Multiple sequence alignment - TraesCS2B01G491200

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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 TraesCS2B01G491200 chr2B 100.000 4459 0 0 1 4459 689488189 689483731 0.000000e+00 8235.0
1 TraesCS2B01G491200 chr2B 78.710 310 43 10 4163 4459 629647179 629647478 7.620000e-43 185.0
2 TraesCS2B01G491200 chr2D 91.930 2243 88 26 1374 3564 573845279 573843078 0.000000e+00 3053.0
3 TraesCS2B01G491200 chr2D 90.476 1323 84 14 1 1298 573846963 573845658 0.000000e+00 1707.0
4 TraesCS2B01G491200 chr2D 83.714 350 43 7 4115 4459 573841583 573841243 7.200000e-83 318.0
5 TraesCS2B01G491200 chr2D 79.038 291 49 5 4165 4452 502833682 502833401 5.890000e-44 189.0
6 TraesCS2B01G491200 chr2D 79.286 140 26 3 67 205 88755389 88755526 1.320000e-15 95.3
7 TraesCS2B01G491200 chr5B 91.279 1892 120 19 1281 3141 120040557 120042434 0.000000e+00 2538.0
8 TraesCS2B01G491200 chr5B 89.829 1465 95 21 1281 2713 55089623 55088181 0.000000e+00 1831.0
9 TraesCS2B01G491200 chr5B 89.545 440 36 8 2705 3144 55056503 55056074 2.340000e-152 549.0
10 TraesCS2B01G491200 chr5B 75.743 202 33 9 9 207 554793686 554793874 2.210000e-13 87.9
11 TraesCS2B01G491200 chr4B 89.747 1463 123 17 1692 3141 302517815 302519263 0.000000e+00 1845.0
12 TraesCS2B01G491200 chr4B 91.304 368 27 5 1281 1645 302517448 302517813 8.610000e-137 497.0
13 TraesCS2B01G491200 chr4B 82.812 192 27 6 23 211 574424852 574424664 2.760000e-37 167.0
14 TraesCS2B01G491200 chr4B 78.519 135 25 4 1 133 641589324 641589456 7.950000e-13 86.1
15 TraesCS2B01G491200 chr4B 77.778 135 26 4 1 133 641665672 641665804 3.700000e-11 80.5
16 TraesCS2B01G491200 chr2A 90.337 1335 97 17 290 1610 712312057 712310741 0.000000e+00 1722.0
17 TraesCS2B01G491200 chr2A 91.233 730 35 15 2127 2841 712309477 712308762 0.000000e+00 966.0
18 TraesCS2B01G491200 chr2A 90.593 691 39 13 2882 3564 712308555 712307883 0.000000e+00 893.0
19 TraesCS2B01G491200 chr2A 86.235 247 33 1 17 262 712312301 712312055 2.640000e-67 267.0
20 TraesCS2B01G491200 chr2A 90.099 202 18 2 1745 1945 712309888 712309688 1.230000e-65 261.0
21 TraesCS2B01G491200 chr2A 80.137 292 40 8 4173 4459 712307009 712306731 7.560000e-48 202.0
22 TraesCS2B01G491200 chr2A 84.667 150 5 2 1612 1743 712310086 712309937 2.800000e-27 134.0
23 TraesCS2B01G491200 chr2A 86.408 103 6 3 3805 3903 712307601 712307503 6.100000e-19 106.0
24 TraesCS2B01G491200 chrUn 91.924 421 19 9 3155 3564 154747787 154748203 3.870000e-160 575.0
25 TraesCS2B01G491200 chrUn 94.382 89 5 0 3600 3688 154748311 154748399 2.160000e-28 137.0
26 TraesCS2B01G491200 chrUn 78.519 135 25 4 1 133 337385383 337385251 7.950000e-13 86.1
27 TraesCS2B01G491200 chrUn 78.519 135 25 4 1 133 353374534 353374666 7.950000e-13 86.1
28 TraesCS2B01G491200 chr5D 91.469 422 21 7 3155 3564 366923899 366924317 2.330000e-157 566.0
29 TraesCS2B01G491200 chr5D 89.583 432 32 7 3143 3564 28571516 28571944 1.830000e-148 536.0
30 TraesCS2B01G491200 chr5D 94.382 89 5 0 3600 3688 28572052 28572140 2.160000e-28 137.0
31 TraesCS2B01G491200 chr1D 91.190 420 24 7 3155 3564 79841551 79841135 3.900000e-155 558.0
32 TraesCS2B01G491200 chr1D 90.278 432 29 8 3143 3564 41782124 41782552 1.810000e-153 553.0
33 TraesCS2B01G491200 chr1D 79.264 299 48 7 4163 4457 370101506 370101794 3.520000e-46 196.0
34 TraesCS2B01G491200 chr1D 94.382 89 5 0 3600 3688 79841027 79840939 2.160000e-28 137.0
35 TraesCS2B01G491200 chr6D 89.762 420 30 8 3155 3564 396277613 396278029 3.950000e-145 525.0
36 TraesCS2B01G491200 chr6D 94.382 89 5 0 3600 3688 396278137 396278225 2.160000e-28 137.0
37 TraesCS2B01G491200 chr4A 80.170 353 56 11 4111 4459 625287654 625287312 7.400000e-63 252.0
38 TraesCS2B01G491200 chr4A 76.961 204 41 6 10 210 8965704 8965904 1.310000e-20 111.0
39 TraesCS2B01G491200 chr3B 82.520 246 30 8 4217 4459 513495085 513495320 2.100000e-48 204.0
40 TraesCS2B01G491200 chr3B 77.457 346 58 17 4119 4459 150283720 150283390 5.890000e-44 189.0
41 TraesCS2B01G491200 chr4D 84.615 169 23 3 4288 4454 343552500 343552667 9.920000e-37 165.0


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 TraesCS2B01G491200 chr2B 689483731 689488189 4458 True 8235.000000 8235 100.000000 1 4459 1 chr2B.!!$R1 4458
1 TraesCS2B01G491200 chr2D 573841243 573846963 5720 True 1692.666667 3053 88.706667 1 4459 3 chr2D.!!$R2 4458
2 TraesCS2B01G491200 chr5B 120040557 120042434 1877 False 2538.000000 2538 91.279000 1281 3141 1 chr5B.!!$F1 1860
3 TraesCS2B01G491200 chr5B 55088181 55089623 1442 True 1831.000000 1831 89.829000 1281 2713 1 chr5B.!!$R2 1432
4 TraesCS2B01G491200 chr4B 302517448 302519263 1815 False 1171.000000 1845 90.525500 1281 3141 2 chr4B.!!$F3 1860
5 TraesCS2B01G491200 chr2A 712306731 712312301 5570 True 568.875000 1722 87.463625 17 4459 8 chr2A.!!$R1 4442
6 TraesCS2B01G491200 chrUn 154747787 154748399 612 False 356.000000 575 93.153000 3155 3688 2 chrUn.!!$F2 533
7 TraesCS2B01G491200 chr5D 28571516 28572140 624 False 336.500000 536 91.982500 3143 3688 2 chr5D.!!$F2 545
8 TraesCS2B01G491200 chr1D 79840939 79841551 612 True 347.500000 558 92.786000 3155 3688 2 chr1D.!!$R1 533
9 TraesCS2B01G491200 chr6D 396277613 396278225 612 False 331.000000 525 92.072000 3155 3688 2 chr6D.!!$F1 533

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
300 302 0.947244 GTTAGCCAATCCCATCAGCG 59.053 55.000 0.0 0.0 0.00 5.18 F
865 889 1.271217 GGTAGTTGGTTTCCGCTTCCT 60.271 52.381 0.0 0.0 0.00 3.36 F
1815 2873 0.251386 TTGCCCCTTCCGTTGCATTA 60.251 50.000 0.0 0.0 33.08 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1159 1190 0.107897 CGATGATTTGGGTCGGGACA 60.108 55.000 0.75 0.0 0.00 4.02 R
1846 2904 1.142870 CTTCCTCCCAACCAGTGTTCA 59.857 52.381 0.00 0.0 30.42 3.18 R
3597 5015 0.179000 CCAGTCCAGGCTCATGGTAC 59.821 60.000 0.23 0.0 41.43 3.34 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
28 29 4.811024 TGAGCCGATACATCATTTTGAGAC 59.189 41.667 0.00 0.00 0.00 3.36
62 63 2.266055 GGTGCCTCCGGAGTCAAG 59.734 66.667 29.25 15.36 0.00 3.02
69 70 2.227089 CTCCGGAGTCAAGGGGAACG 62.227 65.000 24.04 0.00 0.00 3.95
78 79 1.157751 AAGGGGAACGTCTCCTCCA 59.842 57.895 11.57 0.00 46.81 3.86
87 88 1.971357 ACGTCTCCTCCAACTGAATGT 59.029 47.619 0.00 0.00 0.00 2.71
89 90 3.056749 ACGTCTCCTCCAACTGAATGTAC 60.057 47.826 0.00 0.00 0.00 2.90
96 97 2.027653 TCCAACTGAATGTACATCGCCA 60.028 45.455 9.23 7.05 0.00 5.69
114 115 7.542130 ACATCGCCAAAAAGTCTGAAATAAATC 59.458 33.333 0.00 0.00 0.00 2.17
150 152 3.129287 CACCAATGCCAAGTTCTATGACC 59.871 47.826 0.00 0.00 0.00 4.02
152 154 3.379372 CCAATGCCAAGTTCTATGACCTG 59.621 47.826 0.00 0.00 0.00 4.00
157 159 3.307762 GCCAAGTTCTATGACCTGAACCT 60.308 47.826 0.00 0.00 42.32 3.50
176 178 2.291800 CCTTGATGGGTTGATTCCACCT 60.292 50.000 6.85 0.00 37.08 4.00
198 200 5.280215 CCTCAAAGAACCTAACCATCTGAGT 60.280 44.000 0.00 0.00 0.00 3.41
300 302 0.947244 GTTAGCCAATCCCATCAGCG 59.053 55.000 0.00 0.00 0.00 5.18
304 306 1.528824 CCAATCCCATCAGCGAGGT 59.471 57.895 0.00 0.00 0.00 3.85
329 331 8.500773 GTGTTGTTTCAAAGGAACGATTATCTA 58.499 33.333 0.00 0.00 31.35 1.98
421 423 3.940319 TGCCATAGCATTGCACAAAATT 58.060 36.364 11.91 0.00 46.52 1.82
552 556 1.391485 CACTTCTCTATGTGCACGTGC 59.609 52.381 33.11 33.11 42.50 5.34
680 699 7.040686 AGCCACGTTTAATAACAAGACAATTCT 60.041 33.333 0.00 0.00 33.75 2.40
818 842 7.164008 CCTTTGCAAATTCGAATTGAAACAAAC 59.836 33.333 23.38 8.08 40.71 2.93
820 844 7.065216 TGCAAATTCGAATTGAAACAAACAA 57.935 28.000 23.38 0.00 40.71 2.83
821 845 7.521529 TGCAAATTCGAATTGAAACAAACAAA 58.478 26.923 23.38 0.00 40.71 2.83
865 889 1.271217 GGTAGTTGGTTTCCGCTTCCT 60.271 52.381 0.00 0.00 0.00 3.36
1007 1038 4.091939 CCCTCCCGTTTCCCCGTC 62.092 72.222 0.00 0.00 0.00 4.79
1008 1039 3.001406 CCTCCCGTTTCCCCGTCT 61.001 66.667 0.00 0.00 0.00 4.18
1058 1089 2.342648 GTCGCAAACCCTCGTCCT 59.657 61.111 0.00 0.00 0.00 3.85
1085 1116 3.067480 GAATCCCGCGACCCACGTA 62.067 63.158 8.23 0.00 44.60 3.57
1159 1190 2.483014 TTTGACCCGATCGATTTGGT 57.517 45.000 18.66 15.30 0.00 3.67
1162 1193 1.287425 GACCCGATCGATTTGGTGTC 58.713 55.000 18.66 18.01 0.00 3.67
1170 1201 1.377229 GATTTGGTGTCCCGACCCA 59.623 57.895 0.00 2.12 34.79 4.51
1179 1210 1.153249 TCCCGACCCAAATCATCGC 60.153 57.895 0.00 0.00 34.52 4.58
1245 1276 2.442188 GGTCGATCGGTGCGTGTTC 61.442 63.158 16.41 0.00 0.00 3.18
1252 1283 2.279918 GGTGCGTGTTCTCGTGGT 60.280 61.111 0.00 0.00 0.00 4.16
1381 1715 5.041191 TCATGCTCCCCTCTTTTCTTATC 57.959 43.478 0.00 0.00 0.00 1.75
1385 1719 4.164221 TGCTCCCCTCTTTTCTTATCGAAT 59.836 41.667 0.00 0.00 0.00 3.34
1388 1722 6.095580 GCTCCCCTCTTTTCTTATCGAATTTT 59.904 38.462 0.00 0.00 0.00 1.82
1438 1775 3.743396 GGCTGTGCTATCTGCTGTATTAC 59.257 47.826 0.00 0.00 43.37 1.89
1539 1877 7.172361 GCAAGGATTCATAGGAATTCTGTAGAC 59.828 40.741 11.59 0.00 46.57 2.59
1541 1879 6.551601 AGGATTCATAGGAATTCTGTAGACGT 59.448 38.462 10.12 0.00 45.72 4.34
1743 2801 6.372931 TCATCTAAATTAATCTGGGGGTTGG 58.627 40.000 0.00 0.00 0.00 3.77
1752 2810 0.774908 CTGGGGGTTGGTAAACTGGA 59.225 55.000 0.00 0.00 36.48 3.86
1778 2836 9.974980 AAAACGATTCTTTGGTGTAACAATTAT 57.025 25.926 0.00 0.00 39.98 1.28
1815 2873 0.251386 TTGCCCCTTCCGTTGCATTA 60.251 50.000 0.00 0.00 33.08 1.90
1859 2917 4.286297 TCTATCCTTGAACACTGGTTGG 57.714 45.455 0.00 0.00 37.36 3.77
1999 3061 7.120138 ACGTAGACTTTTACCATTGGTTATTGG 59.880 37.037 14.78 4.09 37.09 3.16
2005 3067 8.695456 ACTTTTACCATTGGTTATTGGATCATC 58.305 33.333 14.78 0.00 37.09 2.92
2093 3156 6.935167 TCACTTGTGATGATCTGCTAGTTAA 58.065 36.000 0.00 0.00 0.00 2.01
2095 3158 7.877612 TCACTTGTGATGATCTGCTAGTTAAAA 59.122 33.333 0.00 0.00 0.00 1.52
2154 3287 2.886081 ACTCTTGTTCTATCTGCTGCG 58.114 47.619 0.00 0.00 0.00 5.18
2167 3300 1.808945 CTGCTGCGACCTTGATCTTTT 59.191 47.619 0.00 0.00 0.00 2.27
2459 3611 4.164822 AGTTCCGCTCAAACATTTCATG 57.835 40.909 0.00 0.00 0.00 3.07
2541 3695 2.949644 AGCAGTTGGTGTTGTTAAGGTC 59.050 45.455 0.00 0.00 0.00 3.85
2752 3913 4.042187 GGGCTGAAGTGATGGGATTAGTAT 59.958 45.833 0.00 0.00 0.00 2.12
2753 3914 5.456763 GGGCTGAAGTGATGGGATTAGTATT 60.457 44.000 0.00 0.00 0.00 1.89
2809 3970 1.122227 ACACCATTTGCACAGGCTTT 58.878 45.000 0.00 0.00 41.91 3.51
2843 4004 7.577303 ACATGTACTATTGGAATCCACATCTT 58.423 34.615 0.00 0.00 30.78 2.40
2857 4018 6.588719 TCCACATCTTTATGGTTCAAAAGG 57.411 37.500 0.00 0.00 37.43 3.11
2865 4026 6.218730 TCTTTATGGTTCAAAAGGAGGGGATA 59.781 38.462 0.00 0.00 34.22 2.59
2899 4226 6.507958 TCAAAACTTTGTCTCATGTCACAA 57.492 33.333 7.79 7.79 39.18 3.33
2939 4266 4.885907 CCATTATTGACCATCAGCTGTTCT 59.114 41.667 14.67 0.00 0.00 3.01
2940 4267 6.057533 CCATTATTGACCATCAGCTGTTCTA 58.942 40.000 14.67 4.08 0.00 2.10
2985 4312 1.038280 CATACAGGTACCTCGTCCCC 58.962 60.000 12.84 0.00 0.00 4.81
2997 4324 4.503314 GTCCCCGCCGACCTTACG 62.503 72.222 0.00 0.00 0.00 3.18
3015 4342 1.342174 ACGGTTGGACAGTTCGTGTAT 59.658 47.619 0.00 0.00 40.56 2.29
3141 4468 4.636206 CCTGAACAAACTTATGCCTACCTC 59.364 45.833 0.00 0.00 0.00 3.85
3427 4757 4.892934 TGCACAACCAAGAAAACCTATTCT 59.107 37.500 0.00 0.00 41.34 2.40
3442 4772 9.765795 AAAACCTATTCTTATCCTGACTTATCG 57.234 33.333 0.00 0.00 0.00 2.92
3536 4877 1.796151 CATGCCGCTGTGGTTACTG 59.204 57.895 9.31 0.00 41.21 2.74
3537 4878 1.377202 ATGCCGCTGTGGTTACTGG 60.377 57.895 9.31 0.00 41.21 4.00
3538 4879 2.032071 GCCGCTGTGGTTACTGGT 59.968 61.111 9.31 0.00 41.21 4.00
3551 4892 1.593196 TACTGGTTGTTCACTGCTGC 58.407 50.000 0.00 0.00 0.00 5.25
3564 4905 3.686241 TCACTGCTGCTGATGTAATGTTC 59.314 43.478 13.69 0.00 0.00 3.18
3565 4906 3.437741 CACTGCTGCTGATGTAATGTTCA 59.562 43.478 13.69 0.00 0.00 3.18
3566 4907 3.438087 ACTGCTGCTGATGTAATGTTCAC 59.562 43.478 13.69 0.00 0.00 3.18
3567 4908 2.749076 TGCTGCTGATGTAATGTTCACC 59.251 45.455 0.00 0.00 0.00 4.02
3568 4909 2.223112 GCTGCTGATGTAATGTTCACCG 60.223 50.000 0.00 0.00 0.00 4.94
3575 4968 6.429791 TGATGTAATGTTCACCGGTAATTG 57.570 37.500 6.87 0.00 0.00 2.32
3597 5015 1.063166 GACTAAGGTCGCCGGTACG 59.937 63.158 1.90 0.00 41.76 3.67
3627 5045 0.758734 CTGGACTGGTGGTGACTTCA 59.241 55.000 0.00 0.00 0.00 3.02
3644 5064 5.302568 TGACTTCAACTCCGTTTAGGTTCTA 59.697 40.000 0.00 0.00 41.99 2.10
3649 5069 6.395629 TCAACTCCGTTTAGGTTCTATTGAG 58.604 40.000 0.00 0.00 41.99 3.02
3693 5150 2.756207 GAGAGGGTGTCAGGACTTCTAC 59.244 54.545 0.65 0.00 0.00 2.59
3701 5158 3.271225 TGTCAGGACTTCTACCCTATGGA 59.729 47.826 0.65 0.00 34.81 3.41
3720 5177 3.825585 TGGACAAGCAGTGAATTGCATTA 59.174 39.130 8.07 0.00 46.47 1.90
3723 5180 4.751060 ACAAGCAGTGAATTGCATTATGG 58.249 39.130 8.07 0.00 46.47 2.74
3724 5181 4.463539 ACAAGCAGTGAATTGCATTATGGA 59.536 37.500 8.07 0.00 46.47 3.41
3725 5182 5.128171 ACAAGCAGTGAATTGCATTATGGAT 59.872 36.000 8.07 0.00 46.47 3.41
3726 5183 5.449107 AGCAGTGAATTGCATTATGGATC 57.551 39.130 0.00 0.00 46.47 3.36
3727 5184 4.280174 AGCAGTGAATTGCATTATGGATCC 59.720 41.667 4.20 4.20 46.47 3.36
3728 5185 4.280174 GCAGTGAATTGCATTATGGATCCT 59.720 41.667 14.23 0.89 43.53 3.24
3729 5186 5.564259 GCAGTGAATTGCATTATGGATCCTC 60.564 44.000 14.23 0.00 43.53 3.71
3730 5187 5.048224 CAGTGAATTGCATTATGGATCCTCC 60.048 44.000 14.23 0.00 36.96 4.30
3738 5195 3.805928 TGGATCCTCCAACACGCT 58.194 55.556 14.23 0.00 45.00 5.07
3739 5196 1.296392 TGGATCCTCCAACACGCTG 59.704 57.895 14.23 0.00 45.00 5.18
3740 5197 1.450312 GGATCCTCCAACACGCTGG 60.450 63.158 3.84 0.00 36.28 4.85
3741 5198 2.045926 ATCCTCCAACACGCTGGC 60.046 61.111 0.00 0.00 36.32 4.85
3742 5199 3.958147 ATCCTCCAACACGCTGGCG 62.958 63.158 13.56 13.56 46.03 5.69
3779 5236 4.915704 CACACAAAGTGTTTCAATACGGT 58.084 39.130 0.00 0.00 45.08 4.83
3780 5237 5.336744 CACACAAAGTGTTTCAATACGGTT 58.663 37.500 0.00 0.00 45.08 4.44
3781 5238 5.802956 CACACAAAGTGTTTCAATACGGTTT 59.197 36.000 0.00 0.00 45.08 3.27
3782 5239 6.309251 CACACAAAGTGTTTCAATACGGTTTT 59.691 34.615 0.00 0.00 45.08 2.43
3783 5240 6.528774 ACACAAAGTGTTTCAATACGGTTTTC 59.471 34.615 0.00 0.00 45.08 2.29
3784 5241 6.528423 CACAAAGTGTTTCAATACGGTTTTCA 59.472 34.615 0.00 0.00 0.00 2.69
3785 5242 7.221838 CACAAAGTGTTTCAATACGGTTTTCAT 59.778 33.333 0.00 0.00 0.00 2.57
3786 5243 8.407064 ACAAAGTGTTTCAATACGGTTTTCATA 58.593 29.630 0.00 0.00 0.00 2.15
3787 5244 8.687301 CAAAGTGTTTCAATACGGTTTTCATAC 58.313 33.333 0.00 0.00 0.00 2.39
3788 5245 7.499321 AGTGTTTCAATACGGTTTTCATACA 57.501 32.000 0.00 0.00 0.00 2.29
3789 5246 8.106247 AGTGTTTCAATACGGTTTTCATACAT 57.894 30.769 0.00 0.00 0.00 2.29
3790 5247 8.020819 AGTGTTTCAATACGGTTTTCATACATG 58.979 33.333 0.00 0.00 0.00 3.21
3791 5248 8.018520 GTGTTTCAATACGGTTTTCATACATGA 58.981 33.333 0.00 0.00 34.44 3.07
3792 5249 8.568794 TGTTTCAATACGGTTTTCATACATGAA 58.431 29.630 0.00 0.45 44.42 2.57
3815 5272 5.656213 AATACATAGTCGTACCTATGGCC 57.344 43.478 17.99 0.00 45.61 5.36
3816 5273 2.245582 ACATAGTCGTACCTATGGCCC 58.754 52.381 17.99 0.00 45.61 5.80
3824 5281 1.072331 GTACCTATGGCCCTGATGTGG 59.928 57.143 0.00 0.00 0.00 4.17
3833 5290 2.715749 CCCTGATGTGGCACTATTCA 57.284 50.000 19.83 16.64 0.00 2.57
3834 5291 3.219176 CCCTGATGTGGCACTATTCAT 57.781 47.619 19.83 2.90 0.00 2.57
3835 5292 3.144506 CCCTGATGTGGCACTATTCATC 58.855 50.000 19.83 13.03 37.68 2.92
3836 5293 3.181447 CCCTGATGTGGCACTATTCATCT 60.181 47.826 19.83 0.00 37.93 2.90
3851 5308 8.644619 CACTATTCATCTGATTTTGCAAGTTTG 58.355 33.333 0.00 0.00 0.00 2.93
3855 5312 4.320608 TCTGATTTTGCAAGTTTGTCCC 57.679 40.909 0.00 0.00 0.00 4.46
3866 5323 0.395312 GTTTGTCCCCTTCGACCTCA 59.605 55.000 0.00 0.00 31.35 3.86
3870 5327 2.542550 TGTCCCCTTCGACCTCATTTA 58.457 47.619 0.00 0.00 31.35 1.40
3900 5357 5.163513 AGGCATTTCATTGAATTGTTCGAC 58.836 37.500 17.83 5.66 0.00 4.20
3901 5358 5.047802 AGGCATTTCATTGAATTGTTCGACT 60.048 36.000 17.83 9.30 0.00 4.18
3902 5359 6.150976 AGGCATTTCATTGAATTGTTCGACTA 59.849 34.615 17.83 0.00 0.00 2.59
3904 5361 7.008628 GGCATTTCATTGAATTGTTCGACTAAG 59.991 37.037 17.83 0.00 0.00 2.18
3905 5362 7.008628 GCATTTCATTGAATTGTTCGACTAAGG 59.991 37.037 17.83 0.00 0.00 2.69
3906 5363 6.494893 TTCATTGAATTGTTCGACTAAGGG 57.505 37.500 0.00 0.00 0.00 3.95
3907 5364 5.800296 TCATTGAATTGTTCGACTAAGGGA 58.200 37.500 0.00 0.00 0.00 4.20
3908 5365 5.874810 TCATTGAATTGTTCGACTAAGGGAG 59.125 40.000 0.00 0.00 0.00 4.30
3909 5366 4.884668 TGAATTGTTCGACTAAGGGAGT 57.115 40.909 0.00 0.00 42.90 3.85
3912 5436 6.570692 TGAATTGTTCGACTAAGGGAGTATC 58.429 40.000 0.00 0.00 39.06 2.24
3940 5464 3.058520 CAGAAGCGTGCAATTCATTTTCG 59.941 43.478 9.47 0.00 0.00 3.46
3970 5510 1.603802 CTGTGCGTTGATGACCTTTGT 59.396 47.619 0.00 0.00 0.00 2.83
3973 5513 1.234821 GCGTTGATGACCTTTGTCCA 58.765 50.000 0.00 0.00 41.01 4.02
3975 5515 2.494059 CGTTGATGACCTTTGTCCAGT 58.506 47.619 0.00 0.00 41.01 4.00
3977 5517 3.744660 GTTGATGACCTTTGTCCAGTCT 58.255 45.455 0.00 0.00 41.01 3.24
3978 5518 4.137543 GTTGATGACCTTTGTCCAGTCTT 58.862 43.478 0.00 0.00 41.01 3.01
4003 5551 1.334160 TTCTCTACGCAGGTTCCACA 58.666 50.000 0.00 0.00 0.00 4.17
4006 5554 2.426024 TCTCTACGCAGGTTCCACATAC 59.574 50.000 0.00 0.00 0.00 2.39
4009 5557 1.519408 ACGCAGGTTCCACATACAAC 58.481 50.000 0.00 0.00 0.00 3.32
4010 5558 0.802494 CGCAGGTTCCACATACAACC 59.198 55.000 0.00 0.00 42.26 3.77
4011 5559 1.880221 CGCAGGTTCCACATACAACCA 60.880 52.381 3.77 0.00 44.10 3.67
4012 5560 1.812571 GCAGGTTCCACATACAACCAG 59.187 52.381 3.77 0.00 44.10 4.00
4013 5561 2.436417 CAGGTTCCACATACAACCAGG 58.564 52.381 3.77 0.00 44.10 4.45
4015 5563 2.445525 AGGTTCCACATACAACCAGGTT 59.554 45.455 0.00 0.00 44.10 3.50
4016 5564 3.117284 AGGTTCCACATACAACCAGGTTT 60.117 43.478 0.44 0.00 44.10 3.27
4019 5567 1.959985 CCACATACAACCAGGTTTGCA 59.040 47.619 0.44 0.00 0.00 4.08
4020 5568 2.562298 CCACATACAACCAGGTTTGCAT 59.438 45.455 0.44 0.00 0.00 3.96
4021 5569 3.577667 CACATACAACCAGGTTTGCATG 58.422 45.455 0.44 8.82 36.62 4.06
4022 5570 3.255395 CACATACAACCAGGTTTGCATGA 59.745 43.478 18.45 0.00 34.88 3.07
4023 5571 4.082081 CACATACAACCAGGTTTGCATGAT 60.082 41.667 18.45 6.02 34.88 2.45
4025 5573 5.125417 ACATACAACCAGGTTTGCATGATAC 59.875 40.000 18.45 0.00 34.88 2.24
4027 5575 2.746904 CAACCAGGTTTGCATGATACGA 59.253 45.455 0.44 0.00 0.00 3.43
4028 5576 2.632377 ACCAGGTTTGCATGATACGAG 58.368 47.619 0.00 0.00 0.00 4.18
4029 5577 2.027192 ACCAGGTTTGCATGATACGAGT 60.027 45.455 0.00 0.00 0.00 4.18
4030 5578 3.196901 ACCAGGTTTGCATGATACGAGTA 59.803 43.478 0.00 0.00 0.00 2.59
4031 5579 4.141711 ACCAGGTTTGCATGATACGAGTAT 60.142 41.667 0.00 0.00 0.00 2.12
4032 5580 5.069914 ACCAGGTTTGCATGATACGAGTATA 59.930 40.000 0.00 0.00 0.00 1.47
4033 5581 5.635280 CCAGGTTTGCATGATACGAGTATAG 59.365 44.000 0.00 0.00 0.00 1.31
4037 5585 6.807230 GGTTTGCATGATACGAGTATAGTAGG 59.193 42.308 0.00 0.00 27.29 3.18
4038 5586 5.562506 TGCATGATACGAGTATAGTAGGC 57.437 43.478 0.00 1.23 27.29 3.93
4042 5590 4.648651 TGATACGAGTATAGTAGGCTGCA 58.351 43.478 5.14 0.00 27.29 4.41
4044 5592 1.955080 ACGAGTATAGTAGGCTGCACC 59.045 52.381 5.14 0.00 39.61 5.01
4052 5695 3.433306 AGTAGGCTGCACCATTGTTTA 57.567 42.857 5.14 0.00 43.14 2.01
4055 5698 0.108662 GGCTGCACCATTGTTTAGCC 60.109 55.000 0.50 0.00 38.44 3.93
4056 5699 0.890683 GCTGCACCATTGTTTAGCCT 59.109 50.000 0.00 0.00 0.00 4.58
4059 5702 0.456653 GCACCATTGTTTAGCCTGCG 60.457 55.000 0.00 0.00 0.00 5.18
4089 5732 5.355350 CGAATCTTAAAACATCTCCCAGCTT 59.645 40.000 0.00 0.00 0.00 3.74
4094 5737 2.123982 CATCTCCCAGCTTGGCCC 60.124 66.667 0.00 0.00 35.79 5.80
4096 5739 3.978241 ATCTCCCAGCTTGGCCCCT 62.978 63.158 0.00 0.00 35.79 4.79
4102 5745 0.897621 CCAGCTTGGCCCCTTTTTAG 59.102 55.000 0.00 0.00 0.00 1.85
4106 5749 1.819288 GCTTGGCCCCTTTTTAGAGAC 59.181 52.381 0.00 0.00 0.00 3.36
4109 5752 2.344592 TGGCCCCTTTTTAGAGACAGA 58.655 47.619 0.00 0.00 0.00 3.41
4111 5754 2.306219 GGCCCCTTTTTAGAGACAGACT 59.694 50.000 0.00 0.00 0.00 3.24
4112 5755 3.339141 GCCCCTTTTTAGAGACAGACTG 58.661 50.000 0.00 0.00 0.00 3.51
4117 6809 5.233988 CCTTTTTAGAGACAGACTGAGGTG 58.766 45.833 10.08 0.00 0.00 4.00
4121 6813 0.037790 GAGACAGACTGAGGTGGCAC 60.038 60.000 9.70 9.70 0.00 5.01
4133 6825 1.066858 AGGTGGCACGTGATCTGTTAG 60.067 52.381 22.23 0.00 0.00 2.34
4134 6826 1.359848 GTGGCACGTGATCTGTTAGG 58.640 55.000 22.23 0.00 0.00 2.69
4138 6830 3.196901 TGGCACGTGATCTGTTAGGTTAT 59.803 43.478 22.23 0.00 0.00 1.89
4157 6849 5.662456 GTTATCTCCTAACCTTGTCCACTC 58.338 45.833 0.00 0.00 34.75 3.51
4182 6874 9.042450 TCATTAGTCCCTTCTAATCTACACAAA 57.958 33.333 0.00 0.00 38.19 2.83
4183 6875 9.319143 CATTAGTCCCTTCTAATCTACACAAAG 57.681 37.037 0.00 0.00 38.19 2.77
4191 6883 7.361286 CCTTCTAATCTACACAAAGTTGCTTCC 60.361 40.741 0.00 0.00 0.00 3.46
4210 6906 7.394016 TGCTTCCATTTGAGATAAAGTCTACA 58.606 34.615 0.00 0.00 37.29 2.74
4211 6907 7.334421 TGCTTCCATTTGAGATAAAGTCTACAC 59.666 37.037 0.00 0.00 37.29 2.90
4235 6935 5.940192 AAAAGAAGCACATCGATGTTGTA 57.060 34.783 28.04 0.00 39.39 2.41
4242 6942 5.103000 AGCACATCGATGTTGTAGTTCTAC 58.897 41.667 28.04 7.78 39.39 2.59
4266 6966 5.789521 TCAGATGATTGGTTCGTAGTTTCA 58.210 37.500 0.00 0.00 0.00 2.69
4271 6971 6.236017 TGATTGGTTCGTAGTTTCATTCAC 57.764 37.500 0.00 0.00 0.00 3.18
4283 6983 8.279800 CGTAGTTTCATTCACTGTAAATGTTCA 58.720 33.333 3.70 0.00 35.92 3.18
4284 6984 9.944663 GTAGTTTCATTCACTGTAAATGTTCAA 57.055 29.630 3.70 0.00 35.92 2.69
4286 6986 9.467258 AGTTTCATTCACTGTAAATGTTCAATG 57.533 29.630 3.70 0.00 35.92 2.82
4287 6987 9.248291 GTTTCATTCACTGTAAATGTTCAATGT 57.752 29.630 3.70 0.00 35.92 2.71
4288 6988 8.800231 TTCATTCACTGTAAATGTTCAATGTG 57.200 30.769 3.70 0.00 35.92 3.21
4289 6989 7.939782 TCATTCACTGTAAATGTTCAATGTGT 58.060 30.769 3.70 0.00 35.92 3.72
4290 6990 8.412456 TCATTCACTGTAAATGTTCAATGTGTT 58.588 29.630 3.70 0.00 35.92 3.32
4291 6991 9.676195 CATTCACTGTAAATGTTCAATGTGTTA 57.324 29.630 0.00 0.00 31.00 2.41
4298 6998 9.175060 TGTAAATGTTCAATGTGTTAAATGTCG 57.825 29.630 0.00 0.00 0.00 4.35
4311 7011 7.742525 TGTGTTAAATGTCGTATTCATGTTTCG 59.257 33.333 0.00 0.00 0.00 3.46
4368 7069 3.120442 ACGGTCGATCGTTTGAAATTTCC 60.120 43.478 19.89 0.00 40.85 3.13
4429 7130 2.535934 TGTTGCACGTGTTCTGTTTC 57.464 45.000 18.38 0.00 0.00 2.78
4437 7138 3.978855 CACGTGTTCTGTTTCGATAGTCA 59.021 43.478 7.58 0.00 37.40 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.812127 TGTCAGTCTCAAAATGATGTATCGG 59.188 40.000 0.00 0.00 0.00 4.18
28 29 2.332063 ACCTGTGGTGACTTTGTCAG 57.668 50.000 0.20 0.00 43.57 3.51
55 56 0.246910 GGAGACGTTCCCCTTGACTC 59.753 60.000 0.00 0.00 40.37 3.36
69 70 4.537135 TGTACATTCAGTTGGAGGAGAC 57.463 45.455 0.00 0.00 0.00 3.36
78 79 5.009610 ACTTTTTGGCGATGTACATTCAGTT 59.990 36.000 10.30 0.00 0.00 3.16
87 88 5.957842 ATTTCAGACTTTTTGGCGATGTA 57.042 34.783 0.00 0.00 0.00 2.29
89 90 7.541783 TGATTTATTTCAGACTTTTTGGCGATG 59.458 33.333 0.00 0.00 0.00 3.84
128 130 3.129287 GGTCATAGAACTTGGCATTGGTG 59.871 47.826 0.00 0.00 0.00 4.17
157 159 2.378208 TGAGGTGGAATCAACCCATCAA 59.622 45.455 2.53 0.00 37.27 2.57
176 178 5.825593 ACTCAGATGGTTAGGTTCTTTGA 57.174 39.130 0.00 0.00 0.00 2.69
198 200 6.348458 CGAAAGAATGTGTCAAATGAGCCTAA 60.348 38.462 0.00 0.00 0.00 2.69
210 212 6.251801 GTCTACTAGAAGCGAAAGAATGTGTC 59.748 42.308 0.00 0.00 0.00 3.67
213 215 6.518208 AGTCTACTAGAAGCGAAAGAATGT 57.482 37.500 0.00 0.00 0.00 2.71
300 302 3.375922 TCGTTCCTTTGAAACAACACCTC 59.624 43.478 0.00 0.00 30.79 3.85
304 306 7.504924 AGATAATCGTTCCTTTGAAACAACA 57.495 32.000 0.00 0.00 30.79 3.33
421 423 4.647424 AAAATGTTCTTCGGTCTTGCAA 57.353 36.364 0.00 0.00 0.00 4.08
532 535 1.391485 GCACGTGCACATAGAGAAGTG 59.609 52.381 34.52 14.41 41.59 3.16
588 607 5.669477 TCCATGCAGCCCAATATTTTAAAC 58.331 37.500 0.00 0.00 0.00 2.01
709 730 7.432869 TGGAACATTGAGAGTTTATTTTGTGG 58.567 34.615 0.00 0.00 0.00 4.17
717 738 9.273016 CTTCTAACTTGGAACATTGAGAGTTTA 57.727 33.333 0.00 0.00 36.11 2.01
779 803 0.318441 GCAAAGGAAAGCAACCTCCC 59.682 55.000 0.00 0.00 36.67 4.30
818 842 1.303309 GGTGGCCATCGATCTCTTTG 58.697 55.000 9.72 0.00 0.00 2.77
820 844 1.443407 CGGTGGCCATCGATCTCTT 59.557 57.895 35.04 0.00 37.01 2.85
821 845 2.502492 CCGGTGGCCATCGATCTCT 61.502 63.158 39.33 0.00 37.01 3.10
865 889 2.348243 CGCCTACGTTTCCCCCAA 59.652 61.111 0.00 0.00 33.53 4.12
999 1030 3.951769 GAGACGGGGAGACGGGGAA 62.952 68.421 0.00 0.00 38.39 3.97
1000 1031 4.437587 GAGACGGGGAGACGGGGA 62.438 72.222 0.00 0.00 38.39 4.81
1055 1086 1.812686 CGGGATTCGGCGGATTAGGA 61.813 60.000 7.21 0.00 34.75 2.94
1058 1089 2.029964 GCGGGATTCGGCGGATTA 59.970 61.111 7.21 0.00 39.69 1.75
1082 1113 2.588877 CCAGGGCGGATGCTTACG 60.589 66.667 0.00 0.00 42.25 3.18
1085 1116 2.044946 GAACCAGGGCGGATGCTT 60.045 61.111 0.00 0.00 42.25 3.91
1159 1190 0.107897 CGATGATTTGGGTCGGGACA 60.108 55.000 0.75 0.00 0.00 4.02
1162 1193 2.534019 CGCGATGATTTGGGTCGGG 61.534 63.158 0.00 0.00 40.85 5.14
1170 1201 2.618709 GAGAAAATCCCCGCGATGATTT 59.381 45.455 22.09 22.09 41.63 2.17
1179 1210 0.252197 AGAACCCGAGAAAATCCCCG 59.748 55.000 0.00 0.00 0.00 5.73
1245 1276 1.071471 AACAGAGCCCAACCACGAG 59.929 57.895 0.00 0.00 0.00 4.18
1252 1283 2.507484 CAGATCAACAACAGAGCCCAA 58.493 47.619 0.00 0.00 0.00 4.12
1381 1715 3.692593 ACCCCCTAATTCGACAAAATTCG 59.307 43.478 0.00 0.00 40.53 3.34
1401 1735 1.207329 ACAGCCTCCATAAGACGAACC 59.793 52.381 0.00 0.00 0.00 3.62
1497 1835 8.632679 TGAATCCTTGCAGTTATTCCAATAATC 58.367 33.333 11.96 0.00 33.79 1.75
1743 2801 6.416750 CACCAAAGAATCGTTTTCCAGTTTAC 59.583 38.462 0.00 0.00 0.00 2.01
1752 2810 9.974980 ATAATTGTTACACCAAAGAATCGTTTT 57.025 25.926 0.00 0.00 0.00 2.43
1778 2836 7.217906 AGGGGCAACGAAATTGTTAAAAATAA 58.782 30.769 0.00 0.00 40.77 1.40
1780 2838 5.616270 AGGGGCAACGAAATTGTTAAAAAT 58.384 33.333 0.00 0.00 40.77 1.82
1794 2852 4.038080 GCAACGGAAGGGGCAACG 62.038 66.667 0.00 0.00 34.89 4.10
1846 2904 1.142870 CTTCCTCCCAACCAGTGTTCA 59.857 52.381 0.00 0.00 30.42 3.18
1859 2917 6.372937 CCAAAACTCATAGAAGAACTTCCTCC 59.627 42.308 10.41 0.00 40.33 4.30
1999 3061 7.902387 ACATACATGTCAATAGCTGATGATC 57.098 36.000 0.00 0.00 35.87 2.92
2005 3067 9.102757 AGAGTAAAACATACATGTCAATAGCTG 57.897 33.333 0.00 0.00 40.80 4.24
2612 3773 2.237143 CTGAGTTATCAGCAGGAACCCA 59.763 50.000 0.00 0.00 46.19 4.51
2680 3841 2.445492 AAAGGACCCATGGGCCACAG 62.445 60.000 32.96 13.09 39.32 3.66
2752 3913 2.697751 CCAACCCAATTTCCAGTGACAA 59.302 45.455 0.00 0.00 0.00 3.18
2753 3914 2.315176 CCAACCCAATTTCCAGTGACA 58.685 47.619 0.00 0.00 0.00 3.58
2843 4004 4.965283 ATCCCCTCCTTTTGAACCATAA 57.035 40.909 0.00 0.00 0.00 1.90
2899 4226 1.412079 TGGCCAATCTTGTGCTTTGT 58.588 45.000 0.61 0.00 0.00 2.83
2939 4266 8.472413 GTTGGGTGACGGCTATTAGAATATATA 58.528 37.037 0.00 0.00 0.00 0.86
2940 4267 7.328737 GTTGGGTGACGGCTATTAGAATATAT 58.671 38.462 0.00 0.00 0.00 0.86
2997 4324 2.762745 ACATACACGAACTGTCCAACC 58.237 47.619 0.00 0.00 33.91 3.77
3162 4489 5.584551 AGGAACTTTGGGTTAGAACATCT 57.415 39.130 0.00 0.00 38.41 2.90
3490 4828 4.503910 ACGCATGAGCAGTAGAAATTACA 58.496 39.130 0.00 0.00 42.27 2.41
3536 4877 1.068748 CATCAGCAGCAGTGAACAACC 60.069 52.381 0.00 0.00 0.00 3.77
3537 4878 1.605710 ACATCAGCAGCAGTGAACAAC 59.394 47.619 0.00 0.00 0.00 3.32
3538 4879 1.971481 ACATCAGCAGCAGTGAACAA 58.029 45.000 0.00 0.00 0.00 2.83
3551 4892 6.486248 CAATTACCGGTGAACATTACATCAG 58.514 40.000 19.93 0.00 0.00 2.90
3564 4905 3.374058 CCTTAGTCAAGCAATTACCGGTG 59.626 47.826 19.93 0.19 0.00 4.94
3565 4906 3.008704 ACCTTAGTCAAGCAATTACCGGT 59.991 43.478 13.98 13.98 0.00 5.28
3566 4907 3.606687 ACCTTAGTCAAGCAATTACCGG 58.393 45.455 0.00 0.00 0.00 5.28
3567 4908 3.306166 CGACCTTAGTCAAGCAATTACCG 59.694 47.826 0.00 0.00 43.73 4.02
3568 4909 3.063588 GCGACCTTAGTCAAGCAATTACC 59.936 47.826 0.00 0.00 43.73 2.85
3575 4968 1.810030 CCGGCGACCTTAGTCAAGC 60.810 63.158 9.30 0.00 43.73 4.01
3597 5015 0.179000 CCAGTCCAGGCTCATGGTAC 59.821 60.000 0.23 0.00 41.43 3.34
3644 5064 1.682854 CTTGCAACACCACCACTCAAT 59.317 47.619 0.00 0.00 0.00 2.57
3649 5069 2.354074 CTGCCTTGCAACACCACCAC 62.354 60.000 0.00 0.00 38.41 4.16
3693 5150 2.787473 TTCACTGCTTGTCCATAGGG 57.213 50.000 0.00 0.00 0.00 3.53
3701 5158 4.463539 TCCATAATGCAATTCACTGCTTGT 59.536 37.500 0.00 0.00 43.07 3.16
3723 5180 2.109126 GCCAGCGTGTTGGAGGATC 61.109 63.158 6.95 0.00 40.87 3.36
3724 5181 2.045926 GCCAGCGTGTTGGAGGAT 60.046 61.111 6.95 0.00 40.87 3.24
3725 5182 4.680237 CGCCAGCGTGTTGGAGGA 62.680 66.667 6.95 0.00 40.87 3.71
3747 5204 3.148026 CACTTTGTGTGTTCATGCACA 57.852 42.857 0.00 0.00 45.85 4.57
3757 5214 4.915704 ACCGTATTGAAACACTTTGTGTG 58.084 39.130 4.01 0.00 46.79 3.82
3759 5216 6.528423 TGAAAACCGTATTGAAACACTTTGTG 59.472 34.615 0.00 0.00 39.75 3.33
3760 5217 6.622549 TGAAAACCGTATTGAAACACTTTGT 58.377 32.000 0.00 0.00 0.00 2.83
3761 5218 7.692908 ATGAAAACCGTATTGAAACACTTTG 57.307 32.000 0.00 0.00 0.00 2.77
3762 5219 8.407064 TGTATGAAAACCGTATTGAAACACTTT 58.593 29.630 0.00 0.00 0.00 2.66
3763 5220 7.932335 TGTATGAAAACCGTATTGAAACACTT 58.068 30.769 0.00 0.00 0.00 3.16
3764 5221 7.499321 TGTATGAAAACCGTATTGAAACACT 57.501 32.000 0.00 0.00 0.00 3.55
3765 5222 8.018520 TCATGTATGAAAACCGTATTGAAACAC 58.981 33.333 0.00 0.00 33.08 3.32
3766 5223 8.100508 TCATGTATGAAAACCGTATTGAAACA 57.899 30.769 0.00 0.00 33.08 2.83
3767 5224 8.958175 TTCATGTATGAAAACCGTATTGAAAC 57.042 30.769 4.89 0.00 43.26 2.78
3782 5239 9.687210 GGTACGACTATGTATTTTCATGTATGA 57.313 33.333 0.00 0.00 34.44 2.15
3783 5240 9.692749 AGGTACGACTATGTATTTTCATGTATG 57.307 33.333 0.00 0.00 0.00 2.39
3786 5243 9.692749 CATAGGTACGACTATGTATTTTCATGT 57.307 33.333 14.15 0.00 43.30 3.21
3787 5244 9.140286 CCATAGGTACGACTATGTATTTTCATG 57.860 37.037 18.12 0.00 45.61 3.07
3788 5245 7.817962 GCCATAGGTACGACTATGTATTTTCAT 59.182 37.037 18.12 0.00 45.61 2.57
3789 5246 7.149973 GCCATAGGTACGACTATGTATTTTCA 58.850 38.462 18.12 0.00 45.61 2.69
3790 5247 6.589139 GGCCATAGGTACGACTATGTATTTTC 59.411 42.308 18.12 6.66 45.61 2.29
3791 5248 6.461640 GGCCATAGGTACGACTATGTATTTT 58.538 40.000 18.12 0.00 45.61 1.82
3792 5249 5.046807 GGGCCATAGGTACGACTATGTATTT 60.047 44.000 4.39 0.00 45.61 1.40
3793 5250 4.465305 GGGCCATAGGTACGACTATGTATT 59.535 45.833 4.39 0.00 45.61 1.89
3794 5251 4.021916 GGGCCATAGGTACGACTATGTAT 58.978 47.826 4.39 0.00 45.61 2.29
3795 5252 3.074985 AGGGCCATAGGTACGACTATGTA 59.925 47.826 6.18 0.00 45.61 2.29
3796 5253 2.158355 AGGGCCATAGGTACGACTATGT 60.158 50.000 6.18 4.71 45.61 2.29
3797 5254 2.231478 CAGGGCCATAGGTACGACTATG 59.769 54.545 6.18 14.93 46.27 2.23
3798 5255 2.109480 TCAGGGCCATAGGTACGACTAT 59.891 50.000 6.18 0.00 34.06 2.12
3799 5256 1.496001 TCAGGGCCATAGGTACGACTA 59.504 52.381 6.18 0.00 0.00 2.59
3800 5257 0.260816 TCAGGGCCATAGGTACGACT 59.739 55.000 6.18 0.00 0.00 4.18
3801 5258 1.000955 CATCAGGGCCATAGGTACGAC 59.999 57.143 6.18 0.00 0.00 4.34
3802 5259 1.338107 CATCAGGGCCATAGGTACGA 58.662 55.000 6.18 0.00 0.00 3.43
3803 5260 1.048601 ACATCAGGGCCATAGGTACG 58.951 55.000 6.18 0.00 0.00 3.67
3815 5272 3.813724 CAGATGAATAGTGCCACATCAGG 59.186 47.826 0.00 0.00 40.74 3.86
3816 5273 4.700700 TCAGATGAATAGTGCCACATCAG 58.299 43.478 0.00 0.00 40.74 2.90
3824 5281 6.327934 ACTTGCAAAATCAGATGAATAGTGC 58.672 36.000 0.00 0.00 0.00 4.40
3825 5282 8.644619 CAAACTTGCAAAATCAGATGAATAGTG 58.355 33.333 0.00 0.00 0.00 2.74
3826 5283 8.362639 ACAAACTTGCAAAATCAGATGAATAGT 58.637 29.630 0.00 0.00 0.00 2.12
3827 5284 8.752766 ACAAACTTGCAAAATCAGATGAATAG 57.247 30.769 0.00 0.00 0.00 1.73
3828 5285 7.814107 GGACAAACTTGCAAAATCAGATGAATA 59.186 33.333 0.00 0.00 0.00 1.75
3831 5288 5.509501 GGGACAAACTTGCAAAATCAGATGA 60.510 40.000 0.00 0.00 0.00 2.92
3832 5289 4.687483 GGGACAAACTTGCAAAATCAGATG 59.313 41.667 0.00 0.00 0.00 2.90
3833 5290 4.262592 GGGGACAAACTTGCAAAATCAGAT 60.263 41.667 0.00 0.00 0.00 2.90
3834 5291 3.069443 GGGGACAAACTTGCAAAATCAGA 59.931 43.478 0.00 0.00 0.00 3.27
3835 5292 3.070015 AGGGGACAAACTTGCAAAATCAG 59.930 43.478 0.00 0.00 0.00 2.90
3836 5293 3.037549 AGGGGACAAACTTGCAAAATCA 58.962 40.909 0.00 0.00 0.00 2.57
3851 5308 2.500504 AGTAAATGAGGTCGAAGGGGAC 59.499 50.000 0.00 0.00 36.18 4.46
3855 5312 3.887621 TGGAGTAAATGAGGTCGAAGG 57.112 47.619 0.00 0.00 0.00 3.46
3866 5323 8.537728 TTCAATGAAATGCCTATGGAGTAAAT 57.462 30.769 0.00 0.00 0.00 1.40
3870 5327 6.381994 ACAATTCAATGAAATGCCTATGGAGT 59.618 34.615 10.66 0.00 0.00 3.85
3900 5357 4.386867 TCTGTTTGCGATACTCCCTTAG 57.613 45.455 0.00 0.00 0.00 2.18
3901 5358 4.755411 CTTCTGTTTGCGATACTCCCTTA 58.245 43.478 0.00 0.00 0.00 2.69
3902 5359 3.600388 CTTCTGTTTGCGATACTCCCTT 58.400 45.455 0.00 0.00 0.00 3.95
3904 5361 1.666189 GCTTCTGTTTGCGATACTCCC 59.334 52.381 0.00 0.00 0.00 4.30
3940 5464 5.790495 GTCATCAACGCACAGAACTATTTTC 59.210 40.000 0.00 0.00 0.00 2.29
3973 5513 2.028112 TGCGTAGAGAATGCCAAAGACT 60.028 45.455 0.00 0.00 39.57 3.24
3975 5515 2.621338 CTGCGTAGAGAATGCCAAAGA 58.379 47.619 0.00 0.00 39.57 2.52
3977 5517 1.003118 ACCTGCGTAGAGAATGCCAAA 59.997 47.619 0.53 0.00 39.57 3.28
3978 5518 0.613260 ACCTGCGTAGAGAATGCCAA 59.387 50.000 0.53 0.00 39.57 4.52
3982 5530 2.271800 GTGGAACCTGCGTAGAGAATG 58.728 52.381 0.53 0.00 0.00 2.67
3985 5533 1.557099 ATGTGGAACCTGCGTAGAGA 58.443 50.000 0.53 0.00 34.36 3.10
4003 5551 4.335315 CGTATCATGCAAACCTGGTTGTAT 59.665 41.667 13.79 9.39 34.59 2.29
4006 5554 2.746904 TCGTATCATGCAAACCTGGTTG 59.253 45.455 13.79 8.58 0.00 3.77
4009 5557 2.632377 ACTCGTATCATGCAAACCTGG 58.368 47.619 0.00 0.00 0.00 4.45
4010 5558 6.216569 ACTATACTCGTATCATGCAAACCTG 58.783 40.000 0.00 0.00 0.00 4.00
4011 5559 6.406692 ACTATACTCGTATCATGCAAACCT 57.593 37.500 0.00 0.00 0.00 3.50
4012 5560 6.807230 CCTACTATACTCGTATCATGCAAACC 59.193 42.308 0.00 0.00 0.00 3.27
4013 5561 6.308282 GCCTACTATACTCGTATCATGCAAAC 59.692 42.308 0.00 0.00 0.00 2.93
4015 5563 5.710567 AGCCTACTATACTCGTATCATGCAA 59.289 40.000 0.00 0.00 0.00 4.08
4016 5564 5.123979 CAGCCTACTATACTCGTATCATGCA 59.876 44.000 0.00 0.00 0.00 3.96
4019 5567 5.124138 GTGCAGCCTACTATACTCGTATCAT 59.876 44.000 0.00 0.00 0.00 2.45
4020 5568 4.454847 GTGCAGCCTACTATACTCGTATCA 59.545 45.833 0.00 0.00 0.00 2.15
4021 5569 4.142643 GGTGCAGCCTACTATACTCGTATC 60.143 50.000 4.03 0.00 0.00 2.24
4022 5570 3.757493 GGTGCAGCCTACTATACTCGTAT 59.243 47.826 4.03 0.00 0.00 3.06
4023 5571 3.144506 GGTGCAGCCTACTATACTCGTA 58.855 50.000 4.03 0.00 0.00 3.43
4025 5573 1.954382 TGGTGCAGCCTACTATACTCG 59.046 52.381 14.36 0.00 38.35 4.18
4027 5575 3.711704 ACAATGGTGCAGCCTACTATACT 59.288 43.478 14.36 0.00 38.35 2.12
4028 5576 4.073293 ACAATGGTGCAGCCTACTATAC 57.927 45.455 14.36 0.00 38.35 1.47
4029 5577 4.771114 AACAATGGTGCAGCCTACTATA 57.229 40.909 14.36 0.00 38.35 1.31
4030 5578 3.652057 AACAATGGTGCAGCCTACTAT 57.348 42.857 14.36 0.00 38.35 2.12
4031 5579 3.433306 AAACAATGGTGCAGCCTACTA 57.567 42.857 14.36 0.00 38.35 1.82
4032 5580 2.292828 AAACAATGGTGCAGCCTACT 57.707 45.000 14.36 0.00 38.35 2.57
4033 5581 2.159379 GCTAAACAATGGTGCAGCCTAC 60.159 50.000 14.36 0.00 38.35 3.18
4037 5585 0.890683 AGGCTAAACAATGGTGCAGC 59.109 50.000 9.47 9.47 35.15 5.25
4038 5586 1.403249 GCAGGCTAAACAATGGTGCAG 60.403 52.381 0.00 0.00 0.00 4.41
4042 5590 2.356135 CTACGCAGGCTAAACAATGGT 58.644 47.619 0.00 0.00 0.00 3.55
4044 5592 1.737236 TGCTACGCAGGCTAAACAATG 59.263 47.619 0.00 0.00 33.32 2.82
4052 5695 1.519455 GATTCGTGCTACGCAGGCT 60.519 57.895 3.86 0.00 43.03 4.58
4055 5698 4.143200 TGTTTTAAGATTCGTGCTACGCAG 60.143 41.667 4.15 0.00 42.21 5.18
4056 5699 3.741856 TGTTTTAAGATTCGTGCTACGCA 59.258 39.130 4.15 0.00 42.21 5.24
4059 5702 6.238130 GGGAGATGTTTTAAGATTCGTGCTAC 60.238 42.308 0.00 0.00 0.00 3.58
4065 5708 4.878397 AGCTGGGAGATGTTTTAAGATTCG 59.122 41.667 0.00 0.00 0.00 3.34
4069 5712 4.335416 CCAAGCTGGGAGATGTTTTAAGA 58.665 43.478 0.00 0.00 32.67 2.10
4071 5714 2.825532 GCCAAGCTGGGAGATGTTTTAA 59.174 45.455 12.85 0.00 38.19 1.52
4073 5716 1.260544 GCCAAGCTGGGAGATGTTTT 58.739 50.000 12.85 0.00 38.19 2.43
4079 5722 4.682714 AGGGGCCAAGCTGGGAGA 62.683 66.667 12.85 0.00 38.19 3.71
4089 5732 2.039879 GTCTGTCTCTAAAAAGGGGCCA 59.960 50.000 4.39 0.00 0.00 5.36
4094 5737 5.233988 CACCTCAGTCTGTCTCTAAAAAGG 58.766 45.833 0.00 0.00 0.00 3.11
4096 5739 4.503296 GCCACCTCAGTCTGTCTCTAAAAA 60.503 45.833 0.00 0.00 0.00 1.94
4102 5745 0.037790 GTGCCACCTCAGTCTGTCTC 60.038 60.000 0.00 0.00 0.00 3.36
4106 5749 1.665916 CACGTGCCACCTCAGTCTG 60.666 63.158 0.82 0.00 0.00 3.51
4109 5752 1.188219 AGATCACGTGCCACCTCAGT 61.188 55.000 11.67 0.00 0.00 3.41
4111 5754 1.293179 CAGATCACGTGCCACCTCA 59.707 57.895 11.67 0.00 0.00 3.86
4112 5755 0.320771 AACAGATCACGTGCCACCTC 60.321 55.000 11.67 2.44 0.00 3.85
4117 6809 2.094762 AACCTAACAGATCACGTGCC 57.905 50.000 11.67 5.10 0.00 5.01
4121 6813 5.776173 AGGAGATAACCTAACAGATCACG 57.224 43.478 0.00 0.00 38.65 4.35
4134 6826 5.187186 TGAGTGGACAAGGTTAGGAGATAAC 59.813 44.000 0.00 0.00 42.68 1.89
4138 6830 3.254093 TGAGTGGACAAGGTTAGGAGA 57.746 47.619 0.00 0.00 0.00 3.71
4146 6838 2.840651 AGGGACTAATGAGTGGACAAGG 59.159 50.000 0.00 0.00 36.02 3.61
4149 6841 3.791320 AGAAGGGACTAATGAGTGGACA 58.209 45.455 0.00 0.00 38.49 4.02
4157 6849 9.319143 CTTTGTGTAGATTAGAAGGGACTAATG 57.681 37.037 0.00 0.00 41.34 1.90
4182 6874 6.944862 AGACTTTATCTCAAATGGAAGCAACT 59.055 34.615 0.00 0.00 28.16 3.16
4183 6875 7.150783 AGACTTTATCTCAAATGGAAGCAAC 57.849 36.000 0.00 0.00 28.16 4.17
4210 6906 5.470098 ACAACATCGATGTGCTTCTTTTAGT 59.530 36.000 30.57 8.41 41.61 2.24
4211 6907 5.931532 ACAACATCGATGTGCTTCTTTTAG 58.068 37.500 30.57 12.67 41.61 1.85
4235 6935 5.186021 ACGAACCAATCATCTGAGTAGAACT 59.814 40.000 0.00 0.00 36.32 3.01
4242 6942 5.869344 TGAAACTACGAACCAATCATCTGAG 59.131 40.000 0.00 0.00 0.00 3.35
4283 6983 9.906660 AAACATGAATACGACATTTAACACATT 57.093 25.926 0.00 0.00 0.00 2.71
4284 6984 9.554724 GAAACATGAATACGACATTTAACACAT 57.445 29.630 0.00 0.00 0.00 3.21
4285 6985 7.742525 CGAAACATGAATACGACATTTAACACA 59.257 33.333 0.00 0.00 0.00 3.72
4286 6986 7.742963 ACGAAACATGAATACGACATTTAACAC 59.257 33.333 0.00 0.00 0.00 3.32
4287 6987 7.742525 CACGAAACATGAATACGACATTTAACA 59.257 33.333 0.00 0.00 0.00 2.41
4288 6988 7.742963 ACACGAAACATGAATACGACATTTAAC 59.257 33.333 0.00 0.00 0.00 2.01
4289 6989 7.798801 ACACGAAACATGAATACGACATTTAA 58.201 30.769 0.00 0.00 0.00 1.52
4290 6990 7.354025 ACACGAAACATGAATACGACATTTA 57.646 32.000 0.00 0.00 0.00 1.40
4291 6991 6.236017 ACACGAAACATGAATACGACATTT 57.764 33.333 0.00 0.00 0.00 2.32
4298 6998 8.846607 GTCCAAAATAACACGAAACATGAATAC 58.153 33.333 0.00 0.00 0.00 1.89
4300 7000 6.580791 CGTCCAAAATAACACGAAACATGAAT 59.419 34.615 0.00 0.00 34.06 2.57
4343 7044 0.597898 TTCAAACGATCGACCGTGCA 60.598 50.000 24.34 1.32 42.54 4.57
4368 7069 3.862267 CGAGATGAAGCTACTGGTCAAAG 59.138 47.826 0.00 0.00 0.00 2.77
4429 7130 7.969508 TGTAGATCTACTCGTCTATGACTATCG 59.030 40.741 28.53 0.00 37.00 2.92


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

AutoCloner maintained by Alex Coulton.