Multiple sequence alignment - TraesCS5B01G522300

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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 TraesCS5B01G522300 chr5B 100.000 2900 0 0 1 2900 684048660 684051559 0.000000e+00 5356.0
1 TraesCS5B01G522300 chr5B 83.887 1384 159 40 925 2263 684031968 684033332 0.000000e+00 1262.0
2 TraesCS5B01G522300 chr5B 84.412 1251 140 30 925 2143 684038969 684040196 0.000000e+00 1179.0
3 TraesCS5B01G522300 chr5B 78.635 1245 205 46 1042 2265 685069429 685070633 0.000000e+00 769.0
4 TraesCS5B01G522300 chr5B 96.667 300 9 1 2602 2900 684055711 684056010 5.580000e-137 497.0
5 TraesCS5B01G522300 chr5B 78.277 534 78 23 1620 2132 684113217 684113733 2.810000e-80 309.0
6 TraesCS5B01G522300 chr5B 93.277 119 8 0 652 770 38365241 38365123 2.970000e-40 176.0
7 TraesCS5B01G522300 chr5B 93.860 114 7 0 656 769 691516947 691517060 3.840000e-39 172.0
8 TraesCS5B01G522300 chr5B 90.909 121 11 0 649 769 611922699 611922819 2.310000e-36 163.0
9 TraesCS5B01G522300 chr4A 91.083 1671 119 15 904 2554 626990403 626988743 0.000000e+00 2233.0
10 TraesCS5B01G522300 chr4A 84.779 1268 142 25 925 2175 627004506 627003273 0.000000e+00 1225.0
11 TraesCS5B01G522300 chr4A 91.935 682 53 2 904 1583 627052580 627051899 0.000000e+00 953.0
12 TraesCS5B01G522300 chr4A 91.508 683 53 5 904 1583 627255896 627255216 0.000000e+00 935.0
13 TraesCS5B01G522300 chr4A 90.776 683 59 4 904 1583 627119515 627118834 0.000000e+00 909.0
14 TraesCS5B01G522300 chr4A 85.068 663 63 20 1 647 627053419 627052777 0.000000e+00 643.0
15 TraesCS5B01G522300 chr4A 85.068 663 62 21 1 647 627120353 627119712 2.440000e-180 641.0
16 TraesCS5B01G522300 chr4A 85.238 630 64 15 33 647 627256708 627256093 3.170000e-174 621.0
17 TraesCS5B01G522300 chr4A 78.860 965 160 33 1070 2016 625736681 625735743 1.910000e-171 612.0
18 TraesCS5B01G522300 chr4A 83.058 667 56 25 1 647 626991242 626990613 1.170000e-153 553.0
19 TraesCS5B01G522300 chr4A 93.084 347 23 1 2555 2900 626988442 626988096 9.270000e-140 507.0
20 TraesCS5B01G522300 chr4A 77.820 532 81 23 1620 2132 626940008 626939495 7.860000e-76 294.0
21 TraesCS5B01G522300 chr4A 81.044 364 53 10 1941 2302 626976659 626976310 2.850000e-70 276.0
22 TraesCS5B01G522300 chr4A 100.000 30 0 0 2525 2554 626995326 626995297 4.040000e-04 56.5
23 TraesCS5B01G522300 chr4A 100.000 30 0 0 2525 2554 627081187 627081158 4.040000e-04 56.5
24 TraesCS5B01G522300 chr4A 100.000 30 0 0 2525 2554 627284008 627283979 4.040000e-04 56.5
25 TraesCS5B01G522300 chr5D 83.495 1551 176 46 925 2420 541990238 541991763 0.000000e+00 1373.0
26 TraesCS5B01G522300 chr5D 84.919 1293 159 19 1029 2302 542385275 542386550 0.000000e+00 1275.0
27 TraesCS5B01G522300 chr5D 78.477 1129 186 36 1011 2103 543440802 543441909 0.000000e+00 686.0
28 TraesCS5B01G522300 chr5D 88.728 346 36 2 2555 2897 542295241 542295586 1.240000e-113 420.0
29 TraesCS5B01G522300 chr5D 80.822 365 53 16 1941 2302 542097402 542097752 1.320000e-68 270.0
30 TraesCS5B01G522300 chr5D 86.585 164 18 2 2303 2466 542386639 542386798 8.260000e-41 178.0
31 TraesCS5B01G522300 chr5D 93.860 114 7 0 656 769 547545548 547545661 3.840000e-39 172.0
32 TraesCS5B01G522300 chr7B 93.860 114 7 0 656 769 712100750 712100637 3.840000e-39 172.0
33 TraesCS5B01G522300 chr2D 92.241 116 9 0 656 771 549737464 549737349 6.430000e-37 165.0
34 TraesCS5B01G522300 chr2D 90.244 123 12 0 646 768 543312498 543312620 8.320000e-36 161.0
35 TraesCS5B01G522300 chr1D 89.764 127 11 2 648 773 209564268 209564143 8.320000e-36 161.0
36 TraesCS5B01G522300 chr3B 87.786 131 14 2 640 769 679712641 679712770 5.010000e-33 152.0


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 TraesCS5B01G522300 chr5B 684048660 684051559 2899 False 5356.000000 5356 100.0000 1 2900 1 chr5B.!!$F4 2899
1 TraesCS5B01G522300 chr5B 684031968 684033332 1364 False 1262.000000 1262 83.8870 925 2263 1 chr5B.!!$F2 1338
2 TraesCS5B01G522300 chr5B 684038969 684040196 1227 False 1179.000000 1179 84.4120 925 2143 1 chr5B.!!$F3 1218
3 TraesCS5B01G522300 chr5B 685069429 685070633 1204 False 769.000000 769 78.6350 1042 2265 1 chr5B.!!$F7 1223
4 TraesCS5B01G522300 chr5B 684113217 684113733 516 False 309.000000 309 78.2770 1620 2132 1 chr5B.!!$F6 512
5 TraesCS5B01G522300 chr4A 627003273 627004506 1233 True 1225.000000 1225 84.7790 925 2175 1 chr4A.!!$R5 1250
6 TraesCS5B01G522300 chr4A 626988096 626991242 3146 True 1097.666667 2233 89.0750 1 2900 3 chr4A.!!$R8 2899
7 TraesCS5B01G522300 chr4A 627051899 627053419 1520 True 798.000000 953 88.5015 1 1583 2 chr4A.!!$R9 1582
8 TraesCS5B01G522300 chr4A 627255216 627256708 1492 True 778.000000 935 88.3730 33 1583 2 chr4A.!!$R11 1550
9 TraesCS5B01G522300 chr4A 627118834 627120353 1519 True 775.000000 909 87.9220 1 1583 2 chr4A.!!$R10 1582
10 TraesCS5B01G522300 chr4A 625735743 625736681 938 True 612.000000 612 78.8600 1070 2016 1 chr4A.!!$R1 946
11 TraesCS5B01G522300 chr4A 626939495 626940008 513 True 294.000000 294 77.8200 1620 2132 1 chr4A.!!$R2 512
12 TraesCS5B01G522300 chr5D 541990238 541991763 1525 False 1373.000000 1373 83.4950 925 2420 1 chr5D.!!$F1 1495
13 TraesCS5B01G522300 chr5D 542385275 542386798 1523 False 726.500000 1275 85.7520 1029 2466 2 chr5D.!!$F6 1437
14 TraesCS5B01G522300 chr5D 543440802 543441909 1107 False 686.000000 686 78.4770 1011 2103 1 chr5D.!!$F4 1092

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
209 211 0.106708 GACATTCGCATAGGGGAGCA 59.893 55.0 0.0 0.0 37.28 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2034 2223 0.110056 CAGATGCGTTTGCCTGACAC 60.11 55.0 0.0 0.0 41.78 3.67 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
24 25 3.262405 TCACGTATAAGCCTTTTCCCAGT 59.738 43.478 0.00 0.00 0.00 4.00
25 26 4.467082 TCACGTATAAGCCTTTTCCCAGTA 59.533 41.667 0.00 0.00 0.00 2.74
26 27 4.809426 CACGTATAAGCCTTTTCCCAGTAG 59.191 45.833 0.00 0.00 0.00 2.57
27 28 4.468868 ACGTATAAGCCTTTTCCCAGTAGT 59.531 41.667 0.00 0.00 0.00 2.73
28 29 4.809426 CGTATAAGCCTTTTCCCAGTAGTG 59.191 45.833 0.00 0.00 0.00 2.74
29 30 2.586648 AAGCCTTTTCCCAGTAGTGG 57.413 50.000 9.89 9.89 44.56 4.00
30 31 1.446016 AGCCTTTTCCCAGTAGTGGT 58.554 50.000 15.60 0.00 43.23 4.16
66 67 1.475930 GCTGAATTAGAGTCTGGGCCC 60.476 57.143 17.59 17.59 0.00 5.80
94 95 4.689612 AATAGCATCTACAACCGGACAT 57.310 40.909 9.46 0.00 0.00 3.06
97 98 2.159043 AGCATCTACAACCGGACATGAG 60.159 50.000 9.46 0.00 0.00 2.90
134 136 9.696917 AAACTTGATTTCCTAATTGTCACATTC 57.303 29.630 0.00 0.00 0.00 2.67
136 138 9.739276 ACTTGATTTCCTAATTGTCACATTCTA 57.261 29.630 0.00 0.00 0.00 2.10
162 164 5.361857 AGGAAGTAAATCGACGAATTCCCTA 59.638 40.000 14.98 0.00 36.26 3.53
191 193 4.439153 CGCTAGTTGTGGTAAATAGTCGGA 60.439 45.833 0.00 0.00 0.00 4.55
204 206 0.389391 AGTCGGACATTCGCATAGGG 59.611 55.000 11.27 0.00 0.00 3.53
209 211 0.106708 GACATTCGCATAGGGGAGCA 59.893 55.000 0.00 0.00 37.28 4.26
210 212 0.107456 ACATTCGCATAGGGGAGCAG 59.893 55.000 0.00 0.00 37.28 4.24
211 213 0.604780 CATTCGCATAGGGGAGCAGG 60.605 60.000 0.00 0.00 37.28 4.85
240 242 1.077716 GACCCATGTGTAGCCACCC 60.078 63.158 0.00 0.00 41.09 4.61
248 250 2.045926 GTAGCCACCCCAGTGCAG 60.046 66.667 0.00 0.00 43.09 4.41
253 255 3.663176 CACCCCAGTGCAGCGTTG 61.663 66.667 0.00 0.00 37.14 4.10
256 258 1.599518 CCCCAGTGCAGCGTTGTTA 60.600 57.895 0.00 0.00 0.00 2.41
257 259 1.169661 CCCCAGTGCAGCGTTGTTAA 61.170 55.000 0.00 0.00 0.00 2.01
347 349 6.669631 TCCTTTCTATTTATTTGTCTCCCCC 58.330 40.000 0.00 0.00 0.00 5.40
440 446 7.885297 TGGAGATACTCAAAAACTTTTCATGG 58.115 34.615 0.00 0.00 31.08 3.66
520 536 1.751351 TCAATTGTTTGGCCAACGTGA 59.249 42.857 20.35 13.94 38.36 4.35
521 537 2.363680 TCAATTGTTTGGCCAACGTGAT 59.636 40.909 20.35 7.33 38.36 3.06
522 538 2.437200 ATTGTTTGGCCAACGTGATG 57.563 45.000 20.35 0.00 38.36 3.07
523 539 1.393603 TTGTTTGGCCAACGTGATGA 58.606 45.000 20.35 0.00 38.36 2.92
532 548 2.540361 GCCAACGTGATGATGATGCTTC 60.540 50.000 0.00 0.00 0.00 3.86
546 562 3.882888 TGATGCTTCGGAAGTGTTTTTCT 59.117 39.130 18.32 0.00 0.00 2.52
587 603 4.021229 GGGGTGGAAGGAAAATAACGAAT 58.979 43.478 0.00 0.00 0.00 3.34
658 681 9.511144 CGAAACCTTTTTATTGTACATATTCCC 57.489 33.333 0.00 0.00 0.00 3.97
661 684 8.762481 ACCTTTTTATTGTACATATTCCCTCC 57.238 34.615 0.00 0.00 0.00 4.30
662 685 7.501225 ACCTTTTTATTGTACATATTCCCTCCG 59.499 37.037 0.00 0.00 0.00 4.63
663 686 7.501225 CCTTTTTATTGTACATATTCCCTCCGT 59.499 37.037 0.00 0.00 0.00 4.69
664 687 8.441312 TTTTTATTGTACATATTCCCTCCGTC 57.559 34.615 0.00 0.00 0.00 4.79
665 688 6.989155 TTATTGTACATATTCCCTCCGTCT 57.011 37.500 0.00 0.00 0.00 4.18
666 689 4.665833 TTGTACATATTCCCTCCGTCTG 57.334 45.455 0.00 0.00 0.00 3.51
667 690 2.963101 TGTACATATTCCCTCCGTCTGG 59.037 50.000 0.00 0.00 0.00 3.86
668 691 2.471815 ACATATTCCCTCCGTCTGGA 57.528 50.000 0.00 0.00 43.88 3.86
669 692 2.759355 ACATATTCCCTCCGTCTGGAA 58.241 47.619 0.00 0.00 45.87 3.53
671 694 3.716872 ACATATTCCCTCCGTCTGGAATT 59.283 43.478 12.89 0.00 46.68 2.17
672 695 4.905456 ACATATTCCCTCCGTCTGGAATTA 59.095 41.667 12.89 3.30 46.68 1.40
673 696 3.840124 ATTCCCTCCGTCTGGAATTAC 57.160 47.619 4.30 0.00 46.68 1.89
674 697 2.544844 TCCCTCCGTCTGGAATTACT 57.455 50.000 0.00 0.00 45.87 2.24
675 698 2.829023 TCCCTCCGTCTGGAATTACTT 58.171 47.619 0.00 0.00 45.87 2.24
676 699 2.500098 TCCCTCCGTCTGGAATTACTTG 59.500 50.000 0.00 0.00 45.87 3.16
677 700 2.236395 CCCTCCGTCTGGAATTACTTGT 59.764 50.000 0.00 0.00 45.87 3.16
678 701 3.522553 CCTCCGTCTGGAATTACTTGTC 58.477 50.000 0.00 0.00 45.87 3.18
679 702 3.179830 CTCCGTCTGGAATTACTTGTCG 58.820 50.000 0.00 0.00 45.87 4.35
680 703 2.559668 TCCGTCTGGAATTACTTGTCGT 59.440 45.455 0.00 0.00 42.85 4.34
681 704 3.758023 TCCGTCTGGAATTACTTGTCGTA 59.242 43.478 0.00 0.00 42.85 3.43
682 705 4.400251 TCCGTCTGGAATTACTTGTCGTAT 59.600 41.667 0.00 0.00 42.85 3.06
683 706 5.589855 TCCGTCTGGAATTACTTGTCGTATA 59.410 40.000 0.00 0.00 42.85 1.47
684 707 6.095300 TCCGTCTGGAATTACTTGTCGTATAA 59.905 38.462 0.00 0.00 42.85 0.98
685 708 6.753279 CCGTCTGGAATTACTTGTCGTATAAA 59.247 38.462 0.00 0.00 37.49 1.40
686 709 7.437267 CCGTCTGGAATTACTTGTCGTATAAAT 59.563 37.037 0.00 0.00 37.49 1.40
687 710 8.266682 CGTCTGGAATTACTTGTCGTATAAATG 58.733 37.037 0.00 0.00 0.00 2.32
688 711 8.548721 GTCTGGAATTACTTGTCGTATAAATGG 58.451 37.037 0.00 0.00 0.00 3.16
689 712 8.479689 TCTGGAATTACTTGTCGTATAAATGGA 58.520 33.333 0.00 0.00 0.00 3.41
690 713 9.273016 CTGGAATTACTTGTCGTATAAATGGAT 57.727 33.333 0.00 0.00 0.00 3.41
698 721 9.661563 ACTTGTCGTATAAATGGATAAAACTGA 57.338 29.630 0.00 0.00 0.00 3.41
701 724 9.104965 TGTCGTATAAATGGATAAAACTGAAGG 57.895 33.333 0.00 0.00 0.00 3.46
702 725 9.106070 GTCGTATAAATGGATAAAACTGAAGGT 57.894 33.333 0.00 0.00 0.00 3.50
740 763 9.915629 AAATACGTCTAGATACATCCATTTCTC 57.084 33.333 0.00 0.00 0.00 2.87
741 764 6.334102 ACGTCTAGATACATCCATTTCTCC 57.666 41.667 0.00 0.00 0.00 3.71
742 765 5.048643 ACGTCTAGATACATCCATTTCTCCG 60.049 44.000 0.00 0.00 0.00 4.63
743 766 5.181433 CGTCTAGATACATCCATTTCTCCGA 59.819 44.000 0.00 0.00 0.00 4.55
744 767 6.383415 GTCTAGATACATCCATTTCTCCGAC 58.617 44.000 0.00 0.00 0.00 4.79
745 768 6.016192 GTCTAGATACATCCATTTCTCCGACA 60.016 42.308 0.00 0.00 0.00 4.35
746 769 5.614324 AGATACATCCATTTCTCCGACAA 57.386 39.130 0.00 0.00 0.00 3.18
747 770 5.605534 AGATACATCCATTTCTCCGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
748 771 3.703001 ACATCCATTTCTCCGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
749 772 4.819105 ACATCCATTTCTCCGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
750 773 5.359194 ACATCCATTTCTCCGACAAGTAT 57.641 39.130 0.00 0.00 0.00 2.12
751 774 5.745227 ACATCCATTTCTCCGACAAGTATT 58.255 37.500 0.00 0.00 0.00 1.89
752 775 6.180472 ACATCCATTTCTCCGACAAGTATTT 58.820 36.000 0.00 0.00 0.00 1.40
753 776 6.316390 ACATCCATTTCTCCGACAAGTATTTC 59.684 38.462 0.00 0.00 0.00 2.17
754 777 5.183228 TCCATTTCTCCGACAAGTATTTCC 58.817 41.667 0.00 0.00 0.00 3.13
755 778 4.034048 CCATTTCTCCGACAAGTATTTCCG 59.966 45.833 0.00 0.00 0.00 4.30
756 779 2.953466 TCTCCGACAAGTATTTCCGG 57.047 50.000 0.00 0.00 41.36 5.14
757 780 1.479323 TCTCCGACAAGTATTTCCGGG 59.521 52.381 0.00 0.00 40.48 5.73
758 781 0.108041 TCCGACAAGTATTTCCGGGC 60.108 55.000 0.00 0.00 40.48 6.13
759 782 1.426041 CCGACAAGTATTTCCGGGCG 61.426 60.000 0.00 0.00 36.81 6.13
760 783 1.426041 CGACAAGTATTTCCGGGCGG 61.426 60.000 0.00 0.00 0.00 6.13
761 784 0.108041 GACAAGTATTTCCGGGCGGA 60.108 55.000 0.00 0.00 43.52 5.54
762 785 0.107848 ACAAGTATTTCCGGGCGGAG 60.108 55.000 0.00 0.00 46.06 4.63
763 786 0.814010 CAAGTATTTCCGGGCGGAGG 60.814 60.000 0.00 0.00 46.06 4.30
764 787 1.979619 AAGTATTTCCGGGCGGAGGG 61.980 60.000 0.00 0.00 46.06 4.30
765 788 2.041715 TATTTCCGGGCGGAGGGA 60.042 61.111 0.00 0.00 46.06 4.20
766 789 2.138179 TATTTCCGGGCGGAGGGAG 61.138 63.158 0.00 0.00 46.06 4.30
771 794 1.532316 CCGGGCGGAGGGAGTATAA 60.532 63.158 0.00 0.00 37.50 0.98
782 805 4.477581 GGAGGGAGTATAAAAGAGGGGTTT 59.522 45.833 0.00 0.00 0.00 3.27
794 818 3.956744 AGAGGGGTTTGTTCTAGAATGC 58.043 45.455 8.75 0.00 0.00 3.56
801 825 5.189180 GGTTTGTTCTAGAATGCCTGATCT 58.811 41.667 8.75 0.00 0.00 2.75
817 841 2.101415 TGATCTCGTCCAATAGCAGGTG 59.899 50.000 0.00 0.00 0.00 4.00
820 844 2.688446 TCTCGTCCAATAGCAGGTGTAG 59.312 50.000 0.00 0.00 0.00 2.74
823 847 2.738643 CGTCCAATAGCAGGTGTAGTGG 60.739 54.545 0.00 0.00 37.04 4.00
824 848 2.500098 GTCCAATAGCAGGTGTAGTGGA 59.500 50.000 0.00 0.00 41.24 4.02
825 849 2.766263 TCCAATAGCAGGTGTAGTGGAG 59.234 50.000 0.00 0.00 39.20 3.86
826 850 2.501723 CCAATAGCAGGTGTAGTGGAGT 59.498 50.000 0.00 0.00 37.76 3.85
827 851 3.704566 CCAATAGCAGGTGTAGTGGAGTA 59.295 47.826 0.00 0.00 37.76 2.59
828 852 4.202161 CCAATAGCAGGTGTAGTGGAGTAG 60.202 50.000 0.00 0.00 37.76 2.57
829 853 1.187087 AGCAGGTGTAGTGGAGTAGC 58.813 55.000 0.00 0.00 0.00 3.58
830 854 0.895530 GCAGGTGTAGTGGAGTAGCA 59.104 55.000 0.00 0.00 0.00 3.49
831 855 1.482593 GCAGGTGTAGTGGAGTAGCAT 59.517 52.381 0.00 0.00 0.00 3.79
832 856 2.693591 GCAGGTGTAGTGGAGTAGCATA 59.306 50.000 0.00 0.00 0.00 3.14
836 860 5.986135 CAGGTGTAGTGGAGTAGCATAAATC 59.014 44.000 0.00 0.00 0.00 2.17
862 909 4.345271 AAATCGTTCGGGGATTTTAACG 57.655 40.909 0.00 0.00 40.26 3.18
884 931 5.191059 CGTAAAAATACATTCGCAGAGCTC 58.809 41.667 5.27 5.27 38.43 4.09
887 934 5.476752 AAAATACATTCGCAGAGCTCTTC 57.523 39.130 15.27 8.73 38.43 2.87
888 935 2.194800 TACATTCGCAGAGCTCTTCG 57.805 50.000 26.87 26.87 38.43 3.79
889 936 0.459237 ACATTCGCAGAGCTCTTCGG 60.459 55.000 30.61 19.33 38.43 4.30
891 938 0.459237 ATTCGCAGAGCTCTTCGGTG 60.459 55.000 30.61 18.90 38.43 4.94
893 940 0.958876 TCGCAGAGCTCTTCGGTGTA 60.959 55.000 30.61 12.66 33.57 2.90
894 941 0.109272 CGCAGAGCTCTTCGGTGTAA 60.109 55.000 25.44 0.00 0.00 2.41
895 942 1.351153 GCAGAGCTCTTCGGTGTAAC 58.649 55.000 15.27 0.00 0.00 2.50
896 943 1.067495 GCAGAGCTCTTCGGTGTAACT 60.067 52.381 15.27 0.00 36.74 2.24
898 945 3.760537 CAGAGCTCTTCGGTGTAACTAC 58.239 50.000 15.27 0.00 36.74 2.73
899 946 3.190744 CAGAGCTCTTCGGTGTAACTACA 59.809 47.826 15.27 0.00 36.74 2.74
901 948 4.463186 AGAGCTCTTCGGTGTAACTACAAT 59.537 41.667 11.45 0.00 38.04 2.71
902 949 4.495422 AGCTCTTCGGTGTAACTACAATG 58.505 43.478 0.00 0.00 38.04 2.82
948 1064 5.106876 ACTACGGCCCAGTTATTATGTTT 57.893 39.130 0.00 0.00 0.00 2.83
951 1071 3.697542 ACGGCCCAGTTATTATGTTTTCC 59.302 43.478 0.00 0.00 0.00 3.13
1013 1158 4.181010 CCCCATGGAGGCACGGAG 62.181 72.222 15.22 0.00 35.39 4.63
1333 1496 4.309950 ACGGTCGCGCCCTCTTTT 62.310 61.111 4.01 0.00 0.00 2.27
1334 1497 3.788766 CGGTCGCGCCCTCTTTTG 61.789 66.667 4.01 0.00 0.00 2.44
1521 1684 0.249699 TGGCGTTCGTGTTCAGTCAT 60.250 50.000 0.00 0.00 0.00 3.06
1525 1688 2.394708 CGTTCGTGTTCAGTCATCAGT 58.605 47.619 0.00 0.00 0.00 3.41
1602 1765 6.201044 GTGAGATCACTTCCATTGTTATACCG 59.799 42.308 5.72 0.00 43.25 4.02
1733 1899 1.492176 AGTTGAGGAGGTGCCATATGG 59.508 52.381 18.07 18.07 40.02 2.74
1770 1951 1.227764 CATGCCGACAGAGGATGGG 60.228 63.158 0.00 0.00 0.00 4.00
1787 1968 2.566529 GTGCCTTGGTTTAGCCGC 59.433 61.111 0.00 0.00 41.21 6.53
1806 1993 2.222886 CGCAGTGGAACGATTCAATCTG 60.223 50.000 0.00 0.00 45.86 2.90
1831 2018 1.150536 TGGTCAAAGGTGGTGAGCC 59.849 57.895 1.57 0.00 41.72 4.70
1889 2077 7.972832 GTCATTGATCTCAAAAAGATTCTTCCC 59.027 37.037 0.00 0.00 45.06 3.97
1891 2079 5.891198 TGATCTCAAAAAGATTCTTCCCCA 58.109 37.500 0.00 0.00 45.06 4.96
1909 2097 0.892755 CACGAAGTAGTGGCAGGGTA 59.107 55.000 0.00 0.00 41.61 3.69
2031 2220 1.340405 CCATGAAGGTCAAGGAGGTGG 60.340 57.143 0.00 0.00 37.42 4.61
2032 2221 1.630369 CATGAAGGTCAAGGAGGTGGA 59.370 52.381 0.00 0.00 0.00 4.02
2033 2222 1.352083 TGAAGGTCAAGGAGGTGGAG 58.648 55.000 0.00 0.00 0.00 3.86
2034 2223 0.615850 GAAGGTCAAGGAGGTGGAGG 59.384 60.000 0.00 0.00 0.00 4.30
2035 2224 0.104409 AAGGTCAAGGAGGTGGAGGT 60.104 55.000 0.00 0.00 0.00 3.85
2036 2225 0.838122 AGGTCAAGGAGGTGGAGGTG 60.838 60.000 0.00 0.00 0.00 4.00
2132 2328 2.158449 CCAATGTCGCAGAGTTCACTTC 59.842 50.000 0.00 0.00 36.95 3.01
2160 2381 4.922206 TCCAAATGTATCTGCCTTGAAGT 58.078 39.130 0.00 0.00 0.00 3.01
2186 2411 9.791801 TTGCTTTCAAATATATGAGCCATAGTA 57.208 29.630 0.00 0.00 29.42 1.82
2215 2440 9.753674 TTTATAGATGACAAGTTTTCCTGGAAT 57.246 29.630 10.45 0.00 0.00 3.01
2230 2455 6.639632 TCCTGGAATTTCTTGTGAAAGAAG 57.360 37.500 0.00 0.00 44.25 2.85
2241 2467 9.897744 TTTCTTGTGAAAGAAGTGCTTATTATG 57.102 29.630 1.59 0.00 38.55 1.90
2350 2676 2.102578 GTATGTGAAGCCCTGGCATTT 58.897 47.619 11.38 0.00 44.88 2.32
2485 2811 2.023673 TCTTGTTGTTCAGTTGGGCTG 58.976 47.619 0.00 0.00 46.34 4.85
2504 2830 7.047891 TGGGCTGTACATTTAGATCTAAACAG 58.952 38.462 26.70 26.70 37.80 3.16
2554 2880 3.623510 GCTAGAGTTTGGGCTTGTACATC 59.376 47.826 0.00 0.00 0.00 3.06
2556 2882 3.944087 AGAGTTTGGGCTTGTACATCTC 58.056 45.455 0.00 0.00 0.00 2.75
2557 2883 3.584848 AGAGTTTGGGCTTGTACATCTCT 59.415 43.478 0.00 0.00 0.00 3.10
2558 2884 4.777896 AGAGTTTGGGCTTGTACATCTCTA 59.222 41.667 0.00 0.00 31.50 2.43
2619 3245 3.017442 GGGAACTTGGGATTTAGAGTGC 58.983 50.000 0.00 0.00 0.00 4.40
2622 3248 4.156739 GGAACTTGGGATTTAGAGTGCTTG 59.843 45.833 0.00 0.00 0.00 4.01
2625 3251 2.991250 TGGGATTTAGAGTGCTTGCTC 58.009 47.619 0.00 0.00 35.82 4.26
2631 3257 5.391416 GGATTTAGAGTGCTTGCTCAGTTTC 60.391 44.000 6.36 0.11 37.94 2.78
2643 3269 4.321718 TGCTCAGTTTCTTGATTCTCTGG 58.678 43.478 0.00 0.00 0.00 3.86
2646 3272 3.328931 TCAGTTTCTTGATTCTCTGGCCT 59.671 43.478 3.32 0.00 0.00 5.19
2678 3304 9.273016 CTTGATTCTGAAGTGTAGGAAAAGTTA 57.727 33.333 0.00 0.00 0.00 2.24
2726 3353 9.277783 ACTAAACTTCATCAGATATTATGCACC 57.722 33.333 0.00 0.00 0.00 5.01
2761 3388 5.600484 TGGACTTGTAACAATGAATGGGTTT 59.400 36.000 0.00 0.00 0.00 3.27
2783 3410 9.976255 GGTTTACACCAAAACAATTCTAAAAAC 57.024 29.630 0.00 0.00 43.61 2.43
2791 3418 7.650104 CCAAAACAATTCTAAAAACGCTTCCTA 59.350 33.333 0.00 0.00 0.00 2.94
2794 3421 7.130303 ACAATTCTAAAAACGCTTCCTAGTC 57.870 36.000 0.00 0.00 0.00 2.59
2795 3422 6.148976 ACAATTCTAAAAACGCTTCCTAGTCC 59.851 38.462 0.00 0.00 0.00 3.85
2832 3459 3.999046 ACCGTATTCTTCGTTTTGAGGT 58.001 40.909 0.00 0.00 0.00 3.85
2838 3465 6.019801 CGTATTCTTCGTTTTGAGGTAGATGG 60.020 42.308 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.123936 CCACTACTGGGAAAAGGCTTATAC 58.876 45.833 0.00 0.00 33.23 1.47
15 16 4.165372 AGACTGAAACCACTACTGGGAAAA 59.835 41.667 0.00 0.00 42.74 2.29
24 25 8.372459 TCAGCTAATAAAAGACTGAAACCACTA 58.628 33.333 0.00 0.00 34.59 2.74
25 26 7.224297 TCAGCTAATAAAAGACTGAAACCACT 58.776 34.615 0.00 0.00 34.59 4.00
26 27 7.435068 TCAGCTAATAAAAGACTGAAACCAC 57.565 36.000 0.00 0.00 34.59 4.16
27 28 8.635765 ATTCAGCTAATAAAAGACTGAAACCA 57.364 30.769 7.72 0.00 46.88 3.67
66 67 6.929049 TCCGGTTGTAGATGCTATTAAAGATG 59.071 38.462 0.00 0.00 0.00 2.90
134 136 7.541437 GGGAATTCGTCGATTTACTTCCTATAG 59.459 40.741 10.94 0.00 32.98 1.31
136 138 6.041751 AGGGAATTCGTCGATTTACTTCCTAT 59.958 38.462 10.94 4.06 32.98 2.57
137 139 5.361857 AGGGAATTCGTCGATTTACTTCCTA 59.638 40.000 10.94 0.00 32.98 2.94
139 141 4.439968 AGGGAATTCGTCGATTTACTTCC 58.560 43.478 10.94 10.57 0.00 3.46
140 142 7.710766 AATAGGGAATTCGTCGATTTACTTC 57.289 36.000 10.94 3.74 0.00 3.01
145 147 4.036380 GGCAAATAGGGAATTCGTCGATTT 59.964 41.667 0.00 0.00 0.00 2.17
149 151 1.260561 CGGCAAATAGGGAATTCGTCG 59.739 52.381 0.00 0.00 0.00 5.12
162 164 2.483014 TACCACAACTAGCGGCAAAT 57.517 45.000 1.45 0.00 0.00 2.32
180 182 5.466819 CCTATGCGAATGTCCGACTATTTA 58.533 41.667 0.00 0.00 0.00 1.40
191 193 0.107456 CTGCTCCCCTATGCGAATGT 59.893 55.000 0.00 0.00 0.00 2.71
204 206 3.890926 GGCCCATACCCCTGCTCC 61.891 72.222 0.00 0.00 0.00 4.70
231 233 2.045926 CTGCACTGGGGTGGCTAC 60.046 66.667 0.00 0.00 43.18 3.58
240 242 2.704725 AATTAACAACGCTGCACTGG 57.295 45.000 0.00 0.00 0.00 4.00
265 267 9.463443 CCAAGAAAGAATGAAACTACGAAAATT 57.537 29.630 0.00 0.00 0.00 1.82
266 268 8.846211 TCCAAGAAAGAATGAAACTACGAAAAT 58.154 29.630 0.00 0.00 0.00 1.82
267 269 8.215926 TCCAAGAAAGAATGAAACTACGAAAA 57.784 30.769 0.00 0.00 0.00 2.29
268 270 7.795482 TCCAAGAAAGAATGAAACTACGAAA 57.205 32.000 0.00 0.00 0.00 3.46
269 271 7.979444 ATCCAAGAAAGAATGAAACTACGAA 57.021 32.000 0.00 0.00 0.00 3.85
270 272 7.979444 AATCCAAGAAAGAATGAAACTACGA 57.021 32.000 0.00 0.00 0.00 3.43
271 273 9.118236 GAAAATCCAAGAAAGAATGAAACTACG 57.882 33.333 0.00 0.00 0.00 3.51
274 276 8.146412 CCTGAAAATCCAAGAAAGAATGAAACT 58.854 33.333 0.00 0.00 0.00 2.66
288 290 0.709992 CCCCCTCCCTGAAAATCCAA 59.290 55.000 0.00 0.00 0.00 3.53
323 325 6.669631 GGGGGAGACAAATAAATAGAAAGGA 58.330 40.000 0.00 0.00 0.00 3.36
347 349 7.690454 AAATTTATGAATTTAAGGGAGGGGG 57.310 36.000 6.41 0.00 42.21 5.40
516 532 1.856802 TCCGAAGCATCATCATCACG 58.143 50.000 0.00 0.00 0.00 4.35
520 536 3.272574 ACACTTCCGAAGCATCATCAT 57.727 42.857 8.11 0.00 0.00 2.45
521 537 2.768253 ACACTTCCGAAGCATCATCA 57.232 45.000 8.11 0.00 0.00 3.07
522 538 4.425577 AAAACACTTCCGAAGCATCATC 57.574 40.909 8.11 0.00 0.00 2.92
523 539 4.520492 AGAAAAACACTTCCGAAGCATCAT 59.480 37.500 8.11 0.00 0.00 2.45
615 637 6.752168 AGGTTTCGTTTAGTATACTGTGTGT 58.248 36.000 15.90 0.00 0.00 3.72
644 667 4.040461 CCAGACGGAGGGAATATGTACAAT 59.960 45.833 0.00 0.00 0.00 2.71
645 668 3.386726 CCAGACGGAGGGAATATGTACAA 59.613 47.826 0.00 0.00 0.00 2.41
647 670 3.228453 TCCAGACGGAGGGAATATGTAC 58.772 50.000 0.00 0.00 35.91 2.90
648 671 3.605726 TCCAGACGGAGGGAATATGTA 57.394 47.619 0.00 0.00 35.91 2.29
649 672 2.471815 TCCAGACGGAGGGAATATGT 57.528 50.000 0.00 0.00 35.91 2.29
654 677 2.829023 AGTAATTCCAGACGGAGGGAA 58.171 47.619 6.43 6.43 46.48 3.97
655 678 2.500098 CAAGTAATTCCAGACGGAGGGA 59.500 50.000 0.00 0.00 44.10 4.20
656 679 2.236395 ACAAGTAATTCCAGACGGAGGG 59.764 50.000 0.00 0.00 44.10 4.30
657 680 3.522553 GACAAGTAATTCCAGACGGAGG 58.477 50.000 0.00 0.00 44.10 4.30
658 681 3.179830 CGACAAGTAATTCCAGACGGAG 58.820 50.000 0.00 0.00 44.10 4.63
659 682 2.559668 ACGACAAGTAATTCCAGACGGA 59.440 45.455 0.00 0.00 40.60 4.69
660 683 2.955614 ACGACAAGTAATTCCAGACGG 58.044 47.619 0.00 0.00 0.00 4.79
661 684 7.745022 TTTATACGACAAGTAATTCCAGACG 57.255 36.000 0.00 0.00 39.04 4.18
662 685 8.548721 CCATTTATACGACAAGTAATTCCAGAC 58.451 37.037 0.00 0.00 39.04 3.51
663 686 8.479689 TCCATTTATACGACAAGTAATTCCAGA 58.520 33.333 0.00 0.00 39.04 3.86
664 687 8.657074 TCCATTTATACGACAAGTAATTCCAG 57.343 34.615 0.00 0.00 39.04 3.86
672 695 9.661563 TCAGTTTTATCCATTTATACGACAAGT 57.338 29.630 0.00 0.00 0.00 3.16
675 698 9.104965 CCTTCAGTTTTATCCATTTATACGACA 57.895 33.333 0.00 0.00 0.00 4.35
676 699 9.106070 ACCTTCAGTTTTATCCATTTATACGAC 57.894 33.333 0.00 0.00 0.00 4.34
714 737 9.915629 GAGAAATGGATGTATCTAGACGTATTT 57.084 33.333 0.00 0.00 0.00 1.40
715 738 8.524487 GGAGAAATGGATGTATCTAGACGTATT 58.476 37.037 0.00 0.00 0.00 1.89
716 739 7.148222 CGGAGAAATGGATGTATCTAGACGTAT 60.148 40.741 0.00 0.00 0.00 3.06
717 740 6.148976 CGGAGAAATGGATGTATCTAGACGTA 59.851 42.308 0.00 0.00 0.00 3.57
718 741 5.048643 CGGAGAAATGGATGTATCTAGACGT 60.049 44.000 0.00 0.00 0.00 4.34
719 742 5.181433 TCGGAGAAATGGATGTATCTAGACG 59.819 44.000 0.00 0.00 0.00 4.18
720 743 6.016192 TGTCGGAGAAATGGATGTATCTAGAC 60.016 42.308 0.00 0.00 39.69 2.59
721 744 6.068670 TGTCGGAGAAATGGATGTATCTAGA 58.931 40.000 0.00 0.00 39.69 2.43
722 745 6.332735 TGTCGGAGAAATGGATGTATCTAG 57.667 41.667 0.00 0.00 39.69 2.43
723 746 6.323996 ACTTGTCGGAGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 39.69 1.98
724 747 5.129485 ACTTGTCGGAGAAATGGATGTATCT 59.871 40.000 0.00 0.00 39.69 1.98
725 748 5.360591 ACTTGTCGGAGAAATGGATGTATC 58.639 41.667 0.00 0.00 39.69 2.24
726 749 5.359194 ACTTGTCGGAGAAATGGATGTAT 57.641 39.130 0.00 0.00 39.69 2.29
727 750 4.819105 ACTTGTCGGAGAAATGGATGTA 57.181 40.909 0.00 0.00 39.69 2.29
728 751 3.703001 ACTTGTCGGAGAAATGGATGT 57.297 42.857 0.00 0.00 39.69 3.06
729 752 6.238484 GGAAATACTTGTCGGAGAAATGGATG 60.238 42.308 0.00 0.00 39.69 3.51
730 753 5.823045 GGAAATACTTGTCGGAGAAATGGAT 59.177 40.000 0.00 0.00 39.69 3.41
731 754 5.183228 GGAAATACTTGTCGGAGAAATGGA 58.817 41.667 0.00 0.00 39.69 3.41
732 755 4.034048 CGGAAATACTTGTCGGAGAAATGG 59.966 45.833 0.00 0.00 39.69 3.16
733 756 4.034048 CCGGAAATACTTGTCGGAGAAATG 59.966 45.833 0.00 0.00 42.94 2.32
734 757 4.189231 CCGGAAATACTTGTCGGAGAAAT 58.811 43.478 0.00 0.00 42.94 2.17
735 758 3.592059 CCGGAAATACTTGTCGGAGAAA 58.408 45.455 0.00 0.00 42.94 2.52
736 759 2.093869 CCCGGAAATACTTGTCGGAGAA 60.094 50.000 0.73 0.00 42.94 2.87
737 760 1.479323 CCCGGAAATACTTGTCGGAGA 59.521 52.381 0.73 0.00 42.94 3.71
738 761 1.935933 CCCGGAAATACTTGTCGGAG 58.064 55.000 0.73 0.00 42.94 4.63
739 762 0.108041 GCCCGGAAATACTTGTCGGA 60.108 55.000 0.73 0.00 42.94 4.55
740 763 1.426041 CGCCCGGAAATACTTGTCGG 61.426 60.000 0.73 0.00 40.32 4.79
741 764 1.426041 CCGCCCGGAAATACTTGTCG 61.426 60.000 0.73 0.00 37.50 4.35
742 765 0.108041 TCCGCCCGGAAATACTTGTC 60.108 55.000 0.73 0.00 42.05 3.18
743 766 0.107848 CTCCGCCCGGAAATACTTGT 60.108 55.000 0.73 0.00 44.66 3.16
744 767 0.814010 CCTCCGCCCGGAAATACTTG 60.814 60.000 0.73 0.00 44.66 3.16
745 768 1.525442 CCTCCGCCCGGAAATACTT 59.475 57.895 0.73 0.00 44.66 2.24
746 769 2.440817 CCCTCCGCCCGGAAATACT 61.441 63.158 0.73 0.00 44.66 2.12
747 770 2.110420 CCCTCCGCCCGGAAATAC 59.890 66.667 0.73 0.00 44.66 1.89
748 771 2.041715 TCCCTCCGCCCGGAAATA 60.042 61.111 0.73 0.00 44.66 1.40
749 772 2.884179 TACTCCCTCCGCCCGGAAAT 62.884 60.000 0.73 0.00 44.66 2.17
750 773 2.884179 ATACTCCCTCCGCCCGGAAA 62.884 60.000 0.73 0.00 44.66 3.13
751 774 2.010412 TATACTCCCTCCGCCCGGAA 62.010 60.000 0.73 0.00 44.66 4.30
752 775 2.010412 TTATACTCCCTCCGCCCGGA 62.010 60.000 0.73 9.31 42.90 5.14
753 776 1.117142 TTTATACTCCCTCCGCCCGG 61.117 60.000 0.00 0.00 0.00 5.73
754 777 0.754472 TTTTATACTCCCTCCGCCCG 59.246 55.000 0.00 0.00 0.00 6.13
755 778 2.037381 CTCTTTTATACTCCCTCCGCCC 59.963 54.545 0.00 0.00 0.00 6.13
756 779 2.037381 CCTCTTTTATACTCCCTCCGCC 59.963 54.545 0.00 0.00 0.00 6.13
757 780 2.037381 CCCTCTTTTATACTCCCTCCGC 59.963 54.545 0.00 0.00 0.00 5.54
758 781 2.633481 CCCCTCTTTTATACTCCCTCCG 59.367 54.545 0.00 0.00 0.00 4.63
759 782 3.666568 ACCCCTCTTTTATACTCCCTCC 58.333 50.000 0.00 0.00 0.00 4.30
760 783 5.045066 ACAAACCCCTCTTTTATACTCCCTC 60.045 44.000 0.00 0.00 0.00 4.30
761 784 4.856182 ACAAACCCCTCTTTTATACTCCCT 59.144 41.667 0.00 0.00 0.00 4.20
762 785 5.188988 ACAAACCCCTCTTTTATACTCCC 57.811 43.478 0.00 0.00 0.00 4.30
763 786 6.482524 AGAACAAACCCCTCTTTTATACTCC 58.517 40.000 0.00 0.00 0.00 3.85
764 787 8.537858 TCTAGAACAAACCCCTCTTTTATACTC 58.462 37.037 0.00 0.00 0.00 2.59
765 788 8.445361 TCTAGAACAAACCCCTCTTTTATACT 57.555 34.615 0.00 0.00 0.00 2.12
766 789 9.682465 ATTCTAGAACAAACCCCTCTTTTATAC 57.318 33.333 7.48 0.00 0.00 1.47
771 794 4.767409 GCATTCTAGAACAAACCCCTCTTT 59.233 41.667 7.48 0.00 0.00 2.52
782 805 3.701542 ACGAGATCAGGCATTCTAGAACA 59.298 43.478 7.48 0.00 0.00 3.18
794 818 2.288702 CCTGCTATTGGACGAGATCAGG 60.289 54.545 0.00 0.00 34.64 3.86
801 825 2.165641 CACTACACCTGCTATTGGACGA 59.834 50.000 0.00 0.00 0.00 4.20
817 841 4.617959 TGCGATTTATGCTACTCCACTAC 58.382 43.478 0.00 0.00 0.00 2.73
820 844 6.539649 TTTATGCGATTTATGCTACTCCAC 57.460 37.500 0.00 0.00 0.00 4.02
823 847 7.050281 ACGATTTATGCGATTTATGCTACTC 57.950 36.000 0.00 0.00 0.00 2.59
824 848 7.421530 AACGATTTATGCGATTTATGCTACT 57.578 32.000 0.00 0.00 0.00 2.57
825 849 6.458592 CGAACGATTTATGCGATTTATGCTAC 59.541 38.462 0.00 0.00 0.00 3.58
826 850 6.400621 CCGAACGATTTATGCGATTTATGCTA 60.401 38.462 0.00 0.00 0.00 3.49
827 851 5.374080 CGAACGATTTATGCGATTTATGCT 58.626 37.500 0.00 0.00 0.00 3.79
828 852 4.549599 CCGAACGATTTATGCGATTTATGC 59.450 41.667 0.00 0.00 0.00 3.14
829 853 5.079406 CCCGAACGATTTATGCGATTTATG 58.921 41.667 0.00 0.00 0.00 1.90
830 854 4.153475 CCCCGAACGATTTATGCGATTTAT 59.847 41.667 0.00 0.00 0.00 1.40
831 855 3.495377 CCCCGAACGATTTATGCGATTTA 59.505 43.478 0.00 0.00 0.00 1.40
832 856 2.289547 CCCCGAACGATTTATGCGATTT 59.710 45.455 0.00 0.00 0.00 2.17
836 860 1.508632 ATCCCCGAACGATTTATGCG 58.491 50.000 0.00 0.00 0.00 4.73
862 909 6.351327 AGAGCTCTGCGAATGTATTTTTAC 57.649 37.500 17.42 0.00 0.00 2.01
884 931 3.611113 CCGTCATTGTAGTTACACCGAAG 59.389 47.826 0.00 0.00 35.64 3.79
887 934 1.657094 GCCGTCATTGTAGTTACACCG 59.343 52.381 0.00 0.00 35.64 4.94
888 935 2.004733 GGCCGTCATTGTAGTTACACC 58.995 52.381 0.00 0.00 35.64 4.16
889 936 2.004733 GGGCCGTCATTGTAGTTACAC 58.995 52.381 0.00 0.00 35.64 2.90
891 938 2.389962 TGGGCCGTCATTGTAGTTAC 57.610 50.000 0.00 0.00 0.00 2.50
893 940 2.279935 TTTGGGCCGTCATTGTAGTT 57.720 45.000 0.00 0.00 0.00 2.24
894 941 2.279935 TTTTGGGCCGTCATTGTAGT 57.720 45.000 0.00 0.00 0.00 2.73
895 942 2.817258 TCTTTTTGGGCCGTCATTGTAG 59.183 45.455 0.00 0.00 0.00 2.74
896 943 2.865079 TCTTTTTGGGCCGTCATTGTA 58.135 42.857 0.00 0.00 0.00 2.41
898 945 2.799978 GTTTCTTTTTGGGCCGTCATTG 59.200 45.455 0.00 0.00 0.00 2.82
899 946 2.544903 CGTTTCTTTTTGGGCCGTCATT 60.545 45.455 0.00 0.00 0.00 2.57
901 948 0.382515 CGTTTCTTTTTGGGCCGTCA 59.617 50.000 0.00 0.00 0.00 4.35
902 949 0.664224 TCGTTTCTTTTTGGGCCGTC 59.336 50.000 0.00 0.00 0.00 4.79
965 1085 0.106918 GGGAAAGTGGGTGTGTGTCA 60.107 55.000 0.00 0.00 0.00 3.58
1096 1253 4.821589 GGCGCGGAAGAGGTGGAG 62.822 72.222 8.83 0.00 0.00 3.86
1213 1370 0.322906 GGAGGCCCTTTCTGGTTGAG 60.323 60.000 0.00 0.00 0.00 3.02
1333 1496 3.774528 CCTAGTGCGGCAGCTCCA 61.775 66.667 10.92 0.00 45.42 3.86
1334 1497 3.461773 TCCTAGTGCGGCAGCTCC 61.462 66.667 10.92 0.39 45.42 4.70
1521 1684 3.619733 CGGAGGTGATGAAATTGGACTGA 60.620 47.826 0.00 0.00 0.00 3.41
1525 1688 1.004161 TGCGGAGGTGATGAAATTGGA 59.996 47.619 0.00 0.00 0.00 3.53
1570 1733 4.084051 ATGGAAGTGATCTCACCCCAGAA 61.084 47.826 19.87 5.04 46.07 3.02
1602 1765 4.354587 GCTTTGCCTGAACTAATGCATAC 58.645 43.478 0.00 0.00 33.08 2.39
1746 1927 1.069668 TCCTCTGTCGGCATGATGATG 59.930 52.381 0.00 0.00 0.00 3.07
1770 1951 2.200170 CTGCGGCTAAACCAAGGCAC 62.200 60.000 0.00 0.00 41.95 5.01
1787 1968 5.808042 ATTCAGATTGAATCGTTCCACTG 57.192 39.130 0.00 0.00 43.03 3.66
1806 1993 2.554032 CACCACCTTTGACCACAGATTC 59.446 50.000 0.00 0.00 0.00 2.52
1831 2018 1.405526 CCATGTCACTACCCCGTCAAG 60.406 57.143 0.00 0.00 0.00 3.02
1891 2079 1.861982 ATACCCTGCCACTACTTCGT 58.138 50.000 0.00 0.00 0.00 3.85
1909 2097 5.047306 TCCGCTCGAATATCTTGAACCATAT 60.047 40.000 0.00 0.00 0.00 1.78
2031 2220 1.237285 ATGCGTTTGCCTGACACCTC 61.237 55.000 0.00 0.00 41.78 3.85
2032 2221 1.228245 ATGCGTTTGCCTGACACCT 60.228 52.632 0.00 0.00 41.78 4.00
2033 2222 1.210155 GATGCGTTTGCCTGACACC 59.790 57.895 0.00 0.00 41.78 4.16
2034 2223 0.110056 CAGATGCGTTTGCCTGACAC 60.110 55.000 0.00 0.00 41.78 3.67
2035 2224 1.855213 GCAGATGCGTTTGCCTGACA 61.855 55.000 10.26 0.00 41.78 3.58
2036 2225 1.154150 GCAGATGCGTTTGCCTGAC 60.154 57.895 10.26 0.00 41.78 3.51
2132 2328 6.543465 TCAAGGCAGATACATTTGGAATAGTG 59.457 38.462 0.00 0.00 0.00 2.74
2160 2381 8.696043 ACTATGGCTCATATATTTGAAAGCAA 57.304 30.769 8.80 0.19 0.00 3.91
2186 2411 8.960591 CCAGGAAAACTTGTCATCTATAAATGT 58.039 33.333 0.00 0.00 0.00 2.71
2215 2440 9.897744 CATAATAAGCACTTCTTTCACAAGAAA 57.102 29.630 0.00 0.00 46.35 2.52
2230 2455 5.734855 ACGGTTCATCACATAATAAGCAC 57.265 39.130 0.00 0.00 0.00 4.40
2241 2467 4.868171 TGCAGAGTATTAACGGTTCATCAC 59.132 41.667 0.00 0.00 0.00 3.06
2485 2811 8.703604 TGCTCACTGTTTAGATCTAAATGTAC 57.296 34.615 26.46 16.83 37.37 2.90
2504 2830 5.998454 ACATATAATGCTCAGTTGCTCAC 57.002 39.130 0.00 0.00 0.00 3.51
2520 2846 8.217799 AGCCCAAACTCTAGCAATAAACATATA 58.782 33.333 0.00 0.00 0.00 0.86
2521 2847 7.062957 AGCCCAAACTCTAGCAATAAACATAT 58.937 34.615 0.00 0.00 0.00 1.78
2554 2880 6.822676 AGCAAATGAGAAGGAAACATCTAGAG 59.177 38.462 0.00 0.00 38.79 2.43
2556 2882 6.998968 AGCAAATGAGAAGGAAACATCTAG 57.001 37.500 0.00 0.00 38.79 2.43
2557 2883 6.942005 TCAAGCAAATGAGAAGGAAACATCTA 59.058 34.615 0.00 0.00 38.79 1.98
2558 2884 5.771666 TCAAGCAAATGAGAAGGAAACATCT 59.228 36.000 0.00 0.00 42.01 2.90
2573 3199 5.846203 ACATAACACAAAGCTCAAGCAAAT 58.154 33.333 4.59 0.00 45.16 2.32
2619 3245 5.106634 CCAGAGAATCAAGAAACTGAGCAAG 60.107 44.000 0.00 0.00 37.82 4.01
2622 3248 3.126686 GCCAGAGAATCAAGAAACTGAGC 59.873 47.826 0.00 0.00 37.82 4.26
2625 3251 3.439476 CAGGCCAGAGAATCAAGAAACTG 59.561 47.826 5.01 0.00 37.82 3.16
2631 3257 2.054232 ATGCAGGCCAGAGAATCAAG 57.946 50.000 5.01 0.00 37.82 3.02
2643 3269 3.442977 ACTTCAGAATCAAGAATGCAGGC 59.557 43.478 0.00 0.00 0.00 4.85
2646 3272 5.645067 CCTACACTTCAGAATCAAGAATGCA 59.355 40.000 0.00 0.00 0.00 3.96
2678 3304 1.561076 TGCAGGCATACCAGAGTGAAT 59.439 47.619 0.00 0.00 39.06 2.57
2711 3337 7.286087 AGCAAAAGAATGGTGCATAATATCTGA 59.714 33.333 0.00 0.00 40.83 3.27
2712 3338 7.381408 CAGCAAAAGAATGGTGCATAATATCTG 59.619 37.037 0.00 0.00 41.33 2.90
2726 3353 5.830912 TGTTACAAGTCCAGCAAAAGAATG 58.169 37.500 0.00 0.00 0.00 2.67
2761 3388 7.259161 AGCGTTTTTAGAATTGTTTTGGTGTA 58.741 30.769 0.00 0.00 0.00 2.90
2783 3410 3.870633 AGTTTACTGGACTAGGAAGCG 57.129 47.619 0.00 0.00 35.73 4.68


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

AutoCloner maintained by Alex Coulton.