Multiple sequence alignment - TraesCS7A01G134800

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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 TraesCS7A01G134800 chr7A 100.000 4019 0 0 1 4019 87329095 87325077 0.000000e+00 7422.0
1 TraesCS7A01G134800 chr7A 88.235 51 6 0 605 655 521949642 521949592 1.210000e-05 62.1
2 TraesCS7A01G134800 chr7D 94.510 3133 130 15 909 4018 85917656 85914543 0.000000e+00 4795.0
3 TraesCS7A01G134800 chr7D 89.408 321 27 4 731 1046 85925093 85924775 8.090000e-107 398.0
4 TraesCS7A01G134800 chr7D 77.364 645 111 24 60 679 446421211 446421845 2.300000e-92 350.0
5 TraesCS7A01G134800 chr7D 75.419 358 55 26 36 379 570832219 570832557 4.190000e-30 143.0
6 TraesCS7A01G134800 chr7D 79.348 184 22 9 474 653 26182736 26182565 9.130000e-22 115.0
7 TraesCS7A01G134800 chr7D 80.374 107 18 3 547 651 606679334 606679229 1.200000e-10 78.7
8 TraesCS7A01G134800 chr7B 95.399 2782 80 16 810 3584 35091981 35089241 0.000000e+00 4385.0
9 TraesCS7A01G134800 chr7B 97.319 373 9 1 3624 3995 35089241 35088869 2.040000e-177 632.0
10 TraesCS7A01G134800 chr7B 78.477 302 48 15 85 375 486742412 486742707 8.870000e-42 182.0
11 TraesCS7A01G134800 chr7B 80.128 156 27 4 13 166 595784092 595784245 3.280000e-21 113.0
12 TraesCS7A01G134800 chr5D 76.459 514 90 23 177 674 555655569 555656067 2.400000e-62 250.0
13 TraesCS7A01G134800 chr5D 79.736 227 37 8 163 385 377945455 377945676 5.380000e-34 156.0
14 TraesCS7A01G134800 chr2B 82.609 253 34 9 49 298 596084737 596084492 8.750000e-52 215.0
15 TraesCS7A01G134800 chr2B 78.893 289 48 10 165 446 154188595 154188877 2.470000e-42 183.0
16 TraesCS7A01G134800 chr2B 77.397 292 42 17 165 442 674043070 674042789 6.960000e-33 152.0
17 TraesCS7A01G134800 chr4D 77.287 317 47 13 88 384 373660489 373660178 3.210000e-36 163.0
18 TraesCS7A01G134800 chr4A 81.604 212 26 10 239 444 692541712 692541916 3.210000e-36 163.0
19 TraesCS7A01G134800 chr6B 82.143 196 27 3 474 661 714046980 714046785 1.160000e-35 161.0
20 TraesCS7A01G134800 chr6B 80.090 221 32 9 165 381 566281242 566281454 1.930000e-33 154.0
21 TraesCS7A01G134800 chr6B 79.310 116 12 10 88 193 718326489 718326602 2.000000e-08 71.3
22 TraesCS7A01G134800 chr4B 79.476 229 38 7 12 233 489349507 489349733 1.930000e-33 154.0
23 TraesCS7A01G134800 chr4B 84.472 161 19 5 529 685 520219190 520219348 1.930000e-33 154.0
24 TraesCS7A01G134800 chr4B 78.440 218 37 4 475 682 647307484 647307701 2.520000e-27 134.0
25 TraesCS7A01G134800 chr3D 79.032 186 30 8 36 214 519664377 519664560 7.060000e-23 119.0
26 TraesCS7A01G134800 chr2D 77.251 211 40 3 473 675 14643832 14644042 2.540000e-22 117.0
27 TraesCS7A01G134800 chr2A 92.857 56 3 1 602 656 413486575 413486520 3.330000e-11 80.5


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 TraesCS7A01G134800 chr7A 87325077 87329095 4018 True 7422.0 7422 100.000 1 4019 1 chr7A.!!$R1 4018
1 TraesCS7A01G134800 chr7D 85914543 85917656 3113 True 4795.0 4795 94.510 909 4018 1 chr7D.!!$R2 3109
2 TraesCS7A01G134800 chr7D 446421211 446421845 634 False 350.0 350 77.364 60 679 1 chr7D.!!$F1 619
3 TraesCS7A01G134800 chr7B 35088869 35091981 3112 True 2508.5 4385 96.359 810 3995 2 chr7B.!!$R1 3185

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
133 134 0.034616 GCTTCTGTGAGAGGCACTGT 59.965 55.0 3.03 0.0 45.45 3.55 F
624 647 0.109597 CTCAGGTTGCGACAAATGGC 60.110 55.0 6.39 0.0 0.00 4.40 F
663 686 0.172578 TGTCGCAACCTACGGAGATG 59.827 55.0 0.00 0.0 0.00 2.90 F
2097 2125 0.109086 TGGCACCAAACACAAACACG 60.109 50.0 0.00 0.0 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1111 1139 0.108041 GCATCTGGGGTGCAAAATGG 60.108 55.000 0.0 0.0 42.08 3.16 R
1899 1927 2.173356 CCCAATCTTACAGAGCCCATCA 59.827 50.000 0.0 0.0 0.00 3.07 R
2658 2686 1.187087 CCCGTGCTTCCTCTAGTCTT 58.813 55.000 0.0 0.0 0.00 3.01 R
3613 3665 3.119101 TCAGAGGCTTCGGATTGTAGAAC 60.119 47.826 0.0 0.0 0.00 3.01 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
24 25 7.562454 TTTTTCTTTTGTGAGAGGTACGATT 57.438 32.000 0.00 0.00 0.00 3.34
25 26 7.562454 TTTTCTTTTGTGAGAGGTACGATTT 57.438 32.000 0.00 0.00 0.00 2.17
26 27 7.562454 TTTCTTTTGTGAGAGGTACGATTTT 57.438 32.000 0.00 0.00 0.00 1.82
27 28 6.539649 TCTTTTGTGAGAGGTACGATTTTG 57.460 37.500 0.00 0.00 0.00 2.44
28 29 4.742438 TTTGTGAGAGGTACGATTTTGC 57.258 40.909 0.00 0.00 0.00 3.68
29 30 2.695359 TGTGAGAGGTACGATTTTGCC 58.305 47.619 0.00 0.00 0.00 4.52
30 31 2.301870 TGTGAGAGGTACGATTTTGCCT 59.698 45.455 0.00 0.00 0.00 4.75
31 32 2.930682 GTGAGAGGTACGATTTTGCCTC 59.069 50.000 0.00 0.00 45.75 4.70
34 35 3.247006 GAGGTACGATTTTGCCTCTGA 57.753 47.619 0.00 0.00 42.99 3.27
35 36 3.190874 GAGGTACGATTTTGCCTCTGAG 58.809 50.000 0.00 0.00 42.99 3.35
36 37 2.832129 AGGTACGATTTTGCCTCTGAGA 59.168 45.455 6.17 0.00 0.00 3.27
37 38 3.118956 AGGTACGATTTTGCCTCTGAGAG 60.119 47.826 6.17 1.57 0.00 3.20
38 39 3.119101 GGTACGATTTTGCCTCTGAGAGA 60.119 47.826 11.82 0.00 0.00 3.10
39 40 3.244033 ACGATTTTGCCTCTGAGAGAG 57.756 47.619 11.82 2.23 41.96 3.20
40 41 2.828520 ACGATTTTGCCTCTGAGAGAGA 59.171 45.455 11.82 0.00 45.07 3.10
41 42 3.186119 CGATTTTGCCTCTGAGAGAGAC 58.814 50.000 11.82 0.53 45.07 3.36
42 43 3.367806 CGATTTTGCCTCTGAGAGAGACA 60.368 47.826 11.82 3.37 45.07 3.41
43 44 3.393089 TTTTGCCTCTGAGAGAGACAC 57.607 47.619 11.82 0.00 45.07 3.67
44 45 0.884514 TTGCCTCTGAGAGAGACACG 59.115 55.000 11.82 0.00 45.07 4.49
45 46 0.962855 TGCCTCTGAGAGAGACACGG 60.963 60.000 11.82 0.00 45.07 4.94
46 47 0.678366 GCCTCTGAGAGAGACACGGA 60.678 60.000 11.82 0.00 45.07 4.69
47 48 2.021723 GCCTCTGAGAGAGACACGGAT 61.022 57.143 11.82 0.00 45.07 4.18
48 49 1.675483 CCTCTGAGAGAGACACGGATG 59.325 57.143 11.82 0.00 45.07 3.51
49 50 2.364632 CTCTGAGAGAGACACGGATGT 58.635 52.381 2.60 0.00 45.07 3.06
50 51 2.097304 CTCTGAGAGAGACACGGATGTG 59.903 54.545 2.60 0.00 45.07 3.21
51 52 5.569008 CTCTGAGAGAGACACGGATGTGC 62.569 56.522 2.60 0.00 45.07 4.57
60 61 2.602257 CACGGATGTGCCTCTCATAA 57.398 50.000 0.00 0.00 39.67 1.90
61 62 2.905075 CACGGATGTGCCTCTCATAAA 58.095 47.619 0.00 0.00 39.67 1.40
62 63 2.609459 CACGGATGTGCCTCTCATAAAC 59.391 50.000 0.00 0.00 39.67 2.01
63 64 1.860950 CGGATGTGCCTCTCATAAACG 59.139 52.381 0.00 0.00 0.00 3.60
102 103 6.806751 TCTCTCTTCTTTTTCTTTCGTGAGA 58.193 36.000 0.00 0.00 39.20 3.27
104 105 5.986135 TCTCTTCTTTTTCTTTCGTGAGAGG 59.014 40.000 0.00 0.00 43.69 3.69
105 106 5.671493 TCTTCTTTTTCTTTCGTGAGAGGT 58.329 37.500 0.00 0.00 43.69 3.85
106 107 6.812998 TCTTCTTTTTCTTTCGTGAGAGGTA 58.187 36.000 0.00 0.00 43.69 3.08
107 108 7.270047 TCTTCTTTTTCTTTCGTGAGAGGTAA 58.730 34.615 0.00 0.00 43.69 2.85
109 110 5.989777 TCTTTTTCTTTCGTGAGAGGTAAGG 59.010 40.000 0.00 0.00 43.69 2.69
112 113 4.950205 TCTTTCGTGAGAGGTAAGGTTT 57.050 40.909 0.00 0.00 43.69 3.27
113 114 5.286267 TCTTTCGTGAGAGGTAAGGTTTT 57.714 39.130 0.00 0.00 43.69 2.43
119 120 4.390264 GTGAGAGGTAAGGTTTTGCTTCT 58.610 43.478 0.00 0.00 37.90 2.85
121 122 4.141482 TGAGAGGTAAGGTTTTGCTTCTGT 60.141 41.667 0.00 0.00 35.92 3.41
126 127 4.214332 GGTAAGGTTTTGCTTCTGTGAGAG 59.786 45.833 0.00 0.00 0.00 3.20
132 133 2.838286 GCTTCTGTGAGAGGCACTG 58.162 57.895 3.03 0.00 45.45 3.66
133 134 0.034616 GCTTCTGTGAGAGGCACTGT 59.965 55.000 3.03 0.00 45.45 3.55
154 155 5.000591 TGTCATGCCTATCAGAAACGAAAA 58.999 37.500 0.00 0.00 0.00 2.29
155 156 5.647658 TGTCATGCCTATCAGAAACGAAAAT 59.352 36.000 0.00 0.00 0.00 1.82
157 158 7.335673 TGTCATGCCTATCAGAAACGAAAATAA 59.664 33.333 0.00 0.00 0.00 1.40
158 159 7.640240 GTCATGCCTATCAGAAACGAAAATAAC 59.360 37.037 0.00 0.00 0.00 1.89
159 160 6.102006 TGCCTATCAGAAACGAAAATAACG 57.898 37.500 0.00 0.00 0.00 3.18
160 161 4.962151 GCCTATCAGAAACGAAAATAACGC 59.038 41.667 0.00 0.00 0.00 4.84
161 162 5.188194 CCTATCAGAAACGAAAATAACGCG 58.812 41.667 3.53 3.53 0.00 6.01
162 163 4.657075 ATCAGAAACGAAAATAACGCGT 57.343 36.364 5.58 5.58 40.35 6.01
184 191 1.878953 TTTCCTTTCGTGAGAGGCAC 58.121 50.000 1.64 0.00 43.69 5.01
194 201 1.165907 TGAGAGGCACGGTTTTGCTG 61.166 55.000 0.00 0.00 42.56 4.41
332 349 4.415881 AACCGCATTTTCCCTTCTTTTT 57.584 36.364 0.00 0.00 0.00 1.94
358 375 5.806366 TCATTACATGAGATGCACAGTTG 57.194 39.130 0.00 0.00 33.59 3.16
368 385 3.736483 CACAGTTGTGCTTCCGCT 58.264 55.556 0.00 0.00 39.39 5.52
380 397 2.227089 CTTCCGCTAGAGGCACGGTT 62.227 60.000 7.80 0.00 46.92 4.44
381 398 1.823169 TTCCGCTAGAGGCACGGTTT 61.823 55.000 7.80 0.00 46.92 3.27
390 407 3.744559 GCACGGTTTTGCCTCTCA 58.255 55.556 0.00 0.00 36.42 3.27
396 413 1.946768 CGGTTTTGCCTCTCAGAAACA 59.053 47.619 0.00 0.00 34.54 2.83
398 415 2.294512 GGTTTTGCCTCTCAGAAACAGG 59.705 50.000 0.00 0.00 34.54 4.00
430 447 8.179615 ACACGTTTTCTATTTTTCTTCTTTCGT 58.820 29.630 0.00 0.00 0.00 3.85
439 456 3.685139 TTCTTCTTTCGTGAGAGGCAT 57.315 42.857 0.00 0.00 43.69 4.40
447 464 2.151202 TCGTGAGAGGCATGGTTTTTC 58.849 47.619 0.00 0.00 34.18 2.29
448 465 1.135972 CGTGAGAGGCATGGTTTTTCG 60.136 52.381 0.00 0.00 0.00 3.46
449 466 1.880027 GTGAGAGGCATGGTTTTTCGT 59.120 47.619 0.00 0.00 0.00 3.85
450 467 2.095718 GTGAGAGGCATGGTTTTTCGTC 60.096 50.000 0.00 0.00 0.00 4.20
452 469 1.202879 AGAGGCATGGTTTTTCGTCCA 60.203 47.619 0.00 0.00 38.14 4.02
495 512 8.408043 TTTGTCAAAACCTATGAACATGAGAT 57.592 30.769 0.00 0.00 0.00 2.75
499 516 9.383519 GTCAAAACCTATGAACATGAGATCTAA 57.616 33.333 0.00 0.00 0.00 2.10
518 535 8.380743 GATCTAATTGTGAAGATCTTGATGCT 57.619 34.615 14.00 0.00 43.14 3.79
527 550 6.709397 GTGAAGATCTTGATGCTCCAATGATA 59.291 38.462 14.00 0.00 0.00 2.15
535 558 5.603596 TGATGCTCCAATGATAAAAATGGC 58.396 37.500 0.00 0.00 32.87 4.40
544 567 8.199449 TCCAATGATAAAAATGGCTTGAGATTC 58.801 33.333 0.00 0.00 32.87 2.52
545 568 7.982919 CCAATGATAAAAATGGCTTGAGATTCA 59.017 33.333 0.00 0.00 0.00 2.57
549 572 4.691860 AAAATGGCTTGAGATTCAGACG 57.308 40.909 0.00 0.00 0.00 4.18
560 583 1.659098 GATTCAGACGCACGGTTTAGG 59.341 52.381 0.00 0.00 0.00 2.69
569 592 4.510571 ACGCACGGTTTAGGAGATAAAAT 58.489 39.130 0.00 0.00 35.16 1.82
570 593 5.663456 ACGCACGGTTTAGGAGATAAAATA 58.337 37.500 0.00 0.00 35.16 1.40
614 637 4.655762 AAAAGGAAAACTCTCAGGTTGC 57.344 40.909 0.00 0.00 0.00 4.17
615 638 1.884235 AGGAAAACTCTCAGGTTGCG 58.116 50.000 0.00 0.00 0.00 4.85
616 639 1.416401 AGGAAAACTCTCAGGTTGCGA 59.584 47.619 0.00 0.00 0.00 5.10
617 640 1.531578 GGAAAACTCTCAGGTTGCGAC 59.468 52.381 0.00 0.00 0.00 5.19
618 641 2.210116 GAAAACTCTCAGGTTGCGACA 58.790 47.619 6.39 0.00 0.00 4.35
619 642 2.325583 AAACTCTCAGGTTGCGACAA 57.674 45.000 6.39 0.00 0.00 3.18
620 643 2.325583 AACTCTCAGGTTGCGACAAA 57.674 45.000 6.39 0.00 0.00 2.83
621 644 2.550830 ACTCTCAGGTTGCGACAAAT 57.449 45.000 6.39 0.00 0.00 2.32
622 645 2.146342 ACTCTCAGGTTGCGACAAATG 58.854 47.619 6.39 1.71 0.00 2.32
623 646 1.466167 CTCTCAGGTTGCGACAAATGG 59.534 52.381 6.39 0.00 0.00 3.16
624 647 0.109597 CTCAGGTTGCGACAAATGGC 60.110 55.000 6.39 0.00 0.00 4.40
625 648 0.821301 TCAGGTTGCGACAAATGGCA 60.821 50.000 6.39 0.00 37.85 4.92
626 649 0.244450 CAGGTTGCGACAAATGGCAT 59.756 50.000 6.39 0.00 39.53 4.40
627 650 1.472082 CAGGTTGCGACAAATGGCATA 59.528 47.619 6.39 0.00 39.53 3.14
628 651 2.099592 CAGGTTGCGACAAATGGCATAT 59.900 45.455 6.39 0.00 39.53 1.78
629 652 3.314913 CAGGTTGCGACAAATGGCATATA 59.685 43.478 6.39 0.00 39.53 0.86
630 653 4.022935 CAGGTTGCGACAAATGGCATATAT 60.023 41.667 6.39 0.00 39.53 0.86
631 654 4.022935 AGGTTGCGACAAATGGCATATATG 60.023 41.667 8.45 8.45 39.53 1.78
644 667 3.564235 CATATATGCAGCGTGCCATTT 57.436 42.857 0.00 1.41 44.23 2.32
645 668 3.239254 CATATATGCAGCGTGCCATTTG 58.761 45.455 0.00 3.87 44.23 2.32
646 669 1.105457 ATATGCAGCGTGCCATTTGT 58.895 45.000 0.00 0.00 44.23 2.83
647 670 0.451383 TATGCAGCGTGCCATTTGTC 59.549 50.000 0.00 0.00 44.23 3.18
648 671 2.502510 GCAGCGTGCCATTTGTCG 60.503 61.111 0.00 0.00 37.42 4.35
651 674 2.050533 GCGTGCCATTTGTCGCAA 60.051 55.556 0.00 0.00 46.40 4.85
652 675 2.364311 GCGTGCCATTTGTCGCAAC 61.364 57.895 0.00 0.00 46.40 4.17
653 676 1.729131 CGTGCCATTTGTCGCAACC 60.729 57.895 0.00 0.00 36.60 3.77
654 677 1.659794 GTGCCATTTGTCGCAACCT 59.340 52.632 0.00 0.00 36.60 3.50
655 678 0.878416 GTGCCATTTGTCGCAACCTA 59.122 50.000 0.00 0.00 36.60 3.08
656 679 0.878416 TGCCATTTGTCGCAACCTAC 59.122 50.000 0.00 0.00 30.46 3.18
657 680 0.179200 GCCATTTGTCGCAACCTACG 60.179 55.000 0.00 0.00 0.00 3.51
658 681 0.446222 CCATTTGTCGCAACCTACGG 59.554 55.000 0.00 0.00 0.00 4.02
659 682 1.434555 CATTTGTCGCAACCTACGGA 58.565 50.000 0.00 0.00 0.00 4.69
660 683 1.393539 CATTTGTCGCAACCTACGGAG 59.606 52.381 0.00 0.00 0.00 4.63
661 684 0.675083 TTTGTCGCAACCTACGGAGA 59.325 50.000 0.00 0.00 0.00 3.71
662 685 0.892755 TTGTCGCAACCTACGGAGAT 59.107 50.000 0.00 0.00 0.00 2.75
663 686 0.172578 TGTCGCAACCTACGGAGATG 59.827 55.000 0.00 0.00 0.00 2.90
664 687 1.141019 TCGCAACCTACGGAGATGC 59.859 57.895 13.59 13.59 34.06 3.91
665 688 1.153647 CGCAACCTACGGAGATGCA 60.154 57.895 20.73 0.00 35.96 3.96
666 689 0.739462 CGCAACCTACGGAGATGCAA 60.739 55.000 20.73 0.00 35.96 4.08
667 690 1.009829 GCAACCTACGGAGATGCAAG 58.990 55.000 17.42 0.00 36.14 4.01
668 691 1.676014 GCAACCTACGGAGATGCAAGT 60.676 52.381 17.42 0.00 36.14 3.16
669 692 2.002586 CAACCTACGGAGATGCAAGTG 58.997 52.381 0.00 0.00 0.00 3.16
670 693 1.557099 ACCTACGGAGATGCAAGTGA 58.443 50.000 0.00 0.00 0.00 3.41
671 694 1.204941 ACCTACGGAGATGCAAGTGAC 59.795 52.381 0.00 0.00 0.00 3.67
672 695 1.478510 CCTACGGAGATGCAAGTGACT 59.521 52.381 0.00 0.00 0.00 3.41
673 696 2.093973 CCTACGGAGATGCAAGTGACTT 60.094 50.000 0.00 0.00 0.00 3.01
674 697 2.550830 ACGGAGATGCAAGTGACTTT 57.449 45.000 0.00 0.00 0.00 2.66
675 698 2.851195 ACGGAGATGCAAGTGACTTTT 58.149 42.857 0.00 0.00 0.00 2.27
676 699 4.002906 ACGGAGATGCAAGTGACTTTTA 57.997 40.909 0.00 0.00 0.00 1.52
677 700 4.385825 ACGGAGATGCAAGTGACTTTTAA 58.614 39.130 0.00 0.00 0.00 1.52
678 701 4.819630 ACGGAGATGCAAGTGACTTTTAAA 59.180 37.500 0.00 0.00 0.00 1.52
679 702 5.298276 ACGGAGATGCAAGTGACTTTTAAAA 59.702 36.000 0.00 0.00 0.00 1.52
680 703 5.853282 CGGAGATGCAAGTGACTTTTAAAAG 59.147 40.000 23.38 23.38 41.73 2.27
681 704 6.293407 CGGAGATGCAAGTGACTTTTAAAAGA 60.293 38.462 29.97 9.76 39.31 2.52
682 705 7.425606 GGAGATGCAAGTGACTTTTAAAAGAA 58.574 34.615 29.97 16.78 39.31 2.52
683 706 7.592903 GGAGATGCAAGTGACTTTTAAAAGAAG 59.407 37.037 29.97 9.17 39.31 2.85
684 707 8.000780 AGATGCAAGTGACTTTTAAAAGAAGT 57.999 30.769 29.97 18.34 39.90 3.01
685 708 8.470002 AGATGCAAGTGACTTTTAAAAGAAGTT 58.530 29.630 29.97 21.96 37.46 2.66
686 709 9.087424 GATGCAAGTGACTTTTAAAAGAAGTTT 57.913 29.630 29.97 16.82 37.46 2.66
687 710 8.825667 TGCAAGTGACTTTTAAAAGAAGTTTT 57.174 26.923 29.97 15.69 37.46 2.43
688 711 9.267084 TGCAAGTGACTTTTAAAAGAAGTTTTT 57.733 25.926 29.97 14.84 37.46 1.94
712 735 8.661352 TTTTTGAGGGATGCTTTTAAAAGAAG 57.339 30.769 28.11 6.58 38.28 2.85
713 736 6.976934 TTGAGGGATGCTTTTAAAAGAAGT 57.023 33.333 28.11 14.20 38.28 3.01
714 737 8.472007 TTTGAGGGATGCTTTTAAAAGAAGTA 57.528 30.769 28.11 12.89 38.28 2.24
715 738 7.448748 TGAGGGATGCTTTTAAAAGAAGTAC 57.551 36.000 28.11 14.45 38.28 2.73
716 739 7.231467 TGAGGGATGCTTTTAAAAGAAGTACT 58.769 34.615 28.11 19.07 38.28 2.73
717 740 7.390718 TGAGGGATGCTTTTAAAAGAAGTACTC 59.609 37.037 28.11 24.45 38.28 2.59
718 741 6.659668 AGGGATGCTTTTAAAAGAAGTACTCC 59.340 38.462 28.11 20.66 38.28 3.85
719 742 6.659668 GGGATGCTTTTAAAAGAAGTACTCCT 59.340 38.462 28.11 4.05 38.28 3.69
720 743 7.148222 GGGATGCTTTTAAAAGAAGTACTCCTC 60.148 40.741 28.11 12.25 38.28 3.71
721 744 7.608376 GGATGCTTTTAAAAGAAGTACTCCTCT 59.392 37.037 28.11 2.62 38.28 3.69
722 745 9.654663 GATGCTTTTAAAAGAAGTACTCCTCTA 57.345 33.333 28.11 2.24 38.28 2.43
757 780 6.851222 ACTCAAATAGTGATTTCGGCTATG 57.149 37.500 0.00 0.00 36.93 2.23
758 781 5.760253 ACTCAAATAGTGATTTCGGCTATGG 59.240 40.000 0.00 0.00 36.93 2.74
759 782 5.924356 TCAAATAGTGATTTCGGCTATGGA 58.076 37.500 0.00 0.00 32.73 3.41
760 783 6.353323 TCAAATAGTGATTTCGGCTATGGAA 58.647 36.000 0.00 0.00 32.73 3.53
761 784 6.483307 TCAAATAGTGATTTCGGCTATGGAAG 59.517 38.462 0.00 0.00 32.73 3.46
762 785 5.808366 ATAGTGATTTCGGCTATGGAAGA 57.192 39.130 0.00 0.00 0.00 2.87
763 786 3.798202 AGTGATTTCGGCTATGGAAGAC 58.202 45.455 0.00 0.00 0.00 3.01
764 787 3.197766 AGTGATTTCGGCTATGGAAGACA 59.802 43.478 0.00 0.00 29.38 3.41
765 788 3.309954 GTGATTTCGGCTATGGAAGACAC 59.690 47.826 0.00 0.00 29.38 3.67
766 789 2.396590 TTTCGGCTATGGAAGACACC 57.603 50.000 0.00 0.00 29.38 4.16
767 790 1.271856 TTCGGCTATGGAAGACACCA 58.728 50.000 0.00 0.00 44.41 4.17
773 796 4.819783 TGGAAGACACCATGGCAC 57.180 55.556 13.04 3.29 34.77 5.01
774 797 1.302431 TGGAAGACACCATGGCACG 60.302 57.895 13.04 2.89 34.77 5.34
775 798 2.040544 GGAAGACACCATGGCACGG 61.041 63.158 13.04 0.00 0.00 4.94
776 799 2.672996 AAGACACCATGGCACGGC 60.673 61.111 13.04 2.31 0.00 5.68
786 809 4.579127 GGCACGGCCCATCTAATT 57.421 55.556 0.00 0.00 44.06 1.40
787 810 3.717842 GGCACGGCCCATCTAATTA 57.282 52.632 0.00 0.00 44.06 1.40
788 811 1.523758 GGCACGGCCCATCTAATTAG 58.476 55.000 6.11 6.11 44.06 1.73
789 812 0.875059 GCACGGCCCATCTAATTAGC 59.125 55.000 7.67 0.00 0.00 3.09
790 813 1.148310 CACGGCCCATCTAATTAGCG 58.852 55.000 7.67 6.95 0.00 4.26
791 814 0.756903 ACGGCCCATCTAATTAGCGT 59.243 50.000 7.67 7.56 0.00 5.07
792 815 1.148310 CGGCCCATCTAATTAGCGTG 58.852 55.000 7.67 8.76 0.00 5.34
793 816 0.875059 GGCCCATCTAATTAGCGTGC 59.125 55.000 7.67 7.42 0.00 5.34
794 817 0.875059 GCCCATCTAATTAGCGTGCC 59.125 55.000 7.67 0.81 0.00 5.01
795 818 1.543429 GCCCATCTAATTAGCGTGCCT 60.543 52.381 7.67 0.00 0.00 4.75
796 819 2.289444 GCCCATCTAATTAGCGTGCCTA 60.289 50.000 7.67 0.00 0.00 3.93
797 820 3.589988 CCCATCTAATTAGCGTGCCTAG 58.410 50.000 7.67 0.00 0.00 3.02
798 821 2.996621 CCATCTAATTAGCGTGCCTAGC 59.003 50.000 7.67 0.00 0.00 3.42
799 822 2.814280 TCTAATTAGCGTGCCTAGCC 57.186 50.000 7.67 0.00 34.64 3.93
800 823 1.000607 TCTAATTAGCGTGCCTAGCCG 60.001 52.381 7.67 0.00 34.64 5.52
801 824 0.748450 TAATTAGCGTGCCTAGCCGT 59.252 50.000 0.00 0.00 34.64 5.68
802 825 0.810031 AATTAGCGTGCCTAGCCGTG 60.810 55.000 0.00 0.00 34.64 4.94
803 826 4.508128 TAGCGTGCCTAGCCGTGC 62.508 66.667 0.00 0.00 34.64 5.34
806 829 4.742201 CGTGCCTAGCCGTGCTGT 62.742 66.667 8.44 0.00 40.10 4.40
807 830 3.121030 GTGCCTAGCCGTGCTGTG 61.121 66.667 8.44 1.57 40.10 3.66
811 834 4.742201 CTAGCCGTGCTGTGCCGT 62.742 66.667 8.44 0.00 40.10 5.68
876 904 1.140852 TCTGTCCAGGTTTGTCCACAG 59.859 52.381 0.00 0.00 38.39 3.66
895 923 1.444895 CAAGCATTTGCACGGGCTC 60.445 57.895 12.74 0.00 45.16 4.70
1209 1237 3.893763 ATCGCGGCACTCTCCTCG 61.894 66.667 6.13 0.00 35.80 4.63
1546 1574 2.351276 GAATGGTGACCCGTGGCT 59.649 61.111 0.00 0.00 0.00 4.75
1627 1655 2.610859 TGGAGGAGGTGGAAGCCC 60.611 66.667 0.00 0.00 32.25 5.19
1668 1696 1.302907 AGGGATTCTGCCTGGACAAT 58.697 50.000 0.00 0.00 36.59 2.71
1899 1927 1.647346 ACACACACACGTCGTTGATT 58.353 45.000 12.45 0.00 0.00 2.57
1925 1953 2.420687 GGCTCTGTAAGATTGGGTGGAG 60.421 54.545 0.00 0.00 45.62 3.86
2097 2125 0.109086 TGGCACCAAACACAAACACG 60.109 50.000 0.00 0.00 0.00 4.49
2256 2284 6.956435 AGAAAGGAAAAATTGAAGAGGCCTAT 59.044 34.615 4.42 0.00 0.00 2.57
2488 2516 3.266510 AGCTGTTTGACAAGTGTCTCA 57.733 42.857 12.43 8.18 44.99 3.27
2491 2519 2.930040 CTGTTTGACAAGTGTCTCACGT 59.070 45.455 12.43 0.00 44.99 4.49
2610 2638 0.817013 TTCAAAATGGATGCCTCGCC 59.183 50.000 0.00 0.00 0.00 5.54
2658 2686 0.322816 GTGGGCTCTGCAAGGAATCA 60.323 55.000 0.00 0.00 0.00 2.57
2784 2812 4.563580 GGAAGGACAAGTGTTGCTCTATCA 60.564 45.833 0.00 0.00 0.00 2.15
2910 2938 1.721691 AGGGTTTTGGATGGGGATTCA 59.278 47.619 0.00 0.00 0.00 2.57
2912 2940 2.559705 GGGTTTTGGATGGGGATTCAGT 60.560 50.000 0.00 0.00 0.00 3.41
2973 3001 0.388134 ACGCGAACAATAGACACGCT 60.388 50.000 15.93 0.00 45.64 5.07
3003 3031 9.926158 GCTTCTGAAATATCTGATAAGATCTCA 57.074 33.333 0.00 0.00 34.06 3.27
3112 3140 7.792032 TGGAAGAAATATTCTACAGTAGGTGG 58.208 38.462 7.79 0.00 39.61 4.61
3123 3151 3.032017 CAGTAGGTGGTCACTGTTCTG 57.968 52.381 0.93 2.59 37.87 3.02
3211 3239 8.970859 TTCACAATATTGGTTGGTCAAAATTT 57.029 26.923 19.37 0.00 33.40 1.82
3273 3301 6.465035 GGCCAAGATCTATATGACCTGACTTT 60.465 42.308 0.00 0.00 0.00 2.66
3286 3314 6.010850 TGACCTGACTTTCACTAGTGTATCT 58.989 40.000 21.99 4.37 0.00 1.98
3287 3315 7.173032 TGACCTGACTTTCACTAGTGTATCTA 58.827 38.462 21.99 0.00 0.00 1.98
3342 3370 4.142534 CCCTGTGCATAAACATGTGAGAAG 60.143 45.833 0.00 0.00 0.00 2.85
3343 3371 4.696877 CCTGTGCATAAACATGTGAGAAGA 59.303 41.667 0.00 0.00 0.00 2.87
3344 3372 5.181811 CCTGTGCATAAACATGTGAGAAGAA 59.818 40.000 0.00 0.00 0.00 2.52
3345 3373 6.294120 CCTGTGCATAAACATGTGAGAAGAAA 60.294 38.462 0.00 0.00 0.00 2.52
3382 3414 7.386025 TGTTGATAGTCTGAAGAAACTGTGATG 59.614 37.037 0.00 0.00 0.00 3.07
3474 3522 7.696992 TTCTTTTTGTACAGGAGAACAACTT 57.303 32.000 11.38 0.00 35.43 2.66
3558 3608 7.726738 ACCCTAGATTCCTACTTCTCAAGATAC 59.273 40.741 0.00 0.00 0.00 2.24
3613 3665 3.987220 TGTTCACTGACACGTCACATATG 59.013 43.478 0.00 0.00 35.46 1.78
3704 3756 9.599866 CAGAGTATATTGTTTCCTGTGTTGATA 57.400 33.333 0.00 0.00 0.00 2.15
3763 3818 4.613925 AATTCAGCTGTCTCAGTTCTCA 57.386 40.909 14.67 0.00 33.43 3.27
3836 3891 4.927425 TGTTATTCTGCGTTCACCTTAGAC 59.073 41.667 0.00 0.00 0.00 2.59
3897 3952 8.945057 TCTTCACATGATCATAATTTCGTTCAA 58.055 29.630 8.15 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.562454 AATCGTACCTCTCACAAAAGAAAAA 57.438 32.000 0.00 0.00 0.00 1.94
1 2 7.562454 AAATCGTACCTCTCACAAAAGAAAA 57.438 32.000 0.00 0.00 0.00 2.29
3 4 6.512741 GCAAAATCGTACCTCTCACAAAAGAA 60.513 38.462 0.00 0.00 0.00 2.52
4 5 5.049680 GCAAAATCGTACCTCTCACAAAAGA 60.050 40.000 0.00 0.00 0.00 2.52
6 7 4.023536 GGCAAAATCGTACCTCTCACAAAA 60.024 41.667 0.00 0.00 0.00 2.44
7 8 3.500680 GGCAAAATCGTACCTCTCACAAA 59.499 43.478 0.00 0.00 0.00 2.83
8 9 3.071479 GGCAAAATCGTACCTCTCACAA 58.929 45.455 0.00 0.00 0.00 3.33
9 10 2.301870 AGGCAAAATCGTACCTCTCACA 59.698 45.455 0.00 0.00 0.00 3.58
10 11 2.930682 GAGGCAAAATCGTACCTCTCAC 59.069 50.000 0.00 0.00 44.41 3.51
11 12 3.247006 GAGGCAAAATCGTACCTCTCA 57.753 47.619 0.00 0.00 44.41 3.27
15 16 2.832129 TCTCAGAGGCAAAATCGTACCT 59.168 45.455 0.00 0.00 34.43 3.08
16 17 3.119101 TCTCTCAGAGGCAAAATCGTACC 60.119 47.826 0.57 0.00 0.00 3.34
17 18 4.109050 CTCTCTCAGAGGCAAAATCGTAC 58.891 47.826 0.57 0.00 38.67 3.67
18 19 4.017126 TCTCTCTCAGAGGCAAAATCGTA 58.983 43.478 0.57 0.00 42.54 3.43
19 20 2.828520 TCTCTCTCAGAGGCAAAATCGT 59.171 45.455 0.57 0.00 42.54 3.73
20 21 3.186119 GTCTCTCTCAGAGGCAAAATCG 58.814 50.000 0.57 0.00 45.89 3.34
27 28 0.678366 TCCGTGTCTCTCTCAGAGGC 60.678 60.000 0.57 0.03 46.75 4.70
28 29 1.675483 CATCCGTGTCTCTCTCAGAGG 59.325 57.143 0.57 0.00 42.54 3.69
29 30 2.097304 CACATCCGTGTCTCTCTCAGAG 59.903 54.545 0.00 0.00 37.70 3.35
30 31 2.087646 CACATCCGTGTCTCTCTCAGA 58.912 52.381 0.00 0.00 38.41 3.27
31 32 1.468908 GCACATCCGTGTCTCTCTCAG 60.469 57.143 0.00 0.00 45.50 3.35
32 33 0.528017 GCACATCCGTGTCTCTCTCA 59.472 55.000 0.00 0.00 45.50 3.27
33 34 0.179124 GGCACATCCGTGTCTCTCTC 60.179 60.000 0.00 0.00 44.67 3.20
34 35 1.893786 GGCACATCCGTGTCTCTCT 59.106 57.895 0.00 0.00 44.67 3.10
35 36 4.504132 GGCACATCCGTGTCTCTC 57.496 61.111 0.00 0.00 44.67 3.20
40 41 1.485124 TATGAGAGGCACATCCGTGT 58.515 50.000 0.00 0.00 45.50 4.49
41 42 2.602257 TTATGAGAGGCACATCCGTG 57.398 50.000 0.00 0.00 46.56 4.94
42 43 2.738643 CGTTTATGAGAGGCACATCCGT 60.739 50.000 0.00 0.00 40.77 4.69
43 44 1.860950 CGTTTATGAGAGGCACATCCG 59.139 52.381 0.00 0.00 40.77 4.18
44 45 3.179443 TCGTTTATGAGAGGCACATCC 57.821 47.619 0.00 0.00 0.00 3.51
45 46 5.545658 TTTTCGTTTATGAGAGGCACATC 57.454 39.130 0.00 0.00 0.00 3.06
46 47 5.957842 TTTTTCGTTTATGAGAGGCACAT 57.042 34.783 0.00 0.00 0.00 3.21
72 73 7.549488 ACGAAAGAAAAAGAAGAGAGAGAACAA 59.451 33.333 0.00 0.00 0.00 2.83
73 74 7.010552 CACGAAAGAAAAAGAAGAGAGAGAACA 59.989 37.037 0.00 0.00 0.00 3.18
74 75 7.222999 TCACGAAAGAAAAAGAAGAGAGAGAAC 59.777 37.037 0.00 0.00 0.00 3.01
77 78 6.920758 TCTCACGAAAGAAAAAGAAGAGAGAG 59.079 38.462 0.00 0.00 0.00 3.20
83 84 5.993106 ACCTCTCACGAAAGAAAAAGAAG 57.007 39.130 0.00 0.00 0.00 2.85
91 92 4.950205 AAACCTTACCTCTCACGAAAGA 57.050 40.909 0.00 0.00 0.00 2.52
102 103 4.137543 CTCACAGAAGCAAAACCTTACCT 58.862 43.478 0.00 0.00 0.00 3.08
104 105 4.214332 CCTCTCACAGAAGCAAAACCTTAC 59.786 45.833 0.00 0.00 0.00 2.34
105 106 4.389374 CCTCTCACAGAAGCAAAACCTTA 58.611 43.478 0.00 0.00 0.00 2.69
106 107 3.217626 CCTCTCACAGAAGCAAAACCTT 58.782 45.455 0.00 0.00 0.00 3.50
107 108 2.856222 CCTCTCACAGAAGCAAAACCT 58.144 47.619 0.00 0.00 0.00 3.50
109 110 1.949525 TGCCTCTCACAGAAGCAAAAC 59.050 47.619 0.00 0.00 38.61 2.43
112 113 0.761187 AGTGCCTCTCACAGAAGCAA 59.239 50.000 0.00 0.00 42.67 3.91
131 132 3.885724 TCGTTTCTGATAGGCATGACA 57.114 42.857 0.00 0.00 0.00 3.58
132 133 5.545658 TTTTCGTTTCTGATAGGCATGAC 57.454 39.130 0.00 0.00 0.00 3.06
133 134 7.465379 CGTTATTTTCGTTTCTGATAGGCATGA 60.465 37.037 0.00 0.00 0.00 3.07
141 142 4.657075 ACGCGTTATTTTCGTTTCTGAT 57.343 36.364 5.58 0.00 31.89 2.90
184 191 2.175184 CTCTCGTGGCAGCAAAACCG 62.175 60.000 0.00 0.00 0.00 4.44
257 273 2.317230 CGGAAGCAAAACCGTGTCT 58.683 52.632 0.00 0.00 43.53 3.41
336 353 5.122711 CACAACTGTGCATCTCATGTAATGA 59.877 40.000 12.33 0.00 44.83 2.57
380 397 3.576078 TTCCTGTTTCTGAGAGGCAAA 57.424 42.857 0.00 0.00 38.68 3.68
381 398 3.576078 TTTCCTGTTTCTGAGAGGCAA 57.424 42.857 0.00 0.00 38.68 4.52
404 421 8.179615 ACGAAAGAAGAAAAATAGAAAACGTGT 58.820 29.630 0.00 0.00 0.00 4.49
405 422 8.461398 CACGAAAGAAGAAAAATAGAAAACGTG 58.539 33.333 0.00 0.00 37.92 4.49
406 423 8.392612 TCACGAAAGAAGAAAAATAGAAAACGT 58.607 29.630 0.00 0.00 0.00 3.99
407 424 8.762149 TCACGAAAGAAGAAAAATAGAAAACG 57.238 30.769 0.00 0.00 0.00 3.60
421 438 2.005451 CCATGCCTCTCACGAAAGAAG 58.995 52.381 0.00 0.00 0.00 2.85
422 439 1.347707 ACCATGCCTCTCACGAAAGAA 59.652 47.619 0.00 0.00 0.00 2.52
423 440 0.976641 ACCATGCCTCTCACGAAAGA 59.023 50.000 0.00 0.00 0.00 2.52
430 447 2.151202 GACGAAAAACCATGCCTCTCA 58.849 47.619 0.00 0.00 0.00 3.27
468 485 8.690884 TCTCATGTTCATAGGTTTTGACAAAAA 58.309 29.630 14.75 0.59 32.82 1.94
469 486 8.231692 TCTCATGTTCATAGGTTTTGACAAAA 57.768 30.769 9.30 9.30 0.00 2.44
470 487 7.815840 TCTCATGTTCATAGGTTTTGACAAA 57.184 32.000 0.00 0.00 0.00 2.83
471 488 7.884877 AGATCTCATGTTCATAGGTTTTGACAA 59.115 33.333 0.00 0.00 0.00 3.18
472 489 7.397221 AGATCTCATGTTCATAGGTTTTGACA 58.603 34.615 0.00 0.00 0.00 3.58
473 490 7.856145 AGATCTCATGTTCATAGGTTTTGAC 57.144 36.000 0.00 0.00 0.00 3.18
495 512 6.765036 GGAGCATCAAGATCTTCACAATTAGA 59.235 38.462 4.57 0.00 36.25 2.10
499 516 4.851843 TGGAGCATCAAGATCTTCACAAT 58.148 39.130 4.57 0.00 36.25 2.71
502 519 4.880120 TCATTGGAGCATCAAGATCTTCAC 59.120 41.667 4.57 0.00 36.25 3.18
512 529 5.364446 AGCCATTTTTATCATTGGAGCATCA 59.636 36.000 0.00 0.00 36.25 3.07
515 532 5.187381 TCAAGCCATTTTTATCATTGGAGCA 59.813 36.000 0.00 0.00 0.00 4.26
517 534 7.104043 TCTCAAGCCATTTTTATCATTGGAG 57.896 36.000 0.00 0.00 0.00 3.86
518 535 7.664552 ATCTCAAGCCATTTTTATCATTGGA 57.335 32.000 0.00 0.00 0.00 3.53
527 550 4.616835 GCGTCTGAATCTCAAGCCATTTTT 60.617 41.667 0.00 0.00 0.00 1.94
535 558 0.994995 CCGTGCGTCTGAATCTCAAG 59.005 55.000 0.00 0.00 0.00 3.02
544 567 0.242825 TCTCCTAAACCGTGCGTCTG 59.757 55.000 0.00 0.00 0.00 3.51
545 568 1.183549 ATCTCCTAAACCGTGCGTCT 58.816 50.000 0.00 0.00 0.00 4.18
549 572 9.233232 CAAAATATTTTATCTCCTAAACCGTGC 57.767 33.333 12.98 0.00 0.00 5.34
592 615 4.440112 CGCAACCTGAGAGTTTTCCTTTTT 60.440 41.667 0.00 0.00 0.00 1.94
593 616 3.066760 CGCAACCTGAGAGTTTTCCTTTT 59.933 43.478 0.00 0.00 0.00 2.27
594 617 2.618709 CGCAACCTGAGAGTTTTCCTTT 59.381 45.455 0.00 0.00 0.00 3.11
595 618 2.158813 TCGCAACCTGAGAGTTTTCCTT 60.159 45.455 0.00 0.00 0.00 3.36
596 619 1.416401 TCGCAACCTGAGAGTTTTCCT 59.584 47.619 0.00 0.00 0.00 3.36
597 620 1.531578 GTCGCAACCTGAGAGTTTTCC 59.468 52.381 0.00 0.00 0.00 3.13
598 621 2.210116 TGTCGCAACCTGAGAGTTTTC 58.790 47.619 0.00 0.00 0.00 2.29
599 622 2.325583 TGTCGCAACCTGAGAGTTTT 57.674 45.000 0.00 0.00 0.00 2.43
600 623 2.325583 TTGTCGCAACCTGAGAGTTT 57.674 45.000 0.00 0.00 0.00 2.66
601 624 2.325583 TTTGTCGCAACCTGAGAGTT 57.674 45.000 0.00 0.00 0.00 3.01
602 625 2.146342 CATTTGTCGCAACCTGAGAGT 58.854 47.619 0.00 0.00 0.00 3.24
603 626 1.466167 CCATTTGTCGCAACCTGAGAG 59.534 52.381 0.00 0.00 0.00 3.20
604 627 1.522668 CCATTTGTCGCAACCTGAGA 58.477 50.000 0.00 0.00 0.00 3.27
605 628 0.109597 GCCATTTGTCGCAACCTGAG 60.110 55.000 0.00 0.00 0.00 3.35
606 629 0.821301 TGCCATTTGTCGCAACCTGA 60.821 50.000 0.00 0.00 30.46 3.86
607 630 0.244450 ATGCCATTTGTCGCAACCTG 59.756 50.000 0.00 0.00 38.75 4.00
608 631 1.832883 TATGCCATTTGTCGCAACCT 58.167 45.000 0.00 0.00 38.75 3.50
609 632 2.869233 ATATGCCATTTGTCGCAACC 57.131 45.000 0.00 0.00 38.75 3.77
631 654 2.502510 CGACAAATGGCACGCTGC 60.503 61.111 0.00 1.92 44.08 5.25
632 655 2.502510 GCGACAAATGGCACGCTG 60.503 61.111 11.56 1.87 46.06 5.18
635 658 1.729131 GGTTGCGACAAATGGCACG 60.729 57.895 6.39 0.00 39.54 5.34
636 659 0.878416 TAGGTTGCGACAAATGGCAC 59.122 50.000 6.39 0.00 39.54 5.01
637 660 0.878416 GTAGGTTGCGACAAATGGCA 59.122 50.000 6.39 0.00 37.85 4.92
638 661 0.179200 CGTAGGTTGCGACAAATGGC 60.179 55.000 6.39 0.00 0.00 4.40
639 662 3.967734 CGTAGGTTGCGACAAATGG 57.032 52.632 6.39 0.00 0.00 3.16
653 676 2.949451 AGTCACTTGCATCTCCGTAG 57.051 50.000 0.00 0.00 0.00 3.51
654 677 3.678056 AAAGTCACTTGCATCTCCGTA 57.322 42.857 0.00 0.00 0.00 4.02
655 678 2.550830 AAAGTCACTTGCATCTCCGT 57.449 45.000 0.00 0.00 0.00 4.69
656 679 5.356882 TTTAAAAGTCACTTGCATCTCCG 57.643 39.130 0.00 0.00 0.00 4.63
657 680 6.970484 TCTTTTAAAAGTCACTTGCATCTCC 58.030 36.000 23.75 0.00 37.31 3.71
658 681 8.131731 ACTTCTTTTAAAAGTCACTTGCATCTC 58.868 33.333 23.75 0.00 37.31 2.75
659 682 8.000780 ACTTCTTTTAAAAGTCACTTGCATCT 57.999 30.769 23.75 0.00 37.31 2.90
660 683 8.634475 AACTTCTTTTAAAAGTCACTTGCATC 57.366 30.769 23.75 0.00 35.96 3.91
661 684 9.435688 AAAACTTCTTTTAAAAGTCACTTGCAT 57.564 25.926 23.75 4.95 35.96 3.96
662 685 8.825667 AAAACTTCTTTTAAAAGTCACTTGCA 57.174 26.923 23.75 3.19 35.96 4.08
687 710 8.264347 ACTTCTTTTAAAAGCATCCCTCAAAAA 58.736 29.630 20.93 6.60 35.99 1.94
688 711 7.791029 ACTTCTTTTAAAAGCATCCCTCAAAA 58.209 30.769 20.93 7.04 35.99 2.44
689 712 7.360113 ACTTCTTTTAAAAGCATCCCTCAAA 57.640 32.000 20.93 7.66 35.99 2.69
690 713 6.976934 ACTTCTTTTAAAAGCATCCCTCAA 57.023 33.333 20.93 8.27 35.99 3.02
691 714 7.231467 AGTACTTCTTTTAAAAGCATCCCTCA 58.769 34.615 20.93 0.86 35.99 3.86
692 715 7.148222 GGAGTACTTCTTTTAAAAGCATCCCTC 60.148 40.741 20.93 19.41 35.99 4.30
693 716 6.659668 GGAGTACTTCTTTTAAAAGCATCCCT 59.340 38.462 20.93 13.73 35.99 4.20
694 717 6.659668 AGGAGTACTTCTTTTAAAAGCATCCC 59.340 38.462 20.93 14.44 35.99 3.85
695 718 7.608376 AGAGGAGTACTTCTTTTAAAAGCATCC 59.392 37.037 20.93 18.28 35.99 3.51
696 719 8.554835 AGAGGAGTACTTCTTTTAAAAGCATC 57.445 34.615 20.93 12.68 35.99 3.91
734 757 5.760253 CCATAGCCGAAATCACTATTTGAGT 59.240 40.000 0.00 0.00 37.77 3.41
735 758 5.991606 TCCATAGCCGAAATCACTATTTGAG 59.008 40.000 0.00 0.00 37.77 3.02
736 759 5.924356 TCCATAGCCGAAATCACTATTTGA 58.076 37.500 0.00 0.00 35.41 2.69
737 760 6.483307 TCTTCCATAGCCGAAATCACTATTTG 59.517 38.462 0.00 0.00 35.41 2.32
738 761 6.483640 GTCTTCCATAGCCGAAATCACTATTT 59.516 38.462 0.00 0.00 38.03 1.40
739 762 5.992217 GTCTTCCATAGCCGAAATCACTATT 59.008 40.000 0.00 0.00 0.00 1.73
740 763 5.070446 TGTCTTCCATAGCCGAAATCACTAT 59.930 40.000 0.00 0.00 0.00 2.12
741 764 4.404394 TGTCTTCCATAGCCGAAATCACTA 59.596 41.667 0.00 0.00 0.00 2.74
742 765 3.197766 TGTCTTCCATAGCCGAAATCACT 59.802 43.478 0.00 0.00 0.00 3.41
743 766 3.309954 GTGTCTTCCATAGCCGAAATCAC 59.690 47.826 0.00 0.00 0.00 3.06
744 767 3.531538 GTGTCTTCCATAGCCGAAATCA 58.468 45.455 0.00 0.00 0.00 2.57
745 768 2.872858 GGTGTCTTCCATAGCCGAAATC 59.127 50.000 0.00 0.00 0.00 2.17
746 769 2.238646 TGGTGTCTTCCATAGCCGAAAT 59.761 45.455 0.00 0.00 31.96 2.17
747 770 1.626321 TGGTGTCTTCCATAGCCGAAA 59.374 47.619 0.00 0.00 31.96 3.46
748 771 1.271856 TGGTGTCTTCCATAGCCGAA 58.728 50.000 0.00 0.00 31.96 4.30
749 772 1.138859 CATGGTGTCTTCCATAGCCGA 59.861 52.381 0.00 0.00 45.23 5.54
750 773 1.586422 CATGGTGTCTTCCATAGCCG 58.414 55.000 0.00 0.00 45.23 5.52
751 774 1.972872 CCATGGTGTCTTCCATAGCC 58.027 55.000 2.57 0.00 45.23 3.93
752 775 1.312815 GCCATGGTGTCTTCCATAGC 58.687 55.000 14.67 1.12 45.23 2.97
753 776 2.292267 GTGCCATGGTGTCTTCCATAG 58.708 52.381 14.67 0.00 45.23 2.23
754 777 1.406751 CGTGCCATGGTGTCTTCCATA 60.407 52.381 14.67 0.00 45.23 2.74
756 779 1.302431 CGTGCCATGGTGTCTTCCA 60.302 57.895 14.67 0.00 42.01 3.53
757 780 2.040544 CCGTGCCATGGTGTCTTCC 61.041 63.158 14.67 0.00 0.00 3.46
758 781 2.690778 GCCGTGCCATGGTGTCTTC 61.691 63.158 14.67 0.00 0.00 2.87
759 782 2.672996 GCCGTGCCATGGTGTCTT 60.673 61.111 14.67 0.00 0.00 3.01
770 793 0.875059 GCTAATTAGATGGGCCGTGC 59.125 55.000 16.85 0.00 0.00 5.34
771 794 1.148310 CGCTAATTAGATGGGCCGTG 58.852 55.000 16.85 0.00 0.00 4.94
772 795 0.756903 ACGCTAATTAGATGGGCCGT 59.243 50.000 16.85 11.51 0.00 5.68
773 796 1.148310 CACGCTAATTAGATGGGCCG 58.852 55.000 16.85 10.89 0.00 6.13
774 797 0.875059 GCACGCTAATTAGATGGGCC 59.125 55.000 16.85 0.00 0.00 5.80
775 798 0.875059 GGCACGCTAATTAGATGGGC 59.125 55.000 16.85 18.05 0.00 5.36
776 799 2.550830 AGGCACGCTAATTAGATGGG 57.449 50.000 16.85 9.56 0.00 4.00
777 800 2.996621 GCTAGGCACGCTAATTAGATGG 59.003 50.000 16.85 6.84 0.00 3.51
778 801 2.996621 GGCTAGGCACGCTAATTAGATG 59.003 50.000 16.85 13.51 0.00 2.90
779 802 2.352814 CGGCTAGGCACGCTAATTAGAT 60.353 50.000 16.85 0.20 0.00 1.98
780 803 1.000607 CGGCTAGGCACGCTAATTAGA 60.001 52.381 16.85 0.00 0.00 2.10
781 804 1.269621 ACGGCTAGGCACGCTAATTAG 60.270 52.381 17.45 8.20 0.00 1.73
782 805 0.748450 ACGGCTAGGCACGCTAATTA 59.252 50.000 17.45 0.00 0.00 1.40
783 806 0.810031 CACGGCTAGGCACGCTAATT 60.810 55.000 17.45 0.00 0.00 1.40
784 807 1.227263 CACGGCTAGGCACGCTAAT 60.227 57.895 17.45 0.00 0.00 1.73
785 808 2.183300 CACGGCTAGGCACGCTAA 59.817 61.111 17.45 0.00 0.00 3.09
786 809 4.508128 GCACGGCTAGGCACGCTA 62.508 66.667 17.45 0.00 0.00 4.26
789 812 4.742201 ACAGCACGGCTAGGCACG 62.742 66.667 17.45 7.34 36.40 5.34
790 813 3.121030 CACAGCACGGCTAGGCAC 61.121 66.667 17.45 4.99 36.40 5.01
794 817 4.742201 ACGGCACAGCACGGCTAG 62.742 66.667 0.00 0.00 36.40 3.42
810 833 1.525306 GGTTATACGGGCCAGGCAC 60.525 63.158 15.19 9.32 0.00 5.01
811 834 2.748513 GGGTTATACGGGCCAGGCA 61.749 63.158 15.19 0.00 0.00 4.75
812 835 2.112507 GGGTTATACGGGCCAGGC 59.887 66.667 8.08 1.26 0.00 4.85
813 836 1.450211 CTGGGTTATACGGGCCAGG 59.550 63.158 8.08 0.00 0.00 4.45
817 840 1.068585 CGACCTGGGTTATACGGGC 59.931 63.158 0.00 0.00 37.93 6.13
860 888 0.257328 TTGCTGTGGACAAACCTGGA 59.743 50.000 0.00 0.00 39.86 3.86
911 939 0.955919 GGGTGCCTCTGAAAGAACCG 60.956 60.000 0.00 0.00 46.34 4.44
945 973 4.657814 TTCCTGCCCTCTGAATAACTTT 57.342 40.909 0.00 0.00 0.00 2.66
946 974 4.568592 CCTTTCCTGCCCTCTGAATAACTT 60.569 45.833 0.00 0.00 0.00 2.66
947 975 3.054065 CCTTTCCTGCCCTCTGAATAACT 60.054 47.826 0.00 0.00 0.00 2.24
948 976 3.054361 TCCTTTCCTGCCCTCTGAATAAC 60.054 47.826 0.00 0.00 0.00 1.89
950 978 2.774234 CTCCTTTCCTGCCCTCTGAATA 59.226 50.000 0.00 0.00 0.00 1.75
951 979 1.563410 CTCCTTTCCTGCCCTCTGAAT 59.437 52.381 0.00 0.00 0.00 2.57
1034 1062 2.108168 TGAGTACGAAATGGAGGAGGG 58.892 52.381 0.00 0.00 0.00 4.30
1107 1135 1.891722 CTGGGGTGCAAAATGGAGGC 61.892 60.000 0.00 0.00 0.00 4.70
1108 1136 0.251742 TCTGGGGTGCAAAATGGAGG 60.252 55.000 0.00 0.00 0.00 4.30
1109 1137 1.479323 CATCTGGGGTGCAAAATGGAG 59.521 52.381 0.00 0.00 0.00 3.86
1110 1138 1.559368 CATCTGGGGTGCAAAATGGA 58.441 50.000 0.00 0.00 0.00 3.41
1111 1139 0.108041 GCATCTGGGGTGCAAAATGG 60.108 55.000 0.00 0.00 42.08 3.16
1112 1140 0.108041 GGCATCTGGGGTGCAAAATG 60.108 55.000 5.15 0.00 44.25 2.32
1113 1141 1.606885 CGGCATCTGGGGTGCAAAAT 61.607 55.000 5.15 0.00 44.25 1.82
1114 1142 2.274645 CGGCATCTGGGGTGCAAAA 61.275 57.895 5.15 0.00 44.25 2.44
1627 1655 2.259204 CCACATTGCCGCCAACAG 59.741 61.111 0.00 0.00 32.95 3.16
1899 1927 2.173356 CCCAATCTTACAGAGCCCATCA 59.827 50.000 0.00 0.00 0.00 3.07
2097 2125 2.798680 CCACTGATCAGCGTAGTGTAC 58.201 52.381 22.83 0.00 40.04 2.90
2256 2284 3.081409 GCCCTCCGGAGCACCTTA 61.081 66.667 26.87 0.00 0.00 2.69
2488 2516 3.749609 GTGGTTGGCACTAATTCTAACGT 59.250 43.478 0.00 0.00 0.00 3.99
2491 2519 4.720046 TGTGTGGTTGGCACTAATTCTAA 58.280 39.130 0.00 0.00 37.70 2.10
2581 2609 7.068702 AGGCATCCATTTTGAACCATTCTATA 58.931 34.615 0.00 0.00 0.00 1.31
2610 2638 6.811253 AGAGCTCCATAAGTTATAGAGTCG 57.189 41.667 16.53 0.00 0.00 4.18
2658 2686 1.187087 CCCGTGCTTCCTCTAGTCTT 58.813 55.000 0.00 0.00 0.00 3.01
2784 2812 6.525629 CCGTTTATCCAGTCTATCCAAGATT 58.474 40.000 0.00 0.00 36.36 2.40
2910 2938 7.606456 CCAGTATAAGTTACATGGTCAACAACT 59.394 37.037 0.00 0.00 0.00 3.16
2912 2940 6.373216 GCCAGTATAAGTTACATGGTCAACAA 59.627 38.462 0.00 0.00 0.00 2.83
3003 3031 6.365520 TCTTGAAAGCTAGAGGGTTCTTTTT 58.634 36.000 0.00 0.00 34.22 1.94
3123 3151 5.757850 ACCATTTTACTATAGCAAGCTGC 57.242 39.130 4.53 0.00 45.46 5.25
3211 3239 4.223700 AGACCAGTGAGTATGCAAGATGAA 59.776 41.667 0.00 0.00 0.00 2.57
3286 3314 4.551702 TGCCATCAAGCAGTTCTTACTA 57.448 40.909 0.00 0.00 38.00 1.82
3287 3315 3.423539 TGCCATCAAGCAGTTCTTACT 57.576 42.857 0.00 0.00 38.00 2.24
3342 3370 7.857885 CAGACTATCAACAACAAACCTTCTTTC 59.142 37.037 0.00 0.00 0.00 2.62
3343 3371 7.556275 TCAGACTATCAACAACAAACCTTCTTT 59.444 33.333 0.00 0.00 0.00 2.52
3344 3372 7.054124 TCAGACTATCAACAACAAACCTTCTT 58.946 34.615 0.00 0.00 0.00 2.52
3345 3373 6.591935 TCAGACTATCAACAACAAACCTTCT 58.408 36.000 0.00 0.00 0.00 2.85
3426 3474 9.438291 GAAACATTCAGAATGGTAAATCATACG 57.562 33.333 24.22 0.00 37.99 3.06
3454 3502 6.827586 ACAAAGTTGTTCTCCTGTACAAAA 57.172 33.333 0.00 0.00 38.47 2.44
3530 3580 7.827787 TCTTGAGAAGTAGGAATCTAGGGTAT 58.172 38.462 0.00 0.00 0.00 2.73
3538 3588 9.823647 TGAATTGTATCTTGAGAAGTAGGAATC 57.176 33.333 0.00 0.00 0.00 2.52
3558 3608 8.517056 TGCTATGAATAAGCATACCATGAATTG 58.483 33.333 0.00 0.00 44.78 2.32
3603 3655 5.278604 TCGGATTGTAGAACATATGTGACG 58.721 41.667 9.63 4.44 0.00 4.35
3613 3665 3.119101 TCAGAGGCTTCGGATTGTAGAAC 60.119 47.826 0.00 0.00 0.00 3.01
3763 3818 9.468532 GCAACTTCTTACAAGAATTTTCTGAAT 57.531 29.630 4.93 0.00 43.52 2.57
3897 3952 3.515602 AGGATGTGAACAAGGAAGCTT 57.484 42.857 0.00 0.00 0.00 3.74


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

AutoCloner maintained by Alex Coulton.