Multiple sequence alignment - TraesCS7A01G324300

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 TraesCS7A01G324300 chr7A 100.000 3897 0 0 1 3897 471549485 471553381 0.000000e+00 7197
1 TraesCS7A01G324300 chr7A 87.307 646 59 12 3203 3829 68341571 68342212 0.000000e+00 717
2 TraesCS7A01G324300 chr7A 85.457 722 65 18 3198 3897 121613161 121612458 0.000000e+00 715
3 TraesCS7A01G324300 chr7A 79.839 496 74 12 3407 3897 639324591 639324117 4.820000e-89 339
4 TraesCS7A01G324300 chr7A 98.438 64 1 0 1 64 117356358 117356421 3.180000e-21 113
5 TraesCS7A01G324300 chr7A 94.521 73 2 2 1 72 703568659 703568730 1.140000e-20 111
6 TraesCS7A01G324300 chr7A 84.466 103 16 0 2198 2300 107916705 107916603 6.890000e-18 102
7 TraesCS7A01G324300 chr7D 95.750 2212 65 11 827 3036 410523690 410521506 0.000000e+00 3537
8 TraesCS7A01G324300 chr7D 89.231 520 24 14 57 545 410524239 410523721 4.280000e-174 621
9 TraesCS7A01G324300 chr7D 80.962 499 60 17 3407 3897 553599773 553599302 2.860000e-96 363
10 TraesCS7A01G324300 chr7D 94.355 124 5 2 3083 3205 410521027 410520905 5.140000e-44 189
11 TraesCS7A01G324300 chr7D 92.771 83 5 1 462 544 610826673 610826754 6.840000e-23 119
12 TraesCS7A01G324300 chr7D 90.361 83 7 1 462 544 610837682 610837763 1.480000e-19 108
13 TraesCS7A01G324300 chr7B 94.383 1086 43 6 877 1959 425157566 425158636 0.000000e+00 1652
14 TraesCS7A01G324300 chr7B 93.004 1115 47 18 1956 3058 425158892 425159987 0.000000e+00 1598
15 TraesCS7A01G324300 chr7B 85.761 309 33 7 3596 3896 600014049 600013744 2.260000e-82 316
16 TraesCS7A01G324300 chr7B 87.379 103 13 0 2198 2300 61627839 61627737 6.840000e-23 119
17 TraesCS7A01G324300 chr7B 83.962 106 16 1 2195 2300 61746188 61746084 2.480000e-17 100
18 TraesCS7A01G324300 chr2A 87.616 646 56 12 3203 3829 7510152 7510792 0.000000e+00 728
19 TraesCS7A01G324300 chr2A 92.920 226 15 1 538 762 509549481 509549256 1.040000e-85 327
20 TraesCS7A01G324300 chr2A 98.462 65 0 1 1 65 115096149 115096212 3.180000e-21 113
21 TraesCS7A01G324300 chr3A 87.172 647 59 14 3203 3829 58844756 58845398 0.000000e+00 713
22 TraesCS7A01G324300 chr3A 91.416 233 18 1 544 774 62432931 62433163 6.280000e-83 318
23 TraesCS7A01G324300 chr4A 84.972 712 87 14 3199 3897 7467704 7468408 0.000000e+00 704
24 TraesCS7A01G324300 chr4A 93.607 219 14 0 544 762 58348767 58348985 1.040000e-85 327
25 TraesCS7A01G324300 chr4A 91.463 82 6 1 463 544 537537232 537537312 1.140000e-20 111
26 TraesCS7A01G324300 chr4A 90.000 80 6 2 1 80 274942692 274942615 6.890000e-18 102
27 TraesCS7A01G324300 chr4A 86.813 91 11 1 59 148 734428008 734427918 2.480000e-17 100
28 TraesCS7A01G324300 chr1A 86.883 648 60 13 3200 3829 47517833 47518473 0.000000e+00 702
29 TraesCS7A01G324300 chr1A 94.444 216 12 0 542 757 351584653 351584438 2.240000e-87 333
30 TraesCS7A01G324300 chr1A 92.544 228 15 1 535 762 399599691 399599916 3.750000e-85 326
31 TraesCS7A01G324300 chr1A 84.539 304 26 9 3596 3892 522151563 522151274 8.240000e-72 281
32 TraesCS7A01G324300 chr1A 91.358 81 4 3 1 78 42115817 42115737 1.480000e-19 108
33 TraesCS7A01G324300 chrUn 86.553 647 63 13 3203 3829 81839034 81838392 0.000000e+00 691
34 TraesCS7A01G324300 chr5A 86.265 648 68 13 3200 3829 603796284 603796928 0.000000e+00 684
35 TraesCS7A01G324300 chr5A 94.619 223 12 0 540 762 549412667 549412445 2.880000e-91 346
36 TraesCS7A01G324300 chr5A 81.114 413 65 9 1974 2381 413429412 413429816 6.280000e-83 318
37 TraesCS7A01G324300 chr5A 100.000 62 0 0 1 62 503040076 503040015 8.850000e-22 115
38 TraesCS7A01G324300 chr1D 82.309 667 103 8 3205 3867 102780496 102779841 7.310000e-157 564
39 TraesCS7A01G324300 chr6B 93.243 222 15 0 541 762 307574233 307574012 1.040000e-85 327
40 TraesCS7A01G324300 chr6B 92.000 75 6 0 462 536 153541275 153541349 5.330000e-19 106
41 TraesCS7A01G324300 chr6B 90.123 81 7 1 464 544 482469403 482469482 1.920000e-18 104
42 TraesCS7A01G324300 chr3D 91.915 235 15 3 539 770 108290836 108291069 3.750000e-85 326
43 TraesCS7A01G324300 chr3D 92.105 76 5 1 462 536 426880954 426881029 5.330000e-19 106
44 TraesCS7A01G324300 chr3D 89.412 85 5 3 1 85 587206641 587206561 1.920000e-18 104
45 TraesCS7A01G324300 chr1B 91.139 237 18 3 533 769 444057327 444057094 6.280000e-83 318
46 TraesCS7A01G324300 chr1B 84.043 188 15 5 3713 3897 642609931 642609756 2.410000e-37 167
47 TraesCS7A01G324300 chr5D 80.630 413 67 9 1974 2381 320873913 320873509 1.360000e-79 307
48 TraesCS7A01G324300 chr5B 80.241 415 69 9 1974 2383 372081688 372081282 2.280000e-77 300
49 TraesCS7A01G324300 chr2B 83.077 325 40 10 3578 3897 684861155 684860841 8.240000e-72 281
50 TraesCS7A01G324300 chr6D 96.970 66 2 0 1 66 7489790 7489855 1.140000e-20 111
51 TraesCS7A01G324300 chr6D 90.909 77 6 1 462 537 2899997 2900073 6.890000e-18 102
52 TraesCS7A01G324300 chr6D 89.157 83 8 1 462 544 34399220 34399139 6.890000e-18 102
53 TraesCS7A01G324300 chr2D 94.521 73 2 2 1 71 530301036 530300964 1.140000e-20 111
54 TraesCS7A01G324300 chr2D 79.310 116 17 6 2198 2310 100432469 100432580 1.500000e-09 75


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 TraesCS7A01G324300 chr7A 471549485 471553381 3896 False 7197 7197 100.0000 1 3897 1 chr7A.!!$F3 3896
1 TraesCS7A01G324300 chr7A 68341571 68342212 641 False 717 717 87.3070 3203 3829 1 chr7A.!!$F1 626
2 TraesCS7A01G324300 chr7A 121612458 121613161 703 True 715 715 85.4570 3198 3897 1 chr7A.!!$R2 699
3 TraesCS7A01G324300 chr7D 410520905 410524239 3334 True 1449 3537 93.1120 57 3205 3 chr7D.!!$R2 3148
4 TraesCS7A01G324300 chr7B 425157566 425159987 2421 False 1625 1652 93.6935 877 3058 2 chr7B.!!$F1 2181
5 TraesCS7A01G324300 chr2A 7510152 7510792 640 False 728 728 87.6160 3203 3829 1 chr2A.!!$F1 626
6 TraesCS7A01G324300 chr3A 58844756 58845398 642 False 713 713 87.1720 3203 3829 1 chr3A.!!$F1 626
7 TraesCS7A01G324300 chr4A 7467704 7468408 704 False 704 704 84.9720 3199 3897 1 chr4A.!!$F1 698
8 TraesCS7A01G324300 chr1A 47517833 47518473 640 False 702 702 86.8830 3200 3829 1 chr1A.!!$F1 629
9 TraesCS7A01G324300 chrUn 81838392 81839034 642 True 691 691 86.5530 3203 3829 1 chrUn.!!$R1 626
10 TraesCS7A01G324300 chr5A 603796284 603796928 644 False 684 684 86.2650 3200 3829 1 chr5A.!!$F2 629
11 TraesCS7A01G324300 chr1D 102779841 102780496 655 True 564 564 82.3090 3205 3867 1 chr1D.!!$R1 662

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
738 770 0.098376 CTAGGAGTACACGCACGTCC 59.902 60.0 0.0 0.0 0.0 4.79 F
746 778 0.103572 ACACGCACGTCCTGTAAACT 59.896 50.0 0.0 0.0 0.0 2.66 F
2372 2666 0.252881 AGATCACCTCCCCAAGCTCA 60.253 55.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2372 2666 0.172803 GTCAGATGGCTTACGACGGT 59.827 55.000 0.00 0.0 0.0 4.83 R
2638 2933 3.691342 TCCGGCCTGAACTCGTGG 61.691 66.667 0.00 0.0 0.0 4.94 R
3310 4050 1.468914 GGTCAAAATCGAGACAAGGGC 59.531 52.381 5.09 0.0 36.5 5.19 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
32 33 6.537453 ACATCTAGATACATCCATACCTGC 57.463 41.667 4.54 0.00 0.00 4.85
33 34 5.126222 ACATCTAGATACATCCATACCTGCG 59.874 44.000 4.54 0.00 0.00 5.18
34 35 4.918588 TCTAGATACATCCATACCTGCGA 58.081 43.478 0.00 0.00 0.00 5.10
35 36 3.944055 AGATACATCCATACCTGCGAC 57.056 47.619 0.00 0.00 0.00 5.19
36 37 3.230976 AGATACATCCATACCTGCGACA 58.769 45.455 0.00 0.00 0.00 4.35
37 38 3.641436 AGATACATCCATACCTGCGACAA 59.359 43.478 0.00 0.00 0.00 3.18
38 39 2.315925 ACATCCATACCTGCGACAAG 57.684 50.000 0.00 0.00 0.00 3.16
39 40 1.555075 ACATCCATACCTGCGACAAGT 59.445 47.619 0.00 0.00 0.00 3.16
40 41 2.764010 ACATCCATACCTGCGACAAGTA 59.236 45.455 0.00 0.00 0.00 2.24
41 42 3.196901 ACATCCATACCTGCGACAAGTAA 59.803 43.478 0.00 0.00 0.00 2.24
42 43 4.141711 ACATCCATACCTGCGACAAGTAAT 60.142 41.667 0.00 0.00 0.00 1.89
43 44 4.481368 TCCATACCTGCGACAAGTAATT 57.519 40.909 0.00 0.00 0.00 1.40
44 45 4.439057 TCCATACCTGCGACAAGTAATTC 58.561 43.478 0.00 0.00 0.00 2.17
45 46 3.245284 CCATACCTGCGACAAGTAATTCG 59.755 47.826 0.00 0.00 38.31 3.34
46 47 2.736144 ACCTGCGACAAGTAATTCGA 57.264 45.000 0.00 0.00 37.43 3.71
47 48 3.034721 ACCTGCGACAAGTAATTCGAA 57.965 42.857 0.00 0.00 37.43 3.71
48 49 3.395639 ACCTGCGACAAGTAATTCGAAA 58.604 40.909 0.00 0.00 37.43 3.46
49 50 3.185797 ACCTGCGACAAGTAATTCGAAAC 59.814 43.478 0.00 0.00 37.43 2.78
50 51 3.395671 CTGCGACAAGTAATTCGAAACG 58.604 45.455 0.00 0.09 37.43 3.60
51 52 2.156117 TGCGACAAGTAATTCGAAACGG 59.844 45.455 0.00 0.00 37.43 4.44
52 53 2.409378 GCGACAAGTAATTCGAAACGGA 59.591 45.455 0.00 0.00 37.43 4.69
53 54 3.481467 GCGACAAGTAATTCGAAACGGAG 60.481 47.826 0.00 0.00 37.43 4.63
54 55 3.060363 CGACAAGTAATTCGAAACGGAGG 59.940 47.826 0.00 0.00 37.43 4.30
55 56 3.332034 ACAAGTAATTCGAAACGGAGGG 58.668 45.455 0.00 0.00 0.00 4.30
183 185 7.700611 GTCAAGACGTATTTAAAATTGGTCG 57.299 36.000 0.00 0.00 0.00 4.79
202 205 7.827819 TGGTCGTATTTCAAAGACTTATCAG 57.172 36.000 0.00 0.00 34.34 2.90
211 214 7.750229 TTCAAAGACTTATCAGAAGCAACAT 57.250 32.000 0.00 0.00 0.00 2.71
217 220 9.624373 AAGACTTATCAGAAGCAACATGAATAT 57.376 29.630 0.00 0.00 0.00 1.28
224 227 5.865013 CAGAAGCAACATGAATATGCAAACA 59.135 36.000 0.00 0.00 42.45 2.83
229 232 8.774890 AGCAACATGAATATGCAAACAAAATA 57.225 26.923 0.00 0.00 42.45 1.40
256 259 7.533426 AGATTGGACTTTCGATTCAAAAGATG 58.467 34.615 4.14 0.00 37.22 2.90
259 262 7.364522 TGGACTTTCGATTCAAAAGATGTAG 57.635 36.000 4.14 0.00 37.22 2.74
293 296 5.534207 TGACATGTCAAAAGGAAAAGCAT 57.466 34.783 26.02 0.00 36.53 3.79
358 361 6.072112 AGTTGTACTACCAAAAACTGCATG 57.928 37.500 3.72 0.00 30.17 4.06
359 362 5.592688 AGTTGTACTACCAAAAACTGCATGT 59.407 36.000 3.72 0.00 30.17 3.21
442 473 2.552373 GGGCGCTATAGCAAAATAGGGT 60.552 50.000 23.99 0.00 41.83 4.34
445 476 4.003648 GCGCTATAGCAAAATAGGGTCAT 58.996 43.478 23.99 0.00 41.83 3.06
505 537 8.860088 TCCAGATCTATTATCAAAGTTCATCGA 58.140 33.333 0.00 0.00 0.00 3.59
526 558 4.629065 GAAAGTACAAAGCATCTCGAACG 58.371 43.478 0.00 0.00 0.00 3.95
537 569 8.725046 CAAAGCATCTCGAACGTAATAAAAATC 58.275 33.333 0.00 0.00 0.00 2.17
553 585 8.904099 AATAAAAATCACTATTACTCCCTCCG 57.096 34.615 0.00 0.00 0.00 4.63
554 586 5.952347 AAAATCACTATTACTCCCTCCGT 57.048 39.130 0.00 0.00 0.00 4.69
555 587 5.532664 AAATCACTATTACTCCCTCCGTC 57.467 43.478 0.00 0.00 0.00 4.79
556 588 3.657398 TCACTATTACTCCCTCCGTCA 57.343 47.619 0.00 0.00 0.00 4.35
557 589 3.285484 TCACTATTACTCCCTCCGTCAC 58.715 50.000 0.00 0.00 0.00 3.67
558 590 3.021695 CACTATTACTCCCTCCGTCACA 58.978 50.000 0.00 0.00 0.00 3.58
559 591 3.066900 CACTATTACTCCCTCCGTCACAG 59.933 52.174 0.00 0.00 0.00 3.66
560 592 2.233305 ATTACTCCCTCCGTCACAGT 57.767 50.000 0.00 0.00 0.00 3.55
561 593 2.005370 TTACTCCCTCCGTCACAGTT 57.995 50.000 0.00 0.00 0.00 3.16
562 594 2.005370 TACTCCCTCCGTCACAGTTT 57.995 50.000 0.00 0.00 0.00 2.66
563 595 2.005370 ACTCCCTCCGTCACAGTTTA 57.995 50.000 0.00 0.00 0.00 2.01
564 596 1.617357 ACTCCCTCCGTCACAGTTTAC 59.383 52.381 0.00 0.00 0.00 2.01
565 597 1.616865 CTCCCTCCGTCACAGTTTACA 59.383 52.381 0.00 0.00 0.00 2.41
566 598 2.036733 CTCCCTCCGTCACAGTTTACAA 59.963 50.000 0.00 0.00 0.00 2.41
567 599 2.036733 TCCCTCCGTCACAGTTTACAAG 59.963 50.000 0.00 0.00 0.00 3.16
568 600 2.224209 CCCTCCGTCACAGTTTACAAGT 60.224 50.000 0.00 0.00 0.00 3.16
569 601 3.057734 CCTCCGTCACAGTTTACAAGTC 58.942 50.000 0.00 0.00 0.00 3.01
570 602 3.057734 CTCCGTCACAGTTTACAAGTCC 58.942 50.000 0.00 0.00 0.00 3.85
571 603 2.696707 TCCGTCACAGTTTACAAGTCCT 59.303 45.455 0.00 0.00 0.00 3.85
572 604 3.890756 TCCGTCACAGTTTACAAGTCCTA 59.109 43.478 0.00 0.00 0.00 2.94
573 605 3.985925 CCGTCACAGTTTACAAGTCCTAC 59.014 47.826 0.00 0.00 0.00 3.18
574 606 3.667261 CGTCACAGTTTACAAGTCCTACG 59.333 47.826 0.00 0.00 0.00 3.51
575 607 3.427863 GTCACAGTTTACAAGTCCTACGC 59.572 47.826 0.00 0.00 0.00 4.42
576 608 2.407361 CACAGTTTACAAGTCCTACGCG 59.593 50.000 3.53 3.53 0.00 6.01
577 609 2.035066 ACAGTTTACAAGTCCTACGCGT 59.965 45.455 19.17 19.17 0.00 6.01
578 610 3.253188 ACAGTTTACAAGTCCTACGCGTA 59.747 43.478 19.40 19.40 0.00 4.42
579 611 4.082571 ACAGTTTACAAGTCCTACGCGTAT 60.083 41.667 20.91 5.41 0.00 3.06
580 612 5.123820 ACAGTTTACAAGTCCTACGCGTATA 59.876 40.000 20.91 8.44 0.00 1.47
581 613 6.183360 ACAGTTTACAAGTCCTACGCGTATAT 60.183 38.462 20.91 3.11 0.00 0.86
582 614 6.359087 CAGTTTACAAGTCCTACGCGTATATC 59.641 42.308 20.91 12.33 0.00 1.63
583 615 6.261826 AGTTTACAAGTCCTACGCGTATATCT 59.738 38.462 20.91 14.33 0.00 1.98
584 616 7.442364 AGTTTACAAGTCCTACGCGTATATCTA 59.558 37.037 20.91 0.00 0.00 1.98
585 617 5.859521 ACAAGTCCTACGCGTATATCTAG 57.140 43.478 20.91 8.56 0.00 2.43
586 618 4.694509 ACAAGTCCTACGCGTATATCTAGG 59.305 45.833 20.91 18.03 0.00 3.02
587 619 4.550076 AGTCCTACGCGTATATCTAGGT 57.450 45.455 20.91 0.00 0.00 3.08
588 620 4.904241 AGTCCTACGCGTATATCTAGGTT 58.096 43.478 20.91 8.23 0.00 3.50
589 621 4.694509 AGTCCTACGCGTATATCTAGGTTG 59.305 45.833 20.91 3.59 0.00 3.77
590 622 4.453819 GTCCTACGCGTATATCTAGGTTGT 59.546 45.833 20.91 0.00 0.00 3.32
591 623 4.692625 TCCTACGCGTATATCTAGGTTGTC 59.307 45.833 20.91 0.00 0.00 3.18
592 624 4.453478 CCTACGCGTATATCTAGGTTGTCA 59.547 45.833 20.91 0.00 0.00 3.58
593 625 4.906065 ACGCGTATATCTAGGTTGTCAA 57.094 40.909 11.67 0.00 0.00 3.18
594 626 5.449107 ACGCGTATATCTAGGTTGTCAAT 57.551 39.130 11.67 0.00 0.00 2.57
595 627 5.839621 ACGCGTATATCTAGGTTGTCAATT 58.160 37.500 11.67 0.00 0.00 2.32
596 628 6.278363 ACGCGTATATCTAGGTTGTCAATTT 58.722 36.000 11.67 0.00 0.00 1.82
597 629 6.759827 ACGCGTATATCTAGGTTGTCAATTTT 59.240 34.615 11.67 0.00 0.00 1.82
598 630 7.922278 ACGCGTATATCTAGGTTGTCAATTTTA 59.078 33.333 11.67 0.00 0.00 1.52
599 631 8.922676 CGCGTATATCTAGGTTGTCAATTTTAT 58.077 33.333 0.00 0.00 0.00 1.40
659 691 8.558973 ACCTTCTGAAAATAGAACATCTGAAG 57.441 34.615 11.82 11.82 42.59 3.02
660 692 8.160106 ACCTTCTGAAAATAGAACATCTGAAGT 58.840 33.333 15.39 5.92 41.97 3.01
661 693 9.007901 CCTTCTGAAAATAGAACATCTGAAGTT 57.992 33.333 15.39 0.00 41.97 2.66
714 746 9.513906 TGACTTGTATTAGATTGGTCAAATTGA 57.486 29.630 0.00 0.00 30.81 2.57
715 747 9.774742 GACTTGTATTAGATTGGTCAAATTGAC 57.225 33.333 17.16 17.16 46.23 3.18
730 762 7.965045 GTCAAATTGACAATCTAGGAGTACAC 58.035 38.462 20.08 0.00 46.22 2.90
731 763 6.811665 TCAAATTGACAATCTAGGAGTACACG 59.188 38.462 0.05 0.00 0.00 4.49
732 764 3.777465 TGACAATCTAGGAGTACACGC 57.223 47.619 0.00 0.00 0.00 5.34
733 765 3.086282 TGACAATCTAGGAGTACACGCA 58.914 45.455 0.00 0.00 0.00 5.24
734 766 3.119602 TGACAATCTAGGAGTACACGCAC 60.120 47.826 0.00 0.00 0.00 5.34
735 767 2.159421 ACAATCTAGGAGTACACGCACG 60.159 50.000 0.00 0.00 0.00 5.34
736 768 1.747709 ATCTAGGAGTACACGCACGT 58.252 50.000 0.00 0.00 0.00 4.49
737 769 1.081892 TCTAGGAGTACACGCACGTC 58.918 55.000 0.00 0.00 0.00 4.34
738 770 0.098376 CTAGGAGTACACGCACGTCC 59.902 60.000 0.00 0.00 0.00 4.79
739 771 0.321919 TAGGAGTACACGCACGTCCT 60.322 55.000 5.79 5.79 40.79 3.85
740 772 1.443872 GGAGTACACGCACGTCCTG 60.444 63.158 0.00 0.00 0.00 3.86
741 773 1.285023 GAGTACACGCACGTCCTGT 59.715 57.895 0.00 0.00 0.00 4.00
742 774 0.518636 GAGTACACGCACGTCCTGTA 59.481 55.000 0.00 0.00 0.00 2.74
743 775 0.953727 AGTACACGCACGTCCTGTAA 59.046 50.000 0.00 0.00 0.00 2.41
744 776 1.337703 AGTACACGCACGTCCTGTAAA 59.662 47.619 0.00 0.00 0.00 2.01
745 777 1.453148 GTACACGCACGTCCTGTAAAC 59.547 52.381 0.00 0.00 0.00 2.01
746 778 0.103572 ACACGCACGTCCTGTAAACT 59.896 50.000 0.00 0.00 0.00 2.66
747 779 1.337703 ACACGCACGTCCTGTAAACTA 59.662 47.619 0.00 0.00 0.00 2.24
748 780 2.223782 ACACGCACGTCCTGTAAACTAA 60.224 45.455 0.00 0.00 0.00 2.24
749 781 2.407361 CACGCACGTCCTGTAAACTAAG 59.593 50.000 0.00 0.00 0.00 2.18
750 782 2.294233 ACGCACGTCCTGTAAACTAAGA 59.706 45.455 0.00 0.00 0.00 2.10
751 783 2.915463 CGCACGTCCTGTAAACTAAGAG 59.085 50.000 0.00 0.00 0.00 2.85
752 784 3.365666 CGCACGTCCTGTAAACTAAGAGA 60.366 47.826 0.00 0.00 0.00 3.10
753 785 4.167268 GCACGTCCTGTAAACTAAGAGAG 58.833 47.826 0.00 0.00 0.00 3.20
754 786 4.734917 CACGTCCTGTAAACTAAGAGAGG 58.265 47.826 0.00 0.00 0.00 3.69
755 787 3.762823 ACGTCCTGTAAACTAAGAGAGGG 59.237 47.826 0.00 0.00 0.00 4.30
756 788 3.130693 CGTCCTGTAAACTAAGAGAGGGG 59.869 52.174 0.00 0.00 0.00 4.79
757 789 3.451540 GTCCTGTAAACTAAGAGAGGGGG 59.548 52.174 0.00 0.00 0.00 5.40
792 824 5.615289 ACAGAGTGCTTTAGTTCAGACATT 58.385 37.500 0.00 0.00 0.00 2.71
793 825 5.468072 ACAGAGTGCTTTAGTTCAGACATTG 59.532 40.000 0.00 0.00 0.00 2.82
794 826 5.468072 CAGAGTGCTTTAGTTCAGACATTGT 59.532 40.000 0.00 0.00 0.00 2.71
795 827 6.646653 CAGAGTGCTTTAGTTCAGACATTGTA 59.353 38.462 0.00 0.00 0.00 2.41
796 828 6.647067 AGAGTGCTTTAGTTCAGACATTGTAC 59.353 38.462 0.00 0.00 0.00 2.90
797 829 6.288294 AGTGCTTTAGTTCAGACATTGTACA 58.712 36.000 0.00 0.00 30.17 2.90
798 830 6.425114 AGTGCTTTAGTTCAGACATTGTACAG 59.575 38.462 0.00 0.00 30.17 2.74
799 831 6.202954 GTGCTTTAGTTCAGACATTGTACAGT 59.797 38.462 0.00 0.00 30.17 3.55
800 832 6.202762 TGCTTTAGTTCAGACATTGTACAGTG 59.797 38.462 16.11 16.11 30.17 3.66
801 833 6.423905 GCTTTAGTTCAGACATTGTACAGTGA 59.576 38.462 23.54 7.46 30.17 3.41
802 834 7.118390 GCTTTAGTTCAGACATTGTACAGTGAT 59.882 37.037 23.54 9.70 30.17 3.06
803 835 8.902540 TTTAGTTCAGACATTGTACAGTGATT 57.097 30.769 23.54 9.04 30.17 2.57
804 836 8.902540 TTAGTTCAGACATTGTACAGTGATTT 57.097 30.769 23.54 2.57 30.17 2.17
805 837 9.990360 TTAGTTCAGACATTGTACAGTGATTTA 57.010 29.630 23.54 5.04 30.17 1.40
807 839 9.507329 AGTTCAGACATTGTACAGTGATTTATT 57.493 29.630 23.54 1.09 30.17 1.40
811 843 9.708222 CAGACATTGTACAGTGATTTATTTAGC 57.292 33.333 23.54 1.88 0.00 3.09
812 844 9.672673 AGACATTGTACAGTGATTTATTTAGCT 57.327 29.630 23.54 0.00 0.00 3.32
821 853 8.616076 ACAGTGATTTATTTAGCTAGACATTGC 58.384 33.333 0.00 0.00 0.00 3.56
822 854 8.834465 CAGTGATTTATTTAGCTAGACATTGCT 58.166 33.333 0.00 0.00 42.67 3.91
823 855 9.401058 AGTGATTTATTTAGCTAGACATTGCTT 57.599 29.630 0.00 0.00 40.35 3.91
837 869 6.475207 AGACATTGCTTAAAACGCTATAACG 58.525 36.000 0.00 0.00 39.50 3.18
858 890 9.909644 ATAACGTTCTATTAGTGGTGCTATAAG 57.090 33.333 2.82 0.00 0.00 1.73
1008 1041 4.022329 CAGTTCCTGTCCAAAATGTTACCC 60.022 45.833 0.00 0.00 0.00 3.69
1303 1336 3.275999 GAGTGGGCCACGTATGTTAATT 58.724 45.455 29.76 9.29 39.64 1.40
1601 1634 2.347490 GCCGACAAGCTCAAGGGA 59.653 61.111 0.00 0.00 0.00 4.20
1778 1811 1.986575 GCAAGCGCATCTTCCACCTC 61.987 60.000 11.47 0.00 38.36 3.85
1909 1943 9.774742 CAGTTTTGAAAATATCTAGTAAGTGCC 57.225 33.333 0.00 0.00 0.00 5.01
1924 1959 3.004752 AGTGCCTTTCATGGTGATACC 57.995 47.619 0.00 0.00 39.22 2.73
1959 1994 7.458409 TCTCTGTCGTGGTTTAAAGTAGTAT 57.542 36.000 0.00 0.00 0.00 2.12
1960 1995 8.565896 TCTCTGTCGTGGTTTAAAGTAGTATA 57.434 34.615 0.00 0.00 0.00 1.47
1996 2290 3.694566 GGTATTTCCCAAGCAAGTACAGG 59.305 47.826 0.00 0.00 0.00 4.00
2035 2329 3.334054 GGGGAGCTGGAGCAGGTT 61.334 66.667 0.00 0.00 42.53 3.50
2191 2485 2.279517 GAGCTGGGGTACGATGCG 60.280 66.667 0.00 0.00 0.00 4.73
2304 2598 4.087892 CCCCGAGTGGCAGGACAG 62.088 72.222 0.00 0.00 0.00 3.51
2372 2666 0.252881 AGATCACCTCCCCAAGCTCA 60.253 55.000 0.00 0.00 0.00 4.26
2449 2744 4.804608 TGTCAATGTTTAACACGTGGAG 57.195 40.909 21.57 0.00 0.00 3.86
2450 2745 4.193090 TGTCAATGTTTAACACGTGGAGT 58.807 39.130 21.57 7.20 0.00 3.85
2614 2909 2.591753 CTGGCCATCCACCACGAT 59.408 61.111 5.51 0.00 37.47 3.73
2615 2910 1.829456 CTGGCCATCCACCACGATA 59.171 57.895 5.51 0.00 37.47 2.92
2762 3057 2.043652 CCATGGTGGAGGCCAAGG 60.044 66.667 5.01 0.00 40.96 3.61
2911 3214 2.044555 GTAGGCCGGCTTGGGTTTC 61.045 63.158 28.56 6.68 38.63 2.78
2938 3241 3.469629 CGTACTCGCAATTTTGAGTGTG 58.530 45.455 16.13 7.35 44.74 3.82
2940 3243 3.338818 ACTCGCAATTTTGAGTGTGTG 57.661 42.857 8.23 0.00 43.52 3.82
2941 3244 2.682856 ACTCGCAATTTTGAGTGTGTGT 59.317 40.909 8.23 0.00 43.52 3.72
2942 3245 3.038017 CTCGCAATTTTGAGTGTGTGTG 58.962 45.455 0.00 0.00 0.00 3.82
2943 3246 2.421775 TCGCAATTTTGAGTGTGTGTGT 59.578 40.909 0.00 0.00 0.00 3.72
2944 3247 3.119673 TCGCAATTTTGAGTGTGTGTGTT 60.120 39.130 0.00 0.00 0.00 3.32
2945 3248 3.611986 CGCAATTTTGAGTGTGTGTGTTT 59.388 39.130 0.00 0.00 0.00 2.83
3005 3308 2.602878 TGTGCTTCGATTCGGAACTAC 58.397 47.619 6.18 0.00 0.00 2.73
3009 3312 3.441222 TGCTTCGATTCGGAACTACAGTA 59.559 43.478 6.18 0.00 0.00 2.74
3071 3790 1.293963 GGTGGGACGGACGTTAAAGC 61.294 60.000 0.00 0.00 0.00 3.51
3072 3791 0.320160 GTGGGACGGACGTTAAAGCT 60.320 55.000 0.00 0.00 0.00 3.74
3073 3792 1.067635 GTGGGACGGACGTTAAAGCTA 60.068 52.381 0.00 0.00 0.00 3.32
3075 3794 2.036992 TGGGACGGACGTTAAAGCTAAA 59.963 45.455 0.00 0.00 0.00 1.85
3077 3796 3.686241 GGGACGGACGTTAAAGCTAAAAT 59.314 43.478 0.00 0.00 0.00 1.82
3078 3797 4.869861 GGGACGGACGTTAAAGCTAAAATA 59.130 41.667 0.00 0.00 0.00 1.40
3079 3798 5.220472 GGGACGGACGTTAAAGCTAAAATAC 60.220 44.000 0.00 0.00 0.00 1.89
3080 3799 5.578336 GGACGGACGTTAAAGCTAAAATACT 59.422 40.000 0.00 0.00 0.00 2.12
3081 3800 6.399204 ACGGACGTTAAAGCTAAAATACTG 57.601 37.500 0.00 0.00 0.00 2.74
3258 3997 7.093333 GGTGAAATTTAGATTTGGTCCCTCAAT 60.093 37.037 0.00 0.00 35.65 2.57
3274 4013 3.258123 CCTCAATTCCAAAACCGGACAAT 59.742 43.478 9.46 0.00 33.75 2.71
3304 4044 3.057806 CCCAACTAATGAAACCGGACAAC 60.058 47.826 9.46 0.00 0.00 3.32
3315 4055 2.281276 GGACAACGTTCGGCCCTT 60.281 61.111 10.51 0.00 0.00 3.95
3391 4131 6.521821 GCTGACTCAAATTCGCGTAATTTTTA 59.478 34.615 19.59 13.12 43.75 1.52
3506 4252 9.710900 ACCTTTTTCAAATCCATGAACTATTTC 57.289 29.630 0.00 0.00 38.95 2.17
3611 4392 9.019764 GTTCGTGTAATTTTATCAAATCCATGG 57.980 33.333 4.97 4.97 30.80 3.66
3630 4430 5.276773 CCATGGTGTTTTTGAAATTCACGTG 60.277 40.000 9.94 9.94 0.00 4.49
3643 4443 6.312426 TGAAATTCACGTGCTTGTTTCAAATT 59.688 30.769 22.79 13.93 33.97 1.82
3645 4445 7.763172 AATTCACGTGCTTGTTTCAAATTTA 57.237 28.000 11.67 0.00 0.00 1.40
3705 4506 5.365025 TGTGTTCCTTTTCCAATCCATGAAA 59.635 36.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 8.700051 GCAGGTATGGATGTATCTAGATGTATT 58.300 37.037 15.79 0.00 0.00 1.89
7 8 7.013750 CGCAGGTATGGATGTATCTAGATGTAT 59.986 40.741 15.79 9.11 0.00 2.29
8 9 6.318900 CGCAGGTATGGATGTATCTAGATGTA 59.681 42.308 15.79 4.44 0.00 2.29
9 10 5.126222 CGCAGGTATGGATGTATCTAGATGT 59.874 44.000 15.79 1.25 0.00 3.06
10 11 5.358160 TCGCAGGTATGGATGTATCTAGATG 59.642 44.000 15.79 0.00 0.00 2.90
11 12 5.358442 GTCGCAGGTATGGATGTATCTAGAT 59.642 44.000 10.73 10.73 0.00 1.98
12 13 4.700692 GTCGCAGGTATGGATGTATCTAGA 59.299 45.833 0.00 0.00 0.00 2.43
13 14 4.459337 TGTCGCAGGTATGGATGTATCTAG 59.541 45.833 0.00 0.00 0.00 2.43
14 15 4.403734 TGTCGCAGGTATGGATGTATCTA 58.596 43.478 0.00 0.00 0.00 1.98
15 16 3.230976 TGTCGCAGGTATGGATGTATCT 58.769 45.455 0.00 0.00 0.00 1.98
16 17 3.660501 TGTCGCAGGTATGGATGTATC 57.339 47.619 0.00 0.00 0.00 2.24
17 18 3.388024 ACTTGTCGCAGGTATGGATGTAT 59.612 43.478 0.00 0.00 0.00 2.29
18 19 2.764010 ACTTGTCGCAGGTATGGATGTA 59.236 45.455 0.00 0.00 0.00 2.29
19 20 1.555075 ACTTGTCGCAGGTATGGATGT 59.445 47.619 0.00 0.00 0.00 3.06
20 21 2.315925 ACTTGTCGCAGGTATGGATG 57.684 50.000 0.00 0.00 0.00 3.51
21 22 4.689612 ATTACTTGTCGCAGGTATGGAT 57.310 40.909 3.46 0.00 0.00 3.41
22 23 4.439057 GAATTACTTGTCGCAGGTATGGA 58.561 43.478 3.46 0.00 0.00 3.41
23 24 3.245284 CGAATTACTTGTCGCAGGTATGG 59.755 47.826 3.46 0.00 0.00 2.74
24 25 4.109766 TCGAATTACTTGTCGCAGGTATG 58.890 43.478 3.46 0.00 37.19 2.39
25 26 4.380841 TCGAATTACTTGTCGCAGGTAT 57.619 40.909 3.46 0.00 37.19 2.73
26 27 3.853831 TCGAATTACTTGTCGCAGGTA 57.146 42.857 0.00 0.00 37.19 3.08
27 28 2.736144 TCGAATTACTTGTCGCAGGT 57.264 45.000 0.00 0.91 37.19 4.00
28 29 3.720920 CGTTTCGAATTACTTGTCGCAGG 60.721 47.826 0.00 0.00 37.19 4.85
29 30 3.395671 CGTTTCGAATTACTTGTCGCAG 58.604 45.455 0.00 0.00 37.19 5.18
30 31 2.156117 CCGTTTCGAATTACTTGTCGCA 59.844 45.455 0.00 0.00 37.19 5.10
31 32 2.409378 TCCGTTTCGAATTACTTGTCGC 59.591 45.455 0.00 0.00 37.19 5.19
32 33 3.060363 CCTCCGTTTCGAATTACTTGTCG 59.940 47.826 0.00 0.00 38.62 4.35
33 34 3.370061 CCCTCCGTTTCGAATTACTTGTC 59.630 47.826 0.00 0.00 0.00 3.18
34 35 3.007182 TCCCTCCGTTTCGAATTACTTGT 59.993 43.478 0.00 0.00 0.00 3.16
35 36 3.592059 TCCCTCCGTTTCGAATTACTTG 58.408 45.455 0.00 0.00 0.00 3.16
36 37 3.260128 ACTCCCTCCGTTTCGAATTACTT 59.740 43.478 0.00 0.00 0.00 2.24
37 38 2.830321 ACTCCCTCCGTTTCGAATTACT 59.170 45.455 0.00 0.00 0.00 2.24
38 39 3.242549 ACTCCCTCCGTTTCGAATTAC 57.757 47.619 0.00 0.00 0.00 1.89
39 40 3.181483 GCTACTCCCTCCGTTTCGAATTA 60.181 47.826 0.00 0.00 0.00 1.40
40 41 2.418334 GCTACTCCCTCCGTTTCGAATT 60.418 50.000 0.00 0.00 0.00 2.17
41 42 1.136500 GCTACTCCCTCCGTTTCGAAT 59.864 52.381 0.00 0.00 0.00 3.34
42 43 0.529378 GCTACTCCCTCCGTTTCGAA 59.471 55.000 0.00 0.00 0.00 3.71
43 44 0.323178 AGCTACTCCCTCCGTTTCGA 60.323 55.000 0.00 0.00 0.00 3.71
44 45 0.531200 AAGCTACTCCCTCCGTTTCG 59.469 55.000 0.00 0.00 0.00 3.46
45 46 2.742589 CAAAAGCTACTCCCTCCGTTTC 59.257 50.000 0.00 0.00 0.00 2.78
46 47 2.370849 TCAAAAGCTACTCCCTCCGTTT 59.629 45.455 0.00 0.00 0.00 3.60
47 48 1.975680 TCAAAAGCTACTCCCTCCGTT 59.024 47.619 0.00 0.00 0.00 4.44
48 49 1.640917 TCAAAAGCTACTCCCTCCGT 58.359 50.000 0.00 0.00 0.00 4.69
49 50 2.990066 ATCAAAAGCTACTCCCTCCG 57.010 50.000 0.00 0.00 0.00 4.63
50 51 5.990668 TCTAAATCAAAAGCTACTCCCTCC 58.009 41.667 0.00 0.00 0.00 4.30
51 52 7.275920 TGATCTAAATCAAAAGCTACTCCCTC 58.724 38.462 0.00 0.00 38.97 4.30
52 53 7.200434 TGATCTAAATCAAAAGCTACTCCCT 57.800 36.000 0.00 0.00 38.97 4.20
53 54 8.457238 AATGATCTAAATCAAAAGCTACTCCC 57.543 34.615 0.00 0.00 44.85 4.30
103 105 5.906113 TGCGGCAGGAATTTAAAGATTAA 57.094 34.783 0.00 0.00 0.00 1.40
183 185 9.548208 GTTGCTTCTGATAAGTCTTTGAAATAC 57.452 33.333 0.00 0.00 0.00 1.89
202 205 6.709145 TTGTTTGCATATTCATGTTGCTTC 57.291 33.333 11.72 5.53 37.28 3.86
217 220 9.638239 GAAAGTCCAATCTATATTTTGTTTGCA 57.362 29.630 0.00 0.00 0.00 4.08
229 232 8.792830 TCTTTTGAATCGAAAGTCCAATCTAT 57.207 30.769 19.27 0.00 36.52 1.98
293 296 1.281199 CCCACCCATCCCATCTCACA 61.281 60.000 0.00 0.00 0.00 3.58
325 328 5.223449 TGGTAGTACAACTTTTGGGAGAG 57.777 43.478 2.06 0.00 34.12 3.20
358 361 9.261180 TGTGATTAGAGCTTAATTAGTGCATAC 57.739 33.333 12.82 6.08 0.00 2.39
359 362 9.830975 TTGTGATTAGAGCTTAATTAGTGCATA 57.169 29.630 12.82 5.08 0.00 3.14
417 448 5.186198 CCTATTTTGCTATAGCGCCCTATT 58.814 41.667 19.55 3.82 45.83 1.73
422 453 2.742589 GACCCTATTTTGCTATAGCGCC 59.257 50.000 19.55 0.00 45.83 6.53
500 532 4.562789 TCGAGATGCTTTGTACTTTCGATG 59.437 41.667 0.00 0.00 31.74 3.84
505 537 4.056050 ACGTTCGAGATGCTTTGTACTTT 58.944 39.130 0.00 0.00 0.00 2.66
508 540 5.697848 ATTACGTTCGAGATGCTTTGTAC 57.302 39.130 0.00 0.00 0.00 2.90
515 547 7.399523 AGTGATTTTTATTACGTTCGAGATGC 58.600 34.615 0.00 0.00 0.00 3.91
537 569 3.021695 TGTGACGGAGGGAGTAATAGTG 58.978 50.000 0.00 0.00 0.00 2.74
543 575 2.005370 AAACTGTGACGGAGGGAGTA 57.995 50.000 0.00 0.00 0.00 2.59
544 576 1.617357 GTAAACTGTGACGGAGGGAGT 59.383 52.381 0.00 0.00 0.00 3.85
545 577 1.616865 TGTAAACTGTGACGGAGGGAG 59.383 52.381 0.00 0.00 0.00 4.30
546 578 1.707106 TGTAAACTGTGACGGAGGGA 58.293 50.000 0.00 0.00 0.00 4.20
547 579 2.224209 ACTTGTAAACTGTGACGGAGGG 60.224 50.000 0.00 0.00 0.00 4.30
548 580 3.057734 GACTTGTAAACTGTGACGGAGG 58.942 50.000 0.00 0.00 0.00 4.30
549 581 3.057734 GGACTTGTAAACTGTGACGGAG 58.942 50.000 0.00 0.00 0.00 4.63
550 582 2.696707 AGGACTTGTAAACTGTGACGGA 59.303 45.455 0.00 0.00 0.00 4.69
551 583 3.107642 AGGACTTGTAAACTGTGACGG 57.892 47.619 0.00 0.00 0.00 4.79
552 584 3.667261 CGTAGGACTTGTAAACTGTGACG 59.333 47.826 0.00 0.00 0.00 4.35
553 585 3.427863 GCGTAGGACTTGTAAACTGTGAC 59.572 47.826 0.00 0.00 0.00 3.67
554 586 3.645884 GCGTAGGACTTGTAAACTGTGA 58.354 45.455 0.00 0.00 0.00 3.58
555 587 2.407361 CGCGTAGGACTTGTAAACTGTG 59.593 50.000 0.00 0.00 0.00 3.66
556 588 2.035066 ACGCGTAGGACTTGTAAACTGT 59.965 45.455 11.67 0.00 0.00 3.55
557 589 2.669364 ACGCGTAGGACTTGTAAACTG 58.331 47.619 11.67 0.00 0.00 3.16
558 590 4.708726 ATACGCGTAGGACTTGTAAACT 57.291 40.909 24.78 0.00 0.00 2.66
559 591 6.433766 AGATATACGCGTAGGACTTGTAAAC 58.566 40.000 24.78 8.64 0.00 2.01
560 592 6.624352 AGATATACGCGTAGGACTTGTAAA 57.376 37.500 24.78 0.00 0.00 2.01
561 593 6.369890 CCTAGATATACGCGTAGGACTTGTAA 59.630 42.308 24.78 0.00 34.99 2.41
562 594 5.871524 CCTAGATATACGCGTAGGACTTGTA 59.128 44.000 24.78 10.35 34.99 2.41
563 595 4.694509 CCTAGATATACGCGTAGGACTTGT 59.305 45.833 24.78 8.30 34.99 3.16
564 596 4.694509 ACCTAGATATACGCGTAGGACTTG 59.305 45.833 25.95 20.57 36.34 3.16
565 597 4.904241 ACCTAGATATACGCGTAGGACTT 58.096 43.478 25.95 11.92 36.34 3.01
566 598 4.550076 ACCTAGATATACGCGTAGGACT 57.450 45.455 25.95 22.48 36.34 3.85
567 599 4.453819 ACAACCTAGATATACGCGTAGGAC 59.546 45.833 25.95 17.64 36.34 3.85
568 600 4.645535 ACAACCTAGATATACGCGTAGGA 58.354 43.478 25.95 16.64 36.34 2.94
569 601 4.453478 TGACAACCTAGATATACGCGTAGG 59.547 45.833 24.78 21.85 38.45 3.18
570 602 5.602458 TGACAACCTAGATATACGCGTAG 57.398 43.478 24.78 11.28 0.00 3.51
571 603 6.564709 ATTGACAACCTAGATATACGCGTA 57.435 37.500 22.94 22.94 0.00 4.42
572 604 4.906065 TTGACAACCTAGATATACGCGT 57.094 40.909 19.17 19.17 0.00 6.01
573 605 6.764877 AAATTGACAACCTAGATATACGCG 57.235 37.500 3.53 3.53 0.00 6.01
633 665 9.658799 CTTCAGATGTTCTATTTTCAGAAGGTA 57.341 33.333 0.00 0.00 35.25 3.08
634 666 8.160106 ACTTCAGATGTTCTATTTTCAGAAGGT 58.840 33.333 0.00 0.00 36.56 3.50
635 667 8.558973 ACTTCAGATGTTCTATTTTCAGAAGG 57.441 34.615 0.00 0.00 36.56 3.46
688 720 9.513906 TCAATTTGACCAATCTAATACAAGTCA 57.486 29.630 0.00 0.00 31.15 3.41
689 721 9.774742 GTCAATTTGACCAATCTAATACAAGTC 57.225 33.333 17.07 0.00 41.37 3.01
690 722 9.295825 TGTCAATTTGACCAATCTAATACAAGT 57.704 29.630 23.22 0.00 46.40 3.16
697 729 9.177608 CCTAGATTGTCAATTTGACCAATCTAA 57.822 33.333 31.76 24.56 46.40 2.10
698 730 8.548025 TCCTAGATTGTCAATTTGACCAATCTA 58.452 33.333 31.17 31.17 46.40 1.98
699 731 7.405292 TCCTAGATTGTCAATTTGACCAATCT 58.595 34.615 31.76 31.76 46.40 2.40
700 732 7.337942 ACTCCTAGATTGTCAATTTGACCAATC 59.662 37.037 26.50 26.50 46.40 2.67
701 733 7.177878 ACTCCTAGATTGTCAATTTGACCAAT 58.822 34.615 23.22 20.57 46.40 3.16
702 734 6.542821 ACTCCTAGATTGTCAATTTGACCAA 58.457 36.000 23.22 17.62 46.40 3.67
703 735 6.126863 ACTCCTAGATTGTCAATTTGACCA 57.873 37.500 23.22 15.04 46.40 4.02
704 736 7.064728 GTGTACTCCTAGATTGTCAATTTGACC 59.935 40.741 23.22 10.69 46.40 4.02
706 738 6.811665 CGTGTACTCCTAGATTGTCAATTTGA 59.188 38.462 0.00 0.00 0.00 2.69
707 739 6.455646 GCGTGTACTCCTAGATTGTCAATTTG 60.456 42.308 0.00 0.00 0.00 2.32
708 740 5.581085 GCGTGTACTCCTAGATTGTCAATTT 59.419 40.000 0.00 0.00 0.00 1.82
709 741 5.109903 GCGTGTACTCCTAGATTGTCAATT 58.890 41.667 0.00 0.00 0.00 2.32
710 742 4.159693 TGCGTGTACTCCTAGATTGTCAAT 59.840 41.667 0.00 0.00 0.00 2.57
711 743 3.508402 TGCGTGTACTCCTAGATTGTCAA 59.492 43.478 0.00 0.00 0.00 3.18
712 744 3.086282 TGCGTGTACTCCTAGATTGTCA 58.914 45.455 0.00 0.00 0.00 3.58
713 745 3.436496 GTGCGTGTACTCCTAGATTGTC 58.564 50.000 0.00 0.00 0.00 3.18
714 746 2.159421 CGTGCGTGTACTCCTAGATTGT 60.159 50.000 0.00 0.00 0.00 2.71
715 747 2.159421 ACGTGCGTGTACTCCTAGATTG 60.159 50.000 0.00 0.00 0.00 2.67
716 748 2.089980 ACGTGCGTGTACTCCTAGATT 58.910 47.619 0.00 0.00 0.00 2.40
717 749 1.669779 GACGTGCGTGTACTCCTAGAT 59.330 52.381 0.67 0.00 0.00 1.98
718 750 1.081892 GACGTGCGTGTACTCCTAGA 58.918 55.000 0.67 0.00 0.00 2.43
719 751 0.098376 GGACGTGCGTGTACTCCTAG 59.902 60.000 0.67 0.00 0.00 3.02
720 752 0.321919 AGGACGTGCGTGTACTCCTA 60.322 55.000 0.67 0.00 31.12 2.94
721 753 1.602888 AGGACGTGCGTGTACTCCT 60.603 57.895 0.67 0.00 0.00 3.69
722 754 1.443872 CAGGACGTGCGTGTACTCC 60.444 63.158 0.67 0.00 27.68 3.85
723 755 0.518636 TACAGGACGTGCGTGTACTC 59.481 55.000 13.01 0.00 43.29 2.59
724 756 0.953727 TTACAGGACGTGCGTGTACT 59.046 50.000 15.20 0.00 44.78 2.73
725 757 1.453148 GTTTACAGGACGTGCGTGTAC 59.547 52.381 15.20 7.46 44.78 2.90
726 758 1.337703 AGTTTACAGGACGTGCGTGTA 59.662 47.619 13.01 12.87 43.29 2.90
727 759 0.103572 AGTTTACAGGACGTGCGTGT 59.896 50.000 14.33 14.33 46.45 4.49
728 760 2.054687 TAGTTTACAGGACGTGCGTG 57.945 50.000 13.01 9.22 38.32 5.34
729 761 2.294233 TCTTAGTTTACAGGACGTGCGT 59.706 45.455 0.00 5.61 0.00 5.24
730 762 2.915463 CTCTTAGTTTACAGGACGTGCG 59.085 50.000 0.00 0.00 0.00 5.34
731 763 4.167268 CTCTCTTAGTTTACAGGACGTGC 58.833 47.826 0.00 0.00 0.00 5.34
732 764 4.380655 CCCTCTCTTAGTTTACAGGACGTG 60.381 50.000 0.00 0.00 0.00 4.49
733 765 3.762823 CCCTCTCTTAGTTTACAGGACGT 59.237 47.826 0.00 0.00 0.00 4.34
734 766 3.130693 CCCCTCTCTTAGTTTACAGGACG 59.869 52.174 0.00 0.00 0.00 4.79
735 767 3.451540 CCCCCTCTCTTAGTTTACAGGAC 59.548 52.174 0.00 0.00 0.00 3.85
736 768 3.721021 CCCCCTCTCTTAGTTTACAGGA 58.279 50.000 0.00 0.00 0.00 3.86
755 787 1.838077 ACTCTGTAACATGCTACCCCC 59.162 52.381 3.88 0.00 0.00 5.40
756 788 2.906354 CACTCTGTAACATGCTACCCC 58.094 52.381 3.88 0.00 0.00 4.95
757 789 2.093447 AGCACTCTGTAACATGCTACCC 60.093 50.000 3.88 0.00 46.36 3.69
758 790 3.252974 AGCACTCTGTAACATGCTACC 57.747 47.619 3.88 0.00 46.36 3.18
770 802 5.468072 ACAATGTCTGAACTAAAGCACTCTG 59.532 40.000 0.00 0.00 0.00 3.35
795 827 8.616076 GCAATGTCTAGCTAAATAAATCACTGT 58.384 33.333 0.00 0.00 0.00 3.55
796 828 8.834465 AGCAATGTCTAGCTAAATAAATCACTG 58.166 33.333 0.00 0.00 39.78 3.66
797 829 8.970859 AGCAATGTCTAGCTAAATAAATCACT 57.029 30.769 0.00 0.00 39.78 3.41
803 835 9.982291 CGTTTTAAGCAATGTCTAGCTAAATAA 57.018 29.630 0.00 0.00 40.90 1.40
804 836 8.120465 GCGTTTTAAGCAATGTCTAGCTAAATA 58.880 33.333 0.00 0.00 40.90 1.40
805 837 6.967199 GCGTTTTAAGCAATGTCTAGCTAAAT 59.033 34.615 0.00 0.00 40.90 1.40
806 838 6.148811 AGCGTTTTAAGCAATGTCTAGCTAAA 59.851 34.615 0.00 0.00 40.90 1.85
807 839 5.642063 AGCGTTTTAAGCAATGTCTAGCTAA 59.358 36.000 0.00 0.00 40.90 3.09
808 840 5.175859 AGCGTTTTAAGCAATGTCTAGCTA 58.824 37.500 0.00 0.00 40.90 3.32
809 841 4.003648 AGCGTTTTAAGCAATGTCTAGCT 58.996 39.130 0.00 0.00 44.31 3.32
810 842 4.342352 AGCGTTTTAAGCAATGTCTAGC 57.658 40.909 0.00 0.00 37.01 3.42
811 843 7.787935 CGTTATAGCGTTTTAAGCAATGTCTAG 59.212 37.037 0.19 0.00 37.01 2.43
812 844 7.276218 ACGTTATAGCGTTTTAAGCAATGTCTA 59.724 33.333 8.97 0.00 43.04 2.59
813 845 6.091713 ACGTTATAGCGTTTTAAGCAATGTCT 59.908 34.615 8.97 0.00 43.04 3.41
814 846 6.245724 ACGTTATAGCGTTTTAAGCAATGTC 58.754 36.000 8.97 0.00 43.04 3.06
815 847 6.173191 ACGTTATAGCGTTTTAAGCAATGT 57.827 33.333 8.97 0.00 43.04 2.71
837 869 6.522054 TGCCTTATAGCACCACTAATAGAAC 58.478 40.000 0.00 0.00 38.00 3.01
873 905 2.425143 TGATTGGGCCAAGATCACTC 57.575 50.000 25.16 15.93 0.00 3.51
911 943 7.413000 CGTGCCTATATATAAACACAATGGAGC 60.413 40.741 18.13 0.00 0.00 4.70
1008 1041 1.941294 ACGAGCACTAGGACTATGACG 59.059 52.381 0.00 0.00 0.00 4.35
1601 1634 3.256960 ACCATGTGCCCGACCCTT 61.257 61.111 0.00 0.00 0.00 3.95
1682 1715 4.471908 ATGTGCGCGCCCATCTCA 62.472 61.111 30.77 17.22 0.00 3.27
1778 1811 2.960659 CGCTGCAGCTCCTCGATG 60.961 66.667 34.22 14.00 39.32 3.84
1899 1933 6.631766 GGTATCACCATGAAAGGCACTTACTA 60.632 42.308 0.00 0.00 43.52 1.82
1900 1934 5.861778 GGTATCACCATGAAAGGCACTTACT 60.862 44.000 0.00 0.00 43.52 2.24
1901 1935 4.335594 GGTATCACCATGAAAGGCACTTAC 59.664 45.833 0.00 0.00 43.52 2.34
1909 1943 3.003689 GGAATGCGGTATCACCATGAAAG 59.996 47.826 0.00 0.00 38.47 2.62
1924 1959 2.069273 ACGACAGAGAAAAGGAATGCG 58.931 47.619 0.00 0.00 0.00 4.73
1981 2275 1.902508 TCTCTCCTGTACTTGCTTGGG 59.097 52.381 0.00 0.00 0.00 4.12
1984 2278 4.348486 TCATCTCTCTCCTGTACTTGCTT 58.652 43.478 0.00 0.00 0.00 3.91
1996 2290 2.926838 GTTCAGCCGTTTCATCTCTCTC 59.073 50.000 0.00 0.00 0.00 3.20
2035 2329 1.107114 GCTGGATCGACTCCTTGAGA 58.893 55.000 12.97 0.00 45.21 3.27
2191 2485 1.585668 CACTCGTCAATGATCGTCTGC 59.414 52.381 5.47 0.00 0.00 4.26
2290 2584 4.767255 GCCCTGTCCTGCCACTCG 62.767 72.222 0.00 0.00 0.00 4.18
2372 2666 0.172803 GTCAGATGGCTTACGACGGT 59.827 55.000 0.00 0.00 0.00 4.83
2630 2925 4.353437 GAACTCGTGGGCGTCCGT 62.353 66.667 0.00 0.00 39.49 4.69
2638 2933 3.691342 TCCGGCCTGAACTCGTGG 61.691 66.667 0.00 0.00 0.00 4.94
2762 3057 3.807538 CAGCATGGCCAGCACGAC 61.808 66.667 23.46 5.81 0.00 4.34
2892 3187 3.912745 AAACCCAAGCCGGCCTACG 62.913 63.158 26.15 11.50 43.80 3.51
2966 3269 5.988561 AGCACAAAAACTCTCTCTACTCAAG 59.011 40.000 0.00 0.00 0.00 3.02
2967 3270 5.918608 AGCACAAAAACTCTCTCTACTCAA 58.081 37.500 0.00 0.00 0.00 3.02
2968 3271 5.537300 AGCACAAAAACTCTCTCTACTCA 57.463 39.130 0.00 0.00 0.00 3.41
2969 3272 5.117897 CGAAGCACAAAAACTCTCTCTACTC 59.882 44.000 0.00 0.00 0.00 2.59
2970 3273 4.985409 CGAAGCACAAAAACTCTCTCTACT 59.015 41.667 0.00 0.00 0.00 2.57
2971 3274 4.982916 TCGAAGCACAAAAACTCTCTCTAC 59.017 41.667 0.00 0.00 0.00 2.59
3009 3312 3.181461 GCCACTGCCTTCATAGACAGTAT 60.181 47.826 0.00 0.00 41.28 2.12
3058 3777 5.928264 ACAGTATTTTAGCTTTAACGTCCGT 59.072 36.000 0.00 0.00 0.00 4.69
3075 3794 9.758651 TTGTTAATGCGTATGATCTACAGTATT 57.241 29.630 0.00 5.46 0.00 1.89
3078 3797 9.193133 GTATTGTTAATGCGTATGATCTACAGT 57.807 33.333 0.00 0.00 0.00 3.55
3079 3798 9.191995 TGTATTGTTAATGCGTATGATCTACAG 57.808 33.333 0.00 0.00 0.00 2.74
3080 3799 8.974408 GTGTATTGTTAATGCGTATGATCTACA 58.026 33.333 0.00 0.00 0.00 2.74
3081 3800 8.974408 TGTGTATTGTTAATGCGTATGATCTAC 58.026 33.333 0.00 0.00 0.00 2.59
3201 3940 8.508875 GTTGAGGGACGAAAAATATACTTTTCA 58.491 33.333 16.98 0.00 42.82 2.69
3258 3997 2.168521 TGCAAATTGTCCGGTTTTGGAA 59.831 40.909 17.23 0.22 40.44 3.53
3274 4013 2.685106 TCATTAGTTGGGGGTGCAAA 57.315 45.000 0.00 0.00 0.00 3.68
3304 4044 2.558554 ATCGAGACAAGGGCCGAACG 62.559 60.000 0.00 0.00 34.59 3.95
3310 4050 1.468914 GGTCAAAATCGAGACAAGGGC 59.531 52.381 5.09 0.00 36.50 5.19
3315 4055 2.536761 AACCGGTCAAAATCGAGACA 57.463 45.000 8.04 0.00 36.50 3.41
3427 4167 7.092716 CCTTGAAAAACCTATGTGGATTTGAG 58.907 38.462 0.00 0.00 39.48 3.02
3611 4392 5.164002 ACAAGCACGTGAATTTCAAAAACAC 60.164 36.000 22.23 0.00 0.00 3.32
3678 4478 5.017294 TGGATTGGAAAAGGAACACAAAC 57.983 39.130 0.00 0.00 0.00 2.93
3680 4480 4.898265 TCATGGATTGGAAAAGGAACACAA 59.102 37.500 0.00 0.00 0.00 3.33
3686 4486 7.077050 ACAAATTTCATGGATTGGAAAAGGA 57.923 32.000 0.00 0.00 36.67 3.36
3687 4487 7.748691 AACAAATTTCATGGATTGGAAAAGG 57.251 32.000 0.00 0.00 36.67 3.11


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

AutoCloner maintained by Alex Coulton.