Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006319.1 Hibiscus syriacus cultivar Beakdansim tig00015099_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: 74163
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:186 original size:13 final size:12
Alignment explanation
Indices: 159--201 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
149 ATTTTTTTAT
*
159 GTATAGTGAACA
1 GTATAGTGAATA
*
171 GTATCCGTGAATA
1 GTAT-AGTGAATA
184 GTAATAGTGAATA
1 GT-ATAGTGAATA
197 GTATA
1 GTATA
202 CATGAACAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 7 0.27
13 17 0.65
14 2 0.08
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (12 bp):
GTATAGTGAATA
Found at i:723 original size:45 final size:46
Alignment explanation
Indices: 672--781 Score: 134
Period size: 47 Copynumber: 2.4 Consensus size: 46
662 ATAAAACTCT
* * * *
672 TTACCATTTATCCCATAAGCTTGTAGGCTTA-TTTTACCAAAATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTTACCAAAACAC
*
717 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTACCAATACAC
1 TTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTTACCAAAACAC
*
765 TTGCCA-TTATTCCATAA
1 TTACCATTTATTCCATAA
782 CCATATACCA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
45 18 0.32
47 21 0.38
48 17 0.30
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (46 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTTACCAAAACAC
Found at i:803 original size:20 final size:20
Alignment explanation
Indices: 778--820 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
768 CCATTATTCC
* *
778 ATAACCATATACCATAGAAA
1 ATAACCATAAACAATAGAAA
*
798 ATAACCATAAACAATAGACA
1 ATAACCATAAACAATAGAAA
818 ATA
1 ATA
821 GCCCAATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.58, C:0.19, G:0.05, T:0.19
Consensus pattern (20 bp):
ATAACCATAAACAATAGAAA
Found at i:983 original size:60 final size:59
Alignment explanation
Indices: 885--1009 Score: 187
Period size: 60 Copynumber: 2.1 Consensus size: 59
875 GTGCAATCCT
* **
885 GAATATGACACATAAGGTCGTGTCCACCATATGTACTAGGTATCCTTAAGTACAGTTCCC
1 GAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACA-TTCCC
* **
945 GAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTATTCCC
1 GAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACATTCCC
1004 GAATAT
1 GAATAT
1010 ACAGCCTGCT
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
59 11 0.19
60 48 0.81
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (59 bp):
GAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACATTCCC
Found at i:8392 original size:20 final size:20
Alignment explanation
Indices: 8367--8409 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
8357 CCATTATTCC
* *
8367 ATAACCATATACCATAGAAA
1 ATAACCATAAACAATAGAAA
*
8387 ATAACCATAAACAATAGACA
1 ATAACCATAAACAATAGAAA
8407 ATA
1 ATA
8410 GCCCAATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.58, C:0.19, G:0.05, T:0.19
Consensus pattern (20 bp):
ATAACCATAAACAATAGAAA
Found at i:8573 original size:60 final size:59
Alignment explanation
Indices: 8475--8600 Score: 162
Period size: 60 Copynumber: 2.1 Consensus size: 59
8465 GTGCAATTCT
* * * ** *
8475 GAATATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTTTCCTTAAGTACAGTTCCC
1 GAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTACA-TTCCC
* **
8535 GAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTTAGTGTATTCCC
1 GAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTACATTCCC
8594 GAATATG
1 GAATATG
8601 CAGCCTGCTG
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
59 12 0.21
60 45 0.79
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (59 bp):
GAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTACATTCCC
Found at i:12726 original size:29 final size:28
Alignment explanation
Indices: 12670--12802 Score: 167
Period size: 29 Copynumber: 4.6 Consensus size: 28
12660 AAAGTCAATT
* *
12670 ATTACAAAAATAGCACCCTTTTTCAAAATA
1 ATTACCAAAATATCA-CC-TTTTCAAAATA
12700 ATTACCAAAATATCACCTTTTACAAAATA
1 ATTACCAAAATATCACCTTTT-CAAAATA
* *
12729 ATTACCAAAATATTACCATTTCAAAATA
1 ATTACCAAAATATCACCTTTTCAAAATA
*
12757 ATTACCAAAATATCACCATTTTCAAAAAA
1 ATTACCAAAATATCACC-TTTTCAAAATA
* *
12786 AATCCCAAAATATCACC
1 ATTACCAAAATATCACC
12803 GGGTCGGGTC
Statistics
Matches: 92, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
28 27 0.29
29 52 0.57
30 13 0.14
ACGTcount: A:0.49, C:0.22, G:0.01, T:0.29
Consensus pattern (28 bp):
ATTACCAAAATATCACCTTTTCAAAATA
Found at i:12759 original size:57 final size:57
Alignment explanation
Indices: 12690--12798 Score: 175
Period size: 57 Copynumber: 1.9 Consensus size: 57
12680 TAGCACCCTT
* *
12690 TTTCAAAATAATTACCAAAATATCACC-TTTTACAAAATAATTACCAAAATATTACCA
1 TTTCAAAATAATTACCAAAATATCACCATTTT-CAAAAAAAATACCAAAATATTACCA
*
12747 TTTCAAAATAATTACCAAAATATCACCATTTTCAAAAAAAATCCCAAAATAT
1 TTTCAAAATAATTACCAAAATATCACCATTTTCAAAAAAAATACCAAAATAT
12799 CACCGGGTCG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
57 44 0.92
58 4 0.08
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.30
Consensus pattern (57 bp):
TTTCAAAATAATTACCAAAATATCACCATTTTCAAAAAAAATACCAAAATATTACCA
Found at i:14915 original size:27 final size:26
Alignment explanation
Indices: 14887--14965 Score: 52
Period size: 29 Copynumber: 2.8 Consensus size: 26
14877 ATAAATAAAA
* *
14887 AAAATAAAAAATAAAAAAT-AAAAATA
1 AAAAT-AAAAAGAAAAAATAAAAAAAA
*
14913 AAAATAAAAAGAGGAAAAAGAAAAAGAAA
1 AAAATAAAAAGA--AAAAATAAAAA-AAA
* *
14942 TAAATAAATAAAAAAAGAATAAAA
1 AAAATAAA-AAGAAAA-AATAAAA
14966 GAATAAATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
25 6 0.15
26 5 0.12
27 5 0.12
28 7 0.17
29 15 0.37
30 3 0.07
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (26 bp):
AAAATAAAAAGAAAAAATAAAAAAAA
Found at i:14920 original size:35 final size:34
Alignment explanation
Indices: 14879--14986 Score: 96
Period size: 35 Copynumber: 3.1 Consensus size: 34
14869 CTGAAGAAAT
*
14879 AAATAAAAAAAATAAAAAATAAAAAATAAAAATAA
1 AAATAAAAAGAATAAAAAATAAAAAA-AAAAATAA
** *
14914 AAATAAAAAGAGGAAAAAGA-AAAAGAAATAAATAA
1 AAATAAAAAGAATAAAAA-ATAAAA-AAAAAAATAA
*
14949 ATAA-AAAAAGAATAAAAGAATAAATAAGAAAAA-AA
1 A-AATAAAAAGAATAAAA-AATAAA-AAAAAAAATAA
14984 AAA
1 AAA
14987 GTGGGTTCAA
Statistics
Matches: 59, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
34 2 0.03
35 42 0.71
36 14 0.24
37 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.11
Consensus pattern (34 bp):
AAATAAAAAGAATAAAAAATAAAAAAAAAAATAA
Found at i:14970 original size:27 final size:27
Alignment explanation
Indices: 14927--14985 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
14917 TAAAAAGAGG
*
14927 AAAAAGAAAAAGAAATAAATAA-ATAA
1 AAAAAGAAAAAGAAATAAATAAGAAAA
14953 AAAAAGAATAAA-AGAATAAATAAGAAAA
1 AAAAAGAA-AAAGA-AATAAATAAGAAAA
14981 AAAAA
1 AAAAA
14986 AGTGGGTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 9 0.31
27 12 0.41
28 8 0.28
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.10
Consensus pattern (27 bp):
AAAAAGAAAAAGAAATAAATAAGAAAA
Found at i:14978 original size:44 final size:44
Alignment explanation
Indices: 14895--14981 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
14885 AAAAAATAAA
*
14895 AAATAAAAAATAAAAATAAAAATAAAAAGAGGAAAAAGAAAAAG
1 AAATAAAAAATAAAAATAAAAATAAAAAGAAGAAAAAGAAAAAG
* *
14939 AAATAAATAAATAAAAA-AAGAAT-AAAAGAATAAATAAGAAAAA
1 AAATAAA-AAATAAAAATAAAAATAAAAAGAAGAAA-AAGAAAAA
14982 AAAAAGTGGG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 9 0.24
44 20 0.53
45 9 0.24
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.11
Consensus pattern (44 bp):
AAATAAAAAATAAAAATAAAAATAAAAAGAAGAAAAAGAAAAAG
Found at i:16456 original size:134 final size:133
Alignment explanation
Indices: 16210--16653 Score: 423
Period size: 134 Copynumber: 3.3 Consensus size: 133
16200 AAAATCAAAT
* * * * * * * *
16210 TCGATTCAACCTTCCCTAAATAACAGTAGAATGAATTAACATCCCCATATATGATATTCCTTTCA
1 TCGATTCAATCTTCCCTGAGTAACAGTAGAATGAATCAACATCCTCAAATATGATTTTCC-CTCA
* * *
16275 GA-AA-AAGCAGAACATATCCCTCTCTTTCAAGATTTAAAATTCTCTGAGTAACAATGGAACAAG
65 -ATAAGAAGCAGAACATATCCCTCTCTTTCAAGATTTGATATTC-CTGAGTAACAGTGGAACAAG
*
16338 TCTGCC
128 TCTACC
* * * * * * *
16344 TCGATTCAATCTTCCATGCGTAACAGTTGAATGAATCAACGTCC-CTAGATTTGATTTTCCCTCG
1 TCGATTCAATCTTCCCTGAGTAACAGTAGAATGAATCAACATCCTC-AAATATGATTTTCCCTCA
* ** * * *
16408 ATAAGAAGCAGAACAGATCTTTCTCTTTCAAGATTTGATATTCACTGAGTAGCAGTAGAATAAGT
65 ATAAGAAGCAGAACATATCCCTCTCTTTCAAGATTTGATATTC-CTGAGTAACAGTGGAACAAGT
* *
16473 ATATC
129 CTACC
* * *
16478 TCGATTCAATCTTCCCTGAAG-AATAGAAGAATGAATTGAA-ATCCTCAAATATGATTTTCCCTC
1 TCGATTCAATCTTCCCTG-AGTAACAGTAGAATGAA-TCAACATCCTCAAATATGATTTTCCCTC
* * * * *
16541 AATAAGAAGCGGAATATATCCCTCTCTTGT-AAGATTTGGTATTTCCTTAGTGACAGTGGAACAA
64 AATAAGAAGCAGAACATATCCCTCTCTT-TCAAGATTTGATA-TTCCTGAGTAACAGTGGAACAA
16605 GTCTACC
127 GTCTACC
* * *
16612 TCGATTAAATCTTCCCTGAATAACAGTAGAATGAGTCAACAT
1 TCGATTCAATCTTCCCTGAGTAACAGTAGAATGAATCAACAT
16654 TTCTCGATCT
Statistics
Matches: 245, Mismatches: 55, Indels: 20
0.77 0.17 0.06
Matches are distributed among these distances:
132 1 0.00
133 9 0.04
134 226 0.92
135 9 0.04
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (133 bp):
TCGATTCAATCTTCCCTGAGTAACAGTAGAATGAATCAACATCCTCAAATATGATTTTCCCTCAA
TAAGAAGCAGAACATATCCCTCTCTTTCAAGATTTGATATTCCTGAGTAACAGTGGAACAAGTCT
ACC
Found at i:16853 original size:3 final size:3
Alignment explanation
Indices: 16847--16890 Score: 61
Period size: 3 Copynumber: 14.0 Consensus size: 3
16837 TCAATAATAA
*
16847 TAT TAT TATT TAT TAT TAT TAT TAT TAT TAT TGAA TAT TAT TAT
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT
16891 AGACTTTTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 32 0.86
4 5 0.14
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:16856 original size:19 final size:19
Alignment explanation
Indices: 16832--16875 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
16822 CGAATTTAAC
16832 ATTATTCAATAATAATATT
1 ATTATTCAATAATAATATT
* * * *
16851 ATTATTTATTATTATTATT
1 ATTATTCAATAATAATATT
16870 ATTATT
1 ATTATT
16876 ATTGAATATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTATTCAATAATAATATT
Found at i:16875 original size:22 final size:22
Alignment explanation
Indices: 16847--16890 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
16837 TCAATAATAA
* *
16847 TATTATTATTTATTATTATTAT
1 TATTATTATTGAATATTATTAT
16869 TATTATTATTGAATATTATTAT
1 TATTATTATTGAATATTATTAT
16891 AGACTTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TATTATTATTGAATATTATTAT
Found at i:18616 original size:23 final size:23
Alignment explanation
Indices: 18567--18617 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
18557 GGTTTCGATC
* * *
18567 AATATATGTATATTAGTATTTTT
1 AATATATATATATTAGTATATTA
18590 AATATATATATATATA-TATATTA
1 AATATATATATAT-TAGTATATTA
18613 AATAT
1 AATAT
18618 TATTTTGTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
AATATATATATATTAGTATATTA
Found at i:18879 original size:141 final size:145
Alignment explanation
Indices: 18646--18951 Score: 317
Period size: 141 Copynumber: 2.1 Consensus size: 145
18636 TATAGAAACG
* *
18646 CGCCTTAACTGACAAGTAGTACGTTTCCAAGAATTGTTCAAACAAAATAATACCTTTTATATTCG
1 CGCCTTAACTGACAAGGAGTACGTTCCCAAGAATTGTTCAAACAAAATAATACCTTTTATATTCG
*
18711 AATGAATTTTTTTAAAATATTTAATATATG-TA-T-AAGCTAAGACAATATTATTTTGTATGG-G
66 AATGAATTTTTTTAAAATATTTAATATATGTTATTAAAACTAAGACAATATTATTTTGTATGGAG
*
18772 AAATCTATGGAAATG-
131 -AATCCATGGAAATGC
* * * * *
18787 TGCCTTAACTGACAAGGA-TCACGTTCCCAATG-ATTTTTCATACAGAGTAATACCTTTTTATAT
1 CGCCTTAACTGACAAGGAGT-ACGTTCCCAA-GAATTGTTCAAACAAAATAATACC-TTTTATAT
* * * * * * *
18850 TTG-A-G-TTTTTTTTAAATTATTATGTATATATGATTTATTAAAATTAGGGCAATATTATTTTG
63 TCGAATGAATTTTTTTAAAATATT-T-AATATATG--TTATTAAAACTAAGACAATATTATTTTG
18912 TATGGAGAATCCATGGAAATGC
124 TATGGAGAATCCATGGAAATGC
*
18934 CCCCTTAACTGACAAGGA
1 CGCCTTAACTGACAAGGA
18952 AGGTATTTTC
Statistics
Matches: 135, Mismatches: 18, Indels: 18
0.79 0.11 0.11
Matches are distributed among these distances:
139 14 0.10
140 3 0.02
141 51 0.38
142 11 0.08
144 2 0.01
145 1 0.01
146 36 0.27
147 17 0.13
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (145 bp):
CGCCTTAACTGACAAGGAGTACGTTCCCAAGAATTGTTCAAACAAAATAATACCTTTTATATTCG
AATGAATTTTTTTAAAATATTTAATATATGTTATTAAAACTAAGACAATATTATTTTGTATGGAG
AATCCATGGAAATGC
Found at i:20325 original size:31 final size:30
Alignment explanation
Indices: 20241--20331 Score: 173
Period size: 30 Copynumber: 3.0 Consensus size: 30
20231 ATGACTTGTA
20241 ATTTAACCAAATGTTAGGGTATAAACATTT
1 ATTTAACCAAATGTTAGGGTATAAACATTT
20271 ATTTAACCAAATGTTAGGGTATAAACATTT
1 ATTTAACCAAATGTTAGGGTATAAACATTT
20301 ATTTAACCAAATGTTAGGGGTATAAACATTT
1 ATTTAACCAAATGTTA-GGGTATAAACATTT
20332 TATTATACTT
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 46 0.77
31 14 0.23
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (30 bp):
ATTTAACCAAATGTTAGGGTATAAACATTT
Found at i:20613 original size:26 final size:26
Alignment explanation
Indices: 20584--20648 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
20574 AAATACAATA
20584 AATAATATTATTTATAATAAAAACT-T
1 AATAATATTATTTATAA-AAAAACTAT
* * * *
20610 AATATTATTATTTTTAAAAATATTAT
1 AATAATATTATTTATAAAAAAACTAT
20636 AATAAT-TTATTTA
1 AATAATATTATTTA
20649 ATATTATTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
25 11 0.34
26 21 0.66
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
AATAATATTATTTATAAAAAAACTAT
Found at i:20797 original size:27 final size:27
Alignment explanation
Indices: 20759--20821 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 27
20749 TTATGCTAGT
20759 TATTATTAAAATAAGTATAT-TATATT-A
1 TATTATTAAAATAA-TATATAT-TATTAA
20786 TATTATTAAAATAATATATATTATTAA
1 TATTATTAAAATAATATATATTATTAA
*
20813 TTTTATTAA
1 TATTATTAA
20822 TTACTTATGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
26 9 0.27
27 24 0.73
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (27 bp):
TATTATTAAAATAATATATATTATTAA
Found at i:21149 original size:35 final size:35
Alignment explanation
Indices: 21084--21166 Score: 89
Period size: 35 Copynumber: 2.3 Consensus size: 35
21074 TAATATTATA
* *
21084 TTATTAAAATTATTAATAAATATAT-TTTAAATAAT
1 TTATTAATATTATTAATAAATATATATTAAAAT-AT
* *
21119 TTATTAATATTTTTATTAAA-ATAATATTAAAATAT
1 TTATTAATATTATTAATAAATAT-ATATTAAAATAT
21154 TATATTAATATTA
1 T-TATTAATATTA
21167 AATACATAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
34 2 0.05
35 22 0.55
36 16 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (35 bp):
TTATTAATATTATTAATAAATATATATTAAAATAT
Found at i:21660 original size:63 final size:63
Alignment explanation
Indices: 21556--21688 Score: 239
Period size: 63 Copynumber: 2.1 Consensus size: 63
21546 CCATTTCTCG
* *
21556 CCAATTTTTAGCTACTTTACAACCACCCGTCTTCCATCTTGTAAGCAACCTTTATAAACAACC
1 CCAAGTTTTAGCTACTTTACAACCACCCATCTTCCATCTTGTAAGCAACCTTTATAAACAACC
*
21619 CCAAGTTTTAGCTGCTTTACAACCACCCATCTTCCATCTTGTAAGCAACCTTTATAAACAACC
1 CCAAGTTTTAGCTACTTTACAACCACCCATCTTCCATCTTGTAAGCAACCTTTATAAACAACC
21682 CCAAGTT
1 CCAAGTT
21689 CACATTCACC
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.30, C:0.32, G:0.08, T:0.31
Consensus pattern (63 bp):
CCAAGTTTTAGCTACTTTACAACCACCCATCTTCCATCTTGTAAGCAACCTTTATAAACAACC
Found at i:23027 original size:33 final size:34
Alignment explanation
Indices: 23007--23078 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 34
22997 ATGCGGTGGC
23007 CGGTGGGTAGGTCGTCGGT-GGAGGCGGCAGTGA
1 CGGTGGGTAGGTCGTCGGTGGGAGGCGGCAGTGA
23040 CGGTGGGTAGGTCGTCGGT-GGAGGCGGCAGTGA
1 CGGTGGGTAGGTCGTCGGTGGGAGGCGGCAGTGA
23073 CGGTGG
1 CGGTGG
23079 ACGATCGATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.11, C:0.15, G:0.56, T:0.18
Consensus pattern (34 bp):
CGGTGGGTAGGTCGTCGGTGGGAGGCGGCAGTGA
Found at i:23045 original size:18 final size:18
Alignment explanation
Indices: 23022--23079 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
23012 GGTAGGTCGT
23022 CGGTGGAGGCGGCAGTGA
1 CGGTGGAGGCGGCAGTGA
**
23040 CGGTGG-GTAGGTC-GT--
1 CGGTGGAGGCGG-CAGTGA
23055 CGGTGGAGGCGGCAGTGA
1 CGGTGGAGGCGGCAGTGA
23073 CGGTGGA
1 CGGTGGA
23080 CGATCGATGG
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
15 7 0.23
16 5 0.16
17 5 0.16
18 14 0.45
ACGTcount: A:0.14, C:0.16, G:0.55, T:0.16
Consensus pattern (18 bp):
CGGTGGAGGCGGCAGTGA
Found at i:23202 original size:13 final size:13
Alignment explanation
Indices: 23184--23208 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23174 TAATTTTAAT
23184 TTTTTTTAAAATA
1 TTTTTTTAAAATA
23197 TTTTTTTAAAAT
1 TTTTTTTAAAAT
23209 TTGTTAAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTTTAAAATA
Found at i:26367 original size:311 final size:312
Alignment explanation
Indices: 25788--26408 Score: 1199
Period size: 311 Copynumber: 2.0 Consensus size: 312
25778 TTTTCTTTAT
* *
25788 AGCCGACCCAAAAATTCCTTCAACTCCATATCCGAAATATTTAGTAGGTCTAAACTTGTTGGGTT
1 AGCCGACCCAAAAATACCTTCAACCCCATATCCGAAATATTTAGTAGGTCTAAACTTGTTGGGTT
25853 GTTTTTGAAAATATTGAATGCTGATGAGAAGTTTGAAAAGATTTATTTGATTTGGTTTGGTTTTG
66 GTTTTTGAAAATATTGAATGCTGATGAGAAGTTTGAAAAGATTTATTTGATTTGGTTTGGTTTTG
* *
25918 GCTACTAGCAAAGAAAGAGACCTTTTCCCAAGTTTATCCTGACTACAAGCTTGAGTACAAGCTCT
131 GCTACTAGCAAAGAAAGAGACCTTTTCCCAAATTTACCCTGACTACAAGCTTGAGTACAAGCTCT
25983 TTCTCTTGGAACGGAGTAATGTTATGGACAATTTCTATTTCAGAAAAGGCCATTAGTTAATTTTG
196 TTCTCTTGGAACGGAGTAATGTTATGGACAATTTCTATTTCAGAAAAGGCCATTAGTTAATTTTG
26048 ATCCTCTAGTTAAGGCTTAGGTTGTGATTTTATTTCTTTCCTTAGGTTTAAG
261 ATCCTCTAGTTAAGGCTTAGGTTGTGATTTTATTTCTTTCCTTAGGTTTAAG
26100 AGCCGACCCAAAAA-ACCTTCAACCCCATATCCGAAATATTTAGTAGGTCTAAACTTGTTGGGTT
1 AGCCGACCCAAAAATACCTTCAACCCCATATCCGAAATATTTAGTAGGTCTAAACTTGTTGGGTT
26164 GTTTTTGAAAATATTGAATGCTGATGAGAAGTTTGAAAAGATTTATTTGATTTGGTTTGGTTTTG
66 GTTTTTGAAAATATTGAATGCTGATGAGAAGTTTGAAAAGATTTATTTGATTTGGTTTGGTTTTG
26229 GCTACTAGCAAAGAAAGAGACCTTTTCCCAAATTTACCCTGACTACAAGCTTGAGTACAAGCTCT
131 GCTACTAGCAAAGAAAGAGACCTTTTCCCAAATTTACCCTGACTACAAGCTTGAGTACAAGCTCT
26294 TTCTCTTGGAACGGAGTAATGTTATGGACAATTTCTATTTCAGAAAAGGCCATTAGTTAATTTTG
196 TTCTCTTGGAACGGAGTAATGTTATGGACAATTTCTATTTCAGAAAAGGCCATTAGTTAATTTTG
26359 ATCCTCTAGTTAAGGCTTAGGTTGTGATTTTATTTCTTTCCTTAGGTTTA
261 ATCCTCTAGTTAAGGCTTAGGTTGTGATTTTATTTCTTTCCTTAGGTTTA
26409 TTGATTATGT
Statistics
Matches: 305, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
311 291 0.95
312 14 0.05
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (312 bp):
AGCCGACCCAAAAATACCTTCAACCCCATATCCGAAATATTTAGTAGGTCTAAACTTGTTGGGTT
GTTTTTGAAAATATTGAATGCTGATGAGAAGTTTGAAAAGATTTATTTGATTTGGTTTGGTTTTG
GCTACTAGCAAAGAAAGAGACCTTTTCCCAAATTTACCCTGACTACAAGCTTGAGTACAAGCTCT
TTCTCTTGGAACGGAGTAATGTTATGGACAATTTCTATTTCAGAAAAGGCCATTAGTTAATTTTG
ATCCTCTAGTTAAGGCTTAGGTTGTGATTTTATTTCTTTCCTTAGGTTTAAG
Found at i:30345 original size:35 final size:34
Alignment explanation
Indices: 30282--30360 Score: 122
Period size: 35 Copynumber: 2.3 Consensus size: 34
30272 TAAAATTTTT
* * *
30282 TTTAAAATATGTTTAAATATATATTTATTAATAA
1 TTTAAAATATATTAAAATATATAATTATTAATAA
30316 TTTAAAATATATTCAAAATATATAATTATTAATAA
1 TTTAAAATATATT-AAAATATATAATTATTAATAA
30351 TTTAAAATAT
1 TTTAAAATAT
30361 TTTTTATAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
34 12 0.29
35 29 0.71
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (34 bp):
TTTAAAATATATTAAAATATATAATTATTAATAA
Found at i:30359 original size:10 final size:11
Alignment explanation
Indices: 30282--30360 Score: 63
Period size: 11 Copynumber: 6.9 Consensus size: 11
30272 TAAAATTTTT
*
30282 TTTAAAATATG
1 TTTAAAATATA
30293 TTTAAATATATA
1 TTTAAA-ATATA
*
30305 TTTATTAATA-A
1 TTTA-AAATATA
30316 TTTAAAATATA
1 TTTAAAATATA
*
30327 TTCAAAATATA
1 TTTAAAATATA
*
30338 TAATTATTAATA-A
1 T--TTA-AAATATA
30351 TTTAAAATAT
1 TTTAAAATAT
30361 TTTTTATAGT
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
10 8 0.15
11 26 0.48
12 11 0.20
13 5 0.09
14 4 0.07
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (11 bp):
TTTAAAATATA
Found at i:35614 original size:42 final size:42
Alignment explanation
Indices: 35555--35647 Score: 168
Period size: 42 Copynumber: 2.2 Consensus size: 42
35545 ATGCCAACTG
*
35555 ATAGATCGTGGAGGTTTAGGGATTGTCGATTGGATATTAAGA
1 ATAGAGCGTGGAGGTTTAGGGATTGTCGATTGGATATTAAGA
*
35597 ATAGAGCGTGGAGGTTTAGGGATTGTCGATTGGATTTTAAGA
1 ATAGAGCGTGGAGGTTTAGGGATTGTCGATTGGATATTAAGA
35639 ATAGAGCGT
1 ATAGAGCGT
35648 TGCTAGTTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.28, C:0.05, G:0.34, T:0.32
Consensus pattern (42 bp):
ATAGAGCGTGGAGGTTTAGGGATTGTCGATTGGATATTAAGA
Found at i:38525 original size:12 final size:12
Alignment explanation
Indices: 38510--38539 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
38500 AACAAACTAC
38510 CAAAATCGGGCA
1 CAAAATCGGGCA
38522 CAAAATCGGGCA
1 CAAAATCGGGCA
38534 CAAAAT
1 CAAAAT
38540 GGAAACGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (12 bp):
CAAAATCGGGCA
Found at i:39476 original size:64 final size:64
Alignment explanation
Indices: 39375--39494 Score: 204
Period size: 64 Copynumber: 1.9 Consensus size: 64
39365 TATGTTATAT
* * *
39375 CATTTAACTGGAAATATTATCAAGTATAATAACATATTAAGTAGCGCTTATATAATAAAATAGG
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAAGCAGCGCTTATATAATAAAATAGG
*
39439 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGCAGCGCTTATATAAT
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAAGCAGCGCTTATATAAT
39495 GTAGTAGGTA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 52 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (64 bp):
CATTTAACCGGAAATATTATCAAGTACAATAACATATTAAGCAGCGCTTATATAATAAAATAGG
Found at i:40000 original size:197 final size:196
Alignment explanation
Indices: 39542--40226 Score: 866
Period size: 196 Copynumber: 3.5 Consensus size: 196
39532 AAACCGGTTT
* * * * *
39542 ATTTATACCGGTAACATTGCAGATTTACCTATTACATTATAATTATCGGTTTCAATATTTTTGGG
1 ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATATTTTTGGG
** * * *
39607 ATCGATACAATTT-TAAATGTATCAACACTTTATACATGCACCTCATTGGGCATTCATTCTGGA-
66 ATCGATACTTTTTATAAATGTATCGACACTTTAT-CGTGCACCTCATTTGGCATTCATTCTGGAC
* * * * *
39670 AAAAAGTATCGACACAAACTT-AAAAAGTGTCGATTCATTATGTAGA-ACTATTTTCTCATAAAA
130 AAAAAGTATCGACAC-AAGTTCCACAAGTGTCGATACATTATGTAGACA-TATTTTTTCATAAAA
39733 CCGAGA
193 CC-A-A
* * * * *
39739 TATTTCTATCGGGTACATTGTAAATTTACCTATTACATTGTAATTATCAGTTTCGATGTTTTTGG
1 -ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATATTTTTGG
* * * **
39804 GATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCCCATTTGGCATTCATTTTAAA
65 GATCGATACTTTTTATAAATGTATCGACACTTTAT-CGTGCACCTCATTTGGCATTCATTCTGGA
39869 CAAAAAGTATCGACACAAGTTCCACAAGTGTCGATACATTATGTAGACATATTTTTTCATAAAAC
129 CAAAAAGTATCGACACAAGTTCCACAAGTGTCGATACATTATGTAGACATATTTTTTCATAAAAC
39934 CAA
194 CAA
* * **
39937 ATTTCTACCGGTTACATTGTAAATTTACATATTACATTATAATTATGGGTTTCGATATTTTTGGG
1 ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATATTTTTGGG
* * *
40002 ATCGATACTTTTTATAAATATATCGATACTTTAT-GTGCA-CTCTTTTGGGCATTCATTCTGGAC
66 ATCGATACTTTTTATAAATGTATCGACACTTTATCGTGCACCTCATTT-GGCATTCATTCTGGAC
*
40065 ---AAGTATCGACACAAGTTCCACAAGTGTCGATACATTATATAGACATATTTTTTTCATAAAAC
130 AAAAAGTATCGACACAAGTTCCACAAGTGTCGATACATTATGTAGACATA-TTTTTTCATAAAAC
*
40127 TGATAA
194 ---CAA
* * *
40133 ATTTATACCGGTTACATTGTAAATTTATCTATTACATTATAATTATGAGTTTCGATGTTTTTGGG
1 ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATATTTTTGGG
40198 ATCGATACTTTTTATAAATGTATCGACAC
66 ATCGATACTTTTTATAAATGTATCGACAC
40227 ATATTTAGGT
Statistics
Matches: 428, Mismatches: 50, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
192 46 0.11
193 14 0.03
194 5 0.01
195 18 0.04
196 89 0.21
197 89 0.21
198 66 0.15
199 47 0.11
200 53 0.12
201 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.39
Consensus pattern (196 bp):
ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATATTTTTGGG
ATCGATACTTTTTATAAATGTATCGACACTTTATCGTGCACCTCATTTGGCATTCATTCTGGACA
AAAAGTATCGACACAAGTTCCACAAGTGTCGATACATTATGTAGACATATTTTTTCATAAAACCA
A
Found at i:40196 original size:196 final size:194
Alignment explanation
Indices: 39542--40226 Score: 828
Period size: 197 Copynumber: 3.5 Consensus size: 194
39532 AAACCGGTTT
* * * *
39542 ATTTATACCGGTAACATTGCAGATTTACCTATTACATTATAATTATCG-GTTTCAATATTTTTGG
1 ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTAT-GAGTTTCGATATTTTTGG
** * * *
39606 GATCGATACAATTT-TAAATGTATCAACACTTTATACATGCACCTCATTGGGCATTCATTCTGGA
65 GATCGATACTTTTTATAAATGTATCGACACTTTAT-CGTGCACCT-TTTGGGCATTCATTCTGG-
* * * * * *
39670 AAAAAGTATCGACACAAACTT-AAAAAGTGTCGATTCATTATGTAGA-ACTATTTTCTCATAAAA
127 -ACAAGTATCGACAC-AAGTTCCACAAGTGTCGATACATTATGTAGACA-TATTTTTTCATAAAA
* *
39733 CCGAGAT
189 -CGACAA
* * * * * *
39740 ATTTCTATCGGGTACATTGTAAATTTACCTATTACATTGTAATTATCAGTTTCGATGTTTTTGGG
1 ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGAGTTTCGATATTTTTGGG
* * * **
39805 ATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCCCATTT-GGCATTCATTTTAAA
66 ATCGATACTTTTTATAAATGTATCGACACTTTAT-CGTGCA--CCTTTTGGGCATTCATTCTGGA
39869 CAAAAAGTATCGACACAAGTTCCACAAGTGTCGATACATTATGTAGACATATTTTTTCATAAAAC
128 C---AAGTATCGACACAAGTTCCACAAGTGTCGATACATTATGTAGACATATTTTTTCATAAAAC
39934 --CAA
190 GACAA
* * *
39937 ATTTCTACCGGTTACATTGTAAATTTACATATTACATTATAATTATGGGTTTCGATATTTTTGGG
1 ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGAGTTTCGATATTTTTGGG
* *
40002 ATCGATACTTTTTATAAATATATCGATACTTTAT-GTGCACTCTTTTGGGCATTCATTCTGGACA
66 ATCGATACTTTTTATAAATGTATCGACACTTTATCGTGCAC-CTTTTGGGCATTCATTCTGGACA
* *
40066 AGTATCGACACAAGTTCCACAAGTGTCGATACATTATATAGACATATTTTTTTCATAAAACTGAT
130 AGTATCGACACAAGTTCCACAAGTGTCGATACATTATGTAGACATA-TTTTTTCATAAAAC-GAC
40131 AA
193 AA
* *
40133 ATTTATACCGGTTACATTGTAAATTTATCTATTACATTATAATTATGAGTTTCGATGTTTTTGGG
1 ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGAGTTTCGATATTTTTGGG
40198 ATCGATACTTTTTATAAATGTATCGACAC
66 ATCGATACTTTTTATAAATGTATCGACAC
40227 ATATTTAGGT
Statistics
Matches: 420, Mismatches: 52, Indels: 32
0.83 0.10 0.06
Matches are distributed among these distances:
192 46 0.11
193 15 0.04
194 4 0.01
195 18 0.04
196 89 0.21
197 91 0.22
198 64 0.15
199 40 0.10
200 50 0.12
201 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.39
Consensus pattern (194 bp):
ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGAGTTTCGATATTTTTGGG
ATCGATACTTTTTATAAATGTATCGACACTTTATCGTGCACCTTTTGGGCATTCATTCTGGACAA
GTATCGACACAAGTTCCACAAGTGTCGATACATTATGTAGACATATTTTTTCATAAAACGACAA
Found at i:42736 original size:19 final size:19
Alignment explanation
Indices: 42708--42755 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
42698 TTACATTCAC
*
42708 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATAGT
* *
42727 ATAGAAAATTATGAATAGT
1 ATACAAAATTATAAATAGT
42746 ATACAAAATT
1 ATACAAAATT
42756 TCCCTTACAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATAGT
Found at i:44895 original size:199 final size:198
Alignment explanation
Indices: 44369--45762 Score: 1642
Period size: 199 Copynumber: 7.0 Consensus size: 198
44359 ACGTAATTTA
* * ** * * * *
44369 AAAAAGCATCGACACAACTTTAAAAAGTGTCGATACATTATGCAAACCTATTTTCGAATTAACCG
1 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCG
* * * * * *
44434 GTATATTTATACCGTTTACATTGGAAATTGGCCTATTACATTATAATTATATTATTTGATGTTTA
66 GTATATTTCTACCGGTTACATTGTAAATTGACCTATTACATTATAATTATATTATTCGATGTTTT
* **
44499 TGGGATCGATACTTTTTATAAATGTATTGACACTTTATTCGTGCACCC-TGGTTGGTCATTCATT
131 TGGGATCGATACTTTTTATAAATGTATCGACACTTTATGAGTGCACCCAT--TTGG-CATTCATT
44563 CTGGAC
193 CTGGAC
** ** * * *
44569 AAAAAGTATTAACAC-AATTTAAAAAGTGTCGATACATTATGTATACCACCTATTTTCAAATTAA
1 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATG--TA-GACCTATTTTCTAATTAA
* * * * * **
44633 CCGATATATTTCTATCGGTTACATTATAAATTTACATATTACATTATAATTATGGGT-TTCGATG
63 CCGGTATATTTCTACCGGTTACATTGTAAATTGACCTATTACATTATAATTAT-ATTATTCGATG
* * *
44697 TTTTTGGGATCGATACTTTTTATAAATATATTGAGACTTTATGAGTGCACCCATTTAGGCATTCA
127 TTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGAGTGCACCCATTT-GGCATTCA
44762 TTCTGGAC
191 TTCTGGAC
* * * *
44770 AAAAAGTATCGATACAAATTCCACAAGTATCGATACATGATGTAGACCTATTGTCTAATTAACCG
1 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCG
* * *
44835 GTATATTTCTACCAGTTACATTGGAAATTGACCTATTACATTATAATTATATTATTCGATGTTTA
66 GTATATTTCTACCGGTTACATTGTAAATTGACCTATTACATTATAATTATATTATTCGATGTTTT
* * ** ** *
44900 TGGAATCGATACTTTTTATAAATGTATCGACACTGTATTTGTGCACCCCGGTTGGTCTTTCATTC
131 TGGGATCGATACTTTTTATAAATGTATCGACACTTTATGAGTGCA-CCCATTTGG-CATTCATTC
44965 TGGAC
194 TGGAC
** * * * *
44970 AAAAAGTATCGACAC-AATTTAAAAAGTGTCGATGCATTATGTAAACCTATTTTCAAATTAACCG
1 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCG
* **
45034 GTATATTTCTACCGGTTACATTGTAAAGTT-ACCTATTATATTATAATTATCGGT-TTCGATGTT
66 GTATATTTCTACCGGTTACATTGTAAA-TTGACCTATTACATTATAATTAT-ATTATTCGATGTT
* * * *
45097 TTTGGGATCGATACTATTT-TAAATGTATCAACACTTTATGAGTGCACTCATTTAGGCATTTATT
129 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGAGTGCACCCATTT-GGCATTCATT
45161 CTGGAC
193 CTGGAC
* * * * *
45167 AAAAAGCATCGACACAAATTCCACAACTGTCGATACATGATATAGACATATTTTCTAATTAACCG
1 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCG
* * * *
45232 GTATATTTATACCGCTTACATTGGAAATTGACCTATTACATTATAATTATATTATTCGATGTTTA
66 GTATATTTCTACCGGTTACATTGTAAATTGACCTATTACATTATAATTATATTATTCGATGTTTT
* * * *
45297 TGGGATCGATACGTTTTATAAATGTATCGACACTTTATGCGTGCACCCCTTTTGGGCATTCATTT
131 TGGGATCGATACTTTTTATAAATGTATCGACACTTTATGAGTGCA-CCCATTT-GGCATTCATTC
45362 TGGAC
194 TGGAC
* * * * *
45367 AAAAAATATTGACACAAATTCCACAAGTGTCGATACA-TATGTAGACCTATTCTCCAATTAACCA
1 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCG
* * *
45431 GCATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCTTATTCGATGTTTT
66 GTATATTTCTACCGGTTACATTGTAAATTGACCTATTACATTATAATTATATTATTCGATGTTTT
* * *
45496 TGGGATCGATACTTTTTATAAATGTATCGATACTTTATGAGTGCAACCTTTTGGGCATTCATTCT
131 TGGGATCGATACTTTTTATAAATGTATCGACACTTTATGAGTGCACCCATTT-GGCATTCATTCT
45561 GGAC
195 GGAC
* * * * * *
45565 AAAACGTATCAACACAAGTTCCACAAGTGTCAATATATTATGTAGACCTATTTTGTAATTAACCG
1 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCG
* * *
45630 GTATATATCTACCAGTTACATTGTAAA-TGTACCTATTACATTATAATTATCTTATT-GATGTTT
66 GTATATTTCTACCGGTTACATTGTAAATTG-ACCTATTACATTATAATTATATTATTCGATGTTT
* * *
45693 TTGAGATCGATA-TTTTTAATAAATGTATCGACACTTTATTCA-TGCACCTCAGTTGGACATTCA
130 TTGGGATCGATACTTTTT-ATAAATGTATCGACACTTTA-TGAGTGCACC-CATTTGG-CATTCA
45756 TTCTGGA
191 TTCTGGA
45763 GATTACTGAA
Statistics
Matches: 1018, Mismatches: 152, Indels: 49
0.84 0.12 0.04
Matches are distributed among these distances:
197 38 0.04
198 230 0.23
199 482 0.47
200 101 0.10
201 29 0.03
202 136 0.13
203 2 0.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (198 bp):
AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCG
GTATATTTCTACCGGTTACATTGTAAATTGACCTATTACATTATAATTATATTATTCGATGTTTT
TGGGATCGATACTTTTTATAAATGTATCGACACTTTATGAGTGCACCCATTTGGCATTCATTCTG
GAC
Found at i:45286 original size:397 final size:397
Alignment explanation
Indices: 44369--45762 Score: 1915
Period size: 397 Copynumber: 3.5 Consensus size: 397
44359 ACGTAATTTA
* ** * * * * *
44369 AAAAAGCATCGACACAACTTTAAAAAGTGTCGATACATTATGCAAACCTATTTTCGAATTAACCG
1 AAAAAGCATCGACACAAATTCCACAAGTGTCGATACATGATGTAGACCTATTTTCTAATTAACCG
* *
44434 GTATATTTATACC-GTTTACATTGGAAATTGGCCTATTACATTATAATTATATTATTTGATGTTT
66 GTATATTTATACCAG-TTACATTGGAAATTGACCTATTACATTATAATTATATTATTCGATGTTT
* * *
44498 ATGGGATCGATACTTTTTATAAATGTATTGACACTTTATTCGTGCACCCTGGTTGGTCATTCATT
130 ATGGAATCGATACTTTTTATAAATGTATCGACACTTTATTCGTGCACCCCGGTTGGTCATTCATT
*
44563 CTGGACAAAAAGTATTAACACAATTTAAAAAGTGTCGATACATTATGTATACCACCTATTTTCAA
195 CTGGACAAAAAGTATTGACACAATTTAAAAAGTGTCGATACATTATGTA-A--ACCTATTTTCAA
* * * * *
44628 ATTAACCGATATATTTCTATCGGTTACATTATAAATTTACATATTACATTATAATTATGGGTTTC
257 ATTAACCGGTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTC
* * *
44693 GATGTTTTTGGGATCGATACTTTTTATAAATATATTGAGACTTTATGAGTGCACCCATTTAGGCA
322 GATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGAGTGCA-CCATTTAGGCA
44758 TTCATTCTGGAC
386 TTCATTCTGGAC
* * * *
44770 AAAAAGTATCGATACAAATTCCACAAGTATCGATACATGATGTAGACCTATTGTCTAATTAACCG
1 AAAAAGCATCGACACAAATTCCACAAGTGTCGATACATGATGTAGACCTATTTTCTAATTAACCG
*
44835 GTATATTTCTACCAGTTACATTGGAAATTGACCTATTACATTATAATTATATTATTCGATGTTTA
66 GTATATTTATACCAGTTACATTGGAAATTGACCTATTACATTATAATTATATTATTCGATGTTTA
* * *
44900 TGGAATCGATACTTTTTATAAATGTATCGACACTGTATTTGTGCACCCCGGTTGGTCTTTCATTC
131 TGGAATCGATACTTTTTATAAATGTATCGACACTTTATTCGTGCACCCCGGTTGGTCATTCATTC
* *
44965 TGGACAAAAAGTATCGACACAATTTAAAAAGTGTCGATGCATTATGTAAACCTATTTTCAAATTA
196 TGGACAAAAAGTATTGACACAATTTAAAAAGTGTCGATACATTATGTAAACCTATTTTCAAATTA
* *
45030 ACCGGTATATTTCTACCGGTTACATTGTAAAGTTACCTATTATATTATAATTATCGGTTTCGATG
261 ACCGGTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATG
* * *
45095 TTTTTGGGATCGATACTATTT-TAAATGTATCAACACTTTATGAGTGCACTCATTTAGGCATTTA
326 TTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGAGTGCAC-CATTTAGGCATTCA
45159 TTCTGGAC
390 TTCTGGAC
* * *
45167 AAAAAGCATCGACACAAATTCCACAACTGTCGATACATGATATAGACATATTTTCTAATTAACCG
1 AAAAAGCATCGACACAAATTCCACAAGTGTCGATACATGATGTAGACCTATTTTCTAATTAACCG
45232 GTATATTTATACC-GCTTACATTGGAAATTGACCTATTACATTATAATTATATTATTCGATGTTT
66 GTATATTTATACCAG-TTACATTGGAAATTGACCTATTACATTATAATTATATTATTCGATGTTT
* * * ** *
45296 ATGGGATCGATACGTTTTATAAATGTATCGACACTTTATGCGTGCACCCCTTTTGGGCATTCATT
130 ATGGAATCGATACTTTTTATAAATGTATCGACACTTTATTCGTGCACCCCGGTTGGTCATTCATT
* * ** * * * *
45361 TTGGACAAAAAATATTGACACAAATTCCACAAGTGTCGATACA-TATGTAGACCTATTCTCCAAT
195 CTGGACAAAAAGTATTGACAC-AATTTAAAAAGTGTCGATACATTATGTAAACCTATTTTCAAAT
* * *
45425 TAACCAGCATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATC-TTATTCG
259 TAACCGGTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGT-TTCG
* * *
45489 ATGTTTTTGGGATCGATACTTTTTATAAATGTATCGATACTTTATGAGTGCAACCTTTTGGGCAT
323 ATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGAGTGC-ACCATTTAGGCAT
45554 TCATTCTGGAC
387 TCATTCTGGAC
* * * * * * * *
45565 AAAACGTATCAACACAAGTTCCACAAGTGTCAATATATTATGTAGACCTATTTTGTAATTAACCG
1 AAAAAGCATCGACACAAATTCCACAAGTGTCGATACATGATGTAGACCTATTTTCTAATTAACCG
* * * *
45630 GTATATATCTACCAGTTACATTGTAAA-TGTACCTATTACATTATAATTATCTTATT-GATGTTT
66 GTATATTTATACCAGTTACATTGGAAATTG-ACCTATTACATTATAATTATATTATTCGATGTTT
* * * * *
45693 -TTGAGATCGATA-TTTTTAATAAATGTATCGACACTTTATTCATGCACCTCAGTTGGACATTCA
130 ATGGA-ATCGATACTTTTT-ATAAATGTATCGACACTTTATTCGTGCACCCCGGTTGGTCATTCA
45756 TTCTGGA
193 TTCTGGA
45763 GATTACTGAA
Statistics
Matches: 882, Mismatches: 100, Indels: 26
0.88 0.10 0.03
Matches are distributed among these distances:
396 9 0.01
397 396 0.45
398 255 0.29
399 3 0.00
400 1 0.00
401 217 0.25
402 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (397 bp):
AAAAAGCATCGACACAAATTCCACAAGTGTCGATACATGATGTAGACCTATTTTCTAATTAACCG
GTATATTTATACCAGTTACATTGGAAATTGACCTATTACATTATAATTATATTATTCGATGTTTA
TGGAATCGATACTTTTTATAAATGTATCGACACTTTATTCGTGCACCCCGGTTGGTCATTCATTC
TGGACAAAAAGTATTGACACAATTTAAAAAGTGTCGATACATTATGTAAACCTATTTTCAAATTA
ACCGGTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATG
TTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGAGTGCACCATTTAGGCATTCAT
TCTGGAC
Found at i:45467 original size:596 final size:595
Alignment explanation
Indices: 44369--45762 Score: 1739
Period size: 596 Copynumber: 2.3 Consensus size: 595
44359 ACGTAATTTA
* * *
44369 AAAAAGCATCGACACAACTTTAAAAAGTGTCGATACATTATGCAAACCTATTTTCGAATTAACCG
1 AAAAAGTATCGACACAACTTTAAAAAGTGTCGATACATTATGTAAACCTATTTTCAAATTAACCG
* * * * * *
44434 GTATATTTATACCGTTTACATTGGAAATTGGCCTATTACATTATAATTATATTATTTGATGTTTA
66 GTATATTTCTACCGGTTACATTGTAAATT-ACCTATTACATTATAATTAT-CT-TTTGATGTTTT
* ** *
44499 TGGGATCGATACTTTTTATAAATGTATTGACACTTTATTCGTGCACCCTGGTTGGTCATTCATTC
128 TGGGATCGATACTTTTTATAAATGTATCGACACTTTATGAGTGCACCAT-GTTGGTCATTCATTC
* * * * * *
44564 TGGACAAAAAGTATTAACACAATTTAAAAAGTGTCGATACATTATGTATACCACCTATTTTCAAA
192 TGGACAAAAAGCATCAACACAATTCAAAAACTGTCGATACATGA-GTATACCACATATTTTCAAA
* * * * * *
44629 TTAACCGATATATTTCTATCGGTTACATTATAAATTTACATATTACATTATAATTATGGGTTTCG
256 TTAACCGATATATTTATACCGCTTACATTAGAAATTGACATATTACATTATAATTATGAGTTTCG
* * * *
44694 ATGTTTTTGGGATCGATACTTTTTATAAATATATTGAGACTTTATGAGTGCACCCATTTAGGCAT
321 ATGTTTATGGGATCGATACGTTTTATAAATATATCGACACTTTATGAGTGCACCCATTTAGGCAT
* * *
44759 TCATTCTGGACAAAAAGTATCGATACAAATTCCACAAGTATCGATACATGATGTAGACCTATTGT
386 TCATTCTGGACAAAAAATATCGACACAAATTCCACAAGTATCGATACATGATGTAGACCTATTCT
* * *
44824 CTAATTAACCGGTATATTTCTACCAGTTACATTGGAAATTGACCTATTACATTATAATTATATTA
451 CCAATTAACCAGCATATTTCTACCAGTTACATTGGAAATTGACCTATTACATTATAATTATATTA
** *
44889 TTCGATGTTTATGGAATCGATACTTTTTATAAATGTATCGACACTGTATTTGTGCACCCCGGTTG
516 TTCGATGTTTATGGAATCGATACTTTTTATAAATGTATCGACACTGTATGAGTGCA-ACCGGTTG
* *
44954 GTCTTTCATTCTGGAC
580 GGCATTCATTCTGGAC
*
44970 AAAAAGTATCGACACAA-TTTAAAAAGTGTCGATGCATTATGTAAACCTATTTTCAAATTAACCG
1 AAAAAGTATCGACACAACTTTAAAAAGTGTCGATACATTATGTAAACCTATTTTCAAATTAACCG
* *
45034 GTATATTTCTACCGGTTACATTGTAAAGTTACCTATTATATTATAATTATCGGTTTCGATGTTTT
66 GTATATTTCTACCGGTTACATTGTAAA-TTACCTATTACATTATAATTATC--TTTTGATGTTTT
* * *
45099 TGGGATCGATACTATTT-TAAATGTATCAACACTTTATGAGTGCACTCAT-TTAGG-CATTTATT
128 TGGGATCGATACTTTTTATAAATGTATCGACACTTTATGAGTGCAC-CATGTT-GGTCATTCATT
* * * * *
45161 CTGGACAAAAAGCATCGACACAAATTCCACAACTGTCGATACATGA-TATA-GACATATTTTCTA
191 CTGGACAAAAAGCATCAACAC-AATTCAAAAACTGTCGATACATGAGTATACCACATATTTTCAA
* * * *
45224 ATTAACCGGTATATTTATACCGCTTACATTGGAAATTGACCTATTACATTATAATTAT-ATTATT
255 ATTAACCGATATATTTATACCGCTTACATTAGAAATTGACATATTACATTATAATTATGAGT-TT
* * * *
45288 CGATGTTTATGGGATCGATACGTTTTATAAATGTATCGACACTTTATGCGTGCACCCCTTTTGGG
319 CGATGTTTATGGGATCGATACGTTTTATAAATATATCGACACTTTATGAGTGCA-CCCATTTAGG
* * *
45353 CATTCATTTTGGACAAAAAATATTGACACAAATTCCACAAGTGTCGATACAT-ATGTAGACCTAT
383 CATTCATTCTGGACAAAAAATATCGACACAAATTCCACAAGTATCGATACATGATGTAGACCTAT
* * * *
45417 TCTCCAATTAACCAGCATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATC
448 TCTCCAATTAACCAGCATATTTCTACCAGTTACATTGGAAATTGACCTATTACATTATAATTATA
* * * * **
45482 TTATTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGATACTTTATGAGTGCAACCTTT
513 TTATTCGATGTTTATGGAATCGATACTTTTTATAAATGTATCGACACTGTATGAGTGCAACCGGT
45547 TGGGCATTCATTCTGGAC
578 TGGGCATTCATTCTGGAC
* * * ** * * * * **
45565 AAAACGTATCAACACAAGTTCCACAAGTGTCAATATATTATGTAGACCTATTTTGTAATTAACCG
1 AAAAAGTATCGACACAACTTTAAAAAGTGTCGATACATTATGTAAACCTATTTTCAAATTAACCG
* *
45630 GTATATATCTACCAGTTACATTGTAAATGTACCTATTACATTATAATTATCTTATTGATGTTTTT
66 GTATATTTCTACCGGTTACATTGTAAAT-TACCTATTACATTATAATTATCTT-TTGATGTTTTT
* * *
45695 GAGATCGATA-TTTTTAATAAATGTATCGACACTTTATTCA-TGCACC-TCAGTTGGACATTCAT
129 GGGATCGATACTTTTT-ATAAATGTATCGACACTTTA-TGAGTGCACCAT--GTTGGTCATTCAT
45757 TCTGGA
190 TCTGGA
45763 GATTACTGAA
Statistics
Matches: 683, Mismatches: 92, Indels: 40
0.84 0.11 0.05
Matches are distributed among these distances:
594 7 0.01
595 56 0.08
596 341 0.50
597 75 0.11
598 27 0.04
599 45 0.07
600 113 0.17
601 19 0.03
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (595 bp):
AAAAAGTATCGACACAACTTTAAAAAGTGTCGATACATTATGTAAACCTATTTTCAAATTAACCG
GTATATTTCTACCGGTTACATTGTAAATTACCTATTACATTATAATTATCTTTTGATGTTTTTGG
GATCGATACTTTTTATAAATGTATCGACACTTTATGAGTGCACCATGTTGGTCATTCATTCTGGA
CAAAAAGCATCAACACAATTCAAAAACTGTCGATACATGAGTATACCACATATTTTCAAATTAAC
CGATATATTTATACCGCTTACATTAGAAATTGACATATTACATTATAATTATGAGTTTCGATGTT
TATGGGATCGATACGTTTTATAAATATATCGACACTTTATGAGTGCACCCATTTAGGCATTCATT
CTGGACAAAAAATATCGACACAAATTCCACAAGTATCGATACATGATGTAGACCTATTCTCCAAT
TAACCAGCATATTTCTACCAGTTACATTGGAAATTGACCTATTACATTATAATTATATTATTCGA
TGTTTATGGAATCGATACTTTTTATAAATGTATCGACACTGTATGAGTGCAACCGGTTGGGCATT
CATTCTGGAC
Found at i:53626 original size:59 final size:58
Alignment explanation
Indices: 53076--53617 Score: 694
Period size: 59 Copynumber: 9.2 Consensus size: 58
53066 CATATGTTAT
* *
53076 CATTTTAGCGCAC-AAGGTGCCCAATACAGAAATTCATACACTTAGTATGAATTTCTTAA
1 CATTTTAGCACACGAA-GTGCCCTATAC-GAAATTCATACACTTAGTATGAATTTCTTAA
* *
53135 CATTTTAGCACACGAAGTGACCTATACAGAAATTCATACACTTAGTATGAATTTCTTAT
1 CATTTTAGCACACGAAGTGCCCTATAC-GAAATTCATACACTTAGTATGAATTTCTTAA
* *
53194 CATTTTAGCACATGAAGTGCCCTATACGAAAATTCATACACTTAATATGAATTTCTTAA
1 CATTTTAGCACACGAAGTGCCCTATACG-AAATTCATACACTTAGTATGAATTTCTTAA
* * * *
53253 CATTTTAGTACATGAAGTTCCCTATACGAAAATTCATACACTTAGTATGATTTTCTTAA
1 CATTTTAGCACACGAAGTGCCCTATACG-AAATTCATACACTTAGTATGAATTTCTTAA
* * * * *
53312 CATTTTAGCACACGAAGTACCATATATGGAAATTCATGCACTTAGTATAAATTTCTTAA
1 CATTTTAGCACACGAAGTGCCCTATA-CGAAATTCATACACTTAGTATGAATTTCTTAA
* * * * * *
53371 TATTTTAACACATGAAGTG-CATATACGGAAATTTATGCACTTAGTATGAATTTCTTAA
1 CATTTTAGCACACGAAGTGCCCTATAC-GAAATTCATACACTTAGTATGAATTTCTTAA
* * * * *
53429 CATTTTAGCACACGAAGTGCCCTGTATGAAAATTAAGACACTTAGTATGAATTTCTTAT
1 CATTTTAGCACACGAAGTGCCCTATACG-AAATTCATACACTTAGTATGAATTTCTTAA
*
53488 CATTTTAGCACACGAAGTGCCCTATACGAAAATTCATACACTTAGTATGAATATCTTAA
1 CATTTTAGCACACGAAGTGCCCTATACG-AAATTCATACACTTAGTATGAATTTCTTAA
* * *
53547 CATTTTAGCAAACAAAGTGCCCTATACAGAAATTCATACACTTAATATGAATTTCTTCAA
1 CATTTTAGCACACGAAGTGCCCTATAC-GAAATTCATACACTTAGTATGAATTTCTT-AA
53607 -ATTTTAGCACA
1 CATTTTAGCACA
53618 TTTAGTGCCA
Statistics
Matches: 427, Mismatches: 48, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
58 53 0.12
59 368 0.86
60 6 0.01
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (58 bp):
CATTTTAGCACACGAAGTGCCCTATACGAAATTCATACACTTAGTATGAATTTCTTAA
Found at i:54077 original size:17 final size:17
Alignment explanation
Indices: 54055--54098 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
54045 TTTTTTATTC
* *
54055 AATTCAATATGGTTCCT
1 AATTCAATATAGTCCCT
54072 AATTCAATATAGTCCCT
1 AATTCAATATAGTCCCT
*
54089 AAATCAATAT
1 AATTCAATAT
54099 TTAGGGCATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (17 bp):
AATTCAATATAGTCCCT
Found at i:59573 original size:59 final size:59
Alignment explanation
Indices: 59499--59840 Score: 555
Period size: 59 Copynumber: 5.8 Consensus size: 59
59489 ATAATTTCCC
* * *
59499 ATACGAAAACTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAATTGCCCT
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCT
** *
59558 ATACGGAAATTCATACACTTAGTATGAATTTCTTATTATTTTAGCACAC-AAGGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAA-GTGCCCT
* * *
59617 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTCGCACACAAATTGCCCT
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCT
*
59676 ATACGGAAATTCATACACTTAGTAT-AATTTCTTAACATTTTAGAACACGAAGTGCCC-
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCT
*
59733 ATACGGAAATTCATACACTTAGTATGAATTTCTTTACATTTTAGCACACGAAGTGCCCT
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCT
59792 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACAC
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACAC
59841 TTAGTTCCAT
Statistics
Matches: 261, Mismatches: 18, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
57 25 0.10
58 60 0.23
59 174 0.67
60 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (59 bp):
ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCT
Found at i:59758 original size:175 final size:176
Alignment explanation
Indices: 59491--59840 Score: 573
Period size: 175 Copynumber: 2.0 Consensus size: 176
59481 TTGTAAAAAT
* * *
59491 AATTTCCCATACGAAAACTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAATTGCC
1 AATTGCCCATACGAAAACTCATACACTTAGTATGAATTTCTTAACATTTTAGAACACGAAGTGCC
*
59556 CTATACGGAAATTCATACACTTAGTATGAATTTC-TTATTATTTTAGCACAC-AAGGTGCCCAAT
66 CTATACGGAAATTCATACACTTAGTATGAATTTCTTTA-CATTTTAGCACACGAA-GTGCCCAAT
*
59619 ACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTCGCACACA
129 ACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACA
* *
59667 AATTGCCCTATACGGAAATTCATACACTTAGTAT-AATTTCTTAACATTTTAGAACACGAAGTGC
1 AATTGCCC-ATACGAAAACTCATACACTTAGTATGAATTTCTTAACATTTTAGAACACGAAGTGC
*
59731 CC-ATACGGAAATTCATACACTTAGTATGAATTTCTTTACATTTTAGCACACGAAGTGCCCTATA
65 CCTATACGGAAATTCATACACTTAGTATGAATTTCTTTACATTTTAGCACACGAAGTGCCCAATA
59795 CGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACAC
130 CGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACAC
59841 TTAGTTCCAT
Statistics
Matches: 163, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
175 98 0.60
176 42 0.26
177 23 0.14
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (176 bp):
AATTGCCCATACGAAAACTCATACACTTAGTATGAATTTCTTAACATTTTAGAACACGAAGTGCC
CTATACGGAAATTCATACACTTAGTATGAATTTCTTTACATTTTAGCACACGAAGTGCCCAATAC
GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACA
Found at i:63757 original size:1 final size:1
Alignment explanation
Indices: 63748--63791 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
63738 TAAAAAAATC
* * * *
63748 AAAACAAAAAAAAAAAAAAAAAAAAAAACAAAAGAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
63792 GGTTTAAAGA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.91, C:0.05, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:63769 original size:24 final size:24
Alignment explanation
Indices: 63739--63791 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
63729 TCCGGTTAAT
**
63739 AAAAAAATCAAAACAAAAAAAAAA
1 AAAAAAAAAAAAACAAAAAAAAAA
* *
63763 AAAAAAAAAAAAACAAAAGAAAGA
1 AAAAAAAAAAAAACAAAAAAAAAA
63787 AAAAA
1 AAAAA
63792 GGTTTAAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.89, C:0.06, G:0.04, T:0.02
Consensus pattern (24 bp):
AAAAAAAAAAAAACAAAAAAAAAA
Found at i:63847 original size:45 final size:46
Alignment explanation
Indices: 63782--63882 Score: 186
Period size: 45 Copynumber: 2.2 Consensus size: 46
63772 AAAACAAAAG
*
63782 AAAGAAAAAAGGTTTAAAGAGGGAGGGTGTAATTCTTTTCATCTTT
1 AAAGAAAAAAGGTTTAAAGAGGGAGGGAGTAATTCTTTTCATCTTT
63828 AAAGAAAAAA-GTTTAAAGAGGGAGGGAGTAATTCTTTTCATCTTT
1 AAAGAAAAAAGGTTTAAAGAGGGAGGGAGTAATTCTTTTCATCTTT
63873 AAAGAAAAAA
1 AAAGAAAAAA
63883 AATATTTATG
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 44 0.81
46 10 0.19
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.29
Consensus pattern (46 bp):
AAAGAAAAAAGGTTTAAAGAGGGAGGGAGTAATTCTTTTCATCTTT
Found at i:68927 original size:17 final size:17
Alignment explanation
Indices: 68907--68949 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
68897 TTTAGGGAAG
68907 TAGTTCATTAATCAAAC
1 TAGTTCATTAATCAAAC
*
68924 TAGTTCATTCATCAAAC
1 TAGTTCATTAATCAAAC
68941 TAGTTCATT
1 TAGTTCATT
68950 TTTTTAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.40
Consensus pattern (17 bp):
TAGTTCATTAATCAAAC
Found at i:71341 original size:72 final size:71
Alignment explanation
Indices: 71237--71442 Score: 220
Period size: 72 Copynumber: 2.9 Consensus size: 71
71227 GCTCCTTAAG
*
71237 AGGAGGAGGAGGAGACTTGTACTTGTACACTGGAGGAGGTGGAGGTGGAGACTTGTATTTGTATG
1 AGGAGGAGGAGGAGACTTATACTTGTACACTGGAGGAGGTGGA-GTGGAGACTTGTATTTGTATG
*
71302 ACTCTTT
65 ACTCCTT
* * * *
71309 AGGAGGAGGAGGAGACTTATACTTGTAGACTGGTGGGGGTGGCAGTGGTGACTTGTATTTGTATG
1 AGGAGGAGGAGGAGACTTATACTTGTACACTGGAGGAGGTGG-AGTGGAGACTTGTATTTGTATG
**
71374 GTTCCTT
65 ACTCCTT
* * * * * * * *
71381 GGGAGGAGGATGA-A--GAGACTTGTACACTGAAGAAGGTGGAAGTGGAGATTTGTACTTGTATG
1 AGGAGGAGGAGGAGACTTATACTTGTACACTGGAGGAGGTGG-AGTGGAGACTTGTATTTGTATG
71443 GCTTCTTGAG
Statistics
Matches: 112, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
69 37 0.33
71 1 0.01
72 73 0.65
73 1 0.01
ACGTcount: A:0.24, C:0.09, G:0.38, T:0.29
Consensus pattern (71 bp):
AGGAGGAGGAGGAGACTTATACTTGTACACTGGAGGAGGTGGAGTGGAGACTTGTATTTGTATGA
CTCCTT
Found at i:71425 original size:69 final size:71
Alignment explanation
Indices: 71211--71457 Score: 212
Period size: 72 Copynumber: 3.4 Consensus size: 71
71201 TGGCCATGGT
* * * **
71211 GACTTATACTTGTATGGCTCCTTAAGAGGAGGAGGAGGAGACTTGTACTTGTACACTGGAGGAGG
1 GACTTGTATTTGTATGGTTCCTT--G-GGAGGAGGAGGAGACGAG-ACTTGTACACTGGAGGAGG
*
71276 TGGAGGTGGA
62 TGGAAGTGGA
** * * * * * * *
71286 GACTTGTATTTGTATGACTCTTTAGGAGGAGGAGGAGACTTATACTTGTAGACTGGTGGGGGTGG
1 GACTTGTATTTGTATGGTTCCTTGGGAGGAGGAGGAGAC-GAGACTTGTACACTGGAGGAGGTGG
* *
71351 CAGTGGT
65 AAGTGGA
* * *
71358 GACTTGTATTTGTATGGTTCCTTGGGAGGAGGATGA-A-GAGACTTGTACACTGAAGAAGGTGGA
1 GACTTGTATTTGTATGGTTCCTTGGGAGGAGGAGGAGACGAGACTTGTACACTGGAGGAGGTGGA
71421 AGTGGA
66 AGTGGA
* * *
71427 GATTTGTACTTGTATGGCTT-CTTGAGAGGAG
1 GACTTGTATTTGTATGG-TTCCTTGGGAGGAG
71458 TTGGAGACAT
Statistics
Matches: 140, Mismatches: 30, Indels: 10
0.78 0.17 0.06
Matches are distributed among these distances:
69 48 0.34
70 2 0.01
71 1 0.01
72 69 0.49
73 1 0.01
75 19 0.14
ACGTcount: A:0.24, C:0.10, G:0.36, T:0.30
Consensus pattern (71 bp):
GACTTGTATTTGTATGGTTCCTTGGGAGGAGGAGGAGACGAGACTTGTACACTGGAGGAGGTGGA
AGTGGA
Found at i:73101 original size:23 final size:22
Alignment explanation
Indices: 73046--73101 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
73036 TTAGCATGTT
* *
73046 TAAAAATAAAACTTAAAATAAA
1 TAAAAAGAAAACTTAAAAGAAA
73068 TAAAAATGAAAACTTGAAAAGAAA
1 TAAAAA-GAAAACTT-AAAAGAAA
73092 -AGAAAAGAAA
1 TA-AAAAGAAA
73102 GAACTTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 6 0.21
23 12 0.41
24 11 0.38
ACGTcount: A:0.71, C:0.04, G:0.09, T:0.16
Consensus pattern (22 bp):
TAAAAAGAAAACTTAAAAGAAA
Done.