Multiple sequence alignment - TraesCS3D01G291800

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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 TraesCS3D01G291800 chr3D 100.000 4055 0 0 1 4055 401877894 401873840 0.000000e+00 7489.0
1 TraesCS3D01G291800 chr3D 90.551 127 8 1 565 691 609987539 609987661 9.020000e-37 165.0
2 TraesCS3D01G291800 chr3D 85.806 155 9 6 562 716 546704866 546705007 7.020000e-33 152.0
3 TraesCS3D01G291800 chr3A 92.138 1361 58 26 2672 4010 522178113 522176780 0.000000e+00 1875.0
4 TraesCS3D01G291800 chr3A 95.080 752 28 6 721 1467 522180310 522179563 0.000000e+00 1175.0
5 TraesCS3D01G291800 chr3A 95.609 501 20 2 1961 2460 522179063 522178564 0.000000e+00 802.0
6 TraesCS3D01G291800 chr3A 91.495 388 27 3 11 398 522181123 522180742 2.780000e-146 529.0
7 TraesCS3D01G291800 chr3A 88.338 343 24 13 1635 1974 522179435 522179106 8.170000e-107 398.0
8 TraesCS3D01G291800 chr3A 93.960 149 8 1 390 538 522180530 522180383 1.470000e-54 224.0
9 TraesCS3D01G291800 chr3A 94.286 70 3 1 499 567 522180382 522180313 5.540000e-19 106.0
10 TraesCS3D01G291800 chr3B 87.266 1068 76 27 1635 2668 527299175 527298134 0.000000e+00 1164.0
11 TraesCS3D01G291800 chr3B 90.440 910 47 13 729 1621 527300162 527299276 0.000000e+00 1162.0
12 TraesCS3D01G291800 chr3B 92.011 751 45 6 2672 3410 527298091 527297344 0.000000e+00 1040.0
13 TraesCS3D01G291800 chr3B 91.948 534 28 10 3475 4006 527297324 527296804 0.000000e+00 734.0
14 TraesCS3D01G291800 chr3B 89.683 126 9 2 566 691 532643869 532643990 1.510000e-34 158.0
15 TraesCS3D01G291800 chr3B 95.556 45 2 0 4011 4055 527296728 527296684 5.620000e-09 73.1
16 TraesCS3D01G291800 chr3B 94.444 36 2 0 441 476 527300280 527300245 5.660000e-04 56.5
17 TraesCS3D01G291800 chr4A 92.105 836 41 14 1635 2460 225579428 225580248 0.000000e+00 1155.0
18 TraesCS3D01G291800 chr4A 85.351 983 88 30 2678 3639 225582555 225583502 0.000000e+00 966.0
19 TraesCS3D01G291800 chr4A 84.044 1009 85 28 2678 3642 195313074 195312098 0.000000e+00 902.0
20 TraesCS3D01G291800 chr4A 89.330 731 35 19 1635 2353 195313945 195313246 0.000000e+00 878.0
21 TraesCS3D01G291800 chr4A 88.529 401 33 9 1238 1635 225578959 225579349 1.320000e-129 473.0
22 TraesCS3D01G291800 chr4A 87.750 400 38 8 1238 1635 195314414 195314024 1.330000e-124 457.0
23 TraesCS3D01G291800 chr4A 96.774 62 2 0 2399 2460 195313245 195313184 1.990000e-18 104.0
24 TraesCS3D01G291800 chr5B 91.895 839 37 17 1635 2460 261375857 261375037 0.000000e+00 1144.0
25 TraesCS3D01G291800 chr5B 83.040 1079 88 37 2678 3725 261374925 261373911 0.000000e+00 891.0
26 TraesCS3D01G291800 chr5B 92.621 393 25 4 1245 1635 261376326 261375936 2.740000e-156 562.0
27 TraesCS3D01G291800 chr5B 89.305 187 17 3 2275 2460 543865632 543865816 8.770000e-57 231.0
28 TraesCS3D01G291800 chr5D 91.776 839 30 19 1635 2460 437572544 437571732 0.000000e+00 1131.0
29 TraesCS3D01G291800 chr5D 84.940 996 81 22 2678 3642 437571620 437570663 0.000000e+00 944.0
30 TraesCS3D01G291800 chr5D 91.294 402 28 6 1238 1635 437573021 437572623 3.570000e-150 542.0
31 TraesCS3D01G291800 chr7D 91.270 126 7 1 566 691 156813378 156813499 6.970000e-38 169.0
32 TraesCS3D01G291800 chr7D 88.976 127 9 2 565 691 556132592 556132713 7.020000e-33 152.0
33 TraesCS3D01G291800 chr7B 87.261 157 8 5 565 721 508191348 508191492 6.970000e-38 169.0
34 TraesCS3D01G291800 chr2B 86.076 158 10 5 565 722 288972060 288971915 4.200000e-35 159.0
35 TraesCS3D01G291800 chr2D 89.683 126 9 1 566 691 154002078 154002199 1.510000e-34 158.0
36 TraesCS3D01G291800 chr2D 86.093 151 9 5 566 716 602111497 602111635 7.020000e-33 152.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G291800 chr3D 401873840 401877894 4054 True 7489.000000 7489 100.000000 1 4055 1 chr3D.!!$R1 4054
1 TraesCS3D01G291800 chr3A 522176780 522181123 4343 True 729.857143 1875 92.986571 11 4010 7 chr3A.!!$R1 3999
2 TraesCS3D01G291800 chr3B 527296684 527300280 3596 True 704.933333 1164 91.944167 441 4055 6 chr3B.!!$R1 3614
3 TraesCS3D01G291800 chr4A 225578959 225583502 4543 False 864.666667 1155 88.661667 1238 3639 3 chr4A.!!$F1 2401
4 TraesCS3D01G291800 chr4A 195312098 195314414 2316 True 585.250000 902 89.474500 1238 3642 4 chr4A.!!$R1 2404
5 TraesCS3D01G291800 chr5B 261373911 261376326 2415 True 865.666667 1144 89.185333 1245 3725 3 chr5B.!!$R1 2480
6 TraesCS3D01G291800 chr5D 437570663 437573021 2358 True 872.333333 1131 89.336667 1238 3642 3 chr5D.!!$R1 2404

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
664 925 0.036732 TTCATTCAACTCCGCCAGCT 59.963 50.0 0.0 0.0 0.00 4.24 F
767 1028 0.038801 GGAAGCAGAGCCAAACTTGC 60.039 55.0 0.0 0.0 34.54 4.01 F
1511 1804 0.389025 GCACTGTTGTTTTGGGGGAG 59.611 55.0 0.0 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 1859 0.039074 ACAGAACTTCTCGCGTCAGG 60.039 55.000 5.77 0.0 0.00 3.86 R
1747 2149 1.320555 CTATTTCCTTCGCGACACACG 59.679 52.381 9.15 0.0 45.66 4.49 R
3126 6088 0.383002 CACAACACGCGCTACACAAG 60.383 55.000 5.73 0.0 0.00 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
114 115 0.523546 CGTCGAAGTCGTGGGATCTG 60.524 60.000 0.00 0.00 40.80 2.90
123 124 1.275291 TCGTGGGATCTGACTCCAAAC 59.725 52.381 2.86 3.17 37.01 2.93
157 158 4.052229 CGAGGGTCGAGGCAACGT 62.052 66.667 0.00 0.00 43.74 3.99
163 164 1.080093 GTCGAGGCAACGTCCATGA 60.080 57.895 0.00 0.00 46.39 3.07
207 208 1.600636 CAGGAAGCGGTCAAAGGCA 60.601 57.895 0.00 0.00 0.00 4.75
208 209 1.302832 AGGAAGCGGTCAAAGGCAG 60.303 57.895 0.00 0.00 0.00 4.85
216 217 1.745489 GTCAAAGGCAGCCCTACGG 60.745 63.158 8.22 0.00 41.90 4.02
226 227 2.590092 CCCTACGGCAAGGAAGGG 59.410 66.667 4.49 4.16 39.15 3.95
227 228 2.124695 CCTACGGCAAGGAAGGGC 60.125 66.667 0.00 0.00 39.15 5.19
270 271 0.178990 GCAGCGGGAGGGGAAAATAT 60.179 55.000 0.00 0.00 0.00 1.28
271 272 1.897560 CAGCGGGAGGGGAAAATATC 58.102 55.000 0.00 0.00 0.00 1.63
272 273 1.142870 CAGCGGGAGGGGAAAATATCA 59.857 52.381 0.00 0.00 0.00 2.15
273 274 1.143073 AGCGGGAGGGGAAAATATCAC 59.857 52.381 0.00 0.00 0.00 3.06
291 292 3.519579 TCACTCACGTCAAACCGTTTTA 58.480 40.909 0.00 0.00 39.45 1.52
296 297 1.860326 ACGTCAAACCGTTTTAGGACG 59.140 47.619 23.34 23.34 42.52 4.79
310 311 1.374758 GGACGGTGTGAGCTCCAAG 60.375 63.158 12.15 8.87 0.00 3.61
314 315 0.957395 CGGTGTGAGCTCCAAGCATT 60.957 55.000 12.15 0.00 45.56 3.56
349 350 0.767375 AATATGATGGCTCGTGGGCT 59.233 50.000 0.00 0.00 41.48 5.19
365 366 4.547859 CTCGATTTGGAGCCCCTG 57.452 61.111 0.00 0.00 0.00 4.45
366 367 1.907739 CTCGATTTGGAGCCCCTGA 59.092 57.895 0.00 0.00 0.00 3.86
373 374 1.995376 TTGGAGCCCCTGAAAAACTC 58.005 50.000 0.00 0.00 0.00 3.01
387 388 5.487433 TGAAAAACTCTAGCGATCAATGGA 58.513 37.500 0.00 0.00 0.00 3.41
395 396 1.106285 GCGATCAATGGAGGCCTTTT 58.894 50.000 6.77 0.00 0.00 2.27
405 626 1.340114 GGAGGCCTTTTCGTCCAAGAT 60.340 52.381 6.77 0.00 39.95 2.40
423 644 4.537135 AGATCGTCATAATGGCGGTTAT 57.463 40.909 0.00 0.00 39.82 1.89
433 654 3.620427 ATGGCGGTTATTATGGCGATA 57.380 42.857 0.00 0.00 0.00 2.92
510 731 8.824159 ATATGTTTATCCTGAAGTGAAGATCG 57.176 34.615 0.00 0.00 0.00 3.69
526 747 3.234353 AGATCGAGCCTCCAATGATACA 58.766 45.455 0.00 0.00 0.00 2.29
568 829 4.825546 ACGTGAGTGTCGTTATATAGGG 57.174 45.455 0.00 0.00 46.97 3.53
569 830 3.567164 ACGTGAGTGTCGTTATATAGGGG 59.433 47.826 0.00 0.00 46.97 4.79
571 832 3.573110 GTGAGTGTCGTTATATAGGGGCT 59.427 47.826 0.00 0.00 0.00 5.19
572 833 3.572682 TGAGTGTCGTTATATAGGGGCTG 59.427 47.826 0.00 0.00 0.00 4.85
573 834 3.573110 GAGTGTCGTTATATAGGGGCTGT 59.427 47.826 0.00 0.00 0.00 4.40
574 835 3.965347 AGTGTCGTTATATAGGGGCTGTT 59.035 43.478 0.00 0.00 0.00 3.16
575 836 4.038883 AGTGTCGTTATATAGGGGCTGTTC 59.961 45.833 0.00 0.00 0.00 3.18
576 837 3.005050 TGTCGTTATATAGGGGCTGTTCG 59.995 47.826 0.00 0.00 0.00 3.95
577 838 2.559668 TCGTTATATAGGGGCTGTTCGG 59.440 50.000 0.00 0.00 0.00 4.30
578 839 2.696506 GTTATATAGGGGCTGTTCGGC 58.303 52.381 0.00 0.00 37.49 5.54
579 840 2.018355 TATATAGGGGCTGTTCGGCA 57.982 50.000 5.97 0.00 40.61 5.69
580 841 1.136828 ATATAGGGGCTGTTCGGCAA 58.863 50.000 5.97 0.00 40.61 4.52
582 843 0.179018 ATAGGGGCTGTTCGGCAATC 60.179 55.000 5.97 0.00 40.61 2.67
583 844 2.265467 TAGGGGCTGTTCGGCAATCC 62.265 60.000 5.97 4.34 40.61 3.01
584 845 2.361104 GGGCTGTTCGGCAATCCA 60.361 61.111 5.97 0.00 40.61 3.41
585 846 2.700773 GGGCTGTTCGGCAATCCAC 61.701 63.158 5.97 0.00 40.61 4.02
586 847 1.675641 GGCTGTTCGGCAATCCACT 60.676 57.895 5.97 0.00 38.25 4.00
587 848 0.392461 GGCTGTTCGGCAATCCACTA 60.392 55.000 5.97 0.00 38.25 2.74
588 849 0.727398 GCTGTTCGGCAATCCACTAC 59.273 55.000 0.00 0.00 0.00 2.73
590 851 2.271800 CTGTTCGGCAATCCACTACTC 58.728 52.381 0.00 0.00 0.00 2.59
591 852 1.066430 TGTTCGGCAATCCACTACTCC 60.066 52.381 0.00 0.00 0.00 3.85
592 853 0.539986 TTCGGCAATCCACTACTCCC 59.460 55.000 0.00 0.00 0.00 4.30
593 854 0.325296 TCGGCAATCCACTACTCCCT 60.325 55.000 0.00 0.00 0.00 4.20
594 855 0.179073 CGGCAATCCACTACTCCCTG 60.179 60.000 0.00 0.00 0.00 4.45
595 856 1.204146 GGCAATCCACTACTCCCTGA 58.796 55.000 0.00 0.00 0.00 3.86
596 857 1.559682 GGCAATCCACTACTCCCTGAA 59.440 52.381 0.00 0.00 0.00 3.02
597 858 2.026262 GGCAATCCACTACTCCCTGAAA 60.026 50.000 0.00 0.00 0.00 2.69
598 859 3.372025 GGCAATCCACTACTCCCTGAAAT 60.372 47.826 0.00 0.00 0.00 2.17
599 860 4.273318 GCAATCCACTACTCCCTGAAATT 58.727 43.478 0.00 0.00 0.00 1.82
600 861 4.336713 GCAATCCACTACTCCCTGAAATTC 59.663 45.833 0.00 0.00 0.00 2.17
601 862 5.500234 CAATCCACTACTCCCTGAAATTCA 58.500 41.667 0.00 0.00 0.00 2.57
602 863 5.779241 ATCCACTACTCCCTGAAATTCAA 57.221 39.130 0.00 0.00 0.00 2.69
603 864 5.165961 TCCACTACTCCCTGAAATTCAAG 57.834 43.478 0.00 0.00 0.00 3.02
604 865 4.019321 TCCACTACTCCCTGAAATTCAAGG 60.019 45.833 4.27 4.27 29.12 3.61
605 866 4.019321 CCACTACTCCCTGAAATTCAAGGA 60.019 45.833 12.34 12.34 34.75 3.36
606 867 5.339530 CCACTACTCCCTGAAATTCAAGGAT 60.340 44.000 13.22 7.14 36.48 3.24
607 868 5.819901 CACTACTCCCTGAAATTCAAGGATC 59.180 44.000 13.22 0.00 36.48 3.36
608 869 5.728741 ACTACTCCCTGAAATTCAAGGATCT 59.271 40.000 13.22 5.28 36.48 2.75
609 870 4.853007 ACTCCCTGAAATTCAAGGATCTG 58.147 43.478 13.22 5.50 36.48 2.90
610 871 3.624777 TCCCTGAAATTCAAGGATCTGC 58.375 45.455 9.15 0.00 32.31 4.26
611 872 3.010472 TCCCTGAAATTCAAGGATCTGCA 59.990 43.478 9.15 0.00 32.31 4.41
612 873 3.380637 CCCTGAAATTCAAGGATCTGCAG 59.619 47.826 7.63 7.63 29.32 4.41
613 874 4.267536 CCTGAAATTCAAGGATCTGCAGA 58.732 43.478 20.79 20.79 0.00 4.26
614 875 4.335874 CCTGAAATTCAAGGATCTGCAGAG 59.664 45.833 22.96 8.09 0.00 3.35
615 876 3.693085 TGAAATTCAAGGATCTGCAGAGC 59.307 43.478 23.68 23.68 0.00 4.09
616 877 3.361281 AATTCAAGGATCTGCAGAGCA 57.639 42.857 31.24 12.67 36.92 4.26
617 878 2.105006 TTCAAGGATCTGCAGAGCAC 57.895 50.000 31.24 20.62 33.79 4.40
618 879 0.251354 TCAAGGATCTGCAGAGCACC 59.749 55.000 31.24 25.95 33.79 5.01
619 880 0.252479 CAAGGATCTGCAGAGCACCT 59.748 55.000 31.24 27.47 33.79 4.00
620 881 0.252479 AAGGATCTGCAGAGCACCTG 59.748 55.000 31.24 0.00 45.67 4.00
635 896 2.759973 CTGCTCCCCCGCTCTGTA 60.760 66.667 0.00 0.00 0.00 2.74
636 897 3.075005 TGCTCCCCCGCTCTGTAC 61.075 66.667 0.00 0.00 0.00 2.90
637 898 2.760385 GCTCCCCCGCTCTGTACT 60.760 66.667 0.00 0.00 0.00 2.73
638 899 2.359967 GCTCCCCCGCTCTGTACTT 61.360 63.158 0.00 0.00 0.00 2.24
639 900 1.900545 GCTCCCCCGCTCTGTACTTT 61.901 60.000 0.00 0.00 0.00 2.66
640 901 0.613777 CTCCCCCGCTCTGTACTTTT 59.386 55.000 0.00 0.00 0.00 2.27
641 902 1.003233 CTCCCCCGCTCTGTACTTTTT 59.997 52.381 0.00 0.00 0.00 1.94
642 903 2.235402 CTCCCCCGCTCTGTACTTTTTA 59.765 50.000 0.00 0.00 0.00 1.52
643 904 2.027837 TCCCCCGCTCTGTACTTTTTAC 60.028 50.000 0.00 0.00 0.00 2.01
644 905 2.353323 CCCCGCTCTGTACTTTTTACC 58.647 52.381 0.00 0.00 0.00 2.85
645 906 2.027469 CCCCGCTCTGTACTTTTTACCT 60.027 50.000 0.00 0.00 0.00 3.08
646 907 3.558533 CCCCGCTCTGTACTTTTTACCTT 60.559 47.826 0.00 0.00 0.00 3.50
647 908 3.683340 CCCGCTCTGTACTTTTTACCTTC 59.317 47.826 0.00 0.00 0.00 3.46
648 909 4.312443 CCGCTCTGTACTTTTTACCTTCA 58.688 43.478 0.00 0.00 0.00 3.02
649 910 4.935808 CCGCTCTGTACTTTTTACCTTCAT 59.064 41.667 0.00 0.00 0.00 2.57
650 911 5.411669 CCGCTCTGTACTTTTTACCTTCATT 59.588 40.000 0.00 0.00 0.00 2.57
651 912 6.402226 CCGCTCTGTACTTTTTACCTTCATTC 60.402 42.308 0.00 0.00 0.00 2.67
652 913 6.147164 CGCTCTGTACTTTTTACCTTCATTCA 59.853 38.462 0.00 0.00 0.00 2.57
653 914 7.307751 CGCTCTGTACTTTTTACCTTCATTCAA 60.308 37.037 0.00 0.00 0.00 2.69
654 915 7.803659 GCTCTGTACTTTTTACCTTCATTCAAC 59.196 37.037 0.00 0.00 0.00 3.18
655 916 8.974060 TCTGTACTTTTTACCTTCATTCAACT 57.026 30.769 0.00 0.00 0.00 3.16
656 917 9.052759 TCTGTACTTTTTACCTTCATTCAACTC 57.947 33.333 0.00 0.00 0.00 3.01
657 918 8.161699 TGTACTTTTTACCTTCATTCAACTCC 57.838 34.615 0.00 0.00 0.00 3.85
658 919 6.313744 ACTTTTTACCTTCATTCAACTCCG 57.686 37.500 0.00 0.00 0.00 4.63
659 920 4.759516 TTTTACCTTCATTCAACTCCGC 57.240 40.909 0.00 0.00 0.00 5.54
660 921 2.396590 TACCTTCATTCAACTCCGCC 57.603 50.000 0.00 0.00 0.00 6.13
661 922 0.400213 ACCTTCATTCAACTCCGCCA 59.600 50.000 0.00 0.00 0.00 5.69
662 923 1.089920 CCTTCATTCAACTCCGCCAG 58.910 55.000 0.00 0.00 0.00 4.85
663 924 0.449388 CTTCATTCAACTCCGCCAGC 59.551 55.000 0.00 0.00 0.00 4.85
664 925 0.036732 TTCATTCAACTCCGCCAGCT 59.963 50.000 0.00 0.00 0.00 4.24
665 926 0.391661 TCATTCAACTCCGCCAGCTC 60.392 55.000 0.00 0.00 0.00 4.09
666 927 1.078143 ATTCAACTCCGCCAGCTCC 60.078 57.895 0.00 0.00 0.00 4.70
667 928 2.859273 ATTCAACTCCGCCAGCTCCG 62.859 60.000 0.00 0.00 0.00 4.63
689 950 2.438614 CGAGAGCCTGGAGTCGGA 60.439 66.667 0.00 0.00 0.00 4.55
690 951 2.477176 CGAGAGCCTGGAGTCGGAG 61.477 68.421 0.00 0.00 0.00 4.63
691 952 2.757917 AGAGCCTGGAGTCGGAGC 60.758 66.667 0.00 0.00 0.00 4.70
692 953 3.844090 GAGCCTGGAGTCGGAGCC 61.844 72.222 0.00 0.00 0.00 4.70
693 954 4.390556 AGCCTGGAGTCGGAGCCT 62.391 66.667 0.00 0.00 0.00 4.58
694 955 3.844090 GCCTGGAGTCGGAGCCTC 61.844 72.222 0.00 0.00 0.00 4.70
695 956 3.522731 CCTGGAGTCGGAGCCTCG 61.523 72.222 0.00 0.00 0.00 4.63
696 957 3.522731 CTGGAGTCGGAGCCTCGG 61.523 72.222 0.00 0.00 0.00 4.63
697 958 3.997400 CTGGAGTCGGAGCCTCGGA 62.997 68.421 0.00 0.00 0.00 4.55
698 959 3.213402 GGAGTCGGAGCCTCGGAG 61.213 72.222 1.73 0.00 0.00 4.63
699 960 3.213402 GAGTCGGAGCCTCGGAGG 61.213 72.222 19.95 19.95 38.80 4.30
700 961 4.824515 AGTCGGAGCCTCGGAGGG 62.825 72.222 24.81 8.80 35.37 4.30
701 962 4.816984 GTCGGAGCCTCGGAGGGA 62.817 72.222 24.81 11.04 35.37 4.20
702 963 3.822035 TCGGAGCCTCGGAGGGAT 61.822 66.667 24.81 5.09 35.37 3.85
703 964 3.610669 CGGAGCCTCGGAGGGATG 61.611 72.222 24.81 0.32 35.37 3.51
704 965 3.934962 GGAGCCTCGGAGGGATGC 61.935 72.222 24.81 10.71 35.37 3.91
705 966 3.934962 GAGCCTCGGAGGGATGCC 61.935 72.222 24.81 8.24 37.02 4.40
712 973 2.190578 GGAGGGATGCCGAACAGG 59.809 66.667 0.00 0.00 44.97 4.00
724 985 3.644884 CCGAACAGGCCTATAGTACTG 57.355 52.381 3.98 15.54 37.01 2.74
725 986 2.957006 CCGAACAGGCCTATAGTACTGT 59.043 50.000 3.98 16.55 45.34 3.55
767 1028 0.038801 GGAAGCAGAGCCAAACTTGC 60.039 55.000 0.00 0.00 34.54 4.01
771 1032 1.081641 CAGAGCCAAACTTGCGCAG 60.082 57.895 11.31 7.81 0.00 5.18
775 1036 1.200020 GAGCCAAACTTGCGCAGTAAT 59.800 47.619 11.31 1.59 32.94 1.89
829 1090 0.887387 TAGCGACCAACTTGGCCAAC 60.887 55.000 16.05 2.30 42.67 3.77
838 1099 2.718731 TTGGCCAACAAGCGAACG 59.281 55.556 16.05 0.00 33.18 3.95
911 1172 1.151172 GCCAAACCAAACCAGCAACG 61.151 55.000 0.00 0.00 0.00 4.10
1189 1451 1.007118 TGCCTCTGATCCTGGTGTCTA 59.993 52.381 0.00 0.00 0.00 2.59
1277 1539 2.218603 TCTTCCTTCCGTGTTTCTTGC 58.781 47.619 0.00 0.00 0.00 4.01
1345 1627 4.909894 GCTTATTAGAAAAAGCGTGAGGG 58.090 43.478 0.00 0.00 38.80 4.30
1373 1655 7.878036 TGCCTCTGTTTTTACTGGTTAATTAC 58.122 34.615 0.00 0.00 0.00 1.89
1381 1663 8.757789 GTTTTTACTGGTTAATTACAAGTTGGC 58.242 33.333 7.96 0.00 37.81 4.52
1401 1683 3.653344 GCGACAGCATTGGTCTGATATA 58.347 45.455 0.00 0.00 44.35 0.86
1467 1749 2.433436 GCGATTTAGGTCACCCTGTTT 58.567 47.619 0.00 0.00 42.67 2.83
1468 1750 2.418976 GCGATTTAGGTCACCCTGTTTC 59.581 50.000 0.00 0.00 42.67 2.78
1469 1751 3.868754 GCGATTTAGGTCACCCTGTTTCT 60.869 47.826 0.00 0.00 42.67 2.52
1470 1752 4.622220 GCGATTTAGGTCACCCTGTTTCTA 60.622 45.833 0.00 0.00 42.67 2.10
1471 1753 5.671493 CGATTTAGGTCACCCTGTTTCTAT 58.329 41.667 0.00 0.00 42.67 1.98
1472 1754 5.523916 CGATTTAGGTCACCCTGTTTCTATG 59.476 44.000 0.00 0.00 42.67 2.23
1473 1755 6.629515 CGATTTAGGTCACCCTGTTTCTATGA 60.630 42.308 0.00 0.00 42.67 2.15
1474 1756 6.636454 TTTAGGTCACCCTGTTTCTATGAT 57.364 37.500 0.00 0.00 42.67 2.45
1475 1757 7.743116 TTTAGGTCACCCTGTTTCTATGATA 57.257 36.000 0.00 0.00 42.67 2.15
1476 1758 7.743116 TTAGGTCACCCTGTTTCTATGATAA 57.257 36.000 0.00 0.00 42.67 1.75
1477 1759 6.831664 AGGTCACCCTGTTTCTATGATAAT 57.168 37.500 0.00 0.00 40.58 1.28
1478 1760 6.595682 AGGTCACCCTGTTTCTATGATAATG 58.404 40.000 0.00 0.00 40.58 1.90
1479 1761 5.765182 GGTCACCCTGTTTCTATGATAATGG 59.235 44.000 0.00 0.00 0.00 3.16
1504 1797 3.376859 TCAATCACTCGCACTGTTGTTTT 59.623 39.130 0.00 0.00 0.00 2.43
1511 1804 0.389025 GCACTGTTGTTTTGGGGGAG 59.611 55.000 0.00 0.00 0.00 4.30
1544 1837 4.083537 TGTGAACGCCAATGTAGTTTGATC 60.084 41.667 0.00 0.00 0.00 2.92
1574 1867 1.666553 TGCAACCTTACCTGACGCG 60.667 57.895 3.53 3.53 0.00 6.01
1576 1869 1.352156 GCAACCTTACCTGACGCGAG 61.352 60.000 15.93 0.00 0.00 5.03
1614 1915 8.251026 TGTGGACACATAGTAGTTATTTGAGAG 58.749 37.037 0.13 0.00 36.21 3.20
1741 2143 8.788238 ATGCTATCTATGTGGATATATGTGGA 57.212 34.615 0.00 0.00 0.00 4.02
1742 2144 8.788238 TGCTATCTATGTGGATATATGTGGAT 57.212 34.615 0.00 0.00 0.00 3.41
1743 2145 9.881773 TGCTATCTATGTGGATATATGTGGATA 57.118 33.333 0.00 0.00 0.00 2.59
1747 2149 8.470657 TCTATGTGGATATATGTGGATAGAGC 57.529 38.462 0.00 0.00 0.00 4.09
1748 2150 5.582689 TGTGGATATATGTGGATAGAGCG 57.417 43.478 0.00 0.00 0.00 5.03
2021 2478 4.005650 CTGACAAGATGTATGCCACACTT 58.994 43.478 0.00 0.00 40.86 3.16
2192 2649 1.902508 TCTGGACCTGAATGGACTGTC 59.097 52.381 0.00 0.00 39.71 3.51
2215 2672 7.491372 TGTCGAGTTATTAACAGCTTTCCATAG 59.509 37.037 9.15 0.00 0.00 2.23
2497 5198 4.558226 ATTTGCATCACTCTCTGGTACA 57.442 40.909 0.00 0.00 0.00 2.90
2506 5207 2.293677 ACTCTCTGGTACACGTTGACTG 59.706 50.000 0.00 0.00 0.00 3.51
2507 5208 1.611977 TCTCTGGTACACGTTGACTGG 59.388 52.381 0.00 0.00 0.00 4.00
2510 5211 2.132762 CTGGTACACGTTGACTGGAAC 58.867 52.381 0.00 0.00 0.00 3.62
2526 5228 6.970043 TGACTGGAACGTTTTCACTTTTAATG 59.030 34.615 0.46 0.00 32.80 1.90
2533 5392 7.172654 ACGTTTTCACTTTTAATGAAATGGC 57.827 32.000 4.09 0.00 43.65 4.40
2559 5419 0.179156 CATCACGTGATGCAAAGGCC 60.179 55.000 37.56 0.00 44.44 5.19
2560 5420 1.647545 ATCACGTGATGCAAAGGCCG 61.648 55.000 29.49 0.00 40.13 6.13
2561 5421 2.031919 ACGTGATGCAAAGGCCGA 59.968 55.556 0.00 0.00 40.13 5.54
2570 5430 2.689771 AAAGGCCGACCGGGGTAT 60.690 61.111 6.32 0.00 42.76 2.73
2693 5619 5.046304 ACTGCTAGTAATCTGTGTTGTGGAT 60.046 40.000 0.00 0.00 0.00 3.41
2706 5632 5.419155 TGTGTTGTGGATTCTACTCTCTAGG 59.581 44.000 1.69 0.00 0.00 3.02
2761 5690 7.445121 TCTTATCCTGCACTTACATATCAAGG 58.555 38.462 0.00 0.00 0.00 3.61
2822 5762 5.525378 CCCTACATACAATCTTGTCAAGAGC 59.475 44.000 19.64 0.00 41.61 4.09
2843 5784 3.196463 CTGTGCAGAGATGATCAACTCC 58.804 50.000 24.71 13.79 34.13 3.85
2873 5816 7.603404 TCATGTTTGAAAATGGCAGGAAATAAG 59.397 33.333 0.00 0.00 0.00 1.73
2877 5820 5.090139 TGAAAATGGCAGGAAATAAGGGAA 58.910 37.500 0.00 0.00 0.00 3.97
2889 5832 6.010739 AGGAAATAAGGGAAAAGATGGAGGAA 60.011 38.462 0.00 0.00 0.00 3.36
2928 5871 1.817099 GATGAAGCTGAGGGTGGCG 60.817 63.158 0.00 0.00 0.00 5.69
2997 5940 2.154074 AAGGGCCTTCACTTCCGGT 61.154 57.895 14.48 0.00 0.00 5.28
3126 6088 2.035442 GGAAACCCAGCGCTGAGAC 61.035 63.158 38.06 21.68 0.00 3.36
3187 6149 1.538047 TTGGTCTGAATTGGAGCTGC 58.462 50.000 0.00 0.00 33.06 5.25
3211 6178 6.825721 GCCGATGGAGGATGATATATTCTTTT 59.174 38.462 0.00 0.00 0.00 2.27
3212 6179 7.011857 GCCGATGGAGGATGATATATTCTTTTC 59.988 40.741 0.00 0.00 0.00 2.29
3273 6252 3.421844 GAGGTGCCTGGAATTGTAGTTT 58.578 45.455 0.00 0.00 0.00 2.66
3410 6389 2.088423 AGCAGAACAAACACGGAACAA 58.912 42.857 0.00 0.00 0.00 2.83
3430 6409 9.617975 GGAACAAACATTGAAAAATTTTGTCAA 57.382 25.926 15.34 15.34 35.83 3.18
3443 6422 4.536364 TTTTGTCAAGAAGCGAAGAGTG 57.464 40.909 0.00 0.00 0.00 3.51
3446 6425 2.362397 TGTCAAGAAGCGAAGAGTGAGT 59.638 45.455 0.00 0.00 0.00 3.41
3448 6427 4.218635 TGTCAAGAAGCGAAGAGTGAGTAT 59.781 41.667 0.00 0.00 0.00 2.12
3449 6428 4.560819 GTCAAGAAGCGAAGAGTGAGTATG 59.439 45.833 0.00 0.00 0.00 2.39
3451 6430 5.048013 TCAAGAAGCGAAGAGTGAGTATGAA 60.048 40.000 0.00 0.00 0.00 2.57
3452 6431 4.739195 AGAAGCGAAGAGTGAGTATGAAC 58.261 43.478 0.00 0.00 0.00 3.18
3453 6432 3.512033 AGCGAAGAGTGAGTATGAACC 57.488 47.619 0.00 0.00 0.00 3.62
3457 6436 3.119955 CGAAGAGTGAGTATGAACCACGA 60.120 47.826 0.00 0.00 34.13 4.35
3458 6437 4.615223 CGAAGAGTGAGTATGAACCACGAA 60.615 45.833 0.00 0.00 34.13 3.85
3459 6438 4.866508 AGAGTGAGTATGAACCACGAAA 57.133 40.909 0.00 0.00 34.13 3.46
3460 6439 4.557205 AGAGTGAGTATGAACCACGAAAC 58.443 43.478 0.00 0.00 34.13 2.78
3461 6440 3.314553 AGTGAGTATGAACCACGAAACG 58.685 45.455 0.00 0.00 34.13 3.60
3462 6441 3.005050 AGTGAGTATGAACCACGAAACGA 59.995 43.478 0.00 0.00 34.13 3.85
3463 6442 3.924686 GTGAGTATGAACCACGAAACGAT 59.075 43.478 0.00 0.00 0.00 3.73
3464 6443 3.924073 TGAGTATGAACCACGAAACGATG 59.076 43.478 0.00 0.00 0.00 3.84
3465 6444 3.259064 AGTATGAACCACGAAACGATGG 58.741 45.455 0.00 0.00 42.13 3.51
3466 6445 2.465860 ATGAACCACGAAACGATGGA 57.534 45.000 15.26 0.29 39.46 3.41
3467 6446 2.465860 TGAACCACGAAACGATGGAT 57.534 45.000 15.26 7.23 39.46 3.41
3468 6447 2.073056 TGAACCACGAAACGATGGATG 58.927 47.619 15.26 0.00 39.46 3.51
3469 6448 2.289133 TGAACCACGAAACGATGGATGA 60.289 45.455 15.26 1.18 39.46 2.92
3470 6449 2.010145 ACCACGAAACGATGGATGAG 57.990 50.000 15.26 0.00 39.46 2.90
3471 6450 1.548719 ACCACGAAACGATGGATGAGA 59.451 47.619 15.26 0.00 39.46 3.27
4052 7117 7.436376 GCACTTTGTATTTCTTGCTTCTTCTTT 59.564 33.333 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.239879 AAAACCTATGCCGTTGCGTG 59.760 50.000 0.00 0.00 41.78 5.34
1 2 0.239879 CAAAACCTATGCCGTTGCGT 59.760 50.000 0.00 0.00 41.78 5.24
88 89 1.299620 ACGACTTCGACGGTGGTTG 60.300 57.895 5.47 0.00 43.02 3.77
114 115 4.766891 TCCAATTTCCATCAGTTTGGAGTC 59.233 41.667 0.00 0.00 46.22 3.36
123 124 1.328680 CTCGCGTCCAATTTCCATCAG 59.671 52.381 5.77 0.00 0.00 2.90
132 133 3.064987 CTCGACCCTCGCGTCCAAT 62.065 63.158 5.77 0.00 40.21 3.16
157 158 0.036858 TTTGCCGACGATGTCATGGA 60.037 50.000 1.37 0.00 32.09 3.41
163 164 0.670546 CCAGTCTTTGCCGACGATGT 60.671 55.000 0.00 0.00 38.90 3.06
216 217 3.066814 CAGCCTGCCCTTCCTTGC 61.067 66.667 0.00 0.00 0.00 4.01
256 257 3.744530 CGTGAGTGATATTTTCCCCTCCC 60.745 52.174 0.00 0.00 0.00 4.30
258 259 4.138487 ACGTGAGTGATATTTTCCCCTC 57.862 45.455 0.00 0.00 46.97 4.30
291 292 1.821061 CTTGGAGCTCACACCGTCCT 61.821 60.000 17.19 0.00 0.00 3.85
296 297 0.807496 GAATGCTTGGAGCTCACACC 59.193 55.000 17.19 0.00 42.97 4.16
298 299 1.673923 CGAGAATGCTTGGAGCTCACA 60.674 52.381 17.19 8.45 42.97 3.58
310 311 1.523938 GGTGGTAGGGCGAGAATGC 60.524 63.158 0.00 0.00 0.00 3.56
314 315 1.868713 TATTTGGTGGTAGGGCGAGA 58.131 50.000 0.00 0.00 0.00 4.04
349 350 0.695924 TTTCAGGGGCTCCAAATCGA 59.304 50.000 4.79 0.00 34.83 3.59
365 366 5.007136 CCTCCATTGATCGCTAGAGTTTTTC 59.993 44.000 0.00 0.00 0.00 2.29
366 367 4.878397 CCTCCATTGATCGCTAGAGTTTTT 59.122 41.667 0.00 0.00 0.00 1.94
373 374 0.683973 AGGCCTCCATTGATCGCTAG 59.316 55.000 0.00 0.00 0.00 3.42
395 396 3.798889 GCCATTATGACGATCTTGGACGA 60.799 47.826 0.00 0.00 0.00 4.20
405 626 4.932799 CCATAATAACCGCCATTATGACGA 59.067 41.667 16.92 0.00 44.05 4.20
418 639 2.004733 GCCCGTATCGCCATAATAACC 58.995 52.381 0.00 0.00 0.00 2.85
433 654 2.969300 AATCCACACAAACGGCCCGT 62.969 55.000 1.02 1.02 43.97 5.28
484 705 9.265901 CGATCTTCACTTCAGGATAAACATATT 57.734 33.333 0.00 0.00 0.00 1.28
510 731 3.281727 TGGTTGTATCATTGGAGGCTC 57.718 47.619 5.78 5.78 0.00 4.70
526 747 2.851263 TGTATGCGTCCTCTTTGGTT 57.149 45.000 0.00 0.00 37.07 3.67
564 825 1.223487 GATTGCCGAACAGCCCCTA 59.777 57.895 0.00 0.00 0.00 3.53
568 829 0.392461 TAGTGGATTGCCGAACAGCC 60.392 55.000 0.00 0.00 36.79 4.85
569 830 0.727398 GTAGTGGATTGCCGAACAGC 59.273 55.000 0.00 0.00 36.79 4.40
571 832 1.066430 GGAGTAGTGGATTGCCGAACA 60.066 52.381 0.00 0.00 36.79 3.18
572 833 1.653151 GGAGTAGTGGATTGCCGAAC 58.347 55.000 0.00 0.00 36.79 3.95
573 834 0.539986 GGGAGTAGTGGATTGCCGAA 59.460 55.000 0.00 0.00 36.79 4.30
574 835 0.325296 AGGGAGTAGTGGATTGCCGA 60.325 55.000 0.00 0.00 36.79 5.54
575 836 0.179073 CAGGGAGTAGTGGATTGCCG 60.179 60.000 0.00 0.00 36.79 5.69
576 837 1.204146 TCAGGGAGTAGTGGATTGCC 58.796 55.000 0.00 0.00 0.00 4.52
577 838 3.350219 TTTCAGGGAGTAGTGGATTGC 57.650 47.619 0.00 0.00 0.00 3.56
578 839 5.500234 TGAATTTCAGGGAGTAGTGGATTG 58.500 41.667 0.00 0.00 0.00 2.67
579 840 5.779241 TGAATTTCAGGGAGTAGTGGATT 57.221 39.130 0.00 0.00 0.00 3.01
580 841 5.339530 CCTTGAATTTCAGGGAGTAGTGGAT 60.340 44.000 19.97 0.00 45.53 3.41
582 843 4.019321 TCCTTGAATTTCAGGGAGTAGTGG 60.019 45.833 22.47 5.92 46.11 4.00
583 844 5.165961 TCCTTGAATTTCAGGGAGTAGTG 57.834 43.478 22.47 0.36 46.11 2.74
590 851 3.359033 TGCAGATCCTTGAATTTCAGGG 58.641 45.455 18.89 18.89 44.20 4.45
591 852 4.267536 TCTGCAGATCCTTGAATTTCAGG 58.732 43.478 13.74 1.69 0.00 3.86
592 853 4.201930 GCTCTGCAGATCCTTGAATTTCAG 60.202 45.833 18.63 0.90 0.00 3.02
593 854 3.693085 GCTCTGCAGATCCTTGAATTTCA 59.307 43.478 18.63 0.00 0.00 2.69
594 855 3.693085 TGCTCTGCAGATCCTTGAATTTC 59.307 43.478 18.63 0.00 33.32 2.17
595 856 3.442977 GTGCTCTGCAGATCCTTGAATTT 59.557 43.478 18.63 0.00 40.08 1.82
596 857 3.015327 GTGCTCTGCAGATCCTTGAATT 58.985 45.455 18.63 0.00 40.08 2.17
597 858 2.641305 GTGCTCTGCAGATCCTTGAAT 58.359 47.619 18.63 0.00 40.08 2.57
598 859 1.339438 GGTGCTCTGCAGATCCTTGAA 60.339 52.381 18.63 0.00 40.08 2.69
599 860 0.251354 GGTGCTCTGCAGATCCTTGA 59.749 55.000 18.63 0.00 40.08 3.02
600 861 0.252479 AGGTGCTCTGCAGATCCTTG 59.748 55.000 18.63 6.18 40.08 3.61
601 862 0.252479 CAGGTGCTCTGCAGATCCTT 59.748 55.000 23.63 8.71 40.08 3.36
602 863 1.906253 CAGGTGCTCTGCAGATCCT 59.094 57.895 18.63 20.60 40.08 3.24
603 864 4.536316 CAGGTGCTCTGCAGATCC 57.464 61.111 18.63 18.77 40.08 3.36
618 879 2.759973 TACAGAGCGGGGGAGCAG 60.760 66.667 0.00 0.00 40.15 4.24
619 880 3.075005 GTACAGAGCGGGGGAGCA 61.075 66.667 0.00 0.00 40.15 4.26
620 881 1.900545 AAAGTACAGAGCGGGGGAGC 61.901 60.000 0.00 0.00 37.41 4.70
621 882 0.613777 AAAAGTACAGAGCGGGGGAG 59.386 55.000 0.00 0.00 0.00 4.30
622 883 1.061546 AAAAAGTACAGAGCGGGGGA 58.938 50.000 0.00 0.00 0.00 4.81
623 884 2.353323 GTAAAAAGTACAGAGCGGGGG 58.647 52.381 0.00 0.00 0.00 5.40
624 885 2.027469 AGGTAAAAAGTACAGAGCGGGG 60.027 50.000 0.00 0.00 0.00 5.73
625 886 3.329929 AGGTAAAAAGTACAGAGCGGG 57.670 47.619 0.00 0.00 0.00 6.13
626 887 4.312443 TGAAGGTAAAAAGTACAGAGCGG 58.688 43.478 0.00 0.00 0.00 5.52
627 888 6.147164 TGAATGAAGGTAAAAAGTACAGAGCG 59.853 38.462 0.00 0.00 0.00 5.03
628 889 7.435068 TGAATGAAGGTAAAAAGTACAGAGC 57.565 36.000 0.00 0.00 0.00 4.09
629 890 9.057089 AGTTGAATGAAGGTAAAAAGTACAGAG 57.943 33.333 0.00 0.00 0.00 3.35
630 891 8.974060 AGTTGAATGAAGGTAAAAAGTACAGA 57.026 30.769 0.00 0.00 0.00 3.41
631 892 8.290325 GGAGTTGAATGAAGGTAAAAAGTACAG 58.710 37.037 0.00 0.00 0.00 2.74
632 893 7.041644 CGGAGTTGAATGAAGGTAAAAAGTACA 60.042 37.037 0.00 0.00 0.00 2.90
633 894 7.295930 CGGAGTTGAATGAAGGTAAAAAGTAC 58.704 38.462 0.00 0.00 0.00 2.73
634 895 6.072893 GCGGAGTTGAATGAAGGTAAAAAGTA 60.073 38.462 0.00 0.00 0.00 2.24
635 896 5.278315 GCGGAGTTGAATGAAGGTAAAAAGT 60.278 40.000 0.00 0.00 0.00 2.66
636 897 5.154222 GCGGAGTTGAATGAAGGTAAAAAG 58.846 41.667 0.00 0.00 0.00 2.27
637 898 4.022676 GGCGGAGTTGAATGAAGGTAAAAA 60.023 41.667 0.00 0.00 0.00 1.94
638 899 3.504520 GGCGGAGTTGAATGAAGGTAAAA 59.495 43.478 0.00 0.00 0.00 1.52
639 900 3.078837 GGCGGAGTTGAATGAAGGTAAA 58.921 45.455 0.00 0.00 0.00 2.01
640 901 2.039216 TGGCGGAGTTGAATGAAGGTAA 59.961 45.455 0.00 0.00 0.00 2.85
641 902 1.626321 TGGCGGAGTTGAATGAAGGTA 59.374 47.619 0.00 0.00 0.00 3.08
642 903 0.400213 TGGCGGAGTTGAATGAAGGT 59.600 50.000 0.00 0.00 0.00 3.50
643 904 1.089920 CTGGCGGAGTTGAATGAAGG 58.910 55.000 0.00 0.00 0.00 3.46
644 905 0.449388 GCTGGCGGAGTTGAATGAAG 59.551 55.000 0.00 0.00 0.00 3.02
645 906 0.036732 AGCTGGCGGAGTTGAATGAA 59.963 50.000 0.00 0.00 0.00 2.57
646 907 0.391661 GAGCTGGCGGAGTTGAATGA 60.392 55.000 0.00 0.00 0.00 2.57
647 908 1.372087 GGAGCTGGCGGAGTTGAATG 61.372 60.000 0.00 0.00 0.00 2.67
648 909 1.078143 GGAGCTGGCGGAGTTGAAT 60.078 57.895 0.00 0.00 0.00 2.57
649 910 2.347490 GGAGCTGGCGGAGTTGAA 59.653 61.111 0.00 0.00 0.00 2.69
650 911 4.069232 CGGAGCTGGCGGAGTTGA 62.069 66.667 0.00 0.00 0.00 3.18
667 928 3.535962 CTCCAGGCTCTCGCTCCC 61.536 72.222 0.00 0.00 36.09 4.30
668 929 2.757917 ACTCCAGGCTCTCGCTCC 60.758 66.667 0.00 0.00 36.09 4.70
669 930 2.804856 GACTCCAGGCTCTCGCTC 59.195 66.667 0.00 0.00 36.09 5.03
670 931 3.137459 CGACTCCAGGCTCTCGCT 61.137 66.667 0.00 0.00 36.09 4.93
671 932 4.200283 CCGACTCCAGGCTCTCGC 62.200 72.222 0.00 0.00 0.00 5.03
672 933 2.438614 TCCGACTCCAGGCTCTCG 60.439 66.667 0.00 0.00 0.00 4.04
673 934 2.781158 GCTCCGACTCCAGGCTCTC 61.781 68.421 0.00 0.00 0.00 3.20
674 935 2.757917 GCTCCGACTCCAGGCTCT 60.758 66.667 0.00 0.00 0.00 4.09
675 936 3.844090 GGCTCCGACTCCAGGCTC 61.844 72.222 0.00 0.00 32.47 4.70
676 937 4.390556 AGGCTCCGACTCCAGGCT 62.391 66.667 0.00 0.00 40.58 4.58
677 938 3.844090 GAGGCTCCGACTCCAGGC 61.844 72.222 2.15 0.00 30.04 4.85
678 939 3.522731 CGAGGCTCCGACTCCAGG 61.523 72.222 9.32 0.00 33.37 4.45
679 940 3.522731 CCGAGGCTCCGACTCCAG 61.523 72.222 9.32 0.00 33.37 3.86
680 941 3.997400 CTCCGAGGCTCCGACTCCA 62.997 68.421 9.32 0.00 33.37 3.86
681 942 3.213402 CTCCGAGGCTCCGACTCC 61.213 72.222 9.32 0.00 33.37 3.85
682 943 3.213402 CCTCCGAGGCTCCGACTC 61.213 72.222 9.32 0.00 33.67 3.36
683 944 4.824515 CCCTCCGAGGCTCCGACT 62.825 72.222 9.17 0.00 32.73 4.18
684 945 4.816984 TCCCTCCGAGGCTCCGAC 62.817 72.222 9.17 0.00 32.73 4.79
685 946 3.822035 ATCCCTCCGAGGCTCCGA 61.822 66.667 9.17 7.18 32.73 4.55
686 947 3.610669 CATCCCTCCGAGGCTCCG 61.611 72.222 9.17 2.21 32.73 4.63
687 948 3.934962 GCATCCCTCCGAGGCTCC 61.935 72.222 9.17 0.00 44.95 4.70
695 956 2.190578 CCTGTTCGGCATCCCTCC 59.809 66.667 0.00 0.00 0.00 4.30
704 965 2.957006 ACAGTACTATAGGCCTGTTCGG 59.043 50.000 17.99 6.23 34.64 4.30
705 966 3.630769 TCACAGTACTATAGGCCTGTTCG 59.369 47.826 17.99 6.22 36.06 3.95
706 967 5.793030 ATCACAGTACTATAGGCCTGTTC 57.207 43.478 17.99 2.52 36.06 3.18
707 968 5.900123 AGAATCACAGTACTATAGGCCTGTT 59.100 40.000 17.99 5.24 36.06 3.16
708 969 5.303078 CAGAATCACAGTACTATAGGCCTGT 59.697 44.000 17.99 12.48 38.64 4.00
709 970 5.777802 CAGAATCACAGTACTATAGGCCTG 58.222 45.833 17.99 15.54 0.00 4.85
710 971 4.282195 GCAGAATCACAGTACTATAGGCCT 59.718 45.833 11.78 11.78 0.00 5.19
711 972 4.282195 AGCAGAATCACAGTACTATAGGCC 59.718 45.833 4.43 0.00 0.00 5.19
712 973 5.461032 AGCAGAATCACAGTACTATAGGC 57.539 43.478 4.43 0.00 0.00 3.93
713 974 5.335269 CGGAGCAGAATCACAGTACTATAGG 60.335 48.000 4.43 0.00 0.00 2.57
714 975 5.239744 ACGGAGCAGAATCACAGTACTATAG 59.760 44.000 0.00 0.00 0.00 1.31
715 976 5.131067 ACGGAGCAGAATCACAGTACTATA 58.869 41.667 0.00 0.00 0.00 1.31
716 977 3.954904 ACGGAGCAGAATCACAGTACTAT 59.045 43.478 0.00 0.00 0.00 2.12
717 978 3.353557 ACGGAGCAGAATCACAGTACTA 58.646 45.455 0.00 0.00 0.00 1.82
718 979 2.171840 ACGGAGCAGAATCACAGTACT 58.828 47.619 0.00 0.00 0.00 2.73
719 980 2.656560 ACGGAGCAGAATCACAGTAC 57.343 50.000 0.00 0.00 0.00 2.73
720 981 2.096980 CGTACGGAGCAGAATCACAGTA 59.903 50.000 7.57 0.00 0.00 2.74
721 982 1.135373 CGTACGGAGCAGAATCACAGT 60.135 52.381 7.57 0.00 0.00 3.55
722 983 1.550065 CGTACGGAGCAGAATCACAG 58.450 55.000 7.57 0.00 0.00 3.66
723 984 0.457853 GCGTACGGAGCAGAATCACA 60.458 55.000 18.39 0.00 34.19 3.58
724 985 0.179134 AGCGTACGGAGCAGAATCAC 60.179 55.000 18.39 0.00 37.01 3.06
725 986 0.100682 GAGCGTACGGAGCAGAATCA 59.899 55.000 18.39 0.00 37.01 2.57
775 1036 7.593273 GTGTCCGTGAACAATTCATCAATAAAA 59.407 33.333 0.00 0.00 42.47 1.52
805 1066 1.607148 GCCAAGTTGGTCGCTAGTTTT 59.393 47.619 22.85 0.00 40.46 2.43
829 1090 3.777925 CGGGCAGTCGTTCGCTTG 61.778 66.667 0.00 0.00 0.00 4.01
1249 1511 4.740235 GGAAGGAAGATCCGCTCG 57.260 61.111 0.00 0.00 42.75 5.03
1345 1627 1.541588 CCAGTAAAAACAGAGGCAGGC 59.458 52.381 0.00 0.00 0.00 4.85
1373 1655 0.387622 CCAATGCTGTCGCCAACTTG 60.388 55.000 0.00 0.00 34.43 3.16
1381 1663 4.560427 CGATATATCAGACCAATGCTGTCG 59.440 45.833 13.11 0.00 37.80 4.35
1421 1703 4.424566 CCACACGCCCAAGCATGC 62.425 66.667 10.51 10.51 34.95 4.06
1467 1749 7.976175 GCGAGTGATTGATACCATTATCATAGA 59.024 37.037 0.00 0.00 43.02 1.98
1468 1750 7.761249 TGCGAGTGATTGATACCATTATCATAG 59.239 37.037 0.00 0.00 43.02 2.23
1469 1751 7.545615 GTGCGAGTGATTGATACCATTATCATA 59.454 37.037 0.00 0.00 43.02 2.15
1470 1752 6.369890 GTGCGAGTGATTGATACCATTATCAT 59.630 38.462 0.00 0.00 43.02 2.45
1471 1753 5.696270 GTGCGAGTGATTGATACCATTATCA 59.304 40.000 0.00 0.00 42.05 2.15
1472 1754 5.928839 AGTGCGAGTGATTGATACCATTATC 59.071 40.000 0.00 0.00 35.51 1.75
1473 1755 5.698089 CAGTGCGAGTGATTGATACCATTAT 59.302 40.000 0.00 0.00 0.00 1.28
1474 1756 5.049828 CAGTGCGAGTGATTGATACCATTA 58.950 41.667 0.00 0.00 0.00 1.90
1475 1757 3.873361 CAGTGCGAGTGATTGATACCATT 59.127 43.478 0.00 0.00 0.00 3.16
1476 1758 3.118629 ACAGTGCGAGTGATTGATACCAT 60.119 43.478 0.00 0.00 0.00 3.55
1477 1759 2.233676 ACAGTGCGAGTGATTGATACCA 59.766 45.455 0.00 0.00 0.00 3.25
1478 1760 2.893637 ACAGTGCGAGTGATTGATACC 58.106 47.619 0.00 0.00 0.00 2.73
1479 1761 3.679980 ACAACAGTGCGAGTGATTGATAC 59.320 43.478 0.00 0.00 0.00 2.24
1504 1797 1.075374 CACAGGAATCAAACTCCCCCA 59.925 52.381 0.00 0.00 32.95 4.96
1511 1804 1.606668 TGGCGTTCACAGGAATCAAAC 59.393 47.619 0.00 0.00 35.05 2.93
1544 1837 1.331214 AGGTTGCACCAACAATCTGG 58.669 50.000 9.93 0.00 45.11 3.86
1566 1859 0.039074 ACAGAACTTCTCGCGTCAGG 60.039 55.000 5.77 0.00 0.00 3.86
1574 1867 5.297547 TGTGTCCACATTACAGAACTTCTC 58.702 41.667 0.00 0.00 36.21 2.87
1599 1892 7.763528 CAGCATTCAGACTCTCAAATAACTACT 59.236 37.037 0.00 0.00 0.00 2.57
1606 1899 4.008330 CACCAGCATTCAGACTCTCAAAT 58.992 43.478 0.00 0.00 0.00 2.32
1614 1915 6.595716 AGAGTTATTAACACCAGCATTCAGAC 59.404 38.462 9.15 0.00 0.00 3.51
1723 2121 7.013750 ACGCTCTATCCACATATATCCACATAG 59.986 40.741 0.00 0.00 0.00 2.23
1724 2122 6.833933 ACGCTCTATCCACATATATCCACATA 59.166 38.462 0.00 0.00 0.00 2.29
1734 2136 2.032924 CGACACACGCTCTATCCACATA 59.967 50.000 0.00 0.00 34.51 2.29
1737 2139 2.945315 CGACACACGCTCTATCCAC 58.055 57.895 0.00 0.00 34.51 4.02
1747 2149 1.320555 CTATTTCCTTCGCGACACACG 59.679 52.381 9.15 0.00 45.66 4.49
1748 2150 2.602878 TCTATTTCCTTCGCGACACAC 58.397 47.619 9.15 0.00 0.00 3.82
1861 2263 2.887152 ACAGAAGAGGACATGGCAAAAC 59.113 45.455 0.00 0.00 0.00 2.43
1908 2310 5.860182 CCAGAGCGCATCCAAATTTATAATG 59.140 40.000 11.47 0.00 0.00 1.90
1971 2428 4.379708 GCAATCACACTCACACAATGCATA 60.380 41.667 0.00 0.00 0.00 3.14
1974 2431 2.030540 AGCAATCACACTCACACAATGC 60.031 45.455 0.00 0.00 0.00 3.56
2021 2478 1.686355 ACGATGGTTTGCCTGAACAA 58.314 45.000 0.00 0.00 35.27 2.83
2192 2649 7.621991 CACTATGGAAAGCTGTTAATAACTCG 58.378 38.462 4.67 0.00 0.00 4.18
2215 2672 5.297029 GGGTTTCTAGTTCTTCCATATGCAC 59.703 44.000 0.00 0.00 0.00 4.57
2233 2690 5.406477 GCAGATTCTTGAATTGTTGGGTTTC 59.594 40.000 0.00 0.00 0.00 2.78
2506 5207 8.272866 CCATTTCATTAAAAGTGAAAACGTTCC 58.727 33.333 0.00 0.00 45.50 3.62
2507 5208 7.792048 GCCATTTCATTAAAAGTGAAAACGTTC 59.208 33.333 0.00 0.00 45.50 3.95
2510 5211 7.042791 ACAGCCATTTCATTAAAAGTGAAAACG 60.043 33.333 6.77 2.80 45.50 3.60
2554 5414 2.689771 AATACCCCGGTCGGCCTT 60.690 61.111 3.66 0.00 0.00 4.35
2655 5543 5.080969 ACTAGCAGTAATGTTTTCCGCTA 57.919 39.130 0.00 0.00 0.00 4.26
2657 5545 5.789710 TTACTAGCAGTAATGTTTTCCGC 57.210 39.130 5.10 0.00 35.89 5.54
2667 5555 6.014925 TCCACAACACAGATTACTAGCAGTAA 60.015 38.462 10.01 10.01 43.95 2.24
2668 5556 5.479027 TCCACAACACAGATTACTAGCAGTA 59.521 40.000 0.00 0.00 0.00 2.74
2669 5557 4.283467 TCCACAACACAGATTACTAGCAGT 59.717 41.667 0.00 0.00 0.00 4.40
2670 5558 4.820897 TCCACAACACAGATTACTAGCAG 58.179 43.478 0.00 0.00 0.00 4.24
2737 5666 6.652481 CCCTTGATATGTAAGTGCAGGATAAG 59.348 42.308 0.00 0.00 0.00 1.73
2761 5690 3.243068 ACTGTCAGCGATTTGTTTTGTCC 60.243 43.478 0.00 0.00 0.00 4.02
2822 5762 3.118702 AGGAGTTGATCATCTCTGCACAG 60.119 47.826 25.67 0.00 0.00 3.66
2843 5784 5.759273 TCCTGCCATTTTCAAACATGAAAAG 59.241 36.000 18.22 9.64 46.64 2.27
2873 5816 2.236395 TCGAGTTCCTCCATCTTTTCCC 59.764 50.000 0.00 0.00 0.00 3.97
2877 5820 2.763448 CCTCTCGAGTTCCTCCATCTTT 59.237 50.000 13.13 0.00 0.00 2.52
2889 5832 1.633774 TCTGCTTTTCCCTCTCGAGT 58.366 50.000 13.13 0.00 0.00 4.18
2928 5871 4.083862 GTCACCCGCTCCACCTCC 62.084 72.222 0.00 0.00 0.00 4.30
3078 6035 2.098117 GGAATCATTCAAGGAACTGCCG 59.902 50.000 0.00 0.00 40.86 5.69
3126 6088 0.383002 CACAACACGCGCTACACAAG 60.383 55.000 5.73 0.00 0.00 3.16
3187 6149 8.263640 AGAAAAGAATATATCATCCTCCATCGG 58.736 37.037 0.00 0.00 0.00 4.18
3224 6195 6.146760 ACTACCAGGAACATATCATCCTCTT 58.853 40.000 0.00 0.00 44.26 2.85
3410 6389 7.904461 CGCTTCTTGACAAAATTTTTCAATGTT 59.096 29.630 19.54 0.00 0.00 2.71
3430 6409 4.381079 GGTTCATACTCACTCTTCGCTTCT 60.381 45.833 0.00 0.00 0.00 2.85
3443 6422 3.306166 CCATCGTTTCGTGGTTCATACTC 59.694 47.826 0.00 0.00 0.00 2.59
3446 6425 3.596310 TCCATCGTTTCGTGGTTCATA 57.404 42.857 9.24 0.00 36.84 2.15
3448 6427 2.073056 CATCCATCGTTTCGTGGTTCA 58.927 47.619 9.24 0.00 36.84 3.18
3449 6428 2.343101 TCATCCATCGTTTCGTGGTTC 58.657 47.619 9.24 0.00 36.84 3.62
3451 6430 1.548719 TCTCATCCATCGTTTCGTGGT 59.451 47.619 9.24 0.00 36.84 4.16
3452 6431 1.927174 GTCTCATCCATCGTTTCGTGG 59.073 52.381 0.00 0.00 36.82 4.94
3453 6432 2.881074 AGTCTCATCCATCGTTTCGTG 58.119 47.619 0.00 0.00 0.00 4.35
4006 7000 8.507524 AAGTGCTTTCTTTAGTTTAGTTGAGT 57.492 30.769 0.00 0.00 0.00 3.41
4007 7001 9.226345 CAAAGTGCTTTCTTTAGTTTAGTTGAG 57.774 33.333 0.00 0.00 36.12 3.02
4009 7003 8.911247 ACAAAGTGCTTTCTTTAGTTTAGTTG 57.089 30.769 0.00 0.00 36.12 3.16


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

AutoCloner maintained by Alex Coulton.