Multiple sequence alignment - TraesCS3B01G505900

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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 TraesCS3B01G505900 chr3B 100.000 3224 0 0 1 3224 749724776 749727999 0.000000e+00 5954
1 TraesCS3B01G505900 chr3B 87.515 1658 157 24 926 2558 749859847 749861479 0.000000e+00 1869
2 TraesCS3B01G505900 chr3B 80.690 1362 216 32 948 2288 749979287 749980622 0.000000e+00 1014
3 TraesCS3B01G505900 chr3B 78.054 1449 249 49 993 2411 748779500 748778091 0.000000e+00 850
4 TraesCS3B01G505900 chr3B 78.730 1260 205 36 872 2100 749648141 749649368 0.000000e+00 784
5 TraesCS3B01G505900 chr3B 76.765 1218 208 50 944 2110 749025876 749024683 2.130000e-171 612
6 TraesCS3B01G505900 chr3B 88.190 525 42 9 1 507 661208652 661209174 2.750000e-170 608
7 TraesCS3B01G505900 chr3B 89.894 188 18 1 3037 3224 749861809 749861995 1.160000e-59 241
8 TraesCS3B01G505900 chr3B 87.264 212 18 6 2743 2951 749861582 749861787 1.930000e-57 233
9 TraesCS3B01G505900 chr3B 93.878 98 5 1 2680 2776 749981572 749981669 2.590000e-31 147
10 TraesCS3B01G505900 chr3B 86.538 104 12 2 630 731 749647933 749648036 2.630000e-21 113
11 TraesCS3B01G505900 chr3D 92.506 2095 113 15 864 2951 562504073 562506130 0.000000e+00 2959
12 TraesCS3B01G505900 chr3D 86.545 2029 206 39 957 2951 562538208 562540203 0.000000e+00 2172
13 TraesCS3B01G505900 chr3D 81.149 1358 203 36 948 2288 562545103 562546424 0.000000e+00 1040
14 TraesCS3B01G505900 chr3D 77.735 1572 263 59 993 2513 561462583 561461048 0.000000e+00 883
15 TraesCS3B01G505900 chr3D 79.884 1203 191 32 926 2100 562348011 562349190 0.000000e+00 833
16 TraesCS3B01G505900 chr3D 79.836 977 136 44 926 1880 562433113 562434050 0.000000e+00 656
17 TraesCS3B01G505900 chr3D 76.407 1208 217 47 944 2110 561711715 561710535 9.960000e-165 590
18 TraesCS3B01G505900 chr3D 97.354 189 4 1 3037 3224 562506152 562506340 1.440000e-83 320
19 TraesCS3B01G505900 chr3D 89.362 188 17 1 3037 3224 562540225 562540409 1.930000e-57 233
20 TraesCS3B01G505900 chr3D 77.647 340 43 14 2475 2791 562565289 562565618 3.310000e-40 176
21 TraesCS3B01G505900 chr3D 81.633 147 23 3 624 769 562432781 562432924 5.650000e-23 119
22 TraesCS3B01G505900 chr3D 80.392 153 27 2 617 769 562347666 562347815 2.630000e-21 113
23 TraesCS3B01G505900 chr3A 92.308 1560 78 18 1190 2747 697617717 697619236 0.000000e+00 2178
24 TraesCS3B01G505900 chr3A 85.203 2041 218 44 948 2951 697673424 697675417 0.000000e+00 2019
25 TraesCS3B01G505900 chr3A 80.502 1354 214 31 948 2288 697679895 697681211 0.000000e+00 992
26 TraesCS3B01G505900 chr3A 92.553 188 8 5 3037 3224 697619535 697619716 6.860000e-67 265
27 TraesCS3B01G505900 chr3A 89.806 206 11 2 2746 2951 697619318 697619513 4.130000e-64 255
28 TraesCS3B01G505900 chr3A 83.065 248 22 12 633 865 697617456 697617698 1.170000e-49 207
29 TraesCS3B01G505900 chr3A 78.171 339 42 14 2475 2791 697681655 697681983 1.530000e-43 187
30 TraesCS3B01G505900 chr3A 97.500 80 2 0 2952 3031 36486890 36486811 1.560000e-28 137
31 TraesCS3B01G505900 chr4D 87.759 531 42 9 1 508 468857472 468856942 1.660000e-167 599
32 TraesCS3B01G505900 chr4D 97.701 87 2 0 2952 3038 85613456 85613370 2.000000e-32 150
33 TraesCS3B01G505900 chr2B 87.573 515 54 7 1 507 686821756 686821244 3.580000e-164 588
34 TraesCS3B01G505900 chr6D 85.714 518 61 10 1 508 50727162 50726648 4.730000e-148 534
35 TraesCS3B01G505900 chr6D 85.631 515 57 9 1 505 429002508 429002001 2.850000e-145 525
36 TraesCS3B01G505900 chr5A 83.588 524 60 19 1 508 485573822 485573309 4.870000e-128 468
37 TraesCS3B01G505900 chr5A 83.661 508 67 13 1 502 561113871 561114368 6.300000e-127 464
38 TraesCS3B01G505900 chr4A 83.142 522 64 15 1 508 609571946 609572457 3.790000e-124 455
39 TraesCS3B01G505900 chr4A 95.699 93 3 1 2952 3044 614697971 614697880 7.210000e-32 148
40 TraesCS3B01G505900 chr4A 96.591 88 3 0 2952 3039 695807873 695807786 2.590000e-31 147
41 TraesCS3B01G505900 chr4A 95.455 88 4 0 2952 3039 695874174 695874087 1.210000e-29 141
42 TraesCS3B01G505900 chr6A 83.074 514 63 18 1 503 109133534 109133034 2.280000e-121 446
43 TraesCS3B01G505900 chr4B 97.753 89 1 1 2952 3039 635010467 635010379 5.570000e-33 152
44 TraesCS3B01G505900 chr1B 96.739 92 1 2 2952 3041 429962085 429962176 5.570000e-33 152
45 TraesCS3B01G505900 chr7A 97.674 86 2 0 2952 3037 603953409 603953324 7.210000e-32 148
46 TraesCS3B01G505900 chr1A 96.471 85 3 0 2952 3036 298125546 298125630 1.210000e-29 141


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 TraesCS3B01G505900 chr3B 749724776 749727999 3223 False 5954.00 5954 100.000000 1 3224 1 chr3B.!!$F2 3223
1 TraesCS3B01G505900 chr3B 748778091 748779500 1409 True 850.00 850 78.054000 993 2411 1 chr3B.!!$R1 1418
2 TraesCS3B01G505900 chr3B 749859847 749861995 2148 False 781.00 1869 88.224333 926 3224 3 chr3B.!!$F4 2298
3 TraesCS3B01G505900 chr3B 749024683 749025876 1193 True 612.00 612 76.765000 944 2110 1 chr3B.!!$R2 1166
4 TraesCS3B01G505900 chr3B 661208652 661209174 522 False 608.00 608 88.190000 1 507 1 chr3B.!!$F1 506
5 TraesCS3B01G505900 chr3B 749979287 749981669 2382 False 580.50 1014 87.284000 948 2776 2 chr3B.!!$F5 1828
6 TraesCS3B01G505900 chr3B 749647933 749649368 1435 False 448.50 784 82.634000 630 2100 2 chr3B.!!$F3 1470
7 TraesCS3B01G505900 chr3D 562504073 562506340 2267 False 1639.50 2959 94.930000 864 3224 2 chr3D.!!$F5 2360
8 TraesCS3B01G505900 chr3D 562538208 562540409 2201 False 1202.50 2172 87.953500 957 3224 2 chr3D.!!$F6 2267
9 TraesCS3B01G505900 chr3D 562545103 562546424 1321 False 1040.00 1040 81.149000 948 2288 1 chr3D.!!$F1 1340
10 TraesCS3B01G505900 chr3D 561461048 561462583 1535 True 883.00 883 77.735000 993 2513 1 chr3D.!!$R1 1520
11 TraesCS3B01G505900 chr3D 561710535 561711715 1180 True 590.00 590 76.407000 944 2110 1 chr3D.!!$R2 1166
12 TraesCS3B01G505900 chr3D 562347666 562349190 1524 False 473.00 833 80.138000 617 2100 2 chr3D.!!$F3 1483
13 TraesCS3B01G505900 chr3D 562432781 562434050 1269 False 387.50 656 80.734500 624 1880 2 chr3D.!!$F4 1256
14 TraesCS3B01G505900 chr3A 697673424 697675417 1993 False 2019.00 2019 85.203000 948 2951 1 chr3A.!!$F1 2003
15 TraesCS3B01G505900 chr3A 697617456 697619716 2260 False 726.25 2178 89.433000 633 3224 4 chr3A.!!$F2 2591
16 TraesCS3B01G505900 chr3A 697679895 697681983 2088 False 589.50 992 79.336500 948 2791 2 chr3A.!!$F3 1843
17 TraesCS3B01G505900 chr4D 468856942 468857472 530 True 599.00 599 87.759000 1 508 1 chr4D.!!$R2 507
18 TraesCS3B01G505900 chr2B 686821244 686821756 512 True 588.00 588 87.573000 1 507 1 chr2B.!!$R1 506
19 TraesCS3B01G505900 chr6D 50726648 50727162 514 True 534.00 534 85.714000 1 508 1 chr6D.!!$R1 507
20 TraesCS3B01G505900 chr6D 429002001 429002508 507 True 525.00 525 85.631000 1 505 1 chr6D.!!$R2 504
21 TraesCS3B01G505900 chr5A 485573309 485573822 513 True 468.00 468 83.588000 1 508 1 chr5A.!!$R1 507
22 TraesCS3B01G505900 chr4A 609571946 609572457 511 False 455.00 455 83.142000 1 508 1 chr4A.!!$F1 507
23 TraesCS3B01G505900 chr6A 109133034 109133534 500 True 446.00 446 83.074000 1 503 1 chr6A.!!$R1 502

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
508 551 0.033228 CGGCTGGAGATGCTCTAAGG 59.967 60.0 0.0 0.0 0.00 2.69 F
561 604 0.033781 CCGAGGGACAACACGGTTAA 59.966 55.0 0.0 0.0 40.42 2.01 F
587 630 0.036010 CCTGGTCTGGCTCGTCAATT 60.036 55.0 0.0 0.0 0.00 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 1954 0.689745 TATAGTTGCCCCGCACTCCT 60.690 55.000 0.0 0.0 38.71 3.69 R
2210 2395 1.916181 AGGGGGATCATTCTTCACGTT 59.084 47.619 0.0 0.0 0.00 3.99 R
2516 3136 4.434593 GCTGCTTGTCATTTTTATTTGGCG 60.435 41.667 0.0 0.0 0.00 5.69 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
51 52 0.678048 GGAGACAGAAGCCCGCAAAT 60.678 55.000 0.00 0.00 0.00 2.32
104 108 2.097918 GACAGCGACGACGACGAT 59.902 61.111 22.94 14.51 42.66 3.73
350 375 9.936759 AATATGTTTAAATTTGAATGAACCCGT 57.063 25.926 0.00 0.00 0.00 5.28
407 444 4.537135 TTTTAAAAATACATGGGCGCCA 57.463 36.364 30.85 15.30 38.19 5.69
416 454 2.982643 ATGGGCGCCATGACTGGAA 61.983 57.895 30.85 1.46 46.37 3.53
418 456 2.268920 GGCGCCATGACTGGAAGA 59.731 61.111 24.80 0.00 46.37 2.87
474 517 3.598678 GGAAACGATGTTTAGCGCC 57.401 52.632 2.29 0.00 39.81 6.53
475 518 1.084289 GGAAACGATGTTTAGCGCCT 58.916 50.000 2.29 0.00 39.81 5.52
476 519 1.062148 GGAAACGATGTTTAGCGCCTC 59.938 52.381 2.29 0.00 39.81 4.70
477 520 1.062148 GAAACGATGTTTAGCGCCTCC 59.938 52.381 2.29 0.00 39.81 4.30
478 521 0.249398 AACGATGTTTAGCGCCTCCT 59.751 50.000 2.29 0.00 39.81 3.69
479 522 0.460284 ACGATGTTTAGCGCCTCCTG 60.460 55.000 2.29 0.00 39.81 3.86
480 523 1.154205 CGATGTTTAGCGCCTCCTGG 61.154 60.000 2.29 0.00 0.00 4.45
481 524 0.815615 GATGTTTAGCGCCTCCTGGG 60.816 60.000 2.29 0.00 38.36 4.45
482 525 1.271840 ATGTTTAGCGCCTCCTGGGA 61.272 55.000 2.29 0.00 37.23 4.37
483 526 1.153349 GTTTAGCGCCTCCTGGGAG 60.153 63.158 2.29 9.53 41.63 4.30
491 534 4.101448 CTCCTGGGAGGCCAACGG 62.101 72.222 5.01 0.00 38.51 4.44
503 546 3.805267 CAACGGCTGGAGATGCTC 58.195 61.111 0.00 0.00 0.00 4.26
504 547 1.220206 CAACGGCTGGAGATGCTCT 59.780 57.895 0.00 0.00 0.00 4.09
505 548 0.461548 CAACGGCTGGAGATGCTCTA 59.538 55.000 0.00 0.00 0.00 2.43
506 549 1.134699 CAACGGCTGGAGATGCTCTAA 60.135 52.381 0.00 0.00 0.00 2.10
507 550 0.749649 ACGGCTGGAGATGCTCTAAG 59.250 55.000 0.00 0.00 0.00 2.18
508 551 0.033228 CGGCTGGAGATGCTCTAAGG 59.967 60.000 0.00 0.00 0.00 2.69
509 552 0.250252 GGCTGGAGATGCTCTAAGGC 60.250 60.000 0.00 0.00 34.71 4.35
510 553 0.758123 GCTGGAGATGCTCTAAGGCT 59.242 55.000 0.00 0.00 0.00 4.58
511 554 1.140652 GCTGGAGATGCTCTAAGGCTT 59.859 52.381 4.58 4.58 0.00 4.35
512 555 2.806382 GCTGGAGATGCTCTAAGGCTTC 60.806 54.545 1.30 0.00 36.87 3.86
513 556 2.433604 CTGGAGATGCTCTAAGGCTTCA 59.566 50.000 1.30 0.00 38.37 3.02
514 557 2.840038 TGGAGATGCTCTAAGGCTTCAA 59.160 45.455 1.30 0.00 38.37 2.69
515 558 3.118482 TGGAGATGCTCTAAGGCTTCAAG 60.118 47.826 1.30 3.55 38.37 3.02
516 559 3.133721 GGAGATGCTCTAAGGCTTCAAGA 59.866 47.826 1.30 0.58 38.37 3.02
517 560 4.370917 GAGATGCTCTAAGGCTTCAAGAG 58.629 47.826 18.61 18.61 39.81 2.85
531 574 5.100751 CTTCAAGAGCTTTTCGTTCATGT 57.899 39.130 0.00 0.00 0.00 3.21
532 575 5.499139 TTCAAGAGCTTTTCGTTCATGTT 57.501 34.783 0.00 0.00 0.00 2.71
533 576 6.612247 TTCAAGAGCTTTTCGTTCATGTTA 57.388 33.333 0.00 0.00 0.00 2.41
534 577 6.801539 TCAAGAGCTTTTCGTTCATGTTAT 57.198 33.333 0.00 0.00 0.00 1.89
535 578 7.202016 TCAAGAGCTTTTCGTTCATGTTATT 57.798 32.000 0.00 0.00 0.00 1.40
536 579 7.648142 TCAAGAGCTTTTCGTTCATGTTATTT 58.352 30.769 0.00 0.00 0.00 1.40
537 580 7.591057 TCAAGAGCTTTTCGTTCATGTTATTTG 59.409 33.333 0.00 0.00 0.00 2.32
538 581 6.970484 AGAGCTTTTCGTTCATGTTATTTGT 58.030 32.000 0.00 0.00 0.00 2.83
539 582 7.078228 AGAGCTTTTCGTTCATGTTATTTGTC 58.922 34.615 0.00 0.00 0.00 3.18
540 583 6.734137 AGCTTTTCGTTCATGTTATTTGTCA 58.266 32.000 0.00 0.00 0.00 3.58
541 584 6.636850 AGCTTTTCGTTCATGTTATTTGTCAC 59.363 34.615 0.00 0.00 0.00 3.67
542 585 6.129194 GCTTTTCGTTCATGTTATTTGTCACC 60.129 38.462 0.00 0.00 0.00 4.02
543 586 5.365403 TTCGTTCATGTTATTTGTCACCC 57.635 39.130 0.00 0.00 0.00 4.61
544 587 3.433957 TCGTTCATGTTATTTGTCACCCG 59.566 43.478 0.00 0.00 0.00 5.28
545 588 3.433957 CGTTCATGTTATTTGTCACCCGA 59.566 43.478 0.00 0.00 0.00 5.14
546 589 4.435518 CGTTCATGTTATTTGTCACCCGAG 60.436 45.833 0.00 0.00 0.00 4.63
547 590 3.605634 TCATGTTATTTGTCACCCGAGG 58.394 45.455 0.00 0.00 0.00 4.63
548 591 2.483014 TGTTATTTGTCACCCGAGGG 57.517 50.000 6.63 6.63 42.03 4.30
549 592 1.979308 TGTTATTTGTCACCCGAGGGA 59.021 47.619 16.26 0.00 38.96 4.20
550 593 2.289819 TGTTATTTGTCACCCGAGGGAC 60.290 50.000 16.26 4.03 38.96 4.46
551 594 1.646912 TATTTGTCACCCGAGGGACA 58.353 50.000 16.26 0.00 41.93 4.02
553 596 1.448497 TTGTCACCCGAGGGACAAC 59.552 57.895 11.07 9.83 46.01 3.32
554 597 1.338890 TTGTCACCCGAGGGACAACA 61.339 55.000 11.07 12.20 46.01 3.33
555 598 1.301479 GTCACCCGAGGGACAACAC 60.301 63.158 16.26 0.06 38.96 3.32
556 599 2.357034 CACCCGAGGGACAACACG 60.357 66.667 16.26 0.00 38.96 4.49
557 600 3.622826 ACCCGAGGGACAACACGG 61.623 66.667 16.26 0.00 44.16 4.94
558 601 3.622826 CCCGAGGGACAACACGGT 61.623 66.667 0.84 0.00 43.22 4.83
559 602 2.424302 CCGAGGGACAACACGGTT 59.576 61.111 0.00 0.00 40.42 4.44
560 603 1.667151 CCGAGGGACAACACGGTTA 59.333 57.895 0.00 0.00 40.42 2.85
561 604 0.033781 CCGAGGGACAACACGGTTAA 59.966 55.000 0.00 0.00 40.42 2.01
562 605 1.338389 CCGAGGGACAACACGGTTAAT 60.338 52.381 0.00 0.00 40.42 1.40
563 606 1.730064 CGAGGGACAACACGGTTAATG 59.270 52.381 0.00 0.00 0.00 1.90
564 607 2.610976 CGAGGGACAACACGGTTAATGA 60.611 50.000 0.00 0.00 0.00 2.57
565 608 3.404899 GAGGGACAACACGGTTAATGAA 58.595 45.455 0.00 0.00 0.00 2.57
566 609 3.143728 AGGGACAACACGGTTAATGAAC 58.856 45.455 0.00 0.00 34.56 3.18
567 610 3.143728 GGGACAACACGGTTAATGAACT 58.856 45.455 0.00 0.00 35.74 3.01
568 611 3.187842 GGGACAACACGGTTAATGAACTC 59.812 47.826 0.00 0.00 35.74 3.01
569 612 3.187842 GGACAACACGGTTAATGAACTCC 59.812 47.826 0.00 0.00 35.74 3.85
570 613 4.062991 GACAACACGGTTAATGAACTCCT 58.937 43.478 0.00 0.00 35.74 3.69
571 614 3.813166 ACAACACGGTTAATGAACTCCTG 59.187 43.478 0.00 0.00 35.74 3.86
572 615 3.053831 ACACGGTTAATGAACTCCTGG 57.946 47.619 0.00 0.00 35.74 4.45
573 616 2.370849 ACACGGTTAATGAACTCCTGGT 59.629 45.455 0.00 0.00 35.74 4.00
574 617 3.000727 CACGGTTAATGAACTCCTGGTC 58.999 50.000 0.00 0.00 35.74 4.02
575 618 2.904434 ACGGTTAATGAACTCCTGGTCT 59.096 45.455 0.00 0.00 35.74 3.85
576 619 3.262420 CGGTTAATGAACTCCTGGTCTG 58.738 50.000 0.00 0.00 35.74 3.51
577 620 3.610911 GGTTAATGAACTCCTGGTCTGG 58.389 50.000 0.00 0.00 35.74 3.86
578 621 3.010420 GTTAATGAACTCCTGGTCTGGC 58.990 50.000 0.00 0.00 32.40 4.85
579 622 1.366319 AATGAACTCCTGGTCTGGCT 58.634 50.000 0.00 0.00 0.00 4.75
580 623 0.908198 ATGAACTCCTGGTCTGGCTC 59.092 55.000 0.00 0.00 0.00 4.70
581 624 1.216710 GAACTCCTGGTCTGGCTCG 59.783 63.158 0.00 0.00 0.00 5.03
582 625 1.534235 AACTCCTGGTCTGGCTCGT 60.534 57.895 0.00 0.00 0.00 4.18
583 626 1.536943 AACTCCTGGTCTGGCTCGTC 61.537 60.000 0.00 0.00 0.00 4.20
584 627 1.979155 CTCCTGGTCTGGCTCGTCA 60.979 63.158 0.00 0.00 0.00 4.35
585 628 1.533033 TCCTGGTCTGGCTCGTCAA 60.533 57.895 0.00 0.00 0.00 3.18
586 629 0.904865 TCCTGGTCTGGCTCGTCAAT 60.905 55.000 0.00 0.00 0.00 2.57
587 630 0.036010 CCTGGTCTGGCTCGTCAATT 60.036 55.000 0.00 0.00 0.00 2.32
588 631 1.611673 CCTGGTCTGGCTCGTCAATTT 60.612 52.381 0.00 0.00 0.00 1.82
589 632 1.734465 CTGGTCTGGCTCGTCAATTTC 59.266 52.381 0.00 0.00 0.00 2.17
590 633 1.347707 TGGTCTGGCTCGTCAATTTCT 59.652 47.619 0.00 0.00 0.00 2.52
591 634 1.734465 GGTCTGGCTCGTCAATTTCTG 59.266 52.381 0.00 0.00 0.00 3.02
592 635 2.417719 GTCTGGCTCGTCAATTTCTGT 58.582 47.619 0.00 0.00 0.00 3.41
593 636 3.585862 GTCTGGCTCGTCAATTTCTGTA 58.414 45.455 0.00 0.00 0.00 2.74
594 637 3.614616 GTCTGGCTCGTCAATTTCTGTAG 59.385 47.826 0.00 0.00 0.00 2.74
595 638 3.258372 TCTGGCTCGTCAATTTCTGTAGT 59.742 43.478 0.00 0.00 0.00 2.73
596 639 3.325870 TGGCTCGTCAATTTCTGTAGTG 58.674 45.455 0.00 0.00 0.00 2.74
597 640 3.006430 TGGCTCGTCAATTTCTGTAGTGA 59.994 43.478 0.00 0.00 0.00 3.41
598 641 3.994392 GGCTCGTCAATTTCTGTAGTGAA 59.006 43.478 0.00 0.00 0.00 3.18
599 642 4.451096 GGCTCGTCAATTTCTGTAGTGAAA 59.549 41.667 0.00 0.00 39.79 2.69
600 643 5.049680 GGCTCGTCAATTTCTGTAGTGAAAA 60.050 40.000 0.00 0.00 39.08 2.29
601 644 6.074005 GCTCGTCAATTTCTGTAGTGAAAAG 58.926 40.000 0.00 0.00 39.08 2.27
602 645 6.073765 GCTCGTCAATTTCTGTAGTGAAAAGA 60.074 38.462 0.00 0.00 39.08 2.52
603 646 7.173863 TCGTCAATTTCTGTAGTGAAAAGAC 57.826 36.000 0.00 0.00 39.08 3.01
604 647 6.202188 TCGTCAATTTCTGTAGTGAAAAGACC 59.798 38.462 14.31 0.00 39.31 3.85
605 648 6.018262 CGTCAATTTCTGTAGTGAAAAGACCA 60.018 38.462 14.31 0.00 39.31 4.02
606 649 7.307989 CGTCAATTTCTGTAGTGAAAAGACCAT 60.308 37.037 14.31 0.00 39.31 3.55
607 650 8.352942 GTCAATTTCTGTAGTGAAAAGACCATT 58.647 33.333 0.00 0.00 39.08 3.16
608 651 9.567776 TCAATTTCTGTAGTGAAAAGACCATTA 57.432 29.630 0.00 0.00 39.08 1.90
612 655 8.974060 TTCTGTAGTGAAAAGACCATTAAAGT 57.026 30.769 0.00 0.00 0.00 2.66
614 657 9.485206 TCTGTAGTGAAAAGACCATTAAAGTAC 57.515 33.333 0.00 0.00 0.00 2.73
615 658 9.490379 CTGTAGTGAAAAGACCATTAAAGTACT 57.510 33.333 0.00 0.00 0.00 2.73
616 659 9.485206 TGTAGTGAAAAGACCATTAAAGTACTC 57.515 33.333 0.00 0.00 0.00 2.59
617 660 9.708092 GTAGTGAAAAGACCATTAAAGTACTCT 57.292 33.333 0.00 0.00 0.00 3.24
618 661 8.608844 AGTGAAAAGACCATTAAAGTACTCTG 57.391 34.615 0.00 0.00 0.00 3.35
619 662 8.429641 AGTGAAAAGACCATTAAAGTACTCTGA 58.570 33.333 0.00 0.00 0.00 3.27
620 663 9.220767 GTGAAAAGACCATTAAAGTACTCTGAT 57.779 33.333 0.00 0.00 0.00 2.90
640 683 9.597170 CTCTGATATAATAAGGATCATGTGTGG 57.403 37.037 0.00 0.00 0.00 4.17
648 691 1.656652 GATCATGTGTGGGACGAAGG 58.343 55.000 0.00 0.00 0.00 3.46
653 696 1.331399 TGTGTGGGACGAAGGTGACA 61.331 55.000 0.00 0.00 0.00 3.58
720 763 8.504815 TCGTAATCCAACGATGAAAAATAAACA 58.495 29.630 0.00 0.00 46.29 2.83
722 765 9.620660 GTAATCCAACGATGAAAAATAAACAGT 57.379 29.630 0.00 0.00 0.00 3.55
723 766 8.519492 AATCCAACGATGAAAAATAAACAGTG 57.481 30.769 0.00 0.00 0.00 3.66
726 769 6.920758 CCAACGATGAAAAATAAACAGTGGAA 59.079 34.615 0.00 0.00 0.00 3.53
727 770 7.598493 CCAACGATGAAAAATAAACAGTGGAAT 59.402 33.333 0.00 0.00 0.00 3.01
729 772 9.620660 AACGATGAAAAATAAACAGTGGAATAC 57.379 29.630 0.00 0.00 0.00 1.89
743 786 4.716784 AGTGGAATACTACTGGAGCATGAA 59.283 41.667 0.00 0.00 38.04 2.57
775 838 2.388232 GCGAAAATGACGCGAGGGT 61.388 57.895 15.93 0.00 46.05 4.34
801 868 1.891150 CACCCGTTACTAGTGTCCTGT 59.109 52.381 5.39 0.00 0.00 4.00
802 869 3.084039 CACCCGTTACTAGTGTCCTGTA 58.916 50.000 5.39 0.00 0.00 2.74
823 897 4.823790 ATATAATCCAACGCCGGAAAAC 57.176 40.909 5.05 0.00 38.95 2.43
836 910 3.999229 CGGAAAACGGATCAAGAAGAG 57.001 47.619 0.00 0.00 39.42 2.85
838 912 3.614616 CGGAAAACGGATCAAGAAGAGAG 59.385 47.826 0.00 0.00 39.42 3.20
840 914 4.867608 GGAAAACGGATCAAGAAGAGAGAG 59.132 45.833 0.00 0.00 0.00 3.20
843 917 3.702792 ACGGATCAAGAAGAGAGAGGAA 58.297 45.455 0.00 0.00 0.00 3.36
845 919 3.068024 CGGATCAAGAAGAGAGAGGAAGG 59.932 52.174 0.00 0.00 0.00 3.46
846 920 4.285863 GGATCAAGAAGAGAGAGGAAGGA 58.714 47.826 0.00 0.00 0.00 3.36
847 921 4.714308 GGATCAAGAAGAGAGAGGAAGGAA 59.286 45.833 0.00 0.00 0.00 3.36
848 922 5.188751 GGATCAAGAAGAGAGAGGAAGGAAA 59.811 44.000 0.00 0.00 0.00 3.13
849 923 5.476091 TCAAGAAGAGAGAGGAAGGAAAC 57.524 43.478 0.00 0.00 0.00 2.78
850 924 4.021894 TCAAGAAGAGAGAGGAAGGAAACG 60.022 45.833 0.00 0.00 0.00 3.60
851 925 2.232696 AGAAGAGAGAGGAAGGAAACGC 59.767 50.000 0.00 0.00 0.00 4.84
852 926 1.633774 AGAGAGAGGAAGGAAACGCA 58.366 50.000 0.00 0.00 0.00 5.24
853 927 2.183679 AGAGAGAGGAAGGAAACGCAT 58.816 47.619 0.00 0.00 0.00 4.73
854 928 2.569404 AGAGAGAGGAAGGAAACGCATT 59.431 45.455 0.00 0.00 0.00 3.56
855 929 3.008485 AGAGAGAGGAAGGAAACGCATTT 59.992 43.478 0.00 0.00 0.00 2.32
856 930 3.753797 GAGAGAGGAAGGAAACGCATTTT 59.246 43.478 0.00 0.00 0.00 1.82
857 931 3.753797 AGAGAGGAAGGAAACGCATTTTC 59.246 43.478 0.05 0.05 42.74 2.29
858 932 3.486383 AGAGGAAGGAAACGCATTTTCA 58.514 40.909 9.39 0.00 44.95 2.69
859 933 3.888930 AGAGGAAGGAAACGCATTTTCAA 59.111 39.130 9.39 0.00 44.95 2.69
860 934 4.340950 AGAGGAAGGAAACGCATTTTCAAA 59.659 37.500 9.39 0.00 44.95 2.69
861 935 5.017294 AGGAAGGAAACGCATTTTCAAAA 57.983 34.783 9.39 0.00 44.95 2.44
862 936 5.423886 AGGAAGGAAACGCATTTTCAAAAA 58.576 33.333 9.39 0.00 44.95 1.94
923 998 9.429359 GTATCCATTCTGTCTACATATTTCCTG 57.571 37.037 0.00 0.00 0.00 3.86
924 999 6.291377 TCCATTCTGTCTACATATTTCCTGC 58.709 40.000 0.00 0.00 0.00 4.85
925 1000 6.100279 TCCATTCTGTCTACATATTTCCTGCT 59.900 38.462 0.00 0.00 0.00 4.24
926 1001 6.426328 CCATTCTGTCTACATATTTCCTGCTC 59.574 42.308 0.00 0.00 0.00 4.26
927 1002 5.537300 TCTGTCTACATATTTCCTGCTCC 57.463 43.478 0.00 0.00 0.00 4.70
1079 1186 2.432628 CGACGACAACCTCCTGCC 60.433 66.667 0.00 0.00 0.00 4.85
1117 1224 3.650950 GCTTCCCCACCTGCCTCA 61.651 66.667 0.00 0.00 0.00 3.86
1566 1720 3.117701 TCACCTTGGTGAATCTGTGGAAA 60.118 43.478 18.98 0.00 0.00 3.13
1782 1954 4.326600 TTTCACCCTAGAGCTACCAGTA 57.673 45.455 0.00 0.00 0.00 2.74
1956 2132 2.282391 GGTCAGGCATGCACACCA 60.282 61.111 21.36 0.00 0.00 4.17
2137 2322 5.756347 GCAGATGAATGTGGGTATAAACGTA 59.244 40.000 0.00 0.00 0.00 3.57
2241 2432 1.991813 TGATCCCCCTGTGTTTGATCA 59.008 47.619 0.00 0.00 39.45 2.92
2297 2491 7.650104 GCAATAGAGAGGTATGTACTTTGAGTC 59.350 40.741 0.00 0.00 0.00 3.36
2340 2930 8.996271 ACAATAGATATTGCAGTCATGTATGTG 58.004 33.333 11.59 0.00 45.24 3.21
2341 2931 8.996271 CAATAGATATTGCAGTCATGTATGTGT 58.004 33.333 0.00 0.00 36.94 3.72
2429 3032 1.610038 CCAGCAAAACTGCACTGATCA 59.390 47.619 0.00 0.00 45.78 2.92
2433 3038 3.190744 AGCAAAACTGCACTGATCATCTG 59.809 43.478 0.00 0.00 37.25 2.90
2516 3136 7.973944 AGTTGTGTAGAAAAACTTTGAATGGTC 59.026 33.333 0.00 0.00 29.98 4.02
2543 3163 6.852345 CCAAATAAAAATGACAAGCAGCAAAC 59.148 34.615 0.00 0.00 0.00 2.93
2621 3241 1.019673 CAGGGATGGCTCAAACGATG 58.980 55.000 0.00 0.00 0.00 3.84
2622 3242 0.749454 AGGGATGGCTCAAACGATGC 60.749 55.000 0.00 0.00 0.00 3.91
2623 3243 1.728490 GGGATGGCTCAAACGATGCC 61.728 60.000 0.00 0.00 46.26 4.40
2629 3249 2.797491 GGCTCAAACGATGCCATTAAC 58.203 47.619 0.00 0.00 45.46 2.01
2630 3250 2.423538 GGCTCAAACGATGCCATTAACT 59.576 45.455 0.00 0.00 45.46 2.24
2631 3251 3.429085 GCTCAAACGATGCCATTAACTG 58.571 45.455 0.00 0.00 0.00 3.16
2632 3252 3.126858 GCTCAAACGATGCCATTAACTGA 59.873 43.478 0.00 0.00 0.00 3.41
2633 3253 4.379394 GCTCAAACGATGCCATTAACTGAA 60.379 41.667 0.00 0.00 0.00 3.02
2634 3254 5.697473 TCAAACGATGCCATTAACTGAAA 57.303 34.783 0.00 0.00 0.00 2.69
2635 3255 6.078202 TCAAACGATGCCATTAACTGAAAA 57.922 33.333 0.00 0.00 0.00 2.29
2758 3649 6.870439 GGGAAAATTTGATAGATGCCATTAGC 59.130 38.462 0.00 0.00 44.14 3.09
2776 3667 7.428826 CCATTAGCTGAAGTTTTATCCCAATC 58.571 38.462 0.00 0.00 0.00 2.67
2779 3670 3.378427 GCTGAAGTTTTATCCCAATCGCT 59.622 43.478 0.00 0.00 0.00 4.93
2978 3873 7.663043 TTTTACTTTCTGGTTACCCATTTGT 57.337 32.000 0.00 0.00 40.90 2.83
2979 3874 8.763984 TTTTACTTTCTGGTTACCCATTTGTA 57.236 30.769 0.00 0.00 40.90 2.41
2980 3875 8.763984 TTTACTTTCTGGTTACCCATTTGTAA 57.236 30.769 0.00 1.09 40.90 2.41
2981 3876 6.644248 ACTTTCTGGTTACCCATTTGTAAC 57.356 37.500 0.00 5.69 46.29 2.50
2991 3886 7.596494 GTTACCCATTTGTAACCTTTTACTCC 58.404 38.462 3.31 0.00 42.99 3.85
2992 3887 5.960704 ACCCATTTGTAACCTTTTACTCCT 58.039 37.500 0.00 0.00 38.78 3.69
2993 3888 6.378745 ACCCATTTGTAACCTTTTACTCCTT 58.621 36.000 0.00 0.00 38.78 3.36
2994 3889 6.492429 ACCCATTTGTAACCTTTTACTCCTTC 59.508 38.462 0.00 0.00 38.78 3.46
2995 3890 6.719829 CCCATTTGTAACCTTTTACTCCTTCT 59.280 38.462 0.00 0.00 38.78 2.85
2996 3891 7.886446 CCCATTTGTAACCTTTTACTCCTTCTA 59.114 37.037 0.00 0.00 38.78 2.10
2997 3892 9.292195 CCATTTGTAACCTTTTACTCCTTCTAA 57.708 33.333 0.00 0.00 38.78 2.10
3000 3895 8.767478 TTGTAACCTTTTACTCCTTCTAATCG 57.233 34.615 0.00 0.00 38.78 3.34
3001 3896 6.815142 TGTAACCTTTTACTCCTTCTAATCGC 59.185 38.462 0.00 0.00 38.78 4.58
3002 3897 5.416271 ACCTTTTACTCCTTCTAATCGCA 57.584 39.130 0.00 0.00 0.00 5.10
3003 3898 5.801380 ACCTTTTACTCCTTCTAATCGCAA 58.199 37.500 0.00 0.00 0.00 4.85
3004 3899 6.415573 ACCTTTTACTCCTTCTAATCGCAAT 58.584 36.000 0.00 0.00 0.00 3.56
3005 3900 6.316390 ACCTTTTACTCCTTCTAATCGCAATG 59.684 38.462 0.00 0.00 0.00 2.82
3006 3901 6.538742 CCTTTTACTCCTTCTAATCGCAATGA 59.461 38.462 0.00 0.00 0.00 2.57
3007 3902 7.065803 CCTTTTACTCCTTCTAATCGCAATGAA 59.934 37.037 0.00 0.00 0.00 2.57
3008 3903 7.915293 TTTACTCCTTCTAATCGCAATGAAA 57.085 32.000 0.00 0.00 0.00 2.69
3009 3904 7.539712 TTACTCCTTCTAATCGCAATGAAAG 57.460 36.000 0.00 0.00 0.00 2.62
3010 3905 4.333926 ACTCCTTCTAATCGCAATGAAAGC 59.666 41.667 0.00 0.00 0.00 3.51
3011 3906 4.260985 TCCTTCTAATCGCAATGAAAGCA 58.739 39.130 0.00 0.00 0.00 3.91
3012 3907 4.333649 TCCTTCTAATCGCAATGAAAGCAG 59.666 41.667 0.00 0.00 0.00 4.24
3013 3908 3.680642 TCTAATCGCAATGAAAGCAGC 57.319 42.857 0.00 0.00 0.00 5.25
3014 3909 2.355756 TCTAATCGCAATGAAAGCAGCC 59.644 45.455 0.00 0.00 0.00 4.85
3015 3910 0.889994 AATCGCAATGAAAGCAGCCA 59.110 45.000 0.00 0.00 0.00 4.75
3016 3911 0.889994 ATCGCAATGAAAGCAGCCAA 59.110 45.000 0.00 0.00 0.00 4.52
3017 3912 0.241749 TCGCAATGAAAGCAGCCAAG 59.758 50.000 0.00 0.00 0.00 3.61
3018 3913 1.349259 CGCAATGAAAGCAGCCAAGC 61.349 55.000 0.00 0.00 0.00 4.01
3028 3923 4.085876 AGCCAAGCTGCATTTCGT 57.914 50.000 1.02 0.00 37.57 3.85
3029 3924 1.878775 AGCCAAGCTGCATTTCGTC 59.121 52.632 1.02 0.00 37.57 4.20
3030 3925 0.890542 AGCCAAGCTGCATTTCGTCA 60.891 50.000 1.02 0.00 37.57 4.35
3031 3926 0.039256 GCCAAGCTGCATTTCGTCAA 60.039 50.000 1.02 0.00 0.00 3.18
3032 3927 1.602668 GCCAAGCTGCATTTCGTCAAA 60.603 47.619 1.02 0.00 0.00 2.69
3033 3928 2.741612 CCAAGCTGCATTTCGTCAAAA 58.258 42.857 1.02 0.00 0.00 2.44
3034 3929 3.122297 CCAAGCTGCATTTCGTCAAAAA 58.878 40.909 1.02 0.00 0.00 1.94
3085 3980 7.041440 TGACTCTTCTTCATTTTTACGCATTCA 60.041 33.333 0.00 0.00 0.00 2.57
3141 4040 3.702045 ACACTCCTGACCATAGCTAACTC 59.298 47.826 0.00 0.00 0.00 3.01
3181 4080 4.379793 CACAAAAGCAAAGATTACACGAGC 59.620 41.667 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.213537 CCACATTTGCGGGCTTCTG 59.786 57.895 0.00 0.00 0.00 3.02
136 140 2.764128 TGCATCCCTCTCCCGGTC 60.764 66.667 0.00 0.00 0.00 4.79
143 147 2.041762 TCCCTGCTGCATCCCTCT 59.958 61.111 1.31 0.00 0.00 3.69
274 294 3.441290 CCTCGCCGTCTTCCTCGT 61.441 66.667 0.00 0.00 0.00 4.18
280 300 4.443266 GCTGCTCCTCGCCGTCTT 62.443 66.667 0.00 0.00 38.05 3.01
347 372 0.302288 TTCAACGCAAACTTCGACGG 59.698 50.000 0.00 0.00 0.00 4.79
350 375 2.786578 GCAAATTCAACGCAAACTTCGA 59.213 40.909 0.00 0.00 0.00 3.71
407 444 1.406069 GGCGTGATGTCTTCCAGTCAT 60.406 52.381 0.00 0.00 0.00 3.06
458 501 1.084289 GGAGGCGCTAAACATCGTTT 58.916 50.000 7.64 0.00 0.00 3.60
459 502 0.249398 AGGAGGCGCTAAACATCGTT 59.751 50.000 7.64 0.00 0.00 3.85
460 503 0.460284 CAGGAGGCGCTAAACATCGT 60.460 55.000 7.64 0.00 0.00 3.73
461 504 1.154205 CCAGGAGGCGCTAAACATCG 61.154 60.000 7.64 0.00 0.00 3.84
462 505 0.815615 CCCAGGAGGCGCTAAACATC 60.816 60.000 7.64 0.00 0.00 3.06
463 506 1.224592 CCCAGGAGGCGCTAAACAT 59.775 57.895 7.64 0.00 0.00 2.71
464 507 1.899437 CTCCCAGGAGGCGCTAAACA 61.899 60.000 7.64 0.00 38.51 2.83
465 508 1.153349 CTCCCAGGAGGCGCTAAAC 60.153 63.158 7.64 0.00 38.51 2.01
466 509 3.309582 CTCCCAGGAGGCGCTAAA 58.690 61.111 7.64 0.00 38.51 1.85
474 517 4.101448 CCGTTGGCCTCCCAGGAG 62.101 72.222 3.32 6.73 43.37 3.69
486 529 3.805267 GAGCATCTCCAGCCGTTG 58.195 61.111 0.00 0.00 0.00 4.10
509 552 5.100751 ACATGAACGAAAAGCTCTTGAAG 57.899 39.130 0.00 0.00 0.00 3.02
510 553 5.499139 AACATGAACGAAAAGCTCTTGAA 57.501 34.783 0.00 0.00 0.00 2.69
511 554 6.801539 ATAACATGAACGAAAAGCTCTTGA 57.198 33.333 0.00 0.00 0.00 3.02
512 555 7.379529 ACAAATAACATGAACGAAAAGCTCTTG 59.620 33.333 0.00 0.00 0.00 3.02
513 556 7.425606 ACAAATAACATGAACGAAAAGCTCTT 58.574 30.769 0.00 0.00 0.00 2.85
514 557 6.970484 ACAAATAACATGAACGAAAAGCTCT 58.030 32.000 0.00 0.00 0.00 4.09
515 558 6.855914 TGACAAATAACATGAACGAAAAGCTC 59.144 34.615 0.00 0.00 0.00 4.09
516 559 6.636850 GTGACAAATAACATGAACGAAAAGCT 59.363 34.615 0.00 0.00 0.00 3.74
517 560 6.129194 GGTGACAAATAACATGAACGAAAAGC 60.129 38.462 0.00 0.00 0.00 3.51
518 561 6.362283 GGGTGACAAATAACATGAACGAAAAG 59.638 38.462 0.00 0.00 0.00 2.27
519 562 6.210078 GGGTGACAAATAACATGAACGAAAA 58.790 36.000 0.00 0.00 0.00 2.29
520 563 5.561145 CGGGTGACAAATAACATGAACGAAA 60.561 40.000 0.00 0.00 0.00 3.46
521 564 4.083749 CGGGTGACAAATAACATGAACGAA 60.084 41.667 0.00 0.00 0.00 3.85
522 565 3.433957 CGGGTGACAAATAACATGAACGA 59.566 43.478 0.00 0.00 0.00 3.85
523 566 3.433957 TCGGGTGACAAATAACATGAACG 59.566 43.478 0.00 0.00 0.00 3.95
524 567 4.142687 CCTCGGGTGACAAATAACATGAAC 60.143 45.833 0.00 0.00 0.00 3.18
525 568 4.006989 CCTCGGGTGACAAATAACATGAA 58.993 43.478 0.00 0.00 0.00 2.57
526 569 3.605634 CCTCGGGTGACAAATAACATGA 58.394 45.455 0.00 0.00 0.00 3.07
527 570 2.682856 CCCTCGGGTGACAAATAACATG 59.317 50.000 0.00 0.00 0.00 3.21
528 571 2.574369 TCCCTCGGGTGACAAATAACAT 59.426 45.455 1.18 0.00 36.47 2.71
529 572 1.979308 TCCCTCGGGTGACAAATAACA 59.021 47.619 1.18 0.00 36.47 2.41
530 573 2.289819 TGTCCCTCGGGTGACAAATAAC 60.290 50.000 0.00 0.00 38.48 1.89
531 574 1.979308 TGTCCCTCGGGTGACAAATAA 59.021 47.619 0.00 0.00 38.48 1.40
532 575 1.646912 TGTCCCTCGGGTGACAAATA 58.353 50.000 0.00 0.00 38.48 1.40
533 576 0.768622 TTGTCCCTCGGGTGACAAAT 59.231 50.000 11.13 0.00 45.64 2.32
534 577 2.222885 TTGTCCCTCGGGTGACAAA 58.777 52.632 11.13 0.00 45.64 2.83
535 578 1.338890 TGTTGTCCCTCGGGTGACAA 61.339 55.000 9.43 9.43 46.23 3.18
536 579 1.762858 TGTTGTCCCTCGGGTGACA 60.763 57.895 0.00 0.00 39.61 3.58
537 580 1.301479 GTGTTGTCCCTCGGGTGAC 60.301 63.158 1.18 0.00 36.47 3.67
538 581 2.863346 CGTGTTGTCCCTCGGGTGA 61.863 63.158 1.18 0.00 36.47 4.02
539 582 2.357034 CGTGTTGTCCCTCGGGTG 60.357 66.667 1.18 0.00 36.47 4.61
540 583 3.622826 CCGTGTTGTCCCTCGGGT 61.623 66.667 1.18 0.00 39.41 5.28
541 584 1.818959 TAACCGTGTTGTCCCTCGGG 61.819 60.000 7.34 0.00 46.06 5.14
542 585 0.033781 TTAACCGTGTTGTCCCTCGG 59.966 55.000 0.00 0.00 46.98 4.63
543 586 1.730064 CATTAACCGTGTTGTCCCTCG 59.270 52.381 0.23 0.00 0.00 4.63
544 587 3.048337 TCATTAACCGTGTTGTCCCTC 57.952 47.619 0.23 0.00 0.00 4.30
545 588 3.143728 GTTCATTAACCGTGTTGTCCCT 58.856 45.455 0.23 0.00 0.00 4.20
546 589 3.143728 AGTTCATTAACCGTGTTGTCCC 58.856 45.455 0.23 0.00 36.15 4.46
547 590 3.187842 GGAGTTCATTAACCGTGTTGTCC 59.812 47.826 0.23 0.00 36.15 4.02
548 591 4.062991 AGGAGTTCATTAACCGTGTTGTC 58.937 43.478 0.23 0.00 36.15 3.18
549 592 3.813166 CAGGAGTTCATTAACCGTGTTGT 59.187 43.478 0.23 0.00 36.15 3.32
550 593 3.188460 CCAGGAGTTCATTAACCGTGTTG 59.812 47.826 0.23 0.00 36.15 3.33
551 594 3.181448 ACCAGGAGTTCATTAACCGTGTT 60.181 43.478 0.00 0.00 36.15 3.32
552 595 2.370849 ACCAGGAGTTCATTAACCGTGT 59.629 45.455 0.00 0.00 36.15 4.49
553 596 3.000727 GACCAGGAGTTCATTAACCGTG 58.999 50.000 0.00 0.00 36.15 4.94
554 597 2.904434 AGACCAGGAGTTCATTAACCGT 59.096 45.455 0.00 0.00 36.15 4.83
555 598 3.262420 CAGACCAGGAGTTCATTAACCG 58.738 50.000 0.00 0.00 36.15 4.44
556 599 3.610911 CCAGACCAGGAGTTCATTAACC 58.389 50.000 0.00 0.00 36.15 2.85
557 600 3.010420 GCCAGACCAGGAGTTCATTAAC 58.990 50.000 0.00 0.00 35.72 2.01
558 601 2.912956 AGCCAGACCAGGAGTTCATTAA 59.087 45.455 0.00 0.00 0.00 1.40
559 602 2.501723 GAGCCAGACCAGGAGTTCATTA 59.498 50.000 0.00 0.00 0.00 1.90
560 603 1.280421 GAGCCAGACCAGGAGTTCATT 59.720 52.381 0.00 0.00 0.00 2.57
561 604 0.908198 GAGCCAGACCAGGAGTTCAT 59.092 55.000 0.00 0.00 0.00 2.57
562 605 1.536073 CGAGCCAGACCAGGAGTTCA 61.536 60.000 0.00 0.00 0.00 3.18
563 606 1.216710 CGAGCCAGACCAGGAGTTC 59.783 63.158 0.00 0.00 0.00 3.01
564 607 1.534235 ACGAGCCAGACCAGGAGTT 60.534 57.895 0.00 0.00 0.00 3.01
565 608 1.979693 GACGAGCCAGACCAGGAGT 60.980 63.158 0.00 0.00 0.00 3.85
566 609 1.536073 TTGACGAGCCAGACCAGGAG 61.536 60.000 0.00 0.00 0.00 3.69
567 610 0.904865 ATTGACGAGCCAGACCAGGA 60.905 55.000 0.00 0.00 0.00 3.86
568 611 0.036010 AATTGACGAGCCAGACCAGG 60.036 55.000 0.00 0.00 0.00 4.45
569 612 1.734465 GAAATTGACGAGCCAGACCAG 59.266 52.381 0.00 0.00 0.00 4.00
570 613 1.347707 AGAAATTGACGAGCCAGACCA 59.652 47.619 0.00 0.00 0.00 4.02
571 614 1.734465 CAGAAATTGACGAGCCAGACC 59.266 52.381 0.00 0.00 0.00 3.85
572 615 2.417719 ACAGAAATTGACGAGCCAGAC 58.582 47.619 0.00 0.00 0.00 3.51
573 616 2.839486 ACAGAAATTGACGAGCCAGA 57.161 45.000 0.00 0.00 0.00 3.86
574 617 3.369147 CACTACAGAAATTGACGAGCCAG 59.631 47.826 0.00 0.00 0.00 4.85
575 618 3.006430 TCACTACAGAAATTGACGAGCCA 59.994 43.478 0.00 0.00 0.00 4.75
576 619 3.585862 TCACTACAGAAATTGACGAGCC 58.414 45.455 0.00 0.00 0.00 4.70
577 620 5.591643 TTTCACTACAGAAATTGACGAGC 57.408 39.130 0.00 0.00 32.88 5.03
578 621 7.284351 GTCTTTTCACTACAGAAATTGACGAG 58.716 38.462 0.00 0.00 37.35 4.18
579 622 6.202188 GGTCTTTTCACTACAGAAATTGACGA 59.798 38.462 0.00 0.00 39.48 4.20
580 623 6.018262 TGGTCTTTTCACTACAGAAATTGACG 60.018 38.462 0.72 0.00 39.48 4.35
581 624 7.259290 TGGTCTTTTCACTACAGAAATTGAC 57.741 36.000 0.00 0.00 38.78 3.18
582 625 8.463930 AATGGTCTTTTCACTACAGAAATTGA 57.536 30.769 0.00 0.00 37.35 2.57
586 629 9.403583 ACTTTAATGGTCTTTTCACTACAGAAA 57.596 29.630 0.00 0.00 35.82 2.52
587 630 8.974060 ACTTTAATGGTCTTTTCACTACAGAA 57.026 30.769 0.00 0.00 0.00 3.02
588 631 9.485206 GTACTTTAATGGTCTTTTCACTACAGA 57.515 33.333 0.00 0.00 0.00 3.41
589 632 9.490379 AGTACTTTAATGGTCTTTTCACTACAG 57.510 33.333 0.00 0.00 0.00 2.74
590 633 9.485206 GAGTACTTTAATGGTCTTTTCACTACA 57.515 33.333 0.00 0.00 0.00 2.74
591 634 9.708092 AGAGTACTTTAATGGTCTTTTCACTAC 57.292 33.333 0.00 0.00 0.00 2.73
592 635 9.706691 CAGAGTACTTTAATGGTCTTTTCACTA 57.293 33.333 0.00 0.00 0.00 2.74
593 636 8.429641 TCAGAGTACTTTAATGGTCTTTTCACT 58.570 33.333 0.00 0.00 0.00 3.41
594 637 8.603242 TCAGAGTACTTTAATGGTCTTTTCAC 57.397 34.615 0.00 0.00 0.00 3.18
614 657 9.597170 CCACACATGATCCTTATTATATCAGAG 57.403 37.037 0.00 0.00 33.40 3.35
615 658 8.542926 CCCACACATGATCCTTATTATATCAGA 58.457 37.037 0.00 0.00 33.40 3.27
616 659 8.542926 TCCCACACATGATCCTTATTATATCAG 58.457 37.037 0.00 0.00 33.40 2.90
617 660 8.321353 GTCCCACACATGATCCTTATTATATCA 58.679 37.037 0.00 0.00 34.35 2.15
618 661 7.492669 CGTCCCACACATGATCCTTATTATATC 59.507 40.741 0.00 0.00 0.00 1.63
619 662 7.180229 TCGTCCCACACATGATCCTTATTATAT 59.820 37.037 0.00 0.00 0.00 0.86
620 663 6.495526 TCGTCCCACACATGATCCTTATTATA 59.504 38.462 0.00 0.00 0.00 0.98
621 664 5.306937 TCGTCCCACACATGATCCTTATTAT 59.693 40.000 0.00 0.00 0.00 1.28
622 665 4.651962 TCGTCCCACACATGATCCTTATTA 59.348 41.667 0.00 0.00 0.00 0.98
623 666 3.454447 TCGTCCCACACATGATCCTTATT 59.546 43.478 0.00 0.00 0.00 1.40
624 667 3.038280 TCGTCCCACACATGATCCTTAT 58.962 45.455 0.00 0.00 0.00 1.73
625 668 2.462723 TCGTCCCACACATGATCCTTA 58.537 47.619 0.00 0.00 0.00 2.69
626 669 1.275666 TCGTCCCACACATGATCCTT 58.724 50.000 0.00 0.00 0.00 3.36
627 670 1.208052 CTTCGTCCCACACATGATCCT 59.792 52.381 0.00 0.00 0.00 3.24
628 671 1.656652 CTTCGTCCCACACATGATCC 58.343 55.000 0.00 0.00 0.00 3.36
629 672 1.066143 ACCTTCGTCCCACACATGATC 60.066 52.381 0.00 0.00 0.00 2.92
630 673 0.984230 ACCTTCGTCCCACACATGAT 59.016 50.000 0.00 0.00 0.00 2.45
631 674 0.034756 CACCTTCGTCCCACACATGA 59.965 55.000 0.00 0.00 0.00 3.07
632 675 0.034756 TCACCTTCGTCCCACACATG 59.965 55.000 0.00 0.00 0.00 3.21
633 676 0.034896 GTCACCTTCGTCCCACACAT 59.965 55.000 0.00 0.00 0.00 3.21
634 677 1.331399 TGTCACCTTCGTCCCACACA 61.331 55.000 0.00 0.00 0.00 3.72
640 683 1.829222 TCCCTTATGTCACCTTCGTCC 59.171 52.381 0.00 0.00 0.00 4.79
648 691 2.550978 CCACGTCATCCCTTATGTCAC 58.449 52.381 0.00 0.00 36.89 3.67
653 696 1.705997 GCCCCCACGTCATCCCTTAT 61.706 60.000 0.00 0.00 0.00 1.73
716 759 4.286032 TGCTCCAGTAGTATTCCACTGTTT 59.714 41.667 0.00 0.00 40.47 2.83
720 763 4.290093 TCATGCTCCAGTAGTATTCCACT 58.710 43.478 0.00 0.00 41.62 4.00
722 765 5.692115 TTTCATGCTCCAGTAGTATTCCA 57.308 39.130 0.00 0.00 0.00 3.53
723 766 6.551385 CATTTCATGCTCCAGTAGTATTCC 57.449 41.667 0.00 0.00 0.00 3.01
738 781 2.600556 CGCCTCATACGTGCATTTCATG 60.601 50.000 0.00 0.00 37.70 3.07
743 786 1.732941 TTTCGCCTCATACGTGCATT 58.267 45.000 0.00 0.00 0.00 3.56
749 792 1.332028 GCGTCATTTTCGCCTCATACG 60.332 52.381 0.00 0.00 46.61 3.06
750 793 2.368980 GCGTCATTTTCGCCTCATAC 57.631 50.000 0.00 0.00 46.61 2.39
775 838 3.230134 ACACTAGTAACGGGTGGTTGTA 58.770 45.455 0.00 0.00 39.75 2.41
801 868 4.448395 CGTTTTCCGGCGTTGGATTATATA 59.552 41.667 6.01 0.00 38.00 0.86
802 869 3.249080 CGTTTTCCGGCGTTGGATTATAT 59.751 43.478 6.01 0.00 38.00 0.86
823 897 3.068024 CCTTCCTCTCTCTTCTTGATCCG 59.932 52.174 0.00 0.00 0.00 4.18
836 910 3.502211 TGAAAATGCGTTTCCTTCCTCTC 59.498 43.478 3.96 0.00 44.41 3.20
838 912 3.915437 TGAAAATGCGTTTCCTTCCTC 57.085 42.857 3.96 0.00 44.41 3.71
840 914 5.726729 TTTTTGAAAATGCGTTTCCTTCC 57.273 34.783 3.96 0.00 44.41 3.46
860 934 5.034797 CGAGCGTTTCCTTTTCTTCTTTTT 58.965 37.500 0.00 0.00 0.00 1.94
861 935 4.334481 TCGAGCGTTTCCTTTTCTTCTTTT 59.666 37.500 0.00 0.00 0.00 2.27
862 936 3.875134 TCGAGCGTTTCCTTTTCTTCTTT 59.125 39.130 0.00 0.00 0.00 2.52
863 937 3.463944 TCGAGCGTTTCCTTTTCTTCTT 58.536 40.909 0.00 0.00 0.00 2.52
864 938 3.107642 TCGAGCGTTTCCTTTTCTTCT 57.892 42.857 0.00 0.00 0.00 2.85
865 939 4.084013 TGAATCGAGCGTTTCCTTTTCTTC 60.084 41.667 10.18 0.00 0.00 2.87
866 940 3.813166 TGAATCGAGCGTTTCCTTTTCTT 59.187 39.130 10.18 0.00 0.00 2.52
867 941 3.399330 TGAATCGAGCGTTTCCTTTTCT 58.601 40.909 10.18 0.00 0.00 2.52
868 942 3.737305 CTGAATCGAGCGTTTCCTTTTC 58.263 45.455 10.18 0.00 0.00 2.29
869 943 2.095718 GCTGAATCGAGCGTTTCCTTTT 60.096 45.455 10.18 0.00 0.00 2.27
870 944 1.464997 GCTGAATCGAGCGTTTCCTTT 59.535 47.619 10.18 0.00 0.00 3.11
936 1011 1.354168 TTTGGAGGGGTTTCGGTGGA 61.354 55.000 0.00 0.00 0.00 4.02
1079 1186 1.872197 GAGGCGGATGAGGATCTCGG 61.872 65.000 0.00 0.00 34.92 4.63
1117 1224 4.241555 GATGAGGGCGGCGTGGAT 62.242 66.667 9.59 0.17 0.00 3.41
1332 1443 3.430862 TGCTTGATTCGCGGGCAC 61.431 61.111 6.13 0.00 0.00 5.01
1566 1720 2.162681 GCATACACTTTTGGCCAGTCT 58.837 47.619 5.11 0.00 0.00 3.24
1782 1954 0.689745 TATAGTTGCCCCGCACTCCT 60.690 55.000 0.00 0.00 38.71 3.69
1933 2109 3.064324 GCATGCCTGACCCACACC 61.064 66.667 6.36 0.00 0.00 4.16
1956 2132 2.356313 CAACTGTCCTCTGCGCGT 60.356 61.111 8.43 0.00 0.00 6.01
2017 2202 6.369890 TGATCTAAGAACACAAAGTCAGCATC 59.630 38.462 0.00 0.00 0.00 3.91
2210 2395 1.916181 AGGGGGATCATTCTTCACGTT 59.084 47.619 0.00 0.00 0.00 3.99
2340 2930 6.619801 ATGAAACACAGGTTCTTAAGACAC 57.380 37.500 4.18 6.93 35.82 3.67
2341 2931 7.338196 TGAAATGAAACACAGGTTCTTAAGACA 59.662 33.333 4.18 0.00 35.82 3.41
2429 3032 4.881019 ACAAACTACTGTCAGCTCAGAT 57.119 40.909 9.28 0.00 38.63 2.90
2516 3136 4.434593 GCTGCTTGTCATTTTTATTTGGCG 60.435 41.667 0.00 0.00 0.00 5.69
2543 3163 9.651718 GCTATATTTTCAGTTATTTGTCTTCCG 57.348 33.333 0.00 0.00 0.00 4.30
2577 3197 5.293569 TCGAGAACACAAAAGAAACTTCCTC 59.706 40.000 0.00 0.00 0.00 3.71
2621 3241 6.757947 ACACATGCATATTTTCAGTTAATGGC 59.242 34.615 0.00 0.00 0.00 4.40
2622 3242 8.597227 CAACACATGCATATTTTCAGTTAATGG 58.403 33.333 0.00 0.00 0.00 3.16
2623 3243 9.142515 ACAACACATGCATATTTTCAGTTAATG 57.857 29.630 0.00 0.00 0.00 1.90
2626 3246 7.880105 TCACAACACATGCATATTTTCAGTTA 58.120 30.769 0.00 0.00 0.00 2.24
2628 3248 6.330004 TCACAACACATGCATATTTTCAGT 57.670 33.333 0.00 0.00 0.00 3.41
2629 3249 6.809689 ACATCACAACACATGCATATTTTCAG 59.190 34.615 0.00 0.00 0.00 3.02
2630 3250 6.689554 ACATCACAACACATGCATATTTTCA 58.310 32.000 0.00 0.00 0.00 2.69
2631 3251 6.254157 GGACATCACAACACATGCATATTTTC 59.746 38.462 0.00 0.00 0.00 2.29
2632 3252 6.101332 GGACATCACAACACATGCATATTTT 58.899 36.000 0.00 0.00 0.00 1.82
2633 3253 5.185442 TGGACATCACAACACATGCATATTT 59.815 36.000 0.00 0.00 0.00 1.40
2634 3254 4.705991 TGGACATCACAACACATGCATATT 59.294 37.500 0.00 0.00 0.00 1.28
2635 3255 4.271661 TGGACATCACAACACATGCATAT 58.728 39.130 0.00 0.00 0.00 1.78
2758 3649 4.731773 GCAGCGATTGGGATAAAACTTCAG 60.732 45.833 0.00 0.00 0.00 3.02
2799 3690 2.099098 GTGGAGTTTGTGGACACCAAAG 59.901 50.000 0.00 0.00 41.03 2.77
2800 3691 2.096248 GTGGAGTTTGTGGACACCAAA 58.904 47.619 0.00 0.00 41.03 3.28
2968 3863 7.093965 AGGAGTAAAAGGTTACAAATGGGTA 57.906 36.000 0.00 0.00 41.88 3.69
2971 3866 7.761038 AGAAGGAGTAAAAGGTTACAAATGG 57.239 36.000 0.00 0.00 41.88 3.16
2974 3869 9.211485 CGATTAGAAGGAGTAAAAGGTTACAAA 57.789 33.333 0.00 0.00 41.88 2.83
2975 3870 7.332678 GCGATTAGAAGGAGTAAAAGGTTACAA 59.667 37.037 0.00 0.00 41.88 2.41
2976 3871 6.815142 GCGATTAGAAGGAGTAAAAGGTTACA 59.185 38.462 0.00 0.00 41.88 2.41
2977 3872 6.815142 TGCGATTAGAAGGAGTAAAAGGTTAC 59.185 38.462 0.00 0.00 40.05 2.50
2978 3873 6.938507 TGCGATTAGAAGGAGTAAAAGGTTA 58.061 36.000 0.00 0.00 0.00 2.85
2979 3874 5.801380 TGCGATTAGAAGGAGTAAAAGGTT 58.199 37.500 0.00 0.00 0.00 3.50
2980 3875 5.416271 TGCGATTAGAAGGAGTAAAAGGT 57.584 39.130 0.00 0.00 0.00 3.50
2981 3876 6.538742 TCATTGCGATTAGAAGGAGTAAAAGG 59.461 38.462 0.00 0.00 0.00 3.11
2982 3877 7.539712 TCATTGCGATTAGAAGGAGTAAAAG 57.460 36.000 0.00 0.00 0.00 2.27
2983 3878 7.915293 TTCATTGCGATTAGAAGGAGTAAAA 57.085 32.000 0.00 0.00 0.00 1.52
2984 3879 7.414098 GCTTTCATTGCGATTAGAAGGAGTAAA 60.414 37.037 1.55 0.00 0.00 2.01
2985 3880 6.037172 GCTTTCATTGCGATTAGAAGGAGTAA 59.963 38.462 1.55 0.00 0.00 2.24
2986 3881 5.523916 GCTTTCATTGCGATTAGAAGGAGTA 59.476 40.000 1.55 0.00 0.00 2.59
2987 3882 4.333926 GCTTTCATTGCGATTAGAAGGAGT 59.666 41.667 1.55 0.00 0.00 3.85
2988 3883 4.333649 TGCTTTCATTGCGATTAGAAGGAG 59.666 41.667 1.55 0.00 0.00 3.69
2989 3884 4.260985 TGCTTTCATTGCGATTAGAAGGA 58.739 39.130 1.55 0.00 0.00 3.36
2990 3885 4.595116 CTGCTTTCATTGCGATTAGAAGG 58.405 43.478 0.00 0.00 0.00 3.46
2991 3886 4.033684 GCTGCTTTCATTGCGATTAGAAG 58.966 43.478 0.00 0.00 0.00 2.85
2992 3887 3.181497 GGCTGCTTTCATTGCGATTAGAA 60.181 43.478 0.00 0.00 0.00 2.10
2993 3888 2.355756 GGCTGCTTTCATTGCGATTAGA 59.644 45.455 0.00 0.00 0.00 2.10
2994 3889 2.097954 TGGCTGCTTTCATTGCGATTAG 59.902 45.455 0.00 0.00 0.00 1.73
2995 3890 2.090760 TGGCTGCTTTCATTGCGATTA 58.909 42.857 0.00 0.00 0.00 1.75
2996 3891 0.889994 TGGCTGCTTTCATTGCGATT 59.110 45.000 0.00 0.00 0.00 3.34
2997 3892 0.889994 TTGGCTGCTTTCATTGCGAT 59.110 45.000 0.00 0.00 0.00 4.58
2998 3893 0.241749 CTTGGCTGCTTTCATTGCGA 59.758 50.000 0.00 0.00 0.00 5.10
2999 3894 1.349259 GCTTGGCTGCTTTCATTGCG 61.349 55.000 0.00 0.00 0.00 4.85
3000 3895 0.037605 AGCTTGGCTGCTTTCATTGC 60.038 50.000 0.00 0.00 40.93 3.56
3011 3906 0.890542 TGACGAAATGCAGCTTGGCT 60.891 50.000 0.00 0.00 40.77 4.75
3012 3907 0.039256 TTGACGAAATGCAGCTTGGC 60.039 50.000 0.00 0.00 0.00 4.52
3013 3908 2.420628 TTTGACGAAATGCAGCTTGG 57.579 45.000 0.00 0.00 0.00 3.61
3034 3929 5.586643 GGATTCGAGATAGGCTGAACTTTTT 59.413 40.000 0.00 0.00 0.00 1.94
3035 3930 5.104735 AGGATTCGAGATAGGCTGAACTTTT 60.105 40.000 0.00 0.00 0.00 2.27
3141 4040 3.616956 TGTGAGGGAGCAAAGTGATAG 57.383 47.619 0.00 0.00 0.00 2.08
3181 4080 8.674263 AAACTCCATCTAATGAATTCTAGCAG 57.326 34.615 7.05 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.