Multiple sequence alignment - TraesCS3D01G209400

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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 TraesCS3D01G209400 chr3D 100.000 5586 0 0 1 5586 276755280 276749695 0.000000e+00 10316.0
1 TraesCS3D01G209400 chr3B 88.904 2848 126 69 2837 5586 373620309 373623064 0.000000e+00 3334.0
2 TraesCS3D01G209400 chr3B 95.089 733 30 1 1229 1955 373614276 373615008 0.000000e+00 1149.0
3 TraesCS3D01G209400 chr3B 94.050 605 22 5 1 594 373612874 373613475 0.000000e+00 905.0
4 TraesCS3D01G209400 chr3B 92.308 351 16 4 2133 2480 373619642 373619984 6.500000e-134 488.0
5 TraesCS3D01G209400 chr3B 90.823 316 21 6 861 1171 373613837 373614149 3.110000e-112 416.0
6 TraesCS3D01G209400 chr3B 90.204 245 14 4 581 820 373613500 373613739 1.510000e-80 311.0
7 TraesCS3D01G209400 chr3B 95.897 195 2 2 2653 2841 373620021 373620215 1.510000e-80 311.0
8 TraesCS3D01G209400 chr3B 100.000 42 0 0 2506 2547 373619988 373620029 1.670000e-10 78.7
9 TraesCS3D01G209400 chr3A 90.069 2477 125 37 1 2406 362896561 362898987 0.000000e+00 3099.0
10 TraesCS3D01G209400 chr3A 92.336 1879 70 26 3146 4987 362899844 362901685 0.000000e+00 2604.0
11 TraesCS3D01G209400 chr3A 91.993 612 15 7 5004 5583 362901671 362902280 0.000000e+00 828.0
12 TraesCS3D01G209400 chr3A 91.876 517 20 8 2653 3147 362899167 362899683 0.000000e+00 702.0
13 TraesCS3D01G209400 chr3A 86.420 162 6 2 2401 2547 362899015 362899175 4.480000e-36 163.0
14 TraesCS3D01G209400 chr5B 90.526 95 9 0 2547 2641 666859733 666859827 5.870000e-25 126.0
15 TraesCS3D01G209400 chr5A 89.362 94 10 0 2560 2653 661660543 661660450 9.830000e-23 119.0


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 TraesCS3D01G209400 chr3D 276749695 276755280 5585 True 10316.000 10316 100.00000 1 5586 1 chr3D.!!$R1 5585
1 TraesCS3D01G209400 chr3B 373619642 373623064 3422 False 1052.925 3334 94.27725 2133 5586 4 chr3B.!!$F2 3453
2 TraesCS3D01G209400 chr3B 373612874 373615008 2134 False 695.250 1149 92.54150 1 1955 4 chr3B.!!$F1 1954
3 TraesCS3D01G209400 chr3A 362896561 362902280 5719 False 1479.200 3099 90.53880 1 5583 5 chr3A.!!$F1 5582

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
475 489 2.187424 CTCTCCTCTGCTGCAGCC 59.813 66.667 34.64 17.82 41.18 4.85 F
1323 1550 1.800805 AAGACATCACGCCAGTCAAG 58.199 50.000 0.00 0.00 34.80 3.02 F
2503 2785 0.252479 TTACTATTTCGGCGGCCCAA 59.748 50.000 14.55 3.64 0.00 4.12 F
2559 2856 0.035820 TTATTTTGGACGCGGCTCCT 60.036 50.000 13.91 0.00 0.00 3.69 F
3335 3940 0.249953 TGCTTGCAATTTGGCAGTGG 60.250 50.000 6.97 0.00 45.88 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1443 1671 2.061773 GTCAGGTTGATGTCAGTGTCG 58.938 52.381 0.00 0.0 0.00 4.35 R
2541 2838 0.461339 GAGGAGCCGCGTCCAAAATA 60.461 55.000 17.08 0.0 39.34 1.40 R
3555 4178 0.174617 GGAGACAGAAGGAAGCCGAG 59.825 60.000 0.00 0.0 0.00 4.63 R
3945 4580 4.227197 TGTCCTTCTCTCCTTGTTCTTCT 58.773 43.478 0.00 0.0 0.00 2.85 R
5077 5746 2.337359 AGGTGAACCCTGGCTAAGTA 57.663 50.000 0.00 0.0 44.08 2.24 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
187 193 3.678072 ACATAAACGTGTTCATCACTCGG 59.322 43.478 0.00 0.00 44.91 4.63
475 489 2.187424 CTCTCCTCTGCTGCAGCC 59.813 66.667 34.64 17.82 41.18 4.85
506 520 3.887621 TTCTCATCGTACCCAGGAAAG 57.112 47.619 0.00 0.00 0.00 2.62
522 536 7.013834 CCCAGGAAAGTAGGTAAGATATCTCT 58.986 42.308 5.51 1.63 0.00 3.10
524 538 8.364142 CCAGGAAAGTAGGTAAGATATCTCTTG 58.636 40.741 5.51 0.00 41.83 3.02
527 541 8.085909 GGAAAGTAGGTAAGATATCTCTTGCTC 58.914 40.741 5.51 0.26 42.04 4.26
532 546 6.010219 AGGTAAGATATCTCTTGCTCTCCTC 58.990 44.000 5.51 0.00 42.04 3.71
533 547 5.185056 GGTAAGATATCTCTTGCTCTCCTCC 59.815 48.000 5.51 0.00 42.04 4.30
545 559 5.053978 TGCTCTCCTCCTTTCTTTTTCTT 57.946 39.130 0.00 0.00 0.00 2.52
546 560 5.449553 TGCTCTCCTCCTTTCTTTTTCTTT 58.550 37.500 0.00 0.00 0.00 2.52
579 593 3.679639 GCGCCTTTTGGAATGATTGGATT 60.680 43.478 0.00 0.00 44.07 3.01
624 676 5.007724 GTGGTTAGATGGACGGATCATTTTC 59.992 44.000 0.00 0.00 0.00 2.29
625 677 5.104527 TGGTTAGATGGACGGATCATTTTCT 60.105 40.000 0.00 0.00 0.00 2.52
626 678 5.823045 GGTTAGATGGACGGATCATTTTCTT 59.177 40.000 0.00 0.00 0.00 2.52
627 679 6.318900 GGTTAGATGGACGGATCATTTTCTTT 59.681 38.462 0.00 0.00 0.00 2.52
628 680 7.148069 GGTTAGATGGACGGATCATTTTCTTTT 60.148 37.037 0.00 0.00 0.00 2.27
629 681 6.442513 AGATGGACGGATCATTTTCTTTTC 57.557 37.500 0.00 0.00 0.00 2.29
636 688 7.038154 ACGGATCATTTTCTTTTCTGTTTGA 57.962 32.000 0.00 0.00 0.00 2.69
684 745 2.430704 TTTGCTTGGGCCCCTCTCTG 62.431 60.000 22.27 3.79 37.74 3.35
733 797 4.013728 GGTTGGTACATGAGGCAATACAA 58.986 43.478 0.00 0.00 39.30 2.41
804 885 4.039730 TGAGCCAGCTATTACAAGGAGATC 59.960 45.833 0.00 0.00 0.00 2.75
852 1007 3.550437 AGGCACGAGCTATTCAGAATT 57.450 42.857 4.48 0.00 41.70 2.17
853 1008 4.672587 AGGCACGAGCTATTCAGAATTA 57.327 40.909 4.48 0.00 41.70 1.40
854 1009 4.626042 AGGCACGAGCTATTCAGAATTAG 58.374 43.478 4.48 0.00 41.70 1.73
855 1010 4.342378 AGGCACGAGCTATTCAGAATTAGA 59.658 41.667 4.48 0.00 41.70 2.10
856 1011 5.011533 AGGCACGAGCTATTCAGAATTAGAT 59.988 40.000 4.48 0.00 41.70 1.98
857 1012 5.347364 GGCACGAGCTATTCAGAATTAGATC 59.653 44.000 4.48 4.75 41.70 2.75
858 1013 5.347364 GCACGAGCTATTCAGAATTAGATCC 59.653 44.000 0.00 0.00 37.91 3.36
859 1014 5.570973 CACGAGCTATTCAGAATTAGATCCG 59.429 44.000 0.00 1.66 0.00 4.18
860 1015 5.473846 ACGAGCTATTCAGAATTAGATCCGA 59.526 40.000 0.00 0.00 0.00 4.55
861 1016 6.151985 ACGAGCTATTCAGAATTAGATCCGAT 59.848 38.462 0.00 0.00 0.00 4.18
862 1017 6.471841 CGAGCTATTCAGAATTAGATCCGATG 59.528 42.308 0.00 0.00 0.00 3.84
863 1018 6.105333 AGCTATTCAGAATTAGATCCGATGC 58.895 40.000 0.00 0.00 0.00 3.91
864 1019 5.871524 GCTATTCAGAATTAGATCCGATGCA 59.128 40.000 0.00 0.00 0.00 3.96
865 1020 6.369890 GCTATTCAGAATTAGATCCGATGCAA 59.630 38.462 0.00 0.00 0.00 4.08
866 1021 5.991328 TTCAGAATTAGATCCGATGCAAC 57.009 39.130 0.00 0.00 0.00 4.17
867 1022 5.022282 TCAGAATTAGATCCGATGCAACA 57.978 39.130 0.00 0.00 0.00 3.33
868 1023 5.427378 TCAGAATTAGATCCGATGCAACAA 58.573 37.500 0.00 0.00 0.00 2.83
869 1024 5.294306 TCAGAATTAGATCCGATGCAACAAC 59.706 40.000 0.00 0.00 0.00 3.32
890 1045 6.149474 ACAACAATGGACTAGCAAATCAGTAC 59.851 38.462 0.00 0.00 0.00 2.73
891 1046 5.804639 ACAATGGACTAGCAAATCAGTACA 58.195 37.500 0.00 0.00 39.88 2.90
893 1048 6.714810 ACAATGGACTAGCAAATCAGTACAAA 59.285 34.615 0.00 0.00 39.05 2.83
894 1049 7.394359 ACAATGGACTAGCAAATCAGTACAAAT 59.606 33.333 0.00 0.00 39.05 2.32
895 1050 7.944729 ATGGACTAGCAAATCAGTACAAATT 57.055 32.000 0.00 0.00 39.05 1.82
897 1052 8.492673 TGGACTAGCAAATCAGTACAAATTAG 57.507 34.615 0.00 0.00 32.60 1.73
898 1053 7.065803 TGGACTAGCAAATCAGTACAAATTAGC 59.934 37.037 0.00 0.00 32.60 3.09
900 1055 8.511604 ACTAGCAAATCAGTACAAATTAGCAT 57.488 30.769 0.00 0.00 0.00 3.79
902 1057 9.793252 CTAGCAAATCAGTACAAATTAGCATTT 57.207 29.630 0.00 0.00 32.36 2.32
904 1059 9.573133 AGCAAATCAGTACAAATTAGCATTTAC 57.427 29.630 0.00 0.00 30.90 2.01
905 1060 9.352784 GCAAATCAGTACAAATTAGCATTTACA 57.647 29.630 0.00 0.00 30.90 2.41
957 1115 7.639850 CGGTATGTTGTTTTATACATGCTCTTG 59.360 37.037 0.00 0.00 37.47 3.02
970 1128 3.838244 TGCTCTTGTCTACACCAACTT 57.162 42.857 0.00 0.00 0.00 2.66
978 1136 4.771903 TGTCTACACCAACTTTTGCAGTA 58.228 39.130 0.00 0.00 32.94 2.74
1183 1374 6.861055 GTCATTTCGTTTCAAGAATGCCTTTA 59.139 34.615 0.00 0.00 31.42 1.85
1184 1375 7.381139 GTCATTTCGTTTCAAGAATGCCTTTAA 59.619 33.333 0.00 0.00 31.42 1.52
1233 1424 5.481824 TCTCAGCTCTTGAACCTTTCATAGA 59.518 40.000 0.00 3.36 39.84 1.98
1243 1470 9.495572 CTTGAACCTTTCATAGAAGTAGAGTTT 57.504 33.333 0.00 0.00 39.84 2.66
1308 1535 4.455877 CCCATGGTCAGTTCAGTAAAAGAC 59.544 45.833 11.73 0.00 0.00 3.01
1312 1539 5.924356 TGGTCAGTTCAGTAAAAGACATCA 58.076 37.500 0.00 0.00 0.00 3.07
1315 1542 4.447724 TCAGTTCAGTAAAAGACATCACGC 59.552 41.667 0.00 0.00 0.00 5.34
1316 1543 3.746492 AGTTCAGTAAAAGACATCACGCC 59.254 43.478 0.00 0.00 0.00 5.68
1323 1550 1.800805 AAGACATCACGCCAGTCAAG 58.199 50.000 0.00 0.00 34.80 3.02
1443 1671 4.590850 AGGCCAGAAGAACAACATTTTC 57.409 40.909 5.01 0.00 0.00 2.29
1593 1821 2.971330 TGCACATTTCTCCCAAATTGGT 59.029 40.909 11.52 0.00 35.17 3.67
1597 1825 5.367302 CACATTTCTCCCAAATTGGTTGTT 58.633 37.500 11.52 0.00 35.17 2.83
1631 1859 6.071051 TGACAGACAGTTGGCTATATGTAACA 60.071 38.462 0.00 0.00 0.00 2.41
1821 2055 3.707793 GCTCGAAGGAACTAGGTACATG 58.292 50.000 0.00 0.00 38.49 3.21
1867 2101 4.279922 ACTTGAAACGAAAATTTCCGGGAT 59.720 37.500 0.00 0.00 37.72 3.85
1925 2159 5.885352 TCACCTTCTGTTGATTCTGTTTGAA 59.115 36.000 0.00 0.00 39.24 2.69
2043 2278 3.579335 AACTGAGAGAGACGTTTAGGC 57.421 47.619 0.00 0.00 0.00 3.93
2053 2288 5.790593 AGAGACGTTTAGGCAAAATACAGA 58.209 37.500 0.00 0.00 0.00 3.41
2088 2323 3.382083 TCACTCAGGAGGCAGTACATA 57.618 47.619 0.83 0.00 0.00 2.29
2126 2361 5.710513 TGCAAAAGTAGATGCTTGAACAT 57.289 34.783 0.00 0.00 42.97 2.71
2127 2362 6.816134 TGCAAAAGTAGATGCTTGAACATA 57.184 33.333 0.00 0.00 42.97 2.29
2128 2363 6.611381 TGCAAAAGTAGATGCTTGAACATAC 58.389 36.000 0.00 0.00 42.97 2.39
2146 2381 6.974932 ACATACTAGATGTTTGCTTCACTG 57.025 37.500 0.00 0.00 32.05 3.66
2176 2412 6.995511 TTCTTAAGCATAAAACGCATAGGT 57.004 33.333 0.00 0.00 0.00 3.08
2208 2446 3.712091 AACGCTAGTCTGTGTATAGGC 57.288 47.619 0.00 0.00 0.00 3.93
2213 2451 3.058777 GCTAGTCTGTGTATAGGCGAGAC 60.059 52.174 0.00 0.00 34.47 3.36
2223 2461 2.981859 TAGGCGAGACATCCTTTTCC 57.018 50.000 0.00 0.00 34.02 3.13
2228 2466 2.795470 GCGAGACATCCTTTTCCGATAC 59.205 50.000 0.00 0.00 0.00 2.24
2261 2499 3.242870 GGAAATCAACGAGGCATGTGATC 60.243 47.826 0.00 0.00 0.00 2.92
2502 2784 0.462403 GTTACTATTTCGGCGGCCCA 60.462 55.000 14.55 0.00 0.00 5.36
2503 2785 0.252479 TTACTATTTCGGCGGCCCAA 59.748 50.000 14.55 3.64 0.00 4.12
2541 2838 9.899226 GAGTTTAGTTTTGAGCATTTCATAGTT 57.101 29.630 0.00 0.00 35.27 2.24
2550 2847 9.638239 TTTGAGCATTTCATAGTTATTTTGGAC 57.362 29.630 0.00 0.00 35.27 4.02
2551 2848 7.471721 TGAGCATTTCATAGTTATTTTGGACG 58.528 34.615 0.00 0.00 0.00 4.79
2552 2849 6.265577 AGCATTTCATAGTTATTTTGGACGC 58.734 36.000 0.00 0.00 0.00 5.19
2553 2850 5.171337 GCATTTCATAGTTATTTTGGACGCG 59.829 40.000 3.53 3.53 0.00 6.01
2554 2851 4.868450 TTCATAGTTATTTTGGACGCGG 57.132 40.909 12.47 0.00 0.00 6.46
2555 2852 2.610374 TCATAGTTATTTTGGACGCGGC 59.390 45.455 12.47 7.53 0.00 6.53
2556 2853 2.389962 TAGTTATTTTGGACGCGGCT 57.610 45.000 13.91 0.00 0.00 5.52
2557 2854 1.084289 AGTTATTTTGGACGCGGCTC 58.916 50.000 13.91 1.82 0.00 4.70
2558 2855 0.098200 GTTATTTTGGACGCGGCTCC 59.902 55.000 13.91 10.88 0.00 4.70
2559 2856 0.035820 TTATTTTGGACGCGGCTCCT 60.036 50.000 13.91 0.00 0.00 3.69
2560 2857 0.461339 TATTTTGGACGCGGCTCCTC 60.461 55.000 13.91 0.00 0.00 3.71
2561 2858 2.185310 ATTTTGGACGCGGCTCCTCT 62.185 55.000 13.91 0.00 0.00 3.69
2562 2859 3.589654 TTTGGACGCGGCTCCTCTG 62.590 63.158 13.91 0.00 0.00 3.35
2564 2861 4.500116 GGACGCGGCTCCTCTGAC 62.500 72.222 13.91 0.00 0.00 3.51
2565 2862 4.838486 GACGCGGCTCCTCTGACG 62.838 72.222 12.47 0.00 42.16 4.35
2569 2866 4.803426 CGGCTCCTCTGACGTGCC 62.803 72.222 0.00 8.95 40.14 5.01
2570 2867 4.803426 GGCTCCTCTGACGTGCCG 62.803 72.222 0.00 0.00 33.96 5.69
2571 2868 4.057428 GCTCCTCTGACGTGCCGT 62.057 66.667 0.00 0.00 45.10 5.68
2572 2869 2.126307 CTCCTCTGACGTGCCGTG 60.126 66.667 4.94 0.00 41.37 4.94
2573 2870 2.596338 TCCTCTGACGTGCCGTGA 60.596 61.111 4.94 0.00 41.37 4.35
2574 2871 1.938657 CTCCTCTGACGTGCCGTGAT 61.939 60.000 4.94 0.00 41.37 3.06
2575 2872 1.807165 CCTCTGACGTGCCGTGATG 60.807 63.158 4.94 0.00 41.37 3.07
2576 2873 2.432456 TCTGACGTGCCGTGATGC 60.432 61.111 4.94 0.00 41.37 3.91
2577 2874 3.490759 CTGACGTGCCGTGATGCC 61.491 66.667 4.94 0.00 41.37 4.40
2582 2879 2.267642 GTGCCGTGATGCCCACTA 59.732 61.111 5.07 0.00 43.53 2.74
2583 2880 1.376683 GTGCCGTGATGCCCACTAA 60.377 57.895 5.07 0.00 43.53 2.24
2584 2881 1.376683 TGCCGTGATGCCCACTAAC 60.377 57.895 5.07 0.00 43.53 2.34
2585 2882 1.376683 GCCGTGATGCCCACTAACA 60.377 57.895 5.07 0.00 43.53 2.41
2586 2883 0.748005 GCCGTGATGCCCACTAACAT 60.748 55.000 5.07 0.00 43.53 2.71
2587 2884 1.016627 CCGTGATGCCCACTAACATG 58.983 55.000 0.00 0.00 43.53 3.21
2588 2885 1.678728 CCGTGATGCCCACTAACATGT 60.679 52.381 0.00 0.00 43.53 3.21
2589 2886 1.398041 CGTGATGCCCACTAACATGTG 59.602 52.381 0.00 0.00 43.53 3.21
2595 2892 3.903783 CACTAACATGTGGCCCCG 58.096 61.111 0.00 0.00 34.56 5.73
2596 2893 1.748879 CACTAACATGTGGCCCCGG 60.749 63.158 0.00 0.00 34.56 5.73
2597 2894 2.124320 CTAACATGTGGCCCCGGG 60.124 66.667 15.80 15.80 0.00 5.73
2611 2908 4.742201 CGGGCCCACGAGTCAGTG 62.742 72.222 24.92 0.00 41.53 3.66
2617 2914 2.661537 CACGAGTCAGTGGCGCAA 60.662 61.111 10.83 0.00 38.40 4.85
2618 2915 2.661866 ACGAGTCAGTGGCGCAAC 60.662 61.111 6.88 6.88 0.00 4.17
2619 2916 3.767230 CGAGTCAGTGGCGCAACG 61.767 66.667 9.79 4.80 0.00 4.10
2620 2917 3.414700 GAGTCAGTGGCGCAACGG 61.415 66.667 9.79 9.37 0.00 4.44
2637 2934 4.830765 GCAGCGGGCCATACGTCA 62.831 66.667 4.39 0.00 36.11 4.35
2638 2935 2.586079 CAGCGGGCCATACGTCAG 60.586 66.667 4.39 0.00 0.00 3.51
2639 2936 2.758327 AGCGGGCCATACGTCAGA 60.758 61.111 4.39 0.00 0.00 3.27
2640 2937 2.279517 GCGGGCCATACGTCAGAG 60.280 66.667 4.39 0.00 0.00 3.35
2641 2938 2.417516 CGGGCCATACGTCAGAGG 59.582 66.667 4.39 0.00 0.00 3.69
2642 2939 2.125326 CGGGCCATACGTCAGAGGA 61.125 63.158 4.39 0.00 0.00 3.71
2643 2940 1.464376 CGGGCCATACGTCAGAGGAT 61.464 60.000 4.39 0.00 0.00 3.24
2644 2941 0.759346 GGGCCATACGTCAGAGGATT 59.241 55.000 4.39 0.00 0.00 3.01
2645 2942 1.141053 GGGCCATACGTCAGAGGATTT 59.859 52.381 4.39 0.00 0.00 2.17
2646 2943 2.213499 GGCCATACGTCAGAGGATTTG 58.787 52.381 0.00 0.00 0.00 2.32
2647 2944 1.599542 GCCATACGTCAGAGGATTTGC 59.400 52.381 0.00 0.00 0.00 3.68
2648 2945 2.743183 GCCATACGTCAGAGGATTTGCT 60.743 50.000 0.00 0.00 0.00 3.91
2649 2946 3.535561 CCATACGTCAGAGGATTTGCTT 58.464 45.455 0.00 0.00 0.00 3.91
2650 2947 3.557595 CCATACGTCAGAGGATTTGCTTC 59.442 47.826 0.00 0.00 0.00 3.86
2651 2948 2.100605 ACGTCAGAGGATTTGCTTCC 57.899 50.000 0.00 0.00 35.90 3.46
2652 2949 1.347707 ACGTCAGAGGATTTGCTTCCA 59.652 47.619 0.00 0.00 38.32 3.53
2653 2950 2.005451 CGTCAGAGGATTTGCTTCCAG 58.995 52.381 4.16 0.00 38.32 3.86
2654 2951 2.613977 CGTCAGAGGATTTGCTTCCAGT 60.614 50.000 4.16 0.00 38.32 4.00
2882 3287 1.895798 AGCAGAGACTTTGTCGGATGA 59.104 47.619 0.00 0.00 37.67 2.92
2935 3356 1.815003 CAGCTCAAGGACCCAATGTTC 59.185 52.381 0.00 0.00 0.00 3.18
2949 3370 3.504906 CCAATGTTCTTGCTGTGTCATCT 59.495 43.478 0.00 0.00 0.00 2.90
2968 3389 2.184020 TTAGCTGGCGTCCATGTGCT 62.184 55.000 12.98 12.98 36.67 4.40
2971 3398 2.125147 TGGCGTCCATGTGCTAGC 60.125 61.111 8.10 8.10 0.00 3.42
3083 3514 0.733150 GAATAACGCAGGGCAGGAAC 59.267 55.000 0.00 0.00 0.00 3.62
3242 3846 4.698201 TGGACCAAATGACACTCTGTAA 57.302 40.909 0.00 0.00 0.00 2.41
3243 3847 5.241403 TGGACCAAATGACACTCTGTAAT 57.759 39.130 0.00 0.00 0.00 1.89
3244 3848 5.003160 TGGACCAAATGACACTCTGTAATG 58.997 41.667 0.00 0.00 0.00 1.90
3256 3860 7.553760 TGACACTCTGTAATGTATGATGCAAAT 59.446 33.333 0.00 0.00 0.00 2.32
3329 3934 5.811399 ATCAATCAATGCTTGCAATTTGG 57.189 34.783 0.00 0.00 0.00 3.28
3335 3940 0.249953 TGCTTGCAATTTGGCAGTGG 60.250 50.000 6.97 0.00 45.88 4.00
3390 4007 3.717294 CGCCCTGCCCTACCAGTT 61.717 66.667 0.00 0.00 0.00 3.16
3391 4008 2.044946 GCCCTGCCCTACCAGTTG 60.045 66.667 0.00 0.00 0.00 3.16
3392 4009 2.907179 GCCCTGCCCTACCAGTTGT 61.907 63.158 0.00 0.00 0.00 3.32
3393 4010 1.559065 GCCCTGCCCTACCAGTTGTA 61.559 60.000 0.00 0.00 0.00 2.41
3395 4012 1.141053 CCCTGCCCTACCAGTTGTATC 59.859 57.143 0.00 0.00 0.00 2.24
3396 4013 1.837439 CCTGCCCTACCAGTTGTATCA 59.163 52.381 0.00 0.00 0.00 2.15
3397 4014 2.439507 CCTGCCCTACCAGTTGTATCAT 59.560 50.000 0.00 0.00 0.00 2.45
3400 4017 2.158755 GCCCTACCAGTTGTATCATGCT 60.159 50.000 0.00 0.00 0.00 3.79
3401 4018 3.685550 GCCCTACCAGTTGTATCATGCTT 60.686 47.826 0.00 0.00 0.00 3.91
3402 4019 4.130118 CCCTACCAGTTGTATCATGCTTC 58.870 47.826 0.00 0.00 0.00 3.86
3403 4020 3.804325 CCTACCAGTTGTATCATGCTTCG 59.196 47.826 0.00 0.00 0.00 3.79
3404 4021 2.632377 ACCAGTTGTATCATGCTTCGG 58.368 47.619 0.00 0.00 0.00 4.30
3405 4022 1.331756 CCAGTTGTATCATGCTTCGGC 59.668 52.381 0.00 0.00 42.19 5.54
3415 4032 3.567797 GCTTCGGCATCGGCAGTC 61.568 66.667 0.00 0.00 43.71 3.51
3416 4033 2.185350 CTTCGGCATCGGCAGTCT 59.815 61.111 0.00 0.00 43.71 3.24
3459 4077 3.119352 CCAAAACATTAGCCTGCTTCTCC 60.119 47.826 0.00 0.00 0.00 3.71
3478 4096 4.996793 CTCCTGATCTAGATCAAGGAGGA 58.003 47.826 37.54 33.08 46.03 3.71
3520 4143 3.575687 CCAAACCCAGAATTCTTGAGCTT 59.424 43.478 4.86 0.00 0.00 3.74
3524 4147 3.586618 ACCCAGAATTCTTGAGCTTCTCT 59.413 43.478 4.86 0.00 0.00 3.10
3526 4149 4.635324 CCCAGAATTCTTGAGCTTCTCTTC 59.365 45.833 4.86 0.00 0.00 2.87
3527 4150 5.490159 CCAGAATTCTTGAGCTTCTCTTCT 58.510 41.667 4.86 0.00 0.00 2.85
3555 4178 7.073342 ACAAATTATTAGAAGGTCGTGCTTC 57.927 36.000 0.00 0.00 0.00 3.86
3635 4258 4.362677 AGATTCCAACTGGTAAGGCTCTA 58.637 43.478 0.00 0.00 36.34 2.43
3863 4495 9.134734 TCAAATCGATAATACCAAAGTTTTTGC 57.865 29.630 0.00 0.00 0.00 3.68
3878 4510 4.094739 AGTTTTTGCAGTTGAAATGCCAAC 59.905 37.500 15.35 14.06 44.92 3.77
3889 4524 7.617041 GTTGAAATGCCAACTATAGTCTCTT 57.383 36.000 5.70 0.00 42.20 2.85
3922 4557 4.455606 AGTTTCTTCAGGTCAAGGAAGTG 58.544 43.478 0.00 0.00 40.98 3.16
3923 4558 4.164221 AGTTTCTTCAGGTCAAGGAAGTGA 59.836 41.667 0.00 0.00 40.98 3.41
3924 4559 4.771114 TTCTTCAGGTCAAGGAAGTGAA 57.229 40.909 0.00 0.00 40.98 3.18
3925 4560 4.342862 TCTTCAGGTCAAGGAAGTGAAG 57.657 45.455 4.37 4.37 43.61 3.02
3926 4561 3.967326 TCTTCAGGTCAAGGAAGTGAAGA 59.033 43.478 8.62 8.62 46.81 2.87
3927 4562 4.408921 TCTTCAGGTCAAGGAAGTGAAGAA 59.591 41.667 9.96 0.00 46.29 2.52
3928 4563 4.342862 TCAGGTCAAGGAAGTGAAGAAG 57.657 45.455 0.00 0.00 0.00 2.85
3929 4564 3.967326 TCAGGTCAAGGAAGTGAAGAAGA 59.033 43.478 0.00 0.00 0.00 2.87
3930 4565 4.408921 TCAGGTCAAGGAAGTGAAGAAGAA 59.591 41.667 0.00 0.00 0.00 2.52
3931 4566 4.754114 CAGGTCAAGGAAGTGAAGAAGAAG 59.246 45.833 0.00 0.00 0.00 2.85
3932 4567 4.656112 AGGTCAAGGAAGTGAAGAAGAAGA 59.344 41.667 0.00 0.00 0.00 2.87
3933 4568 5.131142 AGGTCAAGGAAGTGAAGAAGAAGAA 59.869 40.000 0.00 0.00 0.00 2.52
3934 4569 5.468409 GGTCAAGGAAGTGAAGAAGAAGAAG 59.532 44.000 0.00 0.00 0.00 2.85
3935 4570 6.284459 GTCAAGGAAGTGAAGAAGAAGAAGA 58.716 40.000 0.00 0.00 0.00 2.87
3936 4571 6.763610 GTCAAGGAAGTGAAGAAGAAGAAGAA 59.236 38.462 0.00 0.00 0.00 2.52
3937 4572 6.989169 TCAAGGAAGTGAAGAAGAAGAAGAAG 59.011 38.462 0.00 0.00 0.00 2.85
3938 4573 6.739331 AGGAAGTGAAGAAGAAGAAGAAGA 57.261 37.500 0.00 0.00 0.00 2.87
3939 4574 7.130681 AGGAAGTGAAGAAGAAGAAGAAGAA 57.869 36.000 0.00 0.00 0.00 2.52
3940 4575 7.216494 AGGAAGTGAAGAAGAAGAAGAAGAAG 58.784 38.462 0.00 0.00 0.00 2.85
3941 4576 7.070571 AGGAAGTGAAGAAGAAGAAGAAGAAGA 59.929 37.037 0.00 0.00 0.00 2.87
3942 4577 7.713073 GGAAGTGAAGAAGAAGAAGAAGAAGAA 59.287 37.037 0.00 0.00 0.00 2.52
3943 4578 8.661352 AAGTGAAGAAGAAGAAGAAGAAGAAG 57.339 34.615 0.00 0.00 0.00 2.85
3944 4579 8.017418 AGTGAAGAAGAAGAAGAAGAAGAAGA 57.983 34.615 0.00 0.00 0.00 2.87
3945 4580 8.482128 AGTGAAGAAGAAGAAGAAGAAGAAGAA 58.518 33.333 0.00 0.00 0.00 2.52
4245 4893 7.972832 ACTAGTAATGTTTTGACGATTTGGA 57.027 32.000 0.00 0.00 0.00 3.53
4304 4955 4.148825 CCGAGGCCGAGGACAAGG 62.149 72.222 13.48 0.00 38.22 3.61
4387 5038 4.518970 GTGGAAGAAATTCAGGCTGTTGTA 59.481 41.667 15.27 0.00 0.00 2.41
4602 5253 1.468506 TAGTTCCGTGTCAGCTGCCA 61.469 55.000 9.47 0.00 0.00 4.92
4621 5272 6.628844 GCTGCCAGATTTATCCATTTGTCTTT 60.629 38.462 0.00 0.00 0.00 2.52
4680 5331 2.153645 TGGATGCTGTACAGTTTGCAG 58.846 47.619 23.44 0.00 40.77 4.41
4696 5347 3.932545 TGCAGTTGTGTGTTCTTTTGT 57.067 38.095 0.00 0.00 0.00 2.83
4942 5597 5.467902 TTTCACATGCACAAAAAGAAAGC 57.532 34.783 0.00 0.00 0.00 3.51
5077 5746 6.962311 TGAGGCTATAGGGAACTGATTCATAT 59.038 38.462 1.04 0.00 43.88 1.78
5120 5795 6.899393 TTTCATTTTTGCTGACCTATGTCT 57.101 33.333 0.00 0.00 42.28 3.41
5121 5796 6.899393 TTCATTTTTGCTGACCTATGTCTT 57.101 33.333 0.00 0.00 42.28 3.01
5125 5823 6.757897 TTTTTGCTGACCTATGTCTTATGG 57.242 37.500 0.00 0.00 42.28 2.74
5169 5870 7.113544 GCAGCTCAAAACTACTGTACATTTTTC 59.886 37.037 0.00 0.00 32.65 2.29
5170 5871 8.345565 CAGCTCAAAACTACTGTACATTTTTCT 58.654 33.333 0.00 0.00 0.00 2.52
5492 6195 3.496884 TCGTGAAACCAATAGCAACTGAC 59.503 43.478 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 1.272490 CACAAGGAGTCTCGTTAGCCA 59.728 52.381 7.45 0.00 0.00 4.75
187 193 0.098728 AGCGCAACCATGTTTATCGC 59.901 50.000 11.47 11.87 41.16 4.58
475 489 1.204941 ACGATGAGAAAACGGAGAGGG 59.795 52.381 0.00 0.00 0.00 4.30
483 497 3.604875 TCCTGGGTACGATGAGAAAAC 57.395 47.619 0.00 0.00 0.00 2.43
506 520 6.946009 AGGAGAGCAAGAGATATCTTACCTAC 59.054 42.308 6.70 1.57 0.00 3.18
522 536 5.053978 AGAAAAAGAAAGGAGGAGAGCAA 57.946 39.130 0.00 0.00 0.00 3.91
524 538 6.398234 AAAAGAAAAAGAAAGGAGGAGAGC 57.602 37.500 0.00 0.00 0.00 4.09
545 559 6.334102 TCCAAAAGGCGCTAGAAATAAAAA 57.666 33.333 7.64 0.00 0.00 1.94
546 560 5.968528 TCCAAAAGGCGCTAGAAATAAAA 57.031 34.783 7.64 0.00 0.00 1.52
550 564 4.016444 TCATTCCAAAAGGCGCTAGAAAT 58.984 39.130 7.64 0.00 0.00 2.17
599 651 2.747177 TGATCCGTCCATCTAACCACT 58.253 47.619 0.00 0.00 0.00 4.00
625 677 9.663904 CGAGAAAAGATAACATCAAACAGAAAA 57.336 29.630 0.00 0.00 0.00 2.29
626 678 9.051679 TCGAGAAAAGATAACATCAAACAGAAA 57.948 29.630 0.00 0.00 0.00 2.52
627 679 8.601845 TCGAGAAAAGATAACATCAAACAGAA 57.398 30.769 0.00 0.00 0.00 3.02
628 680 7.872993 ACTCGAGAAAAGATAACATCAAACAGA 59.127 33.333 21.68 0.00 0.00 3.41
629 681 8.023050 ACTCGAGAAAAGATAACATCAAACAG 57.977 34.615 21.68 0.00 0.00 3.16
636 688 5.583495 CCGAGACTCGAGAAAAGATAACAT 58.417 41.667 26.11 0.00 43.74 2.71
684 745 6.084277 GTCCGTTCATGGTTACTGAAATTTC 58.916 40.000 11.41 11.41 34.59 2.17
733 797 4.320935 GGTTGGTTGTCGTGAAGCATTATT 60.321 41.667 2.71 0.00 33.53 1.40
764 845 6.183360 GCTGGCTCAGTTTTGAATTTTGAAAA 60.183 34.615 0.00 0.00 33.43 2.29
765 846 5.294060 GCTGGCTCAGTTTTGAATTTTGAAA 59.706 36.000 4.45 0.00 33.43 2.69
782 863 4.565022 GATCTCCTTGTAATAGCTGGCTC 58.435 47.826 0.00 0.00 0.00 4.70
786 867 3.986572 CAGCGATCTCCTTGTAATAGCTG 59.013 47.826 0.00 3.02 40.84 4.24
804 885 4.929808 AGGTAGTACAAGATGAAAACAGCG 59.070 41.667 2.06 0.00 0.00 5.18
834 989 5.347364 GGATCTAATTCTGAATAGCTCGTGC 59.653 44.000 2.85 0.07 40.05 5.34
838 993 6.255453 GCATCGGATCTAATTCTGAATAGCTC 59.745 42.308 2.85 3.55 34.77 4.09
852 1007 3.627123 CCATTGTTGTTGCATCGGATCTA 59.373 43.478 0.00 0.00 0.00 1.98
853 1008 2.424601 CCATTGTTGTTGCATCGGATCT 59.575 45.455 0.00 0.00 0.00 2.75
854 1009 2.423185 TCCATTGTTGTTGCATCGGATC 59.577 45.455 0.00 0.00 0.00 3.36
855 1010 2.164219 GTCCATTGTTGTTGCATCGGAT 59.836 45.455 0.00 0.00 0.00 4.18
856 1011 1.539388 GTCCATTGTTGTTGCATCGGA 59.461 47.619 0.00 0.00 0.00 4.55
857 1012 1.541147 AGTCCATTGTTGTTGCATCGG 59.459 47.619 0.00 0.00 0.00 4.18
858 1013 2.995466 AGTCCATTGTTGTTGCATCG 57.005 45.000 0.00 0.00 0.00 3.84
859 1014 3.191162 TGCTAGTCCATTGTTGTTGCATC 59.809 43.478 0.00 0.00 0.00 3.91
860 1015 3.156293 TGCTAGTCCATTGTTGTTGCAT 58.844 40.909 0.00 0.00 0.00 3.96
861 1016 2.580962 TGCTAGTCCATTGTTGTTGCA 58.419 42.857 0.00 0.00 0.00 4.08
862 1017 3.641437 TTGCTAGTCCATTGTTGTTGC 57.359 42.857 0.00 0.00 0.00 4.17
863 1018 5.771469 TGATTTGCTAGTCCATTGTTGTTG 58.229 37.500 0.00 0.00 0.00 3.33
864 1019 5.536161 ACTGATTTGCTAGTCCATTGTTGTT 59.464 36.000 0.00 0.00 0.00 2.83
865 1020 5.072741 ACTGATTTGCTAGTCCATTGTTGT 58.927 37.500 0.00 0.00 0.00 3.32
866 1021 5.633830 ACTGATTTGCTAGTCCATTGTTG 57.366 39.130 0.00 0.00 0.00 3.33
867 1022 6.237901 TGTACTGATTTGCTAGTCCATTGTT 58.762 36.000 0.00 0.00 0.00 2.83
868 1023 5.804639 TGTACTGATTTGCTAGTCCATTGT 58.195 37.500 0.00 0.00 0.00 2.71
869 1024 6.741992 TTGTACTGATTTGCTAGTCCATTG 57.258 37.500 0.00 0.00 0.00 2.82
890 1045 9.793252 AAGAATGCTACTGTAAATGCTAATTTG 57.207 29.630 0.00 0.00 36.65 2.32
891 1046 9.793252 CAAGAATGCTACTGTAAATGCTAATTT 57.207 29.630 0.00 0.00 39.38 1.82
893 1048 8.737168 TCAAGAATGCTACTGTAAATGCTAAT 57.263 30.769 0.26 0.00 0.00 1.73
894 1049 7.824289 ACTCAAGAATGCTACTGTAAATGCTAA 59.176 33.333 0.26 0.00 0.00 3.09
895 1050 7.331026 ACTCAAGAATGCTACTGTAAATGCTA 58.669 34.615 0.26 0.00 0.00 3.49
897 1052 6.428385 ACTCAAGAATGCTACTGTAAATGC 57.572 37.500 0.00 0.00 0.00 3.56
898 1053 7.613146 CGTACTCAAGAATGCTACTGTAAATG 58.387 38.462 0.00 0.00 0.00 2.32
900 1055 5.575606 GCGTACTCAAGAATGCTACTGTAAA 59.424 40.000 0.00 0.00 0.00 2.01
902 1057 4.398358 AGCGTACTCAAGAATGCTACTGTA 59.602 41.667 0.00 0.00 0.00 2.74
903 1058 3.193691 AGCGTACTCAAGAATGCTACTGT 59.806 43.478 0.00 0.00 0.00 3.55
904 1059 3.549471 CAGCGTACTCAAGAATGCTACTG 59.451 47.826 0.00 0.00 0.00 2.74
905 1060 3.775202 CAGCGTACTCAAGAATGCTACT 58.225 45.455 0.00 0.00 0.00 2.57
906 1061 2.282820 GCAGCGTACTCAAGAATGCTAC 59.717 50.000 0.00 0.00 0.00 3.58
957 1115 5.941948 ATACTGCAAAAGTTGGTGTAGAC 57.058 39.130 10.61 0.00 40.56 2.59
970 1128 4.905429 TGTGCTTCCTCTTATACTGCAAA 58.095 39.130 0.00 0.00 0.00 3.68
978 1136 4.537135 TTCGTTCTGTGCTTCCTCTTAT 57.463 40.909 0.00 0.00 0.00 1.73
1183 1374 2.755952 AGAGGTTTGTTGGAAGCCTT 57.244 45.000 0.00 0.00 0.00 4.35
1184 1375 2.175715 AGAAGAGGTTTGTTGGAAGCCT 59.824 45.455 0.00 0.00 0.00 4.58
1233 1424 5.295152 CCTGTGTCGGTTAAAACTCTACTT 58.705 41.667 0.00 0.00 0.00 2.24
1243 1470 1.274167 CCTAGTGCCTGTGTCGGTTAA 59.726 52.381 0.00 0.00 0.00 2.01
1245 1472 0.830444 TCCTAGTGCCTGTGTCGGTT 60.830 55.000 0.00 0.00 0.00 4.44
1247 1474 1.251527 ACTCCTAGTGCCTGTGTCGG 61.252 60.000 0.00 0.00 0.00 4.79
1308 1535 3.684305 TCATTTACTTGACTGGCGTGATG 59.316 43.478 0.00 0.00 0.00 3.07
1312 1539 5.705609 ATTTTCATTTACTTGACTGGCGT 57.294 34.783 0.00 0.00 0.00 5.68
1315 1542 9.708222 CGATTCTATTTTCATTTACTTGACTGG 57.292 33.333 0.00 0.00 0.00 4.00
1316 1543 9.214953 GCGATTCTATTTTCATTTACTTGACTG 57.785 33.333 0.00 0.00 0.00 3.51
1443 1671 2.061773 GTCAGGTTGATGTCAGTGTCG 58.938 52.381 0.00 0.00 0.00 4.35
1631 1859 6.071320 GGTCAGGCAGGAGGAAATTATTAAT 58.929 40.000 0.00 0.00 0.00 1.40
1821 2055 4.584325 TGGCCCTGAATTGAATATTACTGC 59.416 41.667 0.00 0.00 0.00 4.40
1867 2101 5.581126 AGGAAATTTGCGATATTTGCAGA 57.419 34.783 3.87 1.08 44.28 4.26
1963 2197 8.759481 TGAGCTGAATCATACTCCTATATAGG 57.241 38.462 21.21 21.21 45.02 2.57
1964 2198 8.352201 GCTGAGCTGAATCATACTCCTATATAG 58.648 40.741 0.00 2.46 0.00 1.31
1965 2199 8.058235 AGCTGAGCTGAATCATACTCCTATATA 58.942 37.037 5.97 0.00 37.57 0.86
1966 2200 6.896860 AGCTGAGCTGAATCATACTCCTATAT 59.103 38.462 5.97 0.00 37.57 0.86
1967 2201 6.252233 AGCTGAGCTGAATCATACTCCTATA 58.748 40.000 5.97 0.00 37.57 1.31
1968 2202 5.085920 AGCTGAGCTGAATCATACTCCTAT 58.914 41.667 5.97 0.00 37.57 2.57
1969 2203 4.478203 AGCTGAGCTGAATCATACTCCTA 58.522 43.478 5.97 0.00 37.57 2.94
1970 2204 3.307506 AGCTGAGCTGAATCATACTCCT 58.692 45.455 5.97 0.71 37.57 3.69
1971 2205 3.749665 AGCTGAGCTGAATCATACTCC 57.250 47.619 5.97 0.00 37.57 3.85
1972 2206 5.006552 GTGAAAGCTGAGCTGAATCATACTC 59.993 44.000 8.16 6.51 39.62 2.59
1973 2207 4.874966 GTGAAAGCTGAGCTGAATCATACT 59.125 41.667 8.16 0.00 39.62 2.12
1974 2208 4.034975 GGTGAAAGCTGAGCTGAATCATAC 59.965 45.833 8.16 7.27 39.62 2.39
2031 2266 6.476243 TTCTGTATTTTGCCTAAACGTCTC 57.524 37.500 0.00 0.00 0.00 3.36
2101 2336 4.145876 TCAAGCATCTACTTTTGCAACG 57.854 40.909 0.00 0.00 41.35 4.10
2108 2343 9.539825 CATCTAGTATGTTCAAGCATCTACTTT 57.460 33.333 0.00 0.00 0.00 2.66
2117 2352 6.428385 AGCAAACATCTAGTATGTTCAAGC 57.572 37.500 16.06 17.61 40.94 4.01
2126 2361 4.690748 GCACAGTGAAGCAAACATCTAGTA 59.309 41.667 4.15 0.00 0.00 1.82
2127 2362 3.499918 GCACAGTGAAGCAAACATCTAGT 59.500 43.478 4.15 0.00 0.00 2.57
2128 2363 3.424039 CGCACAGTGAAGCAAACATCTAG 60.424 47.826 4.15 0.00 0.00 2.43
2208 2446 3.043586 CGTATCGGAAAAGGATGTCTCG 58.956 50.000 0.00 0.00 0.00 4.04
2223 2461 3.447918 TTTCCTTCTAAGGCCGTATCG 57.552 47.619 0.00 0.00 46.06 2.92
2228 2466 2.351726 CGTTGATTTCCTTCTAAGGCCG 59.648 50.000 3.73 0.00 46.06 6.13
2261 2499 6.062434 TGTTACGTCACCCTTTTGTAATTG 57.938 37.500 0.00 0.00 0.00 2.32
2480 2762 1.215244 GCCGCCGAAATAGTAACCTC 58.785 55.000 0.00 0.00 0.00 3.85
2502 2784 9.403583 TCAAAACTAAACTCTAGTTTGATGGTT 57.596 29.630 16.48 12.49 46.56 3.67
2503 2785 8.974060 TCAAAACTAAACTCTAGTTTGATGGT 57.026 30.769 16.48 8.29 46.56 3.55
2541 2838 0.461339 GAGGAGCCGCGTCCAAAATA 60.461 55.000 17.08 0.00 39.34 1.40
2542 2839 1.745489 GAGGAGCCGCGTCCAAAAT 60.745 57.895 17.08 0.00 39.34 1.82
2543 2840 2.358247 GAGGAGCCGCGTCCAAAA 60.358 61.111 17.08 0.00 39.34 2.44
2544 2841 3.311110 AGAGGAGCCGCGTCCAAA 61.311 61.111 17.08 0.00 39.34 3.28
2545 2842 4.069232 CAGAGGAGCCGCGTCCAA 62.069 66.667 17.08 0.00 39.34 3.53
2547 2844 4.500116 GTCAGAGGAGCCGCGTCC 62.500 72.222 4.92 6.49 36.79 4.79
2548 2845 4.838486 CGTCAGAGGAGCCGCGTC 62.838 72.222 4.92 0.00 0.00 5.19
2552 2849 4.803426 GGCACGTCAGAGGAGCCG 62.803 72.222 14.71 0.00 35.42 5.52
2578 2875 1.748879 CCGGGGCCACATGTTAGTG 60.749 63.158 5.46 0.00 39.21 2.74
2579 2876 2.674754 CCGGGGCCACATGTTAGT 59.325 61.111 5.46 0.00 0.00 2.24
2580 2877 2.124320 CCCGGGGCCACATGTTAG 60.124 66.667 14.71 0.00 0.00 2.34
2581 2878 4.434354 GCCCGGGGCCACATGTTA 62.434 66.667 28.23 0.00 44.06 2.41
2594 2891 4.742201 CACTGACTCGTGGGCCCG 62.742 72.222 19.37 6.11 0.00 6.13
2600 2897 2.661537 TTGCGCCACTGACTCGTG 60.662 61.111 4.18 0.00 34.71 4.35
2601 2898 2.661866 GTTGCGCCACTGACTCGT 60.662 61.111 4.18 0.00 0.00 4.18
2602 2899 3.767230 CGTTGCGCCACTGACTCG 61.767 66.667 10.16 0.00 0.00 4.18
2603 2900 3.414700 CCGTTGCGCCACTGACTC 61.415 66.667 10.16 0.00 0.00 3.36
2620 2917 4.830765 TGACGTATGGCCCGCTGC 62.831 66.667 0.00 0.00 40.16 5.25
2621 2918 2.586079 CTGACGTATGGCCCGCTG 60.586 66.667 0.00 0.00 0.00 5.18
2622 2919 2.758327 TCTGACGTATGGCCCGCT 60.758 61.111 0.00 0.00 0.00 5.52
2623 2920 2.279517 CTCTGACGTATGGCCCGC 60.280 66.667 0.00 0.00 0.00 6.13
2624 2921 1.464376 ATCCTCTGACGTATGGCCCG 61.464 60.000 0.00 0.00 0.00 6.13
2625 2922 0.759346 AATCCTCTGACGTATGGCCC 59.241 55.000 0.00 0.00 0.00 5.80
2626 2923 2.213499 CAAATCCTCTGACGTATGGCC 58.787 52.381 0.00 0.00 0.00 5.36
2627 2924 1.599542 GCAAATCCTCTGACGTATGGC 59.400 52.381 0.00 0.00 0.00 4.40
2628 2925 3.185246 AGCAAATCCTCTGACGTATGG 57.815 47.619 0.00 0.00 0.00 2.74
2629 2926 3.557595 GGAAGCAAATCCTCTGACGTATG 59.442 47.826 0.00 0.00 36.50 2.39
2630 2927 3.197766 TGGAAGCAAATCCTCTGACGTAT 59.802 43.478 0.00 0.00 40.35 3.06
2631 2928 2.565391 TGGAAGCAAATCCTCTGACGTA 59.435 45.455 0.00 0.00 40.35 3.57
2632 2929 1.347707 TGGAAGCAAATCCTCTGACGT 59.652 47.619 0.00 0.00 40.35 4.34
2633 2930 2.005451 CTGGAAGCAAATCCTCTGACG 58.995 52.381 5.04 0.00 40.35 4.35
2634 2931 3.064900 ACTGGAAGCAAATCCTCTGAC 57.935 47.619 5.04 0.00 40.35 3.51
2635 2932 3.795688 AACTGGAAGCAAATCCTCTGA 57.204 42.857 5.04 0.00 40.35 3.27
2636 2933 6.521151 AAATAACTGGAAGCAAATCCTCTG 57.479 37.500 5.04 0.00 40.35 3.35
2637 2934 7.544804 AAAAATAACTGGAAGCAAATCCTCT 57.455 32.000 5.04 0.00 40.35 3.69
2907 3328 2.224548 GGGTCCTTGAGCTGTAAACTGT 60.225 50.000 0.00 0.00 0.00 3.55
2935 3356 2.676839 CCAGCTAAGATGACACAGCAAG 59.323 50.000 0.00 0.00 36.47 4.01
2949 3370 1.745115 GCACATGGACGCCAGCTAA 60.745 57.895 0.00 0.00 36.75 3.09
2968 3389 1.828595 TCAACTAACCATCTGGCGCTA 59.171 47.619 7.64 0.00 39.32 4.26
2971 3398 1.066143 AGGTCAACTAACCATCTGGCG 60.066 52.381 0.00 0.00 42.12 5.69
3083 3514 6.916387 AGAATATACGACGTAACAGTTGGATG 59.084 38.462 12.40 0.00 31.69 3.51
3174 3778 6.551385 ACACATCAATGTTCTTCTGTCTTC 57.449 37.500 0.00 0.00 39.39 2.87
3256 3860 1.226688 GCTCGCACGATGCAGAGTA 60.227 57.895 20.41 0.00 45.36 2.59
3329 3934 3.679824 ACACTACTTCTTACCCACTGC 57.320 47.619 0.00 0.00 0.00 4.40
3335 3940 8.248945 TGACAGCTAAATACACTACTTCTTACC 58.751 37.037 0.00 0.00 0.00 2.85
3400 4017 2.184322 GAGACTGCCGATGCCGAA 59.816 61.111 0.00 0.00 38.22 4.30
3401 4018 2.755876 AGAGACTGCCGATGCCGA 60.756 61.111 0.00 0.00 38.22 5.54
3402 4019 2.004808 TACAGAGACTGCCGATGCCG 62.005 60.000 0.00 0.00 34.37 5.69
3403 4020 0.390860 ATACAGAGACTGCCGATGCC 59.609 55.000 0.00 0.00 34.37 4.40
3404 4021 3.584406 ATATACAGAGACTGCCGATGC 57.416 47.619 0.00 0.00 34.37 3.91
3405 4022 7.413644 CACTATATATACAGAGACTGCCGATG 58.586 42.308 0.00 0.00 34.37 3.84
3406 4023 6.038825 GCACTATATATACAGAGACTGCCGAT 59.961 42.308 0.00 0.00 34.37 4.18
3407 4024 5.354513 GCACTATATATACAGAGACTGCCGA 59.645 44.000 0.00 0.00 34.37 5.54
3408 4025 5.449314 GGCACTATATATACAGAGACTGCCG 60.449 48.000 5.02 0.00 34.37 5.69
3409 4026 5.163499 GGGCACTATATATACAGAGACTGCC 60.163 48.000 10.49 10.49 39.83 4.85
3410 4027 5.419155 TGGGCACTATATATACAGAGACTGC 59.581 44.000 0.00 0.00 34.37 4.40
3412 4029 5.654650 GCTGGGCACTATATATACAGAGACT 59.345 44.000 10.13 0.00 0.00 3.24
3413 4030 5.163499 GGCTGGGCACTATATATACAGAGAC 60.163 48.000 10.13 0.00 0.00 3.36
3414 4031 4.956700 GGCTGGGCACTATATATACAGAGA 59.043 45.833 10.13 0.00 0.00 3.10
3415 4032 4.100189 GGGCTGGGCACTATATATACAGAG 59.900 50.000 10.13 0.00 0.00 3.35
3416 4033 4.030913 GGGCTGGGCACTATATATACAGA 58.969 47.826 10.13 0.00 0.00 3.41
3488 4111 0.179000 CTGGGTTTGGATCTCCGAGG 59.821 60.000 0.00 0.00 39.43 4.63
3524 4147 8.755977 ACGACCTTCTAATAATTTGTAGGAGAA 58.244 33.333 0.00 0.00 0.00 2.87
3526 4149 7.042658 GCACGACCTTCTAATAATTTGTAGGAG 60.043 40.741 0.00 0.00 0.00 3.69
3527 4150 6.759827 GCACGACCTTCTAATAATTTGTAGGA 59.240 38.462 0.00 0.00 0.00 2.94
3543 4166 2.048127 GCCGAGAAGCACGACCTT 60.048 61.111 0.00 0.00 0.00 3.50
3544 4167 2.493907 GAAGCCGAGAAGCACGACCT 62.494 60.000 0.00 0.00 34.23 3.85
3545 4168 2.048127 AAGCCGAGAAGCACGACC 60.048 61.111 0.00 0.00 34.23 4.79
3555 4178 0.174617 GGAGACAGAAGGAAGCCGAG 59.825 60.000 0.00 0.00 0.00 4.63
3635 4258 6.498651 TCAAACTAGTGAAGAGGAGGAAGAAT 59.501 38.462 0.00 0.00 0.00 2.40
3889 4524 8.241497 TGACCTGAAGAAACTAACTAGTGTTA 57.759 34.615 0.00 0.00 36.50 2.41
3901 4536 4.451900 TCACTTCCTTGACCTGAAGAAAC 58.548 43.478 6.28 0.00 40.30 2.78
3922 4557 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
3923 4558 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
3924 4559 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
3925 4560 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
3926 4561 9.325198 GTTCTTCTTCTTCTTCTTCTTCTTCTT 57.675 33.333 0.00 0.00 0.00 2.52
3927 4562 8.482128 TGTTCTTCTTCTTCTTCTTCTTCTTCT 58.518 33.333 0.00 0.00 0.00 2.85
3928 4563 8.655651 TGTTCTTCTTCTTCTTCTTCTTCTTC 57.344 34.615 0.00 0.00 0.00 2.87
3929 4564 9.108284 CTTGTTCTTCTTCTTCTTCTTCTTCTT 57.892 33.333 0.00 0.00 0.00 2.52
3930 4565 7.714813 CCTTGTTCTTCTTCTTCTTCTTCTTCT 59.285 37.037 0.00 0.00 0.00 2.85
3931 4566 7.713073 TCCTTGTTCTTCTTCTTCTTCTTCTTC 59.287 37.037 0.00 0.00 0.00 2.87
3932 4567 7.569240 TCCTTGTTCTTCTTCTTCTTCTTCTT 58.431 34.615 0.00 0.00 0.00 2.52
3933 4568 7.070571 TCTCCTTGTTCTTCTTCTTCTTCTTCT 59.929 37.037 0.00 0.00 0.00 2.85
3934 4569 7.213678 TCTCCTTGTTCTTCTTCTTCTTCTTC 58.786 38.462 0.00 0.00 0.00 2.87
3935 4570 7.070571 TCTCTCCTTGTTCTTCTTCTTCTTCTT 59.929 37.037 0.00 0.00 0.00 2.52
3936 4571 6.553100 TCTCTCCTTGTTCTTCTTCTTCTTCT 59.447 38.462 0.00 0.00 0.00 2.85
3937 4572 6.754193 TCTCTCCTTGTTCTTCTTCTTCTTC 58.246 40.000 0.00 0.00 0.00 2.87
3938 4573 6.739331 TCTCTCCTTGTTCTTCTTCTTCTT 57.261 37.500 0.00 0.00 0.00 2.52
3939 4574 6.239572 CCTTCTCTCCTTGTTCTTCTTCTTCT 60.240 42.308 0.00 0.00 0.00 2.85
3940 4575 5.931724 CCTTCTCTCCTTGTTCTTCTTCTTC 59.068 44.000 0.00 0.00 0.00 2.87
3941 4576 5.604650 TCCTTCTCTCCTTGTTCTTCTTCTT 59.395 40.000 0.00 0.00 0.00 2.52
3942 4577 5.011635 GTCCTTCTCTCCTTGTTCTTCTTCT 59.988 44.000 0.00 0.00 0.00 2.85
3943 4578 5.221541 TGTCCTTCTCTCCTTGTTCTTCTTC 60.222 44.000 0.00 0.00 0.00 2.87
3944 4579 4.656112 TGTCCTTCTCTCCTTGTTCTTCTT 59.344 41.667 0.00 0.00 0.00 2.52
3945 4580 4.227197 TGTCCTTCTCTCCTTGTTCTTCT 58.773 43.478 0.00 0.00 0.00 2.85
4621 5272 7.013559 CCATATGCAGACCATTCAGTTTTGATA 59.986 37.037 0.00 0.00 35.34 2.15
4680 5331 9.900264 GAAATAAATCACAAAAGAACACACAAC 57.100 29.630 0.00 0.00 0.00 3.32
4696 5347 8.824783 AGGACAATCCCAAAATGAAATAAATCA 58.175 29.630 0.00 0.00 37.19 2.57
4831 5486 4.156739 GGGAAATTACACTGAAGCCTTGAG 59.843 45.833 0.00 0.00 0.00 3.02
4962 5622 9.160496 GATCACATGAAGATCTTTGTCTACTTT 57.840 33.333 9.87 0.00 39.01 2.66
4998 5658 7.600065 CAAAGATCACATGAAGACCTTGAATT 58.400 34.615 0.00 0.00 0.00 2.17
4999 5659 6.349944 GCAAAGATCACATGAAGACCTTGAAT 60.350 38.462 0.00 0.00 0.00 2.57
5002 5662 4.670992 CGCAAAGATCACATGAAGACCTTG 60.671 45.833 0.00 3.50 0.00 3.61
5003 5663 3.438087 CGCAAAGATCACATGAAGACCTT 59.562 43.478 0.00 0.00 0.00 3.50
5077 5746 2.337359 AGGTGAACCCTGGCTAAGTA 57.663 50.000 0.00 0.00 44.08 2.24
5417 6120 1.347817 CTCCACGCGAGAAAGCTCAC 61.348 60.000 15.93 0.00 41.63 3.51
5492 6195 2.017049 GATCCATTTCAGGTTGTCCCG 58.983 52.381 0.00 0.00 38.74 5.14


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

AutoCloner maintained by Alex Coulton.