Multiple sequence alignment - TraesCS2B01G011800

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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 TraesCS2B01G011800 chr2B 100.000 5342 0 0 1 5342 6140962 6135621 0.000000e+00 9865.0
1 TraesCS2B01G011800 chr2B 95.372 4192 176 6 642 4823 6040661 6036478 0.000000e+00 6650.0
2 TraesCS2B01G011800 chr2B 81.584 2020 361 8 1872 3887 6058245 6056233 0.000000e+00 1659.0
3 TraesCS2B01G011800 chr2B 85.018 1128 160 7 1001 2122 6159869 6158745 0.000000e+00 1138.0
4 TraesCS2B01G011800 chr2B 94.203 414 23 1 4872 5285 6036479 6036067 9.760000e-177 630.0
5 TraesCS2B01G011800 chr2B 78.474 367 73 3 3980 4343 6056100 6055737 8.940000e-58 235.0
6 TraesCS2B01G011800 chr2B 76.786 336 78 0 1728 2063 17830227 17829892 7.060000e-44 189.0
7 TraesCS2B01G011800 chr2B 80.288 208 38 3 1569 1775 6058907 6058702 2.580000e-33 154.0
8 TraesCS2B01G011800 chr2B 94.253 87 5 0 486 572 6140392 6140306 3.360000e-27 134.0
9 TraesCS2B01G011800 chr2B 94.253 87 5 0 571 657 6140477 6140391 3.360000e-27 134.0
10 TraesCS2B01G011800 chr2B 81.928 83 15 0 4629 4711 775110758 775110840 2.670000e-08 71.3
11 TraesCS2B01G011800 chr2B 100.000 28 0 0 614 641 17833159 17833132 1.000000e-02 52.8
12 TraesCS2B01G011800 chr2D 93.128 4220 242 13 584 4788 5388360 5392546 0.000000e+00 6143.0
13 TraesCS2B01G011800 chr2D 77.474 2739 557 49 1705 4407 12774077 12771363 0.000000e+00 1585.0
14 TraesCS2B01G011800 chr2D 81.337 1795 317 16 2099 3884 11425526 11423741 0.000000e+00 1443.0
15 TraesCS2B01G011800 chr2D 79.370 1270 218 31 803 2046 11427046 11425795 0.000000e+00 854.0
16 TraesCS2B01G011800 chr2D 87.543 578 39 21 1 572 5387884 5388434 5.830000e-179 638.0
17 TraesCS2B01G011800 chr2D 75.551 454 105 6 1720 2170 12774350 12773900 9.010000e-53 219.0
18 TraesCS2B01G011800 chr2D 76.855 337 76 2 1728 2063 11425969 11425634 7.060000e-44 189.0
19 TraesCS2B01G011800 chr2A 92.953 4229 268 14 584 4794 4037303 4041519 0.000000e+00 6131.0
20 TraesCS2B01G011800 chr2A 79.321 2355 433 42 2067 4387 3976140 3978474 0.000000e+00 1602.0
21 TraesCS2B01G011800 chr2A 78.580 2479 470 39 1971 4408 2334734 2337192 0.000000e+00 1580.0
22 TraesCS2B01G011800 chr2A 83.188 1029 157 14 1032 2050 3974959 3975981 0.000000e+00 928.0
23 TraesCS2B01G011800 chr2A 83.577 274 18 12 301 572 4037129 4037377 1.160000e-56 231.0
24 TraesCS2B01G011800 chr4B 78.871 2693 508 51 1718 4384 6039926 6042583 0.000000e+00 1764.0
25 TraesCS2B01G011800 chr4B 78.243 2652 507 59 1791 4396 4953649 4951022 0.000000e+00 1637.0
26 TraesCS2B01G011800 chr4B 74.755 713 175 3 1420 2128 6056152 6056863 1.120000e-81 315.0
27 TraesCS2B01G011800 chr4B 75.426 411 99 2 1718 2127 6056597 6057006 1.170000e-46 198.0
28 TraesCS2B01G011800 chr3B 79.101 2469 448 46 1971 4389 52892619 52890169 0.000000e+00 1639.0
29 TraesCS2B01G011800 chr4D 79.396 2184 420 27 1718 3887 3713880 3716047 0.000000e+00 1513.0
30 TraesCS2B01G011800 chrUn 79.380 1033 186 18 3345 4357 18052581 18053606 0.000000e+00 702.0
31 TraesCS2B01G011800 chr1D 77.156 661 130 17 3714 4363 456177187 456177837 1.090000e-96 364.0
32 TraesCS2B01G011800 chr1D 90.909 132 10 2 4491 4621 119408452 119408322 5.500000e-40 176.0
33 TraesCS2B01G011800 chr7A 75.393 764 163 21 1421 2170 736692398 736691646 3.960000e-91 346.0
34 TraesCS2B01G011800 chr7A 75.758 594 132 12 1583 2170 736691945 736691358 6.770000e-74 289.0
35 TraesCS2B01G011800 chr5D 93.701 127 8 0 4502 4628 69071478 69071352 1.960000e-44 191.0
36 TraesCS2B01G011800 chr5D 87.179 156 17 3 4476 4630 416831209 416831056 1.980000e-39 174.0
37 TraesCS2B01G011800 chr5B 89.928 139 14 0 4489 4627 161033523 161033385 4.250000e-41 180.0
38 TraesCS2B01G011800 chr7B 88.112 143 17 0 4489 4631 449541454 449541312 2.560000e-38 171.0
39 TraesCS2B01G011800 chr3D 86.842 152 19 1 4476 4627 296065134 296065284 9.200000e-38 169.0
40 TraesCS2B01G011800 chr7D 76.307 287 62 6 1837 2120 631685811 631686094 1.200000e-31 148.0
41 TraesCS2B01G011800 chr1A 88.312 77 9 0 4628 4704 1245542 1245618 5.700000e-15 93.5


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 TraesCS2B01G011800 chr2B 6135621 6140962 5341 True 3377.666667 9865 96.168667 1 5342 3 chr2B.!!$R4 5341
1 TraesCS2B01G011800 chr2B 6036067 6040661 4594 True 3640.000000 6650 94.787500 642 5285 2 chr2B.!!$R2 4643
2 TraesCS2B01G011800 chr2B 6158745 6159869 1124 True 1138.000000 1138 85.018000 1001 2122 1 chr2B.!!$R1 1121
3 TraesCS2B01G011800 chr2B 6055737 6058907 3170 True 682.666667 1659 80.115333 1569 4343 3 chr2B.!!$R3 2774
4 TraesCS2B01G011800 chr2D 5387884 5392546 4662 False 3390.500000 6143 90.335500 1 4788 2 chr2D.!!$F1 4787
5 TraesCS2B01G011800 chr2D 12771363 12774350 2987 True 902.000000 1585 76.512500 1705 4407 2 chr2D.!!$R2 2702
6 TraesCS2B01G011800 chr2D 11423741 11427046 3305 True 828.666667 1443 79.187333 803 3884 3 chr2D.!!$R1 3081
7 TraesCS2B01G011800 chr2A 4037129 4041519 4390 False 3181.000000 6131 88.265000 301 4794 2 chr2A.!!$F3 4493
8 TraesCS2B01G011800 chr2A 2334734 2337192 2458 False 1580.000000 1580 78.580000 1971 4408 1 chr2A.!!$F1 2437
9 TraesCS2B01G011800 chr2A 3974959 3978474 3515 False 1265.000000 1602 81.254500 1032 4387 2 chr2A.!!$F2 3355
10 TraesCS2B01G011800 chr4B 6039926 6042583 2657 False 1764.000000 1764 78.871000 1718 4384 1 chr4B.!!$F1 2666
11 TraesCS2B01G011800 chr4B 4951022 4953649 2627 True 1637.000000 1637 78.243000 1791 4396 1 chr4B.!!$R1 2605
12 TraesCS2B01G011800 chr4B 6056152 6057006 854 False 256.500000 315 75.090500 1420 2128 2 chr4B.!!$F2 708
13 TraesCS2B01G011800 chr3B 52890169 52892619 2450 True 1639.000000 1639 79.101000 1971 4389 1 chr3B.!!$R1 2418
14 TraesCS2B01G011800 chr4D 3713880 3716047 2167 False 1513.000000 1513 79.396000 1718 3887 1 chr4D.!!$F1 2169
15 TraesCS2B01G011800 chrUn 18052581 18053606 1025 False 702.000000 702 79.380000 3345 4357 1 chrUn.!!$F1 1012
16 TraesCS2B01G011800 chr1D 456177187 456177837 650 False 364.000000 364 77.156000 3714 4363 1 chr1D.!!$F1 649
17 TraesCS2B01G011800 chr7A 736691358 736692398 1040 True 317.500000 346 75.575500 1421 2170 2 chr7A.!!$R1 749

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
518 522 0.250295 CCCTTGAAACGAGGAGCACA 60.250 55.000 6.61 0.0 36.33 4.57 F
580 584 0.676736 TTGGCGGTTTCATTCAACCC 59.323 50.000 0.00 0.0 43.12 4.11 F
1985 2675 0.040958 GTGAAACTCACTGGCTTGCG 60.041 55.000 0.00 0.0 43.73 4.85 F
2237 3143 0.902048 CTCTCTGGTCCTCTGCCACA 60.902 60.000 0.00 0.0 31.85 4.17 F
3110 4016 1.133199 TGTTGTGAAAGGATTGCCCCT 60.133 47.619 0.00 0.0 38.42 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1968 2658 0.235926 GACGCAAGCCAGTGAGTTTC 59.764 55.000 0.00 0.00 45.62 2.78 R
2326 3232 1.469308 ACGAACTCTGACTAGGCTTCG 59.531 52.381 14.28 14.28 38.30 3.79 R
3110 4016 4.948341 TTCTGAGGTGCACTACTACAAA 57.052 40.909 17.98 0.44 0.00 2.83 R
3160 4066 7.652105 CGTAGTAGTAACCATGATTAGTGCAAT 59.348 37.037 5.64 0.00 0.00 3.56 R
4846 5869 0.402121 AGTTCCTTTGGAGCTGGTCC 59.598 55.000 18.72 18.72 41.62 4.46 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
86 88 2.043450 CTCTCTGTCCCCGAGCCT 60.043 66.667 0.00 0.00 0.00 4.58
105 107 2.317040 CTAGGAAGGCGGATACTCCAA 58.683 52.381 0.00 0.00 46.86 3.53
148 150 8.731605 TGTTATTTGATAAAAACTACCATCGCA 58.268 29.630 0.00 0.00 0.00 5.10
191 194 2.789409 ATCTTTGAGAAACTCCCGGG 57.211 50.000 16.85 16.85 0.00 5.73
192 195 1.430992 TCTTTGAGAAACTCCCGGGT 58.569 50.000 22.86 0.00 0.00 5.28
193 196 1.071699 TCTTTGAGAAACTCCCGGGTG 59.928 52.381 22.86 21.86 0.00 4.61
198 201 2.438763 TGAGAAACTCCCGGGTGTTTTA 59.561 45.455 39.79 29.43 40.45 1.52
212 215 6.768861 CCGGGTGTTTTATAGGACAATATTGA 59.231 38.462 22.16 0.00 0.00 2.57
270 273 6.050432 TGTACAATAAACTGACGTCTGGTTT 58.950 36.000 27.44 28.03 37.08 3.27
368 371 5.336451 CCTTAATTTTTGGCCACCAGAGTAC 60.336 44.000 3.88 0.00 33.81 2.73
369 372 1.600023 TTTTTGGCCACCAGAGTACG 58.400 50.000 3.88 0.00 33.81 3.67
370 373 0.470766 TTTTGGCCACCAGAGTACGT 59.529 50.000 3.88 0.00 33.81 3.57
371 374 1.340088 TTTGGCCACCAGAGTACGTA 58.660 50.000 3.88 0.00 33.81 3.57
372 375 1.563924 TTGGCCACCAGAGTACGTAT 58.436 50.000 3.88 0.00 33.81 3.06
373 376 0.821517 TGGCCACCAGAGTACGTATG 59.178 55.000 0.00 0.00 0.00 2.39
374 377 1.108776 GGCCACCAGAGTACGTATGA 58.891 55.000 0.00 0.00 0.00 2.15
375 378 1.687123 GGCCACCAGAGTACGTATGAT 59.313 52.381 0.00 0.00 0.00 2.45
376 379 2.889045 GGCCACCAGAGTACGTATGATA 59.111 50.000 0.00 0.00 0.00 2.15
377 380 3.305199 GGCCACCAGAGTACGTATGATAC 60.305 52.174 0.00 0.00 0.00 2.24
400 403 1.092348 TGCAGCTTTAGCATCAGCAG 58.908 50.000 4.33 0.00 45.49 4.24
401 404 0.381089 GCAGCTTTAGCATCAGCAGG 59.619 55.000 4.33 0.00 45.49 4.85
402 405 1.747709 CAGCTTTAGCATCAGCAGGT 58.252 50.000 4.33 0.00 45.49 4.00
403 406 2.910199 CAGCTTTAGCATCAGCAGGTA 58.090 47.619 4.33 0.00 45.49 3.08
405 408 3.250280 CAGCTTTAGCATCAGCAGGTATG 59.750 47.826 4.33 0.00 45.49 2.39
406 409 2.551459 GCTTTAGCATCAGCAGGTATGG 59.449 50.000 0.00 0.00 45.49 2.74
407 410 3.813443 CTTTAGCATCAGCAGGTATGGT 58.187 45.455 0.00 0.00 45.49 3.55
408 411 3.475566 TTAGCATCAGCAGGTATGGTC 57.524 47.619 0.00 0.00 45.49 4.02
409 412 1.206878 AGCATCAGCAGGTATGGTCA 58.793 50.000 0.00 0.00 45.49 4.02
417 420 3.949754 CAGCAGGTATGGTCAAACATGAT 59.050 43.478 0.00 0.00 34.07 2.45
420 423 4.439153 GCAGGTATGGTCAAACATGATGTG 60.439 45.833 0.00 0.00 32.39 3.21
426 429 3.814842 TGGTCAAACATGATGTGACAGTC 59.185 43.478 21.23 0.00 42.81 3.51
444 447 3.573772 CTGGGACGAGCGCACTCAA 62.574 63.158 11.47 0.00 43.66 3.02
449 452 0.582005 GACGAGCGCACTCAAGTTTT 59.418 50.000 11.47 0.00 43.66 2.43
450 453 0.304705 ACGAGCGCACTCAAGTTTTG 59.695 50.000 11.47 0.00 43.66 2.44
451 454 0.384725 CGAGCGCACTCAAGTTTTGG 60.385 55.000 11.47 0.00 43.66 3.28
452 455 0.944386 GAGCGCACTCAAGTTTTGGA 59.056 50.000 11.47 0.00 42.93 3.53
453 456 0.947244 AGCGCACTCAAGTTTTGGAG 59.053 50.000 11.47 0.00 37.18 3.86
460 464 3.190118 CACTCAAGTTTTGGAGAGATGGC 59.810 47.826 0.00 0.00 35.17 4.40
496 500 3.194968 ACTTGTACCTGTCATTCTACCCG 59.805 47.826 0.00 0.00 0.00 5.28
497 501 2.104967 TGTACCTGTCATTCTACCCGG 58.895 52.381 0.00 0.00 0.00 5.73
498 502 1.117150 TACCTGTCATTCTACCCGGC 58.883 55.000 0.00 0.00 0.00 6.13
499 503 1.146263 CCTGTCATTCTACCCGGCC 59.854 63.158 0.00 0.00 0.00 6.13
500 504 1.146263 CTGTCATTCTACCCGGCCC 59.854 63.158 0.00 0.00 0.00 5.80
501 505 2.325393 CTGTCATTCTACCCGGCCCC 62.325 65.000 0.00 0.00 0.00 5.80
502 506 2.070650 GTCATTCTACCCGGCCCCT 61.071 63.158 0.00 0.00 0.00 4.79
503 507 1.307517 TCATTCTACCCGGCCCCTT 60.308 57.895 0.00 0.00 0.00 3.95
504 508 1.152963 CATTCTACCCGGCCCCTTG 60.153 63.158 0.00 0.00 0.00 3.61
505 509 1.307517 ATTCTACCCGGCCCCTTGA 60.308 57.895 0.00 0.00 0.00 3.02
506 510 0.917333 ATTCTACCCGGCCCCTTGAA 60.917 55.000 0.00 0.00 0.00 2.69
507 511 1.135068 TTCTACCCGGCCCCTTGAAA 61.135 55.000 0.00 0.00 0.00 2.69
508 512 1.378119 CTACCCGGCCCCTTGAAAC 60.378 63.158 0.00 0.00 0.00 2.78
509 513 3.256824 TACCCGGCCCCTTGAAACG 62.257 63.158 0.00 0.00 0.00 3.60
510 514 4.338710 CCCGGCCCCTTGAAACGA 62.339 66.667 0.00 0.00 0.00 3.85
511 515 2.746277 CCGGCCCCTTGAAACGAG 60.746 66.667 0.00 0.00 0.00 4.18
512 516 2.746277 CGGCCCCTTGAAACGAGG 60.746 66.667 0.00 0.00 0.00 4.63
513 517 2.754375 GGCCCCTTGAAACGAGGA 59.246 61.111 6.61 0.00 36.33 3.71
514 518 1.377333 GGCCCCTTGAAACGAGGAG 60.377 63.158 6.61 0.00 36.33 3.69
515 519 2.041115 GCCCCTTGAAACGAGGAGC 61.041 63.158 6.61 1.50 36.33 4.70
516 520 1.374947 CCCCTTGAAACGAGGAGCA 59.625 57.895 6.61 0.00 36.33 4.26
517 521 0.955919 CCCCTTGAAACGAGGAGCAC 60.956 60.000 6.61 0.00 36.33 4.40
518 522 0.250295 CCCTTGAAACGAGGAGCACA 60.250 55.000 6.61 0.00 36.33 4.57
519 523 1.151668 CCTTGAAACGAGGAGCACAG 58.848 55.000 0.00 0.00 36.33 3.66
520 524 1.270305 CCTTGAAACGAGGAGCACAGA 60.270 52.381 0.00 0.00 36.33 3.41
521 525 2.064762 CTTGAAACGAGGAGCACAGAG 58.935 52.381 0.00 0.00 0.00 3.35
522 526 1.328279 TGAAACGAGGAGCACAGAGA 58.672 50.000 0.00 0.00 0.00 3.10
523 527 1.270826 TGAAACGAGGAGCACAGAGAG 59.729 52.381 0.00 0.00 0.00 3.20
524 528 1.542030 GAAACGAGGAGCACAGAGAGA 59.458 52.381 0.00 0.00 0.00 3.10
525 529 1.846007 AACGAGGAGCACAGAGAGAT 58.154 50.000 0.00 0.00 0.00 2.75
526 530 1.388547 ACGAGGAGCACAGAGAGATC 58.611 55.000 0.00 0.00 0.00 2.75
527 531 1.064758 ACGAGGAGCACAGAGAGATCT 60.065 52.381 0.00 0.00 0.00 2.75
528 532 2.023673 CGAGGAGCACAGAGAGATCTT 58.976 52.381 0.00 0.00 0.00 2.40
529 533 2.426738 CGAGGAGCACAGAGAGATCTTT 59.573 50.000 0.00 0.00 0.00 2.52
530 534 3.119173 CGAGGAGCACAGAGAGATCTTTT 60.119 47.826 0.00 0.00 0.00 2.27
531 535 4.432712 GAGGAGCACAGAGAGATCTTTTC 58.567 47.826 0.00 0.00 0.00 2.29
532 536 3.119173 AGGAGCACAGAGAGATCTTTTCG 60.119 47.826 0.00 0.00 0.00 3.46
533 537 3.367910 GGAGCACAGAGAGATCTTTTCGT 60.368 47.826 0.00 0.00 0.00 3.85
534 538 4.241681 GAGCACAGAGAGATCTTTTCGTT 58.758 43.478 0.00 0.00 0.00 3.85
535 539 3.993081 AGCACAGAGAGATCTTTTCGTTG 59.007 43.478 0.00 2.82 0.00 4.10
536 540 3.990469 GCACAGAGAGATCTTTTCGTTGA 59.010 43.478 0.00 0.00 0.00 3.18
537 541 4.449068 GCACAGAGAGATCTTTTCGTTGAA 59.551 41.667 0.00 0.00 0.00 2.69
538 542 5.121454 GCACAGAGAGATCTTTTCGTTGAAT 59.879 40.000 0.00 0.00 0.00 2.57
539 543 6.671879 GCACAGAGAGATCTTTTCGTTGAATC 60.672 42.308 0.00 0.00 0.00 2.52
540 544 5.872070 ACAGAGAGATCTTTTCGTTGAATCC 59.128 40.000 0.00 0.00 0.00 3.01
541 545 5.871524 CAGAGAGATCTTTTCGTTGAATCCA 59.128 40.000 0.00 0.00 0.00 3.41
542 546 6.369890 CAGAGAGATCTTTTCGTTGAATCCAA 59.630 38.462 0.00 0.00 0.00 3.53
543 547 7.065563 CAGAGAGATCTTTTCGTTGAATCCAAT 59.934 37.037 0.00 0.00 34.39 3.16
544 548 7.279758 AGAGAGATCTTTTCGTTGAATCCAATC 59.720 37.037 0.00 0.00 34.39 2.67
545 549 6.317391 AGAGATCTTTTCGTTGAATCCAATCC 59.683 38.462 0.00 0.00 34.39 3.01
546 550 5.358160 AGATCTTTTCGTTGAATCCAATCCC 59.642 40.000 0.00 0.00 34.39 3.85
547 551 3.761752 TCTTTTCGTTGAATCCAATCCCC 59.238 43.478 0.00 0.00 34.39 4.81
548 552 2.889170 TTCGTTGAATCCAATCCCCA 57.111 45.000 0.00 0.00 34.39 4.96
549 553 2.122783 TCGTTGAATCCAATCCCCAC 57.877 50.000 0.00 0.00 34.39 4.61
550 554 1.102978 CGTTGAATCCAATCCCCACC 58.897 55.000 0.00 0.00 34.39 4.61
551 555 1.340991 CGTTGAATCCAATCCCCACCT 60.341 52.381 0.00 0.00 34.39 4.00
552 556 2.820178 GTTGAATCCAATCCCCACCTT 58.180 47.619 0.00 0.00 34.39 3.50
553 557 2.760650 GTTGAATCCAATCCCCACCTTC 59.239 50.000 0.00 0.00 34.39 3.46
554 558 2.287584 TGAATCCAATCCCCACCTTCT 58.712 47.619 0.00 0.00 0.00 2.85
555 559 2.242196 TGAATCCAATCCCCACCTTCTC 59.758 50.000 0.00 0.00 0.00 2.87
556 560 2.293598 ATCCAATCCCCACCTTCTCT 57.706 50.000 0.00 0.00 0.00 3.10
557 561 2.059756 TCCAATCCCCACCTTCTCTT 57.940 50.000 0.00 0.00 0.00 2.85
558 562 2.358258 TCCAATCCCCACCTTCTCTTT 58.642 47.619 0.00 0.00 0.00 2.52
559 563 2.308866 TCCAATCCCCACCTTCTCTTTC 59.691 50.000 0.00 0.00 0.00 2.62
560 564 2.310052 CCAATCCCCACCTTCTCTTTCT 59.690 50.000 0.00 0.00 0.00 2.52
561 565 3.245407 CCAATCCCCACCTTCTCTTTCTT 60.245 47.826 0.00 0.00 0.00 2.52
562 566 4.411013 CAATCCCCACCTTCTCTTTCTTT 58.589 43.478 0.00 0.00 0.00 2.52
563 567 3.508845 TCCCCACCTTCTCTTTCTTTG 57.491 47.619 0.00 0.00 0.00 2.77
564 568 2.108250 TCCCCACCTTCTCTTTCTTTGG 59.892 50.000 0.00 0.00 0.00 3.28
565 569 1.889170 CCCACCTTCTCTTTCTTTGGC 59.111 52.381 0.00 0.00 0.00 4.52
566 570 1.537202 CCACCTTCTCTTTCTTTGGCG 59.463 52.381 0.00 0.00 0.00 5.69
567 571 1.537202 CACCTTCTCTTTCTTTGGCGG 59.463 52.381 0.00 0.00 0.00 6.13
568 572 1.143073 ACCTTCTCTTTCTTTGGCGGT 59.857 47.619 0.00 0.00 0.00 5.68
569 573 2.230660 CCTTCTCTTTCTTTGGCGGTT 58.769 47.619 0.00 0.00 0.00 4.44
570 574 2.623416 CCTTCTCTTTCTTTGGCGGTTT 59.377 45.455 0.00 0.00 0.00 3.27
571 575 3.304726 CCTTCTCTTTCTTTGGCGGTTTC 60.305 47.826 0.00 0.00 0.00 2.78
572 576 2.925724 TCTCTTTCTTTGGCGGTTTCA 58.074 42.857 0.00 0.00 0.00 2.69
573 577 3.486383 TCTCTTTCTTTGGCGGTTTCAT 58.514 40.909 0.00 0.00 0.00 2.57
574 578 3.888930 TCTCTTTCTTTGGCGGTTTCATT 59.111 39.130 0.00 0.00 0.00 2.57
575 579 4.023193 TCTCTTTCTTTGGCGGTTTCATTC 60.023 41.667 0.00 0.00 0.00 2.67
576 580 3.634448 TCTTTCTTTGGCGGTTTCATTCA 59.366 39.130 0.00 0.00 0.00 2.57
577 581 4.098654 TCTTTCTTTGGCGGTTTCATTCAA 59.901 37.500 0.00 0.00 0.00 2.69
578 582 3.363341 TCTTTGGCGGTTTCATTCAAC 57.637 42.857 0.00 0.00 0.00 3.18
579 583 2.035321 TCTTTGGCGGTTTCATTCAACC 59.965 45.455 0.00 0.00 42.68 3.77
580 584 0.676736 TTGGCGGTTTCATTCAACCC 59.323 50.000 0.00 0.00 43.12 4.11
581 585 1.211709 GGCGGTTTCATTCAACCCG 59.788 57.895 0.00 0.00 43.12 5.28
582 586 1.211709 GCGGTTTCATTCAACCCGG 59.788 57.895 0.00 0.00 43.12 5.73
583 587 1.211709 CGGTTTCATTCAACCCGGC 59.788 57.895 0.00 0.00 43.12 6.13
584 588 1.589630 GGTTTCATTCAACCCGGCC 59.410 57.895 0.00 0.00 40.53 6.13
585 589 1.589630 GTTTCATTCAACCCGGCCC 59.410 57.895 0.00 0.00 0.00 5.80
586 590 1.608046 TTTCATTCAACCCGGCCCC 60.608 57.895 0.00 0.00 0.00 5.80
587 591 2.087857 TTTCATTCAACCCGGCCCCT 62.088 55.000 0.00 0.00 0.00 4.79
588 592 2.037208 CATTCAACCCGGCCCCTT 59.963 61.111 0.00 0.00 0.00 3.95
589 593 2.037208 ATTCAACCCGGCCCCTTG 59.963 61.111 0.00 0.00 0.00 3.61
594 598 1.609210 AACCCGGCCCCTTGAAATG 60.609 57.895 0.00 0.00 0.00 2.32
596 600 1.754234 CCCGGCCCCTTGAAATGAG 60.754 63.158 0.00 0.00 0.00 2.90
650 654 3.181476 TGCTCACCTTTTCTTTCTTTGGC 60.181 43.478 0.00 0.00 0.00 4.52
1130 1166 1.172175 GCTCTTCTTGCCTGGAAAGG 58.828 55.000 14.55 0.00 0.00 3.11
1164 1200 1.305623 CCCTGCCCAGCTTCAATCT 59.694 57.895 0.00 0.00 0.00 2.40
1391 1430 1.577328 CCCGGCATTGTGTCACTCAC 61.577 60.000 4.27 0.00 46.31 3.51
1574 1616 9.151471 GCTTAACTTATCTGACAATCACTTGTA 57.849 33.333 0.00 0.00 45.57 2.41
1587 1629 1.846439 CACTTGTATGGTCCCATCCCT 59.154 52.381 1.17 0.00 37.82 4.20
1698 1740 7.482169 TCTCACTAAACTCACCATCTTGTAT 57.518 36.000 0.00 0.00 0.00 2.29
1750 2008 3.009916 TCCTCGAGAACTAGGTTACCTGT 59.990 47.826 15.71 7.39 34.61 4.00
1810 2068 0.771755 GGGTTCCATCCCTGATACCC 59.228 60.000 0.00 0.00 43.85 3.69
1856 2258 3.555168 GGCTTGTATCTCTGGGATAACGG 60.555 52.174 0.00 0.00 38.48 4.44
1968 2658 4.705023 CCTAATACCTTTGGGAGTTTGGTG 59.295 45.833 0.00 0.00 36.25 4.17
1985 2675 0.040958 GTGAAACTCACTGGCTTGCG 60.041 55.000 0.00 0.00 43.73 4.85
2237 3143 0.902048 CTCTCTGGTCCTCTGCCACA 60.902 60.000 0.00 0.00 31.85 4.17
2389 3295 7.024368 AGAAGGAGATATTTCTGAGATGGGAT 58.976 38.462 0.00 0.00 30.30 3.85
2552 3458 5.129485 TGGGGCAAATGTTTCAACTAAAGAA 59.871 36.000 0.00 0.00 0.00 2.52
2784 3690 6.127925 TGCTTCGCTCATTTAATTTGAGACAT 60.128 34.615 16.24 0.00 42.63 3.06
2830 3736 2.042979 ACTGTTCTGGGGGTATTGCAAT 59.957 45.455 17.56 17.56 0.00 3.56
3110 4016 1.133199 TGTTGTGAAAGGATTGCCCCT 60.133 47.619 0.00 0.00 38.42 4.79
3160 4066 8.028652 AGGGAAAATGAAAGGATACAAAACAA 57.971 30.769 0.00 0.00 41.41 2.83
3169 4075 8.417106 TGAAAGGATACAAAACAATTGCACTAA 58.583 29.630 5.05 0.00 41.41 2.24
3237 4143 1.060729 TGTTCCGACATGGGAGGAAA 58.939 50.000 16.76 7.97 44.56 3.13
3446 4352 3.729716 GCGGTGAAGAAGATACATACGAC 59.270 47.826 0.00 0.00 0.00 4.34
3556 4462 7.924541 ACTATTTGGGTATTGTTCCTGTAGAA 58.075 34.615 0.00 0.00 0.00 2.10
4252 5264 2.803155 ATCACGCAGACCAACGGCAT 62.803 55.000 0.00 0.00 39.54 4.40
4643 5666 3.463944 CGACACTACCCCAAATCCATAC 58.536 50.000 0.00 0.00 0.00 2.39
4644 5667 3.463944 GACACTACCCCAAATCCATACG 58.536 50.000 0.00 0.00 0.00 3.06
4668 5691 3.153919 ACCATGCAAACGTTGTTCCTAT 58.846 40.909 0.00 0.00 0.00 2.57
4704 5727 9.421806 CATAGAAAGTAGAAATCTGGCATAGAG 57.578 37.037 0.00 0.00 39.20 2.43
4705 5728 7.430760 AGAAAGTAGAAATCTGGCATAGAGT 57.569 36.000 0.00 0.00 39.20 3.24
4840 5863 9.847224 TTAATACCATTGAAGATAAGAGGTTCC 57.153 33.333 0.00 0.00 0.00 3.62
4841 5864 5.779241 ACCATTGAAGATAAGAGGTTCCA 57.221 39.130 0.00 0.00 0.00 3.53
4842 5865 6.332976 ACCATTGAAGATAAGAGGTTCCAT 57.667 37.500 0.00 0.00 0.00 3.41
4843 5866 6.125029 ACCATTGAAGATAAGAGGTTCCATG 58.875 40.000 0.00 0.00 0.00 3.66
4844 5867 6.125029 CCATTGAAGATAAGAGGTTCCATGT 58.875 40.000 0.00 0.00 0.00 3.21
4845 5868 7.092444 ACCATTGAAGATAAGAGGTTCCATGTA 60.092 37.037 0.00 0.00 0.00 2.29
4846 5869 7.443575 CCATTGAAGATAAGAGGTTCCATGTAG 59.556 40.741 0.00 0.00 0.00 2.74
4847 5870 6.485830 TGAAGATAAGAGGTTCCATGTAGG 57.514 41.667 0.00 0.00 39.47 3.18
4856 5879 2.916355 TCCATGTAGGACCAGCTCC 58.084 57.895 0.00 0.00 43.07 4.70
4857 5880 0.042581 TCCATGTAGGACCAGCTCCA 59.957 55.000 0.00 0.00 43.07 3.86
4858 5881 0.911769 CCATGTAGGACCAGCTCCAA 59.088 55.000 0.00 0.00 42.46 3.53
4859 5882 1.281867 CCATGTAGGACCAGCTCCAAA 59.718 52.381 0.00 0.00 42.46 3.28
4860 5883 2.636830 CATGTAGGACCAGCTCCAAAG 58.363 52.381 0.00 0.00 42.46 2.77
4861 5884 0.984230 TGTAGGACCAGCTCCAAAGG 59.016 55.000 0.00 0.00 42.46 3.11
4862 5885 1.276622 GTAGGACCAGCTCCAAAGGA 58.723 55.000 0.00 0.00 42.46 3.36
4863 5886 1.628846 GTAGGACCAGCTCCAAAGGAA 59.371 52.381 0.00 0.00 42.46 3.36
4864 5887 0.402121 AGGACCAGCTCCAAAGGAAC 59.598 55.000 0.00 0.00 42.46 3.62
4865 5888 0.402121 GGACCAGCTCCAAAGGAACT 59.598 55.000 0.00 0.00 39.03 3.01
4866 5889 3.568043 AGGACCAGCTCCAAAGGAACTT 61.568 50.000 0.00 0.00 44.35 2.66
4893 5916 4.978580 GCAATTAAAAATCAGAGGCGGATC 59.021 41.667 0.00 0.00 0.00 3.36
4899 5922 0.105760 ATCAGAGGCGGATCTCACCT 60.106 55.000 1.96 1.96 36.30 4.00
4912 5935 4.148825 CACCTCTTCCTCGCCGGG 62.149 72.222 2.18 0.00 0.00 5.73
4956 5979 3.834799 GGACTCGGGGTAGGCGTG 61.835 72.222 0.00 0.00 0.00 5.34
4994 6017 1.188791 CATCATCGTCATCGCTGTTCG 59.811 52.381 0.00 0.00 35.19 3.95
5006 6029 1.153745 CTGTTCGAAGCGGAGGAGG 60.154 63.158 0.00 0.00 0.00 4.30
5026 6049 2.354203 GGAGGACGATATGAAGATGCCC 60.354 54.545 0.00 0.00 0.00 5.36
5030 6053 1.354337 CGATATGAAGATGCCCGCCG 61.354 60.000 0.00 0.00 0.00 6.46
5081 6104 1.169577 GAGCTGAGGTCGTCTCTTCA 58.830 55.000 0.00 1.46 42.86 3.02
5101 6124 3.121030 GTCGTCGCTGGCTGCATT 61.121 61.111 16.76 0.00 43.06 3.56
5143 6166 2.338015 CGCCATGCAGAGCACCTTT 61.338 57.895 10.95 0.00 43.04 3.11
5144 6167 1.214589 GCCATGCAGAGCACCTTTG 59.785 57.895 5.90 0.00 43.04 2.77
5220 6243 1.458398 TGGTTACAATGTCGGCATGG 58.542 50.000 1.74 1.83 35.15 3.66
5285 6308 2.648059 GGCAGTGCACTTTCCATCTAT 58.352 47.619 18.94 0.00 0.00 1.98
5286 6309 2.357009 GGCAGTGCACTTTCCATCTATG 59.643 50.000 18.94 3.64 0.00 2.23
5287 6310 3.012518 GCAGTGCACTTTCCATCTATGT 58.987 45.455 18.94 0.00 0.00 2.29
5288 6311 3.064545 GCAGTGCACTTTCCATCTATGTC 59.935 47.826 18.94 0.00 0.00 3.06
5289 6312 4.511527 CAGTGCACTTTCCATCTATGTCT 58.488 43.478 18.94 0.00 0.00 3.41
5290 6313 4.940046 CAGTGCACTTTCCATCTATGTCTT 59.060 41.667 18.94 0.00 0.00 3.01
5291 6314 6.108687 CAGTGCACTTTCCATCTATGTCTTA 58.891 40.000 18.94 0.00 0.00 2.10
5292 6315 6.036517 CAGTGCACTTTCCATCTATGTCTTAC 59.963 42.308 18.94 0.00 0.00 2.34
5293 6316 5.874810 GTGCACTTTCCATCTATGTCTTACA 59.125 40.000 10.32 0.00 0.00 2.41
5294 6317 6.036517 GTGCACTTTCCATCTATGTCTTACAG 59.963 42.308 10.32 0.00 0.00 2.74
5295 6318 6.109359 GCACTTTCCATCTATGTCTTACAGT 58.891 40.000 0.00 0.00 0.00 3.55
5296 6319 6.256757 GCACTTTCCATCTATGTCTTACAGTC 59.743 42.308 0.00 0.00 0.00 3.51
5297 6320 6.758886 CACTTTCCATCTATGTCTTACAGTCC 59.241 42.308 0.00 0.00 0.00 3.85
5298 6321 6.670027 ACTTTCCATCTATGTCTTACAGTCCT 59.330 38.462 0.00 0.00 0.00 3.85
5299 6322 7.181125 ACTTTCCATCTATGTCTTACAGTCCTT 59.819 37.037 0.00 0.00 0.00 3.36
5300 6323 7.496346 TTCCATCTATGTCTTACAGTCCTTT 57.504 36.000 0.00 0.00 0.00 3.11
5301 6324 7.496346 TCCATCTATGTCTTACAGTCCTTTT 57.504 36.000 0.00 0.00 0.00 2.27
5302 6325 7.918076 TCCATCTATGTCTTACAGTCCTTTTT 58.082 34.615 0.00 0.00 0.00 1.94
5326 6349 5.766150 TTTTTGGCATGAATATACGAGGG 57.234 39.130 0.00 0.00 0.00 4.30
5327 6350 2.472695 TGGCATGAATATACGAGGGC 57.527 50.000 0.00 0.00 0.00 5.19
5328 6351 1.696884 TGGCATGAATATACGAGGGCA 59.303 47.619 0.00 0.00 0.00 5.36
5329 6352 2.289631 TGGCATGAATATACGAGGGCAG 60.290 50.000 0.00 0.00 0.00 4.85
5330 6353 1.734465 GCATGAATATACGAGGGCAGC 59.266 52.381 0.00 0.00 0.00 5.25
5331 6354 2.871637 GCATGAATATACGAGGGCAGCA 60.872 50.000 0.00 0.00 0.00 4.41
5332 6355 3.402110 CATGAATATACGAGGGCAGCAA 58.598 45.455 0.00 0.00 0.00 3.91
5333 6356 3.769739 TGAATATACGAGGGCAGCAAT 57.230 42.857 0.00 0.00 0.00 3.56
5334 6357 4.882842 TGAATATACGAGGGCAGCAATA 57.117 40.909 0.00 0.00 0.00 1.90
5335 6358 5.420725 TGAATATACGAGGGCAGCAATAT 57.579 39.130 0.00 0.00 0.00 1.28
5336 6359 5.419542 TGAATATACGAGGGCAGCAATATC 58.580 41.667 0.00 0.00 0.00 1.63
5337 6360 5.187772 TGAATATACGAGGGCAGCAATATCT 59.812 40.000 0.00 0.00 0.00 1.98
5338 6361 2.820059 TACGAGGGCAGCAATATCTG 57.180 50.000 0.00 0.00 37.15 2.90
5339 6362 0.833287 ACGAGGGCAGCAATATCTGT 59.167 50.000 0.00 0.00 36.49 3.41
5340 6363 2.039418 ACGAGGGCAGCAATATCTGTA 58.961 47.619 0.00 0.00 36.49 2.74
5341 6364 2.634940 ACGAGGGCAGCAATATCTGTAT 59.365 45.455 0.00 0.00 36.49 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 66 3.151022 CGGGGACAGAGAGCCTCC 61.151 72.222 0.00 0.00 0.00 4.30
75 77 2.134933 CCTTCCTAGGCTCGGGGAC 61.135 68.421 2.96 0.00 33.99 4.46
163 166 9.162764 CGGGAGTTTCTCAAAGATTTTAATCTA 57.837 33.333 5.47 0.00 37.20 1.98
166 169 6.152831 CCCGGGAGTTTCTCAAAGATTTTAAT 59.847 38.462 18.48 0.00 31.08 1.40
187 190 6.768861 TCAATATTGTCCTATAAAACACCCGG 59.231 38.462 14.97 0.00 0.00 5.73
188 191 7.497909 ACTCAATATTGTCCTATAAAACACCCG 59.502 37.037 14.97 0.00 0.00 5.28
198 201 9.745880 CGTAAGTTACACTCAATATTGTCCTAT 57.254 33.333 14.97 2.08 0.00 2.57
212 215 6.164176 CCTGGATTTTCTCGTAAGTTACACT 58.836 40.000 13.33 0.00 39.48 3.55
221 224 5.223449 ACAAAGACCTGGATTTTCTCGTA 57.777 39.130 0.00 0.00 0.00 3.43
270 273 7.823745 ACCTTCAAGCTTTCTCAAAGAATTA 57.176 32.000 0.00 0.00 41.02 1.40
354 357 0.821517 CATACGTACTCTGGTGGCCA 59.178 55.000 0.00 0.00 0.00 5.36
381 384 1.092348 CTGCTGATGCTAAAGCTGCA 58.908 50.000 1.02 0.00 44.95 4.41
382 385 0.381089 CCTGCTGATGCTAAAGCTGC 59.619 55.000 3.26 0.00 42.66 5.25
383 386 1.747709 ACCTGCTGATGCTAAAGCTG 58.252 50.000 3.26 6.00 42.66 4.24
384 387 3.474600 CATACCTGCTGATGCTAAAGCT 58.525 45.455 3.26 0.00 42.66 3.74
398 401 4.943093 TCACATCATGTTTGACCATACCTG 59.057 41.667 0.00 0.00 33.85 4.00
400 403 4.699735 TGTCACATCATGTTTGACCATACC 59.300 41.667 16.32 0.00 39.16 2.73
401 404 5.412594 ACTGTCACATCATGTTTGACCATAC 59.587 40.000 16.32 0.00 39.16 2.39
402 405 5.559770 ACTGTCACATCATGTTTGACCATA 58.440 37.500 16.32 3.57 39.16 2.74
403 406 4.401022 ACTGTCACATCATGTTTGACCAT 58.599 39.130 16.32 6.55 39.16 3.55
405 408 4.067896 AGACTGTCACATCATGTTTGACC 58.932 43.478 10.88 6.34 39.16 4.02
406 409 4.083643 CCAGACTGTCACATCATGTTTGAC 60.084 45.833 10.88 13.71 40.14 3.18
407 410 4.067192 CCAGACTGTCACATCATGTTTGA 58.933 43.478 10.88 0.00 36.00 2.69
408 411 3.189910 CCCAGACTGTCACATCATGTTTG 59.810 47.826 10.88 0.00 0.00 2.93
409 412 3.072915 TCCCAGACTGTCACATCATGTTT 59.927 43.478 10.88 0.00 0.00 2.83
417 420 1.806461 GCTCGTCCCAGACTGTCACA 61.806 60.000 10.88 0.00 0.00 3.58
420 423 2.179517 CGCTCGTCCCAGACTGTC 59.820 66.667 0.00 0.00 0.00 3.51
426 429 3.573772 TTGAGTGCGCTCGTCCCAG 62.574 63.158 21.66 0.00 44.48 4.45
444 447 3.683802 CTTGAGCCATCTCTCCAAAACT 58.316 45.455 0.00 0.00 40.03 2.66
449 452 1.283347 AAGCTTGAGCCATCTCTCCA 58.717 50.000 0.00 0.00 43.38 3.86
450 453 2.433970 ACTAAGCTTGAGCCATCTCTCC 59.566 50.000 9.86 0.00 43.38 3.71
451 454 3.456280 CACTAAGCTTGAGCCATCTCTC 58.544 50.000 9.86 0.00 43.38 3.20
452 455 2.419851 GCACTAAGCTTGAGCCATCTCT 60.420 50.000 9.86 0.00 43.38 3.10
453 456 1.939255 GCACTAAGCTTGAGCCATCTC 59.061 52.381 9.86 0.00 43.38 2.75
460 464 3.433615 GGTACAAGTGCACTAAGCTTGAG 59.566 47.826 22.01 5.36 45.94 3.02
496 500 1.377333 CTCCTCGTTTCAAGGGGCC 60.377 63.158 0.00 0.00 34.46 5.80
497 501 4.303257 CTCCTCGTTTCAAGGGGC 57.697 61.111 0.00 0.00 34.46 5.80
498 502 0.955919 GTGCTCCTCGTTTCAAGGGG 60.956 60.000 0.00 0.00 37.45 4.79
499 503 0.250295 TGTGCTCCTCGTTTCAAGGG 60.250 55.000 0.00 0.00 34.46 3.95
500 504 1.151668 CTGTGCTCCTCGTTTCAAGG 58.848 55.000 0.00 0.00 35.05 3.61
501 505 2.064762 CTCTGTGCTCCTCGTTTCAAG 58.935 52.381 0.00 0.00 0.00 3.02
502 506 1.686587 TCTCTGTGCTCCTCGTTTCAA 59.313 47.619 0.00 0.00 0.00 2.69
503 507 1.270826 CTCTCTGTGCTCCTCGTTTCA 59.729 52.381 0.00 0.00 0.00 2.69
504 508 1.542030 TCTCTCTGTGCTCCTCGTTTC 59.458 52.381 0.00 0.00 0.00 2.78
505 509 1.621992 TCTCTCTGTGCTCCTCGTTT 58.378 50.000 0.00 0.00 0.00 3.60
506 510 1.748493 GATCTCTCTGTGCTCCTCGTT 59.252 52.381 0.00 0.00 0.00 3.85
507 511 1.064758 AGATCTCTCTGTGCTCCTCGT 60.065 52.381 0.00 0.00 0.00 4.18
508 512 1.679139 AGATCTCTCTGTGCTCCTCG 58.321 55.000 0.00 0.00 0.00 4.63
509 513 4.432712 GAAAAGATCTCTCTGTGCTCCTC 58.567 47.826 0.00 0.00 0.00 3.71
510 514 3.119173 CGAAAAGATCTCTCTGTGCTCCT 60.119 47.826 0.00 0.00 0.00 3.69
511 515 3.186119 CGAAAAGATCTCTCTGTGCTCC 58.814 50.000 0.00 0.00 0.00 4.70
512 516 3.843999 ACGAAAAGATCTCTCTGTGCTC 58.156 45.455 0.00 0.00 0.00 4.26
513 517 3.951775 ACGAAAAGATCTCTCTGTGCT 57.048 42.857 0.00 0.00 0.00 4.40
514 518 3.990469 TCAACGAAAAGATCTCTCTGTGC 59.010 43.478 0.00 0.00 0.00 4.57
515 519 6.183360 GGATTCAACGAAAAGATCTCTCTGTG 60.183 42.308 0.00 0.00 0.00 3.66
516 520 5.872070 GGATTCAACGAAAAGATCTCTCTGT 59.128 40.000 0.00 0.00 0.00 3.41
517 521 5.871524 TGGATTCAACGAAAAGATCTCTCTG 59.128 40.000 0.00 0.00 0.00 3.35
518 522 6.042638 TGGATTCAACGAAAAGATCTCTCT 57.957 37.500 0.00 0.00 0.00 3.10
519 523 6.727824 TTGGATTCAACGAAAAGATCTCTC 57.272 37.500 0.00 0.00 0.00 3.20
520 524 6.317391 GGATTGGATTCAACGAAAAGATCTCT 59.683 38.462 0.00 0.00 35.48 3.10
521 525 6.458888 GGGATTGGATTCAACGAAAAGATCTC 60.459 42.308 0.00 0.00 35.48 2.75
522 526 5.358160 GGGATTGGATTCAACGAAAAGATCT 59.642 40.000 0.00 0.00 35.48 2.75
523 527 5.450550 GGGGATTGGATTCAACGAAAAGATC 60.451 44.000 0.00 0.00 35.48 2.75
524 528 4.402474 GGGGATTGGATTCAACGAAAAGAT 59.598 41.667 0.00 0.00 35.48 2.40
525 529 3.761752 GGGGATTGGATTCAACGAAAAGA 59.238 43.478 0.00 0.00 35.48 2.52
526 530 3.509575 TGGGGATTGGATTCAACGAAAAG 59.490 43.478 0.00 0.00 35.48 2.27
527 531 3.257127 GTGGGGATTGGATTCAACGAAAA 59.743 43.478 0.00 0.00 35.48 2.29
528 532 2.823154 GTGGGGATTGGATTCAACGAAA 59.177 45.455 0.00 0.00 35.48 3.46
529 533 2.442413 GTGGGGATTGGATTCAACGAA 58.558 47.619 0.00 0.00 35.48 3.85
530 534 1.340600 GGTGGGGATTGGATTCAACGA 60.341 52.381 0.00 0.00 35.48 3.85
531 535 1.102978 GGTGGGGATTGGATTCAACG 58.897 55.000 0.00 0.00 35.48 4.10
532 536 2.532250 AGGTGGGGATTGGATTCAAC 57.468 50.000 0.00 0.00 35.48 3.18
533 537 2.654385 AGAAGGTGGGGATTGGATTCAA 59.346 45.455 0.00 0.00 37.28 2.69
534 538 2.242196 GAGAAGGTGGGGATTGGATTCA 59.758 50.000 0.00 0.00 0.00 2.57
535 539 2.511637 AGAGAAGGTGGGGATTGGATTC 59.488 50.000 0.00 0.00 0.00 2.52
536 540 2.577970 AGAGAAGGTGGGGATTGGATT 58.422 47.619 0.00 0.00 0.00 3.01
537 541 2.293598 AGAGAAGGTGGGGATTGGAT 57.706 50.000 0.00 0.00 0.00 3.41
538 542 2.059756 AAGAGAAGGTGGGGATTGGA 57.940 50.000 0.00 0.00 0.00 3.53
539 543 2.310052 AGAAAGAGAAGGTGGGGATTGG 59.690 50.000 0.00 0.00 0.00 3.16
540 544 3.728385 AGAAAGAGAAGGTGGGGATTG 57.272 47.619 0.00 0.00 0.00 2.67
541 545 4.411013 CAAAGAAAGAGAAGGTGGGGATT 58.589 43.478 0.00 0.00 0.00 3.01
542 546 3.245407 CCAAAGAAAGAGAAGGTGGGGAT 60.245 47.826 0.00 0.00 0.00 3.85
543 547 2.108250 CCAAAGAAAGAGAAGGTGGGGA 59.892 50.000 0.00 0.00 0.00 4.81
544 548 2.519013 CCAAAGAAAGAGAAGGTGGGG 58.481 52.381 0.00 0.00 0.00 4.96
545 549 1.889170 GCCAAAGAAAGAGAAGGTGGG 59.111 52.381 0.00 0.00 0.00 4.61
546 550 1.537202 CGCCAAAGAAAGAGAAGGTGG 59.463 52.381 0.00 0.00 0.00 4.61
547 551 1.537202 CCGCCAAAGAAAGAGAAGGTG 59.463 52.381 0.00 0.00 0.00 4.00
548 552 1.143073 ACCGCCAAAGAAAGAGAAGGT 59.857 47.619 0.00 0.00 0.00 3.50
549 553 1.897560 ACCGCCAAAGAAAGAGAAGG 58.102 50.000 0.00 0.00 0.00 3.46
550 554 3.315191 TGAAACCGCCAAAGAAAGAGAAG 59.685 43.478 0.00 0.00 0.00 2.85
551 555 3.283751 TGAAACCGCCAAAGAAAGAGAA 58.716 40.909 0.00 0.00 0.00 2.87
552 556 2.925724 TGAAACCGCCAAAGAAAGAGA 58.074 42.857 0.00 0.00 0.00 3.10
553 557 3.923017 ATGAAACCGCCAAAGAAAGAG 57.077 42.857 0.00 0.00 0.00 2.85
554 558 3.634448 TGAATGAAACCGCCAAAGAAAGA 59.366 39.130 0.00 0.00 0.00 2.52
555 559 3.976169 TGAATGAAACCGCCAAAGAAAG 58.024 40.909 0.00 0.00 0.00 2.62
556 560 4.116238 GTTGAATGAAACCGCCAAAGAAA 58.884 39.130 0.00 0.00 0.00 2.52
557 561 3.491792 GGTTGAATGAAACCGCCAAAGAA 60.492 43.478 0.00 0.00 40.28 2.52
558 562 2.035321 GGTTGAATGAAACCGCCAAAGA 59.965 45.455 0.00 0.00 40.28 2.52
559 563 2.403259 GGTTGAATGAAACCGCCAAAG 58.597 47.619 0.00 0.00 40.28 2.77
560 564 2.517650 GGTTGAATGAAACCGCCAAA 57.482 45.000 0.00 0.00 40.28 3.28
567 571 1.589630 GGGCCGGGTTGAATGAAAC 59.410 57.895 2.18 0.00 0.00 2.78
568 572 1.608046 GGGGCCGGGTTGAATGAAA 60.608 57.895 2.18 0.00 0.00 2.69
569 573 2.036572 GGGGCCGGGTTGAATGAA 59.963 61.111 2.18 0.00 0.00 2.57
570 574 2.543797 AAGGGGCCGGGTTGAATGA 61.544 57.895 2.18 0.00 0.00 2.57
571 575 2.037208 AAGGGGCCGGGTTGAATG 59.963 61.111 2.18 0.00 0.00 2.67
572 576 2.037208 CAAGGGGCCGGGTTGAAT 59.963 61.111 2.18 0.00 0.00 2.57
573 577 2.299727 TTTCAAGGGGCCGGGTTGAA 62.300 55.000 18.26 18.26 38.19 2.69
574 578 2.087857 ATTTCAAGGGGCCGGGTTGA 62.088 55.000 2.18 9.77 0.00 3.18
575 579 1.609210 ATTTCAAGGGGCCGGGTTG 60.609 57.895 2.18 1.12 0.00 3.77
576 580 1.609210 CATTTCAAGGGGCCGGGTT 60.609 57.895 2.18 0.00 0.00 4.11
577 581 2.037208 CATTTCAAGGGGCCGGGT 59.963 61.111 2.18 0.00 0.00 5.28
578 582 1.754234 CTCATTTCAAGGGGCCGGG 60.754 63.158 2.18 0.00 0.00 5.73
579 583 1.754234 CCTCATTTCAAGGGGCCGG 60.754 63.158 0.00 0.00 0.00 6.13
580 584 0.749454 CTCCTCATTTCAAGGGGCCG 60.749 60.000 0.00 0.00 34.46 6.13
581 585 3.197664 CTCCTCATTTCAAGGGGCC 57.802 57.895 0.00 0.00 34.46 5.80
583 587 1.272092 TGTGCTCCTCATTTCAAGGGG 60.272 52.381 0.00 0.00 37.45 4.79
584 588 2.089980 CTGTGCTCCTCATTTCAAGGG 58.910 52.381 0.00 0.00 34.46 3.95
585 589 3.008330 CTCTGTGCTCCTCATTTCAAGG 58.992 50.000 0.00 0.00 35.05 3.61
586 590 3.933955 CTCTCTGTGCTCCTCATTTCAAG 59.066 47.826 0.00 0.00 0.00 3.02
587 591 3.580022 TCTCTCTGTGCTCCTCATTTCAA 59.420 43.478 0.00 0.00 0.00 2.69
588 592 3.168292 TCTCTCTGTGCTCCTCATTTCA 58.832 45.455 0.00 0.00 0.00 2.69
589 593 3.883830 TCTCTCTGTGCTCCTCATTTC 57.116 47.619 0.00 0.00 0.00 2.17
594 598 4.432712 GAAAAGATCTCTCTGTGCTCCTC 58.567 47.826 0.00 0.00 0.00 3.71
596 600 3.186119 CGAAAAGATCTCTCTGTGCTCC 58.814 50.000 0.00 0.00 0.00 4.70
650 654 3.670625 TGTTGTCCCTCATAAGAAACCG 58.329 45.455 0.00 0.00 0.00 4.44
1130 1166 2.622436 CAGGGTAGCTTTCTAGTGTGC 58.378 52.381 0.00 0.00 0.00 4.57
1164 1200 2.043227 GTGTTGTTTCCCATTCCCCAA 58.957 47.619 0.00 0.00 0.00 4.12
1391 1430 2.125350 GCAGGAACCGGAGCTCTG 60.125 66.667 16.14 16.14 0.00 3.35
1517 1559 6.744112 AGATTCTCTAGTTCTCCTATTTGCG 58.256 40.000 0.00 0.00 0.00 4.85
1574 1616 2.127708 GTTCACTAGGGATGGGACCAT 58.872 52.381 2.93 2.93 39.69 3.55
1587 1629 6.096564 GCTTCTTTAGGTAGCCTAGTTCACTA 59.903 42.308 0.00 0.00 37.42 2.74
1750 2008 3.260884 AGGGACAGCTCTCGTAAATTCAA 59.739 43.478 0.00 0.00 0.00 2.69
1810 2068 4.645588 AGTGAGGTTAATTAGACTCCCGAG 59.354 45.833 12.99 0.00 0.00 4.63
1968 2658 0.235926 GACGCAAGCCAGTGAGTTTC 59.764 55.000 0.00 0.00 45.62 2.78
1985 2675 5.880887 CCAGAAAGTTGGTTATCCCTTAGAC 59.119 44.000 0.00 0.00 33.38 2.59
2097 3003 7.346751 AGTGAGCTTAGTCAAATTTCCAAAA 57.653 32.000 0.00 0.00 0.00 2.44
2154 3060 2.478539 GCCGATTTCTTGAGGAACATGC 60.479 50.000 0.00 0.00 33.13 4.06
2237 3143 2.030893 CGACCACTGATGCACAAATTGT 60.031 45.455 0.00 0.00 0.00 2.71
2326 3232 1.469308 ACGAACTCTGACTAGGCTTCG 59.531 52.381 14.28 14.28 38.30 3.79
2389 3295 8.533569 TCTATGTACACTAGATTTGGATGACA 57.466 34.615 0.00 0.00 0.00 3.58
2467 3373 8.311109 TGAGATACTTAGCATGTCAAGTTTACA 58.689 33.333 16.07 10.74 36.44 2.41
2476 3382 7.364522 TGTTGTTTGAGATACTTAGCATGTC 57.635 36.000 0.00 0.00 0.00 3.06
2552 3458 7.047460 AGCTTGTTTGATGAAAGATCAAGTT 57.953 32.000 7.82 1.08 39.49 2.66
3110 4016 4.948341 TTCTGAGGTGCACTACTACAAA 57.052 40.909 17.98 0.44 0.00 2.83
3160 4066 7.652105 CGTAGTAGTAACCATGATTAGTGCAAT 59.348 37.037 5.64 0.00 0.00 3.56
3169 4075 8.865420 AGACATATCGTAGTAGTAACCATGAT 57.135 34.615 0.00 0.00 29.71 2.45
3237 4143 9.956720 CTAGAACTGACAATTGACTTTGATTTT 57.043 29.630 13.59 0.00 0.00 1.82
3946 4958 9.729023 GTAATTAGCATATGTATGTGTTGCAAA 57.271 29.630 0.00 0.00 36.11 3.68
4252 5264 2.124612 CTCATCACGGGCATGCCA 60.125 61.111 36.56 18.14 37.98 4.92
4323 5338 3.449737 GGCACTACTGTGTAGGAATGGTA 59.550 47.826 9.20 0.00 45.44 3.25
4522 5545 3.142951 CACGATGTTTTACCCAGGTTCA 58.857 45.455 0.00 0.00 0.00 3.18
4643 5666 1.833860 ACAACGTTTGCATGGTTTCG 58.166 45.000 0.00 0.00 0.00 3.46
4644 5667 2.538037 GGAACAACGTTTGCATGGTTTC 59.462 45.455 0.00 0.00 0.00 2.78
4722 5745 7.117812 ACTGTGTTAAGTTTCTATGTCCAATCG 59.882 37.037 0.00 0.00 0.00 3.34
4771 5794 9.408069 CTTTAAGTAGTTAAGTGATGAACTCGT 57.592 33.333 3.09 0.00 38.56 4.18
4823 5846 6.672218 TCCTACATGGAACCTCTTATCTTCAA 59.328 38.462 0.00 0.00 42.94 2.69
4825 5848 6.463190 GGTCCTACATGGAACCTCTTATCTTC 60.463 46.154 0.00 0.00 46.80 2.87
4827 5850 4.902448 GGTCCTACATGGAACCTCTTATCT 59.098 45.833 0.00 0.00 46.80 1.98
4828 5851 5.216614 GGTCCTACATGGAACCTCTTATC 57.783 47.826 0.00 0.00 46.80 1.75
4838 5861 2.916355 GGAGCTGGTCCTACATGGA 58.084 57.895 18.30 0.00 42.99 3.41
4843 5866 6.329530 AAGTTCCTTTGGAGCTGGTCCTAC 62.330 50.000 24.79 13.21 42.34 3.18
4844 5867 4.274309 AAGTTCCTTTGGAGCTGGTCCTA 61.274 47.826 24.79 16.03 42.34 2.94
4845 5868 3.568043 AAGTTCCTTTGGAGCTGGTCCT 61.568 50.000 24.79 0.94 42.34 3.85
4846 5869 0.402121 AGTTCCTTTGGAGCTGGTCC 59.598 55.000 18.72 18.72 41.62 4.46
4847 5870 2.278332 AAGTTCCTTTGGAGCTGGTC 57.722 50.000 3.81 0.00 42.34 4.02
4848 5871 2.310538 CAAAGTTCCTTTGGAGCTGGT 58.689 47.619 8.50 0.00 42.34 4.00
4857 5880 9.171877 TGATTTTTAATTGCACAAAGTTCCTTT 57.828 25.926 0.00 0.00 33.58 3.11
4858 5881 8.729805 TGATTTTTAATTGCACAAAGTTCCTT 57.270 26.923 0.00 0.00 0.00 3.36
4859 5882 8.203485 TCTGATTTTTAATTGCACAAAGTTCCT 58.797 29.630 0.00 0.00 0.00 3.36
4860 5883 8.364129 TCTGATTTTTAATTGCACAAAGTTCC 57.636 30.769 0.00 0.00 0.00 3.62
4861 5884 8.490355 CCTCTGATTTTTAATTGCACAAAGTTC 58.510 33.333 0.00 0.00 0.00 3.01
4862 5885 7.041848 GCCTCTGATTTTTAATTGCACAAAGTT 60.042 33.333 0.00 0.00 0.00 2.66
4863 5886 6.424812 GCCTCTGATTTTTAATTGCACAAAGT 59.575 34.615 0.00 0.00 0.00 2.66
4864 5887 6.400303 CGCCTCTGATTTTTAATTGCACAAAG 60.400 38.462 0.00 0.00 0.00 2.77
4865 5888 5.404968 CGCCTCTGATTTTTAATTGCACAAA 59.595 36.000 0.00 0.00 0.00 2.83
4866 5889 4.922692 CGCCTCTGATTTTTAATTGCACAA 59.077 37.500 0.00 0.00 0.00 3.33
4867 5890 4.484236 CGCCTCTGATTTTTAATTGCACA 58.516 39.130 0.00 0.00 0.00 4.57
4868 5891 3.859386 CCGCCTCTGATTTTTAATTGCAC 59.141 43.478 0.00 0.00 0.00 4.57
4869 5892 3.761218 TCCGCCTCTGATTTTTAATTGCA 59.239 39.130 0.00 0.00 0.00 4.08
4870 5893 4.370364 TCCGCCTCTGATTTTTAATTGC 57.630 40.909 0.00 0.00 0.00 3.56
4871 5894 6.038603 TGAGATCCGCCTCTGATTTTTAATTG 59.961 38.462 0.00 0.00 34.38 2.32
4872 5895 6.038714 GTGAGATCCGCCTCTGATTTTTAATT 59.961 38.462 0.00 0.00 34.38 1.40
4873 5896 5.529060 GTGAGATCCGCCTCTGATTTTTAAT 59.471 40.000 0.00 0.00 34.38 1.40
4874 5897 4.876107 GTGAGATCCGCCTCTGATTTTTAA 59.124 41.667 0.00 0.00 34.38 1.52
4875 5898 4.442706 GTGAGATCCGCCTCTGATTTTTA 58.557 43.478 0.00 0.00 34.38 1.52
4876 5899 3.274288 GTGAGATCCGCCTCTGATTTTT 58.726 45.455 0.00 0.00 34.38 1.94
4877 5900 2.420687 GGTGAGATCCGCCTCTGATTTT 60.421 50.000 6.55 0.00 42.19 1.82
4878 5901 1.139853 GGTGAGATCCGCCTCTGATTT 59.860 52.381 6.55 0.00 42.19 2.17
4893 5916 2.492090 CGGCGAGGAAGAGGTGAG 59.508 66.667 0.00 0.00 0.00 3.51
4912 5935 1.003233 AGACCCCAAGAAGAAGCGC 60.003 57.895 0.00 0.00 0.00 5.92
4919 5942 3.702048 CCGCCGAGACCCCAAGAA 61.702 66.667 0.00 0.00 0.00 2.52
4947 5970 4.509737 GAGACGCCCACGCCTACC 62.510 72.222 0.00 0.00 45.53 3.18
4967 5990 0.936764 GATGACGATGATGACGCGCT 60.937 55.000 5.73 0.00 0.00 5.92
4994 6017 2.776913 CGTCCTCCTCCTCCGCTTC 61.777 68.421 0.00 0.00 0.00 3.86
5006 6029 2.672478 CGGGCATCTTCATATCGTCCTC 60.672 54.545 0.00 0.00 0.00 3.71
5066 6089 0.536687 ACGGTGAAGAGACGACCTCA 60.537 55.000 11.01 0.00 44.40 3.86
5068 6091 1.575576 CGACGGTGAAGAGACGACCT 61.576 60.000 0.00 0.00 0.00 3.85
5143 6166 0.660005 GTCGTCGCTGCAAAAATGCA 60.660 50.000 3.23 3.23 43.22 3.96
5144 6167 1.655697 CGTCGTCGCTGCAAAAATGC 61.656 55.000 0.00 0.00 0.00 3.56
5304 6327 4.037446 GCCCTCGTATATTCATGCCAAAAA 59.963 41.667 0.00 0.00 0.00 1.94
5305 6328 3.568007 GCCCTCGTATATTCATGCCAAAA 59.432 43.478 0.00 0.00 0.00 2.44
5306 6329 3.146066 GCCCTCGTATATTCATGCCAAA 58.854 45.455 0.00 0.00 0.00 3.28
5307 6330 2.105649 TGCCCTCGTATATTCATGCCAA 59.894 45.455 0.00 0.00 0.00 4.52
5308 6331 1.696884 TGCCCTCGTATATTCATGCCA 59.303 47.619 0.00 0.00 0.00 4.92
5309 6332 2.350522 CTGCCCTCGTATATTCATGCC 58.649 52.381 0.00 0.00 0.00 4.40
5310 6333 1.734465 GCTGCCCTCGTATATTCATGC 59.266 52.381 0.00 0.00 0.00 4.06
5311 6334 3.044235 TGCTGCCCTCGTATATTCATG 57.956 47.619 0.00 0.00 0.00 3.07
5312 6335 3.769739 TTGCTGCCCTCGTATATTCAT 57.230 42.857 0.00 0.00 0.00 2.57
5313 6336 3.769739 ATTGCTGCCCTCGTATATTCA 57.230 42.857 0.00 0.00 0.00 2.57
5314 6337 5.521735 CAGATATTGCTGCCCTCGTATATTC 59.478 44.000 0.00 0.00 0.00 1.75
5315 6338 5.046304 ACAGATATTGCTGCCCTCGTATATT 60.046 40.000 0.00 0.00 39.51 1.28
5316 6339 4.467795 ACAGATATTGCTGCCCTCGTATAT 59.532 41.667 0.00 0.00 39.51 0.86
5317 6340 3.832490 ACAGATATTGCTGCCCTCGTATA 59.168 43.478 0.00 0.00 39.51 1.47
5318 6341 2.634940 ACAGATATTGCTGCCCTCGTAT 59.365 45.455 0.00 0.00 39.51 3.06
5319 6342 2.039418 ACAGATATTGCTGCCCTCGTA 58.961 47.619 0.00 0.00 39.51 3.43
5320 6343 0.833287 ACAGATATTGCTGCCCTCGT 59.167 50.000 0.00 0.00 39.51 4.18
5321 6344 2.820059 TACAGATATTGCTGCCCTCG 57.180 50.000 0.00 0.00 39.51 4.63


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

AutoCloner maintained by Alex Coulton.