Multiple sequence alignment - TraesCS5A01G089200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5A01G089200 chr5A 100.000 4952 0 0 1 4952 119438118 119443069 0.000000e+00 9145.0
1 TraesCS5A01G089200 chr5A 92.202 436 34 0 224 659 484071290 484071725 7.040000e-173 617.0
2 TraesCS5A01G089200 chr5A 91.533 437 36 1 224 659 439444557 439444121 7.090000e-168 601.0
3 TraesCS5A01G089200 chr5A 90.787 445 39 2 224 668 262287354 262286912 1.190000e-165 593.0
4 TraesCS5A01G089200 chr5A 100.000 30 0 0 99 128 650496090 650496061 6.920000e-04 56.5
5 TraesCS5A01G089200 chr5A 100.000 29 0 0 99 127 557123407 557123435 2.000000e-03 54.7
6 TraesCS5A01G089200 chr5D 93.155 2133 119 16 1155 3277 114349540 114351655 0.000000e+00 3105.0
7 TraesCS5A01G089200 chr5D 93.135 1413 65 16 3537 4943 114352047 114353433 0.000000e+00 2043.0
8 TraesCS5A01G089200 chr5D 95.393 521 21 3 659 1179 114348996 114349513 0.000000e+00 826.0
9 TraesCS5A01G089200 chr5B 96.203 1659 49 12 660 2311 125228167 125229818 0.000000e+00 2702.0
10 TraesCS5A01G089200 chr5B 93.209 1664 90 11 3283 4943 125230989 125232632 0.000000e+00 2425.0
11 TraesCS5A01G089200 chr5B 95.380 974 30 6 2306 3278 125229938 125230897 0.000000e+00 1535.0
12 TraesCS5A01G089200 chr7A 91.724 435 36 0 225 659 403182607 403182173 5.480000e-169 604.0
13 TraesCS5A01G089200 chr7A 91.743 436 34 2 225 659 403188603 403188169 5.480000e-169 604.0
14 TraesCS5A01G089200 chr7A 91.264 435 38 0 225 659 403186909 403186475 1.190000e-165 593.0
15 TraesCS5A01G089200 chr7A 81.373 102 18 1 4797 4898 306231603 306231703 1.140000e-11 82.4
16 TraesCS5A01G089200 chr2A 91.116 439 39 0 224 662 645251288 645250850 3.300000e-166 595.0
17 TraesCS5A01G089200 chr3A 90.888 439 39 1 219 657 729301822 729302259 5.520000e-164 588.0
18 TraesCS5A01G089200 chr3A 81.115 323 57 4 3630 3950 189280282 189280602 6.360000e-64 255.0
19 TraesCS5A01G089200 chr3A 93.233 133 9 0 999 1131 189276072 189276204 3.910000e-46 196.0
20 TraesCS5A01G089200 chr3A 93.284 134 7 2 1000 1132 266451191 266451323 3.910000e-46 196.0
21 TraesCS5A01G089200 chr3A 82.609 161 23 5 4637 4794 313520450 313520292 2.400000e-28 137.0
22 TraesCS5A01G089200 chr1A 89.978 459 41 4 202 659 585232164 585232618 5.520000e-164 588.0
23 TraesCS5A01G089200 chr1A 84.472 161 21 4 4637 4794 218525374 218525215 6.640000e-34 156.0
24 TraesCS5A01G089200 chr1A 83.544 158 22 4 4637 4791 357771633 357771789 1.440000e-30 145.0
25 TraesCS5A01G089200 chr3D 80.186 323 60 4 3630 3950 160908837 160908517 6.410000e-59 239.0
26 TraesCS5A01G089200 chr3D 93.233 133 9 0 999 1131 160912166 160912034 3.910000e-46 196.0
27 TraesCS5A01G089200 chr3D 93.284 134 7 2 1000 1132 193598104 193597972 3.910000e-46 196.0
28 TraesCS5A01G089200 chr3D 81.875 160 25 4 4637 4794 199220759 199220602 1.120000e-26 132.0
29 TraesCS5A01G089200 chr3D 100.000 28 0 0 98 125 95954214 95954241 9.000000e-03 52.8
30 TraesCS5A01G089200 chr3B 93.233 133 9 0 999 1131 237648052 237647920 3.910000e-46 196.0
31 TraesCS5A01G089200 chr3B 93.284 134 7 2 1000 1132 276849193 276849325 3.910000e-46 196.0
32 TraesCS5A01G089200 chr3B 81.988 161 24 5 4637 4794 284396814 284396972 1.120000e-26 132.0
33 TraesCS5A01G089200 chr4B 83.648 159 20 6 4637 4791 472395605 472395761 1.440000e-30 145.0
34 TraesCS5A01G089200 chr4B 100.000 29 0 0 99 127 627709734 627709706 2.000000e-03 54.7
35 TraesCS5A01G089200 chr1D 84.138 145 20 3 4652 4794 155719862 155719719 2.400000e-28 137.0
36 TraesCS5A01G089200 chr2B 83.761 117 18 1 9 124 409401378 409401262 5.240000e-20 110.0
37 TraesCS5A01G089200 chr2B 100.000 28 0 0 101 128 233554701 233554674 9.000000e-03 52.8
38 TraesCS5A01G089200 chr6D 100.000 30 0 0 99 128 4684557 4684586 6.920000e-04 56.5
39 TraesCS5A01G089200 chr1B 100.000 29 0 0 99 127 169782331 169782303 2.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G089200 chr5A 119438118 119443069 4951 False 9145.000000 9145 100.000000 1 4952 1 chr5A.!!$F1 4951
1 TraesCS5A01G089200 chr5D 114348996 114353433 4437 False 1991.333333 3105 93.894333 659 4943 3 chr5D.!!$F1 4284
2 TraesCS5A01G089200 chr5B 125228167 125232632 4465 False 2220.666667 2702 94.930667 660 4943 3 chr5B.!!$F1 4283
3 TraesCS5A01G089200 chr7A 403182173 403188603 6430 True 600.333333 604 91.577000 225 659 3 chr7A.!!$R1 434
4 TraesCS5A01G089200 chr3D 160908517 160912166 3649 True 217.500000 239 86.709500 999 3950 2 chr3D.!!$R3 2951

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
781 2992 0.107831 TCTCCAAACCACCCAACTCG 59.892 55.0 0.00 0.00 0.00 4.18 F
1477 5445 0.596341 AATTTTCACGGTGCGTTGCC 60.596 50.0 2.51 0.00 38.32 4.52 F
1828 5800 1.188863 AATTCAGGGGCATGCAAGTC 58.811 50.0 21.36 0.93 0.00 3.01 F
3513 11182 0.391130 TGCATGGCGGTCTCTGTTAC 60.391 55.0 0.00 0.00 0.00 2.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2554 10116 0.680280 GGAGTACTGGAGTCGGCTGA 60.680 60.000 0.00 0.0 0.00 4.26 R
3012 10575 0.319728 CCTGCTGCACACTCTACAGT 59.680 55.000 0.00 0.0 33.87 3.55 R
3621 11371 1.074405 ACTGCATCAACCTGACCACAT 59.926 47.619 0.00 0.0 0.00 3.21 R
4803 12582 0.105593 TCTTCGGATGGCTCATCAGC 59.894 55.000 14.57 0.0 42.13 4.26 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 9.869757 TTACAGAATCACATCAATATATACCGG 57.130 33.333 0.00 0.00 0.00 5.28
65 66 7.907389 ACAGAATCACATCAATATATACCGGT 58.093 34.615 13.98 13.98 0.00 5.28
66 67 9.031537 ACAGAATCACATCAATATATACCGGTA 57.968 33.333 18.46 18.46 0.00 4.02
67 68 9.521503 CAGAATCACATCAATATATACCGGTAG 57.478 37.037 20.91 5.17 0.00 3.18
68 69 9.475620 AGAATCACATCAATATATACCGGTAGA 57.524 33.333 20.91 16.72 0.00 2.59
71 72 8.817092 TCACATCAATATATACCGGTAGATCA 57.183 34.615 24.41 11.91 0.00 2.92
72 73 8.683615 TCACATCAATATATACCGGTAGATCAC 58.316 37.037 24.41 0.00 0.00 3.06
73 74 7.644157 CACATCAATATATACCGGTAGATCACG 59.356 40.741 24.41 13.74 0.00 4.35
80 81 2.965572 CCGGTAGATCACGGGTTAAA 57.034 50.000 13.68 0.00 46.08 1.52
81 82 3.249986 CCGGTAGATCACGGGTTAAAA 57.750 47.619 13.68 0.00 46.08 1.52
82 83 3.800531 CCGGTAGATCACGGGTTAAAAT 58.199 45.455 13.68 0.00 46.08 1.82
83 84 4.947645 CCGGTAGATCACGGGTTAAAATA 58.052 43.478 13.68 0.00 46.08 1.40
84 85 4.746611 CCGGTAGATCACGGGTTAAAATAC 59.253 45.833 13.68 0.00 46.08 1.89
85 86 5.452356 CCGGTAGATCACGGGTTAAAATACT 60.452 44.000 13.68 0.00 46.08 2.12
86 87 6.239008 CCGGTAGATCACGGGTTAAAATACTA 60.239 42.308 13.68 0.00 46.08 1.82
87 88 6.860023 CGGTAGATCACGGGTTAAAATACTAG 59.140 42.308 0.00 0.00 0.00 2.57
88 89 7.255242 CGGTAGATCACGGGTTAAAATACTAGA 60.255 40.741 0.00 0.00 0.00 2.43
89 90 8.416329 GGTAGATCACGGGTTAAAATACTAGAA 58.584 37.037 0.00 0.00 0.00 2.10
90 91 9.978044 GTAGATCACGGGTTAAAATACTAGAAT 57.022 33.333 0.00 0.00 0.00 2.40
105 106 8.902540 AATACTAGAATATTTGATCCGTTGCA 57.097 30.769 0.00 0.00 0.00 4.08
106 107 8.902540 ATACTAGAATATTTGATCCGTTGCAA 57.097 30.769 0.00 0.00 0.00 4.08
107 108 7.016361 ACTAGAATATTTGATCCGTTGCAAC 57.984 36.000 19.89 19.89 0.00 4.17
116 117 3.931130 CGTTGCAACGCACGGACA 61.931 61.111 35.89 0.00 46.06 4.02
117 118 2.405594 GTTGCAACGCACGGACAA 59.594 55.556 14.90 0.00 38.71 3.18
118 119 1.008995 GTTGCAACGCACGGACAAT 60.009 52.632 14.90 0.00 38.71 2.71
119 120 0.593773 GTTGCAACGCACGGACAATT 60.594 50.000 14.90 0.00 38.71 2.32
120 121 0.945099 TTGCAACGCACGGACAATTA 59.055 45.000 0.00 0.00 38.71 1.40
121 122 0.945099 TGCAACGCACGGACAATTAA 59.055 45.000 0.00 0.00 31.71 1.40
122 123 1.323791 GCAACGCACGGACAATTAAC 58.676 50.000 0.00 0.00 0.00 2.01
123 124 1.069500 GCAACGCACGGACAATTAACT 60.069 47.619 0.00 0.00 0.00 2.24
124 125 2.158058 GCAACGCACGGACAATTAACTA 59.842 45.455 0.00 0.00 0.00 2.24
125 126 3.723835 GCAACGCACGGACAATTAACTAG 60.724 47.826 0.00 0.00 0.00 2.57
126 127 3.308438 ACGCACGGACAATTAACTAGT 57.692 42.857 0.00 0.00 0.00 2.57
127 128 4.439305 ACGCACGGACAATTAACTAGTA 57.561 40.909 0.00 0.00 0.00 1.82
128 129 4.808558 ACGCACGGACAATTAACTAGTAA 58.191 39.130 0.00 0.00 0.00 2.24
129 130 4.860907 ACGCACGGACAATTAACTAGTAAG 59.139 41.667 0.00 0.00 0.00 2.34
130 131 5.097529 CGCACGGACAATTAACTAGTAAGA 58.902 41.667 0.00 0.00 0.00 2.10
131 132 5.004156 CGCACGGACAATTAACTAGTAAGAC 59.996 44.000 0.00 0.00 0.00 3.01
132 133 6.098017 GCACGGACAATTAACTAGTAAGACT 58.902 40.000 0.00 0.00 0.00 3.24
133 134 7.253422 GCACGGACAATTAACTAGTAAGACTA 58.747 38.462 0.00 0.00 0.00 2.59
134 135 7.756722 GCACGGACAATTAACTAGTAAGACTAA 59.243 37.037 0.00 0.00 29.00 2.24
135 136 9.630098 CACGGACAATTAACTAGTAAGACTAAA 57.370 33.333 0.00 0.00 29.00 1.85
213 214 8.955061 ATTCAAACTTCAGAAAATACATGTCG 57.045 30.769 0.00 0.00 0.00 4.35
214 215 7.490962 TCAAACTTCAGAAAATACATGTCGT 57.509 32.000 0.00 0.00 0.00 4.34
215 216 8.596271 TCAAACTTCAGAAAATACATGTCGTA 57.404 30.769 0.00 0.00 0.00 3.43
216 217 9.047371 TCAAACTTCAGAAAATACATGTCGTAA 57.953 29.630 0.00 0.00 32.59 3.18
217 218 9.103048 CAAACTTCAGAAAATACATGTCGTAAC 57.897 33.333 0.00 0.00 32.59 2.50
218 219 8.603242 AACTTCAGAAAATACATGTCGTAACT 57.397 30.769 0.00 0.00 32.59 2.24
219 220 8.603242 ACTTCAGAAAATACATGTCGTAACTT 57.397 30.769 0.00 0.00 32.59 2.66
220 221 9.052759 ACTTCAGAAAATACATGTCGTAACTTT 57.947 29.630 0.00 0.00 32.59 2.66
221 222 9.878599 CTTCAGAAAATACATGTCGTAACTTTT 57.121 29.630 0.00 0.61 32.59 2.27
222 223 9.658475 TTCAGAAAATACATGTCGTAACTTTTG 57.342 29.630 0.00 0.00 32.59 2.44
223 224 9.047371 TCAGAAAATACATGTCGTAACTTTTGA 57.953 29.630 0.00 0.00 32.59 2.69
232 233 3.314357 GTCGTAACTTTTGAGGCCAACTT 59.686 43.478 5.01 0.00 30.88 2.66
236 237 1.676006 ACTTTTGAGGCCAACTTCACG 59.324 47.619 5.01 0.00 30.88 4.35
256 257 0.252197 GCGTGACCCATTTCTACCCT 59.748 55.000 0.00 0.00 0.00 4.34
261 262 4.574828 CGTGACCCATTTCTACCCTAAATG 59.425 45.833 0.00 0.00 41.77 2.32
281 282 1.008329 GTCCGTTTGTGTCCGTTTGA 58.992 50.000 0.00 0.00 0.00 2.69
282 283 1.004292 GTCCGTTTGTGTCCGTTTGAG 60.004 52.381 0.00 0.00 0.00 3.02
283 284 1.134759 TCCGTTTGTGTCCGTTTGAGA 60.135 47.619 0.00 0.00 0.00 3.27
309 310 5.692613 AACGAATAAATCAAACGACCCAA 57.307 34.783 0.00 0.00 0.00 4.12
310 311 5.038247 ACGAATAAATCAAACGACCCAAC 57.962 39.130 0.00 0.00 0.00 3.77
325 326 0.747644 CCAACGCATGGGAGCATACA 60.748 55.000 17.76 0.00 46.27 2.29
354 355 2.663852 CGGTCCGTGTCCGCTTTT 60.664 61.111 2.08 0.00 41.48 2.27
382 383 2.260844 TCCAGACCAAAGTTGCTCTG 57.739 50.000 8.73 8.73 39.47 3.35
415 416 3.016474 GCAGACAGAAAGCGGACGC 62.016 63.158 8.91 8.91 42.33 5.19
419 420 1.227853 ACAGAAAGCGGACGCCTTT 60.228 52.632 13.63 12.48 43.17 3.11
433 434 1.663702 CCTTTGCGTCCTCGTCGTT 60.664 57.895 0.00 0.00 39.49 3.85
455 456 4.988716 TGTGTCCGCCTCGACCCT 62.989 66.667 0.00 0.00 31.35 4.34
486 487 3.835395 CTCTCTCCTTTTCTGTACCTGGT 59.165 47.826 4.05 4.05 0.00 4.00
490 491 3.256704 TCCTTTTCTGTACCTGGTCCAT 58.743 45.455 0.63 0.00 0.00 3.41
493 494 4.324563 CCTTTTCTGTACCTGGTCCATCAT 60.325 45.833 0.63 0.00 0.00 2.45
499 500 0.322816 ACCTGGTCCATCATGTGCAC 60.323 55.000 10.75 10.75 0.00 4.57
505 506 2.486504 CATCATGTGCACCCACGC 59.513 61.111 15.69 0.00 45.04 5.34
539 540 2.025699 GGGTGAAAATGGGGTAGTAGCA 60.026 50.000 1.13 0.00 0.00 3.49
540 541 3.014623 GGTGAAAATGGGGTAGTAGCAC 58.985 50.000 1.13 0.00 0.00 4.40
624 2319 4.513198 GGACAAAATCCGGACAAAATGA 57.487 40.909 6.12 0.00 37.88 2.57
641 2336 9.832445 GACAAAATGAGTATAGATTTAGGGTCA 57.168 33.333 0.00 0.00 0.00 4.02
663 2358 2.529744 GGTGGAGTTGGCCTGACCT 61.530 63.158 3.32 0.00 40.22 3.85
681 2376 2.039348 ACCTAAGGGTTACACGTTGCAT 59.961 45.455 0.00 0.00 44.73 3.96
692 2387 1.608590 CACGTTGCATATGGAATCCCC 59.391 52.381 13.12 0.00 0.00 4.81
781 2992 0.107831 TCTCCAAACCACCCAACTCG 59.892 55.000 0.00 0.00 0.00 4.18
797 3008 0.736053 CTCGCACCTACTCCTCTGAC 59.264 60.000 0.00 0.00 0.00 3.51
941 3337 1.480219 CGAGATCCGTTAACAGGCGC 61.480 60.000 6.39 0.00 0.00 6.53
1131 4864 1.204704 CACATGCTCAAGGACGAGGTA 59.795 52.381 0.00 0.00 33.36 3.08
1139 4872 2.565834 TCAAGGACGAGGTAGGGAAAAG 59.434 50.000 0.00 0.00 0.00 2.27
1242 5209 3.517901 ACGAGGTTGGAGGAATTGTGATA 59.482 43.478 0.00 0.00 0.00 2.15
1278 5245 3.328382 TGATCCGTGTGGTTTTAGGAG 57.672 47.619 0.00 0.00 34.14 3.69
1408 5376 4.202161 CCAGTAGATGTTCATCTTAGCGGT 60.202 45.833 18.43 0.00 32.36 5.68
1477 5445 0.596341 AATTTTCACGGTGCGTTGCC 60.596 50.000 2.51 0.00 38.32 4.52
1623 5594 4.462483 TGGACAGATTTCATTTTGGTAGCC 59.538 41.667 0.00 0.00 0.00 3.93
1694 5666 9.220767 GAAAACTCCCATATAGCACCTTATAAG 57.779 37.037 5.43 5.43 0.00 1.73
1761 5733 4.098349 TGATTTCTTCAATGCTACCATGCC 59.902 41.667 0.00 0.00 0.00 4.40
1828 5800 1.188863 AATTCAGGGGCATGCAAGTC 58.811 50.000 21.36 0.93 0.00 3.01
1848 5820 2.823747 TCAGATCTGCTGCAAATGCTTT 59.176 40.909 18.36 0.00 44.52 3.51
1931 5903 4.504514 GGGGGATCTTTTTACTATCCGACC 60.505 50.000 0.00 0.00 40.15 4.79
2011 5983 8.181904 ACATAATCAAGTTCAACATGGAAAGT 57.818 30.769 0.00 0.00 0.00 2.66
2034 6860 3.123959 GCATGCCAAATCACATGTTTGTC 59.876 43.478 6.36 0.00 44.43 3.18
2434 9994 9.770097 AAATGTCATTATCAGTGGATAGTAGTG 57.230 33.333 0.00 0.00 37.31 2.74
2443 10003 1.206132 TGGATAGTAGTGGTTGGCACG 59.794 52.381 0.00 0.00 0.00 5.34
2554 10116 5.296748 GGTTAGTGCATTTTGAACCACAAT 58.703 37.500 7.34 0.00 39.51 2.71
2555 10117 5.405269 GGTTAGTGCATTTTGAACCACAATC 59.595 40.000 7.34 0.00 39.51 2.67
2745 10308 2.631062 CAGTGGTTTTCCTTTTACCCCC 59.369 50.000 0.00 0.00 41.38 5.40
2796 10359 7.217200 TGCTGTGACTTTTGTTCTTATCTACT 58.783 34.615 0.00 0.00 0.00 2.57
2953 10516 2.069273 GGTGACACAATCGAACTCTGG 58.931 52.381 8.08 0.00 0.00 3.86
3126 10689 2.225167 GGTGGAACAAAGGGGGACATAA 60.225 50.000 0.00 0.00 44.16 1.90
3202 10765 2.301346 CAATGGACACTTGGATAGGGC 58.699 52.381 0.00 0.00 0.00 5.19
3232 10795 4.869451 ACTAAGAGGGAGATAAGAACGGT 58.131 43.478 0.00 0.00 0.00 4.83
3233 10796 5.270794 ACTAAGAGGGAGATAAGAACGGTT 58.729 41.667 0.00 0.00 0.00 4.44
3303 10953 9.967346 TGTATAGTATCAGATAAACTCAGCAAC 57.033 33.333 0.00 0.00 0.00 4.17
3372 11022 9.410556 CGCCCTGAATAATAAGGATTTATTTTG 57.589 33.333 0.00 0.00 39.55 2.44
3457 11122 6.484977 AGAAGGCTTAACTGCTTAATCATAGC 59.515 38.462 0.00 0.00 39.10 2.97
3513 11182 0.391130 TGCATGGCGGTCTCTGTTAC 60.391 55.000 0.00 0.00 0.00 2.50
3541 11210 7.490725 CCTGATGATGTTGTTCTGACTTAGTAG 59.509 40.741 0.00 0.00 0.00 2.57
3621 11371 4.224991 TGATGCCATCTTCTGATTGTCA 57.775 40.909 6.21 0.00 0.00 3.58
3981 11754 2.673258 GGGGGAGTGGTGAAAGAAAAA 58.327 47.619 0.00 0.00 0.00 1.94
4032 11805 8.736244 TGATAATCTTGTTTTACCTTACCTTGC 58.264 33.333 0.00 0.00 0.00 4.01
4036 11809 3.224269 TGTTTTACCTTACCTTGCCACC 58.776 45.455 0.00 0.00 0.00 4.61
4154 11927 7.809546 TGGTTGAGTTATTACAACAATGTGA 57.190 32.000 0.00 0.00 45.27 3.58
4155 11928 8.402798 TGGTTGAGTTATTACAACAATGTGAT 57.597 30.769 0.00 0.00 45.27 3.06
4156 11929 8.296000 TGGTTGAGTTATTACAACAATGTGATG 58.704 33.333 0.00 0.00 45.27 3.07
4157 11930 8.296713 GGTTGAGTTATTACAACAATGTGATGT 58.703 33.333 0.00 0.00 45.27 3.06
4158 11931 9.329913 GTTGAGTTATTACAACAATGTGATGTC 57.670 33.333 0.00 0.00 43.66 3.06
4159 11932 8.846943 TGAGTTATTACAACAATGTGATGTCT 57.153 30.769 0.00 0.00 40.84 3.41
4179 11952 6.003326 TGTCTGAAAAGGTGATATGCTTTGA 58.997 36.000 0.00 0.00 0.00 2.69
4253 12026 3.691118 GTGCATCCAGATTTGCTGTTCTA 59.309 43.478 0.00 0.00 43.33 2.10
4280 12053 5.764686 TGTTTTTGCTATTCTCTGAAGCTGA 59.235 36.000 0.00 0.00 37.16 4.26
4284 12057 2.475864 GCTATTCTCTGAAGCTGATGCG 59.524 50.000 0.00 0.00 45.42 4.73
4286 12059 0.037046 TTCTCTGAAGCTGATGCGCA 60.037 50.000 14.96 14.96 45.42 6.09
4310 12083 3.279116 GCTGGTGCGCTGACACAA 61.279 61.111 9.73 0.00 42.55 3.33
4325 12098 6.566564 CGCTGACACAACTTTCATCAGTATTT 60.567 38.462 0.00 0.00 39.21 1.40
4354 12127 8.522830 TCAATTTGAGGGTTGTCATCTATTTTC 58.477 33.333 0.00 0.00 0.00 2.29
4356 12129 8.655935 ATTTGAGGGTTGTCATCTATTTTCTT 57.344 30.769 0.00 0.00 0.00 2.52
4437 12213 2.191354 TACTCGTGGTTGACTCGCCG 62.191 60.000 0.00 0.00 36.12 6.46
4490 12266 6.945435 TGGTTTTATTCTTGGACTTGCTCATA 59.055 34.615 0.00 0.00 0.00 2.15
4527 12303 7.784037 TGCTGAGAATAATTGCAATAAACCAT 58.216 30.769 13.39 0.00 0.00 3.55
4529 12305 9.748708 GCTGAGAATAATTGCAATAAACCATTA 57.251 29.630 13.39 0.30 0.00 1.90
4573 12350 3.799281 TTGACCTTGCAACCAAAAGAG 57.201 42.857 0.00 0.00 0.00 2.85
4604 12381 6.933521 TGCTAAAGAATTTAAGCATGGCAAAA 59.066 30.769 0.00 0.00 40.54 2.44
4605 12382 7.607223 TGCTAAAGAATTTAAGCATGGCAAAAT 59.393 29.630 0.00 0.00 40.54 1.82
4606 12383 9.097257 GCTAAAGAATTTAAGCATGGCAAAATA 57.903 29.630 0.00 0.00 40.54 1.40
4670 12448 1.067821 GAAGGCGATGGTCCTAGACTG 59.932 57.143 0.00 0.00 32.65 3.51
4698 12476 1.056660 TTGAGGTGTGGGGAAGTCTC 58.943 55.000 0.00 0.00 0.00 3.36
4726 12504 7.110810 AGACATAGCGATAGTATGGCTAACTA 58.889 38.462 24.95 9.71 46.99 2.24
4729 12507 7.610692 ACATAGCGATAGTATGGCTAACTAAGA 59.389 37.037 24.95 8.13 46.99 2.10
4765 12544 4.083003 TGTTTCGTCAAATAAGATGCCCAC 60.083 41.667 0.00 0.00 0.00 4.61
4767 12546 3.680490 TCGTCAAATAAGATGCCCACAA 58.320 40.909 0.00 0.00 0.00 3.33
4796 12575 8.914011 TGGAGACGGAATATATTAGTATCATGG 58.086 37.037 20.36 0.56 0.00 3.66
4831 12610 2.036992 AGCCATCCGAAGAAGCTATGAG 59.963 50.000 0.00 0.00 30.46 2.90
4835 12614 4.749099 CCATCCGAAGAAGCTATGAGAAAG 59.251 45.833 0.00 0.00 0.00 2.62
4848 12627 6.602406 AGCTATGAGAAAGAAACATTGAGCAT 59.398 34.615 0.00 0.00 31.86 3.79
4851 12630 4.088823 AGAAAGAAACATTGAGCATCGC 57.911 40.909 0.00 0.00 38.61 4.58
4859 12638 5.824904 AACATTGAGCATCGCTTAAGAAT 57.175 34.783 6.67 0.00 39.88 2.40
4873 12652 6.106877 GCTTAAGAATAATGACAAGCGTGA 57.893 37.500 6.65 0.00 30.29 4.35
4874 12653 6.719365 GCTTAAGAATAATGACAAGCGTGAT 58.281 36.000 6.65 0.00 30.29 3.06
4875 12654 6.848296 GCTTAAGAATAATGACAAGCGTGATC 59.152 38.462 6.65 1.04 30.29 2.92
4876 12655 7.465916 GCTTAAGAATAATGACAAGCGTGATCA 60.466 37.037 6.65 6.99 30.29 2.92
4877 12656 6.741992 AAGAATAATGACAAGCGTGATCAA 57.258 33.333 6.65 0.00 0.00 2.57
4878 12657 6.741992 AGAATAATGACAAGCGTGATCAAA 57.258 33.333 6.65 0.84 0.00 2.69
4879 12658 7.144722 AGAATAATGACAAGCGTGATCAAAA 57.855 32.000 6.65 0.52 0.00 2.44
4900 12679 4.853924 ACTCAGTTTGGTTTTATGCCTG 57.146 40.909 0.00 0.00 0.00 4.85
4919 12698 7.701539 TGCCTGATACAACAACTTATGAAAT 57.298 32.000 0.00 0.00 0.00 2.17
4948 12727 8.924511 AGAGGAAAATAAGAACTTCAATGTGA 57.075 30.769 0.00 0.00 0.00 3.58
4949 12728 9.007901 AGAGGAAAATAAGAACTTCAATGTGAG 57.992 33.333 0.00 0.00 0.00 3.51
4950 12729 8.924511 AGGAAAATAAGAACTTCAATGTGAGA 57.075 30.769 0.00 0.00 0.00 3.27
4951 12730 8.787852 AGGAAAATAAGAACTTCAATGTGAGAC 58.212 33.333 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.947433 AAATGTTTACCAAATCATGTTCATGAT 57.053 25.926 18.83 18.83 42.62 2.45
38 39 9.869757 CCGGTATATATTGATGTGATTCTGTAA 57.130 33.333 0.00 0.00 0.00 2.41
39 40 9.031537 ACCGGTATATATTGATGTGATTCTGTA 57.968 33.333 4.49 0.00 0.00 2.74
40 41 7.907389 ACCGGTATATATTGATGTGATTCTGT 58.093 34.615 4.49 0.00 0.00 3.41
41 42 9.521503 CTACCGGTATATATTGATGTGATTCTG 57.478 37.037 16.25 0.00 0.00 3.02
42 43 9.475620 TCTACCGGTATATATTGATGTGATTCT 57.524 33.333 16.25 0.00 0.00 2.40
45 46 9.421399 TGATCTACCGGTATATATTGATGTGAT 57.579 33.333 16.25 9.40 0.00 3.06
46 47 8.683615 GTGATCTACCGGTATATATTGATGTGA 58.316 37.037 16.25 4.47 0.00 3.58
47 48 7.644157 CGTGATCTACCGGTATATATTGATGTG 59.356 40.741 16.25 0.00 0.00 3.21
48 49 7.201794 CCGTGATCTACCGGTATATATTGATGT 60.202 40.741 16.25 0.00 39.38 3.06
49 50 7.139392 CCGTGATCTACCGGTATATATTGATG 58.861 42.308 16.25 0.00 39.38 3.07
50 51 6.264744 CCCGTGATCTACCGGTATATATTGAT 59.735 42.308 16.25 12.92 42.67 2.57
51 52 5.591472 CCCGTGATCTACCGGTATATATTGA 59.409 44.000 16.25 8.15 42.67 2.57
52 53 5.359009 ACCCGTGATCTACCGGTATATATTG 59.641 44.000 16.25 1.97 42.67 1.90
53 54 5.513233 ACCCGTGATCTACCGGTATATATT 58.487 41.667 16.25 0.00 42.67 1.28
54 55 5.121380 ACCCGTGATCTACCGGTATATAT 57.879 43.478 16.25 9.29 42.67 0.86
55 56 4.574674 ACCCGTGATCTACCGGTATATA 57.425 45.455 16.25 4.26 42.67 0.86
56 57 3.446442 ACCCGTGATCTACCGGTATAT 57.554 47.619 16.25 13.91 42.67 0.86
57 58 2.957402 ACCCGTGATCTACCGGTATA 57.043 50.000 16.25 8.72 42.67 1.47
58 59 2.077687 AACCCGTGATCTACCGGTAT 57.922 50.000 16.25 1.10 39.54 2.73
59 60 2.727123 TAACCCGTGATCTACCGGTA 57.273 50.000 14.95 14.95 39.54 4.02
60 61 1.851304 TTAACCCGTGATCTACCGGT 58.149 50.000 13.98 13.98 41.78 5.28
61 62 2.965572 TTTAACCCGTGATCTACCGG 57.034 50.000 0.00 0.00 43.82 5.28
62 63 5.594926 AGTATTTTAACCCGTGATCTACCG 58.405 41.667 0.00 0.00 0.00 4.02
63 64 7.945134 TCTAGTATTTTAACCCGTGATCTACC 58.055 38.462 0.00 0.00 0.00 3.18
64 65 9.978044 ATTCTAGTATTTTAACCCGTGATCTAC 57.022 33.333 0.00 0.00 0.00 2.59
79 80 9.337396 TGCAACGGATCAAATATTCTAGTATTT 57.663 29.630 0.00 0.00 35.27 1.40
80 81 8.902540 TGCAACGGATCAAATATTCTAGTATT 57.097 30.769 0.00 0.00 0.00 1.89
81 82 8.774586 GTTGCAACGGATCAAATATTCTAGTAT 58.225 33.333 14.90 0.00 0.00 2.12
82 83 8.138365 GTTGCAACGGATCAAATATTCTAGTA 57.862 34.615 14.90 0.00 0.00 1.82
83 84 7.016361 GTTGCAACGGATCAAATATTCTAGT 57.984 36.000 14.90 0.00 0.00 2.57
100 101 0.593773 AATTGTCCGTGCGTTGCAAC 60.594 50.000 19.89 19.89 41.47 4.17
101 102 0.945099 TAATTGTCCGTGCGTTGCAA 59.055 45.000 0.00 0.00 41.47 4.08
102 103 0.945099 TTAATTGTCCGTGCGTTGCA 59.055 45.000 0.00 0.00 35.60 4.08
103 104 1.069500 AGTTAATTGTCCGTGCGTTGC 60.069 47.619 0.00 0.00 0.00 4.17
104 105 2.961522 AGTTAATTGTCCGTGCGTTG 57.038 45.000 0.00 0.00 0.00 4.10
105 106 3.656559 ACTAGTTAATTGTCCGTGCGTT 58.343 40.909 0.00 0.00 0.00 4.84
106 107 3.308438 ACTAGTTAATTGTCCGTGCGT 57.692 42.857 0.00 0.00 0.00 5.24
107 108 5.004156 GTCTTACTAGTTAATTGTCCGTGCG 59.996 44.000 0.00 0.00 0.00 5.34
108 109 6.098017 AGTCTTACTAGTTAATTGTCCGTGC 58.902 40.000 0.00 0.00 0.00 5.34
109 110 9.630098 TTTAGTCTTACTAGTTAATTGTCCGTG 57.370 33.333 0.00 0.00 31.47 4.94
187 188 9.398170 CGACATGTATTTTCTGAAGTTTGAATT 57.602 29.630 0.00 0.00 0.00 2.17
188 189 8.567948 ACGACATGTATTTTCTGAAGTTTGAAT 58.432 29.630 0.00 0.00 0.00 2.57
189 190 7.925993 ACGACATGTATTTTCTGAAGTTTGAA 58.074 30.769 0.00 0.00 0.00 2.69
190 191 7.490962 ACGACATGTATTTTCTGAAGTTTGA 57.509 32.000 0.00 0.00 0.00 2.69
191 192 9.103048 GTTACGACATGTATTTTCTGAAGTTTG 57.897 33.333 0.00 0.00 31.81 2.93
192 193 9.052759 AGTTACGACATGTATTTTCTGAAGTTT 57.947 29.630 0.00 0.00 31.81 2.66
193 194 8.603242 AGTTACGACATGTATTTTCTGAAGTT 57.397 30.769 0.00 0.00 31.81 2.66
194 195 8.603242 AAGTTACGACATGTATTTTCTGAAGT 57.397 30.769 0.00 0.00 31.81 3.01
195 196 9.878599 AAAAGTTACGACATGTATTTTCTGAAG 57.121 29.630 0.00 0.00 31.81 3.02
196 197 9.658475 CAAAAGTTACGACATGTATTTTCTGAA 57.342 29.630 0.00 0.00 31.81 3.02
197 198 9.047371 TCAAAAGTTACGACATGTATTTTCTGA 57.953 29.630 0.00 0.00 31.81 3.27
198 199 9.318041 CTCAAAAGTTACGACATGTATTTTCTG 57.682 33.333 0.00 0.00 31.81 3.02
199 200 8.504005 CCTCAAAAGTTACGACATGTATTTTCT 58.496 33.333 0.00 0.00 31.81 2.52
200 201 7.270579 GCCTCAAAAGTTACGACATGTATTTTC 59.729 37.037 0.00 0.00 31.81 2.29
201 202 7.081976 GCCTCAAAAGTTACGACATGTATTTT 58.918 34.615 0.00 0.00 31.81 1.82
202 203 6.349033 GGCCTCAAAAGTTACGACATGTATTT 60.349 38.462 0.00 0.00 31.81 1.40
203 204 5.123344 GGCCTCAAAAGTTACGACATGTATT 59.877 40.000 0.00 0.00 31.81 1.89
204 205 4.634443 GGCCTCAAAAGTTACGACATGTAT 59.366 41.667 0.00 0.00 31.81 2.29
205 206 3.998341 GGCCTCAAAAGTTACGACATGTA 59.002 43.478 0.00 0.00 0.00 2.29
206 207 2.812011 GGCCTCAAAAGTTACGACATGT 59.188 45.455 0.00 0.00 0.00 3.21
207 208 2.811431 TGGCCTCAAAAGTTACGACATG 59.189 45.455 3.32 0.00 0.00 3.21
208 209 3.134574 TGGCCTCAAAAGTTACGACAT 57.865 42.857 3.32 0.00 0.00 3.06
209 210 2.614983 GTTGGCCTCAAAAGTTACGACA 59.385 45.455 3.32 0.00 34.28 4.35
210 211 2.876550 AGTTGGCCTCAAAAGTTACGAC 59.123 45.455 3.32 0.00 34.28 4.34
211 212 3.202829 AGTTGGCCTCAAAAGTTACGA 57.797 42.857 3.32 0.00 34.28 3.43
212 213 3.314080 TGAAGTTGGCCTCAAAAGTTACG 59.686 43.478 3.32 0.00 34.28 3.18
213 214 4.607955 GTGAAGTTGGCCTCAAAAGTTAC 58.392 43.478 3.32 0.00 34.28 2.50
214 215 3.314080 CGTGAAGTTGGCCTCAAAAGTTA 59.686 43.478 3.32 0.00 34.28 2.24
215 216 2.099098 CGTGAAGTTGGCCTCAAAAGTT 59.901 45.455 3.32 0.00 34.28 2.66
216 217 1.676006 CGTGAAGTTGGCCTCAAAAGT 59.324 47.619 3.32 0.00 34.28 2.66
217 218 1.001378 CCGTGAAGTTGGCCTCAAAAG 60.001 52.381 3.32 0.00 34.28 2.27
218 219 1.028905 CCGTGAAGTTGGCCTCAAAA 58.971 50.000 3.32 0.00 34.28 2.44
219 220 1.452145 GCCGTGAAGTTGGCCTCAAA 61.452 55.000 3.32 0.00 45.73 2.69
220 221 1.896660 GCCGTGAAGTTGGCCTCAA 60.897 57.895 3.32 0.00 45.73 3.02
221 222 2.281484 GCCGTGAAGTTGGCCTCA 60.281 61.111 3.32 0.00 45.73 3.86
232 233 1.669760 GAAATGGGTCACGCCGTGA 60.670 57.895 17.22 17.22 40.50 4.35
236 237 0.746923 GGGTAGAAATGGGTCACGCC 60.747 60.000 0.00 0.00 0.00 5.68
256 257 2.144730 CGGACACAAACGGACCATTTA 58.855 47.619 0.00 0.00 0.00 1.40
261 262 0.028374 CAAACGGACACAAACGGACC 59.972 55.000 0.00 0.00 0.00 4.46
281 282 8.179615 GGGTCGTTTGATTTATTCGTTTTATCT 58.820 33.333 0.00 0.00 0.00 1.98
282 283 7.964011 TGGGTCGTTTGATTTATTCGTTTTATC 59.036 33.333 0.00 0.00 0.00 1.75
283 284 7.818642 TGGGTCGTTTGATTTATTCGTTTTAT 58.181 30.769 0.00 0.00 0.00 1.40
291 292 3.253677 TGCGTTGGGTCGTTTGATTTATT 59.746 39.130 0.00 0.00 0.00 1.40
293 294 2.219458 TGCGTTGGGTCGTTTGATTTA 58.781 42.857 0.00 0.00 0.00 1.40
309 310 0.179073 GTCTGTATGCTCCCATGCGT 60.179 55.000 0.00 0.00 36.93 5.24
310 311 1.217585 CGTCTGTATGCTCCCATGCG 61.218 60.000 0.00 0.00 36.93 4.73
325 326 1.300388 CGGACCGGACAAAACGTCT 60.300 57.895 9.46 0.00 44.70 4.18
340 341 2.975799 GGCAAAAGCGGACACGGA 60.976 61.111 0.00 0.00 41.36 4.69
354 355 0.189574 TTTGGTCTGGAAATGGGGCA 59.810 50.000 0.00 0.00 0.00 5.36
382 383 2.846754 TGCTTTGGCCCCAAACCC 60.847 61.111 8.35 4.09 40.51 4.11
399 400 2.048127 GGCGTCCGCTTTCTGTCT 60.048 61.111 11.82 0.00 41.60 3.41
400 401 1.228657 AAAGGCGTCCGCTTTCTGTC 61.229 55.000 9.49 0.00 39.52 3.51
415 416 1.615107 GAACGACGAGGACGCAAAGG 61.615 60.000 0.00 0.00 43.96 3.11
427 428 3.103911 GGACACAGGCGAACGACG 61.104 66.667 0.00 0.00 45.66 5.12
436 437 4.436998 GGTCGAGGCGGACACAGG 62.437 72.222 12.59 0.00 38.70 4.00
455 456 5.540337 ACAGAAAAGGAGAGAGTGACATGTA 59.460 40.000 0.00 0.00 0.00 2.29
486 487 1.377072 CGTGGGTGCACATGATGGA 60.377 57.895 20.43 0.00 0.00 3.41
499 500 4.137872 ATACGTCGTGGGCGTGGG 62.138 66.667 8.47 0.00 42.87 4.61
539 540 1.366111 ACAAACTCGTTGCACGCAGT 61.366 50.000 4.15 6.09 42.21 4.40
540 541 0.925267 CACAAACTCGTTGCACGCAG 60.925 55.000 4.15 5.60 42.21 5.18
549 2244 2.665185 GAGGCCGCACAAACTCGT 60.665 61.111 0.00 0.00 0.00 4.18
573 2268 3.521947 AGAAATAGGGAGAACGAACGG 57.478 47.619 0.00 0.00 0.00 4.44
578 2273 3.036091 TGGGGTAGAAATAGGGAGAACG 58.964 50.000 0.00 0.00 0.00 3.95
624 2319 4.838986 ACCGCATGACCCTAAATCTATACT 59.161 41.667 0.00 0.00 0.00 2.12
641 2336 3.650950 AGGCCAACTCCACCGCAT 61.651 61.111 5.01 0.00 0.00 4.73
663 2358 4.081031 TCCATATGCAACGTGTAACCCTTA 60.081 41.667 0.00 0.00 0.00 2.69
674 2369 1.979855 TGGGGATTCCATATGCAACG 58.020 50.000 4.80 0.00 41.46 4.10
678 2373 5.612725 TTTTCTTTGGGGATTCCATATGC 57.387 39.130 4.80 0.00 46.52 3.14
781 2992 1.331399 GGGGTCAGAGGAGTAGGTGC 61.331 65.000 0.00 0.00 0.00 5.01
1131 4864 0.251209 GGGCGGAAGTTCTTTTCCCT 60.251 55.000 2.25 0.00 43.02 4.20
1139 4872 2.484742 TAAGGAAAGGGCGGAAGTTC 57.515 50.000 0.00 0.00 0.00 3.01
1242 5209 3.760580 GATCATCCCGATCCAAGAACT 57.239 47.619 0.00 0.00 44.25 3.01
1278 5245 5.066913 AGGGGAAGGGATCAATCAATTAC 57.933 43.478 0.00 0.00 0.00 1.89
1408 5376 5.324832 AAGAAAATCCCCAAGAACTCTCA 57.675 39.130 0.00 0.00 0.00 3.27
1623 5594 1.526887 TCAAAGAAAGAACGCAGCTCG 59.473 47.619 4.36 4.36 45.38 5.03
1694 5666 5.123979 ACGGATTACTGGAAGAAGCAAAATC 59.876 40.000 0.00 0.00 37.43 2.17
1828 5800 2.941453 AAGCATTTGCAGCAGATCTG 57.059 45.000 18.84 18.84 45.16 2.90
1876 5848 5.404366 TCGATAAGTGTGCAAACTTACTGAC 59.596 40.000 27.88 18.38 43.53 3.51
1910 5882 5.298347 CAGGTCGGATAGTAAAAAGATCCC 58.702 45.833 0.00 0.00 36.55 3.85
1931 5903 8.166422 ACTTAAAAGACTGATTACCAAACCAG 57.834 34.615 0.00 0.00 0.00 4.00
2011 5983 3.067833 CAAACATGTGATTTGGCATGCA 58.932 40.909 21.36 2.54 44.43 3.96
2034 6860 6.535963 AGATTTTATTCAGCCAAAAGGAGG 57.464 37.500 0.00 0.00 0.00 4.30
2390 9949 9.700831 ATGACATTTAATAGAACTTTTAGGGCT 57.299 29.630 0.00 0.00 0.00 5.19
2443 10003 6.998802 AGTTAGGACATATTCTAGTGCATCC 58.001 40.000 0.00 0.00 0.00 3.51
2554 10116 0.680280 GGAGTACTGGAGTCGGCTGA 60.680 60.000 0.00 0.00 0.00 4.26
2555 10117 0.681564 AGGAGTACTGGAGTCGGCTG 60.682 60.000 0.00 0.00 0.00 4.85
2796 10359 4.919774 TGGGGTAGAAGCAACATCTAAA 57.080 40.909 0.00 0.00 31.52 1.85
2848 10411 4.895668 ATCCAACATGCCAAAATGACTT 57.104 36.364 0.00 0.00 0.00 3.01
2953 10516 5.202004 TGGGACTAGATCACTTAAGACTCC 58.798 45.833 10.09 1.09 0.00 3.85
3012 10575 0.319728 CCTGCTGCACACTCTACAGT 59.680 55.000 0.00 0.00 33.87 3.55
3065 10628 6.640518 TGGTTTGGCAAATTTAGTTACACAA 58.359 32.000 16.74 0.00 0.00 3.33
3126 10689 2.121948 TGCCAGCACCAGAGATATTCT 58.878 47.619 0.00 0.00 36.25 2.40
3202 10765 7.957002 TCTTATCTCCCTCTTAGTAATTGCAG 58.043 38.462 0.00 0.00 0.00 4.41
3232 10795 9.238368 CAACTATGAACTTATTCTACCCCAAAA 57.762 33.333 0.00 0.00 35.69 2.44
3233 10796 8.607713 TCAACTATGAACTTATTCTACCCCAAA 58.392 33.333 0.00 0.00 35.69 3.28
3278 10841 9.413048 GGTTGCTGAGTTTATCTGATACTATAC 57.587 37.037 0.00 0.00 0.00 1.47
3279 10842 9.143155 TGGTTGCTGAGTTTATCTGATACTATA 57.857 33.333 0.00 0.00 0.00 1.31
3281 10844 7.418337 TGGTTGCTGAGTTTATCTGATACTA 57.582 36.000 0.00 0.00 0.00 1.82
3303 10953 2.993264 CTTGCCCAGCCAGGTTGG 60.993 66.667 15.61 15.61 41.55 3.77
3388 11053 5.246145 AGAGTTCGGTGCTACAGTATTAC 57.754 43.478 0.00 0.00 0.00 1.89
3457 11122 6.060028 AGTATACGCATAATGCACCAAAAG 57.940 37.500 0.00 0.00 45.36 2.27
3474 11139 4.571984 TGCATGCAGACAACATGAGTATAC 59.428 41.667 18.46 0.00 46.33 1.47
3513 11182 4.829968 AGTCAGAACAACATCATCAGGAG 58.170 43.478 0.00 0.00 0.00 3.69
3541 11210 7.868415 AGTACTCAGAATGACAGAAAAGTACAC 59.132 37.037 14.89 0.00 42.56 2.90
3621 11371 1.074405 ACTGCATCAACCTGACCACAT 59.926 47.619 0.00 0.00 0.00 3.21
4014 11787 3.637694 GGTGGCAAGGTAAGGTAAAACAA 59.362 43.478 0.00 0.00 0.00 2.83
4032 11805 0.250513 GCTCCCTAACACTCTGGTGG 59.749 60.000 1.29 0.00 46.85 4.61
4036 11809 2.100584 CAGCTAGCTCCCTAACACTCTG 59.899 54.545 16.15 0.00 0.00 3.35
4147 11920 5.694231 TCACCTTTTCAGACATCACATTG 57.306 39.130 0.00 0.00 0.00 2.82
4148 11921 7.415989 GCATATCACCTTTTCAGACATCACATT 60.416 37.037 0.00 0.00 0.00 2.71
4149 11922 6.039047 GCATATCACCTTTTCAGACATCACAT 59.961 38.462 0.00 0.00 0.00 3.21
4150 11923 5.355071 GCATATCACCTTTTCAGACATCACA 59.645 40.000 0.00 0.00 0.00 3.58
4151 11924 5.587844 AGCATATCACCTTTTCAGACATCAC 59.412 40.000 0.00 0.00 0.00 3.06
4154 11927 6.660521 TCAAAGCATATCACCTTTTCAGACAT 59.339 34.615 0.00 0.00 0.00 3.06
4155 11928 6.003326 TCAAAGCATATCACCTTTTCAGACA 58.997 36.000 0.00 0.00 0.00 3.41
4156 11929 6.500684 TCAAAGCATATCACCTTTTCAGAC 57.499 37.500 0.00 0.00 0.00 3.51
4157 11930 6.716628 AGTTCAAAGCATATCACCTTTTCAGA 59.283 34.615 0.00 0.00 0.00 3.27
4158 11931 6.917533 AGTTCAAAGCATATCACCTTTTCAG 58.082 36.000 0.00 0.00 0.00 3.02
4159 11932 6.071952 GGAGTTCAAAGCATATCACCTTTTCA 60.072 38.462 0.00 0.00 0.00 2.69
4179 11952 0.610232 GGAGCACCAGCAATGGAGTT 60.610 55.000 0.31 0.00 45.49 3.01
4253 12026 6.208204 AGCTTCAGAGAATAGCAAAAACACAT 59.792 34.615 0.00 0.00 37.37 3.21
4325 12098 6.126863 AGATGACAACCCTCAAATTGACTA 57.873 37.500 0.00 0.00 0.00 2.59
4354 12127 2.493278 CTGTTCATTTGTAGGGGCCAAG 59.507 50.000 4.39 0.00 0.00 3.61
4356 12129 1.427368 ACTGTTCATTTGTAGGGGCCA 59.573 47.619 4.39 0.00 0.00 5.36
4437 12213 7.519008 CGAATATGGTAGAGTTTCAAAGATGCC 60.519 40.741 0.00 0.00 0.00 4.40
4536 12312 8.401709 GCAAGGTCAATTTTGGATTTTAAAACA 58.598 29.630 1.97 0.00 30.64 2.83
4538 12314 8.511604 TGCAAGGTCAATTTTGGATTTTAAAA 57.488 26.923 2.51 2.51 0.00 1.52
4552 12328 3.070015 CCTCTTTTGGTTGCAAGGTCAAT 59.930 43.478 0.00 0.00 0.00 2.57
4573 12350 7.225341 CCATGCTTAAATTCTTTAGCATTTCCC 59.775 37.037 8.24 0.00 37.62 3.97
4693 12471 4.382291 ACTATCGCTATGTCTTCGAGACT 58.618 43.478 13.65 5.12 45.27 3.24
4698 12476 4.099120 GCCATACTATCGCTATGTCTTCG 58.901 47.826 0.00 0.00 0.00 3.79
4709 12487 9.692749 TGAAAATCTTAGTTAGCCATACTATCG 57.307 33.333 0.00 0.00 0.00 2.92
4726 12504 9.743057 TTGACGAAACATAATGTTGAAAATCTT 57.257 25.926 0.00 0.00 40.14 2.40
4743 12521 4.083003 TGTGGGCATCTTATTTGACGAAAC 60.083 41.667 0.00 0.00 0.00 2.78
4786 12565 7.821359 GCTCATCAGCTTAATTCCATGATACTA 59.179 37.037 0.00 0.00 43.09 1.82
4791 12570 4.139786 GGCTCATCAGCTTAATTCCATGA 58.860 43.478 0.00 0.00 46.03 3.07
4796 12575 3.188048 CGGATGGCTCATCAGCTTAATTC 59.812 47.826 14.57 0.00 46.03 2.17
4803 12582 0.105593 TCTTCGGATGGCTCATCAGC 59.894 55.000 14.57 0.00 42.13 4.26
4816 12595 5.639506 TGTTTCTTTCTCATAGCTTCTTCGG 59.360 40.000 0.00 0.00 0.00 4.30
4818 12597 8.725148 TCAATGTTTCTTTCTCATAGCTTCTTC 58.275 33.333 0.00 0.00 0.00 2.87
4831 12610 4.088823 AGCGATGCTCAATGTTTCTTTC 57.911 40.909 0.00 0.00 30.62 2.62
4835 12614 5.221891 TCTTAAGCGATGCTCAATGTTTC 57.778 39.130 0.00 0.00 38.25 2.78
4851 12630 7.909267 TGATCACGCTTGTCATTATTCTTAAG 58.091 34.615 0.00 0.00 0.00 1.85
4859 12638 5.468409 TGAGTTTTGATCACGCTTGTCATTA 59.532 36.000 0.00 0.00 0.00 1.90
4873 12652 6.705825 GGCATAAAACCAAACTGAGTTTTGAT 59.294 34.615 15.04 1.39 43.90 2.57
4874 12653 6.045955 GGCATAAAACCAAACTGAGTTTTGA 58.954 36.000 15.04 0.00 43.90 2.69
4875 12654 6.018832 CAGGCATAAAACCAAACTGAGTTTTG 60.019 38.462 8.03 7.74 43.90 2.44
4876 12655 6.048509 CAGGCATAAAACCAAACTGAGTTTT 58.951 36.000 8.03 6.18 45.51 2.43
4877 12656 5.362430 TCAGGCATAAAACCAAACTGAGTTT 59.638 36.000 4.45 4.45 37.80 2.66
4878 12657 4.892934 TCAGGCATAAAACCAAACTGAGTT 59.107 37.500 0.00 0.00 0.00 3.01
4879 12658 4.469657 TCAGGCATAAAACCAAACTGAGT 58.530 39.130 0.00 0.00 0.00 3.41


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.