Multiple sequence alignment - TraesCS7D01G498200

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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 TraesCS7D01G498200 chr7D 100.000 3869 0 0 1 3869 604904548 604908416 0.000000e+00 7145.0
1 TraesCS7D01G498200 chr7D 96.109 2673 73 17 990 3649 605090225 605092879 0.000000e+00 4331.0
2 TraesCS7D01G498200 chr7D 74.952 1577 298 68 1324 2869 605647463 605645953 5.450000e-178 634.0
3 TraesCS7D01G498200 chr7D 75.048 1547 292 63 1331 2860 605598256 605596787 1.960000e-177 632.0
4 TraesCS7D01G498200 chr7D 75.442 1018 199 29 1921 2920 605610574 605609590 7.630000e-122 448.0
5 TraesCS7D01G498200 chr7D 86.788 386 36 9 301 685 605082124 605082495 2.150000e-112 416.0
6 TraesCS7D01G498200 chr7D 87.762 286 33 1 1 286 605000123 605000406 2.230000e-87 333.0
7 TraesCS7D01G498200 chr7D 78.333 420 75 12 3231 3639 575341933 575342347 1.380000e-64 257.0
8 TraesCS7D01G498200 chr7D 93.269 104 4 2 904 1006 605082573 605082674 2.410000e-32 150.0
9 TraesCS7D01G498200 chr7D 97.222 36 1 0 871 906 605082562 605082597 1.160000e-05 62.1
10 TraesCS7D01G498200 chr7B 88.725 816 55 10 913 1720 686139034 686138248 0.000000e+00 963.0
11 TraesCS7D01G498200 chr7B 86.283 678 69 13 1 673 687478782 687479440 0.000000e+00 715.0
12 TraesCS7D01G498200 chr7B 89.245 530 49 5 161 685 686139834 686139308 0.000000e+00 656.0
13 TraesCS7D01G498200 chr7B 74.936 1572 299 65 1326 2870 688821173 688819670 1.960000e-177 632.0
14 TraesCS7D01G498200 chr7B 74.888 1561 293 66 1326 2860 688813676 688812189 1.530000e-173 619.0
15 TraesCS7D01G498200 chr7B 76.268 927 156 37 1304 2209 688547306 688548189 5.940000e-118 435.0
16 TraesCS7D01G498200 chr7B 73.580 1056 205 54 1840 2870 688783402 688782396 1.720000e-88 337.0
17 TraesCS7D01G498200 chr7B 82.011 378 59 5 1332 1706 688930128 688929757 2.900000e-81 313.0
18 TraesCS7D01G498200 chr7B 87.739 261 24 2 978 1230 687545416 687545676 8.130000e-77 298.0
19 TraesCS7D01G498200 chr7B 85.333 150 22 0 2932 3081 11200683 11200832 5.180000e-34 156.0
20 TraesCS7D01G498200 chr7B 94.366 71 4 0 841 911 686139230 686139160 4.090000e-20 110.0
21 TraesCS7D01G498200 chr7A 76.146 851 147 33 1273 2111 696982097 696981291 2.800000e-106 396.0
22 TraesCS7D01G498200 chr7A 82.016 367 63 2 1347 1713 696991006 696990643 3.750000e-80 309.0
23 TraesCS7D01G498200 chr7A 82.534 292 48 3 2931 3219 651644727 651645018 1.780000e-63 254.0
24 TraesCS7D01G498200 chr3D 97.738 221 5 0 3649 3869 456956703 456956923 7.840000e-102 381.0
25 TraesCS7D01G498200 chr3D 97.260 219 6 0 3648 3866 131348462 131348680 4.720000e-99 372.0
26 TraesCS7D01G498200 chr3D 95.982 224 9 0 3643 3866 521590656 521590879 7.900000e-97 364.0
27 TraesCS7D01G498200 chr3D 77.451 408 78 10 3243 3639 424477367 424476963 8.360000e-57 231.0
28 TraesCS7D01G498200 chr3D 79.675 123 24 1 2934 3055 57090802 57090680 1.910000e-13 87.9
29 TraesCS7D01G498200 chr3B 97.285 221 6 0 3649 3869 147162405 147162625 3.650000e-100 375.0
30 TraesCS7D01G498200 chr3B 96.380 221 8 0 3649 3869 698625997 698626217 7.900000e-97 364.0
31 TraesCS7D01G498200 chr5D 96.833 221 7 0 3649 3869 300114408 300114188 1.700000e-98 370.0
32 TraesCS7D01G498200 chr5D 86.154 130 16 2 3512 3639 434423390 434423261 5.210000e-29 139.0
33 TraesCS7D01G498200 chr1D 96.429 224 8 0 3646 3869 320824025 320824248 1.700000e-98 370.0
34 TraesCS7D01G498200 chr1D 95.614 228 8 2 3644 3869 434156515 434156742 7.900000e-97 364.0
35 TraesCS7D01G498200 chr4D 96.396 222 8 0 3648 3869 221285317 221285096 2.200000e-97 366.0
36 TraesCS7D01G498200 chr3A 78.697 399 76 7 3250 3640 25149577 25149974 1.380000e-64 257.0
37 TraesCS7D01G498200 chr3A 77.059 340 62 7 3243 3575 703739018 703739348 8.540000e-42 182.0
38 TraesCS7D01G498200 chr2D 77.477 333 69 5 3310 3640 102727600 102727272 1.100000e-45 195.0
39 TraesCS7D01G498200 chr5A 78.644 295 59 4 2928 3219 667064193 667063900 3.940000e-45 193.0
40 TraesCS7D01G498200 chrUn 78.521 284 52 7 2930 3212 429341586 429341861 1.100000e-40 178.0
41 TraesCS7D01G498200 chr6B 87.597 129 14 2 784 911 75040831 75040704 8.660000e-32 148.0
42 TraesCS7D01G498200 chr1B 80.311 193 30 8 3453 3639 2515367 2515557 5.210000e-29 139.0
43 TraesCS7D01G498200 chr1B 87.097 93 10 2 3549 3639 2452396 2452488 1.900000e-18 104.0


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 TraesCS7D01G498200 chr7D 604904548 604908416 3868 False 7145.000000 7145 100.000000 1 3869 1 chr7D.!!$F2 3868
1 TraesCS7D01G498200 chr7D 605090225 605092879 2654 False 4331.000000 4331 96.109000 990 3649 1 chr7D.!!$F4 2659
2 TraesCS7D01G498200 chr7D 605645953 605647463 1510 True 634.000000 634 74.952000 1324 2869 1 chr7D.!!$R3 1545
3 TraesCS7D01G498200 chr7D 605596787 605598256 1469 True 632.000000 632 75.048000 1331 2860 1 chr7D.!!$R1 1529
4 TraesCS7D01G498200 chr7D 605609590 605610574 984 True 448.000000 448 75.442000 1921 2920 1 chr7D.!!$R2 999
5 TraesCS7D01G498200 chr7D 605082124 605082674 550 False 209.366667 416 92.426333 301 1006 3 chr7D.!!$F5 705
6 TraesCS7D01G498200 chr7B 687478782 687479440 658 False 715.000000 715 86.283000 1 673 1 chr7B.!!$F2 672
7 TraesCS7D01G498200 chr7B 688819670 688821173 1503 True 632.000000 632 74.936000 1326 2870 1 chr7B.!!$R3 1544
8 TraesCS7D01G498200 chr7B 688812189 688813676 1487 True 619.000000 619 74.888000 1326 2860 1 chr7B.!!$R2 1534
9 TraesCS7D01G498200 chr7B 686138248 686139834 1586 True 576.333333 963 90.778667 161 1720 3 chr7B.!!$R5 1559
10 TraesCS7D01G498200 chr7B 688547306 688548189 883 False 435.000000 435 76.268000 1304 2209 1 chr7B.!!$F4 905
11 TraesCS7D01G498200 chr7B 688782396 688783402 1006 True 337.000000 337 73.580000 1840 2870 1 chr7B.!!$R1 1030
12 TraesCS7D01G498200 chr7A 696981291 696982097 806 True 396.000000 396 76.146000 1273 2111 1 chr7A.!!$R1 838

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
805 829 0.107165 TAGTCGCTCTGAGCAGGCTA 60.107 55.000 27.46 24.57 42.58 3.93 F
836 860 0.108424 CTCGGCAGAAGACCTCCTTG 60.108 60.000 0.00 0.00 34.68 3.61 F
839 863 1.004440 GCAGAAGACCTCCTTGCGT 60.004 57.895 0.00 0.00 34.68 5.24 F
1722 1892 1.439353 CCCAATGATCTTGACGCCGG 61.439 60.000 0.00 0.00 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1678 1848 0.532573 GGTCACTGATCCGAAGCAGA 59.467 55.000 0.00 0.00 0.0 4.26 R
1827 2000 2.050918 GGAGAAATCTAGAGGGTGGGG 58.949 57.143 0.00 0.00 0.0 4.96 R
2011 2196 4.394712 GGTCCAGGTGCACGAGGG 62.395 72.222 21.64 17.17 0.0 4.30 R
3177 3395 0.038251 TGTCGCCTGCTCTACAACAG 60.038 55.000 0.00 0.00 0.0 3.16 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
21 22 1.370609 TACTTCGAGAGACTGAGCCG 58.629 55.000 2.28 0.00 41.84 5.52
22 23 0.321741 ACTTCGAGAGACTGAGCCGA 60.322 55.000 2.28 0.00 41.84 5.54
37 40 8.535335 AGACTGAGCCGACATATAAATATCATT 58.465 33.333 0.00 0.00 0.00 2.57
40 43 9.764870 CTGAGCCGACATATAAATATCATTTTG 57.235 33.333 0.00 0.00 0.00 2.44
41 44 9.283768 TGAGCCGACATATAAATATCATTTTGT 57.716 29.630 0.00 0.00 0.00 2.83
42 45 9.546909 GAGCCGACATATAAATATCATTTTGTG 57.453 33.333 0.00 0.00 0.00 3.33
67 70 1.016130 CGAAGTCATCAACAGCGCCT 61.016 55.000 2.29 0.00 0.00 5.52
73 76 2.939103 GTCATCAACAGCGCCTCTTATT 59.061 45.455 2.29 0.00 0.00 1.40
90 93 7.555087 CCTCTTATTCTATTATCCAGCCTCAG 58.445 42.308 0.00 0.00 0.00 3.35
131 134 1.446966 GCGTCTCTCACCCTCAAGC 60.447 63.158 0.00 0.00 0.00 4.01
142 146 2.328099 CCTCAAGCCGTGTTGCTCC 61.328 63.158 0.00 0.00 41.80 4.70
147 151 2.660258 AAGCCGTGTTGCTCCGAGTT 62.660 55.000 0.00 0.00 41.80 3.01
199 203 0.328258 GCCAAGGGGAGAACAAGCTA 59.672 55.000 0.00 0.00 35.59 3.32
230 234 4.639171 GGCCACGTTTTGCGGTGG 62.639 66.667 0.00 5.86 46.52 4.61
262 267 1.340889 GAATTCTGCAAGTGTTGGCCA 59.659 47.619 0.00 0.00 33.76 5.36
265 270 2.043551 TGCAAGTGTTGGCCACCA 60.044 55.556 3.88 0.00 45.74 4.17
292 302 3.057315 ACAAGCTGCACAATATCAACCAC 60.057 43.478 1.02 0.00 0.00 4.16
360 370 0.883153 TGCCACAATGTCTCATGTGC 59.117 50.000 0.51 0.00 44.32 4.57
361 371 0.883153 GCCACAATGTCTCATGTGCA 59.117 50.000 0.51 0.00 44.32 4.57
368 378 2.916702 TGTCTCATGTGCAGTGAGTT 57.083 45.000 21.91 0.00 42.82 3.01
385 395 1.427368 AGTTAATGTTGTGGAGGGGCA 59.573 47.619 0.00 0.00 0.00 5.36
386 396 2.042979 AGTTAATGTTGTGGAGGGGCAT 59.957 45.455 0.00 0.00 0.00 4.40
405 428 3.959943 CATCATCATGCTGCGAAAATGA 58.040 40.909 3.30 3.30 34.96 2.57
406 429 4.546570 CATCATCATGCTGCGAAAATGAT 58.453 39.130 7.21 7.21 40.77 2.45
408 431 3.702330 CATCATGCTGCGAAAATGATGT 58.298 40.909 22.61 1.82 46.57 3.06
409 432 3.853831 TCATGCTGCGAAAATGATGTT 57.146 38.095 0.00 0.00 0.00 2.71
410 433 3.503891 TCATGCTGCGAAAATGATGTTG 58.496 40.909 0.00 0.00 0.00 3.33
411 434 3.190953 TCATGCTGCGAAAATGATGTTGA 59.809 39.130 0.00 0.00 0.00 3.18
419 442 4.437930 GCGAAAATGATGTTGAGGAGGAAG 60.438 45.833 0.00 0.00 0.00 3.46
425 448 3.769300 TGATGTTGAGGAGGAAGATCGAA 59.231 43.478 0.00 0.00 0.00 3.71
461 484 2.161486 GGTGACAGCATCGCTCGTC 61.161 63.158 0.00 9.95 36.40 4.20
488 511 2.355010 AGTCTGCTTGCAAACCTCTT 57.645 45.000 0.00 0.00 0.00 2.85
625 648 1.483415 GATGCAGCCCAAATTGGATGT 59.517 47.619 14.62 0.00 43.74 3.06
682 706 2.612221 GCCAACACTTAGTAGTCGGCTT 60.612 50.000 0.00 0.00 37.86 4.35
683 707 3.367703 GCCAACACTTAGTAGTCGGCTTA 60.368 47.826 0.00 0.00 37.86 3.09
684 708 4.421948 CCAACACTTAGTAGTCGGCTTAG 58.578 47.826 0.00 0.00 30.26 2.18
685 709 4.157289 CCAACACTTAGTAGTCGGCTTAGA 59.843 45.833 0.00 0.00 30.26 2.10
686 710 5.336213 CCAACACTTAGTAGTCGGCTTAGAA 60.336 44.000 0.00 0.00 30.26 2.10
687 711 5.564048 ACACTTAGTAGTCGGCTTAGAAG 57.436 43.478 0.00 0.00 30.26 2.85
688 712 5.008980 ACACTTAGTAGTCGGCTTAGAAGT 58.991 41.667 0.00 0.00 30.26 3.01
689 713 5.476254 ACACTTAGTAGTCGGCTTAGAAGTT 59.524 40.000 0.00 0.00 30.26 2.66
690 714 5.800941 CACTTAGTAGTCGGCTTAGAAGTTG 59.199 44.000 0.00 0.00 30.26 3.16
691 715 3.870633 AGTAGTCGGCTTAGAAGTTGG 57.129 47.619 0.00 0.00 0.00 3.77
692 716 2.094130 AGTAGTCGGCTTAGAAGTTGGC 60.094 50.000 0.00 0.00 0.00 4.52
693 717 0.977395 AGTCGGCTTAGAAGTTGGCT 59.023 50.000 0.00 0.00 0.00 4.75
694 718 2.176889 AGTCGGCTTAGAAGTTGGCTA 58.823 47.619 0.00 0.00 0.00 3.93
695 719 2.565834 AGTCGGCTTAGAAGTTGGCTAA 59.434 45.455 0.00 0.00 0.00 3.09
696 720 3.007614 AGTCGGCTTAGAAGTTGGCTAAA 59.992 43.478 0.00 0.00 0.00 1.85
697 721 3.749609 GTCGGCTTAGAAGTTGGCTAAAA 59.250 43.478 0.00 0.00 0.00 1.52
698 722 4.214758 GTCGGCTTAGAAGTTGGCTAAAAA 59.785 41.667 0.00 0.00 0.00 1.94
787 811 1.841277 AGCCCAACCCAATGACGTATA 59.159 47.619 0.00 0.00 0.00 1.47
799 823 2.303707 GACGTATAGTCGCTCTGAGC 57.696 55.000 19.53 19.53 40.43 4.26
800 824 1.598132 GACGTATAGTCGCTCTGAGCA 59.402 52.381 27.46 13.12 42.58 4.26
801 825 1.600013 ACGTATAGTCGCTCTGAGCAG 59.400 52.381 27.46 19.65 42.58 4.24
802 826 1.069568 CGTATAGTCGCTCTGAGCAGG 60.070 57.143 27.46 13.56 42.58 4.85
803 827 0.955178 TATAGTCGCTCTGAGCAGGC 59.045 55.000 27.46 20.71 42.58 4.85
804 828 0.754957 ATAGTCGCTCTGAGCAGGCT 60.755 55.000 27.46 25.47 42.58 4.58
805 829 0.107165 TAGTCGCTCTGAGCAGGCTA 60.107 55.000 27.46 24.57 42.58 3.93
806 830 1.226831 GTCGCTCTGAGCAGGCTAC 60.227 63.158 27.46 13.63 42.58 3.58
807 831 2.278466 CGCTCTGAGCAGGCTACG 60.278 66.667 27.46 7.22 42.58 3.51
808 832 2.105930 GCTCTGAGCAGGCTACGG 59.894 66.667 24.02 0.00 41.89 4.02
809 833 2.105930 CTCTGAGCAGGCTACGGC 59.894 66.667 0.00 0.00 38.13 5.68
814 838 3.956377 AGCAGGCTACGGCTATGT 58.044 55.556 0.00 0.00 46.44 2.29
815 839 1.443407 AGCAGGCTACGGCTATGTG 59.557 57.895 0.00 0.00 46.44 3.21
816 840 1.595382 GCAGGCTACGGCTATGTGG 60.595 63.158 0.00 0.00 36.44 4.17
817 841 1.595382 CAGGCTACGGCTATGTGGC 60.595 63.158 4.55 4.55 44.66 5.01
818 842 1.762460 AGGCTACGGCTATGTGGCT 60.762 57.895 11.02 0.00 44.75 4.75
819 843 1.301009 GGCTACGGCTATGTGGCTC 60.301 63.158 11.02 0.00 44.75 4.70
820 844 1.661821 GCTACGGCTATGTGGCTCG 60.662 63.158 5.63 0.00 42.41 5.03
821 845 1.007271 CTACGGCTATGTGGCTCGG 60.007 63.158 0.00 0.00 39.32 4.63
822 846 3.146726 TACGGCTATGTGGCTCGGC 62.147 63.158 0.00 0.00 39.32 5.54
823 847 4.529219 CGGCTATGTGGCTCGGCA 62.529 66.667 0.00 0.00 39.32 5.69
824 848 2.590007 GGCTATGTGGCTCGGCAG 60.590 66.667 0.00 0.00 38.32 4.85
825 849 2.501128 GCTATGTGGCTCGGCAGA 59.499 61.111 0.00 0.00 0.00 4.26
826 850 1.153369 GCTATGTGGCTCGGCAGAA 60.153 57.895 0.00 0.00 0.00 3.02
827 851 1.156645 GCTATGTGGCTCGGCAGAAG 61.157 60.000 0.00 0.00 0.00 2.85
828 852 0.461548 CTATGTGGCTCGGCAGAAGA 59.538 55.000 0.00 0.00 0.00 2.87
829 853 0.175760 TATGTGGCTCGGCAGAAGAC 59.824 55.000 0.00 0.00 0.00 3.01
830 854 2.435059 GTGGCTCGGCAGAAGACC 60.435 66.667 0.00 0.00 0.00 3.85
831 855 2.604686 TGGCTCGGCAGAAGACCT 60.605 61.111 0.00 0.00 0.00 3.85
832 856 2.185608 GGCTCGGCAGAAGACCTC 59.814 66.667 0.00 0.00 0.00 3.85
833 857 2.185608 GCTCGGCAGAAGACCTCC 59.814 66.667 0.00 0.00 0.00 4.30
834 858 2.355193 GCTCGGCAGAAGACCTCCT 61.355 63.158 0.00 0.00 0.00 3.69
835 859 1.893919 GCTCGGCAGAAGACCTCCTT 61.894 60.000 0.00 0.00 37.93 3.36
836 860 0.108424 CTCGGCAGAAGACCTCCTTG 60.108 60.000 0.00 0.00 34.68 3.61
837 861 1.743252 CGGCAGAAGACCTCCTTGC 60.743 63.158 0.00 0.00 34.68 4.01
838 862 1.743252 GGCAGAAGACCTCCTTGCG 60.743 63.158 0.00 0.00 34.68 4.85
839 863 1.004440 GCAGAAGACCTCCTTGCGT 60.004 57.895 0.00 0.00 34.68 5.24
960 1110 7.152645 TCAACTTTACTCTAAGGACACATGAC 58.847 38.462 0.00 0.00 0.00 3.06
1021 1171 4.525100 GCATTTTTAAGGGGTGTCCAACTA 59.475 41.667 0.00 0.00 38.24 2.24
1027 1177 4.772886 AAGGGGTGTCCAACTATACATC 57.227 45.455 0.00 0.00 38.24 3.06
1035 1185 6.815142 GGTGTCCAACTATACATCGTACTTTT 59.185 38.462 0.00 0.00 0.00 2.27
1143 1297 5.934402 AGTTTGTATGGATTCGTAGACCT 57.066 39.130 0.00 0.00 34.32 3.85
1221 1375 4.809070 GGCAACTCTGTGCTCCTT 57.191 55.556 0.00 0.00 44.31 3.36
1585 1745 3.187227 TCGCCGTCTATAAGGAATACGAC 59.813 47.826 0.00 0.00 35.66 4.34
1620 1786 2.185350 CAGCAACGGAGATCGCCT 59.815 61.111 14.01 0.00 43.89 5.52
1675 1845 2.103538 GCCTTGTCATGCCATGCG 59.896 61.111 0.00 0.00 0.00 4.73
1678 1848 3.042842 CTTGTCATGCCATGCGCGT 62.043 57.895 8.43 0.00 42.08 6.01
1722 1892 1.439353 CCCAATGATCTTGACGCCGG 61.439 60.000 0.00 0.00 0.00 6.13
1724 1894 1.586422 CAATGATCTTGACGCCGGAT 58.414 50.000 5.05 0.00 0.00 4.18
1725 1895 2.547855 CCAATGATCTTGACGCCGGATA 60.548 50.000 5.05 0.00 0.00 2.59
1726 1896 2.440539 ATGATCTTGACGCCGGATAC 57.559 50.000 5.05 0.00 0.00 2.24
2011 2196 2.952310 GTGCCCTCATTTCTATCCCAAC 59.048 50.000 0.00 0.00 0.00 3.77
2393 2603 4.394729 GAACCTGATTTTGGACCACTACA 58.605 43.478 0.00 0.00 0.00 2.74
2717 2933 9.761504 TGAGCAAATCAACATCAAGAAAATAAA 57.238 25.926 0.00 0.00 34.02 1.40
2732 2948 7.938140 AGAAAATAAATTGATCTTCCCACGA 57.062 32.000 0.00 0.00 0.00 4.35
2814 3030 6.223138 TGTGTGAAGTTTAGTAATGCTTCG 57.777 37.500 16.34 0.00 39.91 3.79
2862 3080 8.701908 ATGTGTAAATGATAAGCATCAAGGAT 57.298 30.769 0.00 0.00 44.27 3.24
2929 3147 7.926018 GGTGATATTTTAAAATTCCGCAATCCT 59.074 33.333 18.14 0.00 0.00 3.24
2980 3198 0.179258 GCGTAACTTTGCCGAGTTCG 60.179 55.000 5.22 9.63 40.24 3.95
3086 3304 5.452078 TTGACTTTGCCTAGTTCAAATGG 57.548 39.130 7.56 2.00 33.54 3.16
3087 3305 4.469657 TGACTTTGCCTAGTTCAAATGGT 58.530 39.130 7.56 4.46 33.54 3.55
3142 3360 7.009999 CAGAATCTCAAGTTTATCGAGTTCCAG 59.990 40.741 0.00 0.00 0.00 3.86
3166 3384 4.637091 GCTAAAAAGCCCGGTAAAGTATGA 59.363 41.667 0.00 0.00 0.00 2.15
3177 3395 5.337330 CCGGTAAAGTATGATAGATGGGTCC 60.337 48.000 0.00 0.00 0.00 4.46
3196 3414 0.038251 CTGTTGTAGAGCAGGCGACA 60.038 55.000 0.00 0.00 0.00 4.35
3233 3451 3.270877 CCTTGTTGGACATACTAGTGCC 58.729 50.000 5.39 2.41 38.35 5.01
3466 3688 2.161609 GGTAGGAACTCGGCAAACATTG 59.838 50.000 0.00 0.00 41.75 2.82
3507 3729 4.552355 TCGCAATAGAAAGAACTCGACAA 58.448 39.130 0.00 0.00 0.00 3.18
3574 3796 2.163818 TGGCACTCGACGAAGATTTT 57.836 45.000 0.00 0.00 0.00 1.82
3596 3818 2.293399 GCCAAGTTTATTATGGGCTCCG 59.707 50.000 0.00 0.00 38.37 4.63
3649 3871 7.147724 GGCCATTCTAGTAGTGCCATGTATATA 60.148 40.741 0.00 0.00 38.73 0.86
3650 3872 7.923344 GCCATTCTAGTAGTGCCATGTATATAG 59.077 40.741 0.00 0.00 0.00 1.31
3651 3873 8.417106 CCATTCTAGTAGTGCCATGTATATAGG 58.583 40.741 0.00 0.00 0.00 2.57
3652 3874 7.956328 TTCTAGTAGTGCCATGTATATAGGG 57.044 40.000 0.00 0.00 0.00 3.53
3653 3875 5.892119 TCTAGTAGTGCCATGTATATAGGGC 59.108 44.000 17.24 17.24 46.58 5.19
3654 3876 4.689062 AGTAGTGCCATGTATATAGGGCT 58.311 43.478 23.11 9.03 46.53 5.19
3655 3877 3.988976 AGTGCCATGTATATAGGGCTG 57.011 47.619 23.11 0.00 46.53 4.85
3656 3878 2.026822 AGTGCCATGTATATAGGGCTGC 60.027 50.000 23.11 16.27 46.53 5.25
3657 3879 1.984424 TGCCATGTATATAGGGCTGCA 59.016 47.619 23.11 3.41 46.53 4.41
3658 3880 2.374839 TGCCATGTATATAGGGCTGCAA 59.625 45.455 23.11 3.06 46.53 4.08
3659 3881 3.012518 GCCATGTATATAGGGCTGCAAG 58.987 50.000 16.87 0.00 43.09 4.01
3660 3882 3.307691 GCCATGTATATAGGGCTGCAAGA 60.308 47.826 16.87 0.00 43.09 3.02
3661 3883 4.807303 GCCATGTATATAGGGCTGCAAGAA 60.807 45.833 16.87 0.00 43.09 2.52
3662 3884 5.316167 CCATGTATATAGGGCTGCAAGAAA 58.684 41.667 0.50 0.00 34.07 2.52
3663 3885 5.769662 CCATGTATATAGGGCTGCAAGAAAA 59.230 40.000 0.50 0.00 34.07 2.29
3664 3886 6.072286 CCATGTATATAGGGCTGCAAGAAAAG 60.072 42.308 0.50 0.00 34.07 2.27
3665 3887 4.821805 TGTATATAGGGCTGCAAGAAAAGC 59.178 41.667 0.50 0.00 38.76 3.51
3666 3888 2.521547 ATAGGGCTGCAAGAAAAGCT 57.478 45.000 0.50 0.00 39.46 3.74
3667 3889 1.826385 TAGGGCTGCAAGAAAAGCTC 58.174 50.000 0.50 0.00 40.40 4.09
3668 3890 1.211190 GGGCTGCAAGAAAAGCTCG 59.789 57.895 0.50 0.00 39.46 5.03
3669 3891 1.237285 GGGCTGCAAGAAAAGCTCGA 61.237 55.000 0.50 0.00 39.46 4.04
3670 3892 0.167689 GGCTGCAAGAAAAGCTCGAG 59.832 55.000 8.45 8.45 39.46 4.04
3671 3893 0.167689 GCTGCAAGAAAAGCTCGAGG 59.832 55.000 15.58 0.00 36.47 4.63
3672 3894 0.167689 CTGCAAGAAAAGCTCGAGGC 59.832 55.000 15.58 6.83 37.39 4.70
3674 3896 4.064266 CTGCAAGAAAAGCTCGAGGCTC 62.064 54.545 15.58 3.87 44.86 4.70
3690 3912 2.824489 TCGTGAGCCGCTCGAGAT 60.824 61.111 18.75 0.00 37.56 2.75
3691 3913 2.352915 CGTGAGCCGCTCGAGATC 60.353 66.667 18.75 8.44 35.64 2.75
3692 3914 2.352915 GTGAGCCGCTCGAGATCG 60.353 66.667 18.75 11.22 41.45 3.69
3694 3916 2.051703 GAGCCGCTCGAGATCGAC 60.052 66.667 18.75 3.34 44.22 4.20
3695 3917 2.515057 AGCCGCTCGAGATCGACT 60.515 61.111 18.75 5.99 44.22 4.18
3696 3918 2.054140 GAGCCGCTCGAGATCGACTT 62.054 60.000 18.75 0.10 44.22 3.01
3697 3919 1.941734 GCCGCTCGAGATCGACTTG 60.942 63.158 18.75 0.00 44.22 3.16
3698 3920 1.429825 CCGCTCGAGATCGACTTGT 59.570 57.895 18.75 0.00 44.22 3.16
3699 3921 0.179161 CCGCTCGAGATCGACTTGTT 60.179 55.000 18.75 0.00 44.22 2.83
3700 3922 1.618861 CGCTCGAGATCGACTTGTTT 58.381 50.000 18.75 0.00 44.22 2.83
3701 3923 1.986378 CGCTCGAGATCGACTTGTTTT 59.014 47.619 18.75 0.00 44.22 2.43
3702 3924 2.408704 CGCTCGAGATCGACTTGTTTTT 59.591 45.455 18.75 0.00 44.22 1.94
3735 3957 4.471942 GAGATCGACTCGAAAAGAAACG 57.528 45.455 5.00 0.00 39.99 3.60
3736 3958 4.156664 AGATCGACTCGAAAAGAAACGA 57.843 40.909 5.00 0.00 39.99 3.85
3742 3964 3.696711 CTCGAAAAGAAACGAGCTGAG 57.303 47.619 0.00 0.00 46.54 3.35
3743 3965 3.053455 CTCGAAAAGAAACGAGCTGAGT 58.947 45.455 0.00 0.00 46.54 3.41
3744 3966 3.454375 TCGAAAAGAAACGAGCTGAGTT 58.546 40.909 0.00 0.00 34.49 3.01
3745 3967 3.869246 TCGAAAAGAAACGAGCTGAGTTT 59.131 39.130 14.54 14.54 43.60 2.66
3746 3968 3.962481 CGAAAAGAAACGAGCTGAGTTTG 59.038 43.478 18.25 3.27 41.32 2.93
3747 3969 4.260212 CGAAAAGAAACGAGCTGAGTTTGA 60.260 41.667 18.25 0.00 41.32 2.69
3748 3970 5.560966 AAAAGAAACGAGCTGAGTTTGAA 57.439 34.783 18.25 0.00 41.32 2.69
3749 3971 4.537936 AAGAAACGAGCTGAGTTTGAAC 57.462 40.909 18.25 7.30 41.32 3.18
3750 3972 3.531538 AGAAACGAGCTGAGTTTGAACA 58.468 40.909 18.25 0.00 41.32 3.18
3751 3973 3.309954 AGAAACGAGCTGAGTTTGAACAC 59.690 43.478 18.25 6.74 41.32 3.32
3752 3974 2.604046 ACGAGCTGAGTTTGAACACT 57.396 45.000 0.00 0.00 0.00 3.55
3753 3975 2.906354 ACGAGCTGAGTTTGAACACTT 58.094 42.857 0.00 0.00 0.00 3.16
3754 3976 3.270877 ACGAGCTGAGTTTGAACACTTT 58.729 40.909 0.00 0.00 0.00 2.66
3755 3977 4.439057 ACGAGCTGAGTTTGAACACTTTA 58.561 39.130 0.00 0.00 0.00 1.85
3756 3978 5.057149 ACGAGCTGAGTTTGAACACTTTAT 58.943 37.500 0.00 0.00 0.00 1.40
3757 3979 5.050091 ACGAGCTGAGTTTGAACACTTTATG 60.050 40.000 0.00 0.00 0.00 1.90
3758 3980 5.050091 CGAGCTGAGTTTGAACACTTTATGT 60.050 40.000 0.00 0.00 46.42 2.29
3759 3981 6.145534 CGAGCTGAGTTTGAACACTTTATGTA 59.854 38.462 0.00 0.00 42.31 2.29
3760 3982 7.426929 AGCTGAGTTTGAACACTTTATGTAG 57.573 36.000 0.00 0.00 42.31 2.74
3761 3983 6.073003 AGCTGAGTTTGAACACTTTATGTAGC 60.073 38.462 0.00 0.00 42.31 3.58
3762 3984 6.073003 GCTGAGTTTGAACACTTTATGTAGCT 60.073 38.462 0.00 0.00 42.31 3.32
3763 3985 7.421530 TGAGTTTGAACACTTTATGTAGCTC 57.578 36.000 0.00 0.00 42.31 4.09
3764 3986 6.145534 TGAGTTTGAACACTTTATGTAGCTCG 59.854 38.462 0.00 0.00 42.31 5.03
3765 3987 6.220930 AGTTTGAACACTTTATGTAGCTCGA 58.779 36.000 0.00 0.00 42.31 4.04
3766 3988 6.145696 AGTTTGAACACTTTATGTAGCTCGAC 59.854 38.462 0.00 0.00 42.31 4.20
3767 3989 4.491676 TGAACACTTTATGTAGCTCGACC 58.508 43.478 0.00 0.00 42.31 4.79
3768 3990 4.021807 TGAACACTTTATGTAGCTCGACCA 60.022 41.667 0.00 0.00 42.31 4.02
3769 3991 4.530710 ACACTTTATGTAGCTCGACCAA 57.469 40.909 0.00 0.00 40.88 3.67
3770 3992 4.495422 ACACTTTATGTAGCTCGACCAAG 58.505 43.478 0.00 0.00 40.88 3.61
3771 3993 4.219944 ACACTTTATGTAGCTCGACCAAGA 59.780 41.667 0.00 0.00 40.88 3.02
3772 3994 5.168569 CACTTTATGTAGCTCGACCAAGAA 58.831 41.667 0.00 0.00 0.00 2.52
3773 3995 5.637810 CACTTTATGTAGCTCGACCAAGAAA 59.362 40.000 0.00 0.00 0.00 2.52
3774 3996 5.638234 ACTTTATGTAGCTCGACCAAGAAAC 59.362 40.000 0.00 0.00 0.00 2.78
3775 3997 2.060326 TGTAGCTCGACCAAGAAACG 57.940 50.000 0.00 0.00 0.00 3.60
3776 3998 1.610038 TGTAGCTCGACCAAGAAACGA 59.390 47.619 0.00 0.00 34.90 3.85
3779 4001 2.446341 CTCGACCAAGAAACGAGCC 58.554 57.895 0.00 0.00 44.67 4.70
3780 4002 1.344942 CTCGACCAAGAAACGAGCCG 61.345 60.000 0.00 0.00 44.67 5.52
3781 4003 1.372499 CGACCAAGAAACGAGCCGA 60.372 57.895 1.50 0.00 0.00 5.54
3782 4004 0.736325 CGACCAAGAAACGAGCCGAT 60.736 55.000 1.50 0.00 0.00 4.18
3783 4005 1.000145 GACCAAGAAACGAGCCGATC 59.000 55.000 1.50 0.58 0.00 3.69
3784 4006 0.608640 ACCAAGAAACGAGCCGATCT 59.391 50.000 1.50 2.63 0.00 2.75
3785 4007 1.002087 ACCAAGAAACGAGCCGATCTT 59.998 47.619 1.50 7.72 37.18 2.40
3786 4008 1.394917 CCAAGAAACGAGCCGATCTTG 59.605 52.381 23.45 23.45 44.64 3.02
3787 4009 2.337583 CAAGAAACGAGCCGATCTTGA 58.662 47.619 24.66 0.00 46.08 3.02
3788 4010 2.285827 AGAAACGAGCCGATCTTGAG 57.714 50.000 1.50 0.00 0.00 3.02
3789 4011 0.647925 GAAACGAGCCGATCTTGAGC 59.352 55.000 1.50 0.00 0.00 4.26
3790 4012 0.741221 AAACGAGCCGATCTTGAGCC 60.741 55.000 1.50 0.00 0.00 4.70
3791 4013 1.888436 AACGAGCCGATCTTGAGCCA 61.888 55.000 1.50 0.00 0.00 4.75
3792 4014 1.153568 CGAGCCGATCTTGAGCCAA 60.154 57.895 0.00 0.00 0.00 4.52
3793 4015 0.531532 CGAGCCGATCTTGAGCCAAT 60.532 55.000 0.00 0.00 0.00 3.16
3794 4016 0.942962 GAGCCGATCTTGAGCCAATG 59.057 55.000 0.00 0.00 0.00 2.82
3795 4017 0.254178 AGCCGATCTTGAGCCAATGT 59.746 50.000 0.00 0.00 0.00 2.71
3796 4018 1.098050 GCCGATCTTGAGCCAATGTT 58.902 50.000 0.00 0.00 0.00 2.71
3797 4019 1.202222 GCCGATCTTGAGCCAATGTTG 60.202 52.381 0.00 0.00 0.00 3.33
3806 4028 2.787249 CCAATGTTGGCTCGCTCG 59.213 61.111 0.00 0.00 42.21 5.03
3807 4029 1.741401 CCAATGTTGGCTCGCTCGA 60.741 57.895 0.00 0.00 42.21 4.04
3808 4030 1.091771 CCAATGTTGGCTCGCTCGAT 61.092 55.000 0.00 0.00 42.21 3.59
3809 4031 0.729116 CAATGTTGGCTCGCTCGATT 59.271 50.000 0.00 0.00 0.00 3.34
3810 4032 1.131126 CAATGTTGGCTCGCTCGATTT 59.869 47.619 0.00 0.00 0.00 2.17
3811 4033 1.453155 ATGTTGGCTCGCTCGATTTT 58.547 45.000 0.00 0.00 0.00 1.82
3812 4034 2.087501 TGTTGGCTCGCTCGATTTTA 57.912 45.000 0.00 0.00 0.00 1.52
3813 4035 2.627945 TGTTGGCTCGCTCGATTTTAT 58.372 42.857 0.00 0.00 0.00 1.40
3814 4036 3.006940 TGTTGGCTCGCTCGATTTTATT 58.993 40.909 0.00 0.00 0.00 1.40
3815 4037 3.438781 TGTTGGCTCGCTCGATTTTATTT 59.561 39.130 0.00 0.00 0.00 1.40
3816 4038 3.944422 TGGCTCGCTCGATTTTATTTC 57.056 42.857 0.00 0.00 0.00 2.17
3817 4039 2.284150 TGGCTCGCTCGATTTTATTTCG 59.716 45.455 0.00 0.00 37.94 3.46
3818 4040 2.538449 GGCTCGCTCGATTTTATTTCGA 59.462 45.455 0.00 0.00 42.87 3.71
3819 4041 3.184581 GGCTCGCTCGATTTTATTTCGAT 59.815 43.478 0.00 0.00 43.93 3.59
3820 4042 4.384846 GGCTCGCTCGATTTTATTTCGATA 59.615 41.667 0.00 0.00 43.93 2.92
3821 4043 5.443431 GGCTCGCTCGATTTTATTTCGATAG 60.443 44.000 0.00 0.00 43.93 2.08
3822 4044 5.496330 TCGCTCGATTTTATTTCGATAGC 57.504 39.130 0.00 0.00 43.93 2.97
3823 4045 5.220381 TCGCTCGATTTTATTTCGATAGCT 58.780 37.500 0.00 0.00 43.93 3.32
3824 4046 5.342525 TCGCTCGATTTTATTTCGATAGCTC 59.657 40.000 0.00 0.00 43.93 4.09
3825 4047 5.533827 GCTCGATTTTATTTCGATAGCTCG 58.466 41.667 0.00 0.00 43.93 5.03
3843 4065 9.579768 GATAGCTCGACAGAATATCATTATGTT 57.420 33.333 0.00 0.00 30.97 2.71
3846 4068 9.764363 AGCTCGACAGAATATCATTATGTTAAA 57.236 29.630 1.16 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.393132 ATGTCGGCTCAGTCTCTCGA 60.393 55.000 0.00 0.00 0.00 4.04
12 13 8.709386 AATGATATTTATATGTCGGCTCAGTC 57.291 34.615 0.00 0.00 0.00 3.51
46 49 0.093705 GCGCTGTTGATGACTTCGTC 59.906 55.000 0.00 0.00 0.00 4.20
49 52 0.723981 GAGGCGCTGTTGATGACTTC 59.276 55.000 7.64 0.00 0.00 3.01
56 59 4.672587 ATAGAATAAGAGGCGCTGTTGA 57.327 40.909 7.64 0.00 0.00 3.18
60 63 5.724328 TGGATAATAGAATAAGAGGCGCTG 58.276 41.667 7.64 0.00 0.00 5.18
61 64 5.625656 GCTGGATAATAGAATAAGAGGCGCT 60.626 44.000 7.64 0.00 0.00 5.92
62 65 4.568760 GCTGGATAATAGAATAAGAGGCGC 59.431 45.833 0.00 0.00 0.00 6.53
67 70 7.094162 CGACTGAGGCTGGATAATAGAATAAGA 60.094 40.741 0.00 0.00 0.00 2.10
73 76 2.558795 GCGACTGAGGCTGGATAATAGA 59.441 50.000 0.00 0.00 0.00 1.98
90 93 1.227002 GGGATGAGGAACGAGCGAC 60.227 63.158 0.00 0.00 0.00 5.19
131 134 2.317609 CCAACTCGGAGCAACACGG 61.318 63.158 4.58 0.00 36.56 4.94
142 146 1.493950 GCGCCATCATCTCCAACTCG 61.494 60.000 0.00 0.00 0.00 4.18
147 151 0.829990 TTGTAGCGCCATCATCTCCA 59.170 50.000 2.29 0.00 0.00 3.86
174 178 2.459969 TTCTCCCCTTGGCAGCACA 61.460 57.895 0.00 0.00 0.00 4.57
199 203 3.300765 GGCCAAGCTTGCAGCACT 61.301 61.111 21.43 0.00 45.56 4.40
241 246 1.666888 GGCCAACACTTGCAGAATTCG 60.667 52.381 0.00 0.00 0.00 3.34
262 267 0.181114 TGTGCAGCTTGTTCTCTGGT 59.819 50.000 0.00 0.00 0.00 4.00
265 270 4.582869 TGATATTGTGCAGCTTGTTCTCT 58.417 39.130 0.00 0.00 0.00 3.10
360 370 3.753272 CCCTCCACAACATTAACTCACTG 59.247 47.826 0.00 0.00 0.00 3.66
361 371 3.244911 CCCCTCCACAACATTAACTCACT 60.245 47.826 0.00 0.00 0.00 3.41
368 378 1.638070 TGATGCCCCTCCACAACATTA 59.362 47.619 0.00 0.00 0.00 1.90
385 395 4.848562 ATCATTTTCGCAGCATGATGAT 57.151 36.364 16.67 5.81 39.69 2.45
394 417 3.181503 CCTCCTCAACATCATTTTCGCAG 60.182 47.826 0.00 0.00 0.00 5.18
398 421 6.238320 CGATCTTCCTCCTCAACATCATTTTC 60.238 42.308 0.00 0.00 0.00 2.29
399 422 5.587844 CGATCTTCCTCCTCAACATCATTTT 59.412 40.000 0.00 0.00 0.00 1.82
400 423 5.104776 TCGATCTTCCTCCTCAACATCATTT 60.105 40.000 0.00 0.00 0.00 2.32
401 424 4.406972 TCGATCTTCCTCCTCAACATCATT 59.593 41.667 0.00 0.00 0.00 2.57
402 425 3.963374 TCGATCTTCCTCCTCAACATCAT 59.037 43.478 0.00 0.00 0.00 2.45
403 426 3.365472 TCGATCTTCCTCCTCAACATCA 58.635 45.455 0.00 0.00 0.00 3.07
404 427 4.392921 TTCGATCTTCCTCCTCAACATC 57.607 45.455 0.00 0.00 0.00 3.06
405 428 6.485830 TTATTCGATCTTCCTCCTCAACAT 57.514 37.500 0.00 0.00 0.00 2.71
406 429 5.932619 TTATTCGATCTTCCTCCTCAACA 57.067 39.130 0.00 0.00 0.00 3.33
407 430 6.516718 TCATTATTCGATCTTCCTCCTCAAC 58.483 40.000 0.00 0.00 0.00 3.18
408 431 6.239430 CCTCATTATTCGATCTTCCTCCTCAA 60.239 42.308 0.00 0.00 0.00 3.02
409 432 5.244851 CCTCATTATTCGATCTTCCTCCTCA 59.755 44.000 0.00 0.00 0.00 3.86
410 433 5.337169 CCCTCATTATTCGATCTTCCTCCTC 60.337 48.000 0.00 0.00 0.00 3.71
411 434 4.530161 CCCTCATTATTCGATCTTCCTCCT 59.470 45.833 0.00 0.00 0.00 3.69
419 442 5.163953 CGCAACATACCCTCATTATTCGATC 60.164 44.000 0.00 0.00 0.00 3.69
425 448 3.135712 TCACCGCAACATACCCTCATTAT 59.864 43.478 0.00 0.00 0.00 1.28
488 511 4.334552 TCAACATGAGCCATTTTGAGCTA 58.665 39.130 0.00 0.00 40.11 3.32
578 601 5.406649 CAGCTGACCTGTTTTTACAACAAA 58.593 37.500 8.42 0.00 36.79 2.83
579 602 4.142271 CCAGCTGACCTGTTTTTACAACAA 60.142 41.667 17.39 0.00 40.06 2.83
593 616 2.777969 CTGCATCTTCCAGCTGACC 58.222 57.895 17.39 0.00 32.24 4.02
610 633 0.039618 ACGGACATCCAATTTGGGCT 59.960 50.000 15.37 0.87 38.32 5.19
641 664 1.961277 GGCTTATGCACGGATCGGG 60.961 63.158 5.18 0.00 41.91 5.14
653 677 1.280998 ACTAAGTGTTGGCCGGCTTAT 59.719 47.619 28.56 8.44 0.00 1.73
700 724 9.694137 GTTGATTATCTAAGCCGACTACTATTT 57.306 33.333 0.00 0.00 0.00 1.40
701 725 9.080097 AGTTGATTATCTAAGCCGACTACTATT 57.920 33.333 0.00 0.00 0.00 1.73
702 726 8.638629 AGTTGATTATCTAAGCCGACTACTAT 57.361 34.615 0.00 0.00 0.00 2.12
703 727 8.461249 AAGTTGATTATCTAAGCCGACTACTA 57.539 34.615 0.00 0.00 0.00 1.82
704 728 6.963083 AGTTGATTATCTAAGCCGACTACT 57.037 37.500 0.00 0.00 0.00 2.57
705 729 7.167801 GTGAAGTTGATTATCTAAGCCGACTAC 59.832 40.741 0.00 0.00 0.00 2.73
706 730 7.068348 AGTGAAGTTGATTATCTAAGCCGACTA 59.932 37.037 0.00 0.00 0.00 2.59
707 731 6.043411 GTGAAGTTGATTATCTAAGCCGACT 58.957 40.000 0.00 0.00 0.00 4.18
708 732 6.043411 AGTGAAGTTGATTATCTAAGCCGAC 58.957 40.000 0.00 0.00 0.00 4.79
709 733 6.096987 AGAGTGAAGTTGATTATCTAAGCCGA 59.903 38.462 0.00 0.00 0.00 5.54
710 734 6.276847 AGAGTGAAGTTGATTATCTAAGCCG 58.723 40.000 0.00 0.00 0.00 5.52
711 735 9.255304 CTTAGAGTGAAGTTGATTATCTAAGCC 57.745 37.037 6.23 0.00 38.39 4.35
712 736 9.255304 CCTTAGAGTGAAGTTGATTATCTAAGC 57.745 37.037 11.69 0.00 41.37 3.09
718 742 7.568349 TGCATCCTTAGAGTGAAGTTGATTAT 58.432 34.615 0.00 0.00 0.00 1.28
787 811 1.379176 TAGCCTGCTCAGAGCGACT 60.379 57.895 17.81 15.72 46.26 4.18
795 819 1.043116 ACATAGCCGTAGCCTGCTCA 61.043 55.000 0.00 0.00 41.25 4.26
796 820 0.598680 CACATAGCCGTAGCCTGCTC 60.599 60.000 0.00 0.00 41.25 4.26
797 821 1.443407 CACATAGCCGTAGCCTGCT 59.557 57.895 0.00 0.00 41.25 4.24
798 822 1.595382 CCACATAGCCGTAGCCTGC 60.595 63.158 0.00 0.00 41.25 4.85
799 823 1.595382 GCCACATAGCCGTAGCCTG 60.595 63.158 0.00 0.00 41.25 4.85
800 824 1.749334 GAGCCACATAGCCGTAGCCT 61.749 60.000 0.00 0.00 41.25 4.58
801 825 1.301009 GAGCCACATAGCCGTAGCC 60.301 63.158 0.00 0.00 41.25 3.93
802 826 1.661821 CGAGCCACATAGCCGTAGC 60.662 63.158 0.00 0.00 40.32 3.58
803 827 1.007271 CCGAGCCACATAGCCGTAG 60.007 63.158 0.00 0.00 0.00 3.51
804 828 3.125607 CCGAGCCACATAGCCGTA 58.874 61.111 0.00 0.00 0.00 4.02
805 829 4.530857 GCCGAGCCACATAGCCGT 62.531 66.667 0.00 0.00 0.00 5.68
806 830 4.529219 TGCCGAGCCACATAGCCG 62.529 66.667 0.00 0.00 0.00 5.52
807 831 2.590007 CTGCCGAGCCACATAGCC 60.590 66.667 0.00 0.00 0.00 3.93
808 832 1.153369 TTCTGCCGAGCCACATAGC 60.153 57.895 0.00 0.00 0.00 2.97
809 833 0.461548 TCTTCTGCCGAGCCACATAG 59.538 55.000 0.00 0.00 0.00 2.23
810 834 0.175760 GTCTTCTGCCGAGCCACATA 59.824 55.000 0.00 0.00 0.00 2.29
811 835 1.078848 GTCTTCTGCCGAGCCACAT 60.079 57.895 0.00 0.00 0.00 3.21
812 836 2.343758 GTCTTCTGCCGAGCCACA 59.656 61.111 0.00 0.00 0.00 4.17
813 837 2.435059 GGTCTTCTGCCGAGCCAC 60.435 66.667 0.00 0.00 0.00 5.01
814 838 2.604686 AGGTCTTCTGCCGAGCCA 60.605 61.111 0.00 0.00 0.00 4.75
815 839 2.185608 GAGGTCTTCTGCCGAGCC 59.814 66.667 0.00 0.00 0.00 4.70
816 840 1.893919 AAGGAGGTCTTCTGCCGAGC 61.894 60.000 0.00 0.00 33.99 5.03
817 841 0.108424 CAAGGAGGTCTTCTGCCGAG 60.108 60.000 0.00 0.00 33.99 4.63
818 842 1.975327 CAAGGAGGTCTTCTGCCGA 59.025 57.895 0.00 0.00 33.99 5.54
819 843 1.743252 GCAAGGAGGTCTTCTGCCG 60.743 63.158 0.00 0.00 33.99 5.69
820 844 1.743252 CGCAAGGAGGTCTTCTGCC 60.743 63.158 0.00 0.00 33.99 4.85
821 845 0.603975 AACGCAAGGAGGTCTTCTGC 60.604 55.000 0.00 0.00 46.39 4.26
822 846 1.151668 CAACGCAAGGAGGTCTTCTG 58.848 55.000 0.00 0.00 46.39 3.02
823 847 1.001406 CTCAACGCAAGGAGGTCTTCT 59.999 52.381 0.00 0.00 46.39 2.85
824 848 1.433534 CTCAACGCAAGGAGGTCTTC 58.566 55.000 0.00 0.00 46.39 2.87
825 849 0.035458 CCTCAACGCAAGGAGGTCTT 59.965 55.000 6.41 0.00 44.59 3.01
826 850 1.674057 CCTCAACGCAAGGAGGTCT 59.326 57.895 6.41 0.00 44.59 3.85
827 851 4.285851 CCTCAACGCAAGGAGGTC 57.714 61.111 6.41 0.00 44.59 3.85
830 854 1.001406 AGAGTTCCTCAACGCAAGGAG 59.999 52.381 1.83 0.00 43.65 3.69
831 855 1.048601 AGAGTTCCTCAACGCAAGGA 58.951 50.000 0.00 0.00 41.21 3.36
832 856 1.532868 CAAGAGTTCCTCAACGCAAGG 59.467 52.381 0.00 0.00 37.61 3.61
833 857 1.069636 GCAAGAGTTCCTCAACGCAAG 60.070 52.381 0.00 0.00 37.61 4.01
834 858 0.944386 GCAAGAGTTCCTCAACGCAA 59.056 50.000 0.00 0.00 37.61 4.85
835 859 0.884704 GGCAAGAGTTCCTCAACGCA 60.885 55.000 0.00 0.00 37.61 5.24
836 860 0.884704 TGGCAAGAGTTCCTCAACGC 60.885 55.000 0.00 0.00 37.61 4.84
837 861 1.593196 TTGGCAAGAGTTCCTCAACG 58.407 50.000 0.00 0.00 37.61 4.10
838 862 3.214328 TCTTTGGCAAGAGTTCCTCAAC 58.786 45.455 0.00 0.00 33.80 3.18
839 863 3.576078 TCTTTGGCAAGAGTTCCTCAA 57.424 42.857 0.00 0.00 33.80 3.02
852 876 6.430000 TCAAGGTAGAGTTACAATTCTTTGGC 59.570 38.462 0.00 0.00 37.15 4.52
858 882 8.738645 ATTCCATCAAGGTAGAGTTACAATTC 57.261 34.615 0.00 0.00 39.02 2.17
942 1092 6.822667 TTTACGTCATGTGTCCTTAGAGTA 57.177 37.500 0.00 0.00 0.00 2.59
1109 1263 0.183014 TACAAACTTTGGCCCGTGGA 59.817 50.000 0.00 0.00 34.12 4.02
1110 1264 1.067915 CATACAAACTTTGGCCCGTGG 60.068 52.381 0.00 0.00 34.12 4.94
1113 1267 1.540267 TCCATACAAACTTTGGCCCG 58.460 50.000 0.00 0.00 34.12 6.13
1221 1375 4.393155 AGCCGCCGCACAAGATGA 62.393 61.111 0.00 0.00 37.52 2.92
1513 1667 0.175989 GGAGGACGATGAGGTGGTTC 59.824 60.000 0.00 0.00 0.00 3.62
1585 1745 3.133464 TCGTAGTACCCACCGCCG 61.133 66.667 0.00 0.00 0.00 6.46
1620 1786 1.103803 GATGTACTGGGAGTGCTCGA 58.896 55.000 0.00 0.00 31.77 4.04
1675 1845 1.153745 ACTGATCCGAAGCAGACGC 60.154 57.895 0.00 0.00 38.99 5.19
1678 1848 0.532573 GGTCACTGATCCGAAGCAGA 59.467 55.000 0.00 0.00 0.00 4.26
1827 2000 2.050918 GGAGAAATCTAGAGGGTGGGG 58.949 57.143 0.00 0.00 0.00 4.96
2011 2196 4.394712 GGTCCAGGTGCACGAGGG 62.395 72.222 21.64 17.17 0.00 4.30
2393 2603 5.217978 TGGTGACCAACGTAGAAAGTAAT 57.782 39.130 0.00 0.00 0.00 1.89
2717 2933 5.989477 TGACTTTATCGTGGGAAGATCAAT 58.011 37.500 0.00 0.00 0.00 2.57
2917 3135 4.161565 TCTTGTAGTGTAGGATTGCGGAAT 59.838 41.667 0.12 0.12 0.00 3.01
2929 3147 9.431887 GTCATAAAACCAGATTCTTGTAGTGTA 57.568 33.333 0.00 0.00 0.00 2.90
2980 3198 2.396590 TGCCAAGTTCCCGATAGAAC 57.603 50.000 5.19 5.19 45.34 3.01
3040 3258 2.177394 TTGCCGAGTTGCTTATCACA 57.823 45.000 0.00 0.00 0.00 3.58
3086 3304 9.797556 AGTTATTTTTGTTTGTGAGTCCTTTAC 57.202 29.630 0.00 0.00 0.00 2.01
3091 3309 5.912955 CCGAGTTATTTTTGTTTGTGAGTCC 59.087 40.000 0.00 0.00 0.00 3.85
3155 3373 6.270231 ACAGGACCCATCTATCATACTTTACC 59.730 42.308 0.00 0.00 0.00 2.85
3162 3380 6.620429 TCTACAACAGGACCCATCTATCATA 58.380 40.000 0.00 0.00 0.00 2.15
3166 3384 3.643792 GCTCTACAACAGGACCCATCTAT 59.356 47.826 0.00 0.00 0.00 1.98
3177 3395 0.038251 TGTCGCCTGCTCTACAACAG 60.038 55.000 0.00 0.00 0.00 3.16
3456 3678 7.329717 TCGGTGAATATTTAAACAATGTTTGCC 59.670 33.333 20.40 7.92 0.00 4.52
3466 3688 5.860641 TGCGAACTCGGTGAATATTTAAAC 58.139 37.500 0.69 0.00 40.23 2.01
3507 3729 3.091545 CGGGCCCAGCAATCATTAATAT 58.908 45.455 24.92 0.00 0.00 1.28
3558 3780 1.798223 TGGCAAAATCTTCGTCGAGTG 59.202 47.619 0.00 0.00 0.00 3.51
3574 3796 3.295973 GGAGCCCATAATAAACTTGGCA 58.704 45.455 0.00 0.00 41.33 4.92
3596 3818 2.851534 CGGATTTCAAAGAAACTCGGC 58.148 47.619 0.00 0.00 0.00 5.54
3649 3871 1.239968 CGAGCTTTTCTTGCAGCCCT 61.240 55.000 0.00 0.00 36.62 5.19
3650 3872 1.211190 CGAGCTTTTCTTGCAGCCC 59.789 57.895 0.00 0.00 36.62 5.19
3651 3873 0.167689 CTCGAGCTTTTCTTGCAGCC 59.832 55.000 0.00 0.00 36.62 4.85
3652 3874 0.167689 CCTCGAGCTTTTCTTGCAGC 59.832 55.000 6.99 0.00 36.16 5.25
3653 3875 0.167689 GCCTCGAGCTTTTCTTGCAG 59.832 55.000 6.99 0.00 38.99 4.41
3654 3876 2.247790 GCCTCGAGCTTTTCTTGCA 58.752 52.632 6.99 0.00 38.99 4.08
3675 3897 2.352915 CGATCTCGAGCGGCTCAC 60.353 66.667 27.83 12.77 43.02 3.51
3676 3898 2.513897 TCGATCTCGAGCGGCTCA 60.514 61.111 27.83 14.76 44.22 4.26
3714 3936 4.156915 TCGTTTCTTTTCGAGTCGATCTC 58.843 43.478 17.34 0.00 35.23 2.75
3715 3937 4.156664 TCGTTTCTTTTCGAGTCGATCT 57.843 40.909 17.34 0.00 35.23 2.75
3716 3938 4.471942 CTCGTTTCTTTTCGAGTCGATC 57.528 45.455 17.34 1.07 45.37 3.69
3723 3945 3.093717 ACTCAGCTCGTTTCTTTTCGA 57.906 42.857 0.00 0.00 34.88 3.71
3724 3946 3.861569 AACTCAGCTCGTTTCTTTTCG 57.138 42.857 0.00 0.00 0.00 3.46
3725 3947 5.156804 TCAAACTCAGCTCGTTTCTTTTC 57.843 39.130 7.50 0.00 32.64 2.29
3726 3948 5.106317 TGTTCAAACTCAGCTCGTTTCTTTT 60.106 36.000 7.50 0.00 32.64 2.27
3727 3949 4.394920 TGTTCAAACTCAGCTCGTTTCTTT 59.605 37.500 7.50 0.00 32.64 2.52
3728 3950 3.938963 TGTTCAAACTCAGCTCGTTTCTT 59.061 39.130 7.50 0.00 32.64 2.52
3729 3951 3.309954 GTGTTCAAACTCAGCTCGTTTCT 59.690 43.478 7.50 0.00 32.64 2.52
3730 3952 3.309954 AGTGTTCAAACTCAGCTCGTTTC 59.690 43.478 7.50 0.03 32.64 2.78
3731 3953 3.270877 AGTGTTCAAACTCAGCTCGTTT 58.729 40.909 5.12 5.12 35.12 3.60
3732 3954 2.906354 AGTGTTCAAACTCAGCTCGTT 58.094 42.857 0.00 0.00 0.00 3.85
3733 3955 2.604046 AGTGTTCAAACTCAGCTCGT 57.396 45.000 0.00 0.00 0.00 4.18
3734 3956 3.951979 AAAGTGTTCAAACTCAGCTCG 57.048 42.857 0.00 0.00 0.00 5.03
3735 3957 6.305693 ACATAAAGTGTTCAAACTCAGCTC 57.694 37.500 0.00 0.00 38.01 4.09
3736 3958 6.073003 GCTACATAAAGTGTTCAAACTCAGCT 60.073 38.462 0.00 0.00 42.29 4.24
3737 3959 6.073003 AGCTACATAAAGTGTTCAAACTCAGC 60.073 38.462 0.00 0.00 42.29 4.26
3738 3960 7.426929 AGCTACATAAAGTGTTCAAACTCAG 57.573 36.000 0.00 0.00 42.29 3.35
3739 3961 6.145534 CGAGCTACATAAAGTGTTCAAACTCA 59.854 38.462 0.00 0.00 42.29 3.41
3740 3962 6.365247 TCGAGCTACATAAAGTGTTCAAACTC 59.635 38.462 0.00 0.00 42.29 3.01
3741 3963 6.145696 GTCGAGCTACATAAAGTGTTCAAACT 59.854 38.462 0.00 0.00 42.29 2.66
3742 3964 6.297353 GTCGAGCTACATAAAGTGTTCAAAC 58.703 40.000 0.00 0.00 42.29 2.93
3743 3965 5.407387 GGTCGAGCTACATAAAGTGTTCAAA 59.593 40.000 7.51 0.00 42.29 2.69
3744 3966 4.927425 GGTCGAGCTACATAAAGTGTTCAA 59.073 41.667 7.51 0.00 42.29 2.69
3745 3967 4.021807 TGGTCGAGCTACATAAAGTGTTCA 60.022 41.667 16.64 0.00 42.29 3.18
3746 3968 4.491676 TGGTCGAGCTACATAAAGTGTTC 58.508 43.478 16.64 0.00 42.29 3.18
3747 3969 4.530710 TGGTCGAGCTACATAAAGTGTT 57.469 40.909 16.64 0.00 42.29 3.32
3748 3970 4.219944 TCTTGGTCGAGCTACATAAAGTGT 59.780 41.667 16.64 0.00 44.95 3.55
3749 3971 4.744570 TCTTGGTCGAGCTACATAAAGTG 58.255 43.478 16.64 0.00 0.00 3.16
3750 3972 5.401531 TTCTTGGTCGAGCTACATAAAGT 57.598 39.130 16.64 0.00 0.00 2.66
3751 3973 5.220228 CGTTTCTTGGTCGAGCTACATAAAG 60.220 44.000 16.64 9.71 0.00 1.85
3752 3974 4.624024 CGTTTCTTGGTCGAGCTACATAAA 59.376 41.667 16.64 6.63 0.00 1.40
3753 3975 4.082625 TCGTTTCTTGGTCGAGCTACATAA 60.083 41.667 16.64 0.00 0.00 1.90
3754 3976 3.441222 TCGTTTCTTGGTCGAGCTACATA 59.559 43.478 16.64 0.00 0.00 2.29
3755 3977 2.230508 TCGTTTCTTGGTCGAGCTACAT 59.769 45.455 16.64 0.00 0.00 2.29
3756 3978 1.610038 TCGTTTCTTGGTCGAGCTACA 59.390 47.619 16.64 0.00 0.00 2.74
3757 3979 2.251893 CTCGTTTCTTGGTCGAGCTAC 58.748 52.381 16.64 5.44 42.94 3.58
3758 3980 2.631418 CTCGTTTCTTGGTCGAGCTA 57.369 50.000 16.64 7.43 42.94 3.32
3759 3981 3.498676 CTCGTTTCTTGGTCGAGCT 57.501 52.632 16.64 0.00 42.94 4.09
3762 3984 1.372499 CGGCTCGTTTCTTGGTCGA 60.372 57.895 0.00 0.00 0.00 4.20
3763 3985 0.736325 ATCGGCTCGTTTCTTGGTCG 60.736 55.000 0.00 0.00 0.00 4.79
3764 3986 1.000145 GATCGGCTCGTTTCTTGGTC 59.000 55.000 0.00 0.00 0.00 4.02
3765 3987 0.608640 AGATCGGCTCGTTTCTTGGT 59.391 50.000 0.00 0.00 0.00 3.67
3766 3988 1.394917 CAAGATCGGCTCGTTTCTTGG 59.605 52.381 20.85 11.59 40.54 3.61
3767 3989 2.337583 TCAAGATCGGCTCGTTTCTTG 58.662 47.619 21.65 21.65 42.78 3.02
3768 3990 2.611518 CTCAAGATCGGCTCGTTTCTT 58.388 47.619 8.50 8.50 33.53 2.52
3769 3991 1.737363 GCTCAAGATCGGCTCGTTTCT 60.737 52.381 0.00 0.00 0.00 2.52
3770 3992 0.647925 GCTCAAGATCGGCTCGTTTC 59.352 55.000 0.00 0.00 0.00 2.78
3771 3993 0.741221 GGCTCAAGATCGGCTCGTTT 60.741 55.000 0.00 0.00 0.00 3.60
3772 3994 1.153549 GGCTCAAGATCGGCTCGTT 60.154 57.895 0.00 0.00 0.00 3.85
3773 3995 1.888436 TTGGCTCAAGATCGGCTCGT 61.888 55.000 0.00 0.00 0.00 4.18
3774 3996 0.531532 ATTGGCTCAAGATCGGCTCG 60.532 55.000 0.00 0.00 0.00 5.03
3775 3997 0.942962 CATTGGCTCAAGATCGGCTC 59.057 55.000 0.00 0.00 0.00 4.70
3776 3998 0.254178 ACATTGGCTCAAGATCGGCT 59.746 50.000 0.00 0.00 0.00 5.52
3777 3999 1.098050 AACATTGGCTCAAGATCGGC 58.902 50.000 0.00 0.00 0.00 5.54
3778 4000 1.402968 CCAACATTGGCTCAAGATCGG 59.597 52.381 0.00 0.00 42.21 4.18
3779 4001 2.838386 CCAACATTGGCTCAAGATCG 57.162 50.000 0.00 0.00 42.21 3.69
3790 4012 0.729116 AATCGAGCGAGCCAACATTG 59.271 50.000 0.00 0.00 0.00 2.82
3791 4013 1.453155 AAATCGAGCGAGCCAACATT 58.547 45.000 0.00 0.00 0.00 2.71
3792 4014 1.453155 AAAATCGAGCGAGCCAACAT 58.547 45.000 0.00 0.00 0.00 2.71
3793 4015 2.087501 TAAAATCGAGCGAGCCAACA 57.912 45.000 0.00 0.00 0.00 3.33
3794 4016 3.675467 AATAAAATCGAGCGAGCCAAC 57.325 42.857 0.00 0.00 0.00 3.77
3795 4017 3.242284 CGAAATAAAATCGAGCGAGCCAA 60.242 43.478 0.00 0.00 42.76 4.52
3796 4018 2.284150 CGAAATAAAATCGAGCGAGCCA 59.716 45.455 0.00 0.00 42.76 4.75
3797 4019 2.538449 TCGAAATAAAATCGAGCGAGCC 59.462 45.455 0.00 0.00 43.76 4.70
3798 4020 3.836229 TCGAAATAAAATCGAGCGAGC 57.164 42.857 0.00 0.00 43.76 5.03
3817 4039 9.579768 AACATAATGATATTCTGTCGAGCTATC 57.420 33.333 0.00 0.00 0.00 2.08
3820 4042 9.764363 TTTAACATAATGATATTCTGTCGAGCT 57.236 29.630 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.