Multiple sequence alignment - TraesCS6B01G123200

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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 TraesCS6B01G123200 chr6B 100.000 2879 0 0 1 2879 118187952 118185074 0.000000e+00 5317.0
1 TraesCS6B01G123200 chr6B 92.715 302 19 3 2578 2879 123917084 123916786 1.580000e-117 433.0
2 TraesCS6B01G123200 chr6A 94.792 2304 93 14 1 2287 61876638 61874345 0.000000e+00 3565.0
3 TraesCS6B01G123200 chr6A 93.388 121 8 0 2456 2576 61868649 61868529 2.280000e-41 180.0
4 TraesCS6B01G123200 chr6A 82.099 162 21 2 2303 2456 29492026 29491865 6.470000e-27 132.0
5 TraesCS6B01G123200 chr6A 97.297 37 0 1 2298 2333 438581673 438581709 8.610000e-06 62.1
6 TraesCS6B01G123200 chr6D 93.369 2443 102 24 1 2404 53564388 53566809 0.000000e+00 3559.0
7 TraesCS6B01G123200 chr6D 81.890 127 21 1 2330 2454 149243761 149243635 3.920000e-19 106.0
8 TraesCS6B01G123200 chr6D 97.297 37 0 1 2299 2334 287025408 287025372 8.610000e-06 62.1
9 TraesCS6B01G123200 chr6D 94.595 37 1 1 2293 2329 178849190 178849225 4.010000e-04 56.5
10 TraesCS6B01G123200 chr2B 94.059 303 17 1 2578 2879 195594011 195593709 2.610000e-125 459.0
11 TraesCS6B01G123200 chr2B 83.465 127 18 2 2331 2454 206736476 206736350 6.520000e-22 115.0
12 TraesCS6B01G123200 chr4B 93.377 302 20 0 2578 2879 451287024 451286723 5.660000e-122 448.0
13 TraesCS6B01G123200 chr4B 93.046 302 21 0 2578 2879 451220998 451220697 2.630000e-120 442.0
14 TraesCS6B01G123200 chr4B 90.789 304 25 3 2578 2879 10787822 10788124 1.240000e-108 403.0
15 TraesCS6B01G123200 chr3B 92.557 309 16 2 2578 2879 694173204 694172896 1.220000e-118 436.0
16 TraesCS6B01G123200 chr3B 90.728 302 27 1 2578 2879 670657840 670657540 4.470000e-108 401.0
17 TraesCS6B01G123200 chr3B 83.077 130 15 5 2331 2454 444135065 444134937 8.430000e-21 111.0
18 TraesCS6B01G123200 chr7B 92.131 305 21 3 2578 2879 600493236 600492932 7.370000e-116 427.0
19 TraesCS6B01G123200 chr5B 91.776 304 23 1 2578 2879 546057602 546057905 3.430000e-114 422.0
20 TraesCS6B01G123200 chr3A 82.143 168 19 5 2302 2459 291805647 291805481 1.800000e-27 134.0
21 TraesCS6B01G123200 chr3A 76.970 165 29 9 2302 2457 208233790 208233954 5.110000e-13 86.1
22 TraesCS6B01G123200 chr3D 80.791 177 21 10 2292 2458 167555113 167554940 3.010000e-25 126.0
23 TraesCS6B01G123200 chr7A 84.127 126 17 2 2331 2454 589751121 589751245 5.040000e-23 119.0
24 TraesCS6B01G123200 chr7A 98.077 52 1 0 1 52 217584136 217584187 1.100000e-14 91.6
25 TraesCS6B01G123200 chr1A 79.755 163 23 3 2303 2455 108075786 108075948 3.030000e-20 110.0
26 TraesCS6B01G123200 chr7D 79.518 166 23 5 2300 2454 64104587 64104752 1.090000e-19 108.0
27 TraesCS6B01G123200 chr4A 100.000 36 0 0 2294 2329 405565350 405565315 1.850000e-07 67.6
28 TraesCS6B01G123200 chr4A 96.970 33 1 0 2303 2335 716495157 716495125 4.010000e-04 56.5
29 TraesCS6B01G123200 chr2D 92.683 41 1 2 2291 2329 593217626 593217666 1.110000e-04 58.4


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 TraesCS6B01G123200 chr6B 118185074 118187952 2878 True 5317 5317 100.000 1 2879 1 chr6B.!!$R1 2878
1 TraesCS6B01G123200 chr6A 61874345 61876638 2293 True 3565 3565 94.792 1 2287 1 chr6A.!!$R3 2286
2 TraesCS6B01G123200 chr6D 53564388 53566809 2421 False 3559 3559 93.369 1 2404 1 chr6D.!!$F1 2403

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
30 31 3.003480 GTGCTACTGATCAGGAACCAAC 58.997 50.000 26.08 12.49 0.0 3.77 F
1444 1476 1.003118 CTAACCAACCCAGCTGCTACA 59.997 52.381 8.66 0.00 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1467 1499 0.179936 GGTTGCAGATCTCCTCCTGG 59.820 60.0 0.00 0.00 0.0 4.45 R
2467 2523 0.033601 TATCCCGTGGCAAGGCATTT 60.034 50.0 14.49 0.86 0.0 2.32 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
30 31 3.003480 GTGCTACTGATCAGGAACCAAC 58.997 50.000 26.08 12.49 0.00 3.77
176 181 4.990526 AGAAGATTCACTGGTGATTTGGT 58.009 39.130 4.19 0.00 39.64 3.67
177 182 5.388654 AGAAGATTCACTGGTGATTTGGTT 58.611 37.500 4.19 0.00 39.64 3.67
250 255 3.134804 AGATTGCATACTGGTGAGTACCC 59.865 47.826 0.00 0.00 46.96 3.69
348 359 6.067263 AGATGCTAGATGAACGTCTTAGAC 57.933 41.667 1.64 1.64 0.00 2.59
383 394 6.408858 AAATTACAGCTACATCGTGACAAG 57.591 37.500 0.00 0.00 0.00 3.16
398 409 6.464222 TCGTGACAAGATTTCAGTTCCTAAT 58.536 36.000 0.00 0.00 0.00 1.73
424 437 5.360714 TCTGCTTGTGGAAACAAAAAGAGAT 59.639 36.000 0.00 0.00 46.06 2.75
456 469 6.183360 GCTTGCCTTTTTAGCACAAACATATC 60.183 38.462 0.00 0.00 40.69 1.63
461 474 9.586435 GCCTTTTTAGCACAAACATATCTTTAT 57.414 29.630 0.00 0.00 0.00 1.40
599 621 5.466728 CCTTGTTCACTTTCTCATTCTTCGA 59.533 40.000 0.00 0.00 0.00 3.71
629 654 6.804677 AGAATGCATCACTGTTCTCTAGTAG 58.195 40.000 0.00 0.00 0.00 2.57
790 815 4.811555 TGCGTGATAGATTGGTTTATGC 57.188 40.909 0.00 0.00 0.00 3.14
831 856 4.157840 GTGACCACAAACAACTTCCTTTCT 59.842 41.667 0.00 0.00 0.00 2.52
1065 1090 2.363795 AGAATCGCCGGGGAGTCA 60.364 61.111 38.95 15.17 33.68 3.41
1077 1102 2.126031 GAGTCAACGACGCCCCTC 60.126 66.667 0.00 0.00 37.67 4.30
1146 1171 2.159653 CCTTTCCTTTCTGATGTTCGCG 60.160 50.000 0.00 0.00 0.00 5.87
1175 1200 3.191162 TGTGAAATGATGCAAGGTGCTAC 59.809 43.478 0.00 0.00 45.31 3.58
1366 1398 1.971357 CTACATCCTCGGCCTGGTAAT 59.029 52.381 0.00 0.00 0.00 1.89
1384 1416 2.604046 ATGTCTGAAGCACGGATACC 57.396 50.000 0.00 0.00 36.21 2.73
1391 1423 2.213499 GAAGCACGGATACCCATCTTG 58.787 52.381 0.00 0.00 0.00 3.02
1398 1430 3.070018 CGGATACCCATCTTGCAGAATC 58.930 50.000 0.00 0.00 0.00 2.52
1414 1446 4.673580 GCAGAATCGCATCATGTTCAGTTT 60.674 41.667 0.00 0.00 0.00 2.66
1421 1453 4.555313 CGCATCATGTTCAGTTTGTTCACT 60.555 41.667 0.00 0.00 0.00 3.41
1422 1454 5.284079 GCATCATGTTCAGTTTGTTCACTT 58.716 37.500 0.00 0.00 0.00 3.16
1436 1468 2.270352 TCACTTGCTAACCAACCCAG 57.730 50.000 0.00 0.00 0.00 4.45
1444 1476 1.003118 CTAACCAACCCAGCTGCTACA 59.997 52.381 8.66 0.00 0.00 2.74
1465 1497 7.752686 GCTACAATTCTGACATTTTCTTCCTTC 59.247 37.037 0.00 0.00 0.00 3.46
1467 1499 4.749245 TTCTGACATTTTCTTCCTTCGC 57.251 40.909 0.00 0.00 0.00 4.70
1524 1556 3.314331 CTCCAGCACCTCCACCGT 61.314 66.667 0.00 0.00 0.00 4.83
1677 1709 3.012518 CAAGATCAAGATTGCCTCCGTT 58.987 45.455 0.00 0.00 0.00 4.44
1870 1902 3.254411 TGAATACCGCAAATTTGTGCAGA 59.746 39.130 23.38 12.20 45.19 4.26
1881 1913 5.705609 AATTTGTGCAGAGGATTTAACGT 57.294 34.783 0.00 0.00 0.00 3.99
1998 2030 3.777087 TCTGCCATCCCAATTTTTCTCA 58.223 40.909 0.00 0.00 0.00 3.27
2020 2054 6.299141 TCATTCCTATTAAAGCTGGCTTAGG 58.701 40.000 8.30 11.06 34.84 2.69
2062 2100 7.827729 GGTGGTTAGGTAGTGATATTTTCTTGT 59.172 37.037 0.00 0.00 0.00 3.16
2151 2190 7.553881 TTTTATTTCGGCCATTTTTGTGAAA 57.446 28.000 2.24 1.75 0.00 2.69
2156 2195 3.118956 TCGGCCATTTTTGTGAAAACTGT 60.119 39.130 2.24 0.00 37.56 3.55
2275 2321 1.553704 GTTATGAACCTCCCCACGAGT 59.446 52.381 0.00 0.00 36.82 4.18
2290 2336 1.202302 ACGAGTGTATCATGGAGCGTG 60.202 52.381 0.00 0.00 0.00 5.34
2293 2339 2.860735 GAGTGTATCATGGAGCGTGAAC 59.139 50.000 0.00 0.00 32.88 3.18
2297 2343 3.699538 TGTATCATGGAGCGTGAACTAGT 59.300 43.478 0.00 0.00 32.88 2.57
2308 2354 3.864003 GCGTGAACTAGTCATTTACTCCC 59.136 47.826 0.00 0.00 38.90 4.30
2311 2357 5.662456 GTGAACTAGTCATTTACTCCCTCC 58.338 45.833 0.00 0.00 38.90 4.30
2312 2358 5.187186 GTGAACTAGTCATTTACTCCCTCCA 59.813 44.000 0.00 0.00 38.90 3.86
2315 2361 6.487299 ACTAGTCATTTACTCCCTCCATTC 57.513 41.667 0.00 0.00 39.80 2.67
2329 2375 7.794683 ACTCCCTCCATTCCTAAATATAAGTCA 59.205 37.037 0.00 0.00 0.00 3.41
2352 2406 9.485591 GTCAATTTCAATATAAACTACACACGG 57.514 33.333 0.00 0.00 0.00 4.94
2353 2407 8.670135 TCAATTTCAATATAAACTACACACGGG 58.330 33.333 0.00 0.00 0.00 5.28
2354 2408 8.455682 CAATTTCAATATAAACTACACACGGGT 58.544 33.333 0.00 0.00 0.00 5.28
2355 2409 9.669887 AATTTCAATATAAACTACACACGGGTA 57.330 29.630 0.00 0.00 0.00 3.69
2365 2419 8.801715 AAACTACACACGGGTATATATAAACG 57.198 34.615 13.00 13.00 0.00 3.60
2413 2469 8.572828 TTTTGCTTTGTATGTAGTTCATGTTG 57.427 30.769 0.00 0.00 37.91 3.33
2414 2470 6.875948 TGCTTTGTATGTAGTTCATGTTGT 57.124 33.333 0.00 0.00 37.91 3.32
2415 2471 7.971183 TGCTTTGTATGTAGTTCATGTTGTA 57.029 32.000 0.00 0.00 37.91 2.41
2416 2472 8.384607 TGCTTTGTATGTAGTTCATGTTGTAA 57.615 30.769 0.00 0.00 37.91 2.41
2417 2473 9.008965 TGCTTTGTATGTAGTTCATGTTGTAAT 57.991 29.630 0.00 0.00 37.91 1.89
2418 2474 9.490663 GCTTTGTATGTAGTTCATGTTGTAATC 57.509 33.333 0.00 0.00 37.91 1.75
2429 2485 9.220767 AGTTCATGTTGTAATCTCTAAAAGGAC 57.779 33.333 0.00 0.00 0.00 3.85
2430 2486 9.220767 GTTCATGTTGTAATCTCTAAAAGGACT 57.779 33.333 0.00 0.00 0.00 3.85
2431 2487 9.793259 TTCATGTTGTAATCTCTAAAAGGACTT 57.207 29.630 0.00 0.00 0.00 3.01
2448 2504 8.959705 AAAGGACTTATATTTAAGAACGGAGG 57.040 34.615 9.58 0.00 38.56 4.30
2449 2505 7.909485 AGGACTTATATTTAAGAACGGAGGA 57.091 36.000 9.58 0.00 38.56 3.71
2450 2506 8.315220 AGGACTTATATTTAAGAACGGAGGAA 57.685 34.615 9.58 0.00 38.56 3.36
2451 2507 8.422566 AGGACTTATATTTAAGAACGGAGGAAG 58.577 37.037 9.58 0.00 38.56 3.46
2452 2508 8.202811 GGACTTATATTTAAGAACGGAGGAAGT 58.797 37.037 9.58 0.00 38.56 3.01
2459 2515 8.768957 ATTTAAGAACGGAGGAAGTACTTAAC 57.231 34.615 8.42 4.88 31.33 2.01
2460 2516 5.796424 AAGAACGGAGGAAGTACTTAACA 57.204 39.130 8.42 0.00 0.00 2.41
2461 2517 5.796424 AGAACGGAGGAAGTACTTAACAA 57.204 39.130 8.42 0.00 0.00 2.83
2462 2518 5.536260 AGAACGGAGGAAGTACTTAACAAC 58.464 41.667 8.42 0.00 0.00 3.32
2463 2519 4.942761 ACGGAGGAAGTACTTAACAACA 57.057 40.909 8.42 0.00 0.00 3.33
2464 2520 4.879598 ACGGAGGAAGTACTTAACAACAG 58.120 43.478 8.42 6.80 0.00 3.16
2465 2521 3.678548 CGGAGGAAGTACTTAACAACAGC 59.321 47.826 8.42 0.00 0.00 4.40
2466 2522 3.678548 GGAGGAAGTACTTAACAACAGCG 59.321 47.826 8.42 0.00 0.00 5.18
2467 2523 4.553323 GAGGAAGTACTTAACAACAGCGA 58.447 43.478 8.42 0.00 0.00 4.93
2468 2524 4.952460 AGGAAGTACTTAACAACAGCGAA 58.048 39.130 8.42 0.00 0.00 4.70
2469 2525 5.362263 AGGAAGTACTTAACAACAGCGAAA 58.638 37.500 8.42 0.00 0.00 3.46
2470 2526 5.995897 AGGAAGTACTTAACAACAGCGAAAT 59.004 36.000 8.42 0.00 0.00 2.17
2471 2527 6.073222 AGGAAGTACTTAACAACAGCGAAATG 60.073 38.462 8.42 0.00 0.00 2.32
2472 2528 5.030874 AGTACTTAACAACAGCGAAATGC 57.969 39.130 0.00 0.00 46.98 3.56
2481 2537 2.504681 GCGAAATGCCTTGCCACG 60.505 61.111 0.00 0.00 37.76 4.94
2482 2538 2.179018 CGAAATGCCTTGCCACGG 59.821 61.111 0.00 0.00 0.00 4.94
2483 2539 2.573340 GAAATGCCTTGCCACGGG 59.427 61.111 0.00 0.00 0.00 5.28
2484 2540 1.976474 GAAATGCCTTGCCACGGGA 60.976 57.895 0.00 0.00 0.00 5.14
2485 2541 1.305213 AAATGCCTTGCCACGGGAT 60.305 52.632 0.00 0.00 33.66 3.85
2486 2542 0.033601 AAATGCCTTGCCACGGGATA 60.034 50.000 0.00 0.00 31.83 2.59
2487 2543 0.033601 AATGCCTTGCCACGGGATAA 60.034 50.000 0.00 0.00 31.83 1.75
2488 2544 0.751643 ATGCCTTGCCACGGGATAAC 60.752 55.000 0.00 0.00 30.14 1.89
2489 2545 1.377987 GCCTTGCCACGGGATAACA 60.378 57.895 0.00 0.00 0.00 2.41
2490 2546 0.963355 GCCTTGCCACGGGATAACAA 60.963 55.000 0.00 0.00 0.00 2.83
2491 2547 1.540267 CCTTGCCACGGGATAACAAA 58.460 50.000 0.00 0.00 0.00 2.83
2492 2548 1.889829 CCTTGCCACGGGATAACAAAA 59.110 47.619 0.00 0.00 0.00 2.44
2493 2549 2.094752 CCTTGCCACGGGATAACAAAAG 60.095 50.000 0.00 0.00 0.00 2.27
2494 2550 2.570415 TGCCACGGGATAACAAAAGA 57.430 45.000 0.00 0.00 0.00 2.52
2495 2551 3.080300 TGCCACGGGATAACAAAAGAT 57.920 42.857 0.00 0.00 0.00 2.40
2496 2552 4.223556 TGCCACGGGATAACAAAAGATA 57.776 40.909 0.00 0.00 0.00 1.98
2497 2553 4.787551 TGCCACGGGATAACAAAAGATAT 58.212 39.130 0.00 0.00 0.00 1.63
2498 2554 5.197451 TGCCACGGGATAACAAAAGATATT 58.803 37.500 0.00 0.00 0.00 1.28
2499 2555 5.654650 TGCCACGGGATAACAAAAGATATTT 59.345 36.000 0.00 0.00 0.00 1.40
2500 2556 6.829298 TGCCACGGGATAACAAAAGATATTTA 59.171 34.615 0.00 0.00 0.00 1.40
2501 2557 7.504238 TGCCACGGGATAACAAAAGATATTTAT 59.496 33.333 0.00 0.00 0.00 1.40
2502 2558 9.005777 GCCACGGGATAACAAAAGATATTTATA 57.994 33.333 0.00 0.00 0.00 0.98
2505 2561 9.227777 ACGGGATAACAAAAGATATTTATAGGC 57.772 33.333 0.00 0.00 0.00 3.93
2506 2562 9.226606 CGGGATAACAAAAGATATTTATAGGCA 57.773 33.333 0.00 0.00 0.00 4.75
2520 2576 7.709269 ATTTATAGGCACACTAACATACACG 57.291 36.000 0.00 0.00 34.79 4.49
2521 2577 2.380084 AGGCACACTAACATACACGG 57.620 50.000 0.00 0.00 0.00 4.94
2522 2578 1.066430 AGGCACACTAACATACACGGG 60.066 52.381 0.00 0.00 0.00 5.28
2523 2579 1.066716 GGCACACTAACATACACGGGA 60.067 52.381 0.00 0.00 0.00 5.14
2524 2580 2.419574 GGCACACTAACATACACGGGAT 60.420 50.000 0.00 0.00 0.00 3.85
2525 2581 3.181473 GGCACACTAACATACACGGGATA 60.181 47.826 0.00 0.00 0.00 2.59
2526 2582 4.435425 GCACACTAACATACACGGGATAA 58.565 43.478 0.00 0.00 0.00 1.75
2527 2583 4.269363 GCACACTAACATACACGGGATAAC 59.731 45.833 0.00 0.00 0.00 1.89
2528 2584 5.412640 CACACTAACATACACGGGATAACA 58.587 41.667 0.00 0.00 0.00 2.41
2529 2585 5.870433 CACACTAACATACACGGGATAACAA 59.130 40.000 0.00 0.00 0.00 2.83
2530 2586 6.369340 CACACTAACATACACGGGATAACAAA 59.631 38.462 0.00 0.00 0.00 2.83
2531 2587 6.935771 ACACTAACATACACGGGATAACAAAA 59.064 34.615 0.00 0.00 0.00 2.44
2532 2588 7.444792 ACACTAACATACACGGGATAACAAAAA 59.555 33.333 0.00 0.00 0.00 1.94
2533 2589 7.960738 CACTAACATACACGGGATAACAAAAAG 59.039 37.037 0.00 0.00 0.00 2.27
2534 2590 6.887626 AACATACACGGGATAACAAAAAGT 57.112 33.333 0.00 0.00 0.00 2.66
2535 2591 7.982761 AACATACACGGGATAACAAAAAGTA 57.017 32.000 0.00 0.00 0.00 2.24
2536 2592 8.570068 AACATACACGGGATAACAAAAAGTAT 57.430 30.769 0.00 0.00 0.00 2.12
2537 2593 8.570068 ACATACACGGGATAACAAAAAGTATT 57.430 30.769 0.00 0.00 0.00 1.89
2538 2594 9.016438 ACATACACGGGATAACAAAAAGTATTT 57.984 29.630 0.00 0.00 42.41 1.40
2563 2619 9.577110 TTATAGACACACTAACGTAAAAGATGG 57.423 33.333 0.00 0.00 34.56 3.51
2564 2620 5.235516 AGACACACTAACGTAAAAGATGGG 58.764 41.667 0.00 0.00 0.00 4.00
2565 2621 3.749609 ACACACTAACGTAAAAGATGGGC 59.250 43.478 0.00 0.00 0.00 5.36
2566 2622 2.997986 ACACTAACGTAAAAGATGGGCG 59.002 45.455 0.00 0.00 0.00 6.13
2567 2623 3.255725 CACTAACGTAAAAGATGGGCGA 58.744 45.455 0.00 0.00 0.00 5.54
2568 2624 3.869246 CACTAACGTAAAAGATGGGCGAT 59.131 43.478 0.00 0.00 0.00 4.58
2569 2625 3.869246 ACTAACGTAAAAGATGGGCGATG 59.131 43.478 0.00 0.00 0.00 3.84
2570 2626 2.684001 ACGTAAAAGATGGGCGATGA 57.316 45.000 0.00 0.00 0.00 2.92
2571 2627 2.277084 ACGTAAAAGATGGGCGATGAC 58.723 47.619 0.00 0.00 0.00 3.06
2572 2628 1.257936 CGTAAAAGATGGGCGATGACG 59.742 52.381 0.00 0.00 42.93 4.35
2573 2629 2.277084 GTAAAAGATGGGCGATGACGT 58.723 47.619 0.00 0.00 41.98 4.34
2574 2630 2.684001 AAAAGATGGGCGATGACGTA 57.316 45.000 0.00 0.00 41.98 3.57
2575 2631 2.225068 AAAGATGGGCGATGACGTAG 57.775 50.000 0.00 0.00 41.98 3.51
2596 2652 2.702847 GGAATGTATCCGGTGCACC 58.297 57.895 26.78 26.78 38.79 5.01
2597 2653 0.818040 GGAATGTATCCGGTGCACCC 60.818 60.000 29.95 15.85 38.79 4.61
2598 2654 0.107410 GAATGTATCCGGTGCACCCA 60.107 55.000 29.95 21.07 0.00 4.51
2599 2655 0.393808 AATGTATCCGGTGCACCCAC 60.394 55.000 29.95 21.00 41.32 4.61
2600 2656 1.558167 ATGTATCCGGTGCACCCACA 61.558 55.000 29.95 25.35 43.88 4.17
2601 2657 1.743995 GTATCCGGTGCACCCACAC 60.744 63.158 29.95 17.89 43.88 3.82
2602 2658 1.916273 TATCCGGTGCACCCACACT 60.916 57.895 29.95 12.63 43.88 3.55
2603 2659 1.485294 TATCCGGTGCACCCACACTT 61.485 55.000 29.95 11.40 43.88 3.16
2604 2660 3.286751 CCGGTGCACCCACACTTG 61.287 66.667 29.95 13.72 43.88 3.16
2605 2661 2.515991 CGGTGCACCCACACTTGT 60.516 61.111 29.95 0.00 43.88 3.16
2606 2662 2.833533 CGGTGCACCCACACTTGTG 61.834 63.158 29.95 8.78 43.88 3.33
2616 2672 3.966215 CACTTGTGGTGCTACCGG 58.034 61.111 0.00 0.00 42.58 5.28
2617 2673 1.070786 CACTTGTGGTGCTACCGGT 59.929 57.895 13.98 13.98 42.58 5.28
2618 2674 1.070786 ACTTGTGGTGCTACCGGTG 59.929 57.895 19.93 8.61 42.58 4.94
2619 2675 2.281208 TTGTGGTGCTACCGGTGC 60.281 61.111 19.93 19.04 42.58 5.01
2620 2676 3.108288 TTGTGGTGCTACCGGTGCA 62.108 57.895 19.93 21.51 42.58 4.57
2674 2730 8.335356 TCTGAATAAATTCTAGCATGTTAACGC 58.665 33.333 0.26 0.00 37.67 4.84
2675 2731 7.980062 TGAATAAATTCTAGCATGTTAACGCA 58.020 30.769 8.00 0.00 37.67 5.24
2676 2732 8.454894 TGAATAAATTCTAGCATGTTAACGCAA 58.545 29.630 8.00 0.00 37.67 4.85
2677 2733 9.450807 GAATAAATTCTAGCATGTTAACGCAAT 57.549 29.630 8.00 0.00 34.05 3.56
2681 2737 7.728847 ATTCTAGCATGTTAACGCAATATCA 57.271 32.000 8.00 0.00 0.00 2.15
2682 2738 7.546778 TTCTAGCATGTTAACGCAATATCAA 57.453 32.000 8.00 0.00 0.00 2.57
2683 2739 7.728847 TCTAGCATGTTAACGCAATATCAAT 57.271 32.000 8.00 0.00 0.00 2.57
2684 2740 7.575365 TCTAGCATGTTAACGCAATATCAATG 58.425 34.615 8.00 1.37 0.00 2.82
2685 2741 6.135290 AGCATGTTAACGCAATATCAATGT 57.865 33.333 8.00 0.00 0.00 2.71
2686 2742 7.258022 AGCATGTTAACGCAATATCAATGTA 57.742 32.000 8.00 0.00 0.00 2.29
2687 2743 7.874940 AGCATGTTAACGCAATATCAATGTAT 58.125 30.769 8.00 0.00 0.00 2.29
2688 2744 7.804600 AGCATGTTAACGCAATATCAATGTATG 59.195 33.333 8.00 0.00 0.00 2.39
2689 2745 7.802720 GCATGTTAACGCAATATCAATGTATGA 59.197 33.333 0.26 0.00 43.67 2.15
2758 2814 8.851541 ACAAAAATGATAAATTTGGCATCAGT 57.148 26.923 0.00 0.00 38.14 3.41
2759 2815 8.723311 ACAAAAATGATAAATTTGGCATCAGTG 58.277 29.630 0.00 5.88 38.14 3.66
2760 2816 8.723311 CAAAAATGATAAATTTGGCATCAGTGT 58.277 29.630 0.00 0.00 32.51 3.55
2761 2817 7.837202 AAATGATAAATTTGGCATCAGTGTG 57.163 32.000 0.00 0.00 32.51 3.82
2762 2818 6.778834 ATGATAAATTTGGCATCAGTGTGA 57.221 33.333 0.00 0.00 32.51 3.58
2763 2819 6.587206 TGATAAATTTGGCATCAGTGTGAA 57.413 33.333 0.00 0.00 0.00 3.18
2764 2820 6.990798 TGATAAATTTGGCATCAGTGTGAAA 58.009 32.000 0.00 0.00 0.00 2.69
2765 2821 7.440198 TGATAAATTTGGCATCAGTGTGAAAA 58.560 30.769 0.00 0.00 0.00 2.29
2766 2822 8.095792 TGATAAATTTGGCATCAGTGTGAAAAT 58.904 29.630 0.00 0.00 0.00 1.82
2767 2823 6.548441 AAATTTGGCATCAGTGTGAAAATG 57.452 33.333 0.00 0.00 0.00 2.32
2768 2824 3.663995 TTGGCATCAGTGTGAAAATGG 57.336 42.857 0.00 0.00 0.00 3.16
2769 2825 1.894466 TGGCATCAGTGTGAAAATGGG 59.106 47.619 0.00 0.00 0.00 4.00
2770 2826 1.404583 GGCATCAGTGTGAAAATGGGC 60.405 52.381 0.00 0.00 0.00 5.36
2771 2827 1.404583 GCATCAGTGTGAAAATGGGCC 60.405 52.381 0.00 0.00 0.00 5.80
2772 2828 1.894466 CATCAGTGTGAAAATGGGCCA 59.106 47.619 9.61 9.61 0.00 5.36
2773 2829 2.079170 TCAGTGTGAAAATGGGCCAA 57.921 45.000 11.89 0.00 0.00 4.52
2774 2830 2.392662 TCAGTGTGAAAATGGGCCAAA 58.607 42.857 11.89 0.00 0.00 3.28
2775 2831 2.971330 TCAGTGTGAAAATGGGCCAAAT 59.029 40.909 11.89 0.00 0.00 2.32
2776 2832 3.006752 TCAGTGTGAAAATGGGCCAAATC 59.993 43.478 11.89 10.05 0.00 2.17
2777 2833 3.007182 CAGTGTGAAAATGGGCCAAATCT 59.993 43.478 11.89 0.00 0.00 2.40
2778 2834 4.220382 CAGTGTGAAAATGGGCCAAATCTA 59.780 41.667 11.89 0.00 0.00 1.98
2779 2835 4.837860 AGTGTGAAAATGGGCCAAATCTAA 59.162 37.500 11.89 0.00 0.00 2.10
2780 2836 5.306678 AGTGTGAAAATGGGCCAAATCTAAA 59.693 36.000 11.89 0.00 0.00 1.85
2781 2837 5.639082 GTGTGAAAATGGGCCAAATCTAAAG 59.361 40.000 11.89 0.00 0.00 1.85
2782 2838 4.631377 GTGAAAATGGGCCAAATCTAAAGC 59.369 41.667 11.89 0.00 0.00 3.51
2783 2839 3.912496 AAATGGGCCAAATCTAAAGCC 57.088 42.857 11.89 0.00 44.99 4.35
2787 2843 2.967599 GGCCAAATCTAAAGCCCAAG 57.032 50.000 0.00 0.00 39.60 3.61
2788 2844 2.456577 GGCCAAATCTAAAGCCCAAGA 58.543 47.619 0.00 0.00 39.60 3.02
2789 2845 3.033909 GGCCAAATCTAAAGCCCAAGAT 58.966 45.455 0.00 0.00 39.60 2.40
2790 2846 4.215109 GGCCAAATCTAAAGCCCAAGATA 58.785 43.478 0.00 0.00 39.60 1.98
2791 2847 4.649218 GGCCAAATCTAAAGCCCAAGATAA 59.351 41.667 0.00 0.00 39.60 1.75
2792 2848 5.305386 GGCCAAATCTAAAGCCCAAGATAAT 59.695 40.000 0.00 0.00 39.60 1.28
2793 2849 6.218746 GCCAAATCTAAAGCCCAAGATAATG 58.781 40.000 0.00 0.00 32.17 1.90
2794 2850 6.183360 GCCAAATCTAAAGCCCAAGATAATGT 60.183 38.462 0.00 0.00 32.17 2.71
2795 2851 7.633553 GCCAAATCTAAAGCCCAAGATAATGTT 60.634 37.037 0.00 0.00 32.17 2.71
2796 2852 8.912988 CCAAATCTAAAGCCCAAGATAATGTTA 58.087 33.333 0.00 0.00 32.17 2.41
2799 2855 9.646522 AATCTAAAGCCCAAGATAATGTTATGT 57.353 29.630 0.00 0.00 32.17 2.29
2801 2857 9.555727 TCTAAAGCCCAAGATAATGTTATGTAC 57.444 33.333 0.00 0.00 0.00 2.90
2802 2858 9.561069 CTAAAGCCCAAGATAATGTTATGTACT 57.439 33.333 0.00 0.00 0.00 2.73
2806 2862 9.726438 AGCCCAAGATAATGTTATGTACTATTC 57.274 33.333 0.00 0.00 0.00 1.75
2807 2863 9.502091 GCCCAAGATAATGTTATGTACTATTCA 57.498 33.333 0.00 0.00 0.00 2.57
2871 2927 9.985318 TCAAATTTTGATTTGAAATGTTGTGAC 57.015 25.926 7.74 0.00 44.64 3.67
2872 2928 9.770503 CAAATTTTGATTTGAAATGTTGTGACA 57.229 25.926 2.88 0.00 42.47 3.58
2874 2930 9.771915 AATTTTGATTTGAAATGTTGTGACAAC 57.228 25.926 20.81 20.81 39.66 3.32
2875 2931 6.900568 TTGATTTGAAATGTTGTGACAACC 57.099 33.333 24.05 10.28 39.66 3.77
2876 2932 6.219417 TGATTTGAAATGTTGTGACAACCT 57.781 33.333 24.05 12.95 39.66 3.50
2877 2933 7.340122 TGATTTGAAATGTTGTGACAACCTA 57.660 32.000 24.05 8.40 39.66 3.08
2878 2934 7.199766 TGATTTGAAATGTTGTGACAACCTAC 58.800 34.615 24.05 13.59 39.66 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.509052 TCTCAGAACAGTGTGGAACG 57.491 50.000 0.00 0.00 42.39 3.95
96 97 8.958119 TCAGAACGATTTTATTTAGGCTGTAT 57.042 30.769 0.00 0.00 0.00 2.29
152 157 4.397417 CCAAATCACCAGTGAATCTTCTCC 59.603 45.833 4.31 0.00 43.58 3.71
176 181 4.334203 ACAACATTCGTGACAGCAACTAAA 59.666 37.500 0.00 0.00 0.00 1.85
177 182 3.874543 ACAACATTCGTGACAGCAACTAA 59.125 39.130 0.00 0.00 0.00 2.24
250 255 3.433306 TGGTAGTCAAATTGGGTGAGG 57.567 47.619 0.00 0.00 0.00 3.86
364 375 4.983671 ATCTTGTCACGATGTAGCTGTA 57.016 40.909 0.00 0.00 0.00 2.74
383 394 6.597280 ACAAGCAGAGATTAGGAACTGAAATC 59.403 38.462 0.00 0.00 41.52 2.17
398 409 4.704540 TCTTTTTGTTTCCACAAGCAGAGA 59.295 37.500 0.00 0.00 43.92 3.10
424 437 5.207110 TGCTAAAAAGGCAAGCACAAATA 57.793 34.783 0.00 0.00 41.15 1.40
461 474 7.610305 GGTGAGAAAAGGGTCTGATTTATACAA 59.390 37.037 0.00 0.00 0.00 2.41
599 621 3.988976 ACAGTGATGCATTCTAGTGGT 57.011 42.857 0.00 0.00 0.00 4.16
1146 1171 4.624024 CCTTGCATCATTTCACAATCACAC 59.376 41.667 0.00 0.00 0.00 3.82
1175 1200 3.744426 TGAAGAGATACATGCGCATGATG 59.256 43.478 46.90 29.44 41.20 3.07
1343 1375 0.833834 CCAGGCCGAGGATGTAGGAT 60.834 60.000 11.49 0.00 0.00 3.24
1366 1398 0.535335 GGGTATCCGTGCTTCAGACA 59.465 55.000 0.00 0.00 0.00 3.41
1391 1423 2.353889 ACTGAACATGATGCGATTCTGC 59.646 45.455 0.00 0.00 0.00 4.26
1398 1430 3.665409 GTGAACAAACTGAACATGATGCG 59.335 43.478 0.00 0.00 0.00 4.73
1414 1446 2.303175 GGGTTGGTTAGCAAGTGAACA 58.697 47.619 0.00 0.00 0.00 3.18
1421 1453 1.178534 GCAGCTGGGTTGGTTAGCAA 61.179 55.000 17.12 0.00 39.84 3.91
1422 1454 1.603455 GCAGCTGGGTTGGTTAGCA 60.603 57.895 17.12 0.00 39.84 3.49
1436 1468 5.947443 AGAAAATGTCAGAATTGTAGCAGC 58.053 37.500 0.00 0.00 0.00 5.25
1444 1476 5.335976 GGCGAAGGAAGAAAATGTCAGAATT 60.336 40.000 0.00 0.00 0.00 2.17
1465 1497 1.964608 TTGCAGATCTCCTCCTGGCG 61.965 60.000 0.00 0.00 0.00 5.69
1467 1499 0.179936 GGTTGCAGATCTCCTCCTGG 59.820 60.000 0.00 0.00 0.00 4.45
1476 1508 0.539986 TTCCCCTACGGTTGCAGATC 59.460 55.000 0.00 0.00 0.00 2.75
1548 1580 4.155733 CCGATGGTGTAGGCCGCA 62.156 66.667 0.00 0.00 0.00 5.69
1881 1913 5.584649 CCGACAGCCTACTAATGAATCAAAA 59.415 40.000 0.00 0.00 0.00 2.44
1911 1943 0.666374 ACAACTTTTACTGCCGGCAC 59.334 50.000 29.03 0.00 0.00 5.01
1998 2030 5.073428 GCCTAAGCCAGCTTTAATAGGAAT 58.927 41.667 18.78 0.00 37.47 3.01
2020 2054 3.451894 CCGGGGATGGCAAAGTGC 61.452 66.667 0.00 0.00 44.08 4.40
2062 2100 3.872603 ACGCAAGCCAGTGACCCA 61.873 61.111 0.00 0.00 45.62 4.51
2151 2190 1.133199 TGGGGCAGGAATTTGACAGTT 60.133 47.619 0.00 0.00 0.00 3.16
2156 2195 1.146774 TGAGTTGGGGCAGGAATTTGA 59.853 47.619 0.00 0.00 0.00 2.69
2275 2321 3.699538 ACTAGTTCACGCTCCATGATACA 59.300 43.478 0.00 0.00 0.00 2.29
2290 2336 5.934402 TGGAGGGAGTAAATGACTAGTTC 57.066 43.478 0.00 0.00 39.06 3.01
2293 2339 5.604650 AGGAATGGAGGGAGTAAATGACTAG 59.395 44.000 0.00 0.00 39.06 2.57
2297 2343 6.901615 TTTAGGAATGGAGGGAGTAAATGA 57.098 37.500 0.00 0.00 0.00 2.57
2329 2375 8.570068 ACCCGTGTGTAGTTTATATTGAAATT 57.430 30.769 0.00 0.00 0.00 1.82
2339 2393 9.891828 CGTTTATATATACCCGTGTGTAGTTTA 57.108 33.333 0.00 0.00 0.00 2.01
2387 2443 9.195411 CAACATGAACTACATACAAAGCAAAAT 57.805 29.630 0.00 0.00 37.46 1.82
2404 2460 9.220767 AGTCCTTTTAGAGATTACAACATGAAC 57.779 33.333 0.00 0.00 0.00 3.18
2405 2461 9.793259 AAGTCCTTTTAGAGATTACAACATGAA 57.207 29.630 0.00 0.00 0.00 2.57
2422 2478 9.392259 CCTCCGTTCTTAAATATAAGTCCTTTT 57.608 33.333 0.00 0.00 39.65 2.27
2423 2479 8.765517 TCCTCCGTTCTTAAATATAAGTCCTTT 58.234 33.333 0.00 0.00 39.65 3.11
2424 2480 8.315220 TCCTCCGTTCTTAAATATAAGTCCTT 57.685 34.615 0.00 0.00 39.65 3.36
2425 2481 7.909485 TCCTCCGTTCTTAAATATAAGTCCT 57.091 36.000 0.00 0.00 39.65 3.85
2426 2482 8.202811 ACTTCCTCCGTTCTTAAATATAAGTCC 58.797 37.037 0.00 0.00 39.65 3.85
2433 2489 9.860898 GTTAAGTACTTCCTCCGTTCTTAAATA 57.139 33.333 12.39 0.00 36.60 1.40
2434 2490 8.370182 TGTTAAGTACTTCCTCCGTTCTTAAAT 58.630 33.333 12.39 0.00 36.60 1.40
2435 2491 7.725251 TGTTAAGTACTTCCTCCGTTCTTAAA 58.275 34.615 12.39 0.00 36.60 1.52
2436 2492 7.288810 TGTTAAGTACTTCCTCCGTTCTTAA 57.711 36.000 12.39 0.00 34.23 1.85
2437 2493 6.899393 TGTTAAGTACTTCCTCCGTTCTTA 57.101 37.500 12.39 0.00 0.00 2.10
2438 2494 5.796424 TGTTAAGTACTTCCTCCGTTCTT 57.204 39.130 12.39 0.00 0.00 2.52
2439 2495 5.069516 TGTTGTTAAGTACTTCCTCCGTTCT 59.930 40.000 12.39 0.00 0.00 3.01
2440 2496 5.291971 TGTTGTTAAGTACTTCCTCCGTTC 58.708 41.667 12.39 0.00 0.00 3.95
2441 2497 5.280654 TGTTGTTAAGTACTTCCTCCGTT 57.719 39.130 12.39 0.00 0.00 4.44
2442 2498 4.798593 GCTGTTGTTAAGTACTTCCTCCGT 60.799 45.833 12.39 0.00 0.00 4.69
2443 2499 3.678548 GCTGTTGTTAAGTACTTCCTCCG 59.321 47.826 12.39 0.00 0.00 4.63
2444 2500 3.678548 CGCTGTTGTTAAGTACTTCCTCC 59.321 47.826 12.39 0.00 0.00 4.30
2445 2501 4.553323 TCGCTGTTGTTAAGTACTTCCTC 58.447 43.478 12.39 4.67 0.00 3.71
2446 2502 4.595762 TCGCTGTTGTTAAGTACTTCCT 57.404 40.909 12.39 0.00 0.00 3.36
2447 2503 5.662211 TTTCGCTGTTGTTAAGTACTTCC 57.338 39.130 12.39 4.83 0.00 3.46
2448 2504 5.564127 GCATTTCGCTGTTGTTAAGTACTTC 59.436 40.000 12.39 0.00 37.77 3.01
2449 2505 5.449304 GCATTTCGCTGTTGTTAAGTACTT 58.551 37.500 13.68 13.68 37.77 2.24
2450 2506 4.083484 GGCATTTCGCTGTTGTTAAGTACT 60.083 41.667 0.00 0.00 41.91 2.73
2451 2507 4.083484 AGGCATTTCGCTGTTGTTAAGTAC 60.083 41.667 0.00 0.00 41.91 2.73
2452 2508 4.069304 AGGCATTTCGCTGTTGTTAAGTA 58.931 39.130 0.00 0.00 41.91 2.24
2453 2509 2.884639 AGGCATTTCGCTGTTGTTAAGT 59.115 40.909 0.00 0.00 41.91 2.24
2454 2510 3.559238 AGGCATTTCGCTGTTGTTAAG 57.441 42.857 0.00 0.00 41.91 1.85
2455 2511 3.637432 CAAGGCATTTCGCTGTTGTTAA 58.363 40.909 0.00 0.00 41.91 2.01
2456 2512 2.606795 GCAAGGCATTTCGCTGTTGTTA 60.607 45.455 0.00 0.00 41.91 2.41
2457 2513 1.869342 GCAAGGCATTTCGCTGTTGTT 60.869 47.619 0.00 0.00 41.91 2.83
2458 2514 0.318955 GCAAGGCATTTCGCTGTTGT 60.319 50.000 0.00 0.00 41.91 3.32
2459 2515 1.010419 GGCAAGGCATTTCGCTGTTG 61.010 55.000 0.00 0.00 41.91 3.33
2460 2516 1.290009 GGCAAGGCATTTCGCTGTT 59.710 52.632 0.00 0.00 41.91 3.16
2461 2517 1.902918 TGGCAAGGCATTTCGCTGT 60.903 52.632 0.00 0.00 41.91 4.40
2462 2518 1.444895 GTGGCAAGGCATTTCGCTG 60.445 57.895 0.00 0.00 41.91 5.18
2463 2519 2.964978 GTGGCAAGGCATTTCGCT 59.035 55.556 0.00 0.00 41.91 4.93
2464 2520 2.504681 CGTGGCAAGGCATTTCGC 60.505 61.111 0.00 0.00 41.28 4.70
2465 2521 2.179018 CCGTGGCAAGGCATTTCG 59.821 61.111 6.51 0.00 0.00 3.46
2466 2522 1.322538 ATCCCGTGGCAAGGCATTTC 61.323 55.000 14.49 0.00 0.00 2.17
2467 2523 0.033601 TATCCCGTGGCAAGGCATTT 60.034 50.000 14.49 0.86 0.00 2.32
2468 2524 0.033601 TTATCCCGTGGCAAGGCATT 60.034 50.000 14.49 3.32 0.00 3.56
2469 2525 0.751643 GTTATCCCGTGGCAAGGCAT 60.752 55.000 14.49 7.61 0.00 4.40
2470 2526 1.377987 GTTATCCCGTGGCAAGGCA 60.378 57.895 14.49 0.00 0.00 4.75
2471 2527 0.963355 TTGTTATCCCGTGGCAAGGC 60.963 55.000 14.49 0.41 0.00 4.35
2472 2528 1.540267 TTTGTTATCCCGTGGCAAGG 58.460 50.000 12.93 12.93 0.00 3.61
2473 2529 2.817258 TCTTTTGTTATCCCGTGGCAAG 59.183 45.455 0.00 0.00 0.00 4.01
2474 2530 2.865079 TCTTTTGTTATCCCGTGGCAA 58.135 42.857 0.00 0.00 0.00 4.52
2475 2531 2.570415 TCTTTTGTTATCCCGTGGCA 57.430 45.000 0.00 0.00 0.00 4.92
2476 2532 5.767816 AATATCTTTTGTTATCCCGTGGC 57.232 39.130 0.00 0.00 0.00 5.01
2479 2535 9.227777 GCCTATAAATATCTTTTGTTATCCCGT 57.772 33.333 0.00 0.00 0.00 5.28
2480 2536 9.226606 TGCCTATAAATATCTTTTGTTATCCCG 57.773 33.333 0.00 0.00 0.00 5.14
2494 2550 9.419297 CGTGTATGTTAGTGTGCCTATAAATAT 57.581 33.333 0.00 0.00 0.00 1.28
2495 2551 7.868922 CCGTGTATGTTAGTGTGCCTATAAATA 59.131 37.037 0.00 0.00 0.00 1.40
2496 2552 6.704493 CCGTGTATGTTAGTGTGCCTATAAAT 59.296 38.462 0.00 0.00 0.00 1.40
2497 2553 6.044046 CCGTGTATGTTAGTGTGCCTATAAA 58.956 40.000 0.00 0.00 0.00 1.40
2498 2554 5.452216 CCCGTGTATGTTAGTGTGCCTATAA 60.452 44.000 0.00 0.00 0.00 0.98
2499 2555 4.038282 CCCGTGTATGTTAGTGTGCCTATA 59.962 45.833 0.00 0.00 0.00 1.31
2500 2556 3.181469 CCCGTGTATGTTAGTGTGCCTAT 60.181 47.826 0.00 0.00 0.00 2.57
2501 2557 2.166870 CCCGTGTATGTTAGTGTGCCTA 59.833 50.000 0.00 0.00 0.00 3.93
2502 2558 1.066430 CCCGTGTATGTTAGTGTGCCT 60.066 52.381 0.00 0.00 0.00 4.75
2503 2559 1.066716 TCCCGTGTATGTTAGTGTGCC 60.067 52.381 0.00 0.00 0.00 5.01
2504 2560 2.373540 TCCCGTGTATGTTAGTGTGC 57.626 50.000 0.00 0.00 0.00 4.57
2505 2561 5.412640 TGTTATCCCGTGTATGTTAGTGTG 58.587 41.667 0.00 0.00 0.00 3.82
2506 2562 5.664294 TGTTATCCCGTGTATGTTAGTGT 57.336 39.130 0.00 0.00 0.00 3.55
2507 2563 6.971527 TTTGTTATCCCGTGTATGTTAGTG 57.028 37.500 0.00 0.00 0.00 2.74
2508 2564 7.662669 ACTTTTTGTTATCCCGTGTATGTTAGT 59.337 33.333 0.00 0.00 0.00 2.24
2509 2565 8.036273 ACTTTTTGTTATCCCGTGTATGTTAG 57.964 34.615 0.00 0.00 0.00 2.34
2510 2566 7.982761 ACTTTTTGTTATCCCGTGTATGTTA 57.017 32.000 0.00 0.00 0.00 2.41
2511 2567 6.887626 ACTTTTTGTTATCCCGTGTATGTT 57.112 33.333 0.00 0.00 0.00 2.71
2512 2568 8.570068 AATACTTTTTGTTATCCCGTGTATGT 57.430 30.769 0.00 0.00 0.00 2.29
2537 2593 9.577110 CCATCTTTTACGTTAGTGTGTCTATAA 57.423 33.333 0.00 0.00 0.00 0.98
2538 2594 8.192774 CCCATCTTTTACGTTAGTGTGTCTATA 58.807 37.037 0.00 0.00 0.00 1.31
2539 2595 7.039882 CCCATCTTTTACGTTAGTGTGTCTAT 58.960 38.462 0.00 0.00 0.00 1.98
2540 2596 6.392354 CCCATCTTTTACGTTAGTGTGTCTA 58.608 40.000 0.00 0.00 0.00 2.59
2541 2597 5.235516 CCCATCTTTTACGTTAGTGTGTCT 58.764 41.667 0.00 0.00 0.00 3.41
2542 2598 4.142966 GCCCATCTTTTACGTTAGTGTGTC 60.143 45.833 0.00 0.00 0.00 3.67
2543 2599 3.749609 GCCCATCTTTTACGTTAGTGTGT 59.250 43.478 0.00 0.00 0.00 3.72
2544 2600 3.181524 CGCCCATCTTTTACGTTAGTGTG 60.182 47.826 0.00 0.00 0.00 3.82
2545 2601 2.997986 CGCCCATCTTTTACGTTAGTGT 59.002 45.455 0.00 0.00 0.00 3.55
2546 2602 3.255725 TCGCCCATCTTTTACGTTAGTG 58.744 45.455 0.00 0.00 0.00 2.74
2547 2603 3.598019 TCGCCCATCTTTTACGTTAGT 57.402 42.857 0.00 0.00 0.00 2.24
2548 2604 4.025979 GTCATCGCCCATCTTTTACGTTAG 60.026 45.833 0.00 0.00 0.00 2.34
2549 2605 3.866910 GTCATCGCCCATCTTTTACGTTA 59.133 43.478 0.00 0.00 0.00 3.18
2550 2606 2.676342 GTCATCGCCCATCTTTTACGTT 59.324 45.455 0.00 0.00 0.00 3.99
2551 2607 2.277084 GTCATCGCCCATCTTTTACGT 58.723 47.619 0.00 0.00 0.00 3.57
2552 2608 1.257936 CGTCATCGCCCATCTTTTACG 59.742 52.381 0.00 0.00 0.00 3.18
2553 2609 2.277084 ACGTCATCGCCCATCTTTTAC 58.723 47.619 0.00 0.00 41.18 2.01
2554 2610 2.684001 ACGTCATCGCCCATCTTTTA 57.316 45.000 0.00 0.00 41.18 1.52
2555 2611 2.093658 ACTACGTCATCGCCCATCTTTT 60.094 45.455 0.00 0.00 41.18 2.27
2556 2612 1.480954 ACTACGTCATCGCCCATCTTT 59.519 47.619 0.00 0.00 41.18 2.52
2557 2613 1.112113 ACTACGTCATCGCCCATCTT 58.888 50.000 0.00 0.00 41.18 2.40
2558 2614 0.385751 CACTACGTCATCGCCCATCT 59.614 55.000 0.00 0.00 41.18 2.90
2559 2615 0.597637 CCACTACGTCATCGCCCATC 60.598 60.000 0.00 0.00 41.18 3.51
2560 2616 1.441729 CCACTACGTCATCGCCCAT 59.558 57.895 0.00 0.00 41.18 4.00
2561 2617 2.717044 CCCACTACGTCATCGCCCA 61.717 63.158 0.00 0.00 41.18 5.36
2562 2618 1.952102 TTCCCACTACGTCATCGCCC 61.952 60.000 0.00 0.00 41.18 6.13
2563 2619 0.104304 ATTCCCACTACGTCATCGCC 59.896 55.000 0.00 0.00 41.18 5.54
2564 2620 1.209128 CATTCCCACTACGTCATCGC 58.791 55.000 0.00 0.00 41.18 4.58
2565 2621 2.579207 ACATTCCCACTACGTCATCG 57.421 50.000 0.00 0.00 43.34 3.84
2566 2622 4.557205 GGATACATTCCCACTACGTCATC 58.443 47.826 0.00 0.00 38.75 2.92
2567 2623 3.005472 CGGATACATTCCCACTACGTCAT 59.995 47.826 0.00 0.00 42.06 3.06
2568 2624 2.359848 CGGATACATTCCCACTACGTCA 59.640 50.000 0.00 0.00 42.06 4.35
2569 2625 2.288030 CCGGATACATTCCCACTACGTC 60.288 54.545 0.00 0.00 42.06 4.34
2570 2626 1.684983 CCGGATACATTCCCACTACGT 59.315 52.381 0.00 0.00 42.06 3.57
2571 2627 1.684983 ACCGGATACATTCCCACTACG 59.315 52.381 9.46 0.00 42.06 3.51
2572 2628 2.805657 GCACCGGATACATTCCCACTAC 60.806 54.545 9.46 0.00 42.06 2.73
2573 2629 1.414919 GCACCGGATACATTCCCACTA 59.585 52.381 9.46 0.00 42.06 2.74
2574 2630 0.180406 GCACCGGATACATTCCCACT 59.820 55.000 9.46 0.00 42.06 4.00
2575 2631 0.107410 TGCACCGGATACATTCCCAC 60.107 55.000 9.46 0.00 42.06 4.61
2576 2632 0.107410 GTGCACCGGATACATTCCCA 60.107 55.000 9.46 0.00 42.06 4.37
2577 2633 0.818040 GGTGCACCGGATACATTCCC 60.818 60.000 22.49 0.00 42.06 3.97
2578 2634 0.818040 GGGTGCACCGGATACATTCC 60.818 60.000 29.08 7.74 41.59 3.01
2579 2635 0.107410 TGGGTGCACCGGATACATTC 60.107 55.000 29.08 12.57 44.64 2.67
2580 2636 0.393808 GTGGGTGCACCGGATACATT 60.394 55.000 29.08 0.00 44.64 2.71
2581 2637 1.223487 GTGGGTGCACCGGATACAT 59.777 57.895 29.08 0.00 44.64 2.29
2582 2638 2.217745 TGTGGGTGCACCGGATACA 61.218 57.895 29.08 24.96 44.64 2.29
2583 2639 1.743995 GTGTGGGTGCACCGGATAC 60.744 63.158 29.08 22.91 44.64 2.24
2584 2640 1.485294 AAGTGTGGGTGCACCGGATA 61.485 55.000 29.08 13.90 44.64 2.59
2585 2641 2.829384 AAGTGTGGGTGCACCGGAT 61.829 57.895 29.08 10.62 44.64 4.18
2586 2642 3.484806 AAGTGTGGGTGCACCGGA 61.485 61.111 29.08 15.83 44.64 5.14
2587 2643 3.286751 CAAGTGTGGGTGCACCGG 61.287 66.667 29.08 0.00 44.64 5.28
2588 2644 2.515991 ACAAGTGTGGGTGCACCG 60.516 61.111 29.08 15.85 44.64 4.94
2589 2645 3.119193 CACAAGTGTGGGTGCACC 58.881 61.111 28.57 28.57 42.10 5.01
2600 2656 1.070786 CACCGGTAGCACCACAAGT 59.929 57.895 6.87 0.00 38.47 3.16
2601 2657 2.325082 GCACCGGTAGCACCACAAG 61.325 63.158 19.85 0.99 38.47 3.16
2602 2658 2.281208 GCACCGGTAGCACCACAA 60.281 61.111 19.85 0.00 38.47 3.33
2603 2659 3.551407 TGCACCGGTAGCACCACA 61.551 61.111 22.47 5.12 38.47 4.17
2648 2704 8.335356 GCGTTAACATGCTAGAATTTATTCAGA 58.665 33.333 6.39 0.00 34.22 3.27
2649 2705 8.122330 TGCGTTAACATGCTAGAATTTATTCAG 58.878 33.333 6.39 2.56 36.23 3.02
2650 2706 7.980062 TGCGTTAACATGCTAGAATTTATTCA 58.020 30.769 6.39 0.00 36.23 2.57
2651 2707 8.835467 TTGCGTTAACATGCTAGAATTTATTC 57.165 30.769 6.39 0.00 35.72 1.75
2655 2711 8.620416 TGATATTGCGTTAACATGCTAGAATTT 58.380 29.630 6.39 0.00 35.72 1.82
2656 2712 8.153479 TGATATTGCGTTAACATGCTAGAATT 57.847 30.769 6.39 0.00 35.72 2.17
2657 2713 7.728847 TGATATTGCGTTAACATGCTAGAAT 57.271 32.000 6.39 1.53 35.72 2.40
2658 2714 7.546778 TTGATATTGCGTTAACATGCTAGAA 57.453 32.000 6.39 0.00 35.72 2.10
2659 2715 7.226523 ACATTGATATTGCGTTAACATGCTAGA 59.773 33.333 6.39 0.00 35.72 2.43
2660 2716 7.355017 ACATTGATATTGCGTTAACATGCTAG 58.645 34.615 6.39 0.00 35.72 3.42
2661 2717 7.258022 ACATTGATATTGCGTTAACATGCTA 57.742 32.000 6.39 0.00 35.72 3.49
2662 2718 6.135290 ACATTGATATTGCGTTAACATGCT 57.865 33.333 6.39 0.00 35.72 3.79
2663 2719 7.802720 TCATACATTGATATTGCGTTAACATGC 59.197 33.333 6.39 2.42 35.21 4.06
2664 2720 9.830294 ATCATACATTGATATTGCGTTAACATG 57.170 29.630 6.39 1.20 43.43 3.21
2665 2721 9.830294 CATCATACATTGATATTGCGTTAACAT 57.170 29.630 6.39 0.00 43.40 2.71
2666 2722 8.835439 ACATCATACATTGATATTGCGTTAACA 58.165 29.630 6.39 0.00 43.40 2.41
2667 2723 9.318041 GACATCATACATTGATATTGCGTTAAC 57.682 33.333 0.00 0.00 43.40 2.01
2668 2724 9.050601 TGACATCATACATTGATATTGCGTTAA 57.949 29.630 0.00 0.00 43.40 2.01
2669 2725 8.495148 GTGACATCATACATTGATATTGCGTTA 58.505 33.333 0.00 0.00 43.40 3.18
2670 2726 7.012232 TGTGACATCATACATTGATATTGCGTT 59.988 33.333 0.00 0.00 43.40 4.84
2671 2727 6.482973 TGTGACATCATACATTGATATTGCGT 59.517 34.615 0.00 0.00 43.40 5.24
2672 2728 6.890558 TGTGACATCATACATTGATATTGCG 58.109 36.000 0.00 0.00 43.40 4.85
2673 2729 9.518906 TTTTGTGACATCATACATTGATATTGC 57.481 29.630 0.00 0.00 43.40 3.56
2732 2788 9.941325 ACTGATGCCAAATTTATCATTTTTGTA 57.059 25.926 3.23 0.00 31.11 2.41
2733 2789 8.723311 CACTGATGCCAAATTTATCATTTTTGT 58.277 29.630 3.23 0.00 31.11 2.83
2734 2790 8.723311 ACACTGATGCCAAATTTATCATTTTTG 58.277 29.630 3.23 5.08 31.11 2.44
2735 2791 8.723311 CACACTGATGCCAAATTTATCATTTTT 58.277 29.630 3.23 0.00 31.11 1.94
2736 2792 8.095792 TCACACTGATGCCAAATTTATCATTTT 58.904 29.630 3.23 0.00 31.11 1.82
2737 2793 7.613585 TCACACTGATGCCAAATTTATCATTT 58.386 30.769 3.23 0.00 31.11 2.32
2738 2794 7.172868 TCACACTGATGCCAAATTTATCATT 57.827 32.000 3.23 0.00 31.11 2.57
2739 2795 6.778834 TCACACTGATGCCAAATTTATCAT 57.221 33.333 3.23 3.92 31.11 2.45
2740 2796 6.587206 TTCACACTGATGCCAAATTTATCA 57.413 33.333 2.88 2.88 0.00 2.15
2741 2797 7.887996 TTTTCACACTGATGCCAAATTTATC 57.112 32.000 0.00 0.00 0.00 1.75
2742 2798 7.334921 CCATTTTCACACTGATGCCAAATTTAT 59.665 33.333 0.00 0.00 0.00 1.40
2743 2799 6.649973 CCATTTTCACACTGATGCCAAATTTA 59.350 34.615 0.00 0.00 0.00 1.40
2744 2800 5.470777 CCATTTTCACACTGATGCCAAATTT 59.529 36.000 0.00 0.00 0.00 1.82
2745 2801 4.998672 CCATTTTCACACTGATGCCAAATT 59.001 37.500 0.00 0.00 0.00 1.82
2746 2802 4.563993 CCCATTTTCACACTGATGCCAAAT 60.564 41.667 0.00 0.00 0.00 2.32
2747 2803 3.244146 CCCATTTTCACACTGATGCCAAA 60.244 43.478 0.00 0.00 0.00 3.28
2748 2804 2.299582 CCCATTTTCACACTGATGCCAA 59.700 45.455 0.00 0.00 0.00 4.52
2749 2805 1.894466 CCCATTTTCACACTGATGCCA 59.106 47.619 0.00 0.00 0.00 4.92
2750 2806 1.404583 GCCCATTTTCACACTGATGCC 60.405 52.381 0.00 0.00 0.00 4.40
2751 2807 1.404583 GGCCCATTTTCACACTGATGC 60.405 52.381 0.00 0.00 0.00 3.91
2752 2808 1.894466 TGGCCCATTTTCACACTGATG 59.106 47.619 0.00 0.00 0.00 3.07
2753 2809 2.307496 TGGCCCATTTTCACACTGAT 57.693 45.000 0.00 0.00 0.00 2.90
2754 2810 2.079170 TTGGCCCATTTTCACACTGA 57.921 45.000 0.00 0.00 0.00 3.41
2755 2811 2.906691 TTTGGCCCATTTTCACACTG 57.093 45.000 0.00 0.00 0.00 3.66
2756 2812 3.242011 AGATTTGGCCCATTTTCACACT 58.758 40.909 0.00 0.00 0.00 3.55
2757 2813 3.683365 AGATTTGGCCCATTTTCACAC 57.317 42.857 0.00 0.00 0.00 3.82
2758 2814 5.792741 CTTTAGATTTGGCCCATTTTCACA 58.207 37.500 0.00 0.00 0.00 3.58
2759 2815 4.631377 GCTTTAGATTTGGCCCATTTTCAC 59.369 41.667 0.00 0.00 0.00 3.18
2760 2816 4.323409 GGCTTTAGATTTGGCCCATTTTCA 60.323 41.667 0.00 0.00 38.77 2.69
2761 2817 4.191544 GGCTTTAGATTTGGCCCATTTTC 58.808 43.478 0.00 0.00 38.77 2.29
2762 2818 4.220693 GGCTTTAGATTTGGCCCATTTT 57.779 40.909 0.00 0.00 38.77 1.82
2763 2819 3.912496 GGCTTTAGATTTGGCCCATTT 57.088 42.857 0.00 0.00 38.77 2.32
2768 2824 2.456577 TCTTGGGCTTTAGATTTGGCC 58.543 47.619 0.00 0.00 45.24 5.36
2769 2825 5.852282 TTATCTTGGGCTTTAGATTTGGC 57.148 39.130 0.00 0.00 33.38 4.52
2770 2826 7.352079 ACATTATCTTGGGCTTTAGATTTGG 57.648 36.000 0.00 0.00 33.38 3.28
2773 2829 9.646522 ACATAACATTATCTTGGGCTTTAGATT 57.353 29.630 0.00 0.00 33.38 2.40
2775 2831 9.555727 GTACATAACATTATCTTGGGCTTTAGA 57.444 33.333 0.00 0.00 0.00 2.10
2776 2832 9.561069 AGTACATAACATTATCTTGGGCTTTAG 57.439 33.333 0.00 0.00 0.00 1.85
2780 2836 9.726438 GAATAGTACATAACATTATCTTGGGCT 57.274 33.333 0.00 0.00 0.00 5.19
2781 2837 9.502091 TGAATAGTACATAACATTATCTTGGGC 57.498 33.333 0.00 0.00 0.00 5.36
2848 2904 9.771915 GTTGTCACAACATTTCAAATCAAAATT 57.228 25.926 16.14 0.00 34.73 1.82
2849 2905 8.397148 GGTTGTCACAACATTTCAAATCAAAAT 58.603 29.630 22.13 0.00 34.73 1.82
2850 2906 7.605691 AGGTTGTCACAACATTTCAAATCAAAA 59.394 29.630 22.13 0.00 34.73 2.44
2851 2907 7.102346 AGGTTGTCACAACATTTCAAATCAAA 58.898 30.769 22.13 0.00 34.73 2.69
2852 2908 6.638610 AGGTTGTCACAACATTTCAAATCAA 58.361 32.000 22.13 0.00 34.73 2.57
2853 2909 6.219417 AGGTTGTCACAACATTTCAAATCA 57.781 33.333 22.13 0.00 34.73 2.57
2854 2910 7.623268 GTAGGTTGTCACAACATTTCAAATC 57.377 36.000 22.13 1.54 34.73 2.17


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

AutoCloner maintained by Alex Coulton.