Multiple sequence alignment - TraesCS7B01G171100

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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 TraesCS7B01G171100 chr7B 100.000 4463 0 0 1 4463 244135361 244139823 0.000000e+00 8242.0
1 TraesCS7B01G171100 chr7D 91.903 2149 133 17 2337 4451 263892933 263895074 0.000000e+00 2966.0
2 TraesCS7B01G171100 chr7D 95.812 1170 31 7 765 1926 263889750 263890909 0.000000e+00 1873.0
3 TraesCS7B01G171100 chr7D 82.492 931 144 13 988 1916 591206890 591207803 0.000000e+00 798.0
4 TraesCS7B01G171100 chr7D 87.838 444 26 14 222 664 263889336 263889752 3.100000e-136 496.0
5 TraesCS7B01G171100 chr7D 90.476 168 13 1 1 165 263889154 263889321 7.520000e-53 219.0
6 TraesCS7B01G171100 chr7D 92.857 126 8 1 1980 2104 263892510 263892635 9.860000e-42 182.0
7 TraesCS7B01G171100 chr7A 93.355 1505 74 13 2484 3981 286996401 286997886 0.000000e+00 2202.0
8 TraesCS7B01G171100 chr7A 89.827 865 47 18 1492 2341 286995186 286996024 0.000000e+00 1072.0
9 TraesCS7B01G171100 chr7A 94.350 531 21 4 889 1417 286994662 286995185 0.000000e+00 806.0
10 TraesCS7B01G171100 chr7A 92.812 320 16 5 212 530 286993990 286994303 1.460000e-124 457.0
11 TraesCS7B01G171100 chr7A 93.254 252 17 0 4050 4301 286997891 286998142 5.450000e-99 372.0
12 TraesCS7B01G171100 chr7A 82.234 197 18 9 1 180 286993794 286993990 2.150000e-33 154.0
13 TraesCS7B01G171100 chr7A 92.079 101 5 1 768 868 286994310 286994407 6.020000e-29 139.0
14 TraesCS7B01G171100 chr2D 78.897 943 163 22 988 1921 3035760 3034845 1.370000e-169 606.0
15 TraesCS7B01G171100 chr2D 75.431 232 47 7 2629 2853 94420147 94420375 2.200000e-18 104.0
16 TraesCS7B01G171100 chr2A 78.564 933 153 30 988 1910 2655799 2656694 5.010000e-159 571.0
17 TraesCS7B01G171100 chr2A 78.182 935 168 19 994 1916 551721513 551722423 8.380000e-157 564.0
18 TraesCS7B01G171100 chr2A 70.700 843 199 40 1096 1914 682635518 682634700 1.290000e-30 145.0
19 TraesCS7B01G171100 chrUn 77.025 605 122 10 3078 3676 24020559 24019966 9.250000e-87 331.0
20 TraesCS7B01G171100 chr5B 76.591 440 80 17 2438 2862 268519908 268519477 2.090000e-53 220.0
21 TraesCS7B01G171100 chr3D 76.562 448 76 19 2438 2862 517771635 517772076 7.520000e-53 219.0
22 TraesCS7B01G171100 chr3B 81.818 154 23 4 2710 2862 168673369 168673518 1.690000e-24 124.0
23 TraesCS7B01G171100 chr3B 75.000 228 44 11 2640 2859 737778286 737778508 4.750000e-15 93.5
24 TraesCS7B01G171100 chr3A 84.127 126 15 2 2733 2853 653348099 653348224 2.820000e-22 117.0
25 TraesCS7B01G171100 chr4A 80.597 134 12 6 2712 2844 38735903 38736023 1.710000e-14 91.6
26 TraesCS7B01G171100 chr2B 100.000 33 0 0 2674 2706 251104204 251104172 1.340000e-05 62.1


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 TraesCS7B01G171100 chr7B 244135361 244139823 4462 False 8242.000000 8242 100.000000 1 4463 1 chr7B.!!$F1 4462
1 TraesCS7B01G171100 chr7D 263889154 263895074 5920 False 1147.200000 2966 91.777200 1 4451 5 chr7D.!!$F2 4450
2 TraesCS7B01G171100 chr7D 591206890 591207803 913 False 798.000000 798 82.492000 988 1916 1 chr7D.!!$F1 928
3 TraesCS7B01G171100 chr7A 286993794 286998142 4348 False 743.142857 2202 91.130143 1 4301 7 chr7A.!!$F1 4300
4 TraesCS7B01G171100 chr2D 3034845 3035760 915 True 606.000000 606 78.897000 988 1921 1 chr2D.!!$R1 933
5 TraesCS7B01G171100 chr2A 2655799 2656694 895 False 571.000000 571 78.564000 988 1910 1 chr2A.!!$F1 922
6 TraesCS7B01G171100 chr2A 551721513 551722423 910 False 564.000000 564 78.182000 994 1916 1 chr2A.!!$F2 922
7 TraesCS7B01G171100 chrUn 24019966 24020559 593 True 331.000000 331 77.025000 3078 3676 1 chrUn.!!$R1 598

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
464 495 0.251077 CAGCCTGGGAGAGCAAAGTT 60.251 55.0 0.00 0.0 0.00 2.66 F
465 496 0.251077 AGCCTGGGAGAGCAAAGTTG 60.251 55.0 0.00 0.0 0.00 3.16 F
679 711 0.254747 CATACCCCTCCGCTTCCAAA 59.745 55.0 0.00 0.0 0.00 3.28 F
680 712 0.996583 ATACCCCTCCGCTTCCAAAA 59.003 50.0 0.00 0.0 0.00 2.44 F
682 714 0.996583 ACCCCTCCGCTTCCAAAATA 59.003 50.0 0.00 0.0 0.00 1.40 F
976 1246 1.073964 CACATCACGTCTCTGCAAGG 58.926 55.0 0.00 0.0 0.00 3.61 F
2659 4793 1.178534 ACAAGTGTCCGGCCAAATGG 61.179 55.0 2.24 0.0 38.53 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1606 1897 0.108329 CCCAACTCGCGGATGTACTT 60.108 55.000 6.13 0.00 0.00 2.24 R
2341 4283 1.132527 TCCCCCAAACCTCTCTCAAGA 60.133 52.381 0.00 0.00 0.00 3.02 R
2475 4426 1.295423 GTGGTACATCGGTGGCAGT 59.705 57.895 0.00 0.00 44.52 4.40 R
2636 4770 1.978455 TTGGCCGGACACTTGTCAGT 61.978 55.000 11.33 0.00 46.47 3.41 R
2710 4844 4.996788 TTTATCCTCCTTCACCGAGTAC 57.003 45.455 0.00 0.00 0.00 2.73 R
2787 4921 2.959707 ACGTTACCAAAATTTCAGGGCA 59.040 40.909 12.65 0.22 0.00 5.36 R
3500 5640 0.188342 AAAACATCCCAGGGCACTGT 59.812 50.000 16.38 1.12 43.36 3.55 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
32 33 3.964031 CCTAGTCCCTACTGATTTGCTCT 59.036 47.826 0.00 0.00 36.36 4.09
132 152 0.251787 GCCCCACCCTTCTCAAATGT 60.252 55.000 0.00 0.00 0.00 2.71
143 166 5.046304 CCCTTCTCAAATGTAGTCCTCTTCA 60.046 44.000 0.00 0.00 0.00 3.02
147 170 4.556233 TCAAATGTAGTCCTCTTCACGTG 58.444 43.478 9.94 9.94 0.00 4.49
153 176 1.602605 TCCTCTTCACGTGCTCGGA 60.603 57.895 11.67 10.83 41.85 4.55
172 195 3.217626 GGACACTTTCCATCCCATCATC 58.782 50.000 0.00 0.00 45.10 2.92
175 198 5.222007 GGACACTTTCCATCCCATCATCTAT 60.222 44.000 0.00 0.00 45.10 1.98
180 203 5.752036 TTCCATCCCATCATCTATGAGTC 57.248 43.478 0.00 0.00 40.64 3.36
181 204 3.766051 TCCATCCCATCATCTATGAGTCG 59.234 47.826 0.00 0.00 40.64 4.18
182 205 3.513119 CCATCCCATCATCTATGAGTCGT 59.487 47.826 0.00 0.00 40.64 4.34
183 206 4.381398 CCATCCCATCATCTATGAGTCGTC 60.381 50.000 0.00 0.00 40.64 4.20
184 207 3.832527 TCCCATCATCTATGAGTCGTCA 58.167 45.455 0.00 0.00 40.64 4.35
186 209 4.835056 TCCCATCATCTATGAGTCGTCATT 59.165 41.667 0.00 0.00 40.84 2.57
189 212 6.484643 CCCATCATCTATGAGTCGTCATTTTT 59.515 38.462 0.00 0.00 40.84 1.94
190 213 7.307632 CCCATCATCTATGAGTCGTCATTTTTC 60.308 40.741 0.00 0.00 40.84 2.29
191 214 7.440556 CCATCATCTATGAGTCGTCATTTTTCT 59.559 37.037 0.00 0.00 40.84 2.52
192 215 7.993821 TCATCTATGAGTCGTCATTTTTCTC 57.006 36.000 0.00 0.00 40.84 2.87
193 216 7.547227 TCATCTATGAGTCGTCATTTTTCTCA 58.453 34.615 0.00 0.00 40.84 3.27
194 217 8.034804 TCATCTATGAGTCGTCATTTTTCTCAA 58.965 33.333 0.00 0.00 40.84 3.02
195 218 8.659491 CATCTATGAGTCGTCATTTTTCTCAAA 58.341 33.333 0.00 0.00 40.84 2.69
196 219 8.601845 TCTATGAGTCGTCATTTTTCTCAAAA 57.398 30.769 0.00 0.00 40.84 2.44
197 220 9.051679 TCTATGAGTCGTCATTTTTCTCAAAAA 57.948 29.630 0.00 0.00 40.84 1.94
240 263 5.230306 GTCGTCATAGTTGGAGAAAGATTCG 59.770 44.000 0.00 0.00 34.02 3.34
252 275 5.886516 AGAAAGATTCGTCCGCATACGGG 62.887 52.174 4.12 0.00 46.97 5.28
449 480 1.035932 ACCATTCTCATGCTGCAGCC 61.036 55.000 34.64 17.82 41.18 4.85
464 495 0.251077 CAGCCTGGGAGAGCAAAGTT 60.251 55.000 0.00 0.00 0.00 2.66
465 496 0.251077 AGCCTGGGAGAGCAAAGTTG 60.251 55.000 0.00 0.00 0.00 3.16
466 497 0.538287 GCCTGGGAGAGCAAAGTTGT 60.538 55.000 0.00 0.00 0.00 3.32
467 498 1.271379 GCCTGGGAGAGCAAAGTTGTA 60.271 52.381 0.00 0.00 0.00 2.41
468 499 2.704572 CCTGGGAGAGCAAAGTTGTAG 58.295 52.381 0.00 0.00 0.00 2.74
475 506 3.839293 AGAGCAAAGTTGTAGAGTAGCG 58.161 45.455 0.00 0.00 0.00 4.26
477 508 2.561419 AGCAAAGTTGTAGAGTAGCGGA 59.439 45.455 0.00 0.00 0.00 5.54
493 524 8.639761 AGAGTAGCGGACATTTAATTACATACT 58.360 33.333 0.00 0.00 0.00 2.12
497 529 7.703328 AGCGGACATTTAATTACATACTTTGG 58.297 34.615 0.00 0.00 0.00 3.28
543 575 3.664107 GGCTATGATCGCCATTGTCTTA 58.336 45.455 2.74 0.00 46.77 2.10
558 590 8.243426 GCCATTGTCTTACATGATTGTCTTTTA 58.757 33.333 0.00 0.00 37.28 1.52
584 616 0.758685 CCAGCGATCTTCCTCCCTCT 60.759 60.000 0.00 0.00 0.00 3.69
592 624 1.286553 TCTTCCTCCCTCTCTGTCTCC 59.713 57.143 0.00 0.00 0.00 3.71
599 631 2.033602 TCTCTGTCTCCGCACGGA 59.966 61.111 11.90 11.90 42.90 4.69
630 662 0.815095 TGCATCAAAGCAGCTGATGG 59.185 50.000 20.43 7.83 46.81 3.51
641 673 2.093288 GCAGCTGATGGCAGGCTATATA 60.093 50.000 20.43 0.00 44.79 0.86
642 674 3.529533 CAGCTGATGGCAGGCTATATAC 58.470 50.000 8.42 0.00 44.79 1.47
646 678 5.426509 AGCTGATGGCAGGCTATATACATAA 59.573 40.000 9.99 0.00 44.79 1.90
665 697 6.624423 ACATAACCGGACGTTATATCATACC 58.376 40.000 9.46 0.00 44.30 2.73
666 698 4.525912 AACCGGACGTTATATCATACCC 57.474 45.455 9.46 0.00 30.96 3.69
667 699 2.827921 ACCGGACGTTATATCATACCCC 59.172 50.000 9.46 0.00 0.00 4.95
668 700 3.094572 CCGGACGTTATATCATACCCCT 58.905 50.000 0.00 0.00 0.00 4.79
669 701 3.129988 CCGGACGTTATATCATACCCCTC 59.870 52.174 0.00 0.00 0.00 4.30
670 702 3.129988 CGGACGTTATATCATACCCCTCC 59.870 52.174 0.00 0.00 0.00 4.30
671 703 3.129988 GGACGTTATATCATACCCCTCCG 59.870 52.174 0.00 0.00 0.00 4.63
672 704 2.494870 ACGTTATATCATACCCCTCCGC 59.505 50.000 0.00 0.00 0.00 5.54
673 705 2.758979 CGTTATATCATACCCCTCCGCT 59.241 50.000 0.00 0.00 0.00 5.52
674 706 3.194968 CGTTATATCATACCCCTCCGCTT 59.805 47.826 0.00 0.00 0.00 4.68
675 707 4.677250 CGTTATATCATACCCCTCCGCTTC 60.677 50.000 0.00 0.00 0.00 3.86
676 708 1.640917 TATCATACCCCTCCGCTTCC 58.359 55.000 0.00 0.00 0.00 3.46
677 709 0.399949 ATCATACCCCTCCGCTTCCA 60.400 55.000 0.00 0.00 0.00 3.53
678 710 0.619255 TCATACCCCTCCGCTTCCAA 60.619 55.000 0.00 0.00 0.00 3.53
679 711 0.254747 CATACCCCTCCGCTTCCAAA 59.745 55.000 0.00 0.00 0.00 3.28
680 712 0.996583 ATACCCCTCCGCTTCCAAAA 59.003 50.000 0.00 0.00 0.00 2.44
681 713 0.996583 TACCCCTCCGCTTCCAAAAT 59.003 50.000 0.00 0.00 0.00 1.82
682 714 0.996583 ACCCCTCCGCTTCCAAAATA 59.003 50.000 0.00 0.00 0.00 1.40
683 715 1.356398 ACCCCTCCGCTTCCAAAATAA 59.644 47.619 0.00 0.00 0.00 1.40
684 716 2.225167 ACCCCTCCGCTTCCAAAATAAA 60.225 45.455 0.00 0.00 0.00 1.40
685 717 2.829120 CCCCTCCGCTTCCAAAATAAAA 59.171 45.455 0.00 0.00 0.00 1.52
686 718 3.259625 CCCCTCCGCTTCCAAAATAAAAA 59.740 43.478 0.00 0.00 0.00 1.94
687 719 4.081142 CCCCTCCGCTTCCAAAATAAAAAT 60.081 41.667 0.00 0.00 0.00 1.82
688 720 5.128008 CCCCTCCGCTTCCAAAATAAAAATA 59.872 40.000 0.00 0.00 0.00 1.40
689 721 6.351456 CCCCTCCGCTTCCAAAATAAAAATAA 60.351 38.462 0.00 0.00 0.00 1.40
690 722 6.533723 CCCTCCGCTTCCAAAATAAAAATAAC 59.466 38.462 0.00 0.00 0.00 1.89
691 723 7.320399 CCTCCGCTTCCAAAATAAAAATAACT 58.680 34.615 0.00 0.00 0.00 2.24
692 724 7.275560 CCTCCGCTTCCAAAATAAAAATAACTG 59.724 37.037 0.00 0.00 0.00 3.16
693 725 7.662897 TCCGCTTCCAAAATAAAAATAACTGT 58.337 30.769 0.00 0.00 0.00 3.55
694 726 7.810759 TCCGCTTCCAAAATAAAAATAACTGTC 59.189 33.333 0.00 0.00 0.00 3.51
695 727 7.812669 CCGCTTCCAAAATAAAAATAACTGTCT 59.187 33.333 0.00 0.00 0.00 3.41
696 728 8.850452 CGCTTCCAAAATAAAAATAACTGTCTC 58.150 33.333 0.00 0.00 0.00 3.36
697 729 9.691362 GCTTCCAAAATAAAAATAACTGTCTCA 57.309 29.630 0.00 0.00 0.00 3.27
740 772 9.106070 AGTACAAAATTACATTAAGATCGGGAC 57.894 33.333 0.00 0.00 0.00 4.46
741 773 7.931578 ACAAAATTACATTAAGATCGGGACA 57.068 32.000 0.00 0.00 0.00 4.02
742 774 7.758495 ACAAAATTACATTAAGATCGGGACAC 58.242 34.615 0.00 0.00 0.00 3.67
743 775 7.610305 ACAAAATTACATTAAGATCGGGACACT 59.390 33.333 0.00 0.00 0.00 3.55
744 776 8.458843 CAAAATTACATTAAGATCGGGACACTT 58.541 33.333 0.00 0.00 0.00 3.16
745 777 9.675464 AAAATTACATTAAGATCGGGACACTTA 57.325 29.630 0.00 0.00 0.00 2.24
746 778 9.675464 AAATTACATTAAGATCGGGACACTTAA 57.325 29.630 0.00 0.00 39.36 1.85
747 779 9.847224 AATTACATTAAGATCGGGACACTTAAT 57.153 29.630 0.00 0.00 43.19 1.40
748 780 9.847224 ATTACATTAAGATCGGGACACTTAATT 57.153 29.630 14.40 10.94 41.65 1.40
749 781 9.675464 TTACATTAAGATCGGGACACTTAATTT 57.325 29.630 14.40 12.42 41.65 1.82
751 783 9.326413 ACATTAAGATCGGGACACTTAATTTAG 57.674 33.333 14.40 0.00 41.65 1.85
752 784 9.542462 CATTAAGATCGGGACACTTAATTTAGA 57.458 33.333 14.40 0.00 41.65 2.10
754 786 9.595823 TTAAGATCGGGACACTTAATTTAGAAG 57.404 33.333 0.00 0.00 33.22 2.85
755 787 6.583562 AGATCGGGACACTTAATTTAGAAGG 58.416 40.000 0.00 0.00 0.00 3.46
756 788 5.093849 TCGGGACACTTAATTTAGAAGGG 57.906 43.478 0.00 0.00 33.29 3.95
757 789 4.778958 TCGGGACACTTAATTTAGAAGGGA 59.221 41.667 0.00 0.00 31.42 4.20
758 790 5.105064 TCGGGACACTTAATTTAGAAGGGAG 60.105 44.000 0.00 0.00 31.42 4.30
759 791 5.437946 GGGACACTTAATTTAGAAGGGAGG 58.562 45.833 0.00 0.00 31.42 4.30
760 792 5.437946 GGACACTTAATTTAGAAGGGAGGG 58.562 45.833 0.00 0.00 31.42 4.30
761 793 5.437946 GACACTTAATTTAGAAGGGAGGGG 58.562 45.833 0.00 0.00 31.42 4.79
762 794 4.229812 ACACTTAATTTAGAAGGGAGGGGG 59.770 45.833 0.00 0.00 31.42 5.40
763 795 4.229812 CACTTAATTTAGAAGGGAGGGGGT 59.770 45.833 0.00 0.00 27.89 4.95
843 875 8.701895 CCATCCCTACTGTATTTGTTTCTACTA 58.298 37.037 0.00 0.00 0.00 1.82
844 876 9.530633 CATCCCTACTGTATTTGTTTCTACTAC 57.469 37.037 0.00 0.00 0.00 2.73
845 877 8.890410 TCCCTACTGTATTTGTTTCTACTACT 57.110 34.615 0.00 0.00 0.00 2.57
904 1170 2.910199 TGATGCTCCAGAGTTGCATAC 58.090 47.619 0.00 0.00 45.90 2.39
907 1173 2.635714 TGCTCCAGAGTTGCATACATG 58.364 47.619 0.00 0.00 0.00 3.21
938 1204 1.376543 TCGAGGCCGTCACTTACTAG 58.623 55.000 0.00 0.00 37.05 2.57
976 1246 1.073964 CACATCACGTCTCTGCAAGG 58.926 55.000 0.00 0.00 0.00 3.61
1079 1355 4.544689 CGAGCTCTCCCGTCGCAG 62.545 72.222 12.85 0.00 0.00 5.18
1080 1356 4.200283 GAGCTCTCCCGTCGCAGG 62.200 72.222 6.43 0.00 0.00 4.85
1081 1357 4.742649 AGCTCTCCCGTCGCAGGA 62.743 66.667 0.00 0.00 0.00 3.86
1082 1358 3.760035 GCTCTCCCGTCGCAGGAA 61.760 66.667 0.00 0.00 31.49 3.36
1083 1359 2.182030 CTCTCCCGTCGCAGGAAC 59.818 66.667 0.00 0.00 31.49 3.62
1084 1360 2.599281 TCTCCCGTCGCAGGAACA 60.599 61.111 0.00 0.00 31.49 3.18
1462 1753 2.750637 GCGTCAGGACCGAGGAGA 60.751 66.667 9.29 0.00 0.00 3.71
1848 2139 1.744741 GGAAGTGCTGCTCAGGCTC 60.745 63.158 0.00 0.00 39.59 4.70
1921 2212 5.622914 GCCGTCATGTTTGTAAGTACTCCTA 60.623 44.000 0.00 0.00 0.00 2.94
1922 2213 5.803967 CCGTCATGTTTGTAAGTACTCCTAC 59.196 44.000 0.00 0.00 0.00 3.18
1925 2216 7.597743 CGTCATGTTTGTAAGTACTCCTACTTT 59.402 37.037 0.00 0.00 39.79 2.66
1926 2217 9.918630 GTCATGTTTGTAAGTACTCCTACTTTA 57.081 33.333 0.00 0.00 39.79 1.85
1927 2218 9.918630 TCATGTTTGTAAGTACTCCTACTTTAC 57.081 33.333 0.00 0.00 39.79 2.01
1930 2221 9.754382 TGTTTGTAAGTACTCCTACTTTACAAG 57.246 33.333 11.75 0.00 39.79 3.16
1931 2222 8.706936 GTTTGTAAGTACTCCTACTTTACAAGC 58.293 37.037 11.75 11.10 39.79 4.01
1932 2223 6.928520 TGTAAGTACTCCTACTTTACAAGCC 58.071 40.000 0.00 0.00 39.79 4.35
1933 2224 4.715527 AGTACTCCTACTTTACAAGCCG 57.284 45.455 0.00 0.00 27.62 5.52
1934 2225 4.338879 AGTACTCCTACTTTACAAGCCGA 58.661 43.478 0.00 0.00 27.62 5.54
1935 2226 3.870633 ACTCCTACTTTACAAGCCGAG 57.129 47.619 0.00 0.00 0.00 4.63
1951 2404 8.271312 ACAAGCCGAGTAGTATCTATCTATTC 57.729 38.462 0.00 0.00 0.00 1.75
1952 2405 7.337436 ACAAGCCGAGTAGTATCTATCTATTCC 59.663 40.741 0.00 0.00 0.00 3.01
2054 3898 5.820947 GGAACTCCAAGAAAACACAGAAGTA 59.179 40.000 0.00 0.00 35.64 2.24
2059 3903 7.661847 ACTCCAAGAAAACACAGAAGTATTAGG 59.338 37.037 0.00 0.00 0.00 2.69
2108 3952 8.758829 TCTACCAGCATATCACTTTCTTTCTTA 58.241 33.333 0.00 0.00 0.00 2.10
2110 3954 8.443953 ACCAGCATATCACTTTCTTTCTTATC 57.556 34.615 0.00 0.00 0.00 1.75
2111 3955 8.270744 ACCAGCATATCACTTTCTTTCTTATCT 58.729 33.333 0.00 0.00 0.00 1.98
2112 3956 9.770097 CCAGCATATCACTTTCTTTCTTATCTA 57.230 33.333 0.00 0.00 0.00 1.98
2298 4143 4.278170 TCAGTTCGCCTCAAATGTTTGAAT 59.722 37.500 9.24 0.00 45.61 2.57
2314 4159 6.227522 TGTTTGAATCGGACAGTTCAGATAA 58.772 36.000 0.00 0.00 35.81 1.75
2320 4165 8.236586 TGAATCGGACAGTTCAGATAATTTTTG 58.763 33.333 0.00 0.00 35.81 2.44
2321 4166 7.687941 ATCGGACAGTTCAGATAATTTTTGT 57.312 32.000 0.00 0.00 35.17 2.83
2323 4168 8.610248 TCGGACAGTTCAGATAATTTTTGTTA 57.390 30.769 0.00 0.00 0.00 2.41
2324 4169 9.226606 TCGGACAGTTCAGATAATTTTTGTTAT 57.773 29.630 0.00 0.00 0.00 1.89
2325 4170 9.490663 CGGACAGTTCAGATAATTTTTGTTATC 57.509 33.333 0.00 0.00 40.01 1.75
2334 4179 9.787532 CAGATAATTTTTGTTATCAACGATGGT 57.212 29.630 8.76 0.00 41.42 3.55
2341 4283 4.584874 TGTTATCAACGATGGTCACCAAT 58.415 39.130 0.00 0.00 36.95 3.16
2374 4316 1.306997 GGGGGAGTCTGGATGTCCA 60.307 63.158 1.17 1.17 45.30 4.02
2397 4339 2.675423 TCTGACTCCGACACCCCG 60.675 66.667 0.00 0.00 0.00 5.73
2459 4410 2.114616 CTCCCCTTGTGCTCTGTATCT 58.885 52.381 0.00 0.00 0.00 1.98
2475 4426 3.970410 CTGCACCCTTGGAGGCCA 61.970 66.667 5.01 0.00 37.53 5.36
2496 4630 2.587889 CCACCGATGTACCACCCC 59.412 66.667 0.00 0.00 0.00 4.95
2534 4668 2.494918 CGAACCTCCGCCTTCGAT 59.505 61.111 0.00 0.00 41.47 3.59
2535 4669 1.589196 CGAACCTCCGCCTTCGATC 60.589 63.158 0.00 0.00 41.47 3.69
2636 4770 1.473844 TCCAGGGAGGACACCATGA 59.526 57.895 2.04 0.00 43.28 3.07
2659 4793 1.178534 ACAAGTGTCCGGCCAAATGG 61.179 55.000 2.24 0.00 38.53 3.16
2710 4844 3.675481 TGAAACAAACACGATGACAACG 58.325 40.909 3.29 3.29 0.00 4.10
2717 4851 1.256652 CACGATGACAACGTACTCGG 58.743 55.000 10.60 0.00 42.07 4.63
2746 4880 5.705441 GGAGGATAAATTGTTGTGTGAGACA 59.295 40.000 0.00 0.00 0.00 3.41
2781 4915 4.074970 AGTGTGGAGTTTTAAGGCATGAG 58.925 43.478 0.00 0.00 0.00 2.90
2782 4916 2.819608 TGTGGAGTTTTAAGGCATGAGC 59.180 45.455 0.00 0.00 41.10 4.26
2783 4917 3.084786 GTGGAGTTTTAAGGCATGAGCT 58.915 45.455 0.00 0.00 41.70 4.09
2787 4921 5.951747 TGGAGTTTTAAGGCATGAGCTAAAT 59.048 36.000 0.00 0.00 41.70 1.40
2788 4922 6.127647 TGGAGTTTTAAGGCATGAGCTAAATG 60.128 38.462 0.00 4.78 41.70 2.32
2795 4929 2.026641 GCATGAGCTAAATGCCCTGAA 58.973 47.619 18.82 0.00 43.78 3.02
3096 5232 0.185901 AGGACATGTTTGCTGGTGGT 59.814 50.000 0.00 0.00 0.00 4.16
3115 5251 1.275856 GTACGGATACCACCACAACCA 59.724 52.381 0.00 0.00 0.00 3.67
3407 5547 7.466746 TTTCCAGTCAAGATATTGGGAAAAG 57.533 36.000 15.39 0.00 39.29 2.27
3620 5760 6.203530 GTCTGACTTCATTTGACATGTCTGAA 59.796 38.462 25.55 23.03 35.40 3.02
3629 5769 8.202811 TCATTTGACATGTCTGAAAAATTTGGA 58.797 29.630 25.55 13.22 0.00 3.53
3696 5836 3.640029 ACGGGTGGACGTCAAAGATATAT 59.360 43.478 18.91 0.00 45.08 0.86
3708 5848 8.656849 ACGTCAAAGATATATTGTTGAAGTGAC 58.343 33.333 20.07 11.88 39.91 3.67
3902 6042 8.516234 TGTACTAGTTTTGTGTTTGTGAACATT 58.484 29.630 0.00 0.00 46.63 2.71
3948 6088 8.698973 TGGAAGTAACATGGTCTTTTATTTGA 57.301 30.769 0.00 0.00 0.00 2.69
3959 6099 9.685276 ATGGTCTTTTATTTGATCTGACACATA 57.315 29.630 0.00 0.00 0.00 2.29
4047 6188 7.609056 ATGGTCACATTTACTAAGTCGTTAGT 58.391 34.615 4.15 4.15 42.19 2.24
4048 6189 6.864685 TGGTCACATTTACTAAGTCGTTAGTG 59.135 38.462 8.32 0.00 46.91 2.74
4084 6248 4.305989 AGCGTGTGAACAAATTGTGAAT 57.694 36.364 0.00 0.00 0.00 2.57
4085 6249 4.681744 AGCGTGTGAACAAATTGTGAATT 58.318 34.783 0.00 0.00 0.00 2.17
4111 6275 3.576078 TTTCATGGATTGTATCGCCCT 57.424 42.857 0.00 0.00 0.00 5.19
4134 6298 3.571590 AGAGCGGTAGAAATCATCTCCT 58.428 45.455 0.00 0.00 39.71 3.69
4284 6448 2.812836 TCCATCGTGGACTACCTACA 57.187 50.000 3.02 0.00 42.67 2.74
4369 6533 6.642131 CGTTGAAATGTTGAGGATTTGTTCAT 59.358 34.615 0.00 0.00 0.00 2.57
4377 6541 8.862325 TGTTGAGGATTTGTTCATATGTTAGT 57.138 30.769 1.90 0.00 0.00 2.24
4383 6547 8.432805 AGGATTTGTTCATATGTTAGTAGGGAG 58.567 37.037 1.90 0.00 0.00 4.30
4401 6565 8.858094 AGTAGGGAGTATCTAGGAAAAATAACG 58.142 37.037 0.00 0.00 33.73 3.18
4413 6577 5.359860 AGGAAAAATAACGAGCCCTTATTGG 59.640 40.000 0.00 0.00 0.00 3.16
4454 6618 8.553459 AGAAAAAGCCATCTTATATATCCACG 57.447 34.615 0.00 0.00 31.02 4.94
4455 6619 8.157476 AGAAAAAGCCATCTTATATATCCACGT 58.843 33.333 0.00 0.00 31.02 4.49
4456 6620 9.431887 GAAAAAGCCATCTTATATATCCACGTA 57.568 33.333 0.00 0.00 31.02 3.57
4457 6621 9.787435 AAAAAGCCATCTTATATATCCACGTAA 57.213 29.630 0.00 0.00 31.02 3.18
4458 6622 8.773404 AAAGCCATCTTATATATCCACGTAAC 57.227 34.615 0.00 0.00 31.02 2.50
4459 6623 6.875076 AGCCATCTTATATATCCACGTAACC 58.125 40.000 0.00 0.00 0.00 2.85
4460 6624 6.668283 AGCCATCTTATATATCCACGTAACCT 59.332 38.462 0.00 0.00 0.00 3.50
4461 6625 6.979238 GCCATCTTATATATCCACGTAACCTC 59.021 42.308 0.00 0.00 0.00 3.85
4462 6626 7.363530 GCCATCTTATATATCCACGTAACCTCA 60.364 40.741 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 4.293494 ACTCTAATTGCTCTGAGGATGGA 58.707 43.478 6.83 0.00 0.00 3.41
87 107 3.261137 GCCTAGGAAAATATAGAGCCGGT 59.739 47.826 14.75 0.00 0.00 5.28
132 152 0.803117 CGAGCACGTGAAGAGGACTA 59.197 55.000 22.23 0.00 34.56 2.59
143 166 1.300697 GGAAAGTGTCCGAGCACGT 60.301 57.895 2.18 0.00 43.61 4.49
153 176 5.370584 TCATAGATGATGGGATGGAAAGTGT 59.629 40.000 0.00 0.00 36.08 3.55
205 228 9.529325 CTCCAACTATGACGACTCATAATTTTA 57.471 33.333 0.00 0.00 38.64 1.52
206 229 8.258007 TCTCCAACTATGACGACTCATAATTTT 58.742 33.333 0.00 0.00 38.64 1.82
207 230 7.782049 TCTCCAACTATGACGACTCATAATTT 58.218 34.615 0.00 0.00 38.64 1.82
208 231 7.348080 TCTCCAACTATGACGACTCATAATT 57.652 36.000 0.00 0.00 38.64 1.40
209 232 6.961360 TCTCCAACTATGACGACTCATAAT 57.039 37.500 0.00 0.00 38.64 1.28
210 233 6.769134 TTCTCCAACTATGACGACTCATAA 57.231 37.500 0.00 0.00 38.64 1.90
211 234 6.602009 TCTTTCTCCAACTATGACGACTCATA 59.398 38.462 0.00 0.00 38.21 2.15
212 235 5.419155 TCTTTCTCCAACTATGACGACTCAT 59.581 40.000 0.00 0.00 40.47 2.90
213 236 4.765339 TCTTTCTCCAACTATGACGACTCA 59.235 41.667 0.00 0.00 0.00 3.41
214 237 5.312120 TCTTTCTCCAACTATGACGACTC 57.688 43.478 0.00 0.00 0.00 3.36
215 238 5.923733 ATCTTTCTCCAACTATGACGACT 57.076 39.130 0.00 0.00 0.00 4.18
216 239 5.230306 CGAATCTTTCTCCAACTATGACGAC 59.770 44.000 0.00 0.00 0.00 4.34
217 240 5.105877 ACGAATCTTTCTCCAACTATGACGA 60.106 40.000 0.00 0.00 0.00 4.20
218 241 5.103000 ACGAATCTTTCTCCAACTATGACG 58.897 41.667 0.00 0.00 0.00 4.35
219 242 5.520649 GGACGAATCTTTCTCCAACTATGAC 59.479 44.000 0.00 0.00 31.46 3.06
220 243 5.661458 GGACGAATCTTTCTCCAACTATGA 58.339 41.667 0.00 0.00 31.46 2.15
252 275 2.202810 GAGGCCTGAGCGCTACAC 60.203 66.667 12.00 0.00 41.24 2.90
449 480 3.007398 ACTCTACAACTTTGCTCTCCCAG 59.993 47.826 0.00 0.00 0.00 4.45
464 495 7.774134 TGTAATTAAATGTCCGCTACTCTACA 58.226 34.615 0.00 0.00 0.00 2.74
465 496 8.813643 ATGTAATTAAATGTCCGCTACTCTAC 57.186 34.615 0.00 0.00 0.00 2.59
466 497 9.903682 GTATGTAATTAAATGTCCGCTACTCTA 57.096 33.333 0.00 0.00 0.00 2.43
467 498 8.639761 AGTATGTAATTAAATGTCCGCTACTCT 58.360 33.333 0.00 0.00 0.00 3.24
468 499 8.813643 AGTATGTAATTAAATGTCCGCTACTC 57.186 34.615 0.00 0.00 0.00 2.59
543 575 8.031277 GCTGGAGAAAATAAAAGACAATCATGT 58.969 33.333 0.00 0.00 44.25 3.21
558 590 3.432890 GGAGGAAGATCGCTGGAGAAAAT 60.433 47.826 0.00 0.00 0.00 1.82
592 624 2.791158 GCAAAATAATCACCTCCGTGCG 60.791 50.000 0.00 0.00 40.04 5.34
599 631 6.040209 TGCTTTGATGCAAAATAATCACCT 57.960 33.333 0.00 0.00 40.29 4.00
630 662 4.430908 GTCCGGTTATGTATATAGCCTGC 58.569 47.826 0.00 0.00 37.84 4.85
646 678 2.827921 GGGGTATGATATAACGTCCGGT 59.172 50.000 0.00 0.00 0.00 5.28
661 693 0.996583 TTTTGGAAGCGGAGGGGTAT 59.003 50.000 0.00 0.00 0.00 2.73
662 694 0.996583 ATTTTGGAAGCGGAGGGGTA 59.003 50.000 0.00 0.00 0.00 3.69
663 695 0.996583 TATTTTGGAAGCGGAGGGGT 59.003 50.000 0.00 0.00 0.00 4.95
664 696 2.137810 TTATTTTGGAAGCGGAGGGG 57.862 50.000 0.00 0.00 0.00 4.79
665 697 4.529109 TTTTTATTTTGGAAGCGGAGGG 57.471 40.909 0.00 0.00 0.00 4.30
666 698 7.275560 CAGTTATTTTTATTTTGGAAGCGGAGG 59.724 37.037 0.00 0.00 0.00 4.30
667 699 7.812669 ACAGTTATTTTTATTTTGGAAGCGGAG 59.187 33.333 0.00 0.00 0.00 4.63
668 700 7.662897 ACAGTTATTTTTATTTTGGAAGCGGA 58.337 30.769 0.00 0.00 0.00 5.54
669 701 7.812669 AGACAGTTATTTTTATTTTGGAAGCGG 59.187 33.333 0.00 0.00 0.00 5.52
670 702 8.742554 AGACAGTTATTTTTATTTTGGAAGCG 57.257 30.769 0.00 0.00 0.00 4.68
671 703 9.691362 TGAGACAGTTATTTTTATTTTGGAAGC 57.309 29.630 0.00 0.00 0.00 3.86
714 746 9.106070 GTCCCGATCTTAATGTAATTTTGTACT 57.894 33.333 0.00 0.00 37.87 2.73
715 747 8.885722 TGTCCCGATCTTAATGTAATTTTGTAC 58.114 33.333 0.00 0.00 37.87 2.90
716 748 8.885722 GTGTCCCGATCTTAATGTAATTTTGTA 58.114 33.333 0.00 0.00 37.87 2.41
717 749 7.610305 AGTGTCCCGATCTTAATGTAATTTTGT 59.390 33.333 0.00 0.00 37.87 2.83
718 750 7.985476 AGTGTCCCGATCTTAATGTAATTTTG 58.015 34.615 0.00 0.00 37.87 2.44
719 751 8.575649 AAGTGTCCCGATCTTAATGTAATTTT 57.424 30.769 0.00 0.00 37.87 1.82
720 752 9.675464 TTAAGTGTCCCGATCTTAATGTAATTT 57.325 29.630 0.00 0.00 37.87 1.82
721 753 9.847224 ATTAAGTGTCCCGATCTTAATGTAATT 57.153 29.630 12.63 0.00 40.51 1.40
722 754 9.847224 AATTAAGTGTCCCGATCTTAATGTAAT 57.153 29.630 13.46 0.00 40.88 1.89
723 755 9.675464 AAATTAAGTGTCCCGATCTTAATGTAA 57.325 29.630 13.46 0.00 40.88 2.41
725 757 9.326413 CTAAATTAAGTGTCCCGATCTTAATGT 57.674 33.333 13.46 11.81 40.88 2.71
726 758 9.542462 TCTAAATTAAGTGTCCCGATCTTAATG 57.458 33.333 13.46 6.67 40.88 1.90
728 760 9.595823 CTTCTAAATTAAGTGTCCCGATCTTAA 57.404 33.333 0.00 0.00 37.81 1.85
729 761 8.202137 CCTTCTAAATTAAGTGTCCCGATCTTA 58.798 37.037 0.00 0.00 0.00 2.10
730 762 7.048512 CCTTCTAAATTAAGTGTCCCGATCTT 58.951 38.462 0.00 0.00 0.00 2.40
731 763 6.408206 CCCTTCTAAATTAAGTGTCCCGATCT 60.408 42.308 0.00 0.00 0.00 2.75
732 764 5.758784 CCCTTCTAAATTAAGTGTCCCGATC 59.241 44.000 0.00 0.00 0.00 3.69
733 765 5.427481 TCCCTTCTAAATTAAGTGTCCCGAT 59.573 40.000 0.00 0.00 0.00 4.18
734 766 4.778958 TCCCTTCTAAATTAAGTGTCCCGA 59.221 41.667 0.00 0.00 0.00 5.14
735 767 5.093849 TCCCTTCTAAATTAAGTGTCCCG 57.906 43.478 0.00 0.00 0.00 5.14
736 768 5.437946 CCTCCCTTCTAAATTAAGTGTCCC 58.562 45.833 0.00 0.00 0.00 4.46
737 769 5.437946 CCCTCCCTTCTAAATTAAGTGTCC 58.562 45.833 0.00 0.00 0.00 4.02
738 770 5.437946 CCCCTCCCTTCTAAATTAAGTGTC 58.562 45.833 0.00 0.00 0.00 3.67
739 771 4.229812 CCCCCTCCCTTCTAAATTAAGTGT 59.770 45.833 0.00 0.00 0.00 3.55
740 772 4.229812 ACCCCCTCCCTTCTAAATTAAGTG 59.770 45.833 0.00 0.00 0.00 3.16
741 773 4.455161 ACCCCCTCCCTTCTAAATTAAGT 58.545 43.478 0.00 0.00 0.00 2.24
742 774 6.781857 ATACCCCCTCCCTTCTAAATTAAG 57.218 41.667 0.00 0.00 0.00 1.85
747 779 9.739737 GAATATATATACCCCCTCCCTTCTAAA 57.260 37.037 0.00 0.00 0.00 1.85
748 780 8.302102 GGAATATATATACCCCCTCCCTTCTAA 58.698 40.741 0.00 0.00 0.00 2.10
749 781 7.146631 GGGAATATATATACCCCCTCCCTTCTA 60.147 44.444 16.19 0.00 38.61 2.10
750 782 6.357608 GGGAATATATATACCCCCTCCCTTCT 60.358 46.154 16.19 0.00 38.61 2.85
751 783 5.850583 GGGAATATATATACCCCCTCCCTTC 59.149 48.000 16.19 6.33 38.61 3.46
752 784 5.811896 GGGAATATATATACCCCCTCCCTT 58.188 45.833 16.19 0.00 38.61 3.95
753 785 5.075542 AGGGAATATATATACCCCCTCCCT 58.924 45.833 18.89 18.89 45.51 4.20
754 786 5.451056 AGGGAATATATATACCCCCTCCC 57.549 47.826 20.45 18.61 39.89 4.30
755 787 7.782695 AAAAGGGAATATATATACCCCCTCC 57.217 40.000 23.85 12.78 42.95 4.30
786 818 0.245539 CACCTATGTCGTGGTCCGTT 59.754 55.000 0.00 0.00 37.94 4.44
800 832 3.199946 GGATGGACTTTGATGGTCACCTA 59.800 47.826 0.00 0.00 35.61 3.08
904 1170 1.068333 CCTCGAAGTTTGGTTGGCATG 60.068 52.381 0.00 0.00 0.00 4.06
907 1173 1.285950 GCCTCGAAGTTTGGTTGGC 59.714 57.895 6.85 6.85 0.00 4.52
955 1221 0.033920 TTGCAGAGACGTGATGTGCT 59.966 50.000 17.11 0.00 37.79 4.40
956 1222 0.441533 CTTGCAGAGACGTGATGTGC 59.558 55.000 11.36 11.36 37.45 4.57
957 1223 1.073964 CCTTGCAGAGACGTGATGTG 58.926 55.000 0.00 0.00 0.00 3.21
959 1225 1.073964 CACCTTGCAGAGACGTGATG 58.926 55.000 0.00 0.00 0.00 3.07
976 1246 1.952635 GCAGCTTGTTGGCTTGCAC 60.953 57.895 0.00 0.00 41.00 4.57
1079 1355 3.193479 CAGCTTCTTATTGGGGTTGTTCC 59.807 47.826 0.00 0.00 0.00 3.62
1080 1356 3.367395 GCAGCTTCTTATTGGGGTTGTTC 60.367 47.826 0.00 0.00 0.00 3.18
1081 1357 2.562738 GCAGCTTCTTATTGGGGTTGTT 59.437 45.455 0.00 0.00 0.00 2.83
1082 1358 2.171003 GCAGCTTCTTATTGGGGTTGT 58.829 47.619 0.00 0.00 0.00 3.32
1083 1359 1.478105 GGCAGCTTCTTATTGGGGTTG 59.522 52.381 0.00 0.00 0.00 3.77
1084 1360 1.359130 AGGCAGCTTCTTATTGGGGTT 59.641 47.619 0.00 0.00 0.00 4.11
1110 1398 1.762522 CGATGGGGAGAGTCCATGGG 61.763 65.000 13.02 0.00 44.34 4.00
1462 1753 2.125106 GCGAAGGAGGTTGCCGAT 60.125 61.111 0.00 0.00 0.00 4.18
1606 1897 0.108329 CCCAACTCGCGGATGTACTT 60.108 55.000 6.13 0.00 0.00 2.24
1716 2007 1.403687 GGCCGTAGCTCCTCCTCATT 61.404 60.000 0.00 0.00 39.73 2.57
1925 2216 9.381033 GAATAGATAGATACTACTCGGCTTGTA 57.619 37.037 0.00 0.00 0.00 2.41
1926 2217 7.337436 GGAATAGATAGATACTACTCGGCTTGT 59.663 40.741 0.00 0.00 0.00 3.16
1927 2218 7.201750 GGGAATAGATAGATACTACTCGGCTTG 60.202 44.444 0.00 0.00 0.00 4.01
1929 2220 6.358991 GGGAATAGATAGATACTACTCGGCT 58.641 44.000 0.00 0.00 0.00 5.52
1930 2221 5.532032 GGGGAATAGATAGATACTACTCGGC 59.468 48.000 0.00 0.00 0.00 5.54
1931 2222 6.063404 GGGGGAATAGATAGATACTACTCGG 58.937 48.000 0.00 0.00 0.00 4.63
2054 3898 4.196971 GGTCAGTAAATCGGCAACCTAAT 58.803 43.478 0.00 0.00 0.00 1.73
2059 3903 3.270877 AGATGGTCAGTAAATCGGCAAC 58.729 45.455 0.00 0.00 0.00 4.17
2186 4031 9.383519 CTGTATGTTTGCGGGATATCTTTATAT 57.616 33.333 2.05 0.00 0.00 0.86
2187 4032 8.590204 TCTGTATGTTTGCGGGATATCTTTATA 58.410 33.333 2.05 0.00 0.00 0.98
2188 4033 7.450074 TCTGTATGTTTGCGGGATATCTTTAT 58.550 34.615 2.05 0.00 0.00 1.40
2189 4034 6.822442 TCTGTATGTTTGCGGGATATCTTTA 58.178 36.000 2.05 0.00 0.00 1.85
2190 4035 5.680619 TCTGTATGTTTGCGGGATATCTTT 58.319 37.500 2.05 0.00 0.00 2.52
2191 4036 5.290493 TCTGTATGTTTGCGGGATATCTT 57.710 39.130 2.05 0.00 0.00 2.40
2192 4037 4.955811 TCTGTATGTTTGCGGGATATCT 57.044 40.909 2.05 0.00 0.00 1.98
2193 4038 6.313905 CCTTATCTGTATGTTTGCGGGATATC 59.686 42.308 0.00 0.00 0.00 1.63
2194 4039 6.173339 CCTTATCTGTATGTTTGCGGGATAT 58.827 40.000 0.00 0.00 0.00 1.63
2195 4040 5.071250 ACCTTATCTGTATGTTTGCGGGATA 59.929 40.000 0.00 0.00 0.00 2.59
2196 4041 4.141482 ACCTTATCTGTATGTTTGCGGGAT 60.141 41.667 0.00 0.00 0.00 3.85
2197 4042 3.199071 ACCTTATCTGTATGTTTGCGGGA 59.801 43.478 0.00 0.00 0.00 5.14
2198 4043 3.541632 ACCTTATCTGTATGTTTGCGGG 58.458 45.455 0.00 0.00 0.00 6.13
2199 4044 6.260050 ACATAACCTTATCTGTATGTTTGCGG 59.740 38.462 0.00 0.00 0.00 5.69
2200 4045 7.011016 TGACATAACCTTATCTGTATGTTTGCG 59.989 37.037 0.00 0.00 0.00 4.85
2201 4046 8.208718 TGACATAACCTTATCTGTATGTTTGC 57.791 34.615 0.00 0.00 0.00 3.68
2298 4143 7.504924 AACAAAAATTATCTGAACTGTCCGA 57.495 32.000 0.00 0.00 0.00 4.55
2314 4159 6.015856 TGGTGACCATCGTTGATAACAAAAAT 60.016 34.615 0.00 0.00 37.77 1.82
2320 4165 4.876107 AGATTGGTGACCATCGTTGATAAC 59.124 41.667 4.56 0.00 31.53 1.89
2321 4166 5.097742 AGATTGGTGACCATCGTTGATAA 57.902 39.130 4.56 0.00 31.53 1.75
2323 4168 3.634397 AGATTGGTGACCATCGTTGAT 57.366 42.857 4.56 0.00 31.53 2.57
2324 4169 3.073678 CAAGATTGGTGACCATCGTTGA 58.926 45.455 4.56 0.00 31.53 3.18
2325 4170 3.073678 TCAAGATTGGTGACCATCGTTG 58.926 45.455 4.56 9.42 31.53 4.10
2326 4171 3.007940 TCTCAAGATTGGTGACCATCGTT 59.992 43.478 4.56 0.00 31.53 3.85
2327 4172 2.567169 TCTCAAGATTGGTGACCATCGT 59.433 45.455 4.56 0.88 31.53 3.73
2328 4173 3.118992 TCTCTCAAGATTGGTGACCATCG 60.119 47.826 4.56 0.00 31.53 3.84
2330 4175 3.199508 CCTCTCTCAAGATTGGTGACCAT 59.800 47.826 4.56 0.00 31.53 3.55
2331 4176 2.568956 CCTCTCTCAAGATTGGTGACCA 59.431 50.000 0.00 0.00 0.00 4.02
2333 4178 3.971245 ACCTCTCTCAAGATTGGTGAC 57.029 47.619 4.07 0.00 31.51 3.67
2334 4179 4.505566 CCAAACCTCTCTCAAGATTGGTGA 60.506 45.833 5.28 0.00 32.67 4.02
2335 4180 3.755378 CCAAACCTCTCTCAAGATTGGTG 59.245 47.826 5.28 0.00 32.67 4.17
2341 4283 1.132527 TCCCCCAAACCTCTCTCAAGA 60.133 52.381 0.00 0.00 0.00 3.02
2374 4316 1.527611 TGTCGGAGTCAGACGTGGT 60.528 57.895 17.00 0.00 41.24 4.16
2459 4410 4.284550 GTGGCCTCCAAGGGTGCA 62.285 66.667 3.32 0.00 35.37 4.57
2475 4426 1.295423 GTGGTACATCGGTGGCAGT 59.705 57.895 0.00 0.00 44.52 4.40
2519 4653 2.494918 CGATCGAAGGCGGAGGTT 59.505 61.111 10.26 0.00 38.28 3.50
2611 4745 2.285368 TCCTCCCTGGATGGCGTT 60.285 61.111 0.00 0.00 40.56 4.84
2636 4770 1.978455 TTGGCCGGACACTTGTCAGT 61.978 55.000 11.33 0.00 46.47 3.41
2710 4844 4.996788 TTTATCCTCCTTCACCGAGTAC 57.003 45.455 0.00 0.00 0.00 2.73
2717 4851 6.206634 TCACACAACAATTTATCCTCCTTCAC 59.793 38.462 0.00 0.00 0.00 3.18
2781 4915 4.578871 ACCAAAATTTCAGGGCATTTAGC 58.421 39.130 12.65 0.00 44.65 3.09
2782 4916 6.310224 CGTTACCAAAATTTCAGGGCATTTAG 59.690 38.462 12.65 0.00 0.00 1.85
2783 4917 6.159988 CGTTACCAAAATTTCAGGGCATTTA 58.840 36.000 12.65 0.00 0.00 1.40
2787 4921 2.959707 ACGTTACCAAAATTTCAGGGCA 59.040 40.909 12.65 0.22 0.00 5.36
2788 4922 3.243602 ACACGTTACCAAAATTTCAGGGC 60.244 43.478 12.65 3.94 0.00 5.19
2789 4923 4.295051 CACACGTTACCAAAATTTCAGGG 58.705 43.478 12.65 7.90 0.00 4.45
2792 4926 4.371855 TGCACACGTTACCAAAATTTCA 57.628 36.364 0.00 0.00 0.00 2.69
2793 4927 4.742659 ACATGCACACGTTACCAAAATTTC 59.257 37.500 0.00 0.00 0.00 2.17
2795 4929 4.314740 ACATGCACACGTTACCAAAATT 57.685 36.364 0.00 0.00 0.00 1.82
2919 5054 8.747538 AACTTCCACATAACTTGTTTAAGAGT 57.252 30.769 0.00 0.00 36.00 3.24
3096 5232 1.642112 TGGTTGTGGTGGTATCCGTA 58.358 50.000 0.00 0.00 0.00 4.02
3109 5245 1.047801 GCCCACTCCAAAATGGTTGT 58.952 50.000 0.00 0.00 39.03 3.32
3115 5251 2.643551 CGACATAGCCCACTCCAAAAT 58.356 47.619 0.00 0.00 0.00 1.82
3206 5342 7.886629 ATGTCACAATTGGTAATGATAGCTT 57.113 32.000 10.83 0.00 0.00 3.74
3407 5547 1.087501 CGGGCTTAAACTCTTCAGGC 58.912 55.000 0.00 0.00 32.04 4.85
3497 5637 4.101448 ATCCCAGGGCACTGTCGC 62.101 66.667 16.38 0.00 43.36 5.19
3500 5640 0.188342 AAAACATCCCAGGGCACTGT 59.812 50.000 16.38 1.12 43.36 3.55
3632 5772 8.367911 TGCAGGTCATATCTTCGTCTTATTATT 58.632 33.333 0.00 0.00 0.00 1.40
3634 5774 7.284919 TGCAGGTCATATCTTCGTCTTATTA 57.715 36.000 0.00 0.00 0.00 0.98
3682 5822 8.656849 GTCACTTCAACAATATATCTTTGACGT 58.343 33.333 10.37 10.37 32.43 4.34
3696 5836 3.238441 GTTGTTTGCGTCACTTCAACAA 58.762 40.909 0.00 0.00 36.31 2.83
3708 5848 5.991328 AGATAGATACCATGTTGTTTGCG 57.009 39.130 0.00 0.00 0.00 4.85
3794 5934 6.370718 GTCCCAACGAGCTTTTCTTATTCTAA 59.629 38.462 0.00 0.00 0.00 2.10
3948 6088 8.806429 TGGTAAACAAATCATATGTGTCAGAT 57.194 30.769 1.90 0.00 0.00 2.90
4009 6150 9.906660 GTAAATGTGACCATAAATCAAAAGACA 57.093 29.630 0.00 0.00 0.00 3.41
4047 6188 6.342111 TCACACGCTTTGTTGGATATATACA 58.658 36.000 0.00 0.00 35.67 2.29
4048 6189 6.838198 TCACACGCTTTGTTGGATATATAC 57.162 37.500 0.00 0.00 35.67 1.47
4094 6258 2.037641 TCTCAGGGCGATACAATCCATG 59.962 50.000 0.00 0.00 33.38 3.66
4111 6275 3.319405 GGAGATGATTTCTACCGCTCTCA 59.681 47.826 0.00 0.00 33.74 3.27
4207 6371 4.837860 TCAAGCACCCCTCAATTAAAACAT 59.162 37.500 0.00 0.00 0.00 2.71
4224 6388 5.554070 TCAAAGTCAGAGATCAATCAAGCA 58.446 37.500 0.00 0.00 0.00 3.91
4343 6507 5.766150 ACAAATCCTCAACATTTCAACGA 57.234 34.783 0.00 0.00 0.00 3.85
4345 6509 7.951530 ATGAACAAATCCTCAACATTTCAAC 57.048 32.000 0.00 0.00 0.00 3.18
4354 6518 9.613428 CCTACTAACATATGAACAAATCCTCAA 57.387 33.333 10.38 0.00 0.00 3.02
4357 6521 8.331931 TCCCTACTAACATATGAACAAATCCT 57.668 34.615 10.38 0.00 0.00 3.24
4377 6541 9.075678 CTCGTTATTTTTCCTAGATACTCCCTA 57.924 37.037 0.00 0.00 0.00 3.53
4383 6547 6.522946 AGGGCTCGTTATTTTTCCTAGATAC 58.477 40.000 0.00 0.00 0.00 2.24
4413 6577 9.705290 TGGCTTTTTCTTATTTGATTAAGAACC 57.295 29.630 6.23 5.65 44.05 3.62
4432 6596 9.216117 GTTACGTGGATATATAAGATGGCTTTT 57.784 33.333 0.00 0.00 35.56 2.27
4436 6600 6.875076 AGGTTACGTGGATATATAAGATGGC 58.125 40.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.