Multiple sequence alignment - TraesCS1B01G392900

Loading Multiple Alignment...

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 TraesCS1B01G392900 chr1B 100.000 4033 0 0 1 4033 626083215 626087247 0.000000e+00 7448.0
1 TraesCS1B01G392900 chr1D 95.014 3129 122 16 921 4033 455748290 455751400 0.000000e+00 4883.0
2 TraesCS1B01G392900 chr1D 88.832 779 41 18 20 764 455747379 455748145 0.000000e+00 915.0
3 TraesCS1B01G392900 chr1D 90.647 139 10 3 835 971 455748161 455748298 8.900000e-42 182.0
4 TraesCS1B01G392900 chr1D 91.818 110 8 1 3830 3939 455765638 455765746 6.980000e-33 152.0
5 TraesCS1B01G392900 chr1D 97.368 38 0 1 2331 2367 455749776 455749813 3.370000e-06 63.9
6 TraesCS1B01G392900 chr1A 93.405 743 39 2 2605 3345 549289546 549290280 0.000000e+00 1092.0
7 TraesCS1B01G392900 chr1A 81.818 209 26 5 3753 3959 549312745 549312943 8.970000e-37 165.0
8 TraesCS1B01G392900 chr4B 80.117 855 156 12 2428 3270 666565298 666564446 3.420000e-175 625.0
9 TraesCS1B01G392900 chrUn 79.062 917 174 13 2428 3328 134238337 134237423 7.410000e-172 614.0
10 TraesCS1B01G392900 chr3B 84.152 631 96 4 2428 3056 820286873 820286245 3.450000e-170 608.0
11 TraesCS1B01G392900 chr3B 83.518 631 100 3 2428 3056 820447577 820446949 1.610000e-163 586.0
12 TraesCS1B01G392900 chr3B 81.354 724 126 7 2425 3140 820150461 820151183 7.510000e-162 580.0
13 TraesCS1B01G392900 chr3B 79.493 473 89 6 994 1462 818202411 818202879 3.000000e-86 329.0
14 TraesCS1B01G392900 chr3B 79.493 473 89 6 994 1462 818237948 818238416 3.000000e-86 329.0
15 TraesCS1B01G392900 chr3B 75.670 448 90 15 1890 2329 811305803 811305367 5.280000e-49 206.0
16 TraesCS1B01G392900 chr3D 82.979 611 100 4 2430 3038 609585764 609585156 2.120000e-152 549.0
17 TraesCS1B01G392900 chr3A 81.295 556 95 8 2504 3055 742420361 742420911 3.700000e-120 442.0
18 TraesCS1B01G392900 chr6A 90.909 66 6 0 3946 4011 586326328 586326263 5.550000e-14 89.8
19 TraesCS1B01G392900 chr7D 85.333 75 4 3 3935 4003 567735110 567735183 2.010000e-08 71.3
20 TraesCS1B01G392900 chr7B 83.750 80 4 6 3935 4006 622269320 622269398 2.600000e-07 67.6


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G392900 chr1B 626083215 626087247 4032 False 7448.000 7448 100.00000 1 4033 1 chr1B.!!$F1 4032
1 TraesCS1B01G392900 chr1D 455747379 455751400 4021 False 1510.975 4883 92.96525 20 4033 4 chr1D.!!$F2 4013
2 TraesCS1B01G392900 chr1A 549289546 549290280 734 False 1092.000 1092 93.40500 2605 3345 1 chr1A.!!$F1 740
3 TraesCS1B01G392900 chr4B 666564446 666565298 852 True 625.000 625 80.11700 2428 3270 1 chr4B.!!$R1 842
4 TraesCS1B01G392900 chrUn 134237423 134238337 914 True 614.000 614 79.06200 2428 3328 1 chrUn.!!$R1 900
5 TraesCS1B01G392900 chr3B 820286245 820286873 628 True 608.000 608 84.15200 2428 3056 1 chr3B.!!$R2 628
6 TraesCS1B01G392900 chr3B 820446949 820447577 628 True 586.000 586 83.51800 2428 3056 1 chr3B.!!$R3 628
7 TraesCS1B01G392900 chr3B 820150461 820151183 722 False 580.000 580 81.35400 2425 3140 1 chr3B.!!$F3 715
8 TraesCS1B01G392900 chr3D 609585156 609585764 608 True 549.000 549 82.97900 2430 3038 1 chr3D.!!$R1 608
9 TraesCS1B01G392900 chr3A 742420361 742420911 550 False 442.000 442 81.29500 2504 3055 1 chr3A.!!$F1 551

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
574 588 0.178767 TGGCAGATTCTCCATGTCGG 59.821 55.0 0.0 0.0 0.0 4.79 F
1410 1490 0.108424 AGCCTGATCTGTCGAAGCAC 60.108 55.0 0.0 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1723 1803 0.327924 TGGTTGATGGACCAAGCGAT 59.672 50.0 0.0 0.0 46.33 4.58 R
3217 3310 1.475403 TCTCTGGAGACCGAATCACC 58.525 55.0 0.0 0.0 38.51 4.02 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
54 55 4.742659 GCATTTTTCGTATGGTGTTGTTGT 59.257 37.500 0.00 0.00 0.00 3.32
55 56 5.108027 GCATTTTTCGTATGGTGTTGTTGTC 60.108 40.000 0.00 0.00 0.00 3.18
61 62 6.656314 TCGTATGGTGTTGTTGTCATATTC 57.344 37.500 0.00 0.00 0.00 1.75
69 70 7.779326 TGGTGTTGTTGTCATATTCCATGATAT 59.221 33.333 0.00 0.00 0.00 1.63
170 176 5.048504 GGCAAAGATGTCATCACAAGAAAGA 60.049 40.000 15.20 0.00 35.64 2.52
211 217 7.839680 AACATAAATTGGGCTATCCTTAAGG 57.160 36.000 15.98 15.98 36.20 2.69
292 298 1.944177 GCTAGGGATATCCTCAGCCA 58.056 55.000 25.66 6.95 44.06 4.75
293 299 2.260822 GCTAGGGATATCCTCAGCCAA 58.739 52.381 25.66 6.14 44.06 4.52
294 300 2.639839 GCTAGGGATATCCTCAGCCAAA 59.360 50.000 25.66 4.29 44.06 3.28
295 301 3.558109 GCTAGGGATATCCTCAGCCAAAC 60.558 52.174 25.66 8.30 44.06 2.93
296 302 1.777272 AGGGATATCCTCAGCCAAACC 59.223 52.381 21.18 0.65 44.06 3.27
320 326 0.321346 CAAACCAAATGCCCCCTGAC 59.679 55.000 0.00 0.00 0.00 3.51
321 327 0.835971 AAACCAAATGCCCCCTGACC 60.836 55.000 0.00 0.00 0.00 4.02
322 328 2.364186 CCAAATGCCCCCTGACCC 60.364 66.667 0.00 0.00 0.00 4.46
323 329 2.772924 CAAATGCCCCCTGACCCT 59.227 61.111 0.00 0.00 0.00 4.34
324 330 1.683365 CAAATGCCCCCTGACCCTG 60.683 63.158 0.00 0.00 0.00 4.45
325 331 1.856873 AAATGCCCCCTGACCCTGA 60.857 57.895 0.00 0.00 0.00 3.86
342 348 2.020720 CTGAGTGCTAGGATGACGACT 58.979 52.381 0.00 0.00 0.00 4.18
349 355 2.924290 GCTAGGATGACGACTGTGTTTC 59.076 50.000 0.00 0.00 0.00 2.78
350 356 3.614150 GCTAGGATGACGACTGTGTTTCA 60.614 47.826 0.00 0.00 0.00 2.69
351 357 3.685139 AGGATGACGACTGTGTTTCAT 57.315 42.857 0.00 0.00 0.00 2.57
376 382 6.070021 TGGAGTCATGATCAGATTAAAGGTGT 60.070 38.462 0.00 0.00 0.00 4.16
382 388 6.769134 TGATCAGATTAAAGGTGTAGTCGA 57.231 37.500 0.00 0.00 0.00 4.20
389 395 5.664294 TTAAAGGTGTAGTCGAATGGCTA 57.336 39.130 0.00 0.00 0.00 3.93
404 410 3.696281 TGGCTAATCAAATGTCATGCG 57.304 42.857 0.00 0.00 0.00 4.73
461 467 9.239002 CTTCATCTTCCGACTACTTAATTACTG 57.761 37.037 0.00 0.00 0.00 2.74
484 490 1.748879 GGCATTAGTTCAGCGGGCA 60.749 57.895 0.00 0.00 0.00 5.36
556 570 4.886489 GGGTAACTGTACTACCTCCTACTG 59.114 50.000 9.08 0.00 39.11 2.74
566 580 2.393646 ACCTCCTACTGGCAGATTCTC 58.606 52.381 23.66 0.00 0.00 2.87
571 585 2.437281 CCTACTGGCAGATTCTCCATGT 59.563 50.000 23.66 0.00 0.00 3.21
574 588 0.178767 TGGCAGATTCTCCATGTCGG 59.821 55.000 0.00 0.00 0.00 4.79
607 621 0.179176 GTGCGCGCATTTATGGTCAA 60.179 50.000 38.62 6.07 0.00 3.18
608 622 0.179176 TGCGCGCATTTATGGTCAAC 60.179 50.000 33.09 0.00 0.00 3.18
622 636 9.847224 ATTTATGGTCAACGAATATAAAGAGGT 57.153 29.630 0.00 0.00 29.79 3.85
690 710 9.868160 CCACTATATGTATAGATATCCCACTGA 57.132 37.037 12.71 0.00 38.30 3.41
697 717 9.781425 ATGTATAGATATCCCACTGAAGAGAAT 57.219 33.333 0.00 0.00 0.00 2.40
704 724 8.970859 ATATCCCACTGAAGAGAATTAAACAG 57.029 34.615 0.00 0.00 0.00 3.16
705 725 5.003804 TCCCACTGAAGAGAATTAAACAGC 58.996 41.667 0.00 0.00 0.00 4.40
718 754 7.664758 AGAATTAAACAGCAGCATTTCTCTTT 58.335 30.769 0.00 0.00 0.00 2.52
719 755 7.811713 AGAATTAAACAGCAGCATTTCTCTTTC 59.188 33.333 0.00 0.00 0.00 2.62
720 756 6.639632 TTAAACAGCAGCATTTCTCTTTCT 57.360 33.333 0.00 0.00 0.00 2.52
722 758 3.080319 ACAGCAGCATTTCTCTTTCTCC 58.920 45.455 0.00 0.00 0.00 3.71
723 759 2.422832 CAGCAGCATTTCTCTTTCTCCC 59.577 50.000 0.00 0.00 0.00 4.30
753 789 1.774254 TCCAGTGCCTTTCCTTTGAGA 59.226 47.619 0.00 0.00 0.00 3.27
764 800 4.982241 TTCCTTTGAGATCAGGTGAGTT 57.018 40.909 0.00 0.00 0.00 3.01
765 801 6.433847 TTTCCTTTGAGATCAGGTGAGTTA 57.566 37.500 0.00 0.00 0.00 2.24
769 805 6.724441 TCCTTTGAGATCAGGTGAGTTACTTA 59.276 38.462 0.00 0.00 0.00 2.24
771 807 6.911250 TTGAGATCAGGTGAGTTACTTACA 57.089 37.500 9.43 0.00 0.00 2.41
772 808 6.516739 TGAGATCAGGTGAGTTACTTACAG 57.483 41.667 9.43 1.76 0.00 2.74
775 811 6.926313 AGATCAGGTGAGTTACTTACAGTTC 58.074 40.000 9.43 5.97 0.00 3.01
776 812 5.464030 TCAGGTGAGTTACTTACAGTTCC 57.536 43.478 9.43 0.00 0.00 3.62
777 813 4.897076 TCAGGTGAGTTACTTACAGTTCCA 59.103 41.667 9.43 0.00 0.00 3.53
778 814 5.542635 TCAGGTGAGTTACTTACAGTTCCAT 59.457 40.000 9.43 0.00 0.00 3.41
779 815 5.869888 CAGGTGAGTTACTTACAGTTCCATC 59.130 44.000 9.43 0.00 0.00 3.51
780 816 4.863131 GGTGAGTTACTTACAGTTCCATCG 59.137 45.833 9.43 0.00 0.00 3.84
781 817 5.336213 GGTGAGTTACTTACAGTTCCATCGA 60.336 44.000 9.43 0.00 0.00 3.59
782 818 5.800941 GTGAGTTACTTACAGTTCCATCGAG 59.199 44.000 2.29 0.00 0.00 4.04
783 819 5.475909 TGAGTTACTTACAGTTCCATCGAGT 59.524 40.000 0.00 0.00 0.00 4.18
784 820 6.015688 TGAGTTACTTACAGTTCCATCGAGTT 60.016 38.462 0.00 0.00 0.00 3.01
785 821 7.175467 TGAGTTACTTACAGTTCCATCGAGTTA 59.825 37.037 0.00 0.00 0.00 2.24
786 822 7.889469 AGTTACTTACAGTTCCATCGAGTTAA 58.111 34.615 0.00 0.00 0.00 2.01
787 823 8.529476 AGTTACTTACAGTTCCATCGAGTTAAT 58.471 33.333 0.00 0.00 0.00 1.40
788 824 9.148104 GTTACTTACAGTTCCATCGAGTTAATT 57.852 33.333 0.00 0.00 0.00 1.40
789 825 9.715121 TTACTTACAGTTCCATCGAGTTAATTT 57.285 29.630 0.00 0.00 0.00 1.82
791 827 9.367444 ACTTACAGTTCCATCGAGTTAATTTAG 57.633 33.333 0.00 0.00 0.00 1.85
792 828 8.712285 TTACAGTTCCATCGAGTTAATTTAGG 57.288 34.615 0.00 0.00 0.00 2.69
793 829 5.585047 ACAGTTCCATCGAGTTAATTTAGGC 59.415 40.000 0.00 0.00 0.00 3.93
794 830 5.817816 CAGTTCCATCGAGTTAATTTAGGCT 59.182 40.000 0.00 0.00 0.00 4.58
795 831 6.316390 CAGTTCCATCGAGTTAATTTAGGCTT 59.684 38.462 0.00 0.00 0.00 4.35
796 832 7.494625 CAGTTCCATCGAGTTAATTTAGGCTTA 59.505 37.037 0.00 0.00 0.00 3.09
797 833 7.494952 AGTTCCATCGAGTTAATTTAGGCTTAC 59.505 37.037 0.00 0.00 0.00 2.34
798 834 6.880484 TCCATCGAGTTAATTTAGGCTTACA 58.120 36.000 0.00 0.00 0.00 2.41
799 835 7.506114 TCCATCGAGTTAATTTAGGCTTACAT 58.494 34.615 0.00 0.00 0.00 2.29
800 836 7.990886 TCCATCGAGTTAATTTAGGCTTACATT 59.009 33.333 0.00 0.00 0.00 2.71
801 837 8.621286 CCATCGAGTTAATTTAGGCTTACATTT 58.379 33.333 0.00 0.00 0.00 2.32
802 838 9.438291 CATCGAGTTAATTTAGGCTTACATTTG 57.562 33.333 0.00 0.00 0.00 2.32
803 839 7.469260 TCGAGTTAATTTAGGCTTACATTTGC 58.531 34.615 0.00 0.00 0.00 3.68
804 840 7.335924 TCGAGTTAATTTAGGCTTACATTTGCT 59.664 33.333 0.00 0.00 0.00 3.91
805 841 8.609176 CGAGTTAATTTAGGCTTACATTTGCTA 58.391 33.333 0.00 0.00 0.00 3.49
806 842 9.717892 GAGTTAATTTAGGCTTACATTTGCTAC 57.282 33.333 0.00 0.00 0.00 3.58
807 843 9.238368 AGTTAATTTAGGCTTACATTTGCTACA 57.762 29.630 0.00 0.00 0.00 2.74
808 844 9.503427 GTTAATTTAGGCTTACATTTGCTACAG 57.497 33.333 0.00 0.00 0.00 2.74
809 845 7.703058 AATTTAGGCTTACATTTGCTACAGT 57.297 32.000 0.00 0.00 0.00 3.55
810 846 7.703058 ATTTAGGCTTACATTTGCTACAGTT 57.297 32.000 0.00 0.00 0.00 3.16
811 847 8.801882 ATTTAGGCTTACATTTGCTACAGTTA 57.198 30.769 0.00 0.00 0.00 2.24
812 848 7.605410 TTAGGCTTACATTTGCTACAGTTAC 57.395 36.000 0.00 0.00 0.00 2.50
813 849 5.805728 AGGCTTACATTTGCTACAGTTACT 58.194 37.500 0.00 0.00 0.00 2.24
814 850 6.238648 AGGCTTACATTTGCTACAGTTACTT 58.761 36.000 0.00 0.00 0.00 2.24
815 851 6.149474 AGGCTTACATTTGCTACAGTTACTTG 59.851 38.462 0.00 0.00 0.00 3.16
816 852 6.072673 GGCTTACATTTGCTACAGTTACTTGT 60.073 38.462 0.00 0.00 35.09 3.16
817 853 7.360361 GCTTACATTTGCTACAGTTACTTGTT 58.640 34.615 0.00 0.00 32.56 2.83
818 854 7.860872 GCTTACATTTGCTACAGTTACTTGTTT 59.139 33.333 0.00 0.00 32.56 2.83
819 855 9.382244 CTTACATTTGCTACAGTTACTTGTTTC 57.618 33.333 0.00 0.00 32.56 2.78
820 856 6.735130 ACATTTGCTACAGTTACTTGTTTCC 58.265 36.000 0.00 0.00 32.56 3.13
821 857 6.546034 ACATTTGCTACAGTTACTTGTTTCCT 59.454 34.615 0.00 0.00 32.56 3.36
822 858 6.613755 TTTGCTACAGTTACTTGTTTCCTC 57.386 37.500 0.00 0.00 32.56 3.71
823 859 5.546621 TGCTACAGTTACTTGTTTCCTCT 57.453 39.130 0.00 0.00 32.56 3.69
824 860 6.659745 TGCTACAGTTACTTGTTTCCTCTA 57.340 37.500 0.00 0.00 32.56 2.43
825 861 6.688578 TGCTACAGTTACTTGTTTCCTCTAG 58.311 40.000 0.00 0.00 32.56 2.43
826 862 6.267014 TGCTACAGTTACTTGTTTCCTCTAGT 59.733 38.462 0.00 0.00 32.56 2.57
827 863 7.153315 GCTACAGTTACTTGTTTCCTCTAGTT 58.847 38.462 0.00 0.00 32.56 2.24
828 864 8.302438 GCTACAGTTACTTGTTTCCTCTAGTTA 58.698 37.037 0.00 0.00 32.56 2.24
857 893 8.655651 TTTTGAATAATTTTGCGGAACTTTCT 57.344 26.923 0.00 0.00 0.00 2.52
868 904 4.929808 TGCGGAACTTTCTGAGTAGAATTC 59.070 41.667 0.00 0.00 42.25 2.17
900 936 8.064814 GCTCGGTTAATTTAGCAGATTTTCTAG 58.935 37.037 0.00 0.00 35.05 2.43
907 943 7.928307 ATTTAGCAGATTTTCTAGTTGCTCA 57.072 32.000 0.00 0.00 43.47 4.26
908 944 6.974932 TTAGCAGATTTTCTAGTTGCTCAG 57.025 37.500 0.00 0.00 43.47 3.35
941 979 8.668510 TCCTCAGCAGTTAAAATCAAGATATC 57.331 34.615 0.00 0.00 0.00 1.63
942 980 8.267183 TCCTCAGCAGTTAAAATCAAGATATCA 58.733 33.333 5.32 0.00 0.00 2.15
971 1009 5.233902 CAGACAATACATCAGCAGCTAGTTC 59.766 44.000 0.00 0.00 0.00 3.01
973 1011 5.678583 ACAATACATCAGCAGCTAGTTCAT 58.321 37.500 0.00 0.00 0.00 2.57
974 1012 5.757320 ACAATACATCAGCAGCTAGTTCATC 59.243 40.000 0.00 0.00 0.00 2.92
975 1013 2.819115 ACATCAGCAGCTAGTTCATCG 58.181 47.619 0.00 0.00 0.00 3.84
976 1014 2.167281 ACATCAGCAGCTAGTTCATCGT 59.833 45.455 0.00 0.00 0.00 3.73
981 1061 1.861575 GCAGCTAGTTCATCGTAAGGC 59.138 52.381 0.00 0.00 38.47 4.35
988 1068 0.604073 TTCATCGTAAGGCGGACACA 59.396 50.000 0.00 0.00 41.72 3.72
1085 1165 3.752747 TCGCAAGATCAAAGCATTCTTCA 59.247 39.130 0.00 0.00 45.01 3.02
1089 1169 5.348986 CAAGATCAAAGCATTCTTCATGGG 58.651 41.667 0.00 0.00 32.81 4.00
1097 1177 3.766051 AGCATTCTTCATGGGAAAACTCC 59.234 43.478 0.00 0.00 32.81 3.85
1146 1226 1.644437 CCATCCATGGCCACCAGGTA 61.644 60.000 8.16 1.48 41.75 3.08
1252 1332 1.746615 CGTGGCTGGGTCTCATTGG 60.747 63.158 0.00 0.00 0.00 3.16
1263 1343 2.746362 GGTCTCATTGGCTTCTGTCTTG 59.254 50.000 0.00 0.00 0.00 3.02
1274 1354 0.108472 TCTGTCTTGCTCCGATGCTG 60.108 55.000 0.00 0.00 0.00 4.41
1278 1358 4.393155 TTGCTCCGATGCTGCCGT 62.393 61.111 0.00 0.00 0.00 5.68
1303 1383 1.648467 GCGGTTGAGTGAGGCAATCC 61.648 60.000 0.00 0.00 0.00 3.01
1398 1478 1.421480 TGATAGCAGCAGAGCCTGAT 58.579 50.000 6.40 0.00 34.77 2.90
1410 1490 0.108424 AGCCTGATCTGTCGAAGCAC 60.108 55.000 0.00 0.00 0.00 4.40
1462 1542 2.660490 TCGCGGCAAAGAGAAATTTTG 58.340 42.857 6.13 0.00 38.30 2.44
1473 1553 8.982925 CAAAGAGAAATTTTGCAGATGTTTTC 57.017 30.769 0.00 0.00 0.00 2.29
1551 1631 1.434696 GCATGCCGCAGCTACAAAT 59.565 52.632 6.36 0.00 41.79 2.32
1585 1665 2.168521 GAGACCTAGGTGCACAGCATAA 59.831 50.000 22.10 0.00 41.91 1.90
1586 1666 2.169352 AGACCTAGGTGCACAGCATAAG 59.831 50.000 22.10 5.84 41.91 1.73
1678 1758 7.443272 CAGCATAGTTGATGTTATGATTCCTCA 59.557 37.037 0.00 0.00 37.90 3.86
1729 1809 2.100252 CCAAAGGCAATCATCATCGCTT 59.900 45.455 0.00 0.00 0.00 4.68
1732 1812 1.027357 GGCAATCATCATCGCTTGGT 58.973 50.000 0.00 0.00 0.00 3.67
1736 1816 2.882761 CAATCATCATCGCTTGGTCCAT 59.117 45.455 0.00 0.00 0.00 3.41
1737 1817 2.245159 TCATCATCGCTTGGTCCATC 57.755 50.000 0.00 0.00 0.00 3.51
1738 1818 1.485895 TCATCATCGCTTGGTCCATCA 59.514 47.619 0.00 0.00 0.00 3.07
1739 1819 2.093021 TCATCATCGCTTGGTCCATCAA 60.093 45.455 0.00 0.00 0.00 2.57
1740 1820 1.737838 TCATCGCTTGGTCCATCAAC 58.262 50.000 0.00 0.00 0.00 3.18
1741 1821 0.734889 CATCGCTTGGTCCATCAACC 59.265 55.000 0.00 0.00 39.94 3.77
1761 1841 8.291191 TCAACCATCATTAACTAATTCATGCA 57.709 30.769 0.00 0.00 0.00 3.96
1783 1863 7.755591 TGCATCTTGACTATTTTTCAGACATC 58.244 34.615 0.00 0.00 0.00 3.06
1795 1875 7.851822 TTTTTCAGACATCGCTACAAAAATC 57.148 32.000 0.00 0.00 0.00 2.17
1864 1944 3.222173 ACACCAGCAAGATTGGTTGTA 57.778 42.857 1.73 0.00 46.57 2.41
1928 2008 8.511604 ACATGATTGTTCTTTAGGGTATGAAG 57.488 34.615 0.00 0.00 29.55 3.02
1946 2026 5.146010 TGAAGTGAGCACAAAAGGTTTTT 57.854 34.783 3.19 0.00 0.00 1.94
1991 2071 5.529581 TCGAGGTCATATTGATGTTGCTA 57.470 39.130 0.00 0.00 34.41 3.49
2044 2124 7.769044 GCTCCTTATTGTCAAGTAGATAACCAA 59.231 37.037 0.00 0.00 29.65 3.67
2076 2156 9.865321 TTTGACACTCCTACATACAACTATAAC 57.135 33.333 0.00 0.00 0.00 1.89
2077 2157 8.004087 TGACACTCCTACATACAACTATAACC 57.996 38.462 0.00 0.00 0.00 2.85
2095 2175 4.942761 AACCAACAATCATGCAGAGTTT 57.057 36.364 0.00 0.00 0.00 2.66
2096 2176 4.247267 ACCAACAATCATGCAGAGTTTG 57.753 40.909 9.82 9.82 0.00 2.93
2122 2202 1.271856 TTATCCTGAGGACACCGCAA 58.728 50.000 1.77 0.00 32.01 4.85
2162 2242 3.518634 TGCAAGACAACCAAGGAAAAC 57.481 42.857 0.00 0.00 0.00 2.43
2224 2304 1.134965 GTCGCTGCCTTACTGTCTCAT 60.135 52.381 0.00 0.00 0.00 2.90
2287 2367 1.754226 GCAACTTGGGAACTGTGGAAA 59.246 47.619 0.00 0.00 0.00 3.13
2305 2385 4.701651 TGGAAAGTCATACAGAATGCCAAG 59.298 41.667 0.00 0.00 42.53 3.61
2308 2388 4.558226 AGTCATACAGAATGCCAAGACA 57.442 40.909 0.00 0.00 42.53 3.41
2331 2411 9.101655 GACATTAAACTGGGTACGTATGTTATT 57.898 33.333 0.00 0.00 0.00 1.40
2367 2447 5.220912 GCAGAATGAAGTGTGCATGCTTATA 60.221 40.000 20.33 0.00 39.69 0.98
2368 2448 6.514541 GCAGAATGAAGTGTGCATGCTTATAT 60.515 38.462 20.33 2.19 39.69 0.86
2369 2449 6.856426 CAGAATGAAGTGTGCATGCTTATATG 59.144 38.462 20.33 0.22 39.69 1.78
2370 2450 8.462910 CAGAATGAAGTGTGCATGCTTATATGC 61.463 40.741 20.33 3.70 46.37 3.14
2423 2503 8.464404 GGTCATTTGTACCTTCCCTTTTATTAC 58.536 37.037 0.00 0.00 33.97 1.89
2600 2680 6.459670 TCGTTAGTAGCAATCCTCATTACA 57.540 37.500 0.00 0.00 0.00 2.41
2993 3074 2.604046 TGAGGCTTAGATTTCGGCTC 57.396 50.000 0.00 0.00 46.76 4.70
3057 3138 5.011090 TCAGATATTTGTCTTCTGGTCCG 57.989 43.478 0.00 0.00 37.93 4.79
3081 3169 6.195244 CGTGTAACATTTTGCAATCTATCTGC 59.805 38.462 0.00 0.00 37.15 4.26
3217 3310 8.447833 TCTTGTATTCCACTTAAACTAAATGCG 58.552 33.333 0.00 0.00 0.00 4.73
3231 3326 0.462047 AATGCGGTGATTCGGTCTCC 60.462 55.000 0.00 0.00 37.18 3.71
3324 3421 7.062605 GTCATGAAACCATACAAAAAGATGCTG 59.937 37.037 0.00 0.00 0.00 4.41
3350 3447 9.722056 GAAAGCACCACAGAAAAGTATATTATG 57.278 33.333 0.00 0.00 0.00 1.90
3351 3448 9.461312 AAAGCACCACAGAAAAGTATATTATGA 57.539 29.630 0.00 0.00 0.00 2.15
3353 3450 9.113838 AGCACCACAGAAAAGTATATTATGAAG 57.886 33.333 0.00 0.00 0.00 3.02
3354 3451 9.109393 GCACCACAGAAAAGTATATTATGAAGA 57.891 33.333 0.00 0.00 0.00 2.87
3387 3487 6.346477 ACTGTTGAGCACTAGTAAGATTGA 57.654 37.500 0.00 0.00 0.00 2.57
3446 3552 4.494199 GCAGTCTGTTTAATACCGATGTGC 60.494 45.833 0.93 0.00 31.02 4.57
3461 3567 5.359576 ACCGATGTGCACAAATAATTGGTAT 59.640 36.000 25.72 1.57 41.01 2.73
3462 3568 6.544197 ACCGATGTGCACAAATAATTGGTATA 59.456 34.615 25.72 0.00 41.01 1.47
3509 3615 3.909776 TTCTTGCAAGCAGAATCACAG 57.090 42.857 21.99 0.00 0.00 3.66
3567 3673 6.861065 ATCACGGCAAAATATAACCTGTAG 57.139 37.500 0.00 0.00 0.00 2.74
3568 3674 5.736813 TCACGGCAAAATATAACCTGTAGT 58.263 37.500 0.00 0.00 0.00 2.73
3638 3744 9.575868 TGTAAGGACCACAAAATCACTAAATTA 57.424 29.630 0.00 0.00 0.00 1.40
3675 3781 5.895534 ACAACAAATCAGGAGCCATGAATAT 59.104 36.000 0.00 0.00 0.00 1.28
3689 3795 9.339850 GAGCCATGAATATTAATGATAGCAGAT 57.660 33.333 13.69 0.00 0.00 2.90
3750 3856 1.831736 CACCCGGATCAAGGACTTAGT 59.168 52.381 0.73 0.00 0.00 2.24
3822 3928 2.747822 GCAGTGCTGTCTGATGGCG 61.748 63.158 8.18 0.00 37.61 5.69
3864 3970 3.555966 CTTGGTTCTCAGTTTCTGGGTT 58.444 45.455 0.00 0.00 33.01 4.11
3865 3971 3.662759 TGGTTCTCAGTTTCTGGGTTT 57.337 42.857 0.00 0.00 33.01 3.27
3866 3972 3.287222 TGGTTCTCAGTTTCTGGGTTTG 58.713 45.455 0.00 0.00 33.01 2.93
3881 3987 4.018490 TGGGTTTGAGATTGTGATGATGG 58.982 43.478 0.00 0.00 0.00 3.51
3926 4032 6.791303 TGAAACAGAACAGGTAACATTTCAC 58.209 36.000 0.00 0.00 41.41 3.18
3952 4058 5.066117 TCAGTTATACTACTGCCTCTGTTCG 59.934 44.000 0.00 0.00 44.10 3.95
3964 4070 3.371285 GCCTCTGTTCGGAAATAAGTGAC 59.629 47.826 0.00 0.00 0.00 3.67
3969 4075 3.062042 GTTCGGAAATAAGTGACGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
4011 4117 4.994852 CACTCCACTTATTTCCGAACAGAA 59.005 41.667 0.00 0.00 0.00 3.02
4024 4130 5.067273 TCCGAACAGAATTTGCTAAAAGGA 58.933 37.500 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.352682 TGTAAACATATCCATGCGTACAAC 57.647 37.500 0.00 0.00 34.34 3.32
1 2 6.986904 TTGTAAACATATCCATGCGTACAA 57.013 33.333 0.00 8.51 39.73 2.41
2 3 6.203915 GGATTGTAAACATATCCATGCGTACA 59.796 38.462 14.31 0.00 34.94 2.90
3 4 6.203915 TGGATTGTAAACATATCCATGCGTAC 59.796 38.462 16.40 0.00 37.96 3.67
4 5 6.292150 TGGATTGTAAACATATCCATGCGTA 58.708 36.000 16.40 0.00 37.96 4.42
5 6 5.129634 TGGATTGTAAACATATCCATGCGT 58.870 37.500 16.40 0.00 37.96 5.24
6 7 5.687770 TGGATTGTAAACATATCCATGCG 57.312 39.130 16.40 0.00 37.96 4.73
7 8 6.366877 GCATTGGATTGTAAACATATCCATGC 59.633 38.462 22.86 22.86 40.13 4.06
8 9 7.435305 TGCATTGGATTGTAAACATATCCATG 58.565 34.615 18.95 18.22 40.13 3.66
9 10 7.600231 TGCATTGGATTGTAAACATATCCAT 57.400 32.000 18.95 11.52 40.13 3.41
10 11 7.600231 ATGCATTGGATTGTAAACATATCCA 57.400 32.000 16.40 16.40 39.47 3.41
11 12 8.891671 AAATGCATTGGATTGTAAACATATCC 57.108 30.769 13.82 13.16 35.75 2.59
14 15 8.867935 CGAAAAATGCATTGGATTGTAAACATA 58.132 29.630 13.82 0.00 0.00 2.29
15 16 7.387397 ACGAAAAATGCATTGGATTGTAAACAT 59.613 29.630 13.82 0.00 0.00 2.71
16 17 6.703607 ACGAAAAATGCATTGGATTGTAAACA 59.296 30.769 13.82 0.00 0.00 2.83
17 18 7.116061 ACGAAAAATGCATTGGATTGTAAAC 57.884 32.000 13.82 0.00 0.00 2.01
18 19 8.867935 CATACGAAAAATGCATTGGATTGTAAA 58.132 29.630 13.82 0.00 0.00 2.01
31 32 4.742659 ACAACAACACCATACGAAAAATGC 59.257 37.500 0.00 0.00 0.00 3.56
154 160 7.323420 AGACGAATATCTTTCTTGTGATGACA 58.677 34.615 0.00 0.00 0.00 3.58
164 170 8.311836 TGTTTGGTTAGAGACGAATATCTTTCT 58.688 33.333 0.00 0.00 0.00 2.52
165 171 8.475331 TGTTTGGTTAGAGACGAATATCTTTC 57.525 34.615 0.00 0.00 0.00 2.62
203 209 2.574824 GAGGTGGTTAAGGCCTTAAGGA 59.425 50.000 33.51 21.56 35.90 3.36
211 217 5.497474 TCTAAATTGAGAGGTGGTTAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
292 298 3.020274 GGCATTTGGTTTGGTTTGGTTT 58.980 40.909 0.00 0.00 0.00 3.27
293 299 2.649190 GGCATTTGGTTTGGTTTGGTT 58.351 42.857 0.00 0.00 0.00 3.67
294 300 1.133945 GGGCATTTGGTTTGGTTTGGT 60.134 47.619 0.00 0.00 0.00 3.67
295 301 1.603456 GGGCATTTGGTTTGGTTTGG 58.397 50.000 0.00 0.00 0.00 3.28
296 302 1.603456 GGGGCATTTGGTTTGGTTTG 58.397 50.000 0.00 0.00 0.00 2.93
320 326 0.387202 CGTCATCCTAGCACTCAGGG 59.613 60.000 0.00 0.00 33.66 4.45
321 327 1.066303 GTCGTCATCCTAGCACTCAGG 59.934 57.143 0.00 0.00 34.20 3.86
322 328 2.020720 AGTCGTCATCCTAGCACTCAG 58.979 52.381 0.00 0.00 0.00 3.35
323 329 1.745653 CAGTCGTCATCCTAGCACTCA 59.254 52.381 0.00 0.00 0.00 3.41
324 330 1.746220 ACAGTCGTCATCCTAGCACTC 59.254 52.381 0.00 0.00 0.00 3.51
325 331 1.474478 CACAGTCGTCATCCTAGCACT 59.526 52.381 0.00 0.00 0.00 4.40
350 356 6.996879 CACCTTTAATCTGATCATGACTCCAT 59.003 38.462 0.00 0.00 0.00 3.41
351 357 6.070021 ACACCTTTAATCTGATCATGACTCCA 60.070 38.462 0.00 0.00 0.00 3.86
360 366 7.169982 CCATTCGACTACACCTTTAATCTGATC 59.830 40.741 0.00 0.00 0.00 2.92
368 374 5.664294 TTAGCCATTCGACTACACCTTTA 57.336 39.130 0.00 0.00 0.00 1.85
376 382 6.345298 TGACATTTGATTAGCCATTCGACTA 58.655 36.000 0.00 0.00 0.00 2.59
382 388 4.613944 CGCATGACATTTGATTAGCCATT 58.386 39.130 0.00 0.00 0.00 3.16
389 395 2.482316 CCATGGCGCATGACATTTGATT 60.482 45.455 10.83 0.00 42.91 2.57
404 410 4.097892 CCCACTAAACTAATGTTCCATGGC 59.902 45.833 6.96 0.00 34.96 4.40
461 467 2.290641 CCCGCTGAACTAATGCCATAAC 59.709 50.000 0.00 0.00 0.00 1.89
464 470 1.103398 GCCCGCTGAACTAATGCCAT 61.103 55.000 0.00 0.00 0.00 4.40
484 490 9.558396 TTCTGCAAAATTAGACAAAATTTGGAT 57.442 25.926 10.71 0.73 38.68 3.41
546 560 2.393646 GAGAATCTGCCAGTAGGAGGT 58.606 52.381 0.00 0.00 36.89 3.85
556 570 0.179000 ACCGACATGGAGAATCTGCC 59.821 55.000 0.00 0.00 42.00 4.85
566 580 2.698803 TGTGAAGATCAACCGACATGG 58.301 47.619 0.00 0.00 46.41 3.66
571 585 2.076100 GCACATGTGAAGATCAACCGA 58.924 47.619 29.80 0.00 0.00 4.69
574 588 1.787989 CGCGCACATGTGAAGATCAAC 60.788 52.381 29.80 7.84 0.00 3.18
607 621 9.457436 ACAACCAATAAACCTCTTTATATTCGT 57.543 29.630 0.00 0.00 32.29 3.85
622 636 8.043710 ACCAGTTGATGAAAAACAACCAATAAA 58.956 29.630 0.00 0.00 44.79 1.40
690 710 7.176340 AGAGAAATGCTGCTGTTTAATTCTCTT 59.824 33.333 9.98 0.00 45.69 2.85
692 712 6.850555 AGAGAAATGCTGCTGTTTAATTCTC 58.149 36.000 0.00 4.11 40.97 2.87
693 713 6.830873 AGAGAAATGCTGCTGTTTAATTCT 57.169 33.333 0.00 0.00 0.00 2.40
694 714 7.811713 AGAAAGAGAAATGCTGCTGTTTAATTC 59.188 33.333 0.00 5.69 29.13 2.17
695 715 7.664758 AGAAAGAGAAATGCTGCTGTTTAATT 58.335 30.769 0.00 0.00 29.13 1.40
697 717 6.294176 GGAGAAAGAGAAATGCTGCTGTTTAA 60.294 38.462 0.00 0.00 29.13 1.52
699 719 4.022503 GGAGAAAGAGAAATGCTGCTGTTT 60.023 41.667 0.00 2.17 31.29 2.83
701 721 3.080319 GGAGAAAGAGAAATGCTGCTGT 58.920 45.455 0.00 0.00 0.00 4.40
702 722 2.422832 GGGAGAAAGAGAAATGCTGCTG 59.577 50.000 0.00 0.00 0.00 4.41
704 724 1.399791 CGGGAGAAAGAGAAATGCTGC 59.600 52.381 0.00 0.00 0.00 5.25
705 725 2.417933 CACGGGAGAAAGAGAAATGCTG 59.582 50.000 0.00 0.00 0.00 4.41
739 775 2.751806 CACCTGATCTCAAAGGAAAGGC 59.248 50.000 3.90 0.00 37.01 4.35
769 805 5.585047 GCCTAAATTAACTCGATGGAACTGT 59.415 40.000 0.00 0.00 0.00 3.55
771 807 5.990668 AGCCTAAATTAACTCGATGGAACT 58.009 37.500 0.00 0.00 0.00 3.01
772 808 6.679327 AAGCCTAAATTAACTCGATGGAAC 57.321 37.500 0.00 0.00 0.00 3.62
775 811 7.730364 ATGTAAGCCTAAATTAACTCGATGG 57.270 36.000 0.00 0.00 0.00 3.51
776 812 9.438291 CAAATGTAAGCCTAAATTAACTCGATG 57.562 33.333 0.00 0.00 0.00 3.84
777 813 8.129211 GCAAATGTAAGCCTAAATTAACTCGAT 58.871 33.333 0.00 0.00 0.00 3.59
778 814 7.335924 AGCAAATGTAAGCCTAAATTAACTCGA 59.664 33.333 0.00 0.00 0.00 4.04
779 815 7.472543 AGCAAATGTAAGCCTAAATTAACTCG 58.527 34.615 0.00 0.00 0.00 4.18
780 816 9.717892 GTAGCAAATGTAAGCCTAAATTAACTC 57.282 33.333 0.00 0.00 0.00 3.01
781 817 9.238368 TGTAGCAAATGTAAGCCTAAATTAACT 57.762 29.630 0.00 0.00 0.00 2.24
782 818 9.503427 CTGTAGCAAATGTAAGCCTAAATTAAC 57.497 33.333 0.00 0.00 0.00 2.01
783 819 9.238368 ACTGTAGCAAATGTAAGCCTAAATTAA 57.762 29.630 0.00 0.00 0.00 1.40
784 820 8.801882 ACTGTAGCAAATGTAAGCCTAAATTA 57.198 30.769 0.00 0.00 0.00 1.40
785 821 7.703058 ACTGTAGCAAATGTAAGCCTAAATT 57.297 32.000 0.00 0.00 0.00 1.82
786 822 7.703058 AACTGTAGCAAATGTAAGCCTAAAT 57.297 32.000 0.00 0.00 0.00 1.40
787 823 7.881232 AGTAACTGTAGCAAATGTAAGCCTAAA 59.119 33.333 0.00 0.00 0.00 1.85
788 824 7.391620 AGTAACTGTAGCAAATGTAAGCCTAA 58.608 34.615 0.00 0.00 0.00 2.69
789 825 6.942976 AGTAACTGTAGCAAATGTAAGCCTA 58.057 36.000 0.00 0.00 0.00 3.93
790 826 5.805728 AGTAACTGTAGCAAATGTAAGCCT 58.194 37.500 0.00 0.00 0.00 4.58
791 827 6.072673 ACAAGTAACTGTAGCAAATGTAAGCC 60.073 38.462 0.00 0.00 0.00 4.35
792 828 6.899114 ACAAGTAACTGTAGCAAATGTAAGC 58.101 36.000 0.00 0.00 0.00 3.09
793 829 9.382244 GAAACAAGTAACTGTAGCAAATGTAAG 57.618 33.333 0.00 0.00 0.00 2.34
794 830 8.347035 GGAAACAAGTAACTGTAGCAAATGTAA 58.653 33.333 0.00 0.00 0.00 2.41
795 831 7.717875 AGGAAACAAGTAACTGTAGCAAATGTA 59.282 33.333 0.00 0.00 0.00 2.29
796 832 6.546034 AGGAAACAAGTAACTGTAGCAAATGT 59.454 34.615 0.00 0.00 0.00 2.71
797 833 6.970484 AGGAAACAAGTAACTGTAGCAAATG 58.030 36.000 0.00 0.00 0.00 2.32
798 834 6.998673 AGAGGAAACAAGTAACTGTAGCAAAT 59.001 34.615 0.00 0.00 0.00 2.32
799 835 6.354130 AGAGGAAACAAGTAACTGTAGCAAA 58.646 36.000 0.00 0.00 0.00 3.68
800 836 5.925509 AGAGGAAACAAGTAACTGTAGCAA 58.074 37.500 0.00 0.00 0.00 3.91
801 837 5.546621 AGAGGAAACAAGTAACTGTAGCA 57.453 39.130 0.00 0.00 0.00 3.49
802 838 6.689554 ACTAGAGGAAACAAGTAACTGTAGC 58.310 40.000 0.00 0.00 30.68 3.58
828 864 9.705290 AAGTTCCGCAAAATTATTCAAAAGTAT 57.295 25.926 0.00 0.00 0.00 2.12
829 865 9.535878 AAAGTTCCGCAAAATTATTCAAAAGTA 57.464 25.926 0.00 0.00 0.00 2.24
830 866 8.432110 AAAGTTCCGCAAAATTATTCAAAAGT 57.568 26.923 0.00 0.00 0.00 2.66
831 867 8.764287 AGAAAGTTCCGCAAAATTATTCAAAAG 58.236 29.630 0.00 0.00 0.00 2.27
832 868 8.547069 CAGAAAGTTCCGCAAAATTATTCAAAA 58.453 29.630 0.00 0.00 0.00 2.44
833 869 7.923344 TCAGAAAGTTCCGCAAAATTATTCAAA 59.077 29.630 0.00 0.00 0.00 2.69
837 873 6.981722 ACTCAGAAAGTTCCGCAAAATTATT 58.018 32.000 0.00 0.00 33.03 1.40
857 893 3.068732 CCGAGCTCCATGAATTCTACTCA 59.931 47.826 8.47 0.00 0.00 3.41
868 904 3.876914 TGCTAAATTAACCGAGCTCCATG 59.123 43.478 8.47 0.00 35.89 3.66
914 952 6.114187 TCTTGATTTTAACTGCTGAGGAGA 57.886 37.500 8.31 0.00 0.00 3.71
921 959 8.139989 GCCATTGATATCTTGATTTTAACTGCT 58.860 33.333 3.98 0.00 0.00 4.24
922 960 7.922278 TGCCATTGATATCTTGATTTTAACTGC 59.078 33.333 3.98 0.00 0.00 4.40
930 968 7.834881 ATTGTCTGCCATTGATATCTTGATT 57.165 32.000 3.98 0.00 0.00 2.57
941 979 3.379057 TGCTGATGTATTGTCTGCCATTG 59.621 43.478 0.00 0.00 39.08 2.82
942 980 3.623703 TGCTGATGTATTGTCTGCCATT 58.376 40.909 0.00 0.00 39.08 3.16
974 1012 1.068474 CTCTTTGTGTCCGCCTTACG 58.932 55.000 0.00 0.00 43.15 3.18
975 1013 0.796927 GCTCTTTGTGTCCGCCTTAC 59.203 55.000 0.00 0.00 0.00 2.34
976 1014 0.321298 GGCTCTTTGTGTCCGCCTTA 60.321 55.000 0.00 0.00 37.76 2.69
981 1061 0.249868 TCTGTGGCTCTTTGTGTCCG 60.250 55.000 0.00 0.00 0.00 4.79
988 1068 0.036010 CGGTCCATCTGTGGCTCTTT 60.036 55.000 0.00 0.00 45.63 2.52
1085 1165 0.611896 CCCTTGCGGAGTTTTCCCAT 60.612 55.000 0.00 0.00 40.67 4.00
1089 1169 1.001706 GTGTTCCCTTGCGGAGTTTTC 60.002 52.381 0.00 0.00 43.39 2.29
1097 1177 3.365265 GGCAGGTGTTCCCTTGCG 61.365 66.667 0.00 0.00 42.73 4.85
1137 1217 0.525761 CCGTGCAAAATACCTGGTGG 59.474 55.000 10.23 0.00 39.83 4.61
1160 1240 1.450312 GATTCCTCCAGTGCCACCG 60.450 63.158 0.00 0.00 0.00 4.94
1252 1332 1.005340 CATCGGAGCAAGACAGAAGC 58.995 55.000 0.00 0.00 0.00 3.86
1263 1343 3.567797 GAACGGCAGCATCGGAGC 61.568 66.667 0.00 0.00 0.00 4.70
1278 1358 1.300620 CTCACTCAACCGCCGTGAA 60.301 57.895 0.00 0.00 37.24 3.18
1303 1383 0.386352 CCATGCGTGTCTTGTTGCAG 60.386 55.000 4.96 0.00 41.19 4.41
1398 1478 1.007734 GGTCACGTGCTTCGACAGA 60.008 57.895 11.67 0.00 42.86 3.41
1410 1490 3.059597 GTGAGTCATTGAACTTGGTCACG 60.060 47.826 0.00 0.00 0.00 4.35
1462 1542 3.330267 AGAGTTCCTCGAAAACATCTGC 58.670 45.455 11.62 0.00 35.36 4.26
1473 1553 5.907207 TCTGGAATATTCAAGAGTTCCTCG 58.093 41.667 17.20 0.00 40.55 4.63
1489 1569 3.470709 CCGCATGACTACAATCTGGAAT 58.529 45.455 0.00 0.00 0.00 3.01
1499 1579 1.518572 CACCGTCCCGCATGACTAC 60.519 63.158 0.00 0.00 32.97 2.73
1539 1619 1.066002 CCATTCCCATTTGTAGCTGCG 59.934 52.381 0.00 0.00 0.00 5.18
1551 1631 2.696864 GGTCTCACCTCCATTCCCA 58.303 57.895 0.00 0.00 34.73 4.37
1611 1691 5.376625 TCAATCCCATGGCTACTTTGATAC 58.623 41.667 6.09 0.00 0.00 2.24
1612 1692 5.645056 TCAATCCCATGGCTACTTTGATA 57.355 39.130 6.09 0.00 0.00 2.15
1620 1700 6.439487 TCCTAAATTTTCAATCCCATGGCTA 58.561 36.000 6.09 0.00 0.00 3.93
1621 1701 5.279685 TCCTAAATTTTCAATCCCATGGCT 58.720 37.500 6.09 0.00 0.00 4.75
1659 1739 6.690194 AAGCTGAGGAATCATAACATCAAC 57.310 37.500 0.00 0.00 0.00 3.18
1671 1751 4.592942 TGTAGATGCAAAAGCTGAGGAAT 58.407 39.130 0.00 0.00 0.00 3.01
1723 1803 0.327924 TGGTTGATGGACCAAGCGAT 59.672 50.000 0.00 0.00 46.33 4.58
1725 1805 4.395519 TGGTTGATGGACCAAGCG 57.604 55.556 0.00 0.00 46.33 4.68
1732 1812 9.645128 ATGAATTAGTTAATGATGGTTGATGGA 57.355 29.630 0.00 0.00 0.00 3.41
1736 1816 8.291191 TGCATGAATTAGTTAATGATGGTTGA 57.709 30.769 0.00 0.00 28.83 3.18
1737 1817 9.188588 GATGCATGAATTAGTTAATGATGGTTG 57.811 33.333 2.46 0.00 28.83 3.77
1738 1818 9.139734 AGATGCATGAATTAGTTAATGATGGTT 57.860 29.630 2.46 0.00 28.83 3.67
1739 1819 8.701908 AGATGCATGAATTAGTTAATGATGGT 57.298 30.769 2.46 0.00 28.83 3.55
1740 1820 9.406828 CAAGATGCATGAATTAGTTAATGATGG 57.593 33.333 2.46 0.00 28.83 3.51
1761 1841 6.820656 AGCGATGTCTGAAAAATAGTCAAGAT 59.179 34.615 0.00 0.00 0.00 2.40
1783 1863 4.285292 GCATCCTCATGATTTTTGTAGCG 58.715 43.478 0.00 0.00 30.57 4.26
1795 1875 2.028420 TTTCAGGTCGCATCCTCATG 57.972 50.000 0.00 0.00 35.37 3.07
1864 1944 7.148474 CGTAGCATGTCAACCTTGTTATAAAGT 60.148 37.037 0.00 0.00 0.00 2.66
1928 2008 3.118775 AGGGAAAAACCTTTTGTGCTCAC 60.119 43.478 0.00 0.00 37.69 3.51
1991 2071 7.911651 TCAGGACAATGTTTAAGAATCTCTCT 58.088 34.615 0.00 0.00 35.13 3.10
2044 2124 5.483937 TGTATGTAGGAGTGTCAAACCATCT 59.516 40.000 0.00 0.00 0.00 2.90
2052 2132 7.616542 TGGTTATAGTTGTATGTAGGAGTGTCA 59.383 37.037 0.00 0.00 0.00 3.58
2095 2175 3.055819 GTGTCCTCAGGATAAAGTCAGCA 60.056 47.826 0.00 0.00 32.73 4.41
2096 2176 3.526534 GTGTCCTCAGGATAAAGTCAGC 58.473 50.000 0.00 0.00 32.73 4.26
2098 2178 2.496070 CGGTGTCCTCAGGATAAAGTCA 59.504 50.000 0.00 0.00 32.73 3.41
2101 2181 1.207089 TGCGGTGTCCTCAGGATAAAG 59.793 52.381 0.00 0.00 32.73 1.85
2162 2242 2.039084 GGACTGCATAATGTAGAGGGGG 59.961 54.545 0.00 0.00 34.09 5.40
2224 2304 9.243105 TCGATCATTGTTACATCTATATCCTCA 57.757 33.333 0.00 0.00 0.00 3.86
2287 2367 4.558226 TGTCTTGGCATTCTGTATGACT 57.442 40.909 1.73 0.00 43.22 3.41
2305 2385 6.973229 AACATACGTACCCAGTTTAATGTC 57.027 37.500 0.00 0.00 0.00 3.06
2344 2424 3.570926 AAGCATGCACACTTCATTCTG 57.429 42.857 21.98 0.00 0.00 3.02
2367 2447 6.101150 TCTGGGTACAAATGACCTTATAGCAT 59.899 38.462 0.00 0.00 37.13 3.79
2368 2448 5.427157 TCTGGGTACAAATGACCTTATAGCA 59.573 40.000 0.00 0.00 37.13 3.49
2369 2449 5.925509 TCTGGGTACAAATGACCTTATAGC 58.074 41.667 0.00 0.00 37.13 2.97
2370 2450 8.210946 TCATTCTGGGTACAAATGACCTTATAG 58.789 37.037 0.00 0.00 37.13 1.31
2423 2503 5.050644 TGCACACTTCATTCTGCATTAAG 57.949 39.130 0.00 0.00 34.73 1.85
2426 2506 3.845178 CATGCACACTTCATTCTGCATT 58.155 40.909 1.26 0.00 45.91 3.56
2993 3074 6.305693 AGATCAGAGTTGAAAGTTTTTCCG 57.694 37.500 0.00 0.00 36.78 4.30
3057 3138 7.441878 GCAGATAGATTGCAAAATGTTACAC 57.558 36.000 1.71 0.00 41.17 2.90
3163 3253 3.636679 TGACCACATTCTGTCCCAAAAA 58.363 40.909 0.00 0.00 0.00 1.94
3217 3310 1.475403 TCTCTGGAGACCGAATCACC 58.525 55.000 0.00 0.00 38.51 4.02
3231 3326 5.298197 GCAGATGGCATGAATTATCTCTG 57.702 43.478 3.81 4.53 43.97 3.35
3324 3421 9.722056 CATAATATACTTTTCTGTGGTGCTTTC 57.278 33.333 0.00 0.00 0.00 2.62
3350 3447 5.470098 TGCTCAACAGTACCTGAATTTCTTC 59.530 40.000 0.00 0.00 35.18 2.87
3351 3448 5.239525 GTGCTCAACAGTACCTGAATTTCTT 59.760 40.000 0.00 0.00 35.18 2.52
3353 3450 4.757149 AGTGCTCAACAGTACCTGAATTTC 59.243 41.667 0.00 0.00 35.92 2.17
3354 3451 4.718961 AGTGCTCAACAGTACCTGAATTT 58.281 39.130 0.00 0.00 35.92 1.82
3387 3487 3.932710 AGTCGATACATTCATTGCACGTT 59.067 39.130 0.00 0.00 0.00 3.99
3461 3567 9.935241 TTTGCAAATAAGTGATTATTTGGCTTA 57.065 25.926 24.14 12.48 46.81 3.09
3462 3568 8.845413 TTTGCAAATAAGTGATTATTTGGCTT 57.155 26.923 24.14 0.00 46.81 4.35
3490 3596 2.854963 ACTGTGATTCTGCTTGCAAGA 58.145 42.857 30.39 13.73 0.00 3.02
3504 3610 8.105097 TGCATTTTTACAAGCTAATACTGTGA 57.895 30.769 0.00 0.00 0.00 3.58
3509 3615 9.586435 AAGGATTGCATTTTTACAAGCTAATAC 57.414 29.630 0.00 0.00 32.89 1.89
3525 3631 7.875041 GCCGTGATATATCTATAAGGATTGCAT 59.125 37.037 13.79 0.00 0.00 3.96
3526 3632 7.147742 TGCCGTGATATATCTATAAGGATTGCA 60.148 37.037 13.79 5.67 0.00 4.08
3559 3665 7.811117 TGTGCTTTAAAATGTACTACAGGTT 57.189 32.000 0.00 0.00 0.00 3.50
3609 3715 4.218417 AGTGATTTTGTGGTCCTTACATGC 59.782 41.667 0.00 0.00 0.00 4.06
3641 3747 8.736244 GGCTCCTGATTTGTTGTAATAAAAGTA 58.264 33.333 0.00 0.00 0.00 2.24
3689 3795 8.717821 GTTGCTTCAACTTATTACACTATGTCA 58.282 33.333 2.71 0.00 40.73 3.58
3750 3856 1.280133 CCAAGGAGATGAGAGCCAACA 59.720 52.381 0.00 0.00 0.00 3.33
3822 3928 2.288518 GGAGCAACAGATACCTCGGATC 60.289 54.545 0.00 0.00 0.00 3.36
3864 3970 3.374988 GCGTTCCATCATCACAATCTCAA 59.625 43.478 0.00 0.00 0.00 3.02
3865 3971 2.938451 GCGTTCCATCATCACAATCTCA 59.062 45.455 0.00 0.00 0.00 3.27
3866 3972 2.938451 TGCGTTCCATCATCACAATCTC 59.062 45.455 0.00 0.00 0.00 2.75
3881 3987 3.044059 GCTGTGGCCTCATGCGTTC 62.044 63.158 8.18 0.00 42.61 3.95
3952 4058 7.749126 CAGATTAAAACCACGTCACTTATTTCC 59.251 37.037 0.00 0.00 0.00 3.13
3969 4075 8.626526 GTGGAGTGGTTTTAGTTCAGATTAAAA 58.373 33.333 0.00 0.00 0.00 1.52
3990 4096 6.743575 AATTCTGTTCGGAAATAAGTGGAG 57.256 37.500 0.00 0.00 0.00 3.86
3991 4097 6.569610 GCAAATTCTGTTCGGAAATAAGTGGA 60.570 38.462 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.