Multiple sequence alignment - TraesCS5B01G041800

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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 TraesCS5B01G041800 chr5B 100.000 4822 0 0 1 4822 45878218 45873397 0.000000e+00 8905.0
1 TraesCS5B01G041800 chr5D 92.304 3690 182 31 332 3964 45688684 45685040 0.000000e+00 5147.0
2 TraesCS5B01G041800 chr5D 91.964 336 27 0 1 336 45717736 45717401 5.650000e-129 472.0
3 TraesCS5B01G041800 chr5D 85.130 269 24 10 3975 4237 45684988 45684730 1.330000e-65 261.0
4 TraesCS5B01G041800 chr5D 76.852 216 37 8 176 388 310685665 310685460 5.100000e-20 110.0
5 TraesCS5B01G041800 chr5D 87.500 56 4 2 169 223 247608846 247608793 1.450000e-05 62.1
6 TraesCS5B01G041800 chr5A 91.017 2349 149 18 573 2897 36496751 36494441 0.000000e+00 3112.0
7 TraesCS5B01G041800 chr5A 93.182 880 37 8 2939 3799 36494440 36493565 0.000000e+00 1271.0
8 TraesCS5B01G041800 chr5A 92.510 494 36 1 1 493 36499002 36498509 0.000000e+00 706.0
9 TraesCS5B01G041800 chr5A 86.740 362 25 9 3797 4156 36493461 36493121 9.790000e-102 381.0
10 TraesCS5B01G041800 chr5A 91.477 176 9 2 4648 4822 36492420 36492250 2.240000e-58 237.0
11 TraesCS5B01G041800 chr5A 88.750 160 12 2 4663 4822 36491538 36491385 1.770000e-44 191.0
12 TraesCS5B01G041800 chr5A 78.632 117 20 4 189 304 294260788 294260676 6.690000e-09 73.1
13 TraesCS5B01G041800 chr4A 75.269 372 75 14 6 368 41852258 41852621 1.390000e-35 161.0
14 TraesCS5B01G041800 chr6B 90.196 51 5 0 4436 4486 572512163 572512213 3.110000e-07 67.6


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 TraesCS5B01G041800 chr5B 45873397 45878218 4821 True 8905 8905 100.000000 1 4822 1 chr5B.!!$R1 4821
1 TraesCS5B01G041800 chr5D 45684730 45688684 3954 True 2704 5147 88.717000 332 4237 2 chr5D.!!$R4 3905
2 TraesCS5B01G041800 chr5A 36491385 36499002 7617 True 983 3112 90.612667 1 4822 6 chr5A.!!$R2 4821

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
233 235 0.881600 GCCACCACCTCGTTAACGTT 60.882 55.000 25.98 5.88 40.80 3.99 F
634 2336 1.005037 GGTGATGTGCGTCCAGTGA 60.005 57.895 0.00 0.00 0.00 3.41 F
2107 3835 0.107945 GTGATGGTGCTCCTCTGGAC 60.108 60.000 6.34 0.00 34.23 4.02 F
2456 4190 1.603802 TGCAAGAAGTTGAAGGAAGCG 59.396 47.619 0.00 0.00 35.46 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1310 3038 0.108945 GAAGCAGCCAATTCACAGCC 60.109 55.0 0.00 0.0 0.00 4.85 R
2456 4190 0.112412 TCTTCTTTGGCAGGGGGTTC 59.888 55.0 0.00 0.0 0.00 3.62 R
3600 5367 0.251077 ACTGACCGAGTAACGAGGGT 60.251 55.0 0.00 0.0 45.77 4.34 R
4178 6104 0.179018 ACACTCTTTTGGGCGCTCTT 60.179 50.0 9.62 0.0 0.00 2.85 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
22 23 3.426159 CGAACCATGCCACAGAACAATAC 60.426 47.826 0.00 0.00 0.00 1.89
34 35 6.402983 CCACAGAACAATACAGAAGAAGATGC 60.403 42.308 0.00 0.00 0.00 3.91
126 127 4.445448 GGGAAGCAATAGATCTGGTGACAT 60.445 45.833 5.18 0.00 41.51 3.06
127 128 5.221722 GGGAAGCAATAGATCTGGTGACATA 60.222 44.000 5.18 0.00 41.51 2.29
134 135 8.462016 GCAATAGATCTGGTGACATAAACTTTT 58.538 33.333 5.18 0.00 41.51 2.27
148 149 6.919662 ACATAAACTTTTACAGTCTTCGTCGA 59.080 34.615 0.00 0.00 32.94 4.20
154 155 2.127345 AGTCTTCGTCGACGCACG 60.127 61.111 32.19 21.13 41.36 5.34
181 182 3.632333 ACATTGTCGAGGTATGGAGAGA 58.368 45.455 0.00 0.00 0.00 3.10
191 192 5.124776 CGAGGTATGGAGAGATCCAATAGAC 59.875 48.000 0.29 0.00 43.83 2.59
194 195 5.782845 GGTATGGAGAGATCCAATAGACCTT 59.217 44.000 0.29 0.00 43.83 3.50
206 208 5.827797 TCCAATAGACCTTATTCCAACATGC 59.172 40.000 0.00 0.00 0.00 4.06
230 232 2.030958 CCGCCACCACCTCGTTAAC 61.031 63.158 0.00 0.00 0.00 2.01
233 235 0.881600 GCCACCACCTCGTTAACGTT 60.882 55.000 25.98 5.88 40.80 3.99
238 240 1.262151 CCACCTCGTTAACGTTGTTGG 59.738 52.381 25.98 21.77 40.80 3.77
273 275 7.818997 ACCTAAGGGAAAGAAAACTAAACAG 57.181 36.000 0.00 0.00 36.25 3.16
279 281 5.538813 GGGAAAGAAAACTAAACAGATGGGT 59.461 40.000 0.00 0.00 0.00 4.51
304 306 1.945354 TTCCTCTTGCCGCCGACTAG 61.945 60.000 0.00 0.00 0.00 2.57
311 313 3.129502 CCGCCGACTAGACCGTCA 61.130 66.667 0.00 0.00 33.54 4.35
312 314 2.693762 CCGCCGACTAGACCGTCAA 61.694 63.158 0.00 0.00 33.54 3.18
353 355 3.480133 GGGGCAGCGTGTAGGGAT 61.480 66.667 0.00 0.00 0.00 3.85
355 357 2.109181 GGCAGCGTGTAGGGATCC 59.891 66.667 1.92 1.92 0.00 3.36
412 414 3.490348 CTCCAAACACCCTCTTTGTGAT 58.510 45.455 0.00 0.00 37.18 3.06
445 448 6.855763 ATTCCAGGTAAAGCAATGATGAAA 57.144 33.333 0.00 0.00 0.00 2.69
462 465 3.734463 TGAAAAGTTACATGAGCGGACA 58.266 40.909 0.00 0.00 0.00 4.02
465 468 5.935206 TGAAAAGTTACATGAGCGGACATTA 59.065 36.000 0.00 0.00 0.00 1.90
564 2266 6.808008 TGGAAGTCATTCAAGATTCAAGTC 57.192 37.500 0.00 0.00 37.15 3.01
565 2267 5.707298 TGGAAGTCATTCAAGATTCAAGTCC 59.293 40.000 0.00 0.00 37.15 3.85
566 2268 5.942826 GGAAGTCATTCAAGATTCAAGTCCT 59.057 40.000 0.00 0.00 37.15 3.85
567 2269 7.106239 GGAAGTCATTCAAGATTCAAGTCCTA 58.894 38.462 0.00 0.00 37.15 2.94
568 2270 7.279758 GGAAGTCATTCAAGATTCAAGTCCTAG 59.720 40.741 0.00 0.00 37.15 3.02
571 2273 7.180051 AGTCATTCAAGATTCAAGTCCTAGACT 59.820 37.037 0.00 0.00 45.64 3.24
584 2286 4.461081 AGTCCTAGACTTGACACTGATGTC 59.539 45.833 0.37 0.37 43.39 3.06
585 2287 6.558742 AGTCCTAGACTTGACACTGATGTCC 61.559 48.000 5.04 0.00 43.69 4.02
604 2306 4.338118 TGTCCGCATTTTCCTGGATTTATC 59.662 41.667 0.00 0.00 32.18 1.75
634 2336 1.005037 GGTGATGTGCGTCCAGTGA 60.005 57.895 0.00 0.00 0.00 3.41
646 2348 3.082548 CGTCCAGTGAGAGGAGACTTTA 58.917 50.000 0.00 0.00 44.43 1.85
684 2386 3.978855 CGTCTGTGACAAACTTCGTCATA 59.021 43.478 0.00 0.00 44.70 2.15
729 2432 2.014857 TCGATAGGTCCTGAACGTCAG 58.985 52.381 0.00 7.72 43.91 3.51
738 2456 2.347697 CTGAACGTCAGGATCGAACA 57.652 50.000 0.00 0.00 40.71 3.18
758 2476 8.920665 TCGAACAATTTTTGTGGCAATTTATAG 58.079 29.630 0.00 0.00 44.59 1.31
832 2551 7.965718 ACTCTTCCAAATTTGAATTCATTCCA 58.034 30.769 19.86 0.00 35.97 3.53
1259 2985 2.438614 TCGCCACCTCTCTCTCCG 60.439 66.667 0.00 0.00 0.00 4.63
1289 3016 1.810197 GCGTGTATTGTCATTTCGGC 58.190 50.000 0.00 0.00 0.00 5.54
1330 3058 0.108945 GCTGTGAATTGGCTGCTTCC 60.109 55.000 0.00 0.00 0.00 3.46
1413 3141 1.884579 TCAAGGTACCTCTGTCACGAC 59.115 52.381 16.64 0.00 0.00 4.34
1414 3142 1.887198 CAAGGTACCTCTGTCACGACT 59.113 52.381 16.64 0.00 0.00 4.18
1415 3143 1.823797 AGGTACCTCTGTCACGACTC 58.176 55.000 9.21 0.00 0.00 3.36
1416 3144 1.073444 AGGTACCTCTGTCACGACTCA 59.927 52.381 9.21 0.00 0.00 3.41
1417 3145 1.199558 GGTACCTCTGTCACGACTCAC 59.800 57.143 4.06 0.00 0.00 3.51
1419 3147 0.534427 ACCTCTGTCACGACTCACGA 60.534 55.000 0.00 0.00 45.77 4.35
1549 3277 0.252479 CTCCAGGAGCTGACATTGCT 59.748 55.000 2.60 0.00 44.24 3.91
1553 3281 2.758089 GGAGCTGACATTGCTGCGG 61.758 63.158 0.00 0.00 41.30 5.69
1588 3316 5.048713 AGGTAGCTGCATCTTTGTTTGTTAC 60.049 40.000 3.61 0.00 0.00 2.50
1602 3330 9.268268 CTTTGTTTGTTACTATGAGTTGTCCTA 57.732 33.333 0.00 0.00 0.00 2.94
1609 3337 7.015877 TGTTACTATGAGTTGTCCTAGTTTGGT 59.984 37.037 0.00 0.00 36.09 3.67
1610 3338 8.526147 GTTACTATGAGTTGTCCTAGTTTGGTA 58.474 37.037 0.00 0.00 36.09 3.25
1732 3460 0.179018 AGAACAAGAAAGGCGGTGCT 60.179 50.000 0.00 0.00 0.00 4.40
1737 3465 0.890996 AAGAAAGGCGGTGCTGAAGG 60.891 55.000 0.00 0.00 0.00 3.46
1741 3469 2.045926 GGCGGTGCTGAAGGTCAT 60.046 61.111 0.00 0.00 0.00 3.06
1747 3475 1.354040 GTGCTGAAGGTCATGAGTCG 58.646 55.000 0.00 0.00 0.00 4.18
1751 3479 1.135915 CTGAAGGTCATGAGTCGGAGG 59.864 57.143 0.00 0.00 0.00 4.30
1757 3485 1.112113 TCATGAGTCGGAGGGTAAGC 58.888 55.000 0.00 0.00 0.00 3.09
1810 3538 0.387202 AGAAGGCGGATGATGAGACG 59.613 55.000 0.00 0.00 0.00 4.18
1939 3667 6.968131 AAGAAAAGCAAGAAACAGGAAAAC 57.032 33.333 0.00 0.00 0.00 2.43
2038 3766 4.990526 AGGTTGATGACAAGAAATCTGGT 58.009 39.130 0.00 0.00 36.64 4.00
2082 3810 2.089201 TGATGAGGCTAACGAGAACGA 58.911 47.619 0.00 0.00 42.66 3.85
2107 3835 0.107945 GTGATGGTGCTCCTCTGGAC 60.108 60.000 6.34 0.00 34.23 4.02
2143 3871 9.937175 AAAAAGAAGAAGAGTAAATCAACTTCG 57.063 29.630 0.00 0.00 42.17 3.79
2220 3948 6.949352 ATCTAATGGTGCCAGTGAAAATAG 57.051 37.500 1.01 0.00 0.00 1.73
2222 3950 4.789012 AATGGTGCCAGTGAAAATAGTG 57.211 40.909 0.00 0.00 0.00 2.74
2245 3973 3.248024 TGCTGTAGGAGAAGGGAAAGAA 58.752 45.455 0.00 0.00 0.00 2.52
2248 3976 4.263112 GCTGTAGGAGAAGGGAAAGAAGTT 60.263 45.833 0.00 0.00 0.00 2.66
2380 4114 3.118482 AGACTGCGATGGACATTGAGAAT 60.118 43.478 3.73 0.00 0.00 2.40
2428 4162 5.241285 TGATGATGCAGTTGTTAGCAAGAAA 59.759 36.000 0.00 0.00 44.88 2.52
2438 4172 4.932146 TGTTAGCAAGAAAAGGAAACTGC 58.068 39.130 0.00 0.00 42.68 4.40
2456 4190 1.603802 TGCAAGAAGTTGAAGGAAGCG 59.396 47.619 0.00 0.00 35.46 4.68
2630 4372 7.275888 TCTTTGAGTATTGCTTGTTTGTCAT 57.724 32.000 0.00 0.00 0.00 3.06
2667 4409 4.141390 ACCCTGACAGTTGAAAGTCTCAAT 60.141 41.667 0.93 0.00 45.74 2.57
2718 4460 9.959721 TTCTCTTACATGAAACCTTATTTAGCT 57.040 29.630 0.00 0.00 0.00 3.32
2846 4594 8.691797 ACTTATTATTGTTGTTGTTGTTCCTGT 58.308 29.630 0.00 0.00 0.00 4.00
2847 4595 9.528018 CTTATTATTGTTGTTGTTGTTCCTGTT 57.472 29.630 0.00 0.00 0.00 3.16
2913 4661 9.162764 GAAATATGTTTCAGTTAGAAGCTACCA 57.837 33.333 9.81 0.00 42.61 3.25
2931 4679 7.506971 AGCTACCAGTAAGTAAAAGTTCACTT 58.493 34.615 7.68 7.68 38.50 3.16
3011 4759 5.372373 GCTTTTAGGATATGCTGACCTCTT 58.628 41.667 7.05 0.00 35.52 2.85
3085 4851 7.014038 GGCAAGATCTTGATTATCCATGTCTTT 59.986 37.037 34.43 0.00 42.93 2.52
3236 5003 8.613060 TGAGGTTTATTGATCATAAGCTCATC 57.387 34.615 26.68 13.50 39.07 2.92
3270 5037 7.542025 ACCATTTCTCAATGATGCTAAACTTC 58.458 34.615 0.00 0.00 42.35 3.01
3402 5169 5.092781 TGTTTTCTTCGTCTTTTGCTGAAC 58.907 37.500 0.00 0.00 0.00 3.18
3406 5173 2.613026 TCGTCTTTTGCTGAACTCCA 57.387 45.000 0.00 0.00 0.00 3.86
3442 5209 6.172136 TGGTTTCATGATTGGTGTTCAATT 57.828 33.333 0.00 0.00 45.36 2.32
3600 5367 2.156117 CGTGCGACGTTTTCCATTCTTA 59.844 45.455 0.00 0.00 36.74 2.10
3659 5426 3.634225 GAAGGCATGCCTGCTTTGCAA 62.634 52.381 39.18 0.00 46.53 4.08
3894 5771 4.098349 TCACAGAAATTGCAAAGCTGTCTT 59.902 37.500 21.81 1.97 35.42 3.01
3923 5801 4.637483 TTGAACTGAGGCTGTTTTCTTG 57.363 40.909 0.00 0.00 0.00 3.02
3924 5802 3.884895 TGAACTGAGGCTGTTTTCTTGA 58.115 40.909 0.00 0.00 0.00 3.02
3925 5803 3.879295 TGAACTGAGGCTGTTTTCTTGAG 59.121 43.478 0.00 0.00 0.00 3.02
4123 6044 1.133025 GGCGTGATCAGTTGGATTTGG 59.867 52.381 0.00 0.00 36.00 3.28
4156 6082 7.430502 GGCTATGCTAATGCGAAATGAAATATC 59.569 37.037 0.00 0.00 43.34 1.63
4157 6083 8.180267 GCTATGCTAATGCGAAATGAAATATCT 58.820 33.333 0.00 0.00 43.34 1.98
4158 6084 9.699985 CTATGCTAATGCGAAATGAAATATCTC 57.300 33.333 0.00 0.00 43.34 2.75
4159 6085 6.902341 TGCTAATGCGAAATGAAATATCTCC 58.098 36.000 0.00 0.00 43.34 3.71
4160 6086 6.017933 GCTAATGCGAAATGAAATATCTCCG 58.982 40.000 0.00 0.00 0.00 4.63
4161 6087 6.347725 GCTAATGCGAAATGAAATATCTCCGT 60.348 38.462 0.00 0.00 0.00 4.69
4162 6088 6.377327 AATGCGAAATGAAATATCTCCGTT 57.623 33.333 0.00 0.00 0.00 4.44
4163 6089 5.403897 TGCGAAATGAAATATCTCCGTTC 57.596 39.130 0.00 0.00 0.00 3.95
4164 6090 4.873259 TGCGAAATGAAATATCTCCGTTCA 59.127 37.500 0.00 0.00 35.83 3.18
4165 6091 5.198274 GCGAAATGAAATATCTCCGTTCAC 58.802 41.667 0.00 0.00 34.28 3.18
4166 6092 5.006746 GCGAAATGAAATATCTCCGTTCACT 59.993 40.000 0.00 0.00 34.28 3.41
4167 6093 6.456988 GCGAAATGAAATATCTCCGTTCACTT 60.457 38.462 0.00 0.00 34.28 3.16
4168 6094 7.464358 CGAAATGAAATATCTCCGTTCACTTT 58.536 34.615 0.00 0.00 34.28 2.66
4180 6106 8.263940 TCTCCGTTCACTTTTATATTTCCAAG 57.736 34.615 0.00 0.00 0.00 3.61
4192 6121 0.673437 TTTCCAAGAGCGCCCAAAAG 59.327 50.000 2.29 0.00 0.00 2.27
4215 6144 5.998363 AGAGTGTGAAAAGACATTTCTACCC 59.002 40.000 4.91 0.00 46.27 3.69
4216 6145 5.941788 AGTGTGAAAAGACATTTCTACCCT 58.058 37.500 4.91 0.00 46.27 4.34
4217 6146 5.765182 AGTGTGAAAAGACATTTCTACCCTG 59.235 40.000 4.91 0.00 46.27 4.45
4218 6147 5.048713 GTGTGAAAAGACATTTCTACCCTGG 60.049 44.000 4.91 0.00 46.27 4.45
4233 6163 2.884639 ACCCTGGTCAGTTTGAATTTCG 59.115 45.455 0.00 0.00 0.00 3.46
4237 6167 5.393962 CCTGGTCAGTTTGAATTTCGAATC 58.606 41.667 0.00 0.00 0.00 2.52
4238 6168 5.048782 CCTGGTCAGTTTGAATTTCGAATCA 60.049 40.000 0.00 0.00 0.00 2.57
4254 6184 0.957395 ATCATGATCGCGATTGCCCC 60.957 55.000 24.55 10.50 38.08 5.80
4255 6185 1.893335 CATGATCGCGATTGCCCCA 60.893 57.895 24.55 16.23 38.08 4.96
4256 6186 1.893808 ATGATCGCGATTGCCCCAC 60.894 57.895 24.55 8.94 38.08 4.61
4263 6193 4.179579 GATTGCCCCACGCGCTTC 62.180 66.667 5.73 0.00 42.08 3.86
4264 6194 4.722700 ATTGCCCCACGCGCTTCT 62.723 61.111 5.73 0.00 42.08 2.85
4265 6195 4.947147 TTGCCCCACGCGCTTCTT 62.947 61.111 5.73 0.00 42.08 2.52
4268 6198 4.394712 CCCCACGCGCTTCTTCCT 62.395 66.667 5.73 0.00 0.00 3.36
4269 6199 2.358737 CCCACGCGCTTCTTCCTT 60.359 61.111 5.73 0.00 0.00 3.36
4270 6200 2.680913 CCCACGCGCTTCTTCCTTG 61.681 63.158 5.73 0.00 0.00 3.61
4271 6201 2.174349 CACGCGCTTCTTCCTTGC 59.826 61.111 5.73 0.00 0.00 4.01
4272 6202 3.050275 ACGCGCTTCTTCCTTGCC 61.050 61.111 5.73 0.00 0.00 4.52
4273 6203 2.743928 CGCGCTTCTTCCTTGCCT 60.744 61.111 5.56 0.00 0.00 4.75
4274 6204 1.447838 CGCGCTTCTTCCTTGCCTA 60.448 57.895 5.56 0.00 0.00 3.93
4275 6205 1.424493 CGCGCTTCTTCCTTGCCTAG 61.424 60.000 5.56 0.00 0.00 3.02
4276 6206 0.108138 GCGCTTCTTCCTTGCCTAGA 60.108 55.000 0.00 0.00 0.00 2.43
4277 6207 1.474143 GCGCTTCTTCCTTGCCTAGAT 60.474 52.381 0.00 0.00 0.00 1.98
4278 6208 2.208431 CGCTTCTTCCTTGCCTAGATG 58.792 52.381 0.00 0.00 0.00 2.90
4279 6209 2.419297 CGCTTCTTCCTTGCCTAGATGT 60.419 50.000 0.00 0.00 0.00 3.06
4280 6210 3.615155 GCTTCTTCCTTGCCTAGATGTT 58.385 45.455 0.00 0.00 0.00 2.71
4281 6211 3.376546 GCTTCTTCCTTGCCTAGATGTTG 59.623 47.826 0.00 0.00 0.00 3.33
4282 6212 2.991250 TCTTCCTTGCCTAGATGTTGC 58.009 47.619 0.00 0.00 0.00 4.17
4283 6213 2.019984 CTTCCTTGCCTAGATGTTGCC 58.980 52.381 0.00 0.00 0.00 4.52
4284 6214 0.991146 TCCTTGCCTAGATGTTGCCA 59.009 50.000 0.00 0.00 0.00 4.92
4285 6215 1.065199 TCCTTGCCTAGATGTTGCCAG 60.065 52.381 0.00 0.00 0.00 4.85
4286 6216 1.065199 CCTTGCCTAGATGTTGCCAGA 60.065 52.381 0.00 0.00 0.00 3.86
4287 6217 2.286872 CTTGCCTAGATGTTGCCAGAG 58.713 52.381 0.00 0.00 0.00 3.35
4288 6218 0.543277 TGCCTAGATGTTGCCAGAGG 59.457 55.000 0.00 0.00 0.00 3.69
4289 6219 0.179034 GCCTAGATGTTGCCAGAGGG 60.179 60.000 0.00 0.00 37.18 4.30
4290 6220 0.471617 CCTAGATGTTGCCAGAGGGG 59.528 60.000 0.00 0.00 40.85 4.79
4291 6221 1.500474 CTAGATGTTGCCAGAGGGGA 58.500 55.000 0.00 0.00 40.01 4.81
4292 6222 1.415659 CTAGATGTTGCCAGAGGGGAG 59.584 57.143 0.00 0.00 40.01 4.30
4293 6223 0.548682 AGATGTTGCCAGAGGGGAGT 60.549 55.000 0.00 0.00 40.01 3.85
4294 6224 0.393537 GATGTTGCCAGAGGGGAGTG 60.394 60.000 0.00 0.00 40.01 3.51
4295 6225 2.360475 GTTGCCAGAGGGGAGTGC 60.360 66.667 0.00 0.00 40.01 4.40
4296 6226 2.853542 TTGCCAGAGGGGAGTGCA 60.854 61.111 0.00 0.00 40.01 4.57
4297 6227 2.233566 TTGCCAGAGGGGAGTGCAT 61.234 57.895 0.00 0.00 40.01 3.96
4298 6228 2.191641 GCCAGAGGGGAGTGCATC 59.808 66.667 0.00 0.00 40.01 3.91
4299 6229 2.373707 GCCAGAGGGGAGTGCATCT 61.374 63.158 0.00 0.00 40.01 2.90
4300 6230 1.050988 GCCAGAGGGGAGTGCATCTA 61.051 60.000 0.00 0.00 40.01 1.98
4301 6231 0.755686 CCAGAGGGGAGTGCATCTAC 59.244 60.000 0.00 0.00 40.01 2.59
4302 6232 1.690845 CCAGAGGGGAGTGCATCTACT 60.691 57.143 0.00 0.00 40.01 2.57
4303 6233 2.114616 CAGAGGGGAGTGCATCTACTT 58.885 52.381 0.00 0.00 0.00 2.24
4304 6234 2.114616 AGAGGGGAGTGCATCTACTTG 58.885 52.381 0.00 0.00 0.00 3.16
4305 6235 0.543749 AGGGGAGTGCATCTACTTGC 59.456 55.000 0.00 0.00 43.07 4.01
4313 6243 1.012841 GCATCTACTTGCAGTGCTCC 58.987 55.000 17.60 0.00 42.31 4.70
4314 6244 1.661341 CATCTACTTGCAGTGCTCCC 58.339 55.000 17.60 0.00 0.00 4.30
4315 6245 0.176680 ATCTACTTGCAGTGCTCCCG 59.823 55.000 17.60 4.44 0.00 5.14
4316 6246 1.185618 TCTACTTGCAGTGCTCCCGT 61.186 55.000 17.60 10.07 0.00 5.28
4317 6247 0.320771 CTACTTGCAGTGCTCCCGTT 60.321 55.000 17.60 0.00 0.00 4.44
4318 6248 0.602638 TACTTGCAGTGCTCCCGTTG 60.603 55.000 17.60 1.35 0.00 4.10
4319 6249 3.259425 CTTGCAGTGCTCCCGTTGC 62.259 63.158 17.60 0.00 37.09 4.17
4322 6252 2.743928 CAGTGCTCCCGTTGCCTC 60.744 66.667 0.00 0.00 0.00 4.70
4323 6253 4.021925 AGTGCTCCCGTTGCCTCC 62.022 66.667 0.00 0.00 0.00 4.30
4324 6254 4.021925 GTGCTCCCGTTGCCTCCT 62.022 66.667 0.00 0.00 0.00 3.69
4325 6255 3.706373 TGCTCCCGTTGCCTCCTC 61.706 66.667 0.00 0.00 0.00 3.71
4326 6256 4.475135 GCTCCCGTTGCCTCCTCC 62.475 72.222 0.00 0.00 0.00 4.30
4327 6257 3.003173 CTCCCGTTGCCTCCTCCA 61.003 66.667 0.00 0.00 0.00 3.86
4328 6258 3.316573 CTCCCGTTGCCTCCTCCAC 62.317 68.421 0.00 0.00 0.00 4.02
4329 6259 4.410400 CCCGTTGCCTCCTCCACC 62.410 72.222 0.00 0.00 0.00 4.61
4330 6260 3.636231 CCGTTGCCTCCTCCACCA 61.636 66.667 0.00 0.00 0.00 4.17
4331 6261 2.358737 CGTTGCCTCCTCCACCAC 60.359 66.667 0.00 0.00 0.00 4.16
4332 6262 2.034221 GTTGCCTCCTCCACCACC 59.966 66.667 0.00 0.00 0.00 4.61
4333 6263 2.121963 TTGCCTCCTCCACCACCT 60.122 61.111 0.00 0.00 0.00 4.00
4334 6264 2.224159 TTGCCTCCTCCACCACCTC 61.224 63.158 0.00 0.00 0.00 3.85
4335 6265 3.403558 GCCTCCTCCACCACCTCC 61.404 72.222 0.00 0.00 0.00 4.30
4336 6266 2.689034 CCTCCTCCACCACCTCCC 60.689 72.222 0.00 0.00 0.00 4.30
4337 6267 2.689034 CTCCTCCACCACCTCCCC 60.689 72.222 0.00 0.00 0.00 4.81
4338 6268 4.348495 TCCTCCACCACCTCCCCC 62.348 72.222 0.00 0.00 0.00 5.40
4357 6287 3.450115 GAGTAGCCGCTCCACCGT 61.450 66.667 0.00 0.00 0.00 4.83
4358 6288 3.412879 GAGTAGCCGCTCCACCGTC 62.413 68.421 0.00 0.00 0.00 4.79
4359 6289 4.849329 GTAGCCGCTCCACCGTCG 62.849 72.222 0.00 0.00 0.00 5.12
4392 6322 2.388232 GCAACGGGTTACTGCGAGG 61.388 63.158 0.00 0.00 0.00 4.63
4411 6346 1.005294 GCTGTGACGCAATTTGCCAG 61.005 55.000 15.45 16.01 41.12 4.85
4459 6403 1.681264 AGTGTGGTGGCTAAAACAAGC 59.319 47.619 0.00 0.00 41.99 4.01
4466 6410 0.243636 GGCTAAAACAAGCGCCACAT 59.756 50.000 2.29 0.00 43.74 3.21
4467 6411 1.617740 GCTAAAACAAGCGCCACATC 58.382 50.000 2.29 0.00 31.76 3.06
4483 6427 4.559153 CCACATCTTTGGCGAAAATTTCT 58.441 39.130 4.09 0.00 0.00 2.52
4485 6429 5.572896 CCACATCTTTGGCGAAAATTTCTAC 59.427 40.000 4.09 0.00 0.00 2.59
4493 6463 3.417185 GCGAAAATTTCTACTGCCGAAG 58.583 45.455 4.09 0.00 0.00 3.79
4509 6479 2.409975 CGAAGCTTCGTAAGGAACCAA 58.590 47.619 34.97 0.00 45.09 3.67
4513 6483 1.399343 GCTTCGTAAGGAACCAAACGC 60.399 52.381 11.30 0.00 35.40 4.84
4514 6484 1.196127 CTTCGTAAGGAACCAAACGCC 59.804 52.381 11.30 0.00 35.40 5.68
4516 6486 1.617850 TCGTAAGGAACCAAACGCCTA 59.382 47.619 11.30 0.00 35.40 3.93
4518 6488 2.079158 GTAAGGAACCAAACGCCTACC 58.921 52.381 0.00 0.00 0.00 3.18
4527 6497 1.732259 CAAACGCCTACCTAGCAAGTG 59.268 52.381 0.00 0.00 0.00 3.16
4528 6498 0.974383 AACGCCTACCTAGCAAGTGT 59.026 50.000 0.00 0.00 0.00 3.55
4529 6499 1.843368 ACGCCTACCTAGCAAGTGTA 58.157 50.000 0.00 0.00 0.00 2.90
4531 6501 1.536284 CGCCTACCTAGCAAGTGTAGC 60.536 57.143 0.00 0.00 32.47 3.58
4532 6502 1.536284 GCCTACCTAGCAAGTGTAGCG 60.536 57.143 0.00 0.00 37.01 4.26
4538 6531 2.418197 CCTAGCAAGTGTAGCGGCTAAA 60.418 50.000 11.98 2.92 38.29 1.85
4554 6547 2.863704 GCTAAAGCTGGCAACCAAACAG 60.864 50.000 0.00 0.00 38.21 3.16
4563 6556 3.731766 AACCAAACAGCCCCTGCGT 62.732 57.895 0.00 0.00 44.33 5.24
4565 6558 3.726517 CAAACAGCCCCTGCGTCG 61.727 66.667 0.00 0.00 44.33 5.12
4592 6590 3.603671 CTAGTACCGCCGCCCCTC 61.604 72.222 0.00 0.00 0.00 4.30
4637 6635 4.832608 GTGCCGGGATCCACGACC 62.833 72.222 20.20 12.63 0.00 4.79
4640 6638 4.508128 CCGGGATCCACGACCACG 62.508 72.222 20.20 10.11 45.75 4.94
4669 6947 2.342910 AACCGTTAGTACTGACTGCG 57.657 50.000 15.06 3.10 36.28 5.18
4711 6989 0.990374 ATGCAAAGCTCTCTGTCCCT 59.010 50.000 0.00 0.00 0.00 4.20
4724 7002 6.531503 TCTCTGTCCCTGATTTACTGTTAG 57.468 41.667 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 6.592994 TCAGCATCTTCTTCTGTATTGTTCTG 59.407 38.462 0.00 0.00 0.00 3.02
22 23 4.753610 TGACAACTTCAGCATCTTCTTCTG 59.246 41.667 0.00 0.00 0.00 3.02
34 35 7.379529 GGTTGAATATTTGTGTGACAACTTCAG 59.620 37.037 0.00 0.00 37.90 3.02
79 80 1.470098 AGATCTTGACAATTGGTGCGC 59.530 47.619 10.83 0.00 0.00 6.09
126 127 5.396362 CGTCGACGAAGACTGTAAAAGTTTA 59.604 40.000 33.35 0.00 39.78 2.01
127 128 4.205792 CGTCGACGAAGACTGTAAAAGTTT 59.794 41.667 33.35 0.00 39.78 2.66
134 135 0.110509 GTGCGTCGACGAAGACTGTA 60.111 55.000 39.74 12.41 43.02 2.74
148 149 1.076533 GACAATGTCCGATCGTGCGT 61.077 55.000 15.09 4.74 0.00 5.24
154 155 3.309388 CATACCTCGACAATGTCCGATC 58.691 50.000 7.91 0.00 34.08 3.69
181 182 6.491403 GCATGTTGGAATAAGGTCTATTGGAT 59.509 38.462 0.00 0.00 0.00 3.41
191 192 2.287788 GCGATGGCATGTTGGAATAAGG 60.288 50.000 3.81 0.00 39.62 2.69
194 195 1.317613 GGCGATGGCATGTTGGAATA 58.682 50.000 3.81 0.00 42.47 1.75
233 235 4.162509 CCTTAGGTTTTTGTTTCCCCAACA 59.837 41.667 0.00 0.00 44.11 3.33
238 240 5.364446 TCTTTCCCTTAGGTTTTTGTTTCCC 59.636 40.000 0.00 0.00 0.00 3.97
273 275 2.747799 GCAAGAGGAATGAGGACCCATC 60.748 54.545 0.00 0.00 0.00 3.51
279 281 1.221840 GCGGCAAGAGGAATGAGGA 59.778 57.895 0.00 0.00 0.00 3.71
311 313 1.639722 CCCCCTCATTTTTCCCGTTT 58.360 50.000 0.00 0.00 0.00 3.60
312 314 0.902984 GCCCCCTCATTTTTCCCGTT 60.903 55.000 0.00 0.00 0.00 4.44
318 320 1.361204 CCTTTGGCCCCCTCATTTTT 58.639 50.000 0.00 0.00 0.00 1.94
341 343 1.330655 CCACAGGATCCCTACACGCT 61.331 60.000 8.55 0.00 29.64 5.07
375 377 0.321996 GGAGGCACGAAAAGACTCCT 59.678 55.000 7.82 0.00 43.37 3.69
412 414 5.489637 TGCTTTACCTGGAATAGAACCCTAA 59.510 40.000 0.00 0.00 0.00 2.69
445 448 4.442706 CCTAATGTCCGCTCATGTAACTT 58.557 43.478 0.00 0.00 0.00 2.66
462 465 7.010160 TCTCCATCTTTTCAACAAACCCTAAT 58.990 34.615 0.00 0.00 0.00 1.73
465 468 4.803452 TCTCCATCTTTTCAACAAACCCT 58.197 39.130 0.00 0.00 0.00 4.34
515 2217 9.920133 AATTTAGAATTTGGAAGAGCTTTCTTC 57.080 29.630 7.08 7.08 43.86 2.87
528 2230 9.709495 TTGAATGACTTCCAATTTAGAATTTGG 57.291 29.630 8.88 8.88 43.10 3.28
584 2286 4.243007 GGATAAATCCAGGAAAATGCGG 57.757 45.455 4.04 0.00 46.38 5.69
618 2320 0.244721 CTCTCACTGGACGCACATCA 59.755 55.000 0.00 0.00 0.00 3.07
628 2330 2.820787 ACGTAAAGTCTCCTCTCACTGG 59.179 50.000 0.00 0.00 0.00 4.00
704 2407 2.015587 GTTCAGGACCTATCGACGTCT 58.984 52.381 14.70 0.00 0.00 4.18
709 2412 2.014857 CTGACGTTCAGGACCTATCGA 58.985 52.381 15.65 0.00 40.71 3.59
720 2423 2.804697 TTGTTCGATCCTGACGTTCA 57.195 45.000 0.00 0.00 0.00 3.18
729 2432 3.648009 TGCCACAAAAATTGTTCGATCC 58.352 40.909 0.00 0.00 43.23 3.36
832 2551 4.442375 TTCATTTTGTTTGTCCACACGT 57.558 36.364 0.00 0.00 0.00 4.49
850 2569 3.075882 ACCAATGGGAGTGATTCCTTTCA 59.924 43.478 3.55 0.00 45.98 2.69
892 2611 1.078214 CATGACATGTGGGACCGCT 60.078 57.895 1.15 0.00 0.00 5.52
1240 2964 1.077357 GGAGAGAGAGGTGGCGAGA 60.077 63.158 0.00 0.00 0.00 4.04
1242 2966 2.272230 ATCGGAGAGAGAGGTGGCGA 62.272 60.000 0.00 0.00 43.63 5.54
1295 3022 2.037144 ACAGCCTCCCGACGTAATAAT 58.963 47.619 0.00 0.00 0.00 1.28
1302 3029 1.079127 AATTCACAGCCTCCCGACG 60.079 57.895 0.00 0.00 0.00 5.12
1310 3038 0.108945 GAAGCAGCCAATTCACAGCC 60.109 55.000 0.00 0.00 0.00 4.85
1330 3058 0.179936 GACCTCCAAGCATCTCCCTG 59.820 60.000 0.00 0.00 0.00 4.45
1413 3141 4.433186 ACAATGAAGACTCTCTCGTGAG 57.567 45.455 8.20 8.20 41.51 3.51
1414 3142 4.038042 ACAACAATGAAGACTCTCTCGTGA 59.962 41.667 0.00 0.00 0.00 4.35
1415 3143 4.302455 ACAACAATGAAGACTCTCTCGTG 58.698 43.478 0.00 0.00 0.00 4.35
1416 3144 4.592485 ACAACAATGAAGACTCTCTCGT 57.408 40.909 0.00 0.00 0.00 4.18
1417 3145 7.408132 TTTAACAACAATGAAGACTCTCTCG 57.592 36.000 0.00 0.00 0.00 4.04
1418 3146 9.604626 CAATTTAACAACAATGAAGACTCTCTC 57.395 33.333 0.00 0.00 0.00 3.20
1419 3147 8.078596 GCAATTTAACAACAATGAAGACTCTCT 58.921 33.333 0.00 0.00 0.00 3.10
1429 3157 7.011295 ACCAACAGAAGCAATTTAACAACAATG 59.989 33.333 0.00 0.00 0.00 2.82
1529 3257 0.251354 GCAATGTCAGCTCCTGGAGA 59.749 55.000 27.53 6.18 31.51 3.71
1549 3277 2.476852 TACCTTGCTCATTGCCCGCA 62.477 55.000 0.00 0.00 42.00 5.69
1553 3281 0.737219 CAGCTACCTTGCTCATTGCC 59.263 55.000 0.00 0.00 41.98 4.52
1588 3316 9.132923 TCTATACCAAACTAGGACAACTCATAG 57.867 37.037 0.00 0.00 36.92 2.23
1609 3337 6.795144 TCAAAAGGGAATACACGGTCTATA 57.205 37.500 0.00 0.00 0.00 1.31
1610 3338 5.687166 TCAAAAGGGAATACACGGTCTAT 57.313 39.130 0.00 0.00 0.00 1.98
1617 3345 4.220602 AGCACCAATCAAAAGGGAATACAC 59.779 41.667 0.00 0.00 0.00 2.90
1652 3380 4.963373 TCATCTGTTTTCTCGGTACCAAA 58.037 39.130 13.54 1.98 0.00 3.28
1656 3384 3.309954 GGCATCATCTGTTTTCTCGGTAC 59.690 47.826 0.00 0.00 0.00 3.34
1658 3386 2.359900 GGCATCATCTGTTTTCTCGGT 58.640 47.619 0.00 0.00 0.00 4.69
1660 3388 2.002586 ACGGCATCATCTGTTTTCTCG 58.997 47.619 0.00 0.00 0.00 4.04
1732 3460 1.186200 CCTCCGACTCATGACCTTCA 58.814 55.000 0.00 0.00 0.00 3.02
1737 3465 1.202428 GCTTACCCTCCGACTCATGAC 60.202 57.143 0.00 0.00 0.00 3.06
1741 3469 0.543410 TTGGCTTACCCTCCGACTCA 60.543 55.000 0.00 0.00 33.59 3.41
1747 3475 0.393132 GCTCACTTGGCTTACCCTCC 60.393 60.000 0.00 0.00 33.59 4.30
1751 3479 0.393132 GAGGGCTCACTTGGCTTACC 60.393 60.000 0.00 0.00 0.00 2.85
1757 3485 2.045536 GGCAGAGGGCTCACTTGG 60.046 66.667 0.00 0.00 44.01 3.61
1810 3538 7.694886 TCTTCTTCTTCCGTTTCTTTTCTTTC 58.305 34.615 0.00 0.00 0.00 2.62
1901 3629 4.084171 GCTTTTCTTTTTCTTGCCATCAGC 60.084 41.667 0.00 0.00 44.14 4.26
1939 3667 3.388308 CCTAGCTTCAACATCCTCATCG 58.612 50.000 0.00 0.00 0.00 3.84
2038 3766 4.935578 TCTGAGTCTTAGGTTCATCCTCA 58.064 43.478 0.00 0.00 44.42 3.86
2074 3802 3.061295 CACCATCACTCAAATCGTTCTCG 59.939 47.826 0.00 0.00 38.55 4.04
2082 3810 2.575279 AGAGGAGCACCATCACTCAAAT 59.425 45.455 2.07 0.00 38.94 2.32
2107 3835 5.830457 ACTCTTCTTCTTTTTCTTCCCCTTG 59.170 40.000 0.00 0.00 0.00 3.61
2143 3871 4.261994 GCATCAGTCTTATCTGAGGTCTCC 60.262 50.000 9.43 0.00 45.70 3.71
2182 3910 1.860641 TAGATTTCACCTCGGCCTCA 58.139 50.000 0.00 0.00 0.00 3.86
2220 3948 2.111384 TCCCTTCTCCTACAGCATCAC 58.889 52.381 0.00 0.00 0.00 3.06
2222 3950 3.452627 TCTTTCCCTTCTCCTACAGCATC 59.547 47.826 0.00 0.00 0.00 3.91
2380 4114 2.644299 TGAAGCCTTTCCATCTTCTCCA 59.356 45.455 0.00 0.00 37.63 3.86
2428 4162 4.098501 CCTTCAACTTCTTGCAGTTTCCTT 59.901 41.667 0.00 0.00 34.60 3.36
2438 4172 3.304057 GGTTCGCTTCCTTCAACTTCTTG 60.304 47.826 0.00 0.00 0.00 3.02
2456 4190 0.112412 TCTTCTTTGGCAGGGGGTTC 59.888 55.000 0.00 0.00 0.00 3.62
2614 4348 5.299028 ACTGTGACATGACAAACAAGCAATA 59.701 36.000 0.00 0.00 0.00 1.90
2630 4372 3.389656 TGTCAGGGTGATTAACTGTGACA 59.610 43.478 7.03 7.03 43.34 3.58
2667 4409 6.927416 TGTAAGAAGCTACCAGAAAATACGA 58.073 36.000 0.00 0.00 0.00 3.43
2913 4661 7.571025 TCTTGGGAAGTGAACTTTTACTTACT 58.429 34.615 8.35 0.00 37.77 2.24
2931 4679 0.615331 GTCACATCAGCCTCTTGGGA 59.385 55.000 0.00 0.00 37.23 4.37
3085 4851 2.857186 TAGGCTGCAGTGAATGAACA 57.143 45.000 16.64 0.00 0.00 3.18
3236 5003 3.469899 TTGAGAAATGGTCGAATTGCG 57.530 42.857 0.00 0.00 42.69 4.85
3246 5013 6.976925 GGAAGTTTAGCATCATTGAGAAATGG 59.023 38.462 0.00 0.00 0.00 3.16
3270 5037 6.098982 AGGAGATAAGTACAGATCAACCAAGG 59.901 42.308 17.09 0.00 0.00 3.61
3402 5169 3.272574 ACCATGTTCAGCAGTATGGAG 57.727 47.619 8.93 0.00 42.05 3.86
3406 5173 5.255687 TCATGAAACCATGTTCAGCAGTAT 58.744 37.500 0.00 0.00 40.72 2.12
3591 5358 3.379372 CGAGTAACGAGGGTAAGAATGGA 59.621 47.826 0.00 0.00 45.77 3.41
3600 5367 0.251077 ACTGACCGAGTAACGAGGGT 60.251 55.000 0.00 0.00 45.77 4.34
3659 5426 6.534793 ACAATTCAATGTTTTTGCTTCTTCGT 59.465 30.769 0.00 0.00 0.00 3.85
3819 5692 4.457496 GCTAGAGGCACGGCAGCA 62.457 66.667 0.00 0.00 41.35 4.41
3898 5775 6.959639 AGAAAACAGCCTCAGTTCAATAAA 57.040 33.333 0.00 0.00 0.00 1.40
3899 5776 6.545666 TCAAGAAAACAGCCTCAGTTCAATAA 59.454 34.615 0.00 0.00 0.00 1.40
3900 5777 6.061441 TCAAGAAAACAGCCTCAGTTCAATA 58.939 36.000 0.00 0.00 0.00 1.90
3901 5778 4.889409 TCAAGAAAACAGCCTCAGTTCAAT 59.111 37.500 0.00 0.00 0.00 2.57
3904 5782 4.130118 TCTCAAGAAAACAGCCTCAGTTC 58.870 43.478 0.00 0.00 0.00 3.01
3964 5843 6.597832 AATATATCCTGCTATCCGCCTATC 57.402 41.667 0.00 0.00 38.05 2.08
3966 5845 6.808321 AAAATATATCCTGCTATCCGCCTA 57.192 37.500 0.00 0.00 38.05 3.93
3967 5846 5.700402 AAAATATATCCTGCTATCCGCCT 57.300 39.130 0.00 0.00 38.05 5.52
4156 6082 8.263940 TCTTGGAAATATAAAAGTGAACGGAG 57.736 34.615 0.00 0.00 0.00 4.63
4157 6083 7.148306 GCTCTTGGAAATATAAAAGTGAACGGA 60.148 37.037 0.00 0.00 0.00 4.69
4158 6084 6.967199 GCTCTTGGAAATATAAAAGTGAACGG 59.033 38.462 0.00 0.00 0.00 4.44
4159 6085 6.682863 CGCTCTTGGAAATATAAAAGTGAACG 59.317 38.462 0.00 0.00 0.00 3.95
4160 6086 6.469275 GCGCTCTTGGAAATATAAAAGTGAAC 59.531 38.462 0.00 0.00 0.00 3.18
4161 6087 6.404293 GGCGCTCTTGGAAATATAAAAGTGAA 60.404 38.462 7.64 0.00 0.00 3.18
4162 6088 5.065988 GGCGCTCTTGGAAATATAAAAGTGA 59.934 40.000 7.64 0.00 0.00 3.41
4163 6089 5.273944 GGCGCTCTTGGAAATATAAAAGTG 58.726 41.667 7.64 0.00 0.00 3.16
4164 6090 4.338400 GGGCGCTCTTGGAAATATAAAAGT 59.662 41.667 7.64 0.00 0.00 2.66
4165 6091 4.338118 TGGGCGCTCTTGGAAATATAAAAG 59.662 41.667 9.62 0.00 0.00 2.27
4166 6092 4.274147 TGGGCGCTCTTGGAAATATAAAA 58.726 39.130 9.62 0.00 0.00 1.52
4167 6093 3.892284 TGGGCGCTCTTGGAAATATAAA 58.108 40.909 9.62 0.00 0.00 1.40
4168 6094 3.569194 TGGGCGCTCTTGGAAATATAA 57.431 42.857 9.62 0.00 0.00 0.98
4178 6104 0.179018 ACACTCTTTTGGGCGCTCTT 60.179 50.000 9.62 0.00 0.00 2.85
4180 6106 0.884704 TCACACTCTTTTGGGCGCTC 60.885 55.000 7.64 2.47 0.00 5.03
4192 6121 5.998363 AGGGTAGAAATGTCTTTTCACACTC 59.002 40.000 12.33 9.58 45.19 3.51
4215 6144 6.000891 TGATTCGAAATTCAAACTGACCAG 57.999 37.500 0.00 0.00 0.00 4.00
4216 6145 6.206438 TCATGATTCGAAATTCAAACTGACCA 59.794 34.615 0.00 0.00 0.00 4.02
4217 6146 6.611381 TCATGATTCGAAATTCAAACTGACC 58.389 36.000 0.00 0.00 0.00 4.02
4218 6147 7.163195 CGATCATGATTCGAAATTCAAACTGAC 59.837 37.037 10.14 0.00 0.00 3.51
4233 6163 1.135859 GGGCAATCGCGATCATGATTC 60.136 52.381 23.92 10.59 39.92 2.52
4237 6167 1.893335 TGGGGCAATCGCGATCATG 60.893 57.895 23.92 18.82 39.92 3.07
4238 6168 1.893808 GTGGGGCAATCGCGATCAT 60.894 57.895 23.92 4.44 39.92 2.45
4254 6184 2.174349 GCAAGGAAGAAGCGCGTG 59.826 61.111 8.43 0.00 0.00 5.34
4255 6185 2.167398 TAGGCAAGGAAGAAGCGCGT 62.167 55.000 8.43 0.00 0.00 6.01
4256 6186 1.424493 CTAGGCAAGGAAGAAGCGCG 61.424 60.000 0.00 0.00 0.00 6.86
4258 6188 2.208431 CATCTAGGCAAGGAAGAAGCG 58.792 52.381 0.00 0.00 0.00 4.68
4259 6189 3.274095 ACATCTAGGCAAGGAAGAAGC 57.726 47.619 0.00 0.00 0.00 3.86
4260 6190 3.376546 GCAACATCTAGGCAAGGAAGAAG 59.623 47.826 0.00 0.00 0.00 2.85
4261 6191 3.347216 GCAACATCTAGGCAAGGAAGAA 58.653 45.455 0.00 0.00 0.00 2.52
4262 6192 2.356125 GGCAACATCTAGGCAAGGAAGA 60.356 50.000 0.00 0.00 0.00 2.87
4263 6193 2.019984 GGCAACATCTAGGCAAGGAAG 58.980 52.381 0.00 0.00 0.00 3.46
4264 6194 1.354031 TGGCAACATCTAGGCAAGGAA 59.646 47.619 0.00 0.00 46.17 3.36
4265 6195 0.991146 TGGCAACATCTAGGCAAGGA 59.009 50.000 0.00 0.00 46.17 3.36
4266 6196 3.575506 TGGCAACATCTAGGCAAGG 57.424 52.632 0.00 0.00 46.17 3.61
4278 6208 2.360475 GCACTCCCCTCTGGCAAC 60.360 66.667 0.00 0.00 0.00 4.17
4279 6209 2.202236 GATGCACTCCCCTCTGGCAA 62.202 60.000 0.00 0.00 38.08 4.52
4280 6210 2.611800 ATGCACTCCCCTCTGGCA 60.612 61.111 0.00 0.00 39.03 4.92
4281 6211 1.050988 TAGATGCACTCCCCTCTGGC 61.051 60.000 0.00 0.00 0.00 4.85
4282 6212 0.755686 GTAGATGCACTCCCCTCTGG 59.244 60.000 0.00 0.00 0.00 3.86
4283 6213 1.786937 AGTAGATGCACTCCCCTCTG 58.213 55.000 0.00 0.00 0.00 3.35
4284 6214 2.114616 CAAGTAGATGCACTCCCCTCT 58.885 52.381 0.00 0.00 0.00 3.69
4285 6215 1.474143 GCAAGTAGATGCACTCCCCTC 60.474 57.143 0.00 0.00 45.70 4.30
4286 6216 0.543749 GCAAGTAGATGCACTCCCCT 59.456 55.000 0.00 0.00 45.70 4.79
4287 6217 3.086733 GCAAGTAGATGCACTCCCC 57.913 57.895 0.00 0.00 45.70 4.81
4301 6231 2.949106 CAACGGGAGCACTGCAAG 59.051 61.111 3.30 0.00 42.29 4.01
4302 6232 3.286751 GCAACGGGAGCACTGCAA 61.287 61.111 3.30 0.00 34.51 4.08
4305 6235 2.743928 GAGGCAACGGGAGCACTG 60.744 66.667 0.00 0.00 46.39 3.66
4306 6236 4.021925 GGAGGCAACGGGAGCACT 62.022 66.667 0.00 0.00 46.39 4.40
4307 6237 3.959991 GAGGAGGCAACGGGAGCAC 62.960 68.421 0.00 0.00 46.39 4.40
4308 6238 3.706373 GAGGAGGCAACGGGAGCA 61.706 66.667 0.00 0.00 46.39 4.26
4309 6239 4.475135 GGAGGAGGCAACGGGAGC 62.475 72.222 0.00 0.00 46.39 4.70
4310 6240 3.003173 TGGAGGAGGCAACGGGAG 61.003 66.667 0.00 0.00 46.39 4.30
4311 6241 3.319198 GTGGAGGAGGCAACGGGA 61.319 66.667 0.00 0.00 46.39 5.14
4312 6242 4.410400 GGTGGAGGAGGCAACGGG 62.410 72.222 0.00 0.00 46.39 5.28
4313 6243 3.636231 TGGTGGAGGAGGCAACGG 61.636 66.667 0.00 0.00 46.39 4.44
4314 6244 2.358737 GTGGTGGAGGAGGCAACG 60.359 66.667 0.00 0.00 46.39 4.10
4315 6245 2.034221 GGTGGTGGAGGAGGCAAC 59.966 66.667 0.00 0.00 0.00 4.17
4316 6246 2.121963 AGGTGGTGGAGGAGGCAA 60.122 61.111 0.00 0.00 0.00 4.52
4317 6247 2.607750 GAGGTGGTGGAGGAGGCA 60.608 66.667 0.00 0.00 0.00 4.75
4318 6248 3.403558 GGAGGTGGTGGAGGAGGC 61.404 72.222 0.00 0.00 0.00 4.70
4319 6249 2.689034 GGGAGGTGGTGGAGGAGG 60.689 72.222 0.00 0.00 0.00 4.30
4320 6250 2.689034 GGGGAGGTGGTGGAGGAG 60.689 72.222 0.00 0.00 0.00 3.69
4321 6251 4.348495 GGGGGAGGTGGTGGAGGA 62.348 72.222 0.00 0.00 0.00 3.71
4340 6270 3.412879 GACGGTGGAGCGGCTACTC 62.413 68.421 14.37 9.91 35.86 2.59
4341 6271 3.450115 GACGGTGGAGCGGCTACT 61.450 66.667 14.37 0.00 0.00 2.57
4342 6272 4.849329 CGACGGTGGAGCGGCTAC 62.849 72.222 4.92 4.92 0.00 3.58
4368 6298 3.729698 GTAACCCGTTGCGGCCAC 61.730 66.667 2.24 0.00 46.86 5.01
4369 6299 3.943691 AGTAACCCGTTGCGGCCA 61.944 61.111 2.24 0.00 46.86 5.36
4370 6300 3.428282 CAGTAACCCGTTGCGGCC 61.428 66.667 1.51 0.00 46.86 6.13
4376 6306 2.047560 GCCTCGCAGTAACCCGTT 60.048 61.111 0.00 0.00 0.00 4.44
4377 6307 2.995574 AGCCTCGCAGTAACCCGT 60.996 61.111 0.00 0.00 0.00 5.28
4381 6311 1.344942 CGTCACAGCCTCGCAGTAAC 61.345 60.000 0.00 0.00 0.00 2.50
4389 6319 0.730494 GCAAATTGCGTCACAGCCTC 60.730 55.000 0.90 0.00 31.71 4.70
4392 6322 1.005294 CTGGCAAATTGCGTCACAGC 61.005 55.000 12.15 0.00 46.21 4.40
4437 6372 3.795488 GCTTGTTTTAGCCACCACACTTC 60.795 47.826 0.00 0.00 35.06 3.01
4438 6373 2.100749 GCTTGTTTTAGCCACCACACTT 59.899 45.455 0.00 0.00 35.06 3.16
4439 6374 1.681264 GCTTGTTTTAGCCACCACACT 59.319 47.619 0.00 0.00 35.06 3.55
4440 6375 1.599419 CGCTTGTTTTAGCCACCACAC 60.599 52.381 0.00 0.00 37.90 3.82
4441 6376 0.665835 CGCTTGTTTTAGCCACCACA 59.334 50.000 0.00 0.00 37.90 4.17
4466 6410 4.320935 GGCAGTAGAAATTTTCGCCAAAGA 60.321 41.667 16.32 0.00 37.98 2.52
4467 6411 3.920412 GGCAGTAGAAATTTTCGCCAAAG 59.080 43.478 16.32 4.01 37.98 2.77
4498 6468 2.079158 GGTAGGCGTTTGGTTCCTTAC 58.921 52.381 0.00 0.00 0.00 2.34
4503 6473 1.338389 TGCTAGGTAGGCGTTTGGTTC 60.338 52.381 0.00 0.00 0.00 3.62
4509 6479 0.974383 ACACTTGCTAGGTAGGCGTT 59.026 50.000 0.00 0.00 0.00 4.84
4513 6483 1.067212 CCGCTACACTTGCTAGGTAGG 59.933 57.143 18.11 11.71 36.02 3.18
4514 6484 1.536284 GCCGCTACACTTGCTAGGTAG 60.536 57.143 14.70 14.70 38.00 3.18
4516 6486 1.218316 GCCGCTACACTTGCTAGGT 59.782 57.895 0.00 0.00 0.00 3.08
4518 6488 2.579207 TTAGCCGCTACACTTGCTAG 57.421 50.000 0.00 0.00 37.59 3.42
4527 6497 1.024579 TTGCCAGCTTTAGCCGCTAC 61.025 55.000 0.00 0.00 43.38 3.58
4528 6498 1.024579 GTTGCCAGCTTTAGCCGCTA 61.025 55.000 11.30 0.00 43.38 4.26
4529 6499 2.034066 TTGCCAGCTTTAGCCGCT 59.966 55.556 0.00 0.00 43.38 5.52
4531 6501 1.523154 TTGGTTGCCAGCTTTAGCCG 61.523 55.000 0.00 0.00 43.38 5.52
4532 6502 0.678950 TTTGGTTGCCAGCTTTAGCC 59.321 50.000 0.00 0.00 43.38 3.93
4538 6531 3.132084 GCTGTTTGGTTGCCAGCT 58.868 55.556 3.75 0.00 46.23 4.24
4618 6616 3.080765 TCGTGGATCCCGGCACAT 61.081 61.111 18.67 0.00 0.00 3.21
4623 6621 4.508128 CGTGGTCGTGGATCCCGG 62.508 72.222 18.67 0.00 0.00 5.73
4637 6635 2.088950 AACGGTTAATCAGGGACGTG 57.911 50.000 0.00 0.00 34.54 4.49
4640 6638 5.126061 TCAGTACTAACGGTTAATCAGGGAC 59.874 44.000 0.00 0.00 0.00 4.46
4645 6643 5.404946 GCAGTCAGTACTAACGGTTAATCA 58.595 41.667 0.00 0.00 33.48 2.57
4646 6644 4.498323 CGCAGTCAGTACTAACGGTTAATC 59.502 45.833 0.00 0.00 33.48 1.75
4669 6947 7.530863 CATTTTCTTCAAGTAGTAGAAAGGGC 58.469 38.462 0.00 0.00 42.25 5.19
4757 7035 6.012658 TCAAACAGATAGCTTCGCATTTTT 57.987 33.333 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.