Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005201.1 Hibiscus syriacus cultivar Beakdansim tig00011754_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: 64473
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1863 original size:13 final size:13
Alignment explanation
Indices: 1845--1877 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1835 TTCAATTCCG
1845 TTATTTTTTATTT
1 TTATTTTTTATTT
1858 TTATTTTTTATTT
1 TTATTTTTTATTT
1871 TT-TTTTT
1 TTATTTTT
1878 CCGATTAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTATTTTTTATTT
Found at i:1866 original size:8 final size:7
Alignment explanation
Indices: 1845--1877 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
1835 TTCAATTCCG
1845 TTATTTT
1 TTATTTT
1852 TTA-TTT
1 TTATTTT
1858 TTATTTT
1 TTATTTT
1865 TTATTTT
1 TTATTTT
1872 TT-TTTT
1 TTATTTT
1878 CCGATTAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 10 0.40
7 15 0.60
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTATTTT
Found at i:9091 original size:14 final size:15
Alignment explanation
Indices: 9067--9101 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
9057 TATACATATA
9067 ATAATAATAATGAAT
1 ATAATAATAATGAAT
9082 ATAA-AATAATGAAT
1 ATAATAATAATGAAT
*
9096 AAAATA
1 ATAATA
9102 TCCATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (15 bp):
ATAATAATAATGAAT
Found at i:9546 original size:37 final size:36
Alignment explanation
Indices: 9457--9556 Score: 121
Period size: 37 Copynumber: 2.8 Consensus size: 36
9447 GTGCTTGTGG
* * * * *
9457 ATCCTATCTTTAGGAATTTAAATCTTAGAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGAAAACTCT
* *
9493 ATCCTA-TTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAG-AAAACTCT
9529 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
9557 TAGGACGAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
35 17 0.31
36 17 0.31
37 21 0.38
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGAAAACTCT
Found at i:10505 original size:104 final size:105
Alignment explanation
Indices: 10098--10722 Score: 860
Period size: 104 Copynumber: 6.0 Consensus size: 105
10088 GCATTGTTCC
* * ** *
10098 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACA
* * * * * *
10162 ACCAGCCGTCCCTTCGTTGTGAAATTGAACTTGTGTTGTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
10204 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* * * *
10264 TA-CGGTCCCTTCATCGTGGAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
10303 GAGTCCAATATCCTTCGTTGTGAAGTT-AAATTGGCT-TGAGATTGGGAAGTTG-T-TTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
10364 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
10404 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
10469 CA-CGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
10508 AAGTCCAATATCCTTCGTTGGGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
10573 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
10613 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
* * * * *
10678 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
10719 GAGT
1 GAGT
10723 GTCACGATAT
Statistics
Matches: 469, Mismatches: 37, Indels: 26
0.88 0.07 0.05
Matches are distributed among these distances:
97 3 0.01
98 9 0.02
99 56 0.12
100 20 0.04
101 67 0.14
102 15 0.03
103 16 0.03
104 99 0.21
105 98 0.21
106 86 0.18
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:10632 original size:209 final size:206
Alignment explanation
Indices: 10099--10717 Score: 863
Period size: 209 Copynumber: 3.0 Consensus size: 206
10089 CATTGTTCCG
* * * ** * *
10099 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTT-AAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAAG
* * * * * *
10164 CAGCCGTCCCTTCGTTGTGAAATTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAG
64 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
* * * * *
10229 TTGAAATTGACTCTGAA-T-GAAATT-TTGTTGACAAGTACGGTCCCTTCATCGTGGAGTTGAAC
129 TTGAAATTGGCTCTGAATTGGAAGTTGTTGTTGACAAGCACGGTCCCTTCGTCGTGAAGTTGAAC
* *
10291 TTGCATTGTCTGG
194 TTGCGTTGTCTGA
*
10304 AGTCCAATATCCTTCGTTGTGAAGTTAAATTGGCT-TGAGATTGGGAAGTTG-T-TTGACAAGCA
1 AGTCCAATATCCTTCGTTGTGAAGTTAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGCA
10366 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
*
10431 GAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCACGGTCCCTTTGTCGTGAAGTTGAAC
131 GAAATTGGCTCTGA-ATT-GGAAGTTGTTGTTGACAAGCACGGTCCCTTCGTCGTGAAGTTGAAC
10496 TTGCGTTGTCTGA
194 TTGCGTTGTCTGA
* *
10509 AGTCCAATATCCTTCGTTGGGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTT-AAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGC
10574 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
* * *
10639 TGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTG
130 TGAAATTGGCTCTG-AATTG-GAAGTTG-TTGTTGACAAGCA-CGGTCCCTTCGTCGTGAAGTTG
*
10704 AACTTGTGTTGTCT
191 AACTTGCGTTGTCT
10718 CGAGTGTCAC
Statistics
Matches: 371, Mismatches: 30, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
200 81 0.22
201 2 0.01
202 1 0.00
203 11 0.03
204 14 0.04
205 94 0.25
206 9 0.02
207 14 0.04
208 2 0.01
209 98 0.26
210 13 0.04
211 32 0.09
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (206 bp):
AGTCCAATATCCTTCGTTGTGAAGTTAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGCA
GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
GAAATTGGCTCTGAATTGGAAGTTGTTGTTGACAAGCACGGTCCCTTCGTCGTGAAGTTGAACTT
GCGTTGTCTGA
Found at i:10982 original size:35 final size:36
Alignment explanation
Indices: 10915--10989 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 36
10905 TATTTGGAGA
* * *
10915 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
*
10951 GAAACTATCTCAAGCGAGA-TAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
10986 GAAA
1 GAAA
10990 TGTTTTCAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
35 18 0.51
36 17 0.49
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:11104 original size:102 final size:102
Alignment explanation
Indices: 10912--11202 Score: 489
Period size: 102 Copynumber: 2.9 Consensus size: 102
10902 GTTTATTTGG
* * *
10912 AGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGGAAACTATCTCAAGCGAGATAAA
1 AGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGAGA-AAAAA
10974 TTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCA
65 TTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCA
* *
11012 AGAGAAACTATCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGAGAAAAAAA
1 AGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGAGAAAAAAT
11077 TCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCA
66 TCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCA
*
11114 AGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAGGAGAAAAAAT
1 AGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGAGAAAAAAT
*
11179 TAATTTCAAGGGAAATGTTTTCAA
66 TCATTTCAAGGGAAATGTTTTCAA
11203 GAGAAACTCT
Statistics
Matches: 179, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
100 26 0.15
102 129 0.72
103 24 0.13
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (102 bp):
AGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGAGAAAAAAT
TCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCA
Found at i:11161 original size:39 final size:37
Alignment explanation
Indices: 11107--11179 Score: 92
Period size: 39 Copynumber: 1.9 Consensus size: 37
11097 TCAATGTTTA
* *
11107 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTC
1 TGTTTCAAGAGAAACTATCTC-A-GGAGAAAAAATTTTC
* *
11146 TGTTTCGAGGGAAACTATCTCAGGAGAAAAAATT
1 TGTTTCAAGAGAAACTATCTCAGGAGAAAAAATT
11180 AATTTCAAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 11 0.37
38 1 0.03
39 18 0.60
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAGGAGAAAAAATTTTC
Found at i:11373 original size:36 final size:36
Alignment explanation
Indices: 11328--11442 Score: 108
Period size: 36 Copynumber: 3.2 Consensus size: 36
11318 GGTCTCAAGC
*
11328 GAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGT
1 GAGATAAATCTTGTTTTAAGAAAAACAATCTTGAGT
* * ** * **
11364 GAAATAAATCTTCTTTCGAGAAAAACAGTCTCAAGT
1 GAGATAAATCTTGTTTTAAGAAAAACAATCTTGAGT
* *
11400 GAGACAAAGT-ATGTTTTAAGAAAAACAAAT-TTGAGT
1 GAGATAAA-TCTTGTTTTAAGAAAAAC-AATCTTGAGT
11436 GAGATAA
1 GAGATAA
11443 TCATCTGCAT
Statistics
Matches: 59, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
36 56 0.95
37 3 0.05
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.28
Consensus pattern (36 bp):
GAGATAAATCTTGTTTTAAGAAAAACAATCTTGAGT
Found at i:11395 original size:72 final size:75
Alignment explanation
Indices: 11281--11442 Score: 208
Period size: 72 Copynumber: 2.2 Consensus size: 75
11271 AAAAAATAGC
* * * *
11281 CTTGAGTGAAATGAAATGTCTTCTTTCTAGTGAAAACGGTCTCAAGCGAGACAAA-TCTTGTTTT
1 CTTGAGTGAAAT-AAA-GTCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAAGT-ATGTTTT
11345 AAGAAAAAC-AAT
63 AAGAAAAACAAAT
*
11357 CTTGAGTGAAATAAA-TCTTCTTTCGAG-AAAAACAGTCTCAAGTGAGACAAAGTATGTTTTAAG
1 CTTGAGTGAAATAAAGTCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAAGTATGTTTTAAG
11420 AAAAACAAAT
66 AAAAACAAAT
*
11430 -TTGAGTGAGATAA
1 CTTGAGTGAAATAA
11443 TCATCTGCAT
Statistics
Matches: 78, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
72 48 0.62
73 15 0.19
75 3 0.04
76 12 0.15
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (75 bp):
CTTGAGTGAAATAAAGTCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAAGTATGTTTTAAG
AAAAACAAAT
Found at i:12950 original size:182 final size:182
Alignment explanation
Indices: 12558--13091 Score: 928
Period size: 182 Copynumber: 2.9 Consensus size: 182
12548 ATCAGGTTTA
* ** *
12558 ACTGAAGGGTTCATCTCATCACAAGTCTTTGATCTGACAAAAGCAGTAGAGCAAACACCGAATTG
1 ACTGAAGGATTCATCTCATCACAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTG
* **
12623 CCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAG-CAGGGCTTTCGAGTT
66 CCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
*
12686 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGTGGGACAAATC
130 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* *
12739 ACTGAAGGATTCGTCTCATCATAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGATTCATCTCATCA-CAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
12804 ACCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
65 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
*
12869 TCCTCTATAACCAATTACCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
130 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
12922 ACTGAAGGATTCATCTCATCACAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTG
1 ACTGAAGGATTCATCTCATCACAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTG
12987 CCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTT
66 CCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTT
13052 CCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 CCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
13092 CGGATTTAAT
Statistics
Matches: 334, Mismatches: 16, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
181 19 0.06
182 228 0.68
183 87 0.26
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (182 bp):
ACTGAAGGATTCATCTCATCACAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTG
CCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTT
CCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:17372 original size:18 final size:17
Alignment explanation
Indices: 17349--17391 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
17339 ATATATACAT
17349 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
17367 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
17384 ATAA-AATA
1 ATAATAATA
17392 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:17796 original size:37 final size:37
Alignment explanation
Indices: 17746--17846 Score: 130
Period size: 37 Copynumber: 2.7 Consensus size: 37
17736 GTGCTTGTGG
* * * * *
17746 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
* *
17783 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
*
17820 ATCCTATTTTTAGGAGTTTGAATCCTA
1 ATCCTATTTTTAGGAGTTTAAATCCTA
17847 ATAGGACGAA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
Found at i:20220 original size:26 final size:24
Alignment explanation
Indices: 20172--20227 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 24
20162 CACTCTCTCT
20172 AAAAAATTTTAAAAAAAAAAGAAA
1 AAAAAATTTTAAAAAAAAAAGAAA
***
20196 AATAAAATGTTTAAAAAAGGCAGAAA
1 AA-AAAAT-TTTAAAAAAAAAAGAAA
20222 AAAAAA
1 AAAAAA
20228 GGGAGAAGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 2 0.07
25 9 0.33
26 16 0.59
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (24 bp):
AAAAAATTTTAAAAAAAAAAGAAA
Found at i:20439 original size:21 final size:20
Alignment explanation
Indices: 20413--20466 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
20403 TGATGTTGTT
20413 TTATTTTAATTTAGTC-ACTG
1 TTATTTTAATTT-GTCTACTG
* *
20433 TTAATTTCTGATTTTTCTACTG
1 TT-ATTT-TAATTTGTCTACTG
20455 TTATTTTAATTT
1 TTATTTTAATTT
20467 TTGCATTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.25
21 10 0.36
22 11 0.39
ACGTcount: A:0.22, C:0.09, G:0.07, T:0.61
Consensus pattern (20 bp):
TTATTTTAATTTGTCTACTG
Found at i:20468 original size:21 final size:20
Alignment explanation
Indices: 20413--20468 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 20
20403 TGATGTTGTT
**
20413 TTATTTTAATTTAGTCACTG
1 TTATTTTAATTTTTTCACTG
*
20433 TTAATTTCTGA-TTTTTCTACTG
1 TT-ATTT-TAATTTTTTC-ACTG
20455 TTATTTTAATTTTT
1 TTATTTTAATTTTT
20469 GCATTTTGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
20 4 0.14
21 16 0.57
22 8 0.29
ACGTcount: A:0.21, C:0.09, G:0.07, T:0.62
Consensus pattern (20 bp):
TTATTTTAATTTTTTCACTG
Found at i:24892 original size:39 final size:39
Alignment explanation
Indices: 24837--25256 Score: 632
Period size: 39 Copynumber: 10.8 Consensus size: 39
24827 ATTTTTTTAA
* * * * * *
24837 AGAATATTTTATCTCACTTGAGATGGTTTCTCTTGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
24876 AAAAGATTTTGTCTCACTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
*
24915 AGAAGA-TTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
*
24953 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
*
24992 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
25031 AGAAGA-TTTATCTTGCTTGAGATAGTTTTCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
25069 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
25108 AGAAGATTTTGTCTCGCTTGAGATA-TTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
*
25146 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
25185 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * *
25224 AGAA-AGTTTTGTCTCCCTTAAGACAATTTCCCT
1 AGAAGA-TTTTGTCTCGCTTGAGATAGTTTCCCT
25257 TAAAAAAATT
Statistics
Matches: 353, Mismatches: 24, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
38 108 0.31
39 245 0.69
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (39 bp):
AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
Found at i:24973 original size:77 final size:78
Alignment explanation
Indices: 24837--25227 Score: 635
Period size: 77 Copynumber: 5.1 Consensus size: 78
24827 ATTTTTTTAA
* * * * * * *
24837 AGAATATTTTATCTCACTTGAGATGGTTTCTCTTGAAACAAAAGATTTTGTCTCACTTGAGATAG
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTGTCTCGCTTGAGATAG
24902 TTTCCCTCGAAAC
66 TTTCCCTCGAAAC
24915 AGAAGA-TTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTGTCTCGCTTGAGATAG
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTGTCTCGCTTGAGATAG
*
24979 TTTCCCTTGAAAC
66 TTTCCCTCGAAAC
* * * *
24992 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAGAAGA-TTTATCTTGCTTGAGATAG
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTGTCTCGCTTGAGATAG
*
25056 TTTTCCTCGAAAC
66 TTTCCCTCGAAAC
*
25069 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTGTCTCGCTTGAGATA-
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTGTCTCGCTTGAGATAG
25133 TTTCCCTCGAAAC
66 TTTCCCTCGAAAC
25146 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTGTCTCGCTTGAGATAG
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTGTCTCGCTTGAGATAG
25211 TTTCCCTCGAAAC
66 TTTCCCTCGAAAC
25224 AGAA
1 AGAA
25228 AGTTTTGTCT
Statistics
Matches: 291, Mismatches: 19, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
77 217 0.75
78 74 0.25
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (78 bp):
AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTGTCTCGCTTGAGATAG
TTTCCCTCGAAAC
Found at i:25049 original size:116 final size:116
Alignment explanation
Indices: 24837--25256 Score: 664
Period size: 116 Copynumber: 3.6 Consensus size: 116
24827 ATTTTTTTAA
* * * * * * * *
24837 AGAATATTTTATCTCACTTGAGATGGTTTCTCTTGAAACAAAAGATTTTGTCTCACTTGAGATAG
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTGTCTCGCTTGAGATAG
24902 TTTCCCTCGAAACAGAAGATTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
66 TTTCCCTCGAAACAGAAGATTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
24953 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAGAAGATTTTGTCTCGCTTGAGATAG
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTGTCTCGCTTGAGATAG
* * *
25018 TTTCCCTTGAAACAGAAGATTTATCTTGCTTGAGATAGTTTTCCTCGAAAC
66 TTTCCCTCGAAACAGAAGATTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
25069 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTGTCTCGCTTGAGATA-
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTGTCTCGCTTGAGATAG
25133 TTTCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
66 TTTCCCTCGAAACAGAAGA-TTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
25185 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAA-AGTTTTGTCTCCCTTAAGACA
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGA-TTTTGTCTCGCTTGAGATA
*
25249 ATTTCCCT
65 GTTTCCCT
25257 TAAAAAAATT
Statistics
Matches: 284, Mismatches: 17, Indels: 5
0.93 0.06 0.02
Matches are distributed among these distances:
115 19 0.07
116 258 0.91
117 7 0.02
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (116 bp):
AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTGTCTCGCTTGAGATAG
TTTCCCTCGAAACAGAAGATTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
Found at i:25389 original size:36 final size:36
Alignment explanation
Indices: 25349--25511 Score: 126
Period size: 36 Copynumber: 4.6 Consensus size: 36
25339 ATCATTTCCC
**
25349 CTTGAAATGAATTTTGTCTCTCTTGAAACAGTTTCT
1 CTTGAAACAAATTTTGTCTCTCTTGAAACAGTTTCT
* *
25385 CTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCT
1 CTTGAAACAAATTTTGTCTCTCTTGAAACAGTTTCT
** * *
25421 CTTGAAACACAA-----AATCT-TTGAATA-TGTTTCC
1 CTTGAAACA-AATTTTGTCTCTCTTGAA-ACAGTTTCT
** * *
25452 CTTGAAAC-AATATTCATCTCCCTTGAGACAGTTTCT
1 CTTGAAACAAAT-TTTGTCTCTCTTGAAACAGTTTCT
25488 CTTGAAACAAAGTTTTGTCTCTCT
1 CTTGAAACAAA-TTTTGTCTCTCT
25512 ATAGTCAATT
Statistics
Matches: 97, Mismatches: 18, Indels: 23
0.70 0.13 0.17
Matches are distributed among these distances:
29 2 0.02
31 17 0.18
32 4 0.04
35 3 0.03
36 58 0.60
37 12 0.12
38 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (36 bp):
CTTGAAACAAATTTTGTCTCTCTTGAAACAGTTTCT
Found at i:25441 original size:103 final size:104
Alignment explanation
Indices: 25312--25511 Score: 289
Period size: 103 Copynumber: 1.9 Consensus size: 104
25302 CTTTGAAAAT
* ** *
25312 GTTTCCCTTAAAACACAAAATCTTTGAATCAT-TTCCCCTTGAAATGAAT-TTTGTCTCTCTTGA
1 GTTTCCCTTAAAACACAAAATCTTTGAAT-ATGTTCCCCTTGAAA-CAATATTCATCTCCCTTGA
25375 AACAGTTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGATA
64 AACAGTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGATA
* * * *
25415 GTTTCTCTTGAAACACAAAATCTTTGAATATGTTTCCCTTGAAACAATATTCATCTCCCTTGAGA
1 GTTTCCCTTAAAACACAAAATCTTTGAATATGTTCCCCTTGAAACAATATTCATCTCCCTTGAAA
25480 CAGTTTCTCTTGAAACAAAGTTTTGTCTCTCT
66 CAGTTTCTCTTGAAACAAAGTTTTGTCTCTCT
25512 ATAGTCAATT
Statistics
Matches: 86, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
102 5 0.06
103 69 0.80
104 12 0.14
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (104 bp):
GTTTCCCTTAAAACACAAAATCTTTGAATATGTTCCCCTTGAAACAATATTCATCTCCCTTGAAA
CAGTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGATA
Found at i:25903 original size:92 final size:92
Alignment explanation
Indices: 25746--25914 Score: 286
Period size: 92 Copynumber: 1.8 Consensus size: 92
25736 AAATTTCAAA
* *
25746 TGGAGAGTTCATAATGAGAAGAACTTATCTAATGAGGGAGAATAAGTTCATAATGAGAAGAACTT
1 TGGAGAGTTCATAATGAGAAGAACTCATCTAATGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
*
25811 GTTCGACCTTGGATTAACATTTTCCAG
66 GTTCAACCTTGGATTAACATTTTCCAG
*
25838 TGGAGAGTTCATAATGAGAAGAACTCAT-TCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACT
1 TGGAGAGTTCATAATGAGAAGAACTCATCT-AATGAGGGAGAAGAAGTTCATAATGAGAAGAACT
25902 TGTTCAACCTTGG
65 TGTTCAACCTTGG
25915 TTCAATTCCA
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
91 1 0.01
92 71 0.99
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (92 bp):
TGGAGAGTTCATAATGAGAAGAACTCATCTAATGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
GTTCAACCTTGGATTAACATTTTCCAG
Found at i:25906 original size:20 final size:19
Alignment explanation
Indices: 25844--25907 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
25834 CCAGTGGAGA
25844 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* **
25863 CATTCGATGAGGGAGAAGAA--
1 -GTTC-AT-AATGAGAAGAACT
25883 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
25903 GTTCA
1 GTTCA
25908 ACCTTGGTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 9 0.27
18 2 0.06
19 3 0.09
20 8 0.24
21 2 0.06
22 9 0.27
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:26062 original size:91 final size:91
Alignment explanation
Indices: 25961--26214 Score: 409
Period size: 91 Copynumber: 2.8 Consensus size: 91
25951 CCAATGGGAG
* * * * * *
25961 AGTTCATAATGAGAAGAACTCGTTTAACCTTGGCTCAACATTTCTAGTAGAGAGTTCATAATGAG
1 AGTTCATAATGAGAAGAACTTGTTCAACCTTGGCTCAGCATTTCCAATGGAGAGTTCATAATGAG
26026 AAGAACTCATCCAACAAGGGAGAAGA
66 AAGAACTCATCCAACAAGGGAGAAGA
*
26052 AGTTCATAATGAGAAGAACTTGTTCAACCTGGGCTCAGCATTTCCAATGGAGAGTTCATAATGAG
1 AGTTCATAATGAGAAGAACTTGTTCAACCTTGGCTCAGCATTTCCAATGGAGAGTTCATAATGAG
26117 AAGAACTCATCCAACAAGGGAGAAGA
66 AAGAACTCATCCAACAAGGGAGAAGA
* * *
26143 AGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTCGGTATTTCCAATGGAGAGTTCATAATGAG
1 AGTTCATAATGAGAAGAACTTGTTCAACCTTGGCTCAGCATTTCCAATGGAGAGTTCATAATGAG
*
26208 AATAACT
66 AAGAACT
26215 TATTCAACCT
Statistics
Matches: 151, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 151 1.00
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.26
Consensus pattern (91 bp):
AGTTCATAATGAGAAGAACTTGTTCAACCTTGGCTCAGCATTTCCAATGGAGAGTTCATAATGAG
AAGAACTCATCCAACAAGGGAGAAGA
Found at i:26482 original size:86 final size:87
Alignment explanation
Indices: 26317--26482 Score: 248
Period size: 88 Copynumber: 1.9 Consensus size: 87
26307 CAACTTTTAG
* *
26317 CTCGATTCTATCACAGAAGGAGGTAGATTAGCACCGAAATCTTGTTCGATTCCATCACGGAATGA
1 CTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGAAATC-TGTTCGATTCCATCACAGAATGA
*
26382 GAGGGATCGACATTTTCATTTCA
65 GAGGGATCAACATTTTCATTTCA
*
26405 CTCGATTCTATCACAGAATGAGGTAGATCAGCACC-AATATC-GTTCGATTCCATCACAGAATGA
1 CTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGAA-ATCTGTTCGATTCCATCACAGAATGA
26468 G-GTGGATCAACATTT
65 GAG-GGATCAACATTT
26483 CAATATAATG
Statistics
Matches: 72, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
85 1 0.01
86 33 0.46
87 2 0.03
88 36 0.50
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (87 bp):
CTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGAAATCTGTTCGATTCCATCACAGAATGAG
AGGGATCAACATTTTCATTTCA
Found at i:27701 original size:25 final size:25
Alignment explanation
Indices: 27656--27720 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
27646 TTTTATTTTA
* ** *
27656 TATTTTTAATTGTTTTTATTATCTT
1 TATTTTTAATTATTTCAATTAACTT
*
27681 T-TGTTTTAATTATTTCAATTAAGTT
1 TAT-TTTTAATTATTTCAATTAACTT
27706 TATTTTTAATTATTT
1 TATTTTTAATTATTT
27721 TGTTTCATAG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
24 1 0.03
25 31 0.94
26 1 0.03
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.68
Consensus pattern (25 bp):
TATTTTTAATTATTTCAATTAACTT
Found at i:33021 original size:36 final size:35
Alignment explanation
Indices: 32946--33041 Score: 104
Period size: 36 Copynumber: 2.7 Consensus size: 35
32936 CACAATTATC
* *
32946 AATTACATTCTAAACCCCAAATTCCAAAATGATTC
1 AATTACATTCTAAACCCCAAATTCAAAAATGATTA
* *
32981 AATTACATTTTAAACCTCAAATTCTAAAAAT-ACTTA
1 AATTACATTCTAAACCCCAAATTC-AAAAATGA-TTA
** *
33017 AATTACATTCCCAACCCTAAATTCA
1 AATTACATTCTAAACCCCAAATTCA
33042 TAATCCATTC
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
35 24 0.48
36 26 0.52
ACGTcount: A:0.44, C:0.24, G:0.01, T:0.31
Consensus pattern (35 bp):
AATTACATTCTAAACCCCAAATTCAAAAATGATTA
Found at i:35107 original size:25 final size:24
Alignment explanation
Indices: 35054--35112 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
35044 TTTAAATTGT
* **
35054 ATTAAAAATTTTAGAAGATGTGGA
1 ATTATAAATTTTAGAAGATGTAAA
* *
35078 GTTATGAAATTTTAGGAGATGTAAA
1 ATTAT-AAATTTTAGAAGATGTAAA
35103 ATTATAAATT
1 ATTATAAATT
35113 AAATAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
24 8 0.29
25 20 0.71
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.37
Consensus pattern (24 bp):
ATTATAAATTTTAGAAGATGTAAA
Found at i:36679 original size:37 final size:38
Alignment explanation
Indices: 36610--36682 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
36600 AGGCAAAGAG
*
36610 TTTGTAAAAGCATAACTTTGCCACAATGGTACTATGAA
1 TTTGTAAAAGCATAACTTTGCCACAATAGTACTATGAA
* **
36648 TTTGTAAAAGTATAAC-TTGCCTGAATAGTACTATG
1 TTTGTAAAAGCATAACTTTGCCACAATAGTACTATG
36683 TGCAAGAAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 16 0.52
38 15 0.48
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (38 bp):
TTTGTAAAAGCATAACTTTGCCACAATAGTACTATGAA
Found at i:36962 original size:12 final size:12
Alignment explanation
Indices: 36934--36970 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
36924 TTTGGTAATC
36934 CCCGCCCCGATTA
1 CCCGCCCCGA-TA
36947 CCCGCCCCGATA
1 CCCGCCCCGATA
*
36959 CCCGACCCGATA
1 CCCGCCCCGATA
36971 AATATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.19, C:0.54, G:0.16, T:0.11
Consensus pattern (12 bp):
CCCGCCCCGATA
Found at i:36997 original size:2 final size:2
Alignment explanation
Indices: 36990--37085 Score: 69
Period size: 2 Copynumber: 51.0 Consensus size: 2
36980 AATAATTATT
*
36990 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA -A TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
37029 TT TA -A TT TA AA TA -A AA TA TA TA TA TT TA TA TA TT TA -A TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
37068 TA AA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
37086 CCCGACCCAA
Statistics
Matches: 71, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
1 6 0.08
2 65 0.92
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:37107 original size:11 final size:11
Alignment explanation
Indices: 37087--37145 Score: 64
Period size: 11 Copynumber: 5.2 Consensus size: 11
37077 ATATATATAC
*
37087 CCGACCCAATT
1 CCGACCCAATA
*
37098 CCGGCCCAATA
1 CCGACCCAATA
37109 CCGACCCAATA
1 CCGACCCAATA
*
37120 CCCGACCTAATA
1 -CCGACCCAATA
*
37132 CCCGGCCCAATA
1 -CCGACCCAATA
37144 CC
1 CC
37146 CGTTTAAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
11 21 0.51
12 20 0.49
ACGTcount: A:0.29, C:0.47, G:0.12, T:0.12
Consensus pattern (11 bp):
CCGACCCAATA
Found at i:37126 original size:12 final size:12
Alignment explanation
Indices: 37083--37147 Score: 80
Period size: 12 Copynumber: 5.6 Consensus size: 12
37073 ATATATATAT
37083 ATACCCGACCCA
1 ATACCCGACCCA
* *
37095 AT-TCCGGCCCA
1 ATACCCGACCCA
37106 ATA-CCGACCCA
1 ATACCCGACCCA
*
37117 ATACCCGACCTA
1 ATACCCGACCCA
*
37129 ATACCCGGCCCA
1 ATACCCGACCCA
37141 ATACCCG
1 ATACCCG
37148 TTTAAATAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
11 19 0.42
12 26 0.58
ACGTcount: A:0.29, C:0.46, G:0.12, T:0.12
Consensus pattern (12 bp):
ATACCCGACCCA
Found at i:49365 original size:13 final size:14
Alignment explanation
Indices: 49342--49370 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
49332 GCCAATTTTC
49342 TTTTCTCTTTGTTT
1 TTTTCTCTTTGTTT
49356 TTTTCT-TTTGTTT
1 TTTTCTCTTTGTTT
49369 TT
1 TT
49371 AATAAGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (14 bp):
TTTTCTCTTTGTTT
Found at i:49561 original size:21 final size:21
Alignment explanation
Indices: 49535--49578 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
49525 CTTACTCGAA
49535 ATCTTGTTGATCTTCCCTGCT
1 ATCTTGTTGATCTTCCCTGCT
49556 ATCTTGTTGATCTTCCCTGCT
1 ATCTTGTTGATCTTCCCTGCT
49577 AT
1 AT
49579 GGACCGTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.11, C:0.27, G:0.14, T:0.48
Consensus pattern (21 bp):
ATCTTGTTGATCTTCCCTGCT
Found at i:50399 original size:30 final size:31
Alignment explanation
Indices: 50365--50423 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
50355 TTTATTATAT
50365 TTCT-ATAAATTTAA-TTTTTTAAAAATAATC
1 TTCTAATAAA-TTAATTTTTTTAAAAATAATC
*
50395 TTCTAATAAATTAATTTTTTTTAAAATAA
1 TTCTAATAAATTAATTTTTTTAAAAATAA
50424 CTTATTCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (31 bp):
TTCTAATAAATTAATTTTTTTAAAAATAATC
Found at i:50435 original size:32 final size:30
Alignment explanation
Indices: 50365--50437 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
50355 TTTATTATAT
*
50365 TTCT-ATAAATTTAATTTTTTAAAAATAATC
1 TTCTAATAAA-TTAATTTTTTAAAAATAATA
*
50395 TTCTAATAAATTAATTTTTTTTAAAATAACTTA
1 TTCTAATAAATTAA-TTTTTTAAAAATAA--TA
50428 TTC-AATAAAT
1 TTCTAATAAAT
50438 GAAGTGAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
30 8 0.22
31 18 0.49
32 7 0.19
33 4 0.11
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (30 bp):
TTCTAATAAATTAATTTTTTAAAAATAATA
Found at i:53508 original size:18 final size:18
Alignment explanation
Indices: 53487--53522 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
53477 GGGGGTTTTG
*
53487 GTAAAATGAGAGTAAATA
1 GTAAAAAGAGAGTAAATA
*
53505 GTAAAAAGAGATTAAATA
1 GTAAAAAGAGAGTAAATA
53523 AATAAAAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.22
Consensus pattern (18 bp):
GTAAAAAGAGAGTAAATA
Found at i:59645 original size:10 final size:10
Alignment explanation
Indices: 59630--59705 Score: 54
Period size: 10 Copynumber: 7.7 Consensus size: 10
59620 CATTTAATAA
59630 ATAAACGAAC
1 ATAAACGAAC
59640 ATAAACGAAC
1 ATAAACGAAC
59650 ----ACGAAC
1 ATAAACGAAC
59656 ATAAACGAAC
1 ATAAACGAAC
** *
59666 ACGAAC-ATAA
1 ATAAACGA-AC
59676 ATGAACACGGAAC
1 AT-AA-AC-GAAC
59689 ATAAACGAAC
1 ATAAACGAAC
59699 ATAAACG
1 ATAAACG
59706 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 18
0.68 0.08 0.24
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 33 0.65
11 3 0.06
12 4 0.08
13 3 0.06
14 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.13, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:59655 original size:16 final size:16
Alignment explanation
Indices: 59634--59699 Score: 114
Period size: 16 Copynumber: 4.1 Consensus size: 16
59624 TAATAAATAA
59634 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
59650 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
59666 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
59682 ACGGAACATAAACGAAC
1 AC-GAACATAAACGAAC
59699 A
1 A
59700 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
16 33 0.70
17 14 0.30
ACGTcount: A:0.56, C:0.23, G:0.14, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:60452 original size:24 final size:25
Alignment explanation
Indices: 60425--60479 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 25
60415 GATTGTGTTA
*
60425 AACATAAAT-GAATGAACATAAACG
1 AACATAAATCGAACGAACATAAACG
60449 AACAT-AATCGAACGAACATAAACG
1 AACATAAATCGAACGAACATAAACG
60473 AACATAA
1 AACATAA
60480 CCGAACGTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 3 0.11
24 24 0.86
25 1 0.04
ACGTcount: A:0.58, C:0.16, G:0.11, T:0.15
Consensus pattern (25 bp):
AACATAAATCGAACGAACATAAACG
Found at i:60453 original size:10 final size:10
Alignment explanation
Indices: 60438--60485 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
60428 ATAAATGAAT
60438 GAACATAAAC
1 GAACATAAAC
60448 GAACATAATCGAAC
1 GAACAT-A---AAC
60462 GAACATAAAC
1 GAACATAAAC
*
60472 GAACATAACC
1 GAACATAAAC
60482 GAAC
1 GAAC
60486 GTTCACGAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:60462 original size:14 final size:14
Alignment explanation
Indices: 60445--60475 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
60435 AATGAACATA
*
60445 AACGAACATAATCG
1 AACGAACATAAACG
60459 AACGAACATAAACG
1 AACGAACATAAACG
60473 AAC
1 AAC
60476 ATAACCGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.23, G:0.13, T:0.10
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:60484 original size:24 final size:24
Alignment explanation
Indices: 60438--60486 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
60428 ATAAATGAAT
*
60438 GAACATAAACGAACATAATCGAAC
1 GAACATAAACGAACATAACCGAAC
60462 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
60486 G
1 G
60487 TTCACGAACG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.22, G:0.14, T:0.10
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:61611 original size:18 final size:19
Alignment explanation
Indices: 61579--61614 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
61569 CAAGTCAATC
*
61579 TTTGATTTTTGAAAACTAT
1 TTTGATTTTTAAAAACTAT
61598 TTTGA-TTTTAAAAACTA
1 TTTGATTTTTAAAAACTA
61615 GGAACGAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.50
Consensus pattern (19 bp):
TTTGATTTTTAAAAACTAT
Found at i:62833 original size:37 final size:37
Alignment explanation
Indices: 62764--62905 Score: 130
Period size: 37 Copynumber: 3.8 Consensus size: 37
62754 AATCAAAGTG
*
62764 TTGTCTCGCTAGAGACAATTTTTTTCTTAAAAACAAATT
1 TTGTCTCGCTAGAGAC-A-TTTTTTCTTAAAAAAAAATT
* *
62803 TTGTCTCGCTAGAGTCATTTTTTCTTAAAAAAACAAGT
1 TTGTCTCGCTAGAGACATTTTTTCTTAAAAAAA-AATT
* * * *
62841 TT-TCTCACTTA-AGACA-GTTTTCTTTAAAATAAATT
1 TTGTCTCGC-TAGAGACATTTTTTCTTAAAAAAAAATT
* *
62876 TTGTCTCGCTTA-AGACAATTTTTCTCAAAA
1 TTGTCTCGC-TAGAGACATTTTTTCTTAAAA
62906 CACAAGTTTT
Statistics
Matches: 86, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
35 5 0.06
36 25 0.29
37 33 0.38
38 8 0.09
39 15 0.17
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (37 bp):
TTGTCTCGCTAGAGACATTTTTTCTTAAAAAAAAATT
Found at i:62888 original size:36 final size:36
Alignment explanation
Indices: 62785--62897 Score: 113
Period size: 36 Copynumber: 3.1 Consensus size: 36
62775 GAGACAATTT
* * *
62785 TTTTCTTAAAAACAAATTTTGTCTCGC-TAGAGTCATT
1 TTTTCTTAAAAAAAAATTTTGTCTCGCTTA-AGACA-A
* * *
62822 TTTTCTTAAAAAAACAAGTTT-TCTCACTTAAGACAG
1 TTTTCTTAAAAAAA-AATTTTGTCTCGCTTAAGACAA
* *
62858 TTTTCTTTAAAATAAATTTTGTCTCGCTTAAGACAA
1 TTTTCTTAAAAAAAAATTTTGTCTCGCTTAAGACAA
62894 TTTT
1 TTTT
62898 TCTCAAAACA
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
35 5 0.08
36 29 0.46
37 22 0.35
38 7 0.11
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (36 bp):
TTTTCTTAAAAAAAAATTTTGTCTCGCTTAAGACAA
Found at i:63224 original size:63 final size:65
Alignment explanation
Indices: 62920--63237 Score: 432
Period size: 65 Copynumber: 5.0 Consensus size: 65
62910 AGTTTTTTTT
* * *
62920 TCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCTCTTGAAATGAATTTTGTCTC
1 TCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTAAAATGAATTTTGTCTA
* * * *
62985 TCTTGAGACAATTTCTCTTGAAACATCATCTGTGAGATC-ATTCCCTCAAAATGAA-TTTGTCTC
1 TCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTAAAATGAATTTTGTCT-
63048 A
65 A
* ** *
63049 -CTTGATACAGTTTCTCTTGAAAC-TCATCTTTGAGATTATTTCCCTTAAAATGAATTTTGTCTC
1 TCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTAAAATGAATTTTGTCTA
* * *
63112 TCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAAATCGTTTCCCTTTAAATGAATCTTGTCTA
1 TCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTAAAATGAATTTTGTCTA
* * *
63177 TCTTGAGACA-ATTCTCTTGAAA-ATCATCTTTGAGATCGTTTCCCTTTAAACGAATTTTGTC
1 TCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTAAAATGAATTTTGTC
63238 CCTCTTGAAA
Statistics
Matches: 223, Mismatches: 25, Indels: 12
0.86 0.10 0.05
Matches are distributed among these distances:
62 12 0.05
63 78 0.35
64 52 0.23
65 81 0.36
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (65 bp):
TCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTAAAATGAATTTTGTCTA
Found at i:63244 original size:63 final size:65
Alignment explanation
Indices: 62920--63245 Score: 455
Period size: 63 Copynumber: 5.1 Consensus size: 65
62910 AGTTTTTTTT
* *
62920 TCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCTCTTGAAATGAATTTTGTCTC
1 TCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTAAAATGAATTTTGTCTC
* * * *
62985 TCTTGAGACAATTTCTCTTGAAACATCATCTGTGAGATC-ATTCCCTCAAAATGAA-TTTGTCTC
1 TCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTAAAATGAATTTTGTCTC
* * **
63048 ACTTGATACAGTTTCTCTTGAAAC-TCATCTTTGAGATTATTTCCCTTAAAATGAATTTTGTCTC
1 TCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTAAAATGAATTTTGTCTC
* * * *
63112 TCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAAATCGTTTCCCTTTAAATGAATCTTGTCTA
1 TCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTAAAATGAATTTTGTCTC
* * * *
63177 TCTTGAGACA-ATTCTCTTGAAA-ATCATCTTTGAGATCGTTTCCCTTTAAACGAATTTTGTCCC
1 TCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTAAAATGAATTTTGTCTC
63240 TCTTGA
1 TCTTGA
63246 AACATAATCT
Statistics
Matches: 231, Mismatches: 27, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
62 12 0.05
63 85 0.37
64 53 0.23
65 81 0.35
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (65 bp):
TCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTAAAATGAATTTTGTCTC
Found at i:63581 original size:131 final size:132
Alignment explanation
Indices: 63281--63638 Score: 359
Period size: 131 Copynumber: 2.7 Consensus size: 132
63271 TTGAAACATT
*** * * *
63281 ATCCCTAAAGATGGCCAGTCATCCTCATCGCGTAGGAATCATGTCATCCACTGACCAGATCTCCT
1 ATCCCTAAAGATGATAAGCCATCCTCATCACGTAGGAAT-ATGTCATCCACCGACCAGATCTCCT
** * *
63346 CATCACGTAGGAGTTGCGTCACCCTTAGATAACCAGCCGTCCTCATCACATAGGAACAGGTTATC
65 CATCACGTAGGAGCCGCGTCACCCTTAGATAACCAGCCATCCTCATCACATAGAAACAGGTTATC
63411 ATC
130 ATC
* ** * * *
63414 ATCCCTTAAA-ATGGCTAA-CCATTTTCATCACATAGGAACTGTGTCATCCACCAACCAGATCTC
1 ATCCC-TAAAGAT-GATAAGCCATCCTCATCACGTAGGAA-TATGTCATCCACCGACCAGATCTC
** * **
63477 CTCATCACGTAGG-GCCGCGTCA-CCTTAGATAACCA-TTATCCTTATCGTATAGAAATC-GTGT
63 CTCATCACGTAGGAGCCGCGTCACCCTTAGATAACCAGCCATCCTCATCACATAGAAA-CAG-GT
63538 TATCATC
126 TATCATC
* * *
63545 ATCCCTAAAGATGATAAGCCATCCTCATCATGTAGGAAATATGTTATCCATCGACCAGATCTCCT
1 ATCCCTAAAGATGATAAGCCATCCTCATCACGTAGG-AATATGTCATCCACCGACCAGATCTCCT
* * * *
63610 CATCACATAGGAGACGTGTCACCCGTAGA
65 CATCACGTAGGAGCCGCGTCACCCTTAGA
63639 CGACCAAAAC
Statistics
Matches: 182, Mismatches: 33, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
130 22 0.12
131 76 0.42
132 16 0.09
133 61 0.34
134 7 0.04
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (132 bp):
ATCCCTAAAGATGATAAGCCATCCTCATCACGTAGGAATATGTCATCCACCGACCAGATCTCCTC
ATCACGTAGGAGCCGCGTCACCCTTAGATAACCAGCCATCCTCATCACATAGAAACAGGTTATCA
TC
Found at i:63825 original size:3 final size:3
Alignment explanation
Indices: 63817--63845 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
63807 GTCTTAAAAA
63817 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
63846 CATATTTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Done.