Multiple sequence alignment - TraesCS4D01G271600

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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 TraesCS4D01G271600 chr4D 100.000 3189 0 0 4195 7383 442209412 442212600 0.000000e+00 5890.0
1 TraesCS4D01G271600 chr4D 100.000 2722 0 0 1 2722 442205218 442207939 0.000000e+00 5027.0
2 TraesCS4D01G271600 chr4D 100.000 614 0 0 3052 3665 442208269 442208882 0.000000e+00 1134.0
3 TraesCS4D01G271600 chr4D 84.028 288 38 5 3188 3474 468406844 468407124 3.390000e-68 270.0
4 TraesCS4D01G271600 chr4D 89.147 129 13 1 3189 3317 18214613 18214740 7.670000e-35 159.0
5 TraesCS4D01G271600 chr4B 92.211 2555 157 19 91 2628 550392858 550395387 0.000000e+00 3578.0
6 TraesCS4D01G271600 chr4B 95.041 726 30 2 6217 6942 550397907 550398626 0.000000e+00 1136.0
7 TraesCS4D01G271600 chr4B 92.956 724 41 3 4195 4918 550395390 550396103 0.000000e+00 1046.0
8 TraesCS4D01G271600 chr4B 90.755 530 25 10 5692 6220 550397239 550397745 0.000000e+00 686.0
9 TraesCS4D01G271600 chr4B 92.818 362 23 2 5313 5672 550396719 550397079 8.490000e-144 521.0
10 TraesCS4D01G271600 chr4B 92.042 377 18 7 4920 5294 550396146 550396512 3.050000e-143 520.0
11 TraesCS4D01G271600 chr4B 85.339 457 55 10 3188 3636 584620675 584620223 5.220000e-126 462.0
12 TraesCS4D01G271600 chr4B 83.784 444 56 8 6942 7383 550398924 550399353 2.480000e-109 407.0
13 TraesCS4D01G271600 chr4A 90.500 2642 185 30 39 2645 24944476 24941866 0.000000e+00 3428.0
14 TraesCS4D01G271600 chr4A 94.269 1518 67 16 5541 7054 24939764 24938263 0.000000e+00 2303.0
15 TraesCS4D01G271600 chr4A 95.023 1306 52 6 4195 5491 24941063 24939762 0.000000e+00 2039.0
16 TraesCS4D01G271600 chr4A 90.000 630 26 9 3052 3645 24941809 24941181 0.000000e+00 780.0
17 TraesCS4D01G271600 chr7B 86.614 508 44 15 3143 3632 131181655 131182156 2.340000e-149 540.0
18 TraesCS4D01G271600 chr7B 86.111 288 24 9 3190 3474 424497364 424497638 5.600000e-76 296.0
19 TraesCS4D01G271600 chr7D 87.021 470 49 9 3134 3596 519403640 519404104 3.050000e-143 520.0
20 TraesCS4D01G271600 chr7D 87.108 287 35 2 3189 3474 151707728 151708013 2.570000e-84 324.0
21 TraesCS4D01G271600 chr7D 100.000 28 0 0 2667 2694 515395630 515395657 1.300000e-02 52.8
22 TraesCS4D01G271600 chr2D 87.723 448 43 9 3189 3627 54599213 54599657 5.110000e-141 512.0
23 TraesCS4D01G271600 chr2D 88.889 45 4 1 5646 5690 247830363 247830406 4.000000e-03 54.7
24 TraesCS4D01G271600 chr2B 87.168 452 48 9 3184 3632 436519152 436519596 8.550000e-139 505.0
25 TraesCS4D01G271600 chr2B 82.670 352 39 13 3143 3474 460609576 460609925 7.250000e-75 292.0
26 TraesCS4D01G271600 chr2B 83.232 328 37 9 3143 3452 786242609 786242936 1.210000e-72 285.0
27 TraesCS4D01G271600 chr7A 86.768 461 50 7 3143 3596 595278273 595278729 3.070000e-138 503.0
28 TraesCS4D01G271600 chr2A 86.652 457 50 7 3189 3636 779159377 779159831 5.150000e-136 496.0
29 TraesCS4D01G271600 chr5A 85.144 451 63 3 3188 3637 510075594 510076041 6.750000e-125 459.0
30 TraesCS4D01G271600 chr3A 86.411 287 38 1 3189 3474 620621847 620622133 5.560000e-81 313.0
31 TraesCS4D01G271600 chr3A 91.111 45 1 3 5636 5677 738316885 738316929 2.880000e-04 58.4
32 TraesCS4D01G271600 chr6D 85.985 264 30 5 3188 3450 306699613 306699870 7.300000e-70 276.0
33 TraesCS4D01G271600 chr1A 84.507 71 7 4 5646 5714 12091214 12091282 4.780000e-07 67.6
34 TraesCS4D01G271600 chr1A 86.538 52 4 3 5643 5691 307037675 307037726 4.000000e-03 54.7
35 TraesCS4D01G271600 chr6B 88.235 51 3 3 5644 5691 471675230 471675180 2.880000e-04 58.4
36 TraesCS4D01G271600 chr6B 100.000 28 0 0 2667 2694 592472288 592472261 1.300000e-02 52.8
37 TraesCS4D01G271600 chr6A 88.235 51 3 3 5644 5691 409430730 409430680 2.880000e-04 58.4
38 TraesCS4D01G271600 chr5B 81.250 80 8 7 5642 5717 324964803 324964727 2.880000e-04 58.4
39 TraesCS4D01G271600 chrUn 90.244 41 4 0 2667 2707 24462084 24462124 4.000000e-03 54.7
40 TraesCS4D01G271600 chr3D 100.000 28 0 0 2667 2694 395006025 395006052 1.300000e-02 52.8
41 TraesCS4D01G271600 chr1D 100.000 28 0 0 2667 2694 203458251 203458278 1.300000e-02 52.8
42 TraesCS4D01G271600 chr1B 100.000 28 0 0 2667 2694 641173409 641173382 1.300000e-02 52.8


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 TraesCS4D01G271600 chr4D 442205218 442212600 7382 False 4017.000000 5890 100.000000 1 7383 3 chr4D.!!$F3 7382
1 TraesCS4D01G271600 chr4B 550392858 550399353 6495 False 1127.714286 3578 91.372429 91 7383 7 chr4B.!!$F1 7292
2 TraesCS4D01G271600 chr4A 24938263 24944476 6213 True 2137.500000 3428 92.448000 39 7054 4 chr4A.!!$R1 7015
3 TraesCS4D01G271600 chr7B 131181655 131182156 501 False 540.000000 540 86.614000 3143 3632 1 chr7B.!!$F1 489

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
36 37 0.037697 ATATCGCCGTGTGTGTGTGT 60.038 50.0 0.00 0.00 0.00 3.72 F
839 863 0.519175 CAGCGAACGCAATAGTGTGC 60.519 55.0 20.66 0.00 44.88 4.57 F
1070 1106 1.054978 GGTCCGCCCCTTATTCCTCT 61.055 60.0 0.00 0.00 0.00 3.69 F
2664 2708 0.172803 GGACGCGGTCTAGATGTGTT 59.827 55.0 12.47 1.32 32.47 3.32 F
2688 2732 0.107214 CATCCAACGTGGGCCTGTAT 60.107 55.0 3.23 0.00 38.32 2.29 F
2689 2733 0.180406 ATCCAACGTGGGCCTGTATC 59.820 55.0 3.23 0.00 38.32 2.24 F
3076 3120 0.329261 CCCACCTTTCTCTGCATCCA 59.671 55.0 0.00 0.00 0.00 3.41 F
3095 3141 0.734889 ATTTTCTCTTGCATCCGCGG 59.265 50.0 22.12 22.12 42.97 6.46 F
4624 4748 0.902531 TCTGCTTTAGGCGCTTAGGT 59.097 50.0 7.64 0.00 45.43 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 1762 1.071385 ACAACAAGCAGAGTCTCCCTG 59.929 52.381 0.00 0.0 34.88 4.45 R
2645 2689 0.172803 AACACATCTAGACCGCGTCC 59.827 55.000 4.92 0.0 32.18 4.79 R
2670 2714 0.180406 GATACAGGCCCACGTTGGAT 59.820 55.000 10.41 0.0 40.96 3.41 R
4220 4344 0.248289 TCTACTTTAGCACGCCCCAC 59.752 55.000 0.00 0.0 0.00 4.61 R
4476 4600 1.328680 GGTGCACAGCGACTTCATATG 59.671 52.381 20.43 0.0 0.00 1.78 R
4624 4748 2.194597 GCACCAACCACCCTGACA 59.805 61.111 0.00 0.0 0.00 3.58 R
4775 4899 4.082300 CAGTTAATACTTTGGGCATGTGCA 60.082 41.667 7.36 0.0 35.99 4.57 R
4870 4994 4.439253 AAGTAACTCCACAGGAAGCTTT 57.561 40.909 0.00 0.0 0.00 3.51 R
6621 7336 0.175760 TTCTAGCCGGAGTGTGATGC 59.824 55.000 5.05 0.0 0.00 3.91 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
21 22 4.825546 TTCCACTCGTTCCGACTATATC 57.174 45.455 0.00 0.00 0.00 1.63
30 31 3.839654 CGACTATATCGCCGTGTGT 57.160 52.632 0.00 0.00 45.52 3.72
31 32 1.395670 CGACTATATCGCCGTGTGTG 58.604 55.000 0.00 0.00 45.52 3.82
32 33 1.268386 CGACTATATCGCCGTGTGTGT 60.268 52.381 0.00 0.00 45.52 3.72
33 34 2.117137 GACTATATCGCCGTGTGTGTG 58.883 52.381 0.00 0.00 0.00 3.82
34 35 1.475280 ACTATATCGCCGTGTGTGTGT 59.525 47.619 0.00 0.00 0.00 3.72
35 36 1.852280 CTATATCGCCGTGTGTGTGTG 59.148 52.381 0.00 0.00 0.00 3.82
36 37 0.037697 ATATCGCCGTGTGTGTGTGT 60.038 50.000 0.00 0.00 0.00 3.72
37 38 0.941936 TATCGCCGTGTGTGTGTGTG 60.942 55.000 0.00 0.00 0.00 3.82
38 39 2.916502 ATCGCCGTGTGTGTGTGTGT 62.917 55.000 0.00 0.00 0.00 3.72
39 40 2.403186 GCCGTGTGTGTGTGTGTG 59.597 61.111 0.00 0.00 0.00 3.82
40 41 3.097672 CCGTGTGTGTGTGTGTGG 58.902 61.111 0.00 0.00 0.00 4.17
41 42 2.468670 CCGTGTGTGTGTGTGTGGG 61.469 63.158 0.00 0.00 0.00 4.61
42 43 2.468670 CGTGTGTGTGTGTGTGGGG 61.469 63.158 0.00 0.00 0.00 4.96
43 44 2.118404 GTGTGTGTGTGTGTGGGGG 61.118 63.158 0.00 0.00 0.00 5.40
63 64 4.252493 GGGTGTTCTCCTCCCCTT 57.748 61.111 0.00 0.00 35.52 3.95
64 65 1.685820 GGGTGTTCTCCTCCCCTTG 59.314 63.158 0.00 0.00 35.52 3.61
69 70 1.290134 GTTCTCCTCCCCTTGGATGT 58.710 55.000 0.00 0.00 40.80 3.06
70 71 2.225779 TGTTCTCCTCCCCTTGGATGTA 60.226 50.000 0.00 0.00 40.80 2.29
71 72 3.049344 GTTCTCCTCCCCTTGGATGTAT 58.951 50.000 0.00 0.00 40.80 2.29
75 76 1.477558 CCTCCCCTTGGATGTATGCAC 60.478 57.143 0.00 0.00 40.80 4.57
83 84 2.080693 TGGATGTATGCACGTTGGTTC 58.919 47.619 0.00 0.00 0.00 3.62
94 95 4.277174 TGCACGTTGGTTCTGTGATTTTAT 59.723 37.500 0.00 0.00 35.66 1.40
99 100 5.469479 GTTGGTTCTGTGATTTTATGGGTG 58.531 41.667 0.00 0.00 0.00 4.61
102 103 5.222027 TGGTTCTGTGATTTTATGGGTGAGA 60.222 40.000 0.00 0.00 0.00 3.27
107 108 6.599244 TCTGTGATTTTATGGGTGAGATTGTC 59.401 38.462 0.00 0.00 0.00 3.18
134 135 1.149174 CCAGTGGAGTTGGTGCAGT 59.851 57.895 1.68 0.00 0.00 4.40
162 163 5.809001 ACTTGAGACTAATGGCTCATTGAA 58.191 37.500 2.19 0.00 40.51 2.69
178 179 5.070001 TCATTGAATTTTCCCAAGTCGACT 58.930 37.500 13.58 13.58 0.00 4.18
179 180 6.234920 TCATTGAATTTTCCCAAGTCGACTA 58.765 36.000 20.39 0.64 0.00 2.59
185 186 2.297698 TCCCAAGTCGACTACTTCCA 57.702 50.000 20.39 0.00 45.64 3.53
192 193 1.022735 TCGACTACTTCCATCGGAGC 58.977 55.000 0.00 0.00 36.51 4.70
224 225 1.482593 AGTCGAGGATGGTGTTGATCC 59.517 52.381 0.00 0.00 39.94 3.36
241 242 4.520846 CGCAATCGTTCAGCCCGC 62.521 66.667 0.00 0.00 0.00 6.13
262 263 3.142951 CCGTGATTAGGGTTTTGTCACA 58.857 45.455 0.00 0.00 39.20 3.58
312 313 2.542178 CGTGACGTGATTTTGTTCTCCA 59.458 45.455 0.00 0.00 0.00 3.86
323 324 5.835113 TTTTGTTCTCCAGTTCCTTCTTG 57.165 39.130 0.00 0.00 0.00 3.02
387 395 1.272203 TGTGTCCCTCTCCTCTGTCTC 60.272 57.143 0.00 0.00 0.00 3.36
397 406 1.978580 TCCTCTGTCTCCCCAAACTTC 59.021 52.381 0.00 0.00 0.00 3.01
417 426 2.707791 TCAGATTATCTTCTGGCCCCTG 59.292 50.000 0.00 0.00 42.78 4.45
457 466 5.503002 TCGGGTCATCGATTAGTCCATATA 58.497 41.667 0.00 0.00 33.92 0.86
502 513 5.882040 TCTATATCGATGACTTCTCCACCT 58.118 41.667 8.54 0.00 0.00 4.00
509 520 2.889512 TGACTTCTCCACCTCTGCTTA 58.110 47.619 0.00 0.00 0.00 3.09
535 554 2.092429 ACTCTTGAACAAGGTTGCTCCA 60.092 45.455 13.46 0.00 38.88 3.86
543 562 4.634012 ACAAGGTTGCTCCAGTAATACA 57.366 40.909 0.00 0.00 39.02 2.29
544 563 4.980573 ACAAGGTTGCTCCAGTAATACAA 58.019 39.130 0.00 0.00 39.02 2.41
652 671 9.859427 CTTGTAATTTCATATTCTTTCAAGGCA 57.141 29.630 0.00 0.00 0.00 4.75
654 673 9.638239 TGTAATTTCATATTCTTTCAAGGCAAC 57.362 29.630 0.00 0.00 0.00 4.17
839 863 0.519175 CAGCGAACGCAATAGTGTGC 60.519 55.000 20.66 0.00 44.88 4.57
1057 1093 1.519455 CTCCTCAACATCGGTCCGC 60.519 63.158 6.34 0.00 0.00 5.54
1070 1106 1.054978 GGTCCGCCCCTTATTCCTCT 61.055 60.000 0.00 0.00 0.00 3.69
1482 1518 6.863275 TGCTCGTAATAGATTCAGAAACTCA 58.137 36.000 0.00 0.00 0.00 3.41
1500 1536 8.641541 AGAAACTCACCATTGTACATTTGATTT 58.358 29.630 0.00 0.00 0.00 2.17
1679 1719 4.009675 CCCAGAAAATCAGATTTCGTGGA 58.990 43.478 25.44 0.00 42.73 4.02
1691 1731 6.322456 TCAGATTTCGTGGACTGAATCTATCT 59.678 38.462 0.00 0.00 36.63 1.98
1722 1762 9.988815 TTGATCTATCTAAGCTTGTAAGATTCC 57.011 33.333 13.97 5.55 35.96 3.01
1755 1797 3.253188 TGCTTGTTGTTCTCTATTGCCAC 59.747 43.478 0.00 0.00 0.00 5.01
1831 1873 7.648142 TGATAAAGTCGAACAAGCAATTTTCT 58.352 30.769 0.00 0.00 0.00 2.52
2126 2168 3.259064 ACTGTATCATTAACGCGTTGCT 58.741 40.909 33.40 17.71 0.00 3.91
2165 2209 1.350684 TGGTGGAAGCTGCACATTCTA 59.649 47.619 1.02 0.00 40.73 2.10
2203 2247 8.673711 GCAAATTTACATGAGTAAGATACACCA 58.326 33.333 0.00 0.00 41.00 4.17
2223 2267 4.533707 ACCATCAATCTTCTTCTGGTCTCA 59.466 41.667 0.00 0.00 31.51 3.27
2406 2450 4.615452 GCAAATCTTCAAGAAGCTGTCCTG 60.615 45.833 4.95 0.00 38.28 3.86
2488 2532 8.694540 CCCCAAATCATGTATTTAACTTGATCA 58.305 33.333 0.00 0.00 46.71 2.92
2501 2545 8.519492 TTTAACTTGATCACAGCTTATTTTGC 57.481 30.769 0.00 0.00 0.00 3.68
2503 2547 6.088016 ACTTGATCACAGCTTATTTTGCAA 57.912 33.333 0.00 0.00 0.00 4.08
2507 2551 7.966246 TGATCACAGCTTATTTTGCAATTTT 57.034 28.000 0.00 0.00 0.00 1.82
2508 2552 8.380743 TGATCACAGCTTATTTTGCAATTTTT 57.619 26.923 0.00 0.00 0.00 1.94
2557 2601 7.617041 ATCGCTAAAGTAAATCTGAAGCTTT 57.383 32.000 0.00 0.00 34.54 3.51
2558 2602 7.061752 TCGCTAAAGTAAATCTGAAGCTTTC 57.938 36.000 0.00 0.00 34.54 2.62
2562 2606 7.553044 GCTAAAGTAAATCTGAAGCTTTCCCTA 59.447 37.037 0.00 0.00 34.15 3.53
2570 2614 5.661458 TCTGAAGCTTTCCCTATTTCTACG 58.339 41.667 0.00 0.00 0.00 3.51
2578 2622 7.447545 AGCTTTCCCTATTTCTACGTTTTCTTT 59.552 33.333 0.00 0.00 0.00 2.52
2595 2639 3.963129 TCTTTCCTTTGTGACCACTGTT 58.037 40.909 1.62 0.00 0.00 3.16
2628 2672 6.371389 GCAGTTCTTTGTAACTTACCATGTC 58.629 40.000 0.00 0.00 37.61 3.06
2638 2682 2.171448 ACTTACCATGTCAGGGCATCTC 59.829 50.000 2.72 0.00 0.00 2.75
2645 2689 1.078214 TCAGGGCATCTCCAAAGCG 60.078 57.895 0.00 0.00 36.21 4.68
2646 2690 2.117156 CAGGGCATCTCCAAAGCGG 61.117 63.158 0.00 0.00 36.21 5.52
2647 2691 2.272146 GGGCATCTCCAAAGCGGA 59.728 61.111 0.00 0.00 43.61 5.54
2648 2692 2.115291 GGGCATCTCCAAAGCGGAC 61.115 63.158 0.00 0.00 39.64 4.79
2649 2693 2.464459 GGCATCTCCAAAGCGGACG 61.464 63.158 0.00 0.00 39.64 4.79
2650 2694 3.093278 CATCTCCAAAGCGGACGC 58.907 61.111 8.91 8.91 39.64 5.19
2660 2704 2.353607 GCGGACGCGGTCTAGATG 60.354 66.667 12.47 0.00 32.47 2.90
2661 2705 3.108343 CGGACGCGGTCTAGATGT 58.892 61.111 12.47 0.00 32.47 3.06
2662 2706 1.298413 CGGACGCGGTCTAGATGTG 60.298 63.158 12.47 1.14 32.47 3.21
2664 2708 0.172803 GGACGCGGTCTAGATGTGTT 59.827 55.000 12.47 1.32 32.47 3.32
2665 2709 1.403780 GGACGCGGTCTAGATGTGTTT 60.404 52.381 12.47 0.00 32.47 2.83
2666 2710 2.159338 GGACGCGGTCTAGATGTGTTTA 60.159 50.000 12.47 0.00 32.47 2.01
2668 2712 1.852895 CGCGGTCTAGATGTGTTTAGC 59.147 52.381 0.00 0.00 0.00 3.09
2670 2714 2.418197 GCGGTCTAGATGTGTTTAGCCA 60.418 50.000 0.00 0.00 0.00 4.75
2671 2715 3.741388 GCGGTCTAGATGTGTTTAGCCAT 60.741 47.826 0.00 0.00 0.00 4.40
2672 2716 4.051922 CGGTCTAGATGTGTTTAGCCATC 58.948 47.826 0.00 0.00 38.17 3.51
2674 2718 4.141711 GGTCTAGATGTGTTTAGCCATCCA 60.142 45.833 0.00 0.00 38.57 3.41
2675 2719 5.428253 GTCTAGATGTGTTTAGCCATCCAA 58.572 41.667 0.00 0.00 38.57 3.53
2676 2720 5.294552 GTCTAGATGTGTTTAGCCATCCAAC 59.705 44.000 0.00 0.00 38.57 3.77
2678 2722 2.264005 TGTGTTTAGCCATCCAACGT 57.736 45.000 0.00 0.00 0.00 3.99
2679 2723 1.876799 TGTGTTTAGCCATCCAACGTG 59.123 47.619 0.00 0.00 0.00 4.49
2680 2724 1.199097 GTGTTTAGCCATCCAACGTGG 59.801 52.381 0.00 0.00 39.43 4.94
2681 2725 0.808755 GTTTAGCCATCCAACGTGGG 59.191 55.000 1.09 1.09 38.32 4.61
2685 2729 2.751436 CCATCCAACGTGGGCCTG 60.751 66.667 3.23 4.18 38.32 4.85
2686 2730 2.034066 CATCCAACGTGGGCCTGT 59.966 61.111 3.23 0.00 38.32 4.00
2687 2731 1.298340 CATCCAACGTGGGCCTGTA 59.702 57.895 3.23 0.00 38.32 2.74
2688 2732 0.107214 CATCCAACGTGGGCCTGTAT 60.107 55.000 3.23 0.00 38.32 2.29
2689 2733 0.180406 ATCCAACGTGGGCCTGTATC 59.820 55.000 3.23 0.00 38.32 2.24
2690 2734 1.813753 CCAACGTGGGCCTGTATCG 60.814 63.158 4.53 4.67 32.67 2.92
2691 2735 1.813753 CAACGTGGGCCTGTATCGG 60.814 63.158 4.53 0.00 0.00 4.18
2692 2736 2.288025 AACGTGGGCCTGTATCGGT 61.288 57.895 4.53 0.00 0.00 4.69
2693 2737 2.106332 CGTGGGCCTGTATCGGTC 59.894 66.667 4.53 0.00 0.00 4.79
2694 2738 2.717044 CGTGGGCCTGTATCGGTCA 61.717 63.158 4.53 0.00 0.00 4.02
2695 2739 1.600107 GTGGGCCTGTATCGGTCAA 59.400 57.895 4.53 0.00 0.00 3.18
2696 2740 0.743345 GTGGGCCTGTATCGGTCAAC 60.743 60.000 4.53 0.00 0.00 3.18
2720 2764 2.981350 GTCCCCGCAAAGCCGAAA 60.981 61.111 0.00 0.00 0.00 3.46
2721 2765 2.034999 TCCCCGCAAAGCCGAAAT 59.965 55.556 0.00 0.00 0.00 2.17
3076 3120 0.329261 CCCACCTTTCTCTGCATCCA 59.671 55.000 0.00 0.00 0.00 3.41
3080 3124 3.512724 CCACCTTTCTCTGCATCCATTTT 59.487 43.478 0.00 0.00 0.00 1.82
3094 3140 1.532505 CCATTTTCTCTTGCATCCGCG 60.533 52.381 0.00 0.00 42.97 6.46
3095 3141 0.734889 ATTTTCTCTTGCATCCGCGG 59.265 50.000 22.12 22.12 42.97 6.46
3148 3210 4.293671 CCGTTTCCCCCTTGCCCA 62.294 66.667 0.00 0.00 0.00 5.36
3149 3211 2.676471 CGTTTCCCCCTTGCCCAG 60.676 66.667 0.00 0.00 0.00 4.45
3374 3471 1.402968 CAGAATCCGGCCACATTTGAG 59.597 52.381 2.24 0.00 0.00 3.02
3410 3507 7.760131 AATGCATCAACAAATTCTTTATCGG 57.240 32.000 0.00 0.00 0.00 4.18
3447 3544 5.893897 ACTGAAGGAAGATTTGATTGAGC 57.106 39.130 0.00 0.00 0.00 4.26
3487 3584 4.654262 AGGGGACAACTAGTACATATGTGG 59.346 45.833 18.81 8.22 30.17 4.17
3574 3671 6.639632 AGAACTACTGTTGCATTTGAACAT 57.360 33.333 0.00 0.00 36.39 2.71
3632 3729 1.144969 TGAGCGTGCGGACTTAAAAG 58.855 50.000 5.27 0.00 0.00 2.27
3637 3734 2.912366 CGTGCGGACTTAAAAGAAACC 58.088 47.619 5.27 0.00 0.00 3.27
3645 3742 1.271379 CTTAAAAGAAACCGGGTGGCC 59.729 52.381 6.32 0.00 39.70 5.36
4220 4344 1.615384 CCTTTGCCCTCTCTTTCCCTG 60.615 57.143 0.00 0.00 0.00 4.45
4285 4409 9.905713 AGATTCTTATAAGTTGCTATGGTTCAA 57.094 29.630 12.19 0.00 0.00 2.69
4410 4534 5.984926 CAGGTTTGCAAATTGTTGTGAGTAT 59.015 36.000 16.21 0.00 37.06 2.12
4476 4600 1.827969 AGTCCCTGCTGACATAGTGAC 59.172 52.381 0.00 0.00 37.73 3.67
4492 4616 3.914555 GTGACATATGAAGTCGCTGTG 57.085 47.619 10.38 0.00 41.86 3.66
4624 4748 0.902531 TCTGCTTTAGGCGCTTAGGT 59.097 50.000 7.64 0.00 45.43 3.08
4655 4779 2.879462 GTGCTCGTCTTACCGCCG 60.879 66.667 0.00 0.00 0.00 6.46
4676 4800 4.399112 CGTATAAACAATGACGCAAAGCA 58.601 39.130 0.00 0.00 0.00 3.91
4775 4899 4.649674 TCCGAAATATGTAAGCAGAGTCCT 59.350 41.667 0.00 0.00 0.00 3.85
4805 4929 5.890985 TGCCCAAAGTATTAACTGCATACAT 59.109 36.000 0.00 0.00 35.62 2.29
4870 4994 8.642432 CATTCTTCCCTAGATAGTCACATGTAA 58.358 37.037 0.00 0.00 31.54 2.41
4913 5037 8.080083 ACTTTTAGCAATTCAAAAAGCATCAG 57.920 30.769 12.85 0.00 34.73 2.90
5083 5248 8.915654 GGTGTTGATTATTTCATTTCTTGTGTC 58.084 33.333 0.00 0.00 33.34 3.67
5131 5298 3.134804 AGAATGCTAATCTTACGGGTGCT 59.865 43.478 0.00 0.00 0.00 4.40
5242 5409 4.511527 ACAGTCTGCTGATTATCTGGTTG 58.488 43.478 11.79 0.00 45.28 3.77
5341 5696 4.670221 GCCTGTTCATCGTAAAGCTTGAAG 60.670 45.833 0.00 0.00 0.00 3.02
5538 5946 5.648330 GGATTTCCCTCCCTTAACTGTAT 57.352 43.478 0.00 0.00 0.00 2.29
5539 5947 5.377478 GGATTTCCCTCCCTTAACTGTATG 58.623 45.833 0.00 0.00 0.00 2.39
5540 5948 5.104067 GGATTTCCCTCCCTTAACTGTATGT 60.104 44.000 0.00 0.00 0.00 2.29
5541 5949 5.853572 TTTCCCTCCCTTAACTGTATGTT 57.146 39.130 0.00 0.00 42.31 2.71
5542 5950 5.853572 TTCCCTCCCTTAACTGTATGTTT 57.146 39.130 0.00 0.00 39.89 2.83
5586 5994 3.195698 GGATCGAACGTGGCTGGC 61.196 66.667 0.00 0.00 0.00 4.85
5674 6082 7.977853 TCCCTCTGTAAACAAATATAAGACGTC 59.022 37.037 7.70 7.70 0.00 4.34
5687 6095 9.647797 AAATATAAGACGTCTAACATTCACACA 57.352 29.630 20.39 0.00 0.00 3.72
5688 6096 9.647797 AATATAAGACGTCTAACATTCACACAA 57.352 29.630 20.39 0.00 0.00 3.33
5689 6097 5.907197 AAGACGTCTAACATTCACACAAG 57.093 39.130 20.39 0.00 0.00 3.16
5690 6098 4.945246 AGACGTCTAACATTCACACAAGT 58.055 39.130 18.46 0.00 0.00 3.16
5692 6100 6.509656 AGACGTCTAACATTCACACAAGTTA 58.490 36.000 18.46 0.00 0.00 2.24
5693 6101 7.152645 AGACGTCTAACATTCACACAAGTTAT 58.847 34.615 18.46 0.00 0.00 1.89
5695 6103 7.793902 ACGTCTAACATTCACACAAGTTATTC 58.206 34.615 0.00 0.00 0.00 1.75
5759 6306 6.813649 TCTCTGTAAGCATCTAACATTCACAC 59.186 38.462 0.00 0.00 0.00 3.82
5768 6315 8.292448 AGCATCTAACATTCACACAAGTTAAAG 58.708 33.333 0.00 0.00 0.00 1.85
5870 6417 6.915349 TGTTATGTAAGCCATGTTGTTTACC 58.085 36.000 6.35 0.00 34.86 2.85
5911 6459 8.004087 AGCATGCATAAATGAAAGACATTAGT 57.996 30.769 21.98 0.00 46.90 2.24
5912 6460 8.472413 AGCATGCATAAATGAAAGACATTAGTT 58.528 29.630 21.98 0.00 46.90 2.24
5971 6519 5.276461 TGTATTCGCATACTTGTCCTCAT 57.724 39.130 6.76 0.00 36.87 2.90
5986 6534 8.267183 ACTTGTCCTCATTATGTCATTCATACA 58.733 33.333 0.00 0.00 38.55 2.29
6119 6668 8.574251 TGTATGTTGTCCTGTTTGCTATTTAT 57.426 30.769 0.00 0.00 0.00 1.40
6292 7007 6.478512 TGCATTCTTTTGTTTACCTCCTTT 57.521 33.333 0.00 0.00 0.00 3.11
6496 7211 3.438781 AGAAGAGCAGTACGTCTGAAGAG 59.561 47.826 16.09 0.00 46.27 2.85
6540 7255 1.001815 CAAACGTTCAGGCATTCGGTT 60.002 47.619 0.00 0.00 33.48 4.44
6581 7296 3.013921 CGGGGCAAATAGTTTCTTGCTA 58.986 45.455 6.73 0.00 45.79 3.49
6691 7406 6.978659 TGTTAGATACCTGTGCTAAATCTTCG 59.021 38.462 0.00 0.00 0.00 3.79
6738 7453 0.332632 ACAGCTGTTGCATATGGGGT 59.667 50.000 15.25 0.00 42.74 4.95
6879 7596 4.524328 TCAGAGCAGTCACATTCTCACTTA 59.476 41.667 0.00 0.00 0.00 2.24
6883 7600 6.939163 AGAGCAGTCACATTCTCACTTATTTT 59.061 34.615 0.00 0.00 0.00 1.82
6926 7643 1.006922 GTTTTGACAGCAGCAGGGC 60.007 57.895 0.00 0.00 0.00 5.19
6927 7644 2.554636 TTTTGACAGCAGCAGGGCG 61.555 57.895 0.00 0.00 39.27 6.13
6963 7978 0.179094 TACAACCACCGATCGGATGC 60.179 55.000 39.55 0.00 38.96 3.91
6999 8014 5.065218 GGACTGAGATCATATTTGCACGTTT 59.935 40.000 0.00 0.00 0.00 3.60
7019 8034 3.536956 TTTTAGGCCACGTATCTCCAG 57.463 47.619 5.01 0.00 0.00 3.86
7022 8037 1.220749 GGCCACGTATCTCCAGCAA 59.779 57.895 0.00 0.00 0.00 3.91
7027 8042 1.204704 CACGTATCTCCAGCAAGGACA 59.795 52.381 0.00 0.00 43.07 4.02
7030 8045 2.166459 CGTATCTCCAGCAAGGACAGAA 59.834 50.000 0.00 0.00 43.07 3.02
7036 8051 4.471025 TCTCCAGCAAGGACAGAAATCATA 59.529 41.667 0.00 0.00 43.07 2.15
7044 8060 1.537202 GACAGAAATCATATGGGGCGC 59.463 52.381 0.00 0.00 0.00 6.53
7071 8087 3.439129 GGTTGAGTGCATTAGGTACAACC 59.561 47.826 12.09 12.09 45.11 3.77
7083 8099 2.201708 TACAACCAGACCCGTGCGA 61.202 57.895 0.00 0.00 0.00 5.10
7086 8102 4.760047 ACCAGACCCGTGCGATGC 62.760 66.667 0.00 0.00 0.00 3.91
7092 8108 1.852067 GACCCGTGCGATGCAGTTTT 61.852 55.000 0.00 0.00 40.08 2.43
7110 8126 0.829333 TTGGCATGTTTGGTTGCTGT 59.171 45.000 0.00 0.00 38.88 4.40
7113 8129 1.885887 GGCATGTTTGGTTGCTGTCTA 59.114 47.619 0.00 0.00 38.88 2.59
7129 8145 5.476752 CTGTCTAGCACCAAAATCTTAGC 57.523 43.478 0.00 0.00 0.00 3.09
7144 8160 2.300723 TCTTAGCCTGCACGAACCTTAA 59.699 45.455 0.00 0.00 0.00 1.85
7152 8168 1.607148 GCACGAACCTTAAAGCACCTT 59.393 47.619 0.00 0.00 0.00 3.50
7158 8174 0.322546 CCTTAAAGCACCTTCGGGCT 60.323 55.000 0.00 0.00 43.46 5.19
7162 8178 3.570212 AGCACCTTCGGGCTTGGT 61.570 61.111 0.00 0.00 36.92 3.67
7177 8193 0.472471 TTGGTTGAGGAGGAACGCTT 59.528 50.000 0.00 0.00 0.00 4.68
7178 8194 0.250295 TGGTTGAGGAGGAACGCTTG 60.250 55.000 0.00 0.00 0.00 4.01
7183 8199 1.623311 TGAGGAGGAACGCTTGAATCA 59.377 47.619 0.00 0.00 0.00 2.57
7184 8200 2.038426 TGAGGAGGAACGCTTGAATCAA 59.962 45.455 0.00 0.00 0.00 2.57
7207 8223 2.199652 TTTTTCACAGCCAGGCCCG 61.200 57.895 8.22 1.62 0.00 6.13
7227 8243 0.671781 AGTGATGCAACTCGAGGCAC 60.672 55.000 18.41 13.56 43.75 5.01
7228 8244 0.950555 GTGATGCAACTCGAGGCACA 60.951 55.000 18.41 14.14 43.75 4.57
7231 8247 0.321919 ATGCAACTCGAGGCACATGT 60.322 50.000 18.41 0.00 43.75 3.21
7245 8261 1.402968 CACATGTGCATTGGAGGCTAC 59.597 52.381 13.94 0.00 0.00 3.58
7256 8272 3.759766 GAGGCTACACGCGAGGAGC 62.760 68.421 29.78 29.78 40.44 4.70
7259 8275 2.808315 CTACACGCGAGGAGCCAT 59.192 61.111 15.93 0.00 44.76 4.40
7260 8276 1.589993 CTACACGCGAGGAGCCATG 60.590 63.158 15.93 0.00 44.76 3.66
7261 8277 3.716539 TACACGCGAGGAGCCATGC 62.717 63.158 15.93 0.00 44.76 4.06
7262 8278 4.827087 CACGCGAGGAGCCATGCT 62.827 66.667 15.93 0.00 44.76 3.79
7281 8297 0.891373 TCTCCTTGAGAGTGCTTCCG 59.109 55.000 0.00 0.00 43.71 4.30
7306 8322 2.056906 GCCGCCATAACTCCCCTCAT 62.057 60.000 0.00 0.00 0.00 2.90
7317 8333 2.249743 ACTCCCCTCATCCTTCTCTCAT 59.750 50.000 0.00 0.00 0.00 2.90
7319 8335 2.248423 TCCCCTCATCCTTCTCTCATCA 59.752 50.000 0.00 0.00 0.00 3.07
7328 8344 4.671831 TCCTTCTCTCATCACTCACTCTT 58.328 43.478 0.00 0.00 0.00 2.85
7350 8366 2.289320 CCCTTTCTCCACTCTCACACTG 60.289 54.545 0.00 0.00 0.00 3.66
7352 8368 0.681733 TTCTCCACTCTCACACTGGC 59.318 55.000 0.00 0.00 0.00 4.85
7375 8391 0.169009 GGCGAGCACAAGATTTGGAC 59.831 55.000 0.00 0.00 34.12 4.02
7378 8394 1.523758 GAGCACAAGATTTGGACGGT 58.476 50.000 0.00 0.00 34.12 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.117137 CACACACACGGCGATATAGTC 58.883 52.381 16.62 0.00 0.00 2.59
14 15 1.475280 ACACACACACGGCGATATAGT 59.525 47.619 16.62 3.29 0.00 2.12
15 16 1.852280 CACACACACACGGCGATATAG 59.148 52.381 16.62 2.57 0.00 1.31
16 17 1.202817 ACACACACACACGGCGATATA 59.797 47.619 16.62 0.00 0.00 0.86
17 18 0.037697 ACACACACACACGGCGATAT 60.038 50.000 16.62 0.00 0.00 1.63
18 19 0.941936 CACACACACACACGGCGATA 60.942 55.000 16.62 0.00 0.00 2.92
19 20 2.108157 ACACACACACACGGCGAT 59.892 55.556 16.62 0.00 0.00 4.58
20 21 2.888051 CACACACACACACGGCGA 60.888 61.111 16.62 0.00 0.00 5.54
21 22 3.192230 ACACACACACACACGGCG 61.192 61.111 4.80 4.80 0.00 6.46
22 23 2.403186 CACACACACACACACGGC 59.597 61.111 0.00 0.00 0.00 5.68
23 24 2.468670 CCCACACACACACACACGG 61.469 63.158 0.00 0.00 0.00 4.94
24 25 2.468670 CCCCACACACACACACACG 61.469 63.158 0.00 0.00 0.00 4.49
25 26 2.118404 CCCCCACACACACACACAC 61.118 63.158 0.00 0.00 0.00 3.82
26 27 2.273776 CCCCCACACACACACACA 59.726 61.111 0.00 0.00 0.00 3.72
63 64 2.080693 GAACCAACGTGCATACATCCA 58.919 47.619 0.00 0.00 0.00 3.41
64 65 2.095853 CAGAACCAACGTGCATACATCC 59.904 50.000 0.00 0.00 0.00 3.51
69 70 2.535012 TCACAGAACCAACGTGCATA 57.465 45.000 0.00 0.00 0.00 3.14
70 71 1.896220 ATCACAGAACCAACGTGCAT 58.104 45.000 0.00 0.00 0.00 3.96
71 72 1.674359 AATCACAGAACCAACGTGCA 58.326 45.000 0.00 0.00 0.00 4.57
75 76 4.217550 ACCCATAAAATCACAGAACCAACG 59.782 41.667 0.00 0.00 0.00 4.10
83 84 6.183360 GGACAATCTCACCCATAAAATCACAG 60.183 42.308 0.00 0.00 0.00 3.66
94 95 4.324254 GGTGATAAAGGACAATCTCACCCA 60.324 45.833 8.06 0.00 44.36 4.51
99 100 4.878397 CCACTGGTGATAAAGGACAATCTC 59.122 45.833 1.93 0.00 0.00 2.75
102 103 4.289672 ACTCCACTGGTGATAAAGGACAAT 59.710 41.667 4.09 0.00 0.00 2.71
107 108 3.244911 ACCAACTCCACTGGTGATAAAGG 60.245 47.826 4.09 1.97 45.67 3.11
134 135 4.040339 TGAGCCATTAGTCTCAAGTTGTCA 59.960 41.667 2.11 0.00 36.50 3.58
178 179 1.320344 ACGCTGCTCCGATGGAAGTA 61.320 55.000 0.00 0.00 0.00 2.24
179 180 2.172483 AACGCTGCTCCGATGGAAGT 62.172 55.000 0.00 0.00 0.00 3.01
185 186 0.602638 TTTGTCAACGCTGCTCCGAT 60.603 50.000 0.00 0.00 0.00 4.18
192 193 0.508641 CCTCGACTTTGTCAACGCTG 59.491 55.000 0.00 0.00 32.09 5.18
224 225 4.520846 GCGGGCTGAACGATTGCG 62.521 66.667 0.00 0.00 44.79 4.85
241 242 3.142951 TGTGACAAAACCCTAATCACGG 58.857 45.455 0.00 0.00 42.09 4.94
285 286 3.872354 ACAAAATCACGTCACGATGTTG 58.128 40.909 2.91 13.15 41.81 3.33
286 287 4.272504 AGAACAAAATCACGTCACGATGTT 59.727 37.500 2.91 5.15 32.89 2.71
323 324 4.133013 TCTGGCTAAACTTTATCGGACC 57.867 45.455 0.00 0.00 0.00 4.46
352 353 1.002792 GACACAAACCTCGCAAGTTCC 60.003 52.381 0.00 0.00 39.48 3.62
353 354 1.002792 GGACACAAACCTCGCAAGTTC 60.003 52.381 0.00 0.00 39.48 3.01
354 355 1.021968 GGACACAAACCTCGCAAGTT 58.978 50.000 0.00 0.00 39.48 2.66
397 406 2.813354 GCAGGGGCCAGAAGATAATCTG 60.813 54.545 4.39 0.00 45.19 2.90
423 432 1.739338 ATGACCCGAGAAGGCTAGCG 61.739 60.000 9.00 0.00 39.21 4.26
430 439 3.304794 GGACTAATCGATGACCCGAGAAG 60.305 52.174 0.00 0.00 42.21 2.85
433 442 1.954382 TGGACTAATCGATGACCCGAG 59.046 52.381 0.00 0.00 42.21 4.63
457 466 2.693591 TCAGAAGACGTCTTTGACCACT 59.306 45.455 30.22 18.77 36.11 4.00
509 520 8.127481 GGAGCAACCTTGTTCAAGAGTTGAAT 62.127 42.308 28.78 22.03 42.40 2.57
523 535 4.396166 CCTTGTATTACTGGAGCAACCTTG 59.604 45.833 1.91 0.00 39.86 3.61
524 536 4.288626 TCCTTGTATTACTGGAGCAACCTT 59.711 41.667 5.45 0.00 39.86 3.50
525 537 3.844211 TCCTTGTATTACTGGAGCAACCT 59.156 43.478 5.45 0.00 39.86 3.50
526 538 3.939592 GTCCTTGTATTACTGGAGCAACC 59.060 47.826 8.64 0.00 39.54 3.77
527 539 3.939592 GGTCCTTGTATTACTGGAGCAAC 59.060 47.826 21.96 9.03 43.95 4.17
535 554 6.971340 TCTGACTCTAGGTCCTTGTATTACT 58.029 40.000 0.00 0.00 43.89 2.24
557 576 1.424635 GCGTCGCGAGTAGAGTTCT 59.575 57.895 10.24 0.00 0.00 3.01
581 600 1.003580 GTCCTCCTTCTGCAACCATCA 59.996 52.381 0.00 0.00 0.00 3.07
586 605 2.508526 ACATTGTCCTCCTTCTGCAAC 58.491 47.619 0.00 0.00 0.00 4.17
707 727 8.703604 TGTAAATGTTCAAATTTTCGGTTTGA 57.296 26.923 0.00 0.00 42.14 2.69
828 852 0.657840 CTTAGCCCGCACACTATTGC 59.342 55.000 0.00 0.00 39.28 3.56
839 863 2.737830 GCTCCCTAGCTTAGCCCG 59.262 66.667 0.00 0.00 45.85 6.13
1057 1093 1.343069 CGGGAGAGAGGAATAAGGGG 58.657 60.000 0.00 0.00 0.00 4.79
1482 1518 8.144862 ACCCATTAAATCAAATGTACAATGGT 57.855 30.769 13.63 4.75 39.40 3.55
1500 1536 4.407621 TGATTCCGAAGCTAGAACCCATTA 59.592 41.667 0.00 0.00 0.00 1.90
1502 1538 2.771943 TGATTCCGAAGCTAGAACCCAT 59.228 45.455 0.00 0.00 0.00 4.00
1679 1719 4.906664 AGATCAAGGCCAGATAGATTCAGT 59.093 41.667 5.01 0.00 0.00 3.41
1691 1731 4.410228 ACAAGCTTAGATAGATCAAGGCCA 59.590 41.667 5.01 0.00 0.00 5.36
1722 1762 1.071385 ACAACAAGCAGAGTCTCCCTG 59.929 52.381 0.00 0.00 34.88 4.45
1755 1797 3.307242 GGAATCGCAGCTGTAAACAGTAG 59.693 47.826 16.64 5.92 45.45 2.57
1772 1814 7.947282 AGATAAGCTGACTAAGTACAGGAATC 58.053 38.462 0.00 0.00 35.05 2.52
2165 2209 7.215789 TCATGTAAATTTGCCTGTTCAAATGT 58.784 30.769 10.40 0.76 43.56 2.71
2203 2247 7.911130 TCTATGAGACCAGAAGAAGATTGAT 57.089 36.000 0.00 0.00 0.00 2.57
2300 2344 9.294030 CAAACAAAAATCAGCATATAAGGAGAC 57.706 33.333 0.00 0.00 0.00 3.36
2301 2345 9.023962 ACAAACAAAAATCAGCATATAAGGAGA 57.976 29.630 0.00 0.00 0.00 3.71
2406 2450 2.854805 GCTTTGAACGTTTGCTCTGTCC 60.855 50.000 0.46 0.00 0.00 4.02
2510 2554 9.820229 CGATATACAGTGTGTGTAAACAAAAAT 57.180 29.630 5.88 0.00 45.00 1.82
2521 2565 7.980742 TTACTTTAGCGATATACAGTGTGTG 57.019 36.000 5.88 0.00 0.00 3.82
2535 2579 6.251549 GGAAAGCTTCAGATTTACTTTAGCG 58.748 40.000 0.00 0.00 37.46 4.26
2557 2601 7.012661 AGGAAAGAAAACGTAGAAATAGGGA 57.987 36.000 0.00 0.00 0.00 4.20
2558 2602 7.683437 AAGGAAAGAAAACGTAGAAATAGGG 57.317 36.000 0.00 0.00 0.00 3.53
2562 2606 7.913821 GTCACAAAGGAAAGAAAACGTAGAAAT 59.086 33.333 0.00 0.00 0.00 2.17
2570 2614 5.102313 CAGTGGTCACAAAGGAAAGAAAAC 58.898 41.667 3.82 0.00 0.00 2.43
2578 2622 3.013921 GTGAAACAGTGGTCACAAAGGA 58.986 45.455 19.09 0.00 43.02 3.36
2595 2639 3.857157 ACAAAGAACTGCCCTAGTGAA 57.143 42.857 0.00 0.00 40.26 3.18
2628 2672 2.117156 CCGCTTTGGAGATGCCCTG 61.117 63.158 0.00 0.00 42.00 4.45
2638 2682 3.636313 TAGACCGCGTCCGCTTTGG 62.636 63.158 4.92 6.34 39.32 3.28
2645 2689 0.172803 AACACATCTAGACCGCGTCC 59.827 55.000 4.92 0.00 32.18 4.79
2646 2690 1.992170 AAACACATCTAGACCGCGTC 58.008 50.000 4.92 2.66 0.00 5.19
2647 2691 2.734492 GCTAAACACATCTAGACCGCGT 60.734 50.000 4.92 0.00 0.00 6.01
2648 2692 1.852895 GCTAAACACATCTAGACCGCG 59.147 52.381 0.00 0.00 0.00 6.46
2649 2693 2.202566 GGCTAAACACATCTAGACCGC 58.797 52.381 0.00 0.00 0.00 5.68
2650 2694 3.520290 TGGCTAAACACATCTAGACCG 57.480 47.619 0.00 0.00 0.00 4.79
2653 2697 5.428253 GTTGGATGGCTAAACACATCTAGA 58.572 41.667 0.00 0.00 42.34 2.43
2656 2700 3.009723 CGTTGGATGGCTAAACACATCT 58.990 45.455 0.00 0.00 42.34 2.90
2657 2701 2.747446 ACGTTGGATGGCTAAACACATC 59.253 45.455 0.00 0.00 42.05 3.06
2658 2702 2.487762 CACGTTGGATGGCTAAACACAT 59.512 45.455 0.00 0.00 0.00 3.21
2659 2703 1.876799 CACGTTGGATGGCTAAACACA 59.123 47.619 0.00 0.00 0.00 3.72
2660 2704 1.199097 CCACGTTGGATGGCTAAACAC 59.801 52.381 0.00 0.00 40.96 3.32
2661 2705 1.529226 CCACGTTGGATGGCTAAACA 58.471 50.000 0.00 0.00 40.96 2.83
2662 2706 0.808755 CCCACGTTGGATGGCTAAAC 59.191 55.000 0.00 0.00 40.96 2.01
2664 2708 1.377987 GCCCACGTTGGATGGCTAA 60.378 57.895 10.41 0.00 40.96 3.09
2665 2709 2.270850 GCCCACGTTGGATGGCTA 59.729 61.111 10.41 0.00 40.96 3.93
2666 2710 4.740822 GGCCCACGTTGGATGGCT 62.741 66.667 10.41 0.00 40.96 4.75
2668 2712 2.191786 TACAGGCCCACGTTGGATGG 62.192 60.000 10.41 0.00 40.96 3.51
2670 2714 0.180406 GATACAGGCCCACGTTGGAT 59.820 55.000 10.41 0.00 40.96 3.41
2671 2715 1.600107 GATACAGGCCCACGTTGGA 59.400 57.895 10.41 0.00 40.96 3.53
2672 2716 1.813753 CGATACAGGCCCACGTTGG 60.814 63.158 0.00 0.16 37.25 3.77
2674 2718 2.234913 GACCGATACAGGCCCACGTT 62.235 60.000 0.00 0.00 33.69 3.99
2675 2719 2.682494 ACCGATACAGGCCCACGT 60.682 61.111 0.00 0.00 33.69 4.49
2676 2720 2.106332 GACCGATACAGGCCCACG 59.894 66.667 0.00 0.00 33.69 4.94
2678 2722 1.600107 GTTGACCGATACAGGCCCA 59.400 57.895 0.00 0.00 33.69 5.36
2679 2723 1.153229 GGTTGACCGATACAGGCCC 60.153 63.158 0.00 0.00 33.69 5.80
2680 2724 4.534401 GGTTGACCGATACAGGCC 57.466 61.111 0.00 0.00 33.69 5.19
2703 2747 2.340328 ATTTCGGCTTTGCGGGGAC 61.340 57.895 0.00 0.00 0.00 4.46
2704 2748 2.034999 ATTTCGGCTTTGCGGGGA 59.965 55.556 0.00 0.00 0.00 4.81
3061 3105 4.948621 AGAGAAAATGGATGCAGAGAAAGG 59.051 41.667 0.00 0.00 0.00 3.11
3076 3120 0.734889 CCGCGGATGCAAGAGAAAAT 59.265 50.000 24.07 0.00 42.97 1.82
3080 3124 4.838152 GGCCGCGGATGCAAGAGA 62.838 66.667 33.48 0.00 42.97 3.10
3102 3159 4.722700 CAAGGGTGTGGCGGGAGG 62.723 72.222 0.00 0.00 0.00 4.30
3129 3191 2.361230 GGCAAGGGGGAAACGGAG 60.361 66.667 0.00 0.00 0.00 4.63
3135 3197 1.155155 GTTTCTGGGCAAGGGGGAA 59.845 57.895 0.00 0.00 0.00 3.97
3148 3210 4.759183 CCTTTCTAGCTGCTTCTTGTTTCT 59.241 41.667 7.79 0.00 0.00 2.52
3149 3211 4.757149 TCCTTTCTAGCTGCTTCTTGTTTC 59.243 41.667 7.79 0.00 0.00 2.78
3374 3471 5.049167 TGTTGATGCATTTGAACAAACTCC 58.951 37.500 14.19 0.00 32.51 3.85
3410 3507 1.527034 TCAGTTGCTCATGAGTTGCC 58.473 50.000 23.38 7.78 0.00 4.52
3447 3544 1.211457 CCCTTTGACCTCCCAGAGATG 59.789 57.143 0.00 0.00 0.00 2.90
3581 3678 7.155328 CCGCATATCTAGTTCCAGTTTAGATT 58.845 38.462 0.00 0.00 36.06 2.40
4220 4344 0.248289 TCTACTTTAGCACGCCCCAC 59.752 55.000 0.00 0.00 0.00 4.61
4285 4409 6.325919 TCAATCGCTTCATACTTGGTTTTT 57.674 33.333 0.00 0.00 0.00 1.94
4302 4426 6.237648 GCAAAATTGGTCTAGCAAATCAATCG 60.238 38.462 0.00 0.00 0.00 3.34
4342 4466 3.519107 TGTCTCAATGAAGCTACATCCCA 59.481 43.478 0.00 0.00 0.00 4.37
4410 4534 7.446013 ACAGGGAACGTTTATGAAGAAATACAA 59.554 33.333 0.46 0.00 0.00 2.41
4428 4552 3.370672 CAGCAAAACACAAAACAGGGAAC 59.629 43.478 0.00 0.00 0.00 3.62
4476 4600 1.328680 GGTGCACAGCGACTTCATATG 59.671 52.381 20.43 0.00 0.00 1.78
4624 4748 2.194597 GCACCAACCACCCTGACA 59.805 61.111 0.00 0.00 0.00 3.58
4655 4779 7.186804 AGTATGCTTTGCGTCATTGTTTATAC 58.813 34.615 0.00 0.00 0.00 1.47
4676 4800 7.659390 GTGGCAGAATTAGCATCTAAGAAGTAT 59.341 37.037 4.92 0.00 0.00 2.12
4775 4899 4.082300 CAGTTAATACTTTGGGCATGTGCA 60.082 41.667 7.36 0.00 35.99 4.57
4844 4968 7.060383 ACATGTGACTATCTAGGGAAGAATG 57.940 40.000 0.00 0.00 37.89 2.67
4845 4969 8.783660 TTACATGTGACTATCTAGGGAAGAAT 57.216 34.615 9.11 0.00 37.89 2.40
4870 4994 4.439253 AAGTAACTCCACAGGAAGCTTT 57.561 40.909 0.00 0.00 0.00 3.51
4913 5037 7.370383 TGAAGTTCAAAATTCAGGCATTAGTC 58.630 34.615 2.20 0.00 37.99 2.59
4923 5088 7.815840 TGTCCTGTATGAAGTTCAAAATTCA 57.184 32.000 10.14 7.93 45.47 2.57
4927 5092 9.528018 GAAATTTGTCCTGTATGAAGTTCAAAA 57.472 29.630 10.14 3.74 0.00 2.44
5051 5216 7.598493 AGAAATGAAATAATCAACACCCAAACG 59.402 33.333 0.00 0.00 42.54 3.60
5088 5253 9.695526 CATTCTGAAAGTTCATTGGAATTTACA 57.304 29.630 0.00 0.00 36.46 2.41
5089 5254 8.650714 GCATTCTGAAAGTTCATTGGAATTTAC 58.349 33.333 0.00 0.00 36.46 2.01
5091 5256 7.447594 AGCATTCTGAAAGTTCATTGGAATTT 58.552 30.769 0.00 0.00 36.46 1.82
5131 5298 5.569355 TCAAGGTTAGCTCCATTCAAATCA 58.431 37.500 0.00 0.00 0.00 2.57
5208 5375 0.603569 CAGACTGTAGCGGTGAGGTT 59.396 55.000 0.00 0.00 0.00 3.50
5209 5376 1.878656 GCAGACTGTAGCGGTGAGGT 61.879 60.000 3.99 0.00 0.00 3.85
5242 5409 7.875041 ACAAGATATTGTGCCACACTAGATATC 59.125 37.037 15.00 15.00 35.20 1.63
5303 5473 7.761249 CGATGAACAGGCATGTATGATATAGAA 59.239 37.037 3.57 0.00 39.29 2.10
5375 5730 6.376864 TCAAACTCTTCAGTTCCAAACATGAA 59.623 34.615 0.00 0.00 42.45 2.57
5516 5924 5.104067 ACATACAGTTAAGGGAGGGAAATCC 60.104 44.000 0.00 0.00 38.76 3.01
5517 5925 6.002653 ACATACAGTTAAGGGAGGGAAATC 57.997 41.667 0.00 0.00 0.00 2.17
5518 5926 6.402981 AACATACAGTTAAGGGAGGGAAAT 57.597 37.500 0.00 0.00 39.09 2.17
5519 5927 5.853572 AACATACAGTTAAGGGAGGGAAA 57.146 39.130 0.00 0.00 39.09 3.13
5520 5928 5.853572 AAACATACAGTTAAGGGAGGGAA 57.146 39.130 0.00 0.00 40.26 3.97
5521 5929 5.853572 AAAACATACAGTTAAGGGAGGGA 57.146 39.130 0.00 0.00 40.26 4.20
5541 5949 6.045106 AGGGAGGTCACATTTCTACCTAAAAA 59.955 38.462 0.00 0.00 43.69 1.94
5542 5950 5.550403 AGGGAGGTCACATTTCTACCTAAAA 59.450 40.000 0.00 0.00 43.69 1.52
5586 5994 1.160137 GCTCACAGGTGTAAGCTTGG 58.840 55.000 9.86 0.00 46.63 3.61
5599 6007 1.483827 CTTGGATGGCTAGAGCTCACA 59.516 52.381 17.77 9.58 41.70 3.58
5626 6034 5.866633 GGAGTAGATGTTTGTGAGAACTGAG 59.133 44.000 0.00 0.00 0.00 3.35
5674 6082 9.950680 AAACAGAATAACTTGTGTGAATGTTAG 57.049 29.630 0.00 0.00 37.86 2.34
5676 6084 9.730420 GTAAACAGAATAACTTGTGTGAATGTT 57.270 29.630 0.00 0.00 37.86 2.71
5678 6086 9.385902 CTGTAAACAGAATAACTTGTGTGAATG 57.614 33.333 3.99 0.00 46.59 2.67
5695 6103 7.040062 CCTGATAGATACTCCCTCTGTAAACAG 60.040 44.444 3.64 3.64 45.08 3.16
5714 6261 6.760770 CAGAGAACTAAAGAAAGCCCTGATAG 59.239 42.308 0.00 0.00 0.00 2.08
5759 6306 7.215085 ACTGAGGGTTAGTACACTTTAACTTG 58.785 38.462 0.00 0.00 38.42 3.16
5768 6315 8.059798 TGATAGTTTACTGAGGGTTAGTACAC 57.940 38.462 0.00 0.00 33.60 2.90
5796 6343 1.486310 TGATGGGTACTGACTCCATGC 59.514 52.381 5.44 0.03 36.99 4.06
5851 6398 7.120579 CAGAATAGGTAAACAACATGGCTTACA 59.879 37.037 0.00 0.00 0.00 2.41
5870 6417 5.886992 TGCATGCTTCATCAAACAGAATAG 58.113 37.500 20.33 0.00 0.00 1.73
5971 6519 9.710900 CTTAGCATAGGTGTATGAATGACATAA 57.289 33.333 0.00 0.00 42.19 1.90
5986 6534 3.917300 ACCAGACTAGCTTAGCATAGGT 58.083 45.455 7.07 2.59 0.00 3.08
6141 6690 9.853555 TTGTTCGAATTATGCATGAAGTAAAAT 57.146 25.926 10.16 0.00 0.00 1.82
6177 6726 9.305925 GCTCTTTGTATTCTCAAAATAATTGGG 57.694 33.333 0.00 0.00 36.96 4.12
6301 7016 8.755028 TGTTACCAGAGCAGACATAGTTTAATA 58.245 33.333 0.00 0.00 0.00 0.98
6319 7034 3.687698 CACCGGTTAAATCCTGTTACCAG 59.312 47.826 2.97 0.00 38.50 4.00
6496 7211 3.575965 ACCCATTTGCATTCGAGTTTC 57.424 42.857 0.00 0.00 0.00 2.78
6540 7255 1.269309 GGCGTGCATGTGTTTTGGTAA 60.269 47.619 7.93 0.00 0.00 2.85
6581 7296 3.928005 ATCAACACTGAGAGGCATGAT 57.072 42.857 0.00 0.00 34.23 2.45
6621 7336 0.175760 TTCTAGCCGGAGTGTGATGC 59.824 55.000 5.05 0.00 0.00 3.91
6691 7406 1.134694 GAATTCCTTGCGCCACGAC 59.865 57.895 4.18 0.00 0.00 4.34
6738 7453 7.066163 CCAACAATTCAGATACAGATACAGCAA 59.934 37.037 0.00 0.00 0.00 3.91
6879 7596 9.056005 GGAAAAGATAAAACTTTGCCTCAAAAT 57.944 29.630 10.04 0.00 46.56 1.82
6927 7644 5.048504 TGGTTGTACATACGCTATACCTAGC 60.049 44.000 9.78 0.00 45.79 3.42
6932 7649 3.976942 CGGTGGTTGTACATACGCTATAC 59.023 47.826 0.00 0.00 0.00 1.47
6963 7978 1.272490 TCTCAGTCCCTGCAACTTACG 59.728 52.381 0.00 0.00 0.00 3.18
6999 8014 2.419574 GCTGGAGATACGTGGCCTAAAA 60.420 50.000 3.32 0.00 0.00 1.52
7002 8017 0.396556 TGCTGGAGATACGTGGCCTA 60.397 55.000 3.32 0.00 0.00 3.93
7019 8034 3.571401 CCCCATATGATTTCTGTCCTTGC 59.429 47.826 3.65 0.00 0.00 4.01
7022 8037 2.224621 CGCCCCATATGATTTCTGTCCT 60.225 50.000 3.65 0.00 0.00 3.85
7027 8042 0.606401 CCGCGCCCCATATGATTTCT 60.606 55.000 3.65 0.00 0.00 2.52
7030 8045 1.150536 AACCGCGCCCCATATGATT 59.849 52.632 3.65 0.00 0.00 2.57
7044 8060 1.468520 CCTAATGCACTCAACCAACCG 59.531 52.381 0.00 0.00 0.00 4.44
7054 8070 3.307480 GGTCTGGTTGTACCTAATGCACT 60.307 47.826 0.00 0.00 39.58 4.40
7071 8087 3.190849 CTGCATCGCACGGGTCTG 61.191 66.667 0.00 0.00 33.79 3.51
7086 8102 2.031930 GCAACCAAACATGCCAAAACTG 59.968 45.455 0.00 0.00 36.56 3.16
7092 8108 0.388659 GACAGCAACCAAACATGCCA 59.611 50.000 0.00 0.00 43.57 4.92
7110 8126 4.517285 CAGGCTAAGATTTTGGTGCTAGA 58.483 43.478 0.00 0.00 0.00 2.43
7113 8129 1.821136 GCAGGCTAAGATTTTGGTGCT 59.179 47.619 0.00 0.00 0.00 4.40
7127 8143 1.523758 CTTTAAGGTTCGTGCAGGCT 58.476 50.000 0.35 0.00 0.00 4.58
7129 8145 1.069227 GTGCTTTAAGGTTCGTGCAGG 60.069 52.381 0.00 0.00 0.00 4.85
7152 8168 2.592993 CCTCCTCAACCAAGCCCGA 61.593 63.158 0.00 0.00 0.00 5.14
7158 8174 0.472471 AAGCGTTCCTCCTCAACCAA 59.528 50.000 0.00 0.00 0.00 3.67
7162 8178 2.038426 TGATTCAAGCGTTCCTCCTCAA 59.962 45.455 0.00 0.00 0.00 3.02
7203 8219 3.490890 GAGTTGCATCACTCGGGC 58.509 61.111 2.87 0.00 34.12 6.13
7207 8223 0.390340 TGCCTCGAGTTGCATCACTC 60.390 55.000 12.31 8.27 40.02 3.51
7210 8226 0.036105 ATGTGCCTCGAGTTGCATCA 60.036 50.000 17.57 16.32 40.07 3.07
7227 8243 1.402968 GTGTAGCCTCCAATGCACATG 59.597 52.381 0.00 0.00 0.00 3.21
7228 8244 1.755179 GTGTAGCCTCCAATGCACAT 58.245 50.000 0.00 0.00 0.00 3.21
7231 8247 1.745115 GCGTGTAGCCTCCAATGCA 60.745 57.895 0.00 0.00 40.81 3.96
7236 8252 3.449227 CCTCGCGTGTAGCCTCCA 61.449 66.667 5.77 0.00 44.76 3.86
7237 8253 3.127352 CTCCTCGCGTGTAGCCTCC 62.127 68.421 5.77 0.00 44.76 4.30
7245 8261 4.827087 AGCATGGCTCCTCGCGTG 62.827 66.667 5.77 2.75 40.44 5.34
7262 8278 0.891373 CGGAAGCACTCTCAAGGAGA 59.109 55.000 0.00 0.00 44.45 3.71
7263 8279 0.108424 CCGGAAGCACTCTCAAGGAG 60.108 60.000 0.00 0.00 46.87 3.69
7264 8280 0.541998 TCCGGAAGCACTCTCAAGGA 60.542 55.000 0.00 0.00 0.00 3.36
7265 8281 0.321671 TTCCGGAAGCACTCTCAAGG 59.678 55.000 14.35 0.00 0.00 3.61
7281 8297 2.513897 AGTTATGGCGGCGCTTCC 60.514 61.111 32.30 15.98 0.00 3.46
7293 8309 4.078336 TGAGAGAAGGATGAGGGGAGTTAT 60.078 45.833 0.00 0.00 0.00 1.89
7295 8311 2.045047 TGAGAGAAGGATGAGGGGAGTT 59.955 50.000 0.00 0.00 0.00 3.01
7306 8322 4.314522 AGAGTGAGTGATGAGAGAAGGA 57.685 45.455 0.00 0.00 0.00 3.36
7317 8333 2.900546 GGAGAAAGGGAAGAGTGAGTGA 59.099 50.000 0.00 0.00 0.00 3.41
7319 8335 2.635427 GTGGAGAAAGGGAAGAGTGAGT 59.365 50.000 0.00 0.00 0.00 3.41
7328 8344 1.971357 GTGTGAGAGTGGAGAAAGGGA 59.029 52.381 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.