Multiple sequence alignment - TraesCS7A01G137900

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7A01G137900 chr7A 100.000 3785 0 0 1 3785 90475408 90479192 0.000000e+00 6990.0
1 TraesCS7A01G137900 chr7A 94.355 124 7 0 3320 3443 473023840 473023717 1.390000e-44 191.0
2 TraesCS7A01G137900 chr7A 83.146 89 15 0 3240 3328 509222367 509222455 8.710000e-12 82.4
3 TraesCS7A01G137900 chr7A 97.059 34 0 1 528 561 15096507 15096475 5.280000e-04 56.5
4 TraesCS7A01G137900 chr7B 92.663 2576 101 23 699 3243 40193330 40195848 0.000000e+00 3629.0
5 TraesCS7A01G137900 chr7B 93.559 621 38 1 1 621 40191673 40192291 0.000000e+00 924.0
6 TraesCS7A01G137900 chr7B 94.853 136 7 0 3199 3334 40196317 40196452 2.960000e-51 213.0
7 TraesCS7A01G137900 chr7B 83.444 151 19 4 3293 3443 547472516 547472372 6.590000e-28 135.0
8 TraesCS7A01G137900 chr7B 88.571 105 9 1 3599 3703 40196111 40196212 1.430000e-24 124.0
9 TraesCS7A01G137900 chr7B 86.747 83 10 1 3249 3330 638921347 638921265 1.450000e-14 91.6
10 TraesCS7A01G137900 chr7B 93.182 44 0 2 522 563 48123640 48123682 1.140000e-05 62.1
11 TraesCS7A01G137900 chr7D 91.587 1153 64 13 1824 2954 89289668 89290809 0.000000e+00 1561.0
12 TraesCS7A01G137900 chr7D 93.920 625 38 0 1 625 89285988 89286612 0.000000e+00 944.0
13 TraesCS7A01G137900 chr7D 93.014 501 33 2 817 1316 89286981 89287480 0.000000e+00 730.0
14 TraesCS7A01G137900 chr7D 93.333 495 28 5 1303 1794 89289188 89289680 0.000000e+00 726.0
15 TraesCS7A01G137900 chr7D 90.572 297 12 5 2961 3246 89290865 89291156 2.760000e-101 379.0
16 TraesCS7A01G137900 chr7D 90.000 90 6 1 3599 3688 89291326 89291412 3.090000e-21 113.0
17 TraesCS7A01G137900 chr3B 85.149 1212 107 31 995 2194 99698093 99696943 0.000000e+00 1173.0
18 TraesCS7A01G137900 chr3B 89.263 624 60 4 2176 2796 99696768 99696149 0.000000e+00 774.0
19 TraesCS7A01G137900 chr3B 90.927 507 43 2 1 507 99700691 99700188 0.000000e+00 678.0
20 TraesCS7A01G137900 chr3B 84.414 648 91 7 2197 2838 408345509 408344866 2.480000e-176 628.0
21 TraesCS7A01G137900 chr3B 78.585 1018 164 24 1794 2798 580787380 580786404 1.150000e-174 623.0
22 TraesCS7A01G137900 chr3B 77.982 327 39 14 145 470 408364252 408363958 1.400000e-39 174.0
23 TraesCS7A01G137900 chr3B 82.692 104 13 5 3314 3415 805128852 805128752 1.870000e-13 87.9
24 TraesCS7A01G137900 chr5B 78.128 1079 201 25 1775 2840 57117117 57116061 0.000000e+00 652.0
25 TraesCS7A01G137900 chr5B 76.119 268 54 9 995 1257 24146487 24146225 8.530000e-27 132.0
26 TraesCS7A01G137900 chr5B 81.325 166 25 3 1517 1682 57117880 57117721 3.070000e-26 130.0
27 TraesCS7A01G137900 chr5B 79.885 174 28 7 3241 3412 565770566 565770398 1.850000e-23 121.0
28 TraesCS7A01G137900 chr6D 83.688 705 96 13 2149 2840 155840588 155839890 0.000000e+00 647.0
29 TraesCS7A01G137900 chr6D 92.481 133 9 1 3336 3467 464671861 464671993 4.990000e-44 189.0
30 TraesCS7A01G137900 chr6B 75.974 1232 242 31 1550 2771 700250461 700251648 1.510000e-163 586.0
31 TraesCS7A01G137900 chr6B 74.708 514 85 25 1 490 700057776 700058268 1.800000e-43 187.0
32 TraesCS7A01G137900 chr6B 74.118 510 83 26 1 490 699814919 699815399 8.410000e-37 165.0
33 TraesCS7A01G137900 chr6B 74.067 509 84 25 1 490 699894305 699894784 8.410000e-37 165.0
34 TraesCS7A01G137900 chr6B 73.674 509 86 25 1 490 699854653 699855132 1.820000e-33 154.0
35 TraesCS7A01G137900 chr6B 81.053 95 13 4 693 783 700249677 700249770 1.890000e-08 71.3
36 TraesCS7A01G137900 chr5D 77.096 1109 187 42 1742 2835 54198852 54197796 2.530000e-161 579.0
37 TraesCS7A01G137900 chr5D 77.547 579 104 13 2206 2774 33656188 33655626 3.650000e-85 326.0
38 TraesCS7A01G137900 chr5D 78.495 465 77 17 921 1377 54201252 54200803 2.230000e-72 283.0
39 TraesCS7A01G137900 chr5D 97.321 112 3 0 3332 3443 424123660 424123549 1.390000e-44 191.0
40 TraesCS7A01G137900 chr5D 92.063 126 8 2 3337 3461 134808380 134808256 3.890000e-40 176.0
41 TraesCS7A01G137900 chr5D 84.536 97 11 1 1522 1618 54200600 54200508 4.030000e-15 93.5
42 TraesCS7A01G137900 chr5D 90.909 44 1 3 518 561 558898439 558898479 5.280000e-04 56.5
43 TraesCS7A01G137900 chr3D 83.417 597 90 5 2205 2798 442975914 442975324 2.570000e-151 545.0
44 TraesCS7A01G137900 chr3D 94.400 125 5 2 3324 3447 98597613 98597490 1.390000e-44 191.0
45 TraesCS7A01G137900 chr3D 81.250 80 15 0 3255 3334 454901782 454901703 8.780000e-07 65.8
46 TraesCS7A01G137900 chr3D 90.909 44 2 2 528 571 571136183 571136224 1.470000e-04 58.4
47 TraesCS7A01G137900 chr5A 78.280 465 78 18 921 1377 42285514 42285065 1.040000e-70 278.0
48 TraesCS7A01G137900 chr5A 91.852 135 6 4 3331 3461 69844782 69844915 2.320000e-42 183.0
49 TraesCS7A01G137900 chr5A 77.273 220 37 9 1517 1732 42283368 42283158 2.390000e-22 117.0
50 TraesCS7A01G137900 chr5A 94.595 37 2 0 3327 3363 6288535 6288499 1.470000e-04 58.4
51 TraesCS7A01G137900 chr2B 97.297 111 3 0 3333 3443 446213655 446213545 4.990000e-44 189.0
52 TraesCS7A01G137900 chr4A 92.913 127 7 1 3317 3443 416231377 416231501 2.320000e-42 183.0
53 TraesCS7A01G137900 chr6A 91.045 134 8 4 3313 3443 32793159 32793027 1.080000e-40 178.0
54 TraesCS7A01G137900 chr6A 97.059 34 0 1 528 561 555769191 555769159 5.280000e-04 56.5
55 TraesCS7A01G137900 chr1D 86.957 92 12 0 3244 3335 138347291 138347200 1.860000e-18 104.0
56 TraesCS7A01G137900 chr1A 86.957 92 12 0 3244 3335 154576865 154576774 1.860000e-18 104.0
57 TraesCS7A01G137900 chr3A 88.235 85 10 0 3244 3328 621324961 621324877 6.690000e-18 102.0
58 TraesCS7A01G137900 chr1B 84.270 89 14 0 3244 3332 212748889 212748977 1.870000e-13 87.9
59 TraesCS7A01G137900 chr1B 97.297 37 0 1 528 564 503829902 503829937 1.140000e-05 62.1
60 TraesCS7A01G137900 chr2A 80.899 89 17 0 3240 3328 676609717 676609805 1.890000e-08 71.3
61 TraesCS7A01G137900 chr4D 84.615 65 7 3 3415 3476 505012114 505012178 1.140000e-05 62.1
62 TraesCS7A01G137900 chr2D 97.059 34 0 1 528 561 199123540 199123508 5.280000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G137900 chr7A 90475408 90479192 3784 False 6990.000000 6990 100.000000 1 3785 1 chr7A.!!$F1 3784
1 TraesCS7A01G137900 chr7B 40191673 40196452 4779 False 1222.500000 3629 92.411500 1 3703 4 chr7B.!!$F2 3702
2 TraesCS7A01G137900 chr7D 89285988 89291412 5424 False 742.166667 1561 92.071000 1 3688 6 chr7D.!!$F1 3687
3 TraesCS7A01G137900 chr3B 99696149 99700691 4542 True 875.000000 1173 88.446333 1 2796 3 chr3B.!!$R5 2795
4 TraesCS7A01G137900 chr3B 408344866 408345509 643 True 628.000000 628 84.414000 2197 2838 1 chr3B.!!$R1 641
5 TraesCS7A01G137900 chr3B 580786404 580787380 976 True 623.000000 623 78.585000 1794 2798 1 chr3B.!!$R3 1004
6 TraesCS7A01G137900 chr5B 57116061 57117880 1819 True 391.000000 652 79.726500 1517 2840 2 chr5B.!!$R3 1323
7 TraesCS7A01G137900 chr6D 155839890 155840588 698 True 647.000000 647 83.688000 2149 2840 1 chr6D.!!$R1 691
8 TraesCS7A01G137900 chr6B 700249677 700251648 1971 False 328.650000 586 78.513500 693 2771 2 chr6B.!!$F5 2078
9 TraesCS7A01G137900 chr5D 33655626 33656188 562 True 326.000000 326 77.547000 2206 2774 1 chr5D.!!$R1 568
10 TraesCS7A01G137900 chr5D 54197796 54201252 3456 True 318.500000 579 80.042333 921 2835 3 chr5D.!!$R4 1914
11 TraesCS7A01G137900 chr3D 442975324 442975914 590 True 545.000000 545 83.417000 2205 2798 1 chr3D.!!$R2 593

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
321 322 1.489481 AGTGATGCGAATCCCTCTCA 58.511 50.000 0.0 0.0 0.00 3.27 F
1084 3358 1.531149 GTGTTGTGCATTCTGTACGCT 59.469 47.619 0.0 0.0 35.67 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1166 3440 1.926561 TGAATCCAGACAATCTCGCG 58.073 50.0 0.0 0.0 0.0 5.87 R
2888 8802 0.595310 GACGAACTGGAGATAGCCGC 60.595 60.0 0.0 0.0 0.0 6.53 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
49 50 5.587388 CTTGATGGCAAGGAACATTACAT 57.413 39.130 0.00 0.00 46.13 2.29
67 68 4.799564 ACATTACATGGCCAAACGAATT 57.200 36.364 10.96 0.00 33.60 2.17
321 322 1.489481 AGTGATGCGAATCCCTCTCA 58.511 50.000 0.00 0.00 0.00 3.27
465 468 5.748592 GTGAAACTGGTTAGCACAAAGTAG 58.251 41.667 11.68 0.00 32.07 2.57
466 469 5.526111 GTGAAACTGGTTAGCACAAAGTAGA 59.474 40.000 11.68 0.00 32.07 2.59
519 522 7.154191 TCAAAATAGCTAATCCCTCCAATCT 57.846 36.000 0.00 0.00 0.00 2.40
612 615 9.878667 TTTTGTGATAAATAATACTCACTCGGA 57.121 29.630 0.00 0.00 38.98 4.55
625 628 4.529377 ACTCACTCGGACCCAAAATAAGTA 59.471 41.667 0.00 0.00 0.00 2.24
627 630 5.424757 TCACTCGGACCCAAAATAAGTATG 58.575 41.667 0.00 0.00 0.00 2.39
628 631 5.188163 TCACTCGGACCCAAAATAAGTATGA 59.812 40.000 0.00 0.00 0.00 2.15
629 632 5.878116 CACTCGGACCCAAAATAAGTATGAA 59.122 40.000 0.00 0.00 0.00 2.57
631 634 6.373495 ACTCGGACCCAAAATAAGTATGAAAC 59.627 38.462 0.00 0.00 0.00 2.78
632 635 6.478129 TCGGACCCAAAATAAGTATGAAACT 58.522 36.000 0.00 0.00 41.49 2.66
633 636 6.596497 TCGGACCCAAAATAAGTATGAAACTC 59.404 38.462 0.00 0.00 37.50 3.01
634 637 6.456449 CGGACCCAAAATAAGTATGAAACTCG 60.456 42.308 0.00 0.00 37.50 4.18
635 638 6.190954 ACCCAAAATAAGTATGAAACTCGC 57.809 37.500 0.00 0.00 37.50 5.03
800 3064 3.570125 GCTTGGCTCCTGAAAGTTTTACT 59.430 43.478 0.00 0.00 0.00 2.24
801 3065 4.038042 GCTTGGCTCCTGAAAGTTTTACTT 59.962 41.667 0.00 0.00 40.80 2.24
802 3066 7.589356 AGCTTGGCTCCTGAAAGTTTTACTTT 61.589 38.462 4.59 4.59 42.55 2.66
803 3067 8.988930 AGCTTGGCTCCTGAAAGTTTTACTTTT 61.989 37.037 6.29 0.00 40.88 2.27
980 3249 8.904099 AGTTGTGCTATTTATGGTAAGTATCC 57.096 34.615 0.00 0.00 0.00 2.59
1028 3302 6.183360 GCACAACTAGAGCCAATGATGTTATT 60.183 38.462 0.00 0.00 0.00 1.40
1056 3330 3.138304 CACTGATTGTTTTCCTGACCGA 58.862 45.455 0.00 0.00 0.00 4.69
1067 3341 2.248248 TCCTGACCGAGAAAGATGTGT 58.752 47.619 0.00 0.00 0.00 3.72
1084 3358 1.531149 GTGTTGTGCATTCTGTACGCT 59.469 47.619 0.00 0.00 35.67 5.07
1157 3431 5.392767 AGCTCGGTACAACTATATGGATG 57.607 43.478 0.00 0.00 0.00 3.51
1166 3440 7.707035 GGTACAACTATATGGATGTATAGCTGC 59.293 40.741 11.45 0.00 37.92 5.25
1236 3510 2.485479 GGACGATCCCATTACAGTGCAT 60.485 50.000 0.00 0.00 0.00 3.96
1654 6733 7.615582 TGGCAGTTACTCAGAAAAGATATTG 57.384 36.000 0.00 0.00 0.00 1.90
1766 7367 5.964887 TTCTTTTTGTTTCCTTGAATGCG 57.035 34.783 0.00 0.00 0.00 4.73
1879 7531 8.853077 AAGTGAAATGTTATCATCTTCACTCA 57.147 30.769 24.94 8.36 46.23 3.41
1937 7603 9.784531 CCAGTTTGAATATCTTATCTGTATGGT 57.215 33.333 0.00 0.00 0.00 3.55
1947 7613 2.078849 TCTGTATGGTGTCTTGCGTG 57.921 50.000 0.00 0.00 0.00 5.34
2011 7687 6.234177 GTGTTCTCCTTGCATATATTAGGCT 58.766 40.000 0.00 0.00 36.27 4.58
2021 7697 9.890629 CTTGCATATATTAGGCTAGTTTATGGA 57.109 33.333 20.66 17.53 34.53 3.41
2108 7784 2.945668 GTGGGTTGAGAATCTATGCCAC 59.054 50.000 0.00 0.00 34.92 5.01
2109 7785 2.575735 TGGGTTGAGAATCTATGCCACA 59.424 45.455 0.00 0.00 34.92 4.17
2121 7797 5.756195 TCTATGCCACATCACTTAAATGC 57.244 39.130 0.00 0.00 0.00 3.56
2223 8102 6.642540 GCAATTTAATAATAGTTCTGCAGGGC 59.357 38.462 15.13 7.11 0.00 5.19
2539 8428 1.900981 TTTGCCGGTGGGTCACATG 60.901 57.895 1.90 0.00 35.86 3.21
2564 8453 4.153655 GGGAATCGAACTCTTTTGTGGTAC 59.846 45.833 0.00 0.00 0.00 3.34
2748 8639 7.337480 ACAAATAATACTTGAGCATGCATCA 57.663 32.000 21.98 17.04 0.00 3.07
2806 8701 9.103048 GATAAAGTCGTTGTGTTTTGTATTCAG 57.897 33.333 0.00 0.00 0.00 3.02
2817 8712 7.771361 TGTGTTTTGTATTCAGACTTTACTGGA 59.229 33.333 0.00 0.00 38.31 3.86
2840 8735 5.587388 ATTATTTGGTCTTGCACTGGATG 57.413 39.130 0.00 0.00 0.00 3.51
2841 8736 1.619654 TTTGGTCTTGCACTGGATGG 58.380 50.000 0.00 0.00 0.00 3.51
2844 8739 2.195727 TGGTCTTGCACTGGATGGATA 58.804 47.619 0.00 0.00 0.00 2.59
2845 8740 2.092968 TGGTCTTGCACTGGATGGATAC 60.093 50.000 0.00 0.00 0.00 2.24
2942 8856 3.378339 GAAGCAGATAATGTTGCATGGC 58.622 45.455 0.00 0.00 42.67 4.40
2954 8868 0.035152 TGCATGGCTCATTCCTCGTT 60.035 50.000 0.00 0.00 0.00 3.85
2958 8872 3.732212 CATGGCTCATTCCTCGTTCATA 58.268 45.455 0.00 0.00 0.00 2.15
3013 8976 3.666334 GCGTCAGAAGCTTCATATAGTCG 59.334 47.826 27.57 19.73 0.00 4.18
3164 9141 2.029649 TGCTCTGCCTTTCATTGCTTTC 60.030 45.455 0.00 0.00 0.00 2.62
3180 9157 7.549134 TCATTGCTTTCGATCTTGTATACAACT 59.451 33.333 14.35 5.03 0.00 3.16
3247 9224 8.304202 CTGAATAGCAGGTAAATCATGTACTC 57.696 38.462 0.00 0.00 41.07 2.59
3250 9227 4.040755 AGCAGGTAAATCATGTACTCCCT 58.959 43.478 0.00 0.00 0.00 4.20
3251 9228 4.475016 AGCAGGTAAATCATGTACTCCCTT 59.525 41.667 0.00 0.00 0.00 3.95
3252 9229 4.816925 GCAGGTAAATCATGTACTCCCTTC 59.183 45.833 0.00 0.00 0.00 3.46
3253 9230 5.629133 GCAGGTAAATCATGTACTCCCTTCA 60.629 44.000 0.00 0.00 0.00 3.02
3256 9233 8.378565 CAGGTAAATCATGTACTCCCTTCATAT 58.621 37.037 0.00 0.00 0.00 1.78
3257 9234 8.598041 AGGTAAATCATGTACTCCCTTCATATC 58.402 37.037 0.00 0.00 0.00 1.63
3258 9235 8.375506 GGTAAATCATGTACTCCCTTCATATCA 58.624 37.037 0.00 0.00 0.00 2.15
3289 9266 7.440523 AAGATGTTTTTGTAGGCTAGTTCAG 57.559 36.000 0.00 0.00 0.00 3.02
3291 9268 6.998673 AGATGTTTTTGTAGGCTAGTTCAGTT 59.001 34.615 0.00 0.00 0.00 3.16
3292 9269 7.502561 AGATGTTTTTGTAGGCTAGTTCAGTTT 59.497 33.333 0.00 0.00 0.00 2.66
3293 9270 8.685838 ATGTTTTTGTAGGCTAGTTCAGTTTA 57.314 30.769 0.00 0.00 0.00 2.01
3294 9271 7.922837 TGTTTTTGTAGGCTAGTTCAGTTTAC 58.077 34.615 0.00 0.00 0.00 2.01
3295 9272 7.553402 TGTTTTTGTAGGCTAGTTCAGTTTACA 59.447 33.333 0.00 0.00 0.00 2.41
3296 9273 8.400186 GTTTTTGTAGGCTAGTTCAGTTTACAA 58.600 33.333 0.00 0.00 35.38 2.41
3299 9276 8.508883 TTGTAGGCTAGTTCAGTTTACAAAAA 57.491 30.769 0.00 0.00 34.81 1.94
3308 9285 7.312899 AGTTCAGTTTACAAAAAGGTCTTGTG 58.687 34.615 0.00 0.00 37.56 3.33
3312 9289 8.145122 TCAGTTTACAAAAAGGTCTTGTGTTTT 58.855 29.630 5.87 0.00 37.56 2.43
3313 9290 8.220434 CAGTTTACAAAAAGGTCTTGTGTTTTG 58.780 33.333 6.25 6.25 43.40 2.44
3314 9291 8.145122 AGTTTACAAAAAGGTCTTGTGTTTTGA 58.855 29.630 13.07 0.00 41.38 2.69
3323 9300 7.259088 AGGTCTTGTGTTTTGATATAGAGGT 57.741 36.000 0.00 0.00 0.00 3.85
3351 9328 2.305009 AGTATTACTCCCTCCGTTCCG 58.695 52.381 0.00 0.00 0.00 4.30
3354 9331 1.856629 TTACTCCCTCCGTTCCGAAT 58.143 50.000 0.00 0.00 0.00 3.34
3357 9334 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
3358 9335 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
3361 9338 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
3363 9340 3.581755 CTCCGTTCCGAATTACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
3367 9344 4.377022 CCGTTCCGAATTACTTGTCACAAG 60.377 45.833 16.42 16.42 0.00 3.16
3369 9346 5.403166 CGTTCCGAATTACTTGTCACAAGTA 59.597 40.000 23.96 23.96 0.00 2.24
3372 9349 5.872617 TCCGAATTACTTGTCACAAGTATGG 59.127 40.000 27.30 23.89 33.27 2.74
3374 9351 6.538742 CCGAATTACTTGTCACAAGTATGGAT 59.461 38.462 27.30 16.93 33.27 3.41
3375 9352 7.401860 CGAATTACTTGTCACAAGTATGGATG 58.598 38.462 27.30 14.53 33.27 3.51
3376 9353 7.064609 CGAATTACTTGTCACAAGTATGGATGT 59.935 37.037 27.30 11.61 33.27 3.06
3377 9354 9.378551 GAATTACTTGTCACAAGTATGGATGTA 57.621 33.333 27.30 13.53 33.27 2.29
3379 9356 8.942338 TTACTTGTCACAAGTATGGATGTATC 57.058 34.615 27.30 0.00 33.27 2.24
3383 9360 8.533569 TTGTCACAAGTATGGATGTATCTAGA 57.466 34.615 0.00 0.00 0.00 2.43
3384 9361 8.712228 TGTCACAAGTATGGATGTATCTAGAT 57.288 34.615 10.73 10.73 0.00 1.98
3385 9362 8.579863 TGTCACAAGTATGGATGTATCTAGATG 58.420 37.037 15.79 0.00 0.00 2.90
3387 9364 9.807921 TCACAAGTATGGATGTATCTAGATGTA 57.192 33.333 15.79 4.44 0.00 2.29
3417 9394 8.693120 AGTTCTAGATACATCCATTTCTACGA 57.307 34.615 0.00 0.00 0.00 3.43
3418 9395 8.569641 AGTTCTAGATACATCCATTTCTACGAC 58.430 37.037 0.00 0.00 0.00 4.34
3419 9396 7.130303 TCTAGATACATCCATTTCTACGACG 57.870 40.000 0.00 0.00 0.00 5.12
3420 9397 6.932960 TCTAGATACATCCATTTCTACGACGA 59.067 38.462 0.00 0.00 0.00 4.20
3421 9398 6.003234 AGATACATCCATTTCTACGACGAG 57.997 41.667 0.00 0.00 0.00 4.18
3424 9401 5.571784 ACATCCATTTCTACGACGAGTAA 57.428 39.130 0.00 0.00 34.45 2.24
3444 9421 2.845363 TTTGGAACGGAGGGAGTAAC 57.155 50.000 0.00 0.00 0.00 2.50
3447 9424 0.971386 GGAACGGAGGGAGTAACACA 59.029 55.000 0.00 0.00 0.00 3.72
3460 9437 7.290061 AGGGAGTAACACATAACATGCAATAT 58.710 34.615 0.00 0.00 0.00 1.28
3463 9440 8.840321 GGAGTAACACATAACATGCAATATCTT 58.160 33.333 0.00 0.00 0.00 2.40
3519 9511 8.095937 GTTCATAACCAAGCTAAACAAGTACT 57.904 34.615 0.00 0.00 0.00 2.73
3520 9512 7.900782 TCATAACCAAGCTAAACAAGTACTC 57.099 36.000 0.00 0.00 0.00 2.59
3521 9513 6.877322 TCATAACCAAGCTAAACAAGTACTCC 59.123 38.462 0.00 0.00 0.00 3.85
3522 9514 4.017177 ACCAAGCTAAACAAGTACTCCC 57.983 45.455 0.00 0.00 0.00 4.30
3523 9515 3.651423 ACCAAGCTAAACAAGTACTCCCT 59.349 43.478 0.00 0.00 0.00 4.20
3524 9516 4.104261 ACCAAGCTAAACAAGTACTCCCTT 59.896 41.667 0.00 0.00 0.00 3.95
3525 9517 4.695928 CCAAGCTAAACAAGTACTCCCTTC 59.304 45.833 0.00 0.00 0.00 3.46
3526 9518 4.189639 AGCTAAACAAGTACTCCCTTCG 57.810 45.455 0.00 0.00 0.00 3.79
3527 9519 3.056035 AGCTAAACAAGTACTCCCTTCGG 60.056 47.826 0.00 0.00 0.00 4.30
3528 9520 2.180432 AAACAAGTACTCCCTTCGGC 57.820 50.000 0.00 0.00 0.00 5.54
3529 9521 1.349067 AACAAGTACTCCCTTCGGCT 58.651 50.000 0.00 0.00 0.00 5.52
3530 9522 1.349067 ACAAGTACTCCCTTCGGCTT 58.651 50.000 0.00 0.00 0.00 4.35
3531 9523 1.002087 ACAAGTACTCCCTTCGGCTTG 59.998 52.381 0.00 0.00 39.16 4.01
3532 9524 0.036294 AAGTACTCCCTTCGGCTTGC 60.036 55.000 0.00 0.00 0.00 4.01
3533 9525 1.192146 AGTACTCCCTTCGGCTTGCA 61.192 55.000 0.00 0.00 0.00 4.08
3534 9526 0.321298 GTACTCCCTTCGGCTTGCAA 60.321 55.000 0.00 0.00 0.00 4.08
3535 9527 0.398696 TACTCCCTTCGGCTTGCAAA 59.601 50.000 0.00 0.00 0.00 3.68
3536 9528 0.467290 ACTCCCTTCGGCTTGCAAAA 60.467 50.000 0.00 0.00 0.00 2.44
3537 9529 0.890683 CTCCCTTCGGCTTGCAAAAT 59.109 50.000 0.00 0.00 0.00 1.82
3538 9530 2.091541 CTCCCTTCGGCTTGCAAAATA 58.908 47.619 0.00 0.00 0.00 1.40
3539 9531 2.491693 CTCCCTTCGGCTTGCAAAATAA 59.508 45.455 0.00 0.00 0.00 1.40
3540 9532 3.096092 TCCCTTCGGCTTGCAAAATAAT 58.904 40.909 0.00 0.00 0.00 1.28
3541 9533 3.130340 TCCCTTCGGCTTGCAAAATAATC 59.870 43.478 0.00 0.00 0.00 1.75
3542 9534 3.131046 CCCTTCGGCTTGCAAAATAATCT 59.869 43.478 0.00 0.00 0.00 2.40
3543 9535 4.381932 CCCTTCGGCTTGCAAAATAATCTT 60.382 41.667 0.00 0.00 0.00 2.40
3544 9536 5.163561 CCCTTCGGCTTGCAAAATAATCTTA 60.164 40.000 0.00 0.00 0.00 2.10
3545 9537 6.461509 CCCTTCGGCTTGCAAAATAATCTTAT 60.462 38.462 0.00 0.00 0.00 1.73
3546 9538 7.255451 CCCTTCGGCTTGCAAAATAATCTTATA 60.255 37.037 0.00 0.00 0.00 0.98
3547 9539 7.591426 CCTTCGGCTTGCAAAATAATCTTATAC 59.409 37.037 0.00 0.00 0.00 1.47
3548 9540 7.801716 TCGGCTTGCAAAATAATCTTATACT 57.198 32.000 0.00 0.00 0.00 2.12
3549 9541 8.220755 TCGGCTTGCAAAATAATCTTATACTT 57.779 30.769 0.00 0.00 0.00 2.24
3550 9542 9.332502 TCGGCTTGCAAAATAATCTTATACTTA 57.667 29.630 0.00 0.00 0.00 2.24
3565 9557 9.608718 ATCTTATACTTATGAAACCCTCTAGCT 57.391 33.333 0.00 0.00 0.00 3.32
3566 9558 9.435570 TCTTATACTTATGAAACCCTCTAGCTT 57.564 33.333 0.00 0.00 0.00 3.74
3567 9559 9.482627 CTTATACTTATGAAACCCTCTAGCTTG 57.517 37.037 0.00 0.00 0.00 4.01
3568 9560 4.518249 ACTTATGAAACCCTCTAGCTTGC 58.482 43.478 0.00 0.00 0.00 4.01
3569 9561 4.019321 ACTTATGAAACCCTCTAGCTTGCA 60.019 41.667 0.00 0.00 0.00 4.08
3570 9562 2.949177 TGAAACCCTCTAGCTTGCAA 57.051 45.000 0.00 0.00 0.00 4.08
3571 9563 3.222173 TGAAACCCTCTAGCTTGCAAA 57.778 42.857 0.00 0.00 0.00 3.68
3572 9564 3.561143 TGAAACCCTCTAGCTTGCAAAA 58.439 40.909 0.00 0.00 0.00 2.44
3573 9565 3.317993 TGAAACCCTCTAGCTTGCAAAAC 59.682 43.478 0.00 0.00 0.00 2.43
3574 9566 1.523758 ACCCTCTAGCTTGCAAAACG 58.476 50.000 0.00 0.00 0.00 3.60
3575 9567 1.071699 ACCCTCTAGCTTGCAAAACGA 59.928 47.619 0.00 0.00 0.00 3.85
3576 9568 2.290323 ACCCTCTAGCTTGCAAAACGAT 60.290 45.455 0.00 0.00 0.00 3.73
3577 9569 2.352960 CCCTCTAGCTTGCAAAACGATC 59.647 50.000 0.00 0.00 0.00 3.69
3578 9570 3.265791 CCTCTAGCTTGCAAAACGATCT 58.734 45.455 0.00 0.00 0.00 2.75
3579 9571 3.686726 CCTCTAGCTTGCAAAACGATCTT 59.313 43.478 0.00 0.00 0.00 2.40
3580 9572 4.870426 CCTCTAGCTTGCAAAACGATCTTA 59.130 41.667 0.00 0.00 0.00 2.10
3581 9573 5.525378 CCTCTAGCTTGCAAAACGATCTTAT 59.475 40.000 0.00 0.00 0.00 1.73
3582 9574 6.701841 CCTCTAGCTTGCAAAACGATCTTATA 59.298 38.462 0.00 0.00 0.00 0.98
3583 9575 7.386299 CCTCTAGCTTGCAAAACGATCTTATAT 59.614 37.037 0.00 0.00 0.00 0.86
3584 9576 8.662781 TCTAGCTTGCAAAACGATCTTATATT 57.337 30.769 0.00 0.00 0.00 1.28
3585 9577 9.758651 TCTAGCTTGCAAAACGATCTTATATTA 57.241 29.630 0.00 0.00 0.00 0.98
3586 9578 9.798885 CTAGCTTGCAAAACGATCTTATATTAC 57.201 33.333 0.00 0.00 0.00 1.89
3587 9579 8.208718 AGCTTGCAAAACGATCTTATATTACA 57.791 30.769 0.00 0.00 0.00 2.41
3588 9580 8.673711 AGCTTGCAAAACGATCTTATATTACAA 58.326 29.630 0.00 0.00 0.00 2.41
3589 9581 9.284594 GCTTGCAAAACGATCTTATATTACAAA 57.715 29.630 0.00 0.00 0.00 2.83
3592 9584 9.268255 TGCAAAACGATCTTATATTACAAAACG 57.732 29.630 0.00 0.00 0.00 3.60
3593 9585 9.480538 GCAAAACGATCTTATATTACAAAACGA 57.519 29.630 0.00 0.00 0.00 3.85
3608 9600 6.445357 ACAAAACGAATGGAGTAACACTTT 57.555 33.333 0.00 0.00 0.00 2.66
3617 9609 7.065803 CGAATGGAGTAACACTTTACAATCCAT 59.934 37.037 10.42 10.42 46.01 3.41
3691 9683 1.454663 GGGGAGCCCAAGAATCAGC 60.455 63.158 8.02 0.00 44.65 4.26
3692 9684 1.304282 GGGAGCCCAAGAATCAGCA 59.696 57.895 0.00 0.00 35.81 4.41
3703 9695 1.410517 AGAATCAGCATGGTCGACGAT 59.589 47.619 9.92 8.58 36.16 3.73
3704 9696 2.159043 AGAATCAGCATGGTCGACGATT 60.159 45.455 10.65 11.52 36.16 3.34
3705 9697 2.315925 ATCAGCATGGTCGACGATTT 57.684 45.000 10.65 0.00 36.16 2.17
3706 9698 1.640428 TCAGCATGGTCGACGATTTC 58.360 50.000 10.65 5.96 36.16 2.17
3710 9702 1.732259 GCATGGTCGACGATTTCAACT 59.268 47.619 10.65 0.00 0.00 3.16
3712 9704 2.074547 TGGTCGACGATTTCAACTCC 57.925 50.000 9.92 0.00 0.00 3.85
3713 9705 1.341852 TGGTCGACGATTTCAACTCCA 59.658 47.619 9.92 0.00 0.00 3.86
3714 9706 1.993370 GGTCGACGATTTCAACTCCAG 59.007 52.381 9.92 0.00 0.00 3.86
3715 9707 1.993370 GTCGACGATTTCAACTCCAGG 59.007 52.381 0.00 0.00 0.00 4.45
3716 9708 1.067142 TCGACGATTTCAACTCCAGGG 60.067 52.381 0.00 0.00 0.00 4.45
3717 9709 1.739067 GACGATTTCAACTCCAGGGG 58.261 55.000 0.00 0.00 0.00 4.79
3718 9710 0.322546 ACGATTTCAACTCCAGGGGC 60.323 55.000 0.00 0.00 0.00 5.80
3719 9711 0.322456 CGATTTCAACTCCAGGGGCA 60.322 55.000 0.00 0.00 0.00 5.36
3720 9712 1.177401 GATTTCAACTCCAGGGGCAC 58.823 55.000 0.00 0.00 0.00 5.01
3733 9725 4.424711 GGCACCAGGGCCGAATGA 62.425 66.667 0.00 0.00 45.40 2.57
3734 9726 2.124151 GCACCAGGGCCGAATGAT 60.124 61.111 0.00 0.00 0.00 2.45
3735 9727 2.484062 GCACCAGGGCCGAATGATG 61.484 63.158 0.00 0.00 0.00 3.07
3737 9729 2.000701 ACCAGGGCCGAATGATGGA 61.001 57.895 13.67 0.00 34.99 3.41
3738 9730 1.227102 CCAGGGCCGAATGATGGAA 59.773 57.895 1.04 0.00 32.55 3.53
3740 9732 0.820891 CAGGGCCGAATGATGGAAGG 60.821 60.000 0.00 0.00 0.00 3.46
3741 9733 0.988145 AGGGCCGAATGATGGAAGGA 60.988 55.000 0.00 0.00 0.00 3.36
3742 9734 0.819666 GGGCCGAATGATGGAAGGAC 60.820 60.000 0.00 0.00 0.00 3.85
3744 9736 1.160329 GCCGAATGATGGAAGGACCG 61.160 60.000 0.00 0.00 42.61 4.79
3745 9737 0.532862 CCGAATGATGGAAGGACCGG 60.533 60.000 0.00 0.00 42.61 5.28
3747 9739 1.539065 CGAATGATGGAAGGACCGGAG 60.539 57.143 9.46 0.00 42.61 4.63
3761 9753 4.500116 GGAGGCAGCGAGGACGAC 62.500 72.222 0.00 0.00 42.66 4.34
3762 9754 4.838486 GAGGCAGCGAGGACGACG 62.838 72.222 0.00 0.00 42.66 5.12
3769 9761 3.417224 CGAGGACGACGTCGGTGA 61.417 66.667 37.89 0.00 46.22 4.02
3771 9763 3.036783 GAGGACGACGTCGGTGAGG 62.037 68.421 37.89 13.31 44.95 3.86
3773 9765 3.735029 GACGACGTCGGTGAGGCT 61.735 66.667 37.89 18.30 44.95 4.58
3774 9766 3.948086 GACGACGTCGGTGAGGCTG 62.948 68.421 37.89 11.09 44.95 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 4.493547 CAATTCGTTTGGCCATGTAATGT 58.506 39.130 6.09 0.00 44.81 2.71
67 68 2.224695 TGGTCTGAGTCGACTTACTCCA 60.225 50.000 21.08 21.04 44.40 3.86
141 142 2.919602 TCTATTCTTCCCTTTGGTGGCT 59.080 45.455 0.00 0.00 0.00 4.75
321 322 7.732222 TCCCAAATTAAAAGGAGCAATACAT 57.268 32.000 0.00 0.00 0.00 2.29
375 376 6.939730 TCATGTACATTCAGCCTCAAACTTTA 59.060 34.615 5.37 0.00 0.00 1.85
448 449 6.631016 TGTAGATCTACTTTGTGCTAACCAG 58.369 40.000 28.53 0.00 37.00 4.00
568 571 9.981460 ATCACAAAATTTCTAACTATTCCCTCT 57.019 29.630 0.00 0.00 0.00 3.69
610 613 6.677187 GCGAGTTTCATACTTATTTTGGGTCC 60.677 42.308 0.00 0.00 37.17 4.46
612 615 5.708230 TGCGAGTTTCATACTTATTTTGGGT 59.292 36.000 0.00 0.00 37.17 4.51
634 637 8.961294 AAATCTATCAATTATCGCAAATCTGC 57.039 30.769 0.00 0.00 45.75 4.26
694 2955 7.056800 CGTGCATGACAAAATGTAAAAAGAAC 58.943 34.615 0.00 0.00 0.00 3.01
697 2958 5.689514 TCCGTGCATGACAAAATGTAAAAAG 59.310 36.000 7.72 0.00 0.00 2.27
993 3267 5.412594 TGGCTCTAGTTGTGCTTCATAAAAG 59.587 40.000 0.00 0.00 35.67 2.27
1028 3302 3.075882 AGGAAAACAATCAGTGGGATCCA 59.924 43.478 15.23 0.00 34.28 3.41
1056 3330 4.581824 ACAGAATGCACAACACATCTTTCT 59.418 37.500 0.00 0.00 42.53 2.52
1067 3341 3.033368 TGTAGCGTACAGAATGCACAA 57.967 42.857 0.00 0.00 43.05 3.33
1166 3440 1.926561 TGAATCCAGACAATCTCGCG 58.073 50.000 0.00 0.00 0.00 5.87
1230 3504 3.430042 AAGATGTTCACCTGATGCACT 57.570 42.857 0.00 0.00 0.00 4.40
1236 3510 5.012458 AGAGATGTGAAAGATGTTCACCTGA 59.988 40.000 14.76 0.00 46.01 3.86
1263 3537 7.390996 TGAACTATTAAAAATGACTGCGGGTAA 59.609 33.333 0.00 0.00 0.00 2.85
1548 5604 7.981225 AGCAAATATTCATCCATAACACCAAAC 59.019 33.333 0.00 0.00 0.00 2.93
1622 5680 4.820897 TCTGAGTAACTGCCATTACACAG 58.179 43.478 19.67 19.67 46.55 3.66
1627 5685 9.905713 AATATCTTTTCTGAGTAACTGCCATTA 57.094 29.630 0.00 0.00 0.00 1.90
1654 6733 4.976224 ATTTCACACCTATTTAACCGGC 57.024 40.909 0.00 0.00 0.00 6.13
1879 7531 9.685276 TCTTCACCACATCTCAAATGTTTATAT 57.315 29.630 0.00 0.00 0.00 0.86
1937 7603 2.290008 ACATGTATTCCCACGCAAGACA 60.290 45.455 0.00 0.00 43.62 3.41
1938 7604 2.095853 CACATGTATTCCCACGCAAGAC 59.904 50.000 0.00 0.00 43.62 3.01
1947 7613 2.301346 CTCCAAGGCACATGTATTCCC 58.699 52.381 0.00 0.00 0.00 3.97
2108 7784 5.883661 ACAAAGGATCGCATTTAAGTGATG 58.116 37.500 1.56 0.00 38.75 3.07
2109 7785 5.647658 TGACAAAGGATCGCATTTAAGTGAT 59.352 36.000 1.56 0.00 41.16 3.06
2121 7797 4.191544 TCTAGCCAATTGACAAAGGATCG 58.808 43.478 7.12 4.40 0.00 3.69
2539 8428 3.437049 CCACAAAAGAGTTCGATTCCCTC 59.563 47.826 0.00 0.00 0.00 4.30
2564 8453 1.410517 AGCCACATGACTCACCGATAG 59.589 52.381 0.00 0.00 0.00 2.08
2748 8639 2.613977 CCAAGTCACCTTCAGCGAGATT 60.614 50.000 0.00 0.00 0.00 2.40
2806 8701 7.755373 GCAAGACCAAATAATTCCAGTAAAGTC 59.245 37.037 0.00 0.00 0.00 3.01
2817 8712 5.105228 CCATCCAGTGCAAGACCAAATAATT 60.105 40.000 0.00 0.00 0.00 1.40
2840 8735 2.678190 GCCGGCAGGAGATTATGTATCC 60.678 54.545 24.80 0.00 41.02 2.59
2841 8736 2.028112 TGCCGGCAGGAGATTATGTATC 60.028 50.000 29.03 0.00 41.02 2.24
2844 8739 0.767375 ATGCCGGCAGGAGATTATGT 59.233 50.000 35.36 11.04 41.02 2.29
2845 8740 1.162698 CATGCCGGCAGGAGATTATG 58.837 55.000 36.51 21.40 41.02 1.90
2846 8741 0.607489 GCATGCCGGCAGGAGATTAT 60.607 55.000 42.53 17.78 41.02 1.28
2847 8742 1.227943 GCATGCCGGCAGGAGATTA 60.228 57.895 42.53 13.95 41.02 1.75
2888 8802 0.595310 GACGAACTGGAGATAGCCGC 60.595 60.000 0.00 0.00 0.00 6.53
2942 8856 6.137794 ACAGTACTATGAACGAGGAATGAG 57.862 41.667 0.00 0.00 0.00 2.90
3034 9001 3.054166 TGGTCTTGTACGTGATGTTTCG 58.946 45.455 0.00 0.00 0.00 3.46
3078 9045 0.946221 CAGGTTCGCACAGAGGTGTC 60.946 60.000 0.00 0.00 46.95 3.67
3210 9187 5.221342 ACCTGCTATTCAGTCAGCTACATAC 60.221 44.000 0.00 0.00 41.25 2.39
3269 9246 7.553402 TGTAAACTGAACTAGCCTACAAAAACA 59.447 33.333 0.00 0.00 0.00 2.83
3270 9247 7.922837 TGTAAACTGAACTAGCCTACAAAAAC 58.077 34.615 0.00 0.00 0.00 2.43
3271 9248 8.508883 TTGTAAACTGAACTAGCCTACAAAAA 57.491 30.769 0.00 0.00 35.49 1.94
3275 9252 7.227910 CCTTTTTGTAAACTGAACTAGCCTACA 59.772 37.037 0.00 0.00 0.00 2.74
3277 9254 7.284820 ACCTTTTTGTAAACTGAACTAGCCTA 58.715 34.615 0.00 0.00 0.00 3.93
3278 9255 6.127101 ACCTTTTTGTAAACTGAACTAGCCT 58.873 36.000 0.00 0.00 0.00 4.58
3279 9256 6.262496 AGACCTTTTTGTAAACTGAACTAGCC 59.738 38.462 0.00 0.00 0.00 3.93
3280 9257 7.260558 AGACCTTTTTGTAAACTGAACTAGC 57.739 36.000 0.00 0.00 0.00 3.42
3284 9261 7.088272 ACACAAGACCTTTTTGTAAACTGAAC 58.912 34.615 0.00 0.00 36.67 3.18
3285 9262 7.222000 ACACAAGACCTTTTTGTAAACTGAA 57.778 32.000 0.00 0.00 36.67 3.02
3286 9263 6.827586 ACACAAGACCTTTTTGTAAACTGA 57.172 33.333 0.00 0.00 36.67 3.41
3287 9264 7.883229 AAACACAAGACCTTTTTGTAAACTG 57.117 32.000 0.00 0.00 36.67 3.16
3288 9265 8.145122 TCAAAACACAAGACCTTTTTGTAAACT 58.855 29.630 0.00 0.00 39.13 2.66
3289 9266 8.300495 TCAAAACACAAGACCTTTTTGTAAAC 57.700 30.769 0.00 0.00 39.13 2.01
3293 9270 9.965824 CTATATCAAAACACAAGACCTTTTTGT 57.034 29.630 0.00 0.00 39.13 2.83
3296 9273 9.014297 CCTCTATATCAAAACACAAGACCTTTT 57.986 33.333 0.00 0.00 0.00 2.27
3299 9276 7.259088 ACCTCTATATCAAAACACAAGACCT 57.741 36.000 0.00 0.00 0.00 3.85
3323 9300 7.380423 ACGGAGGGAGTAATACTTAGTACTA 57.620 40.000 0.00 0.00 37.24 1.82
3327 9304 4.892345 GGAACGGAGGGAGTAATACTTAGT 59.108 45.833 0.00 0.00 0.00 2.24
3351 9328 8.268850 ACATCCATACTTGTGACAAGTAATTC 57.731 34.615 33.69 0.00 36.45 2.17
3354 9331 8.758829 AGATACATCCATACTTGTGACAAGTAA 58.241 33.333 33.69 21.95 36.45 2.24
3357 9334 8.633561 TCTAGATACATCCATACTTGTGACAAG 58.366 37.037 22.73 22.73 0.00 3.16
3358 9335 8.533569 TCTAGATACATCCATACTTGTGACAA 57.466 34.615 0.00 0.00 0.00 3.18
3361 9338 8.712228 ACATCTAGATACATCCATACTTGTGA 57.288 34.615 4.54 0.00 0.00 3.58
3391 9368 9.788889 TCGTAGAAATGGATGTATCTAGAACTA 57.211 33.333 0.00 0.00 0.00 2.24
3393 9370 7.534578 CGTCGTAGAAATGGATGTATCTAGAAC 59.465 40.741 0.00 0.00 39.69 3.01
3394 9371 7.443272 TCGTCGTAGAAATGGATGTATCTAGAA 59.557 37.037 0.00 0.00 39.69 2.10
3396 9373 7.095144 ACTCGTCGTAGAAATGGATGTATCTAG 60.095 40.741 0.00 0.00 39.69 2.43
3397 9374 6.709397 ACTCGTCGTAGAAATGGATGTATCTA 59.291 38.462 0.00 0.00 39.69 1.98
3398 9375 5.531659 ACTCGTCGTAGAAATGGATGTATCT 59.468 40.000 0.00 0.00 39.69 1.98
3400 9377 5.769484 ACTCGTCGTAGAAATGGATGTAT 57.231 39.130 0.00 0.00 39.69 2.29
3401 9378 6.682423 TTACTCGTCGTAGAAATGGATGTA 57.318 37.500 0.00 0.00 39.69 2.29
3403 9380 7.337718 CAAATTACTCGTCGTAGAAATGGATG 58.662 38.462 0.00 0.00 39.69 3.51
3404 9381 6.479001 CCAAATTACTCGTCGTAGAAATGGAT 59.521 38.462 0.00 0.00 39.69 3.41
3405 9382 5.808540 CCAAATTACTCGTCGTAGAAATGGA 59.191 40.000 0.00 0.00 39.69 3.41
3406 9383 5.808540 TCCAAATTACTCGTCGTAGAAATGG 59.191 40.000 0.00 0.00 39.69 3.16
3407 9384 6.880822 TCCAAATTACTCGTCGTAGAAATG 57.119 37.500 0.00 0.00 39.69 2.32
3408 9385 6.034256 CGTTCCAAATTACTCGTCGTAGAAAT 59.966 38.462 0.00 0.00 39.69 2.17
3409 9386 5.343058 CGTTCCAAATTACTCGTCGTAGAAA 59.657 40.000 0.00 0.00 39.69 2.52
3410 9387 4.853196 CGTTCCAAATTACTCGTCGTAGAA 59.147 41.667 0.00 0.00 39.69 2.10
3411 9388 4.406069 CGTTCCAAATTACTCGTCGTAGA 58.594 43.478 0.00 0.00 0.00 2.59
3412 9389 3.545078 CCGTTCCAAATTACTCGTCGTAG 59.455 47.826 0.00 0.00 0.00 3.51
3413 9390 3.190327 TCCGTTCCAAATTACTCGTCGTA 59.810 43.478 0.00 0.00 0.00 3.43
3414 9391 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
3415 9392 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
3416 9393 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
3417 9394 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
3418 9395 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
3419 9396 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
3420 9397 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
3421 9398 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
3424 9401 2.640826 TGTTACTCCCTCCGTTCCAAAT 59.359 45.455 0.00 0.00 0.00 2.32
3479 9457 2.031258 TGAACCTGAACGCTTGTTGA 57.969 45.000 0.00 0.00 35.50 3.18
3522 9514 8.345565 AGTATAAGATTATTTTGCAAGCCGAAG 58.654 33.333 0.00 0.00 0.00 3.79
3523 9515 8.220755 AGTATAAGATTATTTTGCAAGCCGAA 57.779 30.769 0.00 0.00 0.00 4.30
3524 9516 7.801716 AGTATAAGATTATTTTGCAAGCCGA 57.198 32.000 0.00 0.00 0.00 5.54
3539 9531 9.608718 AGCTAGAGGGTTTCATAAGTATAAGAT 57.391 33.333 0.00 0.00 0.00 2.40
3540 9532 9.435570 AAGCTAGAGGGTTTCATAAGTATAAGA 57.564 33.333 0.00 0.00 30.77 2.10
3541 9533 9.482627 CAAGCTAGAGGGTTTCATAAGTATAAG 57.517 37.037 0.00 0.00 32.86 1.73
3542 9534 7.931948 GCAAGCTAGAGGGTTTCATAAGTATAA 59.068 37.037 0.00 0.00 32.86 0.98
3543 9535 7.070696 TGCAAGCTAGAGGGTTTCATAAGTATA 59.929 37.037 0.00 0.00 32.86 1.47
3544 9536 6.126768 TGCAAGCTAGAGGGTTTCATAAGTAT 60.127 38.462 0.00 0.00 32.86 2.12
3545 9537 5.188948 TGCAAGCTAGAGGGTTTCATAAGTA 59.811 40.000 0.00 0.00 32.86 2.24
3546 9538 4.019321 TGCAAGCTAGAGGGTTTCATAAGT 60.019 41.667 0.00 0.00 32.86 2.24
3547 9539 4.517285 TGCAAGCTAGAGGGTTTCATAAG 58.483 43.478 0.00 0.00 32.86 1.73
3548 9540 4.568072 TGCAAGCTAGAGGGTTTCATAA 57.432 40.909 0.00 0.00 32.86 1.90
3549 9541 4.568072 TTGCAAGCTAGAGGGTTTCATA 57.432 40.909 0.00 0.00 32.86 2.15
3550 9542 3.439857 TTGCAAGCTAGAGGGTTTCAT 57.560 42.857 0.00 0.00 32.86 2.57
3551 9543 2.949177 TTGCAAGCTAGAGGGTTTCA 57.051 45.000 0.00 0.00 32.86 2.69
3552 9544 3.609409 CGTTTTGCAAGCTAGAGGGTTTC 60.609 47.826 0.00 0.00 32.86 2.78
3553 9545 2.293399 CGTTTTGCAAGCTAGAGGGTTT 59.707 45.455 0.00 0.00 32.86 3.27
3554 9546 1.880027 CGTTTTGCAAGCTAGAGGGTT 59.120 47.619 0.00 0.00 35.89 4.11
3555 9547 1.071699 TCGTTTTGCAAGCTAGAGGGT 59.928 47.619 0.00 0.00 0.00 4.34
3556 9548 1.808411 TCGTTTTGCAAGCTAGAGGG 58.192 50.000 0.00 0.00 0.00 4.30
3557 9549 3.265791 AGATCGTTTTGCAAGCTAGAGG 58.734 45.455 0.00 0.00 0.00 3.69
3558 9550 4.935885 AAGATCGTTTTGCAAGCTAGAG 57.064 40.909 0.00 0.00 0.00 2.43
3559 9551 8.662781 AATATAAGATCGTTTTGCAAGCTAGA 57.337 30.769 0.00 0.00 0.00 2.43
3560 9552 9.798885 GTAATATAAGATCGTTTTGCAAGCTAG 57.201 33.333 0.00 0.00 0.00 3.42
3561 9553 9.320352 TGTAATATAAGATCGTTTTGCAAGCTA 57.680 29.630 0.00 0.00 0.00 3.32
3562 9554 8.208718 TGTAATATAAGATCGTTTTGCAAGCT 57.791 30.769 0.00 0.00 0.00 3.74
3563 9555 8.835467 TTGTAATATAAGATCGTTTTGCAAGC 57.165 30.769 0.00 0.00 0.00 4.01
3566 9558 9.268255 CGTTTTGTAATATAAGATCGTTTTGCA 57.732 29.630 0.00 0.00 0.00 4.08
3567 9559 9.480538 TCGTTTTGTAATATAAGATCGTTTTGC 57.519 29.630 0.00 0.00 0.00 3.68
3572 9564 9.537192 TCCATTCGTTTTGTAATATAAGATCGT 57.463 29.630 0.00 0.00 0.00 3.73
3580 9572 9.444600 AGTGTTACTCCATTCGTTTTGTAATAT 57.555 29.630 0.00 0.00 0.00 1.28
3581 9573 8.836268 AGTGTTACTCCATTCGTTTTGTAATA 57.164 30.769 0.00 0.00 0.00 0.98
3582 9574 7.739498 AGTGTTACTCCATTCGTTTTGTAAT 57.261 32.000 0.00 0.00 0.00 1.89
3583 9575 7.556733 AAGTGTTACTCCATTCGTTTTGTAA 57.443 32.000 0.00 0.00 0.00 2.41
3584 9576 7.556733 AAAGTGTTACTCCATTCGTTTTGTA 57.443 32.000 0.00 0.00 0.00 2.41
3585 9577 6.445357 AAAGTGTTACTCCATTCGTTTTGT 57.555 33.333 0.00 0.00 0.00 2.83
3586 9578 7.411274 TGTAAAGTGTTACTCCATTCGTTTTG 58.589 34.615 0.00 0.00 40.35 2.44
3587 9579 7.556733 TGTAAAGTGTTACTCCATTCGTTTT 57.443 32.000 0.00 0.00 40.35 2.43
3588 9580 7.556733 TTGTAAAGTGTTACTCCATTCGTTT 57.443 32.000 0.00 0.00 40.35 3.60
3589 9581 7.094933 GGATTGTAAAGTGTTACTCCATTCGTT 60.095 37.037 0.00 0.00 40.35 3.85
3590 9582 6.370718 GGATTGTAAAGTGTTACTCCATTCGT 59.629 38.462 0.00 0.00 40.35 3.85
3591 9583 6.370442 TGGATTGTAAAGTGTTACTCCATTCG 59.630 38.462 4.38 0.00 38.60 3.34
3592 9584 7.681939 TGGATTGTAAAGTGTTACTCCATTC 57.318 36.000 4.38 0.00 38.60 2.67
3593 9585 7.122650 CCATGGATTGTAAAGTGTTACTCCATT 59.877 37.037 5.56 3.07 44.80 3.16
3594 9586 6.603201 CCATGGATTGTAAAGTGTTACTCCAT 59.397 38.462 5.56 11.68 46.36 3.41
3595 9587 5.943416 CCATGGATTGTAAAGTGTTACTCCA 59.057 40.000 5.56 8.98 43.41 3.86
3596 9588 5.944007 ACCATGGATTGTAAAGTGTTACTCC 59.056 40.000 21.47 0.00 40.35 3.85
3597 9589 6.622896 GCACCATGGATTGTAAAGTGTTACTC 60.623 42.308 21.47 0.00 40.35 2.59
3605 9597 3.674138 GCACAGCACCATGGATTGTAAAG 60.674 47.826 21.47 8.71 0.00 1.85
3608 9600 1.271817 TGCACAGCACCATGGATTGTA 60.272 47.619 21.47 4.22 31.71 2.41
3629 9621 3.433306 TCCCCACATCTTTACTGTTGG 57.567 47.619 0.00 0.00 31.00 3.77
3630 9622 3.129287 GCATCCCCACATCTTTACTGTTG 59.871 47.826 0.00 0.00 0.00 3.33
3631 9623 3.245229 TGCATCCCCACATCTTTACTGTT 60.245 43.478 0.00 0.00 0.00 3.16
3632 9624 2.308570 TGCATCCCCACATCTTTACTGT 59.691 45.455 0.00 0.00 0.00 3.55
3633 9625 2.684881 GTGCATCCCCACATCTTTACTG 59.315 50.000 0.00 0.00 35.80 2.74
3691 9683 2.348666 GGAGTTGAAATCGTCGACCATG 59.651 50.000 10.58 0.00 41.13 3.66
3692 9684 2.028476 TGGAGTTGAAATCGTCGACCAT 60.028 45.455 10.58 0.00 41.13 3.55
3703 9695 1.152830 GGTGCCCCTGGAGTTGAAA 59.847 57.895 0.00 0.00 0.00 2.69
3704 9696 2.067932 CTGGTGCCCCTGGAGTTGAA 62.068 60.000 0.00 0.00 0.00 2.69
3705 9697 2.449518 TGGTGCCCCTGGAGTTGA 60.450 61.111 0.00 0.00 0.00 3.18
3706 9698 2.034687 CTGGTGCCCCTGGAGTTG 59.965 66.667 0.00 0.00 0.00 3.16
3717 9709 2.124151 ATCATTCGGCCCTGGTGC 60.124 61.111 0.00 0.00 0.00 5.01
3718 9710 1.825191 CCATCATTCGGCCCTGGTG 60.825 63.158 0.00 0.00 0.00 4.17
3719 9711 1.570857 TTCCATCATTCGGCCCTGGT 61.571 55.000 0.00 0.00 0.00 4.00
3720 9712 0.820891 CTTCCATCATTCGGCCCTGG 60.821 60.000 0.00 0.00 0.00 4.45
3722 9714 0.988145 TCCTTCCATCATTCGGCCCT 60.988 55.000 0.00 0.00 0.00 5.19
3724 9716 0.819666 GGTCCTTCCATCATTCGGCC 60.820 60.000 0.00 0.00 35.97 6.13
3725 9717 1.160329 CGGTCCTTCCATCATTCGGC 61.160 60.000 0.00 0.00 35.57 5.54
3726 9718 0.532862 CCGGTCCTTCCATCATTCGG 60.533 60.000 0.00 0.00 35.57 4.30
3728 9720 1.202698 CCTCCGGTCCTTCCATCATTC 60.203 57.143 0.00 0.00 35.57 2.67
3729 9721 0.839946 CCTCCGGTCCTTCCATCATT 59.160 55.000 0.00 0.00 35.57 2.57
3730 9722 1.700042 GCCTCCGGTCCTTCCATCAT 61.700 60.000 0.00 0.00 35.57 2.45
3731 9723 2.367202 GCCTCCGGTCCTTCCATCA 61.367 63.158 0.00 0.00 35.57 3.07
3732 9724 2.317149 CTGCCTCCGGTCCTTCCATC 62.317 65.000 0.00 0.00 35.57 3.51
3733 9725 2.285368 TGCCTCCGGTCCTTCCAT 60.285 61.111 0.00 0.00 35.57 3.41
3734 9726 3.003173 CTGCCTCCGGTCCTTCCA 61.003 66.667 0.00 0.00 35.57 3.53
3735 9727 4.475135 GCTGCCTCCGGTCCTTCC 62.475 72.222 0.00 0.00 0.00 3.46
3744 9736 4.500116 GTCGTCCTCGCTGCCTCC 62.500 72.222 0.00 0.00 36.96 4.30
3745 9737 4.838486 CGTCGTCCTCGCTGCCTC 62.838 72.222 0.00 0.00 36.96 4.70
3749 9741 4.813526 CCGACGTCGTCCTCGCTG 62.814 72.222 33.49 14.06 37.74 5.18
3752 9744 3.364249 CTCACCGACGTCGTCCTCG 62.364 68.421 33.49 21.22 37.74 4.63
3754 9746 3.054503 CCTCACCGACGTCGTCCT 61.055 66.667 33.49 14.92 37.74 3.85
3755 9747 4.773117 GCCTCACCGACGTCGTCC 62.773 72.222 33.49 12.89 37.74 4.79
3756 9748 3.735029 AGCCTCACCGACGTCGTC 61.735 66.667 33.49 15.51 37.74 4.20


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

AutoCloner maintained by Alex Coulton.