Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006638.1 Hibiscus syriacus cultivar Beakdansim tig00016349_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: 193951
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:118575 original size:20 final size:20
Alignment explanation
Indices: 118547--118599 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
118537 GCGCTATGTA
*
118547 AATCGCGTTGCGAAAGTCAG
1 AATCACGTTGCGAAAGTCAG
118567 AATCACGTTGCGAAAGTCAG
1 AATCACGTTGCGAAAGTCAG
* *
118587 TATCTCGTTGCGA
1 AATCACGTTGCGA
118600 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (20 bp):
AATCACGTTGCGAAAGTCAG
Found at i:118633 original size:20 final size:20
Alignment explanation
Indices: 118608--118661 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
118598 GATTTTGTAT
118608 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
118628 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
118648 TATCGCATTGCGAT
1 TATCGCATTGCGAT
118662 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:118680 original size:61 final size:61
Alignment explanation
Indices: 118548--118682 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
118538 CGCTATGTAA
* * * * * ** *
118548 ATCGCGTTGCGAAAGTCAGAATCACGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCACATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * * *
118609 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCACATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
118671 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
118683 TTACTTATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCACATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:118772 original size:21 final size:21
Alignment explanation
Indices: 118732--118772 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
118722 ACTGTATACC
**
118732 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
118753 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
118773 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:122649 original size:43 final size:43
Alignment explanation
Indices: 122585--122713 Score: 170
Period size: 43 Copynumber: 3.0 Consensus size: 43
122575 TTTTTAAACT
* * *
122585 CCAAAGTAATAATCCATAAATACACTAAAATAACAAATTACAA
1 CCAAAGTAACAATCCACAAATACACTAAAATAACATATTACAA
*
122628 CCAAAGTAACATTCCACAAATACA-TCAAAATAACATATTACAA
1 CCAAAGTAACAATCCACAAATACACT-AAAATAACATATTACAA
* * * *
122671 CTAAAGTAACAATCCACAAGTACACCAAACTAACATATTACAA
1 CCAAAGTAACAATCCACAAATACACTAAAATAACATATTACAA
122714 TTATACTTAA
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
42 1 0.01
43 74 0.99
ACGTcount: A:0.54, C:0.22, G:0.03, T:0.20
Consensus pattern (43 bp):
CCAAAGTAACAATCCACAAATACACTAAAATAACATATTACAA
Found at i:129668 original size:65 final size:64
Alignment explanation
Indices: 129612--129754 Score: 193
Period size: 65 Copynumber: 2.2 Consensus size: 64
129602 CATTGAGGCG
* *
129612 TAAAATGCATTCGATGTTT-CA-AACAA-GCATGTAGTGCATCGATGCATGGTCTGTGCATCGAT
1 TAAAATGCATTCGATGTTTCCATAA-AATGC-TG-AGTGCATCAATGCATGGT-AGTGCATCGAT
129674 GCA
62 GCA
* *
129677 TAAAATGAATTCGATGTTTCCATAAAATTCTGAGTGCATCAATGCATGGTAGTGCATCGATGCA
1 TAAAATGCATTCGATGTTTCCATAAAATGCTGAGTGCATCAATGCATGGTAGTGCATCGATGCA
129741 TAAAATGCATTCGA
1 TAAAATGCATTCGA
129755 AATGGGGTGT
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
64 26 0.37
65 35 0.50
66 6 0.09
67 3 0.04
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (64 bp):
TAAAATGCATTCGATGTTTCCATAAAATGCTGAGTGCATCAATGCATGGTAGTGCATCGATGCA
Found at i:130388 original size:27 final size:27
Alignment explanation
Indices: 130358--130414 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
130348 CTAAATGATG
* * *
130358 CAAAAATCTAATAAACCAATATAAGTT
1 CAAAAACCAAATAAACAAATATAAGTT
* *
130385 CAAAAACCAAATATATAAATATAAGTT
1 CAAAAACCAAATAAACAAATATAAGTT
130412 CAA
1 CAA
130415 GCATTCAAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.58, C:0.14, G:0.04, T:0.25
Consensus pattern (27 bp):
CAAAAACCAAATAAACAAATATAAGTT
Found at i:132421 original size:23 final size:22
Alignment explanation
Indices: 132394--132473 Score: 90
Period size: 23 Copynumber: 3.6 Consensus size: 22
132384 CACTGCTGAG
132394 TGCATCGATGCACATTCAAGGA
1 TGCATCGATGCACATTCAAGGA
* * *
132416 GTGCATCGGTGCACCTTC-ATGA
1 -TGCATCGATGCACATTCAAGGA
* *
132438 TGTATCGATTCACATTCATAGGA
1 TGCATCGATGCACATTCA-AGGA
132461 TGCATCGATGCAC
1 TGCATCGATGCAC
132474 TGGATAGTGT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
21 13 0.29
22 3 0.07
23 29 0.64
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:137934 original size:65 final size:64
Alignment explanation
Indices: 137865--138012 Score: 194
Period size: 65 Copynumber: 2.3 Consensus size: 64
137855 TGTACTAAGG
*
137865 GTGCATCGATGCATAAAATACATTCGATGTTT-CA-AACAAGCA-TGGAGTGCATCGATGCATGG
1 GTGCATCGATGCATAAAATACATTCAATGTTTCCATAA-AA-CACT-GAGTGCATCGATGCATGG
*
137927 TCT
63 T-A
* * *
137930 GTGCATCGATACATAAAATGCATTCAATGTTTCCATAAAATACTGAGTGCATCGATGCATGGTA
1 GTGCATCGATGCATAAAATACATTCAATGTTTCCATAAAACACTGAGTGCATCGATGCATGGTA
137994 GTGCATCGATGCATAAAAT
1 GTGCATCGATGCATAAAAT
138013 GCTTTCGAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
64 18 0.24
65 49 0.66
66 5 0.07
67 2 0.03
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATACATTCAATGTTTCCATAAAACACTGAGTGCATCGATGCATGGTA
Found at i:147987 original size:58 final size:57
Alignment explanation
Indices: 147752--148159 Score: 335
Period size: 58 Copynumber: 7.0 Consensus size: 57
147742 AATCTTGTGT
* * * * *
147752 TGATTCT-AGTTTCGTAAGGAAAATAAATAGTT-AGATTTATTTACTTGAGAATATTTAA
1 TGATTCTAACTTT-GTAAGGAAAATAAATTGTTGA-ATTTATTT-TTTGAGAATCTTGAA
* *
147810 TGATTCTAACTTTGTAAGGAAAATAAATTATTGAATTTATTTCTTTGAGAATCTTAAA
1 TGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATTT-TTTGAGAATCTTGAA
*
147868 TGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATTTCATTG-GAAATCTTGAA
1 TGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATTT-TTTGAG-AATCTTGAA
* * * *
147926 TGATTTTAACTTTGTAAGGAAAATAAATTGTCGAATTTATTTTGTTGAGAATCGTGGA
1 TGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATTTT-TTGAGAATCTTGAA
* * * ** * *
147984 TGATTCTATCCTCT-AAAAAAGAAATAAATTGTTAAATTTATTTCTCTTGAGAATCTTAAA
1 TGATTCTA-ACTTTGTAAGGA-AAATAAATTGTTGAATTTATTT-T-TTGAGAATCTTGAA
* * * * ** * * * *
148044 AGATTAT-ATTTTGTAAAAGTTAATTAATTGTTAAATTTATTTTTTTGAGAATCATAAA
1 TGATTCTAACTTTGT-AAGGAAAATAAATTGTTGAATTTA-TTTTTTGAGAATCTTGAA
* * * *
148102 TGATTCT-ATTTTGTTAAAGG-AAATAAATTGTTAAATTTATTTTCTAAGAATCTTGAA
1 TGATTCTAACTTTG-T-AAGGAAAATAAATTGTTGAATTTATTTTTTGAGAATCTTGAA
148159 T
1 T
148160 AAAGAAATAA
Statistics
Matches: 291, Mismatches: 47, Indels: 25
0.80 0.13 0.07
Matches are distributed among these distances:
57 16 0.05
58 200 0.69
59 52 0.18
60 23 0.08
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.43
Consensus pattern (57 bp):
TGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATTTTTTGAGAATCTTGAA
Found at i:148164 original size:118 final size:119
Alignment explanation
Indices: 147811--148164 Score: 307
Period size: 118 Copynumber: 3.0 Consensus size: 119
147801 AATATTTAAT
* * * ** * *
147811 GATTCTAACTTTGTAAGGAAAATAAATTATTGAATTTATTTCTTTGAGAATCTTAAATGATTCTA
1 GATTATAACTTTGTAAAGAAAATAAATTGTCAAATTTATTTTTTTGAGAATCATAAATGATTCT-
* * **
147876 ACTTTG-T-AAGGAAAATAAATTGTTGAATTTA-TTTCATTGGAAATCTTGAAT---
65 ATTTTGTTAAAGG-AAATAAATTGTTAAATTTATTTTCATAAG-AATCTTGAATAAA
* * * * * **
147927 GATTTTAACTTTGTAAGGAAAATAAATTGTCGAATTTATTTTGTTGAGAATCGTGGATGATTCTA
1 GATTATAACTTTGTAAAGAAAATAAATTGTCAAATTTATTTTTTTGAGAATCATAAATGATTCTA
** * * * * *
147992 TCCTCTAAAAAAGAAATAAATTGTTAAATTTATTTCTCTTGAGAATCTT--A-AAA
66 TTTTGT-TAAAGGAAATAAATTGTTAAATTTATTT-TCATAAGAATCTTGAATAAA
* ** * *
148045 GATTAT-ATTTTGTAAAAGTTAATTAATTGTTAAATTTATTTTTTTGAGAATCATAAATGATTCT
1 GATTATAACTTTGT-AAAGAAAATAAATTGTCAAATTTATTTTTTTGAGAATCATAAATGATTCT
148109 ATTTTGTTAAAGGAAATAAATTGTTAAATTTATTTTC-TAAGAATCTTGAATAAA
65 ATTTTGTTAAAGGAAATAAATTGTTAAATTTATTTTCATAAGAATCTTGAATAAA
148163 GA
1 GA
148165 AATAAAATTT
Statistics
Matches: 190, Mismatches: 36, Indels: 22
0.77 0.15 0.09
Matches are distributed among these distances:
115 11 0.06
116 59 0.31
117 51 0.27
118 65 0.34
119 4 0.02
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (119 bp):
GATTATAACTTTGTAAAGAAAATAAATTGTCAAATTTATTTTTTTGAGAATCATAAATGATTCTA
TTTTGTTAAAGGAAATAAATTGTTAAATTTATTTTCATAAGAATCTTGAATAAA
Found at i:148606 original size:175 final size:172
Alignment explanation
Indices: 148333--148647 Score: 377
Period size: 175 Copynumber: 1.8 Consensus size: 172
148323 CACATGATTC
* * * * * * *
148333 TGATTTGTAAAAGTATATAAATCGTTAGATTTATTTTCTTATTTGATGAAAGTAAATAACTCATT
1 TGATGTGTAAAAGGAGATAAATCGTTAGATTTATTTTCCTATTTGATAAAAGGAAATAACTCATA
* * ** *
148398 GAGTTTATTTTCCTGTTTTATGAAAGAAAATAAATTGGTGGATTTATTTTTCCTGTTTTGAAAAA
66 GAATTTAGTTTCCTGTTTTA-GAAAGAAAATAAATCAGTGGATTTA-TTTTCCTATTTTGAAAAA
148463 AAGGAAATAAATAGATAAATTTATTTTCTTAAGAATCTTGTATGA
129 AA-GAAATAAATAGATAAATTTATTTTCTTAAGAATCTTGTATGA
148508 TGATGTGTAAAAGGAGATAAATCGTT-GAATTTATTTTCCTATTTCGA-AAAAGGAAATAAAC-C
1 TGATGTGTAAAAGGAGATAAATCGTTAG-ATTTATTTTCCTATTT-GATAAAAGGAAAT-AACTC
* * * *
148570 ATAGAATTTAGTTTCCTAGTTTGTA-AAAGGAAATAAATCATTGGATTTATTTTCTTATTTTGTA
63 ATAGAATTTAGTTTCCT-GTTT-TAGAAAGAAAATAAATCAGTGGATTTATTTTCCTATTTTGAA
*
148634 AAAAATAAATAAAT
126 AAAAAGAAATAAAT
148648 CATTGGATTT
Statistics
Matches: 118, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
173 8 0.07
174 18 0.15
175 81 0.69
176 9 0.08
177 2 0.02
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.41
Consensus pattern (172 bp):
TGATGTGTAAAAGGAGATAAATCGTTAGATTTATTTTCCTATTTGATAAAAGGAAATAACTCATA
GAATTTAGTTTCCTGTTTTAGAAAGAAAATAAATCAGTGGATTTATTTTCCTATTTTGAAAAAAA
GAAATAAATAGATAAATTTATTTTCTTAAGAATCTTGTATGA
Found at i:148653 original size:40 final size:40
Alignment explanation
Indices: 148516--148790 Score: 245
Period size: 39 Copynumber: 6.7 Consensus size: 40
148506 GATGATGTGT
* * * *
148516 AAAAGGAGATAAATCGTTGAATTTATTTTCCTATTTCG-A
1 AAAAGGAAATAAATCATTGGATTTATTTTCCTATTTTGTA
* * * * *
148555 AAAAGGAAATAAACCATAGAATTTAGTTTCCTAGTTTGT-
1 AAAAGGAAATAAATCATTGGATTTATTTTCCTATTTTGTA
*
148594 AAAAGGAAATAAATCATTGGATTTATTTTCTTATTTTGTA
1 AAAAGGAAATAAATCATTGGATTTATTTTCCTATTTTGTA
** *
148634 AAAAATAAATAAATCATTGGATTTAGTTTCCTATTTTGT-
1 AAAAGGAAATAAATCATTGGATTTATTTTCCTATTTTGTA
* * *
148673 AAAAGAAAATAAATCGAAACAAATAGTTTGATTTATTTTTCCTGTTTTGT-
1 AAAAGGAAATAAAT-----C----A-TTGGATTTA-TTTTCCTATTTTGTA
* * *
148723 GAAAGGAAATAAATCGTTGGATTTATTTTCCTATTTT-TT
1 AAAAGGAAATAAATCATTGGATTTATTTTCCTATTTTGTA
148762 AAAAGGAAATAAATCATTGGATTTATTTT
1 AAAAGGAAATAAATCATTGGATTTATTTT
148791 TTTGGGAATC
Statistics
Matches: 193, Mismatches: 29, Indels: 28
0.77 0.12 0.11
Matches are distributed among these distances:
38 1 0.01
39 114 0.59
40 43 0.22
44 1 0.01
45 1 0.01
48 1 0.01
49 8 0.04
50 24 0.12
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (40 bp):
AAAAGGAAATAAATCATTGGATTTATTTTCCTATTTTGTA
Found at i:152078 original size:20 final size:20
Alignment explanation
Indices: 152053--152148 Score: 165
Period size: 20 Copynumber: 4.8 Consensus size: 20
152043 TTTTCCAAAT
152053 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
152073 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
* *
152093 TCGAAATGTGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
152113 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
*
152133 TCGCAATGCGATTATG
1 TCGCAATGCGAATATG
152149 ACTATCACAA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 71 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.27
Consensus pattern (20 bp):
TCGCAATGCGAATATGTAAA
Found at i:152159 original size:20 final size:20
Alignment explanation
Indices: 152132--152239 Score: 144
Period size: 20 Copynumber: 5.4 Consensus size: 20
152122 GAATATGTAA
* *
152132 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
* * *
152152 ATCACAATGCAATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
152172 ATCGCAACGCGATTCTGATT
1 ATCGCAACGCGATTCTGACT
*
152192 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
152212 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
152232 GTCGCAAC
1 ATCGCAAC
152240 ACTGAATTTC
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 77 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.27
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:152176 original size:60 final size:60
Alignment explanation
Indices: 152053--152238 Score: 148
Period size: 60 Copynumber: 3.1 Consensus size: 60
152043 TTTTCCAAAT
* * * * *
152053 TCGCAATGCGAATATGTAAATCGCAATGCGAATATGTA-AATCGA-AATGTGAA-TATGTA-AA
1 TCGCAATGCGAATATGTAAATCGCAATGCGATTATG-ACTATC-ACAATG-CAATTCTG-ACTA
152113 TCGCAATGCGAATATGTAAATCGCAATGCGATTATGACTATCACAATGCAATTCTGACTA
1 TCGCAATGCGAATATGTAAATCGCAATGCGATTATGACTATCACAATGCAATTCTGACTA
* * * * * * * * * * *
152173 TCGCAACGCGATTCTG-ATTATCGCAACGAGATTCTGACTATCGCAACGCGATTCTGACTG
1 TCGCAATGCGAATATGTA-AATCGCAATGCGATTATGACTATCACAATGCAATTCTGACTA
152233 TCGCAA
1 TCGCAA
152239 CACTGAATTT
Statistics
Matches: 105, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
59 6 0.06
60 99 0.94
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (60 bp):
TCGCAATGCGAATATGTAAATCGCAATGCGATTATGACTATCACAATGCAATTCTGACTA
Found at i:153084 original size:24 final size:24
Alignment explanation
Indices: 153052--153105 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
153042 GTATTCAAAA
153052 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
153076 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
153100 TTTGAT
1 TTTGAT
153106 AATGTTTCAG
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:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:155580 original size:20 final size:20
Alignment explanation
Indices: 155555--155727 Score: 154
Period size: 20 Copynumber: 9.2 Consensus size: 20
155545 TTACACATTC
*
155555 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
155575 ATTTGACTATCACAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
155595 ATTTGATTATCGTAACTC-A
1 ATTTGACTATCGCAACGCGA
*
155614 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
155629 ATTTGATTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
155649 ATTTGACTATCGCAA--CGA
1 ATTTGACTATCGCAACGCGA
** *
155667 A----AAAATTGCAACGCGA
1 ATTTGACTATCGCAACGCGA
155683 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
155703 ATTTGACTATTGCAACGTGA
1 ATTTGACTATCGCAACGCGA
155723 ATTTG
1 ATTTG
155728 GTTATCACAA
Statistics
Matches: 122, Mismatches: 19, Indels: 24
0.74 0.12 0.15
Matches are distributed among these distances:
14 15 0.12
15 3 0.02
16 4 0.03
18 4 0.03
19 3 0.02
20 93 0.76
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:155645 original size:54 final size:54
Alignment explanation
Indices: 155563--155719 Score: 242
Period size: 54 Copynumber: 2.9 Consensus size: 54
155553 TCATTTGAAT
* * * **
155563 ATCGCAACGCGAATTTGACTATCACAACGCGAATTTGATTATCGTAACTCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAAAAA
*
155617 ATCGCAACGCGAATTTGATTATCGCAACGCGAATTTGACTATCGCAACGAAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAAAAA
* *
155671 ATTGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATTGCAACG
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACG
155720 TGAATTTGGT
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 94 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (54 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAAAAA
Found at i:155695 original size:74 final size:74
Alignment explanation
Indices: 155617--155789 Score: 222
Period size: 74 Copynumber: 2.4 Consensus size: 74
155607 TAACTCAAAA
* * * *
155617 ATCGCAACGCGAATTTGATTATCGCAACGCGAATTTGACTATCGCAACGAAAAAATTGCAACGCG
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCACAACGAAAAAATCGCAAAGCG
*
155682 AATTTGACT
66 AATTAGACT
* * ** *
155691 ATCGCAACGCGAATTTGACTATTGCAACGTGAATTTGGTTATCACAACGAGAAAATCGCAAAGCG
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCACAACGAAAAAATCGCAAAGCG
*
155756 TATTAGACT
66 AATTAGACT
* *
155765 ATCGCAACACGAA-TTGACTTTCGCA
1 ATCGCAACGCGAATTTGACTATCGCA
155790 TTGCAATTTT
Statistics
Matches: 85, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
73 10 0.12
74 75 0.88
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (74 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCACAACGAAAAAATCGCAAAGCG
AATTAGACT
Found at i:155807 original size:20 final size:20
Alignment explanation
Indices: 155782--155820 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
155772 CACGAATTGA
155782 CTTTCGCATTGCAATTTTGG
1 CTTTCGCATTGCAATTTTGG
*
155802 CTTTCGCATTGCGATTTTG
1 CTTTCGCATTGCAATTTTG
155821 AGTTTAACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.46
Consensus pattern (20 bp):
CTTTCGCATTGCAATTTTGG
Found at i:155994 original size:14 final size:14
Alignment explanation
Indices: 155957--155995 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
155947 TCAATATTAA
*
155957 ACAAATCAACTTTT
1 ACAAATCAATTTTT
155971 ACAAATCAATTTTT
1 ACAAATCAATTTTT
155985 ACAAATCAATT
1 ACAAATCAATT
155996 AAACAAGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (14 bp):
ACAAATCAATTTTT
Found at i:157502 original size:42 final size:42
Alignment explanation
Indices: 157395--157505 Score: 109
Period size: 42 Copynumber: 2.6 Consensus size: 42
157385 TCTAGAATAT
* * *
157395 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCATGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAGGGGCCTCATGAACGA
* * ** * *
157437 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCATGAACGA
157479 TAGGG-GAGGCCTCTTGAACGATGACAG
1 T-GGGAGAGGCCTCTTGAACGATGACAG
157506 ATGAGTCGGG
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
42 49 0.91
43 5 0.09
ACGTcount: A:0.23, C:0.19, G:0.38, T:0.20
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCATGAACGA
Found at i:158026 original size:20 final size:18
Alignment explanation
Indices: 157988--158034 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 18
157978 GAAACTTAAA
*
157988 ATCGCAACACGAATGACT
1 ATCGCAACGCGAATGACT
158006 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAA--TGACT
158026 ATCGCAACG
1 ATCGCAACG
158035 AGAGAATCGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 12 0.46
20 14 0.54
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (18 bp):
ATCGCAACGCGAATGACT
Found at i:158102 original size:20 final size:20
Alignment explanation
Indices: 158077--158144 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
158067 GCGATTCTTT
**
158077 TGTTGCGATAGTCAAATTCG
1 TGTTGCGATAGTCATTTTCG
158097 TGTTGCGATAGTCATTTTCG
1 TGTTGCGATAGTCATTTTCG
158117 TGTTGCGATAGTCATTTTCG
1 TGTTGCGATAGTCATTTTCG
*
158137 CGTTGCGA
1 TGTTGCGA
158145 AAGTGAACTA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.18, C:0.16, G:0.26, T:0.40
Consensus pattern (20 bp):
TGTTGCGATAGTCATTTTCG
Found at i:158315 original size:18 final size:18
Alignment explanation
Indices: 158292--158341 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
158282 TTTACTAATC
*
158292 AATCTAAGTAAAATAGTT
1 AATCTAAGTGAAATAGTT
*
158310 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATAGTT
158328 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
158342 TACGAGTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATAGTT
Found at i:160112 original size:20 final size:20
Alignment explanation
Indices: 160066--160106 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
160056 TCTGAAACTT
160066 AAAATCGCAATACGAAAATG
1 AAAATCGCAATACGAAAATG
*
160086 AAAATCGTAATACGAAAATG
1 AAAATCGCAATACGAAAATG
160106 A
1 A
160107 CTATCGCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.56, C:0.12, G:0.15, T:0.17
Consensus pattern (20 bp):
AAAATCGCAATACGAAAATG
Found at i:160121 original size:20 final size:20
Alignment explanation
Indices: 160098--160181 Score: 98
Period size: 20 Copynumber: 4.2 Consensus size: 20
160088 AATCGTAATA
160098 CGAAAATGACTATCGCAACG
1 CGAAAATGACTATCGCAACG
**
160118 CGAATTTGACTATCGCAACG
1 CGAAAATGACTATCGCAACG
**
160138 CGAATTTGACTATCGCAACG
1 CGAAAATGACTATCGCAACG
** *
160158 CG-AAATGAAAATCACAACG
1 CGAAAATGACTATCGCAACG
160177 CGAAA
1 CGAAA
160182 CTAAAATCGC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
19 14 0.25
20 42 0.75
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.18
Consensus pattern (20 bp):
CGAAAATGACTATCGCAACG
Found at i:160605 original size:22 final size:22
Alignment explanation
Indices: 160574--160630 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
160564 GATGGAGATA
160574 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* **
160596 GACTGATTTCGTAGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
160618 GACGGATGTCGCC
1 GACGGATTTCGCC
160631 TTAGAGAGTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.19, C:0.18, G:0.42, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:160872 original size:20 final size:20
Alignment explanation
Indices: 160779--160864 Score: 145
Period size: 20 Copynumber: 4.3 Consensus size: 20
160769 GCGCTTTGAA
*
160779 AATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
160799 CATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
160819 AATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
160839 AATCGCGTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
160859 AATCGC
1 AATCGC
160865 ATTACGATTT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:160879 original size:20 final size:20
Alignment explanation
Indices: 160856--160899 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
160846 TTGCGATAGT
160856 CATAATCGCATTACGATTTA
1 CATAATCGCATTACGATTTA
* * *
160876 CATATTCGTATTGCGATTTA
1 CATAATCGCATTACGATTTA
160896 CATA
1 CATA
160900 TTCTCATTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (20 bp):
CATAATCGCATTACGATTTA
Found at i:160900 original size:20 final size:20
Alignment explanation
Indices: 160864--160911 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
160854 GTCATAATCG
*
160864 CATTACGATTTACATATTCGT
1 CATTGCGATTTACATATTC-T
160885 -ATTGCGATTTACATATTCT
1 CATTGCGATTTACATATTCT
160904 CATTGCGA
1 CATTGCGA
160912 ATTCGGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (20 bp):
CATTGCGATTTACATATTCT
Found at i:160935 original size:21 final size:21
Alignment explanation
Indices: 160909--160948 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
160899 ATTCTCATTG
160909 CGAATTCGGAAAATCGCAACA
1 CGAATTCGGAAAATCGCAACA
*
160930 CGAATTTGGAAAATCGCAA
1 CGAATTCGGAAAATCGCAA
160949 TGCGATAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.17
Consensus pattern (21 bp):
CGAATTCGGAAAATCGCAACA
Found at i:163139 original size:17 final size:18
Alignment explanation
Indices: 163102--163142 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
163092 ATATTATGTA
*
163102 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
163120 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
163137 TTTACT
1 TTTACT
163143 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:164792 original size:18 final size:18
Alignment explanation
Indices: 164769--164807 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
164759 ACAGCAGCCA
*
164769 CCGCAACCATTTATGATG
1 CCGCAACCATATATGATG
164787 CCGCAACCATATATGATG
1 CCGCAACCATATATGATG
164805 CCG
1 CCG
164808 TCATCACCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (18 bp):
CCGCAACCATATATGATG
Found at i:165162 original size:3 final size:3
Alignment explanation
Indices: 165154--165197 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
165144 ACCTGCTCAG
* * * *
165154 GAC GAC GAC GAT GAC GAT GAC GAC GAC GAC GAT GAC GAC AAC GA
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GA
165198 TGATGACAGC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.36, C:0.25, G:0.32, T:0.07
Consensus pattern (3 bp):
GAC
Found at i:165177 original size:15 final size:15
Alignment explanation
Indices: 165157--165204 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
165147 TGCTCAGGAC
*
165157 GACGACGATGACGAT
1 GACGACGACGACGAT
165172 GACGACGACGACGAT
1 GACGACGACGACGAT
* *
165187 GACGACAACGATGAT
1 GACGACGACGACGAT
165202 GAC
1 GAC
165205 AGCGAGGAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.35, C:0.23, G:0.31, T:0.10
Consensus pattern (15 bp):
GACGACGACGACGAT
Found at i:169995 original size:17 final size:17
Alignment explanation
Indices: 169952--169995 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
169942 TTTATTTTGA
* *
169952 ATAAAAATAATTTATTCT
1 ATAAAAA-AATTTACTAT
*
169970 ATTAAAAAATTTACTAT
1 ATAAAAAAATTTACTAT
169987 ATAAAAAAA
1 ATAAAAAAA
169996 AAGATCATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAAAAAAATTTACTAT
Found at i:170483 original size:15 final size:15
Alignment explanation
Indices: 170453--170500 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
170443 AATTTTATAA
*
170453 TCTTTGAAAG-AATG
1 TCTTTAAAAGAAATG
170467 TCTTTAAAAGAAATG
1 TCTTTAAAAGAAATG
170482 TCTTTAAAAGAAATG
1 TCTTTAAAAGAAATG
170497 TCTT
1 TCTT
170501 GAATACTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
14 9 0.28
15 23 0.72
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.38
Consensus pattern (15 bp):
TCTTTAAAAGAAATG
Found at i:172962 original size:26 final size:25
Alignment explanation
Indices: 172915--172977 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
172905 TAAGGTATTT
*
172915 TTTATTATGTTATAATTATTTAATA
1 TTTATTATTTTATAATTATTTAATA
* *
172940 GTTTATTATTTTATTA-TATTTTACTA
1 -TTTATTATTTTATAATTA-TTTAATA
172966 TATTATTATTTT
1 T-TTATTATTTT
172978 TGCTTTTCGC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 3 0.09
26 29 0.91
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (25 bp):
TTTATTATTTTATAATTATTTAATA
Found at i:183759 original size:2 final size:2
Alignment explanation
Indices: 183752--183778 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
183742 TATCAAATGC
183752 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
183779 TCTAGTTCTT
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:184023 original size:16 final size:16
Alignment explanation
Indices: 184002--184032 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
183992 TAATAAATAA
184002 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
184018 ACGAACATAAACGAA
1 ACGAACATAAACGAA
184033 TAAATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:184124 original size:16 final size:16
Alignment explanation
Indices: 184103--184147 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
184093 TAATAAATAA
184103 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
**
184119 ACGAACATAAATAAAC
1 ACGAACATAAACGAAC
*
184135 ACGAAAATAAACG
1 ACGAACATAAACG
184148 TTGGAGACCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.60, C:0.20, G:0.11, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:191475 original size:94 final size:95
Alignment explanation
Indices: 191218--192320 Score: 1404
Period size: 94 Copynumber: 11.2 Consensus size: 95
191208 AAAAGTTGTC
* ***
191218 TGTCAATAAACAATTTC-CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAA
1 TGTCAATAAACAATTTCACCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAA
**
191282 GTTCAACTTCACGACGAAGGGACCGCTGAC
66 GTTCAACTTCACGACGAAGGGACCGCTGGT
*** *
191312 TGTCAACTTCTCAA-TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTCCAGACAAC
1 TGTCAA-TAAACAATTTC--A-CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
191376 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
62 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* ***
191410 TGTCAATAAACAATTTC-CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAA
1 TGTCAATAAACAATTTCACCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAA
**
191474 GTTCAACTTCACGACGAAGGGACCGCTGAC
66 GTTCAACTTCACGACGAAGGGACCGCTGGT
191504 TGTCAATAAACAACTCTCAATTTCAGAGCCAATTTCAACTTCACAACG-AGGATATTGGACTCCA
1 TGTCAAT--A-AA----CAATTTC--A-CCAATTTCAACTTCACAACGAAGGATATTGGACTCCA
*
191568 GACAACGCAAGTTCAACTTCACGACGAAGGTACCGCTGGT
56 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
191608 TGTCAATAAACAATTTC-CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC-ACGCAA
1 TGTCAATAAACAATTTCACCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAA
191671 GTTCAACTTCACGACGAAGGGACCGCTGGT
66 GTTCAACTTCACGACGAAGGGACCGCTGGT
*
191701 TGTCAATAACAACTTCTCAATTTCAGAGCAATTTCAACTTCACAACGAAGGATATTGGACTCCAG
1 TGTCAAT-A-AA-----CAATTTC--ACCAATTTCAACTTCACAACGAAGGATATTGGACTCCAG
*
191766 ATAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
57 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
191805 TGTCAATAAA-AATTTC-CCAACTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAA
1 TGTCAATAAACAATTTCACCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAA
191868 GTTCAACTTCACGACGAAGGGACCGCTGGT
66 GTTCAACTTCACGACGAAGGGACCGCTGGT
191898 TGTCAATAAAACTTCTCAA-TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAG
1 TGTCAAT-AAA-----CAATTTC--A-CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAG
*
191962 ACAACGCAAGTTCAACTTAACGACGAAGGGACCGCTGGT
57 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
192001 TGTCAATAAACAATTTC-CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAA
1 TGTCAATAAACAATTTCACCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAA
*
192065 GTTCAACTTCACGACGAAGGGACCACTGGT
66 GTTCAACTTCACGACGAAGGGACCGCTGGT
192095 TGTCAATAAACAACTTCTCAATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAAT--A-AA-----CAATTTC---ACCAATTTCAACTTCACAACGAAGGATATTGGACTCC
192160 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
55 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
192201 TGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG-AGGATATTGGACTCC
1 TGTCAAT--A-AA-----CAATTTC--A-CCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
192265 ATG-C-ACACAAGTTCAACTTCACAACGAAGGGACCGCTGGT
55 A-GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
192305 TGTCAATAAACAATTT
1 TGTCAATAAACAATTT
192321 TCCAGTTCCA
Statistics
Matches: 912, Mismatches: 42, Indels: 108
0.86 0.04 0.10
Matches are distributed among these distances:
93 143 0.16
94 191 0.21
95 6 0.01
96 14 0.02
97 18 0.02
98 82 0.09
99 3 0.00
100 9 0.01
101 11 0.01
102 14 0.02
103 121 0.13
104 140 0.15
105 38 0.04
106 122 0.13
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (95 bp):
TGTCAATAAACAATTTCACCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAA
GTTCAACTTCACGACGAAGGGACCGCTGGT
Found at i:191791 original size:197 final size:199
Alignment explanation
Indices: 191218--192349 Score: 1775
Period size: 197 Copynumber: 5.7 Consensus size: 199
191208 AAAAGTTGTC
*
191218 TGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACA-GTACAA
1 TGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACACG--CAA
**
191282 GTTCAACTTCACGACGAAGGGACCGCTGACTG----T---CAACTTCTCAA-TTCAGAGCCAATT
64 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATT
*
191339 TCAACTTCACAACGAAGGATATTGAACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
129 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
191404 GCTGGT
194 GCTGGT
*
191410 TGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACA-GTACAA
1 TGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACACG--CAA
**
191474 GTTCAACTTCACGACGAAGGGACCGCTGACTGTCAATAAACAAC-TCTCAATTTCAGAGCCAATT
64 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATT
*
191538 TCAACTTCACAACG-AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGTACC
129 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
191602 GCTGGT
194 GCTGGT
191608 TGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACACGCAAGT
1 TGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACACGCAAGT
191673 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT-AACAACTTCTCAATTTCAGAG-CAATTTC
66 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTC
*
191736 AACTTCACAACGAAGGATATTGGACTCCAGATAACGCAAGTTCAACTTCACGACGAAGGGACCGC
131 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
191801 TGGT
196 TGGT
*
191805 TGTCAATAAA-AATTTCCCAACTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC-ACGCAAG
191869 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT-AA-AACTTCTCAA-TTCAGAGCCAATTT
65 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTT
*
191931 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTAACGACGAAGGGACCG
130 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
191996 CTGGT
195 CTGGT
192001 TGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC-ACGCAAG
* *
192066 TTCAACTTCACGACGAAGGGACCACTGGTTGTCAATAAACAACTTCTCAATTTCAGAACCAATTT
65 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTT
192131 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
130 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
192196 CTGGT
195 CTGGT
192201 TGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG-AGGATATTGGACTCC
1 TGTCAAT--A-AA-----CAATTTC----CCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * * *
192265 ATG-CACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAA-TTTTCCAGTT
54 A-GACACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCT-CAATT
*
192328 CCAGAGCCAATTTCAACTTCAC
117 TCAGAGCCAATTTCAACTTCAC
192350 GGCGGAGGAA
Statistics
Matches: 888, Mismatches: 21, Indels: 44
0.93 0.02 0.05
Matches are distributed among these distances:
192 96 0.11
195 7 0.01
196 165 0.19
197 249 0.28
198 119 0.13
199 42 0.05
200 89 0.10
202 1 0.00
203 2 0.00
208 7 0.01
209 3 0.00
210 70 0.08
211 17 0.02
212 21 0.02
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (199 bp):
TGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACACGCAAGT
TCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTC
AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
TGGT
Found at i:191794 original size:43 final size:43
Alignment explanation
Indices: 191728--191887 Score: 131
Period size: 43 Copynumber: 3.6 Consensus size: 43
191718 CAATTTCAGA
*
191728 GCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGATAAC
1 GCAAGTTCAACTTCACAACGAAGGATATTGGACTCCAGATAAC
* * * * ** * **
191771 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAAAATTTC
1 GCAAGTTCAACTTCACAACGAA-GGA----T-ATTG-GACTCCAGATAAC
* * *
191821 CCAACTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
1 GCAAGTTCAACTTCACAACGAAGGATATTGGACTCCAGATAAC
*
191864 GCAAGTTCAACTTCACGACGAAGG
1 GCAAGTTCAACTTCACAACGAAGG
191888 GACCGCTGGT
Statistics
Matches: 85, Mismatches: 25, Indels: 14
0.69 0.20 0.11
Matches are distributed among these distances:
43 46 0.54
44 6 0.07
45 1 0.01
48 1 0.01
49 6 0.07
50 25 0.29
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (43 bp):
GCAAGTTCAACTTCACAACGAAGGATATTGGACTCCAGATAAC
Found at i:191990 original size:43 final size:43
Alignment explanation
Indices: 191929--192084 Score: 132
Period size: 43 Copynumber: 3.4 Consensus size: 43
191919 CAGAGCCAAT
191929 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * *** ** * * * *
191972 TTCAACTTAACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA---CGCAAG
192023 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
192066 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
192085 GACCACTGGT
Statistics
Matches: 82, Mismatches: 23, Indels: 16
0.68 0.19 0.13
Matches are distributed among these distances:
43 37 0.45
44 3 0.04
45 3 0.04
46 7 0.09
48 7 0.09
49 3 0.04
50 3 0.04
51 19 0.23
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:192203 original size:106 final size:106
Alignment explanation
Indices: 191821--192349 Score: 826
Period size: 106 Copynumber: 5.2 Consensus size: 106
191811 TAAAAATTTC
*
191821 CCAACTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
191886 GGGACCGCTGGTTGTCAAT-AA-AACTTCTCAA-TTCAGAG
66 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
*
191924 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTAACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
191989 GGGACCGCTGGTTGTCAAT--A-AA-----CAATTTC----
66 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
192018 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
192083 GGGACCACTGGTTGTCAATAAACAACTTCTCAATTTCAGAA
66 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
192124 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
192189 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
66 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
* *
192230 CCAATTTCAACTTCACAACG-AGGATATTGGACTCCATG-C-ACACAAGTTCAACTTCACAACGA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCA-GACAACGCAAGTTCAACTTCACGACGA
* * *
192292 AGGGACCGCTGGTTGTCAATAAACAA-TTTTCCAGTTCCAGAG
65 AGGGACCGCTGGTTGTCAATAAACAACTTCT-CAATTTCAGAG
192334 CCAATTTCAACTTCAC
1 CCAATTTCAACTTCAC
192350 GGCGGAGGAA
Statistics
Matches: 400, Mismatches: 11, Indels: 29
0.91 0.03 0.07
Matches are distributed among these distances:
94 82 0.20
96 1 0.00
97 5 0.01
98 3 0.01
102 10 0.03
103 85 0.21
104 72 0.18
105 17 0.04
106 125 0.31
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (106 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
Found at i:193044 original size:37 final size:37
Alignment explanation
Indices: 192980--193075 Score: 106
Period size: 37 Copynumber: 2.6 Consensus size: 37
192970 ATATCTATAT
* *
192980 ATATAA-ATAGTTTTTAAAACCCCATTTTTTGAAATAC
1 ATATAATATAGTTTTTAAAACACAATTTTTTGAAAT-C
* *
193017 ATATAATATAGTTTTTAAAA-ATAATTTTTTGAAATT
1 ATATAATATAGTTTTTAAAACACAATTTTTTGAAATC
* *
193053 ATATATTATATGATTTTAAAACA
1 ATATAATATA-GTTTTTAAAACA
193076 TTTATTTACT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
36 9 0.18
37 27 0.54
38 14 0.28
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (37 bp):
ATATAATATAGTTTTTAAAACACAATTTTTTGAAATC
Done.