Multiple sequence alignment - TraesCS4D01G074500

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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 TraesCS4D01G074500 chr4D 100.000 4685 0 0 1 4685 49087549 49082865 0.000000e+00 8652.0
1 TraesCS4D01G074500 chr4D 83.061 673 89 15 39 707 428973545 428972894 5.220000e-164 588.0
2 TraesCS4D01G074500 chr4D 98.077 52 1 0 3836 3887 49083661 49083610 1.800000e-14 91.6
3 TraesCS4D01G074500 chr4D 98.077 52 1 0 3889 3940 49083714 49083663 1.800000e-14 91.6
4 TraesCS4D01G074500 chr4A 90.825 2474 132 47 886 3292 548341616 548344061 0.000000e+00 3223.0
5 TraesCS4D01G074500 chr4A 89.367 790 47 12 3296 4063 548344175 548344949 0.000000e+00 959.0
6 TraesCS4D01G074500 chr4A 98.077 52 1 0 3889 3940 548344732 548344783 1.800000e-14 91.6
7 TraesCS4D01G074500 chr4B 94.691 1149 47 5 886 2022 72167303 72168449 0.000000e+00 1772.0
8 TraesCS4D01G074500 chr4B 86.514 1698 126 38 2170 3790 72168534 72170205 0.000000e+00 1772.0
9 TraesCS4D01G074500 chr4B 90.123 81 8 0 3892 3972 72170202 72170282 6.410000e-19 106.0
10 TraesCS4D01G074500 chr4B 100.000 39 0 0 3903 3941 552857569 552857607 6.500000e-09 73.1
11 TraesCS4D01G074500 chr1D 94.462 650 11 6 4060 4685 478814135 478814783 0.000000e+00 977.0
12 TraesCS4D01G074500 chr1D 97.368 38 1 0 3850 3887 212719257 212719294 1.090000e-06 65.8
13 TraesCS4D01G074500 chr3A 90.154 650 37 12 4060 4685 696045911 696045265 0.000000e+00 821.0
14 TraesCS4D01G074500 chr3A 92.840 419 27 2 4267 4685 634712987 634712572 5.190000e-169 604.0
15 TraesCS4D01G074500 chr3A 88.694 513 30 12 4060 4547 628703317 628702808 6.710000e-168 601.0
16 TraesCS4D01G074500 chr3A 92.958 213 8 3 4060 4265 634724298 634724086 2.120000e-78 303.0
17 TraesCS4D01G074500 chr3A 80.734 109 19 2 758 865 83301264 83301157 3.000000e-12 84.2
18 TraesCS4D01G074500 chr3B 90.108 647 37 11 4063 4685 80093439 80094082 0.000000e+00 815.0
19 TraesCS4D01G074500 chr7D 90.015 651 34 12 4062 4685 621220842 621221488 0.000000e+00 813.0
20 TraesCS4D01G074500 chr7D 89.164 646 43 12 4063 4685 578840201 578839560 0.000000e+00 780.0
21 TraesCS4D01G074500 chr7D 88.000 650 44 15 4063 4685 579045234 579044592 0.000000e+00 737.0
22 TraesCS4D01G074500 chr7D 78.276 290 54 5 106 395 351351232 351351512 1.340000e-40 178.0
23 TraesCS4D01G074500 chr7A 89.969 648 40 11 4062 4685 127659191 127659837 0.000000e+00 813.0
24 TraesCS4D01G074500 chr3D 90.108 647 35 10 4066 4685 345757870 345757226 0.000000e+00 813.0
25 TraesCS4D01G074500 chr3D 81.699 836 126 22 37 865 526190827 526191642 0.000000e+00 671.0
26 TraesCS4D01G074500 chr3D 76.776 366 65 13 37 395 598485921 598485569 2.230000e-43 187.0
27 TraesCS4D01G074500 chr3D 92.222 90 6 1 311 400 557604312 557604400 4.920000e-25 126.0
28 TraesCS4D01G074500 chr3D 100.000 39 0 0 3903 3941 13182050 13182088 6.500000e-09 73.1
29 TraesCS4D01G074500 chr6A 89.692 650 41 10 4060 4685 36402980 36402333 0.000000e+00 806.0
30 TraesCS4D01G074500 chr6A 76.190 231 45 8 648 876 489508476 489508698 3.830000e-21 113.0
31 TraesCS4D01G074500 chr1B 89.432 634 38 16 4075 4685 18123434 18122807 0.000000e+00 773.0
32 TraesCS4D01G074500 chr1B 81.915 94 12 5 774 864 569929987 569929896 1.810000e-09 75.0
33 TraesCS4D01G074500 chr1B 100.000 38 0 0 3850 3887 302512165 302512128 2.340000e-08 71.3
34 TraesCS4D01G074500 chr5B 86.349 630 47 16 4063 4685 572382728 572383325 0.000000e+00 651.0
35 TraesCS4D01G074500 chr5B 85.572 402 53 4 39 440 678906763 678907159 2.610000e-112 416.0
36 TraesCS4D01G074500 chr5B 100.000 39 0 0 3903 3941 65592607 65592645 6.500000e-09 73.1
37 TraesCS4D01G074500 chr1A 86.637 449 52 6 69 515 243603567 243603125 1.510000e-134 490.0
38 TraesCS4D01G074500 chr1A 77.741 301 62 5 576 872 59950320 59950619 3.720000e-41 180.0
39 TraesCS4D01G074500 chr1A 76.221 307 68 4 113 418 459169295 459169597 1.750000e-34 158.0
40 TraesCS4D01G074500 chr1A 75.896 307 69 4 113 418 459164613 459164915 8.120000e-33 152.0
41 TraesCS4D01G074500 chr1A 100.000 35 0 0 3853 3887 269573837 269573871 1.090000e-06 65.8
42 TraesCS4D01G074500 chr1A 80.488 82 16 0 784 865 14159864 14159945 3.910000e-06 63.9
43 TraesCS4D01G074500 chr2B 88.000 225 22 4 1 223 765087876 765088097 1.290000e-65 261.0
44 TraesCS4D01G074500 chr2B 94.737 38 2 0 3850 3887 747178655 747178692 5.060000e-05 60.2
45 TraesCS4D01G074500 chr5D 76.577 222 44 4 646 865 37122035 37122250 1.070000e-21 115.0
46 TraesCS4D01G074500 chr5A 81.250 112 21 0 754 865 535653088 535653199 1.800000e-14 91.6
47 TraesCS4D01G074500 chr6D 77.953 127 25 3 740 865 193094962 193094838 5.030000e-10 76.8
48 TraesCS4D01G074500 chr6B 100.000 39 0 0 3903 3941 284652742 284652704 6.500000e-09 73.1
49 TraesCS4D01G074500 chr2A 100.000 39 0 0 3903 3941 364478324 364478362 6.500000e-09 73.1
50 TraesCS4D01G074500 chr2D 97.561 41 1 0 3903 3943 98907733 98907773 2.340000e-08 71.3


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 TraesCS4D01G074500 chr4D 49082865 49087549 4684 True 2945.066667 8652 98.718000 1 4685 3 chr4D.!!$R2 4684
1 TraesCS4D01G074500 chr4D 428972894 428973545 651 True 588.000000 588 83.061000 39 707 1 chr4D.!!$R1 668
2 TraesCS4D01G074500 chr4A 548341616 548344949 3333 False 1424.533333 3223 92.756333 886 4063 3 chr4A.!!$F1 3177
3 TraesCS4D01G074500 chr4B 72167303 72170282 2979 False 1216.666667 1772 90.442667 886 3972 3 chr4B.!!$F2 3086
4 TraesCS4D01G074500 chr1D 478814135 478814783 648 False 977.000000 977 94.462000 4060 4685 1 chr1D.!!$F2 625
5 TraesCS4D01G074500 chr3A 696045265 696045911 646 True 821.000000 821 90.154000 4060 4685 1 chr3A.!!$R5 625
6 TraesCS4D01G074500 chr3A 628702808 628703317 509 True 601.000000 601 88.694000 4060 4547 1 chr3A.!!$R2 487
7 TraesCS4D01G074500 chr3B 80093439 80094082 643 False 815.000000 815 90.108000 4063 4685 1 chr3B.!!$F1 622
8 TraesCS4D01G074500 chr7D 621220842 621221488 646 False 813.000000 813 90.015000 4062 4685 1 chr7D.!!$F2 623
9 TraesCS4D01G074500 chr7D 578839560 578840201 641 True 780.000000 780 89.164000 4063 4685 1 chr7D.!!$R1 622
10 TraesCS4D01G074500 chr7D 579044592 579045234 642 True 737.000000 737 88.000000 4063 4685 1 chr7D.!!$R2 622
11 TraesCS4D01G074500 chr7A 127659191 127659837 646 False 813.000000 813 89.969000 4062 4685 1 chr7A.!!$F1 623
12 TraesCS4D01G074500 chr3D 345757226 345757870 644 True 813.000000 813 90.108000 4066 4685 1 chr3D.!!$R1 619
13 TraesCS4D01G074500 chr3D 526190827 526191642 815 False 671.000000 671 81.699000 37 865 1 chr3D.!!$F2 828
14 TraesCS4D01G074500 chr6A 36402333 36402980 647 True 806.000000 806 89.692000 4060 4685 1 chr6A.!!$R1 625
15 TraesCS4D01G074500 chr1B 18122807 18123434 627 True 773.000000 773 89.432000 4075 4685 1 chr1B.!!$R1 610
16 TraesCS4D01G074500 chr5B 572382728 572383325 597 False 651.000000 651 86.349000 4063 4685 1 chr5B.!!$F2 622

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
944 950 0.031314 CGCTCACACTCACTCACTGT 59.969 55.0 0.0 0.0 0.0 3.55 F
2292 2340 0.036388 TTGGATCAGTTGGGCGTCTC 60.036 55.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2401 2449 0.109342 CTGAGGCAGGTTTGACTGGT 59.891 55.0 0.00 0.00 44.85 4.0 R
3825 4108 0.250510 TTCACACTGCGGTGCCATAA 60.251 50.0 25.67 11.46 46.57 1.9 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
176 180 5.693769 ATATGCACTAACAGGTACTTGGT 57.306 39.130 10.04 5.22 34.60 3.67
184 188 2.966915 ACAGGTACTTGGTGTAGTGGA 58.033 47.619 10.04 0.00 34.60 4.02
187 191 5.278061 ACAGGTACTTGGTGTAGTGGATAT 58.722 41.667 10.04 0.00 34.60 1.63
192 196 3.967987 ACTTGGTGTAGTGGATATCTCCC 59.032 47.826 2.05 0.00 41.29 4.30
202 206 3.009916 GTGGATATCTCCCATGCTTCCAT 59.990 47.826 2.05 0.00 41.29 3.41
210 214 2.041485 TCCCATGCTTCCATGTTCAAGA 59.959 45.455 3.34 0.00 45.90 3.02
225 229 9.551734 CCATGTTCAAGATCTACAGATTGATTA 57.448 33.333 0.00 0.00 34.37 1.75
230 234 7.996385 TCAAGATCTACAGATTGATTACGTCA 58.004 34.615 0.00 0.00 34.37 4.35
235 239 4.801330 ACAGATTGATTACGTCACTCCA 57.199 40.909 0.00 0.00 37.25 3.86
236 240 5.344743 ACAGATTGATTACGTCACTCCAT 57.655 39.130 0.00 0.00 37.25 3.41
291 295 3.350219 ACGAACTTATGCTTGACCCAT 57.650 42.857 0.00 0.00 0.00 4.00
310 314 4.101448 GACAGATGGGCCCTGCGT 62.101 66.667 25.70 14.91 35.14 5.24
364 368 6.028368 CACGTTGTTAGTATCCTACTGACTG 58.972 44.000 9.67 4.15 43.40 3.51
396 400 6.428295 CACCCCTAAATTACCCATTAGACAA 58.572 40.000 0.00 0.00 32.10 3.18
432 436 3.390135 TCTGATTGACGGACACAAACTC 58.610 45.455 0.00 0.00 0.00 3.01
440 444 0.531974 GGACACAAACTCGACAGGCA 60.532 55.000 0.00 0.00 0.00 4.75
453 457 3.441222 TCGACAGGCAGTTTCGTCTAATA 59.559 43.478 0.00 0.00 34.35 0.98
457 461 6.481954 ACAGGCAGTTTCGTCTAATAAAAG 57.518 37.500 0.00 0.00 0.00 2.27
480 484 9.816354 AAAGAAAGTTTAGTTGTGCATGTTTAT 57.184 25.926 0.00 0.00 0.00 1.40
488 492 4.340666 AGTTGTGCATGTTTATTGTCCACA 59.659 37.500 0.00 0.00 0.00 4.17
515 519 1.899814 GGTGGGATGGATATGCGTCTA 59.100 52.381 15.15 3.66 0.00 2.59
517 521 3.055094 GGTGGGATGGATATGCGTCTAAT 60.055 47.826 15.15 0.00 0.00 1.73
518 522 4.161565 GGTGGGATGGATATGCGTCTAATA 59.838 45.833 15.15 0.00 0.00 0.98
519 523 5.163301 GGTGGGATGGATATGCGTCTAATAT 60.163 44.000 15.15 0.00 0.00 1.28
520 524 6.041637 GGTGGGATGGATATGCGTCTAATATA 59.958 42.308 15.15 0.00 0.00 0.86
521 525 7.418597 GGTGGGATGGATATGCGTCTAATATAA 60.419 40.741 15.15 0.00 0.00 0.98
522 526 7.985184 GTGGGATGGATATGCGTCTAATATAAA 59.015 37.037 15.15 0.00 0.00 1.40
523 527 7.985184 TGGGATGGATATGCGTCTAATATAAAC 59.015 37.037 15.15 0.00 0.00 2.01
524 528 7.441458 GGGATGGATATGCGTCTAATATAAACC 59.559 40.741 15.15 2.38 0.00 3.27
526 530 9.250624 GATGGATATGCGTCTAATATAAACCTC 57.749 37.037 9.06 0.00 0.00 3.85
528 532 8.758829 TGGATATGCGTCTAATATAAACCTCAT 58.241 33.333 0.00 0.00 0.00 2.90
532 536 7.526142 TGCGTCTAATATAAACCTCATCTCT 57.474 36.000 0.00 0.00 0.00 3.10
534 538 8.421784 TGCGTCTAATATAAACCTCATCTCTTT 58.578 33.333 0.00 0.00 0.00 2.52
535 539 9.262358 GCGTCTAATATAAACCTCATCTCTTTT 57.738 33.333 0.00 0.00 0.00 2.27
542 546 5.363979 AAACCTCATCTCTTTTTCTTCGC 57.636 39.130 0.00 0.00 0.00 4.70
543 547 2.996621 ACCTCATCTCTTTTTCTTCGCG 59.003 45.455 0.00 0.00 0.00 5.87
544 548 3.254060 CCTCATCTCTTTTTCTTCGCGA 58.746 45.455 3.71 3.71 0.00 5.87
545 549 3.305629 CCTCATCTCTTTTTCTTCGCGAG 59.694 47.826 9.59 3.89 0.00 5.03
546 550 4.169508 CTCATCTCTTTTTCTTCGCGAGA 58.830 43.478 9.59 6.53 35.46 4.04
573 577 4.109050 GTTCGAACCTCATCTGACTCATC 58.891 47.826 17.68 0.00 0.00 2.92
574 578 3.356290 TCGAACCTCATCTGACTCATCA 58.644 45.455 0.00 0.00 0.00 3.07
619 623 7.223193 GCCTTTCGCGGGTAATTAAATAAATTT 59.777 33.333 6.13 0.00 38.71 1.82
624 628 8.675504 TCGCGGGTAATTAAATAAATTTCAAGA 58.324 29.630 6.13 0.00 38.71 3.02
674 679 0.322906 TCACCCAACACTTGTGCACA 60.323 50.000 17.42 17.42 0.00 4.57
683 688 0.401738 ACTTGTGCACACCTAGCCAT 59.598 50.000 21.56 0.00 0.00 4.40
712 717 3.554342 CCTCCGGCAGGCTAGCAT 61.554 66.667 18.24 6.55 34.56 3.79
713 718 2.280660 CTCCGGCAGGCTAGCATG 60.281 66.667 24.52 24.52 37.47 4.06
714 719 3.083349 TCCGGCAGGCTAGCATGT 61.083 61.111 28.24 4.41 37.47 3.21
726 732 1.598132 CTAGCATGTCATGTGAGCAGC 59.402 52.381 14.26 0.00 0.00 5.25
730 736 0.679002 ATGTCATGTGAGCAGCCCAC 60.679 55.000 0.00 0.00 35.23 4.61
734 740 3.907260 ATGTGAGCAGCCCACACGG 62.907 63.158 12.59 0.00 45.87 4.94
771 777 5.581085 GGAAGCACTGTATTTACACGAGAAT 59.419 40.000 0.00 0.00 31.93 2.40
773 779 5.479306 AGCACTGTATTTACACGAGAATGT 58.521 37.500 0.00 0.00 36.56 2.71
834 840 5.399013 AGCACCAAACTAAATATCAAACGC 58.601 37.500 0.00 0.00 0.00 4.84
852 858 1.336517 CGCAAGTCCTGTAACTTCCGA 60.337 52.381 0.00 0.00 41.80 4.55
857 863 4.392921 AGTCCTGTAACTTCCGATGATG 57.607 45.455 0.00 0.00 0.00 3.07
865 871 3.821421 ACTTCCGATGATGTTACCTCC 57.179 47.619 0.00 0.00 0.00 4.30
866 872 3.375699 ACTTCCGATGATGTTACCTCCT 58.624 45.455 0.00 0.00 0.00 3.69
867 873 3.133003 ACTTCCGATGATGTTACCTCCTG 59.867 47.826 0.00 0.00 0.00 3.86
868 874 3.026707 TCCGATGATGTTACCTCCTGA 57.973 47.619 0.00 0.00 0.00 3.86
869 875 3.576861 TCCGATGATGTTACCTCCTGAT 58.423 45.455 0.00 0.00 0.00 2.90
870 876 4.736473 TCCGATGATGTTACCTCCTGATA 58.264 43.478 0.00 0.00 0.00 2.15
871 877 5.144832 TCCGATGATGTTACCTCCTGATAA 58.855 41.667 0.00 0.00 0.00 1.75
872 878 5.600898 TCCGATGATGTTACCTCCTGATAAA 59.399 40.000 0.00 0.00 0.00 1.40
873 879 6.099125 TCCGATGATGTTACCTCCTGATAAAA 59.901 38.462 0.00 0.00 0.00 1.52
874 880 6.425114 CCGATGATGTTACCTCCTGATAAAAG 59.575 42.308 0.00 0.00 0.00 2.27
875 881 6.986817 CGATGATGTTACCTCCTGATAAAAGT 59.013 38.462 0.00 0.00 0.00 2.66
876 882 8.141909 CGATGATGTTACCTCCTGATAAAAGTA 58.858 37.037 0.00 0.00 0.00 2.24
877 883 9.262358 GATGATGTTACCTCCTGATAAAAGTAC 57.738 37.037 0.00 0.00 0.00 2.73
878 884 8.375493 TGATGTTACCTCCTGATAAAAGTACT 57.625 34.615 0.00 0.00 0.00 2.73
879 885 8.475639 TGATGTTACCTCCTGATAAAAGTACTC 58.524 37.037 0.00 0.00 0.00 2.59
880 886 6.860080 TGTTACCTCCTGATAAAAGTACTCG 58.140 40.000 0.00 0.00 0.00 4.18
881 887 4.388378 ACCTCCTGATAAAAGTACTCGC 57.612 45.455 0.00 0.00 0.00 5.03
882 888 4.024670 ACCTCCTGATAAAAGTACTCGCT 58.975 43.478 0.00 0.00 0.00 4.93
883 889 4.098196 ACCTCCTGATAAAAGTACTCGCTC 59.902 45.833 0.00 0.00 0.00 5.03
884 890 4.098044 CCTCCTGATAAAAGTACTCGCTCA 59.902 45.833 0.00 0.00 0.00 4.26
887 893 4.563184 CCTGATAAAAGTACTCGCTCACAC 59.437 45.833 0.00 0.00 0.00 3.82
941 947 0.387878 CCTCGCTCACACTCACTCAC 60.388 60.000 0.00 0.00 0.00 3.51
944 950 0.031314 CGCTCACACTCACTCACTGT 59.969 55.000 0.00 0.00 0.00 3.55
977 989 4.601794 CCCACTGCTGCCACCCAA 62.602 66.667 0.00 0.00 0.00 4.12
978 990 2.987547 CCACTGCTGCCACCCAAG 60.988 66.667 0.00 0.00 0.00 3.61
979 991 3.677648 CACTGCTGCCACCCAAGC 61.678 66.667 0.00 0.00 0.00 4.01
980 992 3.894638 ACTGCTGCCACCCAAGCT 61.895 61.111 0.00 0.00 0.00 3.74
981 993 2.352422 CTGCTGCCACCCAAGCTA 59.648 61.111 0.00 0.00 0.00 3.32
982 994 1.303561 CTGCTGCCACCCAAGCTAA 60.304 57.895 0.00 0.00 0.00 3.09
983 995 0.682209 CTGCTGCCACCCAAGCTAAT 60.682 55.000 0.00 0.00 0.00 1.73
985 997 0.174162 GCTGCCACCCAAGCTAATTG 59.826 55.000 0.00 0.00 38.74 2.32
987 999 1.203052 CTGCCACCCAAGCTAATTGTG 59.797 52.381 0.00 0.00 37.17 3.33
1009 1027 1.498865 GCCAGTGATAATGCCGTCCG 61.499 60.000 0.00 0.00 0.00 4.79
1495 1513 3.108343 TCGACTCGCCGAGATTCC 58.892 61.111 22.80 5.87 34.19 3.01
1496 1514 1.451567 TCGACTCGCCGAGATTCCT 60.452 57.895 22.80 0.00 34.19 3.36
1512 1530 1.176619 TCCTCTCGTTCTTGCACGGA 61.177 55.000 0.00 0.00 40.74 4.69
1554 1572 1.019278 ACGCCGCTGTGATTTACCAG 61.019 55.000 0.00 0.00 0.00 4.00
1557 1575 1.676014 GCCGCTGTGATTTACCAGTCT 60.676 52.381 0.00 0.00 0.00 3.24
2123 2170 4.396166 CCTGTAGTGTTCCAATGATTCCAC 59.604 45.833 0.00 0.00 0.00 4.02
2126 2173 2.821969 AGTGTTCCAATGATTCCACTGC 59.178 45.455 0.00 0.00 0.00 4.40
2292 2340 0.036388 TTGGATCAGTTGGGCGTCTC 60.036 55.000 0.00 0.00 0.00 3.36
2406 2454 4.986054 TGTAATGGAAGGTACAACCAGT 57.014 40.909 9.90 9.62 41.95 4.00
2407 2455 4.901868 TGTAATGGAAGGTACAACCAGTC 58.098 43.478 8.06 0.00 41.95 3.51
2415 2463 1.607148 GGTACAACCAGTCAAACCTGC 59.393 52.381 0.00 0.00 38.42 4.85
2416 2464 1.607148 GTACAACCAGTCAAACCTGCC 59.393 52.381 0.00 0.00 0.00 4.85
2418 2466 0.954452 CAACCAGTCAAACCTGCCTC 59.046 55.000 0.00 0.00 0.00 4.70
2482 2540 1.690352 GCATTAGGGCAGCAATCCATT 59.310 47.619 0.00 0.00 0.00 3.16
2493 2551 4.748102 GCAGCAATCCATTTGGTTCATATG 59.252 41.667 0.00 0.00 43.35 1.78
2534 2592 4.687483 GCTGCAATGTTGTTTTGATAGCTT 59.313 37.500 0.00 0.00 35.12 3.74
2535 2593 5.164022 GCTGCAATGTTGTTTTGATAGCTTC 60.164 40.000 0.00 0.00 35.12 3.86
2536 2594 5.229423 TGCAATGTTGTTTTGATAGCTTCC 58.771 37.500 0.00 0.00 0.00 3.46
2537 2595 5.221402 TGCAATGTTGTTTTGATAGCTTCCA 60.221 36.000 0.00 0.00 0.00 3.53
2538 2596 5.870978 GCAATGTTGTTTTGATAGCTTCCAT 59.129 36.000 0.00 0.00 0.00 3.41
2542 2603 5.304101 TGTTGTTTTGATAGCTTCCATTGGT 59.696 36.000 1.86 0.00 0.00 3.67
2549 2610 0.532862 AGCTTCCATTGGTATCCGCG 60.533 55.000 0.00 0.00 0.00 6.46
2558 2619 4.098960 CCATTGGTATCCGCGGTATATACT 59.901 45.833 27.15 7.40 0.00 2.12
2560 2621 3.689347 TGGTATCCGCGGTATATACTGT 58.311 45.455 27.15 5.83 35.04 3.55
2561 2622 3.441222 TGGTATCCGCGGTATATACTGTG 59.559 47.826 27.15 23.04 41.51 3.66
2563 2624 4.156556 GGTATCCGCGGTATATACTGTGAA 59.843 45.833 28.96 15.48 43.85 3.18
2564 2625 5.163581 GGTATCCGCGGTATATACTGTGAAT 60.164 44.000 28.96 20.56 43.85 2.57
2565 2626 4.859304 TCCGCGGTATATACTGTGAATT 57.141 40.909 28.96 0.00 43.85 2.17
2566 2627 4.552355 TCCGCGGTATATACTGTGAATTG 58.448 43.478 28.96 16.25 43.85 2.32
2570 2646 5.460748 CGCGGTATATACTGTGAATTGTTGA 59.539 40.000 24.93 0.00 43.85 3.18
2720 2803 4.326504 ACATAAAATTGCTAGCCATGCC 57.673 40.909 13.29 0.00 0.00 4.40
2735 2838 3.366374 GCCATGCCTTCTGTGTAAGAAAC 60.366 47.826 0.00 0.00 44.38 2.78
2737 2840 4.460382 CCATGCCTTCTGTGTAAGAAACAT 59.540 41.667 0.00 0.00 44.38 2.71
2748 2853 8.311109 TCTGTGTAAGAAACATAGCAGACATTA 58.689 33.333 0.00 0.00 44.61 1.90
2749 2854 8.840833 TGTGTAAGAAACATAGCAGACATTAA 57.159 30.769 0.00 0.00 41.10 1.40
2750 2855 8.717821 TGTGTAAGAAACATAGCAGACATTAAC 58.282 33.333 0.00 0.00 41.10 2.01
2751 2856 8.717821 GTGTAAGAAACATAGCAGACATTAACA 58.282 33.333 0.00 0.00 41.10 2.41
2752 2857 8.935844 TGTAAGAAACATAGCAGACATTAACAG 58.064 33.333 0.00 0.00 31.43 3.16
2753 2858 9.151471 GTAAGAAACATAGCAGACATTAACAGA 57.849 33.333 0.00 0.00 0.00 3.41
2754 2859 7.602517 AGAAACATAGCAGACATTAACAGAC 57.397 36.000 0.00 0.00 0.00 3.51
2814 2923 6.013725 AGTCAACATCACACCCTAATCTGTTA 60.014 38.462 0.00 0.00 0.00 2.41
2864 2973 4.038402 CCAGGTCTGCATCTTCTTTTTGTT 59.962 41.667 0.00 0.00 0.00 2.83
2870 2979 6.089954 GTCTGCATCTTCTTTTTGTTAATGGC 59.910 38.462 0.00 0.00 0.00 4.40
2876 2985 5.988561 TCTTCTTTTTGTTAATGGCGCATTT 59.011 32.000 10.83 4.27 35.54 2.32
2907 3016 8.918202 ATTTGTCAGATGTTAGGTTTCTGTTA 57.082 30.769 0.00 0.00 38.39 2.41
2953 3062 4.574599 ATTTTTCACTGACAAGCACTCC 57.425 40.909 0.00 0.00 0.00 3.85
2956 3065 2.174363 TCACTGACAAGCACTCCATG 57.826 50.000 0.00 0.00 0.00 3.66
2971 3080 7.315142 AGCACTCCATGTATTGTTAAACATTG 58.685 34.615 0.00 0.00 34.12 2.82
3012 3121 3.454082 ACAAGGAATCCACCTCTGAGATC 59.546 47.826 6.17 0.00 39.62 2.75
3087 3196 3.184628 TGGATTCCTCTCTGTGGTTGAT 58.815 45.455 3.95 0.00 0.00 2.57
3114 3223 8.879759 CGGCTGAAAGAGATAATTAAGTACAAA 58.120 33.333 0.00 0.00 34.07 2.83
3292 3423 4.944930 TGTTGGGTAAGTATGCACCATAAC 59.055 41.667 0.00 0.00 36.48 1.89
3294 3425 5.381184 TGGGTAAGTATGCACCATAACAT 57.619 39.130 0.00 0.00 36.48 2.71
3331 3572 3.777106 TCCACATCTTCCCTGCATATC 57.223 47.619 0.00 0.00 0.00 1.63
3367 3609 6.149474 AGGAGCACATGTTAACTGTTTATCAC 59.851 38.462 7.22 0.00 0.00 3.06
3376 3618 9.719355 ATGTTAACTGTTTATCACACAGATACA 57.281 29.630 7.22 7.73 43.90 2.29
3378 3620 8.984764 GTTAACTGTTTATCACACAGATACACA 58.015 33.333 7.06 0.00 43.85 3.72
3388 3630 4.010349 ACACAGATACACAGACGATCAGA 58.990 43.478 0.00 0.00 0.00 3.27
3478 3720 5.148651 AGACTTTGTCGCTAAACAGGTAT 57.851 39.130 0.00 0.00 37.67 2.73
3506 3748 4.495422 AGGTATTTGACACAGCTACTTCG 58.505 43.478 0.00 0.00 0.00 3.79
3514 3756 4.035324 TGACACAGCTACTTCGCTCTATAC 59.965 45.833 0.00 0.00 38.41 1.47
3551 3817 1.281899 GAGCCTAATGACTGTCGTGC 58.718 55.000 2.78 3.13 0.00 5.34
3553 3819 0.721718 GCCTAATGACTGTCGTGCAC 59.278 55.000 6.82 6.82 0.00 4.57
3753 4019 6.968263 TGTTGGGAACATTAAAGTCATTCA 57.032 33.333 0.00 0.00 42.32 2.57
3757 4040 5.105392 TGGGAACATTAAAGTCATTCATGCC 60.105 40.000 0.00 0.00 33.40 4.40
3808 4091 2.106857 TCTCCCGGTTGTGTAAAATGGT 59.893 45.455 0.00 0.00 0.00 3.55
3816 4099 4.082949 GGTTGTGTAAAATGGTAGGAGTGC 60.083 45.833 0.00 0.00 0.00 4.40
3820 4103 4.634443 GTGTAAAATGGTAGGAGTGCGAAT 59.366 41.667 0.00 0.00 0.00 3.34
3822 4105 6.314400 GTGTAAAATGGTAGGAGTGCGAATAA 59.686 38.462 0.00 0.00 0.00 1.40
3825 4108 4.755266 ATGGTAGGAGTGCGAATAAACT 57.245 40.909 0.00 0.00 0.00 2.66
3833 4116 4.495844 GGAGTGCGAATAAACTTATGGCAC 60.496 45.833 20.48 20.48 45.24 5.01
3907 4195 4.716784 TCAGGCAGTGTGAAATACTCCTAT 59.283 41.667 0.00 0.00 35.46 2.57
3939 4227 9.733556 AAGATGTTATTACAACCAATGTACTCA 57.266 29.630 0.00 0.00 44.11 3.41
3941 4229 9.935682 GATGTTATTACAACCAATGTACTCATG 57.064 33.333 0.00 0.00 44.11 3.07
3951 4239 8.554528 CAACCAATGTACTCATGTCAGATATTC 58.445 37.037 0.00 0.00 34.19 1.75
3972 4260 4.205587 TCTTGCTGTTAAACCCCGTTAAA 58.794 39.130 0.00 0.00 0.00 1.52
3988 4276 2.510064 TAAACCCCGTCGCTCGCATT 62.510 55.000 0.00 0.00 38.35 3.56
3997 4285 1.209898 CGCTCGCATTGCAGGAAAA 59.790 52.632 9.69 0.00 0.00 2.29
4000 4288 2.724349 GCTCGCATTGCAGGAAAATAG 58.276 47.619 9.69 0.00 0.00 1.73
4002 4290 1.405105 TCGCATTGCAGGAAAATAGGC 59.595 47.619 9.69 0.00 0.00 3.93
4042 4330 1.544724 GCTGTCATGGCAACCCTTTA 58.455 50.000 0.00 0.00 0.00 1.85
4277 4593 2.604914 CAGCTACACTCTAATTGCCACG 59.395 50.000 0.00 0.00 0.00 4.94
4409 4725 1.329292 GACGTTTGCAGCTTGTGTACA 59.671 47.619 0.00 0.00 0.00 2.90
4530 4850 2.789569 GAGCGCTTTCTCGGTTTTAG 57.210 50.000 13.26 0.00 40.51 1.85
4647 4970 6.814644 TCCAAACGACTCAACGTATTGAATAT 59.185 34.615 0.07 0.00 44.28 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 102 7.201661 GGCCACGACAATTACTTGTATTGATTA 60.202 37.037 0.00 0.00 45.57 1.75
110 112 4.864704 ATTTTGGCCACGACAATTACTT 57.135 36.364 3.88 0.00 27.33 2.24
115 117 6.930731 AGTTTTATATTTTGGCCACGACAAT 58.069 32.000 3.88 4.31 27.33 2.71
150 153 8.104566 ACCAAGTACCTGTTAGTGCATATAAAA 58.895 33.333 0.00 0.00 0.00 1.52
166 169 5.778542 AGATATCCACTACACCAAGTACCT 58.221 41.667 0.00 0.00 0.00 3.08
176 180 3.861846 AGCATGGGAGATATCCACTACA 58.138 45.455 8.98 0.00 37.08 2.74
184 188 4.105217 TGAACATGGAAGCATGGGAGATAT 59.895 41.667 0.00 0.00 36.91 1.63
187 191 1.634973 TGAACATGGAAGCATGGGAGA 59.365 47.619 0.00 0.00 36.91 3.71
192 196 5.587443 TGTAGATCTTGAACATGGAAGCATG 59.413 40.000 0.00 0.00 38.46 4.06
202 206 8.251026 ACGTAATCAATCTGTAGATCTTGAACA 58.749 33.333 0.00 0.00 32.75 3.18
279 283 2.885135 TCTGTCAATGGGTCAAGCAT 57.115 45.000 0.00 0.00 0.00 3.79
291 295 2.356278 GCAGGGCCCATCTGTCAA 59.644 61.111 27.56 0.00 34.89 3.18
310 314 7.940688 GGCTAACCAGGTAATTAGGCTAATTTA 59.059 37.037 31.13 17.42 45.67 1.40
400 404 6.071334 TGTCCGTCAATCAGATAAAGAGACTT 60.071 38.462 0.00 0.00 0.00 3.01
403 407 5.185056 TGTGTCCGTCAATCAGATAAAGAGA 59.815 40.000 0.00 0.00 0.00 3.10
432 436 2.060326 TTAGACGAAACTGCCTGTCG 57.940 50.000 0.00 0.00 40.56 4.35
453 457 8.546597 AAACATGCACAACTAAACTTTCTTTT 57.453 26.923 0.00 0.00 0.00 2.27
457 461 9.030301 ACAATAAACATGCACAACTAAACTTTC 57.970 29.630 0.00 0.00 0.00 2.62
480 484 3.872603 ACCAGCGCCTGTGGACAA 61.873 61.111 19.97 0.00 38.57 3.18
517 521 7.010183 CGCGAAGAAAAAGAGATGAGGTTTATA 59.990 37.037 0.00 0.00 0.00 0.98
518 522 6.183360 CGCGAAGAAAAAGAGATGAGGTTTAT 60.183 38.462 0.00 0.00 0.00 1.40
519 523 5.120208 CGCGAAGAAAAAGAGATGAGGTTTA 59.880 40.000 0.00 0.00 0.00 2.01
520 524 4.083802 CGCGAAGAAAAAGAGATGAGGTTT 60.084 41.667 0.00 0.00 0.00 3.27
521 525 3.433615 CGCGAAGAAAAAGAGATGAGGTT 59.566 43.478 0.00 0.00 0.00 3.50
522 526 2.996621 CGCGAAGAAAAAGAGATGAGGT 59.003 45.455 0.00 0.00 0.00 3.85
523 527 3.254060 TCGCGAAGAAAAAGAGATGAGG 58.746 45.455 6.20 0.00 0.00 3.86
524 528 4.169508 TCTCGCGAAGAAAAAGAGATGAG 58.830 43.478 11.33 0.00 33.58 2.90
526 530 4.910746 TTCTCGCGAAGAAAAAGAGATG 57.089 40.909 11.33 0.00 41.10 2.90
535 539 1.792006 GAACCCTTTCTCGCGAAGAA 58.208 50.000 11.33 13.22 42.35 2.52
537 541 0.388134 TCGAACCCTTTCTCGCGAAG 60.388 55.000 11.33 4.53 35.04 3.79
538 542 0.032403 TTCGAACCCTTTCTCGCGAA 59.968 50.000 11.33 0.00 35.69 4.70
539 543 0.665369 GTTCGAACCCTTTCTCGCGA 60.665 55.000 17.68 9.26 35.04 5.87
540 544 1.623973 GGTTCGAACCCTTTCTCGCG 61.624 60.000 33.02 0.00 43.43 5.87
541 545 2.160063 GGTTCGAACCCTTTCTCGC 58.840 57.895 33.02 7.79 43.43 5.03
599 603 8.844441 TCTTGAAATTTATTTAATTACCCGCG 57.156 30.769 0.00 0.00 35.39 6.46
641 646 1.220749 GGTGACCTTAGCATGCGGA 59.779 57.895 15.99 4.19 0.00 5.54
674 679 0.620556 CCACCTGTCAATGGCTAGGT 59.379 55.000 3.70 3.70 44.05 3.08
702 707 2.210961 CTCACATGACATGCTAGCCTG 58.789 52.381 17.32 17.32 0.00 4.85
708 713 1.030488 GGCTGCTCACATGACATGCT 61.030 55.000 15.49 0.24 0.00 3.79
711 716 0.679002 GTGGGCTGCTCACATGACAT 60.679 55.000 26.87 0.00 35.39 3.06
712 717 1.302752 GTGGGCTGCTCACATGACA 60.303 57.895 26.87 0.00 35.39 3.58
713 718 1.302752 TGTGGGCTGCTCACATGAC 60.303 57.895 30.19 5.64 39.83 3.06
714 719 1.302752 GTGTGGGCTGCTCACATGA 60.303 57.895 35.08 12.84 45.32 3.07
726 732 2.802787 CTCTTATAGAGCCGTGTGGG 57.197 55.000 0.00 0.00 35.30 4.61
737 743 3.444703 ACAGTGCTTCCGCTCTTATAG 57.555 47.619 0.00 0.00 37.86 1.31
738 744 5.531122 AATACAGTGCTTCCGCTCTTATA 57.469 39.130 0.00 0.00 37.86 0.98
742 748 2.770164 AAATACAGTGCTTCCGCTCT 57.230 45.000 0.00 0.00 40.37 4.09
746 752 3.247442 TCGTGTAAATACAGTGCTTCCG 58.753 45.455 0.00 0.00 36.78 4.30
807 813 9.400638 CGTTTGATATTTAGTTTGGTGCTAAAA 57.599 29.630 0.00 0.00 40.44 1.52
808 814 7.539366 GCGTTTGATATTTAGTTTGGTGCTAAA 59.461 33.333 0.00 0.00 41.04 1.85
811 817 5.048364 TGCGTTTGATATTTAGTTTGGTGCT 60.048 36.000 0.00 0.00 0.00 4.40
812 818 5.157781 TGCGTTTGATATTTAGTTTGGTGC 58.842 37.500 0.00 0.00 0.00 5.01
822 828 6.430000 AGTTACAGGACTTGCGTTTGATATTT 59.570 34.615 0.00 0.00 0.00 1.40
823 829 5.938125 AGTTACAGGACTTGCGTTTGATATT 59.062 36.000 0.00 0.00 0.00 1.28
825 831 4.890088 AGTTACAGGACTTGCGTTTGATA 58.110 39.130 0.00 0.00 0.00 2.15
834 840 4.188247 TCATCGGAAGTTACAGGACTTG 57.812 45.455 0.00 0.00 39.84 3.16
837 843 4.124851 ACATCATCGGAAGTTACAGGAC 57.875 45.455 0.00 0.00 0.00 3.85
844 850 3.775316 AGGAGGTAACATCATCGGAAGTT 59.225 43.478 0.00 0.00 38.41 2.66
849 855 5.468540 TTATCAGGAGGTAACATCATCGG 57.531 43.478 0.00 0.00 41.41 4.18
852 858 8.993424 AGTACTTTTATCAGGAGGTAACATCAT 58.007 33.333 0.00 0.00 41.41 2.45
857 863 5.747675 GCGAGTACTTTTATCAGGAGGTAAC 59.252 44.000 0.00 0.00 0.00 2.50
865 871 5.403246 AGTGTGAGCGAGTACTTTTATCAG 58.597 41.667 0.00 0.00 0.00 2.90
866 872 5.048294 TGAGTGTGAGCGAGTACTTTTATCA 60.048 40.000 0.00 0.00 0.00 2.15
867 873 5.399858 TGAGTGTGAGCGAGTACTTTTATC 58.600 41.667 0.00 0.00 0.00 1.75
868 874 5.386958 TGAGTGTGAGCGAGTACTTTTAT 57.613 39.130 0.00 0.00 0.00 1.40
869 875 4.841443 TGAGTGTGAGCGAGTACTTTTA 57.159 40.909 0.00 0.00 0.00 1.52
870 876 3.728076 TGAGTGTGAGCGAGTACTTTT 57.272 42.857 0.00 0.00 0.00 2.27
871 877 3.318275 TCTTGAGTGTGAGCGAGTACTTT 59.682 43.478 0.00 0.00 0.00 2.66
872 878 2.885266 TCTTGAGTGTGAGCGAGTACTT 59.115 45.455 0.00 0.00 0.00 2.24
873 879 2.505405 TCTTGAGTGTGAGCGAGTACT 58.495 47.619 0.00 0.00 0.00 2.73
874 880 2.991434 TCTTGAGTGTGAGCGAGTAC 57.009 50.000 0.00 0.00 0.00 2.73
875 881 3.146847 TCTTCTTGAGTGTGAGCGAGTA 58.853 45.455 0.00 0.00 0.00 2.59
876 882 1.957177 TCTTCTTGAGTGTGAGCGAGT 59.043 47.619 0.00 0.00 0.00 4.18
877 883 2.594321 CTCTTCTTGAGTGTGAGCGAG 58.406 52.381 0.00 0.00 37.99 5.03
878 884 1.336332 GCTCTTCTTGAGTGTGAGCGA 60.336 52.381 0.00 0.00 44.41 4.93
879 885 1.066914 GCTCTTCTTGAGTGTGAGCG 58.933 55.000 0.00 0.00 44.41 5.03
881 887 3.383620 ACTGCTCTTCTTGAGTGTGAG 57.616 47.619 0.00 0.00 44.41 3.51
882 888 3.827008 AACTGCTCTTCTTGAGTGTGA 57.173 42.857 0.00 0.00 44.41 3.58
883 889 3.060003 CGAAACTGCTCTTCTTGAGTGTG 60.060 47.826 0.00 0.00 44.41 3.82
884 890 3.126831 CGAAACTGCTCTTCTTGAGTGT 58.873 45.455 0.00 0.00 44.41 3.55
887 893 3.557595 ACAACGAAACTGCTCTTCTTGAG 59.442 43.478 0.00 0.00 45.33 3.02
941 947 4.846551 TGGGACACGACACAACAG 57.153 55.556 0.00 0.00 0.00 3.16
977 989 1.630369 TCACTGGCTCCACAATTAGCT 59.370 47.619 0.00 0.00 38.80 3.32
978 990 2.113860 TCACTGGCTCCACAATTAGC 57.886 50.000 0.00 0.00 38.03 3.09
979 991 5.278169 GCATTATCACTGGCTCCACAATTAG 60.278 44.000 0.00 0.00 0.00 1.73
980 992 4.580167 GCATTATCACTGGCTCCACAATTA 59.420 41.667 0.00 0.00 0.00 1.40
981 993 3.382546 GCATTATCACTGGCTCCACAATT 59.617 43.478 0.00 0.00 0.00 2.32
982 994 2.954318 GCATTATCACTGGCTCCACAAT 59.046 45.455 0.00 0.00 0.00 2.71
983 995 2.368439 GCATTATCACTGGCTCCACAA 58.632 47.619 0.00 0.00 0.00 3.33
985 997 1.312815 GGCATTATCACTGGCTCCAC 58.687 55.000 0.00 0.00 36.34 4.02
987 999 0.179045 ACGGCATTATCACTGGCTCC 60.179 55.000 0.00 0.00 37.06 4.70
1251 1269 4.899239 CCGCGGGAGATGTGGAGC 62.899 72.222 20.10 0.00 39.39 4.70
1495 1513 1.009389 GGTCCGTGCAAGAACGAGAG 61.009 60.000 1.33 0.00 46.49 3.20
1496 1514 1.006571 GGTCCGTGCAAGAACGAGA 60.007 57.895 1.33 0.00 46.49 4.04
1529 1547 4.758251 TCACAGCGGCGTCCATGG 62.758 66.667 9.37 4.97 0.00 3.66
1554 1572 2.916052 TATCGCCGCCGGATCAGAC 61.916 63.158 7.68 0.00 34.56 3.51
1557 1575 2.910479 AGTATCGCCGCCGGATCA 60.910 61.111 7.68 0.00 34.56 2.92
1936 1954 1.127343 ATAAGCTCTGGTGAGAGGGC 58.873 55.000 0.00 0.00 45.40 5.19
2155 2202 9.407380 TCAGTAGCCATAATCAACAATACAAAT 57.593 29.630 0.00 0.00 0.00 2.32
2165 2213 8.486210 AGTTAACTCATCAGTAGCCATAATCAA 58.514 33.333 1.12 0.00 30.14 2.57
2166 2214 8.023021 AGTTAACTCATCAGTAGCCATAATCA 57.977 34.615 1.12 0.00 30.14 2.57
2167 2215 8.768955 CAAGTTAACTCATCAGTAGCCATAATC 58.231 37.037 8.95 0.00 30.14 1.75
2168 2216 7.227512 GCAAGTTAACTCATCAGTAGCCATAAT 59.772 37.037 8.95 0.00 30.14 1.28
2169 2217 6.538742 GCAAGTTAACTCATCAGTAGCCATAA 59.461 38.462 8.95 0.00 30.14 1.90
2170 2218 6.049149 GCAAGTTAACTCATCAGTAGCCATA 58.951 40.000 8.95 0.00 30.14 2.74
2171 2219 4.878397 GCAAGTTAACTCATCAGTAGCCAT 59.122 41.667 8.95 0.00 30.14 4.40
2172 2220 4.253685 GCAAGTTAACTCATCAGTAGCCA 58.746 43.478 8.95 0.00 30.14 4.75
2173 2221 4.093556 GTGCAAGTTAACTCATCAGTAGCC 59.906 45.833 8.95 0.00 30.14 3.93
2401 2449 0.109342 CTGAGGCAGGTTTGACTGGT 59.891 55.000 0.00 0.00 44.85 4.00
2406 2454 0.473755 TTCAGCTGAGGCAGGTTTGA 59.526 50.000 17.43 0.00 40.40 2.69
2407 2455 1.321474 TTTCAGCTGAGGCAGGTTTG 58.679 50.000 17.43 0.00 40.40 2.93
2415 2463 5.801350 TGATCGTTATTTTTCAGCTGAGG 57.199 39.130 17.43 0.00 0.00 3.86
2416 2464 6.779117 ACATGATCGTTATTTTTCAGCTGAG 58.221 36.000 17.43 2.60 0.00 3.35
2418 2466 8.950961 CATAACATGATCGTTATTTTTCAGCTG 58.049 33.333 7.63 7.63 39.50 4.24
2482 2540 5.190992 GCATGATTGCTCATATGAACCAA 57.809 39.130 16.39 16.39 45.77 3.67
2506 2564 3.063725 TCAAAACAACATTGCAGCAAAGC 59.936 39.130 12.97 0.00 0.00 3.51
2534 2592 1.344065 ATACCGCGGATACCAATGGA 58.656 50.000 35.90 0.00 0.00 3.41
2535 2593 3.536956 ATATACCGCGGATACCAATGG 57.463 47.619 35.90 0.00 0.00 3.16
2536 2594 5.041287 CAGTATATACCGCGGATACCAATG 58.959 45.833 35.90 18.23 0.00 2.82
2537 2595 4.708421 ACAGTATATACCGCGGATACCAAT 59.292 41.667 35.90 17.36 0.00 3.16
2538 2596 4.081406 ACAGTATATACCGCGGATACCAA 58.919 43.478 35.90 11.04 0.00 3.67
2542 2603 6.071784 ACAATTCACAGTATATACCGCGGATA 60.072 38.462 35.90 23.89 0.00 2.59
2558 2619 5.830457 TCCCACTGTAAATCAACAATTCACA 59.170 36.000 0.00 0.00 0.00 3.58
2560 2621 6.303054 TCTCCCACTGTAAATCAACAATTCA 58.697 36.000 0.00 0.00 0.00 2.57
2561 2622 6.127897 CCTCTCCCACTGTAAATCAACAATTC 60.128 42.308 0.00 0.00 0.00 2.17
2563 2624 5.256474 CCTCTCCCACTGTAAATCAACAAT 58.744 41.667 0.00 0.00 0.00 2.71
2564 2625 4.506625 CCCTCTCCCACTGTAAATCAACAA 60.507 45.833 0.00 0.00 0.00 2.83
2565 2626 3.009033 CCCTCTCCCACTGTAAATCAACA 59.991 47.826 0.00 0.00 0.00 3.33
2566 2627 3.610911 CCCTCTCCCACTGTAAATCAAC 58.389 50.000 0.00 0.00 0.00 3.18
2570 2646 2.197465 GTCCCCTCTCCCACTGTAAAT 58.803 52.381 0.00 0.00 0.00 1.40
2667 2744 2.484264 GCAGTCATCAACAGTTACACCC 59.516 50.000 0.00 0.00 0.00 4.61
2720 2803 6.646653 TGTCTGCTATGTTTCTTACACAGAAG 59.353 38.462 0.00 0.00 42.76 2.85
2735 2838 6.020281 GTCTTCGTCTGTTAATGTCTGCTATG 60.020 42.308 0.00 0.00 0.00 2.23
2737 2840 5.048294 TGTCTTCGTCTGTTAATGTCTGCTA 60.048 40.000 0.00 0.00 0.00 3.49
2748 2853 4.836125 ATGCAAATTGTCTTCGTCTGTT 57.164 36.364 0.00 0.00 0.00 3.16
2749 2854 4.836125 AATGCAAATTGTCTTCGTCTGT 57.164 36.364 0.00 0.00 0.00 3.41
2750 2855 6.636447 TGTAAAATGCAAATTGTCTTCGTCTG 59.364 34.615 0.00 0.00 0.00 3.51
2751 2856 6.734137 TGTAAAATGCAAATTGTCTTCGTCT 58.266 32.000 0.00 0.00 0.00 4.18
2752 2857 6.984740 TGTAAAATGCAAATTGTCTTCGTC 57.015 33.333 0.00 0.00 0.00 4.20
2753 2858 7.144661 TCATGTAAAATGCAAATTGTCTTCGT 58.855 30.769 0.00 0.00 0.00 3.85
2754 2859 7.565450 TCATGTAAAATGCAAATTGTCTTCG 57.435 32.000 0.00 0.00 0.00 3.79
2814 2923 7.714377 CAGAAAGCAATATCCATCAAGACTAGT 59.286 37.037 0.00 0.00 0.00 2.57
2864 2973 4.097741 ACAAATCTGCTAAATGCGCCATTA 59.902 37.500 4.18 3.14 46.63 1.90
2870 2979 4.604843 TCTGACAAATCTGCTAAATGCG 57.395 40.909 0.00 0.00 46.63 4.73
2876 2985 6.299805 ACCTAACATCTGACAAATCTGCTA 57.700 37.500 0.00 0.00 0.00 3.49
2929 3038 5.460091 GGAGTGCTTGTCAGTGAAAAATTTC 59.540 40.000 0.00 0.00 37.69 2.17
2947 3056 6.531240 CCAATGTTTAACAATACATGGAGTGC 59.469 38.462 5.01 0.00 35.29 4.40
2971 3080 5.425196 TTGTCACCAAGGTAACCTATACC 57.575 43.478 0.00 0.00 37.86 2.73
3012 3121 2.821969 CAACCACCCTTCAGAATCCAAG 59.178 50.000 0.00 0.00 0.00 3.61
3087 3196 7.778083 TGTACTTAATTATCTCTTTCAGCCGA 58.222 34.615 0.00 0.00 0.00 5.54
3312 3553 3.497103 TGATATGCAGGGAAGATGTGG 57.503 47.619 0.00 0.00 0.00 4.17
3331 3572 2.118313 TGTGCTCCTCATGATGGTTG 57.882 50.000 0.00 0.25 0.00 3.77
3367 3609 4.095632 AGTCTGATCGTCTGTGTATCTGTG 59.904 45.833 0.00 0.00 0.00 3.66
3376 3618 0.960861 TCGCCAGTCTGATCGTCTGT 60.961 55.000 0.00 0.00 0.00 3.41
3378 3620 0.678366 ACTCGCCAGTCTGATCGTCT 60.678 55.000 0.00 0.00 0.00 4.18
3450 3692 5.747565 TGTTTAGCGACAAAGTCTTTGATG 58.252 37.500 28.07 20.01 43.26 3.07
3478 3720 5.483685 AGCTGTGTCAAATACCTAGTTCA 57.516 39.130 0.00 0.00 0.00 3.18
3506 3748 6.809196 GGCTATGTCTACACATTGTATAGAGC 59.191 42.308 5.06 5.50 40.66 4.09
3514 3756 2.797156 GCTCGGCTATGTCTACACATTG 59.203 50.000 0.00 0.00 40.66 2.82
3753 4019 9.000978 ACTATCCATGATCTATTTATCAGGCAT 57.999 33.333 0.00 0.00 39.18 4.40
3757 4040 9.526713 CGGAACTATCCATGATCTATTTATCAG 57.473 37.037 0.00 0.00 46.97 2.90
3808 4091 5.054477 GCCATAAGTTTATTCGCACTCCTA 58.946 41.667 0.00 0.00 0.00 2.94
3816 4099 2.353269 TGCGGTGCCATAAGTTTATTCG 59.647 45.455 0.00 0.00 0.00 3.34
3820 4103 2.080693 CACTGCGGTGCCATAAGTTTA 58.919 47.619 13.81 0.00 36.61 2.01
3822 4105 0.250727 ACACTGCGGTGCCATAAGTT 60.251 50.000 25.67 0.00 46.57 2.66
3825 4108 0.250510 TTCACACTGCGGTGCCATAA 60.251 50.000 25.67 11.46 46.57 1.90
3833 4116 2.386661 AGGAGTATTTCACACTGCGG 57.613 50.000 0.00 0.00 39.16 5.69
3872 4155 3.326588 ACACTGCCTGAGTACATTGGTTA 59.673 43.478 0.00 0.00 31.73 2.85
3916 4204 9.461312 ACATGAGTACATTGGTTGTAATAACAT 57.539 29.630 0.00 0.00 42.37 2.71
3922 4210 6.764379 TCTGACATGAGTACATTGGTTGTAA 58.236 36.000 0.00 0.00 42.37 2.41
3923 4211 6.353404 TCTGACATGAGTACATTGGTTGTA 57.647 37.500 0.00 0.00 39.87 2.41
3924 4212 5.227569 TCTGACATGAGTACATTGGTTGT 57.772 39.130 0.00 0.00 42.62 3.32
3925 4213 8.442632 AATATCTGACATGAGTACATTGGTTG 57.557 34.615 0.00 0.00 34.15 3.77
3926 4214 8.489489 AGAATATCTGACATGAGTACATTGGTT 58.511 33.333 0.00 0.00 34.15 3.67
3927 4215 8.027524 AGAATATCTGACATGAGTACATTGGT 57.972 34.615 0.00 0.00 34.15 3.67
3928 4216 8.771766 CAAGAATATCTGACATGAGTACATTGG 58.228 37.037 0.00 0.00 34.15 3.16
3929 4217 8.281194 GCAAGAATATCTGACATGAGTACATTG 58.719 37.037 0.00 0.00 34.15 2.82
3930 4218 8.209584 AGCAAGAATATCTGACATGAGTACATT 58.790 33.333 0.00 0.00 34.15 2.71
3931 4219 7.656542 CAGCAAGAATATCTGACATGAGTACAT 59.343 37.037 0.00 0.00 37.19 2.29
3932 4220 6.982724 CAGCAAGAATATCTGACATGAGTACA 59.017 38.462 0.00 0.00 0.00 2.90
3933 4221 6.983307 ACAGCAAGAATATCTGACATGAGTAC 59.017 38.462 0.00 0.00 0.00 2.73
3934 4222 7.117285 ACAGCAAGAATATCTGACATGAGTA 57.883 36.000 0.00 0.00 0.00 2.59
3935 4223 5.987098 ACAGCAAGAATATCTGACATGAGT 58.013 37.500 0.00 0.00 0.00 3.41
3939 4227 7.067494 GGGTTTAACAGCAAGAATATCTGACAT 59.933 37.037 0.00 0.00 0.00 3.06
3941 4229 6.183360 GGGGTTTAACAGCAAGAATATCTGAC 60.183 42.308 0.00 0.00 0.00 3.51
3951 4239 4.292599 GTTTAACGGGGTTTAACAGCAAG 58.707 43.478 0.00 0.00 35.83 4.01
4002 4290 0.314935 AAAAACGCTGCCATGACAGG 59.685 50.000 11.26 3.79 38.16 4.00
4042 4330 3.006859 GCCTAACTGAAAGCAAAACCCAT 59.993 43.478 0.00 0.00 37.60 4.00
4049 4337 4.367039 AACTAGGCCTAACTGAAAGCAA 57.633 40.909 14.85 0.00 37.60 3.91
4277 4593 1.105457 TGCAAGGCTGAATGCATACC 58.895 50.000 8.22 0.00 46.87 2.73
4409 4725 1.453762 GGCTAGAGGCGGACGTACAT 61.454 60.000 0.00 0.00 42.94 2.29


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

AutoCloner maintained by Alex Coulton.