Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000744.1 Hibiscus syriacus cultivar Beakdansim tig00001435_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: 85776
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:168 original size:33 final size:35
Alignment explanation
Indices: 111--176 Score: 109
Period size: 33 Copynumber: 1.9 Consensus size: 35
101 TAAAGGCTGG
111 CAAAATGCAACTATCATATTGAGCAAACCAAACCGA
1 CAAAATGCAAC-ATCATATTGAGCAAACCAAACCGA
147 CAAAATGCAAC-T-ATATTGAGCAAACCAAAC
1 CAAAATGCAACATCATATTGAGCAAACCAAAC
177 GATCGATCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
33 18 0.60
34 1 0.03
36 11 0.37
ACGTcount: A:0.48, C:0.24, G:0.11, T:0.17
Consensus pattern (35 bp):
CAAAATGCAACATCATATTGAGCAAACCAAACCGA
Found at i:8919 original size:3 final size:3
Alignment explanation
Indices: 8913--8942 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
8903 ATAATAATAT
8913 TTA TTA TTA TTA TTA TTA TTA TTA TATA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
8943 CTAAAGCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:9102 original size:31 final size:31
Alignment explanation
Indices: 9064--9137 Score: 139
Period size: 31 Copynumber: 2.4 Consensus size: 31
9054 ACCAACGGCT
9064 ACTAACGTTATCGATATGTAATAAAATGGTC
1 ACTAACGTTATCGATATGTAATAAAATGGTC
9095 ACTAACGTTATCGATATGTAATAAAATGGTC
1 ACTAACGTTATCGATATGTAATAAAATGGTC
9126 ACTAACGATTAT
1 ACTAACG-TTAT
9138 AACAATTATC
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 38 0.90
32 4 0.10
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (31 bp):
ACTAACGTTATCGATATGTAATAAAATGGTC
Found at i:17285 original size:29 final size:29
Alignment explanation
Indices: 17225--17323 Score: 80
Period size: 29 Copynumber: 3.5 Consensus size: 29
17215 ATGAAGAATA
* * *
17225 AAAATAAGTAAA-AAA-AAATAAAAG-GA
1 AAAATAAATAAATAAATAAATAAATGAGT
*
17251 AAAATAAATAAATAAATAAATGAAAT-ATT
1 AAAATAAATAAATAAATAAAT-AAATGAGT
* * * *
17280 AAAATATATATATATATATATAAATGAGT
1 AAAATAAATAAATAAATAAATAAATGAGT
*
17309 AAAATAAAAAAATAA
1 AAAATAAATAAATAA
17324 TAATCATAAC
Statistics
Matches: 55, Mismatches: 13, Indels: 7
0.73 0.17 0.09
Matches are distributed among these distances:
26 11 0.20
27 3 0.05
28 8 0.15
29 33 0.60
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (29 bp):
AAAATAAATAAATAAATAAATAAATGAGT
Found at i:17374 original size:19 final size:19
Alignment explanation
Indices: 17319--17373 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
17309 AAAATAAAAA
* *
17319 AATAATAATCATAACAATAAT
1 AATAGTAAT-ATAAAAAT-AT
*
17340 AATAGTAATATTAAAATAT
1 AATAGTAATATAAAAATAT
17359 AATA-TAATATAAAAA
1 AATAGTAATATAAAAA
17374 AAACCAAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 10 0.33
19 6 0.20
20 6 0.20
21 8 0.27
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.31
Consensus pattern (19 bp):
AATAGTAATATAAAAATAT
Found at i:17616 original size:19 final size:19
Alignment explanation
Indices: 17585--17622 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
17575 ATATATATAT
*
17585 ATATATATATAAATAATAA
1 ATATATATATAAAAAATAA
17604 ATATAGTAT-TAAAAAATAA
1 ATATA-TATATAAAAAATAA
17623 TCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
ATATATATATAAAAAATAA
Found at i:18202 original size:37 final size:37
Alignment explanation
Indices: 18148--18286 Score: 197
Period size: 37 Copynumber: 3.8 Consensus size: 37
18138 GTGCTTGTGG
* * * * * *
18148 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
* *
18185 ATCATATTTTTAAGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
*
18222 ATCCTATTTTTAGGAGTTTGAATCTTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
18259 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
18287 TAGGACGAAA
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 90 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
Found at i:19229 original size:106 final size:106
Alignment explanation
Indices: 18918--20611 Score: 2542
Period size: 106 Copynumber: 16.0 Consensus size: 106
18908 GCATTGTTCT
* * * ** * *
18918 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
18983 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
19024 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * * *
19083 TCAGTC-GCCCCTTCGTCTTGAAGTTGAGCTTGTGTTGTCTTG
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * *
19125 G-GTCCAAGATCATTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
19189 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
19230 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * *
19295 CCAGCAGTCCCTTCATCGTTAAGTTGAAATTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
19336 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTAACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
19401 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
19442 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
19507 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
19548 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTTGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
19613 CCAGCGGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
19654 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
19719 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
19760 GAGTCCAATATCTTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
19825 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
19866 GAGTCCAATATCCTACGTTGTGAAGTTGAAATTGGCTCTGAAATTTGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
19931 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
19972 GAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
20037 TCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
20078 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
20143 CCAGCGGGCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
20184 AAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
20249 CCAGTGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
20290 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
20355 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
20396 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
20461 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCTTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
20502 GAGTCCAATATTCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
20567 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
20608 GAGT
1 GAGT
20612 GGCACGATAT
Statistics
Matches: 1444, Mismatches: 135, Indels: 18
0.90 0.08 0.01
Matches are distributed among these distances:
100 79 0.05
101 5 0.00
102 4 0.00
104 3 0.00
105 5 0.00
106 1348 0.93
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:21217 original size:24 final size:24
Alignment explanation
Indices: 21188--21248 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
21178 AATATCAATA
*
21188 AAGAGTTTCGAAAGATGTTTAATC
1 AAGAGTTTTGAAAGATGTTTAATC
*
21212 AAGAGTTTTGAAAGATGTTTAATT
1 AAGAGTTTTGAAAGATGTTTAATC
*
21236 AAAAGTTTTGAAA
1 AAGAGTTTTGAAA
21249 ATATTGTCCC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.41, C:0.03, G:0.20, T:0.36
Consensus pattern (24 bp):
AAGAGTTTTGAAAGATGTTTAATC
Found at i:21472 original size:22 final size:22
Alignment explanation
Indices: 21445--21508 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
21435 GTTTGGTCAA
21445 ATTTGATGCTCAAAGGTTTGGC
1 ATTTGATGCTCAAAGGTTTGGC
*
21467 ATTTGATGCTCATAGGTTTGGC
1 ATTTGATGCTCAAAGGTTTGGC
* *
21489 ATTTAATGCTCAATGGTTTG
1 ATTTGATGCTCAAAGGTTTG
21509 ATGGGGTAGC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.22, C:0.12, G:0.25, T:0.41
Consensus pattern (22 bp):
ATTTGATGCTCAAAGGTTTGGC
Found at i:22131 original size:13 final size:13
Alignment explanation
Indices: 22115--22188 Score: 60
Period size: 14 Copynumber: 5.4 Consensus size: 13
22105 TTTTTGTCCC
*
22115 TTTTTCTTTTTGA
1 TTTTTCTTTTTGT
* *
22128 TTTTTGTTCTTTCT
1 TTTTTCTT-TTTGT
22142 TTTTTC-TTTTGT
1 TTTTTCTTTTTGT
22154 TTTATTCTTTTTTGTT
1 TTT-TTC-TTTTTG-T
*
22170 TTTTTGTTTTTTGT
1 TTTTT-CTTTTTGT
22184 TTTTT
1 TTTTT
22189 TTTCTTTTTG
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
12 7 0.14
13 11 0.22
14 14 0.29
15 13 0.27
16 4 0.08
ACGTcount: A:0.03, C:0.07, G:0.08, T:0.82
Consensus pattern (13 bp):
TTTTTCTTTTTGT
Found at i:22147 original size:7 final size:7
Alignment explanation
Indices: 22115--22197 Score: 50
Period size: 7 Copynumber: 12.6 Consensus size: 7
22105 TTTTTGTCCC
22115 TTTTTC-
1 TTTTTCT
**
22121 TTTTTGA
1 TTTTTCT
*
22128 TTTTTGT
1 TTTTTCT
*
22135 TCTTTCT
1 TTTTTCT
22142 TTTTTCT
1 TTTTTCT
*
22149 TTTGT-T
1 TTTTTCT
*
22155 TTATTCT
1 TTTTTCT
*
22162 TTTTTGT
1 TTTTTCT
22169 TTTTT-T
1 TTTTTCT
*
22175 GTTTT-T
1 TTTTTCT
*
22181 TGTTT-T
1 TTTTTCT
22187 TTTTTCT
1 TTTTTCT
22194 TTTT
1 TTTT
22198 GTTCTGATTG
Statistics
Matches: 60, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
6 23 0.38
7 37 0.62
ACGTcount: A:0.02, C:0.07, G:0.07, T:0.83
Consensus pattern (7 bp):
TTTTTCT
Found at i:22151 original size:20 final size:20
Alignment explanation
Indices: 22117--22172 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
22107 TTTGTCCCTT
*
22117 TTTCTTTTTGATTTTTGTTC
1 TTTCTTTTTTATTTTTGTTC
* *
22137 TTTCTTTTTT-CTTTTGTTT
1 TTTCTTTTTTATTTTTGTTC
*
22156 TATTCTTTTTTGTTTTT
1 T-TTCTTTTTTATTTTT
22173 TTGTTTTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 8 0.27
20 18 0.60
21 4 0.13
ACGTcount: A:0.04, C:0.09, G:0.07, T:0.80
Consensus pattern (20 bp):
TTTCTTTTTTATTTTTGTTC
Found at i:22168 original size:15 final size:15
Alignment explanation
Indices: 22148--22200 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
22138 TTCTTTTTTC
*
22148 TTTTGTTTTATTCTT
1 TTTTGTTTTTTTCTT
*
22163 TTTTGTTTTTTTGTT
1 TTTTGTTTTTTTCTT
*
22178 TTTTGTTTTTTTTTCT
1 TTTTGTTTTTTTCT-T
22194 TTTTGTT
1 TTTTGTT
22201 CTGATTGAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
15 26 0.76
16 8 0.24
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.85
Consensus pattern (15 bp):
TTTTGTTTTTTTCTT
Found at i:22171 original size:27 final size:27
Alignment explanation
Indices: 22115--22173 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
22105 TTTTTGTCCC
*
22115 TTTTTCTTTTTGATTTTTGTTCTTTCT
1 TTTTTCTTTTTGATTTTTCTTCTTTCT
* * *
22142 TTTTTC-TTTTGTTTTATTCTTTTTTGT
1 TTTTTCTTTTTGATTT-TTCTTCTTTCT
22169 TTTTT
1 TTTTT
22174 TGTTTTTTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 8 0.30
27 19 0.70
ACGTcount: A:0.03, C:0.08, G:0.07, T:0.81
Consensus pattern (27 bp):
TTTTTCTTTTTGATTTTTCTTCTTTCT
Found at i:22178 original size:23 final size:21
Alignment explanation
Indices: 22115--22196 Score: 74
Period size: 24 Copynumber: 3.5 Consensus size: 21
22105 TTTTTGTCCC
*
22115 TTTTTCTTTTTGATTTTTGTTCTT
1 TTTTTTTTTTTG--TTTT-TTCTT
22139 TCTTTTTTCTTTTGTTTTATTCTT
1 T-TTTTTT-TTTTGTTTT-TTCTT
*
22163 TTTTGTTTTTTTGTTTTTTGTT
1 TTTT-TTTTTTTGTTTTTTCTT
22185 TTTTTTTCTTTT
1 TTTTTTT-TTTT
22197 TGTTCTGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
21 3 0.06
22 12 0.24
23 12 0.24
24 14 0.27
25 5 0.10
26 5 0.10
ACGTcount: A:0.02, C:0.07, G:0.07, T:0.83
Consensus pattern (21 bp):
TTTTTTTTTTTGTTTTTTCTT
Found at i:26675 original size:25 final size:24
Alignment explanation
Indices: 26647--26714 Score: 59
Period size: 25 Copynumber: 2.7 Consensus size: 24
26637 GGGAAAAATG
*
26647 AATAAATGAAAAAATGAAGAA-TAAA
1 AATAAAT-AAAAAATGAA-AAGGAAA
*
26672 AATAAGTAAAAAAAAT-AAAAGGAAA
1 AATAA--ATAAAAAATGAAAAGGAAA
26697 AATAAATAAATAAATGAA
1 AATAAATAAA-AAATGAA
26715 TGAAATATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
23 4 0.11
24 6 0.17
25 17 0.49
26 7 0.20
27 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (24 bp):
AATAAATAAAAAATGAAAAGGAAA
Found at i:26703 original size:16 final size:16
Alignment explanation
Indices: 26666--26706 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
26656 AAAAATGAAG
*
26666 AATAAA-AATAAGTAAA
1 AATAAATAA-AAGGAAA
26682 AA-AAATAAAAGGAAA
1 AATAAATAAAAGGAAA
26697 AATAAATAAA
1 AATAAATAAA
26707 TAAATGAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (16 bp):
AATAAATAAAAGGAAA
Found at i:26735 original size:2 final size:2
Alignment explanation
Indices: 26728--26770 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
26718 AATATTTAAA
26728 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
26770 A
1 A
26771 AATGAGTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27176 original size:66 final size:64
Alignment explanation
Indices: 27029--27177 Score: 151
Period size: 66 Copynumber: 2.3 Consensus size: 64
27019 GCTTATAAGT
* *
27029 AAAATATTTTAAAAAAAGTATATATATATATATAATAAATATAGTATTAAAAAATAATCAAATG
1 AAAATATTTAAAAAAAAGTATATATATATATATAATAAATATAGTAGTAAAAAATAATCAAATG
* * * *
27093 AATATAAATAAATAAAAAATTATATGTATATATATAATAATAATATATAGT-GT-AAAAA-AATC
1 AAAAT-ATTTAA-AAAAAAGTATA--TATATATAT-ATAATAA-ATATAGTAGTAAAAAATAATC
*
27155 AATTG
60 AAATG
27160 AAAATCATTTAAAAAAAA
1 AAAAT-ATTTAAAAAAAA
27178 CATACGAATA
Statistics
Matches: 68, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
64 4 0.06
65 3 0.04
66 16 0.24
67 16 0.24
68 14 0.21
69 8 0.12
70 7 0.10
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (64 bp):
AAAATATTTAAAAAAAAGTATATATATATATATAATAAATATAGTAGTAAAAAATAATCAAATG
Found at i:27666 original size:37 final size:37
Alignment explanation
Indices: 27620--27716 Score: 115
Period size: 37 Copynumber: 2.6 Consensus size: 37
27610 GGATCCTATC
* * *
27620 TTTAGGAGTTTAAATCATAGTAGAACTCTATCATATT
1 TTTAAGAGTTTGAATCCTAGTAGAACTCTATCATATT
* * * *
27657 TTTAAGAGTTTGAATCCTAGCAAAATTCTATCTTATT
1 TTTAAGAGTTTGAATCCTAGTAGAACTCTATCATATT
27694 TTT-AGAAGTTTGAATCCTAGTAG
1 TTTAAG-AGTTTGAATCCTAGTAG
27717 GACGAAAAGG
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
36 2 0.04
37 48 0.96
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.41
Consensus pattern (37 bp):
TTTAAGAGTTTGAATCCTAGTAGAACTCTATCATATT
Found at i:29748 original size:295 final size:287
Alignment explanation
Indices: 29177--30132 Score: 1142
Period size: 295 Copynumber: 3.3 Consensus size: 287
29167 CATGCCGTTA
* * *
29177 AAAACTTTAATTTTTGTTTCATTTTAATACTCCGTTTAAAATTTAACGTTTAGTTTTGAACAAAA
1 AAAA-TTT-ATTTTT-TTTCATTTTAGTACTCCGTTCAAAATTTAACGTTGAGTTTTGAACAAAA
* *
29242 TGAAAGTTTAGTACAAAACGGACTAAAACTGATAGTTTAGGTACTAAACACATTAAATTTTAATA
63 TGAAAGTTTAGTACAAAACGGACCAAAACTGATAGTTTAGGTACTAAACACATTAAGTTTT--TA
29307 A-AGGGGTACTAAATGAAATGAAAACTAAACATTAGGTATGATTTTGAAAAAAA-TGAAAGTTTA
126 ACAGGGGTACTAAATGAAATGAAAACTAAACATTAGGTATGA-TTT-AAAAAAATTGAAAGTTTA
* * * *
29370 GGTACTAAAACAAGCCAAAATTGATAGTTTAGGTATTAAATGAGTAATTTTCCCTAAAATAAAAT
189 GGTACTAAAACAGGCCAAAATCGATAGTTTAGGTATTAAATGTGTAATTTACCCTAAAATAAAAT
* * *
29435 CTAGAGAGTATATTTCATTTTAGCACCCGTCGTT
254 ATAGAGAGTATGTTTCATTTTAGCACCCGTCATT
* *
29469 AAACATTTTAGTTTTTGTTTCATTTTAGTACACTGTTCAAAATTTAACGTTGAGTTTTGAACAAA
1 AAA-A-TTTA-TTTTT-TTTCATTTTAGTACTCCGTTCAAAATTTAACGTTGAGTTTTGAACAAA
* ** * *
29534 ATGAAA-ATTATGTACTAAAACATACCAAAATTGATATTTTAGGTACTAAACACATTAAGTTTTT
62 ATGAAAGTTTA-GTAC-AAAACGGACCAAAACTGATAGTTTAGGTACTAAACACATTAAGTTTTT
* * * * * *
29598 AACAGCGGGTACTAAAATGATATAAAAATTAAATATTAGGTATAACTTTAAAAAAATTGGAAGTT
125 AACAG-GGGTACT-AAATGAAATGAAAACTAAACATTAGGTATGA-TTTAAAAAAATTGAAAGTT
** * * * *
29663 TTTGTACTGAAACAGGCTAAAAACGATAGTTTAGGTATTAAATGTTTAATTTACCCTAAAATAAA
187 TAGGTACTAAAACAGGCCAAAATCGATAGTTTAGGTATTAAATGTGTAATTTACCCTAAAATAAA
*
29728 ATGTAGAGAGTATGTTTCATTTTAGCACCCGTCATT
252 ATATAGAGAGTATGTTTCATTTTAGCACCCGTCATT
* *
29764 AAAAACTT-TTTTTTTTCATTTTAGTA-TCTCGTTCAAAATTTAACATTGAGTTTTGAACAAAAT
1 -AAAATTTATTTTTTTTCATTTTAGTACTC-CGTTCAAAATTTAACGTTGAGTTTTGAACAAAAT
** * * *
29827 GAAAGTTTAGTACAAAACGGACCAAAAGAGTTAGTTTAAGTACTAAATACA-TAAGTTTTTAACA
64 GAAAGTTTAGTACAAAACGGACCAAAACTGATAGTTTAGGTACTAAACACATTAAGTTTTTAACA
* * * * ** * *
29891 GTTGGTACTAAATAAAATGAAAACTAAACGTTAGATATGATTTTGAAAAATTCAAAGTTTAGGAA
129 G-GGGTACTAAATGAAATGAAAACTAAACATTAGGTATGATTTAAAAAAATTGAAAGTTTAGGTA
*
29956 CTAAAACAGGCCACAATCGATAGTTTAGGTATTAAATGTGTAATTTACCCTAAAATAAAATATAG
193 CTAAAACAGGCCAAAATCGATAGTTTAGGTATTAAATGTGTAATTTACCCTAAAATAAAATATAG
* *
30021 AGAGTATGTTTTATTTTAGC-TCCGTCATT
258 AGAGTATGTTTCATTTTAGCACCCGTCATT
*
30050 AAAA---ACTTTTTTTTCATTTTAGTA-TCCCGTTCAAAATTTAACGTTGAGTTTTGAATAAAAA
1 AAAATTTA-TTTTTTTTCATTTTAGTACT-CCGTTCAAAATTTAACGTTGAGTTTTGAA-CAAAA
*
30111 AGAGAAGTTTAGGTACTAAAAC
63 TGA-AAGTTTA-GTAC-AAAAC
30133 AAGCCAAAAT
Statistics
Matches: 572, Mismatches: 74, Indels: 40
0.83 0.11 0.06
Matches are distributed among these distances:
284 46 0.08
285 11 0.02
286 15 0.03
287 100 0.17
288 28 0.05
289 20 0.03
290 31 0.05
291 53 0.09
292 18 0.03
293 65 0.11
294 57 0.10
295 125 0.22
296 3 0.01
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (287 bp):
AAAATTTATTTTTTTTCATTTTAGTACTCCGTTCAAAATTTAACGTTGAGTTTTGAACAAAATGA
AAGTTTAGTACAAAACGGACCAAAACTGATAGTTTAGGTACTAAACACATTAAGTTTTTAACAGG
GGTACTAAATGAAATGAAAACTAAACATTAGGTATGATTTAAAAAAATTGAAAGTTTAGGTACTA
AAACAGGCCAAAATCGATAGTTTAGGTATTAAATGTGTAATTTACCCTAAAATAAAATATAGAGA
GTATGTTTCATTTTAGCACCCGTCATT
Found at i:33419 original size:20 final size:20
Alignment explanation
Indices: 33389--33585 Score: 137
Period size: 20 Copynumber: 9.7 Consensus size: 20
33379 GTTTCCAGAT
*
33389 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* * *
33409 TCGCATTGCGATTTTCTAAAT-
1 TCGCAATGCGA--TTCTGACTA
**
33430 TCGCGTTGCGATTTTCTGACTA
1 TCGCAATGCGA--TTCTGACTA
* * * *
33452 TCGCAATGTGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
* *
33472 TCGCAATGCGAGTATGACTA
1 TCGCAATGCGATTCTGACTA
* *
33492 TCGCAAAGCGATTCTCACTA
1 TCGCAATGCGATTCTGACTA
* * *
33512 TCGCAACGAGATTTTGACTA
1 TCGCAATGCGATTCTGACTA
*
33532 TCGCAACGCGATTTCTGACTA
1 TCGCAATGCGA-TTCTGACTA
* * *
33553 TCGTAACGCGATGCTGACTA
1 TCGCAATGCGATTCTGACTA
33573 TCGCAATGCGATT
1 TCGCAATGCGATT
33586 TTCAAAACGC
Statistics
Matches: 140, Mismatches: 31, Indels: 12
0.77 0.17 0.07
Matches are distributed among these distances:
19 1 0.01
20 88 0.63
21 37 0.26
22 14 0.10
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:33571 original size:41 final size:41
Alignment explanation
Indices: 33486--33586 Score: 132
Period size: 41 Copynumber: 2.5 Consensus size: 41
33476 AATGCGAGTA
**
33486 TGACTATCGCAAAGCGA-TTCTCACTATCGCAACGAGATTT
1 TGACTATCGCAAAGCGATTTCTCACTATCGCAACGAGATGC
* * * *
33526 TGACTATCGCAACGCGATTTCTGACTATCGTAACGCGATGC
1 TGACTATCGCAAAGCGATTTCTCACTATCGCAACGAGATGC
*
33567 TGACTATCGCAATGCGATTT
1 TGACTATCGCAAAGCGATTT
33587 TCAAAACGCC
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 16 0.30
41 37 0.70
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.29
Consensus pattern (41 bp):
TGACTATCGCAAAGCGATTTCTCACTATCGCAACGAGATGC
Found at i:33801 original size:22 final size:22
Alignment explanation
Indices: 33750--33802 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
33740 CACTCTCTAA
* *
33750 GGCGACATCCGTCCCCATCTCC
1 GGCGAAATCAGTCCCCATCTCC
* *
33772 GACAAAATCAGTCCCCATCTCC
1 GGCGAAATCAGTCCCCATCTCC
33794 GGCGAAATC
1 GGCGAAATC
33803 CGTCTATCTC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.42, G:0.17, T:0.17
Consensus pattern (22 bp):
GGCGAAATCAGTCCCCATCTCC
Found at i:34244 original size:20 final size:20
Alignment explanation
Indices: 34199--34271 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 20
34189 GCGATTTTAG
**
34199 TTTCGCGTTGCGATTTTC-A
1 TTTCGCGTTGCGATAGTCAA
34218 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAA
* *
34238 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAA
*
34258 TTTCGTGTTGCGAT
1 TTTCGCGTTGCGAT
34272 TTTAAGTTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 16 0.34
20 31 0.66
ACGTcount: A:0.15, C:0.19, G:0.25, T:0.41
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAA
Found at i:34281 original size:20 final size:19
Alignment explanation
Indices: 34188--34281 Score: 80
Period size: 20 Copynumber: 4.8 Consensus size: 19
34178 AGAATCGCAA
*
34188 TGCGATTTTAGTTTCGCGT
1 TGCGATTTTAATTTCGCGT
*
34207 TGCGATTTTCATTTCGCGT
1 TGCGATTTTAATTTCGCGT
* * *
34226 TGCGATAGTCAAATTCGCGT
1 TGCGAT-TTTAATTTCGCGT
* * * *
34246 TGCGATAGTCATTTTCGTGT
1 TGCGAT-TTTAATTTCGCGT
34266 TGCGATTTTAAGTTTC
1 TGCGATTTTAA-TTTC
34282 AGAAACTATT
Statistics
Matches: 61, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
19 25 0.41
20 36 0.59
ACGTcount: A:0.16, C:0.17, G:0.23, T:0.44
Consensus pattern (19 bp):
TGCGATTTTAATTTCGCGT
Found at i:36281 original size:20 final size:20
Alignment explanation
Indices: 36252--36307 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
36242 GCGATTCTCT
36252 CGTTGCGATAGTCATTTTCA
1 CGTTGCGATAGTCATTTTCA
* *
36272 CGTTGTGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCA
36292 CGTTGCGATAGTCATT
1 CGTTGCGATAGTCATT
36308 CGTGTTGCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCA
Found at i:36314 original size:18 final size:19
Alignment explanation
Indices: 36252--36318 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
36242 GCGATTCTCT
*
36252 CGTTGCGATAGTCATTTTCA
1 CGTTGCGATAGTCA-TTTCG
*
36272 CGTTGTGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
36292 CGTTGCGATAGTCA-TTCG
1 CGTTGCGATAGTCATTTCG
*
36310 TGTTGCGAT
1 CGTTGCGAT
36319 TTTAAGTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.28
20 31 0.72
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:36849 original size:18 final size:19
Alignment explanation
Indices: 36810--36851 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
36800 CTCACCTGTC
36810 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
36831 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
36849 ATC
1 ATC
36852 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:36905 original size:42 final size:42
Alignment explanation
Indices: 36805--36908 Score: 111
Period size: 42 Copynumber: 2.5 Consensus size: 42
36795 CCCGACTCAC
* * *
36805 CTGTCATCGTTCAAGAGGCCTCCCCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGGCCTCCCCCACCGTTCAAGAGGCCA
* ** * *
36847 CTATCATCCCTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCTA
1 CTGTCATCGTTCAAGAGGCCTCC-CCCACCGTTCAAGAGGCCA
*
36889 CTGTCATCGTTGAAGAGGCC
1 CTGTCATCGTTCAAGAGGCC
36909 CATATCGAAT
Statistics
Matches: 48, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
41 2 0.04
42 46 0.96
ACGTcount: A:0.21, C:0.36, G:0.20, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGGCCTCCCCCACCGTTCAAGAGGCCA
Found at i:38341 original size:36 final size:30
Alignment explanation
Indices: 38261--38326 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
38251 ATAAGAGTTG
38261 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
38291 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
38321 ATTTGT
1 ATTTGT
38327 GCTTGTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.29, C:0.03, G:0.14, T:0.55
Consensus pattern (30 bp):
ATTTGTTTAATTGATGTGTAAATAATTCTT
Found at i:38504 original size:20 final size:20
Alignment explanation
Indices: 38476--38739 Score: 203
Period size: 20 Copynumber: 13.8 Consensus size: 20
38466 GCGATTTTCT
* *
38476 CGTTACGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
*
38496 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
38516 CATTGCGATAGTC-ATTTCG
1 CGTTGCGATAGTCAAATTCG
*
38535 AGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
38555 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCG
** **
38575 CGTTGCGATAGTCATTTTTA
1 CGTTGCGATAGTCAAATTCG
* **
38595 TGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
38615 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
**
38629 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
**
38649 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
38669 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
* *
38683 CGTTGCAATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
* *
38703 CGTTGCGATAGTCATATTCA
1 CGTTGCGATAGTCAAATTCG
38723 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
38740 GAATGTGTAA
Statistics
Matches: 196, Mismatches: 35, Indels: 26
0.76 0.14 0.10
Matches are distributed among these distances:
14 19 0.10
16 2 0.01
18 2 0.01
19 17 0.09
20 156 0.80
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:38544 original size:39 final size:40
Alignment explanation
Indices: 38481--38584 Score: 129
Period size: 39 Copynumber: 2.6 Consensus size: 40
38471 TTTCTCGTTA
* **
38481 CGATAGTCAAATTCCCGTTGCGATAATCAAATTCGCATTG
1 CGATAGTTAAATTCGAGTTGCGATAATCAAATTCGCATTG
* * * *
38521 CGATAG-TCATTTCGAGTTGCGATAGTCAAATTCGCGTTG
1 CGATAGTTAAATTCGAGTTGCGATAATCAAATTCGCATTG
*
38560 CGATAGTTAAATTCGCGTTGCGATA
1 CGATAGTTAAATTCGAGTTGCGATA
38585 GTCATTTTTA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
39 32 0.60
40 21 0.40
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (40 bp):
CGATAGTTAAATTCGAGTTGCGATAATCAAATTCGCATTG
Found at i:38643 original size:54 final size:54
Alignment explanation
Indices: 38518--38731 Score: 250
Period size: 54 Copynumber: 3.9 Consensus size: 54
38508 CAAATTCGCA
* ** * *
38518 TTGCGATAGTCA-TTTCGAGTTGCGATAGTCAAATTCGCGTTGCGATAGTTAAATTCGCG
1 TTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCATTGCG--A-TT--A-TCCCG
***
38577 TTGCGATAGTCATTTTTATGTTGCGATAGTCATTTTCGCATTGCGATTATCCCG
1 TTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCG
38631 TTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCG
1 TTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCG
* * * * *
38685 TTGCAATAGTCATATTCGCGTTGCGATAGTCATATTCACGTTGCGAT
1 TTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCATTGCGAT
38732 AGTCAAATGA
Statistics
Matches: 139, Mismatches: 15, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
54 97 0.70
55 1 0.01
57 2 0.01
58 1 0.01
59 12 0.09
60 26 0.19
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (54 bp):
TTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCG
Found at i:38937 original size:18 final size:18
Alignment explanation
Indices: 38914--38948 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
38904 AAGCCGGTTG
*
38914 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
38932 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
38949 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:41243 original size:24 final size:24
Alignment explanation
Indices: 41209--41262 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
41199 CTGAAACATC
41209 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
41233 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
41257 ATCAAA
1 ATCAAA
41263 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:42092 original size:20 final size:20
Alignment explanation
Indices: 42069--42125 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
42059 GTGTTGTGAC
* *
42069 AGTCAGAATCGCGTTGTAAT
1 AGTCAGAATCGCATTGCAAT
*
42089 AGTCAGAATCGCATTGCGAT
1 AGTCAGAATCGCATTGCAAT
*
42109 AGTCATAATCGCATTGC
1 AGTCAGAATCGCATTGC
42126 GATTTACATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (20 bp):
AGTCAGAATCGCATTGCAAT
Found at i:42126 original size:20 final size:20
Alignment explanation
Indices: 42087--42270 Score: 124
Period size: 20 Copynumber: 9.1 Consensus size: 20
42077 TCGCGTTGTA
*
42087 ATAGTCAGAATCGCATTGCG
1 ATAGTCATAATCGCATTGCG
42107 ATAGTCATAATCGCATTGCG
1 ATAGTCATAATCGCATTGCG
* *
42127 AT-TTACATATTCGCATTGCG
1 ATAGT-CATAATCGCATTGCG
* * *
42147 AT-TTACATATTCGCGTTGCG
1 ATAGT-CATAATCGCATTGCG
*
42167 ATAGTCATACTCGCATTGCG
1 ATAGTCATAATCGCATTGCG
* *
42187 AT-TTACATATTCGCATTGCG
1 ATAGT-CATAATCGCATTGCG
* **
42207 ATAGTCGGAAAATCGCAACGCG
1 ATAGTC--ATAATCGCATTGCG
* * *
42229 A-ATTCGGAAAATCGCAATGCG
1 ATAGTC--ATAATCGCATTGCG
* *
42250 ATAGTCAGAATCGCGTTGCG
1 ATAGTCATAATCGCATTGCG
42270 A
1 A
42271 ATCTGGAAAC
Statistics
Matches: 137, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
19 2 0.01
20 100 0.73
21 21 0.15
22 14 0.10
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Consensus pattern (20 bp):
ATAGTCATAATCGCATTGCG
Found at i:42141 original size:40 final size:40
Alignment explanation
Indices: 42087--42212 Score: 157
Period size: 40 Copynumber: 3.1 Consensus size: 40
42077 TCGCGTTGTA
* * * *
42087 ATAGTCAGAATCGCATTGCGATAGT-CATAATCGCATTGCG
1 ATAGTCATACTCGCATTGCGAT-TTACATATTCGCATTGCG
* * *
42127 AT-TTACATATTCGCATTGCGATTTACATATTCGCGTTGCG
1 ATAGT-CATACTCGCATTGCGATTTACATATTCGCATTGCG
42167 ATAGTCATACTCGCATTGCGATTTACATATTCGCATTGCG
1 ATAGTCATACTCGCATTGCGATTTACATATTCGCATTGCG
42207 ATAGTC
1 ATAGTC
42213 GGAAAATCGC
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
39 2 0.03
40 71 0.96
41 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (40 bp):
ATAGTCATACTCGCATTGCGATTTACATATTCGCATTGCG
Found at i:42237 original size:21 final size:21
Alignment explanation
Indices: 42211--42250 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
42201 ATTGCGATAG
42211 TCGGAAAATCGCAACGCGAAT
1 TCGGAAAATCGCAACGCGAAT
*
42232 TCGGAAAATCGCAATGCGA
1 TCGGAAAATCGCAACGCGA
42251 TAGTCAGAAT
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:0.38, C:0.23, G:0.25, T:0.15
Consensus pattern (21 bp):
TCGGAAAATCGCAACGCGAAT
Found at i:51499 original size:24 final size:24
Alignment explanation
Indices: 51467--51513 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
51457 AGAAACTGTT
51467 GCTGGAGCCGGAGCTGGTACCGAC
1 GCTGGAGCCGGAGCTGGTACCGAC
* *
51491 GCTGGAGCCGGGGCTGGTGCCGA
1 GCTGGAGCCGGAGCTGGTACCGA
51514 TGATGGTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.13, C:0.28, G:0.47, T:0.13
Consensus pattern (24 bp):
GCTGGAGCCGGAGCTGGTACCGAC
Found at i:53842 original size:106 final size:106
Alignment explanation
Indices: 53706--54747 Score: 1789
Period size: 106 Copynumber: 9.8 Consensus size: 106
53696 GAATTGGATA
*
53706 TCCC-TCGTCGTGAAGTTGAACATGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
* *
53770 TTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGG
* *
53811 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
53876 TTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGG
* * *
53917 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTTTAA
1 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAG-TTGAA
53982 ATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGG
65 ATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGG
*
54024 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTAGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
54089 TTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGG
* *
54130 TCCCTTCGTCGTGAAGTTGAACATGTGTTGTCTGGAGTCCAATATCCTTCGCTGTAAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
*
54195 TTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGG
*
54236 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAACTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
54301 TTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGG
* *
54342 TCCCTTCGTCGTGAAGTTGAACATGTGTTGTCTGGAGTCCAATATCCTTCGCTGTAAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
* *
54407 TTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGG
* *
54448 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
* *
54513 TTGGCTCTAAAATTGAGAAGTTGTTTATTGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGG
*
54554 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
* * * * *
54619 TTGACTATAAAATTGGGAAGTTGTTTATTGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGG
* * * *
54660 TCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCACTATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
54725 TTGGCTCTGAAATTGAGAAGTTG
66 TTGGCTCTGAAATTGAGAAGTTG
54748 ATTGAGGTGT
Statistics
Matches: 895, Mismatches: 40, Indels: 3
0.95 0.04 0.00
Matches are distributed among these distances:
105 4 0.00
106 789 0.88
107 102 0.11
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (106 bp):
TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
TTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGG
Found at i:59500 original size:24 final size:24
Alignment explanation
Indices: 59468--59514 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
59458 AGAAACTGTT
59468 GCTGGAGCCGGAGCTGGTACCGAC
1 GCTGGAGCCGGAGCTGGTACCGAC
* *
59492 GCTGGAGCCGGGGCTGGTGCCGA
1 GCTGGAGCCGGAGCTGGTACCGA
59515 TGATGGTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.13, C:0.28, G:0.47, T:0.13
Consensus pattern (24 bp):
GCTGGAGCCGGAGCTGGTACCGAC
Found at i:68643 original size:20 final size:20
Alignment explanation
Indices: 68629--68688 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
68619 TTCGCAACGT
68629 GAATCTGTAAATCGCAACAC
1 GAATCTGTAAATCGCAACAC
68649 GAATCTGTAAATCGCAACAC
1 GAATCTGTAAATCGCAACAC
*
68669 GAATTTGTAAATCGCAACAC
1 GAATCTGTAAATCGCAACAC
68689 ATAAGTCAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.22
Consensus pattern (20 bp):
GAATCTGTAAATCGCAACAC
Found at i:68703 original size:20 final size:20
Alignment explanation
Indices: 68680--68806 Score: 111
Period size: 20 Copynumber: 6.3 Consensus size: 20
68670 AATTTGTAAA
68680 TCGCAACACATAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
*
68700 TCGCAACGCGAT-AGTCAAAT
1 TCGCAACAC-ATAAGTCAAAT
**
68720 TCGCAACGTGA-ATTTGT-AAA-
1 TCGCAAC---ACATAAGTCAAAT
68740 TCGCAACACATAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
*
68760 TCGCAACGCGAT-AGTCAAAT
1 TCGCAACAC-ATAAGTCAAAT
* * *
68780 TTGCAACACAAAACTCAAAT
1 TCGCAACACATAAGTCAAAT
68800 TCGCAAC
1 TCGCAAC
68807 GCGGAATTTC
Statistics
Matches: 86, Mismatches: 11, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
17 1 0.01
18 4 0.05
19 4 0.05
20 66 0.77
21 9 0.10
22 2 0.02
ACGTcount: A:0.40, C:0.24, G:0.14, T:0.21
Consensus pattern (20 bp):
TCGCAACACATAAGTCAAAT
Found at i:68704 original size:40 final size:41
Alignment explanation
Indices: 68614--68706 Score: 102
Period size: 40 Copynumber: 2.3 Consensus size: 41
68604 AACCCAGTTT
* ** **
68614 TCAATTTCGCAACGTGAATCTGTAAATCGCAACACGAATCTG
1 TCAAATTCGCAACACGAATCTGTAAATCGCAACAC-AATAAG
*
68656 T-AAA-TCGCAACACGAATTTGTAAATCGCAACAC-ATAAG
1 TCAAATTCGCAACACGAATCTGTAAATCGCAACACAATAAG
68694 TCAAATTCGCAAC
1 TCAAATTCGCAAC
68707 GCGATAGTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
38 4 0.09
39 3 0.07
40 33 0.77
41 2 0.05
42 1 0.02
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.24
Consensus pattern (41 bp):
TCAAATTCGCAACACGAATCTGTAAATCGCAACACAATAAG
Found at i:68704 original size:60 final size:60
Alignment explanation
Indices: 68660--68788 Score: 213
Period size: 60 Copynumber: 2.1 Consensus size: 60
68650 AATCTGTAAA
*
68660 TCGCAACACGAATTTGTAAATCGCAACACATAAGTCAAATTCGCAACGCGATAGTCAAAT
1 TCGCAACACGAATTTGTAAATCGCAACACATAAGTCAAATTCGCAACACGATAGTCAAAT
** *
68720 TCGCAACGTGAATTTGTAAATCGCAACACATAAGTCAAATTCGCAACGCGATAGTCAAAT
1 TCGCAACACGAATTTGTAAATCGCAACACATAAGTCAAATTCGCAACACGATAGTCAAAT
*
68780 TTGCAACAC
1 TCGCAACAC
68789 AAAACTCAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22
Consensus pattern (60 bp):
TCGCAACACGAATTTGTAAATCGCAACACATAAGTCAAATTCGCAACACGATAGTCAAAT
Found at i:68786 original size:40 final size:42
Alignment explanation
Indices: 68692--68827 Score: 151
Period size: 40 Copynumber: 3.4 Consensus size: 42
68682 GCAACACATA
* *
68692 AGTCAAATTCGCAACGCGAT-AGTCAAATTCGCAACGTGAATT
1 AGTCAAATTCGCAACAC-ATAAGTCAAATTCGCAACGCGAATT
*
68734 TGT-AAA-TCGCAACACATAAGTCAAATTCGCAACGCG-A-T
1 AGTCAAATTCGCAACACATAAGTCAAATTCGCAACGCGAATT
* * *
68772 AGTCAAATTTGCAACACAAAACTCAAATTCGCAACGCGGAATT
1 AGTCAAATTCGCAACACATAAGTCAAATTCGCAACGC-GAATT
68815 --TCAAATTCGCAAC
1 AGTCAAATTCGCAAC
68828 TGAATTTCAA
Statistics
Matches: 80, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
38 3 0.04
39 6 0.08
40 51 0.64
41 16 0.20
42 3 0.04
43 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (42 bp):
AGTCAAATTCGCAACACATAAGTCAAATTCGCAACGCGAATT
Found at i:68804 original size:60 final size:60
Alignment explanation
Indices: 68677--68806 Score: 181
Period size: 60 Copynumber: 2.2 Consensus size: 60
68667 ACGAATTTGT
*** ** *
68677 AAATCGCAACACATAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGTGAATTTGT
1 AAATCGCAACACATAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAACTGC
*
68737 AAATCGCAACACATAAGTCAAATTCGCAACGCGATAGTCAAATTTGCAACACAAAACT-C
1 AAATCGCAACACATAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAACTGC
68796 AAATTCGCAAC
1 AAA-TCGCAAC
68807 GCGGAATTTC
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 3 0.05
60 59 0.95
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.21
Consensus pattern (60 bp):
AAATCGCAACACATAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAACTGC
Found at i:68879 original size:20 final size:19
Alignment explanation
Indices: 68794--68885 Score: 121
Period size: 19 Copynumber: 4.7 Consensus size: 19
68784 AACACAAAAC
*
68794 TCAAATTCGCAACGCGGAATT
1 TCAAATTCGCAA--CTGAATT
68815 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
68834 TCAAATTCGAAACTGAATT
1 TCAAATTCGCAACTGAATT
*
68853 TCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACT-GAATT
*
68873 TCGAATTCGCAAC
1 TCAAATTCGCAAC
68886 ACGAATTTAA
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
19 37 0.57
20 16 0.25
21 12 0.18
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:68904 original size:39 final size:40
Alignment explanation
Indices: 68794--68893 Score: 134
Period size: 38 Copynumber: 2.5 Consensus size: 40
68784 AACACAAAAC
*
68794 TCAAATTCGCAACGCGGAATTTCAAATTCGCAACTGAATT
1 TCAAATTCGCAACACGGAATTTCAAATTCGCAACTGAATT
* *
68834 TCAAATTCG-AA-ACTGAATTTCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACACGGAATTTCAAATTCGCAACT-GAATT
*
68873 TCGAATTCGCAACAC-GAATTT
1 TCAAATTCGCAACACGGAATTT
68894 AATTTTGCAA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
38 20 0.38
39 14 0.26
40 17 0.32
41 2 0.04
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (40 bp):
TCAAATTCGCAACACGGAATTTCAAATTCGCAACTGAATT
Found at i:69044 original size:22 final size:22
Alignment explanation
Indices: 69019--69062 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
69009 CTCTCTCCGG
69019 CGACATCCGTTCCT-ATATCTAA
1 CGACATCC-TTCCTCATATCTAA
*
69041 CGACATCCTTCCTCATCTCTAA
1 CGACATCCTTCCTCATATCTAA
69063 TTTTTTTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.25, C:0.36, G:0.07, T:0.32
Consensus pattern (22 bp):
CGACATCCTTCCTCATATCTAA
Found at i:69713 original size:12 final size:12
Alignment explanation
Indices: 69692--69725 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
69682 ACCACATTTC
*
69692 CAATACCAAACA
1 CAATATCAAACA
69704 CAATATCAAACA
1 CAATATCAAACA
*
69716 CAATCTCAAA
1 CAATATCAAA
69726 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:70214 original size:20 final size:20
Alignment explanation
Indices: 70175--70214 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
70165 AAAATCGCAG
* * *
70175 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGAATTTAAGTTTC
70195 GTGTTGCGAATTTAAGTTTC
1 GTGTTGCGAATTTAAGTTTC
70215 AAAAGCTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.23, T:0.50
Consensus pattern (20 bp):
GTGTTGCGAATTTAAGTTTC
Found at i:70576 original size:22 final size:21
Alignment explanation
Indices: 70549--70599 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 21
70539 GATGGAGATA
*
70549 GACGGATTCAGTCGGAGATGGG
1 GACGGATTC-GTCAGAGATGGG
70571 GACGGATTTCGTCAGAGATGGG
1 GACGGA-TTCGTCAGAGATGGG
70593 GACGGAT
1 GACGGAT
70600 GTCGCCGTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 1 0.04
22 23 0.85
23 3 0.11
ACGTcount: A:0.24, C:0.14, G:0.43, T:0.20
Consensus pattern (21 bp):
GACGGATTCGTCAGAGATGGG
Found at i:70726 original size:20 final size:20
Alignment explanation
Indices: 70701--70802 Score: 132
Period size: 20 Copynumber: 5.1 Consensus size: 20
70691 TAATATTGTG
70701 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* *
70721 TTTCGCGTTGAGAAATTGAC
1 TTTCGCGTTGCGAATTTGAC
* *
70741 TATCGCGTTACGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* *
70761 TTTTGTGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
**
70781 TACCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
70801 TT
1 TT
70803 ATGTGTTGCG
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.39
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:70808 original size:40 final size:39
Alignment explanation
Indices: 70704--70813 Score: 148
Period size: 40 Copynumber: 2.7 Consensus size: 39
70694 TATTGTGTTT
* * *
70704 CGCGTTGCGAATTTGACTTTCGCGTTGAGAAATTGACTAT
1 CGCGTTGCGAATTTGACTTT-GTGTTGCGAAATTGACTAC
* *
70744 CGCGTTACGAATTTGACTTTTGTGTTGCGAATTTGACTAC
1 CGCGTTGCGAATTTGAC-TTTGTGTTGCGAAATTGACTAC
70784 CGCGTTGCGAATTTGACTTATGTGTTGCGA
1 CGCGTTGCGAATTTGACTT-TGTGTTGCGA
70814 TTTACAAATT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
39 2 0.03
40 57 0.92
41 3 0.05
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.37
Consensus pattern (39 bp):
CGCGTTGCGAATTTGACTTTGTGTTGCGAAATTGACTAC
Found at i:70810 original size:20 final size:20
Alignment explanation
Indices: 70705--70813 Score: 107
Period size: 20 Copynumber: 5.5 Consensus size: 20
70695 ATTGTGTTTC
70705 GCGTTGCGAATTTGACTT-T
1 GCGTTGCGAATTTGACTTAT
* *
70724 CGCGTTGAGAAATTGAC-TAT
1 -GCGTTGCGAATTTGACTTAT
* *
70744 CGCGTTACGAATTTGACTTTT
1 -GCGTTGCGAATTTGACTTAT
* *
70765 GTGTTGCGAATTTGAC-TACC
1 GCGTTGCGAATTTGACTTA-T
70785 GCGTTGCGAATTTGACTTAT
1 GCGTTGCGAATTTGACTTAT
*
70805 GTGTTGCGA
1 GCGTTGCGA
70814 TTTACAAATT
Statistics
Matches: 72, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
19 2 0.03
20 66 0.92
21 4 0.06
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.38
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTTAT
Found at i:70828 original size:40 final size:40
Alignment explanation
Indices: 70703--70833 Score: 142
Period size: 40 Copynumber: 3.3 Consensus size: 40
70693 ATATTGTGTT
* * * *
70703 TCGCGTTGCGAATTTGACTT-TCGCGTTGAGAAATTGACTA
1 TCGCGTTGCGAATTTGACTTAT-GTGTTGCGAATTTGACAA
* * *
70743 TCGCGTTACGAATTTGACTTTTGTGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTTATGTGTTGCGAATTTGACAA
*
70783 CCGCGTTGCGAATTTGACTTATGTGTTGCG-ATTT-ACAAA
1 TCGCGTTGCGAATTTGACTTATGTGTTGCGAATTTGAC-AA
70822 TTCGCGTTGCGA
1 -TCGCGTTGCGA
70834 TTTACAGATT
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
38 2 0.03
39 5 0.06
40 71 0.90
41 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGAATTTGACTTATGTGTTGCGAATTTGACAA
Found at i:70830 original size:20 final size:20
Alignment explanation
Indices: 70807--70971 Score: 143
Period size: 20 Copynumber: 8.2 Consensus size: 20
70797 TGACTTATGT
70807 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
* *
70827 GTTGCGATTTACAGATTCAC
1 GTTGCGATTTACAAATTCGC
* *
70847 GTTACGAATTTGA-AAAATCGC
1 GTTGCG-ATTT-ACAAATTCGC
**
70868 AATGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
**
70888 AATGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
* *
70908 GTTGCGATTTACATATTCAC
1 GTTGCGATTTACAAATTCGC
* ** *
70928 GTTACGAATTTGGAAAATCGC
1 GTTGCG-ATTTACAAATTCGC
** *
70949 AATGCGATTTACATATTCGC
1 GTTGCGATTTACAAATTCGC
70969 GTT
1 GTT
70972 ACGAAATTGG
Statistics
Matches: 112, Mismatches: 29, Indels: 8
0.75 0.19 0.05
Matches are distributed among these distances:
19 1 0.01
20 86 0.77
21 24 0.21
22 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:70900 original size:81 final size:81
Alignment explanation
Indices: 70809--70968 Score: 293
Period size: 81 Copynumber: 2.0 Consensus size: 81
70799 ACTTATGTGT
70809 TGCGATTTACAAATTCGCGTTGCGATTTACAGATTCACGTTACGAATTTGAAAAATCGCAATGCG
1 TGCGATTTACAAATTCGCGTTGCGATTTACAGATTCACGTTACGAATTTGAAAAATCGCAATGCG
70874 ATTTACAAATTCGCAA
66 ATTTACAAATTCGCAA
* *
70890 TGCGATTTACAAATTCGCGTTGCGATTTACATATTCACGTTACGAATTTGGAAAATCGCAATGCG
1 TGCGATTTACAAATTCGCGTTGCGATTTACAGATTCACGTTACGAATTTGAAAAATCGCAATGCG
*
70955 ATTTACATATTCGC
66 ATTTACAAATTCGC
70969 GTTACGAAAT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 76 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (81 bp):
TGCGATTTACAAATTCGCGTTGCGATTTACAGATTCACGTTACGAATTTGAAAAATCGCAATGCG
ATTTACAAATTCGCAA
Found at i:70972 original size:41 final size:41
Alignment explanation
Indices: 70829--70984 Score: 179
Period size: 41 Copynumber: 3.8 Consensus size: 41
70819 AAATTCGCGT
* *
70829 TGCGATTTACAGATTCACGTTACGAATTTGAAAAATCGCAA
1 TGCGATTTACATATTCACGTTACGAATTTGGAAAATCGCAA
* * ** * ** * **
70870 TGCGATTTACAAATTCGCAATGCG-ATTTACAAATTCGCGT
1 TGCGATTTACATATTCACGTTACGAATTTGGAAAATCGCAA
70910 TGCGATTTACATATTCACGTTACGAATTTGGAAAATCGCAA
1 TGCGATTTACATATTCACGTTACGAATTTGGAAAATCGCAA
* *
70951 TGCGATTTACATATTCGCGTTACGAAATTGGAAA
1 TGCGATTTACATATTCACGTTACGAATTTGGAAA
70985 CTGGGTTGCG
Statistics
Matches: 92, Mismatches: 22, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
40 30 0.33
41 62 0.67
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (41 bp):
TGCGATTTACATATTCACGTTACGAATTTGGAAAATCGCAA
Found at i:80425 original size:2 final size:2
Alignment explanation
Indices: 80418--80442 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
80408 TTTGCATAAC
80418 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 T
80443 CAAGGGATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:81357 original size:2 final size:2
Alignment explanation
Indices: 81350--81377 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
81340 TACCCTAATA
81350 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
81378 CCTTATTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.