Multiple sequence alignment - TraesCS1D01G207300

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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 TraesCS1D01G207300 chr1D 100.000 2831 0 0 1 2831 293606641 293609471 0.000000e+00 5228
1 TraesCS1D01G207300 chr1B 89.197 2379 139 38 1 2315 394857595 394859919 0.000000e+00 2861
2 TraesCS1D01G207300 chr1B 89.318 440 35 11 2331 2764 394875572 394876005 2.480000e-150 542
3 TraesCS1D01G207300 chr1A 91.484 822 53 10 1603 2413 365541972 365542787 0.000000e+00 1114
4 TraesCS1D01G207300 chr1A 88.930 813 53 13 1 788 365541080 365541880 0.000000e+00 968
5 TraesCS1D01G207300 chr3D 90.102 394 22 9 2434 2821 418216322 418215940 1.960000e-136 496
6 TraesCS1D01G207300 chr5B 86.216 399 42 9 2428 2821 340615313 340615703 1.210000e-113 420
7 TraesCS1D01G207300 chr5B 88.352 352 32 8 2472 2820 554639621 554639966 5.640000e-112 414
8 TraesCS1D01G207300 chr6B 83.879 397 49 14 2427 2819 573628185 573627800 5.760000e-97 364
9 TraesCS1D01G207300 chr6B 83.166 398 53 10 2428 2820 707212751 707213139 4.490000e-93 351
10 TraesCS1D01G207300 chr2B 84.021 388 50 8 2434 2820 65476947 65476571 2.070000e-96 363
11 TraesCS1D01G207300 chr2D 85.673 349 43 4 2473 2818 639827919 639828263 7.460000e-96 361
12 TraesCS1D01G207300 chr7B 80.098 407 63 13 2424 2820 384192092 384192490 1.280000e-73 287


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 TraesCS1D01G207300 chr1D 293606641 293609471 2830 False 5228 5228 100.000 1 2831 1 chr1D.!!$F1 2830
1 TraesCS1D01G207300 chr1B 394857595 394859919 2324 False 2861 2861 89.197 1 2315 1 chr1B.!!$F1 2314
2 TraesCS1D01G207300 chr1A 365541080 365542787 1707 False 1041 1114 90.207 1 2413 2 chr1A.!!$F1 2412

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
29 30 0.179000 CATCGGCAACTAGGGCTTCT 59.821 55.0 8.33 0.0 0.0 2.85 F
1485 1592 0.384309 TACTCGACGCCATCATGTCC 59.616 55.0 0.00 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1593 1700 0.594540 CGCTTCTCATCTCGCTGAGG 60.595 60.0 8.86 0.0 42.42 3.86 R
2776 2896 0.032912 TGCTCCACACCCCTATACGA 60.033 55.0 0.00 0.0 0.00 3.43 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
29 30 0.179000 CATCGGCAACTAGGGCTTCT 59.821 55.000 8.33 0.00 0.00 2.85
31 32 0.690762 TCGGCAACTAGGGCTTCTTT 59.309 50.000 8.33 0.00 0.00 2.52
56 57 1.469251 CCCCGTCATGTGACTTACTCG 60.469 57.143 11.03 0.00 42.66 4.18
177 181 4.400884 AGGCATGTTCACTGTTTGTGTTAA 59.599 37.500 0.00 0.00 46.27 2.01
178 182 5.068987 AGGCATGTTCACTGTTTGTGTTAAT 59.931 36.000 0.00 0.00 46.27 1.40
179 183 5.752955 GGCATGTTCACTGTTTGTGTTAATT 59.247 36.000 0.00 0.00 46.27 1.40
180 184 6.257630 GGCATGTTCACTGTTTGTGTTAATTT 59.742 34.615 0.00 0.00 46.27 1.82
181 185 7.118724 GCATGTTCACTGTTTGTGTTAATTTG 58.881 34.615 0.00 0.00 46.27 2.32
182 186 7.201513 GCATGTTCACTGTTTGTGTTAATTTGT 60.202 33.333 0.00 0.00 46.27 2.83
183 187 8.655092 CATGTTCACTGTTTGTGTTAATTTGTT 58.345 29.630 0.00 0.00 46.27 2.83
223 227 8.252417 TGCTGATATTGCATGTTTTTCTATGTT 58.748 29.630 0.00 0.00 35.31 2.71
312 316 5.577835 TGTGTACAATTGCACTTTCACTTC 58.422 37.500 10.12 3.95 39.02 3.01
477 485 8.702408 TTAATCGGTAATTGATATTTTTCGCG 57.298 30.769 0.00 0.00 0.00 5.87
490 498 3.332761 TTTTCGCGTTGGATGATATGC 57.667 42.857 5.77 0.00 0.00 3.14
625 636 3.744940 ATGGCAGATCTTTTTCAGGGA 57.255 42.857 0.00 0.00 0.00 4.20
629 640 4.281688 TGGCAGATCTTTTTCAGGGAAAAG 59.718 41.667 6.48 6.48 41.55 2.27
641 652 3.573967 TCAGGGAAAAGAAAATGGCAGAC 59.426 43.478 0.00 0.00 0.00 3.51
642 653 2.899900 AGGGAAAAGAAAATGGCAGACC 59.100 45.455 0.00 0.00 0.00 3.85
643 654 2.899900 GGGAAAAGAAAATGGCAGACCT 59.100 45.455 0.00 0.00 36.63 3.85
644 655 3.324846 GGGAAAAGAAAATGGCAGACCTT 59.675 43.478 0.00 0.00 36.63 3.50
699 741 0.875059 GTGAGGGAAAGAAAGTGGCG 59.125 55.000 0.00 0.00 0.00 5.69
738 807 1.950472 CGCTAGAACAAAAACCGCAG 58.050 50.000 0.00 0.00 0.00 5.18
991 1078 4.514577 CCGTCCTACAGCGCCCTG 62.515 72.222 2.29 0.00 44.80 4.45
1109 1204 3.978491 GGCCCTCGCGATCATCGA 61.978 66.667 12.38 6.84 43.74 3.59
1404 1511 1.517257 CGTCCACGACAGGCATCTC 60.517 63.158 0.00 0.00 43.02 2.75
1405 1512 1.517257 GTCCACGACAGGCATCTCG 60.517 63.158 0.00 0.00 35.96 4.04
1406 1513 2.887568 CCACGACAGGCATCTCGC 60.888 66.667 0.00 0.00 41.28 5.03
1485 1592 0.384309 TACTCGACGCCATCATGTCC 59.616 55.000 0.00 0.00 0.00 4.02
1491 1598 2.903855 GCCATCATGTCCCGCCTG 60.904 66.667 0.00 0.00 0.00 4.85
1536 1643 2.394563 GCTGCTCCTCAAGGCGAAC 61.395 63.158 0.00 0.00 34.44 3.95
1593 1700 1.878953 TCAGCGAGGTTTTCAAGGTC 58.121 50.000 0.00 0.00 0.00 3.85
1597 1704 1.542547 GCGAGGTTTTCAAGGTCCTCA 60.543 52.381 10.07 0.00 44.53 3.86
1599 1706 2.155279 GAGGTTTTCAAGGTCCTCAGC 58.845 52.381 0.00 0.00 43.95 4.26
1680 1787 1.144936 CCAGCCCGAAGAGGTCATC 59.855 63.158 0.00 0.00 38.74 2.92
1681 1788 1.617018 CCAGCCCGAAGAGGTCATCA 61.617 60.000 0.00 0.00 38.74 3.07
1831 1938 5.012893 TGAGTGGCTCGTATGATAGATGAT 58.987 41.667 0.00 0.00 32.35 2.45
1941 2049 0.678048 GGCCTACCACAAGCAAGGAG 60.678 60.000 0.00 0.00 35.26 3.69
2044 2155 3.149196 ACGAGCAAAGAATTGACATGGT 58.851 40.909 0.00 0.00 38.94 3.55
2049 2160 2.819608 CAAAGAATTGACATGGTCGGGT 59.180 45.455 0.00 0.00 38.94 5.28
2051 2162 4.503714 AAGAATTGACATGGTCGGGTAT 57.496 40.909 0.00 0.00 34.95 2.73
2052 2163 3.808728 AGAATTGACATGGTCGGGTATG 58.191 45.455 0.00 0.00 34.95 2.39
2235 2352 3.402628 TTTCAAGCAGTACCTCCACTC 57.597 47.619 0.00 0.00 0.00 3.51
2283 2402 2.845363 TAGGTCGGTCCACCTTTTTC 57.155 50.000 15.56 0.00 45.24 2.29
2287 2406 2.292569 GGTCGGTCCACCTTTTTCTTTC 59.707 50.000 3.87 0.00 35.97 2.62
2290 2409 2.304092 GGTCCACCTTTTTCTTTCCGT 58.696 47.619 0.00 0.00 0.00 4.69
2296 2415 4.261447 CCACCTTTTTCTTTCCGTCGAAAT 60.261 41.667 0.00 0.00 37.36 2.17
2315 2434 8.907685 GTCGAAATCATAGAACAATAGCTCTAC 58.092 37.037 0.00 0.00 0.00 2.59
2381 2501 1.831736 CTACCCGTCCCAGTCAAATCT 59.168 52.381 0.00 0.00 0.00 2.40
2390 2510 5.248640 GTCCCAGTCAAATCTCTCATCAAA 58.751 41.667 0.00 0.00 0.00 2.69
2396 2516 7.555554 CCAGTCAAATCTCTCATCAAAGGTTAT 59.444 37.037 0.00 0.00 0.00 1.89
2413 2533 7.907841 AAGGTTATAATATTGGGGTTTGGTC 57.092 36.000 0.00 0.00 0.00 4.02
2414 2534 6.378745 AGGTTATAATATTGGGGTTTGGTCC 58.621 40.000 0.00 0.00 0.00 4.46
2415 2535 5.242171 GGTTATAATATTGGGGTTTGGTCCG 59.758 44.000 0.00 0.00 0.00 4.79
2416 2536 2.153034 AATATTGGGGTTTGGTCCGG 57.847 50.000 0.00 0.00 0.00 5.14
2417 2537 1.300927 ATATTGGGGTTTGGTCCGGA 58.699 50.000 0.00 0.00 0.00 5.14
2418 2538 1.073931 TATTGGGGTTTGGTCCGGAA 58.926 50.000 5.23 0.00 0.00 4.30
2419 2539 0.188834 ATTGGGGTTTGGTCCGGAAA 59.811 50.000 5.23 0.00 0.00 3.13
2420 2540 0.032416 TTGGGGTTTGGTCCGGAAAA 60.032 50.000 5.23 0.20 0.00 2.29
2421 2541 0.188834 TGGGGTTTGGTCCGGAAAAT 59.811 50.000 5.23 0.00 0.00 1.82
2422 2542 1.428139 TGGGGTTTGGTCCGGAAAATA 59.572 47.619 5.23 0.00 0.00 1.40
2423 2543 1.820519 GGGGTTTGGTCCGGAAAATAC 59.179 52.381 5.23 2.48 0.00 1.89
2424 2544 2.516906 GGGTTTGGTCCGGAAAATACA 58.483 47.619 5.23 0.00 0.00 2.29
2425 2545 2.229543 GGGTTTGGTCCGGAAAATACAC 59.770 50.000 5.23 0.00 0.00 2.90
2426 2546 2.885894 GGTTTGGTCCGGAAAATACACA 59.114 45.455 5.23 0.00 0.00 3.72
2427 2547 3.057806 GGTTTGGTCCGGAAAATACACAG 60.058 47.826 5.23 0.00 0.00 3.66
2428 2548 2.483014 TGGTCCGGAAAATACACAGG 57.517 50.000 5.23 0.00 0.00 4.00
2429 2549 1.979308 TGGTCCGGAAAATACACAGGA 59.021 47.619 5.23 0.00 0.00 3.86
2430 2550 2.027561 TGGTCCGGAAAATACACAGGAG 60.028 50.000 5.23 0.00 31.82 3.69
2431 2551 2.007608 GTCCGGAAAATACACAGGAGC 58.992 52.381 5.23 0.00 31.82 4.70
2432 2552 1.906574 TCCGGAAAATACACAGGAGCT 59.093 47.619 0.00 0.00 0.00 4.09
2433 2553 2.093658 TCCGGAAAATACACAGGAGCTC 60.094 50.000 0.00 4.71 0.00 4.09
2434 2554 2.354704 CCGGAAAATACACAGGAGCTCA 60.355 50.000 17.19 0.00 0.00 4.26
2435 2555 2.673368 CGGAAAATACACAGGAGCTCAC 59.327 50.000 17.19 5.01 0.00 3.51
2436 2556 3.674997 GGAAAATACACAGGAGCTCACA 58.325 45.455 17.19 0.00 0.00 3.58
2437 2557 3.437049 GGAAAATACACAGGAGCTCACAC 59.563 47.826 17.19 0.00 0.00 3.82
2438 2558 2.770164 AATACACAGGAGCTCACACC 57.230 50.000 17.19 0.00 0.00 4.16
2439 2559 0.905357 ATACACAGGAGCTCACACCC 59.095 55.000 17.19 0.00 0.00 4.61
2440 2560 1.192146 TACACAGGAGCTCACACCCC 61.192 60.000 17.19 0.00 0.00 4.95
2441 2561 2.205462 ACAGGAGCTCACACCCCT 59.795 61.111 17.19 0.00 0.00 4.79
2442 2562 0.904865 CACAGGAGCTCACACCCCTA 60.905 60.000 17.19 0.00 0.00 3.53
2443 2563 0.043334 ACAGGAGCTCACACCCCTAT 59.957 55.000 17.19 0.00 0.00 2.57
2444 2564 1.291033 ACAGGAGCTCACACCCCTATA 59.709 52.381 17.19 0.00 0.00 1.31
2445 2565 1.689273 CAGGAGCTCACACCCCTATAC 59.311 57.143 17.19 0.00 0.00 1.47
2446 2566 0.674534 GGAGCTCACACCCCTATACG 59.325 60.000 17.19 0.00 0.00 3.06
2447 2567 1.688772 GAGCTCACACCCCTATACGA 58.311 55.000 9.40 0.00 0.00 3.43
2448 2568 2.029623 GAGCTCACACCCCTATACGAA 58.970 52.381 9.40 0.00 0.00 3.85
2449 2569 2.628657 GAGCTCACACCCCTATACGAAT 59.371 50.000 9.40 0.00 0.00 3.34
2450 2570 3.825014 GAGCTCACACCCCTATACGAATA 59.175 47.826 9.40 0.00 0.00 1.75
2451 2571 4.417437 AGCTCACACCCCTATACGAATAT 58.583 43.478 0.00 0.00 0.00 1.28
2452 2572 4.838986 AGCTCACACCCCTATACGAATATT 59.161 41.667 0.00 0.00 0.00 1.28
2453 2573 6.014647 AGCTCACACCCCTATACGAATATTA 58.985 40.000 0.00 0.00 0.00 0.98
2454 2574 6.495872 AGCTCACACCCCTATACGAATATTAA 59.504 38.462 0.00 0.00 0.00 1.40
2455 2575 7.015877 AGCTCACACCCCTATACGAATATTAAA 59.984 37.037 0.00 0.00 0.00 1.52
2456 2576 7.822822 GCTCACACCCCTATACGAATATTAAAT 59.177 37.037 0.00 0.00 0.00 1.40
2457 2577 9.151471 CTCACACCCCTATACGAATATTAAATG 57.849 37.037 0.00 0.00 0.00 2.32
2458 2578 8.653191 TCACACCCCTATACGAATATTAAATGT 58.347 33.333 0.00 0.00 0.00 2.71
2459 2579 9.932207 CACACCCCTATACGAATATTAAATGTA 57.068 33.333 0.00 0.00 0.00 2.29
2509 2629 9.671279 AAAATCTGAAATTTGGGGATATCAAAC 57.329 29.630 4.83 0.00 37.00 2.93
2510 2630 6.790232 TCTGAAATTTGGGGATATCAAACC 57.210 37.500 4.83 4.34 37.00 3.27
2511 2631 6.502138 TCTGAAATTTGGGGATATCAAACCT 58.498 36.000 4.83 0.00 37.00 3.50
2512 2632 6.380846 TCTGAAATTTGGGGATATCAAACCTG 59.619 38.462 4.83 0.00 37.00 4.00
2513 2633 5.424895 TGAAATTTGGGGATATCAAACCTGG 59.575 40.000 4.83 0.00 37.00 4.45
2514 2634 4.625225 ATTTGGGGATATCAAACCTGGT 57.375 40.909 4.83 0.00 37.00 4.00
2515 2635 4.412060 TTTGGGGATATCAAACCTGGTT 57.588 40.909 6.18 6.18 0.00 3.67
2516 2636 4.412060 TTGGGGATATCAAACCTGGTTT 57.588 40.909 18.84 18.84 36.05 3.27
2517 2637 3.976015 TGGGGATATCAAACCTGGTTTC 58.024 45.455 21.49 10.43 33.10 2.78
2518 2638 3.596046 TGGGGATATCAAACCTGGTTTCT 59.404 43.478 21.49 14.10 33.10 2.52
2519 2639 4.207955 GGGGATATCAAACCTGGTTTCTC 58.792 47.826 21.49 10.40 33.10 2.87
2520 2640 4.325030 GGGGATATCAAACCTGGTTTCTCA 60.325 45.833 21.49 9.38 33.10 3.27
2521 2641 5.261216 GGGATATCAAACCTGGTTTCTCAA 58.739 41.667 21.49 8.45 33.10 3.02
2522 2642 5.893824 GGGATATCAAACCTGGTTTCTCAAT 59.106 40.000 21.49 14.27 33.10 2.57
2523 2643 6.039829 GGGATATCAAACCTGGTTTCTCAATC 59.960 42.308 21.49 18.74 33.10 2.67
2524 2644 6.830838 GGATATCAAACCTGGTTTCTCAATCT 59.169 38.462 21.49 6.50 33.10 2.40
2525 2645 7.993183 GGATATCAAACCTGGTTTCTCAATCTA 59.007 37.037 21.49 6.63 33.10 1.98
2526 2646 9.566432 GATATCAAACCTGGTTTCTCAATCTAT 57.434 33.333 21.49 10.40 33.10 1.98
2527 2647 9.927081 ATATCAAACCTGGTTTCTCAATCTATT 57.073 29.630 21.49 0.00 33.10 1.73
2528 2648 7.687941 TCAAACCTGGTTTCTCAATCTATTC 57.312 36.000 21.49 0.00 33.10 1.75
2529 2649 6.659242 TCAAACCTGGTTTCTCAATCTATTCC 59.341 38.462 21.49 0.00 33.10 3.01
2530 2650 6.394345 AACCTGGTTTCTCAATCTATTCCT 57.606 37.500 6.18 0.00 0.00 3.36
2531 2651 5.749462 ACCTGGTTTCTCAATCTATTCCTG 58.251 41.667 0.00 0.00 0.00 3.86
2532 2652 5.251700 ACCTGGTTTCTCAATCTATTCCTGT 59.748 40.000 0.00 0.00 0.00 4.00
2533 2653 5.587844 CCTGGTTTCTCAATCTATTCCTGTG 59.412 44.000 0.00 0.00 0.00 3.66
2534 2654 6.126863 TGGTTTCTCAATCTATTCCTGTGT 57.873 37.500 0.00 0.00 0.00 3.72
2535 2655 5.939883 TGGTTTCTCAATCTATTCCTGTGTG 59.060 40.000 0.00 0.00 0.00 3.82
2536 2656 6.173339 GGTTTCTCAATCTATTCCTGTGTGA 58.827 40.000 0.00 0.00 0.00 3.58
2537 2657 6.655003 GGTTTCTCAATCTATTCCTGTGTGAA 59.345 38.462 0.00 0.00 0.00 3.18
2538 2658 7.174946 GGTTTCTCAATCTATTCCTGTGTGAAA 59.825 37.037 0.00 0.00 32.39 2.69
2539 2659 8.734386 GTTTCTCAATCTATTCCTGTGTGAAAT 58.266 33.333 0.00 0.00 35.44 2.17
2540 2660 8.868522 TTCTCAATCTATTCCTGTGTGAAATT 57.131 30.769 0.00 0.00 0.00 1.82
2541 2661 8.868522 TCTCAATCTATTCCTGTGTGAAATTT 57.131 30.769 0.00 0.00 0.00 1.82
2542 2662 8.950210 TCTCAATCTATTCCTGTGTGAAATTTC 58.050 33.333 11.41 11.41 0.00 2.17
2543 2663 8.634335 TCAATCTATTCCTGTGTGAAATTTCA 57.366 30.769 16.91 16.91 34.20 2.69
2544 2664 9.246670 TCAATCTATTCCTGTGTGAAATTTCAT 57.753 29.630 23.05 7.89 39.73 2.57
2545 2665 9.297586 CAATCTATTCCTGTGTGAAATTTCATG 57.702 33.333 23.05 13.35 39.73 3.07
2546 2666 8.812513 ATCTATTCCTGTGTGAAATTTCATGA 57.187 30.769 23.05 10.91 39.73 3.07
2547 2667 8.634335 TCTATTCCTGTGTGAAATTTCATGAA 57.366 30.769 23.05 18.50 39.73 2.57
2548 2668 9.076781 TCTATTCCTGTGTGAAATTTCATGAAA 57.923 29.630 23.05 22.52 39.73 2.69
2549 2669 9.695526 CTATTCCTGTGTGAAATTTCATGAAAA 57.304 29.630 23.91 13.16 39.73 2.29
2550 2670 8.597662 ATTCCTGTGTGAAATTTCATGAAAAG 57.402 30.769 23.91 15.26 39.73 2.27
2551 2671 7.345422 TCCTGTGTGAAATTTCATGAAAAGA 57.655 32.000 23.91 13.18 39.73 2.52
2552 2672 7.780064 TCCTGTGTGAAATTTCATGAAAAGAA 58.220 30.769 23.91 8.29 39.73 2.52
2553 2673 8.423349 TCCTGTGTGAAATTTCATGAAAAGAAT 58.577 29.630 23.91 10.82 39.73 2.40
2554 2674 9.695526 CCTGTGTGAAATTTCATGAAAAGAATA 57.304 29.630 23.91 7.96 39.73 1.75
2556 2676 9.474920 TGTGTGAAATTTCATGAAAAGAATACC 57.525 29.630 23.91 11.19 39.73 2.73
2557 2677 9.474920 GTGTGAAATTTCATGAAAAGAATACCA 57.525 29.630 23.91 12.11 39.73 3.25
2558 2678 9.695526 TGTGAAATTTCATGAAAAGAATACCAG 57.304 29.630 23.91 0.00 39.73 4.00
2559 2679 9.912634 GTGAAATTTCATGAAAAGAATACCAGA 57.087 29.630 23.91 0.00 39.73 3.86
2564 2684 8.795786 TTTCATGAAAAGAATACCAGAAAACG 57.204 30.769 18.45 0.00 0.00 3.60
2565 2685 7.504924 TCATGAAAAGAATACCAGAAAACGT 57.495 32.000 0.00 0.00 0.00 3.99
2566 2686 8.610248 TCATGAAAAGAATACCAGAAAACGTA 57.390 30.769 0.00 0.00 0.00 3.57
2567 2687 9.226606 TCATGAAAAGAATACCAGAAAACGTAT 57.773 29.630 0.00 0.00 0.00 3.06
2568 2688 9.490663 CATGAAAAGAATACCAGAAAACGTATC 57.509 33.333 0.00 0.00 0.00 2.24
2569 2689 8.842358 TGAAAAGAATACCAGAAAACGTATCT 57.158 30.769 0.00 0.00 0.00 1.98
2570 2690 8.717821 TGAAAAGAATACCAGAAAACGTATCTG 58.282 33.333 19.31 19.31 43.15 2.90
2571 2691 8.617290 AAAAGAATACCAGAAAACGTATCTGT 57.383 30.769 22.51 15.63 42.19 3.41
2572 2692 7.596749 AAGAATACCAGAAAACGTATCTGTG 57.403 36.000 22.51 17.64 42.19 3.66
2573 2693 6.106673 AGAATACCAGAAAACGTATCTGTGG 58.893 40.000 22.51 15.03 42.19 4.17
2574 2694 2.423577 ACCAGAAAACGTATCTGTGGC 58.576 47.619 22.51 0.00 42.19 5.01
2575 2695 1.393539 CCAGAAAACGTATCTGTGGCG 59.606 52.381 22.51 9.45 42.19 5.69
2576 2696 2.333926 CAGAAAACGTATCTGTGGCGA 58.666 47.619 18.42 0.00 39.54 5.54
2577 2697 2.734606 CAGAAAACGTATCTGTGGCGAA 59.265 45.455 18.42 0.00 39.54 4.70
2578 2698 2.993899 AGAAAACGTATCTGTGGCGAAG 59.006 45.455 3.20 0.00 0.00 3.79
2579 2699 1.722011 AAACGTATCTGTGGCGAAGG 58.278 50.000 0.00 0.00 0.00 3.46
2580 2700 0.892755 AACGTATCTGTGGCGAAGGA 59.107 50.000 0.00 0.00 0.00 3.36
2581 2701 0.892755 ACGTATCTGTGGCGAAGGAA 59.107 50.000 0.00 0.00 0.00 3.36
2582 2702 1.274167 ACGTATCTGTGGCGAAGGAAA 59.726 47.619 0.00 0.00 0.00 3.13
2583 2703 2.093658 ACGTATCTGTGGCGAAGGAAAT 60.094 45.455 0.00 0.00 0.00 2.17
2584 2704 3.131577 ACGTATCTGTGGCGAAGGAAATA 59.868 43.478 0.00 0.00 0.00 1.40
2585 2705 4.202223 ACGTATCTGTGGCGAAGGAAATAT 60.202 41.667 0.00 0.00 0.00 1.28
2586 2706 4.750098 CGTATCTGTGGCGAAGGAAATATT 59.250 41.667 0.00 0.00 0.00 1.28
2587 2707 5.333339 CGTATCTGTGGCGAAGGAAATATTG 60.333 44.000 0.00 0.00 0.00 1.90
2588 2708 3.950397 TCTGTGGCGAAGGAAATATTGT 58.050 40.909 0.00 0.00 0.00 2.71
2589 2709 3.938963 TCTGTGGCGAAGGAAATATTGTC 59.061 43.478 0.00 0.00 0.00 3.18
2590 2710 3.013921 TGTGGCGAAGGAAATATTGTCC 58.986 45.455 8.01 8.01 35.17 4.02
2591 2711 2.031683 GTGGCGAAGGAAATATTGTCCG 59.968 50.000 9.58 0.00 40.36 4.79
2592 2712 2.093394 TGGCGAAGGAAATATTGTCCGA 60.093 45.455 9.58 0.00 40.36 4.55
2593 2713 2.544267 GGCGAAGGAAATATTGTCCGAG 59.456 50.000 9.58 7.37 40.36 4.63
2594 2714 2.032808 GCGAAGGAAATATTGTCCGAGC 60.033 50.000 9.58 11.35 40.36 5.03
2595 2715 3.194861 CGAAGGAAATATTGTCCGAGCA 58.805 45.455 9.58 0.00 40.36 4.26
2596 2716 3.621268 CGAAGGAAATATTGTCCGAGCAA 59.379 43.478 9.58 0.00 40.36 3.91
2597 2717 4.094294 CGAAGGAAATATTGTCCGAGCAAA 59.906 41.667 9.58 0.00 40.36 3.68
2598 2718 5.391523 CGAAGGAAATATTGTCCGAGCAAAA 60.392 40.000 9.58 0.00 40.36 2.44
2599 2719 5.975693 AGGAAATATTGTCCGAGCAAAAA 57.024 34.783 9.58 0.00 40.36 1.94
2600 2720 6.530019 AGGAAATATTGTCCGAGCAAAAAT 57.470 33.333 9.58 0.00 40.36 1.82
2601 2721 6.564328 AGGAAATATTGTCCGAGCAAAAATC 58.436 36.000 9.58 0.00 40.36 2.17
2602 2722 6.378280 AGGAAATATTGTCCGAGCAAAAATCT 59.622 34.615 9.58 0.00 40.36 2.40
2603 2723 6.473455 GGAAATATTGTCCGAGCAAAAATCTG 59.527 38.462 0.00 0.00 31.63 2.90
2604 2724 6.515272 AATATTGTCCGAGCAAAAATCTGT 57.485 33.333 0.00 0.00 31.63 3.41
2605 2725 3.896648 TTGTCCGAGCAAAAATCTGTC 57.103 42.857 0.00 0.00 0.00 3.51
2606 2726 2.151202 TGTCCGAGCAAAAATCTGTCC 58.849 47.619 0.00 0.00 0.00 4.02
2607 2727 2.151202 GTCCGAGCAAAAATCTGTCCA 58.849 47.619 0.00 0.00 0.00 4.02
2608 2728 2.552315 GTCCGAGCAAAAATCTGTCCAA 59.448 45.455 0.00 0.00 0.00 3.53
2609 2729 3.004315 GTCCGAGCAAAAATCTGTCCAAA 59.996 43.478 0.00 0.00 0.00 3.28
2610 2730 3.004315 TCCGAGCAAAAATCTGTCCAAAC 59.996 43.478 0.00 0.00 0.00 2.93
2611 2731 3.243367 CCGAGCAAAAATCTGTCCAAACA 60.243 43.478 0.00 0.00 0.00 2.83
2612 2732 4.549458 CGAGCAAAAATCTGTCCAAACAT 58.451 39.130 0.00 0.00 34.13 2.71
2613 2733 4.984161 CGAGCAAAAATCTGTCCAAACATT 59.016 37.500 0.00 0.00 34.13 2.71
2614 2734 5.463061 CGAGCAAAAATCTGTCCAAACATTT 59.537 36.000 0.00 0.00 34.13 2.32
2615 2735 6.018832 CGAGCAAAAATCTGTCCAAACATTTT 60.019 34.615 0.00 0.00 34.13 1.82
2616 2736 7.465781 CGAGCAAAAATCTGTCCAAACATTTTT 60.466 33.333 0.00 0.00 37.75 1.94
2666 2786 5.811399 TTTGCTACGGATACATTTTCTGG 57.189 39.130 0.00 0.00 0.00 3.86
2667 2787 4.481368 TGCTACGGATACATTTTCTGGT 57.519 40.909 0.00 0.00 0.00 4.00
2668 2788 5.601583 TGCTACGGATACATTTTCTGGTA 57.398 39.130 0.00 0.00 0.00 3.25
2669 2789 6.169557 TGCTACGGATACATTTTCTGGTAT 57.830 37.500 0.00 0.00 33.10 2.73
2670 2790 6.588204 TGCTACGGATACATTTTCTGGTATT 58.412 36.000 0.00 0.00 30.68 1.89
2671 2791 7.051623 TGCTACGGATACATTTTCTGGTATTT 58.948 34.615 0.00 0.00 30.68 1.40
2672 2792 7.554835 TGCTACGGATACATTTTCTGGTATTTT 59.445 33.333 0.00 0.00 30.68 1.82
2673 2793 8.403236 GCTACGGATACATTTTCTGGTATTTTT 58.597 33.333 0.00 0.00 30.68 1.94
2695 2815 7.504922 TTTTTCACGAAATTTCACACAGAAG 57.495 32.000 17.99 1.90 37.57 2.85
2696 2816 4.209452 TCACGAAATTTCACACAGAAGC 57.791 40.909 17.99 0.00 37.57 3.86
2697 2817 3.625313 TCACGAAATTTCACACAGAAGCA 59.375 39.130 17.99 0.00 37.57 3.91
2698 2818 3.970610 CACGAAATTTCACACAGAAGCAG 59.029 43.478 17.99 0.06 37.57 4.24
2699 2819 3.003689 ACGAAATTTCACACAGAAGCAGG 59.996 43.478 17.99 0.00 37.57 4.85
2700 2820 3.003689 CGAAATTTCACACAGAAGCAGGT 59.996 43.478 17.99 0.00 37.57 4.00
2701 2821 4.540824 GAAATTTCACACAGAAGCAGGTC 58.459 43.478 13.40 0.00 37.57 3.85
2702 2822 1.581934 TTTCACACAGAAGCAGGTCG 58.418 50.000 0.00 0.00 37.57 4.79
2703 2823 0.249868 TTCACACAGAAGCAGGTCGG 60.250 55.000 0.00 0.00 0.00 4.79
2704 2824 1.669115 CACACAGAAGCAGGTCGGG 60.669 63.158 0.00 0.00 0.00 5.14
2705 2825 1.837051 ACACAGAAGCAGGTCGGGA 60.837 57.895 0.00 0.00 0.00 5.14
2706 2826 1.371183 CACAGAAGCAGGTCGGGAA 59.629 57.895 0.00 0.00 0.00 3.97
2707 2827 0.951040 CACAGAAGCAGGTCGGGAAC 60.951 60.000 0.00 0.00 0.00 3.62
2723 2843 1.947456 GGAACCCAGGTTTGATATCGC 59.053 52.381 3.05 0.00 38.60 4.58
2724 2844 2.639065 GAACCCAGGTTTGATATCGCA 58.361 47.619 3.05 0.00 38.60 5.10
2725 2845 2.799126 ACCCAGGTTTGATATCGCAA 57.201 45.000 0.00 0.00 0.00 4.85
2726 2846 3.080300 ACCCAGGTTTGATATCGCAAA 57.920 42.857 0.00 0.00 35.54 3.68
2727 2847 3.426615 ACCCAGGTTTGATATCGCAAAA 58.573 40.909 0.00 0.00 39.26 2.44
2728 2848 4.023291 ACCCAGGTTTGATATCGCAAAAT 58.977 39.130 0.00 0.00 39.26 1.82
2729 2849 4.097892 ACCCAGGTTTGATATCGCAAAATC 59.902 41.667 0.00 0.00 39.26 2.17
2730 2850 4.339247 CCCAGGTTTGATATCGCAAAATCT 59.661 41.667 0.00 0.00 39.26 2.40
2731 2851 5.506317 CCCAGGTTTGATATCGCAAAATCTC 60.506 44.000 0.00 0.00 39.26 2.75
2732 2852 5.066375 CCAGGTTTGATATCGCAAAATCTCA 59.934 40.000 0.00 0.00 39.26 3.27
2733 2853 6.197276 CAGGTTTGATATCGCAAAATCTCAG 58.803 40.000 0.00 0.00 39.26 3.35
2734 2854 6.037500 CAGGTTTGATATCGCAAAATCTCAGA 59.962 38.462 0.00 0.00 39.26 3.27
2735 2855 6.769822 AGGTTTGATATCGCAAAATCTCAGAT 59.230 34.615 0.00 0.00 39.26 2.90
2736 2856 7.284034 AGGTTTGATATCGCAAAATCTCAGATT 59.716 33.333 0.00 0.00 39.26 2.40
2737 2857 7.917505 GGTTTGATATCGCAAAATCTCAGATTT 59.082 33.333 6.83 6.83 39.26 2.17
2738 2858 9.294030 GTTTGATATCGCAAAATCTCAGATTTT 57.706 29.630 18.17 18.17 39.26 1.82
2739 2859 9.859427 TTTGATATCGCAAAATCTCAGATTTTT 57.141 25.926 20.80 10.55 35.03 1.94
2791 2911 8.857694 AATTTAATATTCGTATAGGGGTGTGG 57.142 34.615 0.00 0.00 0.00 4.17
2792 2912 7.615039 TTTAATATTCGTATAGGGGTGTGGA 57.385 36.000 0.00 0.00 0.00 4.02
2793 2913 5.740290 AATATTCGTATAGGGGTGTGGAG 57.260 43.478 0.00 0.00 0.00 3.86
2794 2914 1.117150 TTCGTATAGGGGTGTGGAGC 58.883 55.000 0.00 0.00 0.00 4.70
2795 2915 0.032912 TCGTATAGGGGTGTGGAGCA 60.033 55.000 0.00 0.00 0.00 4.26
2796 2916 0.104304 CGTATAGGGGTGTGGAGCAC 59.896 60.000 0.00 0.00 46.97 4.40
2814 2934 1.468520 CACCCAGGTGCTACAAATTCG 59.531 52.381 3.41 0.00 39.39 3.34
2815 2935 0.451783 CCCAGGTGCTACAAATTCGC 59.548 55.000 0.00 0.00 0.00 4.70
2816 2936 1.453155 CCAGGTGCTACAAATTCGCT 58.547 50.000 0.00 0.00 0.00 4.93
2817 2937 1.812571 CCAGGTGCTACAAATTCGCTT 59.187 47.619 0.00 0.00 0.00 4.68
2818 2938 2.159517 CCAGGTGCTACAAATTCGCTTC 60.160 50.000 0.00 0.00 0.00 3.86
2819 2939 2.084546 AGGTGCTACAAATTCGCTTCC 58.915 47.619 0.00 0.00 0.00 3.46
2820 2940 1.202031 GGTGCTACAAATTCGCTTCCG 60.202 52.381 0.00 0.00 0.00 4.30
2821 2941 1.083489 TGCTACAAATTCGCTTCCGG 58.917 50.000 0.00 0.00 34.56 5.14
2822 2942 1.084289 GCTACAAATTCGCTTCCGGT 58.916 50.000 0.00 0.00 34.56 5.28
2823 2943 1.467342 GCTACAAATTCGCTTCCGGTT 59.533 47.619 0.00 0.00 34.56 4.44
2824 2944 2.095415 GCTACAAATTCGCTTCCGGTTT 60.095 45.455 0.00 0.00 34.56 3.27
2825 2945 2.415697 ACAAATTCGCTTCCGGTTTG 57.584 45.000 0.00 5.58 41.60 2.93
2826 2946 1.000717 ACAAATTCGCTTCCGGTTTGG 60.001 47.619 13.89 0.00 40.91 3.28
2827 2947 1.000717 CAAATTCGCTTCCGGTTTGGT 60.001 47.619 0.00 0.00 37.10 3.67
2828 2948 1.324383 AATTCGCTTCCGGTTTGGTT 58.676 45.000 0.00 0.00 39.52 3.67
2829 2949 0.879090 ATTCGCTTCCGGTTTGGTTC 59.121 50.000 0.00 0.00 39.52 3.62
2830 2950 1.500512 TTCGCTTCCGGTTTGGTTCG 61.501 55.000 0.00 0.00 39.52 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.812571 CATGACGGGGTTGGAAAGAAG 59.187 52.381 0.00 0.00 0.00 2.85
29 30 0.474614 TCACATGACGGGGTTGGAAA 59.525 50.000 0.00 0.00 0.00 3.13
31 32 1.373435 GTCACATGACGGGGTTGGA 59.627 57.895 0.00 0.00 35.12 3.53
149 153 1.795768 ACAGTGAACATGCCTACGTG 58.204 50.000 0.00 0.00 38.85 4.49
199 203 9.791820 TGAACATAGAAAAACATGCAATATCAG 57.208 29.630 0.00 0.00 0.00 2.90
203 207 9.409312 CAGTTGAACATAGAAAAACATGCAATA 57.591 29.630 0.00 0.00 0.00 1.90
260 264 9.719279 AAGTCACAATTGCAAAAATACAAAATG 57.281 25.926 1.71 0.00 0.00 2.32
383 389 5.689383 AACAATTGCAACGAGTACAGATT 57.311 34.783 0.00 0.00 0.00 2.40
384 390 5.689383 AAACAATTGCAACGAGTACAGAT 57.311 34.783 0.00 0.00 0.00 2.90
386 392 5.510671 AGAAAACAATTGCAACGAGTACAG 58.489 37.500 0.00 0.00 0.00 2.74
430 436 1.202639 TCTCTTTGCACCTCTTCGCAA 60.203 47.619 0.00 0.00 45.93 4.85
474 482 1.059692 GATCGCATATCATCCAACGCG 59.940 52.381 3.53 3.53 43.80 6.01
477 485 4.692155 TCACATGATCGCATATCATCCAAC 59.308 41.667 0.00 0.00 36.69 3.77
490 498 1.001624 ACGTGCATGTCACATGATCG 58.998 50.000 22.56 23.29 45.92 3.69
509 517 0.179150 GTTGGCGCAACTCACACAAA 60.179 50.000 10.83 0.00 40.73 2.83
620 631 3.306294 GGTCTGCCATTTTCTTTTCCCTG 60.306 47.826 0.00 0.00 34.09 4.45
654 665 8.924691 CAAAAACAAATCTGTCACTTTCTTTCA 58.075 29.630 0.00 0.00 33.45 2.69
674 685 5.109210 CCACTTTCTTTCCCTCACAAAAAC 58.891 41.667 0.00 0.00 0.00 2.43
965 1052 1.439679 CTGTAGGACGGAAACCTTGC 58.560 55.000 0.00 0.00 38.76 4.01
974 1061 4.514577 CAGGGCGCTGTAGGACGG 62.515 72.222 21.92 0.00 0.00 4.79
991 1078 3.285215 CATCTGCATGGCGAGGGC 61.285 66.667 0.00 0.00 38.90 5.19
1042 1137 3.918220 CTTGATCAGCGCCGCGAC 61.918 66.667 18.91 8.07 0.00 5.19
1077 1172 2.617274 GGCCACGTTCTGCAGTTCC 61.617 63.158 14.67 1.79 0.00 3.62
1252 1359 1.368850 GCGTGTTGTTGAAGGCGAC 60.369 57.895 0.00 0.00 0.00 5.19
1346 1453 1.890979 GGCGAGATGCTGATGGTGG 60.891 63.158 0.00 0.00 45.43 4.61
1593 1700 0.594540 CGCTTCTCATCTCGCTGAGG 60.595 60.000 8.86 0.00 42.42 3.86
1597 1704 1.001487 CATCTCGCTTCTCATCTCGCT 60.001 52.381 0.00 0.00 0.00 4.93
1599 1706 1.606189 TCCATCTCGCTTCTCATCTCG 59.394 52.381 0.00 0.00 0.00 4.04
1692 1799 1.579698 CGTGCTCATCTTGATCTGGG 58.420 55.000 0.00 0.00 0.00 4.45
1698 1805 1.446099 GTCGGCGTGCTCATCTTGA 60.446 57.895 6.85 0.00 0.00 3.02
1831 1938 2.926901 AATAACGTGCCGCGGCCATA 62.927 55.000 44.42 30.26 46.52 2.74
1922 2030 0.678048 CTCCTTGCTTGTGGTAGGCC 60.678 60.000 0.00 0.00 0.00 5.19
1944 2052 3.074999 GCCGCTCTGGTCTCTGGAG 62.075 68.421 0.00 0.00 41.21 3.86
2044 2155 4.481368 AACATTGCTAAGACATACCCGA 57.519 40.909 0.00 0.00 0.00 5.14
2049 2160 7.986889 TCAGCTTGATAACATTGCTAAGACATA 59.013 33.333 0.00 0.00 35.59 2.29
2051 2162 6.092670 GTCAGCTTGATAACATTGCTAAGACA 59.907 38.462 10.79 0.00 35.59 3.41
2052 2163 6.092670 TGTCAGCTTGATAACATTGCTAAGAC 59.907 38.462 0.00 9.67 35.59 3.01
2235 2352 2.743664 TCAGTCAACAATGATGCGAAGG 59.256 45.455 0.00 0.00 38.01 3.46
2283 2402 6.403333 TTGTTCTATGATTTCGACGGAAAG 57.597 37.500 0.00 0.00 44.81 2.62
2287 2406 5.692204 AGCTATTGTTCTATGATTTCGACGG 59.308 40.000 0.00 0.00 0.00 4.79
2290 2409 7.803659 CGTAGAGCTATTGTTCTATGATTTCGA 59.196 37.037 12.64 0.00 42.14 3.71
2342 2461 6.255020 CGGGTAGACGGCATTTATACATATTC 59.745 42.308 0.00 0.00 0.00 1.75
2351 2470 0.461135 GGACGGGTAGACGGCATTTA 59.539 55.000 0.00 0.00 45.67 1.40
2357 2476 2.362120 ACTGGGACGGGTAGACGG 60.362 66.667 0.00 0.00 40.47 4.79
2381 2501 8.732854 ACCCCAATATTATAACCTTTGATGAGA 58.267 33.333 5.76 0.00 0.00 3.27
2390 2510 6.378745 GGACCAAACCCCAATATTATAACCT 58.621 40.000 0.00 0.00 0.00 3.50
2396 2516 2.851194 TCCGGACCAAACCCCAATATTA 59.149 45.455 0.00 0.00 0.00 0.98
2398 2518 1.300927 TCCGGACCAAACCCCAATAT 58.699 50.000 0.00 0.00 0.00 1.28
2402 2522 0.188834 ATTTTCCGGACCAAACCCCA 59.811 50.000 1.83 0.00 0.00 4.96
2404 2524 2.229543 GTGTATTTTCCGGACCAAACCC 59.770 50.000 1.83 0.00 0.00 4.11
2413 2533 2.280628 GAGCTCCTGTGTATTTTCCGG 58.719 52.381 0.87 0.00 0.00 5.14
2414 2534 2.673368 GTGAGCTCCTGTGTATTTTCCG 59.327 50.000 12.15 0.00 0.00 4.30
2415 2535 3.437049 GTGTGAGCTCCTGTGTATTTTCC 59.563 47.826 12.15 0.00 0.00 3.13
2416 2536 3.437049 GGTGTGAGCTCCTGTGTATTTTC 59.563 47.826 12.15 0.00 0.00 2.29
2417 2537 3.412386 GGTGTGAGCTCCTGTGTATTTT 58.588 45.455 12.15 0.00 0.00 1.82
2418 2538 2.290323 GGGTGTGAGCTCCTGTGTATTT 60.290 50.000 12.15 0.00 0.00 1.40
2419 2539 1.279271 GGGTGTGAGCTCCTGTGTATT 59.721 52.381 12.15 0.00 0.00 1.89
2420 2540 0.905357 GGGTGTGAGCTCCTGTGTAT 59.095 55.000 12.15 0.00 0.00 2.29
2421 2541 1.192146 GGGGTGTGAGCTCCTGTGTA 61.192 60.000 12.15 0.00 0.00 2.90
2422 2542 2.520536 GGGGTGTGAGCTCCTGTGT 61.521 63.158 12.15 0.00 0.00 3.72
2423 2543 0.904865 TAGGGGTGTGAGCTCCTGTG 60.905 60.000 12.15 0.00 0.00 3.66
2424 2544 0.043334 ATAGGGGTGTGAGCTCCTGT 59.957 55.000 12.15 0.00 0.00 4.00
2425 2545 1.689273 GTATAGGGGTGTGAGCTCCTG 59.311 57.143 12.15 0.00 0.00 3.86
2426 2546 1.754555 CGTATAGGGGTGTGAGCTCCT 60.755 57.143 12.15 2.58 0.00 3.69
2427 2547 0.674534 CGTATAGGGGTGTGAGCTCC 59.325 60.000 12.15 3.09 0.00 4.70
2428 2548 1.688772 TCGTATAGGGGTGTGAGCTC 58.311 55.000 6.82 6.82 0.00 4.09
2429 2549 2.154567 TTCGTATAGGGGTGTGAGCT 57.845 50.000 0.00 0.00 0.00 4.09
2430 2550 4.803098 ATATTCGTATAGGGGTGTGAGC 57.197 45.455 0.00 0.00 0.00 4.26
2431 2551 9.151471 CATTTAATATTCGTATAGGGGTGTGAG 57.849 37.037 0.00 0.00 0.00 3.51
2432 2552 8.653191 ACATTTAATATTCGTATAGGGGTGTGA 58.347 33.333 0.00 0.00 0.00 3.58
2433 2553 8.842358 ACATTTAATATTCGTATAGGGGTGTG 57.158 34.615 0.00 0.00 0.00 3.82
2483 2603 9.671279 GTTTGATATCCCCAAATTTCAGATTTT 57.329 29.630 0.00 0.00 36.14 1.82
2484 2604 8.267183 GGTTTGATATCCCCAAATTTCAGATTT 58.733 33.333 0.00 0.00 36.14 2.17
2485 2605 7.624879 AGGTTTGATATCCCCAAATTTCAGATT 59.375 33.333 0.00 0.00 36.14 2.40
2486 2606 7.070322 CAGGTTTGATATCCCCAAATTTCAGAT 59.930 37.037 0.00 0.00 36.14 2.90
2487 2607 6.380846 CAGGTTTGATATCCCCAAATTTCAGA 59.619 38.462 0.00 0.00 36.14 3.27
2488 2608 6.407299 CCAGGTTTGATATCCCCAAATTTCAG 60.407 42.308 0.00 0.00 36.14 3.02
2489 2609 5.424895 CCAGGTTTGATATCCCCAAATTTCA 59.575 40.000 0.00 0.00 36.14 2.69
2490 2610 5.425217 ACCAGGTTTGATATCCCCAAATTTC 59.575 40.000 0.00 0.00 36.14 2.17
2491 2611 5.349690 ACCAGGTTTGATATCCCCAAATTT 58.650 37.500 0.00 0.00 36.14 1.82
2492 2612 4.959080 ACCAGGTTTGATATCCCCAAATT 58.041 39.130 0.00 0.00 36.14 1.82
2493 2613 4.625225 ACCAGGTTTGATATCCCCAAAT 57.375 40.909 0.00 0.00 36.14 2.32
2494 2614 4.412060 AACCAGGTTTGATATCCCCAAA 57.588 40.909 0.00 0.00 0.00 3.28
2495 2615 4.045334 AGAAACCAGGTTTGATATCCCCAA 59.955 41.667 22.98 0.00 35.77 4.12
2496 2616 3.596046 AGAAACCAGGTTTGATATCCCCA 59.404 43.478 22.98 0.00 35.77 4.96
2497 2617 4.207955 GAGAAACCAGGTTTGATATCCCC 58.792 47.826 22.98 5.21 35.77 4.81
2498 2618 4.855340 TGAGAAACCAGGTTTGATATCCC 58.145 43.478 22.98 5.95 35.77 3.85
2499 2619 6.830838 AGATTGAGAAACCAGGTTTGATATCC 59.169 38.462 22.98 6.69 35.77 2.59
2500 2620 7.872113 AGATTGAGAAACCAGGTTTGATATC 57.128 36.000 22.98 16.90 35.77 1.63
2501 2621 9.927081 AATAGATTGAGAAACCAGGTTTGATAT 57.073 29.630 22.98 9.80 35.77 1.63
2502 2622 9.396022 GAATAGATTGAGAAACCAGGTTTGATA 57.604 33.333 22.98 5.05 35.77 2.15
2503 2623 7.340487 GGAATAGATTGAGAAACCAGGTTTGAT 59.660 37.037 22.98 10.57 35.77 2.57
2504 2624 6.659242 GGAATAGATTGAGAAACCAGGTTTGA 59.341 38.462 22.98 5.95 35.77 2.69
2505 2625 6.660949 AGGAATAGATTGAGAAACCAGGTTTG 59.339 38.462 22.98 0.00 35.77 2.93
2506 2626 6.660949 CAGGAATAGATTGAGAAACCAGGTTT 59.339 38.462 18.10 18.10 38.54 3.27
2507 2627 6.183347 CAGGAATAGATTGAGAAACCAGGTT 58.817 40.000 0.00 0.00 0.00 3.50
2508 2628 5.251700 ACAGGAATAGATTGAGAAACCAGGT 59.748 40.000 0.00 0.00 0.00 4.00
2509 2629 5.587844 CACAGGAATAGATTGAGAAACCAGG 59.412 44.000 0.00 0.00 0.00 4.45
2510 2630 6.093219 CACACAGGAATAGATTGAGAAACCAG 59.907 42.308 0.00 0.00 0.00 4.00
2511 2631 5.939883 CACACAGGAATAGATTGAGAAACCA 59.060 40.000 0.00 0.00 0.00 3.67
2512 2632 6.173339 TCACACAGGAATAGATTGAGAAACC 58.827 40.000 0.00 0.00 0.00 3.27
2513 2633 7.672983 TTCACACAGGAATAGATTGAGAAAC 57.327 36.000 0.00 0.00 0.00 2.78
2514 2634 8.868522 ATTTCACACAGGAATAGATTGAGAAA 57.131 30.769 0.00 0.00 0.00 2.52
2515 2635 8.868522 AATTTCACACAGGAATAGATTGAGAA 57.131 30.769 0.00 0.00 0.00 2.87
2516 2636 8.868522 AAATTTCACACAGGAATAGATTGAGA 57.131 30.769 0.00 0.00 0.00 3.27
2517 2637 8.733458 TGAAATTTCACACAGGAATAGATTGAG 58.267 33.333 16.91 0.00 31.01 3.02
2518 2638 8.634335 TGAAATTTCACACAGGAATAGATTGA 57.366 30.769 16.91 0.00 31.01 2.57
2519 2639 9.297586 CATGAAATTTCACACAGGAATAGATTG 57.702 33.333 22.71 8.39 40.49 2.67
2520 2640 9.246670 TCATGAAATTTCACACAGGAATAGATT 57.753 29.630 22.71 0.00 40.49 2.40
2521 2641 8.812513 TCATGAAATTTCACACAGGAATAGAT 57.187 30.769 22.71 0.00 40.49 1.98
2522 2642 8.634335 TTCATGAAATTTCACACAGGAATAGA 57.366 30.769 22.71 5.99 40.49 1.98
2523 2643 9.695526 TTTTCATGAAATTTCACACAGGAATAG 57.304 29.630 22.71 4.00 40.49 1.73
2524 2644 9.695526 CTTTTCATGAAATTTCACACAGGAATA 57.304 29.630 22.71 13.94 40.49 1.75
2525 2645 8.423349 TCTTTTCATGAAATTTCACACAGGAAT 58.577 29.630 22.71 1.94 40.49 3.01
2526 2646 7.780064 TCTTTTCATGAAATTTCACACAGGAA 58.220 30.769 22.71 16.65 40.49 3.36
2527 2647 7.345422 TCTTTTCATGAAATTTCACACAGGA 57.655 32.000 22.71 13.41 40.49 3.86
2528 2648 8.597662 ATTCTTTTCATGAAATTTCACACAGG 57.402 30.769 22.71 11.55 40.49 4.00
2530 2650 9.474920 GGTATTCTTTTCATGAAATTTCACACA 57.525 29.630 22.71 7.19 40.49 3.72
2531 2651 9.474920 TGGTATTCTTTTCATGAAATTTCACAC 57.525 29.630 22.71 13.93 40.49 3.82
2532 2652 9.695526 CTGGTATTCTTTTCATGAAATTTCACA 57.304 29.630 22.71 10.04 40.49 3.58
2533 2653 9.912634 TCTGGTATTCTTTTCATGAAATTTCAC 57.087 29.630 22.71 14.37 40.49 3.18
2538 2658 9.410556 CGTTTTCTGGTATTCTTTTCATGAAAT 57.589 29.630 21.10 9.25 0.00 2.17
2539 2659 8.410141 ACGTTTTCTGGTATTCTTTTCATGAAA 58.590 29.630 16.91 16.91 0.00 2.69
2540 2660 7.936584 ACGTTTTCTGGTATTCTTTTCATGAA 58.063 30.769 3.38 3.38 0.00 2.57
2541 2661 7.504924 ACGTTTTCTGGTATTCTTTTCATGA 57.495 32.000 0.00 0.00 0.00 3.07
2542 2662 9.490663 GATACGTTTTCTGGTATTCTTTTCATG 57.509 33.333 0.00 0.00 29.86 3.07
2543 2663 9.449719 AGATACGTTTTCTGGTATTCTTTTCAT 57.550 29.630 0.00 0.00 29.86 2.57
2544 2664 8.717821 CAGATACGTTTTCTGGTATTCTTTTCA 58.282 33.333 16.44 0.00 37.53 2.69
2545 2665 8.718734 ACAGATACGTTTTCTGGTATTCTTTTC 58.281 33.333 23.87 0.00 43.95 2.29
2546 2666 8.504005 CACAGATACGTTTTCTGGTATTCTTTT 58.496 33.333 23.87 5.30 43.95 2.27
2547 2667 7.119262 CCACAGATACGTTTTCTGGTATTCTTT 59.881 37.037 23.87 5.83 43.95 2.52
2548 2668 6.594159 CCACAGATACGTTTTCTGGTATTCTT 59.406 38.462 23.87 6.37 43.95 2.52
2549 2669 6.106673 CCACAGATACGTTTTCTGGTATTCT 58.893 40.000 23.87 6.91 43.95 2.40
2550 2670 5.220605 GCCACAGATACGTTTTCTGGTATTC 60.221 44.000 23.87 10.48 43.95 1.75
2551 2671 4.634443 GCCACAGATACGTTTTCTGGTATT 59.366 41.667 23.87 7.73 43.95 1.89
2552 2672 4.189231 GCCACAGATACGTTTTCTGGTAT 58.811 43.478 23.87 8.00 43.95 2.73
2553 2673 3.592059 GCCACAGATACGTTTTCTGGTA 58.408 45.455 23.87 0.00 43.95 3.25
2554 2674 2.423577 GCCACAGATACGTTTTCTGGT 58.576 47.619 23.87 12.25 43.95 4.00
2555 2675 1.393539 CGCCACAGATACGTTTTCTGG 59.606 52.381 23.87 14.03 43.95 3.86
2556 2676 2.333926 TCGCCACAGATACGTTTTCTG 58.666 47.619 20.50 20.50 44.95 3.02
2557 2677 2.736144 TCGCCACAGATACGTTTTCT 57.264 45.000 0.00 0.00 0.00 2.52
2558 2678 2.093783 CCTTCGCCACAGATACGTTTTC 59.906 50.000 0.00 0.00 0.00 2.29
2559 2679 2.073816 CCTTCGCCACAGATACGTTTT 58.926 47.619 0.00 0.00 0.00 2.43
2560 2680 1.274167 TCCTTCGCCACAGATACGTTT 59.726 47.619 0.00 0.00 0.00 3.60
2561 2681 0.892755 TCCTTCGCCACAGATACGTT 59.107 50.000 0.00 0.00 0.00 3.99
2562 2682 0.892755 TTCCTTCGCCACAGATACGT 59.107 50.000 0.00 0.00 0.00 3.57
2563 2683 2.004583 TTTCCTTCGCCACAGATACG 57.995 50.000 0.00 0.00 0.00 3.06
2564 2684 5.527582 ACAATATTTCCTTCGCCACAGATAC 59.472 40.000 0.00 0.00 0.00 2.24
2565 2685 5.680619 ACAATATTTCCTTCGCCACAGATA 58.319 37.500 0.00 0.00 0.00 1.98
2566 2686 4.526970 ACAATATTTCCTTCGCCACAGAT 58.473 39.130 0.00 0.00 0.00 2.90
2567 2687 3.938963 GACAATATTTCCTTCGCCACAGA 59.061 43.478 0.00 0.00 0.00 3.41
2568 2688 3.065371 GGACAATATTTCCTTCGCCACAG 59.935 47.826 8.56 0.00 0.00 3.66
2569 2689 3.013921 GGACAATATTTCCTTCGCCACA 58.986 45.455 8.56 0.00 0.00 4.17
2570 2690 2.031683 CGGACAATATTTCCTTCGCCAC 59.968 50.000 12.12 0.00 0.00 5.01
2571 2691 2.093394 TCGGACAATATTTCCTTCGCCA 60.093 45.455 12.12 0.00 0.00 5.69
2572 2692 2.544267 CTCGGACAATATTTCCTTCGCC 59.456 50.000 12.12 0.00 0.00 5.54
2573 2693 2.032808 GCTCGGACAATATTTCCTTCGC 60.033 50.000 12.12 8.93 0.00 4.70
2574 2694 3.194861 TGCTCGGACAATATTTCCTTCG 58.805 45.455 12.12 2.69 0.00 3.79
2575 2695 5.560966 TTTGCTCGGACAATATTTCCTTC 57.439 39.130 12.12 4.98 0.00 3.46
2576 2696 5.975693 TTTTGCTCGGACAATATTTCCTT 57.024 34.783 12.12 0.00 0.00 3.36
2577 2697 5.975693 TTTTTGCTCGGACAATATTTCCT 57.024 34.783 12.12 0.00 0.00 3.36
2578 2698 6.473455 CAGATTTTTGCTCGGACAATATTTCC 59.527 38.462 6.60 6.60 0.00 3.13
2579 2699 7.029563 ACAGATTTTTGCTCGGACAATATTTC 58.970 34.615 0.00 0.00 0.00 2.17
2580 2700 6.924111 ACAGATTTTTGCTCGGACAATATTT 58.076 32.000 0.00 0.00 0.00 1.40
2581 2701 6.404734 GGACAGATTTTTGCTCGGACAATATT 60.405 38.462 0.00 0.00 0.00 1.28
2582 2702 5.066505 GGACAGATTTTTGCTCGGACAATAT 59.933 40.000 0.00 0.00 0.00 1.28
2583 2703 4.394920 GGACAGATTTTTGCTCGGACAATA 59.605 41.667 0.00 0.00 0.00 1.90
2584 2704 3.191371 GGACAGATTTTTGCTCGGACAAT 59.809 43.478 0.00 0.00 0.00 2.71
2585 2705 2.552315 GGACAGATTTTTGCTCGGACAA 59.448 45.455 0.00 0.00 0.00 3.18
2586 2706 2.151202 GGACAGATTTTTGCTCGGACA 58.849 47.619 0.00 0.00 0.00 4.02
2587 2707 2.151202 TGGACAGATTTTTGCTCGGAC 58.849 47.619 0.00 0.00 0.00 4.79
2588 2708 2.559698 TGGACAGATTTTTGCTCGGA 57.440 45.000 0.00 0.00 0.00 4.55
2589 2709 3.243367 TGTTTGGACAGATTTTTGCTCGG 60.243 43.478 0.00 0.00 0.00 4.63
2590 2710 3.963665 TGTTTGGACAGATTTTTGCTCG 58.036 40.909 0.00 0.00 0.00 5.03
2591 2711 6.849588 AAATGTTTGGACAGATTTTTGCTC 57.150 33.333 0.00 0.00 39.58 4.26
2592 2712 7.628769 AAAAATGTTTGGACAGATTTTTGCT 57.371 28.000 0.00 0.00 36.94 3.91
2642 2762 6.207810 ACCAGAAAATGTATCCGTAGCAAAAA 59.792 34.615 0.00 0.00 0.00 1.94
2643 2763 5.708230 ACCAGAAAATGTATCCGTAGCAAAA 59.292 36.000 0.00 0.00 0.00 2.44
2644 2764 5.250200 ACCAGAAAATGTATCCGTAGCAAA 58.750 37.500 0.00 0.00 0.00 3.68
2645 2765 4.839121 ACCAGAAAATGTATCCGTAGCAA 58.161 39.130 0.00 0.00 0.00 3.91
2646 2766 4.481368 ACCAGAAAATGTATCCGTAGCA 57.519 40.909 0.00 0.00 0.00 3.49
2647 2767 7.492352 AAATACCAGAAAATGTATCCGTAGC 57.508 36.000 0.00 0.00 0.00 3.58
2671 2791 6.034470 GCTTCTGTGTGAAATTTCGTGAAAAA 59.966 34.615 13.34 3.78 33.79 1.94
2672 2792 5.514914 GCTTCTGTGTGAAATTTCGTGAAAA 59.485 36.000 13.34 3.33 33.79 2.29
2673 2793 5.034152 GCTTCTGTGTGAAATTTCGTGAAA 58.966 37.500 13.34 0.00 33.79 2.69
2674 2794 4.095632 TGCTTCTGTGTGAAATTTCGTGAA 59.904 37.500 13.34 10.83 33.79 3.18
2675 2795 3.625313 TGCTTCTGTGTGAAATTTCGTGA 59.375 39.130 13.34 4.45 33.79 4.35
2676 2796 3.951306 TGCTTCTGTGTGAAATTTCGTG 58.049 40.909 13.34 2.32 33.79 4.35
2677 2797 3.003689 CCTGCTTCTGTGTGAAATTTCGT 59.996 43.478 13.34 0.00 33.79 3.85
2678 2798 3.003689 ACCTGCTTCTGTGTGAAATTTCG 59.996 43.478 13.34 0.00 33.79 3.46
2679 2799 4.540824 GACCTGCTTCTGTGTGAAATTTC 58.459 43.478 11.41 11.41 33.79 2.17
2680 2800 3.003689 CGACCTGCTTCTGTGTGAAATTT 59.996 43.478 0.00 0.00 33.79 1.82
2681 2801 2.549754 CGACCTGCTTCTGTGTGAAATT 59.450 45.455 0.00 0.00 33.79 1.82
2682 2802 2.146342 CGACCTGCTTCTGTGTGAAAT 58.854 47.619 0.00 0.00 33.79 2.17
2683 2803 1.581934 CGACCTGCTTCTGTGTGAAA 58.418 50.000 0.00 0.00 33.79 2.69
2684 2804 0.249868 CCGACCTGCTTCTGTGTGAA 60.250 55.000 0.00 0.00 0.00 3.18
2685 2805 1.367471 CCGACCTGCTTCTGTGTGA 59.633 57.895 0.00 0.00 0.00 3.58
2686 2806 1.669115 CCCGACCTGCTTCTGTGTG 60.669 63.158 0.00 0.00 0.00 3.82
2687 2807 1.407656 TTCCCGACCTGCTTCTGTGT 61.408 55.000 0.00 0.00 0.00 3.72
2688 2808 0.951040 GTTCCCGACCTGCTTCTGTG 60.951 60.000 0.00 0.00 0.00 3.66
2689 2809 1.371558 GTTCCCGACCTGCTTCTGT 59.628 57.895 0.00 0.00 0.00 3.41
2690 2810 1.376037 GGTTCCCGACCTGCTTCTG 60.376 63.158 0.00 0.00 45.55 3.02
2691 2811 3.069778 GGTTCCCGACCTGCTTCT 58.930 61.111 0.00 0.00 45.55 2.85
2699 2819 0.037734 ATCAAACCTGGGTTCCCGAC 59.962 55.000 5.42 0.00 37.35 4.79
2700 2820 1.659022 TATCAAACCTGGGTTCCCGA 58.341 50.000 5.42 4.01 37.35 5.14
2701 2821 2.572290 GATATCAAACCTGGGTTCCCG 58.428 52.381 5.42 0.00 37.35 5.14
2702 2822 2.572290 CGATATCAAACCTGGGTTCCC 58.428 52.381 5.42 0.12 37.35 3.97
2703 2823 1.947456 GCGATATCAAACCTGGGTTCC 59.053 52.381 5.42 0.00 37.35 3.62
2704 2824 2.639065 TGCGATATCAAACCTGGGTTC 58.361 47.619 5.42 0.00 37.35 3.62
2705 2825 2.799126 TGCGATATCAAACCTGGGTT 57.201 45.000 3.12 0.00 40.45 4.11
2706 2826 2.799126 TTGCGATATCAAACCTGGGT 57.201 45.000 3.12 0.00 0.00 4.51
2707 2827 4.339247 AGATTTTGCGATATCAAACCTGGG 59.661 41.667 3.12 0.00 35.86 4.45
2708 2828 5.066375 TGAGATTTTGCGATATCAAACCTGG 59.934 40.000 3.12 0.00 35.86 4.45
2709 2829 6.037500 TCTGAGATTTTGCGATATCAAACCTG 59.962 38.462 3.12 0.00 35.86 4.00
2710 2830 6.115446 TCTGAGATTTTGCGATATCAAACCT 58.885 36.000 3.12 0.00 35.86 3.50
2711 2831 6.363577 TCTGAGATTTTGCGATATCAAACC 57.636 37.500 3.12 0.00 35.86 3.27
2712 2832 8.847444 AAATCTGAGATTTTGCGATATCAAAC 57.153 30.769 14.34 0.00 35.86 2.93
2713 2833 9.859427 AAAAATCTGAGATTTTGCGATATCAAA 57.141 25.926 28.00 0.00 34.47 2.69
2765 2885 9.292195 CCACACCCCTATACGAATATTAAATTT 57.708 33.333 0.00 0.00 0.00 1.82
2766 2886 8.662255 TCCACACCCCTATACGAATATTAAATT 58.338 33.333 0.00 0.00 0.00 1.82
2767 2887 8.209802 TCCACACCCCTATACGAATATTAAAT 57.790 34.615 0.00 0.00 0.00 1.40
2768 2888 7.615039 TCCACACCCCTATACGAATATTAAA 57.385 36.000 0.00 0.00 0.00 1.52
2769 2889 6.295462 GCTCCACACCCCTATACGAATATTAA 60.295 42.308 0.00 0.00 0.00 1.40
2770 2890 5.186409 GCTCCACACCCCTATACGAATATTA 59.814 44.000 0.00 0.00 0.00 0.98
2771 2891 4.020485 GCTCCACACCCCTATACGAATATT 60.020 45.833 0.00 0.00 0.00 1.28
2772 2892 3.514309 GCTCCACACCCCTATACGAATAT 59.486 47.826 0.00 0.00 0.00 1.28
2773 2893 2.895404 GCTCCACACCCCTATACGAATA 59.105 50.000 0.00 0.00 0.00 1.75
2774 2894 1.692519 GCTCCACACCCCTATACGAAT 59.307 52.381 0.00 0.00 0.00 3.34
2775 2895 1.117150 GCTCCACACCCCTATACGAA 58.883 55.000 0.00 0.00 0.00 3.85
2776 2896 0.032912 TGCTCCACACCCCTATACGA 60.033 55.000 0.00 0.00 0.00 3.43
2777 2897 0.104304 GTGCTCCACACCCCTATACG 59.896 60.000 0.00 0.00 44.02 3.06
2795 2915 1.821216 CGAATTTGTAGCACCTGGGT 58.179 50.000 0.00 0.00 0.00 4.51
2796 2916 0.451783 GCGAATTTGTAGCACCTGGG 59.548 55.000 0.00 0.00 0.00 4.45
2797 2917 1.453155 AGCGAATTTGTAGCACCTGG 58.547 50.000 0.00 0.00 0.00 4.45
2798 2918 2.159517 GGAAGCGAATTTGTAGCACCTG 60.160 50.000 0.00 0.00 0.00 4.00
2799 2919 2.084546 GGAAGCGAATTTGTAGCACCT 58.915 47.619 0.00 0.00 0.00 4.00
2800 2920 1.202031 CGGAAGCGAATTTGTAGCACC 60.202 52.381 0.00 0.00 0.00 5.01
2801 2921 1.202031 CCGGAAGCGAATTTGTAGCAC 60.202 52.381 0.00 0.00 0.00 4.40
2802 2922 1.083489 CCGGAAGCGAATTTGTAGCA 58.917 50.000 0.00 0.00 0.00 3.49
2803 2923 1.084289 ACCGGAAGCGAATTTGTAGC 58.916 50.000 9.46 0.00 0.00 3.58
2804 2924 3.488489 CAAACCGGAAGCGAATTTGTAG 58.512 45.455 9.46 0.00 0.00 2.74
2805 2925 2.226912 CCAAACCGGAAGCGAATTTGTA 59.773 45.455 9.46 0.00 36.56 2.41
2806 2926 1.000717 CCAAACCGGAAGCGAATTTGT 60.001 47.619 9.46 0.00 36.56 2.83
2807 2927 1.000717 ACCAAACCGGAAGCGAATTTG 60.001 47.619 9.46 6.45 38.63 2.32
2808 2928 1.324383 ACCAAACCGGAAGCGAATTT 58.676 45.000 9.46 0.00 38.63 1.82
2809 2929 1.268625 GAACCAAACCGGAAGCGAATT 59.731 47.619 9.46 0.00 38.63 2.17
2810 2930 0.879090 GAACCAAACCGGAAGCGAAT 59.121 50.000 9.46 0.00 38.63 3.34
2811 2931 1.500512 CGAACCAAACCGGAAGCGAA 61.501 55.000 9.46 0.00 38.63 4.70
2812 2932 1.957186 CGAACCAAACCGGAAGCGA 60.957 57.895 9.46 0.00 38.63 4.93
2813 2933 2.554272 CGAACCAAACCGGAAGCG 59.446 61.111 9.46 0.00 38.63 4.68


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

AutoCloner maintained by Alex Coulton.