Multiple sequence alignment - TraesCS6D01G287200

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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 TraesCS6D01G287200 chr6D 100.000 4407 0 0 1 4407 396451627 396447221 0.000000e+00 8139.0
1 TraesCS6D01G287200 chr6D 97.619 42 1 0 3646 3687 87467560 87467519 6.110000e-09 73.1
2 TraesCS6D01G287200 chr6D 97.619 42 0 1 3647 3687 106837869 106837828 2.200000e-08 71.3
3 TraesCS6D01G287200 chr6B 95.821 1388 44 5 980 2356 592946540 592945156 0.000000e+00 2230.0
4 TraesCS6D01G287200 chr6B 96.193 683 26 0 2805 3487 592944905 592944223 0.000000e+00 1118.0
5 TraesCS6D01G287200 chr6B 81.928 747 85 37 3536 4254 592941049 592940325 1.770000e-163 586.0
6 TraesCS6D01G287200 chr6B 94.737 76 4 0 2385 2460 592945158 592945083 7.740000e-23 119.0
7 TraesCS6D01G287200 chr6A 94.808 1329 57 6 980 2301 542711376 542710053 0.000000e+00 2061.0
8 TraesCS6D01G287200 chr6A 92.778 720 31 12 2977 3687 542709029 542708322 0.000000e+00 1022.0
9 TraesCS6D01G287200 chr6A 79.887 353 42 19 3741 4078 542706020 542705682 9.530000e-57 231.0
10 TraesCS6D01G287200 chr6A 82.031 128 14 3 2734 2853 542709154 542709028 2.800000e-17 100.0
11 TraesCS6D01G287200 chr3A 80.977 962 140 24 1 936 660439547 660440491 0.000000e+00 723.0
12 TraesCS6D01G287200 chr3A 76.910 589 97 32 285 858 142876757 142877321 9.270000e-77 298.0
13 TraesCS6D01G287200 chr3A 79.845 258 45 7 646 898 17480859 17481114 9.740000e-42 182.0
14 TraesCS6D01G287200 chr7D 83.438 797 93 21 1 765 482241777 482240988 0.000000e+00 704.0
15 TraesCS6D01G287200 chr7D 80.323 930 132 19 1 883 32821633 32820708 0.000000e+00 656.0
16 TraesCS6D01G287200 chr7D 80.131 916 119 32 1 868 32701071 32700171 3.740000e-175 625.0
17 TraesCS6D01G287200 chr7D 77.617 965 132 49 1 936 37539651 37540560 3.930000e-140 508.0
18 TraesCS6D01G287200 chr7D 79.760 751 112 26 22 741 91057460 91056719 3.930000e-140 508.0
19 TraesCS6D01G287200 chr7D 77.997 609 91 24 156 737 46130867 46131459 4.220000e-90 342.0
20 TraesCS6D01G287200 chr2A 81.009 932 127 26 14 898 17755981 17755053 0.000000e+00 695.0
21 TraesCS6D01G287200 chr2A 90.196 51 4 1 3635 3684 125205704 125205754 1.020000e-06 65.8
22 TraesCS6D01G287200 chr2D 82.367 845 103 20 1 807 158099689 158100525 0.000000e+00 693.0
23 TraesCS6D01G287200 chr2D 80.305 919 137 24 10 890 492298886 492297974 0.000000e+00 654.0
24 TraesCS6D01G287200 chr2D 88.571 280 30 2 1 279 496376675 496376397 5.460000e-89 339.0
25 TraesCS6D01G287200 chr4D 78.834 926 109 42 2 882 421511146 421510263 1.080000e-150 544.0
26 TraesCS6D01G287200 chr4D 92.208 154 12 0 1 154 417432746 417432593 7.420000e-53 219.0
27 TraesCS6D01G287200 chr4D 97.436 39 1 0 3646 3684 5786199 5786237 2.840000e-07 67.6
28 TraesCS6D01G287200 chr3D 80.685 730 102 21 201 898 31748151 31748873 8.390000e-147 531.0
29 TraesCS6D01G287200 chr3D 77.268 959 142 46 24 935 268950116 268949187 1.100000e-135 494.0
30 TraesCS6D01G287200 chr1B 79.843 764 115 18 2 726 665832999 665833762 5.050000e-144 521.0
31 TraesCS6D01G287200 chr7B 77.754 917 135 45 22 883 43946489 43947391 2.370000e-137 499.0
32 TraesCS6D01G287200 chr7B 79.945 364 52 11 536 881 242914669 242914309 9.470000e-62 248.0
33 TraesCS6D01G287200 chr4A 80.841 642 86 25 156 765 396763702 396763066 1.860000e-128 470.0
34 TraesCS6D01G287200 chr4A 78.803 401 60 17 517 898 677243345 677242951 3.400000e-61 246.0
35 TraesCS6D01G287200 chr1D 82.264 530 63 15 3 505 63606230 63606755 3.150000e-116 429.0
36 TraesCS6D01G287200 chr1D 76.687 489 82 24 247 726 282936690 282937155 4.400000e-60 243.0
37 TraesCS6D01G287200 chr1D 76.507 481 86 25 281 742 33337138 33337610 2.050000e-58 237.0
38 TraesCS6D01G287200 chr5B 79.074 497 83 16 284 762 525529713 525529220 5.500000e-84 322.0
39 TraesCS6D01G287200 chr3B 83.333 330 40 7 568 883 327867633 327867305 1.550000e-74 291.0
40 TraesCS6D01G287200 chrUn 80.612 294 50 7 603 892 239310831 239311121 2.060000e-53 220.0
41 TraesCS6D01G287200 chrUn 80.333 300 52 7 603 898 318150059 318149763 2.060000e-53 220.0
42 TraesCS6D01G287200 chr7A 77.500 320 51 12 536 841 238034603 238034291 5.860000e-39 172.0
43 TraesCS6D01G287200 chr7A 95.238 42 2 0 3646 3687 411492989 411492948 2.840000e-07 67.6
44 TraesCS6D01G287200 chr5D 90.741 54 4 1 3635 3687 29901046 29900993 2.200000e-08 71.3
45 TraesCS6D01G287200 chr2B 95.455 44 1 1 3646 3688 174395603 174395560 7.910000e-08 69.4


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 TraesCS6D01G287200 chr6D 396447221 396451627 4406 True 8139.00 8139 100.00000 1 4407 1 chr6D.!!$R3 4406
1 TraesCS6D01G287200 chr6B 592940325 592946540 6215 True 1013.25 2230 92.16975 980 4254 4 chr6B.!!$R1 3274
2 TraesCS6D01G287200 chr6A 542705682 542711376 5694 True 853.50 2061 87.37600 980 4078 4 chr6A.!!$R1 3098
3 TraesCS6D01G287200 chr3A 660439547 660440491 944 False 723.00 723 80.97700 1 936 1 chr3A.!!$F3 935
4 TraesCS6D01G287200 chr3A 142876757 142877321 564 False 298.00 298 76.91000 285 858 1 chr3A.!!$F2 573
5 TraesCS6D01G287200 chr7D 482240988 482241777 789 True 704.00 704 83.43800 1 765 1 chr7D.!!$R4 764
6 TraesCS6D01G287200 chr7D 32820708 32821633 925 True 656.00 656 80.32300 1 883 1 chr7D.!!$R2 882
7 TraesCS6D01G287200 chr7D 32700171 32701071 900 True 625.00 625 80.13100 1 868 1 chr7D.!!$R1 867
8 TraesCS6D01G287200 chr7D 37539651 37540560 909 False 508.00 508 77.61700 1 936 1 chr7D.!!$F1 935
9 TraesCS6D01G287200 chr7D 91056719 91057460 741 True 508.00 508 79.76000 22 741 1 chr7D.!!$R3 719
10 TraesCS6D01G287200 chr7D 46130867 46131459 592 False 342.00 342 77.99700 156 737 1 chr7D.!!$F2 581
11 TraesCS6D01G287200 chr2A 17755053 17755981 928 True 695.00 695 81.00900 14 898 1 chr2A.!!$R1 884
12 TraesCS6D01G287200 chr2D 158099689 158100525 836 False 693.00 693 82.36700 1 807 1 chr2D.!!$F1 806
13 TraesCS6D01G287200 chr2D 492297974 492298886 912 True 654.00 654 80.30500 10 890 1 chr2D.!!$R1 880
14 TraesCS6D01G287200 chr4D 421510263 421511146 883 True 544.00 544 78.83400 2 882 1 chr4D.!!$R2 880
15 TraesCS6D01G287200 chr3D 31748151 31748873 722 False 531.00 531 80.68500 201 898 1 chr3D.!!$F1 697
16 TraesCS6D01G287200 chr3D 268949187 268950116 929 True 494.00 494 77.26800 24 935 1 chr3D.!!$R1 911
17 TraesCS6D01G287200 chr1B 665832999 665833762 763 False 521.00 521 79.84300 2 726 1 chr1B.!!$F1 724
18 TraesCS6D01G287200 chr7B 43946489 43947391 902 False 499.00 499 77.75400 22 883 1 chr7B.!!$F1 861
19 TraesCS6D01G287200 chr4A 396763066 396763702 636 True 470.00 470 80.84100 156 765 1 chr4A.!!$R1 609
20 TraesCS6D01G287200 chr1D 63606230 63606755 525 False 429.00 429 82.26400 3 505 1 chr1D.!!$F2 502

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
885 1037 0.168128 CCGACGAAAAATGGGCTGTC 59.832 55.000 0.00 0.00 0.00 3.51 F
1173 1331 0.041238 TCCTCCATCTCGTCAACCCT 59.959 55.000 0.00 0.00 0.00 4.34 F
2435 2729 1.064463 ACCGGCAGTTCATCATCCAAT 60.064 47.619 0.00 0.00 0.00 3.16 F
2549 2905 0.750850 TCTAGAACAGTATGCCGGCC 59.249 55.000 26.77 8.84 42.53 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2536 2892 0.396811 GGAATAGGCCGGCATACTGT 59.603 55.000 30.85 14.75 0.00 3.55 R
2541 2897 2.320681 TACTAGGAATAGGCCGGCAT 57.679 50.000 30.85 26.24 0.00 4.40 R
3319 4050 1.293498 GCTCAAGCTCGAGAACCCA 59.707 57.895 18.75 0.00 38.21 4.51 R
3798 9912 1.670791 GATTCGGAGGTCTCGTCTCT 58.329 55.000 0.00 0.00 0.00 3.10 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
111 113 3.575247 TGACGCCCCACCATTGGT 61.575 61.111 1.37 1.37 42.10 3.67
224 249 0.892358 TACCTCGTCTGGTTCTGCGT 60.892 55.000 3.26 0.00 41.22 5.24
327 352 4.742201 GCGCTCAGCCTCCACGAA 62.742 66.667 0.00 0.00 40.81 3.85
483 558 1.734388 GCGAAGAGAGAGGGGAGAGC 61.734 65.000 0.00 0.00 0.00 4.09
530 622 3.375443 TTCGGCGAGAGGGGGAGAT 62.375 63.158 10.46 0.00 0.00 2.75
552 650 1.965930 TTGTGGCGAGGATGTGTGC 60.966 57.895 0.00 0.00 0.00 4.57
553 651 2.358615 GTGGCGAGGATGTGTGCA 60.359 61.111 0.00 0.00 0.00 4.57
744 888 0.389948 GATGAGGACGACAAAGGCGT 60.390 55.000 0.00 0.00 45.79 5.68
803 949 2.989422 AAAAATGTTTCTCTCGGCGG 57.011 45.000 7.21 0.00 0.00 6.13
860 1012 2.675075 ACCGGCACCAAATTCGGG 60.675 61.111 0.00 0.77 45.97 5.14
883 1035 0.596082 AACCGACGAAAAATGGGCTG 59.404 50.000 0.00 0.00 0.00 4.85
884 1036 0.536460 ACCGACGAAAAATGGGCTGT 60.536 50.000 0.00 0.00 0.00 4.40
885 1037 0.168128 CCGACGAAAAATGGGCTGTC 59.832 55.000 0.00 0.00 0.00 3.51
950 1108 3.170360 GGGGGAGTTTCGGCTTTAG 57.830 57.895 0.00 0.00 0.00 1.85
951 1109 0.616891 GGGGGAGTTTCGGCTTTAGA 59.383 55.000 0.00 0.00 0.00 2.10
952 1110 1.212195 GGGGGAGTTTCGGCTTTAGAT 59.788 52.381 0.00 0.00 0.00 1.98
953 1111 2.436911 GGGGGAGTTTCGGCTTTAGATA 59.563 50.000 0.00 0.00 0.00 1.98
954 1112 3.072622 GGGGGAGTTTCGGCTTTAGATAT 59.927 47.826 0.00 0.00 0.00 1.63
955 1113 4.065789 GGGGAGTTTCGGCTTTAGATATG 58.934 47.826 0.00 0.00 0.00 1.78
956 1114 3.498777 GGGAGTTTCGGCTTTAGATATGC 59.501 47.826 0.00 0.00 0.00 3.14
957 1115 3.498777 GGAGTTTCGGCTTTAGATATGCC 59.501 47.826 0.00 0.00 42.27 4.40
962 1120 1.809684 GGCTTTAGATATGCCGGACC 58.190 55.000 5.05 0.00 37.33 4.46
963 1121 1.429463 GCTTTAGATATGCCGGACCG 58.571 55.000 5.05 6.99 0.00 4.79
964 1122 1.270147 GCTTTAGATATGCCGGACCGT 60.270 52.381 13.94 0.00 0.00 4.83
965 1123 2.404215 CTTTAGATATGCCGGACCGTG 58.596 52.381 13.94 5.55 0.00 4.94
966 1124 1.405872 TTAGATATGCCGGACCGTGT 58.594 50.000 13.94 0.47 0.00 4.49
967 1125 0.956633 TAGATATGCCGGACCGTGTC 59.043 55.000 13.94 2.31 0.00 3.67
968 1126 1.040893 AGATATGCCGGACCGTGTCA 61.041 55.000 13.94 8.11 33.68 3.58
969 1127 0.179094 GATATGCCGGACCGTGTCAA 60.179 55.000 13.94 0.00 33.68 3.18
970 1128 0.250793 ATATGCCGGACCGTGTCAAA 59.749 50.000 13.94 0.00 33.68 2.69
971 1129 0.390603 TATGCCGGACCGTGTCAAAG 60.391 55.000 13.94 0.00 33.68 2.77
972 1130 3.047877 GCCGGACCGTGTCAAAGG 61.048 66.667 13.94 0.00 33.68 3.11
973 1131 2.358247 CCGGACCGTGTCAAAGGG 60.358 66.667 13.94 0.00 39.88 3.95
977 1135 3.541072 ACCGTGTCAAAGGGTCGA 58.459 55.556 1.27 0.00 43.78 4.20
978 1136 1.366366 ACCGTGTCAAAGGGTCGAG 59.634 57.895 0.00 0.00 43.78 4.04
1062 1220 0.811616 GCCGCTCACATCCTAACCTG 60.812 60.000 0.00 0.00 0.00 4.00
1173 1331 0.041238 TCCTCCATCTCGTCAACCCT 59.959 55.000 0.00 0.00 0.00 4.34
1287 1445 2.079158 ACATGGCTTCGTGACAATCTG 58.921 47.619 0.00 0.00 37.17 2.90
1291 1449 4.406648 TGGCTTCGTGACAATCTGATAT 57.593 40.909 0.00 0.00 0.00 1.63
1373 1531 1.270274 TGGTACGAGAAGCTTTACGCA 59.730 47.619 20.36 9.67 42.61 5.24
1424 1582 9.871238 TCTTATGAAGCCGAGGTATATAATTTC 57.129 33.333 0.00 0.00 0.00 2.17
1622 1780 7.034685 TCCTATCTGAATGAATTGCACAATG 57.965 36.000 0.00 0.00 0.00 2.82
1731 1889 1.869767 CACTTGGAGTGCTGTTCTGTC 59.130 52.381 0.00 0.00 39.62 3.51
2028 2189 3.884037 ATTGGGGTGGATCCTAACATC 57.116 47.619 14.23 0.71 36.25 3.06
2133 2301 1.597742 ATGGTGCCTTATGATCGTGC 58.402 50.000 0.00 0.00 0.00 5.34
2333 2508 7.711846 TCTTTGCAGCAGTGATTTTTAAGTTA 58.288 30.769 0.00 0.00 0.00 2.24
2380 2555 4.632538 ATTTGTAAGGCAATTAGACGGC 57.367 40.909 0.00 0.00 36.89 5.68
2388 2682 3.477530 GGCAATTAGACGGCCTAAGAAT 58.522 45.455 0.00 0.00 44.32 2.40
2395 2689 6.982160 TTAGACGGCCTAAGAATATACCAA 57.018 37.500 0.00 0.00 32.67 3.67
2435 2729 1.064463 ACCGGCAGTTCATCATCCAAT 60.064 47.619 0.00 0.00 0.00 3.16
2456 2750 7.571892 CCAATAAACAAAAAGTATTGGCACAC 58.428 34.615 8.34 0.00 44.33 3.82
2457 2751 7.225538 CCAATAAACAAAAAGTATTGGCACACA 59.774 33.333 8.34 0.00 44.33 3.72
2458 2752 7.945033 ATAAACAAAAAGTATTGGCACACAG 57.055 32.000 0.00 0.00 39.29 3.66
2460 2754 6.458232 AACAAAAAGTATTGGCACACAGTA 57.542 33.333 0.00 0.00 39.29 2.74
2461 2755 6.458232 ACAAAAAGTATTGGCACACAGTAA 57.542 33.333 0.00 0.00 39.29 2.24
2464 2758 7.651704 ACAAAAAGTATTGGCACACAGTAATTC 59.348 33.333 0.00 0.00 39.29 2.17
2465 2759 6.892658 AAAGTATTGGCACACAGTAATTCA 57.107 33.333 0.00 0.00 39.29 2.57
2467 2761 5.804639 AGTATTGGCACACAGTAATTCAGA 58.195 37.500 0.00 0.00 39.29 3.27
2468 2762 6.237901 AGTATTGGCACACAGTAATTCAGAA 58.762 36.000 0.00 0.00 39.29 3.02
2469 2763 5.633830 ATTGGCACACAGTAATTCAGAAG 57.366 39.130 0.00 0.00 39.29 2.85
2470 2764 4.085357 TGGCACACAGTAATTCAGAAGT 57.915 40.909 0.00 0.00 0.00 3.01
2471 2765 4.065088 TGGCACACAGTAATTCAGAAGTC 58.935 43.478 0.00 0.00 0.00 3.01
2472 2766 3.123621 GGCACACAGTAATTCAGAAGTCG 59.876 47.826 0.00 0.00 0.00 4.18
2473 2767 3.987868 GCACACAGTAATTCAGAAGTCGA 59.012 43.478 0.00 0.00 0.00 4.20
2474 2768 4.447724 GCACACAGTAATTCAGAAGTCGAA 59.552 41.667 0.00 0.00 0.00 3.71
2475 2769 5.050363 GCACACAGTAATTCAGAAGTCGAAA 60.050 40.000 0.00 0.00 0.00 3.46
2476 2770 6.347725 GCACACAGTAATTCAGAAGTCGAAAT 60.348 38.462 0.00 0.00 0.00 2.17
2477 2771 7.011773 CACACAGTAATTCAGAAGTCGAAATG 58.988 38.462 0.00 0.00 0.00 2.32
2478 2772 6.147821 ACACAGTAATTCAGAAGTCGAAATGG 59.852 38.462 0.00 0.00 0.00 3.16
2497 2853 3.289836 TGGTCAACATAGGGCATTCATG 58.710 45.455 0.00 0.00 0.00 3.07
2521 2877 6.484643 TGTACCGATAACTCCTACATACAGAC 59.515 42.308 0.00 0.00 0.00 3.51
2523 2879 4.083431 CCGATAACTCCTACATACAGACCG 60.083 50.000 0.00 0.00 0.00 4.79
2531 2887 5.657474 TCCTACATACAGACCGTTGAATTC 58.343 41.667 0.00 0.00 0.00 2.17
2532 2888 5.421056 TCCTACATACAGACCGTTGAATTCT 59.579 40.000 7.05 0.00 0.00 2.40
2536 2892 6.931838 ACATACAGACCGTTGAATTCTAGAA 58.068 36.000 7.82 7.82 0.00 2.10
2541 2897 6.015688 ACAGACCGTTGAATTCTAGAACAGTA 60.016 38.462 7.48 0.00 0.00 2.74
2544 2900 5.581085 ACCGTTGAATTCTAGAACAGTATGC 59.419 40.000 7.48 0.00 42.53 3.14
2545 2901 5.006746 CCGTTGAATTCTAGAACAGTATGCC 59.993 44.000 7.48 0.00 42.53 4.40
2549 2905 0.750850 TCTAGAACAGTATGCCGGCC 59.249 55.000 26.77 8.84 42.53 6.13
2550 2906 0.753262 CTAGAACAGTATGCCGGCCT 59.247 55.000 26.77 18.16 42.53 5.19
2560 2916 2.320681 ATGCCGGCCTATTCCTAGTA 57.679 50.000 26.77 0.00 0.00 1.82
2563 2919 2.103601 TGCCGGCCTATTCCTAGTAAAC 59.896 50.000 26.77 0.00 0.00 2.01
2567 2923 5.374071 CCGGCCTATTCCTAGTAAACAAAT 58.626 41.667 0.00 0.00 0.00 2.32
2569 2925 6.993902 CCGGCCTATTCCTAGTAAACAAATAA 59.006 38.462 0.00 0.00 0.00 1.40
2570 2926 7.664318 CCGGCCTATTCCTAGTAAACAAATAAT 59.336 37.037 0.00 0.00 0.00 1.28
2571 2927 9.715121 CGGCCTATTCCTAGTAAACAAATAATA 57.285 33.333 0.00 0.00 0.00 0.98
2593 2949 8.803397 AATAATTCCACAGTAAAAGGACTACC 57.197 34.615 0.00 0.00 0.00 3.18
2610 2966 6.000219 GGACTACCATGCTATGTCATCAATT 59.000 40.000 0.00 0.00 35.97 2.32
2611 2967 6.148480 GGACTACCATGCTATGTCATCAATTC 59.852 42.308 0.00 0.00 35.97 2.17
2612 2968 6.835174 ACTACCATGCTATGTCATCAATTCT 58.165 36.000 0.00 0.00 0.00 2.40
2613 2969 7.285566 ACTACCATGCTATGTCATCAATTCTT 58.714 34.615 0.00 0.00 0.00 2.52
2614 2970 8.432013 ACTACCATGCTATGTCATCAATTCTTA 58.568 33.333 0.00 0.00 0.00 2.10
2615 2971 7.502120 ACCATGCTATGTCATCAATTCTTAC 57.498 36.000 0.00 0.00 0.00 2.34
2616 2972 7.285566 ACCATGCTATGTCATCAATTCTTACT 58.714 34.615 0.00 0.00 0.00 2.24
2617 2973 7.776969 ACCATGCTATGTCATCAATTCTTACTT 59.223 33.333 0.00 0.00 0.00 2.24
2618 2974 8.288208 CCATGCTATGTCATCAATTCTTACTTC 58.712 37.037 0.00 0.00 0.00 3.01
2619 2975 9.053840 CATGCTATGTCATCAATTCTTACTTCT 57.946 33.333 0.00 0.00 0.00 2.85
2620 2976 8.654230 TGCTATGTCATCAATTCTTACTTCTC 57.346 34.615 0.00 0.00 0.00 2.87
2621 2977 8.481314 TGCTATGTCATCAATTCTTACTTCTCT 58.519 33.333 0.00 0.00 0.00 3.10
2622 2978 8.763356 GCTATGTCATCAATTCTTACTTCTCTG 58.237 37.037 0.00 0.00 0.00 3.35
2625 2981 9.730705 ATGTCATCAATTCTTACTTCTCTGAAA 57.269 29.630 0.00 0.00 0.00 2.69
2626 2982 9.730705 TGTCATCAATTCTTACTTCTCTGAAAT 57.269 29.630 0.00 0.00 0.00 2.17
2672 3028 9.793259 TGAAAGTCATTGTCTTTTCCTTAGTAT 57.207 29.630 9.69 0.00 35.62 2.12
2732 3455 1.202222 GCAATGCATGTGCCTAGACAC 60.202 52.381 17.74 1.65 41.18 3.67
2743 3466 2.371841 TGCCTAGACACAAAGACCACAT 59.628 45.455 0.00 0.00 0.00 3.21
2792 3515 3.405831 CATCACACTGACCATGAGTTGT 58.594 45.455 0.00 0.00 0.00 3.32
2839 3570 9.078753 AGTTTCATTTTTACGTTTTGGTACTTG 57.921 29.630 0.00 0.00 0.00 3.16
2886 3617 6.564709 TTTGTCATCTCCATCTTTTCTGTG 57.435 37.500 0.00 0.00 0.00 3.66
2900 3631 3.569194 TTCTGTGCTTTCCACCTTACA 57.431 42.857 0.00 0.00 44.01 2.41
2940 3671 1.937191 TCTTTCCCTTCATTTGCCCC 58.063 50.000 0.00 0.00 0.00 5.80
2943 3674 1.643310 TTCCCTTCATTTGCCCCTTG 58.357 50.000 0.00 0.00 0.00 3.61
2960 3691 3.274288 CCTTGCCTGGAGAATACACTTC 58.726 50.000 0.00 0.00 0.00 3.01
3199 3930 2.915349 TGCTTGATCTCCTGCTCATTC 58.085 47.619 0.00 0.00 0.00 2.67
3228 3959 2.024273 TCGTAGATGGTTCCTTCCTCCT 60.024 50.000 1.86 0.00 0.00 3.69
3319 4050 3.255149 CAGCTGAAAACATCAAGGAAGCT 59.745 43.478 8.42 0.00 37.67 3.74
3340 4071 0.818296 GGTTCTCGAGCTTGAGCCTA 59.182 55.000 24.19 10.45 43.38 3.93
3445 4176 2.260869 CGGAGCCCTGTGGTGTTTG 61.261 63.158 0.00 0.00 0.00 2.93
3507 5580 4.115199 CCCCTGGAGGCCTTTCCG 62.115 72.222 6.77 1.23 40.27 4.30
3562 7421 3.166489 GCAGGCACTTCGAATACTACT 57.834 47.619 0.00 0.00 34.60 2.57
3566 7425 4.563184 CAGGCACTTCGAATACTACTGTTC 59.437 45.833 0.00 0.00 34.60 3.18
3640 7502 0.684153 GCAGGCTTTTCCATAGGCCA 60.684 55.000 5.01 0.00 46.23 5.36
3718 7611 3.614092 TGCTTGATGAAGGGCTAGAAAG 58.386 45.455 0.00 0.00 0.00 2.62
3737 7630 7.807977 AGAAAGCATTACCATGGTATAACTG 57.192 36.000 25.12 18.96 40.38 3.16
3738 7631 7.346471 AGAAAGCATTACCATGGTATAACTGT 58.654 34.615 25.12 16.35 40.38 3.55
3739 7632 8.491134 AGAAAGCATTACCATGGTATAACTGTA 58.509 33.333 25.12 9.01 40.38 2.74
3769 9883 8.357402 GGATACATTTGTGTCTGTTAGGTTTTT 58.643 33.333 7.28 0.00 36.56 1.94
3794 9908 0.670546 GCAGCGCTTTGTCTCACCTA 60.671 55.000 7.50 0.00 0.00 3.08
3797 9911 3.521560 CAGCGCTTTGTCTCACCTAATA 58.478 45.455 7.50 0.00 0.00 0.98
3798 9912 3.932710 CAGCGCTTTGTCTCACCTAATAA 59.067 43.478 7.50 0.00 0.00 1.40
3808 9922 6.051646 GTCTCACCTAATAAGAGACGAGAC 57.948 45.833 6.11 0.00 45.88 3.36
3813 9927 3.499157 CCTAATAAGAGACGAGACCTCCG 59.501 52.174 0.00 0.00 0.00 4.63
3842 9962 1.814634 CGTAGGGCGATAGGAGTCACT 60.815 57.143 0.00 0.00 44.77 3.41
3855 9975 3.334751 TCACTCAAACGCGCACCG 61.335 61.111 5.73 0.00 44.21 4.94
4081 10213 9.914923 AAAATGTTTTCACTTTTCTTAAATCGC 57.085 25.926 0.00 0.00 30.85 4.58
4082 10214 8.641499 AATGTTTTCACTTTTCTTAAATCGCA 57.359 26.923 0.00 0.00 0.00 5.10
4084 10216 8.467402 TGTTTTCACTTTTCTTAAATCGCAAA 57.533 26.923 0.00 0.00 0.00 3.68
4172 10306 8.767478 ATCATGAAATTTTCAACAATGACTCC 57.233 30.769 15.34 0.00 43.95 3.85
4174 10308 5.527951 TGAAATTTTCAACAATGACTCCCG 58.472 37.500 9.36 0.00 36.59 5.14
4177 10311 2.270352 TTCAACAATGACTCCCGCTT 57.730 45.000 0.00 0.00 34.61 4.68
4178 10312 2.270352 TCAACAATGACTCCCGCTTT 57.730 45.000 0.00 0.00 0.00 3.51
4179 10313 2.582052 TCAACAATGACTCCCGCTTTT 58.418 42.857 0.00 0.00 0.00 2.27
4181 10315 4.138290 TCAACAATGACTCCCGCTTTTTA 58.862 39.130 0.00 0.00 0.00 1.52
4182 10316 4.580995 TCAACAATGACTCCCGCTTTTTAA 59.419 37.500 0.00 0.00 0.00 1.52
4187 10321 6.433093 ACAATGACTCCCGCTTTTTAATAGTT 59.567 34.615 0.00 0.00 0.00 2.24
4215 10352 6.502652 TCACGAATTCAAACAATGTTCACAT 58.497 32.000 6.22 0.00 38.41 3.21
4256 10393 7.922505 TCAAAAACTCAATAAATGTTCACCG 57.077 32.000 0.00 0.00 0.00 4.94
4257 10394 6.920758 TCAAAAACTCAATAAATGTTCACCGG 59.079 34.615 0.00 0.00 0.00 5.28
4258 10395 6.399639 AAAACTCAATAAATGTTCACCGGT 57.600 33.333 0.00 0.00 0.00 5.28
4259 10396 6.399639 AAACTCAATAAATGTTCACCGGTT 57.600 33.333 2.97 0.00 0.00 4.44
4260 10397 5.622770 ACTCAATAAATGTTCACCGGTTC 57.377 39.130 2.97 0.00 0.00 3.62
4261 10398 5.067273 ACTCAATAAATGTTCACCGGTTCA 58.933 37.500 2.97 5.21 0.00 3.18
4262 10399 5.533154 ACTCAATAAATGTTCACCGGTTCAA 59.467 36.000 2.97 0.00 0.00 2.69
4263 10400 6.039941 ACTCAATAAATGTTCACCGGTTCAAA 59.960 34.615 2.97 0.00 0.00 2.69
4264 10401 6.987386 TCAATAAATGTTCACCGGTTCAAAT 58.013 32.000 2.97 0.00 0.00 2.32
4265 10402 8.112016 TCAATAAATGTTCACCGGTTCAAATA 57.888 30.769 2.97 0.00 0.00 1.40
4266 10403 8.577296 TCAATAAATGTTCACCGGTTCAAATAA 58.423 29.630 2.97 0.00 0.00 1.40
4267 10404 9.364989 CAATAAATGTTCACCGGTTCAAATAAT 57.635 29.630 2.97 0.00 0.00 1.28
4268 10405 8.925161 ATAAATGTTCACCGGTTCAAATAATG 57.075 30.769 2.97 0.00 0.00 1.90
4269 10406 5.975693 ATGTTCACCGGTTCAAATAATGT 57.024 34.783 2.97 0.00 0.00 2.71
4270 10407 5.776173 TGTTCACCGGTTCAAATAATGTT 57.224 34.783 2.97 0.00 0.00 2.71
4271 10408 5.524284 TGTTCACCGGTTCAAATAATGTTG 58.476 37.500 2.97 0.00 0.00 3.33
4272 10409 4.167554 TCACCGGTTCAAATAATGTTGC 57.832 40.909 2.97 0.00 0.00 4.17
4273 10410 2.914214 CACCGGTTCAAATAATGTTGCG 59.086 45.455 2.97 0.00 0.00 4.85
4274 10411 1.917303 CCGGTTCAAATAATGTTGCGC 59.083 47.619 0.00 0.00 0.00 6.09
4275 10412 2.590073 CGGTTCAAATAATGTTGCGCA 58.410 42.857 5.66 5.66 0.00 6.09
4276 10413 3.178267 CGGTTCAAATAATGTTGCGCAT 58.822 40.909 12.75 0.00 40.03 4.73
4278 10415 4.091220 CGGTTCAAATAATGTTGCGCATTT 59.909 37.500 12.75 4.45 44.82 2.32
4279 10416 5.550070 GGTTCAAATAATGTTGCGCATTTC 58.450 37.500 12.75 5.82 44.82 2.17
4280 10417 5.119898 GGTTCAAATAATGTTGCGCATTTCA 59.880 36.000 12.75 12.00 44.82 2.69
4281 10418 6.347240 GGTTCAAATAATGTTGCGCATTTCAA 60.347 34.615 12.75 0.00 44.82 2.69
4282 10419 6.775939 TCAAATAATGTTGCGCATTTCAAA 57.224 29.167 12.75 4.93 44.82 2.69
4283 10420 7.182361 TCAAATAATGTTGCGCATTTCAAAA 57.818 28.000 12.75 4.58 44.82 2.44
4284 10421 7.633621 TCAAATAATGTTGCGCATTTCAAAAA 58.366 26.923 12.75 0.00 44.82 1.94
4354 10491 8.973182 ACACCGGGATTTATAAATTTATTGTGT 58.027 29.630 15.64 16.15 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 113 2.111999 CTCAACTCCGAGGGGCAACA 62.112 60.000 0.00 0.00 39.74 3.33
113 115 3.068881 CTCAACTCCGAGGGGCAA 58.931 61.111 0.00 0.00 0.00 4.52
212 237 1.300931 GAGCACACGCAGAACCAGA 60.301 57.895 0.00 0.00 42.27 3.86
377 402 3.461773 ACGAGGATGAGGCCCACG 61.462 66.667 0.00 0.00 35.44 4.94
379 404 1.001120 TACACGAGGATGAGGCCCA 59.999 57.895 0.00 0.00 0.00 5.36
444 469 4.129737 ACGACCATGACCGAGCGG 62.130 66.667 7.48 7.48 42.03 5.52
507 584 2.756283 CCCTCTCGCCGAAGACCT 60.756 66.667 0.00 0.00 0.00 3.85
530 622 2.350895 CATCCTCGCCACAACCCA 59.649 61.111 0.00 0.00 0.00 4.51
665 782 2.617788 CCGGTCAACCTCCATTGATTCA 60.618 50.000 0.00 0.00 40.60 2.57
744 888 3.461773 GCCTAGTGAGCGGCTGGA 61.462 66.667 7.50 0.00 42.98 3.86
754 898 1.515954 CTGGTGTACCCGCCTAGTG 59.484 63.158 0.00 0.00 42.08 2.74
841 992 1.969064 CCGAATTTGGTGCCGGTGA 60.969 57.895 1.90 0.00 37.40 4.02
860 1012 1.131693 CCCATTTTTCGTCGGTTAGGC 59.868 52.381 0.00 0.00 0.00 3.93
936 1094 4.733972 GGCATATCTAAAGCCGAAACTC 57.266 45.455 0.00 0.00 38.86 3.01
943 1101 1.809684 GGTCCGGCATATCTAAAGCC 58.190 55.000 0.00 0.00 44.89 4.35
944 1102 1.270147 ACGGTCCGGCATATCTAAAGC 60.270 52.381 17.28 0.00 0.00 3.51
945 1103 2.223971 ACACGGTCCGGCATATCTAAAG 60.224 50.000 17.28 0.00 0.00 1.85
946 1104 1.758280 ACACGGTCCGGCATATCTAAA 59.242 47.619 17.28 0.00 0.00 1.85
947 1105 1.338973 GACACGGTCCGGCATATCTAA 59.661 52.381 17.28 0.00 0.00 2.10
948 1106 0.956633 GACACGGTCCGGCATATCTA 59.043 55.000 17.28 0.00 0.00 1.98
949 1107 1.040893 TGACACGGTCCGGCATATCT 61.041 55.000 17.28 0.00 0.00 1.98
950 1108 0.179094 TTGACACGGTCCGGCATATC 60.179 55.000 17.28 5.94 0.00 1.63
951 1109 0.250793 TTTGACACGGTCCGGCATAT 59.749 50.000 17.28 0.00 0.00 1.78
952 1110 0.390603 CTTTGACACGGTCCGGCATA 60.391 55.000 17.28 5.28 0.00 3.14
953 1111 1.671054 CTTTGACACGGTCCGGCAT 60.671 57.895 17.28 0.00 0.00 4.40
954 1112 2.280524 CTTTGACACGGTCCGGCA 60.281 61.111 17.28 7.93 0.00 5.69
955 1113 3.047877 CCTTTGACACGGTCCGGC 61.048 66.667 17.28 5.16 0.00 6.13
956 1114 2.358247 CCCTTTGACACGGTCCGG 60.358 66.667 17.28 7.22 0.00 5.14
957 1115 1.666872 GACCCTTTGACACGGTCCG 60.667 63.158 10.48 10.48 40.23 4.79
958 1116 1.666872 CGACCCTTTGACACGGTCC 60.667 63.158 9.06 0.00 42.65 4.46
959 1117 0.666577 CTCGACCCTTTGACACGGTC 60.667 60.000 5.74 5.74 42.27 4.79
960 1118 1.366366 CTCGACCCTTTGACACGGT 59.634 57.895 0.00 0.00 0.00 4.83
961 1119 2.027625 GCTCGACCCTTTGACACGG 61.028 63.158 0.00 0.00 0.00 4.94
962 1120 2.027625 GGCTCGACCCTTTGACACG 61.028 63.158 0.00 0.00 0.00 4.49
963 1121 2.027625 CGGCTCGACCCTTTGACAC 61.028 63.158 0.00 0.00 33.26 3.67
964 1122 2.035237 AACGGCTCGACCCTTTGACA 62.035 55.000 1.50 0.00 33.26 3.58
965 1123 1.289800 GAACGGCTCGACCCTTTGAC 61.290 60.000 0.00 0.00 33.26 3.18
966 1124 1.005394 GAACGGCTCGACCCTTTGA 60.005 57.895 0.00 0.00 33.26 2.69
967 1125 2.033194 GGAACGGCTCGACCCTTTG 61.033 63.158 0.00 0.00 33.26 2.77
968 1126 2.346365 GGAACGGCTCGACCCTTT 59.654 61.111 1.50 0.00 33.26 3.11
969 1127 3.703127 GGGAACGGCTCGACCCTT 61.703 66.667 18.39 0.00 40.87 3.95
972 1130 4.011517 TTGGGGAACGGCTCGACC 62.012 66.667 1.50 4.80 0.00 4.79
973 1131 2.741211 GTTGGGGAACGGCTCGAC 60.741 66.667 1.50 0.00 0.00 4.20
974 1132 2.515996 GATGTTGGGGAACGGCTCGA 62.516 60.000 1.50 0.00 0.00 4.04
975 1133 2.046314 ATGTTGGGGAACGGCTCG 60.046 61.111 0.00 0.00 0.00 5.03
976 1134 0.744771 GAGATGTTGGGGAACGGCTC 60.745 60.000 0.00 0.00 0.00 4.70
977 1135 1.299976 GAGATGTTGGGGAACGGCT 59.700 57.895 0.00 0.00 0.00 5.52
978 1136 1.749258 GGAGATGTTGGGGAACGGC 60.749 63.158 0.00 0.00 0.00 5.68
1062 1220 3.431725 CTTCTGCGGCGGGGTTTC 61.432 66.667 9.78 0.00 0.00 2.78
1287 1445 7.116233 CACAAAGCCACACCAAGTAAAAATATC 59.884 37.037 0.00 0.00 0.00 1.63
1291 1449 4.499183 CACAAAGCCACACCAAGTAAAAA 58.501 39.130 0.00 0.00 0.00 1.94
1373 1531 2.035626 CCCTTGTCCATGGCCGTT 59.964 61.111 6.96 0.00 0.00 4.44
1424 1582 3.636764 GCAGTGGAACAAATATTAGGGGG 59.363 47.826 0.00 0.00 44.16 5.40
1456 1614 3.374678 GGTTAACACGTGACAAACTTGGA 59.625 43.478 25.01 0.00 32.40 3.53
1622 1780 2.046283 TCACGAGTTCACGATGTCAC 57.954 50.000 0.00 0.00 37.03 3.67
1803 1964 5.800296 TCTCCGTTCCTGAAAACATATGAA 58.200 37.500 10.38 0.00 0.00 2.57
2028 2189 6.007076 TGCTCTAGAATACTCCTCCATGTAG 58.993 44.000 0.00 0.00 0.00 2.74
2133 2301 8.589338 AGAAAACATAGGCATAGATACCTAGTG 58.411 37.037 0.00 0.00 41.74 2.74
2357 2532 5.277828 GGCCGTCTAATTGCCTTACAAATAG 60.278 44.000 0.00 0.00 42.86 1.73
2359 2534 3.380320 GGCCGTCTAATTGCCTTACAAAT 59.620 43.478 0.00 0.00 42.86 2.32
2362 2537 2.032680 GGCCGTCTAATTGCCTTACA 57.967 50.000 0.00 0.00 42.01 2.41
2377 2552 7.860872 GTCAAAAATTGGTATATTCTTAGGCCG 59.139 37.037 0.00 0.00 0.00 6.13
2388 2682 9.739276 AGAGAGAATGTGTCAAAAATTGGTATA 57.261 29.630 0.00 0.00 0.00 1.47
2395 2689 5.643777 CCGGTAGAGAGAATGTGTCAAAAAT 59.356 40.000 0.00 0.00 0.00 1.82
2435 2729 6.868622 ACTGTGTGCCAATACTTTTTGTTTA 58.131 32.000 0.00 0.00 0.00 2.01
2456 2750 6.368791 TGACCATTTCGACTTCTGAATTACTG 59.631 38.462 0.00 0.00 0.00 2.74
2457 2751 6.464222 TGACCATTTCGACTTCTGAATTACT 58.536 36.000 0.00 0.00 0.00 2.24
2458 2752 6.721571 TGACCATTTCGACTTCTGAATTAC 57.278 37.500 0.00 0.00 0.00 1.89
2460 2754 5.530915 TGTTGACCATTTCGACTTCTGAATT 59.469 36.000 0.00 0.00 39.23 2.17
2461 2755 5.063204 TGTTGACCATTTCGACTTCTGAAT 58.937 37.500 0.00 0.00 39.23 2.57
2464 2758 5.063944 CCTATGTTGACCATTTCGACTTCTG 59.936 44.000 0.00 0.00 39.23 3.02
2465 2759 5.178797 CCTATGTTGACCATTTCGACTTCT 58.821 41.667 0.00 0.00 39.23 2.85
2467 2761 4.261801 CCCTATGTTGACCATTTCGACTT 58.738 43.478 0.00 0.00 39.23 3.01
2468 2762 3.873910 CCCTATGTTGACCATTTCGACT 58.126 45.455 0.00 0.00 39.23 4.18
2469 2763 2.354821 GCCCTATGTTGACCATTTCGAC 59.645 50.000 0.00 0.00 38.96 4.20
2470 2764 2.026729 TGCCCTATGTTGACCATTTCGA 60.027 45.455 0.00 0.00 34.86 3.71
2471 2765 2.364632 TGCCCTATGTTGACCATTTCG 58.635 47.619 0.00 0.00 34.86 3.46
2472 2766 4.402155 TGAATGCCCTATGTTGACCATTTC 59.598 41.667 0.00 0.00 34.86 2.17
2473 2767 4.352009 TGAATGCCCTATGTTGACCATTT 58.648 39.130 0.00 0.00 34.86 2.32
2474 2768 3.979911 TGAATGCCCTATGTTGACCATT 58.020 40.909 0.00 0.00 34.86 3.16
2475 2769 3.668141 TGAATGCCCTATGTTGACCAT 57.332 42.857 0.00 0.00 37.58 3.55
2476 2770 3.289836 CATGAATGCCCTATGTTGACCA 58.710 45.455 0.00 0.00 0.00 4.02
2477 2771 3.290710 ACATGAATGCCCTATGTTGACC 58.709 45.455 0.00 0.00 31.38 4.02
2478 2772 4.275936 GGTACATGAATGCCCTATGTTGAC 59.724 45.833 0.00 0.00 36.52 3.18
2497 2853 6.072783 GGTCTGTATGTAGGAGTTATCGGTAC 60.073 46.154 0.00 0.00 0.00 3.34
2521 2877 5.006746 GGCATACTGTTCTAGAATTCAACGG 59.993 44.000 8.75 10.76 33.35 4.44
2523 2879 5.006746 CCGGCATACTGTTCTAGAATTCAAC 59.993 44.000 8.75 4.29 0.00 3.18
2531 2887 0.753262 AGGCCGGCATACTGTTCTAG 59.247 55.000 30.85 0.00 0.00 2.43
2532 2888 2.076207 TAGGCCGGCATACTGTTCTA 57.924 50.000 30.85 14.65 0.00 2.10
2536 2892 0.396811 GGAATAGGCCGGCATACTGT 59.603 55.000 30.85 14.75 0.00 3.55
2541 2897 2.320681 TACTAGGAATAGGCCGGCAT 57.679 50.000 30.85 26.24 0.00 4.40
2544 2900 4.411256 TTGTTTACTAGGAATAGGCCGG 57.589 45.455 0.00 0.00 0.00 6.13
2545 2901 8.617290 ATTATTTGTTTACTAGGAATAGGCCG 57.383 34.615 0.00 0.00 0.00 6.13
2567 2923 9.895138 GGTAGTCCTTTTACTGTGGAATTATTA 57.105 33.333 0.00 0.00 30.51 0.98
2569 2925 7.924541 TGGTAGTCCTTTTACTGTGGAATTAT 58.075 34.615 0.00 0.00 34.23 1.28
2570 2926 7.319052 TGGTAGTCCTTTTACTGTGGAATTA 57.681 36.000 0.00 0.00 34.23 1.40
2571 2927 6.195600 TGGTAGTCCTTTTACTGTGGAATT 57.804 37.500 0.00 0.00 34.23 2.17
2572 2928 5.836024 TGGTAGTCCTTTTACTGTGGAAT 57.164 39.130 0.00 0.00 34.23 3.01
2576 2932 4.579869 AGCATGGTAGTCCTTTTACTGTG 58.420 43.478 0.00 0.00 34.23 3.66
2578 2934 6.349300 ACATAGCATGGTAGTCCTTTTACTG 58.651 40.000 10.82 2.46 34.23 2.74
2579 2935 6.156256 TGACATAGCATGGTAGTCCTTTTACT 59.844 38.462 21.30 0.00 34.23 2.24
2586 2942 4.607293 TGATGACATAGCATGGTAGTCC 57.393 45.455 21.30 13.11 33.60 3.85
2592 2948 7.741027 AGTAAGAATTGATGACATAGCATGG 57.259 36.000 0.00 0.00 33.60 3.66
2593 2949 9.053840 AGAAGTAAGAATTGATGACATAGCATG 57.946 33.333 0.00 0.00 0.00 4.06
2628 2984 9.507329 TGACTTTCAGCTAGACAAGATTTTATT 57.493 29.630 0.00 0.00 0.00 1.40
2629 2985 9.678260 ATGACTTTCAGCTAGACAAGATTTTAT 57.322 29.630 0.00 0.00 0.00 1.40
2630 2986 9.507329 AATGACTTTCAGCTAGACAAGATTTTA 57.493 29.630 0.00 0.00 0.00 1.52
2631 2987 7.992754 ATGACTTTCAGCTAGACAAGATTTT 57.007 32.000 0.00 0.00 0.00 1.82
2632 2988 7.446625 ACAATGACTTTCAGCTAGACAAGATTT 59.553 33.333 0.00 0.00 0.00 2.17
2633 2989 6.939163 ACAATGACTTTCAGCTAGACAAGATT 59.061 34.615 0.00 0.00 0.00 2.40
2634 2990 6.471146 ACAATGACTTTCAGCTAGACAAGAT 58.529 36.000 0.00 0.00 0.00 2.40
2672 3028 8.976353 ACCATAATTCAGTAATGCAAATGGTAA 58.024 29.630 13.81 0.00 35.96 2.85
2728 3451 5.689383 ATGTGTTATGTGGTCTTTGTGTC 57.311 39.130 0.00 0.00 0.00 3.67
2732 3455 6.563422 CCCATAATGTGTTATGTGGTCTTTG 58.437 40.000 7.23 0.00 43.64 2.77
2792 3515 9.444600 GAAACTTAGGTCAGTATTCAATAACCA 57.555 33.333 0.54 0.00 0.00 3.67
2802 3525 9.498176 ACGTAAAAATGAAACTTAGGTCAGTAT 57.502 29.630 0.00 0.00 0.00 2.12
2886 3617 5.003804 TCTTCTCAATGTAAGGTGGAAAGC 58.996 41.667 0.00 0.00 0.00 3.51
2900 3631 5.991861 AGATTGCTCAGATGTCTTCTCAAT 58.008 37.500 2.55 2.55 32.16 2.57
2940 3671 3.942829 TGAAGTGTATTCTCCAGGCAAG 58.057 45.455 0.00 0.00 0.00 4.01
2943 3674 3.879892 GGATTGAAGTGTATTCTCCAGGC 59.120 47.826 0.00 0.00 0.00 4.85
2960 3691 5.025826 GCGGTTCTAATTTGTTACGGATTG 58.974 41.667 0.00 0.00 0.00 2.67
3155 3886 2.487934 CACAGCAGCACAGGGATATAC 58.512 52.381 0.00 0.00 0.00 1.47
3199 3930 0.456221 AACCATCTACGAGCGGACAG 59.544 55.000 0.00 0.00 0.00 3.51
3319 4050 1.293498 GCTCAAGCTCGAGAACCCA 59.707 57.895 18.75 0.00 38.21 4.51
3439 4170 7.813852 ACGAGTATTATCTCAGAACAAACAC 57.186 36.000 0.00 0.00 34.46 3.32
3440 4171 8.737175 AGTACGAGTATTATCTCAGAACAAACA 58.263 33.333 0.00 0.00 34.46 2.83
3445 4176 6.144175 GCCAGTACGAGTATTATCTCAGAAC 58.856 44.000 0.00 0.00 34.46 3.01
3541 7400 1.852895 GTAGTATTCGAAGTGCCTGCG 59.147 52.381 3.35 0.00 33.08 5.18
3562 7421 6.072230 TCCATTTCATAGAAATGCAACGAACA 60.072 34.615 21.18 0.00 36.56 3.18
3566 7425 5.639757 TGTCCATTTCATAGAAATGCAACG 58.360 37.500 21.18 11.43 36.56 4.10
3640 7502 8.691661 ATATAAGACGTTTTGATAGGCCATTT 57.308 30.769 5.01 0.00 0.00 2.32
3650 7512 9.015367 TCCATTCCAAAATATAAGACGTTTTGA 57.985 29.630 0.83 0.00 42.47 2.69
3718 7611 9.162764 CCTTATACAGTTATACCATGGTAATGC 57.837 37.037 27.93 18.89 33.99 3.56
3739 7632 8.548877 ACCTAACAGACACAAATGTATCCTTAT 58.451 33.333 0.00 0.00 39.95 1.73
3769 9883 2.203337 ACAAAGCGCTGCCTGGAA 60.203 55.556 12.58 0.00 0.00 3.53
3770 9884 2.669569 GACAAAGCGCTGCCTGGA 60.670 61.111 12.58 0.00 0.00 3.86
3774 9888 2.558313 GTGAGACAAAGCGCTGCC 59.442 61.111 12.58 0.00 0.00 4.85
3794 9908 3.278668 TCGGAGGTCTCGTCTCTTATT 57.721 47.619 0.00 0.00 0.00 1.40
3797 9911 2.018515 GATTCGGAGGTCTCGTCTCTT 58.981 52.381 0.00 0.00 0.00 2.85
3798 9912 1.670791 GATTCGGAGGTCTCGTCTCT 58.329 55.000 0.00 0.00 0.00 3.10
3805 9919 3.155167 GCGGGGATTCGGAGGTCT 61.155 66.667 0.00 0.00 0.00 3.85
3808 9922 3.208884 CTACGCGGGGATTCGGAGG 62.209 68.421 12.47 0.00 33.25 4.30
3860 9980 1.832883 AAAGGGCGCATGTTGTATCA 58.167 45.000 10.83 0.00 0.00 2.15
3887 10007 4.781959 CACTGCCGCGCAAATGGG 62.782 66.667 8.75 0.00 38.41 4.00
3903 10023 3.558033 ACGAAAAAGAAAAGTAGGGGCA 58.442 40.909 0.00 0.00 0.00 5.36
3999 10124 8.132362 CCGATGAATGTTTAAATCCGGATTTAA 58.868 33.333 39.92 39.92 45.93 1.52
4000 10125 7.499563 TCCGATGAATGTTTAAATCCGGATTTA 59.500 33.333 35.30 35.30 40.99 1.40
4004 10129 4.771903 TCCGATGAATGTTTAAATCCGGA 58.228 39.130 6.61 6.61 0.00 5.14
4005 10130 5.493133 TTCCGATGAATGTTTAAATCCGG 57.507 39.130 0.00 0.00 0.00 5.14
4006 10131 7.985634 ATTTTCCGATGAATGTTTAAATCCG 57.014 32.000 0.00 0.00 0.00 4.18
4021 10152 6.868339 GTGAACATTTCCTGAAATTTTCCGAT 59.132 34.615 20.44 1.21 42.41 4.18
4035 10166 9.786105 ACATTTTTCAAAATTGTGAACATTTCC 57.214 25.926 10.70 0.00 37.24 3.13
4063 10195 8.864069 TCAATTTGCGATTTAAGAAAAGTGAA 57.136 26.923 0.00 0.00 38.00 3.18
4146 10280 9.211485 GGAGTCATTGTTGAAAATTTCATGATT 57.789 29.630 9.41 6.96 39.84 2.57
4148 10282 7.153985 GGGAGTCATTGTTGAAAATTTCATGA 58.846 34.615 9.41 7.37 39.84 3.07
4149 10283 6.089820 CGGGAGTCATTGTTGAAAATTTCATG 59.910 38.462 9.41 5.09 39.84 3.07
4153 10287 4.039124 AGCGGGAGTCATTGTTGAAAATTT 59.961 37.500 0.00 0.00 32.48 1.82
4155 10289 3.157087 AGCGGGAGTCATTGTTGAAAAT 58.843 40.909 0.00 0.00 32.48 1.82
4156 10290 2.582052 AGCGGGAGTCATTGTTGAAAA 58.418 42.857 0.00 0.00 32.48 2.29
4157 10291 2.270352 AGCGGGAGTCATTGTTGAAA 57.730 45.000 0.00 0.00 32.48 2.69
4158 10292 2.270352 AAGCGGGAGTCATTGTTGAA 57.730 45.000 0.00 0.00 32.48 2.69
4159 10293 2.270352 AAAGCGGGAGTCATTGTTGA 57.730 45.000 0.00 0.00 0.00 3.18
4160 10294 3.369546 AAAAAGCGGGAGTCATTGTTG 57.630 42.857 0.00 0.00 0.00 3.33
4161 10295 5.722021 ATTAAAAAGCGGGAGTCATTGTT 57.278 34.783 0.00 0.00 0.00 2.83
4162 10296 5.944007 ACTATTAAAAAGCGGGAGTCATTGT 59.056 36.000 0.00 0.00 0.00 2.71
4163 10297 6.436843 ACTATTAAAAAGCGGGAGTCATTG 57.563 37.500 0.00 0.00 0.00 2.82
4166 10300 6.887626 AAAACTATTAAAAAGCGGGAGTCA 57.112 33.333 0.00 0.00 0.00 3.41
4187 10321 8.165428 GTGAACATTGTTTGAATTCGTGAAAAA 58.835 29.630 3.08 0.00 0.00 1.94
4232 10369 6.920758 CCGGTGAACATTTATTGAGTTTTTGA 59.079 34.615 0.00 0.00 0.00 2.69
4233 10370 6.699642 ACCGGTGAACATTTATTGAGTTTTTG 59.300 34.615 6.12 0.00 0.00 2.44
4238 10375 5.067273 TGAACCGGTGAACATTTATTGAGT 58.933 37.500 8.52 0.00 0.00 3.41
4239 10376 5.621197 TGAACCGGTGAACATTTATTGAG 57.379 39.130 8.52 0.00 0.00 3.02
4241 10378 8.749841 TTATTTGAACCGGTGAACATTTATTG 57.250 30.769 8.52 0.00 0.00 1.90
4246 10383 6.339587 ACATTATTTGAACCGGTGAACATT 57.660 33.333 8.52 0.00 0.00 2.71
4247 10384 5.975693 ACATTATTTGAACCGGTGAACAT 57.024 34.783 8.52 0.15 0.00 2.71
4248 10385 5.524284 CAACATTATTTGAACCGGTGAACA 58.476 37.500 8.52 6.57 0.00 3.18
4249 10386 4.384547 GCAACATTATTTGAACCGGTGAAC 59.615 41.667 8.52 3.49 0.00 3.18
4250 10387 4.551388 GCAACATTATTTGAACCGGTGAA 58.449 39.130 8.52 4.02 0.00 3.18
4251 10388 3.365465 CGCAACATTATTTGAACCGGTGA 60.365 43.478 8.52 0.00 0.00 4.02
4252 10389 2.914214 CGCAACATTATTTGAACCGGTG 59.086 45.455 8.52 0.00 0.00 4.94
4253 10390 2.669950 GCGCAACATTATTTGAACCGGT 60.670 45.455 0.00 0.00 0.00 5.28
4254 10391 1.917303 GCGCAACATTATTTGAACCGG 59.083 47.619 0.30 0.00 0.00 5.28
4255 10392 2.590073 TGCGCAACATTATTTGAACCG 58.410 42.857 8.16 0.00 0.00 4.44
4328 10465 8.973182 ACACAATAAATTTATAAATCCCGGTGT 58.027 29.630 19.22 19.22 0.00 4.16


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

AutoCloner maintained by Alex Coulton.