Multiple sequence alignment - TraesCS1A01G005100

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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 TraesCS1A01G005100 chr1A 100.000 4219 0 0 1 4219 2982121 2977903 0.000000e+00 7792.0
1 TraesCS1A01G005100 chr1A 90.916 2543 147 35 1687 4219 3448358 3450826 0.000000e+00 3339.0
2 TraesCS1A01G005100 chr1A 91.221 729 48 8 3494 4219 3676822 3677537 0.000000e+00 977.0
3 TraesCS1A01G005100 chr1A 83.311 749 98 17 1773 2509 27218556 27217823 0.000000e+00 665.0
4 TraesCS1A01G005100 chr1A 91.848 368 24 5 1882 2248 2988313 2987951 3.760000e-140 508.0
5 TraesCS1A01G005100 chr1A 82.552 533 63 13 2928 3458 3676321 3676825 3.870000e-120 442.0
6 TraesCS1A01G005100 chr1A 89.344 366 18 8 1676 2041 3469505 3469849 1.390000e-119 440.0
7 TraesCS1A01G005100 chr1A 83.924 423 48 12 2383 2796 3675810 3676221 1.840000e-103 387.0
8 TraesCS1A01G005100 chr1A 80.899 356 47 14 3537 3876 3487657 3488007 1.160000e-65 261.0
9 TraesCS1A01G005100 chr1A 83.704 135 18 3 368 498 3018113 3017979 1.590000e-24 124.0
10 TraesCS1A01G005100 chr1A 97.143 35 1 0 244 278 3697870 3697904 4.560000e-05 60.2
11 TraesCS1A01G005100 chr1B 93.981 2492 112 16 1686 4150 4477278 4479758 0.000000e+00 3736.0
12 TraesCS1A01G005100 chr1B 88.428 1279 113 20 2917 4167 4556420 4557691 0.000000e+00 1509.0
13 TraesCS1A01G005100 chr1B 84.247 1022 121 27 1689 2689 3948205 3947203 0.000000e+00 959.0
14 TraesCS1A01G005100 chr1B 80.372 1238 186 39 2363 3580 4126982 4125782 0.000000e+00 887.0
15 TraesCS1A01G005100 chr1B 92.281 583 34 7 3572 4150 4119036 4118461 0.000000e+00 817.0
16 TraesCS1A01G005100 chr1B 87.844 617 49 13 1 602 4562086 4562691 0.000000e+00 701.0
17 TraesCS1A01G005100 chr1B 75.166 1506 246 72 1899 3334 4818728 4820175 3.630000e-165 592.0
18 TraesCS1A01G005100 chr1B 78.434 830 105 38 1985 2795 4032004 4031230 1.370000e-129 473.0
19 TraesCS1A01G005100 chr1B 73.920 1250 228 54 2154 3340 4497183 4498397 3.040000e-111 412.0
20 TraesCS1A01G005100 chr1B 81.159 483 50 29 3132 3596 3947036 3946577 2.410000e-92 350.0
21 TraesCS1A01G005100 chr1B 84.314 357 44 9 2363 2713 4555794 4556144 5.230000e-89 339.0
22 TraesCS1A01G005100 chr1B 80.538 483 56 25 2069 2521 4189389 4188915 1.880000e-88 337.0
23 TraesCS1A01G005100 chr1B 85.782 211 17 8 3027 3230 687790161 687789957 1.190000e-50 211.0
24 TraesCS1A01G005100 chr1B 76.275 451 64 18 2576 2998 4527348 4527783 2.570000e-47 200.0
25 TraesCS1A01G005100 chr1B 94.531 128 3 1 929 1056 4148903 4148780 1.200000e-45 195.0
26 TraesCS1A01G005100 chr1B 87.006 177 12 9 252 422 3941497 3941326 5.570000e-44 189.0
27 TraesCS1A01G005100 chr1B 92.969 128 5 1 929 1056 4911108 4911231 2.590000e-42 183.0
28 TraesCS1A01G005100 chr1B 86.400 125 10 2 2675 2799 4188867 4188750 3.420000e-26 130.0
29 TraesCS1A01G005100 chr1B 87.500 112 13 1 814 925 4950204 4950314 1.230000e-25 128.0
30 TraesCS1A01G005100 chr1B 86.667 90 10 1 3945 4034 4587627 4587714 9.650000e-17 99.0
31 TraesCS1A01G005100 chr1B 88.889 63 5 1 3972 4034 4498758 4498818 4.520000e-10 76.8
32 TraesCS1A01G005100 chr1D 89.652 2561 170 29 1686 4191 614683 617203 0.000000e+00 3173.0
33 TraesCS1A01G005100 chr1D 94.152 855 32 4 713 1565 456561 455723 0.000000e+00 1286.0
34 TraesCS1A01G005100 chr1D 86.038 838 86 20 3130 3946 452206 451379 0.000000e+00 870.0
35 TraesCS1A01G005100 chr1D 85.812 585 52 13 1 568 458119 457549 3.630000e-165 592.0
36 TraesCS1A01G005100 chr1D 88.281 512 36 14 1738 2248 464450 463962 3.630000e-165 592.0
37 TraesCS1A01G005100 chr1D 84.094 635 73 17 1685 2297 398318 397690 4.700000e-164 588.0
38 TraesCS1A01G005100 chr1D 84.551 356 43 4 1686 2029 692893 693248 4.040000e-90 342.0
39 TraesCS1A01G005100 chr1D 84.054 370 43 6 2406 2767 693797 694158 4.040000e-90 342.0
40 TraesCS1A01G005100 chr1D 91.099 191 17 0 2134 2324 693579 693769 4.180000e-65 259.0
41 TraesCS1A01G005100 chr1D 96.491 57 2 0 1676 1732 464563 464507 1.250000e-15 95.3
42 TraesCS1A01G005100 chr1D 77.143 105 17 5 3974 4078 396693 396596 2.000000e-03 54.7
43 TraesCS1A01G005100 chr5D 90.102 293 15 3 1333 1620 497870554 497870271 6.660000e-98 368.0
44 TraesCS1A01G005100 chr3D 82.171 387 51 9 2913 3287 560071856 560072236 2.450000e-82 316.0
45 TraesCS1A01G005100 chr3D 77.252 444 59 24 3379 3786 560072278 560072715 5.490000e-54 222.0
46 TraesCS1A01G005100 chr5B 87.556 225 15 3 1335 1557 617173748 617173535 9.060000e-62 248.0
47 TraesCS1A01G005100 chrUn 90.604 149 10 1 940 1088 318172896 318172752 1.200000e-45 195.0
48 TraesCS1A01G005100 chrUn 83.704 135 18 3 368 498 318173886 318173752 1.590000e-24 124.0
49 TraesCS1A01G005100 chr7D 100.000 28 0 0 1568 1595 311872943 311872916 8.000000e-03 52.8


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 TraesCS1A01G005100 chr1A 2977903 2982121 4218 True 7792.000000 7792 100.000000 1 4219 1 chr1A.!!$R1 4218
1 TraesCS1A01G005100 chr1A 3448358 3450826 2468 False 3339.000000 3339 90.916000 1687 4219 1 chr1A.!!$F1 2532
2 TraesCS1A01G005100 chr1A 27217823 27218556 733 True 665.000000 665 83.311000 1773 2509 1 chr1A.!!$R4 736
3 TraesCS1A01G005100 chr1A 3675810 3677537 1727 False 602.000000 977 85.899000 2383 4219 3 chr1A.!!$F5 1836
4 TraesCS1A01G005100 chr1B 4477278 4479758 2480 False 3736.000000 3736 93.981000 1686 4150 1 chr1B.!!$F1 2464
5 TraesCS1A01G005100 chr1B 4555794 4557691 1897 False 924.000000 1509 86.371000 2363 4167 2 chr1B.!!$F9 1804
6 TraesCS1A01G005100 chr1B 4125782 4126982 1200 True 887.000000 887 80.372000 2363 3580 1 chr1B.!!$R4 1217
7 TraesCS1A01G005100 chr1B 4118461 4119036 575 True 817.000000 817 92.281000 3572 4150 1 chr1B.!!$R3 578
8 TraesCS1A01G005100 chr1B 4562086 4562691 605 False 701.000000 701 87.844000 1 602 1 chr1B.!!$F3 601
9 TraesCS1A01G005100 chr1B 3946577 3948205 1628 True 654.500000 959 82.703000 1689 3596 2 chr1B.!!$R7 1907
10 TraesCS1A01G005100 chr1B 4818728 4820175 1447 False 592.000000 592 75.166000 1899 3334 1 chr1B.!!$F5 1435
11 TraesCS1A01G005100 chr1B 4031230 4032004 774 True 473.000000 473 78.434000 1985 2795 1 chr1B.!!$R2 810
12 TraesCS1A01G005100 chr1B 4497183 4498818 1635 False 244.400000 412 81.404500 2154 4034 2 chr1B.!!$F8 1880
13 TraesCS1A01G005100 chr1B 4188750 4189389 639 True 233.500000 337 83.469000 2069 2799 2 chr1B.!!$R8 730
14 TraesCS1A01G005100 chr1D 614683 617203 2520 False 3173.000000 3173 89.652000 1686 4191 1 chr1D.!!$F1 2505
15 TraesCS1A01G005100 chr1D 451379 458119 6740 True 916.000000 1286 88.667333 1 3946 3 chr1D.!!$R2 3945
16 TraesCS1A01G005100 chr1D 463962 464563 601 True 343.650000 592 92.386000 1676 2248 2 chr1D.!!$R3 572
17 TraesCS1A01G005100 chr1D 396596 398318 1722 True 321.350000 588 80.618500 1685 4078 2 chr1D.!!$R1 2393
18 TraesCS1A01G005100 chr1D 692893 694158 1265 False 314.333333 342 86.568000 1686 2767 3 chr1D.!!$F2 1081
19 TraesCS1A01G005100 chr3D 560071856 560072715 859 False 269.000000 316 79.711500 2913 3786 2 chr3D.!!$F1 873

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
583 608 0.033504 ACACCGTCTGCGTTGAATCT 59.966 50.0 0.00 0.0 34.07 2.40 F
706 731 0.042731 TTAGGTGCCTGCCTACCTCT 59.957 55.0 4.58 0.0 43.69 3.69 F
1601 2515 0.316841 TCCGTTCCAAAATGCTTGCC 59.683 50.0 0.00 0.0 0.00 4.52 F
1605 2519 1.035923 TTCCAAAATGCTTGCCGTGA 58.964 45.0 0.00 0.0 0.00 4.35 F
2268 5934 1.429463 GGCGGTATGGCTCTTATTCG 58.571 55.0 0.00 0.0 40.72 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1584 2498 0.318614 ACGGCAAGCATTTTGGAACG 60.319 50.000 0.00 0.0 0.00 3.95 R
1754 5054 2.375174 TGTAGGGAAAGCATGTGGAGTT 59.625 45.455 0.00 0.0 0.00 3.01 R
2487 6202 2.614057 CAGCAAACAGAGAACCGTCTTT 59.386 45.455 0.00 0.0 32.80 2.52 R
3053 6949 4.406648 TGTGCCGTCTGAGATATTCAAT 57.593 40.909 0.00 0.0 34.81 2.57 R
3824 7945 0.178953 ACCTTGTGCCAAGCAGGAAT 60.179 50.000 8.85 0.0 40.08 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
26 27 8.514330 TTTTCAGTTGGTACATAGAACAAACT 57.486 30.769 0.00 0.00 40.92 2.66
37 44 7.190920 ACATAGAACAAACTGTTTAGCTCAC 57.809 36.000 5.31 0.00 41.28 3.51
41 48 3.537580 ACAAACTGTTTAGCTCACGGAA 58.462 40.909 5.31 0.00 0.00 4.30
55 62 2.668632 GGAATCGTGGCTGGTGGA 59.331 61.111 0.00 0.00 0.00 4.02
66 73 1.648720 CTGGTGGAGCAACACAACG 59.351 57.895 12.04 0.00 43.08 4.10
74 81 2.788786 GGAGCAACACAACGACAAATTG 59.211 45.455 0.00 0.00 0.00 2.32
86 93 5.529581 ACGACAAATTGTGGGAAAATTCT 57.470 34.783 12.51 0.00 29.89 2.40
105 112 5.957842 TTCTGTGCTGGTGGTAAAAATAG 57.042 39.130 0.00 0.00 0.00 1.73
112 119 5.242838 TGCTGGTGGTAAAAATAGAGGTTTG 59.757 40.000 0.00 0.00 0.00 2.93
113 120 5.336451 GCTGGTGGTAAAAATAGAGGTTTGG 60.336 44.000 0.00 0.00 0.00 3.28
117 124 5.537295 GTGGTAAAAATAGAGGTTTGGGTGT 59.463 40.000 0.00 0.00 0.00 4.16
131 138 4.927978 TTGGGTGTTGAATTGTGGTTAG 57.072 40.909 0.00 0.00 0.00 2.34
187 206 2.613977 CGAGGAAAATGACAGAGTGGCT 60.614 50.000 0.00 0.00 0.00 4.75
210 231 6.929049 GCTCTGTACAACCATGCAAGTATATA 59.071 38.462 0.00 0.00 0.00 0.86
211 232 7.604164 GCTCTGTACAACCATGCAAGTATATAT 59.396 37.037 0.00 0.00 0.00 0.86
216 237 9.878599 GTACAACCATGCAAGTATATATTGTTC 57.121 33.333 0.00 0.00 0.00 3.18
259 280 2.105477 CCTATACAACCAGGCAGCATCT 59.895 50.000 0.00 0.00 0.00 2.90
285 307 4.099266 ACCACACAAGCTGAAGCAAAAATA 59.901 37.500 4.90 0.00 45.16 1.40
295 317 5.463061 GCTGAAGCAAAAATACAAGCTCAAA 59.537 36.000 0.00 0.00 41.59 2.69
377 402 1.774254 TCCGACATGCCAATATTCCCT 59.226 47.619 0.00 0.00 0.00 4.20
391 416 1.089123 TTCCCTGGTATGCCCCTTTT 58.911 50.000 0.00 0.00 0.00 2.27
428 453 2.086610 AAAGGGTGCAAATCCACTGT 57.913 45.000 0.00 0.00 36.03 3.55
446 471 3.517901 ACTGTTCAACCTCCGATATTCCA 59.482 43.478 0.00 0.00 0.00 3.53
464 489 2.159043 TCCATCGAACATCTGAGAAGGC 60.159 50.000 0.00 0.00 0.00 4.35
465 490 2.419159 CCATCGAACATCTGAGAAGGCA 60.419 50.000 0.00 0.00 0.00 4.75
466 491 3.464907 CATCGAACATCTGAGAAGGCAT 58.535 45.455 0.00 0.00 0.00 4.40
468 493 3.264947 TCGAACATCTGAGAAGGCATTG 58.735 45.455 0.00 0.00 0.00 2.82
471 496 3.278668 ACATCTGAGAAGGCATTGAGG 57.721 47.619 0.00 0.00 0.00 3.86
476 501 1.340405 TGAGAAGGCATTGAGGAAGGC 60.340 52.381 0.00 0.00 38.17 4.35
508 533 5.783111 ACTTGTTTTGGAATAATGTGAGCC 58.217 37.500 0.00 0.00 0.00 4.70
509 534 5.304101 ACTTGTTTTGGAATAATGTGAGCCA 59.696 36.000 0.00 0.00 0.00 4.75
510 535 5.132897 TGTTTTGGAATAATGTGAGCCAC 57.867 39.130 0.00 0.00 34.56 5.01
511 536 4.832266 TGTTTTGGAATAATGTGAGCCACT 59.168 37.500 6.83 0.00 35.11 4.00
512 537 5.048083 TGTTTTGGAATAATGTGAGCCACTC 60.048 40.000 6.83 0.00 35.11 3.51
513 538 4.574674 TTGGAATAATGTGAGCCACTCT 57.425 40.909 6.83 0.00 35.11 3.24
514 539 4.142609 TGGAATAATGTGAGCCACTCTC 57.857 45.455 6.83 0.00 42.23 3.20
515 540 3.776969 TGGAATAATGTGAGCCACTCTCT 59.223 43.478 6.83 0.00 42.38 3.10
525 550 3.287222 GAGCCACTCTCTGTCTCTGTAT 58.713 50.000 0.00 0.00 38.78 2.29
529 554 3.130164 CCACTCTCTGTCTCTGTATGGTG 59.870 52.174 0.00 0.00 0.00 4.17
535 560 4.412843 TCTGTCTCTGTATGGTGGTTGTA 58.587 43.478 0.00 0.00 0.00 2.41
542 567 5.274015 TCTGTATGGTGGTTGTACATCCTA 58.726 41.667 20.93 10.02 0.00 2.94
569 594 7.601073 ATTATATAGCATGTCAATCACACCG 57.399 36.000 0.00 0.00 38.04 4.94
571 596 1.442769 AGCATGTCAATCACACCGTC 58.557 50.000 0.00 0.00 38.04 4.79
572 597 1.002430 AGCATGTCAATCACACCGTCT 59.998 47.619 0.00 0.00 38.04 4.18
573 598 1.129251 GCATGTCAATCACACCGTCTG 59.871 52.381 0.00 0.00 38.04 3.51
574 599 1.129251 CATGTCAATCACACCGTCTGC 59.871 52.381 0.00 0.00 38.04 4.26
575 600 0.943835 TGTCAATCACACCGTCTGCG 60.944 55.000 0.00 0.00 37.95 5.18
576 601 0.944311 GTCAATCACACCGTCTGCGT 60.944 55.000 0.00 0.00 36.15 5.24
577 602 0.249699 TCAATCACACCGTCTGCGTT 60.250 50.000 0.00 0.00 36.15 4.84
578 603 0.110688 CAATCACACCGTCTGCGTTG 60.111 55.000 0.00 0.00 36.56 4.10
579 604 0.249699 AATCACACCGTCTGCGTTGA 60.250 50.000 0.00 0.00 34.07 3.18
581 606 0.249699 TCACACCGTCTGCGTTGAAT 60.250 50.000 0.00 0.00 34.07 2.57
583 608 0.033504 ACACCGTCTGCGTTGAATCT 59.966 50.000 0.00 0.00 34.07 2.40
585 610 0.732880 ACCGTCTGCGTTGAATCTCG 60.733 55.000 0.00 0.00 36.15 4.04
586 611 0.456142 CCGTCTGCGTTGAATCTCGA 60.456 55.000 3.18 0.00 36.15 4.04
587 612 1.550065 CGTCTGCGTTGAATCTCGAT 58.450 50.000 0.00 0.00 0.00 3.59
590 615 1.476488 TCTGCGTTGAATCTCGATGGA 59.524 47.619 0.00 0.00 0.00 3.41
592 617 2.868583 CTGCGTTGAATCTCGATGGAAT 59.131 45.455 0.00 0.00 0.00 3.01
593 618 2.609002 TGCGTTGAATCTCGATGGAATG 59.391 45.455 0.00 0.00 0.00 2.67
596 621 4.437390 GCGTTGAATCTCGATGGAATGTTT 60.437 41.667 0.00 0.00 0.00 2.83
597 622 5.220586 GCGTTGAATCTCGATGGAATGTTTA 60.221 40.000 0.00 0.00 0.00 2.01
598 623 6.414079 CGTTGAATCTCGATGGAATGTTTAG 58.586 40.000 0.00 0.00 0.00 1.85
599 624 6.510157 CGTTGAATCTCGATGGAATGTTTAGG 60.510 42.308 0.00 0.00 0.00 2.69
600 625 5.989477 TGAATCTCGATGGAATGTTTAGGT 58.011 37.500 0.00 0.00 0.00 3.08
602 627 6.316140 TGAATCTCGATGGAATGTTTAGGTTG 59.684 38.462 0.00 0.00 0.00 3.77
603 628 4.513442 TCTCGATGGAATGTTTAGGTTGG 58.487 43.478 0.00 0.00 0.00 3.77
604 629 4.224147 TCTCGATGGAATGTTTAGGTTGGA 59.776 41.667 0.00 0.00 0.00 3.53
605 630 4.912586 TCGATGGAATGTTTAGGTTGGAA 58.087 39.130 0.00 0.00 0.00 3.53
607 632 5.414454 TCGATGGAATGTTTAGGTTGGAAAG 59.586 40.000 0.00 0.00 0.00 2.62
608 633 4.864704 TGGAATGTTTAGGTTGGAAAGC 57.135 40.909 0.00 0.00 46.62 3.51
617 642 1.856802 GGTTGGAAAGCAAGCACAAG 58.143 50.000 0.00 0.00 45.31 3.16
620 645 3.054878 GTTGGAAAGCAAGCACAAGATG 58.945 45.455 0.00 0.00 0.00 2.90
622 647 2.957680 TGGAAAGCAAGCACAAGATGAA 59.042 40.909 0.00 0.00 0.00 2.57
624 649 4.171754 GGAAAGCAAGCACAAGATGAATC 58.828 43.478 0.00 0.00 0.00 2.52
625 650 4.082354 GGAAAGCAAGCACAAGATGAATCT 60.082 41.667 0.00 0.00 39.22 2.40
626 651 4.436242 AAGCAAGCACAAGATGAATCTG 57.564 40.909 0.00 0.00 37.19 2.90
627 652 3.418995 AGCAAGCACAAGATGAATCTGT 58.581 40.909 0.00 0.00 37.19 3.41
628 653 4.582869 AGCAAGCACAAGATGAATCTGTA 58.417 39.130 0.00 0.00 37.19 2.74
630 655 5.651139 AGCAAGCACAAGATGAATCTGTATT 59.349 36.000 0.00 0.00 37.19 1.89
631 656 6.825213 AGCAAGCACAAGATGAATCTGTATTA 59.175 34.615 0.00 0.00 37.19 0.98
632 657 7.012138 AGCAAGCACAAGATGAATCTGTATTAG 59.988 37.037 0.00 0.00 37.19 1.73
633 658 7.011763 GCAAGCACAAGATGAATCTGTATTAGA 59.988 37.037 0.00 0.00 40.37 2.10
634 659 8.886719 CAAGCACAAGATGAATCTGTATTAGAA 58.113 33.333 0.00 0.00 39.30 2.10
635 660 9.453572 AAGCACAAGATGAATCTGTATTAGAAA 57.546 29.630 0.00 0.00 39.30 2.52
636 661 9.107177 AGCACAAGATGAATCTGTATTAGAAAG 57.893 33.333 0.00 0.00 39.30 2.62
649 674 8.129840 TCTGTATTAGAAAGTGATAACGAGAGC 58.870 37.037 0.00 0.00 30.84 4.09
650 675 7.997482 TGTATTAGAAAGTGATAACGAGAGCT 58.003 34.615 0.00 0.00 0.00 4.09
651 676 7.915923 TGTATTAGAAAGTGATAACGAGAGCTG 59.084 37.037 0.00 0.00 0.00 4.24
653 678 5.140747 AGAAAGTGATAACGAGAGCTGTT 57.859 39.130 0.00 0.00 0.00 3.16
654 679 5.164954 AGAAAGTGATAACGAGAGCTGTTC 58.835 41.667 0.00 0.00 0.00 3.18
655 680 4.792521 AAGTGATAACGAGAGCTGTTCT 57.207 40.909 0.00 0.00 39.43 3.01
666 691 3.377346 GAGCTGTTCTCTGAACTCACA 57.623 47.619 11.06 0.00 38.78 3.58
667 692 3.056304 GAGCTGTTCTCTGAACTCACAC 58.944 50.000 11.06 0.00 38.78 3.82
671 696 4.302455 CTGTTCTCTGAACTCACACGATT 58.698 43.478 11.06 0.00 0.00 3.34
672 697 4.051237 TGTTCTCTGAACTCACACGATTG 58.949 43.478 11.06 0.00 0.00 2.67
673 698 4.051922 GTTCTCTGAACTCACACGATTGT 58.948 43.478 3.49 0.00 35.84 2.71
674 699 4.322080 TCTCTGAACTCACACGATTGTT 57.678 40.909 0.00 0.00 31.66 2.83
678 703 4.053469 TGAACTCACACGATTGTTCAGA 57.947 40.909 0.00 0.00 42.25 3.27
680 705 3.735237 ACTCACACGATTGTTCAGAGT 57.265 42.857 6.17 6.17 33.67 3.24
682 707 5.392767 ACTCACACGATTGTTCAGAGTAT 57.607 39.130 9.15 0.00 35.68 2.12
683 708 5.784177 ACTCACACGATTGTTCAGAGTATT 58.216 37.500 9.15 0.00 35.68 1.89
684 709 6.920817 ACTCACACGATTGTTCAGAGTATTA 58.079 36.000 9.15 0.00 35.68 0.98
685 710 7.548097 ACTCACACGATTGTTCAGAGTATTAT 58.452 34.615 9.15 0.00 35.68 1.28
686 711 7.489435 ACTCACACGATTGTTCAGAGTATTATG 59.511 37.037 9.15 0.00 35.68 1.90
687 712 7.320399 TCACACGATTGTTCAGAGTATTATGT 58.680 34.615 0.00 0.00 31.66 2.29
688 713 7.817478 TCACACGATTGTTCAGAGTATTATGTT 59.183 33.333 0.00 0.00 31.66 2.71
689 714 9.083080 CACACGATTGTTCAGAGTATTATGTTA 57.917 33.333 0.00 0.00 31.66 2.41
690 715 9.302345 ACACGATTGTTCAGAGTATTATGTTAG 57.698 33.333 0.00 0.00 28.43 2.34
691 716 8.755941 CACGATTGTTCAGAGTATTATGTTAGG 58.244 37.037 0.00 0.00 0.00 2.69
692 717 8.475639 ACGATTGTTCAGAGTATTATGTTAGGT 58.524 33.333 0.00 0.00 0.00 3.08
693 718 8.755941 CGATTGTTCAGAGTATTATGTTAGGTG 58.244 37.037 0.00 0.00 0.00 4.00
694 719 7.843490 TTGTTCAGAGTATTATGTTAGGTGC 57.157 36.000 0.00 0.00 0.00 5.01
695 720 6.346096 TGTTCAGAGTATTATGTTAGGTGCC 58.654 40.000 0.00 0.00 0.00 5.01
696 721 6.156256 TGTTCAGAGTATTATGTTAGGTGCCT 59.844 38.462 0.00 0.00 0.00 4.75
697 722 6.161855 TCAGAGTATTATGTTAGGTGCCTG 57.838 41.667 0.12 0.00 0.00 4.85
698 723 4.752101 CAGAGTATTATGTTAGGTGCCTGC 59.248 45.833 0.12 0.00 0.00 4.85
699 724 4.065789 GAGTATTATGTTAGGTGCCTGCC 58.934 47.826 0.12 0.00 0.00 4.85
700 725 3.716872 AGTATTATGTTAGGTGCCTGCCT 59.283 43.478 0.12 0.00 42.43 4.75
701 726 4.905456 AGTATTATGTTAGGTGCCTGCCTA 59.095 41.667 0.12 0.00 39.94 3.93
702 727 3.553828 TTATGTTAGGTGCCTGCCTAC 57.446 47.619 0.12 0.00 40.53 3.18
703 728 0.546598 ATGTTAGGTGCCTGCCTACC 59.453 55.000 0.12 0.00 40.53 3.18
705 730 0.178301 GTTAGGTGCCTGCCTACCTC 59.822 60.000 4.58 0.00 43.69 3.85
706 731 0.042731 TTAGGTGCCTGCCTACCTCT 59.957 55.000 4.58 0.00 43.69 3.69
707 732 0.397254 TAGGTGCCTGCCTACCTCTC 60.397 60.000 4.58 0.00 43.69 3.20
708 733 1.687493 GGTGCCTGCCTACCTCTCT 60.687 63.158 0.00 0.00 34.11 3.10
709 734 1.681486 GGTGCCTGCCTACCTCTCTC 61.681 65.000 0.00 0.00 34.11 3.20
711 736 0.396417 TGCCTGCCTACCTCTCTCTC 60.396 60.000 0.00 0.00 0.00 3.20
717 1585 2.038659 GCCTACCTCTCTCTCTGCAAT 58.961 52.381 0.00 0.00 0.00 3.56
835 1703 8.467402 ACATATTTCTGAACTCTTAAGTCGTG 57.533 34.615 1.63 0.00 33.48 4.35
869 1737 7.121315 GGCTTAGTGTCATGAAAGATACCTTTT 59.879 37.037 8.71 0.00 42.30 2.27
922 1790 9.871238 CCTAGCTTGATCTTACTAGTAAAACAA 57.129 33.333 15.95 17.67 32.03 2.83
925 1793 9.780186 AGCTTGATCTTACTAGTAAAACAAACT 57.220 29.630 15.95 16.59 0.00 2.66
972 1840 9.613428 AATTCTATTGATGGTTTCTATGTTCGA 57.387 29.630 0.00 0.00 0.00 3.71
991 1859 8.251750 TGTTCGATTGAGGTTAAGACAAATAG 57.748 34.615 0.00 0.00 0.00 1.73
998 1866 4.828829 AGGTTAAGACAAATAGTGGACCG 58.171 43.478 0.00 0.00 0.00 4.79
999 1867 3.373130 GGTTAAGACAAATAGTGGACCGC 59.627 47.826 0.00 0.00 0.00 5.68
1000 1868 2.851263 AAGACAAATAGTGGACCGCA 57.149 45.000 7.99 0.00 0.00 5.69
1001 1869 3.350219 AAGACAAATAGTGGACCGCAT 57.650 42.857 7.99 0.00 0.00 4.73
1113 1981 5.640189 AAAAGTCTACTACTAGCGCTTCA 57.360 39.130 18.68 0.00 37.50 3.02
1138 2006 0.391130 GTCTGCTGGATTGCCGTGTA 60.391 55.000 0.00 0.00 36.79 2.90
1178 2046 3.985877 CCACGATGGCTCTTTGCA 58.014 55.556 0.00 0.00 45.15 4.08
1228 2096 4.278975 AGACATTTTCCTTCTTCTCGCT 57.721 40.909 0.00 0.00 0.00 4.93
1231 2099 3.433615 ACATTTTCCTTCTTCTCGCTTCG 59.566 43.478 0.00 0.00 0.00 3.79
1276 2144 4.204799 CTCAGCCATCATTTCATTCCAGA 58.795 43.478 0.00 0.00 0.00 3.86
1314 2182 6.485313 TGTTGGTTTTCGAATGATAGTGAGTT 59.515 34.615 0.00 0.00 0.00 3.01
1322 2190 8.703604 TTCGAATGATAGTGAGTTCTAAAAGG 57.296 34.615 0.00 0.00 0.00 3.11
1339 2207 4.338379 AAAGGAGGTGTTCTCTGTACAC 57.662 45.455 0.00 0.00 43.96 2.90
1355 2223 6.134055 TCTGTACACCCTATAGTTAGCATGT 58.866 40.000 0.00 0.00 0.00 3.21
1366 2234 3.148412 AGTTAGCATGTGTGTGATTGCA 58.852 40.909 0.00 0.00 37.56 4.08
1454 2324 6.710597 ATTTGCTAGTTCTCGTACCATCTA 57.289 37.500 0.00 0.00 0.00 1.98
1464 2334 4.350225 TCTCGTACCATCTATACTCACCCT 59.650 45.833 0.00 0.00 0.00 4.34
1471 2341 5.364157 ACCATCTATACTCACCCTTTCTGTC 59.636 44.000 0.00 0.00 0.00 3.51
1509 2379 5.128919 AGGCATGTAGAAATAAGAAGGCTG 58.871 41.667 0.00 0.00 0.00 4.85
1510 2380 4.884164 GGCATGTAGAAATAAGAAGGCTGT 59.116 41.667 0.00 0.00 0.00 4.40
1511 2381 6.055588 GGCATGTAGAAATAAGAAGGCTGTA 58.944 40.000 0.00 0.00 0.00 2.74
1512 2382 6.712547 GGCATGTAGAAATAAGAAGGCTGTAT 59.287 38.462 0.00 0.00 0.00 2.29
1513 2383 7.308229 GGCATGTAGAAATAAGAAGGCTGTATG 60.308 40.741 0.00 0.00 0.00 2.39
1514 2384 7.442364 GCATGTAGAAATAAGAAGGCTGTATGA 59.558 37.037 0.00 0.00 0.00 2.15
1515 2385 9.499479 CATGTAGAAATAAGAAGGCTGTATGAT 57.501 33.333 0.00 0.00 0.00 2.45
1525 2395 5.760253 AGAAGGCTGTATGATATTTGTTCCG 59.240 40.000 0.00 0.00 0.00 4.30
1584 2498 3.321396 GCCACATAAGTACTACTCCCTCC 59.679 52.174 0.00 0.00 0.00 4.30
1601 2515 0.316841 TCCGTTCCAAAATGCTTGCC 59.683 50.000 0.00 0.00 0.00 4.52
1605 2519 1.035923 TTCCAAAATGCTTGCCGTGA 58.964 45.000 0.00 0.00 0.00 4.35
1873 5174 3.976793 AAAGATGCTCAACACACTGTG 57.023 42.857 7.68 7.68 39.75 3.66
2268 5934 1.429463 GGCGGTATGGCTCTTATTCG 58.571 55.000 0.00 0.00 40.72 3.34
2399 6098 9.739276 AATTTGATTCAGTACACTCTCCATTTA 57.261 29.630 0.00 0.00 0.00 1.40
2487 6202 7.020602 CGTCATGCATGTGTTAATTTACAGAA 58.979 34.615 25.43 0.00 0.00 3.02
2522 6240 6.494842 TCTGTTTGCTGTTCTCATTTTGTAC 58.505 36.000 0.00 0.00 0.00 2.90
2533 6254 8.622157 TGTTCTCATTTTGTACGTTGGAAAATA 58.378 29.630 0.00 0.00 30.07 1.40
3053 6949 5.868454 TCATGATGAACTTTGAAGTCTCCA 58.132 37.500 0.00 0.00 38.57 3.86
3059 6955 7.449395 TGATGAACTTTGAAGTCTCCATTGAAT 59.551 33.333 0.00 0.00 38.57 2.57
3291 7249 3.922240 GCACTTTGTTTATGCATGGACAG 59.078 43.478 10.16 5.83 39.23 3.51
3522 7626 4.034510 GTCACGGCTTTTTCCTATCATCTG 59.965 45.833 0.00 0.00 0.00 2.90
3534 7638 6.854091 TCCTATCATCTGATCTCATCCTTG 57.146 41.667 0.00 0.00 36.05 3.61
3619 7726 7.011576 TCGTTACAAGTGCTTGAAATTAAGTGA 59.988 33.333 17.62 5.37 42.93 3.41
3667 7774 4.710375 TCCTAAGGACAAGGACTACACATC 59.290 45.833 0.00 0.00 38.24 3.06
3721 7837 2.434702 CCCTACAATCCTCCGTAAGCTT 59.565 50.000 3.48 3.48 0.00 3.74
3771 7892 7.051623 TCTTGTTTTATGCACCTATATCCGTT 58.948 34.615 0.00 0.00 0.00 4.44
3824 7945 7.677041 GCATCGAACACTTGATCATTGTGATTA 60.677 37.037 26.07 13.25 37.20 1.75
3836 7957 4.098349 TCATTGTGATTATTCCTGCTTGGC 59.902 41.667 0.00 0.00 35.26 4.52
3876 8020 6.061022 TGATACCCAGAGAACAATAAAGCA 57.939 37.500 0.00 0.00 0.00 3.91
4160 8335 1.419922 GACAACATGGTACTGCGCG 59.580 57.895 0.00 0.00 0.00 6.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.717875 AGCTAAACAGTTTGTTCTATGTACCAA 59.282 33.333 8.93 0.00 40.14 3.67
37 44 2.819595 CCACCAGCCACGATTCCG 60.820 66.667 0.00 0.00 42.50 4.30
55 62 3.178267 CACAATTTGTCGTTGTGTTGCT 58.822 40.909 10.04 0.00 46.97 3.91
66 73 5.050159 GCACAGAATTTTCCCACAATTTGTC 60.050 40.000 0.00 0.00 0.00 3.18
74 81 1.963515 ACCAGCACAGAATTTTCCCAC 59.036 47.619 0.00 0.00 0.00 4.61
86 93 4.202524 ACCTCTATTTTTACCACCAGCACA 60.203 41.667 0.00 0.00 0.00 4.57
105 112 3.492482 CCACAATTCAACACCCAAACCTC 60.492 47.826 0.00 0.00 0.00 3.85
112 119 7.690952 TTATACTAACCACAATTCAACACCC 57.309 36.000 0.00 0.00 0.00 4.61
113 120 9.567848 CATTTATACTAACCACAATTCAACACC 57.432 33.333 0.00 0.00 0.00 4.16
117 124 8.354711 TGGCATTTATACTAACCACAATTCAA 57.645 30.769 0.00 0.00 0.00 2.69
131 138 6.509418 TCCAACAAGACTTGGCATTTATAC 57.491 37.500 19.16 0.00 40.66 1.47
187 206 9.271828 CAATATATACTTGCATGGTTGTACAGA 57.728 33.333 4.44 0.00 0.00 3.41
210 231 3.485463 TTCCACAGGACTTCGAACAAT 57.515 42.857 0.00 0.00 0.00 2.71
211 232 2.992124 TTCCACAGGACTTCGAACAA 57.008 45.000 0.00 0.00 0.00 2.83
216 237 4.332819 GGTTATGAATTCCACAGGACTTCG 59.667 45.833 2.27 0.00 42.07 3.79
237 258 1.285280 TGCTGCCTGGTTGTATAGGT 58.715 50.000 0.00 0.00 36.44 3.08
259 280 1.024271 GCTTCAGCTTGTGTGGTCAA 58.976 50.000 0.00 0.00 38.21 3.18
285 307 2.233271 CAGTGACCCATTTGAGCTTGT 58.767 47.619 0.00 0.00 0.00 3.16
295 317 2.034879 CGAAAGCGCAGTGACCCAT 61.035 57.895 11.47 0.00 0.00 4.00
377 402 7.621683 ACTCATAAATTAAAAAGGGGCATACCA 59.378 33.333 0.00 0.00 42.91 3.25
428 453 3.639561 TCGATGGAATATCGGAGGTTGAA 59.360 43.478 9.13 0.00 41.45 2.69
446 471 3.834489 ATGCCTTCTCAGATGTTCGAT 57.166 42.857 0.00 0.00 0.00 3.59
464 489 3.688673 GTCTTCTTCTGCCTTCCTCAATG 59.311 47.826 0.00 0.00 0.00 2.82
465 490 3.586618 AGTCTTCTTCTGCCTTCCTCAAT 59.413 43.478 0.00 0.00 0.00 2.57
466 491 2.975489 AGTCTTCTTCTGCCTTCCTCAA 59.025 45.455 0.00 0.00 0.00 3.02
468 493 3.244387 ACAAGTCTTCTTCTGCCTTCCTC 60.244 47.826 0.00 0.00 0.00 3.71
471 496 5.277047 CAAAACAAGTCTTCTTCTGCCTTC 58.723 41.667 0.00 0.00 0.00 3.46
476 501 9.403110 CATTATTCCAAAACAAGTCTTCTTCTG 57.597 33.333 0.00 0.00 0.00 3.02
508 533 3.130164 CCACCATACAGAGACAGAGAGTG 59.870 52.174 0.00 0.00 0.00 3.51
509 534 3.245443 ACCACCATACAGAGACAGAGAGT 60.245 47.826 0.00 0.00 0.00 3.24
510 535 3.360867 ACCACCATACAGAGACAGAGAG 58.639 50.000 0.00 0.00 0.00 3.20
511 536 3.458044 ACCACCATACAGAGACAGAGA 57.542 47.619 0.00 0.00 0.00 3.10
512 537 3.259374 ACAACCACCATACAGAGACAGAG 59.741 47.826 0.00 0.00 0.00 3.35
513 538 3.239449 ACAACCACCATACAGAGACAGA 58.761 45.455 0.00 0.00 0.00 3.41
514 539 3.685139 ACAACCACCATACAGAGACAG 57.315 47.619 0.00 0.00 0.00 3.51
515 540 3.898741 TGTACAACCACCATACAGAGACA 59.101 43.478 0.00 0.00 0.00 3.41
548 573 4.960938 ACGGTGTGATTGACATGCTATAT 58.039 39.130 0.00 0.00 36.78 0.86
549 574 4.099419 AGACGGTGTGATTGACATGCTATA 59.901 41.667 0.00 0.00 36.78 1.31
550 575 3.118629 AGACGGTGTGATTGACATGCTAT 60.119 43.478 0.00 0.00 36.78 2.97
551 576 2.233676 AGACGGTGTGATTGACATGCTA 59.766 45.455 0.00 0.00 36.78 3.49
552 577 1.002430 AGACGGTGTGATTGACATGCT 59.998 47.619 0.00 0.00 36.78 3.79
569 594 1.590238 CCATCGAGATTCAACGCAGAC 59.410 52.381 0.00 0.00 0.00 3.51
571 596 1.926561 TCCATCGAGATTCAACGCAG 58.073 50.000 0.00 0.00 0.00 5.18
572 597 2.378445 TTCCATCGAGATTCAACGCA 57.622 45.000 0.00 0.00 0.00 5.24
573 598 2.609459 ACATTCCATCGAGATTCAACGC 59.391 45.455 0.00 0.00 0.00 4.84
574 599 4.864916 AACATTCCATCGAGATTCAACG 57.135 40.909 0.00 0.00 0.00 4.10
575 600 6.316390 ACCTAAACATTCCATCGAGATTCAAC 59.684 38.462 0.00 0.00 0.00 3.18
576 601 6.414732 ACCTAAACATTCCATCGAGATTCAA 58.585 36.000 0.00 0.00 0.00 2.69
577 602 5.989477 ACCTAAACATTCCATCGAGATTCA 58.011 37.500 0.00 0.00 0.00 2.57
578 603 6.238484 CCAACCTAAACATTCCATCGAGATTC 60.238 42.308 0.00 0.00 0.00 2.52
579 604 5.590259 CCAACCTAAACATTCCATCGAGATT 59.410 40.000 0.00 0.00 0.00 2.40
581 606 4.224147 TCCAACCTAAACATTCCATCGAGA 59.776 41.667 0.00 0.00 0.00 4.04
583 608 4.561500 TCCAACCTAAACATTCCATCGA 57.438 40.909 0.00 0.00 0.00 3.59
585 610 5.047377 TGCTTTCCAACCTAAACATTCCATC 60.047 40.000 0.00 0.00 0.00 3.51
586 611 4.837860 TGCTTTCCAACCTAAACATTCCAT 59.162 37.500 0.00 0.00 0.00 3.41
587 612 4.219115 TGCTTTCCAACCTAAACATTCCA 58.781 39.130 0.00 0.00 0.00 3.53
590 615 4.100808 TGCTTGCTTTCCAACCTAAACATT 59.899 37.500 0.00 0.00 0.00 2.71
592 617 3.027412 TGCTTGCTTTCCAACCTAAACA 58.973 40.909 0.00 0.00 0.00 2.83
593 618 3.181480 TGTGCTTGCTTTCCAACCTAAAC 60.181 43.478 0.00 0.00 0.00 2.01
596 621 2.356665 TGTGCTTGCTTTCCAACCTA 57.643 45.000 0.00 0.00 0.00 3.08
597 622 1.410153 CTTGTGCTTGCTTTCCAACCT 59.590 47.619 0.00 0.00 0.00 3.50
598 623 1.408702 TCTTGTGCTTGCTTTCCAACC 59.591 47.619 0.00 0.00 0.00 3.77
599 624 2.869233 TCTTGTGCTTGCTTTCCAAC 57.131 45.000 0.00 0.00 0.00 3.77
600 625 2.957680 TCATCTTGTGCTTGCTTTCCAA 59.042 40.909 0.00 0.00 0.00 3.53
602 627 3.648339 TTCATCTTGTGCTTGCTTTCC 57.352 42.857 0.00 0.00 0.00 3.13
603 628 4.857588 CAGATTCATCTTGTGCTTGCTTTC 59.142 41.667 0.00 0.00 34.22 2.62
604 629 4.280174 ACAGATTCATCTTGTGCTTGCTTT 59.720 37.500 0.00 0.00 34.22 3.51
605 630 3.825014 ACAGATTCATCTTGTGCTTGCTT 59.175 39.130 0.00 0.00 34.22 3.91
607 632 3.844577 ACAGATTCATCTTGTGCTTGC 57.155 42.857 0.00 0.00 34.22 4.01
608 633 8.429493 TCTAATACAGATTCATCTTGTGCTTG 57.571 34.615 0.00 0.00 34.22 4.01
610 635 9.107177 CTTTCTAATACAGATTCATCTTGTGCT 57.893 33.333 0.00 0.00 34.22 4.40
611 636 8.887717 ACTTTCTAATACAGATTCATCTTGTGC 58.112 33.333 0.00 0.00 34.22 4.57
624 649 8.132362 AGCTCTCGTTATCACTTTCTAATACAG 58.868 37.037 0.00 0.00 0.00 2.74
625 650 7.915923 CAGCTCTCGTTATCACTTTCTAATACA 59.084 37.037 0.00 0.00 0.00 2.29
626 651 7.916450 ACAGCTCTCGTTATCACTTTCTAATAC 59.084 37.037 0.00 0.00 0.00 1.89
627 652 7.997482 ACAGCTCTCGTTATCACTTTCTAATA 58.003 34.615 0.00 0.00 0.00 0.98
628 653 6.868622 ACAGCTCTCGTTATCACTTTCTAAT 58.131 36.000 0.00 0.00 0.00 1.73
630 655 5.899120 ACAGCTCTCGTTATCACTTTCTA 57.101 39.130 0.00 0.00 0.00 2.10
631 656 4.792521 ACAGCTCTCGTTATCACTTTCT 57.207 40.909 0.00 0.00 0.00 2.52
632 657 5.164954 AGAACAGCTCTCGTTATCACTTTC 58.835 41.667 0.00 0.00 0.00 2.62
633 658 5.140747 AGAACAGCTCTCGTTATCACTTT 57.859 39.130 0.00 0.00 0.00 2.66
634 659 4.739195 GAGAACAGCTCTCGTTATCACTT 58.261 43.478 5.45 0.00 41.34 3.16
635 660 4.364415 GAGAACAGCTCTCGTTATCACT 57.636 45.455 5.45 0.00 41.34 3.41
646 671 3.056304 GTGTGAGTTCAGAGAACAGCTC 58.944 50.000 11.92 2.48 44.29 4.09
649 674 3.355626 TCGTGTGAGTTCAGAGAACAG 57.644 47.619 11.92 0.00 0.00 3.16
650 675 4.051237 CAATCGTGTGAGTTCAGAGAACA 58.949 43.478 11.92 0.00 0.00 3.18
651 676 4.051922 ACAATCGTGTGAGTTCAGAGAAC 58.948 43.478 1.77 1.77 36.31 3.01
653 678 4.202111 TGAACAATCGTGTGAGTTCAGAGA 60.202 41.667 0.00 0.00 43.66 3.10
654 679 4.051237 TGAACAATCGTGTGAGTTCAGAG 58.949 43.478 0.00 0.00 43.66 3.35
655 680 4.053469 TGAACAATCGTGTGAGTTCAGA 57.947 40.909 0.00 0.00 43.66 3.27
658 683 4.051922 ACTCTGAACAATCGTGTGAGTTC 58.948 43.478 0.00 0.00 35.90 3.01
659 684 4.060038 ACTCTGAACAATCGTGTGAGTT 57.940 40.909 0.00 0.00 35.90 3.01
660 685 3.735237 ACTCTGAACAATCGTGTGAGT 57.265 42.857 0.00 0.00 38.27 3.41
661 686 7.489435 ACATAATACTCTGAACAATCGTGTGAG 59.511 37.037 0.00 0.00 38.27 3.51
662 687 7.320399 ACATAATACTCTGAACAATCGTGTGA 58.680 34.615 0.00 0.00 38.27 3.58
663 688 7.525688 ACATAATACTCTGAACAATCGTGTG 57.474 36.000 0.00 0.00 38.27 3.82
664 689 9.302345 CTAACATAATACTCTGAACAATCGTGT 57.698 33.333 0.00 0.00 40.75 4.49
665 690 8.755941 CCTAACATAATACTCTGAACAATCGTG 58.244 37.037 0.00 0.00 0.00 4.35
666 691 8.475639 ACCTAACATAATACTCTGAACAATCGT 58.524 33.333 0.00 0.00 0.00 3.73
667 692 8.755941 CACCTAACATAATACTCTGAACAATCG 58.244 37.037 0.00 0.00 0.00 3.34
671 696 6.156256 AGGCACCTAACATAATACTCTGAACA 59.844 38.462 0.00 0.00 0.00 3.18
672 697 6.480320 CAGGCACCTAACATAATACTCTGAAC 59.520 42.308 0.00 0.00 0.00 3.18
673 698 6.582636 CAGGCACCTAACATAATACTCTGAA 58.417 40.000 0.00 0.00 0.00 3.02
674 699 5.453339 GCAGGCACCTAACATAATACTCTGA 60.453 44.000 0.00 0.00 0.00 3.27
678 703 3.716872 AGGCAGGCACCTAACATAATACT 59.283 43.478 0.00 0.00 38.67 2.12
680 705 5.223449 GTAGGCAGGCACCTAACATAATA 57.777 43.478 7.78 0.00 43.91 0.98
682 707 3.553828 GTAGGCAGGCACCTAACATAA 57.446 47.619 7.78 0.00 43.91 1.90
686 711 4.957164 GGTAGGCAGGCACCTAAC 57.043 61.111 7.78 6.86 43.91 2.34
687 712 0.042731 AGAGGTAGGCAGGCACCTAA 59.957 55.000 15.23 0.00 45.32 2.69
688 713 0.397254 GAGAGGTAGGCAGGCACCTA 60.397 60.000 15.23 2.43 45.32 3.08
690 715 1.681486 GAGAGAGGTAGGCAGGCACC 61.681 65.000 0.00 2.03 34.86 5.01
691 716 0.686112 AGAGAGAGGTAGGCAGGCAC 60.686 60.000 0.00 0.00 0.00 5.01
692 717 0.396417 GAGAGAGAGGTAGGCAGGCA 60.396 60.000 0.00 0.00 0.00 4.75
693 718 0.106217 AGAGAGAGAGGTAGGCAGGC 60.106 60.000 0.00 0.00 0.00 4.85
694 719 1.691196 CAGAGAGAGAGGTAGGCAGG 58.309 60.000 0.00 0.00 0.00 4.85
695 720 1.032014 GCAGAGAGAGAGGTAGGCAG 58.968 60.000 0.00 0.00 0.00 4.85
696 721 0.332972 TGCAGAGAGAGAGGTAGGCA 59.667 55.000 0.00 0.00 0.00 4.75
697 722 1.479709 TTGCAGAGAGAGAGGTAGGC 58.520 55.000 0.00 0.00 0.00 3.93
698 723 4.405358 AGAAATTGCAGAGAGAGAGGTAGG 59.595 45.833 0.00 0.00 0.00 3.18
699 724 5.596836 AGAAATTGCAGAGAGAGAGGTAG 57.403 43.478 0.00 0.00 0.00 3.18
700 725 7.667575 ATTAGAAATTGCAGAGAGAGAGGTA 57.332 36.000 0.00 0.00 0.00 3.08
701 726 6.558488 ATTAGAAATTGCAGAGAGAGAGGT 57.442 37.500 0.00 0.00 0.00 3.85
702 727 9.638239 GTATATTAGAAATTGCAGAGAGAGAGG 57.362 37.037 0.00 0.00 0.00 3.69
703 728 9.638239 GGTATATTAGAAATTGCAGAGAGAGAG 57.362 37.037 0.00 0.00 0.00 3.20
704 729 9.147732 TGGTATATTAGAAATTGCAGAGAGAGA 57.852 33.333 0.00 0.00 0.00 3.10
705 730 9.941325 ATGGTATATTAGAAATTGCAGAGAGAG 57.059 33.333 0.00 0.00 0.00 3.20
706 731 9.716531 CATGGTATATTAGAAATTGCAGAGAGA 57.283 33.333 0.00 0.00 0.00 3.10
707 732 8.449397 GCATGGTATATTAGAAATTGCAGAGAG 58.551 37.037 0.00 0.00 0.00 3.20
708 733 8.159447 AGCATGGTATATTAGAAATTGCAGAGA 58.841 33.333 0.00 0.00 0.00 3.10
709 734 8.332996 AGCATGGTATATTAGAAATTGCAGAG 57.667 34.615 0.00 0.00 0.00 3.35
711 736 8.235226 CAGAGCATGGTATATTAGAAATTGCAG 58.765 37.037 0.00 0.00 0.00 4.41
755 1623 9.205719 CTCAATTAGATCATGTGACAGGATAAG 57.794 37.037 13.10 0.60 34.96 1.73
835 1703 6.985188 TTCATGACACTAAGCCTGAAATAC 57.015 37.500 0.00 0.00 0.00 1.89
869 1737 2.354510 CTCAGTTCTTCGCACCAACAAA 59.645 45.455 0.00 0.00 0.00 2.83
972 1840 6.884836 GGTCCACTATTTGTCTTAACCTCAAT 59.115 38.462 0.00 0.00 0.00 2.57
991 1859 1.237285 AAGACTTGCATGCGGTCCAC 61.237 55.000 28.16 13.38 0.00 4.02
998 1866 2.035066 ACTTCCAACAAGACTTGCATGC 59.965 45.455 15.24 11.82 0.00 4.06
999 1867 3.316029 TGACTTCCAACAAGACTTGCATG 59.684 43.478 15.24 13.61 0.00 4.06
1000 1868 3.554934 TGACTTCCAACAAGACTTGCAT 58.445 40.909 15.24 1.67 0.00 3.96
1001 1869 2.997980 TGACTTCCAACAAGACTTGCA 58.002 42.857 15.24 0.00 0.00 4.08
1086 1954 4.034510 GCGCTAGTAGTAGACTTTTACCGA 59.965 45.833 8.87 0.00 39.81 4.69
1113 1981 1.656652 GCAATCCAGCAGACGTACAT 58.343 50.000 0.00 0.00 0.00 2.29
1228 2096 2.548067 GGAGCAGGTTGAAAGAGACGAA 60.548 50.000 0.00 0.00 0.00 3.85
1231 2099 2.694213 GAGGAGCAGGTTGAAAGAGAC 58.306 52.381 0.00 0.00 0.00 3.36
1288 2156 6.147821 ACTCACTATCATTCGAAAACCAACAG 59.852 38.462 0.00 0.00 0.00 3.16
1314 2182 5.836898 TGTACAGAGAACACCTCCTTTTAGA 59.163 40.000 0.00 0.00 42.97 2.10
1339 2207 5.276461 TCACACACATGCTAACTATAGGG 57.724 43.478 4.43 0.00 0.00 3.53
1343 2211 4.943093 TGCAATCACACACATGCTAACTAT 59.057 37.500 0.00 0.00 39.49 2.12
1355 2223 2.566833 AGGCTAGTTGCAATCACACA 57.433 45.000 0.59 0.00 45.15 3.72
1416 2284 6.499436 ACTAGCAAATACCCCAATAACCTTT 58.501 36.000 0.00 0.00 0.00 3.11
1419 2287 6.127101 AGAACTAGCAAATACCCCAATAACC 58.873 40.000 0.00 0.00 0.00 2.85
1420 2288 6.018180 CGAGAACTAGCAAATACCCCAATAAC 60.018 42.308 0.00 0.00 0.00 1.89
1454 2324 7.259088 ACTTATTGACAGAAAGGGTGAGTAT 57.741 36.000 4.47 0.00 0.00 2.12
1464 2334 7.090173 GCCTAATGCAAACTTATTGACAGAAA 58.910 34.615 0.00 0.00 40.77 2.52
1509 2379 6.018994 GGACTGACACGGAACAAATATCATAC 60.019 42.308 0.00 0.00 0.00 2.39
1510 2380 6.046593 GGACTGACACGGAACAAATATCATA 58.953 40.000 0.00 0.00 0.00 2.15
1511 2381 4.876107 GGACTGACACGGAACAAATATCAT 59.124 41.667 0.00 0.00 0.00 2.45
1512 2382 4.020573 AGGACTGACACGGAACAAATATCA 60.021 41.667 0.00 0.00 0.00 2.15
1513 2383 4.330074 CAGGACTGACACGGAACAAATATC 59.670 45.833 0.00 0.00 0.00 1.63
1514 2384 4.253685 CAGGACTGACACGGAACAAATAT 58.746 43.478 0.00 0.00 0.00 1.28
1515 2385 3.659786 CAGGACTGACACGGAACAAATA 58.340 45.455 0.00 0.00 0.00 1.40
1516 2386 2.494059 CAGGACTGACACGGAACAAAT 58.506 47.619 0.00 0.00 0.00 2.32
1517 2387 1.948104 CAGGACTGACACGGAACAAA 58.052 50.000 0.00 0.00 0.00 2.83
1518 2388 0.531974 GCAGGACTGACACGGAACAA 60.532 55.000 3.00 0.00 0.00 2.83
1519 2389 1.069090 GCAGGACTGACACGGAACA 59.931 57.895 3.00 0.00 0.00 3.18
1520 2390 1.668151 GGCAGGACTGACACGGAAC 60.668 63.158 3.00 0.00 38.82 3.62
1584 2498 0.318614 ACGGCAAGCATTTTGGAACG 60.319 50.000 0.00 0.00 0.00 3.95
1669 2631 5.063880 GGTAATCAGTGCCCTTTATACAGG 58.936 45.833 0.00 0.00 0.00 4.00
1754 5054 2.375174 TGTAGGGAAAGCATGTGGAGTT 59.625 45.455 0.00 0.00 0.00 3.01
1796 5097 7.112779 AGATTATAAGTTTGGTTGGACAGGAG 58.887 38.462 0.00 0.00 0.00 3.69
2124 5775 4.334759 GCATGCTCTGCGGATGATTATTAT 59.665 41.667 11.37 0.00 43.46 1.28
2268 5934 9.832445 TGAATTATCTGAGAATAACCAACTACC 57.168 33.333 0.00 0.00 0.00 3.18
2298 5964 4.217767 GGAAAACTAGTTGGCCAAGTAAGG 59.782 45.833 28.68 21.52 0.00 2.69
2347 6045 6.766452 ACTACGAAACTTTTACTGAAGAGC 57.234 37.500 0.00 0.00 0.00 4.09
2399 6098 9.753674 TTTCAGATGAAACCTAAGACCAATATT 57.246 29.630 3.91 0.00 38.94 1.28
2487 6202 2.614057 CAGCAAACAGAGAACCGTCTTT 59.386 45.455 0.00 0.00 32.80 2.52
2522 6240 5.327091 CATCAAGCTCTGTATTTTCCAACG 58.673 41.667 0.00 0.00 0.00 4.10
3053 6949 4.406648 TGTGCCGTCTGAGATATTCAAT 57.593 40.909 0.00 0.00 34.81 2.57
3059 6955 6.459670 TTAAAGTATGTGCCGTCTGAGATA 57.540 37.500 0.00 0.00 0.00 1.98
3291 7249 8.887717 GGTATATGAGGCAAGATACAATGAATC 58.112 37.037 7.13 0.00 0.00 2.52
3522 7626 8.738645 ATACAAACTTAACCAAGGATGAGATC 57.261 34.615 0.00 0.00 35.97 2.75
3534 7638 8.276252 TCTTGATGCCTAATACAAACTTAACC 57.724 34.615 0.00 0.00 0.00 2.85
3642 7749 4.710375 TGTGTAGTCCTTGTCCTTAGGATC 59.290 45.833 3.52 0.00 43.39 3.36
3667 7774 2.764269 TCCTTGTCCTTAGGATGGAGG 58.236 52.381 16.46 16.46 36.88 4.30
3771 7892 5.255710 ACGGAACAAATGAATGTGAACAA 57.744 34.783 0.00 0.00 32.81 2.83
3824 7945 0.178953 ACCTTGTGCCAAGCAGGAAT 60.179 50.000 8.85 0.00 40.08 3.01
3836 7957 8.343168 TGGGTATCAAAGTAAAATACCTTGTG 57.657 34.615 9.85 0.00 42.94 3.33


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

AutoCloner maintained by Alex Coulton.