Multiple sequence alignment - TraesCS1B01G133400

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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 TraesCS1B01G133400 chr1B 100.000 4586 0 0 1 4586 168620686 168625271 0.000000e+00 8469.0
1 TraesCS1B01G133400 chr1B 90.950 1337 89 17 2519 3843 168417741 168419057 0.000000e+00 1770.0
2 TraesCS1B01G133400 chr1B 85.738 603 58 6 1692 2293 168417063 168417638 3.030000e-171 612.0
3 TraesCS1B01G133400 chr1B 90.865 416 32 4 1115 1524 168416254 168416669 1.860000e-153 553.0
4 TraesCS1B01G133400 chr1B 86.982 507 43 10 1 496 36352472 36352966 2.410000e-152 549.0
5 TraesCS1B01G133400 chr1B 89.610 154 12 3 692 844 168415878 168416028 4.680000e-45 193.0
6 TraesCS1B01G133400 chr1B 86.607 112 12 3 1540 1650 15285319 15285210 2.240000e-23 121.0
7 TraesCS1B01G133400 chr1A 94.008 3421 131 31 497 3879 115975350 115978734 0.000000e+00 5114.0
8 TraesCS1B01G133400 chr1A 91.366 1332 100 13 2519 3843 115971113 115972436 0.000000e+00 1808.0
9 TraesCS1B01G133400 chr1A 84.765 617 59 10 1692 2305 115970440 115971024 1.840000e-163 586.0
10 TraesCS1B01G133400 chr1A 90.338 414 34 4 1115 1522 115949689 115950102 5.220000e-149 538.0
11 TraesCS1B01G133400 chr1A 91.033 368 33 0 4216 4583 115978864 115979231 8.860000e-137 497.0
12 TraesCS1B01G133400 chr1A 85.774 239 16 7 607 844 115949197 115949418 2.130000e-58 237.0
13 TraesCS1B01G133400 chr1A 85.938 128 11 7 1542 1666 137739650 137739773 3.720000e-26 130.0
14 TraesCS1B01G133400 chr1D 91.741 3378 136 53 560 3897 110659165 110662439 0.000000e+00 4560.0
15 TraesCS1B01G133400 chr1D 91.592 1332 97 11 2519 3843 110604891 110606214 0.000000e+00 1825.0
16 TraesCS1B01G133400 chr1D 85.362 608 55 18 943 1524 110603223 110603822 2.360000e-167 599.0
17 TraesCS1B01G133400 chr1D 85.222 609 60 8 1692 2299 110604215 110604794 2.360000e-167 599.0
18 TraesCS1B01G133400 chr1D 91.690 361 28 2 4227 4586 110662469 110662828 2.460000e-137 499.0
19 TraesCS1B01G133400 chr1D 86.122 245 18 9 607 844 110602977 110603212 2.740000e-62 250.0
20 TraesCS1B01G133400 chr1D 93.750 64 4 0 497 560 110656767 110656830 3.780000e-16 97.1
21 TraesCS1B01G133400 chr3D 89.567 508 38 8 1 500 561759340 561759840 8.370000e-177 630.0
22 TraesCS1B01G133400 chr3D 82.963 270 33 7 4114 4370 472105952 472106221 9.920000e-57 231.0
23 TraesCS1B01G133400 chr3D 83.929 56 7 2 405 459 578734147 578734201 8.000000e-03 52.8
24 TraesCS1B01G133400 chr5D 89.087 504 35 10 1 496 552096462 552095971 3.920000e-170 608.0
25 TraesCS1B01G133400 chr5D 90.323 93 8 1 2426 2518 139441007 139440916 2.240000e-23 121.0
26 TraesCS1B01G133400 chr4A 85.185 513 57 12 1 496 611225791 611225281 4.090000e-140 508.0
27 TraesCS1B01G133400 chr4A 83.058 242 37 3 2811 3049 547298075 547297835 2.780000e-52 217.0
28 TraesCS1B01G133400 chr4B 84.559 272 28 8 4112 4369 66802667 66802938 1.640000e-64 257.0
29 TraesCS1B01G133400 chr4B 83.395 271 31 6 4113 4369 187444513 187444243 5.930000e-59 239.0
30 TraesCS1B01G133400 chr4B 88.991 109 9 3 1542 1649 639958587 639958481 1.040000e-26 132.0
31 TraesCS1B01G133400 chr4B 88.235 102 10 2 2426 2526 511163800 511163700 2.240000e-23 121.0
32 TraesCS1B01G133400 chr6B 99.291 141 1 0 3898 4038 592484862 592485002 5.890000e-64 255.0
33 TraesCS1B01G133400 chr6B 82.686 283 34 9 4104 4371 66742544 66742262 2.130000e-58 237.0
34 TraesCS1B01G133400 chr6B 80.541 185 23 7 324 496 642353882 642354065 3.720000e-26 130.0
35 TraesCS1B01G133400 chr6B 78.641 103 19 3 399 500 256481223 256481323 1.060000e-06 65.8
36 TraesCS1B01G133400 chr2B 83.643 269 30 8 4113 4367 221723770 221723502 1.650000e-59 241.0
37 TraesCS1B01G133400 chr2B 88.288 111 10 3 1540 1649 664218184 664218292 3.720000e-26 130.0
38 TraesCS1B01G133400 chr2B 87.273 110 11 3 1542 1650 92488917 92488810 6.230000e-24 122.0
39 TraesCS1B01G133400 chr2B 93.478 46 3 0 4114 4159 32969098 32969053 8.230000e-08 69.4
40 TraesCS1B01G133400 chr2D 83.150 273 33 7 4110 4369 625392508 625392780 2.130000e-58 237.0
41 TraesCS1B01G133400 chr2A 97.143 140 3 1 3900 4039 434558267 434558405 7.670000e-58 235.0
42 TraesCS1B01G133400 chr3B 85.455 220 28 4 4160 4375 763250529 763250310 4.620000e-55 226.0
43 TraesCS1B01G133400 chr3B 78.571 266 36 8 4113 4369 795181904 795181651 6.140000e-34 156.0
44 TraesCS1B01G133400 chr7B 85.849 212 25 5 2 211 211941520 211941728 2.150000e-53 220.0
45 TraesCS1B01G133400 chr5B 91.156 147 10 3 3900 4046 531695298 531695155 3.620000e-46 196.0
46 TraesCS1B01G133400 chr5B 89.109 101 9 2 2426 2525 474466617 474466716 1.730000e-24 124.0
47 TraesCS1B01G133400 chr5B 87.736 106 11 2 2413 2518 166379079 166379182 6.230000e-24 122.0
48 TraesCS1B01G133400 chr5B 89.000 100 10 1 2426 2525 378998966 378998868 6.230000e-24 122.0
49 TraesCS1B01G133400 chr5B 78.212 179 27 6 330 496 673908379 673908201 2.260000e-18 104.0
50 TraesCS1B01G133400 chr5B 84.466 103 14 2 395 496 184275897 184275998 2.920000e-17 100.0
51 TraesCS1B01G133400 chr4D 92.708 96 7 0 1554 1649 13244491 13244586 6.190000e-29 139.0
52 TraesCS1B01G133400 chr4D 88.235 102 11 1 2426 2526 414999654 414999553 2.240000e-23 121.0
53 TraesCS1B01G133400 chr4D 79.310 145 22 7 388 530 327039105 327038967 1.360000e-15 95.3
54 TraesCS1B01G133400 chr3A 92.000 100 6 2 2424 2522 438607901 438607803 6.190000e-29 139.0
55 TraesCS1B01G133400 chr6D 88.182 110 11 2 1542 1650 218447224 218447332 3.720000e-26 130.0
56 TraesCS1B01G133400 chr6A 86.207 116 12 4 1542 1655 14162993 14162880 6.230000e-24 122.0
57 TraesCS1B01G133400 chr7D 80.583 103 16 4 396 496 60544655 60544755 4.920000e-10 76.8
58 TraesCS1B01G133400 chr7A 79.245 106 18 4 395 498 413612991 413612888 2.290000e-08 71.3


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 TraesCS1B01G133400 chr1B 168620686 168625271 4585 False 8469.00 8469 100.000000 1 4586 1 chr1B.!!$F2 4585
1 TraesCS1B01G133400 chr1B 168415878 168419057 3179 False 782.00 1770 89.290750 692 3843 4 chr1B.!!$F3 3151
2 TraesCS1B01G133400 chr1A 115970440 115979231 8791 False 2001.25 5114 90.293000 497 4583 4 chr1A.!!$F3 4086
3 TraesCS1B01G133400 chr1A 115949197 115950102 905 False 387.50 538 88.056000 607 1522 2 chr1A.!!$F2 915
4 TraesCS1B01G133400 chr1D 110656767 110662828 6061 False 1718.70 4560 92.393667 497 4586 3 chr1D.!!$F2 4089
5 TraesCS1B01G133400 chr1D 110602977 110606214 3237 False 818.25 1825 87.074500 607 3843 4 chr1D.!!$F1 3236
6 TraesCS1B01G133400 chr3D 561759340 561759840 500 False 630.00 630 89.567000 1 500 1 chr3D.!!$F2 499
7 TraesCS1B01G133400 chr4A 611225281 611225791 510 True 508.00 508 85.185000 1 496 1 chr4A.!!$R2 495

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
958 7724 0.467659 GGAGGAGGAGGCTACGCTTA 60.468 60.0 0.00 0.0 0.00 3.09 F
1451 8315 0.898326 TACCCGAAGAGACAGCTGCA 60.898 55.0 15.27 0.0 0.00 4.41 F
3253 10484 0.409484 ACCATTTAGGCCCTGCAACT 59.591 50.0 0.00 0.0 43.14 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2719 9939 2.285083 TGTGTTCCAAGGAGTTTGTCG 58.715 47.619 0.0 0.0 34.87 4.35 R
3366 10600 0.676782 GCACCTAGAACGCCACCATT 60.677 55.000 0.0 0.0 0.00 3.16 R
4178 11415 0.471617 CAAGCCTAGATGTGAGGGGG 59.528 60.000 0.0 0.0 34.35 5.40 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
140 141 1.614317 CCATCTCTTTCACACACCCCC 60.614 57.143 0.00 0.00 0.00 5.40
189 190 2.347322 GCTCCTCTCCTCTGTGCGT 61.347 63.158 0.00 0.00 0.00 5.24
226 227 2.579201 CAGGTCGCATCGGGACTT 59.421 61.111 10.49 0.92 43.54 3.01
253 282 2.412112 GACGCGGTCGCTCCTATT 59.588 61.111 12.47 0.00 39.84 1.73
387 424 2.140717 GGGTCAGTTAACACAGAACGG 58.859 52.381 8.61 0.00 26.55 4.44
460 497 1.136197 CCGAAAACGCAAATCGCTGTA 60.136 47.619 0.00 0.00 43.23 2.74
461 498 2.566036 CGAAAACGCAAATCGCTGTAA 58.434 42.857 0.00 0.00 43.23 2.41
467 504 1.394917 CGCAAATCGCTGTAAGAGCTT 59.605 47.619 0.00 0.00 46.64 3.74
468 505 2.159653 CGCAAATCGCTGTAAGAGCTTT 60.160 45.455 0.00 0.00 46.64 3.51
479 516 4.456535 TGTAAGAGCTTTGTTTAGGTGCA 58.543 39.130 0.00 0.00 0.00 4.57
487 524 5.414765 AGCTTTGTTTAGGTGCACTTATACC 59.585 40.000 21.11 9.92 37.23 2.73
530 4950 3.503748 CCTGCAGTCTTTTGAAACTAGGG 59.496 47.826 13.81 0.00 0.00 3.53
581 7336 3.845860 TCCTCATAGGATGTGACCCTAC 58.154 50.000 0.00 0.00 40.06 3.18
722 7482 2.646175 GGCAGCCAGAGTCACCGTA 61.646 63.158 6.55 0.00 0.00 4.02
876 7641 0.468226 TTTTGGGTGTGTCGCTCTCT 59.532 50.000 0.00 0.00 0.00 3.10
958 7724 0.467659 GGAGGAGGAGGCTACGCTTA 60.468 60.000 0.00 0.00 0.00 3.09
1104 7933 1.544724 AGCGCCCATGTATGTGTTTT 58.455 45.000 2.29 0.00 0.00 2.43
1116 7975 3.552132 ATGTGTTTTCCCCCACAAAAC 57.448 42.857 0.00 1.84 44.10 2.43
1151 8010 9.828852 GATCTGAATTTGATGATCTTGCTATTC 57.171 33.333 0.00 0.00 34.27 1.75
1295 8159 1.811266 CGCCTCCGTCATTGTCCTG 60.811 63.158 0.00 0.00 0.00 3.86
1302 8166 1.354337 CGTCATTGTCCTGGTGCTCG 61.354 60.000 0.00 0.00 0.00 5.03
1451 8315 0.898326 TACCCGAAGAGACAGCTGCA 60.898 55.000 15.27 0.00 0.00 4.41
1482 8347 3.621715 GGTAACCAGCAATTTACTCCTCG 59.378 47.826 0.00 0.00 0.00 4.63
1485 8350 3.535561 ACCAGCAATTTACTCCTCGATG 58.464 45.455 0.00 0.00 0.00 3.84
1526 8391 4.877823 TGTTGCATCAGATTCAGATGGTAC 59.122 41.667 17.60 5.16 42.38 3.34
1550 8435 4.566004 TCAAATTCAACTGTACTCCTCCG 58.434 43.478 0.00 0.00 0.00 4.63
1556 8441 2.005370 ACTGTACTCCTCCGTTTCCA 57.995 50.000 0.00 0.00 0.00 3.53
1566 8451 4.975631 TCCTCCGTTTCCAAATTACTTGA 58.024 39.130 0.00 0.00 37.17 3.02
1571 8456 5.008217 TCCGTTTCCAAATTACTTGACACAG 59.992 40.000 0.00 0.00 37.17 3.66
1592 8477 8.200792 ACACAGAAATGGATGTATCTAGAACTC 58.799 37.037 0.00 0.00 0.00 3.01
1621 8506 9.512435 AATACGTCTATATACATCCATTTACGC 57.488 33.333 0.00 0.00 0.00 4.42
1676 8571 6.074249 GCGTATTGAACCTAATAGTCTTCAGC 60.074 42.308 0.00 0.00 0.00 4.26
1745 8956 2.756760 CAACCATGATGAAAGGAGGTGG 59.243 50.000 0.00 0.00 0.00 4.61
1853 9065 8.710749 AAATCCAATATCTTAATGCAAGCCTA 57.289 30.769 0.00 0.00 33.94 3.93
1856 9073 8.710749 TCCAATATCTTAATGCAAGCCTATTT 57.289 30.769 0.00 0.00 33.94 1.40
1995 9212 6.558771 TGTTTTCATGATGTAACACTGGAG 57.441 37.500 12.07 0.00 0.00 3.86
2056 9273 4.677584 CAGGAAGAGAACCTATGAAGTCG 58.322 47.826 0.00 0.00 35.84 4.18
2085 9302 7.266905 AGTAAATATGACTGGGTGGTTTACT 57.733 36.000 0.00 0.00 36.57 2.24
2099 9316 5.180680 GGTGGTTTACTGGTATGTGAAACTC 59.819 44.000 0.00 0.00 38.04 3.01
2214 9431 8.311836 CCAGTGGATTTTACACTAAGAGAACTA 58.688 37.037 1.68 0.00 46.76 2.24
2274 9492 8.603304 AGGGATCAACAGTATAATGGTATAACC 58.397 37.037 5.03 0.00 39.22 2.85
2329 9548 7.432350 TTTTTATTGCATTTTACTGCCCTTG 57.568 32.000 0.00 0.00 41.58 3.61
2396 9615 8.746751 CATATTAGTCTCAGTCGTGTGTAATTG 58.253 37.037 0.00 0.00 0.00 2.32
2398 9617 2.412089 GTCTCAGTCGTGTGTAATTGGC 59.588 50.000 0.00 0.00 0.00 4.52
2411 9630 4.339247 GTGTAATTGGCATGCCTTGATACT 59.661 41.667 35.53 15.89 36.94 2.12
2451 9670 4.299155 CGATCCATAATAAGTGTCGCAGT 58.701 43.478 0.00 0.00 0.00 4.40
2452 9671 4.745125 CGATCCATAATAAGTGTCGCAGTT 59.255 41.667 5.48 5.48 0.00 3.16
2453 9672 5.234329 CGATCCATAATAAGTGTCGCAGTTT 59.766 40.000 5.46 0.00 0.00 2.66
2454 9673 6.238103 CGATCCATAATAAGTGTCGCAGTTTT 60.238 38.462 5.46 3.95 0.00 2.43
2455 9674 6.176975 TCCATAATAAGTGTCGCAGTTTTG 57.823 37.500 5.46 1.31 0.00 2.44
2456 9675 5.935206 TCCATAATAAGTGTCGCAGTTTTGA 59.065 36.000 5.46 0.00 0.00 2.69
2457 9676 6.428465 TCCATAATAAGTGTCGCAGTTTTGAA 59.572 34.615 5.46 0.00 0.00 2.69
2458 9677 6.523201 CCATAATAAGTGTCGCAGTTTTGAAC 59.477 38.462 5.46 0.00 0.00 3.18
2459 9678 5.751243 AATAAGTGTCGCAGTTTTGAACT 57.249 34.783 5.46 0.00 44.06 3.01
2529 9748 7.395489 GGATCGGAGGGAGTACTATTTAATGTA 59.605 40.741 0.00 0.00 0.00 2.29
2690 9910 7.646884 ACCCAGAGATCAAGAATCCTATTTTT 58.353 34.615 0.00 0.00 34.67 1.94
2702 9922 8.593945 AGAATCCTATTTTTATCAACCAGCAA 57.406 30.769 0.00 0.00 0.00 3.91
2719 9939 3.421844 AGCAAGTAGGTGATTTCAACCC 58.578 45.455 0.00 0.00 32.98 4.11
2996 10224 7.147312 TCTCAAACATTACAAATGCTCCAAAG 58.853 34.615 0.00 0.00 0.00 2.77
3109 10340 4.773674 TCATCACCCGAAAACTCCTAGTTA 59.226 41.667 0.00 0.00 37.47 2.24
3182 10413 1.922570 TCTCGCGTTCATAAGGAAGC 58.077 50.000 5.77 0.00 35.82 3.86
3218 10449 2.629617 GGGCCATGGAAGGATACAATTG 59.370 50.000 18.40 3.24 41.41 2.32
3253 10484 0.409484 ACCATTTAGGCCCTGCAACT 59.591 50.000 0.00 0.00 43.14 3.16
3320 10553 8.454106 GCAACACATTTCTCTCTGTTATACATT 58.546 33.333 0.00 0.00 0.00 2.71
3362 10596 5.344884 GTCTTAGATGACAGTACCTTGCTC 58.655 45.833 0.00 0.00 36.97 4.26
3366 10600 5.939764 AGATGACAGTACCTTGCTCAATA 57.060 39.130 0.00 0.00 0.00 1.90
3569 10803 5.994668 ACCAAAACAAAGAAAAGAAGTGCAA 59.005 32.000 0.00 0.00 0.00 4.08
3644 10878 5.131142 AGCTTAGGTTGCCAAGTCTGTATAT 59.869 40.000 0.00 0.00 0.00 0.86
3645 10879 6.326583 AGCTTAGGTTGCCAAGTCTGTATATA 59.673 38.462 0.00 0.00 0.00 0.86
3678 10912 4.970662 TGAGGAGCTATTTCATTGTTGC 57.029 40.909 0.00 0.00 0.00 4.17
3811 11046 7.572814 AGTGAAAAATTTCTTCCCATTTTGGA 58.427 30.769 7.36 0.00 37.64 3.53
3830 11065 3.054287 TGGAGGGATATGCCAACGTTTTA 60.054 43.478 16.46 0.00 38.95 1.52
3843 11078 6.697892 TGCCAACGTTTTAAAAACTGGATAAG 59.302 34.615 20.48 0.00 0.00 1.73
3861 11096 1.242076 AGTTGGCATGCAGTCTGAAC 58.758 50.000 21.36 11.16 0.00 3.18
3898 11133 3.145551 GAGGAGGCGGCCGACTTA 61.146 66.667 38.50 0.00 30.74 2.24
3899 11134 3.140225 GAGGAGGCGGCCGACTTAG 62.140 68.421 38.50 0.51 30.74 2.18
3900 11135 4.222847 GGAGGCGGCCGACTTAGG 62.223 72.222 38.50 0.00 30.74 2.69
3908 11143 3.782042 CCGACTTAGGCGCTGTTC 58.218 61.111 7.64 0.00 0.00 3.18
3909 11144 2.158959 CCGACTTAGGCGCTGTTCG 61.159 63.158 7.64 8.80 42.12 3.95
3910 11145 2.158959 CGACTTAGGCGCTGTTCGG 61.159 63.158 7.64 0.00 38.94 4.30
3911 11146 1.810030 GACTTAGGCGCTGTTCGGG 60.810 63.158 7.64 0.00 38.94 5.14
3912 11147 2.221906 GACTTAGGCGCTGTTCGGGA 62.222 60.000 7.64 0.00 38.94 5.14
3913 11148 1.519455 CTTAGGCGCTGTTCGGGAG 60.519 63.158 7.64 0.00 38.94 4.30
3914 11149 2.227089 CTTAGGCGCTGTTCGGGAGT 62.227 60.000 7.64 0.00 38.94 3.85
3915 11150 2.221906 TTAGGCGCTGTTCGGGAGTC 62.222 60.000 7.64 0.00 38.94 3.36
3917 11152 4.373116 GCGCTGTTCGGGAGTCCA 62.373 66.667 12.30 0.00 38.94 4.02
3918 11153 2.432628 CGCTGTTCGGGAGTCCAC 60.433 66.667 12.30 0.86 33.78 4.02
3919 11154 2.047179 GCTGTTCGGGAGTCCACC 60.047 66.667 12.30 0.00 0.00 4.61
3928 11163 4.436998 GAGTCCACCGGCTCCGTG 62.437 72.222 0.00 5.87 37.81 4.94
3929 11164 4.988716 AGTCCACCGGCTCCGTGA 62.989 66.667 0.00 0.00 37.81 4.35
3930 11165 3.998672 GTCCACCGGCTCCGTGAA 61.999 66.667 0.00 0.00 37.81 3.18
3931 11166 3.235481 TCCACCGGCTCCGTGAAA 61.235 61.111 0.00 0.00 37.81 2.69
3932 11167 2.281208 CCACCGGCTCCGTGAAAA 60.281 61.111 0.00 0.00 37.81 2.29
3933 11168 1.674322 CCACCGGCTCCGTGAAAAT 60.674 57.895 0.00 0.00 37.81 1.82
3934 11169 1.241315 CCACCGGCTCCGTGAAAATT 61.241 55.000 0.00 0.00 37.81 1.82
3935 11170 1.444836 CACCGGCTCCGTGAAAATTA 58.555 50.000 0.00 0.00 37.81 1.40
3936 11171 1.807742 CACCGGCTCCGTGAAAATTAA 59.192 47.619 0.00 0.00 37.81 1.40
3937 11172 2.081462 ACCGGCTCCGTGAAAATTAAG 58.919 47.619 0.00 0.00 37.81 1.85
3938 11173 2.289819 ACCGGCTCCGTGAAAATTAAGA 60.290 45.455 0.00 0.00 37.81 2.10
3939 11174 2.745281 CCGGCTCCGTGAAAATTAAGAA 59.255 45.455 7.59 0.00 37.81 2.52
3940 11175 3.377172 CCGGCTCCGTGAAAATTAAGAAT 59.623 43.478 7.59 0.00 37.81 2.40
3941 11176 4.495844 CCGGCTCCGTGAAAATTAAGAATC 60.496 45.833 7.59 0.00 37.81 2.52
3942 11177 4.332819 CGGCTCCGTGAAAATTAAGAATCT 59.667 41.667 0.00 0.00 34.35 2.40
3943 11178 5.502544 CGGCTCCGTGAAAATTAAGAATCTC 60.503 44.000 0.00 0.00 34.35 2.75
3944 11179 5.586643 GGCTCCGTGAAAATTAAGAATCTCT 59.413 40.000 0.00 0.00 0.00 3.10
3945 11180 6.457528 GGCTCCGTGAAAATTAAGAATCTCTG 60.458 42.308 0.00 0.00 0.00 3.35
3946 11181 6.457528 GCTCCGTGAAAATTAAGAATCTCTGG 60.458 42.308 0.00 0.00 0.00 3.86
3947 11182 6.707290 TCCGTGAAAATTAAGAATCTCTGGA 58.293 36.000 0.00 0.00 0.00 3.86
3948 11183 6.818644 TCCGTGAAAATTAAGAATCTCTGGAG 59.181 38.462 0.00 0.00 0.00 3.86
3949 11184 6.595716 CCGTGAAAATTAAGAATCTCTGGAGT 59.404 38.462 0.00 0.00 0.00 3.85
3950 11185 7.764443 CCGTGAAAATTAAGAATCTCTGGAGTA 59.236 37.037 0.00 0.00 0.00 2.59
3951 11186 8.596380 CGTGAAAATTAAGAATCTCTGGAGTAC 58.404 37.037 0.00 0.00 0.00 2.73
3952 11187 8.884726 GTGAAAATTAAGAATCTCTGGAGTACC 58.115 37.037 0.00 0.00 0.00 3.34
3953 11188 7.764443 TGAAAATTAAGAATCTCTGGAGTACCG 59.236 37.037 0.00 0.00 39.42 4.02
3954 11189 6.793505 AATTAAGAATCTCTGGAGTACCGT 57.206 37.500 0.00 0.00 39.42 4.83
3955 11190 6.793505 ATTAAGAATCTCTGGAGTACCGTT 57.206 37.500 0.00 0.00 39.42 4.44
3956 11191 6.600882 TTAAGAATCTCTGGAGTACCGTTT 57.399 37.500 0.00 0.00 39.42 3.60
3957 11192 4.722361 AGAATCTCTGGAGTACCGTTTC 57.278 45.455 0.00 0.00 39.42 2.78
3958 11193 3.128938 AGAATCTCTGGAGTACCGTTTCG 59.871 47.826 0.00 0.00 39.42 3.46
3959 11194 0.524862 TCTCTGGAGTACCGTTTCGC 59.475 55.000 0.00 0.00 39.42 4.70
3960 11195 0.526662 CTCTGGAGTACCGTTTCGCT 59.473 55.000 0.00 0.00 39.42 4.93
3961 11196 0.242825 TCTGGAGTACCGTTTCGCTG 59.757 55.000 0.00 0.00 39.42 5.18
3962 11197 0.736325 CTGGAGTACCGTTTCGCTGG 60.736 60.000 0.00 0.00 39.42 4.85
3963 11198 2.098831 GGAGTACCGTTTCGCTGGC 61.099 63.158 0.00 0.00 0.00 4.85
3964 11199 1.080025 GAGTACCGTTTCGCTGGCT 60.080 57.895 0.00 0.00 0.00 4.75
3965 11200 1.077089 GAGTACCGTTTCGCTGGCTC 61.077 60.000 0.00 0.00 0.00 4.70
3966 11201 2.098831 GTACCGTTTCGCTGGCTCC 61.099 63.158 0.00 0.00 0.00 4.70
3967 11202 3.636313 TACCGTTTCGCTGGCTCCG 62.636 63.158 0.00 0.00 0.00 4.63
3970 11205 4.090057 GTTTCGCTGGCTCCGCAC 62.090 66.667 0.00 0.00 0.00 5.34
3971 11206 4.314440 TTTCGCTGGCTCCGCACT 62.314 61.111 0.00 0.00 0.00 4.40
3972 11207 3.825160 TTTCGCTGGCTCCGCACTT 62.825 57.895 0.00 0.00 0.00 3.16
3973 11208 3.825160 TTCGCTGGCTCCGCACTTT 62.825 57.895 0.00 0.00 0.00 2.66
3974 11209 3.357079 CGCTGGCTCCGCACTTTT 61.357 61.111 0.00 0.00 0.00 2.27
3975 11210 2.908073 CGCTGGCTCCGCACTTTTT 61.908 57.895 0.00 0.00 0.00 1.94
3995 11230 6.645790 TTTTTACTAGAACTCCGTCAGACT 57.354 37.500 0.00 0.00 0.00 3.24
3996 11231 5.876612 TTTACTAGAACTCCGTCAGACTC 57.123 43.478 0.00 0.00 0.00 3.36
3997 11232 3.706600 ACTAGAACTCCGTCAGACTCT 57.293 47.619 0.00 0.00 0.00 3.24
3998 11233 3.340034 ACTAGAACTCCGTCAGACTCTG 58.660 50.000 0.00 0.00 0.00 3.35
3999 11234 1.540267 AGAACTCCGTCAGACTCTGG 58.460 55.000 6.20 0.00 31.51 3.86
4000 11235 0.528470 GAACTCCGTCAGACTCTGGG 59.472 60.000 6.20 0.96 31.51 4.45
4001 11236 0.112606 AACTCCGTCAGACTCTGGGA 59.887 55.000 6.20 5.23 31.51 4.37
4002 11237 0.322997 ACTCCGTCAGACTCTGGGAG 60.323 60.000 21.35 21.35 42.02 4.30
4003 11238 1.662438 CTCCGTCAGACTCTGGGAGC 61.662 65.000 14.87 1.48 34.78 4.70
4004 11239 2.487428 CGTCAGACTCTGGGAGCG 59.513 66.667 6.20 3.23 32.04 5.03
4005 11240 2.888863 GTCAGACTCTGGGAGCGG 59.111 66.667 6.20 0.00 32.04 5.52
4006 11241 3.071206 TCAGACTCTGGGAGCGGC 61.071 66.667 6.20 0.00 32.04 6.53
4007 11242 4.154347 CAGACTCTGGGAGCGGCC 62.154 72.222 0.00 0.00 32.04 6.13
4008 11243 4.390556 AGACTCTGGGAGCGGCCT 62.391 66.667 0.00 0.00 36.66 5.19
4009 11244 3.844090 GACTCTGGGAGCGGCCTC 61.844 72.222 0.00 0.00 37.37 4.70
4034 11269 3.787001 GGAGGGGCTCCGAACAGG 61.787 72.222 0.00 0.00 41.08 4.00
4035 11270 4.475135 GAGGGGCTCCGAACAGGC 62.475 72.222 0.00 0.00 40.77 4.85
4039 11274 4.035102 GGCTCCGAACAGGCCCTT 62.035 66.667 0.00 0.00 39.96 3.95
4040 11275 2.666098 GGCTCCGAACAGGCCCTTA 61.666 63.158 0.00 0.00 39.96 2.69
4041 11276 1.527370 GCTCCGAACAGGCCCTTAT 59.473 57.895 0.00 0.00 40.77 1.73
4078 11313 0.669077 CCGGTCATCTACCCTTCTCG 59.331 60.000 0.00 0.00 46.62 4.04
4084 11319 1.025812 ATCTACCCTTCTCGCTGACG 58.974 55.000 0.00 0.00 42.01 4.35
4085 11320 0.322277 TCTACCCTTCTCGCTGACGT 60.322 55.000 0.00 0.00 41.18 4.34
4090 11325 3.288308 CTTCTCGCTGACGTGCCCT 62.288 63.158 0.00 0.00 41.18 5.19
4091 11326 1.934220 CTTCTCGCTGACGTGCCCTA 61.934 60.000 0.00 0.00 41.18 3.53
4095 11330 2.970639 GCTGACGTGCCCTACTCA 59.029 61.111 0.00 0.00 0.00 3.41
4097 11332 1.153745 CTGACGTGCCCTACTCAGC 60.154 63.158 0.00 0.00 32.11 4.26
4098 11333 2.202623 GACGTGCCCTACTCAGCG 60.203 66.667 0.00 0.00 0.00 5.18
4100 11335 4.514577 CGTGCCCTACTCAGCGGG 62.515 72.222 0.00 0.00 43.60 6.13
4122 11359 6.472163 CGGGCAAAGTTATGTGTATTGAATTC 59.528 38.462 0.00 0.00 0.00 2.17
4136 11373 8.686334 GTGTATTGAATTCATACTCCAACCAAT 58.314 33.333 9.40 0.00 0.00 3.16
4141 11378 8.365060 TGAATTCATACTCCAACCAATTCATT 57.635 30.769 3.38 0.00 36.04 2.57
4151 11388 5.365025 TCCAACCAATTCATTCAAAAGTCCA 59.635 36.000 0.00 0.00 0.00 4.02
4152 11389 6.054295 CCAACCAATTCATTCAAAAGTCCAA 58.946 36.000 0.00 0.00 0.00 3.53
4161 11398 9.880157 ATTCATTCAAAAGTCCAAATTGATAGG 57.120 29.630 0.00 0.00 33.45 2.57
4162 11399 7.322664 TCATTCAAAAGTCCAAATTGATAGGC 58.677 34.615 0.00 0.00 33.45 3.93
4164 11401 6.662865 TCAAAAGTCCAAATTGATAGGCAA 57.337 33.333 0.00 0.00 41.53 4.52
4166 11403 8.359875 TCAAAAGTCCAAATTGATAGGCAATA 57.640 30.769 0.00 0.00 46.25 1.90
4167 11404 8.980596 TCAAAAGTCCAAATTGATAGGCAATAT 58.019 29.630 0.00 0.00 46.25 1.28
4179 11416 7.759489 TGATAGGCAATATATTTCAACACCC 57.241 36.000 0.00 0.00 0.00 4.61
4180 11417 6.719370 TGATAGGCAATATATTTCAACACCCC 59.281 38.462 0.00 0.00 0.00 4.95
4181 11418 4.223144 AGGCAATATATTTCAACACCCCC 58.777 43.478 0.00 0.00 0.00 5.40
4195 11432 4.737346 CCCCCTCACATCTAGGCT 57.263 61.111 0.00 0.00 32.34 4.58
4196 11433 2.936823 CCCCCTCACATCTAGGCTT 58.063 57.895 0.00 0.00 32.34 4.35
4197 11434 0.471617 CCCCCTCACATCTAGGCTTG 59.528 60.000 0.00 0.00 32.34 4.01
4198 11435 1.207791 CCCCTCACATCTAGGCTTGT 58.792 55.000 0.00 0.00 32.34 3.16
4199 11436 1.561542 CCCCTCACATCTAGGCTTGTT 59.438 52.381 0.00 0.00 32.34 2.83
4200 11437 2.025887 CCCCTCACATCTAGGCTTGTTT 60.026 50.000 0.00 0.00 32.34 2.83
4201 11438 3.199946 CCCCTCACATCTAGGCTTGTTTA 59.800 47.826 0.00 0.00 32.34 2.01
4202 11439 4.446371 CCCTCACATCTAGGCTTGTTTAG 58.554 47.826 0.00 0.00 32.34 1.85
4203 11440 4.080863 CCCTCACATCTAGGCTTGTTTAGT 60.081 45.833 0.00 0.00 32.34 2.24
4204 11441 5.112686 CCTCACATCTAGGCTTGTTTAGTC 58.887 45.833 0.00 0.00 0.00 2.59
4205 11442 5.086104 TCACATCTAGGCTTGTTTAGTCC 57.914 43.478 0.00 0.00 0.00 3.85
4206 11443 4.777896 TCACATCTAGGCTTGTTTAGTCCT 59.222 41.667 0.00 0.00 35.46 3.85
4207 11444 5.248477 TCACATCTAGGCTTGTTTAGTCCTT 59.752 40.000 0.00 0.00 33.93 3.36
4208 11445 5.352569 CACATCTAGGCTTGTTTAGTCCTTG 59.647 44.000 0.00 0.00 33.93 3.61
4209 11446 4.553330 TCTAGGCTTGTTTAGTCCTTGG 57.447 45.455 0.00 0.00 33.93 3.61
4210 11447 4.164981 TCTAGGCTTGTTTAGTCCTTGGA 58.835 43.478 0.00 0.00 33.93 3.53
4211 11448 3.141767 AGGCTTGTTTAGTCCTTGGAC 57.858 47.619 11.59 11.59 29.47 4.02
4212 11449 1.804748 GGCTTGTTTAGTCCTTGGACG 59.195 52.381 13.41 0.08 0.00 4.79
4213 11450 2.490991 GCTTGTTTAGTCCTTGGACGT 58.509 47.619 13.41 0.00 0.00 4.34
4214 11451 2.223377 GCTTGTTTAGTCCTTGGACGTG 59.777 50.000 13.41 2.89 0.00 4.49
4229 11466 2.158871 GGACGTGGGATTTATGTAGGCA 60.159 50.000 0.00 0.00 0.00 4.75
4235 11472 5.542779 GTGGGATTTATGTAGGCAGTAGAG 58.457 45.833 0.00 0.00 0.00 2.43
4238 11475 5.279556 GGGATTTATGTAGGCAGTAGAGTCC 60.280 48.000 0.00 0.00 0.00 3.85
4311 11548 7.609146 TCTGATACCATATTGAATTCATGCTCC 59.391 37.037 9.40 0.00 0.00 4.70
4332 11569 3.152341 CAGCCAACTCATCCAAAAGTCT 58.848 45.455 0.00 0.00 0.00 3.24
4351 11588 2.041755 TCTGAACTGGTAGAGAGAGGCA 59.958 50.000 0.00 0.00 0.00 4.75
4354 11591 0.707616 ACTGGTAGAGAGAGGCAGGT 59.292 55.000 0.00 0.00 0.00 4.00
4461 11698 4.034742 GCCTGTGTTAGTTCTTTTTGTCGA 59.965 41.667 0.00 0.00 0.00 4.20
4498 11735 0.606673 GGTGGAGAGAGTTGTTGGGC 60.607 60.000 0.00 0.00 0.00 5.36
4499 11736 0.606673 GTGGAGAGAGTTGTTGGGCC 60.607 60.000 0.00 0.00 0.00 5.80
4506 11743 0.893727 GAGTTGTTGGGCCGGTCAAT 60.894 55.000 9.07 0.00 0.00 2.57
4557 11794 4.752101 GTGGCCACTGATAGTGTTCATATC 59.248 45.833 29.12 0.00 44.50 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
140 141 0.870307 GTCGGTCGATTGGATCCACG 60.870 60.000 15.91 16.30 0.00 4.94
226 227 1.153449 GACCGCGTCCATCCAATCA 60.153 57.895 4.92 0.00 0.00 2.57
253 282 0.623723 ATGGGCTTCGCTAAAAGGGA 59.376 50.000 0.00 0.00 35.23 4.20
272 301 0.037326 CGCTAAAGCTGGTCCACTCA 60.037 55.000 0.00 0.00 39.32 3.41
341 378 0.540365 CCTGTGGGTTGTTGCTCCAT 60.540 55.000 0.00 0.00 32.71 3.41
349 386 1.602237 CGGCTATCCTGTGGGTTGT 59.398 57.895 0.00 0.00 0.00 3.32
387 424 1.669760 TCCGATTTCGTGGGTGTGC 60.670 57.895 0.00 0.00 37.74 4.57
460 497 3.555966 AGTGCACCTAAACAAAGCTCTT 58.444 40.909 14.63 0.00 0.00 2.85
461 498 3.214696 AGTGCACCTAAACAAAGCTCT 57.785 42.857 14.63 0.00 0.00 4.09
467 504 4.897140 ACGGTATAAGTGCACCTAAACAA 58.103 39.130 14.63 0.00 32.29 2.83
468 505 4.497300 GACGGTATAAGTGCACCTAAACA 58.503 43.478 14.63 0.00 32.29 2.83
479 516 9.729281 TGAAGAAAATTTAAGGACGGTATAAGT 57.271 29.630 0.00 0.00 0.00 2.24
487 524 4.083484 AGGCGTGAAGAAAATTTAAGGACG 60.083 41.667 0.00 0.00 0.00 4.79
581 7336 0.096976 CGCTGGGTTCACTAATTGCG 59.903 55.000 0.00 0.00 36.41 4.85
722 7482 3.081804 GTCGGAATTCCACTGGACAAAT 58.918 45.455 24.09 0.00 35.14 2.32
876 7641 2.486548 GCCTGGCACGGAATATTCCTTA 60.487 50.000 27.86 11.37 45.33 2.69
958 7724 3.457749 CCTTGCTTCCTTCTCCTCCTTAT 59.542 47.826 0.00 0.00 0.00 1.73
1104 7933 1.057851 AGTCGAGGTTTTGTGGGGGA 61.058 55.000 0.00 0.00 0.00 4.81
1116 7975 5.814188 TCATCAAATTCAGATCAAGTCGAGG 59.186 40.000 0.00 0.00 0.00 4.63
1151 8010 0.382158 TGCGCTACTCCGAGATTCAG 59.618 55.000 9.73 0.00 0.00 3.02
1295 8159 2.158957 TCCTCCAATGAATACGAGCACC 60.159 50.000 0.00 0.00 0.00 5.01
1302 8166 3.686726 GCATCGGATCCTCCAATGAATAC 59.313 47.826 10.75 0.00 35.91 1.89
1451 8315 5.937975 AATTGCTGGTTACCAAATATGCT 57.062 34.783 5.31 0.00 30.80 3.79
1482 8347 2.797177 AGAAGGAAGGGCAAGTCATC 57.203 50.000 0.00 0.00 0.00 2.92
1485 8350 3.636153 ACATAGAAGGAAGGGCAAGTC 57.364 47.619 0.00 0.00 0.00 3.01
1526 8391 5.063944 CGGAGGAGTACAGTTGAATTTGATG 59.936 44.000 0.00 0.00 0.00 3.07
1527 8392 5.178797 CGGAGGAGTACAGTTGAATTTGAT 58.821 41.667 0.00 0.00 0.00 2.57
1550 8435 8.755018 CATTTCTGTGTCAAGTAATTTGGAAAC 58.245 33.333 0.00 0.00 37.39 2.78
1556 8441 8.181904 ACATCCATTTCTGTGTCAAGTAATTT 57.818 30.769 0.00 0.00 0.00 1.82
1566 8451 8.083828 AGTTCTAGATACATCCATTTCTGTGT 57.916 34.615 0.00 0.00 0.00 3.72
1619 8504 0.643820 GTCCGGAATTACTTGTCGCG 59.356 55.000 5.23 0.00 0.00 5.87
1620 8505 0.643820 CGTCCGGAATTACTTGTCGC 59.356 55.000 5.23 0.00 0.00 5.19
1621 8506 1.135315 TCCGTCCGGAATTACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
1676 8571 6.680874 ATTATACTATAGTCTTCTCGGGCG 57.319 41.667 9.12 0.00 0.00 6.13
1745 8956 4.887748 TCTTCGGGATATTCTTCAGCATC 58.112 43.478 0.00 0.00 0.00 3.91
1863 9080 6.691388 GCACAAATATATTCAGGTTCGGTTTC 59.309 38.462 0.00 0.00 0.00 2.78
1995 9212 2.442188 GGCGATGTCGGTCGTGTTC 61.442 63.158 4.44 0.00 43.27 3.18
2056 9273 4.202367 CCACCCAGTCATATTTACTCCCTC 60.202 50.000 0.00 0.00 0.00 4.30
2085 9302 5.541845 CTTGAGACAGAGTTTCACATACCA 58.458 41.667 0.00 0.00 0.00 3.25
2099 9316 4.040376 GCAACAAAAGAAGCTTGAGACAG 58.960 43.478 2.10 0.00 0.00 3.51
2274 9492 8.782144 AGAAAGCAAGAAATAGAGAAGACAAAG 58.218 33.333 0.00 0.00 0.00 2.77
2396 9615 6.884280 ACTAAATAAGTATCAAGGCATGCC 57.116 37.500 30.12 30.12 36.36 4.40
2451 9670 6.399743 GGTTAGTTCAAAACCCAGTTCAAAA 58.600 36.000 0.00 0.00 40.49 2.44
2452 9671 5.968254 GGTTAGTTCAAAACCCAGTTCAAA 58.032 37.500 0.00 0.00 40.49 2.69
2453 9672 5.585820 GGTTAGTTCAAAACCCAGTTCAA 57.414 39.130 0.00 0.00 40.49 2.69
2690 9910 5.435686 AATCACCTACTTGCTGGTTGATA 57.564 39.130 0.00 0.00 33.75 2.15
2702 9922 2.635915 TGTCGGGTTGAAATCACCTACT 59.364 45.455 0.00 0.00 0.00 2.57
2719 9939 2.285083 TGTGTTCCAAGGAGTTTGTCG 58.715 47.619 0.00 0.00 34.87 4.35
2996 10224 5.163683 TGTGGTGTCGTCTATTAGAAGTAGC 60.164 44.000 6.54 7.38 0.00 3.58
3109 10340 5.324409 TGCAGGTTAGAAATGGTCTTTGAT 58.676 37.500 0.00 0.00 37.84 2.57
3182 10413 2.396608 TGGCCCAATCCCAATTACATG 58.603 47.619 0.00 0.00 0.00 3.21
3233 10464 0.817654 GTTGCAGGGCCTAAATGGTC 59.182 55.000 5.28 0.00 40.45 4.02
3253 10484 2.359850 GCCCGTGCCACAAGATCA 60.360 61.111 0.00 0.00 0.00 2.92
3320 10553 9.541884 TCTAAGACCTGGCATATGTATATGTAA 57.458 33.333 12.14 2.51 41.63 2.41
3362 10596 3.312421 CACCTAGAACGCCACCATTATTG 59.688 47.826 0.00 0.00 0.00 1.90
3366 10600 0.676782 GCACCTAGAACGCCACCATT 60.677 55.000 0.00 0.00 0.00 3.16
3569 10803 1.767681 GATCTCATGCAGGAGGTCCTT 59.232 52.381 27.31 8.97 46.09 3.36
3678 10912 1.206371 AGTCCATTTTCTCGGTACCGG 59.794 52.381 32.80 22.89 40.25 5.28
3751 10985 2.101415 TGGAACTCCATGATGCTCTACG 59.899 50.000 0.00 0.00 42.01 3.51
3811 11046 5.986501 TTTTAAAACGTTGGCATATCCCT 57.013 34.783 0.00 0.00 0.00 4.20
3816 11051 6.145338 TCCAGTTTTTAAAACGTTGGCATA 57.855 33.333 18.32 4.98 0.00 3.14
3830 11065 4.040217 TGCATGCCAACTTATCCAGTTTTT 59.960 37.500 16.68 0.00 43.89 1.94
3843 11078 0.242017 GGTTCAGACTGCATGCCAAC 59.758 55.000 16.68 6.11 0.00 3.77
3861 11096 1.017387 GCCTATGCTCAGGAAAACGG 58.983 55.000 8.21 0.00 38.00 4.44
3897 11132 2.678934 ACTCCCGAACAGCGCCTA 60.679 61.111 2.29 0.00 39.11 3.93
3898 11133 4.070552 GACTCCCGAACAGCGCCT 62.071 66.667 2.29 0.00 39.11 5.52
3900 11135 4.373116 TGGACTCCCGAACAGCGC 62.373 66.667 0.00 0.00 39.11 5.92
3901 11136 2.432628 GTGGACTCCCGAACAGCG 60.433 66.667 0.00 0.00 40.47 5.18
3902 11137 2.047179 GGTGGACTCCCGAACAGC 60.047 66.667 0.00 0.00 34.29 4.40
3911 11146 4.436998 CACGGAGCCGGTGGACTC 62.437 72.222 14.07 0.00 44.69 3.36
3912 11147 4.988716 TCACGGAGCCGGTGGACT 62.989 66.667 14.07 0.00 44.69 3.85
3913 11148 2.999739 TTTTCACGGAGCCGGTGGAC 63.000 60.000 14.07 0.00 44.69 4.02
3914 11149 2.119484 ATTTTCACGGAGCCGGTGGA 62.119 55.000 14.07 5.09 44.69 4.02
3915 11150 1.241315 AATTTTCACGGAGCCGGTGG 61.241 55.000 14.07 2.71 44.69 4.61
3916 11151 1.444836 TAATTTTCACGGAGCCGGTG 58.555 50.000 14.07 9.13 44.69 4.94
3917 11152 2.081462 CTTAATTTTCACGGAGCCGGT 58.919 47.619 14.07 0.00 44.69 5.28
3918 11153 2.352388 TCTTAATTTTCACGGAGCCGG 58.648 47.619 14.07 0.00 44.69 6.13
3919 11154 4.332819 AGATTCTTAATTTTCACGGAGCCG 59.667 41.667 7.48 7.48 46.03 5.52
3920 11155 5.586643 AGAGATTCTTAATTTTCACGGAGCC 59.413 40.000 0.00 0.00 0.00 4.70
3921 11156 6.457528 CCAGAGATTCTTAATTTTCACGGAGC 60.458 42.308 0.00 0.00 0.00 4.70
3922 11157 6.818644 TCCAGAGATTCTTAATTTTCACGGAG 59.181 38.462 0.00 0.00 0.00 4.63
3923 11158 6.707290 TCCAGAGATTCTTAATTTTCACGGA 58.293 36.000 0.00 0.00 0.00 4.69
3924 11159 6.595716 ACTCCAGAGATTCTTAATTTTCACGG 59.404 38.462 0.70 0.00 0.00 4.94
3925 11160 7.602517 ACTCCAGAGATTCTTAATTTTCACG 57.397 36.000 0.70 0.00 0.00 4.35
3926 11161 8.884726 GGTACTCCAGAGATTCTTAATTTTCAC 58.115 37.037 0.70 0.00 0.00 3.18
3927 11162 7.764443 CGGTACTCCAGAGATTCTTAATTTTCA 59.236 37.037 0.70 0.00 0.00 2.69
3928 11163 7.764901 ACGGTACTCCAGAGATTCTTAATTTTC 59.235 37.037 0.70 0.00 0.00 2.29
3929 11164 7.621796 ACGGTACTCCAGAGATTCTTAATTTT 58.378 34.615 0.70 0.00 0.00 1.82
3930 11165 7.184067 ACGGTACTCCAGAGATTCTTAATTT 57.816 36.000 0.70 0.00 0.00 1.82
3931 11166 6.793505 ACGGTACTCCAGAGATTCTTAATT 57.206 37.500 0.70 0.00 0.00 1.40
3932 11167 6.793505 AACGGTACTCCAGAGATTCTTAAT 57.206 37.500 0.70 0.00 0.00 1.40
3933 11168 6.600882 AAACGGTACTCCAGAGATTCTTAA 57.399 37.500 0.70 0.00 0.00 1.85
3934 11169 5.163683 CGAAACGGTACTCCAGAGATTCTTA 60.164 44.000 0.70 0.00 0.00 2.10
3935 11170 4.380655 CGAAACGGTACTCCAGAGATTCTT 60.381 45.833 0.70 0.00 0.00 2.52
3936 11171 3.128938 CGAAACGGTACTCCAGAGATTCT 59.871 47.826 0.70 0.00 0.00 2.40
3937 11172 3.436496 CGAAACGGTACTCCAGAGATTC 58.564 50.000 0.70 0.00 0.00 2.52
3938 11173 2.416972 GCGAAACGGTACTCCAGAGATT 60.417 50.000 0.70 0.00 0.00 2.40
3939 11174 1.134560 GCGAAACGGTACTCCAGAGAT 59.865 52.381 0.70 0.00 0.00 2.75
3940 11175 0.524862 GCGAAACGGTACTCCAGAGA 59.475 55.000 0.70 0.00 0.00 3.10
3941 11176 0.526662 AGCGAAACGGTACTCCAGAG 59.473 55.000 0.00 0.00 35.27 3.35
3942 11177 0.242825 CAGCGAAACGGTACTCCAGA 59.757 55.000 0.00 0.00 35.27 3.86
3943 11178 0.736325 CCAGCGAAACGGTACTCCAG 60.736 60.000 0.00 0.00 35.27 3.86
3944 11179 1.290955 CCAGCGAAACGGTACTCCA 59.709 57.895 0.00 0.00 35.27 3.86
3945 11180 2.098831 GCCAGCGAAACGGTACTCC 61.099 63.158 0.00 0.00 35.27 3.85
3946 11181 1.077089 GAGCCAGCGAAACGGTACTC 61.077 60.000 0.00 0.00 35.27 2.59
3947 11182 1.080025 GAGCCAGCGAAACGGTACT 60.080 57.895 0.00 0.00 35.27 2.73
3948 11183 2.098831 GGAGCCAGCGAAACGGTAC 61.099 63.158 0.00 0.00 35.27 3.34
3949 11184 2.263540 GGAGCCAGCGAAACGGTA 59.736 61.111 0.00 0.00 35.27 4.02
3984 11219 1.662438 GCTCCCAGAGTCTGACGGAG 61.662 65.000 28.28 28.28 40.48 4.63
3985 11220 1.679305 GCTCCCAGAGTCTGACGGA 60.679 63.158 22.09 18.03 32.44 4.69
3986 11221 2.888863 GCTCCCAGAGTCTGACGG 59.111 66.667 22.09 14.74 32.44 4.79
3987 11222 2.487428 CGCTCCCAGAGTCTGACG 59.513 66.667 22.09 14.62 32.44 4.35
3988 11223 2.888863 CCGCTCCCAGAGTCTGAC 59.111 66.667 22.09 6.99 32.44 3.51
3989 11224 3.071206 GCCGCTCCCAGAGTCTGA 61.071 66.667 22.09 1.24 32.44 3.27
3990 11225 4.154347 GGCCGCTCCCAGAGTCTG 62.154 72.222 13.56 13.56 31.39 3.51
3991 11226 4.390556 AGGCCGCTCCCAGAGTCT 62.391 66.667 0.00 0.00 34.51 3.24
3992 11227 3.844090 GAGGCCGCTCCCAGAGTC 61.844 72.222 0.00 0.00 34.51 3.36
4017 11252 3.787001 CCTGTTCGGAGCCCCTCC 61.787 72.222 1.10 1.10 46.44 4.30
4018 11253 4.475135 GCCTGTTCGGAGCCCCTC 62.475 72.222 0.00 0.00 33.16 4.30
4022 11257 1.984288 ATAAGGGCCTGTTCGGAGCC 61.984 60.000 6.92 0.00 46.37 4.70
4023 11258 0.756903 TATAAGGGCCTGTTCGGAGC 59.243 55.000 6.92 0.00 33.16 4.70
4024 11259 2.040178 ACTATAAGGGCCTGTTCGGAG 58.960 52.381 6.92 1.49 33.16 4.63
4025 11260 2.170012 ACTATAAGGGCCTGTTCGGA 57.830 50.000 6.92 0.00 33.16 4.55
4026 11261 3.493873 GGTTACTATAAGGGCCTGTTCGG 60.494 52.174 6.92 0.00 0.00 4.30
4027 11262 3.493873 GGGTTACTATAAGGGCCTGTTCG 60.494 52.174 6.92 0.00 0.00 3.95
4028 11263 3.715315 AGGGTTACTATAAGGGCCTGTTC 59.285 47.826 6.92 0.00 0.00 3.18
4029 11264 3.744309 AGGGTTACTATAAGGGCCTGTT 58.256 45.455 6.92 0.00 0.00 3.16
4030 11265 3.433088 AGGGTTACTATAAGGGCCTGT 57.567 47.619 6.92 2.48 0.00 4.00
4031 11266 3.261137 GCTAGGGTTACTATAAGGGCCTG 59.739 52.174 6.92 0.00 0.00 4.85
4032 11267 3.518639 GCTAGGGTTACTATAAGGGCCT 58.481 50.000 0.00 0.00 0.00 5.19
4033 11268 2.570752 GGCTAGGGTTACTATAAGGGCC 59.429 54.545 0.00 0.00 32.82 5.80
4034 11269 2.233186 CGGCTAGGGTTACTATAAGGGC 59.767 54.545 0.00 0.00 0.00 5.19
4035 11270 2.233186 GCGGCTAGGGTTACTATAAGGG 59.767 54.545 0.00 0.00 0.00 3.95
4036 11271 2.094854 CGCGGCTAGGGTTACTATAAGG 60.095 54.545 0.00 0.00 0.00 2.69
4037 11272 2.816087 TCGCGGCTAGGGTTACTATAAG 59.184 50.000 6.13 0.00 0.00 1.73
4038 11273 2.554032 GTCGCGGCTAGGGTTACTATAA 59.446 50.000 1.90 0.00 0.00 0.98
4039 11274 2.154462 GTCGCGGCTAGGGTTACTATA 58.846 52.381 1.90 0.00 0.00 1.31
4040 11275 0.957362 GTCGCGGCTAGGGTTACTAT 59.043 55.000 1.90 0.00 0.00 2.12
4041 11276 1.103398 GGTCGCGGCTAGGGTTACTA 61.103 60.000 11.94 0.00 0.00 1.82
4078 11313 1.153745 CTGAGTAGGGCACGTCAGC 60.154 63.158 3.49 0.00 30.74 4.26
4090 11325 2.027561 ACATAACTTTGCCCGCTGAGTA 60.028 45.455 0.00 0.00 0.00 2.59
4091 11326 1.271379 ACATAACTTTGCCCGCTGAGT 60.271 47.619 0.00 0.00 0.00 3.41
4095 11330 2.483014 TACACATAACTTTGCCCGCT 57.517 45.000 0.00 0.00 0.00 5.52
4097 11332 4.955925 TCAATACACATAACTTTGCCCG 57.044 40.909 0.00 0.00 0.00 6.13
4098 11333 7.319646 TGAATTCAATACACATAACTTTGCCC 58.680 34.615 5.45 0.00 0.00 5.36
4122 11359 8.090214 ACTTTTGAATGAATTGGTTGGAGTATG 58.910 33.333 0.00 0.00 0.00 2.39
4125 11362 6.462909 GGACTTTTGAATGAATTGGTTGGAGT 60.463 38.462 0.00 0.00 0.00 3.85
4136 11373 7.818930 GCCTATCAATTTGGACTTTTGAATGAA 59.181 33.333 0.00 0.00 33.45 2.57
4141 11378 6.662865 TTGCCTATCAATTTGGACTTTTGA 57.337 33.333 0.00 0.00 34.18 2.69
4160 11397 4.600692 GGGGGTGTTGAAATATATTGCC 57.399 45.455 0.00 0.00 0.00 4.52
4178 11415 0.471617 CAAGCCTAGATGTGAGGGGG 59.528 60.000 0.00 0.00 34.35 5.40
4179 11416 1.207791 ACAAGCCTAGATGTGAGGGG 58.792 55.000 0.00 0.00 34.35 4.79
4180 11417 3.356529 AAACAAGCCTAGATGTGAGGG 57.643 47.619 0.00 0.00 34.35 4.30
4181 11418 5.091261 ACTAAACAAGCCTAGATGTGAGG 57.909 43.478 0.00 0.00 37.12 3.86
4182 11419 5.105146 AGGACTAAACAAGCCTAGATGTGAG 60.105 44.000 0.00 0.00 32.11 3.51
4183 11420 4.777896 AGGACTAAACAAGCCTAGATGTGA 59.222 41.667 0.00 0.00 32.11 3.58
4184 11421 5.091261 AGGACTAAACAAGCCTAGATGTG 57.909 43.478 0.00 0.00 32.11 3.21
4185 11422 5.491982 CAAGGACTAAACAAGCCTAGATGT 58.508 41.667 0.00 0.00 33.13 3.06
4186 11423 4.878397 CCAAGGACTAAACAAGCCTAGATG 59.122 45.833 0.00 0.00 33.13 2.90
4187 11424 4.783227 TCCAAGGACTAAACAAGCCTAGAT 59.217 41.667 0.00 0.00 33.13 1.98
4188 11425 4.020485 GTCCAAGGACTAAACAAGCCTAGA 60.020 45.833 11.94 0.00 41.57 2.43
4189 11426 4.254492 GTCCAAGGACTAAACAAGCCTAG 58.746 47.826 11.94 0.00 41.57 3.02
4190 11427 3.306502 CGTCCAAGGACTAAACAAGCCTA 60.307 47.826 16.57 0.00 42.54 3.93
4191 11428 2.550208 CGTCCAAGGACTAAACAAGCCT 60.550 50.000 16.57 0.00 42.54 4.58
4192 11429 1.804748 CGTCCAAGGACTAAACAAGCC 59.195 52.381 16.57 0.00 42.54 4.35
4193 11430 2.223377 CACGTCCAAGGACTAAACAAGC 59.777 50.000 16.57 0.00 42.54 4.01
4194 11431 2.806244 CCACGTCCAAGGACTAAACAAG 59.194 50.000 16.57 2.59 42.54 3.16
4195 11432 2.485835 CCCACGTCCAAGGACTAAACAA 60.486 50.000 16.57 0.00 42.54 2.83
4196 11433 1.071071 CCCACGTCCAAGGACTAAACA 59.929 52.381 16.57 0.00 42.54 2.83
4197 11434 1.345415 TCCCACGTCCAAGGACTAAAC 59.655 52.381 16.57 0.00 42.54 2.01
4198 11435 1.719529 TCCCACGTCCAAGGACTAAA 58.280 50.000 16.57 0.00 42.54 1.85
4199 11436 1.946984 ATCCCACGTCCAAGGACTAA 58.053 50.000 16.57 0.00 42.54 2.24
4200 11437 1.946984 AATCCCACGTCCAAGGACTA 58.053 50.000 16.57 0.00 42.54 2.59
4201 11438 1.064825 AAATCCCACGTCCAAGGACT 58.935 50.000 16.57 2.05 42.54 3.85
4202 11439 2.773993 TAAATCCCACGTCCAAGGAC 57.226 50.000 9.22 9.22 41.40 3.85
4203 11440 2.574369 ACATAAATCCCACGTCCAAGGA 59.426 45.455 0.00 0.00 0.00 3.36
4204 11441 2.999331 ACATAAATCCCACGTCCAAGG 58.001 47.619 0.00 0.00 0.00 3.61
4205 11442 4.127171 CCTACATAAATCCCACGTCCAAG 58.873 47.826 0.00 0.00 0.00 3.61
4206 11443 3.683281 GCCTACATAAATCCCACGTCCAA 60.683 47.826 0.00 0.00 0.00 3.53
4207 11444 2.158871 GCCTACATAAATCCCACGTCCA 60.159 50.000 0.00 0.00 0.00 4.02
4208 11445 2.158871 TGCCTACATAAATCCCACGTCC 60.159 50.000 0.00 0.00 0.00 4.79
4209 11446 3.131396 CTGCCTACATAAATCCCACGTC 58.869 50.000 0.00 0.00 0.00 4.34
4210 11447 2.504175 ACTGCCTACATAAATCCCACGT 59.496 45.455 0.00 0.00 0.00 4.49
4211 11448 3.194005 ACTGCCTACATAAATCCCACG 57.806 47.619 0.00 0.00 0.00 4.94
4212 11449 5.070580 ACTCTACTGCCTACATAAATCCCAC 59.929 44.000 0.00 0.00 0.00 4.61
4213 11450 5.216622 ACTCTACTGCCTACATAAATCCCA 58.783 41.667 0.00 0.00 0.00 4.37
4214 11451 5.279556 GGACTCTACTGCCTACATAAATCCC 60.280 48.000 0.00 0.00 0.00 3.85
4244 11481 7.344612 AGTTCAAGACCATACCATCACAGTATA 59.655 37.037 0.00 0.00 0.00 1.47
4311 11548 3.057736 CAGACTTTTGGATGAGTTGGCTG 60.058 47.826 0.00 0.00 0.00 4.85
4332 11569 2.451490 CTGCCTCTCTCTACCAGTTCA 58.549 52.381 0.00 0.00 0.00 3.18
4404 11641 2.344535 CCCAACCAGGCTCAAACAG 58.655 57.895 0.00 0.00 35.39 3.16
4461 11698 3.202151 CCACCCACCAAGTAAGACCATAT 59.798 47.826 0.00 0.00 0.00 1.78
4498 11735 3.500299 TGTTACAACATCACATTGACCGG 59.500 43.478 0.00 0.00 33.17 5.28
4499 11736 4.024472 TGTGTTACAACATCACATTGACCG 60.024 41.667 0.00 0.00 41.59 4.79
4557 11794 1.477700 CATGGTGTTTGTATGGGGCTG 59.522 52.381 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.