Multiple sequence alignment - TraesCS2D01G049500

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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 TraesCS2D01G049500 chr2D 100.000 5744 0 0 1 5744 18229525 18235268 0.000000e+00 10608
1 TraesCS2D01G049500 chr2D 90.878 888 53 16 1258 2131 50817762 50816889 0.000000e+00 1166
2 TraesCS2D01G049500 chrUn 90.130 5066 297 76 1 4996 12589510 12594442 0.000000e+00 6397
3 TraesCS2D01G049500 chrUn 93.447 763 37 7 4988 5741 12594546 12595304 0.000000e+00 1120
4 TraesCS2D01G049500 chrUn 89.782 871 73 9 4887 5744 178512287 178511420 0.000000e+00 1101
5 TraesCS2D01G049500 chrUn 89.323 871 77 9 4887 5744 178477362 178476495 0.000000e+00 1079
6 TraesCS2D01G049500 chr2B 92.851 2266 129 15 2014 4265 30156688 30158934 0.000000e+00 3256
7 TraesCS2D01G049500 chr2B 90.483 1450 89 22 4325 5744 30158931 30160361 0.000000e+00 1868
8 TraesCS2D01G049500 chr2B 89.667 871 74 9 4887 5744 30172831 30173698 0.000000e+00 1096
9 TraesCS2D01G049500 chr2B 89.667 871 74 9 4887 5744 30229100 30229967 0.000000e+00 1096
10 TraesCS2D01G049500 chr2B 89.437 871 76 9 4887 5744 30186550 30187417 0.000000e+00 1085
11 TraesCS2D01G049500 chr2B 89.208 871 75 10 4887 5744 30208064 30208928 0.000000e+00 1070
12 TraesCS2D01G049500 chr2B 88.848 816 66 17 1112 1914 30155883 30156686 0.000000e+00 979
13 TraesCS2D01G049500 chr2B 79.179 341 54 10 1 339 30154672 30154997 2.690000e-53 220
14 TraesCS2D01G049500 chr7D 90.929 893 59 13 1258 2136 539125164 539124280 0.000000e+00 1181
15 TraesCS2D01G049500 chr7D 90.370 893 60 15 1258 2136 577474987 577475867 0.000000e+00 1149
16 TraesCS2D01G049500 chr7D 90.268 894 61 12 1261 2136 8616116 8617001 0.000000e+00 1146
17 TraesCS2D01G049500 chr2A 93.447 763 37 7 4988 5741 19346327 19347085 0.000000e+00 1120
18 TraesCS2D01G049500 chr2A 89.651 889 68 14 1198 2072 160096765 160097643 0.000000e+00 1110
19 TraesCS2D01G049500 chr2A 89.815 108 10 1 2259 2366 40143168 40143062 2.790000e-28 137
20 TraesCS2D01G049500 chr3D 89.752 888 63 16 1258 2131 426387482 426386609 0.000000e+00 1110
21 TraesCS2D01G049500 chr3B 88.183 897 64 18 4820 5696 557609481 557608607 0.000000e+00 1031
22 TraesCS2D01G049500 chr4A 89.342 441 36 6 1261 1694 619801495 619801059 1.410000e-150 544


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 TraesCS2D01G049500 chr2D 18229525 18235268 5743 False 10608.00 10608 100.00000 1 5744 1 chr2D.!!$F1 5743
1 TraesCS2D01G049500 chr2D 50816889 50817762 873 True 1166.00 1166 90.87800 1258 2131 1 chr2D.!!$R1 873
2 TraesCS2D01G049500 chrUn 12589510 12595304 5794 False 3758.50 6397 91.78850 1 5741 2 chrUn.!!$F1 5740
3 TraesCS2D01G049500 chrUn 178511420 178512287 867 True 1101.00 1101 89.78200 4887 5744 1 chrUn.!!$R2 857
4 TraesCS2D01G049500 chrUn 178476495 178477362 867 True 1079.00 1079 89.32300 4887 5744 1 chrUn.!!$R1 857
5 TraesCS2D01G049500 chr2B 30154672 30160361 5689 False 1580.75 3256 87.84025 1 5744 4 chr2B.!!$F5 5743
6 TraesCS2D01G049500 chr2B 30172831 30173698 867 False 1096.00 1096 89.66700 4887 5744 1 chr2B.!!$F1 857
7 TraesCS2D01G049500 chr2B 30229100 30229967 867 False 1096.00 1096 89.66700 4887 5744 1 chr2B.!!$F4 857
8 TraesCS2D01G049500 chr2B 30186550 30187417 867 False 1085.00 1085 89.43700 4887 5744 1 chr2B.!!$F2 857
9 TraesCS2D01G049500 chr2B 30208064 30208928 864 False 1070.00 1070 89.20800 4887 5744 1 chr2B.!!$F3 857
10 TraesCS2D01G049500 chr7D 539124280 539125164 884 True 1181.00 1181 90.92900 1258 2136 1 chr7D.!!$R1 878
11 TraesCS2D01G049500 chr7D 577474987 577475867 880 False 1149.00 1149 90.37000 1258 2136 1 chr7D.!!$F2 878
12 TraesCS2D01G049500 chr7D 8616116 8617001 885 False 1146.00 1146 90.26800 1261 2136 1 chr7D.!!$F1 875
13 TraesCS2D01G049500 chr2A 19346327 19347085 758 False 1120.00 1120 93.44700 4988 5741 1 chr2A.!!$F1 753
14 TraesCS2D01G049500 chr2A 160096765 160097643 878 False 1110.00 1110 89.65100 1198 2072 1 chr2A.!!$F2 874
15 TraesCS2D01G049500 chr3D 426386609 426387482 873 True 1110.00 1110 89.75200 1258 2131 1 chr3D.!!$R1 873
16 TraesCS2D01G049500 chr3B 557608607 557609481 874 True 1031.00 1031 88.18300 4820 5696 1 chr3B.!!$R1 876

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
268 269 0.036952 CGACTCATGTGCCCTTGTCT 60.037 55.000 0.00 0.00 0.0 3.41 F
1533 1682 0.042731 TGGTGTCCCCTAGCTAGCTT 59.957 55.000 24.88 7.25 0.0 3.74 F
2065 2227 0.248012 ACACCGAACACACAGACACA 59.752 50.000 0.00 0.00 0.0 3.72 F
2072 2234 0.461870 ACACACAGACACACGCACAT 60.462 50.000 0.00 0.00 0.0 3.21 F
3504 3702 1.000843 GCGATCAAAGCCCCAAGTTTT 59.999 47.619 0.00 0.00 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2051 2213 0.026285 GTGCGTGTGTCTGTGTGTTC 59.974 55.0 0.00 0.0 0.00 3.18 R
3001 3199 0.591659 CATCAGCAATCATGGCTCCG 59.408 55.0 0.00 0.0 40.23 4.63 R
3734 3932 0.843309 TCCTTGCTGTCCCAAGTTGA 59.157 50.0 3.87 0.0 40.40 3.18 R
3779 3977 0.969149 CCGCATCTGCTATGAGGGTA 59.031 55.0 12.44 0.0 39.32 3.69 R
5228 5559 0.179240 CGCTGTGACAAGATGTTCGC 60.179 55.0 0.00 0.0 0.00 4.70 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
68 69 7.387673 AGCCAAACAAAAGGTTATTGCTTATTC 59.612 33.333 0.00 0.00 39.29 1.75
128 129 9.397280 TCTCGCATGCTTATCTATAACTATAGT 57.603 33.333 17.13 0.00 37.51 2.12
195 196 2.972505 CGGCTGGTCGCAAGTTGT 60.973 61.111 4.48 0.00 41.67 3.32
265 266 0.518636 CAACGACTCATGTGCCCTTG 59.481 55.000 0.00 0.00 0.00 3.61
267 268 0.320771 ACGACTCATGTGCCCTTGTC 60.321 55.000 0.00 0.00 0.00 3.18
268 269 0.036952 CGACTCATGTGCCCTTGTCT 60.037 55.000 0.00 0.00 0.00 3.41
269 270 1.446907 GACTCATGTGCCCTTGTCTG 58.553 55.000 0.00 0.00 0.00 3.51
270 271 0.607489 ACTCATGTGCCCTTGTCTGC 60.607 55.000 0.00 0.00 0.00 4.26
271 272 1.642037 CTCATGTGCCCTTGTCTGCG 61.642 60.000 0.00 0.00 0.00 5.18
277 280 2.281761 CCCTTGTCTGCGGCAACT 60.282 61.111 3.44 0.00 0.00 3.16
290 293 3.118920 TGCGGCAACTAGTCTAATGCTTA 60.119 43.478 15.07 2.22 38.79 3.09
306 309 8.543774 TCTAATGCTTATCTCCTTTCTTCAGTT 58.456 33.333 0.00 0.00 0.00 3.16
307 310 9.171877 CTAATGCTTATCTCCTTTCTTCAGTTT 57.828 33.333 0.00 0.00 0.00 2.66
313 317 4.499472 TCTCCTTTCTTCAGTTTCCCCTA 58.501 43.478 0.00 0.00 0.00 3.53
323 327 2.598787 TTTCCCCTACTGCCACCGG 61.599 63.158 0.00 0.00 0.00 5.28
344 348 0.321564 CGATCCACCTGCCTTTGTCA 60.322 55.000 0.00 0.00 0.00 3.58
346 350 0.773644 ATCCACCTGCCTTTGTCACT 59.226 50.000 0.00 0.00 0.00 3.41
347 351 0.550914 TCCACCTGCCTTTGTCACTT 59.449 50.000 0.00 0.00 0.00 3.16
354 358 1.391157 GCCTTTGTCACTTGTGGCCA 61.391 55.000 0.00 0.00 34.81 5.36
423 427 0.802222 CCATCGTCGTGCATTCGTCT 60.802 55.000 0.00 0.00 0.00 4.18
458 462 1.209275 CTAAAGCTCGCGCGCACTAT 61.209 55.000 32.61 13.58 42.32 2.12
489 493 1.013596 TAGCCCGCAATTGAATCGTG 58.986 50.000 10.34 0.00 0.00 4.35
498 502 2.672874 CAATTGAATCGTGAAGCTCCGA 59.327 45.455 0.00 5.69 37.51 4.55
522 526 2.755876 TCCGCCTGAGACATCGCT 60.756 61.111 0.00 0.00 0.00 4.93
542 546 1.431036 CGAGCTGCATCGTCTCTGA 59.569 57.895 1.02 0.00 37.91 3.27
551 555 2.544685 CATCGTCTCTGACCATGGTTC 58.455 52.381 20.85 12.76 29.80 3.62
557 561 2.632996 TCTCTGACCATGGTTCGTTCTT 59.367 45.455 20.85 0.00 0.00 2.52
599 603 2.202932 CCAGGCATCGCTACGCTT 60.203 61.111 0.00 0.00 0.00 4.68
600 604 2.528743 CCAGGCATCGCTACGCTTG 61.529 63.158 0.00 0.00 35.19 4.01
642 646 1.674764 CTCAGTGCCGCTCCTCATCT 61.675 60.000 0.00 0.00 0.00 2.90
656 660 2.965147 CCTCATCTCCTCCTTCCTTCTC 59.035 54.545 0.00 0.00 0.00 2.87
657 661 2.965147 CTCATCTCCTCCTTCCTTCTCC 59.035 54.545 0.00 0.00 0.00 3.71
666 670 2.435805 TCCTTCCTTCTCCCATGAATCG 59.564 50.000 0.00 0.00 0.00 3.34
684 688 2.785562 TCGACCAACCCAAATTCGAAT 58.214 42.857 4.39 4.39 35.86 3.34
685 689 3.940319 TCGACCAACCCAAATTCGAATA 58.060 40.909 11.83 0.00 35.86 1.75
687 691 5.672503 TCGACCAACCCAAATTCGAATATA 58.327 37.500 11.83 0.00 35.86 0.86
698 724 6.249893 CCAAATTCGAATATATTGCGCTCATG 59.750 38.462 11.83 0.00 0.00 3.07
702 732 5.108517 TCGAATATATTGCGCTCATGCATA 58.891 37.500 9.73 0.00 45.78 3.14
719 749 9.569167 CTCATGCATACAATCAATTCCATAATC 57.431 33.333 0.00 0.00 0.00 1.75
754 784 8.596293 AGAATACAAAATTCAAATCCACACCAT 58.404 29.630 1.01 0.00 0.00 3.55
771 801 2.038820 ACCATTTTCACCTTTGCCCATG 59.961 45.455 0.00 0.00 0.00 3.66
772 802 2.078392 CATTTTCACCTTTGCCCATGC 58.922 47.619 0.00 0.00 38.26 4.06
773 803 0.396060 TTTTCACCTTTGCCCATGCC 59.604 50.000 0.00 0.00 36.33 4.40
774 804 0.762082 TTTCACCTTTGCCCATGCCA 60.762 50.000 0.00 0.00 36.33 4.92
775 805 0.762082 TTCACCTTTGCCCATGCCAA 60.762 50.000 0.00 0.00 36.33 4.52
776 806 0.762082 TCACCTTTGCCCATGCCAAA 60.762 50.000 8.77 8.77 36.33 3.28
778 808 0.397564 ACCTTTGCCCATGCCAAAAG 59.602 50.000 9.92 7.77 36.33 2.27
780 810 0.956902 CTTTGCCCATGCCAAAAGCC 60.957 55.000 9.92 0.00 42.71 4.35
781 811 2.408880 TTTGCCCATGCCAAAAGCCC 62.409 55.000 7.14 0.00 42.71 5.19
782 812 4.100084 GCCCATGCCAAAAGCCCC 62.100 66.667 0.00 0.00 42.71 5.80
783 813 3.401804 CCCATGCCAAAAGCCCCC 61.402 66.667 0.00 0.00 42.71 5.40
784 814 2.284847 CCATGCCAAAAGCCCCCT 60.285 61.111 0.00 0.00 42.71 4.79
785 815 1.001503 CCATGCCAAAAGCCCCCTA 59.998 57.895 0.00 0.00 42.71 3.53
786 816 0.617249 CCATGCCAAAAGCCCCCTAA 60.617 55.000 0.00 0.00 42.71 2.69
787 817 1.274712 CATGCCAAAAGCCCCCTAAA 58.725 50.000 0.00 0.00 42.71 1.85
788 818 1.839354 CATGCCAAAAGCCCCCTAAAT 59.161 47.619 0.00 0.00 42.71 1.40
789 819 2.930109 TGCCAAAAGCCCCCTAAATA 57.070 45.000 0.00 0.00 42.71 1.40
790 820 2.462723 TGCCAAAAGCCCCCTAAATAC 58.537 47.619 0.00 0.00 42.71 1.89
791 821 2.043801 TGCCAAAAGCCCCCTAAATACT 59.956 45.455 0.00 0.00 42.71 2.12
792 822 2.693591 GCCAAAAGCCCCCTAAATACTC 59.306 50.000 0.00 0.00 34.35 2.59
793 823 3.296854 CCAAAAGCCCCCTAAATACTCC 58.703 50.000 0.00 0.00 0.00 3.85
794 824 3.052869 CCAAAAGCCCCCTAAATACTCCT 60.053 47.826 0.00 0.00 0.00 3.69
795 825 4.167307 CCAAAAGCCCCCTAAATACTCCTA 59.833 45.833 0.00 0.00 0.00 2.94
796 826 5.162980 CCAAAAGCCCCCTAAATACTCCTAT 60.163 44.000 0.00 0.00 0.00 2.57
797 827 5.584551 AAAGCCCCCTAAATACTCCTATG 57.415 43.478 0.00 0.00 0.00 2.23
798 828 4.229718 AGCCCCCTAAATACTCCTATGT 57.770 45.455 0.00 0.00 0.00 2.29
799 829 5.364620 AGCCCCCTAAATACTCCTATGTA 57.635 43.478 0.00 0.00 0.00 2.29
800 830 5.734078 AGCCCCCTAAATACTCCTATGTAA 58.266 41.667 0.00 0.00 0.00 2.41
801 831 5.546887 AGCCCCCTAAATACTCCTATGTAAC 59.453 44.000 0.00 0.00 0.00 2.50
802 832 5.308759 GCCCCCTAAATACTCCTATGTAACA 59.691 44.000 0.00 0.00 0.00 2.41
844 874 2.232298 GAGACGCCTCAACCCCTCTG 62.232 65.000 0.00 0.00 39.24 3.35
856 886 2.234296 CCCTCTGCCTCCAAACCCT 61.234 63.158 0.00 0.00 0.00 4.34
857 887 1.001641 CCTCTGCCTCCAAACCCTG 60.002 63.158 0.00 0.00 0.00 4.45
858 888 1.763770 CTCTGCCTCCAAACCCTGT 59.236 57.895 0.00 0.00 0.00 4.00
859 889 0.322008 CTCTGCCTCCAAACCCTGTC 60.322 60.000 0.00 0.00 0.00 3.51
860 890 1.303643 CTGCCTCCAAACCCTGTCC 60.304 63.158 0.00 0.00 0.00 4.02
893 924 1.244019 AAAGCCACGCAACCTCATCC 61.244 55.000 0.00 0.00 0.00 3.51
926 958 0.247460 CTCACCGTTCTGCCTCATCA 59.753 55.000 0.00 0.00 0.00 3.07
928 960 1.081892 CACCGTTCTGCCTCATCAAG 58.918 55.000 0.00 0.00 0.00 3.02
968 1000 2.432510 CTCCACCTTATCCTCACCTCAC 59.567 54.545 0.00 0.00 0.00 3.51
973 1005 2.432510 CCTTATCCTCACCTCACCTCAC 59.567 54.545 0.00 0.00 0.00 3.51
978 1010 0.894141 CTCACCTCACCTCACCTCAG 59.106 60.000 0.00 0.00 0.00 3.35
979 1011 1.188219 TCACCTCACCTCACCTCAGC 61.188 60.000 0.00 0.00 0.00 4.26
980 1012 1.157276 ACCTCACCTCACCTCAGCT 59.843 57.895 0.00 0.00 0.00 4.24
1140 1268 2.587194 CCTCAATCTGCGGCCTCG 60.587 66.667 0.00 0.00 39.81 4.63
1156 1284 2.202427 CGTTGGCCGAATTTCCGC 60.202 61.111 0.00 1.64 39.56 5.54
1157 1285 2.958576 GTTGGCCGAATTTCCGCA 59.041 55.556 11.04 0.00 0.00 5.69
1158 1286 1.510844 GTTGGCCGAATTTCCGCAT 59.489 52.632 11.04 0.00 0.00 4.73
1159 1287 0.801836 GTTGGCCGAATTTCCGCATG 60.802 55.000 11.04 0.00 0.00 4.06
1160 1288 1.247419 TTGGCCGAATTTCCGCATGT 61.247 50.000 11.04 0.00 0.00 3.21
1161 1289 1.226660 GGCCGAATTTCCGCATGTG 60.227 57.895 11.04 0.00 0.00 3.21
1162 1290 1.506262 GCCGAATTTCCGCATGTGT 59.494 52.632 5.38 0.00 0.00 3.72
1163 1291 0.109319 GCCGAATTTCCGCATGTGTT 60.109 50.000 5.38 0.00 0.00 3.32
1164 1292 1.668628 GCCGAATTTCCGCATGTGTTT 60.669 47.619 5.38 0.00 0.00 2.83
1165 1293 2.671596 CCGAATTTCCGCATGTGTTTT 58.328 42.857 5.38 0.00 0.00 2.43
1166 1294 3.056304 CCGAATTTCCGCATGTGTTTTT 58.944 40.909 5.38 0.00 0.00 1.94
1192 1325 3.951306 TGAATTGTGTGTTCTTGCGAAG 58.049 40.909 0.00 0.00 0.00 3.79
1204 1337 0.313672 TTGCGAAGTTGTGATTGCCC 59.686 50.000 0.00 0.00 0.00 5.36
1251 1385 1.892474 CCGGGTTGATGTGAAATTGGT 59.108 47.619 0.00 0.00 0.00 3.67
1252 1386 3.085533 CCGGGTTGATGTGAAATTGGTA 58.914 45.455 0.00 0.00 0.00 3.25
1253 1387 3.508012 CCGGGTTGATGTGAAATTGGTAA 59.492 43.478 0.00 0.00 0.00 2.85
1254 1388 4.021894 CCGGGTTGATGTGAAATTGGTAAA 60.022 41.667 0.00 0.00 0.00 2.01
1264 1399 5.419155 TGTGAAATTGGTAAAGGTTGTGACA 59.581 36.000 0.00 0.00 0.00 3.58
1460 1595 2.501128 GTGATGCTCAGCCGCCTA 59.499 61.111 0.00 0.00 0.00 3.93
1462 1597 0.948141 GTGATGCTCAGCCGCCTATC 60.948 60.000 0.00 0.00 0.00 2.08
1477 1617 2.072298 CCTATCTAATTGCAGCTCGCC 58.928 52.381 5.82 0.00 41.33 5.54
1484 1625 1.180029 ATTGCAGCTCGCCTTTCATT 58.820 45.000 5.82 0.00 41.33 2.57
1519 1664 2.695127 TTTCCGTGTTACTGTGGTGT 57.305 45.000 0.00 0.00 0.00 4.16
1522 1671 0.601841 CCGTGTTACTGTGGTGTCCC 60.602 60.000 0.00 0.00 0.00 4.46
1529 1678 0.412244 ACTGTGGTGTCCCCTAGCTA 59.588 55.000 0.00 0.00 0.00 3.32
1530 1679 1.115467 CTGTGGTGTCCCCTAGCTAG 58.885 60.000 14.20 14.20 0.00 3.42
1531 1680 0.976073 TGTGGTGTCCCCTAGCTAGC 60.976 60.000 15.74 6.62 0.00 3.42
1532 1681 0.688087 GTGGTGTCCCCTAGCTAGCT 60.688 60.000 23.12 23.12 0.00 3.32
1533 1682 0.042731 TGGTGTCCCCTAGCTAGCTT 59.957 55.000 24.88 7.25 0.00 3.74
1590 1740 1.055849 TCTGCTGCCAAACCTGACTA 58.944 50.000 0.00 0.00 0.00 2.59
1605 1755 4.159879 ACCTGACTACGTGCTAGCTAATTT 59.840 41.667 17.23 0.00 0.00 1.82
1606 1756 5.109903 CCTGACTACGTGCTAGCTAATTTT 58.890 41.667 17.23 0.00 0.00 1.82
1914 2070 4.319477 CGTACCAAGATTGAACACAACCTG 60.319 45.833 0.00 0.00 0.00 4.00
2044 2206 8.947115 AGATTACTAAGCAATACAAGACCAAAC 58.053 33.333 0.00 0.00 0.00 2.93
2051 2213 4.286910 CAATACAAGACCAAACAACACCG 58.713 43.478 0.00 0.00 0.00 4.94
2059 2221 1.200252 CCAAACAACACCGAACACACA 59.800 47.619 0.00 0.00 0.00 3.72
2060 2222 2.514902 CAAACAACACCGAACACACAG 58.485 47.619 0.00 0.00 0.00 3.66
2061 2223 2.102070 AACAACACCGAACACACAGA 57.898 45.000 0.00 0.00 0.00 3.41
2062 2224 1.365699 ACAACACCGAACACACAGAC 58.634 50.000 0.00 0.00 0.00 3.51
2063 2225 1.338294 ACAACACCGAACACACAGACA 60.338 47.619 0.00 0.00 0.00 3.41
2064 2226 1.062002 CAACACCGAACACACAGACAC 59.938 52.381 0.00 0.00 0.00 3.67
2065 2227 0.248012 ACACCGAACACACAGACACA 59.752 50.000 0.00 0.00 0.00 3.72
2066 2228 0.650512 CACCGAACACACAGACACAC 59.349 55.000 0.00 0.00 0.00 3.82
2072 2234 0.461870 ACACACAGACACACGCACAT 60.462 50.000 0.00 0.00 0.00 3.21
2090 2264 7.164990 CACGCACATTTCGTATTATTTGCATAA 59.835 33.333 0.00 0.00 38.19 1.90
2158 2332 8.812147 AACTAGCTACTTAATTTTTGTTTGCC 57.188 30.769 0.00 0.00 0.00 4.52
2159 2333 7.947282 ACTAGCTACTTAATTTTTGTTTGCCA 58.053 30.769 0.00 0.00 0.00 4.92
2256 2437 9.236691 TCATTTTCTGAAACGAAAGAAGAAATG 57.763 29.630 1.58 0.23 36.89 2.32
2265 2446 6.687081 ACGAAAGAAGAAATGTTGGTGTTA 57.313 33.333 0.00 0.00 0.00 2.41
2276 2457 7.599998 AGAAATGTTGGTGTTAAATTGCAGATC 59.400 33.333 0.00 0.00 0.00 2.75
2302 2483 5.247862 TGTCATGCAAGCTCTAATCTTTGA 58.752 37.500 0.00 0.00 0.00 2.69
2304 2485 6.026513 GTCATGCAAGCTCTAATCTTTGAAC 58.973 40.000 0.00 0.00 0.00 3.18
2414 2595 3.444029 AGCTAACCCAATGGAAAATGCT 58.556 40.909 0.00 0.78 34.81 3.79
2517 2698 3.758023 TCCTAATGCATGTTGTCCACTTG 59.242 43.478 0.00 0.00 34.32 3.16
2539 2720 5.316167 TGTTCATGATTGAAGGTTGCTAGT 58.684 37.500 0.00 0.00 42.41 2.57
2686 2867 3.077359 CAAAACTGTCCAGGGTCTGATC 58.923 50.000 0.00 0.00 32.44 2.92
2820 3015 6.474140 TGTGACAACAAGGTAGTCTTTCTA 57.526 37.500 0.00 0.00 32.41 2.10
2888 3083 1.976045 GCGCCTAATTTGACGTTTGTG 59.024 47.619 0.00 0.00 0.00 3.33
2896 3091 6.359617 CCTAATTTGACGTTTGTGCTTTAGTG 59.640 38.462 0.00 0.00 0.00 2.74
2951 3149 7.510675 AATAGGTTCCTAACTTGGATTCTGA 57.489 36.000 2.53 0.00 35.83 3.27
3001 3199 5.348986 TCTGCTGGTAACGATGAACTTATC 58.651 41.667 0.00 0.00 42.51 1.75
3064 3262 1.201647 GGTGTCCTTTCGATCGAGTCA 59.798 52.381 18.54 8.18 0.00 3.41
3236 3434 9.136323 TCTCTTCCTGAAGCTTTCTTAAATTTT 57.864 29.630 0.00 0.00 38.28 1.82
3238 3436 8.143835 TCTTCCTGAAGCTTTCTTAAATTTTGG 58.856 33.333 0.00 0.00 38.28 3.28
3441 3639 1.234821 TTACTGGTGAAGCTTTGGCG 58.765 50.000 0.00 0.00 44.37 5.69
3504 3702 1.000843 GCGATCAAAGCCCCAAGTTTT 59.999 47.619 0.00 0.00 0.00 2.43
3680 3878 6.641474 ACTTATCCTACAACTACTTTCAGGC 58.359 40.000 0.00 0.00 0.00 4.85
3686 3884 1.728971 CAACTACTTTCAGGCGCTGAG 59.271 52.381 7.64 0.81 41.75 3.35
3692 3890 1.476891 CTTTCAGGCGCTGAGTACCTA 59.523 52.381 7.64 0.00 41.75 3.08
3779 3977 5.745312 TCACAATCCATCAGACTACAACT 57.255 39.130 0.00 0.00 0.00 3.16
3971 4169 2.487428 CTCGAGGACCGTCAGCTG 59.513 66.667 7.63 7.63 39.75 4.24
4061 4259 1.135083 GCGTATGTGCACCTGTCTACT 60.135 52.381 15.69 0.00 34.15 2.57
4064 4262 4.103357 CGTATGTGCACCTGTCTACTTAC 58.897 47.826 15.69 0.00 0.00 2.34
4070 4268 1.475682 CACCTGTCTACTTACGTCCCC 59.524 57.143 0.00 0.00 0.00 4.81
4085 4283 0.675522 TCCCCGCGATCAAAGAAACC 60.676 55.000 8.23 0.00 0.00 3.27
4097 4295 4.651778 TCAAAGAAACCATCGAAGACCAT 58.348 39.130 0.00 0.00 42.51 3.55
4100 4298 4.494091 AGAAACCATCGAAGACCATGAT 57.506 40.909 0.00 0.00 42.51 2.45
4127 4325 2.821378 CCTTGGTGCTGACATCATTCAA 59.179 45.455 0.00 0.00 36.60 2.69
4174 4372 7.439356 CGATATGTTGATGGACTGAACTACATT 59.561 37.037 0.00 0.00 32.97 2.71
4188 4386 7.551974 ACTGAACTACATTGATCTCTTTCATGG 59.448 37.037 0.00 0.00 0.00 3.66
4189 4387 7.623630 TGAACTACATTGATCTCTTTCATGGA 58.376 34.615 0.00 0.00 0.00 3.41
4193 4391 8.105829 ACTACATTGATCTCTTTCATGGAAACT 58.894 33.333 0.00 0.00 0.00 2.66
4277 4477 7.869937 GCTTGTCTATACTGATAGAGAATGCAA 59.130 37.037 0.00 7.47 43.38 4.08
4279 4479 7.661968 TGTCTATACTGATAGAGAATGCAACC 58.338 38.462 0.00 0.00 43.84 3.77
4286 4486 2.957402 AGAGAATGCAACCAAGGACA 57.043 45.000 0.00 0.00 0.00 4.02
4359 4559 2.680339 GTTTCAGGCTAAGGATGTGAGC 59.320 50.000 0.00 0.00 35.39 4.26
4381 4581 5.867716 AGCCACAATACTTTAGTACTTGTCG 59.132 40.000 0.00 0.00 33.87 4.35
4423 4623 4.691326 TGTGGAATAACACCTGTGTACA 57.309 40.909 2.92 0.00 44.13 2.90
4426 4626 5.304871 TGTGGAATAACACCTGTGTACAGTA 59.695 40.000 10.80 0.00 44.13 2.74
4433 4633 6.415206 AACACCTGTGTACAGTACTTACAT 57.585 37.500 12.07 3.68 44.13 2.29
4436 4636 7.954835 ACACCTGTGTACAGTACTTACATTAA 58.045 34.615 12.07 8.38 42.90 1.40
4698 4898 2.815647 GTCGAGAAGCCCAAGCCG 60.816 66.667 0.00 0.00 41.25 5.52
4704 4904 3.927481 GAAGCCCAAGCCGAAGCCT 62.927 63.158 0.00 0.00 41.25 4.58
4745 4945 1.519719 GGCAGCTCTCCGTCTGATT 59.480 57.895 0.00 0.00 32.26 2.57
4761 4965 6.036470 CGTCTGATTGAGCTGTATGTAAAGA 58.964 40.000 0.00 0.00 0.00 2.52
4782 4986 1.954362 CTCTTCAGGCCTCCTCCGTG 61.954 65.000 0.00 0.00 0.00 4.94
4804 5011 6.292865 CGTGTTTTTAGATGCTTCAGTTCAGA 60.293 38.462 2.07 0.00 0.00 3.27
4885 5095 2.368655 AGGATTGCCATTTTTGCGAC 57.631 45.000 0.00 0.00 36.29 5.19
4895 5105 1.850377 TTTTTGCGACTCGAACGGTA 58.150 45.000 1.63 0.00 0.00 4.02
4937 5152 7.448420 TCTGAACTCTTGTGAATCAGAGAAAT 58.552 34.615 5.20 0.00 38.86 2.17
4938 5153 8.588472 TCTGAACTCTTGTGAATCAGAGAAATA 58.412 33.333 5.20 0.00 38.86 1.40
4942 5158 8.729805 ACTCTTGTGAATCAGAGAAATATTCC 57.270 34.615 5.20 0.00 33.09 3.01
4984 5200 8.807948 AAATAAATACTGATAACACCACAGCT 57.192 30.769 0.00 0.00 35.38 4.24
5062 5391 4.011698 TGCACATCACATATTTCACTGCT 58.988 39.130 0.00 0.00 0.00 4.24
5389 5729 4.087892 CACTCGTCCAGCCCCAGG 62.088 72.222 0.00 0.00 0.00 4.45
5432 5772 4.790962 CCTGCAGCTGGGCGATGT 62.791 66.667 17.12 0.00 36.28 3.06
5660 6006 0.818040 GAGGACGGAGGAGAGAGCTC 60.818 65.000 5.27 5.27 40.54 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 5.450818 TTTGTTTGGCTCATATAGGACCT 57.549 39.130 0.00 0.00 0.00 3.85
93 94 5.530171 AGATAAGCATGCGAGATCAACATTT 59.470 36.000 22.99 8.41 0.00 2.32
98 99 7.606349 AGTTATAGATAAGCATGCGAGATCAA 58.394 34.615 22.99 11.72 0.00 2.57
131 132 8.316046 GCATGATCAACATTCGAATAAAGTTTG 58.684 33.333 10.97 9.25 37.07 2.93
132 133 8.028354 TGCATGATCAACATTCGAATAAAGTTT 58.972 29.630 10.97 0.00 37.07 2.66
133 134 7.537715 TGCATGATCAACATTCGAATAAAGTT 58.462 30.769 10.97 8.36 37.07 2.66
134 135 7.087409 TGCATGATCAACATTCGAATAAAGT 57.913 32.000 10.97 1.77 37.07 2.66
135 136 9.836076 ATATGCATGATCAACATTCGAATAAAG 57.164 29.630 10.97 1.07 37.07 1.85
140 141 8.782339 AGATATATGCATGATCAACATTCGAA 57.218 30.769 19.78 0.00 37.07 3.71
142 143 8.193250 TGAGATATATGCATGATCAACATTCG 57.807 34.615 19.78 0.00 37.07 3.34
143 144 9.937175 CATGAGATATATGCATGATCAACATTC 57.063 33.333 19.78 10.48 41.35 2.67
144 145 9.462606 ACATGAGATATATGCATGATCAACATT 57.537 29.630 22.56 9.54 41.35 2.71
146 147 9.595823 CTACATGAGATATATGCATGATCAACA 57.404 33.333 22.56 18.23 41.35 3.33
147 148 9.043079 CCTACATGAGATATATGCATGATCAAC 57.957 37.037 22.56 14.81 41.35 3.18
148 149 8.208903 CCCTACATGAGATATATGCATGATCAA 58.791 37.037 22.56 11.37 41.35 2.57
149 150 7.202066 CCCCTACATGAGATATATGCATGATCA 60.202 40.741 22.56 0.00 41.35 2.92
150 151 7.015974 TCCCCTACATGAGATATATGCATGATC 59.984 40.741 22.56 11.98 41.35 2.92
151 152 6.848099 TCCCCTACATGAGATATATGCATGAT 59.152 38.462 22.56 2.15 41.35 2.45
152 153 6.098838 GTCCCCTACATGAGATATATGCATGA 59.901 42.308 22.56 0.00 41.35 3.07
153 154 6.286758 GTCCCCTACATGAGATATATGCATG 58.713 44.000 10.16 17.45 43.70 4.06
154 155 5.367937 GGTCCCCTACATGAGATATATGCAT 59.632 44.000 3.79 3.79 0.00 3.96
155 156 4.716784 GGTCCCCTACATGAGATATATGCA 59.283 45.833 0.00 0.00 0.00 3.96
183 184 6.576551 TTATTTTTCAAACAACTTGCGACC 57.423 33.333 0.00 0.00 34.76 4.79
195 196 8.260818 TCAACTGACCACCAATTATTTTTCAAA 58.739 29.630 0.00 0.00 0.00 2.69
265 266 2.649331 TTAGACTAGTTGCCGCAGAC 57.351 50.000 0.00 0.00 0.00 3.51
267 268 1.594862 GCATTAGACTAGTTGCCGCAG 59.405 52.381 6.06 0.00 0.00 5.18
268 269 1.207089 AGCATTAGACTAGTTGCCGCA 59.793 47.619 12.56 0.00 35.71 5.69
269 270 1.941325 AGCATTAGACTAGTTGCCGC 58.059 50.000 12.56 5.60 35.71 6.53
270 271 5.533482 AGATAAGCATTAGACTAGTTGCCG 58.467 41.667 12.56 0.00 35.71 5.69
271 272 5.929415 GGAGATAAGCATTAGACTAGTTGCC 59.071 44.000 12.56 0.00 35.71 4.52
277 280 9.201989 TGAAGAAAGGAGATAAGCATTAGACTA 57.798 33.333 0.00 0.00 31.76 2.59
290 293 3.919554 AGGGGAAACTGAAGAAAGGAGAT 59.080 43.478 0.00 0.00 0.00 2.75
306 309 3.006728 CCGGTGGCAGTAGGGGAA 61.007 66.667 0.00 0.00 0.00 3.97
307 310 4.326227 ACCGGTGGCAGTAGGGGA 62.326 66.667 6.12 0.00 0.00 4.81
313 317 3.771160 GGATCGACCGGTGGCAGT 61.771 66.667 14.63 0.00 0.00 4.40
323 327 0.321653 ACAAAGGCAGGTGGATCGAC 60.322 55.000 0.00 0.00 0.00 4.20
354 358 4.715130 TAGTGCAGGAGGGGCGGT 62.715 66.667 0.00 0.00 0.00 5.68
360 364 0.392193 CACAAGGCTAGTGCAGGAGG 60.392 60.000 0.00 0.00 41.91 4.30
389 393 1.229951 ATGGGTGGAGCTGAGGGAA 60.230 57.895 0.00 0.00 0.00 3.97
423 427 1.596006 TTAGGGGGATGGTCGAGGGA 61.596 60.000 0.00 0.00 0.00 4.20
489 493 4.516195 GAGGCGGGTCGGAGCTTC 62.516 72.222 7.19 0.00 32.57 3.86
508 512 3.260483 CGCAGCGATGTCTCAGGC 61.260 66.667 9.98 0.00 0.00 4.85
511 515 2.202663 GCTCGCAGCGATGTCTCA 60.203 61.111 19.91 0.00 34.61 3.27
532 536 1.135139 CGAACCATGGTCAGAGACGAT 59.865 52.381 20.07 0.00 31.45 3.73
542 546 1.142060 TGTCCAAGAACGAACCATGGT 59.858 47.619 13.00 13.00 32.90 3.55
551 555 0.593128 CAAGGCCTTGTCCAAGAACG 59.407 55.000 33.46 7.51 40.79 3.95
579 583 4.609018 CGTAGCGATGCCTGGGGG 62.609 72.222 0.00 0.00 0.00 5.40
621 625 4.828925 GAGGAGCGGCACTGAGGC 62.829 72.222 1.45 0.00 39.93 4.70
623 627 1.227205 GATGAGGAGCGGCACTGAG 60.227 63.158 1.45 0.00 0.00 3.35
626 630 2.430610 GGAGATGAGGAGCGGCACT 61.431 63.158 1.45 0.00 0.00 4.40
627 631 2.107953 GGAGATGAGGAGCGGCAC 59.892 66.667 1.45 0.00 0.00 5.01
632 636 1.047801 GGAAGGAGGAGATGAGGAGC 58.952 60.000 0.00 0.00 0.00 4.70
633 637 2.773525 AGGAAGGAGGAGATGAGGAG 57.226 55.000 0.00 0.00 0.00 3.69
642 646 1.366082 TCATGGGAGAAGGAAGGAGGA 59.634 52.381 0.00 0.00 0.00 3.71
656 660 0.034574 TGGGTTGGTCGATTCATGGG 60.035 55.000 0.00 0.00 0.00 4.00
657 661 1.832883 TTGGGTTGGTCGATTCATGG 58.167 50.000 0.00 0.00 0.00 3.66
666 670 6.640907 GCAATATATTCGAATTTGGGTTGGTC 59.359 38.462 17.19 0.00 0.00 4.02
684 688 5.642919 TGATTGTATGCATGAGCGCAATATA 59.357 36.000 11.47 0.00 46.87 0.86
685 689 4.456566 TGATTGTATGCATGAGCGCAATAT 59.543 37.500 11.47 0.00 46.87 1.28
687 691 2.619646 TGATTGTATGCATGAGCGCAAT 59.380 40.909 11.47 11.34 46.87 3.56
728 758 7.961351 TGGTGTGGATTTGAATTTTGTATTCT 58.039 30.769 0.00 0.00 0.00 2.40
739 769 4.653341 AGGTGAAAATGGTGTGGATTTGAA 59.347 37.500 0.00 0.00 0.00 2.69
754 784 0.396060 GGCATGGGCAAAGGTGAAAA 59.604 50.000 0.00 0.00 43.71 2.29
771 801 2.693591 GAGTATTTAGGGGGCTTTTGGC 59.306 50.000 0.00 0.00 45.19 4.52
772 802 3.052869 AGGAGTATTTAGGGGGCTTTTGG 60.053 47.826 0.00 0.00 0.00 3.28
773 803 4.251103 AGGAGTATTTAGGGGGCTTTTG 57.749 45.455 0.00 0.00 0.00 2.44
774 804 5.435373 ACATAGGAGTATTTAGGGGGCTTTT 59.565 40.000 0.00 0.00 0.00 2.27
775 805 4.982302 ACATAGGAGTATTTAGGGGGCTTT 59.018 41.667 0.00 0.00 0.00 3.51
776 806 4.578128 ACATAGGAGTATTTAGGGGGCTT 58.422 43.478 0.00 0.00 0.00 4.35
778 808 5.308759 TGTTACATAGGAGTATTTAGGGGGC 59.691 44.000 0.00 0.00 0.00 5.80
780 810 9.689501 TTTTTGTTACATAGGAGTATTTAGGGG 57.310 33.333 0.00 0.00 0.00 4.79
824 854 3.358076 GAGGGGTTGAGGCGTCTCG 62.358 68.421 13.21 0.00 42.79 4.04
844 874 1.002011 GAGGACAGGGTTTGGAGGC 60.002 63.158 0.00 0.00 0.00 4.70
856 886 3.330701 GCTTTATATGGGGATGGAGGACA 59.669 47.826 0.00 0.00 0.00 4.02
857 887 3.308473 GGCTTTATATGGGGATGGAGGAC 60.308 52.174 0.00 0.00 0.00 3.85
858 888 2.919602 GGCTTTATATGGGGATGGAGGA 59.080 50.000 0.00 0.00 0.00 3.71
859 889 2.649312 TGGCTTTATATGGGGATGGAGG 59.351 50.000 0.00 0.00 0.00 4.30
860 890 3.690460 GTGGCTTTATATGGGGATGGAG 58.310 50.000 0.00 0.00 0.00 3.86
893 924 1.279749 GGTGAGGGAGGGGGTTTAGG 61.280 65.000 0.00 0.00 0.00 2.69
926 958 1.869452 AGGGGAGGAGGAGGGACTT 60.869 63.158 0.00 0.00 41.55 3.01
928 960 2.041405 CAGGGGAGGAGGAGGGAC 60.041 72.222 0.00 0.00 0.00 4.46
968 1000 1.516892 GAGCTGAGCTGAGGTGAGG 59.483 63.158 13.71 0.00 39.88 3.86
973 1005 4.527583 GGGCGAGCTGAGCTGAGG 62.528 72.222 13.71 1.49 39.88 3.86
1140 1268 0.801836 CATGCGGAAATTCGGCCAAC 60.802 55.000 20.21 0.00 41.34 3.77
1163 1291 6.036953 GCAAGAACACACAATTCATGGAAAAA 59.963 34.615 0.00 0.00 0.00 1.94
1164 1292 5.523188 GCAAGAACACACAATTCATGGAAAA 59.477 36.000 0.00 0.00 0.00 2.29
1165 1293 5.049167 GCAAGAACACACAATTCATGGAAA 58.951 37.500 0.00 0.00 0.00 3.13
1166 1294 4.619973 GCAAGAACACACAATTCATGGAA 58.380 39.130 0.00 0.00 0.00 3.53
1167 1295 3.304592 CGCAAGAACACACAATTCATGGA 60.305 43.478 0.00 0.00 43.02 3.41
1168 1296 2.981805 CGCAAGAACACACAATTCATGG 59.018 45.455 0.00 0.00 43.02 3.66
1192 1325 1.573829 TTCGAGCGGGCAATCACAAC 61.574 55.000 0.00 0.00 0.00 3.32
1204 1337 4.294523 TGGGGACAAATTCGAGCG 57.705 55.556 0.00 0.00 37.44 5.03
1251 1385 3.550820 ACAGCACATGTCACAACCTTTA 58.449 40.909 0.00 0.00 37.75 1.85
1252 1386 2.378038 ACAGCACATGTCACAACCTTT 58.622 42.857 0.00 0.00 37.75 3.11
1253 1387 2.057137 ACAGCACATGTCACAACCTT 57.943 45.000 0.00 0.00 37.75 3.50
1254 1388 1.677576 CAACAGCACATGTCACAACCT 59.322 47.619 0.00 0.00 43.00 3.50
1264 1399 3.084039 CTCATTACACCCAACAGCACAT 58.916 45.455 0.00 0.00 0.00 3.21
1477 1617 4.583871 AGCTAGTGGTTCAGGAATGAAAG 58.416 43.478 0.00 0.00 0.00 2.62
1484 1625 2.289444 CGGAAAAGCTAGTGGTTCAGGA 60.289 50.000 0.00 0.00 32.90 3.86
1519 1664 2.775490 TCATGAAGCTAGCTAGGGGA 57.225 50.000 19.70 11.10 0.00 4.81
1522 1671 5.736951 ACCTTATCATGAAGCTAGCTAGG 57.263 43.478 19.70 19.75 0.00 3.02
1529 1678 5.426689 TCTGACAACCTTATCATGAAGCT 57.573 39.130 0.00 0.00 0.00 3.74
1530 1679 6.150140 ACTTTCTGACAACCTTATCATGAAGC 59.850 38.462 0.00 0.00 0.00 3.86
1531 1680 7.678947 ACTTTCTGACAACCTTATCATGAAG 57.321 36.000 0.00 0.00 0.00 3.02
1532 1681 7.174946 GGAACTTTCTGACAACCTTATCATGAA 59.825 37.037 0.00 0.00 0.00 2.57
1533 1682 6.655003 GGAACTTTCTGACAACCTTATCATGA 59.345 38.462 0.00 0.00 0.00 3.07
1590 1740 6.908825 TGAAATGAAAAATTAGCTAGCACGT 58.091 32.000 18.83 0.00 0.00 4.49
1605 1755 7.420002 CAGAAGATGCCGATTATGAAATGAAA 58.580 34.615 0.00 0.00 0.00 2.69
1606 1756 6.962686 CAGAAGATGCCGATTATGAAATGAA 58.037 36.000 0.00 0.00 0.00 2.57
1699 1855 6.202570 CAGTGTCAAACCCCAAAATTACAATG 59.797 38.462 0.00 0.00 0.00 2.82
1803 1959 3.608796 TCAATTCGATCCATGCTTGTGA 58.391 40.909 0.00 0.00 0.00 3.58
1914 2070 8.371770 ACAGTGTGAAAGAAATCTAGAAAGAC 57.628 34.615 0.00 0.00 33.57 3.01
2044 2206 1.062002 GTGTCTGTGTGTTCGGTGTTG 59.938 52.381 0.00 0.00 0.00 3.33
2051 2213 0.026285 GTGCGTGTGTCTGTGTGTTC 59.974 55.000 0.00 0.00 0.00 3.18
2059 2221 2.143008 TACGAAATGTGCGTGTGTCT 57.857 45.000 0.00 0.00 42.62 3.41
2060 2222 3.449322 AATACGAAATGTGCGTGTGTC 57.551 42.857 0.00 0.00 42.62 3.67
2061 2223 5.539582 AATAATACGAAATGTGCGTGTGT 57.460 34.783 0.00 0.00 42.62 3.72
2062 2224 5.275234 GCAAATAATACGAAATGTGCGTGTG 60.275 40.000 0.00 0.00 42.62 3.82
2063 2225 4.791163 GCAAATAATACGAAATGTGCGTGT 59.209 37.500 0.00 0.00 42.62 4.49
2064 2226 4.790651 TGCAAATAATACGAAATGTGCGTG 59.209 37.500 0.00 0.00 42.62 5.34
2065 2227 4.975788 TGCAAATAATACGAAATGTGCGT 58.024 34.783 0.00 0.00 38.88 5.24
2066 2228 7.601881 TTATGCAAATAATACGAAATGTGCG 57.398 32.000 0.00 0.00 38.88 5.34
2136 2310 9.771534 AATTGGCAAACAAAAATTAAGTAGCTA 57.228 25.926 3.01 0.00 43.46 3.32
2159 2333 7.173047 GGTTTCATACAAAGTCAATTGCCAATT 59.827 33.333 0.00 0.00 33.52 2.32
2167 2341 5.183904 GCCTCAGGTTTCATACAAAGTCAAT 59.816 40.000 0.00 0.00 0.00 2.57
2181 2355 0.178981 ATGCACACAGCCTCAGGTTT 60.179 50.000 0.00 0.00 44.83 3.27
2243 2424 7.979115 TTTAACACCAACATTTCTTCTTTCG 57.021 32.000 0.00 0.00 0.00 3.46
2245 2426 8.611757 GCAATTTAACACCAACATTTCTTCTTT 58.388 29.630 0.00 0.00 0.00 2.52
2256 2437 6.701400 ACAAAGATCTGCAATTTAACACCAAC 59.299 34.615 0.00 0.00 0.00 3.77
2265 2446 5.142061 TGCATGACAAAGATCTGCAATTT 57.858 34.783 0.00 0.00 39.68 1.82
2276 2457 5.814764 AGATTAGAGCTTGCATGACAAAG 57.185 39.130 3.33 0.00 37.96 2.77
2302 2483 2.486918 CGTTCCTCCCTGTAAAACGTT 58.513 47.619 0.00 0.00 38.24 3.99
2304 2485 2.159327 ACGTTCCTCCCTGTAAAACG 57.841 50.000 4.58 4.58 45.90 3.60
2414 2595 0.671472 CACGAATCAGAGCTGCACCA 60.671 55.000 1.02 0.00 0.00 4.17
2517 2698 5.886960 ACTAGCAACCTTCAATCATGAAC 57.113 39.130 0.00 0.00 40.59 3.18
2539 2720 4.019411 TCACCAGCAGAATCATTGGTCTTA 60.019 41.667 1.26 0.00 41.81 2.10
2888 3083 1.442688 GCAACAGCCGCACTAAAGC 60.443 57.895 0.00 0.00 0.00 3.51
3001 3199 0.591659 CATCAGCAATCATGGCTCCG 59.408 55.000 0.00 0.00 40.23 4.63
3064 3262 8.370940 TCAACAGTAGTCTCAAAAGATGAAGAT 58.629 33.333 0.00 0.00 37.67 2.40
3236 3434 2.125552 CTCGGTCAATCTGCGCCA 60.126 61.111 4.18 0.00 0.00 5.69
3238 3436 2.629050 TAGCCTCGGTCAATCTGCGC 62.629 60.000 0.00 0.00 0.00 6.09
3622 3820 8.581253 AAGAAATCGGGAAAGATAACAAGATT 57.419 30.769 0.00 0.00 0.00 2.40
3686 3884 2.694109 ACCAAGATCCTTCGCTAGGTAC 59.306 50.000 3.73 0.00 45.03 3.34
3692 3890 1.270907 ACAGACCAAGATCCTTCGCT 58.729 50.000 0.00 0.00 0.00 4.93
3734 3932 0.843309 TCCTTGCTGTCCCAAGTTGA 59.157 50.000 3.87 0.00 40.40 3.18
3779 3977 0.969149 CCGCATCTGCTATGAGGGTA 59.031 55.000 12.44 0.00 39.32 3.69
3971 4169 2.508439 TTCGCGTCCTCAATCCGC 60.508 61.111 5.77 0.00 43.74 5.54
3977 4175 1.447838 GGCATTCTTCGCGTCCTCA 60.448 57.895 5.77 0.00 0.00 3.86
4070 4268 1.658596 TCGATGGTTTCTTTGATCGCG 59.341 47.619 0.00 0.00 38.05 5.87
4085 4283 1.791204 CGCTCATCATGGTCTTCGATG 59.209 52.381 0.00 0.00 38.29 3.84
4097 4295 2.747460 GCACCAAGGCGCTCATCA 60.747 61.111 7.64 0.00 0.00 3.07
4100 4298 3.939939 TCAGCACCAAGGCGCTCA 61.940 61.111 7.64 0.00 35.96 4.26
4127 4325 9.998106 ATATCGATATGTAAGCAAGTTACCTTT 57.002 29.630 17.08 0.00 40.49 3.11
4143 4341 7.816513 AGTTCAGTCCATCAACATATCGATATG 59.183 37.037 33.70 33.70 44.37 1.78
4145 4343 7.290110 AGTTCAGTCCATCAACATATCGATA 57.710 36.000 7.75 7.75 0.00 2.92
4149 4347 8.554528 CAATGTAGTTCAGTCCATCAACATATC 58.445 37.037 0.00 0.00 0.00 1.63
4157 4355 6.815089 AGAGATCAATGTAGTTCAGTCCATC 58.185 40.000 0.00 0.00 0.00 3.51
4162 4360 7.551974 CCATGAAAGAGATCAATGTAGTTCAGT 59.448 37.037 0.00 0.00 32.06 3.41
4163 4361 7.767659 TCCATGAAAGAGATCAATGTAGTTCAG 59.232 37.037 0.00 0.00 32.06 3.02
4174 4372 5.884232 CCATCAGTTTCCATGAAAGAGATCA 59.116 40.000 0.00 0.00 31.87 2.92
4188 4386 9.076596 GTAAATGCAATTTCTACCATCAGTTTC 57.923 33.333 0.00 0.00 44.81 2.78
4189 4387 8.034804 GGTAAATGCAATTTCTACCATCAGTTT 58.965 33.333 0.00 0.00 44.81 2.66
4277 4477 7.213178 ACTATCCTAAATGATTGTCCTTGGT 57.787 36.000 0.00 0.00 0.00 3.67
4359 4559 5.579511 CCCGACAAGTACTAAAGTATTGTGG 59.420 44.000 16.02 14.83 35.01 4.17
4361 4561 6.594788 TCCCGACAAGTACTAAAGTATTGT 57.405 37.500 0.00 13.19 36.22 2.71
4368 4568 9.139734 AGATATACAATCCCGACAAGTACTAAA 57.860 33.333 0.00 0.00 0.00 1.85
4381 4581 8.816894 TCCACATTTCTAGAGATATACAATCCC 58.183 37.037 0.00 0.00 0.00 3.85
4433 4633 6.757897 ATGCCTGAAGAATCGACAAATTAA 57.242 33.333 0.00 0.00 0.00 1.40
4436 4636 4.676196 GCAATGCCTGAAGAATCGACAAAT 60.676 41.667 0.00 0.00 0.00 2.32
4449 4649 2.628696 CGGTGCTTGCAATGCCTGA 61.629 57.895 15.29 0.00 35.91 3.86
4526 4726 1.456705 ATCTCCCACTCGCTCTCCC 60.457 63.158 0.00 0.00 0.00 4.30
4698 4898 1.227002 CTCGGCGACCTTAGGCTTC 60.227 63.158 4.99 0.00 0.00 3.86
4704 4904 4.143333 GCTGGCTCGGCGACCTTA 62.143 66.667 22.60 8.50 0.00 2.69
4745 4945 7.410120 TGAAGAGATCTTTACATACAGCTCA 57.590 36.000 0.00 0.00 36.11 4.26
4761 4965 0.758685 CGGAGGAGGCCTGAAGAGAT 60.759 60.000 12.00 0.00 31.76 2.75
4782 4986 6.959361 TGTCTGAACTGAAGCATCTAAAAAC 58.041 36.000 0.00 0.00 0.00 2.43
4804 5011 2.887151 AATTCTACTGCTTGGCCTGT 57.113 45.000 3.32 0.00 0.00 4.00
4885 5095 2.603953 GAGGAAGGTTTACCGTTCGAG 58.396 52.381 0.00 0.00 42.08 4.04
4895 5105 1.065854 CAGATCAGGCGAGGAAGGTTT 60.066 52.381 0.00 0.00 0.00 3.27
5062 5391 7.315142 CGGAAGAAAAATGATCATCTTTTCCA 58.685 34.615 28.85 1.46 39.02 3.53
5226 5557 1.800805 CTGTGACAAGATGTTCGCCT 58.199 50.000 0.00 0.00 0.00 5.52
5228 5559 0.179240 CGCTGTGACAAGATGTTCGC 60.179 55.000 0.00 0.00 0.00 4.70
5346 5686 1.514087 GATTACGCCTGGACCGTGA 59.486 57.895 9.23 2.19 39.54 4.35
5542 5885 1.080025 GGCGCAGGACTACGACTTT 60.080 57.895 10.83 0.00 33.47 2.66
5627 5970 2.043450 CCTCCTCCTGCTCCTCGT 60.043 66.667 0.00 0.00 0.00 4.18
5660 6006 3.866582 GACCATGGCCCCTCTCCG 61.867 72.222 13.04 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.