Multiple sequence alignment - TraesCS7A01G261100

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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 TraesCS7A01G261100 chr7A 100.000 3820 0 0 1 3820 254895588 254899407 0.000000e+00 7055.0
1 TraesCS7A01G261100 chr7D 89.796 3283 134 78 610 3788 242785877 242782692 0.000000e+00 4021.0
2 TraesCS7A01G261100 chr7D 91.339 381 14 11 1 374 242786587 242786219 1.580000e-138 503.0
3 TraesCS7A01G261100 chr7D 89.412 85 3 3 37 115 242785880 242785796 6.750000e-18 102.0
4 TraesCS7A01G261100 chr7D 100.000 33 0 0 3788 3820 242782671 242782639 1.150000e-05 62.1
5 TraesCS7A01G261100 chr7B 89.944 3192 131 82 723 3788 218549862 218546735 0.000000e+00 3941.0
6 TraesCS7A01G261100 chr7B 92.893 197 7 4 3 193 218550931 218550736 2.910000e-71 279.0
7 TraesCS7A01G261100 chr7B 84.862 218 19 9 178 390 218550524 218550316 1.390000e-49 207.0
8 TraesCS7A01G261100 chr5D 78.912 588 95 17 1815 2380 393995090 393994510 4.660000e-99 372.0
9 TraesCS7A01G261100 chr5D 90.323 93 9 0 440 532 386648832 386648924 5.180000e-24 122.0
10 TraesCS7A01G261100 chr5A 78.596 584 98 17 1816 2380 496011465 496010890 1.010000e-95 361.0
11 TraesCS7A01G261100 chr5A 90.909 99 9 0 434 532 677160839 677160937 2.390000e-27 134.0
12 TraesCS7A01G261100 chr5B 82.031 384 61 7 1815 2194 473872373 473871994 1.710000e-83 320.0
13 TraesCS7A01G261100 chr6A 94.444 90 5 0 445 534 614304754 614304665 5.150000e-29 139.0
14 TraesCS7A01G261100 chr6A 93.407 91 5 1 446 536 596336265 596336176 2.390000e-27 134.0
15 TraesCS7A01G261100 chr6A 89.796 98 9 1 432 528 601226121 601226024 1.440000e-24 124.0
16 TraesCS7A01G261100 chr2D 95.402 87 4 0 446 532 612817346 612817260 5.150000e-29 139.0
17 TraesCS7A01G261100 chr2A 95.294 85 4 0 444 528 585208694 585208778 6.660000e-28 135.0
18 TraesCS7A01G261100 chr4D 93.258 89 6 0 446 534 19442647 19442559 8.610000e-27 132.0
19 TraesCS7A01G261100 chr3D 93.103 87 6 0 446 532 206978512 206978598 1.110000e-25 128.0


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 TraesCS7A01G261100 chr7A 254895588 254899407 3819 False 7055.000000 7055 100.00000 1 3820 1 chr7A.!!$F1 3819
1 TraesCS7A01G261100 chr7D 242782639 242786587 3948 True 1172.025000 4021 92.63675 1 3820 4 chr7D.!!$R1 3819
2 TraesCS7A01G261100 chr7B 218546735 218550931 4196 True 1475.666667 3941 89.23300 3 3788 3 chr7B.!!$R1 3785
3 TraesCS7A01G261100 chr5D 393994510 393995090 580 True 372.000000 372 78.91200 1815 2380 1 chr5D.!!$R1 565
4 TraesCS7A01G261100 chr5A 496010890 496011465 575 True 361.000000 361 78.59600 1816 2380 1 chr5A.!!$R1 564

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
608 880 0.171007 CCAGCCGATCATTTTGCGTT 59.829 50.0 0.00 0.00 0.00 4.84 F
1208 1863 0.034283 TAGGTTGGCTCATGCATGCA 60.034 50.0 25.04 25.04 41.91 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1793 2476 0.672342 ACCCATACCGTATCGTCAGC 59.328 55.0 0.00 0.00 0.0 4.26 R
3149 3927 0.374758 GACCAGTACACATGCATGCG 59.625 55.0 26.53 19.79 0.0 4.73 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 3.175929 CCAGACACACGTTTTCAAAACC 58.824 45.455 7.44 0.00 0.00 3.27
105 107 1.454847 CAGAGGGGAGAGGGAGACG 60.455 68.421 0.00 0.00 0.00 4.18
115 118 1.379309 AGGGAGACGGAGACAGAGC 60.379 63.158 0.00 0.00 0.00 4.09
210 444 4.036498 CCTGTAGAGGTATCACTAACACCG 59.964 50.000 0.00 0.00 37.42 4.94
211 445 3.379372 TGTAGAGGTATCACTAACACCGC 59.621 47.826 0.00 0.00 37.42 5.68
256 491 1.557443 CGGAGCGTGAAGACACAACC 61.557 60.000 0.00 0.00 46.20 3.77
257 492 1.557443 GGAGCGTGAAGACACAACCG 61.557 60.000 0.00 0.00 46.20 4.44
298 536 1.226491 GCAACGCTGATGATGCACC 60.226 57.895 0.00 0.00 38.63 5.01
346 589 9.936329 AAGAAAGAAATACTCCTATCTCTCTCT 57.064 33.333 0.00 0.00 0.00 3.10
375 618 8.500753 TTAATACAGCAGTATACAAGGTTTGG 57.499 34.615 5.50 0.00 40.00 3.28
380 623 5.705441 CAGCAGTATACAAGGTTTGGAGAAA 59.295 40.000 5.50 0.00 34.12 2.52
394 666 7.716560 AGGTTTGGAGAAATTGATTTTCCTTTG 59.283 33.333 13.65 0.00 44.06 2.77
419 691 8.144478 TGTATACTAGACAAAGAATGAGATGGC 58.856 37.037 4.17 0.00 0.00 4.40
420 692 4.437239 ACTAGACAAAGAATGAGATGGCG 58.563 43.478 0.00 0.00 0.00 5.69
421 693 3.340814 AGACAAAGAATGAGATGGCGT 57.659 42.857 0.00 0.00 0.00 5.68
422 694 3.005554 AGACAAAGAATGAGATGGCGTG 58.994 45.455 0.00 0.00 0.00 5.34
423 695 3.002791 GACAAAGAATGAGATGGCGTGA 58.997 45.455 0.00 0.00 0.00 4.35
424 696 3.005554 ACAAAGAATGAGATGGCGTGAG 58.994 45.455 0.00 0.00 0.00 3.51
425 697 3.005554 CAAAGAATGAGATGGCGTGAGT 58.994 45.455 0.00 0.00 0.00 3.41
426 698 3.340814 AAGAATGAGATGGCGTGAGTT 57.659 42.857 0.00 0.00 0.00 3.01
427 699 2.625737 AGAATGAGATGGCGTGAGTTG 58.374 47.619 0.00 0.00 0.00 3.16
428 700 1.667724 GAATGAGATGGCGTGAGTTGG 59.332 52.381 0.00 0.00 0.00 3.77
429 701 0.615331 ATGAGATGGCGTGAGTTGGT 59.385 50.000 0.00 0.00 0.00 3.67
430 702 0.396435 TGAGATGGCGTGAGTTGGTT 59.604 50.000 0.00 0.00 0.00 3.67
431 703 1.621317 TGAGATGGCGTGAGTTGGTTA 59.379 47.619 0.00 0.00 0.00 2.85
432 704 2.236146 TGAGATGGCGTGAGTTGGTTAT 59.764 45.455 0.00 0.00 0.00 1.89
433 705 3.270877 GAGATGGCGTGAGTTGGTTATT 58.729 45.455 0.00 0.00 0.00 1.40
434 706 3.009723 AGATGGCGTGAGTTGGTTATTG 58.990 45.455 0.00 0.00 0.00 1.90
435 707 2.264005 TGGCGTGAGTTGGTTATTGT 57.736 45.000 0.00 0.00 0.00 2.71
436 708 2.577700 TGGCGTGAGTTGGTTATTGTT 58.422 42.857 0.00 0.00 0.00 2.83
437 709 2.292016 TGGCGTGAGTTGGTTATTGTTG 59.708 45.455 0.00 0.00 0.00 3.33
438 710 2.292292 GGCGTGAGTTGGTTATTGTTGT 59.708 45.455 0.00 0.00 0.00 3.32
439 711 3.499157 GGCGTGAGTTGGTTATTGTTGTA 59.501 43.478 0.00 0.00 0.00 2.41
440 712 4.023878 GGCGTGAGTTGGTTATTGTTGTAA 60.024 41.667 0.00 0.00 0.00 2.41
441 713 5.144359 GCGTGAGTTGGTTATTGTTGTAAG 58.856 41.667 0.00 0.00 0.00 2.34
442 714 5.277634 GCGTGAGTTGGTTATTGTTGTAAGT 60.278 40.000 0.00 0.00 0.00 2.24
443 715 6.073657 GCGTGAGTTGGTTATTGTTGTAAGTA 60.074 38.462 0.00 0.00 0.00 2.24
444 716 7.285788 CGTGAGTTGGTTATTGTTGTAAGTAC 58.714 38.462 0.00 0.00 0.00 2.73
445 717 7.170320 CGTGAGTTGGTTATTGTTGTAAGTACT 59.830 37.037 0.00 0.00 0.00 2.73
446 718 9.480053 GTGAGTTGGTTATTGTTGTAAGTACTA 57.520 33.333 0.00 0.00 0.00 1.82
447 719 9.480053 TGAGTTGGTTATTGTTGTAAGTACTAC 57.520 33.333 0.00 0.00 33.53 2.73
448 720 9.702494 GAGTTGGTTATTGTTGTAAGTACTACT 57.298 33.333 0.00 0.00 33.96 2.57
449 721 9.702494 AGTTGGTTATTGTTGTAAGTACTACTC 57.298 33.333 0.00 0.00 33.96 2.59
450 722 8.929746 GTTGGTTATTGTTGTAAGTACTACTCC 58.070 37.037 0.00 0.00 33.96 3.85
451 723 7.614494 TGGTTATTGTTGTAAGTACTACTCCC 58.386 38.462 0.00 0.00 33.96 4.30
452 724 7.455638 TGGTTATTGTTGTAAGTACTACTCCCT 59.544 37.037 0.00 0.00 33.96 4.20
453 725 7.978414 GGTTATTGTTGTAAGTACTACTCCCTC 59.022 40.741 0.00 0.00 33.96 4.30
454 726 5.990120 TTGTTGTAAGTACTACTCCCTCC 57.010 43.478 0.00 0.00 33.96 4.30
455 727 4.012374 TGTTGTAAGTACTACTCCCTCCG 58.988 47.826 0.00 0.00 33.96 4.63
456 728 4.013050 GTTGTAAGTACTACTCCCTCCGT 58.987 47.826 0.00 0.00 0.00 4.69
457 729 5.186198 GTTGTAAGTACTACTCCCTCCGTA 58.814 45.833 0.00 0.00 0.00 4.02
458 730 5.435686 TGTAAGTACTACTCCCTCCGTAA 57.564 43.478 0.00 0.00 0.00 3.18
459 731 5.815581 TGTAAGTACTACTCCCTCCGTAAA 58.184 41.667 0.00 0.00 0.00 2.01
460 732 5.882557 TGTAAGTACTACTCCCTCCGTAAAG 59.117 44.000 0.00 0.00 0.00 1.85
461 733 4.851639 AGTACTACTCCCTCCGTAAAGA 57.148 45.455 0.00 0.00 0.00 2.52
462 734 5.184892 AGTACTACTCCCTCCGTAAAGAA 57.815 43.478 0.00 0.00 0.00 2.52
463 735 5.574188 AGTACTACTCCCTCCGTAAAGAAA 58.426 41.667 0.00 0.00 0.00 2.52
464 736 4.797800 ACTACTCCCTCCGTAAAGAAAC 57.202 45.455 0.00 0.00 0.00 2.78
465 737 4.154942 ACTACTCCCTCCGTAAAGAAACA 58.845 43.478 0.00 0.00 0.00 2.83
466 738 4.776308 ACTACTCCCTCCGTAAAGAAACAT 59.224 41.667 0.00 0.00 0.00 2.71
467 739 5.954150 ACTACTCCCTCCGTAAAGAAACATA 59.046 40.000 0.00 0.00 0.00 2.29
468 740 5.750352 ACTCCCTCCGTAAAGAAACATAA 57.250 39.130 0.00 0.00 0.00 1.90
469 741 5.731591 ACTCCCTCCGTAAAGAAACATAAG 58.268 41.667 0.00 0.00 0.00 1.73
470 742 5.482878 ACTCCCTCCGTAAAGAAACATAAGA 59.517 40.000 0.00 0.00 0.00 2.10
471 743 5.974108 TCCCTCCGTAAAGAAACATAAGAG 58.026 41.667 0.00 0.00 0.00 2.85
472 744 5.482878 TCCCTCCGTAAAGAAACATAAGAGT 59.517 40.000 0.00 0.00 0.00 3.24
473 745 5.581085 CCCTCCGTAAAGAAACATAAGAGTG 59.419 44.000 0.00 0.00 0.00 3.51
474 746 6.164176 CCTCCGTAAAGAAACATAAGAGTGT 58.836 40.000 0.00 0.00 0.00 3.55
475 747 6.649557 CCTCCGTAAAGAAACATAAGAGTGTT 59.350 38.462 0.00 0.00 43.78 3.32
527 799 9.667107 TGTTCTTATATTTGTTTACAGAGGGAG 57.333 33.333 0.00 0.00 0.00 4.30
528 800 8.613482 GTTCTTATATTTGTTTACAGAGGGAGC 58.387 37.037 0.00 0.00 0.00 4.70
529 801 7.857456 TCTTATATTTGTTTACAGAGGGAGCA 58.143 34.615 0.00 0.00 0.00 4.26
530 802 7.769044 TCTTATATTTGTTTACAGAGGGAGCAC 59.231 37.037 0.00 0.00 0.00 4.40
531 803 3.857157 TTTGTTTACAGAGGGAGCACT 57.143 42.857 0.00 0.00 0.00 4.40
532 804 3.857157 TTGTTTACAGAGGGAGCACTT 57.143 42.857 0.00 0.00 0.00 3.16
533 805 4.967084 TTGTTTACAGAGGGAGCACTTA 57.033 40.909 0.00 0.00 0.00 2.24
534 806 4.537135 TGTTTACAGAGGGAGCACTTAG 57.463 45.455 0.00 0.00 0.00 2.18
535 807 3.260884 TGTTTACAGAGGGAGCACTTAGG 59.739 47.826 0.00 0.00 0.00 2.69
536 808 2.921834 TACAGAGGGAGCACTTAGGT 57.078 50.000 0.00 0.00 0.00 3.08
537 809 2.921834 ACAGAGGGAGCACTTAGGTA 57.078 50.000 0.00 0.00 0.00 3.08
538 810 2.458620 ACAGAGGGAGCACTTAGGTAC 58.541 52.381 0.00 0.00 0.00 3.34
539 811 2.225293 ACAGAGGGAGCACTTAGGTACA 60.225 50.000 0.00 0.00 0.00 2.90
540 812 2.428890 CAGAGGGAGCACTTAGGTACAG 59.571 54.545 0.00 0.00 0.00 2.74
541 813 2.312140 AGAGGGAGCACTTAGGTACAGA 59.688 50.000 0.00 0.00 0.00 3.41
542 814 2.691011 GAGGGAGCACTTAGGTACAGAG 59.309 54.545 0.00 0.00 0.00 3.35
543 815 2.312140 AGGGAGCACTTAGGTACAGAGA 59.688 50.000 0.00 0.00 0.00 3.10
544 816 2.427812 GGGAGCACTTAGGTACAGAGAC 59.572 54.545 0.00 0.00 0.00 3.36
545 817 2.427812 GGAGCACTTAGGTACAGAGACC 59.572 54.545 0.00 0.00 40.08 3.85
553 825 1.640917 GGTACAGAGACCTGGGTTCA 58.359 55.000 0.00 0.00 44.60 3.18
554 826 1.975680 GGTACAGAGACCTGGGTTCAA 59.024 52.381 0.00 0.00 44.60 2.69
555 827 2.370849 GGTACAGAGACCTGGGTTCAAA 59.629 50.000 0.00 0.00 44.60 2.69
556 828 3.009143 GGTACAGAGACCTGGGTTCAAAT 59.991 47.826 0.00 0.00 44.60 2.32
557 829 3.425162 ACAGAGACCTGGGTTCAAATC 57.575 47.619 0.00 0.00 44.60 2.17
558 830 2.982488 ACAGAGACCTGGGTTCAAATCT 59.018 45.455 0.00 0.00 44.60 2.40
559 831 3.395941 ACAGAGACCTGGGTTCAAATCTT 59.604 43.478 0.00 0.00 44.60 2.40
560 832 3.755378 CAGAGACCTGGGTTCAAATCTTG 59.245 47.826 0.00 0.00 36.77 3.02
561 833 3.652869 AGAGACCTGGGTTCAAATCTTGA 59.347 43.478 0.00 0.00 38.04 3.02
562 834 4.006319 GAGACCTGGGTTCAAATCTTGAG 58.994 47.826 0.00 0.00 41.38 3.02
566 838 3.698040 CCTGGGTTCAAATCTTGAGATGG 59.302 47.826 0.00 0.00 41.38 3.51
569 841 4.082125 GGGTTCAAATCTTGAGATGGTGT 58.918 43.478 0.00 0.00 41.38 4.16
578 850 7.771927 AATCTTGAGATGGTGTTTCTTTCAT 57.228 32.000 0.00 0.00 34.49 2.57
603 875 3.939564 GGCCCAGCCGATCATTTT 58.060 55.556 0.00 0.00 39.62 1.82
605 877 1.227060 GCCCAGCCGATCATTTTGC 60.227 57.895 0.00 0.00 0.00 3.68
608 880 0.171007 CCAGCCGATCATTTTGCGTT 59.829 50.000 0.00 0.00 0.00 4.84
627 1214 5.003967 TGCGTTCGTTTTCAAAACTCATTTC 59.996 36.000 11.23 0.00 0.00 2.17
652 1239 2.898705 ACGTTCCAAATGCAGCAAAAA 58.101 38.095 0.00 0.00 0.00 1.94
659 1246 4.025061 TCCAAATGCAGCAAAAATGTTTCG 60.025 37.500 0.00 0.00 0.00 3.46
787 1414 1.630148 GCGTCTATATAAGCCAGCGG 58.370 55.000 0.00 0.00 0.00 5.52
911 1540 0.895530 TCGGGACTAGTTCTTGGCTG 59.104 55.000 0.01 0.00 0.00 4.85
931 1572 0.565674 AGATCTTCTCCCTCCCTCCC 59.434 60.000 0.00 0.00 0.00 4.30
932 1573 0.565674 GATCTTCTCCCTCCCTCCCT 59.434 60.000 0.00 0.00 0.00 4.20
933 1574 0.565674 ATCTTCTCCCTCCCTCCCTC 59.434 60.000 0.00 0.00 0.00 4.30
934 1575 1.074850 CTTCTCCCTCCCTCCCTCC 60.075 68.421 0.00 0.00 0.00 4.30
935 1576 2.613576 CTTCTCCCTCCCTCCCTCCC 62.614 70.000 0.00 0.00 0.00 4.30
936 1577 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
937 1578 3.036959 TCCCTCCCTCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
938 1579 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
939 1580 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
940 1581 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
941 1582 3.036959 TCCCTCCCTCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
942 1583 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
969 1611 1.339610 CTCCCTCAGCTGATACCTTCG 59.660 57.143 18.63 3.16 0.00 3.79
975 1617 0.676736 AGCTGATACCTTCGCTAGCC 59.323 55.000 9.66 0.00 34.12 3.93
991 1633 2.103143 CCAGCAGTAGCCGAGTCG 59.897 66.667 5.29 5.29 43.56 4.18
992 1634 2.580867 CAGCAGTAGCCGAGTCGC 60.581 66.667 7.12 2.73 43.56 5.19
1092 1746 6.209986 TCATGGAGAAAATGCAGTTTCATTCT 59.790 34.615 33.48 18.35 39.52 2.40
1109 1763 9.248291 GTTTCATTCTGTGTTTGTATGTCATTT 57.752 29.630 0.00 0.00 0.00 2.32
1161 1816 2.700371 TCCTTCTTGTTGAGCAGTCTGA 59.300 45.455 3.32 0.00 0.00 3.27
1171 1826 2.486592 TGAGCAGTCTGATGTGCATTTG 59.513 45.455 14.90 0.00 42.47 2.32
1197 1852 1.609555 AGATCGATCGTCTAGGTTGGC 59.390 52.381 19.33 0.00 0.00 4.52
1200 1855 0.738975 CGATCGTCTAGGTTGGCTCA 59.261 55.000 7.03 0.00 0.00 4.26
1206 1861 1.945394 GTCTAGGTTGGCTCATGCATG 59.055 52.381 21.07 21.07 41.91 4.06
1207 1862 0.666913 CTAGGTTGGCTCATGCATGC 59.333 55.000 22.25 11.82 41.91 4.06
1208 1863 0.034283 TAGGTTGGCTCATGCATGCA 60.034 50.000 25.04 25.04 41.91 3.96
1209 1864 0.686441 AGGTTGGCTCATGCATGCAT 60.686 50.000 27.46 27.46 41.91 3.96
1210 1865 1.034356 GGTTGGCTCATGCATGCATA 58.966 50.000 31.73 18.59 41.91 3.14
1211 1866 1.000607 GGTTGGCTCATGCATGCATAG 60.001 52.381 31.73 26.06 41.91 2.23
1244 1911 0.539438 AAGCGCATCTCCAAAACCCA 60.539 50.000 11.47 0.00 0.00 4.51
1277 1944 5.416952 CCAATTCTAGCAAGAACACATCCTT 59.583 40.000 0.00 0.00 44.40 3.36
1278 1945 6.320171 CAATTCTAGCAAGAACACATCCTTG 58.680 40.000 0.00 0.00 44.40 3.61
1279 1946 4.890158 TCTAGCAAGAACACATCCTTGA 57.110 40.909 0.00 0.00 41.56 3.02
1280 1947 4.569943 TCTAGCAAGAACACATCCTTGAC 58.430 43.478 0.00 0.00 41.56 3.18
1293 1960 1.230635 CCTTGACCGGTTGCTGACAG 61.231 60.000 9.42 0.00 0.00 3.51
1296 1963 2.022129 GACCGGTTGCTGACAGACG 61.022 63.158 9.42 4.59 0.00 4.18
1300 1967 1.548973 CGGTTGCTGACAGACGACAC 61.549 60.000 6.65 2.24 0.00 3.67
1302 1969 1.286501 GTTGCTGACAGACGACACAA 58.713 50.000 6.65 0.00 0.00 3.33
1307 1974 2.267426 CTGACAGACGACACAAACACA 58.733 47.619 0.00 0.00 0.00 3.72
1308 1975 2.866156 CTGACAGACGACACAAACACAT 59.134 45.455 0.00 0.00 0.00 3.21
1309 1976 3.266636 TGACAGACGACACAAACACATT 58.733 40.909 0.00 0.00 0.00 2.71
1310 1977 3.687212 TGACAGACGACACAAACACATTT 59.313 39.130 0.00 0.00 0.00 2.32
1311 1978 4.870991 TGACAGACGACACAAACACATTTA 59.129 37.500 0.00 0.00 0.00 1.40
1313 1980 4.272504 ACAGACGACACAAACACATTTAGG 59.727 41.667 0.00 0.00 0.00 2.69
1318 1985 4.290155 GACACAAACACATTTAGGCACAG 58.710 43.478 0.00 0.00 0.00 3.66
1319 1986 3.951037 ACACAAACACATTTAGGCACAGA 59.049 39.130 0.00 0.00 0.00 3.41
1320 1987 4.584325 ACACAAACACATTTAGGCACAGAT 59.416 37.500 0.00 0.00 0.00 2.90
1321 1988 5.156355 CACAAACACATTTAGGCACAGATC 58.844 41.667 0.00 0.00 0.00 2.75
1346 2013 4.755411 TCGATCACACCTAAAAGGCTAAG 58.245 43.478 0.00 0.00 39.63 2.18
1347 2014 4.464951 TCGATCACACCTAAAAGGCTAAGA 59.535 41.667 0.00 0.00 39.63 2.10
1415 2083 1.735920 GCTCACCGTGCACTCTCTG 60.736 63.158 16.19 4.54 0.00 3.35
1601 2272 6.993079 AGGTGCCAAAAGAACTAATTAAAGG 58.007 36.000 0.00 0.00 0.00 3.11
1760 2435 5.107760 TGTTCAAGTAATCTTTGACGTACGC 60.108 40.000 16.72 8.98 0.00 4.42
1793 2476 1.068125 CATGCATGTGGTGGTGTTGAG 60.068 52.381 18.91 0.00 0.00 3.02
1802 2485 1.067142 GGTGGTGTTGAGCTGACGATA 60.067 52.381 0.00 0.00 0.00 2.92
1803 2486 1.993370 GTGGTGTTGAGCTGACGATAC 59.007 52.381 0.00 0.00 0.00 2.24
1805 2488 1.269166 GTGTTGAGCTGACGATACGG 58.731 55.000 0.00 0.00 0.00 4.02
1806 2489 0.885879 TGTTGAGCTGACGATACGGT 59.114 50.000 0.00 0.00 0.00 4.83
1807 2490 2.086094 TGTTGAGCTGACGATACGGTA 58.914 47.619 0.00 0.00 0.00 4.02
1808 2491 2.686405 TGTTGAGCTGACGATACGGTAT 59.314 45.455 0.00 0.00 0.00 2.73
1931 2624 2.500442 CTACGCGCTGCTCAAGACG 61.500 63.158 5.73 0.00 34.27 4.18
1934 2627 2.774774 GCGCTGCTCAAGACGAAG 59.225 61.111 0.00 0.00 0.00 3.79
2450 3197 0.036105 CTGCCACTGCCACTGATACA 60.036 55.000 0.00 0.00 36.33 2.29
2474 3221 0.827368 GTGGGTGGATCTCTGACTCC 59.173 60.000 0.00 0.00 0.00 3.85
2537 3284 0.174389 TCTTCAGCTGCGTCCAGATC 59.826 55.000 9.47 0.00 41.77 2.75
2726 3473 1.662629 GTGCACAAGATCGAGGTCATG 59.337 52.381 13.17 0.00 0.00 3.07
2825 3581 4.742201 CCCGCCGTGTGAGACAGG 62.742 72.222 0.00 0.00 34.07 4.00
3030 3802 0.685097 ACTGGATTGTACTGCGTGGT 59.315 50.000 0.00 0.00 0.00 4.16
3149 3927 4.152402 CCTACTACTTGTGCATGTTGTGAC 59.848 45.833 12.66 0.00 0.00 3.67
3190 3968 3.835378 TTCATGCTGTATGTTGCAGTG 57.165 42.857 5.64 0.00 42.74 3.66
3191 3969 3.056588 TCATGCTGTATGTTGCAGTGA 57.943 42.857 5.64 0.00 42.74 3.41
3192 3970 3.004862 TCATGCTGTATGTTGCAGTGAG 58.995 45.455 5.64 0.00 42.74 3.51
3199 3977 3.829026 TGTATGTTGCAGTGAGTCTCTCT 59.171 43.478 0.65 0.00 0.00 3.10
3221 3999 2.626840 GTCTCAGACCTTGCCTGATTC 58.373 52.381 0.00 0.00 39.62 2.52
3234 4012 2.487934 CCTGATTCGTGTCATCCATCC 58.512 52.381 0.00 0.00 0.00 3.51
3308 4119 8.818622 TTGGCTGTCTCTTTCTACTTATACTA 57.181 34.615 0.00 0.00 0.00 1.82
3309 4120 8.223177 TGGCTGTCTCTTTCTACTTATACTAC 57.777 38.462 0.00 0.00 0.00 2.73
3310 4121 8.053963 TGGCTGTCTCTTTCTACTTATACTACT 58.946 37.037 0.00 0.00 0.00 2.57
3323 4134 2.363788 TACTACTGTTTGCTGGCTCG 57.636 50.000 0.00 0.00 0.00 5.03
3366 4177 1.670083 GTCGGCCTACCAAAAGCGT 60.670 57.895 0.00 0.00 34.57 5.07
3371 4182 1.135489 GGCCTACCAAAAGCGTAAAGC 60.135 52.381 0.00 0.00 40.61 3.51
3412 4223 4.543590 ACAGTGGAATCTAGAACACCAG 57.456 45.455 17.04 13.78 34.50 4.00
3479 4303 3.004106 CACTGAAACAAGCTCCAAGGAAG 59.996 47.826 0.00 0.00 0.00 3.46
3493 4317 2.359967 GGAAGCGGGCCTCTACTGT 61.360 63.158 0.84 0.00 0.00 3.55
3519 4343 5.984926 TCAAAGTGCCTGAAAATTCACAATC 59.015 36.000 0.00 0.00 32.90 2.67
3524 4348 3.762779 CCTGAAAATTCACAATCGGAGC 58.237 45.455 0.00 0.00 32.90 4.70
3589 4413 4.659115 AGAAATGTGGGTGTAGGTTTACC 58.341 43.478 0.00 0.00 36.21 2.85
3590 4414 2.773993 ATGTGGGTGTAGGTTTACCG 57.226 50.000 0.00 0.00 42.08 4.02
3609 4435 0.601311 GACACGAGAAGCTTGCCACT 60.601 55.000 2.10 0.00 0.00 4.00
3617 4443 3.815401 GAGAAGCTTGCCACTAGAAACAA 59.185 43.478 2.10 0.00 0.00 2.83
3681 4507 6.237701 GCGATACAAAGACATCAAAGAGAGTC 60.238 42.308 0.00 0.00 0.00 3.36
3721 4547 6.183360 CCATGAACAAAGAACAGTGAGAAAGT 60.183 38.462 0.00 0.00 0.00 2.66
3725 4551 7.389330 TGAACAAAGAACAGTGAGAAAGTTACA 59.611 33.333 0.00 0.00 0.00 2.41
3726 4552 7.073342 ACAAAGAACAGTGAGAAAGTTACAC 57.927 36.000 0.00 0.00 35.15 2.90
3727 4553 6.653320 ACAAAGAACAGTGAGAAAGTTACACA 59.347 34.615 0.00 0.00 37.05 3.72
3731 4557 5.854010 ACAGTGAGAAAGTTACACAGAGA 57.146 39.130 0.00 0.00 37.05 3.10
3734 4560 6.183360 ACAGTGAGAAAGTTACACAGAGACAT 60.183 38.462 0.00 0.00 37.05 3.06
3735 4561 7.014326 ACAGTGAGAAAGTTACACAGAGACATA 59.986 37.037 0.00 0.00 37.05 2.29
3786 4633 5.104693 TGACTTCTTTACCTCCTTGTCAACA 60.105 40.000 0.00 0.00 31.49 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.741878 CGTGTGTCTGGTCTTGGAAAGT 60.742 50.000 0.00 0.00 46.34 2.66
51 52 3.651803 TTTGGAACGTAGGCAAAATGG 57.348 42.857 0.00 0.00 0.00 3.16
105 107 6.018343 GCTATTTCAATAACTGCTCTGTCTCC 60.018 42.308 0.00 0.00 0.00 3.71
168 175 2.171448 AGGAGATGTAGTTGGGTGATGC 59.829 50.000 0.00 0.00 0.00 3.91
210 444 1.635663 CGAGGGACGATGTTGGTTGC 61.636 60.000 0.00 0.00 45.77 4.17
211 445 1.635663 GCGAGGGACGATGTTGGTTG 61.636 60.000 0.00 0.00 45.77 3.77
245 480 2.617274 GCAGGCCGGTTGTGTCTTC 61.617 63.158 1.90 0.00 0.00 2.87
246 481 2.594592 GCAGGCCGGTTGTGTCTT 60.595 61.111 1.90 0.00 0.00 3.01
247 482 4.643387 GGCAGGCCGGTTGTGTCT 62.643 66.667 1.90 0.00 0.00 3.41
257 492 4.722700 ATGTGACACGGGCAGGCC 62.723 66.667 1.81 1.81 0.00 5.19
364 607 8.147704 GGAAAATCAATTTCTCCAAACCTTGTA 58.852 33.333 1.47 0.00 45.57 2.41
394 666 7.327275 CGCCATCTCATTCTTTGTCTAGTATAC 59.673 40.741 0.00 0.00 0.00 1.47
398 670 4.081420 ACGCCATCTCATTCTTTGTCTAGT 60.081 41.667 0.00 0.00 0.00 2.57
399 671 4.269603 CACGCCATCTCATTCTTTGTCTAG 59.730 45.833 0.00 0.00 0.00 2.43
400 672 4.081697 TCACGCCATCTCATTCTTTGTCTA 60.082 41.667 0.00 0.00 0.00 2.59
401 673 3.005554 CACGCCATCTCATTCTTTGTCT 58.994 45.455 0.00 0.00 0.00 3.41
402 674 3.002791 TCACGCCATCTCATTCTTTGTC 58.997 45.455 0.00 0.00 0.00 3.18
404 676 3.005554 ACTCACGCCATCTCATTCTTTG 58.994 45.455 0.00 0.00 0.00 2.77
405 677 3.340814 ACTCACGCCATCTCATTCTTT 57.659 42.857 0.00 0.00 0.00 2.52
407 679 2.625737 CAACTCACGCCATCTCATTCT 58.374 47.619 0.00 0.00 0.00 2.40
408 680 1.667724 CCAACTCACGCCATCTCATTC 59.332 52.381 0.00 0.00 0.00 2.67
409 681 1.003580 ACCAACTCACGCCATCTCATT 59.996 47.619 0.00 0.00 0.00 2.57
410 682 0.615331 ACCAACTCACGCCATCTCAT 59.385 50.000 0.00 0.00 0.00 2.90
411 683 0.396435 AACCAACTCACGCCATCTCA 59.604 50.000 0.00 0.00 0.00 3.27
412 684 2.380084 TAACCAACTCACGCCATCTC 57.620 50.000 0.00 0.00 0.00 2.75
413 685 3.009723 CAATAACCAACTCACGCCATCT 58.990 45.455 0.00 0.00 0.00 2.90
414 686 2.747446 ACAATAACCAACTCACGCCATC 59.253 45.455 0.00 0.00 0.00 3.51
415 687 2.790433 ACAATAACCAACTCACGCCAT 58.210 42.857 0.00 0.00 0.00 4.40
416 688 2.264005 ACAATAACCAACTCACGCCA 57.736 45.000 0.00 0.00 0.00 5.69
417 689 2.292292 ACAACAATAACCAACTCACGCC 59.708 45.455 0.00 0.00 0.00 5.68
418 690 3.619233 ACAACAATAACCAACTCACGC 57.381 42.857 0.00 0.00 0.00 5.34
419 691 6.295039 ACTTACAACAATAACCAACTCACG 57.705 37.500 0.00 0.00 0.00 4.35
420 692 8.374327 AGTACTTACAACAATAACCAACTCAC 57.626 34.615 0.00 0.00 0.00 3.51
421 693 9.480053 GTAGTACTTACAACAATAACCAACTCA 57.520 33.333 0.00 0.00 32.27 3.41
422 694 9.702494 AGTAGTACTTACAACAATAACCAACTC 57.298 33.333 0.00 0.00 34.56 3.01
423 695 9.702494 GAGTAGTACTTACAACAATAACCAACT 57.298 33.333 0.00 0.00 34.56 3.16
424 696 8.929746 GGAGTAGTACTTACAACAATAACCAAC 58.070 37.037 0.00 0.00 34.56 3.77
425 697 8.096414 GGGAGTAGTACTTACAACAATAACCAA 58.904 37.037 0.00 0.00 34.56 3.67
426 698 7.455638 AGGGAGTAGTACTTACAACAATAACCA 59.544 37.037 0.00 0.00 34.56 3.67
427 699 7.845037 AGGGAGTAGTACTTACAACAATAACC 58.155 38.462 0.00 0.00 34.56 2.85
428 700 7.978414 GGAGGGAGTAGTACTTACAACAATAAC 59.022 40.741 0.00 0.00 34.56 1.89
429 701 7.148018 CGGAGGGAGTAGTACTTACAACAATAA 60.148 40.741 0.00 0.00 34.56 1.40
430 702 6.319658 CGGAGGGAGTAGTACTTACAACAATA 59.680 42.308 0.00 0.00 34.56 1.90
431 703 5.126707 CGGAGGGAGTAGTACTTACAACAAT 59.873 44.000 0.00 0.00 34.56 2.71
432 704 4.460382 CGGAGGGAGTAGTACTTACAACAA 59.540 45.833 0.00 0.00 34.56 2.83
433 705 4.012374 CGGAGGGAGTAGTACTTACAACA 58.988 47.826 0.00 0.00 34.56 3.33
434 706 4.013050 ACGGAGGGAGTAGTACTTACAAC 58.987 47.826 0.00 0.00 34.56 3.32
435 707 4.307032 ACGGAGGGAGTAGTACTTACAA 57.693 45.455 0.00 0.00 34.56 2.41
436 708 5.435686 TTACGGAGGGAGTAGTACTTACA 57.564 43.478 0.00 0.00 34.56 2.41
437 709 6.116126 TCTTTACGGAGGGAGTAGTACTTAC 58.884 44.000 0.00 0.97 0.00 2.34
438 710 6.313519 TCTTTACGGAGGGAGTAGTACTTA 57.686 41.667 0.00 0.00 0.00 2.24
439 711 5.184892 TCTTTACGGAGGGAGTAGTACTT 57.815 43.478 0.00 0.00 0.00 2.24
440 712 4.851639 TCTTTACGGAGGGAGTAGTACT 57.148 45.455 1.37 1.37 0.00 2.73
441 713 5.183904 TGTTTCTTTACGGAGGGAGTAGTAC 59.816 44.000 0.00 0.00 0.00 2.73
442 714 5.324409 TGTTTCTTTACGGAGGGAGTAGTA 58.676 41.667 0.00 0.00 0.00 1.82
443 715 4.154942 TGTTTCTTTACGGAGGGAGTAGT 58.845 43.478 0.00 0.00 0.00 2.73
444 716 4.796038 TGTTTCTTTACGGAGGGAGTAG 57.204 45.455 0.00 0.00 0.00 2.57
445 717 6.664816 TCTTATGTTTCTTTACGGAGGGAGTA 59.335 38.462 0.00 0.00 0.00 2.59
446 718 5.482878 TCTTATGTTTCTTTACGGAGGGAGT 59.517 40.000 0.00 0.00 0.00 3.85
447 719 5.974108 TCTTATGTTTCTTTACGGAGGGAG 58.026 41.667 0.00 0.00 0.00 4.30
448 720 5.482878 ACTCTTATGTTTCTTTACGGAGGGA 59.517 40.000 0.00 0.00 0.00 4.20
449 721 5.581085 CACTCTTATGTTTCTTTACGGAGGG 59.419 44.000 0.00 0.00 0.00 4.30
450 722 6.164176 ACACTCTTATGTTTCTTTACGGAGG 58.836 40.000 0.00 0.00 0.00 4.30
451 723 7.653767 AACACTCTTATGTTTCTTTACGGAG 57.346 36.000 0.00 0.00 39.86 4.63
501 773 9.667107 CTCCCTCTGTAAACAAATATAAGAACA 57.333 33.333 0.00 0.00 0.00 3.18
502 774 8.613482 GCTCCCTCTGTAAACAAATATAAGAAC 58.387 37.037 0.00 0.00 0.00 3.01
503 775 8.325787 TGCTCCCTCTGTAAACAAATATAAGAA 58.674 33.333 0.00 0.00 0.00 2.52
504 776 7.769044 GTGCTCCCTCTGTAAACAAATATAAGA 59.231 37.037 0.00 0.00 0.00 2.10
505 777 7.770897 AGTGCTCCCTCTGTAAACAAATATAAG 59.229 37.037 0.00 0.00 0.00 1.73
506 778 7.630082 AGTGCTCCCTCTGTAAACAAATATAA 58.370 34.615 0.00 0.00 0.00 0.98
507 779 7.195374 AGTGCTCCCTCTGTAAACAAATATA 57.805 36.000 0.00 0.00 0.00 0.86
508 780 6.067217 AGTGCTCCCTCTGTAAACAAATAT 57.933 37.500 0.00 0.00 0.00 1.28
509 781 5.499004 AGTGCTCCCTCTGTAAACAAATA 57.501 39.130 0.00 0.00 0.00 1.40
510 782 4.373156 AGTGCTCCCTCTGTAAACAAAT 57.627 40.909 0.00 0.00 0.00 2.32
511 783 3.857157 AGTGCTCCCTCTGTAAACAAA 57.143 42.857 0.00 0.00 0.00 2.83
512 784 3.857157 AAGTGCTCCCTCTGTAAACAA 57.143 42.857 0.00 0.00 0.00 2.83
513 785 3.260884 CCTAAGTGCTCCCTCTGTAAACA 59.739 47.826 0.00 0.00 0.00 2.83
514 786 3.261137 ACCTAAGTGCTCCCTCTGTAAAC 59.739 47.826 0.00 0.00 0.00 2.01
515 787 3.517612 ACCTAAGTGCTCCCTCTGTAAA 58.482 45.455 0.00 0.00 0.00 2.01
516 788 3.185880 ACCTAAGTGCTCCCTCTGTAA 57.814 47.619 0.00 0.00 0.00 2.41
517 789 2.921834 ACCTAAGTGCTCCCTCTGTA 57.078 50.000 0.00 0.00 0.00 2.74
518 790 2.225293 TGTACCTAAGTGCTCCCTCTGT 60.225 50.000 0.00 0.00 0.00 3.41
519 791 2.428890 CTGTACCTAAGTGCTCCCTCTG 59.571 54.545 0.00 0.00 0.00 3.35
520 792 2.312140 TCTGTACCTAAGTGCTCCCTCT 59.688 50.000 0.00 0.00 0.00 3.69
521 793 2.691011 CTCTGTACCTAAGTGCTCCCTC 59.309 54.545 0.00 0.00 0.00 4.30
522 794 2.312140 TCTCTGTACCTAAGTGCTCCCT 59.688 50.000 0.00 0.00 0.00 4.20
523 795 2.427812 GTCTCTGTACCTAAGTGCTCCC 59.572 54.545 0.00 0.00 0.00 4.30
524 796 2.427812 GGTCTCTGTACCTAAGTGCTCC 59.572 54.545 0.00 0.00 36.53 4.70
525 797 3.786516 GGTCTCTGTACCTAAGTGCTC 57.213 52.381 0.00 0.00 36.53 4.26
534 806 1.640917 TGAACCCAGGTCTCTGTACC 58.359 55.000 0.00 0.00 39.31 3.34
535 807 3.764237 TTTGAACCCAGGTCTCTGTAC 57.236 47.619 0.00 0.00 39.31 2.90
536 808 4.168101 AGATTTGAACCCAGGTCTCTGTA 58.832 43.478 0.00 0.00 39.31 2.74
537 809 2.982488 AGATTTGAACCCAGGTCTCTGT 59.018 45.455 0.00 0.00 39.31 3.41
538 810 3.710209 AGATTTGAACCCAGGTCTCTG 57.290 47.619 0.00 0.00 40.59 3.35
539 811 3.652869 TCAAGATTTGAACCCAGGTCTCT 59.347 43.478 0.00 0.00 36.59 3.10
540 812 4.006319 CTCAAGATTTGAACCCAGGTCTC 58.994 47.826 0.00 0.00 39.58 3.36
541 813 3.652869 TCTCAAGATTTGAACCCAGGTCT 59.347 43.478 0.00 0.00 39.58 3.85
542 814 4.021102 TCTCAAGATTTGAACCCAGGTC 57.979 45.455 0.00 0.00 39.58 3.85
543 815 4.338879 CATCTCAAGATTTGAACCCAGGT 58.661 43.478 0.00 0.00 39.58 4.00
544 816 3.698040 CCATCTCAAGATTTGAACCCAGG 59.302 47.826 0.00 0.00 39.58 4.45
545 817 4.157289 CACCATCTCAAGATTTGAACCCAG 59.843 45.833 0.00 0.00 39.58 4.45
546 818 4.081406 CACCATCTCAAGATTTGAACCCA 58.919 43.478 0.00 0.00 39.58 4.51
547 819 4.082125 ACACCATCTCAAGATTTGAACCC 58.918 43.478 5.70 0.00 39.58 4.11
548 820 5.712152 AACACCATCTCAAGATTTGAACC 57.288 39.130 5.70 0.00 39.58 3.62
549 821 6.974965 AGAAACACCATCTCAAGATTTGAAC 58.025 36.000 5.70 0.00 39.58 3.18
550 822 7.587037 AAGAAACACCATCTCAAGATTTGAA 57.413 32.000 5.70 0.00 39.58 2.69
551 823 7.285172 TGAAAGAAACACCATCTCAAGATTTGA 59.715 33.333 5.70 0.00 38.17 2.69
552 824 7.428020 TGAAAGAAACACCATCTCAAGATTTG 58.572 34.615 0.00 0.00 31.21 2.32
553 825 7.587037 TGAAAGAAACACCATCTCAAGATTT 57.413 32.000 0.00 0.00 31.21 2.17
554 826 7.771927 ATGAAAGAAACACCATCTCAAGATT 57.228 32.000 0.00 0.00 31.21 2.40
555 827 7.771927 AATGAAAGAAACACCATCTCAAGAT 57.228 32.000 0.00 0.00 34.56 2.40
556 828 7.587037 AAATGAAAGAAACACCATCTCAAGA 57.413 32.000 0.00 0.00 0.00 3.02
557 829 7.383300 GGAAAATGAAAGAAACACCATCTCAAG 59.617 37.037 0.00 0.00 0.00 3.02
558 830 7.069826 AGGAAAATGAAAGAAACACCATCTCAA 59.930 33.333 0.00 0.00 0.00 3.02
559 831 6.550854 AGGAAAATGAAAGAAACACCATCTCA 59.449 34.615 0.00 0.00 0.00 3.27
560 832 6.986250 AGGAAAATGAAAGAAACACCATCTC 58.014 36.000 0.00 0.00 0.00 2.75
561 833 6.983906 AGGAAAATGAAAGAAACACCATCT 57.016 33.333 0.00 0.00 0.00 2.90
562 834 6.424812 CCAAGGAAAATGAAAGAAACACCATC 59.575 38.462 0.00 0.00 0.00 3.51
566 838 4.511454 GGCCAAGGAAAATGAAAGAAACAC 59.489 41.667 0.00 0.00 0.00 3.32
569 841 3.713764 TGGGCCAAGGAAAATGAAAGAAA 59.286 39.130 2.13 0.00 0.00 2.52
598 870 5.546434 AGTTTTGAAAACGAACGCAAAATG 58.454 33.333 14.38 0.00 40.82 2.32
599 871 5.346281 TGAGTTTTGAAAACGAACGCAAAAT 59.654 32.000 14.38 0.00 40.82 1.82
600 872 4.680110 TGAGTTTTGAAAACGAACGCAAAA 59.320 33.333 14.38 0.00 37.74 2.44
602 874 3.822996 TGAGTTTTGAAAACGAACGCAA 58.177 36.364 14.38 0.00 31.73 4.85
603 875 3.473093 TGAGTTTTGAAAACGAACGCA 57.527 38.095 14.38 7.07 32.11 5.24
605 877 5.633747 CGAAATGAGTTTTGAAAACGAACG 58.366 37.500 14.38 11.48 31.48 3.95
608 880 4.039032 GGCGAAATGAGTTTTGAAAACGA 58.961 39.130 14.38 6.59 31.48 3.85
627 1214 0.096976 CTGCATTTGGAACGTAGGCG 59.903 55.000 0.00 0.00 44.93 5.52
747 1370 2.671177 GCGCTGGTGCTGTACAGTG 61.671 63.158 23.44 5.78 45.44 3.66
767 1391 1.260206 CGCTGGCTTATATAGACGCG 58.740 55.000 3.53 3.53 44.12 6.01
768 1392 1.630148 CCGCTGGCTTATATAGACGC 58.370 55.000 0.00 0.00 32.99 5.19
911 1540 1.482365 GGGAGGGAGGGAGAAGATCTC 60.482 61.905 0.00 0.00 42.66 2.75
931 1572 0.341609 AGAGGAAAGGAGGGAGGGAG 59.658 60.000 0.00 0.00 0.00 4.30
932 1573 0.340208 GAGAGGAAAGGAGGGAGGGA 59.660 60.000 0.00 0.00 0.00 4.20
933 1574 0.692756 GGAGAGGAAAGGAGGGAGGG 60.693 65.000 0.00 0.00 0.00 4.30
934 1575 0.692756 GGGAGAGGAAAGGAGGGAGG 60.693 65.000 0.00 0.00 0.00 4.30
935 1576 0.341609 AGGGAGAGGAAAGGAGGGAG 59.658 60.000 0.00 0.00 0.00 4.30
936 1577 0.340208 GAGGGAGAGGAAAGGAGGGA 59.660 60.000 0.00 0.00 0.00 4.20
937 1578 0.043334 TGAGGGAGAGGAAAGGAGGG 59.957 60.000 0.00 0.00 0.00 4.30
938 1579 1.494960 CTGAGGGAGAGGAAAGGAGG 58.505 60.000 0.00 0.00 0.00 4.30
939 1580 0.829990 GCTGAGGGAGAGGAAAGGAG 59.170 60.000 0.00 0.00 0.00 3.69
940 1581 0.415429 AGCTGAGGGAGAGGAAAGGA 59.585 55.000 0.00 0.00 0.00 3.36
941 1582 0.540923 CAGCTGAGGGAGAGGAAAGG 59.459 60.000 8.42 0.00 0.00 3.11
942 1583 1.566211 TCAGCTGAGGGAGAGGAAAG 58.434 55.000 13.74 0.00 0.00 2.62
975 1617 2.580867 GCGACTCGGCTACTGCTG 60.581 66.667 0.00 0.00 46.48 4.41
1092 1746 4.098501 TGTGCCAAATGACATACAAACACA 59.901 37.500 6.97 6.97 32.37 3.72
1109 1763 2.126596 CCAAAGGTGTGCTGTGCCA 61.127 57.895 0.00 0.00 0.00 4.92
1161 1816 2.476686 CGATCTTGCGACAAATGCACAT 60.477 45.455 0.00 0.00 43.10 3.21
1171 1826 2.566036 CTAGACGATCGATCTTGCGAC 58.434 52.381 24.34 10.64 43.79 5.19
1182 1837 2.748605 CATGAGCCAACCTAGACGATC 58.251 52.381 0.00 0.00 0.00 3.69
1206 1861 1.952621 TCCCTACCCTATGCCTATGC 58.047 55.000 0.00 0.00 38.26 3.14
1207 1862 2.237392 GCTTCCCTACCCTATGCCTATG 59.763 54.545 0.00 0.00 0.00 2.23
1208 1863 2.552367 GCTTCCCTACCCTATGCCTAT 58.448 52.381 0.00 0.00 0.00 2.57
1209 1864 1.826042 CGCTTCCCTACCCTATGCCTA 60.826 57.143 0.00 0.00 0.00 3.93
1210 1865 1.122019 CGCTTCCCTACCCTATGCCT 61.122 60.000 0.00 0.00 0.00 4.75
1211 1866 1.371558 CGCTTCCCTACCCTATGCC 59.628 63.158 0.00 0.00 0.00 4.40
1244 1911 1.992557 TGCTAGAATTGGGAGGTGGTT 59.007 47.619 0.00 0.00 0.00 3.67
1277 1944 1.069090 GTCTGTCAGCAACCGGTCA 59.931 57.895 8.04 0.00 0.00 4.02
1278 1945 2.022129 CGTCTGTCAGCAACCGGTC 61.022 63.158 8.04 0.00 0.00 4.79
1279 1946 2.029073 CGTCTGTCAGCAACCGGT 59.971 61.111 0.00 0.00 0.00 5.28
1280 1947 2.022129 GTCGTCTGTCAGCAACCGG 61.022 63.158 0.00 0.00 0.00 5.28
1293 1960 3.002862 TGCCTAAATGTGTTTGTGTCGTC 59.997 43.478 0.00 0.00 0.00 4.20
1296 1963 4.036262 TCTGTGCCTAAATGTGTTTGTGTC 59.964 41.667 0.00 0.00 0.00 3.67
1300 1967 4.154015 TCGATCTGTGCCTAAATGTGTTTG 59.846 41.667 0.00 0.00 0.00 2.93
1302 1969 3.937814 TCGATCTGTGCCTAAATGTGTT 58.062 40.909 0.00 0.00 0.00 3.32
1307 1974 4.489810 GATCGATCGATCTGTGCCTAAAT 58.510 43.478 38.45 13.89 45.42 1.40
1308 1975 3.902150 GATCGATCGATCTGTGCCTAAA 58.098 45.455 38.45 8.64 45.42 1.85
1309 1976 3.560902 GATCGATCGATCTGTGCCTAA 57.439 47.619 38.45 8.84 45.42 2.69
1318 1985 6.800090 GCCTTTTAGGTGTGATCGATCGATC 61.800 48.000 38.90 38.90 43.15 3.69
1319 1986 4.621991 CCTTTTAGGTGTGATCGATCGAT 58.378 43.478 29.76 29.76 37.59 3.59
1320 1987 3.737047 GCCTTTTAGGTGTGATCGATCGA 60.737 47.826 21.86 21.86 37.80 3.59
1321 1988 2.540101 GCCTTTTAGGTGTGATCGATCG 59.460 50.000 20.03 9.36 37.80 3.69
1346 2013 0.171007 CACGCACAATTGATGGGGTC 59.829 55.000 13.59 0.00 34.46 4.46
1347 2014 1.876497 GCACGCACAATTGATGGGGT 61.876 55.000 13.59 12.12 34.46 4.95
1415 2083 2.948315 GGAATTTGGCAGAGAGATCCAC 59.052 50.000 0.00 0.00 0.00 4.02
1417 2085 2.174424 AGGGAATTTGGCAGAGAGATCC 59.826 50.000 0.00 0.00 0.00 3.36
1554 2222 9.435570 ACCTATGATTAGTAGTGGAATGTTACT 57.564 33.333 0.00 0.00 0.00 2.24
1555 2223 9.477484 CACCTATGATTAGTAGTGGAATGTTAC 57.523 37.037 0.00 0.00 0.00 2.50
1556 2224 8.148351 GCACCTATGATTAGTAGTGGAATGTTA 58.852 37.037 0.00 0.00 0.00 2.41
1557 2225 6.992715 GCACCTATGATTAGTAGTGGAATGTT 59.007 38.462 0.00 0.00 0.00 2.71
1558 2226 6.464465 GGCACCTATGATTAGTAGTGGAATGT 60.464 42.308 0.00 0.00 0.00 2.71
1564 2232 7.047891 TCTTTTGGCACCTATGATTAGTAGTG 58.952 38.462 0.00 0.00 0.00 2.74
1574 2242 9.573133 CTTTAATTAGTTCTTTTGGCACCTATG 57.427 33.333 0.00 0.00 0.00 2.23
1601 2272 3.364964 CCGTTAGTTTTGTCAGTGGCATC 60.365 47.826 0.00 0.00 0.00 3.91
1793 2476 0.672342 ACCCATACCGTATCGTCAGC 59.328 55.000 0.00 0.00 0.00 4.26
1802 2485 4.109675 GCCCTGCACCCATACCGT 62.110 66.667 0.00 0.00 0.00 4.83
1805 2488 2.513897 GTCGCCCTGCACCCATAC 60.514 66.667 0.00 0.00 0.00 2.39
1806 2489 4.155733 CGTCGCCCTGCACCCATA 62.156 66.667 0.00 0.00 0.00 2.74
2244 2960 2.800629 GCCATATTGCCATGTCAACTGC 60.801 50.000 0.00 0.00 0.00 4.40
2450 3197 2.503356 GTCAGAGATCCACCCACTCAAT 59.497 50.000 0.00 0.00 33.69 2.57
2459 3206 1.323271 TGGCGGAGTCAGAGATCCAC 61.323 60.000 0.00 0.00 36.97 4.02
2501 3248 2.203294 AAGAAGCCGCCCACGTTT 60.203 55.556 0.00 0.00 37.70 3.60
2537 3284 1.437986 GTACCAGCAGTAGAGCCCG 59.562 63.158 0.00 0.00 34.23 6.13
2825 3581 4.678743 GGTGGGTGGGGTGGAAGC 62.679 72.222 0.00 0.00 0.00 3.86
2975 3742 4.817464 ACAAAGTAAGTAATCCACACGCAA 59.183 37.500 0.00 0.00 0.00 4.85
2976 3743 4.382291 ACAAAGTAAGTAATCCACACGCA 58.618 39.130 0.00 0.00 0.00 5.24
3149 3927 0.374758 GACCAGTACACATGCATGCG 59.625 55.000 26.53 19.79 0.00 4.73
3190 3968 2.093658 AGGTCTGAGACGAGAGAGACTC 60.094 54.545 6.50 0.00 41.79 3.36
3191 3969 1.906574 AGGTCTGAGACGAGAGAGACT 59.093 52.381 6.50 0.00 36.02 3.24
3192 3970 2.396590 AGGTCTGAGACGAGAGAGAC 57.603 55.000 6.50 0.00 35.15 3.36
3199 3977 0.539669 TCAGGCAAGGTCTGAGACGA 60.540 55.000 6.50 0.00 39.51 4.20
3221 3999 2.445565 ATCGATGGATGGATGACACG 57.554 50.000 0.00 0.00 0.00 4.49
3234 4012 6.535274 TTGCAGTCTATTGATGAATCGATG 57.465 37.500 0.00 0.00 33.15 3.84
3308 4119 1.598130 GGTCGAGCCAGCAAACAGT 60.598 57.895 2.39 0.00 37.17 3.55
3309 4120 0.037326 TAGGTCGAGCCAGCAAACAG 60.037 55.000 11.73 0.00 40.61 3.16
3310 4121 0.320421 GTAGGTCGAGCCAGCAAACA 60.320 55.000 11.73 0.00 40.61 2.83
3315 4126 1.874872 CTACTAGTAGGTCGAGCCAGC 59.125 57.143 20.44 1.68 40.61 4.85
3366 4177 3.673052 GCTTGATCAACCATTGCGCTTTA 60.673 43.478 9.73 0.00 0.00 1.85
3371 4182 2.350899 TTGCTTGATCAACCATTGCG 57.649 45.000 3.38 0.00 0.00 4.85
3412 4223 6.727824 TCTTGTCTTTATTGTGCTAAGCTC 57.272 37.500 0.00 0.00 0.00 4.09
3446 4261 1.525077 TTTCAGTGCGGGGTGTGTC 60.525 57.895 0.00 0.00 0.00 3.67
3479 4303 1.605058 TTGAGACAGTAGAGGCCCGC 61.605 60.000 0.00 0.00 0.00 6.13
3493 4317 4.644234 TGTGAATTTTCAGGCACTTTGAGA 59.356 37.500 0.00 0.00 37.98 3.27
3519 4343 3.824414 AACCGTTTAAATCTTGCTCCG 57.176 42.857 0.00 0.00 0.00 4.63
3524 4348 5.629435 GCTCCAAGAAACCGTTTAAATCTTG 59.371 40.000 16.46 16.46 44.05 3.02
3589 4413 1.664649 TGGCAAGCTTCTCGTGTCG 60.665 57.895 0.00 0.00 31.22 4.35
3590 4414 0.601311 AGTGGCAAGCTTCTCGTGTC 60.601 55.000 0.00 0.00 0.00 3.67
3609 4435 4.782691 TCAGGTGGGAGATGATTGTTTCTA 59.217 41.667 0.00 0.00 0.00 2.10
3617 4443 2.277008 AAGGTCAGGTGGGAGATGAT 57.723 50.000 0.00 0.00 0.00 2.45
3711 4537 5.854010 TGTCTCTGTGTAACTTTCTCACT 57.146 39.130 0.00 0.00 38.04 3.41
3734 4560 7.397476 AGTTGACCAGACTCTTAACATGATCTA 59.603 37.037 0.00 0.00 0.00 1.98
3735 4561 6.212388 AGTTGACCAGACTCTTAACATGATCT 59.788 38.462 0.00 0.00 0.00 2.75
3770 4596 2.038557 GCCTCTGTTGACAAGGAGGTAA 59.961 50.000 25.51 0.00 45.00 2.85
3786 4633 1.977129 GGATCTAAGGAGCATGCCTCT 59.023 52.381 15.66 9.44 40.57 3.69


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

AutoCloner maintained by Alex Coulton.