Multiple sequence alignment - TraesCS5D01G512700

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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 TraesCS5D01G512700 chr5D 100.000 3957 0 0 369 4325 536871727 536875683 0.000000e+00 7308.0
1 TraesCS5D01G512700 chr5D 87.833 526 60 2 1798 2319 536882521 536883046 8.800000e-172 614.0
2 TraesCS5D01G512700 chr5D 100.000 216 0 0 4568 4783 536875926 536876141 2.680000e-107 399.0
3 TraesCS5D01G512700 chr5D 79.234 496 88 9 3686 4174 536790762 536791249 9.920000e-87 331.0
4 TraesCS5D01G512700 chr5D 100.000 100 0 0 1 100 536871359 536871458 8.170000e-43 185.0
5 TraesCS5D01G512700 chr5D 84.615 156 21 3 2550 2702 536882980 536883135 8.290000e-33 152.0
6 TraesCS5D01G512700 chr5D 94.737 95 5 0 2442 2536 265951011 265950917 1.070000e-31 148.0
7 TraesCS5D01G512700 chr4A 92.216 2004 80 31 369 2345 633077446 633075492 0.000000e+00 2767.0
8 TraesCS5D01G512700 chr4A 92.057 768 40 6 2550 3312 633075234 633074483 0.000000e+00 1061.0
9 TraesCS5D01G512700 chr4A 96.979 629 18 1 3396 4023 633074477 633073849 0.000000e+00 1055.0
10 TraesCS5D01G512700 chr4A 95.814 215 9 0 4569 4783 633073421 633073207 9.850000e-92 348.0
11 TraesCS5D01G512700 chr4A 91.753 194 13 3 4022 4212 633073598 633073405 2.840000e-67 267.0
12 TraesCS5D01G512700 chr4A 95.413 109 4 1 2337 2444 633075331 633075223 6.360000e-39 172.0
13 TraesCS5D01G512700 chr4A 96.000 100 4 0 1 100 633077586 633077487 3.830000e-36 163.0
14 TraesCS5D01G512700 chr4A 88.889 63 6 1 2470 2531 385193907 385193845 5.130000e-10 76.8
15 TraesCS5D01G512700 chr4A 88.889 63 6 1 2470 2531 385201296 385201234 5.130000e-10 76.8
16 TraesCS5D01G512700 chr4A 88.333 60 5 2 1500 1557 614168687 614168628 2.390000e-08 71.3
17 TraesCS5D01G512700 chr5B 93.366 1447 81 3 999 2439 677650578 677649141 0.000000e+00 2126.0
18 TraesCS5D01G512700 chr5B 92.654 844 45 9 2550 3386 677649147 677648314 0.000000e+00 1199.0
19 TraesCS5D01G512700 chr5B 79.876 646 103 17 3549 4177 677666837 677666202 9.440000e-122 448.0
20 TraesCS5D01G512700 chr5A 94.737 95 5 0 2442 2536 354547914 354548008 1.070000e-31 148.0
21 TraesCS5D01G512700 chr2A 79.630 162 26 6 1311 1467 484034026 484034185 5.060000e-20 110.0
22 TraesCS5D01G512700 chr2A 100.000 29 0 0 2470 2498 367493451 367493423 2.000000e-03 54.7
23 TraesCS5D01G512700 chr6D 85.437 103 15 0 1311 1413 372974580 372974682 1.820000e-19 108.0
24 TraesCS5D01G512700 chr3B 83.333 96 15 1 2441 2535 520044717 520044622 2.370000e-13 87.9
25 TraesCS5D01G512700 chr7B 90.164 61 4 1 1496 1554 504227979 504228039 1.430000e-10 78.7
26 TraesCS5D01G512700 chr7B 90.741 54 5 0 2485 2538 221129050 221129103 6.640000e-09 73.1
27 TraesCS5D01G512700 chr3D 88.060 67 7 1 2470 2535 114002989 114002923 1.430000e-10 78.7
28 TraesCS5D01G512700 chr3D 88.060 67 7 1 2470 2535 114003391 114003325 1.430000e-10 78.7
29 TraesCS5D01G512700 chr3A 91.228 57 3 2 1500 1554 586905256 586905312 5.130000e-10 76.8
30 TraesCS5D01G512700 chr2B 81.188 101 12 7 639 735 55858368 55858465 1.850000e-09 75.0
31 TraesCS5D01G512700 chr6A 90.741 54 5 0 2485 2538 487374477 487374424 6.640000e-09 73.1


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 TraesCS5D01G512700 chr5D 536871359 536876141 4782 False 2630.666667 7308 100.000000 1 4783 3 chr5D.!!$F2 4782
1 TraesCS5D01G512700 chr5D 536882521 536883135 614 False 383.000000 614 86.224000 1798 2702 2 chr5D.!!$F3 904
2 TraesCS5D01G512700 chr4A 633073207 633077586 4379 True 833.285714 2767 94.318857 1 4783 7 chr4A.!!$R4 4782
3 TraesCS5D01G512700 chr5B 677648314 677650578 2264 True 1662.500000 2126 93.010000 999 3386 2 chr5B.!!$R2 2387
4 TraesCS5D01G512700 chr5B 677666202 677666837 635 True 448.000000 448 79.876000 3549 4177 1 chr5B.!!$R1 628

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
95 96 0.690762 ACCCCTAGACGCAACACATT 59.309 50.0 0.00 0.00 0.00 2.71 F
915 946 1.028130 GCTAAGAATGAAGCCCAGGC 58.972 55.0 0.00 0.00 42.33 4.85 F
2455 2664 0.034670 GGAATGGAGGCTGCTTCAGT 60.035 55.0 13.97 2.42 33.43 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1554 1591 0.537188 AACACCCATCAGAGTAGGCG 59.463 55.0 0.0 0.0 0.00 5.52 R
2477 2686 0.031994 GGCCCACATGTCAAACACAC 59.968 55.0 0.0 0.0 38.04 3.82 R
4223 4708 0.398098 ATATTCTGTCCCGTCCCGGT 60.398 55.0 0.0 0.0 46.80 5.28 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
51 52 1.151908 TTGTGGTGTTAGTGGGGGC 59.848 57.895 0.00 0.00 0.00 5.80
95 96 0.690762 ACCCCTAGACGCAACACATT 59.309 50.000 0.00 0.00 0.00 2.71
399 400 4.383010 GGGCAAATCCTACAATTTCCTTGG 60.383 45.833 0.00 0.00 35.56 3.61
420 436 4.408596 TGGACATTGCACTCCTATACATCA 59.591 41.667 5.96 0.00 0.00 3.07
434 450 5.719085 CCTATACATCATCAAGTAGCTCCCT 59.281 44.000 0.00 0.00 0.00 4.20
449 465 2.743718 CCTTGTGGCACGTCTCCT 59.256 61.111 13.77 0.00 0.00 3.69
503 519 8.854979 TGTTGTGACTTCTTTTGATAACATTG 57.145 30.769 0.00 0.00 0.00 2.82
896 927 2.103143 CTCGAGCCCAGCTACACG 59.897 66.667 0.00 0.00 39.88 4.49
915 946 1.028130 GCTAAGAATGAAGCCCAGGC 58.972 55.000 0.00 0.00 42.33 4.85
989 1020 1.294659 CTCCACTTGAGCAAGCCGTC 61.295 60.000 9.99 0.00 41.99 4.79
1206 1240 1.602237 GCTCCCCATCTCCAACGAA 59.398 57.895 0.00 0.00 0.00 3.85
1486 1523 2.048222 CGACCTGCGGTGACATGT 60.048 61.111 0.00 0.00 35.25 3.21
1488 1525 1.741770 GACCTGCGGTGACATGTCC 60.742 63.158 22.85 13.66 35.25 4.02
1521 1558 1.136446 GTGTTCGACGAAATTCCCGTG 60.136 52.381 12.67 4.33 40.67 4.94
1524 1561 2.151881 TCGACGAAATTCCCGTGAAA 57.848 45.000 10.04 0.00 40.67 2.69
1563 1600 1.330655 CCATGGTGTCCGCCTACTCT 61.331 60.000 2.57 0.00 0.00 3.24
1644 1681 0.964358 GGCTTGCTGGTGATCTGCTT 60.964 55.000 0.00 0.00 40.43 3.91
1687 1724 2.265739 GGTCATGTGCTCGGCTGA 59.734 61.111 0.00 0.00 0.00 4.26
1758 1795 2.428544 AGAGAGTCTGCGGTGATACT 57.571 50.000 0.00 0.00 0.00 2.12
1899 1939 1.078848 GACAGCTTGCCACCGAGAT 60.079 57.895 0.00 0.00 0.00 2.75
2025 2065 0.254178 AGAACTGCAGGTGCTATGGG 59.746 55.000 19.93 0.00 42.66 4.00
2319 2359 2.437359 AGGTGAGCTGCCGAATGC 60.437 61.111 0.00 0.00 41.77 3.56
2348 2388 0.725686 CTGCTGCACTGCACATCTAC 59.274 55.000 0.00 0.00 38.12 2.59
2436 2645 1.207570 AGAGGACATCTCAAGCTGCTG 59.792 52.381 1.35 0.00 44.81 4.41
2439 2648 1.339438 GGACATCTCAAGCTGCTGGAA 60.339 52.381 8.32 0.12 0.00 3.53
2441 2650 2.355132 GACATCTCAAGCTGCTGGAATG 59.645 50.000 19.06 19.06 0.00 2.67
2442 2651 1.676529 CATCTCAAGCTGCTGGAATGG 59.323 52.381 8.32 0.00 0.00 3.16
2443 2652 0.986527 TCTCAAGCTGCTGGAATGGA 59.013 50.000 8.32 0.00 0.00 3.41
2444 2653 1.065636 TCTCAAGCTGCTGGAATGGAG 60.066 52.381 8.32 6.75 0.00 3.86
2445 2654 0.034767 TCAAGCTGCTGGAATGGAGG 60.035 55.000 3.74 0.00 0.00 4.30
2446 2655 1.379576 AAGCTGCTGGAATGGAGGC 60.380 57.895 1.35 0.00 0.00 4.70
2447 2656 1.860944 AAGCTGCTGGAATGGAGGCT 61.861 55.000 1.35 0.00 0.00 4.58
2448 2657 2.119655 GCTGCTGGAATGGAGGCTG 61.120 63.158 0.00 0.00 0.00 4.85
2449 2658 2.044650 TGCTGGAATGGAGGCTGC 60.045 61.111 0.00 0.00 0.00 5.25
2450 2659 2.274760 GCTGGAATGGAGGCTGCT 59.725 61.111 7.74 0.00 0.00 4.24
2451 2660 1.379576 GCTGGAATGGAGGCTGCTT 60.380 57.895 7.74 0.00 0.00 3.91
2452 2661 1.382692 GCTGGAATGGAGGCTGCTTC 61.383 60.000 7.74 2.75 0.00 3.86
2453 2662 0.034767 CTGGAATGGAGGCTGCTTCA 60.035 55.000 13.97 3.59 0.00 3.02
2454 2663 0.034767 TGGAATGGAGGCTGCTTCAG 60.035 55.000 13.97 0.00 34.12 3.02
2455 2664 0.034670 GGAATGGAGGCTGCTTCAGT 60.035 55.000 13.97 2.42 33.43 3.41
2456 2665 1.093159 GAATGGAGGCTGCTTCAGTG 58.907 55.000 13.97 0.00 33.43 3.66
2457 2666 0.964358 AATGGAGGCTGCTTCAGTGC 60.964 55.000 13.97 0.00 33.43 4.40
2458 2667 1.849975 ATGGAGGCTGCTTCAGTGCT 61.850 55.000 13.97 0.00 33.43 4.40
2459 2668 2.039405 GGAGGCTGCTTCAGTGCTG 61.039 63.158 13.97 0.00 33.43 4.41
2460 2669 1.302351 GAGGCTGCTTCAGTGCTGT 60.302 57.895 6.91 0.00 33.43 4.40
2461 2670 0.036952 GAGGCTGCTTCAGTGCTGTA 60.037 55.000 6.91 0.00 33.43 2.74
2462 2671 0.397941 AGGCTGCTTCAGTGCTGTAA 59.602 50.000 0.00 0.00 33.43 2.41
2463 2672 0.519077 GGCTGCTTCAGTGCTGTAAC 59.481 55.000 0.00 0.00 33.43 2.50
2464 2673 0.164647 GCTGCTTCAGTGCTGTAACG 59.835 55.000 0.00 0.00 33.43 3.18
2465 2674 1.502231 CTGCTTCAGTGCTGTAACGT 58.498 50.000 0.00 0.00 0.00 3.99
2466 2675 1.867233 CTGCTTCAGTGCTGTAACGTT 59.133 47.619 5.88 5.88 0.00 3.99
2467 2676 3.057019 CTGCTTCAGTGCTGTAACGTTA 58.943 45.455 3.29 3.29 0.00 3.18
2468 2677 3.057019 TGCTTCAGTGCTGTAACGTTAG 58.943 45.455 8.60 0.31 0.00 2.34
2469 2678 2.159827 GCTTCAGTGCTGTAACGTTAGC 60.160 50.000 14.76 14.76 40.29 3.09
2470 2679 3.318017 CTTCAGTGCTGTAACGTTAGCT 58.682 45.455 20.54 7.32 40.52 3.32
2471 2680 2.672714 TCAGTGCTGTAACGTTAGCTG 58.327 47.619 20.54 16.38 40.52 4.24
2472 2681 1.126846 CAGTGCTGTAACGTTAGCTGC 59.873 52.381 20.54 21.01 40.52 5.25
2473 2682 0.442699 GTGCTGTAACGTTAGCTGCC 59.557 55.000 20.54 13.99 40.52 4.85
2474 2683 0.320374 TGCTGTAACGTTAGCTGCCT 59.680 50.000 20.54 0.00 40.52 4.75
2475 2684 1.270625 TGCTGTAACGTTAGCTGCCTT 60.271 47.619 20.54 0.00 40.52 4.35
2476 2685 1.804748 GCTGTAACGTTAGCTGCCTTT 59.195 47.619 14.43 0.00 36.99 3.11
2477 2686 2.412847 GCTGTAACGTTAGCTGCCTTTG 60.413 50.000 14.43 0.00 36.99 2.77
2478 2687 2.806244 CTGTAACGTTAGCTGCCTTTGT 59.194 45.455 8.60 0.00 0.00 2.83
2479 2688 2.546368 TGTAACGTTAGCTGCCTTTGTG 59.454 45.455 8.60 0.00 0.00 3.33
2480 2689 1.675552 AACGTTAGCTGCCTTTGTGT 58.324 45.000 0.00 0.00 0.00 3.72
2481 2690 0.944386 ACGTTAGCTGCCTTTGTGTG 59.056 50.000 0.00 0.00 0.00 3.82
2482 2691 0.944386 CGTTAGCTGCCTTTGTGTGT 59.056 50.000 0.00 0.00 0.00 3.72
2483 2692 1.333619 CGTTAGCTGCCTTTGTGTGTT 59.666 47.619 0.00 0.00 0.00 3.32
2484 2693 2.223479 CGTTAGCTGCCTTTGTGTGTTT 60.223 45.455 0.00 0.00 0.00 2.83
2485 2694 3.115554 GTTAGCTGCCTTTGTGTGTTTG 58.884 45.455 0.00 0.00 0.00 2.93
2486 2695 1.473258 AGCTGCCTTTGTGTGTTTGA 58.527 45.000 0.00 0.00 0.00 2.69
2487 2696 1.134946 AGCTGCCTTTGTGTGTTTGAC 59.865 47.619 0.00 0.00 0.00 3.18
2488 2697 1.135141 GCTGCCTTTGTGTGTTTGACA 60.135 47.619 0.00 0.00 0.00 3.58
2489 2698 2.481795 GCTGCCTTTGTGTGTTTGACAT 60.482 45.455 0.00 0.00 36.78 3.06
2490 2699 3.117794 CTGCCTTTGTGTGTTTGACATG 58.882 45.455 0.00 0.00 36.78 3.21
2491 2700 2.495270 TGCCTTTGTGTGTTTGACATGT 59.505 40.909 0.00 0.00 36.78 3.21
2492 2701 2.859538 GCCTTTGTGTGTTTGACATGTG 59.140 45.455 1.15 0.00 36.78 3.21
2493 2702 3.446799 CCTTTGTGTGTTTGACATGTGG 58.553 45.455 1.15 0.00 36.78 4.17
2494 2703 3.446799 CTTTGTGTGTTTGACATGTGGG 58.553 45.455 1.15 0.00 36.78 4.61
2495 2704 0.743688 TGTGTGTTTGACATGTGGGC 59.256 50.000 1.15 0.00 36.78 5.36
2496 2705 0.031994 GTGTGTTTGACATGTGGGCC 59.968 55.000 1.15 0.00 36.78 5.80
2497 2706 0.396278 TGTGTTTGACATGTGGGCCA 60.396 50.000 1.15 0.00 0.00 5.36
2498 2707 0.314935 GTGTTTGACATGTGGGCCAG 59.685 55.000 6.40 0.00 0.00 4.85
2499 2708 0.184692 TGTTTGACATGTGGGCCAGA 59.815 50.000 6.40 5.95 0.00 3.86
2500 2709 0.598065 GTTTGACATGTGGGCCAGAC 59.402 55.000 6.40 0.04 0.00 3.51
2501 2710 0.184692 TTTGACATGTGGGCCAGACA 59.815 50.000 6.40 7.27 0.00 3.41
2502 2711 0.537143 TTGACATGTGGGCCAGACAC 60.537 55.000 6.40 4.05 39.26 3.67
2503 2712 1.675641 GACATGTGGGCCAGACACC 60.676 63.158 6.40 0.00 38.05 4.16
2504 2713 2.129555 GACATGTGGGCCAGACACCT 62.130 60.000 6.40 0.00 38.05 4.00
2505 2714 0.840288 ACATGTGGGCCAGACACCTA 60.840 55.000 6.40 0.00 38.05 3.08
2506 2715 0.548031 CATGTGGGCCAGACACCTAT 59.452 55.000 6.40 0.00 38.05 2.57
2507 2716 1.064463 CATGTGGGCCAGACACCTATT 60.064 52.381 6.40 0.00 38.05 1.73
2508 2717 0.327924 TGTGGGCCAGACACCTATTG 59.672 55.000 6.40 0.00 38.05 1.90
2509 2718 0.394352 GTGGGCCAGACACCTATTGG 60.394 60.000 6.40 0.00 39.83 3.16
2510 2719 1.227383 GGGCCAGACACCTATTGGG 59.773 63.158 4.39 0.00 41.89 4.12
2511 2720 4.242602 GCCAGACACCTATTGGGC 57.757 61.111 0.00 0.00 39.10 5.36
2512 2721 1.453928 GCCAGACACCTATTGGGCC 60.454 63.158 0.00 0.00 39.10 5.80
2513 2722 1.227383 CCAGACACCTATTGGGCCC 59.773 63.158 17.59 17.59 39.10 5.80
2514 2723 1.570857 CCAGACACCTATTGGGCCCA 61.571 60.000 24.45 24.45 39.10 5.36
2515 2724 0.394352 CAGACACCTATTGGGCCCAC 60.394 60.000 28.70 10.83 39.10 4.61
2516 2725 0.844661 AGACACCTATTGGGCCCACA 60.845 55.000 28.70 16.93 39.10 4.17
2517 2726 0.258774 GACACCTATTGGGCCCACAT 59.741 55.000 28.70 22.66 39.10 3.21
2518 2727 0.033208 ACACCTATTGGGCCCACATG 60.033 55.000 28.70 20.09 39.10 3.21
2519 2728 0.033208 CACCTATTGGGCCCACATGT 60.033 55.000 28.70 16.92 39.10 3.21
2520 2729 0.258774 ACCTATTGGGCCCACATGTC 59.741 55.000 28.70 0.00 39.10 3.06
2521 2730 0.258484 CCTATTGGGCCCACATGTCA 59.742 55.000 28.70 9.60 0.00 3.58
2522 2731 1.133388 CCTATTGGGCCCACATGTCAT 60.133 52.381 28.70 17.39 0.00 3.06
2523 2732 2.669781 CTATTGGGCCCACATGTCATT 58.330 47.619 28.70 4.43 0.00 2.57
2524 2733 1.488390 ATTGGGCCCACATGTCATTC 58.512 50.000 28.70 0.00 0.00 2.67
2525 2734 0.113972 TTGGGCCCACATGTCATTCA 59.886 50.000 28.70 1.58 0.00 2.57
2526 2735 0.611618 TGGGCCCACATGTCATTCAC 60.612 55.000 24.45 0.00 0.00 3.18
2527 2736 1.322538 GGGCCCACATGTCATTCACC 61.323 60.000 19.95 0.00 0.00 4.02
2528 2737 0.611618 GGCCCACATGTCATTCACCA 60.612 55.000 0.00 0.00 0.00 4.17
2529 2738 1.255882 GCCCACATGTCATTCACCAA 58.744 50.000 0.00 0.00 0.00 3.67
2530 2739 1.617850 GCCCACATGTCATTCACCAAA 59.382 47.619 0.00 0.00 0.00 3.28
2531 2740 2.353011 GCCCACATGTCATTCACCAAAG 60.353 50.000 0.00 0.00 0.00 2.77
2532 2741 2.231964 CCCACATGTCATTCACCAAAGG 59.768 50.000 0.00 0.00 0.00 3.11
2533 2742 2.353011 CCACATGTCATTCACCAAAGGC 60.353 50.000 0.00 0.00 0.00 4.35
2534 2743 2.296752 CACATGTCATTCACCAAAGGCA 59.703 45.455 0.00 0.00 0.00 4.75
2535 2744 2.297033 ACATGTCATTCACCAAAGGCAC 59.703 45.455 0.00 0.00 0.00 5.01
2536 2745 1.327303 TGTCATTCACCAAAGGCACC 58.673 50.000 0.00 0.00 0.00 5.01
2537 2746 1.133513 TGTCATTCACCAAAGGCACCT 60.134 47.619 0.00 0.00 0.00 4.00
2538 2747 1.963515 GTCATTCACCAAAGGCACCTT 59.036 47.619 0.00 0.00 37.98 3.50
2539 2748 1.962807 TCATTCACCAAAGGCACCTTG 59.037 47.619 1.91 0.00 36.26 3.61
2540 2749 0.681175 ATTCACCAAAGGCACCTTGC 59.319 50.000 1.91 0.00 44.08 4.01
2541 2750 0.396974 TTCACCAAAGGCACCTTGCT 60.397 50.000 1.91 0.00 44.28 3.91
2542 2751 1.108727 TCACCAAAGGCACCTTGCTG 61.109 55.000 1.91 0.00 44.28 4.41
2543 2752 1.076044 ACCAAAGGCACCTTGCTGT 60.076 52.632 1.91 0.00 44.28 4.40
2544 2753 1.109323 ACCAAAGGCACCTTGCTGTC 61.109 55.000 1.91 0.00 44.28 3.51
2545 2754 1.662044 CAAAGGCACCTTGCTGTCC 59.338 57.895 1.91 0.00 44.28 4.02
2546 2755 1.108727 CAAAGGCACCTTGCTGTCCA 61.109 55.000 1.91 0.00 44.28 4.02
2547 2756 0.178953 AAAGGCACCTTGCTGTCCAT 60.179 50.000 1.91 0.00 44.28 3.41
2548 2757 0.896940 AAGGCACCTTGCTGTCCATG 60.897 55.000 0.00 0.00 44.28 3.66
2621 2831 1.067060 CGACCTACGGAATGAGATGCA 59.933 52.381 0.00 0.00 38.46 3.96
2630 2840 3.744942 CGGAATGAGATGCATGACCTTAG 59.255 47.826 2.46 0.00 37.28 2.18
2696 2908 3.008594 TCTCAAGAACGGCCAATAAGGAA 59.991 43.478 2.24 0.00 41.22 3.36
2790 3002 6.258507 TGACACGTCATAATCCAATCATTGAG 59.741 38.462 0.00 0.00 34.14 3.02
2803 3015 2.972625 TCATTGAGACTAGCGGTTTGG 58.027 47.619 0.00 0.00 0.00 3.28
2834 3046 7.474190 GCGTTTGCTTAGGTTTAATAATGGTA 58.526 34.615 0.00 0.00 38.39 3.25
3036 3253 9.250624 GCACTGACCTATATTTCTTTAGTGTAG 57.749 37.037 0.00 0.00 36.36 2.74
3131 3348 5.886715 TTGCAGAATTTTTGTGTGAATCG 57.113 34.783 0.00 0.00 0.00 3.34
3175 3393 1.072173 CCAATCACCACTCCTGTCACA 59.928 52.381 0.00 0.00 0.00 3.58
3200 3418 1.470285 GCATAGCTTGTGCCCATGTTG 60.470 52.381 11.54 0.00 40.80 3.33
3217 3435 6.272318 CCATGTTGTGTTTGTGTATGTCTTT 58.728 36.000 0.00 0.00 0.00 2.52
3260 3478 2.368548 TCTTGCTGTAGAAGGCAGAACA 59.631 45.455 0.00 0.00 39.68 3.18
3368 3586 3.514645 TCACGGGAAATTTCTAGCGTAC 58.485 45.455 17.42 0.00 0.00 3.67
3386 3604 4.200874 CGTACTCCCTTGACTCTCTGTAT 58.799 47.826 0.00 0.00 0.00 2.29
3387 3605 4.641094 CGTACTCCCTTGACTCTCTGTATT 59.359 45.833 0.00 0.00 0.00 1.89
3388 3606 5.821470 CGTACTCCCTTGACTCTCTGTATTA 59.179 44.000 0.00 0.00 0.00 0.98
3389 3607 6.487331 CGTACTCCCTTGACTCTCTGTATTAT 59.513 42.308 0.00 0.00 0.00 1.28
3390 3608 7.660617 CGTACTCCCTTGACTCTCTGTATTATA 59.339 40.741 0.00 0.00 0.00 0.98
3391 3609 9.005777 GTACTCCCTTGACTCTCTGTATTATAG 57.994 40.741 0.00 0.00 0.00 1.31
3394 3612 9.747898 CTCCCTTGACTCTCTGTATTATAGTAT 57.252 37.037 0.00 0.00 0.00 2.12
3419 3637 6.411376 TCCACATCGACAATTACCAATAGTT 58.589 36.000 0.00 0.00 0.00 2.24
3420 3638 6.315144 TCCACATCGACAATTACCAATAGTTG 59.685 38.462 0.00 0.00 34.89 3.16
3589 3807 4.657814 AATGAGGGTGTTACATTGGAGT 57.342 40.909 0.00 0.00 33.79 3.85
3649 3868 2.102357 ACAGTCGACATAGGCGCG 59.898 61.111 19.50 0.00 0.00 6.86
3697 3923 5.885881 TGGTGTTTTATCTGTGTGTTTGTC 58.114 37.500 0.00 0.00 0.00 3.18
3742 3968 2.308811 GCATTTGCAAACCAAAATGCG 58.691 42.857 15.41 0.00 45.80 4.73
3743 3969 2.917296 GCATTTGCAAACCAAAATGCGG 60.917 45.455 15.41 0.00 45.80 5.69
3789 4017 8.893219 TCAATATAAATGCAGTTGAGGACTAG 57.107 34.615 10.14 0.00 36.65 2.57
3852 4080 9.466497 TCTAGCAATTGGAAAACATCTATTCTT 57.534 29.630 7.72 0.00 0.00 2.52
4038 4519 7.882271 ACAATCATATAGAAGAGAAAGGCCATC 59.118 37.037 5.01 2.29 0.00 3.51
4048 4529 6.382869 AGAGAAAGGCCATCAAAAATATCG 57.617 37.500 5.01 0.00 0.00 2.92
4054 4535 3.882888 GGCCATCAAAAATATCGTCTCCA 59.117 43.478 0.00 0.00 0.00 3.86
4177 4662 4.253685 TCATGGCACTTACTGCTTACTTC 58.746 43.478 0.00 0.00 46.25 3.01
4190 4675 1.933853 CTTACTTCCGTATGCAGTGGC 59.066 52.381 0.00 0.00 41.68 5.01
4195 4680 2.586079 CGTATGCAGTGGCGGAGG 60.586 66.667 0.00 0.00 45.35 4.30
4197 4682 1.820581 GTATGCAGTGGCGGAGGTA 59.179 57.895 0.00 0.00 45.35 3.08
4198 4683 0.529992 GTATGCAGTGGCGGAGGTAC 60.530 60.000 0.00 0.00 45.35 3.34
4201 4686 2.126071 CAGTGGCGGAGGTACACG 60.126 66.667 0.00 0.00 39.95 4.49
4202 4687 2.282674 AGTGGCGGAGGTACACGA 60.283 61.111 7.85 0.00 39.95 4.35
4204 4689 1.735559 GTGGCGGAGGTACACGAAC 60.736 63.158 7.85 2.43 32.99 3.95
4205 4690 1.904865 TGGCGGAGGTACACGAACT 60.905 57.895 7.85 0.00 32.99 3.01
4206 4691 1.153881 GGCGGAGGTACACGAACTC 60.154 63.158 7.85 0.00 32.99 3.01
4207 4692 1.593296 GGCGGAGGTACACGAACTCT 61.593 60.000 7.85 0.00 32.99 3.24
4208 4693 0.456312 GCGGAGGTACACGAACTCTG 60.456 60.000 7.85 4.66 39.92 3.35
4209 4694 0.456312 CGGAGGTACACGAACTCTGC 60.456 60.000 0.00 0.00 31.59 4.26
4210 4695 0.108756 GGAGGTACACGAACTCTGCC 60.109 60.000 0.00 0.00 0.00 4.85
4211 4696 0.889306 GAGGTACACGAACTCTGCCT 59.111 55.000 0.00 0.00 0.00 4.75
4212 4697 1.272769 GAGGTACACGAACTCTGCCTT 59.727 52.381 0.00 0.00 0.00 4.35
4213 4698 1.000955 AGGTACACGAACTCTGCCTTG 59.999 52.381 0.00 0.00 0.00 3.61
4214 4699 1.429463 GTACACGAACTCTGCCTTGG 58.571 55.000 0.00 0.00 0.00 3.61
4215 4700 0.320374 TACACGAACTCTGCCTTGGG 59.680 55.000 0.00 0.00 0.00 4.12
4245 4730 2.821991 GGGACGGGACAGAATATGAG 57.178 55.000 0.00 0.00 0.00 2.90
4246 4731 2.317040 GGGACGGGACAGAATATGAGA 58.683 52.381 0.00 0.00 0.00 3.27
4247 4732 2.297597 GGGACGGGACAGAATATGAGAG 59.702 54.545 0.00 0.00 0.00 3.20
4248 4733 2.959707 GGACGGGACAGAATATGAGAGT 59.040 50.000 0.00 0.00 0.00 3.24
4249 4734 3.385111 GGACGGGACAGAATATGAGAGTT 59.615 47.826 0.00 0.00 0.00 3.01
4250 4735 4.500035 GGACGGGACAGAATATGAGAGTTC 60.500 50.000 0.00 0.00 0.00 3.01
4251 4736 4.023980 ACGGGACAGAATATGAGAGTTCA 58.976 43.478 0.00 0.00 37.81 3.18
4252 4737 4.466370 ACGGGACAGAATATGAGAGTTCAA 59.534 41.667 0.00 0.00 36.78 2.69
4253 4738 5.046529 CGGGACAGAATATGAGAGTTCAAG 58.953 45.833 0.00 0.00 36.78 3.02
4254 4739 5.394663 CGGGACAGAATATGAGAGTTCAAGT 60.395 44.000 0.00 0.00 36.78 3.16
4255 4740 6.410540 GGGACAGAATATGAGAGTTCAAGTT 58.589 40.000 0.00 0.00 36.78 2.66
4256 4741 6.881602 GGGACAGAATATGAGAGTTCAAGTTT 59.118 38.462 0.00 0.00 36.78 2.66
4257 4742 7.148340 GGGACAGAATATGAGAGTTCAAGTTTG 60.148 40.741 0.00 0.00 36.78 2.93
4258 4743 7.148340 GGACAGAATATGAGAGTTCAAGTTTGG 60.148 40.741 0.00 0.00 36.78 3.28
4259 4744 6.656693 ACAGAATATGAGAGTTCAAGTTTGGG 59.343 38.462 0.00 0.00 36.78 4.12
4260 4745 6.094603 CAGAATATGAGAGTTCAAGTTTGGGG 59.905 42.308 0.00 0.00 36.78 4.96
4261 4746 2.656947 TGAGAGTTCAAGTTTGGGGG 57.343 50.000 0.00 0.00 0.00 5.40
4299 4784 3.418684 TTTTCCCACCTAAGCTCTCAC 57.581 47.619 0.00 0.00 0.00 3.51
4300 4785 2.327325 TTCCCACCTAAGCTCTCACT 57.673 50.000 0.00 0.00 0.00 3.41
4301 4786 2.327325 TCCCACCTAAGCTCTCACTT 57.673 50.000 0.00 0.00 0.00 3.16
4302 4787 3.468071 TCCCACCTAAGCTCTCACTTA 57.532 47.619 0.00 0.00 0.00 2.24
4303 4788 3.786553 TCCCACCTAAGCTCTCACTTAA 58.213 45.455 0.00 0.00 31.92 1.85
4304 4789 4.164981 TCCCACCTAAGCTCTCACTTAAA 58.835 43.478 0.00 0.00 31.92 1.52
4305 4790 4.783227 TCCCACCTAAGCTCTCACTTAAAT 59.217 41.667 0.00 0.00 31.92 1.40
4306 4791 5.962031 TCCCACCTAAGCTCTCACTTAAATA 59.038 40.000 0.00 0.00 31.92 1.40
4307 4792 6.615726 TCCCACCTAAGCTCTCACTTAAATAT 59.384 38.462 0.00 0.00 31.92 1.28
4308 4793 7.127339 TCCCACCTAAGCTCTCACTTAAATATT 59.873 37.037 0.00 0.00 31.92 1.28
4309 4794 7.775561 CCCACCTAAGCTCTCACTTAAATATTT 59.224 37.037 5.89 5.89 31.92 1.40
4310 4795 8.831550 CCACCTAAGCTCTCACTTAAATATTTC 58.168 37.037 3.39 0.00 31.92 2.17
4311 4796 9.606631 CACCTAAGCTCTCACTTAAATATTTCT 57.393 33.333 3.39 0.00 31.92 2.52
4316 4801 8.729805 AGCTCTCACTTAAATATTTCTTCAGG 57.270 34.615 3.39 0.00 0.00 3.86
4317 4802 8.325046 AGCTCTCACTTAAATATTTCTTCAGGT 58.675 33.333 3.39 0.00 0.00 4.00
4318 4803 9.601217 GCTCTCACTTAAATATTTCTTCAGGTA 57.399 33.333 3.39 0.00 0.00 3.08
4635 5120 9.642327 TCATGTTTGGAAATGATGTTAAAGATG 57.358 29.630 0.00 0.00 33.03 2.90
4724 5209 1.617850 TGGTTTAGCAATTGGGCTGTG 59.382 47.619 7.72 0.00 45.44 3.66
4738 5223 0.816825 GCTGTGGATGGCGATCACAT 60.817 55.000 11.07 0.00 0.00 3.21
4765 5250 1.338579 GCTCACAGGACTCTTTGGAGG 60.339 57.143 0.00 0.00 43.46 4.30
4767 5252 0.689623 CACAGGACTCTTTGGAGGCT 59.310 55.000 0.00 0.00 46.45 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 5.127031 ACACCACAACAAAATAAGCAAGAGT 59.873 36.000 0.00 0.00 0.00 3.24
51 52 8.230486 GTGACCAACTATGACACAAAATAAGAG 58.770 37.037 0.00 0.00 35.40 2.85
399 400 6.226052 TGATGATGTATAGGAGTGCAATGTC 58.774 40.000 0.00 0.00 0.00 3.06
420 436 1.065126 GCCACAAGGGAGCTACTTGAT 60.065 52.381 27.89 14.76 46.27 2.57
434 450 4.454948 CAAGGAGACGTGCCACAA 57.545 55.556 0.00 0.00 31.77 3.33
449 465 3.736433 CGTTGTTGACCAAAATCCAGCAA 60.736 43.478 0.00 0.00 34.07 3.91
622 638 9.383519 TGTTAAAATGTTGACCAAGCATTTAAA 57.616 25.926 16.11 0.00 40.58 1.52
623 639 8.948631 TGTTAAAATGTTGACCAAGCATTTAA 57.051 26.923 16.11 10.35 40.58 1.52
624 640 9.553064 AATGTTAAAATGTTGACCAAGCATTTA 57.447 25.926 16.11 6.67 40.58 1.40
625 641 8.449251 AATGTTAAAATGTTGACCAAGCATTT 57.551 26.923 12.82 12.82 42.46 2.32
626 642 8.449251 AAATGTTAAAATGTTGACCAAGCATT 57.551 26.923 0.00 0.00 34.69 3.56
627 643 8.449251 AAAATGTTAAAATGTTGACCAAGCAT 57.551 26.923 0.00 0.00 0.00 3.79
628 644 7.856145 AAAATGTTAAAATGTTGACCAAGCA 57.144 28.000 0.00 0.00 0.00 3.91
816 841 0.179097 GTAGGGAAGCCTCGCTCAAG 60.179 60.000 4.98 0.00 43.41 3.02
826 851 0.029167 GTAGCGAGACGTAGGGAAGC 59.971 60.000 0.00 0.00 0.00 3.86
878 904 2.496817 GTGTAGCTGGGCTCGAGG 59.503 66.667 15.58 0.00 40.44 4.63
896 927 1.028130 GCCTGGGCTTCATTCTTAGC 58.972 55.000 4.12 0.00 38.26 3.09
915 946 2.930019 TGGTCTGGTCTGGGCTGG 60.930 66.667 0.00 0.00 0.00 4.85
923 954 3.126001 TCAAATGACAGTGGTCTGGTC 57.874 47.619 0.00 0.00 45.14 4.02
1521 1558 1.635663 CCCACGTGATGCCGTCTTTC 61.636 60.000 19.30 0.00 39.45 2.62
1524 1561 4.760047 GCCCACGTGATGCCGTCT 62.760 66.667 19.30 0.00 39.45 4.18
1554 1591 0.537188 AACACCCATCAGAGTAGGCG 59.463 55.000 0.00 0.00 0.00 5.52
1687 1724 1.359130 ACCAAAGCCCCTTAATCTGCT 59.641 47.619 0.00 0.00 35.08 4.24
1758 1795 1.374631 CTGCAGCAGCGAACTACCA 60.375 57.895 10.14 0.00 46.23 3.25
1899 1939 2.673200 GGCCTCATCCAGCAGTCCA 61.673 63.158 0.00 0.00 0.00 4.02
2040 2080 3.908189 CCGTGCTTGATGGCATCA 58.092 55.556 25.63 25.63 44.34 3.07
2319 2359 1.010935 AGTGCAGCAGTCAACGATCG 61.011 55.000 14.88 14.88 0.00 3.69
2348 2388 1.067060 TCTTCGGCACAGATCATACCG 59.933 52.381 9.43 9.43 45.15 4.02
2436 2645 0.034670 ACTGAAGCAGCCTCCATTCC 60.035 55.000 0.00 0.00 34.37 3.01
2439 2648 1.378250 GCACTGAAGCAGCCTCCAT 60.378 57.895 0.00 0.00 34.37 3.41
2441 2650 2.039405 CAGCACTGAAGCAGCCTCC 61.039 63.158 0.00 0.00 34.37 4.30
2442 2651 0.036952 TACAGCACTGAAGCAGCCTC 60.037 55.000 4.31 0.00 34.37 4.70
2443 2652 0.397941 TTACAGCACTGAAGCAGCCT 59.602 50.000 4.31 0.00 34.37 4.58
2444 2653 0.519077 GTTACAGCACTGAAGCAGCC 59.481 55.000 4.31 0.00 34.37 4.85
2445 2654 0.164647 CGTTACAGCACTGAAGCAGC 59.835 55.000 4.31 0.00 34.37 5.25
2446 2655 1.502231 ACGTTACAGCACTGAAGCAG 58.498 50.000 4.31 0.00 37.52 4.24
2447 2656 1.948104 AACGTTACAGCACTGAAGCA 58.052 45.000 0.00 0.00 36.85 3.91
2448 2657 2.159827 GCTAACGTTACAGCACTGAAGC 60.160 50.000 16.35 7.30 37.73 3.86
2449 2658 3.121944 CAGCTAACGTTACAGCACTGAAG 59.878 47.826 21.71 4.68 40.36 3.02
2450 2659 3.057019 CAGCTAACGTTACAGCACTGAA 58.943 45.455 21.71 0.00 40.36 3.02
2451 2660 2.672714 CAGCTAACGTTACAGCACTGA 58.327 47.619 21.71 0.00 40.36 3.41
2452 2661 1.126846 GCAGCTAACGTTACAGCACTG 59.873 52.381 21.71 14.32 40.36 3.66
2453 2662 1.429463 GCAGCTAACGTTACAGCACT 58.571 50.000 21.71 2.94 40.36 4.40
2454 2663 0.442699 GGCAGCTAACGTTACAGCAC 59.557 55.000 21.71 14.17 40.36 4.40
2455 2664 0.320374 AGGCAGCTAACGTTACAGCA 59.680 50.000 21.71 0.00 40.36 4.41
2456 2665 1.439679 AAGGCAGCTAACGTTACAGC 58.560 50.000 13.97 13.97 38.09 4.40
2457 2666 2.806244 ACAAAGGCAGCTAACGTTACAG 59.194 45.455 3.29 0.00 0.00 2.74
2458 2667 2.546368 CACAAAGGCAGCTAACGTTACA 59.454 45.455 3.29 0.00 0.00 2.41
2459 2668 2.546789 ACACAAAGGCAGCTAACGTTAC 59.453 45.455 3.29 2.02 0.00 2.50
2460 2669 2.546368 CACACAAAGGCAGCTAACGTTA 59.454 45.455 7.94 7.94 0.00 3.18
2461 2670 1.333619 CACACAAAGGCAGCTAACGTT 59.666 47.619 5.88 5.88 0.00 3.99
2462 2671 0.944386 CACACAAAGGCAGCTAACGT 59.056 50.000 0.00 0.00 0.00 3.99
2463 2672 0.944386 ACACACAAAGGCAGCTAACG 59.056 50.000 0.00 0.00 0.00 3.18
2464 2673 3.115554 CAAACACACAAAGGCAGCTAAC 58.884 45.455 0.00 0.00 0.00 2.34
2465 2674 3.020274 TCAAACACACAAAGGCAGCTAA 58.980 40.909 0.00 0.00 0.00 3.09
2466 2675 2.357637 GTCAAACACACAAAGGCAGCTA 59.642 45.455 0.00 0.00 0.00 3.32
2467 2676 1.134946 GTCAAACACACAAAGGCAGCT 59.865 47.619 0.00 0.00 0.00 4.24
2468 2677 1.135141 TGTCAAACACACAAAGGCAGC 60.135 47.619 0.00 0.00 0.00 5.25
2469 2678 2.937469 TGTCAAACACACAAAGGCAG 57.063 45.000 0.00 0.00 0.00 4.85
2470 2679 2.495270 ACATGTCAAACACACAAAGGCA 59.505 40.909 0.00 0.00 38.04 4.75
2471 2680 2.859538 CACATGTCAAACACACAAAGGC 59.140 45.455 0.00 0.00 38.04 4.35
2472 2681 3.446799 CCACATGTCAAACACACAAAGG 58.553 45.455 0.00 0.00 38.04 3.11
2473 2682 3.446799 CCCACATGTCAAACACACAAAG 58.553 45.455 0.00 0.00 38.04 2.77
2474 2683 2.417924 GCCCACATGTCAAACACACAAA 60.418 45.455 0.00 0.00 38.04 2.83
2475 2684 1.135915 GCCCACATGTCAAACACACAA 59.864 47.619 0.00 0.00 38.04 3.33
2476 2685 0.743688 GCCCACATGTCAAACACACA 59.256 50.000 0.00 0.00 38.04 3.72
2477 2686 0.031994 GGCCCACATGTCAAACACAC 59.968 55.000 0.00 0.00 38.04 3.82
2478 2687 0.396278 TGGCCCACATGTCAAACACA 60.396 50.000 0.00 0.00 40.18 3.72
2479 2688 0.314935 CTGGCCCACATGTCAAACAC 59.685 55.000 0.00 0.00 0.00 3.32
2480 2689 0.184692 TCTGGCCCACATGTCAAACA 59.815 50.000 0.00 0.00 0.00 2.83
2481 2690 0.598065 GTCTGGCCCACATGTCAAAC 59.402 55.000 0.00 0.00 0.00 2.93
2482 2691 0.184692 TGTCTGGCCCACATGTCAAA 59.815 50.000 0.00 0.00 0.00 2.69
2483 2692 0.537143 GTGTCTGGCCCACATGTCAA 60.537 55.000 7.84 0.00 33.00 3.18
2484 2693 1.073025 GTGTCTGGCCCACATGTCA 59.927 57.895 7.84 0.00 33.00 3.58
2485 2694 1.675641 GGTGTCTGGCCCACATGTC 60.676 63.158 12.01 0.00 34.46 3.06
2486 2695 0.840288 TAGGTGTCTGGCCCACATGT 60.840 55.000 12.01 0.00 34.46 3.21
2487 2696 0.548031 ATAGGTGTCTGGCCCACATG 59.452 55.000 12.01 0.00 34.46 3.21
2488 2697 1.064463 CAATAGGTGTCTGGCCCACAT 60.064 52.381 12.01 7.82 34.46 3.21
2489 2698 0.327924 CAATAGGTGTCTGGCCCACA 59.672 55.000 12.01 6.73 34.46 4.17
2490 2699 0.394352 CCAATAGGTGTCTGGCCCAC 60.394 60.000 0.00 0.11 0.00 4.61
2491 2700 1.570857 CCCAATAGGTGTCTGGCCCA 61.571 60.000 0.00 0.00 0.00 5.36
2492 2701 1.227383 CCCAATAGGTGTCTGGCCC 59.773 63.158 0.00 0.00 0.00 5.80
2493 2702 1.453928 GCCCAATAGGTGTCTGGCC 60.454 63.158 0.00 0.00 38.26 5.36
2494 2703 1.453928 GGCCCAATAGGTGTCTGGC 60.454 63.158 0.00 0.00 38.26 4.85
2495 2704 1.227383 GGGCCCAATAGGTGTCTGG 59.773 63.158 19.95 0.00 38.26 3.86
2496 2705 0.394352 GTGGGCCCAATAGGTGTCTG 60.394 60.000 30.64 0.00 38.26 3.51
2497 2706 0.844661 TGTGGGCCCAATAGGTGTCT 60.845 55.000 30.64 0.00 38.26 3.41
2498 2707 0.258774 ATGTGGGCCCAATAGGTGTC 59.741 55.000 30.64 12.49 38.26 3.67
2499 2708 0.033208 CATGTGGGCCCAATAGGTGT 60.033 55.000 30.64 4.36 38.26 4.16
2500 2709 0.033208 ACATGTGGGCCCAATAGGTG 60.033 55.000 30.64 21.87 38.26 4.00
2501 2710 0.258774 GACATGTGGGCCCAATAGGT 59.741 55.000 30.64 26.07 38.26 3.08
2502 2711 0.258484 TGACATGTGGGCCCAATAGG 59.742 55.000 30.64 22.77 39.47 2.57
2503 2712 2.369983 ATGACATGTGGGCCCAATAG 57.630 50.000 30.64 21.28 0.00 1.73
2504 2713 2.024560 TGAATGACATGTGGGCCCAATA 60.025 45.455 30.64 20.11 0.00 1.90
2505 2714 1.273154 TGAATGACATGTGGGCCCAAT 60.273 47.619 30.64 19.44 0.00 3.16
2506 2715 0.113972 TGAATGACATGTGGGCCCAA 59.886 50.000 30.64 17.87 0.00 4.12
2507 2716 0.611618 GTGAATGACATGTGGGCCCA 60.612 55.000 24.45 24.45 0.00 5.36
2508 2717 1.322538 GGTGAATGACATGTGGGCCC 61.323 60.000 17.59 17.59 0.00 5.80
2509 2718 0.611618 TGGTGAATGACATGTGGGCC 60.612 55.000 1.15 0.00 0.00 5.80
2510 2719 1.255882 TTGGTGAATGACATGTGGGC 58.744 50.000 1.15 0.00 0.00 5.36
2511 2720 2.231964 CCTTTGGTGAATGACATGTGGG 59.768 50.000 1.15 0.00 0.00 4.61
2512 2721 2.353011 GCCTTTGGTGAATGACATGTGG 60.353 50.000 1.15 0.00 0.00 4.17
2513 2722 2.296752 TGCCTTTGGTGAATGACATGTG 59.703 45.455 1.15 0.00 0.00 3.21
2514 2723 2.297033 GTGCCTTTGGTGAATGACATGT 59.703 45.455 0.00 0.00 0.00 3.21
2515 2724 2.353011 GGTGCCTTTGGTGAATGACATG 60.353 50.000 0.00 0.00 0.00 3.21
2516 2725 1.895131 GGTGCCTTTGGTGAATGACAT 59.105 47.619 0.00 0.00 0.00 3.06
2517 2726 1.133513 AGGTGCCTTTGGTGAATGACA 60.134 47.619 0.00 0.00 0.00 3.58
2518 2727 1.620822 AGGTGCCTTTGGTGAATGAC 58.379 50.000 0.00 0.00 0.00 3.06
2519 2728 1.962807 CAAGGTGCCTTTGGTGAATGA 59.037 47.619 0.00 0.00 33.42 2.57
2520 2729 1.606224 GCAAGGTGCCTTTGGTGAATG 60.606 52.381 0.00 0.00 37.42 2.67
2521 2730 0.681175 GCAAGGTGCCTTTGGTGAAT 59.319 50.000 0.00 0.00 37.42 2.57
2522 2731 0.396974 AGCAAGGTGCCTTTGGTGAA 60.397 50.000 0.00 0.00 46.52 3.18
2523 2732 1.108727 CAGCAAGGTGCCTTTGGTGA 61.109 55.000 17.98 0.00 46.52 4.02
2524 2733 1.364901 CAGCAAGGTGCCTTTGGTG 59.635 57.895 12.32 12.32 46.52 4.17
2525 2734 1.076044 ACAGCAAGGTGCCTTTGGT 60.076 52.632 0.00 0.76 46.52 3.67
2526 2735 1.662044 GACAGCAAGGTGCCTTTGG 59.338 57.895 0.00 0.00 46.52 3.28
2527 2736 1.108727 TGGACAGCAAGGTGCCTTTG 61.109 55.000 0.00 1.19 46.52 2.77
2528 2737 0.178953 ATGGACAGCAAGGTGCCTTT 60.179 50.000 0.00 0.00 46.52 3.11
2529 2738 0.896940 CATGGACAGCAAGGTGCCTT 60.897 55.000 0.00 0.00 46.52 4.35
2530 2739 1.303888 CATGGACAGCAAGGTGCCT 60.304 57.895 11.80 0.00 46.52 4.75
2531 2740 1.604593 ACATGGACAGCAAGGTGCC 60.605 57.895 0.00 2.91 46.52 5.01
2532 2741 1.582968 CACATGGACAGCAAGGTGC 59.417 57.895 0.00 0.00 45.46 5.01
2533 2742 0.892358 AGCACATGGACAGCAAGGTG 60.892 55.000 0.00 0.00 0.00 4.00
2534 2743 0.892358 CAGCACATGGACAGCAAGGT 60.892 55.000 0.00 0.00 0.00 3.50
2535 2744 1.880894 CAGCACATGGACAGCAAGG 59.119 57.895 0.00 0.00 0.00 3.61
2609 2819 4.712476 ACTAAGGTCATGCATCTCATTCC 58.288 43.478 0.00 0.00 31.79 3.01
2678 2890 5.506708 AGTAATTCCTTATTGGCCGTTCTT 58.493 37.500 0.00 0.00 35.26 2.52
2696 2908 6.260936 ACAAATAATGCAGCGAGCTAAGTAAT 59.739 34.615 0.00 0.00 45.94 1.89
2749 2961 7.870826 TGACGTGTCATAATCAAATTTTCAGT 58.129 30.769 0.00 0.00 34.14 3.41
2776 2988 4.141620 ACCGCTAGTCTCAATGATTGGATT 60.142 41.667 5.20 1.79 0.00 3.01
2790 3002 1.429423 GCATGCCAAACCGCTAGTC 59.571 57.895 6.36 0.00 0.00 2.59
2803 3015 1.869132 CCTAAGCAAACGCGCATGC 60.869 57.895 24.28 24.28 42.87 4.06
2957 3173 9.979270 GATAACTGTGTGATAGAATGTTTTGAG 57.021 33.333 0.00 0.00 0.00 3.02
3131 3348 6.431278 GCAAAAGAAAGAGTGGTTTAGAGAC 58.569 40.000 0.00 0.00 0.00 3.36
3175 3393 0.393537 GGGCACAAGCTATGCTGAGT 60.394 55.000 19.25 0.00 42.93 3.41
3200 3418 5.339990 ACTGCAAAAGACATACACAAACAC 58.660 37.500 0.00 0.00 0.00 3.32
3368 3586 9.747898 ATACTATAATACAGAGAGTCAAGGGAG 57.252 37.037 0.00 0.00 0.00 4.30
3386 3604 9.701098 GGTAATTGTCGATGTGGAATACTATAA 57.299 33.333 0.00 0.00 0.00 0.98
3387 3605 8.862085 TGGTAATTGTCGATGTGGAATACTATA 58.138 33.333 0.00 0.00 0.00 1.31
3388 3606 7.732025 TGGTAATTGTCGATGTGGAATACTAT 58.268 34.615 0.00 0.00 0.00 2.12
3389 3607 7.114866 TGGTAATTGTCGATGTGGAATACTA 57.885 36.000 0.00 0.00 0.00 1.82
3390 3608 5.984725 TGGTAATTGTCGATGTGGAATACT 58.015 37.500 0.00 0.00 0.00 2.12
3391 3609 6.671614 TTGGTAATTGTCGATGTGGAATAC 57.328 37.500 0.00 0.00 0.00 1.89
3394 3612 6.411376 ACTATTGGTAATTGTCGATGTGGAA 58.589 36.000 0.00 0.00 0.00 3.53
3419 3637 7.438757 GCATTCAATATCATGCAACAATTACCA 59.561 33.333 0.00 0.00 44.49 3.25
3420 3638 7.790000 GCATTCAATATCATGCAACAATTACC 58.210 34.615 0.00 0.00 44.49 2.85
3484 3702 4.446371 ACTAATCTTGAATTGGCTCTCCG 58.554 43.478 0.00 0.00 34.14 4.63
3488 3706 7.699812 GTGAATGAACTAATCTTGAATTGGCTC 59.300 37.037 0.00 0.00 0.00 4.70
3536 3754 9.587772 TTAAACTTCTATCAGAGTGCAAGATAC 57.412 33.333 0.00 0.00 0.00 2.24
3649 3868 3.375299 AGGTGCTCGCAATCTATTCAAAC 59.625 43.478 0.00 0.00 0.00 2.93
3697 3923 7.274904 GCATAAATGTAGCATGCAGATAAATGG 59.725 37.037 21.98 3.98 43.59 3.16
3742 3968 3.991367 AGTACAGATTATTAGCGCACCC 58.009 45.455 11.47 0.00 0.00 4.61
3743 3969 5.047847 TGAAGTACAGATTATTAGCGCACC 58.952 41.667 11.47 0.00 0.00 5.01
4038 4519 5.505173 AGGCATTGGAGACGATATTTTTG 57.495 39.130 0.00 0.00 31.43 2.44
4048 4529 2.159324 GCTAAAGCAAGGCATTGGAGAC 60.159 50.000 13.70 0.00 41.59 3.36
4177 4662 2.586079 CTCCGCCACTGCATACGG 60.586 66.667 9.75 9.75 46.97 4.02
4190 4675 0.456312 GCAGAGTTCGTGTACCTCCG 60.456 60.000 0.00 0.00 0.00 4.63
4195 4680 1.429463 CCAAGGCAGAGTTCGTGTAC 58.571 55.000 0.00 0.00 0.00 2.90
4197 4682 1.071471 CCCAAGGCAGAGTTCGTGT 59.929 57.895 0.00 0.00 0.00 4.49
4198 4683 3.972227 CCCAAGGCAGAGTTCGTG 58.028 61.111 0.00 0.00 0.00 4.35
4222 4707 1.039233 TATTCTGTCCCGTCCCGGTC 61.039 60.000 0.00 0.00 46.80 4.79
4223 4708 0.398098 ATATTCTGTCCCGTCCCGGT 60.398 55.000 0.00 0.00 46.80 5.28
4225 4710 1.000163 CTCATATTCTGTCCCGTCCCG 60.000 57.143 0.00 0.00 0.00 5.14
4226 4711 2.297597 CTCTCATATTCTGTCCCGTCCC 59.702 54.545 0.00 0.00 0.00 4.46
4227 4712 2.959707 ACTCTCATATTCTGTCCCGTCC 59.040 50.000 0.00 0.00 0.00 4.79
4228 4713 4.098044 TGAACTCTCATATTCTGTCCCGTC 59.902 45.833 0.00 0.00 0.00 4.79
4229 4714 4.023980 TGAACTCTCATATTCTGTCCCGT 58.976 43.478 0.00 0.00 0.00 5.28
4230 4715 4.655762 TGAACTCTCATATTCTGTCCCG 57.344 45.455 0.00 0.00 0.00 5.14
4231 4716 5.983540 ACTTGAACTCTCATATTCTGTCCC 58.016 41.667 0.00 0.00 0.00 4.46
4232 4717 7.148340 CCAAACTTGAACTCTCATATTCTGTCC 60.148 40.741 0.00 0.00 0.00 4.02
4233 4718 7.148340 CCCAAACTTGAACTCTCATATTCTGTC 60.148 40.741 0.00 0.00 0.00 3.51
4234 4719 6.656693 CCCAAACTTGAACTCTCATATTCTGT 59.343 38.462 0.00 0.00 0.00 3.41
4235 4720 6.094603 CCCCAAACTTGAACTCTCATATTCTG 59.905 42.308 0.00 0.00 0.00 3.02
4236 4721 6.183347 CCCCAAACTTGAACTCTCATATTCT 58.817 40.000 0.00 0.00 0.00 2.40
4237 4722 5.358160 CCCCCAAACTTGAACTCTCATATTC 59.642 44.000 0.00 0.00 0.00 1.75
4238 4723 5.264395 CCCCCAAACTTGAACTCTCATATT 58.736 41.667 0.00 0.00 0.00 1.28
4239 4724 4.860022 CCCCCAAACTTGAACTCTCATAT 58.140 43.478 0.00 0.00 0.00 1.78
4240 4725 4.301072 CCCCCAAACTTGAACTCTCATA 57.699 45.455 0.00 0.00 0.00 2.15
4241 4726 3.160679 CCCCCAAACTTGAACTCTCAT 57.839 47.619 0.00 0.00 0.00 2.90
4242 4727 2.656947 CCCCCAAACTTGAACTCTCA 57.343 50.000 0.00 0.00 0.00 3.27
4278 4763 3.394606 AGTGAGAGCTTAGGTGGGAAAAA 59.605 43.478 0.00 0.00 0.00 1.94
4279 4764 2.979678 AGTGAGAGCTTAGGTGGGAAAA 59.020 45.455 0.00 0.00 0.00 2.29
4280 4765 2.621070 AGTGAGAGCTTAGGTGGGAAA 58.379 47.619 0.00 0.00 0.00 3.13
4281 4766 2.327325 AGTGAGAGCTTAGGTGGGAA 57.673 50.000 0.00 0.00 0.00 3.97
4282 4767 2.327325 AAGTGAGAGCTTAGGTGGGA 57.673 50.000 0.00 0.00 0.00 4.37
4283 4768 4.553330 TTTAAGTGAGAGCTTAGGTGGG 57.447 45.455 0.00 0.00 33.16 4.61
4284 4769 8.738645 AAATATTTAAGTGAGAGCTTAGGTGG 57.261 34.615 0.00 0.00 33.16 4.61
4285 4770 9.606631 AGAAATATTTAAGTGAGAGCTTAGGTG 57.393 33.333 0.00 0.00 33.16 4.00
4290 4775 9.171877 CCTGAAGAAATATTTAAGTGAGAGCTT 57.828 33.333 0.00 0.00 0.00 3.74
4291 4776 8.325046 ACCTGAAGAAATATTTAAGTGAGAGCT 58.675 33.333 0.00 0.00 0.00 4.09
4292 4777 8.499403 ACCTGAAGAAATATTTAAGTGAGAGC 57.501 34.615 0.00 0.00 0.00 4.09
4567 5052 4.134379 ACAGAGGCAGAGATATGTGTTG 57.866 45.455 0.00 0.00 0.00 3.33
4568 5053 4.833478 AACAGAGGCAGAGATATGTGTT 57.167 40.909 0.00 0.00 0.00 3.32
4569 5054 5.939764 TTAACAGAGGCAGAGATATGTGT 57.060 39.130 0.00 0.00 0.00 3.72
4570 5055 7.615582 TTTTTAACAGAGGCAGAGATATGTG 57.384 36.000 0.00 0.00 0.00 3.21
4724 5209 2.016318 TGTGAAATGTGATCGCCATCC 58.984 47.619 3.31 0.00 0.00 3.51
4738 5223 2.042464 AGAGTCCTGTGAGCTGTGAAA 58.958 47.619 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.