Multiple sequence alignment - TraesCS3A01G495700

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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 TraesCS3A01G495700 chr3A 100.000 3234 0 0 1 3234 721545298 721548531 0.000000e+00 5973
1 TraesCS3A01G495700 chr3A 94.487 2630 96 3 632 3234 741177983 741175376 0.000000e+00 4008
2 TraesCS3A01G495700 chr1A 95.968 2629 78 2 633 3234 376489597 376492224 0.000000e+00 4242
3 TraesCS3A01G495700 chr1A 93.318 2110 94 14 633 2713 549429753 549431844 0.000000e+00 3072
4 TraesCS3A01G495700 chr5A 95.783 2632 83 2 631 3234 509128605 509131236 0.000000e+00 4220
5 TraesCS3A01G495700 chr5A 90.354 622 53 3 16 632 327577960 327577341 0.000000e+00 809
6 TraesCS3A01G495700 chr6A 94.943 2630 101 12 633 3232 532336336 532333709 0.000000e+00 4091
7 TraesCS3A01G495700 chr6A 95.031 2395 111 8 623 3015 615748449 615750837 0.000000e+00 3757
8 TraesCS3A01G495700 chr6A 96.617 1892 62 2 1344 3234 558829543 558831433 0.000000e+00 3138
9 TraesCS3A01G495700 chr2A 94.109 2631 123 9 633 3234 721575155 721577782 0.000000e+00 3971
10 TraesCS3A01G495700 chr4A 97.462 1891 48 0 1344 3234 37984150 37982260 0.000000e+00 3227
11 TraesCS3A01G495700 chr7A 97.197 1891 53 0 1344 3234 704257662 704259552 0.000000e+00 3199
12 TraesCS3A01G495700 chr7A 86.550 171 14 7 2502 2669 704258771 704258935 2.560000e-41 180
13 TraesCS3A01G495700 chr3D 92.716 1977 124 12 633 2605 580652201 580650241 0.000000e+00 2835
14 TraesCS3A01G495700 chr3D 93.382 1904 97 16 633 2508 374010878 374008976 0.000000e+00 2791
15 TraesCS3A01G495700 chr3D 89.810 736 47 15 2502 3234 374009031 374008321 0.000000e+00 918
16 TraesCS3A01G495700 chr3D 89.544 746 45 22 2502 3234 580650377 580649652 0.000000e+00 915
17 TraesCS3A01G495700 chr1B 89.482 618 42 7 16 632 280715069 280714474 0.000000e+00 760


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 TraesCS3A01G495700 chr3A 721545298 721548531 3233 False 5973.0 5973 100.0000 1 3234 1 chr3A.!!$F1 3233
1 TraesCS3A01G495700 chr3A 741175376 741177983 2607 True 4008.0 4008 94.4870 632 3234 1 chr3A.!!$R1 2602
2 TraesCS3A01G495700 chr1A 376489597 376492224 2627 False 4242.0 4242 95.9680 633 3234 1 chr1A.!!$F1 2601
3 TraesCS3A01G495700 chr1A 549429753 549431844 2091 False 3072.0 3072 93.3180 633 2713 1 chr1A.!!$F2 2080
4 TraesCS3A01G495700 chr5A 509128605 509131236 2631 False 4220.0 4220 95.7830 631 3234 1 chr5A.!!$F1 2603
5 TraesCS3A01G495700 chr5A 327577341 327577960 619 True 809.0 809 90.3540 16 632 1 chr5A.!!$R1 616
6 TraesCS3A01G495700 chr6A 532333709 532336336 2627 True 4091.0 4091 94.9430 633 3232 1 chr6A.!!$R1 2599
7 TraesCS3A01G495700 chr6A 615748449 615750837 2388 False 3757.0 3757 95.0310 623 3015 1 chr6A.!!$F2 2392
8 TraesCS3A01G495700 chr6A 558829543 558831433 1890 False 3138.0 3138 96.6170 1344 3234 1 chr6A.!!$F1 1890
9 TraesCS3A01G495700 chr2A 721575155 721577782 2627 False 3971.0 3971 94.1090 633 3234 1 chr2A.!!$F1 2601
10 TraesCS3A01G495700 chr4A 37982260 37984150 1890 True 3227.0 3227 97.4620 1344 3234 1 chr4A.!!$R1 1890
11 TraesCS3A01G495700 chr7A 704257662 704259552 1890 False 1689.5 3199 91.8735 1344 3234 2 chr7A.!!$F1 1890
12 TraesCS3A01G495700 chr3D 580649652 580652201 2549 True 1875.0 2835 91.1300 633 3234 2 chr3D.!!$R2 2601
13 TraesCS3A01G495700 chr3D 374008321 374010878 2557 True 1854.5 2791 91.5960 633 3234 2 chr3D.!!$R1 2601
14 TraesCS3A01G495700 chr1B 280714474 280715069 595 True 760.0 760 89.4820 16 632 1 chr1B.!!$R1 616

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
483 485 0.041982 AGGAACCAGGAGGAGAGGAC 59.958 60.0 0.00 0.00 38.69 3.85 F
566 568 0.096281 AACGCAGTGTGTTGTTCGTG 59.904 50.0 20.85 0.00 45.00 4.35 F
1721 1756 0.393402 CCTGGAGCATGCAAGCACTA 60.393 55.0 21.98 6.98 34.45 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1686 1721 0.458669 CAGGCATGCCATCCTGTTTC 59.541 55.00 37.18 7.34 43.66 2.78 R
1900 1937 4.020543 ACTGGTCAACAACAGCCTTTAAA 58.979 39.13 0.00 0.00 38.25 1.52 R
2841 3006 1.060713 CGTCGTCGTGAAGCAAGAAT 58.939 50.00 0.00 0.00 0.00 2.40 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
68 69 0.175760 CGTGGATGTGGAAGGATCGT 59.824 55.000 0.00 0.00 0.00 3.73
115 116 2.797278 CCGCCTACCGCTTCTCCAT 61.797 63.158 0.00 0.00 35.03 3.41
120 121 1.739338 CTACCGCTTCTCCATCGCCT 61.739 60.000 0.00 0.00 0.00 5.52
136 137 2.034532 CTCACCCACATGCTGCCA 59.965 61.111 0.00 0.00 0.00 4.92
205 207 1.375396 CTTTCGACCATGCCCGTCA 60.375 57.895 5.17 0.00 0.00 4.35
221 223 2.668212 CATCCGCCACAACCGTGT 60.668 61.111 0.00 0.00 41.93 4.49
287 289 3.532155 GCTCTGGCTCCGATCGGT 61.532 66.667 32.15 0.00 36.47 4.69
438 440 3.807538 GCTGTGCGGCCATGTCAG 61.808 66.667 2.24 6.70 0.00 3.51
439 441 2.046988 CTGTGCGGCCATGTCAGA 60.047 61.111 2.24 0.00 0.00 3.27
440 442 1.450848 CTGTGCGGCCATGTCAGAT 60.451 57.895 2.24 0.00 0.00 2.90
441 443 1.712018 CTGTGCGGCCATGTCAGATG 61.712 60.000 2.24 0.00 0.00 2.90
442 444 1.450134 GTGCGGCCATGTCAGATGA 60.450 57.895 2.24 0.00 0.00 2.92
443 445 0.816825 GTGCGGCCATGTCAGATGAT 60.817 55.000 2.24 0.00 0.00 2.45
444 446 0.107066 TGCGGCCATGTCAGATGATT 60.107 50.000 2.24 0.00 0.00 2.57
445 447 0.590195 GCGGCCATGTCAGATGATTC 59.410 55.000 2.24 0.00 0.00 2.52
446 448 1.233019 CGGCCATGTCAGATGATTCC 58.767 55.000 2.24 0.00 0.00 3.01
447 449 1.475571 CGGCCATGTCAGATGATTCCA 60.476 52.381 2.24 0.00 0.00 3.53
448 450 2.812983 CGGCCATGTCAGATGATTCCAT 60.813 50.000 2.24 0.00 35.29 3.41
449 451 2.557056 GGCCATGTCAGATGATTCCATG 59.443 50.000 0.00 5.40 32.09 3.66
454 456 6.650427 CATGTCAGATGATTCCATGGATTT 57.350 37.500 17.06 6.32 32.09 2.17
455 457 6.678878 CATGTCAGATGATTCCATGGATTTC 58.321 40.000 17.06 15.91 32.09 2.17
456 458 5.135383 TGTCAGATGATTCCATGGATTTCC 58.865 41.667 17.06 5.80 32.09 3.13
471 473 4.761163 TCCACAGGGAAGGAACCA 57.239 55.556 0.00 0.00 41.32 3.67
472 474 2.463441 TCCACAGGGAAGGAACCAG 58.537 57.895 0.00 0.00 41.32 4.00
473 475 1.133809 TCCACAGGGAAGGAACCAGG 61.134 60.000 0.00 0.00 41.32 4.45
474 476 1.133809 CCACAGGGAAGGAACCAGGA 61.134 60.000 0.00 0.00 35.59 3.86
475 477 0.326264 CACAGGGAAGGAACCAGGAG 59.674 60.000 0.00 0.00 0.00 3.69
476 478 0.842467 ACAGGGAAGGAACCAGGAGG 60.842 60.000 0.00 0.00 42.21 4.30
477 479 0.547712 CAGGGAAGGAACCAGGAGGA 60.548 60.000 0.00 0.00 38.69 3.71
478 480 0.252927 AGGGAAGGAACCAGGAGGAG 60.253 60.000 0.00 0.00 38.69 3.69
479 481 0.252742 GGGAAGGAACCAGGAGGAGA 60.253 60.000 0.00 0.00 38.69 3.71
480 482 1.199615 GGAAGGAACCAGGAGGAGAG 58.800 60.000 0.00 0.00 38.69 3.20
481 483 1.199615 GAAGGAACCAGGAGGAGAGG 58.800 60.000 0.00 0.00 38.69 3.69
482 484 0.793617 AAGGAACCAGGAGGAGAGGA 59.206 55.000 0.00 0.00 38.69 3.71
483 485 0.041982 AGGAACCAGGAGGAGAGGAC 59.958 60.000 0.00 0.00 38.69 3.85
484 486 0.041982 GGAACCAGGAGGAGAGGACT 59.958 60.000 0.00 0.00 38.69 3.85
485 487 1.480789 GAACCAGGAGGAGAGGACTC 58.519 60.000 0.00 0.00 41.94 3.36
486 488 1.006639 GAACCAGGAGGAGAGGACTCT 59.993 57.143 0.60 0.60 43.78 3.24
487 489 1.089123 ACCAGGAGGAGAGGACTCTT 58.911 55.000 2.97 0.00 40.61 2.85
488 490 2.289467 ACCAGGAGGAGAGGACTCTTA 58.711 52.381 2.97 0.00 40.61 2.10
489 491 2.655407 ACCAGGAGGAGAGGACTCTTAA 59.345 50.000 2.97 0.00 40.61 1.85
490 492 3.295973 CCAGGAGGAGAGGACTCTTAAG 58.704 54.545 2.97 0.00 40.61 1.85
491 493 3.053245 CCAGGAGGAGAGGACTCTTAAGA 60.053 52.174 4.81 4.81 40.61 2.10
492 494 4.387437 CCAGGAGGAGAGGACTCTTAAGAT 60.387 50.000 5.44 0.00 40.61 2.40
493 495 4.584325 CAGGAGGAGAGGACTCTTAAGATG 59.416 50.000 5.44 3.21 40.61 2.90
494 496 3.895041 GGAGGAGAGGACTCTTAAGATGG 59.105 52.174 5.44 0.00 40.61 3.51
495 497 4.542697 GAGGAGAGGACTCTTAAGATGGT 58.457 47.826 5.44 0.94 40.61 3.55
496 498 4.285863 AGGAGAGGACTCTTAAGATGGTG 58.714 47.826 5.44 0.00 40.61 4.17
497 499 4.017037 AGGAGAGGACTCTTAAGATGGTGA 60.017 45.833 5.44 0.00 40.61 4.02
498 500 4.340950 GGAGAGGACTCTTAAGATGGTGAG 59.659 50.000 5.44 0.00 40.61 3.51
499 501 5.197451 GAGAGGACTCTTAAGATGGTGAGA 58.803 45.833 5.44 0.00 40.61 3.27
500 502 5.200483 AGAGGACTCTTAAGATGGTGAGAG 58.800 45.833 5.44 0.00 41.04 3.20
501 503 3.704061 AGGACTCTTAAGATGGTGAGAGC 59.296 47.826 5.44 0.00 39.33 4.09
502 504 3.704061 GGACTCTTAAGATGGTGAGAGCT 59.296 47.826 5.44 0.00 39.33 4.09
503 505 4.441356 GGACTCTTAAGATGGTGAGAGCTG 60.441 50.000 5.44 0.00 39.33 4.24
504 506 4.348486 ACTCTTAAGATGGTGAGAGCTGA 58.652 43.478 5.44 0.00 39.33 4.26
505 507 4.159506 ACTCTTAAGATGGTGAGAGCTGAC 59.840 45.833 5.44 0.00 39.33 3.51
506 508 3.449018 TCTTAAGATGGTGAGAGCTGACC 59.551 47.826 0.00 0.00 37.37 4.02
509 511 3.051210 TGGTGAGAGCTGACCACG 58.949 61.111 4.65 0.00 41.89 4.94
510 512 2.262915 GGTGAGAGCTGACCACGG 59.737 66.667 1.04 0.00 36.81 4.94
511 513 2.574955 GGTGAGAGCTGACCACGGT 61.575 63.158 1.04 0.00 36.81 4.83
512 514 1.373497 GTGAGAGCTGACCACGGTG 60.373 63.158 0.00 0.00 0.00 4.94
513 515 2.433318 GAGAGCTGACCACGGTGC 60.433 66.667 1.68 0.00 0.00 5.01
514 516 3.226429 GAGAGCTGACCACGGTGCA 62.226 63.158 1.68 0.00 0.00 4.57
515 517 2.046892 GAGCTGACCACGGTGCAT 60.047 61.111 1.68 0.00 0.00 3.96
516 518 2.359107 AGCTGACCACGGTGCATG 60.359 61.111 1.68 0.00 0.00 4.06
517 519 3.434319 GCTGACCACGGTGCATGG 61.434 66.667 1.68 3.18 43.43 3.66
518 520 2.747460 CTGACCACGGTGCATGGG 60.747 66.667 9.58 2.42 41.97 4.00
519 521 4.343323 TGACCACGGTGCATGGGG 62.343 66.667 9.58 9.06 41.97 4.96
527 529 4.856801 GTGCATGGGGCCGACGAT 62.857 66.667 0.00 0.00 43.89 3.73
528 530 4.854924 TGCATGGGGCCGACGATG 62.855 66.667 0.00 0.00 43.89 3.84
530 532 4.935495 CATGGGGCCGACGATGGG 62.935 72.222 0.00 0.00 0.00 4.00
562 564 2.941891 CGATAACGCAGTGTGTTGTT 57.058 45.000 28.07 17.05 45.00 2.83
563 565 2.822827 CGATAACGCAGTGTGTTGTTC 58.177 47.619 28.07 22.13 45.00 3.18
564 566 2.717595 CGATAACGCAGTGTGTTGTTCG 60.718 50.000 28.07 27.58 45.00 3.95
565 567 1.642728 TAACGCAGTGTGTTGTTCGT 58.357 45.000 28.07 8.01 45.00 3.85
566 568 0.096281 AACGCAGTGTGTTGTTCGTG 59.904 50.000 20.85 0.00 45.00 4.35
567 569 1.017177 ACGCAGTGTGTTGTTCGTGT 61.017 50.000 2.75 0.00 42.51 4.49
568 570 0.924777 CGCAGTGTGTTGTTCGTGTA 59.075 50.000 0.00 0.00 0.00 2.90
569 571 1.331680 CGCAGTGTGTTGTTCGTGTAC 60.332 52.381 0.00 0.00 0.00 2.90
570 572 1.661617 GCAGTGTGTTGTTCGTGTACA 59.338 47.619 0.00 0.00 0.00 2.90
571 573 2.094575 GCAGTGTGTTGTTCGTGTACAA 59.905 45.455 0.00 0.00 35.75 2.41
572 574 3.425094 GCAGTGTGTTGTTCGTGTACAAA 60.425 43.478 0.00 0.00 39.54 2.83
573 575 4.729458 GCAGTGTGTTGTTCGTGTACAAAT 60.729 41.667 0.00 0.00 39.54 2.32
574 576 5.502706 GCAGTGTGTTGTTCGTGTACAAATA 60.503 40.000 0.00 0.00 39.54 1.40
575 577 6.479436 CAGTGTGTTGTTCGTGTACAAATAA 58.521 36.000 0.00 0.00 39.54 1.40
576 578 6.627276 CAGTGTGTTGTTCGTGTACAAATAAG 59.373 38.462 0.00 0.00 39.54 1.73
577 579 5.905181 GTGTGTTGTTCGTGTACAAATAAGG 59.095 40.000 0.00 0.00 39.54 2.69
578 580 5.007823 TGTGTTGTTCGTGTACAAATAAGGG 59.992 40.000 0.00 0.00 39.54 3.95
579 581 4.515944 TGTTGTTCGTGTACAAATAAGGGG 59.484 41.667 0.00 0.00 39.54 4.79
580 582 3.677190 TGTTCGTGTACAAATAAGGGGG 58.323 45.455 0.00 0.00 0.00 5.40
581 583 3.072768 TGTTCGTGTACAAATAAGGGGGT 59.927 43.478 0.00 0.00 0.00 4.95
582 584 3.615224 TCGTGTACAAATAAGGGGGTC 57.385 47.619 0.00 0.00 0.00 4.46
583 585 2.236893 TCGTGTACAAATAAGGGGGTCC 59.763 50.000 0.00 0.00 0.00 4.46
584 586 2.635714 GTGTACAAATAAGGGGGTCCG 58.364 52.381 0.00 0.00 38.33 4.79
585 587 2.026915 GTGTACAAATAAGGGGGTCCGT 60.027 50.000 0.00 0.00 38.33 4.69
586 588 3.197549 GTGTACAAATAAGGGGGTCCGTA 59.802 47.826 0.00 0.00 38.33 4.02
587 589 3.843027 TGTACAAATAAGGGGGTCCGTAA 59.157 43.478 0.00 0.00 38.33 3.18
588 590 3.639672 ACAAATAAGGGGGTCCGTAAG 57.360 47.619 0.00 0.00 38.33 2.34
601 603 3.920144 CGTAAGGAGTAGTGAGCGG 57.080 57.895 0.00 0.00 0.00 5.52
602 604 1.376543 CGTAAGGAGTAGTGAGCGGA 58.623 55.000 0.00 0.00 0.00 5.54
603 605 1.741706 CGTAAGGAGTAGTGAGCGGAA 59.258 52.381 0.00 0.00 0.00 4.30
604 606 2.223294 CGTAAGGAGTAGTGAGCGGAAG 60.223 54.545 0.00 0.00 0.00 3.46
618 620 2.105323 CGGAAGCAACACAAGACAAC 57.895 50.000 0.00 0.00 0.00 3.32
619 621 1.400142 CGGAAGCAACACAAGACAACA 59.600 47.619 0.00 0.00 0.00 3.33
620 622 2.033299 CGGAAGCAACACAAGACAACAT 59.967 45.455 0.00 0.00 0.00 2.71
621 623 3.632189 GGAAGCAACACAAGACAACATC 58.368 45.455 0.00 0.00 0.00 3.06
622 624 3.066621 GGAAGCAACACAAGACAACATCA 59.933 43.478 0.00 0.00 0.00 3.07
623 625 3.976793 AGCAACACAAGACAACATCAG 57.023 42.857 0.00 0.00 0.00 2.90
624 626 2.033801 AGCAACACAAGACAACATCAGC 59.966 45.455 0.00 0.00 0.00 4.26
625 627 2.223548 GCAACACAAGACAACATCAGCA 60.224 45.455 0.00 0.00 0.00 4.41
626 628 3.624900 CAACACAAGACAACATCAGCAG 58.375 45.455 0.00 0.00 0.00 4.24
627 629 1.605710 ACACAAGACAACATCAGCAGC 59.394 47.619 0.00 0.00 0.00 5.25
628 630 1.605232 CACAAGACAACATCAGCAGCA 59.395 47.619 0.00 0.00 0.00 4.41
629 631 1.605710 ACAAGACAACATCAGCAGCAC 59.394 47.619 0.00 0.00 0.00 4.40
652 654 4.083110 CGAGAGTGAATTGCAAGAAACCAT 60.083 41.667 4.94 0.00 0.00 3.55
686 688 5.334569 GGCTTATCTTGCAGAAAACAACGTA 60.335 40.000 0.00 0.00 0.00 3.57
740 742 6.803807 GGATTCAGTAACAGTTTTGCAGATTC 59.196 38.462 0.00 0.00 0.00 2.52
854 856 1.289109 TTGCTTAAGACAGACGCGGC 61.289 55.000 12.47 7.86 0.00 6.53
878 880 3.386237 GCCAGAGACAGACCGCCT 61.386 66.667 0.00 0.00 0.00 5.52
881 883 2.601666 AGAGACAGACCGCCTGCA 60.602 61.111 3.38 0.00 46.81 4.41
910 912 2.425312 ACATCTCGCTCGATTTCTCTGT 59.575 45.455 0.00 0.00 0.00 3.41
954 956 3.764466 CACTCGCTCGCTCCCCTT 61.764 66.667 0.00 0.00 0.00 3.95
956 958 3.144193 CTCGCTCGCTCCCCTTCT 61.144 66.667 0.00 0.00 0.00 2.85
1028 1030 1.112916 TGGACCGACAGTGAGAGCAA 61.113 55.000 0.00 0.00 0.00 3.91
1059 1061 1.729470 CCGCGCAGTACATCTCCTCT 61.729 60.000 8.75 0.00 0.00 3.69
1062 1064 1.339610 GCGCAGTACATCTCCTCTGAT 59.660 52.381 0.30 0.00 0.00 2.90
1098 1100 5.269505 AGGTCAGAACATTCTATTCCTCG 57.730 43.478 0.00 0.00 35.34 4.63
1132 1134 5.707495 AGGGTTTGTAGGGTTGAACATTTA 58.293 37.500 0.00 0.00 0.00 1.40
1194 1196 1.258982 CTACAATTGATGAGCCGTCGC 59.741 52.381 13.59 0.00 0.00 5.19
1397 1426 6.154706 CCTGTTCTAGGGTTCATAGTTACTGT 59.845 42.308 0.00 0.00 43.33 3.55
1721 1756 0.393402 CCTGGAGCATGCAAGCACTA 60.393 55.000 21.98 6.98 34.45 2.74
2011 2048 7.227156 AGAAGGAAAAGTTGAGCTCTGATAAA 58.773 34.615 16.19 0.00 0.00 1.40
2023 2060 6.072199 AGCTCTGATAAAAGGACTTTGGAT 57.928 37.500 0.00 0.00 32.36 3.41
2249 2361 5.865085 AGGACTAATTTGTGTTGCTGTCTA 58.135 37.500 0.00 0.00 0.00 2.59
2688 2806 5.924825 ACTAACATACTGACGAAACTGAACC 59.075 40.000 0.00 0.00 0.00 3.62
2787 2952 1.729131 CATTGTTGTTCACCGCCGC 60.729 57.895 0.00 0.00 0.00 6.53
2788 2953 2.914908 ATTGTTGTTCACCGCCGCC 61.915 57.895 0.00 0.00 0.00 6.13
2793 2958 4.699522 GTTCACCGCCGCCCTCTT 62.700 66.667 0.00 0.00 0.00 2.85
2794 2959 4.388499 TTCACCGCCGCCCTCTTC 62.388 66.667 0.00 0.00 0.00 2.87
2796 2961 4.394712 CACCGCCGCCCTCTTCTT 62.395 66.667 0.00 0.00 0.00 2.52
2797 2962 4.083862 ACCGCCGCCCTCTTCTTC 62.084 66.667 0.00 0.00 0.00 2.87
2798 2963 3.775654 CCGCCGCCCTCTTCTTCT 61.776 66.667 0.00 0.00 0.00 2.85
2799 2964 2.266055 CGCCGCCCTCTTCTTCTT 59.734 61.111 0.00 0.00 0.00 2.52
2800 2965 2.103042 CGCCGCCCTCTTCTTCTTG 61.103 63.158 0.00 0.00 0.00 3.02
2801 2966 1.746991 GCCGCCCTCTTCTTCTTGG 60.747 63.158 0.00 0.00 0.00 3.61
2802 2967 1.746991 CCGCCCTCTTCTTCTTGGC 60.747 63.158 0.00 0.00 38.74 4.52
2803 2968 1.746991 CGCCCTCTTCTTCTTGGCC 60.747 63.158 0.00 0.00 38.92 5.36
2804 2969 1.746991 GCCCTCTTCTTCTTGGCCG 60.747 63.158 0.00 0.00 36.07 6.13
2805 2970 1.078143 CCCTCTTCTTCTTGGCCGG 60.078 63.158 0.00 0.00 0.00 6.13
2806 2971 1.746991 CCTCTTCTTCTTGGCCGGC 60.747 63.158 21.18 21.18 0.00 6.13
2807 2972 2.047274 TCTTCTTCTTGGCCGGCG 60.047 61.111 22.54 6.96 0.00 6.46
3034 3199 0.328592 TGTCAGAGGAGTAGCCGTCT 59.671 55.000 0.00 0.00 43.43 4.18
3222 3394 0.036765 GAGCGGTACATCCACCAACA 60.037 55.000 0.00 0.00 38.61 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.072839 GGAAACGGAGAGGAGACATTTTT 58.927 43.478 0.00 0.00 0.00 1.94
9 10 3.328050 AGGAAACGGAGAGGAGACATTTT 59.672 43.478 0.00 0.00 0.00 1.82
10 11 2.907042 AGGAAACGGAGAGGAGACATTT 59.093 45.455 0.00 0.00 0.00 2.32
11 12 2.498078 GAGGAAACGGAGAGGAGACATT 59.502 50.000 0.00 0.00 0.00 2.71
12 13 2.104170 GAGGAAACGGAGAGGAGACAT 58.896 52.381 0.00 0.00 0.00 3.06
13 14 1.546961 GAGGAAACGGAGAGGAGACA 58.453 55.000 0.00 0.00 0.00 3.41
14 15 0.818938 GGAGGAAACGGAGAGGAGAC 59.181 60.000 0.00 0.00 0.00 3.36
68 69 1.546476 GAGAAACCTCGGAGCTTCTCA 59.454 52.381 26.76 0.00 42.16 3.27
115 116 3.321648 AGCATGTGGGTGAGGCGA 61.322 61.111 0.00 0.00 0.00 5.54
221 223 1.790541 AGGTGGAGTCCCATCCTGA 59.209 57.895 6.74 0.00 44.88 3.86
257 259 1.079543 CAGAGCAGGGTGTCCTTCG 60.080 63.158 0.00 0.00 42.67 3.79
287 289 1.186200 CTGAACCCCAGAGTCGATCA 58.814 55.000 0.00 0.00 45.78 2.92
421 423 3.807538 CTGACATGGCCGCACAGC 61.808 66.667 0.00 0.00 0.00 4.40
422 424 1.450848 ATCTGACATGGCCGCACAG 60.451 57.895 0.00 5.48 0.00 3.66
423 425 1.746239 CATCTGACATGGCCGCACA 60.746 57.895 0.00 0.00 0.00 4.57
424 426 0.816825 ATCATCTGACATGGCCGCAC 60.817 55.000 0.00 0.00 0.00 5.34
425 427 0.107066 AATCATCTGACATGGCCGCA 60.107 50.000 0.00 0.00 0.00 5.69
426 428 0.590195 GAATCATCTGACATGGCCGC 59.410 55.000 0.00 0.00 0.00 6.53
427 429 1.233019 GGAATCATCTGACATGGCCG 58.767 55.000 0.00 0.00 0.00 6.13
428 430 2.353357 TGGAATCATCTGACATGGCC 57.647 50.000 0.00 0.00 0.00 5.36
429 431 3.917329 CATGGAATCATCTGACATGGC 57.083 47.619 0.00 0.00 36.25 4.40
431 433 6.294564 GGAAATCCATGGAATCATCTGACATG 60.295 42.308 20.67 0.00 38.82 3.21
432 434 5.773680 GGAAATCCATGGAATCATCTGACAT 59.226 40.000 20.67 0.00 35.64 3.06
433 435 5.135383 GGAAATCCATGGAATCATCTGACA 58.865 41.667 20.67 0.00 35.64 3.58
434 436 5.135383 TGGAAATCCATGGAATCATCTGAC 58.865 41.667 20.67 7.02 42.01 3.51
435 437 5.391577 TGGAAATCCATGGAATCATCTGA 57.608 39.130 20.67 3.63 42.01 3.27
454 456 1.133809 CCTGGTTCCTTCCCTGTGGA 61.134 60.000 0.00 0.00 39.54 4.02
455 457 1.133809 TCCTGGTTCCTTCCCTGTGG 61.134 60.000 0.00 0.00 0.00 4.17
456 458 0.326264 CTCCTGGTTCCTTCCCTGTG 59.674 60.000 0.00 0.00 0.00 3.66
457 459 0.842467 CCTCCTGGTTCCTTCCCTGT 60.842 60.000 0.00 0.00 0.00 4.00
458 460 0.547712 TCCTCCTGGTTCCTTCCCTG 60.548 60.000 0.00 0.00 34.23 4.45
459 461 0.252927 CTCCTCCTGGTTCCTTCCCT 60.253 60.000 0.00 0.00 34.23 4.20
460 462 0.252742 TCTCCTCCTGGTTCCTTCCC 60.253 60.000 0.00 0.00 34.23 3.97
461 463 1.199615 CTCTCCTCCTGGTTCCTTCC 58.800 60.000 0.00 0.00 34.23 3.46
462 464 1.199615 CCTCTCCTCCTGGTTCCTTC 58.800 60.000 0.00 0.00 34.23 3.46
463 465 0.793617 TCCTCTCCTCCTGGTTCCTT 59.206 55.000 0.00 0.00 34.23 3.36
464 466 0.041982 GTCCTCTCCTCCTGGTTCCT 59.958 60.000 0.00 0.00 34.23 3.36
465 467 0.041982 AGTCCTCTCCTCCTGGTTCC 59.958 60.000 0.00 0.00 34.23 3.62
466 468 1.006639 AGAGTCCTCTCCTCCTGGTTC 59.993 57.143 0.00 0.00 41.26 3.62
467 469 1.089123 AGAGTCCTCTCCTCCTGGTT 58.911 55.000 0.00 0.00 41.26 3.67
468 470 1.089123 AAGAGTCCTCTCCTCCTGGT 58.911 55.000 0.00 0.00 41.26 4.00
469 471 3.053245 TCTTAAGAGTCCTCTCCTCCTGG 60.053 52.174 0.00 0.00 41.26 4.45
470 472 4.243793 TCTTAAGAGTCCTCTCCTCCTG 57.756 50.000 0.00 0.00 41.26 3.86
471 473 4.387437 CCATCTTAAGAGTCCTCTCCTCCT 60.387 50.000 11.53 0.00 41.26 3.69
472 474 3.895041 CCATCTTAAGAGTCCTCTCCTCC 59.105 52.174 11.53 0.00 41.26 4.30
473 475 4.340950 CACCATCTTAAGAGTCCTCTCCTC 59.659 50.000 11.53 0.00 41.26 3.71
474 476 4.017037 TCACCATCTTAAGAGTCCTCTCCT 60.017 45.833 11.53 0.00 41.26 3.69
475 477 4.282496 TCACCATCTTAAGAGTCCTCTCC 58.718 47.826 11.53 0.00 41.26 3.71
476 478 5.197451 TCTCACCATCTTAAGAGTCCTCTC 58.803 45.833 11.53 0.00 39.39 3.20
477 479 5.199982 TCTCACCATCTTAAGAGTCCTCT 57.800 43.478 11.53 0.00 42.75 3.69
478 480 4.202111 GCTCTCACCATCTTAAGAGTCCTC 60.202 50.000 11.53 0.00 38.01 3.71
479 481 3.704061 GCTCTCACCATCTTAAGAGTCCT 59.296 47.826 11.53 0.00 38.01 3.85
480 482 3.704061 AGCTCTCACCATCTTAAGAGTCC 59.296 47.826 11.53 0.00 38.01 3.85
481 483 4.400884 TCAGCTCTCACCATCTTAAGAGTC 59.599 45.833 11.53 0.00 38.01 3.36
482 484 4.159506 GTCAGCTCTCACCATCTTAAGAGT 59.840 45.833 11.53 1.34 38.01 3.24
483 485 4.441356 GGTCAGCTCTCACCATCTTAAGAG 60.441 50.000 11.53 0.67 38.61 2.85
484 486 3.449018 GGTCAGCTCTCACCATCTTAAGA 59.551 47.826 7.82 7.82 32.33 2.10
485 487 3.196469 TGGTCAGCTCTCACCATCTTAAG 59.804 47.826 4.82 0.00 37.78 1.85
486 488 3.055819 GTGGTCAGCTCTCACCATCTTAA 60.056 47.826 11.10 0.00 44.60 1.85
487 489 2.497675 GTGGTCAGCTCTCACCATCTTA 59.502 50.000 11.10 0.00 44.60 2.10
488 490 1.277557 GTGGTCAGCTCTCACCATCTT 59.722 52.381 11.10 0.00 44.60 2.40
489 491 0.901124 GTGGTCAGCTCTCACCATCT 59.099 55.000 11.10 0.00 44.60 2.90
490 492 0.459237 CGTGGTCAGCTCTCACCATC 60.459 60.000 11.10 5.64 44.60 3.51
491 493 1.593787 CGTGGTCAGCTCTCACCAT 59.406 57.895 11.10 0.00 44.60 3.55
492 494 2.574018 CCGTGGTCAGCTCTCACCA 61.574 63.158 4.82 4.82 40.56 4.17
493 495 2.262915 CCGTGGTCAGCTCTCACC 59.737 66.667 0.00 0.00 0.00 4.02
494 496 1.373497 CACCGTGGTCAGCTCTCAC 60.373 63.158 0.00 0.00 0.00 3.51
495 497 3.051210 CACCGTGGTCAGCTCTCA 58.949 61.111 0.00 0.00 0.00 3.27
496 498 2.433318 GCACCGTGGTCAGCTCTC 60.433 66.667 0.00 0.00 0.00 3.20
497 499 2.587247 ATGCACCGTGGTCAGCTCT 61.587 57.895 0.00 0.00 0.00 4.09
498 500 2.046892 ATGCACCGTGGTCAGCTC 60.047 61.111 0.00 0.00 0.00 4.09
499 501 2.359107 CATGCACCGTGGTCAGCT 60.359 61.111 0.00 0.00 0.00 4.24
500 502 3.434319 CCATGCACCGTGGTCAGC 61.434 66.667 0.00 0.00 35.92 4.26
501 503 2.747460 CCCATGCACCGTGGTCAG 60.747 66.667 4.19 0.00 38.76 3.51
502 504 4.343323 CCCCATGCACCGTGGTCA 62.343 66.667 4.19 0.00 38.76 4.02
510 512 4.856801 ATCGTCGGCCCCATGCAC 62.857 66.667 0.00 0.00 43.89 4.57
511 513 4.854924 CATCGTCGGCCCCATGCA 62.855 66.667 0.00 0.00 43.89 3.96
513 515 4.935495 CCCATCGTCGGCCCCATG 62.935 72.222 0.00 0.00 0.00 3.66
531 533 2.582226 TTATCGCTGCTCGCCGTG 60.582 61.111 0.00 0.00 38.27 4.94
532 534 2.582498 GTTATCGCTGCTCGCCGT 60.582 61.111 0.00 0.00 38.27 5.68
533 535 3.682315 CGTTATCGCTGCTCGCCG 61.682 66.667 0.00 0.00 38.27 6.46
543 545 2.717595 CGAACAACACACTGCGTTATCG 60.718 50.000 4.07 4.07 40.37 2.92
544 546 2.220133 ACGAACAACACACTGCGTTATC 59.780 45.455 0.00 0.00 0.00 1.75
545 547 2.033236 CACGAACAACACACTGCGTTAT 60.033 45.455 0.00 0.00 0.00 1.89
546 548 1.325037 CACGAACAACACACTGCGTTA 59.675 47.619 0.00 0.00 0.00 3.18
547 549 0.096281 CACGAACAACACACTGCGTT 59.904 50.000 0.00 0.00 0.00 4.84
548 550 1.017177 ACACGAACAACACACTGCGT 61.017 50.000 0.00 0.00 0.00 5.24
549 551 0.924777 TACACGAACAACACACTGCG 59.075 50.000 0.00 0.00 0.00 5.18
550 552 1.661617 TGTACACGAACAACACACTGC 59.338 47.619 0.00 0.00 0.00 4.40
551 553 4.329296 TTTGTACACGAACAACACACTG 57.671 40.909 0.00 0.00 39.02 3.66
552 554 6.238266 CCTTATTTGTACACGAACAACACACT 60.238 38.462 0.00 0.00 39.02 3.55
553 555 5.905181 CCTTATTTGTACACGAACAACACAC 59.095 40.000 0.00 0.00 39.02 3.82
554 556 5.007823 CCCTTATTTGTACACGAACAACACA 59.992 40.000 0.00 0.00 39.02 3.72
555 557 5.445845 CCCTTATTTGTACACGAACAACAC 58.554 41.667 0.00 0.00 39.02 3.32
556 558 4.515944 CCCCTTATTTGTACACGAACAACA 59.484 41.667 0.00 0.00 39.02 3.33
557 559 4.083164 CCCCCTTATTTGTACACGAACAAC 60.083 45.833 0.00 0.00 39.02 3.32
558 560 4.073549 CCCCCTTATTTGTACACGAACAA 58.926 43.478 0.00 0.00 37.58 2.83
559 561 3.072768 ACCCCCTTATTTGTACACGAACA 59.927 43.478 0.00 0.00 0.00 3.18
560 562 3.678289 ACCCCCTTATTTGTACACGAAC 58.322 45.455 0.00 0.00 0.00 3.95
561 563 3.307621 GGACCCCCTTATTTGTACACGAA 60.308 47.826 0.00 0.00 0.00 3.85
562 564 2.236893 GGACCCCCTTATTTGTACACGA 59.763 50.000 0.00 0.00 0.00 4.35
563 565 2.635714 GGACCCCCTTATTTGTACACG 58.364 52.381 0.00 0.00 0.00 4.49
564 566 2.026915 ACGGACCCCCTTATTTGTACAC 60.027 50.000 0.00 0.00 0.00 2.90
565 567 2.268107 ACGGACCCCCTTATTTGTACA 58.732 47.619 0.00 0.00 0.00 2.90
566 568 4.445453 CTTACGGACCCCCTTATTTGTAC 58.555 47.826 0.00 0.00 0.00 2.90
567 569 3.455543 CCTTACGGACCCCCTTATTTGTA 59.544 47.826 0.00 0.00 0.00 2.41
568 570 2.240414 CCTTACGGACCCCCTTATTTGT 59.760 50.000 0.00 0.00 0.00 2.83
569 571 2.506644 TCCTTACGGACCCCCTTATTTG 59.493 50.000 0.00 0.00 33.30 2.32
570 572 2.775960 CTCCTTACGGACCCCCTTATTT 59.224 50.000 0.00 0.00 34.92 1.40
571 573 2.293385 ACTCCTTACGGACCCCCTTATT 60.293 50.000 0.00 0.00 34.92 1.40
572 574 1.293153 ACTCCTTACGGACCCCCTTAT 59.707 52.381 0.00 0.00 34.92 1.73
573 575 0.712380 ACTCCTTACGGACCCCCTTA 59.288 55.000 0.00 0.00 34.92 2.69
574 576 0.712380 TACTCCTTACGGACCCCCTT 59.288 55.000 0.00 0.00 34.92 3.95
575 577 0.261109 CTACTCCTTACGGACCCCCT 59.739 60.000 0.00 0.00 34.92 4.79
576 578 0.032714 ACTACTCCTTACGGACCCCC 60.033 60.000 0.00 0.00 34.92 5.40
577 579 1.109609 CACTACTCCTTACGGACCCC 58.890 60.000 0.00 0.00 34.92 4.95
578 580 2.022934 CTCACTACTCCTTACGGACCC 58.977 57.143 0.00 0.00 34.92 4.46
579 581 1.404748 GCTCACTACTCCTTACGGACC 59.595 57.143 0.00 0.00 34.92 4.46
580 582 1.063764 CGCTCACTACTCCTTACGGAC 59.936 57.143 0.00 0.00 34.92 4.79
581 583 1.376543 CGCTCACTACTCCTTACGGA 58.623 55.000 0.00 0.00 37.82 4.69
582 584 0.381089 CCGCTCACTACTCCTTACGG 59.619 60.000 0.00 0.00 0.00 4.02
583 585 1.376543 TCCGCTCACTACTCCTTACG 58.623 55.000 0.00 0.00 0.00 3.18
584 586 2.479901 GCTTCCGCTCACTACTCCTTAC 60.480 54.545 0.00 0.00 0.00 2.34
585 587 1.749634 GCTTCCGCTCACTACTCCTTA 59.250 52.381 0.00 0.00 0.00 2.69
586 588 0.533032 GCTTCCGCTCACTACTCCTT 59.467 55.000 0.00 0.00 0.00 3.36
587 589 0.612174 TGCTTCCGCTCACTACTCCT 60.612 55.000 0.00 0.00 36.97 3.69
588 590 0.246635 TTGCTTCCGCTCACTACTCC 59.753 55.000 0.00 0.00 36.97 3.85
589 591 1.336887 TGTTGCTTCCGCTCACTACTC 60.337 52.381 0.00 0.00 36.97 2.59
590 592 0.679505 TGTTGCTTCCGCTCACTACT 59.320 50.000 0.00 0.00 36.97 2.57
591 593 0.790814 GTGTTGCTTCCGCTCACTAC 59.209 55.000 0.00 0.00 38.05 2.73
592 594 0.391228 TGTGTTGCTTCCGCTCACTA 59.609 50.000 11.68 1.27 39.97 2.74
593 595 0.463654 TTGTGTTGCTTCCGCTCACT 60.464 50.000 11.68 0.00 39.97 3.41
594 596 0.040958 CTTGTGTTGCTTCCGCTCAC 60.041 55.000 0.00 0.00 39.84 3.51
595 597 0.179059 TCTTGTGTTGCTTCCGCTCA 60.179 50.000 0.00 0.00 36.97 4.26
596 598 0.235926 GTCTTGTGTTGCTTCCGCTC 59.764 55.000 0.00 0.00 36.97 5.03
597 599 0.463654 TGTCTTGTGTTGCTTCCGCT 60.464 50.000 0.00 0.00 36.97 5.52
598 600 0.380378 TTGTCTTGTGTTGCTTCCGC 59.620 50.000 0.00 0.00 0.00 5.54
599 601 1.400142 TGTTGTCTTGTGTTGCTTCCG 59.600 47.619 0.00 0.00 0.00 4.30
600 602 3.066621 TGATGTTGTCTTGTGTTGCTTCC 59.933 43.478 0.00 0.00 0.00 3.46
601 603 4.285292 CTGATGTTGTCTTGTGTTGCTTC 58.715 43.478 0.00 0.00 0.00 3.86
602 604 3.489738 GCTGATGTTGTCTTGTGTTGCTT 60.490 43.478 0.00 0.00 0.00 3.91
603 605 2.033801 GCTGATGTTGTCTTGTGTTGCT 59.966 45.455 0.00 0.00 0.00 3.91
604 606 2.223548 TGCTGATGTTGTCTTGTGTTGC 60.224 45.455 0.00 0.00 0.00 4.17
605 607 3.624900 CTGCTGATGTTGTCTTGTGTTG 58.375 45.455 0.00 0.00 0.00 3.33
606 608 2.033801 GCTGCTGATGTTGTCTTGTGTT 59.966 45.455 0.00 0.00 0.00 3.32
607 609 1.605710 GCTGCTGATGTTGTCTTGTGT 59.394 47.619 0.00 0.00 0.00 3.72
608 610 1.605232 TGCTGCTGATGTTGTCTTGTG 59.395 47.619 0.00 0.00 0.00 3.33
609 611 1.605710 GTGCTGCTGATGTTGTCTTGT 59.394 47.619 0.00 0.00 0.00 3.16
610 612 1.399343 CGTGCTGCTGATGTTGTCTTG 60.399 52.381 0.00 0.00 0.00 3.02
611 613 0.870393 CGTGCTGCTGATGTTGTCTT 59.130 50.000 0.00 0.00 0.00 3.01
612 614 0.033920 TCGTGCTGCTGATGTTGTCT 59.966 50.000 0.00 0.00 0.00 3.41
613 615 0.441533 CTCGTGCTGCTGATGTTGTC 59.558 55.000 0.00 0.00 0.00 3.18
614 616 0.033920 TCTCGTGCTGCTGATGTTGT 59.966 50.000 0.00 0.00 0.00 3.32
615 617 0.720027 CTCTCGTGCTGCTGATGTTG 59.280 55.000 0.00 0.00 0.00 3.33
616 618 0.319728 ACTCTCGTGCTGCTGATGTT 59.680 50.000 0.00 0.00 0.00 2.71
617 619 0.389556 CACTCTCGTGCTGCTGATGT 60.390 55.000 0.00 0.00 33.82 3.06
618 620 0.108945 TCACTCTCGTGCTGCTGATG 60.109 55.000 0.00 0.00 40.99 3.07
619 621 0.605083 TTCACTCTCGTGCTGCTGAT 59.395 50.000 0.00 0.00 40.99 2.90
620 622 0.605083 ATTCACTCTCGTGCTGCTGA 59.395 50.000 0.00 0.00 40.99 4.26
621 623 1.128136 CAATTCACTCTCGTGCTGCTG 59.872 52.381 0.00 0.00 40.99 4.41
622 624 1.436600 CAATTCACTCTCGTGCTGCT 58.563 50.000 0.00 0.00 40.99 4.24
623 625 0.179205 GCAATTCACTCTCGTGCTGC 60.179 55.000 0.00 0.00 40.99 5.25
624 626 1.150827 TGCAATTCACTCTCGTGCTG 58.849 50.000 0.00 0.00 40.99 4.41
625 627 1.802960 CTTGCAATTCACTCTCGTGCT 59.197 47.619 0.00 0.00 40.99 4.40
626 628 1.800586 TCTTGCAATTCACTCTCGTGC 59.199 47.619 0.00 0.00 40.99 5.34
627 629 4.214437 GTTTCTTGCAATTCACTCTCGTG 58.786 43.478 0.00 0.00 42.59 4.35
628 630 3.251004 GGTTTCTTGCAATTCACTCTCGT 59.749 43.478 0.00 0.00 0.00 4.18
629 631 3.250762 TGGTTTCTTGCAATTCACTCTCG 59.749 43.478 0.00 0.00 0.00 4.04
652 654 2.760092 GCAAGATAAGCCCCAAATGTGA 59.240 45.455 0.00 0.00 0.00 3.58
686 688 4.168760 GCTTTTGCAAATGATTAGCGACT 58.831 39.130 24.70 0.00 46.58 4.18
740 742 2.559668 AGCCAAATGACATGTTCAGTGG 59.440 45.455 17.38 17.38 42.61 4.00
854 856 4.135153 CTGTCTCTGGCGACCCGG 62.135 72.222 0.00 0.00 38.98 5.73
878 880 2.662596 GAGATGTGGTCGGGTGCA 59.337 61.111 0.00 0.00 0.00 4.57
881 883 2.680352 AGCGAGATGTGGTCGGGT 60.680 61.111 0.00 0.00 37.91 5.28
910 912 0.675208 AGAGAGAGCGAGCGTGAGAA 60.675 55.000 0.00 0.00 0.00 2.87
954 956 3.571590 GGAGAGGAGAGGAGCAAATAGA 58.428 50.000 0.00 0.00 0.00 1.98
956 958 2.311463 CGGAGAGGAGAGGAGCAAATA 58.689 52.381 0.00 0.00 0.00 1.40
992 994 2.927856 AGGACACCATGGCGGACA 60.928 61.111 13.04 0.00 38.63 4.02
1059 1061 1.279496 CCTTGACAGGGGAGTCATCA 58.721 55.000 0.00 0.00 46.90 3.07
1062 1064 0.105194 TGACCTTGACAGGGGAGTCA 60.105 55.000 8.68 0.00 46.01 3.41
1098 1100 5.001874 CCCTACAAACCCTAGAACAGAAAC 58.998 45.833 0.00 0.00 0.00 2.78
1132 1134 4.976987 ACAAAAACGTGTTCAAATCGAGT 58.023 34.783 0.00 0.00 0.00 4.18
1194 1196 1.153939 CGTCAGCAAGACCCTCGAG 60.154 63.158 5.13 5.13 44.66 4.04
1397 1426 8.258007 CAGTAACTATGAACCCTAGAACATGAA 58.742 37.037 0.00 0.00 0.00 2.57
1686 1721 0.458669 CAGGCATGCCATCCTGTTTC 59.541 55.000 37.18 7.34 43.66 2.78
1721 1756 4.541973 TCTGCTGTGTGAGATTGTGTAT 57.458 40.909 0.00 0.00 0.00 2.29
1900 1937 4.020543 ACTGGTCAACAACAGCCTTTAAA 58.979 39.130 0.00 0.00 38.25 1.52
2011 2048 6.040166 CAGCATAGCAAATATCCAAAGTCCTT 59.960 38.462 0.00 0.00 0.00 3.36
2023 2060 5.357742 TCTTCAGGTCAGCATAGCAAATA 57.642 39.130 0.00 0.00 0.00 1.40
2249 2361 4.401022 AGACATCATTGACACACATGGTT 58.599 39.130 0.00 0.00 0.00 3.67
2787 2952 1.078143 CCGGCCAAGAAGAAGAGGG 60.078 63.158 2.24 0.00 0.00 4.30
2788 2953 1.746991 GCCGGCCAAGAAGAAGAGG 60.747 63.158 18.11 0.00 0.00 3.69
2789 2954 2.103042 CGCCGGCCAAGAAGAAGAG 61.103 63.158 23.46 0.00 0.00 2.85
2790 2955 2.047274 CGCCGGCCAAGAAGAAGA 60.047 61.111 23.46 0.00 0.00 2.87
2791 2956 3.804193 GCGCCGGCCAAGAAGAAG 61.804 66.667 23.46 4.03 0.00 2.85
2792 2957 4.329545 AGCGCCGGCCAAGAAGAA 62.330 61.111 23.46 0.00 41.24 2.52
2841 3006 1.060713 CGTCGTCGTGAAGCAAGAAT 58.939 50.000 0.00 0.00 0.00 2.40
2944 3109 2.045634 GATGTGCAGCTCCTGGCA 60.046 61.111 0.00 0.00 44.79 4.92
3006 3171 1.248486 CTCCTCTGACAACGAGGTGA 58.752 55.000 9.85 0.00 46.49 4.02
3034 3199 2.347755 CGACTACGACTCTGACGAATCA 59.652 50.000 0.00 0.00 42.66 2.57
3108 3279 1.134220 CCTACTGGGAAAGGCGCAATA 60.134 52.381 10.83 0.00 39.13 1.90
3154 3326 1.079819 CATCACTGACGCCGTCCTT 60.080 57.895 15.60 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.