Multiple sequence alignment - TraesCS2A01G162600

Loading Multiple Alignment...

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 TraesCS2A01G162600 chr2A 100.000 4848 0 0 1 4848 115113212 115118059 0.000000e+00 8953.0
1 TraesCS2A01G162600 chr2B 95.350 3462 124 18 906 4337 164082701 164086155 0.000000e+00 5467.0
2 TraesCS2A01G162600 chr2B 86.335 161 9 4 4390 4541 164086153 164086309 3.880000e-36 163.0
3 TraesCS2A01G162600 chr2B 98.305 59 1 0 818 876 164079650 164079708 2.390000e-18 104.0
4 TraesCS2A01G162600 chr2B 94.030 67 4 0 653 719 496929550 496929484 8.580000e-18 102.0
5 TraesCS2A01G162600 chr2D 90.644 1646 88 25 768 2373 113486963 113488582 0.000000e+00 2126.0
6 TraesCS2A01G162600 chr2D 89.427 681 46 20 2373 3033 113488629 113489303 0.000000e+00 835.0
7 TraesCS2A01G162600 chr2D 93.860 456 21 4 3592 4047 113490491 113490939 0.000000e+00 680.0
8 TraesCS2A01G162600 chr2D 80.713 814 94 33 4062 4846 113500349 113501128 4.210000e-160 575.0
9 TraesCS2A01G162600 chr2D 85.196 358 42 8 4 355 113486410 113486762 1.660000e-94 357.0
10 TraesCS2A01G162600 chr2D 85.294 102 7 6 561 658 113486871 113486968 1.110000e-16 99.0
11 TraesCS2A01G162600 chrUn 79.050 358 43 22 2873 3202 93415035 93415388 2.940000e-52 217.0
12 TraesCS2A01G162600 chrUn 78.841 345 41 23 2873 3189 403668335 403668675 2.290000e-48 204.0
13 TraesCS2A01G162600 chrUn 82.353 204 17 12 2873 3057 455370039 455370242 5.020000e-35 159.0
14 TraesCS2A01G162600 chrUn 88.372 86 7 2 2873 2955 61042608 61042523 3.090000e-17 100.0
15 TraesCS2A01G162600 chr5D 78.771 358 44 21 2873 3202 503215184 503214831 1.370000e-50 211.0
16 TraesCS2A01G162600 chr1D 77.933 358 47 22 2873 3202 254523035 254522682 1.380000e-45 195.0
17 TraesCS2A01G162600 chr1D 88.372 86 7 2 2873 2955 185379167 185379082 3.090000e-17 100.0
18 TraesCS2A01G162600 chr4A 94.030 67 4 0 653 719 646297751 646297817 8.580000e-18 102.0
19 TraesCS2A01G162600 chr5B 92.647 68 5 0 652 719 478928874 478928941 1.110000e-16 99.0
20 TraesCS2A01G162600 chr7D 92.537 67 5 0 653 719 293961617 293961683 3.990000e-16 97.1
21 TraesCS2A01G162600 chr7D 92.537 67 5 0 653 719 294114629 294114563 3.990000e-16 97.1
22 TraesCS2A01G162600 chr6B 90.411 73 7 0 653 725 269146239 269146167 3.990000e-16 97.1
23 TraesCS2A01G162600 chr4D 92.537 67 5 0 653 719 302343248 302343182 3.990000e-16 97.1
24 TraesCS2A01G162600 chr1B 92.537 67 5 0 653 719 30123195 30123261 3.990000e-16 97.1
25 TraesCS2A01G162600 chr6A 89.333 75 6 1 647 719 439775744 439775818 5.170000e-15 93.5


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 TraesCS2A01G162600 chr2A 115113212 115118059 4847 False 8953.000000 8953 100.0000 1 4848 1 chr2A.!!$F1 4847
1 TraesCS2A01G162600 chr2B 164079650 164086309 6659 False 1911.333333 5467 93.3300 818 4541 3 chr2B.!!$F1 3723
2 TraesCS2A01G162600 chr2D 113486410 113490939 4529 False 819.400000 2126 88.8842 4 4047 5 chr2D.!!$F2 4043
3 TraesCS2A01G162600 chr2D 113500349 113501128 779 False 575.000000 575 80.7130 4062 4846 1 chr2D.!!$F1 784

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
664 675 0.325765 GCTGTCCTACTCCCTCCCTT 60.326 60.000 0.00 0.0 0.00 3.95 F
1422 4435 0.328926 TGTCTGATTGCTGCATGGGA 59.671 50.000 1.84 0.0 0.00 4.37 F
1602 4615 0.900421 TCTCTGGTGGAGATGCACTG 59.100 55.000 4.44 0.0 45.20 3.66 F
2816 5884 2.097825 GAACTGGCTGAGGATTGCATT 58.902 47.619 0.00 0.0 0.00 3.56 F
3749 7483 0.512952 AGAATTGCGACTGTTGCGAC 59.487 50.000 12.13 0.0 34.24 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1655 4668 0.387622 CAGTCAATTTGCAGCCCGTG 60.388 55.000 0.0 0.0 0.00 4.94 R
2625 5688 1.411394 CTTCAGCACGCAAACAATGG 58.589 50.000 0.0 0.0 0.00 3.16 R
3073 6516 3.589988 CGACTCTTTACTGTTGCTCCAT 58.410 45.455 0.0 0.0 0.00 3.41 R
3790 7524 0.032813 CTTGGCACATCCCCTGGAAT 60.033 55.000 0.0 0.0 39.30 3.01 R
4723 8486 0.035176 GATGCCTCCTCATCCTCAGC 59.965 60.000 0.0 0.0 37.47 4.26 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
26 27 3.799281 TGCTTCCTTGTCCAAACTTTG 57.201 42.857 0.00 0.00 0.00 2.77
32 33 6.016610 GCTTCCTTGTCCAAACTTTGTATACA 60.017 38.462 0.08 0.08 0.00 2.29
34 35 7.504924 TCCTTGTCCAAACTTTGTATACAAG 57.495 36.000 17.36 21.21 40.22 3.16
36 37 8.212312 TCCTTGTCCAAACTTTGTATACAAGTA 58.788 33.333 23.48 14.91 39.62 2.24
37 38 9.010029 CCTTGTCCAAACTTTGTATACAAGTAT 57.990 33.333 23.48 5.61 39.62 2.12
154 159 1.202359 GCCAAAAGTTCGCTTTCCACA 60.202 47.619 0.00 0.00 45.86 4.17
158 163 3.971032 AAAGTTCGCTTTCCACAAGAG 57.029 42.857 0.00 0.00 43.39 2.85
170 175 1.343075 CCACAAGAGCTCCCCTACCTA 60.343 57.143 10.93 0.00 0.00 3.08
173 178 2.857498 ACAAGAGCTCCCCTACCTACTA 59.143 50.000 10.93 0.00 0.00 1.82
175 180 2.500590 AGAGCTCCCCTACCTACTACA 58.499 52.381 10.93 0.00 0.00 2.74
178 183 2.518834 AGCTCCCCTACCTACTACACAT 59.481 50.000 0.00 0.00 0.00 3.21
179 184 2.892215 GCTCCCCTACCTACTACACATC 59.108 54.545 0.00 0.00 0.00 3.06
181 186 4.145807 CTCCCCTACCTACTACACATCTG 58.854 52.174 0.00 0.00 0.00 2.90
184 189 3.296854 CCTACCTACTACACATCTGGCA 58.703 50.000 0.00 0.00 0.00 4.92
190 195 4.528206 CCTACTACACATCTGGCATGGATA 59.472 45.833 0.00 0.00 0.00 2.59
194 199 7.078249 ACTACACATCTGGCATGGATATTTA 57.922 36.000 0.00 0.00 0.00 1.40
196 201 8.825774 ACTACACATCTGGCATGGATATTTATA 58.174 33.333 0.00 0.00 0.00 0.98
203 209 7.988937 TCTGGCATGGATATTTATAAAGGACT 58.011 34.615 3.94 0.00 0.00 3.85
205 211 7.754624 TGGCATGGATATTTATAAAGGACTGA 58.245 34.615 3.94 0.00 0.00 3.41
228 234 5.120399 ACACGGTCTAGTTTTGTGAAATCA 58.880 37.500 11.93 0.00 34.72 2.57
229 235 5.763204 ACACGGTCTAGTTTTGTGAAATCAT 59.237 36.000 11.93 0.00 34.72 2.45
238 244 7.775053 AGTTTTGTGAAATCATTTAGGCCTA 57.225 32.000 8.91 8.91 0.00 3.93
239 245 8.366359 AGTTTTGTGAAATCATTTAGGCCTAT 57.634 30.769 14.74 0.00 0.00 2.57
392 403 9.127277 GGTATGTAGGATAGAGACCTTCATATC 57.873 40.741 13.36 10.54 42.39 1.63
412 423 9.187996 TCATATCTTAAAGGAATGCATCAAACA 57.812 29.630 0.00 0.00 0.00 2.83
425 436 3.569701 GCATCAAACAACCTCTCTTTCCA 59.430 43.478 0.00 0.00 0.00 3.53
427 438 5.706916 CATCAAACAACCTCTCTTTCCATG 58.293 41.667 0.00 0.00 0.00 3.66
438 449 5.184479 CCTCTCTTTCCATGCAGAAATTGAA 59.816 40.000 1.97 0.00 35.30 2.69
440 451 7.235935 TCTCTTTCCATGCAGAAATTGAAAT 57.764 32.000 1.97 0.00 35.30 2.17
543 554 7.892771 AGGGCTAGAAGATGATTTTCTTTTCTT 59.107 33.333 3.43 0.00 36.10 2.52
545 556 9.566530 GGCTAGAAGATGATTTTCTTTTCTTTC 57.433 33.333 3.43 0.00 36.10 2.62
589 600 9.790344 AGATGATTTTCTTCTCTCTCTTTTTGA 57.210 29.630 0.00 0.00 0.00 2.69
592 603 9.050601 TGATTTTCTTCTCTCTCTTTTTGAGAC 57.949 33.333 0.00 0.00 46.03 3.36
593 604 8.970859 ATTTTCTTCTCTCTCTTTTTGAGACA 57.029 30.769 0.00 0.00 46.03 3.41
594 605 8.792830 TTTTCTTCTCTCTCTTTTTGAGACAA 57.207 30.769 0.00 0.00 46.03 3.18
595 606 8.430801 TTTCTTCTCTCTCTTTTTGAGACAAG 57.569 34.615 0.00 0.00 46.03 3.16
596 607 7.353414 TCTTCTCTCTCTTTTTGAGACAAGA 57.647 36.000 7.16 7.16 46.03 3.02
597 608 7.961351 TCTTCTCTCTCTTTTTGAGACAAGAT 58.039 34.615 7.16 0.00 46.03 2.40
598 609 7.871973 TCTTCTCTCTCTTTTTGAGACAAGATG 59.128 37.037 7.16 0.00 46.03 2.90
599 610 7.295322 TCTCTCTCTTTTTGAGACAAGATGA 57.705 36.000 0.00 0.00 46.03 2.92
600 611 7.905265 TCTCTCTCTTTTTGAGACAAGATGAT 58.095 34.615 0.00 0.00 46.03 2.45
601 612 8.373981 TCTCTCTCTTTTTGAGACAAGATGATT 58.626 33.333 0.00 0.00 46.03 2.57
602 613 8.915057 TCTCTCTTTTTGAGACAAGATGATTT 57.085 30.769 0.00 0.00 46.03 2.17
603 614 9.347240 TCTCTCTTTTTGAGACAAGATGATTTT 57.653 29.630 0.00 0.00 46.03 1.82
604 615 9.609950 CTCTCTTTTTGAGACAAGATGATTTTC 57.390 33.333 0.00 0.00 46.03 2.29
605 616 9.347240 TCTCTTTTTGAGACAAGATGATTTTCT 57.653 29.630 0.00 0.00 46.03 2.52
606 617 9.962783 CTCTTTTTGAGACAAGATGATTTTCTT 57.037 29.630 0.00 0.00 45.39 2.52
654 665 3.391049 AGTTCGTTCTTTGCTGTCCTAC 58.609 45.455 0.00 0.00 0.00 3.18
655 666 3.069729 AGTTCGTTCTTTGCTGTCCTACT 59.930 43.478 0.00 0.00 0.00 2.57
656 667 3.299340 TCGTTCTTTGCTGTCCTACTC 57.701 47.619 0.00 0.00 0.00 2.59
657 668 2.029290 TCGTTCTTTGCTGTCCTACTCC 60.029 50.000 0.00 0.00 0.00 3.85
658 669 2.701107 GTTCTTTGCTGTCCTACTCCC 58.299 52.381 0.00 0.00 0.00 4.30
659 670 2.303311 GTTCTTTGCTGTCCTACTCCCT 59.697 50.000 0.00 0.00 0.00 4.20
660 671 2.180276 TCTTTGCTGTCCTACTCCCTC 58.820 52.381 0.00 0.00 0.00 4.30
661 672 1.208293 CTTTGCTGTCCTACTCCCTCC 59.792 57.143 0.00 0.00 0.00 4.30
662 673 0.617820 TTGCTGTCCTACTCCCTCCC 60.618 60.000 0.00 0.00 0.00 4.30
663 674 1.311747 GCTGTCCTACTCCCTCCCT 59.688 63.158 0.00 0.00 0.00 4.20
664 675 0.325765 GCTGTCCTACTCCCTCCCTT 60.326 60.000 0.00 0.00 0.00 3.95
665 676 1.902141 GCTGTCCTACTCCCTCCCTTT 60.902 57.143 0.00 0.00 0.00 3.11
666 677 2.112190 CTGTCCTACTCCCTCCCTTTC 58.888 57.143 0.00 0.00 0.00 2.62
667 678 1.112950 GTCCTACTCCCTCCCTTTCG 58.887 60.000 0.00 0.00 0.00 3.46
668 679 1.005228 TCCTACTCCCTCCCTTTCGA 58.995 55.000 0.00 0.00 0.00 3.71
669 680 1.574339 TCCTACTCCCTCCCTTTCGAT 59.426 52.381 0.00 0.00 0.00 3.59
670 681 2.023307 TCCTACTCCCTCCCTTTCGATT 60.023 50.000 0.00 0.00 0.00 3.34
671 682 2.772515 CCTACTCCCTCCCTTTCGATTT 59.227 50.000 0.00 0.00 0.00 2.17
672 683 3.965347 CCTACTCCCTCCCTTTCGATTTA 59.035 47.826 0.00 0.00 0.00 1.40
673 684 4.593634 CCTACTCCCTCCCTTTCGATTTAT 59.406 45.833 0.00 0.00 0.00 1.40
674 685 5.778750 CCTACTCCCTCCCTTTCGATTTATA 59.221 44.000 0.00 0.00 0.00 0.98
675 686 5.810080 ACTCCCTCCCTTTCGATTTATAG 57.190 43.478 0.00 0.00 0.00 1.31
676 687 4.593634 ACTCCCTCCCTTTCGATTTATAGG 59.406 45.833 0.00 0.00 0.00 2.57
678 689 3.559384 CCCTCCCTTTCGATTTATAGGGC 60.559 52.174 9.07 0.00 45.76 5.19
679 690 3.328050 CCTCCCTTTCGATTTATAGGGCT 59.672 47.826 0.00 0.00 45.76 5.19
680 691 4.563786 CCTCCCTTTCGATTTATAGGGCTC 60.564 50.000 0.00 0.00 45.76 4.70
681 692 3.971305 TCCCTTTCGATTTATAGGGCTCA 59.029 43.478 0.00 0.00 45.76 4.26
682 693 4.410883 TCCCTTTCGATTTATAGGGCTCAA 59.589 41.667 0.00 0.00 45.76 3.02
683 694 5.104277 TCCCTTTCGATTTATAGGGCTCAAA 60.104 40.000 0.00 0.00 45.76 2.69
684 695 5.770162 CCCTTTCGATTTATAGGGCTCAAAT 59.230 40.000 0.00 0.00 40.84 2.32
685 696 6.072452 CCCTTTCGATTTATAGGGCTCAAATC 60.072 42.308 0.00 0.00 40.84 2.17
686 697 6.712547 CCTTTCGATTTATAGGGCTCAAATCT 59.287 38.462 6.37 0.00 36.81 2.40
687 698 7.095017 CCTTTCGATTTATAGGGCTCAAATCTC 60.095 40.741 6.37 0.00 36.81 2.75
688 699 6.419484 TCGATTTATAGGGCTCAAATCTCA 57.581 37.500 6.37 0.00 36.81 3.27
689 700 6.826668 TCGATTTATAGGGCTCAAATCTCAA 58.173 36.000 6.37 0.00 36.81 3.02
690 701 7.279615 TCGATTTATAGGGCTCAAATCTCAAA 58.720 34.615 6.37 0.00 36.81 2.69
691 702 7.939039 TCGATTTATAGGGCTCAAATCTCAAAT 59.061 33.333 6.37 0.00 36.81 2.32
692 703 8.233190 CGATTTATAGGGCTCAAATCTCAAATC 58.767 37.037 6.37 0.00 36.81 2.17
693 704 9.294614 GATTTATAGGGCTCAAATCTCAAATCT 57.705 33.333 1.56 0.00 36.29 2.40
694 705 8.682936 TTTATAGGGCTCAAATCTCAAATCTC 57.317 34.615 0.00 0.00 0.00 2.75
695 706 4.581309 AGGGCTCAAATCTCAAATCTCA 57.419 40.909 0.00 0.00 0.00 3.27
696 707 5.126699 AGGGCTCAAATCTCAAATCTCAT 57.873 39.130 0.00 0.00 0.00 2.90
697 708 5.131784 AGGGCTCAAATCTCAAATCTCATC 58.868 41.667 0.00 0.00 0.00 2.92
698 709 4.885907 GGGCTCAAATCTCAAATCTCATCA 59.114 41.667 0.00 0.00 0.00 3.07
699 710 5.359009 GGGCTCAAATCTCAAATCTCATCAA 59.641 40.000 0.00 0.00 0.00 2.57
700 711 6.264088 GGCTCAAATCTCAAATCTCATCAAC 58.736 40.000 0.00 0.00 0.00 3.18
701 712 6.264088 GCTCAAATCTCAAATCTCATCAACC 58.736 40.000 0.00 0.00 0.00 3.77
702 713 6.426980 TCAAATCTCAAATCTCATCAACCG 57.573 37.500 0.00 0.00 0.00 4.44
703 714 6.172630 TCAAATCTCAAATCTCATCAACCGA 58.827 36.000 0.00 0.00 0.00 4.69
704 715 6.314648 TCAAATCTCAAATCTCATCAACCGAG 59.685 38.462 0.00 0.00 0.00 4.63
705 716 4.128925 TCTCAAATCTCATCAACCGAGG 57.871 45.455 0.00 0.00 0.00 4.63
706 717 2.611292 CTCAAATCTCATCAACCGAGGC 59.389 50.000 0.00 0.00 0.00 4.70
707 718 2.027285 TCAAATCTCATCAACCGAGGCA 60.027 45.455 0.00 0.00 0.00 4.75
708 719 2.947652 CAAATCTCATCAACCGAGGCAT 59.052 45.455 0.00 0.00 0.00 4.40
709 720 3.287867 AATCTCATCAACCGAGGCATT 57.712 42.857 0.00 0.00 0.00 3.56
710 721 2.315925 TCTCATCAACCGAGGCATTC 57.684 50.000 0.00 0.00 0.00 2.67
711 722 1.833630 TCTCATCAACCGAGGCATTCT 59.166 47.619 0.00 0.00 0.00 2.40
712 723 1.938577 CTCATCAACCGAGGCATTCTG 59.061 52.381 0.00 0.00 0.00 3.02
713 724 1.278985 TCATCAACCGAGGCATTCTGT 59.721 47.619 0.00 0.00 0.00 3.41
714 725 2.499693 TCATCAACCGAGGCATTCTGTA 59.500 45.455 0.00 0.00 0.00 2.74
715 726 3.055458 TCATCAACCGAGGCATTCTGTAA 60.055 43.478 0.00 0.00 0.00 2.41
716 727 2.972625 TCAACCGAGGCATTCTGTAAG 58.027 47.619 0.00 0.00 0.00 2.34
717 728 2.301870 TCAACCGAGGCATTCTGTAAGT 59.698 45.455 0.00 0.00 33.76 2.24
718 729 2.386661 ACCGAGGCATTCTGTAAGTG 57.613 50.000 0.00 0.00 33.76 3.16
719 730 1.899814 ACCGAGGCATTCTGTAAGTGA 59.100 47.619 0.00 0.00 33.76 3.41
720 731 2.301870 ACCGAGGCATTCTGTAAGTGAA 59.698 45.455 0.00 0.00 33.76 3.18
721 732 3.244422 ACCGAGGCATTCTGTAAGTGAAA 60.244 43.478 0.00 0.00 33.76 2.69
722 733 3.751175 CCGAGGCATTCTGTAAGTGAAAA 59.249 43.478 0.00 0.00 33.76 2.29
723 734 4.215399 CCGAGGCATTCTGTAAGTGAAAAA 59.785 41.667 0.00 0.00 33.76 1.94
751 762 7.404671 AAAAAGTTGAGACAAGCCTTAGAAA 57.595 32.000 0.00 0.00 0.00 2.52
752 763 6.625873 AAAGTTGAGACAAGCCTTAGAAAG 57.374 37.500 0.00 0.00 0.00 2.62
780 791 5.360144 TGAGTATTACTTAGTCCAGTCCAGC 59.640 44.000 0.00 0.00 30.30 4.85
879 911 6.978080 TGAAAAGCTGAGAAAACACAAATACC 59.022 34.615 0.00 0.00 0.00 2.73
881 913 3.502211 AGCTGAGAAAACACAAATACCCG 59.498 43.478 0.00 0.00 0.00 5.28
885 917 6.452494 TGAGAAAACACAAATACCCGAAAA 57.548 33.333 0.00 0.00 0.00 2.29
886 918 6.864342 TGAGAAAACACAAATACCCGAAAAA 58.136 32.000 0.00 0.00 0.00 1.94
925 3920 5.279306 GGAGAAGATACGAGAGAGCTCTAGA 60.279 48.000 18.25 0.32 40.61 2.43
960 3955 0.736053 GAACGAGCGAGAGAGGACAT 59.264 55.000 0.00 0.00 0.00 3.06
1169 4172 2.478890 ATCGCTACCCGTCCGTCTG 61.479 63.158 0.00 0.00 38.35 3.51
1184 4187 1.553706 GTCTGGACCTAGGGTTTCGA 58.446 55.000 14.81 0.00 35.25 3.71
1208 4211 4.278310 CCCCCTTTCGGTTAATTGAATCT 58.722 43.478 0.00 0.00 0.00 2.40
1422 4435 0.328926 TGTCTGATTGCTGCATGGGA 59.671 50.000 1.84 0.00 0.00 4.37
1602 4615 0.900421 TCTCTGGTGGAGATGCACTG 59.100 55.000 4.44 0.00 45.20 3.66
1609 4622 2.422519 GGTGGAGATGCACTGAATCCAT 60.423 50.000 9.56 0.00 41.81 3.41
1626 4639 9.918630 CTGAATCCATGTTTTTGTAATCTCTTT 57.081 29.630 0.00 0.00 0.00 2.52
2029 5043 6.128472 GCATTTGCTTATTTTTGTCTTCAGGG 60.128 38.462 0.00 0.00 38.21 4.45
2278 5292 5.187967 TCATTGTCTTCTTACTCCCCTTCTC 59.812 44.000 0.00 0.00 0.00 2.87
2625 5688 6.919721 TGTTAACCCAAGTGCATATCTTTTC 58.080 36.000 2.48 0.00 0.00 2.29
2638 5704 5.220265 GCATATCTTTTCCATTGTTTGCGTG 60.220 40.000 0.00 0.00 0.00 5.34
2691 5757 7.247456 TGTTGGTACTGTCATCCAATACTTA 57.753 36.000 12.60 0.63 42.10 2.24
2816 5884 2.097825 GAACTGGCTGAGGATTGCATT 58.902 47.619 0.00 0.00 0.00 3.56
3275 6727 4.521639 GGCCATAATCTGAATTCTGCATCA 59.478 41.667 7.05 0.00 0.00 3.07
3426 7048 3.807209 GCGCCAGTATTATGTCCTTCCAT 60.807 47.826 0.00 0.00 0.00 3.41
3747 7481 1.321016 CAAGAATTGCGACTGTTGCG 58.679 50.000 14.90 0.00 40.39 4.85
3748 7482 1.069973 CAAGAATTGCGACTGTTGCGA 60.070 47.619 12.27 12.27 40.39 5.10
3749 7483 0.512952 AGAATTGCGACTGTTGCGAC 59.487 50.000 12.13 0.00 34.24 5.19
3750 7484 0.785708 GAATTGCGACTGTTGCGACG 60.786 55.000 12.13 0.00 34.24 5.12
3753 7487 3.995669 GCGACTGTTGCGACGCAA 61.996 61.111 30.11 30.11 46.80 4.85
3779 7513 9.606631 ACTCTGATGTCTTGACCTAATAATTTC 57.393 33.333 0.00 0.00 0.00 2.17
3790 7524 8.146053 TGACCTAATAATTTCTCTTCTGGTCA 57.854 34.615 0.00 0.00 45.06 4.02
3881 7615 0.531532 GATGCAGTCGTGATCCTGGG 60.532 60.000 0.00 0.00 0.00 4.45
3887 7621 4.838152 CGTGATCCTGGGGCCGTG 62.838 72.222 0.00 0.00 0.00 4.94
3952 7686 1.743431 CGCCAGTGTTATGCATCCTCA 60.743 52.381 0.19 0.00 0.00 3.86
3963 7697 0.579156 GCATCCTCAAGCGATTCGTC 59.421 55.000 8.03 0.28 0.00 4.20
3972 7706 1.414897 GCGATTCGTCGAACGCTTT 59.585 52.632 30.02 11.37 46.06 3.51
3992 7726 5.762045 CTTTTGTACAACCTGGAGACATTG 58.238 41.667 8.07 0.00 41.51 2.82
4123 7858 3.117360 AGCCTATGCCAAAAGCTCCTAAT 60.117 43.478 0.00 0.00 44.23 1.73
4133 7868 8.196771 TGCCAAAAGCTCCTAATATTATTGTTG 58.803 33.333 0.00 0.00 44.23 3.33
4156 7891 3.761897 TCCGAACAAAGGATTCATGGTT 58.238 40.909 0.00 0.00 31.86 3.67
4159 7894 4.475944 CGAACAAAGGATTCATGGTTGTC 58.524 43.478 0.00 0.00 31.41 3.18
4193 7928 1.541233 CCTACCTGCATTCATCCCGAC 60.541 57.143 0.00 0.00 0.00 4.79
4242 7986 2.575461 GCACTCATGCCTTTGCCC 59.425 61.111 0.00 0.00 46.97 5.36
4246 7990 1.305623 CTCATGCCTTTGCCCCTCT 59.694 57.895 0.00 0.00 36.33 3.69
4291 8035 4.431416 TCAAAACCCTAGCTTTGAGTCA 57.569 40.909 0.00 0.00 36.79 3.41
4301 8045 3.471680 AGCTTTGAGTCACTTCTCCAAC 58.528 45.455 0.00 0.00 33.93 3.77
4339 8084 3.189606 TGACCACCCCTAGATCACATTT 58.810 45.455 0.00 0.00 0.00 2.32
4340 8085 3.054434 TGACCACCCCTAGATCACATTTG 60.054 47.826 0.00 0.00 0.00 2.32
4343 8088 2.684881 CACCCCTAGATCACATTTGTGC 59.315 50.000 5.81 0.00 45.25 4.57
4384 8129 2.238646 TGGTTGTCTCTGTGGTTTGTCT 59.761 45.455 0.00 0.00 0.00 3.41
4496 8250 3.912496 CATGACTATGGTGGAGGTCAA 57.088 47.619 0.00 0.00 41.14 3.18
4547 8301 0.541764 ATGGTTGTTGATGGGGCGTT 60.542 50.000 0.00 0.00 0.00 4.84
4554 8308 1.459455 TTGATGGGGCGTTGGTGTTG 61.459 55.000 0.00 0.00 0.00 3.33
4556 8310 4.904590 TGGGGCGTTGGTGTTGGG 62.905 66.667 0.00 0.00 0.00 4.12
4557 8311 4.906537 GGGGCGTTGGTGTTGGGT 62.907 66.667 0.00 0.00 0.00 4.51
4558 8312 3.601685 GGGCGTTGGTGTTGGGTG 61.602 66.667 0.00 0.00 0.00 4.61
4559 8313 3.601685 GGCGTTGGTGTTGGGTGG 61.602 66.667 0.00 0.00 0.00 4.61
4562 8316 2.811799 GTTGGTGTTGGGTGGCAC 59.188 61.111 9.70 9.70 35.07 5.01
4563 8317 1.756561 GTTGGTGTTGGGTGGCACT 60.757 57.895 18.45 0.00 36.03 4.40
4564 8318 1.454847 TTGGTGTTGGGTGGCACTC 60.455 57.895 18.45 15.20 36.03 3.51
4565 8319 2.597510 GGTGTTGGGTGGCACTCC 60.598 66.667 16.28 15.90 42.03 3.85
4566 8320 2.515901 GTGTTGGGTGGCACTCCT 59.484 61.111 16.28 0.00 42.45 3.69
4567 8321 1.898574 GTGTTGGGTGGCACTCCTG 60.899 63.158 16.28 0.00 42.45 3.86
4568 8322 2.282462 GTTGGGTGGCACTCCTGG 60.282 66.667 16.28 0.00 42.45 4.45
4569 8323 2.449518 TTGGGTGGCACTCCTGGA 60.450 61.111 16.28 0.00 42.45 3.86
4570 8324 2.528818 TTGGGTGGCACTCCTGGAG 61.529 63.158 22.00 22.00 42.45 3.86
4571 8325 3.721706 GGGTGGCACTCCTGGAGG 61.722 72.222 26.56 16.41 42.45 4.30
4572 8326 2.607750 GGTGGCACTCCTGGAGGA 60.608 66.667 26.56 1.34 43.08 3.71
4623 8377 2.444624 CGTCGCGACCATGGTTGAG 61.445 63.158 32.76 29.11 0.00 3.02
4628 8382 3.134127 GACCATGGTTGAGGCGGC 61.134 66.667 20.85 0.00 0.00 6.53
4683 8446 0.251916 CCTCCATACAAAGCGGTCCA 59.748 55.000 0.00 0.00 0.00 4.02
4707 8470 2.970324 GGCAACTCCGCGTCAACA 60.970 61.111 4.92 0.00 0.00 3.33
4708 8471 2.539338 GGCAACTCCGCGTCAACAA 61.539 57.895 4.92 0.00 0.00 2.83
4709 8472 1.353804 GCAACTCCGCGTCAACAAA 59.646 52.632 4.92 0.00 0.00 2.83
4711 8474 1.599419 GCAACTCCGCGTCAACAAAAT 60.599 47.619 4.92 0.00 0.00 1.82
4712 8475 2.043411 CAACTCCGCGTCAACAAAATG 58.957 47.619 4.92 0.00 0.00 2.32
4713 8476 0.040425 ACTCCGCGTCAACAAAATGC 60.040 50.000 4.92 0.00 0.00 3.56
4715 8478 3.435915 CGCGTCAACAAAATGCGG 58.564 55.556 0.00 0.00 45.83 5.69
4717 8480 1.327292 CGCGTCAACAAAATGCGGTC 61.327 55.000 0.00 0.00 45.83 4.79
4718 8481 0.040425 GCGTCAACAAAATGCGGTCT 60.040 50.000 0.00 0.00 0.00 3.85
4719 8482 1.195900 GCGTCAACAAAATGCGGTCTA 59.804 47.619 0.00 0.00 0.00 2.59
4720 8483 2.724839 GCGTCAACAAAATGCGGTCTAG 60.725 50.000 0.00 0.00 0.00 2.43
4722 8485 1.463056 TCAACAAAATGCGGTCTAGCG 59.537 47.619 0.00 0.00 40.67 4.26
4723 8486 0.802494 AACAAAATGCGGTCTAGCGG 59.198 50.000 3.55 0.00 40.67 5.52
4732 8509 1.365633 GGTCTAGCGGCTGAGGATG 59.634 63.158 13.86 0.00 0.00 3.51
4742 8519 0.035176 GCTGAGGATGAGGAGGCATC 59.965 60.000 0.00 0.00 43.04 3.91
4743 8520 1.421480 CTGAGGATGAGGAGGCATCA 58.579 55.000 0.00 0.00 45.03 3.07
4758 8535 0.512518 CATCAAAGCAGCACGACGAA 59.487 50.000 0.00 0.00 0.00 3.85
4772 8549 0.165944 GACGAAGATGCAAACCACGG 59.834 55.000 0.00 0.00 0.00 4.94
4773 8550 0.534203 ACGAAGATGCAAACCACGGT 60.534 50.000 0.00 0.00 0.00 4.83
4817 8594 2.880879 CGTCTGGTGCGATGGTCG 60.881 66.667 0.00 0.00 43.89 4.79
4821 8598 3.336715 CTGGTGCGATGGTCGTCGA 62.337 63.158 15.67 0.00 44.06 4.20
4846 8623 6.171213 CCTTACCTCCGACAAAGAGTAAATT 58.829 40.000 0.00 0.00 0.00 1.82
4847 8624 6.653740 CCTTACCTCCGACAAAGAGTAAATTT 59.346 38.462 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.590850 AAGTTTGGACAAGGAAGCATTC 57.409 40.909 0.00 0.00 46.67 2.67
4 5 4.162131 ACAAAGTTTGGACAAGGAAGCATT 59.838 37.500 19.45 0.00 34.12 3.56
5 6 3.706086 ACAAAGTTTGGACAAGGAAGCAT 59.294 39.130 19.45 0.00 34.12 3.79
6 7 3.096092 ACAAAGTTTGGACAAGGAAGCA 58.904 40.909 19.45 0.00 34.12 3.91
7 8 3.801114 ACAAAGTTTGGACAAGGAAGC 57.199 42.857 19.45 0.00 34.12 3.86
96 100 7.333528 CACACCCTATATGTGCAGTATTTTT 57.666 36.000 0.00 0.00 40.94 1.94
97 101 6.942532 CACACCCTATATGTGCAGTATTTT 57.057 37.500 0.00 0.00 40.94 1.82
124 129 1.172812 AACTTTTGGCTCTCGGGTGC 61.173 55.000 0.00 0.00 0.00 5.01
154 159 2.857498 TGTAGTAGGTAGGGGAGCTCTT 59.143 50.000 14.64 2.43 37.09 2.85
158 163 2.449137 TGTGTAGTAGGTAGGGGAGC 57.551 55.000 0.00 0.00 0.00 4.70
170 175 5.573380 AATATCCATGCCAGATGTGTAGT 57.427 39.130 0.00 0.00 0.00 2.73
173 178 8.938801 TTTATAAATATCCATGCCAGATGTGT 57.061 30.769 0.00 0.00 0.00 3.72
175 180 8.393259 TCCTTTATAAATATCCATGCCAGATGT 58.607 33.333 0.00 0.00 0.00 3.06
178 183 7.884877 CAGTCCTTTATAAATATCCATGCCAGA 59.115 37.037 0.00 0.00 0.00 3.86
179 184 7.884877 TCAGTCCTTTATAAATATCCATGCCAG 59.115 37.037 0.00 0.00 0.00 4.85
181 186 7.665559 TGTCAGTCCTTTATAAATATCCATGCC 59.334 37.037 0.00 0.00 0.00 4.40
184 189 7.878127 CCGTGTCAGTCCTTTATAAATATCCAT 59.122 37.037 0.00 0.00 0.00 3.41
190 195 6.295719 AGACCGTGTCAGTCCTTTATAAAT 57.704 37.500 0.00 0.00 34.60 1.40
194 199 4.342359 ACTAGACCGTGTCAGTCCTTTAT 58.658 43.478 0.00 0.00 34.60 1.40
196 201 2.595238 ACTAGACCGTGTCAGTCCTTT 58.405 47.619 0.00 0.00 34.60 3.11
203 209 3.804786 TCACAAAACTAGACCGTGTCA 57.195 42.857 0.00 0.00 34.60 3.58
205 211 5.120399 TGATTTCACAAAACTAGACCGTGT 58.880 37.500 0.00 0.00 0.00 4.49
228 234 9.984590 TTCCTACAAACTAAAATAGGCCTAAAT 57.015 29.630 18.42 6.05 35.17 1.40
229 235 9.984590 ATTCCTACAAACTAAAATAGGCCTAAA 57.015 29.630 18.42 0.00 35.17 1.85
303 309 7.633789 TCCATTTCTATAAACCAAAGAGCTCT 58.366 34.615 11.45 11.45 0.00 4.09
357 363 3.655615 ATCCTACATACCCCGCAAAAA 57.344 42.857 0.00 0.00 0.00 1.94
358 364 3.968649 TCTATCCTACATACCCCGCAAAA 59.031 43.478 0.00 0.00 0.00 2.44
359 365 3.576982 CTCTATCCTACATACCCCGCAAA 59.423 47.826 0.00 0.00 0.00 3.68
360 366 3.162666 CTCTATCCTACATACCCCGCAA 58.837 50.000 0.00 0.00 0.00 4.85
361 367 2.377531 TCTCTATCCTACATACCCCGCA 59.622 50.000 0.00 0.00 0.00 5.69
362 368 2.754002 GTCTCTATCCTACATACCCCGC 59.246 54.545 0.00 0.00 0.00 6.13
363 369 3.010361 AGGTCTCTATCCTACATACCCCG 59.990 52.174 0.00 0.00 33.04 5.73
364 370 4.678538 AGGTCTCTATCCTACATACCCC 57.321 50.000 0.00 0.00 33.04 4.95
365 371 5.642165 TGAAGGTCTCTATCCTACATACCC 58.358 45.833 0.00 0.00 34.56 3.69
366 372 9.127277 GATATGAAGGTCTCTATCCTACATACC 57.873 40.741 0.00 0.00 34.56 2.73
367 373 9.914834 AGATATGAAGGTCTCTATCCTACATAC 57.085 37.037 0.00 0.00 34.56 2.39
392 403 6.458210 AGGTTGTTTGATGCATTCCTTTAAG 58.542 36.000 0.00 0.00 0.00 1.85
411 422 3.063510 TCTGCATGGAAAGAGAGGTTG 57.936 47.619 0.00 0.00 0.00 3.77
412 423 3.795688 TTCTGCATGGAAAGAGAGGTT 57.204 42.857 0.00 0.00 0.00 3.50
425 436 9.139734 AGGTGATATGTATTTCAATTTCTGCAT 57.860 29.630 0.00 0.00 0.00 3.96
427 438 8.623903 TGAGGTGATATGTATTTCAATTTCTGC 58.376 33.333 0.00 0.00 0.00 4.26
512 523 9.533831 AAGAAAATCATCTTCTAGCCCTAAAAA 57.466 29.630 0.00 0.00 34.60 1.94
513 524 9.533831 AAAGAAAATCATCTTCTAGCCCTAAAA 57.466 29.630 0.00 0.00 38.69 1.52
514 525 9.533831 AAAAGAAAATCATCTTCTAGCCCTAAA 57.466 29.630 0.00 0.00 38.69 1.85
515 526 9.178758 GAAAAGAAAATCATCTTCTAGCCCTAA 57.821 33.333 0.00 0.00 38.69 2.69
516 527 8.552296 AGAAAAGAAAATCATCTTCTAGCCCTA 58.448 33.333 0.00 0.00 38.69 3.53
517 528 7.409358 AGAAAAGAAAATCATCTTCTAGCCCT 58.591 34.615 0.00 0.00 38.69 5.19
518 529 7.637631 AGAAAAGAAAATCATCTTCTAGCCC 57.362 36.000 0.00 0.00 38.69 5.19
519 530 9.566530 GAAAGAAAAGAAAATCATCTTCTAGCC 57.433 33.333 0.00 0.00 38.69 3.93
580 591 9.962783 AAGAAAATCATCTTGTCTCAAAAAGAG 57.037 29.630 0.00 0.00 40.67 2.85
601 612 9.929180 CTCATTCGGTTCATAGGATATAAGAAA 57.071 33.333 0.00 0.00 0.00 2.52
602 613 8.531982 CCTCATTCGGTTCATAGGATATAAGAA 58.468 37.037 0.00 0.00 0.00 2.52
603 614 7.363880 GCCTCATTCGGTTCATAGGATATAAGA 60.364 40.741 0.00 0.00 0.00 2.10
604 615 6.758886 GCCTCATTCGGTTCATAGGATATAAG 59.241 42.308 0.00 0.00 0.00 1.73
605 616 6.351881 GGCCTCATTCGGTTCATAGGATATAA 60.352 42.308 0.00 0.00 0.00 0.98
606 617 5.128827 GGCCTCATTCGGTTCATAGGATATA 59.871 44.000 0.00 0.00 0.00 0.86
607 618 4.080863 GGCCTCATTCGGTTCATAGGATAT 60.081 45.833 0.00 0.00 0.00 1.63
608 619 3.260884 GGCCTCATTCGGTTCATAGGATA 59.739 47.826 0.00 0.00 0.00 2.59
609 620 2.039084 GGCCTCATTCGGTTCATAGGAT 59.961 50.000 0.00 0.00 0.00 3.24
610 621 1.416401 GGCCTCATTCGGTTCATAGGA 59.584 52.381 0.00 0.00 0.00 2.94
611 622 1.417890 AGGCCTCATTCGGTTCATAGG 59.582 52.381 0.00 0.00 0.00 2.57
612 623 2.918712 AGGCCTCATTCGGTTCATAG 57.081 50.000 0.00 0.00 0.00 2.23
613 624 3.709653 ACTAAGGCCTCATTCGGTTCATA 59.290 43.478 5.23 0.00 0.00 2.15
614 625 2.505819 ACTAAGGCCTCATTCGGTTCAT 59.494 45.455 5.23 0.00 0.00 2.57
615 626 1.906574 ACTAAGGCCTCATTCGGTTCA 59.093 47.619 5.23 0.00 0.00 3.18
616 627 2.693267 ACTAAGGCCTCATTCGGTTC 57.307 50.000 5.23 0.00 0.00 3.62
654 665 5.153950 CCTATAAATCGAAAGGGAGGGAG 57.846 47.826 0.00 0.00 0.00 4.30
661 672 6.712547 AGATTTGAGCCCTATAAATCGAAAGG 59.287 38.462 0.00 0.00 42.61 3.11
662 673 7.442364 TGAGATTTGAGCCCTATAAATCGAAAG 59.558 37.037 0.00 0.00 42.61 2.62
663 674 7.279615 TGAGATTTGAGCCCTATAAATCGAAA 58.720 34.615 0.00 0.00 42.61 3.46
664 675 6.826668 TGAGATTTGAGCCCTATAAATCGAA 58.173 36.000 0.00 0.00 42.61 3.71
665 676 6.419484 TGAGATTTGAGCCCTATAAATCGA 57.581 37.500 0.00 0.00 42.61 3.59
666 677 7.496529 TTTGAGATTTGAGCCCTATAAATCG 57.503 36.000 0.00 0.00 42.61 3.34
667 678 9.294614 AGATTTGAGATTTGAGCCCTATAAATC 57.705 33.333 0.00 0.00 39.76 2.17
668 679 9.294614 GAGATTTGAGATTTGAGCCCTATAAAT 57.705 33.333 0.00 0.00 0.00 1.40
669 680 8.274322 TGAGATTTGAGATTTGAGCCCTATAAA 58.726 33.333 0.00 0.00 0.00 1.40
670 681 7.805163 TGAGATTTGAGATTTGAGCCCTATAA 58.195 34.615 0.00 0.00 0.00 0.98
671 682 7.379059 TGAGATTTGAGATTTGAGCCCTATA 57.621 36.000 0.00 0.00 0.00 1.31
672 683 6.257994 TGAGATTTGAGATTTGAGCCCTAT 57.742 37.500 0.00 0.00 0.00 2.57
673 684 5.698741 TGAGATTTGAGATTTGAGCCCTA 57.301 39.130 0.00 0.00 0.00 3.53
674 685 4.581309 TGAGATTTGAGATTTGAGCCCT 57.419 40.909 0.00 0.00 0.00 5.19
675 686 4.885907 TGATGAGATTTGAGATTTGAGCCC 59.114 41.667 0.00 0.00 0.00 5.19
676 687 6.264088 GTTGATGAGATTTGAGATTTGAGCC 58.736 40.000 0.00 0.00 0.00 4.70
677 688 6.264088 GGTTGATGAGATTTGAGATTTGAGC 58.736 40.000 0.00 0.00 0.00 4.26
678 689 6.314648 TCGGTTGATGAGATTTGAGATTTGAG 59.685 38.462 0.00 0.00 0.00 3.02
679 690 6.172630 TCGGTTGATGAGATTTGAGATTTGA 58.827 36.000 0.00 0.00 0.00 2.69
680 691 6.426980 TCGGTTGATGAGATTTGAGATTTG 57.573 37.500 0.00 0.00 0.00 2.32
681 692 5.587844 CCTCGGTTGATGAGATTTGAGATTT 59.412 40.000 0.00 0.00 35.43 2.17
682 693 5.121811 CCTCGGTTGATGAGATTTGAGATT 58.878 41.667 0.00 0.00 35.43 2.40
683 694 4.701765 CCTCGGTTGATGAGATTTGAGAT 58.298 43.478 0.00 0.00 35.43 2.75
684 695 3.679917 GCCTCGGTTGATGAGATTTGAGA 60.680 47.826 0.00 0.00 35.43 3.27
685 696 2.611292 GCCTCGGTTGATGAGATTTGAG 59.389 50.000 0.00 0.00 35.43 3.02
686 697 2.027285 TGCCTCGGTTGATGAGATTTGA 60.027 45.455 0.00 0.00 35.43 2.69
687 698 2.358957 TGCCTCGGTTGATGAGATTTG 58.641 47.619 0.00 0.00 35.43 2.32
688 699 2.787473 TGCCTCGGTTGATGAGATTT 57.213 45.000 0.00 0.00 35.43 2.17
689 700 3.118112 AGAATGCCTCGGTTGATGAGATT 60.118 43.478 0.00 0.00 35.43 2.40
690 701 2.437281 AGAATGCCTCGGTTGATGAGAT 59.563 45.455 0.00 0.00 35.43 2.75
691 702 1.833630 AGAATGCCTCGGTTGATGAGA 59.166 47.619 0.00 0.00 35.43 3.27
692 703 1.938577 CAGAATGCCTCGGTTGATGAG 59.061 52.381 0.00 0.00 0.00 2.90
693 704 1.278985 ACAGAATGCCTCGGTTGATGA 59.721 47.619 0.00 0.00 42.53 2.92
694 705 1.742761 ACAGAATGCCTCGGTTGATG 58.257 50.000 0.00 0.00 42.53 3.07
695 706 3.055094 ACTTACAGAATGCCTCGGTTGAT 60.055 43.478 0.00 0.00 42.53 2.57
696 707 2.301870 ACTTACAGAATGCCTCGGTTGA 59.698 45.455 0.00 0.00 42.53 3.18
697 708 2.416547 CACTTACAGAATGCCTCGGTTG 59.583 50.000 0.00 0.00 42.53 3.77
698 709 2.301870 TCACTTACAGAATGCCTCGGTT 59.698 45.455 0.00 0.00 42.53 4.44
699 710 1.899814 TCACTTACAGAATGCCTCGGT 59.100 47.619 0.00 0.00 42.53 4.69
700 711 2.672961 TCACTTACAGAATGCCTCGG 57.327 50.000 0.00 0.00 42.53 4.63
701 712 5.356882 TTTTTCACTTACAGAATGCCTCG 57.643 39.130 0.00 0.00 42.53 4.63
727 738 7.404671 TTTCTAAGGCTTGTCTCAACTTTTT 57.595 32.000 10.69 0.00 0.00 1.94
728 739 6.039829 CCTTTCTAAGGCTTGTCTCAACTTTT 59.960 38.462 10.69 0.00 42.78 2.27
729 740 5.532779 CCTTTCTAAGGCTTGTCTCAACTTT 59.467 40.000 10.69 0.00 42.78 2.66
730 741 5.066593 CCTTTCTAAGGCTTGTCTCAACTT 58.933 41.667 10.69 0.00 42.78 2.66
731 742 4.646572 CCTTTCTAAGGCTTGTCTCAACT 58.353 43.478 10.69 0.00 42.78 3.16
746 757 9.406113 GGACTAAGTAATACTCACTCCTTTCTA 57.594 37.037 0.00 0.00 0.00 2.10
747 758 7.894364 TGGACTAAGTAATACTCACTCCTTTCT 59.106 37.037 0.00 0.00 0.00 2.52
748 759 8.064336 TGGACTAAGTAATACTCACTCCTTTC 57.936 38.462 0.00 0.00 0.00 2.62
749 760 7.674772 ACTGGACTAAGTAATACTCACTCCTTT 59.325 37.037 0.00 0.00 0.00 3.11
750 761 7.183460 ACTGGACTAAGTAATACTCACTCCTT 58.817 38.462 0.00 0.00 0.00 3.36
751 762 6.733509 ACTGGACTAAGTAATACTCACTCCT 58.266 40.000 0.00 0.00 0.00 3.69
752 763 6.039605 GGACTGGACTAAGTAATACTCACTCC 59.960 46.154 0.00 0.00 0.00 3.85
753 764 6.602406 TGGACTGGACTAAGTAATACTCACTC 59.398 42.308 0.00 0.00 0.00 3.51
754 765 6.491383 TGGACTGGACTAAGTAATACTCACT 58.509 40.000 0.00 0.00 0.00 3.41
755 766 6.680872 GCTGGACTGGACTAAGTAATACTCAC 60.681 46.154 0.00 0.00 0.00 3.51
756 767 5.360144 GCTGGACTGGACTAAGTAATACTCA 59.640 44.000 0.00 0.00 0.00 3.41
757 768 5.505985 CGCTGGACTGGACTAAGTAATACTC 60.506 48.000 0.00 0.00 0.00 2.59
758 769 4.338682 CGCTGGACTGGACTAAGTAATACT 59.661 45.833 0.00 0.00 0.00 2.12
759 770 4.499357 CCGCTGGACTGGACTAAGTAATAC 60.499 50.000 0.00 0.00 0.00 1.89
760 771 3.635373 CCGCTGGACTGGACTAAGTAATA 59.365 47.826 0.00 0.00 0.00 0.98
761 772 2.431057 CCGCTGGACTGGACTAAGTAAT 59.569 50.000 0.00 0.00 0.00 1.89
762 773 1.822990 CCGCTGGACTGGACTAAGTAA 59.177 52.381 0.00 0.00 0.00 2.24
763 774 1.471119 CCGCTGGACTGGACTAAGTA 58.529 55.000 0.00 0.00 0.00 2.24
764 775 1.258445 CCCGCTGGACTGGACTAAGT 61.258 60.000 0.00 0.00 0.00 2.24
765 776 1.517832 CCCGCTGGACTGGACTAAG 59.482 63.158 0.00 0.00 0.00 2.18
766 777 2.656069 GCCCGCTGGACTGGACTAA 61.656 63.158 0.00 0.00 0.00 2.24
767 778 3.075005 GCCCGCTGGACTGGACTA 61.075 66.667 0.00 0.00 0.00 2.59
780 791 4.148825 CCGACCTTCCAGAGCCCG 62.149 72.222 0.00 0.00 0.00 6.13
820 832 0.808125 TGTGATGTTTGGGCGCATAC 59.192 50.000 10.83 15.81 0.00 2.39
879 911 8.357402 TCTCCTTTTCTTTTTCCTATTTTTCGG 58.643 33.333 0.00 0.00 0.00 4.30
886 918 9.384764 CGTATCTTCTCCTTTTCTTTTTCCTAT 57.615 33.333 0.00 0.00 0.00 2.57
925 3920 2.567497 TTCCCTCGCTCGTTCCGTT 61.567 57.895 0.00 0.00 0.00 4.44
943 3938 1.944024 CTTATGTCCTCTCTCGCTCGT 59.056 52.381 0.00 0.00 0.00 4.18
960 3955 1.953559 CCTTGCCTGCTATTCGCTTA 58.046 50.000 0.00 0.00 40.11 3.09
1208 4211 4.500887 GCCCTAGTTTGACACGCAGATATA 60.501 45.833 0.00 0.00 0.00 0.86
1422 4435 2.619849 CCATTCTCCCTGAACTGCACAT 60.620 50.000 0.00 0.00 37.52 3.21
1655 4668 0.387622 CAGTCAATTTGCAGCCCGTG 60.388 55.000 0.00 0.00 0.00 4.94
2029 5043 7.981102 AAACCAAACTGGATAGAGAAAGTAC 57.019 36.000 0.00 0.00 40.96 2.73
2123 5137 7.761038 AATGGTCTAACCTGTTCCTTTTTAG 57.239 36.000 0.00 0.00 39.58 1.85
2251 5265 4.019231 AGGGGAGTAAGAAGACAATGAACC 60.019 45.833 0.00 0.00 0.00 3.62
2256 5270 5.346270 AGAGAAGGGGAGTAAGAAGACAAT 58.654 41.667 0.00 0.00 0.00 2.71
2589 5652 2.896044 TGGGTTAACAAGCATGCAATCA 59.104 40.909 21.98 5.22 0.00 2.57
2625 5688 1.411394 CTTCAGCACGCAAACAATGG 58.589 50.000 0.00 0.00 0.00 3.16
2638 5704 9.508567 CATTACTTAAATAAAGAAGGCTTCAGC 57.491 33.333 27.70 3.02 38.67 4.26
2765 5833 9.680315 CATTTACATTTTGTTGGCATGATTTTT 57.320 25.926 0.00 0.00 0.00 1.94
3073 6516 3.589988 CGACTCTTTACTGTTGCTCCAT 58.410 45.455 0.00 0.00 0.00 3.41
3453 7075 7.147915 GGACCATTGGCATTAATTTCTCTGTTA 60.148 37.037 1.54 0.00 0.00 2.41
3743 7477 0.599991 ACATCAGAGTTGCGTCGCAA 60.600 50.000 27.85 27.85 46.80 4.85
3744 7478 1.006220 ACATCAGAGTTGCGTCGCA 60.006 52.632 17.58 17.58 36.47 5.10
3745 7479 0.734253 AGACATCAGAGTTGCGTCGC 60.734 55.000 11.10 11.10 33.93 5.19
3746 7480 1.388093 CAAGACATCAGAGTTGCGTCG 59.612 52.381 0.00 0.00 33.93 5.12
3747 7481 2.410053 GTCAAGACATCAGAGTTGCGTC 59.590 50.000 0.00 0.00 0.00 5.19
3748 7482 2.408050 GTCAAGACATCAGAGTTGCGT 58.592 47.619 0.00 0.00 0.00 5.24
3749 7483 1.728971 GGTCAAGACATCAGAGTTGCG 59.271 52.381 2.29 0.00 0.00 4.85
3750 7484 3.051081 AGGTCAAGACATCAGAGTTGC 57.949 47.619 2.29 0.00 0.00 4.17
3751 7485 8.954950 ATTATTAGGTCAAGACATCAGAGTTG 57.045 34.615 2.29 0.00 0.00 3.16
3752 7486 9.965902 AAATTATTAGGTCAAGACATCAGAGTT 57.034 29.630 2.29 0.00 0.00 3.01
3753 7487 9.606631 GAAATTATTAGGTCAAGACATCAGAGT 57.393 33.333 2.29 0.00 0.00 3.24
3756 7490 9.829507 AGAGAAATTATTAGGTCAAGACATCAG 57.170 33.333 2.29 0.00 0.00 2.90
3790 7524 0.032813 CTTGGCACATCCCCTGGAAT 60.033 55.000 0.00 0.00 39.30 3.01
3855 7589 2.524569 TCACGACTGCATCAACTTCA 57.475 45.000 0.00 0.00 0.00 3.02
3881 7615 4.788521 GCAACTATATGTAAAAGCACGGCC 60.789 45.833 0.00 0.00 0.00 6.13
3887 7621 6.436843 ACAGGTGCAACTATATGTAAAAGC 57.563 37.500 2.54 0.00 36.74 3.51
3963 7697 2.601266 CCAGGTTGTACAAAAGCGTTCG 60.601 50.000 10.51 0.00 32.80 3.95
3972 7706 4.431416 ACAATGTCTCCAGGTTGTACAA 57.569 40.909 3.59 3.59 33.39 2.41
4133 7868 3.506067 ACCATGAATCCTTTGTTCGGAAC 59.494 43.478 13.86 13.86 33.55 3.62
4137 7872 4.475944 GACAACCATGAATCCTTTGTTCG 58.524 43.478 0.00 0.00 30.60 3.95
4150 7885 0.320683 TCCTGACAGCGACAACCATG 60.321 55.000 0.00 0.00 0.00 3.66
4156 7891 0.904865 AGGGAATCCTGACAGCGACA 60.905 55.000 0.00 0.00 42.98 4.35
4159 7894 0.105039 GGTAGGGAATCCTGACAGCG 59.895 60.000 0.00 0.00 44.61 5.18
4242 7986 3.655211 AGGGGCAAGGCACAGAGG 61.655 66.667 0.00 0.00 30.93 3.69
4246 7990 0.114168 AATAACAGGGGCAAGGCACA 59.886 50.000 0.00 0.00 30.93 4.57
4291 8035 1.325355 TCTCGAACGGTTGGAGAAGT 58.675 50.000 26.61 0.00 40.81 3.01
4301 8045 0.446616 TCAGACGACATCTCGAACGG 59.553 55.000 0.00 0.00 43.06 4.44
4339 8084 1.514678 GATGGCGAACAACAGGCACA 61.515 55.000 0.00 0.00 45.57 4.57
4340 8085 1.210155 GATGGCGAACAACAGGCAC 59.790 57.895 0.00 0.00 45.57 5.01
4343 8088 0.950836 TTGTGATGGCGAACAACAGG 59.049 50.000 0.00 0.00 32.06 4.00
4369 8114 2.115427 TCCACAGACAAACCACAGAGA 58.885 47.619 0.00 0.00 0.00 3.10
4384 8129 0.396435 CCTAGCACCAAGTGTCCACA 59.604 55.000 0.00 0.00 35.75 4.17
4393 8138 0.114168 AAATGTGGGCCTAGCACCAA 59.886 50.000 4.53 0.00 38.73 3.67
4444 8189 1.323271 CCACTCCTTCGAGCTAGGCA 61.323 60.000 0.00 0.00 40.03 4.75
4496 8250 1.303155 GCAGGCTGTTCTGGCTCTT 60.303 57.895 17.16 0.00 41.04 2.85
4547 8301 2.194597 GAGTGCCACCCAACACCA 59.805 61.111 0.00 0.00 37.51 4.17
4554 8308 3.721706 CCTCCAGGAGTGCCACCC 61.722 72.222 15.86 0.00 37.39 4.61
4563 8317 0.907486 CAAGTGATGCTCCTCCAGGA 59.093 55.000 0.00 0.00 43.08 3.86
4564 8318 0.107312 CCAAGTGATGCTCCTCCAGG 60.107 60.000 0.00 0.00 0.00 4.45
4565 8319 0.617413 ACCAAGTGATGCTCCTCCAG 59.383 55.000 0.00 0.00 0.00 3.86
4566 8320 0.325933 CACCAAGTGATGCTCCTCCA 59.674 55.000 0.00 0.00 35.23 3.86
4567 8321 0.393537 CCACCAAGTGATGCTCCTCC 60.394 60.000 0.00 0.00 35.23 4.30
4568 8322 0.615331 TCCACCAAGTGATGCTCCTC 59.385 55.000 0.00 0.00 35.23 3.71
4569 8323 0.617413 CTCCACCAAGTGATGCTCCT 59.383 55.000 0.00 0.00 35.23 3.69
4570 8324 0.393537 CCTCCACCAAGTGATGCTCC 60.394 60.000 0.00 0.00 35.23 4.70
4571 8325 1.028868 GCCTCCACCAAGTGATGCTC 61.029 60.000 0.00 0.00 35.23 4.26
4572 8326 1.001641 GCCTCCACCAAGTGATGCT 60.002 57.895 0.00 0.00 35.23 3.79
4573 8327 1.001641 AGCCTCCACCAAGTGATGC 60.002 57.895 0.00 0.00 35.23 3.91
4574 8328 0.742281 CGAGCCTCCACCAAGTGATG 60.742 60.000 0.00 0.00 35.23 3.07
4575 8329 1.599047 CGAGCCTCCACCAAGTGAT 59.401 57.895 0.00 0.00 35.23 3.06
4576 8330 2.583441 CCGAGCCTCCACCAAGTGA 61.583 63.158 0.00 0.00 35.23 3.41
4577 8331 2.046892 CCGAGCCTCCACCAAGTG 60.047 66.667 0.00 0.00 0.00 3.16
4578 8332 4.021925 GCCGAGCCTCCACCAAGT 62.022 66.667 0.00 0.00 0.00 3.16
4579 8333 3.259633 AAGCCGAGCCTCCACCAAG 62.260 63.158 0.00 0.00 0.00 3.61
4606 8360 2.100631 CCTCAACCATGGTCGCGAC 61.101 63.158 30.67 30.67 0.00 5.19
4609 8363 3.499737 CGCCTCAACCATGGTCGC 61.500 66.667 20.07 15.94 0.00 5.19
4610 8364 2.819595 CCGCCTCAACCATGGTCG 60.820 66.667 20.07 16.65 0.00 4.79
4623 8377 4.759205 ACAATTCCTGGGGCCGCC 62.759 66.667 18.45 10.45 0.00 6.13
4628 8382 1.019278 CACGTCGACAATTCCTGGGG 61.019 60.000 17.16 0.00 0.00 4.96
4632 8386 1.792006 GGTTCACGTCGACAATTCCT 58.208 50.000 17.16 0.00 0.00 3.36
4633 8387 0.437295 CGGTTCACGTCGACAATTCC 59.563 55.000 17.16 9.64 37.93 3.01
4635 8389 0.947180 CCCGGTTCACGTCGACAATT 60.947 55.000 17.16 0.00 42.24 2.32
4683 8446 4.681978 GCGGAGTTGCCTCACGGT 62.682 66.667 0.00 0.00 39.64 4.83
4686 8449 3.112709 GACGCGGAGTTGCCTCAC 61.113 66.667 12.47 0.00 39.64 3.51
4692 8455 2.043411 CATTTTGTTGACGCGGAGTTG 58.957 47.619 12.47 0.00 0.00 3.16
4694 8457 0.040425 GCATTTTGTTGACGCGGAGT 60.040 50.000 12.47 0.00 0.00 3.85
4696 8459 1.082431 CGCATTTTGTTGACGCGGA 60.082 52.632 12.47 0.00 42.13 5.54
4699 8462 0.040425 AGACCGCATTTTGTTGACGC 60.040 50.000 0.00 0.00 0.00 5.19
4701 8464 2.724839 CGCTAGACCGCATTTTGTTGAC 60.725 50.000 0.00 0.00 0.00 3.18
4702 8465 1.463056 CGCTAGACCGCATTTTGTTGA 59.537 47.619 0.00 0.00 0.00 3.18
4703 8466 1.465689 CCGCTAGACCGCATTTTGTTG 60.466 52.381 0.00 0.00 0.00 3.33
4705 8468 1.644786 GCCGCTAGACCGCATTTTGT 61.645 55.000 0.00 0.00 0.00 2.83
4706 8469 1.062525 GCCGCTAGACCGCATTTTG 59.937 57.895 0.00 0.00 0.00 2.44
4707 8470 1.078426 AGCCGCTAGACCGCATTTT 60.078 52.632 0.00 0.00 0.00 1.82
4708 8471 1.815421 CAGCCGCTAGACCGCATTT 60.815 57.895 0.00 0.00 0.00 2.32
4709 8472 2.202932 CAGCCGCTAGACCGCATT 60.203 61.111 0.00 0.00 0.00 3.56
4711 8474 3.826754 CTCAGCCGCTAGACCGCA 61.827 66.667 0.00 0.00 0.00 5.69
4712 8475 4.577246 CCTCAGCCGCTAGACCGC 62.577 72.222 0.00 0.00 0.00 5.68
4713 8476 2.196925 ATCCTCAGCCGCTAGACCG 61.197 63.158 0.00 0.00 0.00 4.79
4714 8477 1.109920 TCATCCTCAGCCGCTAGACC 61.110 60.000 0.00 0.00 0.00 3.85
4715 8478 0.313672 CTCATCCTCAGCCGCTAGAC 59.686 60.000 0.00 0.00 0.00 2.59
4717 8480 0.825425 TCCTCATCCTCAGCCGCTAG 60.825 60.000 0.00 0.00 0.00 3.42
4718 8481 0.825425 CTCCTCATCCTCAGCCGCTA 60.825 60.000 0.00 0.00 0.00 4.26
4719 8482 2.042537 TCCTCATCCTCAGCCGCT 60.043 61.111 0.00 0.00 0.00 5.52
4720 8483 2.420890 CTCCTCATCCTCAGCCGC 59.579 66.667 0.00 0.00 0.00 6.53
4722 8485 1.417288 ATGCCTCCTCATCCTCAGCC 61.417 60.000 0.00 0.00 0.00 4.85
4723 8486 0.035176 GATGCCTCCTCATCCTCAGC 59.965 60.000 0.00 0.00 37.47 4.26
4732 8509 0.679002 TGCTGCTTTGATGCCTCCTC 60.679 55.000 0.00 0.00 0.00 3.71
4742 8519 0.792640 ATCTTCGTCGTGCTGCTTTG 59.207 50.000 0.00 0.00 0.00 2.77
4743 8520 0.792640 CATCTTCGTCGTGCTGCTTT 59.207 50.000 0.00 0.00 0.00 3.51
4758 8535 2.268076 GCCACCGTGGTTTGCATCT 61.268 57.895 18.95 0.00 40.46 2.90
4786 8563 3.827898 GACGGTCCAGCCTCCTCG 61.828 72.222 0.00 0.00 34.25 4.63
4789 8566 3.775654 CCAGACGGTCCAGCCTCC 61.776 72.222 4.14 0.00 34.25 4.30
4821 8598 2.606378 ACTCTTTGTCGGAGGTAAGGT 58.394 47.619 0.00 0.00 35.34 3.50


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

AutoCloner maintained by Alex Coulton.