Multiple sequence alignment - TraesCS4A01G186000

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4A01G186000 chr4A 100.000 3878 0 0 1 3878 465274101 465277978 0.000000e+00 7162.0
1 TraesCS4A01G186000 chr4D 91.922 3714 202 50 1 3684 111981554 111977909 0.000000e+00 5107.0
2 TraesCS4A01G186000 chr4B 94.848 2795 133 6 898 3683 172722769 172719977 0.000000e+00 4353.0
3 TraesCS4A01G186000 chr3A 91.457 199 14 1 3680 3878 45864846 45864651 1.780000e-68 270.0
4 TraesCS4A01G186000 chr3A 83.529 85 12 2 3511 3594 632368946 632369029 1.160000e-10 78.7
5 TraesCS4A01G186000 chr7A 91.327 196 14 1 3683 3878 62186332 62186524 8.260000e-67 265.0
6 TraesCS4A01G186000 chr2A 90.909 198 16 1 3681 3878 211337031 211336836 8.260000e-67 265.0
7 TraesCS4A01G186000 chr2D 90.909 198 14 4 3682 3878 131235439 131235633 2.970000e-66 263.0
8 TraesCS4A01G186000 chr2D 90.500 200 16 1 3679 3878 501303974 501303778 1.070000e-65 261.0
9 TraesCS4A01G186000 chr1D 90.909 198 15 3 3681 3878 411194952 411194758 2.970000e-66 263.0
10 TraesCS4A01G186000 chr1D 100.000 31 0 0 3514 3544 50947981 50948011 1.500000e-04 58.4
11 TraesCS4A01G186000 chr1A 90.863 197 15 1 3682 3878 121359819 121360012 1.070000e-65 261.0
12 TraesCS4A01G186000 chr6A 90.452 199 15 2 3681 3878 308187935 308188130 3.840000e-65 259.0
13 TraesCS4A01G186000 chr6A 81.013 79 11 2 3257 3331 83331701 83331779 4.180000e-05 60.2
14 TraesCS4A01G186000 chr5A 90.452 199 15 3 3681 3878 36128793 36128988 3.840000e-65 259.0
15 TraesCS4A01G186000 chr2B 77.841 176 38 1 3509 3684 689136608 689136782 1.470000e-19 108.0


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 TraesCS4A01G186000 chr4A 465274101 465277978 3877 False 7162 7162 100.000 1 3878 1 chr4A.!!$F1 3877
1 TraesCS4A01G186000 chr4D 111977909 111981554 3645 True 5107 5107 91.922 1 3684 1 chr4D.!!$R1 3683
2 TraesCS4A01G186000 chr4B 172719977 172722769 2792 True 4353 4353 94.848 898 3683 1 chr4B.!!$R1 2785

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
279 289 0.034896 CCGGCTATATCCCGCAAAGT 59.965 55.0 8.76 0.0 44.27 2.66 F
875 897 0.040425 GAAATTGCTTCGTGCCACGT 60.040 50.0 17.83 0.0 43.14 4.49 F
1563 1586 0.249447 TCGATTGTATGCCGCTGAGG 60.249 55.0 0.00 0.0 44.97 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2087 2110 0.877071 ATCGACAAAACAGCTGGCAG 59.123 50.0 19.93 10.94 0.00 4.85 R
2645 2668 0.683973 CCTCAGCTCCGAGGCATTAT 59.316 55.0 7.14 0.00 45.95 1.28 R
3486 3519 0.467384 CCTCCTCGTGCATCCAGAAT 59.533 55.0 0.00 0.00 0.00 2.40 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
19 20 2.672188 TGCAACATTTGGTAACGACG 57.328 45.000 0.00 0.00 42.51 5.12
26 27 1.700523 TTTGGTAACGACGGATGACG 58.299 50.000 0.00 0.00 46.05 4.35
40 41 0.452184 ATGACGTAGCTCAGGTGACG 59.548 55.000 3.01 3.01 41.02 4.35
42 43 3.238232 ACGTAGCTCAGGTGACGTA 57.762 52.632 8.27 0.00 45.97 3.57
87 91 0.038159 CAACCTTCTTCGAGCCGACT 60.038 55.000 0.00 0.00 34.89 4.18
88 92 1.201647 CAACCTTCTTCGAGCCGACTA 59.798 52.381 0.00 0.00 34.89 2.59
105 109 0.801451 CTAGCTGCTCGTGACTGCTG 60.801 60.000 4.91 0.00 41.66 4.41
122 126 2.055689 CTGGTGTGAGGCTTGACCCA 62.056 60.000 7.76 7.48 40.58 4.51
135 139 4.464008 GCTTGACCCAATCCTTGATGATA 58.536 43.478 0.00 0.00 0.00 2.15
138 142 6.688922 GCTTGACCCAATCCTTGATGATACTA 60.689 42.308 0.00 0.00 0.00 1.82
150 154 6.295575 CCTTGATGATACTAAGGATGGTCTCC 60.296 46.154 0.00 0.00 42.82 3.71
171 175 1.244697 GGTCGGAGCTCTGAGACACA 61.245 60.000 25.75 0.00 35.49 3.72
178 182 0.387878 GCTCTGAGACACAGTGACCG 60.388 60.000 7.81 0.00 45.86 4.79
179 183 0.955178 CTCTGAGACACAGTGACCGT 59.045 55.000 7.81 0.00 45.86 4.83
191 195 1.007336 GTGACCGTGACGCGAATTCT 61.007 55.000 15.93 0.00 44.77 2.40
192 196 0.522626 TGACCGTGACGCGAATTCTA 59.477 50.000 15.93 0.00 44.77 2.10
239 248 4.388499 GTCTTCCCCGCGCCTTCA 62.388 66.667 0.00 0.00 0.00 3.02
250 259 2.049156 GCCTTCAAAGCCGGTTGC 60.049 61.111 1.90 0.00 41.71 4.17
275 285 1.982395 CCTCCGGCTATATCCCGCA 60.982 63.158 0.00 0.00 44.27 5.69
277 287 0.320374 CTCCGGCTATATCCCGCAAA 59.680 55.000 0.00 0.00 44.27 3.68
279 289 0.034896 CCGGCTATATCCCGCAAAGT 59.965 55.000 8.76 0.00 44.27 2.66
280 290 1.148310 CGGCTATATCCCGCAAAGTG 58.852 55.000 2.25 0.00 39.22 3.16
281 291 1.270094 CGGCTATATCCCGCAAAGTGA 60.270 52.381 2.25 0.00 39.22 3.41
282 292 2.805295 CGGCTATATCCCGCAAAGTGAA 60.805 50.000 2.25 0.00 39.22 3.18
283 293 2.808543 GGCTATATCCCGCAAAGTGAAG 59.191 50.000 0.00 0.00 0.00 3.02
284 294 3.494398 GGCTATATCCCGCAAAGTGAAGA 60.494 47.826 0.00 0.00 0.00 2.87
285 295 3.495001 GCTATATCCCGCAAAGTGAAGAC 59.505 47.826 0.00 0.00 0.00 3.01
286 296 2.004583 TATCCCGCAAAGTGAAGACG 57.995 50.000 0.00 0.00 0.00 4.18
287 297 0.320374 ATCCCGCAAAGTGAAGACGA 59.680 50.000 0.00 0.00 0.00 4.20
288 298 0.599204 TCCCGCAAAGTGAAGACGAC 60.599 55.000 0.00 0.00 0.00 4.34
289 299 1.566018 CCCGCAAAGTGAAGACGACC 61.566 60.000 0.00 0.00 0.00 4.79
290 300 1.566018 CCGCAAAGTGAAGACGACCC 61.566 60.000 0.00 0.00 0.00 4.46
291 301 1.566018 CGCAAAGTGAAGACGACCCC 61.566 60.000 0.00 0.00 0.00 4.95
292 302 1.235281 GCAAAGTGAAGACGACCCCC 61.235 60.000 0.00 0.00 0.00 5.40
293 303 0.949105 CAAAGTGAAGACGACCCCCG 60.949 60.000 0.00 0.00 45.44 5.73
294 304 2.726822 AAAGTGAAGACGACCCCCGC 62.727 60.000 0.00 0.00 43.32 6.13
295 305 4.754667 GTGAAGACGACCCCCGCC 62.755 72.222 0.00 0.00 43.32 6.13
316 326 4.424711 GATCCCAAGGCCGTGGCA 62.425 66.667 30.41 18.99 44.11 4.92
333 343 2.366973 ACTGGCCTCCGGTGGATA 59.633 61.111 26.61 12.30 42.23 2.59
344 355 2.202837 GTGGATACCACGGTCGCC 60.203 66.667 5.17 0.00 44.95 5.54
402 413 2.525248 CGATCCCGCGACAATGTGG 61.525 63.158 8.23 0.00 39.29 4.17
403 414 1.449601 GATCCCGCGACAATGTGGT 60.450 57.895 8.23 0.00 37.84 4.16
416 427 0.320334 ATGTGGTCACGCATGAACGA 60.320 50.000 0.00 0.00 46.50 3.85
424 435 1.519455 CGCATGAACGACTCCTCCC 60.519 63.158 0.00 0.00 34.06 4.30
429 440 1.153804 GAACGACTCCTCCCGCTTC 60.154 63.158 0.00 0.00 0.00 3.86
438 449 1.821332 CTCCCGCTTCAAGATGGGC 60.821 63.158 9.79 0.00 41.65 5.36
454 465 1.683365 GGCATGCCCATGAACTGGT 60.683 57.895 27.24 0.00 44.30 4.00
456 467 1.252904 GCATGCCCATGAACTGGTGT 61.253 55.000 6.36 0.00 44.30 4.16
465 476 2.847234 AACTGGTGTCGGCCTCCA 60.847 61.111 0.00 3.38 0.00 3.86
483 494 3.717294 GTGGATCCCACGGCCACT 61.717 66.667 9.90 0.00 44.95 4.00
505 516 4.047059 GACACGCGGGGAAGTCGA 62.047 66.667 15.46 0.00 0.00 4.20
559 570 3.499737 CATGCACGAACGCCCCTC 61.500 66.667 0.00 0.00 0.00 4.30
560 571 3.706373 ATGCACGAACGCCCCTCT 61.706 61.111 0.00 0.00 0.00 3.69
561 572 2.355986 ATGCACGAACGCCCCTCTA 61.356 57.895 0.00 0.00 0.00 2.43
606 618 1.381872 CTGACCCCAGGATCTCGGT 60.382 63.158 0.00 0.00 36.77 4.69
611 623 3.147595 CCAGGATCTCGGTCGGCA 61.148 66.667 0.00 0.00 0.00 5.69
628 640 1.140589 CATCCAGCGACGCTCTCTT 59.859 57.895 21.67 2.08 36.40 2.85
629 641 0.869454 CATCCAGCGACGCTCTCTTC 60.869 60.000 21.67 0.00 36.40 2.87
631 643 2.177038 CAGCGACGCTCTCTTCGT 59.823 61.111 21.67 0.00 43.49 3.85
658 670 4.918201 GGGCGGCGAATGAGGGAG 62.918 72.222 12.98 0.00 0.00 4.30
659 671 4.918201 GGCGGCGAATGAGGGAGG 62.918 72.222 12.98 0.00 0.00 4.30
660 672 3.849951 GCGGCGAATGAGGGAGGA 61.850 66.667 12.98 0.00 0.00 3.71
661 673 2.419198 CGGCGAATGAGGGAGGAG 59.581 66.667 0.00 0.00 0.00 3.69
663 675 1.745264 GGCGAATGAGGGAGGAGAG 59.255 63.158 0.00 0.00 0.00 3.20
667 679 1.385206 AATGAGGGAGGAGAGGGGC 60.385 63.158 0.00 0.00 0.00 5.80
682 704 2.359975 GGCAACGGAGTGGGGAAG 60.360 66.667 0.00 0.00 45.00 3.46
699 721 1.156322 AAGGAGTGGAGGGAGGAGGA 61.156 60.000 0.00 0.00 0.00 3.71
712 734 3.327404 GAGGAAGGCGTGGGGGAA 61.327 66.667 0.00 0.00 0.00 3.97
747 769 2.228480 TAGTGGGGTGGCTGGGTTC 61.228 63.158 0.00 0.00 0.00 3.62
748 770 2.993038 TAGTGGGGTGGCTGGGTTCA 62.993 60.000 0.00 0.00 0.00 3.18
750 772 2.043953 GGGGTGGCTGGGTTCATC 60.044 66.667 0.00 0.00 0.00 2.92
767 789 4.308458 CCGGGCGACACACCTTCA 62.308 66.667 0.00 0.00 0.00 3.02
785 807 1.614903 TCAACCCGAACGAGCTTCTAA 59.385 47.619 0.00 0.00 0.00 2.10
792 814 2.223294 CGAACGAGCTTCTAAGGACGAT 60.223 50.000 0.00 0.00 0.00 3.73
804 826 2.483745 GACGATGTGGCGAGTCGA 59.516 61.111 18.61 0.00 38.63 4.20
807 829 1.583967 CGATGTGGCGAGTCGAGAC 60.584 63.158 18.61 11.89 37.55 3.36
820 842 1.209383 CGAGACCGTCGTGATGTGT 59.791 57.895 0.00 0.00 44.20 3.72
821 843 1.065572 CGAGACCGTCGTGATGTGTG 61.066 60.000 0.00 0.00 44.20 3.82
822 844 1.344942 GAGACCGTCGTGATGTGTGC 61.345 60.000 0.00 0.00 0.00 4.57
823 845 1.663388 GACCGTCGTGATGTGTGCA 60.663 57.895 0.00 0.00 0.00 4.57
826 848 0.516877 CCGTCGTGATGTGTGCATTT 59.483 50.000 0.00 0.00 35.07 2.32
827 849 1.464023 CCGTCGTGATGTGTGCATTTC 60.464 52.381 0.00 0.00 35.07 2.17
829 851 2.349343 CGTCGTGATGTGTGCATTTCAA 60.349 45.455 0.00 0.00 35.07 2.69
830 852 3.667695 CGTCGTGATGTGTGCATTTCAAT 60.668 43.478 0.00 0.00 35.07 2.57
831 853 3.848019 GTCGTGATGTGTGCATTTCAATC 59.152 43.478 0.00 0.00 35.07 2.67
832 854 2.841907 CGTGATGTGTGCATTTCAATCG 59.158 45.455 0.00 0.00 35.07 3.34
834 856 4.475028 GTGATGTGTGCATTTCAATCGAA 58.525 39.130 0.00 0.00 35.07 3.71
835 857 4.321745 GTGATGTGTGCATTTCAATCGAAC 59.678 41.667 0.00 0.00 35.07 3.95
836 858 3.978718 TGTGTGCATTTCAATCGAACA 57.021 38.095 0.00 0.00 0.00 3.18
837 859 4.502171 TGTGTGCATTTCAATCGAACAT 57.498 36.364 0.00 0.00 0.00 2.71
838 860 4.475028 TGTGTGCATTTCAATCGAACATC 58.525 39.130 0.00 0.00 0.00 3.06
839 861 4.023365 TGTGTGCATTTCAATCGAACATCA 60.023 37.500 0.00 0.00 0.00 3.07
840 862 4.916831 GTGTGCATTTCAATCGAACATCAA 59.083 37.500 0.00 0.00 0.00 2.57
848 870 5.966636 TCAATCGAACATCAATAAGGACG 57.033 39.130 0.00 0.00 0.00 4.79
852 874 4.811908 TCGAACATCAATAAGGACGTCAA 58.188 39.130 18.91 2.11 0.00 3.18
874 896 2.712077 GAAATTGCTTCGTGCCACG 58.288 52.632 11.80 11.80 44.19 4.94
875 897 0.040425 GAAATTGCTTCGTGCCACGT 60.040 50.000 17.83 0.00 43.14 4.49
876 898 0.317770 AAATTGCTTCGTGCCACGTG 60.318 50.000 17.83 9.08 43.14 4.49
877 899 1.444119 AATTGCTTCGTGCCACGTGT 61.444 50.000 17.83 0.00 43.14 4.49
878 900 1.841663 ATTGCTTCGTGCCACGTGTC 61.842 55.000 17.83 0.98 43.14 3.67
879 901 2.661866 GCTTCGTGCCACGTGTCT 60.662 61.111 17.83 0.00 43.14 3.41
880 902 2.943345 GCTTCGTGCCACGTGTCTG 61.943 63.158 17.83 0.00 43.14 3.51
881 903 1.299850 CTTCGTGCCACGTGTCTGA 60.300 57.895 17.83 1.12 43.14 3.27
882 904 1.548973 CTTCGTGCCACGTGTCTGAC 61.549 60.000 17.83 0.00 43.14 3.51
883 905 2.279186 CGTGCCACGTGTCTGACA 60.279 61.111 15.65 6.36 36.74 3.58
884 906 2.585869 CGTGCCACGTGTCTGACAC 61.586 63.158 26.86 26.86 45.26 3.67
885 907 1.227263 GTGCCACGTGTCTGACACT 60.227 57.895 31.34 19.12 46.46 3.55
886 908 0.810031 GTGCCACGTGTCTGACACTT 60.810 55.000 31.34 23.26 46.46 3.16
887 909 0.747852 TGCCACGTGTCTGACACTTA 59.252 50.000 31.34 14.58 46.46 2.24
888 910 1.343142 TGCCACGTGTCTGACACTTAT 59.657 47.619 31.34 17.95 46.46 1.73
889 911 1.993370 GCCACGTGTCTGACACTTATC 59.007 52.381 31.34 16.99 46.46 1.75
890 912 2.609491 GCCACGTGTCTGACACTTATCA 60.609 50.000 31.34 0.00 46.46 2.15
891 913 3.849911 CCACGTGTCTGACACTTATCAT 58.150 45.455 31.34 12.26 46.46 2.45
892 914 4.245660 CCACGTGTCTGACACTTATCATT 58.754 43.478 31.34 9.83 46.46 2.57
893 915 4.690748 CCACGTGTCTGACACTTATCATTT 59.309 41.667 31.34 8.67 46.46 2.32
894 916 5.389830 CCACGTGTCTGACACTTATCATTTG 60.390 44.000 31.34 18.27 46.46 2.32
895 917 5.405269 CACGTGTCTGACACTTATCATTTGA 59.595 40.000 31.34 0.00 46.46 2.69
896 918 5.635280 ACGTGTCTGACACTTATCATTTGAG 59.365 40.000 31.34 17.25 46.46 3.02
900 922 8.725148 GTGTCTGACACTTATCATTTGAGATTT 58.275 33.333 28.73 0.00 45.27 2.17
1167 1190 3.461773 CTCATGCCGTCCCCGACT 61.462 66.667 0.00 0.00 35.63 4.18
1185 1208 3.075884 GACTCTCGTCTCCTACAACACT 58.924 50.000 0.00 0.00 37.19 3.55
1194 1217 2.160205 TCCTACAACACTGTCCTCTCG 58.840 52.381 0.00 0.00 36.96 4.04
1290 1313 4.308458 TGGTCCTGGAACACCGCG 62.308 66.667 11.16 0.00 35.15 6.46
1419 1442 3.725459 TGCTGCGGCGTTGACATG 61.725 61.111 13.96 0.00 42.25 3.21
1563 1586 0.249447 TCGATTGTATGCCGCTGAGG 60.249 55.000 0.00 0.00 44.97 3.86
1755 1778 4.820897 TGCAGGTACACTCAGTTATTCTG 58.179 43.478 0.00 0.00 44.85 3.02
1848 1871 2.687935 TGACTTGGCCAAGAAACTGTTC 59.312 45.455 44.50 30.56 40.79 3.18
1885 1908 0.250124 GGATGTTGTGTCGTGGACCA 60.250 55.000 0.00 0.00 0.00 4.02
2087 2110 4.340381 TGGGTTAGAACTCGTTCCTATAGC 59.660 45.833 6.20 0.55 40.33 2.97
2179 2202 3.599730 TGCCACAGAGAGACATTGTAG 57.400 47.619 0.00 0.00 0.00 2.74
2199 2222 4.252971 AGCTTGGAATGCAATGATATGC 57.747 40.909 0.00 0.00 46.58 3.14
2225 2248 3.996921 AGCTCAGAATGGTCAATCAGT 57.003 42.857 0.00 0.00 36.16 3.41
2351 2374 2.622942 GTGATGTCCAGAAAGGTTGCAA 59.377 45.455 0.00 0.00 39.02 4.08
2358 2381 4.023963 GTCCAGAAAGGTTGCAACTACTTC 60.024 45.833 27.64 23.73 39.02 3.01
2469 2492 5.754406 AGATGAAGCAGAAGAGATCATTTCG 59.246 40.000 0.00 0.00 31.24 3.46
2538 2561 6.736110 AATGGCTGCAGAAAATATGGTAAT 57.264 33.333 20.43 0.00 0.00 1.89
2645 2668 6.990798 TGTACATTGCAAATGAAGAATGGAA 58.009 32.000 1.71 0.00 31.34 3.53
2676 2699 1.117749 AGCTGAGGGATGCTGCGATA 61.118 55.000 0.00 0.00 38.21 2.92
2840 2863 1.835483 GCTGACAAGCTGGTCACACG 61.835 60.000 20.42 11.89 46.60 4.49
2993 3017 7.870509 TTCTATGCGAGAAGGTTAGTTACTA 57.129 36.000 0.00 0.00 39.36 1.82
3025 3049 3.196463 ACCTACTACATCAGTCGACTCG 58.804 50.000 16.96 11.66 38.80 4.18
3090 3114 4.345271 AACACCACGTTTGTTTGAGTAC 57.655 40.909 6.50 0.00 33.23 2.73
3106 3130 4.173256 TGAGTACATACGTTGCAGATGTG 58.827 43.478 10.45 3.44 35.48 3.21
3107 3131 4.082463 TGAGTACATACGTTGCAGATGTGA 60.082 41.667 10.45 0.00 35.48 3.58
3234 3261 0.250381 TTCGGGTTTTCCAGCGCTAA 60.250 50.000 10.99 0.00 42.91 3.09
3278 3305 3.181462 CCATCTACTACAAGGAGCATGCA 60.181 47.826 21.98 0.00 0.00 3.96
3325 3352 1.064803 CGGTTCAGTCTCTCGGAGATG 59.935 57.143 8.39 4.48 40.98 2.90
3334 3361 0.106015 TCTCGGAGATGCTCATGGGA 60.106 55.000 2.97 0.00 33.89 4.37
3370 3397 5.664908 AGAAAGATAGAGGAGGCATTTCAGA 59.335 40.000 0.00 0.00 0.00 3.27
3473 3506 1.519408 ACAAACAAATCGAGGGACCG 58.481 50.000 0.00 0.00 0.00 4.79
3478 3511 1.071071 ACAAATCGAGGGACCGTTTCA 59.929 47.619 0.00 0.00 0.00 2.69
3481 3514 0.682852 ATCGAGGGACCGTTTCACAA 59.317 50.000 0.00 0.00 0.00 3.33
3486 3519 3.469739 GAGGGACCGTTTCACAAAAGTA 58.530 45.455 0.00 0.00 0.00 2.24
3490 3523 4.517832 GGGACCGTTTCACAAAAGTATTCT 59.482 41.667 0.00 0.00 0.00 2.40
3494 3527 5.768164 ACCGTTTCACAAAAGTATTCTGGAT 59.232 36.000 0.00 0.00 0.00 3.41
3512 3546 2.029623 GATGCACGAGGAGGGTACTTA 58.970 52.381 0.00 0.00 0.00 2.24
3610 3644 3.778954 AGCTTGGAGTTTCAGTAAGCT 57.221 42.857 0.00 0.00 46.52 3.74
3618 3652 5.221641 TGGAGTTTCAGTAAGCTAGCTTTCA 60.222 40.000 33.50 15.48 37.47 2.69
3668 3702 2.427232 CACAAATGTGCTGAACCCAG 57.573 50.000 0.00 0.00 43.22 4.45
3684 3718 4.744795 ACCCAGTTGCTGATCTACTTAG 57.255 45.455 0.00 0.00 32.44 2.18
3685 3719 3.452627 ACCCAGTTGCTGATCTACTTAGG 59.547 47.826 0.00 0.00 32.44 2.69
3686 3720 3.181461 CCCAGTTGCTGATCTACTTAGGG 60.181 52.174 0.00 0.00 32.44 3.53
3687 3721 3.462021 CAGTTGCTGATCTACTTAGGGC 58.538 50.000 0.00 0.00 32.44 5.19
3688 3722 2.436173 AGTTGCTGATCTACTTAGGGCC 59.564 50.000 0.00 0.00 0.00 5.80
3689 3723 2.436173 GTTGCTGATCTACTTAGGGCCT 59.564 50.000 12.58 12.58 0.00 5.19
3690 3724 2.042464 TGCTGATCTACTTAGGGCCTG 58.958 52.381 18.53 2.03 0.00 4.85
3691 3725 2.043227 GCTGATCTACTTAGGGCCTGT 58.957 52.381 18.53 9.27 0.00 4.00
3692 3726 2.436173 GCTGATCTACTTAGGGCCTGTT 59.564 50.000 18.53 2.05 0.00 3.16
3693 3727 3.118223 GCTGATCTACTTAGGGCCTGTTT 60.118 47.826 18.53 1.64 0.00 2.83
3694 3728 4.446371 CTGATCTACTTAGGGCCTGTTTG 58.554 47.826 18.53 5.84 0.00 2.93
3695 3729 3.199946 TGATCTACTTAGGGCCTGTTTGG 59.800 47.826 18.53 3.76 39.35 3.28
3696 3730 2.627933 TCTACTTAGGGCCTGTTTGGT 58.372 47.619 18.53 9.80 38.35 3.67
3697 3731 2.983898 TCTACTTAGGGCCTGTTTGGTT 59.016 45.455 18.53 0.00 38.35 3.67
3698 3732 2.767644 ACTTAGGGCCTGTTTGGTTT 57.232 45.000 18.53 0.00 38.35 3.27
3699 3733 3.040655 ACTTAGGGCCTGTTTGGTTTT 57.959 42.857 18.53 0.00 38.35 2.43
3700 3734 4.187506 ACTTAGGGCCTGTTTGGTTTTA 57.812 40.909 18.53 0.00 38.35 1.52
3701 3735 4.548669 ACTTAGGGCCTGTTTGGTTTTAA 58.451 39.130 18.53 0.00 38.35 1.52
3702 3736 5.152193 ACTTAGGGCCTGTTTGGTTTTAAT 58.848 37.500 18.53 0.00 38.35 1.40
3703 3737 6.316513 ACTTAGGGCCTGTTTGGTTTTAATA 58.683 36.000 18.53 0.00 38.35 0.98
3704 3738 6.783482 ACTTAGGGCCTGTTTGGTTTTAATAA 59.217 34.615 18.53 0.00 38.35 1.40
3705 3739 5.738619 AGGGCCTGTTTGGTTTTAATAAG 57.261 39.130 4.50 0.00 38.35 1.73
3706 3740 5.152193 AGGGCCTGTTTGGTTTTAATAAGT 58.848 37.500 4.50 0.00 38.35 2.24
3707 3741 5.245301 AGGGCCTGTTTGGTTTTAATAAGTC 59.755 40.000 4.50 0.00 38.35 3.01
3708 3742 5.011227 GGGCCTGTTTGGTTTTAATAAGTCA 59.989 40.000 0.84 0.00 38.35 3.41
3709 3743 6.295632 GGGCCTGTTTGGTTTTAATAAGTCAT 60.296 38.462 0.84 0.00 38.35 3.06
3710 3744 6.811665 GGCCTGTTTGGTTTTAATAAGTCATC 59.188 38.462 0.00 0.00 38.35 2.92
3711 3745 7.309805 GGCCTGTTTGGTTTTAATAAGTCATCT 60.310 37.037 0.00 0.00 38.35 2.90
3712 3746 7.542130 GCCTGTTTGGTTTTAATAAGTCATCTG 59.458 37.037 0.00 0.00 38.35 2.90
3713 3747 8.028938 CCTGTTTGGTTTTAATAAGTCATCTGG 58.971 37.037 0.00 0.00 0.00 3.86
3714 3748 7.375053 TGTTTGGTTTTAATAAGTCATCTGGC 58.625 34.615 0.00 0.00 0.00 4.85
3715 3749 7.232534 TGTTTGGTTTTAATAAGTCATCTGGCT 59.767 33.333 0.00 0.00 0.00 4.75
3716 3750 7.775053 TTGGTTTTAATAAGTCATCTGGCTT 57.225 32.000 2.24 2.24 43.26 4.35
3717 3751 8.871629 TTGGTTTTAATAAGTCATCTGGCTTA 57.128 30.769 6.71 6.71 45.06 3.09
3744 3778 5.758924 GTCAGGTGACTTAAAACCAATGAC 58.241 41.667 2.72 6.43 41.65 3.06
3745 3779 5.531287 GTCAGGTGACTTAAAACCAATGACT 59.469 40.000 2.72 0.00 38.06 3.41
3746 3780 6.039382 GTCAGGTGACTTAAAACCAATGACTT 59.961 38.462 2.72 0.00 38.06 3.01
3747 3781 7.227910 GTCAGGTGACTTAAAACCAATGACTTA 59.772 37.037 2.72 0.00 38.06 2.24
3748 3782 7.942341 TCAGGTGACTTAAAACCAATGACTTAT 59.058 33.333 4.87 0.00 40.21 1.73
3749 3783 9.226606 CAGGTGACTTAAAACCAATGACTTATA 57.773 33.333 4.87 0.00 40.21 0.98
3750 3784 9.802039 AGGTGACTTAAAACCAATGACTTATAA 57.198 29.630 4.87 0.00 37.44 0.98
3766 3800 5.850614 ACTTATAAGTCACGTCTGTTTGGT 58.149 37.500 12.50 0.00 32.86 3.67
3767 3801 6.285990 ACTTATAAGTCACGTCTGTTTGGTT 58.714 36.000 12.50 0.00 32.86 3.67
3768 3802 6.202188 ACTTATAAGTCACGTCTGTTTGGTTG 59.798 38.462 12.50 0.00 32.86 3.77
3769 3803 2.396590 AGTCACGTCTGTTTGGTTGT 57.603 45.000 0.00 0.00 0.00 3.32
3770 3804 2.277084 AGTCACGTCTGTTTGGTTGTC 58.723 47.619 0.00 0.00 0.00 3.18
3771 3805 2.004017 GTCACGTCTGTTTGGTTGTCA 58.996 47.619 0.00 0.00 0.00 3.58
3772 3806 2.612212 GTCACGTCTGTTTGGTTGTCAT 59.388 45.455 0.00 0.00 0.00 3.06
3773 3807 2.869801 TCACGTCTGTTTGGTTGTCATC 59.130 45.455 0.00 0.00 0.00 2.92
3774 3808 2.872245 CACGTCTGTTTGGTTGTCATCT 59.128 45.455 0.00 0.00 0.00 2.90
3775 3809 2.872245 ACGTCTGTTTGGTTGTCATCTG 59.128 45.455 0.00 0.00 0.00 2.90
3776 3810 3.130633 CGTCTGTTTGGTTGTCATCTGA 58.869 45.455 0.00 0.00 0.00 3.27
3777 3811 3.059597 CGTCTGTTTGGTTGTCATCTGAC 60.060 47.826 3.34 3.34 44.97 3.51
3778 3812 4.130118 GTCTGTTTGGTTGTCATCTGACT 58.870 43.478 11.35 0.00 44.99 3.41
3779 3813 4.576463 GTCTGTTTGGTTGTCATCTGACTT 59.424 41.667 11.35 0.00 44.99 3.01
3780 3814 5.758296 GTCTGTTTGGTTGTCATCTGACTTA 59.242 40.000 11.35 0.00 44.99 2.24
3781 3815 6.428159 GTCTGTTTGGTTGTCATCTGACTTAT 59.572 38.462 11.35 0.00 44.99 1.73
3782 3816 7.602644 GTCTGTTTGGTTGTCATCTGACTTATA 59.397 37.037 11.35 0.00 44.99 0.98
3783 3817 8.154203 TCTGTTTGGTTGTCATCTGACTTATAA 58.846 33.333 11.35 0.00 44.99 0.98
3784 3818 8.322906 TGTTTGGTTGTCATCTGACTTATAAG 57.677 34.615 11.05 11.05 44.99 1.73
3785 3819 7.936847 TGTTTGGTTGTCATCTGACTTATAAGT 59.063 33.333 18.05 18.05 44.99 2.24
3798 3832 5.148651 ACTTATAAGTCACCTGACCACAC 57.851 43.478 12.50 0.00 45.85 3.82
3799 3833 4.020485 ACTTATAAGTCACCTGACCACACC 60.020 45.833 12.50 0.00 45.85 4.16
3800 3834 2.097110 TAAGTCACCTGACCACACCT 57.903 50.000 1.66 0.00 45.85 4.00
3801 3835 1.213296 AAGTCACCTGACCACACCTT 58.787 50.000 1.66 0.00 45.85 3.50
3802 3836 0.759346 AGTCACCTGACCACACCTTC 59.241 55.000 1.66 0.00 45.85 3.46
3803 3837 0.759346 GTCACCTGACCACACCTTCT 59.241 55.000 0.00 0.00 39.07 2.85
3804 3838 1.048601 TCACCTGACCACACCTTCTC 58.951 55.000 0.00 0.00 0.00 2.87
3805 3839 0.758734 CACCTGACCACACCTTCTCA 59.241 55.000 0.00 0.00 0.00 3.27
3806 3840 1.349026 CACCTGACCACACCTTCTCAT 59.651 52.381 0.00 0.00 0.00 2.90
3807 3841 1.625818 ACCTGACCACACCTTCTCATC 59.374 52.381 0.00 0.00 0.00 2.92
3808 3842 1.905215 CCTGACCACACCTTCTCATCT 59.095 52.381 0.00 0.00 0.00 2.90
3809 3843 2.304180 CCTGACCACACCTTCTCATCTT 59.696 50.000 0.00 0.00 0.00 2.40
3810 3844 3.332919 CTGACCACACCTTCTCATCTTG 58.667 50.000 0.00 0.00 0.00 3.02
3811 3845 2.705658 TGACCACACCTTCTCATCTTGT 59.294 45.455 0.00 0.00 0.00 3.16
3812 3846 3.136443 TGACCACACCTTCTCATCTTGTT 59.864 43.478 0.00 0.00 0.00 2.83
3813 3847 4.137543 GACCACACCTTCTCATCTTGTTT 58.862 43.478 0.00 0.00 0.00 2.83
3814 3848 4.536765 ACCACACCTTCTCATCTTGTTTT 58.463 39.130 0.00 0.00 0.00 2.43
3815 3849 4.956075 ACCACACCTTCTCATCTTGTTTTT 59.044 37.500 0.00 0.00 0.00 1.94
3843 3877 1.571955 AAAAAGGGTGGGATCCATGC 58.428 50.000 15.23 2.35 35.28 4.06
3844 3878 0.413037 AAAAGGGTGGGATCCATGCA 59.587 50.000 15.23 0.00 35.28 3.96
3845 3879 0.413037 AAAGGGTGGGATCCATGCAA 59.587 50.000 15.23 0.00 35.28 4.08
3846 3880 0.413037 AAGGGTGGGATCCATGCAAA 59.587 50.000 15.23 0.00 35.28 3.68
3847 3881 0.413037 AGGGTGGGATCCATGCAAAA 59.587 50.000 15.23 0.00 35.28 2.44
3848 3882 0.826062 GGGTGGGATCCATGCAAAAG 59.174 55.000 15.23 0.00 35.28 2.27
3849 3883 0.826062 GGTGGGATCCATGCAAAAGG 59.174 55.000 15.23 0.00 35.28 3.11
3850 3884 0.826062 GTGGGATCCATGCAAAAGGG 59.174 55.000 15.23 0.00 35.28 3.95
3851 3885 0.325484 TGGGATCCATGCAAAAGGGG 60.325 55.000 15.23 0.00 0.00 4.79
3852 3886 0.032217 GGGATCCATGCAAAAGGGGA 60.032 55.000 15.23 0.00 0.00 4.81
3853 3887 1.413517 GGGATCCATGCAAAAGGGGAT 60.414 52.381 15.23 0.00 42.66 3.85
3854 3888 1.690352 GGATCCATGCAAAAGGGGATG 59.310 52.381 6.95 0.00 40.15 3.51
3855 3889 2.669781 GATCCATGCAAAAGGGGATGA 58.330 47.619 10.65 0.00 40.15 2.92
3856 3890 1.851304 TCCATGCAAAAGGGGATGAC 58.149 50.000 0.00 0.00 38.73 3.06
3857 3891 1.358787 TCCATGCAAAAGGGGATGACT 59.641 47.619 0.00 0.00 38.73 3.41
3858 3892 2.181975 CCATGCAAAAGGGGATGACTT 58.818 47.619 0.00 0.00 38.73 3.01
3859 3893 3.011144 TCCATGCAAAAGGGGATGACTTA 59.989 43.478 0.00 0.00 38.73 2.24
3860 3894 3.962718 CCATGCAAAAGGGGATGACTTAT 59.037 43.478 0.00 0.00 38.73 1.73
3861 3895 5.103728 TCCATGCAAAAGGGGATGACTTATA 60.104 40.000 0.00 0.00 38.73 0.98
3862 3896 5.598005 CCATGCAAAAGGGGATGACTTATAA 59.402 40.000 0.00 0.00 38.73 0.98
3863 3897 6.239120 CCATGCAAAAGGGGATGACTTATAAG 60.239 42.308 11.05 11.05 38.73 1.73
3864 3898 5.826643 TGCAAAAGGGGATGACTTATAAGT 58.173 37.500 18.05 18.05 43.16 2.24
3865 3899 6.252995 TGCAAAAGGGGATGACTTATAAGTT 58.747 36.000 18.96 4.55 39.88 2.66
3866 3900 6.723977 TGCAAAAGGGGATGACTTATAAGTTT 59.276 34.615 18.96 10.17 39.88 2.66
3867 3901 7.234577 TGCAAAAGGGGATGACTTATAAGTTTT 59.765 33.333 18.96 10.67 39.88 2.43
3868 3902 8.745590 GCAAAAGGGGATGACTTATAAGTTTTA 58.254 33.333 18.96 9.55 39.88 1.52
3873 3907 9.462606 AGGGGATGACTTATAAGTTTTAAGTTG 57.537 33.333 18.96 0.00 39.40 3.16
3874 3908 8.683615 GGGGATGACTTATAAGTTTTAAGTTGG 58.316 37.037 18.96 0.00 39.40 3.77
3875 3909 8.683615 GGGATGACTTATAAGTTTTAAGTTGGG 58.316 37.037 18.96 0.00 39.40 4.12
3876 3910 8.683615 GGATGACTTATAAGTTTTAAGTTGGGG 58.316 37.037 18.96 0.00 39.40 4.96
3877 3911 9.239551 GATGACTTATAAGTTTTAAGTTGGGGT 57.760 33.333 18.96 5.40 39.40 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.103803 TCACCTGAGCTACGTCATCC 58.896 55.000 0.00 0.00 0.00 3.51
26 27 1.135170 GGGTTACGTCACCTGAGCTAC 60.135 57.143 18.03 0.00 36.97 3.58
33 34 1.005394 CGCAAGGGTTACGTCACCT 60.005 57.895 18.03 9.15 36.97 4.00
56 57 3.976701 AAGGTTGGCCTCATCGCGG 62.977 63.158 6.13 0.00 46.33 6.46
72 73 0.736053 AGCTAGTCGGCTCGAAGAAG 59.264 55.000 0.00 0.00 38.24 2.85
87 91 1.213799 CAGCAGTCACGAGCAGCTA 59.786 57.895 0.00 0.00 33.59 3.32
88 92 2.048409 CAGCAGTCACGAGCAGCT 60.048 61.111 0.00 0.00 35.63 4.24
105 109 0.251341 ATTGGGTCAAGCCTCACACC 60.251 55.000 0.00 0.00 37.43 4.16
150 154 0.962855 TGTCTCAGAGCTCCGACCTG 60.963 60.000 19.59 9.15 0.00 4.00
171 175 1.006571 AATTCGCGTCACGGTCACT 60.007 52.632 5.77 0.00 43.89 3.41
178 182 1.717194 TGGGTTAGAATTCGCGTCAC 58.283 50.000 5.77 0.00 0.00 3.67
179 183 2.459060 TTGGGTTAGAATTCGCGTCA 57.541 45.000 5.77 0.00 0.00 4.35
191 195 4.569015 GCCCTCTACAGGAATTTTGGGTTA 60.569 45.833 0.00 0.00 43.65 2.85
192 196 3.817931 GCCCTCTACAGGAATTTTGGGTT 60.818 47.826 0.00 0.00 43.65 4.11
259 268 0.320374 CTTTGCGGGATATAGCCGGA 59.680 55.000 17.90 4.04 0.00 5.14
267 277 1.546923 TCGTCTTCACTTTGCGGGATA 59.453 47.619 0.00 0.00 0.00 2.59
275 285 1.370064 CGGGGGTCGTCTTCACTTT 59.630 57.895 0.00 0.00 0.00 2.66
277 287 3.692406 GCGGGGGTCGTCTTCACT 61.692 66.667 0.00 0.00 41.72 3.41
290 300 4.856801 CTTGGGATCCACGGCGGG 62.857 72.222 15.23 7.16 30.78 6.13
291 301 4.856801 CCTTGGGATCCACGGCGG 62.857 72.222 15.23 2.24 36.16 6.13
294 304 4.856801 CGGCCTTGGGATCCACGG 62.857 72.222 15.23 11.26 44.59 4.94
295 305 4.096003 ACGGCCTTGGGATCCACG 62.096 66.667 15.23 9.97 30.78 4.94
296 306 2.438434 CACGGCCTTGGGATCCAC 60.438 66.667 15.23 3.53 30.78 4.02
297 307 3.727258 CCACGGCCTTGGGATCCA 61.727 66.667 20.65 0.00 32.35 3.41
299 309 4.424711 TGCCACGGCCTTGGGATC 62.425 66.667 28.25 13.27 41.09 3.36
300 310 4.740822 GTGCCACGGCCTTGGGAT 62.741 66.667 28.25 0.00 39.49 3.85
392 403 0.179217 CATGCGTGACCACATTGTCG 60.179 55.000 0.00 0.00 38.11 4.35
396 407 0.516877 CGTTCATGCGTGACCACATT 59.483 50.000 8.48 0.00 33.11 2.71
402 413 0.388649 AGGAGTCGTTCATGCGTGAC 60.389 55.000 8.48 3.38 33.11 3.67
403 414 0.109272 GAGGAGTCGTTCATGCGTGA 60.109 55.000 3.97 3.97 0.00 4.35
410 421 1.874345 GAAGCGGGAGGAGTCGTTCA 61.874 60.000 0.00 0.00 0.00 3.18
416 427 0.539051 CATCTTGAAGCGGGAGGAGT 59.461 55.000 0.00 0.00 0.00 3.85
424 435 1.065273 GCATGCCCATCTTGAAGCG 59.935 57.895 6.36 0.00 0.00 4.68
454 465 2.284625 ATCCACTGGAGGCCGACA 60.285 61.111 3.62 0.00 34.05 4.35
456 467 2.764128 GGATCCACTGGAGGCCGA 60.764 66.667 6.95 0.00 34.05 5.54
485 496 3.934391 GACTTCCCCGCGTGTCCAG 62.934 68.421 4.92 0.00 0.00 3.86
518 529 1.153025 ATCGTCTCGGGGTCGATGA 60.153 57.895 9.15 1.15 45.04 2.92
520 531 1.453379 ACATCGTCTCGGGGTCGAT 60.453 57.895 4.17 4.17 45.04 3.59
523 534 2.202756 GCACATCGTCTCGGGGTC 60.203 66.667 0.00 0.00 0.00 4.46
559 570 1.067821 GTGTCCCCATCTCGAAGCTAG 59.932 57.143 0.00 0.00 0.00 3.42
560 571 1.112113 GTGTCCCCATCTCGAAGCTA 58.888 55.000 0.00 0.00 0.00 3.32
561 572 1.617947 GGTGTCCCCATCTCGAAGCT 61.618 60.000 0.00 0.00 0.00 3.74
578 589 0.405585 CTGGGGTCAGGTTCATTGGT 59.594 55.000 0.00 0.00 37.36 3.67
611 623 1.435515 GAAGAGAGCGTCGCTGGAT 59.564 57.895 27.16 10.37 39.88 3.41
646 658 1.745264 CCTCTCCTCCCTCATTCGC 59.255 63.158 0.00 0.00 0.00 4.70
651 663 2.880612 TTGCCCCTCTCCTCCCTCA 61.881 63.158 0.00 0.00 0.00 3.86
658 670 3.003763 ACTCCGTTGCCCCTCTCC 61.004 66.667 0.00 0.00 0.00 3.71
659 671 2.266055 CACTCCGTTGCCCCTCTC 59.734 66.667 0.00 0.00 0.00 3.20
660 672 3.322466 CCACTCCGTTGCCCCTCT 61.322 66.667 0.00 0.00 0.00 3.69
661 673 4.410400 CCCACTCCGTTGCCCCTC 62.410 72.222 0.00 0.00 0.00 4.30
667 679 1.296715 CTCCTTCCCCACTCCGTTG 59.703 63.158 0.00 0.00 0.00 4.10
682 704 0.689412 CTTCCTCCTCCCTCCACTCC 60.689 65.000 0.00 0.00 0.00 3.85
712 734 5.368989 CCCACTACTCTGTCTTCACTTTTT 58.631 41.667 0.00 0.00 0.00 1.94
724 746 1.599047 CAGCCACCCCACTACTCTG 59.401 63.158 0.00 0.00 0.00 3.35
747 769 3.605749 AAGGTGTGTCGCCCGGATG 62.606 63.158 0.73 0.00 33.99 3.51
748 770 3.310860 GAAGGTGTGTCGCCCGGAT 62.311 63.158 0.73 0.00 33.99 4.18
750 772 3.818121 TTGAAGGTGTGTCGCCCGG 62.818 63.158 0.00 0.00 33.99 5.73
755 777 0.531090 TTCGGGTTGAAGGTGTGTCG 60.531 55.000 0.00 0.00 31.44 4.35
767 789 1.067071 CCTTAGAAGCTCGTTCGGGTT 60.067 52.381 0.00 0.00 40.49 4.11
785 807 2.885861 GACTCGCCACATCGTCCT 59.114 61.111 0.00 0.00 0.00 3.85
792 814 3.733960 CGGTCTCGACTCGCCACA 61.734 66.667 0.00 0.00 39.00 4.17
804 826 1.372997 GCACACATCACGACGGTCT 60.373 57.895 6.57 0.00 0.00 3.85
807 829 0.516877 AAATGCACACATCACGACGG 59.483 50.000 0.00 0.00 34.62 4.79
818 840 4.762956 TGATGTTCGATTGAAATGCACA 57.237 36.364 0.00 0.00 35.46 4.57
820 842 6.974048 CCTTATTGATGTTCGATTGAAATGCA 59.026 34.615 0.00 0.00 35.46 3.96
821 843 7.166473 GTCCTTATTGATGTTCGATTGAAATGC 59.834 37.037 0.00 0.00 35.46 3.56
822 844 7.374228 CGTCCTTATTGATGTTCGATTGAAATG 59.626 37.037 0.00 0.00 35.46 2.32
823 845 7.065803 ACGTCCTTATTGATGTTCGATTGAAAT 59.934 33.333 0.00 0.00 35.46 2.17
826 848 5.416083 ACGTCCTTATTGATGTTCGATTGA 58.584 37.500 0.00 0.00 30.33 2.57
827 849 5.290885 TGACGTCCTTATTGATGTTCGATTG 59.709 40.000 14.12 0.00 34.68 2.67
829 851 5.006153 TGACGTCCTTATTGATGTTCGAT 57.994 39.130 14.12 0.00 34.68 3.59
830 852 4.443913 TGACGTCCTTATTGATGTTCGA 57.556 40.909 14.12 0.00 34.68 3.71
831 853 4.862574 TCTTGACGTCCTTATTGATGTTCG 59.137 41.667 14.12 0.00 34.68 3.95
832 854 5.220228 CGTCTTGACGTCCTTATTGATGTTC 60.220 44.000 14.12 0.00 34.68 3.18
834 856 4.082408 TCGTCTTGACGTCCTTATTGATGT 60.082 41.667 20.30 0.00 37.20 3.06
835 857 4.421058 TCGTCTTGACGTCCTTATTGATG 58.579 43.478 20.30 7.58 0.00 3.07
836 858 4.713824 TCGTCTTGACGTCCTTATTGAT 57.286 40.909 20.30 0.00 0.00 2.57
837 859 4.508461 TTCGTCTTGACGTCCTTATTGA 57.492 40.909 20.30 1.19 0.00 2.57
838 860 5.779806 ATTTCGTCTTGACGTCCTTATTG 57.220 39.130 20.30 0.00 0.00 1.90
839 861 5.390567 GCAATTTCGTCTTGACGTCCTTATT 60.391 40.000 20.30 11.74 0.00 1.40
840 862 4.092968 GCAATTTCGTCTTGACGTCCTTAT 59.907 41.667 20.30 7.43 0.00 1.73
856 878 0.040425 ACGTGGCACGAAGCAATTTC 60.040 50.000 42.65 0.00 46.05 2.17
858 880 1.282570 CACGTGGCACGAAGCAATT 59.717 52.632 42.65 18.80 46.05 2.32
859 881 1.841663 GACACGTGGCACGAAGCAAT 61.842 55.000 42.65 19.57 46.05 3.56
875 897 8.724229 CAAATCTCAAATGATAAGTGTCAGACA 58.276 33.333 0.00 0.00 0.00 3.41
876 898 8.939929 TCAAATCTCAAATGATAAGTGTCAGAC 58.060 33.333 0.00 0.00 0.00 3.51
877 899 9.676861 ATCAAATCTCAAATGATAAGTGTCAGA 57.323 29.630 0.00 0.00 32.25 3.27
976 999 5.069318 TCATTCAACTGTGGCAATGAGTTA 58.931 37.500 7.31 0.00 31.70 2.24
1167 1190 2.812591 GACAGTGTTGTAGGAGACGAGA 59.187 50.000 0.00 0.00 37.76 4.04
1290 1313 2.607892 GCGTGCAAGGCCGGATATC 61.608 63.158 5.05 0.00 43.00 1.63
1335 1358 1.086634 GCGTCATCTGCAGGAACCTC 61.087 60.000 15.13 0.00 0.00 3.85
1417 1440 4.592192 CTGACGCGCGGATCCCAT 62.592 66.667 35.22 11.27 0.00 4.00
1563 1586 3.252701 GCACATTCCATGACATCAGATCC 59.747 47.826 0.00 0.00 0.00 3.36
1755 1778 6.943899 AGATCCCTAAGATACCCAGATTTC 57.056 41.667 0.00 0.00 34.42 2.17
1848 1871 3.103447 TCCTTCTCAAGCATAGCATCG 57.897 47.619 0.00 0.00 0.00 3.84
1885 1908 1.251251 GCAAGCCCTGAAATCACAGT 58.749 50.000 0.00 0.00 36.30 3.55
1967 1990 1.067635 CAAAGGTGAAGGAATTGGGCG 60.068 52.381 0.00 0.00 0.00 6.13
2087 2110 0.877071 ATCGACAAAACAGCTGGCAG 59.123 50.000 19.93 10.94 0.00 4.85
2179 2202 2.984471 CGCATATCATTGCATTCCAAGC 59.016 45.455 0.00 0.00 42.91 4.01
2199 2222 3.459232 TGACCATTCTGAGCTAATCCG 57.541 47.619 0.00 0.00 0.00 4.18
2225 2248 5.832060 TCATCATACAGCTCAAGAGATCTCA 59.168 40.000 24.39 3.25 0.00 3.27
2340 2363 4.574828 TGAGTGAAGTAGTTGCAACCTTTC 59.425 41.667 25.62 23.31 0.00 2.62
2351 2374 8.157476 AGTCATTAACCATTTGAGTGAAGTAGT 58.843 33.333 0.00 0.00 0.00 2.73
2358 2381 6.016360 TGTGGAAGTCATTAACCATTTGAGTG 60.016 38.462 0.00 0.00 34.87 3.51
2439 2462 5.078411 TCTCTTCTGCTTCATCTAACCAC 57.922 43.478 0.00 0.00 0.00 4.16
2469 2492 6.583806 CAGCATCATGTTTGAAAGGTAAGTTC 59.416 38.462 0.00 0.00 34.96 3.01
2538 2561 2.767536 GCGCTTAGCCATGTCAAGA 58.232 52.632 0.00 0.00 40.81 3.02
2645 2668 0.683973 CCTCAGCTCCGAGGCATTAT 59.316 55.000 7.14 0.00 45.95 1.28
2676 2699 6.600822 CCATGACTTTATGAGTTCCACTTGAT 59.399 38.462 0.00 0.00 39.19 2.57
2955 2979 8.763049 TCTCGCATAGAAATACTATCCAAATG 57.237 34.615 0.00 0.00 39.50 2.32
2993 3017 4.949238 TGATGTAGTAGGTTGCATTGCATT 59.051 37.500 12.95 4.25 38.76 3.56
3025 3049 7.320443 TCAGGAACACATGATTTAGTATTGC 57.680 36.000 0.00 0.00 0.00 3.56
3090 3114 3.928992 AGTTCTCACATCTGCAACGTATG 59.071 43.478 0.00 0.00 0.00 2.39
3095 3119 4.320057 CCAAAGAGTTCTCACATCTGCAAC 60.320 45.833 2.64 0.00 0.00 4.17
3106 3130 5.705609 TGGCATAAAACCAAAGAGTTCTC 57.294 39.130 0.00 0.00 33.12 2.87
3218 3245 1.751437 AGATTAGCGCTGGAAAACCC 58.249 50.000 22.90 2.04 0.00 4.11
3234 3261 4.202441 GGCACATCATACCACTGAAAGAT 58.798 43.478 0.00 0.00 37.43 2.40
3285 3312 4.022762 ACCGATAGATCTTGAGATTGACGG 60.023 45.833 0.00 18.42 39.92 4.79
3325 3352 4.220821 TCTTCCTACGATATTCCCATGAGC 59.779 45.833 0.00 0.00 0.00 4.26
3334 3361 9.238368 CTCCTCTATCTTTCTTCCTACGATATT 57.762 37.037 0.00 0.00 0.00 1.28
3370 3397 6.780198 TTAATTCATTCTAGCCCCTACCAT 57.220 37.500 0.00 0.00 0.00 3.55
3473 3506 6.363357 GTGCATCCAGAATACTTTTGTGAAAC 59.637 38.462 0.00 0.00 37.35 2.78
3478 3511 4.323417 TCGTGCATCCAGAATACTTTTGT 58.677 39.130 0.00 0.00 0.00 2.83
3481 3514 3.197766 TCCTCGTGCATCCAGAATACTTT 59.802 43.478 0.00 0.00 0.00 2.66
3486 3519 0.467384 CCTCCTCGTGCATCCAGAAT 59.533 55.000 0.00 0.00 0.00 2.40
3490 3523 1.001120 TACCCTCCTCGTGCATCCA 59.999 57.895 0.00 0.00 0.00 3.41
3494 3527 2.154567 ATAAGTACCCTCCTCGTGCA 57.845 50.000 0.00 0.00 0.00 4.57
3610 3644 1.605457 CGTGCCTGTCACTGAAAGCTA 60.605 52.381 0.00 0.00 43.46 3.32
3618 3652 3.399105 TTGCACCGTGCCTGTCACT 62.399 57.895 20.67 0.00 44.23 3.41
3659 3693 2.486472 AGATCAGCAACTGGGTTCAG 57.514 50.000 0.00 0.00 46.10 3.02
3662 3696 4.080863 CCTAAGTAGATCAGCAACTGGGTT 60.081 45.833 0.00 0.00 31.51 4.11
3664 3698 3.181461 CCCTAAGTAGATCAGCAACTGGG 60.181 52.174 0.00 0.00 31.51 4.45
3668 3702 2.436173 AGGCCCTAAGTAGATCAGCAAC 59.564 50.000 0.00 0.00 0.00 4.17
3684 3718 5.011227 TGACTTATTAAAACCAAACAGGCCC 59.989 40.000 0.00 0.00 43.14 5.80
3685 3719 6.091718 TGACTTATTAAAACCAAACAGGCC 57.908 37.500 0.00 0.00 43.14 5.19
3686 3720 7.542130 CAGATGACTTATTAAAACCAAACAGGC 59.458 37.037 0.00 0.00 43.14 4.85
3687 3721 8.028938 CCAGATGACTTATTAAAACCAAACAGG 58.971 37.037 0.00 0.00 45.67 4.00
3688 3722 7.542130 GCCAGATGACTTATTAAAACCAAACAG 59.458 37.037 0.00 0.00 0.00 3.16
3689 3723 7.232534 AGCCAGATGACTTATTAAAACCAAACA 59.767 33.333 0.00 0.00 0.00 2.83
3690 3724 7.602753 AGCCAGATGACTTATTAAAACCAAAC 58.397 34.615 0.00 0.00 0.00 2.93
3691 3725 7.775053 AGCCAGATGACTTATTAAAACCAAA 57.225 32.000 0.00 0.00 0.00 3.28
3692 3726 7.775053 AAGCCAGATGACTTATTAAAACCAA 57.225 32.000 0.00 0.00 0.00 3.67
3700 3734 8.153550 CCTGACTTATAAGCCAGATGACTTATT 58.846 37.037 25.33 0.00 38.61 1.40
3701 3735 7.291182 ACCTGACTTATAAGCCAGATGACTTAT 59.709 37.037 25.33 6.63 38.61 1.73
3702 3736 6.611642 ACCTGACTTATAAGCCAGATGACTTA 59.388 38.462 25.33 0.00 38.61 2.24
3703 3737 5.426833 ACCTGACTTATAAGCCAGATGACTT 59.573 40.000 25.33 4.46 38.61 3.01
3704 3738 4.965532 ACCTGACTTATAAGCCAGATGACT 59.034 41.667 25.33 4.40 38.61 3.41
3705 3739 5.053145 CACCTGACTTATAAGCCAGATGAC 58.947 45.833 25.33 4.25 38.61 3.06
3706 3740 4.962362 TCACCTGACTTATAAGCCAGATGA 59.038 41.667 25.33 22.21 36.80 2.92
3707 3741 5.053145 GTCACCTGACTTATAAGCCAGATG 58.947 45.833 25.33 20.47 38.61 2.90
3708 3742 5.283457 GTCACCTGACTTATAAGCCAGAT 57.717 43.478 25.33 9.94 38.61 2.90
3709 3743 4.737855 GTCACCTGACTTATAAGCCAGA 57.262 45.455 25.33 7.56 38.61 3.86
3721 3755 5.531287 AGTCATTGGTTTTAAGTCACCTGAC 59.469 40.000 11.35 11.35 45.08 3.51
3722 3756 5.690865 AGTCATTGGTTTTAAGTCACCTGA 58.309 37.500 3.10 0.00 33.76 3.86
3723 3757 6.391227 AAGTCATTGGTTTTAAGTCACCTG 57.609 37.500 3.10 0.00 33.76 4.00
3724 3758 9.802039 TTATAAGTCATTGGTTTTAAGTCACCT 57.198 29.630 3.10 0.00 33.76 4.00
3743 3777 5.850614 ACCAAACAGACGTGACTTATAAGT 58.149 37.500 18.05 18.05 43.16 2.24
3744 3778 6.202188 ACAACCAAACAGACGTGACTTATAAG 59.798 38.462 11.05 11.05 0.00 1.73
3745 3779 6.050432 ACAACCAAACAGACGTGACTTATAA 58.950 36.000 0.00 0.00 0.00 0.98
3746 3780 5.603596 ACAACCAAACAGACGTGACTTATA 58.396 37.500 0.00 0.00 0.00 0.98
3747 3781 4.448210 ACAACCAAACAGACGTGACTTAT 58.552 39.130 0.00 0.00 0.00 1.73
3748 3782 3.864243 ACAACCAAACAGACGTGACTTA 58.136 40.909 0.00 0.00 0.00 2.24
3749 3783 2.676342 GACAACCAAACAGACGTGACTT 59.324 45.455 0.00 0.00 0.00 3.01
3750 3784 2.277084 GACAACCAAACAGACGTGACT 58.723 47.619 0.00 0.00 0.00 3.41
3751 3785 2.004017 TGACAACCAAACAGACGTGAC 58.996 47.619 0.00 0.00 0.00 3.67
3752 3786 2.388310 TGACAACCAAACAGACGTGA 57.612 45.000 0.00 0.00 0.00 4.35
3753 3787 2.872245 AGATGACAACCAAACAGACGTG 59.128 45.455 0.00 0.00 0.00 4.49
3754 3788 2.872245 CAGATGACAACCAAACAGACGT 59.128 45.455 0.00 0.00 0.00 4.34
3755 3789 3.059597 GTCAGATGACAACCAAACAGACG 60.060 47.826 8.09 0.00 44.18 4.18
3756 3790 4.474226 GTCAGATGACAACCAAACAGAC 57.526 45.455 8.09 0.00 44.18 3.51
3776 3810 4.020485 GGTGTGGTCAGGTGACTTATAAGT 60.020 45.833 18.05 18.05 44.20 2.24
3777 3811 4.223032 AGGTGTGGTCAGGTGACTTATAAG 59.777 45.833 11.05 11.05 44.20 1.73
3778 3812 4.164981 AGGTGTGGTCAGGTGACTTATAA 58.835 43.478 9.90 0.00 44.20 0.98
3779 3813 3.786553 AGGTGTGGTCAGGTGACTTATA 58.213 45.455 9.90 0.00 44.20 0.98
3780 3814 2.621070 AGGTGTGGTCAGGTGACTTAT 58.379 47.619 9.90 0.00 44.20 1.73
3781 3815 2.097110 AGGTGTGGTCAGGTGACTTA 57.903 50.000 9.90 0.00 44.20 2.24
3782 3816 1.141053 GAAGGTGTGGTCAGGTGACTT 59.859 52.381 9.90 0.00 44.20 3.01
3783 3817 0.759346 GAAGGTGTGGTCAGGTGACT 59.241 55.000 9.90 0.00 44.20 3.41
3784 3818 0.759346 AGAAGGTGTGGTCAGGTGAC 59.241 55.000 1.17 1.17 44.04 3.67
3785 3819 1.048601 GAGAAGGTGTGGTCAGGTGA 58.951 55.000 0.00 0.00 0.00 4.02
3786 3820 0.758734 TGAGAAGGTGTGGTCAGGTG 59.241 55.000 0.00 0.00 0.00 4.00
3787 3821 1.625818 GATGAGAAGGTGTGGTCAGGT 59.374 52.381 0.00 0.00 0.00 4.00
3788 3822 1.905215 AGATGAGAAGGTGTGGTCAGG 59.095 52.381 0.00 0.00 0.00 3.86
3789 3823 3.244353 ACAAGATGAGAAGGTGTGGTCAG 60.244 47.826 0.00 0.00 0.00 3.51
3790 3824 2.705658 ACAAGATGAGAAGGTGTGGTCA 59.294 45.455 0.00 0.00 0.00 4.02
3791 3825 3.409026 ACAAGATGAGAAGGTGTGGTC 57.591 47.619 0.00 0.00 0.00 4.02
3792 3826 3.864789 AACAAGATGAGAAGGTGTGGT 57.135 42.857 0.00 0.00 0.00 4.16
3793 3827 5.520376 AAAAACAAGATGAGAAGGTGTGG 57.480 39.130 0.00 0.00 0.00 4.17
3824 3858 1.203288 TGCATGGATCCCACCCTTTTT 60.203 47.619 9.90 0.00 35.80 1.94
3825 3859 0.413037 TGCATGGATCCCACCCTTTT 59.587 50.000 9.90 0.00 35.80 2.27
3826 3860 0.413037 TTGCATGGATCCCACCCTTT 59.587 50.000 9.90 0.00 35.80 3.11
3827 3861 0.413037 TTTGCATGGATCCCACCCTT 59.587 50.000 9.90 0.00 35.80 3.95
3828 3862 0.413037 TTTTGCATGGATCCCACCCT 59.587 50.000 9.90 0.00 35.80 4.34
3829 3863 0.826062 CTTTTGCATGGATCCCACCC 59.174 55.000 9.90 0.00 35.80 4.61
3830 3864 0.826062 CCTTTTGCATGGATCCCACC 59.174 55.000 9.90 0.00 35.80 4.61
3831 3865 0.826062 CCCTTTTGCATGGATCCCAC 59.174 55.000 9.90 0.00 35.80 4.61
3832 3866 0.325484 CCCCTTTTGCATGGATCCCA 60.325 55.000 9.90 0.00 38.19 4.37
3833 3867 0.032217 TCCCCTTTTGCATGGATCCC 60.032 55.000 9.90 0.00 0.00 3.85
3834 3868 1.690352 CATCCCCTTTTGCATGGATCC 59.310 52.381 4.20 4.20 35.43 3.36
3835 3869 2.363359 GTCATCCCCTTTTGCATGGATC 59.637 50.000 0.00 0.00 35.43 3.36
3836 3870 2.023695 AGTCATCCCCTTTTGCATGGAT 60.024 45.455 0.00 0.00 38.12 3.41
3837 3871 1.358787 AGTCATCCCCTTTTGCATGGA 59.641 47.619 0.00 0.00 0.00 3.41
3838 3872 1.856629 AGTCATCCCCTTTTGCATGG 58.143 50.000 0.00 0.00 0.00 3.66
3839 3873 6.322201 ACTTATAAGTCATCCCCTTTTGCATG 59.678 38.462 12.50 0.00 32.86 4.06
3840 3874 6.435164 ACTTATAAGTCATCCCCTTTTGCAT 58.565 36.000 12.50 0.00 32.86 3.96
3841 3875 5.826643 ACTTATAAGTCATCCCCTTTTGCA 58.173 37.500 12.50 0.00 32.86 4.08
3842 3876 6.775594 AACTTATAAGTCATCCCCTTTTGC 57.224 37.500 18.28 0.00 38.57 3.68
3847 3881 9.462606 CAACTTAAAACTTATAAGTCATCCCCT 57.537 33.333 18.28 0.00 41.49 4.79
3848 3882 8.683615 CCAACTTAAAACTTATAAGTCATCCCC 58.316 37.037 18.28 0.00 41.49 4.81
3849 3883 8.683615 CCCAACTTAAAACTTATAAGTCATCCC 58.316 37.037 18.28 0.00 41.49 3.85
3850 3884 8.683615 CCCCAACTTAAAACTTATAAGTCATCC 58.316 37.037 18.28 0.00 41.49 3.51
3851 3885 9.239551 ACCCCAACTTAAAACTTATAAGTCATC 57.760 33.333 18.28 0.00 41.49 2.92


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

AutoCloner maintained by Alex Coulton.