Multiple sequence alignment - TraesCS5A01G297800

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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 TraesCS5A01G297800 chr5A 100.000 2634 0 0 725 3358 505489135 505491768 0.000000e+00 4865.0
1 TraesCS5A01G297800 chr5A 100.000 441 0 0 1 441 505488411 505488851 0.000000e+00 815.0
2 TraesCS5A01G297800 chr5A 73.200 500 98 19 1758 2230 505353009 505353499 7.510000e-32 148.0
3 TraesCS5A01G297800 chr5A 97.368 38 1 0 8 45 127986360 127986323 7.780000e-07 65.8
4 TraesCS5A01G297800 chr5B 88.433 1340 95 32 1654 2979 479816751 479818044 0.000000e+00 1561.0
5 TraesCS5A01G297800 chr5B 93.405 925 36 2 726 1650 479815815 479816714 0.000000e+00 1347.0
6 TraesCS5A01G297800 chr5B 93.182 440 25 4 1 440 479815296 479815730 2.820000e-180 641.0
7 TraesCS5A01G297800 chr5B 88.514 296 33 1 3017 3312 479818152 479818446 1.150000e-94 357.0
8 TraesCS5A01G297800 chr5D 95.992 474 18 1 1104 1577 399928140 399928612 0.000000e+00 769.0
9 TraesCS5A01G297800 chr5D 87.970 399 35 7 725 1112 399909703 399910099 3.050000e-125 459.0
10 TraesCS5A01G297800 chr5D 80.481 374 65 5 1038 1404 399735672 399736044 2.550000e-71 279.0
11 TraesCS5A01G297800 chr5D 74.155 503 94 20 1758 2233 399793480 399793973 3.440000e-40 176.0
12 TraesCS5A01G297800 chr5D 74.935 387 62 19 1213 1566 399792889 399793273 9.710000e-31 145.0
13 TraesCS5A01G297800 chr2A 80.747 696 108 12 978 1651 47796127 47795436 1.380000e-143 520.0
14 TraesCS5A01G297800 chr2A 82.675 329 51 5 983 1306 47825340 47825013 1.520000e-73 287.0
15 TraesCS5A01G297800 chr2A 85.714 63 6 3 376 438 61383390 61383449 2.800000e-06 63.9
16 TraesCS5A01G297800 chr2B 80.265 679 104 16 997 1651 69036068 69035396 5.040000e-133 484.0
17 TraesCS5A01G297800 chr2B 79.070 645 106 18 1029 1651 69003759 69004396 1.860000e-112 416.0
18 TraesCS5A01G297800 chr2D 80.031 641 100 11 1029 1649 43988225 43987593 1.840000e-122 449.0
19 TraesCS5A01G297800 chr2D 80.110 543 90 11 1119 1651 43974757 43975291 4.060000e-104 388.0
20 TraesCS5A01G297800 chr2D 88.462 52 5 1 376 427 60789987 60790037 1.010000e-05 62.1
21 TraesCS5A01G297800 chr7A 88.889 72 8 0 5 76 263716032 263715961 4.610000e-14 89.8
22 TraesCS5A01G297800 chr7A 85.882 85 11 1 5 89 563503544 563503627 4.610000e-14 89.8
23 TraesCS5A01G297800 chr7A 85.135 74 11 0 3 76 625711427 625711500 3.590000e-10 76.8
24 TraesCS5A01G297800 chr7B 92.982 57 4 0 5 61 223173149 223173093 2.150000e-12 84.2
25 TraesCS5A01G297800 chr7B 83.529 85 13 1 5 89 526425887 526425970 9.990000e-11 78.7
26 TraesCS5A01G297800 chr7D 91.228 57 5 0 3 59 544366786 544366842 9.990000e-11 78.7
27 TraesCS5A01G297800 chr7D 90.909 55 5 0 8 62 129802620 129802674 1.290000e-09 75.0
28 TraesCS5A01G297800 chr1B 72.908 251 59 6 1992 2234 180552276 180552027 9.990000e-11 78.7
29 TraesCS5A01G297800 chr1B 91.304 46 4 0 3313 3358 413929649 413929604 2.800000e-06 63.9


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 TraesCS5A01G297800 chr5A 505488411 505491768 3357 False 2840.0 4865 100.0000 1 3358 2 chr5A.!!$F2 3357
1 TraesCS5A01G297800 chr5B 479815296 479818446 3150 False 976.5 1561 90.8835 1 3312 4 chr5B.!!$F1 3311
2 TraesCS5A01G297800 chr2A 47795436 47796127 691 True 520.0 520 80.7470 978 1651 1 chr2A.!!$R1 673
3 TraesCS5A01G297800 chr2B 69035396 69036068 672 True 484.0 484 80.2650 997 1651 1 chr2B.!!$R1 654
4 TraesCS5A01G297800 chr2B 69003759 69004396 637 False 416.0 416 79.0700 1029 1651 1 chr2B.!!$F1 622
5 TraesCS5A01G297800 chr2D 43987593 43988225 632 True 449.0 449 80.0310 1029 1649 1 chr2D.!!$R1 620
6 TraesCS5A01G297800 chr2D 43974757 43975291 534 False 388.0 388 80.1100 1119 1651 1 chr2D.!!$F1 532

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
78 79 0.248289 ACAAACGAGGTATGGTCCGG 59.752 55.0 0.0 0.0 0.00 5.14 F
868 869 0.390472 CTCGGAGCACTTTGACCTCC 60.390 60.0 0.0 0.0 41.35 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 2118 0.301687 GTCATAGCGAACCACATGCG 59.698 55.0 0.00 0.0 0.0 4.73 R
2847 2930 0.041400 TTGTGCAATGAAGTCGCGTG 60.041 50.0 5.77 0.0 0.0 5.34 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
63 64 0.749818 TCCAGTTCTGCGGCAACAAA 60.750 50.000 3.44 0.00 0.00 2.83
78 79 0.248289 ACAAACGAGGTATGGTCCGG 59.752 55.000 0.00 0.00 0.00 5.14
85 86 2.223665 CGAGGTATGGTCCGGTTTAGAC 60.224 54.545 0.00 0.00 0.00 2.59
128 129 5.754406 TGGCATGACTTCAAATCAACAAAAG 59.246 36.000 0.00 0.00 0.00 2.27
131 132 6.345250 GCATGACTTCAAATCAACAAAAGACG 60.345 38.462 0.00 0.00 0.00 4.18
159 160 6.154877 TGCAACATGGATGAGGTGAAAATATT 59.845 34.615 0.00 0.00 0.00 1.28
160 161 7.341512 TGCAACATGGATGAGGTGAAAATATTA 59.658 33.333 0.00 0.00 0.00 0.98
293 294 7.441836 TGGTACAAAGGCATATCATAGTACAG 58.558 38.462 0.00 0.00 33.99 2.74
321 322 9.816354 ATACTGCCCAAAAATAAATATCAACAC 57.184 29.630 0.00 0.00 0.00 3.32
330 331 9.751542 AAAAATAAATATCAACACGAAACCACA 57.248 25.926 0.00 0.00 0.00 4.17
831 832 4.301027 AGATCCGCCGCCCGAATC 62.301 66.667 0.00 0.00 40.02 2.52
868 869 0.390472 CTCGGAGCACTTTGACCTCC 60.390 60.000 0.00 0.00 41.35 4.30
873 874 1.899142 GAGCACTTTGACCTCCTCTCT 59.101 52.381 0.00 0.00 0.00 3.10
878 879 3.831911 CACTTTGACCTCCTCTCTCTTCT 59.168 47.826 0.00 0.00 0.00 2.85
1014 1015 3.134458 GCTCCATCCTTACATTTCCTCG 58.866 50.000 0.00 0.00 0.00 4.63
1110 1125 4.477975 GTGCTCGACGACCTCCCG 62.478 72.222 0.00 0.00 0.00 5.14
1294 1315 1.600636 CCGCAGAAAACCAGCCTCA 60.601 57.895 0.00 0.00 0.00 3.86
1429 1450 1.511850 CACGGTGCATGAGTTCTTCA 58.488 50.000 0.00 0.00 40.85 3.02
1448 1469 1.779061 AATCTGCAACCCGGTCACCT 61.779 55.000 0.00 0.00 0.00 4.00
1616 1655 0.907230 TGTCATGTCGGTGGGATCCA 60.907 55.000 15.23 0.00 0.00 3.41
1669 1741 2.431942 CCGTTACGTGAGCGGCTT 60.432 61.111 2.97 0.00 43.45 4.35
1704 1776 1.331399 TATCCGCCAATCGACCACCA 61.331 55.000 0.00 0.00 41.67 4.17
1765 1837 2.635427 TGATGCCGGCTACATAATGGTA 59.365 45.455 29.70 1.81 0.00 3.25
1789 1861 6.395426 TTCAAGACAGCAGATGAAACATTT 57.605 33.333 0.00 0.00 0.00 2.32
1801 1873 4.909696 TGAAACATTTCGGTTGATGTGT 57.090 36.364 0.18 0.00 40.01 3.72
1807 1879 2.631160 TTCGGTTGATGTGTTGTCCT 57.369 45.000 0.00 0.00 0.00 3.85
1808 1880 2.163818 TCGGTTGATGTGTTGTCCTC 57.836 50.000 0.00 0.00 0.00 3.71
1911 1983 5.473504 CCATAGATATTTGGGTGGTACAAGC 59.526 44.000 0.00 0.00 44.16 4.01
1918 1990 2.487775 TGGGTGGTACAAGCCTATGAT 58.512 47.619 19.20 0.00 44.16 2.45
1920 1992 2.438021 GGGTGGTACAAGCCTATGATGA 59.562 50.000 11.48 0.00 44.16 2.92
1949 2021 2.503765 TGGTCCTTCAAGCATCGGATTA 59.496 45.455 0.00 0.00 0.00 1.75
2046 2118 2.284190 GCTGATCCAGTTTGCTCCTAC 58.716 52.381 0.00 0.00 33.43 3.18
2061 2133 0.179121 CCTACGCATGTGGTTCGCTA 60.179 55.000 11.65 0.00 0.00 4.26
2068 2140 2.032549 GCATGTGGTTCGCTATGACATC 60.033 50.000 0.00 0.00 0.00 3.06
2112 2184 2.104111 TGAAAAGCGAAGAGGACCAAGA 59.896 45.455 0.00 0.00 0.00 3.02
2200 2272 1.601759 GCAAGAAGGAGGTGCTGCA 60.602 57.895 0.00 0.00 35.36 4.41
2248 2324 4.000331 GCTATAGCCTTGCTTCATCTGA 58.000 45.455 14.13 0.00 40.44 3.27
2249 2325 4.577875 GCTATAGCCTTGCTTCATCTGAT 58.422 43.478 14.13 0.00 40.44 2.90
2250 2326 4.392445 GCTATAGCCTTGCTTCATCTGATG 59.608 45.833 14.13 11.42 40.44 3.07
2255 2331 3.675228 GCCTTGCTTCATCTGATGGTTTG 60.675 47.826 17.06 6.74 0.00 2.93
2310 2386 9.220767 ACTATTGTCATTGTTCTTAGTTCTTCC 57.779 33.333 0.00 0.00 0.00 3.46
2360 2436 6.176183 AGAATGAAACACTTCGGATGATTCT 58.824 36.000 0.00 0.00 33.94 2.40
2368 2444 6.276847 ACACTTCGGATGATTCTGTATTCTC 58.723 40.000 0.00 0.00 0.00 2.87
2386 2462 2.170397 TCTCAAACTGCTTCTGTCCACA 59.830 45.455 0.00 0.00 0.00 4.17
2387 2463 3.144506 CTCAAACTGCTTCTGTCCACAT 58.855 45.455 0.00 0.00 0.00 3.21
2395 2473 4.002982 TGCTTCTGTCCACATATTGTCAC 58.997 43.478 0.00 0.00 0.00 3.67
2397 2475 4.142816 GCTTCTGTCCACATATTGTCACAC 60.143 45.833 0.00 0.00 0.00 3.82
2425 2503 5.385509 TTTTTCCTAGCAATTACACTGGC 57.614 39.130 0.00 0.00 0.00 4.85
2426 2504 4.301072 TTTCCTAGCAATTACACTGGCT 57.699 40.909 0.00 0.00 40.26 4.75
2427 2505 3.266510 TCCTAGCAATTACACTGGCTG 57.733 47.619 0.00 0.00 37.17 4.85
2428 2506 2.092968 TCCTAGCAATTACACTGGCTGG 60.093 50.000 0.00 0.00 37.17 4.85
2433 2511 2.493278 GCAATTACACTGGCTGGTTGAT 59.507 45.455 0.00 0.00 0.00 2.57
2454 2532 4.098914 TCAACTGCCCTGAAATTGTACT 57.901 40.909 0.00 0.00 0.00 2.73
2465 2543 5.238432 CCTGAAATTGTACTAGTGTTGTGCA 59.762 40.000 5.39 0.00 0.00 4.57
2469 2547 7.860373 TGAAATTGTACTAGTGTTGTGCAAATC 59.140 33.333 5.39 0.00 41.67 2.17
2481 2560 2.158645 TGTGCAAATCGGAACACATACG 59.841 45.455 0.00 0.00 38.07 3.06
2488 2567 6.675971 GCAAATCGGAACACATACGGATTTTA 60.676 38.462 0.00 0.00 40.95 1.52
2489 2568 7.414436 CAAATCGGAACACATACGGATTTTAT 58.586 34.615 0.00 0.00 40.95 1.40
2494 2573 6.399669 CGGAACACATACGGATTTTATCGATC 60.400 42.308 0.00 0.00 0.00 3.69
2505 2584 4.855298 TTTTATCGATCCCTTCCCTTGT 57.145 40.909 0.00 0.00 0.00 3.16
2531 2610 6.014012 TCCTTTTCCCGTTTCCAGAATAATT 58.986 36.000 0.00 0.00 0.00 1.40
2532 2611 6.071616 TCCTTTTCCCGTTTCCAGAATAATTG 60.072 38.462 0.00 0.00 0.00 2.32
2533 2612 5.652994 TTTCCCGTTTCCAGAATAATTGG 57.347 39.130 0.00 0.00 37.04 3.16
2534 2613 4.577988 TCCCGTTTCCAGAATAATTGGA 57.422 40.909 0.00 0.00 42.81 3.53
2535 2614 4.266714 TCCCGTTTCCAGAATAATTGGAC 58.733 43.478 0.00 0.00 44.13 4.02
2536 2615 4.013728 CCCGTTTCCAGAATAATTGGACA 58.986 43.478 0.00 0.00 44.13 4.02
2539 2618 5.861787 CCGTTTCCAGAATAATTGGACAAAC 59.138 40.000 0.00 0.00 44.13 2.93
2545 2624 5.577945 CCAGAATAATTGGACAAACATGTGC 59.422 40.000 0.00 0.00 37.96 4.57
2554 2633 4.155826 TGGACAAACATGTGCTATGCTTAC 59.844 41.667 0.00 0.00 0.00 2.34
2555 2634 4.155826 GGACAAACATGTGCTATGCTTACA 59.844 41.667 0.00 0.00 0.00 2.41
2557 2636 5.003160 ACAAACATGTGCTATGCTTACAGA 58.997 37.500 0.00 0.00 0.00 3.41
2558 2637 5.122869 ACAAACATGTGCTATGCTTACAGAG 59.877 40.000 0.00 0.00 38.20 3.35
2559 2638 4.478206 ACATGTGCTATGCTTACAGAGT 57.522 40.909 0.00 0.00 37.45 3.24
2560 2639 4.836825 ACATGTGCTATGCTTACAGAGTT 58.163 39.130 0.00 0.00 37.45 3.01
2561 2640 5.977635 ACATGTGCTATGCTTACAGAGTTA 58.022 37.500 0.00 0.00 37.45 2.24
2562 2641 5.812642 ACATGTGCTATGCTTACAGAGTTAC 59.187 40.000 0.00 0.00 37.45 2.50
2563 2642 5.400066 TGTGCTATGCTTACAGAGTTACA 57.600 39.130 0.00 0.00 37.45 2.41
2564 2643 5.410924 TGTGCTATGCTTACAGAGTTACAG 58.589 41.667 0.00 0.00 37.45 2.74
2565 2644 5.047306 TGTGCTATGCTTACAGAGTTACAGT 60.047 40.000 0.00 0.00 37.45 3.55
2566 2645 6.152154 TGTGCTATGCTTACAGAGTTACAGTA 59.848 38.462 0.00 0.00 37.45 2.74
2567 2646 7.033791 GTGCTATGCTTACAGAGTTACAGTAA 58.966 38.462 0.00 0.00 37.45 2.24
2568 2647 7.544566 GTGCTATGCTTACAGAGTTACAGTAAA 59.455 37.037 0.00 0.00 37.45 2.01
2569 2648 8.092068 TGCTATGCTTACAGAGTTACAGTAAAA 58.908 33.333 0.00 0.00 37.45 1.52
2570 2649 8.596380 GCTATGCTTACAGAGTTACAGTAAAAG 58.404 37.037 0.00 0.00 37.45 2.27
2578 2657 6.018994 ACAGAGTTACAGTAAAAGAGCAAACG 60.019 38.462 0.00 0.00 0.00 3.60
2585 2664 9.872757 TTACAGTAAAAGAGCAAACGAAATTAG 57.127 29.630 0.00 0.00 0.00 1.73
2591 2670 6.695292 AAGAGCAAACGAAATTAGCAAATG 57.305 33.333 0.00 0.00 0.00 2.32
2598 2677 5.262588 ACGAAATTAGCAAATGATTCCCC 57.737 39.130 0.00 0.00 0.00 4.81
2611 2690 3.689347 TGATTCCCCACACTTCATTCTG 58.311 45.455 0.00 0.00 0.00 3.02
2617 2696 4.536090 TCCCCACACTTCATTCTGTATCTT 59.464 41.667 0.00 0.00 0.00 2.40
2619 2698 5.124457 CCCCACACTTCATTCTGTATCTTTG 59.876 44.000 0.00 0.00 0.00 2.77
2620 2699 5.392380 CCCACACTTCATTCTGTATCTTTGC 60.392 44.000 0.00 0.00 0.00 3.68
2621 2700 5.181811 CCACACTTCATTCTGTATCTTTGCA 59.818 40.000 0.00 0.00 0.00 4.08
2622 2701 6.127814 CCACACTTCATTCTGTATCTTTGCAT 60.128 38.462 0.00 0.00 0.00 3.96
2623 2702 7.310664 CACACTTCATTCTGTATCTTTGCATT 58.689 34.615 0.00 0.00 0.00 3.56
2624 2703 8.453320 CACACTTCATTCTGTATCTTTGCATTA 58.547 33.333 0.00 0.00 0.00 1.90
2656 2736 5.163088 ACTGTTGGAAAGGTCCTTACAAGAT 60.163 40.000 17.50 7.43 45.22 2.40
2660 2740 5.805728 TGGAAAGGTCCTTACAAGATCTTC 58.194 41.667 4.57 0.00 45.22 2.87
2661 2741 5.309543 TGGAAAGGTCCTTACAAGATCTTCA 59.690 40.000 4.57 0.00 45.22 3.02
2662 2742 6.183361 TGGAAAGGTCCTTACAAGATCTTCAA 60.183 38.462 4.57 2.00 45.22 2.69
2667 2747 7.234355 AGGTCCTTACAAGATCTTCAAAATGT 58.766 34.615 4.57 2.70 0.00 2.71
2668 2748 7.175641 AGGTCCTTACAAGATCTTCAAAATGTG 59.824 37.037 4.57 0.00 0.00 3.21
2672 2752 9.533253 CCTTACAAGATCTTCAAAATGTGTTTT 57.467 29.630 4.57 0.00 38.03 2.43
2695 2775 0.109342 AGAAGCAGGTTCAGTGTGGG 59.891 55.000 14.73 0.00 37.67 4.61
2698 2778 0.109342 AGCAGGTTCAGTGTGGGAAG 59.891 55.000 0.00 0.00 0.00 3.46
2700 2780 1.879796 GCAGGTTCAGTGTGGGAAGAG 60.880 57.143 0.00 0.00 0.00 2.85
2712 2792 6.825721 CAGTGTGGGAAGAGCTTTAAGATATT 59.174 38.462 0.00 0.00 0.00 1.28
2714 2794 7.554476 AGTGTGGGAAGAGCTTTAAGATATTTC 59.446 37.037 0.00 0.00 0.00 2.17
2715 2795 6.828785 TGTGGGAAGAGCTTTAAGATATTTCC 59.171 38.462 7.87 7.87 31.32 3.13
2716 2796 6.828785 GTGGGAAGAGCTTTAAGATATTTCCA 59.171 38.462 12.92 12.92 38.08 3.53
2717 2797 7.339466 GTGGGAAGAGCTTTAAGATATTTCCAA 59.661 37.037 17.73 8.65 41.59 3.53
2718 2798 7.557719 TGGGAAGAGCTTTAAGATATTTCCAAG 59.442 37.037 14.35 0.00 37.52 3.61
2719 2799 7.013750 GGGAAGAGCTTTAAGATATTTCCAAGG 59.986 40.741 20.07 0.00 31.04 3.61
2720 2800 7.558081 GGAAGAGCTTTAAGATATTTCCAAGGT 59.442 37.037 16.15 0.00 31.59 3.50
2721 2801 9.614792 GAAGAGCTTTAAGATATTTCCAAGGTA 57.385 33.333 0.00 0.00 0.00 3.08
2731 2811 9.642343 AAGATATTTCCAAGGTATTTAGGGAAC 57.358 33.333 0.00 0.00 37.36 3.62
2743 2823 8.783903 AGGTATTTAGGGAACATGGTTTACATA 58.216 33.333 0.00 0.00 37.84 2.29
2764 2844 7.907389 ACATATAACAGAAGACAAAGACCAGA 58.093 34.615 0.00 0.00 0.00 3.86
2772 2852 6.422400 CAGAAGACAAAGACCAGAGTTTACTC 59.578 42.308 1.59 1.59 43.17 2.59
2775 2855 4.381411 ACAAAGACCAGAGTTTACTCAGC 58.619 43.478 12.10 0.00 45.21 4.26
2785 2865 8.540388 ACCAGAGTTTACTCAGCTGATAAATTA 58.460 33.333 18.63 1.14 45.21 1.40
2845 2928 9.547279 AATTTCATATTTTACCCTCTTTGGACT 57.453 29.630 0.00 0.00 38.35 3.85
2846 2929 8.950007 TTTCATATTTTACCCTCTTTGGACTT 57.050 30.769 0.00 0.00 38.35 3.01
2847 2930 8.575649 TTCATATTTTACCCTCTTTGGACTTC 57.424 34.615 0.00 0.00 38.35 3.01
2848 2931 7.695055 TCATATTTTACCCTCTTTGGACTTCA 58.305 34.615 0.00 0.00 38.35 3.02
2849 2932 7.610305 TCATATTTTACCCTCTTTGGACTTCAC 59.390 37.037 0.00 0.00 38.35 3.18
2864 2947 0.234625 TTCACGCGACTTCATTGCAC 59.765 50.000 15.93 0.00 37.61 4.57
2886 2969 5.241506 CACAATGATAAGAACACCCACAGTT 59.758 40.000 0.00 0.00 0.00 3.16
2896 2979 8.706322 AAGAACACCCACAGTTAAGAAAATAT 57.294 30.769 0.00 0.00 0.00 1.28
2902 2985 9.410556 CACCCACAGTTAAGAAAATATGAAAAG 57.589 33.333 0.00 0.00 0.00 2.27
2907 2990 8.306761 ACAGTTAAGAAAATATGAAAAGCTGGG 58.693 33.333 0.00 0.00 0.00 4.45
2939 3022 5.422012 CCAAGCATATTTCACCCCTTACTTT 59.578 40.000 0.00 0.00 0.00 2.66
2947 3030 0.775542 ACCCCTTACTTTGACCACCC 59.224 55.000 0.00 0.00 0.00 4.61
2962 3046 3.161866 ACCACCCTTGCAAATATTTCGT 58.838 40.909 0.00 0.00 0.00 3.85
2969 3053 8.134895 CACCCTTGCAAATATTTCGTGTATAAT 58.865 33.333 0.00 0.00 0.00 1.28
2995 3111 1.471676 CGGGATCTACTTGCAGACACC 60.472 57.143 0.00 0.00 0.00 4.16
3002 3118 3.699538 TCTACTTGCAGACACCATACGAT 59.300 43.478 0.00 0.00 0.00 3.73
3015 3131 1.198408 CATACGATGGATGCCATGTGC 59.802 52.381 3.25 0.00 45.26 4.57
3039 3193 6.016276 GCAAACTTCCTAAAATCTCAGGTGAA 60.016 38.462 0.00 0.00 33.37 3.18
3076 3230 0.040157 CATGACATTTATGCCCCGCG 60.040 55.000 0.00 0.00 0.00 6.46
3090 3244 2.876645 CGCGGCGACTGTTCTCTC 60.877 66.667 19.16 0.00 0.00 3.20
3093 3247 1.512310 CGGCGACTGTTCTCTCGAC 60.512 63.158 0.00 0.00 34.37 4.20
3096 3250 1.498166 CGACTGTTCTCTCGACGCT 59.502 57.895 0.00 0.00 31.24 5.07
3099 3253 0.889638 ACTGTTCTCTCGACGCTGGA 60.890 55.000 0.00 0.00 0.00 3.86
3115 3269 3.689161 CGCTGGATGGTCTGTTATTTTCA 59.311 43.478 0.00 0.00 0.00 2.69
3117 3271 5.585390 GCTGGATGGTCTGTTATTTTCATG 58.415 41.667 0.00 0.00 0.00 3.07
3119 3273 6.350445 GCTGGATGGTCTGTTATTTTCATGTT 60.350 38.462 0.00 0.00 0.00 2.71
3184 3338 0.392729 GGATCAGCAGCTGCAACTCT 60.393 55.000 38.24 16.73 45.16 3.24
3200 3354 7.414984 GCTGCAACTCTTCTTTTATGAAGCTAT 60.415 37.037 0.00 0.00 42.15 2.97
3236 3390 7.123997 TGGAAATATATGTGGCATGTCAAAGTT 59.876 33.333 0.00 0.00 0.00 2.66
3237 3391 8.629158 GGAAATATATGTGGCATGTCAAAGTTA 58.371 33.333 0.00 0.00 0.00 2.24
3251 3405 5.408299 TGTCAAAGTTACTCACCGAATCATG 59.592 40.000 0.00 0.00 0.00 3.07
3261 3415 3.057596 TCACCGAATCATGGTTTTGCTTC 60.058 43.478 0.00 0.00 37.72 3.86
3266 3420 5.091431 CGAATCATGGTTTTGCTTCTTCTC 58.909 41.667 0.00 0.00 0.00 2.87
3268 3422 4.104383 TCATGGTTTTGCTTCTTCTCCT 57.896 40.909 0.00 0.00 0.00 3.69
3269 3423 4.473444 TCATGGTTTTGCTTCTTCTCCTT 58.527 39.130 0.00 0.00 0.00 3.36
3300 3454 7.790823 AAGGATCATTGTTTTTCTTTGGTTG 57.209 32.000 0.00 0.00 0.00 3.77
3303 3457 6.928492 GGATCATTGTTTTTCTTTGGTTGCTA 59.072 34.615 0.00 0.00 0.00 3.49
3305 3459 6.634805 TCATTGTTTTTCTTTGGTTGCTACA 58.365 32.000 0.00 0.00 0.00 2.74
3312 3466 4.032960 TCTTTGGTTGCTACATGTGGAT 57.967 40.909 14.15 0.00 0.00 3.41
3313 3467 5.172687 TCTTTGGTTGCTACATGTGGATA 57.827 39.130 14.15 0.00 0.00 2.59
3314 3468 5.185454 TCTTTGGTTGCTACATGTGGATAG 58.815 41.667 14.15 0.71 0.00 2.08
3315 3469 3.558931 TGGTTGCTACATGTGGATAGG 57.441 47.619 14.15 0.00 0.00 2.57
3316 3470 2.172505 TGGTTGCTACATGTGGATAGGG 59.827 50.000 14.15 0.00 0.00 3.53
3317 3471 2.438021 GGTTGCTACATGTGGATAGGGA 59.562 50.000 14.15 0.00 0.00 4.20
3318 3472 3.073062 GGTTGCTACATGTGGATAGGGAT 59.927 47.826 14.15 0.00 0.00 3.85
3319 3473 4.067896 GTTGCTACATGTGGATAGGGATG 58.932 47.826 14.15 0.00 0.00 3.51
3320 3474 2.038952 TGCTACATGTGGATAGGGATGC 59.961 50.000 14.15 0.81 0.00 3.91
3321 3475 2.038952 GCTACATGTGGATAGGGATGCA 59.961 50.000 14.15 0.00 0.00 3.96
3322 3476 2.945080 ACATGTGGATAGGGATGCAG 57.055 50.000 0.00 0.00 33.52 4.41
3323 3477 1.422781 ACATGTGGATAGGGATGCAGG 59.577 52.381 0.00 0.00 33.52 4.85
3324 3478 1.070604 ATGTGGATAGGGATGCAGGG 58.929 55.000 0.00 0.00 33.52 4.45
3325 3479 1.073897 GTGGATAGGGATGCAGGGC 59.926 63.158 0.00 0.00 33.52 5.19
3326 3480 2.348998 GGATAGGGATGCAGGGCG 59.651 66.667 0.00 0.00 0.00 6.13
3327 3481 2.348998 GATAGGGATGCAGGGCGG 59.651 66.667 0.00 0.00 0.00 6.13
3328 3482 2.448542 ATAGGGATGCAGGGCGGT 60.449 61.111 0.00 0.00 0.00 5.68
3329 3483 2.738213 GATAGGGATGCAGGGCGGTG 62.738 65.000 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 1.225376 TACCTCGTTTGTTGCCGCAG 61.225 55.000 0.00 0.00 0.00 5.18
63 64 1.753073 CTAAACCGGACCATACCTCGT 59.247 52.381 9.46 0.00 0.00 4.18
78 79 7.030768 TGCTTTAGGTTGTTGTTTGTCTAAAC 58.969 34.615 0.00 0.00 45.04 2.01
85 86 3.494251 GCCATGCTTTAGGTTGTTGTTTG 59.506 43.478 0.00 0.00 0.00 2.93
128 129 0.734309 TCATCCATGTTGCATGCGTC 59.266 50.000 14.09 9.05 0.00 5.19
131 132 1.108776 ACCTCATCCATGTTGCATGC 58.891 50.000 11.82 11.82 0.00 4.06
191 192 8.232913 TGGAATACCTGTTGATTATTTTAGCC 57.767 34.615 0.00 0.00 37.04 3.93
261 262 8.710749 ATGATATGCCTTTGTACCATACAATT 57.289 30.769 2.42 0.00 46.89 2.32
276 277 6.871844 CAGTATGCTGTACTATGATATGCCT 58.128 40.000 2.12 0.00 37.92 4.75
301 302 8.652463 GGTTTCGTGTTGATATTTATTTTTGGG 58.348 33.333 0.00 0.00 0.00 4.12
384 385 9.935241 CAAACATAGTCTAGCATAATACTCCAT 57.065 33.333 0.00 0.00 0.00 3.41
397 398 8.131455 ACATATTTGCGACAAACATAGTCTAG 57.869 34.615 7.08 0.00 33.89 2.43
401 402 7.589395 TGAAACATATTTGCGACAAACATAGT 58.411 30.769 7.08 2.88 0.00 2.12
724 725 5.374071 GAAGGGTTTGGGTATCGTCATATT 58.626 41.667 0.00 0.00 0.00 1.28
725 726 4.202430 GGAAGGGTTTGGGTATCGTCATAT 60.202 45.833 0.00 0.00 0.00 1.78
726 727 3.135167 GGAAGGGTTTGGGTATCGTCATA 59.865 47.826 0.00 0.00 0.00 2.15
727 728 2.092592 GGAAGGGTTTGGGTATCGTCAT 60.093 50.000 0.00 0.00 0.00 3.06
827 828 4.814294 ACCTCGCACGGCCGATTC 62.814 66.667 35.90 18.50 36.54 2.52
868 869 4.233789 CGTCTTTGGACAAGAAGAGAGAG 58.766 47.826 0.00 0.00 42.21 3.20
873 874 1.872237 CGGCGTCTTTGGACAAGAAGA 60.872 52.381 0.00 0.00 42.21 2.87
878 879 1.146485 TTCCGGCGTCTTTGGACAA 59.854 52.632 6.01 0.00 42.21 3.18
916 917 3.299977 GGTGGTTTTGCGACCCCC 61.300 66.667 0.00 0.00 39.71 5.40
917 918 0.609681 TATGGTGGTTTTGCGACCCC 60.610 55.000 0.00 3.68 44.25 4.95
918 919 0.808755 CTATGGTGGTTTTGCGACCC 59.191 55.000 0.00 0.00 44.25 4.46
919 920 0.170339 GCTATGGTGGTTTTGCGACC 59.830 55.000 0.00 0.00 44.98 4.79
920 921 1.130561 GAGCTATGGTGGTTTTGCGAC 59.869 52.381 0.00 0.00 0.00 5.19
921 922 1.271108 TGAGCTATGGTGGTTTTGCGA 60.271 47.619 0.00 0.00 0.00 5.10
922 923 1.135689 GTGAGCTATGGTGGTTTTGCG 60.136 52.381 0.00 0.00 0.00 4.85
923 924 2.162681 AGTGAGCTATGGTGGTTTTGC 58.837 47.619 0.00 0.00 0.00 3.68
924 925 4.576463 GGATAGTGAGCTATGGTGGTTTTG 59.424 45.833 0.00 0.00 37.99 2.44
925 926 4.475016 AGGATAGTGAGCTATGGTGGTTTT 59.525 41.667 0.00 0.00 37.99 2.43
926 927 4.040755 AGGATAGTGAGCTATGGTGGTTT 58.959 43.478 0.00 0.00 37.99 3.27
1014 1015 5.220491 CGATTTCGATCTCTGAAAAGGGAAC 60.220 44.000 0.00 0.00 43.02 3.62
1110 1125 1.909302 TCTTCCACAAGGATCCACTCC 59.091 52.381 15.82 0.00 45.26 3.85
1193 1208 2.358737 CGGTGGAGGTGGCACTTC 60.359 66.667 20.39 20.39 0.00 3.01
1294 1315 2.684001 TCGGCGTCAAAGGATAACAT 57.316 45.000 6.85 0.00 0.00 2.71
1429 1450 1.303317 GGTGACCGGGTTGCAGATT 60.303 57.895 6.32 0.00 0.00 2.40
1476 1497 8.475639 TCTGGTAGTAATAGTTCAGTTGATTCC 58.524 37.037 0.00 0.00 0.00 3.01
1546 1570 0.685097 TCGGACAAGAGACCCAAAGG 59.315 55.000 0.00 0.00 40.04 3.11
1603 1642 6.817140 GTCTTATATAATTGGATCCCACCGAC 59.183 42.308 9.90 0.00 30.78 4.79
1604 1643 6.499000 TGTCTTATATAATTGGATCCCACCGA 59.501 38.462 9.90 0.00 30.78 4.69
1669 1741 1.380785 ATAGCCAGACGAACCGGGA 60.381 57.895 6.32 0.00 0.00 5.14
1704 1776 1.975407 GTCCAGTGCAAGCTGCCAT 60.975 57.895 0.00 0.00 44.23 4.40
1765 1837 6.585695 AATGTTTCATCTGCTGTCTTGAAT 57.414 33.333 7.01 0.00 0.00 2.57
1789 1861 1.270625 GGAGGACAACACATCAACCGA 60.271 52.381 0.00 0.00 0.00 4.69
1801 1873 2.840753 GGGCAACTGGGGAGGACAA 61.841 63.158 0.00 0.00 0.00 3.18
1807 1879 2.081787 TTGTGAGGGCAACTGGGGA 61.082 57.895 0.00 0.00 0.00 4.81
1808 1880 1.903404 GTTGTGAGGGCAACTGGGG 60.903 63.158 0.00 0.00 43.74 4.96
1889 1961 5.372661 AGGCTTGTACCACCCAAATATCTAT 59.627 40.000 0.00 0.00 0.00 1.98
1895 1967 3.268334 TCATAGGCTTGTACCACCCAAAT 59.732 43.478 0.00 0.00 0.00 2.32
1911 1983 3.558746 GGACCAGGCTTCATCATCATAGG 60.559 52.174 0.00 0.00 0.00 2.57
1918 1990 1.361204 TGAAGGACCAGGCTTCATCA 58.639 50.000 5.60 0.00 32.89 3.07
1920 1992 1.615384 GCTTGAAGGACCAGGCTTCAT 60.615 52.381 9.62 0.00 37.03 2.57
1949 2021 6.723052 GGTGATTCATCCATCCCTGATAAATT 59.277 38.462 0.00 0.00 0.00 1.82
2046 2118 0.301687 GTCATAGCGAACCACATGCG 59.698 55.000 0.00 0.00 0.00 4.73
2061 2133 3.548770 ACAAATCTGCCATCGATGTCAT 58.451 40.909 23.27 0.38 0.00 3.06
2068 2140 6.424812 TCACATATTCTACAAATCTGCCATCG 59.575 38.462 0.00 0.00 0.00 3.84
2112 2184 3.214328 CTGGTAAGCCACAAGTTCTTGT 58.786 45.455 11.75 11.75 40.46 3.16
2248 2324 2.990967 CACCGGGCTGCAAACCAT 60.991 61.111 6.32 0.00 0.00 3.55
2249 2325 4.514585 ACACCGGGCTGCAAACCA 62.515 61.111 6.32 0.00 0.00 3.67
2250 2326 3.977244 CACACCGGGCTGCAAACC 61.977 66.667 6.32 0.00 0.00 3.27
2255 2331 0.392461 TAATTCTCACACCGGGCTGC 60.392 55.000 6.32 0.00 0.00 5.25
2287 2363 8.697507 AAGGAAGAACTAAGAACAATGACAAT 57.302 30.769 0.00 0.00 0.00 2.71
2328 2404 7.759465 TCCGAAGTGTTTCATTCTACTACTAG 58.241 38.462 0.00 0.00 32.67 2.57
2329 2405 7.692460 TCCGAAGTGTTTCATTCTACTACTA 57.308 36.000 0.00 0.00 32.67 1.82
2330 2406 6.585695 TCCGAAGTGTTTCATTCTACTACT 57.414 37.500 0.00 0.00 32.67 2.57
2331 2407 7.033791 TCATCCGAAGTGTTTCATTCTACTAC 58.966 38.462 0.00 0.00 32.67 2.73
2332 2408 7.165460 TCATCCGAAGTGTTTCATTCTACTA 57.835 36.000 0.00 0.00 32.67 1.82
2333 2409 6.037786 TCATCCGAAGTGTTTCATTCTACT 57.962 37.500 0.00 0.00 32.67 2.57
2334 2410 6.910536 ATCATCCGAAGTGTTTCATTCTAC 57.089 37.500 0.00 0.00 32.67 2.59
2335 2411 7.278646 CAGAATCATCCGAAGTGTTTCATTCTA 59.721 37.037 0.00 0.00 32.67 2.10
2336 2412 6.093219 CAGAATCATCCGAAGTGTTTCATTCT 59.907 38.462 0.00 0.00 32.67 2.40
2341 2417 6.910536 ATACAGAATCATCCGAAGTGTTTC 57.089 37.500 0.00 0.00 0.00 2.78
2342 2418 7.106239 AGAATACAGAATCATCCGAAGTGTTT 58.894 34.615 0.00 0.00 0.00 2.83
2346 2422 6.471233 TGAGAATACAGAATCATCCGAAGT 57.529 37.500 0.00 0.00 0.00 3.01
2350 2426 6.510799 GCAGTTTGAGAATACAGAATCATCCG 60.511 42.308 0.00 0.00 0.00 4.18
2360 2436 4.997395 GGACAGAAGCAGTTTGAGAATACA 59.003 41.667 0.00 0.00 0.00 2.29
2368 2444 5.048504 ACAATATGTGGACAGAAGCAGTTTG 60.049 40.000 0.00 0.00 0.00 2.93
2407 2485 2.092968 CCAGCCAGTGTAATTGCTAGGA 60.093 50.000 0.00 0.00 31.69 2.94
2408 2486 2.292267 CCAGCCAGTGTAATTGCTAGG 58.708 52.381 0.00 0.00 31.69 3.02
2409 2487 2.991250 ACCAGCCAGTGTAATTGCTAG 58.009 47.619 0.00 0.00 31.69 3.42
2412 2490 1.885887 TCAACCAGCCAGTGTAATTGC 59.114 47.619 0.00 0.00 0.00 3.56
2413 2491 3.758023 TGATCAACCAGCCAGTGTAATTG 59.242 43.478 0.00 0.00 0.00 2.32
2415 2493 3.719268 TGATCAACCAGCCAGTGTAAT 57.281 42.857 0.00 0.00 0.00 1.89
2417 2495 2.371841 AGTTGATCAACCAGCCAGTGTA 59.628 45.455 30.34 0.00 42.06 2.90
2418 2496 1.143684 AGTTGATCAACCAGCCAGTGT 59.856 47.619 30.34 9.78 42.06 3.55
2419 2497 1.538512 CAGTTGATCAACCAGCCAGTG 59.461 52.381 30.34 18.30 42.06 3.66
2420 2498 1.901591 CAGTTGATCAACCAGCCAGT 58.098 50.000 30.34 11.17 42.06 4.00
2421 2499 0.524862 GCAGTTGATCAACCAGCCAG 59.475 55.000 30.34 16.38 42.06 4.85
2422 2500 2.644887 GCAGTTGATCAACCAGCCA 58.355 52.632 30.34 0.00 42.06 4.75
2424 2502 0.610232 AGGGCAGTTGATCAACCAGC 60.610 55.000 30.73 30.73 42.06 4.85
2425 2503 1.171308 CAGGGCAGTTGATCAACCAG 58.829 55.000 30.34 24.28 42.06 4.00
2426 2504 0.770499 TCAGGGCAGTTGATCAACCA 59.230 50.000 30.34 7.35 42.06 3.67
2427 2505 1.909700 TTCAGGGCAGTTGATCAACC 58.090 50.000 30.34 18.03 42.06 3.77
2428 2506 4.240096 CAATTTCAGGGCAGTTGATCAAC 58.760 43.478 27.69 27.69 41.45 3.18
2433 2511 4.098914 AGTACAATTTCAGGGCAGTTGA 57.901 40.909 0.00 0.00 0.00 3.18
2454 2532 3.002862 GTGTTCCGATTTGCACAACACTA 59.997 43.478 6.09 0.00 36.90 2.74
2465 2543 5.890424 AAAATCCGTATGTGTTCCGATTT 57.110 34.783 0.00 0.00 0.00 2.17
2469 2547 4.741185 TCGATAAAATCCGTATGTGTTCCG 59.259 41.667 0.00 0.00 0.00 4.30
2481 2560 4.642466 AGGGAAGGGATCGATAAAATCC 57.358 45.455 0.00 4.58 41.74 3.01
2488 2567 2.092375 GGAAACAAGGGAAGGGATCGAT 60.092 50.000 0.00 0.00 0.00 3.59
2489 2568 1.280998 GGAAACAAGGGAAGGGATCGA 59.719 52.381 0.00 0.00 0.00 3.59
2494 2573 2.632996 GGAAAAGGAAACAAGGGAAGGG 59.367 50.000 0.00 0.00 0.00 3.95
2505 2584 3.300239 TCTGGAAACGGGAAAAGGAAA 57.700 42.857 0.00 0.00 37.31 3.13
2531 2610 2.794103 AGCATAGCACATGTTTGTCCA 58.206 42.857 0.00 0.00 32.34 4.02
2532 2611 3.855689 AAGCATAGCACATGTTTGTCC 57.144 42.857 0.00 0.00 32.34 4.02
2533 2612 5.122239 TCTGTAAGCATAGCACATGTTTGTC 59.878 40.000 0.00 5.09 32.34 3.18
2534 2613 5.003160 TCTGTAAGCATAGCACATGTTTGT 58.997 37.500 0.00 0.00 36.15 2.83
2535 2614 5.122869 ACTCTGTAAGCATAGCACATGTTTG 59.877 40.000 0.00 0.00 0.00 2.93
2536 2615 5.248640 ACTCTGTAAGCATAGCACATGTTT 58.751 37.500 0.00 5.87 0.00 2.83
2539 2618 5.812127 TGTAACTCTGTAAGCATAGCACATG 59.188 40.000 0.00 0.00 0.00 3.21
2545 2624 9.856488 TCTTTTACTGTAACTCTGTAAGCATAG 57.144 33.333 0.00 0.00 40.00 2.23
2554 2633 6.200286 TCGTTTGCTCTTTTACTGTAACTCTG 59.800 38.462 0.00 0.00 0.00 3.35
2555 2634 6.278363 TCGTTTGCTCTTTTACTGTAACTCT 58.722 36.000 0.00 0.00 0.00 3.24
2557 2636 6.913873 TTCGTTTGCTCTTTTACTGTAACT 57.086 33.333 0.00 0.00 0.00 2.24
2558 2637 8.556517 AATTTCGTTTGCTCTTTTACTGTAAC 57.443 30.769 0.00 0.00 0.00 2.50
2559 2638 9.872757 CTAATTTCGTTTGCTCTTTTACTGTAA 57.127 29.630 0.00 0.00 0.00 2.41
2560 2639 8.013378 GCTAATTTCGTTTGCTCTTTTACTGTA 58.987 33.333 0.00 0.00 35.95 2.74
2561 2640 6.856426 GCTAATTTCGTTTGCTCTTTTACTGT 59.144 34.615 0.00 0.00 35.95 3.55
2562 2641 6.855914 TGCTAATTTCGTTTGCTCTTTTACTG 59.144 34.615 0.00 0.00 38.99 2.74
2563 2642 6.966021 TGCTAATTTCGTTTGCTCTTTTACT 58.034 32.000 0.00 0.00 38.99 2.24
2564 2643 7.617533 TTGCTAATTTCGTTTGCTCTTTTAC 57.382 32.000 0.00 0.00 38.99 2.01
2565 2644 8.698854 CATTTGCTAATTTCGTTTGCTCTTTTA 58.301 29.630 0.00 0.00 38.99 1.52
2566 2645 7.437862 TCATTTGCTAATTTCGTTTGCTCTTTT 59.562 29.630 0.00 0.00 38.99 2.27
2567 2646 6.922957 TCATTTGCTAATTTCGTTTGCTCTTT 59.077 30.769 0.00 0.00 38.99 2.52
2568 2647 6.446318 TCATTTGCTAATTTCGTTTGCTCTT 58.554 32.000 0.00 0.00 38.99 2.85
2569 2648 6.012658 TCATTTGCTAATTTCGTTTGCTCT 57.987 33.333 0.00 0.00 38.99 4.09
2570 2649 6.875926 ATCATTTGCTAATTTCGTTTGCTC 57.124 33.333 0.00 0.00 38.99 4.26
2578 2657 5.812127 GTGTGGGGAATCATTTGCTAATTTC 59.188 40.000 0.00 0.00 0.00 2.17
2585 2664 2.562298 TGAAGTGTGGGGAATCATTTGC 59.438 45.455 0.00 0.00 0.00 3.68
2591 2670 3.690460 ACAGAATGAAGTGTGGGGAATC 58.310 45.455 0.00 0.00 39.69 2.52
2598 2677 6.245115 TGCAAAGATACAGAATGAAGTGTG 57.755 37.500 0.00 0.00 39.69 3.82
2619 2698 9.051679 ACCTTTCCAACAGTAAAATTTTAATGC 57.948 29.630 28.89 12.06 41.06 3.56
2621 2700 9.772973 GGACCTTTCCAACAGTAAAATTTTAAT 57.227 29.630 12.14 8.61 42.30 1.40
2622 2701 8.983789 AGGACCTTTCCAACAGTAAAATTTTAA 58.016 29.630 12.14 0.00 45.72 1.52
2623 2702 8.541899 AGGACCTTTCCAACAGTAAAATTTTA 57.458 30.769 6.54 6.54 45.72 1.52
2624 2703 7.432148 AGGACCTTTCCAACAGTAAAATTTT 57.568 32.000 8.75 8.75 45.72 1.82
2646 2726 9.533253 AAAACACATTTTGAAGATCTTGTAAGG 57.467 29.630 14.00 8.10 36.64 2.69
2672 2752 2.945008 CACACTGAACCTGCTTCTCAAA 59.055 45.455 0.00 0.00 0.00 2.69
2680 2760 0.108585 TCTTCCCACACTGAACCTGC 59.891 55.000 0.00 0.00 0.00 4.85
2681 2761 1.879796 GCTCTTCCCACACTGAACCTG 60.880 57.143 0.00 0.00 0.00 4.00
2695 2775 8.512966 ACCTTGGAAATATCTTAAAGCTCTTC 57.487 34.615 0.00 0.00 0.00 2.87
2712 2792 5.015817 ACCATGTTCCCTAAATACCTTGGAA 59.984 40.000 0.00 0.00 32.87 3.53
2714 2794 4.867086 ACCATGTTCCCTAAATACCTTGG 58.133 43.478 0.00 0.00 0.00 3.61
2715 2795 6.850752 AAACCATGTTCCCTAAATACCTTG 57.149 37.500 0.00 0.00 0.00 3.61
2716 2796 7.471890 TGTAAACCATGTTCCCTAAATACCTT 58.528 34.615 0.00 0.00 0.00 3.50
2717 2797 7.034967 TGTAAACCATGTTCCCTAAATACCT 57.965 36.000 0.00 0.00 0.00 3.08
2718 2798 7.891498 ATGTAAACCATGTTCCCTAAATACC 57.109 36.000 0.00 0.00 30.69 2.73
2722 2802 9.976776 TGTTATATGTAAACCATGTTCCCTAAA 57.023 29.630 0.00 0.00 34.86 1.85
2723 2803 9.621629 CTGTTATATGTAAACCATGTTCCCTAA 57.378 33.333 0.00 0.00 34.86 2.69
2724 2804 8.994500 TCTGTTATATGTAAACCATGTTCCCTA 58.006 33.333 0.00 0.00 34.86 3.53
2725 2805 7.867921 TCTGTTATATGTAAACCATGTTCCCT 58.132 34.615 0.00 0.00 34.86 4.20
2726 2806 8.514330 TTCTGTTATATGTAAACCATGTTCCC 57.486 34.615 0.00 0.00 34.86 3.97
2727 2807 9.391006 TCTTCTGTTATATGTAAACCATGTTCC 57.609 33.333 0.00 0.00 34.86 3.62
2729 2809 9.733556 TGTCTTCTGTTATATGTAAACCATGTT 57.266 29.630 0.00 0.00 34.86 2.71
2730 2810 9.733556 TTGTCTTCTGTTATATGTAAACCATGT 57.266 29.630 0.00 0.00 34.86 3.21
2743 2823 6.426646 ACTCTGGTCTTTGTCTTCTGTTAT 57.573 37.500 0.00 0.00 0.00 1.89
2824 2907 7.414098 CGTGAAGTCCAAAGAGGGTAAAATATG 60.414 40.741 0.00 0.00 38.24 1.78
2837 2920 1.192534 GAAGTCGCGTGAAGTCCAAAG 59.807 52.381 5.77 0.00 0.00 2.77
2844 2927 0.512518 TGCAATGAAGTCGCGTGAAG 59.487 50.000 5.77 0.00 0.00 3.02
2845 2928 0.234625 GTGCAATGAAGTCGCGTGAA 59.765 50.000 5.77 0.00 0.00 3.18
2846 2929 0.878086 TGTGCAATGAAGTCGCGTGA 60.878 50.000 5.77 0.00 0.00 4.35
2847 2930 0.041400 TTGTGCAATGAAGTCGCGTG 60.041 50.000 5.77 0.00 0.00 5.34
2848 2931 0.874390 ATTGTGCAATGAAGTCGCGT 59.126 45.000 5.77 0.00 0.00 6.01
2849 2932 3.681705 ATTGTGCAATGAAGTCGCG 57.318 47.368 0.00 0.00 0.00 5.87
2864 2947 5.964958 AACTGTGGGTGTTCTTATCATTG 57.035 39.130 0.00 0.00 0.00 2.82
2869 2952 8.706322 ATTTTCTTAACTGTGGGTGTTCTTAT 57.294 30.769 0.00 0.00 0.00 1.73
2875 2958 8.472007 TTTCATATTTTCTTAACTGTGGGTGT 57.528 30.769 0.00 0.00 0.00 4.16
2886 2969 6.630071 GCACCCAGCTTTTCATATTTTCTTA 58.370 36.000 0.00 0.00 41.15 2.10
2914 2997 1.780503 AGGGGTGAAATATGCTTGGC 58.219 50.000 0.00 0.00 0.00 4.52
2916 2999 6.152661 TCAAAGTAAGGGGTGAAATATGCTTG 59.847 38.462 0.00 0.00 0.00 4.01
2918 3001 5.652452 GTCAAAGTAAGGGGTGAAATATGCT 59.348 40.000 0.00 0.00 0.00 3.79
2919 3002 5.163550 GGTCAAAGTAAGGGGTGAAATATGC 60.164 44.000 0.00 0.00 0.00 3.14
2920 3003 5.949354 TGGTCAAAGTAAGGGGTGAAATATG 59.051 40.000 0.00 0.00 0.00 1.78
2921 3004 5.949952 GTGGTCAAAGTAAGGGGTGAAATAT 59.050 40.000 0.00 0.00 0.00 1.28
2922 3005 5.318630 GTGGTCAAAGTAAGGGGTGAAATA 58.681 41.667 0.00 0.00 0.00 1.40
2923 3006 4.149598 GTGGTCAAAGTAAGGGGTGAAAT 58.850 43.478 0.00 0.00 0.00 2.17
2939 3022 3.192422 CGAAATATTTGCAAGGGTGGTCA 59.808 43.478 5.17 0.00 0.00 4.02
2962 3046 8.472413 GCAAGTAGATCCCGGTATTATTATACA 58.528 37.037 0.00 0.00 38.71 2.29
2969 3053 4.280174 GTCTGCAAGTAGATCCCGGTATTA 59.720 45.833 0.00 0.00 33.76 0.98
2979 3063 3.699538 TCGTATGGTGTCTGCAAGTAGAT 59.300 43.478 0.00 0.00 33.76 1.98
2980 3064 3.086282 TCGTATGGTGTCTGCAAGTAGA 58.914 45.455 0.00 0.00 33.76 2.59
2995 3111 1.198408 GCACATGGCATCCATCGTATG 59.802 52.381 0.00 0.00 43.15 2.39
3008 3124 6.029346 AGATTTTAGGAAGTTTGCACATGG 57.971 37.500 0.00 0.00 0.00 3.66
3014 3130 5.473504 TCACCTGAGATTTTAGGAAGTTTGC 59.526 40.000 0.53 0.00 37.52 3.68
3015 3131 7.229506 AGTTCACCTGAGATTTTAGGAAGTTTG 59.770 37.037 0.53 0.00 37.52 2.93
3039 3193 7.759489 TGTCATGCCTCAAAAGTTTAATAGT 57.241 32.000 0.00 0.00 0.00 2.12
3048 3202 5.961395 GCATAAATGTCATGCCTCAAAAG 57.039 39.130 0.00 0.00 42.41 2.27
3073 3227 2.876645 GAGAGAACAGTCGCCGCG 60.877 66.667 6.39 6.39 0.00 6.46
3076 3230 1.512310 CGTCGAGAGAACAGTCGCC 60.512 63.158 0.00 0.00 45.01 5.54
3078 3232 0.791238 CAGCGTCGAGAGAACAGTCG 60.791 60.000 0.00 0.00 45.01 4.18
3079 3233 0.455295 CCAGCGTCGAGAGAACAGTC 60.455 60.000 0.00 0.00 45.01 3.51
3090 3244 0.172578 TAACAGACCATCCAGCGTCG 59.827 55.000 0.00 0.00 34.10 5.12
3093 3247 3.689161 TGAAAATAACAGACCATCCAGCG 59.311 43.478 0.00 0.00 0.00 5.18
3096 3250 6.947733 AGAACATGAAAATAACAGACCATCCA 59.052 34.615 0.00 0.00 0.00 3.41
3099 3253 8.408043 TGAAGAACATGAAAATAACAGACCAT 57.592 30.769 0.00 0.00 0.00 3.55
3143 3297 7.867305 TCCAAACAGTAAATGTGACTACAAA 57.133 32.000 0.00 0.00 43.00 2.83
3184 3338 9.520515 AAGGTTTCTCATAGCTTCATAAAAGAA 57.479 29.630 0.00 0.00 0.00 2.52
3200 3354 6.321181 GCCACATATATTTCCAAGGTTTCTCA 59.679 38.462 0.00 0.00 0.00 3.27
3223 3377 2.159627 CGGTGAGTAACTTTGACATGCC 59.840 50.000 0.00 0.00 0.00 4.40
3236 3390 3.438781 GCAAAACCATGATTCGGTGAGTA 59.561 43.478 0.00 0.00 36.67 2.59
3237 3391 2.228822 GCAAAACCATGATTCGGTGAGT 59.771 45.455 0.00 0.00 36.67 3.41
3274 3428 7.790823 ACCAAAGAAAAACAATGATCCTTTG 57.209 32.000 0.00 0.00 38.89 2.77
3278 3432 5.759763 AGCAACCAAAGAAAAACAATGATCC 59.240 36.000 0.00 0.00 0.00 3.36
3285 3439 5.809562 CACATGTAGCAACCAAAGAAAAACA 59.190 36.000 0.00 0.00 0.00 2.83
3291 3445 3.500448 TCCACATGTAGCAACCAAAGA 57.500 42.857 0.00 0.00 0.00 2.52
3300 3454 2.038952 TGCATCCCTATCCACATGTAGC 59.961 50.000 0.00 0.00 0.00 3.58
3303 3457 1.422781 CCTGCATCCCTATCCACATGT 59.577 52.381 0.00 0.00 0.00 3.21
3305 3459 1.070604 CCCTGCATCCCTATCCACAT 58.929 55.000 0.00 0.00 0.00 3.21
3312 3466 3.479203 CACCGCCCTGCATCCCTA 61.479 66.667 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.