Multiple sequence alignment - TraesCS3D01G313500

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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 TraesCS3D01G313500 chr3D 100.000 4034 0 0 1 4034 427444601 427448634 0.000000e+00 7450.0
1 TraesCS3D01G313500 chr3D 87.164 335 32 7 355 680 13806571 13806239 1.770000e-98 370.0
2 TraesCS3D01G313500 chr3A 94.008 3388 115 24 688 4032 558893710 558890368 0.000000e+00 5051.0
3 TraesCS3D01G313500 chr3A 82.044 362 30 12 4 343 558894064 558893716 3.970000e-70 276.0
4 TraesCS3D01G313500 chr3B 94.444 3276 123 31 792 4032 557086830 557090081 0.000000e+00 4987.0
5 TraesCS3D01G313500 chr3B 86.562 320 31 11 355 671 719907524 719907834 3.860000e-90 342.0
6 TraesCS3D01G313500 chr3B 88.462 182 21 0 162 343 557048117 557048298 1.890000e-53 220.0
7 TraesCS3D01G313500 chr5A 90.691 333 21 6 355 680 358053504 358053833 6.190000e-118 435.0
8 TraesCS3D01G313500 chr5D 90.419 334 21 6 355 680 437262191 437261861 2.880000e-116 429.0
9 TraesCS3D01G313500 chr2D 84.956 339 37 7 355 680 118115505 118115842 8.360000e-87 331.0
10 TraesCS3D01G313500 chr6B 83.631 336 44 3 355 679 469296972 469297307 5.070000e-79 305.0
11 TraesCS3D01G313500 chr5B 82.687 335 46 8 355 680 6465786 6466117 1.830000e-73 287.0
12 TraesCS3D01G313500 chr5B 71.770 712 164 30 2132 2820 63260868 63260171 2.490000e-37 167.0
13 TraesCS3D01G313500 chr6D 82.335 334 40 16 355 680 159982834 159982512 5.140000e-69 272.0
14 TraesCS3D01G313500 chr1A 82.067 329 45 7 355 679 492233391 492233709 6.650000e-68 268.0
15 TraesCS3D01G313500 chr1D 73.822 191 47 2 2099 2289 462335956 462336143 5.590000e-09 73.1
16 TraesCS3D01G313500 chr7B 71.011 376 81 21 2235 2592 683151854 683152219 9.360000e-07 65.8
17 TraesCS3D01G313500 chr7B 72.112 251 56 12 2352 2592 682843644 682843890 3.370000e-06 63.9
18 TraesCS3D01G313500 chr7A 100.000 29 0 0 2564 2592 694198131 694198159 2.000000e-03 54.7


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 TraesCS3D01G313500 chr3D 427444601 427448634 4033 False 7450.0 7450 100.000 1 4034 1 chr3D.!!$F1 4033
1 TraesCS3D01G313500 chr3A 558890368 558894064 3696 True 2663.5 5051 88.026 4 4032 2 chr3A.!!$R1 4028
2 TraesCS3D01G313500 chr3B 557086830 557090081 3251 False 4987.0 4987 94.444 792 4032 1 chr3B.!!$F2 3240

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
505 528 0.108992 TAGACGGCTACGCAAAGTGG 60.109 55.0 0.00 0.00 46.04 4.00 F
1642 1685 0.179134 CCTCTCCTACGGCGACTTTG 60.179 60.0 16.62 0.27 0.00 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2151 2194 1.364171 GATGATGCGTACCTCGGCT 59.636 57.895 0.0 0.0 40.26 5.52 R
3335 3398 0.250553 CTAGTCCCGTTGGTTTGCCA 60.251 55.000 0.0 0.0 44.38 4.92 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
17 18 3.005539 AGTGGAGGTGCAGGCGAT 61.006 61.111 0.00 0.00 0.00 4.58
97 98 4.760047 GGCGTCCACGTCTGGCAT 62.760 66.667 0.36 0.00 41.36 4.40
98 99 3.490759 GCGTCCACGTCTGGCATG 61.491 66.667 0.36 0.00 42.22 4.06
168 191 1.054978 ACGGCTATTCTTCCCCTCCC 61.055 60.000 0.00 0.00 0.00 4.30
181 204 2.047274 CTCCCGTTGATGCACCGT 60.047 61.111 0.00 0.00 0.00 4.83
202 225 1.717937 GCGAGCTTGCCACACATAG 59.282 57.895 15.66 0.00 0.00 2.23
275 298 9.739737 TTAGATTAGGTTAAAAGACTATCCCCT 57.260 33.333 0.00 0.00 0.00 4.79
291 314 6.723977 ACTATCCCCTGCTTTTGTTTATTTGA 59.276 34.615 0.00 0.00 0.00 2.69
292 315 5.208463 TCCCCTGCTTTTGTTTATTTGAC 57.792 39.130 0.00 0.00 0.00 3.18
307 330 9.737427 TGTTTATTTGACATGTATGAAAAACGT 57.263 25.926 0.00 0.00 0.00 3.99
313 336 9.605955 TTTGACATGTATGAAAAACGTAATGAG 57.394 29.630 0.00 0.00 0.00 2.90
361 384 9.846248 CATCTAATTAAACCCATTAAGCTATGC 57.154 33.333 0.00 0.00 36.94 3.14
362 385 8.404107 TCTAATTAAACCCATTAAGCTATGCC 57.596 34.615 0.00 0.00 36.94 4.40
363 386 8.001875 TCTAATTAAACCCATTAAGCTATGCCA 58.998 33.333 0.00 0.00 36.94 4.92
364 387 5.845391 TTAAACCCATTAAGCTATGCCAC 57.155 39.130 0.00 0.00 0.00 5.01
365 388 1.967319 ACCCATTAAGCTATGCCACG 58.033 50.000 0.00 0.00 0.00 4.94
366 389 1.211949 ACCCATTAAGCTATGCCACGT 59.788 47.619 0.00 0.00 0.00 4.49
367 390 1.603802 CCCATTAAGCTATGCCACGTG 59.396 52.381 9.08 9.08 0.00 4.49
368 391 1.603802 CCATTAAGCTATGCCACGTGG 59.396 52.381 30.66 30.66 38.53 4.94
393 416 4.877619 TGGTTGGCCGCGGTGAAA 62.878 61.111 28.70 15.82 37.67 2.69
394 417 3.597728 GGTTGGCCGCGGTGAAAA 61.598 61.111 28.70 13.16 0.00 2.29
395 418 2.413765 GTTGGCCGCGGTGAAAAA 59.586 55.556 28.70 11.29 0.00 1.94
396 419 1.660264 GTTGGCCGCGGTGAAAAAG 60.660 57.895 28.70 0.00 0.00 2.27
397 420 3.492311 TTGGCCGCGGTGAAAAAGC 62.492 57.895 28.70 9.28 0.00 3.51
398 421 3.670377 GGCCGCGGTGAAAAAGCT 61.670 61.111 28.70 0.00 0.00 3.74
399 422 2.335011 GCCGCGGTGAAAAAGCTT 59.665 55.556 28.70 0.00 0.00 3.74
400 423 1.299850 GCCGCGGTGAAAAAGCTTT 60.300 52.632 28.70 5.69 0.00 3.51
401 424 0.874175 GCCGCGGTGAAAAAGCTTTT 60.874 50.000 28.70 18.74 0.00 2.27
402 425 1.600912 GCCGCGGTGAAAAAGCTTTTA 60.601 47.619 28.70 7.58 0.00 1.52
403 426 2.315901 CCGCGGTGAAAAAGCTTTTAG 58.684 47.619 24.11 13.87 0.00 1.85
404 427 2.031508 CCGCGGTGAAAAAGCTTTTAGA 60.032 45.455 24.11 11.29 0.00 2.10
405 428 3.549221 CCGCGGTGAAAAAGCTTTTAGAA 60.549 43.478 24.11 10.45 0.00 2.10
406 429 4.226761 CGCGGTGAAAAAGCTTTTAGAAT 58.773 39.130 24.11 9.18 0.00 2.40
407 430 5.387279 CGCGGTGAAAAAGCTTTTAGAATA 58.613 37.500 24.11 7.06 0.00 1.75
408 431 6.027749 CGCGGTGAAAAAGCTTTTAGAATAT 58.972 36.000 24.11 8.04 0.00 1.28
409 432 6.526674 CGCGGTGAAAAAGCTTTTAGAATATT 59.473 34.615 24.11 7.29 0.00 1.28
410 433 7.694784 CGCGGTGAAAAAGCTTTTAGAATATTA 59.305 33.333 24.11 2.32 0.00 0.98
411 434 9.516314 GCGGTGAAAAAGCTTTTAGAATATTAT 57.484 29.630 24.11 5.79 0.00 1.28
470 493 4.437682 TTTACATGGAGGTGATGATCCC 57.562 45.455 0.00 0.00 34.47 3.85
471 494 1.897473 ACATGGAGGTGATGATCCCA 58.103 50.000 0.00 0.00 34.47 4.37
472 495 2.425818 ACATGGAGGTGATGATCCCAT 58.574 47.619 0.00 0.00 38.07 4.00
473 496 3.601520 ACATGGAGGTGATGATCCCATA 58.398 45.455 0.00 0.00 35.99 2.74
474 497 4.181520 ACATGGAGGTGATGATCCCATAT 58.818 43.478 0.00 0.00 35.99 1.78
475 498 5.353125 ACATGGAGGTGATGATCCCATATA 58.647 41.667 0.00 0.00 35.99 0.86
476 499 5.974994 ACATGGAGGTGATGATCCCATATAT 59.025 40.000 0.00 0.00 35.99 0.86
477 500 6.449368 ACATGGAGGTGATGATCCCATATATT 59.551 38.462 0.00 0.00 35.99 1.28
478 501 6.975471 TGGAGGTGATGATCCCATATATTT 57.025 37.500 3.38 0.00 34.47 1.40
479 502 7.347319 TGGAGGTGATGATCCCATATATTTT 57.653 36.000 3.38 0.00 34.47 1.82
480 503 7.768643 TGGAGGTGATGATCCCATATATTTTT 58.231 34.615 3.38 0.00 34.47 1.94
500 523 5.859521 TTTTTAAATAGACGGCTACGCAA 57.140 34.783 0.00 0.00 46.04 4.85
501 524 5.859521 TTTTAAATAGACGGCTACGCAAA 57.140 34.783 0.00 0.00 46.04 3.68
502 525 5.459110 TTTAAATAGACGGCTACGCAAAG 57.541 39.130 0.00 0.00 46.04 2.77
503 526 2.667473 AATAGACGGCTACGCAAAGT 57.333 45.000 0.00 0.00 46.04 2.66
504 527 1.922570 ATAGACGGCTACGCAAAGTG 58.077 50.000 0.00 0.00 46.04 3.16
505 528 0.108992 TAGACGGCTACGCAAAGTGG 60.109 55.000 0.00 0.00 46.04 4.00
506 529 1.666872 GACGGCTACGCAAAGTGGT 60.667 57.895 0.00 0.00 46.04 4.16
507 530 1.897398 GACGGCTACGCAAAGTGGTG 61.897 60.000 0.00 0.00 46.04 4.17
508 531 2.561373 GGCTACGCAAAGTGGTGC 59.439 61.111 0.00 0.00 41.32 5.01
509 532 1.966451 GGCTACGCAAAGTGGTGCT 60.966 57.895 0.00 0.00 42.62 4.40
510 533 1.515521 GGCTACGCAAAGTGGTGCTT 61.516 55.000 0.00 0.00 42.62 3.91
511 534 0.385974 GCTACGCAAAGTGGTGCTTG 60.386 55.000 0.00 0.00 42.62 4.01
512 535 0.385974 CTACGCAAAGTGGTGCTTGC 60.386 55.000 0.00 0.00 42.62 4.01
513 536 0.817634 TACGCAAAGTGGTGCTTGCT 60.818 50.000 5.37 0.00 42.62 3.91
514 537 1.659335 CGCAAAGTGGTGCTTGCTG 60.659 57.895 5.37 0.00 42.62 4.41
515 538 1.300388 GCAAAGTGGTGCTTGCTGG 60.300 57.895 0.00 0.00 41.51 4.85
516 539 2.019897 GCAAAGTGGTGCTTGCTGGT 62.020 55.000 0.00 0.00 41.51 4.00
517 540 1.317613 CAAAGTGGTGCTTGCTGGTA 58.682 50.000 0.00 0.00 37.52 3.25
518 541 1.267806 CAAAGTGGTGCTTGCTGGTAG 59.732 52.381 0.00 0.00 37.52 3.18
519 542 0.250901 AAGTGGTGCTTGCTGGTAGG 60.251 55.000 0.00 0.00 35.80 3.18
520 543 2.034066 TGGTGCTTGCTGGTAGGC 59.966 61.111 0.00 0.00 0.00 3.93
521 544 2.751837 GGTGCTTGCTGGTAGGCC 60.752 66.667 0.00 0.00 0.00 5.19
522 545 3.127533 GTGCTTGCTGGTAGGCCG 61.128 66.667 0.00 0.00 37.67 6.13
523 546 3.636231 TGCTTGCTGGTAGGCCGT 61.636 61.111 0.00 0.00 37.67 5.68
524 547 3.127533 GCTTGCTGGTAGGCCGTG 61.128 66.667 0.00 0.00 37.67 4.94
525 548 2.347490 CTTGCTGGTAGGCCGTGT 59.653 61.111 0.00 0.00 37.67 4.49
526 549 1.302511 CTTGCTGGTAGGCCGTGTT 60.303 57.895 0.00 0.00 37.67 3.32
527 550 0.889186 CTTGCTGGTAGGCCGTGTTT 60.889 55.000 0.00 0.00 37.67 2.83
528 551 1.169661 TTGCTGGTAGGCCGTGTTTG 61.170 55.000 0.00 0.00 37.67 2.93
529 552 1.599797 GCTGGTAGGCCGTGTTTGT 60.600 57.895 0.00 0.00 37.67 2.83
530 553 1.852067 GCTGGTAGGCCGTGTTTGTG 61.852 60.000 0.00 0.00 37.67 3.33
531 554 0.250124 CTGGTAGGCCGTGTTTGTGA 60.250 55.000 0.00 0.00 37.67 3.58
532 555 0.398696 TGGTAGGCCGTGTTTGTGAT 59.601 50.000 0.00 0.00 37.67 3.06
533 556 1.202830 TGGTAGGCCGTGTTTGTGATT 60.203 47.619 0.00 0.00 37.67 2.57
534 557 1.883926 GGTAGGCCGTGTTTGTGATTT 59.116 47.619 0.00 0.00 0.00 2.17
535 558 2.295070 GGTAGGCCGTGTTTGTGATTTT 59.705 45.455 0.00 0.00 0.00 1.82
536 559 3.243602 GGTAGGCCGTGTTTGTGATTTTT 60.244 43.478 0.00 0.00 0.00 1.94
570 593 9.672673 TTTTACCTCTTTTTCTAGATGGAGATG 57.327 33.333 0.00 0.00 0.00 2.90
571 594 8.609617 TTACCTCTTTTTCTAGATGGAGATGA 57.390 34.615 0.00 0.00 0.00 2.92
572 595 7.123355 ACCTCTTTTTCTAGATGGAGATGAG 57.877 40.000 0.00 0.00 0.00 2.90
573 596 6.099557 ACCTCTTTTTCTAGATGGAGATGAGG 59.900 42.308 15.65 15.65 41.15 3.86
574 597 6.326064 CCTCTTTTTCTAGATGGAGATGAGGA 59.674 42.308 13.59 0.00 38.63 3.71
575 598 7.016465 CCTCTTTTTCTAGATGGAGATGAGGAT 59.984 40.741 13.59 0.00 38.63 3.24
576 599 8.329346 TCTTTTTCTAGATGGAGATGAGGATT 57.671 34.615 0.00 0.00 0.00 3.01
577 600 8.776119 TCTTTTTCTAGATGGAGATGAGGATTT 58.224 33.333 0.00 0.00 0.00 2.17
578 601 9.406113 CTTTTTCTAGATGGAGATGAGGATTTT 57.594 33.333 0.00 0.00 0.00 1.82
579 602 9.759473 TTTTTCTAGATGGAGATGAGGATTTTT 57.241 29.630 0.00 0.00 0.00 1.94
615 638 8.722480 TTTTAGATGAAGGTGATGACTACATG 57.278 34.615 0.00 0.00 36.82 3.21
616 639 5.946942 AGATGAAGGTGATGACTACATGT 57.053 39.130 2.69 2.69 36.82 3.21
617 640 8.533569 TTAGATGAAGGTGATGACTACATGTA 57.466 34.615 5.25 5.25 36.82 2.29
618 641 7.609097 AGATGAAGGTGATGACTACATGTAT 57.391 36.000 5.91 0.00 36.82 2.29
619 642 8.027524 AGATGAAGGTGATGACTACATGTATT 57.972 34.615 5.91 0.00 36.82 1.89
620 643 8.489489 AGATGAAGGTGATGACTACATGTATTT 58.511 33.333 5.91 0.00 36.82 1.40
621 644 9.113838 GATGAAGGTGATGACTACATGTATTTT 57.886 33.333 5.91 0.00 36.82 1.82
622 645 8.862325 TGAAGGTGATGACTACATGTATTTTT 57.138 30.769 5.91 0.00 36.82 1.94
645 668 8.967552 TTTTAAATGAAAACGTGTACACAACT 57.032 26.923 24.98 6.69 31.90 3.16
646 669 8.967552 TTTAAATGAAAACGTGTACACAACTT 57.032 26.923 24.98 13.84 0.00 2.66
647 670 8.603983 TTAAATGAAAACGTGTACACAACTTC 57.396 30.769 24.98 20.67 0.00 3.01
648 671 4.603231 TGAAAACGTGTACACAACTTCC 57.397 40.909 24.98 9.92 0.00 3.46
649 672 4.255301 TGAAAACGTGTACACAACTTCCT 58.745 39.130 24.98 3.01 0.00 3.36
650 673 4.330620 TGAAAACGTGTACACAACTTCCTC 59.669 41.667 24.98 11.78 0.00 3.71
651 674 3.814005 AACGTGTACACAACTTCCTCT 57.186 42.857 24.98 0.00 0.00 3.69
652 675 3.366440 ACGTGTACACAACTTCCTCTC 57.634 47.619 24.98 0.00 0.00 3.20
653 676 2.691526 ACGTGTACACAACTTCCTCTCA 59.308 45.455 24.98 0.00 0.00 3.27
654 677 3.131577 ACGTGTACACAACTTCCTCTCAA 59.868 43.478 24.98 0.00 0.00 3.02
655 678 3.736252 CGTGTACACAACTTCCTCTCAAG 59.264 47.826 24.98 0.38 0.00 3.02
656 679 3.495001 GTGTACACAACTTCCTCTCAAGC 59.505 47.826 21.14 0.00 0.00 4.01
657 680 1.871080 ACACAACTTCCTCTCAAGCG 58.129 50.000 0.00 0.00 0.00 4.68
658 681 1.151668 CACAACTTCCTCTCAAGCGG 58.848 55.000 0.00 0.00 0.00 5.52
659 682 0.603975 ACAACTTCCTCTCAAGCGGC 60.604 55.000 0.00 0.00 0.00 6.53
660 683 1.374758 AACTTCCTCTCAAGCGGCG 60.375 57.895 0.51 0.51 0.00 6.46
661 684 3.191539 CTTCCTCTCAAGCGGCGC 61.192 66.667 26.86 26.86 0.00 6.53
662 685 4.760047 TTCCTCTCAAGCGGCGCC 62.760 66.667 30.40 19.07 0.00 6.53
682 705 3.762247 CAGGTGGCGCCCCAAATG 61.762 66.667 28.68 17.87 44.33 2.32
685 708 3.773404 GTGGCGCCCCAAATGCAT 61.773 61.111 26.77 0.00 44.33 3.96
686 709 3.772281 TGGCGCCCCAAATGCATG 61.772 61.111 26.77 0.00 38.46 4.06
687 710 3.459965 GGCGCCCCAAATGCATGA 61.460 61.111 18.11 0.00 0.00 3.07
688 711 2.578128 GCGCCCCAAATGCATGAA 59.422 55.556 0.00 0.00 0.00 2.57
689 712 1.079266 GCGCCCCAAATGCATGAAA 60.079 52.632 0.00 0.00 0.00 2.69
690 713 0.462403 GCGCCCCAAATGCATGAAAT 60.462 50.000 0.00 0.00 0.00 2.17
691 714 2.013058 GCGCCCCAAATGCATGAAATT 61.013 47.619 0.00 0.00 0.00 1.82
692 715 2.358015 CGCCCCAAATGCATGAAATTT 58.642 42.857 0.00 0.00 0.00 1.82
693 716 2.096174 CGCCCCAAATGCATGAAATTTG 59.904 45.455 19.71 19.71 42.24 2.32
739 762 4.764050 AATGTATGGACACGGTTGGATA 57.236 40.909 0.00 0.00 38.76 2.59
751 774 1.131693 GGTTGGATAAGCCGGTTTTCG 59.868 52.381 9.46 0.00 40.66 3.46
757 780 1.083489 TAAGCCGGTTTTCGCATCAG 58.917 50.000 9.46 0.00 37.59 2.90
758 781 2.200170 AAGCCGGTTTTCGCATCAGC 62.200 55.000 1.90 0.00 37.59 4.26
774 797 2.201022 AGCGTCCGTGAACTGGTCT 61.201 57.895 0.00 0.00 0.00 3.85
775 798 2.022129 GCGTCCGTGAACTGGTCTG 61.022 63.158 0.00 0.00 0.00 3.51
825 849 1.614413 GTTGGAGAGACGGTGACTCTT 59.386 52.381 0.00 0.00 43.55 2.85
831 855 4.035909 GGAGAGACGGTGACTCTTATCTTC 59.964 50.000 0.00 0.00 43.55 2.87
832 856 3.949113 AGAGACGGTGACTCTTATCTTCC 59.051 47.826 0.00 0.00 41.20 3.46
1105 1148 0.250124 CACCTACAACTTCACCGCCA 60.250 55.000 0.00 0.00 0.00 5.69
1639 1682 2.124236 CCCTCTCCTACGGCGACT 60.124 66.667 16.62 0.00 0.00 4.18
1640 1683 1.753463 CCCTCTCCTACGGCGACTT 60.753 63.158 16.62 0.00 0.00 3.01
1642 1685 0.179134 CCTCTCCTACGGCGACTTTG 60.179 60.000 16.62 0.27 0.00 2.77
1643 1686 0.526662 CTCTCCTACGGCGACTTTGT 59.473 55.000 16.62 0.00 0.00 2.83
2726 2769 2.058675 CGGACTGGAGGTTGAAGGT 58.941 57.895 0.00 0.00 0.00 3.50
2845 2888 1.250154 TGCCCTGAAATTTGAGGCGG 61.250 55.000 17.47 6.85 46.92 6.13
2938 2981 2.507110 ATCAGTTGGAGGTGCGTCCG 62.507 60.000 6.46 0.00 39.81 4.79
2970 3013 2.048503 GGCGGCGTTACTGAGTGT 60.049 61.111 9.37 0.00 0.00 3.55
3000 3043 0.684153 GGGCTAATGCTGGCAAAGGA 60.684 55.000 0.00 0.00 39.59 3.36
3035 3078 1.048601 AGACTTCTGGAGCCGTGAAA 58.951 50.000 0.00 0.00 0.00 2.69
3043 3086 1.966451 GAGCCGTGAAAGTGGTGGG 60.966 63.158 0.00 0.00 0.00 4.61
3157 3200 6.204688 TGAGTTGAGTTTGGTTTGTATAGCAG 59.795 38.462 0.00 0.00 0.00 4.24
3159 3202 4.331968 TGAGTTTGGTTTGTATAGCAGGG 58.668 43.478 0.00 0.00 0.00 4.45
3209 3252 5.429130 AGGACCGAACAAGAAGAAATATCC 58.571 41.667 0.00 0.00 0.00 2.59
3210 3253 4.575236 GGACCGAACAAGAAGAAATATCCC 59.425 45.833 0.00 0.00 0.00 3.85
3211 3254 5.174037 ACCGAACAAGAAGAAATATCCCA 57.826 39.130 0.00 0.00 0.00 4.37
3222 3265 4.026052 AGAAATATCCCAAGGCAGTTTGG 58.974 43.478 6.84 6.84 45.83 3.28
3232 3275 1.569072 AGGCAGTTTGGGGTATTAGGG 59.431 52.381 0.00 0.00 0.00 3.53
3244 3290 3.105283 GGTATTAGGGTGAGTCAGGTGT 58.895 50.000 0.00 0.00 0.00 4.16
3272 3318 9.618890 AAAGCTGATAGATTGCTTATAACTTGA 57.381 29.630 0.00 0.00 44.94 3.02
3273 3319 9.618890 AAGCTGATAGATTGCTTATAACTTGAA 57.381 29.630 0.00 0.00 44.04 2.69
3274 3320 9.790344 AGCTGATAGATTGCTTATAACTTGAAT 57.210 29.630 0.00 0.00 32.61 2.57
3275 3321 9.823098 GCTGATAGATTGCTTATAACTTGAATG 57.177 33.333 0.00 0.00 0.00 2.67
3280 3326 8.798859 AGATTGCTTATAACTTGAATGTCACT 57.201 30.769 0.00 0.00 0.00 3.41
3281 3327 8.887717 AGATTGCTTATAACTTGAATGTCACTC 58.112 33.333 0.00 0.00 0.00 3.51
3307 3354 2.420372 GAGATGATAGCCGATACGAGCA 59.580 50.000 0.00 0.00 0.00 4.26
3311 3358 2.059541 GATAGCCGATACGAGCAAACC 58.940 52.381 0.00 0.00 0.00 3.27
3321 3384 1.344438 ACGAGCAAACCAGATGTCAGA 59.656 47.619 0.00 0.00 0.00 3.27
3325 3388 1.200948 GCAAACCAGATGTCAGAAGGC 59.799 52.381 0.00 0.00 0.00 4.35
3328 3391 0.617413 ACCAGATGTCAGAAGGCCAG 59.383 55.000 5.01 0.00 0.00 4.85
3335 3398 0.674895 GTCAGAAGGCCAGACGCAAT 60.675 55.000 5.01 0.00 40.31 3.56
3337 3400 1.377725 AGAAGGCCAGACGCAATGG 60.378 57.895 5.01 0.00 40.31 3.16
3369 3435 2.067013 GACTAGAACACCGCTCAAACC 58.933 52.381 0.00 0.00 0.00 3.27
3372 3438 2.052782 AGAACACCGCTCAAACCTTT 57.947 45.000 0.00 0.00 0.00 3.11
3373 3439 2.375146 AGAACACCGCTCAAACCTTTT 58.625 42.857 0.00 0.00 0.00 2.27
3374 3440 3.547746 AGAACACCGCTCAAACCTTTTA 58.452 40.909 0.00 0.00 0.00 1.52
3375 3441 4.142038 AGAACACCGCTCAAACCTTTTAT 58.858 39.130 0.00 0.00 0.00 1.40
3376 3442 4.215613 AGAACACCGCTCAAACCTTTTATC 59.784 41.667 0.00 0.00 0.00 1.75
3387 3457 8.682710 GCTCAAACCTTTTATCATATACAACCA 58.317 33.333 0.00 0.00 0.00 3.67
3399 3473 6.946340 TCATATACAACCACACTGAACAGAT 58.054 36.000 8.87 0.00 0.00 2.90
3411 3485 2.009051 TGAACAGATGCATGTAAGCCG 58.991 47.619 2.46 0.00 31.70 5.52
3412 3486 0.734889 AACAGATGCATGTAAGCCGC 59.265 50.000 2.46 0.00 31.70 6.53
3539 3615 3.782656 TGAAAGTTAACCTGAGGGTCC 57.217 47.619 2.38 0.00 46.67 4.46
3540 3616 2.374170 TGAAAGTTAACCTGAGGGTCCC 59.626 50.000 2.38 0.00 46.67 4.46
3661 3738 5.313240 AGGCCCCTATAGAAATGCTATTTGA 59.687 40.000 0.00 0.00 40.30 2.69
3872 3949 9.823647 TTTCTCCTGAGACAAATTATACATCTC 57.176 33.333 0.00 0.00 37.14 2.75
3874 3951 9.152327 TCTCCTGAGACAAATTATACATCTCAT 57.848 33.333 2.92 0.00 43.55 2.90
3876 3953 9.152327 TCCTGAGACAAATTATACATCTCATCT 57.848 33.333 2.92 0.00 43.55 2.90
3877 3954 9.775854 CCTGAGACAAATTATACATCTCATCTT 57.224 33.333 2.92 0.00 43.55 2.40
3893 3970 7.175347 TCTCATCTTAGTACTGCATGAAACT 57.825 36.000 5.39 0.00 0.00 2.66
3968 4047 0.252513 TCGAGGACCAATGGGAAGGA 60.253 55.000 3.55 0.00 38.05 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.005539 ATCGCCTGCACCTCCACT 61.006 61.111 0.00 0.00 0.00 4.00
1 2 2.512515 GATCGCCTGCACCTCCAC 60.513 66.667 0.00 0.00 0.00 4.02
2 3 4.147449 CGATCGCCTGCACCTCCA 62.147 66.667 0.26 0.00 0.00 3.86
86 87 2.094659 GTCGACCATGCCAGACGTG 61.095 63.158 3.51 0.00 34.83 4.49
87 88 2.261671 GTCGACCATGCCAGACGT 59.738 61.111 3.51 0.00 0.00 4.34
88 89 1.807165 CTGTCGACCATGCCAGACG 60.807 63.158 14.12 0.00 36.49 4.18
89 90 1.448540 CCTGTCGACCATGCCAGAC 60.449 63.158 14.12 5.94 0.00 3.51
90 91 2.659063 CCCTGTCGACCATGCCAGA 61.659 63.158 14.12 0.00 0.00 3.86
91 92 2.124983 CCCTGTCGACCATGCCAG 60.125 66.667 14.12 2.03 0.00 4.85
92 93 4.408821 GCCCTGTCGACCATGCCA 62.409 66.667 14.12 0.00 0.00 4.92
95 96 4.758251 TGCGCCCTGTCGACCATG 62.758 66.667 14.12 3.19 0.00 3.66
96 97 4.760047 GTGCGCCCTGTCGACCAT 62.760 66.667 14.12 0.00 0.00 3.55
151 174 1.054978 ACGGGAGGGGAAGAATAGCC 61.055 60.000 0.00 0.00 0.00 3.93
152 175 0.837940 AACGGGAGGGGAAGAATAGC 59.162 55.000 0.00 0.00 0.00 2.97
196 219 5.033507 CACACATCTCGTCTTCTCTATGTG 58.966 45.833 10.74 10.74 46.01 3.21
199 222 4.944317 TGTCACACATCTCGTCTTCTCTAT 59.056 41.667 0.00 0.00 0.00 1.98
202 225 3.238441 GTGTCACACATCTCGTCTTCTC 58.762 50.000 2.00 0.00 34.08 2.87
267 290 7.035612 GTCAAATAAACAAAAGCAGGGGATAG 58.964 38.462 0.00 0.00 0.00 2.08
272 295 5.990996 ACATGTCAAATAAACAAAAGCAGGG 59.009 36.000 0.00 0.00 0.00 4.45
275 298 9.755804 TTCATACATGTCAAATAAACAAAAGCA 57.244 25.926 0.00 0.00 0.00 3.91
291 314 9.393249 CAAACTCATTACGTTTTTCATACATGT 57.607 29.630 2.69 2.69 32.64 3.21
292 315 9.605955 TCAAACTCATTACGTTTTTCATACATG 57.394 29.630 0.00 0.00 32.64 3.21
343 366 3.880490 CGTGGCATAGCTTAATGGGTTTA 59.120 43.478 0.00 0.00 0.00 2.01
344 367 2.687935 CGTGGCATAGCTTAATGGGTTT 59.312 45.455 0.00 0.00 0.00 3.27
345 368 2.297701 CGTGGCATAGCTTAATGGGTT 58.702 47.619 0.00 0.00 0.00 4.11
346 369 1.211949 ACGTGGCATAGCTTAATGGGT 59.788 47.619 0.00 0.00 0.00 4.51
347 370 1.603802 CACGTGGCATAGCTTAATGGG 59.396 52.381 7.95 0.00 0.00 4.00
348 371 1.603802 CCACGTGGCATAGCTTAATGG 59.396 52.381 24.02 0.00 0.00 3.16
364 387 4.688419 CAACCAGCTTGCGCCACG 62.688 66.667 4.18 0.00 36.60 4.94
365 388 4.347453 CCAACCAGCTTGCGCCAC 62.347 66.667 4.18 0.00 36.60 5.01
376 399 4.877619 TTTCACCGCGGCCAACCA 62.878 61.111 28.58 0.78 34.57 3.67
377 400 3.140225 TTTTTCACCGCGGCCAACC 62.140 57.895 28.58 0.00 0.00 3.77
378 401 1.660264 CTTTTTCACCGCGGCCAAC 60.660 57.895 28.58 0.00 0.00 3.77
379 402 2.725008 CTTTTTCACCGCGGCCAA 59.275 55.556 28.58 15.88 0.00 4.52
380 403 3.972276 GCTTTTTCACCGCGGCCA 61.972 61.111 28.58 9.25 0.00 5.36
381 404 2.693250 AAAGCTTTTTCACCGCGGCC 62.693 55.000 28.58 3.24 0.00 6.13
382 405 0.874175 AAAAGCTTTTTCACCGCGGC 60.874 50.000 28.58 8.56 0.00 6.53
383 406 2.031508 TCTAAAAGCTTTTTCACCGCGG 60.032 45.455 28.21 26.86 0.00 6.46
384 407 3.262135 TCTAAAAGCTTTTTCACCGCG 57.738 42.857 28.21 0.00 0.00 6.46
385 408 7.812309 AATATTCTAAAAGCTTTTTCACCGC 57.188 32.000 28.21 0.00 0.00 5.68
447 470 5.200483 GGGATCATCACCTCCATGTAAAAA 58.800 41.667 0.00 0.00 32.90 1.94
448 471 4.229353 TGGGATCATCACCTCCATGTAAAA 59.771 41.667 0.00 0.00 32.90 1.52
449 472 3.785325 TGGGATCATCACCTCCATGTAAA 59.215 43.478 0.00 0.00 32.90 2.01
450 473 3.392730 TGGGATCATCACCTCCATGTAA 58.607 45.455 0.00 0.00 32.90 2.41
451 474 3.059051 TGGGATCATCACCTCCATGTA 57.941 47.619 0.00 0.00 32.90 2.29
452 475 1.897473 TGGGATCATCACCTCCATGT 58.103 50.000 0.00 0.00 32.90 3.21
453 476 4.857130 ATATGGGATCATCACCTCCATG 57.143 45.455 7.45 0.00 38.51 3.66
454 477 7.535390 AAATATATGGGATCATCACCTCCAT 57.465 36.000 0.00 0.00 40.78 3.41
455 478 6.975471 AAATATATGGGATCATCACCTCCA 57.025 37.500 0.00 0.00 34.96 3.86
497 520 1.300388 CCAGCAAGCACCACTTTGC 60.300 57.895 1.20 1.20 43.34 3.68
498 521 1.267806 CTACCAGCAAGCACCACTTTG 59.732 52.381 0.00 0.00 36.04 2.77
499 522 1.609208 CTACCAGCAAGCACCACTTT 58.391 50.000 0.00 0.00 36.04 2.66
500 523 0.250901 CCTACCAGCAAGCACCACTT 60.251 55.000 0.00 0.00 40.05 3.16
501 524 1.376466 CCTACCAGCAAGCACCACT 59.624 57.895 0.00 0.00 0.00 4.00
502 525 2.335712 GCCTACCAGCAAGCACCAC 61.336 63.158 0.00 0.00 0.00 4.16
503 526 2.034066 GCCTACCAGCAAGCACCA 59.966 61.111 0.00 0.00 0.00 4.17
504 527 2.751837 GGCCTACCAGCAAGCACC 60.752 66.667 0.00 0.00 35.26 5.01
505 528 3.127533 CGGCCTACCAGCAAGCAC 61.128 66.667 0.00 0.00 34.57 4.40
506 529 3.636231 ACGGCCTACCAGCAAGCA 61.636 61.111 0.00 0.00 34.57 3.91
507 530 3.127533 CACGGCCTACCAGCAAGC 61.128 66.667 0.00 0.00 34.57 4.01
508 531 0.889186 AAACACGGCCTACCAGCAAG 60.889 55.000 0.00 0.00 34.57 4.01
509 532 1.149627 AAACACGGCCTACCAGCAA 59.850 52.632 0.00 0.00 34.57 3.91
510 533 1.599518 CAAACACGGCCTACCAGCA 60.600 57.895 0.00 0.00 34.57 4.41
511 534 1.599797 ACAAACACGGCCTACCAGC 60.600 57.895 0.00 0.00 34.57 4.85
512 535 0.250124 TCACAAACACGGCCTACCAG 60.250 55.000 0.00 0.00 34.57 4.00
513 536 0.398696 ATCACAAACACGGCCTACCA 59.601 50.000 0.00 0.00 34.57 3.25
514 537 1.530323 AATCACAAACACGGCCTACC 58.470 50.000 0.00 0.00 0.00 3.18
515 538 3.636282 AAAATCACAAACACGGCCTAC 57.364 42.857 0.00 0.00 0.00 3.18
544 567 9.672673 CATCTCCATCTAGAAAAAGAGGTAAAA 57.327 33.333 0.00 0.00 0.00 1.52
545 568 9.046846 TCATCTCCATCTAGAAAAAGAGGTAAA 57.953 33.333 0.00 0.00 0.00 2.01
546 569 8.609617 TCATCTCCATCTAGAAAAAGAGGTAA 57.390 34.615 0.00 0.00 0.00 2.85
547 570 7.288852 CCTCATCTCCATCTAGAAAAAGAGGTA 59.711 40.741 0.00 0.00 33.85 3.08
548 571 6.099557 CCTCATCTCCATCTAGAAAAAGAGGT 59.900 42.308 0.00 0.00 33.85 3.85
549 572 6.326064 TCCTCATCTCCATCTAGAAAAAGAGG 59.674 42.308 14.63 14.63 36.60 3.69
550 573 7.358770 TCCTCATCTCCATCTAGAAAAAGAG 57.641 40.000 0.00 1.05 0.00 2.85
551 574 7.927683 ATCCTCATCTCCATCTAGAAAAAGA 57.072 36.000 0.00 0.00 0.00 2.52
552 575 8.977267 AAATCCTCATCTCCATCTAGAAAAAG 57.023 34.615 0.00 0.00 0.00 2.27
553 576 9.759473 AAAAATCCTCATCTCCATCTAGAAAAA 57.241 29.630 0.00 0.00 0.00 1.94
589 612 9.166173 CATGTAGTCATCACCTTCATCTAAAAA 57.834 33.333 0.00 0.00 31.15 1.94
590 613 8.321353 ACATGTAGTCATCACCTTCATCTAAAA 58.679 33.333 0.00 0.00 31.15 1.52
591 614 7.851228 ACATGTAGTCATCACCTTCATCTAAA 58.149 34.615 0.00 0.00 31.15 1.85
592 615 7.423844 ACATGTAGTCATCACCTTCATCTAA 57.576 36.000 0.00 0.00 31.15 2.10
593 616 8.712228 ATACATGTAGTCATCACCTTCATCTA 57.288 34.615 11.91 0.00 31.15 1.98
594 617 5.946942 ACATGTAGTCATCACCTTCATCT 57.053 39.130 0.00 0.00 31.15 2.90
595 618 8.668510 AAATACATGTAGTCATCACCTTCATC 57.331 34.615 11.91 0.00 31.15 2.92
596 619 9.466497 AAAAATACATGTAGTCATCACCTTCAT 57.534 29.630 11.91 0.00 31.15 2.57
597 620 8.862325 AAAAATACATGTAGTCATCACCTTCA 57.138 30.769 11.91 0.00 31.15 3.02
619 642 9.408069 AGTTGTGTACACGTTTTCATTTAAAAA 57.592 25.926 20.61 1.84 38.76 1.94
620 643 8.967552 AGTTGTGTACACGTTTTCATTTAAAA 57.032 26.923 20.61 2.27 34.66 1.52
621 644 8.967552 AAGTTGTGTACACGTTTTCATTTAAA 57.032 26.923 20.61 2.47 0.00 1.52
622 645 7.697291 GGAAGTTGTGTACACGTTTTCATTTAA 59.303 33.333 24.79 9.91 0.00 1.52
623 646 7.066043 AGGAAGTTGTGTACACGTTTTCATTTA 59.934 33.333 24.79 5.29 0.00 1.40
624 647 6.031471 GGAAGTTGTGTACACGTTTTCATTT 58.969 36.000 24.79 12.19 0.00 2.32
625 648 5.355910 AGGAAGTTGTGTACACGTTTTCATT 59.644 36.000 24.79 15.79 0.00 2.57
626 649 4.879545 AGGAAGTTGTGTACACGTTTTCAT 59.120 37.500 24.79 19.73 0.00 2.57
627 650 4.255301 AGGAAGTTGTGTACACGTTTTCA 58.745 39.130 24.79 7.68 0.00 2.69
628 651 4.569564 AGAGGAAGTTGTGTACACGTTTTC 59.430 41.667 20.61 20.02 0.00 2.29
629 652 4.510571 AGAGGAAGTTGTGTACACGTTTT 58.489 39.130 20.61 13.72 0.00 2.43
630 653 4.117685 GAGAGGAAGTTGTGTACACGTTT 58.882 43.478 20.61 14.05 0.00 3.60
631 654 3.131577 TGAGAGGAAGTTGTGTACACGTT 59.868 43.478 20.61 13.64 0.00 3.99
632 655 2.691526 TGAGAGGAAGTTGTGTACACGT 59.308 45.455 20.61 5.55 0.00 4.49
633 656 3.364889 TGAGAGGAAGTTGTGTACACG 57.635 47.619 20.61 0.00 0.00 4.49
634 657 3.495001 GCTTGAGAGGAAGTTGTGTACAC 59.505 47.826 19.36 19.36 0.00 2.90
635 658 3.728845 GCTTGAGAGGAAGTTGTGTACA 58.271 45.455 0.00 0.00 0.00 2.90
636 659 2.731976 CGCTTGAGAGGAAGTTGTGTAC 59.268 50.000 0.00 0.00 0.00 2.90
637 660 2.288825 CCGCTTGAGAGGAAGTTGTGTA 60.289 50.000 0.00 0.00 37.14 2.90
638 661 1.541233 CCGCTTGAGAGGAAGTTGTGT 60.541 52.381 0.00 0.00 37.14 3.72
639 662 1.151668 CCGCTTGAGAGGAAGTTGTG 58.848 55.000 0.00 0.00 37.14 3.33
640 663 0.603975 GCCGCTTGAGAGGAAGTTGT 60.604 55.000 4.87 0.00 37.14 3.32
641 664 1.630244 CGCCGCTTGAGAGGAAGTTG 61.630 60.000 4.87 0.00 37.14 3.16
642 665 1.374758 CGCCGCTTGAGAGGAAGTT 60.375 57.895 4.87 0.00 37.14 2.66
643 666 2.262915 CGCCGCTTGAGAGGAAGT 59.737 61.111 4.87 0.00 37.14 3.01
644 667 3.191539 GCGCCGCTTGAGAGGAAG 61.192 66.667 0.00 0.00 37.14 3.46
645 668 4.760047 GGCGCCGCTTGAGAGGAA 62.760 66.667 12.58 0.00 37.14 3.36
665 688 3.762247 CATTTGGGGCGCCACCTG 61.762 66.667 29.43 17.53 39.10 4.00
668 691 3.773404 ATGCATTTGGGGCGCCAC 61.773 61.111 30.85 28.40 0.00 5.01
669 692 3.772281 CATGCATTTGGGGCGCCA 61.772 61.111 30.85 20.22 0.00 5.69
670 693 2.518973 TTTCATGCATTTGGGGCGCC 62.519 55.000 21.18 21.18 0.00 6.53
671 694 0.462403 ATTTCATGCATTTGGGGCGC 60.462 50.000 0.00 0.00 0.00 6.53
672 695 2.027003 AATTTCATGCATTTGGGGCG 57.973 45.000 0.00 0.00 0.00 6.13
673 696 3.768468 CAAATTTCATGCATTTGGGGC 57.232 42.857 16.73 0.00 37.78 5.80
680 703 9.451002 TGAATAAAATGACCAAATTTCATGCAT 57.549 25.926 0.00 0.00 33.84 3.96
681 704 8.843885 TGAATAAAATGACCAAATTTCATGCA 57.156 26.923 0.00 0.00 33.84 3.96
702 725 9.657419 GTCCATACATTTCAAAGGAATTTGAAT 57.343 29.630 14.81 5.48 46.47 2.57
711 734 3.756434 ACCGTGTCCATACATTTCAAAGG 59.244 43.478 0.00 0.00 38.08 3.11
739 762 1.875963 CTGATGCGAAAACCGGCTT 59.124 52.632 0.00 0.00 39.04 4.35
751 774 1.738099 AGTTCACGGACGCTGATGC 60.738 57.895 0.00 0.00 0.00 3.91
757 780 2.022129 CAGACCAGTTCACGGACGC 61.022 63.158 0.00 0.00 0.00 5.19
758 781 1.372997 CCAGACCAGTTCACGGACG 60.373 63.158 0.00 0.00 0.00 4.79
774 797 7.394077 CCATGTATTTATCTGCATATTGGTCCA 59.606 37.037 0.00 0.00 0.00 4.02
775 798 7.629222 GCCATGTATTTATCTGCATATTGGTCC 60.629 40.741 0.00 0.00 0.00 4.46
784 807 1.879380 GCGGCCATGTATTTATCTGCA 59.121 47.619 2.24 0.00 0.00 4.41
825 849 4.338118 GGTTCATTGGCGAAATGGAAGATA 59.662 41.667 9.99 0.00 45.00 1.98
831 855 2.965572 ATGGTTCATTGGCGAAATGG 57.034 45.000 9.99 0.00 45.00 3.16
832 856 3.181501 ACGTATGGTTCATTGGCGAAATG 60.182 43.478 4.74 4.74 46.10 2.32
1458 1501 2.028476 CCAATCGTTCCTGTAGGTGTCA 60.028 50.000 0.00 0.00 36.34 3.58
1643 1686 2.993264 GAAGGACGTCCGTGGGGA 60.993 66.667 28.16 0.00 42.08 4.81
1926 1969 1.876714 CTCGTCGTACCCCATTGCG 60.877 63.158 0.00 0.00 0.00 4.85
2148 2191 3.716539 GATGCGTACCTCGGCTGCA 62.717 63.158 0.50 0.00 40.23 4.41
2151 2194 1.364171 GATGATGCGTACCTCGGCT 59.636 57.895 0.00 0.00 40.26 5.52
2726 2769 2.171003 TCTGCTTCTCATCGAACTCCA 58.829 47.619 0.00 0.00 0.00 3.86
2938 2981 3.050275 GCCTGGGTTCTGCGTGTC 61.050 66.667 0.00 0.00 0.00 3.67
2970 3013 1.141657 GCATTAGCCCCTGATGACTCA 59.858 52.381 1.70 0.00 30.42 3.41
3000 3043 3.603965 AGTCTATCCCTCACCGAAGAT 57.396 47.619 0.00 0.00 0.00 2.40
3035 3078 1.111277 GCTTCACAAAACCCACCACT 58.889 50.000 0.00 0.00 0.00 4.00
3127 3170 6.767524 ACAAACCAAACTCAACTCATACAA 57.232 33.333 0.00 0.00 0.00 2.41
3157 3200 5.768164 ACCGATATAATCCAACACATTTCCC 59.232 40.000 0.00 0.00 0.00 3.97
3159 3202 7.490962 TGACCGATATAATCCAACACATTTC 57.509 36.000 0.00 0.00 0.00 2.17
3209 3252 1.937191 AATACCCCAAACTGCCTTGG 58.063 50.000 2.99 2.99 44.77 3.61
3210 3253 3.023832 CCTAATACCCCAAACTGCCTTG 58.976 50.000 0.00 0.00 0.00 3.61
3211 3254 2.024369 CCCTAATACCCCAAACTGCCTT 60.024 50.000 0.00 0.00 0.00 4.35
3222 3265 2.434702 CACCTGACTCACCCTAATACCC 59.565 54.545 0.00 0.00 0.00 3.69
3232 3275 3.728845 TCAGCTTTAACACCTGACTCAC 58.271 45.455 0.00 0.00 31.16 3.51
3278 3324 1.335182 CGGCTATCATCTCACACGAGT 59.665 52.381 0.00 0.00 40.44 4.18
3279 3325 1.604278 TCGGCTATCATCTCACACGAG 59.396 52.381 0.00 0.00 40.98 4.18
3280 3326 1.675552 TCGGCTATCATCTCACACGA 58.324 50.000 0.00 0.00 0.00 4.35
3281 3327 2.713895 ATCGGCTATCATCTCACACG 57.286 50.000 0.00 0.00 0.00 4.49
3307 3354 1.425066 TGGCCTTCTGACATCTGGTTT 59.575 47.619 3.32 0.00 0.00 3.27
3311 3358 1.738365 CGTCTGGCCTTCTGACATCTG 60.738 57.143 3.32 0.00 42.30 2.90
3325 3388 1.080569 GGTTTGCCATTGCGTCTGG 60.081 57.895 0.00 0.00 41.78 3.86
3328 3391 1.274798 CGTTGGTTTGCCATTGCGTC 61.275 55.000 0.00 0.00 45.56 5.19
3335 3398 0.250553 CTAGTCCCGTTGGTTTGCCA 60.251 55.000 0.00 0.00 44.38 4.92
3337 3400 1.534163 GTTCTAGTCCCGTTGGTTTGC 59.466 52.381 0.00 0.00 0.00 3.68
3348 3414 2.067013 GTTTGAGCGGTGTTCTAGTCC 58.933 52.381 0.00 0.00 0.00 3.85
3369 3435 9.988350 GTTCAGTGTGGTTGTATATGATAAAAG 57.012 33.333 0.00 0.00 0.00 2.27
3372 3438 8.536175 TCTGTTCAGTGTGGTTGTATATGATAA 58.464 33.333 0.00 0.00 0.00 1.75
3373 3439 8.073467 TCTGTTCAGTGTGGTTGTATATGATA 57.927 34.615 0.00 0.00 0.00 2.15
3374 3440 6.946340 TCTGTTCAGTGTGGTTGTATATGAT 58.054 36.000 0.00 0.00 0.00 2.45
3375 3441 6.353404 TCTGTTCAGTGTGGTTGTATATGA 57.647 37.500 0.00 0.00 0.00 2.15
3376 3442 6.457392 GCATCTGTTCAGTGTGGTTGTATATG 60.457 42.308 0.00 0.00 0.00 1.78
3387 3457 3.438087 GCTTACATGCATCTGTTCAGTGT 59.562 43.478 0.00 0.00 0.00 3.55
3399 3473 1.066502 TCTACTTGCGGCTTACATGCA 60.067 47.619 0.00 0.00 36.72 3.96
3411 3485 6.045318 TCTCAGCACATTCTAATCTACTTGC 58.955 40.000 0.00 0.00 0.00 4.01
3412 3486 8.484641 TTTCTCAGCACATTCTAATCTACTTG 57.515 34.615 0.00 0.00 0.00 3.16
3458 3534 9.582223 GATATAACAAAGCAAAGTATCGTTAGC 57.418 33.333 0.00 0.00 0.00 3.09
3661 3738 8.997301 AGATAAATATTTCTCAGGGGAGGTAT 57.003 34.615 14.06 0.00 41.69 2.73
3872 3949 6.674037 GCACAGTTTCATGCAGTACTAAGATG 60.674 42.308 0.00 0.00 41.65 2.90
3874 3951 4.690748 GCACAGTTTCATGCAGTACTAAGA 59.309 41.667 0.00 0.00 41.65 2.10
3876 3953 4.384940 TGCACAGTTTCATGCAGTACTAA 58.615 39.130 0.00 0.00 46.63 2.24
3877 3954 4.001618 TGCACAGTTTCATGCAGTACTA 57.998 40.909 0.00 0.00 46.63 1.82
3878 3955 2.849942 TGCACAGTTTCATGCAGTACT 58.150 42.857 0.00 0.00 46.63 2.73
3893 3970 5.791666 TGGCAATGAATTTTTAGATGCACA 58.208 33.333 0.00 0.00 34.14 4.57
3968 4047 7.279615 TCGGTTAAATCCTATGTGATGTCAAT 58.720 34.615 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.