Multiple sequence alignment - TraesCS1D01G371700

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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 TraesCS1D01G371700 chr1D 100.000 2823 0 0 583 3405 449846284 449849106 0.000000e+00 5214.0
1 TraesCS1D01G371700 chr1D 88.534 1221 101 22 828 2039 449660074 449661264 0.000000e+00 1443.0
2 TraesCS1D01G371700 chr1D 86.212 1349 127 30 822 2150 449923923 449922614 0.000000e+00 1406.0
3 TraesCS1D01G371700 chr1D 87.137 1205 104 27 843 2039 449674356 449675517 0.000000e+00 1319.0
4 TraesCS1D01G371700 chr1D 83.639 764 81 25 1494 2226 450044896 450044146 0.000000e+00 678.0
5 TraesCS1D01G371700 chr1D 82.362 669 79 22 806 1456 449983769 449983122 2.310000e-151 545.0
6 TraesCS1D01G371700 chr1D 94.225 329 18 1 1093 1421 449752586 449752913 5.070000e-138 501.0
7 TraesCS1D01G371700 chr1D 100.000 237 0 0 1 237 449845702 449845938 4.030000e-119 438.0
8 TraesCS1D01G371700 chr1D 80.741 135 14 5 106 230 449674107 449674239 1.010000e-15 95.3
9 TraesCS1D01G371700 chr1A 87.472 2195 159 59 820 2953 544999880 545002019 0.000000e+00 2423.0
10 TraesCS1D01G371700 chr1A 87.823 928 78 21 1122 2038 544748274 544749177 0.000000e+00 1055.0
11 TraesCS1D01G371700 chr1A 86.989 661 70 10 1533 2184 545009127 545008474 0.000000e+00 730.0
12 TraesCS1D01G371700 chr1A 89.764 508 50 2 1533 2039 544928174 544928680 0.000000e+00 649.0
13 TraesCS1D01G371700 chr1A 89.770 479 34 7 755 1222 544927491 544927965 1.750000e-167 599.0
14 TraesCS1D01G371700 chr1A 81.806 764 89 26 1497 2226 545299321 545298574 2.260000e-166 595.0
15 TraesCS1D01G371700 chr1A 85.371 499 48 15 934 1421 545009701 545009217 8.490000e-136 494.0
16 TraesCS1D01G371700 chr1A 83.077 195 19 7 3224 3405 545002163 545002356 7.560000e-37 165.0
17 TraesCS1D01G371700 chr1A 93.333 75 2 3 106 179 544764897 544764825 1.290000e-19 108.0
18 TraesCS1D01G371700 chr1B 91.438 1238 73 15 1532 2752 615732508 615733729 0.000000e+00 1668.0
19 TraesCS1D01G371700 chr1B 85.834 1073 98 35 979 2039 615581586 615582616 0.000000e+00 1090.0
20 TraesCS1D01G371700 chr1B 80.734 1417 159 63 822 2183 615745547 615744190 0.000000e+00 1000.0
21 TraesCS1D01G371700 chr1B 88.130 615 37 16 848 1451 615731879 615732468 0.000000e+00 699.0
22 TraesCS1D01G371700 chr1B 84.471 586 59 20 856 1417 615625319 615625896 1.790000e-152 549.0
23 TraesCS1D01G371700 chr1B 88.729 417 22 13 2758 3165 615733771 615734171 1.420000e-133 486.0
24 TraesCS1D01G371700 chr1B 94.030 201 10 1 3205 3405 615734177 615734375 1.540000e-78 303.0
25 TraesCS1D01G371700 chr1B 84.699 183 14 9 58 234 615731620 615731794 1.620000e-38 171.0


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 TraesCS1D01G371700 chr1D 449845702 449849106 3404 False 2826.00 5214 100.0000 1 3405 2 chr1D.!!$F4 3404
1 TraesCS1D01G371700 chr1D 449660074 449661264 1190 False 1443.00 1443 88.5340 828 2039 1 chr1D.!!$F1 1211
2 TraesCS1D01G371700 chr1D 449922614 449923923 1309 True 1406.00 1406 86.2120 822 2150 1 chr1D.!!$R1 1328
3 TraesCS1D01G371700 chr1D 449674107 449675517 1410 False 707.15 1319 83.9390 106 2039 2 chr1D.!!$F3 1933
4 TraesCS1D01G371700 chr1D 450044146 450044896 750 True 678.00 678 83.6390 1494 2226 1 chr1D.!!$R3 732
5 TraesCS1D01G371700 chr1D 449983122 449983769 647 True 545.00 545 82.3620 806 1456 1 chr1D.!!$R2 650
6 TraesCS1D01G371700 chr1A 544999880 545002356 2476 False 1294.00 2423 85.2745 820 3405 2 chr1A.!!$F3 2585
7 TraesCS1D01G371700 chr1A 544748274 544749177 903 False 1055.00 1055 87.8230 1122 2038 1 chr1A.!!$F1 916
8 TraesCS1D01G371700 chr1A 544927491 544928680 1189 False 624.00 649 89.7670 755 2039 2 chr1A.!!$F2 1284
9 TraesCS1D01G371700 chr1A 545008474 545009701 1227 True 612.00 730 86.1800 934 2184 2 chr1A.!!$R3 1250
10 TraesCS1D01G371700 chr1A 545298574 545299321 747 True 595.00 595 81.8060 1497 2226 1 chr1A.!!$R2 729
11 TraesCS1D01G371700 chr1B 615581586 615582616 1030 False 1090.00 1090 85.8340 979 2039 1 chr1B.!!$F1 1060
12 TraesCS1D01G371700 chr1B 615744190 615745547 1357 True 1000.00 1000 80.7340 822 2183 1 chr1B.!!$R1 1361
13 TraesCS1D01G371700 chr1B 615731620 615734375 2755 False 665.40 1668 89.4052 58 3405 5 chr1B.!!$F3 3347
14 TraesCS1D01G371700 chr1B 615625319 615625896 577 False 549.00 549 84.4710 856 1417 1 chr1B.!!$F2 561

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
678 691 0.183492 AAAGCACCTCACCAGCAGAA 59.817 50.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2425 2660 0.177604 AGCATGCAGAGTACTCCAGC 59.822 55.0 23.82 23.82 0.0 4.85 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
38 39 4.634012 TTTTCTCCTCCCGAAAAGATGA 57.366 40.909 0.00 0.00 35.95 2.92
39 40 4.844349 TTTCTCCTCCCGAAAAGATGAT 57.156 40.909 0.00 0.00 0.00 2.45
40 41 4.408182 TTCTCCTCCCGAAAAGATGATC 57.592 45.455 0.00 0.00 0.00 2.92
41 42 2.362397 TCTCCTCCCGAAAAGATGATCG 59.638 50.000 0.00 0.00 38.74 3.69
42 43 2.362397 CTCCTCCCGAAAAGATGATCGA 59.638 50.000 0.00 0.00 41.43 3.59
43 44 2.764010 TCCTCCCGAAAAGATGATCGAA 59.236 45.455 0.00 0.00 41.43 3.71
44 45 3.196901 TCCTCCCGAAAAGATGATCGAAA 59.803 43.478 0.00 0.00 41.43 3.46
45 46 3.309954 CCTCCCGAAAAGATGATCGAAAC 59.690 47.826 0.00 0.00 41.43 2.78
46 47 2.927477 TCCCGAAAAGATGATCGAAACG 59.073 45.455 0.00 0.00 41.43 3.60
47 48 2.536928 CCCGAAAAGATGATCGAAACGC 60.537 50.000 0.00 0.00 41.43 4.84
48 49 2.093625 CCGAAAAGATGATCGAAACGCA 59.906 45.455 0.00 0.00 41.43 5.24
49 50 3.242413 CCGAAAAGATGATCGAAACGCAT 60.242 43.478 0.00 0.00 41.43 4.73
50 51 4.334443 CGAAAAGATGATCGAAACGCATT 58.666 39.130 0.00 0.00 41.43 3.56
51 52 5.489335 CGAAAAGATGATCGAAACGCATTA 58.511 37.500 0.00 0.00 41.43 1.90
52 53 6.129393 CGAAAAGATGATCGAAACGCATTAT 58.871 36.000 0.00 0.00 41.43 1.28
53 54 6.298569 CGAAAAGATGATCGAAACGCATTATC 59.701 38.462 0.00 0.00 41.43 1.75
54 55 6.603237 AAAGATGATCGAAACGCATTATCA 57.397 33.333 0.00 0.00 0.00 2.15
55 56 6.603237 AAGATGATCGAAACGCATTATCAA 57.397 33.333 0.00 0.00 30.90 2.57
56 57 6.791887 AGATGATCGAAACGCATTATCAAT 57.208 33.333 0.00 0.00 30.90 2.57
75 76 6.895607 TCAATGTGACGCGATTCTTAATTA 57.104 33.333 15.93 0.00 0.00 1.40
76 77 7.297229 TCAATGTGACGCGATTCTTAATTAA 57.703 32.000 15.93 0.00 0.00 1.40
78 79 8.394877 TCAATGTGACGCGATTCTTAATTAATT 58.605 29.630 15.93 5.89 0.00 1.40
79 80 8.463709 CAATGTGACGCGATTCTTAATTAATTG 58.536 33.333 15.93 3.67 0.00 2.32
80 81 5.963004 TGTGACGCGATTCTTAATTAATTGC 59.037 36.000 15.93 10.74 39.41 3.56
81 82 6.183360 TGTGACGCGATTCTTAATTAATTGCT 60.183 34.615 15.93 7.43 40.25 3.91
82 83 6.354622 GTGACGCGATTCTTAATTAATTGCTC 59.645 38.462 15.93 13.07 40.25 4.26
83 84 6.257849 TGACGCGATTCTTAATTAATTGCTCT 59.742 34.615 15.93 5.92 40.25 4.09
84 85 6.422223 ACGCGATTCTTAATTAATTGCTCTG 58.578 36.000 15.93 7.48 40.25 3.35
85 86 6.037172 ACGCGATTCTTAATTAATTGCTCTGT 59.963 34.615 15.93 7.90 40.25 3.41
86 87 7.223971 ACGCGATTCTTAATTAATTGCTCTGTA 59.776 33.333 15.93 0.00 40.25 2.74
87 88 7.737744 CGCGATTCTTAATTAATTGCTCTGTAG 59.262 37.037 11.05 0.00 40.25 2.74
95 96 1.279496 ATTGCTCTGTAGGCCACTGA 58.721 50.000 5.01 9.86 34.32 3.41
99 100 0.820871 CTCTGTAGGCCACTGAGGTC 59.179 60.000 22.86 0.00 45.03 3.85
108 109 1.572085 CCACTGAGGTCGCAAAGCAG 61.572 60.000 0.00 0.00 0.00 4.24
110 111 1.302033 CTGAGGTCGCAAAGCAGGT 60.302 57.895 0.00 0.00 0.00 4.00
111 112 1.294659 CTGAGGTCGCAAAGCAGGTC 61.295 60.000 0.00 0.00 0.00 3.85
112 113 2.032681 AGGTCGCAAAGCAGGTCC 59.967 61.111 0.00 0.00 0.00 4.46
115 118 4.697756 TCGCAAAGCAGGTCCCCG 62.698 66.667 0.00 0.00 0.00 5.73
182 193 3.672511 CGCACTTAATCTACAGTGTCCGT 60.673 47.826 0.00 0.00 42.19 4.69
216 229 1.912731 AGAGGAAAGAAGGGCTTCCTC 59.087 52.381 19.52 19.52 43.64 3.71
643 656 9.942850 AAAATAAACTGATTTTATGGGAAGGTG 57.057 29.630 0.00 0.00 39.14 4.00
644 657 8.664669 AATAAACTGATTTTATGGGAAGGTGT 57.335 30.769 0.00 0.00 39.14 4.16
645 658 6.994421 AAACTGATTTTATGGGAAGGTGTT 57.006 33.333 0.00 0.00 0.00 3.32
646 659 6.994421 AACTGATTTTATGGGAAGGTGTTT 57.006 33.333 0.00 0.00 0.00 2.83
647 660 8.485578 AAACTGATTTTATGGGAAGGTGTTTA 57.514 30.769 0.00 0.00 0.00 2.01
648 661 8.664669 AACTGATTTTATGGGAAGGTGTTTAT 57.335 30.769 0.00 0.00 0.00 1.40
649 662 8.066612 ACTGATTTTATGGGAAGGTGTTTATG 57.933 34.615 0.00 0.00 0.00 1.90
650 663 7.124147 ACTGATTTTATGGGAAGGTGTTTATGG 59.876 37.037 0.00 0.00 0.00 2.74
651 664 6.382570 TGATTTTATGGGAAGGTGTTTATGGG 59.617 38.462 0.00 0.00 0.00 4.00
652 665 5.538082 TTTATGGGAAGGTGTTTATGGGA 57.462 39.130 0.00 0.00 0.00 4.37
653 666 2.891191 TGGGAAGGTGTTTATGGGAC 57.109 50.000 0.00 0.00 0.00 4.46
674 687 2.175236 GCTAAAGCACCTCACCAGC 58.825 57.895 0.00 0.00 41.59 4.85
675 688 0.606401 GCTAAAGCACCTCACCAGCA 60.606 55.000 0.00 0.00 41.59 4.41
676 689 1.446907 CTAAAGCACCTCACCAGCAG 58.553 55.000 0.00 0.00 0.00 4.24
677 690 1.002430 CTAAAGCACCTCACCAGCAGA 59.998 52.381 0.00 0.00 0.00 4.26
678 691 0.183492 AAAGCACCTCACCAGCAGAA 59.817 50.000 0.00 0.00 0.00 3.02
679 692 0.183492 AAGCACCTCACCAGCAGAAA 59.817 50.000 0.00 0.00 0.00 2.52
680 693 0.403271 AGCACCTCACCAGCAGAAAT 59.597 50.000 0.00 0.00 0.00 2.17
681 694 0.807496 GCACCTCACCAGCAGAAATC 59.193 55.000 0.00 0.00 0.00 2.17
682 695 1.612726 GCACCTCACCAGCAGAAATCT 60.613 52.381 0.00 0.00 0.00 2.40
683 696 2.354259 CACCTCACCAGCAGAAATCTC 58.646 52.381 0.00 0.00 0.00 2.75
684 697 1.280421 ACCTCACCAGCAGAAATCTCC 59.720 52.381 0.00 0.00 0.00 3.71
685 698 1.558756 CCTCACCAGCAGAAATCTCCT 59.441 52.381 0.00 0.00 0.00 3.69
686 699 2.768527 CCTCACCAGCAGAAATCTCCTA 59.231 50.000 0.00 0.00 0.00 2.94
687 700 3.198635 CCTCACCAGCAGAAATCTCCTAA 59.801 47.826 0.00 0.00 0.00 2.69
688 701 4.323792 CCTCACCAGCAGAAATCTCCTAAA 60.324 45.833 0.00 0.00 0.00 1.85
689 702 5.435291 CTCACCAGCAGAAATCTCCTAAAT 58.565 41.667 0.00 0.00 0.00 1.40
690 703 5.819991 TCACCAGCAGAAATCTCCTAAATT 58.180 37.500 0.00 0.00 0.00 1.82
691 704 6.957631 TCACCAGCAGAAATCTCCTAAATTA 58.042 36.000 0.00 0.00 0.00 1.40
692 705 7.577303 TCACCAGCAGAAATCTCCTAAATTAT 58.423 34.615 0.00 0.00 0.00 1.28
693 706 8.713971 TCACCAGCAGAAATCTCCTAAATTATA 58.286 33.333 0.00 0.00 0.00 0.98
694 707 8.997323 CACCAGCAGAAATCTCCTAAATTATAG 58.003 37.037 0.00 0.00 0.00 1.31
695 708 8.938883 ACCAGCAGAAATCTCCTAAATTATAGA 58.061 33.333 0.00 0.00 0.00 1.98
696 709 9.213799 CCAGCAGAAATCTCCTAAATTATAGAC 57.786 37.037 0.00 0.00 0.00 2.59
697 710 9.770097 CAGCAGAAATCTCCTAAATTATAGACA 57.230 33.333 0.00 0.00 0.00 3.41
698 711 9.771534 AGCAGAAATCTCCTAAATTATAGACAC 57.228 33.333 0.00 0.00 0.00 3.67
699 712 8.994170 GCAGAAATCTCCTAAATTATAGACACC 58.006 37.037 0.00 0.00 0.00 4.16
718 731 7.661040 AGACACCTCATAAAAACATTTTGAGG 58.339 34.615 19.53 19.53 40.72 3.86
719 732 6.758254 ACACCTCATAAAAACATTTTGAGGG 58.242 36.000 22.81 16.61 39.92 4.30
720 733 6.553100 ACACCTCATAAAAACATTTTGAGGGA 59.447 34.615 22.81 4.42 39.92 4.20
721 734 7.092716 CACCTCATAAAAACATTTTGAGGGAG 58.907 38.462 22.81 15.02 39.92 4.30
722 735 7.010160 ACCTCATAAAAACATTTTGAGGGAGA 58.990 34.615 22.81 3.30 39.92 3.71
723 736 7.177392 ACCTCATAAAAACATTTTGAGGGAGAG 59.823 37.037 22.81 9.87 39.92 3.20
724 737 7.177392 CCTCATAAAAACATTTTGAGGGAGAGT 59.823 37.037 15.62 0.00 35.69 3.24
725 738 8.477419 TCATAAAAACATTTTGAGGGAGAGTT 57.523 30.769 0.00 0.00 0.00 3.01
726 739 8.923270 TCATAAAAACATTTTGAGGGAGAGTTT 58.077 29.630 0.00 0.00 0.00 2.66
727 740 9.546428 CATAAAAACATTTTGAGGGAGAGTTTT 57.454 29.630 0.00 0.00 38.79 2.43
728 741 9.764363 ATAAAAACATTTTGAGGGAGAGTTTTC 57.236 29.630 0.00 0.00 36.89 2.29
729 742 7.423844 AAAACATTTTGAGGGAGAGTTTTCT 57.576 32.000 0.00 0.00 33.87 2.52
730 743 8.533569 AAAACATTTTGAGGGAGAGTTTTCTA 57.466 30.769 0.00 0.00 33.87 2.10
731 744 8.712228 AAACATTTTGAGGGAGAGTTTTCTAT 57.288 30.769 0.00 0.00 32.53 1.98
732 745 7.693969 ACATTTTGAGGGAGAGTTTTCTATG 57.306 36.000 0.00 0.00 32.53 2.23
733 746 6.660949 ACATTTTGAGGGAGAGTTTTCTATGG 59.339 38.462 0.00 0.00 32.53 2.74
734 747 5.843019 TTTGAGGGAGAGTTTTCTATGGT 57.157 39.130 0.00 0.00 32.53 3.55
735 748 6.945636 TTTGAGGGAGAGTTTTCTATGGTA 57.054 37.500 0.00 0.00 32.53 3.25
736 749 5.934402 TGAGGGAGAGTTTTCTATGGTAC 57.066 43.478 0.00 0.00 32.53 3.34
737 750 5.590818 TGAGGGAGAGTTTTCTATGGTACT 58.409 41.667 0.00 0.00 32.53 2.73
738 751 6.023603 TGAGGGAGAGTTTTCTATGGTACTT 58.976 40.000 0.00 0.00 32.53 2.24
739 752 6.070767 TGAGGGAGAGTTTTCTATGGTACTTG 60.071 42.308 0.00 0.00 32.53 3.16
740 753 5.785940 AGGGAGAGTTTTCTATGGTACTTGT 59.214 40.000 0.00 0.00 32.53 3.16
741 754 6.272558 AGGGAGAGTTTTCTATGGTACTTGTT 59.727 38.462 0.00 0.00 32.53 2.83
742 755 6.371825 GGGAGAGTTTTCTATGGTACTTGTTG 59.628 42.308 0.00 0.00 32.53 3.33
743 756 6.371825 GGAGAGTTTTCTATGGTACTTGTTGG 59.628 42.308 0.00 0.00 32.53 3.77
744 757 7.074653 AGAGTTTTCTATGGTACTTGTTGGA 57.925 36.000 0.00 0.00 0.00 3.53
745 758 7.162082 AGAGTTTTCTATGGTACTTGTTGGAG 58.838 38.462 0.00 0.00 0.00 3.86
746 759 7.016268 AGAGTTTTCTATGGTACTTGTTGGAGA 59.984 37.037 0.00 0.00 0.00 3.71
747 760 7.690256 AGTTTTCTATGGTACTTGTTGGAGAT 58.310 34.615 0.00 0.00 0.00 2.75
748 761 7.607991 AGTTTTCTATGGTACTTGTTGGAGATG 59.392 37.037 0.00 0.00 0.00 2.90
749 762 5.023533 TCTATGGTACTTGTTGGAGATGC 57.976 43.478 0.00 0.00 0.00 3.91
750 763 4.716784 TCTATGGTACTTGTTGGAGATGCT 59.283 41.667 0.00 0.00 0.00 3.79
751 764 3.334583 TGGTACTTGTTGGAGATGCTC 57.665 47.619 0.00 0.00 0.00 4.26
752 765 2.906389 TGGTACTTGTTGGAGATGCTCT 59.094 45.455 0.00 0.00 0.00 4.09
753 766 4.093743 TGGTACTTGTTGGAGATGCTCTA 58.906 43.478 0.00 0.00 0.00 2.43
754 767 4.530553 TGGTACTTGTTGGAGATGCTCTAA 59.469 41.667 0.00 0.00 0.00 2.10
767 780 3.402628 TGCTCTAACAGGGAGAAACAC 57.597 47.619 0.00 0.00 33.03 3.32
768 781 2.288825 TGCTCTAACAGGGAGAAACACG 60.289 50.000 0.00 0.00 33.03 4.49
778 791 1.762222 GAGAAACACGCACAGCACGT 61.762 55.000 0.00 0.00 46.42 4.49
814 852 1.000771 TCCTCCGCTAGAGTGCACT 60.001 57.895 21.88 21.88 41.47 4.40
905 963 3.635734 CTGCGCCTTGCTTCGAACG 62.636 63.158 4.18 0.00 46.63 3.95
1082 1182 4.486090 GATCGCCATTACATACATCGACT 58.514 43.478 0.00 0.00 0.00 4.18
1388 1535 0.252284 AGGAGGAGGACCACATCGTT 60.252 55.000 0.00 0.00 38.94 3.85
1458 1610 2.224079 AGTGCAATGCGTTCAGTTACAG 59.776 45.455 0.00 0.00 0.00 2.74
1462 1614 3.303725 GCAATGCGTTCAGTTACAGTTGA 60.304 43.478 0.00 0.00 0.00 3.18
1471 1623 6.140108 CGTTCAGTTACAGTTGAAATTTTCCG 59.860 38.462 6.68 0.00 35.29 4.30
1483 1635 7.766738 AGTTGAAATTTTCCGGTACAATTTTGT 59.233 29.630 16.71 1.08 44.86 2.83
1547 1718 2.959507 TGTATACTGATGCGTGTGCT 57.040 45.000 4.17 0.00 43.34 4.40
1738 1932 1.549170 GAAGAGGAAGACCGTAAGCCA 59.451 52.381 0.00 0.00 41.83 4.75
1742 1936 1.697982 AGGAAGACCGTAAGCCACTTT 59.302 47.619 0.00 0.00 41.83 2.66
1874 2068 3.089784 CCGCATTGTACGGTCAGC 58.910 61.111 0.00 0.00 45.70 4.26
1878 2072 0.736325 GCATTGTACGGTCAGCTCGT 60.736 55.000 4.27 4.27 43.64 4.18
1934 2128 4.129737 GAGGCGCGGACTACAGCA 62.130 66.667 8.83 0.00 37.07 4.41
1939 2133 2.488355 GCGGACTACAGCAGCGTA 59.512 61.111 0.00 0.00 37.19 4.42
2059 2256 4.431131 CACTGGGGCAAGGCGGAT 62.431 66.667 0.00 0.00 0.00 4.18
2083 2305 2.357396 CAGCAGCACACACCGCTA 60.357 61.111 0.00 0.00 37.72 4.26
2174 2396 7.654022 TTGGAACCATACTTCTGAACTTTTT 57.346 32.000 0.00 0.00 0.00 1.94
2185 2407 7.251281 ACTTCTGAACTTTTTCTTTCTTTCCG 58.749 34.615 0.00 0.00 32.36 4.30
2186 2408 6.753107 TCTGAACTTTTTCTTTCTTTCCGT 57.247 33.333 0.00 0.00 32.36 4.69
2235 2462 2.696707 TCGATTCCCACCCACATACTAC 59.303 50.000 0.00 0.00 0.00 2.73
2236 2463 2.698797 CGATTCCCACCCACATACTACT 59.301 50.000 0.00 0.00 0.00 2.57
2237 2464 3.893200 CGATTCCCACCCACATACTACTA 59.107 47.826 0.00 0.00 0.00 1.82
2379 2611 2.800544 ACACGAGAACATTGCTGTGTAC 59.199 45.455 0.00 0.00 38.65 2.90
2429 2664 9.520204 AAATAAACATTTCTCGAAATATGCTGG 57.480 29.630 4.70 0.00 38.84 4.85
2480 2719 2.224113 TGTGTCCGGGTGTACTTCTTTC 60.224 50.000 0.00 0.00 0.00 2.62
2653 2898 2.560504 CAGCGAGGCCACATTAACATA 58.439 47.619 5.01 0.00 0.00 2.29
2654 2899 2.287915 CAGCGAGGCCACATTAACATAC 59.712 50.000 5.01 0.00 0.00 2.39
2655 2900 2.093181 AGCGAGGCCACATTAACATACA 60.093 45.455 5.01 0.00 0.00 2.29
2656 2901 2.878406 GCGAGGCCACATTAACATACAT 59.122 45.455 5.01 0.00 0.00 2.29
2665 2910 6.016360 GCCACATTAACATACATTGCTATCCA 60.016 38.462 0.00 0.00 0.00 3.41
2696 2944 4.873827 TGGCCGTAATCAATCAGTAGAAAC 59.126 41.667 0.00 0.00 0.00 2.78
2725 2976 3.503748 CCAGGAAGAAAAGCCAGTACTTG 59.496 47.826 0.00 0.00 0.00 3.16
2734 2985 1.414919 AGCCAGTACTTGAACGTGGAA 59.585 47.619 0.00 0.00 0.00 3.53
2740 2991 4.152402 CAGTACTTGAACGTGGAAATCCTG 59.848 45.833 0.00 0.00 36.82 3.86
2744 2995 2.253414 GAACGTGGAAATCCTGCCGC 62.253 60.000 0.44 0.00 36.82 6.53
2876 3187 4.168291 GCTGGGCGGGAGAGAAGG 62.168 72.222 0.00 0.00 0.00 3.46
2920 3231 0.107066 ATGCCATGATTGGAGCACGA 60.107 50.000 0.00 0.00 46.92 4.35
2966 3277 0.389948 GCGACGAGGGTCTCACATTT 60.390 55.000 0.00 0.00 41.16 2.32
2993 3304 2.025155 GTACCAGAAGCGGATCAGAGA 58.975 52.381 0.00 0.00 0.00 3.10
3022 3333 2.027024 GGCACGACACGACACTGA 59.973 61.111 0.00 0.00 0.00 3.41
3023 3334 2.300787 GGCACGACACGACACTGAC 61.301 63.158 0.00 0.00 0.00 3.51
3024 3335 2.636227 GCACGACACGACACTGACG 61.636 63.158 0.00 0.00 35.77 4.35
3026 3337 3.097728 CGACACGACACTGACGGC 61.098 66.667 5.90 0.00 34.93 5.68
3028 3339 4.295119 ACACGACACTGACGGCCC 62.295 66.667 0.00 0.00 34.93 5.80
3177 3517 2.978010 CAGCGCTTTCGGGGTGTT 60.978 61.111 7.50 0.00 43.88 3.32
3178 3518 2.203294 AGCGCTTTCGGGGTGTTT 60.203 55.556 2.64 0.00 35.95 2.83
3179 3519 2.254350 GCGCTTTCGGGGTGTTTC 59.746 61.111 0.00 0.00 35.95 2.78
3180 3520 2.951458 CGCTTTCGGGGTGTTTCC 59.049 61.111 0.00 0.00 0.00 3.13
3181 3521 1.599797 CGCTTTCGGGGTGTTTCCT 60.600 57.895 0.00 0.00 36.25 3.36
3182 3522 1.574702 CGCTTTCGGGGTGTTTCCTC 61.575 60.000 0.00 0.00 36.25 3.71
3187 3527 2.350134 GGGGTGTTTCCTCGGGAC 59.650 66.667 0.00 0.00 36.25 4.46
3188 3528 2.222013 GGGGTGTTTCCTCGGGACT 61.222 63.158 0.00 0.00 36.25 3.85
3189 3529 1.003718 GGGTGTTTCCTCGGGACTG 60.004 63.158 0.00 0.00 36.25 3.51
3190 3530 1.003718 GGTGTTTCCTCGGGACTGG 60.004 63.158 0.00 0.00 0.00 4.00
3191 3531 1.671379 GTGTTTCCTCGGGACTGGC 60.671 63.158 0.00 0.00 0.00 4.85
3192 3532 2.046217 GTTTCCTCGGGACTGGCC 60.046 66.667 0.00 0.00 0.00 5.36
3193 3533 2.203938 TTTCCTCGGGACTGGCCT 60.204 61.111 3.32 0.00 36.66 5.19
3194 3534 2.592993 TTTCCTCGGGACTGGCCTG 61.593 63.158 8.29 8.29 45.07 4.85
3197 3537 4.154347 CTCGGGACTGGCCTGCTC 62.154 72.222 9.95 6.61 43.24 4.26
3212 3552 4.849329 CTCCAGGGCGCGTCGTAC 62.849 72.222 5.25 0.00 0.00 3.67
3219 3559 4.771356 GCGCGTCGTACCAGCTCA 62.771 66.667 8.43 0.00 0.00 4.26
3220 3560 2.577112 CGCGTCGTACCAGCTCAG 60.577 66.667 0.00 0.00 0.00 3.35
3221 3561 2.875485 GCGTCGTACCAGCTCAGA 59.125 61.111 0.00 0.00 0.00 3.27
3222 3562 1.226435 GCGTCGTACCAGCTCAGAG 60.226 63.158 0.00 0.00 0.00 3.35
3223 3563 1.226435 CGTCGTACCAGCTCAGAGC 60.226 63.158 15.25 15.25 42.84 4.09
3274 3614 2.094675 CAGTTAAGCACCTCATTGGGG 58.905 52.381 0.00 0.00 43.81 4.96
3283 3623 1.774254 ACCTCATTGGGGCGATGATAA 59.226 47.619 1.28 0.00 41.11 1.75
3345 3685 0.752009 AGCTAACCGAGGCGAGATGA 60.752 55.000 0.00 0.00 0.00 2.92
3361 3709 1.936547 GATGAGAAGCGTGGATGGAAC 59.063 52.381 0.00 0.00 0.00 3.62
3391 3743 2.283173 TCTGCTCGGCACCAGAGA 60.283 61.111 11.18 0.00 37.93 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.980573 TCATCTTTTCGGGAGGAGAAAAA 58.019 39.130 5.76 0.00 44.02 1.94
17 18 4.634012 TCATCTTTTCGGGAGGAGAAAA 57.366 40.909 4.41 4.41 42.96 2.29
18 19 4.680708 CGATCATCTTTTCGGGAGGAGAAA 60.681 45.833 0.00 0.00 36.00 2.52
19 20 3.181475 CGATCATCTTTTCGGGAGGAGAA 60.181 47.826 0.00 0.00 0.00 2.87
20 21 2.362397 CGATCATCTTTTCGGGAGGAGA 59.638 50.000 0.00 0.00 0.00 3.71
21 22 2.362397 TCGATCATCTTTTCGGGAGGAG 59.638 50.000 0.00 0.00 36.08 3.69
22 23 2.384828 TCGATCATCTTTTCGGGAGGA 58.615 47.619 0.00 0.00 36.08 3.71
23 24 2.890808 TCGATCATCTTTTCGGGAGG 57.109 50.000 0.00 0.00 36.08 4.30
24 25 3.000322 CGTTTCGATCATCTTTTCGGGAG 60.000 47.826 0.00 0.00 36.08 4.30
25 26 2.927477 CGTTTCGATCATCTTTTCGGGA 59.073 45.455 0.00 0.00 36.08 5.14
26 27 2.536928 GCGTTTCGATCATCTTTTCGGG 60.537 50.000 0.00 0.00 36.08 5.14
27 28 2.093625 TGCGTTTCGATCATCTTTTCGG 59.906 45.455 0.00 0.00 36.08 4.30
28 29 3.368321 TGCGTTTCGATCATCTTTTCG 57.632 42.857 0.00 0.00 36.72 3.46
29 30 7.125755 TGATAATGCGTTTCGATCATCTTTTC 58.874 34.615 0.00 0.00 0.00 2.29
30 31 7.015226 TGATAATGCGTTTCGATCATCTTTT 57.985 32.000 0.00 0.00 0.00 2.27
31 32 6.603237 TGATAATGCGTTTCGATCATCTTT 57.397 33.333 0.00 0.00 0.00 2.52
32 33 6.603237 TTGATAATGCGTTTCGATCATCTT 57.397 33.333 0.00 0.00 0.00 2.40
33 34 6.203530 ACATTGATAATGCGTTTCGATCATCT 59.796 34.615 0.00 0.00 42.69 2.90
34 35 6.301607 CACATTGATAATGCGTTTCGATCATC 59.698 38.462 0.00 0.00 42.69 2.92
35 36 6.018016 TCACATTGATAATGCGTTTCGATCAT 60.018 34.615 0.00 0.00 42.69 2.45
36 37 5.293079 TCACATTGATAATGCGTTTCGATCA 59.707 36.000 0.00 0.00 42.69 2.92
37 38 5.617187 GTCACATTGATAATGCGTTTCGATC 59.383 40.000 0.00 0.00 42.69 3.69
38 39 5.501715 GTCACATTGATAATGCGTTTCGAT 58.498 37.500 0.00 0.00 42.69 3.59
39 40 4.491763 CGTCACATTGATAATGCGTTTCGA 60.492 41.667 0.00 0.00 42.69 3.71
40 41 3.714016 CGTCACATTGATAATGCGTTTCG 59.286 43.478 0.00 0.00 42.69 3.46
41 42 3.478516 GCGTCACATTGATAATGCGTTTC 59.521 43.478 0.00 0.00 42.69 2.78
42 43 3.425404 GCGTCACATTGATAATGCGTTT 58.575 40.909 0.00 0.00 42.69 3.60
43 44 2.536728 CGCGTCACATTGATAATGCGTT 60.537 45.455 0.00 0.00 42.69 4.84
44 45 1.005032 CGCGTCACATTGATAATGCGT 60.005 47.619 0.00 0.00 42.69 5.24
45 46 1.257675 TCGCGTCACATTGATAATGCG 59.742 47.619 5.77 13.89 42.69 4.73
46 47 3.526385 ATCGCGTCACATTGATAATGC 57.474 42.857 5.77 0.00 42.69 3.56
47 48 5.334435 AGAATCGCGTCACATTGATAATG 57.666 39.130 5.77 0.28 44.48 1.90
48 49 5.991328 AAGAATCGCGTCACATTGATAAT 57.009 34.783 5.77 0.00 0.00 1.28
49 50 6.895607 TTAAGAATCGCGTCACATTGATAA 57.104 33.333 5.77 0.00 0.00 1.75
50 51 7.477144 AATTAAGAATCGCGTCACATTGATA 57.523 32.000 5.77 0.00 0.00 2.15
51 52 5.991328 ATTAAGAATCGCGTCACATTGAT 57.009 34.783 5.77 0.00 0.00 2.57
52 53 5.794687 AATTAAGAATCGCGTCACATTGA 57.205 34.783 5.77 0.00 0.00 2.57
53 54 8.463709 CAATTAATTAAGAATCGCGTCACATTG 58.536 33.333 5.77 0.05 0.00 2.82
54 55 7.165812 GCAATTAATTAAGAATCGCGTCACATT 59.834 33.333 5.77 0.00 0.00 2.71
55 56 6.632834 GCAATTAATTAAGAATCGCGTCACAT 59.367 34.615 5.77 0.00 0.00 3.21
56 57 5.963004 GCAATTAATTAAGAATCGCGTCACA 59.037 36.000 5.77 0.00 0.00 3.58
75 76 1.630369 TCAGTGGCCTACAGAGCAATT 59.370 47.619 3.32 0.00 0.00 2.32
76 77 1.209019 CTCAGTGGCCTACAGAGCAAT 59.791 52.381 3.32 0.00 36.34 3.56
78 79 1.260538 CCTCAGTGGCCTACAGAGCA 61.261 60.000 16.86 0.00 40.50 4.26
79 80 1.261238 ACCTCAGTGGCCTACAGAGC 61.261 60.000 16.86 0.00 40.50 4.09
80 81 0.820871 GACCTCAGTGGCCTACAGAG 59.179 60.000 15.91 15.91 41.24 3.35
81 82 0.965866 CGACCTCAGTGGCCTACAGA 60.966 60.000 3.32 2.24 40.22 3.41
82 83 1.513158 CGACCTCAGTGGCCTACAG 59.487 63.158 3.32 0.00 40.22 2.74
83 84 2.646175 GCGACCTCAGTGGCCTACA 61.646 63.158 3.32 0.00 41.49 2.74
84 85 2.167398 TTGCGACCTCAGTGGCCTAC 62.167 60.000 3.32 0.00 46.28 3.18
85 86 1.476845 TTTGCGACCTCAGTGGCCTA 61.477 55.000 3.32 0.00 46.28 3.93
86 87 2.738213 CTTTGCGACCTCAGTGGCCT 62.738 60.000 3.32 0.00 46.28 5.19
87 88 2.281484 TTTGCGACCTCAGTGGCC 60.281 61.111 0.00 0.00 46.28 5.36
95 96 2.032681 GGACCTGCTTTGCGACCT 59.967 61.111 0.00 0.00 0.00 3.85
119 122 4.580551 GGCAGCCCATCAATGCGC 62.581 66.667 0.00 0.00 40.90 6.09
182 193 2.364317 CTCTCCGAGAGCCCCCAA 60.364 66.667 12.50 0.00 35.30 4.12
617 630 9.942850 CACCTTCCCATAAAATCAGTTTATTTT 57.057 29.630 0.00 0.00 39.88 1.82
618 631 9.100197 ACACCTTCCCATAAAATCAGTTTATTT 57.900 29.630 0.00 0.00 39.88 1.40
619 632 8.664669 ACACCTTCCCATAAAATCAGTTTATT 57.335 30.769 0.00 0.00 39.88 1.40
620 633 8.664669 AACACCTTCCCATAAAATCAGTTTAT 57.335 30.769 0.00 0.00 42.12 1.40
621 634 8.485578 AAACACCTTCCCATAAAATCAGTTTA 57.514 30.769 0.00 0.00 36.14 2.01
622 635 6.994421 AACACCTTCCCATAAAATCAGTTT 57.006 33.333 0.00 0.00 0.00 2.66
623 636 6.994421 AAACACCTTCCCATAAAATCAGTT 57.006 33.333 0.00 0.00 0.00 3.16
624 637 7.124147 CCATAAACACCTTCCCATAAAATCAGT 59.876 37.037 0.00 0.00 0.00 3.41
625 638 7.417797 CCCATAAACACCTTCCCATAAAATCAG 60.418 40.741 0.00 0.00 0.00 2.90
626 639 6.382570 CCCATAAACACCTTCCCATAAAATCA 59.617 38.462 0.00 0.00 0.00 2.57
627 640 6.609616 TCCCATAAACACCTTCCCATAAAATC 59.390 38.462 0.00 0.00 0.00 2.17
628 641 6.382859 GTCCCATAAACACCTTCCCATAAAAT 59.617 38.462 0.00 0.00 0.00 1.82
629 642 5.717654 GTCCCATAAACACCTTCCCATAAAA 59.282 40.000 0.00 0.00 0.00 1.52
630 643 5.222358 TGTCCCATAAACACCTTCCCATAAA 60.222 40.000 0.00 0.00 0.00 1.40
631 644 4.292571 TGTCCCATAAACACCTTCCCATAA 59.707 41.667 0.00 0.00 0.00 1.90
632 645 3.853181 TGTCCCATAAACACCTTCCCATA 59.147 43.478 0.00 0.00 0.00 2.74
633 646 2.652348 TGTCCCATAAACACCTTCCCAT 59.348 45.455 0.00 0.00 0.00 4.00
634 647 2.066592 TGTCCCATAAACACCTTCCCA 58.933 47.619 0.00 0.00 0.00 4.37
635 648 2.891191 TGTCCCATAAACACCTTCCC 57.109 50.000 0.00 0.00 0.00 3.97
636 649 2.427095 GCATGTCCCATAAACACCTTCC 59.573 50.000 0.00 0.00 0.00 3.46
637 650 3.356290 AGCATGTCCCATAAACACCTTC 58.644 45.455 0.00 0.00 0.00 3.46
638 651 3.456380 AGCATGTCCCATAAACACCTT 57.544 42.857 0.00 0.00 0.00 3.50
639 652 4.584638 TTAGCATGTCCCATAAACACCT 57.415 40.909 0.00 0.00 0.00 4.00
640 653 4.440112 GCTTTAGCATGTCCCATAAACACC 60.440 45.833 0.00 0.00 41.59 4.16
641 654 4.672409 GCTTTAGCATGTCCCATAAACAC 58.328 43.478 0.00 0.00 41.59 3.32
642 655 4.981806 GCTTTAGCATGTCCCATAAACA 57.018 40.909 0.00 0.00 41.59 2.83
656 669 0.606401 TGCTGGTGAGGTGCTTTAGC 60.606 55.000 0.00 0.00 42.50 3.09
657 670 1.002430 TCTGCTGGTGAGGTGCTTTAG 59.998 52.381 0.00 0.00 0.00 1.85
658 671 1.055849 TCTGCTGGTGAGGTGCTTTA 58.944 50.000 0.00 0.00 0.00 1.85
659 672 0.183492 TTCTGCTGGTGAGGTGCTTT 59.817 50.000 0.00 0.00 0.00 3.51
660 673 0.183492 TTTCTGCTGGTGAGGTGCTT 59.817 50.000 0.00 0.00 0.00 3.91
661 674 0.403271 ATTTCTGCTGGTGAGGTGCT 59.597 50.000 0.00 0.00 0.00 4.40
662 675 0.807496 GATTTCTGCTGGTGAGGTGC 59.193 55.000 0.00 0.00 0.00 5.01
663 676 2.354259 GAGATTTCTGCTGGTGAGGTG 58.646 52.381 0.00 0.00 0.00 4.00
664 677 1.280421 GGAGATTTCTGCTGGTGAGGT 59.720 52.381 0.00 0.00 0.00 3.85
665 678 1.558756 AGGAGATTTCTGCTGGTGAGG 59.441 52.381 0.34 0.00 43.25 3.86
666 679 4.478206 TTAGGAGATTTCTGCTGGTGAG 57.522 45.455 11.40 0.00 44.59 3.51
667 680 4.908601 TTTAGGAGATTTCTGCTGGTGA 57.091 40.909 11.40 0.00 44.59 4.02
668 681 7.814264 ATAATTTAGGAGATTTCTGCTGGTG 57.186 36.000 11.40 0.00 44.59 4.17
669 682 8.938883 TCTATAATTTAGGAGATTTCTGCTGGT 58.061 33.333 11.40 0.00 44.59 4.00
670 683 9.213799 GTCTATAATTTAGGAGATTTCTGCTGG 57.786 37.037 11.40 0.00 44.59 4.85
671 684 9.770097 TGTCTATAATTTAGGAGATTTCTGCTG 57.230 33.333 11.40 0.00 44.59 4.41
672 685 9.771534 GTGTCTATAATTTAGGAGATTTCTGCT 57.228 33.333 6.82 6.82 46.60 4.24
673 686 8.994170 GGTGTCTATAATTTAGGAGATTTCTGC 58.006 37.037 0.00 0.00 34.24 4.26
692 705 8.792633 CCTCAAAATGTTTTTATGAGGTGTCTA 58.207 33.333 11.11 0.00 35.12 2.59
693 706 7.255942 CCCTCAAAATGTTTTTATGAGGTGTCT 60.256 37.037 16.46 0.00 36.71 3.41
694 707 6.868339 CCCTCAAAATGTTTTTATGAGGTGTC 59.132 38.462 16.46 0.00 36.71 3.67
695 708 6.553100 TCCCTCAAAATGTTTTTATGAGGTGT 59.447 34.615 16.46 0.00 36.71 4.16
696 709 6.991938 TCCCTCAAAATGTTTTTATGAGGTG 58.008 36.000 16.46 9.67 36.71 4.00
697 710 7.010160 TCTCCCTCAAAATGTTTTTATGAGGT 58.990 34.615 16.46 0.00 36.71 3.85
698 711 7.177392 ACTCTCCCTCAAAATGTTTTTATGAGG 59.823 37.037 12.12 12.12 37.49 3.86
699 712 8.115490 ACTCTCCCTCAAAATGTTTTTATGAG 57.885 34.615 0.00 0.00 0.00 2.90
700 713 8.477419 AACTCTCCCTCAAAATGTTTTTATGA 57.523 30.769 0.00 0.00 0.00 2.15
701 714 9.546428 AAAACTCTCCCTCAAAATGTTTTTATG 57.454 29.630 0.00 0.00 34.01 1.90
702 715 9.764363 GAAAACTCTCCCTCAAAATGTTTTTAT 57.236 29.630 0.00 0.00 36.63 1.40
703 716 8.977412 AGAAAACTCTCCCTCAAAATGTTTTTA 58.023 29.630 0.00 0.00 36.63 1.52
704 717 7.851228 AGAAAACTCTCCCTCAAAATGTTTTT 58.149 30.769 0.00 0.00 36.63 1.94
705 718 7.423844 AGAAAACTCTCCCTCAAAATGTTTT 57.576 32.000 0.00 0.00 38.36 2.43
706 719 8.579863 CATAGAAAACTCTCCCTCAAAATGTTT 58.420 33.333 0.00 0.00 0.00 2.83
707 720 7.177392 CCATAGAAAACTCTCCCTCAAAATGTT 59.823 37.037 0.00 0.00 0.00 2.71
708 721 6.660949 CCATAGAAAACTCTCCCTCAAAATGT 59.339 38.462 0.00 0.00 0.00 2.71
709 722 6.660949 ACCATAGAAAACTCTCCCTCAAAATG 59.339 38.462 0.00 0.00 0.00 2.32
710 723 6.794534 ACCATAGAAAACTCTCCCTCAAAAT 58.205 36.000 0.00 0.00 0.00 1.82
711 724 6.200878 ACCATAGAAAACTCTCCCTCAAAA 57.799 37.500 0.00 0.00 0.00 2.44
712 725 5.843019 ACCATAGAAAACTCTCCCTCAAA 57.157 39.130 0.00 0.00 0.00 2.69
713 726 6.023603 AGTACCATAGAAAACTCTCCCTCAA 58.976 40.000 0.00 0.00 0.00 3.02
714 727 5.590818 AGTACCATAGAAAACTCTCCCTCA 58.409 41.667 0.00 0.00 0.00 3.86
715 728 6.070710 ACAAGTACCATAGAAAACTCTCCCTC 60.071 42.308 0.00 0.00 0.00 4.30
716 729 5.785940 ACAAGTACCATAGAAAACTCTCCCT 59.214 40.000 0.00 0.00 0.00 4.20
717 730 6.051179 ACAAGTACCATAGAAAACTCTCCC 57.949 41.667 0.00 0.00 0.00 4.30
718 731 6.371825 CCAACAAGTACCATAGAAAACTCTCC 59.628 42.308 0.00 0.00 0.00 3.71
719 732 7.159372 TCCAACAAGTACCATAGAAAACTCTC 58.841 38.462 0.00 0.00 0.00 3.20
720 733 7.016268 TCTCCAACAAGTACCATAGAAAACTCT 59.984 37.037 0.00 0.00 0.00 3.24
721 734 7.159372 TCTCCAACAAGTACCATAGAAAACTC 58.841 38.462 0.00 0.00 0.00 3.01
722 735 7.074653 TCTCCAACAAGTACCATAGAAAACT 57.925 36.000 0.00 0.00 0.00 2.66
723 736 7.626452 GCATCTCCAACAAGTACCATAGAAAAC 60.626 40.741 0.00 0.00 0.00 2.43
724 737 6.374333 GCATCTCCAACAAGTACCATAGAAAA 59.626 38.462 0.00 0.00 0.00 2.29
725 738 5.880332 GCATCTCCAACAAGTACCATAGAAA 59.120 40.000 0.00 0.00 0.00 2.52
726 739 5.189736 AGCATCTCCAACAAGTACCATAGAA 59.810 40.000 0.00 0.00 0.00 2.10
727 740 4.716784 AGCATCTCCAACAAGTACCATAGA 59.283 41.667 0.00 0.00 0.00 1.98
728 741 5.028549 AGCATCTCCAACAAGTACCATAG 57.971 43.478 0.00 0.00 0.00 2.23
729 742 5.023533 GAGCATCTCCAACAAGTACCATA 57.976 43.478 0.00 0.00 0.00 2.74
730 743 3.878778 GAGCATCTCCAACAAGTACCAT 58.121 45.455 0.00 0.00 0.00 3.55
731 744 3.334583 GAGCATCTCCAACAAGTACCA 57.665 47.619 0.00 0.00 0.00 3.25
745 758 3.935828 GTGTTTCTCCCTGTTAGAGCATC 59.064 47.826 0.00 0.00 0.00 3.91
746 759 3.617531 CGTGTTTCTCCCTGTTAGAGCAT 60.618 47.826 0.00 0.00 0.00 3.79
747 760 2.288825 CGTGTTTCTCCCTGTTAGAGCA 60.289 50.000 0.00 0.00 0.00 4.26
748 761 2.338500 CGTGTTTCTCCCTGTTAGAGC 58.662 52.381 0.00 0.00 0.00 4.09
749 762 2.288825 TGCGTGTTTCTCCCTGTTAGAG 60.289 50.000 0.00 0.00 0.00 2.43
750 763 1.689813 TGCGTGTTTCTCCCTGTTAGA 59.310 47.619 0.00 0.00 0.00 2.10
751 764 1.798813 GTGCGTGTTTCTCCCTGTTAG 59.201 52.381 0.00 0.00 0.00 2.34
752 765 1.139256 TGTGCGTGTTTCTCCCTGTTA 59.861 47.619 0.00 0.00 0.00 2.41
753 766 0.107410 TGTGCGTGTTTCTCCCTGTT 60.107 50.000 0.00 0.00 0.00 3.16
754 767 0.532862 CTGTGCGTGTTTCTCCCTGT 60.533 55.000 0.00 0.00 0.00 4.00
755 768 1.845809 GCTGTGCGTGTTTCTCCCTG 61.846 60.000 0.00 0.00 0.00 4.45
756 769 1.598130 GCTGTGCGTGTTTCTCCCT 60.598 57.895 0.00 0.00 0.00 4.20
757 770 1.891919 TGCTGTGCGTGTTTCTCCC 60.892 57.895 0.00 0.00 0.00 4.30
767 780 1.799519 GAGAGAGACGTGCTGTGCG 60.800 63.158 0.00 0.00 0.00 5.34
768 781 0.455972 GAGAGAGAGACGTGCTGTGC 60.456 60.000 0.00 0.00 0.00 4.57
778 791 4.219115 GAGGAGAGAGAGAGAGAGAGAGA 58.781 52.174 0.00 0.00 0.00 3.10
905 963 1.281899 GTGAGGCAGCGATCAAGTAC 58.718 55.000 0.69 0.00 0.00 2.73
991 1076 4.100498 GGTGGGTATATATGGTCGGGTATG 59.900 50.000 0.00 0.00 0.00 2.39
1082 1182 1.248785 ACTCCGACGAGCTAGGCAAA 61.249 55.000 0.00 0.00 40.03 3.68
1105 1216 1.816537 CTGCTGGCCTCGTAGCTAA 59.183 57.895 13.45 0.00 40.52 3.09
1313 1460 1.006758 AGGTAGTTGATCCACCGGAGA 59.993 52.381 9.46 4.59 37.42 3.71
1388 1535 2.685017 AGGATCTGGTGGAGCGCA 60.685 61.111 11.47 0.00 0.00 6.09
1458 1610 7.911343 ACAAAATTGTACCGGAAAATTTCAAC 58.089 30.769 9.46 1.26 40.16 3.18
1462 1614 9.549078 ACATTACAAAATTGTACCGGAAAATTT 57.451 25.926 9.46 13.90 42.84 1.82
1471 1623 5.049398 TCCGCACATTACAAAATTGTACC 57.951 39.130 5.53 0.00 42.84 3.34
1483 1635 0.894835 TCACTCTGCTCCGCACATTA 59.105 50.000 0.00 0.00 33.79 1.90
1547 1718 1.471829 ATCTGTGACCACCTGCACGA 61.472 55.000 0.00 0.00 37.83 4.35
1714 1908 0.329261 TACGGTCTTCCTCTTCCGGA 59.671 55.000 0.00 0.00 46.06 5.14
1715 1909 1.134560 CTTACGGTCTTCCTCTTCCGG 59.865 57.143 0.00 0.00 46.06 5.14
1848 2042 3.943479 TACAATGCGGCCGCGTTCT 62.943 57.895 45.71 38.17 46.07 3.01
1874 2068 2.037136 CCTCCTTGCAGCCAACGAG 61.037 63.158 0.00 0.00 35.31 4.18
1918 2112 4.135153 CTGCTGTAGTCCGCGCCT 62.135 66.667 0.00 0.21 0.00 5.52
2059 2256 0.674581 GTGTGTGCTGCTGCTCCATA 60.675 55.000 17.00 8.80 40.48 2.74
2083 2305 1.502163 GCAGCGACAACTTGTGCTCT 61.502 55.000 12.96 0.57 34.30 4.09
2235 2462 5.459107 GTCCTGTACTGACGTGCAAATATAG 59.541 44.000 0.00 0.00 35.30 1.31
2236 2463 5.105675 TGTCCTGTACTGACGTGCAAATATA 60.106 40.000 0.00 0.00 35.30 0.86
2237 2464 4.181578 GTCCTGTACTGACGTGCAAATAT 58.818 43.478 0.00 0.00 35.30 1.28
2316 2544 5.201713 TGTCGTCTCTGAGAAAATCAACT 57.798 39.130 9.31 0.00 37.52 3.16
2415 2650 5.218885 CAGAGTACTCCAGCATATTTCGAG 58.781 45.833 19.38 0.00 0.00 4.04
2425 2660 0.177604 AGCATGCAGAGTACTCCAGC 59.822 55.000 23.82 23.82 0.00 4.85
2426 2661 2.692557 AGTAGCATGCAGAGTACTCCAG 59.307 50.000 21.98 13.26 0.00 3.86
2429 2664 3.490078 GGTCAGTAGCATGCAGAGTACTC 60.490 52.174 21.98 15.41 0.00 2.59
2480 2719 4.999950 AGCCTCCATCGCTAAATTATTGAG 59.000 41.667 0.00 0.00 33.91 3.02
2653 2898 3.154710 CAGCATGGATGGATAGCAATGT 58.845 45.455 0.00 0.00 0.00 2.71
2654 2899 3.850122 CAGCATGGATGGATAGCAATG 57.150 47.619 0.00 0.00 0.00 2.82
2696 2944 3.888930 TGGCTTTTCTTCCTGGTGTTAAG 59.111 43.478 0.00 0.00 0.00 1.85
2725 2976 1.794222 CGGCAGGATTTCCACGTTC 59.206 57.895 0.00 0.00 38.89 3.95
2757 3008 4.554036 GACCGATCTGCAGGGCCC 62.554 72.222 16.46 16.46 0.00 5.80
2799 3110 4.351054 CCTTTGTCCCTGCCCGCT 62.351 66.667 0.00 0.00 0.00 5.52
2804 3115 0.606673 GTGGAGTCCTTTGTCCCTGC 60.607 60.000 11.33 0.00 31.04 4.85
2805 3116 1.059913 AGTGGAGTCCTTTGTCCCTG 58.940 55.000 11.33 0.00 31.04 4.45
2966 3277 1.592400 CCGCTTCTGGTACCACGAGA 61.592 60.000 20.70 10.70 30.95 4.04
3086 3402 2.959599 GTGTCGCACACGCACAGA 60.960 61.111 5.30 0.00 39.53 3.41
3165 3485 0.953960 CCGAGGAAACACCCCGAAAG 60.954 60.000 0.00 0.00 40.05 2.62
3173 3513 1.671379 GCCAGTCCCGAGGAAACAC 60.671 63.158 0.00 0.00 31.38 3.32
3174 3514 2.747686 GCCAGTCCCGAGGAAACA 59.252 61.111 0.00 0.00 31.38 2.83
3175 3515 2.046217 GGCCAGTCCCGAGGAAAC 60.046 66.667 0.00 0.00 31.38 2.78
3176 3516 2.203938 AGGCCAGTCCCGAGGAAA 60.204 61.111 5.01 0.00 31.38 3.13
3177 3517 3.003173 CAGGCCAGTCCCGAGGAA 61.003 66.667 5.01 0.00 31.38 3.36
3180 3520 4.154347 GAGCAGGCCAGTCCCGAG 62.154 72.222 5.01 0.00 34.51 4.63
3195 3535 4.849329 GTACGACGCGCCCTGGAG 62.849 72.222 5.73 0.00 0.00 3.86
3202 3542 4.771356 TGAGCTGGTACGACGCGC 62.771 66.667 5.73 0.00 0.00 6.86
3203 3543 2.577112 CTGAGCTGGTACGACGCG 60.577 66.667 3.53 3.53 0.00 6.01
3204 3544 1.226435 CTCTGAGCTGGTACGACGC 60.226 63.158 0.00 0.00 0.00 5.19
3205 3545 1.226435 GCTCTGAGCTGGTACGACG 60.226 63.158 21.93 0.00 38.45 5.12
3206 3546 1.226435 CGCTCTGAGCTGGTACGAC 60.226 63.158 25.59 0.00 39.60 4.34
3207 3547 2.407428 CCGCTCTGAGCTGGTACGA 61.407 63.158 25.59 0.00 39.60 3.43
3208 3548 2.103143 CCGCTCTGAGCTGGTACG 59.897 66.667 25.59 10.12 39.60 3.67
3209 3549 2.010582 CTCCCGCTCTGAGCTGGTAC 62.011 65.000 30.86 4.16 44.68 3.34
3210 3550 1.754621 CTCCCGCTCTGAGCTGGTA 60.755 63.158 30.86 19.99 44.68 3.25
3211 3551 3.073735 CTCCCGCTCTGAGCTGGT 61.074 66.667 30.86 0.00 44.68 4.00
3212 3552 3.847602 CCTCCCGCTCTGAGCTGG 61.848 72.222 28.07 28.07 45.60 4.85
3213 3553 3.847602 CCCTCCCGCTCTGAGCTG 61.848 72.222 25.59 19.56 39.60 4.24
3274 3614 1.286501 TTCGTGTGGCTTATCATCGC 58.713 50.000 0.00 0.00 0.00 4.58
3283 3623 0.548031 ATCCATGGATTCGTGTGGCT 59.452 50.000 22.15 0.00 0.00 4.75
3290 3630 5.049198 CACAGGACAATTATCCATGGATTCG 60.049 44.000 31.70 18.89 41.73 3.34
3345 3685 1.079127 CCGTTCCATCCACGCTTCT 60.079 57.895 0.00 0.00 36.27 2.85


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

AutoCloner maintained by Alex Coulton.