Multiple sequence alignment - TraesCS1D01G156000

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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 TraesCS1D01G156000 chr1D 100.000 8195 0 0 998 9192 219730976 219722782 0.000000e+00 15134.0
1 TraesCS1D01G156000 chr1D 100.000 688 0 0 1 688 219731973 219731286 0.000000e+00 1271.0
2 TraesCS1D01G156000 chr1D 78.598 271 47 10 301 566 142911196 142911460 1.590000e-37 169.0
3 TraesCS1D01G156000 chr1D 93.137 102 4 1 8466 8564 219710616 219710717 7.440000e-31 147.0
4 TraesCS1D01G156000 chr1D 93.478 46 3 0 7041 7086 283042075 283042030 1.660000e-07 69.4
5 TraesCS1D01G156000 chr1A 95.062 7412 247 52 998 8380 282702290 282694969 0.000000e+00 11550.0
6 TraesCS1D01G156000 chr1A 88.983 472 34 7 4 473 282704673 282704218 1.340000e-157 568.0
7 TraesCS1D01G156000 chr1A 91.935 62 3 2 627 687 282702405 282702345 1.640000e-12 86.1
8 TraesCS1D01G156000 chr1A 93.478 46 3 0 7041 7086 247796299 247796254 1.660000e-07 69.4
9 TraesCS1D01G156000 chr1A 97.500 40 1 0 7041 7080 248034683 248034722 1.660000e-07 69.4
10 TraesCS1D01G156000 chr1B 96.020 6130 193 29 998 7110 314745147 314739052 0.000000e+00 9921.0
11 TraesCS1D01G156000 chr1B 93.169 1259 41 18 7160 8380 314739047 314737796 0.000000e+00 1807.0
12 TraesCS1D01G156000 chr1B 87.615 759 60 14 8466 9192 342028587 342029343 0.000000e+00 850.0
13 TraesCS1D01G156000 chr1B 84.815 540 61 14 5 527 314745854 314745319 2.940000e-144 523.0
14 TraesCS1D01G156000 chr1B 84.874 119 8 6 570 687 314745319 314745210 2.710000e-20 111.0
15 TraesCS1D01G156000 chr7B 89.894 752 50 8 8466 9192 709839709 709840459 0.000000e+00 944.0
16 TraesCS1D01G156000 chr7B 82.609 759 48 29 8466 9192 417609693 417608987 2.210000e-165 593.0
17 TraesCS1D01G156000 chr7B 85.294 68 10 0 4991 5058 145376804 145376737 4.600000e-08 71.3
18 TraesCS1D01G156000 chr5D 87.979 757 58 10 8466 9192 453974499 453975252 0.000000e+00 863.0
19 TraesCS1D01G156000 chr5D 88.048 753 39 11 8466 9192 540990104 540989377 0.000000e+00 845.0
20 TraesCS1D01G156000 chr5D 79.362 470 66 14 10 453 41440989 41441453 1.500000e-77 302.0
21 TraesCS1D01G156000 chr5D 83.401 247 37 3 3 248 155855669 155855912 9.290000e-55 226.0
22 TraesCS1D01G156000 chr5D 80.669 269 41 9 301 566 460100598 460100858 2.020000e-46 198.0
23 TraesCS1D01G156000 chr5D 79.487 273 44 11 300 566 533549516 533549782 5.670000e-42 183.0
24 TraesCS1D01G156000 chr6A 87.664 762 58 12 8466 9192 352671011 352671771 0.000000e+00 854.0
25 TraesCS1D01G156000 chr7D 90.361 664 33 12 8547 9192 186800194 186800844 0.000000e+00 843.0
26 TraesCS1D01G156000 chr7D 87.925 265 17 7 8466 8716 430991288 430991551 1.940000e-76 298.0
27 TraesCS1D01G156000 chr7D 79.008 262 44 10 301 557 37578870 37579125 1.590000e-37 169.0
28 TraesCS1D01G156000 chr7D 89.130 92 7 1 8380 8468 186813538 186813447 2.710000e-20 111.0
29 TraesCS1D01G156000 chr7D 88.889 54 4 2 7037 7089 82903912 82903860 2.140000e-06 65.8
30 TraesCS1D01G156000 chr3D 85.620 758 51 18 8466 9192 143621149 143620419 0.000000e+00 743.0
31 TraesCS1D01G156000 chr3D 76.451 586 85 30 4 546 45355496 45356071 1.520000e-67 268.0
32 TraesCS1D01G156000 chr4A 83.838 792 62 20 8466 9192 130451893 130452683 0.000000e+00 693.0
33 TraesCS1D01G156000 chr3B 89.730 555 30 6 8665 9192 650013332 650013886 0.000000e+00 684.0
34 TraesCS1D01G156000 chr3B 82.695 757 73 23 8466 9192 744513275 744514003 3.650000e-173 619.0
35 TraesCS1D01G156000 chr3B 81.818 759 61 29 8466 9192 240266620 240265907 4.820000e-157 566.0
36 TraesCS1D01G156000 chr4B 90.123 486 30 2 8725 9192 166658000 166657515 4.720000e-172 616.0
37 TraesCS1D01G156000 chr2B 85.328 518 37 15 8466 8959 43628869 43628367 4.960000e-137 499.0
38 TraesCS1D01G156000 chr2B 76.756 598 87 27 3 557 155115123 155115711 4.200000e-73 287.0
39 TraesCS1D01G156000 chr2B 76.223 593 100 20 3 569 295533696 295533119 9.090000e-70 276.0
40 TraesCS1D01G156000 chr2D 85.863 481 40 11 8466 8945 460567708 460567255 3.860000e-133 486.0
41 TraesCS1D01G156000 chr2D 77.138 608 90 28 3 569 171446409 171445810 3.220000e-79 307.0
42 TraesCS1D01G156000 chr2D 97.500 40 1 0 7041 7080 37490034 37490073 1.660000e-07 69.4
43 TraesCS1D01G156000 chr6B 77.408 571 105 20 3 568 58118997 58119548 1.490000e-82 318.0
44 TraesCS1D01G156000 chr5B 76.678 596 91 29 3 557 516087753 516088341 4.200000e-73 287.0
45 TraesCS1D01G156000 chr6D 78.419 468 56 19 10 437 394833175 394833637 7.080000e-66 263.0
46 TraesCS1D01G156000 chr3A 80.297 269 45 7 301 566 638773951 638774214 7.280000e-46 196.0
47 TraesCS1D01G156000 chr5A 79.336 271 46 8 301 568 709284962 709284699 2.040000e-41 182.0
48 TraesCS1D01G156000 chr7A 97.727 44 1 0 7037 7080 411492985 411493028 9.900000e-10 76.8
49 TraesCS1D01G156000 chr2A 97.436 39 1 0 7042 7080 749896831 749896869 5.960000e-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 TraesCS1D01G156000 chr1D 219722782 219731973 9191 True 8202.500000 15134 100.000000 1 9192 2 chr1D.!!$R2 9191
1 TraesCS1D01G156000 chr1A 282694969 282704673 9704 True 4068.033333 11550 91.993333 4 8380 3 chr1A.!!$R2 8376
2 TraesCS1D01G156000 chr1B 314737796 314745854 8058 True 3090.500000 9921 89.719500 5 8380 4 chr1B.!!$R1 8375
3 TraesCS1D01G156000 chr1B 342028587 342029343 756 False 850.000000 850 87.615000 8466 9192 1 chr1B.!!$F1 726
4 TraesCS1D01G156000 chr7B 709839709 709840459 750 False 944.000000 944 89.894000 8466 9192 1 chr7B.!!$F1 726
5 TraesCS1D01G156000 chr7B 417608987 417609693 706 True 593.000000 593 82.609000 8466 9192 1 chr7B.!!$R2 726
6 TraesCS1D01G156000 chr5D 453974499 453975252 753 False 863.000000 863 87.979000 8466 9192 1 chr5D.!!$F3 726
7 TraesCS1D01G156000 chr5D 540989377 540990104 727 True 845.000000 845 88.048000 8466 9192 1 chr5D.!!$R1 726
8 TraesCS1D01G156000 chr6A 352671011 352671771 760 False 854.000000 854 87.664000 8466 9192 1 chr6A.!!$F1 726
9 TraesCS1D01G156000 chr7D 186800194 186800844 650 False 843.000000 843 90.361000 8547 9192 1 chr7D.!!$F2 645
10 TraesCS1D01G156000 chr3D 143620419 143621149 730 True 743.000000 743 85.620000 8466 9192 1 chr3D.!!$R1 726
11 TraesCS1D01G156000 chr3D 45355496 45356071 575 False 268.000000 268 76.451000 4 546 1 chr3D.!!$F1 542
12 TraesCS1D01G156000 chr4A 130451893 130452683 790 False 693.000000 693 83.838000 8466 9192 1 chr4A.!!$F1 726
13 TraesCS1D01G156000 chr3B 650013332 650013886 554 False 684.000000 684 89.730000 8665 9192 1 chr3B.!!$F1 527
14 TraesCS1D01G156000 chr3B 744513275 744514003 728 False 619.000000 619 82.695000 8466 9192 1 chr3B.!!$F2 726
15 TraesCS1D01G156000 chr3B 240265907 240266620 713 True 566.000000 566 81.818000 8466 9192 1 chr3B.!!$R1 726
16 TraesCS1D01G156000 chr2B 43628367 43628869 502 True 499.000000 499 85.328000 8466 8959 1 chr2B.!!$R1 493
17 TraesCS1D01G156000 chr2B 155115123 155115711 588 False 287.000000 287 76.756000 3 557 1 chr2B.!!$F1 554
18 TraesCS1D01G156000 chr2B 295533119 295533696 577 True 276.000000 276 76.223000 3 569 1 chr2B.!!$R2 566
19 TraesCS1D01G156000 chr2D 171445810 171446409 599 True 307.000000 307 77.138000 3 569 1 chr2D.!!$R1 566
20 TraesCS1D01G156000 chr6B 58118997 58119548 551 False 318.000000 318 77.408000 3 568 1 chr6B.!!$F1 565
21 TraesCS1D01G156000 chr5B 516087753 516088341 588 False 287.000000 287 76.678000 3 557 1 chr5B.!!$F1 554

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
45 47 0.246360 CTACACATGTCCGGTGCTGA 59.754 55.0 0.00 0.0 39.87 4.26 F
1278 3077 0.183971 CCTCTCCCTCTTCTCCGCTA 59.816 60.0 0.00 0.0 0.00 4.26 F
2492 4301 0.602905 GTGCGGCTCTTGTTAGTGGT 60.603 55.0 0.00 0.0 0.00 4.16 F
3372 5197 0.108186 TGGTCATACTTGAGGCTGCG 60.108 55.0 0.00 0.0 30.85 5.18 F
5021 6850 0.455410 TGGTTGCTGAACTGTGTTGC 59.545 50.0 0.00 0.0 32.15 4.17 F
6707 8545 0.109342 CAGAAGGTGTCCTTGCCACT 59.891 55.0 5.73 0.0 44.82 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1762 3570 0.387929 CCATCCATGTGGCTCAATGC 59.612 55.000 0.00 0.0 41.94 3.56 R
3118 4943 2.158295 ACCCCTTGTCAGACTAGTGACT 60.158 50.000 0.00 0.0 46.06 3.41 R
3751 5577 1.263356 CGGTTGGGACTTCAGGAGTA 58.737 55.000 0.00 0.0 39.19 2.59 R
5127 6956 0.687757 CTAGCCCCACCTAGACTGCA 60.688 60.000 0.00 0.0 37.57 4.41 R
6850 8688 1.405526 GCTGAGAATTACGAGGCACCA 60.406 52.381 0.00 0.0 0.00 4.17 R
8456 10340 0.108520 GACTCGGCCAAATACGTGGA 60.109 55.000 2.24 0.0 41.65 4.02 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
45 47 0.246360 CTACACATGTCCGGTGCTGA 59.754 55.000 0.00 0.00 39.87 4.26
147 151 0.393944 TCCTCGTCTACGCATGTCCT 60.394 55.000 0.00 0.00 39.60 3.85
455 515 2.061773 ACAACTTCGAGACGCATCAAG 58.938 47.619 0.00 0.00 0.00 3.02
488 557 1.653151 GGGGATGTCGTTCAGCTTAC 58.347 55.000 0.00 0.00 32.48 2.34
490 559 2.614481 GGGGATGTCGTTCAGCTTACAA 60.614 50.000 0.00 0.00 32.48 2.41
491 560 2.415512 GGGATGTCGTTCAGCTTACAAC 59.584 50.000 0.00 0.00 32.48 3.32
492 561 3.326747 GGATGTCGTTCAGCTTACAACT 58.673 45.455 0.00 0.00 32.48 3.16
501 584 6.926826 TCGTTCAGCTTACAACTTTCAGATTA 59.073 34.615 0.00 0.00 0.00 1.75
504 587 9.899226 GTTCAGCTTACAACTTTCAGATTATTT 57.101 29.630 0.00 0.00 0.00 1.40
546 629 1.479323 GCTACCGTTATGACTGTGGGA 59.521 52.381 0.00 0.00 0.00 4.37
557 641 3.213506 TGACTGTGGGAAATGTTGAGTG 58.786 45.455 0.00 0.00 0.00 3.51
1065 2863 0.762418 TCAGTCCTCCCTCGCAAAAA 59.238 50.000 0.00 0.00 0.00 1.94
1236 3034 1.065251 CTTAGACGAGGAAGGTACGCC 59.935 57.143 0.00 0.00 0.00 5.68
1278 3077 0.183971 CCTCTCCCTCTTCTCCGCTA 59.816 60.000 0.00 0.00 0.00 4.26
1343 3149 3.581687 GATCTGGCTCGATCCCGGC 62.582 68.421 2.20 0.00 34.98 6.13
1403 3209 2.935238 GCTGGGACTGAATGCTCGTTTA 60.935 50.000 0.00 0.00 0.00 2.01
1533 3339 2.885113 GCTTGCCCAATCCCGTTC 59.115 61.111 0.00 0.00 0.00 3.95
1591 3397 2.863809 ACGCCCTTCTGATTTCACTTT 58.136 42.857 0.00 0.00 0.00 2.66
1695 3503 3.270877 CCAAGGTACTCCAATGCAGTAC 58.729 50.000 5.94 5.94 43.82 2.73
1740 3548 6.317391 GTGTTTTAGCTATGCTTCTGGATTCT 59.683 38.462 0.00 0.00 40.44 2.40
1762 3570 0.618458 TTGCTGGGCCTGGTAGTTAG 59.382 55.000 12.70 0.00 0.00 2.34
2315 4124 6.535865 TGTTTCATCGCGTGTAGGTTATTATT 59.464 34.615 5.77 0.00 0.00 1.40
2492 4301 0.602905 GTGCGGCTCTTGTTAGTGGT 60.603 55.000 0.00 0.00 0.00 4.16
2616 4425 7.500892 TGCTTTAATTCTAAACAGACAAGTCCA 59.499 33.333 0.00 0.00 0.00 4.02
2980 4797 9.578576 AAGTATGTCCATGAAAACATGCTATAT 57.421 29.630 18.99 8.00 44.63 0.86
2997 4814 6.519382 TGCTATATCTCTGACAAATGACCTG 58.481 40.000 0.00 0.00 0.00 4.00
3010 4827 4.927267 AATGACCTGTGAATGACCCTTA 57.073 40.909 0.00 0.00 0.00 2.69
3051 4876 7.302948 TCTTCCTACTGGGCTATCTAAACATA 58.697 38.462 0.00 0.00 34.39 2.29
3052 4877 7.451877 TCTTCCTACTGGGCTATCTAAACATAG 59.548 40.741 0.00 0.00 34.39 2.23
3053 4878 6.621394 TCCTACTGGGCTATCTAAACATAGT 58.379 40.000 0.00 0.00 34.39 2.12
3054 4879 7.073854 TCCTACTGGGCTATCTAAACATAGTT 58.926 38.462 0.00 0.00 34.39 2.24
3055 4880 7.232941 TCCTACTGGGCTATCTAAACATAGTTC 59.767 40.741 0.00 0.00 34.39 3.01
3056 4881 6.808321 ACTGGGCTATCTAAACATAGTTCA 57.192 37.500 0.00 0.00 0.00 3.18
3057 4882 7.380423 ACTGGGCTATCTAAACATAGTTCAT 57.620 36.000 0.00 0.00 0.00 2.57
3058 4883 7.806180 ACTGGGCTATCTAAACATAGTTCATT 58.194 34.615 0.00 0.00 0.00 2.57
3118 4943 1.821216 GGTTGGCTGTTAGCAAGCTA 58.179 50.000 2.99 0.00 44.75 3.32
3345 5170 0.969894 AGTCCTGTCTCCGGAACAAG 59.030 55.000 5.23 7.28 31.13 3.16
3372 5197 0.108186 TGGTCATACTTGAGGCTGCG 60.108 55.000 0.00 0.00 30.85 5.18
3594 5419 7.267857 TCTGTATGACCTTGATTGTATCACAG 58.732 38.462 0.00 0.00 39.39 3.66
3655 5480 8.534496 AGTTTTATTTCTTCATTCCATCCCTTG 58.466 33.333 0.00 0.00 0.00 3.61
3656 5481 6.469782 TTATTTCTTCATTCCATCCCTTGC 57.530 37.500 0.00 0.00 0.00 4.01
3855 5681 1.197721 GGTTGGAAGATGCAACTGTCG 59.802 52.381 13.22 0.00 46.11 4.35
3879 5705 8.912658 TCGTCTTGTTGATTTTCTATATATCGC 58.087 33.333 0.00 0.00 0.00 4.58
4014 5843 4.283467 GGGAAAAGGCCTTGACTAATTTGT 59.717 41.667 21.33 0.00 0.00 2.83
4017 5846 7.438564 GGAAAAGGCCTTGACTAATTTGTTTA 58.561 34.615 21.33 0.00 0.00 2.01
4168 5997 3.181461 GGGACTGCATGCTCATTACTACT 60.181 47.826 20.33 0.00 0.00 2.57
4174 6003 4.395854 TGCATGCTCATTACTACTTTGGTG 59.604 41.667 20.33 0.00 0.00 4.17
4541 6370 5.817816 ACTAGTTTGCTATCAGCGCTTTTAT 59.182 36.000 7.50 4.32 46.26 1.40
4547 6376 4.747108 TGCTATCAGCGCTTTTATCTTCTC 59.253 41.667 7.50 0.00 46.26 2.87
4753 6582 4.646040 CAGGTGATTGCCAATTCATCCTTA 59.354 41.667 0.00 0.00 0.00 2.69
4793 6622 8.570488 TGTGAAGATACTGAAACTTCGTAGTAA 58.430 33.333 0.00 0.00 41.67 2.24
4794 6623 8.848528 GTGAAGATACTGAAACTTCGTAGTAAC 58.151 37.037 0.00 0.00 41.67 2.50
4795 6624 8.790718 TGAAGATACTGAAACTTCGTAGTAACT 58.209 33.333 0.00 0.00 41.67 2.24
4798 6627 9.447157 AGATACTGAAACTTCGTAGTAACTAGT 57.553 33.333 0.00 0.00 33.17 2.57
4878 6707 6.435591 GGATTTCCTTCTGAAGAAACAGGAAT 59.564 38.462 18.68 7.74 36.45 3.01
4912 6741 6.383147 AGGCAACCTGAAACTATAACTAGCTA 59.617 38.462 0.00 0.00 29.57 3.32
4977 6806 9.472361 CTGTCATTTTGAACAAGAGAATGATTT 57.528 29.630 12.85 0.00 38.52 2.17
5021 6850 0.455410 TGGTTGCTGAACTGTGTTGC 59.545 50.000 0.00 0.00 32.15 4.17
5030 6859 1.064060 GAACTGTGTTGCGCTGACTTT 59.936 47.619 9.73 0.52 0.00 2.66
5043 6872 5.874810 TGCGCTGACTTTCTTTATAATCTGT 59.125 36.000 9.73 0.00 0.00 3.41
5248 7077 2.086869 CAACATACCCCAACAGCTCAG 58.913 52.381 0.00 0.00 0.00 3.35
5258 7087 5.103515 ACCCCAACAGCTCAGGATAAATTAT 60.104 40.000 0.00 0.00 0.00 1.28
5628 7458 7.831691 TGAGGTCAGTGGAAAATTTCATTTA 57.168 32.000 8.09 0.00 0.00 1.40
5690 7520 4.879545 TCCTTTTAATTTCGGAATCCCTCG 59.120 41.667 0.00 0.00 0.00 4.63
5743 7575 5.613795 CGCGCAACTTTATCTGTGAAAGTAA 60.614 40.000 8.75 0.00 44.43 2.24
6026 7862 9.726232 CATCTCAACACTGTTATGATTTAATGG 57.274 33.333 0.00 0.00 0.00 3.16
6301 8137 4.758165 GTGGTCCTTTTCACGGAAGATAAA 59.242 41.667 0.00 0.00 31.13 1.40
6596 8434 0.736053 TGGTGTTTGTTGACGCTTCC 59.264 50.000 0.00 0.00 0.00 3.46
6650 8488 4.527944 AGCCTTTAAGATCCTTGCCTTAC 58.472 43.478 0.00 0.00 0.00 2.34
6707 8545 0.109342 CAGAAGGTGTCCTTGCCACT 59.891 55.000 5.73 0.00 44.82 4.00
6783 8621 6.474140 TGTTCCCGCTATCTCTGTTATTAA 57.526 37.500 0.00 0.00 0.00 1.40
6808 8646 8.682936 ATCTTAATCAAATACCCTCATGTGAC 57.317 34.615 0.00 0.00 0.00 3.67
6848 8686 7.591165 TGCTTCTCATGATTTTCTTTCAGAAG 58.409 34.615 0.00 2.88 35.37 2.85
6850 8688 8.081025 GCTTCTCATGATTTTCTTTCAGAAGTT 58.919 33.333 12.69 0.00 35.37 2.66
6974 8812 9.238368 TCATTTTGGGGTTGACTTTATTAGTAG 57.762 33.333 0.00 0.00 37.17 2.57
7080 8918 8.734386 CATCTTATATTTTGGAATGGAGGTAGC 58.266 37.037 0.00 0.00 0.00 3.58
7104 8943 6.183360 GCACTATTTACCCTTTTAGCAGACAG 60.183 42.308 0.00 0.00 0.00 3.51
7112 8951 5.066593 CCCTTTTAGCAGACAGAAGACTTT 58.933 41.667 0.00 0.00 0.00 2.66
7123 8962 7.148390 GCAGACAGAAGACTTTAGGGTAAAATC 60.148 40.741 0.00 0.00 0.00 2.17
7156 8995 8.246871 TCATAATGTTCTAGACTCTGACAGTTG 58.753 37.037 1.59 0.00 34.41 3.16
7157 8996 6.412362 AATGTTCTAGACTCTGACAGTTGT 57.588 37.500 1.59 3.08 34.41 3.32
7173 9016 4.333649 ACAGTTGTGTCTGACATTTCTGTG 59.666 41.667 26.94 17.71 38.62 3.66
7184 9027 7.702772 GTCTGACATTTCTGTGTAGAATCGTAT 59.297 37.037 2.24 0.00 42.25 3.06
7185 9028 8.899771 TCTGACATTTCTGTGTAGAATCGTATA 58.100 33.333 0.00 0.00 42.25 1.47
7196 9039 8.172484 TGTGTAGAATCGTATACATGTTTTTGC 58.828 33.333 2.30 0.00 34.13 3.68
7200 9043 4.587211 TCGTATACATGTTTTTGCGGAC 57.413 40.909 2.30 0.00 0.00 4.79
7210 9053 6.016276 ACATGTTTTTGCGGACTAAGAAGAAT 60.016 34.615 0.00 0.00 0.00 2.40
7213 9056 7.262048 TGTTTTTGCGGACTAAGAAGAATTTT 58.738 30.769 0.00 0.00 0.00 1.82
7251 9094 6.054941 TGGGTGTGCATCTACATGTAATAAG 58.945 40.000 7.06 0.00 32.43 1.73
7868 9715 1.002624 CAGCGGGCCCAAAGAAGTA 60.003 57.895 24.92 0.00 0.00 2.24
7892 9739 2.859526 TGAAGCTAGCAGTCAGATCG 57.140 50.000 18.83 0.00 0.00 3.69
7945 9792 2.611974 ATTGTTGCGAACGGCTAAAG 57.388 45.000 0.00 0.00 44.05 1.85
8077 9933 1.895131 GGAATCCCACTGTTGTTGCAT 59.105 47.619 0.00 0.00 0.00 3.96
8192 10049 7.560991 TGCAATAATACTGAAATGGAATGTCCT 59.439 33.333 0.00 0.00 37.46 3.85
8197 10054 8.915057 AATACTGAAATGGAATGTCCTATCTG 57.085 34.615 0.00 0.00 37.46 2.90
8198 10055 5.128919 ACTGAAATGGAATGTCCTATCTGC 58.871 41.667 0.00 0.00 37.46 4.26
8199 10056 4.464008 TGAAATGGAATGTCCTATCTGCC 58.536 43.478 0.00 0.00 37.46 4.85
8201 10058 1.140312 TGGAATGTCCTATCTGCCCC 58.860 55.000 0.00 0.00 37.46 5.80
8203 10060 1.777272 GGAATGTCCTATCTGCCCCTT 59.223 52.381 0.00 0.00 32.53 3.95
8204 10061 2.175715 GGAATGTCCTATCTGCCCCTTT 59.824 50.000 0.00 0.00 32.53 3.11
8205 10062 3.394606 GGAATGTCCTATCTGCCCCTTTA 59.605 47.826 0.00 0.00 32.53 1.85
8207 10064 5.458215 GGAATGTCCTATCTGCCCCTTTAAT 60.458 44.000 0.00 0.00 32.53 1.40
8208 10065 4.706842 TGTCCTATCTGCCCCTTTAATC 57.293 45.455 0.00 0.00 0.00 1.75
8210 10067 4.665009 TGTCCTATCTGCCCCTTTAATCAT 59.335 41.667 0.00 0.00 0.00 2.45
8212 10069 6.071320 GTCCTATCTGCCCCTTTAATCATTT 58.929 40.000 0.00 0.00 0.00 2.32
8213 10070 7.147213 TGTCCTATCTGCCCCTTTAATCATTTA 60.147 37.037 0.00 0.00 0.00 1.40
8214 10071 7.890655 GTCCTATCTGCCCCTTTAATCATTTAT 59.109 37.037 0.00 0.00 0.00 1.40
8215 10072 8.109634 TCCTATCTGCCCCTTTAATCATTTATC 58.890 37.037 0.00 0.00 0.00 1.75
8216 10073 8.112183 CCTATCTGCCCCTTTAATCATTTATCT 58.888 37.037 0.00 0.00 0.00 1.98
8225 10104 7.966753 CCCTTTAATCATTTATCTGATGCATCG 59.033 37.037 21.34 15.63 36.03 3.84
8295 10178 1.741327 TAACGGATCACCTAGGCGGC 61.741 60.000 9.30 0.00 35.61 6.53
8345 10229 2.681344 TCTATAACGAGAGCTGCGACAA 59.319 45.455 12.04 0.00 0.00 3.18
8365 10249 7.072030 CGACAAAGATCAATTTAATCGATCCC 58.928 38.462 0.00 0.00 36.95 3.85
8376 10260 2.951229 ATCGATCCCGCCCTTAAATT 57.049 45.000 0.00 0.00 35.37 1.82
8380 10264 5.080969 TCGATCCCGCCCTTAAATTATAG 57.919 43.478 0.00 0.00 35.37 1.31
8381 10265 4.773674 TCGATCCCGCCCTTAAATTATAGA 59.226 41.667 0.00 0.00 35.37 1.98
8382 10266 5.105473 TCGATCCCGCCCTTAAATTATAGAG 60.105 44.000 0.00 0.00 35.37 2.43
8383 10267 5.105473 CGATCCCGCCCTTAAATTATAGAGA 60.105 44.000 0.00 0.00 0.00 3.10
8384 10268 6.573680 CGATCCCGCCCTTAAATTATAGAGAA 60.574 42.308 0.00 0.00 0.00 2.87
8385 10269 6.503560 TCCCGCCCTTAAATTATAGAGAAA 57.496 37.500 0.00 0.00 0.00 2.52
8386 10270 6.902408 TCCCGCCCTTAAATTATAGAGAAAA 58.098 36.000 0.00 0.00 0.00 2.29
8387 10271 7.348033 TCCCGCCCTTAAATTATAGAGAAAAA 58.652 34.615 0.00 0.00 0.00 1.94
8388 10272 8.002459 TCCCGCCCTTAAATTATAGAGAAAAAT 58.998 33.333 0.00 0.00 0.00 1.82
8389 10273 8.638873 CCCGCCCTTAAATTATAGAGAAAAATT 58.361 33.333 0.00 0.00 0.00 1.82
8390 10274 9.678941 CCGCCCTTAAATTATAGAGAAAAATTC 57.321 33.333 0.00 0.00 0.00 2.17
8412 10296 9.825972 AATTCATTGTACGTCATTAAACTTGAG 57.174 29.630 0.00 0.00 0.00 3.02
8413 10297 7.956420 TCATTGTACGTCATTAAACTTGAGT 57.044 32.000 0.00 0.00 0.00 3.41
8414 10298 8.014322 TCATTGTACGTCATTAAACTTGAGTC 57.986 34.615 0.00 0.00 0.00 3.36
8415 10299 6.442487 TTGTACGTCATTAAACTTGAGTCG 57.558 37.500 0.00 0.00 0.00 4.18
8416 10300 4.919168 TGTACGTCATTAAACTTGAGTCGG 59.081 41.667 0.00 0.00 0.00 4.79
8417 10301 3.323243 ACGTCATTAAACTTGAGTCGGG 58.677 45.455 0.00 0.00 0.00 5.14
8418 10302 3.243975 ACGTCATTAAACTTGAGTCGGGT 60.244 43.478 0.00 0.00 0.00 5.28
8419 10303 3.122948 CGTCATTAAACTTGAGTCGGGTG 59.877 47.826 0.00 0.00 0.00 4.61
8420 10304 4.312443 GTCATTAAACTTGAGTCGGGTGA 58.688 43.478 0.00 0.00 0.00 4.02
8421 10305 4.151867 GTCATTAAACTTGAGTCGGGTGAC 59.848 45.833 0.00 0.00 45.86 3.67
8432 10316 2.951726 GTCGGGTGACAGTTTAGTACC 58.048 52.381 0.00 0.00 44.82 3.34
8433 10317 2.297033 GTCGGGTGACAGTTTAGTACCA 59.703 50.000 0.00 0.00 44.82 3.25
8434 10318 2.297033 TCGGGTGACAGTTTAGTACCAC 59.703 50.000 0.00 0.00 33.10 4.16
8435 10319 2.298163 CGGGTGACAGTTTAGTACCACT 59.702 50.000 0.00 0.00 33.10 4.00
8436 10320 3.507233 CGGGTGACAGTTTAGTACCACTA 59.493 47.826 0.00 0.00 33.10 2.74
8437 10321 4.616835 CGGGTGACAGTTTAGTACCACTAC 60.617 50.000 0.00 0.00 28.93 2.73
8438 10322 4.281688 GGGTGACAGTTTAGTACCACTACA 59.718 45.833 0.00 0.00 28.93 2.74
8439 10323 5.221501 GGGTGACAGTTTAGTACCACTACAA 60.222 44.000 0.00 0.00 28.93 2.41
8440 10324 6.282930 GGTGACAGTTTAGTACCACTACAAA 58.717 40.000 0.00 0.00 28.93 2.83
8441 10325 6.762661 GGTGACAGTTTAGTACCACTACAAAA 59.237 38.462 0.00 0.00 28.93 2.44
8442 10326 7.443272 GGTGACAGTTTAGTACCACTACAAAAT 59.557 37.037 0.00 0.00 28.93 1.82
8443 10327 9.480053 GTGACAGTTTAGTACCACTACAAAATA 57.520 33.333 0.00 0.00 28.93 1.40
8444 10328 9.480053 TGACAGTTTAGTACCACTACAAAATAC 57.520 33.333 0.00 0.00 28.93 1.89
8445 10329 8.837788 ACAGTTTAGTACCACTACAAAATACC 57.162 34.615 0.00 0.00 28.93 2.73
8446 10330 7.879677 ACAGTTTAGTACCACTACAAAATACCC 59.120 37.037 0.00 0.00 28.93 3.69
8447 10331 7.063780 CAGTTTAGTACCACTACAAAATACCCG 59.936 40.741 0.00 0.00 28.93 5.28
8448 10332 6.849085 TTAGTACCACTACAAAATACCCGA 57.151 37.500 0.00 0.00 28.93 5.14
8449 10333 5.743636 AGTACCACTACAAAATACCCGAA 57.256 39.130 0.00 0.00 0.00 4.30
8450 10334 5.482006 AGTACCACTACAAAATACCCGAAC 58.518 41.667 0.00 0.00 0.00 3.95
8451 10335 4.628963 ACCACTACAAAATACCCGAACT 57.371 40.909 0.00 0.00 0.00 3.01
8452 10336 5.743636 ACCACTACAAAATACCCGAACTA 57.256 39.130 0.00 0.00 0.00 2.24
8453 10337 5.482006 ACCACTACAAAATACCCGAACTAC 58.518 41.667 0.00 0.00 0.00 2.73
8454 10338 4.563976 CCACTACAAAATACCCGAACTACG 59.436 45.833 0.00 0.00 42.18 3.51
8509 10395 2.281484 GCTTTGACCGCCACCTGA 60.281 61.111 0.00 0.00 0.00 3.86
8515 10401 2.680352 ACCGCCACCTGATCGAGT 60.680 61.111 0.00 0.00 0.00 4.18
8564 10466 3.512033 TTTTGCAAAAACGCCAGTACT 57.488 38.095 21.94 0.00 0.00 2.73
8566 10468 4.634184 TTTGCAAAAACGCCAGTACTTA 57.366 36.364 10.02 0.00 0.00 2.24
8569 10471 3.628487 TGCAAAAACGCCAGTACTTAGTT 59.372 39.130 0.00 0.00 0.00 2.24
8571 10473 4.496840 GCAAAAACGCCAGTACTTAGTTGT 60.497 41.667 0.00 0.00 0.00 3.32
8765 10793 1.303398 TCGTCTTCCAGCTCCGTCT 60.303 57.895 0.00 0.00 0.00 4.18
8865 10893 2.481854 GTCTAGCACTGATGAGCATGG 58.518 52.381 0.00 0.00 32.15 3.66
8889 10917 3.181475 GGATGGATCTTCTACAAGTGCGA 60.181 47.826 0.00 0.00 0.00 5.10
9147 11222 6.868864 GCACTCTGAACTTTATTGTCACTCTA 59.131 38.462 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.511464 CCAGCACGAGTCGTACGTC 60.511 63.158 19.43 10.06 42.07 4.34
1 2 0.950555 TACCAGCACGAGTCGTACGT 60.951 55.000 19.43 13.54 44.83 3.57
66 68 0.524414 CCGGAGACACGTCATGTACA 59.476 55.000 0.00 0.00 43.56 2.90
147 151 2.899838 GTCGGTGTTGCCAGCACA 60.900 61.111 13.79 0.00 39.05 4.57
283 319 3.712907 TTAGCCACCGTGGAGCCC 61.713 66.667 22.37 3.18 40.96 5.19
419 477 2.858344 AGTTGTGACTCGAGTGAAAACG 59.142 45.455 25.92 0.00 0.00 3.60
478 547 9.899226 AAATAATCTGAAAGTTGTAAGCTGAAC 57.101 29.630 0.00 0.00 33.76 3.18
490 559 9.750125 GGTGAAACTGAAAAATAATCTGAAAGT 57.250 29.630 0.00 0.00 36.74 2.66
511 594 0.457853 GTAGCGATGCAGACGGTGAA 60.458 55.000 23.80 8.32 41.38 3.18
546 629 5.163663 ACAACAATCACGACACTCAACATTT 60.164 36.000 0.00 0.00 0.00 2.32
557 641 6.503616 TTGCAATAAAACAACAATCACGAC 57.496 33.333 0.00 0.00 0.00 4.34
631 1802 3.428413 ACTATGGCCACCTAACGTTTT 57.572 42.857 8.16 0.00 0.00 2.43
632 1803 3.244630 TGAACTATGGCCACCTAACGTTT 60.245 43.478 8.16 0.00 0.00 3.60
633 1804 2.303600 TGAACTATGGCCACCTAACGTT 59.696 45.455 8.16 5.88 0.00 3.99
634 1805 1.903860 TGAACTATGGCCACCTAACGT 59.096 47.619 8.16 0.00 0.00 3.99
635 1806 2.684001 TGAACTATGGCCACCTAACG 57.316 50.000 8.16 0.00 0.00 3.18
636 1807 3.560068 CGATTGAACTATGGCCACCTAAC 59.440 47.826 8.16 0.08 0.00 2.34
637 1808 3.452990 TCGATTGAACTATGGCCACCTAA 59.547 43.478 8.16 0.00 0.00 2.69
638 1809 3.035363 TCGATTGAACTATGGCCACCTA 58.965 45.455 8.16 0.00 0.00 3.08
640 1811 2.325583 TCGATTGAACTATGGCCACC 57.674 50.000 8.16 0.00 0.00 4.61
1065 2863 4.535425 CGAGTCTTTGTCTCGCGT 57.465 55.556 5.77 0.00 45.77 6.01
1403 3209 2.162608 CGAGTAGTACTCTGCAGCAAGT 59.837 50.000 24.35 11.16 42.92 3.16
1533 3339 1.988293 TCTAGCGGGAGGAAGATCAG 58.012 55.000 0.00 0.00 0.00 2.90
1591 3397 4.879197 ATGCATCAGTATTCATCCGAGA 57.121 40.909 0.00 0.00 0.00 4.04
1695 3503 6.683974 ACACGATAAAAGAAAGATGGGATG 57.316 37.500 0.00 0.00 0.00 3.51
1740 3548 1.295020 ACTACCAGGCCCAGCAATTA 58.705 50.000 0.00 0.00 0.00 1.40
1762 3570 0.387929 CCATCCATGTGGCTCAATGC 59.612 55.000 0.00 0.00 41.94 3.56
1956 3764 5.646360 AGATCCCCAGTTTAAAACATGTACG 59.354 40.000 0.00 0.00 0.00 3.67
2315 4124 4.344968 TCCTTCATCAGAGAACTTGTCACA 59.655 41.667 0.00 0.00 0.00 3.58
2602 4411 4.396166 CACAACTTCTGGACTTGTCTGTTT 59.604 41.667 0.61 0.00 0.00 2.83
2616 4425 4.464008 TGCTCCATCTTTTCACAACTTCT 58.536 39.130 0.00 0.00 0.00 2.85
2830 4639 6.112927 AGCTTTCAAGAGATTCAAGAGAGT 57.887 37.500 0.00 0.00 0.00 3.24
2831 4640 6.621164 GCAAGCTTTCAAGAGATTCAAGAGAG 60.621 42.308 0.00 0.00 0.00 3.20
2832 4641 5.180868 GCAAGCTTTCAAGAGATTCAAGAGA 59.819 40.000 0.00 0.00 0.00 3.10
2833 4642 5.181622 AGCAAGCTTTCAAGAGATTCAAGAG 59.818 40.000 0.00 0.00 0.00 2.85
2834 4643 5.068636 AGCAAGCTTTCAAGAGATTCAAGA 58.931 37.500 0.00 0.00 0.00 3.02
2835 4644 5.373981 AGCAAGCTTTCAAGAGATTCAAG 57.626 39.130 0.00 0.00 0.00 3.02
2836 4645 6.883217 AGATAGCAAGCTTTCAAGAGATTCAA 59.117 34.615 13.58 0.00 0.00 2.69
2837 4646 6.413052 AGATAGCAAGCTTTCAAGAGATTCA 58.587 36.000 13.58 0.00 0.00 2.57
2838 4647 6.923928 AGATAGCAAGCTTTCAAGAGATTC 57.076 37.500 13.58 0.00 0.00 2.52
2839 4648 8.046107 ACTTAGATAGCAAGCTTTCAAGAGATT 58.954 33.333 19.94 3.96 0.00 2.40
2840 4649 7.563906 ACTTAGATAGCAAGCTTTCAAGAGAT 58.436 34.615 19.94 0.00 0.00 2.75
2980 4797 4.687901 TTCACAGGTCATTTGTCAGAGA 57.312 40.909 0.00 0.00 0.00 3.10
2997 4814 7.855409 GCAAACAAAAATTTAAGGGTCATTCAC 59.145 33.333 0.00 0.00 0.00 3.18
3010 4827 8.882736 CAGTAGGAAGAAAGCAAACAAAAATTT 58.117 29.630 0.00 0.00 0.00 1.82
3118 4943 2.158295 ACCCCTTGTCAGACTAGTGACT 60.158 50.000 0.00 0.00 46.06 3.41
3345 5170 3.629398 CCTCAAGTATGACCATTTCTGCC 59.371 47.826 0.00 0.00 0.00 4.85
3372 5197 5.237344 ACCATTTAGATCAGTTATTGCTCGC 59.763 40.000 0.00 0.00 0.00 5.03
3579 5404 8.298854 TGATTGGAAAACTGTGATACAATCAAG 58.701 33.333 21.88 0.00 45.37 3.02
3655 5480 6.471519 AGAGTGAGTATTTAATACGAACACGC 59.528 38.462 22.74 22.74 40.37 5.34
3656 5481 7.695201 TCAGAGTGAGTATTTAATACGAACACG 59.305 37.037 22.40 15.39 40.37 4.49
3751 5577 1.263356 CGGTTGGGACTTCAGGAGTA 58.737 55.000 0.00 0.00 39.19 2.59
3763 5589 1.453197 GCCCTTATCCACGGTTGGG 60.453 63.158 0.00 0.00 44.11 4.12
3855 5681 8.988934 TGGCGATATATAGAAAATCAACAAGAC 58.011 33.333 0.00 0.00 0.00 3.01
3875 5701 5.299279 CCTGTAAAAACAATAGGATGGCGAT 59.701 40.000 0.00 0.00 0.00 4.58
3876 5702 4.638421 CCTGTAAAAACAATAGGATGGCGA 59.362 41.667 0.00 0.00 0.00 5.54
3877 5703 4.398044 ACCTGTAAAAACAATAGGATGGCG 59.602 41.667 0.00 0.00 32.86 5.69
3878 5704 5.417580 TGACCTGTAAAAACAATAGGATGGC 59.582 40.000 0.00 0.00 32.86 4.40
3879 5705 6.659242 AGTGACCTGTAAAAACAATAGGATGG 59.341 38.462 0.00 0.00 32.86 3.51
3956 5782 8.671384 TTAAGAATGATGGGGTTTTCGTATAG 57.329 34.615 0.00 0.00 0.00 1.31
3988 5817 4.569719 TTAGTCAAGGCCTTTTCCCTAG 57.430 45.455 17.61 2.32 30.93 3.02
4168 5997 6.184789 AGTAGGAACAAAGAAAGACACCAAA 58.815 36.000 0.00 0.00 0.00 3.28
4174 6003 8.884726 GGATCATTAGTAGGAACAAAGAAAGAC 58.115 37.037 0.00 0.00 0.00 3.01
4265 6094 9.372189 TGATCAGAGATTAAACTCTCCATATCA 57.628 33.333 12.01 14.14 44.18 2.15
4514 6343 2.738643 GCGCTGATAGCAAACTAGTGGA 60.739 50.000 0.00 0.00 42.58 4.02
4516 6345 2.544685 AGCGCTGATAGCAAACTAGTG 58.455 47.619 10.39 0.00 42.58 2.74
4541 6370 3.173151 TCCTGCCAACATGTAGAGAAGA 58.827 45.455 0.00 0.00 0.00 2.87
4547 6376 3.614092 AGTTCATCCTGCCAACATGTAG 58.386 45.455 0.00 0.00 0.00 2.74
4642 6471 8.894592 TCTTTAGCATCAGGAATATCCCTAATT 58.105 33.333 0.00 0.00 37.19 1.40
4726 6555 3.499338 TGAATTGGCAATCACCTGAGTT 58.501 40.909 14.04 0.00 0.00 3.01
4753 6582 7.657761 CAGTATCTTCACAGTTAGTTTCCAACT 59.342 37.037 0.00 0.00 45.40 3.16
4766 6595 7.085116 ACTACGAAGTTTCAGTATCTTCACAG 58.915 38.462 0.00 0.00 37.78 3.66
4819 6648 6.268617 AGAGAGCAGAAGGTACATGCATAATA 59.731 38.462 0.00 0.00 42.45 0.98
4826 6655 5.528043 ACATAGAGAGCAGAAGGTACATG 57.472 43.478 0.00 0.00 0.00 3.21
4828 6657 5.756918 AGTACATAGAGAGCAGAAGGTACA 58.243 41.667 0.00 0.00 33.99 2.90
4912 6741 4.918810 AGGAAACAAAGCAAAATCTCGT 57.081 36.364 0.00 0.00 0.00 4.18
5021 6850 6.684555 GCAACAGATTATAAAGAAAGTCAGCG 59.315 38.462 0.00 0.00 0.00 5.18
5043 6872 4.947388 ACTTCCATAGCTATTTTTCCGCAA 59.053 37.500 2.64 0.00 0.00 4.85
5127 6956 0.687757 CTAGCCCCACCTAGACTGCA 60.688 60.000 0.00 0.00 37.57 4.41
5203 7032 6.294508 GGCAAACTGCTTCTACATTCCTTAAA 60.295 38.462 0.00 0.00 44.28 1.52
5676 7506 0.326927 AAAGGCGAGGGATTCCGAAA 59.673 50.000 0.00 0.00 38.33 3.46
5717 7549 2.139917 TCACAGATAAAGTTGCGCGTT 58.860 42.857 8.43 0.00 0.00 4.84
5790 7622 0.038166 TTCTTGCCAGGAAAGCGGAT 59.962 50.000 1.45 0.00 0.00 4.18
6026 7862 5.482006 AGAAAATAAGGCTCCAACAAATGC 58.518 37.500 0.00 0.00 0.00 3.56
6301 8137 2.169352 ACGAGAGCCTCAAAGCATATGT 59.831 45.455 4.29 0.00 34.23 2.29
6596 8434 4.453819 ACTTCTGAAAATTCTTCTGCCTCG 59.546 41.667 0.00 0.00 0.00 4.63
6650 8488 2.499685 GTCTGTCCGGGGGAATCG 59.500 66.667 0.00 0.00 31.38 3.34
6762 8600 7.540474 AGATTAATAACAGAGATAGCGGGAA 57.460 36.000 0.00 0.00 0.00 3.97
6783 8621 7.442364 CGTCACATGAGGGTATTTGATTAAGAT 59.558 37.037 0.00 0.00 0.00 2.40
6808 8646 4.201881 TGAGAAGCATGCTTGATTTGATCG 60.202 41.667 36.48 0.00 36.26 3.69
6848 8686 2.673368 CTGAGAATTACGAGGCACCAAC 59.327 50.000 0.00 0.00 0.00 3.77
6850 8688 1.405526 GCTGAGAATTACGAGGCACCA 60.406 52.381 0.00 0.00 0.00 4.17
6974 8812 7.541244 CTGTACGGAAAACGGAAAGAGTAGAC 61.541 46.154 0.00 0.00 43.95 2.59
7080 8918 7.103641 TCTGTCTGCTAAAAGGGTAAATAGTG 58.896 38.462 0.00 0.00 0.00 2.74
7104 8943 9.736414 AAGGTTAGATTTTACCCTAAAGTCTTC 57.264 33.333 5.42 1.76 40.45 2.87
7123 8962 9.743057 CAGAGTCTAGAACATTATGAAGGTTAG 57.257 37.037 0.00 0.00 35.26 2.34
7156 8995 6.183360 CGATTCTACACAGAAATGTCAGACAC 60.183 42.308 5.05 0.00 43.89 3.67
7157 8996 5.863935 CGATTCTACACAGAAATGTCAGACA 59.136 40.000 5.50 5.50 43.89 3.41
7173 9016 6.844279 CCGCAAAAACATGTATACGATTCTAC 59.156 38.462 0.00 0.00 0.00 2.59
7184 9027 5.992829 TCTTCTTAGTCCGCAAAAACATGTA 59.007 36.000 0.00 0.00 0.00 2.29
7185 9028 4.819630 TCTTCTTAGTCCGCAAAAACATGT 59.180 37.500 0.00 0.00 0.00 3.21
7196 9039 7.010023 CGAACTGAAAAATTCTTCTTAGTCCG 58.990 38.462 0.00 0.00 0.00 4.79
7200 9043 8.989980 AGTACCGAACTGAAAAATTCTTCTTAG 58.010 33.333 0.00 0.00 36.93 2.18
7210 9053 3.628487 CACCCAAGTACCGAACTGAAAAA 59.372 43.478 0.00 0.00 38.88 1.94
7213 9056 1.764134 ACACCCAAGTACCGAACTGAA 59.236 47.619 0.00 0.00 38.88 3.02
7612 9456 5.124138 TGGTACACCAAAACAACAGTACTTG 59.876 40.000 0.00 0.00 44.35 3.16
7868 9715 0.907486 TGACTGCTAGCTTCATGGCT 59.093 50.000 17.23 1.96 45.29 4.75
7892 9739 0.390860 CACTGACCTCCGGATCATCC 59.609 60.000 3.57 0.00 0.00 3.51
7945 9792 2.429927 AAAAACTCCTGCTGGTGGC 58.570 52.632 15.10 0.00 42.22 5.01
8077 9933 2.290367 CTGCGTTGAACAAGAATGGTGA 59.710 45.455 0.00 0.00 0.00 4.02
8121 9978 9.832445 GAGGATATAAGAAAATAGTGTGGTTCA 57.168 33.333 0.00 0.00 0.00 3.18
8192 10049 8.668653 TCAGATAAATGATTAAAGGGGCAGATA 58.331 33.333 0.00 0.00 0.00 1.98
8195 10052 7.600065 CATCAGATAAATGATTAAAGGGGCAG 58.400 38.462 0.00 0.00 37.84 4.85
8196 10053 6.015180 GCATCAGATAAATGATTAAAGGGGCA 60.015 38.462 0.00 0.00 37.84 5.36
8197 10054 6.015180 TGCATCAGATAAATGATTAAAGGGGC 60.015 38.462 0.00 0.00 37.84 5.80
8198 10055 7.528996 TGCATCAGATAAATGATTAAAGGGG 57.471 36.000 0.00 0.00 37.84 4.79
8199 10056 7.966753 CGATGCATCAGATAAATGATTAAAGGG 59.033 37.037 25.70 0.00 37.84 3.95
8205 10062 9.657419 TGTATACGATGCATCAGATAAATGATT 57.343 29.630 25.70 2.78 37.84 2.57
8225 10104 1.137513 GTGCCGAAGCCGATGTATAC 58.862 55.000 0.00 0.00 38.69 1.47
8295 10178 6.996562 TTGAAACGTATATAGCACCGTATG 57.003 37.500 0.00 0.00 32.49 2.39
8300 10183 6.047231 AGGTCTTTGAAACGTATATAGCACC 58.953 40.000 0.00 0.00 0.00 5.01
8345 10229 4.455877 GGCGGGATCGATTAAATTGATCTT 59.544 41.667 13.80 0.00 45.52 2.40
8386 10270 9.825972 CTCAAGTTTAATGACGTACAATGAATT 57.174 29.630 0.00 0.00 0.00 2.17
8387 10271 8.999431 ACTCAAGTTTAATGACGTACAATGAAT 58.001 29.630 0.00 0.00 0.00 2.57
8388 10272 8.373048 ACTCAAGTTTAATGACGTACAATGAA 57.627 30.769 0.00 0.00 0.00 2.57
8389 10273 7.148869 CGACTCAAGTTTAATGACGTACAATGA 60.149 37.037 0.00 0.00 0.00 2.57
8390 10274 6.948228 CGACTCAAGTTTAATGACGTACAATG 59.052 38.462 0.00 0.00 0.00 2.82
8391 10275 6.090358 CCGACTCAAGTTTAATGACGTACAAT 59.910 38.462 0.00 0.00 0.00 2.71
8392 10276 5.403166 CCGACTCAAGTTTAATGACGTACAA 59.597 40.000 0.00 0.00 0.00 2.41
8393 10277 4.919168 CCGACTCAAGTTTAATGACGTACA 59.081 41.667 0.00 0.00 0.00 2.90
8394 10278 4.325472 CCCGACTCAAGTTTAATGACGTAC 59.675 45.833 0.00 0.00 0.00 3.67
8395 10279 4.022068 ACCCGACTCAAGTTTAATGACGTA 60.022 41.667 0.00 0.00 0.00 3.57
8396 10280 3.243975 ACCCGACTCAAGTTTAATGACGT 60.244 43.478 0.00 0.00 0.00 4.34
8397 10281 3.122948 CACCCGACTCAAGTTTAATGACG 59.877 47.826 0.00 0.00 0.00 4.35
8398 10282 4.151867 GTCACCCGACTCAAGTTTAATGAC 59.848 45.833 0.00 0.00 39.22 3.06
8399 10283 4.202274 TGTCACCCGACTCAAGTTTAATGA 60.202 41.667 0.00 0.00 43.06 2.57
8400 10284 4.062293 TGTCACCCGACTCAAGTTTAATG 58.938 43.478 0.00 0.00 43.06 1.90
8401 10285 4.202326 ACTGTCACCCGACTCAAGTTTAAT 60.202 41.667 0.00 0.00 43.06 1.40
8402 10286 3.133362 ACTGTCACCCGACTCAAGTTTAA 59.867 43.478 0.00 0.00 43.06 1.52
8403 10287 2.696707 ACTGTCACCCGACTCAAGTTTA 59.303 45.455 0.00 0.00 43.06 2.01
8404 10288 1.485066 ACTGTCACCCGACTCAAGTTT 59.515 47.619 0.00 0.00 43.06 2.66
8405 10289 1.120530 ACTGTCACCCGACTCAAGTT 58.879 50.000 0.00 0.00 43.06 2.66
8406 10290 1.120530 AACTGTCACCCGACTCAAGT 58.879 50.000 0.00 0.00 43.06 3.16
8407 10291 2.240493 AAACTGTCACCCGACTCAAG 57.760 50.000 0.00 0.00 43.06 3.02
8408 10292 2.696707 ACTAAACTGTCACCCGACTCAA 59.303 45.455 0.00 0.00 43.06 3.02
8409 10293 2.313317 ACTAAACTGTCACCCGACTCA 58.687 47.619 0.00 0.00 43.06 3.41
8410 10294 3.366781 GGTACTAAACTGTCACCCGACTC 60.367 52.174 0.00 0.00 43.06 3.36
8411 10295 2.560105 GGTACTAAACTGTCACCCGACT 59.440 50.000 0.00 0.00 43.06 4.18
8412 10296 2.297033 TGGTACTAAACTGTCACCCGAC 59.703 50.000 0.00 0.00 42.93 4.79
8413 10297 2.297033 GTGGTACTAAACTGTCACCCGA 59.703 50.000 0.00 0.00 0.00 5.14
8414 10298 2.298163 AGTGGTACTAAACTGTCACCCG 59.702 50.000 0.00 0.00 0.00 5.28
8415 10299 4.281688 TGTAGTGGTACTAAACTGTCACCC 59.718 45.833 0.00 0.00 31.62 4.61
8416 10300 5.458041 TGTAGTGGTACTAAACTGTCACC 57.542 43.478 0.00 0.00 31.62 4.02
8417 10301 7.775397 TTTTGTAGTGGTACTAAACTGTCAC 57.225 36.000 0.00 0.00 31.62 3.67
8418 10302 9.480053 GTATTTTGTAGTGGTACTAAACTGTCA 57.520 33.333 0.00 0.00 36.91 3.58
8419 10303 8.929746 GGTATTTTGTAGTGGTACTAAACTGTC 58.070 37.037 0.00 0.00 36.91 3.51
8420 10304 7.879677 GGGTATTTTGTAGTGGTACTAAACTGT 59.120 37.037 0.00 0.00 36.91 3.55
8421 10305 7.063780 CGGGTATTTTGTAGTGGTACTAAACTG 59.936 40.741 0.00 0.00 36.91 3.16
8422 10306 7.039082 TCGGGTATTTTGTAGTGGTACTAAACT 60.039 37.037 0.00 0.00 36.91 2.66
8423 10307 7.096551 TCGGGTATTTTGTAGTGGTACTAAAC 58.903 38.462 0.00 0.00 36.91 2.01
8424 10308 7.238486 TCGGGTATTTTGTAGTGGTACTAAA 57.762 36.000 0.00 0.00 37.96 1.85
8425 10309 6.849085 TCGGGTATTTTGTAGTGGTACTAA 57.151 37.500 0.00 0.00 31.62 2.24
8426 10310 6.437162 AGTTCGGGTATTTTGTAGTGGTACTA 59.563 38.462 0.00 0.00 0.00 1.82
8427 10311 5.246883 AGTTCGGGTATTTTGTAGTGGTACT 59.753 40.000 0.00 0.00 0.00 2.73
8428 10312 5.482006 AGTTCGGGTATTTTGTAGTGGTAC 58.518 41.667 0.00 0.00 0.00 3.34
8429 10313 5.743636 AGTTCGGGTATTTTGTAGTGGTA 57.256 39.130 0.00 0.00 0.00 3.25
8430 10314 4.628963 AGTTCGGGTATTTTGTAGTGGT 57.371 40.909 0.00 0.00 0.00 4.16
8431 10315 4.563976 CGTAGTTCGGGTATTTTGTAGTGG 59.436 45.833 0.00 0.00 35.71 4.00
8432 10316 5.691508 CGTAGTTCGGGTATTTTGTAGTG 57.308 43.478 0.00 0.00 35.71 2.74
8453 10337 2.457778 CGGCCAAATACGTGGACCG 61.458 63.158 2.24 4.85 44.82 4.79
8454 10338 1.078988 TCGGCCAAATACGTGGACC 60.079 57.895 2.24 0.00 44.82 4.46
8455 10339 0.390735 ACTCGGCCAAATACGTGGAC 60.391 55.000 2.24 0.00 44.10 4.02
8456 10340 0.108520 GACTCGGCCAAATACGTGGA 60.109 55.000 2.24 0.00 41.65 4.02
8457 10341 0.390603 TGACTCGGCCAAATACGTGG 60.391 55.000 2.24 0.00 42.05 4.94
8458 10342 0.999406 CTGACTCGGCCAAATACGTG 59.001 55.000 2.24 0.00 0.00 4.49
8459 10343 0.739813 GCTGACTCGGCCAAATACGT 60.740 55.000 2.24 0.00 0.00 3.57
8460 10344 1.752501 CGCTGACTCGGCCAAATACG 61.753 60.000 2.24 0.00 31.00 3.06
8461 10345 1.429148 CCGCTGACTCGGCCAAATAC 61.429 60.000 2.24 0.00 43.18 1.89
8462 10346 1.153449 CCGCTGACTCGGCCAAATA 60.153 57.895 2.24 0.00 43.18 1.40
8463 10347 2.436646 CCGCTGACTCGGCCAAAT 60.437 61.111 2.24 0.00 43.18 2.32
8509 10395 6.190346 ACTAGTATTGACCCTAGACTCGAT 57.810 41.667 0.00 0.00 35.65 3.59
8515 10401 5.642165 GGATGGACTAGTATTGACCCTAGA 58.358 45.833 0.00 0.00 35.65 2.43
8564 10466 2.030007 CGGTCCGACCAAGTACAACTAA 60.030 50.000 17.87 0.00 38.47 2.24
8566 10468 0.316204 CGGTCCGACCAAGTACAACT 59.684 55.000 17.87 0.00 38.47 3.16
8569 10471 4.498346 TCGGTCCGACCAAGTACA 57.502 55.556 17.87 0.00 38.47 2.90
8741 10769 1.066858 GGAGCTGGAAGACGACATGAA 60.067 52.381 0.00 0.00 34.07 2.57
8765 10793 2.281692 ACCACGCAATGCAGAGCA 60.282 55.556 5.91 0.00 44.86 4.26
8832 10860 0.662085 GCTAGACCGGTAGAACCTCG 59.338 60.000 7.34 0.00 35.66 4.63
8865 10893 3.873952 GCACTTGTAGAAGATCCATCCAC 59.126 47.826 6.63 0.00 32.98 4.02
9056 11131 4.734398 TTTTGCAAACATGGACAGTCTT 57.266 36.364 12.39 0.00 0.00 3.01
9066 11141 7.491682 AGTTCTGTCAGTAATTTTGCAAACAT 58.508 30.769 12.39 6.25 0.00 2.71
9147 11222 8.137437 CACAAGTGACCTGAGAACAAAAATTAT 58.863 33.333 0.00 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.