Multiple sequence alignment - TraesCS1A01G106200

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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 TraesCS1A01G106200 chr1A 100.000 6392 0 0 1 6392 103637401 103631010 0.000000e+00 11804.0
1 TraesCS1A01G106200 chr1A 95.349 43 0 2 1477 1517 380957969 380958011 4.140000e-07 67.6
2 TraesCS1A01G106200 chr1B 95.502 4936 128 36 1476 6392 150063718 150058858 0.000000e+00 7799.0
3 TraesCS1A01G106200 chr1B 91.226 718 33 16 752 1466 150064484 150063794 0.000000e+00 950.0
4 TraesCS1A01G106200 chr1B 95.349 43 0 2 1477 1517 410804721 410804763 4.140000e-07 67.6
5 TraesCS1A01G106200 chr1D 96.994 4225 89 22 2179 6392 101579940 101575743 0.000000e+00 7064.0
6 TraesCS1A01G106200 chr1D 92.936 1274 36 11 935 2192 101581211 101579976 0.000000e+00 1805.0
7 TraesCS1A01G106200 chr1D 85.426 693 55 20 1 663 101582414 101581738 0.000000e+00 678.0
8 TraesCS1A01G106200 chr1D 91.667 60 3 2 825 882 101581324 101581265 1.480000e-11 82.4
9 TraesCS1A01G106200 chr1D 95.349 43 0 2 1477 1517 303325604 303325646 4.140000e-07 67.6
10 TraesCS1A01G106200 chr4B 86.755 453 50 5 5639 6085 630376379 630375931 4.450000e-136 496.0
11 TraesCS1A01G106200 chr4B 95.522 67 3 0 6325 6391 630428564 630428498 2.440000e-19 108.0
12 TraesCS1A01G106200 chr5A 95.522 67 3 0 6325 6391 672416360 672416426 2.440000e-19 108.0
13 TraesCS1A01G106200 chr6B 80.374 107 16 5 82 184 579937594 579937699 6.870000e-10 76.8
14 TraesCS1A01G106200 chr3A 95.652 46 0 2 1476 1520 137579600 137579556 8.890000e-09 73.1
15 TraesCS1A01G106200 chr3D 95.455 44 0 2 1476 1518 126949086 126949044 1.150000e-07 69.4
16 TraesCS1A01G106200 chr3B 95.455 44 0 2 1476 1518 181288851 181288809 1.150000e-07 69.4
17 TraesCS1A01G106200 chr6D 95.349 43 0 2 1476 1517 55924952 55924911 4.140000e-07 67.6


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 TraesCS1A01G106200 chr1A 103631010 103637401 6391 True 11804.00 11804 100.00000 1 6392 1 chr1A.!!$R1 6391
1 TraesCS1A01G106200 chr1B 150058858 150064484 5626 True 4374.50 7799 93.36400 752 6392 2 chr1B.!!$R1 5640
2 TraesCS1A01G106200 chr1D 101575743 101582414 6671 True 2407.35 7064 91.75575 1 6392 4 chr1D.!!$R1 6391

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
668 697 0.037697 CGAAAGATCACGGGGTGTCA 60.038 55.000 0.00 0.0 34.79 3.58 F
675 704 0.179067 TCACGGGGTGTCAACAACTC 60.179 55.000 0.00 0.0 34.79 3.01 F
676 705 0.462937 CACGGGGTGTCAACAACTCA 60.463 55.000 0.00 0.0 32.28 3.41 F
677 706 0.463116 ACGGGGTGTCAACAACTCAC 60.463 55.000 0.00 0.0 32.28 3.51 F
2368 2810 0.815213 TCGTGTTGCAAAGCTGAGCT 60.815 50.000 0.00 0.0 42.56 4.09 F
3269 3721 2.821437 AGTGTAGCACTCACTACCCAT 58.179 47.619 6.66 0.0 41.21 4.00 F
4817 5272 0.244721 AGCAATTTCTTTCCAGCGGC 59.755 50.000 0.00 0.0 0.00 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1716 2101 0.665835 CTCTAACGCCTCGAGCTGAT 59.334 55.000 6.99 0.00 40.39 2.90 R
2623 3066 1.344763 ACATTAGCTACATCTCCCCGC 59.655 52.381 0.00 0.00 0.00 6.13 R
2624 3067 3.753294 AACATTAGCTACATCTCCCCG 57.247 47.619 0.00 0.00 0.00 5.73 R
2758 3210 5.832539 AATCGATGGGACCTATCTGAAAT 57.167 39.130 15.20 6.09 0.00 2.17 R
3344 3796 4.479425 AGAGGGTCCTTCTAGCTAACTACT 59.521 45.833 0.63 0.00 0.00 2.57 R
5226 5683 2.759973 ATCTCTGGGAGCGCCGAA 60.760 61.111 2.29 0.00 33.83 4.30 R
6283 6744 0.322975 GTGCTATGGGATCAGCGGAT 59.677 55.000 0.00 0.00 40.79 4.18 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
29 30 0.740868 ATCGTTGCCATGACACGAGG 60.741 55.000 15.89 3.19 36.26 4.63
30 31 1.374125 CGTTGCCATGACACGAGGA 60.374 57.895 0.00 0.00 0.00 3.71
122 123 2.028130 AGTAAGCCGGAGATCTCAGTG 58.972 52.381 23.85 14.30 0.00 3.66
163 164 3.201290 GCATCATGCGGATATAAGGAGG 58.799 50.000 0.00 0.00 33.95 4.30
250 251 1.071567 CGAAGTCGCCGAAGAAGTCC 61.072 60.000 0.00 0.00 0.00 3.85
252 253 1.521450 AAGTCGCCGAAGAAGTCCGA 61.521 55.000 0.00 0.00 0.00 4.55
260 261 1.827399 GAAGAAGTCCGAGGCCACCA 61.827 60.000 5.01 0.00 0.00 4.17
280 281 1.381872 CCCGACACCCATCTCCTCT 60.382 63.158 0.00 0.00 0.00 3.69
283 284 0.684479 CGACACCCATCTCCTCTGGA 60.684 60.000 0.00 0.00 35.70 3.86
288 289 0.396417 CCCATCTCCTCTGGACGAGT 60.396 60.000 0.00 0.00 38.11 4.18
311 312 2.063979 CCGTCTAGGGCCACCATGA 61.064 63.158 6.18 0.00 40.13 3.07
312 313 1.622607 CCGTCTAGGGCCACCATGAA 61.623 60.000 6.18 0.00 40.13 2.57
313 314 0.179073 CGTCTAGGGCCACCATGAAG 60.179 60.000 6.18 0.00 40.13 3.02
314 315 0.464554 GTCTAGGGCCACCATGAAGC 60.465 60.000 6.18 0.00 40.13 3.86
315 316 0.621571 TCTAGGGCCACCATGAAGCT 60.622 55.000 6.18 0.00 40.13 3.74
316 317 0.179034 CTAGGGCCACCATGAAGCTC 60.179 60.000 6.18 0.00 40.13 4.09
317 318 1.635817 TAGGGCCACCATGAAGCTCC 61.636 60.000 6.18 0.00 40.13 4.70
319 320 2.825836 GCCACCATGAAGCTCCGG 60.826 66.667 0.00 0.00 0.00 5.14
320 321 2.825836 CCACCATGAAGCTCCGGC 60.826 66.667 0.00 0.00 39.06 6.13
323 324 4.161295 CCATGAAGCTCCGGCGGA 62.161 66.667 29.14 29.14 44.37 5.54
407 429 4.227134 CCCGAGTCGCCCCTCATG 62.227 72.222 7.12 0.00 0.00 3.07
427 456 3.841379 GAGCGACGTGGCTGTCACA 62.841 63.158 30.34 0.00 46.36 3.58
458 487 4.825634 TGATCGACCCGACTAGTATTCATT 59.174 41.667 0.00 0.00 39.18 2.57
459 488 4.825546 TCGACCCGACTAGTATTCATTC 57.174 45.455 0.00 0.00 0.00 2.67
460 489 4.201657 TCGACCCGACTAGTATTCATTCA 58.798 43.478 0.00 0.00 0.00 2.57
461 490 4.825634 TCGACCCGACTAGTATTCATTCAT 59.174 41.667 0.00 0.00 0.00 2.57
490 519 7.602517 ATCGTAAATGGTCTTCTTTCTTCAG 57.397 36.000 0.00 0.00 0.00 3.02
551 580 4.884961 AGGGCCTACAAATTAGAGAGAGA 58.115 43.478 2.82 0.00 0.00 3.10
584 613 1.539929 GGGAGAGCGATGTCATTGAGG 60.540 57.143 4.07 0.00 0.00 3.86
666 695 2.358039 TCGAAAGATCACGGGGTGT 58.642 52.632 0.00 0.00 32.60 4.16
667 696 0.245539 TCGAAAGATCACGGGGTGTC 59.754 55.000 0.00 0.00 32.60 3.67
668 697 0.037697 CGAAAGATCACGGGGTGTCA 60.038 55.000 0.00 0.00 34.79 3.58
669 698 1.606994 CGAAAGATCACGGGGTGTCAA 60.607 52.381 0.00 0.00 34.79 3.18
670 699 1.804748 GAAAGATCACGGGGTGTCAAC 59.195 52.381 0.00 0.00 34.79 3.18
671 700 0.762418 AAGATCACGGGGTGTCAACA 59.238 50.000 0.00 0.00 34.79 3.33
672 701 0.762418 AGATCACGGGGTGTCAACAA 59.238 50.000 0.00 0.00 34.79 2.83
673 702 0.872388 GATCACGGGGTGTCAACAAC 59.128 55.000 0.00 0.00 34.79 3.32
674 703 0.472471 ATCACGGGGTGTCAACAACT 59.528 50.000 0.00 0.00 34.79 3.16
675 704 0.179067 TCACGGGGTGTCAACAACTC 60.179 55.000 0.00 0.00 34.79 3.01
676 705 0.462937 CACGGGGTGTCAACAACTCA 60.463 55.000 0.00 0.00 32.28 3.41
677 706 0.463116 ACGGGGTGTCAACAACTCAC 60.463 55.000 0.00 0.00 32.28 3.51
683 712 2.906354 GTGTCAACAACTCACCAGTCT 58.094 47.619 0.00 0.00 29.93 3.24
684 713 4.054780 GTGTCAACAACTCACCAGTCTA 57.945 45.455 0.00 0.00 29.93 2.59
685 714 4.051922 GTGTCAACAACTCACCAGTCTAG 58.948 47.826 0.00 0.00 29.93 2.43
686 715 3.060602 GTCAACAACTCACCAGTCTAGC 58.939 50.000 0.00 0.00 29.93 3.42
687 716 2.698274 TCAACAACTCACCAGTCTAGCA 59.302 45.455 0.00 0.00 29.93 3.49
688 717 3.062763 CAACAACTCACCAGTCTAGCAG 58.937 50.000 0.00 0.00 29.93 4.24
689 718 2.320781 ACAACTCACCAGTCTAGCAGT 58.679 47.619 0.00 0.00 29.93 4.40
690 719 2.036475 ACAACTCACCAGTCTAGCAGTG 59.964 50.000 0.00 0.00 29.93 3.66
691 720 2.294449 ACTCACCAGTCTAGCAGTGA 57.706 50.000 0.00 0.00 37.65 3.41
692 721 2.813907 ACTCACCAGTCTAGCAGTGAT 58.186 47.619 0.00 0.00 38.49 3.06
693 722 3.169099 ACTCACCAGTCTAGCAGTGATT 58.831 45.455 0.00 0.00 38.49 2.57
694 723 3.194542 ACTCACCAGTCTAGCAGTGATTC 59.805 47.826 0.00 0.00 38.49 2.52
695 724 3.435275 TCACCAGTCTAGCAGTGATTCT 58.565 45.455 0.00 0.00 34.44 2.40
696 725 3.445450 TCACCAGTCTAGCAGTGATTCTC 59.555 47.826 0.00 0.00 34.44 2.87
697 726 3.446873 CACCAGTCTAGCAGTGATTCTCT 59.553 47.826 0.00 0.00 31.79 3.10
698 727 3.699038 ACCAGTCTAGCAGTGATTCTCTC 59.301 47.826 0.00 0.00 0.00 3.20
699 728 3.953612 CCAGTCTAGCAGTGATTCTCTCT 59.046 47.826 0.00 0.00 0.00 3.10
700 729 4.036734 CCAGTCTAGCAGTGATTCTCTCTC 59.963 50.000 0.00 0.00 0.00 3.20
701 730 4.883585 CAGTCTAGCAGTGATTCTCTCTCT 59.116 45.833 0.00 0.00 0.00 3.10
702 731 5.008019 CAGTCTAGCAGTGATTCTCTCTCTC 59.992 48.000 0.00 0.00 0.00 3.20
703 732 5.104360 AGTCTAGCAGTGATTCTCTCTCTCT 60.104 44.000 0.00 0.00 0.00 3.10
704 733 5.237344 GTCTAGCAGTGATTCTCTCTCTCTC 59.763 48.000 0.00 0.00 0.00 3.20
705 734 4.240881 AGCAGTGATTCTCTCTCTCTCT 57.759 45.455 0.00 0.00 0.00 3.10
706 735 4.202441 AGCAGTGATTCTCTCTCTCTCTC 58.798 47.826 0.00 0.00 0.00 3.20
707 736 4.080129 AGCAGTGATTCTCTCTCTCTCTCT 60.080 45.833 0.00 0.00 0.00 3.10
708 737 4.274459 GCAGTGATTCTCTCTCTCTCTCTC 59.726 50.000 0.00 0.00 0.00 3.20
709 738 5.678583 CAGTGATTCTCTCTCTCTCTCTCT 58.321 45.833 0.00 0.00 0.00 3.10
710 739 5.757320 CAGTGATTCTCTCTCTCTCTCTCTC 59.243 48.000 0.00 0.00 0.00 3.20
711 740 5.664908 AGTGATTCTCTCTCTCTCTCTCTCT 59.335 44.000 0.00 0.00 0.00 3.10
712 741 5.988561 GTGATTCTCTCTCTCTCTCTCTCTC 59.011 48.000 0.00 0.00 0.00 3.20
713 742 5.901853 TGATTCTCTCTCTCTCTCTCTCTCT 59.098 44.000 0.00 0.00 0.00 3.10
714 743 5.860941 TTCTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
715 744 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
716 745 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
717 746 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
718 747 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
719 748 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
720 749 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
721 750 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
722 751 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
723 752 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
724 753 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
725 754 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
726 755 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
727 756 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
728 757 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
729 758 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
730 759 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
731 760 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
732 761 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
733 762 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
734 763 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
735 764 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
736 765 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
737 766 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
738 767 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
739 768 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
740 769 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
741 770 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
742 771 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
743 772 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
744 773 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
745 774 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
746 775 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
747 776 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
748 777 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
749 778 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
750 779 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
776 805 8.499403 TCTCTCTCTTCATGTCCATATATACG 57.501 38.462 0.00 0.00 0.00 3.06
777 806 7.554476 TCTCTCTCTTCATGTCCATATATACGG 59.446 40.741 0.00 0.00 0.00 4.02
778 807 6.603599 TCTCTCTTCATGTCCATATATACGGG 59.396 42.308 0.00 0.00 0.00 5.28
779 808 6.253758 TCTCTTCATGTCCATATATACGGGT 58.746 40.000 0.00 0.00 0.00 5.28
794 823 3.775654 GGTGCCACTCTCCCCTCG 61.776 72.222 0.00 0.00 0.00 4.63
795 824 2.680352 GTGCCACTCTCCCCTCGA 60.680 66.667 0.00 0.00 0.00 4.04
865 1157 1.073025 GTGTCCATCACCCAGCACA 59.927 57.895 0.00 0.00 40.84 4.57
867 1159 1.073025 GTCCATCACCCAGCACACA 59.927 57.895 0.00 0.00 0.00 3.72
869 1161 1.228215 CCATCACCCAGCACACACA 60.228 57.895 0.00 0.00 0.00 3.72
873 1165 1.893808 CACCCAGCACACACACTCC 60.894 63.158 0.00 0.00 0.00 3.85
882 1174 2.796557 CACACACACTCCCTCTCTCTA 58.203 52.381 0.00 0.00 0.00 2.43
949 1263 3.843619 TCTCTCTCTCTCTCTCTCCACAA 59.156 47.826 0.00 0.00 0.00 3.33
962 1276 1.464608 CTCCACAATTCGACGCATTGT 59.535 47.619 18.18 18.18 44.14 2.71
1021 1335 3.542676 TGGTGCCTTCCACGACGT 61.543 61.111 0.00 0.00 45.62 4.34
1104 1418 1.666553 GACGGTTGACATGTCCGCA 60.667 57.895 22.85 2.21 46.92 5.69
1428 1746 3.179830 CTCACGCTTCAGGTACATACAC 58.820 50.000 0.00 0.00 0.00 2.90
1429 1747 2.559231 TCACGCTTCAGGTACATACACA 59.441 45.455 0.00 0.00 0.00 3.72
1430 1748 2.666508 CACGCTTCAGGTACATACACAC 59.333 50.000 0.00 0.00 0.00 3.82
1431 1749 2.297880 ACGCTTCAGGTACATACACACA 59.702 45.455 0.00 0.00 0.00 3.72
1432 1750 3.056107 ACGCTTCAGGTACATACACACAT 60.056 43.478 0.00 0.00 0.00 3.21
1433 1751 4.158949 ACGCTTCAGGTACATACACACATA 59.841 41.667 0.00 0.00 0.00 2.29
1434 1752 4.503007 CGCTTCAGGTACATACACACATAC 59.497 45.833 0.00 0.00 0.00 2.39
1435 1753 5.416083 GCTTCAGGTACATACACACATACA 58.584 41.667 0.00 0.00 0.00 2.29
1527 1909 2.159226 ACAGAGGAGTACATGCTTACGC 60.159 50.000 0.00 0.00 0.00 4.42
1613 1995 6.531594 GGTTTCTTAATCCTGCAAGCATTAAC 59.468 38.462 0.00 0.00 0.00 2.01
1715 2100 6.808212 GCACGGTTTTACTACATAACAGTCTA 59.192 38.462 0.00 0.00 29.81 2.59
1716 2101 7.329226 GCACGGTTTTACTACATAACAGTCTAA 59.671 37.037 0.00 0.00 29.81 2.10
1855 2248 1.337817 CTCAAGACGTCGACAAGCCG 61.338 60.000 17.16 3.32 0.00 5.52
1866 2259 1.854743 CGACAAGCCGATGTGTAGATG 59.145 52.381 0.00 0.00 32.57 2.90
1972 2365 1.266989 GCAGTGCCACTTAACCAACTC 59.733 52.381 2.85 0.00 0.00 3.01
1973 2366 2.571212 CAGTGCCACTTAACCAACTCA 58.429 47.619 0.00 0.00 0.00 3.41
1974 2367 3.149196 CAGTGCCACTTAACCAACTCAT 58.851 45.455 0.00 0.00 0.00 2.90
1982 2375 5.065218 CCACTTAACCAACTCATGACTATGC 59.935 44.000 0.00 0.00 34.21 3.14
1996 2389 2.086869 ACTATGCTGATGTTGGTGTGC 58.913 47.619 0.00 0.00 0.00 4.57
2018 2411 4.380761 GCATGTGATGTGGTTTGCTTATCA 60.381 41.667 0.00 0.00 0.00 2.15
2019 2412 5.680408 GCATGTGATGTGGTTTGCTTATCAT 60.680 40.000 0.00 0.00 31.28 2.45
2020 2413 6.459985 GCATGTGATGTGGTTTGCTTATCATA 60.460 38.462 0.00 0.00 31.28 2.15
2021 2414 7.482474 CATGTGATGTGGTTTGCTTATCATAA 58.518 34.615 0.00 0.00 31.28 1.90
2022 2415 7.643569 TGTGATGTGGTTTGCTTATCATAAT 57.356 32.000 0.00 0.00 31.28 1.28
2023 2416 8.744568 TGTGATGTGGTTTGCTTATCATAATA 57.255 30.769 0.00 0.00 31.28 0.98
2060 2453 2.171027 CTGCCCCATTTGCATATTGGTT 59.829 45.455 6.53 0.00 38.22 3.67
2061 2454 3.378512 TGCCCCATTTGCATATTGGTTA 58.621 40.909 6.53 0.00 32.85 2.85
2062 2455 3.972638 TGCCCCATTTGCATATTGGTTAT 59.027 39.130 6.53 0.00 32.85 1.89
2063 2456 4.202336 TGCCCCATTTGCATATTGGTTATG 60.202 41.667 6.53 0.00 40.67 1.90
2064 2457 4.040217 GCCCCATTTGCATATTGGTTATGA 59.960 41.667 6.53 0.00 40.22 2.15
2065 2458 5.786311 CCCCATTTGCATATTGGTTATGAG 58.214 41.667 6.53 0.00 40.22 2.90
2066 2459 5.279607 CCCCATTTGCATATTGGTTATGAGG 60.280 44.000 6.53 0.00 40.22 3.86
2067 2460 5.305128 CCCATTTGCATATTGGTTATGAGGT 59.695 40.000 8.70 0.00 40.22 3.85
2068 2461 6.183360 CCCATTTGCATATTGGTTATGAGGTT 60.183 38.462 8.70 0.00 40.22 3.50
2069 2462 7.015098 CCCATTTGCATATTGGTTATGAGGTTA 59.985 37.037 8.70 0.00 40.22 2.85
2070 2463 8.084073 CCATTTGCATATTGGTTATGAGGTTAG 58.916 37.037 0.00 0.00 40.22 2.34
2071 2464 6.633500 TTGCATATTGGTTATGAGGTTAGC 57.367 37.500 0.00 0.00 40.22 3.09
2072 2465 5.940617 TGCATATTGGTTATGAGGTTAGCT 58.059 37.500 0.00 0.00 40.22 3.32
2073 2466 7.073457 TGCATATTGGTTATGAGGTTAGCTA 57.927 36.000 0.00 0.00 40.22 3.32
2074 2467 7.161404 TGCATATTGGTTATGAGGTTAGCTAG 58.839 38.462 0.00 0.00 40.22 3.42
2075 2468 6.092807 GCATATTGGTTATGAGGTTAGCTAGC 59.907 42.308 6.62 6.62 40.22 3.42
2176 2569 2.828520 AGAGAGGTGATATATGTGGGCG 59.171 50.000 0.00 0.00 0.00 6.13
2212 2654 4.201851 CGATTTATTTGTGAGGCAGGACTG 60.202 45.833 0.00 0.00 0.00 3.51
2281 2723 1.707632 CACAGAGGACTTTCTGCTCG 58.292 55.000 3.10 0.00 46.77 5.03
2302 2744 2.350772 GGTACAATGCTGTCTTGTGCAC 60.351 50.000 10.75 10.75 42.26 4.57
2368 2810 0.815213 TCGTGTTGCAAAGCTGAGCT 60.815 50.000 0.00 0.00 42.56 4.09
2444 2886 4.151512 TGTTGTGATGCACTACATGTTACG 59.848 41.667 2.30 0.00 42.80 3.18
2518 2960 9.466497 AATATAATTCAAGCCAAAGTGAGAGAA 57.534 29.630 0.00 0.00 0.00 2.87
2614 3057 6.992063 AACTCCAAACAGATGTAGCTAATG 57.008 37.500 0.00 0.00 0.00 1.90
2616 3059 6.476378 ACTCCAAACAGATGTAGCTAATGTT 58.524 36.000 0.00 2.13 35.70 2.71
2735 3184 8.681806 TGTTTTCAGTTCATGACAGAATTAACA 58.318 29.630 0.00 6.11 37.77 2.41
2758 3210 8.851541 ACATCAATATGCACACATATGTATCA 57.148 30.769 8.32 7.14 46.58 2.15
2759 3211 9.457436 ACATCAATATGCACACATATGTATCAT 57.543 29.630 8.32 13.43 46.58 2.45
2818 3270 3.734463 TGAGCACATAGTTTCCGAAACA 58.266 40.909 22.84 11.33 43.79 2.83
3031 3483 9.263446 AGAGTTGTCTAACCCTATACAAACATA 57.737 33.333 0.00 0.00 37.52 2.29
3269 3721 2.821437 AGTGTAGCACTCACTACCCAT 58.179 47.619 6.66 0.00 41.21 4.00
3323 3775 7.121382 TGAGAGCAAAATAAGATGAAAGGGAT 58.879 34.615 0.00 0.00 0.00 3.85
3342 3794 6.663734 AGGGATAATAAAACACTCTCTTGGG 58.336 40.000 0.00 0.00 0.00 4.12
3343 3795 6.217693 AGGGATAATAAAACACTCTCTTGGGT 59.782 38.462 0.00 0.00 0.00 4.51
3344 3796 7.404980 AGGGATAATAAAACACTCTCTTGGGTA 59.595 37.037 0.00 0.00 0.00 3.69
3594 4046 6.881065 AGACAATGATGTATATGCATGTACCC 59.119 38.462 25.31 18.58 40.74 3.69
4493 4947 2.932234 CGGGTTCGGTGAGCACTCT 61.932 63.158 0.16 0.00 0.00 3.24
4732 5187 8.161425 TGCTTATAGGAACTGTTAAAGAAAGGT 58.839 33.333 0.00 0.00 41.52 3.50
4779 5234 4.785914 TCTGGGACCAACCATAAATACTCA 59.214 41.667 0.00 0.00 40.36 3.41
4817 5272 0.244721 AGCAATTTCTTTCCAGCGGC 59.755 50.000 0.00 0.00 0.00 6.53
4837 5292 5.926542 GCGGCTCATATGAACAGATTACTTA 59.073 40.000 10.01 0.00 0.00 2.24
4838 5293 6.591834 GCGGCTCATATGAACAGATTACTTAT 59.408 38.462 10.01 0.00 0.00 1.73
4916 5373 4.318332 TGTCTGATTGGACACTCATGTTC 58.682 43.478 0.00 0.00 39.95 3.18
5064 5521 4.848357 AGCCTAACAGCACAAATCACTAT 58.152 39.130 0.00 0.00 34.23 2.12
5067 5524 5.355350 GCCTAACAGCACAAATCACTATTCT 59.645 40.000 0.00 0.00 0.00 2.40
5226 5683 0.241749 CACCACTGCATGCACGAATT 59.758 50.000 18.46 0.00 0.00 2.17
5255 5712 1.607801 CCAGAGATGGTCACAGCCGA 61.608 60.000 0.00 0.00 32.15 5.54
5492 5949 3.036819 TCTCTGACAGCTATTGCCAGAT 58.963 45.455 6.95 0.00 40.80 2.90
5551 6008 3.434167 CCATGACCTGGCTAGCTTTGTAT 60.434 47.826 15.72 0.12 38.47 2.29
5759 6216 0.671781 ACAGAGGCAGCAATGTCGAC 60.672 55.000 9.11 9.11 0.00 4.20
5847 6304 4.321745 CAGCAGCGCACAAATTTAACTAAG 59.678 41.667 11.47 0.00 0.00 2.18
6024 6482 6.662414 TTGTGCAGTACTTACTATTCATGC 57.338 37.500 0.00 0.00 34.13 4.06
6111 6569 3.242870 GCAAACAGTCTGACAAGGTTCAG 60.243 47.826 10.88 8.62 43.93 3.02
6254 6715 3.416156 GAGAGTGTGCAAGGGAGAAATT 58.584 45.455 0.00 0.00 0.00 1.82
6265 6726 4.982241 AGGGAGAAATTCTTCACTGACA 57.018 40.909 3.40 0.00 33.64 3.58
6283 6744 1.159285 CAAAGGCATCGAAGAGCACA 58.841 50.000 9.57 0.00 43.63 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.097674 GTGTCATGGCAACGATCTGC 59.902 55.000 0.00 0.00 41.85 4.26
7 8 0.371301 CGTGTCATGGCAACGATCTG 59.629 55.000 14.43 0.00 42.51 2.90
13 14 1.197721 CTTTCCTCGTGTCATGGCAAC 59.802 52.381 0.00 0.00 0.00 4.17
21 22 1.544691 TCCTAGTGCTTTCCTCGTGTC 59.455 52.381 0.00 0.00 0.00 3.67
29 30 0.460459 GAGGCGGTCCTAGTGCTTTC 60.460 60.000 0.00 0.00 44.46 2.62
30 31 1.597461 GAGGCGGTCCTAGTGCTTT 59.403 57.895 0.00 0.00 44.46 3.51
101 102 3.215151 CACTGAGATCTCCGGCTTACTA 58.785 50.000 20.03 0.00 0.00 1.82
142 143 3.201290 CCTCCTTATATCCGCATGATGC 58.799 50.000 7.49 7.49 40.69 3.91
145 146 3.506398 TCACCTCCTTATATCCGCATGA 58.494 45.455 0.00 0.00 0.00 3.07
152 153 1.618837 TGCGGCTCACCTCCTTATATC 59.381 52.381 0.00 0.00 0.00 1.63
154 155 0.750850 GTGCGGCTCACCTCCTTATA 59.249 55.000 0.00 0.00 39.79 0.98
219 220 3.575351 GACTTCGGCTGTCGGCTGT 62.575 63.158 12.30 0.00 46.74 4.40
240 241 1.446272 GTGGCCTCGGACTTCTTCG 60.446 63.158 3.32 0.00 0.00 3.79
260 261 2.687566 GGAGATGGGTGTCGGGGT 60.688 66.667 0.00 0.00 0.00 4.95
264 265 0.684479 TCCAGAGGAGATGGGTGTCG 60.684 60.000 0.00 0.00 38.44 4.35
266 267 0.972983 CGTCCAGAGGAGATGGGTGT 60.973 60.000 0.00 0.00 38.44 4.16
267 268 0.684479 TCGTCCAGAGGAGATGGGTG 60.684 60.000 0.00 0.00 38.44 4.61
268 269 0.396417 CTCGTCCAGAGGAGATGGGT 60.396 60.000 11.08 0.00 43.80 4.51
269 270 2.424474 CTCGTCCAGAGGAGATGGG 58.576 63.158 11.08 0.00 43.80 4.00
283 284 3.862402 CTAGACGGCGCGACTCGT 61.862 66.667 12.10 16.66 42.67 4.18
298 299 1.635817 GGAGCTTCATGGTGGCCCTA 61.636 60.000 0.00 0.00 0.00 3.53
335 336 2.881352 CTTCGAAGGACGCCTCGC 60.881 66.667 17.70 0.00 42.26 5.03
371 393 1.439644 CGGAAGACTAGAGCAGCCC 59.560 63.158 0.00 0.00 0.00 5.19
405 427 4.457496 CAGCCACGTCGCTCCCAT 62.457 66.667 4.12 0.00 36.82 4.00
490 519 4.244862 CAGAAATGGGTTGTGTTTATGGC 58.755 43.478 0.00 0.00 0.00 4.40
551 580 1.662686 CTCTCCCTTCCCCTCTGTTT 58.337 55.000 0.00 0.00 0.00 2.83
584 613 8.279103 GTCATGAGCTTAATTGTCTATGCTTAC 58.721 37.037 0.00 0.00 33.68 2.34
647 676 0.902531 ACACCCCGTGATCTTTCGAT 59.097 50.000 0.00 0.00 36.96 3.59
663 692 2.906354 AGACTGGTGAGTTGTTGACAC 58.094 47.619 0.00 0.00 30.16 3.67
664 693 3.492656 GCTAGACTGGTGAGTTGTTGACA 60.493 47.826 0.00 0.00 30.16 3.58
665 694 3.060602 GCTAGACTGGTGAGTTGTTGAC 58.939 50.000 0.00 0.00 30.16 3.18
666 695 2.698274 TGCTAGACTGGTGAGTTGTTGA 59.302 45.455 0.00 0.00 30.16 3.18
667 696 3.062763 CTGCTAGACTGGTGAGTTGTTG 58.937 50.000 0.00 0.00 30.16 3.33
668 697 2.700897 ACTGCTAGACTGGTGAGTTGTT 59.299 45.455 0.00 0.00 30.16 2.83
669 698 2.036475 CACTGCTAGACTGGTGAGTTGT 59.964 50.000 0.00 0.00 30.16 3.32
670 699 2.297315 TCACTGCTAGACTGGTGAGTTG 59.703 50.000 0.00 0.00 34.38 3.16
671 700 2.598565 TCACTGCTAGACTGGTGAGTT 58.401 47.619 0.00 0.00 34.38 3.01
672 701 2.294449 TCACTGCTAGACTGGTGAGT 57.706 50.000 0.00 0.00 34.38 3.41
673 702 3.446873 AGAATCACTGCTAGACTGGTGAG 59.553 47.826 0.00 0.00 41.11 3.51
674 703 3.435275 AGAATCACTGCTAGACTGGTGA 58.565 45.455 0.00 2.06 41.84 4.02
675 704 3.446873 AGAGAATCACTGCTAGACTGGTG 59.553 47.826 0.00 0.00 37.82 4.17
676 705 3.699038 GAGAGAATCACTGCTAGACTGGT 59.301 47.826 0.00 0.00 37.82 4.00
677 706 3.953612 AGAGAGAATCACTGCTAGACTGG 59.046 47.826 0.00 0.00 33.77 4.00
678 707 4.883585 AGAGAGAGAATCACTGCTAGACTG 59.116 45.833 0.00 0.00 35.72 3.51
679 708 5.104360 AGAGAGAGAGAATCACTGCTAGACT 60.104 44.000 0.00 0.00 35.72 3.24
680 709 5.126067 AGAGAGAGAGAATCACTGCTAGAC 58.874 45.833 0.00 0.00 35.72 2.59
681 710 5.130975 AGAGAGAGAGAGAATCACTGCTAGA 59.869 44.000 0.00 0.00 35.72 2.43
682 711 5.371526 AGAGAGAGAGAGAATCACTGCTAG 58.628 45.833 0.00 0.00 35.72 3.42
683 712 5.130975 AGAGAGAGAGAGAGAATCACTGCTA 59.869 44.000 0.00 0.00 35.72 3.49
684 713 4.080129 AGAGAGAGAGAGAGAATCACTGCT 60.080 45.833 0.00 0.00 35.72 4.24
685 714 4.202441 AGAGAGAGAGAGAGAATCACTGC 58.798 47.826 0.00 0.00 35.72 4.40
686 715 5.678583 AGAGAGAGAGAGAGAGAATCACTG 58.321 45.833 0.00 0.00 35.72 3.66
687 716 5.664908 AGAGAGAGAGAGAGAGAGAATCACT 59.335 44.000 0.00 0.00 39.29 3.41
688 717 5.923204 AGAGAGAGAGAGAGAGAGAATCAC 58.077 45.833 0.00 0.00 37.82 3.06
689 718 5.901853 AGAGAGAGAGAGAGAGAGAGAATCA 59.098 44.000 0.00 0.00 37.82 2.57
690 719 6.267471 AGAGAGAGAGAGAGAGAGAGAGAATC 59.733 46.154 0.00 0.00 0.00 2.52
691 720 6.142498 AGAGAGAGAGAGAGAGAGAGAGAAT 58.858 44.000 0.00 0.00 0.00 2.40
692 721 5.523588 AGAGAGAGAGAGAGAGAGAGAGAA 58.476 45.833 0.00 0.00 0.00 2.87
693 722 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
694 723 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
695 724 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
696 725 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
697 726 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
698 727 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
699 728 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
700 729 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
701 730 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
702 731 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
703 732 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
704 733 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
705 734 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
706 735 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
707 736 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
708 737 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
709 738 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
710 739 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
711 740 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
712 741 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
713 742 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
714 743 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
715 744 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
716 745 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
717 746 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
718 747 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
719 748 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
720 749 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
721 750 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
722 751 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
723 752 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
724 753 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
725 754 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
726 755 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
727 756 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
728 757 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
729 758 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
730 759 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
731 760 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
732 761 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
733 762 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
734 763 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
735 764 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
736 765 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
737 766 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
738 767 5.362143 TGAAGAGAGAGAGAGAGAGAGAGAG 59.638 48.000 0.00 0.00 0.00 3.20
739 768 5.272402 TGAAGAGAGAGAGAGAGAGAGAGA 58.728 45.833 0.00 0.00 0.00 3.10
740 769 5.604758 TGAAGAGAGAGAGAGAGAGAGAG 57.395 47.826 0.00 0.00 0.00 3.20
741 770 5.426509 ACATGAAGAGAGAGAGAGAGAGAGA 59.573 44.000 0.00 0.00 0.00 3.10
742 771 5.678583 ACATGAAGAGAGAGAGAGAGAGAG 58.321 45.833 0.00 0.00 0.00 3.20
743 772 5.396772 GGACATGAAGAGAGAGAGAGAGAGA 60.397 48.000 0.00 0.00 0.00 3.10
744 773 4.818546 GGACATGAAGAGAGAGAGAGAGAG 59.181 50.000 0.00 0.00 0.00 3.20
745 774 4.227073 TGGACATGAAGAGAGAGAGAGAGA 59.773 45.833 0.00 0.00 0.00 3.10
746 775 4.525996 TGGACATGAAGAGAGAGAGAGAG 58.474 47.826 0.00 0.00 0.00 3.20
747 776 4.582973 TGGACATGAAGAGAGAGAGAGA 57.417 45.455 0.00 0.00 0.00 3.10
748 777 8.812513 ATATATGGACATGAAGAGAGAGAGAG 57.187 38.462 0.00 0.00 0.00 3.20
749 778 9.679661 GTATATATGGACATGAAGAGAGAGAGA 57.320 37.037 0.00 0.00 0.00 3.10
750 779 8.611757 CGTATATATGGACATGAAGAGAGAGAG 58.388 40.741 0.00 0.00 0.00 3.20
776 805 3.403558 GAGGGGAGAGTGGCACCC 61.404 72.222 15.27 8.32 45.86 4.61
777 806 3.775654 CGAGGGGAGAGTGGCACC 61.776 72.222 15.27 5.99 0.00 5.01
778 807 2.680352 TCGAGGGGAGAGTGGCAC 60.680 66.667 10.29 10.29 0.00 5.01
779 808 2.363018 CTCGAGGGGAGAGTGGCA 60.363 66.667 3.91 0.00 46.23 4.92
810 1102 4.024048 GGAGTTGTGTCATTTGTGTGTAGG 60.024 45.833 0.00 0.00 0.00 3.18
811 1103 4.024048 GGGAGTTGTGTCATTTGTGTGTAG 60.024 45.833 0.00 0.00 0.00 2.74
812 1104 3.880490 GGGAGTTGTGTCATTTGTGTGTA 59.120 43.478 0.00 0.00 0.00 2.90
818 1110 2.227388 GAGCTGGGAGTTGTGTCATTTG 59.773 50.000 0.00 0.00 0.00 2.32
819 1111 2.508526 GAGCTGGGAGTTGTGTCATTT 58.491 47.619 0.00 0.00 0.00 2.32
820 1112 1.609061 CGAGCTGGGAGTTGTGTCATT 60.609 52.381 0.00 0.00 0.00 2.57
821 1113 0.036952 CGAGCTGGGAGTTGTGTCAT 60.037 55.000 0.00 0.00 0.00 3.06
822 1114 1.112916 TCGAGCTGGGAGTTGTGTCA 61.113 55.000 0.00 0.00 0.00 3.58
823 1115 0.247736 ATCGAGCTGGGAGTTGTGTC 59.752 55.000 0.00 0.00 0.00 3.67
912 1226 0.039074 AGAGAGTATGCGCCGTATGC 60.039 55.000 4.18 0.00 0.00 3.14
913 1227 1.537638 AGAGAGAGTATGCGCCGTATG 59.462 52.381 4.18 0.00 0.00 2.39
914 1228 1.807742 GAGAGAGAGTATGCGCCGTAT 59.192 52.381 4.18 0.00 0.00 3.06
915 1229 1.202663 AGAGAGAGAGTATGCGCCGTA 60.203 52.381 4.18 0.00 0.00 4.02
916 1230 0.464735 AGAGAGAGAGTATGCGCCGT 60.465 55.000 4.18 0.00 0.00 5.68
917 1231 0.237235 GAGAGAGAGAGTATGCGCCG 59.763 60.000 4.18 0.00 0.00 6.46
918 1232 1.535462 GAGAGAGAGAGAGTATGCGCC 59.465 57.143 4.18 0.00 0.00 6.53
919 1233 2.480419 GAGAGAGAGAGAGAGTATGCGC 59.520 54.545 0.00 0.00 0.00 6.09
949 1263 2.217847 GTGCGTATACAATGCGTCGAAT 59.782 45.455 3.32 0.00 43.57 3.34
988 1302 2.741985 CACCATCGCGTTGGCTCA 60.742 61.111 31.08 0.00 40.68 4.26
1150 1464 1.003233 GGAAGAAGCCTTGCTCCGT 60.003 57.895 0.00 0.00 38.25 4.69
1527 1909 1.266718 GTGGTATGTGTGTGCCTTGTG 59.733 52.381 0.00 0.00 0.00 3.33
1613 1995 8.647143 AGTATGTTTCATGTTTGAAGGTTTTG 57.353 30.769 0.00 0.00 42.60 2.44
1715 2100 1.066303 CTCTAACGCCTCGAGCTGATT 59.934 52.381 6.99 0.85 40.39 2.57
1716 2101 0.665835 CTCTAACGCCTCGAGCTGAT 59.334 55.000 6.99 0.00 40.39 2.90
1732 2117 4.985538 ACACTGTCTTTCTCTCTCTCTCT 58.014 43.478 0.00 0.00 0.00 3.10
1733 2118 4.759693 TGACACTGTCTTTCTCTCTCTCTC 59.240 45.833 10.54 0.00 33.15 3.20
1734 2119 4.518970 GTGACACTGTCTTTCTCTCTCTCT 59.481 45.833 10.54 0.00 33.15 3.10
1735 2120 4.518970 AGTGACACTGTCTTTCTCTCTCTC 59.481 45.833 7.47 0.00 33.15 3.20
1855 2248 5.294356 TGTATAAACGCCCATCTACACATC 58.706 41.667 0.00 0.00 0.00 3.06
1866 2259 1.666700 TCAACGCATGTATAAACGCCC 59.333 47.619 0.00 0.00 0.00 6.13
1894 2287 4.079090 GTCACATCTGACGCCTCG 57.921 61.111 0.00 0.00 37.67 4.63
1938 2331 1.731160 GCACTGCTGCTAGCTATATGC 59.269 52.381 17.23 14.77 42.97 3.14
1972 2365 3.943381 ACACCAACATCAGCATAGTCATG 59.057 43.478 0.00 0.00 35.07 3.07
1973 2366 3.943381 CACACCAACATCAGCATAGTCAT 59.057 43.478 0.00 0.00 0.00 3.06
1974 2367 3.337358 CACACCAACATCAGCATAGTCA 58.663 45.455 0.00 0.00 0.00 3.41
1982 2375 1.881324 TCACATGCACACCAACATCAG 59.119 47.619 0.00 0.00 0.00 2.90
1996 2389 5.313520 TGATAAGCAAACCACATCACATG 57.686 39.130 0.00 0.00 0.00 3.21
2018 2411 7.069344 GGCAGGCCCAGGATTATTATTATTAT 58.931 38.462 0.00 0.00 0.00 1.28
2019 2412 6.431722 GGCAGGCCCAGGATTATTATTATTA 58.568 40.000 0.00 0.00 0.00 0.98
2020 2413 5.272402 GGCAGGCCCAGGATTATTATTATT 58.728 41.667 0.00 0.00 0.00 1.40
2021 2414 4.871822 GGCAGGCCCAGGATTATTATTAT 58.128 43.478 0.00 0.00 0.00 1.28
2022 2415 4.316025 GGCAGGCCCAGGATTATTATTA 57.684 45.455 0.00 0.00 0.00 0.98
2023 2416 3.175438 GGCAGGCCCAGGATTATTATT 57.825 47.619 0.00 0.00 0.00 1.40
2049 2442 5.940617 AGCTAACCTCATAACCAATATGCA 58.059 37.500 0.00 0.00 41.08 3.96
2071 2464 8.637986 CAAATCTATTAGGGGATAGCTAGCTAG 58.362 40.741 27.42 16.84 31.15 3.42
2072 2465 7.565398 CCAAATCTATTAGGGGATAGCTAGCTA 59.435 40.741 26.09 26.09 31.15 3.32
2073 2466 6.385467 CCAAATCTATTAGGGGATAGCTAGCT 59.615 42.308 23.12 23.12 31.15 3.32
2074 2467 6.384305 TCCAAATCTATTAGGGGATAGCTAGC 59.616 42.308 6.62 6.62 31.15 3.42
2075 2468 7.979786 TCCAAATCTATTAGGGGATAGCTAG 57.020 40.000 0.00 0.00 31.15 3.42
2092 2485 8.398665 GTTGACTGTAACCATATCTTCCAAATC 58.601 37.037 0.00 0.00 0.00 2.17
2176 2569 2.325583 TAAATCGGTCCATGCCTGAC 57.674 50.000 0.00 0.00 0.00 3.51
2212 2654 2.033294 GCCATGCCCTAGCTAGCC 59.967 66.667 15.74 8.77 40.80 3.93
2281 2723 1.879380 TGCACAAGACAGCATTGTACC 59.121 47.619 0.00 0.00 38.80 3.34
2444 2886 3.067106 TCGTCCTTGAAAGAATCTGTGC 58.933 45.455 0.00 0.00 0.00 4.57
2552 2995 2.611751 TCATTCAACAACTGTCCACGTG 59.388 45.455 9.08 9.08 0.00 4.49
2620 3063 1.491668 TAGCTACATCTCCCCGCAAA 58.508 50.000 0.00 0.00 0.00 3.68
2623 3066 1.344763 ACATTAGCTACATCTCCCCGC 59.655 52.381 0.00 0.00 0.00 6.13
2624 3067 3.753294 AACATTAGCTACATCTCCCCG 57.247 47.619 0.00 0.00 0.00 5.73
2758 3210 5.832539 AATCGATGGGACCTATCTGAAAT 57.167 39.130 15.20 6.09 0.00 2.17
2759 3211 6.740944 TTAATCGATGGGACCTATCTGAAA 57.259 37.500 15.20 5.02 0.00 2.69
3031 3483 6.560003 ATTTTCCTGTGTTTTCCTTTTCCT 57.440 33.333 0.00 0.00 0.00 3.36
3104 3556 4.044065 ACCAGGGACAAATGTATCTTTCCA 59.956 41.667 0.00 0.00 0.00 3.53
3269 3721 5.663106 ACTCTGATTAGGCCACTTTCTGATA 59.337 40.000 5.01 0.00 0.00 2.15
3323 3775 9.317827 ACTACTACCCAAGAGAGTGTTTTATTA 57.682 33.333 0.00 0.00 0.00 0.98
3342 3794 5.693961 AGGGTCCTTCTAGCTAACTACTAC 58.306 45.833 0.00 0.00 0.00 2.73
3343 3795 5.671276 AGAGGGTCCTTCTAGCTAACTACTA 59.329 44.000 0.63 0.00 0.00 1.82
3344 3796 4.479425 AGAGGGTCCTTCTAGCTAACTACT 59.521 45.833 0.63 0.00 0.00 2.57
3791 4243 7.721409 TTTATGTTACCATAAAAAGGACCCC 57.279 36.000 3.19 0.00 45.81 4.95
4732 5187 8.637986 AGATCAATGCCTTTAACAGTTTGTTTA 58.362 29.630 0.00 0.00 41.45 2.01
4916 5373 6.540914 TGGAGTGTCTTGGTAAACTAGTTTTG 59.459 38.462 25.07 11.13 34.23 2.44
5226 5683 2.759973 ATCTCTGGGAGCGCCGAA 60.760 61.111 2.29 0.00 33.83 4.30
5313 5770 2.982130 CTGTGGCTTAGGCGGAGT 59.018 61.111 0.40 0.00 39.81 3.85
5340 5797 3.002042 CGTCATCATCAACATGGAAGAGC 59.998 47.826 0.00 0.00 0.00 4.09
5492 5949 9.588096 ACACTACACCATCATAATACTGAGATA 57.412 33.333 0.00 0.00 0.00 1.98
5515 5972 1.330521 GTCATGGACACACACACACAC 59.669 52.381 0.00 0.00 32.09 3.82
5516 5973 1.662517 GTCATGGACACACACACACA 58.337 50.000 0.00 0.00 32.09 3.72
5791 6248 7.448161 TCCAATCATATGTATTTTCTTGCGGAT 59.552 33.333 1.90 0.00 0.00 4.18
5867 6325 6.590292 GCTCGAGCTAATATATGCCTTAAACA 59.410 38.462 29.88 0.00 38.21 2.83
5883 6341 2.134287 GGGGATGTGGCTCGAGCTA 61.134 63.158 34.46 28.17 41.70 3.32
6024 6482 4.423625 AGAAACTCAATCTAATCCCCCG 57.576 45.455 0.00 0.00 0.00 5.73
6254 6715 2.037121 TCGATGCCTTTGTCAGTGAAGA 59.963 45.455 0.00 0.00 0.00 2.87
6265 6726 2.012673 GATGTGCTCTTCGATGCCTTT 58.987 47.619 0.00 0.00 0.00 3.11
6283 6744 0.322975 GTGCTATGGGATCAGCGGAT 59.677 55.000 0.00 0.00 40.79 4.18


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

AutoCloner maintained by Alex Coulton.