48
42 33 0.52
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (42 bp):
ATATTGCGGCATTTGTACTATAAACGCCGCTAAATTATTACT
Found at i:3541446 original size:41 final size:42
Alignment explanation
Indices: 3541370--3541452 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 42
3541360 ATAAACAAAC
* *
3541370 ATATTGCGGCATTTGTACTATAAACGCCGCTAAATTATTACT
1 ATATTGCGGCATTTGTACTACAAACGCCACTAAATTATTACT
*
3541412 ATATTGCGGCATTTTTAC-ACAAACGCCACTAAATTATTACT
1 ATATTGCGGCATTTGTACTACAAACGCCACTAAATTATTACT
3541453 CTACAGCAGC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
41 21 0.55
42 17 0.45
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (42 bp):
ATATTGCGGCATTTGTACTACAAACGCCACTAAATTATTACT
Found at i:3543154 original size:65 final size:64
Alignment explanation
Indices: 3543085--3543234 Score: 144
Period size: 65 Copynumber: 2.3 Consensus size: 64
3543075 TTTTTATAAC
* * * *
3543085 TTTTTTACTGTGACTAAATAAT-TTTGTTACAATTTGTTATTTTGA-AAGAATATTATTTGTCAC
1 TTTTTTA-TATGACTAAATAATATTTGTTACAAATTGTTATTTTGATAA-AATA-AATTTATCAC
*
3543148 CA
63 AA
* * *
3543150 TTTTTTATAATGA-GAAATTAATATTTGTTATAAATTGTTATTTTGATTAAATAAATTTATCACA
1 TTTTTTAT-ATGACTAAA-TAATATTTGTTACAAATTGTTATTTTGATAAAATAAATTTATCACA
3543214 A
64 A
*
3543215 TTTTTTATTTTGACTAAATA
1 TTTTTTA-TATGACTAAATA
3543235 TTGAGACGAA
Statistics
Matches: 69, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
64 4 0.06
65 35 0.51
66 29 0.42
67 1 0.01
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.51
Consensus pattern (64 bp):
TTTTTTATATGACTAAATAATATTTGTTACAAATTGTTATTTTGATAAAATAAATTTATCACAA
Found at i:3547697 original size:417 final size:413
Alignment explanation
Indices: 3546897--3547738 Score: 1137
Period size: 417 Copynumber: 2.0 Consensus size: 413
3546887 TATAAAACTT
* * *
3546897 TTACTATATAACATTTTTGGCACCAAAAAATAGGGAAAATTTTTTATAGTATAATTTTTCATAAT
1 TTACTATATAACATTTTTGACACAAAAAAATAGGGAAAATTTTTGATAGTATAATTTTTCATAAT
*
3546962 GATTAAAATATATAAATACAAAATAATTAATTACAAAAAACTTGAATTTTATTATCTGATGTGAT
66 GATTAAAATATATAAATACAAAATAATTAATTACAAAAAACTTGAA-TTTATTATCTGATATGAT
* * *
3547027 AATTTTTTCTATAACAATTACTATAAATTATAATTACAAAACTTATCAATATAGCTTTTTGAAAC
130 AATTTTTTCTATAACAATAACTATAAATTATAATTACAAAAATTATCAATATAACTTTTTGAAAC
* * * *
3547092 AAAAAAAAAAGTTGAGAAAAAATATTTATCATAATATATGTTATAACTATAATTAAAATTTATTA
195 ---AAAAAAAGTGGAGAAAAAATAATTATCATAATATATGCTATAACTATAATTAAAATTTATAA
* * *
3547157 CTACAAGCATAATTTCTCACAAAAATGTGAATACCATTATTTTTGTGACAATGTTTTTTGTAATA
257 CTACAAACATAATTTCTCACAAAAACGTGAATACCATTATTTTTGTGACAATGTTTTATGTAATA
* *
3547222 ATTATAAACACTTATAGTTACAAAAATTGTTACAATATGATTTTTCTAGTGCAAAAAAATATAGA
322 ATTATAAACACTTATAGTTACAAAAATTGTCACAATATGATTTTTCTAGCGCAAAAAAATATAGA
3547287 -GGAAAATCTTTATGAAAATATATTTTG
387 TGG-AAATCTTTATGAAAATATATTTTG
*
3547314 TTACTATATAACATTTTTGACATTAAAAAAATAGGGAGAAATAGTTTTGATAGTATAATTTTTCA
1 TTACTATATAACATTTTTGACA-CAAAAAAATAGGGA-AAAT--TTTTGATAGTATAATTTTTCA
*
3547379 TAATGATTAAAATATATAAGTACAAAAATAATTTAA-TACAAAAAACTTGAA-TT-TTAT-TGAT
62 TAATGATTAAAATATATAAATAC-AAAATAA-TTAATTACAAAAAACTTGAATTTATTATCTGAT
* *
3547440 ATGAT-ATTTTTTCTATAACAATAACTATAAATTATAATTATAAAAATTGTCAATATAAC-TTTT
125 ATGATAATTTTTTCTATAACAATAACTATAAATTATAATTACAAAAATTATCAATATAACTTTTT
* *
3547503 GAAAC-AAAAAAGTGGAG-AAAAATAATTATGACGATTAATATATGCTATCACTATAGTTAAAAT
190 GAAACAAAAAAAGTGGAGAAAAAATAATTAT--C-A-TAATATATGCTATAACTATAATTAAAAT
* * *
3547566 TTATAACTACAAATATAATTTGTCACAAAAACGTGAATATCATTATTTTTTGTGACAATGTTTTA
251 TTATAACTACAAACATAATTTCTCACAAAAACGTGAATACCATTA-TTTTTGTGACAATGTTTTA
* * * ** *
3547631 TGTAATAATTATTAACATTTATAGTTACAAAATTTGTCATTATATGACTTTTT-TTGCGCAAAAA
315 TGTAATAATTATAAACACTTATAGTTACAAAAATTGTCACAATATGA-TTTTTCTAGCGC-AAAA
* * *
3547695 AAATATGGATGGAAATCTTTGTGACAATATATTTTG
378 AAATATAGATGGAAATCTTTATGAAAATATATTTTG
*
3547731 TCACTATA
1 TTACTATA
3547739 ATTAAAACAT
Statistics
Matches: 376, Mismatches: 35, Indels: 28
0.86 0.08 0.06
Matches are distributed among these distances:
411 11 0.03
412 11 0.03
413 1 0.00
414 1 0.00
415 64 0.17
416 72 0.19
417 116 0.31
418 22 0.06
419 8 0.02
420 2 0.01
421 42 0.11
422 22 0.06
423 4 0.01
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (413 bp):
TTACTATATAACATTTTTGACACAAAAAAATAGGGAAAATTTTTGATAGTATAATTTTTCATAAT
GATTAAAATATATAAATACAAAATAATTAATTACAAAAAACTTGAATTTATTATCTGATATGATA
ATTTTTTCTATAACAATAACTATAAATTATAATTACAAAAATTATCAATATAACTTTTTGAAACA
AAAAAAGTGGAGAAAAAATAATTATCATAATATATGCTATAACTATAATTAAAATTTATAACTAC
AAACATAATTTCTCACAAAAACGTGAATACCATTATTTTTGTGACAATGTTTTATGTAATAATTA
TAAACACTTATAGTTACAAAAATTGTCACAATATGATTTTTCTAGCGCAAAAAAATATAGATGGA
AATCTTTATGAAAATATATTTTG
Found at i:3547845 original size:183 final size:181
Alignment explanation
Indices: 3547550--3547995 Score: 431
Period size: 181 Copynumber: 2.5 Consensus size: 181
3547540 ATATATGCTA
* ** * * * *
3547550 TCACTATAGTTAAAATTTATAACTAC-AAATATAATTTGTCACAA-AAA-CGTGAATATCATTAT
1 TCACTATAATTAAAACATATAACGACAAAAAAAAATTTGTCACAACAAATC-TGAATCTCATTAT
* * * * * ** **
3547612 TTTTTGTGACAATGTTTTATGTAATAATTATTAACATTTATAGTTACAAAATTTGTCATTATATG
65 TTGTTGTGACAATTTTTTTTGTAACAATAATTAACATTTATAGTTACAAAACATGTCACCATATG
*
3547677 ACTTTT-TTTGCGCAAAAAAAATATGGATGGA-AATC-TTTGTGACAATATATTTTG
130 A-TTTTGTTT-CGCAAAAAAAAT-TGGA--GATAATCATTTGTGACAATACATTTTG
* * ** * * * *
3547731 TCACTATAATTAAAACATATCACGACAAACATTATTTTTTTACTAA-AAATTTGAATCTCATTAT
1 TCACTATAATTAAAACATATAACGACAAAAAAAAATTTGTCAC-AACAAATCTGAATCTCATTAT
* * *
3547795 TTGCTGTGACAATTTTTTTTGTAACAATAATTATA-GTTTATAGTTACAAAACATGTGACCATAT
65 TTGTTGTGACAATTTTTTTTGTAACAATAATTA-ACATTTATAGTTACAAAACATGTCACCATAT
*** * * *
3547859 GATTTTGTTTTTTACAAAAAATTGGAGATAATCATTTGTGACTATGCATTTTG
129 GATTTTGTTTCGCAAAAAAAATTGGAGATAATCATTTGTGACAATACATTTTG
** *
3547912 TCACTATAATTAAAACATATAATTACAAAAAAAAATTTGTCACAACAAATCTAAATCTCATTATT
1 TCACTATAATTAAAACATATAACGACAAAAAAAAATTTGTCACAACAAATCTGAATCTCATTATT
3547977 TGTTGTGACAATTTTTTTT
66 TGTTGTGACAATTTTTTTT
3547996 TCATAATTAC
Statistics
Matches: 213, Mismatches: 44, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
179 2 0.01
180 6 0.03
181 110 0.52
182 22 0.10
183 72 0.34
184 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (181 bp):
TCACTATAATTAAAACATATAACGACAAAAAAAAATTTGTCACAACAAATCTGAATCTCATTATT
TGTTGTGACAATTTTTTTTGTAACAATAATTAACATTTATAGTTACAAAACATGTCACCATATGA
TTTTGTTTCGCAAAAAAAATTGGAGATAATCATTTGTGACAATACATTTTG
Found at i:3550988 original size:51 final size:51
Alignment explanation
Indices: 3550912--3551014 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
3550902 ATGTAAATAT
*
3550912 GATTGACAATTTATGCAAATACGACTATCAAAAACACATAAGATACTAATG
1 GATTGACAATTTATGCAAATACGACTATAAAAAACACATAAGATACTAATG
3550963 GATTGACAATTTATGCAAATACGACTATAAAAAACACATAAGATACTAATG
1 GATTGACAATTTATGCAAATACGACTATAAAAAACACATAAGATACTAATG
3551014 G
1 G
3551015 TTAGAGGCTC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.25
Consensus pattern (51 bp):
GATTGACAATTTATGCAAATACGACTATAAAAAACACATAAGATACTAATG
Found at i:3555191 original size:17 final size:17
Alignment explanation
Indices: 3555169--3555210 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
3555159 TGAAATGCAT
3555169 CAAGCATAAATCACAAC
1 CAAGCATAAATCACAAC
3555186 CAAGCATAAATCACAAC
1 CAAGCATAAATCACAAC
*
3555203 AAAGCATA
1 CAAGCATA
3555211 GTAGTGTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.55, C:0.26, G:0.07, T:0.12
Consensus pattern (17 bp):
CAAGCATAAATCACAAC
Found at i:3555970 original size:20 final size:20
Alignment explanation
Indices: 3555919--3555970 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
3555909 CACACCATTG
* *
3555919 ATATTGATACCACAATAACA
1 ATATTGATACCCCAAGAACA
3555939 ATATTGATACCCCAAGAACA
1 ATATTGATACCCCAAGAACA
*
3555959 GTATTGATACCC
1 ATATTGATACCC
3555971 TATGAACATG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.25
Consensus pattern (20 bp):
ATATTGATACCCCAAGAACA
Found at i:3555977 original size:20 final size:20
Alignment explanation
Indices: 3555919--3555978 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
3555909 CACACCATTG
3555919 ATATTGATACCACAAT-AACA
1 ATATTGATACC-CAATGAACA
3555939 ATATTGATACCCCAA-GAACA
1 ATATTGATA-CCCAATGAACA
* *
3555959 GTATTGATACCCTATGAACA
1 ATATTGATACCCAATGAACA
3555979 TGGTACTGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 4 0.11
20 29 0.83
21 2 0.06
ACGTcount: A:0.43, C:0.22, G:0.10, T:0.25
Consensus pattern (20 bp):
ATATTGATACCCAATGAACA
Found at i:3557636 original size:32 final size:32
Alignment explanation
Indices: 3557591--3557656 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
3557581 ACACTTTCAG
3557591 TACCTCAACGATAGAAAGTATATTTGGGTTGT
1 TACCTCAACGATAGAAAGTATATTTGGGTTGT
* * *
3557623 TACCTCAATGATAGAAGGTATGTTTGGGTTGT
1 TACCTCAACGATAGAAAGTATATTTGGGTTGT
3557655 TA
1 TA
3557657 TTTGTTCTTT
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:0.29, C:0.11, G:0.24, T:0.36
Consensus pattern (32 bp):
TACCTCAACGATAGAAAGTATATTTGGGTTGT
Found at i:3566158 original size:24 final size:23
Alignment explanation
Indices: 3566111--3566157 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
3566101 AATCGATTCC
3566111 TAAGCCCTTTTTCAAAATGATTT
1 TAAGCCCTTTTTCAAAATGATTT
3566134 TAAGCCCTTTTTCAAAATGATTT
1 TAAGCCCTTTTTCAAAATGATTT
3566157 T
1 T
3566158 TTGGTTAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.45
Consensus pattern (23 bp):
TAAGCCCTTTTTCAAAATGATTT
Found at i:3566560 original size:16 final size:16
Alignment explanation
Indices: 3566541--3566571 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3566531 AATAGTTGTA
*
3566541 CTAATTTCTGATTTCC
1 CTAATTTCAGATTTCC
3566557 CTAATTTCAGATTTC
1 CTAATTTCAGATTTC
3566572 TGACATATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.48
Consensus pattern (16 bp):
CTAATTTCAGATTTCC
Found at i:3568463 original size:44 final size:44
Alignment explanation
Indices: 3568402--3568647 Score: 366
Period size: 44 Copynumber: 5.6 Consensus size: 44
3568392 AATGCATTAT
* *
3568402 TTATACATTTTCATTTATGGCACATTTCTGCCAATAATGCACCA
1 TTATGCATTTTCATTTATGGCACATTTCTGCCAATAATGCACCG
* * *
3568446 TTATGCATTTTCATTTATTGCACCTTTCTGCCAATAATGCATCG
1 TTATGCATTTTCATTTATGGCACATTTCTGCCAATAATGCACCG
* * *
3568490 TCATGCATTTTCATTTATGACATATTTCTGCCAATAATGCACCG
1 TTATGCATTTTCATTTATGGCACATTTCTGCCAATAATGCACCG
* * *
3568534 TTATACATTTTCATTTATGACACATTTCTGCCAAAAATGCACCG
1 TTATGCATTTTCATTTATGGCACATTTCTGCCAATAATGCACCG
* *
3568578 TTATGCATTTTCATTTATGGCACCTTTCTGTCAATAATGCACCG
1 TTATGCATTTTCATTTATGGCACATTTCTGCCAATAATGCACCG
*
3568622 TTATGCATTTTCATTTATGGTACATT
1 TTATGCATTTTCATTTATGGCACATT
3568648 AATGCCCTCG
Statistics
Matches: 180, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 180 1.00
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (44 bp):
TTATGCATTTTCATTTATGGCACATTTCTGCCAATAATGCACCG
Found at i:3568566 original size:132 final size:132
Alignment explanation
Indices: 3568402--3568640 Score: 415
Period size: 132 Copynumber: 1.8 Consensus size: 132
3568392 AATGCATTAT
* * *
3568402 TTATACATTTTCATTTATGGCACATTTCTGCCAATAATGCACCATTATGCATTTTCATTTATTGC
1 TTATACATTTTCATTTATGACACATTTCTGCCAAAAATGCACCATTATGCATTTTCATTTATGGC
*
3568467 ACCTTTCTGCCAATAATGCATCGTCATGCATTTTCATTTATGACATATTTCTGCCAATAATGCAC
66 ACCTTTCTGCCAATAATGCACCGTCATGCATTTTCATTTATGACATATTTCTGCCAATAATGCAC
3568532 CG
131 CG
*
3568534 TTATACATTTTCATTTATGACACATTTCTGCCAAAAATGCACCGTTATGCATTTTCATTTATGGC
1 TTATACATTTTCATTTATGACACATTTCTGCCAAAAATGCACCATTATGCATTTTCATTTATGGC
* *
3568599 ACCTTTCTGTCAATAATGCACCGTTATGCATTTTCATTTATG
66 ACCTTTCTGCCAATAATGCACCGTCATGCATTTTCATTTATG
3568641 GTACATTAAT
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 100 1.00
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (132 bp):
TTATACATTTTCATTTATGACACATTTCTGCCAAAAATGCACCATTATGCATTTTCATTTATGGC
ACCTTTCTGCCAATAATGCACCGTCATGCATTTTCATTTATGACATATTTCTGCCAATAATGCAC
CG
Found at i:3572707 original size:2 final size:2
Alignment explanation
Indices: 3572700--3572732 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3572690 CCCGAAAAGC
3572700 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3572733 TTACGACATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3578272 original size:2 final size:2
Alignment explanation
Indices: 3578265--3578295 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3578255 CCCAAAAAGC
3578265 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3578296 CTGACATCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3583228 original size:2 final size:2
Alignment explanation
Indices: 3583221--3583247 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3583211 CCCAAAATGC
3583221 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3583248 TTTACTGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3588895 original size:2 final size:2
Alignment explanation
Indices: 3588888--3588928 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3588878 AAGGGACATA
3588888 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3588929 CAAAATAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3592624 original size:29 final size:27
Alignment explanation
Indices: 3592574--3592633 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 27
3592564 AATAAAGAAG
3592574 AATAAAAGAAAGACAAAGAGAATAATAAT
1 AATAAAAGAAAGACAAAGAGAA-AA-AAT
* *
3592603 AATAAAATAAAGATAACA-AGAAAAAAT
1 AATAAAAGAAAGACAA-AGAGAAAAAAT
3592630 AATA
1 AATA
3592634 GAGTCAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 7 0.25
28 2 0.07
29 18 0.64
30 1 0.04
ACGTcount: A:0.72, C:0.03, G:0.10, T:0.15
Consensus pattern (27 bp):
AATAAAAGAAAGACAAAGAGAAAAAAT
Found at i:3613571 original size:15 final size:15
Alignment explanation
Indices: 3613551--3613581 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3613541 TTTCTCTATC
3613551 ACGTAAGGAGTAAGG
1 ACGTAAGGAGTAAGG
3613566 ACGTAAGGAGTAAGG
1 ACGTAAGGAGTAAGG
3613581 A
1 A
3613582 AAAAGCTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.39, T:0.13
Consensus pattern (15 bp):
ACGTAAGGAGTAAGG
Found at i:3617664 original size:29 final size:30
Alignment explanation
Indices: 3617632--3617691 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
3617622 AATAAAGAAG
3617632 AATAAAAGAAAGACAA-AGAG-AAAAATAAT
1 AATAAAAGAAAGACAACA-AGTAAAAATAAT
* *
3617661 AATAAAATAAAGATAACAAGTAAAAATAAT
1 AATAAAAGAAAGACAACAAGTAAAAATAAT
3617691 A
1 A
3617692 GAGTCAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.72, C:0.03, G:0.10, T:0.15
Consensus pattern (30 bp):
AATAAAAGAAAGACAACAAGTAAAAATAAT
Found at i:3617836 original size:2 final size:2
Alignment explanation
Indices: 3617829--3617893 Score: 121
Period size: 2 Copynumber: 32.0 Consensus size: 2
3617819 AAACAAAATA
3617829 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3617871 AT AT AT AT AT AT AT AT ACT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT
3617894 TAATATTAAT
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 60 0.97
3 2 0.03
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3617959 original size:22 final size:23
Alignment explanation
Indices: 3617926--3617972 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
3617916 GGGACAGAAT
*
3617926 ATATATATATATACAAAATAATAAA
1 ATATATATATCTA-AAAA-AATAAA
3617951 ATATA-ATATCTAAAAAAATAAA
1 ATATATATATCTAAAAAAATAAA
3617973 TGAAAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 4 0.19
24 6 0.29
25 5 0.24
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (23 bp):
ATATATATATCTAAAAAAATAAA
Found at i:3619240 original size:18 final size:20
Alignment explanation
Indices: 3619187--3619257 Score: 56
Period size: 21 Copynumber: 3.5 Consensus size: 20
3619177 ATGTAAATAA
* * *
3619187 ATATATTATATATATAGATGA
1 ATATAATATAAATATAGAT-T
* *
3619208 ATATATTTTATAATAT-GATT
1 ATATAATATA-AATATAGATT
*
3619228 -TATAATATAAATATATATT
1 ATATAATATAAATATAGATT
3619247 ATATAATATAA
1 ATATAATATAA
3619258 TAACGTTTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
18 5 0.12
19 10 0.24
20 10 0.24
21 12 0.29
22 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.46
Consensus pattern (20 bp):
ATATAATATAAATATAGATT
Found at i:3619489 original size:44 final size:44
Alignment explanation
Indices: 3619440--3619688 Score: 331
Period size: 44 Copynumber: 5.7 Consensus size: 44
3619430 ACCATTTTTA
*
3619440 CAATAATGCACCGTTAAGCATTTTCATTTATGGCACCTTTCTGC
1 CAATAATGCACCGTTATGCATTTTCATTTATGGCACCTTTCTGC
* *
3619484 TAATAATGCACC-TTATGCATTTTCATTT-TGGAACCTTTCTGC
1 CAATAATGCACCGTTATGCATTTTCATTTATGGCACCTTTCTGC
* * * *
3619526 CAATAATGCATCGTCATGCATTTTCATTTATGGCATCTTTATGC
1 CAATAATGCACCGTTATGCATTTTCATTTATGGCACCTTTCTGC
* * ** *
3619570 CAAAAATGCACCATTATGCATTTTCATTTATGGCAAATTTCTGT
1 CAATAATGCACCGTTATGCATTTTCATTTATGGCACCTTTCTGC
* * *
3619614 CAAAAATGAACTGTTATGCATTTTCATTTATGGCACCTTTCTGC
1 CAATAATGCACCGTTATGCATTTTCATTTATGGCACCTTTCTGC
**
3619658 CAATAATGCATTGTTATGCATTTTCATTTAT
1 CAATAATGCACCGTTATGCATTTTCATTTAT
3619689 TTCGATAACA
Statistics
Matches: 177, Mismatches: 26, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
42 23 0.13
43 30 0.17
44 124 0.70
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (44 bp):
CAATAATGCACCGTTATGCATTTTCATTTATGGCACCTTTCTGC
Found at i:3620168 original size:20 final size:21
Alignment explanation
Indices: 3620134--3620188 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
3620124 AGGCTCAATA
* *
3620134 GTATCGGTAC-CCCTACCATG
1 GTATCGATACTCCATACCATG
*
3620154 GTATCGATACTCCTATACTATG
1 GTATCGATACTCC-ATACCATG
*
3620176 GTATTGATACTCC
1 GTATCGATACTCC
3620189 CTTTCAGCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.31
21 2 0.07
22 18 0.62
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (21 bp):
GTATCGATACTCCATACCATG
Found at i:3628168 original size:2 final size:2
Alignment explanation
Indices: 3628151--3628187 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
3628141 CCTGTATGTG
* *
3628151 TA TA TG TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3628188 TTTCACTCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3631568 original size:69 final size:69
Alignment explanation
Indices: 3631457--3631595 Score: 278
Period size: 69 Copynumber: 2.0 Consensus size: 69
3631447 TCCTTGCTAT
3631457 TTTGATCTATGAGCACCCATTTGATTTGATTTTATTTCTTTCAGTAAAAGTTTGTCGTATATTTA
1 TTTGATCTATGAGCACCCATTTGATTTGATTTTATTTCTTTCAGTAAAAGTTTGTCGTATATTTA
3631522 CCCC
66 CCCC
3631526 TTTGATCTATGAGCACCCATTTGATTTGATTTTATTTCTTTCAGTAAAAGTTTGTCGTATATTTA
1 TTTGATCTATGAGCACCCATTTGATTTGATTTTATTTCTTTCAGTAAAAGTTTGTCGTATATTTA
3631591 CCCC
66 CCCC
3631595 T
1 T
3631596 AAAAACTCTT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.23, C:0.17, G:0.13, T:0.47
Consensus pattern (69 bp):
TTTGATCTATGAGCACCCATTTGATTTGATTTTATTTCTTTCAGTAAAAGTTTGTCGTATATTTA
CCCC
Found at i:3632727 original size:133 final size:132
Alignment explanation
Indices: 3632380--3632755 Score: 366
Period size: 133 Copynumber: 2.8 Consensus size: 132
3632370 GGAGTTAATC
* * * *
3632380 TACCTCAATTTAATCTTCCCTGAAGAGCAGTGAAATGAATCAATTTTTTTCCAGATCTGATCTTT
1 TACCTCAATTTAATCTTCCTTGAAGAGCAGTGAAATGAATCAAATTTTTT-CAAATCTGATCTTC
* ** * *
3632445 CCTAAAGAGTAGTGAAGCATATCCCTTAATCCAAGATTTGATATTCCCTTAAAACAATTGAGCAA
65 CCTAAAGAGTAGTGAAGCAGATCCCTTAATCCAAGATTTGATATTCCCCGAAAACAATGGAACAA
*
3632510 ATC
130 ATA
* * * **** * *
3632513 TACCTCAATTTTAT-TTTCTCTGAAGAGCAGTGAAGTGAAT-AAAAAAATT-ACATATGATCTTC
1 TACCTCAATTTAATCTTCCT-TGAAGAGCAGTGAAATGAATCAAATTTTTTCAAATCTGATCTTC
* ** * * *
3632575 CCTAAAGAGTGGAT-AAGCAGATCCCTTCTTCTAAGGTTTGATCTTCCCCGAAAAGCAATGGAAC
65 CCTAAAGAGTAG-TGAAGCAGATCCCTTAATCCAAGATTTGATATTCCCCGAAAA-CAATGGAAC
3632639 AAATA
128 AAATA
* * * * *
3632644 TACCTCAATTCAATCTTCCTTGAATAGCAGTTAACTGATTCAAATTTTTTCAAATCTGATCTTCC
1 TACCTCAATTTAATCTTCCTTGAAGAGCAGTGAAATGAATCAAATTTTTTCAAATCTGATCTTCC
* ** *
3632709 CTAAAGAGTAGTGGAGCAGATCTATT-ATGTCAAGATTTGATATTCCC
66 CTAAAGAGTAGTGAAGCAGATCCCTTAAT-CCAAGATTTGATATTCCC
3632756 TGAAGAGCAG
Statistics
Matches: 189, Mismatches: 46, Indels: 16
0.75 0.18 0.06
Matches are distributed among these distances:
130 53 0.28
131 40 0.21
132 18 0.10
133 78 0.41
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (132 bp):
TACCTCAATTTAATCTTCCTTGAAGAGCAGTGAAATGAATCAAATTTTTTCAAATCTGATCTTCC
CTAAAGAGTAGTGAAGCAGATCCCTTAATCCAAGATTTGATATTCCCCGAAAACAATGGAACAAA
TA
Found at i:3635420 original size:33 final size:33
Alignment explanation
Indices: 3635378--3635444 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
3635368 GGCGAAAGAA
3635378 TATCGCGGGGAGGCCATATATCCCTAGAGTTCC
1 TATCGCGGGGAGGCCATATATCCCTAGAGTTCC
3635411 TATCGCGGGGAGGCCATATATCCCTAGAGTTCC
1 TATCGCGGGGAGGCCATATATCCCTAGAGTTCC
3635444 T
1 T
3635445 CAATTAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (33 bp):
TATCGCGGGGAGGCCATATATCCCTAGAGTTCC
Found at i:3638511 original size:2 final size:2
Alignment explanation
Indices: 3638504--3638542 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3638494 TTTATCATTA
3638504 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3638543 ATCACACTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3643766 original size:23 final size:23
Alignment explanation
Indices: 3643736--3643796 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
3643726 CTCATATAAA
3643736 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
3643759 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
3643782 TGCACCAAAGTGCCA
1 TGCACCGAAGTGCCA
3643797 TATAAAATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.31, C:0.28, G:0.25, T:0.16
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:3664222 original size:43 final size:43
Alignment explanation
Indices: 3664150--3664418 Score: 405
Period size: 43 Copynumber: 6.3 Consensus size: 43
3664140 TTAATTACCG
* * *
3664150 TTACAGTTACCCCAGGTCCCTTTGTTGTGTGCAAAGGTAAGCC
1 TTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* * *
3664193 TTATAGTTTCCCCAGGTTCCTTTACTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* *
3664236 TTACAGTTT-CCCAGGTTCTTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* *
3664278 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCG
1 TTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* * *
3664321 TTACAATTTCCCCAGGTCCCTTTGCTGTGTACAAGGGTAAGCG
1 TTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
*
3664364 TTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
3664407 TTACAGTTTCCC
1 TTACAGTTTCCC
3664419 ATGTTTTTTT
Statistics
Matches: 205, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
42 39 0.19
43 166 0.81
ACGTcount: A:0.18, C:0.25, G:0.24, T:0.32
Consensus pattern (43 bp):
TTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
Found at i:3670593 original size:10 final size:9
Alignment explanation
Indices: 3670570--3670599 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
3670560 TTGATATAAG
3670570 TATATGTGT
1 TATATGTGT
3670579 TATATGTGAT
1 TATATGTG-T
3670589 TATATGTGT
1 TATATGTGT
3670598 TA
1 TA
3670600 CATGATTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (9 bp):
TATATGTGT
Found at i:3672717 original size:28 final size:28
Alignment explanation
Indices: 3672685--3672747 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
3672675 CATTTAAAAT
* * *
3672685 ATGTCATCTTGTACTTAACCTTTGTAAC
1 ATGTCATCTTATACTCAACATTTGTAAC
*
3672713 ATGTCATTTTATACTCAACATTTGTAAC
1 ATGTCATCTTATACTCAACATTTGTAAC
*
3672741 ATATCAT
1 ATGTCAT
3672748 ATAATACATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.30, C:0.19, G:0.08, T:0.43
Consensus pattern (28 bp):
ATGTCATCTTATACTCAACATTTGTAAC
Found at i:3672754 original size:28 final size:28
Alignment explanation
Indices: 3672696--3672754 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
3672686 TGTCATCTTG
* * * * *
3672696 TACTTAACCTTTGTAACATGTCATTTTA
1 TACTCAACATTTGTAACATATCATATAA
3672724 TACTCAACATTTGTAACATATCATATAA
1 TACTCAACATTTGTAACATATCATATAA
3672752 TAC
1 TAC
3672755 ATTTCACCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.41
Consensus pattern (28 bp):
TACTCAACATTTGTAACATATCATATAA
Found at i:3673050 original size:36 final size:36
Alignment explanation
Indices: 3673010--3673148 Score: 251
Period size: 36 Copynumber: 3.9 Consensus size: 36
3673000 ACGTTGCTGG
3673010 ACATTGATACACGAATGTACCAAAGCTAATATGATA
1 ACATTGATACACGAATGTACCAAAGCTAATATGATA
*
3673046 ACATTGATACACGAATATACCAAAGCTAATATGATA
1 ACATTGATACACGAATGTACCAAAGCTAATATGATA
*
3673082 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTAATATGATA
*
3673118 ACATTGATACACGAATGTACCAAAACTAATA
1 ACATTGATACACGAATGTACCAAAGCTAATA
3673149 ATGGATAAAT
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 98 1.00
ACGTcount: A:0.45, C:0.17, G:0.13, T:0.24
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTAATATGATA
Found at i:3674474 original size:19 final size:20
Alignment explanation
Indices: 3674452--3674500 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
3674442 TTCGGCTTAG
3674452 TCAGACCGGTCCAT-TCGAT
1 TCAGACCGGTCCATATCGAT
* *
3674471 TCAGACCGATTCATATCGAT
1 TCAGACCGGTCCATATCGAT
*
3674491 TCAGATCGGT
1 TCAGACCGGT
3674501 TTAACACGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (20 bp):
TCAGACCGGTCCATATCGAT
Found at i:3674491 original size:20 final size:19
Alignment explanation
Indices: 3674452--3674495 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
3674442 TTCGGCTTAG
*
3674452 TCAGACCGGTCCATTCGAT
1 TCAGACCGATCCATTCGAT
*
3674471 TCAGACCGATTCATATCGAT
1 TCAGACCGATCCAT-TCGAT
3674491 TCAGA
1 TCAGA
3674496 TCGGTTTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (19 bp):
TCAGACCGATCCATTCGAT
Found at i:3675566 original size:15 final size:15
Alignment explanation
Indices: 3675543--3675573 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3675533 ATCATTTATG
3675543 TTACATAGAACATAT
1 TTACATAGAACATAT
*
3675558 TTACTTAGAACATAT
1 TTACATAGAACATAT
3675573 T
1 T
3675574 CATATAACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (15 bp):
TTACATAGAACATAT
Found at i:3679508 original size:18 final size:18
Alignment explanation
Indices: 3679468--3679515 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
3679458 TGCACATATG
3679468 CCATCATTATCAACATCA
1 CCATCATTATCAACATCA
* ** *
3679486 ACATCATTATCATGATCT
1 CCATCATTATCAACATCA
3679504 CCATCATTATCA
1 CCATCATTATCA
3679516 CTAACACATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.33
Consensus pattern (18 bp):
CCATCATTATCAACATCA
Found at i:3679561 original size:28 final size:28
Alignment explanation
Indices: 3679529--3679594 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
3679519 ACACATTTAA
* * *
3679529 AACATGTCATCTTGTACTTAACCTTTGT
1 AACATGTCATCTTATACTCAACATTTGT
* *
3679557 AACATGTCATTTTATACTCAATATTTGT
1 AACATGTCATCTTATACTCAACATTTGT
*
3679585 AACATATCAT
1 AACATGTCAT
3679595 ATAATACATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (28 bp):
AACATGTCATCTTATACTCAACATTTGT
Found at i:3680105 original size:33 final size:33
Alignment explanation
Indices: 3680068--3680131 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
3680058 TAGCTTATGA
*
3680068 AACATTCTTGTATTATCTCATAGATCCTTGTAT
1 AACATTCTTGTATGATCTCATAGATCCTTGTAT
*
3680101 AACATTCTTGTATGATCTCATATATCCTTGT
1 AACATTCTTGTATGATCTCATAGATCCTTGT
3680132 CATATAACCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.27, C:0.19, G:0.09, T:0.45
Consensus pattern (33 bp):
AACATTCTTGTATGATCTCATAGATCCTTGTAT
Found at i:3680285 original size:21 final size:21
Alignment explanation
Indices: 3680230--3680288 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
3680220 ATTTCTCATG
3680230 TGTTCATATA-A-A-CACATA
1 TGTTCATATATATATCACATA
* *
3680248 TG-TCATATCT-TGCTCACATA
1 TGTTCATATATAT-ATCACATA
3680268 TGTTCATATATATATCACATA
1 TGTTCATATATATATCACATA
3680289 GCACATAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
17 6 0.19
18 2 0.06
20 8 0.26
21 14 0.45
22 1 0.03
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.39
Consensus pattern (21 bp):
TGTTCATATATATATCACATA
Found at i:3688048 original size:28 final size:31
Alignment explanation
Indices: 3687991--3688050 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 31
3687981 CCGAATTAAT
* *
3687991 CAAACTTTTTTTCTTTAACTGTTAATCGAAC
1 CAAACTTTTTTTCTTTAACTATTAACCGAAC
3688022 CAAAC-TTTTTT-TTTAA-TATTAACCGAAC
1 CAAACTTTTTTTCTTTAACTATTAACCGAAC
3688050 C
1 C
3688051 GAATAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 11 0.41
29 5 0.19
30 6 0.22
31 5 0.19
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (31 bp):
CAAACTTTTTTTCTTTAACTATTAACCGAAC
Found at i:3693186 original size:18 final size:18
Alignment explanation
Indices: 3693160--3693206 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
3693150 TTTATATATC
*
3693160 TTAACTTAAATTTACATA
1 TTAAATTAAATTTACATA
* *
3693178 TTAAATTAATTTTACATC
1 TTAAATTAAATTTACATA
3693196 TTAATATTAAA
1 TTAA-ATTAAA
3693207 AATATATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAATTAAATTTACATA
Found at i:3693323 original size:30 final size:29
Alignment explanation
Indices: 3693193--3693535 Score: 230
Period size: 30 Copynumber: 11.6 Consensus size: 29
3693183 TTAATTTTAC
* *
3693193 ATCTTAATATTAAAAATATATTTTATTTTT
1 ATCTTAA-CTTAAAAATATATTTTATTCTT
* * * * *
3693223 ATATTAAATTATTATATATAATTTATTCTT
1 ATCTTAACTTA-AAAATATATTTTATTCTT
* *
3693253 ATTTTAACTTAAAAATATAATTTTAGTCTGT
1 ATCTTAACTTAAAAATAT-ATTTTATTCT-T
*
3693284 ATGTTAACTTAAGAAATATATTTTATTCTT
1 ATCTTAACTTAA-AAATATATTTTATTCTT
* * * *
3693314 ATCTTAACTTATTACATAGATTATATTCTT
1 ATCTTAACTTA-AAAATATATTTTATTCTT
* * * * *
3693344 AACTTAAATTATTAAATATATTCTATTTTT
1 ATCTTAACTTA-AAAATATATTTTATTCTT
* * * * * *
3693374 ACCTTAAATTATCAAAATAGAATTAATTCTC
1 ATCTTAACTTA--AAAATATATTTTATTCTT
* * *
3693405 ATTTTAACTTAAAACATGTCTTTTATTCTT
1 ATCTTAACTTAAAA-ATATATTTTATTCTT
*
3693435 ATCTTAACTTAAAAATATTTTTTATT-TT
1 ATCTTAACTTAAAAATATATTTTATTCTT
* *
3693463 AAC-T-AC--AAAAATATATTTTATTTTT
1 ATCTTAACTTAAAAATATATTTTATTCTT
*
3693488 ATCTTAACTACAAAAATATATTTTACTT-TT
1 ATCTTAACT-TAAAAATATATTTTA-TTCTT
* *
3693518 ATCTTAAATTTAAAATAT
1 ATCTTAACTTAAAAATAT
3693536 TATCAAAATA
Statistics
Matches: 248, Mismatches: 51, Indels: 29
0.76 0.16 0.09
Matches are distributed among these distances:
24 15 0.06
25 4 0.02
26 3 0.01
27 3 0.01
28 4 0.02
29 29 0.12
30 142 0.57
31 42 0.17
32 6 0.02
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (29 bp):
ATCTTAACTTAAAAATATATTTTATTCTT
Found at i:3693353 original size:121 final size:120
Alignment explanation
Indices: 3693226--3693445 Score: 266
Period size: 121 Copynumber: 1.8 Consensus size: 120
3693216 TATTTTTATA
* ** * * * *
3693226 TTAAATTATTATATATAATT-TATTCTTATTTTAACTTA-AAAATATAATTTTAGTCTGTATGTT
1 TTAAATTATTAAATAT-ATTCTATTCTTACCTTAAATTACAAAATAGAA-TTAAGTCT-CATGTT
3693289 AACTTAAGAA-ATATATTTTATTCTTATCTTAACTTATTACATAGATTATATTCTTAAC
63 AACTTAA-AACATATATTTTATTCTTATCTTAACTTATTACATAGATTATATTCTTAAC
* * *
3693347 TTAAATTATTAAATATATTCTATTTTTACCTTAAATTATCAAAATAGAATTAATTCTCATTTTAA
1 TTAAATTATTAAATATATTCTATTCTTACCTTAAATTA-CAAAATAGAATTAAGTCTCATGTTAA
* *
3693412 CTTAAAACATGTCTTTTATTCTTATCTTAACTTA
65 CTTAAAACATATATTTTATTCTTATCTTAACTTA
3693446 AAAATATTTT
Statistics
Matches: 83, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
120 5 0.06
121 64 0.77
122 6 0.07
123 8 0.10
ACGTcount: A:0.37, C:0.10, G:0.03, T:0.50
Consensus pattern (120 bp):
TTAAATTATTAAATATATTCTATTCTTACCTTAAATTACAAAATAGAATTAAGTCTCATGTTAAC
TTAAAACATATATTTTATTCTTATCTTAACTTATTACATAGATTATATTCTTAAC
Found at i:3693463 original size:53 final size:54
Alignment explanation
Indices: 3693405--3693525 Score: 147
Period size: 53 Copynumber: 2.2 Consensus size: 54
3693395 ATTAATTCTC
* * * * *
3693405 ATTTTAACTTAAAACATGTCTTTTATTCTTATCTTAACT-TAAAAATATTTTTT
1 ATTTTAACTTAAAAAATATATTTTATTCTTATCTTAACTACAAAAATATATTTT
*
3693458 ATTTTAAC-TACAAAAATATATTTTATTTTTATCTTAACTACAAAAATATATTTT
1 ATTTTAACTTA-AAAAATATATTTTATTCTTATCTTAACTACAAAAATATATTTT
*
3693512 ACTTTTATCTTAAA
1 A-TTTTAACTTAAA
3693526 TTTAAAATAT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
52 2 0.04
53 32 0.56
54 13 0.23
55 8 0.14
56 2 0.04
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.50
Consensus pattern (54 bp):
ATTTTAACTTAAAAAATATATTTTATTCTTATCTTAACTACAAAAATATATTTT
Found at i:3693639 original size:29 final size:29
Alignment explanation
Indices: 3693542--3693676 Score: 99
Period size: 29 Copynumber: 4.5 Consensus size: 29
3693532 ATATTATCAA
* *
3693542 AATAAAATATAAATATTTAAGTTAAGATAAG
1 AATAAAATAT--ATTTTTAAATTAAGATAAG
* *
3693573 AATAAATTATATATTTTTTAATCTAAGATAAT
1 AATAAA--ATATATTTTTAAAT-TAAGATAAG
* *
3693605 ATTAAAATATATTTTTAAATTAAAATAAG
1 AATAAAATATATTTTTAAATTAAGATAAG
* ** * ** * *
3693634 AATAAAAAATAAGTGTAGGTTATGAAAAG
1 AATAAAATATATTTTTAAATTAAGATAAG
3693663 AATAAAATATATTT
1 AATAAAATATATTT
3693677 AATAAGTTAA
Statistics
Matches: 80, Mismatches: 21, Indels: 8
0.73 0.19 0.07
Matches are distributed among these distances:
29 37 0.46
30 13 0.16
31 13 0.16
32 13 0.16
33 4 0.05
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.37
Consensus pattern (29 bp):
AATAAAATATATTTTTAAATTAAGATAAG
Found at i:3693944 original size:16 final size:16
Alignment explanation
Indices: 3693923--3693957 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3693913 GATTGATGAG
* *
3693923 AAAAATATATTAAATT
1 AAAAATAAATTAAAAT
3693939 AAAAATAAATTAAAAT
1 AAAAATAAATTAAAAT
3693955 AAA
1 AAA
3693958 TTTAATCATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAATAAATTAAAAT
Found at i:3695086 original size:66 final size:63
Alignment explanation
Indices: 3694980--3695140 Score: 146
Period size: 64 Copynumber: 2.5 Consensus size: 63
3694970 TTGTTGAAGG
* * * * * *
3694980 TGCATCGATGCACATGGAGTGTATCGTTGCACTCATTTAAATTAAATGAACATCGAATGCCATTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCACTCA-TTAAAATAAA--AACATCGAATACCATTA
3695045 A
63 A
* ** *
3695046 TGCATCGATGCATAAGGAGTGCATCGATGCACCTGC-TTAAAATACAAACATCGAATATGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCA-CT-CATTAAAATAAAAACATCGAATACCATTAA
* *
3695110 TGCACCGATGCAT-GGGTAGTGCATCGATGCA
1 TGCATCGATGCATAAGG-AGTGCATCGATGCA
3695141 TCCGTCAAGG
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
63 2 0.03
64 40 0.50
66 35 0.44
67 2 0.03
68 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCACTCATTAAAATAAAAACATCGAATACCATTAA
Found at i:3695719 original size:22 final size:22
Alignment explanation
Indices: 3695694--3695778 Score: 106
Period size: 22 Copynumber: 4.0 Consensus size: 22
3695684 TTAGTCATTT
3695694 GGGACGTATCCAGTGGTCCTTC
1 GGGACGTATCCAGTGGTCCTTC
*
3695716 GGGACGTATCCAGTGGTCTTTC
1 GGGACGTATCCAGTGGTCCTTC
* * *
3695738 GGGATGTATCCAGTGGTCTTTT
1 GGGACGTATCCAGTGGTCCTTC
3695760 GGGAC--AT--AGTGGTCCTTC
1 GGGACGTATCCAGTGGTCCTTC
3695778 G
1 G
3695779 AGACAAATAC
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
18 10 0.18
20 2 0.04
22 45 0.79
ACGTcount: A:0.14, C:0.21, G:0.33, T:0.32
Consensus pattern (22 bp):
GGGACGTATCCAGTGGTCCTTC
Found at i:3696600 original size:16 final size:16
Alignment explanation
Indices: 3696579--3696609 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3696569 TATAAATAGA
3696579 TTAATGGTACCCATCG
1 TTAATGGTACCCATCG
*
3696595 TTAATGGTACTCATC
1 TTAATGGTACCCATC
3696610 AATTACTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (16 bp):
TTAATGGTACCCATCG
Found at i:3702966 original size:13 final size:13
Alignment explanation
Indices: 3702950--3702988 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
3702940 AGTAAAATAA
*
3702950 AAAAATAATAATT
1 AAAAATAAAAATT
* *
3702963 AAAAATAACAATG
1 AAAAATAAAAATT
3702976 AAAAATAAAAATT
1 AAAAATAAAAATT
3702989 CCTACCCCCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (13 bp):
AAAAATAAAAATT
Found at i:3704068 original size:16 final size:16
Alignment explanation
Indices: 3704017--3704080 Score: 58
Period size: 16 Copynumber: 4.0 Consensus size: 16
3704007 AAAAAAGATG
* *
3704017 AAAT-AAAATAAAACA
1 AAATAAAAATTAAAGA
**
3704032 AAATAAAAAATTAAATT
1 AAAT-AAAAATTAAAGA
* *
3704049 AAATTAAATTTAAAGA
1 AAATAAAAATTAAAGA
3704065 AAATAAAAATTAAAGA
1 AAATAAAAATTAAAGA
3704081 GGGATTAAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
15 4 0.11
16 22 0.58
17 12 0.32
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.23
Consensus pattern (16 bp):
AAATAAAAATTAAAGA
Found at i:3705307 original size:5 final size:5
Alignment explanation
Indices: 3705293--3705482 Score: 93
Period size: 5 Copynumber: 38.2 Consensus size: 5
3705283 TAATTAAATA
3705293 ATAA- ATAAT ATAAT AT-AT AATATAT ATAAT AT-A- ATAAT ATACTAT
1 ATAAT ATAAT ATAAT ATAAT -ATA-AT ATAAT ATAAT ATAAT ATA--AT
3705338 ATAAT -T-AT ATAA- ATAAT AT-AT ACT-AT ATAAT A-ATAT ATAAT ACT-AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT A-TAAT ATAAT ATA-AT ATAAT A-TAAT
* * * **
3705384 ATACTGT GTAA- ATACT ATAAT AT-AT ATATAT ATATAT ATAAT ACCAT
1 ATA--AT ATAAT ATAAT ATAAT ATAAT ATA-AT ATA-AT ATAAT ATAAT
** *
3705431 ACCAT ATAAT AT-AT ATAAA ATAATAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT AT-A-AT ATAAT ATAAT ATAAT ATAAT ATAAT
3705482 A
1 A
3705483 AAAGGAAGCC
Statistics
Matches: 149, Mismatches: 12, Indels: 49
0.71 0.06 0.23
Matches are distributed among these distances:
3 4 0.03
4 30 0.20
5 84 0.56
6 18 0.12
7 13 0.09
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:3705317 original size:2 final size:2
Alignment explanation
Indices: 3705300--3705479 Score: 94
Period size: 2 Copynumber: 96.5 Consensus size: 2
3705290 ATAATAAATA
3705300 AT AT A- AT AT AT A- AT AT AT AT A- AT AT A- AT A- AT AT ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
*
3705338 AT A- AT -T AT AT AA AT A- AT AT AT ACT AT AT A- AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * *
3705376 A- AT ACT AT AT ACT GT GT AA AT ACT AT A- AT AT AT AT AT AT AT
1 AT AT A-T AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
* * *
3705417 AT AT AT A- AT ACC AT ACC AT AT A- AT AT AT AT A- AA AT A- AT AT
1 AT AT AT AT AT A-T AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
3705457 AT A- AT AT A- AT AT A- AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3705480 ATAAAAGGAA
Statistics
Matches: 140, Mismatches: 11, Indels: 54
0.68 0.05 0.26
Matches are distributed among these distances:
1 20 0.14
2 109 0.78
3 11 0.08
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (2 bp):
AT
Found at i:3705342 original size:41 final size:40
Alignment explanation
Indices: 3705289--3705474 Score: 152
Period size: 41 Copynumber: 4.5 Consensus size: 40
3705279 ATAATAATTA
*
3705289 AATA-ATAAATAATATAATATATAATATATATAATATAAT
1 AATATATATATAATATAATATATAATATATATAATATAAT
*
3705328 AATATACTATATAAT-TATATAAATAATATATACT-ATATAAT
1 AATATA-TATATAATATA-ATATATAATATATA-TAATATAAT
* * *
3705369 AATATATA-ATACTATATACTGTGTAA-ATACTATAATATATAT
1 AATATATATATA--ATATAATATATAATATA-TATAATATA-AT
** *
3705411 ATATATATATATAATACCATACCATATAATATATATAAAATAAT
1 A-ATATATATATAAT---ATAATATATAATATATATAATATAAT
3705455 -ATATA-ATATAATATAATATA
1 AATATATATATAATATAATATA
3705475 ATATAATAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 33
0.73 0.07 0.20
Matches are distributed among these distances:
38 6 0.05
39 7 0.06
40 9 0.08
41 53 0.45
42 13 0.11
43 7 0.06
44 5 0.04
45 16 0.13
46 3 0.03
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (40 bp):
AATATATATATAATATAATATATAATATATATAATATAAT
Found at i:3705457 original size:98 final size:98
Alignment explanation
Indices: 3705294--3705477 Score: 252
Period size: 98 Copynumber: 1.9 Consensus size: 98
3705284 AATTAAATAA
* *
3705294 TAAATAATATAATATATAATATATATAATATAATAATATACTATATAATTATATAAATAATATAT
1 TAAATAATATAATATATAATATATATAATATAATAACATACCATATAATTATATAAATAATATAT
3705359 ACT-ATATAATA-ATATATAATACTATATACTGTG
66 A-TAATATAATATA-ATATAATACTATATACTGTG
* *
3705392 TAAATACTATAATATAT-ATATATATATATATAATACCATACCATATAA-TATATATAA-AATAA
1 TAAATAATATAATATATAATATATATA-ATATAATAACATACCATATAATTATATA-AATAAT-A
3705454 TATATAATATAATATAATATAATA
63 TATATAATATAATATAATATAATA
3705478 TAATAAAAGG
Statistics
Matches: 77, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
97 19 0.25
98 57 0.74
99 1 0.01
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (98 bp):
TAAATAATATAATATATAATATATATAATATAATAACATACCATATAATTATATAAATAATATAT
ATAATATAATATAATATAATACTATATACTGTG
Found at i:3705478 original size:36 final size:36
Alignment explanation
Indices: 3705282--3705485 Score: 133
Period size: 36 Copynumber: 5.7 Consensus size: 36
3705272 ACCTAAAATA
*
3705282 ATAAT-TAA-ATAATA-A-ATAATATAATATATAAT
1 ATAATATAATATAATATATATAAAATAATATATAAT
*
3705314 AT-ATATAATATAATA-ATATACTATATAATTATATAA-
1 ATAATATAATATAATATATATA--AAATAA-TATATAAT
* * *
3705350 ATAATAT-ATACTATATAATAATATATAATACTATATACTGT
1 ATAATATAATA-TA-AT-AT-ATATAAAATAATATATA--AT
* * *
3705391 GTAA-ATACTATAATATATAT-ATATATATATATAAT
1 ATAATATAATATAATATATATAAAATA-ATATATAAT
** **
3705426 ACCATACCATATAATATATATAAAATAATATATAAT
1 ATAATATAATATAATATATATAAAATAATATATAAT
3705462 ATAATATAATATAATATA-ATAAAA
1 ATAATATAATATAATATATATAAAA
3705486 GGAAGCCGGA
Statistics
Matches: 132, Mismatches: 21, Indels: 35
0.70 0.11 0.19
Matches are distributed among these distances:
31 2 0.02
32 5 0.04
33 7 0.05
34 3 0.02
35 8 0.06
36 50 0.38
37 27 0.20
38 10 0.08
39 6 0.05
40 4 0.03
41 10 0.08
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (36 bp):
ATAATATAATATAATATATATAAAATAATATATAAT
Found at i:3705802 original size:23 final size:22
Alignment explanation
Indices: 3705757--3705812 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
3705747 AATATTATAA
*
3705757 AATATTCATTTAATATTTAAAAT
1 AATATT-AATTAATATTTAAAAT
*
3705780 CAA-ATTAATTAATTATTTTAAAT
1 -AATATTAATTAA-TATTTAAAAT
3705803 AATATTAATT
1 AATATTAATT
3705813 TTAAATTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 7 0.25
23 19 0.68
24 2 0.07
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (22 bp):
AATATTAATTAATATTTAAAAT
Found at i:3712924 original size:102 final size:102
Alignment explanation
Indices: 3712748--3712954 Score: 414
Period size: 102 Copynumber: 2.0 Consensus size: 102
3712738 TGCCTTGTTG
3712748 ATTGGGGTATTTAATGTTGGGTTGAATTGATTTGTTATTCGCCCGTGGATGTTATGATTGTCCTG
1 ATTGGGGTATTTAATGTTGGGTTGAATTGATTTGTTATTCGCCCGTGGATGTTATGATTGTCCTG
3712813 TTCACTAAAACATTATTTTCTATGTTTTGTTCTTTGT
66 TTCACTAAAACATTATTTTCTATGTTTTGTTCTTTGT
3712850 ATTGGGGTATTTAATGTTGGGTTGAATTGATTTGTTATTCGCCCGTGGATGTTATGATTGTCCTG
1 ATTGGGGTATTTAATGTTGGGTTGAATTGATTTGTTATTCGCCCGTGGATGTTATGATTGTCCTG
3712915 TTCACTAAAACATTATTTTCTATGTTTTGTTCTTTGT
66 TTCACTAAAACATTATTTTCTATGTTTTGTTCTTTGT
3712952 ATT
1 ATT
3712955 TTCTTTTTTT
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 105 1.00
ACGTcount: A:0.19, C:0.11, G:0.21, T:0.49
Consensus pattern (102 bp):
ATTGGGGTATTTAATGTTGGGTTGAATTGATTTGTTATTCGCCCGTGGATGTTATGATTGTCCTG
TTCACTAAAACATTATTTTCTATGTTTTGTTCTTTGT
Found at i:3716003 original size:33 final size:33
Alignment explanation
Indices: 3715961--3716026 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
3715951 TGATACTATG
*
3715961 TAGTTTAATGAGAAAGTGTATTCACAAAAAATA
1 TAGTTTAATGAGAAAGAGTATTCACAAAAAATA
*
3715994 TAGTTTAATGAGAAAGAGTATTCACGAAAAATA
1 TAGTTTAATGAGAAAGAGTATTCACAAAAAATA
3716027 ATTCTCTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.29
Consensus pattern (33 bp):
TAGTTTAATGAGAAAGAGTATTCACAAAAAATA
Found at i:3722550 original size:30 final size:31
Alignment explanation
Indices: 3722482--3722541 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
3722472 AATGATTCAC
* * *
3722482 AACTTTTCCAAATTTTTTGAATTGGTCCCCT
1 AACTTTTCAAAATTTATAGAATTGGTCCCCT
3722513 AACTTTTCAAAATTTATAGAA-TGGTCCCC
1 AACTTTTCAAAATTTATAGAATTGGTCCCC
3722542 AATTTTTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.40
Consensus pattern (31 bp):
AACTTTTCAAAATTTATAGAATTGGTCCCCT
Found at i:3725692 original size:5 final size:5
Alignment explanation
Indices: 3725684--3725724 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
3725674 ATATTTATTA
*
3725684 ATATC ATATC ATATC ATATC ATATTAC ATATC ATATT ATAT
1 ATATC ATATC ATATC ATATC ATA-T-C ATATC ATATC ATAT
3725725 AAATATTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
5 27 0.82
6 2 0.06
7 4 0.12
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (5 bp):
ATATC
Found at i:3725715 original size:12 final size:12
Alignment explanation
Indices: 3725688--3725721 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
3725678 TTATTAATAT
3725688 CATATCATA-T-
1 CATATCATATTA
3725698 CATATCATATTA
1 CATATCATATTA
3725710 CATATCATATTA
1 CATATCATATTA
3725722 TATAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 9 0.41
11 1 0.05
12 12 0.55
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (12 bp):
CATATCATATTA
Found at i:3729705 original size:32 final size:32
Alignment explanation
Indices: 3729619--3729731 Score: 113
Period size: 32 Copynumber: 3.6 Consensus size: 32
3729609 AATTTGCATA
* * **
3729619 ATCTAAATGTGAAACT-AACACTATTGCGCATT
1 ATCTCAATGTGACACTGAA-ACTATTGTACATT
* * * *
3729651 AACT-AATGCGACACTGACACTATTGTCCATT
1 ATCTCAATGTGACACTGAAACTATTGTACATT
*
3729682 ATTTCAATGTGACACTGAAACTATTGTACATT
1 ATCTCAATGTGACACTGAAACTATTGTACATT
*
3729714 ATCTGAATGTGACACTGA
1 ATCTCAATGTGACACTGA
3729732 CACTGCTTTG
Statistics
Matches: 66, Mismatches: 13, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
31 22 0.33
32 44 0.67
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (32 bp):
ATCTCAATGTGACACTGAAACTATTGTACATT
Found at i:3729749 original size:32 final size:32
Alignment explanation
Indices: 3729655--3729756 Score: 98
Period size: 32 Copynumber: 3.2 Consensus size: 32
3729645 CGCATTAACT
* * * * * *
3729655 AATGCGACACTGACACTATTGTCCATTATTTC
1 AATGTGACACTGAAACTATTGTACACTATCTG
*
3729687 AATGTGACACTGAAACTATTGTACATTATCTG
1 AATGTGACACTGAAACTATTGTACACTATCTG
* * *
3729719 AATGTGACACTGACACTGCTT-TGCACTATCTG
1 AATGTGACACTGAAACT-ATTGTACACTATCTG
3729751 AATGTG
1 AATGTG
3729757 TCACAACTAG
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
32 58 0.97
33 2 0.03
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (32 bp):
AATGTGACACTGAAACTATTGTACACTATCTG
Found at i:3730239 original size:20 final size:20
Alignment explanation
Indices: 3730176--3730240 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
3730166 ACACTGATTT
* * *
3730176 GAGTTAACTTAGATTGGTTC
1 GAGTTGACTCAGATCGGTTC
* * * * *
3730196 GATTTGATTCAAATCGATTT
1 GAGTTGACTCAGATCGGTTC
3730216 GAGTTGACTCAGATCGGTTC
1 GAGTTGACTCAGATCGGTTC
3730236 GAGTT
1 GAGTT
3730241 CGGTTTGATC
Statistics
Matches: 32, Mismatches: 13, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (20 bp):
GAGTTGACTCAGATCGGTTC
Found at i:3731583 original size:19 final size:19
Alignment explanation
Indices: 3731559--3731623 Score: 112
Period size: 19 Copynumber: 3.4 Consensus size: 19
3731549 GGGTTTAGCC
3731559 TTGCCATTACCCTTAGGCT
1 TTGCCATTACCCTTAGGCT
*
3731578 TTGCCATTGCCCTTAGGCT
1 TTGCCATTACCCTTAGGCT
*
3731597 TTGCCATTTCCCTTAGGCT
1 TTGCCATTACCCTTAGGCT
3731616 TTGCCATT
1 TTGCCATT
3731624 GCCTTGTTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.12, C:0.31, G:0.17, T:0.40
Consensus pattern (19 bp):
TTGCCATTACCCTTAGGCT
Found at i:3733225 original size:2 final size:2
Alignment explanation
Indices: 3733207--3733263 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
3733197 TTAATATTAC
*
3733207 AT AT AC AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3733248 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
3733264 TAATGTCAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3733627 original size:84 final size:82
Alignment explanation
Indices: 3733455--3733627 Score: 265
Period size: 82 Copynumber: 2.1 Consensus size: 82
3733445 AAGTTACAAG
*
3733455 AAGTCATGATTCGACAAAACCTCTTCGTCACTAACTCATTTATGTATTATATCTTTTTGTCCTTT
1 AAGTCCTGATTCGACAAAACCTCTTCGTCACTAACTCATTTATGTATTATATCTTTTTGTCCTTT
* *
3733520 ATATCTAGAATAGGCAC
66 ATATCTAAAATAAGCAC
* * * *
3733537 AAGTCCTGATTCGACAAAACTTCTTTGTGACTAACTCCTTTATGTATTATATATCTTTTTGTCCT
1 AAGTCCTGATTCGACAAAACCTCTTCGTCACTAACTCATTTATGTA-T-TATATCTTTTTGTCCT
3733602 TTATATCTAAAATAAGCAC
64 TTATATCTAAAATAAGCAC
3733621 AAGTCCT
1 AAGTCCT
3733628 TGAATAATCA
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
82 41 0.50
83 1 0.01
84 40 0.49
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.40
Consensus pattern (82 bp):
AAGTCCTGATTCGACAAAACCTCTTCGTCACTAACTCATTTATGTATTATATCTTTTTGTCCTTT
ATATCTAAAATAAGCAC
Found at i:3739923 original size:57 final size:57
Alignment explanation
Indices: 3739821--3739931 Score: 159
Period size: 57 Copynumber: 1.9 Consensus size: 57
3739811 ATCTCACTTA
3739821 TTCTCTCATCTAAAATGTTCTACAAGGTTTTACTAGCTTTCTACATCTGTTAGTTTC
1 TTCTCTCATCTAAAATGTTCTACAAGGTTTTACTAGCTTTCTACATCTGTTAGTTTC
* * * ** * *
3739878 TTCTCTCATCTAGAATGTTTTATAAGGTTTTTGTAGTTTTTTACATCTGTTAGT
1 TTCTCTCATCTAAAATGTTCTACAAGGTTTTACTAGCTTTCTACATCTGTTAGT
3739932 CCATTAATTG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.22, C:0.16, G:0.13, T:0.50
Consensus pattern (57 bp):
TTCTCTCATCTAAAATGTTCTACAAGGTTTTACTAGCTTTCTACATCTGTTAGTTTC
Found at i:3743954 original size:26 final size:26
Alignment explanation
Indices: 3743865--3743954 Score: 69
Period size: 26 Copynumber: 3.5 Consensus size: 26
3743855 TTAAATTAAT
* *
3743865 ATTTACACTTATATATGAATCATATCA
1 ATTTAAAC-TATATATGAATTATATCA
* *
3743892 ATTTAAACTATA-ATTAATTCA-A-AA
1 ATTTAAACTATATATGAATT-ATATCA
* * *
3743916 AATTATTATTATATATGAATTATATCA
1 ATTTA-AACTATATATGAATTATATCA
3743943 ATTTAAACTATA
1 ATTTAAACTATA
3743955 ATAAAAATAT
Statistics
Matches: 46, Mismatches: 12, Indels: 11
0.67 0.17 0.16
Matches are distributed among these distances:
24 5 0.11
25 12 0.26
26 17 0.37
27 12 0.26
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (26 bp):
ATTTAAACTATATATGAATTATATCA
Found at i:3743973 original size:14 final size:14
Alignment explanation
Indices: 3743954--3744002 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
3743944 TTTAAACTAT
3743954 AATAAAAATATAAA
1 AATAAAAATATAAA
3743968 AATAAAAATA-AAA
1 AATAAAAATATAAA
**
3743981 ATATAATTATAATAAA
1 A-ATAAAAAT-ATAAA
3743997 AATAAA
1 AATAAA
3744003 TTTTATATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 4 0.14
14 16 0.55
15 5 0.17
16 4 0.14
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AATAAAAATATAAA
Found at i:3744012 original size:17 final size:17
Alignment explanation
Indices: 3743951--3744004 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
3743941 CAATTTAAAC
3743951 TATAATAAAAATATAAAAAT
1 TATAATAAAAATAT---AAT
* *
3743971 AAAAATAAAAATATAAT
1 TATAATAAAAATATAAT
3743988 TATAATAAAAATA-AAT
1 TATAATAAAAATATAAT
3744004 T
1 T
3744005 TTATATAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
16 4 0.13
17 14 0.47
20 12 0.40
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
TATAATAAAAATATAAT
Found at i:3744755 original size:18 final size:19
Alignment explanation
Indices: 3744726--3744762 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3744716 TATTTAATAT
*
3744726 TTTATATAAAAATGAAACC
1 TTTATATAAAAAAGAAACC
3744745 TTTAT-TAAAAAAGAAACC
1 TTTATATAAAAAAGAAACC
3744763 ATAAGTGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (19 bp):
TTTATATAAAAAAGAAACC
Found at i:3751143 original size:20 final size:23
Alignment explanation
Indices: 3751099--3751145 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
3751089 TATATTATAA
3751099 AAATAAGTTATTTATGTAGTATT
1 AAATAAGTTATTTATGTAGTATT
3751122 AAATAAGTTATTT-T-TA-TATT
1 AAATAAGTTATTTATGTAGTATT
3751142 AAAT
1 AAAT
3751146 TTAAATAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 8 0.33
21 2 0.08
22 1 0.04
23 13 0.54
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (23 bp):
AAATAAGTTATTTATGTAGTATT
Found at i:3751484 original size:60 final size:59
Alignment explanation
Indices: 3751380--3751508 Score: 143
Period size: 60 Copynumber: 2.2 Consensus size: 59
3751370 AAAGTTTGGG
* ** *
3751380 GGACTAATTTAGGATGAAAATCTTAGCTTGGGGAGGAAAATGAAATGTTCAAAAGTTTAA
1 GGACTAATTTAGGATGAAAATCATAGCTTAAGGAGGAAAATGAAATGTTCAAAAGCTT-A
* * * * *
3751440 GGACTAATTTAGGAT-AATAGTCATAGTTTAAGGATGAAATTGAAATGTTTAAAAGCTTA
1 GGACTAATTTAGGATGAA-AATCATAGCTTAAGGAGGAAAATGAAATGTTCAAAAGCTTA
3751499 GTGACTAATT
1 G-GACTAATT
3751509 CAAAATGAGG
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
59 4 0.07
60 54 0.93
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (59 bp):
GGACTAATTTAGGATGAAAATCATAGCTTAAGGAGGAAAATGAAATGTTCAAAAGCTTA
Found at i:3756394 original size:32 final size:31
Alignment explanation
Indices: 3756321--3756397 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
3756311 CTAATATGAC
* * *
3756321 TCTTAGGTAGGCTCTGCGGCCCTGATATTAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
** * *
3756352 TCTCGGGTAGGCCCTGCGGTCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-TAT
3756384 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
3756398 CACAGCCCTG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 22 0.61
32 14 0.39
ACGTcount: A:0.14, C:0.25, G:0.30, T:0.31
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
Found at i:3756423 original size:63 final size:63
Alignment explanation
Indices: 3756321--3756444 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
3756311 CTAATATGAC
* ** * * *
3756321 TCTTAGGTAGGCTCTGCGGCCCTGATATTATTCTCGGGTAGGCCCTGC-GGTCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACAGCCCTGAAATTATTCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
3756384 TCTTAGGTAGGCCCCACAGCCCTGAAATCTA-TCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACAGCCCTGAAAT-TATTCTCGGGTAGGCCCTCAGGCCCTAAGATGT
3756445 TCCCTTAGGT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 1 0.02
63 48 0.94
64 2 0.04
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.29
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACAGCCCTGAAATTATTCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:3761462 original size:32 final size:32
Alignment explanation
Indices: 3761380--3761513 Score: 100
Period size: 31 Copynumber: 4.2 Consensus size: 32
3761370 CTAATGTGAC
*
3761380 TCTTAGGTAGG-CTCTACGGCCCTGAGAT-TAT
1 TCTTAGGTAGGCCTCTACGGCCCTAAGATGT-T
**
3761411 TCTCGGGTAGGCC-CTACGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCTCTACGGCCCTAAGATGT-T
* * * *
3761443 TCTTAGGTAGGCCTC-ACGGCCCCAAAATCTA
1 TCTTAGGTAGGCCTCTACGGCCCTAAGATGTT
* *
3761474 TATTGGGTAGG-CTCT-CAGGCCCTAAGATGTT
1 TCTTAGGTAGGCCTCTAC-GGCCCTAAGATGTT
*
3761505 CCCTTAGGT
1 -TCTTAGGT
3761514 TAACTCTTTG
Statistics
Matches: 78, Mismatches: 19, Indels: 11
0.72 0.18 0.10
Matches are distributed among these distances:
30 4 0.05
31 42 0.54
32 31 0.40
33 1 0.01
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (32 bp):
TCTTAGGTAGGCCTCTACGGCCCTAAGATGTT
Found at i:3768990 original size:22 final size:22
Alignment explanation
Indices: 3768965--3769008 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3768955 ACGATTGAGT
*
3768965 GGGATTGGATCTCTTTGTAGTA
1 GGGATTGGATCTATTTGTAGTA
* *
3768987 GGGATTGTATCTATTTTTAGTA
1 GGGATTGGATCTATTTGTAGTA
3769009 ATCTTCCATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.20, C:0.07, G:0.27, T:0.45
Consensus pattern (22 bp):
GGGATTGGATCTATTTGTAGTA
Found at i:3770914 original size:23 final size:23
Alignment explanation
Indices: 3770870--3770914 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3770860 AAATCAATAT
3770870 CGATCAACAGTAAAAGTCAACGC
1 CGATCAACAGTAAAAGTCAACGC
**
3770893 CGATCAATGGTAAAAGTCAACG
1 CGATCAACAGTAAAAGTCAACG
3770915 GTGGTGGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.16
Consensus pattern (23 bp):
CGATCAACAGTAAAAGTCAACGC
Found at i:3776794 original size:15 final size:15
Alignment explanation
Indices: 3776776--3776806 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3776766 TTTCTAAACT
3776776 TTTATTTTTATTTTC
1 TTTATTTTTATTTTC
*
3776791 TTTATTTTTGTTTTC
1 TTTATTTTTATTTTC
3776806 T
1 T
3776807 CCTCATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.06, G:0.03, T:0.81
Consensus pattern (15 bp):
TTTATTTTTATTTTC
Found at i:3777547 original size:23 final size:19
Alignment explanation
Indices: 3777496--3777540 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
3777486 TTCAAGATAG
3777496 TTTCTCTTGAAACAAAAGT
1 TTTCTCTTGAAACAAAAGT
3777515 TTTCTCTTGAAACAAAAGT
1 TTTCTCTTGAAACAAAAGT
3777534 TTTCTCT
1 TTTCTCT
3777541 CACTTGAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (19 bp):
TTTCTCTTGAAACAAAAGT
Found at i:3777635 original size:74 final size:75
Alignment explanation
Indices: 3777515--3777662 Score: 181
Period size: 74 Copynumber: 2.0 Consensus size: 75
3777505 AAACAAAAGT
* * * * * *
3777515 TTTCTCTTGAAACAAAAGTTTTCTCTCACTTGAGATAGTTTTCCTCAACAGCAATTTTTGTATCA
1 TTTCTCTCGAAACAAAAGTTTTATCTCACTTGAGAAAGTTTTCCTCAAAAACAATTTTCGTATCA
3777580 CTCAAGACAG
66 CTCAAGACAG
* * * * * *
3777590 TTTCTCTCGGAACAAAA-TTTTATCTTAGTTGAGAAATTTTTCCTCAAAAATAATTTTCGTCTCA
1 TTTCTCTCGAAACAAAAGTTTTATCTCACTTGAGAAAGTTTTCCTCAAAAACAATTTTCGTATCA
3777654 CTCAAGACA
66 CTCAAGACA
3777663 ATTTTCCAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
74 46 0.75
75 15 0.25
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (75 bp):
TTTCTCTCGAAACAAAAGTTTTATCTCACTTGAGAAAGTTTTCCTCAAAAACAATTTTCGTATCA
CTCAAGACAG
Found at i:3778250 original size:22 final size:21
Alignment explanation
Indices: 3778221--3778261 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3778211 ATCCACAATG
*
3778221 AAAAATATTGGACTTAAATAT
1 AAAAATATTCGACTTAAATAT
*
3778242 AAAACATATTCGAGTTAAAT
1 AAAA-ATATTCGACTTAAAT
3778262 TTTGACTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.32
Consensus pattern (21 bp):
AAAAATATTCGACTTAAATAT
Found at i:3778686 original size:20 final size:19
Alignment explanation
Indices: 3778661--3778712 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
3778651 ATATATATAG
3778661 TATATATTTATTCAAAAATA
1 TATATATTTATT-AAAAATA
*
3778681 TATATAGTTT-TTAAATATA
1 TATATA-TTTATTAAAAATA
3778700 T-TATATTATATTA
1 TATATATT-TATTA
3778713 TCATTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 2 0.07
18 5 0.18
19 10 0.36
20 8 0.29
21 3 0.11
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
TATATATTTATTAAAAATA
Found at i:3782533 original size:21 final size:21
Alignment explanation
Indices: 3782486--3782535 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
3782476 AACGACACTC
* *
3782486 AATACAATAATAACTAAACTT
1 AATAAAATGATAACTAAACTT
3782507 AATAAAATGATAACATAAA-TT
1 AATAAAATGATAAC-TAAACTT
*
3782528 ATTAAAAT
1 AATAAAAT
3782536 TTAACTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (21 bp):
AATAAAATGATAACTAAACTT
Found at i:3783841 original size:17 final size:18
Alignment explanation
Indices: 3783808--3783841 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3783798 CTGCTATTAG
3783808 TGAACCGGTCAGAACCGC
1 TGAACCGGTCAGAACCGC
*
3783826 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
3783842 GACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.15
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGC
Found at i:3785407 original size:8 final size:7
Alignment explanation
Indices: 3785400--3785444 Score: 54
Period size: 8 Copynumber: 6.0 Consensus size: 7
3785390 ATGGTATAAT
3785400 ATCCTAA
1 ATCCTAA
*
3785407 TTCCTAA
1 ATCCTAA
3785414 ATTCCTAA
1 A-TCCTAA
3785422 ATCCCTAA
1 AT-CCTAA
3785430 ATCCTAA
1 ATCCTAA
3785437 ATTCCTAA
1 A-TCCTAA
3785445 TTATAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
7 13 0.39
8 20 0.61
ACGTcount: A:0.38, C:0.29, G:0.00, T:0.33
Consensus pattern (7 bp):
ATCCTAA
Found at i:3785421 original size:15 final size:15
Alignment explanation
Indices: 3785396--3785446 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
3785386 ATTAATGGTA
3785396 TAATATCCT-AATTCC
1 TAAT-TCCTAAATTCC
*
3785411 TAAATTCCTAAATCCC
1 T-AATTCCTAAATTCC
*
3785427 TAAATCCTAAATTCC
1 TAATTCCTAAATTCC
3785442 TAATT
1 TAATT
3785447 ATAATTTTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 21 0.70
16 9 0.30
ACGTcount: A:0.37, C:0.25, G:0.00, T:0.37
Consensus pattern (15 bp):
TAATTCCTAAATTCC
Found at i:3790487 original size:13 final size:13
Alignment explanation
Indices: 3790449--3790491 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
3790439 CAGGTAAATA
* *
3790449 ATTATTTAATTAA
1 ATTATTTATTTAT
3790462 ATTATTTACTTTAT
1 ATTATTTA-TTTAT
3790476 ATTATTTATTTAT
1 ATTATTTATTTAT
3790489 ATT
1 ATT
3790492 TGTACATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (13 bp):
ATTATTTATTTAT
Found at i:3790996 original size:15 final size:15
Alignment explanation
Indices: 3790952--3791000 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
3790942 GGTATAATGA
3790952 AATAAAATAAT-AAT
1 AATAAAATAATAAAT
3790966 AAATAAAA-AGGA-AAAT
1 -AATAAAATA--ATAAAT
3790982 AATAAAATAATAAAT
1 AATAAAATAATAAAT
3790997 AATA
1 AATA
3791001 GTAGTAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
14 2 0.07
15 22 0.76
16 5 0.17
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (15 bp):
AATAAAATAATAAAT
Found at i:3791784 original size:73 final size:76
Alignment explanation
Indices: 3791698--3791888 Score: 255
Period size: 76 Copynumber: 2.6 Consensus size: 76
3791688 TAAAACCTCT
* * * * * *
3791698 TAAATCCTAATTAAAACACTTAAAA-ATATTTAAACTAAAATACGTAAAA-ATA-ATAATAT-TT
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
*
3791759 AAAATAATATTC
65 AAAATAATATCC
*
3791771 TAAATCCTAATTAAATTACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
3791836 AAATAATATCC
66 AAATAATATCC
* *
3791847 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATA
3791889 AAAAGATAAA
Statistics
Matches: 103, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
72 5 0.05
73 39 0.38
74 2 0.02
75 6 0.06
76 51 0.50
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.30
Consensus pattern (76 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
AAATAATATCC
Found at i:3791913 original size:76 final size:75
Alignment explanation
Indices: 3791698--3791925 Score: 241
Period size: 76 Copynumber: 3.1 Consensus size: 75
3791688 TAAAACCTCT
* * * ** *
3791698 TAAATCCTAATTAAAACACTTAAAA-ATATTTAAACTAAAATACGTAA-AAATA-ATAATATTTA
1 TAAAACCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACAAAACAAAAATATAATATTTA
*
3791760 AAATAATATTC
65 AAATAATATCC
* * * * *
3791771 TAAATCCTAATTAAATTACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATA-TA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATA-C-AAAACAAAAATATAATATTT
3791835 AAAATAATATCC
64 AAAATAATATCC
* * *
3791847 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATA-AAAAGATAAAATATAATGTTTA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAACA-AAAATATAATATTTA
*
3791911 AAATACTATCC
65 AAATAATATCC
3791922 TAAA
1 TAAA
3791926 CTTGAGTTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
72 5 0.04
73 38 0.29
74 9 0.07
75 18 0.14
76 55 0.42
77 5 0.04
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (75 bp):
TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAACAAAAATATAATATTTAA
AATAATATCC
Found at i:3799133 original size:15 final size:15
Alignment explanation
Indices: 3799089--3799137 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
3799079 GGTATAATGA
3799089 AATAAAATAAT-AAT
1 AATAAAATAATAAAT
*
3799103 AAATAAAAGGAA-AAAT
1 -AATAAAA-TAATAAAT
3799119 AATAAAATAATAAAT
1 AATAAAATAATAAAT
3799134 AATA
1 AATA
3799138 GTAGTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 2 0.07
15 22 0.76
16 5 0.17
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (15 bp):
AATAAAATAATAAAT
Found at i:3799168 original size:12 final size:13
Alignment explanation
Indices: 3799151--3799179 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3799141 GTAAAATAAA
3799151 AAAAG-TGTTTTT
1 AAAAGTTGTTTTT
3799163 AAAAGTTGTTTTT
1 AAAAGTTGTTTTT
3799176 AAAA
1 AAAA
3799180 TAAAAGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (13 bp):
AAAAGTTGTTTTT
Found at i:3799914 original size:71 final size:75
Alignment explanation
Indices: 3799833--3800022 Score: 275
Period size: 76 Copynumber: 2.6 Consensus size: 75
3799823 CTAAAACTCT
* * *
3799833 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCT-AA-AAA-ATAATAT-TTA
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAACAAAGATAAAATATAA
*
3799893 AAATAATATTC
65 AAATAATATCC
3799904 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCT-AAACAAAGATAAAATATAA
3799969 AAATAATATCC
65 AAATAATATCC
3799980 TAAA-CCTTAATTAAAATACTAAAACCTATTTAAACTAAAATAC
1 TAAATCC-TAATTAAAATACTAAAACCTATTTAAACTAAAATAC
3800023 AAAGATAAAA
Statistics
Matches: 108, Mismatches: 4, Indels: 9
0.89 0.03 0.07
Matches are distributed among these distances:
70 5 0.05
71 38 0.35
73 2 0.02
74 3 0.03
75 8 0.07
76 52 0.48
ACGTcount: A:0.56, C:0.14, G:0.01, T:0.29
Consensus pattern (75 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAACAAAGATAAAATATAAA
AATAATATCC
Found at i:3800046 original size:76 final size:70
Alignment explanation
Indices: 3799833--3800059 Score: 258
Period size: 76 Copynumber: 3.1 Consensus size: 70
3799823 CTAAAACTCT
* **
3799833 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAAAATAATATTTAAAAT
1 TAAA-CCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACAAAAAAAATAATATTTAAAAT
*
3799897 AATATTC
64 AATATCC
* *
3799904 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAA-CCTAATTAAAATACTAAAACCTATTTAAACTAAAATA-C-AAAA-AAA-ATAATAT-TTA
3799969 AAATAATATCC
60 AAATAATATCC
*
3799980 TAAACCTTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAATATATTGTTTAA
1 TAAACC-TAATTAAAATACTAAAACCTATTTAAACTAAAATACAAA-A-AAAATA-A-TATTTAA
*
3800045 AATATTATCC
61 AATAATATCC
3800055 TAAAC
1 TAAAC
3800060 TTGAGTTTAA
Statistics
Matches: 135, Mismatches: 11, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
70 5 0.04
71 35 0.26
72 1 0.01
73 2 0.01
74 9 0.07
75 31 0.23
76 52 0.39
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.30
Consensus pattern (70 bp):
TAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAAAAAATAATATTTAAAATAA
TATCC
Found at i:3801437 original size:2 final size:2
Alignment explanation
Indices: 3801432--3801469 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3801422 TATTGTTAAA
3801432 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3801470 TATTCTTGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3804232 original size:22 final size:20
Alignment explanation
Indices: 3804207--3804257 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3804197 GTTTTTAGCA
3804207 CTTTTGAATAGAAAAATAATAG
1 CTTTTGAA-AG-AAAATAATAG
* *
3804229 CTTTCGAAAGGAAATAATAG
1 CTTTTGAAAGAAAATAATAG
3804249 CTTTTGAAA
1 CTTTTGAAA
3804258 ACGTGAGCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 17 0.65
21 2 0.08
22 7 0.27
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.31
Consensus pattern (20 bp):
CTTTTGAAAGAAAATAATAG
Found at i:3804245 original size:20 final size:20
Alignment explanation
Indices: 3804220--3804257 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3804210 TTGAATAGAA
3804220 AAATAATAGCTTTCGAAAGG
1 AAATAATAGCTTTCGAAAGG
*
3804240 AAATAATAGCTTTTGAAA
1 AAATAATAGCTTTCGAAA
3804258 ACGTGAGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.29
Consensus pattern (20 bp):
AAATAATAGCTTTCGAAAGG
Found at i:3805776 original size:41 final size:40
Alignment explanation
Indices: 3805731--3805858 Score: 100
Period size: 41 Copynumber: 3.1 Consensus size: 40
3805721 ATTTTGTGGT
3805731 GTTTTTATGTAAACGCCGCGATAGATTAGCATTATAGAGGC
1 GTTTTTATGTAAACGCCGCGATAGATTAGCA-TATAGAGGC
* ** * * * *
3805772 GTTTTCATACAAACGCCGCAAAATAG-TTGGACA-GTAGTGGC
1 GTTTTTATGTAAACGCCGC--GATAGATTAG-CATATAGAGGC
* *
3805813 GTTTTT-TAGTAAACGCCGCGATAGAGTAGAACTATAGAGGC
1 GTTTTTAT-GTAAACGCCGCGATAGATTAGCA-TATAGAGGC
3805854 GTTTT
1 GTTTT
3805859 CATACAAATG
Statistics
Matches: 64, Mismatches: 16, Indels: 14
0.68 0.17 0.15
Matches are distributed among these distances:
39 5 0.08
40 3 0.05
41 47 0.73
42 3 0.05
43 6 0.09
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (40 bp):
GTTTTTATGTAAACGCCGCGATAGATTAGCATATAGAGGC
Found at i:3805787 original size:82 final size:82
Alignment explanation
Indices: 3805700--3805866 Score: 230
Period size: 82 Copynumber: 2.0 Consensus size: 82
3805690 GTTTGTGTAG
* * * * * *
3805700 AAACGCCGCAAAATAATAGGA-ATTTTGTGGTG-TTTTTATGTAAACGCCGCGATAGATTAGCAT
1 AAACGCCGCAAAATAATAGGACA-GTAGTGGCGTTTTTTA-GTAAACGCCGCGATAGAGTAGAAC
3805763 TATAGAGGCGTTTTCATAC
64 TATAGAGGCGTTTTCATAC
* *
3805782 AAACGCCGCAAAATAGTTGGACAGTAGTGGCGTTTTTTAGTAAACGCCGCGATAGAGTAGAACTA
1 AAACGCCGCAAAATAATAGGACAGTAGTGGCGTTTTTTAGTAAACGCCGCGATAGAGTAGAACTA
3805847 TAGAGGCGTTTTCATAC
66 TAGAGGCGTTTTCATAC
3805864 AAA
1 AAA
3805867 TGTCGCTATA
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
82 68 0.91
83 7 0.09
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (82 bp):
AAACGCCGCAAAATAATAGGACAGTAGTGGCGTTTTTTAGTAAACGCCGCGATAGAGTAGAACTA
TAGAGGCGTTTTCATAC
Found at i:3805882 original size:82 final size:83
Alignment explanation
Indices: 3805732--3805941 Score: 251
Period size: 82 Copynumber: 2.5 Consensus size: 83
3805722 TTTTGTGGTG
* * *
3805732 TTTTTATGTAAACGCCGCGATAGATTAGCATTATAGAGGCGTTTTCATACAAACGCCGCAAAATA
1 TTTTTA-GTAAACGCCGCGATAGAGTAGCACTATAGAGGCGTTTTCATACAAACGCCGCAAAAGA
*
3805797 GTTGGACAGTAGTGGC-GT
65 GTTGGACAATAGTGGCAGT
* * * * *
3805815 TTTTTAGTAAACGCCGCGATAGAGTAGAACTATAGAGGCGTTTTCATACAAATGTCGCTATAGAG
1 TTTTTAGTAAACGCCGCGATAGAGTAGCACTATAGAGGCGTTTTCATACAAACGCCGCAAAAGAG
*
3805880 TTGGACAATAGTGGCATT
66 TTGGACAATAGTGGCAGT
* * * * * *
3805898 TTGTTTTGTAAATGTCGCAATAAAGTAGCACTATAGTGGCGTTT
1 TT-TTTAGTAAACGCCGCGATAGAGTAGCACTATAGAGGCGTTT
3805942 GGTTTACAAA
Statistics
Matches: 108, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
82 65 0.60
83 9 0.08
84 34 0.31
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (83 bp):
TTTTTAGTAAACGCCGCGATAGAGTAGCACTATAGAGGCGTTTTCATACAAACGCCGCAAAAGAG
TTGGACAATAGTGGCAGT
Done.