Multiple sequence alignment - TraesCS2A01G367300

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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 TraesCS2A01G367300 chr2A 100.000 3542 0 0 1 3542 611295160 611298701 0.000000e+00 6541
1 TraesCS2A01G367300 chr2A 87.001 1677 183 20 814 2470 733628714 733630375 0.000000e+00 1857
2 TraesCS2A01G367300 chr2A 81.486 1588 225 38 921 2470 611302751 611304307 0.000000e+00 1240
3 TraesCS2A01G367300 chr2A 91.581 879 74 0 2664 3542 733630366 733631244 0.000000e+00 1214
4 TraesCS2A01G367300 chr2A 98.492 199 3 0 2470 2668 657011302 657011104 5.630000e-93 351
5 TraesCS2A01G367300 chr2A 96.244 213 7 1 2467 2679 746266514 746266303 7.280000e-92 348
6 TraesCS2A01G367300 chr2B 94.699 2471 94 20 20 2470 548608530 548610983 0.000000e+00 3803
7 TraesCS2A01G367300 chr2B 87.650 1579 167 14 901 2470 729766506 729768065 0.000000e+00 1810
8 TraesCS2A01G367300 chr2B 81.624 1589 224 34 921 2470 548623910 548625469 0.000000e+00 1254
9 TraesCS2A01G367300 chr2B 91.126 879 78 0 2664 3542 729768056 729768934 0.000000e+00 1192
10 TraesCS2A01G367300 chr2B 87.654 891 95 10 2664 3542 548625460 548626347 0.000000e+00 1022
11 TraesCS2A01G367300 chr2D 95.382 2317 74 6 175 2470 469983205 469985509 0.000000e+00 3655
12 TraesCS2A01G367300 chr2D 87.937 1575 170 11 901 2470 599926336 599927895 0.000000e+00 1838
13 TraesCS2A01G367300 chr2D 97.156 879 25 0 2664 3542 469985500 469986378 0.000000e+00 1485
14 TraesCS2A01G367300 chr2D 92.150 879 69 0 2664 3542 599927886 599928764 0.000000e+00 1242
15 TraesCS2A01G367300 chr2D 97.386 153 4 0 1 153 469983062 469983214 9.750000e-66 261
16 TraesCS2A01G367300 chr1D 82.949 1519 188 43 985 2470 407672559 407671079 0.000000e+00 1304
17 TraesCS2A01G367300 chr1D 82.086 1563 234 20 935 2470 6714673 6713130 0.000000e+00 1293
18 TraesCS2A01G367300 chr1D 81.418 1566 219 40 939 2470 6721655 6720128 0.000000e+00 1214
19 TraesCS2A01G367300 chr1D 81.003 1595 234 34 916 2469 6898370 6899936 0.000000e+00 1203
20 TraesCS2A01G367300 chr1D 87.613 888 98 4 2664 3542 407671088 407670204 0.000000e+00 1020
21 TraesCS2A01G367300 chr1A 81.893 1585 217 39 921 2471 8331876 8333424 0.000000e+00 1273
22 TraesCS2A01G367300 chr1A 81.847 1559 237 25 939 2470 8144561 8143022 0.000000e+00 1269
23 TraesCS2A01G367300 chr1A 82.091 1502 206 36 999 2470 7834683 7836151 0.000000e+00 1225
24 TraesCS2A01G367300 chr1A 80.961 1581 236 32 921 2470 8341973 8343519 0.000000e+00 1192
25 TraesCS2A01G367300 chr1A 98.974 195 2 0 2471 2665 289512223 289512029 2.020000e-92 350
26 TraesCS2A01G367300 chr5D 82.634 1382 172 37 1000 2353 18083677 18085018 0.000000e+00 1160
27 TraesCS2A01G367300 chr5D 87.964 889 91 10 2664 3542 18085231 18086113 0.000000e+00 1035
28 TraesCS2A01G367300 chr5A 89.040 885 87 7 2664 3542 12192757 12191877 0.000000e+00 1088
29 TraesCS2A01G367300 chr5B 87.950 888 92 8 2664 3542 13774674 13773793 0.000000e+00 1033
30 TraesCS2A01G367300 chrUn 97.653 213 5 0 2458 2670 2228576 2228788 2.010000e-97 366
31 TraesCS2A01G367300 chr4A 98.980 196 2 0 2471 2666 333811145 333811340 5.630000e-93 351
32 TraesCS2A01G367300 chr4A 95.714 210 8 1 2464 2672 120409465 120409674 1.580000e-88 337
33 TraesCS2A01G367300 chr7A 98.974 195 2 0 2471 2665 581263352 581263158 2.020000e-92 350
34 TraesCS2A01G367300 chr7A 95.775 213 8 1 2458 2670 585005525 585005736 3.390000e-90 342
35 TraesCS2A01G367300 chr3A 98.485 198 2 1 2471 2668 387716351 387716155 7.280000e-92 348


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 TraesCS2A01G367300 chr2A 611295160 611298701 3541 False 6541.000000 6541 100.000000 1 3542 1 chr2A.!!$F1 3541
1 TraesCS2A01G367300 chr2A 733628714 733631244 2530 False 1535.500000 1857 89.291000 814 3542 2 chr2A.!!$F3 2728
2 TraesCS2A01G367300 chr2A 611302751 611304307 1556 False 1240.000000 1240 81.486000 921 2470 1 chr2A.!!$F2 1549
3 TraesCS2A01G367300 chr2B 548608530 548610983 2453 False 3803.000000 3803 94.699000 20 2470 1 chr2B.!!$F1 2450
4 TraesCS2A01G367300 chr2B 729766506 729768934 2428 False 1501.000000 1810 89.388000 901 3542 2 chr2B.!!$F3 2641
5 TraesCS2A01G367300 chr2B 548623910 548626347 2437 False 1138.000000 1254 84.639000 921 3542 2 chr2B.!!$F2 2621
6 TraesCS2A01G367300 chr2D 469983062 469986378 3316 False 1800.333333 3655 96.641333 1 3542 3 chr2D.!!$F1 3541
7 TraesCS2A01G367300 chr2D 599926336 599928764 2428 False 1540.000000 1838 90.043500 901 3542 2 chr2D.!!$F2 2641
8 TraesCS2A01G367300 chr1D 6713130 6714673 1543 True 1293.000000 1293 82.086000 935 2470 1 chr1D.!!$R1 1535
9 TraesCS2A01G367300 chr1D 6720128 6721655 1527 True 1214.000000 1214 81.418000 939 2470 1 chr1D.!!$R2 1531
10 TraesCS2A01G367300 chr1D 6898370 6899936 1566 False 1203.000000 1203 81.003000 916 2469 1 chr1D.!!$F1 1553
11 TraesCS2A01G367300 chr1D 407670204 407672559 2355 True 1162.000000 1304 85.281000 985 3542 2 chr1D.!!$R3 2557
12 TraesCS2A01G367300 chr1A 8331876 8333424 1548 False 1273.000000 1273 81.893000 921 2471 1 chr1A.!!$F2 1550
13 TraesCS2A01G367300 chr1A 8143022 8144561 1539 True 1269.000000 1269 81.847000 939 2470 1 chr1A.!!$R1 1531
14 TraesCS2A01G367300 chr1A 7834683 7836151 1468 False 1225.000000 1225 82.091000 999 2470 1 chr1A.!!$F1 1471
15 TraesCS2A01G367300 chr1A 8341973 8343519 1546 False 1192.000000 1192 80.961000 921 2470 1 chr1A.!!$F3 1549
16 TraesCS2A01G367300 chr5D 18083677 18086113 2436 False 1097.500000 1160 85.299000 1000 3542 2 chr5D.!!$F1 2542
17 TraesCS2A01G367300 chr5A 12191877 12192757 880 True 1088.000000 1088 89.040000 2664 3542 1 chr5A.!!$R1 878
18 TraesCS2A01G367300 chr5B 13773793 13774674 881 True 1033.000000 1033 87.950000 2664 3542 1 chr5B.!!$R1 878

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
810 845 0.469705 AAGTCCAAGTGGGCATGCAA 60.47 50.0 21.36 3.78 43.78 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2578 2847 0.10741 TCGGCAAGTTAATCGGCCAT 60.107 50.0 2.24 0.0 46.75 4.4 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
138 140 4.179579 GCTGGCGGCGGAACAATC 62.180 66.667 23.83 0.00 0.00 2.67
219 221 1.334869 CATGCGGGCTCCATTTACTTC 59.665 52.381 0.00 0.00 0.00 3.01
309 318 2.700371 TGGTGAGCTTTCTCTTCTGTCA 59.300 45.455 0.00 0.00 40.03 3.58
310 319 3.134623 TGGTGAGCTTTCTCTTCTGTCAA 59.865 43.478 0.00 0.00 40.03 3.18
383 397 6.462500 ACATATCATCCTGTTCTACATCAGC 58.538 40.000 0.00 0.00 0.00 4.26
388 402 2.906389 TCCTGTTCTACATCAGCCTGTT 59.094 45.455 0.00 0.00 0.00 3.16
455 469 8.638565 GTTTATTACTTGCTGCTTTATGTGTTG 58.361 33.333 0.00 0.00 0.00 3.33
473 487 4.702131 GTGTTGCCATTCTTCCTATTCTGT 59.298 41.667 0.00 0.00 0.00 3.41
481 495 9.678260 GCCATTCTTCCTATTCTGTCAATATAT 57.322 33.333 0.00 0.00 0.00 0.86
486 500 9.749340 TCTTCCTATTCTGTCAATATATACCGA 57.251 33.333 0.00 0.00 0.00 4.69
489 503 9.475620 TCCTATTCTGTCAATATATACCGATGT 57.524 33.333 0.00 0.00 0.00 3.06
615 650 7.282585 CACTATGAGGGAAGTTGGATTTCATA 58.717 38.462 0.00 0.00 0.00 2.15
650 685 1.002430 GGTGAATCCAGTGAGCACTCA 59.998 52.381 0.00 0.00 40.20 3.41
744 779 2.060284 CACACGGTTTTCATGGCAATG 58.940 47.619 0.00 0.00 34.88 2.82
810 845 0.469705 AAGTCCAAGTGGGCATGCAA 60.470 50.000 21.36 3.78 43.78 4.08
937 1001 6.546484 TCTTGTTCCTCTTCCATTTCATCTT 58.454 36.000 0.00 0.00 0.00 2.40
1016 1086 2.423446 CATGCCTCCCCTCTACGC 59.577 66.667 0.00 0.00 0.00 4.42
1098 1177 2.058595 AAGCGATACCCTCACGGCT 61.059 57.895 0.00 0.00 33.26 5.52
1196 1284 3.181450 GCAGGCATAATCAGTAAGTCCCT 60.181 47.826 0.00 0.00 0.00 4.20
1198 1286 3.392616 AGGCATAATCAGTAAGTCCCTGG 59.607 47.826 0.00 0.00 0.00 4.45
1280 1395 1.340600 TGTGTGGGTTGCTAATAGGGC 60.341 52.381 0.00 0.00 0.00 5.19
1385 1518 2.484065 CCGTAGTTTGGTCCACTCACAA 60.484 50.000 0.00 0.00 0.00 3.33
1581 1720 0.822121 GGAACAAGGTCACCGGCTTT 60.822 55.000 0.00 0.00 0.00 3.51
2470 2739 2.543445 GCAAGCATTTTTGGTTTTGGGC 60.543 45.455 0.00 0.00 0.00 5.36
2471 2740 1.979855 AGCATTTTTGGTTTTGGGCC 58.020 45.000 0.00 0.00 0.00 5.80
2472 2741 0.958091 GCATTTTTGGTTTTGGGCCC 59.042 50.000 17.59 17.59 0.00 5.80
2473 2742 1.478471 GCATTTTTGGTTTTGGGCCCT 60.478 47.619 25.70 0.00 0.00 5.19
2474 2743 2.228925 CATTTTTGGTTTTGGGCCCTG 58.771 47.619 25.70 3.78 0.00 4.45
2475 2744 1.290134 TTTTTGGTTTTGGGCCCTGT 58.710 45.000 25.70 0.00 0.00 4.00
2476 2745 1.290134 TTTTGGTTTTGGGCCCTGTT 58.710 45.000 25.70 0.00 0.00 3.16
2477 2746 0.833949 TTTGGTTTTGGGCCCTGTTC 59.166 50.000 25.70 11.06 0.00 3.18
2478 2747 0.325671 TTGGTTTTGGGCCCTGTTCA 60.326 50.000 25.70 12.12 0.00 3.18
2479 2748 0.325671 TGGTTTTGGGCCCTGTTCAA 60.326 50.000 25.70 5.13 0.00 2.69
2480 2749 0.392706 GGTTTTGGGCCCTGTTCAAG 59.607 55.000 25.70 0.00 0.00 3.02
2481 2750 1.408969 GTTTTGGGCCCTGTTCAAGA 58.591 50.000 25.70 0.00 0.00 3.02
2482 2751 1.760029 GTTTTGGGCCCTGTTCAAGAA 59.240 47.619 25.70 2.45 0.00 2.52
2483 2752 2.368548 GTTTTGGGCCCTGTTCAAGAAT 59.631 45.455 25.70 0.00 0.00 2.40
2484 2753 2.397044 TTGGGCCCTGTTCAAGAATT 57.603 45.000 25.70 0.00 0.00 2.17
2485 2754 1.923356 TGGGCCCTGTTCAAGAATTC 58.077 50.000 25.70 0.00 0.00 2.17
2486 2755 1.146774 TGGGCCCTGTTCAAGAATTCA 59.853 47.619 25.70 0.00 0.00 2.57
2487 2756 2.225343 TGGGCCCTGTTCAAGAATTCAT 60.225 45.455 25.70 0.00 0.00 2.57
2488 2757 2.428530 GGGCCCTGTTCAAGAATTCATC 59.571 50.000 17.04 0.00 0.00 2.92
2489 2758 2.428530 GGCCCTGTTCAAGAATTCATCC 59.571 50.000 8.44 0.00 0.00 3.51
2490 2759 2.098117 GCCCTGTTCAAGAATTCATCCG 59.902 50.000 8.44 0.00 0.00 4.18
2491 2760 3.609853 CCCTGTTCAAGAATTCATCCGA 58.390 45.455 8.44 0.00 0.00 4.55
2492 2761 4.202441 CCCTGTTCAAGAATTCATCCGAT 58.798 43.478 8.44 0.00 0.00 4.18
2493 2762 4.641989 CCCTGTTCAAGAATTCATCCGATT 59.358 41.667 8.44 0.00 0.00 3.34
2494 2763 5.822519 CCCTGTTCAAGAATTCATCCGATTA 59.177 40.000 8.44 0.00 0.00 1.75
2495 2764 6.318648 CCCTGTTCAAGAATTCATCCGATTAA 59.681 38.462 8.44 0.00 0.00 1.40
2496 2765 7.189512 CCTGTTCAAGAATTCATCCGATTAAC 58.810 38.462 8.44 1.74 0.00 2.01
2497 2766 7.083875 TGTTCAAGAATTCATCCGATTAACC 57.916 36.000 8.44 0.00 0.00 2.85
2498 2767 6.657117 TGTTCAAGAATTCATCCGATTAACCA 59.343 34.615 8.44 0.00 0.00 3.67
2499 2768 6.925610 TCAAGAATTCATCCGATTAACCAG 57.074 37.500 8.44 0.00 0.00 4.00
2500 2769 6.414732 TCAAGAATTCATCCGATTAACCAGT 58.585 36.000 8.44 0.00 0.00 4.00
2501 2770 6.884295 TCAAGAATTCATCCGATTAACCAGTT 59.116 34.615 8.44 0.00 0.00 3.16
2502 2771 8.044309 TCAAGAATTCATCCGATTAACCAGTTA 58.956 33.333 8.44 0.00 0.00 2.24
2503 2772 8.840321 CAAGAATTCATCCGATTAACCAGTTAT 58.160 33.333 8.44 0.00 0.00 1.89
2504 2773 8.608844 AGAATTCATCCGATTAACCAGTTATC 57.391 34.615 8.44 0.00 0.00 1.75
2505 2774 8.432805 AGAATTCATCCGATTAACCAGTTATCT 58.567 33.333 8.44 0.00 0.00 1.98
2506 2775 8.980481 AATTCATCCGATTAACCAGTTATCTT 57.020 30.769 0.00 0.00 0.00 2.40
2507 2776 7.786178 TTCATCCGATTAACCAGTTATCTTG 57.214 36.000 0.00 0.00 0.00 3.02
2508 2777 6.884832 TCATCCGATTAACCAGTTATCTTGT 58.115 36.000 0.00 0.00 0.00 3.16
2509 2778 6.984474 TCATCCGATTAACCAGTTATCTTGTC 59.016 38.462 0.00 0.00 0.00 3.18
2510 2779 5.345702 TCCGATTAACCAGTTATCTTGTCG 58.654 41.667 0.00 0.00 0.00 4.35
2511 2780 5.125900 TCCGATTAACCAGTTATCTTGTCGA 59.874 40.000 0.00 0.00 0.00 4.20
2512 2781 5.983720 CCGATTAACCAGTTATCTTGTCGAT 59.016 40.000 0.00 0.00 36.11 3.59
2513 2782 6.479001 CCGATTAACCAGTTATCTTGTCGATT 59.521 38.462 0.00 0.00 33.48 3.34
2514 2783 7.650504 CCGATTAACCAGTTATCTTGTCGATTA 59.349 37.037 0.00 0.00 33.48 1.75
2515 2784 9.027129 CGATTAACCAGTTATCTTGTCGATTAA 57.973 33.333 0.00 0.00 33.48 1.40
2518 2787 7.787725 AACCAGTTATCTTGTCGATTAATCC 57.212 36.000 9.87 0.00 33.48 3.01
2519 2788 6.289064 ACCAGTTATCTTGTCGATTAATCCC 58.711 40.000 9.87 1.75 33.48 3.85
2520 2789 6.099845 ACCAGTTATCTTGTCGATTAATCCCT 59.900 38.462 9.87 0.00 33.48 4.20
2521 2790 7.289317 ACCAGTTATCTTGTCGATTAATCCCTA 59.711 37.037 9.87 0.00 33.48 3.53
2522 2791 7.599245 CCAGTTATCTTGTCGATTAATCCCTAC 59.401 40.741 9.87 6.59 33.48 3.18
2523 2792 8.361139 CAGTTATCTTGTCGATTAATCCCTACT 58.639 37.037 9.87 0.00 33.48 2.57
2524 2793 8.578151 AGTTATCTTGTCGATTAATCCCTACTC 58.422 37.037 9.87 0.00 33.48 2.59
2525 2794 6.978674 ATCTTGTCGATTAATCCCTACTCA 57.021 37.500 9.87 0.00 0.00 3.41
2526 2795 6.978674 TCTTGTCGATTAATCCCTACTCAT 57.021 37.500 9.87 0.00 0.00 2.90
2527 2796 8.651589 ATCTTGTCGATTAATCCCTACTCATA 57.348 34.615 9.87 0.00 0.00 2.15
2528 2797 8.112016 TCTTGTCGATTAATCCCTACTCATAG 57.888 38.462 9.87 4.03 0.00 2.23
2529 2798 6.835819 TGTCGATTAATCCCTACTCATAGG 57.164 41.667 9.87 0.00 46.99 2.57
2536 2805 3.053146 CCTACTCATAGGGTCCCCG 57.947 63.158 3.51 0.00 44.06 5.73
2537 2806 0.481567 CCTACTCATAGGGTCCCCGA 59.518 60.000 3.51 0.00 44.06 5.14
2538 2807 1.548128 CCTACTCATAGGGTCCCCGAG 60.548 61.905 15.13 15.13 44.06 4.63
2539 2808 1.145325 CTACTCATAGGGTCCCCGAGT 59.855 57.143 22.47 22.47 41.95 4.18
2540 2809 1.229131 ACTCATAGGGTCCCCGAGTA 58.771 55.000 19.16 0.75 41.95 2.59
2541 2810 1.145325 ACTCATAGGGTCCCCGAGTAG 59.855 57.143 19.16 8.03 41.95 2.57
2542 2811 0.178970 TCATAGGGTCCCCGAGTAGC 60.179 60.000 3.51 0.00 41.95 3.58
2543 2812 1.155624 ATAGGGTCCCCGAGTAGCC 59.844 63.158 3.51 0.00 41.95 3.93
2544 2813 2.710237 ATAGGGTCCCCGAGTAGCCG 62.710 65.000 3.51 0.00 41.95 5.52
2545 2814 4.828296 GGGTCCCCGAGTAGCCGA 62.828 72.222 0.00 0.00 0.00 5.54
2546 2815 2.521224 GGTCCCCGAGTAGCCGAT 60.521 66.667 0.00 0.00 0.00 4.18
2547 2816 2.132352 GGTCCCCGAGTAGCCGATT 61.132 63.158 0.00 0.00 0.00 3.34
2548 2817 0.825010 GGTCCCCGAGTAGCCGATTA 60.825 60.000 0.00 0.00 0.00 1.75
2549 2818 0.313357 GTCCCCGAGTAGCCGATTAC 59.687 60.000 0.00 0.00 0.00 1.89
2550 2819 0.825010 TCCCCGAGTAGCCGATTACC 60.825 60.000 0.00 0.00 0.00 2.85
2551 2820 1.664306 CCCGAGTAGCCGATTACCC 59.336 63.158 0.00 0.00 0.00 3.69
2552 2821 1.285023 CCGAGTAGCCGATTACCCG 59.715 63.158 0.00 0.00 0.00 5.28
2553 2822 1.168407 CCGAGTAGCCGATTACCCGA 61.168 60.000 2.70 0.00 27.60 5.14
2554 2823 0.879765 CGAGTAGCCGATTACCCGAT 59.120 55.000 0.00 0.00 27.60 4.18
2555 2824 2.079158 CGAGTAGCCGATTACCCGATA 58.921 52.381 0.00 0.00 27.60 2.92
2556 2825 2.485426 CGAGTAGCCGATTACCCGATAA 59.515 50.000 0.00 0.00 27.60 1.75
2557 2826 3.058016 CGAGTAGCCGATTACCCGATAAA 60.058 47.826 0.00 0.00 27.60 1.40
2558 2827 4.380233 CGAGTAGCCGATTACCCGATAAAT 60.380 45.833 0.00 0.00 27.60 1.40
2559 2828 5.069501 AGTAGCCGATTACCCGATAAATC 57.930 43.478 0.00 0.00 0.00 2.17
2581 2850 9.677567 AAATCGTCCGATTAATTGATTAAATGG 57.322 29.630 14.61 5.88 43.26 3.16
2582 2851 6.664515 TCGTCCGATTAATTGATTAAATGGC 58.335 36.000 4.10 2.85 36.02 4.40
2583 2852 5.856455 CGTCCGATTAATTGATTAAATGGCC 59.144 40.000 4.10 0.00 36.02 5.36
2584 2853 5.856455 GTCCGATTAATTGATTAAATGGCCG 59.144 40.000 4.10 0.00 36.02 6.13
2585 2854 5.765677 TCCGATTAATTGATTAAATGGCCGA 59.234 36.000 4.10 0.00 36.02 5.54
2586 2855 6.432783 TCCGATTAATTGATTAAATGGCCGAT 59.567 34.615 4.10 0.00 36.02 4.18
2587 2856 7.040062 TCCGATTAATTGATTAAATGGCCGATT 60.040 33.333 4.10 0.00 36.02 3.34
2588 2857 8.240682 CCGATTAATTGATTAAATGGCCGATTA 58.759 33.333 4.10 0.00 36.02 1.75
2589 2858 9.619316 CGATTAATTGATTAAATGGCCGATTAA 57.381 29.630 13.33 13.33 36.02 1.40
2593 2862 8.647143 AATTGATTAAATGGCCGATTAACTTG 57.353 30.769 13.26 0.00 0.00 3.16
2594 2863 5.587289 TGATTAAATGGCCGATTAACTTGC 58.413 37.500 13.26 6.21 0.00 4.01
2595 2864 2.959507 AAATGGCCGATTAACTTGCC 57.040 45.000 0.00 4.44 44.27 4.52
2597 2866 4.211986 GGCCGATTAACTTGCCGA 57.788 55.556 0.00 0.00 33.59 5.54
2598 2867 2.702847 GGCCGATTAACTTGCCGAT 58.297 52.632 0.00 0.00 33.59 4.18
2599 2868 1.021968 GGCCGATTAACTTGCCGATT 58.978 50.000 0.00 0.00 33.59 3.34
2600 2869 2.215196 GGCCGATTAACTTGCCGATTA 58.785 47.619 0.00 0.00 33.59 1.75
2601 2870 2.223377 GGCCGATTAACTTGCCGATTAG 59.777 50.000 0.00 0.00 33.59 1.73
2602 2871 2.349532 GCCGATTAACTTGCCGATTAGC 60.350 50.000 0.00 0.00 0.00 3.09
2603 2872 2.223377 CCGATTAACTTGCCGATTAGCC 59.777 50.000 0.00 0.00 0.00 3.93
2604 2873 3.131396 CGATTAACTTGCCGATTAGCCT 58.869 45.455 0.00 0.00 0.00 4.58
2605 2874 4.304110 CGATTAACTTGCCGATTAGCCTA 58.696 43.478 0.00 0.00 0.00 3.93
2606 2875 4.929808 CGATTAACTTGCCGATTAGCCTAT 59.070 41.667 0.00 0.00 0.00 2.57
2607 2876 5.408604 CGATTAACTTGCCGATTAGCCTATT 59.591 40.000 0.00 0.00 0.00 1.73
2608 2877 6.588756 CGATTAACTTGCCGATTAGCCTATTA 59.411 38.462 0.00 0.00 0.00 0.98
2609 2878 7.117236 CGATTAACTTGCCGATTAGCCTATTAA 59.883 37.037 0.00 0.00 0.00 1.40
2610 2879 8.863872 ATTAACTTGCCGATTAGCCTATTAAT 57.136 30.769 0.00 0.00 0.00 1.40
2611 2880 6.803154 AACTTGCCGATTAGCCTATTAATC 57.197 37.500 0.00 0.00 36.92 1.75
2612 2881 5.246307 ACTTGCCGATTAGCCTATTAATCC 58.754 41.667 0.00 0.00 36.93 3.01
2613 2882 4.216411 TGCCGATTAGCCTATTAATCCC 57.784 45.455 0.00 0.00 36.93 3.85
2614 2883 3.054655 TGCCGATTAGCCTATTAATCCCC 60.055 47.826 0.00 0.00 36.93 4.81
2615 2884 3.200165 GCCGATTAGCCTATTAATCCCCT 59.800 47.826 0.00 0.00 36.93 4.79
2616 2885 4.407945 GCCGATTAGCCTATTAATCCCCTA 59.592 45.833 0.00 0.00 36.93 3.53
2617 2886 5.684291 GCCGATTAGCCTATTAATCCCCTAC 60.684 48.000 0.00 0.00 36.93 3.18
2618 2887 5.661759 CCGATTAGCCTATTAATCCCCTACT 59.338 44.000 0.00 0.00 36.93 2.57
2619 2888 6.183360 CCGATTAGCCTATTAATCCCCTACTC 60.183 46.154 0.00 0.00 36.93 2.59
2620 2889 6.380274 CGATTAGCCTATTAATCCCCTACTCA 59.620 42.308 0.00 0.00 36.93 3.41
2621 2890 6.930068 TTAGCCTATTAATCCCCTACTCAC 57.070 41.667 0.00 0.00 0.00 3.51
2622 2891 4.168883 AGCCTATTAATCCCCTACTCACC 58.831 47.826 0.00 0.00 0.00 4.02
2623 2892 3.908103 GCCTATTAATCCCCTACTCACCA 59.092 47.826 0.00 0.00 0.00 4.17
2624 2893 4.020128 GCCTATTAATCCCCTACTCACCAG 60.020 50.000 0.00 0.00 0.00 4.00
2625 2894 4.020128 CCTATTAATCCCCTACTCACCAGC 60.020 50.000 0.00 0.00 0.00 4.85
2626 2895 1.802553 TAATCCCCTACTCACCAGCC 58.197 55.000 0.00 0.00 0.00 4.85
2627 2896 1.338136 AATCCCCTACTCACCAGCCG 61.338 60.000 0.00 0.00 0.00 5.52
2628 2897 2.238319 ATCCCCTACTCACCAGCCGA 62.238 60.000 0.00 0.00 0.00 5.54
2629 2898 2.722201 CCCCTACTCACCAGCCGAC 61.722 68.421 0.00 0.00 0.00 4.79
2630 2899 2.722201 CCCTACTCACCAGCCGACC 61.722 68.421 0.00 0.00 0.00 4.79
2631 2900 2.490217 CTACTCACCAGCCGACCG 59.510 66.667 0.00 0.00 0.00 4.79
2632 2901 2.034532 TACTCACCAGCCGACCGA 59.965 61.111 0.00 0.00 0.00 4.69
2633 2902 1.994507 CTACTCACCAGCCGACCGAG 61.995 65.000 0.00 0.00 0.00 4.63
2634 2903 4.803426 CTCACCAGCCGACCGAGC 62.803 72.222 0.00 0.00 0.00 5.03
2639 2908 3.826754 CAGCCGACCGAGCAGCTA 61.827 66.667 0.00 0.00 33.33 3.32
2640 2909 3.827898 AGCCGACCGAGCAGCTAC 61.828 66.667 0.00 0.00 32.73 3.58
2641 2910 4.874977 GCCGACCGAGCAGCTACC 62.875 72.222 0.00 0.00 0.00 3.18
2642 2911 3.449227 CCGACCGAGCAGCTACCA 61.449 66.667 0.00 0.00 0.00 3.25
2643 2912 2.103143 CGACCGAGCAGCTACCAG 59.897 66.667 0.00 0.00 0.00 4.00
2644 2913 2.701780 CGACCGAGCAGCTACCAGT 61.702 63.158 0.00 0.00 0.00 4.00
2645 2914 1.592223 GACCGAGCAGCTACCAGTT 59.408 57.895 0.00 0.00 0.00 3.16
2646 2915 0.815734 GACCGAGCAGCTACCAGTTA 59.184 55.000 0.00 0.00 0.00 2.24
2647 2916 1.203994 GACCGAGCAGCTACCAGTTAA 59.796 52.381 0.00 0.00 0.00 2.01
2648 2917 1.067071 ACCGAGCAGCTACCAGTTAAC 60.067 52.381 0.00 0.00 0.00 2.01
2649 2918 1.269166 CGAGCAGCTACCAGTTAACG 58.731 55.000 0.00 0.00 0.00 3.18
2650 2919 1.135489 CGAGCAGCTACCAGTTAACGA 60.135 52.381 0.00 0.00 0.00 3.85
2651 2920 2.479730 CGAGCAGCTACCAGTTAACGAT 60.480 50.000 0.00 0.00 0.00 3.73
2652 2921 3.522553 GAGCAGCTACCAGTTAACGATT 58.477 45.455 0.00 0.00 0.00 3.34
2653 2922 3.933332 GAGCAGCTACCAGTTAACGATTT 59.067 43.478 0.00 0.00 0.00 2.17
2654 2923 3.933332 AGCAGCTACCAGTTAACGATTTC 59.067 43.478 0.00 0.00 0.00 2.17
2655 2924 3.063588 GCAGCTACCAGTTAACGATTTCC 59.936 47.826 0.00 0.00 0.00 3.13
2656 2925 4.504858 CAGCTACCAGTTAACGATTTCCT 58.495 43.478 0.00 0.00 0.00 3.36
2657 2926 4.567159 CAGCTACCAGTTAACGATTTCCTC 59.433 45.833 0.00 0.00 0.00 3.71
2658 2927 4.222145 AGCTACCAGTTAACGATTTCCTCA 59.778 41.667 0.00 0.00 0.00 3.86
2659 2928 4.933400 GCTACCAGTTAACGATTTCCTCAA 59.067 41.667 0.00 0.00 0.00 3.02
2660 2929 5.163884 GCTACCAGTTAACGATTTCCTCAAC 60.164 44.000 0.00 0.00 0.00 3.18
2661 2930 4.710324 ACCAGTTAACGATTTCCTCAACA 58.290 39.130 0.00 0.00 0.00 3.33
2662 2931 5.127491 ACCAGTTAACGATTTCCTCAACAA 58.873 37.500 0.00 0.00 0.00 2.83
2693 2962 4.335594 GGGTTACTAATGCTCATGGTGTTC 59.664 45.833 0.00 0.00 0.00 3.18
2715 2985 9.191479 TGTTCTTACTTATTTGGAGGAACAAAA 57.809 29.630 2.61 0.00 42.91 2.44
2742 3018 2.719705 TGGTGTGGTTCCCCTTTATTCT 59.280 45.455 0.00 0.00 0.00 2.40
2787 3063 5.248477 GGGATTATAGCCTTCAGATACACCA 59.752 44.000 0.00 0.00 0.00 4.17
3404 3680 2.029470 GGTCCTGCTGGAGATCTTATCG 60.029 54.545 13.36 0.00 44.16 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
219 221 2.038269 CCGTGAACCACCGGAATGG 61.038 63.158 9.46 9.49 46.10 3.16
352 363 6.992664 AGAACAGGATGATATGTAAGAGCT 57.007 37.500 0.00 0.00 39.69 4.09
383 397 8.558973 AGAGAGAAGAAATAACAATCAACAGG 57.441 34.615 0.00 0.00 0.00 4.00
455 469 7.992754 ATATTGACAGAATAGGAAGAATGGC 57.007 36.000 0.00 0.00 0.00 4.40
473 487 7.121611 ACATCGGTGTACATCGGTATATATTGA 59.878 37.037 27.14 5.21 36.63 2.57
481 495 3.304861 GCATACATCGGTGTACATCGGTA 60.305 47.826 27.14 21.21 43.21 4.02
483 497 2.058798 GCATACATCGGTGTACATCGG 58.941 52.381 27.14 15.14 43.21 4.18
484 498 3.013276 AGCATACATCGGTGTACATCG 57.987 47.619 22.50 22.50 43.21 3.84
485 499 4.368315 TGAAGCATACATCGGTGTACATC 58.632 43.478 11.47 7.72 43.21 3.06
486 500 4.400529 TGAAGCATACATCGGTGTACAT 57.599 40.909 11.47 0.00 43.21 2.29
488 502 5.277345 GGAAATGAAGCATACATCGGTGTAC 60.277 44.000 11.47 0.00 43.21 2.90
489 503 4.814234 GGAAATGAAGCATACATCGGTGTA 59.186 41.667 11.65 11.65 44.43 2.90
490 504 3.627577 GGAAATGAAGCATACATCGGTGT 59.372 43.478 6.54 6.54 42.39 4.16
615 650 4.530875 GATTCACCCCTTCATGACTGAAT 58.469 43.478 0.00 3.45 40.52 2.57
650 685 0.820871 GATCGACTGGAGCCACTTCT 59.179 55.000 0.00 0.00 0.00 2.85
804 839 1.741706 CTTGAGCTGGGTAGTTGCATG 59.258 52.381 0.00 0.00 0.00 4.06
810 845 1.127567 TGCCACTTGAGCTGGGTAGT 61.128 55.000 0.00 0.00 0.00 2.73
888 923 3.145551 CAAGCATGGAGGCAGGGC 61.146 66.667 0.00 0.00 35.83 5.19
937 1001 6.453476 AGAAGGAAGAAGAGGGTGGATATAA 58.547 40.000 0.00 0.00 0.00 0.98
943 1007 1.557371 GGAGAAGGAAGAAGAGGGTGG 59.443 57.143 0.00 0.00 0.00 4.61
1016 1086 0.375106 GAGAAGCCCGAGCGAAAATG 59.625 55.000 0.00 0.00 46.67 2.32
1182 1267 2.572104 GGTGTCCAGGGACTTACTGATT 59.428 50.000 18.60 0.00 44.80 2.57
1196 1284 2.447572 TGGAGCTGGTGGTGTCCA 60.448 61.111 0.00 0.00 36.72 4.02
1198 1286 2.359230 GCTGGAGCTGGTGGTGTC 60.359 66.667 0.00 0.00 38.21 3.67
1385 1518 6.095440 GCTGGTTTGTGTCCTATTATTGACAT 59.905 38.462 0.00 0.00 42.90 3.06
1581 1720 7.789026 TCTTCTTTGAGATGCTCTGATGAATA 58.211 34.615 0.00 0.00 0.00 1.75
2128 2288 6.942886 TGAACTTGTGATGTTTTTGTTGTC 57.057 33.333 0.00 0.00 0.00 3.18
2470 2739 3.609853 TCGGATGAATTCTTGAACAGGG 58.390 45.455 7.05 0.00 0.00 4.45
2471 2740 5.824904 AATCGGATGAATTCTTGAACAGG 57.175 39.130 7.05 0.00 0.00 4.00
2472 2741 7.148255 TGGTTAATCGGATGAATTCTTGAACAG 60.148 37.037 7.05 0.00 0.00 3.16
2473 2742 6.657117 TGGTTAATCGGATGAATTCTTGAACA 59.343 34.615 7.05 0.00 0.00 3.18
2474 2743 7.083875 TGGTTAATCGGATGAATTCTTGAAC 57.916 36.000 7.05 0.68 0.00 3.18
2475 2744 6.884295 ACTGGTTAATCGGATGAATTCTTGAA 59.116 34.615 7.05 0.00 0.00 2.69
2476 2745 6.414732 ACTGGTTAATCGGATGAATTCTTGA 58.585 36.000 7.05 0.00 0.00 3.02
2477 2746 6.683974 ACTGGTTAATCGGATGAATTCTTG 57.316 37.500 7.05 0.00 0.00 3.02
2478 2747 8.980481 ATAACTGGTTAATCGGATGAATTCTT 57.020 30.769 7.05 0.00 0.00 2.52
2479 2748 8.432805 AGATAACTGGTTAATCGGATGAATTCT 58.567 33.333 7.05 0.00 0.00 2.40
2480 2749 8.608844 AGATAACTGGTTAATCGGATGAATTC 57.391 34.615 0.31 0.00 0.00 2.17
2481 2750 8.840321 CAAGATAACTGGTTAATCGGATGAATT 58.160 33.333 0.31 0.00 0.00 2.17
2482 2751 7.993183 ACAAGATAACTGGTTAATCGGATGAAT 59.007 33.333 0.31 0.00 0.00 2.57
2483 2752 7.335627 ACAAGATAACTGGTTAATCGGATGAA 58.664 34.615 0.31 0.00 0.00 2.57
2484 2753 6.884832 ACAAGATAACTGGTTAATCGGATGA 58.115 36.000 0.31 0.00 0.00 2.92
2485 2754 6.074302 CGACAAGATAACTGGTTAATCGGATG 60.074 42.308 0.31 0.00 29.28 3.51
2486 2755 5.983720 CGACAAGATAACTGGTTAATCGGAT 59.016 40.000 0.31 0.00 29.28 4.18
2487 2756 5.125900 TCGACAAGATAACTGGTTAATCGGA 59.874 40.000 0.31 0.00 29.28 4.55
2488 2757 5.345702 TCGACAAGATAACTGGTTAATCGG 58.654 41.667 0.00 0.00 29.28 4.18
2489 2758 7.464830 AATCGACAAGATAACTGGTTAATCG 57.535 36.000 0.00 0.00 38.98 3.34
2492 2761 9.321562 GGATTAATCGACAAGATAACTGGTTAA 57.678 33.333 9.32 0.00 38.98 2.01
2493 2762 7.929785 GGGATTAATCGACAAGATAACTGGTTA 59.070 37.037 9.32 0.00 38.98 2.85
2494 2763 6.766467 GGGATTAATCGACAAGATAACTGGTT 59.234 38.462 9.32 0.00 38.98 3.67
2495 2764 6.099845 AGGGATTAATCGACAAGATAACTGGT 59.900 38.462 9.32 0.00 38.98 4.00
2496 2765 6.525629 AGGGATTAATCGACAAGATAACTGG 58.474 40.000 9.32 0.00 38.98 4.00
2497 2766 8.361139 AGTAGGGATTAATCGACAAGATAACTG 58.639 37.037 9.32 0.00 38.98 3.16
2498 2767 8.480133 AGTAGGGATTAATCGACAAGATAACT 57.520 34.615 9.32 0.89 38.98 2.24
2499 2768 8.358148 TGAGTAGGGATTAATCGACAAGATAAC 58.642 37.037 9.32 0.00 38.98 1.89
2500 2769 8.473358 TGAGTAGGGATTAATCGACAAGATAA 57.527 34.615 9.32 0.00 38.98 1.75
2501 2770 8.651589 ATGAGTAGGGATTAATCGACAAGATA 57.348 34.615 9.32 0.00 38.98 1.98
2502 2771 6.978674 TGAGTAGGGATTAATCGACAAGAT 57.021 37.500 9.32 0.00 42.43 2.40
2503 2772 6.978674 ATGAGTAGGGATTAATCGACAAGA 57.021 37.500 9.32 0.00 0.00 3.02
2504 2773 7.316640 CCTATGAGTAGGGATTAATCGACAAG 58.683 42.308 9.32 4.73 43.26 3.16
2505 2774 7.228314 CCTATGAGTAGGGATTAATCGACAA 57.772 40.000 9.32 1.80 43.26 3.18
2506 2775 6.835819 CCTATGAGTAGGGATTAATCGACA 57.164 41.667 9.32 3.99 43.26 4.35
2530 2799 0.313357 GTAATCGGCTACTCGGGGAC 59.687 60.000 0.00 0.00 0.00 4.46
2531 2800 0.825010 GGTAATCGGCTACTCGGGGA 60.825 60.000 0.00 0.00 0.00 4.81
2532 2801 1.664306 GGTAATCGGCTACTCGGGG 59.336 63.158 0.00 0.00 0.00 5.73
2533 2802 1.664306 GGGTAATCGGCTACTCGGG 59.336 63.158 0.00 0.00 0.00 5.14
2534 2803 1.168407 TCGGGTAATCGGCTACTCGG 61.168 60.000 14.45 0.84 44.30 4.63
2535 2804 0.879765 ATCGGGTAATCGGCTACTCG 59.120 55.000 9.90 9.90 45.31 4.18
2536 2805 4.510038 TTTATCGGGTAATCGGCTACTC 57.490 45.455 0.00 0.00 0.00 2.59
2537 2806 4.380233 CGATTTATCGGGTAATCGGCTACT 60.380 45.833 14.59 0.00 45.61 2.57
2538 2807 3.855950 CGATTTATCGGGTAATCGGCTAC 59.144 47.826 14.59 0.00 45.61 3.58
2539 2808 4.100707 CGATTTATCGGGTAATCGGCTA 57.899 45.455 14.59 0.00 45.61 3.93
2540 2809 2.955614 CGATTTATCGGGTAATCGGCT 58.044 47.619 14.59 0.00 45.61 5.52
2555 2824 9.677567 CCATTTAATCAATTAATCGGACGATTT 57.322 29.630 22.82 5.63 41.55 2.17
2556 2825 7.807907 GCCATTTAATCAATTAATCGGACGATT 59.192 33.333 21.60 21.60 45.58 3.34
2557 2826 7.305474 GCCATTTAATCAATTAATCGGACGAT 58.695 34.615 0.65 0.65 32.78 3.73
2558 2827 6.293735 GGCCATTTAATCAATTAATCGGACGA 60.294 38.462 0.00 0.00 32.78 4.20
2559 2828 5.856455 GGCCATTTAATCAATTAATCGGACG 59.144 40.000 0.00 0.00 32.78 4.79
2560 2829 5.856455 CGGCCATTTAATCAATTAATCGGAC 59.144 40.000 2.24 9.25 32.60 4.79
2561 2830 5.765677 TCGGCCATTTAATCAATTAATCGGA 59.234 36.000 2.24 0.00 32.78 4.55
2562 2831 6.007936 TCGGCCATTTAATCAATTAATCGG 57.992 37.500 2.24 2.40 32.78 4.18
2563 2832 9.619316 TTAATCGGCCATTTAATCAATTAATCG 57.381 29.630 2.24 0.00 32.78 3.34
2567 2836 9.743057 CAAGTTAATCGGCCATTTAATCAATTA 57.257 29.630 2.24 0.00 0.00 1.40
2568 2837 7.224557 GCAAGTTAATCGGCCATTTAATCAATT 59.775 33.333 2.24 0.00 0.00 2.32
2569 2838 6.701400 GCAAGTTAATCGGCCATTTAATCAAT 59.299 34.615 2.24 0.00 0.00 2.57
2570 2839 6.039616 GCAAGTTAATCGGCCATTTAATCAA 58.960 36.000 2.24 0.00 0.00 2.57
2571 2840 5.451242 GGCAAGTTAATCGGCCATTTAATCA 60.451 40.000 2.24 0.00 45.70 2.57
2572 2841 4.982295 GGCAAGTTAATCGGCCATTTAATC 59.018 41.667 2.24 1.98 45.70 1.75
2573 2842 4.499019 CGGCAAGTTAATCGGCCATTTAAT 60.499 41.667 2.24 0.00 46.75 1.40
2574 2843 3.181495 CGGCAAGTTAATCGGCCATTTAA 60.181 43.478 2.24 3.07 46.75 1.52
2575 2844 2.356382 CGGCAAGTTAATCGGCCATTTA 59.644 45.455 2.24 0.00 46.75 1.40
2576 2845 1.134175 CGGCAAGTTAATCGGCCATTT 59.866 47.619 2.24 0.00 46.75 2.32
2577 2846 0.738389 CGGCAAGTTAATCGGCCATT 59.262 50.000 2.24 4.55 46.75 3.16
2578 2847 0.107410 TCGGCAAGTTAATCGGCCAT 60.107 50.000 2.24 0.00 46.75 4.40
2579 2848 0.107410 ATCGGCAAGTTAATCGGCCA 60.107 50.000 2.24 0.00 46.75 5.36
2580 2849 1.021968 AATCGGCAAGTTAATCGGCC 58.978 50.000 0.00 0.00 42.98 6.13
2581 2850 2.349532 GCTAATCGGCAAGTTAATCGGC 60.350 50.000 0.00 0.00 0.00 5.54
2582 2851 2.223377 GGCTAATCGGCAAGTTAATCGG 59.777 50.000 0.00 0.00 38.25 4.18
2583 2852 3.131396 AGGCTAATCGGCAAGTTAATCG 58.869 45.455 0.00 0.00 41.46 3.34
2584 2853 6.803154 AATAGGCTAATCGGCAAGTTAATC 57.197 37.500 0.00 0.00 41.46 1.75
2585 2854 8.863872 ATTAATAGGCTAATCGGCAAGTTAAT 57.136 30.769 0.00 0.00 41.46 1.40
2586 2855 7.389607 GGATTAATAGGCTAATCGGCAAGTTAA 59.610 37.037 0.00 0.00 38.61 2.01
2587 2856 6.877322 GGATTAATAGGCTAATCGGCAAGTTA 59.123 38.462 0.00 0.00 38.61 2.24
2588 2857 5.705905 GGATTAATAGGCTAATCGGCAAGTT 59.294 40.000 0.00 0.00 38.61 2.66
2589 2858 5.246307 GGATTAATAGGCTAATCGGCAAGT 58.754 41.667 0.00 0.00 38.61 3.16
2590 2859 4.636206 GGGATTAATAGGCTAATCGGCAAG 59.364 45.833 0.00 0.00 38.61 4.01
2591 2860 4.566907 GGGGATTAATAGGCTAATCGGCAA 60.567 45.833 0.00 0.00 38.61 4.52
2592 2861 3.054655 GGGGATTAATAGGCTAATCGGCA 60.055 47.826 0.00 0.00 38.61 5.69
2593 2862 3.200165 AGGGGATTAATAGGCTAATCGGC 59.800 47.826 0.00 0.00 38.61 5.54
2594 2863 5.661759 AGTAGGGGATTAATAGGCTAATCGG 59.338 44.000 0.00 0.00 38.61 4.18
2595 2864 6.380274 TGAGTAGGGGATTAATAGGCTAATCG 59.620 42.308 0.00 0.00 38.61 3.34
2596 2865 7.364851 GGTGAGTAGGGGATTAATAGGCTAATC 60.365 44.444 0.00 0.00 37.50 1.75
2597 2866 6.444171 GGTGAGTAGGGGATTAATAGGCTAAT 59.556 42.308 0.00 0.00 0.00 1.73
2598 2867 5.783875 GGTGAGTAGGGGATTAATAGGCTAA 59.216 44.000 0.00 0.00 0.00 3.09
2599 2868 5.162804 TGGTGAGTAGGGGATTAATAGGCTA 60.163 44.000 0.00 0.00 0.00 3.93
2600 2869 4.168883 GGTGAGTAGGGGATTAATAGGCT 58.831 47.826 0.00 0.00 0.00 4.58
2601 2870 3.908103 TGGTGAGTAGGGGATTAATAGGC 59.092 47.826 0.00 0.00 0.00 3.93
2602 2871 4.020128 GCTGGTGAGTAGGGGATTAATAGG 60.020 50.000 0.00 0.00 0.00 2.57
2603 2872 4.020128 GGCTGGTGAGTAGGGGATTAATAG 60.020 50.000 0.00 0.00 0.00 1.73
2604 2873 3.908103 GGCTGGTGAGTAGGGGATTAATA 59.092 47.826 0.00 0.00 0.00 0.98
2605 2874 2.711547 GGCTGGTGAGTAGGGGATTAAT 59.288 50.000 0.00 0.00 0.00 1.40
2606 2875 2.124411 GGCTGGTGAGTAGGGGATTAA 58.876 52.381 0.00 0.00 0.00 1.40
2607 2876 1.802553 GGCTGGTGAGTAGGGGATTA 58.197 55.000 0.00 0.00 0.00 1.75
2608 2877 1.338136 CGGCTGGTGAGTAGGGGATT 61.338 60.000 0.00 0.00 0.00 3.01
2609 2878 1.762460 CGGCTGGTGAGTAGGGGAT 60.762 63.158 0.00 0.00 0.00 3.85
2610 2879 2.363795 CGGCTGGTGAGTAGGGGA 60.364 66.667 0.00 0.00 0.00 4.81
2611 2880 2.363795 TCGGCTGGTGAGTAGGGG 60.364 66.667 0.00 0.00 0.00 4.79
2612 2881 2.722201 GGTCGGCTGGTGAGTAGGG 61.722 68.421 0.00 0.00 0.00 3.53
2613 2882 2.893398 GGTCGGCTGGTGAGTAGG 59.107 66.667 0.00 0.00 0.00 3.18
2614 2883 1.994507 CTCGGTCGGCTGGTGAGTAG 61.995 65.000 0.00 0.00 0.00 2.57
2615 2884 2.034532 TCGGTCGGCTGGTGAGTA 59.965 61.111 0.00 0.00 0.00 2.59
2616 2885 3.374402 CTCGGTCGGCTGGTGAGT 61.374 66.667 0.00 0.00 0.00 3.41
2617 2886 4.803426 GCTCGGTCGGCTGGTGAG 62.803 72.222 0.00 0.00 0.00 3.51
2624 2893 4.874977 GGTAGCTGCTCGGTCGGC 62.875 72.222 4.91 1.17 38.60 5.54
2625 2894 3.417275 CTGGTAGCTGCTCGGTCGG 62.417 68.421 4.91 0.00 0.00 4.79
2626 2895 2.103143 CTGGTAGCTGCTCGGTCG 59.897 66.667 4.91 0.00 0.00 4.79
2627 2896 0.815734 TAACTGGTAGCTGCTCGGTC 59.184 55.000 4.91 0.00 0.00 4.79
2628 2897 1.067071 GTTAACTGGTAGCTGCTCGGT 60.067 52.381 4.91 0.41 0.00 4.69
2629 2898 1.641577 GTTAACTGGTAGCTGCTCGG 58.358 55.000 4.91 0.00 0.00 4.63
2630 2899 1.135489 TCGTTAACTGGTAGCTGCTCG 60.135 52.381 4.91 0.00 0.00 5.03
2631 2900 2.649331 TCGTTAACTGGTAGCTGCTC 57.351 50.000 4.91 0.00 0.00 4.26
2632 2901 3.611766 AATCGTTAACTGGTAGCTGCT 57.388 42.857 7.57 7.57 0.00 4.24
2633 2902 3.063588 GGAAATCGTTAACTGGTAGCTGC 59.936 47.826 3.71 0.00 0.00 5.25
2634 2903 4.504858 AGGAAATCGTTAACTGGTAGCTG 58.495 43.478 3.71 0.00 0.00 4.24
2635 2904 4.222145 TGAGGAAATCGTTAACTGGTAGCT 59.778 41.667 3.71 0.00 0.00 3.32
2636 2905 4.501071 TGAGGAAATCGTTAACTGGTAGC 58.499 43.478 3.71 0.00 0.00 3.58
2637 2906 5.929992 TGTTGAGGAAATCGTTAACTGGTAG 59.070 40.000 3.71 0.00 33.31 3.18
2638 2907 5.856156 TGTTGAGGAAATCGTTAACTGGTA 58.144 37.500 3.71 0.00 33.31 3.25
2639 2908 4.710324 TGTTGAGGAAATCGTTAACTGGT 58.290 39.130 3.71 0.00 33.31 4.00
2640 2909 5.682943 TTGTTGAGGAAATCGTTAACTGG 57.317 39.130 3.71 0.00 33.31 4.00
2641 2910 6.086222 CCATTGTTGAGGAAATCGTTAACTG 58.914 40.000 3.71 0.00 33.31 3.16
2642 2911 5.768164 ACCATTGTTGAGGAAATCGTTAACT 59.232 36.000 3.71 0.00 33.31 2.24
2643 2912 6.009115 ACCATTGTTGAGGAAATCGTTAAC 57.991 37.500 0.00 0.00 32.93 2.01
2644 2913 6.642707 AACCATTGTTGAGGAAATCGTTAA 57.357 33.333 0.00 0.00 32.13 2.01
2645 2914 6.642707 AAACCATTGTTGAGGAAATCGTTA 57.357 33.333 0.00 0.00 34.13 3.18
2646 2915 5.529581 AAACCATTGTTGAGGAAATCGTT 57.470 34.783 0.00 0.00 34.13 3.85
2647 2916 5.288804 CAAAACCATTGTTGAGGAAATCGT 58.711 37.500 0.00 0.00 34.13 3.73
2648 2917 4.685628 CCAAAACCATTGTTGAGGAAATCG 59.314 41.667 0.00 0.00 34.13 3.34
2649 2918 4.996758 CCCAAAACCATTGTTGAGGAAATC 59.003 41.667 3.10 0.00 34.13 2.17
2650 2919 4.411869 ACCCAAAACCATTGTTGAGGAAAT 59.588 37.500 3.10 0.00 34.13 2.17
2651 2920 3.777522 ACCCAAAACCATTGTTGAGGAAA 59.222 39.130 3.10 0.00 34.13 3.13
2652 2921 3.379452 ACCCAAAACCATTGTTGAGGAA 58.621 40.909 3.10 0.00 34.13 3.36
2653 2922 3.039252 ACCCAAAACCATTGTTGAGGA 57.961 42.857 3.10 0.00 34.13 3.71
2654 2923 3.836365 AACCCAAAACCATTGTTGAGG 57.164 42.857 0.00 0.00 34.13 3.86
2655 2924 5.529581 AGTAACCCAAAACCATTGTTGAG 57.470 39.130 0.00 0.00 34.13 3.02
2656 2925 7.437748 CATTAGTAACCCAAAACCATTGTTGA 58.562 34.615 0.00 0.00 34.13 3.18
2657 2926 6.147000 GCATTAGTAACCCAAAACCATTGTTG 59.853 38.462 0.00 0.00 34.13 3.33
2658 2927 6.042666 AGCATTAGTAACCCAAAACCATTGTT 59.957 34.615 0.00 0.00 35.82 2.83
2659 2928 5.542251 AGCATTAGTAACCCAAAACCATTGT 59.458 36.000 0.00 0.00 0.00 2.71
2660 2929 6.036577 AGCATTAGTAACCCAAAACCATTG 57.963 37.500 0.00 0.00 0.00 2.82
2661 2930 5.777732 TGAGCATTAGTAACCCAAAACCATT 59.222 36.000 0.00 0.00 0.00 3.16
2662 2931 5.329399 TGAGCATTAGTAACCCAAAACCAT 58.671 37.500 0.00 0.00 0.00 3.55
2742 3018 3.307410 CCACCAGCACTACCTTGATTGTA 60.307 47.826 0.00 0.00 0.00 2.41
3197 3473 4.578928 GTGTCCACAAGTATGTTTTCTGGT 59.421 41.667 0.00 0.00 37.82 4.00
3386 3662 1.274728 CCCGATAAGATCTCCAGCAGG 59.725 57.143 0.00 0.00 0.00 4.85
3404 3680 1.916181 TCAGGTGAATTCCTCCTTCCC 59.084 52.381 14.19 0.00 36.67 3.97
3490 3775 0.256752 CACATCTCCCCCATGAAGCA 59.743 55.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.