Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006439.1 Hibiscus syriacus cultivar Beakdansim tig00015555_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: 467271
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:158215 original size:13 final size:13
Alignment explanation
Indices: 158199--158237 Score: 69
Period size: 14 Copynumber: 2.9 Consensus size: 13
158189 TTGTTTAGAT
158199 TTTTTATTTTTTA
1 TTTTTATTTTTTA
158212 TTTTTATTTTTTTA
1 TTTTTA-TTTTTTA
158226 TTTTTATTTTTT
1 TTTTTATTTTTT
158238 GGTAATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:160010 original size:2 final size:2
Alignment explanation
Indices: 160003--160029 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
159993 AAAAATAAAT
160003 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
160030 TTAGGTCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:165319 original size:21 final size:21
Alignment explanation
Indices: 165295--165343 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
165285 TTCAATTAGG
165295 GAGTATGGATACTCAAAC-GAA
1 GAGTATGGATACTCAAACAG-A
* * *
165316 GAGTTTAGATATTCAAACAGA
1 GAGTATGGATACTCAAACAGA
165337 GAGTATG
1 GAGTATG
165344 TGTATTTGAG
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.24
Consensus pattern (21 bp):
GAGTATGGATACTCAAACAGA
Found at i:165388 original size:19 final size:20
Alignment explanation
Indices: 165364--165402 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
165354 TATCGATACT
*
165364 CAATGA-TATTGATACCAAA
1 CAATGAGTATCGATACCAAA
165383 CAATGAGTATCGATACCAAA
1 CAATGAGTATCGATACCAAA
165403 ATGATACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (20 bp):
CAATGAGTATCGATACCAAA
Found at i:166641 original size:2 final size:2
Alignment explanation
Indices: 166630--166662 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
166620 AACAATTAAC
166630 AT AT -T 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
166663 TTGAATAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:169413 original size:40 final size:40
Alignment explanation
Indices: 169358--169490 Score: 115
Period size: 40 Copynumber: 3.2 Consensus size: 40
169348 TTCAGAGCAA
* *
169358 AAAAATGCCACTAATGTTCTGAAATATTGCAGCGCTTAAT
1 AAAAACGCCACTAATGTTCTGAAATATTGCGGCGCTTAAT
** * * *
169398 AAAAACGCCACTAATGTGGTGAAAT-TTGCGGCATTTCTGATT
1 AAAAACGCCACTAATGTTCTGAAATATTGCGGC---GCTTAAT
** * * *
169440 GTAAACGCCACTAATGTTCTAAAATATTACGGCGTTTAAT
1 AAAAACGCCACTAATGTTCTGAAATATTGCGGCGCTTAAT
169480 GAAAAACGCCA
1 -AAAAACGCCA
169491 TTATATGTAA
Statistics
Matches: 69, Mismatches: 19, Indels: 9
0.71 0.20 0.09
Matches are distributed among these distances:
39 6 0.09
40 25 0.36
41 8 0.12
42 24 0.35
43 6 0.09
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (40 bp):
AAAAACGCCACTAATGTTCTGAAATATTGCGGCGCTTAAT
Found at i:172533 original size:35 final size:36
Alignment explanation
Indices: 172459--172539 Score: 137
Period size: 36 Copynumber: 2.3 Consensus size: 36
172449 AACACAATCA
*
172459 TCAATTACATTCTAAACCCCAAATTCCAAAAATATT
1 TCAATTACATTCTAAACCCCAAATTCCAAAAATACT
*
172495 TCAATTACATTCTAAACCTCAAATTCC-AAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAAATACT
172530 TCAATTACAT
1 TCAATTACAT
172540 GCCCAATCTC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
35 17 0.40
36 26 0.60
ACGTcount: A:0.43, C:0.25, G:0.00, T:0.32
Consensus pattern (36 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAAATACT
Found at i:172551 original size:35 final size:36
Alignment explanation
Indices: 172459--172555 Score: 115
Period size: 35 Copynumber: 2.7 Consensus size: 36
172449 AACACAATCA
* * * *
172459 TCAATTACATTCTAAACCCCAAATTCCAAAAATATT
1 TCAATTACATGCCAAACCTCAAATTCCAAAAATACT
* *
172495 TCAATTACATTCTAAACCTCAAATTCC-AAAATACT
1 TCAATTACATGCCAAACCTCAAATTCCAAAAATACT
* *
172530 TCAATTACATGCCCAATCTCAAATTC
1 TCAATTACATGCCAAACCTCAAATTC
172556 ATAATTCATT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
35 29 0.53
36 26 0.47
ACGTcount: A:0.41, C:0.27, G:0.01, T:0.31
Consensus pattern (36 bp):
TCAATTACATGCCAAACCTCAAATTCCAAAAATACT
Found at i:173392 original size:35 final size:35
Alignment explanation
Indices: 173353--173432 Score: 135
Period size: 35 Copynumber: 2.3 Consensus size: 35
173343 GGGGTTGGGC
*
173353 ATGTAATTGAAGTATTTTGGAATTT-GAGGTTTAGA
1 ATGTAATTGAAGCATTTTGGAATTTAG-GGTTTAGA
173388 ATGTAATTGAAGCATTTTGGAATTTAGGGTTTAGA
1 ATGTAATTGAAGCATTTTGGAATTTAGGGTTTAGA
173423 ATGTAATTGA
1 ATGTAATTGA
173433 TGATTGTGTT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
35 42 0.98
36 1 0.02
ACGTcount: A:0.33, C:0.01, G:0.25, T:0.41
Consensus pattern (35 bp):
ATGTAATTGAAGCATTTTGGAATTTAGGGTTTAGA
Found at i:177978 original size:12 final size:12
Alignment explanation
Indices: 177963--177990 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
177953 TAAATAATCT
177963 TTTAAATATGAA
1 TTTAAATATGAA
177975 TTTAAATATGAA
1 TTTAAATATGAA
177987 TTTA
1 TTTA
177991 TTAAGTGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (12 bp):
TTTAAATATGAA
Found at i:183267 original size:29 final size:29
Alignment explanation
Indices: 183191--183276 Score: 91
Period size: 29 Copynumber: 3.0 Consensus size: 29
183181 AGTGACTAAG
* * *
183191 GAATGGGGCCATAACTGTAATGATTAAAA
1 GAATAGGGCCCTAACTGTAAAGATTAAAA
* * **
183220 GAATAAGGCTCTATTTGTAAAGATTAAAA
1 GAATAGGGCCCTAACTGTAAAGATTAAAA
* *
183249 GAATAGGGCCCTAAGTGTAAATATTAAA
1 GAATAGGGCCCTAACTGTAAAGATTAAA
183277 GGAGCGGGCC
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.27
Consensus pattern (29 bp):
GAATAGGGCCCTAACTGTAAAGATTAAAA
Found at i:185653 original size:24 final size:24
Alignment explanation
Indices: 185617--185662 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
185607 CTTCTTTCTT
* *
185617 TTCTCCTCCTTCTGTTTGTCTTTC
1 TTCTCATCCTTCTGTTTCTCTTTC
* *
185641 TTCTCATCTTTCTTTTTCTCTT
1 TTCTCATCCTTCTGTTTCTCTT
185663 CTATTTCATC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.02, C:0.30, G:0.04, T:0.63
Consensus pattern (24 bp):
TTCTCATCCTTCTGTTTCTCTTTC
Found at i:185767 original size:21 final size:21
Alignment explanation
Indices: 185725--185774 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
185715 ATCTTTCTTC
* ** *
185725 TTCTTTTTCTCCTGTTTTTCT
1 TTCTTCTTCTCCTCCTTGTCT
185746 TTCTTCTTCTCCTCCTTGTCT
1 TTCTTCTTCTCCTCCTTGTCT
185767 TTCTTCTT
1 TTCTTCTT
185775 ATCTTTCTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.00, C:0.30, G:0.04, T:0.66
Consensus pattern (21 bp):
TTCTTCTTCTCCTCCTTGTCT
Found at i:185852 original size:129 final size:129
Alignment explanation
Indices: 185632--185866 Score: 298
Period size: 129 Copynumber: 1.8 Consensus size: 129
185622 CTCCTTCTGT
* *
185632 TTGTCTTTCTTCTCATCTTTCTTTTTCTCTTCTATTTCATCATCGTCAGCTTCTTCTACCTCTTC
1 TTGTCTTTCTTCTCATCTTTCTTTGTCTCTTCTATTTCATCATCGTCAGCTTCTTCTACCTCATC
*
185697 CTCTTTATCCTTCTTCTTATCTTTCTTCTTCTTTTTC-TCCTGTTTTTCTTTCTTCTTCTCCTCC
66 CTCTTTATCCTTCTTCTTATCTTTCTT-TTCCTTTTCATCCTGTTTTTCTTTCTTCTTCTCCTCC
* * * * * *
185761 TTGTCTTTCTTCTTATCTTTCTTTGTCTCTTTTATTTCTTTATCTTCATCTTCTTCTACCTCATC
1 TTGTCTTTCTTCTCATCTTTCTTTGTCTCTTCTATTTCATCATCGTCAGCTTCTTCTACCTCATC
* * *
185826 TTTCTTT-TTCTTCATT-TCTGTC-TTCTTTTCCTTTTCATCCT
66 -CTCTTTATCCTTC-TTCT-TATCTTTCTTTTCCTTTTCATCCT
185867 TGCCTTTCTT
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
128 8 0.09
129 72 0.80
130 10 0.11
ACGTcount: A:0.07, C:0.29, G:0.03, T:0.61
Consensus pattern (129 bp):
TTGTCTTTCTTCTCATCTTTCTTTGTCTCTTCTATTTCATCATCGTCAGCTTCTTCTACCTCATC
CTCTTTATCCTTCTTCTTATCTTTCTTTTCCTTTTCATCCTGTTTTTCTTTCTTCTTCTCCTCC
Found at i:185904 original size:15 final size:16
Alignment explanation
Indices: 185870--185912 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
185860 TCATCCTTGC
185870 CTTTCTTCTTCTCCATCT
1 CTTTC-TCTTCTCCA-CT
185888 CTTTCTCTTCTCC-CT
1 CTTTCTCTTCTCCACT
*
185903 CTTCCTCTTC
1 CTTTCTCTTC
185913 ATCTTTCAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 11 0.46
17 8 0.33
18 5 0.21
ACGTcount: A:0.02, C:0.44, G:0.00, T:0.53
Consensus pattern (16 bp):
CTTTCTCTTCTCCACT
Found at i:186043 original size:81 final size:81
Alignment explanation
Indices: 185925--186082 Score: 185
Period size: 81 Copynumber: 2.0 Consensus size: 81
185915 CTTTCAGCTT
* * * * *
185925 CTTTTCTTTCTTTTTCTCCTTATCTTTCTTCTTTTTCTTC-TTCTC-TCCCGTCTCTTCTTCTTC
1 CTTTTCTTTCTTCTTCTCCTTATCCTCCTTCTCTTTCTTCTTTCTCTTCCCATCT-TTC-TCTTC
185988 ATCTACTTCTACCTTGTG
64 ATCTACTTCTACCTTGTG
* * * * *
186006 CTTTTCTTTCTTCTTCTCTTTCTCCTCCTTGTCTTTCTTCTTTTTCTTCTCATCTTTCTCTTCAT
1 CTTTTCTTTCTTCTTCTCCTTATCCTCCTTCTCTTTCTTCTTTCTCTTCCCATCTTTCTCTTCAT
*
186071 CTTCTTCTACCT
66 CTACTTCTACCT
186083 CAACCTCTTT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
81 51 0.80
82 7 0.11
83 6 0.09
ACGTcount: A:0.04, C:0.33, G:0.03, T:0.60
Consensus pattern (81 bp):
CTTTTCTTTCTTCTTCTCCTTATCCTCCTTCTCTTTCTTCTTTCTCTTCCCATCTTTCTCTTCAT
CTACTTCTACCTTGTG
Found at i:186067 original size:27 final size:27
Alignment explanation
Indices: 186006--186076 Score: 65
Period size: 27 Copynumber: 2.6 Consensus size: 27
185996 CTACCTTGTG
*
186006 CTTTTCTTTCTTC-TTCTCTTTCTCCT
1 CTTTTCTTTCTTCTTTCTCTTTCTCAT
* *
186032 CCTTGTCTTTCTTCTTTTTC-TTCTCAT
1 -CTTTTCTTTCTTCTTTCTCTTTCTCAT
186059 CTTTCTCTTCATCTTCTT
1 CTTT-TCTT--TCTTCTT
186077 CTACCTCAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
26 3 0.08
27 22 0.61
28 4 0.11
29 7 0.19
ACGTcount: A:0.03, C:0.32, G:0.01, T:0.63
Consensus pattern (27 bp):
CTTTTCTTTCTTCTTTCTCTTTCTCAT
Found at i:186107 original size:90 final size:89
Alignment explanation
Indices: 186013--186258 Score: 261
Period size: 90 Copynumber: 2.8 Consensus size: 89
186003 GTGCTTTTCT
*
186013 TTCTTCTTCTCTTTCTCCTCCTTGTCTTTCTTCTTTTTCTTCTCATCTTTCTCTTCATCTTCTTC
1 TTCTT-TTCTCTTTCTCCTCCTTATCTTTCTTCTTTTTCTTCTCATCTTTCTCTTCATCTTCTTC
186078 TACCTCAACCTCTTTTTCCTTGTGC
65 TACCTCAACCTCTTTTTCCTTGTGC
* * * * * * *
186103 TTCTTTTCCTTTTTCTTCTCCTTCCCACCTTT-GTC-TTTT-TTCACATCTTTCACTTCATTTTC
1 TTCTTTT-CTCTTTCTCCTCCTT---ATCTTTCTTCTTTTTCTTCTCATCTTTCTCTTCATCTTC
* *
186165 TTCTCCCTCGACCTCTTTTTCCTTGTGC
62 TTCTACCTCAACCTCTTTTTCCTTGTGC
* * * * *
186193 TTCTTTT-TC-TTCTCCTTCTCATC-CTCATCCTTTTTCTTCTCTTCTTTCTCTTCATCTTCTTC
1 TTCTTTTCTCTTTCTCCTCCTTATCTTTC-TTCTTTTTCTTCTCATCTTTCTCTTCATCTTCTTC
186255 TACC
65 TACC
186259 GCCTCTTTAC
Statistics
Matches: 125, Mismatches: 23, Indels: 19
0.75 0.14 0.11
Matches are distributed among these distances:
83 1 0.01
84 2 0.02
85 1 0.01
86 4 0.03
87 33 0.26
88 1 0.01
89 2 0.02
90 71 0.57
91 4 0.03
92 2 0.02
93 4 0.03
ACGTcount: A:0.06, C:0.35, G:0.03, T:0.56
Consensus pattern (89 bp):
TTCTTTTCTCTTTCTCCTCCTTATCTTTCTTCTTTTTCTTCTCATCTTTCTCTTCATCTTCTTCT
ACCTCAACCTCTTTTTCCTTGTGC
Found at i:187830 original size:80 final size:80
Alignment explanation
Indices: 187588--187912 Score: 544
Period size: 80 Copynumber: 4.1 Consensus size: 80
187578 CTCCAAATAT
* * * *
187588 CAAGAATCAAAACAGAAGACATAGATATTCACCCGCATGATACTTATCAGTCCAGATCTTATTCA
1 CAAGAATCGAAACAGCAGACACAGATATTCACCCGCATGATACTAATCAGTCCAGATCTTATTCA
* *
187653 ATCTATACACATAAA
66 ATCTATATACATCAA
* *
187668 AAAGAATCGAAACAGCAGACATAGATATTCACCCGCATGATA-TAATCAGTCCAGATCTTATTCA
1 CAAGAATCGAAACAGCAGACACAGATATTCACCCGCATGATACTAATCAGTCCAGATCTTATTCA
187732 ATCTATATACATCAA
66 ATCTATATACATCAA
*
187747 CAAGAATCGAAACAGCAGACACAGATATTCACCCGCATGATACTAATCAGTCCAGATCGTATTCA
1 CAAGAATCGAAACAGCAGACACAGATATTCACCCGCATGATACTAATCAGTCCAGATCTTATTCA
187812 ATCTATATACATCAA
66 ATCTATATACATCAA
*
187827 CAAGAATCGAAACAGCAGACACAGATATTCACCCGCATGATACTAATCAGTCCAGATCTAATTCA
1 CAAGAATCGAAACAGCAGACACAGATATTCACCCGCATGATACTAATCAGTCCAGATCTTATTCA
*
187892 ATCTATATACATCAG
66 ATCTATATACATCAA
187907 CAAGAA
1 CAAGAA
187913 GGTAGTTGAA
Statistics
Matches: 232, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
79 74 0.32
80 158 0.68
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (80 bp):
CAAGAATCGAAACAGCAGACACAGATATTCACCCGCATGATACTAATCAGTCCAGATCTTATTCA
ATCTATATACATCAA
Found at i:187928 original size:159 final size:159
Alignment explanation
Indices: 187588--187912 Score: 524
Period size: 159 Copynumber: 2.0 Consensus size: 159
187578 CTCCAAATAT
* * * * *
187588 CAAGAATCAAAACAGAAGACATAGATATTCACCCGCATGATACTTATCAGTCCAGATCTTATTCA
1 CAAGAATCGAAACAGAAAACACAGATATTCACCCGCATGATACTAATCAGTCCAGATCGTATTCA
*
187653 ATCTATACACATAAAAAAGAATCGAAACAGCAGACATAGATATTCACCCGCATGATATAATCAGT
66 ATCTATACACATAAAAAAGAATCGAAACAGCAGACACAGATATTCACCCGCATGATATAATCAGT
*
187718 CCAGATCTTATTCAATCTATATACATCAA
131 CCAGATCTAATTCAATCTATATACATCAA
* *
187747 CAAGAATCGAAACAGCAGACACAGATATTCACCCGCATGATACTAATCAGTCCAGATCGTATTCA
1 CAAGAATCGAAACAGAAAACACAGATATTCACCCGCATGATACTAATCAGTCCAGATCGTATTCA
* * *
187812 ATCTATATACATCAACAAGAATCGAAACAGCAGACACAGATATTCACCCGCATGATACTAATCAG
66 ATCTATACACATAAAAAAGAATCGAAACAGCAGACACAGATATTCACCCGCATGATA-TAATCAG
*
187877 TCCAGATCTAATTCAATCTATATACATCAG
130 TCCAGATCTAATTCAATCTATATACATCAA
187907 CAAGAA
1 CAAGAA
187913 GGTAGTTGAA
Statistics
Matches: 154, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
159 113 0.73
160 41 0.27
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (159 bp):
CAAGAATCGAAACAGAAAACACAGATATTCACCCGCATGATACTAATCAGTCCAGATCGTATTCA
ATCTATACACATAAAAAAGAATCGAAACAGCAGACACAGATATTCACCCGCATGATATAATCAGT
CCAGATCTAATTCAATCTATATACATCAA
Found at i:189884 original size:30 final size:35
Alignment explanation
Indices: 189801--189880 Score: 153
Period size: 35 Copynumber: 2.3 Consensus size: 35
189791 ATCTGTATTT
189801 TTTA-AATATTATTATGTTATAGACTTTAGTTTTG
1 TTTATAATATTATTATGTTATAGACTTTAGTTTTG
189835 TTTATAATATTATTATGTTATAGACTTTAGTTTTG
1 TTTATAATATTATTATGTTATAGACTTTAGTTTTG
189870 TTTATAATATT
1 TTTATAATATT
189881 GTTAATAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
34 4 0.09
35 41 0.91
ACGTcount: A:0.30, C:0.03, G:0.10, T:0.57
Consensus pattern (35 bp):
TTTATAATATTATTATGTTATAGACTTTAGTTTTG
Found at i:190150 original size:8 final size:8
Alignment explanation
Indices: 190137--190180 Score: 88
Period size: 8 Copynumber: 5.5 Consensus size: 8
190127 ATTATTAGTT
190137 TTAAAAAA
1 TTAAAAAA
190145 TTAAAAAA
1 TTAAAAAA
190153 TTAAAAAA
1 TTAAAAAA
190161 TTAAAAAA
1 TTAAAAAA
190169 TTAAAAAA
1 TTAAAAAA
190177 TTAA
1 TTAA
190181 TTATAATGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 36 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
TTAAAAAA
Found at i:190242 original size:18 final size:18
Alignment explanation
Indices: 190219--190282 Score: 69
Period size: 17 Copynumber: 3.7 Consensus size: 18
190209 AAATAAAAAG
190219 TAATATTTTATAAATTTT
1 TAATATTTTATAAATTTT
*
190237 TAATA-TTTATAAATATT
1 TAATATTTTATAAATTTT
* * *
190254 AAAGATTTGATAAA-TTT
1 TAATATTTTATAAATTTT
*
190271 TAATATTATATA
1 TAATATTTTATA
190283 TATATATATT
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
17 24 0.67
18 12 0.33
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (18 bp):
TAATATTTTATAAATTTT
Found at i:192307 original size:13 final size:13
Alignment explanation
Indices: 192291--192361 Score: 88
Period size: 13 Copynumber: 5.1 Consensus size: 13
192281 ATAAACAAAT
192291 AATTTAAAGCATA
1 AATTTAAAGCATA
*
192304 AATTTAAATTGTGAATA
1 AATTTAAA----GCATA
192321 AATTTAAAGCATA
1 AATTTAAAGCATA
192334 AATTTAAAGCATA
1 AATTTAAAGCATA
192347 AATTTAAAGGCATA
1 AATTTAAA-GCATA
192361 A
1 A
192362 TGGAAATAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
13 33 0.65
14 6 0.12
17 12 0.24
ACGTcount: A:0.52, C:0.06, G:0.10, T:0.32
Consensus pattern (13 bp):
AATTTAAAGCATA
Found at i:192309 original size:43 final size:42
Alignment explanation
Indices: 192261--192376 Score: 132
Period size: 43 Copynumber: 2.7 Consensus size: 42
192251 TTAATATCGG
192261 AATTTAAAGGCATAATGGAAATAAACAAATAATTTAAAGCATA
1 AATTTAAAGGCATAATGGAAATAAACAAA-AATTTAAAGCATA
* *
192304 AATTTAAATTG--TGAAT--AAATTTAAAGCATAAATTTAAAGCATA
1 AATTTAAA-GGCAT-AATGGAAA--TAAA-CAAAAATTTAAAGCATA
192347 AATTTAAAGGCATAATGGAAATAAACAAAA
1 AATTTAAAGGCATAATGGAAATAAACAAAA
192377 TAAGTTTGAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
41 3 0.05
42 6 0.10
43 43 0.72
44 5 0.08
45 3 0.05
ACGTcount: A:0.55, C:0.06, G:0.11, T:0.28
Consensus pattern (42 bp):
AATTTAAAGGCATAATGGAAATAAACAAAAATTTAAAGCATA
Found at i:203838 original size:30 final size:31
Alignment explanation
Indices: 203771--203870 Score: 139
Period size: 31 Copynumber: 3.3 Consensus size: 31
203761 GTACATATAT
*
203771 CACATTAGGAATTTTGTCGAAGTATAAGTAG
1 CACATTAGGAATTTTGTCAAAGTATAAGTAG
* *
203802 CACATTAAGAATTTTGTCAAAGTATAGGTA-
1 CACATTAGGAATTTTGTCAAAGTATAAGTAG
* *
203832 CACATTAGGCATTTTGTCAAAGTATAAGTAA
1 CACATTAGGAATTTTGTCAAAGTATAAGTAG
*
203863 AACATTAG
1 CACATTAG
203871 ACTTTTTTGA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
30 27 0.44
31 34 0.56
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (31 bp):
CACATTAGGAATTTTGTCAAAGTATAAGTAG
Found at i:205490 original size:16 final size:16
Alignment explanation
Indices: 205469--205500 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
205459 CTGCATGGCC
205469 CTTGTTTGGCTTAACA
1 CTTGTTTGGCTTAACA
205485 CTTGTTTGGCTTAACA
1 CTTGTTTGGCTTAACA
205501 GAGAGTCCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (16 bp):
CTTGTTTGGCTTAACA
Found at i:209092 original size:16 final size:16
Alignment explanation
Indices: 209071--209103 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
209061 TCATTTTCAC
209071 CACCAACAATTCTCAT
1 CACCAACAATTCTCAT
209087 CACCAACAATTCTCAT
1 CACCAACAATTCTCAT
209103 C
1 C
209104 TTGAAACTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.39, G:0.00, T:0.24
Consensus pattern (16 bp):
CACCAACAATTCTCAT
Found at i:210258 original size:80 final size:79
Alignment explanation
Indices: 210120--210374 Score: 375
Period size: 80 Copynumber: 3.2 Consensus size: 79
210110 GACCCTCCAA
* * *
210120 ATACATCAACAAGAATCAAAACAGAAGACAGAGATATTCACCTGCATGATACTTATCAGTCCAGA
1 ATACATCAACAAGAATCGAAACAGAAGACACAGATATTCACC-GCATGATACTAATCAGTCCAGA
210185 TCTTATTCAATCTAT
65 TCTTATTCAATCTAT
* * *
210200 ATACATCAAAAAGAATCGAAACAGCAGACATAGATATTCACTCGCATGATACTAATCAGTCCAGA
1 ATACATCAACAAGAATCGAAACAGAAGACACAGATATTCAC-CGCATGATACTAATCAGTCCAGA
210265 TCTTATTCAATCTAT
65 TCTTATTCAATCTAT
* * * *
210280 ATATATCAACAAGAATAGAAACAGAAGACACATATATTCACCCGCATGATACTAATCAGTCCATA
1 ATACATCAACAAGAATCGAAACAGAAGACACAGATATTCA-CCGCATGATACTAATCAGTCCAGA
*
210345 TCTAATTCAATCTAT
65 TCTTATTCAATCTAT
*
210360 ATACATCAGCAAGAA
1 ATACATCAACAAGAA
210375 GGTAGTTGAA
Statistics
Matches: 158, Mismatches: 15, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
80 156 0.99
81 2 0.01
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.25
Consensus pattern (79 bp):
ATACATCAACAAGAATCGAAACAGAAGACACAGATATTCACCGCATGATACTAATCAGTCCAGAT
CTTATTCAATCTAT
Found at i:211255 original size:35 final size:36
Alignment explanation
Indices: 211216--211311 Score: 83
Period size: 37 Copynumber: 2.7 Consensus size: 36
211206 TATAATATTT
*
211216 TTTTTAGTGTAACCTAAAATGTTATTATTT-TAATA
1 TTTTTAATGTAACCTAAAATGTTATTATTTATAATA
* * *
211251 TTTTTGAT-TGAA-TTGAAAATGTTAATTTTTTATAATA
1 TTTTTAATGT-AACCT-AAAATGTT-ATTATTTATAATA
*
211288 TTTTTAAT-TCAACCTAAAGTGTTA
1 TTTTTAATGT-AACCTAAAATGTTA
211312 AGAAGATTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
34 2 0.04
35 16 0.33
36 7 0.15
37 22 0.46
38 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.09, T:0.51
Consensus pattern (36 bp):
TTTTTAATGTAACCTAAAATGTTATTATTTATAATA
Found at i:211311 original size:37 final size:36
Alignment explanation
Indices: 211226--211312 Score: 97
Period size: 37 Copynumber: 2.4 Consensus size: 36
211216 TTTTTAGTGT
* *
211226 AACCTAAAATGTT-ATTATTTTAATATTTTTGATTG
1 AACCTAAAATGTTAATTATTTTAATATTTTTAATTC
* *
211261 AA-TTGAAAATGTTAATTTTTTATAATATTTTTAATTC
1 AACCT-AAAATGTTAATTATTT-TAATATTTTTAATTC
*
211298 AACCTAAAGTGTTAA
1 AACCTAAAATGTTAA
211313 GAAGATTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
34 1 0.02
35 10 0.24
36 6 0.14
37 24 0.57
38 1 0.02
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (36 bp):
AACCTAAAATGTTAATTATTTTAATATTTTTAATTC
Found at i:212411 original size:17 final size:17
Alignment explanation
Indices: 212389--212444 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
212379 TAATATTTTA
212389 TATAAATTTTTAATATT
1 TATAAATTTTTAATATT
* *
212406 TATAAATTTTAAAGATT
1 TATAAATTTTTAATATT
212423 TGATAAA-TTTTAATATT
1 T-ATAAATTTTTAATATT
212440 ATATA
1 -TATA
212445 TATGTATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 27 0.82
18 6 0.18
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (17 bp):
TATAAATTTTTAATATT
Found at i:214531 original size:28 final size:28
Alignment explanation
Indices: 214500--214595 Score: 77
Period size: 28 Copynumber: 3.2 Consensus size: 28
214490 TGTGAATTTT
**
214500 AAAAATATAAAAATTTA-ATACAAAATAG
1 AAAAATA-AAAAATAAATATACAAAATAG
* *
214528 AAAAATAAATAATAAATATATAAAATAG
1 AAAAATAAAAAATAAATATACAAAATAG
*
214556 AAAAATAATTAAAATATATATATACATAATATG
1 AAAAATAA--AAAATA-A-ATATACAAAATA-G
*
214589 ATAAATA
1 AAAAATA
214596 TTATTATTCA
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
27 6 0.11
28 25 0.46
30 5 0.09
31 1 0.02
32 10 0.19
33 7 0.13
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (28 bp):
AAAAATAAAAAATAAATATACAAAATAG
Found at i:214579 original size:30 final size:29
Alignment explanation
Indices: 214500--214579 Score: 85
Period size: 28 Copynumber: 2.8 Consensus size: 29
214490 TGTGAATTTT
* *
214500 AAAAAT-ATAAAA-ATTTAATACAAAATAG
1 AAAAATAATAAAATATAT-ATATAAAATAG
* *
214528 AAAAATAA-ATAATAAATATATAAAATAG
1 AAAAATAATAAAATATATATATAAAATAG
214556 AAAAATAATTAAAATATATATATA
1 AAAAATAA-TAAAATATATATATA
214580 CATAATATGA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
28 27 0.64
29 3 0.07
30 12 0.29
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.28
Consensus pattern (29 bp):
AAAAATAATAAAATATATATATAAAATAG
Found at i:214629 original size:111 final size:111
Alignment explanation
Indices: 214514--214714 Score: 270
Period size: 113 Copynumber: 1.8 Consensus size: 111
214504 ATATAAAAAT
214514 TTAATACAAAATAGAAAAATAAATAATA-AA-TATAT-AAAA-TAGA-AAAATAAT-TAAAATAT
1 TTAATA-AAAATAGAAAAATAAA-AATAGAAGTATATAAAAATTAGATAAAA-AATAT-AAATAT
214573 ATATATACATAATATGATAAATATTATTATTCAAAAAATATGTATTTATATA
62 ATATATACATAATATGATAAAT-TT-TTATTCAAAAAATATGTATTTATATA
** * *
214625 TTAATAATGATAGAAAAATATAAATAGAAGTATATAAAAATTAGATGAAAAATATAAATATATAT
1 TTAATAAAAATAGAAAAATAAAAATAGAAGTATATAAAAATTAGATAAAAAATATAAATATATAT
214690 ATACATAATATGATAAATTTTTATT
66 ATACATAATATGATAAATTTTTATT
214715 AATTATTTGA
Statistics
Matches: 80, Mismatches: 4, Indels: 12
0.83 0.04 0.12
Matches are distributed among these distances:
109 4 0.05
110 15 0.19
111 16 0.20
112 6 0.08
113 35 0.44
114 4 0.05
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (111 bp):
TTAATAAAAATAGAAAAATAAAAATAGAAGTATATAAAAATTAGATAAAAAATATAAATATATAT
ATACATAATATGATAAATTTTTATTCAAAAAATATGTATTTATATA
Found at i:217730 original size:31 final size:30
Alignment explanation
Indices: 217695--217787 Score: 141
Period size: 30 Copynumber: 3.1 Consensus size: 30
217685 GTACATATAT
*
217695 CACATTAGGAATTTTGTCGAAGTATAAGTA
1 CACATTAGGAATTTTGTCAAAGTATAAGTA
*
217725 GCACATTAGGAATTTTGTCAAAGTATAGGTA
1 -CACATTAGGAATTTTGTCAAAGTATAAGTA
* *
217756 CACATTAGGCATTTTGTCAAAGTATAAATA
1 CACATTAGGAATTTTGTCAAAGTATAAGTA
217786 CA
1 CA
217788 AAATTAGACT
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 29 0.51
31 28 0.49
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (30 bp):
CACATTAGGAATTTTGTCAAAGTATAAGTA
Found at i:217762 original size:30 final size:31
Alignment explanation
Indices: 217695--217782 Score: 142
Period size: 31 Copynumber: 2.9 Consensus size: 31
217685 GTACATATAT
*
217695 CACATTAGGAATTTTGTCGAAGTATAAGTAG
1 CACATTAGGAATTTTGTCAAAGTATAAGTAG
*
217726 CACATTAGGAATTTTGTCAAAGTATAGGTA-
1 CACATTAGGAATTTTGTCAAAGTATAAGTAG
*
217756 CACATTAGGCATTTTGTCAAAGTATAA
1 CACATTAGGAATTTTGTCAAAGTATAA
217783 ATACAAAATT
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 25 0.47
31 28 0.53
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.33
Consensus pattern (31 bp):
CACATTAGGAATTTTGTCAAAGTATAAGTAG
Found at i:217802 original size:31 final size:30
Alignment explanation
Indices: 217705--217803 Score: 92
Period size: 31 Copynumber: 3.2 Consensus size: 30
217695 CACATTAGGA
* * *
217705 ATTTTGTCGAAGTATAAGTAGCACATTAGGA-
1 ATTTTGTCAAAGTATAAATA-CAAATTA-GAC
** * *
217736 ATTTTGTCAAAGTATAGGTACACATTAGGC
1 ATTTTGTCAAAGTATAAATACAAATTAGAC
217766 ATTTTGTCAAAGTATAAATACAAAATTAGAC
1 ATTTTGTCAAAGTATAAATAC-AAATTAGAC
*
217797 TTTTTGT
1 ATTTTGT
217804 GATCAACGCA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
29 1 0.02
30 26 0.45
31 31 0.53
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (30 bp):
ATTTTGTCAAAGTATAAATACAAATTAGAC
Found at i:218595 original size:22 final size:22
Alignment explanation
Indices: 218567--218614 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
218557 AATATTAAGA
218567 GGTACTGATACCCCTATGAAAG
1 GGTACTGATACCCCTATGAAAG
*
218589 GGTACTGATACCCCTATGAATG
1 GGTACTGATACCCCTATGAAAG
218611 GGTA
1 GGTA
218615 TCATGAAGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (22 bp):
GGTACTGATACCCCTATGAAAG
Found at i:225280 original size:20 final size:20
Alignment explanation
Indices: 225255--225315 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
225245 TTTTGATGCA
*
225255 GAAGGAATCGATACCCCCAT
1 GAAGGAACCGATACCCCCAT
* *
225275 GAAGGAACCGATTCCCCCTTT
1 GAAGGAACCGATACCCCC-AT
*
225296 GAAGGGGAACCGATTCCCCC
1 GAA--GGAACCGATACCCCC
225316 CACAGGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 16 0.46
21 4 0.11
23 15 0.43
ACGTcount: A:0.28, C:0.33, G:0.23, T:0.16
Consensus pattern (20 bp):
GAAGGAACCGATACCCCCAT
Found at i:225324 original size:21 final size:21
Alignment explanation
Indices: 225298--225337 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
225288 CCCCCTTTGA
*
225298 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
225319 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
225338 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:226999 original size:17 final size:17
Alignment explanation
Indices: 226973--227014 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
226963 ATTGATCAAT
226973 AACAAGAAACATCAAGC
1 AACAAGAAACATCAAGC
*
226990 AACAATAAACATCAAGC
1 AACAAGAAACATCAAGC
*
227007 AACTAGAA
1 AACAAGAA
227015 TCAAGTGAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.60, C:0.21, G:0.10, T:0.10
Consensus pattern (17 bp):
AACAAGAAACATCAAGC
Found at i:231834 original size:10 final size:10
Alignment explanation
Indices: 231810--231863 Score: 58
Period size: 10 Copynumber: 5.6 Consensus size: 10
231800 ATTTTATTTA
*
231810 TAATAA-TAG
1 TAATAATTAT
231819 TAATAATTAT
1 TAATAATTAT
*
231829 TAATAATAAT
1 TAATAATTAT
*
231839 TAATAATAAT
1 TAATAATTAT
*
231849 T-ATTATTAT
1 TAATAATTAT
231858 TAATAA
1 TAATAA
231864 ACAATCAGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
9 13 0.34
10 25 0.66
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (10 bp):
TAATAATTAT
Found at i:231837 original size:13 final size:13
Alignment explanation
Indices: 231819--231863 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
231809 ATAATAATAG
231819 TAATAATTATTAA
1 TAATAATTATTAA
*
231832 TAATAATTAATAA
1 TAATAATTATTAA
* *
231845 TAATTATTATTAT
1 TAATAATTATTAA
231858 TAATAA
1 TAATAA
231864 ACAATCAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAATAATTATTAA
Found at i:232509 original size:2 final size:2
Alignment explanation
Indices: 232504--232528 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
232494 TGTTTTTTTA
232504 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 A
232529 AAACTTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:233270 original size:31 final size:31
Alignment explanation
Indices: 233235--233299 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
233225 ATTTGGTCGG
* * *
233235 ATTCAAGGGTTAAAATGTTATTTTATTTAAA
1 ATTCAAGGGTCAAAATGATATTTTATATAAA
* *
233266 ATTCAATGGTCAAATTGATATTTTATATAAA
1 ATTCAAGGGTCAAAATGATATTTTATATAAA
233297 ATT
1 ATT
233300 TAGGAATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.45
Consensus pattern (31 bp):
ATTCAAGGGTCAAAATGATATTTTATATAAA
Found at i:233331 original size:30 final size:31
Alignment explanation
Indices: 233278--233336 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
233268 TCAATGGTCA
*
233278 AATTGATATTTTATATAAAATTTAGGAATTT
1 AATTGACATTTTATATAAAATTTAGGAATTT
* *
233309 AATTGACATTTTATCT-AAATTTATGAAT
1 AATTGACATTTTATATAAAATTTAGGAAT
233337 CAGGTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (31 bp):
AATTGACATTTTATATAAAATTTAGGAATTT
Found at i:240535 original size:27 final size:27
Alignment explanation
Indices: 240497--240551 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
240487 GGAAAAGGAG
240497 GCCAATGCCATAGCTCAACTCCTGACA
1 GCCAATGCCATAGCTCAACTCCTGACA
240524 GCCAATGCCATAGCTCAACTCCTGACA
1 GCCAATGCCATAGCTCAACTCCTGACA
240551 G
1 G
240552 AAAAGTCTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.36, G:0.16, T:0.18
Consensus pattern (27 bp):
GCCAATGCCATAGCTCAACTCCTGACA
Found at i:244299 original size:36 final size:34
Alignment explanation
Indices: 244241--244308 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 34
244231 TTTTAACAAC
*
244241 ATTTAATAATTTTTATTCATTTTTAATAAAATTAGA
1 ATTTAATAATTTTTAATCATTTTT--TAAAATTAGA
*
244277 ATTTAATATTTATTTAAT-ATTTTTTAAAATTA
1 ATTTAATAATT-TTTAATCATTTTTTAAAATTA
244309 ATATTAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 8 0.28
36 16 0.55
37 5 0.17
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (34 bp):
ATTTAATAATTTTTAATCATTTTTTAAAATTAGA
Found at i:244407 original size:11 final size:11
Alignment explanation
Indices: 244361--244419 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
244351 GCTTTACATT
244361 TTTTTATTG-A
1 TTTTTATTGTA
*
244371 ATTTTATT-TA
1 TTTTTATTGTA
* * *
244381 CTTTTAATTCTT
1 -TTTTTATTGTA
244393 TTTTTATTGTA
1 TTTTTATTGTA
244404 TTTTTATTG-A
1 TTTTTATTGTA
244414 TTTTTA
1 TTTTTA
244420 AATATATGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
10 15 0.38
11 23 0.59
12 1 0.03
ACGTcount: A:0.20, C:0.03, G:0.05, T:0.71
Consensus pattern (11 bp):
TTTTTATTGTA
Found at i:252189 original size:30 final size:30
Alignment explanation
Indices: 252122--252221 Score: 146
Period size: 31 Copynumber: 3.3 Consensus size: 30
252112 GTACATATAT
*
252122 CACATTAGGAATTTTGTCGAAGTATAAGTA
1 CACATTAGGAATTTTGTCAAAGTATAAGTA
* *
252152 GCACATTAGGAATTATGTCAAAGTATAGGTA
1 -CACATTAGGAATTTTGTCAAAGTATAAGTA
*
252183 CACATTAGGCATTTTGTCAAAGTATAAGTA
1 CACATTAGGAATTTTGTCAAAGTATAAGTA
252213 CAACATTAG
1 C-ACATTAG
252222 ACTTTTTTTG
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
30 28 0.45
31 34 0.55
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (30 bp):
CACATTAGGAATTTTGTCAAAGTATAAGTA
Found at i:253035 original size:22 final size:22
Alignment explanation
Indices: 253007--253072 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
252997 AGAGGTACTG
* *
253007 ATACCCCTATCAATGGGCATCA
1 ATACCCCTATGAATGGGTATCA
* *
253029 ATACCCCTATGAATGGGTACCG
1 ATACCCCTATGAATGGGTATCA
253051 ATACCCCTATGAATGGGTATCA
1 ATACCCCTATGAATGGGTATCA
253073 TGAAGGCTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.24
Consensus pattern (22 bp):
ATACCCCTATGAATGGGTATCA
Found at i:253395 original size:20 final size:20
Alignment explanation
Indices: 253343--253388 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
253333 ACACTTGAAG
*
253343 AAGCAAGAAAACAACTATCC
1 AAGCAAGAAAACAACTATAC
253363 AAGCAAGAAAACAACTATAC
1 AAGCAAGAAAACAACTATAC
253383 AAGCAA
1 AAGCAA
253389 ACAAACACAA
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:0.59, C:0.22, G:0.11, T:0.09
Consensus pattern (20 bp):
AAGCAAGAAAACAACTATAC
Found at i:255445 original size:86 final size:85
Alignment explanation
Indices: 255276--255459 Score: 314
Period size: 88 Copynumber: 2.1 Consensus size: 85
255266 CTTCAACTTT
*
255276 ATCATATAAAATATGTAATCAGATAAGATTTTATAGTCTGAAAACGACAAAGTATTTCCTAAAGT
1 ATCATATAAAATATGTAATCAGAAAAGATTTTATAGTCTGAAAACGACAAAGTATTTCCTAAAGT
255341 TTCCAACTTTAATTTTTTTTA
66 TTCCAACTTTAA-TTTTTTTA
255362 ATCATATAAAATATGTAATCAGAAAAGATTTTTTATAGTCTGAAAACGACAAAGTATTTCCTAAA
1 ATCATATAAAATATGTAATCAGAAAAGA--TTTTATAGTCTGAAAACGACAAAGTATTTCCTAAA
* *
255427 GTTTTCAATTTTAATTTTTTTA
64 GTTTCCAACTTTAATTTTTTTA
255449 ATCATATAAAA
1 ATCATATAAAA
255460 GAAAAAAAGT
Statistics
Matches: 93, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
86 27 0.29
87 19 0.20
88 47 0.51
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (85 bp):
ATCATATAAAATATGTAATCAGAAAAGATTTTATAGTCTGAAAACGACAAAGTATTTCCTAAAGT
TTCCAACTTTAATTTTTTTA
Found at i:255712 original size:14 final size:15
Alignment explanation
Indices: 255693--255722 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
255683 AAAGTCTTTT
255693 AAAATAA-TTTTAAA
1 AAAATAATTTTTAAA
255707 AAAATAATTTTTAAA
1 AAAATAATTTTTAAA
255722 A
1 A
255723 CAAAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAATAATTTTTAAA
Found at i:258114 original size:10 final size:10
Alignment explanation
Indices: 258090--258130 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
258080 ATTTTATTTA
*
258090 TAATAA-TAG
1 TAATAATTAT
258099 TAATAATTAT
1 TAATAATTAT
*
258109 TAATAATAAT
1 TAATAATTAT
258119 TAATAATTAT
1 TAATAATTAT
258129 TA
1 TA
258131 TTATTAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
9 6 0.21
10 22 0.79
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (10 bp):
TAATAATTAT
Found at i:258117 original size:13 final size:13
Alignment explanation
Indices: 258099--258140 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
258089 ATAATAATAG
258099 TAATAATTATTAA
1 TAATAATTATTAA
*
258112 TAATAATTAATAA
1 TAATAATTATTAA
* *
258125 TTATTATTATTAA
1 TAATAATTATTAA
258138 TAA
1 TAA
258141 ACAATCAGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAATAATTATTAA
Found at i:258785 original size:2 final size:2
Alignment explanation
Indices: 258780--258818 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
258770 TGTTTTTTTA
258780 AT AT AT 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 AT AT AT A
258819 CTTTCATGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:259562 original size:31 final size:31
Alignment explanation
Indices: 259527--259588 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
259517 ATTTGGTCGG
* * *
259527 ATTCAAGGGTTAAAATGTTATTTTATTTAAA
1 ATTCAAGGGTCAAAATGATATTTTATATAAA
* *
259558 ATTCAATGGTCAAATTGATATTTTATATAAA
1 ATTCAAGGGTCAAAATGATATTTTATATAAA
259589 TTTAGGAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (31 bp):
ATTCAAGGGTCAAAATGATATTTTATATAAA
Found at i:259604 original size:30 final size:30
Alignment explanation
Indices: 259570--259627 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
259560 TCAATGGTCA
* *
259570 AATTGATATTTTATATAAATTTAGGAATTT
1 AATTGACATTTTATATAAATTTACGAATTT
*
259600 AATTGACATTTTATCTAAATTTACGAAT
1 AATTGACATTTTATATAAATTTACGAAT
259628 CAGGTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.47
Consensus pattern (30 bp):
AATTGACATTTTATATAAATTTACGAATTT
Found at i:264679 original size:6 final size:6
Alignment explanation
Indices: 264668--264723 Score: 76
Period size: 6 Copynumber: 9.3 Consensus size: 6
264658 TTTCTCTATT
* * *
264668 TATATG TATATG TATATG TATATG TATATG TAGATG TAGATG TAGATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
*
264716 TAGATG TA
1 TATATG TA
264724 GACATAGATG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (6 bp):
TATATG
Found at i:264691 original size:18 final size:18
Alignment explanation
Indices: 264668--264723 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
264658 TTTCTCTATT
*
264668 TATATGTATATGTATATG
1 TATATGTATATGTAGATG
264686 TATATGTATATGTAGATG
1 TATATGTATATGTAGATG
* *
264704 TAGATGTAGATGTAGATG
1 TATATGTATATGTAGATG
264722 TA
1 TA
264724 GACATAGATG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (18 bp):
TATATGTATATGTAGATG
Found at i:264731 original size:18 final size:18
Alignment explanation
Indices: 264695--264733 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
264685 GTATATGTAT
**
264695 ATGTAGATGTAGATGTAG
1 ATGTAGATGTAGACATAG
264713 ATGTAGATGTAGACATAG
1 ATGTAGATGTAGACATAG
264731 ATG
1 ATG
264734 ATATATCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.36, C:0.03, G:0.31, T:0.31
Consensus pattern (18 bp):
ATGTAGATGTAGACATAG
Found at i:270723 original size:21 final size:21
Alignment explanation
Indices: 270699--270738 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
270689 TAACAAAGGT
*
270699 AGTACCGATACTCTCTGTAGG
1 AGTACCGATACCCTCTGTAGG
270720 AGTACCGATACCCTCTGTA
1 AGTACCGATACCCTCTGTA
270739 TTGGGTAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.28
Consensus pattern (21 bp):
AGTACCGATACCCTCTGTAGG
Found at i:274199 original size:21 final size:21
Alignment explanation
Indices: 274175--274214 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
274165 TAACAAAGGT
*
274175 AGTACCGATACTCTCTGTAGG
1 AGTACCGATACCCTCTGTAGG
*
274196 AGTATCGATACCCTCTGTA
1 AGTACCGATACCCTCTGTA
274215 TTGGGTAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (21 bp):
AGTACCGATACCCTCTGTAGG
Found at i:280085 original size:19 final size:19
Alignment explanation
Indices: 280061--280111 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
280051 TTATTAAATC
280061 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
280080 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
280099 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
280112 TTCAATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:280150 original size:21 final size:21
Alignment explanation
Indices: 280124--280163 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
280114 CAATTTATTC
280124 ATTGATACATCGATGCATGGT
1 ATTGATACATCGATGCATGGT
* *
280145 ATTGATGCATCGGTGCATG
1 ATTGATACATCGATGCATG
280164 CCTTTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (21 bp):
ATTGATACATCGATGCATGGT
Found at i:281951 original size:20 final size:20
Alignment explanation
Indices: 281915--281965 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
281905 TTAAATTCAG
*
281915 AATTTCGAAAA--AAAAATT
1 AATTTCGAAAATTAAAAATA
*
281933 TATTTCGAAAATTAAAAATA
1 AATTTCGAAAATTAAAAATA
*
281953 AATTTTGAAAATT
1 AATTTCGAAAATT
281966 TGTGAGTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 10 0.37
20 17 0.63
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (20 bp):
AATTTCGAAAATTAAAAATA
Found at i:286217 original size:52 final size:51
Alignment explanation
Indices: 286103--286926 Score: 938
Period size: 52 Copynumber: 15.7 Consensus size: 51
286093 AATCGTGTCT
* * *
286103 GCTCCCTATTTCTTCAGAGAGTATAGAACTCGA-ACATCTTCTTCAAACGGGTTC
1 GCTCCCTCTTTCTTCAGGGAGTATGGAACTCGATA-A---TCTTCAAACGGGTTC
*
286157 GCTCCCTCTTTC-TCTAGGGAGTATGGAACTCAGATAATCTCCAAACGGGTTC
1 GCTCCCTCTTTCTTC-AGGGAGTATGGAACTC-GATAATCTTCAAACGGGTTC
* *
286209 GCTCCCTCTTT-ATCTAGGGAGTATGGAACTCGATCATCTTCAAACGGGTTC
1 GCTCCCTCTTTCTTC-AGGGAGTATGGAACTCGATAATCTTCAAACGGGTTC
* * * * * *
286260 GCTTCCTCTTTTTTTCAGGAAGTATAGAACTCGAACAATCTCCAAACGGGTTC
1 GCTCCCTC-TTTCTTCAGGGAGTATGGAACTCG-ATAATCTTCAAACGGGTTC
*
286313 GCTCCCTCTTTCTTCAGGGAGTATGGAACTCGATCATCTTCAAACGGGTTC
1 GCTCCCTCTTTCTTCAGGGAGTATGGAACTCGATAATCTTCAAACGGGTTC
* * * * *
286364 ACTTCCTCTTTCTTTCAGGAAGTATAGAACTCGAACAATCTTCAAACGGGTTC
1 GCTCCCTCTTTC-TTCAGGGAGTATGGAACTCG-ATAATCTTCAAACGGGTTC
* * *
286417 GCTCCCTCTTTCTTCAGGGAGTATAGAACTCAGACAATCTCCAAACGGGTTC
1 GCTCCCTCTTTCTTCAGGGAGTATGGAACTC-GATAATCTTCAAACGGGTTC
*
286469 GCTCCCTCTTTC-TCTAGGGAGTATGGAACTCGATCATCTTCAAACGGGTTC
1 GCTCCCTCTTTCTTC-AGGGAGTATGGAACTCGATAATCTTCAAACGGGTTC
* * * * * *
286520 GCTTCCTCTTTTTTTCAGGAAGTATAGAACTCGAACAATCTCCAAACGGGTTC
1 GCTCCCTC-TTTCTTCAGGGAGTATGGAACTCG-ATAATCTTCAAACGGGTTC
*
286573 GCTCCCTCTTTCTTCAGGGAGTATGGAACTCGATCATCTTCAAACGGGTTC
1 GCTCCCTCTTTCTTCAGGGAGTATGGAACTCGATAATCTTCAAACGGGTTC
* * * * *
286624 ACTTCCTCTTTCTTTCAGGAAGTATAGAACTCGAACAATCTTCAAACGGGTTC
1 GCTCCCTCTTTC-TTCAGGGAGTATGGAACTCG-ATAATCTTCAAACGGGTTC
* * *
286677 GCTCCCTCTTTCTTCAGGGAGTATAGAGCTCGAAAATCTTCAAACGGGTTC
1 GCTCCCTCTTTCTTCAGGGAGTATGGAACTCGATAATCTTCAAACGGGTTC
* * * *
286728 GCTCCTTCTTTCTTTAAGGAGTATGGAACTCGGAT-ATCTTCGTCAAACGAGTTC
1 GCTCCCTCTTTCTTCAGGGAGTATGGAACTC-GATAATC-T--TCAAACGGGTTC
* * * *
286782 TCTCCCTTTTTCTTCATGGAGTATGGAACTCGAACAATCTTCAAACGGGTTC
1 GCTCCCTCTTTCTTCAGGGAGTATGGAACTCG-ATAATCTTCAAACGGGTTC
* ** *
286834 GCTCCCTCTTTCTTCAGGGAGTATAGAACTCGTACCTCTTCTTCAAACGGGTTT
1 GCTCCCTCTTTCTTCAGGGAGTATGGAACTCG-A--TAATCTTCAAACGGGTTC
286888 GCTCCCTCTTTCTTCAGGGAGTATGGAACTCGAATAATC
1 GCTCCCTCTTTCTTCAGGGAGTATGGAACTCG-ATAATC
286927 CTCATTTGCT
Statistics
Matches: 660, Mismatches: 86, Indels: 50
0.83 0.11 0.06
Matches are distributed among these distances:
51 150 0.23
52 285 0.43
53 108 0.16
54 110 0.17
55 6 0.01
56 1 0.00
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (51 bp):
GCTCCCTCTTTCTTCAGGGAGTATGGAACTCGATAATCTTCAAACGGGTTC
Found at i:286603 original size:260 final size:260
Alignment explanation
Indices: 286122--286926 Score: 1255
Period size: 260 Copynumber: 3.1 Consensus size: 260
286112 TTCTTCAGAG
* *
286122 AGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTC-TCTAGGGAGTATGGAAC
1 AGTATAGAACTCGAACA--ATCTTCAAACGGGTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAAC
* *
286186 TCAGATAATCTCCAAACGGGTTCGCTCCCTCTTTATCTAGGGAGTATGGAACTCGATCATCTTCA
63 TCAGAAAATCTCCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGATCATCTTCA
286251 AACGGGTTCGCTTCCTCTTTTTTTCAGGAAGTATAGAACTCGAACAATCTCCAAACGGGTTCGCT
128 AACGGGTTCGCTTCCTCTTTTTTTCAGGAAGTATAGAACTCGAACAATCTCCAAACGGGTTCGCT
286316 CCCTCTTTCTTCAGGGAGTATGGAACTCGATCATCTTCAAACGGGTTCACTTCCTCTTTCTTTCA
193 CCCTCTTTCTTCAGGGAGTATGGAACTCGATCATCTTCAAACGGGTTCACTTCCTCTTTCTTTCA
286381 GGA
258 GGA
286384 AGTATAGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCA
1 AGTATAGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCA
*
286449 GACAATCTCCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGATCATCTTCAAAC
66 GAAAATCTCCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGATCATCTTCAAAC
286514 GGGTTCGCTTCCTCTTTTTTTCAGGAAGTATAGAACTCGAACAATCTCCAAACGGGTTCGCTCCC
131 GGGTTCGCTTCCTCTTTTTTTCAGGAAGTATAGAACTCGAACAATCTCCAAACGGGTTCGCTCCC
286579 TCTTTCTTCAGGGAGTATGGAACTCGATCATCTTCAAACGGGTTCACTTCCTCTTTCTTTCAGGA
196 TCTTTCTTCAGGGAGTATGGAACTCGATCATCTTCAAACGGGTTCACTTCCTCTTTCTTTCAGGA
*
286644 AGTATAGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAGCTC-
1 AGTATAGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCA
* * * *
286708 GAAAATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGGAT-ATCTTCGTC
66 GAAAATCTCCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC-GATCATC-T--TC
* * * *
286772 AAACGAGTTCTC-TCC-CTTTTTCTTCATGG-AGTATGGAACTCGAACAATCTTCAAACGGGTTC
127 AAACGGGTTCGCTTCCTCTTTTT-TTCA-GGAAGTATAGAACTCGAACAATCTCCAAACGGGTTC
* * ** *
286834 GCTCCCTCTTTCTTCAGGGAGTATAGAACTCGTACCTCTTCTTCAAACGGGTTTGCTCCCTCTTT
190 GCTCCCTCTTTCTTCAGGGAGTATGGAACTCG-A--TCATCTTCAAACGGGTTCACTTCCTCTTT
*
286899 C-TTCAGGG
252 CTTTCAGGA
* *
286907 AGTATGGAACTCGAATAATC
1 AGTATAGAACTCGAACAATC
286927 CTCATTTGCT
Statistics
Matches: 511, Mismatches: 22, Indels: 19
0.93 0.04 0.03
Matches are distributed among these distances:
259 49 0.10
260 309 0.60
261 71 0.14
262 32 0.06
263 24 0.05
264 26 0.05
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.32
Consensus pattern (260 bp):
AGTATAGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCA
GAAAATCTCCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGATCATCTTCAAAC
GGGTTCGCTTCCTCTTTTTTTCAGGAAGTATAGAACTCGAACAATCTCCAAACGGGTTCGCTCCC
TCTTTCTTCAGGGAGTATGGAACTCGATCATCTTCAAACGGGTTCACTTCCTCTTTCTTTCAGGA
Found at i:288173 original size:10 final size:9
Alignment explanation
Indices: 288158--288271 Score: 86
Period size: 10 Copynumber: 11.6 Consensus size: 9
288148 TTTATTCGTA
288158 TTTTTCATTT
1 TTTTTC-TTT
288168 TTTTTCTTT
1 TTTTTCTTT
288177 CCTTTTT-TATAT
1 --TTTTTCT-T-T
*
288189 TTCTTCATTCT
1 TTTTTC-TT-T
*
288200 TTTTTCCTT
1 TTTTTCTTT
*
288209 TTTTTCTTC
1 TTTTTCTTT
288218 TTTTTCTTTT
1 TTTTTC-TTT
288228 TTTTTCCTTT
1 TTTTT-CTTT
288238 TTTTTCCTTT
1 TTTTT-CTTT
*
288248 TTTTCCTTT
1 TTTTTCTTT
288257 TTTTTCCTTT
1 TTTTT-CTTT
288267 TTTTT
1 TTTTT
288272 TCCTTTTTAT
Statistics
Matches: 86, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
9 25 0.29
10 45 0.52
11 14 0.16
12 2 0.02
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:288218 original size:19 final size:20
Alignment explanation
Indices: 288196--288270 Score: 104
Period size: 19 Copynumber: 3.9 Consensus size: 20
288186 TATTTCTTCA
288196 TTCTTTTTTCCTTTTTTT-C
1 TTCTTTTTTCCTTTTTTTCC
*
288215 TTC-TTTTTCTTTTTTTTTCC
1 TTCTTTTTTC-CTTTTTTTCC
288235 TT-TTTTTTCCTTTTTTTCC
1 TTCTTTTTTCCTTTTTTTCC
288254 TT-TTTTTTCCTTTTTTT
1 TTCTTTTTTCCTTTTTTT
288271 TTCCTTTTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
18 6 0.12
19 36 0.71
20 9 0.18
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (20 bp):
TTCTTTTTTCCTTTTTTTCC
Found at i:288278 original size:10 final size:10
Alignment explanation
Indices: 288199--288279 Score: 114
Period size: 10 Copynumber: 8.3 Consensus size: 10
288189 TTCTTCATTC
288199 TTTTTTCC-T
1 TTTTTTCCTT
288208 TTTTTT-CTT
1 TTTTTTCCTT
* *
288217 CTTTTTCTTT
1 TTTTTTCCTT
288227 TTTTTTCCTT
1 TTTTTTCCTT
288237 TTTTTTCC-T
1 TTTTTTCCTT
288246 TTTTTTCCTT
1 TTTTTTCCTT
288256 TTTTTTCCTTT
1 TTTTTTCC-TT
288267 TTTTTTCCTT
1 TTTTTTCCTT
288277 TTT
1 TTT
288280 ATTTTTTAGG
Statistics
Matches: 64, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
8 1 0.02
9 21 0.33
10 32 0.50
11 10 0.16
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTTCCTT
Found at i:288278 original size:19 final size:18
Alignment explanation
Indices: 288167--288279 Score: 81
Period size: 21 Copynumber: 5.9 Consensus size: 18
288157 ATTTTTCATT
*
288167 TTTTTTCTTTCCTTTTTTA
1 TTTTTT-TTTCCTTTTTTC
*
288186 TATTTCTTCATT-CTTTTTTCC
1 T-TTT-TT-TTTCCTTTTTT-C
288207 TTTTTTTCTT-C-TTTTTC
1 TTTTTTT-TTCCTTTTTTC
288224 TTTTTTTTTCCTTTTTT-
1 TTTTTTTTTCCTTTTTTC
288241 TTCCTTTTTTTCCTTTTTTTTCC
1 TT--TTTTTTTCC--TTTTTT-C
288264 TTTTTTTTTCCTTTTT
1 TTTTTTTTTCCTTTTT
288280 ATTTTTTAGG
Statistics
Matches: 79, Mismatches: 3, Indels: 24
0.75 0.03 0.23
Matches are distributed among these distances:
16 2 0.03
17 11 0.14
18 10 0.13
19 20 0.25
20 13 0.16
21 21 0.27
23 2 0.03
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTTTTTCCTTTTTTC
Found at i:288279 original size:9 final size:9
Alignment explanation
Indices: 288199--288270 Score: 92
Period size: 9 Copynumber: 7.7 Consensus size: 9
288189 TTCTTCATTC
288199 TTTTTTCCT
1 TTTTTTCCT
288208 TTTTTT-CT
1 TTTTTTCCT
*
288216 TCTTTTTCTTT
1 T-TTTTTC-CT
288227 TTTTTTCCTT
1 TTTTTTCC-T
288237 TTTTTTCCT
1 TTTTTTCCT
288246 TTTTTTCCTT
1 TTTTTTCC-T
288256 TTTTTTCCT
1 TTTTTTCCT
288265 TTTTTT
1 TTTTTT
288271 TTCCTTTTTA
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
8 3 0.05
9 27 0.48
10 24 0.43
11 2 0.04
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTCCT
Found at i:288286 original size:19 final size:19
Alignment explanation
Indices: 288158--288286 Score: 77
Period size: 19 Copynumber: 6.6 Consensus size: 19
288148 TTTATTCGTA
288158 TTTTTCATTTTTTTTCTTTCC
1 TTTTT-ATTTTTTTT-TTTCC
* ** *
288179 TTTTTTATATTTCTTCATTCT
1 -TTTTTAT-TTTTTTTTTTCC
** *
288200 TTTTTCCTTTTTTTCTT-C
1 TTTTTATTTTTTTTTTTCC
*
288218 -TTTT-TCTTTTTTTTTCC
1 TTTTTATTTTTTTTTTTCC
*
288235 TTTTT-TTTCCTTTTTTTCC
1 TTTTTATTT-TTTTTTTTCC
*
288254 TTTTTTTTCCTTTTTTTTTCC
1 TTTTTATT--TTTTTTTTTCC
288275 TTTTTATTTTTT
1 TTTTTATTTTTT
288287 AGGCAAAATA
Statistics
Matches: 83, Mismatches: 17, Indels: 17
0.71 0.15 0.15
Matches are distributed among these distances:
16 8 0.10
17 5 0.06
18 6 0.07
19 25 0.30
20 7 0.08
21 21 0.25
22 11 0.13
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTATTTTTTTTTTTCC
Found at i:289643 original size:30 final size:31
Alignment explanation
Indices: 289556--289647 Score: 143
Period size: 31 Copynumber: 3.0 Consensus size: 31
289546 CAATTTAAGG
289556 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
*
289587 CAAAATGGTTTTTGTACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
*
289618 CAAAAT-GTTATTTGGA-TTTAATTGAATTTA
1 CAAAATGGTT-TTTGGACTTGAATTGAATTTA
289648 TTCAAAATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
30 16 0.28
31 41 0.72
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:289738 original size:19 final size:19
Alignment explanation
Indices: 289711--289777 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
289701 AAATGTTTTA
* *
289711 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
289730 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
* *
289749 TGAACAGTAAATCACTGTT
1 TGAACAGTAAATTACTATT
289768 TGAACAGTAA
1 TGAACAGTAA
289778 CCCGAGGCTC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.36
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:289909 original size:21 final size:21
Alignment explanation
Indices: 289883--289924 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
289873 ATTTGAATAT
*
289883 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
289904 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
289925 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:289987 original size:21 final size:21
Alignment explanation
Indices: 289953--289992 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
289943 TTTGAGTAGA
*
289953 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
289975 AAAAT-ATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
289993 ATATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 1 0.06
22 5 0.29
ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:290246 original size:34 final size:32
Alignment explanation
Indices: 290207--290276 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
290197 TTTTGTAAAG
*
290207 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
290241 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
290273 GGGA
1 GGGA
290277 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:303081 original size:21 final size:21
Alignment explanation
Indices: 303057--303107 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
303047 GTTTGTTTTT
* *
303057 ATTTTTCA-ATTTTGAAACATC
1 ATTTTTCATATTTT-AAAAATA
303078 ATTTTT-ATATTTTAAAAATA
1 ATTTTTCATATTTTAAAAATA
303098 ATTTTTCATA
1 ATTTTTCATA
303108 ATCCGAAGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (21 bp):
ATTTTTCATATTTTAAAAATA
Found at i:305062 original size:18 final size:17
Alignment explanation
Indices: 305008--305056 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
304998 TTGGACTCCT
* *
305008 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
305026 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
305044 AGTGCATTCGATG
1 AGTGCA-TCGATG
305057 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:305159 original size:19 final size:19
Alignment explanation
Indices: 305135--305173 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
305125 TTATTAAATC
305135 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
305154 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
305173 A
1 A
305174 TTCGATGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.38, T:0.21
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:309838 original size:23 final size:23
Alignment explanation
Indices: 309807--309863 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
309797 CATCCAAGAA
*
309807 TGGATGGAATTCAATTCCCTTGT
1 TGGAGGGAATTCAATTCCCTTGT
309830 TGGAGGGAATTCAATTCCCTTGT
1 TGGAGGGAATTCAATTCCCTTGT
309853 TGGAGGGAATT
1 TGGAGGGAATT
309864 GAAATTTGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.35
Consensus pattern (23 bp):
TGGAGGGAATTCAATTCCCTTGT
Found at i:310313 original size:37 final size:38
Alignment explanation
Indices: 310271--310342 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
310261 TTTATTTTGT
310271 TCGGGTCGGG-TTTTTTAAGTGTGATATTCGGGTCGAG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGAG
310308 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTC
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTC
310343 AGGTTCGGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 10 0.29
38 24 0.71
ACGTcount: A:0.12, C:0.11, G:0.36, T:0.40
Consensus pattern (38 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGAG
Found at i:313947 original size:14 final size:14
Alignment explanation
Indices: 313929--313968 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
313919 CATCCGAAAC
313929 CATCCGACCGAGGG
1 CATCCGACCGAGGG
*
313943 TATCCGACCGAGGG
1 CATCCGACCGAGGG
*
313957 CATCCGAGCGAG
1 CATCCGACCGAG
313969 CTATGCGAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.23, C:0.33, G:0.35, T:0.10
Consensus pattern (14 bp):
CATCCGACCGAGGG
Found at i:314046 original size:29 final size:29
Alignment explanation
Indices: 314007--314081 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
313997 GGAGCAGGAA
314007 GAGTGCATGGCGACCTACAAGGTCGCCAG
1 GAGTGCATGGCGACCTACAAGGTCGCCAG
*
314036 GAGTGCATGGCGACCTACAAGGTCGCCCG
1 GAGTGCATGGCGACCTACAAGGTCGCCAG
314065 GAGTGCATGGCGACCTA
1 GAGTGCATGGCGACCTA
314082 TGCTGGGAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.23, C:0.28, G:0.35, T:0.15
Consensus pattern (29 bp):
GAGTGCATGGCGACCTACAAGGTCGCCAG
Found at i:316231 original size:21 final size:23
Alignment explanation
Indices: 316201--316246 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
316191 TTAATTTAAT
* *
316201 ATTATAATAAT-ATATTTGATAA
1 ATTATAATAATGAGATTTGAAAA
316223 ATTA-AATAATGAGATTTGAAAA
1 ATTATAATAATGAGATTTGAAAA
316245 AT
1 AT
316247 AGAAAACTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (23 bp):
ATTATAATAATGAGATTTGAAAA
Found at i:317506 original size:24 final size:24
Alignment explanation
Indices: 317479--317525 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
317469 GCTTCTTCCC
*
317479 CTTCTTATCTTTCTT-TTTCTCTTT
1 CTTCTT-TCTCTCTTCTTTCTCTTT
*
317503 CTTCTTTGTCTCTTCTTTCTCTT
1 CTTCTTTCTCTCTTCTTTCTCTT
317526 CACCTTCTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.02, C:0.28, G:0.02, T:0.68
Consensus pattern (24 bp):
CTTCTTTCTCTCTTCTTTCTCTTT
Found at i:317583 original size:21 final size:20
Alignment explanation
Indices: 317558--317609 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
317548 GATCATTTTG
317558 TCTTTCCTTCCTTCCTTCACC
1 TCTTTCCTTCCTT-CTTCACC
* **
317579 TCTTTGCCTTTCTTCTTCTTC
1 TCTTT-CCTTCCTTCTTCACC
317600 TCTTT-CTTCC
1 TCTTTCCTTCC
317610 CCTCTTCTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 4 0.15
21 15 0.58
22 7 0.27
ACGTcount: A:0.02, C:0.40, G:0.02, T:0.56
Consensus pattern (20 bp):
TCTTTCCTTCCTTCTTCACC
Found at i:317675 original size:12 final size:12
Alignment explanation
Indices: 317654--317748 Score: 54
Period size: 12 Copynumber: 7.9 Consensus size: 12
317644 CTCTTCCTCT
*
317654 TTATCCTTCTTC
1 TTATCTTTCTTC
317666 TTATCTTTCTTC
1 TTATCTTTCTTC
* *
317678 TTCT-TGTTCTCCTGT
1 TTATCT-TTCT--T-C
*
317693 TTTTCTTTCTTC
1 TTATCTTTCTTC
*
317705 TCATCTTTCTTC
1 TTATCTTTCTTC
* *
317717 TTCTC-CTC-T-
1 TTATCTTTCTTC
*
317726 TTGTCTTTCTTC
1 TTATCTTTCTTC
317738 TTATCTTTCTT
1 TTATCTTTCTT
317749 TGTCTCTTTT
Statistics
Matches: 62, Mismatches: 13, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
9 4 0.06
10 3 0.05
11 4 0.06
12 41 0.66
13 1 0.02
14 1 0.02
15 7 0.11
16 1 0.02
ACGTcount: A:0.04, C:0.28, G:0.03, T:0.64
Consensus pattern (12 bp):
TTATCTTTCTTC
Found at i:317733 original size:21 final size:22
Alignment explanation
Indices: 317708--317753 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
317698 TTTCTTCTCA
*
317708 TCTTTCTTCTTCTC-CTCTTTG
1 TCTTTCTTCTTATCTCTCTTTG
*
317729 TCTTTCTTCTTATCTTTCTTTG
1 TCTTTCTTCTTATCTCTCTTTG
317751 TCT
1 TCT
317754 CTTTTATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.02, C:0.28, G:0.04, T:0.65
Consensus pattern (22 bp):
TCTTTCTTCTTATCTCTCTTTG
Found at i:317744 original size:18 final size:17
Alignment explanation
Indices: 317693--317749 Score: 66
Period size: 16 Copynumber: 3.5 Consensus size: 17
317683 GTTCTCCTGT
317693 TTTTCTTTCTTCTCATC
1 TTTTCTTTCTTCTCATC
*
317710 -TTTC-TTCTTCTCCTC
1 TTTTCTTTCTTCTCATC
*
317725 TTTGTCTTTCTTCTTATC
1 TTT-TCTTTCTTCTCATC
317743 -TTTCTTT
1 TTTTCTTT
317750 GTCTCTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 10 0.29
16 11 0.32
17 4 0.12
18 9 0.26
ACGTcount: A:0.04, C:0.28, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTTCTTTCTTCTCATC
Found at i:317766 original size:33 final size:33
Alignment explanation
Indices: 317678--317748 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
317668 ATCTTTCTTC
* *
317678 TTCTTGTTCTCCTGTTTTTCTTTCTTCTCATCT
1 TTCTTCTTCTCCTCTTTTTCTTTCTTCTCATCT
* *
317711 TTCTTCTTCTCCTCTTTGTCTTTCTTCTTATCT
1 TTCTTCTTCTCCTCTTTTTCTTTCTTCTCATCT
317744 TTCTT
1 TTCTT
317749 TGTCTCTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.03, C:0.28, G:0.04, T:0.65
Consensus pattern (33 bp):
TTCTTCTTCTCCTCTTTTTCTTTCTTCTCATCT
Found at i:317863 original size:17 final size:15
Alignment explanation
Indices: 317835--317877 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
317825 TCATCCTTGC
317835 CTTTCTTCTTCTCCATCT
1 CTTTC-TCTTCTCC--CT
317853 CTTTCTCTTCTCCCT
1 CTTTCTCTTCTCCCT
*
317868 CTTCCTCTTC
1 CTTTCTCTTC
317878 ATCTTTCATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 11 0.46
17 8 0.33
18 5 0.21
ACGTcount: A:0.02, C:0.44, G:0.00, T:0.53
Consensus pattern (15 bp):
CTTTCTCTTCTCCCT
Found at i:317916 original size:42 final size:40
Alignment explanation
Indices: 317852--317946 Score: 101
Period size: 42 Copynumber: 2.4 Consensus size: 40
317842 CTTCTCCATC
317852 TCTTTCTCTTCTC-CCTCTTCCT-CTTCATCTTTCATCTTCTTT
1 TCTTTCT-TTCTCTCCTCTTCCTCCTT-ATCTTTCATC-T-TTT
*
317894 TCTTTCTTTCTCTCCT-TATCCTCCTTATCTTTCTTCTTTT
1 TCTTTCTTTCTCTCCTCT-TCCTCCTTATCTTTCATCTTTT
317934 TC-TTC-TTCTCTCC
1 TCTTTCTTTCTCTCC
317947 CGTCTCTTCT
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
38 8 0.16
39 3 0.06
40 5 0.10
41 7 0.14
42 23 0.47
43 3 0.06
ACGTcount: A:0.04, C:0.37, G:0.00, T:0.59
Consensus pattern (40 bp):
TCTTTCTTTCTCTCCTCTTCCTCCTTATCTTTCATCTTTT
Found at i:317931 original size:90 final size:89
Alignment explanation
Indices: 317805--318042 Score: 216
Period size: 90 Copynumber: 2.7 Consensus size: 89
317795 TTTTTCTTAG
* * * ** *
317805 TTTCTTTCTTCTTTTCCTTTTCATCCTTGCCTTTCTTC---TTCTCCATCTCTTTCTCTTCTCCC
1 TTTCTTTCTTCTTCTCCTTATCCTCCTTATCTTTCTTCTTTTTCTTC-TCTCTTTCTCTTCTCCC
* ** *
317867 TCTTCCTCTTCATCTTTCATCTTCT
65 TCTTCATCTTCATCTACCATCTGCT
* * *
317892 TTTCTTTCTT-TCTCTCCTTATCCTCCTTATCTTTCTTCTTTTTCTTCT-TCTCTCCCGTCTCTT
1 TTTCTTTCTTCT-TCTCCTTATCCTCCTTATCTTTCTTCTTTTTCTTCTCTCTTTCTC-T-TCTC
* * * *
317955 CTTCTTCATCTTCTTCTACCTTGTGCT
63 CCTCTTCATCTTCATCTACCATCTGCT
* * *
317982 TTTCTTTCTTCTTCTCTTTCTCCTCCTTGTCTTTCTTCTTTTTCTTCTCATCTTTCTCTTC
1 TTTCTTTCTTCTTCTCCTTATCCTCCTTATCTTTCTTCTTTTTCTTCTC-TCTTTCTCTTC
318043 ATCTTCTTCT
Statistics
Matches: 120, Mismatches: 22, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
86 1 0.01
87 31 0.26
88 6 0.05
89 2 0.02
90 72 0.60
91 2 0.02
92 6 0.05
ACGTcount: A:0.04, C:0.35, G:0.02, T:0.59
Consensus pattern (89 bp):
TTTCTTTCTTCTTCTCCTTATCCTCCTTATCTTTCTTCTTTTTCTTCTCTCTTTCTCTTCTCCCT
CTTCATCTTCATCTACCATCTGCT
Found at i:318041 original size:27 final size:27
Alignment explanation
Indices: 317980--318050 Score: 65
Period size: 27 Copynumber: 2.6 Consensus size: 27
317970 CTACCTTGTG
*
317980 CTTTTCTTTCTTC-TTCTCTTTCTCCT
1 CTTTTCTTTCTTCTTTCTCTTTCTCAT
* *
318006 CCTTGTCTTTCTTCTTTTTC-TTCTCAT
1 -CTTTTCTTTCTTCTTTCTCTTTCTCAT
318033 CTTTCTCTTCATCTTCTT
1 CTTT-TCTT--TCTTCTT
318051 CTACCTCAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
26 3 0.08
27 22 0.61
28 4 0.11
29 7 0.19
ACGTcount: A:0.03, C:0.32, G:0.01, T:0.63
Consensus pattern (27 bp):
CTTTTCTTTCTTCTTTCTCTTTCTCAT
Found at i:319536 original size:80 final size:80
Alignment explanation
Indices: 319403--319717 Score: 508
Period size: 80 Copynumber: 4.0 Consensus size: 80
319393 ACCATGCCTA
* ** * *
319403 AAACAGAAGACATGGATATTAACCCGCATGATACTTATCAGTCCAGATCTTATTCAATCTATATA
1 AAACAGCAGACACAGATATTCACCCGCATGATACTAATCAGTCCAGATCTTATTCAATCTATATA
*
319468 CATCAAAAAGAATCG
66 CATCAACAAGAATCG
*
319483 AAACAGCAGACATAGATATTCACCCGCATGATACTAATCAGTCCAGATCTTATTCAATCTATATA
1 AAACAGCAGACACAGATATTCACCCGCATGATACTAATCAGTCCAGATCTTATTCAATCTATATA
319548 CATCAACAAGAATCG
66 CATCAACAAGAATCG
319563 AAACAGCAGACACAGATATTCACCCGCATGATAC--ATCAGTCCAGATCTTATTCAATCTATATA
1 AAACAGCAGACACAGATATTCACCCGCATGATACTAATCAGTCCAGATCTTATTCAATCTATATA
*
319626 CATCAACAAGAATTG
66 CATCAACAAGAATCG
* * *
319641 AAAGAGCAGACACAGATATTCACCCGCATGATAGTAATCAGTCCAGATCTAATTCAATCTATATA
1 AAACAGCAGACACAGATATTCACCCGCATGATACTAATCAGTCCAGATCTTATTCAATCTATATA
*
319706 CATCAGCAAGAA
66 CATCAACAAGAA
319718 GGTAGTGGAA
Statistics
Matches: 222, Mismatches: 11, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
78 75 0.34
80 147 0.66
ACGTcount: A:0.41, C:0.23, G:0.12, T:0.24
Consensus pattern (80 bp):
AAACAGCAGACACAGATATTCACCCGCATGATACTAATCAGTCCAGATCTTATTCAATCTATATA
CATCAACAAGAATCG
Found at i:320585 original size:12 final size:12
Alignment explanation
Indices: 320562--320594 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
320552 AAAATGTTAA
320562 TTTTTTT-A-AT
1 TTTTTTTAATAT
320572 TTTTTTTAATAT
1 TTTTTTTAATAT
320584 TTTTTTTAATA
1 TTTTTTTAATA
320595 ATTAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.33
11 1 0.05
12 13 0.62
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTTTAATAT
Found at i:321758 original size:18 final size:18
Alignment explanation
Indices: 321735--321798 Score: 69
Period size: 17 Copynumber: 3.7 Consensus size: 18
321725 AAATAAAACG
321735 TAATATTTTATAAATTTT
1 TAATATTTTATAAATTTT
*
321753 TAATA-TTTATAAATATT
1 TAATATTTTATAAATTTT
* * *
321770 AAAGATTTGATAAA-TTT
1 TAATATTTTATAAATTTT
*
321787 TAATATTATATA
1 TAATATTTTATA
321799 TATATTATAT
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
17 24 0.67
18 12 0.33
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (18 bp):
TAATATTTTATAAATTTT
Found at i:321783 original size:35 final size:35
Alignment explanation
Indices: 321739--321805 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
321729 AAAACGTAAT
*
321739 ATTTTATAAATTTTTAATATT-TATAAATATTAAAG
1 ATTTGATAAA-TTTTAATATTATATAAATATTAAAG
*
321774 ATTTGATAAATTTTAATATTATATATATATTA
1 ATTTGATAAATTTTAATATTATATAAATATTA
321806 TATAATTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 10 0.34
35 19 0.66
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (35 bp):
ATTTGATAAATTTTAATATTATATAAATATTAAAG
Found at i:323555 original size:27 final size:27
Alignment explanation
Indices: 323525--323579 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 27
323515 AATTTAATAC
323525 AAAATAGAAAAATAAATAATA-ATATAT
1 AAAATAGAAAAAT-AATAATATATATAT
323552 AAAATAGAAAAATAATAATATATATAT
1 AAAATAGAAAAATAATAATATATATAT
323579 A
1 A
323580 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 7 0.26
27 20 0.74
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (27 bp):
AAAATAGAAAAATAATAATATATATAT
Found at i:323576 original size:2 final size:2
Alignment explanation
Indices: 323569--323811 Score: 259
Period size: 2 Copynumber: 123.5 Consensus size: 2
323559 AAAAATAATA
323569 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
323611 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
*
323653 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
323694 AT AT -T AT TT CA- AA AA AT AT GT AT TT AT AT AT -T A- AT A- AT
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * * * *
323732 GAT AG AA AA AT AT AA AT AG A- AGT AT AT AA AA AT -T AG AT GAA
1 -AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT -AT
323773 AT AT AT 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 AT AT AT A
323812 CATAATATGA
Statistics
Matches: 208, Mismatches: 21, Indels: 24
0.82 0.08 0.09
Matches are distributed among these distances:
1 8 0.04
2 196 0.94
3 4 0.02
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:325214 original size:27 final size:27
Alignment explanation
Indices: 325176--325230 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
325166 GGAAAAGGAG
325176 GCCAATGCCATAGCTCAACTCCTGACA
1 GCCAATGCCATAGCTCAACTCCTGACA
325203 GCCAATGCCATAGCTCAACTCCTGACA
1 GCCAATGCCATAGCTCAACTCCTGACA
325230 G
1 G
325231 AAAAGTCTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.36, G:0.16, T:0.18
Consensus pattern (27 bp):
GCCAATGCCATAGCTCAACTCCTGACA
Found at i:330982 original size:30 final size:30
Alignment explanation
Indices: 330915--331014 Score: 146
Period size: 31 Copynumber: 3.3 Consensus size: 30
330905 GTACATATAT
*
330915 CACATTAGGAATTTTGTCGAAGTATAAGTA
1 CACATTAGGAATTTTGTCAAAGTATAAGTA
* *
330945 GCACATTAGGAATTATGTCAAAGTATAGGTA
1 -CACATTAGGAATTTTGTCAAAGTATAAGTA
*
330976 CACATTAGGCATTTTGTCAAAGTATAAGTA
1 CACATTAGGAATTTTGTCAAAGTATAAGTA
331006 CAACATTAG
1 C-ACATTAG
331015 ACTTTTTTGA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
30 28 0.45
31 34 0.55
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (30 bp):
CACATTAGGAATTTTGTCAAAGTATAAGTA
Found at i:331822 original size:22 final size:22
Alignment explanation
Indices: 331794--331859 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
331784 AGAGGTACTG
* *
331794 ATACCCCTATCAATGGGCATCA
1 ATACCCCTATGAATGGGTATCA
* *
331816 ATACCCCTATGAATGGGTACCG
1 ATACCCCTATGAATGGGTATCA
331838 ATACCCCTATGAATGGGTATCA
1 ATACCCCTATGAATGGGTATCA
331860 TGAAGGCTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.24
Consensus pattern (22 bp):
ATACCCCTATGAATGGGTATCA
Found at i:334205 original size:86 final size:85
Alignment explanation
Indices: 334036--334219 Score: 314
Period size: 88 Copynumber: 2.1 Consensus size: 85
334026 CTTCAACTTT
*
334036 ATCATATAAAATATGTAATCAGATAAGATTTTATAGTCTGAAAACGACAAAGTATTTCCTAAAGT
1 ATCATATAAAATATGTAATCAGAAAAGATTTTATAGTCTGAAAACGACAAAGTATTTCCTAAAGT
334101 TTCCAACTTTAATTTTTTTTA
66 TTCCAACTTTAA-TTTTTTTA
334122 ATCATATAAAATATGTAATCAGAAAAGATTTTTTATAGTCTGAAAACGACAAAGTATTTCCTAAA
1 ATCATATAAAATATGTAATCAGAAAAGA--TTTTATAGTCTGAAAACGACAAAGTATTTCCTAAA
* *
334187 GTTTTCAATTTTAATTTTTTTA
64 GTTTCCAACTTTAATTTTTTTA
334209 ATCATATAAAA
1 ATCATATAAAA
334220 GAAAAAAAGT
Statistics
Matches: 93, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
86 27 0.29
87 19 0.20
88 47 0.51
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (85 bp):
ATCATATAAAATATGTAATCAGAAAAGATTTTATAGTCTGAAAACGACAAAGTATTTCCTAAAGT
TTCCAACTTTAATTTTTTTA
Found at i:337525 original size:2 final size:2
Alignment explanation
Indices: 337518--337565 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
337508 ATTTTATTTA
337518 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
337560 AT -T AT A
1 AT AT AT A
337566 GTATTTTGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:339431 original size:13 final size:13
Alignment explanation
Indices: 339394--339445 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
339384 TTAGCATATT
*
339394 TTATTTATAATAA
1 TTATTAATAATAA
* *
339407 -TAATAGTAATAA
1 TTATTAATAATAA
339419 TTATTAATAATAA
1 TTATTAATAATAA
*
339432 TTATTATTAATAA
1 TTATTAATAATAA
339445 T
1 T
339446 AAACAATCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
12 9 0.28
13 23 0.72
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (13 bp):
TTATTAATAATAA
Found at i:339432 original size:16 final size:16
Alignment explanation
Indices: 339407--339447 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
339397 TTTATAATAA
*
339407 TAATAGTAATAATTAT
1 TAATAATAATAATTAT
*
339423 TAATAATAATTATTAT
1 TAATAATAATAATTAT
339439 TAATAATAA
1 TAATAATAA
339448 ACAATCAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
TAATAATAATAATTAT
Found at i:340106 original size:2 final size:2
Alignment explanation
Indices: 340101--340137 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
340091 TTGTTTTTTA
*
340101 AT AT AT AT AT AT AC 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 AT AT A
340138 AAACTTTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:349092 original size:6 final size:6
Alignment explanation
Indices: 349083--349119 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
349073 CTCTATTGAT
* *
349083 ATGTAT ATGTAT ATGTAG ATGTAG ATGTAG ATGTAG A
1 ATGTAG ATGTAG ATGTAG ATGTAG ATGTAG ATGTAG A
349120 CATAGATGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.35, C:0.00, G:0.27, T:0.38
Consensus pattern (6 bp):
ATGTAG
Found at i:349110 original size:18 final size:18
Alignment explanation
Indices: 349083--349133 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
349073 CTCTATTGAT
*
349083 ATGTATATGTATATGTAG
1 ATGTAGATGTATATGTAG
*
349101 ATGTAGATGTAGATGTAG
1 ATGTAGATGTATATGTAG
**
349119 ACATAGATGATATAT
1 ATGTAGATG-TATAT
349134 CATACAGCCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (18 bp):
ATGTAGATGTATATGTAG
Found at i:351151 original size:21 final size:21
Alignment explanation
Indices: 351127--351170 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
351117 GCTATGGAGG
351127 CGTGCGGAATTGCAATTGAGA
1 CGTGCGGAATTGCAATTGAGA
351148 CGTGCGGAATTGCAATTGAGA
1 CGTGCGGAATTGCAATTGAGA
351169 CG
1 CG
351171 ATAACCACTT
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:0.27, C:0.16, G:0.34, T:0.23
Consensus pattern (21 bp):
CGTGCGGAATTGCAATTGAGA
Found at i:356438 original size:21 final size:21
Alignment explanation
Indices: 356414--356453 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
356404 TAACAAAGGT
* *
356414 AGTACCGATACTCTTTGTAGG
1 AGTACCAATACCCTTTGTAGG
356435 AGTACCAATACCCTTTGTA
1 AGTACCAATACCCTTTGTA
356454 TTGGGTAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.33
Consensus pattern (21 bp):
AGTACCAATACCCTTTGTAGG
Found at i:366031 original size:19 final size:19
Alignment explanation
Indices: 366007--366045 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
365997 TTATTAAATC
366007 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
366026 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
366045 A
1 A
366046 ATGCATTCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.38, T:0.21
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:366094 original size:21 final size:21
Alignment explanation
Indices: 366070--366109 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
366060 CAATTTATTC
366070 ATTGATACATCGATGCATGGT
1 ATTGATACATCGATGCATGGT
* *
366091 ATTGATGCATCGGTGCATG
1 ATTGATACATCGATGCATG
366110 CCTTTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (21 bp):
ATTGATACATCGATGCATGGT
Found at i:367915 original size:24 final size:24
Alignment explanation
Indices: 367883--367935 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
367873 TTTTTTTATT
367883 TCGATACATATTCAAAGGGATGCA
1 TCGATACATATTCAAAGGGATGCA
367907 TCGATACATATTCAAAGGGATGCA
1 TCGATACATATTCAAAGGGATGCA
367931 TCGAT
1 TCGAT
367936 GCATTGTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (24 bp):
TCGATACATATTCAAAGGGATGCA
Done.