Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009074.1 Hibiscus syriacus cultivar Beakdansim tig00112507_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: 2143704
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 11
Found at i:5294 original size:47 final size:48
Alignment explanation
Indices: 5210--5305 Score: 158
Period size: 47 Copynumber: 2.0 Consensus size: 48
5200 TATTATTGTG
*
5210 AATAAAGTGTTGGTAAAAATGTGAATTGAATTGATGGATTTAATATTT
1 AATAAAGTGTTGGTAAAAAGGTGAATTGAATTGATGGATTTAATATTT
* *
5258 AATAAAGTGTTGG-AAAAAGGTGAATTTAATTTATGGATTTAATATTT
1 AATAAAGTGTTGGTAAAAAGGTGAATTGAATTGATGGATTTAATATTT
5305 A
1 A
5306 TAATAAATTC
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 32 0.71
48 13 0.29
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.40
Consensus pattern (48 bp):
AATAAAGTGTTGGTAAAAAGGTGAATTGAATTGATGGATTTAATATTT
Found at i:5351 original size:17 final size:17
Alignment explanation
Indices: 5329--5363 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5319 TTTTTTTTAC
5329 TATTTTAAATTTAAATA
1 TATTTTAAATTTAAATA
5346 TATTTTAAATTTAAATA
1 TATTTTAAATTTAAATA
5363 T
1 T
5364 TAGTATGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATTTTAAATTTAAATA
Found at i:20221 original size:22 final size:22
Alignment explanation
Indices: 20193--20252 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
20183 AGTGCCTAAT
*
20193 AATAACAAAACCGATATAAAAA
1 AATAACAAAACCGATAGAAAAA
*
20215 AATAACAAAACCGGTAGAAAAA
1 AATAACAAAACCGATAGAAAAA
20237 AATAACAAAACCGATA
1 AATAACAAAACCGATA
20253 AAGCACCCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.65, C:0.15, G:0.08, T:0.12
Consensus pattern (22 bp):
AATAACAAAACCGATAGAAAAA
Found at i:20710 original size:2 final size:2
Alignment explanation
Indices: 20703--20733 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20693 AATTAGTTAT
20703 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20734 GTGTGTGTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20866 original size:16 final size:16
Alignment explanation
Indices: 20827--20878 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
20817 TAATATATGC
20827 ATATATA-TTAATATTAT
1 ATATATACTT-ATA-TAT
*
20844 ATATATACTTATGTAT
1 ATATATACTTATATAT
*
20860 ATTTATACTTATATAT
1 ATATATACTTATATAT
20876 ATA
1 ATA
20879 AAAGTGTACA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 19 0.63
17 9 0.30
18 2 0.07
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATACTTATATAT
Found at i:20886 original size:28 final size:27
Alignment explanation
Indices: 20830--20886 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 27
20820 TATATGCATA
**
20830 TATATTAATATTATATATATACTTATG
1 TATATTAATATTATATATATACAAATG
*
20857 TATATTTATACTTATATATATA-AAAGTG
1 TATATTAATA-TTATATATATACAAA-TG
20885 TA
1 TA
20887 CACACACATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (27 bp):
TATATTAATATTATATATATACAAATG
Found at i:20988 original size:2 final size:2
Alignment explanation
Indices: 20941--20970 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
20931 ATAAGTTTAT
20941 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20971 CAGAAGTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22865 original size:22 final size:22
Alignment explanation
Indices: 22839--22880 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
22829 GATTTATTAA
22839 ATAGCTATATAAATATTAGTTG
1 ATAGCTATATAAATATTAGTTG
*
22861 ATAGCTATATAAATGTTAGT
1 ATAGCTATATAAATATTAGT
22881 ATTTTTAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.40
Consensus pattern (22 bp):
ATAGCTATATAAATATTAGTTG
Found at i:28252 original size:16 final size:16
Alignment explanation
Indices: 28233--28279 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
28223 ATAAGTAAGT
28233 TAAATATCAAGTCGGG
1 TAAATATCAAGTCGGG
* *
28249 TAAATATCAAATCAGG
1 TAAATATCAAGTCGGG
* *
28265 TCAATAACAAGTCGG
1 TAAATATCAAGTCGG
28280 ATTATTTACA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (16 bp):
TAAATATCAAGTCGGG
Found at i:28638 original size:2 final size:2
Alignment explanation
Indices: 28631--28700 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
28621 CTTAAATTTC
28631 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
28673 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
28701 TCACACCTCA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31280 original size:12 final size:12
Alignment explanation
Indices: 31263--31288 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31253 TTCATGCTTG
31263 ACCTATGATCAT
1 ACCTATGATCAT
31275 ACCTATGATCAT
1 ACCTATGATCAT
31287 AC
1 AC
31289 TTGAGAGGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.31
Consensus pattern (12 bp):
ACCTATGATCAT
Found at i:35349 original size:18 final size:18
Alignment explanation
Indices: 35328--35384 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
35318 TCCATAAGAC
35328 CTTATAATACCATTAATG
1 CTTATAATACCATTAATG
* *
35346 CTTATTATA--ATATAAAG
1 CTTATAATACCAT-TAATG
*
35363 -TCATAATACCATTAATG
1 CTTATAATACCATTAATG
35380 CTTAT
1 CTTAT
35385 TATAGAATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
16 8 0.28
17 8 0.28
18 13 0.45
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.40
Consensus pattern (18 bp):
CTTATAATACCATTAATG
Found at i:44981 original size:25 final size:24
Alignment explanation
Indices: 44945--44991 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 24
44935 CTCTTTTATT
44945 TTATTTTCAAGTTTTCGGTTTTTACA
1 TTATTTTCAAGTTTT--GTTTTTACA
44971 TTATTTT-AAGTTTTGTTTTTA
1 TTATTTTCAAGTTTTGTTTTTA
44992 AATATGCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
25 7 0.33
26 7 0.33
ACGTcount: A:0.19, C:0.06, G:0.11, T:0.64
Consensus pattern (24 bp):
TTATTTTCAAGTTTTGTTTTTACA
Found at i:45157 original size:18 final size:19
Alignment explanation
Indices: 45131--45167 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
45121 CTGCGTTTAT
*
45131 TTTTTAAAATCAAA-ATAG
1 TTTTCAAAATCAAAGATAG
45149 TTTTCAAAATCAAAGATAG
1 TTTTCAAAATCAAAGATAG
45168 ACTTTGGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (19 bp):
TTTTCAAAATCAAAGATAG
Found at i:46081 original size:27 final size:28
Alignment explanation
Indices: 46051--46104 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
46041 AAAAGTAAAT
*
46051 AGTTGAAAAAAA-GAAAAGGTTGAAAAA
1 AGTTGAAAAAAAGGAAAAGGTGGAAAAA
*
46078 AGTTGAAAAAAAGGAAAATGTGGAAAA
1 AGTTGAAAAAAAGGAAAAGGTGGAAAA
46105 TGTTAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.15
Consensus pattern (28 bp):
AGTTGAAAAAAAGGAAAAGGTGGAAAAA
Found at i:46095 original size:17 final size:18
Alignment explanation
Indices: 46040--46078 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
46030 AAAAAGTCTG
46040 AAAAAGTAAATA-GTTGAA
1 AAAAAG-AAATAGGTTGAA
46058 AAAAAGAAA-AGGTTGAA
1 AAAAAGAAATAGGTTGAA
46075 AAAA
1 AAAA
46079 GTTGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 1 0.05
17 13 0.65
18 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (18 bp):
AAAAAGAAATAGGTTGAA
Found at i:46113 original size:27 final size:27
Alignment explanation
Indices: 46047--46113 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
46037 CTGAAAAAGT
46047 AAATAGTTGAAAAAAAGAAAAGGTTGAA
1 AAAT-GTTGAAAAAAAGAAAAGGTTGAA
* * *
46075 AAAAGTTGAAAAAAAGGAAAATG-TGGA
1 AAATGTTGAAAAAAA-GAAAAGGTTGAA
46102 AAATGTT-AAAAA
1 AAATGTTGAAAAA
46114 TTGAAAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
26 5 0.15
27 20 0.59
28 9 0.26
ACGTcount: A:0.61, C:0.00, G:0.21, T:0.18
Consensus pattern (27 bp):
AAATGTTGAAAAAAAGAAAAGGTTGAA
Found at i:46224 original size:2 final size:2
Alignment explanation
Indices: 46219--46268 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
46209 AAAAAAGATA
46219 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
46261 AT AT -T AT A
1 AT AT AT AT A
46269 ACAATGTAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48587 original size:86 final size:86
Alignment explanation
Indices: 48348--48633 Score: 400
Period size: 84 Copynumber: 3.4 Consensus size: 86
48338 ATGTGTCATC
* * * * *
48348 GAGCTGAATGAAATCGAACTCGACAG--TTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
1 GAGCTGAGTGTAATCGAACTCGAAAGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
*
48411 CTGTAAATTTGATGTGCCTTT
66 CTGTAAATTGGATGTGCCTTT
* * * *
48432 GAGCTGAGTGTAATCGAACTCGAAGGTC-TTGGAT-ACATATAACCCTTCTCGCCTTGAGTTATG
1 GAGCTGAGTGTAATCGAACTCGAAAGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
*
48495 CTGTAAATTGGATATGCCTTT
66 CTGTAAATTGGATGTGCCTTT
* * *
48516 AAGCAGAGTGTAATCGAACTCGAAAGTCTTTTGTTGACAGATAACCCTTATCGCCTTGAGTTATG
1 GAGCTGAGTGTAATCGAACTCGAAAGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
48581 CTGTAAATTGGATGTGCCTTT
66 CTGTAAATTGGATGTGCCTTT
* *
48602 GAGCTGAGTGTAATCGAACTAGAAGGTCTTTT
1 GAGCTGAGTGTAATCGAACTCGAAAGTCTTTT
48634 ATGACTTTAA
Statistics
Matches: 175, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
84 92 0.53
85 8 0.05
86 75 0.43
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (86 bp):
GAGCTGAGTGTAATCGAACTCGAAAGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
CTGTAAATTGGATGTGCCTTT
Found at i:48768 original size:66 final size:66
Alignment explanation
Indices: 48662--48819 Score: 244
Period size: 66 Copynumber: 2.4 Consensus size: 66
48652 GTTAGGCACA
* * * * *
48662 ATATCCTTCATCGTAAAGTTAAAATTGTGGATGGCTCATTCGTTGCGAAGTTGAGCTTTAAATTG
1 ATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTG
48727 G
66 G
* * *
48728 ATATCTTTCATCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTCAGTTTTGAATTG
1 ATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTG
48793 G
66 G
48794 ATATCCTTCATCGTGAAGTTGAAATC
1 ATATCCTTCATCGTGAAGTTGAAATC
48820 CAAGGGTTGC
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 83 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (66 bp):
ATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTG
G
Found at i:48945 original size:121 final size:121
Alignment explanation
Indices: 48727--49060 Score: 470
Period size: 121 Copynumber: 2.8 Consensus size: 121
48717 CTTTAAATTG
* * * * * *
48727 GATATCTTTCATCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTCAGTTTTGAATT
1 GATATCCTTCATCGTGAAATTAAAATCATGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATT
* *
48792 GGATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTATGGGCAC
66 GGATATCCTTCGTCGTGAAGTTGAAATACAAGGGTTGCATTGCTGCTTATGGGCAC
* * * * *
48848 GATATCCTTCGTTGTGAAATTAATATTATGGATGGCTCCTTCGTTGTGAAGTTGAGCTTTGAATT
1 GATATCCTTCATCGTGAAATTAAAATCATGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATT
* * * *
48913 GGATATTCTTTGTCGTGAAGTTGAAATACAAGGGTTGTATTGCTGCTTGTGGGCAC
66 GGATATCCTTCGTCGTGAAGTTGAAATACAAGGGTTGCATTGCTGCTTATGGGCAC
* * * *
48969 GATATCCTTCATCGTGAAGTTAAAATCGTGGATGGCTCATTTGTTGTAAAGTTGAGCTTTGAATT
1 GATATCCTTCATCGTGAAATTAAAATCATGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATT
*
49034 GGATATCCTTCGTCGTGAAATTGAAAT
66 GGATATCCTTCGTCGTGAAGTTGAAAT
49061 CGTGGATGGC
Statistics
Matches: 184, Mismatches: 29, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
121 184 1.00
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (121 bp):
GATATCCTTCATCGTGAAATTAAAATCATGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATT
GGATATCCTTCGTCGTGAAGTTGAAATACAAGGGTTGCATTGCTGCTTATGGGCAC
Found at i:49041 original size:187 final size:187
Alignment explanation
Indices: 48848--49248 Score: 606
Period size: 187 Copynumber: 2.1 Consensus size: 187
48838 TTATGGGCAC
* * *
48848 GATATCCTTCGTTGTGAAATT-AATATTATGGATGGCTCCTTCGTTGTGAAGTTGAGCTTTGAAT
1 GATATCCTTCGTCGTGAAATTGAA-ATCATGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAAT
* ** *
48912 TGGATATTCTTTGTCGTGAAGTTGAAATACAAGGGTTGTATTGCTGCTTGTGGGCACGATATCCT
65 TGGATATCCTTCATCGTGAAGTTGAAATACAAGGGTTGCATTGCTGCTTGTGGGCACGATATCCT
* * *
48977 TCATCGTGAAGTTAAAATCGTGGATGGCTCATTTGTTGTAAAGTTGAGCTTTGAATTG
130 TCATCGTGAAGTTAAAATCATGGATGGCTCATTCGTTGTAAAGTTGAGCTTTGAATTA
* *
49035 GATATCCTTCGTCGTGAAATTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGTGCTTTGAATT
1 GATATCCTTCGTCGTGAAATTGAAATCATGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATT
* * *
49100 GGATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGCATTGCTTCTTGTGGGCACGATATTCTT
66 GGATATCCTTCATCGTGAAGTTGAAATACAAGGGTTGCATTGCTGCTTGTGGGCACGATATCCTT
* * *
49165 CATCGTTAAGTTGAAATCATGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTA
131 CATCGTGAAGTTAAAATCATGGATGGCTCATTCGTTGTAAAGTTGAGCTTTGAATTA
* *
49222 GATATCCTTTGTCGTGAAGTTGAAATC
1 GATATCCTTCGTCGTGAAATTGAAATC
49249 CAAGGATTGT
Statistics
Matches: 193, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
187 191 0.99
188 2 0.01
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.38
Consensus pattern (187 bp):
GATATCCTTCGTCGTGAAATTGAAATCATGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATT
GGATATCCTTCATCGTGAAGTTGAAATACAAGGGTTGCATTGCTGCTTGTGGGCACGATATCCTT
CATCGTGAAGTTAAAATCATGGATGGCTCATTCGTTGTAAAGTTGAGCTTTGAATTA
Found at i:49050 original size:66 final size:66
Alignment explanation
Indices: 48969--49127 Score: 264
Period size: 66 Copynumber: 2.4 Consensus size: 66
48959 TTGTGGGCAC
* *
48969 GATATCCTTCATCGTGAAGTTAAAATCGTGGATGGCTCATTTGTTGTAAAGTTGAGCTTTGAATT
1 GATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTAAAGTTGAGCTTTGAATT
49034 G
66 G
* * * *
49035 GATATCCTTCGTCGTGAAATTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGTGCTTTGAATT
1 GATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTAAAGTTGAGCTTTGAATT
49100 G
66 G
49101 GATATCCTTCATCGTGAAGTTGAAATC
1 GATATCCTTCATCGTGAAGTTGAAATC
49128 CAAGGGTTGC
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 85 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.37
Consensus pattern (66 bp):
GATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTAAAGTTGAGCTTTGAATT
G
Found at i:49220 original size:308 final size:308
Alignment explanation
Indices: 48656--49258 Score: 956
Period size: 308 Copynumber: 2.0 Consensus size: 308
48646 CGATTCGTTA
* *
48656 GGCACAATATCCTTCATCGTAAAGTTAAAATTGTGGATGGCTCATTCGTTGCGAAGTTGAGCTTT
1 GGCACAATATCCTTCATCGTAAAGTTAAAATCGTGGATGGCTCATTCGTTGCAAAGTTGAGCTTT
* * *
48721 AAATTGGATATCTTTCATCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTCAGTTT
66 AAATTGGATATCCTTCATCGTGAAATTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTCAGCTT
48786 TGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTATGGGCACGAT
131 TGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTATGGGCACGAT
* * * * *
48851 ATCCTTCGTTGTGAAATTAATATTATGGATGGCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGGA
196 ATCCTTCATCGTGAAATTAATATCATGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTAGA
* *
48916 TATTCTTTGTCGTGAAGTTGAAATACAAGGGTTGTATTGCTGCTTGTG
261 TATCCTTTGTCGTGAAGTTGAAATACAAGGATTGTATTGCTGCTTGTG
* * * *
48964 GGCACGATATCCTTCATCGTGAAGTTAAAATCGTGGATGGCTCATTTGTTGTAAAGTTGAGCTTT
1 GGCACAATATCCTTCATCGTAAAGTTAAAATCGTGGATGGCTCATTCGTTGCAAAGTTGAGCTTT
* * **
49029 GAATTGGATATCCTTCGTCGTGAAATTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGTGCTT
66 AAATTGGATATCCTTCATCGTGAAATTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTCAGCTT
* *
49094 TGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGCATTGCTTCTTGTGGGCACGAT
131 TGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTATGGGCACGAT
* * *
49159 ATTCTTCATCGTTAAGTTGAA-ATCATGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTAG
196 ATCCTTCATCGTGAAATT-AATATCATGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTAG
*
49223 ATATCCTTTGTCGTGAAGTTGAAATCCAAGGATTGT
260 ATATCCTTTGTCGTGAAGTTGAAATACAAGGATTGT
49259 TTCACCAAAT
Statistics
Matches: 268, Mismatches: 26, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
308 266 0.99
309 2 0.01
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (308 bp):
GGCACAATATCCTTCATCGTAAAGTTAAAATCGTGGATGGCTCATTCGTTGCAAAGTTGAGCTTT
AAATTGGATATCCTTCATCGTGAAATTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTCAGCTT
TGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTATGGGCACGAT
ATCCTTCATCGTGAAATTAATATCATGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTAGA
TATCCTTTGTCGTGAAGTTGAAATACAAGGATTGTATTGCTGCTTGTG
Found at i:49249 original size:121 final size:121
Alignment explanation
Indices: 49035--49253 Score: 357
Period size: 121 Copynumber: 1.8 Consensus size: 121
49025 CTTTGAATTG
* * *
49035 GATATCCTTCGTCGTGAAATTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGTGCTTTGAATT
1 GATATCCTTCATCGTGAAATTGAAATCATGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATT
*
49100 GGATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGCATTGCTTCTTGTGGGCAC
66 AGATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGCATTGCTTCTTGTGGGCAC
* * *
49156 GATATTCTTCATCGTTAAGTTGAAATCATGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATT
1 GATATCCTTCATCGTGAAATTGAAATCATGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATT
**
49221 AGATATCCTTTGTCGTGAAGTTGAAATCCAAGG
66 AGATATCCTTCATCGTGAAGTTGAAATCCAAGG
49254 ATTGTTTCAC
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
121 89 1.00
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (121 bp):
GATATCCTTCATCGTGAAATTGAAATCATGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATT
AGATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGCATTGCTTCTTGTGGGCAC
Found at i:49354 original size:65 final size:63
Alignment explanation
Indices: 49213--49379 Score: 214
Period size: 65 Copynumber: 2.7 Consensus size: 63
49203 GAAGTTGAGC
* * * *
49213 TTTGAATTAGATATCCTTTGTCGTGAAGTTGAAATCCAA---GGATTGTTTCACCAAATTGGT
1 TTTGAGTTAGATATCCTTCGTCGTGAAGTTGAAATCCAATCTGGATAGTTTCACCAAATTAGT
* * *
49273 TTTGAGTTGGACATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCACCAAATTAGT
1 TTTGAGTTAGATATCCTTCGTCGTGAAGTTGAAATCCAATCTGGA-T-AGTTTCACCAAATTAGT
* *
49338 TTTGAGTTTGATATCCTTCGTTGTGAAGTTGAAATCCAATCT
1 TTTGAGTTAGATATCCTTCGTCGTGAAGTTGAAATCCAATCT
49380 CGTATAAGTT
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
60 35 0.38
63 2 0.02
64 1 0.01
65 54 0.59
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (63 bp):
TTTGAGTTAGATATCCTTCGTCGTGAAGTTGAAATCCAATCTGGATAGTTTCACCAAATTAGT
Found at i:49486 original size:64 final size:64
Alignment explanation
Indices: 49400--50014 Score: 973
Period size: 64 Copynumber: 9.6 Consensus size: 64
49390 GCATTGTTTC
* * * *
49400 GAGTCCAATATACTTCATTGTGAAGTTGAAATTGACTCTGATTGAAAATGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* * *
49464 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACAGGAAAGTTATTTGTT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* * * * *
49528 GAGTTCAATATCCTTTGCTGTGAAGTTGAAATTTACTCTAAATGAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* * *
49592 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTAACTCTGAATGAAACTGGAAAGTTATTTGTT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* *
49656 GAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAACA-TTATTTGTT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAA-AGTTGTTTGTT
*
49720 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGCTTT-TT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTG-TTTGTT
* *
49784 GAGTCCAATATCTTTCGTTGTGTAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
49848 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* * * *
49912 GAGTCCAATAACCTTTGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAACGTTGTTTGTT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
*
49976 GAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGACTCT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCT
50015 AAAAGCTGCA
Statistics
Matches: 509, Mismatches: 38, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
63 4 0.01
64 501 0.98
65 4 0.01
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (64 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
Found at i:52583 original size:48 final size:50
Alignment explanation
Indices: 52509--52636 Score: 183
Period size: 48 Copynumber: 2.6 Consensus size: 50
52499 TTGAAATGAG
* *
52509 GTCCTACCCCACATCATATCTACCCCACATCATATCTACCCA-ACATCA-TA
1 GTCCTACCCAACATCATATCTACCCCACATCATATCTACCCATA-AT-AGAA
52559 -T-CTACCCAACATCATATCTACCCCACATCATATCTACCCATAATAGAA
1 GTCCTACCCAACATCATATCTACCCCACATCATATCTACCCATAATAGAA
*
52607 GTCCTACCCAACATCATATCTACCCAACAT
1 GTCCTACCCAACATCATATCTACCCCACAT
52637 GCTTATTATT
Statistics
Matches: 71, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
47 1 0.01
48 41 0.58
49 3 0.04
50 26 0.37
ACGTcount: A:0.34, C:0.39, G:0.02, T:0.24
Consensus pattern (50 bp):
GTCCTACCCAACATCATATCTACCCCACATCATATCTACCCATAATAGAA
Found at i:52631 original size:16 final size:16
Alignment explanation
Indices: 52512--52636 Score: 164
Period size: 16 Copynumber: 7.7 Consensus size: 16
52502 AAATGAGGTC
*
52512 CTACCCCACATCATAT
1 CTACCCAACATCATAT
*
52528 CTACCCCACATCATAT
1 CTACCCAACATCATAT
52544 CTACCCAACATCATAT
1 CTACCCAACATCATAT
52560 CTACCCAACATCATAT
1 CTACCCAACATCATAT
*
52576 CTACCCCACATCATAT
1 CTACCCAACATCATAT
*
52592 CTACCCATA-AT-AGAAGT
1 CTACCCA-ACATCA-TA-T
52609 CCTACCCAACATCATAT
1 -CTACCCAACATCATAT
52626 CTACCCAACAT
1 CTACCCAACAT
52637 GCTTATTATT
Statistics
Matches: 98, Mismatches: 5, Indels: 12
0.85 0.04 0.10
Matches are distributed among these distances:
15 1 0.01
16 82 0.84
17 4 0.04
18 10 0.10
19 1 0.01
ACGTcount: A:0.35, C:0.39, G:0.02, T:0.24
Consensus pattern (16 bp):
CTACCCAACATCATAT
Found at i:53874 original size:17 final size:17
Alignment explanation
Indices: 53842--53950 Score: 55
Period size: 16 Copynumber: 6.2 Consensus size: 17
53832 AAAAAGGAAA
53842 AAAAAGTAAAAAAATTTG
1 AAAAAGTAAAAAAA-TTG
*
53860 AAAAAGT-AAATAATTG
1 AAAAAGTAAAAAAATTG
*
53876 AAAAA--AAGAAAAGGTTG
1 AAAAAGTAA-AAAA-ATTG
* *
53893 AAAAAGTTGAAAAAAGTTA
1 AAAAAG-T-AAAAAAATTG
* * *
53912 AAAAAG-GAAAAAGTGG
1 AAAAAGTAAAAAAATTG
*
53928 AAAAGGTTAAAAAAAGTTG
1 AAAAAG-TAAAAAAA-TTG
53947 AAAA
1 AAAA
53951 GCGTTTTAAT
Statistics
Matches: 70, Mismatches: 11, Indels: 19
0.70 0.11 0.19
Matches are distributed among these distances:
15 1 0.01
16 23 0.33
17 13 0.19
18 12 0.17
19 15 0.21
20 4 0.06
21 2 0.03
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.17
Consensus pattern (17 bp):
AAAAAGTAAAAAAATTG
Found at i:53901 original size:9 final size:9
Alignment explanation
Indices: 53883--53950 Score: 59
Period size: 9 Copynumber: 7.6 Consensus size: 9
53873 TTGAAAAAAA
*
53883 GAAAAGGTT
1 GAAAAAGTT
53892 GAAAAAGTT
1 GAAAAAGTT
53901 GAAAAAAGTT
1 G-AAAAAGTT
*
53911 AAAAAAG--
1 GAAAAAGTT
*
53918 GAAAAAGTG
1 GAAAAAGTT
*
53927 GAAAAGGTT
1 GAAAAAGTT
*
53936 AAAAAAAGTT
1 -GAAAAAGTT
53946 GAAAA
1 GAAAA
53951 GCGTTTTAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
7 6 0.13
9 26 0.55
10 15 0.32
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (9 bp):
GAAAAAGTT
Found at i:53915 original size:35 final size:35
Alignment explanation
Indices: 53876--53950 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
53866 TAAATAATTG
* * *
53876 AAAAAAAGAAAAGGTTGAAAAAGTTGAAAAAAGTT
1 AAAAAAAGAAAAAGTGGAAAAAGTTAAAAAAAGTT
* *
53911 AAAAAAGGAAAAAGTGGAAAAGGTTAAAAAAAGTT
1 AAAAAAAGAAAAAGTGGAAAAAGTTAAAAAAAGTT
*
53946 GAAAA
1 AAAAA
53951 GCGTTTTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.15
Consensus pattern (35 bp):
AAAAAAAGAAAAAGTGGAAAAAGTTAAAAAAAGTT
Found at i:53943 original size:26 final size:26
Alignment explanation
Indices: 53892--53941 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
53882 AGAAAAGGTT
53892 GAAAAAGTTGAAAAAAGTTAAAAAAG
1 GAAAAAGTTGAAAAAAGTTAAAAAAG
* *
53918 GAAAAAG-TGGAAAAGGTTAAAAAA
1 GAAAAAGTTGAAAAAAGTTAAAAAA
53942 AGTTGAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.64, C:0.00, G:0.22, T:0.14
Consensus pattern (26 bp):
GAAAAAGTTGAAAAAAGTTAAAAAAG
Found at i:53967 original size:4 final size:4
Alignment explanation
Indices: 53958--53982 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
53948 AAAGCGTTTT
53958 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
53983 TAATGTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:54018 original size:2 final size:2
Alignment explanation
Indices: 54011--54053 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
54001 ATAAGAGAAA
54011 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
54053 A
1 A
54054 CAATGTAAAA
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:56725 original size:20 final size:19
Alignment explanation
Indices: 56702--56742 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
56692 GAATTTTGTT
* *
56702 TTCGCAACTCGATTTTAGAA
1 TTCGCAACGCGAATTTA-AA
56722 TTCGCAACGCGAATTTAAA
1 TTCGCAACGCGAATTTAAA
56741 TT
1 TT
56743 TAGCAAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (19 bp):
TTCGCAACGCGAATTTAAA
Found at i:56743 original size:60 final size:60
Alignment explanation
Indices: 56580--56748 Score: 144
Period size: 60 Copynumber: 2.8 Consensus size: 60
56570 AGTTTCCGAA
** * *
56580 TTCGCAACACAGAAGTT-GAATTCGCAACTCGAATTTGACAATTTCA-CAACTCAAATTTCCTT
1 TTCGCAACA-AGATTTTAGAATTCGCAACGCGAATTT-A-AATTT-AGCAACACAAATTTCCTT
** * * * * * * **
56642 TTCGCAACAAGATTTTCTAATTCGCAAAGTGAGTTTCAATTTTGCAACACGAATTTTGTT
1 TTCGCAACAAGATTTTAGAATTCGCAACGCGAATTTAAATTTAGCAACACAAATTTCCTT
**
56702 TTCGCAACTCGATTTTAGAATTCGCAACGCGAATTTAAATTTAGCAA
1 TTCGCAACAAGATTTTAGAATTCGCAACGCGAATTTAAATTTAGCAA
56749 ATCAATTTTT
Statistics
Matches: 83, Mismatches: 22, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
60 55 0.66
61 5 0.06
62 23 0.28
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.34
Consensus pattern (60 bp):
TTCGCAACAAGATTTTAGAATTCGCAACGCGAATTTAAATTTAGCAACACAAATTTCCTT
Found at i:56881 original size:22 final size:22
Alignment explanation
Indices: 56856--56904 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
56846 TCTCTCACTC
*
56856 TCTCCAGCGACATCTGTCCCCA
1 TCTCCAGCGACATCCGTCCCCA
*
56878 TCTCCAGCTACATCCGTCCCCA
1 TCTCCAGCGACATCCGTCCCCA
56900 TCTCC
1 TCTCC
56905 GGCAAGCCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.16, C:0.49, G:0.10, T:0.24
Consensus pattern (22 bp):
TCTCCAGCGACATCCGTCCCCA
Found at i:57289 original size:20 final size:20
Alignment explanation
Indices: 57266--57307 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
57256 AATTCGCAAC
*
57266 ATGAAAATAGCAACTCGAAA
1 ATGAAAATAGCAACACGAAA
* *
57286 ATGAAATTTGCAACACGAAA
1 ATGAAAATAGCAACACGAAA
57306 AT
1 AT
57308 CACAACTCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.52, C:0.14, G:0.14, T:0.19
Consensus pattern (20 bp):
ATGAAAATAGCAACACGAAA
Found at i:57299 original size:34 final size:34
Alignment explanation
Indices: 57255--57329 Score: 116
Period size: 34 Copynumber: 2.2 Consensus size: 34
57245 CAAGAAACTT
*
57255 AAATTCGCAACATGAAAAT-AGCAACTCGAAAATG
1 AAATTCGCAACACGAAAATCA-CAACTCGAAAATG
*
57289 AAATTTGCAACACGAAAATCACAACTCGAAAATG
1 AAATTCGCAACACGAAAATCACAACTCGAAAATG
57323 AAATTCG
1 AAATTCG
57330 AGTTGTGAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 36 0.97
35 1 0.03
ACGTcount: A:0.49, C:0.19, G:0.13, T:0.19
Consensus pattern (34 bp):
AAATTCGCAACACGAAAATCACAACTCGAAAATG
Found at i:57351 original size:20 final size:20
Alignment explanation
Indices: 57326--57442 Score: 106
Period size: 20 Copynumber: 6.2 Consensus size: 20
57316 GAAAATGAAA
*
57326 TTCGAGTTGTGAATTTCATT
1 TTCGAGTTGCGAATTTCATT
*
57346 TTCGAGTTGCGATTTTCA--
1 TTCGAGTTGCGAATTTCATT
57364 -T---GTTGCGAATTT-ATGT
1 TTCGAGTTGCGAATTTCAT-T
* * *
57380 TTCGAATTGCGAATTTAAGT
1 TTCGAGTTGCGAATTTCATT
*
57400 TTCGAATTGCGAA-TTCAATT
1 TTCGAGTTGCGAATTTC-ATT
57420 TTCGAGTTGCGAATTTCATT
1 TTCGAGTTGCGAATTTCATT
57440 TTC
1 TTC
57443 TTGGAATAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
13 1 0.01
14 10 0.13
17 2 0.03
19 2 0.03
20 60 0.76
21 4 0.05
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.45
Consensus pattern (20 bp):
TTCGAGTTGCGAATTTCATT
Found at i:59984 original size:31 final size:31
Alignment explanation
Indices: 59946--60225 Score: 472
Period size: 31 Copynumber: 9.0 Consensus size: 31
59936 AGGGTCGAGG
*
59946 GTTTACCTATGTTTTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
59977 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
60008 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
60039 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
60070 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
60101 GTTTACCTATGTTCTTCGGGACATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
60132 GTTTACCTATGTTATTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
60163 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * * * *
60194 GATTACTTAGGTTTTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
60225 G
1 G
60226 GTCCTTCGGG
Statistics
Matches: 238, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
31 237 1.00
32 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:61523 original size:42 final size:42
Alignment explanation
Indices: 61462--61666 Score: 218
Period size: 42 Copynumber: 5.0 Consensus size: 42
61452 CCCCACTTTT
* *
61462 TCATCGAGTCGATTCTCCACTTCGACATCGAGATCCATCACC
1 TCATCGAGCCGATTCTCCACTTCGACACCGAGATCCATCACC
*
61504 TCATCGAGCCGATTATCCACTTCGACACCGAGATCCATCACC
1 TCATCGAGCCGATTCTCCACTTCGACACCGAGATCCATCACC
*** * *
61546 TCATCGAGTTAATTCTCCACTTAGACACCGAGATCCATCATC
1 TCATCGAGCCGATTCTCCACTTCGACACCGAGATCCATCACC
* * * * ** *
61588 TCATCTAACCGATTCTACACCTAAACACTGAGATCCATCA-C
1 TCATCGAGCCGATTCTCCACTTCGACACCGAGATCCATCACC
* * * *
61629 T--TCTAGCCGACTCTACACCTCGACACCGAGATCCATCA
1 TCATCGAGCCGATTCTCCACTTCGACACCGAGATCCATCA
61667 TCTATTACAT
Statistics
Matches: 140, Mismatches: 23, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
39 32 0.23
41 2 0.01
42 106 0.76
ACGTcount: A:0.28, C:0.36, G:0.12, T:0.24
Consensus pattern (42 bp):
TCATCGAGCCGATTCTCCACTTCGACACCGAGATCCATCACC
Found at i:61660 original size:39 final size:41
Alignment explanation
Indices: 61567--61671 Score: 142
Period size: 39 Copynumber: 2.6 Consensus size: 41
61557 ATTCTCCACT
*
61567 TAGACACCGAGATCCATCATCTCATCTAACCGATTCTACACC
1 TAGACACCGAGATCCATCATCT-ATCTAACCGACTCTACACC
* * *
61609 TAAACACTGAGATCCATCA-CT-TCTAGCCGACTCTACACC
1 TAGACACCGAGATCCATCATCTATCTAACCGACTCTACACC
*
61648 TCGACACCGAGATCCATCATCTAT
1 TAGACACCGAGATCCATCATCTAT
61672 TACATCACAT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
39 32 0.59
40 2 0.04
41 3 0.06
42 17 0.31
ACGTcount: A:0.30, C:0.35, G:0.10, T:0.24
Consensus pattern (41 bp):
TAGACACCGAGATCCATCATCTATCTAACCGACTCTACACC
Found at i:61793 original size:21 final size:21
Alignment explanation
Indices: 61769--61917 Score: 122
Period size: 21 Copynumber: 7.1 Consensus size: 21
61759 ACCTCCATGG
* *
61769 GATGAGTTGGGTGCTTTACAT
1 GATGAGGTAGGTGCTTTACAT
* *
61790 GATGAGGTCA-GTGTTTTACGT
1 GATGAGGT-AGGTGCTTTACAT
* * *
61811 GATGAGGTCGGTACTTTACGT
1 GATGAGGTAGGTGCTTTACAT
** * *
61832 GATGATAATA-GTGGTTTACGT
1 GATGA-GGTAGGTGCTTTACAT
* *
61853 GATGAGGTAGCTACTTTACAT
1 GATGAGGTAGGTGCTTTACAT
*
61874 GGTGAGGTAGGTGCTTTACAT
1 GATGAGGTAGGTGCTTTACAT
* *
61895 GATGAAGTAGGTGCTCTACAT
1 GATGAGGTAGGTGCTTTACAT
61916 GA
1 GA
61918 GATTGTTTCA
Statistics
Matches: 100, Mismatches: 24, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
20 2 0.02
21 97 0.97
22 1 0.01
ACGTcount: A:0.23, C:0.11, G:0.32, T:0.34
Consensus pattern (21 bp):
GATGAGGTAGGTGCTTTACAT
Found at i:61828 original size:42 final size:41
Alignment explanation
Indices: 61782--61917 Score: 137
Period size: 42 Copynumber: 3.2 Consensus size: 41
61772 GAGTTGGGTG
* *
61782 CTTTACATGATGAGGTCAGTGTTTTACGTGATGAGGTCGGTA
1 CTTTACATGATGAGGT-AGTGCTTTACGTGATGAGGTAGGTA
* ** * *
61824 CTTTACGTGATGATAATAGTGGTTTACGTGATGAGGTAGCTA
1 CTTTACATGATGA-GGTAGTGCTTTACGTGATGAGGTAGGTA
* * * *
61866 CTTTACATGGTGAGGTAGGTGCTTTACATGATGAAGTAGGTG
1 CTTTACATGATGAGGTA-GTGCTTTACGTGATGAGGTAGGTA
*
61908 CTCTACATGA
1 CTTTACATGA
61918 GATTGTTTCA
Statistics
Matches: 75, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
41 2 0.03
42 72 0.96
43 1 0.01
ACGTcount: A:0.24, C:0.12, G:0.29, T:0.35
Consensus pattern (41 bp):
CTTTACATGATGAGGTAGTGCTTTACGTGATGAGGTAGGTA
Found at i:62314 original size:21 final size:21
Alignment explanation
Indices: 62290--62385 Score: 117
Period size: 21 Copynumber: 4.6 Consensus size: 21
62280 CCTCATATTT
*
62290 TTCAGGATTCACCTCTCATCG
1 TTCAGGATCCACCTCTCATCG
*
62311 TTCAAGAGA-CC-CCTCCCATCG
1 TTC-AG-GATCCACCTCTCATCG
*
62332 TTCAGGATCCACCTCCCATCG
1 TTCAGGATCCACCTCTCATCG
62353 TTCAGGATCCACC-CTGCATCG
1 TTCAGGATCCACCTCT-CATCG
62374 TTCAGGATCCAC
1 TTCAGGATCCAC
62386 ATTCCATACT
Statistics
Matches: 67, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
19 2 0.03
20 5 0.07
21 55 0.82
22 3 0.04
23 2 0.03
ACGTcount: A:0.21, C:0.39, G:0.16, T:0.25
Consensus pattern (21 bp):
TTCAGGATCCACCTCTCATCG
Found at i:64371 original size:20 final size:20
Alignment explanation
Indices: 64346--64447 Score: 80
Period size: 20 Copynumber: 5.1 Consensus size: 20
64336 CTATCTTTAA
64346 GAAAATCAAATTCGCAACTC
1 GAAAATCAAATTCGCAACTC
** *
64366 GAAAATTGAATTAGCAACTC
1 GAAAATCAAATTCGCAACTC
* *
64386 -AATATTAAAATTCGCAACTC
1 GAA-AATCAAATTCGCAACTC
** * *
64406 GAATTTCAAATTTGCTACTC
1 GAAAATCAAATTCGCAACTC
* * *
64426 AAAAATGAAATTCACAACTC
1 GAAAATCAAATTCGCAACTC
64446 GA
1 GA
64448 TTTTAAGTTG
Statistics
Matches: 61, Mismatches: 19, Indels: 4
0.73 0.23 0.05
Matches are distributed among these distances:
19 2 0.03
20 57 0.93
21 2 0.03
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.26
Consensus pattern (20 bp):
GAAAATCAAATTCGCAACTC
Found at i:64426 original size:40 final size:39
Alignment explanation
Indices: 64347--64447 Score: 103
Period size: 40 Copynumber: 2.5 Consensus size: 39
64337 TATCTTTAAG
* *
64347 AAAATCAAATTCGCAACTCGAAAATTGAATTAGCAACTCA
1 AAAATAAAATTCGCAACTCG-AAATTAAATTAGCAACTCA
* * * * *
64387 ATATTAAAATTCGCAACTCGAATTTCAAATTTGCTACTCA
1 AAAATAAAATTCGCAACTCGAAATT-AAATTAGCAACTCA
* *
64427 AAAATGAAATTCACAACTCGA
1 AAAATAAAATTCGCAACTCGA
64448 TTTTAAGTTG
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
39 4 0.08
40 45 0.92
ACGTcount: A:0.45, C:0.20, G:0.09, T:0.27
Consensus pattern (39 bp):
AAAATAAAATTCGCAACTCGAAATTAAATTAGCAACTCA
Found at i:64477 original size:21 final size:20
Alignment explanation
Indices: 64447--64505 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
64437 TCACAACTCG
64447 ATTTT-AAGTTGCAAATTTCA
1 ATTTTCAAGTTGCAAATTT-A
* * *
64467 TTTTTCAAGTTGAAAAGTTA
1 ATTTTCAAGTTGCAAATTTA
* *
64487 ATTTTCGAGTTGCGAATTT
1 ATTTTCAAGTTGCAAATTT
64506 TAATACCAAG
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (20 bp):
ATTTTCAAGTTGCAAATTTA
Found at i:64559 original size:27 final size:27
Alignment explanation
Indices: 64521--64592 Score: 108
Period size: 27 Copynumber: 2.7 Consensus size: 27
64511 CCAAGTTACG
* *
64521 ATTTTCGGGTTGCGAATTGCGAATTCA
1 ATTTTCGAGTTGCGAATTACGAATTCA
*
64548 ATTTTCGTGTTGCGAATTACGAATTCA
1 ATTTTCGAGTTGCGAATTACGAATTCA
*
64575 ATTTTCGAGTTGTGAATT
1 ATTTTCGAGTTGCGAATT
64593 TGATTTTTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.42
Consensus pattern (27 bp):
ATTTTCGAGTTGCGAATTACGAATTCA
Found at i:64598 original size:20 final size:20
Alignment explanation
Indices: 64575--64613 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
64565 TACGAATTCA
*
64575 ATTTTCGAGTTGTGAATTTG
1 ATTTTCGAGTTGCGAATTTG
*
64595 ATTTTTGAGTTGCGAATTT
1 ATTTTCGAGTTGCGAATTT
64614 TCACTAGGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.05, G:0.23, T:0.51
Consensus pattern (20 bp):
ATTTTCGAGTTGCGAATTTG
Found at i:68309 original size:64 final size:65
Alignment explanation
Indices: 68184--68311 Score: 177
Period size: 65 Copynumber: 2.0 Consensus size: 65
68174 AAGGATATCC
*
68184 TTAGATCCATAGGGTCACCTTAAGCACACAACAAAAGGAAACCAACTTAAGGATATACCTTGGGT
1 TTAGATCCATAGGGTCACCTTAAGCACACAACAAAAGGAAACCAACCTAAGGATATACCTTGGGT
* * * * * * *
68249 TTAGATCCGTATGGTTACCTTAAGCGCACAGCAAATGG-AACCAACCTAAGGATATGCCTTGGG
1 TTAGATCCATAGGGTCACCTTAAGCACACAACAAAAGGAAACCAACCTAAGGATATACCTTGGG
68312 CCTACCCAAG
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
64 23 0.42
65 32 0.58
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (65 bp):
TTAGATCCATAGGGTCACCTTAAGCACACAACAAAAGGAAACCAACCTAAGGATATACCTTGGGT
Found at i:68359 original size:80 final size:80
Alignment explanation
Indices: 68249--68419 Score: 245
Period size: 80 Copynumber: 2.1 Consensus size: 80
68239 TACCTTGGGT
* * * *
68249 TTAGATCCGTATGGTTACCTTAAGCGCACAGCAAATGGAACCAACCTAAGGATATGCCTT-GGGC
1 TTAGATCTGTAGGGTTACCTTAAGCACACAGCAAAGGGAACCAACCTAAGGATATGCCTTGGGGC
*
68313 CTACCCAAGGGCATCC
66 CTACCCAA-GACATCC
* *
68329 TTAGATCTGTAGGGTTACCTTATGCACACAGCAAAGGGAATCAACCTAAGGATATGCCTTGGGGC
1 TTAGATCTGTAGGGTTACCTTAAGCACACAGCAAAGGGAACCAACCTAAGGATATGCCTTGGGGC
*
68394 CTACCCAAGATATCC
66 CTACCCAAGACATCC
*
68409 TTAGGTCTGTA
1 TTAGATCTGTA
68420 AGGACTTACA
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
80 69 0.85
81 12 0.15
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.24
Consensus pattern (80 bp):
TTAGATCTGTAGGGTTACCTTAAGCACACAGCAAAGGGAACCAACCTAAGGATATGCCTTGGGGC
CTACCCAAGACATCC
Found at i:72047 original size:12 final size:12
Alignment explanation
Indices: 72026--72060 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
72016 AGTTGTGGAT
*
72026 TTTGAGATTGTG
1 TTTGATATTGTG
72038 TTTGATATTGTG
1 TTTGATATTGTG
*
72050 TTTGGTATTGT
1 TTTGATATTGT
72061 AAATGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.29, T:0.57
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:72429 original size:22 final size:22
Alignment explanation
Indices: 72395--72450 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
72385 TTAGAGATGG
*
72395 GGAAGGATGTCGTCGGATATGA
1 GGAAGGATGTCGTCGGATATAA
* *
72417 GGAATGATTTCGTCGGATATAA
1 GGAAGGATGTCGTCGGATATAA
*
72439 GGACGGATGTCG
1 GGAAGGATGTCG
72451 CAGGAGAGAG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.27, C:0.11, G:0.38, T:0.25
Consensus pattern (22 bp):
GGAAGGATGTCGTCGGATATAA
Found at i:72591 original size:20 final size:20
Alignment explanation
Indices: 72568--72758 Score: 84
Period size: 20 Copynumber: 9.4 Consensus size: 20
72558 ATAAAAGCTT
72568 TGTTGCGAAATTAAAATTCG
1 TGTTGCGAAATTAAAATTCG
72588 TGTTGCG-AATTCAAAAATT-G
1 TGTTGCGAAATT--AAAATTCG
* *** *
72608 AGTTGCGAAAACGAAATTCC
1 TGTTGCGAAATTAAAATTCG
* * * *
72628 TGTTGTGAAAATGAAACTCG
1 TGTTGCGAAATTAAAATTCG
* * * *
72648 CGTTACG-AATTAGAAAATCT
1 TGTTGCGAAATTA-AAATTCG
*** *
72668 TGTTGCGAAAAGGAAACTCG
1 TGTTGCGAAATTAAAATTCG
* * *
72688 TGTTGCGAATTTAAAAATAG
1 TGTTGCGAAATTAAAATTCG
* *
72708 AGTTGCGAAA-AATAAATTCG
1 TGTTGCGAAATTA-AAATTCG
*
72728 TGTTGCGAAATTGTCAAATTCG
1 TGTTGCGAAA-T-TAAAATTCG
*
72750 AGTTGCGAA
1 TGTTGCGAA
72759 TTCGACTTCT
Statistics
Matches: 122, Mismatches: 39, Indels: 18
0.68 0.22 0.10
Matches are distributed among these distances:
19 13 0.11
20 84 0.69
21 10 0.08
22 15 0.12
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCG
Found at i:72632 original size:60 final size:60
Alignment explanation
Indices: 72568--72703 Score: 141
Period size: 60 Copynumber: 2.3 Consensus size: 60
72558 ATAAAAGCTT
* * * *
72568 TGTTGCGAAATTAAAATTCGTGTTGCGAATTCA-AAAAT-TGAGTTGCGAAAACGAAATTCC
1 TGTTGCGAAATTAAAACTCGCGTTACGAATT-AGAAAATCT-AGTTGCGAAAACGAAACTCC
* * * * * *
72628 TGTTGTGAAAATGAAACTCGCGTTACGAATTAGAAAATCTTGTTGCGAAAAGGAAACTCG
1 TGTTGCGAAATTAAAACTCGCGTTACGAATTAGAAAATCTAGTTGCGAAAACGAAACTCC
*
72688 TGTTGCGAATTTAAAA
1 TGTTGCGAAATTAAAA
72704 ATAGAGTTGC
Statistics
Matches: 60, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
59 1 0.02
60 58 0.97
61 1 0.02
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.29
Consensus pattern (60 bp):
TGTTGCGAAATTAAAACTCGCGTTACGAATTAGAAAATCTAGTTGCGAAAACGAAACTCC
Found at i:72705 original size:40 final size:40
Alignment explanation
Indices: 72628--72736 Score: 112
Period size: 40 Copynumber: 2.7 Consensus size: 40
72618 ACGAAATTCC
* * * * **
72628 TGTTGTGAAAATGAAACTCGCGTTACGAATTAGAAAATCT
1 TGTTGCGAAAAAGAAACTCGTGTTGCGAATTAGAAAATAG
*
72668 TGTTGCGAAAAGGAAACTCGTGTTGCGAATTTA-AAAATAG
1 TGTTGCGAAAAAGAAACTCGTGTTGCGAA-TTAGAAAATAG
* * *
72708 AGTTGCGAAAAATAAATTCGTGTTGCGAA
1 TGTTGCGAAAAAGAAACTCGTGTTGCGAA
72737 ATTGTCAAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 55 0.95
41 3 0.05
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (40 bp):
TGTTGCGAAAAAGAAACTCGTGTTGCGAATTAGAAAATAG
Found at i:75790 original size:12 final size:12
Alignment explanation
Indices: 75775--75807 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
75765 AATAAAAATA
75775 TCAATAGGATGT
1 TCAATAGGATGT
*
75787 TCAATAGGATTT
1 TCAATAGGATGT
75799 TCAATAGGA
1 TCAATAGGA
75808 GAAGGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.33
Consensus pattern (12 bp):
TCAATAGGATGT
Found at i:77862 original size:22 final size:20
Alignment explanation
Indices: 77834--77876 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 20
77824 ATACAATACA
77834 TATAGATTTTGAAGATATATTG
1 TATAGATTTTGAA-A-ATATTG
77856 TATAGATTTTGAAAATATTG
1 TATAGATTTTGAAAATATTG
77876 T
1 T
77877 TGAAAACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.33
21 1 0.05
22 13 0.62
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (20 bp):
TATAGATTTTGAAAATATTG
Found at i:77919 original size:34 final size:34
Alignment explanation
Indices: 77876--77968 Score: 150
Period size: 36 Copynumber: 2.7 Consensus size: 34
77866 GAAAATATTG
77876 TTGAAAACATATAATATATAGTTAAAAAAAGGTT
1 TTGAAAACATATAATATATAGTTAAAAAAAGGTT
* *
77910 TTGAAAACATATAATATATAGTTTTAAAAACAGTTT
1 TTGAAAACATATAATATATAG--TTAAAAAAAGGTT
77946 TTGAAAACATATAATATATAGTT
1 TTGAAAACATATAATATATAGTT
77969 TTTAAAAAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
34 23 0.42
36 32 0.58
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.37
Consensus pattern (34 bp):
TTGAAAACATATAATATATAGTTAAAAAAAGGTT
Found at i:77989 original size:77 final size:70
Alignment explanation
Indices: 77876--78076 Score: 174
Period size: 70 Copynumber: 2.8 Consensus size: 70
77866 GAAAATATTG
77876 TTGAAAACATATAATATATAGTTAAAAAAAGGTTTTGAAAACATATA-ATATATAGTTTTAAAAA
1 TTGAAAACATATAATATATAGTTAAAAAAAGGTTTTGAAAACATATATA-ATATAGTTTTAAAAA
*
77940 CAGT-TT
65 CA-TAAT
* **
77946 TTGAAAACATATAATATATAGTTTTTAAAAAATCGGTTTTTTTGAAAATGTATATAATATAGTTT
1 TTGAAAACATATAATATATAG---TTAAAAAA-AGG---TTTTGAAAACATATATAATATAGTTT
*
78011 TGAAAACATAAT
59 TAAAAACATAAT
* * * ** * **
78023 TTGAAAACAAATAGT-TATCGTTTTAAAACGGCTTTTGAAAATGTATATAATATA
1 TTGAAAACATATAATATATAGTTAAAAAAAGG-TTTTGAAAACATATATAATATA
78077 TATAATTTTT
Statistics
Matches: 111, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
70 43 0.39
72 3 0.03
73 14 0.13
74 2 0.02
76 5 0.05
77 43 0.39
78 1 0.01
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (70 bp):
TTGAAAACATATAATATATAGTTAAAAAAAGGTTTTGAAAACATATATAATATAGTTTTAAAAAC
ATAAT
Found at i:78123 original size:22 final size:23
Alignment explanation
Indices: 78072--78123 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
78062 AATGTATATA
78072 ATATATATAATTTTTAGAAACAT
1 ATATATATAATTTTTAGAAACAT
*
78095 AT-TATATAGTTTTT-GAAA-AT
1 ATATATATAATTTTTAGAAACAT
78115 ATAATATAT
1 AT-ATATAT
78124 GTTATATAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 4 0.15
21 4 0.15
22 16 0.62
23 2 0.08
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (23 bp):
ATATATATAATTTTTAGAAACAT
Found at i:78128 original size:29 final size:26
Alignment explanation
Indices: 78096--78149 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 26
78086 TAGAAACATA
78096 TTATATAGTTTTTGAAAATATAATATATG
1 TTATATAG-TTTT-AAAATA-AATATATG
78125 TTATATAGTTTTAAAATAAATATAT
1 TTATATAGTTTTAAAATAAATATAT
78150 AGTATGTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 7 0.28
27 6 0.24
28 4 0.16
29 8 0.32
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (26 bp):
TTATATAGTTTTAAAATAAATATATG
Found at i:78129 original size:27 final size:25
Alignment explanation
Indices: 78096--78149 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 25
78086 TAGAAACATA
78096 TTATATAGTTTTTGAAAATATAATATATG
1 TTATATA--TTTT-AAAATA-AATATATG
78125 TTATATAGTTTTAAAATAAATATAT
1 TTATATA-TTTTAAAATAAATATAT
78150 AGTATGTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 7 0.29
27 6 0.25
28 4 0.17
29 7 0.29
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (25 bp):
TTATATATTTTAAAATAAATATATG
Found at i:78171 original size:12 final size:11
Alignment explanation
Indices: 78156--78220 Score: 64
Period size: 12 Copynumber: 5.7 Consensus size: 11
78146 ATATAGTATG
78156 TATTATATTATA
1 TATTAT-TTATA
78168 TATTATTTATA
1 TATTATTTATA
78179 GTATTATTTAT-
1 -TATTATTTATA
78190 TATT-TTTATTA
1 TATTATTTA-TA
78201 TATTA-TTATTAA
1 TATTATTTA-T-A
78213 TATTATTT
1 TATTATTT
78221 TTCGGTTTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
9 4 0.09
10 5 0.11
11 14 0.30
12 22 0.47
13 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTATTTATA
Found at i:78183 original size:19 final size:16
Alignment explanation
Indices: 78161--78210 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 16
78151 GTATGTATTA
78161 TATTATATATTATTTAT
1 TATTATATATTATTT-T
*
78178 AGTATTATTTATTATTTT
1 --TATTATATATTATTTT
78196 TATTATATTATTATT
1 TATTATA-TATTATT
78211 AATATTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 6 0.21
17 7 0.25
18 1 0.04
19 14 0.50
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
TATTATATATTATTTT
Found at i:78184 original size:24 final size:25
Alignment explanation
Indices: 78155--78220 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 25
78145 TATATAGTAT
78155 GTATTATATTATATATTATTTA-TA
1 GTATTATATTATATATTATTTATTA
78179 GTATTAT-TTAT-TATT-TTTATTA
1 GTATTATATTATATATTATTTATTA
78201 -TATTATTATTA-ATATTATTT
1 GTATTA-TATTATATATTATTT
78221 TTCGGTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
21 9 0.24
22 7 0.19
23 11 0.30
24 10 0.27
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (25 bp):
GTATTATATTATATATTATTTATTA
Found at i:78186 original size:3 final size:3
Alignment explanation
Indices: 78156--78219 Score: 53
Period size: 3 Copynumber: 21.3 Consensus size: 3
78146 ATATAGTATG
* *
78156 TAT TA- TAT TAT ATAT TAT T-T ATAG TAT TATT TAT TAT TTT TAT TA-
1 TAT TAT TAT TAT -TAT TAT TAT -TAT TAT TA-T TAT TAT TAT TAT TAT
*
78201 TAT TAT TAT TAA TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
78220 TTTCGGTTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
2 5 0.10
3 38 0.78
4 6 0.12
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:89348 original size:5 final size:5
Alignment explanation
Indices: 89338--89376 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
89328 ACCACGATCA
* * *
89338 CGAGC CGAGC CGAGC CGTGC CGAGC TGAGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
89377 ACGGACGGCG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.21, C:0.33, G:0.41, T:0.05
Consensus pattern (5 bp):
CGAGC
Found at i:104052 original size:19 final size:19
Alignment explanation
Indices: 104028--104064 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
104018 AAAAGGTAAA
104028 CATTCTTCCTAATTATGAT
1 CATTCTTCCTAATTATGAT
104047 CATTCTTCCTAATTATGA
1 CATTCTTCCTAATTATGA
104065 GCGTTCTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.22, G:0.05, T:0.46
Consensus pattern (19 bp):
CATTCTTCCTAATTATGAT
Found at i:104071 original size:19 final size:19
Alignment explanation
Indices: 104028--104077 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
104018 AAAAGGTAAA
*
104028 CATTCTTCCTAATTATGAT
1 CATTCTTCCTAATTATGAG
104047 CATTCTTCCTAATTATGAG
1 CATTCTTCCTAATTATGAG
*
104066 CGTTCTTACCTA
1 CATTCTT-CCTA
104078 CCACTGTTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 24 0.86
20 4 0.14
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.44
Consensus pattern (19 bp):
CATTCTTCCTAATTATGAG
Found at i:109792 original size:18 final size:18
Alignment explanation
Indices: 109755--109799 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
109745 AATGAGATAT
*
109755 TTAAAT-AATAAAAACGA
1 TTAAATAAATAAAAACAA
*
109772 TTAAATAAATTAAAACAA
1 TTAAATAAATAAAAACAA
109790 TTAAAGTAAA
1 TTAAA-TAAA
109800 AACATGATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 6 0.25
18 14 0.58
19 4 0.17
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.27
Consensus pattern (18 bp):
TTAAATAAATAAAAACAA
Found at i:112242 original size:20 final size:20
Alignment explanation
Indices: 112217--112262 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
112207 TTTTACTAAT
112217 GTGTGCAAGTCTCCATAGGA
1 GTGTGCAAGTCTCCATAGGA
*
112237 GTGTGCAGGTCTCCATAGGA
1 GTGTGCAAGTCTCCATAGGA
112257 GTGTGC
1 GTGTGC
112263 TAACGTGAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.35, T:0.26
Consensus pattern (20 bp):
GTGTGCAAGTCTCCATAGGA
Found at i:126905 original size:30 final size:32
Alignment explanation
Indices: 126843--126905 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 32
126833 TTCTTTCATG
*
126843 TCTTTTTTTCTTCTTTTTCGAACAGCTTTTTT
1 TCTTTTTTTCTTCTTTTTCGAACAGCTGTTTT
**
126875 TCTTTTTTT-TTC-TTTTCGAATTGCTGTTTT
1 TCTTTTTTTCTTCTTTTTCGAACAGCTGTTTT
126905 T
1 T
126906 TTTCTCTCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 16 0.57
31 3 0.11
32 9 0.32
ACGTcount: A:0.08, C:0.16, G:0.08, T:0.68
Consensus pattern (32 bp):
TCTTTTTTTCTTCTTTTTCGAACAGCTGTTTT
Found at i:127222 original size:226 final size:227
Alignment explanation
Indices: 126828--127278 Score: 854
Period size: 227 Copynumber: 2.0 Consensus size: 227
126818 TTGTTTTCTA
126828 TTTTTTTCTTTCATGTCTTTTTTTCTTCTTTTTCGAACAGCTTTTTTTCTTTTTTTTTCTTTTCG
1 TTTTTTTCTTTCATGTCTTTTTTTCTTCTTTTTCGAACAGCTTTTTTTCTTTTTTTTTCTTTTCG
126893 AATTGCTGTTTTTTTTCTCTCGATGGAGCATACAAATGAAAAATTATTCACTTGCCCTGAAAAGG
66 AATTGCTGTTTTTTTTCTCTCGATGGAGCATACAAATGAAAAATTATTCACTTGCCCTGAAAAGG
126958 TAGAAAAGACGGATAAAATAAAAGGCTTGGGTTTAAGAATATGGTGAAAAC-AAGAAACGAGAAA
131 TAGAAAAGACGGATAAAATAAAAGGCTTGGGTTTAAGAATATGGTGAAAACAAAGAAACGAGAAA
127022 AGGCTCAAAAGTGGTTAACTAAGGGAAAATAT
196 AGGCTCAAAAGTGGTTAACTAAGGGAAAATAT
127054 TTTTTTTCTTTCATGTCTTTTTTTCTTCTTTTTTC-AACAGCTTTTTTTTCTTTTTTTTTCTTTT
1 TTTTTTTCTTTCATGTCTTTTTTTCTTC-TTTTTCGAACAGC-TTTTTTTCTTTTTTTTTCTTTT
127118 CGAATTGCTGTTTTTTTTCTCTCGATGGAGCATACAAATGAAAAATTATTCACTTGCCCTGAAAA
64 CGAATTGCTGTTTTTTTTCTCTCGATGGAGCATACAAATGAAAAATTATTCACTTGCCCTGAAAA
*
127183 GGTAGAAAAGACGGATAATA-AAAAGGCTTGGGTTTAAGAATATGGTGAAAACAAAGAAACGAGA
129 GGTAGAAAAGACGGATAAAATAAAAGGCTTGGGTTTAAGAATATGGTGAAAACAAAGAAACGAGA
127247 AAAGGCTCAAAAGTGGTTAACTAAGGGAAAAT
194 AAAGGCTCAAAAGTGGTTAACTAAGGGAAAAT
127279 GCATGGGTAG
Statistics
Matches: 221, Mismatches: 1, Indels: 5
0.97 0.00 0.02
Matches are distributed among these distances:
226 66 0.30
227 155 0.70
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (227 bp):
TTTTTTTCTTTCATGTCTTTTTTTCTTCTTTTTCGAACAGCTTTTTTTCTTTTTTTTTCTTTTCG
AATTGCTGTTTTTTTTCTCTCGATGGAGCATACAAATGAAAAATTATTCACTTGCCCTGAAAAGG
TAGAAAAGACGGATAAAATAAAAGGCTTGGGTTTAAGAATATGGTGAAAACAAAGAAACGAGAAA
AGGCTCAAAAGTGGTTAACTAAGGGAAAATAT
Found at i:133181 original size:100 final size:100
Alignment explanation
Indices: 132963--133160 Score: 373
Period size: 100 Copynumber: 2.0 Consensus size: 100
132953 AATTTAACGA
132963 TCTCACCGTCAAACTCCATAGTTAAAATTCCGCTTCTCACGTCAATTTTTGTGTGTGCAGTGCTC
1 TCTCACCGTCAAACTCCATAGTTAAAATTCCGCTTCTCACGTCAATTTTTGTGTGTGCAGTGCTC
133028 AGGAAAGGGCGTCCCAAAAGAATATCGACGATGTG
66 AGGAAAGGGCGTCCCAAAAGAATATCGACGATGTG
133063 TCTCACCGTCAAACTCCATAGTTAAAATTCCGCTTCTCACGTCAA-TTTT-TGTGTGCAGTGCTC
1 TCTCACCGTCAAACTCCATAGTTAAAATTCCGCTTCTCACGTCAATTTTTGTGTGTGCAGTGCTC
133126 AGGAAAGGGCGTCCCAAAAGAATATCGGACGATGT
66 AGGAAAGGGCGTCCCAAAAGAATATC-GACGATGT
133161 TTTCGTGCGT
Statistics
Matches: 97, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
98 40 0.41
99 12 0.12
100 45 0.46
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (100 bp):
TCTCACCGTCAAACTCCATAGTTAAAATTCCGCTTCTCACGTCAATTTTTGTGTGTGCAGTGCTC
AGGAAAGGGCGTCCCAAAAGAATATCGACGATGTG
Found at i:135798 original size:3 final size:3
Alignment explanation
Indices: 135790--135816 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
135780 AATGGAACAT
135790 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
135817 CATGAATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:137376 original size:21 final size:22
Alignment explanation
Indices: 137330--137382 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
137320 AATGTGTAAT
*
137330 TATAAATTAATTAAAAATCTAAA
1 TATAAATT-ATTAAAAATCAAAA
*
137353 TATAAATTATTTAAAA-CAAAA
1 TATAAATTATTAAAAATCAAAA
*
137374 TATTAATTA
1 TATAAATTA
137383 CATTGTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 12 0.44
22 7 0.26
23 8 0.30
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
TATAAATTATTAAAAATCAAAA
Found at i:137640 original size:48 final size:48
Alignment explanation
Indices: 137581--137676 Score: 122
Period size: 48 Copynumber: 2.0 Consensus size: 48
137571 ATAATAACAA
***
137581 CAGCAACGGTGGCGGCAGTGATGACAGCA-ACAACAACGATGATGATAG
1 CAGCAACGGTGGCGGCAACAATGACAGCAGA-AACAACGATGATGATAG
* * *
137629 CAGCAATGGTGGGGGCAACAATGACAGTAGAAACAACGATGATGATAG
1 CAGCAACGGTGGCGGCAACAATGACAGCAGAAACAACGATGATGATAG
137677 TAGGGGCGAC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
48 40 0.98
49 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.31, T:0.14
Consensus pattern (48 bp):
CAGCAACGGTGGCGGCAACAATGACAGCAGAAACAACGATGATGATAG
Found at i:138005 original size:17 final size:17
Alignment explanation
Indices: 137983--138027 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
137973 GTCAAATAAT
*
137983 TTTTTAATATCTTTT-TA
1 TTTTTAATAT-TTTTAAA
138000 TTTTTAATATTTTTAAA
1 TTTTTAATATTTTTAAA
138017 TTTTATAATAT
1 TTTT-TAATAT
138028 ATCTTTTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 4 0.16
17 15 0.60
18 6 0.24
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTAATATTTTTAAA
Found at i:138019 original size:8 final size:9
Alignment explanation
Indices: 137979--138027 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
137969 GATAGTCAAA
137979 TAAT-TTTT
1 TAATATTTT
137987 TAATATCTTT
1 TAATAT-TTT
137997 T--TATTTT
1 TAATATTTT
138004 TAATATTTT
1 TAATATTTT
138013 TAA-ATTTT
1 TAATATTTT
138021 ATAATAT
1 -TAATAT
138028 ATCTTTTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
7 4 0.11
8 12 0.34
9 13 0.37
10 6 0.17
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (9 bp):
TAATATTTT
Found at i:140616 original size:2 final size:2
Alignment explanation
Indices: 140609--140641 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
140599 ACAAATGATA
140609 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
140642 CACACACACG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:150098 original size:29 final size:29
Alignment explanation
Indices: 150011--150104 Score: 107
Period size: 29 Copynumber: 3.2 Consensus size: 29
150001 ATGATCTCAC
* **
150011 GCAGAAACAAGACAGAAATATAATCACAT
1 GCAGAATCAAGACAGGGATATAATCACAT
* * * *
150040 ACAGAATCAGGACGGGGATATAATCTCAT
1 GCAGAATCAAGACAGGGATATAATCACAT
*
150069 GCAGAATCAAGACAGGGATATAATCCCAT
1 GCAGAATCAAGACAGGGATATAATCACAT
*
150098 GTAGAAT
1 GCAGAAT
150105 AAGTAATGCA
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.18
Consensus pattern (29 bp):
GCAGAATCAAGACAGGGATATAATCACAT
Found at i:153587 original size:140 final size:139
Alignment explanation
Indices: 153268--153605 Score: 335
Period size: 140 Copynumber: 2.4 Consensus size: 139
153258 TATTGGATCA
* * * * * *
153268 AAAAACTAAAATGGAAA-CTCAAGCATAAATGTGAGGACCAAATAAAAAAATCACCTAAATTAAA
1 AAAAATTAAAAT-GAAACCTCGAGCATAAAAGAGAGGACCAAAT-AAAAATTCACCTAAACTAAA
* * * * * *
153332 AGACTATAGTGAACTTTAAGACTAAAGTGGAGGATCTAATATTAACTCTAATTGATTTTATCCAA
64 AGACTAAAGTGAACATTAAGACTAAAATAGAGGATCTAATATTAACTCTAATTAATTTTAACCAA
* *
153397 TTATTAAATTG
129 GTATGAAATTG
* * * *
153408 AAAAATTAAAAT-AGAACCTCGAGTAGAAATA-AAAAGACCAAATAAAAACTTCACCTAAACTAA
1 AAAAATTAAAATGA-AACCTCGAGCATAAA-AGAGAGGACCAAATAAAAA-TTCACCTAAACTAA
* * * *
153471 AGGACTAAAGTGAA-ATTAAGTCTAAAATAGAGGCTTTAAATATTAA-TCATAATTAATTTTAAC
63 AAGACTAAAGTGAACATTAAGACTAAAATAGAGGATCT-AATATTAACTC-TAATTAATTTTAAC
**
153534 CAAGTATGGGATTG
126 CAAGTATGAAATTG
* *
153548 AAAAATTGAAATGAAACCTCGAGCATAAAAGCGAGGACCAAATAAAATATTCACCTAA
1 AAAAATTAAAATGAAACCTCGAGCATAAAAGAGAGGACCAAATAAAA-ATTCACCTAA
153606 TTTAAAAATG
Statistics
Matches: 159, Mismatches: 30, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
138 1 0.01
139 27 0.17
140 129 0.81
141 2 0.01
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (139 bp):
AAAAATTAAAATGAAACCTCGAGCATAAAAGAGAGGACCAAATAAAAATTCACCTAAACTAAAAG
ACTAAAGTGAACATTAAGACTAAAATAGAGGATCTAATATTAACTCTAATTAATTTTAACCAAGT
ATGAAATTG
Found at i:155799 original size:29 final size:29
Alignment explanation
Indices: 155766--155822 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
155756 AGTTTGGACC
**
155766 GGATCAGGCGATCTGGACCAGTTCAGACT
1 GGATCAGGCGATCCAGACCAGTTCAGACT
155795 GGATCAGGCGATCCAGACCAGTTCAGAC
1 GGATCAGGCGATCCAGACCAGTTCAGAC
155823 CGGTTCCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.26, C:0.26, G:0.30, T:0.18
Consensus pattern (29 bp):
GGATCAGGCGATCCAGACCAGTTCAGACT
Found at i:158147 original size:13 final size:13
Alignment explanation
Indices: 158129--158153 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
158119 ATTTAATTAC
158129 TATTATTATTATT
1 TATTATTATTATT
158142 TATTATTATTAT
1 TATTATTATTAT
158154 AAAATAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTATTATTATT
Found at i:164951 original size:15 final size:15
Alignment explanation
Indices: 164931--164962 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
164921 GATCAATACC
164931 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
164946 TTTTGCATACATTCA
1 TTTTGCATACATGCA
164961 TT
1 TT
164963 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:168743 original size:9 final size:9
Alignment explanation
Indices: 168729--168760 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
168719 AAATGACAAT
168729 CATTCTTTA
1 CATTCTTTA
168738 CATTCTTTA
1 CATTCTTTA
*
168747 CATTTTTTA
1 CATTCTTTA
168756 CATTC
1 CATTC
168761 ATTATTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (9 bp):
CATTCTTTA
Found at i:172617 original size:19 final size:19
Alignment explanation
Indices: 172568--172644 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 19
172558 ATTTATTAAT
172568 AAATTCTAAGTTTATTTTCTCT-
1 AAATTC-AA-TTTATTTT-T-TG
172590 AAATT-AATTTATTTTTTG
1 AAATTCAATTTATTTTTTG
* *
172608 AGATTCAATTTA-TTTTCG
1 AAATTCAATTTATTTTTTG
172626 AAATTCAATTTATTCTTTT
1 AAATTCAATTTATT-TTTT
172645 ATTTTGTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
17 1 0.02
18 21 0.45
19 15 0.32
20 5 0.11
22 5 0.11
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.56
Consensus pattern (19 bp):
AAATTCAATTTATTTTTTG
Found at i:173993 original size:113 final size:113
Alignment explanation
Indices: 173795--174342 Score: 857
Period size: 113 Copynumber: 4.9 Consensus size: 113
173785 ATCCGTCACA
*
173795 ATGGATCAACATTTCCAGA-AAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
1 ATGGATCAACTTTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
*
173859 TTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAACCCATCACTTG
65 TTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTG
* * *
173908 ATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTAAAGAAGGAAGAAGAAGT
1 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
*
173973 TCATAATGAGAAGAGCTTGTTCAATCTTTTGCTCAAATCCATCACTTG
66 TCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTG
*
174021 ATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* * * *
174086 TCATAATGAAAAGAGTTTGTTCAACCTTTTGCTTAAATCCTTCACTTG
66 TCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTG
*
174134 ATGGATC-ACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAAT
1 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
** * * ** * *
174198 TCATAATGAGAAGAATTTGTTCAACTTTTTGTTTGAATTCATCACTCG
66 TCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTG
* *
174246 ATGGATCAACTTTTCCAGAGAAAGTTCATATTGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* *
174311 TCATAATGAGAAAAGCTTGTTCGACCTTTTGC
66 TCATAATGAGAAGAGCTTGTTCAACCTTTTGC
174343 ATGACCCTAT
Statistics
Matches: 401, Mismatches: 32, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
112 102 0.25
113 297 0.74
114 2 0.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (113 bp):
ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
TCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTG
Found at i:174261 original size:225 final size:226
Alignment explanation
Indices: 173795--174342 Score: 861
Period size: 225 Copynumber: 2.4 Consensus size: 226
173785 ATCCGTCACA
*
173795 ATGGATCAACATTTCCAGA-AAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
1 ATGGATCAACTTTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
*
173859 TTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAACCCATCACTTGATGGATCAGCTTTTCC
65 TTCATAATGAAAAGAGCTTGTTCAACCTTTTGCTCAAACCCATCACTTGATGGATCAGCTTTTCC
* * *
173924 AGAGAAAGTTCATAATGAGAAGAACTTATCTAAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGC
130 AGAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGAGAAGAAC
*
173989 TTGTTCAATCTTTTGCTCAAATCCATCACTTG
195 TTGTTCAATCTTTTGCTCAAATCCATCACTCG
*
174021 ATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* * * *
174086 TCATAATGAAAAGAGTTTGTTCAACCTTTTGCTTAAATCCTTCACTTGATGGATCA-CTTTTCCA
66 TCATAATGAAAAGAGCTTGTTCAACCTTTTGCTCAAACCCATCACTTGATGGATCAGCTTTTCCA
* *
174150 GAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATT
131 GAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGAGAAGAACT
* ** *
174215 TGTTCAA-CTTTTTGTTTGAATTCATCACTCG
196 TGTTCAATC-TTTTGCTCAAATCCATCACTCG
* *
174246 ATGGATCAACTTTTCCAGAGAAAGTTCATATTGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
*
174311 TCATAATGAGAAA-AGCTTGTTCGACCTTTTGC
66 TCATAATGA-AAAGAGCTTGTTCAACCTTTTGC
174343 ATGACCCTAT
Statistics
Matches: 297, Mismatches: 22, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
224 1 0.00
225 180 0.61
226 114 0.38
227 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (226 bp):
ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
TCATAATGAAAAGAGCTTGTTCAACCTTTTGCTCAAACCCATCACTTGATGGATCAGCTTTTCCA
GAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGAGAAGAACT
TGTTCAATCTTTTGCTCAAATCCATCACTCG
Found at i:174677 original size:3 final size:3
Alignment explanation
Indices: 174666--174699 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
174656 TTTTCATTTA
*
174666 ATT ACT ATT ATT ATT ATT ATT ATT ATT A-T ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
174700 AAAATAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:176959 original size:37 final size:37
Alignment explanation
Indices: 176914--177013 Score: 146
Period size: 38 Copynumber: 2.6 Consensus size: 37
176904 CTTTATTTTG
* *
176914 TTCGGGTCGGGTCGGGTCGGGTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTTGGGTCGGGTTTTTTAAGTATGATA
* *
176951 TTCGGGTCGAGTTGGGGCGGGTGTTTTTAAGTATGATA
1 TTCGGGTCGGGTTGGGTCGGGT-TTTTTAAGTATGATA
176989 TTCGGGTCGGGTTGGGTTCGGGTTT
1 TTCGGGTCGGGTTGGG-TCGGGTTT
177014 AGGGTGAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
37 19 0.35
38 31 0.56
39 5 0.09
ACGTcount: A:0.10, C:0.10, G:0.42, T:0.38
Consensus pattern (37 bp):
TTCGGGTCGGGTTGGGTCGGGTTTTTTAAGTATGATA
Found at i:177615 original size:18 final size:17
Alignment explanation
Indices: 177579--177624 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
177569 TATGGAATTG
177579 GATTCCAATT-CTGACA
1 GATTCCAATTCCTGACA
*
177595 GATTCCAATTCCTTTACA
1 GATTCCAATTCC-TGACA
177613 GATTCCAATTCC
1 GATTCCAATTCC
177625 CTCAAAACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 10 0.37
17 1 0.04
18 16 0.59
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.35
Consensus pattern (17 bp):
GATTCCAATTCCTGACA
Found at i:190665 original size:19 final size:18
Alignment explanation
Indices: 190643--190692 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
190633 GGAAGATGTT
190643 TAAATATATTATCAATAAA
1 TAAATATATTATCAA-AAA
* **
190662 TAAATAAATTATTTAAAA
1 TAAATATATTATCAAAAA
190680 TAAATATAATTAT
1 TAAATAT-ATTAT
190693 TATATTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAATATATTATCAAAAA
Found at i:198293 original size:23 final size:23
Alignment explanation
Indices: 198221--198302 Score: 91
Period size: 23 Copynumber: 3.6 Consensus size: 23
198211 ACACTTAACA
198221 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCA-CCCTTTGAAT
*
198245 GTGCATCGA--CACTCC-ATGAA-
1 GTGCATCGATGCAC-CCTTTGAAT
*
198265 GATGCATCGATGCACGCTTTGAAT
1 G-TGCATCGATGCACCCTTTGAAT
198289 GTGCATCGATGCAC
1 GTGCATCGATGCAC
198303 AAGGCCATGC
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
20 1 0.02
21 13 0.27
22 5 0.10
23 20 0.41
24 10 0.20
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (23 bp):
GTGCATCGATGCACCCTTTGAAT
Found at i:198315 original size:20 final size:20
Alignment explanation
Indices: 198290--198340 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
198280 GCTTTGAATG
*
198290 TGCATCGATGCACAAGGCCA
1 TGCATCGATGCACAAGACCA
198310 TGCATCGATGCACAAGACCA
1 TGCATCGATGCACAAGACCA
198330 TGCATCGATGC
1 TGCATCGATGC
198341 GTCCGTCGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (20 bp):
TGCATCGATGCACAAGACCA
Found at i:201011 original size:45 final size:45
Alignment explanation
Indices: 200955--201059 Score: 115
Period size: 46 Copynumber: 2.3 Consensus size: 45
200945 GCACCAATCC
* *
200955 ATGCGTCGATGCAC-CATGGAATAAATTG-AACATCAAATGCATTTT
1 ATGCATCGATGCACTCA-GGAATAAA-TGAAACATCAAATGCATTTG
* ** *
201000 ATGCATCGATGCACTCAGGATTTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACTCAGGAATAAATG-AAACATCAAATGCATTTG
201046 ATGCATCGATGCAC
1 ATGCATCGATGCAC
201060 AAGCCATGCA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
44 2 0.04
45 18 0.35
46 31 0.61
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (45 bp):
ATGCATCGATGCACTCAGGAATAAATGAAACATCAAATGCATTTG
Found at i:201070 original size:19 final size:19
Alignment explanation
Indices: 201046--201097 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
201036 AATGCATTTG
201046 ATGCATCGATGCACAAGCC
1 ATGCATCGATGCACAAGCC
* *
201065 ATGCATCAATGCACATGCC
1 ATGCATCGATGCACAAGCC
201084 ATGCATCGATGCAC
1 ATGCATCGATGCAC
201098 TCTTGCTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (19 bp):
ATGCATCGATGCACAAGCC
Found at i:203222 original size:23 final size:22
Alignment explanation
Indices: 203179--203222 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
203169 CATTCCTTTG
*
203179 TTGATTTTTATACCATTCTTCC
1 TTGATTTTTATACCATCCTTCC
**
203201 TTGATTCTTTATTTCATCCTTC
1 TTGATT-TTTATACCATCCTTC
203223 TTCACTTCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.16, C:0.23, G:0.05, T:0.57
Consensus pattern (22 bp):
TTGATTTTTATACCATCCTTCC
Found at i:214353 original size:13 final size:14
Alignment explanation
Indices: 214330--214363 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
214320 ATGATAATTT
214330 TAAAGAAAATAAAG
1 TAAAGAAAATAAAG
214344 TAAA-AAAATAAAG
1 TAAAGAAAATAAAG
*
214357 GAAAGAA
1 TAAAGAA
214364 TAAAACTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.12
Consensus pattern (14 bp):
TAAAGAAAATAAAG
Found at i:219374 original size:25 final size:22
Alignment explanation
Indices: 219315--219383 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
219305 AGAATATTGG
*
219315 TACCATAGTGTAGTAGTATCGG
1 TACCATAGTGTAGTAGTATCGA
219337 TACCATAGTGTAGTAGTATCGA
1 TACCATAGTGTAGTAGTATCGA
* * *
219359 TACTATAGTATAGTAGTACCGA
1 TACCATAGTGTAGTAGTATCGA
219381 TAC
1 TAC
219384 TGAGAGAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (22 bp):
TACCATAGTGTAGTAGTATCGA
Found at i:219894 original size:57 final size:57
Alignment explanation
Indices: 219728--220198 Score: 693
Period size: 57 Copynumber: 8.3 Consensus size: 57
219718 ATTACCGAAT
*
219728 GGCACTTTGTGTGCAAAAAGTTAAGAAATTTATAATAAGTTTATGAATTTCCGTATG
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* *
219785 GGCACTTTGTGTGCAAAAAGTTAAG-AATTCATAATAAGTTTATGAATTTTCGTATT
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
** *
219841 GGTGCTTTGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
219898 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * *
219955 GGCACTTTATGTGCAAAAAGTTAAGAAATTCATAATGAGTTTATGAATTTCTGTATG
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * * * * *
220012 GGCACTGTATGTGCAAAAA-ATAATAAATTCATAATGAGTTTATTAATTTCCGTATG
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
*
220068 GGCA-TTGTGTGTGCAAAAA-CTAAGAAA-TCTATAATAAGTTTATGAATTTCCGTATG
1 GGCACTT-TGTGTGCAAAAAGTTAAGAAATTC-ATAATAAGTTTATGAATTTCCGTATG
*
220124 GGCACTGTGTGTGTGCAAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
1 GGCACT-T-TGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
**
220182 GGCACTACGTGTGCAAA
1 GGCACTTTGTGTGCAAA
220199 CTATAGAGTT
Statistics
Matches: 383, Mismatches: 25, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
55 3 0.01
56 142 0.37
57 182 0.48
58 54 0.14
59 2 0.01
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (57 bp):
GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
Found at i:220152 original size:227 final size:227
Alignment explanation
Indices: 219728--220187 Score: 698
Period size: 227 Copynumber: 2.0 Consensus size: 227
219718 ATTACCGAAT
* * *
219728 GGCACTTTGTGTGCAAAAAGTTAAGAAATTTATAATAAGTTTATGAATTTCCGTATGGGCACTTT
1 GGCACTTTATGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGT
* * * *
219793 GTGTGCAAAAAGTTAAGAATTCATAATAAGTTTATGAATTTTCGTATTGGTGCTTTGTGTGCAAA
66 ATGTGCAAAAAGATAAAAATTCATAATAAGTTTATGAATTTCCGTATTGGTGCTTTGTGTGCAAA
* * *
219858 AAGTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTGTGTGCAAAAAGTTAAG
131 AAGCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAAGCTAAG
219923 AAATTCATAATAAGTTTATGAATTTCCGTATG
196 AAATTCATAATAAGTTTATGAATTTCCGTATG
* *
219955 GGCACTTTATGTGCAAAAAGTTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTGT
1 GGCACTTTATGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGT
* *
220020 ATGTGCAAAAA-ATAATAAATTCATAATGAGTTTATTAATTTCCGTA-TGG-GCATTGTGTGTGC
66 ATGTGCAAAAAGATAA-AAATTCATAATAAGTTTATGAATTTCCGTATTGGTGC-TT-TGTGTGC
220082 AAAAA-CTAAGAAA-TCTATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGTGCAAAAA
128 AAAAAGCTAAGAAATTC-ATAATAAGTTTATGAATTTCCGTATGGGCACT-T-TGTGTGCAAAAA
220145 -CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
190 GCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
220182 GGCACT
1 GGCACT
220188 ACGTGTGCAA
Statistics
Matches: 213, Mismatches: 14, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
225 4 0.02
226 46 0.22
227 151 0.71
228 12 0.06
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36
Consensus pattern (227 bp):
GGCACTTTATGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGT
ATGTGCAAAAAGATAAAAATTCATAATAAGTTTATGAATTTCCGTATTGGTGCTTTGTGTGCAAA
AAGCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAAGCTAAG
AAATTCATAATAAGTTTATGAATTTCCGTATG
Found at i:220197 original size:170 final size:170
Alignment explanation
Indices: 219728--220198 Score: 691
Period size: 170 Copynumber: 2.8 Consensus size: 170
219718 ATTACCGAAT
219728 GGCACTTTGTGTGCAAAAAGTTAAGAAATTTATAATAAGTTTATGAATTTCCGTATGGGCACTTT
1 GGCACTTTGTGTGCAAAAAGTTAAGAAA-TTATAATAAGTTTATGAATTTCCGTATGGGCACTTT
* * ** *
219793 GTGTGCAAAAAGTTAAG-AATTCATAATAAGTTTATGAATTTTCGTATTGGTGCTTTGTGTGCAA
65 GTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTATGTGTGCAA
* *
219857 AAAGTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
130 AAAGATAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
219898 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTT
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATT-ATAATAAGTTTATGAATTTCCGTATGGGCACTTT
* * * * *
219963 ATGTGCAAAAAGTTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTGTATGTGCAA
65 GTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTATGTGTGCAA
* * *
220028 AAA-ATAATAAATTCATAATGAGTTTATTAATTTCCGTATG
130 AAAGATAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
*
220068 GGCA-TTGTGTGTGCAAAAA-CTAAGAAATCTATAATAAGTTTATGAATTTCCGTATGGGCACTG
1 GGCACTT-TGTGTGCAAAAAGTTAAGAAAT-TATAATAAGTTTATGAATTTCCGTATGGGCACT-
* *
220131 TGTGTGTGCAAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTACGTGTG
63 T-TGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTATGTGTG
220195 CAAA
127 CAAA
220199 CTATAGAGTT
Statistics
Matches: 273, Mismatches: 22, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
169 44 0.16
170 176 0.64
171 53 0.19
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (170 bp):
GGCACTTTGTGTGCAAAAAGTTAAGAAATTATAATAAGTTTATGAATTTCCGTATGGGCACTTTG
TGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTATGTGTGCAAA
AAGATAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
Found at i:220336 original size:45 final size:45
Alignment explanation
Indices: 220282--220511 Score: 266
Period size: 45 Copynumber: 5.1 Consensus size: 45
220272 ATAAAATACT
* * *
220282 AAATGCATAACGATGCATTAAAGGCA-GTTAAGGATGTCATAAATG
1 AAATGCATAACGATGCATTAAAGGCATG-AAAGGATGCCATAAATA
* * * *
220327 AAATACATAACGGTGAATTAGAGGCATGAAAGGATGCCATAAATA
1 AAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCATAAATA
* *
220372 AAATGCATAACGATGCATAAAAGGCATGAAATGATGCCATAAATA
1 AAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCATAAATA
* * * * * *
220417 AAATGCATAATGGTGCATAAAAGGCGTGAAATGATGCCATAAATG
1 AAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCATAAATA
* *
220462 AAATGCATAAC-AGTGCATTAAAGGCATGAAATGATGCCCTAAATGA
1 AAATGCATAACGA-TGCATTAAAGGCATGAAAGGATGCCATAAAT-A
220508 AAAT
1 AAAT
220512 AATGAATAAT
Statistics
Matches: 159, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
45 154 0.97
46 5 0.03
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (45 bp):
AAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCATAAATA
Found at i:223486 original size:20 final size:20
Alignment explanation
Indices: 223460--223517 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
223450 GTTAAAAATC
*
223460 TAAAATTTAAAAATTTAT-T
1 TAAAATTTAAAAATTAATAT
*
223479 TCAAAATTTTAAAATATAATAT
1 T-AAAATTTAAAAAT-TAATAT
223501 TAAAATATTAAAAATTA
1 TAAAAT-TTAAAAATTA
223518 TGTGGATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
19 1 0.03
20 12 0.38
21 10 0.31
22 9 0.28
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAAATTTAAAAATTAATAT
Found at i:223505 original size:21 final size:19
Alignment explanation
Indices: 223460--223513 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 19
223450 GTTAAAAATC
* *
223460 TAAAATTTAAAAATTTATT
1 TAAAATTTTAAAATTAATT
223479 TCAAAATTTTAAAATATAATAT
1 T-AAAATTTTAAAAT-TAAT-T
*
223501 TAAAATATTAAAA
1 TAAAATTTTAAAA
223514 ATTATGTGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 12 0.41
21 14 0.48
22 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAAATTTTAAAATTAATT
Found at i:224848 original size:30 final size:30
Alignment explanation
Indices: 224813--224870 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
224803 TCACTCTACG
224813 ATGACATGA-ATTATTTTATTAATATTTTTT
1 ATGACATGATA-TATTTTATTAATATTTTTT
224843 ATGACATGATATATTTTATTAATATTTT
1 ATGACATGATATATTTTATTAATATTTT
224871 ACCATGTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.55
Consensus pattern (30 bp):
ATGACATGATATATTTTATTAATATTTTTT
Found at i:225276 original size:3 final size:3
Alignment explanation
Indices: 225245--225347 Score: 104
Period size: 3 Copynumber: 35.3 Consensus size: 3
225235 AAAATATATA
* *
225245 TAT TA- TAT TAT AAT TAT TAC TAT TA- TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
225291 TAT TAT TAT TAT AAC AAT TA- TAT TAT AAT AAT TAT TAA TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
225338 TAA TAT TAT T
1 TAT TAT TAT T
225348 TATGTTTTCT
Statistics
Matches: 83, Mismatches: 14, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
2 6 0.07
3 77 0.93
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:226943 original size:30 final size:32
Alignment explanation
Indices: 226908--226975 Score: 77
Period size: 33 Copynumber: 2.2 Consensus size: 32
226898 ATAGTTTTTA
226908 TATTTTATAGT-AAT-ATAATTATATAAATAT
1 TATTTTATAGTAAATAATAATTATATAAATAT
* * * *
226938 TATTTTTTATTAAAATAATATTTATATAATTAT
1 TATTTTATAGT-AAATAATAATTATATAAATAT
226971 TATTT
1 TATTT
226976 ATTTAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 9 0.29
32 3 0.10
33 19 0.61
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (32 bp):
TATTTTATAGTAAATAATAATTATATAAATAT
Found at i:226977 original size:30 final size:28
Alignment explanation
Indices: 226936--226999 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 28
226926 TTATATAAAT
* *
226936 ATTATTTTTTATTAAAATAATATTTATATA
1 ATTATTATTTATTAAAAT-ATATTAAT-TA
* *
226966 ATTATTATTTATTTAAATTTATTAATTA
1 ATTATTATTTATTAAAATATATTAATTA
226994 ATTATT
1 ATTATT
227000 TTTTTGTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 8 0.27
29 6 0.20
30 16 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
ATTATTATTTATTAAAATATATTAATTA
Found at i:228380 original size:42 final size:42
Alignment explanation
Indices: 228292--228380 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
228282 TATGATACCC
* * *
228292 AGCCCTCCAGTTCAGATGTCATCTCCTCAAGGGTATATGCCA
1 AGCCCACCAGTTCAGATGTCATCTCCGCAAGGGTACATGCCA
* * * *
228334 AGCCCACCAGTTTATATGTCATCTCCGC-AGGGTTACATTCCT
1 AGCCCACCAGTTCAGATGTCATCTCCGCAAGGG-TACATGCCA
228376 AGCCC
1 AGCCC
228381 TCAAGGTTAC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 4 0.10
42 35 0.90
ACGTcount: A:0.22, C:0.33, G:0.18, T:0.27
Consensus pattern (42 bp):
AGCCCACCAGTTCAGATGTCATCTCCGCAAGGGTACATGCCA
Found at i:228390 original size:21 final size:21
Alignment explanation
Indices: 228358--228430 Score: 101
Period size: 21 Copynumber: 3.5 Consensus size: 21
228348 TATGTCATCT
*
228358 CCGCAGGGTTACATTCCTAGC
1 CCGCAAGGTTACATTCCTAGC
*
228379 CCTCAAGGTTACATTCCTAGC
1 CCGCAAGGTTACATTCCTAGC
* *
228400 CCGCCAGGTTACATGCCTAGC
1 CCGCAAGGTTACATTCCTAGC
*
228421 CCGCAGGGTT
1 CCGCAAGGTT
228431 TTATGACACC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.19, C:0.34, G:0.23, T:0.23
Consensus pattern (21 bp):
CCGCAAGGTTACATTCCTAGC
Found at i:228982 original size:34 final size:34
Alignment explanation
Indices: 228939--229011 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
228929 TTAAATGTTT
*
228939 TTAATATACAAATTATAATATTCGAAATTTAAAA
1 TTAAAATACAAATTATAATATTCGAAATTTAAAA
** *
228973 TTAAAATACAAATTATGGTATTCGAAATTTAACA
1 TTAAAATACAAATTATAATATTCGAAATTTAAAA
229007 TTAAA
1 TTAAA
229012 TTCAACTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (34 bp):
TTAAAATACAAATTATAATATTCGAAATTTAAAA
Found at i:229255 original size:23 final size:22
Alignment explanation
Indices: 229220--229322 Score: 63
Period size: 23 Copynumber: 4.8 Consensus size: 22
229210 TTATCACTTC
* *
229220 ACATGTATTCAATTTATCCATA
1 ACATTTATCCAATTTATCCATA
* *
229242 ACATTTTATCCAATATATTCA-A
1 ACA-TTTATCCAATTTATCCATA
* *
229264 ACA---A-CCAATTGATCACTTA
1 ACATTTATCCAATTTATC-CATA
* *
229283 ACATTTATTCAATTTATTCATA
1 ACATTTATCCAATTTATCCATA
*
229305 ACATTTTATCTAATTTAT
1 ACA-TTTATCCAATTTAT
229323 TCAAACTTCA
Statistics
Matches: 59, Mismatches: 14, Indels: 15
0.67 0.16 0.17
Matches are distributed among these distances:
17 7 0.12
18 2 0.03
19 4 0.07
22 14 0.24
23 32 0.54
ACGTcount: A:0.38, C:0.17, G:0.02, T:0.43
Consensus pattern (22 bp):
ACATTTATCCAATTTATCCATA
Found at i:229305 original size:63 final size:63
Alignment explanation
Indices: 229204--229328 Score: 189
Period size: 63 Copynumber: 2.0 Consensus size: 63
229194 CAATGTCACG
*
229204 ACCAACTTATCACTTCACATGTATTCAATTTATCCATAACATTTTATCCAATATATTCAAACA
1 ACCAACTTATCACTTAACATGTATTCAATTTATCCATAACATTTTATCCAATATATTCAAACA
* * * *
229267 ACCAA-TTGATCACTTAACATTTATTCAATTTATTCATAACATTTTATCTAATTTATTCAAAC
1 ACCAACTT-ATCACTTAACATGTATTCAATTTATCCATAACATTTTATCCAATATATTCAAAC
229329 TTCACATAAC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
62 2 0.04
63 54 0.96
ACGTcount: A:0.38, C:0.21, G:0.02, T:0.40
Consensus pattern (63 bp):
ACCAACTTATCACTTAACATGTATTCAATTTATCCATAACATTTTATCCAATATATTCAAACA
Found at i:229323 original size:23 final size:22
Alignment explanation
Indices: 229281--229325 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
229271 ATTGATCACT
229281 TAACATTTATTCAATTTATTCA
1 TAACATTTATTCAATTTATTCA
229303 TAACATTT-TATCTAATTTATTCA
1 TAACATTTAT-TC-AATTTATTCA
229326 AACTTCACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 1 0.05
22 10 0.48
23 10 0.48
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (22 bp):
TAACATTTATTCAATTTATTCA
Done.