Multiple sequence alignment - TraesCS3B01G526300

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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 TraesCS3B01G526300 chr3B 100.000 4380 0 0 1 4380 768509654 768514033 0.000000e+00 8089.0
1 TraesCS3B01G526300 chr3B 93.825 1749 72 12 2623 4345 766833563 766831825 0.000000e+00 2599.0
2 TraesCS3B01G526300 chr3B 88.742 1288 56 54 778 2011 766836107 766834855 0.000000e+00 1493.0
3 TraesCS3B01G526300 chr3B 84.559 1101 109 36 1434 2487 768261886 768262972 0.000000e+00 1035.0
4 TraesCS3B01G526300 chr3B 94.687 527 13 7 2105 2631 766834842 766834331 0.000000e+00 804.0
5 TraesCS3B01G526300 chr3B 81.434 781 97 34 2110 2866 768671352 768672108 2.920000e-166 595.0
6 TraesCS3B01G526300 chr3B 80.934 792 67 45 3041 3769 768611840 768612610 2.300000e-152 549.0
7 TraesCS3B01G526300 chr3B 79.950 793 99 36 1028 1795 766792382 766791625 3.000000e-146 529.0
8 TraesCS3B01G526300 chr3B 90.060 332 30 3 3105 3434 766790978 766790648 1.130000e-115 427.0
9 TraesCS3B01G526300 chr3B 87.464 343 33 9 2772 3108 766791346 766791008 1.910000e-103 387.0
10 TraesCS3B01G526300 chr3B 94.737 76 3 1 534 608 766836291 766836216 2.770000e-22 117.0
11 TraesCS3B01G526300 chr3B 87.500 88 10 1 3608 3695 766790443 766790357 2.790000e-17 100.0
12 TraesCS3B01G526300 chr3B 87.500 64 4 4 4320 4380 203376729 203376667 2.190000e-08 71.3
13 TraesCS3B01G526300 chr3B 85.507 69 5 3 4314 4379 219461145 219461211 2.830000e-07 67.6
14 TraesCS3B01G526300 chr3B 85.507 69 5 3 4314 4379 220775162 220775228 2.830000e-07 67.6
15 TraesCS3B01G526300 chr3B 93.333 45 2 1 2787 2831 637663680 637663723 1.020000e-06 65.8
16 TraesCS3B01G526300 chr3D 88.472 2559 157 65 1806 4303 577154801 577152320 0.000000e+00 2964.0
17 TraesCS3B01G526300 chr3D 83.142 1833 135 83 778 2508 577156939 577155179 0.000000e+00 1513.0
18 TraesCS3B01G526300 chr3D 89.599 673 54 11 2772 3434 575765494 575764828 0.000000e+00 841.0
19 TraesCS3B01G526300 chr3D 87.311 662 61 15 2929 3572 576890032 576889376 0.000000e+00 736.0
20 TraesCS3B01G526300 chr3D 80.271 1034 108 48 1434 2414 575839879 575838889 0.000000e+00 691.0
21 TraesCS3B01G526300 chr3D 81.125 853 102 41 2037 2866 576854620 576853804 2.880000e-176 628.0
22 TraesCS3B01G526300 chr3D 79.303 1005 99 61 836 1790 577145766 577144821 1.740000e-168 603.0
23 TraesCS3B01G526300 chr3D 79.003 943 120 48 1035 1953 576901464 576900576 1.370000e-159 573.0
24 TraesCS3B01G526300 chr3D 79.258 916 97 51 935 1795 575766649 575765772 1.780000e-153 553.0
25 TraesCS3B01G526300 chr3D 84.884 516 61 10 2901 3403 576853732 576853221 5.060000e-139 505.0
26 TraesCS3B01G526300 chr3D 83.711 485 61 15 2037 2512 577178344 577178819 4.020000e-120 442.0
27 TraesCS3B01G526300 chr3D 81.682 535 46 26 1510 2016 577025195 577024685 8.830000e-107 398.0
28 TraesCS3B01G526300 chr3D 85.373 335 44 5 1037 1370 575840368 575840038 4.190000e-90 342.0
29 TraesCS3B01G526300 chr3D 85.304 313 36 7 995 1298 577025923 577025612 9.140000e-82 315.0
30 TraesCS3B01G526300 chr3D 88.318 214 16 8 2515 2727 577155008 577154803 9.410000e-62 248.0
31 TraesCS3B01G526300 chr3D 83.333 276 25 5 986 1249 576856210 576855944 7.320000e-58 235.0
32 TraesCS3B01G526300 chr3D 88.811 143 13 3 2548 2689 575838088 575837948 5.820000e-39 172.0
33 TraesCS3B01G526300 chr3D 83.537 164 14 6 3544 3695 575764730 575764568 1.640000e-29 141.0
34 TraesCS3B01G526300 chr3D 79.904 209 21 7 2694 2888 575837316 575837115 2.750000e-27 134.0
35 TraesCS3B01G526300 chr3D 88.608 79 8 1 2794 2872 576900075 576899998 1.300000e-15 95.3
36 TraesCS3B01G526300 chr3D 77.473 182 13 12 867 1034 576901656 576901489 2.810000e-12 84.2
37 TraesCS3B01G526300 chr3D 84.932 73 8 3 4309 4380 338925079 338925149 2.190000e-08 71.3
38 TraesCS3B01G526300 chr3A 89.520 2271 140 51 2105 4342 712307552 712309757 0.000000e+00 2785.0
39 TraesCS3B01G526300 chr3A 83.817 1137 104 41 1434 2512 711385168 711384054 0.000000e+00 1007.0
40 TraesCS3B01G526300 chr3A 81.745 1112 138 46 2037 3110 712380507 712381591 0.000000e+00 869.0
41 TraesCS3B01G526300 chr3A 88.368 619 58 10 2830 3437 711302672 711302057 0.000000e+00 732.0
42 TraesCS3B01G526300 chr3A 86.186 666 72 15 2037 2693 711382957 711382303 0.000000e+00 702.0
43 TraesCS3B01G526300 chr3A 79.603 1108 112 56 2039 3103 711382250 711381214 0.000000e+00 689.0
44 TraesCS3B01G526300 chr3A 79.480 1038 125 46 1510 2512 712322856 712323840 0.000000e+00 656.0
45 TraesCS3B01G526300 chr3A 82.143 672 67 32 3177 3823 712354723 712355366 1.080000e-145 527.0
46 TraesCS3B01G526300 chr3A 79.219 871 93 52 2037 2867 712454132 712454954 3.880000e-145 525.0
47 TraesCS3B01G526300 chr3A 85.185 486 54 12 2037 2512 711383497 711383020 2.370000e-132 483.0
48 TraesCS3B01G526300 chr3A 88.493 365 24 11 1647 2011 712307193 712307539 4.050000e-115 425.0
49 TraesCS3B01G526300 chr3A 79.871 621 71 36 1366 1953 712343534 712344133 5.270000e-109 405.0
50 TraesCS3B01G526300 chr3A 78.561 681 71 41 708 1343 711337469 711336819 3.200000e-101 379.0
51 TraesCS3B01G526300 chr3A 86.297 343 38 7 1032 1370 711385662 711385325 8.950000e-97 364.0
52 TraesCS3B01G526300 chr3A 83.784 148 17 5 3544 3691 711301931 711301791 2.750000e-27 134.0
53 TraesCS3B01G526300 chr3A 88.889 72 7 1 2801 2872 712344550 712344620 2.170000e-13 87.9
54 TraesCS3B01G526300 chr3A 92.857 42 2 1 993 1034 712341598 712341638 4.730000e-05 60.2
55 TraesCS3B01G526300 chr4A 98.802 501 6 0 1 501 481092754 481093254 0.000000e+00 893.0
56 TraesCS3B01G526300 chr1A 98.986 493 5 0 1 493 482822183 482822675 0.000000e+00 883.0
57 TraesCS3B01G526300 chr1A 98.364 489 8 0 1 489 146613171 146613659 0.000000e+00 859.0
58 TraesCS3B01G526300 chrUn 98.211 503 9 0 1 503 62689453 62689955 0.000000e+00 880.0
59 TraesCS3B01G526300 chrUn 87.302 63 6 2 4318 4380 37289142 37289202 2.190000e-08 71.3
60 TraesCS3B01G526300 chrUn 87.302 63 6 2 4318 4380 37292318 37292378 2.190000e-08 71.3
61 TraesCS3B01G526300 chr1D 94.757 515 10 2 1 501 334044125 334043614 0.000000e+00 785.0
62 TraesCS3B01G526300 chr7D 94.391 517 11 3 1 502 4420957 4421470 0.000000e+00 778.0
63 TraesCS3B01G526300 chr5D 94.477 507 13 2 1 493 550415615 550415110 0.000000e+00 767.0
64 TraesCS3B01G526300 chr6B 88.029 543 21 10 1 501 279328826 279328286 1.740000e-168 603.0
65 TraesCS3B01G526300 chr5A 93.590 390 10 2 127 501 612382376 612381987 6.360000e-158 568.0
66 TraesCS3B01G526300 chr5A 97.183 71 2 0 1 71 612382447 612382377 2.140000e-23 121.0
67 TraesCS3B01G526300 chr2B 77.801 973 97 50 1510 2418 657054275 657053358 1.420000e-134 490.0
68 TraesCS3B01G526300 chr2B 83.333 78 4 8 4303 4378 9901594 9901664 3.660000e-06 63.9
69 TraesCS3B01G526300 chr4D 81.148 122 15 5 1 115 40412345 40412225 1.680000e-14 91.6
70 TraesCS3B01G526300 chr1B 91.228 57 1 3 4326 4380 476030739 476030793 1.690000e-09 75.0
71 TraesCS3B01G526300 chr2A 87.097 62 6 2 4320 4380 775020172 775020232 7.860000e-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 TraesCS3B01G526300 chr3B 768509654 768514033 4379 False 8089.000000 8089 100.000000 1 4380 1 chr3B.!!$F5 4379
1 TraesCS3B01G526300 chr3B 766831825 766836291 4466 True 1253.250000 2599 92.997750 534 4345 4 chr3B.!!$R3 3811
2 TraesCS3B01G526300 chr3B 768261886 768262972 1086 False 1035.000000 1035 84.559000 1434 2487 1 chr3B.!!$F4 1053
3 TraesCS3B01G526300 chr3B 768671352 768672108 756 False 595.000000 595 81.434000 2110 2866 1 chr3B.!!$F7 756
4 TraesCS3B01G526300 chr3B 768611840 768612610 770 False 549.000000 549 80.934000 3041 3769 1 chr3B.!!$F6 728
5 TraesCS3B01G526300 chr3B 766790357 766792382 2025 True 360.750000 529 86.243500 1028 3695 4 chr3B.!!$R2 2667
6 TraesCS3B01G526300 chr3D 577152320 577156939 4619 True 1575.000000 2964 86.644000 778 4303 3 chr3D.!!$R8 3525
7 TraesCS3B01G526300 chr3D 576889376 576890032 656 True 736.000000 736 87.311000 2929 3572 1 chr3D.!!$R1 643
8 TraesCS3B01G526300 chr3D 577144821 577145766 945 True 603.000000 603 79.303000 836 1790 1 chr3D.!!$R2 954
9 TraesCS3B01G526300 chr3D 575764568 575766649 2081 True 511.666667 841 84.131333 935 3695 3 chr3D.!!$R3 2760
10 TraesCS3B01G526300 chr3D 576853221 576856210 2989 True 456.000000 628 83.114000 986 3403 3 chr3D.!!$R5 2417
11 TraesCS3B01G526300 chr3D 577024685 577025923 1238 True 356.500000 398 83.493000 995 2016 2 chr3D.!!$R7 1021
12 TraesCS3B01G526300 chr3D 575837115 575840368 3253 True 334.750000 691 83.589750 1037 2888 4 chr3D.!!$R4 1851
13 TraesCS3B01G526300 chr3D 576899998 576901656 1658 True 250.833333 573 81.694667 867 2872 3 chr3D.!!$R6 2005
14 TraesCS3B01G526300 chr3A 712307193 712309757 2564 False 1605.000000 2785 89.006500 1647 4342 2 chr3A.!!$F5 2695
15 TraesCS3B01G526300 chr3A 712380507 712381591 1084 False 869.000000 869 81.745000 2037 3110 1 chr3A.!!$F3 1073
16 TraesCS3B01G526300 chr3A 712322856 712323840 984 False 656.000000 656 79.480000 1510 2512 1 chr3A.!!$F1 1002
17 TraesCS3B01G526300 chr3A 711381214 711385662 4448 True 649.000000 1007 84.217600 1032 3103 5 chr3A.!!$R3 2071
18 TraesCS3B01G526300 chr3A 712354723 712355366 643 False 527.000000 527 82.143000 3177 3823 1 chr3A.!!$F2 646
19 TraesCS3B01G526300 chr3A 712454132 712454954 822 False 525.000000 525 79.219000 2037 2867 1 chr3A.!!$F4 830
20 TraesCS3B01G526300 chr3A 711301791 711302672 881 True 433.000000 732 86.076000 2830 3691 2 chr3A.!!$R2 861
21 TraesCS3B01G526300 chr3A 711336819 711337469 650 True 379.000000 379 78.561000 708 1343 1 chr3A.!!$R1 635
22 TraesCS3B01G526300 chr4A 481092754 481093254 500 False 893.000000 893 98.802000 1 501 1 chr4A.!!$F1 500
23 TraesCS3B01G526300 chrUn 62689453 62689955 502 False 880.000000 880 98.211000 1 503 1 chrUn.!!$F1 502
24 TraesCS3B01G526300 chr1D 334043614 334044125 511 True 785.000000 785 94.757000 1 501 1 chr1D.!!$R1 500
25 TraesCS3B01G526300 chr7D 4420957 4421470 513 False 778.000000 778 94.391000 1 502 1 chr7D.!!$F1 501
26 TraesCS3B01G526300 chr5D 550415110 550415615 505 True 767.000000 767 94.477000 1 493 1 chr5D.!!$R1 492
27 TraesCS3B01G526300 chr6B 279328286 279328826 540 True 603.000000 603 88.029000 1 501 1 chr6B.!!$R1 500
28 TraesCS3B01G526300 chr2B 657053358 657054275 917 True 490.000000 490 77.801000 1510 2418 1 chr2B.!!$R1 908

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
660 693 0.039618 GCCCTCTCCACCAATCCAAA 59.960 55.0 0.0 0.0 0.00 3.28 F
1432 2278 0.902516 GGGACAGGACTCTGCTCTGT 60.903 60.0 0.0 0.0 44.59 3.41 F
2664 8382 0.541392 TGCATCAGCGTTCCTACCAT 59.459 50.0 0.0 0.0 46.23 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 3116 0.988145 TGGGAGTGGCATTAGGGGAG 60.988 60.000 0.00 0.0 0.0 4.30 R
3331 9902 1.565759 AGCAGGGCCATGAACAGATTA 59.434 47.619 24.18 0.0 0.0 1.75 R
3903 10669 1.071385 CGGCAGCCCTCTATCAAATCT 59.929 52.381 5.63 0.0 0.0 2.40 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
503 518 4.335594 GCTATCCAAACAACGCCTAAGATT 59.664 41.667 0.00 0.00 0.00 2.40
504 519 4.701956 ATCCAAACAACGCCTAAGATTG 57.298 40.909 0.00 0.00 0.00 2.67
505 520 2.227865 TCCAAACAACGCCTAAGATTGC 59.772 45.455 0.00 0.00 0.00 3.56
506 521 2.228822 CCAAACAACGCCTAAGATTGCT 59.771 45.455 0.00 0.00 0.00 3.91
507 522 3.492313 CAAACAACGCCTAAGATTGCTC 58.508 45.455 0.00 0.00 0.00 4.26
508 523 2.770164 ACAACGCCTAAGATTGCTCT 57.230 45.000 0.00 0.00 0.00 4.09
509 524 3.059352 ACAACGCCTAAGATTGCTCTT 57.941 42.857 0.00 0.00 44.06 2.85
510 525 4.202245 ACAACGCCTAAGATTGCTCTTA 57.798 40.909 0.00 0.00 41.91 2.10
511 526 4.770795 ACAACGCCTAAGATTGCTCTTAT 58.229 39.130 0.00 0.00 41.87 1.73
512 527 5.914033 ACAACGCCTAAGATTGCTCTTATA 58.086 37.500 0.00 0.00 41.87 0.98
513 528 6.525629 ACAACGCCTAAGATTGCTCTTATAT 58.474 36.000 0.00 0.00 41.87 0.86
514 529 7.667557 ACAACGCCTAAGATTGCTCTTATATA 58.332 34.615 0.00 0.00 41.87 0.86
515 530 7.599245 ACAACGCCTAAGATTGCTCTTATATAC 59.401 37.037 0.00 0.00 41.87 1.47
516 531 6.323266 ACGCCTAAGATTGCTCTTATATACG 58.677 40.000 0.00 2.25 41.87 3.06
517 532 5.230306 CGCCTAAGATTGCTCTTATATACGC 59.770 44.000 0.00 0.00 41.87 4.42
518 533 5.230306 GCCTAAGATTGCTCTTATATACGCG 59.770 44.000 3.53 3.53 41.87 6.01
519 534 5.230306 CCTAAGATTGCTCTTATATACGCGC 59.770 44.000 5.73 0.00 41.87 6.86
520 535 3.512680 AGATTGCTCTTATATACGCGCC 58.487 45.455 5.73 0.00 0.00 6.53
521 536 2.074547 TTGCTCTTATATACGCGCCC 57.925 50.000 5.73 0.00 0.00 6.13
522 537 1.254026 TGCTCTTATATACGCGCCCT 58.746 50.000 5.73 0.00 0.00 5.19
523 538 1.067846 TGCTCTTATATACGCGCCCTG 60.068 52.381 5.73 0.00 0.00 4.45
524 539 1.736032 GCTCTTATATACGCGCCCTGG 60.736 57.143 5.73 0.00 0.00 4.45
525 540 0.245539 TCTTATATACGCGCCCTGGC 59.754 55.000 5.73 0.00 37.85 4.85
526 541 0.739813 CTTATATACGCGCCCTGGCC 60.740 60.000 5.73 0.00 37.98 5.36
527 542 2.175035 TTATATACGCGCCCTGGCCC 62.175 60.000 5.73 0.00 37.98 5.80
567 582 3.335534 GTCAACGGCGCAACGACT 61.336 61.111 10.83 0.00 37.61 4.18
608 623 2.125512 GCTCCACGCCATCTCGTT 60.126 61.111 0.00 0.00 41.21 3.85
609 624 2.167861 GCTCCACGCCATCTCGTTC 61.168 63.158 0.00 0.00 41.21 3.95
612 634 0.460109 TCCACGCCATCTCGTTCATG 60.460 55.000 0.00 0.00 41.21 3.07
618 640 1.524355 GCCATCTCGTTCATGATCGTG 59.476 52.381 21.98 19.81 0.00 4.35
629 651 2.577644 GATCGTGTCGCCGCGTAA 60.578 61.111 13.39 0.00 44.70 3.18
640 662 3.834373 CGCGTAACGGGCTCAACG 61.834 66.667 0.00 0.00 38.44 4.10
641 663 3.484547 GCGTAACGGGCTCAACGG 61.485 66.667 5.41 0.00 35.93 4.44
642 664 3.484547 CGTAACGGGCTCAACGGC 61.485 66.667 0.00 0.00 35.23 5.68
656 689 2.190578 CGGCCCTCTCCACCAATC 59.809 66.667 0.00 0.00 0.00 2.67
657 690 2.597903 GGCCCTCTCCACCAATCC 59.402 66.667 0.00 0.00 0.00 3.01
658 691 2.308722 GGCCCTCTCCACCAATCCA 61.309 63.158 0.00 0.00 0.00 3.41
659 692 1.691219 GCCCTCTCCACCAATCCAA 59.309 57.895 0.00 0.00 0.00 3.53
660 693 0.039618 GCCCTCTCCACCAATCCAAA 59.960 55.000 0.00 0.00 0.00 3.28
661 694 1.549950 GCCCTCTCCACCAATCCAAAA 60.550 52.381 0.00 0.00 0.00 2.44
662 695 2.888212 CCCTCTCCACCAATCCAAAAA 58.112 47.619 0.00 0.00 0.00 1.94
663 696 3.444029 CCCTCTCCACCAATCCAAAAAT 58.556 45.455 0.00 0.00 0.00 1.82
664 697 3.448660 CCCTCTCCACCAATCCAAAAATC 59.551 47.826 0.00 0.00 0.00 2.17
665 698 3.448660 CCTCTCCACCAATCCAAAAATCC 59.551 47.826 0.00 0.00 0.00 3.01
666 699 3.088532 TCTCCACCAATCCAAAAATCCG 58.911 45.455 0.00 0.00 0.00 4.18
667 700 3.088532 CTCCACCAATCCAAAAATCCGA 58.911 45.455 0.00 0.00 0.00 4.55
668 701 3.501349 TCCACCAATCCAAAAATCCGAA 58.499 40.909 0.00 0.00 0.00 4.30
669 702 3.898123 TCCACCAATCCAAAAATCCGAAA 59.102 39.130 0.00 0.00 0.00 3.46
670 703 3.993736 CCACCAATCCAAAAATCCGAAAC 59.006 43.478 0.00 0.00 0.00 2.78
671 704 3.993736 CACCAATCCAAAAATCCGAAACC 59.006 43.478 0.00 0.00 0.00 3.27
672 705 3.249917 CCAATCCAAAAATCCGAAACCG 58.750 45.455 0.00 0.00 0.00 4.44
673 706 3.057174 CCAATCCAAAAATCCGAAACCGA 60.057 43.478 0.00 0.00 0.00 4.69
674 707 4.381505 CCAATCCAAAAATCCGAAACCGAT 60.382 41.667 0.00 0.00 0.00 4.18
675 708 3.840890 TCCAAAAATCCGAAACCGATG 57.159 42.857 0.00 0.00 0.00 3.84
676 709 2.490115 TCCAAAAATCCGAAACCGATGG 59.510 45.455 0.00 0.00 0.00 3.51
677 710 2.490115 CCAAAAATCCGAAACCGATGGA 59.510 45.455 0.00 0.00 35.96 3.41
678 711 3.427503 CCAAAAATCCGAAACCGATGGAG 60.428 47.826 0.00 0.00 34.75 3.86
679 712 3.343941 AAAATCCGAAACCGATGGAGA 57.656 42.857 0.00 0.00 34.75 3.71
680 713 3.343941 AAATCCGAAACCGATGGAGAA 57.656 42.857 0.00 0.00 34.75 2.87
681 714 3.343941 AATCCGAAACCGATGGAGAAA 57.656 42.857 0.00 0.00 34.75 2.52
682 715 2.843401 TCCGAAACCGATGGAGAAAA 57.157 45.000 0.00 0.00 0.00 2.29
683 716 3.128852 TCCGAAACCGATGGAGAAAAA 57.871 42.857 0.00 0.00 0.00 1.94
684 717 3.071479 TCCGAAACCGATGGAGAAAAAG 58.929 45.455 0.00 0.00 0.00 2.27
685 718 2.414161 CCGAAACCGATGGAGAAAAAGC 60.414 50.000 0.00 0.00 0.00 3.51
686 719 2.414161 CGAAACCGATGGAGAAAAAGCC 60.414 50.000 0.00 0.00 0.00 4.35
687 720 2.286365 AACCGATGGAGAAAAAGCCA 57.714 45.000 0.00 0.00 38.78 4.75
689 722 2.094675 ACCGATGGAGAAAAAGCCATG 58.905 47.619 0.00 0.00 44.60 3.66
690 723 1.406539 CCGATGGAGAAAAAGCCATGG 59.593 52.381 7.63 7.63 44.60 3.66
691 724 1.406539 CGATGGAGAAAAAGCCATGGG 59.593 52.381 15.13 0.00 44.60 4.00
692 725 2.738743 GATGGAGAAAAAGCCATGGGA 58.261 47.619 15.13 0.00 44.60 4.37
693 726 2.925966 TGGAGAAAAAGCCATGGGAT 57.074 45.000 15.13 0.00 0.00 3.85
694 727 2.459644 TGGAGAAAAAGCCATGGGATG 58.540 47.619 15.13 0.00 0.00 3.51
695 728 2.042842 TGGAGAAAAAGCCATGGGATGA 59.957 45.455 15.13 0.00 0.00 2.92
696 729 3.099141 GGAGAAAAAGCCATGGGATGAA 58.901 45.455 15.13 0.00 0.00 2.57
697 730 3.131755 GGAGAAAAAGCCATGGGATGAAG 59.868 47.826 15.13 0.00 0.00 3.02
698 731 3.102204 AGAAAAAGCCATGGGATGAAGG 58.898 45.455 15.13 0.00 0.00 3.46
699 732 2.925966 AAAAGCCATGGGATGAAGGA 57.074 45.000 15.13 0.00 0.00 3.36
700 733 2.925966 AAAGCCATGGGATGAAGGAA 57.074 45.000 15.13 0.00 0.00 3.36
701 734 2.149973 AAGCCATGGGATGAAGGAAC 57.850 50.000 15.13 0.00 0.00 3.62
702 735 1.002069 AGCCATGGGATGAAGGAACA 58.998 50.000 15.13 0.00 0.00 3.18
703 736 1.572415 AGCCATGGGATGAAGGAACAT 59.428 47.619 15.13 0.00 0.00 2.71
704 737 2.785269 AGCCATGGGATGAAGGAACATA 59.215 45.455 15.13 0.00 0.00 2.29
705 738 3.152341 GCCATGGGATGAAGGAACATAG 58.848 50.000 15.13 0.00 0.00 2.23
725 758 2.429069 AACGTACGGAACCGCGTC 60.429 61.111 21.06 0.00 44.19 5.19
732 765 4.324991 GGAACCGCGTCAACCCCT 62.325 66.667 4.92 0.00 0.00 4.79
733 766 2.281276 GAACCGCGTCAACCCCTT 60.281 61.111 4.92 0.00 0.00 3.95
736 769 1.730451 AACCGCGTCAACCCCTTTTG 61.730 55.000 4.92 0.00 0.00 2.44
743 776 1.686587 GTCAACCCCTTTTGTCCAAGG 59.313 52.381 0.00 0.00 42.91 3.61
745 778 2.023888 TCAACCCCTTTTGTCCAAGGAA 60.024 45.455 0.77 0.00 45.79 3.36
746 779 2.769095 CAACCCCTTTTGTCCAAGGAAA 59.231 45.455 0.77 0.00 45.79 3.13
747 780 2.394632 ACCCCTTTTGTCCAAGGAAAC 58.605 47.619 0.77 0.00 45.79 2.78
748 781 1.691976 CCCCTTTTGTCCAAGGAAACC 59.308 52.381 0.77 0.00 45.79 3.27
749 782 2.393646 CCCTTTTGTCCAAGGAAACCA 58.606 47.619 0.77 0.00 45.79 3.67
750 783 2.102420 CCCTTTTGTCCAAGGAAACCAC 59.898 50.000 0.77 0.00 45.79 4.16
752 785 2.421751 TTTGTCCAAGGAAACCACGA 57.578 45.000 0.00 0.00 0.00 4.35
753 786 2.421751 TTGTCCAAGGAAACCACGAA 57.578 45.000 0.00 0.00 0.00 3.85
755 788 2.018515 TGTCCAAGGAAACCACGAAAC 58.981 47.619 0.00 0.00 0.00 2.78
758 794 3.067601 GTCCAAGGAAACCACGAAACAAT 59.932 43.478 0.00 0.00 0.00 2.71
766 802 1.209127 CACGAAACAATCCCACCGC 59.791 57.895 0.00 0.00 0.00 5.68
773 809 3.743017 AATCCCACCGCCCTGCAT 61.743 61.111 0.00 0.00 0.00 3.96
786 825 2.515290 TGCATCGCATCTGCCTGG 60.515 61.111 0.00 0.00 38.89 4.45
806 845 2.947938 CTAATGGGCCCAGCAGGTCG 62.948 65.000 31.97 9.96 43.46 4.79
821 866 3.481453 CAGGTCGGTCTCTCATCTGATA 58.519 50.000 0.00 0.00 0.00 2.15
824 869 3.823873 GGTCGGTCTCTCATCTGATATGT 59.176 47.826 0.00 0.00 0.00 2.29
827 872 5.240623 GTCGGTCTCTCATCTGATATGTCTT 59.759 44.000 0.00 0.00 0.00 3.01
828 873 5.471797 TCGGTCTCTCATCTGATATGTCTTC 59.528 44.000 0.00 0.00 0.00 2.87
829 874 5.473162 CGGTCTCTCATCTGATATGTCTTCT 59.527 44.000 0.00 0.00 0.00 2.85
830 875 6.652900 CGGTCTCTCATCTGATATGTCTTCTA 59.347 42.308 0.00 0.00 0.00 2.10
831 876 7.336679 CGGTCTCTCATCTGATATGTCTTCTAT 59.663 40.741 0.00 0.00 0.00 1.98
859 910 3.878667 CCTTCTCGGCCCATCCCC 61.879 72.222 0.00 0.00 0.00 4.81
860 911 3.878667 CTTCTCGGCCCATCCCCC 61.879 72.222 0.00 0.00 0.00 5.40
861 912 4.750695 TTCTCGGCCCATCCCCCA 62.751 66.667 0.00 0.00 0.00 4.96
862 913 4.514594 TCTCGGCCCATCCCCCAT 62.515 66.667 0.00 0.00 0.00 4.00
863 914 3.958860 CTCGGCCCATCCCCCATC 61.959 72.222 0.00 0.00 0.00 3.51
871 922 4.335647 ATCCCCCATCGCCATCGC 62.336 66.667 0.00 0.00 35.26 4.58
890 941 2.926242 GTCCCCGTCCCAGTTCCA 60.926 66.667 0.00 0.00 0.00 3.53
900 956 1.001974 TCCCAGTTCCATCAGTTCACG 59.998 52.381 0.00 0.00 0.00 4.35
905 961 1.873591 GTTCCATCAGTTCACGTTGCT 59.126 47.619 0.00 0.00 0.00 3.91
928 992 2.042435 CCTCCCTCTCGCCTTCCT 60.042 66.667 0.00 0.00 0.00 3.36
929 993 2.430610 CCTCCCTCTCGCCTTCCTG 61.431 68.421 0.00 0.00 0.00 3.86
930 994 1.380515 CTCCCTCTCGCCTTCCTGA 60.381 63.158 0.00 0.00 0.00 3.86
931 995 1.380515 TCCCTCTCGCCTTCCTGAG 60.381 63.158 0.00 0.00 0.00 3.35
933 997 2.057408 CCTCTCGCCTTCCTGAGCT 61.057 63.158 0.00 0.00 32.20 4.09
1176 1292 3.692406 GTCGTCAAGGTCCCCGCT 61.692 66.667 0.00 0.00 0.00 5.52
1188 1304 2.383601 CCCCGCTATCCCCCACTTT 61.384 63.158 0.00 0.00 0.00 2.66
1432 2278 0.902516 GGGACAGGACTCTGCTCTGT 60.903 60.000 0.00 0.00 44.59 3.41
1557 2494 6.174720 TGTCCCATCCATGTACTCTTAATC 57.825 41.667 0.00 0.00 0.00 1.75
1558 2495 5.071788 TGTCCCATCCATGTACTCTTAATCC 59.928 44.000 0.00 0.00 0.00 3.01
1576 2522 9.344772 TCTTAATCCTGCTTTACTAGACTAGAG 57.655 37.037 16.55 4.56 0.00 2.43
1694 2648 3.248446 TACCGCCAGAAGCACCCAC 62.248 63.158 0.00 0.00 44.04 4.61
1792 3035 3.403228 AATTGCCTTCCCACCATGTAT 57.597 42.857 0.00 0.00 0.00 2.29
1793 3036 2.917713 TTGCCTTCCCACCATGTATT 57.082 45.000 0.00 0.00 0.00 1.89
1794 3037 2.435372 TGCCTTCCCACCATGTATTC 57.565 50.000 0.00 0.00 0.00 1.75
1795 3038 1.064017 TGCCTTCCCACCATGTATTCC 60.064 52.381 0.00 0.00 0.00 3.01
1847 3112 6.093219 ACTCTGCTCTGCTGTTTATGTAAATG 59.907 38.462 0.00 0.00 0.00 2.32
1851 3116 5.731686 GCTCTGCTGTTTATGTAAATGAGCC 60.732 44.000 12.88 0.90 34.88 4.70
1855 3120 4.036852 GCTGTTTATGTAAATGAGCCTCCC 59.963 45.833 0.00 0.00 32.10 4.30
1864 3129 0.698886 ATGAGCCTCCCCTAATGCCA 60.699 55.000 0.00 0.00 0.00 4.92
1868 3133 1.839894 CCTCCCCTAATGCCACTCC 59.160 63.158 0.00 0.00 0.00 3.85
1885 3162 5.127031 GCCACTCCCATTAATTGTGTTACAT 59.873 40.000 0.00 0.00 0.00 2.29
1945 3233 5.589192 AGTCACTACTATGTACGGCAATTC 58.411 41.667 0.00 0.00 32.84 2.17
2004 3299 0.621082 TGTGTGTGGACTGGGTTCAA 59.379 50.000 0.00 0.00 0.00 2.69
2012 3470 4.956700 TGTGGACTGGGTTCAAAAATACAA 59.043 37.500 0.00 0.00 0.00 2.41
2022 3480 2.030363 TCAAAAATACAAGTGCCGCCAG 60.030 45.455 0.00 0.00 0.00 4.85
2026 3484 2.483014 ATACAAGTGCCGCCAGTTTA 57.517 45.000 0.00 0.00 32.35 2.01
2028 3486 0.881118 ACAAGTGCCGCCAGTTTATG 59.119 50.000 0.00 0.00 32.35 1.90
2032 3494 3.492102 AGTGCCGCCAGTTTATGATAT 57.508 42.857 0.00 0.00 0.00 1.63
2033 3495 4.617253 AGTGCCGCCAGTTTATGATATA 57.383 40.909 0.00 0.00 0.00 0.86
2034 3496 5.165961 AGTGCCGCCAGTTTATGATATAT 57.834 39.130 0.00 0.00 0.00 0.86
2035 3497 4.937620 AGTGCCGCCAGTTTATGATATATG 59.062 41.667 0.00 0.00 0.00 1.78
2064 3565 8.192774 CCATGTGACTATAGTTGATGCATTTTT 58.807 33.333 6.88 0.00 0.00 1.94
2103 3606 3.206150 CAAGTTGTAGCTGTTGGTCACT 58.794 45.455 0.00 0.00 0.00 3.41
2271 4803 9.784531 ATAGAACATTGGTTGGATCTTACATAG 57.215 33.333 0.00 0.00 37.36 2.23
2272 4804 7.633789 AGAACATTGGTTGGATCTTACATAGT 58.366 34.615 0.00 0.00 37.36 2.12
2273 4805 8.768397 AGAACATTGGTTGGATCTTACATAGTA 58.232 33.333 0.00 0.00 37.36 1.82
2299 4834 0.823356 TGCTGTTTCTTCCTGCCACC 60.823 55.000 0.00 0.00 0.00 4.61
2304 4839 1.001706 GTTTCTTCCTGCCACCGTTTC 60.002 52.381 0.00 0.00 0.00 2.78
2373 6519 2.730715 CGTTTGGTCCAATAACATGCCG 60.731 50.000 4.80 0.00 0.00 5.69
2566 7388 6.922957 GCTGGATAAATCGCATTGGATTAAAA 59.077 34.615 2.19 0.00 35.65 1.52
2664 8382 0.541392 TGCATCAGCGTTCCTACCAT 59.459 50.000 0.00 0.00 46.23 3.55
2675 8393 3.128589 CGTTCCTACCATGTCATTTTGGG 59.871 47.826 0.00 0.00 37.32 4.12
2758 9191 6.697019 TGCAGATAGTTTGCTTCTTTTTCAAC 59.303 34.615 0.00 0.00 42.02 3.18
2911 9414 7.722363 TGTTCTTATGCGATATAAAGAGACCA 58.278 34.615 0.00 0.00 0.00 4.02
2932 9439 4.443739 CCACTAAAATAGTCCCGGCATGTA 60.444 45.833 0.00 0.00 36.76 2.29
3280 9851 3.309682 CGGACAACATCATCAAGCGTTAT 59.690 43.478 0.00 0.00 0.00 1.89
3313 9884 4.459089 GTCTGGGCTGCCGTCTCC 62.459 72.222 13.40 0.00 0.00 3.71
3331 9902 4.407296 GTCTCCCTCTACCTTGACATCATT 59.593 45.833 0.00 0.00 0.00 2.57
3579 10269 1.005975 GTGCTGCTGCGTTTACGATAG 60.006 52.381 11.21 4.74 43.34 2.08
3679 10433 4.848357 CACCTATGAATTGGTCTCTTGGT 58.152 43.478 0.00 0.00 33.63 3.67
3769 10535 4.327680 ACCTTCAAAGAGTATGGTGCTTC 58.672 43.478 0.00 0.00 0.00 3.86
3770 10536 4.202461 ACCTTCAAAGAGTATGGTGCTTCA 60.202 41.667 0.00 0.00 0.00 3.02
3771 10537 4.394300 CCTTCAAAGAGTATGGTGCTTCAG 59.606 45.833 0.00 0.00 0.00 3.02
3772 10538 4.623932 TCAAAGAGTATGGTGCTTCAGT 57.376 40.909 0.00 0.00 0.00 3.41
3773 10539 4.318332 TCAAAGAGTATGGTGCTTCAGTG 58.682 43.478 0.00 0.00 0.00 3.66
3774 10540 2.393271 AGAGTATGGTGCTTCAGTGC 57.607 50.000 0.00 0.00 0.00 4.40
3775 10541 1.905215 AGAGTATGGTGCTTCAGTGCT 59.095 47.619 0.00 0.00 0.00 4.40
3776 10542 2.304180 AGAGTATGGTGCTTCAGTGCTT 59.696 45.455 0.00 0.00 0.00 3.91
3789 10555 5.353678 GCTTCAGTGCTTGTAGATTTCATCT 59.646 40.000 0.00 0.00 43.33 2.90
3791 10557 6.041423 TCAGTGCTTGTAGATTTCATCTGA 57.959 37.500 0.00 0.00 40.51 3.27
3797 10563 9.713740 GTGCTTGTAGATTTCATCTGATTAAAG 57.286 33.333 3.69 0.00 40.51 1.85
3826 10592 3.660501 AGCACTGATTACTGACGAACA 57.339 42.857 0.00 0.00 0.00 3.18
3972 10738 7.093814 GGTGGATTCATGCAAAGCCATTATATA 60.094 37.037 11.08 0.00 45.68 0.86
4099 10888 6.506770 ACTGATATGAACATTGGGAGGGATAT 59.493 38.462 0.00 0.00 0.00 1.63
4178 10968 4.350346 TCTTGTTTGCAAAATCACGTGAG 58.650 39.130 24.41 11.20 33.73 3.51
4183 10973 4.566545 TTGCAAAATCACGTGAGAACAT 57.433 36.364 24.41 3.26 0.00 2.71
4225 11015 2.806244 GTTAGTGCGAGAGGCTTCAAAA 59.194 45.455 0.00 0.00 44.05 2.44
4333 11126 6.765036 CAGAGGTGCAGATCTAATGTGTATTT 59.235 38.462 0.00 0.00 0.00 1.40
4335 11128 7.831193 AGAGGTGCAGATCTAATGTGTATTTTT 59.169 33.333 0.00 0.00 0.00 1.94
4349 11142 9.528489 AATGTGTATTTTTGTTATACAGTCCCT 57.472 29.630 0.00 0.00 38.70 4.20
4350 11143 8.556213 TGTGTATTTTTGTTATACAGTCCCTC 57.444 34.615 0.00 0.00 38.70 4.30
4351 11144 7.608761 TGTGTATTTTTGTTATACAGTCCCTCC 59.391 37.037 0.00 0.00 38.70 4.30
4352 11145 6.819649 TGTATTTTTGTTATACAGTCCCTCCG 59.180 38.462 0.00 0.00 34.46 4.63
4353 11146 4.895668 TTTTGTTATACAGTCCCTCCGT 57.104 40.909 0.00 0.00 0.00 4.69
4354 11147 4.895668 TTTGTTATACAGTCCCTCCGTT 57.104 40.909 0.00 0.00 0.00 4.44
4355 11148 4.460948 TTGTTATACAGTCCCTCCGTTC 57.539 45.455 0.00 0.00 0.00 3.95
4356 11149 2.762327 TGTTATACAGTCCCTCCGTTCC 59.238 50.000 0.00 0.00 0.00 3.62
4357 11150 2.762327 GTTATACAGTCCCTCCGTTCCA 59.238 50.000 0.00 0.00 0.00 3.53
4358 11151 1.946984 ATACAGTCCCTCCGTTCCAA 58.053 50.000 0.00 0.00 0.00 3.53
4359 11152 1.719529 TACAGTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
4360 11153 0.841289 ACAGTCCCTCCGTTCCAAAA 59.159 50.000 0.00 0.00 0.00 2.44
4361 11154 1.423921 ACAGTCCCTCCGTTCCAAAAT 59.576 47.619 0.00 0.00 0.00 1.82
4362 11155 2.640826 ACAGTCCCTCCGTTCCAAAATA 59.359 45.455 0.00 0.00 0.00 1.40
4363 11156 3.270877 CAGTCCCTCCGTTCCAAAATAG 58.729 50.000 0.00 0.00 0.00 1.73
4364 11157 3.055385 CAGTCCCTCCGTTCCAAAATAGA 60.055 47.826 0.00 0.00 0.00 1.98
4365 11158 3.780850 AGTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
4366 11159 3.877508 GTCCCTCCGTTCCAAAATAGATG 59.122 47.826 0.00 0.00 0.00 2.90
4367 11160 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
4368 11161 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
4369 11162 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
4370 11163 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
4371 11164 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
4372 11165 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
4373 11166 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
4374 11167 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
4375 11168 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
4376 11169 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
4377 11170 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
4378 11171 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
4379 11172 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
416 431 7.541916 TGATTTTTAGGAAACCCCGTTTTAT 57.458 32.000 0.00 0.00 40.87 1.40
503 518 1.067846 CAGGGCGCGTATATAAGAGCA 60.068 52.381 21.59 0.00 34.87 4.26
504 519 1.630148 CAGGGCGCGTATATAAGAGC 58.370 55.000 14.29 14.29 0.00 4.09
505 520 1.736032 GCCAGGGCGCGTATATAAGAG 60.736 57.143 8.43 0.00 0.00 2.85
506 521 0.245539 GCCAGGGCGCGTATATAAGA 59.754 55.000 8.43 0.00 0.00 2.10
507 522 0.739813 GGCCAGGGCGCGTATATAAG 60.740 60.000 8.43 0.00 43.06 1.73
508 523 1.294138 GGCCAGGGCGCGTATATAA 59.706 57.895 8.43 0.00 43.06 0.98
509 524 2.652095 GGGCCAGGGCGCGTATATA 61.652 63.158 11.79 0.00 43.74 0.86
510 525 4.016706 GGGCCAGGGCGCGTATAT 62.017 66.667 11.79 0.00 43.74 0.86
528 543 1.968017 CATGAGCACGGCCAACTGT 60.968 57.895 2.24 0.00 35.02 3.55
529 544 2.872557 CATGAGCACGGCCAACTG 59.127 61.111 2.24 0.00 0.00 3.16
530 545 3.058160 GCATGAGCACGGCCAACT 61.058 61.111 2.24 0.00 41.58 3.16
531 546 4.465512 CGCATGAGCACGGCCAAC 62.466 66.667 2.24 0.00 42.27 3.77
608 623 2.582226 GCGGCGACACGATCATGA 60.582 61.111 12.98 0.00 35.47 3.07
609 624 3.976375 CGCGGCGACACGATCATG 61.976 66.667 19.16 0.00 38.38 3.07
612 634 2.577644 TTACGCGGCGACACGATC 60.578 61.111 30.94 0.00 38.38 3.69
633 655 3.706373 TGGAGAGGGCCGTTGAGC 61.706 66.667 0.00 0.00 0.00 4.26
634 656 2.266055 GTGGAGAGGGCCGTTGAG 59.734 66.667 0.00 0.00 0.00 3.02
636 658 2.484287 ATTGGTGGAGAGGGCCGTTG 62.484 60.000 0.00 0.00 0.00 4.10
637 659 2.198304 GATTGGTGGAGAGGGCCGTT 62.198 60.000 0.00 0.00 0.00 4.44
638 660 2.610859 ATTGGTGGAGAGGGCCGT 60.611 61.111 0.00 0.00 0.00 5.68
640 662 1.863155 TTGGATTGGTGGAGAGGGCC 61.863 60.000 0.00 0.00 0.00 5.80
641 663 0.039618 TTTGGATTGGTGGAGAGGGC 59.960 55.000 0.00 0.00 0.00 5.19
642 664 2.603075 TTTTGGATTGGTGGAGAGGG 57.397 50.000 0.00 0.00 0.00 4.30
643 665 3.448660 GGATTTTTGGATTGGTGGAGAGG 59.551 47.826 0.00 0.00 0.00 3.69
656 689 2.490115 TCCATCGGTTTCGGATTTTTGG 59.510 45.455 0.00 0.00 36.95 3.28
657 690 3.438781 TCTCCATCGGTTTCGGATTTTTG 59.561 43.478 0.00 0.00 36.95 2.44
658 691 3.681593 TCTCCATCGGTTTCGGATTTTT 58.318 40.909 0.00 0.00 36.95 1.94
659 692 3.343941 TCTCCATCGGTTTCGGATTTT 57.656 42.857 0.00 0.00 36.95 1.82
660 693 3.343941 TTCTCCATCGGTTTCGGATTT 57.656 42.857 0.00 0.00 36.95 2.17
661 694 3.343941 TTTCTCCATCGGTTTCGGATT 57.656 42.857 0.00 0.00 36.95 3.01
662 695 3.343941 TTTTCTCCATCGGTTTCGGAT 57.656 42.857 0.00 0.00 36.95 4.18
663 696 2.843401 TTTTCTCCATCGGTTTCGGA 57.157 45.000 0.00 0.00 36.95 4.55
664 697 2.414161 GCTTTTTCTCCATCGGTTTCGG 60.414 50.000 0.00 0.00 36.95 4.30
665 698 2.414161 GGCTTTTTCTCCATCGGTTTCG 60.414 50.000 0.00 0.00 37.82 3.46
666 699 2.556622 TGGCTTTTTCTCCATCGGTTTC 59.443 45.455 0.00 0.00 0.00 2.78
667 700 2.593026 TGGCTTTTTCTCCATCGGTTT 58.407 42.857 0.00 0.00 0.00 3.27
668 701 2.286365 TGGCTTTTTCTCCATCGGTT 57.714 45.000 0.00 0.00 0.00 4.44
669 702 2.094675 CATGGCTTTTTCTCCATCGGT 58.905 47.619 0.00 0.00 40.88 4.69
670 703 1.406539 CCATGGCTTTTTCTCCATCGG 59.593 52.381 0.00 0.00 40.88 4.18
671 704 1.406539 CCCATGGCTTTTTCTCCATCG 59.593 52.381 6.09 0.00 40.88 3.84
672 705 2.738743 TCCCATGGCTTTTTCTCCATC 58.261 47.619 6.09 0.00 40.88 3.51
673 706 2.925966 TCCCATGGCTTTTTCTCCAT 57.074 45.000 6.09 0.00 43.45 3.41
674 707 2.042842 TCATCCCATGGCTTTTTCTCCA 59.957 45.455 6.09 0.00 36.70 3.86
675 708 2.738743 TCATCCCATGGCTTTTTCTCC 58.261 47.619 6.09 0.00 0.00 3.71
676 709 3.131755 CCTTCATCCCATGGCTTTTTCTC 59.868 47.826 6.09 0.00 0.00 2.87
677 710 3.102204 CCTTCATCCCATGGCTTTTTCT 58.898 45.455 6.09 0.00 0.00 2.52
678 711 3.099141 TCCTTCATCCCATGGCTTTTTC 58.901 45.455 6.09 0.00 0.00 2.29
679 712 3.188880 TCCTTCATCCCATGGCTTTTT 57.811 42.857 6.09 0.00 0.00 1.94
680 713 2.833943 GTTCCTTCATCCCATGGCTTTT 59.166 45.455 6.09 0.00 0.00 2.27
681 714 2.225343 TGTTCCTTCATCCCATGGCTTT 60.225 45.455 6.09 0.00 0.00 3.51
682 715 1.358787 TGTTCCTTCATCCCATGGCTT 59.641 47.619 6.09 0.00 0.00 4.35
683 716 1.002069 TGTTCCTTCATCCCATGGCT 58.998 50.000 6.09 0.00 0.00 4.75
684 717 2.077687 ATGTTCCTTCATCCCATGGC 57.922 50.000 6.09 0.00 0.00 4.40
685 718 3.152341 GCTATGTTCCTTCATCCCATGG 58.848 50.000 4.14 4.14 0.00 3.66
686 719 3.152341 GGCTATGTTCCTTCATCCCATG 58.848 50.000 0.00 0.00 0.00 3.66
687 720 2.785269 TGGCTATGTTCCTTCATCCCAT 59.215 45.455 0.00 0.00 30.18 4.00
688 721 2.204463 TGGCTATGTTCCTTCATCCCA 58.796 47.619 0.00 0.00 31.59 4.37
689 722 2.952310 GTTGGCTATGTTCCTTCATCCC 59.048 50.000 0.00 0.00 0.00 3.85
690 723 2.614057 CGTTGGCTATGTTCCTTCATCC 59.386 50.000 0.00 0.00 0.00 3.51
691 724 3.270877 ACGTTGGCTATGTTCCTTCATC 58.729 45.455 0.00 0.00 0.00 2.92
692 725 3.350219 ACGTTGGCTATGTTCCTTCAT 57.650 42.857 0.00 0.00 0.00 2.57
693 726 2.851263 ACGTTGGCTATGTTCCTTCA 57.149 45.000 0.00 0.00 0.00 3.02
694 727 2.601763 CGTACGTTGGCTATGTTCCTTC 59.398 50.000 7.22 0.00 0.00 3.46
695 728 2.613691 CGTACGTTGGCTATGTTCCTT 58.386 47.619 7.22 0.00 0.00 3.36
696 729 1.134907 CCGTACGTTGGCTATGTTCCT 60.135 52.381 15.21 0.00 0.00 3.36
697 730 1.135024 TCCGTACGTTGGCTATGTTCC 60.135 52.381 15.21 0.00 0.00 3.62
698 731 2.282701 TCCGTACGTTGGCTATGTTC 57.717 50.000 15.21 0.00 0.00 3.18
699 732 2.340337 GTTCCGTACGTTGGCTATGTT 58.660 47.619 15.21 0.00 0.00 2.71
700 733 1.404583 GGTTCCGTACGTTGGCTATGT 60.405 52.381 15.21 0.00 0.00 2.29
701 734 1.283736 GGTTCCGTACGTTGGCTATG 58.716 55.000 15.21 0.00 0.00 2.23
702 735 0.179129 CGGTTCCGTACGTTGGCTAT 60.179 55.000 15.21 0.00 0.00 2.97
703 736 1.212490 CGGTTCCGTACGTTGGCTA 59.788 57.895 15.21 0.00 0.00 3.93
704 737 2.048877 CGGTTCCGTACGTTGGCT 60.049 61.111 15.21 0.00 0.00 4.75
705 738 3.781162 GCGGTTCCGTACGTTGGC 61.781 66.667 15.21 6.41 0.00 4.52
725 758 2.080654 TCCTTGGACAAAAGGGGTTG 57.919 50.000 3.27 0.00 45.85 3.77
732 765 2.724454 TCGTGGTTTCCTTGGACAAAA 58.276 42.857 0.00 0.00 0.00 2.44
733 766 2.421751 TCGTGGTTTCCTTGGACAAA 57.578 45.000 0.00 0.00 0.00 2.83
736 769 2.018515 TGTTTCGTGGTTTCCTTGGAC 58.981 47.619 0.00 0.00 0.00 4.02
743 776 2.287970 GGTGGGATTGTTTCGTGGTTTC 60.288 50.000 0.00 0.00 0.00 2.78
745 778 1.324383 GGTGGGATTGTTTCGTGGTT 58.676 50.000 0.00 0.00 0.00 3.67
746 779 0.887387 CGGTGGGATTGTTTCGTGGT 60.887 55.000 0.00 0.00 0.00 4.16
747 780 1.873165 CGGTGGGATTGTTTCGTGG 59.127 57.895 0.00 0.00 0.00 4.94
748 781 1.209127 GCGGTGGGATTGTTTCGTG 59.791 57.895 0.00 0.00 0.00 4.35
749 782 1.969589 GGCGGTGGGATTGTTTCGT 60.970 57.895 0.00 0.00 0.00 3.85
750 783 2.696759 GGGCGGTGGGATTGTTTCG 61.697 63.158 0.00 0.00 0.00 3.46
752 785 1.606313 CAGGGCGGTGGGATTGTTT 60.606 57.895 0.00 0.00 0.00 2.83
753 786 2.035626 CAGGGCGGTGGGATTGTT 59.964 61.111 0.00 0.00 0.00 2.83
755 788 4.738998 TGCAGGGCGGTGGGATTG 62.739 66.667 0.00 0.00 0.00 2.67
766 802 3.285215 GGCAGATGCGATGCAGGG 61.285 66.667 9.44 0.00 45.68 4.45
773 809 0.533531 CATTAGCCAGGCAGATGCGA 60.534 55.000 15.80 0.00 43.26 5.10
776 815 1.177256 GCCCATTAGCCAGGCAGATG 61.177 60.000 15.80 16.23 46.34 2.90
786 825 2.520260 CCTGCTGGGCCCATTAGC 60.520 66.667 28.82 26.08 37.93 3.09
806 845 6.899393 AGAAGACATATCAGATGAGAGACC 57.101 41.667 0.00 0.00 0.00 3.85
821 866 9.153479 AGAAGGCTCAACTTATATAGAAGACAT 57.847 33.333 13.92 0.00 0.00 3.06
824 869 7.040340 CCGAGAAGGCTCAACTTATATAGAAGA 60.040 40.741 13.92 0.00 41.36 2.87
827 872 6.576662 CCGAGAAGGCTCAACTTATATAGA 57.423 41.667 0.00 0.00 41.36 1.98
852 903 2.034687 GATGGCGATGGGGGATGG 59.965 66.667 0.00 0.00 0.00 3.51
853 904 2.359107 CGATGGCGATGGGGGATG 60.359 66.667 0.00 0.00 40.82 3.51
854 905 4.335647 GCGATGGCGATGGGGGAT 62.336 66.667 0.00 0.00 40.82 3.85
876 927 1.221840 CTGATGGAACTGGGACGGG 59.778 63.158 0.00 0.00 40.47 5.28
884 935 1.873591 GCAACGTGAACTGATGGAACT 59.126 47.619 0.00 0.00 0.00 3.01
885 936 1.873591 AGCAACGTGAACTGATGGAAC 59.126 47.619 0.00 0.00 0.00 3.62
886 937 2.143122 GAGCAACGTGAACTGATGGAA 58.857 47.619 0.00 0.00 0.00 3.53
890 941 1.338200 GGAGGAGCAACGTGAACTGAT 60.338 52.381 0.00 0.00 0.00 2.90
900 956 2.285743 AGGGAGGGGAGGAGCAAC 60.286 66.667 0.00 0.00 0.00 4.17
905 961 4.144727 GCGAGAGGGAGGGGAGGA 62.145 72.222 0.00 0.00 0.00 3.71
928 992 2.616797 TTTTGGCGGGTGTGAGCTCA 62.617 55.000 13.74 13.74 0.00 4.26
929 993 1.896660 TTTTGGCGGGTGTGAGCTC 60.897 57.895 6.82 6.82 0.00 4.09
930 994 2.193536 GTTTTGGCGGGTGTGAGCT 61.194 57.895 0.00 0.00 0.00 4.09
931 995 2.335011 GTTTTGGCGGGTGTGAGC 59.665 61.111 0.00 0.00 0.00 4.26
933 997 1.706995 TAGGGTTTTGGCGGGTGTGA 61.707 55.000 0.00 0.00 0.00 3.58
1176 1292 0.996583 AGGCGAAAAAGTGGGGGATA 59.003 50.000 0.00 0.00 0.00 2.59
1188 1304 2.718073 GGCGTAGGAGGAGGCGAAA 61.718 63.158 0.00 0.00 0.00 3.46
1432 2278 1.745232 CAGGGCACGCAAAGGTAATA 58.255 50.000 0.00 0.00 0.00 0.98
1557 2494 4.339814 CCCACTCTAGTCTAGTAAAGCAGG 59.660 50.000 6.77 3.77 0.00 4.85
1558 2495 5.194432 TCCCACTCTAGTCTAGTAAAGCAG 58.806 45.833 6.77 0.00 0.00 4.24
1576 2522 1.039856 ACAAAGCAACCACATCCCAC 58.960 50.000 0.00 0.00 0.00 4.61
1694 2648 1.579932 CAAGCAGCAGCAGGTTGAG 59.420 57.895 21.63 0.00 44.78 3.02
1792 3035 2.260822 ACAAGCTAGGAGCAGAAGGAA 58.739 47.619 0.64 0.00 45.56 3.36
1793 3036 1.944177 ACAAGCTAGGAGCAGAAGGA 58.056 50.000 0.64 0.00 45.56 3.36
1794 3037 2.235898 AGAACAAGCTAGGAGCAGAAGG 59.764 50.000 0.64 0.00 45.56 3.46
1795 3038 3.608316 AGAACAAGCTAGGAGCAGAAG 57.392 47.619 0.64 0.00 45.56 2.85
1847 3112 1.149401 GTGGCATTAGGGGAGGCTC 59.851 63.158 5.78 5.78 0.00 4.70
1851 3116 0.988145 TGGGAGTGGCATTAGGGGAG 60.988 60.000 0.00 0.00 0.00 4.30
1855 3120 4.895297 ACAATTAATGGGAGTGGCATTAGG 59.105 41.667 0.00 0.00 0.00 2.69
1864 3129 9.120538 GTCATATGTAACACAATTAATGGGAGT 57.879 33.333 1.90 0.00 35.35 3.85
2004 3299 1.616159 ACTGGCGGCACTTGTATTTT 58.384 45.000 7.97 0.00 0.00 1.82
2012 3470 3.492102 ATATCATAAACTGGCGGCACT 57.508 42.857 7.97 0.00 0.00 4.40
2022 3480 6.886459 AGTCACATGGGCCATATATCATAAAC 59.114 38.462 20.73 7.41 0.00 2.01
2026 3484 6.836714 ATAGTCACATGGGCCATATATCAT 57.163 37.500 20.73 6.62 0.00 2.45
2028 3486 7.366847 ACTATAGTCACATGGGCCATATATC 57.633 40.000 20.73 10.44 0.00 1.63
2032 3494 4.904853 TCAACTATAGTCACATGGGCCATA 59.095 41.667 20.73 2.14 0.00 2.74
2033 3495 3.716353 TCAACTATAGTCACATGGGCCAT 59.284 43.478 14.78 14.78 0.00 4.40
2034 3496 3.111484 TCAACTATAGTCACATGGGCCA 58.889 45.455 9.61 9.61 0.00 5.36
2035 3497 3.838244 TCAACTATAGTCACATGGGCC 57.162 47.619 5.70 0.00 0.00 5.80
2064 3565 1.053835 TGGCCCTCAACACAGACTGA 61.054 55.000 10.08 0.00 0.00 3.41
2174 4702 3.688185 CAGCTGAGAATAGCAAAGCAAGA 59.312 43.478 8.42 0.00 46.07 3.02
2271 4803 6.531594 GGCAGGAAGAAACAGCAAATAAATAC 59.468 38.462 0.00 0.00 0.00 1.89
2272 4804 6.210385 TGGCAGGAAGAAACAGCAAATAAATA 59.790 34.615 0.00 0.00 0.00 1.40
2273 4805 5.011943 TGGCAGGAAGAAACAGCAAATAAAT 59.988 36.000 0.00 0.00 0.00 1.40
2299 4834 9.249457 ACATCACTATGTATCATACAAGAAACG 57.751 33.333 0.45 0.00 44.66 3.60
2373 6519 1.807142 GTCAACTTGAGCAGGTTAGCC 59.193 52.381 0.00 0.00 34.23 3.93
2664 8382 2.091278 TGGTACAACCCCCAAAATGACA 60.091 45.455 0.00 0.00 37.50 3.58
2758 9191 5.590104 TTCATGTAAATGACAGTGACACG 57.410 39.130 0.00 0.00 42.79 4.49
2911 9414 3.926058 ACATGCCGGGACTATTTTAGT 57.074 42.857 2.18 0.00 42.86 2.24
2932 9439 1.688197 CCAAAATGACCTTGCCTGTGT 59.312 47.619 0.00 0.00 0.00 3.72
3280 9851 4.395625 CCCAGACATACTCGTCATAGGTA 58.604 47.826 0.00 0.00 38.43 3.08
3313 9884 7.504403 ACAGATTAATGATGTCAAGGTAGAGG 58.496 38.462 0.00 0.00 0.00 3.69
3331 9902 1.565759 AGCAGGGCCATGAACAGATTA 59.434 47.619 24.18 0.00 0.00 1.75
3579 10269 8.256611 TCAGAAACAGTCATAGTAAGAAATGC 57.743 34.615 0.00 0.00 0.00 3.56
3606 10314 2.080693 TCACGTGGCCATACAAATGAC 58.919 47.619 17.00 0.00 34.84 3.06
3789 10555 7.977789 TCAGTGCTAACATCAACTTTAATCA 57.022 32.000 0.00 0.00 0.00 2.57
3797 10563 6.454318 CGTCAGTAATCAGTGCTAACATCAAC 60.454 42.308 0.00 0.00 0.00 3.18
3826 10592 2.047560 GTACGCCTTCACCCGCTT 60.048 61.111 0.00 0.00 0.00 4.68
3903 10669 1.071385 CGGCAGCCCTCTATCAAATCT 59.929 52.381 5.63 0.00 0.00 2.40
3925 10691 4.277423 ACCAGATAAACAAAAACTCCCACG 59.723 41.667 0.00 0.00 0.00 4.94
3932 10698 7.148590 GCATGAATCCACCAGATAAACAAAAAC 60.149 37.037 0.00 0.00 33.66 2.43
4002 10768 5.243730 CCCAGATAAAAGAAGCAACAAGGAA 59.756 40.000 0.00 0.00 0.00 3.36
4067 10833 7.629157 TCCCAATGTTCATATCAGTTTAGTCA 58.371 34.615 0.00 0.00 0.00 3.41
4099 10888 2.159156 ACAAGCACGGCGTGATCTTATA 60.159 45.455 40.94 0.00 40.22 0.98
4178 10968 5.416271 TTCCCCTGTCTACTACAATGTTC 57.584 43.478 0.00 0.00 37.74 3.18
4183 10973 7.897565 ACTAACTTATTCCCCTGTCTACTACAA 59.102 37.037 0.00 0.00 37.74 2.41
4225 11015 6.839124 TTTGCAAGAAGATGAACCACATAT 57.161 33.333 0.00 0.00 39.56 1.78
4333 11126 4.322953 GGAACGGAGGGACTGTATAACAAA 60.323 45.833 0.00 0.00 41.55 2.83
4335 11128 2.762327 GGAACGGAGGGACTGTATAACA 59.238 50.000 0.00 0.00 41.55 2.41
4342 11135 2.200373 ATTTTGGAACGGAGGGACTG 57.800 50.000 0.00 0.00 41.55 3.51
4345 11138 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
4346 11139 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
4347 11140 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
4348 11141 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
4349 11142 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
4350 11143 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
4351 11144 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
4352 11145 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
4353 11146 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53


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

AutoCloner maintained by Alex Coulton.