Multiple sequence alignment - TraesCS2B01G494300

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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 TraesCS2B01G494300 chr2B 100.000 3415 0 0 1 3415 691453928 691450514 0.000000e+00 6307.0
1 TraesCS2B01G494300 chr2A 92.979 2521 125 11 1 2500 713544585 713542096 0.000000e+00 3627.0
2 TraesCS2B01G494300 chr2A 93.632 581 32 4 2839 3415 713541955 713541376 0.000000e+00 863.0
3 TraesCS2B01G494300 chr2A 100.000 35 0 0 2791 2825 713541967 713541933 7.910000e-07 65.8
4 TraesCS2B01G494300 chr2D 92.534 2518 137 14 1 2500 575360329 575357845 0.000000e+00 3561.0
5 TraesCS2B01G494300 chr2D 91.379 580 41 5 2839 3415 575357589 575357016 0.000000e+00 785.0
6 TraesCS2B01G494300 chr2D 91.282 195 9 3 2650 2838 575357747 575357555 3.380000e-65 259.0
7 TraesCS2B01G494300 chr2D 76.254 598 70 37 299 866 140713689 140713134 5.660000e-63 252.0
8 TraesCS2B01G494300 chr2D 93.617 47 3 0 1 47 575360412 575360366 1.700000e-08 71.3
9 TraesCS2B01G494300 chr6D 87.459 1212 131 11 987 2178 472306494 472305284 0.000000e+00 1376.0
10 TraesCS2B01G494300 chr6D 79.417 515 56 23 396 904 472307068 472306598 5.500000e-83 318.0
11 TraesCS2B01G494300 chr6D 95.833 120 4 1 2487 2606 455247239 455247121 3.480000e-45 193.0
12 TraesCS2B01G494300 chr6A 87.427 1193 132 8 987 2171 617686204 617687386 0.000000e+00 1356.0
13 TraesCS2B01G494300 chr6B 87.066 1152 131 9 1029 2174 716976748 716975609 0.000000e+00 1286.0
14 TraesCS2B01G494300 chr6B 99.115 113 1 0 2497 2609 156651440 156651552 1.610000e-48 204.0
15 TraesCS2B01G494300 chr6B 99.099 111 1 0 2496 2606 239360494 239360384 2.080000e-47 200.0
16 TraesCS2B01G494300 chr7D 85.324 293 28 9 582 866 24431643 24431928 4.310000e-74 289.0
17 TraesCS2B01G494300 chr7D 82.012 328 35 14 547 870 73007779 73007472 1.220000e-64 257.0
18 TraesCS2B01G494300 chr7D 81.040 327 37 16 548 870 190196524 190196219 1.580000e-58 237.0
19 TraesCS2B01G494300 chr1D 76.539 601 67 39 299 866 432956219 432955660 9.400000e-66 261.0
20 TraesCS2B01G494300 chrUn 83.113 302 27 13 573 870 96713244 96713525 1.570000e-63 254.0
21 TraesCS2B01G494300 chr5D 81.873 331 32 18 547 870 149768361 149768670 1.570000e-63 254.0
22 TraesCS2B01G494300 chr4D 81.402 328 37 14 547 870 21034780 21035087 2.630000e-61 246.0
23 TraesCS2B01G494300 chr3B 99.099 111 1 0 2496 2606 214560157 214560267 2.080000e-47 200.0
24 TraesCS2B01G494300 chr3B 93.130 131 6 3 2480 2607 169633540 169633670 4.500000e-44 189.0
25 TraesCS2B01G494300 chr7B 97.414 116 2 1 2488 2603 380869735 380869621 2.690000e-46 196.0
26 TraesCS2B01G494300 chr1B 97.391 115 3 0 2489 2603 395248907 395249021 2.690000e-46 196.0
27 TraesCS2B01G494300 chr1B 92.086 139 6 5 2471 2606 535009767 535009903 1.250000e-44 191.0
28 TraesCS2B01G494300 chr3A 94.400 125 5 2 2479 2603 65345882 65345760 1.250000e-44 191.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G494300 chr2B 691450514 691453928 3414 True 6307.000 6307 100.000 1 3415 1 chr2B.!!$R1 3414
1 TraesCS2B01G494300 chr2A 713541376 713544585 3209 True 1518.600 3627 95.537 1 3415 3 chr2A.!!$R1 3414
2 TraesCS2B01G494300 chr2D 575357016 575360412 3396 True 1169.075 3561 92.203 1 3415 4 chr2D.!!$R2 3414
3 TraesCS2B01G494300 chr2D 140713134 140713689 555 True 252.000 252 76.254 299 866 1 chr2D.!!$R1 567
4 TraesCS2B01G494300 chr6D 472305284 472307068 1784 True 847.000 1376 83.438 396 2178 2 chr6D.!!$R2 1782
5 TraesCS2B01G494300 chr6A 617686204 617687386 1182 False 1356.000 1356 87.427 987 2171 1 chr6A.!!$F1 1184
6 TraesCS2B01G494300 chr6B 716975609 716976748 1139 True 1286.000 1286 87.066 1029 2174 1 chr6B.!!$R2 1145
7 TraesCS2B01G494300 chr1D 432955660 432956219 559 True 261.000 261 76.539 299 866 1 chr1D.!!$R1 567

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
90 175 0.179161 GCTGCACGACTCGACAGTAT 60.179 55.0 19.95 0.0 37.1 2.12 F
783 903 0.723981 GAGGCTCACAGTCGCAATTC 59.276 55.0 10.25 0.0 0.0 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1124 1303 0.108233 GAGACTCTGAGCTTGCTGGG 60.108 60.0 4.19 0.00 0.00 4.45 R
2585 2783 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.0 14.79 0.04 33.41 4.30 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
32 33 0.603065 GCAATGTTGAACACCCCCTC 59.397 55.000 0.00 0.00 0.00 4.30
90 175 0.179161 GCTGCACGACTCGACAGTAT 60.179 55.000 19.95 0.00 37.10 2.12
91 176 1.539341 CTGCACGACTCGACAGTATG 58.461 55.000 5.20 0.00 46.00 2.39
122 207 5.011635 GTGGAATTTACAAGGGAATTGGTGT 59.988 40.000 0.00 0.00 43.68 4.16
132 217 4.298626 AGGGAATTGGTGTAGAGCATAGA 58.701 43.478 0.00 0.00 0.00 1.98
210 295 4.336153 TGCATTCTGGTGTGCATAATACAG 59.664 41.667 0.00 0.00 45.60 2.74
256 341 8.825667 AAATTAACCACACACAATTTATCACC 57.174 30.769 0.00 0.00 30.80 4.02
259 344 4.331968 ACCACACACAATTTATCACCGAT 58.668 39.130 0.00 0.00 0.00 4.18
269 354 3.643159 TTATCACCGATCGACAGATGG 57.357 47.619 18.66 0.00 37.19 3.51
315 401 2.010582 TTGTGAACCAAACTGCCGCC 62.011 55.000 0.00 0.00 0.00 6.13
352 443 1.468985 TGACAGAGCAGAGTAGAGCC 58.531 55.000 0.00 0.00 0.00 4.70
511 626 3.004734 CCAGACGCCATTGTTTCTTTCTT 59.995 43.478 0.00 0.00 0.00 2.52
512 627 4.222114 CAGACGCCATTGTTTCTTTCTTC 58.778 43.478 0.00 0.00 0.00 2.87
513 628 4.023707 CAGACGCCATTGTTTCTTTCTTCT 60.024 41.667 0.00 0.00 0.00 2.85
514 629 4.214332 AGACGCCATTGTTTCTTTCTTCTC 59.786 41.667 0.00 0.00 0.00 2.87
515 630 3.882888 ACGCCATTGTTTCTTTCTTCTCA 59.117 39.130 0.00 0.00 0.00 3.27
516 631 4.338118 ACGCCATTGTTTCTTTCTTCTCAA 59.662 37.500 0.00 0.00 0.00 3.02
517 632 4.913924 CGCCATTGTTTCTTTCTTCTCAAG 59.086 41.667 0.00 0.00 0.00 3.02
519 634 5.508657 GCCATTGTTTCTTTCTTCTCAAGCT 60.509 40.000 0.00 0.00 0.00 3.74
520 635 6.294176 GCCATTGTTTCTTTCTTCTCAAGCTA 60.294 38.462 0.00 0.00 0.00 3.32
536 651 3.130734 AGCTAGAAAGGGGGTGATGTA 57.869 47.619 0.00 0.00 0.00 2.29
541 656 5.013183 GCTAGAAAGGGGGTGATGTATGTAT 59.987 44.000 0.00 0.00 0.00 2.29
542 657 5.310409 AGAAAGGGGGTGATGTATGTATG 57.690 43.478 0.00 0.00 0.00 2.39
543 658 4.975147 AGAAAGGGGGTGATGTATGTATGA 59.025 41.667 0.00 0.00 0.00 2.15
723 838 3.310227 CAGAGCATGCTCAGATCAGAAAC 59.690 47.826 40.91 16.97 44.99 2.78
732 847 4.491602 GCTCAGATCAGAAACAAATCGTCG 60.492 45.833 0.00 0.00 0.00 5.12
780 900 2.159819 GAGGAGGCTCACAGTCGCAA 62.160 60.000 17.69 0.00 0.00 4.85
783 903 0.723981 GAGGCTCACAGTCGCAATTC 59.276 55.000 10.25 0.00 0.00 2.17
872 1001 3.735029 GACGACGAGCAGGACGGT 61.735 66.667 0.00 0.00 34.93 4.83
890 1019 3.417224 CATCGCCATCGCCATCGG 61.417 66.667 0.00 0.00 36.13 4.18
914 1043 2.554032 GTTGGTGGTGGAGATTGTTCTG 59.446 50.000 0.00 0.00 30.30 3.02
958 1087 1.067283 CGCCTGTCAGTCACTCTTCAT 60.067 52.381 0.00 0.00 0.00 2.57
963 1092 6.341316 GCCTGTCAGTCACTCTTCATAATAA 58.659 40.000 0.00 0.00 0.00 1.40
1121 1300 2.433145 CGCTGCTCTCCTTTCGCA 60.433 61.111 0.00 0.00 0.00 5.10
1124 1303 1.435408 GCTGCTCTCCTTTCGCATCC 61.435 60.000 0.00 0.00 32.62 3.51
1126 1305 1.524849 GCTCTCCTTTCGCATCCCC 60.525 63.158 0.00 0.00 0.00 4.81
1297 1485 4.295119 GACACCGTGACCGCCACT 62.295 66.667 5.28 0.00 43.53 4.00
1353 1541 3.728373 GGGCATCACCTCCCCGTT 61.728 66.667 0.00 0.00 39.10 4.44
1558 1746 4.415332 GTGGACGCGCTCTTCGGA 62.415 66.667 5.73 0.00 38.94 4.55
1736 1924 2.659016 CACTCCGCCTCTGCTTCA 59.341 61.111 0.00 0.00 34.43 3.02
1802 1990 3.170362 CCCTGCCCAAGAAGGTCA 58.830 61.111 0.00 0.00 34.66 4.02
1811 1999 1.841556 AAGAAGGTCACCCTCGGCA 60.842 57.895 0.00 0.00 41.56 5.69
1828 2016 1.154488 CAACCACGTCCGCAATTCG 60.154 57.895 0.00 0.00 38.08 3.34
2044 2232 3.710677 CTGTCATTGAGGGAGAGGAGAAT 59.289 47.826 0.00 0.00 0.00 2.40
2144 2332 0.469892 TGATAGAGATGGCGCCAGGA 60.470 55.000 35.36 17.43 0.00 3.86
2182 2370 6.449830 AGTTTGGAGTAGGAAGGTACATTT 57.550 37.500 0.00 0.00 0.00 2.32
2183 2371 6.238648 AGTTTGGAGTAGGAAGGTACATTTG 58.761 40.000 0.00 0.00 0.00 2.32
2184 2372 5.836024 TTGGAGTAGGAAGGTACATTTGT 57.164 39.130 0.00 0.00 0.00 2.83
2185 2373 5.416271 TGGAGTAGGAAGGTACATTTGTC 57.584 43.478 0.00 0.00 0.00 3.18
2187 2375 5.187186 TGGAGTAGGAAGGTACATTTGTCTC 59.813 44.000 0.00 1.47 0.00 3.36
2188 2376 5.326200 AGTAGGAAGGTACATTTGTCTCG 57.674 43.478 0.00 0.00 0.00 4.04
2190 2378 5.948162 AGTAGGAAGGTACATTTGTCTCGTA 59.052 40.000 0.00 0.00 0.00 3.43
2197 2385 4.267928 GGTACATTTGTCTCGTATGTCTGC 59.732 45.833 0.00 0.00 34.55 4.26
2199 2387 5.324784 ACATTTGTCTCGTATGTCTGCTA 57.675 39.130 0.00 0.00 0.00 3.49
2233 2421 8.668353 GTGTATTACACTGATTGATCATGTTGT 58.332 33.333 17.77 3.40 45.27 3.32
2234 2422 8.882736 TGTATTACACTGATTGATCATGTTGTC 58.117 33.333 4.33 0.00 36.02 3.18
2235 2423 4.934075 ACACTGATTGATCATGTTGTCG 57.066 40.909 0.00 0.00 36.02 4.35
2236 2424 3.125829 ACACTGATTGATCATGTTGTCGC 59.874 43.478 0.00 0.00 36.02 5.19
2237 2425 2.679837 ACTGATTGATCATGTTGTCGCC 59.320 45.455 0.00 0.00 36.02 5.54
2322 2511 6.141685 CGGTTGCAGTTCTAATTGTTTGTTAC 59.858 38.462 0.00 0.00 0.00 2.50
2395 2584 2.526888 TATCAGTCCCTGACCGAGTT 57.473 50.000 0.00 0.00 43.63 3.01
2433 2622 0.963962 CAGCCTCAAAGCAACATGGT 59.036 50.000 0.00 0.00 34.23 3.55
2449 2638 5.393068 ACATGGTGATGTATCATTCCCTT 57.607 39.130 0.00 0.00 41.27 3.95
2460 2649 9.520204 GATGTATCATTCCCTTTGTTAACATTG 57.480 33.333 9.56 5.33 0.00 2.82
2505 2703 9.847224 TTAAACATTTATGAATCTACTCCCTCC 57.153 33.333 0.00 0.00 0.00 4.30
2506 2704 6.102897 ACATTTATGAATCTACTCCCTCCG 57.897 41.667 0.00 0.00 0.00 4.63
2507 2705 5.602978 ACATTTATGAATCTACTCCCTCCGT 59.397 40.000 0.00 0.00 0.00 4.69
2508 2706 6.099845 ACATTTATGAATCTACTCCCTCCGTT 59.900 38.462 0.00 0.00 0.00 4.44
2509 2707 5.786264 TTATGAATCTACTCCCTCCGTTC 57.214 43.478 0.00 0.00 0.00 3.95
2510 2708 2.022195 TGAATCTACTCCCTCCGTTCG 58.978 52.381 0.00 0.00 0.00 3.95
2511 2709 1.337387 GAATCTACTCCCTCCGTTCGG 59.663 57.143 4.74 4.74 0.00 4.30
2512 2710 0.549950 ATCTACTCCCTCCGTTCGGA 59.450 55.000 13.34 13.34 0.00 4.55
2513 2711 0.329261 TCTACTCCCTCCGTTCGGAA 59.671 55.000 14.79 0.04 33.41 4.30
2514 2712 1.064166 TCTACTCCCTCCGTTCGGAAT 60.064 52.381 14.79 2.09 33.41 3.01
2515 2713 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
2516 2714 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2517 2715 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2518 2716 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2519 2717 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2520 2718 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2521 2719 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2522 2720 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2523 2721 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
2524 2722 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
2525 2723 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
2526 2724 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
2527 2725 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
2528 2726 4.240096 GTTCGGAATTACTTGTCTCGGAA 58.760 43.478 0.00 0.00 0.00 4.30
2529 2727 4.524316 TCGGAATTACTTGTCTCGGAAA 57.476 40.909 0.00 0.00 0.00 3.13
2530 2728 5.080969 TCGGAATTACTTGTCTCGGAAAT 57.919 39.130 0.00 0.00 0.00 2.17
2531 2729 4.868171 TCGGAATTACTTGTCTCGGAAATG 59.132 41.667 0.00 0.00 0.00 2.32
2532 2730 4.034048 CGGAATTACTTGTCTCGGAAATGG 59.966 45.833 0.00 0.00 0.00 3.16
2533 2731 5.183228 GGAATTACTTGTCTCGGAAATGGA 58.817 41.667 0.00 0.00 0.00 3.41
2534 2732 5.823045 GGAATTACTTGTCTCGGAAATGGAT 59.177 40.000 0.00 0.00 0.00 3.41
2535 2733 6.238484 GGAATTACTTGTCTCGGAAATGGATG 60.238 42.308 0.00 0.00 0.00 3.51
2536 2734 3.703001 ACTTGTCTCGGAAATGGATGT 57.297 42.857 0.00 0.00 0.00 3.06
2537 2735 4.819105 ACTTGTCTCGGAAATGGATGTA 57.181 40.909 0.00 0.00 0.00 2.29
2538 2736 5.359194 ACTTGTCTCGGAAATGGATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
2539 2737 5.360591 ACTTGTCTCGGAAATGGATGTATC 58.639 41.667 0.00 0.00 0.00 2.24
2540 2738 5.129485 ACTTGTCTCGGAAATGGATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
2541 2739 6.323996 ACTTGTCTCGGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 0.00 1.98
2542 2740 6.332735 TGTCTCGGAAATGGATGTATCTAG 57.667 41.667 0.00 0.00 0.00 2.43
2543 2741 6.068670 TGTCTCGGAAATGGATGTATCTAGA 58.931 40.000 0.00 0.00 0.00 2.43
2544 2742 6.549736 TGTCTCGGAAATGGATGTATCTAGAA 59.450 38.462 0.00 0.00 0.00 2.10
2545 2743 6.864165 GTCTCGGAAATGGATGTATCTAGAAC 59.136 42.308 0.00 0.00 0.00 3.01
2546 2744 6.778069 TCTCGGAAATGGATGTATCTAGAACT 59.222 38.462 0.00 0.00 0.00 3.01
2547 2745 7.942894 TCTCGGAAATGGATGTATCTAGAACTA 59.057 37.037 0.00 0.00 0.00 2.24
2548 2746 8.473358 TCGGAAATGGATGTATCTAGAACTAA 57.527 34.615 0.00 0.00 0.00 2.24
2549 2747 8.920174 TCGGAAATGGATGTATCTAGAACTAAA 58.080 33.333 0.00 0.00 0.00 1.85
2550 2748 9.542462 CGGAAATGGATGTATCTAGAACTAAAA 57.458 33.333 0.00 0.00 0.00 1.52
2574 2772 8.744008 AATACGTCTAGATACATCCATTTTCG 57.256 34.615 0.00 0.00 0.00 3.46
2575 2773 4.982916 ACGTCTAGATACATCCATTTTCGC 59.017 41.667 0.00 0.00 0.00 4.70
2576 2774 4.088638 CGTCTAGATACATCCATTTTCGCG 59.911 45.833 0.00 0.00 0.00 5.87
2577 2775 5.220381 GTCTAGATACATCCATTTTCGCGA 58.780 41.667 3.71 3.71 0.00 5.87
2578 2776 5.117287 GTCTAGATACATCCATTTTCGCGAC 59.883 44.000 9.15 0.00 0.00 5.19
2579 2777 3.792401 AGATACATCCATTTTCGCGACA 58.208 40.909 9.15 0.00 0.00 4.35
2580 2778 4.188462 AGATACATCCATTTTCGCGACAA 58.812 39.130 9.15 9.93 0.00 3.18
2581 2779 2.900122 ACATCCATTTTCGCGACAAG 57.100 45.000 9.15 2.84 0.00 3.16
2582 2780 2.151202 ACATCCATTTTCGCGACAAGT 58.849 42.857 9.15 0.00 0.00 3.16
2583 2781 3.331150 ACATCCATTTTCGCGACAAGTA 58.669 40.909 9.15 0.00 0.00 2.24
2584 2782 3.749088 ACATCCATTTTCGCGACAAGTAA 59.251 39.130 9.15 0.00 0.00 2.24
2585 2783 4.394920 ACATCCATTTTCGCGACAAGTAAT 59.605 37.500 9.15 0.42 0.00 1.89
2586 2784 5.106317 ACATCCATTTTCGCGACAAGTAATT 60.106 36.000 9.15 0.00 0.00 1.40
2587 2785 4.965062 TCCATTTTCGCGACAAGTAATTC 58.035 39.130 9.15 0.00 0.00 2.17
2588 2786 4.095610 CCATTTTCGCGACAAGTAATTCC 58.904 43.478 9.15 0.00 0.00 3.01
2589 2787 3.443054 TTTTCGCGACAAGTAATTCCG 57.557 42.857 9.15 0.00 0.00 4.30
2590 2788 2.350899 TTCGCGACAAGTAATTCCGA 57.649 45.000 9.15 0.00 0.00 4.55
2591 2789 2.350899 TCGCGACAAGTAATTCCGAA 57.649 45.000 3.71 0.00 0.00 4.30
2592 2790 1.987770 TCGCGACAAGTAATTCCGAAC 59.012 47.619 3.71 0.00 0.00 3.95
2593 2791 1.266211 CGCGACAAGTAATTCCGAACG 60.266 52.381 0.00 0.00 0.00 3.95
2594 2792 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
2595 2793 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
2596 2794 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
2597 2795 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
2598 2796 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
2599 2797 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
2600 2798 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
2601 2799 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
2602 2800 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
2603 2801 1.109609 ATTCCGAACGGAGGGAGTAC 58.890 55.000 15.34 0.00 46.06 2.73
2604 2802 0.038744 TTCCGAACGGAGGGAGTACT 59.961 55.000 15.34 0.00 46.06 2.73
2641 2839 0.963962 TGGTCGTCCTTGTGTCTACC 59.036 55.000 0.00 0.00 34.23 3.18
2642 2840 0.963962 GGTCGTCCTTGTGTCTACCA 59.036 55.000 0.00 0.00 0.00 3.25
2645 2843 3.428589 GGTCGTCCTTGTGTCTACCATAC 60.429 52.174 0.00 0.00 0.00 2.39
2648 2902 3.132289 CGTCCTTGTGTCTACCATACCAT 59.868 47.826 0.00 0.00 0.00 3.55
2661 2915 4.865905 ACCATACCATTACAATGAGGCAA 58.134 39.130 3.48 0.00 38.70 4.52
2671 2925 7.255590 CCATTACAATGAGGCAATAACTAAGGG 60.256 40.741 3.48 0.00 38.70 3.95
2672 2926 3.954258 ACAATGAGGCAATAACTAAGGGC 59.046 43.478 0.00 0.00 0.00 5.19
2695 2949 5.593010 CTGCACTAGTTAGGTGATAGGTTC 58.407 45.833 0.00 0.00 36.89 3.62
2719 2973 1.444933 TGAACCACAAGGATCAGGGT 58.555 50.000 0.00 0.00 41.27 4.34
2732 2986 3.454812 GGATCAGGGTGTACTGGTAATGT 59.545 47.826 0.00 0.00 38.98 2.71
2772 3032 1.303888 CTGTGCTCAACCCAGGCAT 60.304 57.895 0.00 0.00 38.27 4.40
2775 3035 1.604308 TGCTCAACCCAGGCATGTG 60.604 57.895 0.00 0.00 0.00 3.21
2780 3040 0.612732 CAACCCAGGCATGTGGATGT 60.613 55.000 12.01 0.00 40.44 3.06
2790 3050 3.624861 GGCATGTGGATGTAGTGAAAGAG 59.375 47.826 0.00 0.00 31.50 2.85
2791 3051 4.256920 GCATGTGGATGTAGTGAAAGAGT 58.743 43.478 0.00 0.00 31.50 3.24
2792 3052 4.093998 GCATGTGGATGTAGTGAAAGAGTG 59.906 45.833 0.00 0.00 31.50 3.51
2793 3053 4.955811 TGTGGATGTAGTGAAAGAGTGT 57.044 40.909 0.00 0.00 0.00 3.55
2794 3054 6.398095 CATGTGGATGTAGTGAAAGAGTGTA 58.602 40.000 0.00 0.00 0.00 2.90
2795 3055 6.413783 TGTGGATGTAGTGAAAGAGTGTAA 57.586 37.500 0.00 0.00 0.00 2.41
2796 3056 6.822442 TGTGGATGTAGTGAAAGAGTGTAAA 58.178 36.000 0.00 0.00 0.00 2.01
2797 3057 7.276658 TGTGGATGTAGTGAAAGAGTGTAAAA 58.723 34.615 0.00 0.00 0.00 1.52
2798 3058 7.225931 TGTGGATGTAGTGAAAGAGTGTAAAAC 59.774 37.037 0.00 0.00 0.00 2.43
2799 3059 7.441458 GTGGATGTAGTGAAAGAGTGTAAAACT 59.559 37.037 0.00 0.00 43.85 2.66
2800 3060 7.441157 TGGATGTAGTGAAAGAGTGTAAAACTG 59.559 37.037 0.00 0.00 40.07 3.16
2801 3061 7.441458 GGATGTAGTGAAAGAGTGTAAAACTGT 59.559 37.037 0.00 0.00 40.07 3.55
2802 3062 7.766219 TGTAGTGAAAGAGTGTAAAACTGTC 57.234 36.000 0.00 0.00 40.07 3.51
2803 3063 6.759827 TGTAGTGAAAGAGTGTAAAACTGTCC 59.240 38.462 0.00 0.00 40.07 4.02
2804 3064 5.990668 AGTGAAAGAGTGTAAAACTGTCCT 58.009 37.500 0.00 0.00 40.07 3.85
2805 3065 5.817816 AGTGAAAGAGTGTAAAACTGTCCTG 59.182 40.000 0.00 0.00 40.07 3.86
2806 3066 5.585047 GTGAAAGAGTGTAAAACTGTCCTGT 59.415 40.000 0.00 0.00 40.07 4.00
2807 3067 6.093633 GTGAAAGAGTGTAAAACTGTCCTGTT 59.906 38.462 0.00 0.00 40.07 3.16
2865 3150 6.322456 TGTTTTGTATTCACTGTGGAATTGGA 59.678 34.615 8.11 0.00 38.41 3.53
2907 3192 9.853921 GTTGCAAAAAGAAAAATATGTTGAGAG 57.146 29.630 0.00 0.00 0.00 3.20
2908 3193 8.075593 TGCAAAAAGAAAAATATGTTGAGAGC 57.924 30.769 0.00 0.00 0.00 4.09
2909 3194 7.927629 TGCAAAAAGAAAAATATGTTGAGAGCT 59.072 29.630 0.00 0.00 0.00 4.09
3006 3293 3.194329 CAGATACTGACAGTGGAAGCAGA 59.806 47.826 18.58 0.00 32.44 4.26
3008 3295 0.034616 ACTGACAGTGGAAGCAGAGC 59.965 55.000 7.47 0.00 32.86 4.09
3151 3438 3.683847 GCAGGAGGCTACAAGATCACAAT 60.684 47.826 0.00 0.00 40.25 2.71
3168 3455 4.039004 TCACAATTGGTTGGAGGTGATTTG 59.961 41.667 10.83 0.00 39.70 2.32
3182 3469 3.587061 GGTGATTTGGGGGAGGAAAATTT 59.413 43.478 0.00 0.00 0.00 1.82
3242 3529 1.002430 TGGAGGTGTGTTGAGAGATGC 59.998 52.381 0.00 0.00 0.00 3.91
3254 3541 2.025605 TGAGAGATGCCAGCAAGGAAAT 60.026 45.455 0.00 0.00 41.22 2.17
3288 3575 3.207549 TGGATGAGAATAGGAGGAGGACA 59.792 47.826 0.00 0.00 0.00 4.02
3318 3605 6.293298 GGAATGTGACAGATCAGCATGTAATC 60.293 42.308 0.00 0.00 34.75 1.75
3351 3638 3.075148 GGACAGGGCTAAAGTGAAGAAC 58.925 50.000 0.00 0.00 0.00 3.01
3376 3664 3.503748 GGAGTTTCCAATTGGTGAGTCTG 59.496 47.826 23.76 0.00 36.28 3.51
3384 3672 2.550830 TTGGTGAGTCTGCTTCCTTC 57.449 50.000 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.333581 GTTGGCGGTTTGGGTTCG 59.666 61.111 0.00 0.00 0.00 3.95
90 175 6.307776 TCCCTTGTAAATTCCACATGTTACA 58.692 36.000 0.00 0.00 35.28 2.41
91 176 6.827586 TCCCTTGTAAATTCCACATGTTAC 57.172 37.500 0.00 0.00 0.00 2.50
122 207 7.690256 TCCTGTCAGTATACATCTATGCTCTA 58.310 38.462 5.50 0.00 0.00 2.43
132 217 3.451178 AGCCGTTTCCTGTCAGTATACAT 59.549 43.478 5.50 0.00 0.00 2.29
205 290 5.350504 AGATAAACTGCACAGCTCTGTAT 57.649 39.130 1.79 0.00 42.83 2.29
210 295 7.778470 ATTTACTAGATAAACTGCACAGCTC 57.222 36.000 0.00 0.00 35.57 4.09
256 341 0.527600 TTTCGCCCATCTGTCGATCG 60.528 55.000 9.36 9.36 31.96 3.69
259 344 0.034198 TGTTTTCGCCCATCTGTCGA 59.966 50.000 0.00 0.00 0.00 4.20
269 354 4.437390 CCTGTATGAACTGATGTTTTCGCC 60.437 45.833 0.00 0.00 36.39 5.54
352 443 3.909776 TCAGACTTTCAATTGCTGCTG 57.090 42.857 0.00 4.24 0.00 4.41
399 507 2.880890 AGGTGCTGACAATTGACAAGAC 59.119 45.455 13.59 10.78 0.00 3.01
404 512 1.197721 CGGAAGGTGCTGACAATTGAC 59.802 52.381 13.59 6.72 0.00 3.18
511 626 1.909302 CACCCCCTTTCTAGCTTGAGA 59.091 52.381 0.00 0.00 0.00 3.27
512 627 1.909302 TCACCCCCTTTCTAGCTTGAG 59.091 52.381 0.00 0.00 0.00 3.02
513 628 2.038863 TCACCCCCTTTCTAGCTTGA 57.961 50.000 0.00 0.00 0.00 3.02
514 629 2.025887 ACATCACCCCCTTTCTAGCTTG 60.026 50.000 0.00 0.00 0.00 4.01
515 630 2.279173 ACATCACCCCCTTTCTAGCTT 58.721 47.619 0.00 0.00 0.00 3.74
516 631 1.972588 ACATCACCCCCTTTCTAGCT 58.027 50.000 0.00 0.00 0.00 3.32
517 632 3.136626 ACATACATCACCCCCTTTCTAGC 59.863 47.826 0.00 0.00 0.00 3.42
519 634 6.147473 TCATACATACATCACCCCCTTTCTA 58.853 40.000 0.00 0.00 0.00 2.10
520 635 4.975147 TCATACATACATCACCCCCTTTCT 59.025 41.667 0.00 0.00 0.00 2.52
536 651 7.013655 GGCAAGAAAGGTACATCATTCATACAT 59.986 37.037 0.00 0.00 0.00 2.29
541 656 3.689161 CGGCAAGAAAGGTACATCATTCA 59.311 43.478 0.00 0.00 0.00 2.57
542 657 3.938963 TCGGCAAGAAAGGTACATCATTC 59.061 43.478 0.00 0.00 0.00 2.67
543 658 3.689649 GTCGGCAAGAAAGGTACATCATT 59.310 43.478 0.00 0.00 0.00 2.57
732 847 2.200067 CTGATCCAGTCAATCGAGTGC 58.800 52.381 8.24 3.56 40.69 4.40
872 1001 2.356194 CGATGGCGATGGCGATGA 60.356 61.111 1.13 0.00 37.76 2.92
890 1019 1.303317 AATCTCCACCACCAACCGC 60.303 57.895 0.00 0.00 0.00 5.68
1121 1300 0.913451 ACTCTGAGCTTGCTGGGGAT 60.913 55.000 4.19 0.00 0.00 3.85
1124 1303 0.108233 GAGACTCTGAGCTTGCTGGG 60.108 60.000 4.19 0.00 0.00 4.45
1126 1305 0.458197 CGGAGACTCTGAGCTTGCTG 60.458 60.000 5.24 0.00 0.00 4.41
1210 1398 2.283821 GGCCCCAGATTTGCCACA 60.284 61.111 0.00 0.00 44.70 4.17
1658 1846 4.421479 CCGCACGAGGACGAAGCT 62.421 66.667 0.00 0.00 42.66 3.74
1736 1924 1.251527 AACTCAGGCGTGACGAGGAT 61.252 55.000 10.10 0.00 0.00 3.24
1802 1990 4.309950 GACGTGGTTGCCGAGGGT 62.310 66.667 0.00 0.00 0.00 4.34
1811 1999 1.289109 CTCGAATTGCGGACGTGGTT 61.289 55.000 0.00 0.00 41.33 3.67
2144 2332 5.779241 TCCAAACTTGAGGTGGAGATAAT 57.221 39.130 2.56 0.00 36.51 1.28
2182 2370 3.694566 ACACATAGCAGACATACGAGACA 59.305 43.478 0.00 0.00 0.00 3.41
2183 2371 4.294416 ACACATAGCAGACATACGAGAC 57.706 45.455 0.00 0.00 0.00 3.36
2184 2372 5.531287 ACATACACATAGCAGACATACGAGA 59.469 40.000 0.00 0.00 0.00 4.04
2185 2373 5.626955 CACATACACATAGCAGACATACGAG 59.373 44.000 0.00 0.00 0.00 4.18
2187 2375 5.281727 ACACATACACATAGCAGACATACG 58.718 41.667 0.00 0.00 0.00 3.06
2188 2376 8.818141 AATACACATACACATAGCAGACATAC 57.182 34.615 0.00 0.00 0.00 2.39
2190 2378 8.421002 TGTAATACACATACACATAGCAGACAT 58.579 33.333 0.00 0.00 30.04 3.06
2225 2413 1.374125 CCGACAGGCGACAACATGA 60.374 57.895 0.00 0.00 44.57 3.07
2231 2419 0.948623 CAAATCACCGACAGGCGACA 60.949 55.000 0.00 0.00 44.57 4.35
2232 2420 1.635663 CCAAATCACCGACAGGCGAC 61.636 60.000 0.00 0.00 44.57 5.19
2233 2421 1.375396 CCAAATCACCGACAGGCGA 60.375 57.895 0.00 0.00 44.57 5.54
2234 2422 1.671054 ACCAAATCACCGACAGGCG 60.671 57.895 0.00 0.00 42.76 5.52
2235 2423 1.875963 CACCAAATCACCGACAGGC 59.124 57.895 0.00 0.00 42.76 4.85
2236 2424 1.875963 GCACCAAATCACCGACAGG 59.124 57.895 0.00 0.00 45.13 4.00
2237 2425 1.497278 CGCACCAAATCACCGACAG 59.503 57.895 0.00 0.00 0.00 3.51
2322 2511 6.615264 ATCGATCCACTCATTCAGAATTTG 57.385 37.500 0.00 0.00 0.00 2.32
2381 2570 1.668151 GTGCAACTCGGTCAGGGAC 60.668 63.158 0.00 0.00 0.00 4.46
2395 2584 0.455410 GCTGTCCAACAAGTTGTGCA 59.545 50.000 9.79 6.04 38.85 4.57
2433 2622 8.821686 ATGTTAACAAAGGGAATGATACATCA 57.178 30.769 13.23 0.00 41.70 3.07
2449 2638 7.776107 TCCATGAAACAGAACAATGTTAACAA 58.224 30.769 13.23 0.00 42.49 2.83
2500 2698 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
2501 2699 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
2502 2700 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
2503 2701 3.671433 CGAGACAAGTAATTCCGAACGGA 60.671 47.826 12.04 12.04 43.52 4.69
2504 2702 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
2505 2703 2.597305 CCGAGACAAGTAATTCCGAACG 59.403 50.000 0.00 0.00 0.00 3.95
2506 2704 3.841643 TCCGAGACAAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
2507 2705 4.524316 TTCCGAGACAAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
2508 2706 4.524316 TTTCCGAGACAAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
2509 2707 4.034048 CCATTTCCGAGACAAGTAATTCCG 59.966 45.833 0.00 0.00 0.00 4.30
2510 2708 5.183228 TCCATTTCCGAGACAAGTAATTCC 58.817 41.667 0.00 0.00 0.00 3.01
2511 2709 6.316390 ACATCCATTTCCGAGACAAGTAATTC 59.684 38.462 0.00 0.00 0.00 2.17
2512 2710 6.180472 ACATCCATTTCCGAGACAAGTAATT 58.820 36.000 0.00 0.00 0.00 1.40
2513 2711 5.745227 ACATCCATTTCCGAGACAAGTAAT 58.255 37.500 0.00 0.00 0.00 1.89
2514 2712 5.160607 ACATCCATTTCCGAGACAAGTAA 57.839 39.130 0.00 0.00 0.00 2.24
2515 2713 4.819105 ACATCCATTTCCGAGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
2516 2714 3.703001 ACATCCATTTCCGAGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
2517 2715 5.605534 AGATACATCCATTTCCGAGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
2518 2716 5.614324 AGATACATCCATTTCCGAGACAA 57.386 39.130 0.00 0.00 0.00 3.18
2519 2717 6.068670 TCTAGATACATCCATTTCCGAGACA 58.931 40.000 0.00 0.00 0.00 3.41
2520 2718 6.576662 TCTAGATACATCCATTTCCGAGAC 57.423 41.667 0.00 0.00 0.00 3.36
2521 2719 6.778069 AGTTCTAGATACATCCATTTCCGAGA 59.222 38.462 0.00 0.00 0.00 4.04
2522 2720 6.987386 AGTTCTAGATACATCCATTTCCGAG 58.013 40.000 0.00 0.00 0.00 4.63
2523 2721 6.978674 AGTTCTAGATACATCCATTTCCGA 57.021 37.500 0.00 0.00 0.00 4.55
2524 2722 9.542462 TTTTAGTTCTAGATACATCCATTTCCG 57.458 33.333 0.00 0.00 0.00 4.30
2548 2746 9.193133 CGAAAATGGATGTATCTAGACGTATTT 57.807 33.333 0.00 0.00 0.00 1.40
2549 2747 7.328737 GCGAAAATGGATGTATCTAGACGTATT 59.671 37.037 0.00 0.00 0.00 1.89
2550 2748 6.807230 GCGAAAATGGATGTATCTAGACGTAT 59.193 38.462 0.00 0.00 0.00 3.06
2551 2749 6.147581 GCGAAAATGGATGTATCTAGACGTA 58.852 40.000 0.00 0.00 0.00 3.57
2552 2750 4.982916 GCGAAAATGGATGTATCTAGACGT 59.017 41.667 0.00 0.00 0.00 4.34
2553 2751 4.088638 CGCGAAAATGGATGTATCTAGACG 59.911 45.833 0.00 0.00 0.00 4.18
2554 2752 5.117287 GTCGCGAAAATGGATGTATCTAGAC 59.883 44.000 12.06 0.00 0.00 2.59
2555 2753 5.220381 GTCGCGAAAATGGATGTATCTAGA 58.780 41.667 12.06 0.00 0.00 2.43
2556 2754 4.982295 TGTCGCGAAAATGGATGTATCTAG 59.018 41.667 12.06 0.00 0.00 2.43
2557 2755 4.939271 TGTCGCGAAAATGGATGTATCTA 58.061 39.130 12.06 0.00 0.00 1.98
2558 2756 3.792401 TGTCGCGAAAATGGATGTATCT 58.208 40.909 12.06 0.00 0.00 1.98
2559 2757 4.034048 ACTTGTCGCGAAAATGGATGTATC 59.966 41.667 13.05 0.00 0.00 2.24
2560 2758 3.938963 ACTTGTCGCGAAAATGGATGTAT 59.061 39.130 13.05 0.00 0.00 2.29
2561 2759 3.331150 ACTTGTCGCGAAAATGGATGTA 58.669 40.909 13.05 0.00 0.00 2.29
2562 2760 2.151202 ACTTGTCGCGAAAATGGATGT 58.849 42.857 13.05 3.46 0.00 3.06
2563 2761 2.900122 ACTTGTCGCGAAAATGGATG 57.100 45.000 13.05 2.76 0.00 3.51
2564 2762 5.448632 GGAATTACTTGTCGCGAAAATGGAT 60.449 40.000 13.05 3.91 0.00 3.41
2565 2763 4.142773 GGAATTACTTGTCGCGAAAATGGA 60.143 41.667 13.05 0.56 0.00 3.41
2566 2764 4.095610 GGAATTACTTGTCGCGAAAATGG 58.904 43.478 13.05 4.35 0.00 3.16
2567 2765 3.778718 CGGAATTACTTGTCGCGAAAATG 59.221 43.478 13.05 9.32 0.00 2.32
2568 2766 3.680937 TCGGAATTACTTGTCGCGAAAAT 59.319 39.130 13.05 5.74 0.00 1.82
2569 2767 3.058450 TCGGAATTACTTGTCGCGAAAA 58.942 40.909 12.06 12.01 0.00 2.29
2570 2768 2.674954 TCGGAATTACTTGTCGCGAAA 58.325 42.857 12.06 0.54 0.00 3.46
2571 2769 2.350899 TCGGAATTACTTGTCGCGAA 57.649 45.000 12.06 0.00 0.00 4.70
2572 2770 1.987770 GTTCGGAATTACTTGTCGCGA 59.012 47.619 3.71 3.71 0.00 5.87
2573 2771 1.266211 CGTTCGGAATTACTTGTCGCG 60.266 52.381 0.00 0.00 0.00 5.87
2574 2772 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
2575 2773 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
2576 2774 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2577 2775 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2578 2776 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2579 2777 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2580 2778 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2581 2779 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2582 2780 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2583 2781 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
2584 2782 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
2585 2783 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
2586 2784 0.911769 TAGTACTCCCTCCGTTCGGA 59.088 55.000 13.34 13.34 0.00 4.55
2587 2785 1.755179 TTAGTACTCCCTCCGTTCGG 58.245 55.000 0.00 4.74 0.00 4.30
2588 2786 2.159324 GGTTTAGTACTCCCTCCGTTCG 60.159 54.545 0.00 0.00 0.00 3.95
2589 2787 2.167281 GGGTTTAGTACTCCCTCCGTTC 59.833 54.545 10.30 0.00 38.29 3.95
2590 2788 2.182827 GGGTTTAGTACTCCCTCCGTT 58.817 52.381 10.30 0.00 38.29 4.44
2591 2789 1.857965 GGGTTTAGTACTCCCTCCGT 58.142 55.000 10.30 0.00 38.29 4.69
2592 2790 0.743097 CGGGTTTAGTACTCCCTCCG 59.257 60.000 14.52 12.89 39.10 4.63
2593 2791 1.479730 CACGGGTTTAGTACTCCCTCC 59.520 57.143 14.52 7.04 39.10 4.30
2594 2792 1.134877 GCACGGGTTTAGTACTCCCTC 60.135 57.143 14.52 2.59 39.10 4.30
2595 2793 0.900421 GCACGGGTTTAGTACTCCCT 59.100 55.000 14.52 1.70 39.10 4.20
2596 2794 0.609662 TGCACGGGTTTAGTACTCCC 59.390 55.000 0.00 2.92 37.98 4.30
2597 2795 2.685850 ATGCACGGGTTTAGTACTCC 57.314 50.000 0.00 0.00 0.00 3.85
2598 2796 5.366829 AAAAATGCACGGGTTTAGTACTC 57.633 39.130 0.00 0.00 0.00 2.59
2623 2821 0.963962 TGGTAGACACAAGGACGACC 59.036 55.000 0.00 0.00 0.00 4.79
2641 2839 8.169977 AGTTATTGCCTCATTGTAATGGTATG 57.830 34.615 4.89 0.00 37.03 2.39
2642 2840 9.860650 TTAGTTATTGCCTCATTGTAATGGTAT 57.139 29.630 4.89 0.00 37.03 2.73
2645 2843 7.255590 CCCTTAGTTATTGCCTCATTGTAATGG 60.256 40.741 4.89 0.00 37.03 3.16
2648 2902 5.592688 GCCCTTAGTTATTGCCTCATTGTAA 59.407 40.000 0.00 0.00 0.00 2.41
2661 2915 5.070580 CCTAACTAGTGCAGCCCTTAGTTAT 59.929 44.000 15.41 1.64 32.01 1.89
2671 2925 3.385111 ACCTATCACCTAACTAGTGCAGC 59.615 47.826 0.00 0.00 35.14 5.25
2672 2926 5.361285 AGAACCTATCACCTAACTAGTGCAG 59.639 44.000 0.00 0.00 35.14 4.41
2695 2949 4.194640 CCTGATCCTTGTGGTTCATACAG 58.805 47.826 0.00 0.00 40.22 2.74
2711 2965 4.442706 CACATTACCAGTACACCCTGATC 58.557 47.826 0.00 0.00 34.23 2.92
2719 2973 3.868369 GCCTTCTGCACATTACCAGTACA 60.868 47.826 0.00 0.00 40.77 2.90
2732 2986 1.888512 GAAAACATCCAGCCTTCTGCA 59.111 47.619 0.00 0.00 44.83 4.41
2772 3032 4.955811 ACACTCTTTCACTACATCCACA 57.044 40.909 0.00 0.00 0.00 4.17
2775 3035 7.441458 ACAGTTTTACACTCTTTCACTACATCC 59.559 37.037 0.00 0.00 30.92 3.51
2780 3040 6.984474 CAGGACAGTTTTACACTCTTTCACTA 59.016 38.462 0.00 0.00 30.92 2.74
2790 3050 8.185505 TGAATACAAAACAGGACAGTTTTACAC 58.814 33.333 5.45 0.00 46.69 2.90
2791 3051 8.185505 GTGAATACAAAACAGGACAGTTTTACA 58.814 33.333 5.45 0.00 46.69 2.41
2792 3052 8.403236 AGTGAATACAAAACAGGACAGTTTTAC 58.597 33.333 5.45 1.00 46.69 2.01
2793 3053 8.402472 CAGTGAATACAAAACAGGACAGTTTTA 58.598 33.333 5.45 0.00 46.69 1.52
2795 3055 6.377146 ACAGTGAATACAAAACAGGACAGTTT 59.623 34.615 0.00 0.00 43.13 2.66
2796 3056 5.885912 ACAGTGAATACAAAACAGGACAGTT 59.114 36.000 0.00 0.00 0.00 3.16
2797 3057 5.296780 CACAGTGAATACAAAACAGGACAGT 59.703 40.000 0.00 0.00 0.00 3.55
2798 3058 5.277974 CCACAGTGAATACAAAACAGGACAG 60.278 44.000 0.62 0.00 0.00 3.51
2799 3059 4.578516 CCACAGTGAATACAAAACAGGACA 59.421 41.667 0.62 0.00 0.00 4.02
2800 3060 4.819630 TCCACAGTGAATACAAAACAGGAC 59.180 41.667 0.62 0.00 0.00 3.85
2801 3061 5.042463 TCCACAGTGAATACAAAACAGGA 57.958 39.130 0.62 0.00 0.00 3.86
2802 3062 5.530915 TCTTCCACAGTGAATACAAAACAGG 59.469 40.000 0.62 0.00 0.00 4.00
2803 3063 6.618287 TCTTCCACAGTGAATACAAAACAG 57.382 37.500 0.62 0.00 0.00 3.16
2804 3064 7.397892 TTTCTTCCACAGTGAATACAAAACA 57.602 32.000 0.62 0.00 0.00 2.83
2805 3065 6.918022 CCTTTCTTCCACAGTGAATACAAAAC 59.082 38.462 0.62 0.00 0.00 2.43
2806 3066 6.831353 TCCTTTCTTCCACAGTGAATACAAAA 59.169 34.615 0.62 0.00 0.00 2.44
2807 3067 6.361433 TCCTTTCTTCCACAGTGAATACAAA 58.639 36.000 0.62 0.00 0.00 2.83
2890 3175 5.125097 CCTGCAGCTCTCAACATATTTTTCT 59.875 40.000 8.66 0.00 0.00 2.52
2904 3189 0.901124 CTCCAGTTACCTGCAGCTCT 59.099 55.000 8.66 0.20 37.38 4.09
2907 3192 0.737715 CGACTCCAGTTACCTGCAGC 60.738 60.000 8.66 0.00 37.38 5.25
2908 3193 0.888619 TCGACTCCAGTTACCTGCAG 59.111 55.000 6.78 6.78 37.38 4.41
2909 3194 0.888619 CTCGACTCCAGTTACCTGCA 59.111 55.000 0.00 0.00 37.38 4.41
2956 3243 1.820519 CACACCATCCAACATTCTGGG 59.179 52.381 0.00 0.00 37.06 4.45
3006 3293 3.643792 CCTGGTTATTAGCACTAGAGGCT 59.356 47.826 15.82 15.82 45.18 4.58
3008 3295 3.325135 CCCCTGGTTATTAGCACTAGAGG 59.675 52.174 0.00 0.00 0.00 3.69
3140 3427 3.828451 ACCTCCAACCAATTGTGATCTTG 59.172 43.478 4.43 0.00 33.60 3.02
3142 3429 3.074390 TCACCTCCAACCAATTGTGATCT 59.926 43.478 4.43 0.00 33.60 2.75
3151 3438 1.482177 CCCCAAATCACCTCCAACCAA 60.482 52.381 0.00 0.00 0.00 3.67
3168 3455 6.550108 GGTCTCTATTTAAATTTTCCTCCCCC 59.450 42.308 5.91 0.00 0.00 5.40
3182 3469 6.439375 TGCTTGTAAGGTCTGGTCTCTATTTA 59.561 38.462 0.00 0.00 0.00 1.40
3242 3529 7.121759 CCACTATATTATCCATTTCCTTGCTGG 59.878 40.741 0.00 0.00 37.10 4.85
3288 3575 3.607741 CTGATCTGTCACATTCCTGCTT 58.392 45.455 0.00 0.00 0.00 3.91
3318 3605 1.089920 CCCTGTCCATTGCTTTCTCG 58.910 55.000 0.00 0.00 0.00 4.04
3376 3664 5.966742 ACTGTAGGAAATTTGAAGGAAGC 57.033 39.130 0.00 0.00 0.00 3.86
3384 3672 7.384660 TGCAGCATTTAAACTGTAGGAAATTTG 59.615 33.333 0.00 0.00 36.26 2.32


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

AutoCloner maintained by Alex Coulton.