Multiple sequence alignment - TraesCS6D01G369100

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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 TraesCS6D01G369100 chr6D 100.000 3677 0 0 1 3677 455936638 455932962 0.000000e+00 6791.0
1 TraesCS6D01G369100 chr6D 81.623 1306 132 66 744 2001 455970269 455969024 0.000000e+00 983.0
2 TraesCS6D01G369100 chr6D 85.227 704 69 20 1001 1690 455899719 455899037 0.000000e+00 691.0
3 TraesCS6D01G369100 chr6D 83.788 660 76 21 2143 2788 455969017 455968375 6.800000e-167 597.0
4 TraesCS6D01G369100 chr6D 81.119 715 86 31 1001 1690 455907727 455907037 9.040000e-146 527.0
5 TraesCS6D01G369100 chr6D 88.438 320 27 6 2470 2782 455906044 455905728 9.640000e-101 377.0
6 TraesCS6D01G369100 chr6D 87.461 319 32 5 2472 2783 455897797 455897480 9.710000e-96 361.0
7 TraesCS6D01G369100 chr6D 90.583 223 21 0 3066 3288 455933456 455933234 2.780000e-76 296.0
8 TraesCS6D01G369100 chr6D 90.583 223 21 0 3183 3405 455933573 455933351 2.780000e-76 296.0
9 TraesCS6D01G369100 chr6D 88.889 234 26 0 2151 2384 455906375 455906142 4.650000e-74 289.0
10 TraesCS6D01G369100 chr6D 82.008 239 22 14 3371 3606 455912031 455911811 2.260000e-42 183.0
11 TraesCS6D01G369100 chr6D 82.589 224 22 12 3398 3606 455896803 455896582 8.110000e-42 182.0
12 TraesCS6D01G369100 chr6D 79.512 205 16 15 3006 3185 455912187 455911984 4.990000e-24 122.0
13 TraesCS6D01G369100 chr6D 89.474 76 5 3 3228 3301 455912059 455911985 3.910000e-15 93.5
14 TraesCS6D01G369100 chr6A 91.368 1425 76 21 1905 3288 602726120 602724702 0.000000e+00 1906.0
15 TraesCS6D01G369100 chr6A 90.860 930 44 20 982 1908 602727047 602726156 0.000000e+00 1208.0
16 TraesCS6D01G369100 chr6A 86.127 1038 89 29 999 2001 602740571 602739554 0.000000e+00 1068.0
17 TraesCS6D01G369100 chr6A 92.872 477 33 1 1 477 602728150 602727675 0.000000e+00 691.0
18 TraesCS6D01G369100 chr6A 93.157 453 26 4 3183 3633 602724922 602724473 0.000000e+00 660.0
19 TraesCS6D01G369100 chr6A 88.258 511 41 10 1001 1498 602717637 602717133 8.790000e-166 593.0
20 TraesCS6D01G369100 chr6A 80.383 678 87 21 2119 2792 596485816 596486451 1.200000e-129 473.0
21 TraesCS6D01G369100 chr6A 88.125 320 28 6 2470 2782 602715616 602715300 4.480000e-99 372.0
22 TraesCS6D01G369100 chr6A 86.420 243 33 0 2142 2384 602715956 602715714 2.180000e-67 267.0
23 TraesCS6D01G369100 chr6A 82.545 275 24 10 575 848 602727436 602727185 1.720000e-53 220.0
24 TraesCS6D01G369100 chr6A 92.126 127 9 1 3508 3633 602714597 602714471 1.050000e-40 178.0
25 TraesCS6D01G369100 chr6A 80.597 201 17 9 3006 3185 602720710 602720511 6.410000e-28 135.0
26 TraesCS6D01G369100 chr6A 90.805 87 6 2 2818 2903 602715204 602715119 8.340000e-22 115.0
27 TraesCS6D01G369100 chr6B 94.702 906 33 2 1906 2796 693323371 693322466 0.000000e+00 1393.0
28 TraesCS6D01G369100 chr6B 93.113 755 33 6 972 1719 693324382 693323640 0.000000e+00 1088.0
29 TraesCS6D01G369100 chr6B 91.134 485 32 4 2807 3283 693322414 693321933 0.000000e+00 647.0
30 TraesCS6D01G369100 chr6B 82.951 698 81 20 1001 1673 693133126 693132442 2.440000e-166 595.0
31 TraesCS6D01G369100 chr6B 89.371 461 37 8 3183 3639 693322147 693321695 1.480000e-158 569.0
32 TraesCS6D01G369100 chr6B 85.657 502 48 8 1001 1487 693302744 693302252 1.180000e-139 507.0
33 TraesCS6D01G369100 chr6B 87.812 320 28 8 2470 2782 693299969 693299654 7.500000e-97 364.0
34 TraesCS6D01G369100 chr6B 87.500 320 31 6 2472 2783 693131261 693130943 9.710000e-96 361.0
35 TraesCS6D01G369100 chr6B 85.659 258 37 0 2127 2384 693300327 693300070 4.680000e-69 272.0
36 TraesCS6D01G369100 chr6B 87.083 240 18 6 1676 1908 693323641 693323408 3.640000e-65 259.0
37 TraesCS6D01G369100 chr6B 91.367 139 8 3 3486 3622 693130184 693130048 1.740000e-43 187.0
38 TraesCS6D01G369100 chr6B 94.382 89 5 0 2815 2903 693318346 693318258 1.780000e-28 137.0
39 TraesCS6D01G369100 chr6B 88.889 108 8 3 3066 3173 693322031 693321928 2.980000e-26 130.0
40 TraesCS6D01G369100 chr6B 79.310 145 27 3 333 475 591081015 591080872 8.400000e-17 99.0
41 TraesCS6D01G369100 chr6B 88.679 53 0 3 763 815 693133318 693133272 3.970000e-05 60.2
42 TraesCS6D01G369100 chr3D 93.077 130 9 0 1355 1484 457047672 457047801 1.350000e-44 191.0
43 TraesCS6D01G369100 chr3D 95.192 104 5 0 3497 3600 610112992 610113095 8.170000e-37 165.0
44 TraesCS6D01G369100 chr3B 92.793 111 6 2 3488 3598 822111745 822111853 3.800000e-35 159.0
45 TraesCS6D01G369100 chr1A 91.453 117 4 3 3485 3600 554280647 554280536 4.920000e-34 156.0
46 TraesCS6D01G369100 chr1A 86.154 65 8 1 579 643 372647731 372647668 6.590000e-08 69.4
47 TraesCS6D01G369100 chr5D 82.609 69 9 3 576 643 485292699 485292765 1.430000e-04 58.4


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 TraesCS6D01G369100 chr6D 455932962 455936638 3676 True 2461.000000 6791 93.722000 1 3677 3 chr6D.!!$R4 3676
1 TraesCS6D01G369100 chr6D 455968375 455970269 1894 True 790.000000 983 82.705500 744 2788 2 chr6D.!!$R5 2044
2 TraesCS6D01G369100 chr6D 455896582 455899719 3137 True 411.333333 691 85.092333 1001 3606 3 chr6D.!!$R1 2605
3 TraesCS6D01G369100 chr6D 455905728 455907727 1999 True 397.666667 527 86.148667 1001 2782 3 chr6D.!!$R2 1781
4 TraesCS6D01G369100 chr6A 602739554 602740571 1017 True 1068.000000 1068 86.127000 999 2001 1 chr6A.!!$R1 1002
5 TraesCS6D01G369100 chr6A 602714471 602728150 13679 True 576.818182 1906 88.830273 1 3633 11 chr6A.!!$R2 3632
6 TraesCS6D01G369100 chr6A 596485816 596486451 635 False 473.000000 473 80.383000 2119 2792 1 chr6A.!!$F1 673
7 TraesCS6D01G369100 chr6B 693318258 693324382 6124 True 603.285714 1393 91.239143 972 3639 7 chr6B.!!$R4 2667
8 TraesCS6D01G369100 chr6B 693299654 693302744 3090 True 381.000000 507 86.376000 1001 2782 3 chr6B.!!$R3 1781
9 TraesCS6D01G369100 chr6B 693130048 693133318 3270 True 300.800000 595 87.624250 763 3622 4 chr6B.!!$R2 2859

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
647 805 0.036022 GGTCCAGCAGATCCATAGCC 59.964 60.0 0.00 0.0 0.0 3.93 F
648 806 0.036022 GTCCAGCAGATCCATAGCCC 59.964 60.0 0.00 0.0 0.0 5.19 F
686 844 0.179134 CTAAGACCCGACAGAAGCCG 60.179 60.0 0.00 0.0 0.0 5.52 F
1629 1918 0.317160 TGGTCTCACGCGTCTGATTT 59.683 50.0 9.86 0.0 0.0 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 3058 1.682849 TGGCTCACGGCAAAGGTAT 59.317 52.632 0.00 0.0 43.4 2.73 R
2083 4133 3.444742 CCTAGCATTGCATCAAAGTTCCA 59.555 43.478 11.91 0.0 0.0 3.53 R
2093 4143 4.813027 CAGAAAACAACCTAGCATTGCAT 58.187 39.130 11.91 0.0 0.0 3.96 R
3334 5972 0.240945 CGCATTTTCTCGCCCAAACT 59.759 50.000 0.00 0.0 0.0 2.66 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
31 32 5.870978 GCAATTATTCACAATGAGTTTGCCT 59.129 36.000 0.00 0.00 39.03 4.75
43 44 7.231317 ACAATGAGTTTGCCTTTCTTAAGATCA 59.769 33.333 5.89 4.14 39.03 2.92
67 68 8.260818 TCAGTGGATCAAATTGGTTTTTGTAAA 58.739 29.630 0.00 0.00 37.73 2.01
172 173 7.572523 TTAAGCATCAAGTAATTCCAGATGG 57.427 36.000 0.00 0.00 37.23 3.51
220 221 5.861222 TGATGCCTGCAATACAATATACG 57.139 39.130 0.00 0.00 0.00 3.06
250 251 0.457853 TTCGTCGATGGCTCTTTCGG 60.458 55.000 4.48 0.00 36.08 4.30
253 254 1.439679 GTCGATGGCTCTTTCGGTTT 58.560 50.000 0.00 0.00 36.08 3.27
296 297 3.495377 TCGTTTTGGTTTACGGTCATCTG 59.505 43.478 0.00 0.00 38.26 2.90
303 304 3.071479 GTTTACGGTCATCTGGCTTTGA 58.929 45.455 0.00 0.00 0.00 2.69
379 380 6.951971 AGAGTAGTAGATTGTTTGGCAAGAT 58.048 36.000 0.00 0.00 40.86 2.40
421 422 9.250624 GTAGTACAATTTTATGGCTACAGAGAG 57.749 37.037 0.00 0.00 35.20 3.20
426 427 0.827925 TATGGCTACAGAGAGGGCCG 60.828 60.000 0.00 0.00 46.72 6.13
430 431 1.464376 GCTACAGAGAGGGCCGCATA 61.464 60.000 10.70 0.00 0.00 3.14
463 464 7.011857 GGAAATCTTGCCTCTTGATAGTAACTG 59.988 40.741 0.00 0.00 0.00 3.16
477 478 8.997621 TGATAGTAACTGTGTAATTCTGGAAC 57.002 34.615 0.00 0.00 0.00 3.62
478 479 8.812972 TGATAGTAACTGTGTAATTCTGGAACT 58.187 33.333 0.00 0.00 0.00 3.01
481 482 8.191534 AGTAACTGTGTAATTCTGGAACTACT 57.808 34.615 4.11 0.00 0.00 2.57
518 656 2.047179 GGCGGGCCGGAGAATATC 60.047 66.667 29.48 7.80 0.00 1.63
519 657 2.584391 GGCGGGCCGGAGAATATCT 61.584 63.158 29.48 0.00 0.00 1.98
520 658 1.374758 GCGGGCCGGAGAATATCTG 60.375 63.158 29.48 0.00 0.00 2.90
527 665 2.447244 CGGAGAATATCTGGTGCTCC 57.553 55.000 0.00 0.00 41.29 4.70
528 666 1.688735 CGGAGAATATCTGGTGCTCCA 59.311 52.381 7.39 7.39 44.14 3.86
529 667 2.103094 CGGAGAATATCTGGTGCTCCAA 59.897 50.000 9.14 0.85 44.14 3.53
530 668 3.471680 GGAGAATATCTGGTGCTCCAAC 58.528 50.000 9.14 0.00 43.81 3.77
531 669 3.118261 GGAGAATATCTGGTGCTCCAACA 60.118 47.826 9.14 0.00 43.81 3.33
532 670 3.873952 GAGAATATCTGGTGCTCCAACAC 59.126 47.826 9.14 0.00 43.81 3.32
550 688 2.667473 ACCAAGTGCTACGGTGATAC 57.333 50.000 0.00 0.00 0.00 2.24
552 690 1.556564 CAAGTGCTACGGTGATACGG 58.443 55.000 0.00 0.00 38.39 4.02
559 697 2.286891 GCTACGGTGATACGGACTCTTC 60.287 54.545 0.00 0.00 38.39 2.87
582 740 1.696832 GCCGTTGGATCGAAGTCTGC 61.697 60.000 0.00 0.00 0.00 4.26
586 744 2.143122 GTTGGATCGAAGTCTGCAACA 58.857 47.619 14.02 0.00 40.13 3.33
604 762 3.348647 ACATTTTGCATAAAAGCCCCC 57.651 42.857 0.00 0.00 39.01 5.40
608 766 4.817318 TTTTGCATAAAAGCCCCCTAAG 57.183 40.909 0.00 0.00 32.31 2.18
610 768 3.297134 TGCATAAAAGCCCCCTAAGAG 57.703 47.619 0.00 0.00 0.00 2.85
612 770 3.215151 GCATAAAAGCCCCCTAAGAGTC 58.785 50.000 0.00 0.00 0.00 3.36
614 772 4.455606 CATAAAAGCCCCCTAAGAGTCTG 58.544 47.826 0.00 0.00 0.00 3.51
615 773 1.290134 AAAGCCCCCTAAGAGTCTGG 58.710 55.000 0.00 0.00 0.00 3.86
622 780 3.282885 CCCCTAAGAGTCTGGAAATTGC 58.717 50.000 0.00 0.00 0.00 3.56
636 794 0.394216 AATTGCGCATAGGTCCAGCA 60.394 50.000 12.75 0.00 35.90 4.41
647 805 0.036022 GGTCCAGCAGATCCATAGCC 59.964 60.000 0.00 0.00 0.00 3.93
648 806 0.036022 GTCCAGCAGATCCATAGCCC 59.964 60.000 0.00 0.00 0.00 5.19
649 807 1.130054 TCCAGCAGATCCATAGCCCC 61.130 60.000 0.00 0.00 0.00 5.80
667 825 3.131478 CCCCGGTGCGGTTTCATC 61.131 66.667 0.00 0.00 46.80 2.92
673 831 1.659098 CGGTGCGGTTTCATCTAAGAC 59.341 52.381 0.00 0.00 0.00 3.01
681 839 3.194968 GGTTTCATCTAAGACCCGACAGA 59.805 47.826 0.00 0.00 0.00 3.41
682 840 4.322499 GGTTTCATCTAAGACCCGACAGAA 60.322 45.833 0.00 0.00 0.00 3.02
683 841 4.720649 TTCATCTAAGACCCGACAGAAG 57.279 45.455 0.00 0.00 0.00 2.85
684 842 2.427453 TCATCTAAGACCCGACAGAAGC 59.573 50.000 0.00 0.00 0.00 3.86
685 843 1.183549 TCTAAGACCCGACAGAAGCC 58.816 55.000 0.00 0.00 0.00 4.35
686 844 0.179134 CTAAGACCCGACAGAAGCCG 60.179 60.000 0.00 0.00 0.00 5.52
687 845 0.896940 TAAGACCCGACAGAAGCCGT 60.897 55.000 0.00 0.00 0.00 5.68
691 849 2.338620 CCGACAGAAGCCGTGTCA 59.661 61.111 10.36 0.00 43.90 3.58
692 850 2.022129 CCGACAGAAGCCGTGTCAC 61.022 63.158 10.36 0.00 43.90 3.67
693 851 2.365068 CGACAGAAGCCGTGTCACG 61.365 63.158 18.54 18.54 43.90 4.35
695 853 0.388649 GACAGAAGCCGTGTCACGAT 60.389 55.000 26.53 11.80 46.05 3.73
696 854 0.885879 ACAGAAGCCGTGTCACGATA 59.114 50.000 26.53 0.00 46.05 2.92
697 855 1.135373 ACAGAAGCCGTGTCACGATAG 60.135 52.381 26.53 11.10 46.05 2.08
698 856 0.179134 AGAAGCCGTGTCACGATAGC 60.179 55.000 26.53 20.03 46.05 2.97
699 857 0.457853 GAAGCCGTGTCACGATAGCA 60.458 55.000 26.53 0.00 46.05 3.49
700 858 0.736325 AAGCCGTGTCACGATAGCAC 60.736 55.000 26.53 8.36 46.05 4.40
702 860 4.452753 CGTGTCACGATAGCACGT 57.547 55.556 20.75 0.00 46.05 4.49
708 866 3.604629 ACGATAGCACGTGAGCCT 58.395 55.556 22.23 9.70 44.84 4.58
727 885 3.279434 CCTTGGTAGCACTATTTCCCAC 58.721 50.000 0.00 0.00 0.00 4.61
815 974 1.537776 CCACAAAATCAAACCGCTGCA 60.538 47.619 0.00 0.00 0.00 4.41
818 977 0.939106 AAAATCAAACCGCTGCACGC 60.939 50.000 0.00 1.21 41.76 5.34
850 1038 4.416738 GCCTCTGGCCGCCTTCTT 62.417 66.667 11.61 0.00 44.06 2.52
863 1051 3.883744 CTTCTTCGCGGCCACACCT 62.884 63.158 6.13 0.00 35.61 4.00
865 1053 1.895020 TTCTTCGCGGCCACACCTAT 61.895 55.000 6.13 0.00 35.61 2.57
873 1061 1.691976 CGGCCACACCTATAGAATCCA 59.308 52.381 2.24 0.00 35.61 3.41
875 1063 3.477530 GGCCACACCTATAGAATCCAAC 58.522 50.000 0.00 0.00 34.51 3.77
951 1162 2.287909 CCTCCTCCGAATCTCGAATCAC 60.288 54.545 0.00 0.00 43.74 3.06
954 1165 3.194755 TCCTCCGAATCTCGAATCACAAA 59.805 43.478 0.00 0.00 43.74 2.83
955 1166 3.553511 CCTCCGAATCTCGAATCACAAAG 59.446 47.826 0.00 0.00 43.74 2.77
957 1168 2.609459 CCGAATCTCGAATCACAAAGGG 59.391 50.000 0.00 0.00 43.74 3.95
958 1169 3.521560 CGAATCTCGAATCACAAAGGGA 58.478 45.455 0.00 0.00 43.74 4.20
959 1170 3.307242 CGAATCTCGAATCACAAAGGGAC 59.693 47.826 0.00 0.00 43.74 4.46
960 1171 2.762535 TCTCGAATCACAAAGGGACC 57.237 50.000 0.00 0.00 0.00 4.46
961 1172 1.067142 TCTCGAATCACAAAGGGACCG 60.067 52.381 0.00 0.00 0.00 4.79
962 1173 0.970640 TCGAATCACAAAGGGACCGA 59.029 50.000 0.00 0.00 0.00 4.69
963 1174 1.076332 CGAATCACAAAGGGACCGAC 58.924 55.000 0.00 0.00 0.00 4.79
964 1175 1.450025 GAATCACAAAGGGACCGACC 58.550 55.000 0.00 0.00 38.08 4.79
993 1204 2.040544 CCGAACCAAGCAGCGGAAT 61.041 57.895 0.00 0.00 46.29 3.01
1284 1501 0.607489 ACAGGCTCGTGGTACGTACT 60.607 55.000 24.07 0.00 43.14 2.73
1285 1502 1.339055 ACAGGCTCGTGGTACGTACTA 60.339 52.381 24.07 16.71 43.14 1.82
1286 1503 1.063174 CAGGCTCGTGGTACGTACTAC 59.937 57.143 26.93 26.93 43.14 2.73
1351 1580 6.406370 TCTCTAATCAATTGATGGTCGTGTT 58.594 36.000 21.39 6.78 34.49 3.32
1603 1892 4.103357 GCATTTGATCTGATTGTGCTGTC 58.897 43.478 0.00 0.00 0.00 3.51
1629 1918 0.317160 TGGTCTCACGCGTCTGATTT 59.683 50.000 9.86 0.00 0.00 2.17
1698 3058 6.636454 AAGTGGTAGGATGGTAGATCAAAA 57.364 37.500 0.00 0.00 0.00 2.44
1753 3120 3.760684 GGATTTCAGCATGGTTCTGAGTT 59.239 43.478 0.00 0.00 41.10 3.01
1754 3121 4.142513 GGATTTCAGCATGGTTCTGAGTTC 60.143 45.833 0.00 0.48 41.10 3.01
1755 3122 3.777106 TTCAGCATGGTTCTGAGTTCT 57.223 42.857 0.00 0.00 41.10 3.01
1756 3123 3.049708 TCAGCATGGTTCTGAGTTCTG 57.950 47.619 0.00 0.00 35.81 3.02
1757 3124 2.634453 TCAGCATGGTTCTGAGTTCTGA 59.366 45.455 0.00 0.00 35.81 3.27
1758 3125 2.740981 CAGCATGGTTCTGAGTTCTGAC 59.259 50.000 0.00 0.00 33.54 3.51
1896 3282 4.253685 GCTAGTTCCTTCACACATAAGCA 58.746 43.478 0.00 0.00 0.00 3.91
1897 3283 4.331168 GCTAGTTCCTTCACACATAAGCAG 59.669 45.833 0.00 0.00 0.00 4.24
1900 3286 4.757149 AGTTCCTTCACACATAAGCAGAAC 59.243 41.667 0.00 0.00 31.08 3.01
1902 3288 5.738619 TCCTTCACACATAAGCAGAACTA 57.261 39.130 0.00 0.00 0.00 2.24
1903 3289 6.109156 TCCTTCACACATAAGCAGAACTAA 57.891 37.500 0.00 0.00 0.00 2.24
1932 3965 7.684428 GCCCTTTACAACTTTGTTCTTTCTGAT 60.684 37.037 0.00 0.00 42.35 2.90
1949 3982 5.479124 TCTGATCTATGCACAGCACATAT 57.521 39.130 0.00 0.00 43.04 1.78
2083 4133 5.461032 TGATTGGTTTTTGCCTTCGTTAT 57.539 34.783 0.00 0.00 0.00 1.89
2093 4143 3.745799 TGCCTTCGTTATGGAACTTTGA 58.254 40.909 0.00 0.00 33.01 2.69
2124 4174 5.220970 GCTAGGTTGTTTTCTGCAACTTACA 60.221 40.000 7.88 0.00 43.93 2.41
2135 4186 3.963665 TGCAACTTACACTGTTGATTGC 58.036 40.909 10.29 13.26 45.27 3.56
2296 4347 1.971357 ACATGGTCTTCAAGACGACCT 59.029 47.619 21.63 8.78 45.96 3.85
2702 4859 2.066999 GCCCCTGGGATTCGACTCT 61.067 63.158 16.20 0.00 37.50 3.24
2703 4860 1.826024 CCCCTGGGATTCGACTCTG 59.174 63.158 16.20 0.00 37.50 3.35
2800 4970 6.211664 GCTAAAGCATACTATGTGTTACGG 57.788 41.667 0.00 0.00 41.59 4.02
2801 4971 5.981315 GCTAAAGCATACTATGTGTTACGGA 59.019 40.000 0.00 0.00 41.59 4.69
2803 4973 7.170998 GCTAAAGCATACTATGTGTTACGGATT 59.829 37.037 0.00 0.00 41.59 3.01
2804 4974 9.687210 CTAAAGCATACTATGTGTTACGGATTA 57.313 33.333 0.00 0.00 0.00 1.75
2805 4975 8.951787 AAAGCATACTATGTGTTACGGATTAA 57.048 30.769 0.00 0.00 0.00 1.40
2813 5058 5.384063 TGTGTTACGGATTAAGTTACGGA 57.616 39.130 0.00 0.00 0.00 4.69
2855 5111 4.872691 GGTTATGTGAGATCCTTGTGTCTG 59.127 45.833 0.00 0.00 0.00 3.51
2867 5123 1.053835 TGTGTCTGGTGGCTCCTTGA 61.054 55.000 7.19 2.78 37.07 3.02
2911 5205 2.502510 CTTGTCGGCAATGCGCAC 60.503 61.111 14.90 0.00 45.17 5.34
2953 5247 6.272792 AGGATTCTGCAGGATCTCTTCATATT 59.727 38.462 29.85 4.62 0.00 1.28
2966 5589 7.672983 TCTCTTCATATTTGTTTCTGTCACC 57.327 36.000 0.00 0.00 0.00 4.02
2972 5595 9.513906 TTCATATTTGTTTCTGTCACCATCTTA 57.486 29.630 0.00 0.00 0.00 2.10
3027 5660 0.951040 CTTGGGCCGACTGTGAAGAC 60.951 60.000 0.00 0.00 0.00 3.01
3032 5665 1.133407 GGCCGACTGTGAAGACTAGAG 59.867 57.143 0.00 0.00 0.00 2.43
3106 5744 5.050490 TGTCAAGGAAAGAAGAGAGTTTCG 58.950 41.667 0.00 0.00 34.11 3.46
3143 5781 7.702348 GCGCTAGGAAAAATTATGTGAAAGAAT 59.298 33.333 0.00 0.00 0.00 2.40
3180 5818 7.394359 TGCAGCAATAGGATTATATTTTCCTCC 59.606 37.037 8.91 0.00 41.50 4.30
3223 5861 5.050490 TGTCAAGGAAAGAAGAGAGTTTCG 58.950 41.667 0.00 0.00 34.11 3.46
3224 5862 4.449405 GTCAAGGAAAGAAGAGAGTTTCGG 59.551 45.833 0.00 0.00 34.11 4.30
3225 5863 3.046968 AGGAAAGAAGAGAGTTTCGGC 57.953 47.619 0.00 0.00 34.11 5.54
3226 5864 1.727335 GGAAAGAAGAGAGTTTCGGCG 59.273 52.381 0.00 0.00 34.11 6.46
3227 5865 2.609737 GGAAAGAAGAGAGTTTCGGCGA 60.610 50.000 4.99 4.99 34.11 5.54
3228 5866 2.355717 AAGAAGAGAGTTTCGGCGAG 57.644 50.000 10.46 0.00 32.33 5.03
3229 5867 1.535833 AGAAGAGAGTTTCGGCGAGA 58.464 50.000 10.46 1.71 32.33 4.04
3230 5868 1.887198 AGAAGAGAGTTTCGGCGAGAA 59.113 47.619 10.46 5.04 37.01 2.87
3231 5869 2.296471 AGAAGAGAGTTTCGGCGAGAAA 59.704 45.455 10.46 0.00 45.76 2.52
3245 5883 3.740044 CGAGAAAATGCGCTAGGAAAA 57.260 42.857 9.73 0.00 0.00 2.29
3246 5884 4.078363 CGAGAAAATGCGCTAGGAAAAA 57.922 40.909 9.73 0.00 0.00 1.94
3271 5909 9.972106 AAATATGTGAAAGAAAGGAGAGATTCT 57.028 29.630 0.00 0.00 37.49 2.40
3272 5910 8.961294 ATATGTGAAAGAAAGGAGAGATTCTG 57.039 34.615 0.00 0.00 36.09 3.02
3273 5911 4.999950 TGTGAAAGAAAGGAGAGATTCTGC 59.000 41.667 0.00 0.00 36.09 4.26
3274 5912 4.999950 GTGAAAGAAAGGAGAGATTCTGCA 59.000 41.667 0.00 0.00 37.29 4.41
3275 5913 5.122082 GTGAAAGAAAGGAGAGATTCTGCAG 59.878 44.000 7.63 7.63 37.29 4.41
3276 5914 3.264998 AGAAAGGAGAGATTCTGCAGC 57.735 47.619 9.47 0.00 37.29 5.25
3277 5915 2.570752 AGAAAGGAGAGATTCTGCAGCA 59.429 45.455 9.47 0.00 37.29 4.41
3278 5916 3.008813 AGAAAGGAGAGATTCTGCAGCAA 59.991 43.478 9.47 4.90 37.29 3.91
3279 5917 3.648507 AAGGAGAGATTCTGCAGCAAT 57.351 42.857 9.47 9.85 37.29 3.56
3280 5918 4.767578 AAGGAGAGATTCTGCAGCAATA 57.232 40.909 9.47 0.00 37.29 1.90
3281 5919 4.339872 AGGAGAGATTCTGCAGCAATAG 57.660 45.455 9.47 0.00 37.29 1.73
3282 5920 3.071312 AGGAGAGATTCTGCAGCAATAGG 59.929 47.826 9.47 0.00 37.29 2.57
3283 5921 3.070734 GGAGAGATTCTGCAGCAATAGGA 59.929 47.826 9.47 0.00 34.73 2.94
3284 5922 4.262981 GGAGAGATTCTGCAGCAATAGGAT 60.263 45.833 9.47 0.00 34.73 3.24
3285 5923 5.307204 GAGAGATTCTGCAGCAATAGGATT 58.693 41.667 9.47 0.00 0.00 3.01
3286 5924 6.430962 AGAGATTCTGCAGCAATAGGATTA 57.569 37.500 9.47 0.00 0.00 1.75
3287 5925 7.018487 AGAGATTCTGCAGCAATAGGATTAT 57.982 36.000 9.47 0.00 0.00 1.28
3288 5926 7.460071 AGAGATTCTGCAGCAATAGGATTATT 58.540 34.615 9.47 0.00 0.00 1.40
3289 5927 7.943447 AGAGATTCTGCAGCAATAGGATTATTT 59.057 33.333 9.47 0.00 0.00 1.40
3290 5928 8.474710 AGATTCTGCAGCAATAGGATTATTTT 57.525 30.769 9.47 0.00 0.00 1.82
3291 5929 8.921205 AGATTCTGCAGCAATAGGATTATTTTT 58.079 29.630 9.47 0.00 0.00 1.94
3311 5949 6.627395 TTTTTCCTCTAGCGTTTGATGAAA 57.373 33.333 9.15 9.15 0.00 2.69
3312 5950 6.627395 TTTTCCTCTAGCGTTTGATGAAAA 57.373 33.333 17.01 17.01 35.81 2.29
3313 5951 6.627395 TTTCCTCTAGCGTTTGATGAAAAA 57.373 33.333 10.32 0.00 0.00 1.94
3314 5952 5.607119 TCCTCTAGCGTTTGATGAAAAAC 57.393 39.130 0.00 0.00 36.81 2.43
3315 5953 5.305585 TCCTCTAGCGTTTGATGAAAAACT 58.694 37.500 0.00 0.00 37.80 2.66
3316 5954 6.460781 TCCTCTAGCGTTTGATGAAAAACTA 58.539 36.000 0.00 0.00 37.80 2.24
3317 5955 7.103641 TCCTCTAGCGTTTGATGAAAAACTAT 58.896 34.615 0.00 0.00 37.80 2.12
3318 5956 7.064609 TCCTCTAGCGTTTGATGAAAAACTATG 59.935 37.037 0.00 0.00 37.80 2.23
3319 5957 7.148407 CCTCTAGCGTTTGATGAAAAACTATGT 60.148 37.037 0.00 0.00 37.80 2.29
3320 5958 7.739295 TCTAGCGTTTGATGAAAAACTATGTC 58.261 34.615 0.00 0.00 37.80 3.06
3321 5959 6.312399 AGCGTTTGATGAAAAACTATGTCA 57.688 33.333 0.00 0.00 37.80 3.58
3322 5960 6.734137 AGCGTTTGATGAAAAACTATGTCAA 58.266 32.000 0.00 0.00 37.80 3.18
3323 5961 7.199766 AGCGTTTGATGAAAAACTATGTCAAA 58.800 30.769 0.00 0.00 37.80 2.69
3324 5962 7.379529 AGCGTTTGATGAAAAACTATGTCAAAG 59.620 33.333 0.00 0.00 37.80 2.77
3325 5963 7.378461 GCGTTTGATGAAAAACTATGTCAAAGA 59.622 33.333 0.00 0.00 37.80 2.52
3326 5964 9.232082 CGTTTGATGAAAAACTATGTCAAAGAA 57.768 29.630 0.00 0.00 37.80 2.52
3367 6005 1.308998 AATGCGCGAGGGGAAATTAG 58.691 50.000 12.10 0.00 0.00 1.73
3427 6067 5.511386 AGGATTATATTTCCTCTGGCCAG 57.489 43.478 27.87 27.87 39.46 4.85
3473 6118 9.480053 AACATAAATTTGATTCAACTGAACTGG 57.520 29.630 0.00 0.00 36.80 4.00
3557 16216 4.450419 CCTCAGGATCACTCGCATATTTTC 59.550 45.833 0.00 0.00 0.00 2.29
3624 16284 2.621338 GTCTGACGAATGATTCAGGCA 58.379 47.619 5.95 5.79 42.88 4.75
3633 16293 8.344831 TGACGAATGATTCAGGCATTTTTATAG 58.655 33.333 5.95 0.00 36.19 1.31
3634 16294 7.651808 ACGAATGATTCAGGCATTTTTATAGG 58.348 34.615 5.95 0.00 36.19 2.57
3639 16299 5.835113 TTCAGGCATTTTTATAGGCAGAC 57.165 39.130 0.00 0.00 0.00 3.51
3640 16300 3.876914 TCAGGCATTTTTATAGGCAGACG 59.123 43.478 0.00 0.00 0.00 4.18
3643 16303 3.003378 GGCATTTTTATAGGCAGACGGAC 59.997 47.826 0.00 0.00 0.00 4.79
3645 16305 4.260784 GCATTTTTATAGGCAGACGGACAG 60.261 45.833 0.00 0.00 0.00 3.51
3646 16306 3.536956 TTTTATAGGCAGACGGACAGG 57.463 47.619 0.00 0.00 0.00 4.00
3647 16307 2.447408 TTATAGGCAGACGGACAGGA 57.553 50.000 0.00 0.00 0.00 3.86
3650 16310 0.606604 TAGGCAGACGGACAGGAAAC 59.393 55.000 0.00 0.00 0.00 2.78
3651 16311 1.070786 GGCAGACGGACAGGAAACA 59.929 57.895 0.00 0.00 0.00 2.83
3653 16313 1.305201 GCAGACGGACAGGAAACAAA 58.695 50.000 0.00 0.00 0.00 2.83
3656 16316 2.943033 CAGACGGACAGGAAACAAAAGT 59.057 45.455 0.00 0.00 0.00 2.66
3665 16346 5.487433 ACAGGAAACAAAAGTGGAAAAAGG 58.513 37.500 0.00 0.00 0.00 3.11
3667 16348 6.169800 CAGGAAACAAAAGTGGAAAAAGGAA 58.830 36.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 8.742777 CCAATTTGATCCACTGATCTTAAGAAA 58.257 33.333 9.71 0.05 46.34 2.52
43 44 9.625747 AATTTACAAAAACCAATTTGATCCACT 57.374 25.926 6.76 0.00 41.73 4.00
195 196 2.875087 TTGTATTGCAGGCATCATGC 57.125 45.000 0.00 0.00 44.08 4.06
196 197 6.253013 CGTATATTGTATTGCAGGCATCATG 58.747 40.000 0.00 0.00 0.00 3.07
229 230 1.518929 CGAAAGAGCCATCGACGAATC 59.481 52.381 0.00 0.00 41.43 2.52
250 251 7.060518 CGATCGAGATAATCATCACTGAGAAAC 59.939 40.741 10.26 0.00 34.12 2.78
253 254 5.703130 ACGATCGAGATAATCATCACTGAGA 59.297 40.000 24.34 0.00 34.12 3.27
296 297 5.463392 CAAAAGACCTTTAAGCTTCAAAGCC 59.537 40.000 0.00 6.59 41.41 4.35
303 304 9.542462 GAAATTAACCAAAAGACCTTTAAGCTT 57.458 29.630 3.48 3.48 31.63 3.74
386 387 8.823818 GCCATAAAATTGTACTACGTTCAGTAT 58.176 33.333 0.00 0.00 33.71 2.12
394 395 7.919091 TCTCTGTAGCCATAAAATTGTACTACG 59.081 37.037 0.00 0.00 31.75 3.51
399 400 6.591935 CCCTCTCTGTAGCCATAAAATTGTA 58.408 40.000 0.00 0.00 0.00 2.41
403 404 3.181439 GGCCCTCTCTGTAGCCATAAAAT 60.181 47.826 0.00 0.00 45.07 1.82
406 407 1.424638 GGCCCTCTCTGTAGCCATAA 58.575 55.000 0.00 0.00 45.07 1.90
421 422 0.535335 TTCCTCGATATATGCGGCCC 59.465 55.000 0.00 0.00 0.00 5.80
426 427 5.181748 AGGCAAGATTTCCTCGATATATGC 58.818 41.667 0.00 0.00 0.00 3.14
477 478 1.982395 TGGTGGCCTCGTGGAGTAG 60.982 63.158 7.92 0.00 34.57 2.57
478 479 2.118732 TGGTGGCCTCGTGGAGTA 59.881 61.111 7.92 0.00 34.57 2.59
480 481 3.177194 TTGTGGTGGCCTCGTGGAG 62.177 63.158 7.92 0.00 34.57 3.86
481 482 3.164977 TTGTGGTGGCCTCGTGGA 61.165 61.111 7.92 0.00 34.57 4.02
504 642 0.035458 CACCAGATATTCTCCGGCCC 59.965 60.000 0.00 0.00 0.00 5.80
505 643 0.603975 GCACCAGATATTCTCCGGCC 60.604 60.000 0.00 0.00 0.00 6.13
507 645 1.001406 GGAGCACCAGATATTCTCCGG 59.999 57.143 0.00 0.00 34.67 5.14
508 646 1.688735 TGGAGCACCAGATATTCTCCG 59.311 52.381 0.00 0.00 44.67 4.63
521 659 1.103398 AGCACTTGGTGTTGGAGCAC 61.103 55.000 0.00 0.00 35.75 4.40
522 660 0.472044 TAGCACTTGGTGTTGGAGCA 59.528 50.000 0.00 0.00 35.75 4.26
523 661 0.875059 GTAGCACTTGGTGTTGGAGC 59.125 55.000 0.00 0.00 35.75 4.70
524 662 1.148310 CGTAGCACTTGGTGTTGGAG 58.852 55.000 0.00 0.00 35.75 3.86
525 663 0.250124 CCGTAGCACTTGGTGTTGGA 60.250 55.000 0.00 0.00 35.75 3.53
526 664 0.534203 ACCGTAGCACTTGGTGTTGG 60.534 55.000 0.00 0.00 35.75 3.77
527 665 0.586319 CACCGTAGCACTTGGTGTTG 59.414 55.000 11.58 0.00 46.36 3.33
528 666 3.000815 CACCGTAGCACTTGGTGTT 57.999 52.632 11.58 0.00 46.36 3.32
529 667 4.771127 CACCGTAGCACTTGGTGT 57.229 55.556 11.58 0.00 46.36 4.16
531 669 1.135199 CGTATCACCGTAGCACTTGGT 60.135 52.381 0.00 0.00 36.10 3.67
532 670 1.556564 CGTATCACCGTAGCACTTGG 58.443 55.000 0.00 0.00 0.00 3.61
550 688 3.916392 AACGGCTGCGAAGAGTCCG 62.916 63.158 6.42 6.42 45.04 4.79
552 690 2.383527 CCAACGGCTGCGAAGAGTC 61.384 63.158 0.00 0.00 0.00 3.36
559 697 2.802667 CTTCGATCCAACGGCTGCG 61.803 63.158 0.00 0.00 0.00 5.18
582 740 3.439825 GGGGGCTTTTATGCAAAATGTTG 59.560 43.478 0.00 0.00 33.27 3.33
586 744 5.029474 TCTTAGGGGGCTTTTATGCAAAAT 58.971 37.500 0.00 0.00 33.27 1.82
604 762 3.002791 TGCGCAATTTCCAGACTCTTAG 58.997 45.455 8.16 0.00 0.00 2.18
608 766 2.289002 CCTATGCGCAATTTCCAGACTC 59.711 50.000 17.11 0.00 0.00 3.36
610 768 2.017049 ACCTATGCGCAATTTCCAGAC 58.983 47.619 17.11 0.00 0.00 3.51
612 770 1.334869 GGACCTATGCGCAATTTCCAG 59.665 52.381 17.11 4.85 0.00 3.86
614 772 1.334869 CTGGACCTATGCGCAATTTCC 59.665 52.381 17.11 18.20 0.00 3.13
615 773 1.268743 GCTGGACCTATGCGCAATTTC 60.269 52.381 17.11 8.72 0.00 2.17
622 780 0.320247 GGATCTGCTGGACCTATGCG 60.320 60.000 0.00 0.00 0.00 4.73
655 813 2.007608 GGGTCTTAGATGAAACCGCAC 58.992 52.381 0.00 0.00 32.34 5.34
659 817 3.194968 TCTGTCGGGTCTTAGATGAAACC 59.805 47.826 0.00 0.00 0.00 3.27
665 823 1.757699 GGCTTCTGTCGGGTCTTAGAT 59.242 52.381 0.00 0.00 0.00 1.98
667 825 0.179134 CGGCTTCTGTCGGGTCTTAG 60.179 60.000 0.00 0.00 37.69 2.18
681 839 0.736325 GTGCTATCGTGACACGGCTT 60.736 55.000 26.55 14.62 42.81 4.35
682 840 1.153823 GTGCTATCGTGACACGGCT 60.154 57.895 26.55 16.78 42.81 5.52
683 841 3.384927 GTGCTATCGTGACACGGC 58.615 61.111 26.55 21.53 42.81 5.68
691 849 0.458543 CAAGGCTCACGTGCTATCGT 60.459 55.000 11.67 0.00 45.10 3.73
692 850 1.148157 CCAAGGCTCACGTGCTATCG 61.148 60.000 11.67 0.00 0.00 2.92
693 851 0.108138 ACCAAGGCTCACGTGCTATC 60.108 55.000 11.67 0.18 0.00 2.08
695 853 0.530744 CTACCAAGGCTCACGTGCTA 59.469 55.000 11.67 0.00 0.00 3.49
696 854 1.293498 CTACCAAGGCTCACGTGCT 59.707 57.895 11.67 0.00 0.00 4.40
697 855 2.391389 GCTACCAAGGCTCACGTGC 61.391 63.158 11.67 0.00 0.00 5.34
698 856 1.005037 TGCTACCAAGGCTCACGTG 60.005 57.895 9.94 9.94 0.00 4.49
699 857 1.004918 GTGCTACCAAGGCTCACGT 60.005 57.895 0.00 0.00 0.00 4.49
700 858 0.530744 TAGTGCTACCAAGGCTCACG 59.469 55.000 0.00 0.00 33.28 4.35
701 859 2.990066 ATAGTGCTACCAAGGCTCAC 57.010 50.000 0.00 0.00 0.00 3.51
702 860 3.370527 GGAAATAGTGCTACCAAGGCTCA 60.371 47.826 0.00 0.00 0.00 4.26
703 861 3.206964 GGAAATAGTGCTACCAAGGCTC 58.793 50.000 0.00 0.00 0.00 4.70
704 862 2.092375 GGGAAATAGTGCTACCAAGGCT 60.092 50.000 0.00 0.00 0.00 4.58
705 863 2.298610 GGGAAATAGTGCTACCAAGGC 58.701 52.381 0.00 0.00 0.00 4.35
706 864 3.279434 GTGGGAAATAGTGCTACCAAGG 58.721 50.000 0.00 0.00 0.00 3.61
707 865 3.279434 GGTGGGAAATAGTGCTACCAAG 58.721 50.000 0.00 0.00 46.96 3.61
708 866 3.359695 GGTGGGAAATAGTGCTACCAA 57.640 47.619 0.00 0.00 46.96 3.67
744 902 2.682494 GGTAGGAGGACACGGGCA 60.682 66.667 0.00 0.00 0.00 5.36
748 906 1.330655 ATGGCAGGTAGGAGGACACG 61.331 60.000 0.00 0.00 0.00 4.49
815 974 1.615107 GCTTAACGACGAAGCAGCGT 61.615 55.000 14.41 3.45 46.97 5.07
850 1038 1.038681 TTCTATAGGTGTGGCCGCGA 61.039 55.000 8.23 0.00 43.70 5.87
859 1047 3.728845 CACGGGTTGGATTCTATAGGTG 58.271 50.000 0.00 0.00 0.00 4.00
873 1061 2.886730 GATCGCAATCCCCACGGGTT 62.887 60.000 0.41 0.00 44.74 4.11
875 1063 2.591715 GATCGCAATCCCCACGGG 60.592 66.667 0.00 0.00 46.11 5.28
887 1075 2.849162 TCTGGGGATGGGGATCGC 60.849 66.667 0.06 0.06 0.00 4.58
970 1181 3.423154 CTGCTTGGTTCGGTCGGC 61.423 66.667 0.00 0.00 0.00 5.54
993 1204 1.903890 GGCCTCCTCCATCGATCGA 60.904 63.158 21.86 21.86 0.00 3.59
1284 1501 2.731571 GGGGATCAGCGTGCAGGTA 61.732 63.158 8.40 0.00 0.00 3.08
1285 1502 4.101448 GGGGATCAGCGTGCAGGT 62.101 66.667 8.40 0.00 0.00 4.00
1286 1503 2.898920 ATTGGGGATCAGCGTGCAGG 62.899 60.000 1.01 1.01 0.00 4.85
1603 1892 2.551270 GCGTGAGACCACAAAGCG 59.449 61.111 0.00 0.00 43.34 4.68
1698 3058 1.682849 TGGCTCACGGCAAAGGTAT 59.317 52.632 0.00 0.00 43.40 2.73
1874 3252 4.253685 TGCTTATGTGTGAAGGAACTAGC 58.746 43.478 0.00 0.00 38.49 3.42
1881 3267 5.934625 ACTTAGTTCTGCTTATGTGTGAAGG 59.065 40.000 0.00 0.00 0.00 3.46
1896 3282 5.306114 AGTTGTAAAGGGCACTTAGTTCT 57.694 39.130 0.00 0.00 35.41 3.01
1897 3283 6.183360 ACAAAGTTGTAAAGGGCACTTAGTTC 60.183 38.462 0.00 0.00 40.16 3.01
1900 3286 5.767816 ACAAAGTTGTAAAGGGCACTTAG 57.232 39.130 0.00 0.00 40.16 2.18
1902 3288 4.709886 AGAACAAAGTTGTAAAGGGCACTT 59.290 37.500 0.00 0.00 41.31 3.16
1903 3289 4.278310 AGAACAAAGTTGTAAAGGGCACT 58.722 39.130 0.00 0.00 41.31 4.40
1932 3965 5.928264 GTGTCATATATGTGCTGTGCATAGA 59.072 40.000 15.47 0.00 41.91 1.98
1949 3982 7.880105 TCACATTGTTTATGCAAAGTGTCATA 58.120 30.769 11.92 0.00 43.93 2.15
2083 4133 3.444742 CCTAGCATTGCATCAAAGTTCCA 59.555 43.478 11.91 0.00 0.00 3.53
2093 4143 4.813027 CAGAAAACAACCTAGCATTGCAT 58.187 39.130 11.91 0.00 0.00 3.96
2124 4174 6.165577 ACAAAGACAAAAAGCAATCAACAGT 58.834 32.000 0.00 0.00 0.00 3.55
2135 4186 8.311120 GTCACGATTTGTAACAAAGACAAAAAG 58.689 33.333 5.16 5.31 46.70 2.27
2296 4347 6.713450 GGAAAATCCAGCCCGTAGAAATTATA 59.287 38.462 0.00 0.00 36.28 0.98
2702 4859 2.498644 TCATTTACATTGACCCGGCA 57.501 45.000 0.00 0.00 0.00 5.69
2703 4860 5.507315 CCTTATTCATTTACATTGACCCGGC 60.507 44.000 0.00 0.00 0.00 6.13
2796 4966 6.804677 TGCTTAATCCGTAACTTAATCCGTA 58.195 36.000 0.00 0.00 0.00 4.02
2797 4967 5.663456 TGCTTAATCCGTAACTTAATCCGT 58.337 37.500 0.00 0.00 0.00 4.69
2798 4968 5.981315 TCTGCTTAATCCGTAACTTAATCCG 59.019 40.000 0.00 0.00 0.00 4.18
2800 4970 9.651718 CAAATCTGCTTAATCCGTAACTTAATC 57.348 33.333 0.00 0.00 0.00 1.75
2801 4971 8.129211 GCAAATCTGCTTAATCCGTAACTTAAT 58.871 33.333 0.00 0.00 45.74 1.40
2803 4973 7.011828 GCAAATCTGCTTAATCCGTAACTTA 57.988 36.000 0.00 0.00 45.74 2.24
2804 4974 5.880341 GCAAATCTGCTTAATCCGTAACTT 58.120 37.500 0.00 0.00 45.74 2.66
2805 4975 5.485662 GCAAATCTGCTTAATCCGTAACT 57.514 39.130 0.00 0.00 45.74 2.24
2855 5111 0.393537 CCAGATGTCAAGGAGCCACC 60.394 60.000 0.00 0.00 39.35 4.61
2867 5123 5.190528 ACAAGGATCTCACATAACCAGATGT 59.809 40.000 0.00 0.00 40.78 3.06
2911 5205 2.494059 TCCTGCGAGAAAAGAACCTTG 58.506 47.619 0.00 0.00 0.00 3.61
2940 5234 8.394121 GGTGACAGAAACAAATATGAAGAGATC 58.606 37.037 0.00 0.00 0.00 2.75
2966 5589 1.068127 GCAGCCAGGGCAAATAAGATG 59.932 52.381 13.63 0.28 44.88 2.90
2972 5595 2.753043 CTCGCAGCCAGGGCAAAT 60.753 61.111 13.63 0.00 44.88 2.32
3032 5665 9.218440 TGCTTTTTGAATCCAATTTTATCTTCC 57.782 29.630 0.00 0.00 31.46 3.46
3143 5781 2.574006 ATTGCTGCAGAAACTCTCCA 57.426 45.000 20.43 0.00 0.00 3.86
3180 5818 3.506067 ACATAGTTTTTCCTCAAAGGCCG 59.494 43.478 0.00 0.00 34.61 6.13
3225 5863 3.740044 TTTTCCTAGCGCATTTTCTCG 57.260 42.857 11.47 0.00 0.00 4.04
3245 5883 9.972106 AGAATCTCTCCTTTCTTTCACATATTT 57.028 29.630 0.00 0.00 0.00 1.40
3246 5884 9.393512 CAGAATCTCTCCTTTCTTTCACATATT 57.606 33.333 0.00 0.00 29.85 1.28
3247 5885 7.498570 GCAGAATCTCTCCTTTCTTTCACATAT 59.501 37.037 0.00 0.00 29.85 1.78
3248 5886 6.820656 GCAGAATCTCTCCTTTCTTTCACATA 59.179 38.462 0.00 0.00 29.85 2.29
3249 5887 5.647225 GCAGAATCTCTCCTTTCTTTCACAT 59.353 40.000 0.00 0.00 29.85 3.21
3250 5888 4.999950 GCAGAATCTCTCCTTTCTTTCACA 59.000 41.667 0.00 0.00 29.85 3.58
3251 5889 4.999950 TGCAGAATCTCTCCTTTCTTTCAC 59.000 41.667 0.00 0.00 29.85 3.18
3252 5890 5.233083 TGCAGAATCTCTCCTTTCTTTCA 57.767 39.130 0.00 0.00 29.85 2.69
3253 5891 4.094739 GCTGCAGAATCTCTCCTTTCTTTC 59.905 45.833 20.43 0.00 29.85 2.62
3254 5892 4.009002 GCTGCAGAATCTCTCCTTTCTTT 58.991 43.478 20.43 0.00 29.85 2.52
3255 5893 3.008813 TGCTGCAGAATCTCTCCTTTCTT 59.991 43.478 20.43 0.00 29.85 2.52
3256 5894 2.570752 TGCTGCAGAATCTCTCCTTTCT 59.429 45.455 20.43 0.00 32.48 2.52
3257 5895 2.983229 TGCTGCAGAATCTCTCCTTTC 58.017 47.619 20.43 0.00 0.00 2.62
3258 5896 3.430042 TTGCTGCAGAATCTCTCCTTT 57.570 42.857 20.43 0.00 0.00 3.11
3259 5897 3.648507 ATTGCTGCAGAATCTCTCCTT 57.351 42.857 20.43 0.00 0.00 3.36
3260 5898 3.071312 CCTATTGCTGCAGAATCTCTCCT 59.929 47.826 20.43 0.00 0.00 3.69
3261 5899 3.070734 TCCTATTGCTGCAGAATCTCTCC 59.929 47.826 20.43 0.00 0.00 3.71
3262 5900 4.333913 TCCTATTGCTGCAGAATCTCTC 57.666 45.455 20.43 0.00 0.00 3.20
3263 5901 4.978438 ATCCTATTGCTGCAGAATCTCT 57.022 40.909 20.43 0.00 0.00 3.10
3264 5902 7.684937 AATAATCCTATTGCTGCAGAATCTC 57.315 36.000 20.43 0.00 0.00 2.75
3265 5903 8.474710 AAAATAATCCTATTGCTGCAGAATCT 57.525 30.769 20.43 0.00 0.00 2.40
3288 5926 6.627395 TTTCATCAAACGCTAGAGGAAAAA 57.373 33.333 8.35 0.00 40.30 1.94
3289 5927 6.627395 TTTTCATCAAACGCTAGAGGAAAA 57.373 33.333 15.41 15.41 46.06 2.29
3290 5928 6.262273 AGTTTTTCATCAAACGCTAGAGGAAA 59.738 34.615 7.14 7.14 41.15 3.13
3291 5929 5.763204 AGTTTTTCATCAAACGCTAGAGGAA 59.237 36.000 0.00 0.00 40.92 3.36
3292 5930 5.305585 AGTTTTTCATCAAACGCTAGAGGA 58.694 37.500 0.00 0.00 40.92 3.71
3293 5931 5.613358 AGTTTTTCATCAAACGCTAGAGG 57.387 39.130 0.00 0.00 40.92 3.69
3294 5932 7.743104 ACATAGTTTTTCATCAAACGCTAGAG 58.257 34.615 0.00 0.00 40.92 2.43
3295 5933 7.386573 TGACATAGTTTTTCATCAAACGCTAGA 59.613 33.333 0.00 0.00 40.92 2.43
3296 5934 7.518161 TGACATAGTTTTTCATCAAACGCTAG 58.482 34.615 0.00 0.00 40.92 3.42
3297 5935 7.428282 TGACATAGTTTTTCATCAAACGCTA 57.572 32.000 0.00 0.00 40.92 4.26
3298 5936 6.312399 TGACATAGTTTTTCATCAAACGCT 57.688 33.333 0.00 0.00 40.92 5.07
3299 5937 6.984740 TTGACATAGTTTTTCATCAAACGC 57.015 33.333 0.00 0.00 40.92 4.84
3300 5938 8.781067 TCTTTGACATAGTTTTTCATCAAACG 57.219 30.769 0.00 0.00 40.92 3.60
3314 5952 9.455847 CCAAACTCTTTTCTTTCTTTGACATAG 57.544 33.333 0.00 0.00 0.00 2.23
3315 5953 8.413229 CCCAAACTCTTTTCTTTCTTTGACATA 58.587 33.333 0.00 0.00 0.00 2.29
3316 5954 7.267857 CCCAAACTCTTTTCTTTCTTTGACAT 58.732 34.615 0.00 0.00 0.00 3.06
3317 5955 6.630071 CCCAAACTCTTTTCTTTCTTTGACA 58.370 36.000 0.00 0.00 0.00 3.58
3318 5956 5.520288 GCCCAAACTCTTTTCTTTCTTTGAC 59.480 40.000 0.00 0.00 0.00 3.18
3319 5957 5.660460 GCCCAAACTCTTTTCTTTCTTTGA 58.340 37.500 0.00 0.00 0.00 2.69
3320 5958 4.504097 CGCCCAAACTCTTTTCTTTCTTTG 59.496 41.667 0.00 0.00 0.00 2.77
3321 5959 4.401202 TCGCCCAAACTCTTTTCTTTCTTT 59.599 37.500 0.00 0.00 0.00 2.52
3322 5960 3.951680 TCGCCCAAACTCTTTTCTTTCTT 59.048 39.130 0.00 0.00 0.00 2.52
3323 5961 3.551846 TCGCCCAAACTCTTTTCTTTCT 58.448 40.909 0.00 0.00 0.00 2.52
3324 5962 3.564225 TCTCGCCCAAACTCTTTTCTTTC 59.436 43.478 0.00 0.00 0.00 2.62
3325 5963 3.551846 TCTCGCCCAAACTCTTTTCTTT 58.448 40.909 0.00 0.00 0.00 2.52
3326 5964 3.208747 TCTCGCCCAAACTCTTTTCTT 57.791 42.857 0.00 0.00 0.00 2.52
3327 5965 2.930826 TCTCGCCCAAACTCTTTTCT 57.069 45.000 0.00 0.00 0.00 2.52
3328 5966 3.982576 TTTCTCGCCCAAACTCTTTTC 57.017 42.857 0.00 0.00 0.00 2.29
3329 5967 4.620982 CATTTTCTCGCCCAAACTCTTTT 58.379 39.130 0.00 0.00 0.00 2.27
3330 5968 3.552890 GCATTTTCTCGCCCAAACTCTTT 60.553 43.478 0.00 0.00 0.00 2.52
3331 5969 2.029918 GCATTTTCTCGCCCAAACTCTT 60.030 45.455 0.00 0.00 0.00 2.85
3332 5970 1.541588 GCATTTTCTCGCCCAAACTCT 59.458 47.619 0.00 0.00 0.00 3.24
3333 5971 1.729149 CGCATTTTCTCGCCCAAACTC 60.729 52.381 0.00 0.00 0.00 3.01
3334 5972 0.240945 CGCATTTTCTCGCCCAAACT 59.759 50.000 0.00 0.00 0.00 2.66
3335 5973 1.344226 GCGCATTTTCTCGCCCAAAC 61.344 55.000 0.30 0.00 45.01 2.93
3336 5974 1.080839 GCGCATTTTCTCGCCCAAA 60.081 52.632 0.30 0.00 45.01 3.28
3337 5975 2.566010 GCGCATTTTCTCGCCCAA 59.434 55.556 0.30 0.00 45.01 4.12
3367 6005 3.187432 CAGAAACTCTCCTTTCTTTCGCC 59.813 47.826 0.00 0.00 38.24 5.54
3427 6067 7.948278 ATGTTCTACTAATAATCTTCACGGC 57.052 36.000 0.00 0.00 0.00 5.68
3495 6152 4.141041 TCTCTCACCCCATTTCTTTTTCCA 60.141 41.667 0.00 0.00 0.00 3.53
3557 16216 4.516942 CGCGTAGGTCTCATAGCG 57.483 61.111 0.00 0.00 41.56 4.26
3606 16266 4.627611 AAATGCCTGAATCATTCGTCAG 57.372 40.909 0.00 0.00 40.84 3.51
3607 16267 5.389859 AAAAATGCCTGAATCATTCGTCA 57.610 34.783 0.00 0.00 33.41 4.35
3624 16284 4.163458 TCCTGTCCGTCTGCCTATAAAAAT 59.837 41.667 0.00 0.00 0.00 1.82
3633 16293 0.534203 TTGTTTCCTGTCCGTCTGCC 60.534 55.000 0.00 0.00 0.00 4.85
3634 16294 1.305201 TTTGTTTCCTGTCCGTCTGC 58.695 50.000 0.00 0.00 0.00 4.26
3639 16299 2.294074 TCCACTTTTGTTTCCTGTCCG 58.706 47.619 0.00 0.00 0.00 4.79
3640 16300 4.729227 TTTCCACTTTTGTTTCCTGTCC 57.271 40.909 0.00 0.00 0.00 4.02
3643 16303 5.729510 TCCTTTTTCCACTTTTGTTTCCTG 58.270 37.500 0.00 0.00 0.00 3.86
3645 16305 7.415095 CCAATTCCTTTTTCCACTTTTGTTTCC 60.415 37.037 0.00 0.00 0.00 3.13
3646 16306 7.415095 CCCAATTCCTTTTTCCACTTTTGTTTC 60.415 37.037 0.00 0.00 0.00 2.78
3647 16307 6.376864 CCCAATTCCTTTTTCCACTTTTGTTT 59.623 34.615 0.00 0.00 0.00 2.83
3650 16310 4.821260 CCCCAATTCCTTTTTCCACTTTTG 59.179 41.667 0.00 0.00 0.00 2.44
3651 16311 4.688597 GCCCCAATTCCTTTTTCCACTTTT 60.689 41.667 0.00 0.00 0.00 2.27
3653 16313 2.371841 GCCCCAATTCCTTTTTCCACTT 59.628 45.455 0.00 0.00 0.00 3.16
3656 16316 0.972883 CGCCCCAATTCCTTTTTCCA 59.027 50.000 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.