Multiple sequence alignment - TraesCS2B01G333000

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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 TraesCS2B01G333000 chr2B 100.000 7329 0 0 1 7329 476417251 476409923 0.000000e+00 13535.0
1 TraesCS2B01G333000 chr2B 77.806 392 77 8 155 539 88935520 88935132 4.420000e-57 233.0
2 TraesCS2B01G333000 chr2B 94.737 38 1 1 624 660 291569578 291569541 2.860000e-04 58.4
3 TraesCS2B01G333000 chr2B 94.737 38 1 1 620 656 443918547 443918510 2.860000e-04 58.4
4 TraesCS2B01G333000 chr1A 97.174 3220 73 6 2048 5259 20083774 20086983 0.000000e+00 5426.0
5 TraesCS2B01G333000 chr1A 96.029 3223 102 10 2046 5259 312722546 312719341 0.000000e+00 5219.0
6 TraesCS2B01G333000 chr1A 86.487 3234 411 16 2045 5259 58425301 58422075 0.000000e+00 3528.0
7 TraesCS2B01G333000 chr1A 82.400 3233 531 26 2046 5259 449829487 449826274 0.000000e+00 2784.0
8 TraesCS2B01G333000 chr1A 74.213 508 115 14 6695 7194 58465558 58465059 1.610000e-46 198.0
9 TraesCS2B01G333000 chr1A 100.000 29 0 0 656 684 257969294 257969266 4.000000e-03 54.7
10 TraesCS2B01G333000 chr5B 96.866 2872 72 8 2133 4995 617167605 617164743 0.000000e+00 4789.0
11 TraesCS2B01G333000 chr5B 77.836 3235 671 41 2045 5257 392048035 392044825 0.000000e+00 1960.0
12 TraesCS2B01G333000 chr5B 94.072 641 35 3 6691 7329 589576289 589575650 0.000000e+00 970.0
13 TraesCS2B01G333000 chr5B 87.558 643 73 4 6694 7329 476891836 476892478 0.000000e+00 737.0
14 TraesCS2B01G333000 chrUn 92.097 2480 187 7 2787 5259 93944357 93941880 0.000000e+00 3485.0
15 TraesCS2B01G333000 chrUn 87.480 639 73 4 6695 7326 10583001 10583639 0.000000e+00 730.0
16 TraesCS2B01G333000 chr7A 82.218 3228 534 24 2046 5259 664293460 664290259 0.000000e+00 2745.0
17 TraesCS2B01G333000 chr7A 80.093 648 111 11 6691 7329 536146111 536145473 4.000000e-127 466.0
18 TraesCS2B01G333000 chr7B 82.654 2675 434 19 2046 4704 691262315 691259655 0.000000e+00 2342.0
19 TraesCS2B01G333000 chr7B 82.039 2266 386 16 2057 4310 535699200 535701456 0.000000e+00 1910.0
20 TraesCS2B01G333000 chr7B 86.604 642 79 2 6694 7329 228177967 228178607 0.000000e+00 702.0
21 TraesCS2B01G333000 chr1B 77.850 3237 669 41 2044 5257 42060498 42063709 0.000000e+00 1962.0
22 TraesCS2B01G333000 chr1B 77.605 451 81 14 65 507 597440834 597441272 9.440000e-64 255.0
23 TraesCS2B01G333000 chr1B 77.574 272 46 10 285 546 6706845 6707111 4.580000e-32 150.0
24 TraesCS2B01G333000 chr2A 94.468 1157 39 2 5260 6391 539325811 539326967 0.000000e+00 1759.0
25 TraesCS2B01G333000 chr2A 94.329 1111 42 11 790 1895 539324487 539325581 0.000000e+00 1683.0
26 TraesCS2B01G333000 chr2A 87.584 298 13 6 6417 6691 539326968 539327264 2.550000e-84 324.0
27 TraesCS2B01G333000 chr2A 96.875 160 4 1 1891 2049 539325660 539325819 4.360000e-67 267.0
28 TraesCS2B01G333000 chr2A 85.714 196 24 4 1 196 539019129 539019320 3.470000e-48 204.0
29 TraesCS2B01G333000 chr2A 91.667 60 5 0 727 786 539019326 539019385 4.710000e-12 84.2
30 TraesCS2B01G333000 chr2A 100.000 28 0 0 656 683 36193803 36193776 1.300000e-02 52.8
31 TraesCS2B01G333000 chr2D 89.288 1391 97 20 676 2050 402260000 402261354 0.000000e+00 1696.0
32 TraesCS2B01G333000 chr2D 85.171 1342 126 34 5261 6579 402261346 402262637 0.000000e+00 1308.0
33 TraesCS2B01G333000 chr2D 86.688 631 64 7 1 628 402259388 402260001 0.000000e+00 682.0
34 TraesCS2B01G333000 chr2D 76.271 649 137 12 6695 7329 630327772 630327127 5.480000e-86 329.0
35 TraesCS2B01G333000 chr5D 79.471 643 122 6 6695 7329 537338064 537338704 1.450000e-121 448.0
36 TraesCS2B01G333000 chr6D 82.041 490 87 1 6695 7184 179848596 179849084 4.090000e-112 416.0
37 TraesCS2B01G333000 chr5A 76.234 547 114 12 8 546 125189524 125188986 7.240000e-70 276.0
38 TraesCS2B01G333000 chr5A 75.909 220 50 3 155 373 147491305 147491088 7.770000e-20 110.0
39 TraesCS2B01G333000 chr5A 76.923 143 29 4 406 546 19074735 19074875 2.190000e-10 78.7
40 TraesCS2B01G333000 chr5A 94.872 39 1 1 619 656 215147010 215146972 7.940000e-05 60.2
41 TraesCS2B01G333000 chr3B 74.061 559 117 20 9 555 448582819 448583361 3.470000e-48 204.0
42 TraesCS2B01G333000 chr3B 84.106 151 20 2 408 554 151403047 151402897 7.660000e-30 143.0
43 TraesCS2B01G333000 chr3B 95.122 41 2 0 627 667 788914644 788914684 1.710000e-06 65.8
44 TraesCS2B01G333000 chr3B 95.122 41 2 0 627 667 788970665 788970705 1.710000e-06 65.8
45 TraesCS2B01G333000 chr3A 90.000 50 4 1 498 546 650012244 650012195 6.140000e-06 63.9
46 TraesCS2B01G333000 chr3A 90.698 43 3 1 614 656 553159618 553159577 1.000000e-03 56.5
47 TraesCS2B01G333000 chr3A 90.698 43 3 1 614 656 625970324 625970365 1.000000e-03 56.5
48 TraesCS2B01G333000 chr6A 89.130 46 5 0 611 656 22789792 22789747 2.860000e-04 58.4
49 TraesCS2B01G333000 chr6A 92.683 41 2 1 614 653 410872279 410872319 2.860000e-04 58.4
50 TraesCS2B01G333000 chr7D 94.118 34 2 0 650 683 36073536 36073569 1.300000e-02 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 TraesCS2B01G333000 chr2B 476409923 476417251 7328 True 13535.000000 13535 100.000 1 7329 1 chr2B.!!$R4 7328
1 TraesCS2B01G333000 chr1A 20083774 20086983 3209 False 5426.000000 5426 97.174 2048 5259 1 chr1A.!!$F1 3211
2 TraesCS2B01G333000 chr1A 312719341 312722546 3205 True 5219.000000 5219 96.029 2046 5259 1 chr1A.!!$R4 3213
3 TraesCS2B01G333000 chr1A 58422075 58425301 3226 True 3528.000000 3528 86.487 2045 5259 1 chr1A.!!$R1 3214
4 TraesCS2B01G333000 chr1A 449826274 449829487 3213 True 2784.000000 2784 82.400 2046 5259 1 chr1A.!!$R5 3213
5 TraesCS2B01G333000 chr5B 617164743 617167605 2862 True 4789.000000 4789 96.866 2133 4995 1 chr5B.!!$R3 2862
6 TraesCS2B01G333000 chr5B 392044825 392048035 3210 True 1960.000000 1960 77.836 2045 5257 1 chr5B.!!$R1 3212
7 TraesCS2B01G333000 chr5B 589575650 589576289 639 True 970.000000 970 94.072 6691 7329 1 chr5B.!!$R2 638
8 TraesCS2B01G333000 chr5B 476891836 476892478 642 False 737.000000 737 87.558 6694 7329 1 chr5B.!!$F1 635
9 TraesCS2B01G333000 chrUn 93941880 93944357 2477 True 3485.000000 3485 92.097 2787 5259 1 chrUn.!!$R1 2472
10 TraesCS2B01G333000 chrUn 10583001 10583639 638 False 730.000000 730 87.480 6695 7326 1 chrUn.!!$F1 631
11 TraesCS2B01G333000 chr7A 664290259 664293460 3201 True 2745.000000 2745 82.218 2046 5259 1 chr7A.!!$R2 3213
12 TraesCS2B01G333000 chr7A 536145473 536146111 638 True 466.000000 466 80.093 6691 7329 1 chr7A.!!$R1 638
13 TraesCS2B01G333000 chr7B 691259655 691262315 2660 True 2342.000000 2342 82.654 2046 4704 1 chr7B.!!$R1 2658
14 TraesCS2B01G333000 chr7B 535699200 535701456 2256 False 1910.000000 1910 82.039 2057 4310 1 chr7B.!!$F2 2253
15 TraesCS2B01G333000 chr7B 228177967 228178607 640 False 702.000000 702 86.604 6694 7329 1 chr7B.!!$F1 635
16 TraesCS2B01G333000 chr1B 42060498 42063709 3211 False 1962.000000 1962 77.850 2044 5257 1 chr1B.!!$F2 3213
17 TraesCS2B01G333000 chr2A 539324487 539327264 2777 False 1008.250000 1759 93.314 790 6691 4 chr2A.!!$F2 5901
18 TraesCS2B01G333000 chr2D 402259388 402262637 3249 False 1228.666667 1696 87.049 1 6579 3 chr2D.!!$F1 6578
19 TraesCS2B01G333000 chr2D 630327127 630327772 645 True 329.000000 329 76.271 6695 7329 1 chr2D.!!$R1 634
20 TraesCS2B01G333000 chr5D 537338064 537338704 640 False 448.000000 448 79.471 6695 7329 1 chr5D.!!$F1 634
21 TraesCS2B01G333000 chr5A 125188986 125189524 538 True 276.000000 276 76.234 8 546 1 chr5A.!!$R1 538
22 TraesCS2B01G333000 chr3B 448582819 448583361 542 False 204.000000 204 74.061 9 555 1 chr3B.!!$F1 546

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
508 515 0.109412 AGGTACACGCGCAACTACTC 60.109 55.000 5.73 0.0 0.00 2.59 F
879 886 0.383231 GTGCAAAAGCACTGCTCTGT 59.617 50.000 12.91 0.0 38.25 3.41 F
1453 1466 0.039165 CGTACTCTCTGTGCTGTGCA 60.039 55.000 0.00 0.0 35.60 4.57 F
1600 1613 0.253044 TCCAGTACAAGCCCATCAGC 59.747 55.000 0.00 0.0 0.00 4.26 F
1739 1754 0.583438 CATATTTGGCACGGCTCTCG 59.417 55.000 0.00 0.0 45.88 4.04 F
2559 2682 1.228583 TGTCGGCTGTCCAGAGTCT 60.229 57.895 0.00 0.0 0.00 3.24 F
2715 2838 2.034179 TCGGTCGTGTGCTTCCATATAG 59.966 50.000 0.00 0.0 0.00 1.31 F
2741 2864 2.451490 TCCTCTGAAAGCTCATCGAGT 58.549 47.619 14.25 0.0 31.39 4.18 F
4236 4370 1.066143 GTGGAGATTGGACGTGTGGAT 60.066 52.381 0.00 0.0 0.00 3.41 F
5336 5481 0.723414 ATGCGTGACTGCTTTGATCG 59.277 50.000 1.69 0.0 35.36 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1434 1447 0.039165 TGCACAGCACAGAGAGTACG 60.039 55.000 0.00 0.00 31.71 3.67 R
2048 2158 0.465824 TGCCTCGGTTTCGGGAAAAA 60.466 50.000 0.00 0.00 39.73 1.94 R
2478 2601 1.331214 TTGCAAAAGGGAGCAAGAGG 58.669 50.000 0.00 0.00 44.98 3.69 R
3113 3238 2.092103 GGAATATGGTGGCCTTGGTGTA 60.092 50.000 3.32 0.00 0.00 2.90 R
3488 3618 4.792704 GCCCATTCGGTGCAATAATGTTAG 60.793 45.833 13.05 5.78 0.00 2.34 R
4163 4294 0.038890 AAGAAAGAAGGGGCTGAGGC 59.961 55.000 0.00 0.00 37.82 4.70 R
4236 4370 2.034053 GCGTTTCACCAATTTGACTCCA 59.966 45.455 0.00 0.00 0.00 3.86 R
4716 4852 3.669824 GCAACTATCTCACGACGAGTTGA 60.670 47.826 21.92 7.55 43.00 3.18 R
5648 5795 1.350351 AGAAATGCAGCACTGTCTCCT 59.650 47.619 0.00 0.00 0.00 3.69 R
6491 6686 0.034476 AAACGGTCCGGAGAAACTCC 59.966 55.000 17.28 0.00 46.44 3.85 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
45 46 2.028476 TCCAACGATCTTCCGTGTTCAT 60.028 45.455 0.00 0.00 42.54 2.57
85 87 2.491271 GCGCCGTCGTACAACTACG 61.491 63.158 0.00 0.00 46.10 3.51
101 103 2.288948 ACTACGACATTGTTAACGGGCA 60.289 45.455 0.26 0.00 0.00 5.36
147 151 8.562892 CCCTTGCAGACAATATTTATACTCAAG 58.437 37.037 0.00 0.00 34.61 3.02
152 156 7.442364 GCAGACAATATTTATACTCAAGAGGCA 59.558 37.037 1.73 0.00 0.00 4.75
153 157 8.768955 CAGACAATATTTATACTCAAGAGGCAC 58.231 37.037 1.73 0.00 0.00 5.01
155 159 7.573710 ACAATATTTATACTCAAGAGGCACCA 58.426 34.615 1.73 0.00 0.00 4.17
205 211 5.689383 GGCAACAAATAGAGTCACTTTGA 57.311 39.130 18.77 0.00 34.69 2.69
229 235 6.023334 AGGAATGCAAAAAGGAGATAGGAT 57.977 37.500 0.00 0.00 0.00 3.24
236 242 5.135383 CAAAAAGGAGATAGGATGGATGCA 58.865 41.667 0.00 0.00 0.00 3.96
242 248 2.113233 AGATAGGATGGATGCAGGGAGA 59.887 50.000 0.00 0.00 0.00 3.71
252 258 0.251354 TGCAGGGAGAGCATTCAGAC 59.749 55.000 0.00 0.00 37.02 3.51
267 273 0.735632 CAGACTGCTCCAAGCTCGTC 60.736 60.000 11.42 11.42 42.97 4.20
268 274 1.803519 GACTGCTCCAAGCTCGTCG 60.804 63.158 0.11 0.00 42.97 5.12
276 282 2.097036 TCCAAGCTCGTCGAGGAATTA 58.903 47.619 23.09 0.00 0.00 1.40
283 289 4.038042 AGCTCGTCGAGGAATTATTCATCA 59.962 41.667 23.09 4.53 40.29 3.07
286 292 5.902681 TCGTCGAGGAATTATTCATCAAGT 58.097 37.500 17.76 0.00 40.29 3.16
295 301 8.701895 AGGAATTATTCATCAAGTTGCAATGAT 58.298 29.630 9.30 9.30 36.74 2.45
304 310 4.283978 TCAAGTTGCAATGATGTGGGAATT 59.716 37.500 0.59 0.00 0.00 2.17
305 311 5.479724 TCAAGTTGCAATGATGTGGGAATTA 59.520 36.000 0.59 0.00 0.00 1.40
318 324 4.349636 TGTGGGAATTAGAGACTTTGTGGA 59.650 41.667 0.00 0.00 0.00 4.02
374 380 2.526304 TTGTCGAGGACAAGGTGAAG 57.474 50.000 7.07 0.00 45.88 3.02
378 384 1.002011 GAGGACAAGGTGAAGGGGC 60.002 63.158 0.00 0.00 0.00 5.80
379 385 1.774217 AGGACAAGGTGAAGGGGCA 60.774 57.895 0.00 0.00 0.00 5.36
380 386 1.303643 GGACAAGGTGAAGGGGCAG 60.304 63.158 0.00 0.00 0.00 4.85
381 387 1.973812 GACAAGGTGAAGGGGCAGC 60.974 63.158 0.00 0.00 36.57 5.25
392 399 3.804329 GGGCAGCCCGAACCCATA 61.804 66.667 17.05 0.00 43.64 2.74
398 405 2.691011 GCAGCCCGAACCCATAATTTTA 59.309 45.455 0.00 0.00 0.00 1.52
407 414 6.919115 CCGAACCCATAATTTTAATAAACCCG 59.081 38.462 0.00 0.00 0.00 5.28
425 432 1.676014 CCGGAGAACAAGTCCACATCC 60.676 57.143 0.00 0.00 33.14 3.51
426 433 1.676014 CGGAGAACAAGTCCACATCCC 60.676 57.143 0.00 0.00 33.14 3.85
432 439 2.184533 ACAAGTCCACATCCCGTATCA 58.815 47.619 0.00 0.00 0.00 2.15
498 505 1.269166 CGAGATGAACAGGTACACGC 58.731 55.000 0.00 0.00 0.00 5.34
502 509 0.601576 ATGAACAGGTACACGCGCAA 60.602 50.000 5.73 0.00 0.00 4.85
508 515 0.109412 AGGTACACGCGCAACTACTC 60.109 55.000 5.73 0.00 0.00 2.59
515 522 1.927174 ACGCGCAACTACTCAATGATC 59.073 47.619 5.73 0.00 0.00 2.92
549 556 4.015872 GTGGATCCACAGTGAAAACCTA 57.984 45.455 35.21 0.00 45.53 3.08
550 557 4.003648 GTGGATCCACAGTGAAAACCTAG 58.996 47.826 35.21 0.00 45.53 3.02
551 558 3.009033 TGGATCCACAGTGAAAACCTAGG 59.991 47.826 11.44 7.41 0.00 3.02
552 559 3.263425 GGATCCACAGTGAAAACCTAGGA 59.737 47.826 17.98 0.00 0.00 2.94
553 560 4.508662 GATCCACAGTGAAAACCTAGGAG 58.491 47.826 17.98 0.00 0.00 3.69
554 561 3.583228 TCCACAGTGAAAACCTAGGAGA 58.417 45.455 17.98 0.00 0.00 3.71
555 562 3.971305 TCCACAGTGAAAACCTAGGAGAA 59.029 43.478 17.98 0.00 0.00 2.87
556 563 4.410883 TCCACAGTGAAAACCTAGGAGAAA 59.589 41.667 17.98 0.00 0.00 2.52
557 564 5.104277 TCCACAGTGAAAACCTAGGAGAAAA 60.104 40.000 17.98 0.00 0.00 2.29
558 565 5.592688 CCACAGTGAAAACCTAGGAGAAAAA 59.407 40.000 17.98 0.00 0.00 1.94
559 566 6.459710 CCACAGTGAAAACCTAGGAGAAAAAC 60.460 42.308 17.98 6.47 0.00 2.43
560 567 5.296035 ACAGTGAAAACCTAGGAGAAAAACG 59.704 40.000 17.98 0.50 0.00 3.60
561 568 5.526111 CAGTGAAAACCTAGGAGAAAAACGA 59.474 40.000 17.98 0.00 0.00 3.85
571 578 5.752892 AGGAGAAAAACGAAGGAGAAAAC 57.247 39.130 0.00 0.00 0.00 2.43
593 600 6.173427 ACCAAGGAGTTTAATGTTTGCATT 57.827 33.333 0.00 0.00 46.14 3.56
594 601 5.990996 ACCAAGGAGTTTAATGTTTGCATTG 59.009 36.000 3.39 0.00 44.32 2.82
636 643 7.568199 TTTTCTTTTTGAACTACTCCCTCTG 57.432 36.000 0.00 0.00 33.88 3.35
637 644 5.888982 TCTTTTTGAACTACTCCCTCTGT 57.111 39.130 0.00 0.00 0.00 3.41
638 645 6.248569 TCTTTTTGAACTACTCCCTCTGTT 57.751 37.500 0.00 0.00 0.00 3.16
639 646 6.289064 TCTTTTTGAACTACTCCCTCTGTTC 58.711 40.000 0.00 0.00 39.18 3.18
640 647 4.618920 TTTGAACTACTCCCTCTGTTCC 57.381 45.455 0.00 0.00 38.29 3.62
641 648 3.254093 TGAACTACTCCCTCTGTTCCA 57.746 47.619 0.00 0.00 38.29 3.53
642 649 3.583228 TGAACTACTCCCTCTGTTCCAA 58.417 45.455 0.00 0.00 38.29 3.53
643 650 3.971305 TGAACTACTCCCTCTGTTCCAAA 59.029 43.478 0.00 0.00 38.29 3.28
644 651 4.597507 TGAACTACTCCCTCTGTTCCAAAT 59.402 41.667 0.00 0.00 38.29 2.32
645 652 5.073144 TGAACTACTCCCTCTGTTCCAAATT 59.927 40.000 0.00 0.00 38.29 1.82
646 653 6.271391 TGAACTACTCCCTCTGTTCCAAATTA 59.729 38.462 0.00 0.00 38.29 1.40
647 654 6.051179 ACTACTCCCTCTGTTCCAAATTAC 57.949 41.667 0.00 0.00 0.00 1.89
648 655 5.785940 ACTACTCCCTCTGTTCCAAATTACT 59.214 40.000 0.00 0.00 0.00 2.24
649 656 5.167303 ACTCCCTCTGTTCCAAATTACTC 57.833 43.478 0.00 0.00 0.00 2.59
650 657 4.184629 CTCCCTCTGTTCCAAATTACTCG 58.815 47.826 0.00 0.00 0.00 4.18
651 658 3.581332 TCCCTCTGTTCCAAATTACTCGT 59.419 43.478 0.00 0.00 0.00 4.18
652 659 3.933332 CCCTCTGTTCCAAATTACTCGTC 59.067 47.826 0.00 0.00 0.00 4.20
653 660 3.612860 CCTCTGTTCCAAATTACTCGTCG 59.387 47.826 0.00 0.00 0.00 5.12
654 661 4.235360 CTCTGTTCCAAATTACTCGTCGT 58.765 43.478 0.00 0.00 0.00 4.34
655 662 3.985279 TCTGTTCCAAATTACTCGTCGTG 59.015 43.478 0.00 0.00 0.00 4.35
656 663 3.719924 TGTTCCAAATTACTCGTCGTGT 58.280 40.909 5.19 5.19 0.00 4.49
657 664 4.869215 TGTTCCAAATTACTCGTCGTGTA 58.131 39.130 3.14 3.14 0.00 2.90
658 665 5.288015 TGTTCCAAATTACTCGTCGTGTAA 58.712 37.500 18.92 18.92 34.87 2.41
659 666 5.927689 TGTTCCAAATTACTCGTCGTGTAAT 59.072 36.000 21.15 21.15 40.90 1.89
660 667 6.424509 TGTTCCAAATTACTCGTCGTGTAATT 59.575 34.615 27.40 27.40 46.33 1.40
666 673 5.827568 TTACTCGTCGTGTAATTTGGAAC 57.172 39.130 14.17 0.00 0.00 3.62
667 674 2.727798 ACTCGTCGTGTAATTTGGAACG 59.272 45.455 0.00 0.00 37.38 3.95
668 675 2.060284 TCGTCGTGTAATTTGGAACGG 58.940 47.619 0.00 0.00 36.70 4.44
669 676 2.060284 CGTCGTGTAATTTGGAACGGA 58.940 47.619 0.00 0.00 36.70 4.69
670 677 2.091588 CGTCGTGTAATTTGGAACGGAG 59.908 50.000 0.00 0.00 36.70 4.63
671 678 2.414138 GTCGTGTAATTTGGAACGGAGG 59.586 50.000 0.00 0.00 36.70 4.30
672 679 1.735571 CGTGTAATTTGGAACGGAGGG 59.264 52.381 0.00 0.00 32.55 4.30
673 680 2.613474 CGTGTAATTTGGAACGGAGGGA 60.613 50.000 0.00 0.00 32.55 4.20
674 681 3.007635 GTGTAATTTGGAACGGAGGGAG 58.992 50.000 0.00 0.00 0.00 4.30
675 682 2.640826 TGTAATTTGGAACGGAGGGAGT 59.359 45.455 0.00 0.00 0.00 3.85
676 683 3.839490 TGTAATTTGGAACGGAGGGAGTA 59.161 43.478 0.00 0.00 0.00 2.59
687 694 5.277857 ACGGAGGGAGTATGTATTTCAAG 57.722 43.478 0.00 0.00 0.00 3.02
695 702 8.993424 AGGGAGTATGTATTTCAAGTATGAACT 58.007 33.333 0.00 0.00 45.01 3.01
696 703 9.046296 GGGAGTATGTATTTCAAGTATGAACTG 57.954 37.037 0.00 0.00 45.01 3.16
761 768 7.923344 TCTTATGTTTGTAGATGCTCTAAGCTC 59.077 37.037 0.11 0.00 42.97 4.09
762 769 5.405935 TGTTTGTAGATGCTCTAAGCTCA 57.594 39.130 0.11 0.00 42.97 4.26
763 770 5.414360 TGTTTGTAGATGCTCTAAGCTCAG 58.586 41.667 0.11 0.00 42.97 3.35
764 771 5.047021 TGTTTGTAGATGCTCTAAGCTCAGT 60.047 40.000 0.11 0.00 42.97 3.41
765 772 4.645762 TGTAGATGCTCTAAGCTCAGTG 57.354 45.455 0.11 0.00 42.97 3.66
766 773 4.273318 TGTAGATGCTCTAAGCTCAGTGA 58.727 43.478 0.11 0.00 42.97 3.41
767 774 4.337836 TGTAGATGCTCTAAGCTCAGTGAG 59.662 45.833 16.21 16.21 42.97 3.51
768 775 2.694628 AGATGCTCTAAGCTCAGTGAGG 59.305 50.000 21.54 5.09 42.97 3.86
769 776 2.222227 TGCTCTAAGCTCAGTGAGGA 57.778 50.000 21.54 9.18 42.97 3.71
770 777 2.529632 TGCTCTAAGCTCAGTGAGGAA 58.470 47.619 21.54 0.00 42.97 3.36
771 778 2.232452 TGCTCTAAGCTCAGTGAGGAAC 59.768 50.000 21.54 5.25 42.97 3.62
772 779 2.733858 GCTCTAAGCTCAGTGAGGAACG 60.734 54.545 21.54 0.00 38.45 3.95
773 780 2.750166 CTCTAAGCTCAGTGAGGAACGA 59.250 50.000 21.54 0.00 0.00 3.85
787 794 3.458189 AGGAACGAGGATGAATTTAGCG 58.542 45.455 0.00 0.00 0.00 4.26
788 795 2.544267 GGAACGAGGATGAATTTAGCGG 59.456 50.000 0.00 0.00 0.00 5.52
808 815 2.858655 GGGGAAGGCAAAGGGGAA 59.141 61.111 0.00 0.00 0.00 3.97
812 819 1.985159 GGGAAGGCAAAGGGGAAAAAT 59.015 47.619 0.00 0.00 0.00 1.82
816 823 2.688477 AGGCAAAGGGGAAAAATGACA 58.312 42.857 0.00 0.00 0.00 3.58
878 885 0.659417 CGTGCAAAAGCACTGCTCTG 60.659 55.000 17.23 6.37 38.25 3.35
879 886 0.383231 GTGCAAAAGCACTGCTCTGT 59.617 50.000 12.91 0.00 38.25 3.41
886 893 5.388944 CAAAAGCACTGCTCTGTTAGATTC 58.611 41.667 3.40 0.00 38.25 2.52
894 901 0.974010 TCTGTTAGATTCCGGCCGGT 60.974 55.000 41.57 26.32 36.47 5.28
1098 1109 1.667830 CCACATCAACGTCGTGCCT 60.668 57.895 0.00 0.00 0.00 4.75
1190 1201 6.069206 GGTAACCCTCCTTAAACCCTAATTCT 60.069 42.308 0.00 0.00 0.00 2.40
1192 1203 5.105853 ACCCTCCTTAAACCCTAATTCTCA 58.894 41.667 0.00 0.00 0.00 3.27
1349 1360 0.981183 CTTGCCCCTGGTGTACACTA 59.019 55.000 24.55 18.46 0.00 2.74
1422 1435 2.992593 TGCCAATTTGCGATAGTGGTA 58.007 42.857 0.00 0.00 39.35 3.25
1427 1440 4.739716 CCAATTTGCGATAGTGGTAATTGC 59.260 41.667 0.00 0.00 33.96 3.56
1428 1441 4.568152 ATTTGCGATAGTGGTAATTGCC 57.432 40.909 5.49 5.49 33.49 4.52
1429 1442 3.275617 TTGCGATAGTGGTAATTGCCT 57.724 42.857 14.11 0.00 33.49 4.75
1430 1443 2.833794 TGCGATAGTGGTAATTGCCTC 58.166 47.619 14.11 10.23 33.49 4.70
1431 1444 2.169561 TGCGATAGTGGTAATTGCCTCA 59.830 45.455 14.11 2.30 33.49 3.86
1432 1445 3.181455 TGCGATAGTGGTAATTGCCTCAT 60.181 43.478 14.11 6.69 33.49 2.90
1433 1446 3.815401 GCGATAGTGGTAATTGCCTCATT 59.185 43.478 14.11 2.00 39.35 2.57
1434 1447 4.083802 GCGATAGTGGTAATTGCCTCATTC 60.084 45.833 14.11 9.66 39.35 2.67
1453 1466 0.039165 CGTACTCTCTGTGCTGTGCA 60.039 55.000 0.00 0.00 35.60 4.57
1458 1471 1.657594 CTCTCTGTGCTGTGCATAACG 59.342 52.381 0.00 0.00 41.91 3.18
1468 1481 3.845178 CTGTGCATAACGAGTTCACCTA 58.155 45.455 0.00 0.00 0.00 3.08
1474 1487 5.069119 TGCATAACGAGTTCACCTATGATCT 59.931 40.000 0.00 0.00 37.55 2.75
1484 1497 6.212388 AGTTCACCTATGATCTTGAGTGTCTT 59.788 38.462 10.60 0.00 31.96 3.01
1490 1503 5.627182 ATGATCTTGAGTGTCTTATGCCT 57.373 39.130 0.00 0.00 0.00 4.75
1513 1526 8.903820 GCCTTATACCATTTTCAGTTCTACAAT 58.096 33.333 0.00 0.00 0.00 2.71
1600 1613 0.253044 TCCAGTACAAGCCCATCAGC 59.747 55.000 0.00 0.00 0.00 4.26
1690 1703 7.910162 TGCTTAATTCAATCTTTCTATTCACGC 59.090 33.333 0.00 0.00 0.00 5.34
1692 1705 9.214953 CTTAATTCAATCTTTCTATTCACGCAC 57.785 33.333 0.00 0.00 0.00 5.34
1739 1754 0.583438 CATATTTGGCACGGCTCTCG 59.417 55.000 0.00 0.00 45.88 4.04
1772 1787 2.286872 GACAGCTAGTCCGCACTACTA 58.713 52.381 5.33 0.00 41.56 1.82
1795 1810 7.775093 ACTACTTGCAATATCACATGTTATGGT 59.225 33.333 0.00 0.00 33.60 3.55
1803 1818 9.184062 CAATATCACATGTTATGGTGCAATTAC 57.816 33.333 0.00 0.00 35.04 1.89
1811 1826 8.970293 CATGTTATGGTGCAATTACATATGTTG 58.030 33.333 14.77 7.66 0.00 3.33
2039 2149 6.596497 GGTTCTGATAACGGAATGTTAAGGAA 59.404 38.462 0.00 0.00 45.72 3.36
2040 2150 7.413767 GGTTCTGATAACGGAATGTTAAGGAAC 60.414 40.741 0.00 14.80 45.72 3.62
2118 2230 5.740513 GCAGAGAGGAGAGTTTGTTACAACT 60.741 44.000 0.00 0.00 0.00 3.16
2307 2424 1.441738 CATGACACGAGCATGGTCAA 58.558 50.000 23.68 4.92 43.93 3.18
2478 2601 1.380302 ACAAGAGATGTGGCCCACC 59.620 57.895 12.25 0.00 41.93 4.61
2559 2682 1.228583 TGTCGGCTGTCCAGAGTCT 60.229 57.895 0.00 0.00 0.00 3.24
2715 2838 2.034179 TCGGTCGTGTGCTTCCATATAG 59.966 50.000 0.00 0.00 0.00 1.31
2741 2864 2.451490 TCCTCTGAAAGCTCATCGAGT 58.549 47.619 14.25 0.00 31.39 4.18
3113 3238 3.740115 AGCAAACTTATCGGTGTTGAGT 58.260 40.909 0.00 0.00 0.00 3.41
3488 3618 3.823304 ACTCTGAAGAATGTTTCCCAAGC 59.177 43.478 0.00 0.00 0.00 4.01
3831 3962 4.643784 ACCGTTTAAGAGTATCCTCGATGT 59.356 41.667 0.00 0.00 42.86 3.06
3851 3982 3.198236 GAAGTGCAAAGCAGCGCCA 62.198 57.895 2.29 0.00 45.81 5.69
4163 4294 2.969628 AGGCCTAAAGTCAGTGATCG 57.030 50.000 1.29 0.00 0.00 3.69
4236 4370 1.066143 GTGGAGATTGGACGTGTGGAT 60.066 52.381 0.00 0.00 0.00 3.41
4559 4695 1.251251 GCCATGCTTTAGCCTATGGG 58.749 55.000 17.75 0.00 41.96 4.00
4716 4852 1.209747 CTTAAGCCTCGCCCTAAGGTT 59.790 52.381 0.00 0.00 36.21 3.50
4935 5078 4.574674 TGCTAACCACTTCCATGAATCT 57.425 40.909 0.00 0.00 0.00 2.40
5336 5481 0.723414 ATGCGTGACTGCTTTGATCG 59.277 50.000 1.69 0.00 35.36 3.69
5445 5590 1.425066 AGATGTTCTTGGGCAGTTGGA 59.575 47.619 0.00 0.00 0.00 3.53
5446 5591 1.815003 GATGTTCTTGGGCAGTTGGAG 59.185 52.381 0.00 0.00 0.00 3.86
5461 5606 5.122396 GCAGTTGGAGTATTTAAGGACACAG 59.878 44.000 0.00 0.00 0.00 3.66
5579 5724 7.754851 TTCTGGGGTTTTAACAGTATTCTTC 57.245 36.000 0.00 0.00 34.02 2.87
5593 5738 9.530633 AACAGTATTCTTCGGTGATTAAGTATC 57.469 33.333 0.00 0.00 0.00 2.24
5594 5739 8.692710 ACAGTATTCTTCGGTGATTAAGTATCA 58.307 33.333 0.00 0.00 40.96 2.15
5633 5780 1.337703 TCACAGCAGCAAATTGGTCAC 59.662 47.619 0.00 0.00 0.00 3.67
5685 5836 8.454570 TGCATTTCTTCACATGTATACATCAT 57.545 30.769 15.60 4.45 33.61 2.45
5831 5982 0.973496 TAGGTAGCCGCACCACATGA 60.973 55.000 0.00 0.00 41.40 3.07
6070 6222 1.092345 GGTTTGATCTGAGGCTCGGC 61.092 60.000 18.72 6.24 0.00 5.54
6088 6240 2.684881 CGGCTGGAAAGCTGAATATGTT 59.315 45.455 0.02 0.00 43.49 2.71
6188 6361 7.012704 CACTATGTATCAAAAGCCTGCTAACAT 59.987 37.037 0.00 0.00 0.00 2.71
6365 6559 0.250467 GCACACCTGGACAGTGATGT 60.250 55.000 17.94 1.27 35.33 3.06
6374 6568 3.081061 TGGACAGTGATGTTGTTATGGC 58.919 45.455 0.00 0.00 0.00 4.40
6396 6591 2.579207 CGAAGCGAGGGAGTTATTCA 57.421 50.000 0.00 0.00 0.00 2.57
6397 6592 2.888594 CGAAGCGAGGGAGTTATTCAA 58.111 47.619 0.00 0.00 0.00 2.69
6400 6595 3.252974 AGCGAGGGAGTTATTCAACTG 57.747 47.619 0.00 0.00 45.18 3.16
6411 6606 7.834068 GAGTTATTCAACTGCAACTATCTCA 57.166 36.000 0.00 0.00 45.18 3.27
6420 6615 5.251764 ACTGCAACTATCTCAGCAAAATCT 58.748 37.500 0.00 0.00 36.44 2.40
6433 6628 7.177216 TCTCAGCAAAATCTCATGGTTGTTTAT 59.823 33.333 0.00 0.00 0.00 1.40
6435 6630 8.801299 TCAGCAAAATCTCATGGTTGTTTATTA 58.199 29.630 0.00 0.00 0.00 0.98
6436 6631 9.079833 CAGCAAAATCTCATGGTTGTTTATTAG 57.920 33.333 0.00 0.00 0.00 1.73
6579 6796 3.724508 TGTGGTTGGCACATAAAACTG 57.275 42.857 0.00 0.00 39.30 3.16
6635 6852 7.755591 TCTTGCTCATTAGATTTCACATTCAC 58.244 34.615 0.00 0.00 0.00 3.18
6646 6863 4.829064 TTCACATTCACAGCAACCTAAC 57.171 40.909 0.00 0.00 0.00 2.34
6660 6878 5.297278 AGCAACCTAACGTTACATTCAACAA 59.703 36.000 3.29 0.00 31.77 2.83
6664 6882 6.488817 ACCTAACGTTACATTCAACAAACAC 58.511 36.000 3.29 0.00 0.00 3.32
6691 6909 4.040755 AGTAACCTGGGCTACATCTGATT 58.959 43.478 0.00 0.00 0.00 2.57
6692 6910 4.475016 AGTAACCTGGGCTACATCTGATTT 59.525 41.667 0.00 0.00 0.00 2.17
6736 6956 8.034215 CCAAGTTTATTCAGCAAAATCCACATA 58.966 33.333 0.00 0.00 0.00 2.29
7058 7278 2.040145 TGTTGCTGGATCATGAACTCCA 59.960 45.455 15.66 15.66 39.23 3.86
7229 7459 2.483889 GGGGTAGCTCTTACATGCACTC 60.484 54.545 0.00 0.00 33.73 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.101582 GGAGGATAGTGATGTCGTTGCT 59.898 50.000 0.00 0.00 0.00 3.91
6 7 2.159099 TGGAGGATAGTGATGTCGTTGC 60.159 50.000 0.00 0.00 0.00 4.17
45 46 1.146774 TCCCCCATTTGCAAAGTCTCA 59.853 47.619 18.19 0.00 0.00 3.27
85 87 1.136169 GTCGTGCCCGTTAACAATGTC 60.136 52.381 6.39 0.00 35.01 3.06
86 88 0.869730 GTCGTGCCCGTTAACAATGT 59.130 50.000 6.39 0.00 35.01 2.71
87 89 1.153353 AGTCGTGCCCGTTAACAATG 58.847 50.000 6.39 0.00 35.01 2.82
89 91 1.068281 TGTAGTCGTGCCCGTTAACAA 59.932 47.619 6.39 0.00 35.01 2.83
93 95 0.672889 TGTTGTAGTCGTGCCCGTTA 59.327 50.000 0.00 0.00 35.01 3.18
101 103 2.494870 GGAGTACCCATGTTGTAGTCGT 59.505 50.000 15.72 0.00 38.82 4.34
152 156 5.263599 TCAGATATGGCTTTCACAAATGGT 58.736 37.500 0.00 0.00 0.00 3.55
153 157 5.840243 TCAGATATGGCTTTCACAAATGG 57.160 39.130 0.00 0.00 0.00 3.16
155 159 5.537674 GGGATCAGATATGGCTTTCACAAAT 59.462 40.000 0.00 0.00 0.00 2.32
164 169 1.921049 CCATGGGGATCAGATATGGCT 59.079 52.381 2.85 0.00 35.59 4.75
165 170 2.431954 CCATGGGGATCAGATATGGC 57.568 55.000 2.85 0.00 35.59 4.40
197 202 5.128499 TCCTTTTTGCATTCCTTCAAAGTGA 59.872 36.000 0.00 0.00 34.21 3.41
205 211 5.831103 TCCTATCTCCTTTTTGCATTCCTT 58.169 37.500 0.00 0.00 0.00 3.36
229 235 4.078167 ATGCTCTCCCTGCATCCA 57.922 55.556 0.00 0.00 46.80 3.41
236 242 0.540923 GCAGTCTGAATGCTCTCCCT 59.459 55.000 21.50 0.00 40.59 4.20
252 258 1.515952 CTCGACGAGCTTGGAGCAG 60.516 63.158 12.67 0.00 45.56 4.24
267 273 6.122850 TGCAACTTGATGAATAATTCCTCG 57.877 37.500 0.00 0.00 0.00 4.63
268 274 8.192774 TCATTGCAACTTGATGAATAATTCCTC 58.807 33.333 0.00 0.00 0.00 3.71
283 289 4.895668 AATTCCCACATCATTGCAACTT 57.104 36.364 0.00 0.00 0.00 2.66
286 292 5.357878 GTCTCTAATTCCCACATCATTGCAA 59.642 40.000 0.00 0.00 0.00 4.08
295 301 4.349636 TCCACAAAGTCTCTAATTCCCACA 59.650 41.667 0.00 0.00 0.00 4.17
305 311 8.954350 CATCTTATCAATTTCCACAAAGTCTCT 58.046 33.333 0.00 0.00 0.00 3.10
326 332 5.008619 TGTGCAAAATGACACAACATCTT 57.991 34.783 0.00 0.00 43.48 2.40
378 384 4.993029 TTAAAATTATGGGTTCGGGCTG 57.007 40.909 0.00 0.00 0.00 4.85
379 385 7.418139 GGTTTATTAAAATTATGGGTTCGGGCT 60.418 37.037 0.00 0.00 0.00 5.19
380 386 6.702723 GGTTTATTAAAATTATGGGTTCGGGC 59.297 38.462 0.00 0.00 0.00 6.13
381 387 7.211573 GGGTTTATTAAAATTATGGGTTCGGG 58.788 38.462 0.00 0.00 0.00 5.14
392 399 8.185506 ACTTGTTCTCCGGGTTTATTAAAATT 57.814 30.769 0.00 0.00 0.00 1.82
398 405 3.073356 TGGACTTGTTCTCCGGGTTTATT 59.927 43.478 0.00 0.00 0.00 1.40
407 414 1.676014 CGGGATGTGGACTTGTTCTCC 60.676 57.143 0.00 0.00 0.00 3.71
425 432 4.248691 TCTGATCTGCATCTTGATACGG 57.751 45.455 0.00 0.00 0.00 4.02
426 433 8.476657 AATAATCTGATCTGCATCTTGATACG 57.523 34.615 0.00 0.00 0.00 3.06
453 460 9.823647 GGAGATTCTGATGTATCTGTAGAAAAA 57.176 33.333 0.00 0.00 31.77 1.94
460 467 5.380900 TCTCGGAGATTCTGATGTATCTGT 58.619 41.667 2.97 0.00 31.77 3.41
472 479 3.810310 ACCTGTTCATCTCGGAGATTC 57.190 47.619 17.65 11.49 31.32 2.52
498 505 4.201753 CCACAAGATCATTGAGTAGTTGCG 60.202 45.833 10.61 0.00 0.00 4.85
502 509 4.469227 AGCTCCACAAGATCATTGAGTAGT 59.531 41.667 10.61 0.00 0.00 2.73
508 515 4.275196 CCACATAGCTCCACAAGATCATTG 59.725 45.833 0.00 0.00 0.00 2.82
515 522 2.171237 TGGATCCACATAGCTCCACAAG 59.829 50.000 11.44 0.00 32.92 3.16
549 556 4.579340 GGTTTTCTCCTTCGTTTTTCTCCT 59.421 41.667 0.00 0.00 0.00 3.69
550 557 4.337274 TGGTTTTCTCCTTCGTTTTTCTCC 59.663 41.667 0.00 0.00 0.00 3.71
551 558 5.494632 TGGTTTTCTCCTTCGTTTTTCTC 57.505 39.130 0.00 0.00 0.00 2.87
552 559 5.163550 CCTTGGTTTTCTCCTTCGTTTTTCT 60.164 40.000 0.00 0.00 0.00 2.52
553 560 5.041287 CCTTGGTTTTCTCCTTCGTTTTTC 58.959 41.667 0.00 0.00 0.00 2.29
554 561 4.707934 TCCTTGGTTTTCTCCTTCGTTTTT 59.292 37.500 0.00 0.00 0.00 1.94
555 562 4.274978 TCCTTGGTTTTCTCCTTCGTTTT 58.725 39.130 0.00 0.00 0.00 2.43
556 563 3.883489 CTCCTTGGTTTTCTCCTTCGTTT 59.117 43.478 0.00 0.00 0.00 3.60
557 564 3.118000 ACTCCTTGGTTTTCTCCTTCGTT 60.118 43.478 0.00 0.00 0.00 3.85
558 565 2.438392 ACTCCTTGGTTTTCTCCTTCGT 59.562 45.455 0.00 0.00 0.00 3.85
559 566 3.127425 ACTCCTTGGTTTTCTCCTTCG 57.873 47.619 0.00 0.00 0.00 3.79
560 567 6.954487 TTAAACTCCTTGGTTTTCTCCTTC 57.046 37.500 0.00 0.00 39.66 3.46
561 568 6.839134 ACATTAAACTCCTTGGTTTTCTCCTT 59.161 34.615 0.00 0.00 39.66 3.36
571 578 5.990996 ACAATGCAAACATTAAACTCCTTGG 59.009 36.000 0.00 0.00 44.83 3.61
610 617 9.284968 CAGAGGGAGTAGTTCAAAAAGAAAATA 57.715 33.333 0.00 0.00 38.13 1.40
618 625 4.410883 TGGAACAGAGGGAGTAGTTCAAAA 59.589 41.667 0.00 0.00 41.49 2.44
628 635 4.184629 CGAGTAATTTGGAACAGAGGGAG 58.815 47.826 0.00 0.00 42.39 4.30
629 636 3.581332 ACGAGTAATTTGGAACAGAGGGA 59.419 43.478 0.00 0.00 42.39 4.20
630 637 3.933332 GACGAGTAATTTGGAACAGAGGG 59.067 47.826 0.00 0.00 42.39 4.30
631 638 3.612860 CGACGAGTAATTTGGAACAGAGG 59.387 47.826 0.00 0.00 42.39 3.69
632 639 4.090066 CACGACGAGTAATTTGGAACAGAG 59.910 45.833 0.00 0.00 42.39 3.35
633 640 3.985279 CACGACGAGTAATTTGGAACAGA 59.015 43.478 0.00 0.00 42.39 3.41
634 641 3.739300 ACACGACGAGTAATTTGGAACAG 59.261 43.478 0.00 0.00 42.39 3.16
635 642 3.719924 ACACGACGAGTAATTTGGAACA 58.280 40.909 0.00 0.00 0.00 3.18
636 643 5.827568 TTACACGACGAGTAATTTGGAAC 57.172 39.130 12.90 0.00 0.00 3.62
643 650 5.061311 CGTTCCAAATTACACGACGAGTAAT 59.939 40.000 20.44 20.44 42.32 1.89
644 651 4.382457 CGTTCCAAATTACACGACGAGTAA 59.618 41.667 18.01 18.01 36.06 2.24
645 652 3.913763 CGTTCCAAATTACACGACGAGTA 59.086 43.478 0.00 0.26 34.49 2.59
646 653 2.727798 CGTTCCAAATTACACGACGAGT 59.272 45.455 0.00 1.51 34.49 4.18
647 654 2.091588 CCGTTCCAAATTACACGACGAG 59.908 50.000 0.00 0.00 34.49 4.18
648 655 2.060284 CCGTTCCAAATTACACGACGA 58.940 47.619 0.00 0.00 34.49 4.20
649 656 2.060284 TCCGTTCCAAATTACACGACG 58.940 47.619 0.00 0.00 34.49 5.12
650 657 2.414138 CCTCCGTTCCAAATTACACGAC 59.586 50.000 0.00 0.00 34.49 4.34
651 658 2.613474 CCCTCCGTTCCAAATTACACGA 60.613 50.000 0.00 0.00 34.49 4.35
652 659 1.735571 CCCTCCGTTCCAAATTACACG 59.264 52.381 0.00 0.00 0.00 4.49
653 660 3.007635 CTCCCTCCGTTCCAAATTACAC 58.992 50.000 0.00 0.00 0.00 2.90
654 661 2.640826 ACTCCCTCCGTTCCAAATTACA 59.359 45.455 0.00 0.00 0.00 2.41
655 662 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
656 663 4.472108 ACATACTCCCTCCGTTCCAAATTA 59.528 41.667 0.00 0.00 0.00 1.40
657 664 3.265995 ACATACTCCCTCCGTTCCAAATT 59.734 43.478 0.00 0.00 0.00 1.82
658 665 2.844348 ACATACTCCCTCCGTTCCAAAT 59.156 45.455 0.00 0.00 0.00 2.32
659 666 2.262637 ACATACTCCCTCCGTTCCAAA 58.737 47.619 0.00 0.00 0.00 3.28
660 667 1.946984 ACATACTCCCTCCGTTCCAA 58.053 50.000 0.00 0.00 0.00 3.53
661 668 2.832643 TACATACTCCCTCCGTTCCA 57.167 50.000 0.00 0.00 0.00 3.53
662 669 4.100498 TGAAATACATACTCCCTCCGTTCC 59.900 45.833 0.00 0.00 0.00 3.62
663 670 5.272283 TGAAATACATACTCCCTCCGTTC 57.728 43.478 0.00 0.00 0.00 3.95
664 671 5.189145 ACTTGAAATACATACTCCCTCCGTT 59.811 40.000 0.00 0.00 0.00 4.44
665 672 4.715297 ACTTGAAATACATACTCCCTCCGT 59.285 41.667 0.00 0.00 0.00 4.69
666 673 5.277857 ACTTGAAATACATACTCCCTCCG 57.722 43.478 0.00 0.00 0.00 4.63
667 674 7.963532 TCATACTTGAAATACATACTCCCTCC 58.036 38.462 0.00 0.00 0.00 4.30
668 675 9.262358 GTTCATACTTGAAATACATACTCCCTC 57.738 37.037 0.00 0.00 43.29 4.30
669 676 8.993424 AGTTCATACTTGAAATACATACTCCCT 58.007 33.333 0.00 0.00 43.29 4.20
670 677 9.046296 CAGTTCATACTTGAAATACATACTCCC 57.954 37.037 0.00 0.00 43.29 4.30
671 678 9.601217 ACAGTTCATACTTGAAATACATACTCC 57.399 33.333 0.00 0.00 43.29 3.85
673 680 9.944376 ACACAGTTCATACTTGAAATACATACT 57.056 29.630 0.00 0.00 43.29 2.12
721 728 7.995289 ACAAACATAAGAATGTCACAACAGAA 58.005 30.769 0.00 0.00 45.79 3.02
761 768 3.533606 ATTCATCCTCGTTCCTCACTG 57.466 47.619 0.00 0.00 0.00 3.66
762 769 4.559862 AAATTCATCCTCGTTCCTCACT 57.440 40.909 0.00 0.00 0.00 3.41
763 770 4.271291 GCTAAATTCATCCTCGTTCCTCAC 59.729 45.833 0.00 0.00 0.00 3.51
764 771 4.442706 GCTAAATTCATCCTCGTTCCTCA 58.557 43.478 0.00 0.00 0.00 3.86
765 772 3.491267 CGCTAAATTCATCCTCGTTCCTC 59.509 47.826 0.00 0.00 0.00 3.71
766 773 3.458189 CGCTAAATTCATCCTCGTTCCT 58.542 45.455 0.00 0.00 0.00 3.36
767 774 2.544267 CCGCTAAATTCATCCTCGTTCC 59.456 50.000 0.00 0.00 0.00 3.62
768 775 3.245519 GTCCGCTAAATTCATCCTCGTTC 59.754 47.826 0.00 0.00 0.00 3.95
769 776 3.195661 GTCCGCTAAATTCATCCTCGTT 58.804 45.455 0.00 0.00 0.00 3.85
770 777 2.798499 CGTCCGCTAAATTCATCCTCGT 60.798 50.000 0.00 0.00 0.00 4.18
771 778 1.787155 CGTCCGCTAAATTCATCCTCG 59.213 52.381 0.00 0.00 0.00 4.63
772 779 2.135933 CCGTCCGCTAAATTCATCCTC 58.864 52.381 0.00 0.00 0.00 3.71
773 780 1.202651 CCCGTCCGCTAAATTCATCCT 60.203 52.381 0.00 0.00 0.00 3.24
787 794 2.361230 CCTTTGCCTTCCCCGTCC 60.361 66.667 0.00 0.00 0.00 4.79
788 795 2.361230 CCCTTTGCCTTCCCCGTC 60.361 66.667 0.00 0.00 0.00 4.79
808 815 6.200097 GCGTACAAGGACAAAAATGTCATTTT 59.800 34.615 16.26 16.26 40.25 1.82
812 819 3.880490 AGCGTACAAGGACAAAAATGTCA 59.120 39.130 10.75 0.00 40.38 3.58
816 823 6.651643 TGTATACAGCGTACAAGGACAAAAAT 59.348 34.615 0.08 0.00 0.00 1.82
827 834 3.173599 GCGTTTCTGTATACAGCGTACA 58.826 45.455 25.31 7.49 43.46 2.90
920 927 4.760047 GGCAGCGAGGCGGAAAGA 62.760 66.667 0.00 0.00 33.57 2.52
945 953 4.151883 TCTTCTTCCCAGGTGGATTTTTG 58.848 43.478 0.00 0.00 44.66 2.44
946 954 4.469469 TCTTCTTCCCAGGTGGATTTTT 57.531 40.909 0.00 0.00 44.66 1.94
1098 1109 1.962822 CTTGAAGTGCAGCTCGGCA 60.963 57.895 0.00 0.00 42.53 5.69
1174 1185 7.309194 CCAACACTTGAGAATTAGGGTTTAAGG 60.309 40.741 0.00 0.00 35.90 2.69
1190 1201 2.203480 GGGCAGCCCAACACTTGA 60.203 61.111 27.33 0.00 44.65 3.02
1192 1203 2.748058 CTACGGGCAGCCCAACACTT 62.748 60.000 30.86 8.94 45.83 3.16
1349 1360 1.033574 GAGCAGGCGTATACTGTCCT 58.966 55.000 0.56 2.17 38.22 3.85
1422 1435 4.081420 ACAGAGAGTACGAATGAGGCAATT 60.081 41.667 0.00 0.00 0.00 2.32
1427 1440 2.425312 AGCACAGAGAGTACGAATGAGG 59.575 50.000 0.00 0.00 0.00 3.86
1428 1441 3.119673 ACAGCACAGAGAGTACGAATGAG 60.120 47.826 0.00 0.00 0.00 2.90
1429 1442 2.820197 ACAGCACAGAGAGTACGAATGA 59.180 45.455 0.00 0.00 0.00 2.57
1430 1443 2.919859 CACAGCACAGAGAGTACGAATG 59.080 50.000 0.00 0.00 0.00 2.67
1431 1444 2.672478 GCACAGCACAGAGAGTACGAAT 60.672 50.000 0.00 0.00 0.00 3.34
1432 1445 1.335964 GCACAGCACAGAGAGTACGAA 60.336 52.381 0.00 0.00 0.00 3.85
1433 1446 0.241213 GCACAGCACAGAGAGTACGA 59.759 55.000 0.00 0.00 0.00 3.43
1434 1447 0.039165 TGCACAGCACAGAGAGTACG 60.039 55.000 0.00 0.00 31.71 3.67
1453 1466 7.068839 ACTCAAGATCATAGGTGAACTCGTTAT 59.931 37.037 0.00 0.00 36.58 1.89
1458 1471 5.971763 ACACTCAAGATCATAGGTGAACTC 58.028 41.667 13.17 0.00 36.58 3.01
1468 1481 5.627182 AGGCATAAGACACTCAAGATCAT 57.373 39.130 0.00 0.00 0.00 2.45
1474 1487 6.553953 TGGTATAAGGCATAAGACACTCAA 57.446 37.500 0.00 0.00 0.00 3.02
1484 1497 9.555727 GTAGAACTGAAAATGGTATAAGGCATA 57.444 33.333 0.00 0.00 0.00 3.14
1513 1526 5.045651 TGCCTCAAAATCATTCACCTCTAGA 60.046 40.000 0.00 0.00 0.00 2.43
1600 1613 2.033550 GGAGAGTAGCTGTATGTCACCG 59.966 54.545 0.00 0.00 0.00 4.94
1615 1628 4.464597 GTGACTGGTATCTTCTTGGAGAGT 59.535 45.833 0.00 0.00 0.00 3.24
1690 1703 3.325870 TCTTGCTCTCACATAAACGGTG 58.674 45.455 0.00 0.00 37.60 4.94
1692 1705 3.997021 ACTTCTTGCTCTCACATAAACGG 59.003 43.478 0.00 0.00 0.00 4.44
1739 1754 1.968540 GCTGTCAGTTGCCTCACCC 60.969 63.158 0.93 0.00 0.00 4.61
1772 1787 6.681120 GCACCATAACATGTGATATTGCAAGT 60.681 38.462 17.79 0.00 0.00 3.16
1803 1818 4.987408 TGGACAGGCAATTCAACATATG 57.013 40.909 0.00 0.00 0.00 1.78
1811 1826 7.573843 GCATATTAGTACATGGACAGGCAATTC 60.574 40.741 11.55 0.00 0.00 2.17
2048 2158 0.465824 TGCCTCGGTTTCGGGAAAAA 60.466 50.000 0.00 0.00 39.73 1.94
2049 2159 0.465824 TTGCCTCGGTTTCGGGAAAA 60.466 50.000 0.00 0.00 39.73 2.29
2050 2160 0.465824 TTTGCCTCGGTTTCGGGAAA 60.466 50.000 0.00 0.00 39.73 3.13
2051 2161 0.465824 TTTTGCCTCGGTTTCGGGAA 60.466 50.000 0.00 0.00 39.73 3.97
2052 2162 0.887387 CTTTTGCCTCGGTTTCGGGA 60.887 55.000 0.00 0.00 39.73 5.14
2053 2163 1.579429 CTTTTGCCTCGGTTTCGGG 59.421 57.895 0.00 0.00 36.95 5.14
2054 2164 1.170290 ACCTTTTGCCTCGGTTTCGG 61.170 55.000 0.00 0.00 36.95 4.30
2118 2230 1.616374 TCATGCCGTGTAAGAGTGACA 59.384 47.619 0.00 0.00 0.00 3.58
2320 2437 1.897560 CAGGAGTCCCCAACAGAAAC 58.102 55.000 5.25 0.00 37.41 2.78
2478 2601 1.331214 TTGCAAAAGGGAGCAAGAGG 58.669 50.000 0.00 0.00 44.98 3.69
2715 2838 4.981674 CGATGAGCTTTCAGAGGATTCTAC 59.018 45.833 0.00 0.00 30.73 2.59
2741 2864 2.095213 GTCGCTCGTGCATAATTTCCAA 59.905 45.455 10.43 0.00 39.64 3.53
3113 3238 2.092103 GGAATATGGTGGCCTTGGTGTA 60.092 50.000 3.32 0.00 0.00 2.90
3488 3618 4.792704 GCCCATTCGGTGCAATAATGTTAG 60.793 45.833 13.05 5.78 0.00 2.34
3831 3962 1.577328 GGCGCTGCTTTGCACTTCTA 61.577 55.000 7.64 0.00 33.79 2.10
3851 3982 5.895636 TGCAAGTTTCGTAATTGGATCAT 57.104 34.783 0.00 0.00 0.00 2.45
4163 4294 0.038890 AAGAAAGAAGGGGCTGAGGC 59.961 55.000 0.00 0.00 37.82 4.70
4236 4370 2.034053 GCGTTTCACCAATTTGACTCCA 59.966 45.455 0.00 0.00 0.00 3.86
4559 4695 3.942115 GCAAGGAGGAGAAAGAACCATAC 59.058 47.826 0.00 0.00 0.00 2.39
4716 4852 3.669824 GCAACTATCTCACGACGAGTTGA 60.670 47.826 21.92 7.55 43.00 3.18
4935 5078 1.992557 ACTTCTGGGTTTCCATGCCTA 59.007 47.619 0.00 0.00 43.11 3.93
5216 5361 7.787725 AGAACAATAGGAACATTAATCGGAC 57.212 36.000 0.00 0.00 0.00 4.79
5336 5481 7.163001 AGGAGCAATTTCTGAAAAATACTCC 57.837 36.000 23.38 23.38 40.18 3.85
5416 5561 6.106648 TGCCCAAGAACATCTCTATATCAG 57.893 41.667 0.00 0.00 32.46 2.90
5508 5653 1.745115 GGCATGTGTGGCTAAGCGA 60.745 57.895 0.00 0.00 46.64 4.93
5540 5685 4.638865 ACCCCAGAAACGCTATCATTTTAC 59.361 41.667 0.00 0.00 0.00 2.01
5593 5738 7.113965 GCTGTGATTGAAAACTGACAAATAGTG 59.886 37.037 0.00 0.00 0.00 2.74
5594 5739 7.141363 GCTGTGATTGAAAACTGACAAATAGT 58.859 34.615 0.00 0.00 0.00 2.12
5633 5780 4.641396 TGTCTCCTGTGTACCATTTTGAG 58.359 43.478 0.00 0.00 0.00 3.02
5648 5795 1.350351 AGAAATGCAGCACTGTCTCCT 59.650 47.619 0.00 0.00 0.00 3.69
5655 5802 2.889045 ACATGTGAAGAAATGCAGCACT 59.111 40.909 0.00 0.00 0.00 4.40
5685 5836 8.133024 AGGCAAATGGTGTTAAAATCTTATCA 57.867 30.769 0.00 0.00 0.00 2.15
5693 5844 3.471680 GCCAAGGCAAATGGTGTTAAAA 58.528 40.909 6.14 0.00 40.23 1.52
6070 6222 5.884792 AGGAAGAACATATTCAGCTTTCCAG 59.115 40.000 8.72 0.00 37.67 3.86
6088 6240 4.971282 ACATACCCATGAATCTCAGGAAGA 59.029 41.667 0.00 0.00 35.73 2.87
6365 6559 3.183259 GCTTCGCGGCCATAACAA 58.817 55.556 6.13 0.00 0.00 2.83
6383 6578 4.327680 AGTTGCAGTTGAATAACTCCCTC 58.672 43.478 0.00 0.00 45.12 4.30
6392 6587 4.582869 TGCTGAGATAGTTGCAGTTGAAT 58.417 39.130 0.00 0.00 32.39 2.57
6395 6590 4.754372 TTTGCTGAGATAGTTGCAGTTG 57.246 40.909 0.00 0.00 36.75 3.16
6396 6591 5.709164 AGATTTTGCTGAGATAGTTGCAGTT 59.291 36.000 0.00 0.00 36.75 3.16
6397 6592 5.251764 AGATTTTGCTGAGATAGTTGCAGT 58.748 37.500 0.00 0.00 36.75 4.40
6400 6595 5.808042 TGAGATTTTGCTGAGATAGTTGC 57.192 39.130 0.00 0.00 0.00 4.17
6404 6599 6.318144 ACAACCATGAGATTTTGCTGAGATAG 59.682 38.462 0.00 0.00 0.00 2.08
6406 6601 5.014858 ACAACCATGAGATTTTGCTGAGAT 58.985 37.500 0.00 0.00 0.00 2.75
6407 6602 4.401022 ACAACCATGAGATTTTGCTGAGA 58.599 39.130 0.00 0.00 0.00 3.27
6411 6606 8.806146 ACTAATAAACAACCATGAGATTTTGCT 58.194 29.630 0.00 0.00 0.00 3.91
6420 6615 9.126151 TCAAAAGACACTAATAAACAACCATGA 57.874 29.630 0.00 0.00 0.00 3.07
6433 6628 3.951037 TGCAAAGCCTCAAAAGACACTAA 59.049 39.130 0.00 0.00 0.00 2.24
6435 6630 2.378038 TGCAAAGCCTCAAAAGACACT 58.622 42.857 0.00 0.00 0.00 3.55
6436 6631 2.869233 TGCAAAGCCTCAAAAGACAC 57.131 45.000 0.00 0.00 0.00 3.67
6491 6686 0.034476 AAACGGTCCGGAGAAACTCC 59.966 55.000 17.28 0.00 46.44 3.85
6501 6717 0.729140 GAATGCTGCAAAACGGTCCG 60.729 55.000 10.48 10.48 0.00 4.79
6579 6796 4.450053 AGAGCATGAACTCTGAAATAGGC 58.550 43.478 0.00 0.00 45.36 3.93
6635 6852 5.144359 GTTGAATGTAACGTTAGGTTGCTG 58.856 41.667 8.60 0.00 41.28 4.41
6646 6863 3.728718 GCCAGTGTTTGTTGAATGTAACG 59.271 43.478 0.00 0.00 33.28 3.18
6660 6878 0.110486 CCCAGGTTACTGCCAGTGTT 59.890 55.000 7.83 0.00 43.53 3.32
6664 6882 0.107654 GTAGCCCAGGTTACTGCCAG 60.108 60.000 3.64 0.00 43.53 4.85
6736 6956 5.818678 TGACCAGACTTGTATACCACTTT 57.181 39.130 0.00 0.00 0.00 2.66
6750 6970 1.207329 GGGTGTACCTCATGACCAGAC 59.793 57.143 0.44 0.00 35.85 3.51
7058 7278 1.150567 GCGCTGCTCTTGTGATCGAT 61.151 55.000 0.00 0.00 0.00 3.59
7229 7459 2.035449 TCGGTATTATCAGGAACAGGCG 59.965 50.000 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.