Multiple sequence alignment - TraesCS4D01G225700

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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 TraesCS4D01G225700 chr4D 100.000 4254 0 0 1 4254 384669092 384673345 0.000000e+00 7856.0
1 TraesCS4D01G225700 chr4D 71.569 408 86 26 1386 1784 29828330 29828716 2.730000e-12 84.2
2 TraesCS4D01G225700 chr4B 94.323 2783 85 30 505 3265 471651960 471654691 0.000000e+00 4196.0
3 TraesCS4D01G225700 chr4B 85.075 804 73 22 3275 4060 471654868 471655642 0.000000e+00 776.0
4 TraesCS4D01G225700 chr4B 84.867 489 56 13 7 485 447464121 447464601 1.070000e-130 477.0
5 TraesCS4D01G225700 chr4B 88.934 244 11 2 251 485 471648507 471648743 1.940000e-73 287.0
6 TraesCS4D01G225700 chr4B 79.054 296 49 12 3789 4079 37923359 37923072 1.560000e-44 191.0
7 TraesCS4D01G225700 chr4B 83.333 174 12 8 4083 4252 471655635 471655795 1.230000e-30 145.0
8 TraesCS4D01G225700 chr4B 75.543 184 32 11 1606 1784 42395475 42395650 1.270000e-10 78.7
9 TraesCS4D01G225700 chr4A 93.306 2898 103 40 529 3385 66337736 66340583 0.000000e+00 4193.0
10 TraesCS4D01G225700 chr4A 81.878 458 24 10 3383 3822 66342410 66342826 8.820000e-87 331.0
11 TraesCS4D01G225700 chr4A 80.460 435 40 22 3828 4254 66342875 66343272 1.500000e-74 291.0
12 TraesCS4D01G225700 chr4A 80.128 312 37 14 3771 4076 549807618 549807910 4.310000e-50 209.0
13 TraesCS4D01G225700 chr4A 77.143 175 27 11 1615 1784 573326969 573326803 5.860000e-14 89.8
14 TraesCS4D01G225700 chr7A 87.551 490 47 6 7 485 193073408 193072922 4.810000e-154 555.0
15 TraesCS4D01G225700 chr7D 87.190 484 46 6 7 480 185316654 185316177 1.740000e-148 536.0
16 TraesCS4D01G225700 chr5B 86.032 494 47 13 5 485 266020440 266020924 1.060000e-140 510.0
17 TraesCS4D01G225700 chr1B 85.947 491 54 7 7 485 376009069 376008582 1.060000e-140 510.0
18 TraesCS4D01G225700 chr1B 85.540 491 56 7 7 485 375973482 375972995 2.280000e-137 499.0
19 TraesCS4D01G225700 chr1B 80.000 300 51 9 3780 4078 40364985 40364694 3.330000e-51 213.0
20 TraesCS4D01G225700 chr2B 85.510 490 56 7 7 485 472366263 472365778 8.210000e-137 497.0
21 TraesCS4D01G225700 chr3A 84.787 493 59 8 7 485 330339702 330339212 8.270000e-132 481.0
22 TraesCS4D01G225700 chr3A 78.968 252 49 4 1838 2087 623777529 623777778 7.320000e-38 169.0
23 TraesCS4D01G225700 chr3A 79.352 247 39 11 3788 4027 712282328 712282087 3.400000e-36 163.0
24 TraesCS4D01G225700 chr1D 84.929 491 45 13 7 485 50554528 50554055 1.790000e-128 470.0
25 TraesCS4D01G225700 chr2D 78.622 421 49 25 96 482 37204559 37204146 1.530000e-59 241.0
26 TraesCS4D01G225700 chr3B 81.270 315 34 20 3771 4075 766892365 766892664 9.200000e-57 231.0
27 TraesCS4D01G225700 chr3B 82.836 268 34 11 3753 4014 693074683 693074944 3.310000e-56 230.0
28 TraesCS4D01G225700 chr3B 79.608 255 42 9 1838 2087 641805196 641805445 1.570000e-39 174.0
29 TraesCS4D01G225700 chr5D 85.068 221 28 4 3860 4079 427224739 427224955 1.990000e-53 220.0
30 TraesCS4D01G225700 chr3D 78.571 252 50 4 1838 2087 480969939 480970188 3.400000e-36 163.0
31 TraesCS4D01G225700 chr1A 79.787 188 32 6 3867 4053 535294714 535294532 9.600000e-27 132.0
32 TraesCS4D01G225700 chr6D 87.952 83 9 1 3764 3845 18698191 18698273 3.500000e-16 97.1
33 TraesCS4D01G225700 chr5A 83.529 85 13 1 3762 3845 449249111 449249195 1.270000e-10 78.7


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 TraesCS4D01G225700 chr4D 384669092 384673345 4253 False 7856 7856 100.000000 1 4254 1 chr4D.!!$F2 4253
1 TraesCS4D01G225700 chr4B 471648507 471655795 7288 False 1351 4196 87.916250 251 4252 4 chr4B.!!$F3 4001
2 TraesCS4D01G225700 chr4A 66337736 66343272 5536 False 1605 4193 85.214667 529 4254 3 chr4A.!!$F2 3725

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
880 4107 0.041535 TCGCCTTCTACTACCCCCAA 59.958 55.000 0.00 0.00 0.0 4.12 F
882 4109 1.070289 CGCCTTCTACTACCCCCAATC 59.930 57.143 0.00 0.00 0.0 2.67 F
883 4110 2.409570 GCCTTCTACTACCCCCAATCT 58.590 52.381 0.00 0.00 0.0 2.40 F
1365 4610 2.774351 ATCCTGCCCTACCTGCCC 60.774 66.667 0.00 0.00 0.0 5.36 F
2889 6156 1.377333 GGTTGCAGCCTGAGGTACC 60.377 63.158 13.08 2.73 0.0 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1686 4931 0.378962 CGAGAAGAGCGTAGTCCAGG 59.621 60.000 0.0 0.0 0.00 4.45 R
2588 5841 2.024825 GCGGGAGTCACCAGATCTACT 61.025 57.143 0.0 0.0 41.20 2.57 R
2806 6073 2.215625 TCCACCGCCGACCCTTTTA 61.216 57.895 0.0 0.0 0.00 1.52 R
2912 6179 0.803768 CCATCAAGGCGAGAGTGACG 60.804 60.000 0.0 0.0 0.00 4.35 R
4142 9492 0.107066 ATGCAGGATTCGCCATGTCA 60.107 50.000 0.0 0.0 40.02 3.58 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
21 22 4.974368 TCGGTAAATTTTCGCCATGATT 57.026 36.364 0.00 0.00 0.00 2.57
22 23 4.667262 TCGGTAAATTTTCGCCATGATTG 58.333 39.130 0.00 0.00 0.00 2.67
23 24 4.396478 TCGGTAAATTTTCGCCATGATTGA 59.604 37.500 0.00 0.00 0.00 2.57
24 25 5.098893 CGGTAAATTTTCGCCATGATTGAA 58.901 37.500 0.00 0.00 0.00 2.69
25 26 5.229887 CGGTAAATTTTCGCCATGATTGAAG 59.770 40.000 0.00 0.00 0.00 3.02
26 27 6.329496 GGTAAATTTTCGCCATGATTGAAGA 58.671 36.000 0.00 0.00 0.00 2.87
27 28 6.980397 GGTAAATTTTCGCCATGATTGAAGAT 59.020 34.615 0.00 0.00 0.00 2.40
28 29 7.168135 GGTAAATTTTCGCCATGATTGAAGATC 59.832 37.037 0.00 0.00 0.00 2.75
29 30 4.637483 TTTTCGCCATGATTGAAGATCC 57.363 40.909 0.00 0.00 0.00 3.36
30 31 3.565764 TTCGCCATGATTGAAGATCCT 57.434 42.857 0.00 0.00 0.00 3.24
31 32 3.565764 TCGCCATGATTGAAGATCCTT 57.434 42.857 0.00 0.00 0.00 3.36
32 33 3.889815 TCGCCATGATTGAAGATCCTTT 58.110 40.909 0.00 0.00 0.00 3.11
33 34 4.272489 TCGCCATGATTGAAGATCCTTTT 58.728 39.130 0.00 0.00 0.00 2.27
34 35 5.436175 TCGCCATGATTGAAGATCCTTTTA 58.564 37.500 0.00 0.00 0.00 1.52
35 36 6.064060 TCGCCATGATTGAAGATCCTTTTAT 58.936 36.000 0.00 0.00 0.00 1.40
36 37 6.205464 TCGCCATGATTGAAGATCCTTTTATC 59.795 38.462 0.00 0.00 0.00 1.75
37 38 6.206243 CGCCATGATTGAAGATCCTTTTATCT 59.794 38.462 0.00 0.00 37.84 1.98
38 39 7.255381 CGCCATGATTGAAGATCCTTTTATCTT 60.255 37.037 0.00 0.00 46.46 2.40
39 40 8.419442 GCCATGATTGAAGATCCTTTTATCTTT 58.581 33.333 0.00 0.00 44.38 2.52
40 41 9.745880 CCATGATTGAAGATCCTTTTATCTTTG 57.254 33.333 0.00 0.00 44.38 2.77
43 44 9.519191 TGATTGAAGATCCTTTTATCTTTGTCA 57.481 29.630 0.99 3.97 44.38 3.58
44 45 9.780413 GATTGAAGATCCTTTTATCTTTGTCAC 57.220 33.333 0.99 0.00 44.38 3.67
45 46 8.690203 TTGAAGATCCTTTTATCTTTGTCACA 57.310 30.769 0.99 0.00 44.38 3.58
46 47 8.690203 TGAAGATCCTTTTATCTTTGTCACAA 57.310 30.769 0.99 0.00 44.38 3.33
47 48 9.300681 TGAAGATCCTTTTATCTTTGTCACAAT 57.699 29.630 0.00 0.00 44.38 2.71
48 49 9.565213 GAAGATCCTTTTATCTTTGTCACAATG 57.435 33.333 0.00 0.00 44.38 2.82
49 50 8.868522 AGATCCTTTTATCTTTGTCACAATGA 57.131 30.769 8.47 8.47 32.09 2.57
50 51 9.471702 AGATCCTTTTATCTTTGTCACAATGAT 57.528 29.630 19.67 19.67 32.09 2.45
53 54 9.300681 TCCTTTTATCTTTGTCACAATGATTCT 57.699 29.630 20.65 4.21 0.00 2.40
54 55 9.918630 CCTTTTATCTTTGTCACAATGATTCTT 57.081 29.630 20.65 3.89 0.00 2.52
117 118 9.799106 TTTTATTCTGAATTTCTCTGAACCTCT 57.201 29.630 8.38 0.00 42.68 3.69
118 119 9.442047 TTTATTCTGAATTTCTCTGAACCTCTC 57.558 33.333 8.38 0.00 42.68 3.20
119 120 6.425210 TTCTGAATTTCTCTGAACCTCTCA 57.575 37.500 0.00 0.00 37.16 3.27
120 121 6.425210 TCTGAATTTCTCTGAACCTCTCAA 57.575 37.500 0.00 0.00 32.17 3.02
121 122 6.830912 TCTGAATTTCTCTGAACCTCTCAAA 58.169 36.000 0.00 0.00 32.17 2.69
122 123 7.456725 TCTGAATTTCTCTGAACCTCTCAAAT 58.543 34.615 0.00 0.00 32.17 2.32
123 124 8.597167 TCTGAATTTCTCTGAACCTCTCAAATA 58.403 33.333 0.00 0.00 32.17 1.40
124 125 9.393512 CTGAATTTCTCTGAACCTCTCAAATAT 57.606 33.333 0.00 0.00 32.17 1.28
125 126 9.745018 TGAATTTCTCTGAACCTCTCAAATATT 57.255 29.630 0.00 0.00 32.17 1.28
188 189 4.637483 AATGAAGCATAACAATCCACCG 57.363 40.909 0.00 0.00 0.00 4.94
189 190 1.742831 TGAAGCATAACAATCCACCGC 59.257 47.619 0.00 0.00 0.00 5.68
190 191 0.732571 AAGCATAACAATCCACCGCG 59.267 50.000 0.00 0.00 0.00 6.46
191 192 1.298339 GCATAACAATCCACCGCGC 60.298 57.895 0.00 0.00 0.00 6.86
192 193 1.355210 CATAACAATCCACCGCGCC 59.645 57.895 0.00 0.00 0.00 6.53
193 194 1.822186 ATAACAATCCACCGCGCCC 60.822 57.895 0.00 0.00 0.00 6.13
194 195 2.265467 ATAACAATCCACCGCGCCCT 62.265 55.000 0.00 0.00 0.00 5.19
202 203 4.887190 ACCGCGCCCTGGTTTGTT 62.887 61.111 0.00 0.00 35.82 2.83
203 204 4.038080 CCGCGCCCTGGTTTGTTC 62.038 66.667 0.00 0.00 0.00 3.18
204 205 3.283684 CGCGCCCTGGTTTGTTCA 61.284 61.111 0.00 0.00 0.00 3.18
205 206 2.625823 CGCGCCCTGGTTTGTTCAT 61.626 57.895 0.00 0.00 0.00 2.57
206 207 1.212751 GCGCCCTGGTTTGTTCATC 59.787 57.895 0.00 0.00 0.00 2.92
207 208 1.501741 CGCCCTGGTTTGTTCATCG 59.498 57.895 0.00 0.00 0.00 3.84
208 209 1.883021 GCCCTGGTTTGTTCATCGG 59.117 57.895 0.00 0.00 0.00 4.18
209 210 0.608035 GCCCTGGTTTGTTCATCGGA 60.608 55.000 0.00 0.00 0.00 4.55
210 211 1.165270 CCCTGGTTTGTTCATCGGAC 58.835 55.000 0.00 0.00 0.00 4.79
211 212 1.271379 CCCTGGTTTGTTCATCGGACT 60.271 52.381 0.00 0.00 0.00 3.85
212 213 2.504367 CCTGGTTTGTTCATCGGACTT 58.496 47.619 0.00 0.00 0.00 3.01
213 214 2.484264 CCTGGTTTGTTCATCGGACTTC 59.516 50.000 0.00 0.00 0.00 3.01
214 215 3.138304 CTGGTTTGTTCATCGGACTTCA 58.862 45.455 0.00 0.00 0.00 3.02
215 216 3.750371 TGGTTTGTTCATCGGACTTCAT 58.250 40.909 0.00 0.00 0.00 2.57
216 217 4.900684 TGGTTTGTTCATCGGACTTCATA 58.099 39.130 0.00 0.00 0.00 2.15
217 218 4.693566 TGGTTTGTTCATCGGACTTCATAC 59.306 41.667 0.00 0.00 0.00 2.39
218 219 4.693566 GGTTTGTTCATCGGACTTCATACA 59.306 41.667 0.00 0.00 0.00 2.29
219 220 5.354234 GGTTTGTTCATCGGACTTCATACAT 59.646 40.000 0.00 0.00 0.00 2.29
220 221 6.456988 GGTTTGTTCATCGGACTTCATACATC 60.457 42.308 0.00 0.00 0.00 3.06
221 222 5.337578 TGTTCATCGGACTTCATACATCA 57.662 39.130 0.00 0.00 0.00 3.07
222 223 5.109210 TGTTCATCGGACTTCATACATCAC 58.891 41.667 0.00 0.00 0.00 3.06
223 224 5.105351 TGTTCATCGGACTTCATACATCACT 60.105 40.000 0.00 0.00 0.00 3.41
224 225 6.096282 TGTTCATCGGACTTCATACATCACTA 59.904 38.462 0.00 0.00 0.00 2.74
225 226 6.901081 TCATCGGACTTCATACATCACTAT 57.099 37.500 0.00 0.00 0.00 2.12
226 227 6.681777 TCATCGGACTTCATACATCACTATG 58.318 40.000 0.00 0.00 39.17 2.23
303 304 8.871686 AAAATCAATTTCCGATATAACCAAGC 57.128 30.769 0.00 0.00 0.00 4.01
304 305 7.581213 AATCAATTTCCGATATAACCAAGCA 57.419 32.000 0.00 0.00 0.00 3.91
476 486 3.314553 AGAATATTCGTCGCATAACCCG 58.685 45.455 9.78 0.00 0.00 5.28
485 495 6.193514 TCGTCGCATAACCCGAAATATATA 57.806 37.500 0.00 0.00 36.36 0.86
486 496 6.619744 TCGTCGCATAACCCGAAATATATAA 58.380 36.000 0.00 0.00 36.36 0.98
487 497 6.527722 TCGTCGCATAACCCGAAATATATAAC 59.472 38.462 0.00 0.00 36.36 1.89
488 498 6.237648 CGTCGCATAACCCGAAATATATAACC 60.238 42.308 0.00 0.00 36.36 2.85
489 499 6.591062 GTCGCATAACCCGAAATATATAACCA 59.409 38.462 0.00 0.00 36.36 3.67
491 501 7.493320 TCGCATAACCCGAAATATATAACCATC 59.507 37.037 0.00 0.00 0.00 3.51
492 502 7.279090 CGCATAACCCGAAATATATAACCATCA 59.721 37.037 0.00 0.00 0.00 3.07
522 3730 2.450476 GTAAACCGAGGGAGTAGTGGA 58.550 52.381 0.00 0.00 0.00 4.02
523 3731 2.019807 AAACCGAGGGAGTAGTGGAA 57.980 50.000 0.00 0.00 0.00 3.53
524 3732 2.019807 AACCGAGGGAGTAGTGGAAA 57.980 50.000 0.00 0.00 0.00 3.13
525 3733 2.019807 ACCGAGGGAGTAGTGGAAAA 57.980 50.000 0.00 0.00 0.00 2.29
526 3734 2.332117 ACCGAGGGAGTAGTGGAAAAA 58.668 47.619 0.00 0.00 0.00 1.94
527 3735 2.910977 ACCGAGGGAGTAGTGGAAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
621 3834 0.111442 CAGTACGCACCAACGTTTCG 60.111 55.000 0.00 2.70 45.75 3.46
631 3844 1.003262 CAACGTTTCGCATGCTTGGG 61.003 55.000 17.13 10.06 37.15 4.12
705 3918 2.986413 ACAGTCTCTCGTGCCGCT 60.986 61.111 0.00 0.00 0.00 5.52
706 3919 2.505777 CAGTCTCTCGTGCCGCTG 60.506 66.667 0.00 0.00 0.00 5.18
707 3920 4.427661 AGTCTCTCGTGCCGCTGC 62.428 66.667 0.00 0.00 38.26 5.25
735 3948 1.420430 GGATCCCATTCCACGGAGTA 58.580 55.000 0.00 0.00 41.61 2.59
736 3949 1.070289 GGATCCCATTCCACGGAGTAC 59.930 57.143 0.00 0.00 41.61 2.73
737 3950 2.040178 GATCCCATTCCACGGAGTACT 58.960 52.381 0.00 0.00 41.61 2.73
738 3951 1.481871 TCCCATTCCACGGAGTACTC 58.518 55.000 14.87 14.87 41.61 2.59
739 3952 0.464452 CCCATTCCACGGAGTACTCC 59.536 60.000 29.18 29.18 41.61 3.85
802 4016 0.395312 CACGTACAGAACCCCCAACT 59.605 55.000 0.00 0.00 0.00 3.16
807 4021 2.082140 ACAGAACCCCCAACTTTTCC 57.918 50.000 0.00 0.00 0.00 3.13
841 4066 5.576447 AAAGGATATCGCCGTTTCAATTT 57.424 34.783 0.00 0.00 0.00 1.82
851 4078 4.231439 GCCGTTTCAATTTTGTCGGTAAT 58.769 39.130 17.52 0.00 38.76 1.89
873 4100 1.134007 TCACCCGATCGCCTTCTACTA 60.134 52.381 10.32 0.00 0.00 1.82
877 4104 0.597072 CGATCGCCTTCTACTACCCC 59.403 60.000 0.26 0.00 0.00 4.95
878 4105 0.967662 GATCGCCTTCTACTACCCCC 59.032 60.000 0.00 0.00 0.00 5.40
880 4107 0.041535 TCGCCTTCTACTACCCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
881 4108 1.129058 CGCCTTCTACTACCCCCAAT 58.871 55.000 0.00 0.00 0.00 3.16
882 4109 1.070289 CGCCTTCTACTACCCCCAATC 59.930 57.143 0.00 0.00 0.00 2.67
883 4110 2.409570 GCCTTCTACTACCCCCAATCT 58.590 52.381 0.00 0.00 0.00 2.40
884 4111 2.778270 GCCTTCTACTACCCCCAATCTT 59.222 50.000 0.00 0.00 0.00 2.40
885 4112 3.971971 GCCTTCTACTACCCCCAATCTTA 59.028 47.826 0.00 0.00 0.00 2.10
886 4113 4.202336 GCCTTCTACTACCCCCAATCTTAC 60.202 50.000 0.00 0.00 0.00 2.34
887 4114 5.217400 CCTTCTACTACCCCCAATCTTACT 58.783 45.833 0.00 0.00 0.00 2.24
888 4115 5.304871 CCTTCTACTACCCCCAATCTTACTC 59.695 48.000 0.00 0.00 0.00 2.59
889 4116 5.745988 TCTACTACCCCCAATCTTACTCT 57.254 43.478 0.00 0.00 0.00 3.24
890 4117 6.101274 TCTACTACCCCCAATCTTACTCTT 57.899 41.667 0.00 0.00 0.00 2.85
891 4118 6.134754 TCTACTACCCCCAATCTTACTCTTC 58.865 44.000 0.00 0.00 0.00 2.87
895 4122 3.523972 ACCCCCAATCTTACTCTTCCTTC 59.476 47.826 0.00 0.00 0.00 3.46
897 4124 3.117851 CCCCAATCTTACTCTTCCTTCCC 60.118 52.174 0.00 0.00 0.00 3.97
1365 4610 2.774351 ATCCTGCCCTACCTGCCC 60.774 66.667 0.00 0.00 0.00 5.36
1506 4751 2.792290 CGACAAGCAGATCGCCGTG 61.792 63.158 6.02 7.34 44.04 4.94
2194 5439 3.699894 AGCCCACGGTGAGCTCTG 61.700 66.667 11.67 4.39 28.40 3.35
2492 5743 3.055819 CGACCAGATTCTTCTTTCCTCCA 60.056 47.826 0.00 0.00 0.00 3.86
2534 5785 4.370364 TTCTCAGGTTTCAAAACACTGC 57.630 40.909 7.82 0.00 40.63 4.40
2535 5786 3.620488 TCTCAGGTTTCAAAACACTGCT 58.380 40.909 7.82 0.00 40.63 4.24
2578 5831 9.705290 TGAAAAAGGCTTCCAAACTAAATAATC 57.295 29.630 0.00 0.00 0.00 1.75
2579 5832 9.705290 GAAAAAGGCTTCCAAACTAAATAATCA 57.295 29.630 0.00 0.00 0.00 2.57
2583 5836 9.474313 AAGGCTTCCAAACTAAATAATCATACA 57.526 29.630 0.00 0.00 0.00 2.29
2584 5837 9.474313 AGGCTTCCAAACTAAATAATCATACAA 57.526 29.630 0.00 0.00 0.00 2.41
2606 5871 6.127026 ACAAAATAGTAGATCTGGTGACTCCC 60.127 42.308 5.18 0.00 34.77 4.30
2749 6016 8.567948 TGTCCTTTTCTCAGTAAAATCAATGTC 58.432 33.333 0.00 0.00 0.00 3.06
2806 6073 4.932200 TCGTTTGTTTTTGGCTTGTGATTT 59.068 33.333 0.00 0.00 0.00 2.17
2889 6156 1.377333 GGTTGCAGCCTGAGGTACC 60.377 63.158 13.08 2.73 0.00 3.34
2903 6170 2.232452 GAGGTACCGAGATCATCATGGG 59.768 54.545 6.18 0.00 0.00 4.00
2909 6176 1.541889 CGAGATCATCATGGGGTGTGG 60.542 57.143 0.00 0.00 0.00 4.17
2910 6177 1.492176 GAGATCATCATGGGGTGTGGT 59.508 52.381 0.00 0.00 0.00 4.16
2911 6178 1.213678 AGATCATCATGGGGTGTGGTG 59.786 52.381 0.00 0.00 0.00 4.17
2912 6179 0.396139 ATCATCATGGGGTGTGGTGC 60.396 55.000 0.00 0.00 0.00 5.01
2913 6180 2.045045 ATCATGGGGTGTGGTGCG 60.045 61.111 0.00 0.00 0.00 5.34
2914 6181 2.905996 ATCATGGGGTGTGGTGCGT 61.906 57.895 0.00 0.00 0.00 5.24
2962 6230 0.830866 GGGTAGGTGGATAGGACGGG 60.831 65.000 0.00 0.00 0.00 5.28
2965 6233 1.893801 GTAGGTGGATAGGACGGGATG 59.106 57.143 0.00 0.00 0.00 3.51
2972 6240 2.040178 GATAGGACGGGATGGAACTGT 58.960 52.381 0.00 0.00 0.00 3.55
3022 6296 4.819761 TGATCCTCTGCACGGCGC 62.820 66.667 6.90 0.00 42.89 6.53
3048 6322 0.031178 GCTGTTGTGGTTGCTGAAGG 59.969 55.000 0.00 0.00 0.00 3.46
3049 6323 1.392589 CTGTTGTGGTTGCTGAAGGT 58.607 50.000 0.00 0.00 0.00 3.50
3332 6779 7.804600 TCAATTTCATCTGAATTCGTCAACTTG 59.195 33.333 0.04 1.35 35.22 3.16
3344 6791 2.349155 CGTCAACTTGGAGCGGTTAAAC 60.349 50.000 0.00 0.00 0.00 2.01
3347 6794 4.060205 TCAACTTGGAGCGGTTAAACTAC 58.940 43.478 0.00 0.00 0.00 2.73
3408 8685 3.004315 ACTTTTGTAATCTGGCACAACGG 59.996 43.478 0.00 0.00 38.70 4.44
3413 8691 0.606401 AATCTGGCACAACGGTCAGG 60.606 55.000 0.00 0.00 38.70 3.86
3493 8771 3.802866 TGTGTTGTTGCAGTCAGATACA 58.197 40.909 0.00 0.00 0.00 2.29
3499 8777 4.640364 TGTTGCAGTCAGATACACATCAA 58.360 39.130 0.00 0.00 33.21 2.57
3550 8842 8.700644 GTTAATTGAGTGTCTTGTACAGTAGTG 58.299 37.037 0.00 0.00 42.02 2.74
3551 8843 4.848562 TGAGTGTCTTGTACAGTAGTGG 57.151 45.455 1.92 0.00 42.02 4.00
3555 8847 5.628130 AGTGTCTTGTACAGTAGTGGTAGA 58.372 41.667 1.92 0.00 40.09 2.59
3573 8865 5.048364 TGGTAGATGCACACATTTTGGTTAC 60.048 40.000 0.00 0.00 36.35 2.50
3640 8936 1.338769 ACAACTTGGAGCCGGTCATAC 60.339 52.381 1.90 0.00 0.00 2.39
3648 8944 3.118884 TGGAGCCGGTCATACTTCTTAAC 60.119 47.826 1.90 0.00 0.00 2.01
3650 8946 3.858247 AGCCGGTCATACTTCTTAACAC 58.142 45.455 1.90 0.00 0.00 3.32
3681 8977 8.635765 AATTATCACTCCTTGCTAAAAACAGA 57.364 30.769 0.00 0.00 0.00 3.41
3752 9048 2.027653 TGGAACGCACATCAATAGGACA 60.028 45.455 0.00 0.00 0.00 4.02
3768 9064 2.094675 GGACATTTGACATGGAGTGGG 58.905 52.381 0.00 0.00 0.00 4.61
3818 9116 9.358872 GGAGGACTTTATTTCAAATGATTCAAC 57.641 33.333 0.00 0.00 0.00 3.18
3836 9134 9.829507 TGATTCAACAATAACATTTCCAAGTTT 57.170 25.926 0.00 0.00 0.00 2.66
3883 9226 8.981370 TGAAAATTTATACATATTCACGACGC 57.019 30.769 0.00 0.00 0.00 5.19
3929 9272 7.919313 AATATTATGATTTTCAAGCTGCACG 57.081 32.000 1.02 0.00 0.00 5.34
3935 9283 5.049167 TGATTTTCAAGCTGCACGAAAAAT 58.951 33.333 23.72 17.88 40.78 1.82
3942 9290 5.633182 TCAAGCTGCACGAAAAATAAATTCC 59.367 36.000 1.02 0.00 0.00 3.01
3990 9340 6.984474 TCCCATTCTCATCTACGTATTTGTTC 59.016 38.462 0.00 0.00 0.00 3.18
4050 9400 8.980143 ATGAAATTTTCCCTAAACGTGTTATG 57.020 30.769 6.68 0.00 0.00 1.90
4058 9408 9.669887 TTTCCCTAAACGTGTTATGTATGTATT 57.330 29.630 0.00 0.00 0.00 1.89
4060 9410 9.100554 TCCCTAAACGTGTTATGTATGTATTTG 57.899 33.333 0.00 0.00 0.00 2.32
4062 9412 9.697250 CCTAAACGTGTTATGTATGTATTTGTG 57.303 33.333 0.00 0.00 0.00 3.33
4063 9413 9.205916 CTAAACGTGTTATGTATGTATTTGTGC 57.794 33.333 0.00 0.00 0.00 4.57
4064 9414 6.729391 ACGTGTTATGTATGTATTTGTGCA 57.271 33.333 0.00 0.00 0.00 4.57
4071 9421 9.995957 GTTATGTATGTATTTGTGCATGTACAA 57.004 29.630 23.30 23.30 38.69 2.41
4128 9478 0.620700 AGCCCGTCCTCCCTATTTGT 60.621 55.000 0.00 0.00 0.00 2.83
4135 9485 4.765339 CCGTCCTCCCTATTTGTTCTTTTT 59.235 41.667 0.00 0.00 0.00 1.94
4173 9523 6.803807 GGCGAATCCTGCATAAATAGAAAATC 59.196 38.462 0.00 0.00 0.00 2.17
4179 9529 8.750515 TCCTGCATAAATAGAAAATCACATCA 57.249 30.769 0.00 0.00 0.00 3.07
4180 9530 9.358406 TCCTGCATAAATAGAAAATCACATCAT 57.642 29.630 0.00 0.00 0.00 2.45
4181 9531 9.976511 CCTGCATAAATAGAAAATCACATCATT 57.023 29.630 0.00 0.00 0.00 2.57
4203 9553 7.930325 TCATTTTTCCATATGCACAGACAAAAA 59.070 29.630 0.00 8.88 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.396478 TCAATCATGGCGAAAATTTACCGA 59.604 37.500 14.58 2.37 0.00 4.69
1 2 4.667262 TCAATCATGGCGAAAATTTACCG 58.333 39.130 8.11 8.11 0.00 4.02
2 3 6.329496 TCTTCAATCATGGCGAAAATTTACC 58.671 36.000 0.00 0.00 0.00 2.85
3 4 7.168135 GGATCTTCAATCATGGCGAAAATTTAC 59.832 37.037 0.00 0.00 0.00 2.01
4 5 7.068593 AGGATCTTCAATCATGGCGAAAATTTA 59.931 33.333 0.00 0.00 0.00 1.40
5 6 6.044682 GGATCTTCAATCATGGCGAAAATTT 58.955 36.000 0.00 0.00 0.00 1.82
6 7 5.361857 AGGATCTTCAATCATGGCGAAAATT 59.638 36.000 0.00 0.00 0.00 1.82
7 8 4.891756 AGGATCTTCAATCATGGCGAAAAT 59.108 37.500 0.00 0.00 0.00 1.82
8 9 4.272489 AGGATCTTCAATCATGGCGAAAA 58.728 39.130 0.00 0.00 0.00 2.29
9 10 3.889815 AGGATCTTCAATCATGGCGAAA 58.110 40.909 0.00 0.00 0.00 3.46
10 11 3.565764 AGGATCTTCAATCATGGCGAA 57.434 42.857 0.00 0.00 0.00 4.70
11 12 3.565764 AAGGATCTTCAATCATGGCGA 57.434 42.857 0.00 0.00 0.00 5.54
12 13 4.644103 AAAAGGATCTTCAATCATGGCG 57.356 40.909 0.00 0.00 0.00 5.69
13 14 7.521871 AGATAAAAGGATCTTCAATCATGGC 57.478 36.000 0.00 0.00 31.92 4.40
14 15 9.745880 CAAAGATAAAAGGATCTTCAATCATGG 57.254 33.333 0.00 0.00 43.83 3.66
17 18 9.519191 TGACAAAGATAAAAGGATCTTCAATCA 57.481 29.630 0.00 2.33 43.83 2.57
18 19 9.780413 GTGACAAAGATAAAAGGATCTTCAATC 57.220 33.333 0.00 0.17 43.83 2.67
19 20 9.300681 TGTGACAAAGATAAAAGGATCTTCAAT 57.699 29.630 0.00 0.00 43.83 2.57
20 21 8.690203 TGTGACAAAGATAAAAGGATCTTCAA 57.310 30.769 0.00 0.00 43.83 2.69
21 22 8.690203 TTGTGACAAAGATAAAAGGATCTTCA 57.310 30.769 0.00 0.00 43.83 3.02
22 23 9.565213 CATTGTGACAAAGATAAAAGGATCTTC 57.435 33.333 0.62 0.00 43.83 2.87
23 24 9.300681 TCATTGTGACAAAGATAAAAGGATCTT 57.699 29.630 0.62 0.00 46.02 2.40
24 25 8.868522 TCATTGTGACAAAGATAAAAGGATCT 57.131 30.769 0.62 0.00 37.81 2.75
27 28 9.300681 AGAATCATTGTGACAAAGATAAAAGGA 57.699 29.630 15.33 0.00 0.00 3.36
28 29 9.918630 AAGAATCATTGTGACAAAGATAAAAGG 57.081 29.630 15.33 0.00 0.00 3.11
91 92 9.799106 AGAGGTTCAGAGAAATTCAGAATAAAA 57.201 29.630 0.00 0.00 34.38 1.52
92 93 9.442047 GAGAGGTTCAGAGAAATTCAGAATAAA 57.558 33.333 0.00 0.00 34.38 1.40
93 94 8.597167 TGAGAGGTTCAGAGAAATTCAGAATAA 58.403 33.333 0.00 0.00 34.38 1.40
94 95 8.138928 TGAGAGGTTCAGAGAAATTCAGAATA 57.861 34.615 0.00 0.00 34.38 1.75
95 96 7.013823 TGAGAGGTTCAGAGAAATTCAGAAT 57.986 36.000 0.00 0.00 34.38 2.40
96 97 6.425210 TGAGAGGTTCAGAGAAATTCAGAA 57.575 37.500 0.00 0.00 0.00 3.02
97 98 6.425210 TTGAGAGGTTCAGAGAAATTCAGA 57.575 37.500 0.00 0.00 37.07 3.27
98 99 7.684937 ATTTGAGAGGTTCAGAGAAATTCAG 57.315 36.000 0.00 0.00 37.07 3.02
99 100 9.745018 AATATTTGAGAGGTTCAGAGAAATTCA 57.255 29.630 0.00 0.00 37.07 2.57
162 163 8.349245 CGGTGGATTGTTATGCTTCATTAATAA 58.651 33.333 0.00 0.00 0.00 1.40
163 164 7.521423 GCGGTGGATTGTTATGCTTCATTAATA 60.521 37.037 0.00 0.00 0.00 0.98
164 165 6.735694 GCGGTGGATTGTTATGCTTCATTAAT 60.736 38.462 0.00 0.00 0.00 1.40
165 166 5.449862 GCGGTGGATTGTTATGCTTCATTAA 60.450 40.000 0.00 0.00 0.00 1.40
166 167 4.036262 GCGGTGGATTGTTATGCTTCATTA 59.964 41.667 0.00 0.00 0.00 1.90
167 168 3.181487 GCGGTGGATTGTTATGCTTCATT 60.181 43.478 0.00 0.00 0.00 2.57
168 169 2.358898 GCGGTGGATTGTTATGCTTCAT 59.641 45.455 0.00 0.00 0.00 2.57
169 170 1.742831 GCGGTGGATTGTTATGCTTCA 59.257 47.619 0.00 0.00 0.00 3.02
170 171 1.268032 CGCGGTGGATTGTTATGCTTC 60.268 52.381 0.00 0.00 0.00 3.86
171 172 0.732571 CGCGGTGGATTGTTATGCTT 59.267 50.000 0.00 0.00 0.00 3.91
172 173 1.714899 GCGCGGTGGATTGTTATGCT 61.715 55.000 8.83 0.00 0.00 3.79
173 174 1.298339 GCGCGGTGGATTGTTATGC 60.298 57.895 8.83 0.00 0.00 3.14
174 175 1.355210 GGCGCGGTGGATTGTTATG 59.645 57.895 8.83 0.00 0.00 1.90
175 176 1.822186 GGGCGCGGTGGATTGTTAT 60.822 57.895 8.83 0.00 0.00 1.89
176 177 2.437002 GGGCGCGGTGGATTGTTA 60.437 61.111 8.83 0.00 0.00 2.41
177 178 4.344865 AGGGCGCGGTGGATTGTT 62.345 61.111 8.83 0.00 0.00 2.83
185 186 4.887190 AACAAACCAGGGCGCGGT 62.887 61.111 8.83 10.63 38.85 5.68
186 187 4.038080 GAACAAACCAGGGCGCGG 62.038 66.667 8.83 0.00 0.00 6.46
187 188 2.527547 GATGAACAAACCAGGGCGCG 62.528 60.000 0.00 0.00 0.00 6.86
188 189 1.212751 GATGAACAAACCAGGGCGC 59.787 57.895 0.00 0.00 0.00 6.53
189 190 1.501741 CGATGAACAAACCAGGGCG 59.498 57.895 0.00 0.00 0.00 6.13
190 191 0.608035 TCCGATGAACAAACCAGGGC 60.608 55.000 0.00 0.00 0.00 5.19
191 192 1.165270 GTCCGATGAACAAACCAGGG 58.835 55.000 0.00 0.00 0.00 4.45
192 193 2.185004 AGTCCGATGAACAAACCAGG 57.815 50.000 0.00 0.00 0.00 4.45
193 194 3.138304 TGAAGTCCGATGAACAAACCAG 58.862 45.455 0.00 0.00 0.00 4.00
194 195 3.201353 TGAAGTCCGATGAACAAACCA 57.799 42.857 0.00 0.00 0.00 3.67
195 196 4.693566 TGTATGAAGTCCGATGAACAAACC 59.306 41.667 0.00 0.00 0.00 3.27
196 197 5.856126 TGTATGAAGTCCGATGAACAAAC 57.144 39.130 0.00 0.00 0.00 2.93
197 198 6.092122 GTGATGTATGAAGTCCGATGAACAAA 59.908 38.462 0.00 0.00 0.00 2.83
198 199 5.580691 GTGATGTATGAAGTCCGATGAACAA 59.419 40.000 0.00 0.00 0.00 2.83
199 200 5.105351 AGTGATGTATGAAGTCCGATGAACA 60.105 40.000 0.00 0.00 0.00 3.18
200 201 5.352284 AGTGATGTATGAAGTCCGATGAAC 58.648 41.667 0.00 0.00 0.00 3.18
201 202 5.598416 AGTGATGTATGAAGTCCGATGAA 57.402 39.130 0.00 0.00 0.00 2.57
202 203 6.265422 ACATAGTGATGTATGAAGTCCGATGA 59.735 38.462 0.00 0.00 44.77 2.92
203 204 6.450545 ACATAGTGATGTATGAAGTCCGATG 58.549 40.000 0.00 0.00 44.77 3.84
204 205 6.656632 ACATAGTGATGTATGAAGTCCGAT 57.343 37.500 0.00 0.00 44.77 4.18
280 281 7.285401 ACTGCTTGGTTATATCGGAAATTGATT 59.715 33.333 0.00 0.00 0.00 2.57
290 291 2.287915 GTGGCACTGCTTGGTTATATCG 59.712 50.000 11.13 0.00 0.00 2.92
297 298 0.110295 TGTATGTGGCACTGCTTGGT 59.890 50.000 19.83 0.00 0.00 3.67
298 299 1.200716 CTTGTATGTGGCACTGCTTGG 59.799 52.381 19.83 1.75 0.00 3.61
299 300 1.881973 ACTTGTATGTGGCACTGCTTG 59.118 47.619 19.83 7.29 0.00 4.01
300 301 1.881973 CACTTGTATGTGGCACTGCTT 59.118 47.619 19.83 3.84 34.56 3.91
301 302 1.527034 CACTTGTATGTGGCACTGCT 58.473 50.000 19.83 6.19 34.56 4.24
485 495 6.381994 TCGGTTTACCTCTACTATTGATGGTT 59.618 38.462 0.00 0.00 0.00 3.67
486 496 5.895534 TCGGTTTACCTCTACTATTGATGGT 59.104 40.000 0.00 0.00 0.00 3.55
487 497 6.401047 TCGGTTTACCTCTACTATTGATGG 57.599 41.667 0.00 0.00 0.00 3.51
488 498 6.448006 CCTCGGTTTACCTCTACTATTGATG 58.552 44.000 0.00 0.00 0.00 3.07
489 499 5.539193 CCCTCGGTTTACCTCTACTATTGAT 59.461 44.000 0.00 0.00 0.00 2.57
491 501 4.891756 TCCCTCGGTTTACCTCTACTATTG 59.108 45.833 0.00 0.00 0.00 1.90
492 502 5.134725 TCCCTCGGTTTACCTCTACTATT 57.865 43.478 0.00 0.00 0.00 1.73
494 504 3.525199 ACTCCCTCGGTTTACCTCTACTA 59.475 47.826 0.00 0.00 0.00 1.82
496 506 2.732763 ACTCCCTCGGTTTACCTCTAC 58.267 52.381 0.00 0.00 0.00 2.59
497 507 3.525199 ACTACTCCCTCGGTTTACCTCTA 59.475 47.826 0.00 0.00 0.00 2.43
498 508 2.311243 ACTACTCCCTCGGTTTACCTCT 59.689 50.000 0.00 0.00 0.00 3.69
499 509 2.426381 CACTACTCCCTCGGTTTACCTC 59.574 54.545 0.00 0.00 0.00 3.85
500 510 2.454538 CACTACTCCCTCGGTTTACCT 58.545 52.381 0.00 0.00 0.00 3.08
501 511 1.479730 CCACTACTCCCTCGGTTTACC 59.520 57.143 0.00 0.00 0.00 2.85
502 512 2.450476 TCCACTACTCCCTCGGTTTAC 58.550 52.381 0.00 0.00 0.00 2.01
503 513 2.905415 TCCACTACTCCCTCGGTTTA 57.095 50.000 0.00 0.00 0.00 2.01
506 3714 2.019807 TTTTCCACTACTCCCTCGGT 57.980 50.000 0.00 0.00 0.00 4.69
523 3731 8.334632 CGTTGCAAAAGGTCTCATTTTTATTTT 58.665 29.630 0.00 0.00 0.00 1.82
524 3732 7.494298 ACGTTGCAAAAGGTCTCATTTTTATTT 59.506 29.630 0.00 0.00 0.00 1.40
525 3733 6.983890 ACGTTGCAAAAGGTCTCATTTTTATT 59.016 30.769 0.00 0.00 0.00 1.40
526 3734 6.512297 ACGTTGCAAAAGGTCTCATTTTTAT 58.488 32.000 0.00 0.00 0.00 1.40
527 3735 5.897050 ACGTTGCAAAAGGTCTCATTTTTA 58.103 33.333 0.00 0.00 0.00 1.52
631 3844 2.481471 GCTGTATTTCTGGGGCCGC 61.481 63.158 14.01 14.01 0.00 6.53
711 3924 1.066858 CCGTGGAATGGGATCCGATAG 60.067 57.143 9.97 0.29 42.76 2.08
712 3925 0.973632 CCGTGGAATGGGATCCGATA 59.026 55.000 9.97 0.00 42.76 2.92
734 3947 4.774200 GGGTTGTTTACTGGAGTAGGAGTA 59.226 45.833 0.00 0.00 0.00 2.59
735 3948 3.581770 GGGTTGTTTACTGGAGTAGGAGT 59.418 47.826 0.00 0.00 0.00 3.85
736 3949 3.055312 GGGGTTGTTTACTGGAGTAGGAG 60.055 52.174 0.00 0.00 0.00 3.69
737 3950 2.908351 GGGGTTGTTTACTGGAGTAGGA 59.092 50.000 0.00 0.00 0.00 2.94
738 3951 2.026542 GGGGGTTGTTTACTGGAGTAGG 60.027 54.545 0.00 0.00 0.00 3.18
739 3952 2.354403 CGGGGGTTGTTTACTGGAGTAG 60.354 54.545 0.00 0.00 0.00 2.57
851 4078 1.134907 GTAGAAGGCGATCGGGTGAAA 60.135 52.381 18.30 0.00 0.00 2.69
873 4100 3.222394 AGGAAGAGTAAGATTGGGGGT 57.778 47.619 0.00 0.00 0.00 4.95
877 4104 3.117851 GGGGGAAGGAAGAGTAAGATTGG 60.118 52.174 0.00 0.00 0.00 3.16
878 4105 3.523564 TGGGGGAAGGAAGAGTAAGATTG 59.476 47.826 0.00 0.00 0.00 2.67
880 4107 3.116174 GTGGGGGAAGGAAGAGTAAGAT 58.884 50.000 0.00 0.00 0.00 2.40
881 4108 2.158066 TGTGGGGGAAGGAAGAGTAAGA 60.158 50.000 0.00 0.00 0.00 2.10
882 4109 2.027100 GTGTGGGGGAAGGAAGAGTAAG 60.027 54.545 0.00 0.00 0.00 2.34
883 4110 1.982958 GTGTGGGGGAAGGAAGAGTAA 59.017 52.381 0.00 0.00 0.00 2.24
884 4111 1.652947 GTGTGGGGGAAGGAAGAGTA 58.347 55.000 0.00 0.00 0.00 2.59
885 4112 1.134438 GGTGTGGGGGAAGGAAGAGT 61.134 60.000 0.00 0.00 0.00 3.24
886 4113 1.685820 GGTGTGGGGGAAGGAAGAG 59.314 63.158 0.00 0.00 0.00 2.85
887 4114 1.850755 GGGTGTGGGGGAAGGAAGA 60.851 63.158 0.00 0.00 0.00 2.87
888 4115 2.160171 TGGGTGTGGGGGAAGGAAG 61.160 63.158 0.00 0.00 0.00 3.46
889 4116 2.038221 TGGGTGTGGGGGAAGGAA 60.038 61.111 0.00 0.00 0.00 3.36
890 4117 2.856988 GTGGGTGTGGGGGAAGGA 60.857 66.667 0.00 0.00 0.00 3.36
891 4118 3.979497 GGTGGGTGTGGGGGAAGG 61.979 72.222 0.00 0.00 0.00 3.46
897 4124 1.000896 GATTGGAGGTGGGTGTGGG 60.001 63.158 0.00 0.00 0.00 4.61
1686 4931 0.378962 CGAGAAGAGCGTAGTCCAGG 59.621 60.000 0.00 0.00 0.00 4.45
1866 5111 2.987547 TTCTCGTTCGCGTCCCCT 60.988 61.111 5.77 0.00 42.11 4.79
2194 5439 4.572389 TGAACAACTGACAGAGAAAAGAGC 59.428 41.667 10.08 0.00 0.00 4.09
2492 5743 7.093156 TGAGAATGATGTCAAGTTCCTACTCAT 60.093 37.037 0.00 0.00 31.99 2.90
2534 5785 7.223387 CCTTTTTCATTTCCACAAAGAAGTGAG 59.777 37.037 0.00 0.00 41.63 3.51
2535 5786 7.041107 CCTTTTTCATTTCCACAAAGAAGTGA 58.959 34.615 0.00 0.00 42.05 3.41
2577 5830 9.201989 AGTCACCAGATCTACTATTTTGTATGA 57.798 33.333 0.00 0.00 0.00 2.15
2578 5831 9.469807 GAGTCACCAGATCTACTATTTTGTATG 57.530 37.037 0.00 0.00 0.00 2.39
2579 5832 8.643324 GGAGTCACCAGATCTACTATTTTGTAT 58.357 37.037 0.00 0.00 38.79 2.29
2580 5833 7.069578 GGGAGTCACCAGATCTACTATTTTGTA 59.930 40.741 0.00 0.00 41.20 2.41
2581 5834 6.127026 GGGAGTCACCAGATCTACTATTTTGT 60.127 42.308 0.00 0.00 41.20 2.83
2582 5835 6.284459 GGGAGTCACCAGATCTACTATTTTG 58.716 44.000 0.00 0.00 41.20 2.44
2583 5836 5.069251 CGGGAGTCACCAGATCTACTATTTT 59.931 44.000 0.00 0.00 41.20 1.82
2584 5837 4.585162 CGGGAGTCACCAGATCTACTATTT 59.415 45.833 0.00 0.00 41.20 1.40
2585 5838 4.145807 CGGGAGTCACCAGATCTACTATT 58.854 47.826 0.00 0.00 41.20 1.73
2586 5839 3.757270 CGGGAGTCACCAGATCTACTAT 58.243 50.000 0.00 0.00 41.20 2.12
2587 5840 2.748798 GCGGGAGTCACCAGATCTACTA 60.749 54.545 0.00 0.00 41.20 1.82
2588 5841 2.024825 GCGGGAGTCACCAGATCTACT 61.025 57.143 0.00 0.00 41.20 2.57
2606 5871 4.759693 ACTCCAGATCTACTATCTCTTGCG 59.240 45.833 0.00 0.00 0.00 4.85
2749 6016 5.920193 TGAGGAAAGCAATAAAATGAGGG 57.080 39.130 0.00 0.00 0.00 4.30
2806 6073 2.215625 TCCACCGCCGACCCTTTTA 61.216 57.895 0.00 0.00 0.00 1.52
2889 6156 1.541889 CCACACCCCATGATGATCTCG 60.542 57.143 0.00 0.00 0.00 4.04
2903 6170 1.664965 GAGAGTGACGCACCACACC 60.665 63.158 8.00 0.56 39.42 4.16
2912 6179 0.803768 CCATCAAGGCGAGAGTGACG 60.804 60.000 0.00 0.00 0.00 4.35
2913 6180 3.056628 CCATCAAGGCGAGAGTGAC 57.943 57.895 0.00 0.00 0.00 3.67
2923 6190 2.573369 CCTGAATCTCAGCCATCAAGG 58.427 52.381 0.00 0.00 42.98 3.61
2962 6230 1.552337 TCCAGAGCAGACAGTTCCATC 59.448 52.381 0.00 0.00 0.00 3.51
2965 6233 3.830679 CTCCAGAGCAGACAGTTCC 57.169 57.895 0.00 0.00 0.00 3.62
3022 6296 1.536709 GCAACCACAACAGCAAAGGAG 60.537 52.381 0.00 0.00 0.00 3.69
3025 6299 1.134753 TCAGCAACCACAACAGCAAAG 59.865 47.619 0.00 0.00 0.00 2.77
3031 6305 1.476085 CAACCTTCAGCAACCACAACA 59.524 47.619 0.00 0.00 0.00 3.33
3048 6322 2.428890 AGATCCACATCTCGGTCTCAAC 59.571 50.000 0.00 0.00 33.71 3.18
3049 6323 2.428530 CAGATCCACATCTCGGTCTCAA 59.571 50.000 0.00 0.00 37.25 3.02
3232 6512 7.566760 TTTGCACCTCATGTATATTTGTAGG 57.433 36.000 0.00 0.00 0.00 3.18
3332 6779 3.308438 TCACAGTAGTTTAACCGCTCC 57.692 47.619 0.00 0.00 0.00 4.70
3344 6791 5.007039 AGCAATCGCAACATTATCACAGTAG 59.993 40.000 0.00 0.00 42.27 2.57
3347 6794 4.201841 TGAGCAATCGCAACATTATCACAG 60.202 41.667 0.00 0.00 42.27 3.66
3408 8685 5.163652 CCTTTTACCGAATCCATTTCCTGAC 60.164 44.000 0.00 0.00 0.00 3.51
3413 8691 6.151480 TGGTTACCTTTTACCGAATCCATTTC 59.849 38.462 2.07 0.00 37.23 2.17
3493 8771 5.835280 ACCCAGAAGTTTGAATCTTTGATGT 59.165 36.000 0.00 0.00 0.00 3.06
3499 8777 3.960102 TGCAACCCAGAAGTTTGAATCTT 59.040 39.130 0.00 0.00 0.00 2.40
3550 8842 4.519540 AACCAAAATGTGTGCATCTACC 57.480 40.909 0.00 0.00 33.50 3.18
3551 8843 6.007936 TGTAACCAAAATGTGTGCATCTAC 57.992 37.500 0.00 0.00 33.50 2.59
3555 8847 4.556501 CGTCTGTAACCAAAATGTGTGCAT 60.557 41.667 0.00 0.00 36.80 3.96
3573 8865 2.701073 AGTAACGGTTGTCTCGTCTG 57.299 50.000 3.07 0.00 40.18 3.51
3617 8913 1.349688 TGACCGGCTCCAAGTTGTAAT 59.650 47.619 0.00 0.00 0.00 1.89
3622 8918 1.276622 AGTATGACCGGCTCCAAGTT 58.723 50.000 0.00 0.00 0.00 2.66
3626 8922 1.568504 AAGAAGTATGACCGGCTCCA 58.431 50.000 0.00 0.00 0.00 3.86
3681 8977 1.547372 GGGTGCAGCATGACTTTTCAT 59.453 47.619 19.06 0.00 43.80 2.57
3715 9011 0.251742 TCCAAAGAGGCCCAACATGG 60.252 55.000 0.00 2.01 37.29 3.66
3752 9048 3.814504 ACTTCCCACTCCATGTCAAAT 57.185 42.857 0.00 0.00 0.00 2.32
3768 9064 1.875514 GTACCCGTCCACCAAAACTTC 59.124 52.381 0.00 0.00 0.00 3.01
3864 9207 6.921307 ACAGATGCGTCGTGAATATGTATAAA 59.079 34.615 10.98 0.00 0.00 1.40
3877 9220 3.430895 ACGAAATTTTACAGATGCGTCGT 59.569 39.130 0.00 4.59 34.63 4.34
3918 9261 5.633182 GGAATTTATTTTTCGTGCAGCTTGA 59.367 36.000 0.00 0.00 0.00 3.02
3929 9272 4.570930 TGTTGGGCCGGAATTTATTTTTC 58.429 39.130 5.05 0.00 0.00 2.29
3935 9283 1.996798 TGTTGTTGGGCCGGAATTTA 58.003 45.000 5.05 0.00 0.00 1.40
3942 9290 1.726853 TTTTTGTTGTTGTTGGGCCG 58.273 45.000 0.00 0.00 0.00 6.13
3964 9312 6.281405 ACAAATACGTAGATGAGAATGGGAC 58.719 40.000 15.08 0.00 0.00 4.46
3966 9314 6.986817 AGAACAAATACGTAGATGAGAATGGG 59.013 38.462 15.08 0.00 0.00 4.00
3967 9315 8.425577 AAGAACAAATACGTAGATGAGAATGG 57.574 34.615 15.08 0.00 0.00 3.16
4022 9372 8.806177 AACACGTTTAGGGAAAATTTCATAAC 57.194 30.769 8.09 5.12 0.00 1.89
4031 9381 7.982761 ACATACATAACACGTTTAGGGAAAA 57.017 32.000 0.00 0.00 0.00 2.29
4035 9385 8.885722 ACAAATACATACATAACACGTTTAGGG 58.114 33.333 0.00 0.00 0.00 3.53
4039 9389 7.585867 TGCACAAATACATACATAACACGTTT 58.414 30.769 0.00 0.00 0.00 3.60
4082 9432 9.354673 CCATGGTGGACTTAAAAGAACATATAT 57.645 33.333 2.57 0.00 40.96 0.86
4083 9433 8.553153 TCCATGGTGGACTTAAAAGAACATATA 58.447 33.333 12.58 0.00 42.67 0.86
4084 9434 7.410174 TCCATGGTGGACTTAAAAGAACATAT 58.590 34.615 12.58 0.00 42.67 1.78
4085 9435 6.785076 TCCATGGTGGACTTAAAAGAACATA 58.215 36.000 12.58 0.00 42.67 2.29
4086 9436 5.640147 TCCATGGTGGACTTAAAAGAACAT 58.360 37.500 12.58 0.00 42.67 2.71
4087 9437 5.055265 TCCATGGTGGACTTAAAAGAACA 57.945 39.130 12.58 0.00 42.67 3.18
4088 9438 4.082733 GCTCCATGGTGGACTTAAAAGAAC 60.083 45.833 12.58 0.00 42.67 3.01
4089 9439 4.079253 GCTCCATGGTGGACTTAAAAGAA 58.921 43.478 12.58 0.00 42.67 2.52
4090 9440 3.561313 GGCTCCATGGTGGACTTAAAAGA 60.561 47.826 12.58 0.00 42.67 2.52
4091 9441 2.755103 GGCTCCATGGTGGACTTAAAAG 59.245 50.000 12.58 0.00 42.67 2.27
4092 9442 2.556559 GGGCTCCATGGTGGACTTAAAA 60.557 50.000 12.58 0.00 42.67 1.52
4093 9443 1.005450 GGGCTCCATGGTGGACTTAAA 59.995 52.381 12.58 0.00 42.67 1.52
4094 9444 0.623723 GGGCTCCATGGTGGACTTAA 59.376 55.000 12.58 0.00 42.67 1.85
4095 9445 1.622607 CGGGCTCCATGGTGGACTTA 61.623 60.000 12.58 0.00 42.67 2.24
4135 9485 2.487762 GGATTCGCCATGTCAAACTGAA 59.512 45.455 0.00 0.00 36.34 3.02
4136 9486 2.083774 GGATTCGCCATGTCAAACTGA 58.916 47.619 0.00 0.00 36.34 3.41
4137 9487 2.086869 AGGATTCGCCATGTCAAACTG 58.913 47.619 0.00 0.00 40.02 3.16
4138 9488 2.086869 CAGGATTCGCCATGTCAAACT 58.913 47.619 0.00 0.00 40.02 2.66
4139 9489 1.468054 GCAGGATTCGCCATGTCAAAC 60.468 52.381 0.00 0.00 40.02 2.93
4141 9491 0.322366 TGCAGGATTCGCCATGTCAA 60.322 50.000 0.00 0.00 40.02 3.18
4142 9492 0.107066 ATGCAGGATTCGCCATGTCA 60.107 50.000 0.00 0.00 40.02 3.58
4143 9493 1.882912 TATGCAGGATTCGCCATGTC 58.117 50.000 0.00 0.00 40.02 3.06
4173 9523 6.474427 GTCTGTGCATATGGAAAAATGATGTG 59.526 38.462 4.56 0.00 0.00 3.21
4179 9529 8.851541 ATTTTTGTCTGTGCATATGGAAAAAT 57.148 26.923 4.56 6.98 30.63 1.82
4180 9530 8.674263 AATTTTTGTCTGTGCATATGGAAAAA 57.326 26.923 4.56 4.93 0.00 1.94
4181 9531 7.387397 GGAATTTTTGTCTGTGCATATGGAAAA 59.613 33.333 4.56 0.00 0.00 2.29
4182 9532 6.873076 GGAATTTTTGTCTGTGCATATGGAAA 59.127 34.615 4.56 0.00 0.00 3.13
4183 9533 6.014755 TGGAATTTTTGTCTGTGCATATGGAA 60.015 34.615 4.56 0.00 0.00 3.53
4184 9534 5.479724 TGGAATTTTTGTCTGTGCATATGGA 59.520 36.000 4.56 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.