Multiple sequence alignment - TraesCS3B01G178100

Loading Multiple Alignment...

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 TraesCS3B01G178100 chr3B 100.000 4355 0 0 1 4355 182378748 182383102 0.000000e+00 8043.0
1 TraesCS3B01G178100 chr3B 89.796 147 10 5 540 685 109844705 109844563 2.680000e-42 183.0
2 TraesCS3B01G178100 chr3B 89.041 146 12 4 539 683 691456530 691456388 1.240000e-40 178.0
3 TraesCS3B01G178100 chr3B 88.732 142 15 1 544 685 760715719 760715579 5.790000e-39 172.0
4 TraesCS3B01G178100 chr3B 87.912 91 8 3 552 640 786144014 786143925 2.140000e-18 104.0
5 TraesCS3B01G178100 chr3B 80.292 137 22 5 539 671 251652837 251652972 9.970000e-17 99.0
6 TraesCS3B01G178100 chr3B 82.143 84 15 0 305 388 511069584 511069501 6.040000e-09 73.1
7 TraesCS3B01G178100 chr3A 95.012 2065 75 14 1700 3755 140041668 140043713 0.000000e+00 3217.0
8 TraesCS3B01G178100 chr3A 90.159 1006 52 20 685 1662 140040682 140041668 0.000000e+00 1266.0
9 TraesCS3B01G178100 chr3A 88.793 464 29 13 3830 4273 140050013 140050473 8.230000e-152 547.0
10 TraesCS3B01G178100 chr3A 100.000 79 0 0 4277 4355 140050509 140050587 3.510000e-31 147.0
11 TraesCS3B01G178100 chr3A 73.980 196 47 4 3 197 325307 325499 4.670000e-10 76.8
12 TraesCS3B01G178100 chr3D 95.344 2019 71 13 1700 3699 128541820 128543834 0.000000e+00 3186.0
13 TraesCS3B01G178100 chr3D 94.130 988 52 4 678 1662 128540836 128541820 0.000000e+00 1498.0
14 TraesCS3B01G178100 chr3D 87.889 578 47 12 1 559 128540270 128540843 0.000000e+00 658.0
15 TraesCS3B01G178100 chr3D 89.552 469 21 12 3830 4273 128544164 128544629 1.760000e-158 569.0
16 TraesCS3B01G178100 chr3D 98.734 79 1 0 4277 4355 128544666 128544744 1.630000e-29 141.0
17 TraesCS3B01G178100 chr3D 87.903 124 5 3 3701 3814 128544058 128544181 2.110000e-28 137.0
18 TraesCS3B01G178100 chr1B 96.875 128 3 1 556 683 364117465 364117339 3.410000e-51 213.0
19 TraesCS3B01G178100 chr1B 95.455 132 5 1 554 685 409879807 409879937 4.410000e-50 209.0
20 TraesCS3B01G178100 chr7B 95.489 133 5 1 551 683 601600614 601600745 1.230000e-50 211.0
21 TraesCS3B01G178100 chr7B 91.946 149 9 3 540 687 374557983 374557837 5.710000e-49 206.0
22 TraesCS3B01G178100 chr7B 94.161 137 5 3 548 683 646052800 646052666 5.710000e-49 206.0
23 TraesCS3B01G178100 chr4D 94.203 138 7 1 548 685 23352590 23352726 4.410000e-50 209.0
24 TraesCS3B01G178100 chr5B 94.118 136 7 1 548 683 671344456 671344590 5.710000e-49 206.0
25 TraesCS3B01G178100 chr2B 93.525 139 7 2 555 692 436038065 436038202 5.710000e-49 206.0
26 TraesCS3B01G178100 chr2B 73.095 420 103 7 5 423 59654811 59655221 1.630000e-29 141.0
27 TraesCS3B01G178100 chr2B 79.070 129 23 4 126 253 65667986 65668111 7.760000e-13 86.1
28 TraesCS3B01G178100 chr6B 90.446 157 11 4 548 703 688477563 688477716 2.050000e-48 204.0
29 TraesCS3B01G178100 chr2D 74.627 402 76 18 4 401 646210044 646210423 2.100000e-33 154.0
30 TraesCS3B01G178100 chr1D 78.462 195 39 3 9 202 409340480 409340672 1.640000e-24 124.0
31 TraesCS3B01G178100 chr1D 72.201 259 49 13 167 423 372857636 372857399 1.690000e-04 58.4
32 TraesCS3B01G178100 chr5D 82.270 141 24 1 4 144 199739129 199738990 2.130000e-23 121.0
33 TraesCS3B01G178100 chr6A 76.263 198 43 4 4 201 135759415 135759608 7.710000e-18 102.0
34 TraesCS3B01G178100 chrUn 75.127 197 47 2 1 197 60469306 60469500 1.670000e-14 91.6
35 TraesCS3B01G178100 chr4B 79.528 127 25 1 1 127 643487385 643487260 6.000000e-14 89.8


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 TraesCS3B01G178100 chr3B 182378748 182383102 4354 False 8043.0 8043 100.000000 1 4355 1 chr3B.!!$F1 4354
1 TraesCS3B01G178100 chr3A 140040682 140043713 3031 False 2241.5 3217 92.585500 685 3755 2 chr3A.!!$F2 3070
2 TraesCS3B01G178100 chr3A 140050013 140050587 574 False 347.0 547 94.396500 3830 4355 2 chr3A.!!$F3 525
3 TraesCS3B01G178100 chr3D 128540270 128544744 4474 False 1031.5 3186 92.258667 1 4355 6 chr3D.!!$F1 4354

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
572 592 0.038744 AGTACTCCCTCCGTCCGAAA 59.961 55.0 0.00 0.00 0.00 3.46 F
801 830 0.322997 CCGTCCACTCTGAGTCCTCT 60.323 60.0 7.49 0.00 0.00 3.69 F
968 998 0.678048 CCTCCCCTTTTCTTGCGGAG 60.678 60.0 0.00 0.00 39.92 4.63 F
2755 2807 0.810031 ACGCTTGCACGTTCAAGAGT 60.810 50.0 28.39 27.14 46.94 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 1746 0.108207 GCAGCTCAGCCATATGGACT 59.892 55.000 26.47 18.03 37.39 3.85 R
1837 1886 1.002430 AGAATTCACTGAGCGCCTGAA 59.998 47.619 2.29 6.83 0.00 3.02 R
2888 2940 1.266718 GCAATCTGACGAAGGTTTGCA 59.733 47.619 17.38 0.00 41.37 4.08 R
4043 4367 0.108662 TATCAGCGTGCCAGTCTGTG 60.109 55.000 0.00 0.00 0.00 3.66 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
40 41 2.374184 CTCAGGAAGGAGAGACGACAT 58.626 52.381 0.00 0.00 37.05 3.06
58 59 1.414061 ATCGGCTCCCTGAAGATGGG 61.414 60.000 0.00 0.00 45.90 4.00
73 74 0.112412 ATGGGATAATGTTCGCCCCC 59.888 55.000 0.00 0.00 39.93 5.40
74 75 1.599797 GGGATAATGTTCGCCCCCG 60.600 63.158 0.00 0.00 34.39 5.73
114 115 1.136147 GCGTCTAGCCTCGTCGAAA 59.864 57.895 0.00 0.00 40.81 3.46
130 131 1.227853 AAAGGCGTGTGGAGGTGTC 60.228 57.895 0.00 0.00 0.00 3.67
134 135 1.080434 GCGTGTGGAGGTGTCTCTC 60.080 63.158 0.00 0.00 39.86 3.20
135 136 1.528292 GCGTGTGGAGGTGTCTCTCT 61.528 60.000 0.00 0.00 39.86 3.10
146 147 1.895798 GTGTCTCTCTGGTGGATCACA 59.104 52.381 0.00 0.00 35.86 3.58
163 164 1.804151 CACACGGGATTTTGTCGACAT 59.196 47.619 20.80 4.07 0.00 3.06
171 172 5.528870 GGGATTTTGTCGACATTTGTCTTT 58.471 37.500 20.80 0.00 42.66 2.52
176 177 2.616376 TGTCGACATTTGTCTTTGGTGG 59.384 45.455 15.76 0.00 42.66 4.61
180 181 3.119849 CGACATTTGTCTTTGGTGGATCC 60.120 47.826 4.20 4.20 42.66 3.36
204 222 1.071542 TGGATCCAGTCTTTGTTCGCA 59.928 47.619 11.44 0.00 0.00 5.10
255 273 8.012957 TCCTTCCAATCTATACTTCTCTTCAC 57.987 38.462 0.00 0.00 0.00 3.18
258 276 7.353414 TCCAATCTATACTTCTCTTCACCAG 57.647 40.000 0.00 0.00 0.00 4.00
265 283 0.318441 TTCTCTTCACCAGCGGACAG 59.682 55.000 1.50 0.00 0.00 3.51
299 317 1.117142 ATGGTGCATTGGCCCTATGC 61.117 55.000 25.34 25.34 46.63 3.14
303 321 2.508361 GCATTGGCCCTATGCAACT 58.492 52.632 26.49 0.00 45.93 3.16
311 329 1.064060 GCCCTATGCAACTTTAGCACG 59.936 52.381 0.00 0.00 45.95 5.34
330 348 2.485426 ACGACGACTTTCGGATTGTCTA 59.515 45.455 0.00 0.00 45.59 2.59
332 350 3.177487 GACGACTTTCGGATTGTCTACC 58.823 50.000 0.03 0.00 45.59 3.18
349 367 4.036262 GTCTACCACAACAAGATTTGCACA 59.964 41.667 0.00 0.00 0.00 4.57
350 368 3.883830 ACCACAACAAGATTTGCACAA 57.116 38.095 0.00 0.00 0.00 3.33
352 370 3.195396 ACCACAACAAGATTTGCACAACT 59.805 39.130 0.00 0.00 0.00 3.16
353 371 4.400884 ACCACAACAAGATTTGCACAACTA 59.599 37.500 0.00 0.00 0.00 2.24
354 372 5.068987 ACCACAACAAGATTTGCACAACTAT 59.931 36.000 0.00 0.00 0.00 2.12
362 380 2.198827 TTGCACAACTATGGTGAGGG 57.801 50.000 0.00 0.00 38.54 4.30
401 419 2.583593 CCTTCGGCTCGCTACAGC 60.584 66.667 0.00 0.00 38.84 4.40
425 443 4.019792 TGGTAGTCGTCACTAGGTGTAA 57.980 45.455 0.00 0.00 35.67 2.41
426 444 4.592942 TGGTAGTCGTCACTAGGTGTAAT 58.407 43.478 0.00 0.00 35.67 1.89
460 478 3.444034 AGTGCGCTCTGTACTATCTTGAA 59.556 43.478 11.84 0.00 42.19 2.69
461 479 3.794028 GTGCGCTCTGTACTATCTTGAAG 59.206 47.826 9.73 0.00 0.00 3.02
495 513 8.833231 ATGATCGAAAGTTTTCAAGAGTAGAA 57.167 30.769 5.55 0.00 37.01 2.10
534 554 5.867903 ACTTTTCAAAATCCATGTCCACA 57.132 34.783 0.00 0.00 0.00 4.17
549 569 3.054287 TGTCCACAGTTCACCAAACCTAA 60.054 43.478 0.00 0.00 38.76 2.69
559 579 5.416271 TCACCAAACCTAATGGAGTACTC 57.584 43.478 14.87 14.87 40.56 2.59
560 580 7.295398 GTTCACCAAACCTAATGGAGTACTCC 61.295 46.154 31.61 31.61 40.56 3.85
568 588 4.256462 GGAGTACTCCCTCCGTCC 57.744 66.667 28.87 4.17 43.94 4.79
569 589 1.823041 GGAGTACTCCCTCCGTCCG 60.823 68.421 28.87 0.00 43.94 4.79
570 590 1.222936 GAGTACTCCCTCCGTCCGA 59.777 63.158 12.13 0.00 0.00 4.55
571 591 0.393537 GAGTACTCCCTCCGTCCGAA 60.394 60.000 12.13 0.00 0.00 4.30
572 592 0.038744 AGTACTCCCTCCGTCCGAAA 59.961 55.000 0.00 0.00 0.00 3.46
573 593 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
574 594 1.479730 GTACTCCCTCCGTCCGAAAAT 59.520 52.381 0.00 0.00 0.00 1.82
575 595 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
576 596 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
577 597 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
578 598 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
579 599 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
580 600 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
581 601 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
582 602 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
583 603 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
584 604 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
585 605 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
586 606 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
587 607 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
588 608 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
589 609 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
590 610 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
591 611 8.020819 GTCCGAAAATACTTGTCATCAAAATGA 58.979 33.333 0.00 0.00 39.63 2.57
592 612 8.572185 TCCGAAAATACTTGTCATCAAAATGAA 58.428 29.630 0.00 0.00 43.42 2.57
593 613 9.357652 CCGAAAATACTTGTCATCAAAATGAAT 57.642 29.630 0.00 0.00 43.42 2.57
601 621 9.472361 ACTTGTCATCAAAATGAATGAAAAGAG 57.528 29.630 17.77 0.00 43.42 2.85
602 622 9.687210 CTTGTCATCAAAATGAATGAAAAGAGA 57.313 29.630 8.85 0.00 43.42 3.10
604 624 9.634163 TGTCATCAAAATGAATGAAAAGAGATG 57.366 29.630 0.00 0.00 43.42 2.90
605 625 9.635520 GTCATCAAAATGAATGAAAAGAGATGT 57.364 29.630 0.00 0.00 43.42 3.06
657 677 9.710900 ACATCCCTTTTTATTCTTTTTGATGAC 57.289 29.630 0.00 0.00 32.39 3.06
658 678 9.709495 CATCCCTTTTTATTCTTTTTGATGACA 57.291 29.630 0.00 0.00 0.00 3.58
659 679 9.933723 ATCCCTTTTTATTCTTTTTGATGACAG 57.066 29.630 0.00 0.00 0.00 3.51
660 680 8.367156 TCCCTTTTTATTCTTTTTGATGACAGG 58.633 33.333 0.00 0.00 0.00 4.00
661 681 8.150296 CCCTTTTTATTCTTTTTGATGACAGGT 58.850 33.333 0.00 0.00 0.00 4.00
668 688 8.970691 ATTCTTTTTGATGACAGGTATTTTCG 57.029 30.769 0.00 0.00 0.00 3.46
669 689 6.908825 TCTTTTTGATGACAGGTATTTTCGG 58.091 36.000 0.00 0.00 0.00 4.30
670 690 6.712998 TCTTTTTGATGACAGGTATTTTCGGA 59.287 34.615 0.00 0.00 0.00 4.55
671 691 7.393234 TCTTTTTGATGACAGGTATTTTCGGAT 59.607 33.333 0.00 0.00 0.00 4.18
672 692 6.677781 TTTGATGACAGGTATTTTCGGATC 57.322 37.500 0.00 0.00 0.00 3.36
673 693 4.368315 TGATGACAGGTATTTTCGGATCG 58.632 43.478 0.00 0.00 0.00 3.69
674 694 3.173668 TGACAGGTATTTTCGGATCGG 57.826 47.619 0.00 0.00 0.00 4.18
675 695 2.761767 TGACAGGTATTTTCGGATCGGA 59.238 45.455 0.00 0.00 0.00 4.55
676 696 3.181479 TGACAGGTATTTTCGGATCGGAG 60.181 47.826 2.99 0.00 0.00 4.63
677 697 2.102588 ACAGGTATTTTCGGATCGGAGG 59.897 50.000 2.99 0.00 0.00 4.30
678 698 1.692519 AGGTATTTTCGGATCGGAGGG 59.307 52.381 2.99 0.00 0.00 4.30
679 699 1.690352 GGTATTTTCGGATCGGAGGGA 59.310 52.381 2.99 0.00 0.00 4.20
680 700 2.288886 GGTATTTTCGGATCGGAGGGAG 60.289 54.545 2.99 0.00 0.00 4.30
681 701 1.497161 ATTTTCGGATCGGAGGGAGT 58.503 50.000 2.99 0.00 0.00 3.85
682 702 2.148446 TTTTCGGATCGGAGGGAGTA 57.852 50.000 2.99 0.00 0.00 2.59
683 703 1.396653 TTTCGGATCGGAGGGAGTAC 58.603 55.000 2.99 0.00 0.00 2.73
684 704 0.549950 TTCGGATCGGAGGGAGTACT 59.450 55.000 0.00 0.00 0.00 2.73
685 705 0.549950 TCGGATCGGAGGGAGTACTT 59.450 55.000 0.00 0.00 0.00 2.24
686 706 0.953003 CGGATCGGAGGGAGTACTTC 59.047 60.000 0.00 0.00 0.00 3.01
687 707 1.330234 GGATCGGAGGGAGTACTTCC 58.670 60.000 12.91 12.91 46.00 3.46
688 708 1.133419 GGATCGGAGGGAGTACTTCCT 60.133 57.143 23.71 23.71 45.98 3.36
689 709 2.668625 GATCGGAGGGAGTACTTCCTT 58.331 52.381 24.27 8.08 45.98 3.36
690 710 1.848652 TCGGAGGGAGTACTTCCTTG 58.151 55.000 24.27 18.70 45.98 3.61
691 711 1.076677 TCGGAGGGAGTACTTCCTTGT 59.923 52.381 24.27 1.57 45.98 3.16
692 712 1.204941 CGGAGGGAGTACTTCCTTGTG 59.795 57.143 24.27 12.77 45.98 3.33
693 713 1.555533 GGAGGGAGTACTTCCTTGTGG 59.444 57.143 24.27 0.00 45.98 4.17
694 714 2.537143 GAGGGAGTACTTCCTTGTGGA 58.463 52.381 24.27 0.00 45.98 4.02
707 727 3.895041 TCCTTGTGGATTTGGTTTTCCTC 59.105 43.478 0.00 0.00 37.96 3.71
801 830 0.322997 CCGTCCACTCTGAGTCCTCT 60.323 60.000 7.49 0.00 0.00 3.69
808 837 2.043450 CTGAGTCCTCTCCCCGCT 60.043 66.667 0.00 0.00 39.75 5.52
815 844 3.144193 CTCTCCCCGCTCGCTCTT 61.144 66.667 0.00 0.00 0.00 2.85
926 956 2.378634 CCCCGCATTCTCTTCCCCT 61.379 63.158 0.00 0.00 0.00 4.79
967 997 1.378762 CCTCCCCTTTTCTTGCGGA 59.621 57.895 0.00 0.00 0.00 5.54
968 998 0.678048 CCTCCCCTTTTCTTGCGGAG 60.678 60.000 0.00 0.00 39.92 4.63
969 999 0.678048 CTCCCCTTTTCTTGCGGAGG 60.678 60.000 0.00 0.00 37.13 4.30
1104 1134 3.462678 GGCGACCACTCCTCCTCC 61.463 72.222 0.00 0.00 0.00 4.30
1107 1137 2.115911 CGACCACTCCTCCTCCTCG 61.116 68.421 0.00 0.00 0.00 4.63
1110 1140 2.115911 CCACTCCTCCTCCTCGTCG 61.116 68.421 0.00 0.00 0.00 5.12
1374 1417 0.954449 ACGCGTAGATCGGATCGGAT 60.954 55.000 11.67 15.03 40.26 4.18
1402 1445 1.003718 CTGGACGGGTTTGGGTCTC 60.004 63.158 0.00 0.00 33.70 3.36
1484 1529 2.915137 TTTTTGGGCGGCTGGGTC 60.915 61.111 9.56 0.00 0.00 4.46
1543 1588 1.319541 GCTACTGGAGCGACCTGATA 58.680 55.000 14.31 5.17 42.62 2.15
1551 1596 3.867723 GCGACCTGATATACGCTGT 57.132 52.632 0.00 0.00 46.06 4.40
1590 1635 1.725641 TGCAAGCTGTCTTCGTATGG 58.274 50.000 0.00 0.00 0.00 2.74
1598 1643 3.074412 CTGTCTTCGTATGGGTTTTGCT 58.926 45.455 0.00 0.00 0.00 3.91
1604 1649 1.199097 CGTATGGGTTTTGCTGTGGTC 59.801 52.381 0.00 0.00 0.00 4.02
1629 1674 5.988561 GTGCGATCTGATCTTTAAGATTCCT 59.011 40.000 15.16 0.00 34.53 3.36
1633 1678 5.896073 TCTGATCTTTAAGATTCCTCCCC 57.104 43.478 8.99 0.00 34.53 4.81
1643 1688 9.868160 CTTTAAGATTCCTCCCCTGTATTTATT 57.132 33.333 0.00 0.00 0.00 1.40
1648 1693 3.525609 TCCTCCCCTGTATTTATTGTGCA 59.474 43.478 0.00 0.00 0.00 4.57
1662 1710 8.721019 ATTTATTGTGCAAAAATGGATACTGG 57.279 30.769 0.00 0.00 37.61 4.00
1663 1711 5.743636 ATTGTGCAAAAATGGATACTGGT 57.256 34.783 0.00 0.00 37.61 4.00
1664 1712 5.543507 TTGTGCAAAAATGGATACTGGTT 57.456 34.783 0.00 0.00 37.61 3.67
1665 1713 5.543507 TGTGCAAAAATGGATACTGGTTT 57.456 34.783 0.00 0.00 37.61 3.27
1666 1714 5.923204 TGTGCAAAAATGGATACTGGTTTT 58.077 33.333 0.00 0.00 37.61 2.43
1667 1715 6.352516 TGTGCAAAAATGGATACTGGTTTTT 58.647 32.000 0.00 0.00 37.05 1.94
1668 1716 6.259608 TGTGCAAAAATGGATACTGGTTTTTG 59.740 34.615 15.88 15.88 45.65 2.44
1669 1717 6.481644 GTGCAAAAATGGATACTGGTTTTTGA 59.518 34.615 20.71 10.03 45.69 2.69
1670 1718 7.173047 GTGCAAAAATGGATACTGGTTTTTGAT 59.827 33.333 20.71 0.00 45.69 2.57
1671 1719 8.370940 TGCAAAAATGGATACTGGTTTTTGATA 58.629 29.630 20.71 11.55 45.69 2.15
1672 1720 8.872845 GCAAAAATGGATACTGGTTTTTGATAG 58.127 33.333 20.71 4.95 45.69 2.08
1673 1721 9.927668 CAAAAATGGATACTGGTTTTTGATAGT 57.072 29.630 15.45 0.00 45.69 2.12
1697 1745 8.684520 AGTAATAGTAAGTTTATGCTCTGTCGT 58.315 33.333 0.00 0.00 0.00 4.34
1698 1746 9.941664 GTAATAGTAAGTTTATGCTCTGTCGTA 57.058 33.333 0.00 0.00 0.00 3.43
1712 1760 2.623416 CTGTCGTAGTCCATATGGCTGA 59.377 50.000 17.58 8.99 34.44 4.26
1837 1886 3.755378 GTCAGTTTGTGGCAGAATCATCT 59.245 43.478 8.00 0.00 35.88 2.90
2102 2151 1.526887 CCTATGCGCCATTAGTCGTTG 59.473 52.381 4.18 0.00 0.00 4.10
2276 2325 2.156098 TGTTGTGAATCCTTAACGGGC 58.844 47.619 0.00 0.00 0.00 6.13
2314 2363 5.248870 ACTAGTTGTGTTTTCTTGCCTTG 57.751 39.130 0.00 0.00 0.00 3.61
2331 2380 3.181493 GCCTTGCATTGTCACTCCATAAG 60.181 47.826 0.00 0.00 0.00 1.73
2337 2386 5.534278 TGCATTGTCACTCCATAAGTTTTCA 59.466 36.000 0.00 0.00 35.45 2.69
2342 2391 5.991606 TGTCACTCCATAAGTTTTCACAGAG 59.008 40.000 0.00 0.00 35.45 3.35
2347 2396 6.521427 ACTCCATAAGTTTTCACAGAGCATCT 60.521 38.462 0.00 0.00 40.76 2.90
2404 2453 6.969993 ACTCCTTAAACACTGCCAAATTTA 57.030 33.333 0.00 0.00 0.00 1.40
2407 2459 7.451566 ACTCCTTAAACACTGCCAAATTTATCT 59.548 33.333 0.00 0.00 0.00 1.98
2546 2598 2.093306 TATGTGGAGGAACAAGCACG 57.907 50.000 0.00 0.00 32.81 5.34
2738 2790 5.912360 ATCACAGATTACATGTGCATACG 57.088 39.130 9.11 0.00 46.11 3.06
2755 2807 0.810031 ACGCTTGCACGTTCAAGAGT 60.810 50.000 28.39 27.14 46.94 3.24
2760 2812 3.363084 GCTTGCACGTTCAAGAGTTAGTC 60.363 47.826 28.39 7.75 44.61 2.59
2888 2940 4.260170 GTCATGAGATCAACAGAGCCTTT 58.740 43.478 0.00 0.00 0.00 3.11
2977 3029 4.499019 CCATTGTTTACCAAGCGTTGTTCT 60.499 41.667 0.00 0.00 36.25 3.01
2985 3037 3.498397 ACCAAGCGTTGTTCTTACATCAG 59.502 43.478 0.00 0.00 33.44 2.90
3113 3165 5.520748 ACATTGGTAAGGGATCTCAACTT 57.479 39.130 0.00 0.00 0.00 2.66
3114 3166 5.892348 ACATTGGTAAGGGATCTCAACTTT 58.108 37.500 0.00 0.00 0.00 2.66
3127 3179 8.406297 GGGATCTCAACTTTGTATACCATTTTC 58.594 37.037 0.00 0.00 30.74 2.29
3132 3184 7.946207 TCAACTTTGTATACCATTTTCAGCAA 58.054 30.769 0.00 0.00 0.00 3.91
3141 3196 3.160269 CCATTTTCAGCAACTCTTCCCT 58.840 45.455 0.00 0.00 0.00 4.20
3166 3223 4.046286 TGGATTTGGCTAACAGTGGATT 57.954 40.909 0.00 0.00 0.00 3.01
3374 3431 0.249573 AAACGAGTGGTACCGTGTGG 60.250 55.000 7.57 0.00 39.14 4.17
3375 3432 1.108727 AACGAGTGGTACCGTGTGGA 61.109 55.000 7.57 0.00 39.14 4.02
3436 3499 1.879380 TGAGCACCAAATTTCTCACCG 59.121 47.619 3.79 0.00 31.35 4.94
3467 3532 5.057819 TGTGTTATGTAAGGCTGTTTTCGA 58.942 37.500 0.00 0.00 0.00 3.71
3494 3560 2.815478 CGACTTTGATGAGAGTAGCCC 58.185 52.381 0.00 0.00 0.00 5.19
3495 3561 2.482142 CGACTTTGATGAGAGTAGCCCC 60.482 54.545 0.00 0.00 0.00 5.80
3540 3606 0.386838 GCAGAGGCAGCACTTGTTTT 59.613 50.000 0.00 0.00 40.72 2.43
3596 3662 0.390603 TCGCATGGGTACGGTTTCTG 60.391 55.000 9.86 0.00 0.00 3.02
3699 3769 9.222916 CATGTACTCGTTTCTATTGTACTACTG 57.777 37.037 0.00 0.00 35.76 2.74
3706 3998 8.847196 TCGTTTCTATTGTACTACTGCTATCAT 58.153 33.333 0.00 0.00 0.00 2.45
3779 4080 0.672889 TGCATCGTTGGCACACAATT 59.327 45.000 0.00 0.00 41.95 2.32
3801 4102 4.093743 TGCTGGAGTTTCTCTACCACATA 58.906 43.478 0.00 0.00 0.00 2.29
3803 4104 5.112686 GCTGGAGTTTCTCTACCACATAAG 58.887 45.833 0.00 0.00 0.00 1.73
3804 4105 5.337652 GCTGGAGTTTCTCTACCACATAAGT 60.338 44.000 0.00 0.00 0.00 2.24
3805 4106 6.127423 GCTGGAGTTTCTCTACCACATAAGTA 60.127 42.308 0.00 0.00 0.00 2.24
3806 4107 7.406031 TGGAGTTTCTCTACCACATAAGTAG 57.594 40.000 0.00 0.00 38.86 2.57
3807 4108 6.380274 TGGAGTTTCTCTACCACATAAGTAGG 59.620 42.308 0.00 0.00 38.20 3.18
3808 4109 6.606395 GGAGTTTCTCTACCACATAAGTAGGA 59.394 42.308 0.00 0.00 38.20 2.94
3809 4110 7.201839 GGAGTTTCTCTACCACATAAGTAGGAG 60.202 44.444 0.00 0.00 38.20 3.69
3810 4111 7.183460 AGTTTCTCTACCACATAAGTAGGAGT 58.817 38.462 0.00 0.00 38.20 3.85
3811 4112 7.122948 AGTTTCTCTACCACATAAGTAGGAGTG 59.877 40.741 0.00 0.00 38.20 3.51
3819 4120 6.723298 CACATAAGTAGGAGTGGAGATTCT 57.277 41.667 0.00 0.00 0.00 2.40
3820 4121 6.744112 CACATAAGTAGGAGTGGAGATTCTC 58.256 44.000 5.03 5.03 0.00 2.87
3821 4122 5.533154 ACATAAGTAGGAGTGGAGATTCTCG 59.467 44.000 7.57 0.00 0.00 4.04
3822 4123 3.935818 AGTAGGAGTGGAGATTCTCGA 57.064 47.619 7.57 0.68 0.00 4.04
3823 4124 3.815809 AGTAGGAGTGGAGATTCTCGAG 58.184 50.000 5.93 5.93 0.00 4.04
3824 4125 3.456644 AGTAGGAGTGGAGATTCTCGAGA 59.543 47.826 12.08 12.08 0.00 4.04
3825 4126 3.374042 AGGAGTGGAGATTCTCGAGAA 57.626 47.619 28.85 28.85 38.56 2.87
3826 4127 3.702792 AGGAGTGGAGATTCTCGAGAAA 58.297 45.455 30.18 12.02 37.61 2.52
3827 4128 4.090090 AGGAGTGGAGATTCTCGAGAAAA 58.910 43.478 30.18 10.79 37.61 2.29
3828 4129 4.528596 AGGAGTGGAGATTCTCGAGAAAAA 59.471 41.667 30.18 9.99 37.61 1.94
3868 4169 6.127786 GGAAACTTACCGACTAGTGTCAGTAT 60.128 42.308 0.00 0.00 43.06 2.12
3871 4172 6.179040 ACTTACCGACTAGTGTCAGTATTCT 58.821 40.000 0.00 0.00 43.06 2.40
3884 4190 7.118390 AGTGTCAGTATTCTCAAATTGTAGTGC 59.882 37.037 0.00 0.00 0.00 4.40
3927 4237 7.064134 CGCTCATTTACAGTACAAGGATTAACA 59.936 37.037 0.00 0.00 0.00 2.41
3928 4238 8.391106 GCTCATTTACAGTACAAGGATTAACAG 58.609 37.037 0.00 0.00 0.00 3.16
3934 4244 6.154445 ACAGTACAAGGATTAACAGTACACG 58.846 40.000 0.00 0.00 37.96 4.49
3935 4245 5.061808 CAGTACAAGGATTAACAGTACACGC 59.938 44.000 0.00 0.00 37.96 5.34
3951 4273 6.805271 CAGTACACGCTTATTTACAGTACACT 59.195 38.462 0.00 0.00 34.41 3.55
4028 4352 6.232581 AGGAGTTTCACTAGATTCATGAGG 57.767 41.667 0.00 0.00 0.00 3.86
4040 4364 4.657504 AGATTCATGAGGGAAGCATACTGA 59.342 41.667 0.00 0.00 35.70 3.41
4041 4365 5.310068 AGATTCATGAGGGAAGCATACTGAT 59.690 40.000 0.00 0.00 35.70 2.90
4043 4367 5.474578 TCATGAGGGAAGCATACTGATAC 57.525 43.478 0.00 0.00 0.00 2.24
4079 4405 2.292016 TGATACTGTTTTGTGGCCAACG 59.708 45.455 7.24 1.17 0.00 4.10
4093 4419 0.872388 CCAACGACAACCTACCAAGC 59.128 55.000 0.00 0.00 0.00 4.01
4096 4422 0.602905 ACGACAACCTACCAAGCAGC 60.603 55.000 0.00 0.00 0.00 5.25
4123 4449 5.871396 ACTACCTATACACAAGACATGGG 57.129 43.478 0.00 0.00 38.89 4.00
4124 4450 4.654262 ACTACCTATACACAAGACATGGGG 59.346 45.833 0.00 0.00 36.45 4.96
4128 4454 3.864789 ATACACAAGACATGGGGGATC 57.135 47.619 0.00 0.00 36.45 3.36
4169 4495 7.836842 AGGAGCAAAACTAAAAGAAAGAACAA 58.163 30.769 0.00 0.00 0.00 2.83
4212 4538 8.367911 CCCTGCAGATTCATTATTAGTGTAGTA 58.632 37.037 17.39 0.00 0.00 1.82
4273 4600 4.202121 GGCGATAGACTGTCCTTTCATGTA 60.202 45.833 3.76 0.00 44.90 2.29
4274 4601 4.979197 GCGATAGACTGTCCTTTCATGTAG 59.021 45.833 3.76 0.00 39.76 2.74
4275 4602 4.979197 CGATAGACTGTCCTTTCATGTAGC 59.021 45.833 3.76 0.00 39.76 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.827681 TGTCGTCTCTCCTTCCTGAG 58.172 55.000 0.00 0.00 0.00 3.35
40 41 3.634202 CCATCTTCAGGGAGCCGA 58.366 61.111 0.00 0.00 0.00 5.54
58 59 2.258726 GGCGGGGGCGAACATTATC 61.259 63.158 0.00 0.00 0.00 1.75
107 108 2.355363 TCCACACGCCTTTCGACG 60.355 61.111 0.00 0.00 41.67 5.12
112 113 1.227853 GACACCTCCACACGCCTTT 60.228 57.895 0.00 0.00 0.00 3.11
114 115 2.524394 AGACACCTCCACACGCCT 60.524 61.111 0.00 0.00 0.00 5.52
130 131 0.174389 CCGTGTGATCCACCAGAGAG 59.826 60.000 8.25 0.00 41.26 3.20
134 135 0.253044 AATCCCGTGTGATCCACCAG 59.747 55.000 8.25 2.01 41.26 4.00
135 136 0.695924 AAATCCCGTGTGATCCACCA 59.304 50.000 8.25 0.00 41.26 4.17
146 147 2.882137 ACAAATGTCGACAAAATCCCGT 59.118 40.909 24.13 9.97 0.00 5.28
147 148 3.488489 GACAAATGTCGACAAAATCCCG 58.512 45.455 24.13 9.34 35.12 5.14
163 164 1.202879 AGCGGATCCACCAAAGACAAA 60.203 47.619 13.41 0.00 38.90 2.83
180 181 1.813513 ACAAAGACTGGATCCAAGCG 58.186 50.000 17.00 6.93 0.00 4.68
219 237 4.587189 GGAAGGATCCGACCCGCG 62.587 72.222 16.15 0.00 35.59 6.46
265 283 1.241315 ACCATAACAGCAACCACCGC 61.241 55.000 0.00 0.00 0.00 5.68
266 284 0.521291 CACCATAACAGCAACCACCG 59.479 55.000 0.00 0.00 0.00 4.94
275 293 0.461135 GGGCCAATGCACCATAACAG 59.539 55.000 4.39 0.00 40.13 3.16
299 317 3.658342 CGAAAGTCGTCGTGCTAAAGTTG 60.658 47.826 0.00 0.00 36.26 3.16
301 319 2.049228 CGAAAGTCGTCGTGCTAAAGT 58.951 47.619 0.00 0.00 36.26 2.66
303 321 1.001487 TCCGAAAGTCGTCGTGCTAAA 60.001 47.619 0.00 0.00 38.40 1.85
311 329 3.177487 GGTAGACAATCCGAAAGTCGTC 58.823 50.000 0.00 0.00 38.40 4.20
330 348 3.195396 AGTTGTGCAAATCTTGTTGTGGT 59.805 39.130 0.00 0.00 0.00 4.16
332 350 5.403166 CCATAGTTGTGCAAATCTTGTTGTG 59.597 40.000 0.00 0.00 0.00 3.33
349 367 0.617820 ACGCCTCCCTCACCATAGTT 60.618 55.000 0.00 0.00 0.00 2.24
350 368 0.260816 TACGCCTCCCTCACCATAGT 59.739 55.000 0.00 0.00 0.00 2.12
352 370 1.691976 CATTACGCCTCCCTCACCATA 59.308 52.381 0.00 0.00 0.00 2.74
353 371 0.469917 CATTACGCCTCCCTCACCAT 59.530 55.000 0.00 0.00 0.00 3.55
354 372 0.616395 TCATTACGCCTCCCTCACCA 60.616 55.000 0.00 0.00 0.00 4.17
362 380 2.534903 GCCGCCTTCATTACGCCTC 61.535 63.158 0.00 0.00 0.00 4.70
401 419 4.480667 ACACCTAGTGACGACTACCATCG 61.481 52.174 0.96 0.00 41.29 3.84
405 423 5.573337 AATTACACCTAGTGACGACTACC 57.427 43.478 0.96 0.00 36.96 3.18
443 461 5.967088 TCAACCTTCAAGATAGTACAGAGC 58.033 41.667 0.00 0.00 0.00 4.09
460 478 6.824305 AAACTTTCGATCATTCATCAACCT 57.176 33.333 0.00 0.00 0.00 3.50
461 479 7.083858 TGAAAACTTTCGATCATTCATCAACC 58.916 34.615 0.00 0.00 40.01 3.77
510 530 6.047870 TGTGGACATGGATTTTGAAAAGTTG 58.952 36.000 0.00 0.00 0.00 3.16
516 536 4.892345 TGAACTGTGGACATGGATTTTGAA 59.108 37.500 0.00 0.00 0.00 2.69
517 537 4.278170 GTGAACTGTGGACATGGATTTTGA 59.722 41.667 0.00 0.00 0.00 2.69
534 554 4.724279 ACTCCATTAGGTTTGGTGAACT 57.276 40.909 0.00 0.00 38.35 3.01
559 579 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
560 580 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
563 583 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
564 584 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
565 585 8.020819 TCATTTTGATGACAAGTATTTTCGGAC 58.979 33.333 0.00 0.00 37.32 4.79
566 586 8.105097 TCATTTTGATGACAAGTATTTTCGGA 57.895 30.769 0.00 0.00 37.32 4.55
567 587 8.741101 TTCATTTTGATGACAAGTATTTTCGG 57.259 30.769 0.00 0.00 37.32 4.30
575 595 9.472361 CTCTTTTCATTCATTTTGATGACAAGT 57.528 29.630 10.32 0.00 37.32 3.16
576 596 9.687210 TCTCTTTTCATTCATTTTGATGACAAG 57.313 29.630 6.09 6.09 37.32 3.16
578 598 9.634163 CATCTCTTTTCATTCATTTTGATGACA 57.366 29.630 0.00 0.00 32.05 3.58
579 599 9.635520 ACATCTCTTTTCATTCATTTTGATGAC 57.364 29.630 0.00 0.00 33.85 3.06
631 651 9.710900 GTCATCAAAAAGAATAAAAAGGGATGT 57.289 29.630 0.00 0.00 32.47 3.06
632 652 9.709495 TGTCATCAAAAAGAATAAAAAGGGATG 57.291 29.630 0.00 0.00 0.00 3.51
633 653 9.933723 CTGTCATCAAAAAGAATAAAAAGGGAT 57.066 29.630 0.00 0.00 0.00 3.85
634 654 8.367156 CCTGTCATCAAAAAGAATAAAAAGGGA 58.633 33.333 0.00 0.00 0.00 4.20
635 655 8.150296 ACCTGTCATCAAAAAGAATAAAAAGGG 58.850 33.333 0.00 0.00 0.00 3.95
643 663 8.028938 CCGAAAATACCTGTCATCAAAAAGAAT 58.971 33.333 0.00 0.00 0.00 2.40
644 664 7.229707 TCCGAAAATACCTGTCATCAAAAAGAA 59.770 33.333 0.00 0.00 0.00 2.52
645 665 6.712998 TCCGAAAATACCTGTCATCAAAAAGA 59.287 34.615 0.00 0.00 0.00 2.52
646 666 6.908825 TCCGAAAATACCTGTCATCAAAAAG 58.091 36.000 0.00 0.00 0.00 2.27
647 667 6.885952 TCCGAAAATACCTGTCATCAAAAA 57.114 33.333 0.00 0.00 0.00 1.94
648 668 6.183360 CGATCCGAAAATACCTGTCATCAAAA 60.183 38.462 0.00 0.00 0.00 2.44
649 669 5.293324 CGATCCGAAAATACCTGTCATCAAA 59.707 40.000 0.00 0.00 0.00 2.69
650 670 4.808895 CGATCCGAAAATACCTGTCATCAA 59.191 41.667 0.00 0.00 0.00 2.57
651 671 4.368315 CGATCCGAAAATACCTGTCATCA 58.632 43.478 0.00 0.00 0.00 3.07
652 672 3.741344 CCGATCCGAAAATACCTGTCATC 59.259 47.826 0.00 0.00 0.00 2.92
653 673 3.386726 TCCGATCCGAAAATACCTGTCAT 59.613 43.478 0.00 0.00 0.00 3.06
654 674 2.761767 TCCGATCCGAAAATACCTGTCA 59.238 45.455 0.00 0.00 0.00 3.58
655 675 3.381949 CTCCGATCCGAAAATACCTGTC 58.618 50.000 0.00 0.00 0.00 3.51
656 676 2.102588 CCTCCGATCCGAAAATACCTGT 59.897 50.000 0.00 0.00 0.00 4.00
657 677 2.548067 CCCTCCGATCCGAAAATACCTG 60.548 54.545 0.00 0.00 0.00 4.00
658 678 1.692519 CCCTCCGATCCGAAAATACCT 59.307 52.381 0.00 0.00 0.00 3.08
659 679 1.690352 TCCCTCCGATCCGAAAATACC 59.310 52.381 0.00 0.00 0.00 2.73
660 680 2.364647 ACTCCCTCCGATCCGAAAATAC 59.635 50.000 0.00 0.00 0.00 1.89
661 681 2.674420 ACTCCCTCCGATCCGAAAATA 58.326 47.619 0.00 0.00 0.00 1.40
662 682 1.497161 ACTCCCTCCGATCCGAAAAT 58.503 50.000 0.00 0.00 0.00 1.82
663 683 1.753073 GTACTCCCTCCGATCCGAAAA 59.247 52.381 0.00 0.00 0.00 2.29
664 684 1.064166 AGTACTCCCTCCGATCCGAAA 60.064 52.381 0.00 0.00 0.00 3.46
665 685 0.549950 AGTACTCCCTCCGATCCGAA 59.450 55.000 0.00 0.00 0.00 4.30
666 686 0.549950 AAGTACTCCCTCCGATCCGA 59.450 55.000 0.00 0.00 0.00 4.55
667 687 0.953003 GAAGTACTCCCTCCGATCCG 59.047 60.000 0.00 0.00 0.00 4.18
668 688 1.133419 AGGAAGTACTCCCTCCGATCC 60.133 57.143 0.00 0.00 46.81 3.36
669 689 2.362717 CAAGGAAGTACTCCCTCCGATC 59.637 54.545 0.00 0.00 46.81 3.69
670 690 2.292323 ACAAGGAAGTACTCCCTCCGAT 60.292 50.000 0.00 0.00 46.81 4.18
671 691 1.076677 ACAAGGAAGTACTCCCTCCGA 59.923 52.381 0.00 0.00 46.81 4.55
672 692 1.204941 CACAAGGAAGTACTCCCTCCG 59.795 57.143 0.00 0.00 46.81 4.63
673 693 1.555533 CCACAAGGAAGTACTCCCTCC 59.444 57.143 0.00 2.10 46.81 4.30
674 694 2.537143 TCCACAAGGAAGTACTCCCTC 58.463 52.381 0.00 0.00 46.81 4.30
675 695 2.715763 TCCACAAGGAAGTACTCCCT 57.284 50.000 0.00 0.00 46.81 4.20
686 706 3.305335 CGAGGAAAACCAAATCCACAAGG 60.305 47.826 0.00 0.00 38.23 3.61
687 707 3.317993 ACGAGGAAAACCAAATCCACAAG 59.682 43.478 0.00 0.00 38.23 3.16
688 708 3.067461 CACGAGGAAAACCAAATCCACAA 59.933 43.478 0.00 0.00 38.23 3.33
689 709 2.621055 CACGAGGAAAACCAAATCCACA 59.379 45.455 0.00 0.00 38.23 4.17
690 710 2.621526 ACACGAGGAAAACCAAATCCAC 59.378 45.455 0.00 0.00 38.23 4.02
691 711 2.621055 CACACGAGGAAAACCAAATCCA 59.379 45.455 0.00 0.00 38.23 3.41
692 712 2.607038 GCACACGAGGAAAACCAAATCC 60.607 50.000 0.00 0.00 35.88 3.01
693 713 2.293399 AGCACACGAGGAAAACCAAATC 59.707 45.455 0.00 0.00 0.00 2.17
694 714 2.293399 GAGCACACGAGGAAAACCAAAT 59.707 45.455 0.00 0.00 0.00 2.32
790 819 2.043852 GCGGGGAGAGGACTCAGA 60.044 66.667 1.75 0.00 44.22 3.27
815 844 0.682855 GGATTTGGATTGGACGGCCA 60.683 55.000 5.41 5.41 44.17 5.36
926 956 2.970324 GTGCGCGTGGGAGTTGAA 60.970 61.111 8.43 0.00 0.00 2.69
951 981 1.131303 TCCTCCGCAAGAAAAGGGGA 61.131 55.000 0.00 0.00 44.69 4.81
967 997 0.036294 GAAACCCTAACGCTGCTCCT 60.036 55.000 0.00 0.00 0.00 3.69
968 998 1.359459 CGAAACCCTAACGCTGCTCC 61.359 60.000 0.00 0.00 0.00 4.70
969 999 1.359459 CCGAAACCCTAACGCTGCTC 61.359 60.000 0.00 0.00 0.00 4.26
978 1008 2.355412 GGCTTAGCTTTCCGAAACCCTA 60.355 50.000 3.59 0.00 0.00 3.53
1344 1386 3.060363 CGATCTACGCGTTTAAGCAAAGT 59.940 43.478 20.78 0.00 36.85 2.66
1374 1417 1.874129 ACCCGTCCAGATCCACATAA 58.126 50.000 0.00 0.00 0.00 1.90
1402 1445 2.686915 ACCAGATCTAGTACGAAACCCG 59.313 50.000 0.00 0.00 45.44 5.28
1447 1490 2.474410 AGAAGGCTTAAACCTCACCG 57.526 50.000 0.00 0.00 39.93 4.94
1484 1529 1.404717 CGTCCCTGTGGATCTGAACAG 60.405 57.143 13.51 13.51 44.28 3.16
1543 1588 4.472286 CAAATTCGAAACCAACAGCGTAT 58.528 39.130 0.00 0.00 0.00 3.06
1551 1596 4.054671 GCATTGACCAAATTCGAAACCAA 58.945 39.130 0.00 1.17 0.00 3.67
1590 1635 1.299089 GCACGACCACAGCAAAACC 60.299 57.895 0.00 0.00 0.00 3.27
1598 1643 0.179137 GATCAGATCGCACGACCACA 60.179 55.000 0.00 0.00 0.00 4.17
1604 1649 5.107683 GGAATCTTAAAGATCAGATCGCACG 60.108 44.000 4.67 0.00 32.89 5.34
1629 1674 6.672266 TTTTTGCACAATAAATACAGGGGA 57.328 33.333 0.00 0.00 0.00 4.81
1643 1688 5.543507 AAACCAGTATCCATTTTTGCACA 57.456 34.783 0.00 0.00 0.00 4.57
1671 1719 8.684520 ACGACAGAGCATAAACTTACTATTACT 58.315 33.333 0.00 0.00 0.00 2.24
1672 1720 8.853469 ACGACAGAGCATAAACTTACTATTAC 57.147 34.615 0.00 0.00 0.00 1.89
1674 1722 8.684520 ACTACGACAGAGCATAAACTTACTATT 58.315 33.333 0.00 0.00 0.00 1.73
1675 1723 8.223177 ACTACGACAGAGCATAAACTTACTAT 57.777 34.615 0.00 0.00 0.00 2.12
1676 1724 7.201679 GGACTACGACAGAGCATAAACTTACTA 60.202 40.741 0.00 0.00 0.00 1.82
1677 1725 6.404513 GGACTACGACAGAGCATAAACTTACT 60.405 42.308 0.00 0.00 0.00 2.24
1678 1726 5.742926 GGACTACGACAGAGCATAAACTTAC 59.257 44.000 0.00 0.00 0.00 2.34
1679 1727 5.416639 TGGACTACGACAGAGCATAAACTTA 59.583 40.000 0.00 0.00 0.00 2.24
1680 1728 4.219944 TGGACTACGACAGAGCATAAACTT 59.780 41.667 0.00 0.00 0.00 2.66
1681 1729 3.762288 TGGACTACGACAGAGCATAAACT 59.238 43.478 0.00 0.00 0.00 2.66
1682 1730 4.106029 TGGACTACGACAGAGCATAAAC 57.894 45.455 0.00 0.00 0.00 2.01
1683 1731 6.447162 CATATGGACTACGACAGAGCATAAA 58.553 40.000 0.00 0.00 0.00 1.40
1684 1732 5.048013 CCATATGGACTACGACAGAGCATAA 60.048 44.000 17.49 0.00 37.39 1.90
1685 1733 4.459337 CCATATGGACTACGACAGAGCATA 59.541 45.833 17.49 0.00 37.39 3.14
1686 1734 3.256879 CCATATGGACTACGACAGAGCAT 59.743 47.826 17.49 0.00 37.39 3.79
1687 1735 2.623416 CCATATGGACTACGACAGAGCA 59.377 50.000 17.49 0.00 37.39 4.26
1688 1736 2.608261 GCCATATGGACTACGACAGAGC 60.608 54.545 26.47 0.85 37.39 4.09
1689 1737 2.887783 AGCCATATGGACTACGACAGAG 59.112 50.000 26.47 0.00 37.39 3.35
1690 1738 2.623416 CAGCCATATGGACTACGACAGA 59.377 50.000 26.47 0.00 37.39 3.41
1691 1739 2.623416 TCAGCCATATGGACTACGACAG 59.377 50.000 26.47 8.80 37.39 3.51
1692 1740 2.623416 CTCAGCCATATGGACTACGACA 59.377 50.000 26.47 4.08 37.39 4.35
1693 1741 2.608261 GCTCAGCCATATGGACTACGAC 60.608 54.545 26.47 5.54 37.39 4.34
1694 1742 1.613925 GCTCAGCCATATGGACTACGA 59.386 52.381 26.47 13.91 37.39 3.43
1695 1743 1.615883 AGCTCAGCCATATGGACTACG 59.384 52.381 26.47 14.97 37.39 3.51
1696 1744 2.869636 GCAGCTCAGCCATATGGACTAC 60.870 54.545 26.47 7.47 37.39 2.73
1697 1745 1.345741 GCAGCTCAGCCATATGGACTA 59.654 52.381 26.47 7.97 37.39 2.59
1698 1746 0.108207 GCAGCTCAGCCATATGGACT 59.892 55.000 26.47 18.03 37.39 3.85
1837 1886 1.002430 AGAATTCACTGAGCGCCTGAA 59.998 47.619 2.29 6.83 0.00 3.02
2186 2235 3.859386 AGCTCAAGTTCAAAGCAAAAACG 59.141 39.130 4.70 0.00 38.51 3.60
2187 2236 4.627035 ACAGCTCAAGTTCAAAGCAAAAAC 59.373 37.500 4.70 0.00 38.51 2.43
2276 2325 5.990408 CAACTAGTTGTTTAACCTCTGCTG 58.010 41.667 24.70 0.00 36.63 4.41
2314 2363 5.858581 GTGAAAACTTATGGAGTGACAATGC 59.141 40.000 0.00 0.00 39.00 3.56
2331 2380 3.631145 TGCAAGATGCTCTGTGAAAAC 57.369 42.857 3.78 0.00 45.31 2.43
2337 2386 4.595762 AAAATGTTGCAAGATGCTCTGT 57.404 36.364 10.21 0.00 45.31 3.41
2546 2598 2.685897 CACCTAGTACTCCAGCAGAGAC 59.314 54.545 10.46 4.98 46.50 3.36
2738 2790 2.544267 ACTAACTCTTGAACGTGCAAGC 59.456 45.455 28.51 0.00 43.78 4.01
2760 2812 9.358872 GGCAGAATTTAGAACTCATTTTTAAGG 57.641 33.333 0.00 0.00 0.00 2.69
2888 2940 1.266718 GCAATCTGACGAAGGTTTGCA 59.733 47.619 17.38 0.00 41.37 4.08
2977 3029 4.019411 TGAGGCAAATCCAGACTGATGTAA 60.019 41.667 3.32 0.00 37.29 2.41
2985 3037 5.904362 AGTTAAATGAGGCAAATCCAGAC 57.096 39.130 0.00 0.00 37.29 3.51
3113 3165 7.094377 GGAAGAGTTGCTGAAAATGGTATACAA 60.094 37.037 5.01 0.00 0.00 2.41
3114 3166 6.374333 GGAAGAGTTGCTGAAAATGGTATACA 59.626 38.462 5.01 0.00 0.00 2.29
3127 3179 4.963318 TCCATATAGGGAAGAGTTGCTG 57.037 45.455 2.99 0.00 38.24 4.41
3132 3184 4.916424 AGCCAAATCCATATAGGGAAGAGT 59.084 41.667 10.70 0.00 41.12 3.24
3141 3196 6.508030 TCCACTGTTAGCCAAATCCATATA 57.492 37.500 0.00 0.00 0.00 0.86
3374 3431 1.605710 CCAGTCGCCATCATTCCATTC 59.394 52.381 0.00 0.00 0.00 2.67
3375 3432 1.064463 ACCAGTCGCCATCATTCCATT 60.064 47.619 0.00 0.00 0.00 3.16
3436 3499 4.760204 AGCCTTACATAACACAAGACAACC 59.240 41.667 0.00 0.00 0.00 3.77
3467 3532 4.067896 ACTCTCATCAAAGTCGCAAACAT 58.932 39.130 0.00 0.00 0.00 2.71
3540 3606 1.890876 AATCAAACAGCGGTACAGCA 58.109 45.000 20.22 0.00 40.15 4.41
3596 3662 2.729156 GCAAGTAGCAAAATCAGCGTCC 60.729 50.000 0.00 0.00 44.79 4.79
3743 4035 1.835483 GCACTCTGAACACACGCAGG 61.835 60.000 0.00 0.00 33.05 4.85
3775 4076 4.154918 GTGGTAGAGAAACTCCAGCAATTG 59.845 45.833 0.00 0.00 32.35 2.32
3779 4080 2.325484 TGTGGTAGAGAAACTCCAGCA 58.675 47.619 0.00 0.00 28.47 4.41
3801 4102 4.080243 TCTCGAGAATCTCCACTCCTACTT 60.080 45.833 14.01 0.00 0.00 2.24
3803 4104 3.811083 TCTCGAGAATCTCCACTCCTAC 58.189 50.000 14.01 0.00 0.00 3.18
3804 4105 4.505324 TTCTCGAGAATCTCCACTCCTA 57.495 45.455 23.74 0.00 0.00 2.94
3805 4106 3.374042 TTCTCGAGAATCTCCACTCCT 57.626 47.619 23.74 0.00 0.00 3.69
3806 4107 4.457834 TTTTCTCGAGAATCTCCACTCC 57.542 45.455 27.51 0.00 33.54 3.85
3825 4126 8.762481 AAGTTTCCACTCCTACTTATGTTTTT 57.238 30.769 0.00 0.00 30.45 1.94
3826 4127 9.281371 GTAAGTTTCCACTCCTACTTATGTTTT 57.719 33.333 0.00 0.00 36.02 2.43
3827 4128 7.881751 GGTAAGTTTCCACTCCTACTTATGTTT 59.118 37.037 0.00 0.00 36.02 2.83
3828 4129 7.392418 GGTAAGTTTCCACTCCTACTTATGTT 58.608 38.462 0.00 0.00 36.02 2.71
3829 4130 6.350780 CGGTAAGTTTCCACTCCTACTTATGT 60.351 42.308 0.00 0.00 36.02 2.29
3830 4131 6.040878 CGGTAAGTTTCCACTCCTACTTATG 58.959 44.000 0.00 0.00 36.02 1.90
3831 4132 5.954150 TCGGTAAGTTTCCACTCCTACTTAT 59.046 40.000 0.00 0.00 36.02 1.73
3832 4133 5.183904 GTCGGTAAGTTTCCACTCCTACTTA 59.816 44.000 0.00 0.00 33.28 2.24
3833 4134 4.021632 GTCGGTAAGTTTCCACTCCTACTT 60.022 45.833 0.00 0.00 35.25 2.24
3868 4169 5.239306 CCTGAAGTGCACTACAATTTGAGAA 59.761 40.000 22.01 0.00 36.53 2.87
3871 4172 3.253188 GCCTGAAGTGCACTACAATTTGA 59.747 43.478 22.01 0.00 36.53 2.69
3884 4190 1.364626 GCGGTCTCATGCCTGAAGTG 61.365 60.000 0.00 0.00 0.00 3.16
3927 4237 6.917533 AGTGTACTGTAAATAAGCGTGTACT 58.082 36.000 0.00 0.00 32.60 2.73
3928 4238 8.740369 CATAGTGTACTGTAAATAAGCGTGTAC 58.260 37.037 0.00 0.00 0.00 2.90
3931 4241 7.980742 TCATAGTGTACTGTAAATAAGCGTG 57.019 36.000 0.00 0.00 0.00 5.34
4028 4352 5.046529 CAGTCTGTGTATCAGTATGCTTCC 58.953 45.833 0.00 0.00 43.97 3.46
4040 4364 0.390340 CAGCGTGCCAGTCTGTGTAT 60.390 55.000 0.00 0.00 0.00 2.29
4041 4365 1.006220 CAGCGTGCCAGTCTGTGTA 60.006 57.895 0.00 0.00 0.00 2.90
4043 4367 0.108662 TATCAGCGTGCCAGTCTGTG 60.109 55.000 0.00 0.00 0.00 3.66
4079 4405 1.470098 CATGCTGCTTGGTAGGTTGTC 59.530 52.381 7.58 0.00 0.00 3.18
4093 4419 6.477033 GTCTTGTGTATAGGTAGTTCATGCTG 59.523 42.308 0.00 0.00 0.00 4.41
4096 4422 7.439356 CCATGTCTTGTGTATAGGTAGTTCATG 59.561 40.741 0.00 0.00 0.00 3.07
4123 4449 0.461548 TGTGTGCATCTCTCGATCCC 59.538 55.000 0.00 0.00 0.00 3.85
4124 4450 2.299993 TTGTGTGCATCTCTCGATCC 57.700 50.000 0.00 0.00 0.00 3.36
4128 4454 1.998315 CTCCTTTGTGTGCATCTCTCG 59.002 52.381 0.00 0.00 0.00 4.04
4169 4495 3.055602 GCAGGGCAGATCCTTTTGATTTT 60.056 43.478 0.00 0.00 34.31 1.82
4212 4538 2.557317 CCTGTGTTCGGTTGTTGTACT 58.443 47.619 0.00 0.00 0.00 2.73
4275 4602 5.463724 GGAAAGTAGAATAGATGGCGAACAG 59.536 44.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.